Citrus Sinensis ID: 025979

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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-----
Protein Sequence
MAASAMVLDPKPVSEPPPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEEEEEEEEEcccEEEEEcccccEEEEEEcccccccccccccEEEEEccccEEcccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccHHHHHHcccccccEEEEEccccccHHHHHHHHHHccccEEEEEcHHHHHHHHcccccHHHHHcc
Secondary Structure Prediction (SSPRO)
ccHHEEEccccHHccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEEEEEccccEEEEccccccEEEEEEEcccHHHcccccEEEEcccccEEEEcccccccccEEEEcccccccccHHHcccHHHHHHHHHHHHccccccHHHHHHHccccccEEEEEccccccHHHHHHHHHcccccEEEEEHHHHHHHHHHccccHHHHHHc
Coil and Loop (DISEMBL)
maasamvldpkpvsepppstrsdlteqwsdedDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMvdqnngivgsttgsNYYVRILSTINRellkpsasvalhrhsnalvdvlppeadssisllsqsekpdvtyndiggcdiQKQEIREAVELPLTHHELYKqigidpprgvllygppgtgkTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF
Flexible Loop (DISEMBL)
maasamvldpkpvsepppstrsdlteqwsdeDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLsqsekpdvtynDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVwlkhkqif
Low Complexity Region (SEG)
MAASAMVLDPKPVSEPPPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF
Disordered region (IsUnstruct)
****************************************LQRQLEFIDIQEEYVK*********LLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDV*******************VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKH****
Disordered Region (DISOPRED)
*********************************LYSRLKSLQRQLEFIDIQ*************************QSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF
Disordered Region (DISEMBL)
***************************WSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF
Disordered Region (DISPRO)
*******L*PKPVSEPPPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHK*IF
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAASAMVLDPKPVSEPPPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQxxxxxxxxxxxxxxxxxxxxxxxxxxxxPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF
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	245	2.2.26 [Sep-21-2011]
Q9SEI4	408	26S protease regulatory s	yes	no	0.930	0.558	0.889	1e-118
P54778	413	26S protease regulatory s	N/A	no	0.951	0.564	0.894	1e-117
P85200	414	26S protease regulatory s	N/A	no	0.942	0.557	0.883	1e-115
Q4R7L3	418	26S protease regulatory s	N/A	no	0.897	0.526	0.795	1e-100
P43686	418	26S protease regulatory s	yes	no	0.897	0.526	0.795	1e-100
Q3T030	418	26S protease regulatory s	yes	no	0.897	0.526	0.795	1e-100
Q63570	418	26S protease regulatory s	yes	no	0.897	0.526	0.795	1e-100
P54775	418	26S protease regulatory s	yes	no	0.897	0.526	0.795	1e-100
P46507	415	26S protease regulatory s	N/A	no	0.918	0.542	0.769	7e-99
P78578	423	26S protease regulatory s	yes	no	0.885	0.513	0.764	2e-95

>sp|Q9SEI4|PRS6B_ARATH 26S protease regulatory subunit 6B homolog OS=Arabidopsis thaliana GN=RPT3 PE=1 SV=1

 Score =  425 bits (1092), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 209/235 (88%), Positives = 219/235 (93%), Gaps = 7/235 (2%)

Query: 2   AASAMVLDPKPVSEPPPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKN 61
           A ++MVLDPK       ++ + +    +DE+DLY RLKSL+RQLEF DIQEEYVKDEQKN
Sbjct: 5   AVASMVLDPK-------ASPALMDLSTADEEDLYGRLKSLERQLEFTDIQEEYVKDEQKN 57

Query: 62  LKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPS 121
           LKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPS
Sbjct: 58  LKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPS 117

Query: 122 ASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTH 181
           ASVALHRHSNALVDVLPPEADSSISLLSQSEKPDV+YNDIGGCDIQKQEIREAVELPLTH
Sbjct: 118 ASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVSYNDIGGCDIQKQEIREAVELPLTH 177

Query: 182 HELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
           HELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE
Sbjct: 178 HELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 232

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.
Arabidopsis thaliana (taxid: 3702)

>sp|P54778|PRS6B_SOLTU 26S protease regulatory subunit 6B homolog OS=Solanum tuberosum PE=2 SV=1

 Score =  421 bits (1083), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 212/237 (89%), Positives = 223/237 (94%), Gaps = 4/237 (1%)

Query: 3   ASAMVLDPKPVSEPPPSTR--SDLTEQWSD-EDDLYSRLKSLQRQLEFIDIQEEYVKDEQ 59
           A+AMVLDPKP +E  P+TR  + +T+  SD EDDLY+RLKSLQRQLEFI+IQEEYVKDE 
Sbjct: 2   ATAMVLDPKP-AEKLPATRPETSITDVPSDGEDDLYARLKSLQRQLEFIEIQEEYVKDEL 60

Query: 60  KNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLK 119
           KNL+RE LRAQEEVKRIQSVPLVIGQFMEM+DQNN IVGSTTGSNYYVRILSTINRELLK
Sbjct: 61  KNLRREHLRAQEEVKRIQSVPLVIGQFMEMIDQNNAIVGSTTGSNYYVRILSTINRELLK 120

Query: 120 PSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPL 179
           PSASV L RHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPL
Sbjct: 121 PSASVGLDRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPL 180

Query: 180 THHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
           THHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVA+HTTAAFIRVVGSEFVQKYLGE
Sbjct: 181 THHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTAAFIRVVGSEFVQKYLGE 237

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.

Solanum tuberosum (taxid: 4113)

>sp|P85200|PRS6B_HELAN 26S protease regulatory subunit 6B homolog OS=Helianthus annuus PE=1 SV=1

 Score =  412 bits (1060), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 212/240 (88%), Positives = 220/240 (91%), Gaps = 9/240 (3%)

Query: 3   ASAMVLDPKPVSEP------PPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVK 56
           A+ MVLDPKP S P      P +T S  T+    EDDLY+RLK+L RQ+EFIDIQEEYVK
Sbjct: 2   AATMVLDPKPSSTPPPTLPNPYTTDSQSTDS---EDDLYTRLKTLDRQIEFIDIQEEYVK 58

Query: 57  DEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRE 116
           DE KNLKRE LR+QEEVKRIQSVPLVIGQFMEM+DQNNGIVGSTTGSNYYVRILSTINRE
Sbjct: 59  DELKNLKREQLRSQEEVKRIQSVPLVIGQFMEMIDQNNGIVGSTTGSNYYVRILSTINRE 118

Query: 117 LLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVE 176
           LLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVE
Sbjct: 119 LLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVE 178

Query: 177 LPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
           LPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE
Sbjct: 179 LPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 238

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.

Helianthus annuus (taxid: 4232)

>sp|Q4R7L3|PRS6B_MACFA 26S protease regulatory subunit 6B OS=Macaca fascicularis GN=PSMC4 PE=2 SV=1

 Score =  365 bits (936), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 175/220 (79%), Positives = 196/220 (89%)

Query: 17  PPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRI 76
           P +  S L  +  D +DLYSR K LQ++LEF+++QEEY+KDEQKNLK+E L AQEEVKRI
Sbjct: 23  PQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEYIKDEQKNLKKEFLHAQEEVKRI 82

Query: 77  QSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDV 136
           QS+PLVIGQF+E VDQN  IVGSTTGSNYYVRILSTI+RELLKP+ASVALH+HSNALVDV
Sbjct: 83  QSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTIDRELLKPNASVALHKHSNALVDV 142

Query: 137 LPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGV 196
           LPPEADSSI +L+  +KPDV Y DIGG DIQKQE+REAVELPLTH ELYKQIGIDPPRGV
Sbjct: 143 LPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREAVELPLTHFELYKQIGIDPPRGV 202

Query: 197 LLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
           L+YGPPG GKTMLAKAVA+HTTAAFIRVVGSEFVQKYLGE
Sbjct: 203 LMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYLGE 242

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.

Macaca fascicularis (taxid: 9541)

>sp|P43686|PRS6B_HUMAN 26S protease regulatory subunit 6B OS=Homo sapiens GN=PSMC4 PE=1 SV=2

 Score =  365 bits (936), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 175/220 (79%), Positives = 196/220 (89%)

Query: 17  PPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRI 76
           P +  S L  +  D +DLYSR K LQ++LEF+++QEEY+KDEQKNLK+E L AQEEVKRI
Sbjct: 23  PQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEYIKDEQKNLKKEFLHAQEEVKRI 82

Query: 77  QSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDV 136
           QS+PLVIGQF+E VDQN  IVGSTTGSNYYVRILSTI+RELLKP+ASVALH+HSNALVDV
Sbjct: 83  QSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTIDRELLKPNASVALHKHSNALVDV 142

Query: 137 LPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGV 196
           LPPEADSSI +L+  +KPDV Y DIGG DIQKQE+REAVELPLTH ELYKQIGIDPPRGV
Sbjct: 143 LPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREAVELPLTHFELYKQIGIDPPRGV 202

Query: 197 LLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
           L+YGPPG GKTMLAKAVA+HTTAAFIRVVGSEFVQKYLGE
Sbjct: 203 LMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYLGE 242

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.

Homo sapiens (taxid: 9606)

>sp|Q3T030|PRS6B_BOVIN 26S protease regulatory subunit 6B OS=Bos taurus GN=PSMC4 PE=2 SV=1

 Score =  365 bits (936), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 175/220 (79%), Positives = 196/220 (89%)

Query: 17  PPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRI 76
           P +  S L  +  D +DLYSR K LQ++LEF+++QEEY+KDEQKNLK+E L AQEEVKRI
Sbjct: 23  PQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEYIKDEQKNLKKEFLHAQEEVKRI 82

Query: 77  QSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDV 136
           QS+PLVIGQF+E VDQN  IVGSTTGSNYYVRILSTI+RELLKP+ASVALH+HSNALVDV
Sbjct: 83  QSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTIDRELLKPNASVALHKHSNALVDV 142

Query: 137 LPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGV 196
           LPPEADSSI +L+  +KPDV Y DIGG DIQKQE+REAVELPLTH ELYKQIGIDPPRGV
Sbjct: 143 LPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREAVELPLTHFELYKQIGIDPPRGV 202

Query: 197 LLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
           L+YGPPG GKTMLAKAVA+HTTAAFIRVVGSEFVQKYLGE
Sbjct: 203 LMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYLGE 242

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.

Bos taurus (taxid: 9913)

>sp|Q63570|PRS6B_RAT 26S protease regulatory subunit 6B OS=Rattus norvegicus GN=Psmc4 PE=1 SV=1

 Score =  364 bits (935), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 175/220 (79%), Positives = 196/220 (89%)

Query: 17  PPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRI 76
           P +  S L  +  D +DLYSR K LQ++LEF+++QEEY+KDEQKNLK+E L AQEEVKRI
Sbjct: 23  PQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEYIKDEQKNLKKEFLHAQEEVKRI 82

Query: 77  QSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDV 136
           QS+PLVIGQF+E VDQN  IVGSTTGSNYYVRILSTI+RELLKP+ASVALH+HSNALVDV
Sbjct: 83  QSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTIDRELLKPNASVALHKHSNALVDV 142

Query: 137 LPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGV 196
           LPPEADSSI +L+  +KPDV Y DIGG DIQKQE+REAVELPLTH ELYKQIGIDPPRGV
Sbjct: 143 LPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREAVELPLTHFELYKQIGIDPPRGV 202

Query: 197 LLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
           L+YGPPG GKTMLAKAVA+HTTAAFIRVVGSEFVQKYLGE
Sbjct: 203 LMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYLGE 242

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.

Rattus norvegicus (taxid: 10116)

>sp|P54775|PRS6B_MOUSE 26S protease regulatory subunit 6B OS=Mus musculus GN=Psmc4 PE=1 SV=2

 Score =  364 bits (935), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 175/220 (79%), Positives = 196/220 (89%)

Query: 17  PPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRI 76
           P +  S L  +  D +DLYSR K LQ++LEF+++QEEY+KDEQKNLK+E L AQEEVKRI
Sbjct: 23  PQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEYIKDEQKNLKKEFLHAQEEVKRI 82

Query: 77  QSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDV 136
           QS+PLVIGQF+E VDQN  IVGSTTGSNYYVRILSTI+RELLKP+ASVALH+HSNALVDV
Sbjct: 83  QSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTIDRELLKPNASVALHKHSNALVDV 142

Query: 137 LPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGV 196
           LPPEADSSI +L+  +KPDV Y DIGG DIQKQE+REAVELPLTH ELYKQIGIDPPRGV
Sbjct: 143 LPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREAVELPLTHFELYKQIGIDPPRGV 202

Query: 197 LLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
           L+YGPPG GKTMLAKAVA+HTTAAFIRVVGSEFVQKYLGE
Sbjct: 203 LMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYLGE 242

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.

Mus musculus (taxid: 10090)

>sp|P46507|PRS6B_MANSE 26S protease regulatory subunit 6B OS=Manduca sexta PE=2 SV=1

 Score =  360 bits (923), Expect = 7e-99,   Method: Compositional matrix adjust.
 Identities = 177/230 (76%), Positives = 198/230 (86%), Gaps = 5/230 (2%)

Query: 7   VLDPKPVSEPPPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKREL 66
           V D K +    P T  +L     + +DLY++ K LQR LEF+++QEEY+KDEQ+NLK+E 
Sbjct: 15  VTDAKGLPFAGPQTFDEL-----ESEDLYTKYKKLQRMLEFLEVQEEYIKDEQRNLKKEY 69

Query: 67  LRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVAL 126
           L AQEEVKRIQSVPLVIGQF+E VDQN GIVGSTTGSNYYVRILSTI+RELLKPSASVAL
Sbjct: 70  LHAQEEVKRIQSVPLVIGQFLEAVDQNTGIVGSTTGSNYYVRILSTIDRELLKPSASVAL 129

Query: 127 HRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYK 186
           H+HSNALVDVLPPEADSSIS+L   EKPDV Y+DIGG D QKQEIREAVELPLTH ELY+
Sbjct: 130 HKHSNALVDVLPPEADSSISMLQADEKPDVQYSDIGGMDTQKQEIREAVELPLTHVELYR 189

Query: 187 QIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
           QIGI+PPRGVL+YGPPG GKTMLA AVA+HTTAAFIRVVGSEFVQKYLGE
Sbjct: 190 QIGIEPPRGVLMYGPPGCGKTMLANAVAHHTTAAFIRVVGSEFVQKYLGE 239

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.

Manduca sexta (taxid: 7130)

>sp|P78578|PRS6B_ASPNG 26S protease regulatory subunit 6B homolog OS=Aspergillus niger GN=tbpA PE=3 SV=1

 Score =  348 bits (892), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 166/217 (76%), Positives = 191/217 (88%)

Query: 29  SDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFME 88
           +D  D Y+ LK LQR LE+I +QEEY+KDEQ++LKREL+RAQEE+KRIQSVPLVIGQFME
Sbjct: 36  NDGSDEYATLKRLQRHLEYIQLQEEYIKDEQRSLKRELVRAQEEIKRIQSVPLVIGQFME 95

Query: 89  MVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLL 148
            +DQN GIV S+TGSNY VRILST++RE LKPS+SVALHRHSNALVD+LPPEADSSI++L
Sbjct: 96  AIDQNTGIVQSSTGSNYVVRILSTLDREKLKPSSSVALHRHSNALVDILPPEADSSIAML 155

Query: 149 SQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTM 208
            ++EKPDVTY D+GG D+QKQEIREAVELPLT  +LYKQIGIDPPRGVLLYGPPGTGKTM
Sbjct: 156 GENEKPDVTYADVGGLDMQKQEIREAVELPLTQFDLYKQIGIDPPRGVLLYGPPGTGKTM 215

Query: 209 LAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           L KAVAN TTA+FIRV GSEFVQKYLGE     + +F
Sbjct: 216 LVKAVANSTTASFIRVNGSEFVQKYLGEGPRMVRDVF 252

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.

Aspergillus niger (taxid: 5061)

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	245
449444336	418	PREDICTED: 26S protease regulatory subun	0.963	0.564	0.946	1e-126
255565346	415	26S protease regulatory subunit 6b, puta	0.951	0.561	0.933	1e-125
356570019	422	PREDICTED: 26S protease regulatory subun	0.963	0.559	0.922	1e-125
449475799	418	PREDICTED: LOW QUALITY PROTEIN: 26S prot	0.963	0.564	0.942	1e-125
356539715	423	PREDICTED: 26S protease regulatory subun	0.963	0.557	0.914	1e-125
224137580	412	predicted protein [Populus trichocarpa]	0.942	0.560	0.924	1e-120
118487324	412	unknown [Populus trichocarpa]	0.942	0.560	0.924	1e-120
224086733	412	predicted protein [Populus trichocarpa]	0.942	0.560	0.902	1e-117
356539717	413	PREDICTED: 26S protease regulatory subun	0.951	0.564	0.887	1e-117
15237159	408	regulatory particle triple-A ATPase 3 [A	0.930	0.558	0.889	1e-116

>gi|449444336|ref|XP_004139931.1| PREDICTED: 26S protease regulatory subunit 6B homolog [Cucumis sativus]

 Score =  456 bits (1173), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 229/242 (94%), Positives = 229/242 (94%), Gaps = 6/242 (2%)

Query: 1   MAASAMVLDPKPVSEPP---PSTRSDL---TEQWSDEDDLYSRLKSLQRQLEFIDIQEEY 54
           MAASAMVLDPK   EPP   P  RSDL    EQ SDEDDLYSRLKSLQRQLEFIDIQEEY
Sbjct: 1   MAASAMVLDPKSSLEPPASLPPMRSDLQGLAEQSSDEDDLYSRLKSLQRQLEFIDIQEEY 60

Query: 55  VKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTIN 114
           VKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTIN
Sbjct: 61  VKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTIN 120

Query: 115 RELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREA 174
           RELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREA
Sbjct: 121 RELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREA 180

Query: 175 VELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYL 234
           VELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYL
Sbjct: 181 VELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYL 240

Query: 235 GE 236
           GE
Sbjct: 241 GE 242

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255565346|ref|XP_002523664.1| 26S protease regulatory subunit 6b, putative [Ricinus communis] gi|223537064|gb|EEF38699.1| 26S protease regulatory subunit 6b, putative [Ricinus communis]

 Score =  454 bits (1168), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 226/242 (93%), Positives = 230/242 (95%), Gaps = 9/242 (3%)

Query: 1   MAASAMVLDPKPVSEPPPSTRSDLTEQW------SDEDDLYSRLKSLQRQLEFIDIQEEY 54
           MA+SAMVLDPKPVS P   +RSDL +Q       +DEDDLYSRLKSLQRQLEFIDIQEEY
Sbjct: 1   MASSAMVLDPKPVSSP---SRSDLQQQSFSDLTNADEDDLYSRLKSLQRQLEFIDIQEEY 57

Query: 55  VKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTIN 114
           VKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTIN
Sbjct: 58  VKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTIN 117

Query: 115 RELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREA 174
           RELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREA
Sbjct: 118 RELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREA 177

Query: 175 VELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYL 234
           VELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYL
Sbjct: 178 VELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYL 237

Query: 235 GE 236
           GE
Sbjct: 238 GE 239

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356570019|ref|XP_003553190.1| PREDICTED: 26S protease regulatory subunit 6B homolog [Glycine max]

 Score =  454 bits (1167), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 227/246 (92%), Positives = 230/246 (93%), Gaps = 10/246 (4%)

Query: 1   MAASAMVLDPKPVSEPPP---STRSDLTE-------QWSDEDDLYSRLKSLQRQLEFIDI 50
           M +SAMVLDPKP SEPPP   ST+SD  +         SDEDDLYSRLKSLQRQLEFIDI
Sbjct: 1   MGSSAMVLDPKPSSEPPPFLPSTKSDYLQGSFGGDATASDEDDLYSRLKSLQRQLEFIDI 60

Query: 51  QEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRIL 110
           QEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRIL
Sbjct: 61  QEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRIL 120

Query: 111 STINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQE 170
           STINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQE
Sbjct: 121 STINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQE 180

Query: 171 IREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV 230
           IREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV
Sbjct: 181 IREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV 240

Query: 231 QKYLGE 236
           QKYLGE
Sbjct: 241 QKYLGE 246

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449475799|ref|XP_004154554.1| PREDICTED: LOW QUALITY PROTEIN: 26S protease regulatory subunit 6B homolog [Cucumis sativus]

 Score =  454 bits (1167), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 228/242 (94%), Positives = 228/242 (94%), Gaps = 6/242 (2%)

Query: 1   MAASAMVLDPKPVSEPP---PSTRSDL---TEQWSDEDDLYSRLKSLQRQLEFIDIQEEY 54
           MAASAMVLDPK   EPP   P  RSDL    EQ SDEDDLYSRLKSLQRQLEFIDIQEEY
Sbjct: 1   MAASAMVLDPKSSLEPPASLPPMRSDLQGLAEQSSDEDDLYSRLKSLQRQLEFIDIQEEY 60

Query: 55  VKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTIN 114
           VKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTIN
Sbjct: 61  VKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTIN 120

Query: 115 RELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREA 174
           RELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREA
Sbjct: 121 RELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREA 180

Query: 175 VELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYL 234
           VELPLTHHELYKQIGIDPP GVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYL
Sbjct: 181 VELPLTHHELYKQIGIDPPXGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYL 240

Query: 235 GE 236
           GE
Sbjct: 241 GE 242

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356539715|ref|XP_003538340.1| PREDICTED: 26S protease regulatory subunit 6B homolog [Glycine max]

 Score =  453 bits (1165), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 226/247 (91%), Positives = 230/247 (93%), Gaps = 11/247 (4%)

Query: 1   MAASAMVLDPKPVSEPPP---STRSDLTE--------QWSDEDDLYSRLKSLQRQLEFID 49
           M +SAMVLDPKP SEPPP   ST+SD  +          SDEDDLYSRLK+LQRQLEFID
Sbjct: 1   MGSSAMVLDPKPSSEPPPFLASTKSDYLQGGFSGSDATASDEDDLYSRLKTLQRQLEFID 60

Query: 50  IQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRI 109
           IQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRI
Sbjct: 61  IQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRI 120

Query: 110 LSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQ 169
           LSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQ
Sbjct: 121 LSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQ 180

Query: 170 EIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF 229
           EIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF
Sbjct: 181 EIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF 240

Query: 230 VQKYLGE 236
           VQKYLGE
Sbjct: 241 VQKYLGE 247

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224137580|ref|XP_002322593.1| predicted protein [Populus trichocarpa] gi|118489637|gb|ABK96620.1| unknown [Populus trichocarpa x Populus deltoides] gi|222867223|gb|EEF04354.1| predicted protein [Populus trichocarpa]

 Score =  436 bits (1121), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 219/237 (92%), Positives = 222/237 (93%), Gaps = 6/237 (2%)

Query: 4   SAMVLDPKPVSEPPPSTRSDLTEQWS----DEDDLYSRLKSLQRQLEFIDIQEEYVKDEQ 59
           SAMVLDPKP   P    RSDL    S    ++DDLYSRLKSLQRQLEFI+IQEEYVKDEQ
Sbjct: 2   SAMVLDPKPA--PATEPRSDLVLDPSTIPIEDDDLYSRLKSLQRQLEFIEIQEEYVKDEQ 59

Query: 60  KNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLK 119
           KNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLK
Sbjct: 60  KNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLK 119

Query: 120 PSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPL 179
           PSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPL
Sbjct: 120 PSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPL 179

Query: 180 THHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
           THHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE
Sbjct: 180 THHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118487324|gb|ABK95490.1| unknown [Populus trichocarpa]

 Score =  436 bits (1120), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 219/237 (92%), Positives = 222/237 (93%), Gaps = 6/237 (2%)

Query: 4   SAMVLDPKPVSEPPPSTRSDLTEQWS----DEDDLYSRLKSLQRQLEFIDIQEEYVKDEQ 59
           SAMVLDPKP   P    RSDL    S    ++DDLYSRLKSLQRQLEFI+IQEEYVKDEQ
Sbjct: 2   SAMVLDPKPA--PATEPRSDLVLDPSTIPIEDDDLYSRLKSLQRQLEFIEIQEEYVKDEQ 59

Query: 60  KNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLK 119
           KNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLK
Sbjct: 60  KNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLK 119

Query: 120 PSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPL 179
           PSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPL
Sbjct: 120 PSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPL 179

Query: 180 THHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
           THHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE
Sbjct: 180 THHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224086733|ref|XP_002307945.1| predicted protein [Populus trichocarpa] gi|222853921|gb|EEE91468.1| predicted protein [Populus trichocarpa]

 Score =  427 bits (1098), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 214/237 (90%), Positives = 219/237 (92%), Gaps = 6/237 (2%)

Query: 4   SAMVLDPKPVSEPPPSTRSDL----TEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQ 59
           S MVLDP+P   P    RSDL    T    ++DDLYSR KSLQRQLEFIDIQ+EYVKDEQ
Sbjct: 2   STMVLDPRPA--PTVEPRSDLVPDPTTVPMEDDDLYSRFKSLQRQLEFIDIQDEYVKDEQ 59

Query: 60  KNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLK 119
           KNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQ NGIVGSTTGSNYYVRILSTI+RELLK
Sbjct: 60  KNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQTNGIVGSTTGSNYYVRILSTIDRELLK 119

Query: 120 PSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPL 179
           PSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPL
Sbjct: 120 PSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPL 179

Query: 180 THHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
           THHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE
Sbjct: 180 THHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356539717|ref|XP_003538341.1| PREDICTED: 26S protease regulatory subunit 6B homolog [Glycine max]

 Score =  426 bits (1096), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 213/240 (88%), Positives = 220/240 (91%), Gaps = 7/240 (2%)

Query: 1   MAASAMVLDPKPVSEPPPSTRSDLTEQWS----DEDDLYSRLKSLQRQLEFIDIQEEYVK 56
           MAASAMVLDP P     PST+S   +       DE+DLYSRLKSL RQLEF+DIQEEYVK
Sbjct: 1   MAASAMVLDPPPFL---PSTKSAYLQGGDATAFDEEDLYSRLKSLVRQLEFVDIQEEYVK 57

Query: 57  DEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRE 116
           DE KNL+RELLRA EEVKRIQSVPLVIGQFMEM+DQNNGIVGST GSNYYVRILSTINRE
Sbjct: 58  DELKNLRRELLRAMEEVKRIQSVPLVIGQFMEMIDQNNGIVGSTAGSNYYVRILSTINRE 117

Query: 117 LLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVE 176
           LLKPSASVALHRHSNALV+VLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVE
Sbjct: 118 LLKPSASVALHRHSNALVEVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVE 177

Query: 177 LPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
           LPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE
Sbjct: 178 LPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 237

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15237159|ref|NP_200637.1| regulatory particle triple-A ATPase 3 [Arabidopsis thaliana] gi|297793353|ref|XP_002864561.1| hypothetical protein ARALYDRAFT_495939 [Arabidopsis lyrata subsp. lyrata] gi|28558168|sp|Q9SEI4.1|PRS6B_ARATH RecName: Full=26S protease regulatory subunit 6B homolog; AltName: Full=26S protease subunit 6B homolog; AltName: Full=26S proteasome AAA-ATPase subunit RPT3; AltName: Full=Protein BMAA insensitive morphology 409; AltName: Full=Regulatory particle triple-A ATPase subunit 3 gi|6652882|gb|AAF22523.1|AF123392_1 26S proteasome AAA-ATPase subunit RPT3 [Arabidopsis thaliana] gi|8777330|dbj|BAA96920.1| 26S proteasome AAA-ATPase subunit RPT3 [Arabidopsis thaliana] gi|17979231|gb|AAL49932.1| AT4g10340/F24G24_140 [Arabidopsis thaliana] gi|56382019|gb|AAV85728.1| At5g58290 [Arabidopsis thaliana] gi|297310396|gb|EFH40820.1| hypothetical protein ARALYDRAFT_495939 [Arabidopsis lyrata subsp. lyrata] gi|332009646|gb|AED97029.1| regulatory particle triple-A ATPase 3 [Arabidopsis thaliana]

 Score =  425 bits (1092), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 209/235 (88%), Positives = 219/235 (93%), Gaps = 7/235 (2%)

Query: 2   AASAMVLDPKPVSEPPPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKN 61
           A ++MVLDPK       ++ + +    +DE+DLY RLKSL+RQLEF DIQEEYVKDEQKN
Sbjct: 5   AVASMVLDPK-------ASPALMDLSTADEEDLYGRLKSLERQLEFTDIQEEYVKDEQKN 57

Query: 62  LKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPS 121
           LKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPS
Sbjct: 58  LKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPS 117

Query: 122 ASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTH 181
           ASVALHRHSNALVDVLPPEADSSISLLSQSEKPDV+YNDIGGCDIQKQEIREAVELPLTH
Sbjct: 118 ASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVSYNDIGGCDIQKQEIREAVELPLTH 177

Query: 182 HELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
           HELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE
Sbjct: 178 HELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 232

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	245
TAIR|locus:2161258	408	RPT3 "regulatory particle trip	0.930	0.558	0.902	1.4e-105
FB|FBgn0028686	413	Rpt3 "Regulatory particle trip	0.844	0.501	0.845	2.5e-90
UNIPROTKB|F1MG70	417	PSMC4 "26S protease regulatory	0.893	0.525	0.794	3.1e-90
UNIPROTKB|Q3T030	418	PSMC4 "26S protease regulatory	0.897	0.526	0.795	3.1e-90
UNIPROTKB|E2RH48	418	PSMC4 "Uncharacterized protein	0.897	0.526	0.795	3.1e-90
UNIPROTKB|P43686	418	PSMC4 "26S protease regulatory	0.897	0.526	0.795	3.1e-90
UNIPROTKB|Q4R7L3	418	PSMC4 "26S protease regulatory	0.897	0.526	0.795	3.1e-90
MGI|MGI:1346093	418	Psmc4 "proteasome (prosome, ma	0.897	0.526	0.795	3.1e-90
RGD|621102	418	Psmc4 "proteasome (prosome, ma	0.897	0.526	0.795	3.1e-90
ZFIN|ZDB-GENE-030131-5083	418	psmc4 "proteasome (prosome, ma	0.926	0.543	0.770	3.1e-90

TAIR|locus:2161258 RPT3 "regulatory particle triple-A ATPase 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 1045 (372.9 bits), Expect = 1.4e-105, P = 1.4e-105
 Identities = 212/235 (90%), Positives = 220/235 (93%)

Query:     2 AASAMVLDPKPVSEPPPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKN 61
             A ++MVLDPK  + P      DL+   +DE+DLY RLKSL+RQLEF DIQEEYVKDEQKN
Sbjct:     5 AVASMVLDPK--ASP---ALMDLST--ADEEDLYGRLKSLERQLEFTDIQEEYVKDEQKN 57

Query:    62 LKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPS 121
             LKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPS
Sbjct:    58 LKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPS 117

Query:   122 ASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTH 181
             ASVALHRHSNALVDVLPPEADSSISLLSQSEKPDV+YNDIGGCDIQKQEIREAVELPLTH
Sbjct:   118 ASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVSYNDIGGCDIQKQEIREAVELPLTH 177

Query:   182 HELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
             HELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE
Sbjct:   178 HELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 232

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0016887 "ATPase activity" evidence=IGI;ISS

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

GO:0030163 "protein catabolic process" evidence=IEA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=RCA;TAS

GO:0005634 "nucleus" evidence=TAS

GO:0005618 "cell wall" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0000502 "proteasome complex" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

GO:0006094 "gluconeogenesis" evidence=RCA

GO:0006635 "fatty acid beta-oxidation" evidence=RCA

GO:0006888 "ER to Golgi vesicle-mediated transport" evidence=RCA

GO:0007010 "cytoskeleton organization" evidence=RCA

GO:0009407 "toxin catabolic process" evidence=RCA

GO:0009735 "response to cytokinin stimulus" evidence=RCA

GO:0009853 "photorespiration" evidence=RCA

GO:0010498 "proteasomal protein catabolic process" evidence=RCA

GO:0043090 "amino acid import" evidence=RCA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=RCA

GO:0043248 "proteasome assembly" evidence=RCA

GO:0048767 "root hair elongation" evidence=RCA

GO:0051788 "response to misfolded protein" evidence=RCA

GO:0080129 "proteasome core complex assembly" evidence=RCA

GO:0008540 "proteasome regulatory particle, base subcomplex" evidence=IDA

FB|FBgn0028686 Rpt3 "Regulatory particle triple-A ATPase 3" [Drosophila melanogaster (taxid:7227)]

 Score = 901 (322.2 bits), Expect = 2.5e-90, P = 2.5e-90
 Identities = 175/207 (84%), Positives = 191/207 (92%)

Query:    30 DEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEM 89
             D +DLY R K LQ+ LEFI++QEEY+KDEQ+NLK+E L AQEEVKRIQSVPLVIGQF+E 
Sbjct:    31 DMEDLYVRYKKLQKTLEFIEVQEEYIKDEQRNLKKEYLHAQEEVKRIQSVPLVIGQFLEA 90

Query:    90 VDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLS 149
             VDQN GIVGSTTGSNYYVRILSTI+RELLKPSASVALH+HSNALVDVLPPEADSSIS+L 
Sbjct:    91 VDQNTGIVGSTTGSNYYVRILSTIDRELLKPSASVALHKHSNALVDVLPPEADSSISMLQ 150

Query:   150 QSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTML 209
               EKPDV+Y DIGG D+QKQEIREAVELPLTH ELYKQIGIDPPRGVL+YGPPG GKTML
Sbjct:   151 PDEKPDVSYADIGGMDMQKQEIREAVELPLTHFELYKQIGIDPPRGVLMYGPPGCGKTML 210

Query:   210 AKAVANHTTAAFIRVVGSEFVQKYLGE 236
             AKAVA+HTTA+FIRVVGSEFVQKYLGE
Sbjct:   211 AKAVAHHTTASFIRVVGSEFVQKYLGE 237

GO:0008540 "proteasome regulatory particle, base subcomplex" evidence=ISS;NAS

GO:0004175 "endopeptidase activity" evidence=IDA

GO:0006508 "proteolysis" evidence=ISS;IDA

GO:0005838 "proteasome regulatory particle" evidence=ISS;IDA

GO:0001673 "male germ cell nucleus" evidence=IDA

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0030163 "protein catabolic process" evidence=IEA

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

GO:0006974 "response to DNA damage stimulus" evidence=IMP

UNIPROTKB|F1MG70 PSMC4 "26S protease regulatory subunit 6B" [Bos taurus (taxid:9913)]

 Score = 900 (321.9 bits), Expect = 3.1e-90, P = 3.1e-90
 Identities = 174/219 (79%), Positives = 194/219 (88%)

Query:    18 PSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQ 77
             P T      +  D +DLYSR K LQ++LEF+++QEEY+KDEQKNLK+E L AQEEVKRIQ
Sbjct:    23 PQTGLSFLGEPEDLEDLYSRYKKLQQELEFLEVQEEYIKDEQKNLKKEFLHAQEEVKRIQ 82

Query:    78 SVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVL 137
             S+PLVIGQF+E VDQN  IVGSTTGSNYYVRILSTI+RELLKP+ASVALH+HSNALVDVL
Sbjct:    83 SIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTIDRELLKPNASVALHKHSNALVDVL 142

Query:   138 PPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVL 197
             PPEADSSI +L+  +KPDV Y DIGG DIQKQE+REAVELPLTH ELYKQIGIDPPRGVL
Sbjct:   143 PPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREAVELPLTHFELYKQIGIDPPRGVL 202

Query:   198 LYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
             +YGPPG GKTMLAKAVA+HTTAAFIRVVGSEFVQKYLGE
Sbjct:   203 MYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYLGE 241

GO:0022624 "proteasome accessory complex" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0001824 "blastocyst development" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0030163 "protein catabolic process" evidence=IEA

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

UNIPROTKB|Q3T030 PSMC4 "26S protease regulatory subunit 6B" [Bos taurus (taxid:9913)]

 Score = 900 (321.9 bits), Expect = 3.1e-90, P = 3.1e-90
 Identities = 175/220 (79%), Positives = 196/220 (89%)

Query:    17 PPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRI 76
             P +  S L  +  D +DLYSR K LQ++LEF+++QEEY+KDEQKNLK+E L AQEEVKRI
Sbjct:    23 PQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEYIKDEQKNLKKEFLHAQEEVKRI 82

Query:    77 QSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDV 136
             QS+PLVIGQF+E VDQN  IVGSTTGSNYYVRILSTI+RELLKP+ASVALH+HSNALVDV
Sbjct:    83 QSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTIDRELLKPNASVALHKHSNALVDV 142

Query:   137 LPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGV 196
             LPPEADSSI +L+  +KPDV Y DIGG DIQKQE+REAVELPLTH ELYKQIGIDPPRGV
Sbjct:   143 LPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREAVELPLTHFELYKQIGIDPPRGV 202

Query:   197 LLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
             L+YGPPG GKTMLAKAVA+HTTAAFIRVVGSEFVQKYLGE
Sbjct:   203 LMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYLGE 242

GO:0022624 "proteasome accessory complex" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0001824 "blastocyst development" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0030163 "protein catabolic process" evidence=IEA

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

UNIPROTKB|E2RH48 PSMC4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 900 (321.9 bits), Expect = 3.1e-90, P = 3.1e-90
 Identities = 175/220 (79%), Positives = 196/220 (89%)

Query:    17 PPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRI 76
             P +  S L  +  D +DLYSR K LQ++LEF+++QEEY+KDEQKNLK+E L AQEEVKRI
Sbjct:    23 PQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEYIKDEQKNLKKEFLHAQEEVKRI 82

Query:    77 QSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDV 136
             QS+PLVIGQF+E VDQN  IVGSTTGSNYYVRILSTI+RELLKP+ASVALH+HSNALVDV
Sbjct:    83 QSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTIDRELLKPNASVALHKHSNALVDV 142

Query:   137 LPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGV 196
             LPPEADSSI +L+  +KPDV Y DIGG DIQKQE+REAVELPLTH ELYKQIGIDPPRGV
Sbjct:   143 LPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREAVELPLTHFELYKQIGIDPPRGV 202

Query:   197 LLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
             L+YGPPG GKTMLAKAVA+HTTAAFIRVVGSEFVQKYLGE
Sbjct:   203 LMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYLGE 242

GO:0022624 "proteasome accessory complex" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0001824 "blastocyst development" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0030163 "protein catabolic process" evidence=IEA

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

UNIPROTKB|P43686 PSMC4 "26S protease regulatory subunit 6B" [Homo sapiens (taxid:9606)]

 Score = 900 (321.9 bits), Expect = 3.1e-90, P = 3.1e-90
 Identities = 175/220 (79%), Positives = 196/220 (89%)

Query:    17 PPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRI 76
             P +  S L  +  D +DLYSR K LQ++LEF+++QEEY+KDEQKNLK+E L AQEEVKRI
Sbjct:    23 PQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEYIKDEQKNLKKEFLHAQEEVKRI 82

Query:    77 QSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDV 136
             QS+PLVIGQF+E VDQN  IVGSTTGSNYYVRILSTI+RELLKP+ASVALH+HSNALVDV
Sbjct:    83 QSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTIDRELLKPNASVALHKHSNALVDV 142

Query:   137 LPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGV 196
             LPPEADSSI +L+  +KPDV Y DIGG DIQKQE+REAVELPLTH ELYKQIGIDPPRGV
Sbjct:   143 LPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREAVELPLTHFELYKQIGIDPPRGV 202

Query:   197 LLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
             L+YGPPG GKTMLAKAVA+HTTAAFIRVVGSEFVQKYLGE
Sbjct:   203 LMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYLGE 242

GO:0005524 "ATP binding" evidence=IEA

GO:0001824 "blastocyst development" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0022624 "proteasome accessory complex" evidence=ISS

GO:0000502 "proteasome complex" evidence=TAS

GO:0006508 "proteolysis" evidence=TAS

GO:0016887 "ATPase activity" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006521 "regulation of cellular amino acid metabolic process" evidence=TAS

GO:0006915 "apoptotic process" evidence=TAS

GO:0006977 "DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0031145 "anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process" evidence=TAS

GO:0034641 "cellular nitrogen compound metabolic process" evidence=TAS

GO:0042590 "antigen processing and presentation of exogenous peptide antigen via MHC class I" evidence=TAS

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

GO:0044281 "small molecule metabolic process" evidence=TAS

GO:0051436 "negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0051437 "positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0051439 "regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0000075 "cell cycle checkpoint" evidence=TAS

GO:0000082 "G1/S transition of mitotic cell cycle" evidence=TAS

GO:0000084 "S phase of mitotic cell cycle" evidence=TAS

GO:0000209 "protein polyubiquitination" evidence=TAS

GO:0000216 "M/G1 transition of mitotic cell cycle" evidence=TAS

GO:0000278 "mitotic cell cycle" evidence=TAS

GO:0002474 "antigen processing and presentation of peptide antigen via MHC class I" evidence=TAS

GO:0002479 "antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

GO:0006200 "ATP catabolic process" evidence=TAS

UNIPROTKB|Q4R7L3 PSMC4 "26S protease regulatory subunit 6B" [Macaca fascicularis (taxid:9541)]

 Score = 900 (321.9 bits), Expect = 3.1e-90, P = 3.1e-90
 Identities = 175/220 (79%), Positives = 196/220 (89%)

Query:    17 PPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRI 76
             P +  S L  +  D +DLYSR K LQ++LEF+++QEEY+KDEQKNLK+E L AQEEVKRI
Sbjct:    23 PQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEYIKDEQKNLKKEFLHAQEEVKRI 82

Query:    77 QSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDV 136
             QS+PLVIGQF+E VDQN  IVGSTTGSNYYVRILSTI+RELLKP+ASVALH+HSNALVDV
Sbjct:    83 QSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTIDRELLKPNASVALHKHSNALVDV 142

Query:   137 LPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGV 196
             LPPEADSSI +L+  +KPDV Y DIGG DIQKQE+REAVELPLTH ELYKQIGIDPPRGV
Sbjct:   143 LPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREAVELPLTHFELYKQIGIDPPRGV 202

Query:   197 LLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
             L+YGPPG GKTMLAKAVA+HTTAAFIRVVGSEFVQKYLGE
Sbjct:   203 LMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYLGE 242

GO:0022624 "proteasome accessory complex" evidence=ISS

MGI|MGI:1346093 Psmc4 "proteasome (prosome, macropain) 26S subunit, ATPase, 4" [Mus musculus (taxid:10090)]

 Score = 900 (321.9 bits), Expect = 3.1e-90, P = 3.1e-90
 Identities = 175/220 (79%), Positives = 196/220 (89%)

Query:    17 PPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRI 76
             P +  S L  +  D +DLYSR K LQ++LEF+++QEEY+KDEQKNLK+E L AQEEVKRI
Sbjct:    23 PQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEYIKDEQKNLKKEFLHAQEEVKRI 82

Query:    77 QSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDV 136
             QS+PLVIGQF+E VDQN  IVGSTTGSNYYVRILSTI+RELLKP+ASVALH+HSNALVDV
Sbjct:    83 QSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTIDRELLKPNASVALHKHSNALVDV 142

Query:   137 LPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGV 196
             LPPEADSSI +L+  +KPDV Y DIGG DIQKQE+REAVELPLTH ELYKQIGIDPPRGV
Sbjct:   143 LPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREAVELPLTHFELYKQIGIDPPRGV 202

Query:   197 LLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
             L+YGPPG GKTMLAKAVA+HTTAAFIRVVGSEFVQKYLGE
Sbjct:   203 LMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYLGE 242

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000502 "proteasome complex" evidence=IEA

GO:0001824 "blastocyst development" evidence=IMP

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

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

GO:0022624 "proteasome accessory complex" evidence=IDA

GO:0030163 "protein catabolic process" evidence=IEA

RGD|621102 Psmc4 "proteasome (prosome, macropain) 26S subunit, ATPase, 4" [Rattus norvegicus (taxid:10116)]

 Score = 900 (321.9 bits), Expect = 3.1e-90, P = 3.1e-90
 Identities = 175/220 (79%), Positives = 196/220 (89%)

Query:    17 PPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRI 76
             P +  S L  +  D +DLYSR K LQ++LEF+++QEEY+KDEQKNLK+E L AQEEVKRI
Sbjct:    23 PQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEYIKDEQKNLKKEFLHAQEEVKRI 82

Query:    77 QSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDV 136
             QS+PLVIGQF+E VDQN  IVGSTTGSNYYVRILSTI+RELLKP+ASVALH+HSNALVDV
Sbjct:    83 QSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTIDRELLKPNASVALHKHSNALVDV 142

Query:   137 LPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGV 196
             LPPEADSSI +L+  +KPDV Y DIGG DIQKQE+REAVELPLTH ELYKQIGIDPPRGV
Sbjct:   143 LPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREAVELPLTHFELYKQIGIDPPRGV 202

Query:   197 LLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
             L+YGPPG GKTMLAKAVA+HTTAAFIRVVGSEFVQKYLGE
Sbjct:   203 LMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYLGE 242

GO:0001824 "blastocyst development" evidence=IEA;ISO

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0005739 "mitochondrion" evidence=IEA;ISO

GO:0006200 "ATP catabolic process" evidence=TAS

GO:0016887 "ATPase activity" evidence=TAS

GO:0022624 "proteasome accessory complex" evidence=ISO;ISS

GO:0030163 "protein catabolic process" evidence=IEA

GO:0005730 "nucleolus" evidence=ISO

ZFIN|ZDB-GENE-030131-5083 psmc4 "proteasome (prosome, macropain) 26S subunit, ATPase, 4" [Danio rerio (taxid:7955)]

 Score = 900 (321.9 bits), Expect = 3.1e-90, P = 3.1e-90
 Identities = 175/227 (77%), Positives = 199/227 (87%)

Query:    10 PKPVSEPPPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRA 69
             P  ++  P +  S L  +  D +DLYS  K LQ++LEF+++QEEY+KDEQKNLK+E L A
Sbjct:    16 PALLNSRPQTGLSFLAPEPEDLEDLYSIYKKLQQELEFLEVQEEYIKDEQKNLKKEFLHA 75

Query:    70 QEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRH 129
             QEEVKRIQS+PLVIGQF+E VDQN  IVGSTTGSNYYVRILSTI+RELLKP+ASVALH+H
Sbjct:    76 QEEVKRIQSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTIDRELLKPNASVALHKH 135

Query:   130 SNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIG 189
             SNALVDVLPPEADSSI +L+  +KPDV Y+DIGG DIQKQE+REAVELPLTH ELYKQIG
Sbjct:   136 SNALVDVLPPEADSSIMMLTSDQKPDVLYSDIGGMDIQKQEVREAVELPLTHFELYKQIG 195

Query:   190 IDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
             IDPPRGVL+YGPPG GKTMLAKAVA+HTTAAFIRVVGSEFVQKYLGE
Sbjct:   196 IDPPRGVLMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYLGE 242

GO:0016787 "hydrolase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0030163 "protein catabolic process" evidence=IEA

GO:0000502 "proteasome complex" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P34123	PRS6B_DICDI	No assigned EC number	0.7961	0.8408	0.5111	yes	no
Q63570	PRS6B_RAT	No assigned EC number	0.7954	0.8979	0.5263	yes	no
P33298	PRS6B_YEAST	No assigned EC number	0.7549	0.8326	0.4766	yes	no
O74894	PRS6B_SCHPO	No assigned EC number	0.7740	0.8489	0.5347	yes	no
Q9SEI4	PRS6B_ARATH	No assigned EC number	0.8893	0.9306	0.5588	yes	no
P46502	PRS6B_CAEEL	No assigned EC number	0.7104	0.8775	0.5193	yes	no
P54775	PRS6B_MOUSE	No assigned EC number	0.7954	0.8979	0.5263	yes	no
P78578	PRS6B_ASPNG	No assigned EC number	0.7649	0.8857	0.5130	yes	no
Q3T030	PRS6B_BOVIN	No assigned EC number	0.7954	0.8979	0.5263	yes	no
P43686	PRS6B_HUMAN	No assigned EC number	0.7954	0.8979	0.5263	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	245
PTZ00454	398	PTZ00454, PTZ00454, 26S protease regulatory subuni	1e-145
COG1222	406	COG1222, RPT1, ATP-dependent 26S proteasome regula	1e-102
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	1e-84
TIGR01242	364	TIGR01242, 26Sp45, 26S proteasome subunit P45 fami	1e-70
PTZ00361	438	PTZ00361, PTZ00361, 26 proteosome regulatory subun	7e-68
TIGR03689	512	TIGR03689, pup_AAA, proteasome ATPase	3e-37
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	3e-31
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	6e-31
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	2e-29
TIGR01241	495	TIGR01241, FtsH_fam, ATP-dependent metalloprotease	3e-23
CHL00176	638	CHL00176, ftsH, cell division protein; Validated	3e-19
COG0465	596	COG0465, HflB, ATP-dependent Zn proteases [Posttra	5e-17
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	4e-16
PRK10733	644	PRK10733, hflB, ATP-dependent metalloprotease; Rev	4e-15
COG1223	368	COG1223, COG1223, Predicted ATPase (AAA+ superfami	3e-13
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	4e-11
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	4e-10
PRK13342	413	PRK13342, PRK13342, recombination factor protein R	1e-06
smart00382	148	smart00382, AAA, ATPases associated with a variety	7e-06
PRK13341	725	PRK13341, PRK13341, recombination factor protein R	7e-06
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	1e-05
COG0714	329	COG0714, COG0714, MoxR-like ATPases [General funct	2e-05
pfam13191	154	pfam13191, AAA_16, AAA ATPase domain	3e-05
COG2256	436	COG2256, MGS1, ATPase related to the helicase subu	4e-05
PRK08116	268	PRK08116, PRK08116, hypothetical protein; Validate	4e-05
CHL00195	489	CHL00195, ycf46, Ycf46; Provisional	1e-04
pfam07726	131	pfam07726, AAA_3, ATPase family associated with va	2e-04
PRK00080	328	PRK00080, ruvB, Holliday junction DNA helicase Ruv	2e-04
pfam01078	207	pfam01078, Mg_chelatase, Magnesium chelatase, subu	2e-04
COG2255	332	COG2255, RuvB, Holliday junction resolvasome, heli	5e-04
pfam05496	231	pfam05496, RuvB_N, Holliday junction DNA helicase	8e-04
PRK13765	637	PRK13765, PRK13765, ATP-dependent protease Lon; Pr	8e-04
pfam07724	168	pfam07724, AAA_2, AAA domain (Cdc48 subfamily)	0.001
COG1224	450	COG1224, TIP49, DNA helicase TIP49, TBP-interactin	0.001
pfam06068	395	pfam06068, TIP49, TIP49 C-terminus	0.002
pfam01057	271	pfam01057, Parvo_NS1, Parvovirus non-structural pr	0.002
CHL00206	2281	CHL00206, ycf2, Ycf2; Provisional	0.002
pfam13401	124	pfam13401, AAA_22, AAA domain	0.002
COG0466	782	COG0466, Lon, ATP-dependent Lon protease, bacteria	0.003
COG1484	254	COG1484, DnaC, DNA replication protein [DNA replic	0.004

>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like protein; Provisional

 Score =  409 bits (1054), Expect = e-145
 Identities = 173/208 (83%), Positives = 193/208 (92%)

Query: 29  SDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFME 88
             E DLY +LK L+++LEF+DIQEEY+K+EQKNLKREL+RA+EEVKRIQSVPLVIGQF+E
Sbjct: 15  HTERDLYEKLKELEKELEFLDIQEEYIKEEQKNLKRELIRAKEEVKRIQSVPLVIGQFLE 74

Query: 89  MVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLL 148
           M+D N GIV ST+GSNYYVRILST+NRELLKP+ASVALHRHS+A+VD+LPPEADSSI LL
Sbjct: 75  MIDSNYGIVSSTSGSNYYVRILSTLNRELLKPNASVALHRHSHAVVDILPPEADSSIQLL 134

Query: 149 SQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTM 208
             SEKPDVTY+DIGG DIQKQEIREAVELPLT  ELY+QIGIDPPRGVLLYGPPGTGKTM
Sbjct: 135 QMSEKPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTM 194

Query: 209 LAKAVANHTTAAFIRVVGSEFVQKYLGE 236
           LAKAVA+HTTA FIRVVGSEFVQKYLGE
Sbjct: 195 LAKAVAHHTTATFIRVVGSEFVQKYLGE 222

Length = 398

>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

 Score =  301 bits (774), Expect = e-102
 Identities = 111/226 (49%), Positives = 154/226 (68%)

Query: 11  KPVSEPPPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQ 70
               +           Q        ++LK L+++   + ++E+ ++ E   LKRE+ R +
Sbjct: 3   LDALDEILGDLESYEPQEYLNKLEDTKLKLLEKEKRLLLLEEQRLEAEGLRLKREVDRLR 62

Query: 71  EEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHS 130
           EE++R++  PL++G  +E++D    IV S+TG  + V ILS ++R+LL+P   VAL+R S
Sbjct: 63  EEIERLKEPPLIVGTVLEVLDDGRAIVKSSTGPKFVVNILSFVDRDLLEPGMRVALNRDS 122

Query: 131 NALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGI 190
            ++V VLPPE D  +S++   EKPDVTY DIGG D Q QEIRE VELPL + EL++++GI
Sbjct: 123 YSIVRVLPPEVDPRVSVMEVEEKPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGI 182

Query: 191 DPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
           DPP+GVLLYGPPGTGKT+LAKAVAN T A FIRVVGSE VQKY+GE
Sbjct: 183 DPPKGVLLYGPPGTGKTLLAKAVANQTDATFIRVVGSELVQKYIGE 228

Length = 406

>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase; Provisional

 Score =  256 bits (657), Expect = 1e-84
 Identities = 97/208 (46%), Positives = 144/208 (69%)

Query: 29  SDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFME 88
              + L  R   L+ Q+  ++++   ++ E + L+REL R + E+++++S PL++   +E
Sbjct: 1   ERLEALEERNSELEEQIRQLELKLRDLEAENEKLERELERLKSELEKLKSPPLIVATVLE 60

Query: 89  MVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLL 148
           ++D    +V S+ G  + V +   I+RE LKP A VAL++ S A+V+VLP E D  +  +
Sbjct: 61  VLDDGRVVVKSSGGPQFLVNVSPFIDREKLKPGARVALNQQSLAIVEVLPSEKDPRVQAM 120

Query: 149 SQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTM 208
              E P+VTY DIGG + Q +E+REAVELPL   EL++++GI+PP+GVLLYGPPGTGKT+
Sbjct: 121 EVIESPNVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTL 180

Query: 209 LAKAVANHTTAAFIRVVGSEFVQKYLGE 236
           LAKAVA+ T A FIRVVGSE VQK++GE
Sbjct: 181 LAKAVAHETNATFIRVVGSELVQKFIGE 208

Length = 389

>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family

 Score =  220 bits (561), Expect = 1e-70
 Identities = 101/202 (50%), Positives = 146/202 (72%), Gaps = 3/202 (1%)

Query: 35  YSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNN 94
            S L    R+LE    ++  ++ E+  L+REL R + E++R++S PL++G  +E++D N 
Sbjct: 1   ISELDVRIRKLE---DEKRSLEKEKIRLERELERLRSEIERLRSPPLIVGTVLEVLDDNR 57

Query: 95  GIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKP 154
            +V S+TG N+ V + + I+R+ LKP A VAL++ +  +VDVLP   D  +  +   E+P
Sbjct: 58  VVVKSSTGPNFVVNVSAFIDRKSLKPGARVALNQQTLTIVDVLPTSKDPLVKGMEVEERP 117

Query: 155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVA 214
           +V+Y DIGG + Q +EIREAVELPL H EL++++GI+PP+GVLLYGPPGTGKT+LAKAVA
Sbjct: 118 NVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVA 177

Query: 215 NHTTAAFIRVVGSEFVQKYLGE 236
           + T A FIRVVGSE V+KY+GE
Sbjct: 178 HETNATFIRVVGSELVRKYIGE 199

Many proteins may score above the trusted cutoff because an internal. Length = 364

>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like protein; Provisional

 Score =  215 bits (549), Expect = 7e-68
 Identities = 98/203 (48%), Positives = 143/203 (70%), Gaps = 4/203 (1%)

Query: 37  RLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSV---PLVIGQFMEMVDQN 93
           RL  L+R  +++ ++EE++ + Q+  K    + + E+K++  +   PL +G   E++D+N
Sbjct: 59  RLLKLERIKDYLLLEEEFITN-QEAQKPAQEKNEAELKKVDDLRGSPLSVGTLEEIIDEN 117

Query: 94  NGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEK 153
           + IV S+ G  YYV ILS +++E L+P  SV LH  ++++V +L  E D  +S++   + 
Sbjct: 118 HAIVSSSVGPEYYVNILSFVDKEQLEPGCSVLLHNKTHSVVGILLDEVDPLVSVMKVDKA 177

Query: 154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAV 213
           P  +Y DIGG + Q QEI+EAVELPLTH ELY  IGI PP+GV+LYGPPGTGKT+LAKAV
Sbjct: 178 PLESYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAV 237

Query: 214 ANHTTAAFIRVVGSEFVQKYLGE 236
           AN T+A F+RVVGSE +QKYLG+
Sbjct: 238 ANETSATFLRVVGSELIQKYLGD 260

Length = 438

>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase

 Score =  136 bits (344), Expect = 3e-37
 Identities = 61/164 (37%), Positives = 90/164 (54%), Gaps = 13/164 (7%)

Query: 83  IGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEAD 142
           I    E++D    +V   +G    V++   +  E L+P  ++ +   +    + +P    
Sbjct: 109 IVTLKEVLDDGRALVTDRSGEERVVKLAGALADEGLRPGDTLLVDPRAGYAFEAIPRTEV 168

Query: 143 SSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPP 202
             + L    E PDVTY DIGG   Q ++IR+AVELP  H ELY++ G+ PP+GVLLYGPP
Sbjct: 169 EDLVL---EEVPDVTYADIGGLGSQIEQIRDAVELPFLHPELYREYGLKPPKGVLLYGPP 225

Query: 203 GTGKTMLAKAVAN----------HTTAAFIRVVGSEFVQKYLGE 236
           G GKT++AKAVAN             + F+ + G E + KY+GE
Sbjct: 226 GCGKTLIAKAVANSLAARIGAEGGGKSYFLNIKGPELLNKYVGE 269

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 [Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 512

>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

 Score =  119 bits (301), Expect = 3e-31
 Identities = 56/139 (40%), Positives = 86/139 (61%), Gaps = 8/139 (5%)

Query: 115 RELLKPSASVALHRHSNAL---VDVLPPEADSSISLLSQS-----EKPDVTYNDIGGCDI 166
             L K +A   L R  + +   + V   + + ++  +  S     E  DVT +DIGG + 
Sbjct: 190 GALAKEAALRELRRAIDLVGEYIGVTEDDFEEALKKVLPSRGVLFEDEDVTLDDIGGLEE 249

Query: 167 QKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVG 226
            K+E++EA+E PL   EL++++G+ PP+GVLLYGPPGTGKT+LAKAVA  + + FI V G
Sbjct: 250 AKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRSRFISVKG 309

Query: 227 SEFVQKYLGEVWLKHKQIF 245
           SE + K++GE     +++F
Sbjct: 310 SELLSKWVGESEKNIRELF 328

Length = 494

>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily

 Score =  120 bits (301), Expect = 6e-31
 Identities = 54/92 (58%), Positives = 68/92 (73%)

Query: 154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAV 213
           P VTY DIGG    K++IRE VELP+ H EL++ +GI+PP+GVLLYGPPGTGKT+LAKAV
Sbjct: 173 PKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAV 232

Query: 214 ANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           AN   A FI + G E + KY GE   + ++IF
Sbjct: 233 ANEAGAYFISINGPEIMSKYYGESEERLREIF 264

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. Length = 733

>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily

 Score =  115 bits (290), Expect = 2e-29
 Identities = 52/94 (55%), Positives = 71/94 (75%)

Query: 152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAK 211
           E P+V ++DIGG +  KQE+REAVE PL H E+++++GI PP+GVLL+GPPGTGKT+LAK
Sbjct: 446 EVPNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAK 505

Query: 212 AVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           AVA  + A FI V G E + K++GE     ++IF
Sbjct: 506 AVATESGANFIAVRGPEILSKWVGESEKAIREIF 539

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. Length = 733

>gnl|CDD|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH

 Score = 97.0 bits (242), Expect = 3e-23
 Identities = 41/93 (44%), Positives = 58/93 (62%), Gaps = 1/93 (1%)

Query: 143 SSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPP 202
            S + L   EKP VT+ D+ G D  K+E+ E V+  L +   + ++G   P+GVLL GPP
Sbjct: 39  KSKAKLLNEEKPKVTFKDVAGIDEAKEELMEIVDF-LKNPSKFTKLGAKIPKGVLLVGPP 97

Query: 203 GTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLG 235
           GTGKT+LAKAVA      F  + GS+FV+ ++G
Sbjct: 98  GTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVG 130

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 [Cellular processes, Cell division, Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 495

>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated

 Score = 86.3 bits (214), Expect = 3e-19
 Identities = 36/83 (43%), Positives = 49/83 (59%), Gaps = 1/83 (1%)

Query: 153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKA 212
              +T+ DI G +  K+E  E V   L   E +  +G   P+GVLL GPPGTGKT+LAKA
Sbjct: 177 DTGITFRDIAGIEEAKEEFEEVVSF-LKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKA 235

Query: 213 VANHTTAAFIRVVGSEFVQKYLG 235
           +A      F  + GSEFV+ ++G
Sbjct: 236 IAGEAEVPFFSISGSEFVEMFVG 258

Length = 638

>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

 Score = 79.3 bits (196), Expect = 5e-17
 Identities = 37/85 (43%), Positives = 55/85 (64%), Gaps = 1/85 (1%)

Query: 151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLA 210
            ++  VT+ D+ G D  K+E+ E V+  L + + Y+ +G   P+GVLL GPPGTGKT+LA
Sbjct: 142 EDQVKVTFADVAGVDEAKEELSELVD-FLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLA 200

Query: 211 KAVANHTTAAFIRVVGSEFVQKYLG 235
           KAVA      F  + GS+FV+ ++G
Sbjct: 201 KAVAGEAGVPFFSISGSDFVEMFVG 225

Length = 596

>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular activities (AAA)

 Score = 72.2 bits (178), Expect = 4e-16
 Identities = 28/41 (68%), Positives = 31/41 (75%)

Query: 196 VLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
           +LLYGPPGTGKT LAKAVA    A FI + GSE V KY+GE
Sbjct: 1   LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGE 41

AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes. Length = 131

>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed

 Score = 73.9 bits (181), Expect = 4e-15
 Identities = 35/79 (44%), Positives = 52/79 (65%), Gaps = 1/79 (1%)

Query: 157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANH 216
           T+ D+ GCD  K+E+ E VE  L     ++++G   P+GVL+ GPPGTGKT+LAKA+A  
Sbjct: 150 TFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE 208

Query: 217 TTAAFIRVVGSEFVQKYLG 235
               F  + GS+FV+ ++G
Sbjct: 209 AKVPFFTISGSDFVEMFVG 227

Length = 644

>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General function prediction only]

 Score = 67.9 bits (166), Expect = 3e-13
 Identities = 33/121 (27%), Positives = 62/121 (51%), Gaps = 14/121 (11%)

Query: 126 LHRHSNALVDVLPPEA---DSSISLLSQSEK-------PDVTYNDIGGCDIQKQEIREAV 175
              ++  ++ V+P       S+   + ++ +        D+T +D+ G +  K++ R  +
Sbjct: 78  FPDYAFKVIRVVPSGGGIITSTTIFVLETPREEDREIISDITLDDVIGQEEAKRKCRLIM 137

Query: 176 ELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLG 235
           E  L + E +       P+ VL YGPPGTGKTM+AKA+AN      + V  +E + +++G
Sbjct: 138 EY-LENPERFGDWA---PKNVLFYGPPGTGKTMMAKALANEAKVPLLLVKATELIGEHVG 193

Query: 236 E 236
           +
Sbjct: 194 D 194

Length = 368

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

 Score = 59.1 bits (143), Expect = 4e-11
 Identities = 28/78 (35%), Positives = 42/78 (53%), Gaps = 16/78 (20%)

Query: 162 GGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT--- 218
            G +   + +REA+ELP             PP+ +LLYGPPGTGKT LA+A+AN      
Sbjct: 1   VGQEEAIEALREALELP-------------PPKNLLLYGPPGTGKTTLARAIANELFRPG 47

Query: 219 AAFIRVVGSEFVQKYLGE 236
           A F+ +  S+ ++  +  
Sbjct: 48  APFLYLNASDLLEGLVVA 65

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

>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

 Score = 58.7 bits (142), Expect = 4e-10
 Identities = 36/61 (59%), Positives = 49/61 (80%), Gaps = 1/61 (1%)

Query: 176 ELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLG 235
           ELPL   EL+K++GI+PP+GVLL+GPPGTGKT+LA+A+AN   A F+ + G E + KY+G
Sbjct: 1   ELPLKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALAN-EGAEFLSINGPEILSKYVG 59

Query: 236 E 236
           E
Sbjct: 60  E 60

Length = 494

>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed

 Score = 48.5 bits (117), Expect = 1e-06
 Identities = 17/41 (41%), Positives = 24/41 (58%)

Query: 184 LYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRV 224
           L + I       ++L+GPPGTGKT LA+ +A  T A F  +
Sbjct: 27  LRRMIEAGRLSSMILWGPPGTGKTTLARIIAGATDAPFEAL 67

Length = 413

>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular activities

 Score = 44.3 bits (104), Expect = 7e-06
 Identities = 14/34 (41%), Positives = 20/34 (58%)

Query: 192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVV 225
           P   +L+ GPPG+GKT LA+A+A         V+
Sbjct: 1   PGEVILIVGPPGSGKTTLARALARELGPPGGGVI 34

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. Length = 148

>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown domain fusion protein; Reviewed

 Score = 46.2 bits (110), Expect = 7e-06
 Identities = 17/26 (65%), Positives = 20/26 (76%)

Query: 197 LLYGPPGTGKTMLAKAVANHTTAAFI 222
           +LYGPPG GKT LA+ +ANHT A F 
Sbjct: 56  ILYGPPGVGKTTLARIIANHTRAHFS 81

Length = 725

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 45.3 bits (108), Expect = 1e-05
 Identities = 16/24 (66%), Positives = 19/24 (79%)

Query: 192 PPRGVLLYGPPGTGKTMLAKAVAN 215
           P + +LLYGPPG GKT LA A+AN
Sbjct: 38  PKKALLLYGPPGVGKTSLAHALAN 61

Length = 482

>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction only]

 Score = 44.3 bits (105), Expect = 2e-05
 Identities = 16/31 (51%), Positives = 21/31 (67%)

Query: 194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRV 224
             VLL GPPG GKT+LA+A+A      F+R+
Sbjct: 44  GHVLLEGPPGVGKTLLARALARALGLPFVRI 74

Length = 329

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

 Score = 42.6 bits (100), Expect = 3e-05
 Identities = 16/60 (26%), Positives = 24/60 (40%)

Query: 182 HELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKH 241
            +  ++     P  VLL GP GTGKT L + +      A  +   +E    Y     L+ 
Sbjct: 13  LDALRRARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYAFSQALRE 72

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

>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

 Score = 43.8 bits (104), Expect = 4e-05
 Identities = 16/27 (59%), Positives = 20/27 (74%)

Query: 198 LYGPPGTGKTMLAKAVANHTTAAFIRV 224
           L+GPPGTGKT LA+ +A  T AAF  +
Sbjct: 53  LWGPPGTGKTTLARLIAGTTNAAFEAL 79

Length = 436

>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated

 Score = 43.5 bits (103), Expect = 4e-05
 Identities = 14/32 (43%), Positives = 19/32 (59%)

Query: 194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVV 225
            G+LL+G  GTGKT LA  +AN      + V+
Sbjct: 115 VGLLLWGSVGTGKTYLAACIANELIEKGVPVI 146

Length = 268

>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional

 Score = 42.3 bits (100), Expect = 1e-04
 Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 8/74 (10%)

Query: 147 LLSQSE-----KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGP 201
           ++SQ+E       +   +DIGG D  K  +++      +  +     G+  PRG+LL G 
Sbjct: 211 IISQTEILEFYSVNEKISDIGGLDNLKDWLKKRST---SFSKQASNYGLPTPRGLLLVGI 267

Query: 202 PGTGKTMLAKAVAN 215
            GTGK++ AKA+AN
Sbjct: 268 QGTGKSLTAKAIAN 281

Length = 489

>gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular activities (AAA)

 Score = 40.2 bits (95), Expect = 2e-04
 Identities = 13/29 (44%), Positives = 17/29 (58%)

Query: 196 VLLYGPPGTGKTMLAKAVANHTTAAFIRV 224
           VLL G PG  KT+LA+ +A      F R+
Sbjct: 2   VLLEGVPGLAKTLLARTLARSLGLDFRRI 30

This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 131

>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed

 Score = 41.7 bits (99), Expect = 2e-04
 Identities = 15/20 (75%), Positives = 16/20 (80%)

Query: 196 VLLYGPPGTGKTMLAKAVAN 215
           VLLYGPPG GKT LA  +AN
Sbjct: 54  VLLYGPPGLGKTTLANIIAN 73

Length = 328

>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI

 Score = 41.0 bits (97), Expect = 2e-04
 Identities = 12/17 (70%), Positives = 15/17 (88%)

Query: 196 VLLYGPPGTGKTMLAKA 212
           +L+ GPPG+GKTMLAK 
Sbjct: 25  LLMIGPPGSGKTMLAKR 41

Magnesium-chelatase is a three-component enzyme that catalyzes the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa. Length = 207

>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

 Score = 40.2 bits (95), Expect = 5e-04
 Identities = 14/20 (70%), Positives = 16/20 (80%)

Query: 196 VLLYGPPGTGKTMLAKAVAN 215
           VLL+GPPG GKT LA  +AN
Sbjct: 55  VLLFGPPGLGKTTLAHIIAN 74

Length = 332

>gnl|CDD|203260 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB N-terminus

 Score = 39.4 bits (93), Expect = 8e-04
 Identities = 15/20 (75%), Positives = 16/20 (80%)

Query: 196 VLLYGPPGTGKTMLAKAVAN 215
           VLLYGPPG GKT LA  +AN
Sbjct: 53  VLLYGPPGLGKTTLANIIAN 72

The RuvB protein makes up part of the RuvABC revolvasome which catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalyzed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein. Length = 231

>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional

 Score = 40.0 bits (94), Expect = 8e-04
 Identities = 14/21 (66%), Positives = 18/21 (85%)

Query: 194 RGVLLYGPPGTGKTMLAKAVA 214
           R V++ G PGTGK+MLAKA+A
Sbjct: 51  RHVMMIGSPGTGKSMLAKAMA 71

Length = 637

>gnl|CDD|219536 pfam07724, AAA_2, AAA domain (Cdc48 subfamily)

 Score = 38.3 bits (90), Expect = 0.001
 Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 3/42 (7%)

Query: 196 VLLYGPPGTGKTMLAKAVANH---TTAAFIRVVGSEFVQKYL 234
            L  GP G GKT LAKA+A        A IR+  SE+++++ 
Sbjct: 6   FLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHS 47

This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 168

>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein [Transcription]

 Score = 39.3 bits (92), Expect = 0.001
 Identities = 21/46 (45%), Positives = 26/46 (56%), Gaps = 5/46 (10%)

Query: 194 RGVLLYGPPGTGKTMLAKAVANHTTA--AFIRVVGSEFVQKYLGEV 237
           RG+L+ GPPGTGKT LA  +A        F+ + GSE    Y  EV
Sbjct: 66  RGILIVGPPGTGKTALAMGIARELGEDVPFVAISGSEI---YSLEV 108

Length = 450

>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus

 Score = 38.8 bits (91), Expect = 0.002
 Identities = 18/38 (47%), Positives = 22/38 (57%), Gaps = 2/38 (5%)

Query: 194 RGVLLYGPPGTGKTMLAKAVANH--TTAAFIRVVGSEF 229
           R VL+ GPPGTGKT LA A++        F  + GSE 
Sbjct: 51  RAVLIAGPPGTGKTALAIAISKELGEDTPFCPISGSEV 88

This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the pfam00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases. Length = 395

>gnl|CDD|216270 pfam01057, Parvo_NS1, Parvovirus non-structural protein NS1

 Score = 38.5 bits (90), Expect = 0.002
 Identities = 16/31 (51%), Positives = 19/31 (61%), Gaps = 4/31 (12%)

Query: 186 KQIGIDPPRG-VLLYGPPGTGKTMLAKAVAN 215
           KQ G    R  V  YGP  TGKT LA+A+A+
Sbjct: 108 KQGG---KRNTVWFYGPASTGKTNLAQAIAH 135

This family also contains the NS2 protein. Parvoviruses encode two non-structural proteins, NS1 and NS2. The mRNA for NS2 contains the coding sequence for the first 87 amino acids of NS1, then by an alternative splicing mechanism mRNA from a different reading frame, encoding the last 78 amino acids, makes up the full length of the NS2 mRNA. NS1, is the major non-structural protein. It is essential for DNA replication. It is an 83-kDa nuclear phosphoprotein. It has DNA helicase and ATPase activity. Length = 271

>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional

 Score = 39.1 bits (91), Expect = 0.002
 Identities = 17/48 (35%), Positives = 29/48 (60%), Gaps = 4/48 (8%)

Query: 187  QIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYL 234
            ++ + P RG+L+ G  GTG++ L K +A ++   FI V    F+ K+L
Sbjct: 1624 RLALSPSRGILVIGSIGTGRSYLVKYLATNSYVPFITV----FLNKFL 1667

Length = 2281

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

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 8/35 (22%), Positives = 15/35 (42%), Gaps = 3/35 (8%)

Query: 193 PRGVLLYGPPGTGKTMLAKAVAN---HTTAAFIRV 224
               +L G  G+GKT L + +A    +    ++  
Sbjct: 4   AGIGVLTGESGSGKTTLLRRLARQLPNRRVVYVEA 38

Length = 124

>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

 Score = 37.9 bits (89), Expect = 0.003
 Identities = 13/28 (46%), Positives = 17/28 (60%)

Query: 197 LLYGPPGTGKTMLAKAVANHTTAAFIRV 224
            L GPPG GKT L K++A      F+R+
Sbjct: 354 CLVGPPGVGKTSLGKSIAKALGRKFVRI 381

Length = 782

>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication, recombination, and repair]

 Score = 37.0 bits (86), Expect = 0.004
 Identities = 15/35 (42%), Positives = 19/35 (54%)

Query: 190 IDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRV 224
            +    ++L GPPG GKT LA A+ N    A I V
Sbjct: 102 FERGENLVLLGPPGVGKTHLAIAIGNELLKAGISV 136

Length = 254

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	245
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	100.0
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	100.0
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	100.0
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	100.0
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	100.0
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	100.0
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	100.0
PRK03992	389	proteasome-activating nucleotidase; Provisional	100.0
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	100.0
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	99.98
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	99.96
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	99.94
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	99.94
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.93
KOG0736	953	consensus Peroxisome assembly factor 2 containing	99.92
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	99.88
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	99.87
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	99.86
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	99.86
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	99.85
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	99.84
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.83
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	99.83
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.81
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.79
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	99.77
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	99.77
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.76
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	99.75
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	99.74
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	99.73
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.72
CHL00195	489	ycf46 Ycf46; Provisional	99.71
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	99.69
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.68
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	99.66
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.64
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.64
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	99.64
CHL00176	638	ftsH cell division protein; Validated	99.63
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.55
PRK10865	857	protein disaggregation chaperone; Provisional	99.53
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.46
CHL00181	287	cbbX CbbX; Provisional	99.46
CHL00095	821	clpC Clp protease ATP binding subunit	99.45
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	99.44
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	99.43
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.38
CHL00206	2281	ycf2 Ycf2; Provisional	99.33
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	99.32
PF00004	132	AAA: ATPase family associated with various cellula	99.21
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	99.2
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	99.19
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	99.17
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	99.14
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	99.13
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	98.96
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	98.94
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.92
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	98.91
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	98.88
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	98.86
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.85
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.83
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	98.82
PRK04195	482	replication factor C large subunit; Provisional	98.79
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	98.75
CHL00095	821	clpC Clp protease ATP binding subunit	98.75
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	98.73
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	98.68
PRK10865	857	protein disaggregation chaperone; Provisional	98.67
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	98.66
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	98.65
PLN03025	319	replication factor C subunit; Provisional	98.64
PRK13342	413	recombination factor protein RarA; Reviewed	98.64
PRK12402	337	replication factor C small subunit 2; Reviewed	98.63
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	98.6
PHA02544	316	44 clamp loader, small subunit; Provisional	98.59
PRK07940	394	DNA polymerase III subunit delta'; Validated	98.59
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	98.59
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	98.58
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	98.56
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	98.55
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.55
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	98.54
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	98.51
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	98.5
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.49
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	98.49
PRK15455	644	PrkA family serine protein kinase; Provisional	98.49
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	98.48
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	98.47
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	98.47
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	98.46
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	98.46
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	98.46
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	98.46
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	98.45
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	98.44
PRK13341	725	recombination factor protein RarA/unknown domain f	98.44
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	98.43
KOG2028	554	consensus ATPase related to the helicase subunit o	98.43
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	98.42
PRK08903	227	DnaA regulatory inactivator Hda; Validated	98.42
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	98.42
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	98.41
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	98.4
COG1484	254	DnaC DNA replication protein [DNA replication, rec	98.39
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	98.38
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	98.38
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	98.38
PRK00440	319	rfc replication factor C small subunit; Reviewed	98.37
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	98.36
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	98.36
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	98.36
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	98.36
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	98.35
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	98.35
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	98.35
PRK08181	269	transposase; Validated	98.34
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	98.34
smart00382	148	AAA ATPases associated with a variety of cellular	98.34
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	98.34
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	98.34
PF07726	131	AAA_3: ATPase family associated with various cellu	98.32
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	98.32
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	98.32
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	98.31
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	98.31
PRK08116	268	hypothetical protein; Validated	98.31
PRK00149	450	dnaA chromosomal replication initiation protein; R	98.3
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	98.3
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	98.3
PRK12377	248	putative replication protein; Provisional	98.3
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	98.29
PRK08939	306	primosomal protein DnaI; Reviewed	98.28
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	98.27
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	98.26
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	98.25
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	98.25
PRK06893	229	DNA replication initiation factor; Validated	98.25
PRK06835	329	DNA replication protein DnaC; Validated	98.25
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	98.25
PRK06526	254	transposase; Provisional	98.24
KOG1942	456	consensus DNA helicase, TBP-interacting protein [R	98.23
PHA02244	383	ATPase-like protein	98.23
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.22
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	98.22
PRK06620	214	hypothetical protein; Validated	98.2
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	98.2
PRK08084	235	DNA replication initiation factor; Provisional	98.19
PRK07952	244	DNA replication protein DnaC; Validated	98.18
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	98.17
COG0714	329	MoxR-like ATPases [General function prediction onl	98.17
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	98.16
PRK14088	440	dnaA chromosomal replication initiation protein; P	98.15
PRK06921	266	hypothetical protein; Provisional	98.14
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	98.14
PRK13948	182	shikimate kinase; Provisional	98.13
PRK08727	233	hypothetical protein; Validated	98.12
) 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	98.11
COG0606	490	Predicted ATPase with chaperone activity [Posttran	98.11
PRK09183	259	transposase/IS protein; Provisional	98.1
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.09
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	98.06
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	98.04
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	98.02
PRK05642	234	DNA replication initiation factor; Validated	98.01
PRK07471	365	DNA polymerase III subunit delta'; Validated	98.01
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	98.0
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	98.0
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	97.99
PRK05564	313	DNA polymerase III subunit delta'; Validated	97.99
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	97.99
PRK12422	445	chromosomal replication initiation protein; Provis	97.98
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	97.98
KOG0736	953	consensus Peroxisome assembly factor 2 containing	97.97
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	97.97
PRK14086	617	dnaA chromosomal replication initiation protein; P	97.92
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	97.92
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	97.91
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	97.9
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	97.9
PRK13531	498	regulatory ATPase RavA; Provisional	97.89
PHA00729	226	NTP-binding motif containing protein	97.89
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	97.88
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	97.87
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	97.86
PRK13765	637	ATP-dependent protease Lon; Provisional	97.85
PRK13946	184	shikimate kinase; Provisional	97.85
PLN02200	234	adenylate kinase family protein	97.85
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	97.85
PRK07399	314	DNA polymerase III subunit delta'; Validated	97.84
PRK09112	351	DNA polymerase III subunit delta'; Validated	97.8
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.8
KOG1969	877	consensus DNA replication checkpoint protein CHL12	97.78
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	97.78
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	97.76
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	97.76
PHA02624	647	large T antigen; Provisional	97.75
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	97.72
PRK06547	172	hypothetical protein; Provisional	97.7
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.69
PRK08058	329	DNA polymerase III subunit delta'; Validated	97.66
PLN02674	244	adenylate kinase	97.65
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	97.64
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	97.63
PTZ00112	1164	origin recognition complex 1 protein; Provisional	97.61
PLN02199	303	shikimate kinase	97.61
PRK05541	176	adenylylsulfate kinase; Provisional	97.59
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	97.58
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	97.55
PRK09087	226	hypothetical protein; Validated	97.54
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	97.54
PRK15424	538	propionate catabolism operon regulatory protein Pr	97.53
PF13245	76	AAA_19: Part of AAA domain	97.53
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	97.52
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	97.52
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	97.5
PRK11608	326	pspF phage shock protein operon transcriptional ac	97.49
COG0593	408	DnaA ATPase involved in DNA replication initiation	97.48
PRK06696	223	uridine kinase; Validated	97.46
PLN02459	261	probable adenylate kinase	97.44
PRK05022	509	anaerobic nitric oxide reductase transcription reg	97.43
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	97.42
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	97.42
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	97.42
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	97.42
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	97.42
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	97.4
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	97.39
PF06414	199	Zeta_toxin: Zeta toxin; InterPro: IPR010488 This e	97.38
COG1221	403	PspF Transcriptional regulators containing an AAA-	97.35
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	97.35
PF13173	128	AAA_14: AAA domain	97.35
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.34
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	97.34
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	97.34
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	97.32
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	97.32
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	97.31
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	97.31
PF12774	231	AAA_6: Hydrolytic ATP binding site of dynein motor	97.28
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	97.27
cd01394	218	radB RadB. The archaeal protein radB shares simila	97.27
PHA02774	613	E1; Provisional	97.22
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	97.21
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.2
COG3842	352	PotA ABC-type spermidine/putrescine transport syst	97.2
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	97.19
PRK06067	234	flagellar accessory protein FlaH; Validated	97.19
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	97.17
PLN02165	334	adenylate isopentenyltransferase	97.17
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	97.16
KOG3354	191	consensus Gluconate kinase [Carbohydrate transport	97.14
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	97.13
PRK08099	399	bifunctional DNA-binding transcriptional repressor	97.13
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	97.12
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	97.11
PRK05973	237	replicative DNA helicase; Provisional	97.1
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	97.1
PRK03846	198	adenylylsulfate kinase; Provisional	97.09
PLN03210	1153	Resistant to P. syringae 6; Provisional	97.09
PRK00771	437	signal recognition particle protein Srp54; Provisi	97.09
TIGR01526	325	nadR_NMN_Atrans nicotinamide-nucleotide adenylyltr	97.08
PRK08533	230	flagellar accessory protein FlaH; Reviewed	97.08
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.07
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	97.06
TIGR00455	184	apsK adenylylsulfate kinase (apsK). Important resi	97.05
KOG0990	360	consensus Replication factor C, subunit RFC5 [Repl	97.03
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	97.03
PRK08699	325	DNA polymerase III subunit delta'; Validated	97.03
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	97.02
PRK12337	475	2-phosphoglycerate kinase; Provisional	97.02
TIGR00064	272	ftsY signal recognition particle-docking protein F	97.01
PRK05707	328	DNA polymerase III subunit delta'; Validated	97.0
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	97.0
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	96.99
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	96.99
TIGR00376	637	DNA helicase, putative. The gene product may repre	96.95
PRK10416	318	signal recognition particle-docking protein FtsY;	96.95
PRK04328	249	hypothetical protein; Provisional	96.93
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	96.91
smart00350	509	MCM minichromosome maintenance proteins.	96.9
PRK07667	193	uridine kinase; Provisional	96.89
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	96.88
PRK05537	568	bifunctional sulfate adenylyltransferase subunit 1	96.87
cd00983	325	recA RecA is a bacterial enzyme which has roles in	96.87
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	96.87
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	96.85
KOG2680	454	consensus DNA helicase TIP49, TBP-interacting prot	96.85
PRK14738	206	gmk guanylate kinase; Provisional	96.84
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	96.84
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	96.82
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	96.82
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	96.81
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.81
PRK04220	301	2-phosphoglycerate kinase; Provisional	96.8
PRK11823	446	DNA repair protein RadA; Provisional	96.8
PLN02840	421	tRNA dimethylallyltransferase	96.79
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	96.78
TIGR02236	310	recomb_radA DNA repair and recombination protein R	96.78
COG3839	338	MalK ABC-type sugar transport systems, ATPase comp	96.77
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	96.77
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	96.76
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	96.74
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	96.72
PF00005	137	ABC_tran: ABC transporter This structure is on hol	96.72
PRK10536	262	hypothetical protein; Provisional	96.71
COG1855	604	ATPase (PilT family) [General function prediction	96.71
PRK06964	342	DNA polymerase III subunit delta'; Validated	96.71
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.7
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	96.7
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	96.7
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	96.69
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	96.68
PRK13833	323	conjugal transfer protein TrbB; Provisional	96.67
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.66
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	96.64
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	96.63
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	96.63
PRK04301	317	radA DNA repair and recombination protein RadA; Va	96.62
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.62
PTZ00202	550	tuzin; Provisional	96.61
cd03255	218	ABC_MJ0796_Lo1CDE_FtsE This family is comprised of	96.58
cd01918	149	HprK_C HprK/P, the bifunctional histidine-containi	96.58
PRK09354	349	recA recombinase A; Provisional	96.57
PRK13851	344	type IV secretion system protein VirB11; Provision	96.57
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	96.56
PRK13477	512	bifunctional pantoate ligase/cytidylate kinase; Pr	96.56
PRK08769	319	DNA polymerase III subunit delta'; Validated	96.55
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	96.55
cd01128	249	rho_factor Transcription termination factor rho is	96.54
COG0802	149	Predicted ATPase or kinase [General function predi	96.53
PF13555	62	AAA_29: P-loop containing region of AAA domain	96.52
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	96.51
PF00519	432	PPV_E1_C: Papillomavirus helicase; InterPro: IPR00	96.51
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	96.51
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	96.5
PRK13764	602	ATPase; Provisional	96.49
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	96.49
PRK14974	336	cell division protein FtsY; Provisional	96.48
cd03258	233	ABC_MetN_methionine_transporter MetN (also known a	96.45
cd03262	213	ABC_HisP_GlnQ_permeases HisP and GlnQ are the ATP-	96.45
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.45
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	96.44
PRK06871	325	DNA polymerase III subunit delta'; Validated	96.43
COG4619	223	ABC-type uncharacterized transport system, ATPase	96.43
TIGR02673	214	FtsE cell division ATP-binding protein FtsE. This	96.42
TIGR03410	230	urea_trans_UrtE urea ABC transporter, ATP-binding	96.42
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	96.42
cd03292	214	ABC_FtsE_transporter FtsE is a hydrophilic nucleot	96.42
cd03269	210	ABC_putative_ATPase This subfamily is involved in	96.41
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.41
TIGR02315	243	ABC_phnC phosphonate ABC transporter, ATP-binding	96.4
PRK07993	334	DNA polymerase III subunit delta'; Validated	96.4
cd03256	241	ABC_PhnC_transporter ABC-type phosphate/phosphonat	96.4
PLN02748	468	tRNA dimethylallyltransferase	96.39
PRK10867	433	signal recognition particle protein; Provisional	96.39
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	96.38
PRK10646	153	ADP-binding protein; Provisional	96.38
COG2204	464	AtoC Response regulator containing CheY-like recei	96.38
COG4178	604	ABC-type uncharacterized transport system, permeas	96.37
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	96.36
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	96.36
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	96.35
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	96.35
TIGR03608	206	L_ocin_972_ABC putative bacteriocin export ABC tra	96.35
cd03301	213	ABC_MalK_N The N-terminal ATPase domain of the mal	96.34
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	96.33
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	96.33
PRK13541	195	cytochrome c biogenesis protein CcmA; Provisional	96.33
cd03224	222	ABC_TM1139_LivF_branched LivF (TM1139) is part of	96.32
cd03278	197	ABC_SMC_barmotin Barmotin is a tight junction-asso	96.32
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	96.31
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	96.3
cd03260	227	ABC_PstB_phosphate_transporter Phosphate uptake is	96.3
cd03225	211	ABC_cobalt_CbiO_domain1 Domain I of the ABC compon	96.3
TIGR02211	221	LolD_lipo_ex lipoprotein releasing system, ATP-bin	96.3
TIGR01663	526	PNK-3'Pase polynucleotide 5'-kinase 3'-phosphatase	96.29
cd03261	235	ABC_Org_Solvent_Resistant ABC (ATP-binding cassett	96.29
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	96.29
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	96.28
PRK09376	416	rho transcription termination factor Rho; Provisio	96.28
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	96.28
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	96.27
cd03226	205	ABC_cobalt_CbiO_domain2 Domain II of the ABC compo	96.27
cd03234	226	ABCG_White The White subfamily represents ABC tran	96.27
cd03235	213	ABC_Metallic_Cations ABC component of the metal-ty	96.27
PRK11124	242	artP arginine transporter ATP-binding subunit; Pro	96.26
PRK10247	225	putative ABC transporter ATP-binding protein YbbL;	96.26
cd03264	211	ABC_drug_resistance_like ABC-type multidrug transp	96.26
PRK14247	250	phosphate ABC transporter ATP-binding protein; Pro	96.26
PRK09862	506	putative ATP-dependent protease; Provisional	96.25
COG3604	550	FhlA Transcriptional regulator containing GAF, AAA	96.25
cd03296	239	ABC_CysA_sulfate_importer Part of the ABC transpor	96.25
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	96.24
cd03219	236	ABC_Mj1267_LivG_branched The Mj1267/LivG ABC trans	96.23
cd03293	220	ABC_NrtD_SsuB_transporters NrtD and SsuB are the A	96.23
PRK10895	241	lipopolysaccharide ABC transporter ATP-binding pro	96.23
TIGR03864	236	PQQ_ABC_ATP ABC transporter, ATP-binding subunit,	96.22
cd03263	220	ABC_subfamily_A The ABCA subfamily mediates the tr	96.21
cd03218	232	ABC_YhbG The ABC transporters belonging to the Yhb	96.21
cd03216	163	ABC_Carb_Monos_I This family represents the domain	96.2
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	96.2
cd03254	229	ABCC_Glucan_exporter_like Glucan exporter ATP-bind	96.2
cd03257	228	ABC_NikE_OppD_transporters The ABC transporter sub	96.2
TIGR01978	243	sufC FeS assembly ATPase SufC. SufC is part of the	96.19
PRK11629	233	lolD lipoprotein transporter ATP-binding subunit;	96.19
PRK11264	250	putative amino-acid ABC transporter ATP-binding pr	96.19
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	96.19
TIGR03005	252	ectoine_ehuA ectoine/hydroxyectoine ABC transporte	96.18
cd03215	182	ABC_Carb_Monos_II This family represents domain II	96.18
COG4525	259	TauB ABC-type taurine transport system, ATPase com	96.18
cd03251	234	ABCC_MsbA MsbA is an essential ABC transporter, cl	96.18
cd03246	173	ABCC_Protease_Secretion This family represents the	96.17
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	96.16
cd03267	236	ABC_NatA_like Similar in sequence to NatA, this is	96.16
cd03213	194	ABCG_EPDR ABCG transporters are involved in eye pi	96.16
TIGR02770	230	nickel_nikD nickel import ATP-binding protein NikD	96.16
PRK10771	232	thiQ thiamine transporter ATP-binding subunit; Pro	96.15
PRK11860	661	bifunctional 3-phosphoshikimate 1-carboxyvinyltran	96.15
PRK11248	255	tauB taurine transporter ATP-binding subunit; Prov	96.15
PRK10908	222	cell division protein FtsE; Provisional	96.15
cd03265	220	ABC_DrrA DrrA is the ATP-binding protein component	96.14
TIGR01277	213	thiQ thiamine ABC transporter, ATP-binding protein	96.14
PRK09302	509	circadian clock protein KaiC; Reviewed	96.14
cd03266	218	ABC_NatA_sodium_exporter NatA is the ATPase compon	96.13
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	96.13
cd03259	213	ABC_Carb_Solutes_like ABC Carbohydrate and Solute	96.13
TIGR00959	428	ffh signal recognition particle protein. This mode	96.13
cd03244	221	ABCC_MRP_domain2 Domain 2 of the ABC subfamily C.	96.13
PRK13538	204	cytochrome c biogenesis protein CcmA; Provisional	96.12
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	96.12
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	96.12
PRK13540	200	cytochrome c biogenesis protein CcmA; Provisional	96.12
PRK05439	311	pantothenate kinase; Provisional	96.12
cd00879	190	Sar1 Sar1 subfamily. Sar1 is an essential componen	96.11
TIGR02323	253	CP_lyasePhnK phosphonate C-P lyase system protein	96.11
cd03250	204	ABCC_MRP_domain1 Domain 1 of the ABC subfamily C.	96.1
PRK10584	228	putative ABC transporter ATP-binding protein YbbA;	96.1
PRK09493	240	glnQ glutamine ABC transporter ATP-binding protein	96.1
cd03268	208	ABC_BcrA_bacitracin_resist The BcrA subfamily repr	96.1
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	96.1
COG1122	235	CbiO ABC-type cobalt transport system, ATPase comp	96.08
cd03369	207	ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-ty	96.08
PRK14267	253	phosphate ABC transporter ATP-binding protein; Pro	96.08
PF01926	116	MMR_HSR1: 50S ribosome-binding GTPase; InterPro: I	96.08
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	96.08
cd03232	192	ABC_PDR_domain2 The pleiotropic drug resistance-li	96.07
PRK12608	380	transcription termination factor Rho; Provisional	96.07
PRK06090	319	DNA polymerase III subunit delta'; Validated	96.07
TIGR02533	486	type_II_gspE general secretory pathway protein E.	96.07
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	96.06
PRK14250	241	phosphate ABC transporter ATP-binding protein; Pro	96.06
cd04155	173	Arl3 Arl3 subfamily. Arl3 (Arf-like 3) is an Arf f	96.06
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	96.05
PRK14262	250	phosphate ABC transporter ATP-binding protein; Pro	96.05
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	96.05
COG1125	309	OpuBA ABC-type proline/glycine betaine transport s	96.05
cd03249	238	ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6)	96.05
PRK13543	214	cytochrome c biogenesis protein CcmA; Provisional	96.05
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	96.05
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	96.04
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	96.04
cd03253	236	ABCC_ATM1_transporter ATM1 is an ABC transporter t	96.03
PRK13539	207	cytochrome c biogenesis protein CcmA; Provisional	96.03
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	96.03
cd03297	214	ABC_ModC_molybdenum_transporter ModC is an ABC-typ	96.03
cd03245	220	ABCC_bacteriocin_exporters ABC-type bacteriocin ex	96.02
PRK14242	253	phosphate transporter ATP-binding protein; Provisi	96.02
PRK11701	258	phnK phosphonate C-P lyase system protein PhnK; Pr	96.01
PRK11300	255	livG leucine/isoleucine/valine transporter ATP-bin	96.01
TIGR03740	223	galliderm_ABC gallidermin-class lantibiotic protec	96.01
cd03252	237	ABCC_Hemolysin The ABC-transporter hemolysin B is	96.0
PRK13547	272	hmuV hemin importer ATP-binding subunit; Provision	96.0
PRK14256	252	phosphate ABC transporter ATP-binding protein; Pro	96.0
cd03220	224	ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transpo	96.0
PF06431	417	Polyoma_lg_T_C: Polyomavirus large T antigen C-ter	96.0
cd03295	242	ABC_OpuCA_Osmoprotection OpuCA is a the ATP bindin	95.99
cd03237	246	ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 o	95.99
PRK15177	213	Vi polysaccharide export ATP-binding protein VexC;	95.99
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	95.99
PRK11247	257	ssuB aliphatic sulfonates transport ATP-binding su	95.98
KOG0060	659	consensus Long-chain acyl-CoA transporter, ABC sup	95.98
PRK11432	351	fbpC ferric transporter ATP-binding subunit; Provi	95.97
TIGR01189	198	ccmA heme ABC exporter, ATP-binding protein CcmA.	95.97
cd03290	218	ABCC_SUR1_N The SUR domain 1. The sulfonylurea rec	95.97
cd03248	226	ABCC_TAP TAP, the Transporter Associated with Anti	95.96
TIGR01184	230	ntrCD nitrate transport ATP-binding subunits C and	95.96
PRK14261	253	phosphate ABC transporter ATP-binding protein; Pro	95.96
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	95.96
cd03217	200	ABC_FeS_Assembly ABC-type transport system involve	95.95
PRK09984	262	phosphonate/organophosphate ester transporter subu	95.95
TIGR03411	242	urea_trans_UrtD urea ABC transporter, ATP-binding	95.95
cd03233	202	ABC_PDR_domain1 The pleiotropic drug resistance (P	95.95
PRK13645	289	cbiO cobalt transporter ATP-binding subunit; Provi	95.94
KOG1803	649	consensus DNA helicase [Replication, recombination	95.93
PRK10619	257	histidine/lysine/arginine/ornithine transporter su	95.93
PRK10575	265	iron-hydroxamate transporter ATP-binding subunit;	95.93

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

Probab=100.00  E-value=4.7e-49  Score=351.85  Aligned_cols=212  Identities=52%  Similarity=0.864  Sum_probs=199.5

Q ss_pred             HHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhhhcccceeecccCCeeEEEEeecc
Q 025979           34 LYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTI  113 (245)
Q Consensus        34 ~~~~~~~~~~e~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~  113 (245)
                      .+.+...++++...+..+...+..+...++.++..++++++.++++|..++++.+.+++++++++++++++|++++.+++
T Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~l~~~pl~vg~v~e~id~~~~iVks~~g~~~vV~i~~~v  105 (406)
T COG1222          26 EDTKLKLLEKEKRLLLLEEQRLEAEGLRLKREVDRLREEIERLKEPPLIVGTVLEVLDDGRAIVKSSTGPKFVVNILSFV  105 (406)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHhcCCCceEEEEEEEcCCceEEEEeCCCCeEEEeccCCc
Confidence            34455555666655555667777777788889999999999999999999999999999999999999999999999999


Q ss_pred             cccccCCCceeeeeccccccccccCCCccccccccccCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCC
Q 025979          114 NRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPP  193 (245)
Q Consensus       114 ~~~~l~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~  193 (245)
                      ++..++||.+|+++.++++++.++|++.|+.++.|...+.|+++|+||||+++|+++|+|+|++|+++|++|.++|+.||
T Consensus       106 d~~~L~pG~rVal~~~s~~Iv~vLp~~~Dp~V~~M~v~e~PdvtY~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PP  185 (406)
T COG1222         106 DRDLLEPGMRVALNRDSYSIVRVLPPEVDPRVSVMEVEEKPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPP  185 (406)
T ss_pred             CHHHcCCCCEEEEcCCcceeeeeCCCccCchhheeeeccCCCCChhhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhccccccccccC
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge~~~~vr~iF  245 (245)
                      +|||||||||||||+||||+|++.+++|+++.+|+|++||+||+++.||++|
T Consensus       186 KGVLLYGPPGTGKTLLAkAVA~~T~AtFIrvvgSElVqKYiGEGaRlVRelF  237 (406)
T COG1222         186 KGVLLYGPPGTGKTLLAKAVANQTDATFIRVVGSELVQKYIGEGARLVRELF  237 (406)
T ss_pred             CceEeeCCCCCcHHHHHHHHHhccCceEEEeccHHHHHHHhccchHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999998

>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.5e-48  Score=334.41  Aligned_cols=216  Identities=82%  Similarity=1.215  Sum_probs=212.6

Q ss_pred             CchhHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhhhcccceeecccCCeeEEEE
Q 025979           30 DEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRI  109 (245)
Q Consensus        30 ~~~~~~~~~~~~~~e~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  109 (245)
                      ....++.++++++++++.+..+..+|+++..++++|+...+++.+++++.|.++|.+.+.+|.+.+++.+.+|++|++++
T Consensus        26 ~~~dly~r~k~le~~le~l~vqe~yik~e~~~lkre~~~aqeevkriqsvplvigqfle~vdqnt~ivgsttgsny~vri  105 (408)
T KOG0727|consen   26 DKEDLYVRYKKLERELELLEVQEDYIKDEQRNLKRELLHAQEEVKRIQSVPLVIGQFLEAVDQNTAIVGSTTGSNYYVRI  105 (408)
T ss_pred             cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccchHHHHHHHhhhccCceeecccCCceEEee
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccccccCCCceeeeeccccccccccCCCccccccccccCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhc
Q 025979          110 LSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIG  189 (245)
Q Consensus       110 ~~~~~~~~l~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g  189 (245)
                      ++.++++.++|+.+|+++++++++.+++|++.+++++.+...++|+++|.|++|+|-++++|++++++|+.|.++|+.+|
T Consensus       106 lstidrellkps~svalhrhsnalvdvlppeadssi~ml~~~ekpdvsy~diggld~qkqeireavelplt~~~ly~qig  185 (408)
T KOG0727|consen  106 LSTIDRELLKPSASVALHRHSNALVDVLPPEADSSISMLGPDEKPDVSYADIGGLDVQKQEIREAVELPLTHADLYKQIG  185 (408)
T ss_pred             hhhhhHHHcCCccchhhhhcccceeeccCCcccccccccCCCCCCCccccccccchhhHHHHHHHHhccchHHHHHHHhC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhccccccccccC
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge~~~~vr~iF  245 (245)
                      ++||+|||+|||||||||+||||+|+...+.|+++.+|+|++||+||+.++||++|
T Consensus       186 idpprgvllygppg~gktml~kava~~t~a~firvvgsefvqkylgegprmvrdvf  241 (408)
T KOG0727|consen  186 IDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEGPRMVRDVF  241 (408)
T ss_pred             CCCCcceEEeCCCCCcHHHHHHHHhhccchheeeeccHHHHHHHhccCcHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999998

>KOG0726 consensus 26S proteasome regulatory complex, ATPase RPT2 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=3.4e-40  Score=288.57  Aligned_cols=233  Identities=41%  Similarity=0.738  Sum_probs=211.1

Q ss_pred             CCCCCCCcccCCCCCCCC-------------chhHHHHHHHHHHHhhhhhhhHHHHHHHHH--HHHHHHHHHHHHhhhhc
Q 025979           13 VSEPPPSTRSDLTEQWSD-------------EDDLYSRLKSLQRQLEFIDIQEEYVKDEQK--NLKRELLRAQEEVKRIQ   77 (245)
Q Consensus        13 ~~e~~~~~~~e~~~~~~~-------------~~~~~~~~~~~~~e~~~l~~~~~~i~~~~~--~~~~~~~~~~~~~~~~~   77 (245)
                      .++|+...+..-..++.+             ..+|+-++.++++-..+|..+.++|+++..  ...+...+-+.+.++++
T Consensus        24 ~~~~~v~~r~gr~k~~~kGpdAa~klP~V~p~~~C~lrlLk~~RIkDyLLMEEEFI~NQe~~k~~e~~~ee~r~~vd~lR  103 (440)
T KOG0726|consen   24 KYEPPVPTRVGRKKKKGKGPDAASKLPTVTPHTQCKLKLLKLERIKDYLLMEEEFIRNQERLKPQEEKQEEERSKVDDLR  103 (440)
T ss_pred             ccCCCCcchhhhhhhcccCcchhhcCCccccchhHHHHHHHHHHHHHHHHHHHHHHhhccccCCchhhhHHHHhHHHhhc
Confidence            377777777665544442             457788899999988899888888887754  22222233457899999


Q ss_pred             cccchhhhhhhhhhcccceeecccCCeeEEEEeecccccccCCCceeeeeccccccccccCCCccccccccccCCCCCce
Q 025979           78 SVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVT  157 (245)
Q Consensus        78 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~  157 (245)
                      .+|..++++.+.+|++++++.++.+..|++.++++++.+.+.||++|-+++...++..++..+.++.++.|.....|.-+
T Consensus       104 GtPmsvg~leEiidd~haivst~~g~e~Yv~IlSfVdKdlLepgcsvll~~k~~avvGvL~d~~dpmv~vmK~eKaP~Et  183 (440)
T KOG0726|consen  104 GTPMSVGTLEEIIDDNHAIVSTSVGSEYYVSILSFVDKDLLEPGCSVLLNHKVHAVVGVLQDDTDPMVSVMKVEKAPQET  183 (440)
T ss_pred             CCccccccHHHHhcCCceEEecccCchheeeeeeeccHhhcCCCCeeeeccccceEEEEeccCCCccceeeecccCchhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhccc
Q 025979          158 YNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEV  237 (245)
Q Consensus       158 ~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge~  237 (245)
                      |.|++|++.++++|++.+++|+.||++|..+|++||+||+|||+||||||+||+|+|+...++|+|+.+|+++++|.|++
T Consensus       184 y~diGGle~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAVANqTSATFlRvvGseLiQkylGdG  263 (440)
T KOG0726|consen  184 YADIGGLESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDG  263 (440)
T ss_pred             hcccccHHHHHHHHHHhhcCCCCCHHHHHHcCCCCCCeeEEeCCCCCchhHHHHHHhcccchhhhhhhhHHHHHHHhccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccccC
Q 025979          238 WLKHKQIF  245 (245)
Q Consensus       238 ~~~vr~iF  245 (245)
                      .+.||++|
T Consensus       264 pklvRqlF  271 (440)
T KOG0726|consen  264 PKLVRELF  271 (440)
T ss_pred             hHHHHHHH
Confidence            99999998

>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.5e-39  Score=278.51  Aligned_cols=216  Identities=37%  Similarity=0.589  Sum_probs=207.9

Q ss_pred             CchhHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhhhcccceeecccCCeeEEEE
Q 025979           30 DEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRI  109 (245)
Q Consensus        30 ~~~~~~~~~~~~~~e~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  109 (245)
                      -.....+++.++|..+....+.+.+++.+.+++.....-++++++.++.+...++++.+.+++++.+++..++.+|++.+
T Consensus        18 ~~~y~~~ki~~~~~~v~~kt~nlrrleaqrneln~kvr~lreel~~lqe~gsyvgev~k~m~k~kVLVKvhpegKyvvdv   97 (404)
T KOG0728|consen   18 LRQYYLQKIEELQLQVAEKTQNLRRLEAQRNELNAKVRLLREELQLLQEPGSYVGEVVKAMGKKKVLVKVHPEGKYVVDV   97 (404)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhcCcchHHHHHHhcCcceEEEEEcCCCcEEEec
Confidence            34445578899999998888999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccccccCCCceeeeeccccccccccCCCccccccccccCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhc
Q 025979          110 LSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIG  189 (245)
Q Consensus       110 ~~~~~~~~l~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g  189 (245)
                      ...++...+.++.+|++..+++.++.++|...|+.++.|...+.|+.+|+-++|+|.++++|++.|++|.+||++|..+|
T Consensus        98 ~k~i~i~~~~~~~rVaLR~dsY~lhkiLpnKvDpLVsLMmVeKvPDStYeMiGgLd~QIkeIkEVIeLPvKHPELF~aLG  177 (404)
T KOG0728|consen   98 DKNIDISDVTPSSRVALRNDSYTLHKILPNKVDPLVSLMMVEKVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALG  177 (404)
T ss_pred             cCCCcHhhcCCcceEEEeccchHHHHhcccccchhhHHHhhhhCCccHHHHhccHHHHHHHHHHHHhccccCHHHHHhcC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhccccccccccC
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge~~~~vr~iF  245 (245)
                      +..|+|+|||||||||||+||+|+|....+.|+|+++|+++++|+||+.++||++|
T Consensus       178 IaQPKGvlLygppgtGktLlaraVahht~c~firvsgselvqk~igegsrmvrelf  233 (404)
T KOG0728|consen  178 IAQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQKYIGEGSRMVRELF  233 (404)
T ss_pred             CCCCcceEEecCCCCchhHHHHHHHhhcceEEEEechHHHHHHHhhhhHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999998

>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=3.9e-37  Score=266.22  Aligned_cols=217  Identities=31%  Similarity=0.646  Sum_probs=205.8

Q ss_pred             CCchhHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhhhc----------------
Q 025979           29 SDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQ----------------   92 (245)
Q Consensus        29 ~~~~~~~~~~~~~~~e~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~----------------   92 (245)
                      +..+.+.++.+-+..|+..++.+..++..+....++.+.+..++|+-.+..|+.++.+.+.++-                
T Consensus        20 mste~i~~rtrlldnEirI~~sev~ri~he~~~~~ekIkeN~EkIk~Nk~LPYLV~NvvE~ld~~~~~~~e~sg~n~~ld   99 (424)
T KOG0652|consen   20 MSTEEIISRTRLLDNEIRIMKSEVQRINHELQAMKEKIKENTEKIKVNKQLPYLVSNVVELLDMDPNDDEEDSGANIDLD   99 (424)
T ss_pred             ccHHHHHHHHHHhhhHHHHHHHHHHHhhhHHHHHHHHHHhhHHHhhccccCchHHhhHHHHhcCCcccchhccCCccccc
Confidence            3456777888889999999999999999999999999999999999999999999999999972                


Q ss_pred             -----ccceeecccCCeeEEEEeecccccccCCCceeeeeccccccccccCCCccccccccccCCCCCceeccCCcchhh
Q 025979           93 -----NNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQ  167 (245)
Q Consensus        93 -----~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~dv~Gl~~~  167 (245)
                           ..+++++|+...++..+...++.+.++||..|.++.+++-+.+.+|.+.++.+..|...++|.-+|+|++|++.+
T Consensus       100 ~qrkgkcaViktStRqt~fLPvvGLvd~~~LkPgDLVgvnKDsyliletLP~eyDsrVkaMevDekPtE~YsDiGGldkQ  179 (424)
T KOG0652|consen  100 SQRKGKCAVIKTSTRQTYFLPVVGLVDPDKLKPGDLVGVNKDSYLILETLPSEYDSRVKAMEVDEKPTEQYSDIGGLDKQ  179 (424)
T ss_pred             ccccceeEEEecccceeeeeeeecccChhhCCCcceeeecCCceeehhcCChhhhhhcceeeeccCCcccccccccHHHH
Confidence                 123778999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhccccccccccC
Q 025979          168 KQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       168 ~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge~~~~vr~iF  245 (245)
                      ++++.++|.+|+.|++.|.++|+.||+|+|+|||||||||++|||+|...+.+|+.+.++.++++|+|++++.||+.|
T Consensus       180 IqELvEAiVLpmth~ekF~~lgi~pPKGvLmYGPPGTGKTlmARAcAaqT~aTFLKLAgPQLVQMfIGdGAkLVRDAF  257 (424)
T KOG0652|consen  180 IQELVEAIVLPMTHKEKFENLGIRPPKGVLMYGPPGTGKTLMARACAAQTNATFLKLAGPQLVQMFIGDGAKLVRDAF  257 (424)
T ss_pred             HHHHHHHhccccccHHHHHhcCCCCCCceEeeCCCCCcHHHHHHHHHHhccchHHHhcchHHHhhhhcchHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999999987

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

Probab=100.00  E-value=9.1e-37  Score=282.96  Aligned_cols=220  Identities=79%  Similarity=1.170  Sum_probs=211.1

Q ss_pred             CCCCCchhHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhhhcccceeecccCCee
Q 025979           26 EQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNY  105 (245)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~e~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  105 (245)
                      +-+.....++.++.++++++..++.+...+..+++.+++++.++++++++++.+|..++++.+.+++.+++++++++.++
T Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~   91 (398)
T PTZ00454         12 STTHTERDLYEKLKELEKELEFLDIQEEYIKEEQKNLKRELIRAKEEVKRIQSVPLVIGQFLEMIDSNYGIVSSTSGSNY   91 (398)
T ss_pred             cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCceEEEEEEEEcCCEEEEEcCCCCEE
Confidence            44566677888888899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeecccccccCCCceeeeeccccccccccCCCccccccccccCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHH
Q 025979          106 YVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELY  185 (245)
Q Consensus       106 ~~~~~~~~~~~~l~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~  185 (245)
                      ++.+.+.+++..+++|..|.++.++..+.+++|+..++.+..+...+.|+++|+||+|++.++++|++.+.+|+.+|+.|
T Consensus        92 ~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~l~~~~~~~~~~~~~~~~p~v~~~digGl~~~k~~l~~~v~~pl~~~~~~  171 (398)
T PTZ00454         92 YVRILSTLNRELLKPNASVALHRHSHAVVDILPPEADSSIQLLQMSEKPDVTYSDIGGLDIQKQEIREAVELPLTCPELY  171 (398)
T ss_pred             EEecccccCHhhCCCCCEEEeeccchhHHHhccccccchhhhhcccCCCCCCHHHcCCHHHHHHHHHHHHHHHhcCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhccccccccccC
Q 025979          186 KQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       186 ~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge~~~~vr~iF  245 (245)
                      ..+|+.+|+|+|||||||||||++|+++|+.++.+|+++.++++.++|+|++++.++++|
T Consensus       172 ~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l~~~fi~i~~s~l~~k~~ge~~~~lr~lf  231 (398)
T PTZ00454        172 EQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATFIRVVGSEFVQKYLGEGPRMVRDVF  231 (398)
T ss_pred             HhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCCEEEEehHHHHHHhcchhHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999876

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

Probab=100.00  E-value=1.5e-35  Score=277.16  Aligned_cols=215  Identities=45%  Similarity=0.770  Sum_probs=206.8

Q ss_pred             chhHHHHHHHHHHHhhhhhhhHHHHHHHHH--HHHHHHHHHHHHhhhhccccchhhhhhhhhhcccceeecccCCeeEEE
Q 025979           31 EDDLYSRLKSLQRQLEFIDIQEEYVKDEQK--NLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVR  108 (245)
Q Consensus        31 ~~~~~~~~~~~~~e~~~l~~~~~~i~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  108 (245)
                      ...|+-++.++++++.+|..+.++++.+..  .+++++..+++++++++.+|..++++.+.++++++++.+++|.+++++
T Consensus        53 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~  132 (438)
T PTZ00361         53 NTKCRLRLLKLERIKDYLLLEEEFITNQEAQKPAQEKNEAELKKVDDLRGSPLSVGTLEEIIDENHAIVSSSVGPEYYVN  132 (438)
T ss_pred             chhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhhCCCcEEEEEEEEeCCCeEEEEeCCCCEEEEe
Confidence            457888999999999999999999999874  778899999999999999999999999999999999999999999999


Q ss_pred             EeecccccccCCCceeeeeccccccccccCCCccccccccccCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhh
Q 025979          109 ILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQI  188 (245)
Q Consensus       109 ~~~~~~~~~l~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~  188 (245)
                      +.+.++.+.++||..+.++..+..+..++|.+.+..++.|...+.|.++|+||+|++.++++|.+++..|+.+|++|..+
T Consensus       133 ~~~~~~~~~l~~~~~v~l~~~~~~~~~~~~~~~d~~~~~~~~~~~p~~~~~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~  212 (438)
T PTZ00361        133 ILSFVDKEQLEPGCSVLLHNKTHSVVGILLDEVDPLVSVMKVDKAPLESYADIGGLEQQIQEIKEAVELPLTHPELYDDI  212 (438)
T ss_pred             ccCcCCHhhCCCCCEEEEcCCCCceEecCccccchhhhhcccccCCCCCHHHhcCHHHHHHHHHHHHHhhhhCHHHHHhc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhccccccccccC
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge~~~~vr~iF  245 (245)
                      |+.+|+|+|||||||||||++|+++|++++.+|+++++++++++|+|++++.++++|
T Consensus       213 gi~~p~gVLL~GPPGTGKT~LAraIA~el~~~fi~V~~seL~~k~~Ge~~~~vr~lF  269 (438)
T PTZ00361        213 GIKPPKGVILYGPPGTGKTLLAKAVANETSATFLRVVGSELIQKYLGDGPKLVRELF  269 (438)
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHhhCCCEEEEecchhhhhhcchHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999998876

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=100.00  E-value=7.5e-33  Score=256.60  Aligned_cols=214  Identities=46%  Similarity=0.778  Sum_probs=203.2

Q ss_pred             hhHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhhhcccceeecccCCeeEEEEee
Q 025979           32 DDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILS  111 (245)
Q Consensus        32 ~~~~~~~~~~~~e~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~  111 (245)
                      ..+..++.++++++..++.+++.+..+.+..+.++.+++++++.++.+|..++.+.+.+++.+.++..++|.++++++.+
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~v~~~~g~~~~~~~~~   83 (389)
T PRK03992          4 EALEERNSELEEQIRQLELKLRDLEAENEKLERELERLKSELEKLKSPPLIVATVLEVLDDGRVVVKSSGGPQFLVNVSP   83 (389)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceEEEEEEEeCCCeEEEEECCCCEEEEeccc
Confidence            45567778888899999999999999999999999999999999999999999999999999899999999999999999


Q ss_pred             cccccccCCCceeeeeccccccccccCCCccccccccccCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccC
Q 025979          112 TINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGID  191 (245)
Q Consensus       112 ~~~~~~l~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~  191 (245)
                      ++....+.+|..+.++.....+..++|...+..+..+...+.|+++|+||+|+++++++|.+++..|+.+++.|..+|+.
T Consensus        84 ~~~~~~l~~g~~v~~~~~~~~~~~~l~~~~~~~~~~~~~~~~p~~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~  163 (389)
T PRK03992         84 FIDREKLKPGARVALNQQSLAIVEVLPSEKDPRVQAMEVIESPNVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIE  163 (389)
T ss_pred             cCCHhHCCCCCEEEEcCcchhhhhcccccccchhheeeecCCCCCCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCC
Confidence            99999999999999999999999999988888888888899999999999999999999999999999999999999999


Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhccccccccccC
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge~~~~vr~iF  245 (245)
                      +|+|+|||||||||||++|+++|+.++.+|+.++++++.++|+|++++.++.+|
T Consensus       164 ~p~gvLL~GppGtGKT~lAkaia~~~~~~~i~v~~~~l~~~~~g~~~~~i~~~f  217 (389)
T PRK03992        164 PPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQKFIGEGARLVRELF  217 (389)
T ss_pred             CCCceEEECCCCCChHHHHHHHHHHhCCCEEEeehHHHhHhhccchHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999998876

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=100.00  E-value=6.1e-33  Score=254.97  Aligned_cols=206  Identities=48%  Similarity=0.817  Sum_probs=196.0

Q ss_pred             HHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhhhcccceeecccCCeeEEEEeecccccccC
Q 025979           40 SLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLK  119 (245)
Q Consensus        40 ~~~~e~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  119 (245)
                      +++.++..|+++++.++.+.+..++++.++++++++++.+|..++++.+.+++++.+++++++.++++++.+|++...+.
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~   82 (364)
T TIGR01242         3 ELDVRIRKLEDEKRSLEKEKIRLERELERLRSEIERLRSPPLIVGTVLEVLDDNRVVVKSSTGPNFVVNVSAFIDRKSLK   82 (364)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeEEEEEEEEecCCEEEEEeCCCCEEEEeccccCCHhHCC
Confidence            45567888899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCceeeeeccccccccccCCCccccccccccCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeee
Q 025979          120 PSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLY  199 (245)
Q Consensus       120 ~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~  199 (245)
                      +|..+.++.....+..++|...++.+..+...+.|+++|+||+|+++++++|.+++..|+.+++.|..+|+.+|+|+|||
T Consensus        83 ~g~~v~~~~~~~~~~~~l~~~~~~~~~~~~~~~~p~~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~  162 (364)
T TIGR01242        83 PGARVALNQQTLTIVDVLPTSKDPLVKGMEVEERPNVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLY  162 (364)
T ss_pred             CCCEEEEcCCcceEEeecccccccccccceeccCCCCCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEE
Confidence            99999999999999999998888888888889999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCchHHHHHHHHhcccceeeeechhHHHHHHhccccccccccC
Q 025979          200 GPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       200 GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge~~~~vr~iF  245 (245)
                      ||||||||++|+++|+.++.+|+++.++++..+|+|++++.++.+|
T Consensus       163 GppGtGKT~lakaia~~l~~~~~~v~~~~l~~~~~g~~~~~i~~~f  208 (364)
T TIGR01242       163 GPPGTGKTLLAKAVAHETNATFIRVVGSELVRKYIGEGARLVREIF  208 (364)
T ss_pred             CCCCCCHHHHHHHHHHhCCCCEEecchHHHHHHhhhHHHHHHHHHH
Confidence            9999999999999999999999999999999999999998888765

Many proteins may score above the trusted cutoff because an internal

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=99.98  E-value=3.3e-33  Score=242.53  Aligned_cols=168  Identities=42%  Similarity=0.752  Sum_probs=147.6

Q ss_pred             cccchhhhhhhhhhcc----cceeecccCCeeEEEEeecccccccCCCceeeeeccccccccccCCCccccccccccCCC
Q 025979           78 SVPLVIGQFMEMVDQN----NGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEK  153 (245)
Q Consensus        78 ~~~~~~~~~~~~l~~~----~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~  153 (245)
                      ..|..++...+.++.+    +.++....-.+|++.+.+.+....+..|.+|.++++.+.+.-.+|+..++++..|..+++
T Consensus        92 eqplqvarctkii~~~~~d~~yvin~kqiakfvv~lg~~vsptdieegmrvgvdrnkyqi~lplppkidpsvtmm~veek  171 (435)
T KOG0729|consen   92 EQPLQVARCTKIISGNSEDPKYVINVKQIAKFVVGLGDRVSPTDIEEGMRVGVDRNKYQIQLPLPPKIDPSVTMMQVEEK  171 (435)
T ss_pred             cCCceeheeeeecCCCCCCcceeeeHHHHHHHHhccccccCchhhhhhheecccccceeEeccCCCCCCCceeEEEeecC
Confidence            3456666666655443    223333333445555566777788899999999999999999999999999999999999


Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHH
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKY  233 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~  233 (245)
                      |+++|+|++|+.++++.+++.|+.|+.||+.|-++|++||+|||+|||||||||++|+|+|+..++.|++|-+|++++||
T Consensus       172 pdvty~dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanrtdacfirvigselvqky  251 (435)
T KOG0729|consen  172 PDVTYSDVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANRTDACFIRVIGSELVQKY  251 (435)
T ss_pred             CCcccccccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhcccCceEEeehhHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccccccccccC
Q 025979          234 LGEVWLKHKQIF  245 (245)
Q Consensus       234 ~Ge~~~~vr~iF  245 (245)
                      +||++++||++|
T Consensus       252 vgegarmvrelf  263 (435)
T KOG0729|consen  252 VGEGARMVRELF  263 (435)
T ss_pred             hhhhHHHHHHHH
Confidence            999999999998

>KOG0651 consensus 26S proteasome regulatory complex, ATPase RPT4 [Posttranslational modification, protein turnover, chaperones]

Probab=99.96  E-value=1.9e-30  Score=228.62  Aligned_cols=196  Identities=33%  Similarity=0.616  Sum_probs=179.3

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhhhcccceeecccCCeeEEEEeecccccccCCCceeeeec
Q 025979           49 DIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHR  128 (245)
Q Consensus        49 ~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~~~~  128 (245)
                      ...++..+.....+.+........++.++.....++++.+.++..+.+|+.+.|..|++.+...++...+..|+++.++.
T Consensus        23 ~~~lka~~~~~r~l~k~~~ksend~kslqsvg~~~gevlk~l~~~~~iVK~s~Gpryvvg~~~~~D~~~i~~G~rv~ldi  102 (388)
T KOG0651|consen   23 SSALKALRENSRFLGKKYDKSENDLKSLQSVGQIIGEVLKQLEDEKFIVKASSGPRYVVGCRRSVDKEKIARGTRVVLDI  102 (388)
T ss_pred             hhHHHhHHHHHHHHhhhcCcccchHHHhhhcCchhHHHHhhccccceEeecCCCCcEEEEcccccchhhhccCceeeeee
Confidence            34444444444555555556667788888899999999999999999999999999999999999999999999999999


Q ss_pred             cccccccccCCCccccccccccCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHH
Q 025979          129 HSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTM  208 (245)
Q Consensus       129 ~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~  208 (245)
                      +...+...+|.+.+ .+..|......+++|+.++|+-.+..++++.|+.|+.+|++|.++|+++|+|++||||||||||+
T Consensus       103 ttltIm~~lprevd-~vy~m~~e~~~~~s~~~~ggl~~qirelre~ielpl~np~lf~rvgIk~Pkg~ll~GppGtGKTl  181 (388)
T KOG0651|consen  103 TTLTIMRGLPREVD-LVYNMSHEDPRNISFENVGGLFYQIRELREVIELPLTNPELFLRVGIKPPKGLLLYGPPGTGKTL  181 (388)
T ss_pred             eeeehhcccchHHH-HHHHhhhcCccccCHHHhCChHHHHHHHHhheEeeccCchhccccCCCCCceeEEeCCCCCchhH
Confidence            99999999999999 77888888888899999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcccceeeeechhHHHHHHhccccccccccC
Q 025979          209 LAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       209 lAkalA~~l~~~~~~v~~s~l~~~~~Ge~~~~vr~iF  245 (245)
                      +|+++|..+++.|+.++.++++++|+||+++.||+.|
T Consensus       182 la~~Vaa~mg~nfl~v~ss~lv~kyiGEsaRlIRemf  218 (388)
T KOG0651|consen  182 LARAVAATMGVNFLKVVSSALVDKYIGESARLIRDMF  218 (388)
T ss_pred             HHHHHHHhcCCceEEeeHhhhhhhhcccHHHHHHHHH
Confidence            9999999999999999999999999999999999876

>TIGR03689 pup_AAA proteasome ATPase

Probab=99.94  E-value=2.6e-27  Score=224.78  Aligned_cols=204  Identities=35%  Similarity=0.622  Sum_probs=169.5

Q ss_pred             HHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhhhccccchhhhhhhh-hhcccceeecccCCeeEEEEeeccccc
Q 025979           38 LKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEM-VDQNNGIVGSTTGSNYYVRILSTINRE  116 (245)
Q Consensus        38 ~~~~~~e~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-l~~~~~~~~~~~~~~~~~~~~~~~~~~  116 (245)
                      +.++++++..|..++..|.+.++..+.++..++++++++..||...+++.+. .+...+.+ ...|..+.+.+.+.++..
T Consensus         3 ~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~v-~~~g~~~~~~~~~~~~~~   81 (512)
T TIGR03689         3 LRELQATNSSLGARNAKLAELLKAARDKLSKLKSQLEQLAQPPSTYGTFLQTAIDDETAEV-FTAGRRMRVTVSPNVNAA   81 (512)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcceEEEEEeccCCCeEEE-EeCCceEEEEeCCCCCHH
Confidence            4567788888899999999999999999999999999999999999999987 55545555 667888888888888888


Q ss_pred             ccCCCceeeeec-------------------------------------------------------------ccccccc
Q 025979          117 LLKPSASVALHR-------------------------------------------------------------HSNALVD  135 (245)
Q Consensus       117 ~l~~~~~v~~~~-------------------------------------------------------------~~~~~~~  135 (245)
                      .+.+|..|.++.                                                             .......
T Consensus        82 ~l~~g~~v~l~e~~~~v~~~~~~~~g~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~  161 (512)
T TIGR03689        82 ELVPGQTVRLNEALQVVEARDFETVGEIATLKEVLGDGRALVVDHSGEERVVKLAGALADELIRAGDSLLVDPKAGYAFE  161 (512)
T ss_pred             HCCCCCEEEECCcceeeccCCCCCCCceEEEEEEeCCCeEEEEeCCCCeEEeehhhhhCHhhCCCCCEEEEcccchhhhh
Confidence            888888777660                                                             0000011


Q ss_pred             ccCCCccccccccccCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHh
Q 025979          136 VLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       136 il~~~~~~~~~~~~~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      .+|+   ..+..+...+.|+++|+||+|++.++++|++.|..|+.++++|..+|+.+|+|+|||||||||||++|+++|+
T Consensus       162 ~~~~---~~~~~l~~~~~p~v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~  238 (512)
T TIGR03689       162 AVPK---AEVEDLVLEEVPDVTYADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVAN  238 (512)
T ss_pred             cCCH---hHHhcceeecCCCCCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHH
Confidence            1110   1123344567789999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccc----------eeeeechhHHHHHHhccccccccccC
Q 025979          216 HTTA----------AFIRVVGSEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       216 ~l~~----------~~~~v~~s~l~~~~~Ge~~~~vr~iF  245 (245)
                      +++.          .|+.+++++++++|+|+++++++.+|
T Consensus       239 eL~~~i~~~~~~~~~fl~v~~~eLl~kyvGete~~ir~iF  278 (512)
T TIGR03689       239 SLAQRIGAETGDKSYFLNIKGPELLNKYVGETERQIRLIF  278 (512)
T ss_pred             hhccccccccCCceeEEeccchhhcccccchHHHHHHHHH
Confidence            9854          48889999999999999999999876

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.

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

Probab=99.94  E-value=1.5e-27  Score=224.98  Aligned_cols=95  Identities=48%  Similarity=0.824  Sum_probs=93.5

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      .+.|+++|+||||+++++.++..+|.+|+++|+.|+++|++.|.|||||||||||||+||||+|++.+.+|+.|.|++|+
T Consensus       503 ~tVPdVtW~dIGaL~~vR~eL~~aI~~PiK~pd~~k~lGi~~PsGvLL~GPPGCGKTLlAKAVANEag~NFisVKGPELl  582 (802)
T KOG0733|consen  503 ATVPDVTWDDIGALEEVRLELNMAILAPIKRPDLFKALGIDAPSGVLLCGPPGCGKTLLAKAVANEAGANFISVKGPELL  582 (802)
T ss_pred             eecCCCChhhcccHHHHHHHHHHHHhhhccCHHHHHHhCCCCCCceEEeCCCCccHHHHHHHHhhhccCceEeecCHHHH
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhccccccccccC
Q 025979          231 QKYLGEVWLKHKQIF  245 (245)
Q Consensus       231 ~~~~Ge~~~~vr~iF  245 (245)
                      +||+||+|+.||.+|
T Consensus       583 NkYVGESErAVR~vF  597 (802)
T KOG0733|consen  583 NKYVGESERAVRQVF  597 (802)
T ss_pred             HHHhhhHHHHHHHHH
Confidence            999999999999998

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

Probab=99.93  E-value=3.3e-27  Score=224.52  Aligned_cols=95  Identities=49%  Similarity=0.903  Sum_probs=93.4

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      .+.|+++|+||||++++|.++.+.|.+|++||+.|.++|++||+|||||||||||||++|||+|++++.+|+.|++++++
T Consensus       426 ve~p~v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~~~nFlsvkgpEL~  505 (693)
T KOG0730|consen  426 VEMPNVSWDDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEAGMNFLSVKGPELF  505 (693)
T ss_pred             ccCCCCChhhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhhcCCeeeccCHHHH
Confidence            56789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhccccccccccC
Q 025979          231 QKYLGEVWLKHKQIF  245 (245)
Q Consensus       231 ~~~~Ge~~~~vr~iF  245 (245)
                      +||+||+|++||++|
T Consensus       506 sk~vGeSEr~ir~iF  520 (693)
T KOG0730|consen  506 SKYVGESERAIREVF  520 (693)
T ss_pred             HHhcCchHHHHHHHH
Confidence            999999999999998

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

Probab=99.92  E-value=8.1e-26  Score=217.58  Aligned_cols=96  Identities=42%  Similarity=0.806  Sum_probs=91.6

Q ss_pred             ccCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhH
Q 025979          149 SQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSE  228 (245)
Q Consensus       149 ~~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~  228 (245)
                      ...+.|+|+|+||||++++|.+|.+.|..|+.||++|. .|+.+..|||||||||||||++|||+|.++...|+.|.|+|
T Consensus       662 GAPKIPnV~WdDVGGLeevK~eIldTIqlPL~hpeLfs-sglrkRSGILLYGPPGTGKTLlAKAVATEcsL~FlSVKGPE  740 (953)
T KOG0736|consen  662 GAPKIPNVSWDDVGGLEEVKTEILDTIQLPLKHPELFS-SGLRKRSGILLYGPPGTGKTLLAKAVATECSLNFLSVKGPE  740 (953)
T ss_pred             CCCCCCccchhcccCHHHHHHHHHHHhcCcccChhhhh-ccccccceeEEECCCCCchHHHHHHHHhhceeeEEeecCHH
Confidence            34578999999999999999999999999999999986 48888899999999999999999999999999999999999


Q ss_pred             HHHHHhccccccccccC
Q 025979          229 FVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       229 l~~~~~Ge~~~~vr~iF  245 (245)
                      +++||+||+|.|||++|
T Consensus       741 LLNMYVGqSE~NVR~VF  757 (953)
T KOG0736|consen  741 LLNMYVGQSEENVREVF  757 (953)
T ss_pred             HHHHHhcchHHHHHHHH
Confidence            99999999999999998

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.88  E-value=2.4e-23  Score=183.26  Aligned_cols=95  Identities=43%  Similarity=0.744  Sum_probs=90.0

Q ss_pred             cCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHH
Q 025979          150 QSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF  229 (245)
Q Consensus       150 ~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l  229 (245)
                      ..++|++.|+||.|++.+++.|+|+|.+|++.|.+|.. +-.|.+|+||||||||||+.||+|+|.+.+.+|+.|+.|++
T Consensus       124 v~EKPNVkWsDVAGLE~AKeALKEAVILPIKFPqlFtG-kR~PwrgiLLyGPPGTGKSYLAKAVATEAnSTFFSvSSSDL  202 (439)
T KOG0739|consen  124 VREKPNVKWSDVAGLEGAKEALKEAVILPIKFPQLFTG-KRKPWRGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDL  202 (439)
T ss_pred             hccCCCCchhhhccchhHHHHHHhheeecccchhhhcC-CCCcceeEEEeCCCCCcHHHHHHHHHhhcCCceEEeehHHH
Confidence            46899999999999999999999999999999999874 34578999999999999999999999999999999999999


Q ss_pred             HHHHhccccccccccC
Q 025979          230 VQKYLGEVWLKHKQIF  245 (245)
Q Consensus       230 ~~~~~Ge~~~~vr~iF  245 (245)
                      +++|.||+++.|+++|
T Consensus       203 vSKWmGESEkLVknLF  218 (439)
T KOG0739|consen  203 VSKWMGESEKLVKNLF  218 (439)
T ss_pred             HHHHhccHHHHHHHHH
Confidence            9999999999999988

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

Probab=99.87  E-value=5.8e-23  Score=194.14  Aligned_cols=92  Identities=39%  Similarity=0.704  Sum_probs=89.5

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHH
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQK  232 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~  232 (245)
                      .+.++|.|+||++....++++.+.. +.||+.|..+|+.||+|||||||||||||+||+|+|++++.||+.|+++++++.
T Consensus       184 ~snv~f~diGG~d~~~~el~~li~~-i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel~vPf~~isApeivSG  262 (802)
T KOG0733|consen  184 ESNVSFSDIGGLDKTLAELCELIIH-IKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGELGVPFLSISAPEIVSG  262 (802)
T ss_pred             CCCcchhhccChHHHHHHHHHHHHH-hcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhcCCceEeecchhhhcc
Confidence            3468999999999999999999999 999999999999999999999999999999999999999999999999999999


Q ss_pred             HhccccccccccC
Q 025979          233 YLGEVWLKHKQIF  245 (245)
Q Consensus       233 ~~Ge~~~~vr~iF  245 (245)
                      +.||+|++||++|
T Consensus       263 vSGESEkkiRelF  275 (802)
T KOG0733|consen  263 VSGESEKKIRELF  275 (802)
T ss_pred             cCcccHHHHHHHH
Confidence            9999999999998

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

Probab=99.86  E-value=2.2e-22  Score=196.09  Aligned_cols=94  Identities=41%  Similarity=0.742  Sum_probs=90.8

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      ...++++|.||.|+++++++|.|+|.+ +++|+.|.++|...|+|+||+||||||||+||||+|.+.++||+.+++|+|+
T Consensus       303 ~~~t~V~FkDVAG~deAK~El~E~V~f-LKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEAgVPF~svSGSEFv  381 (774)
T KOG0731|consen  303 EGNTGVKFKDVAGVDEAKEELMEFVKF-LKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEAGVPFFSVSGSEFV  381 (774)
T ss_pred             CCCCCCccccccCcHHHHHHHHHHHHH-hcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhcccCCceeeechHHHH
Confidence            445669999999999999999999998 9999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhccccccccccC
Q 025979          231 QKYLGEVWLKHKQIF  245 (245)
Q Consensus       231 ~~~~Ge~~~~vr~iF  245 (245)
                      ++|+|.++..||++|
T Consensus       382 E~~~g~~asrvr~lf  396 (774)
T KOG0731|consen  382 EMFVGVGASRVRDLF  396 (774)
T ss_pred             HHhcccchHHHHHHH
Confidence            999999999999998

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.86  E-value=1.7e-22  Score=182.97  Aligned_cols=94  Identities=40%  Similarity=0.658  Sum_probs=88.9

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      ...|.+.|+||.|+.++|+-|.|+|.+|+..|++|..+ ..|.+|||++||||||||+||||+|.+|+.+||.|+.+.+.
T Consensus       204 ~~np~ikW~DIagl~~AK~lL~EAVvlPi~mPe~F~Gi-rrPWkgvLm~GPPGTGKTlLAKAvATEc~tTFFNVSsstlt  282 (491)
T KOG0738|consen  204 QRNPNIKWDDIAGLHEAKKLLKEAVVLPIWMPEFFKGI-RRPWKGVLMVGPPGTGKTLLAKAVATECGTTFFNVSSSTLT  282 (491)
T ss_pred             ccCCCcChHhhcchHHHHHHHHHHHhhhhhhHHHHhhc-ccccceeeeeCCCCCcHHHHHHHHHHhhcCeEEEechhhhh
Confidence            45688999999999999999999999999999999854 47889999999999999999999999999999999999999


Q ss_pred             HHHhccccccccccC
Q 025979          231 QKYLGEVWLKHKQIF  245 (245)
Q Consensus       231 ~~~~Ge~~~~vr~iF  245 (245)
                      +||-||+|+.||=+|
T Consensus       283 SKwRGeSEKlvRlLF  297 (491)
T KOG0738|consen  283 SKWRGESEKLVRLLF  297 (491)
T ss_pred             hhhccchHHHHHHHH
Confidence            999999999999877

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=99.85  E-value=4.2e-22  Score=186.07  Aligned_cols=93  Identities=41%  Similarity=0.697  Sum_probs=89.8

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHH
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQ  231 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~  231 (245)
                      ...+++|+||.|+|++++++.|.|++ +++|..|.++|-+-|+||||.||||||||+||||+|.+.++|||..++|+|=+
T Consensus       297 ~~~nv~F~dVkG~DEAK~ELeEiVef-LkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA~VPFF~~sGSEFdE  375 (752)
T KOG0734|consen  297 QMKNVTFEDVKGVDEAKQELEEIVEF-LKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEAGVPFFYASGSEFDE  375 (752)
T ss_pred             hhcccccccccChHHHHHHHHHHHHH-hcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcccCCCeEeccccchhh
Confidence            34468999999999999999999998 99999999999999999999999999999999999999999999999999999


Q ss_pred             HHhccccccccccC
Q 025979          232 KYLGEVWLKHKQIF  245 (245)
Q Consensus       232 ~~~Ge~~~~vr~iF  245 (245)
                      +|+|.+++.||++|
T Consensus       376 m~VGvGArRVRdLF  389 (752)
T KOG0734|consen  376 MFVGVGARRVRDLF  389 (752)
T ss_pred             hhhcccHHHHHHHH
Confidence            99999999999998

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

Probab=99.84  E-value=7.8e-22  Score=189.64  Aligned_cols=165  Identities=18%  Similarity=0.212  Sum_probs=135.1

Q ss_pred             hhHHHHHHHHHHHhhhhhhhHHHHHHHHHHH---HHHHHHHHHHhhhhccccchhhhhhhhhhcccceeecccCCeeEEE
Q 025979           32 DDLYSRLKSLQRQLEFIDIQEEYVKDEQKNL---KRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVR  108 (245)
Q Consensus        32 ~~~~~~~~~~~~e~~~l~~~~~~i~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  108 (245)
                      .++++++.+.|||+ +|++|++.|++|++..   ..++..++++++....+..+...+..++++...+.+.|++++++++
T Consensus       216 ~kVk~~meK~QREy-yL~EQlKaIqkELG~~~d~~~e~~~~~~kie~~~~p~evk~k~~~El~kL~~m~~~SaE~~ViRn  294 (782)
T COG0466         216 KKVKEQMEKSQREY-YLREQLKAIQKELGEDDDDKDEVEELREKIEKLKLPKEAKEKAEKELKKLETMSPMSAEATVIRN  294 (782)
T ss_pred             HHHHHHHHHHHHHH-HHHHHHHHHHHHhCCCccchhHHHHHHHHHhhcCCCHHHHHHHHHHHHHHhcCCCCCchHHHHHH
Confidence            35677888999999 9999999999999843   4678899999999999999999999999999999999999999999


Q ss_pred             EeecccccccCCCceeeeeccccccccccCCCccccccccccCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhh
Q 025979          109 ILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQI  188 (245)
Q Consensus       109 ~~~~~~~~~l~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~  188 (245)
                      |++|+  ..++|+......                    ....+..++.-.||+|++++|++|.|++..-...       
T Consensus       295 YlDwl--l~lPW~~~sk~~--------------------~Dl~~a~~iLd~dHYGLekVKeRIlEyLAV~~l~-------  345 (782)
T COG0466         295 YLDWL--LDLPWGKRSKDK--------------------LDLKKAEKILDKDHYGLEKVKERILEYLAVQKLT-------  345 (782)
T ss_pred             HHHHH--HhCCCccccchh--------------------hhHHHHHHHhcccccCchhHHHHHHHHHHHHHHh-------
Confidence            99998  456666543322                    2233334455579999999999999999862111       


Q ss_pred             ccCCCcc--eeeecCCCCchHHHHHHHHhcccceeeeechhH
Q 025979          189 GIDPPRG--VLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSE  228 (245)
Q Consensus       189 g~~~~~g--vLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~  228 (245)
                        +.-+|  +||+||||||||+|+++||+.+++.|+|++..-
T Consensus       346 --~~~kGpILcLVGPPGVGKTSLgkSIA~al~RkfvR~sLGG  385 (782)
T COG0466         346 --KKLKGPILCLVGPPGVGKTSLGKSIAKALGRKFVRISLGG  385 (782)
T ss_pred             --ccCCCcEEEEECCCCCCchhHHHHHHHHhCCCEEEEecCc
Confidence              12234  999999999999999999999999999998543

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

Probab=99.83  E-value=2.1e-21  Score=185.05  Aligned_cols=95  Identities=52%  Similarity=0.910  Sum_probs=92.3

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      ...+.++|+|++|++..++.+.+.+..|+.+++.|...|+.+++|+|||||||||||++|+|+|++++.+|+.+++++++
T Consensus       234 ~~~~~v~~~diggl~~~k~~l~e~v~~~~~~~e~~~~~~~~~~~giLl~GpPGtGKT~lAkava~~~~~~fi~v~~~~l~  313 (494)
T COG0464         234 FEDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSELL  313 (494)
T ss_pred             cCCCCcceehhhcHHHHHHHHHHHHHhHhhChHHHHhcCCCCCCeeEEECCCCCCHHHHHHHHHhhCCCeEEEeeCHHHh
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhccccccccccC
Q 025979          231 QKYLGEVWLKHKQIF  245 (245)
Q Consensus       231 ~~~~Ge~~~~vr~iF  245 (245)
                      ++|+||++++||++|
T Consensus       314 sk~vGesek~ir~~F  328 (494)
T COG0464         314 SKWVGESEKNIRELF  328 (494)
T ss_pred             ccccchHHHHHHHHH
Confidence            999999999999988

>KOG0737 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.83  E-value=1.6e-21  Score=175.81  Aligned_cols=93  Identities=46%  Similarity=0.780  Sum_probs=88.0

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhc-cCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHH
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIG-IDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQ  231 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g-~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~  231 (245)
                      .-.++|+|++|++.+++.+++.|.+|+.+|++|...+ +.+++|+|||||||||||++|+|+|.+.++.|+.|+++.+++
T Consensus        86 ~I~v~f~DIggLe~v~~~L~e~VilPlr~pelF~~g~Ll~p~kGiLL~GPpG~GKTmlAKA~Akeaga~fInv~~s~lt~  165 (386)
T KOG0737|consen   86 EIGVSFDDIGGLEEVKDALQELVILPLRRPELFAKGKLLRPPKGILLYGPPGTGKTMLAKAIAKEAGANFINVSVSNLTS  165 (386)
T ss_pred             hceeehhhccchHHHHHHHHHHHhhcccchhhhcccccccCCccceecCCCCchHHHHHHHHHHHcCCCcceeeccccch
Confidence            3468899999999999999999999999999998655 579999999999999999999999999999999999999999


Q ss_pred             HHhccccccccccC
Q 025979          232 KYLGEVWLKHKQIF  245 (245)
Q Consensus       232 ~~~Ge~~~~vr~iF  245 (245)
                      ||.||+++.++.+|
T Consensus       166 KWfgE~eKlv~AvF  179 (386)
T KOG0737|consen  166 KWFGEAQKLVKAVF  179 (386)
T ss_pred             hhHHHHHHHHHHHH
Confidence            99999999999988

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

Probab=99.81  E-value=1.7e-20  Score=179.94  Aligned_cols=96  Identities=33%  Similarity=0.633  Sum_probs=92.2

Q ss_pred             cCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHH
Q 025979          150 QSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF  229 (245)
Q Consensus       150 ~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l  229 (245)
                      ......+.|+|++|+.++++.+.+.|++|.+.|.+|...++..+.|+|||||||||||+||.|+|..++..|+.|.|+++
T Consensus       658 ~~k~tgi~w~digg~~~~k~~l~~~i~~P~kyp~if~~~plr~~~giLLyGppGcGKT~la~a~a~~~~~~fisvKGPEl  737 (952)
T KOG0735|consen  658 LVKSTGIRWEDIGGLFEAKKVLEEVIEWPSKYPQIFANCPLRLRTGILLYGPPGCGKTLLASAIASNSNLRFISVKGPEL  737 (952)
T ss_pred             ccccCCCCceecccHHHHHHHHHHHHhccccchHHHhhCCcccccceEEECCCCCcHHHHHHHHHhhCCeeEEEecCHHH
Confidence            34455699999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhccccccccccC
Q 025979          230 VQKYLGEVWLKHKQIF  245 (245)
Q Consensus       230 ~~~~~Ge~~~~vr~iF  245 (245)
                      ++||+|.+|.+||++|
T Consensus       738 L~KyIGaSEq~vR~lF  753 (952)
T KOG0735|consen  738 LSKYIGASEQNVRDLF  753 (952)
T ss_pred             HHHHhcccHHHHHHHH
Confidence            9999999999999998

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.79  E-value=6.6e-20  Score=182.33  Aligned_cols=94  Identities=55%  Similarity=0.957  Sum_probs=91.4

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHH
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQ  231 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~  231 (245)
                      +.|.++|+|++|++.+++.|.+.+.+|+.+++.|.++|+.+|+|+|||||||||||++|+++|++++.+|+.++++++++
T Consensus       446 ~~~~~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~~~~fi~v~~~~l~~  525 (733)
T TIGR01243       446 EVPNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGPEILS  525 (733)
T ss_pred             cccccchhhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCCEEEEehHHHhh
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhccccccccccC
Q 025979          232 KYLGEVWLKHKQIF  245 (245)
Q Consensus       232 ~~~Ge~~~~vr~iF  245 (245)
                      +|+|+++++||++|
T Consensus       526 ~~vGese~~i~~~f  539 (733)
T TIGR01243       526 KWVGESEKAIREIF  539 (733)
T ss_pred             cccCcHHHHHHHHH
Confidence            99999999999987

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.

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

Probab=99.77  E-value=1.8e-19  Score=173.04  Aligned_cols=164  Identities=21%  Similarity=0.192  Sum_probs=127.5

Q ss_pred             HHHHHHHHHHhhhhhhhHHHHHHHHHHH---HH-HHHHHHHHhhhhccccchhhhhhhhhhcccceeecccCCeeEEEEe
Q 025979           35 YSRLKSLQRQLEFIDIQEEYVKDEQKNL---KR-ELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRIL  110 (245)
Q Consensus        35 ~~~~~~~~~e~~~l~~~~~~i~~~~~~~---~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~  110 (245)
                      ..++.+-+++| .|++|++.|+.++...   +. ....++++++.+..|..+...+.+++.+.+.+.+++++.++.++|+
T Consensus       306 E~k~~~~~r~y-lL~eQlk~IKkeLg~e~Ddkd~~~~~~~er~~~~~~P~~v~kv~~eEl~kL~~le~~~sEfnvtrNYL  384 (906)
T KOG2004|consen  306 EEKIKQDHREY-LLREQLKAIKKELGIEKDDKDALVEKFRERIKSLKMPDHVLKVIDEELTKLKLLEPSSSEFNVTRNYL  384 (906)
T ss_pred             HhhhhHHHHHH-HHHHHHHHHHHhhCCCccchhhHHHHHHHHhhhccCcHHHHHHHHHHHHHHhccCccccchhHHHHHH
Confidence            34455666677 7888888888888722   22 3556899999998999999999999999999999999999999999


Q ss_pred             ecccccccCCCceeeeeccccccccccCCCccccccccccCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhcc
Q 025979          111 STINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGI  190 (245)
Q Consensus       111 ~~~~~~~l~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~  190 (245)
                      +|+  ..++||.....                    .+.......+.-+|++|++++|++|.|+|..-...       |-
T Consensus       385 dwl--t~LPWgk~S~E--------------------n~dl~~Ak~iLdeDHYgm~dVKeRILEfiAV~kLr-------gs  435 (906)
T KOG2004|consen  385 DWL--TSLPWGKSSTE--------------------NLDLARAKEILDEDHYGMEDVKERILEFIAVGKLR-------GS  435 (906)
T ss_pred             HHH--HhCCCCCCChh--------------------hhhHHHHHHhhcccccchHHHHHHHHHHHHHHhhc-------cc
Confidence            999  56667655332                    22233334455589999999999999999862111       22


Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcccceeeeechhH
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSE  228 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~  228 (245)
                      ..++-+||+||||+|||++||+||..+|+.|+|++..-
T Consensus       436 ~qGkIlCf~GPPGVGKTSI~kSIA~ALnRkFfRfSvGG  473 (906)
T KOG2004|consen  436 VQGKILCFVGPPGVGKTSIAKSIARALNRKFFRFSVGG  473 (906)
T ss_pred             CCCcEEEEeCCCCCCcccHHHHHHHHhCCceEEEeccc
Confidence            23445999999999999999999999999999998543

>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

Probab=99.77  E-value=1.2e-19  Score=173.87  Aligned_cols=94  Identities=40%  Similarity=0.750  Sum_probs=90.7

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      .....++|.|+.|.+++++++.|.|.+ +++|..|..+|...|+|+||+||||||||+||||+|.+.+.||+.+++|+++
T Consensus       142 ~~~~~v~F~DVAG~dEakeel~EiVdf-Lk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgEA~VPFf~iSGS~FV  220 (596)
T COG0465         142 EDQVKVTFADVAGVDEAKEELSELVDF-LKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFV  220 (596)
T ss_pred             ccccCcChhhhcCcHHHHHHHHHHHHH-HhCchhhHhcccccccceeEecCCCCCcHHHHHHHhcccCCCceeccchhhh
Confidence            346779999999999999999999998 9999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhccccccccccC
Q 025979          231 QKYLGEVWLKHKQIF  245 (245)
Q Consensus       231 ~~~~Ge~~~~vr~iF  245 (245)
                      ++|+|-+++.||++|
T Consensus       221 emfVGvGAsRVRdLF  235 (596)
T COG0465         221 EMFVGVGASRVRDLF  235 (596)
T ss_pred             hhhcCCCcHHHHHHH
Confidence            999999999999988

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

Probab=99.76  E-value=2.8e-19  Score=175.51  Aligned_cols=173  Identities=24%  Similarity=0.366  Sum_probs=128.4

Q ss_pred             cccCCCCC---CCCCCCcccCCCCCCCCchhHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhhhccccch
Q 025979            6 MVLDPKPV---SEPPPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLV   82 (245)
Q Consensus         6 ~~~~~k~~---~e~~~~~~~e~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (245)
                      -.||||||   |||+|+.+++.. .|.+.+.+.+++.+++.+...+..+..   +..+....++..+++         ..
T Consensus       376 R~LPDKAIDLiDeA~a~~~l~~~-~p~~l~~~~~~~~~l~~e~~~~~~e~~---~~~k~~~~~~~~~~~---------~~  442 (786)
T COG0542         376 RFLPDKAIDLLDEAGARVRLEID-KPEELDELERELAQLEIEKEALEREQD---EKEKKLIDEIIKLKE---------GR  442 (786)
T ss_pred             CCCCchHHHHHHHHHHHHHhccc-CCcchhHHHHHHHHHHHHHHHHhhhhh---HHHHHHHHHHHHHhh---------hh
Confidence            46999999   999999999999 999999999999999998887776654   111111112222221         00


Q ss_pred             hhhhhhhhhcccceeecccCCeeEEEEeecccccccCCCceeeeeccccccccccCCCccccccccccCCCCC------c
Q 025979           83 IGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPD------V  156 (245)
Q Consensus        83 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~------~  156 (245)
                      .......+.. .                                 .+...+.+++..|++.++..+...+..+      .
T Consensus       443 ~~~~~~~~~~-~---------------------------------v~~~~Ia~vv~~~TgIPv~~l~~~e~~kll~le~~  488 (786)
T COG0542         443 IPELEKELEA-E---------------------------------VDEDDIAEVVARWTGIPVAKLLEDEKEKLLNLERR  488 (786)
T ss_pred             hhhHHHHHhh-c---------------------------------cCHHHHHHHHHHHHCCChhhhchhhHHHHHHHHHH
Confidence            0111111111 0                                 3455677888999999998876665544      3


Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcc----eeeecCCCCchHHHHHHHHhccc---ceeeeechhHH
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRG----VLLYGPPGTGKTMLAKAVANHTT---AAFIRVVGSEF  229 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~g----vLl~GPPGtGKT~lAkalA~~l~---~~~~~v~~s~l  229 (245)
                      ....|+|+++++..+.++|..        .+.|+..|+.    |||.||+|||||.|||+||..+.   ..+++++||+|
T Consensus       489 L~~rViGQd~AV~avs~aIrr--------aRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~e~aliR~DMSEy  560 (786)
T COG0542         489 LKKRVIGQDEAVEAVSDAIRR--------ARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEY  560 (786)
T ss_pred             HhcceeChHHHHHHHHHHHHH--------HhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHhcCCCccceeechHHH
Confidence            345699999999999999987        7788866544    99999999999999999999995   89999999999


Q ss_pred             HHHH
Q 025979          230 VQKY  233 (245)
Q Consensus       230 ~~~~  233 (245)
                      +++|
T Consensus       561 ~EkH  564 (786)
T COG0542         561 MEKH  564 (786)
T ss_pred             HHHH
Confidence            8776

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=99.75  E-value=4.7e-19  Score=153.80  Aligned_cols=91  Identities=33%  Similarity=0.575  Sum_probs=81.8

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      ...++++++||+|+++++..-+-.+.. +.+|+.|.+|   .|++||||||||||||++|||+|++++.||+.+...+++
T Consensus       113 e~~~~it~ddViGqEeAK~kcrli~~y-LenPe~Fg~W---APknVLFyGppGTGKTm~Akalane~kvp~l~vkat~li  188 (368)
T COG1223         113 EIISDITLDDVIGQEEAKRKCRLIMEY-LENPERFGDW---APKNVLFYGPPGTGKTMMAKALANEAKVPLLLVKATELI  188 (368)
T ss_pred             hhhccccHhhhhchHHHHHHHHHHHHH-hhChHHhccc---CcceeEEECCCCccHHHHHHHHhcccCCceEEechHHHH
Confidence            346789999999999999887766655 8899877665   689999999999999999999999999999999999999


Q ss_pred             HHHhccccccccccC
Q 025979          231 QKYLGEVWLKHKQIF  245 (245)
Q Consensus       231 ~~~~Ge~~~~vr~iF  245 (245)
                      ..|+|++++.|+++|
T Consensus       189 GehVGdgar~Ihely  203 (368)
T COG1223         189 GEHVGDGARRIHELY  203 (368)
T ss_pred             HHHhhhHHHHHHHHH
Confidence            999999999999875

>TIGR00763 lon ATP-dependent protease La

Probab=99.74  E-value=6.5e-19  Score=176.13  Aligned_cols=181  Identities=19%  Similarity=0.182  Sum_probs=136.6

Q ss_pred             hhHHHHHHHHHHHhhhhhhhHHHHHHHHHH---HHHHHHHHHHHhhhhccccchhhhhhhhhhcccceeecccCCeeEEE
Q 025979           32 DDLYSRLKSLQRQLEFIDIQEEYVKDEQKN---LKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVR  108 (245)
Q Consensus        32 ~~~~~~~~~~~~e~~~l~~~~~~i~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  108 (245)
                      .++++++.+.|+++ +|++|++.|++|+++   ...++.+++++++....++.....+.+++++.+.+.+.+++.+++++
T Consensus       213 ~~v~~~~~~~qr~~-~Lreqlk~i~~eLg~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~  291 (775)
T TIGR00763       213 KKVEEKMEKTQREY-YLREQLKAIKKELGIEKDDKDELEKLKEKLEELKLPEEVKKVIEKELTKLSLLEPSSSEFTVTRN  291 (775)
T ss_pred             HHHHHHHHHHHHHH-HHHHHHHHHHHhhCCCCCchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHcCCCCCchHHHHHH
Confidence            46677888899999 999999999999974   45678899999999999999999999999999999999999999888


Q ss_pred             EeecccccccCCCceeeeeccccccccccCCCccccccccccCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhh
Q 025979          109 ILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQI  188 (245)
Q Consensus       109 ~~~~~~~~~l~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~  188 (245)
                      |++++  ..++|+......                    ..........-++++|+++++++|.+++..+...       
T Consensus       292 yl~~~--~~ip~~~~~~~~--------------------~~~~~~~~~l~~~~~G~~~~k~~i~~~~~~~~~~-------  342 (775)
T TIGR00763       292 YLDWL--TDLPWGKYSKEN--------------------LDLKRAKEILDEDHYGLKKVKERILEYLAVQKLR-------  342 (775)
T ss_pred             HHHHH--HCCCCcccccch--------------------hhHHHHHHHhhhhcCChHHHHHHHHHHHHHHHhh-------
Confidence            98887  334444321110                    0011112223467999999999999988753211       


Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH---------HHHhcccccccc
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV---------QKYLGEVWLKHK  242 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~---------~~~~Ge~~~~vr  242 (245)
                      +-..+..+|||||||||||++|+++|+.++.+|++++++.+.         ..|+|.....+.
T Consensus       343 ~~~~~~~lll~GppG~GKT~lAk~iA~~l~~~~~~i~~~~~~~~~~i~g~~~~~~g~~~g~i~  405 (775)
T TIGR00763       343 GKMKGPILCLVGPPGVGKTSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHRRTYVGAMPGRII  405 (775)
T ss_pred             cCCCCceEEEECCCCCCHHHHHHHHHHHhcCCeEEEeCCCcccHHHHcCCCCceeCCCCchHH
Confidence            111233699999999999999999999999999999765432         356666655544

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.

>KOG0740 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.73  E-value=1.4e-18  Score=160.86  Aligned_cols=94  Identities=43%  Similarity=0.734  Sum_probs=88.0

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      ...+++.|+|+.|++.+++.+.+++.+|+..+++|..+. .+++|+||+||||||||+|++|||.++++.|+.+++|++.
T Consensus       145 ~~~~~v~~~di~gl~~~k~~l~e~vi~p~lr~d~F~glr-~p~rglLLfGPpgtGKtmL~~aiAsE~~atff~iSassLt  223 (428)
T KOG0740|consen  145 DTLRNVGWDDIAGLEDAKQSLKEAVILPLLRPDLFLGLR-EPVRGLLLFGPPGTGKTMLAKAIATESGATFFNISASSLT  223 (428)
T ss_pred             ccCCcccccCCcchhhHHHHhhhhhhhcccchHhhhccc-cccchhheecCCCCchHHHHHHHHhhhcceEeeccHHHhh
Confidence            345679999999999999999999999999999997654 5778999999999999999999999999999999999999


Q ss_pred             HHHhccccccccccC
Q 025979          231 QKYLGEVWLKHKQIF  245 (245)
Q Consensus       231 ~~~~Ge~~~~vr~iF  245 (245)
                      ++|+|+++++||.+|
T Consensus       224 sK~~Ge~eK~vralf  238 (428)
T KOG0740|consen  224 SKYVGESEKLVRALF  238 (428)
T ss_pred             hhccChHHHHHHHHH
Confidence            999999999999988

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.72  E-value=4.3e-18  Score=162.50  Aligned_cols=94  Identities=43%  Similarity=0.776  Sum_probs=89.6

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      .+.+.++|+|++|++++++++.+.+.. +.+++.|...|..+|+|+|||||||||||++|+++|++++.+|+.++++++.
T Consensus        47 ~~~~~~~~~di~g~~~~k~~l~~~~~~-l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~~~~~~~i~~~~~~  125 (495)
T TIGR01241        47 EEKPKVTFKDVAGIDEAKEELMEIVDF-LKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFV  125 (495)
T ss_pred             CCCCCCCHHHhCCHHHHHHHHHHHHHH-HHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCCeeeccHHHHH
Confidence            457889999999999999999999887 8999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhccccccccccC
Q 025979          231 QKYLGEVWLKHKQIF  245 (245)
Q Consensus       231 ~~~~Ge~~~~vr~iF  245 (245)
                      ++|+|++++.++++|
T Consensus       126 ~~~~g~~~~~l~~~f  140 (495)
T TIGR01241       126 EMFVGVGASRVRDLF  140 (495)
T ss_pred             HHHhcccHHHHHHHH
Confidence            999999999999876

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.

>CHL00195 ycf46 Ycf46; Provisional

Probab=99.71  E-value=5.2e-18  Score=161.18  Aligned_cols=90  Identities=29%  Similarity=0.430  Sum_probs=80.8

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHH
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQK  232 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~  232 (245)
                      .++++|+||+|++.+|+.+.+....   .+....++|+.+|+|+|||||||||||++|+++|++++.+|++++++.++++
T Consensus       222 ~~~~~~~dvgGl~~lK~~l~~~~~~---~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e~~~~~~~l~~~~l~~~  298 (489)
T CHL00195        222 SVNEKISDIGGLDNLKDWLKKRSTS---FSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGKLFGG  298 (489)
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHHHH---hhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEEEhHHhccc
Confidence            4678899999999999999876543   2334567899999999999999999999999999999999999999999999


Q ss_pred             HhccccccccccC
Q 025979          233 YLGEVWLKHKQIF  245 (245)
Q Consensus       233 ~~Ge~~~~vr~iF  245 (245)
                      |+|+++++++++|
T Consensus       299 ~vGese~~l~~~f  311 (489)
T CHL00195        299 IVGESESRMRQMI  311 (489)
T ss_pred             ccChHHHHHHHHH
Confidence            9999999999886

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

Probab=99.69  E-value=6e-18  Score=168.78  Aligned_cols=169  Identities=14%  Similarity=0.159  Sum_probs=134.6

Q ss_pred             chhHHHHHHHHHHHhhhhhhhHHHHHHHHHH---HHHHHHHHHHHhhhhccccchhhhhhhhhhcccceeecccCCeeEE
Q 025979           31 EDDLYSRLKSLQRQLEFIDIQEEYVKDEQKN---LKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYV  107 (245)
Q Consensus        31 ~~~~~~~~~~~~~e~~~l~~~~~~i~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~  107 (245)
                      ..++++++.+.|+++ +|++|++.|+++++.   ...++.+++++++....++.....+.+++++...+.+.+++.++.+
T Consensus       214 ~~~v~~~~~k~q~e~-~lreq~~~i~~elg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~e~~~~~  292 (784)
T PRK10787        214 RNRVKKQMEKSQREY-YLNEQMKAIQKELGEMDDAPDENEALKRKIDAAKMPKEAKEKAEAELQKLKMMSPMSAEATVVR  292 (784)
T ss_pred             HHHHHHHHhhhhhhh-cchhhhhhhcccccCCCcchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCCCCchHHHHH
Confidence            346778889999999 999999999999974   3467888999999999999999999999999999999999999999


Q ss_pred             EEeecccccccCCCceeeeeccccccccccCCCccccccccccCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhh
Q 025979          108 RILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQ  187 (245)
Q Consensus       108 ~~~~~~~~~~l~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~  187 (245)
                      +|++|+  ..++|+.......                    ...+...+.-.+++|++.+|++|.+++.....       
T Consensus       293 ~yl~~~--~~~pw~~~~~~~~--------------------~~~~~~~~l~~~~~g~~~vK~~i~~~l~~~~~-------  343 (784)
T PRK10787        293 GYIDWM--VQVPWNARSKVKK--------------------DLRQAQEILDTDHYGLERVKDRILEYLAVQSR-------  343 (784)
T ss_pred             HHHHHH--HhCCCCCCCcccc--------------------cHHHHHHHhhhhccCHHHHHHHHHHHHHHHHh-------
Confidence            999998  4567765422111                    11222334446899999999999998875211       


Q ss_pred             hccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHH
Q 025979          188 IGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF  229 (245)
Q Consensus       188 ~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l  229 (245)
                      .+-..+..+||+||||||||++++++|..++.+|++++.+..
T Consensus       344 ~~~~~g~~i~l~GppG~GKTtl~~~ia~~l~~~~~~i~~~~~  385 (784)
T PRK10787        344 VNKIKGPILCLVGPPGVGKTSLGQSIAKATGRKYVRMALGGV  385 (784)
T ss_pred             cccCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEEcCCC
Confidence            111123459999999999999999999999999999976543

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.68  E-value=1.5e-17  Score=165.46  Aligned_cols=93  Identities=58%  Similarity=1.003  Sum_probs=89.9

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHH
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQK  232 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~  232 (245)
                      .++++|+||+|++.+++.|++++..|+.+|++|..+|+.+++|+|||||||||||++|+++|++++.+|+.+++++++++
T Consensus       172 ~~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~~~~~i~i~~~~i~~~  251 (733)
T TIGR01243       172 VPKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAYFISINGPEIMSK  251 (733)
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHhCCeEEEEecHHHhcc
Confidence            47799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhccccccccccC
Q 025979          233 YLGEVWLKHKQIF  245 (245)
Q Consensus       233 ~~Ge~~~~vr~iF  245 (245)
                      |.|+++.+++.+|
T Consensus       252 ~~g~~~~~l~~lf  264 (733)
T TIGR01243       252 YYGESEERLREIF  264 (733)
T ss_pred             cccHHHHHHHHHH
Confidence            9999999998876

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.

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.66  E-value=1.2e-16  Score=149.62  Aligned_cols=93  Identities=38%  Similarity=0.667  Sum_probs=81.3

Q ss_pred             CCCceecc--CCcchhhhHHH-HHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccce-eeeechhH
Q 025979          153 KPDVTYND--IGGCDIQKQEI-REAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAA-FIRVVGSE  228 (245)
Q Consensus       153 ~~~~~~~d--v~Gl~~~~~~i-~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~-~~~v~~s~  228 (245)
                      .|+..|++  |||++.....| +++.....-.|+..+++|++.-+|+|||||||||||++||.|...+++. =--|++++
T Consensus       213 ~Pdf~Fe~mGIGGLd~EFs~IFRRAFAsRvFpp~vie~lGi~HVKGiLLyGPPGTGKTLiARqIGkMLNArePKIVNGPe  292 (744)
T KOG0741|consen  213 NPDFNFESMGIGGLDKEFSDIFRRAFASRVFPPEVIEQLGIKHVKGILLYGPPGTGKTLIARQIGKMLNAREPKIVNGPE  292 (744)
T ss_pred             CCCCChhhcccccchHHHHHHHHHHHHhhcCCHHHHHHcCccceeeEEEECCCCCChhHHHHHHHHHhcCCCCcccCcHH
Confidence            46667776  79999887666 7777777889999999999999999999999999999999999999653 22378999


Q ss_pred             HHHHHhccccccccccC
Q 025979          229 FVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       229 l~~~~~Ge~~~~vr~iF  245 (245)
                      +++||+||+|.|||++|
T Consensus       293 IL~KYVGeSE~NvR~LF  309 (744)
T KOG0741|consen  293 ILNKYVGESEENVRKLF  309 (744)
T ss_pred             HHHHhhcccHHHHHHHH
Confidence            99999999999999998

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

Probab=99.64  E-value=1.2e-16  Score=152.83  Aligned_cols=91  Identities=53%  Similarity=0.879  Sum_probs=88.2

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHH
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKY  233 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~  233 (245)
                      +.+. .+++|+..+...+++.++.|+.++..|..+|+++|+|+|+|||||||||.+++++|++.++.++.+++++++++|
T Consensus       180 ~~~~-~~~gg~~~~~~~i~e~v~~pl~~~~~~~s~g~~~prg~Ll~gppg~Gkt~l~~aVa~e~~a~~~~i~~peli~k~  258 (693)
T KOG0730|consen  180 PEVG-DDIGGLKRQLSVIRELVELPLRHPALFKSIGIKPPRGLLLYGPPGTGKTFLVRAVANEYGAFLFLINGPELISKF  258 (693)
T ss_pred             cccc-cccchhHHHHHHHHHHHHhhhcchhhhhhcCCCCCCCccccCCCCCChHHHHHHHHHHhCceeEecccHHHHHhc
Confidence            5566 799999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccccccccccC
Q 025979          234 LGEVWLKHKQIF  245 (245)
Q Consensus       234 ~Ge~~~~vr~iF  245 (245)
                      .||+++++|++|
T Consensus       259 ~gEte~~LR~~f  270 (693)
T KOG0730|consen  259 PGETESNLRKAF  270 (693)
T ss_pred             ccchHHHHHHHH
Confidence            999999999987

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

Probab=99.64  E-value=7.1e-17  Score=147.15  Aligned_cols=88  Identities=17%  Similarity=0.211  Sum_probs=70.2

Q ss_pred             ceeccC-CcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHh
Q 025979          156 VTYNDI-GGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYL  234 (245)
Q Consensus       156 ~~~~dv-~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~  234 (245)
                      .+|+++ +|+--...-+..++...-  .......|+++|++++||||||||||++|+++|++++++|+.++++++.++|+
T Consensus       112 ~~f~~~~g~~~~~p~f~dk~~~hi~--kn~l~~~~ik~PlgllL~GPPGcGKTllAraiA~elg~~~i~vsa~eL~sk~v  189 (413)
T PLN00020        112 RSFDNLVGGYYIAPAFMDKVAVHIA--KNFLALPNIKVPLILGIWGGKGQGKSFQCELVFKKMGIEPIVMSAGELESENA  189 (413)
T ss_pred             cchhhhcCccccCHHHHHHHHHHHH--hhhhhccCCCCCeEEEeeCCCCCCHHHHHHHHHHHcCCCeEEEEHHHhhcCcC
Confidence            345565 666555555544443211  12233468899999999999999999999999999999999999999999999


Q ss_pred             ccccccccccC
Q 025979          235 GEVWLKHKQIF  245 (245)
Q Consensus       235 Ge~~~~vr~iF  245 (245)
                      ||++++||++|
T Consensus       190 GEsEk~IR~~F  200 (413)
T PLN00020        190 GEPGKLIRQRY  200 (413)
T ss_pred             CcHHHHHHHHH
Confidence            99999999987

>KOG0732 consensus AAA+-type ATPase containing the bromodomain [Posttranslational modification, protein turnover, chaperones]

Probab=99.64  E-value=6.7e-17  Score=161.84  Aligned_cols=92  Identities=36%  Similarity=0.697  Sum_probs=87.9

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc-----cceeeeechhH
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT-----TAAFIRVVGSE  228 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l-----~~~~~~v~~s~  228 (245)
                      ..+.|++|||++.++..++|+|-.|+..|+.|..+++.||+|+|||||||||||+.|+++|..+     +..|+.-++.+
T Consensus       260 ~~v~fd~vggl~~~i~~LKEmVl~PLlyPE~f~~~~itpPrgvL~~GppGTGkTl~araLa~~~s~~~~kisffmrkgaD  339 (1080)
T KOG0732|consen  260 SSVGFDSVGGLENYINQLKEMVLLPLLYPEFFDNFNITPPRGVLFHGPPGTGKTLMARALAAACSRGNRKISFFMRKGAD  339 (1080)
T ss_pred             cccCccccccHHHHHHHHHHHHHhHhhhhhHhhhcccCCCcceeecCCCCCchhHHHHhhhhhhcccccccchhhhcCch
Confidence            4589999999999999999999999999999999999999999999999999999999999988     67788899999


Q ss_pred             HHHHHhccccccccccC
Q 025979          229 FVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       229 l~~~~~Ge~~~~vr~iF  245 (245)
                      ..++|+||.++.+|-+|
T Consensus       340 ~lskwvgEaERqlrllF  356 (1080)
T KOG0732|consen  340 CLSKWVGEAERQLRLLF  356 (1080)
T ss_pred             hhccccCcHHHHHHHHH
Confidence            99999999999999887

>CHL00176 ftsH cell division protein; Validated

Probab=99.63  E-value=1.9e-16  Score=154.83  Aligned_cols=94  Identities=39%  Similarity=0.728  Sum_probs=87.8

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      ...+.++|+|++|++++++++.+.+.. +.+++.|..+|...|+|+|||||||||||++|+++|++++.+|+.++++++.
T Consensus       175 ~~~~~~~f~dv~G~~~~k~~l~eiv~~-lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~~~p~i~is~s~f~  253 (638)
T CHL00176        175 EADTGITFRDIAGIEEAKEEFEEVVSF-LKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFV  253 (638)
T ss_pred             ccCCCCCHHhccChHHHHHHHHHHHHH-HhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCCeeeccHHHHH
Confidence            345678999999999999999999877 8899999999999999999999999999999999999999999999999999


Q ss_pred             HHHhccccccccccC
Q 025979          231 QKYLGEVWLKHKQIF  245 (245)
Q Consensus       231 ~~~~Ge~~~~vr~iF  245 (245)
                      +.|+|.+...++++|
T Consensus       254 ~~~~g~~~~~vr~lF  268 (638)
T CHL00176        254 EMFVGVGAARVRDLF  268 (638)
T ss_pred             HHhhhhhHHHHHHHH
Confidence            999999998888776

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.55  E-value=8.6e-16  Score=154.75  Aligned_cols=217  Identities=18%  Similarity=0.205  Sum_probs=129.5

Q ss_pred             cccCCCCC---CCCCCCcccCCCCCCCCchhHHHHHHHHHHHhhhhhhh----------HHHHHHHHHHHHHHHHHHHHH
Q 025979            6 MVLDPKPV---SEPPPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQ----------EEYVKDEQKNLKRELLRAQEE   72 (245)
Q Consensus         6 ~~~~~k~~---~e~~~~~~~e~~~~~~~~~~~~~~~~~~~~e~~~l~~~----------~~~i~~~~~~~~~~~~~~~~~   72 (245)
                      ..||||||   |||+|..+++..+.+...+.+.+++.+++.+...+..+          ...++.++..+++++..++++
T Consensus       393 r~LPDKAIdlldea~a~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  472 (852)
T TIGR03345       393 RQLPDKAVSLLDTACARVALSQNATPAALEDLRRRIAALELELDALEREAALGADHDERLAELRAELAALEAELAALEAR  472 (852)
T ss_pred             ccCccHHHHHHHHHHHHHHHhccCCchhHHHHHHHHHHHHHHHHHHhhhhccccchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56899999   99999999999999999998988888887777665332          112333333444444444444


Q ss_pred             hhhhccccchhhhhhhhhhcccceeecccCCeeEEEEeeccccc--cc-CCCceeeeeccccccccccCCCccccccccc
Q 025979           73 VKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRE--LL-KPSASVALHRHSNALVDVLPPEADSSISLLS  149 (245)
Q Consensus        73 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~--~l-~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~  149 (245)
                      ++.-+.............+..  ..............+..+...  .+ .....+........+..++..|++.++..+.
T Consensus       473 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~i~~vv~~~tgip~~~~~  550 (852)
T TIGR03345       473 WQQEKELVEAILALRAELEAD--ADAPADDDAALRAQLAELEAALASAQGEEPLVFPEVDAQAVAEVVADWTGIPVGRMV  550 (852)
T ss_pred             HHHHHHHHHHHHHHHHHhhhc--ccchhhhhHHHHHHHHHHHHHHHHHhhccccccceecHHHHHHHHHHHHCCCchhhc
Confidence            433221100000000000000  000000000000000000000  00 0011122234556778899999999998776


Q ss_pred             cCCCCC------ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccC---CCcc-eeeecCCCCchHHHHHHHHhcc--
Q 025979          150 QSEKPD------VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGID---PPRG-VLLYGPPGTGKTMLAKAVANHT--  217 (245)
Q Consensus       150 ~~~~~~------~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~---~~~g-vLl~GPPGtGKT~lAkalA~~l--  217 (245)
                      ..+...      ..-..|+|++.+++.+.+.+..        .+.|+.   .|.| +||+||||||||.+|+++|..+  
T Consensus       551 ~~e~~~l~~l~~~L~~~v~GQ~~Av~~v~~~i~~--------~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~l~~  622 (852)
T TIGR03345       551 RDEIEAVLSLPDRLAERVIGQDHALEAIAERIRT--------ARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLYG  622 (852)
T ss_pred             hhHHHHHHHHHHHhcCeEcChHHHHHHHHHHHHH--------HhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHHHhC
Confidence            554432      3446799999999999999875        334443   3444 8999999999999999999998  


Q ss_pred             -cceeeeechhHHHHH
Q 025979          218 -TAAFIRVVGSEFVQK  232 (245)
Q Consensus       218 -~~~~~~v~~s~l~~~  232 (245)
                       ...|+++++++|.++
T Consensus       623 ~~~~~~~~dmse~~~~  638 (852)
T TIGR03345       623 GEQNLITINMSEFQEA  638 (852)
T ss_pred             CCcceEEEeHHHhhhh
Confidence             568999999999765

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.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.53  E-value=2.3e-15  Score=151.85  Aligned_cols=220  Identities=20%  Similarity=0.247  Sum_probs=128.1

Q ss_pred             ccccCCCCC---CCCCCCcccCCCCCCCCchhHHHHHHHHHHHhhhhhhhH--------HHHHHHHHHHHHHHHHHHHHh
Q 025979            5 AMVLDPKPV---SEPPPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQE--------EYVKDEQKNLKRELLRAQEEV   73 (245)
Q Consensus         5 ~~~~~~k~~---~e~~~~~~~e~~~~~~~~~~~~~~~~~~~~e~~~l~~~~--------~~i~~~~~~~~~~~~~~~~~~   73 (245)
                      ...|||||+   |++++..+++..++|...+.+..++..++.++..++.+.        ..+++++...++++..+++++
T Consensus       383 ~~~~pdkAi~LiD~aaa~~rl~~~~kp~~L~rLer~l~~L~~E~e~l~~e~~~~~~~~~~~l~~~l~~lq~e~~~L~eq~  462 (857)
T PRK10865        383 DRQLPDKAIDLIDEAASSIRMQIDSKPEELDRLDRRIIQLKLEQQALMKESDEASKKRLDMLNEELSDKERQYSELEEEW  462 (857)
T ss_pred             CCCCChHHHHHHHHHhcccccccccChHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467999999   999999999999998888888777777777766654332        222333333344444344444


Q ss_pred             hhhccccchhhhhhhhhhcccc-eeecccC------CeeEEEEeecccc-------cccCCCceeeeeccccccccccCC
Q 025979           74 KRIQSVPLVIGQFMEMVDQNNG-IVGSTTG------SNYYVRILSTINR-------ELLKPSASVALHRHSNALVDVLPP  139 (245)
Q Consensus        74 ~~~~~~~~~~~~~~~~l~~~~~-~~~~~~~------~~~~~~~~~~~~~-------~~l~~~~~v~~~~~~~~~~~il~~  139 (245)
                      +..+..-.......+.++.... +......      ...-...+..+..       ..-.....+........+..++..
T Consensus       463 k~~k~el~~~~~~~~ele~l~~kie~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~i~~vv~~  542 (857)
T PRK10865        463 KAEKASLSGTQTIKAELEQAKIAIEQARRVGDLARMSELQYGKIPELEKQLAAATQLEGKTMRLLRNKVTDAEIAEVLAR  542 (857)
T ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHhhhhhhHHHHHHHHHHHhhhccccccccCccCHHHHHHHHHH
Confidence            4332110000011111110000 0000000      0000000000000       000011122223455667889999


Q ss_pred             CccccccccccCCCCC------ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCc----ceeeecCCCCchHHH
Q 025979          140 EADSSISLLSQSEKPD------VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPR----GVLLYGPPGTGKTML  209 (245)
Q Consensus       140 ~~~~~~~~~~~~~~~~------~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~----gvLl~GPPGtGKT~l  209 (245)
                      |++.++..+...+..+      .....+.|++.+++.|.+.|..        .+.|+..|+    .+||+||||||||++
T Consensus       543 ~tgip~~~~~~~~~~~l~~l~~~l~~~viGQ~~ai~~l~~~i~~--------~~~gl~~~~~p~~~~Lf~Gp~G~GKT~l  614 (857)
T PRK10865        543 WTGIPVSRMLESEREKLLRMEQELHHRVIGQNEAVEAVSNAIRR--------SRAGLSDPNRPIGSFLFLGPTGVGKTEL  614 (857)
T ss_pred             HHCCCchhhhhhHHHHHHHHHHHhCCeEeCCHHHHHHHHHHHHH--------HHhcccCCCCCCceEEEECCCCCCHHHH
Confidence            9999998776554332      3456789999999999999876        344544332    489999999999999


Q ss_pred             HHHHHhcc---cceeeeechhHHHHH
Q 025979          210 AKAVANHT---TAAFIRVVGSEFVQK  232 (245)
Q Consensus       210 AkalA~~l---~~~~~~v~~s~l~~~  232 (245)
                      |++||..+   +.+|++++++++.+.
T Consensus       615 A~aLa~~l~~~~~~~i~id~se~~~~  640 (857)
T PRK10865        615 CKALANFMFDSDDAMVRIDMSEFMEK  640 (857)
T ss_pred             HHHHHHHhhcCCCcEEEEEhHHhhhh
Confidence            99999987   567999999998653

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.46  E-value=9.1e-15  Score=147.74  Aligned_cols=96  Identities=25%  Similarity=0.401  Sum_probs=73.7

Q ss_pred             ccccccccccCCCccccccccccCCCCC------ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCC----Cccee
Q 025979          128 RHSNALVDVLPPEADSSISLLSQSEKPD------VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDP----PRGVL  197 (245)
Q Consensus       128 ~~~~~~~~il~~~~~~~~~~~~~~~~~~------~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~----~~gvL  197 (245)
                      .....+..++..|++.++..+...+...      .....|.|++.+++.+.+.+..        .+.|+..    ...+|
T Consensus       528 v~~~~i~~v~~~~tgip~~~~~~~e~~~l~~l~~~l~~~v~GQ~~av~~v~~~i~~--------~~~gl~~~~~p~~~~L  599 (852)
T TIGR03346       528 VTAEEIAEVVSRWTGIPVSKMLEGEREKLLHMEEVLHERVVGQDEAVEAVSDAIRR--------SRAGLSDPNRPIGSFL  599 (852)
T ss_pred             cCHHHHHHHHHHhcCCCcccccHHHHHHHHHHHHHhhcccCCChHHHHHHHHHHHH--------HhccCCCCCCCCeEEE
Confidence            4456677788889888887765443332      2456799999999999999876        3344432    23499


Q ss_pred             eecCCCCchHHHHHHHHhcc---cceeeeechhHHHH
Q 025979          198 LYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQ  231 (245)
Q Consensus       198 l~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~  231 (245)
                      |+||||||||++|+++|..+   +.+|++++++++++
T Consensus       600 f~Gp~GvGKt~lA~~La~~l~~~~~~~i~~d~s~~~~  636 (852)
T TIGR03346       600 FLGPTGVGKTELAKALAEFLFDDEDAMVRIDMSEYME  636 (852)
T ss_pred             EEcCCCCCHHHHHHHHHHHhcCCCCcEEEEechhhcc
Confidence            99999999999999999987   56899999998754

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

>CHL00181 cbbX CbbX; Provisional

Probab=99.46  E-value=5.2e-14  Score=125.84  Aligned_cols=86  Identities=30%  Similarity=0.487  Sum_probs=73.1

Q ss_pred             eccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCc-c--eeeecCCCCchHHHHHHHHhcc-------cceeeeechh
Q 025979          158 YNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPR-G--VLLYGPPGTGKTMLAKAVANHT-------TAAFIRVVGS  227 (245)
Q Consensus       158 ~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~-g--vLl~GPPGtGKT~lAkalA~~l-------~~~~~~v~~s  227 (245)
                      +++++|++.+|++|.+.+.+ +..+..+.+.|+.+++ |  +||+||||||||++|+++|..+       ..+|+.++.+
T Consensus        22 ~~~l~Gl~~vK~~i~e~~~~-~~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~~~  100 (287)
T CHL00181         22 DEELVGLAPVKTRIREIAAL-LLIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVTRD  100 (287)
T ss_pred             HHhcCCcHHHHHHHHHHHHH-HHHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEecHH
Confidence            45899999999999999987 5566777888987653 4  8999999999999999999876       2369999999


Q ss_pred             HHHHHHhcccccccccc
Q 025979          228 EFVQKYLGEVWLKHKQI  244 (245)
Q Consensus       228 ~l~~~~~Ge~~~~vr~i  244 (245)
                      +++++|+|+++..++.+
T Consensus       101 ~l~~~~~g~~~~~~~~~  117 (287)
T CHL00181        101 DLVGQYIGHTAPKTKEV  117 (287)
T ss_pred             HHHHHHhccchHHHHHH
Confidence            99999999998776654

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.45  E-value=6e-14  Score=141.36  Aligned_cols=180  Identities=19%  Similarity=0.261  Sum_probs=114.1

Q ss_pred             cccCCCCC---CCCCCCcccCCCCCCCCchhHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhhhccccch
Q 025979            6 MVLDPKPV---SEPPPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLV   82 (245)
Q Consensus         6 ~~~~~k~~---~e~~~~~~~e~~~~~~~~~~~~~~~~~~~~e~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (245)
                      -.||||||   |+++|..++.....|.....+..++.+++.+...+..+...  .....++.+...+++++..+..    
T Consensus       384 r~lPdkaidlld~a~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~----  457 (821)
T CHL00095        384 RFLPDKAIDLLDEAGSRVRLINSRLPPAARELDKELREILKDKDEAIREQDF--ETAKQLRDREMEVRAQIAAIIQ----  457 (821)
T ss_pred             ccCchHHHHHHHHHHHHHHhhccCCchhHHHHHHHHHHHHHHHHHHHhCcch--HHHHHHHHHHHHHHHHHHHHHH----
Confidence            45899999   99999999988888887778888888777666554322111  0011111111122222221110    


Q ss_pred             hhhhhhhhhcccceeecccCCeeEEEEeecccccccCCCceeeeeccccccccccCCCccccccccccCCCCC------c
Q 025979           83 IGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPD------V  156 (245)
Q Consensus        83 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~------~  156 (245)
                            .......      .                   ...........+..++..|++.++..+...+...      .
T Consensus       458 ------~~~~~~~------~-------------------~~~~~~v~~~~i~~~~~~~tgip~~~~~~~~~~~l~~l~~~  506 (821)
T CHL00095        458 ------SKKTEEE------K-------------------RLEVPVVTEEDIAEIVSAWTGIPVNKLTKSESEKLLHMEET  506 (821)
T ss_pred             ------HHHhhhc------c-------------------cccCCccCHHHHHHHHHHHHCCCchhhchhHHHHHHHHHHH
Confidence                  0000000      0                   0000123455677788889988888776544332      2


Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCC---Cc-ceeeecCCCCchHHHHHHHHhcc---cceeeeechhHH
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDP---PR-GVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEF  229 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~---~~-gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l  229 (245)
                      .-..|+|++.+++.|..++..        .+.|+..   |. .+||+||||||||++|+++|..+   +.++++++++++
T Consensus       507 L~~~v~GQ~~ai~~l~~~i~~--------~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l~~~~~~~~~~d~s~~  578 (821)
T CHL00095        507 LHKRIIGQDEAVVAVSKAIRR--------ARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYFFGSEDAMIRLDMSEY  578 (821)
T ss_pred             hcCcCcChHHHHHHHHHHHHH--------HhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHHhcCCccceEEEEchhc
Confidence            345699999999999999875        3445433   22 38999999999999999999987   478999999988


Q ss_pred             H
Q 025979          230 V  230 (245)
Q Consensus       230 ~  230 (245)
                      .
T Consensus       579 ~  579 (821)
T CHL00095        579 M  579 (821)
T ss_pred             c
Confidence            4

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=99.44  E-value=4.6e-14  Score=124.19  Aligned_cols=87  Identities=25%  Similarity=0.410  Sum_probs=71.0

Q ss_pred             eccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCc---ceeeecCCCCchHHHHHHHHhcc-------cceeeeechh
Q 025979          158 YNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPR---GVLLYGPPGTGKTMLAKAVANHT-------TAAFIRVVGS  227 (245)
Q Consensus       158 ~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~---gvLl~GPPGtGKT~lAkalA~~l-------~~~~~~v~~s  227 (245)
                      .++++|++.+|+.|++.+.++... ......|+.++.   +++||||||||||++|+++|+.+       ..+++.++++
T Consensus         5 l~~~~Gl~~vk~~i~~~~~~~~~~-~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v~~~~~   83 (261)
T TIGR02881         5 LSRMVGLDEVKALIKEIYAWIQIN-EKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEVERA   83 (261)
T ss_pred             HHHhcChHHHHHHHHHHHHHHHHH-HHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceEEecHH
Confidence            468999999999999998875443 333456776444   38999999999999999999864       3478999999


Q ss_pred             HHHHHHhccccccccccC
Q 025979          228 EFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       228 ~l~~~~~Ge~~~~vr~iF  245 (245)
                      +++.+|+|+++..++++|
T Consensus        84 ~l~~~~~g~~~~~~~~~~  101 (261)
T TIGR02881        84 DLVGEYIGHTAQKTREVI  101 (261)
T ss_pred             HhhhhhccchHHHHHHHH
Confidence            999999999988877764

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.

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=99.43  E-value=8.2e-14  Score=124.35  Aligned_cols=86  Identities=29%  Similarity=0.447  Sum_probs=74.2

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCC---CcceeeecCCCCchHHHHHHHHhccc-------ceeeeechhH
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGIDP---PRGVLLYGPPGTGKTMLAKAVANHTT-------AAFIRVVGSE  228 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~---~~gvLl~GPPGtGKT~lAkalA~~l~-------~~~~~v~~s~  228 (245)
                      ++++|++++|++|.+.+.+ +..++.+.+.|+.+   ..++||+||||||||++|+++|..+.       .+|+.+++++
T Consensus        22 ~~l~Gl~~vk~~i~e~~~~-~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~~~~  100 (284)
T TIGR02880        22 RELIGLKPVKTRIREIAAL-LLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTRDD  100 (284)
T ss_pred             HhccCHHHHHHHHHHHHHH-HHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEecHHH
Confidence            3699999999999999988 67788888899875   33699999999999999999998772       3799999999


Q ss_pred             HHHHHhccccccccccC
Q 025979          229 FVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       229 l~~~~~Ge~~~~vr~iF  245 (245)
                      ++++|+|+++.+++++|
T Consensus       101 l~~~~~g~~~~~~~~~~  117 (284)
T TIGR02880       101 LVGQYIGHTAPKTKEIL  117 (284)
T ss_pred             HhHhhcccchHHHHHHH
Confidence            99999999987776654

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.

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.38  E-value=3.4e-13  Score=132.62  Aligned_cols=92  Identities=39%  Similarity=0.751  Sum_probs=85.2

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHH
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQK  232 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~  232 (245)
                      ....+|+|+.|.+..++++.+.+.. +.++..+..++...|+|+||+||||||||++|+++|++++.+|+.++++++.++
T Consensus       146 ~~~~~~~di~g~~~~~~~l~~i~~~-~~~~~~~~~~~~~~~~gill~G~~G~GKt~~~~~~a~~~~~~f~~is~~~~~~~  224 (644)
T PRK10733        146 QIKTTFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEM  224 (644)
T ss_pred             hhhCcHHHHcCHHHHHHHHHHHHHH-hhCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCCEEEEehHHhHHh
Confidence            3457899999999999999999987 677888888899999999999999999999999999999999999999999999


Q ss_pred             HhccccccccccC
Q 025979          233 YLGEVWLKHKQIF  245 (245)
Q Consensus       233 ~~Ge~~~~vr~iF  245 (245)
                      |+|.++..++++|
T Consensus       225 ~~g~~~~~~~~~f  237 (644)
T PRK10733        225 FVGVGASRVRDMF  237 (644)
T ss_pred             hhcccHHHHHHHH
Confidence            9999999998876

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.33  E-value=5.9e-13  Score=139.47  Aligned_cols=54  Identities=28%  Similarity=0.541  Sum_probs=49.9

Q ss_pred             CcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHH
Q 025979          180 THHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKY  233 (245)
Q Consensus       180 ~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~  233 (245)
                      +......++|+.+|+||||+||||||||+||||+|.++++||+.|++++++++|
T Consensus      1617 ~~kP~slrLGl~pPKGILLiGPPGTGKTlLAKALA~es~VPFIsISgs~fl~~~ 1670 (2281)
T CHL00206       1617 HGKPFSLRLALSPSRGILVIGSIGTGRSYLVKYLATNSYVPFITVFLNKFLDNK 1670 (2281)
T ss_pred             cCcCHHHHcCCCCCCceEEECCCCCCHHHHHHHHHHhcCCceEEEEHHHHhhcc
Confidence            345566889999999999999999999999999999999999999999999876

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

Probab=99.32  E-value=5.8e-13  Score=118.97  Aligned_cols=89  Identities=26%  Similarity=0.304  Sum_probs=67.5

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhc-cCCCcceeeecCCCCchHHHHHHHHhcc---------cceeeeech
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIG-IDPPRGVLLYGPPGTGKTMLAKAVANHT---------TAAFIRVVG  226 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g-~~~~~gvLl~GPPGtGKT~lAkalA~~l---------~~~~~~v~~  226 (245)
                      .|+.++=-...|+++..++...+...+.-..-. +...|=+|||||||||||+|+||+|+.+         ...++.+++
T Consensus       140 lWEsLiyds~lK~~ll~Ya~s~l~fsek~vntnlIt~NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEins  219 (423)
T KOG0744|consen  140 LWESLIYDSNLKERLLSYAASALLFSEKKVNTNLITWNRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINS  219 (423)
T ss_pred             hHHHHhhcccHHHHHHHHHHHHHHHHhcCCCCceeeeeeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEeh
Confidence            466666566788899888765433222111111 2344559999999999999999999988         456899999


Q ss_pred             hHHHHHHhccccccccccC
Q 025979          227 SEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       227 s~l~~~~~Ge~~~~vr~iF  245 (245)
                      -.+++||.+|+.+.|..+|
T Consensus       220 hsLFSKWFsESgKlV~kmF  238 (423)
T KOG0744|consen  220 HSLFSKWFSESGKLVAKMF  238 (423)
T ss_pred             hHHHHHHHhhhhhHHHHHH
Confidence            9999999999999998887

>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=99.21  E-value=3.7e-12  Score=99.06  Aligned_cols=50  Identities=46%  Similarity=0.749  Sum_probs=47.0

Q ss_pred             eeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhccccccccccC
Q 025979          196 VLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge~~~~vr~iF  245 (245)
                      +|||||||||||++|+.+|+.++.+|+.++++++.+.+.+++.+.++++|
T Consensus         1 ill~G~~G~GKT~l~~~la~~l~~~~~~i~~~~~~~~~~~~~~~~i~~~~   50 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYLGFPFIEIDGSELISSYAGDSEQKIRDFF   50 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHTTSEEEEEETTHHHTSSTTHHHHHHHHHH
T ss_pred             CEEECcCCCCeeHHHHHHHhhccccccccccccccccccccccccccccc
Confidence            68999999999999999999999999999999999999999998888765

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 ....

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=99.20  E-value=4.3e-12  Score=117.94  Aligned_cols=87  Identities=28%  Similarity=0.467  Sum_probs=67.6

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhh-ccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHH-HHhc-
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQI-GIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQ-KYLG-  235 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~-g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~-~~~G-  235 (245)
                      .-|+|++++++.+..++........+...+ +-.+|+++||+||||||||++|+++|..++.+|+.++++.+.. .|+| 
T Consensus        12 ~~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~l~~~fi~vdat~~~e~g~vG~   91 (441)
T TIGR00390        12 KYIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGR   91 (441)
T ss_pred             hhccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHHhCCeEEEeecceeecCCcccC
Confidence            358999999999988876432211111111 1124688999999999999999999999999999999999985 8999 


Q ss_pred             cccccccccC
Q 025979          236 EVWLKHKQIF  245 (245)
Q Consensus       236 e~~~~vr~iF  245 (245)
                      +.+..+|++|
T Consensus        92 dvE~i~r~l~  101 (441)
T TIGR00390        92 DVESMVRDLT  101 (441)
T ss_pred             CHHHHHHHHH
Confidence            6788888775

This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in PubMed:98389714, is Ser in other members of the seed alignment.

>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=99.19  E-value=1.8e-11  Score=105.20  Aligned_cols=67  Identities=25%  Similarity=0.407  Sum_probs=47.1

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHH
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF  229 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l  229 (245)
                      +-+++|++|++..+..+.-++.....        .-.+...+|||||||||||+||..||++++.+|..++++.+
T Consensus        20 P~~L~efiGQ~~l~~~l~i~i~aa~~--------r~~~l~h~lf~GPPG~GKTTLA~IIA~e~~~~~~~~sg~~i   86 (233)
T PF05496_consen   20 PKSLDEFIGQEHLKGNLKILIRAAKK--------RGEALDHMLFYGPPGLGKTTLARIIANELGVNFKITSGPAI   86 (233)
T ss_dssp             -SSCCCS-S-HHHHHHHHHHHHHHHC--------TTS---EEEEESSTTSSHHHHHHHHHHHCT--EEEEECCC-
T ss_pred             CCCHHHccCcHHHHhhhHHHHHHHHh--------cCCCcceEEEECCCccchhHHHHHHHhccCCCeEeccchhh
Confidence            34789999999999998776653111        11233569999999999999999999999999999887643

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.

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=99.17  E-value=7.8e-12  Score=124.87  Aligned_cols=94  Identities=29%  Similarity=0.390  Sum_probs=71.6

Q ss_pred             ccccccccCCCccccccccccCCCCC------ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCC---cceeeec
Q 025979          130 SNALVDVLPPEADSSISLLSQSEKPD------VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPP---RGVLLYG  200 (245)
Q Consensus       130 ~~~~~~il~~~~~~~~~~~~~~~~~~------~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~---~gvLl~G  200 (245)
                      ...+..+...|++.++......+...      ..-+.|+|+++++..|.++|..        .+.|+..+   -.+||.|
T Consensus       527 ~~~i~~~~s~~tgip~~~~~~~e~~~l~~L~~~L~~~V~gQ~eAv~aIa~AI~~--------sr~gl~~~~~~awflflG  598 (898)
T KOG1051|consen  527 ESDISEVVSRWTGIPVDRLAEAEAERLKKLEERLHERVIGQDEAVAAIAAAIRR--------SRAGLKDPNPDAWFLFLG  598 (898)
T ss_pred             ccchhhhhhhhcCCchhhhhhhHHHHHHHHHHHHHhhccchHHHHHHHHHHHHh--------hhcccCCCCCCeEEEEEC
Confidence            34566677778777766554333222      3345799999999999999987        44555543   3399999


Q ss_pred             CCCCchHHHHHHHHhcc---cceeeeechhHHHH
Q 025979          201 PPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQ  231 (245)
Q Consensus       201 PPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~  231 (245)
                      |.|||||-+|+++|..+   .-.|+++++|+|++
T Consensus       599 pdgvGKt~lAkaLA~~~Fgse~~~IriDmse~~e  632 (898)
T KOG1051|consen  599 PDGVGKTELAKALAEYVFGSEENFIRLDMSEFQE  632 (898)
T ss_pred             CCchhHHHHHHHHHHHHcCCccceEEechhhhhh
Confidence            99999999999999988   66799999999875

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=99.14  E-value=1.1e-11  Score=115.34  Aligned_cols=85  Identities=28%  Similarity=0.475  Sum_probs=66.2

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhhccC---CCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHH-HHh
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGID---PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQ-KYL  234 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~---~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~-~~~  234 (245)
                      ..|+|++++++.+..++........+..  +..   .|+++||+||||||||++|++||..++.+|+++++++|.+ .|+
T Consensus        15 ~~IiGQe~AkkalavAl~~~~~r~~l~~--~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~l~~~fi~vD~t~f~e~Gyv   92 (443)
T PRK05201         15 KYIIGQDDAKRAVAIALRNRWRRMQLPE--ELRDEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYV   92 (443)
T ss_pred             cccCCHHHHHHHHHHHHHHHHHHhcCCc--ccccccCCceEEEECCCCCCHHHHHHHHHHHhCChheeecchhhccCCcc
Confidence            3589999999999888853211111000  111   2578999999999999999999999999999999999996 799


Q ss_pred             c-cccccccccC
Q 025979          235 G-EVWLKHKQIF  245 (245)
Q Consensus       235 G-e~~~~vr~iF  245 (245)
                      | +.+..+|++|
T Consensus        93 G~d~e~~ir~L~  104 (443)
T PRK05201         93 GRDVESIIRDLV  104 (443)
T ss_pred             cCCHHHHHHHHH
Confidence            9 6678888765

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.13  E-value=4.9e-11  Score=110.73  Aligned_cols=74  Identities=30%  Similarity=0.442  Sum_probs=67.4

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHH
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF  229 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l  229 (245)
                      -+|+.+.--.+.+++|.+-+..+.+..+.|.+.|....||.|||||||||||++..|+|+.++-.++-+..+++
T Consensus       198 stF~TlaMd~~~K~~I~~Dl~~F~k~k~~YkrvGkawKRGYLLYGPPGTGKSS~IaAmAn~L~ydIydLeLt~v  271 (457)
T KOG0743|consen  198 STFETLAMDPDLKERIIDDLDDFIKGKDFYKRVGKAWKRGYLLYGPPGTGKSSFIAAMANYLNYDIYDLELTEV  271 (457)
T ss_pred             CCccccccChhHHHHHHHHHHHHHhcchHHHhcCcchhccceeeCCCCCCHHHHHHHHHhhcCCceEEeeeccc
Confidence            78888888888999999999999999999999999999999999999999999999999999888777765443

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

Probab=98.96  E-value=1.6e-10  Score=115.43  Aligned_cols=92  Identities=25%  Similarity=0.362  Sum_probs=67.7

Q ss_pred             ccccccCCCccccccccccCCCCC------ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCC---Ccc-eeeecC
Q 025979          132 ALVDVLPPEADSSISLLSQSEKPD------VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDP---PRG-VLLYGP  201 (245)
Q Consensus       132 ~~~~il~~~~~~~~~~~~~~~~~~------~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~---~~g-vLl~GP  201 (245)
                      .+..++..|++.++..+...+...      .....|+|++.+++.|.+.+..        .+.|+..   |.| +||+||
T Consensus       421 ~i~~~i~~~tgiP~~~~~~~~~~~l~~l~~~l~~~v~GQ~~ai~~l~~~i~~--------~~~g~~~~~~p~~~~lf~Gp  492 (731)
T TIGR02639       421 DIENVVAKMAHIPVKTVSVDDREKLKNLEKNLKAKIFGQDEAIDSLVSSIKR--------SRAGLGNPNKPVGSFLFTGP  492 (731)
T ss_pred             HHHHHHHHHhCCChhhhhhHHHHHHHHHHHHHhcceeCcHHHHHHHHHHHHH--------HhcCCCCCCCCceeEEEECC
Confidence            345555566666655443322222      2355689999999999988865        3455543   344 899999


Q ss_pred             CCCchHHHHHHHHhcccceeeeechhHHHH
Q 025979          202 PGTGKTMLAKAVANHTTAAFIRVVGSEFVQ  231 (245)
Q Consensus       202 PGtGKT~lAkalA~~l~~~~~~v~~s~l~~  231 (245)
                      ||||||++|+++|..++.+|++++++++.+
T Consensus       493 ~GvGKT~lA~~la~~l~~~~~~~d~se~~~  522 (731)
T TIGR02639       493 TGVGKTELAKQLAEALGVHLERFDMSEYME  522 (731)
T ss_pred             CCccHHHHHHHHHHHhcCCeEEEeCchhhh
Confidence            999999999999999999999999999865

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

Probab=98.94  E-value=3.9e-10  Score=112.56  Aligned_cols=93  Identities=23%  Similarity=0.310  Sum_probs=70.7

Q ss_pred             ccccccccCCCccccccccccCCCCC------ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccC---CCc-ceeee
Q 025979          130 SNALVDVLPPEADSSISLLSQSEKPD------VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGID---PPR-GVLLY  199 (245)
Q Consensus       130 ~~~~~~il~~~~~~~~~~~~~~~~~~------~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~---~~~-gvLl~  199 (245)
                      ...+..++..|++.++..+...+...      ..-..|+|++++++.|.++|..        .+.|+.   .|. .+||+
T Consensus       423 ~~~i~~v~~~~tgip~~~~~~~~~~~l~~l~~~L~~~ViGQ~~ai~~l~~~i~~--------~~~gl~~~~kp~~~~Lf~  494 (758)
T PRK11034        423 VADIESVVARIARIPEKSVSQSDRDTLKNLGDRLKMLVFGQDKAIEALTEAIKM--------SRAGLGHEHKPVGSFLFA  494 (758)
T ss_pred             hhhHHHHHHHHhCCChhhhhhhHHHHHHHHHHHhcceEeCcHHHHHHHHHHHHH--------HhccccCCCCCcceEEEE
Confidence            34566778888888877665433222      1234589999999999999875        233443   233 49999


Q ss_pred             cCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          200 GPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       200 GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      ||||||||++|+++|..++.+|++++++++.
T Consensus       495 GP~GvGKT~lAk~LA~~l~~~~i~id~se~~  525 (758)
T PRK11034        495 GPTGVGKTEVTVQLSKALGIELLRFDMSEYM  525 (758)
T ss_pred             CCCCCCHHHHHHHHHHHhCCCcEEeechhhc
Confidence            9999999999999999999999999999984

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.92  E-value=1e-09  Score=98.09  Aligned_cols=63  Identities=29%  Similarity=0.440  Sum_probs=50.4

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechh
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS  227 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s  227 (245)
                      +|++++|+++.++.+..++....        ..-..+..++||||||||||++|+++|++++..+..+.++
T Consensus         2 ~~~~~iG~~~~~~~l~~~l~~~~--------~~~~~~~~~ll~Gp~G~GKT~la~~ia~~~~~~~~~~~~~   64 (305)
T TIGR00635         2 LLAEFIGQEKVKEQLQLFIEAAK--------MRQEALDHLLLYGPPGLGKTTLAHIIANEMGVNLKITSGP   64 (305)
T ss_pred             CHHHHcCHHHHHHHHHHHHHHHH--------hcCCCCCeEEEECCCCCCHHHHHHHHHHHhCCCEEEeccc
Confidence            58899999999999998885421        1113456799999999999999999999998887666544

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.

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=98.91  E-value=5.6e-10  Score=104.52  Aligned_cols=79  Identities=24%  Similarity=0.318  Sum_probs=58.0

Q ss_pred             cCCcchhhhHHHHHHHhcCCCcHHHHhh--hccC-CCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH-HHHhc
Q 025979          160 DIGGCDIQKQEIREAVELPLTHHELYKQ--IGID-PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV-QKYLG  235 (245)
Q Consensus       160 dv~Gl~~~~~~i~e~i~~~~~~~~~~~~--~g~~-~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~-~~~~G  235 (245)
                      .|+|++.+++.+..++..++........  -... +..++||+||||||||++|+++|..++++|++++++.+. ..|+|
T Consensus        72 ~ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~l~~pf~~id~~~l~~~gyvG  151 (412)
T PRK05342         72 YVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVG  151 (412)
T ss_pred             HeeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHHHhCCCceecchhhcccCCccc
Confidence            4899999999998777432211100000  0111 345699999999999999999999999999999999886 46888


Q ss_pred             ccc
Q 025979          236 EVW  238 (245)
Q Consensus       236 e~~  238 (245)
                      +..
T Consensus       152 ~d~  154 (412)
T PRK05342        152 EDV  154 (412)
T ss_pred             chH
Confidence            753

>smart00763 AAA_PrkA PrkA AAA domain

Probab=98.88  E-value=1e-09  Score=100.60  Aligned_cols=77  Identities=16%  Similarity=0.123  Sum_probs=60.4

Q ss_pred             cCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCC-cceeeecCCCCchHHHHHHHHhcccc-------eeeeech----h
Q 025979          160 DIGGCDIQKQEIREAVELPLTHHELYKQIGIDPP-RGVLLYGPPGTGKTMLAKAVANHTTA-------AFIRVVG----S  227 (245)
Q Consensus       160 dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~-~gvLl~GPPGtGKT~lAkalA~~l~~-------~~~~v~~----s  227 (245)
                      ++.|+++.++++.+++...        ..|.... +.++|+||||||||++|++||+.++.       +++.+.+    |
T Consensus        52 ~~~G~~~~i~~lv~~l~~~--------a~g~~~~r~il~L~GPPGsGKStla~~La~~l~~ys~t~eG~~Y~~~~~~~~s  123 (361)
T smart00763       52 DFFGMEEAIERFVNYFKSA--------AQGLEERKQILYLLGPVGGGKSSLVECLKRGLEEYSKTPEGRRYTFKWNGEES  123 (361)
T ss_pred             hccCcHHHHHHHHHHHHHH--------HhcCCCCCcEEEEECCCCCCHHHHHHHHHHHHhhhcccccCceEEEEecCCCC
Confidence            8999999999888877652        2344433 55899999999999999999999977       9999998    7


Q ss_pred             HHHHHHhcccccccccc
Q 025979          228 EFVQKYLGEVWLKHKQI  244 (245)
Q Consensus       228 ~l~~~~~Ge~~~~vr~i  244 (245)
                      .+.+..+|-....+|+.
T Consensus       124 p~~e~Pl~l~p~~~r~~  140 (361)
T smart00763      124 PMHEDPLHLFPDELRED  140 (361)
T ss_pred             CCccCCcccCCHHHHHH
Confidence            77777776666655543

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

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

Probab=98.86  E-value=1.7e-09  Score=108.10  Aligned_cols=76  Identities=21%  Similarity=0.284  Sum_probs=64.2

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc----------cceeeeech
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT----------TAAFIRVVG  226 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l----------~~~~~~v~~  226 (245)
                      .+++++|.++.+.++.+.+..             ....++|||||||||||++|+++|..+          +..++.+++
T Consensus       180 ~l~~~igr~~ei~~~~~~L~~-------------~~~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~~~~  246 (731)
T TIGR02639       180 KIDPLIGREDELERTIQVLCR-------------RKKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYSLDM  246 (731)
T ss_pred             CCCcccCcHHHHHHHHHHHhc-------------CCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEEecH
Confidence            457899999888877766644             134579999999999999999999987          788999999


Q ss_pred             hHHH--HHHhccccccccccC
Q 025979          227 SEFV--QKYLGEVWLKHKQIF  245 (245)
Q Consensus       227 s~l~--~~~~Ge~~~~vr~iF  245 (245)
                      +.++  .+|.|+.+..++++|
T Consensus       247 ~~l~a~~~~~g~~e~~l~~i~  267 (731)
T TIGR02639       247 GSLLAGTKYRGDFEERLKAVV  267 (731)
T ss_pred             HHHhhhccccchHHHHHHHHH
Confidence            9998  589999999988775

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

Probab=98.85  E-value=2.1e-09  Score=98.74  Aligned_cols=60  Identities=35%  Similarity=0.556  Sum_probs=46.7

Q ss_pred             CceeccCCcchhhh---HHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechh
Q 025979          155 DVTYNDIGGCDIQK---QEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS  227 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~---~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s  227 (245)
                      +-++++++|++...   .-|+++|..             +...+++||||||||||++|+.||+.++..|..++..
T Consensus        20 P~~lde~vGQ~HLlg~~~~lrr~v~~-------------~~l~SmIl~GPPG~GKTTlA~liA~~~~~~f~~~sAv   82 (436)
T COG2256          20 PKSLDEVVGQEHLLGEGKPLRRAVEA-------------GHLHSMILWGPPGTGKTTLARLIAGTTNAAFEALSAV   82 (436)
T ss_pred             CCCHHHhcChHhhhCCCchHHHHHhc-------------CCCceeEEECCCCCCHHHHHHHHHHhhCCceEEeccc
Confidence            45678888887654   344555443             3345699999999999999999999999999999754

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=98.83  E-value=3.6e-09  Score=96.07  Aligned_cols=65  Identities=29%  Similarity=0.409  Sum_probs=52.4

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechh
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS  227 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s  227 (245)
                      +.+|++++|.++.++.+..++....        ..-.++.++|||||||||||++|+++|++++..+..++++
T Consensus        21 P~~~~~~vG~~~~~~~l~~~l~~~~--------~~~~~~~~~ll~GppG~GKT~la~~ia~~l~~~~~~~~~~   85 (328)
T PRK00080         21 PKSLDEFIGQEKVKENLKIFIEAAK--------KRGEALDHVLLYGPPGLGKTTLANIIANEMGVNIRITSGP   85 (328)
T ss_pred             cCCHHHhcCcHHHHHHHHHHHHHHH--------hcCCCCCcEEEECCCCccHHHHHHHHHHHhCCCeEEEecc
Confidence            3588999999999999988875411        1113567799999999999999999999999888776654

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

Probab=98.82  E-value=3.7e-09  Score=93.39  Aligned_cols=67  Identities=27%  Similarity=0.405  Sum_probs=54.4

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHH
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF  229 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l  229 (245)
                      +-.++|.+|++.+++.+.=+|.-.        +..-...-.+|||||||.|||+||..+|+++|..+-..+++.+
T Consensus        22 P~~l~efiGQ~~vk~~L~ifI~AA--------k~r~e~lDHvLl~GPPGlGKTTLA~IIA~Emgvn~k~tsGp~l   88 (332)
T COG2255          22 PKTLDEFIGQEKVKEQLQIFIKAA--------KKRGEALDHVLLFGPPGLGKTTLAHIIANELGVNLKITSGPAL   88 (332)
T ss_pred             cccHHHhcChHHHHHHHHHHHHHH--------HhcCCCcCeEEeeCCCCCcHHHHHHHHHHHhcCCeEecccccc
Confidence            456899999999999999888652        2222344559999999999999999999999999888877655

>PRK04195 replication factor C large subunit; Provisional

Probab=98.79  E-value=4.2e-09  Score=100.54  Aligned_cols=69  Identities=39%  Similarity=0.565  Sum_probs=57.0

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHH
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF  229 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l  229 (245)
                      ...+.++++++|.+.+++.+..++....        .| .+++.+|||||||||||++|+++|++++..++.++.++.
T Consensus         7 KyrP~~l~dlvg~~~~~~~l~~~l~~~~--------~g-~~~~~lLL~GppG~GKTtla~ala~el~~~~ielnasd~   75 (482)
T PRK04195          7 KYRPKTLSDVVGNEKAKEQLREWIESWL--------KG-KPKKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQ   75 (482)
T ss_pred             hcCCCCHHHhcCCHHHHHHHHHHHHHHh--------cC-CCCCeEEEECCCCCCHHHHHHHHHHHcCCCEEEEccccc
Confidence            3345678999999999999999986522        11 246789999999999999999999999999999987753

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

Probab=98.75  E-value=6.6e-09  Score=92.62  Aligned_cols=55  Identities=31%  Similarity=0.411  Sum_probs=46.1

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      +..+-+++++.|++.+++.+...+.. .            ....+|||||||||||+.|++.|+++..
T Consensus        29 KYrPkt~de~~gQe~vV~~L~~a~~~-~------------~lp~~LFyGPpGTGKTStalafar~L~~   83 (346)
T KOG0989|consen   29 KYRPKTFDELAGQEHVVQVLKNALLR-R------------ILPHYLFYGPPGTGKTSTALAFARALNC   83 (346)
T ss_pred             HhCCCcHHhhcchHHHHHHHHHHHhh-c------------CCceEEeeCCCCCcHhHHHHHHHHHhcC
Confidence            44556889999999999999998865 1            1234899999999999999999999865

>CHL00095 clpC Clp protease ATP binding subunit

Probab=98.75  E-value=4.9e-09  Score=106.01  Aligned_cols=76  Identities=24%  Similarity=0.362  Sum_probs=64.5

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc----------cceeeeech
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT----------TAAFIRVVG  226 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l----------~~~~~~v~~  226 (245)
                      .+++++|.++.++++.+.+..             ...++++|+||||||||++|+++|..+          +.+|+.+++
T Consensus       177 ~~~~~igr~~ei~~~~~~L~r-------------~~~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~l~~  243 (821)
T CHL00095        177 NLDPVIGREKEIERVIQILGR-------------RTKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVITLDI  243 (821)
T ss_pred             CCCCCCCcHHHHHHHHHHHcc-------------cccCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeH
Confidence            467899999988888887665             245679999999999999999999976          478999999


Q ss_pred             hHHH--HHHhccccccccccC
Q 025979          227 SEFV--QKYLGEVWLKHKQIF  245 (245)
Q Consensus       227 s~l~--~~~~Ge~~~~vr~iF  245 (245)
                      +.++  .+|.|+.+..++++|
T Consensus       244 ~~l~ag~~~~ge~e~rl~~i~  264 (821)
T CHL00095        244 GLLLAGTKYRGEFEERLKRIF  264 (821)
T ss_pred             HHHhccCCCccHHHHHHHHHH
Confidence            9998  589999988888764

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=98.73  E-value=5.5e-09  Score=97.71  Aligned_cols=79  Identities=25%  Similarity=0.394  Sum_probs=56.7

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHH----HhhhccC-CCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH-HH
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHEL----YKQIGID-PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV-QK  232 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~----~~~~g~~-~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~-~~  232 (245)
                      +-|+|++++++.+..++......-..    ...-++. ...++||+||||||||++|+++|..++.+|..++++.+. ..
T Consensus        77 ~~ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~~l~~pf~~~da~~L~~~g  156 (413)
T TIGR00382        77 EYVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAG  156 (413)
T ss_pred             ceecCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCCcCHHHHHHHHHHhcCCCeEEechhhccccc
Confidence            45899999999998877321111000    0000111 134699999999999999999999999999999998876 36


Q ss_pred             Hhccc
Q 025979          233 YLGEV  237 (245)
Q Consensus       233 ~~Ge~  237 (245)
                      |+|+.
T Consensus       157 yvG~d  161 (413)
T TIGR00382       157 YVGED  161 (413)
T ss_pred             ccccc
Confidence            88875

A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.68  E-value=1.9e-08  Score=95.74  Aligned_cols=54  Identities=28%  Similarity=0.404  Sum_probs=45.4

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      .+-+|+|++|++.+++.|..++...            ..+.++|||||||||||++|+++|+.+++
T Consensus         9 RP~~~~divGq~~i~~~L~~~i~~~------------~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~   62 (472)
T PRK14962          9 RPKTFSEVVGQDHVKKLIINALKKN------------SISHAYIFAGPRGTGKTTVARILAKSLNC   62 (472)
T ss_pred             CCCCHHHccCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHHhcc
Confidence            4567899999999999988877652            24567999999999999999999998865

>PRK10865 protein disaggregation chaperone; Provisional

Probab=98.67  E-value=1.7e-08  Score=102.38  Aligned_cols=76  Identities=21%  Similarity=0.326  Sum_probs=61.9

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc----------cceeeeech
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT----------TAAFIRVVG  226 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l----------~~~~~~v~~  226 (245)
                      .+++++|.+..+.++.+.+..             ....+++|+||||||||++|+++|..+          +.+++.++.
T Consensus       176 ~l~~vigr~~ei~~~i~iL~r-------------~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~~~~~~~l~l  242 (857)
T PRK10865        176 KLDPVIGRDEEIRRTIQVLQR-------------RTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDM  242 (857)
T ss_pred             CCCcCCCCHHHHHHHHHHHhc-------------CCcCceEEECCCCCCHHHHHHHHHHHhhcCCCchhhCCCEEEEEeh
Confidence            467899998876666666544             133569999999999999999999987          789999999


Q ss_pred             hHHH--HHHhccccccccccC
Q 025979          227 SEFV--QKYLGEVWLKHKQIF  245 (245)
Q Consensus       227 s~l~--~~~~Ge~~~~vr~iF  245 (245)
                      +.++  .+|.|+.++.++++|
T Consensus       243 ~~l~ag~~~~g~~e~~lk~~~  263 (857)
T PRK10865        243 GALVAGAKYRGEFEERLKGVL  263 (857)
T ss_pred             hhhhhccchhhhhHHHHHHHH
Confidence            9887  679999988888765

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=98.66  E-value=2e-08  Score=91.95  Aligned_cols=74  Identities=28%  Similarity=0.428  Sum_probs=52.8

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc--ceeeeechhHHHHHHh
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT--AAFIRVVGSEFVQKYL  234 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~--~~~~~v~~s~l~~~~~  234 (245)
                      ..+.++|+.++.+..--.+.+        -+.|--.++++||.||||||||.||-++|+++|  .||+.+++|++.+.-+
T Consensus        22 ~~~GlVGQ~~AReAagiiv~m--------Ik~~K~aGr~iLiaGppGtGKTAlA~~ia~eLG~~~PF~~isgSEiyS~e~   93 (398)
T PF06068_consen   22 IADGLVGQEKAREAAGIIVDM--------IKEGKIAGRAILIAGPPGTGKTALAMAIAKELGEDVPFVSISGSEIYSSEV   93 (398)
T ss_dssp             EETTEES-HHHHHHHHHHHHH--------HHTT--TT-EEEEEE-TTSSHHHHHHHHHHHCTTTS-EEEEEGGGG-BTTC
T ss_pred             ccccccChHHHHHHHHHHHHH--------HhcccccCcEEEEeCCCCCCchHHHHHHHHHhCCCCCeeEcccceeeeccc
Confidence            346789999998887766655        112222468899999999999999999999995  9999999999976555


Q ss_pred             cccc
Q 025979          235 GEVW  238 (245)
Q Consensus       235 Ge~~  238 (245)
                      -.+|
T Consensus        94 kKTE   97 (398)
T PF06068_consen   94 KKTE   97 (398)
T ss_dssp             -HHH
T ss_pred             CchH
Confidence            4444

The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=98.65  E-value=1.4e-08  Score=92.26  Aligned_cols=78  Identities=27%  Similarity=0.412  Sum_probs=58.5

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc--cceeeeechhHHHH
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT--TAAFIRVVGSEFVQ  231 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l--~~~~~~v~~s~l~~  231 (245)
                      ++..-+.++|+.++.+.--=.+.+        -+.|--.++|+|+.||||||||.||-+||+++  +.||+.+++|++.+
T Consensus        34 ~k~~~dG~VGQ~~AReAaGvIv~m--------ik~gk~aGrgiLi~GppgTGKTAlA~gIa~eLG~dvPF~~isgsEiYS  105 (450)
T COG1224          34 AKFIGDGLVGQEEAREAAGVIVKM--------IKQGKMAGRGILIVGPPGTGKTALAMGIARELGEDVPFVAISGSEIYS  105 (450)
T ss_pred             EeEcCCcccchHHHHHhhhHHHHH--------HHhCcccccEEEEECCCCCcHHHHHHHHHHHhCCCCCceeeccceeee
Confidence            334456789998887765544443        12233456899999999999999999999999  58999999999976


Q ss_pred             HHhccccc
Q 025979          232 KYLGEVWL  239 (245)
Q Consensus       232 ~~~Ge~~~  239 (245)
                      --+..++.
T Consensus       106 ~E~kKTE~  113 (450)
T COG1224         106 LEVKKTEA  113 (450)
T ss_pred             ecccHHHH
Confidence            55555443

>PLN03025 replication factor C subunit; Provisional

Probab=98.64  E-value=2.8e-08  Score=89.98  Aligned_cols=63  Identities=25%  Similarity=0.317  Sum_probs=48.5

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc-----ceeeeechh
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT-----AAFIRVVGS  227 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~-----~~~~~v~~s  227 (245)
                      ..+.+++|+.|.+++++.|+.++...             ....+|||||||||||++|+++|+++.     ..++.++.+
T Consensus         7 yrP~~l~~~~g~~~~~~~L~~~~~~~-------------~~~~lll~Gp~G~GKTtla~~la~~l~~~~~~~~~~eln~s   73 (319)
T PLN03025          7 YRPTKLDDIVGNEDAVSRLQVIARDG-------------NMPNLILSGPPGTGKTTSILALAHELLGPNYKEAVLELNAS   73 (319)
T ss_pred             cCCCCHHHhcCcHHHHHHHHHHHhcC-------------CCceEEEECCCCCCHHHHHHHHHHHHhcccCccceeeeccc
Confidence            34567899999999999988776541             123499999999999999999999872     346666665


Q ss_pred             H
Q 025979          228 E  228 (245)
Q Consensus       228 ~  228 (245)
                      +
T Consensus        74 d   74 (319)
T PLN03025         74 D   74 (319)
T ss_pred             c
Confidence            4

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.64  E-value=2.3e-08  Score=93.71  Aligned_cols=60  Identities=32%  Similarity=0.511  Sum_probs=49.3

Q ss_pred             CceeccCCcchhhhHH---HHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechh
Q 025979          155 DVTYNDIGGCDIQKQE---IREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS  227 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~---i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s  227 (245)
                      +-+++|++|.+..+..   +..++..             .....++|+||||||||++|+++|+.++..|+.++.+
T Consensus         8 P~~l~d~vGq~~~v~~~~~L~~~i~~-------------~~~~~ilL~GppGtGKTtLA~~ia~~~~~~~~~l~a~   70 (413)
T PRK13342          8 PKTLDEVVGQEHLLGPGKPLRRMIEA-------------GRLSSMILWGPPGTGKTTLARIIAGATDAPFEALSAV   70 (413)
T ss_pred             CCCHHHhcCcHHHhCcchHHHHHHHc-------------CCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEecc
Confidence            3567899999988666   7777754             1234699999999999999999999999999998765

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.63  E-value=3.9e-08  Score=88.68  Aligned_cols=65  Identities=29%  Similarity=0.420  Sum_probs=51.3

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc-----ceeeeechh
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT-----AAFIRVVGS  227 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~-----~~~~~v~~s  227 (245)
                      ..+.+++++.|.+.+++.+..++..+             ....++||||||||||++|+++|+++.     .+++.++++
T Consensus         9 y~P~~~~~~~g~~~~~~~L~~~~~~~-------------~~~~lll~Gp~GtGKT~la~~~~~~l~~~~~~~~~~~i~~~   75 (337)
T PRK12402          9 YRPALLEDILGQDEVVERLSRAVDSP-------------NLPHLLVQGPPGSGKTAAVRALARELYGDPWENNFTEFNVA   75 (337)
T ss_pred             hCCCcHHHhcCCHHHHHHHHHHHhCC-------------CCceEEEECCCCCCHHHHHHHHHHHhcCcccccceEEechh
Confidence            34567899999999999998887541             122599999999999999999999873     356778877


Q ss_pred             HHH
Q 025979          228 EFV  230 (245)
Q Consensus       228 ~l~  230 (245)
                      ++.
T Consensus        76 ~~~   78 (337)
T PRK12402         76 DFF   78 (337)
T ss_pred             hhh
Confidence            764

>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=98.60  E-value=1.4e-08  Score=91.62  Aligned_cols=85  Identities=28%  Similarity=0.435  Sum_probs=61.0

Q ss_pred             cCCcchhhhHHHHHHHhcCCCcHHHHhhhc-cCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH-HHHhcc-
Q 025979          160 DIGGCDIQKQEIREAVELPLTHHELYKQIG-IDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV-QKYLGE-  236 (245)
Q Consensus       160 dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g-~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~-~~~~Ge-  236 (245)
                      -++|++++|+.+.-++.-......+-..+. --.|+++|+.||+|+|||.+||-+|.-.++||+.|-.+.|. -.|+|. 
T Consensus        16 yIIGQ~~AKkaVAIALRNR~RR~qL~~~lr~EV~PKNILMIGpTGVGKTEIARRLAkl~~aPFiKVEATKfTEVGYVGrD   95 (444)
T COG1220          16 YIIGQDEAKKAVAIALRNRWRRMQLEEELRDEVTPKNILMIGPTGVGKTEIARRLAKLAGAPFIKVEATKFTEVGYVGRD   95 (444)
T ss_pred             HhcCcHHHHHHHHHHHHHHHHHHhcCHHHhhccCccceEEECCCCCcHHHHHHHHHHHhCCCeEEEEeeeeeeccccccc
Confidence            479999999988766643211111111111 12579999999999999999999999999999999988876 467774 


Q ss_pred             cccccccc
Q 025979          237 VWLKHKQI  244 (245)
Q Consensus       237 ~~~~vr~i  244 (245)
                      .+.+||++
T Consensus        96 VesivRDL  103 (444)
T COG1220          96 VESIIRDL  103 (444)
T ss_pred             HHHHHHHH
Confidence            45555553

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=98.59  E-value=5e-08  Score=87.67  Aligned_cols=66  Identities=30%  Similarity=0.344  Sum_probs=53.7

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhH
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSE  228 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~  228 (245)
                      .+..+.+++++.|.+..++.+..++..           | ..|+.+|||||||+|||++|+++++.++.+++.+++++
T Consensus        13 ~kyrP~~~~~~~~~~~~~~~l~~~~~~-----------~-~~~~~lll~G~~G~GKT~la~~l~~~~~~~~~~i~~~~   78 (316)
T PHA02544         13 QKYRPSTIDECILPAADKETFKSIVKK-----------G-RIPNMLLHSPSPGTGKTTVAKALCNEVGAEVLFVNGSD   78 (316)
T ss_pred             eccCCCcHHHhcCcHHHHHHHHHHHhc-----------C-CCCeEEEeeCcCCCCHHHHHHHHHHHhCccceEeccCc
Confidence            344557889999999999999988753           1 23455777999999999999999999998888888764

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=98.59  E-value=3.9e-08  Score=91.72  Aligned_cols=60  Identities=25%  Similarity=0.424  Sum_probs=49.2

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      .|++|+|++.+++.|++++..+...+   ...+...+.++||+||||+|||++|+++|..+.+
T Consensus         3 ~f~~IiGq~~~~~~L~~~i~~~~~~~---~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c   62 (394)
T PRK07940          3 VWDDLVGQEAVVAELRAAARAARADV---AAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQC   62 (394)
T ss_pred             hhhhccChHHHHHHHHHHHHhccccc---cccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCC
Confidence            47899999999999999998755432   2334456788999999999999999999987644

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.59  E-value=4.3e-08  Score=94.24  Aligned_cols=56  Identities=16%  Similarity=0.241  Sum_probs=47.3

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      +..+-+|+|++|++.+++.|..++..-            ..+..+||+||||||||++|+++|+.+++
T Consensus         9 kyRP~~f~divGq~~v~~~L~~~~~~~------------~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c   64 (509)
T PRK14958          9 KWRPRCFQEVIGQAPVVRALSNALDQQ------------YLHHAYLFTGTRGVGKTTISRILAKCLNC   64 (509)
T ss_pred             HHCCCCHHHhcCCHHHHHHHHHHHHhC------------CCCeeEEEECCCCCCHHHHHHHHHHHhcC
Confidence            345568999999999999999998641            24567999999999999999999998865

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.58  E-value=4.6e-08  Score=95.73  Aligned_cols=55  Identities=22%  Similarity=0.299  Sum_probs=46.7

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ..+-+|++++|++.+++.|..++..            -..+..+||+||||||||++|+++|+.+++
T Consensus         9 yRPktFddVIGQe~vv~~L~~aI~~------------grl~HAyLF~GPpGvGKTTlAriLAK~LnC   63 (702)
T PRK14960          9 YRPRNFNELVGQNHVSRALSSALER------------GRLHHAYLFTGTRGVGKTTIARILAKCLNC   63 (702)
T ss_pred             hCCCCHHHhcCcHHHHHHHHHHHHc------------CCCCeEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            3456899999999999999988864            124577999999999999999999998865

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.56  E-value=5.4e-08  Score=89.76  Aligned_cols=55  Identities=25%  Similarity=0.277  Sum_probs=46.0

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ..+.+|++++|++..++.+..++...            ..+..+||+||||||||++|+++|+.+.+
T Consensus        10 yrP~~~~~iiGq~~~~~~l~~~~~~~------------~~~h~~L~~Gp~G~GKTtla~~la~~l~c   64 (363)
T PRK14961         10 WRPQYFRDIIGQKHIVTAISNGLSLG------------RIHHAWLLSGTRGVGKTTIARLLAKSLNC   64 (363)
T ss_pred             hCCCchhhccChHHHHHHHHHHHHcC------------CCCeEEEEecCCCCCHHHHHHHHHHHhcC
Confidence            34578999999999999998887641            24567899999999999999999998853

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

Probab=98.55  E-value=8e-08  Score=83.71  Aligned_cols=70  Identities=33%  Similarity=0.461  Sum_probs=57.5

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhH
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSE  228 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~  228 (245)
                      ....+.++++.|.+.+++.|.+....++.        | .|.+.+||||++|||||+++||+..+.   |..++.|...+
T Consensus        20 ~~~~~~l~~L~Gie~Qk~~l~~Nt~~Fl~--------G-~pannvLL~G~rGtGKSSlVkall~~y~~~GLRlIev~k~~   90 (249)
T PF05673_consen   20 HPDPIRLDDLIGIERQKEALIENTEQFLQ--------G-LPANNVLLWGARGTGKSSLVKALLNEYADQGLRLIEVSKED   90 (249)
T ss_pred             CCCCCCHHHhcCHHHHHHHHHHHHHHHHc--------C-CCCcceEEecCCCCCHHHHHHHHHHHHhhcCceEEEECHHH
Confidence            34567889999999999999988866332        2 367789999999999999999999876   78888888766


Q ss_pred             HH
Q 025979          229 FV  230 (245)
Q Consensus       229 l~  230 (245)
                      +.
T Consensus        91 L~   92 (249)
T PF05673_consen   91 LG   92 (249)
T ss_pred             hc
Confidence            53

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

Probab=98.55  E-value=1.5e-07  Score=72.91  Aligned_cols=43  Identities=49%  Similarity=0.923  Sum_probs=36.9

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHHHHh
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQKYL  234 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~~~~  234 (245)
                      ..+.++++||||||||++++.+++.+   +.+++.++.+++...+.
T Consensus        18 ~~~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~~~~~~~~~   63 (151)
T cd00009          18 PPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLV   63 (151)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEehhhhhhhhH
Confidence            45679999999999999999999998   88999999887765443

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.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=98.54  E-value=7e-08  Score=98.07  Aligned_cols=76  Identities=20%  Similarity=0.337  Sum_probs=60.9

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc----------cceeeeech
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT----------TAAFIRVVG  226 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l----------~~~~~~v~~  226 (245)
                      .+++++|.+..+.++.+.+..             ...++++|+||||||||++|+++|..+          +.+++.++.
T Consensus       171 ~~~~~igr~~ei~~~~~~l~r-------------~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~~~~~~~l~~  237 (852)
T TIGR03346       171 KLDPVIGRDEEIRRTIQVLSR-------------RTKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLALDM  237 (852)
T ss_pred             CCCcCCCcHHHHHHHHHHHhc-------------CCCCceEEEcCCCCCHHHHHHHHHHHHhccCCchhhcCCeEEEeeH
Confidence            457799998876666666544             233568999999999999999999875          678999999


Q ss_pred             hHHH--HHHhccccccccccC
Q 025979          227 SEFV--QKYLGEVWLKHKQIF  245 (245)
Q Consensus       227 s~l~--~~~~Ge~~~~vr~iF  245 (245)
                      +.++  .+|.|+.++.++.+|
T Consensus       238 ~~l~a~~~~~g~~e~~l~~~l  258 (852)
T TIGR03346       238 GALIAGAKYRGEFEERLKAVL  258 (852)
T ss_pred             HHHhhcchhhhhHHHHHHHHH
Confidence            9887  679999888877664

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

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.51  E-value=9.4e-08  Score=89.21  Aligned_cols=54  Identities=20%  Similarity=0.310  Sum_probs=45.7

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      .+.+|++|+|++.+++.|+.++..            -..+..+|||||||||||++|+++|+.+.+
T Consensus        11 RP~~~~eiiGq~~~~~~L~~~~~~------------~~~~ha~lf~Gp~G~GKtt~A~~~a~~l~c   64 (397)
T PRK14955         11 RPKKFADITAQEHITRTIQNSLRM------------GRVGHGYIFSGLRGVGKTTAARVFAKAVNC   64 (397)
T ss_pred             CCCcHhhccChHHHHHHHHHHHHh------------CCcceeEEEECCCCCCHHHHHHHHHHHhcC
Confidence            456789999999999999888764            134567999999999999999999998865

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.50  E-value=9.1e-08  Score=90.87  Aligned_cols=55  Identities=20%  Similarity=0.358  Sum_probs=46.1

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ..+-+|+|++|++.++..|..++...            ..+..+|||||||||||++|+++|+.+++
T Consensus        12 yRP~~f~dvVGQe~iv~~L~~~i~~~------------ri~ha~Lf~GP~GtGKTTlAriLAk~Lnc   66 (484)
T PRK14956         12 YRPQFFRDVIHQDLAIGALQNALKSG------------KIGHAYIFFGPRGVGKTTIARILAKRLNC   66 (484)
T ss_pred             hCCCCHHHHhChHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHhcCc
Confidence            34568999999999999999887651            23456899999999999999999999875

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.49  E-value=3.1e-07  Score=78.30  Aligned_cols=65  Identities=23%  Similarity=0.292  Sum_probs=47.0

Q ss_pred             CceeccCC--cchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHH
Q 025979          155 DVTYNDIG--GCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEF  229 (245)
Q Consensus       155 ~~~~~dv~--Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l  229 (245)
                      ..++++..  +.....+.+++.+..             ..+..++|+||||||||++|+++++.+   +.+++.++++++
T Consensus        11 ~~~~~~~~~~~~~~~~~~l~~~~~~-------------~~~~~lll~G~~G~GKT~la~~~~~~~~~~~~~~~~i~~~~~   77 (226)
T TIGR03420        11 DPTFDNFYAGGNAELLAALRQLAAG-------------KGDRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLPLAEL   77 (226)
T ss_pred             chhhcCcCcCCcHHHHHHHHHHHhc-------------CCCCeEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEeHHHH
Confidence            34556654  344456666665431             245679999999999999999999876   467888998887


Q ss_pred             HHH
Q 025979          230 VQK  232 (245)
Q Consensus       230 ~~~  232 (245)
                      ...
T Consensus        78 ~~~   80 (226)
T TIGR03420        78 AQA   80 (226)
T ss_pred             HHh
Confidence            653

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.

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.49  E-value=9.8e-08  Score=91.13  Aligned_cols=54  Identities=28%  Similarity=0.441  Sum_probs=45.1

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      ..+.+|+|++|++.+++.+..++..            -..+.++||+||||||||++|+.+|..++
T Consensus         7 yRP~~f~dliGQe~vv~~L~~a~~~------------~ri~ha~Lf~Gp~G~GKTT~ArilAk~Ln   60 (491)
T PRK14964          7 YRPSSFKDLVGQDVLVRILRNAFTL------------NKIPQSILLVGASGVGKTTCARIISLCLN   60 (491)
T ss_pred             hCCCCHHHhcCcHHHHHHHHHHHHc------------CCCCceEEEECCCCccHHHHHHHHHHHHc
Confidence            3457899999999999999888764            13467899999999999999999998663

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=98.49  E-value=1.2e-07  Score=91.46  Aligned_cols=62  Identities=18%  Similarity=0.306  Sum_probs=47.0

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCC-cceeeecCCCCchHHHHHHHHhcc-cceeeeech
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPP-RGVLLYGPPGTGKTMLAKAVANHT-TAAFIRVVG  226 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~-~gvLl~GPPGtGKT~lAkalA~~l-~~~~~~v~~  226 (245)
                      -|+|+.|+++++++|.+++..        ...|+... +-+||+||||+|||+||++||+.+ ..+++.+.+
T Consensus        74 fF~d~yGlee~ieriv~~l~~--------Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~~le~~~~Y~~kg  137 (644)
T PRK15455         74 AFEEFYGMEEAIEQIVSYFRH--------AAQGLEEKKQILYLLGPVGGGKSSLAERLKSLMERVPIYVLKA  137 (644)
T ss_pred             chhcccCcHHHHHHHHHHHHH--------HHHhcCCCCceEEEecCCCCCchHHHHHHHHHHHhCcceeecC
Confidence            467999999999999988743        22233332 348899999999999999999987 446666654

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.48  E-value=9.8e-08  Score=91.65  Aligned_cols=56  Identities=23%  Similarity=0.356  Sum_probs=46.6

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      +..+.+|+||+|++.+++.|..++...            ..+..+|||||||||||++|+++|+.+.+
T Consensus         7 KyRP~~~~dvvGq~~v~~~L~~~i~~~------------~l~ha~Lf~GppGtGKTTlA~~lA~~l~c   62 (504)
T PRK14963          7 RARPITFDEVVGQEHVKEVLLAALRQG------------RLGHAYLFSGPRGVGKTTTARLIAMAVNC   62 (504)
T ss_pred             hhCCCCHHHhcChHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHHHhc
Confidence            345578999999999999999988751            24456899999999999999999998854

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=98.47  E-value=8.8e-08  Score=97.20  Aligned_cols=77  Identities=16%  Similarity=0.176  Sum_probs=59.9

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc----------cceeeeec
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT----------TAAFIRVV  225 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l----------~~~~~~v~  225 (245)
                      -.+++++|.+..+.++.+.+..             ....+++|+||||||||++|+.+|..+          +..++.++
T Consensus       184 ~~ld~~iGr~~ei~~~i~~l~r-------------~~~~n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~~~i~~l~  250 (852)
T TIGR03345       184 GKIDPVLGRDDEIRQMIDILLR-------------RRQNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLSLD  250 (852)
T ss_pred             CCCCcccCCHHHHHHHHHHHhc-------------CCcCceeEECCCCCCHHHHHHHHHHHHhhCCCCccccCCeEEEee
Confidence            3567899998876666555433             133568999999999999999999875          36688899


Q ss_pred             hhHHH--HHHhccccccccccC
Q 025979          226 GSEFV--QKYLGEVWLKHKQIF  245 (245)
Q Consensus       226 ~s~l~--~~~~Ge~~~~vr~iF  245 (245)
                      .+.+.  .+|.|+.+..++++|
T Consensus       251 l~~l~ag~~~~ge~e~~lk~ii  272 (852)
T TIGR03345       251 LGLLQAGASVKGEFENRLKSVI  272 (852)
T ss_pred             hhhhhcccccchHHHHHHHHHH
Confidence            88887  378999888887764

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.

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

Probab=98.47  E-value=1.3e-07  Score=94.78  Aligned_cols=75  Identities=19%  Similarity=0.266  Sum_probs=59.7

Q ss_pred             eccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc----------cceeeeechh
Q 025979          158 YNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT----------TAAFIRVVGS  227 (245)
Q Consensus       158 ~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l----------~~~~~~v~~s  227 (245)
                      ++.++|-+..+.++.+.+..             ....++||+||||||||++|+++|...          +..++.++.+
T Consensus       185 ~~~liGR~~ei~~~i~iL~r-------------~~~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~l~~~  251 (758)
T PRK11034        185 IDPLIGREKELERAIQVLCR-------------RRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIG  251 (758)
T ss_pred             CCcCcCCCHHHHHHHHHHhc-------------cCCCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEeccHH
Confidence            45788888887777776654             134568999999999999999999764          6778888888


Q ss_pred             HHH--HHHhccccccccccC
Q 025979          228 EFV--QKYLGEVWLKHKQIF  245 (245)
Q Consensus       228 ~l~--~~~~Ge~~~~vr~iF  245 (245)
                      .++  .+|.|+.+..++++|
T Consensus       252 ~llaG~~~~Ge~e~rl~~l~  271 (758)
T PRK11034        252 SLLAGTKYRGDFEKRFKALL  271 (758)
T ss_pred             HHhcccchhhhHHHHHHHHH
Confidence            887  678999888877654

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=98.46  E-value=1.4e-07  Score=90.59  Aligned_cols=56  Identities=20%  Similarity=0.270  Sum_probs=46.8

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      +..+-+|+|++|++..+..+..++..            -..+.++||+||||||||++|+++|+.+++
T Consensus        14 kyRP~~f~dliGq~~vv~~L~~ai~~------------~ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc   69 (507)
T PRK06645         14 KYRPSNFAELQGQEVLVKVLSYTILN------------DRLAGGYLLTGIRGVGKTTSARIIAKAVNC   69 (507)
T ss_pred             hhCCCCHHHhcCcHHHHHHHHHHHHc------------CCCCceEEEECCCCCCHHHHHHHHHHHhcC
Confidence            34567899999999999999887654            124567999999999999999999999865

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=98.46  E-value=6.2e-08  Score=87.92  Aligned_cols=48  Identities=25%  Similarity=0.292  Sum_probs=40.8

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHH--Hhcccc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQK--YLGEVW  238 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~--~~Ge~~  238 (245)
                      ...+.+||.||||||||++|+.+|..+++++++|.++..+..  ++|...
T Consensus        62 ~~~~~ilL~G~pGtGKTtla~~lA~~l~~~~~rV~~~~~l~~~DliG~~~  111 (327)
T TIGR01650        62 AYDRRVMVQGYHGTGKSTHIEQIAARLNWPCVRVNLDSHVSRIDLVGKDA  111 (327)
T ss_pred             hcCCcEEEEeCCCChHHHHHHHHHHHHCCCeEEEEecCCCChhhcCCCce
Confidence            345779999999999999999999999999999988876655  677543

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.

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

Probab=98.46  E-value=9.4e-08  Score=91.39  Aligned_cols=68  Identities=54%  Similarity=1.029  Sum_probs=63.4

Q ss_pred             cCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhccccccccccC
Q 025979          177 LPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       177 ~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge~~~~vr~iF  245 (245)
                      .|+.+++.+..+++.++++++++||||||||++++++|.. +..++.+++++.+++|.|++++..+.+|
T Consensus         2 ~~~~~~~~~~~~~~~~~~~v~~~g~~~~~~t~~~~~~a~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~   69 (494)
T COG0464           2 LPLKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALANE-GAEFLSINGPEILSKYVGESELRLRELF   69 (494)
T ss_pred             CCccCHHHHHHhCCCCCCCceeeCCCCCchhHHHHHHHhc-cCcccccCcchhhhhhhhHHHHHHHHHH
Confidence            4678899999999999999999999999999999999999 8878889999999999999999988765

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=98.46  E-value=9.8e-08  Score=84.22  Aligned_cols=43  Identities=42%  Similarity=0.581  Sum_probs=35.9

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccceeeeech------hHHHHHHhc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVG------SEFVQKYLG  235 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~------s~l~~~~~G  235 (245)
                      .+.+||+||||||||++|+++|..+|.+|+++.+      ++++..|.|
T Consensus        21 g~~vLL~G~~GtGKT~lA~~la~~lg~~~~~i~~~~~~~~~dllg~~~~   69 (262)
T TIGR02640        21 GYPVHLRGPAGTGKTTLAMHVARKRDRPVMLINGDAELTTSDLVGSYAG   69 (262)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHHhCCCEEEEeCCccCCHHHHhhhhcc
Confidence            3569999999999999999999999999999854      466655544

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).

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=98.45  E-value=9.5e-08  Score=92.35  Aligned_cols=64  Identities=28%  Similarity=0.521  Sum_probs=49.9

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc----------ccee
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT----------TAAF  221 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l----------~~~~  221 (245)
                      .....+|++++|.+..++.++..+..             ..+..+||+||||||||++|+++.+.+          +.+|
T Consensus        58 ~~rp~~f~~iiGqs~~i~~l~~al~~-------------~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~s~~~~~~~f  124 (531)
T TIGR02902        58 KTRPKSFDEIIGQEEGIKALKAALCG-------------PNPQHVIIYGPPGVGKTAAARLVLEEAKKNPASPFKEGAAF  124 (531)
T ss_pred             hhCcCCHHHeeCcHHHHHHHHHHHhC-------------CCCceEEEECCCCCCHHHHHHHHHHHhhhccCCCcCCCCCE
Confidence            34557899999999999888866432             134569999999999999999997642          4689


Q ss_pred             eeechhH
Q 025979          222 IRVVGSE  228 (245)
Q Consensus       222 ~~v~~s~  228 (245)
                      +.++++.
T Consensus       125 i~id~~~  131 (531)
T TIGR02902       125 VEIDATT  131 (531)
T ss_pred             EEEcccc
Confidence            9998763

Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.

>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=98.44  E-value=1.3e-07  Score=74.94  Aligned_cols=34  Identities=50%  Similarity=0.685  Sum_probs=30.4

Q ss_pred             ceeeecCCCCchHHHHHHHHhcccceeeeechhH
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSE  228 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~  228 (245)
                      +|||+||||||||++|+.+|..++.+++.+.++.
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~~~~~~~~i~~~~   34 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAALLGRPVIRINCSS   34 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHTCEEEEEE-TT
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhhcceEEEEecc
Confidence            4899999999999999999999999998887664

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.

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

Probab=98.44  E-value=1.8e-07  Score=93.32  Aligned_cols=60  Identities=38%  Similarity=0.572  Sum_probs=47.8

Q ss_pred             CceeccCCcchhhhH---HHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechh
Q 025979          155 DVTYNDIGGCDIQKQ---EIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS  227 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~---~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s  227 (245)
                      +.+++|++|.+..+.   .+++++..             .....++||||||||||++|+++|+.++.+|+.++.+
T Consensus        24 P~tldd~vGQe~ii~~~~~L~~~i~~-------------~~~~slLL~GPpGtGKTTLA~aIA~~~~~~f~~lna~   86 (725)
T PRK13341         24 PRTLEEFVGQDHILGEGRLLRRAIKA-------------DRVGSLILYGPPGVGKTTLARIIANHTRAHFSSLNAV   86 (725)
T ss_pred             CCcHHHhcCcHHHhhhhHHHHHHHhc-------------CCCceEEEECCCCCCHHHHHHHHHHHhcCcceeehhh
Confidence            467889999998774   45555543             1234699999999999999999999999999888765

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.43  E-value=1.6e-07  Score=94.50  Aligned_cols=56  Identities=21%  Similarity=0.256  Sum_probs=46.9

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccce
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAA  220 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~  220 (245)
                      ..+.+|++|+|++.+++.|+.++..-            ..+..+||+||||||||++|+++|+.+++.
T Consensus        10 yRP~tFddIIGQe~Iv~~LknaI~~~------------rl~HAyLFtGPpGtGKTTLARiLAk~Lnce   65 (944)
T PRK14949         10 WRPATFEQMVGQSHVLHALTNALTQQ------------RLHHAYLFTGTRGVGKTSLARLFAKGLNCE   65 (944)
T ss_pred             hCCCCHHHhcCcHHHHHHHHHHHHhC------------CCCeEEEEECCCCCCHHHHHHHHHHhccCc
Confidence            44578999999999999999887641            235668999999999999999999998764

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

Probab=98.43  E-value=1.1e-07  Score=86.81  Aligned_cols=59  Identities=31%  Similarity=0.532  Sum_probs=40.9

Q ss_pred             CceeccCCcchhhhHH---HHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccce---eeeech
Q 025979          155 DVTYNDIGGCDIQKQE---IREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAA---FIRVVG  226 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~---i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~---~~~v~~  226 (245)
                      +-+.+|.+|++....+   |+.+|+.             ..-.+++||||||||||+||+.||+...-+   |+.++.
T Consensus       134 PktL~dyvGQ~hlv~q~gllrs~ieq-------------~~ipSmIlWGppG~GKTtlArlia~tsk~~SyrfvelSA  198 (554)
T KOG2028|consen  134 PKTLDDYVGQSHLVGQDGLLRSLIEQ-------------NRIPSMILWGPPGTGKTTLARLIASTSKKHSYRFVELSA  198 (554)
T ss_pred             cchHHHhcchhhhcCcchHHHHHHHc-------------CCCCceEEecCCCCchHHHHHHHHhhcCCCceEEEEEec
Confidence            3456777777764332   3333332             223459999999999999999999988666   666654

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=98.42  E-value=2.8e-07  Score=78.56  Aligned_cols=46  Identities=39%  Similarity=0.589  Sum_probs=36.3

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .|+||.|++..|..+.-+...               ..++||+||||||||++|++++.-+
T Consensus         1 Df~dI~GQe~aKrAL~iAAaG---------------~h~lLl~GppGtGKTmlA~~l~~lL   46 (206)
T PF01078_consen    1 DFSDIVGQEEAKRALEIAAAG---------------GHHLLLIGPPGTGKTMLARRLPSLL   46 (206)
T ss_dssp             -TCCSSSTHHHHHHHHHHHHC---------------C--EEEES-CCCTHHHHHHHHHHCS
T ss_pred             ChhhhcCcHHHHHHHHHHHcC---------------CCCeEEECCCCCCHHHHHHHHHHhC
Confidence            368999999999888766543               3579999999999999999999765

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=98.42  E-value=5.9e-07  Score=77.10  Aligned_cols=67  Identities=19%  Similarity=0.260  Sum_probs=45.9

Q ss_pred             CCCceeccCC-cc-hhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechh
Q 025979          153 KPDVTYNDIG-GC-DIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       153 ~~~~~~~dv~-Gl-~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      .+..+++++. |. ......+++.+.            +......++|+||||||||++|+++++.+   +.+++.+++.
T Consensus        12 ~~~~~~d~f~~~~~~~~~~~l~~~~~------------~~~~~~~~~l~G~~G~GKT~La~ai~~~~~~~~~~~~~i~~~   79 (227)
T PRK08903         12 PPPPTFDNFVAGENAELVARLRELAA------------GPVADRFFYLWGEAGSGRSHLLQALVADASYGGRNARYLDAA   79 (227)
T ss_pred             CChhhhcccccCCcHHHHHHHHHHHh------------ccCCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEehH
Confidence            3446677754 32 334444444332            23355679999999999999999999875   6678888887


Q ss_pred             HHHH
Q 025979          228 EFVQ  231 (245)
Q Consensus       228 ~l~~  231 (245)
                      ++..
T Consensus        80 ~~~~   83 (227)
T PRK08903         80 SPLL   83 (227)
T ss_pred             HhHH
Confidence            7654

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

Probab=98.42  E-value=2.4e-07  Score=77.35  Aligned_cols=43  Identities=37%  Similarity=0.687  Sum_probs=34.7

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHHHH
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQKY  233 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~~~  233 (245)
                      ..+.|++|+||||||||+||.++|.++   |.+...++.+++++..
T Consensus        45 ~~~~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~~~~~L~~~l   90 (178)
T PF01695_consen   45 ENGENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFITASDLLDEL   90 (178)
T ss_dssp             SC--EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHH
T ss_pred             ccCeEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEeecCceeccc
Confidence            355789999999999999999999877   7788889999998775

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.

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=98.41  E-value=3.7e-08  Score=88.38  Aligned_cols=79  Identities=25%  Similarity=0.380  Sum_probs=56.1

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhh----ccCCC-cceeeecCCCCchHHHHHHHHhcccceeeeechhHHH-HH
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQI----GIDPP-RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV-QK  232 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~----g~~~~-~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~-~~  232 (245)
                      +=|+|++.+|+.+.=+|-   .|.......    .+.-. .++||.||+|||||+||+.+|+.+++||.--+...+. ..
T Consensus        61 ~YVIGQe~AKKvLsVAVY---NHYKRl~~~~~~~dvEL~KSNILLiGPTGsGKTlLAqTLAk~LnVPFaiADATtLTEAG  137 (408)
T COG1219          61 EYVIGQEQAKKVLSVAVY---NHYKRLNNKEDNDDVELSKSNILLIGPTGSGKTLLAQTLAKILNVPFAIADATTLTEAG  137 (408)
T ss_pred             hheecchhhhceeeeeeh---hHHHHHhccCCCCceeeeeccEEEECCCCCcHHHHHHHHHHHhCCCeeeccccchhhcc
Confidence            347888888877654442   222211111    12222 3499999999999999999999999999999999887 67


Q ss_pred             Hhcccccc
Q 025979          233 YLGEVWLK  240 (245)
Q Consensus       233 ~~Ge~~~~  240 (245)
                      |+||--.|
T Consensus       138 YVGEDVEN  145 (408)
T COG1219         138 YVGEDVEN  145 (408)
T ss_pred             ccchhHHH
Confidence            99985433

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.40  E-value=2.2e-07  Score=89.79  Aligned_cols=55  Identities=22%  Similarity=0.321  Sum_probs=46.3

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ..+-+|+|++|.+.+++.+..++...            ..++.+||+||||||||++|+++|+.+++
T Consensus        10 ~rP~~f~divGq~~v~~~L~~~i~~~------------~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c   64 (527)
T PRK14969         10 WRPKSFSELVGQEHVVRALTNALEQQ------------RLHHAYLFTGTRGVGKTTLARILAKSLNC   64 (527)
T ss_pred             hCCCcHHHhcCcHHHHHHHHHHHHcC------------CCCEEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            34568999999999999999888651            24467899999999999999999998865

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

Probab=98.39  E-value=4.9e-07  Score=79.59  Aligned_cols=43  Identities=30%  Similarity=0.537  Sum_probs=38.0

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHHHHh
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQKYL  234 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~~~~  234 (245)
                      .+.+++||||||||||+||-|||+++   |..++.+..+++++..-
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~~~g~sv~f~~~~el~~~Lk  149 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDLLSKLK  149 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEEHHHHHHHHH
Confidence            56789999999999999999999988   78889999999887653

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=98.38  E-value=2.4e-07  Score=91.27  Aligned_cols=56  Identities=23%  Similarity=0.327  Sum_probs=47.3

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      +...-+|+||+|++.+++.|..++...            +.++++||+||||||||++|+++|+.+++
T Consensus         9 KYRP~tFddIIGQe~vv~~L~~ai~~~------------rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC   64 (709)
T PRK08691          9 KWRPKTFADLVGQEHVVKALQNALDEG------------RLHHAYLLTGTRGVGKTTIARILAKSLNC   64 (709)
T ss_pred             HhCCCCHHHHcCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCcHHHHHHHHHHHhcc
Confidence            345678999999999999999988751            24577999999999999999999998754

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.38  E-value=2.6e-07  Score=89.32  Aligned_cols=55  Identities=20%  Similarity=0.314  Sum_probs=45.6

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ..+.+|++++|.+.+++.+...+...            ..+..+||+||||||||++|+++|+.+.+
T Consensus        10 yRP~~f~diiGq~~~v~~L~~~i~~~------------rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c   64 (546)
T PRK14957         10 YRPQSFAEVAGQQHALNSLVHALETQ------------KVHHAYLFTGTRGVGKTTLGRLLAKCLNC   64 (546)
T ss_pred             HCcCcHHHhcCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            34568999999999999999888641            23466899999999999999999997754

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.38  E-value=2.8e-07  Score=89.86  Aligned_cols=55  Identities=22%  Similarity=0.331  Sum_probs=46.1

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ...-+|+|++|++.+++.|..++...            ..+..+||+||+|||||++|+++|+.+++
T Consensus         7 yRP~~f~eivGq~~i~~~L~~~i~~~------------r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c   61 (584)
T PRK14952          7 YRPATFAEVVGQEHVTEPLSSALDAG------------RINHAYLFSGPRGCGKTSSARILARSLNC   61 (584)
T ss_pred             hCCCcHHHhcCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHHhcc
Confidence            34567999999999999999988651            24566899999999999999999998764

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=98.37  E-value=4.5e-07  Score=81.06  Aligned_cols=52  Identities=31%  Similarity=0.370  Sum_probs=43.0

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..+.+|+|+.|.+++++.+..++...             ....++||||||||||++++++++.+
T Consensus        11 yrP~~~~~~~g~~~~~~~l~~~i~~~-------------~~~~~ll~G~~G~GKt~~~~~l~~~l   62 (319)
T PRK00440         11 YRPRTLDEIVGQEEIVERLKSYVKEK-------------NMPHLLFAGPPGTGKTTAALALAREL   62 (319)
T ss_pred             hCCCcHHHhcCcHHHHHHHHHHHhCC-------------CCCeEEEECCCCCCHHHHHHHHHHHH
Confidence            34468899999999999999887541             11248999999999999999999986

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.36  E-value=3.5e-07  Score=89.77  Aligned_cols=55  Identities=20%  Similarity=0.317  Sum_probs=46.4

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ..+.+|++++|++.+++.|+.++..-            ..+.++||+||||||||++|+++|+.+.+
T Consensus        10 yRP~~f~eivGQe~i~~~L~~~i~~~------------ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c   64 (620)
T PRK14954         10 YRPSKFADITAQEHITHTIQNSLRMD------------RVGHGYIFSGLRGVGKTTAARVFAKAVNC   64 (620)
T ss_pred             HCCCCHHHhcCcHHHHHHHHHHHHcC------------CCCeeEEEECCCCCCHHHHHHHHHHHhCC
Confidence            34568999999999999999887641            34567999999999999999999998866

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=98.36  E-value=3.7e-07  Score=88.89  Aligned_cols=54  Identities=24%  Similarity=0.316  Sum_probs=45.3

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      ..+-+|++++|.+.+++.+..++..            -..++++||+||||||||++|+++|+.+.
T Consensus        10 yRP~~F~dIIGQe~iv~~L~~aI~~------------~rl~hA~Lf~GP~GvGKTTlA~~lAk~L~   63 (605)
T PRK05896         10 YRPHNFKQIIGQELIKKILVNAILN------------NKLTHAYIFSGPRGIGKTSIAKIFAKAIN   63 (605)
T ss_pred             hCCCCHHHhcCcHHHHHHHHHHHHc------------CCCCceEEEECCCCCCHHHHHHHHHHHhc
Confidence            3456789999999999999988754            12457799999999999999999999874

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=98.36  E-value=4e-07  Score=82.86  Aligned_cols=54  Identities=28%  Similarity=0.386  Sum_probs=45.1

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      ..+.+|++++|.+..++.+.+.+...            ..++.+|||||||+|||++|+++|+.+.
T Consensus         8 ~rp~~~~~iig~~~~~~~l~~~~~~~------------~~~~~~Ll~G~~G~GKt~~a~~la~~l~   61 (355)
T TIGR02397         8 YRPQTFEDVIGQEHIVQTLKNAIKNG------------RIAHAYLFSGPRGTGKTSIARIFAKALN   61 (355)
T ss_pred             hCCCcHhhccCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            34568999999999999999887541            2456799999999999999999998874

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.

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=98.36  E-value=4.1e-07  Score=89.28  Aligned_cols=80  Identities=28%  Similarity=0.282  Sum_probs=62.1

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccccee----eee--
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAF----IRV--  224 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~----~~v--  224 (245)
                      ...|...++++.|.++.+..+..++..               +++++|+||||||||++|+++|+.++...    +.+  
T Consensus        10 ~~~~~~~~~~viG~~~a~~~l~~a~~~---------------~~~~ll~G~pG~GKT~la~~la~~l~~~~~~~~~~~~n   74 (608)
T TIGR00764        10 IPVPERLIDQVIGQEEAVEIIKKAAKQ---------------KRNVLLIGEPGVGKSMLAKAMAELLPDEELEDILVYPN   74 (608)
T ss_pred             cCcchhhHhhccCHHHHHHHHHHHHHc---------------CCCEEEECCCCCCHHHHHHHHHHHcCchhheeEEEEeC
Confidence            345667889999999999988887764               24789999999999999999999996552    111  


Q ss_pred             ----chhHHHHHHhccccccccccC
Q 025979          225 ----VGSEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       225 ----~~s~l~~~~~Ge~~~~vr~iF  245 (245)
                          ..+-+...+.|.+.++++..|
T Consensus        75 ~~~~~~~~~~~v~~~~g~~~~~~~~   99 (608)
T TIGR00764        75 PEDPNMPRIVEVPAGEGREIVEDYK   99 (608)
T ss_pred             CCCCchHHHHHHHHhhchHHHHHHH
Confidence                234566888899998887654

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=98.35  E-value=3.6e-07  Score=90.58  Aligned_cols=55  Identities=33%  Similarity=0.425  Sum_probs=46.8

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ..+-+|++|+|++.+++.+...+...            ..++.+|||||||||||++|+++|..+.+
T Consensus        12 yRP~~f~dIiGQe~~v~~L~~aI~~~------------rl~HAYLF~GP~GtGKTt~AriLAk~LnC   66 (725)
T PRK07133         12 YRPKTFDDIVGQDHIVQTLKNIIKSN------------KISHAYLFSGPRGTGKTSVAKIFANALNC   66 (725)
T ss_pred             hCCCCHHHhcCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCcHHHHHHHHHHHhcc
Confidence            45568999999999999999988651            24567999999999999999999998865

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.35  E-value=3.2e-07  Score=89.77  Aligned_cols=56  Identities=20%  Similarity=0.283  Sum_probs=47.4

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      +....+|+||+|++.+++.|.+++..-            ..++.+||+||+|||||++|+.+|+.+++
T Consensus         9 KYRPqtFddVIGQe~vv~~L~~al~~g------------RLpHA~LFtGP~GvGKTTLAriLAkaLnC   64 (700)
T PRK12323          9 KWRPRDFTTLVGQEHVVRALTHALEQQ------------RLHHAYLFTGTRGVGKTTLSRILAKSLNC   64 (700)
T ss_pred             HhCCCcHHHHcCcHHHHHHHHHHHHhC------------CCceEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            345578999999999999999998751            24467899999999999999999998865

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.35  E-value=3.6e-07  Score=89.55  Aligned_cols=55  Identities=18%  Similarity=0.290  Sum_probs=46.2

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ...-+|+|++|.+.+++.|..++..-            ..+..+|||||+|||||++|+++|+.+++
T Consensus        10 yRP~~f~dviGQe~vv~~L~~~l~~~------------rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC   64 (618)
T PRK14951         10 YRPRSFSEMVGQEHVVQALTNALTQQ------------RLHHAYLFTGTRGVGKTTVSRILAKSLNC   64 (618)
T ss_pred             HCCCCHHHhcCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            34568999999999999999987651            24566899999999999999999998865

>PRK08181 transposase; Validated

Probab=98.34  E-value=3.7e-07  Score=81.04  Aligned_cols=42  Identities=33%  Similarity=0.505  Sum_probs=35.9

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHHHH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQKY  233 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~~~  233 (245)
                      ...+++|+||||||||+||.|+|.++   |..++.++.++++..+
T Consensus       105 ~~~nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~~~~~L~~~l  149 (269)
T PRK08181        105 KGANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRTTDLVQKL  149 (269)
T ss_pred             cCceEEEEecCCCcHHHHHHHHHHHHHHcCCceeeeeHHHHHHHH
Confidence            44679999999999999999999765   6778888888888765

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=98.34  E-value=3.4e-07  Score=84.69  Aligned_cols=70  Identities=26%  Similarity=0.440  Sum_probs=48.4

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHH
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF  229 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l  229 (245)
                      +-.+++|+-......+|.+...- ..+    .+..-.|-+++|||||||||||++||-||...|..+-.+.+.++
T Consensus       351 k~pl~~ViL~psLe~Rie~lA~a-TaN----TK~h~apfRNilfyGPPGTGKTm~ArelAr~SGlDYA~mTGGDV  420 (630)
T KOG0742|consen  351 KDPLEGVILHPSLEKRIEDLAIA-TAN----TKKHQAPFRNILFYGPPGTGKTMFARELARHSGLDYAIMTGGDV  420 (630)
T ss_pred             CCCcCCeecCHHHHHHHHHHHHH-hcc----cccccchhhheeeeCCCCCCchHHHHHHHhhcCCceehhcCCCc
Confidence            34466666666666666555432 111    11123456789999999999999999999999998887776665

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=98.34  E-value=4.1e-07  Score=69.50  Aligned_cols=38  Identities=37%  Similarity=0.661  Sum_probs=32.2

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccce---eeeechhHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAA---FIRVVGSEFV  230 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~---~~~v~~s~l~  230 (245)
                      +..++|+||||||||++++.+|..+...   ++.++++...
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~~~~~   42 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDIL   42 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhccCCCCCCEEEECCEEcc
Confidence            3568999999999999999999999765   8888877544

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.

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=98.34  E-value=4.1e-07  Score=88.45  Aligned_cols=55  Identities=27%  Similarity=0.386  Sum_probs=46.3

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ..+-+|++++|++.+++.+...+...            ..++.+|||||||||||++|+.+|+.+++
T Consensus        10 ~rP~~f~~viGq~~v~~~L~~~i~~~------------~~~hayLf~Gp~GtGKTt~Ak~lAkal~c   64 (559)
T PRK05563         10 WRPQTFEDVVGQEHITKTLKNAIKQG------------KISHAYLFSGPRGTGKTSAAKIFAKAVNC   64 (559)
T ss_pred             hCCCcHHhccCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            45568999999999999999888651            24567999999999999999999998753

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=98.34  E-value=3.8e-07  Score=89.70  Aligned_cols=55  Identities=22%  Similarity=0.312  Sum_probs=46.5

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ...-+|++|+|++.+++.|...+..-            ..+..+||+||||||||++|+++|+.+++
T Consensus        10 yRP~~f~divGQe~vv~~L~~~l~~~------------rl~hAyLf~Gp~GvGKTTlAr~lAk~L~c   64 (647)
T PRK07994         10 WRPQTFAEVVGQEHVLTALANALDLG------------RLHHAYLFSGTRGVGKTTIARLLAKGLNC   64 (647)
T ss_pred             hCCCCHHHhcCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHhhhh
Confidence            44578999999999999999888651            23456899999999999999999999876

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=98.32  E-value=2.9e-07  Score=72.81  Aligned_cols=41  Identities=44%  Similarity=0.601  Sum_probs=27.7

Q ss_pred             eeeecCCCCchHHHHHHHHhcccceeeeechh-HHH-HHHhcc
Q 025979          196 VLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS-EFV-QKYLGE  236 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s-~l~-~~~~Ge  236 (245)
                      +||+|+||+|||++|+++|..++..|.||.+. +++ +...|-
T Consensus         2 vLleg~PG~GKT~la~~lA~~~~~~f~RIq~tpdllPsDi~G~   44 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALARSLGLSFKRIQFTPDLLPSDILGF   44 (131)
T ss_dssp             EEEES---HHHHHHHHHHHHHTT--EEEEE--TT--HHHHHEE
T ss_pred             EeeECCCccHHHHHHHHHHHHcCCceeEEEecCCCCcccceee
Confidence            79999999999999999999999999999764 443 555553

AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=98.32  E-value=3.9e-07  Score=90.38  Aligned_cols=56  Identities=18%  Similarity=0.239  Sum_probs=46.7

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      +...-+|++|+|++.+++.|..++..-            ..++.+|||||+|||||++|+++|+.+++
T Consensus         9 KYRPqtFdEVIGQe~Vv~~L~~aL~~g------------RL~HAyLFtGPpGvGKTTlAriLAKaLnC   64 (830)
T PRK07003          9 KWRPKDFASLVGQEHVVRALTHALDGG------------RLHHAYLFTGTRGVGKTTLSRIFAKALNC   64 (830)
T ss_pred             HhCCCcHHHHcCcHHHHHHHHHHHhcC------------CCCeEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            345578999999999999999887641            23566899999999999999999998864

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.32  E-value=4.9e-07  Score=88.25  Aligned_cols=55  Identities=22%  Similarity=0.358  Sum_probs=46.6

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ..+-+|+|++|++.+++.|..++..-            ..++.+|||||||||||++|+++|+.+++
T Consensus        10 ~RP~~f~~iiGq~~v~~~L~~~i~~~------------~~~hayLf~Gp~G~GKtt~A~~lak~l~c   64 (576)
T PRK14965         10 YRPQTFSDLTGQEHVSRTLQNAIDTG------------RVAHAFLFTGARGVGKTSTARILAKALNC   64 (576)
T ss_pred             hCCCCHHHccCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHhhcC
Confidence            45578999999999999999888641            24567999999999999999999998854

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=98.31  E-value=5.1e-07  Score=88.31  Aligned_cols=55  Identities=24%  Similarity=0.314  Sum_probs=46.9

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccce
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAA  220 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~  220 (245)
                      ..-+|+|++|++..++.|..++..-            ..+..+|||||||||||++|+++|+.+.+.
T Consensus        19 RP~~f~dliGq~~~v~~L~~~~~~g------------ri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~   73 (598)
T PRK09111         19 RPQTFDDLIGQEAMVRTLTNAFETG------------RIAQAFMLTGVRGVGKTTTARILARALNYE   73 (598)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHcC------------CCCceEEEECCCCCCHHHHHHHHHHhhCcC
Confidence            4468999999999999999887641            346789999999999999999999988654

>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=98.31  E-value=4.3e-07  Score=69.89  Aligned_cols=31  Identities=35%  Similarity=0.656  Sum_probs=27.4

Q ss_pred             eeeecCCCCchHHHHHHHHhcccceeeeech
Q 025979          196 VLLYGPPGTGKTMLAKAVANHTTAAFIRVVG  226 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l~~~~~~v~~  226 (245)
                      +++.||||||||++|+.||+.+|.+++.++.
T Consensus         2 I~I~G~~gsGKST~a~~La~~~~~~~i~~d~   32 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAERLGFPVISMDD   32 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHTCEEEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCeEEEecc
Confidence            6899999999999999999999988765554

...

>PRK08116 hypothetical protein; Validated

Probab=98.31  E-value=6.7e-07  Score=79.34  Aligned_cols=42  Identities=36%  Similarity=0.490  Sum_probs=36.7

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHHHHh
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQKYL  234 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~~~~  234 (245)
                      +.|++||||||||||+||.|+|+++   +.+++.++.+++++.+.
T Consensus       114 ~~gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~~~~~ll~~i~  158 (268)
T PRK08116        114 NVGLLLWGSVGTGKTYLAACIANELIEKGVPVIFVNFPQLLNRIK  158 (268)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHHHHHHHH
Confidence            4679999999999999999999986   78889999998877653

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=98.30  E-value=1.3e-06  Score=82.85  Aligned_cols=43  Identities=28%  Similarity=0.525  Sum_probs=37.2

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc-----cceeeeechhHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT-----TAAFIRVVGSEFVQKYLGE  236 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l-----~~~~~~v~~s~l~~~~~Ge  236 (245)
                      +.++||||||||||+|++++|+++     +..++.+++.++++.+++.
T Consensus       149 ~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~~~~~~~~~~~  196 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTSEKFTNDFVNA  196 (450)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHHHH
Confidence            569999999999999999999987     5668899999988777654

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.30  E-value=6.8e-07  Score=82.24  Aligned_cols=56  Identities=25%  Similarity=0.389  Sum_probs=46.6

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      +..+.+|++++|.+..++.+...+...            ..+..+|||||||+|||++|+++|+.+.+
T Consensus        10 k~rP~~~~~iig~~~~~~~l~~~i~~~------------~~~~~~L~~G~~G~GKt~~a~~la~~l~~   65 (367)
T PRK14970         10 KYRPQTFDDVVGQSHITNTLLNAIENN------------HLAQALLFCGPRGVGKTTCARILARKINQ   65 (367)
T ss_pred             HHCCCcHHhcCCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            345578999999999999999888641            24567999999999999999999998754

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=98.30  E-value=6e-07  Score=85.20  Aligned_cols=54  Identities=28%  Similarity=0.380  Sum_probs=45.4

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      .+.+|+|++|.+.++..+...+..-            ..+..+|||||||+|||++|+++|+.+.+
T Consensus        12 RP~~~~diiGq~~~v~~L~~~i~~~------------~i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c   65 (451)
T PRK06305         12 RPQTFSEILGQDAVVAVLKNALRFN------------RAAHAYLFSGIRGTGKTTLARIFAKALNC   65 (451)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHcC------------CCceEEEEEcCCCCCHHHHHHHHHHHhcC
Confidence            4478999999999999999888641            24567999999999999999999997743

>PRK12377 putative replication protein; Provisional

Probab=98.30  E-value=6.8e-07  Score=78.45  Aligned_cols=41  Identities=29%  Similarity=0.450  Sum_probs=35.0

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQKY  233 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~~~  233 (245)
                      ..+++|+||||||||+||.|+|+.+   +..++.++.++++...
T Consensus       101 ~~~l~l~G~~GtGKThLa~AIa~~l~~~g~~v~~i~~~~l~~~l  144 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVVTVPDVMSRL  144 (248)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEHHHHHHHH
Confidence            3679999999999999999999988   5677888888887644

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=98.29  E-value=1.6e-06  Score=81.01  Aligned_cols=43  Identities=28%  Similarity=0.513  Sum_probs=37.0

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc-----cceeeeechhHHHHHHhc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT-----TAAFIRVVGSEFVQKYLG  235 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l-----~~~~~~v~~s~l~~~~~G  235 (245)
                      .+.++||||||||||+|++++++++     +..++.+++++++..+++
T Consensus       136 ~n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~~~~~~~~~~  183 (405)
T TIGR00362       136 YNPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSSEKFTNDFVN  183 (405)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEHHHHHHHHHH
Confidence            3568999999999999999999987     577899999988877654

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).

>PRK08939 primosomal protein DnaI; Reviewed

Probab=98.28  E-value=8.1e-07  Score=80.28  Aligned_cols=42  Identities=31%  Similarity=0.472  Sum_probs=35.9

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHHHH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQKY  233 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~~~  233 (245)
                      ..+|++||||||||||+||.|+|+++   |.++..+..++++...
T Consensus       155 ~~~gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~~~~~l~~~l  199 (306)
T PRK08939        155 KVKGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLLHFPEFIREL  199 (306)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEEHHHHHHHH
Confidence            45789999999999999999999998   6777778888876554

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=98.27  E-value=7e-07  Score=86.86  Aligned_cols=55  Identities=24%  Similarity=0.412  Sum_probs=46.4

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ..+-+|+|++|++.+++.+...+..-            ..++.+|||||||+|||++|+++|+.+.+
T Consensus        10 yRP~~f~diiGqe~iv~~L~~~i~~~------------~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c   64 (563)
T PRK06647         10 RRPRDFNSLEGQDFVVETLKHSIESN------------KIANAYIFSGPRGVGKTSSARAFARCLNC   64 (563)
T ss_pred             hCCCCHHHccCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHhhcc
Confidence            44568999999999999999988641            24567999999999999999999998854

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.26  E-value=7.6e-07  Score=85.22  Aligned_cols=55  Identities=25%  Similarity=0.414  Sum_probs=45.7

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ..+-+|+++.|++.++..+...+..-            ..++.+|||||||||||++|+.+|..+++
T Consensus        10 yRP~~f~diiGq~~i~~~L~~~i~~~------------~i~hayLf~Gp~G~GKTtlAr~lAk~L~c   64 (486)
T PRK14953         10 YRPKFFKEVIGQEIVVRILKNAVKLQ------------RVSHAYIFAGPRGTGKTTIARILAKVLNC   64 (486)
T ss_pred             hCCCcHHHccChHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            34568899999999999999888641            23456899999999999999999998753

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=98.25  E-value=1e-06  Score=86.63  Aligned_cols=62  Identities=31%  Similarity=0.587  Sum_probs=48.6

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc----------cceeeee
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT----------TAAFIRV  224 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l----------~~~~~~v  224 (245)
                      .-++++++|.+.....+...+..+             .+..++|+||||||||++|+++++..          +.+|+.+
T Consensus       150 p~~~~~iiGqs~~~~~l~~~ia~~-------------~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i  216 (615)
T TIGR02903       150 PRAFSEIVGQERAIKALLAKVASP-------------FPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEV  216 (615)
T ss_pred             cCcHHhceeCcHHHHHHHHHHhcC-------------CCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEE
Confidence            456789999999888887666432             23569999999999999999998655          4578999


Q ss_pred             chhHH
Q 025979          225 VGSEF  229 (245)
Q Consensus       225 ~~s~l  229 (245)
                      +++.+
T Consensus       217 ~~~~l  221 (615)
T TIGR02903       217 DGTTL  221 (615)
T ss_pred             echhc
Confidence            87654

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.

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.25  E-value=7.7e-07  Score=87.05  Aligned_cols=56  Identities=25%  Similarity=0.360  Sum_probs=45.9

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      +...-+|++++|++.+++.|...+...            ..+..+|||||||||||++|+++|+.+++
T Consensus         9 kyRP~~~~eiiGq~~~~~~L~~~i~~~------------~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c   64 (585)
T PRK14950          9 KWRSQTFAELVGQEHVVQTLRNAIAEG------------RVAHAYLFTGPRGVGKTSTARILAKAVNC   64 (585)
T ss_pred             HhCCCCHHHhcCCHHHHHHHHHHHHhC------------CCceEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            345568999999999999998887641            13456899999999999999999988754

>PRK06893 DNA replication initiation factor; Validated

Probab=98.25  E-value=2.1e-06  Score=74.27  Aligned_cols=24  Identities=38%  Similarity=0.528  Sum_probs=21.8

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..++||||||||||+|+.|+|+++
T Consensus        40 ~~l~l~G~~G~GKThL~~ai~~~~   63 (229)
T PRK06893         40 PFFYIWGGKSSGKSHLLKAVSNHY   63 (229)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHH
Confidence            348999999999999999999886

>PRK06835 DNA replication protein DnaC; Validated

Probab=98.25  E-value=1.1e-06  Score=80.07  Aligned_cols=41  Identities=29%  Similarity=0.532  Sum_probs=36.4

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQKY  233 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~~~  233 (245)
                      ..+++||||||||||+||.|+|+++   +..++.++.++++..+
T Consensus       183 ~~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~t~~~l~~~l  226 (329)
T PRK06835        183 NENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYRTADELIEIL  226 (329)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEEHHHHHHHH
Confidence            3789999999999999999999987   7788889999987765

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=98.25  E-value=7.9e-07  Score=89.81  Aligned_cols=55  Identities=22%  Similarity=0.317  Sum_probs=46.2

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ....+|++|+|++.+++.|..++..-            ..++.+|||||+|||||++|+.+|+.+++
T Consensus         9 yRP~~f~eiiGqe~v~~~L~~~i~~~------------ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C   63 (824)
T PRK07764          9 YRPATFAEVIGQEHVTEPLSTALDSG------------RINHAYLFSGPRGCGKTSSARILARSLNC   63 (824)
T ss_pred             hCCCCHHHhcCcHHHHHHHHHHHHhC------------CCCceEEEECCCCCCHHHHHHHHHHHhCc
Confidence            34568999999999999999887641            23466899999999999999999999864

>PRK06526 transposase; Provisional

Probab=98.24  E-value=6.6e-07  Score=78.82  Aligned_cols=42  Identities=29%  Similarity=0.503  Sum_probs=34.7

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHHHH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQKY  233 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~~~  233 (245)
                      .+.+++|+||||||||+||.+|+.++   |..++.++.+++++..
T Consensus        97 ~~~nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f~t~~~l~~~l  141 (254)
T PRK06526         97 GKENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFATAAQWVARL  141 (254)
T ss_pred             cCceEEEEeCCCCchHHHHHHHHHHHHHCCCchhhhhHHHHHHHH
Confidence            45679999999999999999999876   6667777788777655

>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]

Probab=98.23  E-value=7.9e-07  Score=79.35  Aligned_cols=72  Identities=33%  Similarity=0.460  Sum_probs=53.6

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc--cceeeeechhHHHHHHhcc
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT--TAAFIRVVGSEFVQKYLGE  236 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l--~~~~~~v~~s~l~~~~~Ge  236 (245)
                      ..++|+..+.+.---.+.+ ++.    ++   -.++++||.||||||||.||-++++++  +.||..+.+|++.+.-+-.
T Consensus        38 ~g~vGQ~~AReAagiivdl-ik~----Kk---maGravLlaGppgtGKTAlAlaisqELG~kvPFcpmvgSEvyS~EvKK  109 (456)
T KOG1942|consen   38 AGFVGQENAREAAGIIVDL-IKS----KK---MAGRAVLLAGPPGTGKTALALAISQELGPKVPFCPMVGSEVYSNEVKK  109 (456)
T ss_pred             cccccchhhhhhhhHHHHH-HHh----hh---ccCcEEEEecCCCCchhHHHHHHHHHhCCCCCcccccchhhhhhhhhH
Confidence            4678888777665444433 111    11   145789999999999999999999999  6899999999998766555


Q ss_pred             cc
Q 025979          237 VW  238 (245)
Q Consensus       237 ~~  238 (245)
                      ++
T Consensus       110 TE  111 (456)
T KOG1942|consen  110 TE  111 (456)
T ss_pred             HH
Confidence            44

>PHA02244 ATPase-like protein

Probab=98.23  E-value=1.4e-06  Score=80.29  Aligned_cols=34  Identities=26%  Similarity=0.362  Sum_probs=31.3

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccceeeeech
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVG  226 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~  226 (245)
                      ...+||+||||||||++|+++|..++.+|++++.
T Consensus       119 ~~PVLL~GppGtGKTtLA~aLA~~lg~pfv~In~  152 (383)
T PHA02244        119 NIPVFLKGGAGSGKNHIAEQIAEALDLDFYFMNA  152 (383)
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHhCCCEEEEec
Confidence            4569999999999999999999999999999874

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.22  E-value=9.4e-07  Score=80.81  Aligned_cols=60  Identities=32%  Similarity=0.419  Sum_probs=46.2

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc---------ceeeeechh
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT---------AAFIRVVGS  227 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~---------~~~~~v~~s  227 (245)
                      +++.|-++.++.|..++...+.        | ..+.+++++||||||||++++++++.+.         ..++.+++.
T Consensus        15 ~~l~gRe~e~~~l~~~l~~~~~--------~-~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~   83 (365)
T TIGR02928        15 DRIVHRDEQIEELAKALRPILR--------G-SRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQ   83 (365)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHc--------C-CCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECC
Confidence            5789999999999888764221        1 2445699999999999999999998753         567777754

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.

>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=98.22  E-value=1.4e-06  Score=68.84  Aligned_cols=39  Identities=36%  Similarity=0.670  Sum_probs=32.7

Q ss_pred             eeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhcc
Q 025979          196 VLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE  236 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge  236 (245)
                      ++++||||+|||++|+.++..++  +..++..++.....++
T Consensus         2 ii~~G~pgsGKSt~a~~l~~~~~--~~~i~~D~~~~~~~~~   40 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRLAKRLG--AVVISQDEIRRRLAGE   40 (143)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHST--EEEEEHHHHHHHHCCS
T ss_pred             EEEECCCCCCHHHHHHHHHHHCC--CEEEeHHHHHHHHccc
Confidence            68999999999999999999998  5557777777766553

...

>PRK06620 hypothetical protein; Validated

Probab=98.20  E-value=2.1e-06  Score=73.70  Aligned_cols=29  Identities=38%  Similarity=0.508  Sum_probs=25.5

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceee
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFI  222 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~  222 (245)
                      +.++||||||||||+|++++++..+..++
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~~~~~~~   73 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNLSNAYII   73 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhccCCEEc
Confidence            66999999999999999999998876543

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.20  E-value=1.2e-06  Score=85.57  Aligned_cols=55  Identities=22%  Similarity=0.312  Sum_probs=46.0

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ....+|+||+|++.+++.|..++..-            ..+..+||+||||||||++|+++|+.+.+
T Consensus        10 yRP~sf~dIiGQe~v~~~L~~ai~~~------------ri~ha~Lf~GPpG~GKTtiArilAk~L~C   64 (624)
T PRK14959         10 YRPQTFAEVAGQETVKAILSRAAQEN------------RVAPAYLFSGTRGVGKTTIARIFAKALNC   64 (624)
T ss_pred             hCCCCHHHhcCCHHHHHHHHHHHHcC------------CCCceEEEECCCCCCHHHHHHHHHHhccc
Confidence            34567899999999999999888641            12457999999999999999999999865

>PRK08084 DNA replication initiation factor; Provisional

Probab=98.19  E-value=4.2e-06  Score=72.68  Aligned_cols=25  Identities=20%  Similarity=0.383  Sum_probs=22.6

Q ss_pred             cceeeecCCCCchHHHHHHHHhccc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      ..++||||||||||+|++++++.+.
T Consensus        46 ~~l~l~Gp~G~GKThLl~a~~~~~~   70 (235)
T PRK08084         46 GYIYLWSREGAGRSHLLHAACAELS   70 (235)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHH
Confidence            4699999999999999999998764

>PRK07952 DNA replication protein DnaC; Validated

Probab=98.18  E-value=1.7e-06  Score=75.82  Aligned_cols=41  Identities=24%  Similarity=0.434  Sum_probs=36.3

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHHHHh
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQKYL  234 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~~~~  234 (245)
                      .+++|+||||||||+||.++|.++   +..++.++.+++++.+.
T Consensus       100 ~~~~l~G~~GtGKThLa~aia~~l~~~g~~v~~it~~~l~~~l~  143 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAAAICNELLLRGKSVLIITVADIMSAMK  143 (244)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEHHHHHHHHH
Confidence            579999999999999999999988   77888889999887554

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.17  E-value=1.6e-06  Score=85.28  Aligned_cols=54  Identities=22%  Similarity=0.340  Sum_probs=45.6

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ...+|++++|.+.++..|..++..-            ..+.++|||||||||||++|+++|+.+.+
T Consensus        11 RP~~f~~liGq~~i~~~L~~~l~~~------------rl~~a~Lf~Gp~G~GKttlA~~lAk~L~c   64 (620)
T PRK14948         11 RPQRFDELVGQEAIATTLKNALISN------------RIAPAYLFTGPRGTGKTSSARILAKSLNC   64 (620)
T ss_pred             CCCcHhhccChHHHHHHHHHHHHcC------------CCCceEEEECCCCCChHHHHHHHHHHhcC
Confidence            4467899999999999999888751            12356999999999999999999999865

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=98.17  E-value=1.9e-06  Score=78.37  Aligned_cols=36  Identities=44%  Similarity=0.699  Sum_probs=32.9

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccceeeeechhH
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSE  228 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~  228 (245)
                      .+.+||-||||||||++|+++|..++.+|+++.+..
T Consensus        43 ~~~vll~G~PG~gKT~la~~lA~~l~~~~~~i~~t~   78 (329)
T COG0714          43 GGHVLLEGPPGVGKTLLARALARALGLPFVRIQCTP   78 (329)
T ss_pred             CCCEEEECCCCccHHHHHHHHHHHhCCCeEEEecCC
Confidence            356999999999999999999999999999998763

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=98.16  E-value=1.9e-06  Score=78.69  Aligned_cols=51  Identities=29%  Similarity=0.386  Sum_probs=40.7

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ....|+++.|++.+++.+.-+...+             ...++||+||||||||++|+++|+.+
T Consensus         3 ~~~~f~~i~Gq~~~~~~l~~~~~~~-------------~~~~vLl~G~pG~gKT~lar~la~ll   53 (334)
T PRK13407          3 KPFPFSAIVGQEEMKQAMVLTAIDP-------------GIGGVLVFGDRGTGKSTAVRALAALL   53 (334)
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHhcc-------------CCCcEEEEcCCCCCHHHHHHHHHHHC
Confidence            3467899999999988877543221             11469999999999999999999988

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=98.15  E-value=4.4e-06  Score=79.07  Aligned_cols=41  Identities=22%  Similarity=0.480  Sum_probs=35.3

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc-----cceeeeechhHHHHHHh
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT-----TAAFIRVVGSEFVQKYL  234 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l-----~~~~~~v~~s~l~~~~~  234 (245)
                      +.++||||||||||+|++++|+++     +..++.+++++++..+.
T Consensus       131 n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~~~~f~~~~~  176 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKFLNDLV  176 (440)
T ss_pred             CeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHH
Confidence            459999999999999999999986     45788889888877664

>PRK06921 hypothetical protein; Provisional

Probab=98.14  E-value=3.4e-06  Score=74.78  Aligned_cols=41  Identities=29%  Similarity=0.322  Sum_probs=33.5

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc----cceeeeechhHHHHH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT----TAAFIRVVGSEFVQK  232 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l----~~~~~~v~~s~l~~~  232 (245)
                      ...+++|+||||||||+|+.|+|+++    +..++.++..+++..
T Consensus       116 ~~~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~~~~l~~~  160 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFPFVEGFGD  160 (266)
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEEHHHHHHH
Confidence            35679999999999999999999976    566777777776543

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=98.14  E-value=2.3e-06  Score=82.63  Aligned_cols=54  Identities=19%  Similarity=0.234  Sum_probs=45.1

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      ..+.+|++++|++.+++.+...+..-            ..++.+|||||||+|||++|+++|+.+.
T Consensus         8 yRP~~fdeiiGqe~v~~~L~~~I~~g------------rl~hayLf~Gp~G~GKTt~Ar~LAk~L~   61 (535)
T PRK08451          8 YRPKHFDELIGQESVSKTLSLALDNN------------RLAHAYLFSGLRGSGKTSSARIFARALV   61 (535)
T ss_pred             HCCCCHHHccCcHHHHHHHHHHHHcC------------CCCeeEEEECCCCCcHHHHHHHHHHHhc
Confidence            34568999999999999999888641            2456689999999999999999998873

>PRK13948 shikimate kinase; Provisional

Probab=98.13  E-value=2.3e-06  Score=71.73  Aligned_cols=44  Identities=25%  Similarity=0.364  Sum_probs=37.0

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhccc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEV  237 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge~  237 (245)
                      ++..++|.|++|||||++++.+|..++++|+  +...++.+..|.+
T Consensus         9 ~~~~I~LiG~~GsGKSTvg~~La~~lg~~~i--D~D~~ie~~~g~s   52 (182)
T PRK13948          9 PVTWVALAGFMGTGKSRIGWELSRALMLHFI--DTDRYIERVTGKS   52 (182)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHcCCCEE--ECCHHHHHHHhCC
Confidence            5577999999999999999999999999997  5556666666654

>PRK08727 hypothetical protein; Validated

Probab=98.12  E-value=6.9e-06  Score=71.26  Aligned_cols=39  Identities=28%  Similarity=0.275  Sum_probs=30.1

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHHH
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQK  232 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~~  232 (245)
                      ..++||||||||||+|+.|++.++   +...+.++..++...
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~~~~~~~~   83 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLPLQAAAGR   83 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEeHHHhhhh
Confidence            449999999999999999998775   455566666665543

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=98.11  E-value=2.2e-06  Score=67.57  Aligned_cols=51  Identities=22%  Similarity=0.400  Sum_probs=40.8

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcc--eeeecCCCCchHHHHHHHHhcc
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRG--VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~g--vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..+.|++-+++.|..+|...+..+        .|.+-  +.|+||||||||.+++.||+.+
T Consensus        25 ~~l~GQhla~~~v~~ai~~~l~~~--------~p~KpLVlSfHG~tGtGKn~v~~liA~~l   77 (127)
T PF06309_consen   25 RNLFGQHLAVEVVVNAIKGHLANP--------NPRKPLVLSFHGWTGTGKNFVSRLIAEHL   77 (127)
T ss_pred             HHccCcHHHHHHHHHHHHHHHcCC--------CCCCCEEEEeecCCCCcHHHHHHHHHHHH
Confidence            468999999999999987644332        24444  5599999999999999999985

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

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=98.11  E-value=1.9e-06  Score=81.10  Aligned_cols=48  Identities=35%  Similarity=0.552  Sum_probs=40.5

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..++.||.|+...|..+..+...               .+++||+||||||||++|+-+..-+
T Consensus       175 ~~D~~DV~GQ~~AKrAleiAAAG---------------gHnLl~~GpPGtGKTmla~Rl~~lL  222 (490)
T COG0606         175 APDFKDVKGQEQAKRALEIAAAG---------------GHNLLLVGPPGTGKTMLASRLPGLL  222 (490)
T ss_pred             CcchhhhcCcHHHHHHHHHHHhc---------------CCcEEEecCCCCchHHhhhhhcccC
Confidence            45789999999999988866543               4679999999999999999887655

>PRK09183 transposase/IS protein; Provisional

Probab=98.10  E-value=3.3e-06  Score=74.52  Aligned_cols=42  Identities=24%  Similarity=0.389  Sum_probs=33.8

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHHHH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQKY  233 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~~~  233 (245)
                      ...+++|+||||||||+||.+++..+   |..+..++.++++..+
T Consensus       101 ~~~~v~l~Gp~GtGKThLa~al~~~a~~~G~~v~~~~~~~l~~~l  145 (259)
T PRK09183        101 RNENIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTTAADLLLQL  145 (259)
T ss_pred             cCCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeHHHHHHHH
Confidence            45679999999999999999998764   6667777878877544

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.09  E-value=3e-06  Score=78.37  Aligned_cols=62  Identities=31%  Similarity=0.481  Sum_probs=46.9

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc-----cceeeeechh
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT-----TAAFIRVVGS  227 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l-----~~~~~~v~~s  227 (245)
                      ..+.+.|-++..++|...+...+.        | ..+.++++|||||||||++++.+++.+     +..++.+++.
T Consensus        28 ~P~~l~~Re~e~~~l~~~l~~~~~--------~-~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~   94 (394)
T PRK00411         28 VPENLPHREEQIEELAFALRPALR--------G-SRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQ   94 (394)
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHhC--------C-CCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECC
Confidence            345688888888888888753211        1 234569999999999999999999877     4678888764

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=98.06  E-value=2.2e-06  Score=79.85  Aligned_cols=44  Identities=36%  Similarity=0.585  Sum_probs=40.2

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceeeeechhHHH-HHHhccc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV-QKYLGEV  237 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~-~~~~Ge~  237 (245)
                      .+|||.||+|+|||+||+.||+-+++||.-.++..+. ..|+||-
T Consensus       227 SNvLllGPtGsGKTllaqTLAr~ldVPfaIcDcTtLTQAGYVGeD  271 (564)
T KOG0745|consen  227 SNVLLLGPTGSGKTLLAQTLARVLDVPFAICDCTTLTQAGYVGED  271 (564)
T ss_pred             ccEEEECCCCCchhHHHHHHHHHhCCCeEEecccchhhccccccc
Confidence            3599999999999999999999999999999999886 5788873

>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=98.04  E-value=1.2e-05  Score=69.14  Aligned_cols=40  Identities=35%  Similarity=0.692  Sum_probs=33.6

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc-----cceeeeechhHHHHHHh
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT-----TAAFIRVVGSEFVQKYL  234 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l-----~~~~~~v~~s~l~~~~~  234 (245)
                      .+.+|||+|+|||+|..|+++++     +..++.+++.++...+.
T Consensus        36 ~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~~~~f~~~~~   80 (219)
T PF00308_consen   36 PLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLSAEEFIREFA   80 (219)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEEHHHHHHHHH
T ss_pred             ceEEECCCCCCHHHHHHHHHHHHHhccccccceeecHHHHHHHHH
Confidence            48999999999999999999875     56788899888877664

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.

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=98.02  E-value=4.7e-06  Score=76.55  Aligned_cols=54  Identities=28%  Similarity=0.394  Sum_probs=44.8

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+++...|++|+|+++.+..|.-.+..|             ...|+||.||+|||||++||+++..+
T Consensus         9 ~~~~~~pf~~ivGq~~~k~al~~~~~~p-------------~~~~vli~G~~GtGKs~~ar~~~~~l   62 (350)
T CHL00081          9 KERPVFPFTAIVGQEEMKLALILNVIDP-------------KIGGVMIMGDRGTGKSTTIRALVDLL   62 (350)
T ss_pred             ccCCCCCHHHHhChHHHHHHHHHhccCC-------------CCCeEEEEcCCCCCHHHHHHHHHHHH
Confidence            3455678999999999999998776653             22579999999999999999998876

>PRK05642 DNA replication initiation factor; Validated

Probab=98.01  E-value=5.4e-06  Score=71.99  Aligned_cols=40  Identities=18%  Similarity=0.302  Sum_probs=33.0

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQK  232 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~~  232 (245)
                      .+.++||||+|||||+|++|+++++   +...+.++..+++..
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~~~~~~~~   87 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLPLAELLDR   87 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEeeHHHHHhh
Confidence            3568999999999999999999764   567778888887653

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=98.01  E-value=7.2e-06  Score=75.88  Aligned_cols=52  Identities=21%  Similarity=0.209  Sum_probs=44.8

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+.++++|+|.+.+++.+.+++..-            ..+..+||+||+|+||+++|.++|+.+
T Consensus        14 ~P~~~~~iiGq~~~~~~L~~~~~~~------------rl~HA~Lf~Gp~G~GK~~lA~~~A~~L   65 (365)
T PRK07471         14 HPRETTALFGHAAAEAALLDAYRSG------------RLHHAWLIGGPQGIGKATLAYRMARFL   65 (365)
T ss_pred             CCCchhhccChHHHHHHHHHHHHcC------------CCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            4567889999999999999888751            345679999999999999999999977

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=98.00  E-value=7e-06  Score=79.13  Aligned_cols=63  Identities=27%  Similarity=0.340  Sum_probs=45.7

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeee
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRV  224 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v  224 (245)
                      .+.+.+|+.--...+++++..+..-+        .+-.+.+-+||+||||||||++++.||++++..+..-
T Consensus        14 ~P~~~~eLavhkkKv~eV~~wl~~~~--------~~~~~~~iLlLtGP~G~GKtttv~~La~elg~~v~Ew   76 (519)
T PF03215_consen   14 APKTLDELAVHKKKVEEVRSWLEEMF--------SGSSPKRILLLTGPSGCGKTTTVKVLAKELGFEVQEW   76 (519)
T ss_pred             CCCCHHHhhccHHHHHHHHHHHHHHh--------ccCCCcceEEEECCCCCCHHHHHHHHHHHhCCeeEEe
Confidence            34556777777777778887776411        1222334477899999999999999999998776654

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.00  E-value=5.7e-06  Score=81.33  Aligned_cols=53  Identities=23%  Similarity=0.377  Sum_probs=45.1

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      .+.+|++|+|.+.+++.|..++..            -..+..+|||||+|+|||++|+++|..+.
T Consensus        12 RP~~f~~viGq~~~~~~L~~~i~~------------~~l~hayLf~Gp~G~GKtt~A~~lAk~l~   64 (614)
T PRK14971         12 RPSTFESVVGQEALTTTLKNAIAT------------NKLAHAYLFCGPRGVGKTTCARIFAKTIN   64 (614)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHc------------CCCCeeEEEECCCCCCHHHHHHHHHHHhC
Confidence            346899999999999999988864            12456799999999999999999999875

>TIGR00602 rad24 checkpoint protein rad24

Probab=97.99  E-value=4.6e-06  Score=82.06  Aligned_cols=64  Identities=17%  Similarity=0.242  Sum_probs=49.0

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeee
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIR  223 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~  223 (245)
                      ...+.+++++.|.+..++.+..++...        .++..+.+.++|+||||||||++++.+|+.++..++.
T Consensus        77 KyrP~~ldel~~~~~ki~~l~~~l~~~--------~~~~~~~~illL~GP~GsGKTTl~~~la~~l~~~~~E  140 (637)
T TIGR00602        77 KYKPETQHELAVHKKKIEEVETWLKAQ--------VLENAPKRILLITGPSGCGKSTTIKILSKELGIQVQE  140 (637)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHHhc--------ccccCCCcEEEEECCCCCCHHHHHHHHHHHhhhHHHH
Confidence            344567899999999999988887641        1223344559999999999999999999998765533

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

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=97.99  E-value=6.7e-06  Score=74.23  Aligned_cols=49  Identities=24%  Similarity=0.386  Sum_probs=41.9

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +|+++.|++.+++.+...+..            -..++.+||+||+|+|||++|+++|..+
T Consensus         2 ~~~~i~g~~~~~~~l~~~~~~------------~~~~ha~Lf~G~~G~Gk~~la~~~a~~l   50 (313)
T PRK05564          2 SFHTIIGHENIKNRIKNSIIK------------NRFSHAHIIVGEDGIGKSLLAKEIALKI   50 (313)
T ss_pred             ChhhccCcHHHHHHHHHHHHc------------CCCCceEEeECCCCCCHHHHHHHHHHHH
Confidence            578999999999999888754            1245678999999999999999999976

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

Probab=97.99  E-value=5.1e-06  Score=63.41  Aligned_cols=44  Identities=36%  Similarity=0.718  Sum_probs=33.6

Q ss_pred             eeeecCCCCchHHHHHHHHhccc---------ceeeeechhHHHHHHhccccc
Q 025979          196 VLLYGPPGTGKTMLAKAVANHTT---------AAFIRVVGSEFVQKYLGEVWL  239 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l~---------~~~~~v~~s~l~~~~~Ge~~~  239 (245)
                      |.||||||+|||++|+.||..+.         .-+.+-..+++.+.|.|+..-
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~~~~~~~~~~~vy~~~~~~~~w~gY~~q~vv   53 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLLKHIGEPTKDSVYTRNPGDKFWDGYQGQPVV   53 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHHHhccCCCCcEEeCCCccchhhccCCCcEE
Confidence            57999999999999999887663         223345677888999887543

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

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.98  E-value=7e-06  Score=77.84  Aligned_cols=41  Identities=27%  Similarity=0.501  Sum_probs=35.4

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHHHHh
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQKYL  234 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~~~~  234 (245)
                      +.++||||||+|||+|++++++.+   +..++.++.+++...+.
T Consensus       142 npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~~~~f~~~~~  185 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVRSELFTEHLV  185 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEeeHHHHHHHHH
Confidence            569999999999999999999976   67888899888776554

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

Probab=97.98  E-value=1e-05  Score=67.00  Aligned_cols=59  Identities=29%  Similarity=0.432  Sum_probs=40.6

Q ss_pred             CCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHH
Q 025979          161 IGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFV  230 (245)
Q Consensus       161 v~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~  230 (245)
                      ++|-+...+++.+.+...          . ..+..||++|++||||+++|++|-+..   +.||+.|+++.+-
T Consensus         1 liG~s~~m~~~~~~~~~~----------a-~~~~pVlI~GE~GtGK~~lA~~IH~~s~r~~~pfi~vnc~~~~   62 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRA----------A-SSDLPVLITGETGTGKELLARAIHNNSPRKNGPFISVNCAALP   62 (168)
T ss_dssp             SS--SHHHHHHHHHHHHH----------T-TSTS-EEEECSTTSSHHHHHHHHHHCSTTTTS-EEEEETTTS-
T ss_pred             CEeCCHHHHHHHHHHHHH----------h-CCCCCEEEEcCCCCcHHHHHHHHHHhhhcccCCeEEEehhhhh
Confidence            355566666666665431          1 233569999999999999999998866   5799999997664

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 ....

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

Probab=97.97  E-value=1e-05  Score=79.88  Aligned_cols=51  Identities=33%  Similarity=0.416  Sum_probs=42.6

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhcccccccc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHK  242 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge~~~~vr  242 (245)
                      -.-.|||+|+||||||++.+++|+++|.+++.+++.+++..-.+-++-...
T Consensus       430 ~~~~vLLhG~~g~GK~t~V~~vas~lg~h~~evdc~el~~~s~~~~etkl~  480 (953)
T KOG0736|consen  430 LNPSVLLHGPPGSGKTTVVRAVASELGLHLLEVDCYELVAESASHTETKLQ  480 (953)
T ss_pred             cceEEEEeCCCCCChHHHHHHHHHHhCCceEeccHHHHhhcccchhHHHHH
Confidence            334599999999999999999999999999999999998765555554433

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=97.97  E-value=8.3e-06  Score=73.71  Aligned_cols=63  Identities=22%  Similarity=0.332  Sum_probs=43.7

Q ss_pred             hhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhcc
Q 025979          167 QKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE  236 (245)
Q Consensus       167 ~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge  236 (245)
                      ..+.+.+++...+.+..     -+.++..|.|.|+||||||++++.+|..+|++|+.+  ...+....|-
T Consensus       112 ~~~~~~~~l~~~~~~~~-----~~~~~~~I~l~G~~GsGKStvg~~La~~Lg~~~id~--D~~i~~~~G~  174 (309)
T PRK08154        112 QLARVRDALSGMLGAGR-----RAARRRRIALIGLRGAGKSTLGRMLAARLGVPFVEL--NREIEREAGL  174 (309)
T ss_pred             HHHHHHHHHHHHHhhhh-----hccCCCEEEEECCCCCCHHHHHHHHHHHcCCCEEeH--HHHHHHHhCC
Confidence            44555555544222221     145667799999999999999999999999999844  4555554554

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=97.92  E-value=1.2e-05  Score=78.45  Aligned_cols=43  Identities=26%  Similarity=0.495  Sum_probs=37.1

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc-----cceeeeechhHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT-----TAAFIRVVGSEFVQKYLGE  236 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l-----~~~~~~v~~s~l~~~~~Ge  236 (245)
                      +.++||||+|||||+|+.|+++++     +..++++++.+|++.|+..
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yitaeef~~el~~a  362 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVSSEEFTNEFINS  362 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHHHHHHHHH
Confidence            349999999999999999999986     4678999999998887653

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=97.92  E-value=8e-06  Score=65.35  Aligned_cols=30  Identities=33%  Similarity=0.544  Sum_probs=26.7

Q ss_pred             eeeecCCCCchHHHHHHHHhcccceeeeec
Q 025979          196 VLLYGPPGTGKTMLAKAVANHTTAAFIRVV  225 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l~~~~~~v~  225 (245)
                      ++|+||||+|||++|+.++..++..++..+
T Consensus         2 i~l~G~~GsGKST~a~~l~~~~~~~~i~~D   31 (150)
T cd02021           2 IVVMGVSGSGKSTVGKALAERLGAPFIDGD   31 (150)
T ss_pred             EEEEcCCCCCHHHHHHHHHhhcCCEEEeCc
Confidence            689999999999999999999988876554

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

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

Probab=97.91  E-value=1.2e-05  Score=71.86  Aligned_cols=48  Identities=27%  Similarity=0.369  Sum_probs=35.8

Q ss_pred             cCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          160 DIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       160 dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      ++.|.+.....+...+....           ..|..+||+||||||||++|.++|+.+.
T Consensus         2 ~~~~~~~~~~~l~~~~~~~~-----------~~~halL~~Gp~G~Gktt~a~~lA~~l~   49 (325)
T COG0470           2 ELVPWQEAVKRLLVQALESG-----------RLPHALLFYGPPGVGKTTAALALAKELL   49 (325)
T ss_pred             CcccchhHHHHHHHHHHhcC-----------CCCceeeeeCCCCCCHHHHHHHHHHHHh
Confidence            45666666667666655311           2334699999999999999999999886

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

Probab=97.90  E-value=8.7e-06  Score=70.70  Aligned_cols=53  Identities=23%  Similarity=0.307  Sum_probs=42.3

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +..+..+.|++|-++.++++.-+...             ..-..++|.||||||||+.+.++|+++
T Consensus        20 KYrP~~l~dIVGNe~tv~rl~via~~-------------gnmP~liisGpPG~GKTTsi~~LAr~L   72 (333)
T KOG0991|consen   20 KYRPSVLQDIVGNEDTVERLSVIAKE-------------GNMPNLIISGPPGTGKTTSILCLAREL   72 (333)
T ss_pred             hhCchHHHHhhCCHHHHHHHHHHHHc-------------CCCCceEeeCCCCCchhhHHHHHHHHH
Confidence            34456678999999999988866543             122359999999999999999999987

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

Probab=97.90  E-value=1.6e-05  Score=69.24  Aligned_cols=69  Identities=30%  Similarity=0.451  Sum_probs=55.3

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhH
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSE  228 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~  228 (245)
                      ..+.+...++.|.+.+++.+.+....+..        | .|.+.|||||.-|||||++.||+-++.   +..++.|+.++
T Consensus        53 ~~~~i~L~~l~Gvd~qk~~L~~NT~~F~~--------G-~pANnVLLwGaRGtGKSSLVKA~~~e~~~~glrLVEV~k~d  123 (287)
T COG2607          53 DPDPIDLADLVGVDRQKEALVRNTEQFAE--------G-LPANNVLLWGARGTGKSSLVKALLNEYADEGLRLVEVDKED  123 (287)
T ss_pred             CCCCcCHHHHhCchHHHHHHHHHHHHHHc--------C-CcccceEEecCCCCChHHHHHHHHHHHHhcCCeEEEEcHHH
Confidence            34457889999999999999887765321        2 356779999999999999999998877   66788887766


Q ss_pred             H
Q 025979          229 F  229 (245)
Q Consensus       229 l  229 (245)
                      +
T Consensus       124 l  124 (287)
T COG2607         124 L  124 (287)
T ss_pred             H
Confidence            5

>PRK13531 regulatory ATPase RavA; Provisional

Probab=97.89  E-value=1.4e-05  Score=76.21  Aligned_cols=44  Identities=20%  Similarity=0.241  Sum_probs=32.8

Q ss_pred             cCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          160 DIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       160 dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      .++|.+++++.+..++.               ....+||+||||||||++|++++...+
T Consensus        21 ~i~gre~vI~lll~aal---------------ag~hVLL~GpPGTGKT~LAraLa~~~~   64 (498)
T PRK13531         21 GLYERSHAIRLCLLAAL---------------SGESVFLLGPPGIAKSLIARRLKFAFQ   64 (498)
T ss_pred             hccCcHHHHHHHHHHHc---------------cCCCEEEECCCChhHHHHHHHHHHHhc
Confidence            45666666655554432               335599999999999999999999764

>PHA00729 NTP-binding motif containing protein

Probab=97.89  E-value=1.3e-05  Score=69.40  Aligned_cols=25  Identities=32%  Similarity=0.507  Sum_probs=22.6

Q ss_pred             cceeeecCCCCchHHHHHHHHhccc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      ..++++||||||||++|.+||..++
T Consensus        18 ~nIlItG~pGvGKT~LA~aLa~~l~   42 (226)
T PHA00729         18 VSAVIFGKQGSGKTTYALKVARDVF   42 (226)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3699999999999999999999864

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

Probab=97.88  E-value=2e-05  Score=74.51  Aligned_cols=46  Identities=30%  Similarity=0.457  Sum_probs=34.2

Q ss_pred             eccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          158 YNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       158 ~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      .+++.+.+...+.+...+.               ..+.++|+||||||||++|+.+|..++
T Consensus       174 l~d~~i~e~~le~l~~~L~---------------~~~~iil~GppGtGKT~lA~~la~~l~  219 (459)
T PRK11331        174 LNDLFIPETTIETILKRLT---------------IKKNIILQGPPGVGKTFVARRLAYLLT  219 (459)
T ss_pred             hhcccCCHHHHHHHHHHHh---------------cCCCEEEECCCCCCHHHHHHHHHHHhc
Confidence            4556666665555554433               346799999999999999999998874

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

Probab=97.87  E-value=6.7e-06  Score=78.82  Aligned_cols=57  Identities=25%  Similarity=0.374  Sum_probs=48.2

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccce
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAA  220 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~  220 (245)
                      +..+-+|+|+.|++.+...|..++..-            ....+.||.||-|||||++||.+|..+++.
T Consensus         9 KyRP~~F~evvGQe~v~~~L~nal~~~------------ri~hAYlfsG~RGvGKTt~Ari~AkalNC~   65 (515)
T COG2812           9 KYRPKTFDDVVGQEHVVKTLSNALENG------------RIAHAYLFSGPRGVGKTTIARILAKALNCE   65 (515)
T ss_pred             HhCcccHHHhcccHHHHHHHHHHHHhC------------cchhhhhhcCCCCcCchhHHHHHHHHhcCC
Confidence            345568999999999999999998761            244679999999999999999999988654

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

Probab=97.86  E-value=1.2e-05  Score=65.86  Aligned_cols=59  Identities=24%  Similarity=0.413  Sum_probs=36.4

Q ss_pred             CCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccce---eeeechhHH
Q 025979          161 IGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAA---FIRVVGSEF  229 (245)
Q Consensus       161 v~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~---~~~v~~s~l  229 (245)
                      ++|-+++.+++...+.. ..         -..++.++++||||+|||++.+++...+...   ++.+.+...
T Consensus         2 fvgR~~e~~~l~~~l~~-~~---------~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~~~~~~~~~~~~~   63 (185)
T PF13191_consen    2 FVGREEEIERLRDLLDA-AQ---------SGSPRNLLLTGESGSGKTSLLRALLDRLAERGGYVISINCDDS   63 (185)
T ss_dssp             -TT-HHHHHHHHHTTGG-TS---------S-----EEE-B-TTSSHHHHHHHHHHHHHHHT--EEEEEEETT
T ss_pred             CCCHHHHHHHHHHHHHH-HH---------cCCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCEEEEEEEecc
Confidence            46778888888877742 11         1345779999999999999999988877443   665554443

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=97.85  E-value=1.6e-05  Score=78.29  Aligned_cols=56  Identities=36%  Similarity=0.520  Sum_probs=46.3

Q ss_pred             ccCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          149 SQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       149 ~~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      .....|+..|+++.|.+++++.|..++..               .+.++|+||||||||++|+++|..+..
T Consensus        21 ~~~~~~~~~~~~vigq~~a~~~L~~~~~~---------------~~~~l~~G~~G~GKttla~~l~~~l~~   76 (637)
T PRK13765         21 SDIEVPERLIDQVIGQEHAVEVIKKAAKQ---------------RRHVMMIGSPGTGKSMLAKAMAELLPK   76 (637)
T ss_pred             eecccCcccHHHcCChHHHHHHHHHHHHh---------------CCeEEEECCCCCcHHHHHHHHHHHcCh
Confidence            33456778899999999999988877654               136999999999999999999998743

>PRK13946 shikimate kinase; Provisional

Probab=97.85  E-value=1.7e-05  Score=66.14  Aligned_cols=33  Identities=27%  Similarity=0.426  Sum_probs=29.9

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccceeeeec
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVV  225 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~  225 (245)
                      ++.|+|.|+||||||++++.+|..+|++|+..+
T Consensus        10 ~~~I~l~G~~GsGKsti~~~LA~~Lg~~~id~D   42 (184)
T PRK13946         10 KRTVVLVGLMGAGKSTVGRRLATMLGLPFLDAD   42 (184)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHcCCCeECcC
Confidence            456999999999999999999999999997666

>PLN02200 adenylate kinase family protein

Probab=97.85  E-value=1.8e-05  Score=68.92  Aligned_cols=42  Identities=14%  Similarity=0.348  Sum_probs=33.7

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHh
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYL  234 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~  234 (245)
                      ..|.-+++.||||+|||++|+.+|..+|.+  .++.++++.+.+
T Consensus        41 ~~~~ii~I~G~PGSGKsT~a~~La~~~g~~--his~gdllR~~i   82 (234)
T PLN02200         41 KTPFITFVLGGPGSGKGTQCEKIVETFGFK--HLSAGDLLRREI   82 (234)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhCCe--EEEccHHHHHHH
Confidence            345568999999999999999999999865  477777775443

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=97.85  E-value=1.1e-05  Score=63.71  Aligned_cols=30  Identities=27%  Similarity=0.534  Sum_probs=27.5

Q ss_pred             eeeecCCCCchHHHHHHHHhcccceeeeec
Q 025979          196 VLLYGPPGTGKTMLAKAVANHTTAAFIRVV  225 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l~~~~~~v~  225 (245)
                      +++.||||||||++|+.||..++.+++..+
T Consensus         2 I~i~G~~GsGKst~a~~la~~~~~~~~~~~   31 (147)
T cd02020           2 IAIDGPAGSGKSTVAKLLAKKLGLPYLDTG   31 (147)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceeccc
Confidence            578999999999999999999999998765

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=97.84  E-value=1.7e-05  Score=72.03  Aligned_cols=49  Identities=16%  Similarity=0.294  Sum_probs=42.7

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .|++|+|++.+++.+..++..-            ..+..+||+||+|+||+.+|.++|+.+
T Consensus         2 ~f~~iiGq~~~~~~L~~~i~~~------------rl~ha~Lf~G~~G~Gk~~~A~~~a~~l   50 (314)
T PRK07399          2 LFANLIGQPLAIELLTAAIKQN------------RIAPAYLFAGPEGVGRKLAALCFIEGL   50 (314)
T ss_pred             cHHHhCCHHHHHHHHHHHHHhC------------CCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            4789999999999999998651            235679999999999999999999876

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=97.80  E-value=2.6e-05  Score=71.82  Aligned_cols=54  Identities=24%  Similarity=0.290  Sum_probs=45.5

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      .+..+++++|.+.+++.+..++..-            ..+..+||+||+|+|||++|+.+|+.+.+
T Consensus        18 ~P~~~~~l~Gh~~a~~~L~~a~~~g------------rl~ha~L~~G~~G~GKttlA~~lA~~Llc   71 (351)
T PRK09112         18 SPSENTRLFGHEEAEAFLAQAYREG------------KLHHALLFEGPEGIGKATLAFHLANHILS   71 (351)
T ss_pred             CCCchhhccCcHHHHHHHHHHHHcC------------CCCeeEeeECCCCCCHHHHHHHHHHHHcC
Confidence            4457789999999999999988651            24567999999999999999999998854

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.80  E-value=2.3e-05  Score=74.46  Aligned_cols=42  Identities=33%  Similarity=0.504  Sum_probs=36.1

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc-----cceeeeechhHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT-----TAAFIRVVGSEFVQKYLG  235 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l-----~~~~~~v~~s~l~~~~~G  235 (245)
                      +.++||||+|||||+|++|+++++     +..++.+++.+++..+..
T Consensus       142 npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~~~f~~~~~~  188 (450)
T PRK14087        142 NPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSGDEFARKAVD  188 (450)
T ss_pred             CceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHHH
Confidence            569999999999999999999965     567889999998877754

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

Probab=97.78  E-value=1.7e-05  Score=77.89  Aligned_cols=81  Identities=23%  Similarity=0.378  Sum_probs=53.5

Q ss_pred             cccCCCCCceeccCCcchhhhHHHHHHHhcC----CC--cHHH----------HhhhccC----CC-cceeeecCCCCch
Q 025979          148 LSQSEKPDVTYNDIGGCDIQKQEIREAVELP----LT--HHEL----------YKQIGID----PP-RGVLLYGPPGTGK  206 (245)
Q Consensus       148 ~~~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~----~~--~~~~----------~~~~g~~----~~-~gvLl~GPPGtGK  206 (245)
                      +.+.+...-.|.|+.|-+.+-.++.-.+..+    +.  ..++          .-..+++    |+ +-+||+||||-||
T Consensus       260 LWVdky~Pk~FtdLLsDe~tNR~~L~WLK~WD~~VFg~~vsrl~~s~~~~~ke~~~~~~~~s~RP~kKilLL~GppGlGK  339 (877)
T KOG1969|consen  260 LWVDKYRPKKFTDLLSDEKTNRRMLGWLKQWDPCVFGQKVSRLLASKGPTEKEVLDMELDPSKRPPKKILLLCGPPGLGK  339 (877)
T ss_pred             eeecccChhHHHHHhcchhHHHHHHHHHHhhcHHhhcchHhhhccccccchhhhhhcccCccCCCccceEEeecCCCCCh
Confidence            3344455566778888777776666665422    11  0000          0111222    22 2288999999999


Q ss_pred             HHHHHHHHhcccceeeeechhH
Q 025979          207 TMLAKAVANHTTAAFIRVVGSE  228 (245)
Q Consensus       207 T~lAkalA~~l~~~~~~v~~s~  228 (245)
                      |+||+.+|+++|..++.|+.|+
T Consensus       340 TTLAHViAkqaGYsVvEINASD  361 (877)
T KOG1969|consen  340 TTLAHVIAKQAGYSVVEINASD  361 (877)
T ss_pred             hHHHHHHHHhcCceEEEecccc
Confidence            9999999999999999998875

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=97.78  E-value=2.5e-05  Score=77.18  Aligned_cols=48  Identities=27%  Similarity=0.302  Sum_probs=38.1

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .|.+|+|++..+..+.-+...|             ...||||+||||||||++|++++..+
T Consensus         2 pf~~ivGq~~~~~al~~~av~~-------------~~g~vli~G~~GtgKs~lar~l~~~l   49 (633)
T TIGR02442         2 PFTAIVGQEDLKLALLLNAVDP-------------RIGGVLIRGEKGTAKSTAARGLAALL   49 (633)
T ss_pred             CcchhcChHHHHHHHHHHhhCC-------------CCCeEEEEcCCCCcHHHHHHHHHHhC
Confidence            3678999999887776554432             11359999999999999999999887

A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.

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

Probab=97.76  E-value=2.2e-05  Score=72.73  Aligned_cols=62  Identities=21%  Similarity=0.398  Sum_probs=47.3

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccce-----eeeechhHH
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAA-----FIRVVGSEF  229 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~-----~~~v~~s~l  229 (245)
                      +.+.+-++++..+..++...+..         ..|.++++|||||||||.+++-+++++.-.     ++.|++-.+
T Consensus        17 ~~l~~Re~ei~~l~~~l~~~~~~---------~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~   83 (366)
T COG1474          17 EELPHREEEINQLASFLAPALRG---------ERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLEL   83 (366)
T ss_pred             ccccccHHHHHHHHHHHHHHhcC---------CCCccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeC
Confidence            44888899999988886543322         345569999999999999999999988444     777776554

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=97.76  E-value=1.7e-05  Score=64.27  Aligned_cols=32  Identities=38%  Similarity=0.678  Sum_probs=29.8

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceeeeec
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVV  225 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~  225 (245)
                      .++|+.|-||||||++|..||..++.+++.++
T Consensus         8 PNILvtGTPG~GKstl~~~lae~~~~~~i~is   39 (176)
T KOG3347|consen    8 PNILVTGTPGTGKSTLAERLAEKTGLEYIEIS   39 (176)
T ss_pred             CCEEEeCCCCCCchhHHHHHHHHhCCceEehh
Confidence            46999999999999999999999999999886

>PHA02624 large T antigen; Provisional

Probab=97.75  E-value=2.3e-05  Score=76.25  Aligned_cols=39  Identities=28%  Similarity=0.318  Sum_probs=32.0

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechh
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS  227 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s  227 (245)
                      |+...+.+|||||||||||+++.+|++.++...+.|+++
T Consensus       427 giPKk~~il~~GPpnTGKTtf~~sLl~~L~G~vlsVNsP  465 (647)
T PHA02624        427 NVPKRRYWLFKGPVNSGKTTLAAALLDLCGGKSLNVNCP  465 (647)
T ss_pred             cCCCCeEEEEECCCCCCHHHHHHHHHHHcCCeEEEeeCC
Confidence            444445799999999999999999999996667777644

>TIGR01817 nifA Nif-specific regulatory protein

Probab=97.72  E-value=3.1e-05  Score=74.97  Aligned_cols=63  Identities=24%  Similarity=0.340  Sum_probs=51.1

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHH
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEF  229 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l  229 (245)
                      .++++++|.+...+++.+.+...-           .....|||+|+||||||++|++|....   +.+|+.+++..+
T Consensus       193 ~~~~~liG~s~~~~~~~~~~~~~a-----------~~~~pvli~Ge~GtGK~~lA~~ih~~s~r~~~pfv~i~c~~~  258 (534)
T TIGR01817       193 GKEDGIIGKSPAMRQVVDQARVVA-----------RSNSTVLLRGESGTGKELIAKAIHYLSPRAKRPFVKVNCAAL  258 (534)
T ss_pred             CccCceEECCHHHHHHHHHHHHHh-----------CcCCCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeecCCC
Confidence            567889999998888888876521           233459999999999999999998775   679999998655

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

>PRK06547 hypothetical protein; Provisional

Probab=97.70  E-value=2.8e-05  Score=64.53  Aligned_cols=35  Identities=34%  Similarity=0.397  Sum_probs=29.1

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcccceeeeec
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVV  225 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~  225 (245)
                      ..+.-|++.||||+|||++|+.+|+.++.+++.++
T Consensus        13 ~~~~~i~i~G~~GsGKTt~a~~l~~~~~~~~~~~d   47 (172)
T PRK06547         13 GGMITVLIDGRSGSGKTTLAGALAARTGFQLVHLD   47 (172)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhCCCeeccc
Confidence            34556888999999999999999999988776543

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

Probab=97.69  E-value=3.3e-05  Score=59.86  Aligned_cols=36  Identities=36%  Similarity=0.515  Sum_probs=27.8

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc--------cceeeeechhHH
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT--------TAAFIRVVGSEF  229 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l--------~~~~~~v~~s~l  229 (245)
                      +.++++||||+|||++++.++..+        ..+++.+..+..
T Consensus         5 ~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   48 (131)
T PF13401_consen    5 RILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSS   48 (131)
T ss_dssp             --EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHH
T ss_pred             cccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCC
Confidence            458999999999999999999987        677777765543

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=97.66  E-value=3.6e-05  Score=70.16  Aligned_cols=49  Identities=18%  Similarity=0.247  Sum_probs=40.3

Q ss_pred             eeccCCc-chhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          157 TYNDIGG-CDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       157 ~~~dv~G-l~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .|++|.| ++.+++.+...+..            -..+..+|||||+|+|||++|+++|+.+
T Consensus         3 ~~~~i~~~q~~~~~~L~~~~~~------------~~l~ha~Lf~G~~G~gk~~~a~~la~~l   52 (329)
T PRK08058          3 TWEQLTALQPVVVKMLQNSIAK------------NRLSHAYLFEGAKGTGKKATALWLAKSL   52 (329)
T ss_pred             cHHHHHhhHHHHHHHHHHHHHc------------CCCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            4677877 88889988888754            1355779999999999999999999876

>PLN02674 adenylate kinase

Probab=97.65  E-value=5.7e-05  Score=66.20  Aligned_cols=40  Identities=20%  Similarity=0.508  Sum_probs=33.0

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKY  233 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~  233 (245)
                      ++..++|.||||+|||++|+.||..+++++  ++..+++...
T Consensus        30 ~~~~i~l~G~PGsGKgT~a~~La~~~~~~h--is~GdllR~~   69 (244)
T PLN02674         30 PDKRLILIGPPGSGKGTQSPIIKDEYCLCH--LATGDMLRAA   69 (244)
T ss_pred             cCceEEEECCCCCCHHHHHHHHHHHcCCcE--EchhHHHHHH
Confidence            446699999999999999999999998655  6777776554

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=97.64  E-value=5.5e-05  Score=69.28  Aligned_cols=48  Identities=31%  Similarity=0.379  Sum_probs=38.4

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .|..|+|++..+..+.-.+..|             ...++++.||||+|||++++++++.+
T Consensus         2 pf~~ivgq~~~~~al~~~~~~~-------------~~g~vli~G~~G~gKttl~r~~~~~~   49 (337)
T TIGR02030         2 PFTAIVGQDEMKLALLLNVIDP-------------KIGGVMVMGDRGTGKSTAVRALAALL   49 (337)
T ss_pred             CccccccHHHHHHHHHHHhcCC-------------CCCeEEEEcCCCCCHHHHHHHHHHhh
Confidence            3678999999988876554432             12459999999999999999999877

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.

>PF08298 AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 This is entry is found at the N terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length

Probab=97.63  E-value=5e-05  Score=69.54  Aligned_cols=59  Identities=19%  Similarity=0.326  Sum_probs=45.0

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcc-eeeecCCCCchHHHHHHHHhccc-ceeeeec
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRG-VLLYGPPGTGKTMLAKAVANHTT-AAFIRVV  225 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~g-vLl~GPPGtGKT~lAkalA~~l~-~~~~~v~  225 (245)
                      +++.|+++.++++-+++..        ...|+...+. ++|+||+|+|||++++.|-+.+. .+++.+.
T Consensus        61 ~~~~G~~~~i~~lV~~fk~--------AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~~le~y~~Y~l~  121 (358)
T PF08298_consen   61 DEFYGMEETIERLVNYFKS--------AAQGLEERKRILLLLGPVGGGKSSLAELLKRGLEEYPIYTLK  121 (358)
T ss_pred             ccccCcHHHHHHHHHHHHH--------HHhccCccceEEEEECCCCCCHHHHHHHHHHHhheEEEEEec
Confidence            4799999999998887654        4455665555 67899999999999999988773 3444443

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=97.61  E-value=7.7e-05  Score=75.35  Aligned_cols=61  Identities=18%  Similarity=0.214  Sum_probs=44.2

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc----------cceeeeechh
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT----------TAAFIRVVGS  227 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l----------~~~~~~v~~s  227 (245)
                      +.+.|-++++++|..++...+.        |-.+...++++||||||||++++.+..++          .+.++.|++.
T Consensus       755 D~LPhREeEIeeLasfL~paIk--------gsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm  825 (1164)
T PTZ00112        755 KYLPCREKEIKEVHGFLESGIK--------QSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGM  825 (1164)
T ss_pred             CcCCChHHHHHHHHHHHHHHHh--------cCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCC
Confidence            5688888888888888764221        22233335699999999999999998766          2567778763

>PLN02199 shikimate kinase

Probab=97.61  E-value=5.1e-05  Score=68.13  Aligned_cols=43  Identities=23%  Similarity=0.332  Sum_probs=35.6

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHH-hcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKY-LGE  236 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~-~Ge  236 (245)
                      ..+.|+|.|++|+|||++++.+|+.++++|  ++...+++.. -|.
T Consensus       101 ~~~~I~LIG~~GSGKSTVgr~LA~~Lg~~f--IDtD~lIe~~~~G~  144 (303)
T PLN02199        101 NGRSMYLVGMMGSGKTTVGKLMSKVLGYTF--FDCDTLIEQAMNGT  144 (303)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHhCCCE--EehHHHHHHHhcCC
Confidence            456799999999999999999999999998  4666777664 354

>PRK05541 adenylylsulfate kinase; Provisional

Probab=97.59  E-value=7.8e-05  Score=61.37  Aligned_cols=40  Identities=28%  Similarity=0.378  Sum_probs=30.5

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhccc---ceeeeechhHHHH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTT---AAFIRVVGSEFVQ  231 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~---~~~~~v~~s~l~~  231 (245)
                      ++.-++|.||||+|||++|+.++..+.   ...+.+++..+..
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~~l~~~~~~~~~~~~d~~r~   48 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYERLKLKYSNVIYLDGDELRE   48 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEecHHHHh
Confidence            445689999999999999999999885   2345566655543

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

Probab=97.58  E-value=8e-05  Score=60.13  Aligned_cols=36  Identities=22%  Similarity=0.395  Sum_probs=29.6

Q ss_pred             eeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHH
Q 025979          196 VLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQ  231 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~  231 (245)
                      +++.|+||+|||++|+.++..+   +...+.+++..+..
T Consensus         2 i~i~G~~GsGKSTla~~L~~~l~~~g~~~~~i~~d~~r~   40 (149)
T cd02027           2 IWLTGLSGSGKSTIARALEEKLFQRGRPVYVLDGDNVRH   40 (149)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEEcCHHHHH
Confidence            6899999999999999999998   65666677665543

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

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

Probab=97.55  E-value=4.5e-05  Score=58.55  Aligned_cols=22  Identities=41%  Similarity=0.664  Sum_probs=20.7

Q ss_pred             eeeecCCCCchHHHHHHHHhcc
Q 025979          196 VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      |++.|+||||||++|+.|+..+
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            6899999999999999999986

...

>PRK09087 hypothetical protein; Validated

Probab=97.54  E-value=6.1e-05  Score=65.16  Aligned_cols=31  Identities=39%  Similarity=0.493  Sum_probs=26.0

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceeeee
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRV  224 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v  224 (245)
                      +.++||||+|||||+|+++++...++.++..
T Consensus        45 ~~l~l~G~~GsGKThLl~~~~~~~~~~~i~~   75 (226)
T PRK09087         45 PVVVLAGPVGSGKTHLASIWREKSDALLIHP   75 (226)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhcCCEEecH
Confidence            3499999999999999999998877765444

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

Probab=97.54  E-value=7.2e-05  Score=62.95  Aligned_cols=22  Identities=41%  Similarity=0.724  Sum_probs=15.6

Q ss_pred             eeeecCCCCchHHHHHHHHhcc
Q 025979          196 VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+++||||||||+++.+++..+
T Consensus        20 ~~i~GpPGTGKT~~l~~~i~~~   41 (236)
T PF13086_consen   20 TLIQGPPGTGKTTTLASIIAQL   41 (236)
T ss_dssp             EEEE-STTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCChHHHHHHHHHHh
Confidence            7899999999997555554443

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=97.53  E-value=8.5e-05  Score=72.03  Aligned_cols=63  Identities=25%  Similarity=0.404  Sum_probs=50.5

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhc-----------ccceeeee
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANH-----------TTAAFIRV  224 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~-----------l~~~~~~v  224 (245)
                      .++++++|.....+.+.+.+...       .    .....||++|+|||||+++|++|-..           .+.||+.+
T Consensus       216 ~~f~~iiG~S~~m~~~~~~i~~~-------A----~s~~pVLI~GE~GTGKe~~A~~IH~~~~~~~~~~S~r~~~pfv~i  284 (538)
T PRK15424        216 YVLGDLLGQSPQMEQVRQTILLY-------A----RSSAAVLIQGETGTGKELAAQAIHREYFARHDARQGKKSHPFVAV  284 (538)
T ss_pred             cchhheeeCCHHHHHHHHHHHHH-------h----CCCCcEEEECCCCCCHHHHHHHHHHhhcccccccCccCCCCeEEe
Confidence            45788999999888888887641       1    12345999999999999999999765           46799999


Q ss_pred             chhHH
Q 025979          225 VGSEF  229 (245)
Q Consensus       225 ~~s~l  229 (245)
                      +|+.+
T Consensus       285 nCaal  289 (538)
T PRK15424        285 NCGAI  289 (538)
T ss_pred             ecccC
Confidence            98765

>PF13245 AAA_19: Part of AAA domain

Probab=97.53  E-value=9.5e-05  Score=53.19  Aligned_cols=32  Identities=34%  Similarity=0.561  Sum_probs=21.8

Q ss_pred             eeeecCCCCchH-HHHHHHHhcc------cceeeeechh
Q 025979          196 VLLYGPPGTGKT-MLAKAVANHT------TAAFIRVVGS  227 (245)
Q Consensus       196 vLl~GPPGtGKT-~lAkalA~~l------~~~~~~v~~s  227 (245)
                      +++.|||||||| +++..++...      +..++.+..+
T Consensus        13 ~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t   51 (76)
T PF13245_consen   13 FVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPT   51 (76)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCC
Confidence            556999999999 5556665555      4456666544

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=97.52  E-value=8e-05  Score=74.23  Aligned_cols=63  Identities=22%  Similarity=0.395  Sum_probs=49.3

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHH
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEF  229 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l  229 (245)
                      ..+++++|.....+.+.+.+...-           .....||++|+||||||++|++|....   +.+|+.+++..+
T Consensus       373 ~~~~~liG~S~~~~~~~~~~~~~a-----------~~~~pVLI~GE~GTGK~~lA~~ih~~s~r~~~~~v~i~c~~~  438 (686)
T PRK15429        373 SEFGEIIGRSEAMYSVLKQVEMVA-----------QSDSTVLILGETGTGKELIARAIHNLSGRNNRRMVKMNCAAM  438 (686)
T ss_pred             ccccceeecCHHHHHHHHHHHHHh-----------CCCCCEEEECCCCcCHHHHHHHHHHhcCCCCCCeEEEecccC
Confidence            456788898888888877776411           233469999999999999999998754   679999988754

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=97.52  E-value=6.8e-05  Score=64.73  Aligned_cols=23  Identities=48%  Similarity=0.767  Sum_probs=20.7

Q ss_pred             CcceeeecCCCCchHHHHHHHHh
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      |..+||||+||+|||++|+.++.
T Consensus        12 ~~~~liyG~~G~GKtt~a~~~~~   34 (220)
T TIGR01618        12 PNMYLIYGKPGTGKTSTIKYLPG   34 (220)
T ss_pred             CcEEEEECCCCCCHHHHHHhcCC
Confidence            45599999999999999999985

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.

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

Probab=97.50  E-value=6e-05  Score=74.08  Aligned_cols=39  Identities=36%  Similarity=0.375  Sum_probs=33.3

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc----cceeeeechhHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT----TAAFIRVVGSEFVQ  231 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l----~~~~~~v~~s~l~~  231 (245)
                      +..+||+||+|||||.|+++++.+.    -+++.+++++.+-.
T Consensus       431 ~~~Ill~G~~GsGKT~L~kal~~~~~k~~~~hv~~v~Cs~l~~  473 (952)
T KOG0735|consen  431 HGNILLNGPKGSGKTNLVKALFDYYSKDLIAHVEIVSCSTLDG  473 (952)
T ss_pred             cccEEEeCCCCCCHhHHHHHHHHHhccccceEEEEEechhccc
Confidence            3559999999999999999999987    57788889888743

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=97.49  E-value=0.00011  Score=66.84  Aligned_cols=61  Identities=23%  Similarity=0.287  Sum_probs=47.6

Q ss_pred             eccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHH
Q 025979          158 YNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEF  229 (245)
Q Consensus       158 ~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l  229 (245)
                      +++++|.....+.+.+.+....           .....||++|+|||||+++|++|-...   +.+|+.+++..+
T Consensus         5 ~~~liG~S~~~~~~~~~i~~~a-----------~~~~pVlI~GE~GtGK~~lA~~iH~~s~r~~~pfv~v~c~~~   68 (326)
T PRK11608          5 KDNLLGEANSFLEVLEQVSRLA-----------PLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAAL   68 (326)
T ss_pred             cCccEECCHHHHHHHHHHHHHh-----------CCCCCEEEECCCCCcHHHHHHHHHHhCCccCCCeEEEeCCCC
Confidence            4578888888888888776521           233459999999999999999997554   578999998765

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

Probab=97.48  E-value=0.00023  Score=66.58  Aligned_cols=43  Identities=26%  Similarity=0.547  Sum_probs=36.6

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc-----cceeeeechhHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT-----TAAFIRVVGSEFVQKYLGE  236 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l-----~~~~~~v~~s~l~~~~~Ge  236 (245)
                      +-++||||+|.|||+|++|++++.     +..++.++.+.+++.++-.
T Consensus       114 nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~se~f~~~~v~a  161 (408)
T COG0593         114 NPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFTNDFVKA  161 (408)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEeccHHHHHHHHHHH
Confidence            338999999999999999999887     5678999999988777643

>PRK06696 uridine kinase; Validated

Probab=97.46  E-value=0.00013  Score=62.66  Aligned_cols=38  Identities=29%  Similarity=0.391  Sum_probs=31.5

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFV  230 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~  230 (245)
                      +.-|.+.|+||+|||++|+.|+..+   |.+++.+++.+|.
T Consensus        22 ~~iI~I~G~sgsGKSTlA~~L~~~l~~~g~~v~~~~~Ddf~   62 (223)
T PRK06696         22 PLRVAIDGITASGKTTFADELAEEIKKRGRPVIRASIDDFH   62 (223)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEecccccc
Confidence            3448899999999999999999998   6678877766664

>PLN02459 probable adenylate kinase

Probab=97.44  E-value=0.00014  Score=64.23  Aligned_cols=36  Identities=19%  Similarity=0.393  Sum_probs=29.4

Q ss_pred             ceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHH
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQK  232 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~  232 (245)
                      .++|.||||+|||++|+.+|+.++.++  ++..+++-.
T Consensus        31 ~ii~~G~PGsGK~T~a~~la~~~~~~~--is~gdllR~   66 (261)
T PLN02459         31 NWVFLGCPGVGKGTYASRLSKLLGVPH--IATGDLVRE   66 (261)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcE--EeCcHHHHH
Confidence            488899999999999999999998655  566666543

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=97.43  E-value=0.00014  Score=70.01  Aligned_cols=62  Identities=18%  Similarity=0.351  Sum_probs=49.7

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHH
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEF  229 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l  229 (245)
                      ...+++|.....+.+.+.+...           ...+..||++|++|||||++|++|-...   +.+|+.|+|..+
T Consensus       185 ~~~~iig~s~~~~~~~~~i~~~-----------a~~~~pVlI~Ge~GtGK~~~A~~ih~~s~r~~~p~v~v~c~~~  249 (509)
T PRK05022        185 KEGEMIGQSPAMQQLKKEIEVV-----------AASDLNVLILGETGVGKELVARAIHAASPRADKPLVYLNCAAL  249 (509)
T ss_pred             cCCceeecCHHHHHHHHHHHHH-----------hCCCCcEEEECCCCccHHHHHHHHHHhCCcCCCCeEEEEcccC
Confidence            5667889888888888887651           1234569999999999999999998764   679999998765

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=97.42  E-value=9.3e-05  Score=61.64  Aligned_cols=27  Identities=37%  Similarity=0.530  Sum_probs=24.0

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhccc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      .+..+|||||||+|||++|+++|..+.
T Consensus        13 ~~~~~L~~G~~G~gkt~~a~~~~~~l~   39 (188)
T TIGR00678        13 LAHAYLFAGPEGVGKELLALALAKALL   39 (188)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHc
Confidence            456799999999999999999999874

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.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=97.42  E-value=0.00054  Score=61.16  Aligned_cols=26  Identities=31%  Similarity=0.390  Sum_probs=22.2

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.++|+||+|+|||+++..+|..+
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~  218 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARF  218 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            34569999999999999999998765

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=97.42  E-value=0.00013  Score=70.52  Aligned_cols=63  Identities=24%  Similarity=0.414  Sum_probs=50.5

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHH
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEF  229 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l  229 (245)
                      .+|++++|.....+.+.+.+...       .    .....||++|+|||||+++|++|-...   +.||+.++|..+
T Consensus       209 ~~f~~iiG~S~~m~~~~~~i~~~-------A----~~~~pVLI~GE~GTGKe~lA~~IH~~S~r~~~pfv~inC~~l  274 (526)
T TIGR02329       209 YRLDDLLGASAPMEQVRALVRLY-------A----RSDATVLILGESGTGKELVAQAIHQLSGRRDFPFVAINCGAI  274 (526)
T ss_pred             cchhheeeCCHHHHHHHHHHHHH-------h----CCCCcEEEECCCCcCHHHHHHHHHHhcCcCCCCEEEeccccC
Confidence            56788999999888888887641       1    123569999999999999999997653   679999998755

At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.

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

Probab=97.42  E-value=0.00019  Score=58.89  Aligned_cols=43  Identities=28%  Similarity=0.413  Sum_probs=33.3

Q ss_pred             cchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          163 GCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       163 Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      |++++++.+...+..            -..|..+||+||+|+||+++|+++|..+
T Consensus         1 gq~~~~~~L~~~~~~------------~~l~ha~L~~G~~g~gk~~~a~~~a~~l   43 (162)
T PF13177_consen    1 GQEEIIELLKNLIKS------------GRLPHALLFHGPSGSGKKTLALAFARAL   43 (162)
T ss_dssp             S-HHHHHHHHHHHHC------------TC--SEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHc------------CCcceeEEEECCCCCCHHHHHHHHHHHH
Confidence            567777778777754            1356779999999999999999999877

...

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=97.42  E-value=0.00015  Score=71.72  Aligned_cols=64  Identities=23%  Similarity=0.326  Sum_probs=49.7

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHH
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEF  229 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l  229 (245)
                      ..+|+++.|.+....++.+.+....           .....|||+|+|||||+++|++|-...   +.+|+.|++..+
T Consensus       321 ~~~~~~l~g~s~~~~~~~~~~~~~a-----------~~~~pvli~Ge~GtGK~~~A~~ih~~s~r~~~pfv~vnc~~~  387 (638)
T PRK11388        321 SHTFDHMPQDSPQMRRLIHFGRQAA-----------KSSFPVLLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLY  387 (638)
T ss_pred             cccccceEECCHHHHHHHHHHHHHh-----------CcCCCEEEECCCCcCHHHHHHHHHHhCCccCCCeEEEECCCC
Confidence            4568899998888888777765411           123449999999999999999998765   579999997654

>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=97.40  E-value=0.00016  Score=50.70  Aligned_cols=22  Identities=32%  Similarity=0.591  Sum_probs=20.2

Q ss_pred             eeeecCCCCchHHHHHHHHhcc
Q 025979          196 VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.+.|+||+|||+++++++..+
T Consensus         2 i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5688999999999999999984

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.

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

Probab=97.39  E-value=0.00016  Score=72.32  Aligned_cols=76  Identities=21%  Similarity=0.284  Sum_probs=61.8

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc----------cceeeeec
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT----------TAAFIRVV  225 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l----------~~~~~~v~  225 (245)
                      -..+.|+|-++.+.++.+.+.+.             ..++-+|.|+||||||.++..+|...          +..++.++
T Consensus       167 gklDPvIGRd~EI~r~iqIL~RR-------------~KNNPvLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i~sLD  233 (786)
T COG0542         167 GKLDPVIGRDEEIRRTIQILSRR-------------TKNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLD  233 (786)
T ss_pred             CCCCCCcChHHHHHHHHHHHhcc-------------CCCCCeEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCCEEEEec
Confidence            44678999999888888887763             23457899999999999999999765          67899999


Q ss_pred             hhHHH--HHHhcccccccccc
Q 025979          226 GSEFV--QKYLGEVWLKHKQI  244 (245)
Q Consensus       226 ~s~l~--~~~~Ge~~~~vr~i  244 (245)
                      ++.++  .+|-|+-|..++.+
T Consensus       234 ~g~LvAGakyRGeFEeRlk~v  254 (786)
T COG0542         234 LGSLVAGAKYRGEFEERLKAV  254 (786)
T ss_pred             HHHHhccccccCcHHHHHHHH
Confidence            99998  78889887776653

>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=97.38  E-value=0.00011  Score=61.92  Aligned_cols=43  Identities=26%  Similarity=0.481  Sum_probs=33.1

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc-cceeeeechhHHHHHH
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT-TAAFIRVVGSEFVQKY  233 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l-~~~~~~v~~s~l~~~~  233 (245)
                      ..|.-+++.||||+|||+++..+...+ +..++.|+..++...+
T Consensus        13 ~~P~~~i~aG~~GsGKSt~~~~~~~~~~~~~~v~i~~D~~r~~~   56 (199)
T PF06414_consen   13 EKPTLIIIAGQPGSGKSTLARQLLEEFGGGGIVVIDADEFRQFH   56 (199)
T ss_dssp             SS-EEEEEES-TTSTTHHHHHHHHHHT-TT-SEEE-GGGGGGGS
T ss_pred             cCCEEEEEeCCCCCCHHHHHHHhhhhccCCCeEEEehHHHHHhc
Confidence            456779999999999999999999988 7888999988876443

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.

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=97.35  E-value=0.00025  Score=66.26  Aligned_cols=66  Identities=27%  Similarity=0.435  Sum_probs=51.4

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhc----ccceeeeechhHHHH
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANH----TTAAFIRVVGSEFVQ  231 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~----l~~~~~~v~~s~l~~  231 (245)
                      ..+.+++|-+...+++++.+..       |.    .....||++|++||||+++|++|...    .+.||+.++|..|.+
T Consensus        75 ~~~~~LIG~~~~~~~~~eqik~-------~a----p~~~~vLi~GetGtGKel~A~~iH~~s~r~~~~PFI~~NCa~~~e  143 (403)
T COG1221          75 EALDDLIGESPSLQELREQIKA-------YA----PSGLPVLIIGETGTGKELFARLIHALSARRAEAPFIAFNCAAYSE  143 (403)
T ss_pred             hhhhhhhccCHHHHHHHHHHHh-------hC----CCCCcEEEecCCCccHHHHHHHHHHhhhcccCCCEEEEEHHHhCc
Confidence            4567899999888888888765       11    12244999999999999999988743    367999999998864


Q ss_pred             H
Q 025979          232 K  232 (245)
Q Consensus       232 ~  232 (245)
                      .
T Consensus       144 n  144 (403)
T COG1221         144 N  144 (403)
T ss_pred             C
Confidence            4

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=97.35  E-value=0.00023  Score=64.93  Aligned_cols=57  Identities=23%  Similarity=0.272  Sum_probs=40.9

Q ss_pred             CcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHH
Q 025979          162 GGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEF  229 (245)
Q Consensus       162 ~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l  229 (245)
                      +|.....+.+.+.+...           ......|||+|+|||||+++|++|-...   +.+|+.|++..+
T Consensus         2 iG~S~~m~~~~~~~~~~-----------a~~~~pVLI~GE~GtGK~~lAr~iH~~s~r~~~pfv~vnc~~~   61 (329)
T TIGR02974         2 IGESNAFLEVLEQVSRL-----------APLDRPVLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCAAL   61 (329)
T ss_pred             CcCCHHHHHHHHHHHHH-----------hCCCCCEEEECCCCChHHHHHHHHHHhcCccCCCeEEEeCCCC
Confidence            45555666666665441           1233559999999999999999986544   579999998654

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>PF13173 AAA_14: AAA domain

Probab=97.35  E-value=0.00016  Score=56.56  Aligned_cols=36  Identities=28%  Similarity=0.401  Sum_probs=28.8

Q ss_pred             cceeeecCCCCchHHHHHHHHhccc--ceeeeechhHH
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTT--AAFIRVVGSEF  229 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~--~~~~~v~~s~l  229 (245)
                      +-++++||.|||||++++.++..+.  ..++.++..+.
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~~~~~~~yi~~~~~   40 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLLPPENILYINFDDP   40 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhcccccceeeccCCH
Confidence            4488999999999999999998875  66666665543

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.34  E-value=0.00018  Score=60.76  Aligned_cols=40  Identities=25%  Similarity=0.477  Sum_probs=29.6

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhH
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSE  228 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~  228 (245)
                      |+....-++++||||||||++|..++...   +...+.++..+
T Consensus         8 Gi~~g~i~~i~G~~GsGKT~l~~~~~~~~~~~g~~v~yi~~e~   50 (209)
T TIGR02237         8 GVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTEG   50 (209)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECCC
Confidence            44444449999999999999999888644   55666666654

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

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.34  E-value=0.00017  Score=68.93  Aligned_cols=39  Identities=41%  Similarity=0.699  Sum_probs=33.8

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      +-..+||+||||+|||.||-.+|...+.||+++-.++=+
T Consensus       537 ~lvSvLl~Gp~~sGKTaLAA~iA~~S~FPFvKiiSpe~m  575 (744)
T KOG0741|consen  537 PLVSVLLEGPPGSGKTALAAKIALSSDFPFVKIISPEDM  575 (744)
T ss_pred             cceEEEEecCCCCChHHHHHHHHhhcCCCeEEEeChHHc
Confidence            344599999999999999999999999999998766543

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

Probab=97.34  E-value=0.00011  Score=58.39  Aligned_cols=56  Identities=29%  Similarity=0.460  Sum_probs=36.5

Q ss_pred             cchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc---ceeeeechhHH
Q 025979          163 GCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT---AAFIRVVGSEF  229 (245)
Q Consensus       163 Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~---~~~~~v~~s~l  229 (245)
                      |-....+++++.+...       .    .....||++|+|||||+++|++|....+   .+|+.+++..+
T Consensus         2 G~S~~~~~l~~~l~~~-------a----~~~~pvli~GE~GtGK~~~A~~lh~~~~~~~~~~~~~~~~~~   60 (138)
T PF14532_consen    2 GKSPAMRRLRRQLERL-------A----KSSSPVLITGEPGTGKSLLARALHRYSGRANGPFIVIDCASL   60 (138)
T ss_dssp             -SCHHHHHHHHHHHHH-------H----CSSS-EEEECCTTSSHHHHHHCCHHTTTTCCS-CCCCCHHCT
T ss_pred             CCCHHHHHHHHHHHHH-------h----CCCCcEEEEcCCCCCHHHHHHHHHhhcCccCCCeEEechhhC
Confidence            4445556666665431       1    2234599999999999999999998764   46776665543

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=97.32  E-value=0.00024  Score=68.72  Aligned_cols=66  Identities=20%  Similarity=0.262  Sum_probs=49.6

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHH
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFV  230 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~  230 (245)
                      ...+|++++|.....+.+.+.+...       .    .....||++|++||||+++|+++-...   +.+|+.++|+.+-
T Consensus       199 ~~~~f~~~ig~s~~~~~~~~~~~~~-------A----~~~~pvlI~GE~GtGK~~lA~aiH~~s~r~~~pfv~inca~~~  267 (520)
T PRK10820        199 DDSAFSQIVAVSPKMRQVVEQARKL-------A----MLDAPLLITGDTGTGKDLLAYACHLRSPRGKKPFLALNCASIP  267 (520)
T ss_pred             ccccccceeECCHHHHHHHHHHHHH-------h----CCCCCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeccccCC
Confidence            4568889999998777777666431       1    123449999999999999999985443   5789999987653

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=97.32  E-value=0.00019  Score=57.29  Aligned_cols=30  Identities=33%  Similarity=0.337  Sum_probs=25.9

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcccce
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTTAA  220 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~~~  220 (245)
                      .+..-++|.|+.|+|||+++|.+++.++..
T Consensus        20 ~~~~~i~l~G~lGaGKTtl~~~l~~~lg~~   49 (133)
T TIGR00150        20 DFGTVVLLKGDLGAGKTTLVQGLLQGLGIQ   49 (133)
T ss_pred             CCCCEEEEEcCCCCCHHHHHHHHHHHcCCC
Confidence            344558899999999999999999999765

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.

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

Probab=97.31  E-value=0.00016  Score=63.22  Aligned_cols=24  Identities=29%  Similarity=0.450  Sum_probs=21.9

Q ss_pred             ceeeecCCCCchHHHHHHHHhccc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      -++|+||||+|||++++.+++.+.
T Consensus        45 ~~~l~G~~G~GKTtl~~~l~~~l~   68 (269)
T TIGR03015        45 FILITGEVGAGKTTLIRNLLKRLD   68 (269)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHhcC
Confidence            388999999999999999999875

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.

>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=97.31  E-value=0.00023  Score=58.27  Aligned_cols=39  Identities=26%  Similarity=0.348  Sum_probs=33.0

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHHHH
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQKY  233 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~~~  233 (245)
                      -|.|.|.||+|||+||+++...+   +.+.+.+++..+...+
T Consensus         4 vIwltGlsGsGKtTlA~~L~~~L~~~g~~~~~LDgD~lR~~l   45 (156)
T PF01583_consen    4 VIWLTGLSGSGKTTLARALERRLFARGIKVYLLDGDNLRHGL   45 (156)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHTTS-EEEEEHHHHCTTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEecCcchhhcc
Confidence            37899999999999999999987   7889999998886543

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 ....

>PF12774 AAA_6: Hydrolytic ATP binding site of dynein motor region D1; PDB: 3VKH_A 3VKG_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A

Probab=97.28  E-value=0.00022  Score=61.98  Aligned_cols=40  Identities=33%  Similarity=0.287  Sum_probs=32.9

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      ....|-.++||+|||||.+.|.+|+.+|.+++.+++++-+
T Consensus        30 ~~~~~~~~~GpagtGKtetik~La~~lG~~~~vfnc~~~~   69 (231)
T PF12774_consen   30 SLNLGGALSGPAGTGKTETIKDLARALGRFVVVFNCSEQM   69 (231)
T ss_dssp             CTTTEEEEESSTTSSHHHHHHHHHHCTT--EEEEETTSSS
T ss_pred             ccCCCCCCcCCCCCCchhHHHHHHHHhCCeEEEecccccc
Confidence            3446778999999999999999999999999999887643

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=97.27  E-value=0.00027  Score=61.33  Aligned_cols=39  Identities=33%  Similarity=0.397  Sum_probs=28.6

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhc---ccceeeeechh
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANH---TTAAFIRVVGS  227 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~---l~~~~~~v~~s  227 (245)
                      |+.++..+|++||||||||++|-.++.+   .|-+.+.++..
T Consensus        17 G~~~gs~~lI~G~pGsGKT~la~~~l~~~~~~ge~~lyvs~e   58 (237)
T TIGR03877        17 GIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVALE   58 (237)
T ss_pred             CCcCCeEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEEee
Confidence            5666677999999999999999876543   25555555533

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.

>cd01394 radB RadB

Probab=97.27  E-value=0.00024  Score=60.45  Aligned_cols=39  Identities=33%  Similarity=0.497  Sum_probs=29.3

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechh
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      |+....-++++||||||||++|..+|...   +.+.+.++..
T Consensus        15 Gi~~g~i~~i~G~~GsGKT~l~~~~a~~~~~~g~~v~yi~~e   56 (218)
T cd01394          15 GVERGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYIDTE   56 (218)
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEECC
Confidence            44444559999999999999999998765   4566666543

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

>PHA02774 E1; Provisional

Probab=97.22  E-value=0.00028  Score=68.52  Aligned_cols=28  Identities=29%  Similarity=0.660  Sum_probs=24.5

Q ss_pred             cceeeecCCCCchHHHHHHHHhccccee
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAF  221 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~  221 (245)
                      ++++||||||||||++|-+|++.++...
T Consensus       435 nciv~~GPP~TGKS~fa~sL~~~L~G~v  462 (613)
T PHA02774        435 NCLVIYGPPDTGKSMFCMSLIKFLKGKV  462 (613)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCE
Confidence            4699999999999999999999985433

>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=97.21  E-value=0.00071  Score=54.79  Aligned_cols=43  Identities=28%  Similarity=0.471  Sum_probs=33.5

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccceeeeechh-HHHHHHh
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS-EFVQKYL  234 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s-~l~~~~~  234 (245)
                      ..+.+||.+|+|+|||.++-.++..+..+++.+.++ .+.+++.
T Consensus        24 ~~~~~ll~~~tGsGKT~~~~~~~~~l~~~~l~~~p~~~l~~Q~~   67 (184)
T PF04851_consen   24 EERRVLLNAPTGSGKTIIALALILELARKVLIVAPNISLLEQWY   67 (184)
T ss_dssp             GCSEEEEEESTTSSHHHHHHHHHHHHHCEEEEEESSHHHHHHHH
T ss_pred             CCCCEEEEECCCCCcChhhhhhhhccccceeEecCHHHHHHHHH
Confidence            356799999999999999998777776577777655 6666554

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 ....

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.20  E-value=0.00035  Score=59.79  Aligned_cols=39  Identities=28%  Similarity=0.478  Sum_probs=29.8

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechh
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      |+....-++++||||+|||++|..+|...   +.+.+.++..
T Consensus        19 Gi~~g~i~~i~G~~GsGKT~l~~~la~~~~~~~~~v~yi~~e   60 (225)
T PRK09361         19 GFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE   60 (225)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            44444458999999999999999998744   5666666665

>COG3842 PotA ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=97.20  E-value=0.00016  Score=66.53  Aligned_cols=30  Identities=43%  Similarity=0.744  Sum_probs=24.7

Q ss_pred             hccCCCcc--eeeecCCCCchHHHHHHHHhcc
Q 025979          188 IGIDPPRG--VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       188 ~g~~~~~g--vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++..+|  +.|.||+|||||++.|.||..-
T Consensus        24 isl~i~~Gef~~lLGPSGcGKTTlLR~IAGfe   55 (352)
T COG3842          24 ISLDIKKGEFVTLLGPSGCGKTTLLRMIAGFE   55 (352)
T ss_pred             ceeeecCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            34455566  7799999999999999999865

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=97.19  E-value=0.00031  Score=60.16  Aligned_cols=38  Identities=37%  Similarity=0.462  Sum_probs=27.0

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc----cceeeeech
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT----TAAFIRVVG  226 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l----~~~~~~v~~  226 (245)
                      |+..+.-+|+.||||||||++|..++...    |-+.+.++.
T Consensus        15 Gip~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs~   56 (226)
T PF06745_consen   15 GIPKGSVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVSF   56 (226)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEES
T ss_pred             CCCCCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEEe
Confidence            56666669999999999999998766432    556655654

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 ....

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=97.19  E-value=0.00041  Score=59.81  Aligned_cols=39  Identities=26%  Similarity=0.388  Sum_probs=29.3

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechh
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      |+..+..++++||||||||++|..++...   +.+.+.++..
T Consensus        21 G~~~g~~~~i~G~~GsGKt~l~~~~~~~~~~~g~~~~y~~~e   62 (234)
T PRK06067         21 GIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITTE   62 (234)
T ss_pred             CCcCCcEEEEECCCCCChHHHHHHHHHHHHhCCCEEEEEEcC
Confidence            55556669999999999999999997543   5566666543

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=97.17  E-value=0.00042  Score=59.39  Aligned_cols=38  Identities=34%  Similarity=0.373  Sum_probs=28.0

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeech
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVG  226 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~  226 (245)
                      |+.+...++++||||||||+++..++...   +.+.+.++.
T Consensus        16 Gi~~G~~~~i~G~~G~GKT~l~~~~~~~~~~~g~~~~~is~   56 (229)
T TIGR03881        16 GIPRGFFVAVTGEPGTGKTIFCLHFAYKGLRDGDPVIYVTT   56 (229)
T ss_pred             CCcCCeEEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEEc
Confidence            56666669999999999999999876432   445555554

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.

>PLN02165 adenylate isopentenyltransferase

Probab=97.17  E-value=0.00031  Score=64.09  Aligned_cols=31  Identities=26%  Similarity=0.410  Sum_probs=27.4

Q ss_pred             ceeeecCCCCchHHHHHHHHhcccceeeeec
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTTAAFIRVV  225 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~  225 (245)
                      -++|.||+|+|||+||..||..++..++..+
T Consensus        45 iivIiGPTGSGKStLA~~LA~~l~~eIIsaD   75 (334)
T PLN02165         45 VVVIMGATGSGKSRLSVDLATRFPSEIINSD   75 (334)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHcCCceecCC
Confidence            4889999999999999999999988776654

>TIGR00368 Mg chelatase-related protein

Probab=97.16  E-value=0.00029  Score=67.79  Aligned_cols=46  Identities=37%  Similarity=0.618  Sum_probs=35.7

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhc
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ..|+|+.|...+++.+.-.+               .....++|+||||||||++|++++..
T Consensus       189 ~d~~dv~Gq~~~~~al~~aa---------------~~g~~vlliG~pGsGKTtlar~l~~l  234 (499)
T TIGR00368       189 LDLKDIKGQQHAKRALEIAA---------------AGGHNLLLFGPPGSGKTMLASRLQGI  234 (499)
T ss_pred             CCHHHhcCcHHHHhhhhhhc---------------cCCCEEEEEecCCCCHHHHHHHHhcc
Confidence            47889999887766555333               23356999999999999999999864

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>KOG3354 consensus Gluconate kinase [Carbohydrate transport and metabolism]

Probab=97.14  E-value=0.00032  Score=57.40  Aligned_cols=37  Identities=27%  Similarity=0.560  Sum_probs=30.1

Q ss_pred             CCCcc-eeeecCCCCchHHHHHHHHhcccceeeeechhHH
Q 025979          191 DPPRG-VLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF  229 (245)
Q Consensus       191 ~~~~g-vLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l  229 (245)
                      .+.++ +++.|+.|||||+++++++++++++|+  ++.+|
T Consensus         9 ~~~k~~i~vmGvsGsGKSTigk~L~~~l~~~F~--dgDd~   46 (191)
T KOG3354|consen    9 GPFKYVIVVMGVSGSGKSTIGKALSEELGLKFI--DGDDL   46 (191)
T ss_pred             CCCceeEEEEecCCCChhhHHHHHHHHhCCccc--ccccC
Confidence            34554 778899999999999999999999995  44443

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=97.13  E-value=0.00033  Score=61.74  Aligned_cols=38  Identities=21%  Similarity=0.257  Sum_probs=27.2

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeech
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVG  226 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~  226 (245)
                      |+.+..-++++||||||||++|-.+|...   |.+.+.++.
T Consensus        32 Gip~gs~~lI~G~pGtGKT~l~~qf~~~~a~~Ge~vlyis~   72 (259)
T TIGR03878        32 GIPAYSVINITGVSDTGKSLMVEQFAVTQASRGNPVLFVTV   72 (259)
T ss_pred             CeECCcEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEEe
Confidence            45555559999999999999999876542   445555543

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

>PRK08099 bifunctional DNA-binding transcriptional repressor/ NMN adenylyltransferase; Provisional

Probab=97.13  E-value=0.00058  Score=64.00  Aligned_cols=43  Identities=30%  Similarity=0.388  Sum_probs=35.8

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLG  235 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~G  235 (245)
                      .+.|++.|++|||||+|+++||...|..++.--+-+++...+|
T Consensus       219 ~~~IvI~G~~gsGKTTL~~~La~~~g~~~v~E~~R~~~~~~~~  261 (399)
T PRK08099        219 VRTVAILGGESSGKSTLVNKLANIFNTTSAWEYGREYVFSHLG  261 (399)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHhCCCeeeeccHHHHHHhhc
Confidence            3559999999999999999999999988877667777765554

>TIGR02012 tigrfam_recA protein RecA

Probab=97.12  E-value=0.00047  Score=62.75  Aligned_cols=41  Identities=24%  Similarity=0.333  Sum_probs=29.7

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHH
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEF  229 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l  229 (245)
                      |+...+-++++||||||||+||-.++...   +.+.+.++..+-
T Consensus        51 Glp~G~iteI~G~~GsGKTtLaL~~~~~~~~~g~~v~yId~E~~   94 (321)
T TIGR02012        51 GLPRGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHA   94 (321)
T ss_pred             CCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEcccch
Confidence            34444558999999999999988766544   566667766543

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.

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

Probab=97.11  E-value=0.00041  Score=60.89  Aligned_cols=39  Identities=33%  Similarity=0.491  Sum_probs=29.5

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechh
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      |+...+.+|++|+||||||+++...+...   |.+.+.|+.+
T Consensus        19 G~p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge~vlyvs~~   60 (260)
T COG0467          19 GLPRGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTE   60 (260)
T ss_pred             CCcCCcEEEEEcCCCCcHHHHHHHHHHHHHhcCCcEEEEEec
Confidence            45566669999999999999998877654   5666666533

>PRK05973 replicative DNA helicase; Provisional

Probab=97.10  E-value=0.00043  Score=60.42  Aligned_cols=37  Identities=30%  Similarity=0.350  Sum_probs=27.4

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeec
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVV  225 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~  225 (245)
                      |+.+..-+++.|+||+|||++|-.+|...   |.+.+.++
T Consensus        60 Gl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~Ge~vlyfS   99 (237)
T PRK05973         60 QLKPGDLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFT   99 (237)
T ss_pred             CCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            55566669999999999999888776644   55554454

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.10  E-value=0.00026  Score=61.89  Aligned_cols=32  Identities=31%  Similarity=0.640  Sum_probs=26.5

Q ss_pred             hhhccCCCcc--eeeecCCCCchHHHHHHHHhcc
Q 025979          186 KQIGIDPPRG--VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       186 ~~~g~~~~~g--vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.+.++..+|  +.+.||+|||||+|-+.||.-.
T Consensus        20 ~~i~L~v~~GEfvsilGpSGcGKSTLLriiAGL~   53 (248)
T COG1116          20 EDINLSVEKGEFVAILGPSGCGKSTLLRLIAGLE   53 (248)
T ss_pred             ccceeEECCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            4445555666  8999999999999999999876

>PRK03846 adenylylsulfate kinase; Provisional

Probab=97.09  E-value=0.00054  Score=57.72  Aligned_cols=40  Identities=18%  Similarity=0.202  Sum_probs=31.2

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQK  232 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~~  232 (245)
                      +.-+.|.|+||+|||++|+.|+..+   +...+.+++..+...
T Consensus        24 ~~~i~i~G~~GsGKSTla~~l~~~l~~~~~~~~~ld~d~~~~~   66 (198)
T PRK03846         24 GVVLWFTGLSGSGKSTVAGALEEALHELGVSTYLLDGDNVRHG   66 (198)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhCCCCEEEEcCEeHHhh
Confidence            3448899999999999999999977   445667777665543

>PLN03210 Resistant to P

Probab=97.09  E-value=0.00053  Score=72.17  Aligned_cols=54  Identities=22%  Similarity=0.369  Sum_probs=41.8

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ...+++++|.+...+++...+..           +....+-+-++||+|+|||+||+++++.+..
T Consensus       180 ~~~~~~~vG~~~~l~~l~~lL~l-----------~~~~~~vvgI~G~gGiGKTTLA~~l~~~l~~  233 (1153)
T PLN03210        180 SNDFEDFVGIEDHIAKMSSLLHL-----------ESEEVRMVGIWGSSGIGKTTIARALFSRLSR  233 (1153)
T ss_pred             CcccccccchHHHHHHHHHHHcc-----------ccCceEEEEEEcCCCCchHHHHHHHHHHHhh
Confidence            34567899999988888877643           1223455889999999999999999887643

syringae 6; Provisional

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=97.09  E-value=0.00045  Score=65.40  Aligned_cols=37  Identities=27%  Similarity=0.287  Sum_probs=28.4

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechh
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      .+|..++|+||||+|||+++..+|..+   +..+..+++.
T Consensus        93 ~~p~vI~lvG~~GsGKTTtaakLA~~L~~~g~kV~lV~~D  132 (437)
T PRK00771         93 LKPQTIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVAAD  132 (437)
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEecCC
Confidence            356779999999999999999999876   4444445443

>TIGR01526 nadR_NMN_Atrans nicotinamide-nucleotide adenylyltransferase, NadR type

Probab=97.08  E-value=0.00064  Score=61.96  Aligned_cols=41  Identities=24%  Similarity=0.323  Sum_probs=36.5

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHh
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYL  234 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~  234 (245)
                      +.++|.|+||||||+|++.++..++.+++.-.+.+++....
T Consensus       163 ~~~~~~G~~~~gkstl~~~l~~~~~~~~v~E~~R~~~~~~~  203 (325)
T TIGR01526       163 KTVAILGGESTGKSTLVNKLAAVFNTTSAWEYAREYVEEKL  203 (325)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhhCCCEEeehhHHHHHHhc
Confidence            56999999999999999999999999998888888886664

E. coli NadR has also been found to regulate the import of its substrate, nicotinamide ribonucleotide, but it is not known if the other members of this model share that activity.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=97.08  E-value=0.00059  Score=59.12  Aligned_cols=39  Identities=26%  Similarity=0.313  Sum_probs=26.9

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHh-cc--cceeeeechh
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVAN-HT--TAAFIRVVGS  227 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~-~l--~~~~~~v~~s  227 (245)
                      |+.+..-++++||||||||++|..++. .+  +...+.++..
T Consensus        20 gi~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~g~~~~yi~~e   61 (230)
T PRK08533         20 GIPAGSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVSTQ   61 (230)
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEeCC
Confidence            355555699999999999999755444 32  5556666543

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

Probab=97.07  E-value=0.00084  Score=56.69  Aligned_cols=34  Identities=41%  Similarity=0.530  Sum_probs=25.0

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc---cceeeeechh
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      +-+++.||||||||++.+.++..+   +..++-+.++
T Consensus        19 ~~~~l~G~aGtGKT~~l~~~~~~~~~~g~~v~~~apT   55 (196)
T PF13604_consen   19 RVSVLQGPAGTGKTTLLKALAEALEAAGKRVIGLAPT   55 (196)
T ss_dssp             SEEEEEESTTSTHHHHHHHHHHHHHHTT--EEEEESS
T ss_pred             eEEEEEECCCCCHHHHHHHHHHHHHhCCCeEEEECCc
Confidence            447788999999999999988766   4566666544

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=97.06  E-value=0.00048  Score=54.84  Aligned_cols=23  Identities=35%  Similarity=0.638  Sum_probs=20.5

Q ss_pred             eeeecCCCCchHHHHHHHHhccc
Q 025979          196 VLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      +++.||+|+|||++++.++....
T Consensus         2 i~i~GpsGsGKstl~~~L~~~~~   24 (137)
T cd00071           2 IVLSGPSGVGKSTLLKRLLEEFD   24 (137)
T ss_pred             EEEECCCCCCHHHHHHHHHhcCC
Confidence            57899999999999999998753

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.

>TIGR00455 apsK adenylylsulfate kinase (apsK)

Probab=97.05  E-value=0.00079  Score=55.82  Aligned_cols=40  Identities=20%  Similarity=0.253  Sum_probs=31.4

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQ  231 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~  231 (245)
                      ++.-+++.|+||+|||++|++++..+   +...+.+++..+..
T Consensus        17 ~~~~i~i~G~~GsGKstla~~l~~~l~~~~~~~~~l~~d~~r~   59 (184)
T TIGR00455        17 RGVVIWLTGLSGSGKSTIANALEKKLESKGYRVYVLDGDNVRH   59 (184)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECChHHHh
Confidence            44558899999999999999999987   34456677766654

Important residue (active site in E.coli) is residue 100 of the seed alignment.

>KOG0990 consensus Replication factor C, subunit RFC5 [Replication, recombination and repair]

Probab=97.03  E-value=0.00033  Score=63.29  Aligned_cols=55  Identities=24%  Similarity=0.194  Sum_probs=41.5

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ..+.-...|+++..+.+..+.+++..+             .-...|||||||||||....+.|..+-.
T Consensus        34 kyrP~~l~dv~~~~ei~st~~~~~~~~-------------~lPh~L~YgPPGtGktsti~a~a~~ly~   88 (360)
T KOG0990|consen   34 KYRPPFLGIVIKQEPIWSTENRYSGMP-------------GLPHLLFYGPPGTGKTSTILANARDFYS   88 (360)
T ss_pred             CCCCchhhhHhcCCchhhHHHHhccCC-------------CCCcccccCCCCCCCCCchhhhhhhhcC
Confidence            344456678888888888888775431             1126999999999999999999987744

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=97.03  E-value=0.0003  Score=62.06  Aligned_cols=46  Identities=24%  Similarity=0.487  Sum_probs=34.0

Q ss_pred             hhhccCCCcc--eeeecCCCCchHHHHHHHHhccc--ceeeeechhHHHH
Q 025979          186 KQIGIDPPRG--VLLYGPPGTGKTMLAKAVANHTT--AAFIRVVGSEFVQ  231 (245)
Q Consensus       186 ~~~g~~~~~g--vLl~GPPGtGKT~lAkalA~~l~--~~~~~v~~s~l~~  231 (245)
                      +.+.++.+.|  +.+.||.|||||+|.|++++.+.  .--+.+++.++.+
T Consensus        19 ~~ls~~i~~G~i~~iiGpNG~GKSTLLk~l~g~l~p~~G~V~l~g~~i~~   68 (258)
T COG1120          19 DDLSFSIPKGEITGILGPNGSGKSTLLKCLAGLLKPKSGEVLLDGKDIAS   68 (258)
T ss_pred             ecceEEecCCcEEEEECCCCCCHHHHHHHHhccCCCCCCEEEECCCchhh
Confidence            3344444555  88999999999999999999885  3356677766654

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=97.03  E-value=0.00052  Score=62.60  Aligned_cols=28  Identities=32%  Similarity=0.430  Sum_probs=24.8

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      ..+.++||+||+|+|||++|+++|..+.
T Consensus        19 r~~hA~Lf~G~~G~GK~~la~~~a~~ll   46 (325)
T PRK08699         19 RRPNAWLFAGKKGIGKTAFARFAAQALL   46 (325)
T ss_pred             CcceEEEeECCCCCCHHHHHHHHHHHHc
Confidence            4567899999999999999999998863

>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=97.02  E-value=0.00061  Score=57.26  Aligned_cols=26  Identities=50%  Similarity=0.865  Sum_probs=23.0

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +...++++||.|+|||++++.+.+.+
T Consensus        19 ~~~~~~l~G~rg~GKTsLl~~~~~~~   44 (234)
T PF01637_consen   19 PSQHILLYGPRGSGKTSLLKEFINEL   44 (234)
T ss_dssp             -SSEEEEEESTTSSHHHHHHHHHHHC
T ss_pred             cCcEEEEEcCCcCCHHHHHHHHHHHh
Confidence            34669999999999999999999988

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

>PRK12337 2-phosphoglycerate kinase; Provisional

Probab=97.02  E-value=0.00067  Score=64.44  Aligned_cols=43  Identities=28%  Similarity=0.407  Sum_probs=32.9

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccce-eeeechh-HHHHHHh
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAA-FIRVVGS-EFVQKYL  234 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~-~~~v~~s-~l~~~~~  234 (245)
                      .|.-++++|+||||||++|..+|..+++. +++.|.- +.+-.++
T Consensus       254 ~p~vil~~G~~G~GKSt~a~~LA~~lg~~~ii~tD~iR~~lr~~i  298 (475)
T PRK12337        254 RPLHVLIGGVSGVGKSVLASALAYRLGITRIVSTDAVREVLRAMV  298 (475)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHcCCcEEeehhHHHHHHHhhc
Confidence            46679999999999999999999999986 5555542 4343333

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=97.01  E-value=0.00094  Score=59.42  Aligned_cols=36  Identities=28%  Similarity=0.445  Sum_probs=26.8

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc---cceeeeech
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVG  226 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~  226 (245)
                      .+++-++|+||||+|||+++..+|..+   +..+.-+++
T Consensus        70 ~~~~vi~l~G~~G~GKTTt~akLA~~l~~~g~~V~li~~  108 (272)
T TIGR00064        70 NKPNVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLAAG  108 (272)
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEeC
Confidence            345668899999999999999888766   444444443

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.

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=97.00  E-value=0.00043  Score=63.20  Aligned_cols=28  Identities=39%  Similarity=0.592  Sum_probs=24.9

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      .+.++||+||+|+|||++|+++|+.+.+
T Consensus        21 ~~ha~Lf~G~~G~GK~~~A~~~A~~llC   48 (328)
T PRK05707         21 HPHAYLLHGPAGIGKRALAERLAAALLC   48 (328)
T ss_pred             cceeeeeECCCCCCHHHHHHHHHHHHcC
Confidence            4677999999999999999999998744

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=97.00  E-value=0.00065  Score=58.23  Aligned_cols=40  Identities=23%  Similarity=0.318  Sum_probs=29.0

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---------cceeeeechhH
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---------TAAFIRVVGSE  228 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---------~~~~~~v~~s~  228 (245)
                      |+....-+.++||||||||++|..+|...         +...+.++..+
T Consensus        15 Gi~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~   63 (235)
T cd01123          15 GIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEG   63 (235)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCC
Confidence            45555558999999999999999997442         25666666543

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 .

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=96.99  E-value=0.00074  Score=51.84  Aligned_cols=25  Identities=40%  Similarity=0.519  Sum_probs=21.7

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHH
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVA  214 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA  214 (245)
                      +.+...++|.||+|+|||+|++++.
T Consensus        12 i~~ge~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          12 VYGKVGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             EcCCEEEEEEcCCCCCHHHHHHHhh
Confidence            3455669999999999999999987

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

>KOG1970 consensus Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=96.99  E-value=0.00071  Score=65.01  Aligned_cols=31  Identities=29%  Similarity=0.420  Sum_probs=27.0

Q ss_pred             ceeeecCCCCchHHHHHHHHhcccceeeeec
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTTAAFIRVV  225 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~  225 (245)
                      -+||.||+|||||+..+.++.++|..+..-+
T Consensus       112 iLLltGPsGcGKSTtvkvLskelg~~~~Ew~  142 (634)
T KOG1970|consen  112 ILLLTGPSGCGKSTTVKVLSKELGYQLIEWS  142 (634)
T ss_pred             EEEEeCCCCCCchhHHHHHHHhhCceeeeec
Confidence            3788999999999999999999987776554

>TIGR00376 DNA helicase, putative

Probab=96.95  E-value=0.00097  Score=66.07  Aligned_cols=41  Identities=22%  Similarity=0.340  Sum_probs=28.9

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc---cceeeeec-----hhHHHHHHh
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVV-----GSEFVQKYL  234 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~-----~s~l~~~~~  234 (245)
                      ..++++||||||||+++.++...+   |..++.++     ...+.++..
T Consensus       174 ~~~lI~GpPGTGKT~t~~~ii~~~~~~g~~VLv~a~sn~Avd~l~e~l~  222 (637)
T TIGR00376       174 DLFLIHGPPGTGKTRTLVELIRQLVKRGLRVLVTAPSNIAVDNLLERLA  222 (637)
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEEcCcHHHHHHHHHHHH
Confidence            348899999999999888777654   55666666     334555544

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.

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=96.95  E-value=0.00097  Score=60.65  Aligned_cols=35  Identities=26%  Similarity=0.350  Sum_probs=26.4

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc---cceeeeech
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVG  226 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~  226 (245)
                      .+.-++|+||||+|||+++..+|..+   +..+..+++
T Consensus       113 ~~~vi~lvGpnGsGKTTt~~kLA~~l~~~g~~V~Li~~  150 (318)
T PRK10416        113 KPFVILVVGVNGVGKTTTIGKLAHKYKAQGKKVLLAAG  150 (318)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHhcCCeEEEEec
Confidence            34558899999999999999999876   334444443

>PRK04328 hypothetical protein; Provisional

Probab=96.93  E-value=0.00089  Score=58.64  Aligned_cols=38  Identities=32%  Similarity=0.392  Sum_probs=26.9

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhc-c--cceeeeech
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANH-T--TAAFIRVVG  226 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~-l--~~~~~~v~~  226 (245)
                      |+.++..+|++||||||||.+|-.++.. +  |-+.+.++.
T Consensus        19 Gip~gs~ili~G~pGsGKT~l~~~fl~~~~~~ge~~lyis~   59 (249)
T PRK04328         19 GIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGVYVAL   59 (249)
T ss_pred             CCcCCcEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEEe
Confidence            4555566999999999999998876543 2  445555543

>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=96.91  E-value=0.00091  Score=58.77  Aligned_cols=25  Identities=44%  Similarity=0.517  Sum_probs=22.0

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ..+-+.++|++|+|||+||+.+++.
T Consensus        18 ~~~~v~I~G~~G~GKT~LA~~~~~~   42 (287)
T PF00931_consen   18 EVRVVAIVGMGGIGKTTLARQVARD   42 (287)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHCH
T ss_pred             CeEEEEEEcCCcCCcceeeeecccc
Confidence            3455889999999999999999987

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.

>smart00350 MCM minichromosome maintenance proteins

Probab=96.90  E-value=0.001  Score=64.14  Aligned_cols=25  Identities=40%  Similarity=0.615  Sum_probs=22.5

Q ss_pred             ceeeecCCCCchHHHHHHHHhcccc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      .+||+|+||||||.+|+++++....
T Consensus       238 ~vLL~G~pGtGKs~lar~l~~~~~r  262 (509)
T smart00350      238 NILLLGDPGTAKSQLLKYVEKTAPR  262 (509)
T ss_pred             eEEEeCCCChhHHHHHHHHHHHcCc
Confidence            4999999999999999999987743

>PRK07667 uridine kinase; Provisional

Probab=96.89  E-value=0.00075  Score=56.73  Aligned_cols=35  Identities=14%  Similarity=0.234  Sum_probs=27.5

Q ss_pred             eeeecCCCCchHHHHHHHHhcc---cceeeeechhHHH
Q 025979          196 VLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFV  230 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~  230 (245)
                      |.+.|+||+|||++|+.|+..+   +.+...++..++.
T Consensus        20 IgI~G~~gsGKStla~~L~~~l~~~~~~~~~i~~Dd~~   57 (193)
T PRK07667         20 LGIDGLSRSGKTTFVANLKENMKQEGIPFHIFHIDDYI   57 (193)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEEcCccc
Confidence            6789999999999999999987   3455556665543

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=96.88  E-value=0.00086  Score=57.73  Aligned_cols=37  Identities=22%  Similarity=0.391  Sum_probs=28.9

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc----cceeeeec
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT----TAAFIRVV  225 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l----~~~~~~v~  225 (245)
                      |+.+..-+++.||||+|||+++..+|...    +.+++.++
T Consensus         9 Gl~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s   49 (242)
T cd00984           9 GLQPGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFS   49 (242)
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEe
Confidence            66666669999999999999998887654    56666665

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.

>PRK05537 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Validated

Probab=96.87  E-value=0.0011  Score=64.95  Aligned_cols=41  Identities=22%  Similarity=0.291  Sum_probs=32.3

Q ss_pred             ceeeecCCCCchHHHHHHHHhcccc----eeeeechhHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTTA----AFIRVVGSEFVQKYLG  235 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~~----~~~~v~~s~l~~~~~G  235 (245)
                      -++|+|+||+|||++|++||..++.    +++.+++..+.....|
T Consensus       394 ~Ivl~Gl~GSGKSTia~~La~~L~~~~g~~~~~lD~D~vr~~l~g  438 (568)
T PRK05537        394 TVFFTGLSGAGKSTIAKALMVKLMEMRGRPVTLLDGDVVRKHLSS  438 (568)
T ss_pred             EEEEECCCCChHHHHHHHHHHHhhhccCceEEEeCCcHHHHhccC
Confidence            3889999999999999999999875    4566777766544444

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

Probab=96.87  E-value=0.00095  Score=60.87  Aligned_cols=39  Identities=23%  Similarity=0.307  Sum_probs=28.7

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhH
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSE  228 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~  228 (245)
                      +...+-+.+|||||||||+||-.++...   +...+.++..+
T Consensus        52 lp~G~iteI~Gp~GsGKTtLal~~~~~~~~~g~~~vyId~E~   93 (325)
T cd00983          52 YPKGRIIEIYGPESSGKTTLALHAIAEAQKLGGTVAFIDAEH   93 (325)
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEECccc
Confidence            4444448899999999999999877543   56667776543

RecA couples ATP hydrolysis to DNA strand exchange.

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=96.87  E-value=0.0013  Score=49.98  Aligned_cols=35  Identities=29%  Similarity=0.372  Sum_probs=25.6

Q ss_pred             cceeeecCCCCchHHHHHHHHhccc-----ceeeeechhH
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTT-----AAFIRVVGSE  228 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~-----~~~~~v~~s~  228 (245)
                      ++++++||||+|||+++-.++..+.     ..++.+.++.
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~~~~~~lv~~p~~   40 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTR   40 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhcccCCCEEEEcCcH
Confidence            3689999999999998888777663     4455554443

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

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

Probab=96.85  E-value=0.001  Score=56.70  Aligned_cols=39  Identities=26%  Similarity=0.346  Sum_probs=29.2

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---c------ceeeeechh
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---T------AAFIRVVGS  227 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~------~~~~~v~~s  227 (245)
                      |+....-+.++||||+|||++|..+|...   +      ...+.++..
T Consensus        15 G~~~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e   62 (226)
T cd01393          15 GIPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTE   62 (226)
T ss_pred             CCcCCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecC
Confidence            45555558999999999999999988653   3      556666654

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.

>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=96.85  E-value=0.00058  Score=61.49  Aligned_cols=40  Identities=35%  Similarity=0.610  Sum_probs=35.8

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhccc--ceeeeechhHHHH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTT--AAFIRVVGSEFVQ  231 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~--~~~~~v~~s~l~~  231 (245)
                      ..+.+|+.|+||||||.+|-.+|+.+|  .||..+++|++.+
T Consensus        65 aGraiLiaG~pgtGKtAiAmg~sksLG~~tpF~~i~gSEI~S  106 (454)
T KOG2680|consen   65 AGRAILIAGQPGTGKTAIAMGMSKSLGDDTPFTSISGSEIYS  106 (454)
T ss_pred             cceEEEEecCCCCCceeeeeehhhhhCCCCceeeeecceeee
Confidence            457799999999999999999999995  6999999999864

>PRK14738 gmk guanylate kinase; Provisional

Probab=96.84  E-value=0.00082  Score=57.11  Aligned_cols=24  Identities=29%  Similarity=0.549  Sum_probs=20.4

Q ss_pred             CcceeeecCCCCchHHHHHHHHhc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ++-++|.||||||||+|+++|+..
T Consensus        13 ~~~ivi~GpsG~GK~tl~~~L~~~   36 (206)
T PRK14738         13 PLLVVISGPSGVGKDAVLARMRER   36 (206)
T ss_pred             CeEEEEECcCCCCHHHHHHHHHhc
Confidence            344889999999999999999753

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=96.84  E-value=0.00087  Score=55.91  Aligned_cols=28  Identities=29%  Similarity=0.558  Sum_probs=24.1

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.....+++.||+|+|||++.++++..+
T Consensus        22 v~~g~~i~I~G~tGSGKTTll~aL~~~i   49 (186)
T cd01130          22 VEARKNILISGGTGSGKTTLLNALLAFI   49 (186)
T ss_pred             HhCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            3445669999999999999999999876

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.

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=96.82  E-value=0.0013  Score=56.18  Aligned_cols=39  Identities=18%  Similarity=0.216  Sum_probs=28.0

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechh
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      |+.+..-+++.||||+|||.+|..++...   +.+.+.++..
T Consensus        12 Gi~~g~~~li~G~~G~GKt~~~~~~~~~~~~~g~~~~y~s~e   53 (224)
T TIGR03880        12 GFPEGHVIVVIGEYGTGKTTFSLQFLYQGLKNGEKAMYISLE   53 (224)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECC
Confidence            45555559999999999999998887542   5555555543

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.

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]

Probab=96.82  E-value=0.0016  Score=62.55  Aligned_cols=66  Identities=26%  Similarity=0.367  Sum_probs=52.5

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHH
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFV  230 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~  230 (245)
                      ...+|++++|-..+..++.+.+..           .-..+..||++|-+||||.++|++|=+..   +.||+.++|..+-
T Consensus       240 a~y~f~~Iig~S~~m~~~~~~akr-----------~A~tdstVLi~GESGTGKElfA~~IH~~S~R~~~PFIaiNCaAiP  308 (560)
T COG3829         240 AKYTFDDIIGESPAMLRVLELAKR-----------IAKTDSTVLILGESGTGKELFARAIHNLSPRANGPFIAINCAAIP  308 (560)
T ss_pred             cccchhhhccCCHHHHHHHHHHHh-----------hcCCCCcEEEecCCCccHHHHHHHHHhcCcccCCCeEEEecccCC
Confidence            346789999998887777776654           12345669999999999999999997765   7899999987653

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=96.81  E-value=0.00078  Score=53.01  Aligned_cols=31  Identities=29%  Similarity=0.390  Sum_probs=24.8

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhccccee
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTTAAF  221 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~  221 (245)
                      ++..-|+|+|+=|+|||+++|++++.+|..-
T Consensus        13 ~~g~vi~L~GdLGaGKTtf~r~l~~~lg~~~   43 (123)
T PF02367_consen   13 KPGDVILLSGDLGAGKTTFVRGLARALGIDE   43 (123)
T ss_dssp             SS-EEEEEEESTTSSHHHHHHHHHHHTT--S
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHcCCCC
Confidence            4445599999999999999999999997654

They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.81  E-value=0.00084  Score=62.32  Aligned_cols=26  Identities=31%  Similarity=0.399  Sum_probs=22.3

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+..++|+||||||||+++..||..+
T Consensus       136 ~g~ii~lvGptGvGKTTtiakLA~~~  161 (374)
T PRK14722        136 RGGVFALMGPTGVGKTTTTAKLAARC  161 (374)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            34559999999999999999999764

>PRK04220 2-phosphoglycerate kinase; Provisional

Probab=96.80  E-value=0.0011  Score=59.90  Aligned_cols=31  Identities=23%  Similarity=0.314  Sum_probs=27.3

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhccccee
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTTAAF  221 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~  221 (245)
                      ..|--+++.||||||||++|..||..++.+.
T Consensus        90 ~~p~iIlI~G~sgsGKStlA~~La~~l~~~~  120 (301)
T PRK04220         90 KEPIIILIGGASGVGTSTIAFELASRLGIRS  120 (301)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhCCCE
Confidence            3456699999999999999999999998873

>PRK11823 DNA repair protein RadA; Provisional

Probab=96.80  E-value=0.0012  Score=62.64  Aligned_cols=43  Identities=35%  Similarity=0.475  Sum_probs=33.1

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHH
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQ  231 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~  231 (245)
                      |+.+..-++++||||+|||+++..+|...   +.+.+++++.+-.+
T Consensus        76 Gi~~Gs~~lI~G~pG~GKTtL~lq~a~~~a~~g~~vlYvs~Ees~~  121 (446)
T PRK11823         76 GLVPGSVVLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVSGEESAS  121 (446)
T ss_pred             CccCCEEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEccccHH
Confidence            45555559999999999999999998765   56777887765443

>PLN02840 tRNA dimethylallyltransferase

Probab=96.79  E-value=0.0011  Score=62.34  Aligned_cols=32  Identities=28%  Similarity=0.500  Sum_probs=28.6

Q ss_pred             eeeecCCCCchHHHHHHHHhcccceeeeechh
Q 025979          196 VLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS  227 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s  227 (245)
                      +++.||+|+|||++|..||..++..++.++.-
T Consensus        24 i~I~GptgsGKTtla~~La~~~~~~iis~Ds~   55 (421)
T PLN02840         24 IVISGPTGAGKSRLALELAKRLNGEIISADSV   55 (421)
T ss_pred             EEEECCCCCCHHHHHHHHHHHCCCCeEecccc
Confidence            88999999999999999999999888777653

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=96.78  E-value=0.0015  Score=54.59  Aligned_cols=39  Identities=18%  Similarity=0.260  Sum_probs=33.9

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQ  231 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~  231 (245)
                      +.-+.|.|.+|+|||++|.+++..|   |...+.+||..+-.
T Consensus        23 ~~viW~TGLSGsGKSTiA~ale~~L~~~G~~~y~LDGDnvR~   64 (197)
T COG0529          23 GAVIWFTGLSGSGKSTIANALEEKLFAKGYHVYLLDGDNVRH   64 (197)
T ss_pred             CeEEEeecCCCCCHHHHHHHHHHHHHHcCCeEEEecChhHhh
Confidence            3447799999999999999999987   88999999988753

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=96.78  E-value=0.0012  Score=59.34  Aligned_cols=40  Identities=20%  Similarity=0.326  Sum_probs=28.9

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---------cceeeeechhH
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---------TAAFIRVVGSE  228 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---------~~~~~~v~~s~  228 (245)
                      |+..+.-++++||||||||.+|-.+|...         +...+.|+..+
T Consensus        91 Gi~~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~  139 (310)
T TIGR02236        91 GIETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTEN  139 (310)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCC
Confidence            44444448899999999999999887552         23666676544

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.

>COG3839 MalK ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]

Probab=96.77  E-value=0.00061  Score=62.34  Aligned_cols=28  Identities=39%  Similarity=0.714  Sum_probs=23.1

Q ss_pred             cCCCcc--eeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRG--VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~g--vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +....|  +.|.||+|||||++.|.||.-.
T Consensus        24 l~i~~Gef~vllGPSGcGKSTlLr~IAGLe   53 (338)
T COG3839          24 LDIEDGEFVVLLGPSGCGKSTLLRMIAGLE   53 (338)
T ss_pred             EEEcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            333444  8899999999999999999865

>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=96.77  E-value=0.0015  Score=57.50  Aligned_cols=55  Identities=25%  Similarity=0.426  Sum_probs=37.2

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      ....++++++-.....+.+.+++...           +.....+++.||+|+|||++.+++...+.
T Consensus        98 ~~~~sle~l~~~~~~~~~~~~~l~~~-----------v~~~~~ili~G~tGSGKTT~l~all~~i~  152 (270)
T PF00437_consen   98 SKPFSLEDLGESGSIPEEIAEFLRSA-----------VRGRGNILISGPTGSGKTTLLNALLEEIP  152 (270)
T ss_dssp             SS--CHCCCCHTHHCHHHHHHHHHHC-----------HHTTEEEEEEESTTSSHHHHHHHHHHHCH
T ss_pred             cccccHhhccCchhhHHHHHHHHhhc-----------cccceEEEEECCCccccchHHHHHhhhcc
Confidence            34456667665555555666555441           12345699999999999999999998873

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 ....

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=96.76  E-value=0.0013  Score=62.97  Aligned_cols=39  Identities=26%  Similarity=0.305  Sum_probs=29.2

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhc----ccceeeeechh
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANH----TTAAFIRVVGS  227 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~----l~~~~~~v~~s  227 (245)
                      |+.+++.+|+.||||||||++|..++.+    .|-+.+.|+..
T Consensus        17 Glp~g~~~Li~G~pGsGKT~la~qfl~~g~~~~ge~~lyvs~e   59 (484)
T TIGR02655        17 GLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIHFDEPGVFVTFE   59 (484)
T ss_pred             CCCCCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEEEe
Confidence            5666677999999999999999987532    24566666544

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.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.74  E-value=0.0015  Score=61.09  Aligned_cols=26  Identities=35%  Similarity=0.456  Sum_probs=22.2

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .|+-++|+||+|+|||+++.-+|..+
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~~  198 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAIY  198 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            35569999999999999999898754

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=96.72  E-value=0.0022  Score=57.77  Aligned_cols=26  Identities=35%  Similarity=0.576  Sum_probs=23.3

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..+++++.||+|+|||++++++.+.+
T Consensus       131 ~~~~ilI~G~tGSGKTTll~al~~~i  156 (299)
T TIGR02782       131 ARKNILVVGGTGSGKTTLANALLAEI  156 (299)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHHh
Confidence            44679999999999999999999876

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.

>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=96.72  E-value=0.00089  Score=52.36  Aligned_cols=29  Identities=41%  Similarity=0.602  Sum_probs=24.6

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      +.+..-+.++||+|+|||+|.++++....
T Consensus         8 i~~g~~~~i~G~nGsGKStLl~~l~g~~~   36 (137)
T PF00005_consen    8 IKPGEIVAIVGPNGSGKSTLLKALAGLLP   36 (137)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHTTSSH
T ss_pred             EcCCCEEEEEccCCCccccceeeeccccc
Confidence            34555689999999999999999999873

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 ....

>PRK10536 hypothetical protein; Provisional

Probab=96.71  E-value=0.0014  Score=57.87  Aligned_cols=22  Identities=32%  Similarity=0.427  Sum_probs=20.0

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -+++.||+|||||+||.++|-.
T Consensus        76 lV~i~G~aGTGKT~La~a~a~~   97 (262)
T PRK10536         76 LIFATGEAGCGKTWISAAKAAE   97 (262)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            4888999999999999999984

>COG1855 ATPase (PilT family) [General function prediction only]

Probab=96.71  E-value=0.0013  Score=62.06  Aligned_cols=25  Identities=40%  Similarity=0.784  Sum_probs=23.2

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..|+|+.||||.|||++|+|+|..+
T Consensus       263 aeGILIAG~PGaGKsTFaqAlAefy  287 (604)
T COG1855         263 AEGILIAGAPGAGKSTFAQALAEFY  287 (604)
T ss_pred             hcceEEecCCCCChhHHHHHHHHHH
Confidence            3789999999999999999999877

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=96.71  E-value=0.0011  Score=60.93  Aligned_cols=29  Identities=31%  Similarity=0.442  Sum_probs=25.9

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ..+.++||+||+|+||+.+|+++|..+.+
T Consensus        19 rl~ha~Lf~Gp~G~GK~~lA~~~A~~LlC   47 (342)
T PRK06964         19 RLPHALLLHGQAGIGKLDFAQHLAQGLLC   47 (342)
T ss_pred             CcceEEEEECCCCCCHHHHHHHHHHHHcC
Confidence            46778999999999999999999988754

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.70  E-value=0.0031  Score=59.39  Aligned_cols=26  Identities=31%  Similarity=0.483  Sum_probs=21.8

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++-++|.||+|||||+++..+|...
T Consensus       222 ~~~vi~lvGptGvGKTTtaaKLA~~~  247 (432)
T PRK12724        222 QRKVVFFVGPTGSGKTTSIAKLAAKY  247 (432)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            34458899999999999999999754

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=96.70  E-value=0.0015  Score=60.45  Aligned_cols=30  Identities=40%  Similarity=0.744  Sum_probs=26.5

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ..+|+|+.||||+|+|||+|.-...+.+..
T Consensus        59 ~~~~~GlYl~G~vG~GKT~Lmd~f~~~lp~   88 (362)
T PF03969_consen   59 PPPPKGLYLWGPVGRGKTMLMDLFYDSLPI   88 (362)
T ss_pred             CCCCceEEEECCCCCchhHHHHHHHHhCCc
Confidence            457999999999999999999998887744

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=96.70  E-value=0.0024  Score=59.33  Aligned_cols=49  Identities=33%  Similarity=0.460  Sum_probs=34.3

Q ss_pred             cHHHHhhh--ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHH
Q 025979          181 HHELYKQI--GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEF  229 (245)
Q Consensus       181 ~~~~~~~~--g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l  229 (245)
                      .+++.+-+  |+.+..-++++||||+|||+++..+|...   +.+.+.+++.+-
T Consensus        68 i~eLD~vLgGGi~~GslvLI~G~pG~GKStLllq~a~~~a~~g~~VlYvs~EEs  121 (372)
T cd01121          68 IEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVSGEES  121 (372)
T ss_pred             CHHHHHhhcCCccCCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEECCcC
Confidence            33444444  45555559999999999999999988765   356777776543

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.

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=96.69  E-value=0.0013  Score=64.71  Aligned_cols=34  Identities=35%  Similarity=0.488  Sum_probs=29.1

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccc--eeeeechh
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTA--AFIRVVGS  227 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~--~~~~v~~s  227 (245)
                      .+|||.|+||||||++|++++..+..  +|+++..+
T Consensus        17 g~vLl~G~~GtgKs~lar~l~~~~~~~~pfv~i~~~   52 (589)
T TIGR02031        17 GGVAIRARAGTGKTALARALAEILPPIMPFVELPLG   52 (589)
T ss_pred             ceEEEEcCCCcHHHHHHHHHHHhCCcCCCeEecCcc
Confidence            35999999999999999999998754  68888753

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.

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

Probab=96.68  E-value=0.0015  Score=57.23  Aligned_cols=38  Identities=18%  Similarity=0.183  Sum_probs=28.6

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc----cceeeeech
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT----TAAFIRVVG  226 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l----~~~~~~v~~  226 (245)
                      |+.+..-+++.||||+|||+++..+|..+    +.+++.++.
T Consensus        26 G~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~~g~~vl~iS~   67 (271)
T cd01122          26 GLRKGELIILTAGTGVGKTTFLREYALDLITQHGVRVGTISL   67 (271)
T ss_pred             EEcCCcEEEEEcCCCCCHHHHHHHHHHHHHHhcCceEEEEEc
Confidence            45565668999999999999999887654    556555554

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

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=96.67  E-value=0.002  Score=58.77  Aligned_cols=26  Identities=35%  Similarity=0.515  Sum_probs=23.2

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..+++|+.||+|+|||++.++++...
T Consensus       143 ~~~nilI~G~tGSGKTTll~aL~~~i  168 (323)
T PRK13833        143 SRLNIVISGGTGSGKTTLANAVIAEI  168 (323)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHHH
Confidence            44679999999999999999999875

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.66  E-value=0.0021  Score=60.15  Aligned_cols=26  Identities=31%  Similarity=0.411  Sum_probs=22.8

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++-++|+||+|+|||+++..||..+
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~~L  265 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAWQF  265 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHHHH
Confidence            34669999999999999999999766

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=96.64  E-value=0.0012  Score=62.18  Aligned_cols=26  Identities=27%  Similarity=0.571  Sum_probs=23.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ....++++.||||||||++|.+++..
T Consensus       207 e~~~Nli~lGp~GTGKThla~~l~~~  232 (449)
T TIGR02688       207 EPNYNLIELGPKGTGKSYIYNNLSPY  232 (449)
T ss_pred             hcCCcEEEECCCCCCHHHHHHHHhHH
Confidence            45567999999999999999998877

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.63  E-value=0.002  Score=60.01  Aligned_cols=51  Identities=18%  Similarity=0.139  Sum_probs=34.9

Q ss_pred             chhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          164 CDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       164 l~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+.+...+.+.+...+..+..+   .+.+++-++|+||+|||||+++..+|..+
T Consensus       180 ~~~v~~~~~~~L~~~l~~~~~~---~~~~~~ii~lvGptGvGKTTt~akLA~~l  230 (407)
T PRK12726        180 LDDITDWFVPYLSGKLAVEDSF---DLSNHRIISLIGQTGVGKTTTLVKLGWQL  230 (407)
T ss_pred             HHHHHHHHHHHhcCcEeeCCCc---eecCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4566667776665433222211   23456669999999999999999998765

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

Probab=96.63  E-value=0.0032  Score=55.76  Aligned_cols=47  Identities=26%  Similarity=0.426  Sum_probs=34.2

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcc-eeeecCCCCchHHHHHHHHhcc
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRG-VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~g-vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++++++-...+.+.+.+++..               ++| +++.||+|+|||++.+++...+
T Consensus        57 ~~l~~lg~~~~~~~~l~~~~~~---------------~~GlilisG~tGSGKTT~l~all~~i  104 (264)
T cd01129          57 LDLEKLGLKPENLEIFRKLLEK---------------PHGIILVTGPTGSGKTTTLYSALSEL  104 (264)
T ss_pred             CCHHHcCCCHHHHHHHHHHHhc---------------CCCEEEEECCCCCcHHHHHHHHHhhh
Confidence            3456776555666666655543               244 8999999999999999998766

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.

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=96.62  E-value=0.0018  Score=58.59  Aligned_cols=40  Identities=23%  Similarity=0.348  Sum_probs=28.7

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---------cceeeeechhH
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---------TAAFIRVVGSE  228 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---------~~~~~~v~~s~  228 (245)
                      |+..+.-++++||||||||.+|-.+|...         +...+.|+..+
T Consensus        98 Gi~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~  146 (317)
T PRK04301         98 GIETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEG  146 (317)
T ss_pred             CccCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCC
Confidence            45555558899999999999999888553         33566666443

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.62  E-value=0.0039  Score=56.79  Aligned_cols=25  Identities=40%  Similarity=0.683  Sum_probs=22.6

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ..+++++.||||+|||+++++++..
T Consensus       147 ~~~~ilI~G~tGSGKTTll~aL~~~  171 (319)
T PRK13894        147 AHRNILVIGGTGSGKTTLVNAIINE  171 (319)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHh
Confidence            4567999999999999999999976

>PTZ00202 tuzin; Provisional

Probab=96.61  E-value=0.004  Score=59.08  Aligned_cols=58  Identities=17%  Similarity=0.243  Sum_probs=44.7

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeech
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVG  226 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~  226 (245)
                      .+..|-+....++...+..          .....++-+.|.||+|||||++++.++..++.+.+.++.
T Consensus       262 ~~FVGReaEla~Lr~VL~~----------~d~~~privvLtG~~G~GKTTLlR~~~~~l~~~qL~vNp  319 (550)
T PTZ00202        262 RQFVSREAEESWVRQVLRR----------LDTAHPRIVVFTGFRGCGKSSLCRSAVRKEGMPAVFVDV  319 (550)
T ss_pred             cCCCCcHHHHHHHHHHHhc----------cCCCCceEEEEECCCCCCHHHHHHHHHhcCCceEEEECC
Confidence            4788889888888887753          122344557899999999999999999998876665554

>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=96.58  E-value=0.0014  Score=55.62  Aligned_cols=28  Identities=29%  Similarity=0.484  Sum_probs=23.7

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.++|+..+
T Consensus        27 i~~G~~~~l~G~nGsGKSTLl~~i~Gl~   54 (218)
T cd03255          27 IEKGEFVAIVGPSGSGKSTLLNILGGLD   54 (218)
T ss_pred             EcCCCEEEEEcCCCCCHHHHHHHHhCCc
Confidence            3444558999999999999999999876

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.

>cd01918 HprK_C 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

Probab=96.58  E-value=0.0016  Score=52.91  Aligned_cols=24  Identities=42%  Similarity=0.660  Sum_probs=21.7

Q ss_pred             CcceeeecCCCCchHHHHHHHHhc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .+|+||.||+|+|||++|.++...
T Consensus        14 g~gvLi~G~sG~GKStlal~L~~~   37 (149)
T cd01918          14 GIGVLITGPSGIGKSELALELIKR   37 (149)
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHc
Confidence            578999999999999999988775

It catalyzes both the ATP-dependent phosphorylation of Ser-46 of HPr and its dephosphorylation by phosphorolysis. The latter reaction uses inorganic phosphate as substrate and produces pyrophosphate. Phosphoenolpyruvate carboxykinase (PEPCK) and the C-terminal catalytic domain of HprK/P are structurally similar with conserved active site residues suggesting these two phosphotransferases have related functions. The HprK/P N-terminal domain is structurally similar to the N-terminal domains of the MurE and MurF amino acid ligases.

>PRK09354 recA recombinase A; Provisional

Probab=96.57  E-value=0.0022  Score=59.02  Aligned_cols=39  Identities=26%  Similarity=0.316  Sum_probs=28.4

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhH
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSE  228 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~  228 (245)
                      +...+-+++|||||||||+||-.++...   +...+.|+..+
T Consensus        57 ip~G~IteI~G~~GsGKTtLal~~~~~~~~~G~~~~yId~E~   98 (349)
T PRK09354         57 LPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEH   98 (349)
T ss_pred             CcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECCcc
Confidence            4444448899999999999998766443   66667777554

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=96.57  E-value=0.0015  Score=60.06  Aligned_cols=30  Identities=30%  Similarity=0.489  Sum_probs=26.0

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      .+...+++|+.||+|+|||+++++++..+.
T Consensus       158 ~v~~~~nilI~G~tGSGKTTll~aLl~~i~  187 (344)
T PRK13851        158 CVVGRLTMLLCGPTGSGKTTMSKTLISAIP  187 (344)
T ss_pred             HHHcCCeEEEECCCCccHHHHHHHHHcccC
Confidence            455667899999999999999999998873

>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways

Probab=96.56  E-value=0.0016  Score=52.58  Aligned_cols=24  Identities=42%  Similarity=0.803  Sum_probs=21.1

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++|.||+|||||+|+++|-..-
T Consensus         2 krimliG~~g~GKTTL~q~L~~~~   25 (143)
T PF10662_consen    2 KRIMLIGPSGSGKTTLAQALNGEE   25 (143)
T ss_pred             ceEEEECCCCCCHHHHHHHHcCCC
Confidence            458999999999999999998644

Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process

>PRK13477 bifunctional pantoate ligase/cytidylate kinase; Provisional

Probab=96.56  E-value=0.0019  Score=62.33  Aligned_cols=29  Identities=28%  Similarity=0.537  Sum_probs=25.1

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceee
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFI  222 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~  222 (245)
                      .-+.+.||+|||||++|+.||+.++..++
T Consensus       285 ~ii~i~G~sgsGKst~a~~la~~l~~~~~  313 (512)
T PRK13477        285 PIIAIDGPAGAGKSTVTRAVAKKLGLLYL  313 (512)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCCeEe
Confidence            34889999999999999999999986553

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=96.55  E-value=0.0026  Score=57.87  Aligned_cols=26  Identities=42%  Similarity=0.704  Sum_probs=23.6

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .|.++||+||+|+||+++|.++|..+
T Consensus        25 l~HA~Lf~Gp~G~GK~~lA~~lA~~L   50 (319)
T PRK08769         25 LGHGLLICGPEGLGKRAVALALAEHV   50 (319)
T ss_pred             cceeEeeECCCCCCHHHHHHHHHHHH
Confidence            55679999999999999999999876

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=96.55  E-value=0.0027  Score=60.17  Aligned_cols=61  Identities=28%  Similarity=0.388  Sum_probs=44.3

Q ss_pred             eccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHH
Q 025979          158 YNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEF  229 (245)
Q Consensus       158 ~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l  229 (245)
                      +.++.|-......+.+.+..          . ......+++.|++|||||++|+++....   +.+|+.++++.+
T Consensus       137 ~~~lig~s~~~~~l~~~~~~----------~-~~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~i~i~c~~~  200 (469)
T PRK10923        137 TTDIIGEAPAMQDVFRIIGR----------L-SRSSISVLINGESGTGKELVAHALHRHSPRAKAPFIALNMAAI  200 (469)
T ss_pred             cccceecCHHHHHHHHHHHH----------H-hccCCeEEEEeCCCCcHHHHHHHHHhcCCCCCCCeEeeeCCCC
Confidence            34567766666666555542          0 1223459999999999999999998876   578999998765

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

Probab=96.54  E-value=0.002  Score=56.63  Aligned_cols=28  Identities=36%  Similarity=0.513  Sum_probs=24.1

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      .+..++++||+|||||++++.+++.+..
T Consensus        15 ~Gqr~~I~G~~G~GKTTLlr~I~n~l~~   42 (249)
T cd01128          15 KGQRGLIVAPPKAGKTTLLQSIANAITK   42 (249)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcccc
Confidence            4455999999999999999999988754

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.

>COG0802 Predicted ATPase or kinase [General function prediction only]

Probab=96.53  E-value=0.0019  Score=52.37  Aligned_cols=43  Identities=28%  Similarity=0.289  Sum_probs=31.6

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccceeeeechh-HHHHHHh
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS-EFVQKYL  234 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s-~l~~~~~  234 (245)
                      ++.-|+|.|+=|.|||+++|++++.++..-...|++ .+++.|.
T Consensus        24 ~g~Vv~L~GdLGAGKTtf~rgi~~~Lg~~~~V~SPTFtlv~~Y~   67 (149)
T COG0802          24 AGDVVLLSGDLGAGKTTLVRGIAKGLGVDGNVKSPTFTLVEEYE   67 (149)
T ss_pred             CCCEEEEEcCCcCChHHHHHHHHHHcCCCCcccCCCeeeehhhc
Confidence            344489999999999999999999998643333333 4556663

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

Probab=96.52  E-value=0.0023  Score=44.32  Aligned_cols=23  Identities=35%  Similarity=0.573  Sum_probs=20.0

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..+|+||+|+|||++..|+.-.+
T Consensus        25 ~tli~G~nGsGKSTllDAi~~~L   47 (62)
T PF13555_consen   25 VTLITGPNGSGKSTLLDAIQTVL   47 (62)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            49999999999999999986544

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

Probab=96.51  E-value=0.0015  Score=58.19  Aligned_cols=26  Identities=46%  Similarity=0.618  Sum_probs=22.3

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..+.+||+||+|||||.+++..-+.+
T Consensus        32 ~~~pvLl~G~~GtGKT~li~~~l~~l   57 (272)
T PF12775_consen   32 NGRPVLLVGPSGTGKTSLIQNFLSSL   57 (272)
T ss_dssp             CTEEEEEESSTTSSHHHHHHHHHHCS
T ss_pred             cCCcEEEECCCCCchhHHHHhhhccC
Confidence            45679999999999999998877665

>PF00519 PPV_E1_C: Papillomavirus helicase; InterPro: IPR001177 Papillomaviruses are a large family of DNA tumour viruses which give rise to warts in their host species

Probab=96.51  E-value=0.0026  Score=59.15  Aligned_cols=36  Identities=31%  Similarity=0.630  Sum_probs=29.9

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcccceeeee
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRV  224 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v  224 (245)
                      |+...+.++|||||+||||+++-+|-+.++..++..
T Consensus       258 g~PKKnClvi~GPPdTGKS~F~~SLi~Fl~GkViSf  293 (432)
T PF00519_consen  258 GIPKKNCLVIYGPPDTGKSMFCMSLIKFLKGKVISF  293 (432)
T ss_dssp             TBTTSSEEEEESSCCCSHHHHHHHHHHHHTSEEE-G
T ss_pred             CCCcccEEEEECCCCCchhHHHHHHHHHhCCEEEEe
Confidence            555556699999999999999999999998777654

The helicase E1 protein is an ATP-dependent DNA helicase required for initiation of viral DNA replication []. It forms a complex with the viral E2 protein, which is a site-specific DNA-binding transcriptional activator. The E1-E2 complex binds to the replication origin which contains binding sites for both proteins []. The E1 protein is a 70 kDa polypeptide with a central DNA-binding domain and a C-terminal ATPase/helicase domain. It binds specific 18 bp DNA sequences at the origin of replication, melts the DNA duplex and functions as a 3' to 5' helicase []. In addition to E2 it also interacts with DNA polymerase alpha and replication protein A to effect DNA replication. The DNA-binding domain forms a five-stranded antiparallel beta sheet bordered by four loosely packed alpha helices on one side and two tightly packed helices on the other []. Two structural modules within this domain, an extended loop and a helix, contain conserved residues and are critical for DNA binding. In solution E1 is a monomer, but binds DNA as a dimer. Recruitment of more E1 subunits to the complex leads to melting of the origin and ultimately to the formation of an E1 hexamer with helicase activity []. The entry represents the C-terminal region of E1, containing both the DNA-binding and ATPase/helical domains.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1TUE_K 1R9W_A 2V9P_B 2GXA_I 1KSX_J 1KSY_A 1F08_B.

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=96.51  E-value=0.0028  Score=57.02  Aligned_cols=65  Identities=23%  Similarity=0.360  Sum_probs=44.5

Q ss_pred             cCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcc--eeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhc
Q 025979          160 DIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRG--VLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLG  235 (245)
Q Consensus       160 dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~g--vLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~G  235 (245)
                      .+.|+.-+++.|-..+...+.++        .|.|-  +-|||+|||||...++.||+.+-..   -..|.++.+|++
T Consensus        83 ~lfGQHla~~~Vv~alk~~~~n~--------~p~KPLvLSfHG~tGTGKN~Va~iiA~n~~~~---Gl~S~~V~~fva  149 (344)
T KOG2170|consen   83 ALFGQHLAKQLVVNALKSHWANP--------NPRKPLVLSFHGWTGTGKNYVAEIIAENLYRG---GLRSPFVHHFVA  149 (344)
T ss_pred             HhhchHHHHHHHHHHHHHHhcCC--------CCCCCeEEEecCCCCCchhHHHHHHHHHHHhc---cccchhHHHhhh
Confidence            47888888888888876544332        12233  5599999999999999999976221   134556666654

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=96.50  E-value=0.002  Score=61.78  Aligned_cols=44  Identities=25%  Similarity=0.253  Sum_probs=31.4

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHHH
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQK  232 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~~  232 (245)
                      |+.++.-+|+.||||||||+++-.++...   |-+.+.++..+-.+.
T Consensus       259 G~~~gs~~li~G~~G~GKt~l~~~f~~~~~~~ge~~~y~s~eEs~~~  305 (484)
T TIGR02655       259 GFFKDSIILATGATGTGKTLLVSKFLENACANKERAILFAYEESRAQ  305 (484)
T ss_pred             CccCCcEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEeeCCHHH
Confidence            45555559999999999999998888754   556666665544333

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.

>PRK13764 ATPase; Provisional

Probab=96.49  E-value=0.0018  Score=63.54  Aligned_cols=27  Identities=37%  Similarity=0.722  Sum_probs=24.2

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhccc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      ..+++|++||||+|||+++++++..+.
T Consensus       256 ~~~~ILIsG~TGSGKTTll~AL~~~i~  282 (602)
T PRK13764        256 RAEGILIAGAPGAGKSTFAQALAEFYA  282 (602)
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHHHHh
Confidence            457799999999999999999998874

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

Probab=96.49  E-value=0.0031  Score=60.21  Aligned_cols=53  Identities=23%  Similarity=0.350  Sum_probs=41.0

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcc-eeeecCCCCchHHHHHHHHhcccceee
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRG-VLLYGPPGTGKTMLAKAVANHTTAAFI  222 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~g-vLl~GPPGtGKT~lAkalA~~l~~~~~  222 (245)
                      ..++++++......+.+.+.+..               |.| +|+.||+|+|||++..++-+.++.+..
T Consensus       234 ~l~l~~Lg~~~~~~~~~~~~~~~---------------p~GliLvTGPTGSGKTTTLY~~L~~ln~~~~  287 (500)
T COG2804         234 ILDLEKLGMSPFQLARLLRLLNR---------------PQGLILVTGPTGSGKTTTLYAALSELNTPER  287 (500)
T ss_pred             cCCHHHhCCCHHHHHHHHHHHhC---------------CCeEEEEeCCCCCCHHHHHHHHHHHhcCCCc
Confidence            45667777777777777777654               466 778899999999999999988865544

>PRK14974 cell division protein FtsY; Provisional

Probab=96.48  E-value=0.0022  Score=58.78  Aligned_cols=26  Identities=31%  Similarity=0.368  Sum_probs=22.0

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .|.-++|.||||+|||+++..+|..+
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~~l  164 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAYYL  164 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHH
Confidence            35569999999999999888888765

>cd03258 ABC_MetN_methionine_transporter MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport

Probab=96.45  E-value=0.0019  Score=55.40  Aligned_cols=28  Identities=18%  Similarity=0.305  Sum_probs=24.0

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++..+.|.||+|+|||+|.++||..+
T Consensus        28 i~~Ge~~~l~G~nGsGKSTLl~~l~G~~   55 (233)
T cd03258          28 VPKGEIFGIIGRSGAGKSTLIRCINGLE   55 (233)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3455559999999999999999999876

Other members of this system include the MetP permease and the MetQ substrate binding protein. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03262 ABC_HisP_GlnQ_permeases HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively

Probab=96.45  E-value=0.002  Score=54.43  Aligned_cols=28  Identities=25%  Similarity=0.513  Sum_probs=24.0

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.|.||+|+|||+|.++++...
T Consensus        23 i~~G~~~~l~G~nGsGKSTLl~~l~G~~   50 (213)
T cd03262          23 VKKGEVVVIIGPSGSGKSTLLRCINLLE   50 (213)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3455559999999999999999999875

Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP has properties intermediate between those of integral and peripheral membrane proteins and is accessible from both sides of the membrane, presumably by its interaction with HisQ and HisM. The two HisP subunits form a homodimer within the complex. The domain structure of the amino acid uptake systems is typical for prokaryote extracellular solute binding protein-dependent uptake systems. All of the amino acid uptake systems also have at least one, and in a few cases, two extracellular solute binding proteins located in the periplasm of Gram-negative bacteria, or attached to the cell membrane of Gram-positive bacteria. The best-studied member of the PAAT (polar amino acid transport) family is the HisJQM

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.45  E-value=0.0025  Score=60.23  Aligned_cols=37  Identities=24%  Similarity=0.240  Sum_probs=26.2

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc-----cceeeeechhH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT-----TAAFIRVVGSE  228 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l-----~~~~~~v~~s~  228 (245)
                      .++.++|+||+|||||+++..+|..+     +..+..++...
T Consensus       220 ~~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D~  261 (424)
T PRK05703        220 QGGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDT  261 (424)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECCc
Confidence            34568999999999999888887644     23444455444

>TIGR00416 sms DNA repair protein RadA

Probab=96.44  E-value=0.003  Score=60.23  Aligned_cols=50  Identities=34%  Similarity=0.459  Sum_probs=34.9

Q ss_pred             cHHHHhhh--ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHH
Q 025979          181 HHELYKQI--GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFV  230 (245)
Q Consensus       181 ~~~~~~~~--g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~  230 (245)
                      -+++.+-+  |+.+..-++++|+||+|||+++..+|...   +.+.+++++.+-.
T Consensus        80 i~~LD~vLgGGi~~GsvilI~G~pGsGKTTL~lq~a~~~a~~g~kvlYvs~EEs~  134 (454)
T TIGR00416        80 FGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSGEESL  134 (454)
T ss_pred             cHHHHHHhcCCccCCeEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEECcCCH
Confidence            34444434  45555559999999999999999987755   3467777765544

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)).

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=96.43  E-value=0.0037  Score=57.09  Aligned_cols=27  Identities=22%  Similarity=0.319  Sum_probs=24.2

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhccc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      .+.++||+||+|+||+++|+++|..+-
T Consensus        23 l~HA~Lf~G~~G~GK~~lA~~~A~~ll   49 (325)
T PRK06871         23 GHHALLFKADSGLGTEQLIRALAQWLM   49 (325)
T ss_pred             cceeEEeECCCCCCHHHHHHHHHHHHc
Confidence            457899999999999999999998773

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

Probab=96.43  E-value=0.0022  Score=53.41  Aligned_cols=28  Identities=32%  Similarity=0.481  Sum_probs=23.8

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++-.+++.||+||||+++.|++|+-.
T Consensus        26 v~~Ge~iaitGPSG~GKStllk~va~Li   53 (223)
T COG4619          26 VRAGEFIAITGPSGCGKSTLLKIVASLI   53 (223)
T ss_pred             ecCCceEEEeCCCCccHHHHHHHHHhcc
Confidence            4455559999999999999999999865

>TIGR02673 FtsE cell division ATP-binding protein FtsE

Probab=96.42  E-value=0.0021  Score=54.39  Aligned_cols=28  Identities=36%  Similarity=0.463  Sum_probs=23.6

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.|.||+|+|||+|+++|+..+
T Consensus        25 i~~G~~~~l~G~nGsGKSTLl~~i~Gl~   52 (214)
T TIGR02673        25 IRKGEFLFLTGPSGAGKTTLLKLLYGAL   52 (214)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444558999999999999999999875

This model describes FtsE, a member of the ABC transporter ATP-binding protein family. This protein, and its permease partner FtsX, localize to the division site. In a number of species, the ftsEX gene pair is located next to FtsY, the signal recognition particle-docking protein.

>TIGR03410 urea_trans_UrtE urea ABC transporter, ATP-binding protein UrtE

Probab=96.42  E-value=0.0021  Score=55.10  Aligned_cols=28  Identities=25%  Similarity=0.306  Sum_probs=24.0

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.|.||+|+|||+|+++|+..+
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~~l~G~~   50 (230)
T TIGR03410        23 VPKGEVTCVLGRNGVGKTTLLKTLMGLL   50 (230)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3455559999999999999999999876

Members of this protein family are ABC transporter ATP-binding subunits associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity.

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=96.42  E-value=0.0025  Score=48.35  Aligned_cols=22  Identities=27%  Similarity=0.561  Sum_probs=19.9

Q ss_pred             eeeecCCCCchHHHHHHHHhcc
Q 025979          196 VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      |++.|++|+|||+|.+.++...
T Consensus         2 I~V~G~~g~GKTsLi~~l~~~~   23 (119)
T PF08477_consen    2 IVVLGDSGVGKTSLIRRLCGGE   23 (119)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECcCCCCHHHHHHHHhcCC
Confidence            7899999999999999998655

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.

>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=96.42  E-value=0.0022  Score=54.16  Aligned_cols=28  Identities=36%  Similarity=0.548  Sum_probs=23.8

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.+.++..+
T Consensus        24 i~~G~~~~i~G~nGsGKSTLl~~l~G~~   51 (214)
T cd03292          24 ISAGEFVFLVGPSGAGKSTLLKLIYKEE   51 (214)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3444558899999999999999999876

The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=96.41  E-value=0.0023  Score=54.02  Aligned_cols=28  Identities=25%  Similarity=0.368  Sum_probs=23.5

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.++|+..+
T Consensus        23 i~~G~~~~i~G~nGsGKSTLl~~l~G~~   50 (210)
T cd03269          23 VEKGEIFGLLGPNGAGKTTTIRMILGII   50 (210)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444558899999999999999999865

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.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.41  E-value=0.0026  Score=60.10  Aligned_cols=36  Identities=19%  Similarity=0.169  Sum_probs=27.7

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc---cceeeeechh
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      +|.-++|+||+|+|||+++..+|..+   |.....+++.
T Consensus        99 ~~~vi~lvG~~GvGKTTtaaKLA~~l~~~G~kV~lV~~D  137 (429)
T TIGR01425        99 KQNVIMFVGLQGSGKTTTCTKLAYYYQRKGFKPCLVCAD  137 (429)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEcCc
Confidence            45569999999999999999999766   5555555543

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.

>TIGR02315 ABC_phnC phosphonate ABC transporter, ATP-binding protein

Probab=96.40  E-value=0.0022  Score=55.35  Aligned_cols=27  Identities=30%  Similarity=0.586  Sum_probs=23.1

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.++|+..+
T Consensus        26 ~~Ge~~~l~G~nGsGKSTLl~~l~Gl~   52 (243)
T TIGR02315        26 NPGEFVAIIGPSGAGKSTLLRCINRLV   52 (243)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCc
Confidence            344458999999999999999999865

Phosphonates are a class of phosphorus-containing organic compound with a stable direct C-P bond rather than a C-O-P linkage. A number of bacterial species have operons, typically about 14 genes in size, with genes for ATP-dependent transport of phosphonates, degradation, and regulation of the expression of the system. Members of this protein family are the ATP-binding cassette component of tripartite ABC transporters of phosphonates.

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=96.40  E-value=0.0038  Score=57.16  Aligned_cols=27  Identities=22%  Similarity=0.345  Sum_probs=24.2

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..+.++||+||+|+||+++|.++|..+
T Consensus        22 rl~HA~Lf~G~~G~Gk~~lA~~~A~~L   48 (334)
T PRK07993         22 RGHHALLIQALPGMGDDALIYALSRWL   48 (334)
T ss_pred             CcceEEeeECCCCCCHHHHHHHHHHHH
Confidence            356789999999999999999999877

>cd03256 ABC_PhnC_transporter ABC-type phosphate/phosphonate transport system

Probab=96.40  E-value=0.0022  Score=55.21  Aligned_cols=27  Identities=33%  Similarity=0.586  Sum_probs=23.1

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|+++|+..+
T Consensus        25 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   51 (241)
T cd03256          25 NPGEFVALIGPSGAGKSTLLRCLNGLV   51 (241)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCc
Confidence            444458999999999999999999875

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.

>PLN02748 tRNA dimethylallyltransferase

Probab=96.39  E-value=0.003  Score=60.30  Aligned_cols=32  Identities=34%  Similarity=0.544  Sum_probs=28.1

Q ss_pred             ceeeecCCCCchHHHHHHHHhcccceeeeech
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTTAAFIRVVG  226 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~  226 (245)
                      -+++.||+|||||.||..||..++..++..|.
T Consensus        24 ~i~i~GptgsGKs~la~~la~~~~~eii~~Ds   55 (468)
T PLN02748         24 VVVVMGPTGSGKSKLAVDLASHFPVEIINADS   55 (468)
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCeeEEcCch
Confidence            48899999999999999999999988776654

>PRK10867 signal recognition particle protein; Provisional

Probab=96.39  E-value=0.0029  Score=59.88  Aligned_cols=36  Identities=28%  Similarity=0.445  Sum_probs=27.0

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc----cceeeeechh
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT----TAAFIRVVGS  227 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l----~~~~~~v~~s  227 (245)
                      +|.-++|+||||+|||+++.-+|..+    |..+..+++.
T Consensus        99 ~p~vI~~vG~~GsGKTTtaakLA~~l~~~~G~kV~lV~~D  138 (433)
T PRK10867         99 PPTVIMMVGLQGAGKTTTAGKLAKYLKKKKKKKVLLVAAD  138 (433)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHHhcCCcEEEEEcc
Confidence            46679999999999999877777654    4555556554

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=96.38  E-value=0.0013  Score=56.70  Aligned_cols=43  Identities=30%  Similarity=0.590  Sum_probs=30.3

Q ss_pred             hhhccCCCcc--eeeecCCCCchHHHHHHHHhcc--cceeeeechhH
Q 025979          186 KQIGIDPPRG--VLLYGPPGTGKTMLAKAVANHT--TAAFIRVVGSE  228 (245)
Q Consensus       186 ~~~g~~~~~g--vLl~GPPGtGKT~lAkalA~~l--~~~~~~v~~s~  228 (245)
                      +.+.+...+|  +.++||+|+|||++.|+|..--  ..--+.+++..
T Consensus        19 kgi~l~v~~Gevv~iiGpSGSGKSTlLRclN~LE~~~~G~I~i~g~~   65 (240)
T COG1126          19 KGISLSVEKGEVVVIIGPSGSGKSTLLRCLNGLEEPDSGSITVDGED   65 (240)
T ss_pred             cCcceeEcCCCEEEEECCCCCCHHHHHHHHHCCcCCCCceEEECCEe
Confidence            3344445555  8999999999999999997633  44456666643

>PRK10646 ADP-binding protein; Provisional

Probab=96.38  E-value=0.0028  Score=51.70  Aligned_cols=30  Identities=27%  Similarity=0.434  Sum_probs=25.7

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcccce
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTTAA  220 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~~~  220 (245)
                      .++.-|+|.|+=|+|||+++|++++.+|..
T Consensus        26 ~~g~vi~L~GdLGaGKTtf~rgl~~~Lg~~   55 (153)
T PRK10646         26 DGATVIYLYGDLGAGKTTFSRGFLQALGHQ   55 (153)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHcCCC
Confidence            344458999999999999999999999764

>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]

Probab=96.38  E-value=0.0042  Score=59.11  Aligned_cols=64  Identities=23%  Similarity=0.338  Sum_probs=50.8

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHH
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFV  230 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~  230 (245)
                      ..+.+++|.....+++++.+...           ....-.||++|.+||||.++|++|=...   +.||+.|+|..+-
T Consensus       138 ~~~~~liG~S~am~~l~~~i~kv-----------A~s~a~VLI~GESGtGKElvAr~IH~~S~R~~~PFVavNcaAip  204 (464)
T COG2204         138 SLGGELVGESPAMQQLRRLIAKV-----------APSDASVLITGESGTGKELVARAIHQASPRAKGPFIAVNCAAIP  204 (464)
T ss_pred             cccCCceecCHHHHHHHHHHHHH-----------hCCCCCEEEECCCCCcHHHHHHHHHhhCcccCCCceeeecccCC
Confidence            45678999999999999888651           1233459999999999999999997766   5699999987553

>COG4178 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]

Probab=96.37  E-value=0.0022  Score=62.71  Aligned_cols=30  Identities=33%  Similarity=0.521  Sum_probs=25.8

Q ss_pred             hccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          188 IGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       188 ~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++++..+|+.||+|||||++-||||+-.
T Consensus       414 ~~v~~G~~llI~G~SG~GKTsLlRaiaGLW  443 (604)
T COG4178         414 FEVRPGERLLITGESGAGKTSLLRALAGLW  443 (604)
T ss_pred             eeeCCCCEEEEECCCCCCHHHHHHHHhccC
Confidence            345667779999999999999999999865

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=96.36  E-value=0.0023  Score=52.73  Aligned_cols=28  Identities=21%  Similarity=0.437  Sum_probs=23.8

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++..+.+.||+|+|||+|++.++...
T Consensus        25 i~~Ge~~~i~G~nGsGKStLl~~l~G~~   52 (178)
T cd03247          25 LKQGEKIALLGRSGSGKSTLLQLLTGDL   52 (178)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhccC
Confidence            3444558999999999999999999876

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.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=96.36  E-value=0.0031  Score=57.87  Aligned_cols=25  Identities=24%  Similarity=0.449  Sum_probs=21.7

Q ss_pred             cceeeecCCCCchHHHHHHHHhccc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      ..+++.||+|+|||++.+++...+.
T Consensus       123 g~ili~G~tGSGKTT~l~al~~~i~  147 (343)
T TIGR01420       123 GLILVTGPTGSGKSTTLASMIDYIN  147 (343)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhhC
Confidence            3488999999999999999988663

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.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=96.35  E-value=0.0028  Score=57.22  Aligned_cols=30  Identities=23%  Similarity=0.560  Sum_probs=25.9

Q ss_pred             hccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          188 IGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       188 ~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +-+.....+++.||+|+|||+++++++..+
T Consensus       139 ~~v~~~~~ili~G~tGsGKTTll~al~~~~  168 (308)
T TIGR02788       139 LAIASRKNIIISGGTGSGKTTFLKSLVDEI  168 (308)
T ss_pred             HHhhCCCEEEEECCCCCCHHHHHHHHHccC
Confidence            345566789999999999999999999877

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.

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=96.35  E-value=0.0024  Score=53.08  Aligned_cols=28  Identities=21%  Similarity=0.283  Sum_probs=23.6

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.++|+...
T Consensus        15 i~~Ge~~~i~G~nGsGKSTLl~~i~G~~   42 (190)
T TIGR01166        15 AERGEVLALLGANGAGKSTLLLHLNGLL   42 (190)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444558999999999999999999865

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.

>TIGR03608 L_ocin_972_ABC putative bacteriocin export ABC transporter, lactococcin 972 group

Probab=96.35  E-value=0.0023  Score=53.74  Aligned_cols=28  Identities=21%  Similarity=0.361  Sum_probs=23.7

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++..+.+.||+|+|||+|.+.++..+
T Consensus        21 i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   48 (206)
T TIGR03608        21 IEKGKMYAIIGESGSGKSTLLNIIGLLE   48 (206)
T ss_pred             EeCCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            3444558999999999999999999876

A gene pair with a fairly wide distribution consists of a polypeptide related to the lactococcin 972 (see TIGR01653) and multiple-membrane-spanning putative immunity protein (see TIGR01654). This model represents a small clade within the ABC transporters that regularly are found adjacent to these bacteriocin system gene pairs and are likely serve as export proteins.

>cd03301 ABC_MalK_N The N-terminal ATPase domain of the maltose transporter, MalK

Probab=96.34  E-value=0.0027  Score=53.69  Aligned_cols=28  Identities=36%  Similarity=0.496  Sum_probs=23.7

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++..+.|.||+|+|||+|.+.|+..+
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~~l~G~~   50 (213)
T cd03301          23 IADGEFVVLLGPSGCGKTTTLRMIAGLE   50 (213)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444558999999999999999999875

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.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=96.33  E-value=0.0026  Score=58.26  Aligned_cols=29  Identities=21%  Similarity=0.387  Sum_probs=25.2

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      +...+++|+.||+|+|||++.+++.....
T Consensus       157 v~~~~nili~G~tgSGKTTll~aL~~~ip  185 (332)
T PRK13900        157 VISKKNIIISGGTSTGKTTFTNAALREIP  185 (332)
T ss_pred             HHcCCcEEEECCCCCCHHHHHHHHHhhCC
Confidence            44567799999999999999999998773

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=96.33  E-value=0.0025  Score=54.07  Aligned_cols=27  Identities=26%  Similarity=0.367  Sum_probs=23.3

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.+.++..+
T Consensus        27 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   53 (216)
T TIGR00960        27 TKGEMVFLVGHSGAGKSTFLKLILGIE   53 (216)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            344558999999999999999999876

>PRK13541 cytochrome c biogenesis protein CcmA; Provisional

Probab=96.33  E-value=0.003  Score=52.87  Aligned_cols=28  Identities=25%  Similarity=0.364  Sum_probs=23.9

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.++++...
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~~l~G~~   50 (195)
T PRK13541         23 FLPSAITYIKGANGCGKSSLLRMIAGIM   50 (195)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            3455559999999999999999999875

>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=96.32  E-value=0.0024  Score=54.32  Aligned_cols=28  Identities=32%  Similarity=0.386  Sum_probs=23.6

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.+.++...
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   50 (222)
T cd03224          23 VPEGEIVALLGRNGAGKTTLLKTIMGLL   50 (222)
T ss_pred             EcCCeEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444559999999999999999999875

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.

>cd03278 ABC_SMC_barmotin Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function

Probab=96.32  E-value=0.0019  Score=54.59  Aligned_cols=24  Identities=25%  Similarity=0.362  Sum_probs=21.0

Q ss_pred             ceeeecCCCCchHHHHHHHHhccc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      -++|+||+|+|||++.++++..++
T Consensus        24 ~~~i~G~nGsGKStll~al~~l~~   47 (197)
T cd03278          24 LTAIVGPNGSGKSNIIDAIRWVLG   47 (197)
T ss_pred             cEEEECCCCCCHHHHHHHHHHHhc
Confidence            478999999999999999987653

Barmotin belongs to the SMC protein family. SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, w

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=96.31  E-value=0.0033  Score=57.09  Aligned_cols=40  Identities=18%  Similarity=0.205  Sum_probs=28.1

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhc---------ccceeeeechhH
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANH---------TTAAFIRVVGSE  228 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~---------l~~~~~~v~~s~  228 (245)
                      |+....-..++||||||||.+|..+|-.         .+...++|+..+
T Consensus        92 Gi~~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~  140 (313)
T TIGR02238        92 GIESMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEG  140 (313)
T ss_pred             CCcCCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCC
Confidence            4555455889999999999999877631         245666666443

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.

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=96.30  E-value=0.0027  Score=52.06  Aligned_cols=28  Identities=36%  Similarity=0.584  Sum_probs=24.1

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.+.++...
T Consensus        25 i~~G~~~~l~G~nGsGKstLl~~i~G~~   52 (171)
T cd03228          25 IKPGEKVAIVGPSGSGKSTLLKLLLRLY   52 (171)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHHcCC
Confidence            3455559999999999999999999876

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>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=96.30  E-value=0.0027  Score=54.29  Aligned_cols=28  Identities=29%  Similarity=0.420  Sum_probs=23.6

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.++|+...
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~~i~G~~   50 (227)
T cd03260          23 IPKGEITALIGPSGCGKSTLLRLLNRLN   50 (227)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            3444558999999999999999999876

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).

>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=96.30  E-value=0.0029  Score=53.43  Aligned_cols=27  Identities=30%  Similarity=0.466  Sum_probs=23.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.|.||+|+|||+|.+.|+...
T Consensus        25 ~~G~~~~l~G~nGsGKSTLl~~l~G~~   51 (211)
T cd03225          25 KKGEFVLIVGPNGSGKSTLLRLLNGLL   51 (211)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            344448899999999999999999875

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.

>TIGR02211 LolD_lipo_ex lipoprotein releasing system, ATP-binding protein

Probab=96.30  E-value=0.0026  Score=54.04  Aligned_cols=28  Identities=25%  Similarity=0.369  Sum_probs=23.8

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.++|+..+
T Consensus        28 i~~G~~~~i~G~nGsGKSTLl~~i~G~~   55 (221)
T TIGR02211        28 IGKGEIVAIVGSSGSGKSTLLHLLGGLD   55 (221)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3455558899999999999999999875

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.

>TIGR01663 PNK-3'Pase polynucleotide 5'-kinase 3'-phosphatase

Probab=96.29  E-value=0.0033  Score=60.93  Aligned_cols=32  Identities=22%  Similarity=0.296  Sum_probs=25.9

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccceeeee
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAFIRV  224 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v  224 (245)
                      +.=|+|+|+||+|||++|+.++...+...++.
T Consensus       369 p~LVil~G~pGSGKST~A~~l~~~~g~~~vn~  400 (526)
T TIGR01663       369 CEMVIAVGFPGAGKSHFCKKFFQPAGYKHVNA  400 (526)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHcCCeEECc
Confidence            34499999999999999999999877654433

Note that the EC number for the kinase function is: 2.7.1.78

>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=96.29  E-value=0.0029  Score=54.44  Aligned_cols=28  Identities=21%  Similarity=0.441  Sum_probs=23.7

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.|.||+|+|||+|+++|+..+
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~~l~G~~   50 (235)
T cd03261          23 VRRGEILAIIGPSGSGKSTLLRLIVGLL   50 (235)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444558999999999999999999876

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.

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

Probab=96.29  E-value=0.0027  Score=50.84  Aligned_cols=28  Identities=36%  Similarity=0.536  Sum_probs=24.1

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++..+.+.||+|+|||+|.++++...
T Consensus        23 ~~~Ge~~~i~G~nGsGKStLl~~l~G~~   50 (144)
T cd03221          23 INPGDRIGLVGRNGAGKSTLLKLIAGEL   50 (144)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHcCCC
Confidence            4455568999999999999999999876

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.

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=96.28  E-value=0.0047  Score=58.08  Aligned_cols=61  Identities=26%  Similarity=0.340  Sum_probs=43.6

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHH
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFV  230 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~  230 (245)
                      .++.|.....+.+.+.+..          + ......++++|++||||+++|+++-...   +.+|+.+++..+.
T Consensus       139 ~~lig~s~~~~~l~~~i~~----------~-a~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~v~v~c~~~~  202 (445)
T TIGR02915       139 RGLITSSPGMQKICRTIEK----------I-APSDITVLLLGESGTGKEVLARALHQLSDRKDKRFVAINCAAIP  202 (445)
T ss_pred             cceeecCHHHHHHHHHHHH----------H-hCCCCCEEEECCCCcCHHHHHHHHHHhCCcCCCCeEEEECCCCC
Confidence            4566666666666665532          1 1233559999999999999999997655   5789999877653

Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=96.28  E-value=0.0027  Score=59.33  Aligned_cols=24  Identities=42%  Similarity=0.632  Sum_probs=21.6

Q ss_pred             ceeeecCCCCchHHHHHHHHhccc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      ..|++||||||||+|++.|++...
T Consensus       171 R~lIvgppGvGKTTLaK~Ian~I~  194 (416)
T PRK09376        171 RGLIVAPPKAGKTVLLQNIANSIT  194 (416)
T ss_pred             eEEEeCCCCCChhHHHHHHHHHHH
Confidence            399999999999999999998763

>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment

Probab=96.28  E-value=0.0029  Score=52.26  Aligned_cols=27  Identities=33%  Similarity=0.578  Sum_probs=22.9

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|+++++..+
T Consensus        24 ~~G~~~~i~G~nGsGKSTLl~~l~G~~   50 (178)
T cd03229          24 EAGEIVALLGPSGSGKSTLLRCIAGLE   50 (178)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            344458899999999999999999875

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.

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=96.27  E-value=0.0028  Score=67.79  Aligned_cols=37  Identities=43%  Similarity=0.565  Sum_probs=34.1

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccceeeeechhH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSE  228 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~  228 (245)
                      ..+++||-|.||+|||+|..|+|+..|-.++||+.|+
T Consensus      1542 v~kpilLEGsPGVGKTSlItaLAr~tG~kliRINLSe 1578 (4600)
T COG5271        1542 VGKPILLEGSPGVGKTSLITALARKTGKKLIRINLSE 1578 (4600)
T ss_pred             cCCceeecCCCCccHHHHHHHHHHHhcCceEEeeccc
Confidence            4578999999999999999999999999999998773

>cd03226 ABC_cobalt_CbiO_domain2 Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=96.27  E-value=0.0028  Score=53.36  Aligned_cols=28  Identities=36%  Similarity=0.400  Sum_probs=23.6

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.+.++...
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   50 (205)
T cd03226          23 LYAGEIIALTGKNGAGKTTLAKILAGLI   50 (205)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3444558999999999999999999875

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.

>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=96.27  E-value=0.0026  Score=54.42  Aligned_cols=29  Identities=24%  Similarity=0.507  Sum_probs=24.4

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      +.++..+.|.||+|+|||+|++.++..+.
T Consensus        30 i~~Ge~~~l~G~nGsGKSTLlk~l~G~~~   58 (226)
T cd03234          30 VESGQVMAILGSSGSGKTTLLDAISGRVE   58 (226)
T ss_pred             EcCCeEEEEECCCCCCHHHHHHHHhCccC
Confidence            44555699999999999999999998653

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

>cd03235 ABC_Metallic_Cations ABC component of the metal-type transporters

Probab=96.27  E-value=0.0028  Score=53.67  Aligned_cols=27  Identities=33%  Similarity=0.528  Sum_probs=23.2

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.+.|+...
T Consensus        23 ~~Ge~~~l~G~nGsGKSTLl~~l~G~~   49 (213)
T cd03235          23 KPGEFLAIVGPNGAGKSTLLKAILGLL   49 (213)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHcCCC
Confidence            344458999999999999999999875

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.

>PRK11124 artP arginine transporter ATP-binding subunit; Provisional

Probab=96.26  E-value=0.0029  Score=54.64  Aligned_cols=28  Identities=25%  Similarity=0.443  Sum_probs=23.7

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++..+.+.||+|+|||+|++.||...
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   52 (242)
T PRK11124         25 CPQGETLVLLGPSGAGKSSLLRVLNLLE   52 (242)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444558999999999999999999875

>PRK10247 putative ABC transporter ATP-binding protein YbbL; Provisional

Probab=96.26  E-value=0.0029  Score=54.25  Aligned_cols=27  Identities=37%  Similarity=0.465  Sum_probs=23.1

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.++|+...
T Consensus        31 ~~Ge~~~i~G~nGsGKSTLl~~l~G~~   57 (225)
T PRK10247         31 RAGEFKLITGPSGCGKSTLLKIVASLI   57 (225)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhccc
Confidence            444558999999999999999999865

>cd03264 ABC_drug_resistance_like ABC-type multidrug transport system, ATPase component

Probab=96.26  E-value=0.0029  Score=53.48  Aligned_cols=27  Identities=41%  Similarity=0.576  Sum_probs=22.7

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++ -+.+.||+|+|||+|.++++..+
T Consensus        23 i~~g-~~~i~G~nGsGKSTLl~~l~Gl~   49 (211)
T cd03264          23 LGPG-MYGLLGPNGAGKTTLMRILATLT   49 (211)
T ss_pred             EcCC-cEEEECCCCCCHHHHHHHHhCCC
Confidence            3444 57899999999999999999865

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.

>PRK14247 phosphate ABC transporter ATP-binding protein; Provisional

Probab=96.26  E-value=0.003  Score=54.86  Aligned_cols=28  Identities=29%  Similarity=0.432  Sum_probs=23.6

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|++.|+...
T Consensus        26 i~~Ge~~~i~G~nGsGKSTLl~~i~G~~   53 (250)
T PRK14247         26 IPDNTITALMGPSGSGKSTLLRVFNRLI   53 (250)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhccC
Confidence            3444558999999999999999999875

>PRK09862 putative ATP-dependent protease; Provisional

Probab=96.25  E-value=0.0029  Score=60.99  Aligned_cols=46  Identities=35%  Similarity=0.553  Sum_probs=32.6

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+.++.|....++.+.    .           .......++|+||||||||++++.++..+
T Consensus       189 d~~~v~Gq~~~~~al~----l-----------aa~~G~~llliG~~GsGKTtLak~L~gll  234 (506)
T PRK09862        189 DLSDVIGQEQGKRGLE----I-----------TAAGGHNLLLIGPPGTGKTMLASRINGLL  234 (506)
T ss_pred             CeEEEECcHHHHhhhh----e-----------eccCCcEEEEECCCCCcHHHHHHHHhccC
Confidence            5667777665444432    2           12234569999999999999999998765

>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]

Probab=96.25  E-value=0.0066  Score=57.97  Aligned_cols=67  Identities=19%  Similarity=0.348  Sum_probs=53.9

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHH
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQ  231 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~  231 (245)
                      .....+++|...+..++.+.|...           ......||+.|-+||||.++||+|=...   +.||+.++|..+.+
T Consensus       219 ~~~~~~iIG~S~am~~ll~~i~~V-----------A~Sd~tVLi~GETGtGKElvAraIH~~S~R~~kPfV~~NCAAlPe  287 (550)
T COG3604         219 VLEVGGIIGRSPAMRQLLKEIEVV-----------AKSDSTVLIRGETGTGKELVARAIHQLSPRRDKPFVKLNCAALPE  287 (550)
T ss_pred             hcccccceecCHHHHHHHHHHHHH-----------hcCCCeEEEecCCCccHHHHHHHHHhhCcccCCCceeeeccccch
Confidence            456678999999999999888762           1233459999999999999999997665   78999999887654


Q ss_pred             H
Q 025979          232 K  232 (245)
Q Consensus       232 ~  232 (245)
                      .
T Consensus       288 s  288 (550)
T COG3604         288 S  288 (550)
T ss_pred             H
Confidence            3

>cd03296 ABC_CysA_sulfate_importer Part of the ABC transporter complex cysAWTP involved in sulfate import

Probab=96.25  E-value=0.0029  Score=54.60  Aligned_cols=28  Identities=39%  Similarity=0.559  Sum_probs=23.6

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|+++|+...
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   52 (239)
T cd03296          25 IPSGELVALLGPSGSGKTTLLRLIAGLE   52 (239)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444558999999999999999999875

Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a solute-binding protein (cysP). ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

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

Probab=96.24  E-value=0.0032  Score=51.56  Aligned_cols=28  Identities=43%  Similarity=0.661  Sum_probs=24.0

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.+..-+.+.||+|+|||+|++.++..+
T Consensus        24 i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   51 (166)
T cd03223          24 IKPGDRLLITGPSGTGKSSLFRALAGLW   51 (166)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3455559999999999999999999876

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

>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=96.23  E-value=0.0029  Score=54.37  Aligned_cols=27  Identities=33%  Similarity=0.436  Sum_probs=23.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.|.||+|+|||+|.++++..+
T Consensus        24 ~~Ge~~~l~G~nGsGKSTLl~~l~Gl~   50 (236)
T cd03219          24 RPGEIHGLIGPNGAGKTTLFNLISGFL   50 (236)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHcCCC
Confidence            344458899999999999999999865

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).

>cd03293 ABC_NrtD_SsuB_transporters NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively

Probab=96.23  E-value=0.0028  Score=53.96  Aligned_cols=28  Identities=32%  Similarity=0.525  Sum_probs=23.5

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.++|+...
T Consensus        27 i~~G~~~~i~G~nGsGKSTLl~~l~Gl~   54 (220)
T cd03293          27 VEEGEFVALVGPSGCGKSTLLRIIAGLE   54 (220)
T ss_pred             EeCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444558899999999999999999875

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.

>PRK10895 lipopolysaccharide ABC transporter ATP-binding protein; Provisional

Probab=96.23  E-value=0.0031  Score=54.48  Aligned_cols=28  Identities=32%  Similarity=0.364  Sum_probs=24.1

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.|.||+|+|||+|.+.|+..+
T Consensus        26 i~~Ge~~~l~G~nGsGKSTLl~~l~G~~   53 (241)
T PRK10895         26 VNSGEIVGLLGPNGAGKTTTFYMVVGIV   53 (241)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            4455559999999999999999999875

>TIGR03864 PQQ_ABC_ATP ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system

Probab=96.22  E-value=0.0031  Score=54.36  Aligned_cols=28  Identities=32%  Similarity=0.488  Sum_probs=23.9

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|+++|+...
T Consensus        24 i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   51 (236)
T TIGR03864        24 VRPGEFVALLGPNGAGKSTLFSLLTRLY   51 (236)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCc
Confidence            4455558999999999999999999865

Members of this protein family are the ATP-binding subunit of an ABC transporter system that is associated with PQQ biosynthesis and PQQ-dependent alcohol dehydrogenases. While this family shows homology to several efflux ABC transporter subunits, the presence of a periplasmic substrate-binding protein and association with systems for catabolism of alcohols suggests a role in import rather than detoxification.

>cd03263 ABC_subfamily_A The ABCA subfamily mediates the transport of a variety of lipid compounds

Probab=96.21  E-value=0.0034  Score=53.29  Aligned_cols=27  Identities=26%  Similarity=0.199  Sum_probs=23.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.+.|+...
T Consensus        26 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   52 (220)
T cd03263          26 YKGEIFGLLGHNGAGKTTTLKMLTGEL   52 (220)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            344448899999999999999999865

Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency, degenerative retinopathies, and congenital keratinization disorders. The ABCA1 protein is involved in disorders of cholesterol transport and high-density lipoprotein (HDL) biosynthesis. The ABCA4 (ABCR) protein transports vitamin A derivatives in the outer segments of photoreceptor cells, and therefore, performs a crucial step in the visual cycle. The ABCA genes are not present in yeast. However, evolutionary studies of ABCA genes indicate that they arose as transporters that subsequently duplicated and that certain sets of ABCA genes were lost in different eukaryotic lineages.

>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=96.21  E-value=0.0033  Score=53.83  Aligned_cols=28  Identities=29%  Similarity=0.337  Sum_probs=23.6

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.+.|+..+
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~~l~Gl~   50 (232)
T cd03218          23 VKQGEIVGLLGPNGAGKTTTFYMIVGLV   50 (232)
T ss_pred             ecCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444558899999999999999999865

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.

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=96.20  E-value=0.0032  Score=51.37  Aligned_cols=28  Identities=25%  Similarity=0.317  Sum_probs=24.0

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++..+.|.||+|+|||+|.+.++...
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~~i~G~~   50 (163)
T cd03216          23 VRRGEVHALLGENGAGKSTLMKILSGLY   50 (163)
T ss_pred             EeCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            4455559999999999999999999876

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.

>PF12780 AAA_8: P-loop containing dynein motor region D4; InterPro: IPR024317 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases

Probab=96.20  E-value=0.0063  Score=54.07  Aligned_cols=56  Identities=23%  Similarity=0.316  Sum_probs=37.7

Q ss_pred             cCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcc-eeeecCCCCchHHHHHHHHhcccceeeeechh
Q 025979          160 DIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRG-VLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS  227 (245)
Q Consensus       160 dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~g-vLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s  227 (245)
                      +++-.+++.+-|.++...            +..|+| .||.|++|+||++++|..|.-++..++.+..+
T Consensus         9 ~lVlf~~ai~hi~ri~Rv------------L~~~~Gh~LLvG~~GsGr~sl~rLaa~i~~~~~~~i~~~   65 (268)
T PF12780_consen    9 NLVLFDEAIEHIARISRV------------LSQPRGHALLVGVGGSGRQSLARLAAFICGYEVFQIEIT   65 (268)
T ss_dssp             -----HHHHHHHHHHHHH------------HCSTTEEEEEECTTTSCHHHHHHHHHHHTTEEEE-TTTS
T ss_pred             ceeeHHHHHHHHHHHHHH------------HcCCCCCeEEecCCCccHHHHHHHHHHHhccceEEEEee
Confidence            344555655555555433            234455 89999999999999999998889999888643

The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four (D1 - D4) correspond to the ATP binding sites with P-loop signatures described previously, and two (D5, D6) are modules in which the P loop has been lost in evolution. This particular entry represents the D4 ATP-binding domain of the motor [].; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>cd03254 ABCC_Glucan_exporter_like Glucan exporter ATP-binding protein

Probab=96.20  E-value=0.0032  Score=53.81  Aligned_cols=26  Identities=35%  Similarity=0.572  Sum_probs=22.7

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++.-+.+.||+|+|||+|.++||..+
T Consensus        28 ~G~~~~i~G~nGsGKSTLl~~l~G~~   53 (229)
T cd03254          28 PGETVAIVGPTGAGKTTLINLLMRFY   53 (229)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCc
Confidence            34448999999999999999999876

In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide, and lipid export. The MRP-like family, similar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains each composed of six transmembrane (TM) helices and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03257 ABC_NikE_OppD_transporters The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE)

Probab=96.20  E-value=0.0033  Score=53.57  Aligned_cols=27  Identities=30%  Similarity=0.418  Sum_probs=23.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.+.|+...
T Consensus        29 ~~Ge~~~i~G~nGsGKSTLl~~l~G~~   55 (228)
T cd03257          29 KKGETLGLVGESGSGKSTLARAILGLL   55 (228)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            344449999999999999999999875

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.

>TIGR01978 sufC FeS assembly ATPase SufC

Probab=96.19  E-value=0.0033  Score=54.14  Aligned_cols=26  Identities=35%  Similarity=0.597  Sum_probs=22.6

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .++.-+.+.||+|+|||+|.++|+..
T Consensus        24 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl   49 (243)
T TIGR01978        24 KKGEIHAIMGPNGSGKSTLSKTIAGH   49 (243)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            34445999999999999999999987

SufC is part of the SUF system, shown in E. coli to consist of six proteins and believed to act in Fe-S cluster formation during oxidative stress. SufC forms a complex with SufB and SufD. SufC belongs to the ATP-binding cassette transporter family (pfam00005) but is no longer thought to be part of a transporter. The complex is reported as cytosolic (PubMed:12554644) or associated with the membrane (PubMed:11943156). The SUF system also includes a cysteine desulfurase (SufS, enhanced by SufE) and a probable iron-sulfur cluster assembly scaffold protein, SufA.

>PRK11629 lolD lipoprotein transporter ATP-binding subunit; Provisional

Probab=96.19  E-value=0.0035  Score=53.91  Aligned_cols=27  Identities=19%  Similarity=0.325  Sum_probs=23.2

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.+.|+..+
T Consensus        33 ~~Ge~~~l~G~nGsGKSTLl~~l~Gl~   59 (233)
T PRK11629         33 GEGEMMAIVGSSGSGKSTLLHLLGGLD   59 (233)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            344458999999999999999999875

>PRK11264 putative amino-acid ABC transporter ATP-binding protein YecC; Provisional

Probab=96.19  E-value=0.0033  Score=54.50  Aligned_cols=28  Identities=32%  Similarity=0.586  Sum_probs=23.5

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.|.||+|+|||+|+++|+..+
T Consensus        26 i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   53 (250)
T PRK11264         26 VKPGEVVAIIGPSGSGKTTLLRCINLLE   53 (250)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3444458899999999999999999875

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=96.19  E-value=0.0049  Score=56.68  Aligned_cols=39  Identities=23%  Similarity=0.244  Sum_probs=27.1

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---------cceeeeechh
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---------TAAFIRVVGS  227 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---------~~~~~~v~~s  227 (245)
                      |+....-..++||||||||.+|..+|-..         +...++|+..
T Consensus       122 Gi~~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE  169 (344)
T PLN03187        122 GIETRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTE  169 (344)
T ss_pred             CCCCCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcC
Confidence            34444448899999999999999886321         3456666653

>TIGR03005 ectoine_ehuA ectoine/hydroxyectoine ABC transporter, ATP-binding protein

Probab=96.18  E-value=0.0033  Score=54.72  Aligned_cols=28  Identities=25%  Similarity=0.510  Sum_probs=23.9

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.+.|+..+
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   50 (252)
T TIGR03005        23 VAAGEKVALIGPSGSGKSTILRILMTLE   50 (252)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3455559999999999999999999876

Members of this family are the ATP-binding protein of a conserved four gene ABC transporter operon found next to ectoine unilization operons and ectoine biosynthesis operons. Ectoine is a compatible solute that protects enzymes from high osmolarity. It is released by some species in response to hypoosmotic shock, and it is taken up by a number of bacteria as a compatible solute or for consumption. This family shows strong sequence similiarity to a number of amino acid ABC transporter ATP-binding proteins.

>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=96.18  E-value=0.0032  Score=52.12  Aligned_cols=28  Identities=29%  Similarity=0.275  Sum_probs=23.8

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++..+.+.||+|+|||+|.+.|+...
T Consensus        23 i~~G~~~~i~G~nGsGKSTLl~~l~G~~   50 (182)
T cd03215          23 VRAGEIVGIAGLVGNGQTELAEALFGLR   50 (182)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444558999999999999999999876

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.

>COG4525 TauB ABC-type taurine transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=96.18  E-value=0.0039  Score=53.22  Aligned_cols=27  Identities=33%  Similarity=0.521  Sum_probs=22.4

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+.--+.+.||+|||||+|...+|...
T Consensus        29 a~ge~vv~lGpSGcGKTTLLnl~AGf~   55 (259)
T COG4525          29 ASGELVVVLGPSGCGKTTLLNLIAGFV   55 (259)
T ss_pred             cCCCEEEEEcCCCccHHHHHHHHhcCc
Confidence            334448899999999999999999865

>cd03251 ABCC_MsbA MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins

Probab=96.18  E-value=0.0034  Score=53.87  Aligned_cols=28  Identities=32%  Similarity=0.539  Sum_probs=23.5

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|++.+|..+
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   52 (234)
T cd03251          25 IPAGETVALVGPSGSGKSTLVNLIPRFY   52 (234)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhccc
Confidence            3344458999999999999999999876

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.

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=96.17  E-value=0.0043  Score=50.93  Aligned_cols=27  Identities=30%  Similarity=0.650  Sum_probs=23.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.+.|+...
T Consensus        26 ~~Ge~~~i~G~nGsGKStLl~~l~G~~   52 (173)
T cd03246          26 EPGESLAIIGPSGSGKSTLARLILGLL   52 (173)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhcc
Confidence            344448999999999999999999875

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

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=96.16  E-value=0.0034  Score=53.20  Aligned_cols=26  Identities=19%  Similarity=0.503  Sum_probs=22.1

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHh
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      ++..+-++|.||+|+|||++.|.++.
T Consensus        22 l~~g~~~~ltGpNg~GKSTllr~i~~   47 (199)
T cd03283          22 MEKKNGILITGSNMSGKSTFLRTIGV   47 (199)
T ss_pred             EcCCcEEEEECCCCCChHHHHHHHHH
Confidence            34446689999999999999999985

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

>cd03267 ABC_NatA_like Similar in sequence to NatA, this is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled to proton or K+ uptake

Probab=96.16  E-value=0.0031  Score=54.51  Aligned_cols=27  Identities=30%  Similarity=0.358  Sum_probs=23.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.|.||+|+|||+|.+.|+..+
T Consensus        45 ~~Ge~~~i~G~NGsGKSTLl~~i~Gl~   71 (236)
T cd03267          45 EKGEIVGFIGPNGAGKTTTLKILSGLL   71 (236)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCc
Confidence            344458899999999999999999865

NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilis, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of the single ATP-binding protein and the single intergral membrane protein.

>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR)

Probab=96.16  E-value=0.0034  Score=52.61  Aligned_cols=28  Identities=32%  Similarity=0.555  Sum_probs=24.1

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++..+.+.||+|+|||+|.+.||...
T Consensus        32 i~~Ge~~~l~G~nGsGKStLl~~i~Gl~   59 (194)
T cd03213          32 AKPGELTAIMGPSGAGKSTLLNALAGRR   59 (194)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3455559999999999999999999976

DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.

>TIGR02770 nickel_nikD nickel import ATP-binding protein NikD

Probab=96.16  E-value=0.0034  Score=53.90  Aligned_cols=29  Identities=21%  Similarity=0.332  Sum_probs=24.5

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      +.++..+.+.||+|+|||+|.+.|+....
T Consensus         9 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~~   37 (230)
T TIGR02770         9 LKRGEVLALVGESGSGKSLTCLAILGLLP   37 (230)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            34555599999999999999999998764

This family represents the NikD subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase. NikD and NikE are homologous.

>PRK10771 thiQ thiamine transporter ATP-binding subunit; Provisional

Probab=96.15  E-value=0.0037  Score=53.74  Aligned_cols=28  Identities=29%  Similarity=0.561  Sum_probs=24.2

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++..+.|.||+|+|||+|.+.|+...
T Consensus        22 i~~Ge~~~l~G~nGsGKSTLl~~l~Gl~   49 (232)
T PRK10771         22 VERGERVAILGPSGAGKSTLLNLIAGFL   49 (232)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            4555669999999999999999999875

>PRK11860 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidine monophosphate kinase; Provisional

Probab=96.15  E-value=0.0057  Score=60.89  Aligned_cols=34  Identities=21%  Similarity=0.316  Sum_probs=28.7

Q ss_pred             ceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      .+.+.||+|+|||++|+.+|+.++.+|  ++...+.
T Consensus       444 ~i~i~g~~~~gks~~~~~l~~~~~~~~--~~~~~~~  477 (661)
T PRK11860        444 VICIDGPTASGKGTVAARVAEALGYHY--LDSGALY  477 (661)
T ss_pred             eEEeeCCCCCCHHHHHHHHHHHhCCeE--ecHHHhh
Confidence            478899999999999999999999998  5544443

>PRK11248 tauB taurine transporter ATP-binding subunit; Provisional

Probab=96.15  E-value=0.0035  Score=54.93  Aligned_cols=28  Identities=29%  Similarity=0.552  Sum_probs=23.6

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.++|+...
T Consensus        24 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   51 (255)
T PRK11248         24 LESGELLVVLGPSGCGKTTLLNLIAGFV   51 (255)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444558999999999999999999875

>PRK10908 cell division protein FtsE; Provisional

Probab=96.15  E-value=0.0036  Score=53.34  Aligned_cols=28  Identities=29%  Similarity=0.472  Sum_probs=23.9

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.+.|+...
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   52 (222)
T PRK10908         25 MRPGEMAFLTGHSGAGKSTLLKLICGIE   52 (222)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3455558999999999999999999876

>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=96.14  E-value=0.0037  Score=53.21  Aligned_cols=28  Identities=29%  Similarity=0.337  Sum_probs=23.5

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.|.||+|+|||+|.+.|+..+
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~~i~G~~   50 (220)
T cd03265          23 VRRGEIFGLLGPNGAGKTTTIKMLTTLL   50 (220)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444558899999999999999999865

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.

>TIGR01277 thiQ thiamine ABC transporter, ATP-binding protein

Probab=96.14  E-value=0.0033  Score=53.31  Aligned_cols=29  Identities=28%  Similarity=0.480  Sum_probs=25.1

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+.++..+.+.||+|+|||+|.++|+..+
T Consensus        20 ~i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   48 (213)
T TIGR01277        20 NVADGEIVAIMGPSGAGKSTLLNLIAGFI   48 (213)
T ss_pred             EEeCCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            34566669999999999999999999876

This model describes the energy-transducing ATPase subunit ThiQ of the ThiBPQ thiamine (and thiamine pyrophosphate) ABC transporter in several Proteobacteria. This protein is found so far only in Proteobacteria, and is found in complete genomes only if the ThiB and ThiP subunits are also found.

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=96.14  E-value=0.0052  Score=59.18  Aligned_cols=46  Identities=26%  Similarity=0.294  Sum_probs=0.0

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc----cceeeeechhHHHHHHh
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT----TAAFIRVVGSEFVQKYL  234 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l----~~~~~~v~~s~l~~~~~  234 (245)
                      |+.+++-+|++|+||+|||++|..++...    |-+.+.++..+-.+.+.
T Consensus        27 G~p~Gs~~li~G~pGsGKT~l~~qf~~~~~~~~ge~~lyis~ee~~~~i~   76 (509)
T PRK09302         27 GLPKGRPTLVSGTAGTGKTLFALQFLVNGIKRFDEPGVFVTFEESPEDII   76 (509)
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCEEEEEccCCHHHHH

>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=96.13  E-value=0.0036  Score=53.10  Aligned_cols=27  Identities=33%  Similarity=0.449  Sum_probs=23.1

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++..+.+.||+|+|||+|.+.|+...
T Consensus        29 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   55 (218)
T cd03266          29 KPGEVTGLLGPNGAGKTTTLRMLAGLL   55 (218)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhCCc
Confidence            344458999999999999999999875

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.

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=96.13  E-value=0.0036  Score=51.39  Aligned_cols=27  Identities=33%  Similarity=0.394  Sum_probs=23.2

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+...+.+.||+|+|||+|.+.+|..+
T Consensus        24 ~~Ge~~~i~G~nGsGKStLl~~l~G~~   50 (173)
T cd03230          24 EKGEIYGLLGPNGAGKTTLIKIILGLL   50 (173)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            344458999999999999999999875

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.

>cd03259 ABC_Carb_Solutes_like ABC Carbohydrate and Solute Transporters-like subgroup

Probab=96.13  E-value=0.0038  Score=52.83  Aligned_cols=27  Identities=37%  Similarity=0.607  Sum_probs=23.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.+.|+..+
T Consensus        24 ~~Ge~~~i~G~nGsGKSTLl~~l~G~~   50 (213)
T cd03259          24 EPGEFLALLGPSGCGKTTLLRLIAGLE   50 (213)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            344458899999999999999999865

This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR00959 ffh signal recognition particle protein

Probab=96.13  E-value=0.0053  Score=58.09  Aligned_cols=36  Identities=28%  Similarity=0.392  Sum_probs=27.3

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc----cceeeeechh
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT----TAAFIRVVGS  227 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l----~~~~~~v~~s  227 (245)
                      .|.-++|+||||+|||++|.-+|..+    |..+..+++.
T Consensus        98 ~p~vi~~vG~~GsGKTTtaakLA~~l~~~~g~kV~lV~~D  137 (428)
T TIGR00959        98 PPTVILMVGLQGSGKTTTCGKLAYYLKKKQGKKVLLVACD  137 (428)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHHhCCCeEEEEecc
Confidence            45679999999999999988887663    4555556554

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.

>cd03244 ABCC_MRP_domain2 Domain 2 of the ABC subfamily C

Probab=96.13  E-value=0.0031  Score=53.61  Aligned_cols=27  Identities=30%  Similarity=0.388  Sum_probs=22.9

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.+.|+...
T Consensus        28 ~~Ge~~~i~G~nGsGKSTLl~~l~G~~   54 (221)
T cd03244          28 KPGEKVGIVGRTGSGKSSLLLALFRLV   54 (221)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHcCC
Confidence            344448899999999999999999875

This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.

>PRK13538 cytochrome c biogenesis protein CcmA; Provisional

Probab=96.12  E-value=0.0037  Score=52.68  Aligned_cols=28  Identities=32%  Similarity=0.489  Sum_probs=23.6

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.+.|+..+
T Consensus        24 i~~Ge~~~l~G~nGsGKSTLl~~l~G~~   51 (204)
T PRK13538         24 LNAGELVQIEGPNGAGKTSLLRILAGLA   51 (204)
T ss_pred             ECCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444558999999999999999999875

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

Probab=96.12  E-value=0.0038  Score=51.61  Aligned_cols=28  Identities=36%  Similarity=0.504  Sum_probs=23.9

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.+..-+.|.||+|+|||+|.+.++...
T Consensus        22 i~~G~~~~l~G~nGsGKStLl~~i~G~~   49 (180)
T cd03214          22 IEAGEIVGILGPNGAGKSTLLKTLAGLL   49 (180)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3455559999999999999999999876

Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=96.12  E-value=0.0055  Score=57.31  Aligned_cols=50  Identities=30%  Similarity=0.390  Sum_probs=38.3

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ...|.-+.|++..+..|.-....|             .-.|+|+-|+.|||||+++||||.-|
T Consensus        13 ~~pf~aivGqd~lk~aL~l~av~P-------------~iggvLI~G~kGtaKSt~~Rala~LL   62 (423)
T COG1239          13 NLPFTAIVGQDPLKLALGLNAVDP-------------QIGGALIAGEKGTAKSTLARALADLL   62 (423)
T ss_pred             ccchhhhcCchHHHHHHhhhhccc-------------ccceeEEecCCCccHHHHHHHHHHhC
Confidence            355677899988877775432221             22579999999999999999999988

>PRK13540 cytochrome c biogenesis protein CcmA; Provisional

Probab=96.12  E-value=0.0045  Score=52.00  Aligned_cols=27  Identities=33%  Similarity=0.334  Sum_probs=23.4

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.+.|+...
T Consensus        25 ~~Ge~~~l~G~nGsGKSTLl~~i~G~~   51 (200)
T PRK13540         25 PAGGLLHLKGSNGAGKTTLLKLIAGLL   51 (200)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            444559999999999999999999876

>PRK05439 pantothenate kinase; Provisional

Probab=96.12  E-value=0.0051  Score=55.83  Aligned_cols=24  Identities=17%  Similarity=0.188  Sum_probs=21.2

Q ss_pred             ceeeecCCCCchHHHHHHHHhccc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      -|.+.||||+|||++|+.|+..++
T Consensus        88 iIgIaG~~gsGKSTla~~L~~~l~  111 (311)
T PRK05439         88 IIGIAGSVAVGKSTTARLLQALLS  111 (311)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            377899999999999999998764

>cd00879 Sar1 Sar1 subfamily

Probab=96.11  E-value=0.006  Score=50.17  Aligned_cols=30  Identities=23%  Similarity=0.454  Sum_probs=23.2

Q ss_pred             hhhccCCCcc-eeeecCCCCchHHHHHHHHh
Q 025979          186 KQIGIDPPRG-VLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       186 ~~~g~~~~~g-vLl~GPPGtGKT~lAkalA~  215 (245)
                      ..+|+...++ +++.||+|+|||+|.+.+..
T Consensus        11 ~~~~~~~~~~ki~ilG~~~~GKStLi~~l~~   41 (190)
T cd00879          11 SSLGLYNKEAKILFLGLDNAGKTTLLHMLKD   41 (190)
T ss_pred             HHhhcccCCCEEEEECCCCCCHHHHHHHHhc
Confidence            3445443333 99999999999999999986

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.

>TIGR02323 CP_lyasePhnK phosphonate C-P lyase system protein PhnK

Probab=96.11  E-value=0.0037  Score=54.37  Aligned_cols=28  Identities=25%  Similarity=0.401  Sum_probs=23.9

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++..+.+.||+|+|||+|.+.++...
T Consensus        26 i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   53 (253)
T TIGR02323        26 LYPGEVLGIVGESGSGKSTLLGCLAGRL   53 (253)
T ss_pred             EeCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3445559999999999999999999876

Members of this family are the PhnK protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated complex. This protein (PhnK) and the adjacent-encoded PhnL resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this complex rather than part of a transporter per se.

>cd03250 ABCC_MRP_domain1 Domain 1 of the ABC subfamily C

Probab=96.10  E-value=0.004  Score=52.40  Aligned_cols=28  Identities=29%  Similarity=0.428  Sum_probs=23.9

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++..+.+.||+|+|||+|.+.++...
T Consensus        28 i~~G~~~~i~G~nG~GKSTLl~~i~G~~   55 (204)
T cd03250          28 VPKGELVAIVGPVGSGKSSLLSALLGEL   55 (204)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhCcC
Confidence            3455559999999999999999999875

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.

>PRK10584 putative ABC transporter ATP-binding protein YbbA; Provisional

Probab=96.10  E-value=0.0038  Score=53.37  Aligned_cols=28  Identities=25%  Similarity=0.420  Sum_probs=23.9

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.|.||+|+|||+|.+.|+...
T Consensus        33 i~~Ge~~~i~G~nGsGKSTLl~~i~Gl~   60 (228)
T PRK10584         33 VKRGETIALIGESGSGKSTLLAILAGLD   60 (228)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHHcCC
Confidence            3445559999999999999999999875

>PRK09493 glnQ glutamine ABC transporter ATP-binding protein; Reviewed

Probab=96.10  E-value=0.0038  Score=53.84  Aligned_cols=28  Identities=32%  Similarity=0.623  Sum_probs=23.7

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.|.||+|+|||+|++.|+..+
T Consensus        24 i~~Ge~~~l~G~nGsGKSTLl~~l~G~~   51 (240)
T PRK09493         24 IDQGEVVVIIGPSGSGKSTLLRCINKLE   51 (240)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3445558899999999999999999876

>cd03268 ABC_BcrA_bacitracin_resist The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance

Probab=96.10  E-value=0.0038  Score=52.61  Aligned_cols=27  Identities=26%  Similarity=0.287  Sum_probs=23.1

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++..+.+.||+|+|||+|.+.++...
T Consensus        24 ~~G~~~~i~G~nGsGKSTLl~~l~Gl~   50 (208)
T cd03268          24 KKGEIYGFLGPNGAGKTTTMKIILGLI   50 (208)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhCCc
Confidence            344558999999999999999999865

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.

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=96.10  E-value=0.0039  Score=55.48  Aligned_cols=24  Identities=33%  Similarity=0.505  Sum_probs=22.7

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+++++||||+|||++.++++..+
T Consensus       112 ~~~~i~g~~g~GKttl~~~l~~~~  135 (270)
T TIGR02858       112 LNTLIISPPQCGKTTLLRDLARIL  135 (270)
T ss_pred             eEEEEEcCCCCCHHHHHHHHhCcc
Confidence            579999999999999999999987

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

>COG1122 CbiO ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=96.08  E-value=0.0037  Score=54.49  Aligned_cols=40  Identities=33%  Similarity=0.448  Sum_probs=29.6

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcccce--eeeechhHH
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHTTAA--FIRVVGSEF  229 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~--~~~v~~s~l  229 (245)
                      +.+...++++||+|+|||++++.++.-+...  .+.+++..+
T Consensus        27 i~~Ge~~~i~G~nGsGKSTL~~~l~GLl~p~~G~v~~~g~~~   68 (235)
T COG1122          27 IEKGERVLLIGPNGSGKSTLLKLLNGLLKPTSGEVLVDGLDT   68 (235)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHcCcCcCCCCEEEECCeec
Confidence            4455569999999999999999999877322  345665543

>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1)

Probab=96.08  E-value=0.0033  Score=53.02  Aligned_cols=27  Identities=22%  Similarity=0.304  Sum_probs=22.9

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.++|+...
T Consensus        32 ~~G~~~~i~G~nGsGKSTLl~~l~Gl~   58 (207)
T cd03369          32 KAGEKIGIVGRTGAGKSTLILALFRFL   58 (207)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhccc
Confidence            344448999999999999999999865

NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters. Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.

>PRK14267 phosphate ABC transporter ATP-binding protein; Provisional

Probab=96.08  E-value=0.004  Score=54.12  Aligned_cols=28  Identities=29%  Similarity=0.418  Sum_probs=23.6

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.|.||+|+|||+|.+.++..+
T Consensus        27 i~~Ge~~~l~G~nGsGKSTLl~~l~G~~   54 (253)
T PRK14267         27 IPQNGVFALMGPSGCGKSTLLRTFNRLL   54 (253)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhccC
Confidence            3444558899999999999999999875

>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=96.08  E-value=0.0043  Score=47.18  Aligned_cols=21  Identities=33%  Similarity=0.612  Sum_probs=19.5

Q ss_pred             eeeecCCCCchHHHHHHHHhc
Q 025979          196 VLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~  216 (245)
                      |++.|+||+|||+|..++.+.
T Consensus         2 V~iiG~~~~GKSTlin~l~~~   22 (116)
T PF01926_consen    2 VAIIGRPNVGKSTLINALTGK   22 (116)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhcc
Confidence            789999999999999999974

These proteins represent a new subfamily of GTP-binding proteins that has both prokaryote and eukaryote members [].; GO: 0005525 GTP binding, 0005622 intracellular; PDB: 2DWQ_B 2DBY_A 3CNN_A 3CNO_A 3CNL_A 3IBY_A 1PUI_B 1WXQ_A 1LNZ_A 3GEE_A ....

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

Probab=96.08  E-value=0.0041  Score=54.28  Aligned_cols=40  Identities=23%  Similarity=0.365  Sum_probs=29.3

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc--cceeeeechhHHH
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT--TAAFIRVVGSEFV  230 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l--~~~~~~v~~s~l~  230 (245)
                      .++-.+=++||+|||||+|++++|.-.  ..--+.+++..+.
T Consensus        31 ~~Ge~lgivGeSGsGKSTL~r~l~Gl~~p~~G~I~~~G~~~~   72 (252)
T COG1124          31 ERGETLGIVGESGSGKSTLARLLAGLEKPSSGSILLDGKPLA   72 (252)
T ss_pred             cCCCEEEEEcCCCCCHHHHHHHHhcccCCCCceEEECCcccC
Confidence            344447799999999999999999866  3334556665544

>cd03232 ABC_PDR_domain2 The pleiotropic drug resistance-like (PDR) family of ATP-binding cassette (ABC) transporters

Probab=96.07  E-value=0.0039  Score=52.13  Aligned_cols=27  Identities=33%  Similarity=0.514  Sum_probs=22.8

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      +.+..-+.|.||+|+|||+|.+.++..
T Consensus        30 i~~Ge~~~l~G~nGsGKSTLl~~l~G~   56 (192)
T cd03232          30 VKPGTLTALMGESGAGKTTLLDVLAGR   56 (192)
T ss_pred             EeCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            345555899999999999999999974

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK12608 transcription termination factor Rho; Provisional

Probab=96.07  E-value=0.0043  Score=57.58  Aligned_cols=24  Identities=33%  Similarity=0.552  Sum_probs=21.6

Q ss_pred             ceeeecCCCCchHHHHHHHHhccc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      ..|++||||||||++++.+|+.+.
T Consensus       135 R~LIvG~pGtGKTTLl~~la~~i~  158 (380)
T PRK12608        135 RGLIVAPPRAGKTVLLQQIAAAVA  158 (380)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHH
Confidence            489999999999999999998763

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=96.07  E-value=0.0071  Score=55.09  Aligned_cols=26  Identities=23%  Similarity=0.309  Sum_probs=23.7

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+.++||+||.|+||+.+|+++|..+
T Consensus        24 l~hA~L~~G~~G~Gk~~lA~~~a~~l   49 (319)
T PRK06090         24 IPGALLLQSDEGLGVESLVELFSRAL   49 (319)
T ss_pred             cceeEeeECCCCCCHHHHHHHHHHHH
Confidence            56789999999999999999999876

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=96.07  E-value=0.0085  Score=57.61  Aligned_cols=48  Identities=23%  Similarity=0.409  Sum_probs=34.2

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcc-eeeecCCCCchHHHHHHHHhccc
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRG-VLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~g-vLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      .++++++-.+++.+.+.+.+.               .++| +++.||+|+|||++..++.+.+.
T Consensus       219 ~~l~~Lg~~~~~~~~l~~~~~---------------~~~GlilitGptGSGKTTtL~a~L~~l~  267 (486)
T TIGR02533       219 LDLETLGMSPELLSRFERLIR---------------RPHGIILVTGPTGSGKTTTLYAALSRLN  267 (486)
T ss_pred             CCHHHcCCCHHHHHHHHHHHh---------------cCCCEEEEEcCCCCCHHHHHHHHHhccC
Confidence            455666655555666655543               3456 78999999999999998877763

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.

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=96.06  E-value=0.0054  Score=56.73  Aligned_cols=24  Identities=33%  Similarity=0.634  Sum_probs=21.5

Q ss_pred             cc-eeeecCCCCchHHHHHHHHhcc
Q 025979          194 RG-VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~g-vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +| ++++||+|+|||++.+++.+.+
T Consensus       134 ~glilI~GpTGSGKTTtL~aLl~~i  158 (358)
T TIGR02524       134 EGIVFITGATGSGKSTLLAAIIREL  158 (358)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH
Confidence            44 8999999999999999999776

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.

>PRK14250 phosphate ABC transporter ATP-binding protein; Provisional

Probab=96.06  E-value=0.0041  Score=53.83  Aligned_cols=27  Identities=26%  Similarity=0.396  Sum_probs=23.2

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|++.|+..+
T Consensus        27 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   53 (241)
T PRK14250         27 EGGAIYTIVGPSGAGKSTLIKLINRLI   53 (241)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            344458899999999999999999875

>cd04155 Arl3 Arl3 subfamily

Probab=96.06  E-value=0.0042  Score=50.09  Aligned_cols=23  Identities=30%  Similarity=0.499  Sum_probs=20.8

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ..+++.||+|+|||+|.+++.+.
T Consensus        15 ~~v~i~G~~g~GKStLl~~l~~~   37 (173)
T cd04155          15 PRILILGLDNAGKTTILKQLASE   37 (173)
T ss_pred             cEEEEEccCCCCHHHHHHHHhcC
Confidence            44999999999999999999985

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.

>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain

Probab=96.05  E-value=0.007  Score=43.39  Aligned_cols=22  Identities=36%  Similarity=0.531  Sum_probs=20.1

Q ss_pred             eeeecCCCCchHHHHHHHHhcc
Q 025979          196 VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++++|.+|+|||+++..+|..+
T Consensus         2 ~~~~g~~G~Gktt~~~~l~~~l   23 (99)
T cd01983           2 IVVTGKGGVGKTTLAANLAAAL   23 (99)
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            5788999999999999999887

Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.

>PRK14262 phosphate ABC transporter ATP-binding protein; Provisional

Probab=96.05  E-value=0.0041  Score=53.95  Aligned_cols=28  Identities=29%  Similarity=0.444  Sum_probs=23.1

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.++|+...
T Consensus        26 i~~Ge~~~i~G~nGsGKSTLl~~i~Gl~   53 (250)
T PRK14262         26 IFKNQITAIIGPSGCGKTTLLRSINRMN   53 (250)
T ss_pred             ecCCCEEEEECCCCCCHHHHHHHHhccc
Confidence            3444558899999999999999999754

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=96.05  E-value=0.0043  Score=50.00  Aligned_cols=29  Identities=34%  Similarity=0.527  Sum_probs=24.4

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      +.+..-+++.||+|+|||++.++++..+.
T Consensus        22 i~~g~~~~i~G~nGsGKStll~~l~g~~~   50 (157)
T cd00267          22 LKAGEIVALVGPNGSGKSTLLRAIAGLLK   50 (157)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            34555699999999999999999998763

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.

>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=96.05  E-value=0.0021  Score=56.75  Aligned_cols=32  Identities=28%  Similarity=0.558  Sum_probs=25.4

Q ss_pred             hhhccCCCcc--eeeecCCCCchHHHHHHHHhcc
Q 025979          186 KQIGIDPPRG--VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       186 ~~~g~~~~~g--vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.+..+.|  ++|.||+|||||++.|.|-+-.
T Consensus        18 ~~v~l~I~~gef~vliGpSGsGKTTtLkMINrLi   51 (309)
T COG1125          18 DDVNLTIEEGEFLVLIGPSGSGKTTTLKMINRLI   51 (309)
T ss_pred             eeeeEEecCCeEEEEECCCCCcHHHHHHHHhccc
Confidence            4445555566  8899999999999999998755

>cd03249 ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1

Probab=96.05  E-value=0.0048  Score=53.08  Aligned_cols=27  Identities=26%  Similarity=0.459  Sum_probs=23.4

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|+++|+..+
T Consensus        27 ~~Ge~~~l~G~nGsGKSTLl~~i~G~~   53 (238)
T cd03249          27 PPGKTVALVGSSGCGKSTVVSLLERFY   53 (238)
T ss_pred             cCCCEEEEEeCCCCCHHHHHHHHhccC
Confidence            444559999999999999999999876

In fact, the yeast MDL1 (multidrug resistance-like protein 1) and MDL2 (multidrug resistance-like protein 2) transporters are also included in this CD. MDL1 is an ATP-dependent permease that acts as a high-copy suppressor of ATM1 and is thought to have a role in resistance to oxidative stress. Interestingly, subfamily B is more closely related to the carboxyl-terminal component of subfamily C than the two halves of ABCC molecules are with one another.

>PRK13543 cytochrome c biogenesis protein CcmA; Provisional

Probab=96.05  E-value=0.0042  Score=52.82  Aligned_cols=28  Identities=32%  Similarity=0.527  Sum_probs=23.8

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++..+.+.||+|+|||+|.+.++...
T Consensus        34 i~~Ge~~~i~G~nGsGKSTLl~~i~G~~   61 (214)
T PRK13543         34 VDAGEALLVQGDNGAGKTTLLRVLAGLL   61 (214)
T ss_pred             ECCCCEEEEEcCCCCCHHHHHHHHhCCC
Confidence            4455558999999999999999999865

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=96.05  E-value=0.0047  Score=53.18  Aligned_cols=27  Identities=33%  Similarity=0.450  Sum_probs=22.9

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhccc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      .+.-+.|.||+|+|||+|++.|+..+.
T Consensus        32 ~~~iigi~G~~GsGKTTl~~~L~~~l~   58 (229)
T PRK09270         32 RRTIVGIAGPPGAGKSTLAEFLEALLQ   58 (229)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHhh
Confidence            344478999999999999999998874

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=96.04  E-value=0.0043  Score=63.38  Aligned_cols=27  Identities=30%  Similarity=0.580  Sum_probs=24.9

Q ss_pred             eeeecCCCCchHHHHHHHHhcccceee
Q 025979          196 VLLYGPPGTGKTMLAKAVANHTTAAFI  222 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l~~~~~  222 (245)
                      +.+-||||||||++|+.||..+++.|+
T Consensus        37 i~idG~~gsGKst~~~~la~~l~~~~~   63 (863)
T PRK12269         37 IALDGPAGSGKSSVCRLLASRLGAQCL   63 (863)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEE
Confidence            778999999999999999999998764

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=96.04  E-value=0.0066  Score=54.56  Aligned_cols=26  Identities=19%  Similarity=0.282  Sum_probs=21.3

Q ss_pred             CcceeeecCCCCchHHHHHHHHhccc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      |--+.+.||+|+|||++|+.|+..+.
T Consensus        62 p~IIGIaG~~GSGKSTlar~L~~ll~   87 (290)
T TIGR00554        62 PYIISIAGSVAVGKSTTARILQALLS   87 (290)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            33477999999999999998877663

Shown to be a homodimer in E. coli. This enzyme catalyzes the rate-limiting step in the biosynthesis of coenzyme A. It is very well conserved from E. coli to B. subtilis, but differs considerably from known eukaryotic forms, described in a separate model.

>cd03253 ABCC_ATM1_transporter ATM1 is an ABC transporter that is expressed in the mitochondria

Probab=96.03  E-value=0.0042  Score=53.30  Aligned_cols=27  Identities=22%  Similarity=0.468  Sum_probs=23.1

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.++|+...
T Consensus        25 ~~Ge~~~l~G~nGsGKSTLl~~i~Gl~   51 (236)
T cd03253          25 PAGKKVAIVGPSGSGKSTILRLLFRFY   51 (236)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhccc
Confidence            344458899999999999999999876

Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to mitochondrial DNA, and decreased levels of cytosolic heme proteins. 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.

>PRK13539 cytochrome c biogenesis protein CcmA; Provisional

Probab=96.03  E-value=0.0043  Score=52.44  Aligned_cols=27  Identities=33%  Similarity=0.557  Sum_probs=23.2

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.+.++...
T Consensus        26 ~~Ge~~~i~G~nGsGKSTLl~~l~G~~   52 (207)
T PRK13539         26 AAGEALVLTGPNGSGKTTLLRLIAGLL   52 (207)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            344558999999999999999999875

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=96.03  E-value=0.0069  Score=57.03  Aligned_cols=37  Identities=32%  Similarity=0.588  Sum_probs=31.2

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHH
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFV  230 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~  230 (245)
                      ..+|++|++||||+++|+++....   +.+|+.+++..+-
T Consensus       167 ~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~~~i~c~~~~  206 (457)
T PRK11361        167 ASVLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALP  206 (457)
T ss_pred             cEEEEEcCCCccHHHHHHHHHHhCCCCCCCeEEEECCCCC
Confidence            459999999999999999997654   6789999987653

>cd03297 ABC_ModC_molybdenum_transporter ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB

Probab=96.03  E-value=0.0041  Score=52.71  Aligned_cols=27  Identities=22%  Similarity=0.497  Sum_probs=23.9

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.+ .-+.+.||+|+|||+|++.++..+
T Consensus        21 i~~-e~~~i~G~nGsGKSTLl~~l~G~~   47 (214)
T cd03297          21 LNE-EVTGIFGASGAGKSTLLRCIAGLE   47 (214)
T ss_pred             Ecc-eeEEEECCCCCCHHHHHHHHhCCC
Confidence            456 668999999999999999999876

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.

>cd03245 ABCC_bacteriocin_exporters ABC-type bacteriocin exporters

Probab=96.02  E-value=0.0043  Score=52.67  Aligned_cols=27  Identities=30%  Similarity=0.375  Sum_probs=23.1

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.++|+...
T Consensus        28 ~~G~~~~i~G~nGsGKSTLl~~i~G~~   54 (220)
T cd03245          28 RAGEKVAIIGRVGSGKSTLLKLLAGLY   54 (220)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCc
Confidence            344458899999999999999999875

Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two glycine residues in positions -1 and -2. A dedicated ATP-binding cassette (ABC) transporter is responsible for the proteolytic cleavage of the leader peptides and subsequent translocation of the bacteriocins across the cytoplasmic membrane.

>PRK14242 phosphate transporter ATP-binding protein; Provisional

Probab=96.02  E-value=0.0042  Score=54.01  Aligned_cols=28  Identities=21%  Similarity=0.469  Sum_probs=23.2

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.++|+...
T Consensus        29 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   56 (253)
T PRK14242         29 FEQNQVTALIGPSGCGKSTFLRCLNRMN   56 (253)
T ss_pred             EeCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            3444558999999999999999999753

>PRK11701 phnK phosphonate C-P lyase system protein PhnK; Provisional

Probab=96.01  E-value=0.0042  Score=54.29  Aligned_cols=28  Identities=29%  Similarity=0.434  Sum_probs=24.1

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|++.|+..+
T Consensus        29 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   56 (258)
T PRK11701         29 LYPGEVLGIVGESGSGKTTLLNALSARL   56 (258)
T ss_pred             EeCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            4455559999999999999999999876

>PRK11300 livG leucine/isoleucine/valine transporter ATP-binding subunit; Provisional

Probab=96.01  E-value=0.0042  Score=54.02  Aligned_cols=28  Identities=29%  Similarity=0.434  Sum_probs=23.7

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.|.||+|+|||+|.+.|+...
T Consensus        28 i~~Ge~~~l~G~nGsGKSTLl~~l~Gl~   55 (255)
T PRK11300         28 VREQEIVSLIGPNGAGKTTVFNCLTGFY   55 (255)
T ss_pred             EcCCeEEEEECCCCCCHHHHHHHHhCCc
Confidence            3445558999999999999999999875

>TIGR03740 galliderm_ABC gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit

Probab=96.01  E-value=0.0045  Score=52.79  Aligned_cols=28  Identities=29%  Similarity=0.394  Sum_probs=23.8

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++..+.+.||+|+|||+|.+.++..+
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   50 (223)
T TIGR03740        23 VPKNSVYGLLGPNGAGKSTLLKMITGIL   50 (223)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3455558999999999999999999875

Model TIGR03731 represents the family of all lantibiotics related to gallidermin, including epidermin, mutatin, and nisin. This protein family describes the ATP-binding subunit of a gallidermin/epidermin class lantibiotic protection transporter. It is largely restricted to gallidermin-family lantibiotic biosynthesis and export cassettes, but also occurs in orphan transporter cassettes in species that lack candidate lantibiotic precursor and synthetase genes.

>cd03252 ABCC_Hemolysin The ABC-transporter hemolysin B is a central component of the secretion machinery that translocates the toxin, hemolysin A, in a Sec-independent fashion across both membranes of E

Probab=96.00  E-value=0.0044  Score=53.27  Aligned_cols=27  Identities=30%  Similarity=0.458  Sum_probs=23.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|++.|+..+
T Consensus        26 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   52 (237)
T cd03252          26 KPGEVVGIVGRSGSGKSTLTKLIQRFY   52 (237)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCc
Confidence            344449999999999999999999876

coli. The hemolysin A (HlyA) transport machinery is composed of the ATP-binding cassette (ABC) transporter HlyB located in the inner membrane, hemolysin D (HlyD), also anchored in the inner membrane, and TolC, which resides in the outer membrane. HlyD apparently forms a continuous channel that bridges the entire periplasm, interacting with TolC and HlyB. This arrangement prevents the appearance of periplasmic intermediates of HlyA during substrate transport. Little is known about the molecular details of HlyA transport, but it is evident that ATP-hydrolysis by the ABC-transporter HlyB is a necessary source of energy.

>PRK13547 hmuV hemin importer ATP-binding subunit; Provisional

Probab=96.00  E-value=0.0047  Score=54.76  Aligned_cols=28  Identities=43%  Similarity=0.616  Sum_probs=23.8

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.|.||+|+|||+|.++||..+
T Consensus        24 i~~Ge~~~l~G~nGsGKSTLl~~laG~~   51 (272)
T PRK13547         24 IEPGRVTALLGRNGAGKSTLLKALAGDL   51 (272)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3455558999999999999999999876

>PRK14256 phosphate ABC transporter ATP-binding protein; Provisional

Probab=96.00  E-value=0.0053  Score=53.38  Aligned_cols=28  Identities=18%  Similarity=0.401  Sum_probs=23.7

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++..+.+.||+|+|||+|++.|+..+
T Consensus        27 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   54 (252)
T PRK14256         27 FPENSVTAIIGPSGCGKSTVLRSINRMH   54 (252)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHHhcc
Confidence            3445559999999999999999999875

>cd03220 ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export

Probab=96.00  E-value=0.0044  Score=53.13  Aligned_cols=28  Identities=25%  Similarity=0.344  Sum_probs=23.6

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.|.||+|+|||+|.++++...
T Consensus        45 i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   72 (224)
T cd03220          45 VPRGERIGLIGRNGAGKSTLLRLLAGIY   72 (224)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444558999999999999999999865

Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and teichoic acids have been shown to be exported by ABC transporters. A typical system is made of a conserved integral membrane and an ABC. In addition to these proteins, capsular polysaccharide exporter systems require two 'accessory' proteins to perform their function: a periplasmic (E.coli) or a lipid-anchored outer membrane protein called OMA (Neisseria meningitidis and Haemophilus influenzae) and a cytoplasmic membrane protein MPA2.

>PF06431 Polyoma_lg_T_C: Polyomavirus large T antigen C-terminus; InterPro: IPR010932 The group of polyomaviruses is formed by the homonymous murine virus (Py) as well as other representative members such as the simian virus 40 (SV40) and the human BK and JC viruses []

Probab=96.00  E-value=0.0086  Score=55.26  Aligned_cols=37  Identities=30%  Similarity=0.306  Sum_probs=28.4

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcccceeeeechh
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS  227 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s  227 (245)
                      +..|++||-||=.||||++|.|+-.-+|...+.|+++
T Consensus       153 PKkRy~lFkGPvNsGKTTlAAAlLdL~gG~~LNvN~p  189 (417)
T PF06431_consen  153 PKKRYWLFKGPVNSGKTTLAAALLDLCGGKSLNVNCP  189 (417)
T ss_dssp             TTB-EEEEE-STTSSHHHHHHHHHHHH-EEEE-TSS-
T ss_pred             CcceeEEEecCcCCchHHHHHHHHHhcCCceeecCCC
Confidence            3446699999999999999999999998888888765

Their large T antigen (T-ag) protein binds to and activates DNA replication from the origin of DNA replication (ori). Insofar as is known, the T-ag binds to the origin first as a monomer to its pentanucleotide recognition element. The monomers are then thought to assemble into hexamers and double hexamers, which constitute the form that is active in initiation of DNA replication. When bound to the ori, T-ag double hexamers encircle DNA []. T-ag is a multidomain protein that contains an N-terminal J domain, which mediates protein interactions (see PDOC00553 from PROSITEDOC, IPR001623 from INTERPRO), a central origin-binding domain (OBD), and a C-terminal superfamily 3 helicase domain (see PDOC51206 from PROSITEDOC, IPR010932 from INTERPRO) []. This entry represents the helicase domain of LTag, which assembles into a hexameric structure containing a positively charged central channel that can bind both single- and double-stranded DNA []. ATP binding and hydrolysis trigger large conformational changes which are thought to be coupled to the melting of origin DNA and the unwinding of duplex DNA []. These conformational changes cause the angles and orientations between regions of a monomer to alter, creating what was described as an "iris"-like motion in the hexamer. In addition to this, six beta hairpins on the channel surface move longitudinally along the central channel, possibly serving as a motor for pulling DNA into the LTag double hexamer for unwinding.; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 2H1L_H 1SVO_A 1SVM_E 1SVL_B 1N25_A 4E2I_K.

>cd03295 ABC_OpuCA_Osmoprotection OpuCA is a the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment

Probab=95.99  E-value=0.0046  Score=53.45  Aligned_cols=28  Identities=32%  Similarity=0.466  Sum_probs=23.6

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.+.|+...
T Consensus        24 i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   51 (242)
T cd03295          24 IAKGEFLVLIGPSGSGKTTTMKMINRLI   51 (242)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3444558899999999999999999875

ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition, to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03237 ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 of RNase L inhibitor

Probab=95.99  E-value=0.0057  Score=53.45  Aligned_cols=25  Identities=32%  Similarity=0.468  Sum_probs=22.1

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.-+.|.||+|+|||+|.+.|+..+
T Consensus        25 Ge~~~i~G~NGsGKSTLlk~L~G~~   49 (246)
T cd03237          25 SEVIGILGPNGIGKTTFIKMLAGVL   49 (246)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3448899999999999999999875

The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity of more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>PRK15177 Vi polysaccharide export ATP-binding protein VexC; Provisional

Probab=95.99  E-value=0.0048  Score=52.62  Aligned_cols=28  Identities=21%  Similarity=0.406  Sum_probs=23.3

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.|.||+|+|||+|.+.++...
T Consensus        10 i~~Ge~~~l~G~NGsGKSTLlk~i~Gl~   37 (213)
T PRK15177         10 MGYHEHIGILAAPGSGKTTLTRLLCGLD   37 (213)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCc
Confidence            3444558899999999999999999865

>TIGR00750 lao LAO/AO transport system ATPase

Probab=95.99  E-value=0.0069  Score=54.46  Aligned_cols=26  Identities=31%  Similarity=0.471  Sum_probs=22.4

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+..+.+.||||+|||+++..++..+
T Consensus        33 ~~~~i~i~G~~G~GKttl~~~l~~~~   58 (300)
T TIGR00750        33 NAHRVGITGTPGAGKSTLLEALGMEL   58 (300)
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHH
Confidence            44558899999999999999998866

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.

>PRK11247 ssuB aliphatic sulfonates transport ATP-binding subunit; Provisional

Probab=95.98  E-value=0.005  Score=54.16  Aligned_cols=27  Identities=26%  Similarity=0.335  Sum_probs=23.2

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.|.||+|+|||+|.+.|+..+
T Consensus        36 ~~Ge~~~I~G~NGsGKSTLlk~l~Gl~   62 (257)
T PRK11247         36 PAGQFVAVVGRSGCGKSTLLRLLAGLE   62 (257)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            344459999999999999999999876

>KOG0060 consensus Long-chain acyl-CoA transporter, ABC superfamily (involved in peroxisome organization and biogenesis) [Lipid transport and metabolism; General function prediction only]

Probab=95.98  E-value=0.0046  Score=59.93  Aligned_cols=27  Identities=30%  Similarity=0.510  Sum_probs=23.3

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ....++|++||+|||||+|-|.+|.-.
T Consensus       459 ~~g~~LLItG~sG~GKtSLlRvlggLW  485 (659)
T KOG0060|consen  459 PSGQNLLITGPSGCGKTSLLRVLGGLW  485 (659)
T ss_pred             cCCCeEEEECCCCCchhHHHHHHhccc
Confidence            445569999999999999999999755

>PRK11432 fbpC ferric transporter ATP-binding subunit; Provisional

Probab=95.97  E-value=0.0045  Score=57.01  Aligned_cols=28  Identities=39%  Similarity=0.522  Sum_probs=23.7

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.|.||+|||||+|.+.||...
T Consensus        29 i~~Ge~~~llGpsGsGKSTLLr~IaGl~   56 (351)
T PRK11432         29 IKQGTMVTLLGPSGCGKTTVLRLVAGLE   56 (351)
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHHCCC
Confidence            3444558999999999999999999876

>TIGR01189 ccmA heme ABC exporter, ATP-binding protein CcmA

Probab=95.97  E-value=0.0049  Score=51.61  Aligned_cols=28  Identities=29%  Similarity=0.498  Sum_probs=23.8

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.+.++...
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   50 (198)
T TIGR01189        23 LNAGEALQVTGPNGIGKTTLLRILAGLL   50 (198)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444559999999999999999999875

This model describes the cyt c biogenesis protein encoded by ccmA in bacteria. An exception is, an arabidopsis protein. Quite likely this is encoded by an organelle. Bacterial c-type cytocromes are located on the periplasmic side of the cytoplasmic membrane. Several gene products encoded in a locus designated as 'ccm' are implicated in the transport and assembly of the functional cytochrome C. This cluster includes genes: ccmA;B;C;D;E;F;G and H. The posttranslational pathway includes the transport of heme moiety, the secretion of the apoprotein and the covalent attachment of the heme with the apoprotein. The proteins ccmA and B represent an ABC transporter; ccmC and D participate in heme transfer to ccmE, which function as a periplasmic heme chaperone. The presence of ccmF, G and H is suggested to be obligatory for the final functional assembly of cytochrome c.

>cd03290 ABCC_SUR1_N The SUR domain 1

Probab=95.97  E-value=0.0058  Score=51.95  Aligned_cols=27  Identities=22%  Similarity=0.313  Sum_probs=23.2

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.|.||+|+|||+|.++|+...
T Consensus        25 ~~Ge~~~i~G~nGsGKSTLl~~i~G~~   51 (218)
T cd03290          25 PTGQLTMIVGQVGCGKSSLLLAILGEM   51 (218)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhccC
Confidence            344459999999999999999999875

The sulfonylurea receptor SUR is an ATP transporter of the ABCC/MRP family with tandem ATPase binding domains. Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel. Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism. It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity.

>cd03248 ABCC_TAP TAP, the Transporter Associated with Antigen Processing; TAP is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on major histocompatibility complex (MHC) I molecules

Probab=95.96  E-value=0.0053  Score=52.39  Aligned_cols=27  Identities=30%  Similarity=0.525  Sum_probs=23.3

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|+++++..+
T Consensus        38 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   64 (226)
T cd03248          38 HPGEVTALVGPSGSGKSTVVALLENFY   64 (226)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCc
Confidence            344458999999999999999999876

Loaded MHC I leave the ER and display their antigenic cargo on the cell surface to cytotoxic T cells. Subsequently, virus-infected or malignantly transformed cells can be eliminated. TAP belongs to the large family of ATP-binding cassette (ABC) transporters, which translocate a vast variety of solutes across membranes.

>TIGR01184 ntrCD nitrate transport ATP-binding subunits C and D

Probab=95.96  E-value=0.0048  Score=53.07  Aligned_cols=28  Identities=25%  Similarity=0.370  Sum_probs=23.6

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.++++...
T Consensus         8 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   35 (230)
T TIGR01184         8 IQQGEFISLIGHSGCGKSTLLNLISGLA   35 (230)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444558999999999999999999876

This model describes the ATP binding subunits of nitrate transport in bacteria and archaea. This protein belongs to the ATP-binding cassette (ABC) superfamily. It is thought that the two subunits encoded by ntrC and ntrD form the binding surface for interaction with ATP. This model is restricted in identifying ATP binding subunit associated with the nitrate transport. Nitrate assimilation is aided by other proteins derived from the operon which among others include products of ntrA - a regulatory protein; ntrB - a hydropbobic transmembrane permease and narB - a reductase.

>PRK14261 phosphate ABC transporter ATP-binding protein; Provisional

Probab=95.96  E-value=0.0046  Score=53.80  Aligned_cols=28  Identities=32%  Similarity=0.501  Sum_probs=23.0

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|+++|+...
T Consensus        29 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   56 (253)
T PRK14261         29 IPKNRVTALIGPSGCGKSTLLRCFNRMN   56 (253)
T ss_pred             ECCCcEEEEECCCCCCHHHHHHHHhccc
Confidence            3444559999999999999999999753

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=95.96  E-value=0.0059  Score=50.90  Aligned_cols=28  Identities=32%  Similarity=0.464  Sum_probs=23.8

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.+..-+.+.||+|+|||+|.+.++...
T Consensus        22 i~~Ge~~~l~G~nGsGKSTLl~~l~Gl~   49 (177)
T cd03222          22 VKEGEVIGIVGPNGTGKTTAVKILAGQL   49 (177)
T ss_pred             ECCCCEEEEECCCCChHHHHHHHHHcCC
Confidence            3455558899999999999999999865

RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>cd03217 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component

Probab=95.95  E-value=0.0053  Score=51.68  Aligned_cols=27  Identities=41%  Similarity=0.631  Sum_probs=23.7

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      +.++..+.+.||+|+|||+|.+.++..
T Consensus        23 i~~Ge~~~i~G~nGsGKStLl~~l~G~   49 (200)
T cd03217          23 IKKGEVHALMGPNGSGKSTLAKTIMGH   49 (200)
T ss_pred             ECCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            445566999999999999999999997

Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet.

>PRK09984 phosphonate/organophosphate ester transporter subunit; Provisional

Probab=95.95  E-value=0.0048  Score=54.02  Aligned_cols=28  Identities=32%  Similarity=0.503  Sum_probs=23.9

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      .++.-+.|.||+|+|||+|.+.|+..+.
T Consensus        28 ~~Ge~~~i~G~nGsGKSTLl~~i~G~~~   55 (262)
T PRK09984         28 HHGEMVALLGPSGSGKSTLLRHLSGLIT   55 (262)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhccCC
Confidence            4445599999999999999999998763

>TIGR03411 urea_trans_UrtD urea ABC transporter, ATP-binding protein UrtD

Probab=95.95  E-value=0.0049  Score=53.18  Aligned_cols=28  Identities=32%  Similarity=0.641  Sum_probs=23.6

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.|.||+|+|||+|.++|+..+
T Consensus        25 i~~Ge~~~l~G~nGsGKSTLl~~l~G~~   52 (242)
T TIGR03411        25 VDPGELRVIIGPNGAGKTTMMDVITGKT   52 (242)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444558899999999999999999875

Members of this protein family are ABC transporter ATP-binding subunits associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity.

>cd03233 ABC_PDR_domain1 The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters

Probab=95.95  E-value=0.0049  Score=52.02  Aligned_cols=29  Identities=45%  Similarity=0.704  Sum_probs=24.2

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      +.++.-+.+.||+|+|||+|.+.|+....
T Consensus        30 i~~Ge~~~i~G~nGsGKSTLl~~l~G~~~   58 (202)
T cd03233          30 VKPGEMVLVLGRPGSGCSTLLKALANRTE   58 (202)
T ss_pred             ECCCcEEEEECCCCCCHHHHHHHhcccCC
Confidence            34445599999999999999999998754

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK13645 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=95.94  E-value=0.0049  Score=54.89  Aligned_cols=28  Identities=14%  Similarity=0.293  Sum_probs=23.8

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.|.||+|+|||+|.++|+..+
T Consensus        34 i~~Ge~~~l~G~nGsGKSTLl~~l~Gl~   61 (289)
T PRK13645         34 FKKNKVTCVIGTTGSGKSTMIQLTNGLI   61 (289)
T ss_pred             EeCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3444559999999999999999999876

>KOG1803 consensus DNA helicase [Replication, recombination and repair]

Probab=95.93  E-value=0.0041  Score=60.36  Aligned_cols=33  Identities=27%  Similarity=0.424  Sum_probs=22.6

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc---cceeeeechh
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      =++++||||||||....-|-..+   +-.++.+.++
T Consensus       203 l~~I~GPPGTGKT~TlvEiI~qlvk~~k~VLVcaPS  238 (649)
T KOG1803|consen  203 LLIIHGPPGTGKTRTLVEIISQLVKQKKRVLVCAPS  238 (649)
T ss_pred             ceEeeCCCCCCceeeHHHHHHHHHHcCCeEEEEcCc
Confidence            38899999999998665554443   4555555544

>PRK10619 histidine/lysine/arginine/ornithine transporter subunit; Provisional

Probab=95.93  E-value=0.0051  Score=53.74  Aligned_cols=28  Identities=14%  Similarity=0.329  Sum_probs=23.9

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++..+.|.||+|+|||+|+++++...
T Consensus        28 i~~Ge~~~l~G~nGsGKSTLl~~i~G~~   55 (257)
T PRK10619         28 ANAGDVISIIGSSGSGKSTFLRCINFLE   55 (257)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444558899999999999999999876

>PRK10575 iron-hydroxamate transporter ATP-binding subunit; Provisional

Probab=95.93  E-value=0.0049  Score=54.20  Aligned_cols=28  Identities=29%  Similarity=0.413  Sum_probs=23.6

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.|.||+|+|||+|+++|+...
T Consensus        34 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   61 (265)
T PRK10575         34 FPAGKVTGLIGHNGSGKSTLLKMLGRHQ   61 (265)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHcCCC
Confidence            3444558899999999999999999875

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	245
4b4t_K	428	Near-Atomic Resolution Structural Model Of The Yeas		2e-90
4b4t_I	437	Near-Atomic Resolution Structural Model Of The Yeas		8e-49
4b4t_H	467	Near-Atomic Resolution Structural Model Of The Yeas		7e-35
4b4t_J	405	Near-Atomic Resolution Structural Model Of The Yeas		2e-33
4b4t_L	437	Near-Atomic Resolution Structural Model Of The Yeas		2e-32
3h4m_A	285	Aaa Atpase Domain Of The Proteasome- Activating Nuc		1e-31
4b4t_M	434	Near-Atomic Resolution Structural Model Of The Yeas		4e-29
3cf1_A	806	Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Len		6e-24
3hu2_A	489	Structure Of P97 N-D1 R86a Mutant In Complex With A		6e-24
3hu1_A	489	Structure Of P97 N-D1 R95g Mutant In Complex With A		7e-24
3hu3_A	489	Structure Of P97 N-D1 R155h Mutant In Complex With		7e-24
1r7r_A	816	The Crystal Structure Of Murine P97VCP AT 3.6A Leng		1e-23
1e32_A	458	Structure Of The N-Terminal Domain And The D1 Aaa D		1e-23
3cf0_A	301	Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH		9e-20
2rko_A	331	Crystal Structure Of The Vps4p-Dimer Length = 331		3e-17
2qp9_X	355	Crystal Structure Of S.Cerevisiae Vps4 Length = 355		4e-17
3eie_A	322	Crystal Structure Of S.Cerevisiae Vps4 In The So4-B		5e-17
3eih_A	340	Crystal Structure Of S.Cerevisiae Vps4 In The Prese		5e-17
2x8a_A	274	Human Nuclear Valosin Containing Protein Like (Nvl)		9e-17
3vfd_A	389	Human Spastin Aaa Domain Length = 389		1e-15
2r62_A	268	Crystal Structure Of Helicobacter Pylori Atp Depend		1e-15
1lv7_A	257	Crystal Structure Of The Aaa Domain Of Ftsh Length		5e-15
2ce7_A	476	Edta Treated Length = 476		1e-14
3b9p_A	297	Spastin Length = 297		3e-14
3kds_E	465	Apo-ftsh Crystal Structure Length = 465		4e-14
2zam_A	444	Crystal Structure Of Mouse Skd1VPS4B APO-Form Lengt		5e-14
1xwi_A	322	Crystal Structure Of Vps4b Length = 322		6e-14
3d8b_A	357	Crystal Structure Of Human Fidgetin-Like Protein 1		8e-14
2qz4_A	262	Human Paraplegin, Aaa Domain In Complex With Adp Le		4e-12
1iy2_A	278	Crystal Structure Of The Ftsh Atpase Domain From Th		5e-12
2dhr_A	499	Whole Cytosolic Region Of Atp-Dependent Metalloprot		5e-12
4eiw_A	508	Whole Cytosolic Region Of Atp-Dependent Metalloprot		5e-12
1ixz_A	254	Crystal Structure Of The Ftsh Atpase Domain From Th		6e-12
2wg6_A	109	Proteasome-Activating Nucleotidase (Pan) N-Domain (		3e-08
2wg5_A	109	Proteasome-Activating Nucleotidase (Pan) N-Domain (		7e-08
3h43_A	85	N-Terminal Domain Of The Proteasome-Activating Nucl		6e-05

>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 428

Iteration: 1
 Score =  328 bits (841), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 154/204 (75%), Positives = 181/204 (88%)
Query: 33  DLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQ 92
           D+Y +LK L+++ E + +QE+Y+KDEQ++LKREL RAQEEVKRIQSVPLVIGQF+E +DQ
Sbjct: 46  DIYFKLKKLEKEYELLTLQEDYIKDEQRHLKRELKRAQEEVKRIQSVPLVIGQFLEPIDQ 105
Query: 93  NNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSE 152
           N GIV STTG +Y VRILST++RELLKPS SVALHRHSNALVD+LPP++DSSIS++ ++E
Sbjct: 106 NTGIVSSTTGMSYVVRILSTLDRELLKPSMSVALHRHSNALVDILPPDSDSSISVMGENE 165
Query: 153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKA 212
           KPDVTY D+GG D+QKQEIREAVELPL   +LY+QIGIDPPRGVLLYGPPGTGKTML KA
Sbjct: 166 KPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKA 225
Query: 213 VANHTTAAFIRVVGSEFVQKYLGE 236
           VAN T AAFIRV GSEFV KYLGE
Sbjct: 226 VANSTKAAFIRVNGSEFVHKYLGE 249

>pdb|4B4T|I Chain I, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score =  190 bits (482), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 101/230 (43%), Positives = 154/230 (66%), Gaps = 14/230 (6%)
Query: 18  PSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQ--KNLKRELLRAQEEVKR 75
           PSTR  L            +L  ++R  + + ++EE+V + +  K  +++    +++++ 
Sbjct: 51  PSTRCKL------------KLLRMERIKDHLLLEEEFVSNSEILKPFEKKQEEEKKQLEE 98
Query: 76  IQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVD 135
           I+  PL IG   E++D ++ IV S T  +YYV ILS +++ELL+P  SV LH  + ++V 
Sbjct: 99  IRGNPLSIGTLEEIIDDDHAIVTSPTMPDYYVSILSFVDKELLEPGCSVLLHHKTMSIVG 158
Query: 136 VLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRG 195
           VL  +AD  +S++   + P  +Y+DIGG + Q QEI+E+VELPLTH ELY+++GI PP+G
Sbjct: 159 VLQDDADPMVSVMKMDKSPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKG 218
Query: 196 VLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           V+LYG PGTGKT+LAKAVAN T+A F+R+VGSE +QKYLG+     +QIF
Sbjct: 219 VILYGAPGTGKTLLAKAVANQTSATFLRIVGSELIQKYLGDGPRLCRQIF 268

>pdb|4B4T|H Chain H, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 467

Iteration: 1
 Score =  143 bits (361), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 63/109 (57%), Positives = 84/109 (77%)
Query: 137 LPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGV 196
           LPP  D S+++++  EKPDVTY+D+GGC  Q +++RE VELPL   E +  +GIDPP+G+
Sbjct: 187 LPPRIDPSVTMMTVEEKPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGI 246
Query: 197 LLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           LLYGPPGTGKT+ A+AVAN T A FIRV+GSE VQKY+GE     +++F
Sbjct: 247 LLYGPPGTGKTLCARAVANRTDATFIRVIGSELVQKYVGEGARMVRELF 295

>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 405

Iteration: 1
 Score =  139 bits (349), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 82/220 (37%), Positives = 126/220 (57%), Gaps = 9/220 (4%)
Query: 26  EQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQ 85
           EQ   E +L  +++S    +  ++ Q   + D+ + +K EL       + +Q     +G+
Sbjct: 24  EQKIQETEL--KIRSKTENVRRLEAQRNALNDKVRFIKDEL-------RLLQEPGSYVGE 74
Query: 86  FMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSI 145
            +++V     +V       Y V +   IN + LK S  V L   S  L  VL  +AD  +
Sbjct: 75  VIKIVSDKKVLVKVQPEGKYIVDVAKDINVKDLKASQRVCLRSDSYMLHKVLENKADPLV 134
Query: 146 SLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTG 205
           SL+   + PD TY+ +GG   Q +EI+E +ELP+ H EL++ +GI  P+GV+LYGPPGTG
Sbjct: 135 SLMMVEKVPDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTG 194
Query: 206 KTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           KT+LA+AVA+HT   FIRV G+E VQKY+GE     +++F
Sbjct: 195 KTLLARAVAHHTDCKFIRVSGAELVQKYIGEGSRMVRELF 234

>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score =  135 bits (340), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 68/186 (36%), Positives = 118/186 (63%)
Query: 60  KNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLK 119
           ++L++   + + ++K +QS+  +IG+ M+ + +   IV +++G  Y V + ++++R  LK
Sbjct: 82  RDLEKLYDKTENDIKALQSIGQLIGEVMKELSEEKYIVKASSGPRYIVGVRNSVDRSKLK 141
Query: 120 PSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPL 179
               V L   +  ++ +LP E D  +  ++  E+ ++T++ IGG   Q +E+RE +ELPL
Sbjct: 142 KGVRVTLDITTLTIMRILPRETDPLVYNMTSFEQGEITFDGIGGLTEQIRELREVIELPL 201
Query: 180 THHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWL 239
            + E+++++GI PP+GVLLYGPPGTGKT+LAKAVA    A FI    S  V KY+GE   
Sbjct: 202 KNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIGANFIFSPASGIVDKYIGESAR 261
Query: 240 KHKQIF 245
             +++F
Sbjct: 262 IIREMF 267

>pdb|3H4M|A Chain A, Aaa Atpase Domain Of The Proteasome- Activating Nucleotidase Length = 285

Iteration: 1
 Score =  133 bits (334), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 61/95 (64%), Positives = 75/95 (78%)
Query: 151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLA 210
            E+P+V Y DIGG + Q QEIRE VELPL H EL++++GI+PP+G+LLYGPPGTGKT+LA
Sbjct: 9   DERPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLA 68
Query: 211 KAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           KAVA  T A FIRVVGSE V+K++GE     K IF
Sbjct: 69  KAVATETNATFIRVVGSELVKKFIGEGASLVKDIF 103

>pdb|4B4T|M Chain M, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 434

Iteration: 1
 Score =  124 bits (311), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 122/230 (53%), Gaps = 26/230 (11%)
Query: 33  DLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQ 92
           +L +R K L  ++     + + +  E   +  ++   +E++K  + +P ++   +E++D 
Sbjct: 29  ELQTRAKLLDNEIRIFRSELQRLSHENNVMLEKIKDNKEKIKNNRQLPYLVANVVEVMDM 88
Query: 93  NN--------------------------GIVGSTTGSNYYVRILSTINRELLKPSASVAL 126
           N                            +V +++    ++ ++  ++ + LKP+  V +
Sbjct: 89  NEIEDKENSESTTQGGNVNLDNTAVGKAAVVKTSSRQTVFLPMVGLVDPDKLKPNDLVGV 148
Query: 127 HRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYK 186
           ++ S  ++D LP E DS +  +   EKP  TY+D+GG D Q +E+ EA+ LP+   + +K
Sbjct: 149 NKDSYLILDTLPSEFDSRVKAMEVDEKPTETYSDVGGLDKQIEELVEAIVLPMKRADKFK 208
Query: 187 QIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
            +GI  P+G L+YGPPGTGKT+LA+A A  T A F+++   + VQ Y+GE
Sbjct: 209 DMGIRAPKGALMYGPPGTGKTLLARACAAQTNATFLKLAAPQLVQMYIGE 258

>pdb|3CF1|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Length = 806

Iteration: 1
 Score =  107 bits (267), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 49/91 (53%), Positives = 63/91 (69%)
Query: 155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVA 214
           +V Y+DIGGC  Q  +I+E VELPL H  L+K IG+ PPRG+LLYGPPGTGKT++A+AVA
Sbjct: 200 EVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVA 259
Query: 215 NHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           N T A F  + G E + K  GE     ++ F
Sbjct: 260 NETGAFFFLINGPEIMSKLAGESESNLRKAF 290

>pdb|3HU2|A Chain A, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  107 bits (267), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 49/91 (53%), Positives = 63/91 (69%)
Query: 155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVA 214
           +V Y+DIGGC  Q  +I+E VELPL H  L+K IG+ PPRG+LLYGPPGTGKT++A+AVA
Sbjct: 200 EVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVA 259
Query: 215 NHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           N T A F  + G E + K  GE     ++ F
Sbjct: 260 NETGAFFFLINGPEIMSKLAGESESNLRKAF 290

>pdb|3HU1|A Chain A, Structure Of P97 N-D1 R95g Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  107 bits (267), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 49/91 (53%), Positives = 63/91 (69%)
Query: 155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVA 214
           +V Y+DIGGC  Q  +I+E VELPL H  L+K IG+ PPRG+LLYGPPGTGKT++A+AVA
Sbjct: 200 EVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVA 259
Query: 215 NHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           N T A F  + G E + K  GE     ++ F
Sbjct: 260 NETGAFFFLINGPEIMSKLAGESESNLRKAF 290

>pdb|3HU3|A Chain A, Structure Of P97 N-D1 R155h Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  107 bits (266), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 49/91 (53%), Positives = 63/91 (69%)
Query: 155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVA 214
           +V Y+DIGGC  Q  +I+E VELPL H  L+K IG+ PPRG+LLYGPPGTGKT++A+AVA
Sbjct: 200 EVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVA 259
Query: 215 NHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           N T A F  + G E + K  GE     ++ F
Sbjct: 260 NETGAFFFLINGPEIMSKLAGESESNLRKAF 290

>pdb|1R7R|A Chain A, The Crystal Structure Of Murine P97VCP AT 3.6A Length = 816

Iteration: 1
 Score =  106 bits (265), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 48/91 (52%), Positives = 63/91 (69%)
Query: 155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVA 214
           +V Y+D+GGC  Q  +I+E VELPL H  L+K IG+ PPRG+LLYGPPGTGKT++A+AVA
Sbjct: 200 EVGYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVA 259
Query: 215 NHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           N T A F  + G E + K  GE     ++ F
Sbjct: 260 NETGAFFFLINGPEIMSKLAGESESNLRKAF 290

>pdb|1E32|A Chain A, Structure Of The N-Terminal Domain And The D1 Aaa Domain Of Membrane Fusion Atpase P97 Length = 458

Iteration: 1
 Score =  106 bits (265), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 48/91 (52%), Positives = 63/91 (69%)
Query: 155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVA 214
           +V Y+D+GGC  Q  +I+E VELPL H  L+K IG+ PPRG+LLYGPPGTGKT++A+AVA
Sbjct: 200 EVGYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVA 259
Query: 215 NHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           N T A F  + G E + K  GE     ++ F
Sbjct: 260 NETGAFFFLINGPEIMSKLAGESESNLRKAF 290

>pdb|3CF0|A Chain A, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP Length = 301

Iteration: 1
 Score = 93.6 bits (231), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 42/94 (44%), Positives = 61/94 (64%)
Query: 152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAK 211
           E P VT+ DIGG +  K+E++E V+ P+ H + + + G+ P +GVL YGPPG GKT+LAK
Sbjct: 8   EVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAK 67
Query: 212 AVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           A+AN   A FI + G E +  + GE     ++IF
Sbjct: 68  AIANECQANFISIKGPELLTMWFGESEANVREIF 101

>pdb|2RKO|A Chain A, Crystal Structure Of The Vps4p-Dimer Length = 331

Iteration: 1
 Score = 85.1 bits (209), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 44/97 (45%), Positives = 60/97 (61%), Gaps = 1/97 (1%)
Query: 149 SQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTM 208
           S SEKP+V + D+ G +  K+ ++EAV LP+    L+K     P  G+LLYGPPGTGK+ 
Sbjct: 17  SLSEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPGTGKSY 75
Query: 209 LAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           LAKAVA    + F  V  S+ V K++GE     KQ+F
Sbjct: 76  LAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLF 112

>pdb|2QP9|X Chain X, Crystal Structure Of S.Cerevisiae Vps4 Length = 355

Iteration: 1
 Score = 84.7 bits (208), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 43/95 (45%), Positives = 59/95 (62%), Gaps = 1/95 (1%)
Query: 151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLA 210
           SEKP+V + D+ G +  K+ ++EAV LP+    L+K     P  G+LLYGPPGTGK+ LA
Sbjct: 43  SEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPGTGKSYLA 101
Query: 211 KAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           KAVA    + F  V  S+ V K++GE     KQ+F
Sbjct: 102 KAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLF 136

>pdb|3EIE|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The So4-Bound State Length = 322

Iteration: 1
 Score = 84.3 bits (207), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 43/95 (45%), Positives = 59/95 (62%), Gaps = 1/95 (1%)
Query: 151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLA 210
           SEKP+V + D+ G +  K+ ++EAV LP+    L+K     P  G+LLYGPPGTGK+ LA
Sbjct: 10  SEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPGTGKSYLA 68
Query: 211 KAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           KAVA    + F  V  S+ V K++GE     KQ+F
Sbjct: 69  KAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLF 103

>pdb|3EIH|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The Presence Of Atpgammas Length = 340

Iteration: 1
 Score = 84.3 bits (207), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 43/95 (45%), Positives = 59/95 (62%), Gaps = 1/95 (1%)
Query: 151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLA 210
           SEKP+V + D+ G +  K+ ++EAV LP+    L+K     P  G+LLYGPPGTGK+ LA
Sbjct: 28  SEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPGTGKSYLA 86
Query: 211 KAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           KAVA    + F  V  S+ V K++GE     KQ+F
Sbjct: 87  KAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLF 121

>pdb|2X8A|A Chain A, Human Nuclear Valosin Containing Protein Like (Nvl), C- Terminal Aaa-Atpase Domain Length = 274

Iteration: 1
 Score = 83.6 bits (205), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 40/92 (43%), Positives = 59/92 (64%)
Query: 154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAV 213
           P+VT+ DIG  +  ++E+  A+  P+ + + +K +G+  P GVLL GPPG GKT+LAKAV
Sbjct: 5   PNVTWADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAV 64
Query: 214 ANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           AN +   FI V G E +  Y+GE     +Q+F
Sbjct: 65  ANESGLNFISVKGPELLNMYVGESERAVRQVF 96

>pdb|3VFD|A Chain A, Human Spastin Aaa Domain Length = 389

Iteration: 1
 Score = 79.7 bits (195), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 48/122 (39%), Positives = 66/122 (54%), Gaps = 7/122 (5%)
Query: 119 KPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPD----VTYNDIGGCDIQKQEIREA 174
           KPS      R    L +      DS+++ L  +E  D    V ++DI G D+ KQ ++E 
Sbjct: 73  KPSTPTTATRKKKDLKNFR--NVDSNLANLIMNEIVDNGTAVKFDDIAGQDLAKQALQEI 130
Query: 175 VELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYL 234
           V LP    EL+  +   P RG+LL+GPPG GKTMLAKAVA  + A F  +  +    KY+
Sbjct: 131 VILPSLRPELFTGLRA-PARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYV 189
Query: 235 GE 236
           GE
Sbjct: 190 GE 191

>pdb|2R62|A Chain A, Crystal Structure Of Helicobacter Pylori Atp Dependent Protease, Ftsh Length = 268

Iteration: 1
 Score = 79.7 bits (195), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/96 (40%), Positives = 59/96 (61%), Gaps = 1/96 (1%)
Query: 150 QSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTML 209
            +EKP+V + D+ G +  K+E+ E V+  L + E Y  +G   P+GVLL GPPGTGKT+L
Sbjct: 2   NAEKPNVRFKDMAGNEEAKEEVVEIVDF-LKYPERYANLGAKIPKGVLLVGPPGTGKTLL 60
Query: 210 AKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           AKAVA      F  + GS F++ ++G    + + +F
Sbjct: 61  AKAVAGEAHVPFFSMGGSSFIEMFVGLGASRVRDLF 96

>pdb|1LV7|A Chain A, Crystal Structure Of The Aaa Domain Of Ftsh Length = 257

Iteration: 1
 Score = 77.8 bits (190), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 36/89 (40%), Positives = 56/89 (62%), Gaps = 1/89 (1%)
Query: 157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANH 216
           T+ D+ GCD  K+E+ E VE  L     ++++G   P+GVL+ GPPGTGKT+LAKA+A  
Sbjct: 10  TFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE 68
Query: 217 TTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
               F  + GS+FV+ ++G    + + +F
Sbjct: 69  AKVPFFTISGSDFVEMFVGVGASRVRDMF 97

>pdb|2CE7|A Chain A, Edta Treated Length = 476

Iteration: 1
 Score = 76.6 bits (187), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 36/90 (40%), Positives = 56/90 (62%), Gaps = 1/90 (1%)
Query: 156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVAN 215
           VT+ D+GG +   +E++E VE  L     + +IG   P+G+LL GPPGTGKT+LA+AVA 
Sbjct: 13  VTFKDVGGAEEAIEELKEVVEF-LKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAG 71
Query: 216 HTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
                F  + GS+FV+ ++G    + + +F
Sbjct: 72  EANVPFFHISGSDFVELFVGVGAARVRDLF 101

>pdb|3B9P|A Chain A, Spastin Length = 297

Iteration: 1
 Score = 75.5 bits (184), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 34/81 (41%), Positives = 51/81 (62%), Gaps = 1/81 (1%)
Query: 156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVAN 215
           V + DI G D+ KQ ++E V LP    EL+  +   P +G+LL+GPPG GKT+LA+AVA 
Sbjct: 18  VEWTDIAGQDVAKQALQEMVILPSVRPELFTGLRA-PAKGLLLFGPPGNGKTLLARAVAT 76
Query: 216 HTTAAFIRVVGSEFVQKYLGE 236
             +A F+ +  +    KY+G+
Sbjct: 77  ECSATFLNISAASLTSKYVGD 97

>pdb|3KDS|E Chain E, Apo-ftsh Crystal Structure Length = 465

Iteration: 1
 Score = 74.7 bits (182), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 35/90 (38%), Positives = 55/90 (61%), Gaps = 1/90 (1%)
Query: 156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVAN 215
           VT+ D+GG +   +E++E VE  L     + +IG   P+G+LL GPPGTG T+LA+AVA 
Sbjct: 13  VTFKDVGGAEEAIEELKEVVEF-LKDPSKFNRIGARMPKGILLVGPPGTGATLLARAVAG 71
Query: 216 HTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
                F  + GS+FV+ ++G    + + +F
Sbjct: 72  EANVPFFHISGSDFVELFVGVGAARVRDLF 101

>pdb|2ZAM|A Chain A, Crystal Structure Of Mouse Skd1VPS4B APO-Form Length = 444

Iteration: 1
 Score = 74.3 bits (181), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 37/86 (43%), Positives = 55/86 (63%), Gaps = 2/86 (2%)
Query: 152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAK 211
           E+P+V ++D+ G +  K+ ++EAV LP+    L+      P RG+LL+GPPGTGK+ LAK
Sbjct: 127 ERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRT-PWRGILLFGPPGTGKSYLAK 185
Query: 212 AVANH-TTAAFIRVVGSEFVQKYLGE 236
           AVA     + F  +  S+ V K+LGE
Sbjct: 186 AVATEANNSTFFSISSSDLVSKWLGE 211

>pdb|1XWI|A Chain A, Crystal Structure Of Vps4b Length = 322

Iteration: 1
 Score = 74.3 bits (181), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 37/86 (43%), Positives = 55/86 (63%), Gaps = 2/86 (2%)
Query: 152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAK 211
           E+P+V ++D+ G +  K+ ++EAV LP+    L+      P RG+LL+GPPGTGK+ LAK
Sbjct: 5   ERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRT-PWRGILLFGPPGTGKSYLAK 63
Query: 212 AVANH-TTAAFIRVVGSEFVQKYLGE 236
           AVA     + F  +  S+ V K+LGE
Sbjct: 64  AVATEANNSTFFSISSSDLVSKWLGE 89

>pdb|3D8B|A Chain A, Crystal Structure Of Human Fidgetin-Like Protein 1 In Complex With Adp Length = 357

Iteration: 1
 Score = 73.9 bits (180), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 31/83 (37%), Positives = 50/83 (60%), Gaps = 1/83 (1%)
Query: 154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAV 213
           P V + DI G +  K  I+E V  P+   +++  +   PP+G+LL+GPPGTGKT++ K +
Sbjct: 79  PPVNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLR-GPPKGILLFGPPGTGKTLIGKCI 137
Query: 214 ANHTTAAFIRVVGSEFVQKYLGE 236
           A+ + A F  +  S    K++GE
Sbjct: 138 ASQSGATFFSISASSLTSKWVGE 160

>pdb|2QZ4|A Chain A, Human Paraplegin, Aaa Domain In Complex With Adp Length = 262

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 36/90 (40%), Positives = 52/90 (57%), Gaps = 1/90 (1%)
Query: 156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVAN 215
           V++ D+ G    K E+RE V+  L   E + Q+G   P+G LL GPPG GKT+LAKAVA 
Sbjct: 3   VSFKDVAGMHEAKLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVAT 61
Query: 216 HTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
                F+ + G+EFV+   G    + + +F
Sbjct: 62  EAQVPFLAMAGAEFVEVIGGLGAARVRSLF 91

>pdb|1IY2|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 278

Iteration: 1
 Score = 68.2 bits (165), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 41/110 (37%), Positives = 63/110 (57%), Gaps = 6/110 (5%)
Query: 141 ADSSISLLSQ-----SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRG 195
           +DS+ S         +E P VT+ D+ G +  K+E++E VE  L +   + ++G   P+G
Sbjct: 17  SDSAFSFTKSRARVLTEAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKG 75
Query: 196 VLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           VLL GPPG GKT LA+AVA      FI   GS+FV+ ++G    + + +F
Sbjct: 76  VLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFVGVGAARVRDLF 125

>pdb|2DHR|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 499

Iteration: 1
 Score = 67.8 bits (164), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 41/110 (37%), Positives = 63/110 (57%), Gaps = 6/110 (5%)
Query: 141 ADSSISLLSQ-----SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRG 195
           +DS+ S         +E P VT+ D+ G +  K+E++E VE  L +   + ++G   P+G
Sbjct: 8   SDSAFSFTKSRARVLTEAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKG 66
Query: 196 VLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           VLL GPPG GKT LA+AVA      FI   GS+FV+ ++G    + + +F
Sbjct: 67  VLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFVGVGAARVRDLF 116

>pdb|4EIW|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 508

Iteration: 1
 Score = 67.8 bits (164), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 41/110 (37%), Positives = 63/110 (57%), Gaps = 6/110 (5%)
Query: 141 ADSSISLLSQ-----SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRG 195
           +DS+ S         +E P VT+ D+ G +  K+E++E VE  L +   + ++G   P+G
Sbjct: 17  SDSAFSFTKSRARVLTEAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKG 75
Query: 196 VLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           VLL GPPG GKT LA+AVA      FI   GS+FV+ ++G    + + +F
Sbjct: 76  VLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFVGVGAARVRDLF 125

>pdb|1IXZ|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 254

Iteration: 1
 Score = 67.4 bits (163), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 38/95 (40%), Positives = 58/95 (61%), Gaps = 1/95 (1%)
Query: 151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLA 210
           +E P VT+ D+ G +  K+E++E VE  L +   + ++G   P+GVLL GPPG GKT LA
Sbjct: 8   TEAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHLA 66
Query: 211 KAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           +AVA      FI   GS+FV+ ++G    + + +F
Sbjct: 67  RAVAGEARVPFITASGSDFVEMFVGVGAARVRDLF 101

>pdb|2WG6|A Chain A, Proteasome-Activating Nucleotidase (Pan) N-Domain (57-134) From Archaeoglobus Fulgidus Fused To Gcn4, P61a Mutant Length = 109

Iteration: 1
 Score = 55.5 bits (132), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 28/73 (38%), Positives = 45/73 (61%)
Query: 70  QEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRH 129
           + EV R++S PL++G   ++++    +V S+TG  + V     IN E LKP A VAL++ 
Sbjct: 27  ENEVARLRSAPLLVGVVSDILEDGRVVVKSSTGPKFVVNTSQYINEEELKPGARVALNQQ 86
Query: 130 SNALVDVLPPEAD 142
           + A+V+VLP   D
Sbjct: 87  TLAIVNVLPTSKD 99

>pdb|2WG5|A Chain A, Proteasome-Activating Nucleotidase (Pan) N-Domain (57-134) From Archaeoglobus Fulgidus Fused To Gcn4 Length = 109

Iteration: 1
 Score = 54.3 bits (129), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 28/73 (38%), Positives = 45/73 (61%)
Query: 70  QEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRH 129
           + EV R++S PL++G   ++++    +V S+TG  + V     IN E LKP A VAL++ 
Sbjct: 27  ENEVARLRSPPLLVGVVSDILEDGRVVVKSSTGPKFVVNTSQYINEEELKPGARVALNQQ 86
Query: 130 SNALVDVLPPEAD 142
           + A+V+VLP   D
Sbjct: 87  TLAIVNVLPTSKD 99

>pdb|3H43|A Chain A, N-Terminal Domain Of The Proteasome-Activating Nucleotidase Of Methanocaldococcus Jannaschii Length = 85

Iteration: 1
 Score = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 2/74 (2%)
Query: 65  ELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASV 124
           E+LR   E+ R +  PL++G  ++ V +   +V S+TG ++ V +   +N + L P   V
Sbjct: 5   EILR--RELDRXRVPPLIVGTVVDKVGERKVVVKSSTGPSFLVNVSHFVNPDDLAPGKRV 62
Query: 125 ALHRHSNALVDVLP 138
            L++ +  +VDVLP
Sbjct: 63  CLNQQTLTVVDVLP 76

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	245
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	8e-58
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	2e-39
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	7e-39
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	1e-38
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	9e-36
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	2e-32
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	1e-04
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	2e-33
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	6e-33
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	6e-32
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	1e-31
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	3e-31
2wg5_A	109	General control protein GCN4, proteasome-activatin	2e-30
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	3e-30
3h43_A	85	Proteasome-activating nucleotidase; regulatory par	4e-30
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	1e-28
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	6e-27
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	4e-26
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	6e-23
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	2e-22
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	2e-22
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	3e-22
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	9e-22
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	4e-21
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	1e-20
3m9b_A	251	Proteasome-associated ATPase; coil COIL with 5 bet	4e-17
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-14
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-07
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	4e-10
3pvs_A	447	Replication-associated recombination protein A; ma	4e-08
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	8e-06
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	8e-06
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	2e-05
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	4e-05
2qgz_A	308	Helicase loader, putative primosome component; str	4e-05
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	8e-05
2chg_A	226	Replication factor C small subunit; DNA-binding pr	2e-04
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	2e-04
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	3e-04
2chq_A	319	Replication factor C small subunit; DNA-binding pr	3e-04
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	5e-04
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	6e-04
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	6e-04
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	6e-04
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	7e-04

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii} Length = 285

 Score =  184 bits (469), Expect = 8e-58
 Identities = 58/92 (63%), Positives = 73/92 (79%)

Query: 145 ISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGT 204
              +   E+P+V Y DIGG + Q QEIRE VELPL H EL++++GI+PP+G+LLYGPPGT
Sbjct: 3   AKAMEVDERPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGT 62

Query: 205 GKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
           GKT+LAKAVA  T A FIRVVGSE V+K++GE
Sbjct: 63  GKTLLAKAVATETNATFIRVVGSELVKKFIGE 94

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A* 2pjh_B Length = 489

 Score =  141 bits (357), Expect = 2e-39
 Identities = 49/96 (51%), Positives = 64/96 (66%)

Query: 150 QSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTML 209
           +    +V Y+DIGGC  Q  +I+E VELPL H  L+K IG+ PPRG+LLYGPPGTGKT++
Sbjct: 195 EESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLI 254

Query: 210 AKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           A+AVAN T A F  + G E + K  GE     ++ F
Sbjct: 255 ARAVANETGAFFFLINGPEIMSKLAGESESNLRKAF 290

>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} Length = 301

 Score =  135 bits (343), Expect = 7e-39
 Identities = 40/85 (47%), Positives = 57/85 (67%)

Query: 152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAK 211
           E P VT+ DIGG +  K+E++E V+ P+ H + + + G+ P +GVL YGPPG GKT+LAK
Sbjct: 8   EVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAK 67

Query: 212 AVANHTTAAFIRVVGSEFVQKYLGE 236
           A+AN   A FI + G E +  + GE
Sbjct: 68  AIANECQANFISIKGPELLTMWFGE 92

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens} Length = 274

 Score =  134 bits (340), Expect = 1e-38
 Identities = 38/85 (44%), Positives = 55/85 (64%)

Query: 152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAK 211
             P+VT+ DIG  +  ++E+  A+  P+ + + +K +G+  P GVLL GPPG GKT+LAK
Sbjct: 3   TVPNVTWADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAK 62

Query: 212 AVANHTTAAFIRVVGSEFVQKYLGE 236
           AVAN +   FI V G E +  Y+GE
Sbjct: 63  AVANESGLNFISVKGPELLNMYVGE 87

>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 Length = 322

 Score =  122 bits (307), Expect = 2e-33
 Identities = 39/85 (45%), Positives = 54/85 (63%), Gaps = 1/85 (1%)

Query: 152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAK 211
           EKP+V + D+ G +  K+ ++EAV LP+    L+K     P  G+LLYGPPGTGK+ LAK
Sbjct: 11  EKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPGTGKSYLAK 69

Query: 212 AVANHTTAAFIRVVGSEFVQKYLGE 236
           AVA    + F  V  S+ V K++GE
Sbjct: 70  AVATEANSTFFSVSSSDLVSKWMGE 94

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster} Length = 297

 Score =  120 bits (302), Expect = 6e-33
 Identities = 34/85 (40%), Positives = 51/85 (60%), Gaps = 1/85 (1%)

Query: 152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAK 211
               V + DI G D+ KQ ++E V LP    EL+  +   P +G+LL+GPPG GKT+LA+
Sbjct: 14  GGAKVEWTDIAGQDVAKQALQEMVILPSVRPELFTGLR-APAKGLLLFGPPGNGKTLLAR 72

Query: 212 AVANHTTAAFIRVVGSEFVQKYLGE 236
           AVA   +A F+ +  +    KY+G+
Sbjct: 73  AVATECSATFLNISAASLTSKYVGD 97

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens} Length = 322

 Score =  118 bits (297), Expect = 6e-32
 Identities = 37/86 (43%), Positives = 55/86 (63%), Gaps = 2/86 (2%)

Query: 152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAK 211
           E+P+V ++D+ G +  K+ ++EAV LP+    L+      P RG+LL+GPPGTGK+ LAK
Sbjct: 5   ERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGK-RTPWRGILLFGPPGTGKSYLAK 63

Query: 212 AVANHTTAA-FIRVVGSEFVQKYLGE 236
           AVA     + F  +  S+ V K+LGE
Sbjct: 64  AVATEANNSTFFSISSSDLVSKWLGE 89

>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} Length = 357

 Score =  118 bits (297), Expect = 1e-31
 Identities = 31/85 (36%), Positives = 50/85 (58%), Gaps = 1/85 (1%)

Query: 152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAK 211
             P V + DI G +  K  I+E V  P+   +++  +   PP+G+LL+GPPGTGKT++ K
Sbjct: 77  HGPPVNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLR-GPPKGILLFGPPGTGKTLIGK 135

Query: 212 AVANHTTAAFIRVVGSEFVQKYLGE 236
            +A+ + A F  +  S    K++GE
Sbjct: 136 CIASQSGATFFSISASSLTSKWVGE 160

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens} Length = 389

 Score =  117 bits (295), Expect = 3e-31
 Identities = 38/85 (44%), Positives = 51/85 (60%), Gaps = 1/85 (1%)

Query: 152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAK 211
               V ++DI G D+ KQ ++E V LP    EL+  +   P RG+LL+GPPG GKTMLAK
Sbjct: 108 NGTAVKFDDIAGQDLAKQALQEIVILPSLRPELFTGLR-APARGLLLFGPPGNGKTMLAK 166

Query: 212 AVANHTTAAFIRVVGSEFVQKYLGE 236
           AVA  + A F  +  +    KY+GE
Sbjct: 167 AVAAESNATFFNISAASLTSKYVGE 191

>2wg5_A General control protein GCN4, proteasome-activating nucleotidase; transcription hydrolase complex, nucleotide-binding; 2.10A {Saccharomyces cerevisiae} PDB: 2wg6_A Length = 109

 Score =  108 bits (270), Expect = 2e-30
 Identities = 31/112 (27%), Positives = 57/112 (50%), Gaps = 3/112 (2%)

Query: 41  LQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGST 100
           +         + + ++D+ + L  +    + EV R++S PL++G   ++++    +V S+
Sbjct: 1   MHHHHH---HRMKQLEDKVEELLSKNYHLENEVARLRSPPLLVGVVSDILEDGRVVVKSS 57

Query: 101 TGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSE 152
           TG  + V     IN E LKP A VAL++ + A+V+VLP   D  +      E
Sbjct: 58  TGPKFVVNTSQYINEEELKPGARVALNQQTLAIVNVLPTSKDPMVYGFEVEE 109

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A Length = 293

 Score =  112 bits (283), Expect = 3e-30
 Identities = 16/78 (20%), Positives = 25/78 (32%), Gaps = 2/78 (2%)

Query: 159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT 218
           N + G  I    + + V          K   I  P  + ++G  G GK+   + V     
Sbjct: 4   NKLDGFYIAPAFMDKLVVHIT--KNFLKLPNIKVPLILGIWGGKGQGKSFQCELVFRKMG 61

Query: 219 AAFIRVVGSEFVQKYLGE 236
              I +   E      GE
Sbjct: 62  INPIMMSAGELESGNAGE 79

>3h43_A Proteasome-activating nucleotidase; regulatory particle, nucleosidase, ATP-binding, cytoplasm, nucleotide-binding, hydrolase; 2.10A {Methanocaldococcus jannaschii} Length = 85

 Score =  106 bits (267), Expect = 4e-30
 Identities = 22/82 (26%), Positives = 43/82 (52%)

Query: 64  RELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSAS 123
           +E    + E+ R++  PL++G  ++ V +   +V S+TG ++ V +   +N + L P   
Sbjct: 2   KENEILRRELDRMRVPPLIVGTVVDKVGERKVVVKSSTGPSFLVNVSHFVNPDDLAPGKR 61

Query: 124 VALHRHSNALVDVLPPEADSSI 145
           V L++ +  +VDVLP       
Sbjct: 62  VCLNQQTLTVVDVLPELEHHHH 83

>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* Length = 272

 Score =  108 bits (271), Expect = 1e-28
 Identities = 21/106 (19%), Positives = 38/106 (35%), Gaps = 9/106 (8%)

Query: 131 NALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGI 190
            + +D+ P    +               N I         + +  EL +   +   +   
Sbjct: 11  GSTMDIKPAFGTNQEDY------ASYIMNGIIKWGDPVTRVLDDGELLVQQTKNSDR--- 61

Query: 191 DPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE 236
            P   VLL GPP +GKT LA  +A  +   FI++   + +  +   
Sbjct: 62  TPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSET 107

>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* Length = 355

 Score =  105 bits (264), Expect = 6e-27
 Identities = 39/85 (45%), Positives = 54/85 (63%), Gaps = 1/85 (1%)

Query: 152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAK 211
           EKP+V + D+ G +  K+ ++EAV LP+    L+K     P  G+LLYGPPGTGK+ LAK
Sbjct: 44  EKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPGTGKSYLAK 102

Query: 212 AVANHTTAAFIRVVGSEFVQKYLGE 236
           AVA    + F  V  S+ V K++GE
Sbjct: 103 AVATEANSTFFSVSSSDLVSKWMGE 127

>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 Length = 444

 Score =  104 bits (260), Expect = 4e-26
 Identities = 37/86 (43%), Positives = 55/86 (63%), Gaps = 2/86 (2%)

Query: 152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAK 211
           E+P+V ++D+ G +  K+ ++EAV LP+    L+      P RG+LL+GPPGTGK+ LAK
Sbjct: 127 ERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTG-KRTPWRGILLFGPPGTGKSYLAK 185

Query: 212 AVANHTTAA-FIRVVGSEFVQKYLGE 236
           AVA     + F  +  S+ V K+LGE
Sbjct: 186 AVATEANNSTFFSISSSDLVSKWLGE 211

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20 Length = 278

 Score = 93.2 bits (232), Expect = 6e-23
 Identities = 37/86 (43%), Positives = 54/86 (62%), Gaps = 1/86 (1%)

Query: 150 QSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTML 209
            +E P VT+ D+ G +  K+E++E VE  L +   + ++G   P+GVLL GPPG GKT L
Sbjct: 31  LTEAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHL 89

Query: 210 AKAVANHTTAAFIRVVGSEFVQKYLG 235
           A+AVA      FI   GS+FV+ ++G
Sbjct: 90  ARAVAGEARVPFITASGSDFVEMFVG 115

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A* Length = 254

 Score = 91.2 bits (227), Expect = 2e-22
 Identities = 37/88 (42%), Positives = 54/88 (61%), Gaps = 1/88 (1%)

Query: 148 LSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKT 207
              +E P VT+ D+ G +  K+E++E VE  L +   + ++G   P+GVLL GPPG GKT
Sbjct: 5   SVLTEAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKT 63

Query: 208 MLAKAVANHTTAAFIRVVGSEFVQKYLG 235
            LA+AVA      FI   GS+FV+ ++G
Sbjct: 64  HLARAVAGEARVPFITASGSDFVEMFVG 91

>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* Length = 268

 Score = 91.5 bits (228), Expect = 2e-22
 Identities = 38/84 (45%), Positives = 54/84 (64%), Gaps = 1/84 (1%)

Query: 152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAK 211
           EKP+V + D+ G +  K+E+ E V+  L + E Y  +G   P+GVLL GPPGTGKT+LAK
Sbjct: 4   EKPNVRFKDMAGNEEAKEEVVEIVDF-LKYPERYANLGAKIPKGVLLVGPPGTGKTLLAK 62

Query: 212 AVANHTTAAFIRVVGSEFVQKYLG 235
           AVA      F  + GS F++ ++G
Sbjct: 63  AVAGEAHVPFFSMGGSSFIEMFVG 86

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20 Length = 257

 Score = 91.2 bits (227), Expect = 3e-22
 Identities = 35/88 (39%), Positives = 55/88 (62%), Gaps = 1/88 (1%)

Query: 148 LSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKT 207
           +   ++   T+ D+ GCD  K+E+ E VE  L     ++++G   P+GVL+ GPPGTGKT
Sbjct: 1   MLTEDQIKTTFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKT 59

Query: 208 MLAKAVANHTTAAFIRVVGSEFVQKYLG 235
           +LAKA+A      F  + GS+FV+ ++G
Sbjct: 60  LLAKAIAGEAKVPFFTISGSDFVEMFVG 87

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens} Length = 262

 Score = 89.6 bits (223), Expect = 9e-22
 Identities = 35/80 (43%), Positives = 48/80 (60%), Gaps = 1/80 (1%)

Query: 156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVAN 215
           V++ D+ G    K E+RE V+  L   E + Q+G   P+G LL GPPG GKT+LAKAVA 
Sbjct: 3   VSFKDVAGMHEAKLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVAT 61

Query: 216 HTTAAFIRVVGSEFVQKYLG 235
                F+ + G+EFV+   G
Sbjct: 62  EAQVPFLAMAGAEFVEVIGG 81

>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* Length = 476

 Score = 90.3 bits (225), Expect = 4e-21
 Identities = 36/89 (40%), Positives = 54/89 (60%), Gaps = 1/89 (1%)

Query: 147 LLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGK 206
           +   S    VT+ D+GG +   +E++E VE  L     + +IG   P+G+LL GPPGTGK
Sbjct: 4   MYKPSGNKRVTFKDVGGAEEAIEELKEVVEF-LKDPSKFNRIGARMPKGILLVGPPGTGK 62

Query: 207 TMLAKAVANHTTAAFIRVVGSEFVQKYLG 235
           T+LA+AVA      F  + GS+FV+ ++G
Sbjct: 63  TLLARAVAGEANVPFFHISGSDFVELFVG 91

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus} Length = 499

 Score = 89.2 bits (222), Expect = 1e-20
 Identities = 37/86 (43%), Positives = 54/86 (62%), Gaps = 1/86 (1%)

Query: 150 QSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTML 209
            +E P VT+ D+ G +  K+E++E VE  L +   + ++G   P+GVLL GPPG GKT L
Sbjct: 22  LTEAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHL 80

Query: 210 AKAVANHTTAAFIRVVGSEFVQKYLG 235
           A+AVA      FI   GS+FV+ ++G
Sbjct: 81  ARAVAGEARVPFITASGSDFVEMFVG 106

>3m9b_A Proteasome-associated ATPase; coil COIL with 5 beta-strand barrel inter domain, chaperone; 3.94A {Mycobacterium tuberculosis} PDB: 3m9d_A Length = 251

 Score = 77.2 bits (189), Expect = 4e-17
 Identities = 29/181 (16%), Positives = 61/181 (33%), Gaps = 3/181 (1%)

Query: 21  RSDLTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVP 80
           + +              +  L+ +++ +  +   + +  K  +++LL  +EEV R+   P
Sbjct: 39  QLENAVGSHAPTRSARDIHQLEARIDSLAARNSKLMETLKEARQQLLALREEVDRLGQPP 98

Query: 81  LVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPE 140
              G  +   D +   V  T+G    +     I+   LK   +V L+      V+    E
Sbjct: 99  SGYGVLLATHDDDTVDV-FTSGRKMRLTCSPNIDAASLKKGQTVRLNEALTV-VEAGTFE 156

Query: 141 ADSSISLLSQS-EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLY 199
           A   IS L +               + +   + + +        L + +  D     L  
Sbjct: 157 AVGEISTLREILADGHRALVVGHADEERVVWLADPLIAEDLPDGLPEALNDDTRPRKLRP 216

Query: 200 G 200
           G
Sbjct: 217 G 217

>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 = 71.0 bits (173), Expect = 3e-14
 Identities = 35/220 (15%), Positives = 74/220 (33%), Gaps = 65/220 (29%)

Query: 42  QRQLEFIDI----QEEYVKDEQKNLKRELLRA---QEEVKRIQSVPLVIGQFMEMVD--- 91
           + Q ++ DI    ++ +V +      +++ ++   +EE+  I      +   + +     
Sbjct: 13  EHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLL 72

Query: 92  --QNNGI---VGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSIS 146
             Q   +   V      NY   ++S I  E  +PS    ++                   
Sbjct: 73  SKQEEMVQKFVEEVLRINYKF-LMSPIKTEQRQPSMMTRMY------------------- 112

Query: 147 LLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQI-----GIDPPRGVLLYGP 201
                E+ D  YND           +   +  ++  + Y ++      + P + VL+ G 
Sbjct: 113 ----IEQRDRLYNDN----------QVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGV 158

Query: 202 PGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEV-WLK 240
            G+GKT +A  V              +   K   ++ WL 
Sbjct: 159 LGSGKTWVALDVCLS----------YKVQCKMDFKIFWLN 188

>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 = 49.1 bits (116), Expect = 7e-07
 Identities = 26/235 (11%), Positives = 69/235 (29%), Gaps = 46/235 (19%)

Query: 1   MAASAMVLDPKPVSEPP-----------PSTRSDLTEQWSDEDDLYSRLKSLQRQLEFID 49
           +A     L  K   +              S  + L         L  ++           
Sbjct: 166 VALDV-CLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQ----KLLYQIDPNWTSRSDHS 220

Query: 50  IQEEYVKDEQKNLKRELLRAQEEVKR-------IQSVPLVIGQF-----MEMVDQNNGIV 97
              +      +   R LL+  +  +        +Q+       F     + +  +   + 
Sbjct: 221 SNIKLRIHSIQAELRRLLK-SKPYENCLLVLLNVQN-AKAWNAFNLSCKILLTTRFKQVT 278

Query: 98  GSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADS----SISLLSQSEK 153
              + +      L   +  L        L ++ +     LP E  +     +S++++S +
Sbjct: 279 DFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIR 338

Query: 154 PDV----TYNDIGGCDIQKQEIREAVEL--PLTHHELYKQIGIDP-----PRGVL 197
             +     +  +  CD     I  ++ +  P  + +++ ++ + P     P  +L
Sbjct: 339 DGLATWDNWKHV-NCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILL 392

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A* Length = 309

 Score = 57.8 bits (139), Expect = 4e-10
 Identities = 29/124 (23%), Positives = 46/124 (37%), Gaps = 17/124 (13%)

Query: 138 PPEADSSISLLSQSEKPDVT------YNDIGGCDIQKQEIREAVELPLTHHELYKQIGID 191
              A +SI L ++ E             ++ G    K  IRE   L L      +++G+ 
Sbjct: 4   AATAPTSIDLRAEYEGSGAKEVLEELDRELIGLKPVKDRIRETAAL-LLVERARQKLGLA 62

Query: 192 PPRGVL---LYGPPGTGKTMLAKAVANHTTAA-------FIRVVGSEFVQKYLGEVWLKH 241
                L     G PGTGKT +A  +A              + V   + V +Y+G    K 
Sbjct: 63  HETPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTRDDLVGQYIGHTAPKT 122

Query: 242 KQIF 245
           K++ 
Sbjct: 123 KEVL 126

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli} Length = 447

 Score = 52.2 bits (126), Expect = 4e-08
 Identities = 16/41 (39%), Positives = 24/41 (58%)

Query: 184 LYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRV 224
           L + I       ++L+GPPGTGKT LA+ +A +  A   R+
Sbjct: 41  LPRAIEAGHLHSMILWGPPGTGKTTLAEVIARYANADVERI 81

>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 Length = 516

 Score = 45.3 bits (107), Expect = 8e-06
 Identities = 13/23 (56%), Positives = 14/23 (60%)

Query: 194 RGVLLYGPPGTGKTMLAKAVANH 216
           R  +LYGPPG GKT  A  VA  
Sbjct: 78  RAAMLYGPPGIGKTTAAHLVAQE 100

>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* Length = 180

 Score = 43.9 bits (104), Expect = 8e-06
 Identities = 10/31 (32%), Positives = 13/31 (41%)

Query: 186 KQIGIDPPRGVLLYGPPGTGKTMLAKAVANH 216
                +  +G+   G PG GKT LA A    
Sbjct: 31  HNFNPEEGKGLTFVGSPGVGKTHLAVATLKA 61

>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* Length = 456

 Score = 44.2 bits (104), Expect = 2e-05
 Identities = 27/69 (39%), Positives = 35/69 (50%), Gaps = 6/69 (8%)

Query: 169 QEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANH--TTAAFIRVVG 226
           +  REA  + +   EL K   +   R VLL GPPGTGKT LA A+A    +   F  +VG
Sbjct: 43  ENAREACGVIV---ELIKSKKM-AGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVG 98

Query: 227 SEFVQKYLG 235
           SE     + 
Sbjct: 99  SEVYSTEIK 107

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426} Length = 202

 Score = 42.4 bits (100), Expect = 4e-05
 Identities = 11/36 (30%), Positives = 17/36 (47%)

Query: 190 IDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVV 225
               +G+ L+G  G GKT L  A+AN      +  +
Sbjct: 51  GKKMKGLYLHGSFGVGKTYLLAAIANELAKRNVSSL 86

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3} Length = 308

 Score = 42.9 bits (101), Expect = 4e-05
 Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 3/52 (5%)

Query: 165 DIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANH 216
           D+      EA    L   +  +Q      +G+ LYG  G GK+ L  A+A+ 
Sbjct: 127 DVNNASRMEAFSAIL---DFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHE 175

>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} Length = 193

 Score = 41.5 bits (97), Expect = 8e-05
 Identities = 11/35 (31%), Positives = 19/35 (54%)

Query: 189 GIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIR 223
           G+  P  +++ G P TGKT L++A+A       + 
Sbjct: 1   GMQTPALIIVTGHPATGKTTLSQALATGLRLPLLS 35

>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} Length = 226

 Score = 40.7 bits (96), Expect = 2e-04
 Identities = 12/19 (63%), Positives = 13/19 (68%)

Query: 197 LLYGPPGTGKTMLAKAVAN 215
           L  GPPGTGKT  A A+A 
Sbjct: 42  LFSGPPGTGKTATAIALAR 60

>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 Length = 350

 Score = 40.9 bits (96), Expect = 2e-04
 Identities = 10/20 (50%), Positives = 15/20 (75%)

Query: 195 GVLLYGPPGTGKTMLAKAVA 214
           GVL++G  GTGK+   +A+A
Sbjct: 47  GVLVFGDRGTGKSTAVRALA 66

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli} Length = 500

 Score = 40.5 bits (95), Expect = 3e-04
 Identities = 9/30 (30%), Positives = 14/30 (46%), Gaps = 1/30 (3%)

Query: 196 VLLYGPPGTGKTMLAKAVANH-TTAAFIRV 224
           V L GPPG  K+++A+ +      A     
Sbjct: 44  VFLLGPPGIAKSLIARRLKFAFQNARAFEY 73

>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 Length = 319

 Score = 40.0 bits (94), Expect = 3e-04
 Identities = 12/19 (63%), Positives = 13/19 (68%)

Query: 197 LLYGPPGTGKTMLAKAVAN 215
           L  GPPGTGKT  A A+A 
Sbjct: 42  LFSGPPGTGKTATAIALAR 60

>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 Length = 327

 Score = 39.7 bits (93), Expect = 5e-04
 Identities = 11/19 (57%), Positives = 12/19 (63%)

Query: 197 LLYGPPGTGKTMLAKAVAN 215
           L  GPPG GKT  A A+A 
Sbjct: 50  LFAGPPGVGKTTAALALAR 68

>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* Length = 334

 Score = 39.5 bits (93), Expect = 6e-04
 Identities = 13/20 (65%), Positives = 15/20 (75%)

Query: 196 VLLYGPPGTGKTMLAKAVAN 215
           VLL GPPG GKT LA  +A+
Sbjct: 54  VLLAGPPGLGKTTLAHIIAS 73

>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* Length = 324

 Score = 39.5 bits (93), Expect = 6e-04
 Identities = 12/20 (60%), Positives = 16/20 (80%)

Query: 196 VLLYGPPGTGKTMLAKAVAN 215
           +LL+GPPG GKT LA  +A+
Sbjct: 41  LLLFGPPGLGKTTLAHVIAH 60

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp} Length = 338

 Score = 39.5 bits (93), Expect = 6e-04
 Identities = 9/20 (45%), Positives = 12/20 (60%)

Query: 196 VLLYGPPGTGKTMLAKAVAN 215
           +L  GP G GKT LA  ++ 
Sbjct: 58  ILFSGPAGLGKTTLANIISY 77

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus} Length = 604

 Score = 39.3 bits (92), Expect = 7e-04
 Identities = 14/28 (50%), Positives = 19/28 (67%)

Query: 187 QIGIDPPRGVLLYGPPGTGKTMLAKAVA 214
           +   +  R VLL G PGTGK+ML +A+A
Sbjct: 54  KTAANQKRHVLLIGEPGTGKSMLGQAMA 81

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	245
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	100.0
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	100.0
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	100.0
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	100.0
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	100.0
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	100.0
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.85
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.85
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.79
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	99.77
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	99.75
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.74
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.71
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.71
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.7
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.66
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.65
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.65
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.65
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.65
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.62
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.61
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.6
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.59
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.59
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.58
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.58
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.52
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.52
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.47
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	99.45
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	99.42
2wg5_A	109	General control protein GCN4, proteasome-activatin	99.4
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.32
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.31
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.21
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	99.18
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	99.12
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	99.12
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	99.06
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	99.06
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.05
3h43_A	85	Proteasome-activating nucleotidase; regulatory par	99.04
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	99.03
3m9b_A	251	Proteasome-associated ATPase; coil COIL with 5 bet	98.99
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	98.98
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	98.96
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	98.95
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	98.95
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	98.9
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	98.9
3co5_A	143	Putative two-component system transcriptional RES	98.85
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	98.84
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	98.81
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	98.79
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	98.78
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	98.77
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	98.77
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	98.76
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	98.73
3pvs_A	447	Replication-associated recombination protein A; ma	98.73
2r44_A	331	Uncharacterized protein; putative ATPase, structur	98.69
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.67
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	98.66
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	98.65
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	98.63
2chq_A	319	Replication factor C small subunit; DNA-binding pr	98.62
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	98.62
3bos_A	242	Putative DNA replication factor; P-loop containing	98.6
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	98.59
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	98.59
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.57
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	98.55
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.53
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.5
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.47
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.47
2qgz_A	308	Helicase loader, putative primosome component; str	98.46
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	98.46
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.4
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	98.37
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	98.36
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	98.35
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	98.35
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	98.3
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	98.27
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	98.27
1tue_A	212	Replication protein E1; helicase, replication, E1E	98.22
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	98.11
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	98.0
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	97.99
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.99
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	97.99
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	97.98
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	97.97
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	97.94
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	97.93
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	97.91
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	97.91
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	97.89
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	97.87
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	97.85
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	97.84
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	97.83
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	97.83
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	97.8
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	97.8
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	97.78
2fna_A	357	Conserved hypothetical protein; structural genomic	97.76
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	97.75
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	97.72
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	97.72
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	97.71
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	97.67
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	97.66
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	97.66
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	97.62
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	97.59
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	97.54
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	97.52
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	97.52
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	97.51
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	97.49
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.48
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	97.43
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	97.43
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	97.41
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	97.41
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	97.39
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	97.37
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	97.37
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	97.33
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	97.31
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	97.31
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	97.29
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	97.27
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	97.27
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	97.23
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	97.21
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	97.2
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	97.18
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	97.18
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	97.16
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	97.16
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	97.15
2z43_A	324	DNA repair and recombination protein RADA; archaea	97.14
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	97.13
4a74_A	231	DNA repair and recombination protein RADA; hydrola	97.13
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	97.12
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.1
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	97.06
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	97.03
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	97.01
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	96.99
1u94_A	356	RECA protein, recombinase A; homologous recombinat	96.99
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	96.96
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	96.93
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	96.9
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	96.89
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	96.88
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.87
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	96.87
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	96.87
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	96.86
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	96.86
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	96.84
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	96.83
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	96.81
1xp8_A	366	RECA protein, recombinase A; recombination, radior	96.81
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	96.79
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	96.79
2eyu_A	261	Twitching motility protein PILT; pilus retraction	96.76
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	96.72
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	96.72
3u06_A	412	Protein claret segregational; motor domain, stalk	96.71
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	96.71
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	96.7
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	96.64
3hdt_A	223	Putative kinase; structura genomics, PSI-2, protei	96.63
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	96.63
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	96.63
3io5_A	333	Recombination and repair protein; storage dimer, i	96.62
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	96.61
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	96.59
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	96.59
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	96.58
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	96.55
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	96.52
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	96.51
2ewv_A	372	Twitching motility protein PILT; pilus retraction	96.5
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	96.49
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	96.45
3kta_A	182	Chromosome segregation protein SMC; structural mai	96.43
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	96.43
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	96.42
2r6a_A	454	DNAB helicase, replicative helicase; replication,	96.41
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	96.4
2og2_A	359	Putative signal recognition particle receptor; nuc	96.38
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	96.38
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	96.36
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	96.34
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	96.34
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	96.3
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	96.3
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	96.28
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	96.28
1b0u_A	262	Histidine permease; ABC transporter, transport pro	96.28
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	96.26
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	96.25
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	96.25
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	96.23
1g6h_A	257	High-affinity branched-chain amino acid transport	96.19
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	96.19
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	96.18
1p9r_A	418	General secretion pathway protein E; bacterial typ	96.17
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	96.17
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	96.16
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	96.16
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	96.14
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	96.13
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	96.13
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	96.13
2ghi_A	260	Transport protein; multidrug resistance protein, M	96.13
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	96.12
1sgw_A	214	Putative ABC transporter; structural genomics, P p	96.11
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	96.09
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	96.09
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	96.09
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.09
1ji0_A	240	ABC transporter; ATP binding protein, structural g	96.09
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	96.07
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	96.07
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	96.06
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	96.06
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	96.06
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	96.05
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	96.04
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	96.04
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	96.04
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	96.02
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	96.02
2ged_A	193	SR-beta, signal recognition particle receptor beta	96.02
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	96.02
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	96.02
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	96.01
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	96.0
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.0
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	96.0
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	95.98
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	95.97
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	95.96
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	95.96
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	95.96
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	95.95
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	95.95
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	95.93
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	95.89
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	95.88
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	95.86
1nrj_B	218	SR-beta, signal recognition particle receptor beta	95.85
2wji_A	165	Ferrous iron transport protein B homolog; membrane	95.83
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	95.82
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	95.8
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	95.75
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	95.74
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	95.73
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	95.73
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	95.73
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	95.72
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	95.72
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	95.72
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	95.71
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	95.69
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	95.69
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	95.65
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	95.63
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	95.62
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	95.61
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	95.57
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	95.57
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	95.56
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	95.53
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	95.53
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	95.52
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	95.51
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	95.5
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	95.48
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	95.47
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	95.46
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	95.44
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	95.42
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	95.4
3ice_A	422	Transcription termination factor RHO; transcriptio	95.4
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	95.4
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	95.37
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	95.36
4i1u_A	210	Dephospho-COA kinase; structural genomics, niaid,	95.36
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	95.3
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	95.28
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	95.27
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	95.25
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	95.25
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	95.25
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	95.23
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	95.23
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	95.22
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	95.2
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	95.19
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	95.17
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	95.17
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	95.17
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	95.16
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	95.15
3f8t_A	506	Predicted ATPase involved in replication control,	95.14
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	95.14
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	95.13
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	95.13
2xxa_A	433	Signal recognition particle protein; protein trans	95.13
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	95.12
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	95.11
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	95.1
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	95.08
1qhl_A	227	Protein (cell division protein MUKB); SMC, chromos	95.08
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	95.08
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	95.07
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	95.06
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	95.06
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	95.04
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	95.04
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	95.03
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	95.01
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	94.99
3b6e_A	216	Interferon-induced helicase C domain-containing P;	94.98
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	94.98
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	94.97
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	94.97
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	94.97
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	94.97
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	94.95
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	94.95
1knx_A	312	Probable HPR(Ser) kinase/phosphatase; HPR kinase,	94.93
1ko7_A	314	HPR kinase/phosphatase; protein kinase, phosphotra	94.92
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	94.91
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	94.91
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	94.88
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	94.88
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	94.87
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	94.87
3ch4_B	202	Pmkase, phosphomevalonate kinase; parallel beta-sh	94.81
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	94.81
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	94.81
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	94.79
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	94.78
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	94.77
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	94.76
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	94.75
2hf9_A	226	Probable hydrogenase nickel incorporation protein	94.75
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	94.74
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	94.74
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	94.73
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	94.71
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	94.7
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	94.69
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	94.68
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	94.68
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	94.67
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	94.67
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	94.66
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	94.62
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	94.59
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	94.58
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	94.57
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	94.57
3qf7_A	365	RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.	94.56
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	94.56
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	94.51
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	94.49
3qkt_A	339	DNA double-strand break repair RAD50 ATPase; RECA-	94.48
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	94.47
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	94.46
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	94.44
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	94.44
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	94.43
3l0o_A	427	Transcription termination factor RHO; helicase, RH	94.39
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	94.38
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	94.38
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	94.38
3qks_A	203	DNA double-strand break repair RAD50 ATPase; RECA-	94.36
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	94.32
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	94.32
3b60_A	582	Lipid A export ATP-binding/permease protein MSBA;	94.32
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	94.29
3llu_A	196	RAS-related GTP-binding protein C; structural geno	94.26
3euj_A	483	Chromosome partition protein MUKB, linker; MUKB, M	94.23
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	94.22
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	94.2
2o5v_A	359	DNA replication and repair protein RECF; ABC ATPas	94.2
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	94.2
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	94.19
2x77_A	189	ADP-ribosylation factor; GTP-binding protein, smal	94.18
2qnr_A	301	Septin-2, protein NEDD5; structural genomics conso	94.18
3cpj_B	223	GTP-binding protein YPT31/YPT8; RAB GTPase, prenyl	94.16
2yl4_A	595	ATP-binding cassette SUB-family B member 10, mitoc	94.15
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	94.14
3qf4_B	598	Uncharacterized ABC transporter ATP-binding prote	94.1
1t9h_A	307	YLOQ, probable GTPase ENGC; N-terminal beta-barrel	94.09
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	94.08
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	94.01
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	94.01
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	93.99
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	93.96
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	93.93
2yc2_C	208	IFT27, small RAB-related GTPase; transport protein	93.9
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	93.89
1ega_A	301	Protein (GTP-binding protein ERA); GTPase, RNA-bin	93.88
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	93.88
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	93.87
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	93.86
3szr_A	608	Interferon-induced GTP-binding protein MX1; interf	93.86
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	93.81
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	93.76
4a82_A	578	Cystic fibrosis transmembrane conductance regulat;	93.76
3bor_A	237	Human initiation factor 4A-II; translation initiat	93.74
2aka_B	299	Dynamin-1; fusion protein, GTPase domain, myosin,	93.73
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	93.69
2xtp_A	260	GTPase IMAP family member 2; immune system, G prot	93.68
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	93.66
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	93.65
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	93.65
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	93.62
3qf4_A	587	ABC transporter, ATP-binding protein; multidrug tr	93.53
3lxw_A	247	GTPase IMAP family member 1; immunity, structural	93.53
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	93.52
1w1w_A	430	Structural maintenance of chromosome 1; cohesin, c	93.51
3auy_A	371	DNA double-strand break repair RAD50 ATPase; DNA r	93.4
2qtf_A	364	Protein HFLX, GTP-binding protein; beta-alpha-barr	93.32
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	93.24
4djt_A	218	GTP-binding nuclear protein GSP1; structural genom	93.23
1mky_A	439	Probable GTP-binding protein ENGA; GTPase, DER, KH	93.19
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	93.16
2e87_A	357	Hypothetical protein PH1320; GTP-binding, GTPase,	93.1
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	93.07
4dhe_A	223	Probable GTP-binding protein ENGB; melioidosis, RA	92.94
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	92.88
3th5_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	92.01
1jwy_B	315	Dynamin A GTPase domain; dynamin, GTPase, GDP, myo	92.81
1ni3_A	392	YCHF GTPase, YCHF GTP-binding protein; structural	92.8
4aby_A	415	DNA repair protein RECN; hydrolase, double strand	92.79
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	92.73
1e69_A	322	Chromosome segregation SMC protein; structural mai	92.73
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	92.72
3gj0_A	221	GTP-binding nuclear protein RAN; G protein, GDP, a	92.7
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	92.69
2iw3_A	986	Elongation factor 3A; acetylation, ATP-binding, pr	92.57
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	92.51
3bfv_A	271	CAPA1, CAPB2, membrane protein CAPA1, protein tyro	92.44
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	92.43
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	92.34
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	92.29
3cio_A	299	ETK, tyrosine-protein kinase ETK; WZC, escherichia	92.28
3h1t_A	590	Type I site-specific restriction-modification syst	92.26
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	92.25
2qag_A	361	Septin-2, protein NEDD5; cell cycle, cell division	92.14
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	92.13
3ug7_A	349	Arsenical pump-driving ATPase; tail-anchored, memb	92.08
1h65_A	270	Chloroplast outer envelope protein OEP34; GTPase,	92.06
2iw3_A	986	Elongation factor 3A; acetylation, ATP-binding, pr	92.02
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	92.01
1ihu_A	589	Arsenical pump-driving ATPase; aluminum fluoride,	91.94
1udx_A	416	The GTP-binding protein OBG; TGS domain, riken str	91.84
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	91.74
1puj_A	282	YLQF, conserved hypothetical protein YLQF; structu	91.74
3cnl_A	262	YLQF, putative uncharacterized protein; circular p	91.72
3la6_A	286	Tyrosine-protein kinase WZC; P-loop protein, nucle	91.7
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	91.57
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	91.57
3l0i_B	199	RAS-related protein RAB-1A; GEF-GDF-RAB complex, G	91.55
3t5d_A	274	Septin-7; GTP-binding protein, cytoskeleton, signa	91.55
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	91.4
2ohf_A	396	Protein OLA1, GTP-binding protein 9; ATPase, GTPas	91.33
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	91.32
3end_A	307	Light-independent protochlorophyllide reductase ir	91.31
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	91.3
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	91.26
3def_A	262	T7I23.11 protein; chloroplast, TOC33, GTPase, hydr	91.21
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	91.14
3geh_A	462	MNME, tRNA modification GTPase MNME; G protein, U3	91.14
3zq6_A	324	Putative arsenical pump-driving ATPase; tail-ancho	91.13
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	91.08
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	91.0
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	90.89
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	90.85
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	90.76
1zcb_A	362	G alpha I/13; GTP-binding, lipoprotein, membrane,	90.74
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	90.7
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	90.68
3g5u_A	1284	MCG1178, multidrug resistance protein 1A; P-glycop	90.66
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	90.63
3vr4_A	600	V-type sodium ATPase catalytic subunit A; V-ATPase	90.57
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	90.52

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=6.4e-42  Score=318.77  Aligned_cols=215  Identities=72%  Similarity=1.107  Sum_probs=206.8

Q ss_pred             chhHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhhhcccceeecccCCeeEEEEe
Q 025979           31 EDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRIL  110 (245)
Q Consensus        31 ~~~~~~~~~~~~~e~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~  110 (245)
                      ..+++.++++++++++.|..+.++++++...+++++..++++++.++.+|..++++.+.++..+++++++++.++++++.
T Consensus        44 ~~dl~~~lk~le~~~~~L~~e~e~l~~~~~~~~~e~~~~~ee~~~l~~~~~~vg~~~e~~d~~~~iv~~~~~~~~~v~~~  123 (428)
T 4b4t_K           44 NSDIYFKLKKLEKEYELLTLQEDYIKDEQRHLKRELKRAQEEVKRIQSVPLVIGQFLEPIDQNTGIVSSTTGMSYVVRIL  123 (428)
T ss_dssp             ----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSCEEEEEEEEEEETTEEEEEETTSCEEEECBC
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCceeeEEEEEccCCeeEEecCCCCEEEEecc
Confidence            46778899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccccccCCCceeeeeccccccccccCCCccccccccccCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhcc
Q 025979          111 STINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGI  190 (245)
Q Consensus       111 ~~~~~~~l~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~  190 (245)
                      +.++...+++|..+.++..+..+..++|.+.++.++.+...+.|+++|+||+|+++++++|.+.|.+|+.+|+.|.++|+
T Consensus       124 ~~~~~~~~~~~~~v~~~~~~~~~~~~l~~~~d~~v~~~~~~~~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~  203 (428)
T 4b4t_K          124 STLDRELLKPSMSVALHRHSNALVDILPPDSDSSISVMGENEKPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIGI  203 (428)
T ss_dssp             SSSCTTTCCTTCEEEECSSSCCEEEEECSCCCCSSCCCEEESSCSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCC
T ss_pred             ccccHhhCCCCceeeeecchhhHHhhcCcccCcchhhccCCCCCCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhccccccccccC
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge~~~~vr~iF  245 (245)
                      .+|+|+|||||||||||++|+|+|++++++|+.+++++++++|+|+++++||++|
T Consensus       204 ~~prGiLL~GPPGtGKT~lakAiA~~~~~~~~~v~~~~l~~~~~Ge~e~~ir~lF  258 (428)
T 4b4t_K          204 DPPRGVLLYGPPGTGKTMLVKAVANSTKAAFIRVNGSEFVHKYLGEGPRMVRDVF  258 (428)
T ss_dssp             CCCCEEEEESCTTTTHHHHHHHHHHHHTCEEEEEEGGGTCCSSCSHHHHHHHHHH
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHHHhCCCeEEEecchhhccccchhHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999987

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.5e-41  Score=313.45  Aligned_cols=211  Identities=35%  Similarity=0.585  Sum_probs=201.9

Q ss_pred             HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhhhcccceeecccCCeeEEEEeeccc
Q 025979           35 YSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTIN  114 (245)
Q Consensus        35 ~~~~~~~~~e~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  114 (245)
                      ..++.+++.++....++...++.+.+.++++...++++++.++.+|..++++.+.+++.+++++.+++.++++.+.+.++
T Consensus        24 ~~~i~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~e~~~l~~~~~~v~~~~~~~~~~~~iv~~~~~~~~~v~~~~~~~  103 (405)
T 4b4t_J           24 EQKIQETELKIRSKTENVRRLEAQRNALNDKVRFIKDELRLLQEPGSYVGEVIKIVSDKKVLVKVQPEGKYIVDVAKDIN  103 (405)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECTTSCEEEEESSSCEEEECCCTTSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCceEEEEEEEecCCeEEEEeCCCCEEEEecccccC
Confidence            35677888888777788888888888888889999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCceeeeeccccccccccCCCccccccccccCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCc
Q 025979          115 RELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPR  194 (245)
Q Consensus       115 ~~~l~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~  194 (245)
                      ...+++|.+|.++.++..+..++|+..++.+..+...+.|+++|+||+|+++++++|++.|.+|+.+|++|.++|+.+|+
T Consensus       104 ~~~l~~~~~v~l~~~~~~~~~~l~~~~~~~~~~~~~~~~p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~pr  183 (405)
T 4b4t_J          104 VKDLKASQRVCLRSDSYMLHKVLENKADPLVSLMMVEKVPDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPK  183 (405)
T ss_dssp             TTTCCSSCEEEEETTTCSCCEECCCCCSCCTTSCEEECSCSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCC
T ss_pred             HhhCCCcceeeeecccceeeeecCcccCchhhhccccCCCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhccccccccccC
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge~~~~vr~iF  245 (245)
                      |+|||||||||||++|+|+|++++++|+.+++++++++|+|+++++||++|
T Consensus       184 GvLL~GPPGTGKTllAkAiA~e~~~~f~~v~~s~l~sk~vGese~~vr~lF  234 (405)
T 4b4t_J          184 GVILYGPPGTGKTLLARAVAHHTDCKFIRVSGAELVQKYIGEGSRMVRELF  234 (405)
T ss_dssp             CEEEESCSSSSHHHHHHHHHHHHTCEEEEEEGGGGSCSSTTHHHHHHHHHH
T ss_pred             ceEEeCCCCCCHHHHHHHHHHhhCCCceEEEhHHhhccccchHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999987

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.5e-41  Score=314.87  Aligned_cols=232  Identities=43%  Similarity=0.731  Sum_probs=185.0

Q ss_pred             CCCCCCcccCCCCCCCC------------chhHHHHHHHHHHHhhhhhhhHHHHHHH--HHHHHHHHHHHHHHhhhhccc
Q 025979           14 SEPPPSTRSDLTEQWSD------------EDDLYSRLKSLQRQLEFIDIQEEYVKDE--QKNLKRELLRAQEEVKRIQSV   79 (245)
Q Consensus        14 ~e~~~~~~~e~~~~~~~------------~~~~~~~~~~~~~e~~~l~~~~~~i~~~--~~~~~~~~~~~~~~~~~~~~~   79 (245)
                      .|+|...++....+...            ..+|+-++.++++...+|..+.++++.+  ++..+++..+.++++++++.+
T Consensus        23 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  102 (437)
T 4b4t_I           23 YEPPVQSKFGRKKRKGGPATAEKLPNIYPSTRCKLKLLRMERIKDHLLLEEEFVSNSEILKPFEKKQEEEKKQLEEIRGN  102 (437)
T ss_dssp             ----------------------------------------------------CHHHHHHHHHHHHHHHHHHHHHHHHHCS
T ss_pred             CCCCCccccccccCCCCcchhhcCcccCCcchhhHHHHHHHHHHHHHHHHHHHHHhHHhhhhHHHHHHHHHHHHHhhcCC
Confidence            77777776654433311            3355667778888888888777777766  356777788889999999999


Q ss_pred             cchhhhhhhhhhcccceeecccCCeeEEEEeecccccccCCCceeeeeccccccccccCCCccccccccccCCCCCceec
Q 025979           80 PLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYN  159 (245)
Q Consensus        80 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~  159 (245)
                      |..+|++.+.++..+++|+++++.+|++.+.++++...+.||.+|.++..+..+.+++|+..++.++.|...+.|+++|+
T Consensus       103 p~~~g~~~~~~~~~~~iv~~~~~~~~~v~~~~~~~~~~l~~~~~v~l~~~~~~~~~~l~~~~d~~~~~~~~~~~p~v~~~  182 (437)
T 4b4t_I          103 PLSIGTLEEIIDDDHAIVTSPTMPDYYVSILSFVDKELLEPGCSVLLHHKTMSIVGVLQDDADPMVSVMKMDKSPTESYS  182 (437)
T ss_dssp             SEEEEEEEEECTTSEEEEECSSSCCCEEECCTTSCGGGCCTTCEEEECTTTCCEEEEECCCSSCCCCCCEEESSCCCCGG
T ss_pred             CceeEEEEEEecCCEEEEEcCCCCEEEEecccccCHhHccCCcEEEEeccCccceeecCCccCCcceeeeeccCCCCcce
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhccccc
Q 025979          160 DIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWL  239 (245)
Q Consensus       160 dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge~~~  239 (245)
                      ||+|+++++++|.+.|.+|+.+|+.|..+|+.+|+|+|||||||||||++|+|+|++++++|+.+++++++++|+|++++
T Consensus       183 DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~~~~fi~v~~s~l~sk~vGesek  262 (437)
T 4b4t_I          183 DIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSATFLRIVGSELIQKYLGDGPR  262 (437)
T ss_dssp             GTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHHTCEEEEEESGGGCCSSSSHHHH
T ss_pred             ecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHhCCCEEEEEHHHhhhccCchHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccC
Q 025979          240 KHKQIF  245 (245)
Q Consensus       240 ~vr~iF  245 (245)
                      +||++|
T Consensus       263 ~ir~lF  268 (437)
T 4b4t_I          263 LCRQIF  268 (437)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            999987

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.3e-39  Score=303.69  Aligned_cols=215  Identities=31%  Similarity=0.601  Sum_probs=189.6

Q ss_pred             chhHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhhhcc-----------------
Q 025979           31 EDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQN-----------------   93 (245)
Q Consensus        31 ~~~~~~~~~~~~~e~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~-----------------   93 (245)
                      .++++.+.+.++.++..++.+..+++.+...+++++..++++++..+.+|..++.+.+.++..                 
T Consensus        27 ~~~l~~r~~~le~e~~~l~~e~~r~~~e~~~~~~~~~~~~~~i~~~~~~p~~v~~~~e~~d~~~~~~~~~~~~~~~~~~~  106 (434)
T 4b4t_M           27 TQELQTRAKLLDNEIRIFRSELQRLSHENNVMLEKIKDNKEKIKNNRQLPYLVANVVEVMDMNEIEDKENSESTTQGGNV  106 (434)
T ss_dssp             --------------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSSSCCEEEECCC---------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchhhhhhhhhccchhhhhccchhhhhhhhh
Confidence            345566777788888888999999999999999999999999999999999999888877642                 


Q ss_pred             ---------cceeecccCCeeEEEEeecccccccCCCceeeeeccccccccccCCCccccccccccCCCCCceeccCCcc
Q 025979           94 ---------NGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGC  164 (245)
Q Consensus        94 ---------~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~dv~Gl  164 (245)
                               .++++++++.++++.+.+.++...++||.+|.++.++..+.+++|+..++.+..|...+.|+++|+||+|+
T Consensus       107 ~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~l~~~~~v~~~~~~~~~~~~l~~~~d~~~~~~~~~~~p~~t~~digGl  186 (434)
T 4b4t_M          107 NLDNTAVGKAAVVKTSSRQTVFLPMVGLVDPDKLKPNDLVGVNKDSYLILDTLPSEFDSRVKAMEVDEKPTETYSDVGGL  186 (434)
T ss_dssp             ------CCSEEEEEETTSCEEEEECCSSSCTTTSCSSEEEEECSSSCSEEEEEEESSSCSCSCCEEESSCSCCGGGSCSC
T ss_pred             hhhhcccCceEEEEcCCCCeEEEecccccCHhHCCCCCEEeEcCcchhhheecCcccCchhhhcccCCCCCCChHhcCcH
Confidence                     46788999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhcccccccccc
Q 025979          165 DIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQI  244 (245)
Q Consensus       165 ~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge~~~~vr~i  244 (245)
                      ++++++|.+.|.+|+.+|+.|.++|+.+|+|+|||||||||||++|+|+|++++++|+.+++++++++|+|++++++|.+
T Consensus       187 ~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~~~~f~~v~~s~l~~~~vGese~~ir~l  266 (434)
T 4b4t_M          187 DKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTNATFLKLAAPQLVQMYIGEGAKLVRDA  266 (434)
T ss_dssp             HHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCEEEEEEGGGGCSSCSSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHhCCCEEEEehhhhhhcccchHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             C
Q 025979          245 F  245 (245)
Q Consensus       245 F  245 (245)
                      |
T Consensus       267 F  267 (434)
T 4b4t_M          267 F  267 (434)
T ss_dssp             H
T ss_pred             H
Confidence            7

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.8e-39  Score=302.80  Aligned_cols=202  Identities=35%  Similarity=0.605  Sum_probs=189.6

Q ss_pred             HhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhhhcccceeecccCCeeEEEEeecccccccCCCce
Q 025979           44 QLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSAS  123 (245)
Q Consensus        44 e~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  123 (245)
                      +...++.+++.++.+...+++++.+.+++++.++.+|..+|++.+.+++.+.++.+++|+++++++.+.++...+.+|.+
T Consensus        66 ~~~~~e~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~vg~~~~~~~~~~~iv~~~~g~~~~v~~~~~~~~~~l~~g~~  145 (437)
T 4b4t_L           66 EHRRYDDQLKQRRQNIRDLEKLYDKTENDIKALQSIGQLIGEVMKELSEEKYIVKASSGPRYIVGVRNSVDRSKLKKGVR  145 (437)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCCEEEEEEEECSSSSCEEEEETTSCEEEECBCSSSCTTSCCTTCE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCceeeeheeeecCCcEEEEECCCCEEEEecccccCHhhcCCCce
Confidence            33445566666777777777888888899999999999999999999999999999999999999999999999999999


Q ss_pred             eeeeccccccccccCCCccccccccccCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCC
Q 025979          124 VALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPG  203 (245)
Q Consensus       124 v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPG  203 (245)
                      |.++..+..+..++|+..++.+..+...+.|+++|+||+|+++++++|++.|.+|+.+|++|.++|+.+|+|+|||||||
T Consensus       146 v~~~~~~~~~~~~l~~~~d~~~~~~~~~~~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPG  225 (437)
T 4b4t_L          146 VTLDITTLTIMRILPRETDPLVYNMTSFEQGEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPG  225 (437)
T ss_dssp             EEECSSSCSEEEECCCCSCCCCSSCEEEESCSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTT
T ss_pred             eeEcccchhHHHhcCcccCchhheeeeccCCCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CchHHHHHHHHhcccceeeeechhHHHHHHhccccccccccC
Q 025979          204 TGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       204 tGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge~~~~vr~iF  245 (245)
                      ||||++|+|+|++++++|+.+++++++++|+|++++++|.+|
T Consensus       226 tGKTllAkAiA~e~~~~~~~v~~s~l~sk~~Gese~~ir~~F  267 (437)
T 4b4t_L          226 TGKTLLAKAVAATIGANFIFSPASGIVDKYIGESARIIREMF  267 (437)
T ss_dssp             SSHHHHHHHHHHHHTCEEEEEEGGGTCCSSSSHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHhCCCEEEEehhhhccccchHHHHHHHHHH
Confidence            999999999999999999999999999999999999999987

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=9.6e-36  Score=278.19  Aligned_cols=155  Identities=43%  Similarity=0.752  Sum_probs=150.8

Q ss_pred             hcccceeecccCCeeEEEEeecccccccCCCceeeeeccccccccccCCCccccccccccCCCCCceeccCCcchhhhHH
Q 025979           91 DQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSEKPDVTYNDIGGCDIQKQE  170 (245)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~dv~Gl~~~~~~  170 (245)
                      +..+.++..+++.+|++.+.+.++...++||.+|.++.++..+..++|+..|+.+..|...+.|+++|+||+|+++++++
T Consensus       141 ~~~~~~v~~~~~~~~~v~~~~~~~~~~l~~g~~v~l~~~~~~i~~~lp~~~d~~v~~m~v~e~P~vt~~DIgGl~~~k~~  220 (467)
T 4b4t_H          141 EDAKYVINLKQIAKFVVGLGERVSPTDIEEGMRVGVDRSKYNIELPLPPRIDPSVTMMTVEEKPDVTYSDVGGCKDQIEK  220 (467)
T ss_dssp             CCCCCEEEETTSCCBCCCCCTTCCSSSCCTTCEECSCTTSCCCCCSSCSSSCCCCCCCEEESSCSCCCSSCTTCHHHHHH
T ss_pred             CCCcEEEEecCCCeEEEecCCcCCHHHCCCCCEEEEccCcceeeecCCCccCCccceeeecCCCCCCHHHhccHHHHHHH
Confidence            34578889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhccccccccccC
Q 025979          171 IREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       171 i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge~~~~vr~iF  245 (245)
                      |++.|.+|+.+|++|.++|+.+|+|+|||||||||||++|+|+|++++++|+.+++++++++|+|++++++|++|
T Consensus       221 L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~~~~fi~vs~s~L~sk~vGesek~ir~lF  295 (467)
T 4b4t_H          221 LREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDATFIRVIGSELVQKYVGEGARMVRELF  295 (467)
T ss_dssp             HHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHHTCEEEEEEGGGGCCCSSSHHHHHHHHHH
T ss_pred             HHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhccCCCeEEEEhHHhhcccCCHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.85  E-value=1.7e-22  Score=200.36  Aligned_cols=95  Identities=44%  Similarity=0.833  Sum_probs=92.5

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      .+.|+++|+|++|++++++.|.+.|.+|+.+|+.|.++|+.+++|+|||||||||||++|+|+|++++.+|+.+++++++
T Consensus       469 ~~~p~v~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~~~~f~~v~~~~l~  548 (806)
T 3cf2_A          469 VEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELL  548 (806)
T ss_dssp             CBCCCCCSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTTTCEEEECCHHHHH
T ss_pred             ccCCCCCHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHhCCceEEeccchhh
Confidence            35688999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhccccccccccC
Q 025979          231 QKYLGEVWLKHKQIF  245 (245)
Q Consensus       231 ~~~~Ge~~~~vr~iF  245 (245)
                      ++|+|+++++||++|
T Consensus       549 s~~vGese~~vr~lF  563 (806)
T 3cf2_A          549 TMWFGESEANVREIF  563 (806)
T ss_dssp             TTTCSSCHHHHHHHH
T ss_pred             ccccchHHHHHHHHH
Confidence            999999999999988

>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=99.85  E-value=1.4e-22  Score=200.82  Aligned_cols=95  Identities=52%  Similarity=0.898  Sum_probs=92.0

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      ...++++|+||+|+++++++|++.|.+|+.+|++|..+|+.+|+|||||||||||||++|+++|++++.+|+.+++++++
T Consensus       196 ~~~~~v~~~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~elg~~~~~v~~~~l~  275 (806)
T 3cf2_A          196 ESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIM  275 (806)
T ss_dssp             CCSSSCCGGGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTTTCEEEEEEHHHHH
T ss_pred             ccCCCCChhhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHhCCeEEEEEhHHhh
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhccccccccccC
Q 025979          231 QKYLGEVWLKHKQIF  245 (245)
Q Consensus       231 ~~~~Ge~~~~vr~iF  245 (245)
                      ++|+|++++++|++|
T Consensus       276 sk~~gese~~lr~lF  290 (806)
T 3cf2_A          276 SKLAGESESNLRKAF  290 (806)
T ss_dssp             SSCTTHHHHHHHHHH
T ss_pred             cccchHHHHHHHHHH
Confidence            999999999999987

>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=99.79  E-value=5.7e-20  Score=162.99  Aligned_cols=94  Identities=45%  Similarity=0.846  Sum_probs=90.3

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHH
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQ  231 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~  231 (245)
                      +.|.++|+|++|++.+++.|.+.+..|+.+|+.|..+|+.+++++|||||||||||++|+++|+.++.+|+.++++++.+
T Consensus         8 ~~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~~~~~i~v~~~~l~~   87 (301)
T 3cf0_A            8 EVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLT   87 (301)
T ss_dssp             ECCCCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHTTCEEEEECHHHHHH
T ss_pred             cCCCCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHhCCCEEEEEhHHHHh
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhccccccccccC
Q 025979          232 KYLGEVWLKHKQIF  245 (245)
Q Consensus       232 ~~~Ge~~~~vr~iF  245 (245)
                      +|+|++++.++.+|
T Consensus        88 ~~~g~~~~~~~~~f  101 (301)
T 3cf0_A           88 MWFGESEANVREIF  101 (301)
T ss_dssp             HHHTTCTTHHHHHH
T ss_pred             hhcCchHHHHHHHH
Confidence            99999999888765

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=99.77  E-value=2.9e-20  Score=163.40  Aligned_cols=94  Identities=43%  Similarity=0.728  Sum_probs=82.1

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHH
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQ  231 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~  231 (245)
                      +.|+++|+||+|+++++++|.+.+..|+.+++.|..+|+.+++|++|+||||||||++++++|+.++.+++.++++++.+
T Consensus         3 ~~~~~~~~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLakala~~~~~~~i~i~g~~l~~   82 (274)
T 2x8a_A            3 TVPNVTWADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANESGLNFISVKGPELLN   82 (274)
T ss_dssp             ---------CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHHHHHHTTCEEEEEETTTTCS
T ss_pred             CCCCCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHHHHHHcCCCEEEEEcHHHHh
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhccccccccccC
Q 025979          232 KYLGEVWLKHKQIF  245 (245)
Q Consensus       232 ~~~Ge~~~~vr~iF  245 (245)
                      +|+|++++.|+.+|
T Consensus        83 ~~~~~~~~~i~~vf   96 (274)
T 2x8a_A           83 MYVGESERAVRQVF   96 (274)
T ss_dssp             STTHHHHHHHHHHH
T ss_pred             hhhhHHHHHHHHHH
Confidence            99999998888775

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=99.75  E-value=1.2e-19  Score=162.71  Aligned_cols=93  Identities=42%  Similarity=0.751  Sum_probs=86.7

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc-cceeeeechhHHH
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT-TAAFIRVVGSEFV  230 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l-~~~~~~v~~s~l~  230 (245)
                      +.|.++|+||+|++++++.|.+.+.+|+.++++|.. +..+++|+|||||||||||++|+++|+++ +.+|+.++++++.
T Consensus         5 ~~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~-~~~~~~~iLL~GppGtGKT~la~ala~~~~~~~~~~i~~~~l~   83 (322)
T 1xwi_A            5 ERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTG-KRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLV   83 (322)
T ss_dssp             ECCCCCGGGSCSCHHHHHHHHHHHHHHHHCGGGSCT-TCCCCSEEEEESSSSSCHHHHHHHHHHHTTSCEEEEEECCSSC
T ss_pred             cCCCCCHHHhcCHHHHHHHHHHHHHHHHhCHHHHhC-CCCCCceEEEECCCCccHHHHHHHHHHHcCCCcEEEEEhHHHH
Confidence            568899999999999999999999999999999874 36788999999999999999999999999 9999999999999


Q ss_pred             HHHhccccccccccC
Q 025979          231 QKYLGEVWLKHKQIF  245 (245)
Q Consensus       231 ~~~~Ge~~~~vr~iF  245 (245)
                      ++|+|++++.++.+|
T Consensus        84 ~~~~g~~~~~~~~lf   98 (322)
T 1xwi_A           84 SKWLGESEKLVKNLF   98 (322)
T ss_dssp             CSSCCSCHHHHHHHH
T ss_pred             hhhhhHHHHHHHHHH
Confidence            999999999998876

>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=99.74  E-value=3.1e-19  Score=159.52  Aligned_cols=94  Identities=46%  Similarity=0.781  Sum_probs=87.7

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      .+.|+++|+|++|++.+++.|.+++..|+.+++.|.. +..+++++|||||||||||++|+++|++++.+|+.++++++.
T Consensus        10 ~~~~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~-~~~~~~~vLl~GppGtGKT~la~aia~~~~~~~~~v~~~~l~   88 (322)
T 3eie_A           10 SEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLV   88 (322)
T ss_dssp             EECCCCCGGGSCSCHHHHHHHHHHTHHHHHCGGGCCT-TCCCCCEEEEECSSSSCHHHHHHHHHHHHTCEEEEEEHHHHH
T ss_pred             ecCCCCCHHHhcChHHHHHHHHHHHHHHHhCHHHHhc-CCCCCCeEEEECCCCCcHHHHHHHHHHHHCCCEEEEchHHHh
Confidence            4678899999999999999999999999999998876 557889999999999999999999999999999999999999


Q ss_pred             HHHhccccccccccC
Q 025979          231 QKYLGEVWLKHKQIF  245 (245)
Q Consensus       231 ~~~~Ge~~~~vr~iF  245 (245)
                      ++|+|++++.++.+|
T Consensus        89 ~~~~g~~~~~~~~~f  103 (322)
T 3eie_A           89 SKWMGESEKLVKQLF  103 (322)
T ss_dssp             TTTGGGHHHHHHHHH
T ss_pred             hcccchHHHHHHHHH
Confidence            999999999988776

>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=99.71  E-value=1.4e-18  Score=157.78  Aligned_cols=94  Identities=46%  Similarity=0.781  Sum_probs=82.2

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      .+.+.++|+||+|++.+++.|.+.+..|+.+++.|.. +..+++++|||||||||||++|+++|++++.+|+.++++++.
T Consensus        43 ~~~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~-~~~~~~~iLL~GppGtGKT~la~ala~~~~~~~~~v~~~~l~  121 (355)
T 2qp9_X           43 SEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLV  121 (355)
T ss_dssp             ----CCCGGGSCCGGGHHHHHHHHTHHHHHCGGGGCS-SCCCCCCEEEECSTTSCHHHHHHHHHHHHTCEEEEEEHHHHH
T ss_pred             ccCCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHhc-CCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEeeHHHHh
Confidence            4567899999999999999999999999999999886 567889999999999999999999999999999999999999


Q ss_pred             HHHhccccccccccC
Q 025979          231 QKYLGEVWLKHKQIF  245 (245)
Q Consensus       231 ~~~~Ge~~~~vr~iF  245 (245)
                      ++|+|++++.++.+|
T Consensus       122 ~~~~g~~~~~~~~~f  136 (355)
T 2qp9_X          122 SKWMGESEKLVKQLF  136 (355)
T ss_dssp             SCC---CHHHHHHHH
T ss_pred             hhhcchHHHHHHHHH
Confidence            999999999888765

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=99.71  E-value=1.5e-18  Score=151.23  Aligned_cols=98  Identities=62%  Similarity=1.052  Sum_probs=90.9

Q ss_pred             cccCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechh
Q 025979          148 LSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS  227 (245)
Q Consensus       148 ~~~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s  227 (245)
                      +...+.++++|++++|++.+++.|.+++..++.+++.+..+|+.+++++|||||||||||++|+++|+.++.+|+.++++
T Consensus         6 ~~~~~~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~~~~~~~v~~~   85 (285)
T 3h4m_A            6 MEVDERPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGS   85 (285)
T ss_dssp             EEEESSCCCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHTTCEEEEEEGG
T ss_pred             ccccCCCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEehH
Confidence            34456788999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhccccccccccC
Q 025979          228 EFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       228 ~l~~~~~Ge~~~~vr~iF  245 (245)
                      ++...|.|+++..++.+|
T Consensus        86 ~~~~~~~~~~~~~~~~~~  103 (285)
T 3h4m_A           86 ELVKKFIGEGASLVKDIF  103 (285)
T ss_dssp             GGCCCSTTHHHHHHHHHH
T ss_pred             HHHHhccchHHHHHHHHH
Confidence            999999999888777654

>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=99.70  E-value=5.1e-18  Score=158.46  Aligned_cols=95  Identities=41%  Similarity=0.724  Sum_probs=78.4

Q ss_pred             cCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc-cceeeeechhH
Q 025979          150 QSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT-TAAFIRVVGSE  228 (245)
Q Consensus       150 ~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l-~~~~~~v~~s~  228 (245)
                      ..+.+.++|+||+|++.+++.|.+.+..|+.++++|.. +..+++++|||||||||||++|+++|+++ +.+|+.+++++
T Consensus       125 ~~~~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~-~~~~~~~vLL~GppGtGKT~lA~aia~~~~~~~~~~v~~~~  203 (444)
T 2zan_A          125 VIERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTG-KRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSD  203 (444)
T ss_dssp             BCCCCCCCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSG-GGCCCSEEEEECSTTSSHHHHHHHHHHHCCSSEEEEECCC-
T ss_pred             eccCCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhc-cCCCCceEEEECCCCCCHHHHHHHHHHHcCCCCEEEEeHHH
Confidence            34678899999999999999999999999999988874 45678999999999999999999999999 99999999999


Q ss_pred             HHHHHhccccccccccC
Q 025979          229 FVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       229 l~~~~~Ge~~~~vr~iF  245 (245)
                      ++++|+|++++.++.+|
T Consensus       204 l~~~~~g~~~~~~~~~f  220 (444)
T 2zan_A          204 LVSKWLGESEKLVKNLF  220 (444)
T ss_dssp             --------CCCTHHHHH
T ss_pred             HHhhhcchHHHHHHHHH
Confidence            99999999999998876

>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=99.66  E-value=2.7e-17  Score=142.21  Aligned_cols=93  Identities=42%  Similarity=0.749  Sum_probs=86.6

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHH
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQ  231 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~  231 (245)
                      +.++++|++++|.+.+++.+.+.+.. +.+++.|..+|...++|+|||||||||||++|+++|+.++.+|+.++++++.+
T Consensus         4 ~~~~~~~~~i~G~~~~~~~l~~~~~~-~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~v~~~~~~~   82 (268)
T 2r62_A            4 EKPNVRFKDMAGNEEAKEEVVEIVDF-LKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSFIE   82 (268)
T ss_dssp             CCCCCCSTTSSSCTTTHHHHHHHHHH-HHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHHTCCCCCCCSCTTTT
T ss_pred             cCCCCCHHHhCCcHHHHHHHHHHHHH-HHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEechHHHHH
Confidence            45678999999999999999998876 88899999999999999999999999999999999999999999999999999


Q ss_pred             HHhccccccccccC
Q 025979          232 KYLGEVWLKHKQIF  245 (245)
Q Consensus       232 ~~~Ge~~~~vr~iF  245 (245)
                      .|.|.++..++.+|
T Consensus        83 ~~~~~~~~~~~~~~   96 (268)
T 2r62_A           83 MFVGLGASRVRDLF   96 (268)
T ss_dssp             SCSSSCSSSSSTTH
T ss_pred             hhcchHHHHHHHHH
Confidence            99999988887765

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=99.65  E-value=1.2e-17  Score=143.81  Aligned_cols=94  Identities=38%  Similarity=0.745  Sum_probs=80.9

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      .+.+..+|+|++|++.+++.+.+.+.. +.+++.|..+|...++|+|||||||||||++|+++|+.++.+|+.++++++.
T Consensus         4 ~~~~~~~~~~i~G~~~~~~~l~~~~~~-~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~i~~~~~~   82 (257)
T 1lv7_A            4 EDQIKTTFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFV   82 (257)
T ss_dssp             ECSSCCCGGGSCSCHHHHHHTHHHHHH-HHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCCEEEECSCSST
T ss_pred             ccCCCCCHHHhcCcHHHHHHHHHHHHH-HhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHcCCCEEEEeHHHHH
Confidence            345678999999999999999998876 7788888999999999999999999999999999999999999999999999


Q ss_pred             HHHhccccccccccC
Q 025979          231 QKYLGEVWLKHKQIF  245 (245)
Q Consensus       231 ~~~~Ge~~~~vr~iF  245 (245)
                      +.|.|++++.++.+|
T Consensus        83 ~~~~~~~~~~~~~~~   97 (257)
T 1lv7_A           83 EMFVGVGASRVRDMF   97 (257)
T ss_dssp             TSCCCCCHHHHHHHH
T ss_pred             HHhhhhhHHHHHHHH
Confidence            999999888877665

>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=99.65  E-value=1.2e-17  Score=143.19  Aligned_cols=91  Identities=40%  Similarity=0.667  Sum_probs=77.3

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHH
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKY  233 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~  233 (245)
                      |+++|++++|++.+++.+.+.+.. +.+++.|..+|+.+++++|||||||||||++|+++|+.++.+|+.++++++.+.|
T Consensus         1 ~~~~~~~i~G~~~~~~~l~~~~~~-~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~~~~~~~~~~~   79 (262)
T 2qz4_A            1 MGVSFKDVAGMHEAKLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGAEFVEVI   79 (262)
T ss_dssp             CCCCTTSSCSCHHHHHHHHHHHHH-HHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHHTCCEEEEETTTTSSSS
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHH-HHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEechHHHHhhc
Confidence            467899999999999999999876 7788888999999999999999999999999999999999999999999999888


Q ss_pred             hccccccccccC
Q 025979          234 LGEVWLKHKQIF  245 (245)
Q Consensus       234 ~Ge~~~~vr~iF  245 (245)
                      .|+++..++.+|
T Consensus        80 ~~~~~~~~~~~~   91 (262)
T 2qz4_A           80 GGLGAARVRSLF   91 (262)
T ss_dssp             TTHHHHHHHHHH
T ss_pred             cChhHHHHHHHH
Confidence            888877776554

>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=99.65  E-value=3e-17  Score=154.60  Aligned_cols=92  Identities=39%  Similarity=0.771  Sum_probs=86.5

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHH
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQK  232 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~  232 (245)
                      .+.++|+||+|++++++++.+.+.. +.++..|.++|...|+|+||+||||||||++|+++|++++.+|+.++++++.++
T Consensus        10 ~~~~~f~di~G~~~~~~~l~e~v~~-l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~~~~f~~is~~~~~~~   88 (476)
T 2ce7_A           10 NKRVTFKDVGGAEEAIEELKEVVEF-LKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEANVPFFHISGSDFVEL   88 (476)
T ss_dssp             SCCCCGGGCCSCHHHHHHHHHHHHH-HHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGTTTC
T ss_pred             CCCCCHHHhCCcHHHHHHHHHHHHH-hhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHcCCCeeeCCHHHHHHH
Confidence            5778999999999999999999886 778899999999999999999999999999999999999999999999999999


Q ss_pred             HhccccccccccC
Q 025979          233 YLGEVWLKHKQIF  245 (245)
Q Consensus       233 ~~Ge~~~~vr~iF  245 (245)
                      |+|.++..+|.+|
T Consensus        89 ~~g~~~~~~r~lf  101 (476)
T 2ce7_A           89 FVGVGAARVRDLF  101 (476)
T ss_dssp             CTTHHHHHHHHHH
T ss_pred             HhcccHHHHHHHH
Confidence            9999998888765

>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=99.65  E-value=4.2e-17  Score=154.16  Aligned_cols=92  Identities=53%  Similarity=0.933  Sum_probs=87.7

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHH
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKY  233 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~  233 (245)
                      +.++|++++|++.+++.|.+.+..++.+++.|..+|..+++++|||||||||||++|+++|+.++.+|+.++++++.++|
T Consensus       199 ~~~~~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~~~~fv~vn~~~l~~~~  278 (489)
T 3hu3_A          199 NEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKL  278 (489)
T ss_dssp             TCCCGGGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHCSSEEEEEEHHHHHTSC
T ss_pred             CCCCHHHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHhCCCEEEEEchHhhhhh
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccccccccccC
Q 025979          234 LGEVWLKHKQIF  245 (245)
Q Consensus       234 ~Ge~~~~vr~iF  245 (245)
                      .|+++..++.+|
T Consensus       279 ~g~~~~~~~~~f  290 (489)
T 3hu3_A          279 AGESESNLRKAF  290 (489)
T ss_dssp             TTHHHHHHHHHH
T ss_pred             cchhHHHHHHHH
Confidence            999988887765

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=99.62  E-value=4.7e-17  Score=142.68  Aligned_cols=93  Identities=38%  Similarity=0.713  Sum_probs=84.0

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHH
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQ  231 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~  231 (245)
                      +.++++|++++|.+.+++.+.+.+..|..++++|..++ .+++++|||||||||||++|+++|+.++.+|+.++++++..
T Consensus        14 ~~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~-~~~~~vll~Gp~GtGKT~la~~la~~~~~~~~~i~~~~l~~   92 (297)
T 3b9p_A           14 GGAKVEWTDIAGQDVAKQALQEMVILPSVRPELFTGLR-APAKGLLLFGPPGNGKTLLARAVATECSATFLNISAASLTS   92 (297)
T ss_dssp             CSSCCCGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGG-CCCSEEEEESSSSSCHHHHHHHHHHHTTCEEEEEESTTTSS
T ss_pred             CCCCCCHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCC-CCCCeEEEECcCCCCHHHHHHHHHHHhCCCeEEeeHHHHhh
Confidence            45778999999999999999999999988888887665 46789999999999999999999999999999999999999


Q ss_pred             HHhccccccccccC
Q 025979          232 KYLGEVWLKHKQIF  245 (245)
Q Consensus       232 ~~~Ge~~~~vr~iF  245 (245)
                      +|.|+++..++.+|
T Consensus        93 ~~~~~~~~~~~~~~  106 (297)
T 3b9p_A           93 KYVGDGEKLVRALF  106 (297)
T ss_dssp             SSCSCHHHHHHHHH
T ss_pred             cccchHHHHHHHHH
Confidence            99998887777654

>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=99.61  E-value=9.2e-17  Score=145.67  Aligned_cols=94  Identities=34%  Similarity=0.732  Sum_probs=85.4

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      ...+.++|++++|++.+++.|.+.+..|+.+++.|...+ .+++++|||||||||||++|+++|+.++.+|+.++++++.
T Consensus        76 ~~~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~-~~~~~vLl~GppGtGKT~la~aia~~~~~~~~~i~~~~l~  154 (357)
T 3d8b_A           76 DHGPPVNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLR-GPPKGILLFGPPGTGKTLIGKCIASQSGATFFSISASSLT  154 (357)
T ss_dssp             CCSCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGG-SCCSEEEEESSTTSSHHHHHHHHHHHTTCEEEEEEGGGGC
T ss_pred             cCCCCCCHHHhCChHHHHHHHHHHHHHHhhChHhHhhcc-CCCceEEEECCCCCCHHHHHHHHHHHcCCeEEEEehHHhh
Confidence            345788999999999999999999999888888887665 6789999999999999999999999999999999999999


Q ss_pred             HHHhccccccccccC
Q 025979          231 QKYLGEVWLKHKQIF  245 (245)
Q Consensus       231 ~~~~Ge~~~~vr~iF  245 (245)
                      ++|.|+++..++.+|
T Consensus       155 ~~~~g~~~~~~~~~~  169 (357)
T 3d8b_A          155 SKWVGEGEKMVRALF  169 (357)
T ss_dssp             CSSTTHHHHHHHHHH
T ss_pred             ccccchHHHHHHHHH
Confidence            999999888877664

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=99.60  E-value=2.1e-16  Score=144.53  Aligned_cols=94  Identities=41%  Similarity=0.726  Sum_probs=78.7

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      ...+.++|++++|++.+++.|.+++..+..++++|..++ .+++++|||||||||||++|+++|..++.+|+.++++++.
T Consensus       107 ~~~~~~~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~-~~~~~vLL~GppGtGKT~la~aia~~~~~~~~~v~~~~l~  185 (389)
T 3vfd_A          107 DNGTAVKFDDIAGQDLAKQALQEIVILPSLRPELFTGLR-APARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLT  185 (389)
T ss_dssp             CCSCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGG-CCCSEEEEESSTTSCHHHHHHHHHHHTTCEEEEECSCCC-
T ss_pred             ccCCCCChHHhCCHHHHHHHHHHHHHHhccCHHHhcccC-CCCceEEEECCCCCCHHHHHHHHHHhhcCcEEEeeHHHhh
Confidence            345678999999999999999999999888888888776 4678999999999999999999999999999999999999


Q ss_pred             HHHhccccccccccC
Q 025979          231 QKYLGEVWLKHKQIF  245 (245)
Q Consensus       231 ~~~~Ge~~~~vr~iF  245 (245)
                      ..|+|+++..++.+|
T Consensus       186 ~~~~g~~~~~~~~~~  200 (389)
T 3vfd_A          186 SKYVGEGEKLVRALF  200 (389)
T ss_dssp             ------CHHHHHHHH
T ss_pred             ccccchHHHHHHHHH
Confidence            999999988887665

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=99.59  E-value=2.7e-16  Score=148.97  Aligned_cols=91  Identities=41%  Similarity=0.773  Sum_probs=85.6

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHH
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKY  233 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~  233 (245)
                      ++++|+||+|+++++.++.+.+.. +.++..|..+|+..++|+|||||||||||+||+++|+.++.+|+.++++++.++|
T Consensus        26 ~~~~f~dv~G~~~~k~~l~~lv~~-l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~~~~~i~i~g~~~~~~~  104 (499)
T 2dhr_A           26 PKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMF  104 (499)
T ss_dssp             CCCCTTSSCSCHHHHHHHHHHHHH-HHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHTTCCEEEEEGGGGTSSC
T ss_pred             CCCCHHHcCCcHHHHHHHHHHHHH-hhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEehhHHHHhh
Confidence            788999999999999999999876 6778889999999999999999999999999999999999999999999999999


Q ss_pred             hccccccccccC
Q 025979          234 LGEVWLKHKQIF  245 (245)
Q Consensus       234 ~Ge~~~~vr~iF  245 (245)
                      +|.+.+.++.+|
T Consensus       105 ~g~~~~~v~~lf  116 (499)
T 2dhr_A          105 VGVGAARVRDLF  116 (499)
T ss_dssp             TTHHHHHHHHHT
T ss_pred             hhhHHHHHHHHH
Confidence            999988888877

>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=99.58  E-value=9.9e-16  Score=131.61  Aligned_cols=94  Identities=40%  Similarity=0.765  Sum_probs=84.5

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      .+.|.++|++++|++.++.++.+.+.. +.++..+..+++..++|++|+||||||||++++++|+.++.+++.+++.++.
T Consensus         8 ~~~~~~~~~~i~g~~~~~~~l~~l~~~-~~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~i~~~~~~~~i~~~~~~~~   86 (254)
T 1ixz_A            8 TEAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFV   86 (254)
T ss_dssp             CCCCSCCGGGCCSCHHHHHHHHHHHHH-HHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHH
T ss_pred             cCCCCCCHHHhCCcHHHHHHHHHHHHH-HHCHHHHHHcCCCCCCeEEEECCCCCCHHHHHHHHHHHhCCCEEEeeHHHHH
Confidence            456789999999999999999988776 6678889999999999999999999999999999999999999999999999


Q ss_pred             HHHhccccccccccC
Q 025979          231 QKYLGEVWLKHKQIF  245 (245)
Q Consensus       231 ~~~~Ge~~~~vr~iF  245 (245)
                      +.+.|++.+.++.+|
T Consensus        87 ~~~~~~~~~~i~~~~  101 (254)
T 1ixz_A           87 EMFVGVGAARVRDLF  101 (254)
T ss_dssp             HSCTTHHHHHHHHHH
T ss_pred             HHHhhHHHHHHHHHH
Confidence            988888777776554

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=99.52  E-value=6.3e-15  Score=128.59  Aligned_cols=93  Identities=41%  Similarity=0.768  Sum_probs=83.2

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHH
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQ  231 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~  231 (245)
                      +.++++|++++|+++++.++.+.+.. +.++..+..+++..++|++|+||||||||++++++|..++.+++.++++++.+
T Consensus        33 ~~~~~~~~~i~g~~~~~~~l~~l~~~-~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~~~~~i~~~~~~~~~  111 (278)
T 1iy2_A           33 EAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVE  111 (278)
T ss_dssp             CCCCCCGGGSSSCHHHHHHHHHHHHH-HHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHHH
T ss_pred             CCCCCCHHHhCChHHHHHHHHHHHHH-HHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHcCCCEEEecHHHHHH
Confidence            44789999999999999999988775 66788889999999999999999999999999999999999999999999999


Q ss_pred             HHhccccccccccC
Q 025979          232 KYLGEVWLKHKQIF  245 (245)
Q Consensus       232 ~~~Ge~~~~vr~iF  245 (245)
                      .+.|+..+.++.+|
T Consensus       112 ~~~~~~~~~i~~~~  125 (278)
T 1iy2_A          112 MFVGVGAARVRDLF  125 (278)
T ss_dssp             STTTHHHHHHHHHH
T ss_pred             HHhhHHHHHHHHHH
Confidence            88888777766554

>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=99.52  E-value=3.2e-15  Score=139.72  Aligned_cols=85  Identities=31%  Similarity=0.355  Sum_probs=74.5

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc--ceeeeechhHH
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT--AAFIRVVGSEF  229 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~--~~~~~v~~s~l  229 (245)
                      ..+...|++++|++++++.+.+++..        -..|..+++++|||||||||||++|+++|+.++  .+|+.++++++
T Consensus        30 ~~~~~~~~~iiG~~~~~~~l~~~~~~--------~~~~~~~~~~iLl~GppGtGKT~la~ala~~l~~~~~~~~~~~~~~  101 (456)
T 2c9o_A           30 GLAKQAASGLVGQENAREACGVIVEL--------IKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEV  101 (456)
T ss_dssp             SCBCSEETTEESCHHHHHHHHHHHHH--------HHTTCCTTCEEEEECCTTSSHHHHHHHHHHHHCTTSCEEEEEGGGG
T ss_pred             cChhhchhhccCHHHHHHHHHHHHHH--------HHhCCCCCCeEEEECCCcCCHHHHHHHHHHHhCCCceEEEEeHHHH
Confidence            34667899999999999999888754        344667889999999999999999999999998  99999999999


Q ss_pred             HHHHhccccccccccC
Q 025979          230 VQKYLGEVWLKHKQIF  245 (245)
Q Consensus       230 ~~~~~Ge~~~~vr~iF  245 (245)
                      .++|+|++++ ++++|
T Consensus       102 ~~~~~~~~~~-~~~~f  116 (456)
T 2c9o_A          102 YSTEIKKTEV-LMENF  116 (456)
T ss_dssp             CCSSSCHHHH-HHHHH
T ss_pred             HHHhhhhhHH-HHHHH
Confidence            9999999987 76655

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=99.47  E-value=4.2e-15  Score=131.32  Aligned_cols=58  Identities=21%  Similarity=0.200  Sum_probs=51.4

Q ss_pred             hccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhccccccccccC
Q 025979          188 IGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       188 ~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge~~~~vr~iF  245 (245)
                      .+.++|+|+|||||||||||++|+++|++++.+|++++++++.++|+|+++..++++|
T Consensus        31 ~~~~~p~~lLl~GppGtGKT~la~aiA~~l~~~~i~v~~~~l~~~~~g~~~~~i~~~f   88 (293)
T 3t15_A           31 PNIKVPLILGIWGGKGQGKSFQCELVFRKMGINPIMMSAGELESGNAGEPAKLIRQRY   88 (293)
T ss_dssp             TTCCCCSEEEEEECTTSCHHHHHHHHHHHHTCCCEEEEHHHHHCC---HHHHHHHHHH
T ss_pred             CCCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCEEEEeHHHhhhccCchhHHHHHHHH
Confidence            3678899999999999999999999999999999999999999999999999888765

>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=99.45  E-value=5.3e-15  Score=141.33  Aligned_cols=150  Identities=20%  Similarity=0.218  Sum_probs=103.8

Q ss_pred             HHHHHHHHHhhhhccccchhhhhhhhhhcccceeecccCCeeEEEEeecccccccCCCceeeeeccccccccccCCCccc
Q 025979           64 RELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADS  143 (245)
Q Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~~~~~~~~~~~il~~~~~~  143 (245)
                      .++.++++++++.+.++.....+.+++.+...+.+.+.+..+..++++|+  ..++|+....                  
T Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~~~el~~l~~~~~~~~e~~~~~~~l~~~--~~lp~~~~~~------------------   67 (543)
T 3m6a_A            8 GEVQTLTEKIEEAGMPDHVKETALKELNRYEKIPSSSAESSVIRNYIDWL--VALPWTDETD------------------   67 (543)
T ss_dssp             CTTTHHHHHHHSSSCCCHHHHHHHHHHHSSCCCSSSCTTTTHHHHHHHHH--HHSCSSCCCC------------------
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhcCCCCCchHhHHHHHHHHH--hcCCCCcccc------------------
Confidence            35667888999999999999999999999988888888888878888776  2334432211                  


Q ss_pred             cccccccCCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccC-CCcceeeecCCCCchHHHHHHHHhcccceee
Q 025979          144 SISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGID-PPRGVLLYGPPGTGKTMLAKAVANHTTAAFI  222 (245)
Q Consensus       144 ~~~~~~~~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~-~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~  222 (245)
                        ..+...+.....+++++|++++++.+.+.+...        .+... ++..+||+||||||||++|+++|..++.+|+
T Consensus        68 --~~~~~~~~~~~l~~di~G~~~vk~~i~~~~~l~--------~~~~~~~g~~vll~Gp~GtGKTtlar~ia~~l~~~~~  137 (543)
T 3m6a_A           68 --DKLDLKEAGRLLDEEHHGLEKVKERILEYLAVQ--------KLTKSLKGPILCLAGPPGVGKTSLAKSIAKSLGRKFV  137 (543)
T ss_dssp             --CCCCTTTGGGTHHHHCSSCHHHHHHHHHHHHHH--------HHSSSCCSCEEEEESSSSSSHHHHHHHHHHHHTCEEE
T ss_pred             --ccccHHHHHHHHHHHhccHHHHHHHHHHHHHHH--------HhcccCCCCEEEEECCCCCCHHHHHHHHHHhcCCCeE
Confidence              111122334456789999999999998877642        22221 4456999999999999999999999999999


Q ss_pred             eechhHHHH---------HHhccccccccc
Q 025979          223 RVVGSEFVQ---------KYLGEVWLKHKQ  243 (245)
Q Consensus       223 ~v~~s~l~~---------~~~Ge~~~~vr~  243 (245)
                      +++++.+..         .|+|.....++.
T Consensus       138 ~i~~~~~~~~~~~~g~~~~~ig~~~~~~~~  167 (543)
T 3m6a_A          138 RISLGGVRDESEIRGHRRTYVGAMPGRIIQ  167 (543)
T ss_dssp             EECCCC--------------------CHHH
T ss_pred             EEEecccchhhhhhhHHHHHhccCchHHHH
Confidence            998876543         677777666554

>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=99.42  E-value=3.3e-14  Score=132.69  Aligned_cols=88  Identities=26%  Similarity=0.431  Sum_probs=72.0

Q ss_pred             eccCCcchhhhHHHHHHHhcCCCcHHHHhhhccC-CCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHH-HHhc
Q 025979          158 YNDIGGCDIQKQEIREAVELPLTHHELYKQIGID-PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQ-KYLG  235 (245)
Q Consensus       158 ~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~-~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~-~~~G  235 (245)
                      .++|+|++++++.+..++..++.++.++..++.. +++++||+||||||||++|+++|..++.+|+.++++.+.+ +|+|
T Consensus        14 d~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~l~~~~~~v~~~~~~~~g~vG   93 (444)
T 1g41_A           14 DQHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVG   93 (444)
T ss_dssp             HTTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGGGC----CC
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHHcCCCceeecchhhcccceee
Confidence            3579999999999999997766666555444433 5688999999999999999999999999999999999998 6999


Q ss_pred             c-ccccccccC
Q 025979          236 E-VWLKHKQIF  245 (245)
Q Consensus       236 e-~~~~vr~iF  245 (245)
                      + ++..++++|
T Consensus        94 ~d~e~~lr~lf  104 (444)
T 1g41_A           94 KEVDSIIRDLT  104 (444)
T ss_dssp             CCTHHHHHHHH
T ss_pred             ccHHHHHHHHH
Confidence            5 788888765

>2wg5_A General control protein GCN4, proteasome-activating nucleotidase; transcription hydrolase complex, nucleotide-binding; 2.10A {Saccharomyces cerevisiae} PDB: 2wg6_A

Probab=99.40  E-value=2.3e-13  Score=103.79  Aligned_cols=100  Identities=30%  Similarity=0.477  Sum_probs=81.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhhhcccceeecccCCeeEEEEeecccccccCCCceeeeeccc
Q 025979           51 QEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHS  130 (245)
Q Consensus        51 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~~~~~~  130 (245)
                      +++.++.+++.+++++..++++++.++++|..+|++.+.+++.++++++++|.+|++.+.+.++.+.|+||.+|+++.++
T Consensus         8 ~~~~l~~~~~~l~~~i~~lkeel~~L~~~P~~Vg~v~e~~d~~~~iVk~s~g~~~~V~v~~~Vd~~~LkpG~rVaLn~~s   87 (109)
T 2wg5_A            8 RMKQLEDKVEELLSKNYHLENEVARLRSPPLLVGVVSDILEDGRVVVKSSTGPKFVVNTSQYINEEELKPGARVALNQQT   87 (109)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHSCCEEEEEEEEECTTSCEEEEETTSCEEEECBCTTSCTTTCCTTCEEEEETTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhCCCceEEEEEEEecCCEEEEEeCCCCEEEEEcccccCHHHCCCCCEEEECCcc
Confidence            34567777788888888999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccccCCCcccccccccc
Q 025979          131 NALVDVLPPEADSSISLLSQ  150 (245)
Q Consensus       131 ~~~~~il~~~~~~~~~~~~~  150 (245)
                      ..+.+++|++.|+.++.|..
T Consensus        88 ~~Iv~iLp~e~Dp~V~~M~v  107 (109)
T 2wg5_A           88 LAIVNVLPTSKDPMVYGFEV  107 (109)
T ss_dssp             CCEEEEEC------------
T ss_pred             eEeEEeCCCCcCccchheEe
Confidence            99999999999999988764

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=99.32  E-value=2.1e-13  Score=119.64  Aligned_cols=86  Identities=27%  Similarity=0.407  Sum_probs=71.9

Q ss_pred             eccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCc---ceeeecCCCCchHHHHHHHHhcccc-------eeeeechh
Q 025979          158 YNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPR---GVLLYGPPGTGKTMLAKAVANHTTA-------AFIRVVGS  227 (245)
Q Consensus       158 ~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~---gvLl~GPPGtGKT~lAkalA~~l~~-------~~~~v~~s  227 (245)
                      +.+++|++.+++.|.+.+..+. .+..+.+.|+.+++   ++|||||||||||++|+++|+.++.       +|+.++++
T Consensus        30 ~~~i~G~~~~~~~l~~~~~~~~-~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~~  108 (309)
T 3syl_A           30 DRELIGLKPVKDRIRETAALLL-VERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTRD  108 (309)
T ss_dssp             HHHSSSCHHHHHHHHHHHHHHH-HHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEECGG
T ss_pred             HHHccChHHHHHHHHHHHHHHH-hHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEcHH
Confidence            3479999999999999998744 46777788876544   4999999999999999999998844       89999999


Q ss_pred             HHHHHHhcccccccccc
Q 025979          228 EFVQKYLGEVWLKHKQI  244 (245)
Q Consensus       228 ~l~~~~~Ge~~~~vr~i  244 (245)
                      ++.+.|+|.+...++.+
T Consensus       109 ~l~~~~~g~~~~~~~~~  125 (309)
T 3syl_A          109 DLVGQYIGHTAPKTKEV  125 (309)
T ss_dssp             GTCCSSTTCHHHHHHHH
T ss_pred             HhhhhcccccHHHHHHH
Confidence            99999999877766554

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.31  E-value=2.5e-13  Score=134.17  Aligned_cols=177  Identities=21%  Similarity=0.309  Sum_probs=101.6

Q ss_pred             ccCCCCC---CCCCCCcccCCCCCCCCchhHHHHHHHHHHHhhhhhh-----hHHHHHHHHHHHHHHHHHHHHHhhhhcc
Q 025979            7 VLDPKPV---SEPPPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFIDI-----QEEYVKDEQKNLKRELLRAQEEVKRIQS   78 (245)
Q Consensus         7 ~~~~k~~---~e~~~~~~~e~~~~~~~~~~~~~~~~~~~~e~~~l~~-----~~~~i~~~~~~~~~~~~~~~~~~~~~~~   78 (245)
                      .+|||++   |++++..+......+.....+..++..++.+...+..     ....++.++..+++++..++..+.....
T Consensus       369 ~~p~~ai~ll~~a~~~~~~~~~~~p~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~  448 (758)
T 3pxi_A          369 FLPDKAIDLIDEAGSKVRLRSFTTPPNLKELEQKLDEVRKEKDAAVQSQEFEKAASLRDTEQRLREQVEDTKKSWKEKQG  448 (758)
T ss_dssp             CTTHHHHHHHHHHHHHHHHHTTC--CCTHHHHHHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHSGGGHHHH
T ss_pred             cCCcHHHHHHHHHHHHHHhhccCCCcchhhHHHHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            4688888   8888888888888888888888888877766644431     2223333333333333333322222110


Q ss_pred             ccchhhhhhhhhhcccceeecccCCeeEEEEeecccccccCCCceeeeeccccccccccCCCccccccccccCC------
Q 025979           79 VPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADSSISLLSQSE------  152 (245)
Q Consensus        79 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~~~~~~~~~~~il~~~~~~~~~~~~~~~------  152 (245)
                                   ....                               ......+..++..|++.++..+...+      
T Consensus       449 -------------~~~~-------------------------------~v~~~~i~~~v~~~~~ip~~~~~~~~~~~l~~  484 (758)
T 3pxi_A          449 -------------QENS-------------------------------EVTVDDIAMVVSSWTGVPVSKIAQTETDKLLN  484 (758)
T ss_dssp             -------------CC----------------------------------CCTHHHHHHHHTTC-------CHHHHSCC-C
T ss_pred             -------------ccCc-------------------------------ccCHHHHHHHHHHHhCCChHHhhHHHHHHHHH
Confidence                         0000                               00011111222222222222111111      


Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCC---Cc-ceeeecCCCCchHHHHHHHHhcc---cceeeeec
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDP---PR-GVLLYGPPGTGKTMLAKAVANHT---TAAFIRVV  225 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~---~~-gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~  225 (245)
                      .......+++|++.+++.+.+.+..        .+.|+..   |. ++||+||||||||++|+++|+.+   +.+|++++
T Consensus       485 l~~~l~~~viGq~~a~~~l~~~i~~--------~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~~~~~~~i~i~  556 (758)
T 3pxi_A          485 MENILHSRVIGQDEAVVAVAKAVRR--------ARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESIFGDEESMIRID  556 (758)
T ss_dssp             HHHHHHTTSCSCHHHHHHHHHHHHH--------HTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHHHHSCTTCEEEEE
T ss_pred             HHHHHhCcCcChHHHHHHHHHHHHH--------HHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCcceEEEe
Confidence            0112245799999999999999875        2233332   22 59999999999999999999997   78899999


Q ss_pred             hhHHHHHHhc
Q 025979          226 GSEFVQKYLG  235 (245)
Q Consensus       226 ~s~l~~~~~G  235 (245)
                      ++++.+.+.+
T Consensus       557 ~s~~~~~~~~  566 (758)
T 3pxi_A          557 MSEYMEKHST  566 (758)
T ss_dssp             GGGGCSSCCC
T ss_pred             chhccccccc
Confidence            9999876654

>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=99.21  E-value=1.5e-13  Score=137.58  Aligned_cols=93  Identities=26%  Similarity=0.438  Sum_probs=65.6

Q ss_pred             ccccccCCCccccccccccCCC------CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCC----cceeeecC
Q 025979          132 ALVDVLPPEADSSISLLSQSEK------PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPP----RGVLLYGP  201 (245)
Q Consensus       132 ~~~~il~~~~~~~~~~~~~~~~------~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~----~gvLl~GP  201 (245)
                      .+..++..|.+.++..+...+.      +...+++++|.+.+++.+...+..        .+.|+..|    ..+||+||
T Consensus       525 ~l~~~v~~~~~ip~~~~~~~~~~~l~~l~~~l~~~viG~~~a~~~l~~~i~~--------~~~g~~~~~~p~~~vLl~Gp  596 (854)
T 1qvr_A          525 DIAEIVSRWTGIPVSKLLEGEREKLLRLEEELHKRVVGQDEAIRAVADAIRR--------ARAGLKDPNRPIGSFLFLGP  596 (854)
T ss_dssp             HHHHHHHTTSSCHHHHTTCCHHHHHHSHHHHHHHHSCSCHHHHHHHHHHHHH--------HGGGCSCSSSCSEEEEEBSC
T ss_pred             HHHHHHHHHhCCChHhhcHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHHHH--------HhcccCCCCCCceEEEEECC
Confidence            3444555565554443322111      123356899999999999998865        33444332    36999999


Q ss_pred             CCCchHHHHHHHHhcc---cceeeeechhHHHHH
Q 025979          202 PGTGKTMLAKAVANHT---TAAFIRVVGSEFVQK  232 (245)
Q Consensus       202 PGtGKT~lAkalA~~l---~~~~~~v~~s~l~~~  232 (245)
                      ||||||++|+++|..+   +.+|++++++++.+.
T Consensus       597 ~GtGKT~lA~~la~~~~~~~~~~i~i~~~~~~~~  630 (854)
T 1qvr_A          597 TGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEK  630 (854)
T ss_dssp             SSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCSS
T ss_pred             CCCCHHHHHHHHHHHhcCCCCcEEEEechhccch
Confidence            9999999999999998   889999999877543

>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=99.18  E-value=4.4e-12  Score=114.60  Aligned_cols=78  Identities=26%  Similarity=0.332  Sum_probs=59.4

Q ss_pred             cCCcchhhhHHHHHHHhcCCCcHHHHhh-hcc-CCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHH-HHhcc
Q 025979          160 DIGGCDIQKQEIREAVELPLTHHELYKQ-IGI-DPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQ-KYLGE  236 (245)
Q Consensus       160 dv~Gl~~~~~~i~e~i~~~~~~~~~~~~-~g~-~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~-~~~Ge  236 (245)
                      .|+|++.+++.+..++............ .+. .+++++||+||||||||++|+++|+.++.+|+.++++++.. .|+|+
T Consensus        16 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~~~~~~~~~~~~l~~~~~~g~   95 (363)
T 3hws_A           16 YVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTLTEAGYVGE   95 (363)
T ss_dssp             HCCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHTTCHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHcCCCEEEechHHhcccccccc
Confidence            4799999999999988532211110000 011 25678999999999999999999999999999999999884 48887


Q ss_pred             c
Q 025979          237 V  237 (245)
Q Consensus       237 ~  237 (245)
                      +
T Consensus        96 ~   96 (363)
T 3hws_A           96 D   96 (363)
T ss_dssp             H
T ss_pred             c
Confidence            6

>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=99.12  E-value=8.5e-12  Score=108.85  Aligned_cols=78  Identities=28%  Similarity=0.487  Sum_probs=59.1

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhh-ccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHH-HHhcc
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQI-GIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQ-KYLGE  236 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~-g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~-~~~Ge  236 (245)
                      ++++|++.+++.+..++..+.....+.... +-..+.++||+||||||||++|+++|+.++.+|+.++++++.+ .|+|.
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~i~~~~~~~~~~~~~   94 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGK   94 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGGSSCCSGGG
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEcchhcccCCccCc
Confidence            469999999999998886532211111111 1135678999999999999999999999999999999998865 56664

>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=99.12  E-value=1.3e-11  Score=117.09  Aligned_cols=84  Identities=23%  Similarity=0.299  Sum_probs=64.2

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCC-CcHHHHhhhcc---CCCcceeeecCCCCchHHHHHHHHhcccceeeeech
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPL-THHELYKQIGI---DPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVG  226 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~-~~~~~~~~~g~---~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~  226 (245)
                      .+..+.+|++++|.+.+++.+.+.+.... .++..|...|.   .+++++||+||||||||++|+++|++++.+++.+++
T Consensus        31 ekyrP~~~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l~~~~i~in~  110 (516)
T 1sxj_A           31 VKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDILEQNA  110 (516)
T ss_dssp             HHTCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTCEEEEECT
T ss_pred             cccCCCCHHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHcCCCEEEEeC
Confidence            34455689999999999999999987521 11222333333   256789999999999999999999999999999998


Q ss_pred             hHHHHHHh
Q 025979          227 SEFVQKYL  234 (245)
Q Consensus       227 s~l~~~~~  234 (245)
                      +++...++
T Consensus       111 s~~~~~~~  118 (516)
T 1sxj_A          111 SDVRSKTL  118 (516)
T ss_dssp             TSCCCHHH
T ss_pred             CCcchHHH
Confidence            87654443

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=99.06  E-value=6.6e-11  Score=106.15  Aligned_cols=78  Identities=26%  Similarity=0.352  Sum_probs=60.8

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc--eeeeechhHHH
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA--AFIRVVGSEFV  230 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~--~~~~v~~s~l~  230 (245)
                      .|..+|++++|.+.+++.+...+..        -..|..+++++|||||||||||++|+++|+.++.  +|+.+++.++.
T Consensus        38 ~p~~~~~~ivG~~~~~~~l~~l~~~--------~~~~~~~~~~vLl~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~  109 (368)
T 3uk6_A           38 EPRQASQGMVGQLAARRAAGVVLEM--------IREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIF  109 (368)
T ss_dssp             CBCSEETTEESCHHHHHHHHHHHHH--------HHTTCCTTCEEEEEESTTSSHHHHHHHHHHHHCSSCCEEEEEGGGGS
T ss_pred             CcCcchhhccChHHHHHHHHHHHHH--------HHcCCCCCCEEEEECCCCCCHHHHHHHHHHHhcccCCcccccchhhh
Confidence            4566799999999998887665543        2224445688999999999999999999999874  88899888876


Q ss_pred             HHHhcccc
Q 025979          231 QKYLGEVW  238 (245)
Q Consensus       231 ~~~~Ge~~  238 (245)
                      +.+.+.++
T Consensus       110 ~~~~~~~~  117 (368)
T 3uk6_A          110 SLEMSKTE  117 (368)
T ss_dssp             CSSSCHHH
T ss_pred             hcccchhH
Confidence            66665543

>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=99.06  E-value=5.6e-11  Score=107.71  Aligned_cols=79  Identities=24%  Similarity=0.303  Sum_probs=54.5

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHh----------------hhc-cCCCcceeeecCCCCchHHHHHHHHhccccee
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYK----------------QIG-IDPPRGVLLYGPPGTGKTMLAKAVANHTTAAF  221 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~----------------~~g-~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~  221 (245)
                      ++|+|++.+++.|..++..++.......                .-+ ..++.++||+||||||||++|+++|+.++.+|
T Consensus        21 ~~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~la~~l~~~~  100 (376)
T 1um8_A           21 NYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHLDIPI  100 (376)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCE
T ss_pred             hHccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHHHHHHhCCCE
Confidence            4689999999999988843222221100                001 13456799999999999999999999999999


Q ss_pred             eeechhHHH-HHHhccc
Q 025979          222 IRVVGSEFV-QKYLGEV  237 (245)
Q Consensus       222 ~~v~~s~l~-~~~~Ge~  237 (245)
                      +.++++.+. ..|.|+.
T Consensus       101 ~~~~~~~~~~~~~~g~~  117 (376)
T 1um8_A          101 AISDATSLTEAGYVGED  117 (376)
T ss_dssp             EEEEGGGCC--------
T ss_pred             EEecchhhhhcCcCCcc
Confidence            999998875 5677764

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=99.05  E-value=2.2e-10  Score=101.83  Aligned_cols=67  Identities=18%  Similarity=0.243  Sum_probs=55.7

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHH
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF  229 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l  229 (245)
                      ..+|++++|.+..++.+...+....        ..-.++.++||+||||||||++|+++|+.++.+|+.++++.+
T Consensus        25 p~~~~~iiG~~~~~~~l~~~l~~~~--------~~~~~~~~vll~G~~GtGKT~la~~ia~~~~~~~~~~~~~~~   91 (338)
T 3pfi_A           25 PSNFDGYIGQESIKKNLNVFIAAAK--------KRNECLDHILFSGPAGLGKTTLANIISYEMSANIKTTAAPMI   91 (338)
T ss_dssp             CCSGGGCCSCHHHHHHHHHHHHHHH--------HTTSCCCCEEEECSTTSSHHHHHHHHHHHTTCCEEEEEGGGC
T ss_pred             CCCHHHhCChHHHHHHHHHHHHHHH--------hcCCCCCeEEEECcCCCCHHHHHHHHHHHhCCCeEEecchhc
Confidence            3478999999999999998886521        112355679999999999999999999999999999988654

>3h43_A Proteasome-activating nucleotidase; regulatory particle, nucleosidase, ATP-binding, cytoplasm, nucleotide-binding, hydrolase; 2.10A {Methanocaldococcus jannaschii}

Probab=99.04  E-value=1.5e-10  Score=84.28  Aligned_cols=76  Identities=29%  Similarity=0.522  Sum_probs=71.6

Q ss_pred             HHHHHHHHHhhhhccccchhhhhhhhhhcccceeecccCCeeEEEEeecccccccCCCceeeeeccccccccccCC
Q 025979           64 RELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPP  139 (245)
Q Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~v~~~~~~~~~~~il~~  139 (245)
                      +++..++++++.++++|..+|++.+.+++.++++++++|++|++.+.++++.+.++||++|+++.++.++.+++|.
T Consensus         2 ~ev~~lkeei~~L~~~P~~vG~v~e~~dd~~~iVkss~g~~~~V~v~~~Vd~~~LkpG~rVaLn~~s~~Iv~vLp~   77 (85)
T 3h43_A            2 KENEILRRELDRMRVPPLIVGTVVDKVGERKVVVKSSTGPSFLVNVSHFVNPDDLAPGKRVCLNQQTLTVVDVLPE   77 (85)
T ss_dssp             HHHHHHHHHHHHHHSCCEEEEEEEEEEETTEEEEEETTSSEEEEEBCTTSCGGGCCTTCEEEECTTTCCEEEECC-
T ss_pred             cHHHHHHHHHHHhcCCCceEEEEEEEcCCCEEEEEeCCCCeEEEEecCccCHHHCCCCCEEEECCcccCHhhhhhh
Confidence            3677889999999999999999999999999999999999999999999999999999999999999999999983

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=99.03  E-value=1.1e-10  Score=93.53  Aligned_cols=62  Identities=18%  Similarity=0.274  Sum_probs=52.0

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc----------cceeeeec
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT----------TAAFIRVV  225 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l----------~~~~~~v~  225 (245)
                      ..+++++|.++.++.+.+.+..             ..+++++|+||||||||++|+++++.+          +.+++.++
T Consensus        19 ~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (195)
T 1jbk_A           19 GKLDPVIGRDEEIRRTIQVLQR-------------RTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALD   85 (195)
T ss_dssp             TCSCCCCSCHHHHHHHHHHHTS-------------SSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEEC
T ss_pred             ccccccccchHHHHHHHHHHhc-------------CCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCcEEEee
Confidence            4578899999988888877643             245679999999999999999999986          68889999


Q ss_pred             hhHHH
Q 025979          226 GSEFV  230 (245)
Q Consensus       226 ~s~l~  230 (245)
                      ++++.
T Consensus        86 ~~~~~   90 (195)
T 1jbk_A           86 MGALV   90 (195)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            88776

>3m9b_A Proteasome-associated ATPase; coil COIL with 5 beta-strand barrel inter domain, chaperone; 3.94A {Mycobacterium tuberculosis} PDB: 3m9d_A

Probab=98.99  E-value=8.7e-10  Score=94.43  Aligned_cols=108  Identities=21%  Similarity=0.285  Sum_probs=98.7

Q ss_pred             HHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhhhcccceeecccCCeeEEEEeecccc
Q 025979           36 SRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDQNNGIVGSTTGSNYYVRILSTINR  115 (245)
Q Consensus        36 ~~~~~~~~e~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  115 (245)
                      .+++++++++..|..++.+|.++++.+++++.++++++++++++|..+++|.+.+++..+++. ++|.++++.+.+.++.
T Consensus        54 ~~l~eL~~ql~~L~arNe~L~~~Lk~ar~El~~LkeElerL~sPPL~iGtvlev~dd~~aiV~-s~Gr~~~V~Vsp~Vd~  132 (251)
T 3m9b_A           54 RDIHQLEARIDSLAARNSKLMETLKEARQQLLALREEVDRLGQPPSGYGVLLATHDDDTVDVF-TSGRKMRLTCSPNIDA  132 (251)
T ss_dssp             HHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHSCCEEEEEEEEECSSSCEEEE-CSSSCCEECBCTTSCT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCceEEEEEEEcCCCEEEEE-eCCceEEEEeCCCCCH
Confidence            468899999999999999999999999999999999999999999999999999998888887 5889999999999999


Q ss_pred             cccCCCceeeeeccccccccccCCCccccc
Q 025979          116 ELLKPSASVALHRHSNALVDVLPPEADSSI  145 (245)
Q Consensus       116 ~~l~~~~~v~~~~~~~~~~~il~~~~~~~~  145 (245)
                      ..|+||..|.++ ++..+++++|.+..-.+
T Consensus       133 e~LkPG~rVaLN-eSlaVVevLp~E~~Gev  161 (251)
T 3m9b_A          133 ASLKKGQTVRLN-EALTVVEAGTFEAVGEI  161 (251)
T ss_dssp             TTSCSSCEEEEC-TTCCBCCCCCCCCCSEE
T ss_pred             HHCCCCCEEEeC-CccEEEEecCCCCcccE
Confidence            999999999996 68899999987654433

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=98.98  E-value=2.4e-10  Score=107.14  Aligned_cols=74  Identities=23%  Similarity=0.335  Sum_probs=53.3

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc----------cceeeeec
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT----------TAAFIRVV  225 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l----------~~~~~~v~  225 (245)
                      -.+++++|.+..++.+.+.+..             ....++||+||||||||++|+++|..+          +.+|+.++
T Consensus       177 ~~ld~iiGr~~~i~~l~~~l~r-------------~~~~~~LL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~  243 (468)
T 3pxg_A          177 DSLDPVIGRSKEIQRVIEVLSR-------------RTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLD  243 (468)
T ss_dssp             SCSCCCCCCHHHHHHHHHHHHC-------------SSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC-
T ss_pred             CCCCCccCcHHHHHHHHHHHhc-------------cCCCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEee
Confidence            4578899999999998888764             234579999999999999999999986          78899999


Q ss_pred             hhHHHHHHhccccccccccC
Q 025979          226 GSEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       226 ~s~l~~~~~Ge~~~~vr~iF  245 (245)
                      ++   .+|.|+.+..++.+|
T Consensus       244 ~~---~~~~g~~e~~~~~~~  260 (468)
T 3pxg_A          244 MG---TKYRGEFEDRLKKVM  260 (468)
T ss_dssp             ------------CTTHHHHH
T ss_pred             CC---ccccchHHHHHHHHH
Confidence            88   788888877776654

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=98.96  E-value=1.9e-10  Score=92.27  Aligned_cols=63  Identities=17%  Similarity=0.275  Sum_probs=52.0

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc----------cceeeeec
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT----------TAAFIRVV  225 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l----------~~~~~~v~  225 (245)
                      ..+++++|.+...+.+.+.+..             ..+++++|+||||||||++|+++++.+          +.+++.++
T Consensus        19 ~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~vll~G~~G~GKT~la~~~~~~~~~~~~~~~~~~~~~~~~~   85 (187)
T 2p65_A           19 GKLDPVIGRDTEIRRAIQILSR-------------RTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKLVSLD   85 (187)
T ss_dssp             TCSCCCCSCHHHHHHHHHHHTS-------------SSSCEEEEESCGGGCHHHHHHHHHHHHHTTCSCTTTTTCEEEEEC
T ss_pred             cccchhhcchHHHHHHHHHHhC-------------CCCCceEEECCCCCCHHHHHHHHHHHHHhcCCcchhcCCeEEEEe
Confidence            3567899999988888877643             235679999999999999999999987          78899998


Q ss_pred             hhHHHH
Q 025979          226 GSEFVQ  231 (245)
Q Consensus       226 ~s~l~~  231 (245)
                      ++.+..
T Consensus        86 ~~~~~~   91 (187)
T 2p65_A           86 LSSLIA   91 (187)
T ss_dssp             HHHHHH
T ss_pred             HHHhhc
Confidence            887763

>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=98.95  E-value=3.7e-10  Score=97.68  Aligned_cols=67  Identities=30%  Similarity=0.379  Sum_probs=49.2

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhH
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSE  228 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~  228 (245)
                      ..+.|.+...+.+.......   ...+...+..+++++|||||||||||++|+++|+.++.+|+.+++++
T Consensus        33 ~~~i~~~~~~~~i~~~~~~l---~~~l~~~~~~~~~~vLl~G~~GtGKT~la~~ia~~~~~~~~~i~~~~   99 (272)
T 1d2n_A           33 NGIIKWGDPVTRVLDDGELL---VQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPD   99 (272)
T ss_dssp             TCCCCCSHHHHHHHHHHHHH---HHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHTCSEEEEECGG
T ss_pred             cCCCCccHHHHHHHHHHHHH---HHHHhccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCEEEEeCHH
Confidence            45677777766666532110   11223334567788999999999999999999999999999998764

>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=98.95  E-value=5.8e-11  Score=125.28  Aligned_cols=93  Identities=22%  Similarity=0.177  Sum_probs=64.9

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCc----------HHHHhh------hccC----------CCcc--eeeecCCCC
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTH----------HELYKQ------IGID----------PPRG--VLLYGPPGT  204 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~----------~~~~~~------~g~~----------~~~g--vLl~GPPGt  204 (245)
                      .+.+.|+|++|++++++.+.+.+.+|+.+          ++.|+.      .|+.          +|+|  +|+||||||
T Consensus      1014 ~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tG~~glD~~lg~GG~p~g~~~l~~G~~g~ 1093 (1706)
T 3cmw_A         1014 ASGSSTGSMSAIDENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESS 1093 (1706)
T ss_dssp             ----------CTTHHHHHHHHHHHHHHHHHHCGGGSEEGGGCGGGSCCEECCSCHHHHHHTSSSSEETTSEEEEECSTTS
T ss_pred             cCCceeeecCCccHHHHHHHHHHHHHHhhccCcccchhchhhhhccccccccCchhHHHHhccCCCCCCCEEEEEcCCCC
Confidence            34589999999999999999999998844          556665      3333          5677  999999999


Q ss_pred             chHHHHHHHHhcccce-----eeeech--hHHH--------HHHhcc----ccccccccC
Q 025979          205 GKTMLAKAVANHTTAA-----FIRVVG--SEFV--------QKYLGE----VWLKHKQIF  245 (245)
Q Consensus       205 GKT~lAkalA~~l~~~-----~~~v~~--s~l~--------~~~~Ge----~~~~vr~iF  245 (245)
                      |||++|+++|.+....     |+.+..  ++++        ++|+|+    +|+.|+.+|
T Consensus      1094 GKT~la~~~~~~~~~~g~~~~fi~~~~~~~~~~~~~~G~d~~~~~~~~~~~~e~~l~~~~ 1153 (1706)
T 3cmw_A         1094 GKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICD 1153 (1706)
T ss_dssp             SHHHHHHHHHHHHHHTTCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             ChHHHHHHHHHHhhhcCCceeEEEcccchHHHHHHHhCCCHHHHhhccccchHHHHHHHH
Confidence            9999999999877444     666655  5666        778888    888877654

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=98.90  E-value=6.4e-10  Score=109.76  Aligned_cols=74  Identities=23%  Similarity=0.319  Sum_probs=54.4

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc----------cceeeeec
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT----------TAAFIRVV  225 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l----------~~~~~~v~  225 (245)
                      -.+++++|.+..++++.+.+..             ..+.++|||||||||||++|+++|..+          +.+++.++
T Consensus       177 ~~ld~iiG~~~~i~~l~~~l~~-------------~~~~~vLL~G~pGtGKT~la~~la~~l~~~~~p~~l~~~~~~~~~  243 (758)
T 3pxi_A          177 DSLDPVIGRSKEIQRVIEVLSR-------------RTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLD  243 (758)
T ss_dssp             SCSCCCCCCHHHHHHHHHHHHC-------------SSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC-
T ss_pred             CCCCCccCchHHHHHHHHHHhC-------------CCCCCeEEECCCCCCHHHHHHHHHHHHhcCCCChhhcCCeEEEec
Confidence            4578899999999999888754             234579999999999999999999997          88899888


Q ss_pred             hhHHHHHHhccccccccccC
Q 025979          226 GSEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       226 ~s~l~~~~~Ge~~~~vr~iF  245 (245)
                      +   ..+|.|+.+..++.+|
T Consensus       244 ~---g~~~~G~~e~~l~~~~  260 (758)
T 3pxi_A          244 M---GTKYRGEFEDRLKKVM  260 (758)
T ss_dssp             ------------CTTHHHHH
T ss_pred             c---cccccchHHHHHHHHH
Confidence            8   6778999998888765

>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=98.90  E-value=1.2e-09  Score=96.19  Aligned_cols=68  Identities=31%  Similarity=0.460  Sum_probs=54.7

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHH
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF  229 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l  229 (245)
                      ...+|++++|.+..++.+.+.+...       .. +-..+.++||+||||||||++|+++++.++.+|+.++++.+
T Consensus         7 ~p~~~~~~ig~~~~~~~l~~~l~~~-------~~-~~~~~~~vll~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~   74 (324)
T 1hqc_A            7 RPKTLDEYIGQERLKQKLRVYLEAA-------KA-RKEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAI   74 (324)
T ss_dssp             CCCSTTTCCSCHHHHHHHHHHHHHH-------HH-HCSCCCCCEEECCTTCCCHHHHHHHHHHHTCCEEEECTTTC
T ss_pred             CcccHHHhhCHHHHHHHHHHHHHHH-------Hc-cCCCCCcEEEECCCCCCHHHHHHHHHHHhCCCEEEEecccc
Confidence            3457899999999999998887641       11 11355789999999999999999999999999998887643

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=98.85  E-value=7.5e-10  Score=87.21  Aligned_cols=61  Identities=21%  Similarity=0.270  Sum_probs=48.4

Q ss_pred             cCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHH
Q 025979          160 DIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQK  232 (245)
Q Consensus       160 dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~  232 (245)
                      +++|.+...+.+.+.+...           ...+..+||+||||||||++|++++...+ +|+.++++++...
T Consensus         5 ~~iG~s~~~~~l~~~~~~~-----------~~~~~~vll~G~~GtGKt~lA~~i~~~~~-~~~~~~~~~~~~~   65 (143)
T 3co5_A            5 DKLGNSAAIQEMNREVEAA-----------AKRTSPVFLTGEAGSPFETVARYFHKNGT-PWVSPARVEYLID   65 (143)
T ss_dssp             ---CCCHHHHHHHHHHHHH-----------HTCSSCEEEEEETTCCHHHHHGGGCCTTS-CEECCSSTTHHHH
T ss_pred             CceeCCHHHHHHHHHHHHH-----------hCCCCcEEEECCCCccHHHHHHHHHHhCC-CeEEechhhCChH
Confidence            5788888888888887641           12446799999999999999999999988 9999998887554

>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=98.84  E-value=1.5e-09  Score=106.98  Aligned_cols=66  Identities=23%  Similarity=0.388  Sum_probs=54.7

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCC----cceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHH
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPP----RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQK  232 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~----~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~  232 (245)
                      .+++|++.+++.+..++..        .+.|+..+    ..+||+||||||||++|+++|..++.+|+++++++++++
T Consensus       458 ~~v~g~~~~~~~l~~~i~~--------~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l~~~~~~i~~s~~~~~  527 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKM--------ARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMER  527 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHH--------HHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHTCEEEEEEGGGCSSS
T ss_pred             hhccCHHHHHHHHHHHHHH--------HhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHhcCCEEEEechhhcch
Confidence            4588999998888887754        44555422    359999999999999999999999999999999998764

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=98.81  E-value=4.7e-09  Score=92.72  Aligned_cols=64  Identities=27%  Similarity=0.290  Sum_probs=54.4

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHH
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF  229 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l  229 (245)
                      .+.++++++|.+..++.+.+++..            -..++.+|++||||||||++|+++|+.++.+|+.+++++.
T Consensus        21 rP~~~~~ivg~~~~~~~l~~~l~~------------~~~~~~~L~~G~~G~GKT~la~~la~~l~~~~~~i~~~~~   84 (324)
T 3u61_B           21 RPSTIDECILPAFDKETFKSITSK------------GKIPHIILHSPSPGTGKTTVAKALCHDVNADMMFVNGSDC   84 (324)
T ss_dssp             CCCSTTTSCCCHHHHHHHHHHHHT------------TCCCSEEEECSSTTSSHHHHHHHHHHHTTEEEEEEETTTC
T ss_pred             CCCCHHHHhCcHHHHHHHHHHHHc------------CCCCeEEEeeCcCCCCHHHHHHHHHHHhCCCEEEEccccc
Confidence            345789999999999999988873            1345668899999999999999999999999999997653

>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=98.79  E-value=5e-09  Score=92.75  Aligned_cols=73  Identities=26%  Similarity=0.341  Sum_probs=53.2

Q ss_pred             CCceeccCC-cchh--hhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechh
Q 025979          154 PDVTYNDIG-GCDI--QKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       154 ~~~~~~dv~-Gl~~--~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      +..+|++++ |...  ....+..++..+           -..+++++||||||||||++|+++++.+   +.+++.++++
T Consensus         6 ~~~~f~~fv~g~~~~~a~~~~~~~~~~~-----------~~~~~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~~~   74 (324)
T 1l8q_A            6 PKYTLENFIVGEGNRLAYEVVKEALENL-----------GSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSAD   74 (324)
T ss_dssp             TTCCSSSCCCCTTTHHHHHHHHHHHHTT-----------TTSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHH
T ss_pred             CCCCcccCCCCCcHHHHHHHHHHHHhCc-----------CCCCCeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEHH
Confidence            455777875 4332  344444444432           1245679999999999999999999998   8999999999


Q ss_pred             HHHHHHhccc
Q 025979          228 EFVQKYLGEV  237 (245)
Q Consensus       228 ~l~~~~~Ge~  237 (245)
                      ++...+.+..
T Consensus        75 ~~~~~~~~~~   84 (324)
T 1l8q_A           75 DFAQAMVEHL   84 (324)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9987776643

>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=98.78  E-value=5.1e-09  Score=90.03  Aligned_cols=63  Identities=22%  Similarity=0.267  Sum_probs=46.0

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc---ceeeeechhHH
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT---AAFIRVVGSEF  229 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~---~~~~~v~~s~l  229 (245)
                      .+|++++|.+.....+.+.+....           ..+..+||+||||||||++|+++++.+.   .+|+.++++++
T Consensus         3 ~~f~~~ig~~~~~~~~~~~~~~~~-----------~~~~~vll~G~~GtGKt~la~~i~~~~~~~~~~~~~v~~~~~   68 (265)
T 2bjv_A            3 EYKDNLLGEANSFLEVLEQVSHLA-----------PLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAAL   68 (265)
T ss_dssp             -------CCCHHHHHHHHHHHHHT-----------TSCSCEEEECCTTSCHHHHHHHHHHTSTTTTSCEEEEEGGGS
T ss_pred             cccccceeCCHHHHHHHHHHHHHh-----------CCCCCEEEECCCCCcHHHHHHHHHHhcCccCCCeEEEecCCC
Confidence            467889999999888887775421           2346799999999999999999999874   68999998765

>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=98.77  E-value=2.8e-09  Score=106.62  Aligned_cols=76  Identities=20%  Similarity=0.306  Sum_probs=55.7

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc----------cceeeeec
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT----------TAAFIRVV  225 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l----------~~~~~~v~  225 (245)
                      -.+++++|.+..+.++.+.+..             ..++++||+||||||||++|+++|+.+          +.+++.++
T Consensus       167 ~~ld~viGr~~~i~~l~~~l~~-------------~~~~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~  233 (854)
T 1qvr_A          167 GKLDPVIGRDEEIRRVIQILLR-------------RTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQ  233 (854)
T ss_dssp             TCSCCCCSCHHHHHHHHHHHHC-------------SSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEEC
T ss_pred             CCCcccCCcHHHHHHHHHHHhc-------------CCCCceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEEEee
Confidence            4678899999888888877643             245679999999999999999999987          88999999


Q ss_pred             hhHHH--HHHhcccccccccc
Q 025979          226 GSEFV--QKYLGEVWLKHKQI  244 (245)
Q Consensus       226 ~s~l~--~~~~Ge~~~~vr~i  244 (245)
                      ++.++  .+|.|+.+..++.+
T Consensus       234 ~~~l~~g~~~~g~~~~~l~~~  254 (854)
T 1qvr_A          234 MGSLLAGAKYRGEFEERLKAV  254 (854)
T ss_dssp             C-----------CHHHHHHHH
T ss_pred             hHHhhccCccchHHHHHHHHH
Confidence            99987  67888877766654

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=98.77  E-value=1e-08  Score=89.58  Aligned_cols=63  Identities=32%  Similarity=0.522  Sum_probs=50.0

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhhccC----CCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHH
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGID----PPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEF  229 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~----~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l  229 (245)
                      ++++|.+.+++.+...+..        ...++.    +...+||+||||||||++|+++|+.+   +.+|+.++++.+
T Consensus        17 ~~i~G~~~~~~~l~~~i~~--------~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~~~~~~~~~~~~~~~~   86 (311)
T 4fcw_A           17 KRVVGQDEAIRAVADAIRR--------ARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEY   86 (311)
T ss_dssp             TTCCSCHHHHHHHHHHHHH--------HHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHHHHSCGGGEEEEEGGGC
T ss_pred             hhcCCHHHHHHHHHHHHHH--------HhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHHHcCCCcceEEeecccc
Confidence            4688999999999988865        222222    22359999999999999999999988   567999988765

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=98.76  E-value=5.2e-09  Score=82.45  Aligned_cols=59  Identities=20%  Similarity=0.259  Sum_probs=45.6

Q ss_pred             cCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHH
Q 025979          160 DIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFV  230 (245)
Q Consensus       160 dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~  230 (245)
                      +++|.+...+.+.+.+...           ...+..|||+||||||||++|++++...   +.+|+ ++++.+.
T Consensus         2 ~iiG~s~~~~~~~~~~~~~-----------a~~~~~vll~G~~GtGKt~lA~~i~~~~~~~~~~~v-~~~~~~~   63 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQL-----------SETDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFV-YRELTPD   63 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHH-----------TTCCSCEEEESSTTSSHHHHHHHHHHSSTTTTSCCE-EEECCTT
T ss_pred             CceeCCHHHHHHHHHHHHH-----------hCCCCCEEEECCCCCCHHHHHHHHHHhCCccCCCEE-EECCCCC
Confidence            5678888888888777541           1234569999999999999999999987   77899 8887653

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=98.73  E-value=1.4e-08  Score=82.23  Aligned_cols=46  Identities=22%  Similarity=0.270  Sum_probs=37.8

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc----cceeeeechhHHHHHHh
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT----TAAFIRVVGSEFVQKYL  234 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l----~~~~~~v~~s~l~~~~~  234 (245)
                      .+..+.+++|+||||||||++++++++.+    |..++.++..++++.+.
T Consensus        34 ~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~~~~~~~~~~~~   83 (180)
T 3ec2_A           34 NPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFFDTKDLIFRLK   83 (180)
T ss_dssp             CGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCEEEHHHHHHHHH
T ss_pred             cccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEEEEHHHHHHHHH
Confidence            34456789999999999999999999887    56778888888876654

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=98.73  E-value=9.1e-09  Score=96.03  Aligned_cols=60  Identities=28%  Similarity=0.416  Sum_probs=50.3

Q ss_pred             CceeccCCcchhhh---HHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechh
Q 025979          155 DVTYNDIGGCDIQK---QEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS  227 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~---~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s  227 (245)
                      ..++++++|.+..+   ..+...+..             ....++|||||||||||++|+++|+.++.+|+.++..
T Consensus        22 P~~l~~ivGq~~~~~~~~~L~~~i~~-------------~~~~~vLL~GppGtGKTtlAr~ia~~~~~~f~~l~a~   84 (447)
T 3pvs_A           22 PENLAQYIGQQHLLAAGKPLPRAIEA-------------GHLHSMILWGPPGTGKTTLAEVIARYANADVERISAV   84 (447)
T ss_dssp             CCSTTTCCSCHHHHSTTSHHHHHHHH-------------TCCCEEEEECSTTSSHHHHHHHHHHHTTCEEEEEETT
T ss_pred             CCCHHHhCCcHHHHhchHHHHHHHHc-------------CCCcEEEEECCCCCcHHHHHHHHHHHhCCCeEEEEec
Confidence            35688999999988   677777654             1235799999999999999999999999999998864

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=98.69  E-value=1e-08  Score=90.86  Aligned_cols=54  Identities=20%  Similarity=0.199  Sum_probs=46.1

Q ss_pred             eccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeech
Q 025979          158 YNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVG  226 (245)
Q Consensus       158 ~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~  226 (245)
                      ++++.|.+..++.+...+..               +.++|||||||||||++|+++|+.++.+|+++.+
T Consensus        26 ~~~i~g~~~~~~~l~~~l~~---------------~~~vll~G~pGtGKT~la~~la~~~~~~~~~i~~   79 (331)
T 2r44_A           26 GKVVVGQKYMINRLLIGICT---------------GGHILLEGVPGLAKTLSVNTLAKTMDLDFHRIQF   79 (331)
T ss_dssp             TTTCCSCHHHHHHHHHHHHH---------------TCCEEEESCCCHHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             ccceeCcHHHHHHHHHHHHc---------------CCeEEEECCCCCcHHHHHHHHHHHhCCCeEEEec
Confidence            45789999888888766543               2579999999999999999999999999998876

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=98.67  E-value=2.6e-08  Score=81.37  Aligned_cols=61  Identities=34%  Similarity=0.418  Sum_probs=48.3

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc-----cceeeeechh
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT-----TAAFIRVVGS  227 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l-----~~~~~~v~~s  227 (245)
                      +...+++++|.+..++.+.+.+...             .+..++|+||||||||++|+++++.+     ...++.++++
T Consensus        12 ~p~~~~~~~g~~~~~~~l~~~l~~~-------------~~~~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~~~~~   77 (226)
T 2chg_A           12 RPRTLDEVVGQDEVIQRLKGYVERK-------------NIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNAS   77 (226)
T ss_dssp             SCSSGGGCCSCHHHHHHHHHHHHTT-------------CCCCEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEEEETT
T ss_pred             CCCCHHHHcCcHHHHHHHHHHHhCC-------------CCCeEEEECCCCCCHHHHHHHHHHHHhccccccceEEeccc
Confidence            4456889999999999999887641             22349999999999999999999876     4557777654

>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=98.66  E-value=6.4e-09  Score=102.42  Aligned_cols=76  Identities=18%  Similarity=0.234  Sum_probs=58.5

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc----------cceeeeec
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT----------TAAFIRVV  225 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l----------~~~~~~v~  225 (245)
                      -.+++++|.+..++++.+.+..             ..+.++||+||||||||++|+++|..+          +..++.++
T Consensus       183 ~~~d~~iGr~~~i~~l~~~l~~-------------~~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~~~~~  249 (758)
T 1r6b_X          183 GGIDPLIGREKELERAIQVLCR-------------RRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLD  249 (758)
T ss_dssp             TCSCCCCSCHHHHHHHHHHHTS-------------SSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECC
T ss_pred             CCCCCccCCHHHHHHHHHHHhc-------------cCCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEEEEEc
Confidence            3578899999998888887654             245679999999999999999999987          67788888


Q ss_pred             hhHHH--HHHhcccccccccc
Q 025979          226 GSEFV--QKYLGEVWLKHKQI  244 (245)
Q Consensus       226 ~s~l~--~~~~Ge~~~~vr~i  244 (245)
                      .+.+.  .+|.|+.+..++.+
T Consensus       250 ~~~l~~~~~~~g~~e~~l~~~  270 (758)
T 1r6b_X          250 IGSLLAGTKYRGDFEKRFKAL  270 (758)
T ss_dssp             CC---CCCCCSSCHHHHHHHH
T ss_pred             HHHHhccccccchHHHHHHHH
Confidence            88877  46777776665544

>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=98.65  E-value=1.6e-08  Score=89.69  Aligned_cols=55  Identities=25%  Similarity=0.334  Sum_probs=41.0

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      ...+..+|++++|.+..++.+......             ..+.++|||||||||||++|+++|+.++
T Consensus        16 ~~~~~~~f~~i~G~~~~~~~l~~~~~~-------------~~~~~vLl~G~~GtGKT~la~~la~~~~   70 (350)
T 1g8p_A           16 KTRPVFPFSAIVGQEDMKLALLLTAVD-------------PGIGGVLVFGDRGTGKSTAVRALAALLP   70 (350)
T ss_dssp             --CCCCCGGGSCSCHHHHHHHHHHHHC-------------GGGCCEEEECCGGGCTTHHHHHHHHHSC
T ss_pred             CCCCCCCchhccChHHHHHHHHHHhhC-------------CCCceEEEECCCCccHHHHHHHHHHhCc
Confidence            345667899999999877665433322             1224599999999999999999999886

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.63  E-value=2e-08  Score=88.95  Aligned_cols=63  Identities=21%  Similarity=0.354  Sum_probs=49.0

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc------eeeeech
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA------AFIRVVG  226 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~------~~~~v~~  226 (245)
                      ..+.+|++++|.+++++.+...+...             .+.++||+||||||||++|+++|+.++.      .++.+++
T Consensus        31 ~~p~~~~~i~g~~~~~~~l~~~l~~~-------------~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~   97 (353)
T 1sxj_D           31 YRPKNLDEVTAQDHAVTVLKKTLKSA-------------NLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNA   97 (353)
T ss_dssp             TCCSSTTTCCSCCTTHHHHHHHTTCT-------------TCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECS
T ss_pred             cCCCCHHHhhCCHHHHHHHHHHHhcC-------------CCCEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEcc
Confidence            34457899999999999998887541             1233999999999999999999998753      4666665


Q ss_pred             hH
Q 025979          227 SE  228 (245)
Q Consensus       227 s~  228 (245)
                      ++
T Consensus        98 ~~   99 (353)
T 1sxj_D           98 SD   99 (353)
T ss_dssp             SS
T ss_pred             cc
Confidence            44

>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=98.62  E-value=2.2e-08  Score=87.20  Aligned_cols=63  Identities=33%  Similarity=0.422  Sum_probs=49.3

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc-----cceeeeechh
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT-----TAAFIRVVGS  227 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l-----~~~~~~v~~s  227 (245)
                      ..+.+|++++|.+..++.+...+..           | .. ..+|||||||||||++|+++|+.+     +.+|+.++++
T Consensus        11 ~~p~~~~~~~g~~~~~~~l~~~l~~-----------~-~~-~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~   77 (319)
T 2chq_A           11 YRPRTLDEVVGQDEVIQRLKGYVER-----------K-NI-PHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNAS   77 (319)
T ss_dssp             TSCSSGGGSCSCHHHHHHHHTTTTT-----------T-CC-CCEEEESSSSSSHHHHHHHHHHHHHTTCHHHHCEEEETT
T ss_pred             cCCCCHHHHhCCHHHHHHHHHHHhC-----------C-CC-CeEEEECcCCcCHHHHHHHHHHHhcCCcccCCeEEEeCc
Confidence            4456789999999999988877653           1 12 239999999999999999999986     4567777765


Q ss_pred             H
Q 025979          228 E  228 (245)
Q Consensus       228 ~  228 (245)
                      +
T Consensus        78 ~   78 (319)
T 2chq_A           78 D   78 (319)
T ss_dssp             S
T ss_pred             c
Confidence            4

>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=98.62  E-value=3.4e-08  Score=88.27  Aligned_cols=64  Identities=28%  Similarity=0.389  Sum_probs=48.4

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhH
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSE  228 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~  228 (245)
                      ++++++|.+.+++.+...+...        ...-.++..++|+||||||||++|+++|+.+++++...+++.
T Consensus        23 ~l~~~~g~~~~~~~l~~~i~~~--------~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~~l~~~~~~~sg~~   86 (334)
T 1in4_A           23 SLDEFIGQENVKKKLSLALEAA--------KMRGEVLDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPV   86 (334)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHHH--------HHHTCCCCCEEEESSTTSSHHHHHHHHHHHHTCCEEEEETTT
T ss_pred             cHHHccCcHHHHHHHHHHHHHH--------HhcCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEechH
Confidence            6778889888888877666431        001134567999999999999999999999988877666543

>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=98.60  E-value=5.1e-08  Score=81.19  Aligned_cols=65  Identities=18%  Similarity=0.218  Sum_probs=46.1

Q ss_pred             CCceeccCCcc---hhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc---ceeeeechh
Q 025979          154 PDVTYNDIGGC---DIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT---AAFIRVVGS  227 (245)
Q Consensus       154 ~~~~~~dv~Gl---~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~---~~~~~v~~s  227 (245)
                      +..+|+++.|.   ....+.+...+..             ..+++++|+||||||||++|+++++.+.   .+++.++++
T Consensus        23 ~~~~~~~~~~~~~~~~~~~~l~~~~~~-------------~~~~~~ll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~   89 (242)
T 3bos_A           23 DDETFTSYYPAAGNDELIGALKSAASG-------------DGVQAIYLWGPVKSGRTHLIHAACARANELERRSFYIPLG   89 (242)
T ss_dssp             TTCSTTTSCC--CCHHHHHHHHHHHHT-------------CSCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEGG
T ss_pred             CCCChhhccCCCCCHHHHHHHHHHHhC-------------CCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHH
Confidence            34567787762   2445555544432             2457799999999999999999999874   677788877


Q ss_pred             HHHH
Q 025979          228 EFVQ  231 (245)
Q Consensus       228 ~l~~  231 (245)
                      ++..
T Consensus        90 ~~~~   93 (242)
T 3bos_A           90 IHAS   93 (242)
T ss_dssp             GGGG
T ss_pred             HHHH
Confidence            7654

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=98.59  E-value=9.8e-08  Score=78.41  Aligned_cols=42  Identities=31%  Similarity=0.403  Sum_probs=36.2

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHHHHh
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQKYL  234 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~~~~  234 (245)
                      +++++|+||||||||++|+++++.+   +.+++.+++++++..+.
T Consensus        54 ~~~~~l~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~~~~~~~~~   98 (202)
T 2w58_A           54 MKGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVYVPELFRELK   98 (202)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEEHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEhHHHHHHHH
Confidence            3789999999999999999999987   67788888888876654

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=98.59  E-value=4.2e-08  Score=87.49  Aligned_cols=62  Identities=26%  Similarity=0.320  Sum_probs=50.6

Q ss_pred             eccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---------cceeeeechhH
Q 025979          158 YNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---------TAAFIRVVGSE  228 (245)
Q Consensus       158 ~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---------~~~~~~v~~s~  228 (245)
                      .++++|.+...+.+...+...+.         -..+++++|+||||||||++|+++++.+         +.+|+.+++..
T Consensus        18 p~~~~gr~~~~~~l~~~l~~~~~---------~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~   88 (387)
T 2v1u_A           18 PDVLPHREAELRRLAEVLAPALR---------GEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARH   88 (387)
T ss_dssp             CSCCTTCHHHHHHHHHTTGGGTS---------SCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTT
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHc---------CCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCc
Confidence            37899999999999888754221         1356789999999999999999999988         88899998653

>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=98.57  E-value=5.6e-08  Score=84.94  Aligned_cols=63  Identities=29%  Similarity=0.410  Sum_probs=49.2

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc-----ceeeeechh
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT-----AAFIRVVGS  227 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~-----~~~~~v~~s  227 (245)
                      ..+.+|++++|.+..++.+...+..           |  ....+|||||||||||++|+++|+.+.     ..++.++++
T Consensus        19 ~~p~~~~~~~g~~~~~~~l~~~l~~-----------~--~~~~~ll~G~~G~GKT~la~~l~~~l~~~~~~~~~~~~~~~   85 (327)
T 1iqp_A           19 YRPQRLDDIVGQEHIVKRLKHYVKT-----------G--SMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNAS   85 (327)
T ss_dssp             TCCCSTTTCCSCHHHHHHHHHHHHH-----------T--CCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETT
T ss_pred             cCCCCHHHhhCCHHHHHHHHHHHHc-----------C--CCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCceEEeecc
Confidence            3445788999999999999988754           1  223499999999999999999999863     347777765


Q ss_pred             H
Q 025979          228 E  228 (245)
Q Consensus       228 ~  228 (245)
                      +
T Consensus        86 ~   86 (327)
T 1iqp_A           86 D   86 (327)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=98.55  E-value=8.8e-08  Score=85.77  Aligned_cols=63  Identities=21%  Similarity=0.182  Sum_probs=51.2

Q ss_pred             eccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc-----------cceeeeech
Q 025979          158 YNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT-----------TAAFIRVVG  226 (245)
Q Consensus       158 ~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l-----------~~~~~~v~~  226 (245)
                      .++++|.+..++.+.+.+.....         -..+++++|+||||||||++|+++++.+           +.+++.+++
T Consensus        19 p~~l~gr~~~~~~l~~~l~~~~~---------~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~   89 (384)
T 2qby_B           19 FKEIPFREDILRDAAIAIRYFVK---------NEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNC   89 (384)
T ss_dssp             CSSCTTCHHHHHHHHHHHHHHHT---------TCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHc---------CCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEEC
Confidence            37899999999999888754211         1356689999999999999999999987           889999987


Q ss_pred             hHH
Q 025979          227 SEF  229 (245)
Q Consensus       227 s~l  229 (245)
                      ++.
T Consensus        90 ~~~   92 (384)
T 2qby_B           90 REV   92 (384)
T ss_dssp             HHH
T ss_pred             ccC
Confidence            653

>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=98.53  E-value=7.7e-08  Score=89.42  Aligned_cols=72  Identities=22%  Similarity=0.420  Sum_probs=51.7

Q ss_pred             CCCceeccCC-cchhh--hHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc-----cceeeee
Q 025979          153 KPDVTYNDIG-GCDIQ--KQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT-----TAAFIRV  224 (245)
Q Consensus       153 ~~~~~~~dv~-Gl~~~--~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l-----~~~~~~v  224 (245)
                      .+..+|++++ |....  ...+..+...+          + . +++++||||||||||+||+++|+.+     +.+++.+
T Consensus        99 ~~~~tfd~fv~g~~n~~a~~~~~~~a~~~----------~-~-~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v  166 (440)
T 2z4s_A           99 NPDYTFENFVVGPGNSFAYHAALEVAKHP----------G-R-YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYI  166 (440)
T ss_dssp             CTTCSGGGCCCCTTTHHHHHHHHHHHHST----------T-S-SCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEE
T ss_pred             CCCCChhhcCCCCchHHHHHHHHHHHhCC----------C-C-CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEe
Confidence            3556888876 64432  23333333221          1 1 5679999999999999999999988     7889999


Q ss_pred             chhHHHHHHhcc
Q 025979          225 VGSEFVQKYLGE  236 (245)
Q Consensus       225 ~~s~l~~~~~Ge  236 (245)
                      +++++...+.+.
T Consensus       167 ~~~~~~~~~~~~  178 (440)
T 2z4s_A          167 TSEKFLNDLVDS  178 (440)
T ss_dssp             EHHHHHHHHHHH
T ss_pred             eHHHHHHHHHHH
Confidence            999988777654

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.50  E-value=3.5e-08  Score=88.28  Aligned_cols=59  Identities=10%  Similarity=0.008  Sum_probs=44.0

Q ss_pred             CCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc----------cceeeeechhH
Q 025979          161 IGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT----------TAAFIRVVGSE  228 (245)
Q Consensus       161 v~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l----------~~~~~~v~~s~  228 (245)
                      +.|-+++.+.|..++..         .+.-..+.+++||||||||||++++++++++          +..++.+++..
T Consensus        22 L~~Re~E~~~i~~~L~~---------~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~   90 (318)
T 3te6_A           22 LKSQVEDFTRIFLPIYD---------SLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALE   90 (318)
T ss_dssp             HHHHHHHHHHHHHHHHH---------HHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTC
T ss_pred             cCCHHHHHHHHHHHHHH---------HhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccc
Confidence            45556666666666543         2233577889999999999999999999998          35788888654

>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=98.47  E-value=1.3e-07  Score=82.44  Aligned_cols=62  Identities=21%  Similarity=0.375  Sum_probs=48.7

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc-----cceeeeechhH
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT-----TAAFIRVVGSE  228 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l-----~~~~~~v~~s~  228 (245)
                      .+.++++++|.+..++.+...+..           + ..+. +|||||||||||++|+++|+.+     +..++.+++++
T Consensus        16 ~p~~~~~~~g~~~~~~~l~~~l~~-----------~-~~~~-~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~   82 (323)
T 1sxj_B           16 RPQVLSDIVGNKETIDRLQQIAKD-----------G-NMPH-MIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASD   82 (323)
T ss_dssp             CCSSGGGCCSCTHHHHHHHHHHHS-----------C-CCCC-EEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTS
T ss_pred             CCCCHHHHHCCHHHHHHHHHHHHc-----------C-CCCe-EEEECcCCCCHHHHHHHHHHHhcCCcccCCEEEecCcc
Confidence            345678999999999999988754           1 2234 9999999999999999999986     45577776553

>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=98.47  E-value=1.3e-07  Score=84.19  Aligned_cols=63  Identities=19%  Similarity=0.289  Sum_probs=50.4

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc------cceeeeechhH
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT------TAAFIRVVGSE  228 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l------~~~~~~v~~s~  228 (245)
                      ..++++|.+...+.+.+.+...+.         -..+..++|+||||||||++++++++.+      +.+++.+++..
T Consensus        18 ~p~~~~gr~~e~~~l~~~l~~~~~---------~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~   86 (386)
T 2qby_A           18 IPDELPHREDQIRKIASILAPLYR---------EEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQ   86 (386)
T ss_dssp             CCSCCTTCHHHHHHHHHSSGGGGG---------TCCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHHH
T ss_pred             CCCCCCChHHHHHHHHHHHHHHHc---------CCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECCC
Confidence            347899999999999887654211         1345679999999999999999999988      78899988764

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=98.46  E-value=1.6e-07  Score=83.27  Aligned_cols=43  Identities=26%  Similarity=0.375  Sum_probs=37.0

Q ss_pred             CcceeeecCCCCchHHHHHHHHhccc----ceeeeechhHHHHHHhc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTT----AAFIRVVGSEFVQKYLG  235 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~----~~~~~v~~s~l~~~~~G  235 (245)
                      +.+++||||||||||+||+++|..+.    .+++.+..++++..+.+
T Consensus       152 ~~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~~~~~l~~~l~~  198 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHFPSFAIDVKN  198 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEEEHHHHHHHHHC
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEHHHHHHHHHH
Confidence            57899999999999999999998765    67888899988876654

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=98.46  E-value=9.9e-08  Score=84.39  Aligned_cols=60  Identities=18%  Similarity=0.329  Sum_probs=47.8

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHH
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEF  229 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l  229 (245)
                      ++++|.+...+.+.+.+...           ...+..+||+||||||||++|++++...   +.+|+.++++.+
T Consensus         2 ~~iig~s~~~~~~~~~~~~~-----------a~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~~~v~v~~~~~   64 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMV-----------APSDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAAL   64 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHH-----------CSTTSCEEEESCTTSCHHHHHHHHHHHSSCSSSCCCEEECSSC
T ss_pred             CCcEECCHHHHHHHHHHHHH-----------hCCCCcEEEECCCCchHHHHHHHHHHhCcccCCCeEEEeCCCC
Confidence            46788888888888877642           1345679999999999999999999965   678999987654

>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=98.40  E-value=2.4e-07  Score=76.22  Aligned_cols=54  Identities=22%  Similarity=0.318  Sum_probs=43.4

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ....+++++|.+..++.+.+.+...            ..++.++|+||||||||++++++++.++.
T Consensus        18 ~p~~~~~~~g~~~~~~~l~~~l~~~------------~~~~~~ll~G~~G~GKT~l~~~~~~~~~~   71 (250)
T 1njg_A           18 RPQTFADVVGQEHVLTALANGLSLG------------RIHHAYLFSGTRGVGKTSIARLLAKGLNC   71 (250)
T ss_dssp             CCCSGGGCCSCHHHHHHHHHHHHHT------------CCCSEEEEECSTTSCHHHHHHHHHHHHHC
T ss_pred             CCccHHHHhCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            3446788999999999998887541            23457999999999999999999988754

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=98.37  E-value=2.2e-07  Score=87.84  Aligned_cols=45  Identities=20%  Similarity=0.215  Sum_probs=35.8

Q ss_pred             cCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          160 DIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       160 dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      .++|.+..++.+..++..               +.++||+||||||||++|+++|..++.
T Consensus        23 ~ivGq~~~i~~l~~al~~---------------~~~VLL~GpPGtGKT~LAraLa~~l~~   67 (500)
T 3nbx_X           23 GLYERSHAIRLCLLAALS---------------GESVFLLGPPGIAKSLIARRLKFAFQN   67 (500)
T ss_dssp             TCSSCHHHHHHHHHHHHH---------------TCEEEEECCSSSSHHHHHHHGGGGBSS
T ss_pred             hhHHHHHHHHHHHHHHhc---------------CCeeEeecCchHHHHHHHHHHHHHHhh
Confidence            577888877776655432               257999999999999999999998843

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.36  E-value=3.3e-07  Score=81.62  Aligned_cols=61  Identities=31%  Similarity=0.487  Sum_probs=46.1

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc-----ceeeeechh
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT-----AAFIRVVGS  227 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~-----~~~~~v~~s  227 (245)
                      .+.++++++|.+.+++.|...+..           | ..+. ++||||||||||++|+++|+.+.     ..++.++.+
T Consensus        20 rp~~~~~~~g~~~~~~~L~~~i~~-----------g-~~~~-~ll~Gp~G~GKTtla~~la~~l~~~~~~~~~~~~~~~   85 (340)
T 1sxj_C           20 RPETLDEVYGQNEVITTVRKFVDE-----------G-KLPH-LLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNAS   85 (340)
T ss_dssp             CCSSGGGCCSCHHHHHHHHHHHHT-----------T-CCCC-EEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTT
T ss_pred             CCCcHHHhcCcHHHHHHHHHHHhc-----------C-CCce-EEEECCCCCCHHHHHHHHHHHHcCCCccceEEEEcCc
Confidence            445688999999999998888764           1 1233 99999999999999999999863     235555544

>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=98.35  E-value=5e-07  Score=80.72  Aligned_cols=61  Identities=25%  Similarity=0.232  Sum_probs=48.1

Q ss_pred             eccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCc--ceeeecCCCCchHHHHHHHHhcc----cceeeeechh
Q 025979          158 YNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPR--GVLLYGPPGTGKTMLAKAVANHT----TAAFIRVVGS  227 (245)
Q Consensus       158 ~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~--gvLl~GPPGtGKT~lAkalA~~l----~~~~~~v~~s  227 (245)
                      .++++|.+...+.+.+.+....        .| ..+.  .++|+||||||||++++++++.+    +..++.++++
T Consensus        16 p~~l~gr~~~~~~l~~~l~~~~--------~~-~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~~~   82 (389)
T 1fnn_A           16 PKRLPHREQQLQQLDILLGNWL--------RN-PGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGF   82 (389)
T ss_dssp             CSCCTTCHHHHHHHHHHHHHHH--------HS-TTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETT
T ss_pred             CCCCCChHHHHHHHHHHHHHHH--------cC-CCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEeCc
Confidence            3789999999999988875411        11 2334  79999999999999999999988    5778888754

>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=98.35  E-value=3.6e-07  Score=81.45  Aligned_cols=53  Identities=23%  Similarity=0.329  Sum_probs=43.5

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      +.+|++++|.+..++.+...+...            ..+..+||+||||||||++|+++|+.+++
T Consensus        12 p~~~~~~vg~~~~~~~L~~~l~~~------------~~~~~~ll~G~~G~GKT~la~~la~~l~~   64 (373)
T 1jr3_A           12 PQTFADVVGQEHVLTALANGLSLG------------RIHHAYLFSGTRGVGKTSIARLLAKGLNC   64 (373)
T ss_dssp             CCSTTTSCSCHHHHHHHHHHHHHT------------CCCSEEEEESCTTSSHHHHHHHHHHHHSC
T ss_pred             CCchhhccCcHHHHHHHHHHHHhC------------CCCeEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            346789999999999999887531            23456899999999999999999998754

>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=98.30  E-value=3.7e-07  Score=81.12  Aligned_cols=53  Identities=25%  Similarity=0.365  Sum_probs=41.9

Q ss_pred             CCCCceeccCCcchhhhHHHHHHH-hcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAV-ELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i-~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +..+.++++++|.+.+++.+..++ ..           | ..+. ++|+||||||||++++++|+.+
T Consensus         7 kyrP~~~~~~vg~~~~~~~l~~~~~~~-----------~-~~~~-~ll~Gp~G~GKTtl~~~la~~l   60 (354)
T 1sxj_E            7 KYRPKSLNALSHNEELTNFLKSLSDQP-----------R-DLPH-LLLYGPNGTGKKTRCMALLESI   60 (354)
T ss_dssp             TTCCCSGGGCCSCHHHHHHHHTTTTCT-----------T-CCCC-EEEECSTTSSHHHHHHTHHHHH
T ss_pred             ccCCCCHHHhcCCHHHHHHHHHHHhhC-----------C-CCCe-EEEECCCCCCHHHHHHHHHHHH
Confidence            345567899999999988888776 22           1 2334 9999999999999999999964

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=98.27  E-value=6.4e-07  Score=73.74  Aligned_cols=45  Identities=27%  Similarity=0.346  Sum_probs=34.5

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE  236 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge  236 (245)
                      +.+++.++|.||||||||+++++||..++.+|+  +..++.....|.
T Consensus        22 ~~~~~~i~l~G~~GsGKsTl~~~La~~l~~~~i--~~d~~~~~~~g~   66 (199)
T 3vaa_A           22 SNAMVRIFLTGYMGAGKTTLGKAFARKLNVPFI--DLDWYIEERFHK   66 (199)
T ss_dssp             --CCCEEEEECCTTSCHHHHHHHHHHHHTCCEE--EHHHHHHHHHTS
T ss_pred             cCCCCEEEEEcCCCCCHHHHHHHHHHHcCCCEE--cchHHHHHHhCC
Confidence            345566999999999999999999999998885  555665555443

>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=98.27  E-value=2e-07  Score=81.34  Aligned_cols=25  Identities=40%  Similarity=0.680  Sum_probs=22.7

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++++||||||||||++|+|||+.+
T Consensus       104 ~n~~~l~GppgtGKt~~a~ala~~~  128 (267)
T 1u0j_A          104 RNTIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CcEEEEECCCCCCHHHHHHHHHhhh
Confidence            4579999999999999999999864

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=98.22  E-value=4.6e-07  Score=76.31  Aligned_cols=34  Identities=21%  Similarity=0.376  Sum_probs=27.3

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcccceeee
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIR  223 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~  223 (245)
                      +...+++|||||||||||++|.++|+.+....+.
T Consensus        55 iPkkn~ili~GPPGtGKTt~a~ala~~l~g~i~~   88 (212)
T 1tue_A           55 TPKKNCLVFCGPANTGKSYFGMSFIHFIQGAVIS   88 (212)
T ss_dssp             CTTCSEEEEESCGGGCHHHHHHHHHHHHTCEECC
T ss_pred             CCcccEEEEECCCCCCHHHHHHHHHHHhCCCeee
Confidence            3344679999999999999999999988554443

>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=98.11  E-value=2e-06  Score=69.59  Aligned_cols=41  Identities=27%  Similarity=0.330  Sum_probs=34.0

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      +.++.-++|.||||+|||++++.||...+...+.+++.++.
T Consensus         6 i~~g~~i~l~G~~GsGKSTl~~~La~~~~~g~i~i~~d~~~   46 (191)
T 1zp6_A            6 DLGGNILLLSGHPGSGKSTIAEALANLPGVPKVHFHSDDLW   46 (191)
T ss_dssp             CCTTEEEEEEECTTSCHHHHHHHHHTCSSSCEEEECTTHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHhccCCCeEEEcccchh
Confidence            44455589999999999999999999988787888777664

>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=98.00  E-value=3.1e-06  Score=68.09  Aligned_cols=33  Identities=39%  Similarity=0.624  Sum_probs=28.6

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccceeeee
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRV  224 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v  224 (245)
                      .++.++|+||||+|||++++.+|..++.+++.+
T Consensus        10 ~~~~i~i~G~~GsGKst~~~~l~~~~~~~~~~~   42 (180)
T 3iij_A           10 LLPNILLTGTPGVGKTTLGKELASKSGLKYINV   42 (180)
T ss_dssp             CCCCEEEECSTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             cCCeEEEEeCCCCCHHHHHHHHHHHhCCeEEEH
Confidence            345699999999999999999999999887654

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=97.99  E-value=3.4e-06  Score=67.16  Aligned_cols=41  Identities=20%  Similarity=0.295  Sum_probs=33.5

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE  236 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge  236 (245)
                      ..++|.|+||||||++|+.||..++.+|+  +..++.....|.
T Consensus         8 ~~i~l~G~~GsGKSTva~~La~~lg~~~i--d~D~~~~~~~g~   48 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQELGLALKLEVL--DTDMIISERVGL   48 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHHTCCEE--EHHHHHHHHHTS
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCCEE--EChHHHHHHhCC
Confidence            45899999999999999999999999885  555666555554

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.99  E-value=2.6e-06  Score=67.58  Aligned_cols=38  Identities=16%  Similarity=0.247  Sum_probs=31.0

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEF  229 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l  229 (245)
                      +...++|+||+|+|||+|+++++..+   |...+.+++.++
T Consensus        35 ~g~~~~l~G~~G~GKTtL~~~i~~~~~~~g~~~~~~~~~~~   75 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLLQAWVAQALEAGKNAAYIDAASM   75 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHHHHHHHHHHTTTCCEEEEETTTS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEcHHHh
Confidence            44669999999999999999999987   655667776654

>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=97.99  E-value=4.8e-06  Score=76.02  Aligned_cols=37  Identities=32%  Similarity=0.343  Sum_probs=31.9

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcccceeeeec
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVV  225 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~  225 (245)
                      ++.+++.++|+||||+|||+++++++..++..++.+.
T Consensus       165 ~i~~~~~i~l~G~~GsGKSTl~~~l~~~~~g~~~~~~  201 (377)
T 1svm_A          165 NIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVN  201 (377)
T ss_dssp             CCTTCCEEEEECSTTSSHHHHHHHHHHHHCCEEECCS
T ss_pred             ccCCCCEEEEECCCCCCHHHHHHHHHhhcCCcEEEEe
Confidence            6677778999999999999999999998877776654

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=97.98  E-value=6e-06  Score=79.49  Aligned_cols=52  Identities=37%  Similarity=0.534  Sum_probs=43.6

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      ..+...+++++|.+.+++.+...+..               ...++|+||||||||++|+++|+.+.
T Consensus        34 ~~rp~~l~~i~G~~~~l~~l~~~i~~---------------g~~vll~Gp~GtGKTtlar~ia~~l~   85 (604)
T 3k1j_A           34 EVPEKLIDQVIGQEHAVEVIKTAANQ---------------KRHVLLIGEPGTGKSMLGQAMAELLP   85 (604)
T ss_dssp             CCCSSHHHHCCSCHHHHHHHHHHHHT---------------TCCEEEECCTTSSHHHHHHHHHHTSC
T ss_pred             cccccccceEECchhhHhhccccccC---------------CCEEEEEeCCCCCHHHHHHHHhccCC
Confidence            44556789999999998888877653               25799999999999999999999884

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=97.97  E-value=1.7e-06  Score=83.45  Aligned_cols=29  Identities=24%  Similarity=0.456  Sum_probs=26.4

Q ss_pred             ceeeecCCCCchHHHHHHHHhcccceeee
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTTAAFIR  223 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~~~~~~  223 (245)
                      ++||+||||||||++|+++|+.++..++.
T Consensus       329 ~vLL~GppGtGKT~LAr~la~~~~r~~~~  357 (595)
T 3f9v_A          329 HILIIGDPGTAKSQMLQFISRVAPRAVYT  357 (595)
T ss_dssp             CEEEEESSCCTHHHHHHSSSTTCSCEECC
T ss_pred             ceEEECCCchHHHHHHHHHHHhCCCceec
Confidence            69999999999999999999999877655

>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=97.94  E-value=1.1e-05  Score=72.60  Aligned_cols=61  Identities=20%  Similarity=0.140  Sum_probs=45.5

Q ss_pred             eccCCcchhhhHHHHHHH-hcCCCcHHHHhhhcc-CCCcceee--ecCCCCchHHHHHHHHhcc---------cceeeee
Q 025979          158 YNDIGGCDIQKQEIREAV-ELPLTHHELYKQIGI-DPPRGVLL--YGPPGTGKTMLAKAVANHT---------TAAFIRV  224 (245)
Q Consensus       158 ~~dv~Gl~~~~~~i~e~i-~~~~~~~~~~~~~g~-~~~~gvLl--~GPPGtGKT~lAkalA~~l---------~~~~~~v  224 (245)
                      .++++|-+...+.+.+.+ ....        .|. ..+..+++  +||||||||++++++++.+         +..++.+
T Consensus        21 p~~l~gR~~el~~l~~~l~~~~~--------~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~   92 (412)
T 1w5s_A           21 PPELRVRRGEAEALARIYLNRLL--------SGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYV   92 (412)
T ss_dssp             CSSCSSSCHHHHHHHHHHHHHHH--------TSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             CCCCCChHHHHHHHHHHHhHHHh--------cCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEE
Confidence            367899999999998887 4311        011 23456889  9999999999999999876         4567777


Q ss_pred             ch
Q 025979          225 VG  226 (245)
Q Consensus       225 ~~  226 (245)
                      ++
T Consensus        93 ~~   94 (412)
T 1w5s_A           93 NA   94 (412)
T ss_dssp             EG
T ss_pred             EC
Confidence            75

>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=97.93  E-value=5.1e-06  Score=67.48  Aligned_cols=36  Identities=31%  Similarity=0.501  Sum_probs=29.3

Q ss_pred             cceeeecCCCCchHHHHHHHHhc-ccceeeeechhHHHH
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH-TTAAFIRVVGSEFVQ  231 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~-l~~~~~~v~~s~l~~  231 (245)
                      ..++|+||||||||++++.+|.. +|.+|+  +.+++..
T Consensus        11 ~~I~l~G~~GsGKSTv~~~La~~l~g~~~i--d~d~~~~   47 (184)
T 1y63_A           11 INILITGTPGTGKTSMAEMIAAELDGFQHL--EVGKLVK   47 (184)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHSTTEEEE--EHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhcCCCEEe--eHHHHHH
Confidence            44999999999999999999999 788775  4444443

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=97.91  E-value=7.4e-06  Score=72.56  Aligned_cols=52  Identities=10%  Similarity=0.139  Sum_probs=37.0

Q ss_pred             cchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc------cceeeeechh
Q 025979          163 GCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT------TAAFIRVVGS  227 (245)
Q Consensus       163 Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l------~~~~~~v~~s  227 (245)
                      |.+++++.+..++...             ....+|||||||||||++|+++|+.+      ...|+.++++
T Consensus         1 g~~~~~~~L~~~i~~~-------------~~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~   58 (305)
T 2gno_A            1 GAKDQLETLKRIIEKS-------------EGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPE   58 (305)
T ss_dssp             ---CHHHHHHHHHHTC-------------SSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCS
T ss_pred             ChHHHHHHHHHHHHCC-------------CCcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCC
Confidence            5667778888777641             13469999999999999999999864      3456666643

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=97.91  E-value=5.1e-06  Score=72.80  Aligned_cols=38  Identities=37%  Similarity=0.581  Sum_probs=30.7

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccceeeeechhHH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF  229 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l  229 (245)
                      .|.-++|.||||+|||++|+.++..++..++.|++..+
T Consensus        32 ~~~livl~G~sGsGKSTla~~L~~~~~~~~~~Is~D~~   69 (287)
T 1gvn_B           32 SPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDTF   69 (287)
T ss_dssp             SCEEEEEECCTTSCTHHHHHHHHHHTTTCCEEECTHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhCCCeEEEechHh
Confidence            34558999999999999999999988555666776555

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=97.89  E-value=5e-06  Score=67.33  Aligned_cols=34  Identities=15%  Similarity=0.283  Sum_probs=29.7

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccceeeeec
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVV  225 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~  225 (245)
                      .+.-++|.||||+|||++|+.||..++.+++..+
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~La~~l~~~~i~~d   41 (196)
T 2c95_A            8 KTNIIFVVGGPGSGKGTQCEKIVQKYGYTHLSTG   41 (196)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHhCCeEEcHH
Confidence            4456999999999999999999999999887653

>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=97.87  E-value=6.4e-06  Score=67.52  Aligned_cols=31  Identities=39%  Similarity=0.522  Sum_probs=26.9

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceeeee
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRV  224 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v  224 (245)
                      ..|+|.||||+|||++|+.||..++.+++.+
T Consensus        21 ~~I~l~G~~GsGKST~a~~La~~l~~~~i~~   51 (201)
T 2cdn_A           21 MRVLLLGPPGAGKGTQAVKLAEKLGIPQIST   51 (201)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCcEEeh
Confidence            3488999999999999999999999877543

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=97.85  E-value=9.3e-07  Score=80.14  Aligned_cols=29  Identities=28%  Similarity=0.574  Sum_probs=27.0

Q ss_pred             ceeeecCCCCchHHHHHHHHhcccceeee
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTTAAFIR  223 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~~~~~~  223 (245)
                      .++|+||||+|||+++++||..++.+|+.
T Consensus        26 ~i~l~G~~G~GKTTl~~~la~~l~~~f~~   54 (359)
T 2ga8_A           26 CVILVGSPGSGKSTIAEELCQIINEKYHT   54 (359)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHHHhCCCeee
Confidence            48999999999999999999999999865

>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=97.84  E-value=1.3e-05  Score=71.43  Aligned_cols=28  Identities=21%  Similarity=0.310  Sum_probs=24.8

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      .+.++|||||||||||++|+++|+.+.+
T Consensus        23 ~~~a~L~~G~~G~GKt~~a~~la~~l~~   50 (334)
T 1a5t_A           23 GHHALLIQALPGMGDDALIYALSRYLLC   50 (334)
T ss_dssp             CCSEEEEECCTTSCHHHHHHHHHHHHTC
T ss_pred             cceeEEEECCCCchHHHHHHHHHHHHhC
Confidence            4567999999999999999999998753

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=97.83  E-value=1.3e-05  Score=67.66  Aligned_cols=41  Identities=12%  Similarity=0.316  Sum_probs=32.9

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHH
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKY  233 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~  233 (245)
                      ..++-|+|.||||+|||+.|+.||..++.+.  ++..+++-..
T Consensus        27 ~k~kiI~llGpPGsGKgTqa~~L~~~~g~~h--IstGdllR~~   67 (217)
T 3umf_A           27 AKAKVIFVLGGPGSGKGTQCEKLVQKFHFNH--LSSGDLLRAE   67 (217)
T ss_dssp             TSCEEEEEECCTTCCHHHHHHHHHHHHCCEE--ECHHHHHHHH
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHHCCce--EcHHHHHHHH
Confidence            4556688999999999999999999998765  5666666543

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=97.83  E-value=7.4e-06  Score=70.08  Aligned_cols=39  Identities=26%  Similarity=0.481  Sum_probs=32.8

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHH
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF  229 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l  229 (245)
                      ..|..++|.||||+|||++|+.|+..++..++.+++..+
T Consensus        30 ~~~~~i~l~G~~GsGKSTla~~L~~~l~~~~~~~~~D~~   68 (253)
T 2p5t_B           30 KQPIAILLGGQSGAGKTTIHRIKQKEFQGNIVIIDGDSF   68 (253)
T ss_dssp             SSCEEEEEESCGGGTTHHHHHHHHHHTTTCCEEECGGGG
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHhcCCCcEEEecHHH
Confidence            345569999999999999999999999876777777765

>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=97.80  E-value=1e-05  Score=68.16  Aligned_cols=37  Identities=24%  Similarity=0.463  Sum_probs=30.0

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQ  231 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~  231 (245)
                      +..|+|.||||||||++|+.||..++.+++.  ..+++.
T Consensus        16 ~~~I~l~G~~GsGKsT~a~~La~~l~~~~i~--~d~li~   52 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAPKLAKNFCVCHLA--TGDMLR   52 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHTCEEEE--HHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCceec--HHHHHH
Confidence            3459999999999999999999999987754  444443

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=97.80  E-value=8.8e-06  Score=66.00  Aligned_cols=31  Identities=16%  Similarity=0.345  Sum_probs=27.1

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccceeee
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAFIR  223 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~  223 (245)
                      +.-|+|.||||+|||++|+.||..++.+++.
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~~l~~~~i~   42 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVEKYGFTHLS   42 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHTCEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCeEEc
Confidence            4568999999999999999999999977654

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=97.78  E-value=1.2e-05  Score=65.96  Aligned_cols=32  Identities=28%  Similarity=0.551  Sum_probs=27.7

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccceeeee
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAFIRV  224 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v  224 (245)
                      ++-|+|.||||+|||++|+.|+..++..++..
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~~lg~~~i~~   49 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAEACGYPFIEG   49 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHHHHTCCEEEG
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCEEEeC
Confidence            35689999999999999999999998777543

>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=97.76  E-value=3.1e-05  Score=67.81  Aligned_cols=57  Identities=18%  Similarity=0.186  Sum_probs=43.5

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechh
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS  227 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s  227 (245)
                      +......++|-+...+.|.+ +..                +.++++||+|+|||++++.+++.++..++.+++.
T Consensus         8 ~~~~~~~~~gR~~el~~L~~-l~~----------------~~v~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~   64 (357)
T 2fna_A            8 PKDNRKDFFDREKEIEKLKG-LRA----------------PITLVLGLRRTGKSSIIKIGINELNLPYIYLDLR   64 (357)
T ss_dssp             CCCSGGGSCCCHHHHHHHHH-TCS----------------SEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGG
T ss_pred             CCCCHHHhcChHHHHHHHHH-hcC----------------CcEEEECCCCCCHHHHHHHHHHhcCCCEEEEEch
Confidence            34455678888887777776 432                3689999999999999999999876666666654

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=97.75  E-value=1.4e-05  Score=65.41  Aligned_cols=36  Identities=14%  Similarity=0.398  Sum_probs=29.1

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceeeeechhHHHH
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQ  231 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~  231 (245)
                      +-|+|.||||||||++|+.|+..++.+++.  .++++.
T Consensus        16 ~~I~l~G~~GsGKsT~~~~L~~~~g~~~i~--~d~~~~   51 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQCEKLVKDYSFVHLS--AGDLLR   51 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSSCEEEE--HHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCceEEe--HHHHHH
Confidence            448899999999999999999999877654  445544

>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=97.72  E-value=1.5e-05  Score=67.85  Aligned_cols=38  Identities=16%  Similarity=0.386  Sum_probs=30.7

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      .+|..|+|.||||+|||++|+.|+..++.+++  +.++++
T Consensus        27 ~~~~~I~l~G~~GsGKsT~a~~L~~~~g~~~i--s~~~~~   64 (243)
T 3tlx_A           27 KPDGRYIFLGAPGSGKGTQSLNLKKSHCYCHL--STGDLL   64 (243)
T ss_dssp             SCCEEEEEECCTTSSHHHHHHHHHHHHCCEEE--EHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHhCCeEE--ecHHHH
Confidence            45667999999999999999999999987665  444444

>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=97.72  E-value=1.7e-05  Score=63.30  Aligned_cols=32  Identities=34%  Similarity=0.454  Sum_probs=27.8

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceeeeec
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVV  225 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~  225 (245)
                      .-++|.||||+|||++++.++..+|..++..+
T Consensus         9 ~~i~l~G~~GsGKSTl~~~l~~~~g~~~i~~d   40 (175)
T 1knq_A            9 HIYVLMGVSGSGKSAVASEVAHQLHAAFLDGD   40 (175)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHTCEEEEGG
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHhhCcEEEeCc
Confidence            45889999999999999999998888777654

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=97.71  E-value=1.6e-05  Score=68.48  Aligned_cols=40  Identities=25%  Similarity=0.391  Sum_probs=33.0

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHh
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYL  234 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~  234 (245)
                      ...+.|.||||+|||++++.||..++++|+  +...+.....
T Consensus        48 g~~i~l~G~~GsGKSTl~~~La~~lg~~~~--d~d~~~~~~~   87 (250)
T 3nwj_A           48 GRSMYLVGMMGSGKTTVGKIMARSLGYTFF--DCDTLIEQAM   87 (250)
T ss_dssp             TCCEEEECSTTSCHHHHHHHHHHHHTCEEE--EHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhcCCcEE--eCcHHHHHHh
Confidence            456999999999999999999999998875  5556665554

>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=97.67  E-value=2.8e-05  Score=63.83  Aligned_cols=38  Identities=21%  Similarity=0.213  Sum_probs=29.6

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEF  229 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l  229 (245)
                      ++.-+.|.||+|+|||+++++||..+   |...+.+++.++
T Consensus        24 ~g~~i~l~G~sGsGKSTl~~~La~~l~~~G~~~~~~d~d~~   64 (200)
T 3uie_A           24 KGCVIWVTGLSGSGKSTLACALNQMLYQKGKLCYILDGDNV   64 (200)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhcCceEEEecCchh
Confidence            44558899999999999999999988   444346666655

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=97.66  E-value=2.6e-05  Score=63.99  Aligned_cols=36  Identities=39%  Similarity=0.648  Sum_probs=28.4

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccceeeeechhHH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF  229 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l  229 (245)
                      ++.-++|.||||+|||++++.|+..+|..++  ++.++
T Consensus        28 ~g~~i~l~G~~GsGKSTl~~~L~~~~g~~~i--~~d~~   63 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTIAHGVADETGLEFA--EADAF   63 (200)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHHCCEEE--EGGGG
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHhhCCeEE--ccccc
Confidence            3445889999999999999999999876554  44443

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=97.66  E-value=7.2e-05  Score=65.36  Aligned_cols=57  Identities=25%  Similarity=0.232  Sum_probs=43.3

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechh
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS  227 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s  227 (245)
                      +......++|-+...+.|.+.+..           |    +.++++||+|+|||++++.+++..+  ++.+++.
T Consensus         7 ~~~~~~~~~gR~~el~~L~~~l~~-----------~----~~v~i~G~~G~GKT~Ll~~~~~~~~--~~~~~~~   63 (350)
T 2qen_A            7 PKTRREDIFDREEESRKLEESLEN-----------Y----PLTLLLGIRRVGKSSLLRAFLNERP--GILIDCR   63 (350)
T ss_dssp             CCCSGGGSCSCHHHHHHHHHHHHH-----------C----SEEEEECCTTSSHHHHHHHHHHHSS--EEEEEHH
T ss_pred             CCCChHhcCChHHHHHHHHHHHhc-----------C----CeEEEECCCcCCHHHHHHHHHHHcC--cEEEEee
Confidence            334456789999888888877642           1    5699999999999999999999886  4444443

>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=97.62  E-value=2e-05  Score=65.10  Aligned_cols=36  Identities=19%  Similarity=0.227  Sum_probs=29.2

Q ss_pred             ceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHH
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQK  232 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~  232 (245)
                      -+.|.|++|||||++|+.++..+|++++  ++.++...
T Consensus        14 iIgltG~~GSGKSTva~~L~~~lg~~vi--d~D~~~~~   49 (192)
T 2grj_A           14 VIGVTGKIGTGKSTVCEILKNKYGAHVV--NVDRIGHE   49 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCEEE--EHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCCEEE--ECcHHHHH
Confidence            3789999999999999999998888774  55555433

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=97.59  E-value=1.5e-05  Score=71.41  Aligned_cols=36  Identities=22%  Similarity=0.248  Sum_probs=27.8

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcccce--eeee
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHTTAA--FIRV  224 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~--~~~v  224 (245)
                      |+.+++.++|+||||||||+||.++|...+.+  |+.+
T Consensus       119 Gi~~gsviLI~GpPGsGKTtLAlqlA~~~G~~VlyIs~  156 (331)
T 2vhj_A          119 HRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATV  156 (331)
T ss_dssp             EEEESEEEEEECSCSSSHHHHHHHHHHHHHTTSCCEEE
T ss_pred             CCCCCcEEEEEcCCCCCHHHHHHHHHHhCCCCEEEEEe
Confidence            44455558999999999999999999875444  5555

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=97.54  E-value=2.8e-05  Score=63.75  Aligned_cols=33  Identities=15%  Similarity=0.188  Sum_probs=26.8

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccceeeee
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRV  224 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v  224 (245)
                      .+.-|+|.|+||||||++|+.|+..++.+++.+
T Consensus         9 ~~~~I~l~G~~GsGKST~~~~L~~~l~~~~~~~   41 (212)
T 2wwf_A            9 KGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEV   41 (212)
T ss_dssp             CSCEEEEEESTTSSHHHHHHHHHHHHHHTTCCE
T ss_pred             cCCEEEEEcCCCCCHHHHHHHHHHHHHHcCCcE
Confidence            345589999999999999999999887654433

>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=97.52  E-value=3.1e-05  Score=63.52  Aligned_cols=31  Identities=19%  Similarity=0.137  Sum_probs=25.5

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccceee
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAFI  222 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~  222 (245)
                      .+.-|+|.||||+|||++|+.|+..++..++
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~L~~~l~~~~~   38 (215)
T 1nn5_A            8 RGALIVLEGVDRAGKSTQSRKLVEALCAAGH   38 (215)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHHHHTTC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHcCC
Confidence            3456899999999999999999998755433

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=97.52  E-value=8.2e-05  Score=61.17  Aligned_cols=29  Identities=28%  Similarity=0.436  Sum_probs=24.7

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      +..++-++|.||||+|||++++.|+..++
T Consensus         9 ~~~~~~i~l~G~sGsGKsTl~~~L~~~~~   37 (204)
T 2qor_A            9 MARIPPLVVCGPSGVGKGTLIKKVLSEFP   37 (204)
T ss_dssp             CCCCCCEEEECCTTSCHHHHHHHHHHHCT
T ss_pred             cccCCEEEEECCCCCCHHHHHHHHHHhCc
Confidence            34556689999999999999999998873

>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=97.51  E-value=4.8e-05  Score=64.41  Aligned_cols=30  Identities=23%  Similarity=0.510  Sum_probs=25.7

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccceee
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAFI  222 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~~  222 (245)
                      +.-++|.||||+|||++++.||..+|...+
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~~lg~~~~   56 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQNFGLQHL   56 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHCCCCE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeEe
Confidence            456999999999999999999988876543

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=97.49  E-value=6.8e-05  Score=60.53  Aligned_cols=38  Identities=29%  Similarity=0.240  Sum_probs=28.9

Q ss_pred             CcceeeecCCCCchHHHHHHHHhccc---ceeeeechhHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTT---AAFIRVVGSEFV  230 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~---~~~~~v~~s~l~  230 (245)
                      +.-++|.|+||+|||++++.+|..++   ..++.+++..+.
T Consensus        13 ~~~i~l~G~~GsGKsT~~~~L~~~l~~~~~~~~~~~~d~~~   53 (186)
T 2yvu_A           13 GIVVWLTGLPGSGKTTIATRLADLLQKEGYRVEVLDGDWAR   53 (186)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEeeHHHHH
Confidence            34488999999999999999999884   334556655553

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=97.48  E-value=6.4e-05  Score=61.67  Aligned_cols=39  Identities=28%  Similarity=0.310  Sum_probs=30.2

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechh
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS  227 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s  227 (245)
                      |+.++.-++++||||+|||++++.+|...+.+.+.++..
T Consensus        16 gi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~v~~i~~~   54 (220)
T 2cvh_A           16 GFAPGVLTQVYGPYASGKTTLALQTGLLSGKKVAYVDTE   54 (220)
T ss_dssp             SBCTTSEEEEECSTTSSHHHHHHHHHHHHCSEEEEEESS
T ss_pred             CCcCCEEEEEECCCCCCHHHHHHHHHHHcCCcEEEEECC
Confidence            466666699999999999999999998445566666543

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=97.43  E-value=7.7e-05  Score=67.08  Aligned_cols=34  Identities=29%  Similarity=0.381  Sum_probs=29.8

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceeeeechh
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS  227 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s  227 (245)
                      +-+++.||+|||||+||..||..++..|+..|.-
T Consensus        41 ~lIvI~GPTgsGKTtLa~~LA~~l~~eiIs~Ds~   74 (339)
T 3a8t_A           41 KLLVLMGATGTGKSRLSIDLAAHFPLEVINSDKM   74 (339)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTTSCEEEEECCSS
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHCCCcEEccccc
Confidence            3588999999999999999999999988776643

>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=97.43  E-value=0.00011  Score=60.63  Aligned_cols=39  Identities=21%  Similarity=0.288  Sum_probs=30.4

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhccc----ceeeeechhHH
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTT----AAFIRVVGSEF  229 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~----~~~~~v~~s~l  229 (245)
                      ..+.-++|.||||+|||++++.++..++    .+++.+++..+
T Consensus        23 ~~~~~i~~~G~~GsGKsT~~~~l~~~l~~~~g~~~~~~~~d~~   65 (211)
T 1m7g_A           23 QRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNI   65 (211)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEECHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHhccccCCcEEEECChHH
Confidence            3445588999999999999999999875    44666775554

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=97.41  E-value=0.00013  Score=60.66  Aligned_cols=40  Identities=20%  Similarity=0.244  Sum_probs=30.0

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhc--c-------cceeeeechhH
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANH--T-------TAAFIRVVGSE  228 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~--l-------~~~~~~v~~s~  228 (245)
                      |+.++.-++|+||||+|||++++.+|..  +       +...+.+++.+
T Consensus        20 gi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~   68 (243)
T 1n0w_A           20 GIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEG   68 (243)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSS
T ss_pred             CCcCCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCC
Confidence            4555566999999999999999999984  3       34566665443

>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=97.41  E-value=0.00014  Score=60.20  Aligned_cols=27  Identities=30%  Similarity=0.425  Sum_probs=23.1

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhccc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      ++.-+.|.||+|+|||++++.|+..+.
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~~L~~~~~   33 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVREAVFKDPE   33 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHSTT
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHhhCC
Confidence            344588999999999999999998763

>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=97.39  E-value=8.6e-05  Score=63.36  Aligned_cols=33  Identities=27%  Similarity=0.436  Sum_probs=28.6

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccceeeeec
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVV  225 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~  225 (245)
                      +.-+.+.||||+|||++|+.||..++.+++...
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~lg~~~~d~g   41 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARALGARYLDTG   41 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHTCEEEEHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCcccCC
Confidence            345889999999999999999999998887653

>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=97.37  E-value=9.2e-05  Score=63.01  Aligned_cols=38  Identities=13%  Similarity=0.172  Sum_probs=30.5

Q ss_pred             CcceeeecCCCCchHHHHHHHHhccccee--------eeechhHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAF--------IRVVGSEFV  230 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~--------~~v~~s~l~  230 (245)
                      +.-|.+.||||+|||++|+.|+..++.++        +.++..++.
T Consensus        22 ~~iI~I~G~~GSGKST~a~~L~~~lg~~~~d~~~~~~~~i~~D~~~   67 (252)
T 1uj2_A           22 PFLIGVSGGTASGKSSVCAKIVQLLGQNEVDYRQKQVVILSQDSFY   67 (252)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHTTGGGSCGGGCSEEEEEGGGGB
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHhhhhcccccCCceEEEecCccc
Confidence            34588999999999999999999998773        246666654

>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=97.37  E-value=0.00011  Score=60.29  Aligned_cols=32  Identities=28%  Similarity=0.297  Sum_probs=26.3

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc-cceeeeec
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT-TAAFIRVV  225 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l-~~~~~~v~  225 (245)
                      .-+.+.||||+|||++++.++..+ +..++..+
T Consensus        22 ~~i~i~G~~GsGKSTl~~~L~~~~~~~~~i~~D   54 (207)
T 2qt1_A           22 FIIGISGVTNSGKTTLAKNLQKHLPNCSVISQD   54 (207)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTTSTTEEEEEGG
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCcEEEeCC
Confidence            347899999999999999999988 66665443

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=97.33  E-value=0.00013  Score=78.52  Aligned_cols=38  Identities=32%  Similarity=0.409  Sum_probs=32.3

Q ss_pred             CcHHHHhhhc---cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          180 THHELYKQIG---IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       180 ~~~~~~~~~g---~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      -.+++...+|   +.++++++||||||||||+||.++|.+.
T Consensus      1411 G~~~LD~lLG~GGi~~g~~vll~GppGtGKT~LA~ala~ea 1451 (2050)
T 3cmu_A         1411 GSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAA 1451 (2050)
T ss_dssp             SCHHHHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCHHHHHhcCCCCccCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            3456666666   8888999999999999999999998876

>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=97.31  E-value=0.00014  Score=64.82  Aligned_cols=35  Identities=31%  Similarity=0.557  Sum_probs=30.3

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccceeeeechh
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS  227 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s  227 (245)
                      ++-+++.||+|+|||+||..+|..++..++..|.-
T Consensus        10 ~~~i~i~GptgsGKt~la~~La~~~~~~iis~Ds~   44 (316)
T 3foz_A           10 PKAIFLMGPTASGKTALAIELRKILPVELISVDSA   44 (316)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHSCEEEEECCTT
T ss_pred             CcEEEEECCCccCHHHHHHHHHHhCCCcEEecccc
Confidence            45588999999999999999999999888877643

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=97.31  E-value=7.9e-05  Score=82.19  Aligned_cols=37  Identities=38%  Similarity=0.695  Sum_probs=28.9

Q ss_pred             CCCcceeeecCCCCchHHHH-HHHHhcccceeeeechh
Q 025979          191 DPPRGVLLYGPPGTGKTMLA-KAVANHTTAAFIRVVGS  227 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lA-kalA~~l~~~~~~v~~s  227 (245)
                      ..++++||+||||||||++| ++++...+..++.+..+
T Consensus      1265 ~~~~~vLL~GPpGtGKT~la~~~l~~~~~~~~~~infs 1302 (2695)
T 4akg_A         1265 NSKRGIILCGPPGSGKTMIMNNALRNSSLYDVVGINFS 1302 (2695)
T ss_dssp             HHTCEEEEECSTTSSHHHHHHHHHHSCSSCEEEEEECC
T ss_pred             HCCCeEEEECCCCCCHHHHHHHHHhcCCCCceEEEEee
Confidence            45588999999999999999 55665557777777654

>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=97.29  E-value=0.00013  Score=67.07  Aligned_cols=33  Identities=21%  Similarity=0.292  Sum_probs=27.8

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccceeeeec
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVV  225 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~  225 (245)
                      +.-|+|+||||+|||++|+.++..+++.++..+
T Consensus       258 ~~lIil~G~pGSGKSTla~~L~~~~~~~~i~~D  290 (416)
T 3zvl_A          258 PEVVVAVGFPGAGKSTFIQEHLVSAGYVHVNRD  290 (416)
T ss_dssp             CCEEEEESCTTSSHHHHHHHHTGGGTCEECCGG
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhcCcEEEccc
Confidence            445889999999999999999999987775543

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=97.27  E-value=0.0001  Score=60.64  Aligned_cols=29  Identities=34%  Similarity=0.461  Sum_probs=24.3

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      |+.++.-++++||||+|||++++.+|..+
T Consensus        19 gi~~G~~~~i~G~~GsGKTtl~~~l~~~~   47 (235)
T 2w0m_A           19 GIPQGFFIALTGEPGTGKTIFSLHFIAKG   47 (235)
T ss_dssp             SEETTCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCcCCCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            45556668999999999999999999654

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=97.27  E-value=0.00016  Score=61.73  Aligned_cols=35  Identities=26%  Similarity=0.374  Sum_probs=28.6

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      .-+.|.||+|+|||++++.||..+|..++  +...+.
T Consensus        28 ~~I~I~G~~GsGKSTl~k~La~~Lg~~~~--d~g~i~   62 (252)
T 4e22_A           28 PVITVDGPSGAGKGTLCKALAESLNWRLL--DSGAIY   62 (252)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHTTCEEE--EHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCCCcC--CCCcee
Confidence            34889999999999999999999987764  444444

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=97.23  E-value=0.00018  Score=60.48  Aligned_cols=35  Identities=20%  Similarity=0.370  Sum_probs=28.9

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      ..+.|.||||+|||++++.+|..+|.+++  +..++.
T Consensus        17 ~~i~i~G~~gsGKst~~~~l~~~lg~~~~--d~d~~~   51 (236)
T 1q3t_A           17 IQIAIDGPASSGKSTVAKIIAKDFGFTYL--DTGAMY   51 (236)
T ss_dssp             CEEEEECSSCSSHHHHHHHHHHHHCCEEE--EHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCCcee--cCCCee
Confidence            34889999999999999999999997764  555554

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=97.21  E-value=0.00012  Score=80.80  Aligned_cols=37  Identities=27%  Similarity=0.402  Sum_probs=33.9

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccceeeeechhH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSE  228 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~  228 (245)
                      ...|+++.||||||||++++++|+.+|.+++++.+++
T Consensus       644 ~~~~~~l~GpaGtGKTe~vk~LA~~lg~~~v~~nc~e  680 (2695)
T 4akg_A          644 QKYGGCFFGPAGTGKTETVKAFGQNLGRVVVVFNCDD  680 (2695)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHHHTTTCCCEEEETTS
T ss_pred             hCCCCcccCCCCCCcHHHHHHHHHHhCCcEEEEECCC
Confidence            3467999999999999999999999999999998874

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=97.20  E-value=0.00015  Score=60.44  Aligned_cols=38  Identities=37%  Similarity=0.410  Sum_probs=28.0

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeech
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVG  226 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~  226 (245)
                      |+.++.-++++||||+|||++|..+|...   +.+.+.++.
T Consensus        19 Gl~~G~~~~i~G~~GsGKTtl~~~~~~~~~~~~~~v~~~~~   59 (247)
T 2dr3_A           19 GIPERNVVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVAL   59 (247)
T ss_dssp             SEETTCEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEc
Confidence            55566669999999999999998887643   445555543

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=97.18  E-value=0.00016  Score=60.40  Aligned_cols=33  Identities=24%  Similarity=0.215  Sum_probs=21.5

Q ss_pred             HhhhccCCCcc--eeeecCCCCchHHHHHHHHhcc
Q 025979          185 YKQIGIDPPRG--VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       185 ~~~~g~~~~~g--vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +..+.+..++|  +.|.||+|+|||+|++.|+...
T Consensus        13 l~~isl~i~~G~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           13 GLVPRGSMNNIYPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             ---------CCCCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             ccCCceecCCCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            34444444444  8899999999999999999865

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=97.16  E-value=0.00021  Score=58.90  Aligned_cols=34  Identities=32%  Similarity=0.523  Sum_probs=26.9

Q ss_pred             CcceeeecCCCCchHHHHHHHHhccc-----ceeeeech
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTT-----AAFIRVVG  226 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~-----~~~~~v~~  226 (245)
                      +.-+.+.||+|+|||+|++.|+..+.     ..++.+++
T Consensus        22 g~~v~I~G~sGsGKSTl~~~l~~~~~~~g~~~g~v~~d~   60 (208)
T 3c8u_A           22 RQLVALSGAPGSGKSTLSNPLAAALSAQGLPAEVVPMDG   60 (208)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHHHHHHTTCCEEEEESGG
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhhcCCceEEEecCC
Confidence            34488999999999999999999875     45555544

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=97.16  E-value=0.00015  Score=65.65  Aligned_cols=38  Identities=21%  Similarity=0.194  Sum_probs=29.1

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechh
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      +.+..-++++||||+|||+||..+|..+   +...+.++..
T Consensus        58 i~~G~i~~I~GppGsGKSTLal~la~~~~~~gg~VlyId~E   98 (356)
T 3hr8_A           58 YPRGRIVEIFGQESSGKTTLALHAIAEAQKMGGVAAFIDAE   98 (356)
T ss_dssp             EETTEEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEecc
Confidence            4455559999999999999999999875   4455556654

>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=97.15  E-value=0.00023  Score=59.55  Aligned_cols=32  Identities=28%  Similarity=0.346  Sum_probs=26.7

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccceeeeec
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVV  225 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~  225 (245)
                      +++++|.||||+|||++|..++...+ .++..|
T Consensus        34 g~~ilI~GpsGsGKStLA~~La~~g~-~iIsdD   65 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELVQRGH-RLIADD   65 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHHTTTC-EEEESS
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhCC-eEEecc
Confidence            46799999999999999999998875 555444

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=97.14  E-value=0.00035  Score=61.84  Aligned_cols=49  Identities=18%  Similarity=0.283  Sum_probs=34.2

Q ss_pred             CCcHHHHhhh--ccCCCcceeeecCCCCchHHHHHHHHhcc---------cceeeeechh
Q 025979          179 LTHHELYKQI--GIDPPRGVLLYGPPGTGKTMLAKAVANHT---------TAAFIRVVGS  227 (245)
Q Consensus       179 ~~~~~~~~~~--g~~~~~gvLl~GPPGtGKT~lAkalA~~l---------~~~~~~v~~s  227 (245)
                      ...+.+..-+  |+.++.-++++||||+|||++|..+|..+         +...+.++..
T Consensus        91 TG~~~LD~~L~GGl~~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e  150 (324)
T 2z43_A           91 TGSQALDGLLAGGIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTE  150 (324)
T ss_dssp             CSCHHHHHHTTTSEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESS
T ss_pred             CCchhHHHhcCCCCCCCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECC
Confidence            3344444444  46665669999999999999999998754         4455556544

>2axn_A 6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 3 (6PF-2-K/FRU- 2,6-P2ASE brain/placenta-type...; bifunctional enzyme, EDTA complex; HET: F6P EDT ADP; 2.10A {Homo sapiens} PDB: 2dwo_A* 2dwp_A* 2i1v_B* 3qpu_A* 3qpv_A* 3qpw_A*

Probab=97.13  E-value=0.00024  Score=67.24  Aligned_cols=43  Identities=16%  Similarity=0.234  Sum_probs=34.4

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceee---eechhHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFI---RVVGSEFVQKYLGE  236 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~---~v~~s~l~~~~~Ge  236 (245)
                      .-|+|+|+||+|||++|+.||..+++.++   .++..++.....|.
T Consensus        36 ~lIvlvGlpGSGKSTia~~La~~L~~~~~d~~v~s~D~~r~~~~~~   81 (520)
T 2axn_A           36 TVIVMVGLPARGKTYISKKLTRYLNWIGVPTKVFNVGEYRREAVKQ   81 (520)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhhcCCCeEEecccHHHHHhccC
Confidence            44889999999999999999999966554   45777777766654

>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=97.13  E-value=0.00016  Score=59.58  Aligned_cols=28  Identities=36%  Similarity=0.503  Sum_probs=23.8

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhc
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      |+.+..-+.|+||||+|||+|++.++..
T Consensus        21 gi~~G~~~~l~G~nGsGKSTll~~l~g~   48 (231)
T 4a74_A           21 GIETQAITEVFGEFGSGKTQLAHTLAVM   48 (231)
T ss_dssp             SEESSEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            4555556999999999999999999974

>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=97.12  E-value=0.00021  Score=62.19  Aligned_cols=33  Identities=24%  Similarity=0.281  Sum_probs=26.4

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceeeeechhHH
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF  229 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l  229 (245)
                      .-|.|.||||+|||++|+.++ .+|.+++  +..++
T Consensus        76 ~iI~I~G~~GSGKSTva~~La-~lg~~~i--d~D~~  108 (281)
T 2f6r_A           76 YVLGLTGISGSGKSSVAQRLK-NLGAYII--DSDHL  108 (281)
T ss_dssp             EEEEEEECTTSCHHHHHHHHH-HHTCEEE--EHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHH-HCCCcEE--ehhHH
Confidence            348899999999999999999 5787764  44444

>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=97.10  E-value=0.00034  Score=64.84  Aligned_cols=23  Identities=39%  Similarity=0.586  Sum_probs=21.4

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+++.||||||||+++.+++..+
T Consensus        47 ~~li~G~aGTGKT~ll~~~~~~l   69 (459)
T 3upu_A           47 HVTINGPAGTGATTLTKFIIEAL   69 (459)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHH
Confidence            68999999999999999999877

>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=97.06  E-value=0.00038  Score=62.55  Aligned_cols=50  Identities=26%  Similarity=0.340  Sum_probs=33.8

Q ss_pred             CCcHHHHhhh--ccCCCcceeeecCCCCchHHHHHHHHhcc---------cceeeeechhH
Q 025979          179 LTHHELYKQI--GIDPPRGVLLYGPPGTGKTMLAKAVANHT---------TAAFIRVVGSE  228 (245)
Q Consensus       179 ~~~~~~~~~~--g~~~~~gvLl~GPPGtGKT~lAkalA~~l---------~~~~~~v~~s~  228 (245)
                      ...+.+..-+  |+.+..-+.++||||+|||+|++.++...         +...+.+++.+
T Consensus       115 TG~~~LD~lL~ggi~~G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~  175 (349)
T 1pzn_A          115 TGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTEN  175 (349)
T ss_dssp             CSCHHHHHHHTSSEESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSS
T ss_pred             CCCHHHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCC
Confidence            3344444443  44444459999999999999999999876         23446666543

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=97.03  E-value=0.00066  Score=60.70  Aligned_cols=39  Identities=26%  Similarity=0.295  Sum_probs=28.6

Q ss_pred             CCCcHHHHhhh--ccCCCcceeeecCCCCchHHHHHHHHhc
Q 025979          178 PLTHHELYKQI--GIDPPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       178 ~~~~~~~~~~~--g~~~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      +...+.+..-+  |+.++.-++++||||+|||++|..+|..
T Consensus       105 ~TG~~~LD~~LgGGl~~G~i~~I~G~~GsGKTtla~~la~~  145 (343)
T 1v5w_A          105 TTGSQEFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVT  145 (343)
T ss_dssp             CCSCHHHHHHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHH
T ss_pred             ecCChhHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            34445555555  4555555899999999999999999875

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=97.01  E-value=0.00031  Score=63.22  Aligned_cols=38  Identities=24%  Similarity=0.368  Sum_probs=28.2

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeech
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVG  226 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~  226 (245)
                      |+.+..-++++||||+|||+||..+|..+   +.+.+.++.
T Consensus        57 Gl~~G~iv~I~G~pGsGKTtLal~la~~~~~~g~~vlyi~~   97 (349)
T 2zr9_A           57 GLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGIAAFIDA   97 (349)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEC
Confidence            45555669999999999999999998654   344455543

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=96.99  E-value=0.00038  Score=58.16  Aligned_cols=26  Identities=27%  Similarity=0.377  Sum_probs=16.2

Q ss_pred             CCcceeeecCCCCchHHHHHHHH-hcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVA-NHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA-~~l  217 (245)
                      ++.-+.|.||+|+|||++++.|+ ..+
T Consensus        26 ~G~ii~l~Gp~GsGKSTl~~~L~~~~~   52 (231)
T 3lnc_A           26 VGVILVLSSPSGCGKTTVANKLLEKQK   52 (231)
T ss_dssp             CCCEEEEECSCC----CHHHHHHC---
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            34448899999999999999999 654

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=96.99  E-value=0.00057  Score=61.73  Aligned_cols=38  Identities=29%  Similarity=0.377  Sum_probs=29.7

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeech
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVG  226 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~  226 (245)
                      |+.+.+-++++||||+|||++|..+|..+   +.+.+.++.
T Consensus        59 Gl~~G~ii~I~G~pGsGKTtLal~la~~~~~~g~~vlyid~   99 (356)
T 1u94_A           59 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDA   99 (356)
T ss_dssp             SEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeC
Confidence            45566669999999999999999998764   445666665

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=96.96  E-value=0.00038  Score=57.93  Aligned_cols=37  Identities=32%  Similarity=0.338  Sum_probs=26.5

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc----cceeeeec
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT----TAAFIRVV  225 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l----~~~~~~v~  225 (245)
                      |+.++.-++++|+||+|||++|-.+|...    +.+.+.++
T Consensus        26 Gl~~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s   66 (251)
T 2zts_A           26 GFPEGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVT   66 (251)
T ss_dssp             SEETTCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEE
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeec
Confidence            45566669999999999999998776432    44444444

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=96.93  E-value=0.0005  Score=54.92  Aligned_cols=27  Identities=30%  Similarity=0.395  Sum_probs=23.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.|.||.|+|||+|.++++..+
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            344448899999999999999999876

>1x6v_B Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthethase 1; transferase, ATP sulfurylase, APS kinase, PAPS; HET: ADP; 1.75A {Homo sapiens} SCOP: b.122.1.3 c.26.1.5 c.37.1.4 PDB: 1xjq_B* 1xnj_B* 2qjf_A* 2ofx_A* 2ofw_A*

Probab=96.90  E-value=0.00054  Score=66.33  Aligned_cols=36  Identities=25%  Similarity=0.305  Sum_probs=31.6

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc---cceeeeechhHH
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEF  229 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l  229 (245)
                      .-|+|.|+||+|||++|++|+..+   |.+++.+++..+
T Consensus        53 ~lIvLtGlsGSGKSTlAr~La~~L~~~G~~~v~lDgD~i   91 (630)
T 1x6v_B           53 CTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLDGDNI   91 (630)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEESHHHH
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEechHHh
Confidence            448899999999999999999999   899998886554

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=96.89  E-value=0.00091  Score=60.74  Aligned_cols=61  Identities=20%  Similarity=0.245  Sum_probs=44.2

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHH
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFV  230 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~  230 (245)
                      ..+.|.....+.+.+.+..          + ......+|++|++|||||++|+++....   +.+|+.++++.+.
T Consensus       137 ~~~ig~s~~m~~l~~~i~~----------~-a~~~~~vli~Ge~GtGK~~lAr~ih~~s~r~~~~fv~v~~~~~~  200 (387)
T 1ny5_A          137 EEYVFESPKMKEILEKIKK----------I-SCAECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIP  200 (387)
T ss_dssp             CCCCCCSHHHHHHHHHHHH----------H-TTCCSCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSC
T ss_pred             hhhhhccHHhhHHHHHHHH----------h-cCCCCCeEEecCCCcCHHHHHHHHHHhcCCCCCCeEEEecCCCC
Confidence            3566666666666665543          1 1233458999999999999999998766   4789999987653

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=96.88  E-value=0.00043  Score=59.99  Aligned_cols=30  Identities=17%  Similarity=0.269  Sum_probs=25.1

Q ss_pred             hccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          188 IGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       188 ~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .|+.++.-+++.||||+|||+|++.+|..+
T Consensus        30 ~~l~~G~~~~i~G~~G~GKTTl~~~ia~~~   59 (296)
T 1cr0_A           30 LGARGGEVIMVTSGSGMGKSTFVRQQALQW   59 (296)
T ss_dssp             CSBCTTCEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             cCCCCCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            356666669999999999999999999765

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.87  E-value=0.00066  Score=55.64  Aligned_cols=32  Identities=19%  Similarity=0.140  Sum_probs=24.9

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc---cceeeee
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRV  224 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v  224 (245)
                      +.-+.+.||+|+|||++++.++..+   +.+++.+
T Consensus        22 ~~~i~i~G~~GsGKstl~~~l~~~~~~~~~~v~~~   56 (201)
T 1rz3_A           22 RLVLGIDGLSRSGKTTLANQLSQTLREQGISVCVF   56 (201)
T ss_dssp             SEEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhhcCCeEEEe
Confidence            3448899999999999999999875   4444444

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=96.87  E-value=0.00042  Score=58.59  Aligned_cols=25  Identities=12%  Similarity=0.242  Sum_probs=22.5

Q ss_pred             eeeecCCCCchHHHHHHHHhcccce
Q 025979          196 VLLYGPPGTGKTMLAKAVANHTTAA  220 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l~~~  220 (245)
                      +.|.||+|+|||++++.|+..+|..
T Consensus        28 igI~G~~GsGKSTl~k~L~~~lG~~   52 (245)
T 2jeo_A           28 IGVSGGTASGKSTVCEKIMELLGQN   52 (245)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHTGG
T ss_pred             EEEECCCCCCHHHHHHHHHHHhchh
Confidence            7799999999999999999987654

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=96.87  E-value=0.00051  Score=56.49  Aligned_cols=26  Identities=27%  Similarity=0.492  Sum_probs=22.5

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++.-+.|.||+|+|||+|+++|+..+
T Consensus        19 ~Gei~~l~GpnGsGKSTLl~~l~gl~   44 (207)
T 1znw_A           19 VGRVVVLSGPSAVGKSTVVRCLRERI   44 (207)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            44448899999999999999999876

>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=96.86  E-value=0.00039  Score=59.93  Aligned_cols=29  Identities=31%  Similarity=0.362  Sum_probs=23.7

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      |+.+..-++++||||+|||+|++.+|..+
T Consensus        26 gl~~G~i~~i~G~~GsGKTtl~~~l~~~~   54 (279)
T 1nlf_A           26 NMVAGTVGALVSPGGAGKSMLALQLAAQI   54 (279)
T ss_dssp             TEETTSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CccCCCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            45555559999999999999999998643

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=96.86  E-value=0.0013  Score=63.56  Aligned_cols=32  Identities=28%  Similarity=0.449  Sum_probs=21.2

Q ss_pred             eeeecCCCCchHHHHHHHHhcc---cceeeeechh
Q 025979          196 VLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      .|++||||||||++.-.+...+   +..++.++.+
T Consensus       208 ~lI~GPPGTGKT~ti~~~I~~l~~~~~~ILv~a~T  242 (646)
T 4b3f_X          208 AIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPS  242 (646)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             eEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEcCc
Confidence            6899999999998655444333   4455555443

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=96.84  E-value=0.00035  Score=55.98  Aligned_cols=23  Identities=35%  Similarity=0.439  Sum_probs=18.9

Q ss_pred             CCcceeeecCCCCchHHHHHHHH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVA  214 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA  214 (245)
                      ++.-++|+||+|+|||++++++.
T Consensus         8 ~gei~~l~G~nGsGKSTl~~~~~   30 (171)
T 4gp7_A            8 ELSLVVLIGSSGSGKSTFAKKHF   30 (171)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHS
T ss_pred             CCEEEEEECCCCCCHHHHHHHHc
Confidence            34448899999999999999643

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=96.83  E-value=0.00064  Score=56.46  Aligned_cols=24  Identities=21%  Similarity=0.566  Sum_probs=21.2

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +-+.|.||+|+|||+|+++|+...
T Consensus        20 ~~ivl~GPSGaGKsTL~~~L~~~~   43 (197)
T 3ney_A           20 KTLVLIGASGVGRSHIKNALLSQN   43 (197)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CEEEEECcCCCCHHHHHHHHHhhC
Confidence            448899999999999999999765

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=96.81  E-value=0.00044  Score=58.89  Aligned_cols=31  Identities=26%  Similarity=0.395  Sum_probs=28.2

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceeeee
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRV  224 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v  224 (245)
                      ..+-|.||||+|||++|+.||..++.+++.+
T Consensus         9 ~~~~~~G~pGsGKsT~a~~L~~~~g~~~is~   39 (230)
T 3gmt_A            9 MRLILLGAPGAGKGTQANFIKEKFGIPQIST   39 (230)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHTCCEECH
T ss_pred             cceeeECCCCCCHHHHHHHHHHHhCCCeeec
Confidence            4578899999999999999999999998876

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=96.81  E-value=0.00056  Score=62.00  Aligned_cols=38  Identities=32%  Similarity=0.417  Sum_probs=28.6

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeech
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVG  226 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~  226 (245)
                      |+.++.-++++||||+|||++|..+|..+   +.+.+.++.
T Consensus        70 Gl~~G~li~I~G~pGsGKTtlal~la~~~~~~g~~vlyi~~  110 (366)
T 1xp8_A           70 GIPRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDA  110 (366)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             CccCCcEEEEEcCCCCChHHHHHHHHHHHHHCCCeEEEEEC
Confidence            45555669999999999999999988764   445555553

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=96.79  E-value=0.00088  Score=58.90  Aligned_cols=28  Identities=21%  Similarity=0.325  Sum_probs=23.3

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhc
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      |+.+..-++++||||+|||++|..+|..
T Consensus        94 Gl~~g~i~~i~G~~gsGKT~la~~la~~  121 (322)
T 2i1q_A           94 GLESQSVTEFAGVFGSGKTQIMHQSCVN  121 (322)
T ss_dssp             SEETTEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4555555999999999999999998864

>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=96.79  E-value=0.00066  Score=60.08  Aligned_cols=29  Identities=31%  Similarity=0.560  Sum_probs=24.3

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      +.++..+.|+||+|+|||+|++.|++.+.
T Consensus       123 i~~Ge~vaIvGpsGsGKSTLl~lL~gl~~  151 (305)
T 2v9p_A          123 IPKKNCLAFIGPPNTGKSMLCNSLIHFLG  151 (305)
T ss_dssp             CTTCSEEEEECSSSSSHHHHHHHHHHHHT
T ss_pred             ecCCCEEEEECCCCCcHHHHHHHHhhhcC
Confidence            44455599999999999999999998763

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=96.76  E-value=0.00075  Score=58.18  Aligned_cols=29  Identities=21%  Similarity=0.329  Sum_probs=23.7

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      +.+..-+++.||+|+|||++.++++..+.
T Consensus        22 i~~g~~v~i~Gp~GsGKSTll~~l~g~~~   50 (261)
T 2eyu_A           22 HRKMGLILVTGPTGSGKSTTIASMIDYIN   50 (261)
T ss_dssp             GCSSEEEEEECSTTCSHHHHHHHHHHHHH
T ss_pred             hCCCCEEEEECCCCccHHHHHHHHHHhCC
Confidence            33444489999999999999999998763

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=96.72  E-value=0.0089  Score=54.82  Aligned_cols=50  Identities=18%  Similarity=0.257  Sum_probs=30.4

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHH
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLA  210 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lA  210 (245)
                      ...|+.|.+.+..-+.+.+.+. |+-     ..+--.-...|+-||.+|+|||+..
T Consensus       109 ~F~FD~VF~~~~~Q~~Vf~~v~-~lv-----~~~l~G~N~tifAYGqTGSGKTyTM  158 (403)
T 4etp_A          109 EFKFDKIFDQQDTNVDVFKEVG-QLV-----QSSLDGYNVAIFAYGQTGSGKTFTM  158 (403)
T ss_dssp             EEEESEEECTTCCHHHHHHHHH-HHH-----HHHHTTCCEEEEEESCTTSSHHHHH
T ss_pred             EEEcCEEECCCCchHHHHHHHH-HHH-----HHHhCCcceEEEEECCCCCCCceEe
Confidence            3677777777766666655543 211     1111112234778999999999976

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=96.72  E-value=0.00052  Score=73.95  Aligned_cols=55  Identities=22%  Similarity=0.271  Sum_probs=42.8

Q ss_pred             cCCCcHHHHhhh---ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHH
Q 025979          177 LPLTHHELYKQI---GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQ  231 (245)
Q Consensus       177 ~~~~~~~~~~~~---g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~  231 (245)
                      .|...+++..-+   |+.++..++++|+||+|||+||..+|..+   +.+++.+++.+...
T Consensus       713 i~TG~~eLD~llggGGl~~G~lilIaG~PG~GKTtLalqlA~~~a~~g~~VlyiS~Ees~~  773 (2050)
T 3cmu_A          713 ISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALD  773 (2050)
T ss_dssp             ECCSCHHHHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTSCCC
T ss_pred             eecCChHHHHHhccCCcCCCcEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEECCCcHH
Confidence            445567777777   47788889999999999999999999876   44688887765433

>3u06_A Protein claret segregational; motor domain, stalk rotation, power stroke, kinesin-14, MICR binding, NCD, transport, molecular motor; HET: ADP GOL; 2.35A {Drosophila melanogaster} PDB: 2ncd_A* 1n6m_A* 1cz7_A* 3l1c_A*

Probab=96.71  E-value=0.01  Score=54.55  Aligned_cols=50  Identities=22%  Similarity=0.250  Sum_probs=30.9

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHH
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLA  210 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lA  210 (245)
                      ..+|+.|.+.+..-+.+.+.+. |+-     ..+--.-...|+-||.+|+|||+..
T Consensus       107 ~F~FD~VF~~~~~Q~~Vf~~v~-plv-----~~~l~G~n~tifAYGqTGSGKTyTM  156 (412)
T 3u06_A          107 IFSFDQVFHPLSSQSDIFEMVS-PLI-----QSALDGYNICIFAYGQTGSGKTYTM  156 (412)
T ss_dssp             EEECSEEECTTCCHHHHHTTTH-HHH-----HHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             EEeeCeEcCCCCCHHHHHHHHH-HHH-----HHHHCCCceEEEEecCCCCCCeeEe
Confidence            4677888877766666665432 221     1111112234788999999999975

>1m8p_A Sulfate adenylyltransferase; rossmann fold, phosphosulfate binding, T-state; HET: PPS; 2.60A {Penicillium chrysogenum} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1i2d_A*

Probab=96.71  E-value=0.001  Score=63.72  Aligned_cols=38  Identities=18%  Similarity=0.266  Sum_probs=32.0

Q ss_pred             cceeeecCCCCchHHHHHHHHhccc----ceeeeechhHHHH
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTT----AAFIRVVGSEFVQ  231 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~----~~~~~v~~s~l~~  231 (245)
                      .-|+|.|+||+|||++|++|+..++    .+++.+++..+..
T Consensus       397 ~~I~l~GlsGSGKSTiA~~La~~L~~~G~~~~~~lD~D~ir~  438 (573)
T 1m8p_A          397 FTIFLTGYMNSGKDAIARALQVTLNQQGGRSVSLLLGDTVRH  438 (573)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHHCSSCEEEEEHHHHHH
T ss_pred             eEEEeecCCCCCHHHHHHHHHHHhcccCCceEEEECcHHHHH
Confidence            3488999999999999999999986    6788888776544

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=96.70  E-value=0.00077  Score=54.45  Aligned_cols=24  Identities=25%  Similarity=0.364  Sum_probs=21.1

Q ss_pred             CcceeeecCCCCchHHHHHHHHhc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      +.-+.|.||||+|||++|+.||..
T Consensus         8 ~~~I~i~G~~GsGKST~~~~La~~   31 (203)
T 1uf9_A            8 PIIIGITGNIGSGKSTVAALLRSW   31 (203)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHC
Confidence            345889999999999999999964

>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=96.64  E-value=0.0023  Score=53.95  Aligned_cols=42  Identities=24%  Similarity=0.336  Sum_probs=33.1

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceeeeechh-HHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS-EFVQKYLG  235 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s-~l~~~~~G  235 (245)
                      +.++++||+|+|||.+|.+++..++.+.+.+... +++..|..
T Consensus       109 ~~~ll~~~tG~GKT~~a~~~~~~~~~~~liv~P~~~L~~q~~~  151 (237)
T 2fz4_A          109 KRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKE  151 (237)
T ss_dssp             SEEEEEESSSTTHHHHHHHHHHHSCSCEEEEESSHHHHHHHHH
T ss_pred             CCEEEEeCCCCCHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHH
Confidence            3489999999999999999998887666666655 77666543

>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}

Probab=96.63  E-value=0.00093  Score=56.38  Aligned_cols=29  Identities=17%  Similarity=0.246  Sum_probs=26.5

Q ss_pred             ceeeecCCCCchHHHHHHHHhcccceeee
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTTAAFIR  223 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~~~~~~  223 (245)
                      -|.+.|++|||||++|+.||..+|.+|+-
T Consensus        16 iI~i~g~~gsGk~~i~~~la~~lg~~~~d   44 (223)
T 3hdt_A           16 IITIEREYGSGGRIVGKKLAEELGIHFYD   44 (223)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHTCEEEC
T ss_pred             EEEEeCCCCCCHHHHHHHHHHHcCCcEEc
Confidence            47899999999999999999999999854

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=96.63  E-value=0.0013  Score=57.96  Aligned_cols=37  Identities=24%  Similarity=0.204  Sum_probs=27.9

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeec
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVV  225 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~  225 (245)
                      |+.++.-+++.|+||+|||++|..+|...   +.+.+.++
T Consensus        64 Gl~~G~l~li~G~pG~GKTtl~l~ia~~~a~~g~~vl~~s  103 (315)
T 3bh0_A           64 GYKRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHS  103 (315)
T ss_dssp             SBCTTCEEEEECCTTSSHHHHHHHHHHHHHTTTCEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEE
Confidence            56666669999999999999999988654   34444444

>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=96.63  E-value=0.0019  Score=61.80  Aligned_cols=34  Identities=38%  Similarity=0.420  Sum_probs=26.1

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc---cceeeeechh
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      +.+++.||||||||+++.+++..+   +.+++.+..+
T Consensus       205 ~~~~I~G~pGTGKTt~i~~l~~~l~~~g~~Vl~~ApT  241 (574)
T 3e1s_A          205 RLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAPT  241 (574)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEecCc
Confidence            458899999999999999998765   4555555433

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=96.62  E-value=0.00084  Score=59.98  Aligned_cols=37  Identities=14%  Similarity=0.145  Sum_probs=27.0

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc-----cceeeeechh
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT-----TAAFIRVVGS  227 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l-----~~~~~~v~~s  227 (245)
                      +.+. -++++||||+|||+||-.++..+     +...+.++..
T Consensus        26 l~~G-iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E   67 (333)
T 3io5_A           26 MQSG-LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSE   67 (333)
T ss_dssp             BCSE-EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESS
T ss_pred             CcCC-eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEecc
Confidence            4443 47899999999999988776544     4566777754

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=96.61  E-value=0.00088  Score=59.04  Aligned_cols=27  Identities=26%  Similarity=0.389  Sum_probs=23.1

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-++|.||+|+|||++++.+|..+
T Consensus        98 ~~g~vi~lvG~nGsGKTTll~~Lag~l  124 (302)
T 3b9q_A           98 RKPAVIMIVGVNGGGKTTSLGKLAHRL  124 (302)
T ss_dssp             SSCEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            344558899999999999999999876

>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=96.59  E-value=0.001  Score=56.01  Aligned_cols=30  Identities=27%  Similarity=0.359  Sum_probs=24.6

Q ss_pred             cceeeecCCCCchHHHHHHHHhccc--ceeee
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTT--AAFIR  223 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~--~~~~~  223 (245)
                      .-+.|.||||+|||++++.|+..++  ..++.
T Consensus        27 ~~i~i~G~~GsGKsT~~~~l~~~l~~~~~~~~   58 (229)
T 4eaq_A           27 AFITFEGPEGSGKTTVINEVYHRLVKDYDVIM   58 (229)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHTTTSCEEE
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHhcCCCcee
Confidence            3488999999999999999999886  34443

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=96.59  E-value=0.00089  Score=58.67  Aligned_cols=27  Identities=30%  Similarity=0.577  Sum_probs=23.1

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      +.-+.+.||+|+|||++|+.|+..++.
T Consensus        31 ~~ii~I~G~sGsGKSTla~~L~~~l~~   57 (290)
T 1odf_A           31 PLFIFFSGPQGSGKSFTSIQIYNHLME   57 (290)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhhh
Confidence            344789999999999999999998853

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=96.58  E-value=0.0011  Score=55.57  Aligned_cols=28  Identities=21%  Similarity=0.344  Sum_probs=23.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      .++.-+.|.||+|+|||+|.++|+....
T Consensus        14 ~~G~ii~l~GpsGsGKSTLlk~L~g~~~   41 (219)
T 1s96_A           14 AQGTLYIVSAPSGAGKSSLIQALLKTQP   41 (219)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHhccCC
Confidence            3444588999999999999999998764

>1bif_A 6-phosphofructo-2-kinase/ fructose-2,6-bisphospha; transferase (phospho), phosphatase, hydrolase (phosp glycolysis, bifunctional enzyme; HET: AGS; 2.00A {Rattus norvegicus} SCOP: c.37.1.7 c.60.1.4 PDB: 3bif_A* 2bif_A* 1k6m_A* 1c80_A* 1c7z_A* 1c81_A* 1tip_A* 1fbt_A

Probab=96.55  E-value=0.00077  Score=62.69  Aligned_cols=43  Identities=16%  Similarity=0.252  Sum_probs=31.4

Q ss_pred             CcceeeecCCCCchHHHHHHHHhccccee---eeechhHHHHHHhc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAF---IRVVGSEFVQKYLG  235 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~---~~v~~s~l~~~~~G  235 (245)
                      +.-|+|+|+||+|||++++.+|..+++.+   ..++..++..+..|
T Consensus        39 ~~~IvlvGlpGsGKSTia~~La~~l~~~~~~t~~~~~d~~r~~~~g   84 (469)
T 1bif_A           39 PTLIVMVGLPARGKTYISKKLTRYLNFIGVPTREFNVGQYRRDMVK   84 (469)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEHHHHHHHHHC
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHhccCCCceEEecchhhhhhcc
Confidence            34589999999999999999999886544   33444555554444

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=96.52  E-value=0.0017  Score=59.55  Aligned_cols=34  Identities=26%  Similarity=0.396  Sum_probs=25.1

Q ss_pred             cHHHHhhh--ccCCCcceeeecCCCCchHHHHHHHH
Q 025979          181 HHELYKQI--GIDPPRGVLLYGPPGTGKTMLAKAVA  214 (245)
Q Consensus       181 ~~~~~~~~--g~~~~~gvLl~GPPGtGKT~lAkalA  214 (245)
                      .+.+..-+  |+.+..-++|+||||||||+|++.+|
T Consensus       164 ~~~LD~lLgGGI~~Gei~~I~G~sGsGKTTLl~~la  199 (400)
T 3lda_A          164 SKNLDTLLGGGVETGSITELFGEFRTGKSQLCHTLA  199 (400)
T ss_dssp             CHHHHHHTTTSEETTSEEEEEESTTSSHHHHHHHHH
T ss_pred             ChhHHHHhcCCcCCCcEEEEEcCCCCChHHHHHHHH
Confidence            34444444  45555559999999999999999765

>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=96.51  E-value=0.00095  Score=56.92  Aligned_cols=31  Identities=10%  Similarity=0.169  Sum_probs=25.9

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc-cceee
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT-TAAFI  222 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l-~~~~~  222 (245)
                      .+.-|.|.|++|+|||++++.|+..+ +..++
T Consensus        23 ~~~~I~ieG~~GsGKST~~~~L~~~l~~~~~i   54 (263)
T 1p5z_B           23 RIKKISIEGNIAAGKSTFVNILKQLCEDWEVV   54 (263)
T ss_dssp             CCEEEEEECSTTSSHHHHHTTTGGGCTTEEEE
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHhcCCCEEE
Confidence            34458899999999999999999998 55555

>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=96.50  E-value=0.001  Score=60.31  Aligned_cols=33  Identities=18%  Similarity=0.293  Sum_probs=25.7

Q ss_pred             hhhccCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          186 KQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       186 ~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      ..+.+.++..+++.||+|+|||++.++++..+.
T Consensus       129 ~~l~~~~g~~i~ivG~~GsGKTTll~~l~~~~~  161 (372)
T 2ewv_A          129 LELCHRKMGLILVTGPTGSGKSTTIASMIDYIN  161 (372)
T ss_dssp             HHHTTSSSEEEEEECSSSSSHHHHHHHHHHHHH
T ss_pred             HHHhhcCCCEEEEECCCCCCHHHHHHHHHhhcC
Confidence            344344445589999999999999999998763

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=96.49  E-value=0.0012  Score=62.88  Aligned_cols=40  Identities=25%  Similarity=0.303  Sum_probs=31.2

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhccc----ceeeeechhHHHH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTT----AAFIRVVGSEFVQ  231 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~----~~~~~v~~s~l~~  231 (245)
                      .+..+.|.||+|+|||+++++||..++    ..+..+++..+..
T Consensus       368 ~G~iI~LiG~sGSGKSTLar~La~~L~~~~G~~i~~lDgD~~~~  411 (552)
T 3cr8_A          368 QGFTVFFTGLSGAGKSTLARALAARLMEMGGRCVTLLDGDIVRR  411 (552)
T ss_dssp             SCEEEEEEESSCHHHHHHHHHHHHHHHTTCSSCEEEESSHHHHH
T ss_pred             cceEEEEECCCCChHHHHHHHHHHhhcccCCceEEEECCcHHHH
Confidence            344588999999999999999999885    3455577776654

>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=96.45  E-value=0.0016  Score=57.11  Aligned_cols=25  Identities=16%  Similarity=0.205  Sum_probs=22.0

Q ss_pred             cceeeecCCCCchHHHHHHHHhccc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      .-+.|.||+|+|||++++.|+..++
T Consensus        81 ~iigI~G~~GsGKSTl~~~L~~~l~  105 (308)
T 1sq5_A           81 YIISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3378999999999999999999765

>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=96.43  E-value=0.00086  Score=53.55  Aligned_cols=24  Identities=21%  Similarity=0.267  Sum_probs=20.9

Q ss_pred             ceeeecCCCCchHHHHHHHHhccc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      -.+|+||+|+|||++.+||+-.++
T Consensus        28 ~~~i~G~NGsGKStll~ai~~~l~   51 (182)
T 3kta_A           28 FTAIVGANGSGKSNIGDAILFVLG   51 (182)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHTT
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHc
Confidence            367999999999999999987653

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=96.43  E-value=0.0053  Score=55.01  Aligned_cols=46  Identities=17%  Similarity=0.153  Sum_probs=31.7

Q ss_pred             CCcHHHHhhh-ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeee
Q 025979          179 LTHHELYKQI-GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRV  224 (245)
Q Consensus       179 ~~~~~~~~~~-g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v  224 (245)
                      ...+++..-+ |+.+..-+++.|+||+|||++|..+|..+   +.++..+
T Consensus        31 TG~~~LD~~~gGl~~G~LiiIaG~pG~GKTt~al~ia~~~a~~g~~Vl~f   80 (338)
T 4a1f_A           31 TGFVQLDNYTSGFNKGSLVIIGARPSMGKTSLMMNMVLSALNDDRGVAVF   80 (338)
T ss_dssp             CSCHHHHHHHCSBCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCEEEEE
T ss_pred             CCChHHHHHhcCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            3344444443 46665559999999999999999998764   4454444

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=96.42  E-value=0.0014  Score=59.18  Aligned_cols=24  Identities=33%  Similarity=0.488  Sum_probs=21.5

Q ss_pred             ceeeecCCCCchHHHHHHHHhccc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      -+++.||+|+|||++.+++++.+.
T Consensus       125 ~i~I~GptGSGKTTlL~~l~g~~~  148 (356)
T 3jvv_A          125 LVLVTGPTGSGKSTTLAAMLDYLN  148 (356)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHhccc
Confidence            488999999999999999998763

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=96.41  E-value=0.002  Score=59.64  Aligned_cols=37  Identities=19%  Similarity=0.304  Sum_probs=28.1

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc----cceeeeec
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT----TAAFIRVV  225 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l----~~~~~~v~  225 (245)
                      |+.++.-+++.||||+|||++|..+|..+    |.+++.++
T Consensus       199 Gl~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s  239 (454)
T 2r6a_A          199 GFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFS  239 (454)
T ss_dssp             SBCTTCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEE
T ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEE
Confidence            56666669999999999999999988754    43555544

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=96.40  E-value=0.0013  Score=58.09  Aligned_cols=27  Identities=33%  Similarity=0.508  Sum_probs=23.2

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+++-+++.||+|+|||+++..+|..+
T Consensus       102 ~~~~vi~ivG~~GsGKTTl~~~LA~~l  128 (306)
T 1vma_A          102 EPPFVIMVVGVNGTGKTTSCGKLAKMF  128 (306)
T ss_dssp             SSCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCeEEEEEcCCCChHHHHHHHHHHHH
Confidence            345558999999999999999999876

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=96.38  E-value=0.0012  Score=59.60  Aligned_cols=27  Identities=26%  Similarity=0.389  Sum_probs=23.2

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-++|.||+|+|||++++.||..+
T Consensus       155 ~~g~vi~lvG~nGsGKTTll~~Lag~l  181 (359)
T 2og2_A          155 RKPAVIMIVGVNGGGKTTSLGKLAHRL  181 (359)
T ss_dssp             SSSEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCeEEEEEcCCCChHHHHHHHHHhhc
Confidence            344558999999999999999999876

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=96.38  E-value=0.0018  Score=52.93  Aligned_cols=25  Identities=32%  Similarity=0.489  Sum_probs=22.2

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ..+|+||.||+|+|||++|.++...
T Consensus        15 ~G~gvli~G~SGaGKStlal~L~~r   39 (181)
T 3tqf_A           15 DKMGVLITGEANIGKSELSLALIDR   39 (181)
T ss_dssp             TTEEEEEEESSSSSHHHHHHHHHHT
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHc
Confidence            3578999999999999999999874

>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=96.36  E-value=0.0015  Score=55.34  Aligned_cols=28  Identities=29%  Similarity=0.300  Sum_probs=23.6

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.+.|+...
T Consensus        28 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   55 (237)
T 2cbz_A           28 IPEGALVAVVGQVGCGKSSLLSALLAEM   55 (237)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHHHHTTCS
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3444458899999999999999999876

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=96.34  E-value=0.0022  Score=59.16  Aligned_cols=37  Identities=19%  Similarity=0.223  Sum_probs=27.7

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc----cceeeeec
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT----TAAFIRVV  225 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l----~~~~~~v~  225 (245)
                      |+.++.-+++.||||+|||++|..+|...    +.+++.++
T Consensus       196 Gl~~G~l~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~s  236 (444)
T 2q6t_A          196 TLGPGSLNIIAARPAMGKTAFALTIAQNAALKEGVGVGIYS  236 (444)
T ss_dssp             CCCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEE
T ss_pred             CcCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEE
Confidence            46665569999999999999999888654    44555554

>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=96.34  E-value=0.0016  Score=55.16  Aligned_cols=27  Identities=22%  Similarity=0.401  Sum_probs=23.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.+.|+...
T Consensus        29 ~~Ge~~~iiG~nGsGKSTLl~~l~Gl~   55 (235)
T 3tif_A           29 KEGEFVSIMGPSGSGKSTMLNIIGCLD   55 (235)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            344448899999999999999999876

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=96.30  E-value=0.0014  Score=55.03  Aligned_cols=27  Identities=22%  Similarity=0.252  Sum_probs=22.9

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.+.++...
T Consensus        28 ~~Ge~~~iiG~nGsGKSTLl~~l~Gl~   54 (224)
T 2pcj_A           28 KKGEFVSIIGASGSGKSTLLYILGLLD   54 (224)
T ss_dssp             ETTCEEEEEECTTSCHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            344448899999999999999999876

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=96.30  E-value=0.0024  Score=56.84  Aligned_cols=24  Identities=13%  Similarity=0.185  Sum_probs=21.5

Q ss_pred             ceeeecCCCCchHHHHHHHHhccc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      -+.+.||+|||||++++.|+..++
T Consensus        94 iigI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           94 IIGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhc
Confidence            377999999999999999998764

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=96.28  E-value=0.0019  Score=56.95  Aligned_cols=25  Identities=32%  Similarity=0.344  Sum_probs=21.8

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.-+.|.||+|||||++++.+|..+
T Consensus       102 g~vi~lvG~nGsGKTTll~~Lagll  126 (304)
T 1rj9_A          102 GRVVLVVGVNGVGKTTTIAKLGRYY  126 (304)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHH
Confidence            3448899999999999999999765

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=96.28  E-value=0.0037  Score=59.05  Aligned_cols=47  Identities=19%  Similarity=0.163  Sum_probs=36.8

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhc
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ..++|-+...+.|.+.+...           -...+-++++||+|+|||+||+.+++.
T Consensus       124 ~~~vGR~~~l~~L~~~L~~~-----------~~~~~~v~I~G~~GiGKTtLa~~~~~~  170 (591)
T 1z6t_A          124 VVFVTRKKLVNAIQQKLSKL-----------KGEPGWVTIHGMAGCGKSVLAAEAVRD  170 (591)
T ss_dssp             SSCCCCHHHHHHHHHHHTTS-----------TTSCEEEEEECCTTSSHHHHHHHHHCC
T ss_pred             CeecccHHHHHHHHHHHhcc-----------cCCCceEEEEcCCCCCHHHHHHHHHhc
Confidence            46889999999998887541           012345899999999999999999764

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=96.28  E-value=0.0018  Score=55.74  Aligned_cols=27  Identities=15%  Similarity=0.320  Sum_probs=22.9

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.++|+..+
T Consensus        30 ~~Ge~~~liG~nGsGKSTLlk~l~Gl~   56 (262)
T 1b0u_A           30 RAGDVISIIGSSGSGKSTFLRCINFLE   56 (262)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            334448899999999999999999876

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=96.26  E-value=0.0014  Score=61.66  Aligned_cols=25  Identities=32%  Similarity=0.428  Sum_probs=22.0

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.-++|.||+|+|||++++.||..+
T Consensus       293 GeVI~LVGpNGSGKTTLl~~LAgll  317 (503)
T 2yhs_A          293 PFVILMVGVNGVGKTTTIGKLARQF  317 (503)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCcccHHHHHHHHHHHh
Confidence            3448899999999999999999876

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=96.25  E-value=0.002  Score=56.93  Aligned_cols=25  Identities=16%  Similarity=0.130  Sum_probs=21.7

Q ss_pred             cceeeecCCCCchHHHHHHHHhccc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      .-+.+.||+|+|||+|++.|+..+.
T Consensus        91 ~ivgI~G~sGsGKSTL~~~L~gll~  115 (312)
T 3aez_A           91 FIIGVAGSVAVGKSTTARVLQALLA  115 (312)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             EEEEEECCCCchHHHHHHHHHhhcc
Confidence            3378999999999999999998763

>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=96.25  E-value=0.0029  Score=67.36  Aligned_cols=47  Identities=26%  Similarity=0.305  Sum_probs=35.8

Q ss_pred             cHHHHhhh---ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechh
Q 025979          181 HHELYKQI---GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       181 ~~~~~~~~---g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      .+++..-+   |+.++..++++||||+|||+||..+|..+   +.+++.++..
T Consensus       717 ~~eLD~lLg~GGl~~G~lVlI~G~PG~GKTtLal~lA~~aa~~g~~VlyiS~E  769 (1706)
T 3cmw_A          717 SLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAE  769 (1706)
T ss_dssp             CHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECTT
T ss_pred             cHHHHHHhccCCcCCCceEEEECCCCCCcHHHHHHHHHHHHHcCCCeEEEecc
Confidence            35555555   47788889999999999999999998876   3356666654

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A

Probab=96.23  E-value=0.0034  Score=56.60  Aligned_cols=60  Identities=20%  Similarity=0.297  Sum_probs=42.7

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccce--eeeechhHH
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAA--FIRVVGSEF  229 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~--~~~v~~s~l  229 (245)
                      .++.|......++.+.+...       .    .....+|++|++||||+++|+++....+..  |+.++++.+
T Consensus       129 ~~~ig~s~~~~~~~~~~~~~-------a----~~~~~vli~GesGtGKe~lAr~ih~~s~r~~~fv~vnc~~~  190 (368)
T 3dzd_A          129 IEFVGEHPKILEIKRLIPKI-------A----KSKAPVLITGESGTGKEIVARLIHRYSGRKGAFVDLNCASI  190 (368)
T ss_dssp             CCCCCCSHHHHHHHHHHHHH-------H----TSCSCEEEECCTTSSHHHHHHHHHHHHCCCSCEEEEESSSS
T ss_pred             ccccccchHHHHHHhhhhhh-------h----ccchhheEEeCCCchHHHHHHHHHHhccccCCcEEEEcccC
Confidence            35677777666666655431       1    123449999999999999999998776433  999988753

>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=96.19  E-value=0.0017  Score=55.61  Aligned_cols=26  Identities=27%  Similarity=0.503  Sum_probs=22.5

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++.-+.+.||+|+|||+|.+.|+..+
T Consensus        32 ~Ge~~~liG~nGsGKSTLlk~l~Gl~   57 (257)
T 1g6h_A           32 KGDVTLIIGPNGSGKSTLINVITGFL   57 (257)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            34448899999999999999999876

>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=96.19  E-value=0.0024  Score=59.12  Aligned_cols=26  Identities=35%  Similarity=0.409  Sum_probs=22.9

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.++|+||||+|||+++..+|..+
T Consensus        98 ~~~vI~ivG~~GvGKTTla~~La~~l  123 (432)
T 2v3c_C           98 KQNVILLVGIQGSGKTTTAAKLARYI  123 (432)
T ss_dssp             SCCCEEEECCSSSSTTHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            34569999999999999999999876

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=96.18  E-value=0.0023  Score=54.46  Aligned_cols=27  Identities=26%  Similarity=0.521  Sum_probs=23.6

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.+ .-+.+.||+|+|||+|.+.++...
T Consensus        22 i~~-e~~~liG~nGsGKSTLl~~l~Gl~   48 (240)
T 2onk_A           22 MGR-DYCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             ECS-SEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             ECC-EEEEEECCCCCCHHHHHHHHhCCC
Confidence            445 568899999999999999999876

>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=96.17  E-value=0.0043  Score=57.12  Aligned_cols=22  Identities=32%  Similarity=0.504  Sum_probs=20.7

Q ss_pred             eeeecCCCCchHHHHHHHHhcc
Q 025979          196 VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +++.||+|+|||++.++++..+
T Consensus       170 i~I~GpnGSGKTTlL~allg~l  191 (418)
T 1p9r_A          170 ILVTGPTGSGKSTTLYAGLQEL  191 (418)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHhhc
Confidence            7899999999999999999876

>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=96.17  E-value=0.0022  Score=55.32  Aligned_cols=27  Identities=22%  Similarity=0.432  Sum_probs=23.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.|.||+|+|||+|.+.|+..+
T Consensus        48 ~~Gei~~liG~NGsGKSTLlk~l~Gl~   74 (263)
T 2olj_A           48 REGEVVVVIGPSGSGKSTFLRCLNLLE   74 (263)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEEcCCCCcHHHHHHHHHcCC
Confidence            344448899999999999999999876

>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=96.16  E-value=0.0021  Score=54.58  Aligned_cols=27  Identities=22%  Similarity=0.432  Sum_probs=23.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.+.|+...
T Consensus        26 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   52 (243)
T 1mv5_A           26 QPNSIIAFAGPSGGGKSTIFSLLERFY   52 (243)
T ss_dssp             CTTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            344448899999999999999999876

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=96.16  E-value=0.0023  Score=56.17  Aligned_cols=26  Identities=27%  Similarity=0.487  Sum_probs=22.2

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++-++|.||+|+|||+++..+|..+
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~l  129 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAIS  129 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            34558899999999999999999765

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=96.14  E-value=0.002  Score=72.09  Aligned_cols=36  Identities=31%  Similarity=0.381  Sum_probs=32.6

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccceeeeechhH
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSE  228 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~  228 (245)
                      ..|..+.||+|||||.+++.+|+.+|.+++.+++++
T Consensus       604 ~~gg~~~GPaGtGKTet~k~La~~lgr~~~vfnC~~  639 (3245)
T 3vkg_A          604 RMGGNPFGPAGTGKTETVKALGSQLGRFVLVFCCDE  639 (3245)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHTTCCEEEEECSS
T ss_pred             cCCCCCCCCCCCCHHHHHHHHHHHhCCeEEEEeCCC
Confidence            456789999999999999999999999999998764

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=96.13  E-value=0.0023  Score=55.36  Aligned_cols=27  Identities=33%  Similarity=0.502  Sum_probs=23.2

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.|.||+|+|||+|.+.|+..+
T Consensus        43 ~~Ge~~~i~G~nGsGKSTLlk~l~Gl~   69 (271)
T 2ixe_A           43 YPGKVTALVGPNGSGKSTVAALLQNLY   69 (271)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            344448899999999999999999876

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=96.13  E-value=0.0021  Score=54.12  Aligned_cols=27  Identities=22%  Similarity=0.314  Sum_probs=23.1

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.+.|+..+
T Consensus        32 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   58 (229)
T 2pze_A           32 ERGQLLAVAGSTGAGKTSLLMMIMGEL   58 (229)
T ss_dssp             ETTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            344458899999999999999999876

>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=96.13  E-value=0.0028  Score=51.37  Aligned_cols=26  Identities=27%  Similarity=0.135  Sum_probs=22.2

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ...-+.|.||+|+|||++++.++..+
T Consensus         5 ~~~~i~i~G~sGsGKTTl~~~l~~~l   30 (174)
T 1np6_A            5 MIPLLAFAAWSGTGKTTLLKKLIPAL   30 (174)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cceEEEEEeCCCCCHHHHHHHHHHhc
Confidence            34558899999999999999998765

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=96.13  E-value=0.0024  Score=54.96  Aligned_cols=27  Identities=26%  Similarity=0.347  Sum_probs=23.2

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.+.|+..+
T Consensus        44 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   70 (260)
T 2ghi_A           44 PSGTTCALVGHTGSGKSTIAKLLYRFY   70 (260)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhccC
Confidence            344458999999999999999999876

>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=96.12  E-value=0.0036  Score=60.28  Aligned_cols=32  Identities=31%  Similarity=0.539  Sum_probs=22.5

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc----cceeeeech
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT----TAAFIRVVG  226 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l----~~~~~~v~~  226 (245)
                      -++++||||||||+++..++..+    +..++.+..
T Consensus       197 ~~li~GppGTGKT~~~~~~i~~l~~~~~~~ilv~a~  232 (624)
T 2gk6_A          197 LSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAP  232 (624)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHTSSSCCEEEEES
T ss_pred             CeEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEeC
Confidence            47899999999999877666543    344444443

>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=96.11  E-value=0.0024  Score=53.40  Aligned_cols=27  Identities=33%  Similarity=0.452  Sum_probs=23.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.+.++..+
T Consensus        33 ~~Ge~~~iiG~NGsGKSTLlk~l~Gl~   59 (214)
T 1sgw_A           33 EKGNVVNFHGPNGIGKTTLLKTISTYL   59 (214)
T ss_dssp             ETTCCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            344448899999999999999999876

>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=96.09  E-value=0.0022  Score=58.06  Aligned_cols=25  Identities=28%  Similarity=0.477  Sum_probs=22.0

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..-+.|.||+|||||+|.+.||...
T Consensus        30 Ge~~~llGpsGsGKSTLLr~iaGl~   54 (359)
T 3fvq_A           30 GEILFIIGASGCGKTTLLRCLAGFE   54 (359)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCchHHHHHHHHhcCC
Confidence            3338899999999999999999876

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=96.09  E-value=0.0025  Score=56.80  Aligned_cols=26  Identities=31%  Similarity=0.429  Sum_probs=22.5

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++.-+.|.||+|+|||++++.||..+
T Consensus       128 ~g~vi~lvG~nGaGKTTll~~Lag~l  153 (328)
T 3e70_C          128 KPYVIMFVGFNGSGKTTTIAKLANWL  153 (328)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            34458899999999999999999866

>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=96.09  E-value=0.003  Score=54.53  Aligned_cols=26  Identities=31%  Similarity=0.584  Sum_probs=22.4

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .++.-+.|.||+|+|||+|.+.|+..
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            34444889999999999999999996

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=96.09  E-value=0.0029  Score=58.63  Aligned_cols=25  Identities=36%  Similarity=0.448  Sum_probs=21.9

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      |+-++|.||||+|||+++..+|..+
T Consensus        97 ~~vI~lvG~~GsGKTTt~~kLA~~l  121 (433)
T 3kl4_A           97 PFIIMLVGVQGSGKTTTAGKLAYFY  121 (433)
T ss_dssp             SEEEEECCCTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4558899999999999999999766

>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=96.09  E-value=0.0022  Score=54.35  Aligned_cols=26  Identities=35%  Similarity=0.371  Sum_probs=22.5

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++.-+.+.||+|+|||+|.+.|+..+
T Consensus        31 ~Ge~~~l~G~nGsGKSTLl~~l~Gl~   56 (240)
T 1ji0_A           31 RGQIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            33448899999999999999999876

>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=96.07  E-value=0.0023  Score=55.63  Aligned_cols=26  Identities=19%  Similarity=0.222  Sum_probs=22.5

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++.-+.|.||+|+|||+|.++|+..+
T Consensus        33 ~Ge~~~iiGpnGsGKSTLl~~l~Gl~   58 (275)
T 3gfo_A           33 RGEVTAILGGNGVGKSTLFQNFNGIL   58 (275)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHcCC
Confidence            33448899999999999999999876

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=96.07  E-value=0.0024  Score=53.10  Aligned_cols=24  Identities=46%  Similarity=0.517  Sum_probs=21.0

Q ss_pred             CcceeeecCCCCchHHHHHHHHhc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      +.-+.+.||+|+|||+|.++++..
T Consensus        22 Ge~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           22 NTIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             CSEEEEECCTTSSTTHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            344889999999999999999975

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=96.06  E-value=0.0036  Score=57.96  Aligned_cols=44  Identities=25%  Similarity=0.214  Sum_probs=31.0

Q ss_pred             HHHHhhh-ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeec
Q 025979          182 HELYKQI-GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVV  225 (245)
Q Consensus       182 ~~~~~~~-g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~  225 (245)
                      +++..-+ |+.++.-+++.|+||+|||++|-.+|...   |.+++.++
T Consensus       185 ~~LD~~lgGl~~G~liiIaG~pG~GKTtlal~ia~~~a~~g~~vl~fS  232 (444)
T 3bgw_A          185 TELDRMTYGYKRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHS  232 (444)
T ss_dssp             HHHHHHHSSBCSSCEEEEEECSSSSHHHHHHHHHHHHHHTTCEEEEEC
T ss_pred             HHHHhhcCCCCCCcEEEEEeCCCCChHHHHHHHHHHHHHcCCEEEEEE
Confidence            4443333 46555559999999999999999888655   45555554

>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=96.06  E-value=0.0023  Score=54.55  Aligned_cols=27  Identities=22%  Similarity=0.358  Sum_probs=23.1

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.|.||+|+|||+|.+.|+..+
T Consensus        33 ~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   59 (247)
T 2ff7_A           33 KQGEVIGIVGRSGSGKSTLTKLIQRFY   59 (247)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            344448899999999999999999976

>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=96.06  E-value=0.0024  Score=54.66  Aligned_cols=36  Identities=31%  Similarity=0.443  Sum_probs=26.5

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcccc-eeeeech
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTTA-AFIRVVG  226 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~~-~~~~v~~  226 (245)
                      .++.-+.+.||+|+|||+|.+.++..+.. --+.+++
T Consensus        24 ~~Ge~~~liG~NGsGKSTLlk~l~Gl~~p~G~i~~~g   60 (249)
T 2qi9_C           24 RAGEILHLVGPNGAGKSTLLARMAGMTSGKGSIQFAG   60 (249)
T ss_dssp             ETTCEEEEECCTTSSHHHHHHHHTTSSCCEEEEEETT
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhCCCCCCeEEEECC
Confidence            34444889999999999999999987632 3344444

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=96.05  E-value=0.0038  Score=59.40  Aligned_cols=39  Identities=23%  Similarity=0.238  Sum_probs=30.6

Q ss_pred             cceeeecCCCCchHHHHHHHHhccc---ceeeeechhHHHHH
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTT---AAFIRVVGSEFVQK  232 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~---~~~~~v~~s~l~~~  232 (245)
                      .-++|.|+||+|||++|+.|+..++   .++..+++..+...
T Consensus       373 ~~I~l~G~~GsGKSTia~~La~~L~~~G~~~~~ld~D~ir~~  414 (546)
T 2gks_A          373 FCVWLTGLPCAGKSTIAEILATMLQARGRKVTLLDGDVVRTH  414 (546)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECHHHHHHH
T ss_pred             eEEEccCCCCCCHHHHHHHHHHHhhhcCCeEEEECchHhhhh
Confidence            4488999999999999999999875   45666776665443

>1g8f_A Sulfate adenylyltransferase; alpha-beta protein, beta-barrel, rossmann-fold, kinase fold; 1.95A {Saccharomyces cerevisiae} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1g8g_A* 1g8h_A* 1j70_A 1jec_A 1jed_A* 1jee_A*

Probab=96.04  E-value=0.0028  Score=59.87  Aligned_cols=26  Identities=12%  Similarity=0.059  Sum_probs=23.5

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ..+.|.|++|||||++|++||..++.
T Consensus       396 ~~I~l~GlsGsGKSTIa~~La~~L~~  421 (511)
T 1g8f_A          396 FSIVLGNSLTVSREQLSIALLSTFLQ  421 (511)
T ss_dssp             EEEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             eEEEecccCCCCHHHHHHHHHHHHHH
Confidence            34889999999999999999999975

>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=96.04  E-value=0.0028  Score=54.43  Aligned_cols=27  Identities=26%  Similarity=0.363  Sum_probs=23.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.|.||+|+|||+|.+.|+...
T Consensus        39 ~~Gei~~l~G~NGsGKSTLlk~l~Gl~   65 (256)
T 1vpl_A           39 EEGEIFGLIGPNGAGKTTTLRIISTLI   65 (256)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            344448899999999999999999876

>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=96.04  E-value=0.0026  Score=54.30  Aligned_cols=26  Identities=35%  Similarity=0.487  Sum_probs=22.3

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .++.-+.+.||+|+|||+|.+.|+..
T Consensus        27 ~~Ge~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           27 PKGEVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHHTC
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            34444889999999999999999996

>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=96.02  E-value=0.0026  Score=57.46  Aligned_cols=26  Identities=35%  Similarity=0.344  Sum_probs=22.4

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++.-+.|.||+|||||+|.+.||...
T Consensus        28 ~Ge~~~llGpnGsGKSTLLr~iaGl~   53 (359)
T 2yyz_A           28 DGEFVALLGPSGCGKTTTLLMLAGIY   53 (359)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEEcCCCchHHHHHHHHHCCC
Confidence            33448899999999999999999876

>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=96.02  E-value=0.0027  Score=54.85  Aligned_cols=27  Identities=26%  Similarity=0.427  Sum_probs=22.9

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.|.||+|+|||+|.++|+..+
T Consensus        35 ~~Ge~~~liG~nGsGKSTLl~~l~Gl~   61 (266)
T 4g1u_C           35 ASGEMVAIIGPNGAGKSTLLRLLTGYL   61 (266)
T ss_dssp             ETTCEEEEECCTTSCHHHHHHHHTSSS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            344448899999999999999999876

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=96.02  E-value=0.006  Score=48.48  Aligned_cols=25  Identities=24%  Similarity=0.522  Sum_probs=21.5

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ...++++|++|+|||+|..++....
T Consensus        48 ~~~i~vvG~~g~GKSsll~~l~~~~   72 (193)
T 2ged_A           48 QPSIIIAGPQNSGKTSLLTLLTTDS   72 (193)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3459999999999999999998653

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=96.02  E-value=0.0028  Score=54.58  Aligned_cols=27  Identities=30%  Similarity=0.442  Sum_probs=23.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|.+.|+..+
T Consensus        31 ~~Ge~~~liG~nGsGKSTLl~~i~Gl~   57 (266)
T 2yz2_A           31 NEGECLLVAGNTGSGKSTLLQIVAGLI   57 (266)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            344448899999999999999999876

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=96.02  E-value=0.0027  Score=57.46  Aligned_cols=26  Identities=31%  Similarity=0.434  Sum_probs=22.4

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++.-+.|.||+|||||+|.+.||...
T Consensus        28 ~Ge~~~llGpnGsGKSTLLr~iaGl~   53 (362)
T 2it1_A           28 DGEFMALLGPSGSGKSTLLYTIAGIY   53 (362)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCchHHHHHHHHhcCC
Confidence            33448899999999999999999876

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=96.01  E-value=0.0026  Score=55.41  Aligned_cols=27  Identities=30%  Similarity=0.397  Sum_probs=23.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.|.||+|+|||+|.+.|+..+
T Consensus        45 ~~Ge~~~liG~NGsGKSTLlk~l~Gl~   71 (279)
T 2ihy_A           45 AKGDKWILYGLNGAGKTTLLNILNAYE   71 (279)
T ss_dssp             ETTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            344448899999999999999999876

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=96.00  E-value=0.0039  Score=55.31  Aligned_cols=35  Identities=26%  Similarity=0.210  Sum_probs=26.6

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc---cceeeeec
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVV  225 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~  225 (245)
                      .+++-+++.||+|+|||+++..+|..+   +..++.++
T Consensus       103 ~~~~vI~ivG~~G~GKTT~~~~LA~~l~~~g~kVllid  140 (320)
T 1zu4_A          103 NRLNIFMLVGVNGTGKTTSLAKMANYYAELGYKVLIAA  140 (320)
T ss_dssp             TSCEEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            345568999999999999999999876   44444443

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=96.00  E-value=0.0037  Score=58.08  Aligned_cols=26  Identities=31%  Similarity=0.405  Sum_probs=22.4

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +|.-+++.||||+|||+++..+|..+
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~~l  124 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLARYF  124 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHHHH
Confidence            35669999999999999999998765

>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=96.00  E-value=0.0028  Score=57.79  Aligned_cols=26  Identities=31%  Similarity=0.505  Sum_probs=22.4

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++.-+.|.||+|||||+|.+.||...
T Consensus        28 ~Ge~~~llGpsGsGKSTLLr~iaGl~   53 (381)
T 3rlf_A           28 EGEFVVFVGPSGCGKSTLLRMIAGLE   53 (381)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEEcCCCchHHHHHHHHHcCC
Confidence            33348899999999999999999876

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=95.98  E-value=0.0027  Score=59.94  Aligned_cols=27  Identities=19%  Similarity=0.272  Sum_probs=24.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..+.++++.||+|+|||++.++++..+
T Consensus       258 ~~g~~i~I~GptGSGKTTlL~aL~~~i  284 (511)
T 2oap_1          258 EHKFSAIVVGETASGKTTTLNAIMMFI  284 (511)
T ss_dssp             HTTCCEEEEESTTSSHHHHHHHHGGGS
T ss_pred             hCCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            345669999999999999999999877

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=95.97  E-value=0.0031  Score=50.75  Aligned_cols=23  Identities=30%  Similarity=0.491  Sum_probs=20.4

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++|.||+|+|||+|.+.++...
T Consensus        31 kv~lvG~~g~GKSTLl~~l~~~~   53 (191)
T 1oix_A           31 KVVLIGDSGVGKSNLLSRFTRNE   53 (191)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            38999999999999999998754

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=95.96  E-value=0.0026  Score=57.47  Aligned_cols=26  Identities=35%  Similarity=0.503  Sum_probs=22.5

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +..-+.|.||+|||||+|.+.||...
T Consensus        40 ~Ge~~~llGpnGsGKSTLLr~iaGl~   65 (355)
T 1z47_A           40 EGEMVGLLGPSGSGKTTILRLIAGLE   65 (355)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            34448899999999999999999876

>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=95.96  E-value=0.0024  Score=57.52  Aligned_cols=26  Identities=27%  Similarity=0.549  Sum_probs=22.4

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++.-+.|.||+|||||+|.+.||...
T Consensus        25 ~Ge~~~llGpnGsGKSTLLr~iaGl~   50 (348)
T 3d31_A           25 SGEYFVILGPTGAGKTLFLELIAGFH   50 (348)
T ss_dssp             TTCEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCccHHHHHHHHHcCC
Confidence            33448899999999999999999876

>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=95.96  E-value=0.0033  Score=57.11  Aligned_cols=26  Identities=31%  Similarity=0.466  Sum_probs=22.4

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+.-+.|.||+|||||+|.+.||...
T Consensus        36 ~Ge~~~llGpnGsGKSTLLr~iaGl~   61 (372)
T 1v43_A           36 DGEFLVLLGPSGCGKTTTLRMIAGLE   61 (372)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHHcCC
Confidence            33448899999999999999999876

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=95.95  E-value=0.0026  Score=57.29  Aligned_cols=29  Identities=31%  Similarity=0.503  Sum_probs=24.9

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      +.+...+++.||+|+|||+++++++....
T Consensus       172 i~~G~~i~ivG~sGsGKSTll~~l~~~~~  200 (361)
T 2gza_A          172 VQLERVIVVAGETGSGKTTLMKALMQEIP  200 (361)
T ss_dssp             HHTTCCEEEEESSSSCHHHHHHHHHTTSC
T ss_pred             HhcCCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            44556699999999999999999998763

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=95.95  E-value=0.0028  Score=54.27  Aligned_cols=27  Identities=19%  Similarity=0.255  Sum_probs=22.8

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.|.||+|+|||+|.+.++..+
T Consensus        29 ~~Ge~~~l~G~nGsGKSTLl~~l~Gl~   55 (253)
T 2nq2_C           29 NKGDILAVLGQNGCGKSTLLDLLLGIH   55 (253)
T ss_dssp             ETTCEEEEECCSSSSHHHHHHHHTTSS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            344448899999999999999999875

>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=95.93  E-value=0.0033  Score=56.33  Aligned_cols=29  Identities=21%  Similarity=0.338  Sum_probs=24.7

Q ss_pred             CcceeeecCCCCchHHHHHHHHhccccee
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAF  221 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~  221 (245)
                      ...+.+.||+|+|||+|++.|+..+....
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~gl~~~~~  198 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAAVFNTTS  198 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTTCEE
T ss_pred             hCeEEEECCCCCCHHHHHHHHHHHhCCCc
Confidence            34589999999999999999999876543

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=95.89  E-value=0.005  Score=54.88  Aligned_cols=23  Identities=30%  Similarity=0.427  Sum_probs=20.4

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      -+.|.||||+|||+|.++++..+
T Consensus        57 ~v~i~G~~GaGKSTLl~~l~g~~   79 (337)
T 2qm8_A           57 RVGITGVPGVGKSTTIDALGSLL   79 (337)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhh
Confidence            38899999999999999998654

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=95.88  E-value=0.0062  Score=56.37  Aligned_cols=38  Identities=29%  Similarity=0.503  Sum_probs=27.8

Q ss_pred             cCCCcc--eeeecCCCCchHHHHHHHHhcccce--eeeechh
Q 025979          190 IDPPRG--VLLYGPPGTGKTMLAKAVANHTTAA--FIRVVGS  227 (245)
Q Consensus       190 ~~~~~g--vLl~GPPGtGKT~lAkalA~~l~~~--~~~v~~s  227 (245)
                      +..++|  +.|.||+|||||+|.+.||+.....  .+.+.+.
T Consensus       152 l~i~~Gq~~~IvG~sGsGKSTLl~~Iag~~~~~~G~i~~~G~  193 (438)
T 2dpy_A          152 LTVGRGQRMGLFAGSGVGKSVLLGMMARYTRADVIVVGLIGE  193 (438)
T ss_dssp             SCCBTTCEEEEEECTTSSHHHHHHHHHHHSCCSEEEEEEESC
T ss_pred             EEecCCCEEEEECCCCCCHHHHHHHHhcccCCCeEEEEEece
Confidence            344444  8899999999999999999987432  3444443

>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=95.86  E-value=0.0033  Score=57.05  Aligned_cols=26  Identities=31%  Similarity=0.477  Sum_probs=22.5

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++.-+.|.||+|||||+|.+.||...
T Consensus        28 ~Ge~~~llGpnGsGKSTLLr~iaGl~   53 (372)
T 1g29_1           28 DGEFMILLGPSGCGKTTTLRMIAGLE   53 (372)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCcHHHHHHHHHHcCC
Confidence            33448899999999999999999876

>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=95.85  E-value=0.0049  Score=50.20  Aligned_cols=24  Identities=25%  Similarity=0.547  Sum_probs=21.2

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..++|+|+||+|||+|..++....
T Consensus        13 ~~i~~~G~~g~GKTsl~~~l~~~~   36 (218)
T 1nrj_B           13 PSIIIAGPQNSGKTSLLTLLTTDS   36 (218)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCC
Confidence            459999999999999999998754

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=95.83  E-value=0.0041  Score=48.62  Aligned_cols=22  Identities=27%  Similarity=0.542  Sum_probs=20.0

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .+++.|+||+|||+|..++++.
T Consensus         5 ~v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            5 EIALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999999873

>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=95.82  E-value=0.0025  Score=56.75  Aligned_cols=36  Identities=22%  Similarity=0.397  Sum_probs=27.2

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhccc--ceeeeech
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTT--AAFIRVVG  226 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~--~~~~~v~~  226 (245)
                      .+...+++.||+|+|||++.++++....  ...+.+.+
T Consensus       169 ~~g~~v~i~G~~GsGKTTll~~l~g~~~~~~g~i~i~~  206 (330)
T 2pt7_A          169 AIGKNVIVCGGTGSGKTTYIKSIMEFIPKEERIISIED  206 (330)
T ss_dssp             HHTCCEEEEESTTSCHHHHHHHGGGGSCTTSCEEEEES
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCCcCCCcEEEECC
Confidence            3445699999999999999999999873  23444443

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=95.80  E-value=0.0038  Score=58.33  Aligned_cols=38  Identities=8%  Similarity=-0.036  Sum_probs=28.1

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc----cceeeeech
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT----TAAFIRVVG  226 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l----~~~~~~v~~  226 (245)
                      |+.+..-+++.||||+|||++|..+|...    +.+++.++.
T Consensus       238 Gl~~G~l~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s~  279 (503)
T 1q57_A          238 GARGGEVIMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAML  279 (503)
T ss_dssp             CCCTTCEEEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEES
T ss_pred             ccCCCeEEEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEec
Confidence            45555559999999999999999888654    445555543

>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=95.75  E-value=0.0027  Score=57.15  Aligned_cols=26  Identities=27%  Similarity=0.464  Sum_probs=22.3

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++.-+.|.||+|||||+|.+.||...
T Consensus        30 ~Ge~~~llGpnGsGKSTLLr~iaGl~   55 (353)
T 1oxx_K           30 NGERFGILGPSGAGKTTFMRIIAGLD   55 (353)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            33448899999999999999999876

>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=95.74  E-value=0.006  Score=60.63  Aligned_cols=23  Identities=43%  Similarity=0.739  Sum_probs=18.5

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      -+++.||||||||+++..++..+
T Consensus       373 ~~lI~GppGTGKT~ti~~~i~~l  395 (800)
T 2wjy_A          373 LSLIQGPPGTGKTVTSATIVYHL  395 (800)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHH
Confidence            37899999999999877666543

>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=95.73  E-value=0.0043  Score=56.68  Aligned_cols=27  Identities=33%  Similarity=0.444  Sum_probs=22.9

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+..-+.|.||+|||||+|.+.||...
T Consensus        45 ~~Ge~~~llGpsGsGKSTLLr~iaGl~   71 (390)
T 3gd7_A           45 SPGQRVGLLGRTGSGKSTLLSAFLRLL   71 (390)
T ss_dssp             CTTCEEEEEESTTSSHHHHHHHHHTCS
T ss_pred             cCCCEEEEECCCCChHHHHHHHHhCCC
Confidence            344448999999999999999999865

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=95.73  E-value=0.004  Score=69.69  Aligned_cols=37  Identities=30%  Similarity=0.483  Sum_probs=27.0

Q ss_pred             CCCcceeeecCCCCchHHHHHH-HHhcccceeeeechh
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKA-VANHTTAAFIRVVGS  227 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAka-lA~~l~~~~~~v~~s  227 (245)
                      ...+.+||+||||||||.++.. +++..+.+++.++.|
T Consensus      1302 ~~~~pvLL~GptGtGKT~li~~~L~~l~~~~~~~infS 1339 (3245)
T 3vkg_A         1302 SEHRPLILCGPPGSGKTMTLTSTLRAFPDFEVVSLNFS 1339 (3245)
T ss_dssp             HTTCCCEEESSTTSSHHHHHHHHGGGCTTEEEEEECCC
T ss_pred             HCCCcEEEECCCCCCHHHHHHHHHHhCCCCceEEEEee
Confidence            3457799999999999977654 555556677777644

>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=95.73  E-value=0.0069  Score=57.22  Aligned_cols=44  Identities=14%  Similarity=0.092  Sum_probs=34.0

Q ss_pred             CcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHh
Q 025979          162 GGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       162 ~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      .|-+..+++|.+.+...          +-...+-+.++|++|+|||+||+.+++
T Consensus       131 ~GR~~~~~~l~~~L~~~----------~~~~~~vv~I~G~gGvGKTtLA~~v~~  174 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEM----------CDLDSFFLFLHGRAGSGKSVIASQALS  174 (549)
T ss_dssp             CCCHHHHHHHHHHHHHH----------TTSSSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcc----------cCCCceEEEEEcCCCCCHHHHHHHHHH
Confidence            48999899988887431          111235588999999999999999996

>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=95.72  E-value=0.0069  Score=58.21  Aligned_cols=24  Identities=33%  Similarity=0.439  Sum_probs=19.5

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +-+++.||||||||+++..+...+
T Consensus       165 ~~~vi~G~pGTGKTt~l~~ll~~l  188 (608)
T 1w36_D          165 RISVISGGPGTGKTTTVAKLLAAL  188 (608)
T ss_dssp             SEEEEECCTTSTHHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCHHHHHHHHHHHH
Confidence            458999999999999888776544

>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=95.72  E-value=0.0054  Score=49.61  Aligned_cols=21  Identities=24%  Similarity=0.431  Sum_probs=19.3

Q ss_pred             ceeeecCCCCchHHHHHHHHh
Q 025979          195 GVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~  215 (245)
                      .+++.|+||+|||+|..++..
T Consensus        27 ki~lvG~~~vGKSsLi~~l~~   47 (198)
T 1f6b_A           27 KLVFLGLDNAGKTTLLHMLKD   47 (198)
T ss_dssp             EEEEEEETTSSHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            499999999999999999975

>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=95.72  E-value=0.0051  Score=47.32  Aligned_cols=23  Identities=13%  Similarity=0.245  Sum_probs=20.4

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -.+++.|++|+|||+|..++...
T Consensus         6 ~~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            6 IKMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEEECcCCCCHHHHHHHHHcC
Confidence            35899999999999999999864

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=95.71  E-value=0.0042  Score=54.38  Aligned_cols=27  Identities=22%  Similarity=0.314  Sum_probs=22.8

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.|.||+|+|||+|.+.|+..+
T Consensus        62 ~~Ge~~~i~G~NGsGKSTLlk~l~Gl~   88 (290)
T 2bbs_A           62 ERGQLLAVAGSTGAGKTSLLMMIMGEL   88 (290)
T ss_dssp             CTTCEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            333448899999999999999999876

>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=95.69  E-value=0.0027  Score=51.35  Aligned_cols=27  Identities=22%  Similarity=0.316  Sum_probs=21.6

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .....++|.||||+|||+|.++++...
T Consensus        24 ~~~~~v~lvG~~g~GKSTLl~~l~g~~   50 (210)
T 1pui_A           24 DTGIEVAFAGRSNAGKSSALNTLTNQK   50 (210)
T ss_dssp             SCSEEEEEEECTTSSHHHHHTTTCCC-
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            344449999999999999999988644

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=95.69  E-value=0.0066  Score=54.45  Aligned_cols=27  Identities=22%  Similarity=0.416  Sum_probs=23.4

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      +..+.|.||+|+|||+|.+.|++....
T Consensus        71 Gq~~gIiG~nGaGKTTLl~~I~g~~~~   97 (347)
T 2obl_A           71 GQRIGIFAGSGVGKSTLLGMICNGASA   97 (347)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHHSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            344899999999999999999998753

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=95.65  E-value=0.0056  Score=57.06  Aligned_cols=28  Identities=25%  Similarity=0.280  Sum_probs=24.1

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+++.||+|+|||+|+|.|++..
T Consensus       135 i~~Ge~v~IvGpnGsGKSTLlr~L~Gl~  162 (460)
T 2npi_A          135 NFEGPRVVIVGGSQTGKTSLSRTLCSYA  162 (460)
T ss_dssp             SSSCCCEEEEESTTSSHHHHHHHHHHTT
T ss_pred             eCCCCEEEEECCCCCCHHHHHHHHhCcc
Confidence            4455559999999999999999999876

>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=95.63  E-value=0.0047  Score=58.17  Aligned_cols=39  Identities=26%  Similarity=0.277  Sum_probs=27.3

Q ss_pred             cCCCcceeeecCCCCchHHHHHH--HHhcc--cceeeeechhH
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKA--VANHT--TAAFIRVVGSE  228 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAka--lA~~l--~~~~~~v~~s~  228 (245)
                      +.++.-+++.||||+|||+|++.  ++...  +..-+.+++.+
T Consensus        36 i~~Ge~~~l~G~nGsGKSTL~~~~ll~Gl~~~~~g~i~v~g~~   78 (525)
T 1tf7_A           36 LPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEE   78 (525)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEESSS
T ss_pred             CCCCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEEEeC
Confidence            44556699999999999999999  44443  33445555543

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=95.62  E-value=0.0041  Score=54.97  Aligned_cols=28  Identities=25%  Similarity=0.517  Sum_probs=23.8

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|++.|+..+
T Consensus        77 i~~Ge~vaivG~sGsGKSTLl~ll~gl~  104 (306)
T 3nh6_A           77 VMPGQTLALVGPSGAGKSTILRLLFRFY  104 (306)
T ss_dssp             ECTTCEEEEESSSCHHHHHHHHHHTTSS
T ss_pred             EcCCCEEEEECCCCchHHHHHHHHHcCC
Confidence            3444559999999999999999999876

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=95.61  E-value=0.0051  Score=53.05  Aligned_cols=25  Identities=36%  Similarity=0.655  Sum_probs=22.0

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.-+.+.||+|+|||+|.+.|+..+
T Consensus        30 Ge~~~i~G~NGsGKSTLlk~l~Gl~   54 (263)
T 2pjz_A           30 GEKVIILGPNGSGKTTLLRAISGLL   54 (263)
T ss_dssp             SSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEEECCCCCCHHHHHHHHhCCC
Confidence            3448899999999999999999876

>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=95.57  E-value=0.0062  Score=46.61  Aligned_cols=23  Identities=26%  Similarity=0.446  Sum_probs=20.3

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ..+++.|++|+|||+|..++...
T Consensus         5 ~~i~v~G~~~~GKssl~~~l~~~   27 (168)
T 1u8z_A            5 HKVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            45899999999999999999753

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=95.57  E-value=0.0054  Score=51.83  Aligned_cols=24  Identities=21%  Similarity=0.210  Sum_probs=18.6

Q ss_pred             ceeeecCCCCchHHHHHHHHhccc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      -|.|.||+|+|||++++.|+..+.
T Consensus        27 ~I~~eG~~GsGKsT~~~~l~~~l~   50 (227)
T 3v9p_A           27 FITFEGIDGAGKTTHLQWFCDRLQ   50 (227)
T ss_dssp             EEEEECCC---CHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            378899999999999999999884

>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=95.56  E-value=0.0065  Score=46.80  Aligned_cols=24  Identities=25%  Similarity=0.364  Sum_probs=20.7

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      -.+++.|++|+|||+|..++....
T Consensus         7 ~~i~v~G~~~~GKSsli~~l~~~~   30 (170)
T 1z0j_A            7 LKVCLLGDTGVGKSSIMWRFVEDS   30 (170)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            358999999999999999998643

>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=95.53  E-value=0.0053  Score=57.81  Aligned_cols=29  Identities=31%  Similarity=0.447  Sum_probs=24.3

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      |+.+..-+++.||||+|||+|++.++...
T Consensus       277 ~i~~G~i~~i~G~~GsGKSTLl~~l~g~~  305 (525)
T 1tf7_A          277 GFFKDSIILATGATGTGKTLLVSRFVENA  305 (525)
T ss_dssp             SEESSCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            45555669999999999999999999754

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=95.53  E-value=0.0082  Score=46.76  Aligned_cols=24  Identities=33%  Similarity=0.443  Sum_probs=20.8

Q ss_pred             CCcceeeecCCCCchHHHHHHHHh
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      ....|++.|++|+|||+|..++..
T Consensus         7 ~~~~i~v~G~~~~GKssl~~~l~~   30 (178)
T 2lkc_A            7 RPPVVTIMGHVDHGKTTLLDAIRH   30 (178)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhC
Confidence            345599999999999999999975

>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=95.52  E-value=0.006  Score=48.93  Aligned_cols=21  Identities=33%  Similarity=0.491  Sum_probs=19.7

Q ss_pred             ceeeecCCCCchHHHHHHHHh
Q 025979          195 GVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~  215 (245)
                      .+++.|+||+|||+|..++..
T Consensus        25 ki~~vG~~~vGKSsli~~l~~   45 (190)
T 1m2o_B           25 KLLFLGLDNAGKTTLLHMLKN   45 (190)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            499999999999999999986

>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=95.51  E-value=0.0068  Score=47.19  Aligned_cols=23  Identities=30%  Similarity=0.449  Sum_probs=20.2

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -.+++.|+||+|||+|..++...
T Consensus         8 ~~i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A            8 FKVILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            45899999999999999999753

>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=95.50  E-value=0.027  Score=45.30  Aligned_cols=18  Identities=28%  Similarity=0.373  Sum_probs=15.5

Q ss_pred             CcceeeecCCCCchHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLA  210 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lA  210 (245)
                      .+.+++.+|+|+|||..+
T Consensus        38 ~~~~li~~~TGsGKT~~~   55 (207)
T 2gxq_A           38 GKDLIGQARTGTGKTLAF   55 (207)
T ss_dssp             TCCEEEECCTTSCHHHHH
T ss_pred             CCCEEEECCCCChHHHHH
Confidence            366999999999999864

>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=95.48  E-value=0.0072  Score=46.63  Aligned_cols=23  Identities=30%  Similarity=0.309  Sum_probs=20.3

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -.+++.|++|+|||+|..++...
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            7 FKVVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            35899999999999999999854

>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=95.47  E-value=0.0082  Score=46.35  Aligned_cols=23  Identities=26%  Similarity=0.400  Sum_probs=20.3

Q ss_pred             CcceeeecCCCCchHHHHHHHHh
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      ...+++.|++|+|||+|..++..
T Consensus         7 ~~~i~v~G~~~~GKssl~~~l~~   29 (171)
T 1upt_A            7 EMRILILGLDGAGKTTILYRLQV   29 (171)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHHHhc
Confidence            34599999999999999999975

>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=95.46  E-value=0.0072  Score=47.08  Aligned_cols=24  Identities=33%  Similarity=0.465  Sum_probs=20.8

Q ss_pred             CcceeeecCCCCchHHHHHHHHhc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .-.|++.|++|+|||+|...+...
T Consensus         8 ~~~i~v~G~~~~GKSsli~~l~~~   31 (182)
T 1ky3_A            8 ILKVIILGDSGVGKTSLMHRYVND   31 (182)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHHhC
Confidence            356999999999999999988754

>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=95.44  E-value=0.0073  Score=48.57  Aligned_cols=24  Identities=17%  Similarity=0.332  Sum_probs=20.6

Q ss_pred             CcceeeecCCCCchHHHHHHHHhc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .-.|++.|++|+|||+|..++...
T Consensus        28 ~~ki~v~G~~~~GKSsli~~l~~~   51 (199)
T 2p5s_A           28 AYKIVLAGDAAVGKSSFLMRLCKN   51 (199)
T ss_dssp             CEEEEEESSTTSSHHHHHHHHHHC
T ss_pred             CeEEEEECcCCCCHHHHHHHHHhC
Confidence            345999999999999999998753

>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=95.42  E-value=0.0075  Score=46.32  Aligned_cols=21  Identities=24%  Similarity=0.411  Sum_probs=19.4

Q ss_pred             ceeeecCCCCchHHHHHHHHh
Q 025979          195 GVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~  215 (245)
                      .+++.|++|+|||+|..++..
T Consensus         8 ~i~v~G~~~~GKssli~~l~~   28 (170)
T 1r2q_A            8 KLVLLGESAVGKSSLVLRFVK   28 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            489999999999999999985

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=95.40  E-value=0.0084  Score=50.55  Aligned_cols=22  Identities=23%  Similarity=0.159  Sum_probs=19.3

Q ss_pred             eeeecCCCCchHHHHHHHHhcc
Q 025979          196 VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++++||||+|||+++..++..+
T Consensus        15 ~litG~mGsGKTT~ll~~~~r~   36 (223)
T 2b8t_A           15 EFITGPMFAGKTAELIRRLHRL   36 (223)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHHHH
Confidence            7788999999999998888765

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=95.40  E-value=0.0078  Score=55.21  Aligned_cols=26  Identities=35%  Similarity=0.534  Sum_probs=22.2

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+..++++||||||||+|++.||+..
T Consensus       173 rGQr~~IvG~sG~GKTtLl~~Iar~i  198 (422)
T 3ice_A          173 RGQRGLIVAPPKAGKTMLLQNIAQSI  198 (422)
T ss_dssp             TTCEEEEECCSSSSHHHHHHHHHHHH
T ss_pred             CCcEEEEecCCCCChhHHHHHHHHHH
Confidence            34449999999999999999998864

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=95.40  E-value=0.0065  Score=47.31  Aligned_cols=23  Identities=30%  Similarity=0.471  Sum_probs=20.4

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -.|++.|+||+|||+|..++...
T Consensus        10 ~~i~v~G~~~~GKssl~~~l~~~   32 (181)
T 3tw8_B           10 FKLLIIGDSGVGKSSLLLRFADN   32 (181)
T ss_dssp             EEEEEECCTTSCHHHHHHHHCSC
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            45999999999999999999754

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=95.37  E-value=0.0089  Score=59.39  Aligned_cols=22  Identities=45%  Similarity=0.792  Sum_probs=17.5

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -+++.||||||||+++..++..
T Consensus       377 ~~lI~GppGTGKT~~i~~~i~~  398 (802)
T 2xzl_A          377 LSLIQGPPGTGKTVTSATIVYH  398 (802)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            3789999999999977666543

>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=95.36  E-value=0.0079  Score=47.30  Aligned_cols=22  Identities=27%  Similarity=0.353  Sum_probs=19.9

Q ss_pred             cceeeecCCCCchHHHHHHHHh
Q 025979          194 RGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      -.|++.|++|+|||+|..++..
T Consensus        12 ~ki~v~G~~~~GKSsli~~l~~   33 (195)
T 3bc1_A           12 IKFLALGDSGVGKTSVLYQYTD   33 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            3599999999999999999985

>4i1u_A Dephospho-COA kinase; structural genomics, niaid, national institute of allergy AN infectious diseases; 2.05A {Burkholderia vietnamiensis} PDB: 4i1v_A*

Probab=95.36  E-value=0.0093  Score=49.90  Aligned_cols=32  Identities=28%  Similarity=0.284  Sum_probs=28.7

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceeeeech
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVG  226 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~  226 (245)
                      -.|-|.|..|||||++++.++. +|++++..|.
T Consensus        10 ~~iglTGgigsGKStv~~~l~~-~g~~vidaD~   41 (210)
T 4i1u_A           10 YAIGLTGGIGSGKTTVADLFAA-RGASLVDTDL   41 (210)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH-TTCEEEEHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH-CCCcEEECcH
Confidence            4588999999999999999998 9999988774

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=95.30  E-value=0.009  Score=56.34  Aligned_cols=35  Identities=17%  Similarity=0.169  Sum_probs=25.3

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc---cceeeeech
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVG  226 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~  226 (245)
                      .++.|+|+|+||+|||+++..||..+   |.....+++
T Consensus       100 ~~~vI~ivG~~GvGKTTl~~kLA~~l~~~G~kVllVd~  137 (504)
T 2j37_W          100 KQNVIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLICA  137 (504)
T ss_dssp             --EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEec
Confidence            35569999999999999999999665   444444443

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=95.28  E-value=0.011  Score=54.67  Aligned_cols=26  Identities=31%  Similarity=0.231  Sum_probs=22.5

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +++.+++.||+|+|||+++..+|..+
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~~l  122 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLALYY  122 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            45558899999999999999999776

>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=95.27  E-value=0.0081  Score=46.64  Aligned_cols=21  Identities=24%  Similarity=0.357  Sum_probs=19.3

Q ss_pred             ceeeecCCCCchHHHHHHHHh
Q 025979          195 GVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~  215 (245)
                      .+++.|++|+|||+|..++..
T Consensus        16 ~i~v~G~~~~GKssli~~l~~   36 (179)
T 2y8e_A           16 KLVFLGEQSVGKTSLITRFMY   36 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            499999999999999999974

>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=95.25  E-value=0.0089  Score=47.33  Aligned_cols=22  Identities=23%  Similarity=0.469  Sum_probs=19.9

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|++.|++|+|||+|+.+++..
T Consensus        23 ki~vvG~~~~GKSsli~~l~~~   44 (190)
T 3con_A           23 KLVVVGAGGVGKSALTIQLIQN   44 (190)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            4999999999999999999854

>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=95.25  E-value=0.0086  Score=54.25  Aligned_cols=26  Identities=23%  Similarity=0.271  Sum_probs=22.3

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++.-+.+.||+|+|||+|.++|+...
T Consensus        53 ~Gei~~IiGpnGaGKSTLlr~i~GL~   78 (366)
T 3tui_C           53 AGQIYGVIGASGAGKSTLIRCVNLLE   78 (366)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEEcCCCchHHHHHHHHhcCC
Confidence            33348899999999999999999876

>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=95.25  E-value=0.0093  Score=47.10  Aligned_cols=23  Identities=30%  Similarity=0.447  Sum_probs=20.1

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .|++.|+||+|||+|.+.+.+..
T Consensus        16 ki~vvG~~~~GKssL~~~l~~~~   38 (198)
T 3t1o_A           16 KIVYYGPGLSGKTTNLKWIYSKV   38 (198)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhc
Confidence            39999999999999999887644

>3lv8_A DTMP kinase, thymidylate kinase; structural genomics, in diseases, center for structural genomics of infectious DISE ATP-binding; HET: ADP TMP TYD; 1.80A {Vibrio cholerae o1 biovar eltor} PDB: 3n2i_A*

Probab=95.23  E-value=0.0087  Score=50.83  Aligned_cols=25  Identities=20%  Similarity=0.356  Sum_probs=21.9

Q ss_pred             cceeeecCCCCchHHHHHHHHhccc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      .-|.|.||+|+|||++++.++..++
T Consensus        28 ~~i~~eG~~GsGKsT~~~~l~~~l~   52 (236)
T 3lv8_A           28 KFIVIEGLEGAGKSTAIQVVVETLQ   52 (236)
T ss_dssp             CEEEEEESTTSCHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3378899999999999999998873

>1fzq_A ADP-ribosylation factor-like protein 3; protein-GDP complex without magnesium, ARF family, RAS superfamily, G-domain, signaling protein; HET: MES GDP; 1.70A {Mus musculus} SCOP: c.37.1.8 PDB: 3bh7_A* 3bh6_A*

Probab=95.23  E-value=0.0099  Score=47.14  Aligned_cols=23  Identities=39%  Similarity=0.518  Sum_probs=20.5

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ..+++.|+||+|||+|...+...
T Consensus        17 ~ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           17 VRILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             EEEEEEESTTSSHHHHHHHHCCS
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            34999999999999999999864

>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=95.22  E-value=0.0093  Score=47.42  Aligned_cols=22  Identities=36%  Similarity=0.533  Sum_probs=19.8

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|++.|++|+|||+|..++...
T Consensus        27 ki~v~G~~~~GKSsLi~~l~~~   48 (193)
T 2oil_A           27 KVVLIGESGVGKTNLLSRFTRN   48 (193)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            4999999999999999998863

>1moz_A ARL1, ADP-ribosylation factor-like protein 1; GTP-binding, protein binding; HET: GDP; 3.17A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=95.20  E-value=0.01  Score=46.47  Aligned_cols=24  Identities=25%  Similarity=0.360  Sum_probs=20.6

Q ss_pred             CCcceeeecCCCCchHHHHHHHHh
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      ....+++.|+||+|||+|..++..
T Consensus        17 ~~~~i~v~G~~~~GKssli~~l~~   40 (183)
T 1moz_A           17 KELRILILGLDGAGKTTILYRLQI   40 (183)
T ss_dssp             SCEEEEEEEETTSSHHHHHHHTCC
T ss_pred             CccEEEEECCCCCCHHHHHHHHhc
Confidence            344599999999999999999874

>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=95.19  E-value=0.0098  Score=46.18  Aligned_cols=23  Identities=22%  Similarity=0.369  Sum_probs=20.2

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -.+++.|++|+|||+|..++...
T Consensus        16 ~~i~v~G~~~~GKSsli~~l~~~   38 (179)
T 1z0f_A           16 FKYIIIGDMGVGKSCLLHQFTEK   38 (179)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            34999999999999999999854

>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=95.17  E-value=0.0093  Score=46.40  Aligned_cols=23  Identities=22%  Similarity=0.385  Sum_probs=20.5

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ..+++.|++|+|||+|..++...
T Consensus        10 ~~i~v~G~~~~GKssli~~l~~~   32 (181)
T 2fn4_A           10 HKLVVVGGGGVGKSALTIQFIQS   32 (181)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            45999999999999999999864

>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=95.17  E-value=0.01  Score=46.34  Aligned_cols=22  Identities=27%  Similarity=0.463  Sum_probs=19.7

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .+++.|++|+|||+|..++...
T Consensus        14 ki~v~G~~~~GKSsli~~l~~~   35 (181)
T 2efe_B           14 KLVLLGDVGAGKSSLVLRFVKD   35 (181)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            4999999999999999998754

>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=95.17  E-value=0.0099  Score=46.48  Aligned_cols=23  Identities=26%  Similarity=0.446  Sum_probs=20.2

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ..|++.|++|+|||+|..++...
T Consensus        19 ~ki~v~G~~~~GKSsli~~l~~~   41 (187)
T 2a9k_A           19 HKVIMVGSGGVGKSALTLQFMYD   41 (187)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHhhC
Confidence            34999999999999999999853

>1svi_A GTP-binding protein YSXC; ENGB, GTPase, GDP, hydrolase; HET: GDP; 1.95A {Bacillus subtilis} SCOP: c.37.1.8 PDB: 1sul_A* 1svw_A*

Probab=95.16  E-value=0.01  Score=47.04  Aligned_cols=23  Identities=22%  Similarity=0.391  Sum_probs=20.4

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ..+++.|++|+|||+|..++...
T Consensus        24 ~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           24 PEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            45999999999999999999764

>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=95.15  E-value=0.0092  Score=46.90  Aligned_cols=23  Identities=30%  Similarity=0.442  Sum_probs=20.1

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -.+++.|++|+|||+|..++...
T Consensus        11 ~ki~v~G~~~~GKSsli~~l~~~   33 (186)
T 2bme_A           11 FKFLVIGNAGTGKSCLLHQFIEK   33 (186)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            35999999999999999998753

>3f8t_A Predicted ATPase involved in replication control, CDC46/MCM family; helicase, MCM homolog, DNA replication, ATP-binding, DNA-binding; 1.90A {Methanopyrus kandleri AV19}

Probab=95.14  E-value=0.013  Score=54.89  Aligned_cols=25  Identities=24%  Similarity=0.224  Sum_probs=21.4

Q ss_pred             ceeeecCCCCchHHHHHHH-Hhcccce
Q 025979          195 GVLLYGPPGTGKTMLAKAV-ANHTTAA  220 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkal-A~~l~~~  220 (245)
                      .+||.|+||| ||++|+++ ++.+...
T Consensus       241 hVLL~G~PGt-KS~Lar~i~~~i~pR~  266 (506)
T 3f8t_A          241 HVLLAGYPVV-CSEILHHVLDHLAPRG  266 (506)
T ss_dssp             CEEEESCHHH-HHHHHHHHHHHTCSSE
T ss_pred             eEEEECCCCh-HHHHHHHHHHHhCCCe
Confidence            5999999999 99999999 7766443

>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=95.14  E-value=0.01  Score=46.44  Aligned_cols=22  Identities=32%  Similarity=0.457  Sum_probs=19.7

Q ss_pred             eeeecCCCCchHHHHHHHHhcc
Q 025979          196 VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+++||.|+|||++..||.-.+
T Consensus        26 ~~I~G~NGsGKStil~Ai~~~l   47 (149)
T 1f2t_A           26 NLIIGQNGSGKSSLLDAILVGL   47 (149)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            7899999999999999997654

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=95.13  E-value=0.0096  Score=50.19  Aligned_cols=25  Identities=24%  Similarity=0.282  Sum_probs=22.2

Q ss_pred             ceeeecCCCCchHHHHHHHHhcccc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      -|.|.|++|+|||++++.++..++.
T Consensus        23 ~i~~~G~~g~GKst~~~~l~~~l~~   47 (223)
T 3ld9_A           23 FITFEGIDGSGKTTQSHLLAEYLSE   47 (223)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhh
Confidence            3778899999999999999998755

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=95.13  E-value=0.012  Score=51.44  Aligned_cols=26  Identities=31%  Similarity=0.231  Sum_probs=22.0

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +++-+.+.||+|+|||+++..+|..+
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~~  122 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALYY  122 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            34457888999999999999999866

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=95.13  E-value=0.012  Score=54.46  Aligned_cols=35  Identities=29%  Similarity=0.416  Sum_probs=26.2

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc----cceeeeech
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT----TAAFIRVVG  226 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l----~~~~~~v~~  226 (245)
                      +++.++++|++|+|||+++-.||..+    |..+..+++
T Consensus        99 ~~~vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllvd~  137 (433)
T 2xxa_A           99 PPAVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSA  137 (433)
T ss_dssp             SSEEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEEC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEEec
Confidence            45678999999999999999888665    444444443

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=95.12  E-value=0.0088  Score=48.82  Aligned_cols=25  Identities=28%  Similarity=0.441  Sum_probs=21.8

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ...+++.|+||+|||+++..++..+
T Consensus        30 ~~~i~i~G~~g~GKTTl~~~l~~~~   54 (221)
T 2wsm_A           30 TVAVNIMGAIGSGKTLLIERTIERI   54 (221)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHh
Confidence            3458999999999999999998774

>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=95.11  E-value=0.011  Score=47.17  Aligned_cols=23  Identities=22%  Similarity=0.442  Sum_probs=20.4

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -.|++.|++|+|||+|...+...
T Consensus        29 ~ki~v~G~~~vGKSsli~~l~~~   51 (196)
T 2atv_A           29 VKLAIFGRAGVGKSALVVRFLTK   51 (196)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            45999999999999999999764

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=95.10  E-value=0.012  Score=52.49  Aligned_cols=24  Identities=33%  Similarity=0.495  Sum_probs=21.2

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..|.|.|+||+|||+++..++..+
T Consensus        80 ~~I~i~G~~G~GKSTl~~~L~~~l  103 (355)
T 3p32_A           80 HRVGITGVPGVGKSTAIEALGMHL  103 (355)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            348899999999999999998765

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=95.08  E-value=0.01  Score=52.00  Aligned_cols=25  Identities=40%  Similarity=0.495  Sum_probs=21.6

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++-+++.||+|+|||+++..+|..+
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~  122 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFY  122 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4458889999999999999999766

>1qhl_A Protein (cell division protein MUKB); SMC, chromosome partitioning; 2.20A {Escherichia coli} SCOP: c.37.1.12

Probab=95.08  E-value=0.0039  Score=52.73  Aligned_cols=22  Identities=27%  Similarity=0.326  Sum_probs=20.1

Q ss_pred             eeeecCCCCchHHHHHHHHhcc
Q 025979          196 VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++||+|+|||+|.++|+..+
T Consensus        30 ~~i~GpnGsGKSTll~~i~g~~   51 (227)
T 1qhl_A           30 TTLSGGNGAGKSTTMAAFVTAL   51 (227)
T ss_dssp             HHHHSCCSHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhccc
Confidence            5688999999999999999876

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=95.08  E-value=0.025  Score=51.80  Aligned_cols=43  Identities=23%  Similarity=0.332  Sum_probs=35.6

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceeeeechh-HHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS-EFVQKYLGE  236 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s-~l~~~~~Ge  236 (245)
                      +.+++++|+|+|||.++-.++..++.+.+.+.+. ++...|..+
T Consensus       109 ~~~ll~~~TGsGKT~~~l~~i~~~~~~~Lvl~P~~~L~~Q~~~~  152 (472)
T 2fwr_A          109 KRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKER  152 (472)
T ss_dssp             TEEEEECCTTSCHHHHHHHHHHHHCSCEEEEESSHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCHHHHHHHHHHHcCCCEEEEECCHHHHHHHHHH
Confidence            3589999999999999988888888777777777 888777554

>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=95.07  E-value=0.02  Score=57.96  Aligned_cols=48  Identities=21%  Similarity=0.167  Sum_probs=37.6

Q ss_pred             eccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhc
Q 025979          158 YNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       158 ~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ...++|-+...++|.+.+...-           ...+-+.++|++|+|||+||+.+++.
T Consensus       123 ~~~~vgR~~~~~~l~~~l~~~~-----------~~~~~v~i~G~gG~GKTtLa~~~~~~  170 (1249)
T 3sfz_A          123 PVIFVTRKKLVHAIQQKLWKLN-----------GEPGWVTIYGMAGCGKSVLAAEAVRD  170 (1249)
T ss_dssp             CSSCCCCHHHHHHHHHHHHTTT-----------TSCEEEEEECSTTSSHHHHHHHHTCC
T ss_pred             CceeccHHHHHHHHHHHHhhcc-----------CCCCEEEEEeCCCCCHHHHHHHHhcC
Confidence            3468999999999988875310           12345889999999999999999876

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=95.06  E-value=0.0098  Score=49.58  Aligned_cols=21  Identities=33%  Similarity=0.444  Sum_probs=20.0

Q ss_pred             eeeecCCCCchHHHHHHHHhc
Q 025979          196 VLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~  216 (245)
                      +.|.||.|+|||++++.|+..
T Consensus        23 i~i~G~~GsGKSTl~~~L~~~   43 (230)
T 2vp4_A           23 VLIEGNIGSGKTTYLNHFEKY   43 (230)
T ss_dssp             EEEECSTTSCHHHHHHTTGGG
T ss_pred             EEEECCCCCCHHHHHHHHHhc
Confidence            789999999999999999987

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=95.06  E-value=0.012  Score=54.46  Aligned_cols=21  Identities=33%  Similarity=0.542  Sum_probs=19.7

Q ss_pred             eeeecCCCCchHHHHHHHHhc
Q 025979          196 VLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~  216 (245)
                      +.|.||+|+|||+|.++|++.
T Consensus        45 vaLvG~nGaGKSTLln~L~G~   65 (427)
T 2qag_B           45 ILCVGETGLGKSTLMDTLFNT   65 (427)
T ss_dssp             EEEECSTTSSSHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCc
Confidence            779999999999999999876

>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=95.04  E-value=0.011  Score=47.34  Aligned_cols=22  Identities=23%  Similarity=0.305  Sum_probs=19.7

Q ss_pred             cceeeecCCCCchHHHHHHHHh
Q 025979          194 RGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      -.|++.|+||+|||+|...+..
T Consensus        30 ~ki~v~G~~~vGKSsLi~~l~~   51 (192)
T 2b6h_A           30 MRILMVGLDAAGKTTILYKLKL   51 (192)
T ss_dssp             EEEEEEESTTSSHHHHHHHHCS
T ss_pred             cEEEEECCCCCCHHHHHHHHHh
Confidence            4499999999999999999864

>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=95.04  E-value=0.011  Score=46.33  Aligned_cols=22  Identities=23%  Similarity=0.397  Sum_probs=19.8

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|++.|++|+|||+|..++...
T Consensus        20 ki~v~G~~~~GKSsl~~~l~~~   41 (183)
T 3kkq_A           20 KLVVVGDGGVGKSALTIQFFQK   41 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4899999999999999998854

>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=95.03  E-value=0.012  Score=45.98  Aligned_cols=23  Identities=35%  Similarity=0.437  Sum_probs=20.2

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -.+++.|++|+|||+|..++...
T Consensus        11 ~~i~v~G~~~~GKssli~~l~~~   33 (180)
T 2g6b_A           11 FKVMLVGDSGVGKTCLLVRFKDG   33 (180)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHhC
Confidence            45999999999999999998753

>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=95.01  E-value=0.012  Score=46.77  Aligned_cols=22  Identities=32%  Similarity=0.398  Sum_probs=19.8

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|++.|++|+|||+|..++...
T Consensus        24 ki~vvG~~~~GKSsli~~l~~~   45 (189)
T 2gf9_A           24 KLLLIGNSSVGKTSFLFRYADD   45 (189)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4999999999999999998754

>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=94.99  E-value=0.064  Score=43.70  Aligned_cols=23  Identities=35%  Similarity=0.319  Sum_probs=17.4

Q ss_pred             CcceeeecCCCCchHHH-HHHHHh
Q 025979          193 PRGVLLYGPPGTGKTML-AKAVAN  215 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~l-AkalA~  215 (245)
                      .+.+++.+|+|+|||.. +-++..
T Consensus        51 ~~~~lv~~pTGsGKT~~~~~~~l~   74 (224)
T 1qde_A           51 GHDVLAQAQSGTGKTGTFSIAALQ   74 (224)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCEEEECCCCCcHHHHHHHHHHH
Confidence            36699999999999987 333333

>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=94.98  E-value=0.016  Score=46.80  Aligned_cols=24  Identities=29%  Similarity=0.556  Sum_probs=20.4

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.+++++|+|+|||+++-.++...
T Consensus        49 ~~~li~~~tGsGKT~~~~~~~~~~   72 (216)
T 3b6e_A           49 KNIIICLPTGSGKTRVAVYIAKDH   72 (216)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHHH
T ss_pred             CCEEEEcCCCCCHHHHHHHHHHHH
Confidence            569999999999999988777643

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=94.98  E-value=0.01  Score=46.83  Aligned_cols=22  Identities=32%  Similarity=0.434  Sum_probs=19.9

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .+++.|++|+|||+|..++...
T Consensus        25 ~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 3pqc_A           25 EVAFVGRSNVGKSSLLNALFNR   46 (195)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4999999999999999998765

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=94.97  E-value=0.012  Score=46.61  Aligned_cols=22  Identities=36%  Similarity=0.554  Sum_probs=19.9

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|++.|++|+|||+|..++...
T Consensus        18 ki~v~G~~~~GKSsli~~l~~~   39 (196)
T 3tkl_A           18 KLLLIGDSGVGKSCLLLRFADD   39 (196)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            4999999999999999999863

>3c5c_A RAS-like protein 12; GDP, GTPase, structural genomics consortium, SGC, limited proteolysis, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.85A {Homo sapiens}

Probab=94.97  E-value=0.012  Score=46.84  Aligned_cols=21  Identities=24%  Similarity=0.453  Sum_probs=19.1

Q ss_pred             eeeecCCCCchHHHHHHHHhc
Q 025979          196 VLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~  216 (245)
                      |++.|++|+|||+|...+...
T Consensus        24 i~vvG~~~vGKTsLi~~l~~~   44 (187)
T 3c5c_A           24 LAILGRRGAGKSALTVKFLTK   44 (187)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCcHHHHHHHHHhC
Confidence            999999999999999988753

>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=94.97  E-value=0.012  Score=47.16  Aligned_cols=23  Identities=26%  Similarity=0.336  Sum_probs=20.4

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -.|++.|+||+|||+|...+...
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~   31 (203)
T 1zbd_A            9 FKILIIGNSSVGKTSFLFRYADD   31 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTC
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            45999999999999999999764

>1ksh_A ARF-like protein 2; small GTPase, small GTP-binding protein, ARF family; HET: CME GDP; 1.80A {Mus musculus} SCOP: c.37.1.8 PDB: 1ksg_A* 1ksj_A* 3doe_A* 3dof_A*

Probab=94.97  E-value=0.012  Score=46.38  Aligned_cols=25  Identities=24%  Similarity=0.339  Sum_probs=21.3

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ....+++.|+||+|||+|..++...
T Consensus        17 ~~~~i~v~G~~~~GKssl~~~l~~~   41 (186)
T 1ksh_A           17 RELRLLMLGLDNAGKTTILKKFNGE   41 (186)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHTTC
T ss_pred             CeeEEEEECCCCCCHHHHHHHHhcC
Confidence            3445999999999999999999853

>3bwd_D RAC-like GTP-binding protein ARAC6; G domain, cytoplasm, lipoprotein, membrane, methylation, nucleotide-binding, prenylation, ----; HET: GDP; 1.53A {Arabidopsis thaliana} PDB: 2nty_C* 2wbl_C

Probab=94.95  E-value=0.012  Score=45.86  Aligned_cols=24  Identities=21%  Similarity=0.164  Sum_probs=20.9

Q ss_pred             CcceeeecCCCCchHHHHHHHHhc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .-.+++.|++|+|||+|..++...
T Consensus         8 ~~ki~v~G~~~~GKssl~~~~~~~   31 (182)
T 3bwd_D            8 FIKCVTVGDGAVGKTCLLISYTSN   31 (182)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            356999999999999999998754

>3ihw_A Centg3; RAS, centaurin, GTPase, structural genomics, structural genomics consortium, SGC, alternative splicing, ANK repeat, cytoplasm, GTP-binding; 1.92A {Homo sapiens} SCOP: c.37.1.0

Probab=94.95  E-value=0.013  Score=46.80  Aligned_cols=21  Identities=24%  Similarity=0.279  Sum_probs=18.8

Q ss_pred             eeeecCCCCchHHHHHHHHhc
Q 025979          196 VLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~  216 (245)
                      |+|.|++|+|||+|...+...
T Consensus        23 i~ivG~~~vGKSsL~~~~~~~   43 (184)
T 3ihw_A           23 VGIVGNLSSGKSALVHRYLTG   43 (184)
T ss_dssp             EEEECCTTSCHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            999999999999999877653

>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=94.93  E-value=0.013  Score=51.87  Aligned_cols=24  Identities=42%  Similarity=0.465  Sum_probs=21.3

Q ss_pred             CCcceeeecCCCCchHHHHHHHHh
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      ..+|+||.||+|+|||++|-++..
T Consensus       146 ~g~gvli~G~sG~GKStlal~l~~  169 (312)
T 1knx_A          146 FGVGVLLTGRSGIGKSECALDLIN  169 (312)
T ss_dssp             TTEEEEEEESSSSSHHHHHHHHHT
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHH
Confidence            357899999999999999998875

>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=94.92  E-value=0.014  Score=51.72  Aligned_cols=24  Identities=33%  Similarity=0.477  Sum_probs=21.8

Q ss_pred             CcceeeecCCCCchHHHHHHHHhc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .+|++|.|++|+|||++|.++...
T Consensus       144 g~~vl~~G~sG~GKSt~a~~l~~~  167 (314)
T 1ko7_A          144 GVGVLITGDSGIGKSETALELIKR  167 (314)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHT
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHhc
Confidence            578999999999999999999874

>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=94.91  E-value=0.013  Score=52.83  Aligned_cols=25  Identities=28%  Similarity=0.411  Sum_probs=21.9

Q ss_pred             cceeeecCCCCchHHHHHHHHhccc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      .-+.|.||||+|||+|.++|+....
T Consensus       216 ~~~~lvG~sG~GKSTLln~L~g~~~  240 (358)
T 2rcn_A          216 RISIFAGQSGVGKSSLLNALLGLQN  240 (358)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHCCSS
T ss_pred             CEEEEECCCCccHHHHHHHHhcccc
Confidence            3488999999999999999998654

>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=94.91  E-value=0.013  Score=46.31  Aligned_cols=22  Identities=27%  Similarity=0.524  Sum_probs=19.9

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|++.|+||+|||+|..++...
T Consensus        17 ~i~v~G~~~~GKssli~~l~~~   38 (195)
T 1x3s_A           17 KILIIGESGVGKSSLLLRFTDD   38 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4999999999999999999754

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=94.88  E-value=0.014  Score=55.22  Aligned_cols=27  Identities=33%  Similarity=0.409  Sum_probs=23.1

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.|.||+|+|||+|.++|+..+
T Consensus        45 ~~Ge~~~LvG~NGaGKSTLlk~l~Gl~   71 (538)
T 1yqt_A           45 KEGMVVGIVGPNGTGKSTAVKILAGQL   71 (538)
T ss_dssp             CTTSEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            344558999999999999999999876

>1vg8_A RAS-related protein RAB-7; GTP-binding protein, protein transport; HET: GNP; 1.70A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 1vg0_B* 3law_A* 1t91_A* 1yhn_A* 1vg1_A* 1vg9_B*

Probab=94.88  E-value=0.013  Score=46.86  Aligned_cols=24  Identities=33%  Similarity=0.480  Sum_probs=21.0

Q ss_pred             CcceeeecCCCCchHHHHHHHHhc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ...|++.|++|+|||+|..++...
T Consensus         8 ~~ki~v~G~~~~GKSsli~~l~~~   31 (207)
T 1vg8_A            8 LLKVIILGDSGVGKTSLMNQYVNK   31 (207)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcC
Confidence            356999999999999999998764

>2bov_A RAla, RAS-related protein RAL-A; C3BOT, exoenzyme, RAla, GTPase, ribosylating toxin, GTP-binding, lipoprotein, prenylation; HET: GDP; 2.66A {Homo sapiens}

Probab=94.87  E-value=0.013  Score=46.77  Aligned_cols=22  Identities=27%  Similarity=0.457  Sum_probs=19.6

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|++.|++|+|||+|..++...
T Consensus        16 ki~v~G~~~~GKSsli~~l~~~   37 (206)
T 2bov_A           16 KVIMVGSGGVGKSALTLQFMYD   37 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4999999999999999998753

>3dz8_A RAS-related protein RAB-3B; GDP, GTPase, structural genomics consortium, SGC, cell GTP-binding, lipoprotein, membrane, methylation; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=94.87  E-value=0.012  Score=46.79  Aligned_cols=22  Identities=27%  Similarity=0.380  Sum_probs=19.8

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|++.|++|+|||+|...+...
T Consensus        25 ki~v~G~~~~GKSsli~~l~~~   46 (191)
T 3dz8_A           25 KLLIIGNSSVGKTSFLFRYADD   46 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHhcC
Confidence            4999999999999999998864

>3ch4_B Pmkase, phosphomevalonate kinase; parallel beta-sheet with the strand order 23145, walker A motif, cholesterol biosynthesis, lipid synthesis; 1.76A {Homo sapiens}

Probab=94.81  E-value=0.026  Score=46.92  Aligned_cols=40  Identities=20%  Similarity=0.218  Sum_probs=31.2

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccc-eeeeechhHHHH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTA-AFIRVVGSEFVQ  231 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~-~~~~v~~s~l~~  231 (245)
                      |..-+++.|.||+||+++|+.+.+.++. .+..+++++.+.
T Consensus        10 ~~~II~itGk~~SGKd~va~~l~~~~g~~~~~vv~msD~iK   50 (202)
T 3ch4_B           10 PRLVLLFSGKRKSGKDFVTEALQSRLGADVCAVLRLSGPLK   50 (202)
T ss_dssp             CSEEEEEEECTTSSHHHHHHHHHHHHCTTTEEEECTHHHHH
T ss_pred             CCEEEEEECCCCCChHHHHHHHHHHcCCCCceEEEccHHHH
Confidence            5555889999999999999999887753 244567777665

>2fg5_A RAB-22B, RAS-related protein RAB-31; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.80A {Homo sapiens} SCOP: c.37.1.8

Probab=94.81  E-value=0.013  Score=46.72  Aligned_cols=22  Identities=27%  Similarity=0.427  Sum_probs=19.7

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|++.|++|+|||+|..++...
T Consensus        25 ki~vvG~~~~GKSsli~~l~~~   46 (192)
T 2fg5_A           25 KVCLLGDTGVGKSSIVCRFVQD   46 (192)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            4999999999999999999753

>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=94.81  E-value=0.014  Score=46.46  Aligned_cols=22  Identities=27%  Similarity=0.371  Sum_probs=20.0

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|++.|+||+|||+|..++...
T Consensus        25 ki~~vG~~~~GKSsl~~~l~~~   46 (194)
T 3reg_A           25 KIVVVGDGAVGKTCLLLAFSKG   46 (194)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            4999999999999999999864

>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=94.79  E-value=0.014  Score=46.32  Aligned_cols=22  Identities=27%  Similarity=0.363  Sum_probs=19.7

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|++.|++|+|||+|..++...
T Consensus        24 ki~v~G~~~~GKSsli~~l~~~   45 (188)
T 1zd9_A           24 ELTLVGLQYSGKTTFVNVIASG   45 (188)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            3999999999999999999853

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=94.78  E-value=0.017  Score=51.25  Aligned_cols=25  Identities=24%  Similarity=0.348  Sum_probs=21.2

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..-+.+.||||+|||+++.+++..+
T Consensus        56 ~~~i~i~G~~g~GKSTl~~~l~~~~   80 (341)
T 2p67_A           56 TLRLGVTGTPGAGKSTFLEAFGMLL   80 (341)
T ss_dssp             SEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHH
Confidence            3448899999999999999998654

>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=94.77  E-value=0.015  Score=46.10  Aligned_cols=21  Identities=24%  Similarity=0.417  Sum_probs=19.2

Q ss_pred             ceeeecCCCCchHHHHHHHHh
Q 025979          195 GVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~  215 (245)
                      .|++.|++|+|||+|..++..
T Consensus        22 ki~v~G~~~~GKSsli~~l~~   42 (189)
T 1z06_A           22 KIIVIGDSNVGKTCLTYRFCA   42 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            499999999999999999874

>3lxx_A GTPase IMAP family member 4; structural genomics consortium, SGC, coiled coil, GTP- binding, nucleotide-binding, immune system; HET: GDP; 2.15A {Homo sapiens}

Probab=94.76  E-value=0.015  Score=48.50  Aligned_cols=23  Identities=22%  Similarity=0.472  Sum_probs=20.4

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ..|+|.|+||+|||+|..++.+.
T Consensus        30 ~~i~lvG~~g~GKStlin~l~g~   52 (239)
T 3lxx_A           30 LRIVLVGKTGAGKSATGNSILGR   52 (239)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTS
T ss_pred             eEEEEECCCCCCHHHHHHHHcCC
Confidence            34999999999999999999864

>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=94.75  E-value=0.015  Score=46.28  Aligned_cols=21  Identities=24%  Similarity=0.490  Sum_probs=19.2

Q ss_pred             eeeecCCCCchHHHHHHHHhc
Q 025979          196 VLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~  216 (245)
                      +++.|++|+|||+|...+...
T Consensus        24 i~v~G~~~~GKSsli~~l~~~   44 (191)
T 2a5j_A           24 YIIIGDTGVGKSCLLLQFTDK   44 (191)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCCCHHHHHHHHhcC
Confidence            999999999999999998753

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=94.75  E-value=0.016  Score=47.41  Aligned_cols=25  Identities=24%  Similarity=0.391  Sum_probs=21.5

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ...+++.|++|+|||+|+..++...
T Consensus        38 ~~~i~ivG~~gvGKTtl~~~l~~~~   62 (226)
T 2hf9_A           38 VVAFDFMGAIGSGKTLLIEKLIDNL   62 (226)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHh
Confidence            3458899999999999999998764

>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=94.74  E-value=0.015  Score=46.81  Aligned_cols=23  Identities=30%  Similarity=0.478  Sum_probs=20.1

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -.|++.|+||+|||+|..++...
T Consensus        21 ~~i~v~G~~~~GKSsli~~l~~~   43 (213)
T 3cph_A           21 MKILLIGDSGVGKSCLLVRFVED   43 (213)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            45999999999999999998743

>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=94.74  E-value=0.022  Score=51.30  Aligned_cols=34  Identities=21%  Similarity=0.268  Sum_probs=26.5

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc---cceeeeech
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVG  226 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~  226 (245)
                      ...+++.||+|+|||++++.++..+   +..++.++.
T Consensus        35 ~~~~~i~G~~G~GKs~~~~~~~~~~~~~~~~~~~~D~   71 (392)
T 4ag6_A           35 NSNWTILAKPGAGKSFTAKMLLLREYMQGSRVIIIDP   71 (392)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEES
T ss_pred             cCceEEEcCCCCCHHHHHHHHHHHHHHCCCEEEEEeC
Confidence            3458999999999999999988754   555665653

>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=94.73  E-value=0.014  Score=47.00  Aligned_cols=23  Identities=30%  Similarity=0.462  Sum_probs=20.3

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -.|++.|++|+|||+|..++...
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~   31 (206)
T 2bcg_Y            9 FKLLLIGNSGVGKSCLLLRFSDD   31 (206)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            45999999999999999999753

>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=94.71  E-value=0.054  Score=46.91  Aligned_cols=41  Identities=15%  Similarity=0.088  Sum_probs=25.9

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc-----cceeeeechh-HHHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT-----TAAFIRVVGS-EFVQKY  233 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l-----~~~~~~v~~s-~l~~~~  233 (245)
                      .+.+++.+|+|+|||+.+-..+-..     +...+.+.+. ++...+
T Consensus        44 ~~~~l~~~~TGsGKT~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~   90 (367)
T 1hv8_A           44 EYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRELAIQV   90 (367)
T ss_dssp             CSEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHHHHHHH
T ss_pred             CCCEEEECCCCChHHHHHHHHHHHHhcccCCCcEEEEcCCHHHHHHH
Confidence            3679999999999999765444332     4444445443 554443

>1gwn_A RHO-related GTP-binding protein RHOE; GTPase, inactive GTPase, signal transduction; HET: GTP; 2.1A {Mus musculus} SCOP: c.37.1.8

Probab=94.70  E-value=0.014  Score=47.54  Aligned_cols=22  Identities=27%  Similarity=0.427  Sum_probs=20.0

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|++.|++|+|||+|...+...
T Consensus        30 ki~vvG~~~vGKSsLi~~l~~~   51 (205)
T 1gwn_A           30 KIVVVGDSQCGKTALLHVFAKD   51 (205)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4999999999999999999864

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=94.69  E-value=0.01  Score=56.37  Aligned_cols=33  Identities=30%  Similarity=0.554  Sum_probs=25.5

Q ss_pred             HhhhccCCC-cc--eeeecCCCCchHHHHHHHHhcc
Q 025979          185 YKQIGIDPP-RG--VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       185 ~~~~g~~~~-~g--vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      |+-+++..+ +|  +.|.||+|+|||+|.+.|+..+
T Consensus        14 f~l~~l~~~~~Gei~gLiGpNGaGKSTLlkiL~Gl~   49 (538)
T 3ozx_A           14 FKLFGLPTPKNNTILGVLGKNGVGKTTVLKILAGEI   49 (538)
T ss_dssp             CEEECCCCCCTTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             eeecCCCCCCCCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            333455543 44  7899999999999999999876

>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=94.68  E-value=0.011  Score=47.57  Aligned_cols=21  Identities=38%  Similarity=0.615  Sum_probs=18.9

Q ss_pred             ceeeecCCCCchHHHHHHHHh
Q 025979          195 GVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~  215 (245)
                      .|++.|+||+|||+|...+.+
T Consensus        25 ki~vvG~~~vGKSsLi~~l~~   45 (195)
T 3cbq_A           25 KVMLVGESGVGKSTLAGTFGG   45 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            399999999999999999863

>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8

Probab=94.68  E-value=0.013  Score=51.09  Aligned_cols=24  Identities=25%  Similarity=0.320  Sum_probs=21.2

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .-+.|.||+|+|||+|.++|+...
T Consensus       170 eiv~l~G~sG~GKSTll~~l~g~~  193 (301)
T 1u0l_A          170 KISTMAGLSGVGKSSLLNAINPGL  193 (301)
T ss_dssp             SEEEEECSTTSSHHHHHHHHSTTC
T ss_pred             CeEEEECCCCCcHHHHHHHhcccc
Confidence            347899999999999999999865

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=94.67  E-value=0.015  Score=46.80  Aligned_cols=23  Identities=35%  Similarity=0.430  Sum_probs=20.4

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ..|++.|++|+|||+|..++...
T Consensus        25 ~ki~vvG~~~~GKSsli~~l~~~   47 (201)
T 3oes_A           25 RKVVILGYRCVGKTSLAHQFVEG   47 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCcCHHHHHHHHHhC
Confidence            34999999999999999999864

>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=94.67  E-value=0.015  Score=46.16  Aligned_cols=24  Identities=25%  Similarity=0.444  Sum_probs=21.0

Q ss_pred             CCcceeeecCCCCchHHHHHHHHh
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      ..-.|++.|+||+|||+|..++..
T Consensus         7 ~~~ki~vvG~~~~GKSsli~~l~~   30 (199)
T 2gf0_A            7 NDYRVVVFGAGGVGKSSLVLRFVK   30 (199)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CeeEEEEECCCCCcHHHHHHHHHc
Confidence            345699999999999999999975

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=94.66  E-value=0.056  Score=43.99  Aligned_cols=41  Identities=17%  Similarity=0.168  Sum_probs=26.0

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc------cceeeeech-hHHHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT------TAAFIRVVG-SEFVQKY  233 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l------~~~~~~v~~-s~l~~~~  233 (245)
                      .+.+++.+|+|+|||..+-..+-..      +...+.+.+ .++...+
T Consensus        51 ~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~   98 (220)
T 1t6n_A           51 GMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQI   98 (220)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHH
T ss_pred             CCCEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEeCCHHHHHHH
Confidence            3569999999999998766544332      224444444 3555443

>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=94.62  E-value=0.0099  Score=46.69  Aligned_cols=24  Identities=29%  Similarity=0.362  Sum_probs=10.3

Q ss_pred             CcceeeecCCCCchHHHHHHHHhc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .-.|++.|+||+|||+|..++...
T Consensus         8 ~~ki~v~G~~~~GKssl~~~l~~~   31 (183)
T 2fu5_C            8 LFKLLLIGDSGVGKTCVLFRFSED   31 (183)
T ss_dssp             EEEEEEECCCCC------------
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            346999999999999999988643

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=94.59  E-value=0.016  Score=45.87  Aligned_cols=23  Identities=22%  Similarity=0.313  Sum_probs=20.4

Q ss_pred             CcceeeecCCCCchHHHHHHHHh
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      .-.|++.|++|+|||+|..++..
T Consensus        16 ~~~i~v~G~~~~GKssl~~~l~~   38 (187)
T 1zj6_A           16 EHKVIIVGLDNAGKTTILYQFSM   38 (187)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHT
T ss_pred             ccEEEEECCCCCCHHHHHHHHhc
Confidence            34599999999999999999984

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=94.58  E-value=0.062  Score=44.29  Aligned_cols=19  Identities=32%  Similarity=0.345  Sum_probs=15.9

Q ss_pred             CcceeeecCCCCchHHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAK  211 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAk  211 (245)
                      .+.+++.+|+|+|||+.+-
T Consensus        62 ~~~~li~a~TGsGKT~~~~   80 (236)
T 2pl3_A           62 GKDVLGAAKTGSGKTLAFL   80 (236)
T ss_dssp             TCCEEEECCTTSCHHHHHH
T ss_pred             CCCEEEEeCCCCcHHHHHH
Confidence            4679999999999998643

>2ew1_A RAS-related protein RAB-30; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=94.57  E-value=0.016  Score=47.14  Aligned_cols=22  Identities=32%  Similarity=0.566  Sum_probs=19.6

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|++.|++|+|||+|...+...
T Consensus        28 ki~lvG~~~vGKSsLi~~l~~~   49 (201)
T 2ew1_A           28 KIVLIGNAGVGKTCLVRRFTQG   49 (201)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            4999999999999999998753

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=94.57  E-value=0.013  Score=46.52  Aligned_cols=23  Identities=26%  Similarity=0.369  Sum_probs=20.0

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ..|++.|++|+|||+|...+...
T Consensus        18 ~ki~v~G~~~~GKSsl~~~l~~~   40 (199)
T 4bas_A           18 LQVVMCGLDNSGKTTIINQVKPA   40 (199)
T ss_dssp             EEEEEECCTTSCHHHHHHHHSCC
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            34999999999999999998753

>3qf7_A RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga maritima} PDB: 3qg5_A 3tho_A*

Probab=94.56  E-value=0.011  Score=53.30  Aligned_cols=25  Identities=32%  Similarity=0.525  Sum_probs=20.4

Q ss_pred             CCcc-eeeecCCCCchHHHHHHHHhc
Q 025979          192 PPRG-VLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       192 ~~~g-vLl~GPPGtGKT~lAkalA~~  216 (245)
                      .+.| ++++||+|+|||+|..||+-.
T Consensus        21 ~~~g~~~i~G~NGaGKTTll~ai~~a   46 (365)
T 3qf7_A           21 FQSGITVVEGPNGAGKSSLFEAISFA   46 (365)
T ss_dssp             CCSEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            3344 779999999999999998743

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=94.56  E-value=0.017  Score=46.21  Aligned_cols=23  Identities=26%  Similarity=0.320  Sum_probs=19.6

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -.|++.|++|+|||+|...+...
T Consensus        21 ~ki~~~G~~~~GKssl~~~l~~~   43 (201)
T 2q3h_A           21 VKCVLVGDGAVGKTSLVVSYTTN   43 (201)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHC-
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            34999999999999999998753

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=94.51  E-value=0.021  Score=47.87  Aligned_cols=23  Identities=30%  Similarity=0.426  Sum_probs=20.0

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      -+++.|.+|+|||+++..+|..+
T Consensus        16 i~~~~GkgGvGKTTl~~~La~~l   38 (262)
T 1yrb_A           16 IVVFVGTAGSGKTTLTGEFGRYL   38 (262)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEeCCCCCCHHHHHHHHHHHH
Confidence            37889999999999999998654

>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=94.49  E-value=0.016  Score=46.63  Aligned_cols=22  Identities=32%  Similarity=0.472  Sum_probs=19.5

Q ss_pred             cceeeecCCCCchHHHHHHHHh
Q 025979          194 RGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      -.|++.|++|+|||+|..++..
T Consensus        26 ~ki~v~G~~~~GKSsLi~~l~~   47 (200)
T 2o52_A           26 FKFLVIGSAGTGKSCLLHQFIE   47 (200)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHh
Confidence            3499999999999999999874

>3qkt_A DNA double-strand break repair RAD50 ATPase; RECA-like fold, coiled-coils, ATP binding, DNA bindi MRE11, replication; HET: DNA ANP; 1.90A {Pyrococcus furiosus} PDB: 3qku_A* 1ii8_A 3qks_B* 3qkr_B* 1ii8_B

Probab=94.48  E-value=0.0077  Score=53.44  Aligned_cols=22  Identities=32%  Similarity=0.457  Sum_probs=19.1

Q ss_pred             eeeecCCCCchHHHHHHHHhcc
Q 025979          196 VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+|+||+|+|||++..||.-.+
T Consensus        26 ~~i~G~NGsGKS~lleAi~~~l   47 (339)
T 3qkt_A           26 NLIIGQNGSGKSSLLDAILVGL   47 (339)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            7899999999999999986543

>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=94.47  E-value=0.018  Score=45.76  Aligned_cols=22  Identities=32%  Similarity=0.389  Sum_probs=20.0

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .+++.|++|+|||+|...+...
T Consensus        20 ki~v~G~~~~GKssli~~l~~~   41 (194)
T 2atx_A           20 KCVVVGDGAVGKTCLLMSYAND   41 (194)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4999999999999999999864

>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=94.46  E-value=0.014  Score=46.37  Aligned_cols=23  Identities=26%  Similarity=0.362  Sum_probs=20.3

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .|++.|++|+|||+|..++....
T Consensus        23 ki~v~G~~~~GKSsli~~l~~~~   45 (190)
T 2h57_A           23 HVLCLGLDNSGKTTIINKLKPSN   45 (190)
T ss_dssp             EEEEEECTTSSHHHHHHHTSCGG
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            49999999999999999987643

>3b5x_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; 5.50A {Vibrio cholerae}

Probab=94.44  E-value=0.016  Score=55.21  Aligned_cols=38  Identities=24%  Similarity=0.365  Sum_probs=27.8

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhccc--ceeeeechhH
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTT--AAFIRVVGSE  228 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~--~~~~~v~~s~  228 (245)
                      .++.-+.+.||+|+|||++++.+++...  .--+.+++.+
T Consensus       367 ~~G~~~~ivG~sGsGKSTll~~l~g~~~p~~G~i~~~g~~  406 (582)
T 3b5x_A          367 PQGKTVALVGRSGSGKSTIANLFTRFYDVDSGSICLDGHD  406 (582)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcCCCCCCCEEEECCEE
Confidence            3444489999999999999999998763  2244555543

>2f7s_A C25KG, RAS-related protein RAB-27B; G-protein, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2iez_A*

Probab=94.44  E-value=0.019  Score=46.58  Aligned_cols=22  Identities=27%  Similarity=0.442  Sum_probs=19.7

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|+|.|++|+|||+|..++...
T Consensus        27 ki~vvG~~~~GKSsLi~~l~~~   48 (217)
T 2f7s_A           27 KLLALGDSGVGKTTFLYRYTDN   48 (217)
T ss_dssp             EEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            4999999999999999999853

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=94.43  E-value=0.016  Score=46.27  Aligned_cols=21  Identities=33%  Similarity=0.621  Sum_probs=18.8

Q ss_pred             eeeecCCCCchHHHHHHHHhc
Q 025979          196 VLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~  216 (245)
                      |++.|++|+|||+|..++...
T Consensus        29 i~vvG~~~~GKSsLi~~l~~~   49 (192)
T 2il1_A           29 VIIIGSRGVGKTSLMERFTDD   49 (192)
T ss_dssp             EEEECSTTSSHHHHHHHHCC-
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            999999999999999998753

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=94.39  E-value=0.026  Score=51.81  Aligned_cols=24  Identities=33%  Similarity=0.566  Sum_probs=21.1

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ...+++||||||||.|+..||+..
T Consensus       176 QR~lIfg~~g~GKT~Ll~~Ia~~i  199 (427)
T 3l0o_A          176 QRGMIVAPPKAGKTTILKEIANGI  199 (427)
T ss_dssp             CEEEEEECTTCCHHHHHHHHHHHH
T ss_pred             ceEEEecCCCCChhHHHHHHHHHH
Confidence            349999999999999999998864

>2qu8_A Putative nucleolar GTP-binding protein 1; GTPase, malaria, structural genomics, structural genomics consortium, SGC, unknown function; HET: GDP; 2.01A {Plasmodium falciparum}

Probab=94.38  E-value=0.018  Score=47.39  Aligned_cols=23  Identities=26%  Similarity=0.576  Sum_probs=20.2

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ..|++.|++|+|||+|..++...
T Consensus        30 ~kI~vvG~~~vGKSsLin~l~~~   52 (228)
T 2qu8_A           30 KTIILSGAPNVGKSSFMNIVSRA   52 (228)
T ss_dssp             EEEEEECSTTSSHHHHHHHHTTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            34999999999999999999764

>2yv5_A YJEQ protein; hydrolase, GTPase, permutation, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GDP; 1.90A {Aquifex aeolicus}

Probab=94.38  E-value=0.019  Score=50.26  Aligned_cols=23  Identities=26%  Similarity=0.436  Sum_probs=20.4

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .-+.|.||+|+|||+|.++|+ ..
T Consensus       166 ~i~~l~G~sG~GKSTLln~l~-~~  188 (302)
T 2yv5_A          166 FICILAGPSGVGKSSILSRLT-GE  188 (302)
T ss_dssp             CEEEEECSTTSSHHHHHHHHH-SC
T ss_pred             cEEEEECCCCCCHHHHHHHHH-Hh
Confidence            447899999999999999999 55

>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=94.38  E-value=0.016  Score=45.70  Aligned_cols=22  Identities=23%  Similarity=0.344  Sum_probs=19.8

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|++.|++|+|||+|..++...
T Consensus        23 ~i~v~G~~~~GKSsli~~l~~~   44 (181)
T 2h17_A           23 KVIIVGLDNAGKTTILYQFSMN   44 (181)
T ss_dssp             EEEEEEETTSSHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3999999999999999999853

>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=94.36  E-value=0.02  Score=46.98  Aligned_cols=25  Identities=28%  Similarity=0.270  Sum_probs=21.6

Q ss_pred             ceeeecCCCCchHHHHHHHHhcccc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      -.+++||.|+|||++..||.-.++.
T Consensus        25 ~~~I~G~NgsGKStil~ai~~~l~g   49 (203)
T 3qks_A           25 INLIIGQNGSGKSSLLDAILVGLYW   49 (203)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhcC
Confidence            3789999999999999999876654

>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=94.32  E-value=0.019  Score=46.84  Aligned_cols=21  Identities=43%  Similarity=0.548  Sum_probs=19.3

Q ss_pred             ceeeecCCCCchHHHHHHHHh
Q 025979          195 GVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~  215 (245)
                      .|++.|++|+|||+|..++..
T Consensus        36 ki~vvG~~~vGKSsli~~l~~   56 (214)
T 2j1l_A           36 KVVLVGDGGCGKTSLLMVFAD   56 (214)
T ss_dssp             EEEEEECTTSSHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHc
Confidence            499999999999999999975

>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=94.32  E-value=0.02  Score=46.29  Aligned_cols=22  Identities=23%  Similarity=0.336  Sum_probs=19.9

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|++.|++|+|||+|..++...
T Consensus        27 ki~vvG~~~~GKSsli~~l~~~   48 (207)
T 2fv8_A           27 KLVVVGDGACGKTCLLIVFSKD   48 (207)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            4999999999999999999863

>3b60_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; HET: ANP; 3.70A {Salmonella typhimurium} SCOP: c.37.1.12 f.37.1.1 PDB: 3b5y_A* 3b5z_A* 3b5w_A

Probab=94.32  E-value=0.019  Score=54.73  Aligned_cols=38  Identities=26%  Similarity=0.413  Sum_probs=27.8

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhccc--ceeeeechh
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHTT--AAFIRVVGS  227 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l~--~~~~~v~~s  227 (245)
                      +.++.-+.+.||+|+|||+|.+.+++...  .--+.+++.
T Consensus       366 i~~G~~~~ivG~sGsGKSTLl~~l~g~~~p~~G~i~~~g~  405 (582)
T 3b60_A          366 IPAGKTVALVGRSGSGKSTIASLITRFYDIDEGHILMDGH  405 (582)
T ss_dssp             ECTTCEEEEEECTTSSHHHHHHHHTTTTCCSEEEEEETTE
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhhccCCCCCeEEECCE
Confidence            34444599999999999999999998763  224445543

>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=94.29  E-value=0.02  Score=46.15  Aligned_cols=22  Identities=23%  Similarity=0.380  Sum_probs=19.6

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|++.|++|+|||+|...+...
T Consensus        31 ki~vvG~~~vGKSsli~~l~~~   52 (201)
T 2hup_A           31 KLVLVGDASVGKTCVVQRFKTG   52 (201)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhhC
Confidence            4999999999999999998753

>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=94.26  E-value=0.02  Score=45.82  Aligned_cols=22  Identities=32%  Similarity=0.493  Sum_probs=19.7

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|++.|++|+|||+|.+.+.+.
T Consensus        22 ki~~vG~~~vGKTsLi~~l~~~   43 (196)
T 3llu_A           22 RILLMGLRRSGKSSIQKVVFHK   43 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhc
Confidence            3999999999999999988764

>3euj_A Chromosome partition protein MUKB, linker; MUKB, MUKE, chromosome condensation, condensin, SMC, N subunit, ABC-type ATPase, WHD, ATP-binding; HET: AGS; 3.10A {Haemophilus ducreyi} PDB: 3euk_A*

Probab=94.23  E-value=0.022  Score=53.38  Aligned_cols=27  Identities=22%  Similarity=0.239  Sum_probs=22.9

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.+ .-+.|.||+|+|||+|.++|+..+
T Consensus        27 i~~-e~~~liG~nGsGKSTLl~~l~Gl~   53 (483)
T 3euj_A           27 FDE-LVTTLSGGNGAGKSTTMAGFVTAL   53 (483)
T ss_dssp             CCS-SEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             Ecc-ceEEEECCCCCcHHHHHHHHhcCC
Confidence            344 558899999999999999999865

>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=94.22  E-value=0.021  Score=45.92  Aligned_cols=22  Identities=23%  Similarity=0.351  Sum_probs=19.8

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|++.|++|+|||+|..++...
T Consensus        27 ki~vvG~~~~GKSsli~~l~~~   48 (201)
T 2gco_A           27 KLVIVGDGACGKTCLLIVFSKD   48 (201)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4999999999999999999863

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=94.20  E-value=0.021  Score=46.06  Aligned_cols=23  Identities=17%  Similarity=0.200  Sum_probs=20.2

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -.|++.|+||+|||+|...+...
T Consensus        10 ~ki~i~G~~~~GKTsli~~l~~~   32 (212)
T 2j0v_A           10 IKCVTVGDGAVGKTCMLICYTSN   32 (212)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            45999999999999999998853

>2o5v_A DNA replication and repair protein RECF; ABC ATPase, walker A motif, P-loop, signature motif, replication/recombination complex; HET: DNA; 1.61A {Deinococcus radiodurans}

Probab=94.20  E-value=0.011  Score=53.22  Aligned_cols=28  Identities=36%  Similarity=0.521  Sum_probs=22.2

Q ss_pred             cCCCcc-eeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRG-VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~g-vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +..+.| .+|+||+|+|||++..+|+..+
T Consensus        22 ~~~~~g~~~i~G~nG~GKttll~ai~~~~   50 (359)
T 2o5v_A           22 LNFPEGVTGIYGENGAGKTNLLEAAYLAL   50 (359)
T ss_dssp             EECCSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEcCCeEEEECCCCCChhHHHHHHHHhc
Confidence            333444 7799999999999999998644

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=94.20  E-value=0.022  Score=50.88  Aligned_cols=23  Identities=35%  Similarity=0.563  Sum_probs=20.4

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      -+.|.||||+|||+|..+++..+
T Consensus        76 ~v~lvG~pgaGKSTLln~L~~~~   98 (349)
T 2www_A           76 RVGLSGPPGAGKSTFIEYFGKML   98 (349)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHh
Confidence            38899999999999999999753

>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=94.19  E-value=0.017  Score=54.03  Aligned_cols=26  Identities=27%  Similarity=0.488  Sum_probs=21.9

Q ss_pred             CcceeeecCCCCchHHHHHHHHhccc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      +..++|+||||||||+|+..++....
T Consensus       151 Gq~~~i~G~sGvGKTtL~~~l~~~~~  176 (473)
T 1sky_E          151 GGKIGLFGGAGVGKTVLIQELIHNIA  176 (473)
T ss_dssp             TCEEEEECCSSSCHHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCccHHHHHHHhhhh
Confidence            34599999999999999998887653

>2x77_A ADP-ribosylation factor; GTP-binding protein, small GTPase, nucleotide-binding; HET: GDP; 2.10A {Leishmania major}

Probab=94.18  E-value=0.02  Score=45.24  Aligned_cols=24  Identities=25%  Similarity=0.248  Sum_probs=20.5

Q ss_pred             CCcceeeecCCCCchHHHHHHHHh
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      ..-.+++.|+||+|||+|..++..
T Consensus        21 ~~~~i~v~G~~~~GKssli~~l~~   44 (189)
T 2x77_A           21 RKIRVLMLGLDNAGKTSILYRLHL   44 (189)
T ss_dssp             SCEEEEEEEETTSSHHHHHHHTCC
T ss_pred             CceEEEEECCCCCCHHHHHHHHHc
Confidence            344599999999999999999854

>2qnr_A Septin-2, protein NEDD5; structural genomics consortium, SGC, mitosis, GDP, C cycle, cell division, GTP-binding, nucleotide-binding; HET: GDP; 2.60A {Homo sapiens} PDB: 2qa5_A* 3ftq_A*

Probab=94.18  E-value=0.017  Score=50.55  Aligned_cols=21  Identities=24%  Similarity=0.463  Sum_probs=18.7

Q ss_pred             eeeecCCCCchHHHHHHHHhc
Q 025979          196 VLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~  216 (245)
                      |++.||+|+|||+|.+.|+..
T Consensus        21 I~lvG~nG~GKSTLl~~L~g~   41 (301)
T 2qnr_A           21 LMVVGESGLGKSTLINSLFLT   41 (301)
T ss_dssp             EEEEEETTSSHHHHHHHHHC-
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            799999999999999998764

>3cpj_B GTP-binding protein YPT31/YPT8; RAB GTPase, prenylation, vesicular transport, acetylation, golgi apparatus, lipoprotein, membrane; HET: GDP; 2.35A {Saccharomyces cerevisiae}

Probab=94.16  E-value=0.024  Score=46.40  Aligned_cols=22  Identities=27%  Similarity=0.517  Sum_probs=19.9

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|++.|++|+|||+|..++...
T Consensus        15 ki~v~G~~~vGKSsli~~l~~~   36 (223)
T 3cpj_B           15 KIVLIGDSGVGKSNLLSRFTKN   36 (223)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            4999999999999999999854

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=94.14  E-value=0.038  Score=56.70  Aligned_cols=43  Identities=28%  Similarity=0.268  Sum_probs=33.3

Q ss_pred             CcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhc
Q 025979          162 GGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       162 ~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      +|-+..+++|.+.+...            ...+-+.++||+|+|||+||+.+++.
T Consensus       131 VGRe~eLeeL~elL~~~------------d~~RVV~IvGmGGIGKTTLAk~Vy~d  173 (1221)
T 1vt4_I          131 VSRLQPYLKLRQALLEL------------RPAKNVLIDGVLGSGKTWVALDVCLS  173 (1221)
T ss_dssp             CCCHHHHHHHHHHHHHC------------CSSCEEEECCSTTSSHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHhcc------------CCCeEEEEEcCCCccHHHHHHHHHHh
Confidence            77788888888776431            12345889999999999999999863

>3qf4_B Uncharacterized ABC transporter ATP-binding prote TM_0288; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=94.10  E-value=0.023  Score=54.42  Aligned_cols=28  Identities=36%  Similarity=0.619  Sum_probs=23.8

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||++++.+++..
T Consensus       378 i~~G~~~~ivG~sGsGKSTll~~l~g~~  405 (598)
T 3qf4_B          378 IKPGQKVALVGPTGSGKTTIVNLLMRFY  405 (598)
T ss_dssp             CCTTCEEEEECCTTSSTTHHHHHHTTSS
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHhcCc
Confidence            3444459999999999999999999876

>1t9h_A YLOQ, probable GTPase ENGC; N-terminal beta-barrel domain with oligonucleotide binding fold, central GTP binding domain; 1.60A {Bacillus subtilis} SCOP: b.40.4.5 c.37.1.8

Probab=94.09  E-value=0.01  Score=52.36  Aligned_cols=26  Identities=23%  Similarity=0.437  Sum_probs=21.1

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +..-+.|.||||+|||+|.++|+...
T Consensus       172 ~G~~~~lvG~sG~GKSTLln~L~g~~  197 (307)
T 1t9h_A          172 QDKTTVFAGQSGVGKSSLLNAISPEL  197 (307)
T ss_dssp             TTSEEEEEESHHHHHHHHHHHHCC--
T ss_pred             CCCEEEEECCCCCCHHHHHHHhcccc
Confidence            34458999999999999999998755

>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=94.08  E-value=0.022  Score=52.37  Aligned_cols=23  Identities=22%  Similarity=0.401  Sum_probs=20.6

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      -+.|.||+|+|||+|.++|++..
T Consensus        71 ~valvG~nGaGKSTLln~L~Gl~   93 (413)
T 1tq4_A           71 NVAVTGETGSGKSSFINTLRGIG   93 (413)
T ss_dssp             EEEEEECTTSSHHHHHHHHHTCC
T ss_pred             EEEEECCCCCcHHHHHHHHhCCC
Confidence            37899999999999999999844

>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=94.01  E-value=0.025  Score=45.77  Aligned_cols=22  Identities=23%  Similarity=0.259  Sum_probs=19.5

Q ss_pred             cceeeecCCCCchHHHHHHHHh
Q 025979          194 RGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      -.|++.|++|+|||+|...+..
T Consensus        31 ~ki~vvG~~~~GKSsLi~~l~~   52 (204)
T 4gzl_A           31 IKCVVVGDGAVGKTCLLISYTT   52 (204)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEECcCCCCHHHHHHHHHh
Confidence            3499999999999999988875

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=94.01  E-value=0.023  Score=53.92  Aligned_cols=26  Identities=27%  Similarity=0.446  Sum_probs=22.4

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++.-+.|.||+|+|||+|+++|+..+
T Consensus       293 ~Gei~~i~G~nGsGKSTLl~~l~Gl~  318 (538)
T 3ozx_A          293 EGEIIGILGPNGIGKTTFARILVGEI  318 (538)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            34448899999999999999999865

>2qag_C Septin-7; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=93.99  E-value=0.023  Score=52.24  Aligned_cols=22  Identities=23%  Similarity=0.442  Sum_probs=20.0

Q ss_pred             eeeecCCCCchHHHHHHHHhcc
Q 025979          196 VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      |+|.||+|+|||+|.+.+++..
T Consensus        34 I~lvG~sGaGKSTLln~L~g~~   55 (418)
T 2qag_C           34 LMVVGESGLGKSTLINSLFLTD   55 (418)
T ss_dssp             EEEECCTTSSHHHHHHHHTTCC
T ss_pred             EEEECCCCCcHHHHHHHHhCCC
Confidence            6999999999999999998754

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=93.96  E-value=0.025  Score=53.54  Aligned_cols=26  Identities=31%  Similarity=0.429  Sum_probs=22.4

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++.-+.+.||.|+|||+|+++|+..+
T Consensus       311 ~Ge~~~i~G~NGsGKSTLlk~l~Gl~  336 (538)
T 1yqt_A          311 KGEVIGIVGPNGIGKTTFVKMLAGVE  336 (538)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            34448899999999999999999865

>3q3j_B RHO-related GTP-binding protein RHO6; RAS-binding domain, plexin, small GTPase, structural genomic consortium, SGC; HET: GNP; 1.97A {Homo sapiens} PDB: 2rex_B* 2cls_A*

Probab=93.93  E-value=0.028  Score=45.91  Aligned_cols=22  Identities=27%  Similarity=0.428  Sum_probs=19.7

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|++.|++|||||+|...+...
T Consensus        29 ki~vvG~~~vGKSsL~~~l~~~   50 (214)
T 3q3j_B           29 KLVLVGDVQCGKTAMLQVLAKD   50 (214)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            4999999999999999998754

>2yc2_C IFT27, small RAB-related GTPase; transport protein, cilium, IFT complex; 2.59A {Chlamydomonas reinhardtii} PDB: 2yc4_C

Probab=93.90  E-value=0.012  Score=46.97  Aligned_cols=22  Identities=23%  Similarity=0.342  Sum_probs=4.3

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|++.|++|+|||+|..++...
T Consensus        22 ~i~v~G~~~~GKssli~~l~~~   43 (208)
T 2yc2_C           22 KVAVVGEATVGKSALISMFTSK   43 (208)
T ss_dssp             EEEEC-----------------
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4999999999999999988765

>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=93.89  E-value=0.045  Score=43.94  Aligned_cols=19  Identities=32%  Similarity=0.312  Sum_probs=16.0

Q ss_pred             CcceeeecCCCCchHHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAK  211 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAk  211 (245)
                      .+.+++.+|+|+|||..+-
T Consensus        40 ~~~~lv~apTGsGKT~~~~   58 (206)
T 1vec_A           40 GRDILARAKNGTGKSGAYL   58 (206)
T ss_dssp             TCCEEEECCSSSTTHHHHH
T ss_pred             CCCEEEECCCCCchHHHHH
Confidence            3679999999999997554

>1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like, hydrolase; 2.40A {Escherichia coli} SCOP: c.37.1.8 d.52.3.1 PDB: 1x1l_X 3ieu_A* 1x18_X

Probab=93.88  E-value=0.027  Score=49.10  Aligned_cols=22  Identities=23%  Similarity=0.428  Sum_probs=20.2

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -+.+.|+||+|||+|..++...
T Consensus        10 ~VaIvG~~nvGKSTLln~L~g~   31 (301)
T 1ega_A           10 FIAIVGRPNVGKSTLLNKLLGQ   31 (301)
T ss_dssp             EEEEECSSSSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            5999999999999999999865

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=93.88  E-value=0.038  Score=45.72  Aligned_cols=24  Identities=33%  Similarity=0.565  Sum_probs=20.7

Q ss_pred             cc-eeeecCCCCchHHHHHHHHhcc
Q 025979          194 RG-VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~g-vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +| +++|+++|+|||++|-++|-.+
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA   52 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARA   52 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHH
Confidence            44 8899999999999999888655

>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur cluster, adenosine diphosphate, nucleotide-binding; HET: ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*

Probab=93.87  E-value=0.03  Score=53.85  Aligned_cols=26  Identities=38%  Similarity=0.428  Sum_probs=22.4

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++.-+.|.||+|+|||+|.+.|+..+
T Consensus       116 ~Ge~~~LiG~NGsGKSTLlkiL~Gll  141 (607)
T 3bk7_A          116 DGMVVGIVGPNGTGKTTAVKILAGQL  141 (607)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhCCC
Confidence            33448899999999999999999876

>3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA, 30S ribosome ASSE GTP-binding, nucleotide-binding; HET: GNP; 1.90A {Aquifex aeolicus} PDB: 3r9w_A* 3r9x_A*

Probab=93.86  E-value=0.026  Score=49.34  Aligned_cols=25  Identities=28%  Similarity=0.457  Sum_probs=21.1

Q ss_pred             CCcc-eeeecCCCCchHHHHHHHHhc
Q 025979          192 PPRG-VLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       192 ~~~g-vLl~GPPGtGKT~lAkalA~~  216 (245)
                      +|.| |.+.|+||+|||+|..++...
T Consensus         8 ~~~g~v~ivG~~nvGKSTLin~l~g~   33 (308)
T 3iev_A            8 MKVGYVAIVGKPNVGKSTLLNNLLGT   33 (308)
T ss_dssp             CEEEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHhCC
Confidence            4445 889999999999999998764

>3szr_A Interferon-induced GTP-binding protein MX1; interferon-induced antiviral GTPase, membrane associated, PR binding; 3.50A {Homo sapiens} PDB: 3zys_B

Probab=93.86  E-value=0.036  Score=53.25  Aligned_cols=32  Identities=19%  Similarity=0.480  Sum_probs=25.1

Q ss_pred             Hhhhcc----CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          185 YKQIGI----DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       185 ~~~~g~----~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +...|+    +.|. +.+.||+|+|||++.++|++..
T Consensus        34 l~~~gv~~~l~lp~-iaIvG~nGsGKSTLL~~I~Gl~   69 (608)
T 3szr_A           34 LRALGVEQDLALPA-IAVIGDQSSGKSSVLEALSGVA   69 (608)
T ss_dssp             HHHHSCCSSCCCCC-EECCCCTTSCHHHHHHHHHSCC
T ss_pred             HHhCCCCCcccCCe-EEEECCCCChHHHHHHHHhCCC
Confidence            455554    3343 8999999999999999999864

>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=93.81  E-value=0.033  Score=46.33  Aligned_cols=22  Identities=27%  Similarity=0.374  Sum_probs=17.3

Q ss_pred             CcceeeecCCCCchHHHHHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVA  214 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA  214 (245)
                      ++.+++.||+|||||++...+.
T Consensus        76 g~~~~i~g~TGsGKTt~~~~~~   97 (235)
T 3llm_A           76 NSVVIIRGATGCGKTTQVPQFI   97 (235)
T ss_dssp             CSEEEEECCTTSSHHHHHHHHH
T ss_pred             CCEEEEEeCCCCCcHHhHHHHH
Confidence            4569999999999997655443

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=93.76  E-value=0.12  Score=45.36  Aligned_cols=41  Identities=17%  Similarity=0.182  Sum_probs=26.1

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc------cceeeeechh-HHHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT------TAAFIRVVGS-EFVQKY  233 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l------~~~~~~v~~s-~l~~~~  233 (245)
                      .+.+++.+|+|+|||+.+-..+-..      +...+.+.+. ++...+
T Consensus        45 ~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L~~q~   92 (391)
T 1xti_A           45 GMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQI   92 (391)
T ss_dssp             TCCEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHH
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEEEECCCHHHHHHH
Confidence            4679999999999998764433322      3344555444 665544

>4a82_A Cystic fibrosis transmembrane conductance regulat; CFTR, ION channel, transport protein, casse protein; 2.00A {Homo sapiens} PDB: 2onj_A* 2hyd_A

Probab=93.76  E-value=0.019  Score=54.70  Aligned_cols=38  Identities=24%  Similarity=0.340  Sum_probs=27.6

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcccc--eeeeechh
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHTTA--AFIRVVGS  227 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l~~--~~~~v~~s  227 (245)
                      +.++.-+.+.||+|+|||++.+.+++....  --+.+++.
T Consensus       364 i~~G~~~~ivG~sGsGKSTll~~l~g~~~p~~G~i~~~g~  403 (578)
T 4a82_A          364 IEKGETVAFVGMSGGGKSTLINLIPRFYDVTSGQILIDGH  403 (578)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHTTTTTSSCCSEEEEEETTE
T ss_pred             ECCCCEEEEECCCCChHHHHHHHHhcCCCCCCcEEEECCE
Confidence            344445899999999999999999987632  23445543

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=93.74  E-value=0.06  Score=44.67  Aligned_cols=19  Identities=32%  Similarity=0.307  Sum_probs=15.8

Q ss_pred             CcceeeecCCCCchHHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAK  211 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAk  211 (245)
                      .+.+++.+|+|+|||+.+-
T Consensus        67 ~~~~li~apTGsGKT~~~~   85 (237)
T 3bor_A           67 GYDVIAQAQSGTGKTATFA   85 (237)
T ss_dssp             TCCEEECCCSSHHHHHHHH
T ss_pred             CCCEEEECCCCCcHHHHHH
Confidence            3669999999999998643

>2aka_B Dynamin-1; fusion protein, GTPase domain, myosin, contractIle protein; 1.90A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 3l43_A*

Probab=93.73  E-value=0.038  Score=47.18  Aligned_cols=23  Identities=13%  Similarity=0.291  Sum_probs=20.4

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .|++.|.||+|||+|..++.+.-
T Consensus        28 ~i~vvG~~~~GKSSLln~l~g~~   50 (299)
T 2aka_B           28 QIAVVGGQSAGKSSVLENFVGRD   50 (299)
T ss_dssp             EEEEEEBTTSCHHHHHHHHHTSC
T ss_pred             eEEEEeCCCCCHHHHHHHHHCCC
Confidence            49999999999999999998643

>2g3y_A GTP-binding protein GEM; small GTPase, GDP, inactive state, RGK family, structur genomics, structural genomics consortium, SGC, signaling PR; HET: GDP; 2.40A {Homo sapiens} SCOP: c.37.1.8

Probab=93.69  E-value=0.033  Score=46.00  Aligned_cols=21  Identities=43%  Similarity=0.635  Sum_probs=19.1

Q ss_pred             ceeeecCCCCchHHHHHHHHh
Q 025979          195 GVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~  215 (245)
                      .|++.|+||||||+|...+..
T Consensus        39 kVvlvG~~~vGKSSLl~r~~~   59 (211)
T 2g3y_A           39 RVVLIGEQGVGKSTLANIFAG   59 (211)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            389999999999999999874

>2xtp_A GTPase IMAP family member 2; immune system, G protein; HET: MSE; 1.50A {Homo sapiens} PDB: 2xto_A* 2xtm_A* 2xtn_A* 3p1j_A

Probab=93.68  E-value=0.033  Score=46.87  Aligned_cols=23  Identities=26%  Similarity=0.514  Sum_probs=20.3

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ..|+|.|+||+|||+|..++...
T Consensus        23 ~~I~lvG~~g~GKStl~n~l~~~   45 (260)
T 2xtp_A           23 LRIILVGKTGTGKSAAGNSILRK   45 (260)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHTS
T ss_pred             eEEEEECCCCCCHHHHHHHHhCC
Confidence            45999999999999999999754

>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=93.66  E-value=0.064  Score=45.97  Aligned_cols=40  Identities=18%  Similarity=0.198  Sum_probs=29.0

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceeeeechh-HHHHHH
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS-EFVQKY  233 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s-~l~~~~  233 (245)
                      +.+++.+|+|+|||+++-..+-..+...+.+.+. ++...+
T Consensus        32 ~~~lv~~~TGsGKT~~~~~~~~~~~~~~liv~P~~~L~~q~   72 (337)
T 2z0m_A           32 KNVVVRAKTGSGKTAAYAIPILELGMKSLVVTPTRELTRQV   72 (337)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHTCCEEEECSSHHHHHHH
T ss_pred             CCEEEEcCCCCcHHHHHHHHHHhhcCCEEEEeCCHHHHHHH
Confidence            5699999999999998776666556666656554 565544

>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=93.65  E-value=0.037  Score=50.34  Aligned_cols=41  Identities=27%  Similarity=0.454  Sum_probs=31.0

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc---cceeeeechh-HHHHHHh
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS-EFVQKYL  234 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s-~l~~~~~  234 (245)
                      .+++++||||+|||.+.+.+...+   +..++.+|.. ++...|.
T Consensus        54 ~h~~i~G~tGsGKs~~~~~li~~~~~~g~~viv~Dpkge~~~~~~   98 (437)
T 1e9r_A           54 RHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPNGDMLSKFG   98 (437)
T ss_dssp             GCEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEEETTHHHHHHC
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeCCCchhHHhc
Confidence            569999999999999988777654   6677777754 6655553

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=93.65  E-value=0.053  Score=52.54  Aligned_cols=38  Identities=26%  Similarity=0.390  Sum_probs=25.1

Q ss_pred             cCCCcceeeecCCCCchHHHHH-HHHhc---ccceeeeechh
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAK-AVANH---TTAAFIRVVGS  227 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAk-alA~~---l~~~~~~v~~s  227 (245)
                      +...+.+++.||+|+|||+.+- ++...   -+...+.+.+.
T Consensus        43 ~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~il~i~P~   84 (715)
T 2va8_A           43 LLEGNRLLLTSPTGSGKTLIAEMGIISFLLKNGGKAIYVTPL   84 (715)
T ss_dssp             TTTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCSEEEEECSC
T ss_pred             hcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHCCCeEEEEeCc
Confidence            3446779999999999999884 33222   24455555544

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=93.62  E-value=0.038  Score=53.17  Aligned_cols=24  Identities=29%  Similarity=0.365  Sum_probs=21.6

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .-+.|.||+|+|||+|.+.|+..+
T Consensus       104 ei~~LvGpNGaGKSTLLkiL~Gll  127 (608)
T 3j16_B          104 QVLGLVGTNGIGKSTALKILAGKQ  127 (608)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CEEEEECCCCChHHHHHHHHhcCC
Confidence            348899999999999999999876

>3qf4_A ABC transporter, ATP-binding protein; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=93.53  E-value=0.026  Score=53.98  Aligned_cols=29  Identities=24%  Similarity=0.439  Sum_probs=24.2

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      +.++.-+.+.||+|+|||++++.+++...
T Consensus       366 i~~Ge~~~ivG~sGsGKSTll~~l~g~~~  394 (587)
T 3qf4_A          366 VKPGSLVAVLGETGSGKSTLMNLIPRLID  394 (587)
T ss_dssp             ECTTCEEEEECSSSSSHHHHHHTTTTSSC
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCcc
Confidence            34445599999999999999999998763

>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur cluster, adenosine diphosphate, nucleotide-binding; HET: ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*

Probab=93.52  E-value=0.033  Score=53.56  Aligned_cols=26  Identities=31%  Similarity=0.429  Sum_probs=22.3

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++.-+.+.||+|+|||+|.++|+..+
T Consensus       381 ~Gei~~i~G~NGsGKSTLlk~l~Gl~  406 (607)
T 3bk7_A          381 KGEVIGIVGPNGIGKTTFVKMLAGVE  406 (607)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            33448899999999999999999865

>1w1w_A Structural maintenance of chromosome 1; cohesin, chromosome segregation, cell adhesion, kleisin, MIT cell cycle; HET: ATG; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.12

Probab=93.51  E-value=0.042  Score=50.13  Aligned_cols=27  Identities=22%  Similarity=0.345  Sum_probs=22.8

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      +.-.+|+||.|+|||++..+|+..++.
T Consensus        26 ~~~~~i~G~nG~GKstll~ai~~~~~~   52 (430)
T 1w1w_A           26 SNFTSIIGPNGSGKSNMMDAISFVLGV   52 (430)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHHHHTTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhhcc
Confidence            344889999999999999999976643

>3auy_A DNA double-strand break repair RAD50 ATPase; DNA repair, ABC transporter ATPase domain-like; HET: DNA ADP; 2.70A {Methanocaldococcus jannaschii} PDB: 3aux_A* 3av0_B*

Probab=93.40  E-value=0.015  Score=52.16  Aligned_cols=26  Identities=35%  Similarity=0.502  Sum_probs=21.4

Q ss_pred             cCCCcc-eeeecCCCCchHHHHHHHHh
Q 025979          190 IDPPRG-VLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       190 ~~~~~g-vLl~GPPGtGKT~lAkalA~  215 (245)
                      ++...| .+|+||+|+|||++..||.-
T Consensus        21 i~f~~gl~vi~G~NGaGKT~ileAI~~   47 (371)
T 3auy_A           21 IKFEKGIVAIIGENGSGKSSIFEAVFF   47 (371)
T ss_dssp             EECCSEEEEEEECTTSSHHHHHHHHHH
T ss_pred             EecCCCeEEEECCCCCCHHHHHHHHHH
Confidence            344445 78999999999999999985

>2qtf_A Protein HFLX, GTP-binding protein; beta-alpha-barrels, nucleotide-binding, nucleotide binding protein; 2.00A {Sulfolobus solfataricus P2} PDB: 2qth_A* 3kxi_A* 3kxl_A 3kxk_A

Probab=93.32  E-value=0.04  Score=49.61  Aligned_cols=23  Identities=26%  Similarity=0.352  Sum_probs=19.8

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+.+.|+||+|||+|..++++..
T Consensus       181 ~V~lvG~~naGKSTLln~L~~~~  203 (364)
T 2qtf_A          181 SIGIVGYTNSGKTSLFNSLTGLT  203 (364)
T ss_dssp             EEEEECBTTSSHHHHHHHHHCC-
T ss_pred             EEEEECCCCCCHHHHHHHHHCCC
Confidence            38899999999999999998643

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=93.24  E-value=0.025  Score=54.46  Aligned_cols=22  Identities=41%  Similarity=0.605  Sum_probs=20.5

Q ss_pred             eeeecCCCCchHHHHHHHHhcc
Q 025979          196 VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.|.||+|+|||+|.++|+..+
T Consensus       381 v~iiG~NGsGKSTLlk~l~Gl~  402 (608)
T 3j16_B          381 LVMMGENGTGKTTLIKLLAGAL  402 (608)
T ss_dssp             EEEESCTTSSHHHHHHHHHTSS
T ss_pred             EEEECCCCCcHHHHHHHHhcCC
Confidence            7899999999999999999865

>4djt_A GTP-binding nuclear protein GSP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid, RAN family; HET: GDP; 1.80A {Encephalitozoon cuniculi}

Probab=93.23  E-value=0.019  Score=46.65  Aligned_cols=22  Identities=32%  Similarity=0.431  Sum_probs=19.6

Q ss_pred             cceeeecCCCCchHHHHHHHHh
Q 025979          194 RGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      -.|++.|+||+|||+|..++..
T Consensus        12 ~ki~vvG~~~~GKSsli~~l~~   33 (218)
T 4djt_A           12 YKICLIGDGGVGKTTYINRVLD   33 (218)
T ss_dssp             EEEEEECCTTSSHHHHHCBCTT
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            3599999999999999998874

>1mky_A Probable GTP-binding protein ENGA; GTPase, DER, KH-domain, tandem G-domains, ligand binding protein; HET: GDP; 1.90A {Thermotoga maritima} SCOP: c.37.1.8 c.37.1.8 d.52.5.1

Probab=93.19  E-value=0.041  Score=50.48  Aligned_cols=24  Identities=33%  Similarity=0.499  Sum_probs=21.0

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..+.+.|+||+|||+|..++....
T Consensus       181 ~kvaivG~~gvGKSTLln~l~g~~  204 (439)
T 1mky_A          181 IKVAIVGRPNVGKSTLFNAILNKE  204 (439)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTST
T ss_pred             ceEEEECCCCCCHHHHHHHHhCCc
Confidence            358999999999999999998753

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=93.16  E-value=0.18  Score=41.41  Aligned_cols=41  Identities=15%  Similarity=0.240  Sum_probs=25.0

Q ss_pred             CcceeeecCCCCchHHHHH-HHHhcc-----cceeeeechh-HHHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAK-AVANHT-----TAAFIRVVGS-EFVQKY  233 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAk-alA~~l-----~~~~~~v~~s-~l~~~~  233 (245)
                      .+.+++.+|+|+|||..+- .+...+     +...+.+.+. ++...+
T Consensus        61 ~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~  108 (230)
T 2oxc_A           61 GLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQI  108 (230)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHH
T ss_pred             CCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEeCCHHHHHHH
Confidence            4679999999999998633 333332     2344444443 555443

>2e87_A Hypothetical protein PH1320; GTP-binding, GTPase, OBG, bundle, GDP, complex, structural G NPPSFA; HET: GDP; 2.35A {Pyrococcus horikoshii}

Probab=93.10  E-value=0.043  Score=48.86  Aligned_cols=24  Identities=33%  Similarity=0.537  Sum_probs=21.0

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..+++.|+||+|||+|..+++...
T Consensus       168 ~~v~lvG~~gvGKSTLin~L~~~~  191 (357)
T 2e87_A          168 PTVVIAGHPNVGKSTLLKALTTAK  191 (357)
T ss_dssp             CEEEEECSTTSSHHHHHHHHCSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            459999999999999999998753

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=93.07  E-value=0.075  Score=45.28  Aligned_cols=41  Identities=12%  Similarity=0.259  Sum_probs=28.3

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc----cceeeeech-hHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT----TAAFIRVVG-SEFVQKYLG  235 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l----~~~~~~v~~-s~l~~~~~G  235 (245)
                      ..++.+|+|+|||.++-+++...    +.+.+.+.+ .+++..+..
T Consensus       130 ~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~  175 (282)
T 1rif_A          130 RRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMAD  175 (282)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEECSSHHHHHHHHH
T ss_pred             CeEEEcCCCCCcHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHH
Confidence            35779999999999998777643    225555554 477666543

>4dhe_A Probable GTP-binding protein ENGB; melioidosis, RAS-like GTPase, cell division, cell cycle, SEP GTP-binding; 2.20A {Burkholderia thailandensis}

Probab=92.94  E-value=0.031  Score=45.36  Aligned_cols=23  Identities=17%  Similarity=0.349  Sum_probs=20.5

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ..|++.|++|+|||+|..++...
T Consensus        30 ~~i~v~G~~~~GKSslin~l~~~   52 (223)
T 4dhe_A           30 PEIAFAGRSNAGKSTAINVLCNQ   52 (223)
T ss_dssp             CEEEEEESCHHHHHHHHHHHTTC
T ss_pred             CEEEEEcCCCCCHHHHHHHHhCC
Confidence            34999999999999999999865

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19

Probab=92.88  E-value=0.079  Score=47.25  Aligned_cols=42  Identities=21%  Similarity=0.316  Sum_probs=31.7

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc----cceeeeechh-HHHHHHhcc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT----TAAFIRVVGS-EFVQKYLGE  236 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l----~~~~~~v~~s-~l~~~~~Ge  236 (245)
                      ++++.+|+|+|||+.+-+++...    +...+.+.+. +++..|..+
T Consensus        25 ~~ll~~~tG~GKT~~~~~~~~~~~~~~~~~~liv~P~~~L~~q~~~~   71 (494)
T 1wp9_A           25 NCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAES   71 (494)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSSHHHHHHHHHH
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHhcCCCeEEEEECCHHHHHHHHHH
Confidence            78999999999999988876654    5566666665 777666443

>3th5_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTPase, GTP binding, protein binding, signali protein; HET: GNP; 2.30A {Homo sapiens}

Probab=92.01  E-value=0.019  Score=46.14  Aligned_cols=21  Identities=24%  Similarity=0.309  Sum_probs=18.6

Q ss_pred             ceeeecCCCCchHHHHHHHHh
Q 025979          195 GVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~  215 (245)
                      .|++.|+||+|||+|..++..
T Consensus        32 ki~v~G~~~~GKSsli~~l~~   52 (204)
T 3th5_A           32 KCVVVGDGAVGKTCLLISYTT   52 (204)
Confidence            499999999999999987764

>1jwy_B Dynamin A GTPase domain; dynamin, GTPase, GDP, myosin, fusion-protein, hydrolase; HET: BGC ADP GDP; 2.30A {Dictyostelium discoideum} SCOP: c.37.1.8 PDB: 1jx2_B*

Probab=92.81  E-value=0.062  Score=46.33  Aligned_cols=22  Identities=14%  Similarity=0.439  Sum_probs=20.0

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|.+.|+||+|||+|..++.+.
T Consensus        26 ~I~vvG~~~~GKSTlln~l~g~   47 (315)
T 1jwy_B           26 QIVVVGSQSSGKSSVLENIVGR   47 (315)
T ss_dssp             EEEEEECSSSSHHHHHHHHHTS
T ss_pred             eEEEEcCCCCCHHHHHHHHHCC
Confidence            4999999999999999999765

>1ni3_A YCHF GTPase, YCHF GTP-binding protein; structural genomics, GTP1OBG, PSI, protein structure initiative; 2.80A {Schizosaccharomyces pombe} SCOP: c.37.1.8 d.15.10.2

Probab=92.80  E-value=0.058  Score=49.18  Aligned_cols=22  Identities=23%  Similarity=0.398  Sum_probs=20.1

Q ss_pred             cceeeecCCCCchHHHHHHHHh
Q 025979          194 RGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      ..+.|.||||+|||+|.++|++
T Consensus        21 ~~vgiVG~pnaGKSTL~n~Ltg   42 (392)
T 1ni3_A           21 LKTGIVGMPNVGKSTFFRAITK   42 (392)
T ss_dssp             CEEEEEECSSSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHC
Confidence            3488999999999999999998

>4aby_A DNA repair protein RECN; hydrolase, double strand break repair, ATPase, nucleotide binding domain; HET: DNA; 3.00A {Deinococcus radiodurans}

Probab=92.79  E-value=0.02  Score=51.55  Aligned_cols=24  Identities=21%  Similarity=0.303  Sum_probs=20.8

Q ss_pred             ceeeecCCCCchHHHHHHHHhccc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      -+.|+||+|+|||+|.++|+..++
T Consensus        62 ~~~lvG~NGaGKStLl~aI~~l~~   85 (415)
T 4aby_A           62 FCAFTGETGAGKSIIVDALGLLLG   85 (415)
T ss_dssp             EEEEEESHHHHHHHHTHHHHHHTT
T ss_pred             cEEEECCCCCCHHHHHHHHHHHhC
Confidence            478999999999999999976554

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=92.73  E-value=0.066  Score=44.21  Aligned_cols=30  Identities=20%  Similarity=0.309  Sum_probs=23.0

Q ss_pred             eeeecCCCCchH-HHHHHHHhcc--cceeeeec
Q 025979          196 VLLYGPPGTGKT-MLAKAVANHT--TAAFIRVV  225 (245)
Q Consensus       196 vLl~GPPGtGKT-~lAkalA~~l--~~~~~~v~  225 (245)
                      .++|||.|+||| .|.+++.+..  +...+.+.
T Consensus        23 ~fiyG~MgsGKTt~Ll~~i~n~~~~~~kvl~~k   55 (195)
T 1w4r_A           23 QVILGPMFSGKSTELMRRVRRFQIAQYKCLVIK   55 (195)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEc
Confidence            778999999999 8999888755  44455443

>1e69_A Chromosome segregation SMC protein; structural maintenance of chromosomes, coiled coil; 3.1A {Thermotoga maritima} SCOP: c.37.1.12

Probab=92.73  E-value=0.044  Score=48.07  Aligned_cols=23  Identities=26%  Similarity=0.400  Sum_probs=20.0

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      -.+|+||+|+|||++..||.-.+
T Consensus        26 ~~~i~G~NGsGKS~ll~ai~~ll   48 (322)
T 1e69_A           26 VTAIVGPNGSGKSNIIDAIKWVF   48 (322)
T ss_dssp             EEEEECCTTTCSTHHHHHHHHTS
T ss_pred             cEEEECCCCCcHHHHHHHHHHHh
Confidence            47899999999999999998543

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=92.72  E-value=0.1  Score=43.79  Aligned_cols=19  Identities=26%  Similarity=0.314  Sum_probs=16.1

Q ss_pred             CcceeeecCCCCchHHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAK  211 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAk  211 (245)
                      .+.+++.+|+|+|||+.+-
T Consensus        80 ~~~~lv~a~TGsGKT~~~~   98 (249)
T 3ber_A           80 GRDIIGLAETGSGKTGAFA   98 (249)
T ss_dssp             TCCEEEECCTTSCHHHHHH
T ss_pred             CCCEEEEcCCCCCchhHhH
Confidence            4679999999999998643

>3gj0_A GTP-binding nuclear protein RAN; G protein, GDP, acetylation, cytoplasm, HOST- virus interaction, nucleotide-binding, nucleus, phosphoprotein; HET: GDP; 1.48A {Homo sapiens} SCOP: c.37.1.8 PDB: 3gj3_A* 3gj5_A* 3gj4_A* 3gj6_A* 3gj7_A* 3gj8_A* 1i2m_A 1a2k_C 1ibr_A* 1k5d_A* 1k5g_A* 1qbk_C* 3a6p_C* 3ch5_A* 4gmx_A* 4gpt_A* 4hat_A* 4hau_A* 4hav_A* 4haw_A* ...

Probab=92.70  E-value=0.03  Score=45.61  Aligned_cols=19  Identities=42%  Similarity=0.583  Sum_probs=17.3

Q ss_pred             ceeeecCCCCchHHHHHHH
Q 025979          195 GVLLYGPPGTGKTMLAKAV  213 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkal  213 (245)
                      .|++.|++|+|||+|...+
T Consensus        17 ki~v~G~~~~GKSsli~~~   35 (221)
T 3gj0_A           17 KLVLVGDGGTGKTTFVKRH   35 (221)
T ss_dssp             EEEEEECTTSSHHHHHTTB
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            4999999999999999983

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=92.69  E-value=0.07  Score=43.49  Aligned_cols=18  Identities=28%  Similarity=0.242  Sum_probs=15.5

Q ss_pred             cceeeecCCCCchHHHHH
Q 025979          194 RGVLLYGPPGTGKTMLAK  211 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAk  211 (245)
                      +.+++.+|+|+|||..+-
T Consensus        42 ~~~lv~a~TGsGKT~~~~   59 (219)
T 1q0u_A           42 ESMVGQSQTGTGKTHAYL   59 (219)
T ss_dssp             CCEEEECCSSHHHHHHHH
T ss_pred             CCEEEECCCCChHHHHHH
Confidence            569999999999998643

>2iw3_A Elongation factor 3A; acetylation, ATP-binding, protein biosynthesis, nucleotide-binding, phosphorylation, RNA- binding, rRNA-binding; HET: ADP; 2.4A {Saccharomyces cerevisiae} PDB: 2iwh_A* 2ix3_A 2ix8_A

Probab=92.57  E-value=0.048  Score=55.32  Aligned_cols=25  Identities=40%  Similarity=0.643  Sum_probs=21.3

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHh
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      .++.-+.|.||+|+|||+|.+.|++
T Consensus       459 ~~Ge~v~LiGpNGsGKSTLLk~Lag  483 (986)
T 2iw3_A          459 KRARRYGICGPNGCGKSTLMRAIAN  483 (986)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhC
Confidence            3444589999999999999999994

>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=92.51  E-value=0.11  Score=45.35  Aligned_cols=21  Identities=38%  Similarity=0.612  Sum_probs=17.2

Q ss_pred             CCcceeeecCCCCchHHHHHH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKA  212 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAka  212 (245)
                      .++.+++.+|+|+|||+.+-.
T Consensus        43 ~~~~~lv~a~TGsGKT~~~~~   63 (395)
T 3pey_A           43 PPRNMIAQSQSGTGKTAAFSL   63 (395)
T ss_dssp             SCCCEEEECCTTSCHHHHHHH
T ss_pred             CCCeEEEECCCCCcHHHHHHH
Confidence            347799999999999986543

>3bfv_A CAPA1, CAPB2, membrane protein CAPA1, protein tyrosine kinase; chimerical protein, P-loop protein, capsule biogenesis/degradation; HET: ADP; 1.80A {Staphylococcus aureus} PDB: 2ved_A*

Probab=92.44  E-value=0.09  Score=45.10  Aligned_cols=36  Identities=22%  Similarity=0.349  Sum_probs=27.2

Q ss_pred             CCcceeeecC-CCCchHHHHHHHHhcc---cceeeeechh
Q 025979          192 PPRGVLLYGP-PGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       192 ~~~gvLl~GP-PGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      .++-++++|+ ||+|||++|-.+|..+   |..++-|++.
T Consensus        81 ~~kvI~vts~kgG~GKTt~a~nLA~~lA~~G~rVLLID~D  120 (271)
T 3bfv_A           81 AVQSIVITSEAPGAGKSTIAANLAVAYAQAGYKTLIVDGD  120 (271)
T ss_dssp             CCCEEEEECSSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             CCeEEEEECCCCCCcHHHHHHHHHHHHHhCCCeEEEEeCC
Confidence            3456888876 8999999998888766   6666666654

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=92.43  E-value=0.18  Score=44.56  Aligned_cols=20  Identities=35%  Similarity=0.348  Sum_probs=16.4

Q ss_pred             cceeeecCCCCchHHHHHHH
Q 025979          194 RGVLLYGPPGTGKTMLAKAV  213 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkal  213 (245)
                      +.+++.+|+|+|||+.+-..
T Consensus        59 ~~~li~a~TGsGKT~~~~~~   78 (400)
T 1s2m_A           59 RDILARAKNGTGKTAAFVIP   78 (400)
T ss_dssp             CCEEEECCTTSCHHHHHHHH
T ss_pred             CCEEEECCCCcHHHHHHHHH
Confidence            56999999999999865443

>4dkx_A RAS-related protein RAB-6A; GTP binding fold, membrane trafficking, GTP, cytosol, protei transport; HET: GDP; 1.90A {Homo sapiens} PDB: 3bbp_A*

Probab=92.34  E-value=0.068  Score=44.32  Aligned_cols=20  Identities=25%  Similarity=0.393  Sum_probs=18.5

Q ss_pred             eeeecCCCCchHHHHHHHHh
Q 025979          196 VLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~  215 (245)
                      |+|.|.+|||||+|...+..
T Consensus        16 ivlvGd~~VGKTsLi~r~~~   35 (216)
T 4dkx_A           16 LVFLGEQSVGKTSLITRFMY   35 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECcCCcCHHHHHHHHHh
Confidence            99999999999999998874

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=92.29  E-value=0.096  Score=48.55  Aligned_cols=21  Identities=43%  Similarity=0.525  Sum_probs=18.7

Q ss_pred             eeeecCCCCchHHHHHHHHhc
Q 025979          196 VLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~  216 (245)
                      .++.||||||||++.+.++..
T Consensus       164 ~~I~G~aGsGKTt~I~~~~~~  184 (446)
T 3vkw_A          164 VLVDGVPGCGKTKEILSRVNF  184 (446)
T ss_dssp             EEEEECTTSCHHHHHHHHCCT
T ss_pred             EEEEcCCCCCHHHHHHHHhcc
Confidence            778999999999999888764

>3cio_A ETK, tyrosine-protein kinase ETK; WZC, escherichia coli tyrosine kinase domain, signaling protein, transferase, inner membrane, membrane; 2.50A {Escherichia coli}

Probab=92.28  E-value=0.085  Score=45.93  Aligned_cols=35  Identities=17%  Similarity=0.331  Sum_probs=26.6

Q ss_pred             CCcceeeecC-CCCchHHHHHHHHhcc---cceeeeech
Q 025979          192 PPRGVLLYGP-PGTGKTMLAKAVANHT---TAAFIRVVG  226 (245)
Q Consensus       192 ~~~gvLl~GP-PGtGKT~lAkalA~~l---~~~~~~v~~  226 (245)
                      .++.+++.|+ ||+|||++|..+|..+   |..++-|++
T Consensus       103 ~~kvI~vts~kgG~GKTtva~nLA~~lA~~G~rVLLID~  141 (299)
T 3cio_A          103 ENNILMITGATPDSGKTFVSSTLAAVIAQSDQKVLFIDA  141 (299)
T ss_dssp             SCCEEEEEESSSSSCHHHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             CCeEEEEECCCCCCChHHHHHHHHHHHHhCCCcEEEEEC
Confidence            4466888887 8999999998888765   566666654

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=92.26  E-value=0.14  Score=48.34  Aligned_cols=42  Identities=19%  Similarity=0.228  Sum_probs=24.3

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc------------cceeeeech-hHHHHHHh
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT------------TAAFIRVVG-SEFVQKYL  234 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l------------~~~~~~v~~-s~l~~~~~  234 (245)
                      .+++|+++|+|+|||.++-.++..+            +..++.+.+ .+|...+.
T Consensus       198 ~~~~ll~~~TGsGKT~~~~~~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~  252 (590)
T 3h1t_A          198 KKRSLITMATGTGKTVVAFQISWKLWSARWNRTGDYRKPRILFLADRNVLVDDPK  252 (590)
T ss_dssp             CSEEEEEECTTSCHHHHHHHHHHHHHHTTCCSSCSSSCCCEEEEEC---------
T ss_pred             CCceEEEecCCCChHHHHHHHHHHHHhcccccccccCCCeEEEEeCCHHHHHHHH
Confidence            3568999999999999987777653            234444444 67776665

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=92.25  E-value=0.14  Score=41.79  Aligned_cols=19  Identities=26%  Similarity=0.345  Sum_probs=16.0

Q ss_pred             CcceeeecCCCCchHHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAK  211 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAk  211 (245)
                      .+.+++.+|+|+|||+.+-
T Consensus        57 ~~~~l~~apTGsGKT~~~~   75 (228)
T 3iuy_A           57 GIDLIVVAQTGTGKTLSYL   75 (228)
T ss_dssp             TCCEEEECCTTSCHHHHHH
T ss_pred             CCCEEEECCCCChHHHHHH
Confidence            4679999999999998654

>2qag_A Septin-2, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=92.14  E-value=0.061  Score=48.16  Aligned_cols=21  Identities=24%  Similarity=0.450  Sum_probs=18.8

Q ss_pred             ceeeecCCCCchHHHHHHHHh
Q 025979          195 GVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~  215 (245)
                      .|++.|++|+|||+|..+|..
T Consensus        39 ~I~vvG~~g~GKSTLln~L~~   59 (361)
T 2qag_A           39 TLMVVGESGLGKSTLINSLFL   59 (361)
T ss_dssp             CEEECCCTTSCHHHHHHHHTT
T ss_pred             EEEEEcCCCCCHHHHHHHHhC
Confidence            489999999999999999754

>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=92.13  E-value=0.07  Score=43.66  Aligned_cols=25  Identities=16%  Similarity=0.078  Sum_probs=21.1

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+-.+++||+|+|||+.+-.+|..+
T Consensus         8 g~i~v~~G~mgsGKTT~ll~~a~r~   32 (191)
T 1xx6_A            8 GWVEVIVGPMYSGKSEELIRRIRRA   32 (191)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHH
Confidence            4568999999999999888777665

>3ug7_A Arsenical pump-driving ATPase; tail-anchored, membrane protein, targeting factor, ATP-bindi TRC40, ARSA, nucleotide-binding; HET: ADP; 2.90A {Methanocaldococcus jannaschii} PDB: 3ug6_A*

Probab=92.08  E-value=0.11  Score=46.12  Aligned_cols=34  Identities=21%  Similarity=0.239  Sum_probs=24.5

Q ss_pred             CCcc-eeeecCCCCchHHHHHHHHhcc---cceeeeec
Q 025979          192 PPRG-VLLYGPPGTGKTMLAKAVANHT---TAAFIRVV  225 (245)
Q Consensus       192 ~~~g-vLl~GPPGtGKT~lAkalA~~l---~~~~~~v~  225 (245)
                      +.+. +++.|.+|+|||++|-++|..+   |...+-++
T Consensus        24 ~~~~i~v~sgKGGvGKTTvA~~LA~~lA~~G~rVLlvD   61 (349)
T 3ug7_A           24 DGTKYIMFGGKGGVGKTTMSAATGVYLAEKGLKVVIVS   61 (349)
T ss_dssp             CSCEEEEEECSSSTTHHHHHHHHHHHHHHSSCCEEEEE
T ss_pred             CCCEEEEEeCCCCccHHHHHHHHHHHHHHCCCeEEEEe
Confidence            3344 5566999999999999998765   55555554

>1h65_A Chloroplast outer envelope protein OEP34; GTPase, translocon; HET: GDP; 2.0A {Pisum sativum} SCOP: c.37.1.8 PDB: 3bb1_A*

Probab=92.06  E-value=0.069  Score=45.39  Aligned_cols=23  Identities=22%  Similarity=0.437  Sum_probs=20.3

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -.|++.|++|+|||+|..++.+.
T Consensus        40 ~~I~vvG~~g~GKSSLin~l~~~   62 (270)
T 1h65_A           40 LTILVMGKGGVGKSSTVNSIIGE   62 (270)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             eEEEEECCCCCCHHHHHHHHhCC
Confidence            35999999999999999999854

>2iw3_A Elongation factor 3A; acetylation, ATP-binding, protein biosynthesis, nucleotide-binding, phosphorylation, RNA- binding, rRNA-binding; HET: ADP; 2.4A {Saccharomyces cerevisiae} PDB: 2iwh_A* 2ix3_A 2ix8_A

Probab=92.02  E-value=0.046  Score=55.44  Aligned_cols=28  Identities=21%  Similarity=0.436  Sum_probs=23.7

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.++.-+.+.||+|+|||+|.+.|+..+
T Consensus       696 I~~GeivaIiGpNGSGKSTLLklLaGll  723 (986)
T 2iw3_A          696 CSLSSRIAVIGPNGAGKSTLINVLTGEL  723 (986)
T ss_dssp             EETTCEEEECSCCCHHHHHHHHHHTTSS
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444558999999999999999999876

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=92.01  E-value=0.22  Score=45.89  Aligned_cols=42  Identities=14%  Similarity=0.290  Sum_probs=29.2

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc----cceeeeechh-HHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT----TAAFIRVVGS-EFVQKYLG  235 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l----~~~~~~v~~s-~l~~~~~G  235 (245)
                      +.+|++||+|+|||.++-.++...    +...+.+.+. ++...+..
T Consensus       129 ~~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~vlvl~P~~~L~~Q~~~  175 (510)
T 2oca_A          129 RRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMAD  175 (510)
T ss_dssp             SEEEEECCSTTTHHHHHHHHHHHHHHHCSSEEEEEESSHHHHHHHHH
T ss_pred             CCcEEEeCCCCCHHHHHHHHHHHHHhCCCCeEEEEECcHHHHHHHHH
Confidence            568999999999999987666542    3255555544 67665543

>1ihu_A Arsenical pump-driving ATPase; aluminum fluoride, ADP, ARSA ATPase, ATP binding site, hydro; HET: ADP; 2.15A {Escherichia coli} SCOP: c.37.1.10 c.37.1.10 PDB: 1f48_A* 1ii0_A* 1ii9_A*

Probab=91.94  E-value=0.1  Score=49.57  Aligned_cols=36  Identities=25%  Similarity=0.267  Sum_probs=27.4

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc---cceeeeechh
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      +.+-+++.|.+|+|||++|-++|..+   |...+.|+..
T Consensus         7 ~~~i~~~sgkGGvGKTT~a~~lA~~lA~~G~rVLlvd~D   45 (589)
T 1ihu_A            7 IPPYLFFTGKGGVGKTSISCATAIRLAEQGKRVLLVSTD   45 (589)
T ss_dssp             CCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             CCEEEEEeCCCcCHHHHHHHHHHHHHHHCCCcEEEEECC
Confidence            44557888999999999999988766   5565555543

>1udx_A The GTP-binding protein OBG; TGS domain, riken structural genomics/proteomics initiative, RSGI, structural genomics; 2.07A {Thermus thermophilus} SCOP: b.117.1.1 c.37.1.8 d.242.1.1

Probab=91.84  E-value=0.057  Score=49.57  Aligned_cols=24  Identities=33%  Similarity=0.380  Sum_probs=21.2

Q ss_pred             CcceeeecCCCCchHHHHHHHHhc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ..-+.|.||||+|||+|.++++..
T Consensus       157 g~~VgLVG~~gAGKSTLL~~Lsg~  180 (416)
T 1udx_A          157 IADVGLVGYPNAGKSSLLAAMTRA  180 (416)
T ss_dssp             SCSEEEECCGGGCHHHHHHHHCSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHHcC
Confidence            344889999999999999999876

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=91.74  E-value=0.14  Score=47.06  Aligned_cols=42  Identities=14%  Similarity=0.358  Sum_probs=29.5

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc--------cceeeeechh-HHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT--------TAAFIRVVGS-EFVQKYLG  235 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l--------~~~~~~v~~s-~l~~~~~G  235 (245)
                      +.+++.+|+|+|||..+-..+-..        +...+.+.+. +++..+..
T Consensus        20 ~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~   70 (555)
T 3tbk_A           20 KNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQAT   70 (555)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHH
T ss_pred             CCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHH
Confidence            569999999999999866655433        5556666655 77665543

>1puj_A YLQF, conserved hypothetical protein YLQF; structural genomics, nysgxrc T18, GTPase, PSI, protein structure initiative; HET: GNP; 2.00A {Bacillus subtilis} SCOP: c.37.1.8

Probab=91.74  E-value=0.21  Score=43.14  Aligned_cols=53  Identities=19%  Similarity=0.306  Sum_probs=32.5

Q ss_pred             CcchhhhHHHHHHHhcCCCcHHHHhhhcc-CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          162 GGCDIQKQEIREAVELPLTHHELYKQIGI-DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       162 ~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~-~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .|.++..+.+.+.+...   .+....-|. ..+-.+++.|.||+|||++..++.+.-
T Consensus        91 ~gi~~L~~~i~~~l~~~---~~~~~~~~~~~~~~~v~~vG~~nvGKSsliN~l~~~~  144 (282)
T 1puj_A           91 QGLNQIVPASKEILQEK---FDRMRAKGVKPRAIRALIIGIPNVGKSTLINRLAKKN  144 (282)
T ss_dssp             TTGGGHHHHHHHHHHHH---HHHHHHTTCCCCCEEEEEEESTTSSHHHHHHHHHTSC
T ss_pred             ccHHHHHHHHHHHHHHH---HHHHHhcCCCCCCceEEEEecCCCchHHHHHHHhcCc
Confidence            45666666666655321   011122232 233459999999999999999997643

>3cnl_A YLQF, putative uncharacterized protein; circular permutation, GNP, signaling protein; HET: GNP; 2.00A {Thermotoga maritima} PDB: 3cnn_A* 3cno_A*

Probab=91.72  E-value=0.08  Score=45.32  Aligned_cols=24  Identities=29%  Similarity=0.530  Sum_probs=20.8

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..+++.|+||+|||++..++....
T Consensus       100 ~~v~~vG~~~vGKSslin~l~~~~  123 (262)
T 3cnl_A          100 ARVLIVGVPNTGKSTIINKLKGKR  123 (262)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTTC
T ss_pred             hheEEeCCCCCCHHHHHHHHhccc
Confidence            358999999999999999998644

>3la6_A Tyrosine-protein kinase WZC; P-loop protein, nucleotide binding domain, walker A motif, B protein kinase, oligomerization; HET: ADP; 3.20A {Escherichia coli}

Probab=91.70  E-value=0.15  Score=44.21  Aligned_cols=36  Identities=14%  Similarity=0.230  Sum_probs=26.6

Q ss_pred             CCcceeeecC-CCCchHHHHHHHHhcc---cceeeeechh
Q 025979          192 PPRGVLLYGP-PGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       192 ~~~gvLl~GP-PGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      .++-|+++|+ ||+|||++|-.+|..+   |..++-|++.
T Consensus        91 ~~kvI~vts~kgG~GKTtva~nLA~~lA~~G~rVLLID~D  130 (286)
T 3la6_A           91 QNNVLMMTGVSPSIGMTFVCANLAAVISQTNKRVLLIDCD  130 (286)
T ss_dssp             TCCEEEEEESSSSSSHHHHHHHHHHHHHTTTCCEEEEECC
T ss_pred             CCeEEEEECCCCCCcHHHHHHHHHHHHHhCCCCEEEEecc
Confidence            3456777765 8999999999888766   6666666643

>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=91.57  E-value=0.087  Score=50.12  Aligned_cols=19  Identities=26%  Similarity=0.419  Sum_probs=15.3

Q ss_pred             cceeeecCCCCchHHHHHH
Q 025979          194 RGVLLYGPPGTGKTMLAKA  212 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAka  212 (245)
                      ..+++.||||||||+++-.
T Consensus        23 ~~~lV~a~aGsGKT~~l~~   41 (647)
T 3lfu_A           23 SNLLVLAGAGSGKTRVLVH   41 (647)
T ss_dssp             SCEEEEECTTSCHHHHHHH
T ss_pred             CCEEEEECCCCCHHHHHHH
Confidence            3488999999999996543

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=91.57  E-value=0.13  Score=42.69  Aligned_cols=19  Identities=21%  Similarity=0.202  Sum_probs=16.0

Q ss_pred             CcceeeecCCCCchHHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAK  211 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAk  211 (245)
                      .+.+++.+|+|+|||+.+-
T Consensus        66 g~~~l~~apTGsGKT~~~~   84 (242)
T 3fe2_A           66 GLDMVGVAQTGSGKTLSYL   84 (242)
T ss_dssp             TCCEEEEECTTSCHHHHHH
T ss_pred             CCCEEEECCCcCHHHHHHH
Confidence            3579999999999998744

>3l0i_B RAS-related protein RAB-1A; GEF-GDF-RAB complex, GTP-binding, guanine-nucleotide exchang GDI-displacement factor; 2.85A {Homo sapiens}

Probab=91.55  E-value=0.019  Score=46.03  Aligned_cols=21  Identities=38%  Similarity=0.574  Sum_probs=18.6

Q ss_pred             ceeeecCCCCchHHHHHHHHh
Q 025979          195 GVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~  215 (245)
                      .|++.|++|+|||+|..++..
T Consensus        35 ki~vvG~~~~GKSsli~~l~~   55 (199)
T 3l0i_B           35 KLLLIGDSGVGKSCLLLRFAD   55 (199)
T ss_dssp             EEEEECCTTSCCTTTTTSSBC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            499999999999999988764

>3t5d_A Septin-7; GTP-binding protein, cytoskeleton, signaling protein; HET: GDP; 3.30A {Homo sapiens} PDB: 3tw4_A*

Probab=91.55  E-value=0.08  Score=45.13  Aligned_cols=21  Identities=24%  Similarity=0.447  Sum_probs=18.5

Q ss_pred             cceeeecCCCCchHHHHHHHH
Q 025979          194 RGVLLYGPPGTGKTMLAKAVA  214 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA  214 (245)
                      -.|++.|+||+|||+|..++.
T Consensus         9 ~~I~vvG~~g~GKSTLin~L~   29 (274)
T 3t5d_A            9 FTLMVVGESGLGKSTLINSLF   29 (274)
T ss_dssp             EEEEEEECTTSSHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHh
Confidence            358999999999999998864

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=91.40  E-value=0.13  Score=44.99  Aligned_cols=17  Identities=41%  Similarity=0.397  Sum_probs=15.0

Q ss_pred             cceeeecCCCCchHHHH
Q 025979          194 RGVLLYGPPGTGKTMLA  210 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lA  210 (245)
                      +.+++.+|+|+|||+.+
T Consensus        59 ~~~lv~~~TGsGKT~~~   75 (394)
T 1fuu_A           59 HDVLAQAQSGTGKTGTF   75 (394)
T ss_dssp             CCEEECCCSSHHHHHHH
T ss_pred             CCEEEECCCCChHHHHH
Confidence            56999999999999874

>2ohf_A Protein OLA1, GTP-binding protein 9; ATPase, GTPase, P-loop, OBG-like, hydrolase; HET: ACP; 2.70A {Homo sapiens}

Probab=91.33  E-value=0.11  Score=47.32  Aligned_cols=24  Identities=21%  Similarity=0.378  Sum_probs=20.5

Q ss_pred             CcceeeecCCCCchHHHHHHHHhc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      +..+.|.|+||+|||+|..++.+.
T Consensus        22 ~~kvgIVG~pnvGKSTL~n~Ltg~   45 (396)
T 2ohf_A           22 SLKIGIVGLPNVGKSTFFNVLTNS   45 (396)
T ss_dssp             CCCEEEECCSSSSHHHHHHHHHC-
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCC
Confidence            345899999999999999999875

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=91.32  E-value=0.34  Score=43.20  Aligned_cols=41  Identities=20%  Similarity=0.223  Sum_probs=24.9

Q ss_pred             CcceeeecCCCCchHHHHHHHHhc---ccceeeeech-hHHHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANH---TTAAFIRVVG-SEFVQKY  233 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~---l~~~~~~v~~-s~l~~~~  233 (245)
                      .+.+++.+|+|+|||+++-..+-.   -+...+.+.+ .++...+
T Consensus        36 ~~~~lv~apTGsGKT~~~l~~~~~~~~~~~~~lil~Pt~~L~~q~   80 (414)
T 3oiy_A           36 GKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQT   80 (414)
T ss_dssp             TCCEECCSCSSSSHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCHHHHHHHHHHHHhcCCCEEEEEECCHHHHHHH
Confidence            357999999999999955444333   2333444443 3554433

>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=91.30  E-value=0.13  Score=50.87  Aligned_cols=23  Identities=22%  Similarity=0.297  Sum_probs=18.4

Q ss_pred             CcceeeecCCCCchHHHHHHHHh
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      ...+++.||+|+|||++...+..
T Consensus       109 ~~~vii~gpTGSGKTtllp~ll~  131 (773)
T 2xau_A          109 NQIMVFVGETGSGKTTQIPQFVL  131 (773)
T ss_dssp             CSEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH
Confidence            34599999999999997666643

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=91.26  E-value=0.17  Score=46.69  Aligned_cols=42  Identities=19%  Similarity=0.404  Sum_probs=29.1

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc--------cceeeeechh-HHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT--------TAAFIRVVGS-EFVQKYLG  235 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l--------~~~~~~v~~s-~l~~~~~G  235 (245)
                      +.+++.+|+|+|||..+-..+-..        +...+.+.+. +++..+..
T Consensus        23 ~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~   73 (556)
T 4a2p_A           23 KNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKN   73 (556)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHH
T ss_pred             CCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHH
Confidence            569999999999999876555433        4555656554 67665543

>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A* 2j3e_A*

Probab=91.21  E-value=0.098  Score=44.27  Aligned_cols=24  Identities=25%  Similarity=0.415  Sum_probs=20.9

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      -.|++.|++|+|||+|..++...-
T Consensus        37 ~~I~lvG~~g~GKSSLin~l~~~~   60 (262)
T 3def_A           37 MTVLVLGKGGVGKSSTVNSLIGEQ   60 (262)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHTSC
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCC
Confidence            459999999999999999998643

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=91.14  E-value=0.11  Score=50.41  Aligned_cols=37  Identities=22%  Similarity=0.285  Sum_probs=24.6

Q ss_pred             CCCcceeeecCCCCchHHHH-HHHHhcc---cceeeeechh
Q 025979          191 DPPRGVLLYGPPGTGKTMLA-KAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lA-kalA~~l---~~~~~~v~~s  227 (245)
                      ...+.+++.||+|+|||+++ -++...+   +...+.+.+.
T Consensus        37 ~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~~l~i~P~   77 (720)
T 2zj8_A           37 LEGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVPL   77 (720)
T ss_dssp             GGTCEEEEECCGGGCHHHHHHHHHHHHHHHHCSEEEEECSS
T ss_pred             cCCCcEEEEcCCccHHHHHHHHHHHHHHHhCCCEEEEEcCc
Confidence            34577999999999999987 3433322   4455555543

>3geh_A MNME, tRNA modification GTPase MNME; G protein, U34, GTP-binding, HYDR magnesium, metal-binding, nucleotide-binding, potassium, TR processing; HET: GDP FON; 3.20A {Nostoc SP}

Probab=91.14  E-value=0.2  Score=46.47  Aligned_cols=22  Identities=32%  Similarity=0.477  Sum_probs=19.9

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|.+.|+||+|||+|..++...
T Consensus       226 kV~ivG~~nvGKSSLln~L~~~  247 (462)
T 3geh_A          226 KVAIVGRPNVGKSSLLNAWSQS  247 (462)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHhCC
Confidence            3999999999999999998864

>3zq6_A Putative arsenical pump-driving ATPase; tail-anchored, membrane protein; HET: ADP; 2.11A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=91.13  E-value=0.11  Score=45.51  Aligned_cols=31  Identities=26%  Similarity=0.308  Sum_probs=23.2

Q ss_pred             eeeecCCCCchHHHHHHHHhcc---cceeeeech
Q 025979          196 VLLYGPPGTGKTMLAKAVANHT---TAAFIRVVG  226 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~  226 (245)
                      +++.|.+|+|||++|.++|..+   |...+-|+.
T Consensus        17 ~v~sgKGGvGKTTvA~~LA~~lA~~G~rVLlvD~   50 (324)
T 3zq6_A           17 VFIGGKGGVGKTTISAATALWMARSGKKTLVIST   50 (324)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             EEEeCCCCchHHHHHHHHHHHHHHCCCcEEEEeC
Confidence            5566999999999999998765   555554543

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=91.08  E-value=0.18  Score=41.92  Aligned_cols=18  Identities=28%  Similarity=0.436  Sum_probs=15.4

Q ss_pred             cceeeecCCCCchHHHHH
Q 025979          194 RGVLLYGPPGTGKTMLAK  211 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAk  211 (245)
                      +.+++.+|+|+|||+.+-
T Consensus        61 ~~~l~~a~TGsGKT~~~~   78 (253)
T 1wrb_A           61 RDIMACAQTGSGKTAAFL   78 (253)
T ss_dssp             CCEEEECCTTSSHHHHHH
T ss_pred             CCEEEECCCCChHHHHHH
Confidence            569999999999998643

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=91.00  E-value=0.29  Score=43.32  Aligned_cols=18  Identities=28%  Similarity=0.440  Sum_probs=15.3

Q ss_pred             CcceeeecCCCCchHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLA  210 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lA  210 (245)
                      .+.+++.+|+|+|||+.+
T Consensus        52 ~~~~lv~a~TGsGKT~~~   69 (417)
T 2i4i_A           52 KRDLMACAQTGSGKTAAF   69 (417)
T ss_dssp             TCCEEEECCTTSCHHHHH
T ss_pred             CCCEEEEcCCCCHHHHHH
Confidence            467999999999999843

>1wb9_A DNA mismatch repair protein MUTS; DNA-binding, ATP-binding, DNA binding, DNA repair, mismatch recognition; HET: DNA ADP; 2.10A {Escherichia coli} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1wbb_A* 1e3m_A* 1oh5_A* 1oh6_A* 1oh7_A* 1oh8_A* 1w7a_A* 2wtu_A* 1wbd_A* 1ng9_A* 3k0s_A*

Probab=90.89  E-value=0.12  Score=51.24  Aligned_cols=23  Identities=26%  Similarity=0.365  Sum_probs=20.3

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .-+++.||+|+|||++.|.+|..
T Consensus       608 ~i~~ItGpNGsGKSTlLr~iagl  630 (800)
T 1wb9_A          608 RMLIITGPNMGGKSTYMRQTALI  630 (800)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cEEEEECCCCCChHHHHHHHHHH
Confidence            34889999999999999999864

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=90.85  E-value=0.16  Score=44.77  Aligned_cols=18  Identities=33%  Similarity=0.538  Sum_probs=16.0

Q ss_pred             CcceeeecCCCCchHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLA  210 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lA  210 (245)
                      ++.+++.+|+|+|||+.+
T Consensus        64 ~~~~lv~apTGsGKT~~~   81 (412)
T 3fht_A           64 PQNLIAQSQSGTGKTAAF   81 (412)
T ss_dssp             CCCEEEECCTTSCHHHHH
T ss_pred             CCeEEEECCCCchHHHHH
Confidence            477999999999999875

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=90.76  E-value=0.17  Score=47.53  Aligned_cols=27  Identities=26%  Similarity=0.377  Sum_probs=22.9

Q ss_pred             ceeeecCCCCchHHH-HHHHHhccccee
Q 025979          195 GVLLYGPPGTGKTML-AKAVANHTTAAF  221 (245)
Q Consensus       195 gvLl~GPPGtGKT~l-AkalA~~l~~~~  221 (245)
                      .++++|++|||||.| ...|++..+..+
T Consensus       164 R~~Ifg~~g~GKT~Lal~~I~~~~~~dv  191 (502)
T 2qe7_A          164 RELIIGDRQTGKTTIAIDTIINQKGQDV  191 (502)
T ss_dssp             BCEEEECSSSCHHHHHHHHHHGGGSCSE
T ss_pred             EEEEECCCCCCchHHHHHHHHHhhcCCc
Confidence            399999999999999 569998886554

>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=90.74  E-value=0.12  Score=46.39  Aligned_cols=23  Identities=26%  Similarity=0.382  Sum_probs=20.2

Q ss_pred             CCcceeeecCCCCchHHHHHHHH
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVA  214 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA  214 (245)
                      ....+||.|++|+|||+++|.+.
T Consensus        32 ~~~killlG~~~SGKST~~kq~~   54 (362)
T 1zcb_A           32 RLVKILLLGAGESGKSTFLKQMR   54 (362)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHH
T ss_pred             CccEEEEECCCCCcHHHHHHHHH
Confidence            34569999999999999999985

>2wkq_A NPH1-1, RAS-related C3 botulinum toxin substrate 1; transferase, cell adhesion, nucleotide-binding, protein engineering, RAS superfamily LOV2; HET: GTP FMN; 1.60A {Avena sativa} PDB: 2wkr_A* 2wkp_A*

Probab=90.70  E-value=0.11  Score=44.57  Aligned_cols=24  Identities=21%  Similarity=0.199  Sum_probs=20.2

Q ss_pred             CCcceeeecCCCCchHHHHHHHHh
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      ..-.+++.|+||+|||+|...+..
T Consensus       154 ~~~~i~i~G~~~~GKssli~~~~~  177 (332)
T 2wkq_A          154 ELIKCVVVGDGAVGKTCLLISYTT  177 (332)
T ss_dssp             TCEEEEEEESTTSSHHHHHHHHHH
T ss_pred             ceeEEEEECCCCCChHHHHHHHHh
Confidence            334599999999999999988874

>3thx_B DNA mismatch repair protein MSH3; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 3thw_B* 3thy_B* 3thz_B*

Probab=90.68  E-value=0.11  Score=52.44  Aligned_cols=23  Identities=35%  Similarity=0.433  Sum_probs=19.9

Q ss_pred             CcceeeecCCCCchHHHHHHHHh
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      +.-+++.||.|+|||++.|.+|.
T Consensus       673 g~i~~ItGPNGaGKSTlLr~i~~  695 (918)
T 3thx_B          673 ERVMIITGPNMGGKSSYIKQVAL  695 (918)
T ss_dssp             CCEEEEESCCCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCchHHHHHHHHH
Confidence            34488999999999999999874

>3g5u_A MCG1178, multidrug resistance protein 1A; P-glycoprotein, PGP, cyclic peptide, membrane protein; 3.80A {Mus musculus} PDB: 3g61_A* 3g60_A*

Probab=90.66  E-value=0.097  Score=54.52  Aligned_cols=37  Identities=19%  Similarity=0.361  Sum_probs=27.4

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcccc--eeeeech
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHTTA--AFIRVVG  226 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l~~--~~~~v~~  226 (245)
                      +.++.-+.++||+|+|||+|++.|++....  --+.+++
T Consensus       413 i~~G~~~~ivG~sGsGKSTl~~ll~g~~~~~~G~i~i~g  451 (1284)
T 3g5u_A          413 VKSGQTVALVGNSGCGKSTTVQLMQRLYDPLDGMVSIDG  451 (1284)
T ss_dssp             ECTTCEEEEECCSSSSHHHHHHHTTTSSCCSEEEEEETT
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCCCCCCeEEEECC
Confidence            344455999999999999999999987632  2344444

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=90.63  E-value=0.3  Score=43.26  Aligned_cols=41  Identities=20%  Similarity=0.212  Sum_probs=25.2

Q ss_pred             CcceeeecCCCCchHHHHHHHH-hcc-----cceeeeechh-HHHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVA-NHT-----TAAFIRVVGS-EFVQKY  233 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA-~~l-----~~~~~~v~~s-~l~~~~  233 (245)
                      .+.+++.+|+|+|||+.+-..+ ..+     +...+.+.+. ++...+
T Consensus        74 ~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~Pt~~L~~q~  121 (410)
T 2j0s_A           74 GRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQI  121 (410)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHHHHHHH
T ss_pred             CCCEEEECCCCCCchHHHHHHHHHHHhhccCCceEEEEcCcHHHHHHH
Confidence            4669999999999997655333 221     3444445443 555443

>3vr4_A V-type sodium ATPase catalytic subunit A; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_A* 3vr2_A* 3vr5_A 3vr6_A*

Probab=90.57  E-value=0.18  Score=48.25  Aligned_cols=26  Identities=27%  Similarity=0.493  Sum_probs=22.9

Q ss_pred             ceeeecCCCCchHHHHHHHHhcccce
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTTAA  220 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~~~  220 (245)
                      .++++||+|||||.|+..||+..+..
T Consensus       234 r~~Ifgg~g~GKT~L~~~ia~~~~~~  259 (600)
T 3vr4_A          234 AAAVPGPFGAGKTVVQHQIAKWSDVD  259 (600)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHSSCS
T ss_pred             EEeeecCCCccHHHHHHHHHhccCCC
Confidence            39999999999999999999977544

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=90.52  E-value=0.12  Score=54.11  Aligned_cols=28  Identities=21%  Similarity=0.338  Sum_probs=23.9

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      +++.-+.++||+|+|||+|++.|.+...
T Consensus       442 ~~G~~vaivG~sGsGKSTll~ll~~~~~  469 (1321)
T 4f4c_A          442 NAGQTVALVGSSGCGKSTIISLLLRYYD  469 (1321)
T ss_dssp             CTTCEEEEEECSSSCHHHHHHHHTTSSC
T ss_pred             cCCcEEEEEecCCCcHHHHHHHhccccc
Confidence            4444499999999999999999999873

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	245
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	6e-34
d1lv7a_	256	c.37.1.20 (A:) AAA domain of cell division protein	2e-32
d1r7ra3	265	c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p	2e-30
d1e32a2	258	c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p	2e-30
d1svma_	362	c.37.1.20 (A:) Papillomavirus large T antigen heli	4e-16
d1gvnb_	273	c.37.1.21 (B:) Plasmid maintenance system epsilon/	2e-13
d1w44a_	321	c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [Ta	1e-12
d1d2na_	246	c.37.1.20 (A:) Hexamerization domain of N-ethylmal	7e-12
d1sxja2	253	c.37.1.20 (A:295-547) Replication factor C1 {Baker	2e-09
d1ofha_	309	c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId	3e-09
d1ixsb2	239	c.37.1.20 (B:4-242) Holliday junction helicase Ruv	3e-09
d1fnna2	276	c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrob	1e-06
d1g41a_	443	c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId	4e-06
d1in4a2	238	c.37.1.20 (A:17-254) Holliday junction helicase Ru	4e-06
d1w5sa2	287	c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-t	5e-06
d1g8pa_	333	c.37.1.20 (A:) ATPase subunit of magnesium chelata	3e-05
d2i3ba1	189	c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57	2e-04
d1sxje2	252	c.37.1.20 (E:4-255) Replication factor C5 {Baker's	3e-04
d1lw7a2	192	c.37.1.1 (A:220-411) Transcriptional regulator Nad	4e-04
d1um8a_	364	c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 2	0.001
d1qhxa_	178	c.37.1.3 (A:) Chloramphenicol phosphotransferase {	0.001
d1zp6a1	176	c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {	0.002
d2fnaa2	283	c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfo	0.003
d1a5ta2	207	c.37.1.20 (A:1-207) delta prime subunit of DNA pol	0.004
d1n0wa_	242	c.37.1.11 (A:) DNA repair protein Rad51, catalytic	0.004

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]} Length = 247

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]

 Score =  120 bits (302), Expect = 6e-34
 Identities = 38/95 (40%), Positives = 58/95 (61%), Gaps = 1/95 (1%)

Query: 151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLA 210
           +E P VT+ D+ G +  K+E++E VE  L +   + ++G   P+GVLL GPPG GKT LA
Sbjct: 1   TEAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHLA 59

Query: 211 KAVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           +AVA      FI   GS+FV+ ++G    + + +F
Sbjct: 60  RAVAGEARVPFITASGSDFVEMFVGVGAARVRDLF 94

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]} Length = 256

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]

 Score =  116 bits (292), Expect = 2e-32
 Identities = 36/94 (38%), Positives = 58/94 (61%), Gaps = 1/94 (1%)

Query: 152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAK 211
           ++   T+ D+ GCD  K+E+ E VE  L     ++++G   P+GVL+ GPPGTGKT+LAK
Sbjct: 5   DQIKTTFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAK 63

Query: 212 AVANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           A+A      F  + GS+FV+ ++G    + + +F
Sbjct: 64  AIAGEAKVPFFTISGSDFVEMFVGVGASRVRDMF 97

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]} Length = 265

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]

 Score =  111 bits (279), Expect = 2e-30
 Identities = 41/92 (44%), Positives = 60/92 (65%)

Query: 154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAV 213
           P VT+ DIGG +  K+E++E V+ P+ H + + + G+ P +GVL YGPPG GKT+LAKA+
Sbjct: 2   PQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAI 61

Query: 214 ANHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
           AN   A FI + G E +  + GE     ++IF
Sbjct: 62  ANECQANFISIKGPELLTMWFGESEANVREIF 93

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]} Length = 258

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]

 Score =  111 bits (277), Expect = 2e-30
 Identities = 48/90 (53%), Positives = 62/90 (68%)

Query: 156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVAN 215
           V Y+D+GGC  Q  +I+E VELPL H  L+K IG+ PPRG+LLYGPPGTGKT++A+AVAN
Sbjct: 1   VGYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVAN 60

Query: 216 HTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
            T A F  + G E + K  GE     ++ F
Sbjct: 61  ETGAFFFLINGPEIMSKLAGESESNLRKAF 90

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]} Length = 362

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]

 Score = 74.3 bits (182), Expect = 4e-16
 Identities = 36/214 (16%), Positives = 61/214 (28%), Gaps = 22/214 (10%)

Query: 24  LTEQWSDEDDLYSRLKSLQRQLEFIDIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVI 83
           L  +++ E      L  L   LEF    E  +K  +K         ++            
Sbjct: 7   LVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHYKYHEKHYANAAI----- 61

Query: 84  GQFMEMVDQNNGIVGSTTGSNYYVRILSTINRELLKPSASVALHRHSNALVDVLPPEADS 143
             F +  +Q      +        R+      + L+ +    L    N L+D +     S
Sbjct: 62  --FADSKNQKTICQQAVDTVLAKKRV------DSLQLTREQMLTNRFNDLLDRMDIMFGS 113

Query: 144 SISLLSQSEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPG 203
           + S   +     V +           ++   V   L          I   R  L  GP  
Sbjct: 114 TGSADIEEWMAGVAWLHCL-----LPKMDSVVYDFLKC----MVYNIPKKRYWLFKGPID 164

Query: 204 TGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEV 237
           +GKT LA A+        + V        +   V
Sbjct: 165 SGKTTLAAALLELCGGKALNVNLPLDRLNFELGV 198

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]} Length = 273

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]

 Score = 65.8 bits (159), Expect = 2e-13
 Identities = 19/89 (21%), Positives = 31/89 (34%), Gaps = 9/89 (10%)

Query: 156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVAN 215
           V + D    +     + E ++             ++ P   LL G PG+GKT L  A+  
Sbjct: 4   VNFTDKQFENRLNDNLEELIQGKK---------AVESPTAFLLGGQPGSGKTSLRSAIFE 54

Query: 216 HTTAAFIRVVGSEFVQKYLGEVWLKHKQI 244
            T    I +    F Q++     L     
Sbjct: 55  ETQGNVIVIDNDTFKQQHPNFDELVKLYE 83

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]} Length = 321

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]

 Score = 63.9 bits (155), Expect = 1e-12
 Identities = 16/99 (16%), Positives = 29/99 (29%), Gaps = 5/99 (5%)

Query: 152 EKPDVTYNDIGGCDIQKQEIREA--VELPLTHHELYKQIGIDPPRGVLL-YGPPGTGKTM 208
               V   + G      +        EL      + +  G     G+++  G   +GKT 
Sbjct: 79  GSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTP 138

Query: 209 LAKAVANHTTA--AFIRVVGSEFVQKYLGEVWLKHKQIF 245
           L  A+         +  V   E +  Y  +  +    I 
Sbjct: 139 LVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIA 177

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]} Length = 246

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]

 Score = 61.1 bits (147), Expect = 7e-12
 Identities = 17/75 (22%), Positives = 30/75 (40%)

Query: 161 IGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAA 220
           + G       +   ++      +  K     P   VLL GPP +GKT LA  +A  +   
Sbjct: 8   MNGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFP 67

Query: 221 FIRVVGSEFVQKYLG 235
           FI++   + +  +  
Sbjct: 68  FIKICSPDKMIGFSE 82

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 253

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]

 Score = 54.4 bits (129), Expect = 2e-09
 Identities = 19/88 (21%), Positives = 30/88 (34%), Gaps = 4/88 (4%)

Query: 157 TYNDIGGCDIQKQEIREAVELPLTHHE----LYKQIGIDPPRGVLLYGPPGTGKTMLAKA 212
               + G      +++  +       +       + G    R  +LYGPPG GKT  A  
Sbjct: 12  NLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHL 71

Query: 213 VANHTTAAFIRVVGSEFVQKYLGEVWLK 240
           VA       +    S+   K L    +K
Sbjct: 72  VAQELGYDILEQNASDVRSKTLLNAGVK 99

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]} Length = 309

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]

 Score = 54.1 bits (129), Expect = 3e-09
 Identities = 19/80 (23%), Positives = 37/80 (46%), Gaps = 1/80 (1%)

Query: 163 GCDIQKQEIREAVELPLTHHELYKQIGID-PPRGVLLYGPPGTGKTMLAKAVANHTTAAF 221
           G    K+ +  A+       +L + +  +  P+ +L+ GP G GKT +A+ +A    A F
Sbjct: 18  GQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPF 77

Query: 222 IRVVGSEFVQKYLGEVWLKH 241
           I+V  ++F +       +  
Sbjct: 78  IKVEATKFTEVGYVGKEVDS 97

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]} Length = 239

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]

 Score = 53.4 bits (127), Expect = 3e-09
 Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 8/76 (10%)

Query: 157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANH 216
           T ++  G +  KQ++R  +E      E        P   +LL+GPPG GKT LA  +A+ 
Sbjct: 7   TLDEYIGQERLKQKLRVYLEAAKARKE--------PLEHLLLFGPPGLGKTTLAHVIAHE 58

Query: 217 TTAAFIRVVGSEFVQK 232
                    G    + 
Sbjct: 59  LGVNLRVTSGPAIEKP 74

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 276

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]

 Score = 46.0 bits (107), Expect = 1e-06
 Identities = 17/96 (17%), Positives = 31/96 (32%), Gaps = 11/96 (11%)

Query: 154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAV 213
           P      +   + Q Q++   +   L +                L G PGTGKT+  + +
Sbjct: 11  PSYVPKRLPHREQQLQQLDILLGNWLRN-------PGHHYPRATLLGRPGTGKTVTLRKL 63

Query: 214 A----NHTTAAFIRVVGSEFVQKYLGEVWLKHKQIF 245
                + TTA F+ + G  +         +      
Sbjct: 64  WELYKDKTTARFVYINGFIYRNFTAIIGEIARSLNI 99

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]} Length = 443

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]

 Score = 45.1 bits (106), Expect = 4e-06
 Identities = 15/39 (38%), Positives = 25/39 (64%)

Query: 193 PRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQ 231
           P+ +L+ GP G GKT +A+ +A    A FI+V  ++F +
Sbjct: 49  PKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTE 87

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]} Length = 238

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]

 Score = 44.2 bits (103), Expect = 4e-06
 Identities = 20/76 (26%), Positives = 32/76 (42%), Gaps = 8/76 (10%)

Query: 157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANH 216
           + ++  G +  K+++  A+E      E            VLL GPPG GKT LA  +A+ 
Sbjct: 7   SLDEFIGQENVKKKLSLALEAAKMRGE--------VLDHVLLAGPPGLGKTTLAHIIASE 58

Query: 217 TTAAFIRVVGSEFVQK 232
                    G   V++
Sbjct: 59  LQTNIHVTSGPVLVKQ 74

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]} Length = 287

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

 Score = 44.0 bits (102), Expect = 5e-06
 Identities = 11/81 (13%), Positives = 19/81 (23%), Gaps = 4/81 (4%)

Query: 165 DIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRV 224
             + + +       L        + +         G  G GKT LAK      + A  + 
Sbjct: 22  RGEAEALARIYLNRLLSGAGLSDVNM----IYGSIGRVGIGKTTLAKFTVKRVSEAAAKE 77

Query: 225 VGSEFVQKYLGEVWLKHKQIF 245
             +                I 
Sbjct: 78  GLTVKQAYVNAFNAPNLYTIL 98

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]} Length = 333

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]

 Score = 42.2 bits (98), Expect = 3e-05
 Identities = 10/20 (50%), Positives = 15/20 (75%)

Query: 195 GVLLYGPPGTGKTMLAKAVA 214
           GVL++G  GTGK+   +A+A
Sbjct: 30  GVLVFGDRGTGKSTAVRALA 49

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]} Length = 189

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]

 Score = 38.8 bits (89), Expect = 2e-04
 Identities = 13/33 (39%), Positives = 17/33 (51%)

Query: 194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVG 226
           R V L GPPG GKT L    +    ++ + V G
Sbjct: 2   RHVFLTGPPGVGKTTLIHKASEVLKSSGVPVDG 34

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 252

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]

 Score = 38.6 bits (88), Expect = 3e-04
 Identities = 13/60 (21%), Positives = 20/60 (33%), Gaps = 12/60 (20%)

Query: 157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANH 216
           + N +   +     ++   + P     L            LLYGP GTGK     A+   
Sbjct: 9   SLNALSHNEELTNFLKSLSDQPRDLPHL------------LLYGPNGTGKKTRCMALLES 56

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]} Length = 192

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]

 Score = 38.1 bits (87), Expect = 4e-04
 Identities = 10/40 (25%), Positives = 17/40 (42%)

Query: 194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKY 233
           + V + G   +GK++L   +A           G EFV + 
Sbjct: 8   KTVAILGGESSGKSVLVNKLAAVFNTTSAWEYGREFVFEK 47

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]} Length = 364

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

 Score = 37.1 bits (85), Expect = 0.001
 Identities = 11/33 (33%), Positives = 17/33 (51%)

Query: 192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRV 224
               +LL GP G+GKT++A+ +A H        
Sbjct: 67  SKSNILLIGPTGSGKTLMAQTLAKHLDIPIAIS 99

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]} Length = 178

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]

 Score = 36.2 bits (82), Expect = 0.001
 Identities = 5/41 (12%), Positives = 16/41 (39%)

Query: 193 PRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKY 233
            R ++L G    GK+ + + + +     ++       ++  
Sbjct: 3   TRMIILNGGSSAGKSGIVRCLQSVLPEPWLAFGVDSLIEAM 43

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]} Length = 176

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]

 Score = 35.7 bits (81), Expect = 0.002
 Identities = 11/34 (32%), Positives = 19/34 (55%)

Query: 196 VLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF 229
           +LL G PG+GK+ +A+A+AN      +     + 
Sbjct: 7   LLLSGHPGSGKSTIAEALANLPGVPKVHFHSDDL 40

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]} Length = 283

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]

 Score = 35.9 bits (81), Expect = 0.003
 Identities = 9/36 (25%), Positives = 15/36 (41%)

Query: 194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF 229
              L+ G   TGK+ + K   N     +I +   +F
Sbjct: 30  PITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKF 65

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Length = 207

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]

 Score = 35.1 bits (79), Expect = 0.004
 Identities = 6/24 (25%), Positives = 11/24 (45%)

Query: 193 PRGVLLYGPPGTGKTMLAKAVANH 216
              +L+   PG G   L  A++ +
Sbjct: 24  HHALLIQALPGMGDDALIYALSRY 47

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]} Length = 242

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]

 Score = 35.2 bits (79), Expect = 0.004
 Identities = 8/28 (28%), Positives = 13/28 (46%)

Query: 189 GIDPPRGVLLYGPPGTGKTMLAKAVANH 216
           GI+      ++G   TGKT +   +A  
Sbjct: 19  GIETGSITEMFGEFRTGKTQICHTLAVT 46

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	245
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	99.89
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	99.87
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.86
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.84
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.63
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.52
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	99.45
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.45
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	99.44
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	99.34
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	99.3
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	99.24
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	99.21
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.11
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	99.1
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	99.02
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	98.88
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.85
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	98.82
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.82
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.78
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.75
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	98.66
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	98.6
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.53
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	98.51
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.48
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	98.34
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	98.28
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	98.25
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.21
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	98.13
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	98.03
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	98.02
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	98.02
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.0
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	97.96
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	97.64
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	97.59
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.42
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	97.42
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	97.42
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	97.4
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	97.37
d1tuea_	205	Replication protein E1 helicase domain {Human papi	97.33
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	97.22
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	97.14
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	97.06
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	96.9
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.82
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.81
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	96.81
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.79
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	96.72
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	96.69
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	96.65
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.62
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	96.52
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	96.5
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	96.49
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	96.47
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	96.43
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	96.4
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	96.38
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	96.38
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	96.33
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	96.3
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	96.25
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	96.22
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	96.2
d2awna2	232	Maltose transport protein MalK, N-terminal domain	96.17
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	96.14
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	96.11
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	96.1
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	96.1
d1g2912	240	Maltose transport protein MalK, N-terminal domain	96.07
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	96.05
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	96.01
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	95.98
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	95.98
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	95.97
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	95.93
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	95.92
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	95.86
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	95.85
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	95.85
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	95.77
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	95.75
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	95.72
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	95.71
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	95.7
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	95.64
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	95.62
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	95.58
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	95.55
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	95.54
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	95.53
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	95.47
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	95.44
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	95.42
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	95.41
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	95.37
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	95.35
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	95.33
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	95.27
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	95.26
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	95.26
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	95.23
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	95.23
d2ncda_	368	Kinesin motor Ncd (non-claret disjunctional) {Frui	95.19
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	95.14
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	95.12
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	95.08
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	95.08
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	95.05
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	95.04
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	94.98
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	94.83
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	94.83
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	94.82
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	94.81
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	94.71
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	94.7
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	94.69
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	94.66
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	94.56
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	94.55
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	94.54
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	94.42
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	94.42
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	94.28
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	94.15
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	94.15
d1xpua3	289	Transcription termination factor Rho, ATPase domai	93.81
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	93.63
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	93.09
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	92.65
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	92.47
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	91.96
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	91.86
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	91.22
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	90.12
d1j3ba1	318	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	90.1
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	90.07
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	89.92
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	89.91
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	89.82
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	89.31
d2olra1	313	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	89.23
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	89.1
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	89.02
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	89.01
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	89.0
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	88.81
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	88.28
d1ii2a1	323	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	87.98
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	87.46
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	87.36
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	87.27
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	86.51
d1g8fa3	122	ATP sulfurylase C-terminal domain {Baker's yeast (	86.47
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	85.26
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	84.97
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	84.72
d1ry6a_	330	Kinesin {Malaria parasite (Plasmodium falciparum)	83.79
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	83.63
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	83.59
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	83.44
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	83.31
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	82.35
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	81.92
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	81.68

>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=99.89  E-value=2.1e-24  Score=185.44  Aligned_cols=93  Identities=41%  Similarity=0.768  Sum_probs=89.2

Q ss_pred             CCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHH
Q 025979          152 EKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQ  231 (245)
Q Consensus       152 ~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~  231 (245)
                      +.|+++|+||+|+++++++|.+.+.. +.+++.|.++|..+|+|+|||||||||||++|+++|++++++|+.++++++.+
T Consensus         2 ~~p~~~~~di~G~~~~k~~l~~~i~~-l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~~~~~~~i~~~~l~~   80 (247)
T d1ixza_           2 EAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVE   80 (247)
T ss_dssp             CCCSCCGGGCCSCHHHHHHHHHHHHH-HHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHHH
T ss_pred             CCCCCcHHHHccHHHHHHHHHHHHHH-HHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHcCCCEEEEEhHHhhh
Confidence            57899999999999999999998776 88999999999999999999999999999999999999999999999999999


Q ss_pred             HHhccccccccccC
Q 025979          232 KYLGEVWLKHKQIF  245 (245)
Q Consensus       232 ~~~Ge~~~~vr~iF  245 (245)
                      +|+|+++++|+++|
T Consensus        81 ~~~g~~~~~l~~~f   94 (247)
T d1ixza_          81 MFVGVGAARVRDLF   94 (247)
T ss_dssp             SCTTHHHHHHHHHH
T ss_pred             ccccHHHHHHHHHH
Confidence            99999999999887

>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=99.87  E-value=3.9e-24  Score=184.74  Aligned_cols=94  Identities=38%  Similarity=0.745  Sum_probs=84.7

Q ss_pred             CCCCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH
Q 025979          151 SEKPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV  230 (245)
Q Consensus       151 ~~~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~  230 (245)
                      +..++++|+||+|+++++++|.+.|.+ +.+++.|.++|..+|+|+|||||||||||++|+++|++++.+++.+++++++
T Consensus         4 ~~~~~~t~~Di~Gl~~~k~~l~e~v~~-~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~~~~~~~i~~~~l~   82 (256)
T d1lv7a_           4 EDQIKTTFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFV   82 (256)
T ss_dssp             ECSSCCCGGGSCSCHHHHHHTHHHHHH-HHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCCEEEECSCSST
T ss_pred             CCCCCCCHHHHhchHHHHHHHHHHHHH-HHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHcCCCEEEEEhHHhh
Confidence            456789999999999999999999876 8899999999999999999999999999999999999999999999999999


Q ss_pred             HHHhccccccccccC
Q 025979          231 QKYLGEVWLKHKQIF  245 (245)
Q Consensus       231 ~~~~Ge~~~~vr~iF  245 (245)
                      ++|+|+++++++++|
T Consensus        83 ~~~~g~~~~~l~~~f   97 (256)
T d1lv7a_          83 EMFVGVGASRVRDMF   97 (256)
T ss_dssp             TSCCCCCHHHHHHHH
T ss_pred             hcchhHHHHHHHHHH
Confidence            999999999999887

>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=99.86  E-value=2.6e-23  Score=179.24  Aligned_cols=90  Identities=53%  Similarity=0.944  Sum_probs=87.8

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhc
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLG  235 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~G  235 (245)
                      |+|+||+|++.++++|++.|..|+.+|+.|.+.|+.+|+|+|||||||||||++|+++|++++.+|+.++++++.++|+|
T Consensus         1 ~~~~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~~~~~~~i~~~~l~~~~~g   80 (258)
T d1e32a2           1 VGYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAG   80 (258)
T ss_dssp             CCGGGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHTTCEEEEECHHHHTTSCTT
T ss_pred             CChhhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHHhCCeEEEEEchhhcccccc
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccccccC
Q 025979          236 EVWLKHKQIF  245 (245)
Q Consensus       236 e~~~~vr~iF  245 (245)
                      +++.+++++|
T Consensus        81 ~~~~~l~~~f   90 (258)
T d1e32a2          81 ESESNLRKAF   90 (258)
T ss_dssp             HHHHHHHHHH
T ss_pred             cHHHHHHHHH
Confidence            9999999876

>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=99.84  E-value=1.6e-22  Score=175.05  Aligned_cols=93  Identities=44%  Similarity=0.842  Sum_probs=90.0

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHH
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQK  232 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~  232 (245)
                      .|+++|+||+|+++++++|.+.|..|+.+++.|...|+.+++|+|||||||||||++|+++|++++++|+.++++++.+.
T Consensus         1 ~p~~~f~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~~~~~~~~~~~~~l~~~   80 (265)
T d1r7ra3           1 VPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTM   80 (265)
T ss_dssp             CCCCSCSSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHHTTCEEEEECHHHHHTS
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHHhCCcEEEEEHHHhhhc
Confidence            37899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhccccccccccC
Q 025979          233 YLGEVWLKHKQIF  245 (245)
Q Consensus       233 ~~Ge~~~~vr~iF  245 (245)
                      |.|+++.+++++|
T Consensus        81 ~~~~~~~~l~~~f   93 (265)
T d1r7ra3          81 WFGESEANVREIF   93 (265)
T ss_dssp             CTTTHHHHHHHHH
T ss_pred             cccchHHHHHHHH
Confidence            9999999998876

>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=99.63  E-value=1.2e-17  Score=147.07  Aligned_cols=87  Identities=25%  Similarity=0.329  Sum_probs=69.3

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhh-ccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHH--HHHhc
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQI-GIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFV--QKYLG  235 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~-g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~--~~~~G  235 (245)
                      ..|+|++++++.|.++|..++.+..+.... .-.+++|+|||||||||||+|||++|+.++.+|+++++++++  +.|.|
T Consensus        14 ~~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~~~~~~~~i~~s~~~~~~~~~~   93 (309)
T d1ofha_          14 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGK   93 (309)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGGSSCCSGGG
T ss_pred             CcccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhccccchhcccccccccceeEee
Confidence            358999999999999885432222111111 123789999999999999999999999999999999999998  55899


Q ss_pred             cccccccccC
Q 025979          236 EVWLKHKQIF  245 (245)
Q Consensus       236 e~~~~vr~iF  245 (245)
                      ++++.++.+|
T Consensus        94 ~~~~~~~~~f  103 (309)
T d1ofha_          94 EVDSIIRDLT  103 (309)
T ss_dssp             STTHHHHHHH
T ss_pred             eccccccccc
Confidence            9999888765

>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=99.52  E-value=1.4e-16  Score=140.72  Aligned_cols=69  Identities=19%  Similarity=0.129  Sum_probs=62.2

Q ss_pred             cCCCcHHHHhhhccCCCcceee-ecCCCCchHHHHHHHHhccc--ceeeeechhHHHHHHhccccccccccC
Q 025979          177 LPLTHHELYKQIGIDPPRGVLL-YGPPGTGKTMLAKAVANHTT--AAFIRVVGSEFVQKYLGEVWLKHKQIF  245 (245)
Q Consensus       177 ~~~~~~~~~~~~g~~~~~gvLl-~GPPGtGKT~lAkalA~~l~--~~~~~v~~s~l~~~~~Ge~~~~vr~iF  245 (245)
                      ++...|..++.+|...++|++| |||||||||++|+++|.+++  .+|+.+++++++++|+|+++++||++|
T Consensus       106 ~~~~~~~~~~~~~~~~~~g~~l~~G~pG~GKT~la~ala~~~~~~~~~~~~~~~~~~~~~~G~~e~~~~~~f  177 (321)
T d1w44a_         106 LVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIA  177 (321)
T ss_dssp             CCSBCCEEEEETTEEEESEEEEEECSSSSCHHHHHHHHHHHHHTTSCCEEEEBSCSSTTCBCCHHHHHHHHH
T ss_pred             ccccchHHHHHhhcccCCceEEEECCCCccHHHHHHHHHHHhcCCCCeEEEEhhHhhhcccchHHHHHHHHH
Confidence            4456778888888889999655 89999999999999999986  789999999999999999999999987

>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=99.45  E-value=2.8e-14  Score=119.37  Aligned_cols=66  Identities=30%  Similarity=0.452  Sum_probs=56.5

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHH
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF  229 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l  229 (245)
                      .+|+|++|++++++++..++....        .+-.++.++|||||||||||++|+++|++++.+|..++++..
T Consensus         6 ~~~ddivGq~~~~~~L~~~i~~~~--------~~~~~~~~~Ll~GPpG~GKTtla~~la~~~~~~~~~~~~~~~   71 (239)
T d1ixsb2           6 KTLDEYIGQERLKQKLRVYLEAAK--------ARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAI   71 (239)
T ss_dssp             CSGGGSCSCHHHHHHHHHHHHHHT--------TSSSCCCCEEEECCTTSCHHHHHHHHHHHHTCCEEEEETTTC
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHH--------hcCCCCCeEEEECCCCCCHHHHHHHHHHHhCCCeEeccCCcc
Confidence            479999999999999999986522        122356789999999999999999999999999999987765

>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=99.45  E-value=4.6e-15  Score=126.36  Aligned_cols=84  Identities=27%  Similarity=0.364  Sum_probs=60.6

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhccc-
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGEV-  237 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge~-  237 (245)
                      +.++|..+.++.+.+.........   +.....|++|||||||||||||++|++||++++.+|+++++++++.++.|.+ 
T Consensus         9 ~~~i~~~~~i~~i~~~~~~~~~~~---~~~~~~p~~~vLL~GppGtGKT~la~alA~~~~~~~~~i~~~~~~~g~~~~~~   85 (246)
T d1d2na_           9 NGIIKWGDPVTRVLDDGELLVQQT---KNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAK   85 (246)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHH---HHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHTCSEEEEECGGGCTTCCHHHH
T ss_pred             cCCcCcCHHHHHHHHHHHHHHHHH---hccCCCCCeEEEEECcCCCCHHHHHHHHhhcccccccccccccccccccccch
Confidence            456665555555555544322211   2223457889999999999999999999999999999999998877776655 


Q ss_pred             cccccccC
Q 025979          238 WLKHKQIF  245 (245)
Q Consensus       238 ~~~vr~iF  245 (245)
                      .+.+|++|
T Consensus        86 ~~~i~~if   93 (246)
T d1d2na_          86 CQAMKKIF   93 (246)
T ss_dssp             HHHHHHHH
T ss_pred             hhhhhhhh
Confidence            35677665

>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=99.44  E-value=3.5e-14  Score=118.60  Aligned_cols=66  Identities=27%  Similarity=0.360  Sum_probs=55.7

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHH
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF  229 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l  229 (245)
                      -+|+|++|++.+++.|..++..+.        .+-.++.++|||||||||||++|+++|++++.+++.+++++.
T Consensus         6 ~~~~divGqe~~~~~l~~~i~~~~--------~~~~~~~~~L~~GPpGtGKT~lA~~la~~~~~~~~~~~~~~~   71 (238)
T d1in4a2           6 KSLDEFIGQENVKKKLSLALEAAK--------MRGEVLDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVL   71 (238)
T ss_dssp             SSGGGCCSCHHHHHHHHHHHHHHH--------HHTCCCCCEEEESSTTSSHHHHHHHHHHHHTCCEEEEETTTC
T ss_pred             CcHHHcCChHHHHHHHHHHHHHHH--------hcCCCCCeEEEECCCCCcHHHHHHHHHhccCCCcccccCccc
Confidence            378999999999999999986521        122355679999999999999999999999999999887765

>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=99.34  E-value=2.1e-13  Score=114.81  Aligned_cols=69  Identities=26%  Similarity=0.387  Sum_probs=53.4

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHH
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKY  233 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~  233 (245)
                      +++.|..+.+...+.+.+.+...         .+...|+++|||||||||||++|++||++++.+|+.++++++.+.+
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~P~~ilL~GpPGtGKT~la~~la~~~~~~~~~i~~d~~~~~~   72 (273)
T d1gvnb_           4 VNFTDKQFENRLNDNLEELIQGK---------KAVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDTFKQQH   72 (273)
T ss_dssp             TCCCHHHHHHHHHHHHHHHHTTC---------CCCSSCEEEEEECCTTSCTHHHHHHHHHHTTTCCEEECTHHHHTTS
T ss_pred             cccChHHHHHHHHHHHHHHHhcc---------cCCCCCEEEEEECCCCCCHHHHHHHHHHHhhcceEEEecHHHHHHh
Confidence            34556555555566665554432         2456789999999999999999999999999999999999987543

>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=99.30  E-value=1.8e-13  Score=114.72  Aligned_cols=81  Identities=22%  Similarity=0.253  Sum_probs=61.5

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCc-HHH---HhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHH
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTH-HEL---YKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF  229 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~-~~~---~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l  229 (245)
                      .+.+++|++|.+..+++|.+++...... +..   ....+....+++|||||||||||++|+++|++++..++.++++++
T Consensus         9 ~P~~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~~~~~~~~~~~~   88 (253)
T d1sxja2           9 APTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDILEQNASDV   88 (253)
T ss_dssp             CCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTCEEEEECTTSC
T ss_pred             CCCCHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHHhhhhccccccc
Confidence            3457899999999999999988642111 000   112344556779999999999999999999999999999998876


Q ss_pred             HHHHh
Q 025979          230 VQKYL  234 (245)
Q Consensus       230 ~~~~~  234 (245)
                      .+.+.
T Consensus        89 ~~~~~   93 (253)
T d1sxja2          89 RSKTL   93 (253)
T ss_dssp             CCHHH
T ss_pred             hhhHH
Confidence            55443

>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=99.24  E-value=2.1e-12  Score=115.50  Aligned_cols=77  Identities=18%  Similarity=0.060  Sum_probs=60.5

Q ss_pred             cCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHH-hcccc
Q 025979          160 DIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKY-LGEVW  238 (245)
Q Consensus       160 dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~-~Ge~~  238 (245)
                      ++.|++.++..+.+++..        ...|...++++|||||||||||++|+++|+.++.+|+++++|+..+.| +|...
T Consensus       129 l~~~~~~~~~~i~~~l~~--------~~~~~~~~~~~~~~g~~~~gk~~~~~~~~~~~~~~~i~in~s~~rs~~~l~~~~  200 (362)
T d1svma_         129 LHCLLPKMDSVVYDFLKC--------MVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVAI  200 (362)
T ss_dssp             HTTTSTTHHHHHHHHHHH--------HHHCCTTCCEEEEECSTTSSHHHHHHHHHHHHCCEEECCSSCTTTHHHHHGGGT
T ss_pred             HHhcccchHHHHHHHHHH--------HHhCCCCcCeEEEECCCCCCHHHHHHHHHHHcCCCEEEEECcchhhHHHHHhHH
Confidence            456677777777766543        123666777899999999999999999999999999999999988876 77766


Q ss_pred             cccccc
Q 025979          239 LKHKQI  244 (245)
Q Consensus       239 ~~vr~i  244 (245)
                      .....+
T Consensus       201 ~~~~~l  206 (362)
T d1svma_         201 DQFLVV  206 (362)
T ss_dssp             TCSCEE
T ss_pred             HHHHHH
Confidence            655443

>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=99.21  E-value=2.3e-12  Score=118.15  Aligned_cols=71  Identities=30%  Similarity=0.558  Sum_probs=55.9

Q ss_pred             cCCcchhhhHHHHHHHhcCCCcHHHHhhhcc-------CCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHHHH-
Q 025979          160 DIGGCDIQKQEIREAVELPLTHHELYKQIGI-------DPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQ-  231 (245)
Q Consensus       160 dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~-------~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~-  231 (245)
                      -|+|++++|+.+.-+|.-..      ++..+       -.|+++||.||||||||+|||.||+.+++||+.++++.|.+ 
T Consensus        15 yVvGQ~~AKk~lsvav~nhy------rR~~~~~~~~~ei~ksNILliGPTGvGKTlLAr~LAk~l~VPFv~~daT~fTea   88 (443)
T d1g41a_          15 HIIGQADAKRAVAIALRNRW------RRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEV   88 (443)
T ss_dssp             TCCSCHHHHHHHHHHHHHHH------HHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGGGC--
T ss_pred             cccCcHHHHHHHHHHHHHHH------HHhhcccccccccccccEEEECCCCCCHHHHHHHHHHHhCCCEEEeecceeeec
Confidence            48999999999998884311      11111       13678999999999999999999999999999999999984 


Q ss_pred             HHhcc
Q 025979          232 KYLGE  236 (245)
Q Consensus       232 ~~~Ge  236 (245)
                      .|+|+
T Consensus        89 GYvG~   93 (443)
T d1g41a_          89 GYVGK   93 (443)
T ss_dssp             --CCC
T ss_pred             ceeec
Confidence            47775

>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=99.11  E-value=3.1e-11  Score=105.71  Aligned_cols=65  Identities=25%  Similarity=0.417  Sum_probs=54.5

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCC---Cc-ceeeecCCCCchHHHHHHHHhcccceeeeechhHHHH
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGIDP---PR-GVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQ  231 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~---~~-gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~  231 (245)
                      ..|+|++++++.|.++|..        ...|+..   |. .+||+||||||||.||++||..++.+|+++++++|.+
T Consensus        22 ~~viGQ~~a~~~v~~~v~~--------~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~l~~~~i~~d~s~~~~   90 (315)
T d1r6bx3          22 MLVFGQDKAIEALTEAIKM--------ARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYME   90 (315)
T ss_dssp             TTSCSCHHHHHHHHHHHHH--------HHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHTCEEEEEEGGGCSS
T ss_pred             CeecChHHHHHHHHHHHHH--------HHccCCCCCCCceEEEEECCCcchhHHHHHHHHhhccCCeeEeccccccc
Confidence            5689999999999998864        2334332   33 4899999999999999999999999999999999864

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=99.10  E-value=1.8e-11  Score=109.39  Aligned_cols=78  Identities=27%  Similarity=0.350  Sum_probs=54.7

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCc---HHHHh----------hhc----cCCCcceeeecCCCCchHHHHHHHHhccccee
Q 025979          159 NDIGGCDIQKQEIREAVELPLTH---HELYK----------QIG----IDPPRGVLLYGPPGTGKTMLAKAVANHTTAAF  221 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~---~~~~~----------~~g----~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~  221 (245)
                      .-|+|++++++.+..++....+.   +...+          ..|    -.|+.++||.||+|||||.+||+||..++.+|
T Consensus        17 ~~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~~~p~~niLfiGPTGvGKTElAk~LA~~~~~~~   96 (364)
T d1um8a_          17 NYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHLDIPI   96 (364)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCE
T ss_pred             CeecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccccCCCcceeeeCCCCccHHHHHHHHHhhcccce
Confidence            45899999999998887421111   00001          111    23677799999999999999999999999999


Q ss_pred             eeechhHHHH-HHhcc
Q 025979          222 IRVVGSEFVQ-KYLGE  236 (245)
Q Consensus       222 ~~v~~s~l~~-~~~Ge  236 (245)
                      +++++++|++ .|+|.
T Consensus        97 ir~D~s~~~e~gyvg~  112 (364)
T d1um8a_          97 AISDATSLTEAGYVGE  112 (364)
T ss_dssp             EEEEGGGCC-------
T ss_pred             eehhhhhcccchhhHh
Confidence            9999999874 55554

>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=99.02  E-value=1.2e-10  Score=96.30  Aligned_cols=63  Identities=27%  Similarity=0.351  Sum_probs=51.3

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc-----ceeeeechhHH
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT-----AAFIRVVGSEF  229 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~-----~~~~~v~~s~l  229 (245)
                      +-+++|++|.+++++.+..++...             ....+|||||||||||++|+++|++++     ..++.+++++.
T Consensus        20 P~~~~diig~~~~~~~l~~~i~~~-------------~~~~lll~Gp~G~GKTtla~~iak~l~~~~~~~~~~e~n~s~~   86 (231)
T d1iqpa2          20 PQRLDDIVGQEHIVKRLKHYVKTG-------------SMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNASDE   86 (231)
T ss_dssp             CCSTTTCCSCHHHHHHHHHHHHHT-------------CCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETTCH
T ss_pred             CCCHHHccCcHHHHHHHHHHHHcC-------------CCCeEEEECCCCCcHHHHHHHHHHHHHhcccCCCeeEEecCcc
Confidence            347899999999999999998641             224599999999999999999999864     56778877665


Q ss_pred             H
Q 025979          230 V  230 (245)
Q Consensus       230 ~  230 (245)
                      .
T Consensus        87 ~   87 (231)
T d1iqpa2          87 R   87 (231)
T ss_dssp             H
T ss_pred             c
Confidence            4

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.88  E-value=8.1e-10  Score=90.92  Aligned_cols=62  Identities=18%  Similarity=0.227  Sum_probs=48.1

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc-----eeeeechh
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA-----AFIRVVGS  227 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~-----~~~~v~~s  227 (245)
                      ..+-+++|++|.+++++.+..++...             ....+|||||||||||++|+.+|++++.     .++.+..+
T Consensus         9 yrP~~~~d~ig~~~~~~~L~~~~~~~-------------~~~~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~~~n~~   75 (224)
T d1sxjb2           9 YRPQVLSDIVGNKETIDRLQQIAKDG-------------NMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNAS   75 (224)
T ss_dssp             TCCSSGGGCCSCTHHHHHHHHHHHSC-------------CCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTT
T ss_pred             hCCCCHHHhcCCHHHHHHHHHHHHcC-------------CCCeEEEECCCCCCchhhHHHHHHHHhcccccccccccccc
Confidence            34557899999999999999887641             1234999999999999999999998753     35555544

>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=98.85  E-value=7.2e-10  Score=91.99  Aligned_cols=63  Identities=25%  Similarity=0.274  Sum_probs=47.2

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc----cceeeeech
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT----TAAFIRVVG  226 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l----~~~~~~v~~  226 (245)
                      ..+.++|.+.+++.|.+++...+.++      + .++.++||+||||||||++|+++|+.+    +..|+.+.+
T Consensus        14 ~p~~l~~Re~ei~~l~~~l~~~l~~~------~-~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~   80 (276)
T d1fnna2          14 VPKRLPHREQQLQQLDILLGNWLRNP------G-HHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYING   80 (276)
T ss_dssp             CCSCCTTCHHHHHHHHHHHHHHHHST------T-SSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEET
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhCC------C-CCCCceEEECCCCCCHHHHHHHHHHHHhcccCCcEEEecc
Confidence            34568899999999998886533222      1 356789999999999999999999886    345555543

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=98.82  E-value=1.4e-09  Score=95.05  Aligned_cols=65  Identities=31%  Similarity=0.524  Sum_probs=52.6

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhhccC---CCc-ceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHHH
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGID---PPR-GVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFVQ  231 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~---~~~-gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~~  231 (245)
                      ..|.|++++++.|.+.+..        ...|+.   .|. .+||+||||||||.+|+++|..+   +.+|++++++++.+
T Consensus        23 ~~v~GQ~~ai~~v~~~i~~--------~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l~~~~~~~~~~~~~~~~~   94 (315)
T d1qvra3          23 KRVVGQDEAIRAVADAIRR--------ARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYME   94 (315)
T ss_dssp             HHSCSCHHHHHHHHHHHHH--------HGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCS
T ss_pred             CeEeCHHHHHHHHHHHHHH--------HhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHHhcCCCcceEEEecccccc
Confidence            4689999999999988865        223333   234 37899999999999999999998   78999999988753

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.82  E-value=1.6e-09  Score=89.02  Aligned_cols=51  Identities=31%  Similarity=0.429  Sum_probs=42.6

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhccc
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      +-+++|++|.+++++.|+.++...             ....+|||||||||||++|+++|++++
T Consensus        10 P~~~~divg~~~~~~~L~~~i~~~-------------~~~~lLl~Gp~G~GKttl~~~la~~l~   60 (227)
T d1sxjc2          10 PETLDEVYGQNEVITTVRKFVDEG-------------KLPHLLFYGPPGTGKTSTIVALAREIY   60 (227)
T ss_dssp             CSSGGGCCSCHHHHHHHHHHHHTT-------------CCCCEEEECSSSSSHHHHHHHHHHHHH
T ss_pred             CCCHHHccCcHHHHHHHHHHHHcC-------------CCCeEEEECCCCCChhHHHHHHHHHhh
Confidence            357899999999999999987541             122499999999999999999999874

>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=98.78  E-value=1.4e-09  Score=90.23  Aligned_cols=52  Identities=23%  Similarity=0.340  Sum_probs=42.2

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+.+++|++|.+++++.|..++...            ..+.++|||||||||||++|+++|+++
T Consensus         6 ~P~~~~diig~~~~~~~L~~~~~~~------------~~~~~lll~Gp~G~GKTt~~~~la~~l   57 (252)
T d1sxje2           6 RPKSLNALSHNEELTNFLKSLSDQP------------RDLPHLLLYGPNGTGKKTRCMALLESI   57 (252)
T ss_dssp             CCCSGGGCCSCHHHHHHHHTTTTCT------------TCCCCEEEECSTTSSHHHHHHTHHHHH
T ss_pred             CCCCHHHccCcHHHHHHHHHHHHcC------------CCCCeEEEECCCCCCHHHHHHHHHHhh
Confidence            4457999999999888888776532            123359999999999999999999986

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.75  E-value=2.9e-09  Score=87.44  Aligned_cols=51  Identities=24%  Similarity=0.404  Sum_probs=42.3

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+.+++|++|.++.++.|..++...             ....+||+||||||||++++++|+++
T Consensus         7 ~P~~~~diig~~~~~~~l~~~i~~~-------------~~~~lll~Gp~G~GKTtl~~~i~~~l   57 (237)
T d1sxjd2           7 RPKNLDEVTAQDHAVTVLKKTLKSA-------------NLPHMLFYGPPGTGKTSTILALTKEL   57 (237)
T ss_dssp             CCSSTTTCCSCCTTHHHHHHHTTCT-------------TCCCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCCHHHccCcHHHHHHHHHHHHcC-------------CCCeEEEECCCCCChHHHHHHHHHHH
Confidence            3457899999999999999887541             12349999999999999999999986

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.66  E-value=9e-09  Score=85.70  Aligned_cols=52  Identities=23%  Similarity=0.340  Sum_probs=44.5

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      -+++|++|.++.++.+...+...            ..|+++|||||||||||++|+++++.++.
T Consensus         9 ~~~~dlig~~~~~~~L~~~i~~~------------~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~   60 (239)
T d1njfa_           9 QTFADVVGQEHVLTALANGLSLG------------RIHHAYLFSGTRGVGKTSIARLLAKGLNC   60 (239)
T ss_dssp             SSGGGSCSCHHHHHHHHHHHHTT------------CCCSEEEEECSTTSSHHHHHHHHHHHHHC
T ss_pred             CCHHHccChHHHHHHHHHHHHcC------------CCCeeEEEECCCCCcHHHHHHHHHHHhcC
Confidence            48899999999999999887641            34677999999999999999999988743

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.60  E-value=9.6e-09  Score=83.76  Aligned_cols=73  Identities=22%  Similarity=0.327  Sum_probs=57.8

Q ss_pred             ccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc----------cceeeeechhH
Q 025979          159 NDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT----------TAAFIRVVGSE  228 (245)
Q Consensus       159 ~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l----------~~~~~~v~~s~  228 (245)
                      +.++|-++.++++.+.+...             ..++++|+||||||||.++..+|...          +..++.++.+.
T Consensus        22 d~~igRd~Ei~~l~~iL~r~-------------~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~~~   88 (195)
T d1jbka_          22 DPVIGRDEEIRRTIQVLQRR-------------TKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGA   88 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSS-------------SSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHH
T ss_pred             CCCcCcHHHHHHHHHHHhcc-------------CCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeHHH
Confidence            46788898888888877652             33569999999999999999999744          68899999999


Q ss_pred             HH--HHHhcccccccccc
Q 025979          229 FV--QKYLGEVWLKHKQI  244 (245)
Q Consensus       229 l~--~~~~Ge~~~~vr~i  244 (245)
                      ++  .+|.|+-+..++.+
T Consensus        89 LiAg~~~rG~~E~rl~~i  106 (195)
T d1jbka_          89 LVAGAKYRGEFEERLKGV  106 (195)
T ss_dssp             HHTTTCSHHHHHHHHHHH
T ss_pred             HhccCCccHHHHHHHHHH
Confidence            98  56677766655543

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.53  E-value=1.3e-08  Score=86.92  Aligned_cols=74  Identities=19%  Similarity=0.259  Sum_probs=57.2

Q ss_pred             eccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc----------cceeeeechh
Q 025979          158 YNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT----------TAAFIRVVGS  227 (245)
Q Consensus       158 ~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l----------~~~~~~v~~s  227 (245)
                      .+.++|-++.++++.+.+..             ...+++||+||||||||.++..+|...          +..++.++.+
T Consensus        17 ld~~igRd~Ei~~l~~iL~r-------------~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~   83 (268)
T d1r6bx2          17 IDPLIGREKELERAIQVLCR-------------RRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIG   83 (268)
T ss_dssp             SCCCCSCHHHHHHHHHHHTS-------------SSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC
T ss_pred             CCcccChHHHHHHHHHHHhc-------------CccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeec
Confidence            34688999988888888765             234579999999999999999999753          6789999999


Q ss_pred             HHHH--HHhcccccccccc
Q 025979          228 EFVQ--KYLGEVWLKHKQI  244 (245)
Q Consensus       228 ~l~~--~~~Ge~~~~vr~i  244 (245)
                      .++.  +|.|+-+..++.+
T Consensus        84 ~liag~~~~g~~e~r~~~i  102 (268)
T d1r6bx2          84 SLLAGTKYRGDFEKRFKAL  102 (268)
T ss_dssp             ---CCCCCSSCHHHHHHHH
T ss_pred             hHhccCccchhHHHHHHHH
Confidence            9995  7888877766554

>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=98.51  E-value=2.3e-08  Score=87.01  Aligned_cols=51  Identities=31%  Similarity=0.449  Sum_probs=40.0

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      |...|.+|.|++.+|..+.-++..+          |   ..++||+||||||||++||++|.-+
T Consensus         2 ~~~~f~~I~Gq~~~kral~laa~~~----------~---~h~vLl~G~pG~GKT~lar~~~~iL   52 (333)
T d1g8pa_           2 PVFPFSAIVGQEDMKLALLLTAVDP----------G---IGGVLVFGDRGTGKSTAVRALAALL   52 (333)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHHHCG----------G---GCCEEEECCGGGCTTHHHHHHHHHS
T ss_pred             CCCChhhccCcHHHHHHHHHHHhcc----------C---CCeEEEECCCCccHHHHHHHHHHhC
Confidence            4567899999999888776544321          1   1369999999999999999999755

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.48  E-value=4.7e-08  Score=81.09  Aligned_cols=53  Identities=19%  Similarity=0.071  Sum_probs=38.5

Q ss_pred             eccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCc---ceeeecCCCCchHHHHHHHHhcc
Q 025979          158 YNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPR---GVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       158 ~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~---gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+.+.|-+.+++.|.+++..++.+       |..+++   .++||||||||||++++++++.+
T Consensus        15 P~~~~~Re~e~~~l~~~l~~~~~~-------~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l   70 (287)
T d1w5sa2          15 PPELRVRRGEAEALARIYLNRLLS-------GAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRV   70 (287)
T ss_dssp             CSSCSSSCHHHHHHHHHHHHHHHT-------SSCBCCEEEEEECTTCCSSSHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHc-------CCCCCCcceEEEeECCCCCCHHHHHHHHHHHH
Confidence            356788888899998877543211       222222   36789999999999999999987

>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=98.34  E-value=4.2e-07  Score=74.54  Aligned_cols=69  Identities=29%  Similarity=0.404  Sum_probs=46.2

Q ss_pred             CCceeccC-Ccchh--hhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechh
Q 025979          154 PDVTYNDI-GGCDI--QKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       154 ~~~~~~dv-~Gl~~--~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      |+.+|++. +|...  +...+.+++..|          | ...+.++||||||||||+|+.|+++++   +..++.++..
T Consensus         5 ~~~tFdnF~vg~~N~~a~~~~~~~~~~~----------~-~~~n~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~~~   73 (213)
T d1l8qa2           5 PKYTLENFIVGEGNRLAYEVVKEALENL----------G-SLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSAD   73 (213)
T ss_dssp             TTCCSSSCCCCTTTHHHHHHHHHHHHTT----------T-TSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHH
T ss_pred             CCCChhhccCCCcHHHHHHHHHHHHhCc----------C-CCCCcEEEECCCCCcHHHHHHHHHHHhccCccceEEechH
Confidence            56678885 45432  234444444432          1 122448999999999999999999987   4567777877


Q ss_pred             HHHHHH
Q 025979          228 EFVQKY  233 (245)
Q Consensus       228 ~l~~~~  233 (245)
                      ++...+
T Consensus        74 ~~~~~~   79 (213)
T d1l8qa2          74 DFAQAM   79 (213)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            776554

>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=98.28  E-value=1.7e-07  Score=72.43  Aligned_cols=34  Identities=32%  Similarity=0.366  Sum_probs=29.7

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccceeeeech
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVG  226 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~  226 (245)
                      ++=++|+||||||||++|++||+.++.+++..+.
T Consensus         6 ~~iivl~G~~GsGKsT~a~~La~~l~~~~~~~d~   39 (171)
T d1knqa_           6 HHIYVLMGVSGSGKSAVASEVAHQLHAAFLDGDF   39 (171)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHHHTCEEEEGGG
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCeechhh
Confidence            4448899999999999999999999998877763

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=98.25  E-value=3.1e-07  Score=82.07  Aligned_cols=73  Identities=21%  Similarity=0.319  Sum_probs=50.9

Q ss_pred             eccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc----------cceeeeechh
Q 025979          158 YNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT----------TAAFIRVVGS  227 (245)
Q Consensus       158 ~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l----------~~~~~~v~~s  227 (245)
                      ++.++|-++.+.++.+.+..             ...+++||+||||||||.++..+|...          +..++.++.+
T Consensus        21 ld~~~gr~~ei~~~~~~L~r-------------~~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~   87 (387)
T d1qvra2          21 LDPVIGRDEEIRRVIQILLR-------------RTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMG   87 (387)
T ss_dssp             SCCCCSCHHHHHHHHHHHHC-------------SSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-
T ss_pred             CCCCcCcHHHHHHHHHHHhc-------------CCCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHh
Confidence            35688999888888888765             234568999999999999999998754          5779999999


Q ss_pred             HHHH--HHhccccccccc
Q 025979          228 EFVQ--KYLGEVWLKHKQ  243 (245)
Q Consensus       228 ~l~~--~~~Ge~~~~vr~  243 (245)
                      .++.  +|.|+-+..+..
T Consensus        88 ~l~ag~~~~g~~e~r~~~  105 (387)
T d1qvra2          88 SLLAGAKYRGEFEERLKA  105 (387)
T ss_dssp             ----------CHHHHHHH
T ss_pred             hhhcccCcchhHHHHHHH
Confidence            9984  778887766544

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.21  E-value=7.7e-07  Score=73.09  Aligned_cols=57  Identities=18%  Similarity=0.170  Sum_probs=44.7

Q ss_pred             CCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechh
Q 025979          154 PDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS  227 (245)
Q Consensus       154 ~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s  227 (245)
                      |...-++++|-++..++|.+.                 ..+.++++||+|+|||+|++.++..++..+..++..
T Consensus         7 p~~~~~~f~GR~~el~~l~~~-----------------~~~~i~i~G~~G~GKTsLl~~~~~~~~~~~~~i~~~   63 (283)
T d2fnaa2           7 PKDNRKDFFDREKEIEKLKGL-----------------RAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLR   63 (283)
T ss_dssp             CCCSGGGSCCCHHHHHHHHHT-----------------CSSEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGG
T ss_pred             CCCChhhCCChHHHHHHHHhc-----------------cCCEEEEEcCCCCcHHHHHHHHHHHCCCCeEEEEec
Confidence            444557899988877776542                 235699999999999999999999998887777654

>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=98.13  E-value=1e-06  Score=66.80  Aligned_cols=41  Identities=22%  Similarity=0.442  Sum_probs=31.2

Q ss_pred             ceeeecCCCCchHHHHHHHHhcccceeeeechhHHHHHHhcc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQKYLGE  236 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l~~~~~Ge  236 (245)
                      -|+++||||+|||++|+.|+.... .++.++..++.....+.
T Consensus         4 lIii~G~pGsGKTTla~~L~~~~~-~~~~~~~d~~~~~~~~~   44 (152)
T d1ly1a_           4 IILTIGCPGSGKSTWAREFIAKNP-GFYNINRDDYRQSIMAH   44 (152)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHST-TEEEECHHHHHHHHTTS
T ss_pred             EEEEECCCCCCHHHHHHHHHHhCC-CCEEechHHHHHHHhcc
Confidence            378899999999999999876542 35567777887666543

>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=98.03  E-value=3.9e-07  Score=71.76  Aligned_cols=27  Identities=33%  Similarity=0.372  Sum_probs=23.5

Q ss_pred             eeeecCCCCchHHHHHHHHhcccceee
Q 025979          196 VLLYGPPGTGKTMLAKAVANHTTAAFI  222 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l~~~~~  222 (245)
                      |+|+||||+|||++|+.||..++.+++
T Consensus        22 I~L~G~pGSGKTTiAk~La~~l~~~~~   48 (195)
T d1x6va3          22 VWLTGLSGAGKTTVSMALEEYLVCHGI   48 (195)
T ss_dssp             EEEESSCHHHHHHHHHHHHHHHHHTTC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhcCC
Confidence            678899999999999999999866543

>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=98.02  E-value=8.9e-07  Score=70.59  Aligned_cols=33  Identities=15%  Similarity=0.352  Sum_probs=29.4

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccceeeee
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRV  224 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v  224 (245)
                      .++-|+|.||||+|||++|+.||..+|.+++.+
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~~La~~~g~~~is~   39 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCEKIVQKYGYTHLST   39 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHHTCCEEEEH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHhCCeeEec
Confidence            456689999999999999999999999988775

>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=98.02  E-value=1.1e-06  Score=69.94  Aligned_cols=32  Identities=16%  Similarity=0.338  Sum_probs=28.9

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccceeeee
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAFIRV  224 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v  224 (245)
                      ..-++|.||||+|||++|+.||+.+|+.++.+
T Consensus         8 ~~iI~i~GppGSGKsT~a~~La~~~g~~~is~   39 (196)
T d1ukza_           8 VSVIFVLGGPGAGKGTQCEKLVKDYSFVHLSA   39 (196)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHSSCEEEEH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeEEeh
Confidence            45689999999999999999999999988876

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.00  E-value=2.2e-06  Score=69.55  Aligned_cols=26  Identities=23%  Similarity=0.344  Sum_probs=23.9

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .|.++||+||||+|||++|+++|+.+
T Consensus        23 l~h~lLl~Gp~G~GKtt~a~~~a~~l   48 (207)
T d1a5ta2          23 GHHALLIQALPGMGDDALIYALSRYL   48 (207)
T ss_dssp             CCSEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cCeEEEEECCCCCcHHHHHHHHHHhc
Confidence            56789999999999999999999876

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.96  E-value=2.1e-06  Score=67.75  Aligned_cols=32  Identities=22%  Similarity=0.343  Sum_probs=26.8

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccceeee
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAFIR  223 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~  223 (245)
                      .|.-|+++||||||||++|+.++...++.++.
T Consensus        13 ~p~liil~G~pGsGKST~a~~l~~~~~~~~i~   44 (172)
T d1yj5a2          13 NPEVVVAVGFPGAGKSTFIQEHLVSAGYVHVN   44 (172)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHTGGGTCEEEE
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhcCCEEEc
Confidence            45559999999999999999999988866543

>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=97.64  E-value=2.2e-05  Score=65.35  Aligned_cols=58  Identities=19%  Similarity=0.220  Sum_probs=41.7

Q ss_pred             CCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHH
Q 025979          161 IGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEF  229 (245)
Q Consensus       161 v~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l  229 (245)
                      .+|.....+++.+.+...       .    ....-||++||||||||++|++|....   ..+|+.++++.+
T Consensus         2 ~v~~S~~~~~~~~~~~~~-------a----~~~~pvlI~Ge~GtGK~~~A~~ih~~s~~~~~~~~~~~~~~~   62 (247)
T d1ny5a2           2 YVFESPKMKEILEKIKKI-------S----CAECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASI   62 (247)
T ss_dssp             CCCCSHHHHHHHHHHHHH-------T----TCCSCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTS
T ss_pred             eEecCHHHHHHHHHHHHH-------h----CCCCCEEEECCCCcCHHHHHHHHHHhcCCcccccccchhhhh
Confidence            467777777777766541       1    122349999999999999999998655   556888877543

>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=97.59  E-value=1.9e-05  Score=63.99  Aligned_cols=38  Identities=21%  Similarity=0.267  Sum_probs=32.0

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc----cceeeeechhHHHH
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT----TAAFIRVVGSEFVQ  231 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l----~~~~~~v~~s~l~~  231 (245)
                      .-|.|.|+||+|||++|++|+..+    +.+++.+++..+-.
T Consensus        25 ~vIwltGlsGsGKTTia~~L~~~l~~~~~~~~~~ldgD~iR~   66 (208)
T d1m7ga_          25 LTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRF   66 (208)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEECHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHhcCceEEEEcchHHHH
Confidence            348899999999999999999866    56888899888754

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.42  E-value=5.1e-05  Score=61.01  Aligned_cols=26  Identities=8%  Similarity=0.024  Sum_probs=23.5

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+..+|||||||||||.+|+.+|+..
T Consensus        14 ~~~~~l~~G~~g~gk~~~a~~l~~~i   39 (198)
T d2gnoa2          14 EGISILINGEDLSYPREVSLELPEYV   39 (198)
T ss_dssp             SSEEEEEECSSSSHHHHHHHHHHHHH
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHH
Confidence            45679999999999999999999876

>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=97.42  E-value=3.5e-05  Score=61.82  Aligned_cols=28  Identities=29%  Similarity=0.406  Sum_probs=23.4

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhc
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      |+.+.+-++|+||||||||++|-.+|..
T Consensus        30 Gi~~G~~~li~G~pGsGKT~l~lq~~~~   57 (251)
T d1szpa2          30 GVETGSITELFGEFRTGKSQLCHTLAVT   57 (251)
T ss_dssp             SEESSSEEEEEESTTSSHHHHHHHHTTT
T ss_pred             CCcCCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            4666666999999999999999988754

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.42  E-value=4.3e-05  Score=59.42  Aligned_cols=25  Identities=24%  Similarity=0.307  Sum_probs=21.6

Q ss_pred             eeeecCCCCchHHHHHHHHhcccce
Q 025979          196 VLLYGPPGTGKTMLAKAVANHTTAA  220 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l~~~  220 (245)
                      |-+.||+|+|||++|+.|+..++..
T Consensus        25 IgI~G~~GSGKSTla~~L~~~l~~~   49 (198)
T d1rz3a_          25 LGIDGLSRSGKTTLANQLSQTLREQ   49 (198)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHhccc
Confidence            5589999999999999999877543

>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=97.40  E-value=3.5e-05  Score=62.50  Aligned_cols=29  Identities=31%  Similarity=0.447  Sum_probs=24.6

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      |+.+..-++++||||||||++|..+|...
T Consensus        22 Gi~~gsl~li~G~pGsGKT~l~~qia~~~   50 (242)
T d1tf7a2          22 GFFKDSIILATGATGTGKTLLVSRFVENA   50 (242)
T ss_dssp             SEESSCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCcCCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            35566669999999999999999998875

>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=97.37  E-value=3.6e-05  Score=59.81  Aligned_cols=29  Identities=28%  Similarity=0.381  Sum_probs=24.2

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      |+.+..-++++||||+|||++|-.+|...
T Consensus        19 Gi~~G~v~~i~G~~GsGKT~l~l~la~~~   47 (242)
T d1n0wa_          19 GIETGSITEMFGEFRTGKTQICHTLAVTC   47 (242)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCcCCEEEEEEeCCCCCHHHHHHHHHHHH
Confidence            46666669999999999999999888654

>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=97.33  E-value=4e-05  Score=62.05  Aligned_cols=36  Identities=22%  Similarity=0.417  Sum_probs=28.5

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcccceeeee
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRV  224 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v  224 (245)
                      |....+.++|||||+||||++|.+|++.++...+..
T Consensus        49 ~~PKkn~i~~~GP~~TGKS~f~~sl~~~l~G~vis~   84 (205)
T d1tuea_          49 GTPKKNCLVFCGPANTGKSYFGMSFIHFIQGAVISF   84 (205)
T ss_dssp             TCTTCSEEEEESCGGGCHHHHHHHHHHHHTCEECCC
T ss_pred             CCCCceEEEEECCCCccHHHHHHHHHHHhCCEEEec
Confidence            444455699999999999999999999986554433

>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=97.22  E-value=7.3e-05  Score=60.31  Aligned_cols=28  Identities=29%  Similarity=0.341  Sum_probs=23.1

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhc
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      |+.+.+-++++||||||||++|..+|..
T Consensus        33 Gip~G~~~~i~G~~GsGKT~lalq~~~~   60 (258)
T d1v5wa_          33 GIESMAITEAFGEFRTGKTQLSHTLCVT   60 (258)
T ss_dssp             SBCSSEEEEEECCTTCTHHHHHHHHHHH
T ss_pred             CCcCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            4555555999999999999999999853

>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=97.14  E-value=7.3e-05  Score=60.50  Aligned_cols=28  Identities=36%  Similarity=0.503  Sum_probs=22.6

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhc
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      |+...+-++++||||||||++|-.+|..
T Consensus        32 Glp~G~~~li~G~pGsGKT~~~lq~~~~   59 (254)
T d1pzna2          32 GIETQAITEVFGEFGSGKTQLAHTLAVM   59 (254)
T ss_dssp             SEESSEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CccCCEEEEEEcCCCCCHHHHHHHHHHH
Confidence            3555555999999999999999988754

>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=97.06  E-value=0.00012  Score=58.27  Aligned_cols=27  Identities=33%  Similarity=0.533  Sum_probs=22.1

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHh
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      |+.++.-++++||||+|||++|..+|.
T Consensus        22 Gi~~G~~~~I~G~~G~GKT~la~~~~~   48 (242)
T d1tf7a1          22 GLPIGRSTLVSGTSGTGKTLFSIQFLY   48 (242)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCcCCeEEEEEeCCCCCHHHHHHHHHH
Confidence            566666699999999999999976653

>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=96.90  E-value=0.00046  Score=57.76  Aligned_cols=47  Identities=13%  Similarity=0.118  Sum_probs=34.4

Q ss_pred             cCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhc
Q 025979          160 DIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       160 dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      +++|-+..+++|.+.+..          .+-...+-+.+||++|+|||+||+.+.+.
T Consensus        21 ~~~gR~~~~~~i~~~L~~----------~~~~~~~~v~I~GmgGiGKTtLA~~v~~~   67 (277)
T d2a5yb3          21 TCYIREYHVDRVIKKLDE----------MCDLDSFFLFLHGRAGSGKSVIASQALSK   67 (277)
T ss_dssp             CSCCCHHHHHHHHHHHHH----------HTTSSSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ceeCcHHHHHHHHHHHHh----------ccCCCceEEEEECCCCCCHHHHHHHHHHh
Confidence            567888888888877643          11112233779999999999999999765

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=96.82  E-value=0.00026  Score=57.27  Aligned_cols=24  Identities=33%  Similarity=0.272  Sum_probs=19.2

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +-++|.||+|+|||+.+--||..+
T Consensus        11 ~vi~lvGp~GvGKTTTiaKLA~~~   34 (207)
T d1ls1a2          11 NLWFLVGLQGSGKTTTAAKLALYY   34 (207)
T ss_dssp             EEEEEECCTTTTHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHH
Confidence            337889999999999777777655

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=96.81  E-value=0.00029  Score=57.32  Aligned_cols=26  Identities=35%  Similarity=0.493  Sum_probs=20.3

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .|.-++|+||+|+|||+.+--||..+
T Consensus        10 ~p~vi~lvGptGvGKTTTiAKLAa~~   35 (213)
T d1vmaa2          10 PPFVIMVVGVNGTGKTTSCGKLAKMF   35 (213)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            45568999999999999766666544

>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=96.81  E-value=0.00021  Score=56.86  Aligned_cols=28  Identities=18%  Similarity=0.232  Sum_probs=23.4

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.+..-++++||||+|||++|-.+|..+
T Consensus        31 l~~G~l~~i~G~~G~GKT~~~l~~a~~~   58 (258)
T d2i1qa2          31 LESQSVTEFAGVFGSGKTQIMHQSCVNL   58 (258)
T ss_dssp             EETTEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             ccCCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            5555559999999999999999998644

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=96.79  E-value=0.00031  Score=57.02  Aligned_cols=27  Identities=30%  Similarity=0.406  Sum_probs=21.1

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.|.-++|+||+|+|||+.+--+|..+
T Consensus         7 ~~p~vi~lvGptGvGKTTTiAKLA~~~   33 (211)
T d2qy9a2           7 KAPFVILMVGVNGVGKTTTIGKLARQF   33 (211)
T ss_dssp             CTTEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            345668899999999999776667544

>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=96.72  E-value=0.00045  Score=54.50  Aligned_cols=29  Identities=28%  Similarity=0.368  Sum_probs=23.7

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhccccee
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAF  221 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~~  221 (245)
                      ..+|+||.||+|+|||++|-++... |..|
T Consensus        13 ~g~gvl~~G~sG~GKStlal~l~~~-g~~l   41 (176)
T d1kkma_          13 YGLGVLITGDSGVGKSETALELVQR-GHRL   41 (176)
T ss_dssp             TTEEEEEECCTTSCHHHHHHHHHHT-TCEE
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHc-CCeE
Confidence            3578999999999999999988764 4443

>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=96.69  E-value=0.00096  Score=58.10  Aligned_cols=19  Identities=37%  Similarity=0.534  Sum_probs=15.6

Q ss_pred             ceeeecCCCCchHHHHHHH
Q 025979          195 GVLLYGPPGTGKTMLAKAV  213 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkal  213 (245)
                      -+++.||||||||+++..+
T Consensus       165 ~~vI~G~pGTGKTt~i~~~  183 (359)
T d1w36d1         165 ISVISGGPGTGKTTTVAKL  183 (359)
T ss_dssp             EEEEECCTTSTHHHHHHHH
T ss_pred             eEEEEcCCCCCceehHHHH
Confidence            3789999999999987543

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=96.65  E-value=0.00046  Score=57.73  Aligned_cols=39  Identities=28%  Similarity=0.369  Sum_probs=28.6

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechh
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      |+...+-..|+||||+|||++|-.++...   +...+.++..
T Consensus        50 Gi~~g~itei~G~~gsGKTtl~l~~~~~~q~~g~~~vyidtE   91 (263)
T d1u94a1          50 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAE   91 (263)
T ss_dssp             SEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CccCceEEEEecCCCcHHHHHHHHHHHHHHcCCCEEEEEccc
Confidence            34444458899999999999998887665   5556666643

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=96.62  E-value=0.00035  Score=56.66  Aligned_cols=26  Identities=35%  Similarity=0.419  Sum_probs=16.4

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .|.-++|+||||+|||+.+--||..+
T Consensus        11 ~p~vi~lvGptGvGKTTTiAKLA~~~   36 (211)
T d1j8yf2          11 IPYVIMLVGVQGTGKATTAGKLAYFY   36 (211)
T ss_dssp             SSEEEEEECSCCC----HHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            45568999999999999766666544

>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=96.52  E-value=0.00065  Score=53.61  Aligned_cols=29  Identities=38%  Similarity=0.455  Sum_probs=23.4

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhccccee
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAF  221 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~~  221 (245)
                      ..+|+||.||+|+|||++|-.+... |..|
T Consensus        14 ~g~gvli~G~sG~GKS~lal~l~~~-G~~l   42 (177)
T d1knxa2          14 FGVGVLLTGRSGIGKSECALDLINK-NHLF   42 (177)
T ss_dssp             TTEEEEEEESSSSSHHHHHHHHHTT-TCEE
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHc-CCce
Confidence            4578999999999999999888764 4443

>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=96.50  E-value=0.0017  Score=51.64  Aligned_cols=42  Identities=24%  Similarity=0.290  Sum_probs=32.8

Q ss_pred             ceeeecCCCCchHHHHHHHHhcccceeeeech-hHHHHHHhcc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHTTAAFIRVVG-SEFVQKYLGE  236 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~-s~l~~~~~Ge  236 (245)
                      +.++.+|+|+|||.+|-+++..++.+.+.+.. ..+++.|.-+
T Consensus        87 ~~ll~~~tG~GKT~~a~~~~~~~~~~~Liv~p~~~L~~q~~~~  129 (206)
T d2fz4a1          87 RGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKER  129 (206)
T ss_dssp             EEEEEESSSTTHHHHHHHHHHHSCSCEEEEESSHHHHHHHHHH
T ss_pred             CcEEEeCCCCCceehHHhHHHHhcCceeEEEcccchHHHHHHH
Confidence            35678899999999999999988777666666 4777766543

>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=96.49  E-value=6.6e-05  Score=66.51  Aligned_cols=73  Identities=19%  Similarity=0.195  Sum_probs=49.3

Q ss_pred             ccccCCCCC---CCCCCCcccCCCCCCCCchhHHHHHHHHHHHhhhhh--------hhHHHHHHHHHHHHHHHHHHHHHh
Q 025979            5 AMVLDPKPV---SEPPPSTRSDLTEQWSDEDDLYSRLKSLQRQLEFID--------IQEEYVKDEQKNLKRELLRAQEEV   73 (245)
Q Consensus         5 ~~~~~~k~~---~e~~~~~~~e~~~~~~~~~~~~~~~~~~~~e~~~l~--------~~~~~i~~~~~~~~~~~~~~~~~~   73 (245)
                      .-.||||||   |||+|+.+++..++|...+.+..++.+++.+...|.        .++..+..++..++.+...+++++
T Consensus       226 ~r~~PdKAidlld~a~a~~~i~~~s~P~el~~ler~I~qLe~E~~aL~ke~d~~s~~rl~~le~el~~lee~~~~L~~~w  305 (387)
T d1qvra2         226 ERRLPDKAIDLIDEAAARLRMALESAPEEIDALERKKLQLEIEREALKKEKDPDSQERLKAIEAEIAKLTEEIAKLRAEW  305 (387)
T ss_dssp             SSCTHHHHHHHHHHHHHHHHHTTTTHHHHHHHHHHHHHHHHHHHHHHSSCSSHHHHSCTHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccChhhHHHHHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHHHHHhccchHHHHHHhhhhhhhhHHHHHHHHHHHHH
Confidence            457999999   999999999999999988888888877777666553        223334444444444444444444


Q ss_pred             hhhc
Q 025979           74 KRIQ   77 (245)
Q Consensus        74 ~~~~   77 (245)
                      +..+
T Consensus       306 ~~ek  309 (387)
T d1qvra2         306 ERER  309 (387)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4433

>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=96.47  E-value=0.00076  Score=51.20  Aligned_cols=22  Identities=23%  Similarity=0.418  Sum_probs=19.7

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|+|.|+||||||+|..++...
T Consensus        15 kI~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_          15 KLVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             EEEEEEETTSSHHHHHHHHSCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3999999999999999998754

>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=96.43  E-value=0.00083  Score=52.57  Aligned_cols=25  Identities=32%  Similarity=0.417  Sum_probs=21.6

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ..+||||.||+|+|||++|-++...
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            3578999999999999999887765

>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=96.40  E-value=0.0011  Score=51.27  Aligned_cols=29  Identities=28%  Similarity=0.313  Sum_probs=24.8

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccce
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAA  220 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~  220 (245)
                      ++.-|+|.|+=|+|||+++|++++.+|..
T Consensus        32 ~g~ii~L~G~LGaGKTtfvr~~~~~lg~~   60 (158)
T d1htwa_          32 KAIMVYLNGDLGAGKTTLTRGMLQGIGHQ   60 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHTTCC
T ss_pred             CCeEEEEecCCCccHHHHHHHHHhhcccc
Confidence            33348899999999999999999999765

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=96.38  E-value=0.0014  Score=56.04  Aligned_cols=34  Identities=15%  Similarity=0.239  Sum_probs=27.4

Q ss_pred             eeeecCCCCchHHHHHHHHhccc-----ceeeeechhHH
Q 025979          196 VLLYGPPGTGKTMLAKAVANHTT-----AAFIRVVGSEF  229 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l~-----~~~~~v~~s~l  229 (245)
                      |.+.||+|+|||++|+.|+..+.     .....|++.+|
T Consensus        83 IGIaG~sgSGKSTla~~L~~lL~~~~~~~~v~~Is~D~F  121 (308)
T d1sq5a_          83 ISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGF  121 (308)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGGGG
T ss_pred             EEEeCCCCCCCcHHHHHHHHHHhhhcCCCceEEEeeeee
Confidence            77899999999999999998763     44556666665

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=96.38  E-value=0.00063  Score=54.48  Aligned_cols=26  Identities=35%  Similarity=0.434  Sum_probs=22.3

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++.-+.|.||.|+|||+|.+.+++.+
T Consensus        26 ~Gei~~l~G~NGsGKSTLl~~i~gl~   51 (200)
T d1sgwa_          26 KGNVVNFHGPNGIGKTTLLKTISTYL   51 (200)
T ss_dssp             TTCCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhccc
Confidence            33448899999999999999999866

>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=96.33  E-value=0.0012  Score=54.30  Aligned_cols=37  Identities=14%  Similarity=0.159  Sum_probs=27.2

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhc----ccceeeeec
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANH----TTAAFIRVV  225 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~----l~~~~~~v~  225 (245)
                      |+.+..-+++.|+||+|||+++..+|..    .+.+...++
T Consensus        31 G~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s   71 (277)
T d1cr2a_          31 GARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAM   71 (277)
T ss_dssp             SBCTTCEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEE
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHhhhhhcccceeEee
Confidence            5666555999999999999998888753    255555454

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.30  E-value=0.0022  Score=54.16  Aligned_cols=34  Identities=24%  Similarity=0.464  Sum_probs=25.3

Q ss_pred             eeeecCCCCchHHHHHHHHhcc------cceeeeechhHH
Q 025979          196 VLLYGPPGTGKTMLAKAVANHT------TAAFIRVVGSEF  229 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l------~~~~~~v~~s~l  229 (245)
                      |-+.||||+|||++|..|...+      +..+..++..+|
T Consensus        30 IGi~G~qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS~Ddf   69 (286)
T d1odfa_          30 IFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDF   69 (286)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGG
T ss_pred             EEeECCCCCCHHHHHHHHHHHHHHHhCCCcceEeeccCCC
Confidence            5578999999999999887665      334555566665

>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=96.25  E-value=0.0019  Score=56.88  Aligned_cols=51  Identities=22%  Similarity=0.422  Sum_probs=39.9

Q ss_pred             CCCceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcc-eeeecCCCCchHHHHHHHHhccc
Q 025979          153 KPDVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRG-VLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       153 ~~~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~g-vLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      .+..++++++-...+.+.+.+.+..               ++| +|+.||+|+|||++..++-+.++
T Consensus       132 ~~~~~l~~LG~~~~~~~~l~~l~~~---------------~~GliLvtGpTGSGKSTTl~~~l~~~~  183 (401)
T d1p9ra_         132 ATRLDLHSLGMTAHNHDNFRRLIKR---------------PHGIILVTGPTGSGKSTTLYAGLQELN  183 (401)
T ss_dssp             TTCCCGGGSCCCHHHHHHHHHHHTS---------------SSEEEEEECSTTSCHHHHHHHHHHHHC
T ss_pred             ccchhhhhhcccHHHHHHHHHHHhh---------------hhceEEEEcCCCCCccHHHHHHhhhhc
Confidence            3446778888777778888777654               355 88999999999999999988763

>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=96.22  E-value=0.0012  Score=55.09  Aligned_cols=28  Identities=36%  Similarity=0.574  Sum_probs=24.1

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcccc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTA  219 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~  219 (245)
                      ..+.++|+|||+||||+++.+|+..+|.
T Consensus       103 k~n~~~l~G~~~tGKS~f~~~i~~~lg~  130 (267)
T d1u0ja_         103 KRNTIWLFGPATTGKTNIAEAIAHTVPF  130 (267)
T ss_dssp             TCCEEEEECSTTSSHHHHHHHHHHHSSC
T ss_pred             ccEEEEEEcCCCCCHHHHHHHHHHHhcc
Confidence            3455899999999999999999998854

>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=96.20  E-value=0.00096  Score=57.29  Aligned_cols=26  Identities=27%  Similarity=0.480  Sum_probs=23.6

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..+++|+.||+|+|||++.++++...
T Consensus       165 ~~~nili~G~tgSGKTT~l~al~~~i  190 (323)
T d1g6oa_         165 IGKNVIVCGGTGSGKTTYIKSIMEFI  190 (323)
T ss_dssp             HTCCEEEEESTTSSHHHHHHHHGGGS
T ss_pred             hCCCEEEEeeccccchHHHHHHhhhc
Confidence            44679999999999999999999887

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.17  E-value=0.0011  Score=54.32  Aligned_cols=26  Identities=31%  Similarity=0.505  Sum_probs=22.4

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++.-+.|.||+|||||+|.+.++...
T Consensus        25 ~Gei~~liGpsGsGKSTLl~~i~Gl~   50 (232)
T d2awna2          25 EGEFVVFVGPSGCGKSTLLRMIAGLE   50 (232)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcCC
Confidence            33448899999999999999999876

>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=96.14  E-value=0.0012  Score=49.21  Aligned_cols=23  Identities=26%  Similarity=0.387  Sum_probs=20.2

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -.|+|+|+||||||+|..++...
T Consensus         6 ~kI~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           6 MRILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHhCC
Confidence            35899999999999999998764

>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=96.11  E-value=0.0011  Score=54.28  Aligned_cols=25  Identities=36%  Similarity=0.428  Sum_probs=20.3

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      +..-.+|+||||||||+++-.+|..
T Consensus        28 pg~~~~i~G~~G~GKS~l~l~la~~   52 (274)
T d1nlfa_          28 AGTVGALVSPGGAGKSMLALQLAAQ   52 (274)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHH
Confidence            4444889999999999999887754

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=96.10  E-value=0.0012  Score=54.20  Aligned_cols=26  Identities=23%  Similarity=0.410  Sum_probs=22.3

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+.-+.+.||+|||||+|.+.++.-.
T Consensus        30 ~Ge~~~iiG~sGsGKSTLl~~i~gl~   55 (230)
T d1l2ta_          30 EGEFVSIMGPSGSGKSTMLNIIGCLD   55 (230)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCcchhhHhccCCC
Confidence            33448899999999999999999866

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.10  E-value=0.0018  Score=54.14  Aligned_cols=39  Identities=23%  Similarity=0.368  Sum_probs=28.2

Q ss_pred             ccCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechh
Q 025979          189 GIDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       189 g~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      |+..++-..|+||||||||++|-.++...   +...+.|+..
T Consensus        56 G~~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~g~~~vyIDtE   97 (269)
T d1mo6a1          56 GLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAE   97 (269)
T ss_dssp             SBCSSSEEEEECSSSSSHHHHHHHHHHHHHHTTCEEEEEESS
T ss_pred             CcccceeEEEecCCCcHHHHHHHHHHHHHhcCCCEEEEEECC
Confidence            44444558899999999999987666544   6666777643

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=96.07  E-value=0.0011  Score=54.58  Aligned_cols=26  Identities=31%  Similarity=0.477  Sum_probs=22.4

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +..-+.|.||+|||||+++++++...
T Consensus        28 ~Ge~~~liG~sGaGKSTll~~i~gl~   53 (240)
T d1g2912          28 DGEFMILLGPSGCGKTTTLRMIAGLE   53 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcCC
Confidence            33448899999999999999999876

>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=96.05  E-value=0.0015  Score=54.69  Aligned_cols=38  Identities=29%  Similarity=0.361  Sum_probs=28.3

Q ss_pred             cCCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechh
Q 025979          190 IDPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       190 ~~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      +..++-..+|||||||||++|-.++..+   |...+.+|..
T Consensus        54 ip~g~itei~G~~~sGKT~l~l~~~~~aqk~g~~v~yiDtE   94 (268)
T d1xp8a1          54 IPRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAE   94 (268)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             ccCceEEEEecCCccchHHHHHHHHHHHHhCCCEEEEEECC
Confidence            3344448899999999999999888765   5566667643

>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=96.01  E-value=0.0014  Score=55.27  Aligned_cols=32  Identities=28%  Similarity=0.508  Sum_probs=25.6

Q ss_pred             hhhccCCCcc--eeeecCCCCchHHHHHHHHhcc
Q 025979          186 KQIGIDPPRG--VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       186 ~~~g~~~~~g--vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +.+.+..++|  +.+.||+|+|||+|.++|+..+
T Consensus        53 ~~isl~i~~Ge~vaivG~nGsGKSTLl~~i~Gl~   86 (281)
T d1r0wa_          53 KNINLNIEKGEMLAITGSTGSGKTSLLMLILGEL   86 (281)
T ss_dssp             EEEEEEECTTCEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             eCeEEEEcCCCEEEEECCCCChHHHHHHHHhCCC
Confidence            4444444445  8899999999999999999876

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=95.98  E-value=0.0016  Score=53.70  Aligned_cols=25  Identities=32%  Similarity=0.494  Sum_probs=22.0

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..-+.|.||+|||||+|.+.++...
T Consensus        32 Ge~~~liGpsGaGKSTLl~~i~Gl~   56 (239)
T d1v43a3          32 GEFLVLLGPSGCGKTTTLRMIAGLE   56 (239)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCChHHHHHHHHHcCC
Confidence            3348899999999999999999876

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=95.98  E-value=0.0012  Score=53.98  Aligned_cols=25  Identities=28%  Similarity=0.566  Sum_probs=22.1

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..-+.|.||+|||||++.+.++...
T Consensus        26 Ge~~~liGpsGaGKSTll~~l~Gl~   50 (229)
T d3d31a2          26 GEYFVILGPTGAGKTLFLELIAGFH   50 (229)
T ss_dssp             TCEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCc
Confidence            3348899999999999999999876

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=95.97  E-value=0.0016  Score=53.73  Aligned_cols=34  Identities=26%  Similarity=0.585  Sum_probs=25.1

Q ss_pred             eeeecCCCCchHHHHHHHHhccc--ceeeeechhHH
Q 025979          196 VLLYGPPGTGKTMLAKAVANHTT--AAFIRVVGSEF  229 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l~--~~~~~v~~s~l  229 (245)
                      +.|.||+|||||++.+.|+..+.  .--+.+++.++
T Consensus        27 ~~liGpnGaGKSTll~~i~Gl~~p~~G~I~~~G~~i   62 (240)
T d2onka1          27 CVLLGPTGAGKSVFLELIAGIVKPDRGEVRLNGADI   62 (240)
T ss_dssp             EEEECCTTSSHHHHHHHHHTSSCCSEEEEEETTEEC
T ss_pred             EEEECCCCChHHHHHHHHHcCCCCCceEEEECCEEC
Confidence            55899999999999999999772  22344555444

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=95.93  E-value=0.0018  Score=50.26  Aligned_cols=30  Identities=27%  Similarity=0.331  Sum_probs=24.9

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhccccee
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHTTAAF  221 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l~~~~  221 (245)
                      .|.-|.+-|+.|+|||++++.|++.++...
T Consensus         8 kp~~I~ieG~~GsGKTTl~~~L~~~l~~~~   37 (197)
T d2vp4a1           8 QPFTVLIEGNIGSGKTTYLNHFEKYKNDIC   37 (197)
T ss_dssp             CCEEEEEECSTTSCHHHHHHTTGGGTTTEE
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHhCCcE
Confidence            344588999999999999999999996543

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=95.92  E-value=0.0015  Score=54.17  Aligned_cols=27  Identities=26%  Similarity=0.442  Sum_probs=23.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+..-+.++||+|||||+|++.|+...
T Consensus        39 ~~Ge~iaivG~sGsGKSTLl~ll~gl~   65 (253)
T d3b60a1          39 PAGKTVALVGRSGSGKSTIASLITRFY   65 (253)
T ss_dssp             CTTCEEEEEECTTSSHHHHHHHHTTTT
T ss_pred             cCCCEEEEECCCCChHHHHHHHHhccc
Confidence            344449999999999999999999876

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.86  E-value=0.0018  Score=53.66  Aligned_cols=27  Identities=33%  Similarity=0.505  Sum_probs=23.1

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+..-+.+.||+|+|||+|++.|+...
T Consensus        38 ~~Ge~vaivG~sGsGKSTLl~li~gl~   64 (251)
T d1jj7a_          38 RPGEVTALVGPNGSGKSTVAALLQNLY   64 (251)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhccc
Confidence            344449999999999999999999877

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=95.85  E-value=0.0017  Score=53.53  Aligned_cols=27  Identities=22%  Similarity=0.432  Sum_probs=22.9

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+..-+.+.||+|+|||+|++.++...
T Consensus        26 ~~Ge~vaivG~sGsGKSTLl~ll~gl~   52 (242)
T d1mv5a_          26 QPNSIIAFAGPSGGGKSTIFSLLERFY   52 (242)
T ss_dssp             CTTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            334448899999999999999999876

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=95.85  E-value=0.0016  Score=53.70  Aligned_cols=24  Identities=25%  Similarity=0.311  Sum_probs=21.5

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .-+-|.||+|||||+|++.++...
T Consensus        32 e~~~iiG~sGsGKSTLl~~i~Gl~   55 (240)
T d3dhwc1          32 QIYGVIGASGAGKSTLIRCVNLLE   55 (240)
T ss_dssp             CEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHcCCc
Confidence            348899999999999999999876

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=95.77  E-value=0.0017  Score=53.40  Aligned_cols=27  Identities=22%  Similarity=0.358  Sum_probs=23.3

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+.+.||+|+|||+|++.++..+
T Consensus        27 ~~Ge~vaIvG~sGsGKSTLl~ll~gl~   53 (241)
T d2pmka1          27 KQGEVIGIVGRSGSGKSTLTKLIQRFY   53 (241)
T ss_dssp             ETTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHhcC
Confidence            344449999999999999999999977

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=95.75  E-value=0.0021  Score=48.76  Aligned_cols=23  Identities=22%  Similarity=0.338  Sum_probs=20.4

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -.|+|.|.||||||+|..++...
T Consensus        16 ~kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          16 HKVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            34999999999999999998864

>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=95.72  E-value=0.0022  Score=52.79  Aligned_cols=16  Identities=31%  Similarity=0.482  Sum_probs=13.7

Q ss_pred             ceeeecCCCCchHHHH
Q 025979          195 GVLLYGPPGTGKTMLA  210 (245)
Q Consensus       195 gvLl~GPPGtGKT~lA  210 (245)
                      .+|+.||||||||+++
T Consensus        16 ~~lI~g~aGTGKTt~l   31 (306)
T d1uaaa1          16 PCLVLAGAGSGKTRVI   31 (306)
T ss_dssp             EEEECCCTTSCHHHHH
T ss_pred             CEEEEeeCCccHHHHH
Confidence            3889999999999854

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=95.71  E-value=0.0014  Score=54.07  Aligned_cols=26  Identities=27%  Similarity=0.464  Sum_probs=22.3

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+.-+.+.||+|||||++.+.++...
T Consensus        30 ~Ge~~~iiG~sGsGKSTll~~i~gl~   55 (242)
T d1oxxk2          30 NGERFGILGPSGAGKTTFMRIIAGLD   55 (242)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHcCc
Confidence            33448899999999999999999865

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=95.70  E-value=0.0022  Score=53.30  Aligned_cols=25  Identities=16%  Similarity=0.345  Sum_probs=21.7

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..-+.+.||+|+|||+|+++|+...
T Consensus        28 GEi~~iiG~sGsGKSTLl~~i~Gl~   52 (258)
T d1b0ua_          28 GDVISIIGSSGSGKSTFLRCINFLE   52 (258)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHHcCc
Confidence            3338899999999999999999865

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=95.62  E-value=0.0027  Score=48.30  Aligned_cols=21  Identities=29%  Similarity=0.436  Sum_probs=19.1

Q ss_pred             eeeecCCCCchHHHHHHHHhc
Q 025979          196 VLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~  216 (245)
                      ++|.|+||||||+|...+...
T Consensus         8 i~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            899999999999999998753

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.58  E-value=0.0028  Score=47.94  Aligned_cols=20  Identities=25%  Similarity=0.486  Sum_probs=18.5

Q ss_pred             eeeecCCCCchHHHHHHHHh
Q 025979          196 VLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~  215 (245)
                      |++.|.||||||+|...+.+
T Consensus         7 ivlvG~~~vGKTsli~~~~~   26 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTE   26 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            88999999999999998875

>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=95.55  E-value=0.0041  Score=54.13  Aligned_cols=43  Identities=26%  Similarity=0.446  Sum_probs=32.9

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc---cceeeeechh-HHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS-EFVQKYLGE  236 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s-~l~~~~~Ge  236 (245)
                      +.++++|+||+|||.+.+.+...+   +.+++.+|.. ++.+.+.++
T Consensus        51 ~H~~I~G~tGsGKT~~l~~li~~~~~~g~~~iiiD~kge~~~~~~~~   97 (433)
T d1e9ra_          51 RHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPNGDMLSKFGRD   97 (433)
T ss_dssp             GCEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEEETTHHHHHHCCT
T ss_pred             ceEEEEeCCCCcHHHHHHHHHHHHHhCCCCEEEEeCChhHHHHhhcc
Confidence            569999999999999987766544   6777778765 777766543

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.54  E-value=0.0027  Score=48.29  Aligned_cols=20  Identities=35%  Similarity=0.664  Sum_probs=18.8

Q ss_pred             eeeecCCCCchHHHHHHHHh
Q 025979          196 VLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~  215 (245)
                      ++|.|+||||||+|.+.+.+
T Consensus         8 i~lvG~~~vGKTsLi~~l~~   27 (171)
T d2ew1a1           8 IVLIGNAGVGKTCLVRRFTQ   27 (171)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999999885

>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=95.53  E-value=0.0041  Score=45.53  Aligned_cols=40  Identities=18%  Similarity=0.163  Sum_probs=29.2

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceeeeechh-HHHHHH
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGS-EFVQKY  233 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s-~l~~~~  233 (245)
                      +..++.+|+|+|||+++-.++...+...+.+... .+.+.+
T Consensus         9 ~~~ll~apTGsGKT~~~~~~~~~~~~~vli~~P~~~l~~q~   49 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPSVAATLGF   49 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHHHHTTTCCEEEEESCHHHHHHH
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHcCCcEEEEcChHHHHHHH
Confidence            4479999999999998877666777666666554 444444

>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=95.47  E-value=0.004  Score=47.27  Aligned_cols=21  Identities=43%  Similarity=0.615  Sum_probs=19.1

Q ss_pred             eeeecCCCCchHHHHHHHHhc
Q 025979          196 VLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~  216 (245)
                      +++.|+||||||+|...+...
T Consensus        19 I~vvG~~~vGKSsLi~~l~~~   39 (176)
T d1fzqa_          19 ILLLGLDNAGKTTLLKQLASE   39 (176)
T ss_dssp             EEEEESTTSSHHHHHHHHCCS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            999999999999999998653

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=95.44  E-value=0.0028  Score=52.09  Aligned_cols=25  Identities=36%  Similarity=0.397  Sum_probs=22.1

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..-+.|.||+|+|||++.++|+..+
T Consensus        32 Gei~~liGpnGaGKSTl~~~i~Gl~   56 (240)
T d1ji0a_          32 GQIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCC
Confidence            3348899999999999999999877

>d1vpla_ c.37.1.12 (A:) Putative ABC transporter TM0544 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter TM0544
species: Thermotoga maritima [TaxId: 2336]

Probab=95.42  E-value=0.0033  Score=51.57  Aligned_cols=27  Identities=26%  Similarity=0.363  Sum_probs=23.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .++.-+-|.||.|+|||+|.++|+..+
T Consensus        26 ~~Gei~glvG~nGaGKSTLl~~l~G~~   52 (238)
T d1vpla_          26 EEGEIFGLIGPNGAGKTTTLRIISTLI   52 (238)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            344447799999999999999999877

>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=95.41  E-value=0.0024  Score=46.05  Aligned_cols=20  Identities=30%  Similarity=0.177  Sum_probs=16.5

Q ss_pred             CCcceeeecCCCCchHHHHH
Q 025979          192 PPRGVLLYGPPGTGKTMLAK  211 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAk  211 (245)
                      ..+.++|++|||+|||..+-
T Consensus         6 ~~~~~il~~~tGsGKT~~~~   25 (140)
T d1yksa1           6 KGMTTVLDFHPGAGKTRRFL   25 (140)
T ss_dssp             TTCEEEECCCTTSSTTTTHH
T ss_pred             cCCcEEEEcCCCCChhHHHH
Confidence            45669999999999997663

>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=95.37  E-value=0.003  Score=52.60  Aligned_cols=17  Identities=29%  Similarity=0.477  Sum_probs=14.2

Q ss_pred             cceeeecCCCCchHHHH
Q 025979          194 RGVLLYGPPGTGKTMLA  210 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lA  210 (245)
                      ..+|+.||||||||+++
T Consensus        25 g~~lV~g~aGSGKTt~l   41 (318)
T d1pjra1          25 GPLLIMAGAGSGKTRVL   41 (318)
T ss_dssp             SCEEEEECTTSCHHHHH
T ss_pred             CCEEEEecCCccHHHHH
Confidence            34889999999999854

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=95.35  E-value=0.0021  Score=53.33  Aligned_cols=27  Identities=22%  Similarity=0.349  Sum_probs=23.2

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+..-+.+.||+|+|||+|++.++...
T Consensus        42 ~~Ge~vaivG~sGsGKSTLl~ll~gl~   68 (255)
T d2hyda1          42 EKGETVAFVGMSGGGKSTLINLIPRFY   68 (255)
T ss_dssp             CTTCEEEEECSTTSSHHHHHTTTTTSS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHHhcC
Confidence            444459999999999999999999876

>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=95.33  E-value=0.0039  Score=47.33  Aligned_cols=20  Identities=25%  Similarity=0.449  Sum_probs=18.6

Q ss_pred             eeeecCCCCchHHHHHHHHh
Q 025979          196 VLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~  215 (245)
                      |++.|.||||||+|...+..
T Consensus         9 i~vvG~~~vGKTsLi~~l~~   28 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVK   28 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999999884

>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=95.27  E-value=0.0039  Score=47.37  Aligned_cols=20  Identities=25%  Similarity=0.454  Sum_probs=18.5

Q ss_pred             eeeecCCCCchHHHHHHHHh
Q 025979          196 VLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~  215 (245)
                      |+|.|.||||||+|...+..
T Consensus         8 i~lvG~~~vGKTsLi~r~~~   27 (171)
T d2erya1           8 LVVVGGGGVGKSALTIQFIQ   27 (171)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            89999999999999998775

>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=95.26  E-value=0.0042  Score=47.13  Aligned_cols=20  Identities=40%  Similarity=0.597  Sum_probs=18.4

Q ss_pred             eeeecCCCCchHHHHHHHHh
Q 025979          196 VLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~  215 (245)
                      +++.|+||||||+|+..+..
T Consensus         9 i~vvG~~~vGKTsli~~~~~   28 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKD   28 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999998765

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=95.26  E-value=0.0032  Score=52.07  Aligned_cols=26  Identities=27%  Similarity=0.503  Sum_probs=22.4

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ++.-+.|.||.|+|||+|+++|+...
T Consensus        29 ~Gei~~liG~nGaGKSTLl~~i~Gl~   54 (254)
T d1g6ha_          29 KGDVTLIIGPNGSGKSTLINVITGFL   54 (254)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHCCC
Confidence            33348899999999999999999876

>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=95.23  E-value=0.0069  Score=51.83  Aligned_cols=35  Identities=29%  Similarity=0.303  Sum_probs=26.7

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc-----cceeeeechhHH
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT-----TAAFIRVVGSEF  229 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l-----~~~~~~v~~s~l  229 (245)
                      .|-+.||||+|||+|..+++..+     .+.++-++++.-
T Consensus        56 ~IgitG~pGaGKSTLi~~l~~~~~~~g~~vavlavDpss~   95 (327)
T d2p67a1          56 RLGVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAVDPSSP   95 (327)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEECCC--
T ss_pred             EEEeeCCCCCCHHHHHHHHHHHHHhcCCceeeecCCCcee
Confidence            38899999999999999998765     355666776644

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=95.23  E-value=0.0036  Score=48.53  Aligned_cols=21  Identities=24%  Similarity=0.433  Sum_probs=19.3

Q ss_pred             ceeeecCCCCchHHHHHHHHh
Q 025979          195 GVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~  215 (245)
                      .|+|.|+||+|||+|..+|.+
T Consensus        25 ~I~lvG~~n~GKSTLin~L~g   45 (195)
T d1svia_          25 EIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHhcC
Confidence            399999999999999999975

>d2ncda_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {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: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=95.19  E-value=0.012  Score=50.89  Aligned_cols=50  Identities=24%  Similarity=0.347  Sum_probs=30.4

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHH
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLA  210 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lA  210 (245)
                      ...|+.+.+.+..-+.+.+.+. |+-. ..+.  |  ....++-||++|+|||+..
T Consensus        93 ~F~FD~vf~~~~~Q~~Vy~~v~-plv~-~vl~--G--~n~ti~aYGqtGSGKT~Tm  142 (368)
T d2ncda_          93 IFSFDQVFHPLSSQSDIFEMVS-PLIQ-SALD--G--YNICIFAYGQTGSGKTYTM  142 (368)
T ss_dssp             EEECSEEECTTCCHHHHHTTTH-HHHH-HHHT--T--CEEEEEEECSTTSSHHHHH
T ss_pred             eeECCeEECCCCCccchHHHHH-HHHH-HHhc--c--cceeEEeeccCCCccceEe
Confidence            3567777776666666665543 3221 1111  2  2234888999999999864

>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=95.14  E-value=0.0044  Score=46.78  Aligned_cols=22  Identities=23%  Similarity=0.374  Sum_probs=19.6

Q ss_pred             cceeeecCCCCchHHHHHHHHh
Q 025979          194 RGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      ..|++.|++|||||+|...+..
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~   26 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVE   26 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHh
Confidence            4589999999999999999875

>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=95.12  E-value=0.0029  Score=48.24  Aligned_cols=23  Identities=22%  Similarity=0.312  Sum_probs=20.1

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .|+++|+||||||+|...+....
T Consensus        14 kIvlvG~~~vGKTSli~rl~~~~   36 (173)
T d1e0sa_          14 RILMLGLDAAGKTTILYKLKLGQ   36 (173)
T ss_dssp             EEEEEEETTSSHHHHHHHTTCCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            49999999999999999997543

>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=95.08  E-value=0.0052  Score=46.77  Aligned_cols=21  Identities=33%  Similarity=0.523  Sum_probs=18.7

Q ss_pred             ceeeecCCCCchHHHHHHHHh
Q 025979          195 GVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~  215 (245)
                      .|++.|+||||||+|...+..
T Consensus         8 KI~vvG~~~vGKSSli~~~~~   28 (174)
T d1wmsa_           8 KVILLGDGGVGKSSLMNRYVT   28 (174)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            389999999999999988765

>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=95.08  E-value=0.0055  Score=46.89  Aligned_cols=24  Identities=25%  Similarity=0.349  Sum_probs=20.2

Q ss_pred             CcceeeecCCCCchHHHHHHHHhc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .-.|+|.|+||||||+|...+...
T Consensus        17 ~~KI~lvG~~~vGKTsLi~~l~~~   40 (182)
T d1moza_          17 ELRILILGLDGAGKTTILYRLQIG   40 (182)
T ss_dssp             CEEEEEEEETTSSHHHHHHHTCCS
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            334999999999999999988643

>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=95.05  E-value=0.0052  Score=46.94  Aligned_cols=21  Identities=29%  Similarity=0.542  Sum_probs=19.1

Q ss_pred             ceeeecCCCCchHHHHHHHHh
Q 025979          195 GVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~  215 (245)
                      .|++.|.||||||+|...+.+
T Consensus         9 Ki~vvG~~~vGKTsli~~l~~   29 (177)
T d1x3sa1           9 KILIIGESGVGKSSLLLRFTD   29 (177)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            389999999999999999875

>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=95.04  E-value=0.005  Score=46.96  Aligned_cols=22  Identities=23%  Similarity=0.394  Sum_probs=19.3

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -|++.|.||||||+|...+...
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4899999999999999987753

>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=94.83  E-value=0.0088  Score=51.05  Aligned_cols=34  Identities=29%  Similarity=0.339  Sum_probs=26.9

Q ss_pred             eeeecCCCCchHHHHHHHHhcc-----cceeeeechhHH
Q 025979          196 VLLYGPPGTGKTMLAKAVANHT-----TAAFIRVVGSEF  229 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l-----~~~~~~v~~s~l  229 (245)
                      +-+.||||+|||+|.-+++..+     ...++.++.+.-
T Consensus        54 igitG~pGaGKSTli~~l~~~~~~~g~~vaViavDpss~   92 (323)
T d2qm8a1          54 VGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSST   92 (323)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEECGGGG
T ss_pred             EeeeCCCCCCHHHHHHHHHHHHhhcCCceeeeecccccH
Confidence            7799999999999999988754     556677776643

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=94.83  E-value=0.0066  Score=46.07  Aligned_cols=21  Identities=29%  Similarity=0.472  Sum_probs=18.9

Q ss_pred             ceeeecCCCCchHHHHHHHHh
Q 025979          195 GVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~  215 (245)
                      -|++.|.+|||||+|...+..
T Consensus         6 KivlvG~~~vGKTsli~~~~~   26 (168)
T d1u8za_           6 KVIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999998764

>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=94.82  E-value=0.0028  Score=48.03  Aligned_cols=22  Identities=27%  Similarity=0.326  Sum_probs=20.0

Q ss_pred             eeeecCCCCchHHHHHHHHhcc
Q 025979          196 VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+|+||.|+|||++..||.-.+
T Consensus        27 tvi~G~NGsGKStil~Ai~~~L   48 (222)
T d1qhla_          27 TTLSGGNGAGKSTTMAAFVTAL   48 (222)
T ss_dssp             HHHHSCCSHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6889999999999999998765

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.81  E-value=0.0069  Score=45.72  Aligned_cols=20  Identities=30%  Similarity=0.459  Sum_probs=18.5

Q ss_pred             eeeecCCCCchHHHHHHHHh
Q 025979          196 VLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~  215 (245)
                      |++.|.+|||||+|...+..
T Consensus         7 i~lvG~~~vGKTsli~rl~~   26 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVE   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            88999999999999999874

>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=94.71  E-value=0.018  Score=46.85  Aligned_cols=40  Identities=23%  Similarity=0.196  Sum_probs=30.0

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHH
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFV  230 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~  230 (245)
                      ..+...||+|.+|+|||.++-..+...   |...+.+.+...+
T Consensus        74 ~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l~Pt~~L  116 (233)
T d2eyqa3          74 PLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLL  116 (233)
T ss_dssp             SSCCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSHHH
T ss_pred             cCccCeEEEcCCCCCcHHHHHHHHHHHHHcCCceEEEccHHHh
Confidence            355678999999999999887666543   7777777766554

>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=94.70  E-value=0.015  Score=44.86  Aligned_cols=39  Identities=23%  Similarity=0.347  Sum_probs=25.8

Q ss_pred             cceeeecCCCCchHHHHHHHHhc----ccceeeeech-hHHHHH
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH----TTAAFIRVVG-SEFVQK  232 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~----l~~~~~~v~~-s~l~~~  232 (245)
                      +.+|+++|+|+|||.++-.++..    .+...+.+.+ ..++..
T Consensus        24 ~n~lv~~pTGsGKT~i~~~~~~~~~~~~~~~il~i~P~~~L~~q   67 (200)
T d1wp9a1          24 TNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQ   67 (200)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSSHHHHHH
T ss_pred             CCeEEEeCCCCcHHHHHHHHHHHHHHhcCCcEEEEcCchHHHHH
Confidence            35889999999999977666642    2444555654 355443

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=94.69  E-value=0.006  Score=49.60  Aligned_cols=26  Identities=35%  Similarity=0.462  Sum_probs=21.8

Q ss_pred             CCcceeeecCCCCchHHHHHHHHhcc
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .+.-+-|.||.|+|||+|.++++...
T Consensus        24 ~Gei~~iiG~nGaGKSTLl~~l~Gl~   49 (231)
T d1l7vc_          24 AGEILHLVGPNGAGKSTLLARMAGMT   49 (231)
T ss_dssp             TTCEEECBCCTTSSHHHHHHHHHTSC
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            33448899999999999999999844

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=94.66  E-value=0.0035  Score=47.46  Aligned_cols=22  Identities=23%  Similarity=0.374  Sum_probs=19.4

Q ss_pred             ceeeecCCCCchHHHHHHHHhc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      .|.|.|+|++|||+|..+|...
T Consensus        18 ~I~lvG~~NvGKSSL~n~L~~~   39 (188)
T d1puia_          18 EVAFAGRSNAGKSSALNTLTNQ   39 (188)
T ss_dssp             EEEEEECTTSSHHHHHTTTCCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3999999999999999998653

>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=94.56  E-value=0.0049  Score=46.95  Aligned_cols=20  Identities=35%  Similarity=0.537  Sum_probs=8.6

Q ss_pred             eeeecCCCCchHHHHHHHHh
Q 025979          196 VLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~  215 (245)
                      |++.|.||||||+|...+.+
T Consensus         9 i~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEECCCCC-----------
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999987775

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=94.55  E-value=0.011  Score=48.18  Aligned_cols=36  Identities=25%  Similarity=0.283  Sum_probs=28.9

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc---cceeeeech
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVG  226 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~  226 (245)
                      ..|+-++|.|--|||||++|-++|..+   |...+-|+.
T Consensus         6 ~~p~~i~~sGKGGVGKTTvaa~lA~~lA~~G~rVLlvD~   44 (296)
T d1ihua1           6 NIPPYLFFTGKGGVGKTSISCATAIRLAEQGKRVLLVST   44 (296)
T ss_dssp             SCCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             CCCeEEEEECCCcChHHHHHHHHHHHHHHCCCCEEEEeC
Confidence            467888899999999999999988877   556655553

>d1u0la2 c.37.1.8 (A:69-293) Probable GTPase EngC (YjeQ), C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=94.54  E-value=0.013  Score=47.53  Aligned_cols=24  Identities=25%  Similarity=0.320  Sum_probs=20.9

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      +..+|.|++|+|||+|..+|....
T Consensus        96 kt~~~~G~SGVGKSTLiN~L~~~~  119 (225)
T d1u0la2          96 KISTMAGLSGVGKSSLLNAINPGL  119 (225)
T ss_dssp             SEEEEECSTTSSHHHHHHHHSTTC
T ss_pred             CeEEEECCCCCCHHHHHHhhcchh
Confidence            558899999999999999997654

>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=94.42  E-value=0.021  Score=45.62  Aligned_cols=41  Identities=17%  Similarity=0.167  Sum_probs=27.4

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc---cceeeeechh-HHHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS-EFVQKY  233 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s-~l~~~~  233 (245)
                      ++.+++.+|+|+|||+++-..+-.+   +...+.+.+. ++...+
T Consensus        58 g~~~~i~apTGsGKT~~~~~~~~~~~~~~~rvliv~Pt~~La~Q~  102 (237)
T d1gkub1          58 KESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIFPTSLLVIQA  102 (237)
T ss_dssp             TCCEECCCCBTSCSHHHHHHHHHHHHTTSCCEEEEESCHHHHHHH
T ss_pred             CCCEEEEecCCChHHHHHHHHHHHHHHhcCeEEEEeccHHHHHHH
Confidence            4679999999999998766554332   4455555553 565544

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=94.42  E-value=0.0094  Score=45.46  Aligned_cols=23  Identities=35%  Similarity=0.522  Sum_probs=20.2

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -.|++.|.||+|||+|..++.+.
T Consensus         9 ~kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2           9 IKVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
Confidence            35899999999999999999754

>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=94.15  E-value=0.015  Score=45.29  Aligned_cols=41  Identities=27%  Similarity=0.366  Sum_probs=25.1

Q ss_pred             CcceeeecCCCCchHHHHH-HHHhcc--cceeeeech-hHHHHHH
Q 025979          193 PRGVLLYGPPGTGKTMLAK-AVANHT--TAAFIRVVG-SEFVQKY  233 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAk-alA~~l--~~~~~~v~~-s~l~~~~  233 (245)
                      .+.+++.+|+|+|||++|- ++...+  +...+.+.+ ..++..+
T Consensus        40 ~~~~il~apTGsGKT~~a~l~i~~~~~~~~~vl~l~P~~~L~~q~   84 (202)
T d2p6ra3          40 GKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALAGEK   84 (202)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEEESSHHHHHHH
T ss_pred             CCCEEEEcCCCCchhHHHHHHHHHHhhccCcceeecccHHHHHHH
Confidence            3569999999999999873 333332  333444443 3555444

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.15  E-value=0.011  Score=45.55  Aligned_cols=21  Identities=33%  Similarity=0.401  Sum_probs=18.9

Q ss_pred             ceeeecCCCCchHHHHHHHHh
Q 025979          195 GVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~  215 (245)
                      .|++.|.+|||||+|...+..
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~   31 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYAN   31 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhh
Confidence            389999999999999998775

>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=93.81  E-value=0.015  Score=48.97  Aligned_cols=24  Identities=38%  Similarity=0.613  Sum_probs=21.3

Q ss_pred             cceeeecCCCCchHHHHHHHHhcc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l  217 (245)
                      ..+++.||+|||||+|+..+++..
T Consensus        44 Qr~~I~g~~g~GKT~l~~~i~~~~   67 (289)
T d1xpua3          44 QRGLIVAPPKAGKTMLLQNIAQSI   67 (289)
T ss_dssp             CEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             CeeeEeCCCCCCHHHHHHHHHHHH
Confidence            349999999999999999999865

>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=93.63  E-value=0.037  Score=45.77  Aligned_cols=40  Identities=25%  Similarity=0.323  Sum_probs=29.9

Q ss_pred             CCCcceeeecCCCCchHHHHHHHHhcc---cceeeeechhHHH
Q 025979          191 DPPRGVLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGSEFV  230 (245)
Q Consensus       191 ~~~~gvLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s~l~  230 (245)
                      ..+...||+|..|+|||.+|-..+...   |.....+.+.+++
T Consensus       102 ~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~q~~~m~Pt~~L  144 (264)
T d1gm5a3         102 EKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSIL  144 (264)
T ss_dssp             SSCCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSCHHH
T ss_pred             cCcceeeeeccccccccHHHHHHHHHHHhcccceeEEeehHhh
Confidence            456678999999999999887666543   6666667766554

>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=93.09  E-value=0.018  Score=47.31  Aligned_cols=23  Identities=26%  Similarity=0.432  Sum_probs=20.0

Q ss_pred             eeeecCCCCchHHHHHHHHhccc
Q 025979          196 VLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      -+|+||.|+|||++..||+-.++
T Consensus        27 nvlvG~NgsGKS~iL~Ai~~~lg   49 (308)
T d1e69a_          27 TAIVGPNGSGKSNIIDAIKWVFG   49 (308)
T ss_dssp             EEEECCTTTCSTHHHHHHHHTSC
T ss_pred             EEEECCCCCcHHHHHHHHHHHhC
Confidence            58999999999999999976554

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=92.65  E-value=0.025  Score=46.22  Aligned_cols=23  Identities=22%  Similarity=0.437  Sum_probs=20.3

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      -.|+|+|.||+|||++.-+|.+.
T Consensus        33 l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          33 LTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             cEEEEECCCCCcHHHHHHHHhCC
Confidence            45999999999999999999754

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {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: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=92.47  E-value=0.074  Score=43.93  Aligned_cols=42  Identities=14%  Similarity=0.247  Sum_probs=28.3

Q ss_pred             ceeeecCCCCchHHHHHHHHhcc----c-ceeeeechhHHHHHHhcc
Q 025979          195 GVLLYGPPGTGKTMLAKAVANHT----T-AAFIRVVGSEFVQKYLGE  236 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~~l----~-~~~~~v~~s~l~~~~~Ge  236 (245)
                      +.++.-|+|+|||.++-+++..+    + ..++-+...+|+..|..+
T Consensus       130 ~~il~~pTGsGKT~i~~~i~~~~~~~~~~k~Liivp~~~Lv~Q~~~~  176 (282)
T d1rifa_         130 RRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADD  176 (282)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEECSSHHHHHHHHHH
T ss_pred             CceeEEEcccCccHHHHHHHHHhhhcccceEEEEEcCchhHHHHHHH
Confidence            34666799999999988887543    3 345545555787766543

>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=91.96  E-value=0.033  Score=47.31  Aligned_cols=24  Identities=25%  Similarity=0.466  Sum_probs=19.8

Q ss_pred             cc-eeeecCCCCchHHHHHHHHhcc
Q 025979          194 RG-VLLYGPPGTGKTMLAKAVANHT  217 (245)
Q Consensus       194 ~g-vLl~GPPGtGKT~lAkalA~~l  217 (245)
                      .| -+++||.|+|||++..||.=.+
T Consensus        25 ~~l~~i~G~NGsGKS~ileAi~~~l   49 (427)
T d1w1wa_          25 SNFTSIIGPNGSGKSNMMDAISFVL   49 (427)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            44 4899999999999999996444

>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=91.86  E-value=0.016  Score=47.22  Aligned_cols=26  Identities=23%  Similarity=0.426  Sum_probs=20.1

Q ss_pred             CcceeeecCCCCchHHHHHHHHhccc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTT  218 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~  218 (245)
                      ++..+|.|++|+|||+|..+|.....
T Consensus        97 ~~~~vl~G~SGVGKSSLiN~L~~~~~  122 (231)
T d1t9ha2          97 DKTTVFAGQSGVGKSSLLNAISPELG  122 (231)
T ss_dssp             TSEEEEEESHHHHHHHHHHHHCC---
T ss_pred             cceEEEECCCCccHHHHHHhhccHhH
Confidence            34578999999999999999987653

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {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: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=91.22  E-value=0.07  Score=41.79  Aligned_cols=55  Identities=15%  Similarity=0.141  Sum_probs=30.2

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhh----ccCCCcceeeecCCCCchHHHHHHHH
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQI----GIDPPRGVLLYGPPGTGKTMLAKAVA  214 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~----g~~~~~gvLl~GPPGtGKT~lAkalA  214 (245)
                      +|+|++-.+...+.+.+. .  +..|.-.+..    .+...+.++...|+|+|||+.+-..+
T Consensus         5 sf~~l~l~~~l~~~l~~~-g--~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~   63 (208)
T d1hv8a1           5 NFNELNLSDNILNAIRNK-G--FEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPL   63 (208)
T ss_dssp             CGGGSSCCHHHHHHHHHH-T--CCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHH
T ss_pred             CHHHcCCCHHHHHHHHHC-C--CCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeeccc
Confidence            677875444455555432 1  2222111211    12233469999999999999765443

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

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: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=90.12  E-value=0.21  Score=43.62  Aligned_cols=54  Identities=17%  Similarity=0.220  Sum_probs=40.3

Q ss_pred             CcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHHHHHhcccceeeeechhHH
Q 025979          162 GGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF  229 (245)
Q Consensus       162 ~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l  229 (245)
                      |-+..+++.|.+.+..              ..+..+|.|.+|+|||+++.+++...+.+.+.|..+..
T Consensus        14 gDQP~aI~~l~~~l~~--------------g~~~q~l~GltGS~ka~~iA~l~~~~~rp~LVVt~n~~   67 (413)
T d1t5la1          14 GDQPQAIAKLVDGLRR--------------GVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKT   67 (413)
T ss_dssp             TTHHHHHHHHHHHHHH--------------TCSEEEEEECTTSCHHHHHHHHHHHHTCCEEEECSSHH
T ss_pred             CCCHHHHHHHHHHHhc--------------CCCcEEEeCCCCcHHHHHHHHHHHHhCCCEEEEeCCHH
Confidence            4444556666555533              22458899999999999999999999999988876643

>d1j3ba1 c.91.1.1 (A:212-529) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Thermus thermophilus [TaxId: 274]

Probab=90.10  E-value=0.046  Score=46.36  Aligned_cols=17  Identities=41%  Similarity=0.714  Sum_probs=14.9

Q ss_pred             ceeeecCCCCchHHHHH
Q 025979          195 GVLLYGPPGTGKTMLAK  211 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAk  211 (245)
                      -.||+|.+|||||+|.-
T Consensus        16 valffGLSGTGKTTLs~   32 (318)
T d1j3ba1          16 VAVFFGLSGTGKTTLST   32 (318)
T ss_dssp             EEEEEECTTSCHHHHTC
T ss_pred             EEEEEccCCCCcccccc
Confidence            37999999999999764

>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=90.07  E-value=0.085  Score=42.51  Aligned_cols=32  Identities=28%  Similarity=0.367  Sum_probs=24.2

Q ss_pred             eeeecCCCCchHHHHHHHHhcc---cceeeeechh
Q 025979          196 VLLYGPPGTGKTMLAKAVANHT---TAAFIRVVGS  227 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l---~~~~~~v~~s  227 (245)
                      +++.|-=|||||++|-.||..+   |..++.|+..
T Consensus        23 ii~sGKGGVGKTT~a~nLA~~lA~~G~rVllvD~D   57 (279)
T d1ihua2          23 IMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSD   57 (279)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeCC
Confidence            6678999999999877777655   5566666544

>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=89.92  E-value=0.09  Score=42.37  Aligned_cols=22  Identities=27%  Similarity=0.415  Sum_probs=19.8

Q ss_pred             cceeeecCCCCchHHHHHHHHh
Q 025979          194 RGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      +.+++.||..+|||++.|++|-
T Consensus        42 ~~~iiTGpN~~GKSt~lk~i~l   63 (234)
T d1wb9a2          42 RMLIITGPNMGGKSTYMRQTAL   63 (234)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEeccCchhhHHHHHHHHH
Confidence            5589999999999999999884

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {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: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.91  E-value=0.16  Score=39.95  Aligned_cols=53  Identities=19%  Similarity=0.093  Sum_probs=30.2

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhcc---CCCcceeeecCCCCchHHHH
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGI---DPPRGVLLYGPPGTGKTMLA  210 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~---~~~~gvLl~GPPGtGKT~lA  210 (245)
                      -.+|+|++-.+...+.+.+.   -+..|.-.+...+   -.++.++...|+|+|||+..
T Consensus         9 ~~sF~~l~l~~~l~~~L~~~---g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~   64 (212)
T d1qdea_           9 VYKFDDMELDENLLRGVFGY---GFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTF   64 (212)
T ss_dssp             CCCGGGGTCCHHHHHHHHHH---TCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHH
T ss_pred             ccChhhCCCCHHHHHHHHHC---CCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhh
Confidence            35688885444444555432   1333322232221   23566999999999999843

>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=89.82  E-value=0.1  Score=42.22  Aligned_cols=17  Identities=35%  Similarity=0.434  Sum_probs=14.8

Q ss_pred             CCcceeeecCCCCchHH
Q 025979          192 PPRGVLLYGPPGTGKTM  208 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~  208 (245)
                      ..+.+|+.+|+|+|||+
T Consensus         8 ~~~~~lv~~~TGsGKT~   24 (305)
T d2bmfa2           8 KKRLTIMDLHPGAGKTK   24 (305)
T ss_dssp             TTCEEEECCCTTSSTTT
T ss_pred             cCCcEEEEECCCCCHHH
Confidence            45669999999999996

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {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: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.31  E-value=0.14  Score=40.10  Aligned_cols=50  Identities=20%  Similarity=0.110  Sum_probs=28.4

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhcc---CCCcceeeecCCCCchHHH
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGI---DPPRGVLLYGPPGTGKTML  209 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~---~~~~gvLl~GPPGtGKT~l  209 (245)
                      .|+|++-.+...+.|.+.   -+.+|--.+...+   -.++.+++..|+|+|||+.
T Consensus         2 ~F~dl~L~~~l~~~l~~~---g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla   54 (207)
T d1t6na_           2 GFRDFLLKPELLRAIVDC---GFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAV   54 (207)
T ss_dssp             CSTTSCCCHHHHHHHHHT---TCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHH
T ss_pred             CccccCcCHHHHHHHHHC---CCCCCCHHHHHHHHHHHcCCCeEEEeccccccccc
Confidence            467765444445555443   1333322232221   2346799999999999974

>d2olra1 c.91.1.1 (A:228-540) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Escherichia coli [TaxId: 562]

Probab=89.23  E-value=0.067  Score=45.21  Aligned_cols=17  Identities=41%  Similarity=0.714  Sum_probs=14.9

Q ss_pred             ceeeecCCCCchHHHHH
Q 025979          195 GVLLYGPPGTGKTMLAK  211 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAk  211 (245)
                      --||+|.+|||||+|..
T Consensus        16 ~alfFGLSGTGKTTLs~   32 (313)
T d2olra1          16 VAVFFGLSGTGKTTLST   32 (313)
T ss_dssp             EEEEECSTTSSHHHHHC
T ss_pred             EEEEEccCCCCccccee
Confidence            37899999999999873

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {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: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=89.10  E-value=0.091  Score=40.72  Aligned_cols=17  Identities=29%  Similarity=0.309  Sum_probs=14.7

Q ss_pred             CcceeeecCCCCchHHH
Q 025979          193 PRGVLLYGPPGTGKTML  209 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~l  209 (245)
                      ++.+++..|+|||||+.
T Consensus        38 G~dvii~a~TGSGKTla   54 (209)
T d1q0ua_          38 GESMVGQSQTGTGKTHA   54 (209)
T ss_dssp             TCCEEEECCSSHHHHHH
T ss_pred             CCCeEeeccccccccee
Confidence            35699999999999973

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {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: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.02  E-value=0.13  Score=40.71  Aligned_cols=52  Identities=19%  Similarity=0.162  Sum_probs=30.4

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhcc---CCCcceeeecCCCCchHHHH
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGI---DPPRGVLLYGPPGTGKTMLA  210 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~---~~~~gvLl~GPPGtGKT~lA  210 (245)
                      -+|++++-.+...+.|.+.   -+.+|--.+...+   -..+.++...|+|+|||+..
T Consensus        12 ~sF~~l~L~~~l~~~L~~~---g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlay   66 (218)
T d2g9na1          12 DSFDDMNLSESLLRGIYAY---GFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATF   66 (218)
T ss_dssp             CCGGGSCCCHHHHHHHHHH---TCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHH
T ss_pred             CCHHHCCCCHHHHHHHHHC---CCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhh
Confidence            3688875444445555432   2333333333221   13467999999999999844

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {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: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.01  E-value=0.11  Score=40.44  Aligned_cols=50  Identities=26%  Similarity=0.171  Sum_probs=28.2

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhcc---CCCcceeeecCCCCchHHH
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGI---DPPRGVLLYGPPGTGKTML  209 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~---~~~~gvLl~GPPGtGKT~l  209 (245)
                      +|++++-.+...+.|.+.   -+..|--.+...+   -.++.++..+|+|+|||+.
T Consensus         2 sF~~l~L~~~l~~~L~~~---g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTla   54 (206)
T d1s2ma1           2 TFEDFYLKRELLMGIFEA---GFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAA   54 (206)
T ss_dssp             CGGGGCCCHHHHHHHHHT---TCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHH
T ss_pred             ChHHcCCCHHHHHHHHHC---CCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhh
Confidence            577765555555555543   1222222222211   1246699999999999953

>d1goja_ c.37.1.9 (A:) Kinesin {Neurospora crassa [TaxId: 5141]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Neurospora crassa [TaxId: 5141]

Probab=89.00  E-value=0.38  Score=40.63  Aligned_cols=51  Identities=20%  Similarity=0.270  Sum_probs=31.7

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHH
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLA  210 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lA  210 (245)
                      ..+|+.+.+.+..-+.|.+.+..|+-.     .+--.....|+-||++|+|||++.
T Consensus        47 ~f~FD~vf~~~~~q~~vy~~~~~plv~-----~~l~G~n~ti~aYG~tgSGKT~Tm   97 (354)
T d1goja_          47 SFTFDRVFDMSCKQSDIFDFSIKPTVD-----DILNGYNGTVFAYGQTGAGKSYTM   97 (354)
T ss_dssp             EEECSEEECTTCCHHHHHHHHTHHHHH-----HHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             eEECCeEcCCCCCHHHHHHHHHHHHHH-----HhhccCceeEEecccCCCCcceee
Confidence            367777777776666666555443321     111112234888999999999875

>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=88.81  E-value=0.094  Score=43.50  Aligned_cols=23  Identities=35%  Similarity=0.570  Sum_probs=20.2

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ..++++|++|||||+|+..++..
T Consensus        69 Qr~~If~~~g~GKt~l~~~i~~~   91 (276)
T d2jdid3          69 GKIGLFGGAGVGKTVLIMELINN   91 (276)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CEEEeeCCCCCCHHHHHHHHHHH
Confidence            34999999999999999988765

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase 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: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=88.28  E-value=0.24  Score=37.95  Aligned_cols=32  Identities=25%  Similarity=0.264  Sum_probs=21.7

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcccceeeee
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHTTAAFIRV  224 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v  224 (245)
                      .+.+++.-|+|+|||.++....-......+.+
T Consensus        40 g~~vlv~apTGsGKT~~~~~~~~~~~~~~~~v   71 (206)
T d1oywa2          40 GRDCLVVMPTGGGKSLCYQIPALLLNGLTVVV   71 (206)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHHHSSSEEEEE
T ss_pred             CCCEEEEcCCCCCCcchhhhhhhhccCceEEe
Confidence            36799999999999998765444333333333

>d1ii2a1 c.91.1.1 (A:201-523) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Trypanosoma cruzi [TaxId: 5693]

Probab=87.98  E-value=0.092  Score=44.49  Aligned_cols=17  Identities=41%  Similarity=0.702  Sum_probs=14.9

Q ss_pred             ceeeecCCCCchHHHHH
Q 025979          195 GVLLYGPPGTGKTMLAK  211 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAk  211 (245)
                      -.||+|.+|||||+|..
T Consensus        16 ~alfFGLSGTGKTTLs~   32 (323)
T d1ii2a1          16 VTVFFGLSGTGKTTLSA   32 (323)
T ss_dssp             EEEEECCTTSSHHHHHC
T ss_pred             EEEEEccCCCCccccee
Confidence            37899999999999983

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {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: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.46  E-value=0.27  Score=38.92  Aligned_cols=51  Identities=24%  Similarity=0.222  Sum_probs=30.3

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhcc---CCCcceeeecCCCCchHHH
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGI---DPPRGVLLYGPPGTGKTML  209 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~---~~~~gvLl~GPPGtGKT~l  209 (245)
                      .+|++++-.+...+.|.+. .  +..|--.+...+   -.++.++...|+|||||+.
T Consensus        17 ~sF~~l~L~~~l~~~L~~~-g--~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTla   70 (222)
T d2j0sa1          17 PTFDTMGLREDLLRGIYAY-G--FEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTAT   70 (222)
T ss_dssp             CSGGGGCCCHHHHHHHHHH-T--CCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHH
T ss_pred             CCHHHCCCCHHHHHHHHHC-C--CCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhh
Confidence            4788986555556666543 1  222222222211   1356799999999999973

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {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: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.36  E-value=0.17  Score=39.53  Aligned_cols=50  Identities=20%  Similarity=0.092  Sum_probs=27.6

Q ss_pred             eeccCCcchhhhHHHHHHHhcCCCcHHHHhhhcc---CCCcceeeecCCCCchHHH
Q 025979          157 TYNDIGGCDIQKQEIREAVELPLTHHELYKQIGI---DPPRGVLLYGPPGTGKTML  209 (245)
Q Consensus       157 ~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~---~~~~gvLl~GPPGtGKT~l  209 (245)
                      +|+|++-.++..+.|.+.   -+..|.-.+...+   -.++.++...|+|+|||+.
T Consensus         4 ~F~~l~L~~~l~~~l~~~---g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTla   56 (206)
T d1veca_           4 EFEDYCLKRELLMGIFEM---GWEKPSPIQEESIPIALSGRDILARAKNGTGKSGA   56 (206)
T ss_dssp             SGGGSCCCHHHHHHHHTT---TCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHH
T ss_pred             ChhccCcCHHHHHHHHHC---CCCCCCHHHHHHHHHHHcCCCEEeeccCccccccc
Confidence            566765444444444432   1333322232221   1346799999999999963

>d1bg2a_ c.37.1.9 (A:) Kinesin {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: Motor proteins
domain: Kinesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.27  E-value=0.19  Score=41.97  Aligned_cols=51  Identities=10%  Similarity=0.217  Sum_probs=32.3

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHH
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLA  210 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lA  210 (245)
                      ..+|+.+.+.+.--+++.+.+..|+... .+    -.....++-||++|+|||+..
T Consensus        43 ~f~FD~vf~~~~~q~~vf~~~~~~lv~~-~l----~G~n~~i~aYGqtgSGKTyT~   93 (323)
T d1bg2a_          43 PYAFDRVFQSSTSQEQVYNDCAKKIVKD-VL----EGYNGTIFAYGQTSSGKTHTM   93 (323)
T ss_dssp             EEECSEEECTTCCHHHHHHHHTHHHHHH-HH----TTCCEEEEEECSTTSSHHHHH
T ss_pred             eeECCEEECCCCCHHHHHHHHHHHHHHH-HH----cCCCcceeeecccCCCCceec
Confidence            3567777777766666666555443221 11    122344888999999999976

>d1c4oa1 c.37.1.19 (A:2-409) Nucleotide excision repair enzyme UvrB {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: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=86.51  E-value=0.5  Score=40.92  Aligned_cols=36  Identities=28%  Similarity=0.323  Sum_probs=30.8

Q ss_pred             cceeeecCCCCchHHHHHHHHhcccceeeeechhHH
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEF  229 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~l~~~~~~v~~s~l  229 (245)
                      +.++|.|.+|++||+++.+++..++.+++.|..+.-
T Consensus        29 ~~~~L~GlsgS~ka~~~A~l~~~~~rp~LvVt~~~~   64 (408)
T d1c4oa1          29 RFVTLLGATGTGKTVTMAKVIEALGRPALVLAPNKI   64 (408)
T ss_dssp             SEEEEEECTTSCHHHHHHHHHHHHTCCEEEEESSHH
T ss_pred             CcEEEecCCCCHHHHHHHHHHHHhCCCEEEEeCCHH
Confidence            347899999999999999999999999888865543

>d1g8fa3 c.37.1.15 (A:390-511) ATP sulfurylase C-terminal 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: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.47  E-value=0.19  Score=36.50  Aligned_cols=32  Identities=9%  Similarity=0.035  Sum_probs=25.1

Q ss_pred             eeeecCCCCchHHHHHHHHhcc-----cceeeeechh
Q 025979          196 VLLYGPPGTGKTMLAKAVANHT-----TAAFIRVVGS  227 (245)
Q Consensus       196 vLl~GPPGtGKT~lAkalA~~l-----~~~~~~v~~s  227 (245)
                      ++|.|-+|+||+++|+|+...+     ++++-.+++.
T Consensus         9 i~~tg~~~~gk~~ia~al~~~l~q~~G~R~vtll~~~   45 (122)
T d1g8fa3           9 IVLGNSLTVSREQLSIALLSTFLQFGGGRYYKIFEHN   45 (122)
T ss_dssp             EEECTTCCSCHHHHHHHHHHHHTTSCSCCCEEECCCT
T ss_pred             EEEeCCCCCCHHHHHHHHHHHHHHhcCCcceEEecCC
Confidence            7889999999999999997655     4555555544

>d1sdma_ c.37.1.9 (A:) Kinesin heavy chain-like protein {Potato (Solanum tuberosum) [TaxId: 4113]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin heavy chain-like protein
species: Potato (Solanum tuberosum) [TaxId: 4113]

Probab=85.26  E-value=0.32  Score=41.43  Aligned_cols=49  Identities=20%  Similarity=0.327  Sum_probs=29.1

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHH
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLA  210 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lA  210 (245)
                      .+|+.+.+.+..-+++.+.+ .|+-. ..+.  |  ....++-||++|+|||+..
T Consensus        44 f~FD~vf~~~~~q~~vy~~v-~~lv~-~~l~--G--~n~~i~aYGqTGSGKTyTm   92 (364)
T d1sdma_          44 HMYDRVFDGNATQDDVFEDT-KYLVQ-SAVD--G--YNVCIFAYGQTGSGKTFTI   92 (364)
T ss_dssp             EECSEEECTTCCHHHHHHTT-THHHH-HHHT--T--CEEEEEEECSTTSSHHHHH
T ss_pred             EECCeecCCCCCHHHHHHHH-HHHHH-HHhc--C--CceeeeccccCCCCccccc
Confidence            56677766665555665544 22211 1111  1  2234888999999999974

>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=84.97  E-value=0.24  Score=41.04  Aligned_cols=23  Identities=30%  Similarity=0.328  Sum_probs=19.0

Q ss_pred             cceeeecCCCCchHHHHHHHHhc
Q 025979          194 RGVLLYGPPGTGKTMLAKAVANH  216 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~~  216 (245)
                      ..++++|++|||||+++..++..
T Consensus        69 Qr~~If~~~g~GKt~ll~~~~~~   91 (285)
T d2jdia3          69 QRELIIGDRQTGKTSIAIDTIIN   91 (285)
T ss_dssp             CBCEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEeecCCCCChHHHHHHHHHh
Confidence            44999999999999998777643

>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=84.72  E-value=0.23  Score=39.57  Aligned_cols=21  Identities=33%  Similarity=0.441  Sum_probs=19.0

Q ss_pred             ceeeecCCCCchHHHHHHHHh
Q 025979          195 GVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       195 gvLl~GPPGtGKT~lAkalA~  215 (245)
                      .+++.||...|||++.|++|-
T Consensus        37 ~~iiTGpN~~GKSt~lk~i~l   57 (224)
T d1ewqa2          37 LVLITGPNMAGKSTFLRQTAL   57 (224)
T ss_dssp             EEEEESCSSSSHHHHHHHHHH
T ss_pred             EEEEECCCccccchhhhhhHH
Confidence            489999999999999998874

>d1ry6a_ c.37.1.9 (A:) Kinesin {Malaria parasite (Plasmodium falciparum) [TaxId: 5833]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Malaria parasite (Plasmodium falciparum) [TaxId: 5833]

Probab=83.79  E-value=0.19  Score=42.26  Aligned_cols=53  Identities=23%  Similarity=0.322  Sum_probs=32.7

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHHH
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAK  211 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lAk  211 (245)
                      ..+|+.|.+.+..-+++.+.+..|+-.. .+. -|  ....|+-||.+|+|||+..-
T Consensus        51 ~F~fD~Vf~~~~~q~~vy~~~~~plv~~-~~~-~G--~n~~i~aYGqTGSGKTyTm~  103 (330)
T d1ry6a_          51 EFIVDKVFDDTVDNFTVYENTIKPLIID-LYE-NG--CVCSCFAYGQTGSGKTYTML  103 (330)
T ss_dssp             EEECSEEECTTCCHHHHHHHHTHHHHHH-HHH-HC--CEEEEEEECCTTSSHHHHHH
T ss_pred             eEeCCeecCCCCCHHHHHHHHHHHHHHH-HHh-cC--CCeEEEeeeccccccceeee
Confidence            3566777777766677766655443211 111 12  22348889999999998853

>d1f9va_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]

Probab=83.63  E-value=0.5  Score=39.65  Aligned_cols=50  Identities=18%  Similarity=0.240  Sum_probs=30.4

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHH
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLA  210 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lA  210 (245)
                      ..+|+.+.+.+..-+++.+.+. |+-     ..+--.....++-||++|+|||+..
T Consensus        51 ~f~FD~vf~~~~~q~~vy~~v~-~~v-----~~~l~G~n~~i~aYGqtgSGKT~T~  100 (342)
T d1f9va_          51 EFKFDKIFDQQDTNVDVFKEVG-QLV-----QSSLDGYNVCIFAYGQTGSGKTFTM  100 (342)
T ss_dssp             EEEESEEECTTCCHHHHHHHHH-HHH-----GGGGGTCCEEEEEECCTTSSHHHHH
T ss_pred             EeecCeEeCCCCCHHHHHHHhh-hhh-----cchhcccccceeeeeccCCcccccc
Confidence            3667788776665666665543 221     1111112234778999999999865

>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=83.59  E-value=0.31  Score=40.18  Aligned_cols=22  Identities=32%  Similarity=0.350  Sum_probs=18.0

Q ss_pred             cceeeecCCCCchHHHHHHHHh
Q 025979          194 RGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       194 ~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      ..++++|++|||||.++..++.
T Consensus        68 Qr~~Ifg~~g~GKt~l~~~~~~   89 (276)
T d1fx0a3          68 QRELIIGDRQTGKTAVATDTIL   89 (276)
T ss_dssp             CBCBEEESSSSSHHHHHHHHHH
T ss_pred             ceEeeccCCCCChHHHHHHHHh
Confidence            3499999999999999876443

>d1tq4a_ c.37.1.8 (A:) Interferon-inducible GTPase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-inducible GTPase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.44  E-value=0.25  Score=42.63  Aligned_cols=24  Identities=21%  Similarity=0.380  Sum_probs=20.7

Q ss_pred             CCcceeeecCCCCchHHHHHHHHh
Q 025979          192 PPRGVLLYGPPGTGKTMLAKAVAN  215 (245)
Q Consensus       192 ~~~gvLl~GPPGtGKT~lAkalA~  215 (245)
                      .+-.|.+.|.||+|||+|..+|-+
T Consensus        55 ~~l~Iai~G~~n~GKSSLiNaL~G   78 (400)
T d1tq4a_          55 SVLNVAVTGETGSGKSSFINTLRG   78 (400)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhC
Confidence            345699999999999999999964

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {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: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=82.35  E-value=0.47  Score=37.05  Aligned_cols=44  Identities=20%  Similarity=0.232  Sum_probs=33.0

Q ss_pred             CcceeeecCCCCchHHHHHHHHhcc-----cceeeeechhHHHHHHhcc
Q 025979          193 PRGVLLYGPPGTGKTMLAKAVANHT-----TAAFIRVVGSEFVQKYLGE  236 (245)
Q Consensus       193 ~~gvLl~GPPGtGKT~lAkalA~~l-----~~~~~~v~~s~l~~~~~Ge  236 (245)
                      +.|.+|.=++|+|||..|-+++..+     ..+++.|....++..|.-|
T Consensus        31 ~~g~iLaDe~GlGKT~~~i~~~~~~~~~~~~~~~LIv~p~~l~~~W~~e   79 (230)
T d1z63a1          31 GFGICLADDMGLGKTLQTIAVFSDAKKENELTPSLVICPLSVLKNWEEE   79 (230)
T ss_dssp             TCCEEECCCTTSCHHHHHHHHHHHHHHTTCCSSEEEEECSTTHHHHHHH
T ss_pred             CCCEEEEeCCCCChHHHHHHhhhhhhhcccccccceecchhhhhHHHHH
Confidence            4578888899999999998887655     2456667777777777544

>d1v8ka_ c.37.1.9 (A:) Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif2c [TaxId: 10090]

Probab=81.92  E-value=0.33  Score=41.29  Aligned_cols=51  Identities=18%  Similarity=0.308  Sum_probs=32.2

Q ss_pred             CceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHH
Q 025979          155 DVTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLA  210 (245)
Q Consensus       155 ~~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lA  210 (245)
                      ..+|+.+.+.+..-+.+.+.+..|+-.. .+.  |  ....++-||.+|+|||+..
T Consensus        81 ~f~FD~vf~~~~~Q~~Vy~~~~~plv~~-~l~--G--~n~tifaYGqTGSGKTyTm  131 (362)
T d1v8ka_          81 AFCFDFAFDETASNEVVYRFTARPLVQT-IFE--G--GKATCFAYGQTGSGKTHTM  131 (362)
T ss_dssp             EEECSEEECTTCCHHHHHHHTTHHHHHH-HHT--T--CEEEEEEEESTTSSHHHHH
T ss_pred             eEeCCeecCCCCCHHHHHHHHHHHHHHH-HHh--c--cCceEEeeccCCCCCceee
Confidence            3567778777766666766655443221 111  1  2234778999999999875

>d1x88a1 c.37.1.9 (A:18-362) Kinesin {Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]

Probab=81.68  E-value=0.38  Score=40.46  Aligned_cols=50  Identities=24%  Similarity=0.436  Sum_probs=29.4

Q ss_pred             ceeccCCcchhhhHHHHHHHhcCCCcHHHHhhhccCCCcceeeecCCCCchHHHH
Q 025979          156 VTYNDIGGCDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLA  210 (245)
Q Consensus       156 ~~~~dv~Gl~~~~~~i~e~i~~~~~~~~~~~~~g~~~~~gvLl~GPPGtGKT~lA  210 (245)
                      .+|+.+.+.+..-++|.+.+..|+-.. .+.  |  -...++-||+.|+|||+..
T Consensus        49 f~FD~vf~~~~~q~~vy~~~~~~lv~~-~l~--G--~n~~i~aYGqtgSGKTyTm   98 (345)
T d1x88a1          49 YTFDMVFGASTKQIDVYRSVVCPILDE-VIM--G--YNCTIFAYGQTGTGKTFTM   98 (345)
T ss_dssp             EECSEEECTTCCHHHHHHHHHHHHHHH-HHT--T--CEEEEEEEECTTSSHHHHH
T ss_pred             EecCEEeCCCCCHHHHHHHHHHHhHHH-Hhc--c--CCceEEeeeeccccceEEe
Confidence            456666666655556655444333211 111  1  2234888999999999765