Citrus Sinensis ID: 030960

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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-------17
Protein Sequence
MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK
Secondary Structure (PSIPRED)
cHHHHHHHHHHccccEEEEEcccccccccccccccccHHHHHHHHHHHHHcccccccccEEEEEEcccccccccccccccccccccccccccHHHHHHHHHHcccccccHHHHHcccccccHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHcccEEEEEEEEccccccccccccccccHHHHHHHHHHHHcccccccccEEEEEEccccccccHHHccccccccEEEEcccccccHHHHHHHHccccccHHHHHcccccccHHHHHHHHHHHHHHHHHHcccEEcHHHHHHHHHHHHccHHHHHcccc
Coil and Loop (DISEMBL)
MVRDVFRLAkenapaiifiDEVDAIATARfdaqtgadREVQRILMELLNQMDGFDQTVNVKVIMAtnradtldpallrpgrldrkiefplpdrrQKRLVFQmnlsdevdledyvsrpdkiSAAEIAAICQEAGMHavrknryvilpkdfekgyrtnvkkpdtdfefyk
Flexible Loop (DISEMBL)
MVRDVFRLakenapaiifiDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMatnradtldpallrpgrldrkiefplpdrrqkrlvfqmnlsdevdledyvsRPDKISAAEIAAICQEAGMHAVRKNRYVilpkdfekgyrtnvkkpdtdfefyk
Low Complexity Region (SEG)
MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK
Disordered region (IsUnstruct)
****VFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR**************
Disordered Region (DISOPRED)
MVRDVFRLAKENAPAIIFIDEVDAIAT**************RILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT*************
Disordered Region (DISEMBL)
MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK
Disordered Region (DISPRO)
*VRDVFRLAKENAPAIIFIDEVDAIATAR*****GADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDT******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK
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	168	2.2.26 [Sep-21-2011]
Q9SEI4	408	26S protease regulatory s	yes	no	1.0	0.411	0.965	2e-92
P85200	414	26S protease regulatory s	N/A	no	1.0	0.405	0.959	9e-92
P54778	413	26S protease regulatory s	N/A	no	1.0	0.406	0.959	1e-91
P34123	403	26S protease regulatory s	yes	no	0.994	0.414	0.837	5e-82
P46507	415	26S protease regulatory s	N/A	no	1.0	0.404	0.809	1e-80
Q63570	418	26S protease regulatory s	yes	no	1.0	0.401	0.815	2e-78
P54775	418	26S protease regulatory s	yes	no	1.0	0.401	0.815	2e-78
Q4R7L3	418	26S protease regulatory s	N/A	no	1.0	0.401	0.815	2e-78
P43686	418	26S protease regulatory s	yes	no	1.0	0.401	0.815	2e-78
Q3T030	418	26S protease regulatory s	yes	no	1.0	0.401	0.815	2e-78

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

 Score =  337 bits (864), Expect = 2e-92,   Method: Compositional matrix adjust.
 Identities = 167/173 (96%), Positives = 167/173 (96%), Gaps = 5/173 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV
Sbjct: 236 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 295

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
           KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ     MNLSDEVDLEDYVS
Sbjct: 296 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQVCTSKMNLSDEVDLEDYVS 355

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
           RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR NVKKPDTDFEFYK
Sbjct: 356 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRANVKKPDTDFEFYK 408

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

 Score =  335 bits (858), Expect = 9e-92,   Method: Compositional matrix adjust.
 Identities = 166/173 (95%), Positives = 167/173 (96%), Gaps = 5/173 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV
Sbjct: 242 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 301

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
           KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ     MNLSDEVDLEDYVS
Sbjct: 302 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQVCTAKMNLSDEVDLEDYVS 361

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
           RPDKISAAEI AICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDF+FYK
Sbjct: 362 RPDKISAAEITAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFDFYK 414

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

 Score =  334 bits (857), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 166/173 (95%), Positives = 166/173 (95%), Gaps = 5/173 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV
Sbjct: 241 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 300

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
           KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ     MNL DEVDLEDYVS
Sbjct: 301 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQVCTAKMNLGDEVDLEDYVS 360

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
           RPDKISAAEI AICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK
Sbjct: 361 RPDKISAAEITAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 413

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|P34123|PRS6B_DICDI 26S protease regulatory subunit 6B homolog OS=Dictyostelium discoideum GN=psmC4 PE=1 SV=1

 Score =  302 bits (774), Expect = 5e-82,   Method: Compositional matrix adjust.
 Identities = 144/172 (83%), Positives = 157/172 (91%), Gaps = 5/172 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           +VRDVFRLA+EN+PAIIFIDE+DAIAT RFDAQTGADREVQRILMELLNQMDGFD +VNV
Sbjct: 231 LVRDVFRLARENSPAIIFIDEIDAIATKRFDAQTGADREVQRILMELLNQMDGFDVSVNV 290

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
           KVIMATNR DTLDPALLRPGRLDRKIEFPLPDRRQKRL+FQ     MNLSDEVDLEDYVS
Sbjct: 291 KVIMATNRQDTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQVITSKMNLSDEVDLEDYVS 350

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFY 167
           RPDK+S AEI +ICQEAGMHA+RKNRYVILPKDFEKGY+ ++KK   +F FY
Sbjct: 351 RPDKLSGAEIQSICQEAGMHAIRKNRYVILPKDFEKGYKASIKKNTHEFNFY 402

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.

Dictyostelium discoideum (taxid: 44689)

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

 Score =  298 bits (762), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 140/173 (80%), Positives = 162/173 (93%), Gaps = 5/173 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVRDVFRLAKEN+PAIIFIDE+DAIAT RFDAQTGADREVQRIL+ELLNQMDGFDQT NV
Sbjct: 243 MVRDVFRLAKENSPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNV 302

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVF-----QMNLSDEVDLEDYVS 115
           KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRL+F     +MNLS+EVDLE++V+
Sbjct: 303 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITAKMNLSEEVDLEEFVA 362

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
           RPD++S A+I AICQEAGM+AVR+NRY++LPKDFEKGY+ N+KK ++++EFYK
Sbjct: 363 RPDRVSGADINAICQEAGMNAVRENRYIVLPKDFEKGYKNNIKKDESEYEFYK 415

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

 Score =  290 bits (743), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 141/173 (81%), Positives = 157/173 (90%), Gaps = 5/173 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVRDVFRLAKENAPAIIFIDE+DAIAT RFDAQTGADREVQRIL+ELLNQMDGFDQ VNV
Sbjct: 246 MVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFDQNVNV 305

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVF-----QMNLSDEVDLEDYVS 115
           KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRL+F     +MNLS+EVDLEDYV+
Sbjct: 306 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDLEDYVA 365

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
           RPDKIS A+I +ICQE+GM AVR+NRY++L KDFEK Y+T +KK + + EFYK
Sbjct: 366 RPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK 418

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 =  290 bits (743), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 141/173 (81%), Positives = 157/173 (90%), Gaps = 5/173 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVRDVFRLAKENAPAIIFIDE+DAIAT RFDAQTGADREVQRIL+ELLNQMDGFDQ VNV
Sbjct: 246 MVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFDQNVNV 305

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVF-----QMNLSDEVDLEDYVS 115
           KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRL+F     +MNLS+EVDLEDYV+
Sbjct: 306 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDLEDYVA 365

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
           RPDKIS A+I +ICQE+GM AVR+NRY++L KDFEK Y+T +KK + + EFYK
Sbjct: 366 RPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK 418

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

 Score =  290 bits (743), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 141/173 (81%), Positives = 157/173 (90%), Gaps = 5/173 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVRDVFRLAKENAPAIIFIDE+DAIAT RFDAQTGADREVQRIL+ELLNQMDGFDQ VNV
Sbjct: 246 MVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFDQNVNV 305

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVF-----QMNLSDEVDLEDYVS 115
           KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRL+F     +MNLS+EVDLEDYV+
Sbjct: 306 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDLEDYVA 365

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
           RPDKIS A+I +ICQE+GM AVR+NRY++L KDFEK Y+T +KK + + EFYK
Sbjct: 366 RPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK 418

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 =  290 bits (743), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 141/173 (81%), Positives = 157/173 (90%), Gaps = 5/173 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVRDVFRLAKENAPAIIFIDE+DAIAT RFDAQTGADREVQRIL+ELLNQMDGFDQ VNV
Sbjct: 246 MVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFDQNVNV 305

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVF-----QMNLSDEVDLEDYVS 115
           KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRL+F     +MNLS+EVDLEDYV+
Sbjct: 306 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDLEDYVA 365

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
           RPDKIS A+I +ICQE+GM AVR+NRY++L KDFEK Y+T +KK + + EFYK
Sbjct: 366 RPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK 418

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 =  290 bits (743), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 141/173 (81%), Positives = 157/173 (90%), Gaps = 5/173 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVRDVFRLAKENAPAIIFIDE+DAIAT RFDAQTGADREVQRIL+ELLNQMDGFDQ VNV
Sbjct: 246 MVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFDQNVNV 305

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVF-----QMNLSDEVDLEDYVS 115
           KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRL+F     +MNLS+EVDLEDYV+
Sbjct: 306 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDLEDYVA 365

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
           RPDKIS A+I +ICQE+GM AVR+NRY++L KDFEK Y+T +KK + + EFYK
Sbjct: 366 RPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK 418

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)

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	168
255565346	415	26S protease regulatory subunit 6b, puta	1.0	0.404	0.971	3e-91
359478860	418	PREDICTED: 26S protease regulatory subun	1.0	0.401	0.971	4e-91
356570019	422	PREDICTED: 26S protease regulatory subun	1.0	0.398	0.971	5e-91
357460533	415	26S protease regulatory subunit 6B [Medi	1.0	0.404	0.965	5e-91
297745747	328	unnamed protein product [Vitis vinifera]	1.0	0.512	0.971	8e-91
356539715	423	PREDICTED: 26S protease regulatory subun	1.0	0.397	0.965	8e-91
449475799	418	PREDICTED: LOW QUALITY PROTEIN: 26S prot	1.0	0.401	0.965	1e-90
449444336	418	PREDICTED: 26S protease regulatory subun	1.0	0.401	0.965	1e-90
15237159	408	regulatory particle triple-A ATPase 3 [A	1.0	0.411	0.965	1e-90
224086733	412	predicted protein [Populus trichocarpa]	1.0	0.407	0.965	2e-90

>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 =  339 bits (869), Expect = 3e-91,   Method: Compositional matrix adjust.
 Identities = 168/173 (97%), Positives = 168/173 (97%), Gaps = 5/173 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV
Sbjct: 243 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 302

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
           KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ     MNLSDEVDLEDYVS
Sbjct: 303 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQVCTSKMNLSDEVDLEDYVS 362

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
           RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK
Sbjct: 363 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 415

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359478860|ref|XP_002276130.2| PREDICTED: 26S protease regulatory subunit 6B homolog [Vitis vinifera]

 Score =  338 bits (867), Expect = 4e-91,   Method: Compositional matrix adjust.
 Identities = 168/173 (97%), Positives = 168/173 (97%), Gaps = 5/173 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV
Sbjct: 246 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 305

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
           KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ     MNLSDEVDLEDYVS
Sbjct: 306 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQVCTAKMNLSDEVDLEDYVS 365

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
           RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK
Sbjct: 366 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 418

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  338 bits (866), Expect = 5e-91,   Method: Compositional matrix adjust.
 Identities = 168/173 (97%), Positives = 168/173 (97%), Gaps = 5/173 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV
Sbjct: 250 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 309

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
           KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ     MNLSDEVDLEDYVS
Sbjct: 310 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQVCTAKMNLSDEVDLEDYVS 369

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
           RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK
Sbjct: 370 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 422

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357460533|ref|XP_003600548.1| 26S protease regulatory subunit 6B [Medicago truncatula] gi|355489596|gb|AES70799.1| 26S protease regulatory subunit 6B [Medicago truncatula]

 Score =  338 bits (866), Expect = 5e-91,   Method: Compositional matrix adjust.
 Identities = 167/173 (96%), Positives = 168/173 (97%), Gaps = 5/173 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV
Sbjct: 243 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 302

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
           KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ     MNLSDEVDLEDYVS
Sbjct: 303 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQVCTAKMNLSDEVDLEDYVS 362

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
           RPDKISAAEI+AICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK
Sbjct: 363 RPDKISAAEISAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 415

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297745747|emb|CBI15803.3| unnamed protein product [Vitis vinifera]

 Score =  337 bits (865), Expect = 8e-91,   Method: Compositional matrix adjust.
 Identities = 168/173 (97%), Positives = 168/173 (97%), Gaps = 5/173 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV
Sbjct: 156 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 215

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
           KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ     MNLSDEVDLEDYVS
Sbjct: 216 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQVCTAKMNLSDEVDLEDYVS 275

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
           RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK
Sbjct: 276 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 328

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  337 bits (865), Expect = 8e-91,   Method: Compositional matrix adjust.
 Identities = 167/173 (96%), Positives = 168/173 (97%), Gaps = 5/173 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV
Sbjct: 251 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 310

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
           KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ     MNLSDEVDLEDYVS
Sbjct: 311 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQVCTAKMNLSDEVDLEDYVS 370

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
           RPDKISAAEI+AICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK
Sbjct: 371 RPDKISAAEISAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 423

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 =  337 bits (864), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 167/173 (96%), Positives = 167/173 (96%), Gaps = 5/173 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV
Sbjct: 246 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 305

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
           KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ     MNL DEVDLEDYVS
Sbjct: 306 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQVCTAKMNLGDEVDLEDYVS 365

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
           RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK
Sbjct: 366 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 418

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  337 bits (864), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 167/173 (96%), Positives = 167/173 (96%), Gaps = 5/173 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV
Sbjct: 246 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 305

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
           KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ     MNL DEVDLEDYVS
Sbjct: 306 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQVCTAKMNLGDEVDLEDYVS 365

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
           RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK
Sbjct: 366 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 418

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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 =  337 bits (864), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 167/173 (96%), Positives = 167/173 (96%), Gaps = 5/173 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV
Sbjct: 236 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 295

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
           KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ     MNLSDEVDLEDYVS
Sbjct: 296 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQVCTSKMNLSDEVDLEDYVS 355

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
           RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR NVKKPDTDFEFYK
Sbjct: 356 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRANVKKPDTDFEFYK 408

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  336 bits (861), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 167/173 (96%), Positives = 168/173 (97%), Gaps = 5/173 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV
Sbjct: 240 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 299

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
           KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ     MNLSDEVD+EDYVS
Sbjct: 300 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQVCTAKMNLSDEVDMEDYVS 359

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
           RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK
Sbjct: 360 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 412

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	168
TAIR|locus:2161258	408	RPT3 "regulatory particle trip	1.0	0.411	0.965	6.4e-83
DICTYBASE|DDB_G0289003	403	psmC4 "HIV TAT binding-protein	0.994	0.414	0.837	4.6e-73
FB|FBgn0028686	413	Rpt3 "Regulatory particle trip	1.0	0.406	0.826	7.5e-73
UNIPROTKB|F1MG70	417	PSMC4 "26S protease regulatory	1.0	0.402	0.815	6.1e-71
UNIPROTKB|Q3T030	418	PSMC4 "26S protease regulatory	1.0	0.401	0.815	6.1e-71
UNIPROTKB|E2RH48	418	PSMC4 "Uncharacterized protein	1.0	0.401	0.815	6.1e-71
UNIPROTKB|P43686	418	PSMC4 "26S protease regulatory	1.0	0.401	0.815	6.1e-71
UNIPROTKB|Q4R7L3	418	PSMC4 "26S protease regulatory	1.0	0.401	0.815	6.1e-71
MGI|MGI:1346093	418	Psmc4 "proteasome (prosome, ma	1.0	0.401	0.815	6.1e-71
RGD|621102	418	Psmc4 "proteasome (prosome, ma	1.0	0.401	0.815	6.1e-71

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

 Score = 831 (297.6 bits), Expect = 6.4e-83, P = 6.4e-83
 Identities = 167/173 (96%), Positives = 167/173 (96%)

Query:     1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
             MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV
Sbjct:   236 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 295

Query:    61 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
             KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ     MNLSDEVDLEDYVS
Sbjct:   296 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQVCTSKMNLSDEVDLEDYVS 355

Query:   116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
             RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR NVKKPDTDFEFYK
Sbjct:   356 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRANVKKPDTDFEFYK 408

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

DICTYBASE|DDB_G0289003 psmC4 "HIV TAT binding-protein-related" [Dictyostelium discoideum (taxid:44689)]

 Score = 738 (264.8 bits), Expect = 4.6e-73, P = 4.6e-73
 Identities = 144/172 (83%), Positives = 157/172 (91%)

Query:     1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
             +VRDVFRLA+EN+PAIIFIDE+DAIAT RFDAQTGADREVQRILMELLNQMDGFD +VNV
Sbjct:   231 LVRDVFRLARENSPAIIFIDEIDAIATKRFDAQTGADREVQRILMELLNQMDGFDVSVNV 290

Query:    61 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
             KVIMATNR DTLDPALLRPGRLDRKIEFPLPDRRQKRL+FQ     MNLSDEVDLEDYVS
Sbjct:   291 KVIMATNRQDTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQVITSKMNLSDEVDLEDYVS 350

Query:   116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFY 167
             RPDK+S AEI +ICQEAGMHA+RKNRYVILPKDFEKGY+ ++KK   +F FY
Sbjct:   351 RPDKLSGAEIQSICQEAGMHAIRKNRYVILPKDFEKGYKASIKKNTHEFNFY 402

GO:0045335 "phagocytic vesicle" evidence=IDA

GO:0006972 "hyperosmotic response" evidence=IEP

GO:0030163 "protein catabolic process" evidence=IEA

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

GO:0016787 "hydrolase activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006508 "proteolysis" evidence=ISS

GO:0005838 "proteasome regulatory particle" evidence=ISS

GO:0004175 "endopeptidase activity" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0000502 "proteasome complex" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

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

 Score = 736 (264.1 bits), Expect = 7.5e-73, P = 7.5e-73
 Identities = 143/173 (82%), Positives = 159/173 (91%)

Query:     1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
             MVRDVFRLAKENAPAIIFIDE+DAIAT RFDAQTGADREVQRIL+ELLNQMDGFDQT NV
Sbjct:   241 MVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNV 300

Query:    61 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVF-----QMNLSDEVDLEDYVS 115
             KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVF     +MNLS++VDLE++V+
Sbjct:   301 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFSTITSKMNLSEDVDLEEFVA 360

Query:   116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
             RPDKIS A+I AICQEAGMHAVR+NRY++L KDFEKGY+ N+KK + + EFYK
Sbjct:   361 RPDKISGADINAICQEAGMHAVRENRYIVLAKDFEKGYKNNIKKDEQEHEFYK 413

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 = 718 (257.8 bits), Expect = 6.1e-71, P = 6.1e-71
 Identities = 141/173 (81%), Positives = 157/173 (90%)

Query:     1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
             MVRDVFRLAKENAPAIIFIDE+DAIAT RFDAQTGADREVQRIL+ELLNQMDGFDQ VNV
Sbjct:   245 MVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFDQNVNV 304

Query:    61 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVF-----QMNLSDEVDLEDYVS 115
             KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRL+F     +MNLS+EVDLEDYV+
Sbjct:   305 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDLEDYVA 364

Query:   116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
             RPDKIS A+I +ICQE+GM AVR+NRY++L KDFEK Y+T +KK + + EFYK
Sbjct:   365 RPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK 417

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 = 718 (257.8 bits), Expect = 6.1e-71, P = 6.1e-71
 Identities = 141/173 (81%), Positives = 157/173 (90%)

Query:     1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
             MVRDVFRLAKENAPAIIFIDE+DAIAT RFDAQTGADREVQRIL+ELLNQMDGFDQ VNV
Sbjct:   246 MVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFDQNVNV 305

Query:    61 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVF-----QMNLSDEVDLEDYVS 115
             KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRL+F     +MNLS+EVDLEDYV+
Sbjct:   306 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDLEDYVA 365

Query:   116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
             RPDKIS A+I +ICQE+GM AVR+NRY++L KDFEK Y+T +KK + + EFYK
Sbjct:   366 RPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK 418

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 = 718 (257.8 bits), Expect = 6.1e-71, P = 6.1e-71
 Identities = 141/173 (81%), Positives = 157/173 (90%)

Query:     1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
             MVRDVFRLAKENAPAIIFIDE+DAIAT RFDAQTGADREVQRIL+ELLNQMDGFDQ VNV
Sbjct:   246 MVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFDQNVNV 305

Query:    61 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVF-----QMNLSDEVDLEDYVS 115
             KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRL+F     +MNLS+EVDLEDYV+
Sbjct:   306 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDLEDYVA 365

Query:   116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
             RPDKIS A+I +ICQE+GM AVR+NRY++L KDFEK Y+T +KK + + EFYK
Sbjct:   366 RPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK 418

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 = 718 (257.8 bits), Expect = 6.1e-71, P = 6.1e-71
 Identities = 141/173 (81%), Positives = 157/173 (90%)

Query:     1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
             MVRDVFRLAKENAPAIIFIDE+DAIAT RFDAQTGADREVQRIL+ELLNQMDGFDQ VNV
Sbjct:   246 MVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFDQNVNV 305

Query:    61 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVF-----QMNLSDEVDLEDYVS 115
             KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRL+F     +MNLS+EVDLEDYV+
Sbjct:   306 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDLEDYVA 365

Query:   116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
             RPDKIS A+I +ICQE+GM AVR+NRY++L KDFEK Y+T +KK + + EFYK
Sbjct:   366 RPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK 418

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 = 718 (257.8 bits), Expect = 6.1e-71, P = 6.1e-71
 Identities = 141/173 (81%), Positives = 157/173 (90%)

Query:     1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
             MVRDVFRLAKENAPAIIFIDE+DAIAT RFDAQTGADREVQRIL+ELLNQMDGFDQ VNV
Sbjct:   246 MVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFDQNVNV 305

Query:    61 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVF-----QMNLSDEVDLEDYVS 115
             KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRL+F     +MNLS+EVDLEDYV+
Sbjct:   306 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDLEDYVA 365

Query:   116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
             RPDKIS A+I +ICQE+GM AVR+NRY++L KDFEK Y+T +KK + + EFYK
Sbjct:   366 RPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK 418

GO:0022624 "proteasome accessory complex" evidence=ISS

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

 Score = 718 (257.8 bits), Expect = 6.1e-71, P = 6.1e-71
 Identities = 141/173 (81%), Positives = 157/173 (90%)

Query:     1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
             MVRDVFRLAKENAPAIIFIDE+DAIAT RFDAQTGADREVQRIL+ELLNQMDGFDQ VNV
Sbjct:   246 MVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFDQNVNV 305

Query:    61 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVF-----QMNLSDEVDLEDYVS 115
             KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRL+F     +MNLS+EVDLEDYV+
Sbjct:   306 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDLEDYVA 365

Query:   116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
             RPDKIS A+I +ICQE+GM AVR+NRY++L KDFEK Y+T +KK + + EFYK
Sbjct:   366 RPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK 418

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 = 718 (257.8 bits), Expect = 6.1e-71, P = 6.1e-71
 Identities = 141/173 (81%), Positives = 157/173 (90%)

Query:     1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
             MVRDVFRLAKENAPAIIFIDE+DAIAT RFDAQTGADREVQRIL+ELLNQMDGFDQ VNV
Sbjct:   246 MVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFDQNVNV 305

Query:    61 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVF-----QMNLSDEVDLEDYVS 115
             KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRL+F     +MNLS+EVDLEDYV+
Sbjct:   306 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDLEDYVA 365

Query:   116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
             RPDKIS A+I +ICQE+GM AVR+NRY++L KDFEK Y+T +KK + + EFYK
Sbjct:   366 RPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK 418

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

---

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	0.8372	0.9940	0.4143	yes	no
Q63570	PRS6B_RAT	No assigned EC number	0.8150	1.0	0.4019	yes	no
P33298	PRS6B_YEAST	No assigned EC number	0.7102	1.0	0.3925	yes	no
P85200	PRS6B_HELAN	No assigned EC number	0.9595	1.0	0.4057	N/A	no
Q9SEI4	PRS6B_ARATH	No assigned EC number	0.9653	1.0	0.4117	yes	no
O74894	PRS6B_SCHPO	No assigned EC number	0.7257	1.0	0.4318	yes	no
P54778	PRS6B_SOLTU	No assigned EC number	0.9595	1.0	0.4067	N/A	no
P46502	PRS6B_CAEEL	No assigned EC number	0.8092	1.0	0.4057	yes	no
P54775	PRS6B_MOUSE	No assigned EC number	0.8150	1.0	0.4019	yes	no
Q3T030	PRS6B_BOVIN	No assigned EC number	0.8150	1.0	0.4019	yes	no
P43686	PRS6B_HUMAN	No assigned EC number	0.8150	1.0	0.4019	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!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00023924001	SubName- Full=Chromosome chr6 scaffold_3, whole genome shotgun sequence; (418 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00014791001	SubName- Full=Putative uncharacterized protein (Chromosome chr18 scaffold_1, whole genome shotg [...] (309 aa)				•	•	•	•		0.854
	GSVIVG00010470001	SubName- Full=Chromosome chr17 scaffold_263, whole genome shotgun sequence; (386 aa)				•	•	•	•		0.830
	GSVIVG00036762001	SubName- Full=Chromosome chr4 scaffold_83, whole genome shotgun sequence; (440 aa)				•	•	•	•		0.816
	GSVIVG00024499001	RecName- Full=Proteasome subunit beta type; EC=3.4.25.1;; The proteasome is a multicatalytic pr [...] (245 aa)				•	•	•	•		0.695
	GSVIVG00015634001	SubName- Full=Chromosome chr2 scaffold_11, whole genome shotgun sequence; (365 aa)				•	•	•	•		0.684
	GSVIVG00034204001	RecName- Full=Ubiquitin carboxyl-terminal hydrolase; EC=3.1.2.15; (479 aa)				•	•		•		0.682
	GSVIVG00006696001	SubName- Full=Chromosome chr2 scaffold_176, whole genome shotgun sequence; (267 aa)				•	•	•	•		0.678
	GSVIVG00018640001	SubName- Full=Chromosome chr12 scaffold_18, whole genome shotgun sequence; (629 aa)				•	•	•	•		0.649
	GSVIVG00019352001	SubName- Full=Chromosome chr7 scaffold_20, whole genome shotgun sequence; (320 aa)				•	•	•	•		0.629
	GSVIVG00023752001	SubName- Full=Putative uncharacterized protein (Chromosome chr7 scaffold_31, whole genome shotg [...] (205 aa)				•	•	•	•		0.616

---

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	168
PTZ00454	398	PTZ00454, PTZ00454, 26S protease regulatory subuni	1e-123
COG1222	406	COG1222, RPT1, ATP-dependent 26S proteasome regula	6e-88
PTZ00361	438	PTZ00361, PTZ00361, 26 proteosome regulatory subun	2e-67
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	1e-65
TIGR01242	364	TIGR01242, 26Sp45, 26S proteasome subunit P45 fami	3e-55
TIGR01241	495	TIGR01241, FtsH_fam, ATP-dependent metalloprotease	6e-41
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	9e-38
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	2e-35
CHL00176	638	CHL00176, ftsH, cell division protein; Validated	8e-35
COG0465	596	COG0465, HflB, ATP-dependent Zn proteases [Posttra	3e-33
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	3e-30
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	1e-29
PRK10733	644	PRK10733, hflB, ATP-dependent metalloprotease; Rev	2e-29
TIGR03689	512	TIGR03689, pup_AAA, proteasome ATPase	3e-20
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	3e-19
COG1223	368	COG1223, COG1223, Predicted ATPase (AAA+ superfami	1e-17
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	2e-10
smart00382	148	smart00382, AAA, ATPases associated with a variety	1e-09
CHL00195	489	CHL00195, ycf46, Ycf46; Provisional	2e-07

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

 Score =  351 bits (903), Expect = e-123
 Identities = 148/173 (85%), Positives = 161/173 (93%), Gaps = 5/173 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVRDVFRLA+ENAP+IIFIDEVD+IAT RFDAQTGADREVQRIL+ELLNQMDGFDQT NV
Sbjct: 226 MVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNV 285

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
           KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRL+FQ     MNLS+EVDLED+VS
Sbjct: 286 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSEEVDLEDFVS 345

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFYK 168
           RP+KISAA+IAAICQEAGM AVRKNRYVILPKDFEKGY+T V+K D D++FY 
Sbjct: 346 RPEKISAADIAAICQEAGMQAVRKNRYVILPKDFEKGYKTVVRKTDRDYDFYS 398

Length = 398

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

 Score =  262 bits (672), Expect = 6e-88
 Identities = 93/167 (55%), Positives = 115/167 (68%), Gaps = 5/167 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           +VR++F LA+E AP+IIFIDE+DAI   RFD+ T  DREVQR ++ELLNQ+DGFD   NV
Sbjct: 232 LVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRGNV 291

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
           KVIMATNR D LDPALLRPGR DRKIEFPLPD   +  + +     MNL+D+VDLE    
Sbjct: 292 KVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLAR 351

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDT 162
             +  S A++ AIC EAGM A+R+ R  +  +DF K     VKK   
Sbjct: 352 LTEGFSGADLKAICTEAGMFAIRERRDEVTMEDFLKAVEKVVKKKKK 398

Length = 406

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

 Score =  211 bits (538), Expect = 2e-67
 Identities = 86/157 (54%), Positives = 123/157 (78%), Gaps = 5/157 (3%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           +VR++FR+A+ENAP+I+FIDE+DAI T R+DA +G ++E+QR ++ELLNQ+DGFD   +V
Sbjct: 264 LVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGFDSRGDV 323

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
           KVIMATNR ++LDPAL+RPGR+DRKIEFP PD + KR +F+     M L+++VDLE+++ 
Sbjct: 324 KVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDVDLEEFIM 383

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKG 152
             D++S A+I AIC EAG+ A+R+ R  +   DF K 
Sbjct: 384 AKDELSGADIKAICTEAGLLALRERRMKVTQADFRKA 420

Length = 438

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

 Score =  205 bits (523), Expect = 1e-65
 Identities = 87/169 (51%), Positives = 113/169 (66%), Gaps = 5/169 (2%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           +VR++F LA+E AP+IIFIDE+DAIA  R D+ T  DREVQR LM+LL +MDGFD   NV
Sbjct: 212 LVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPRGNV 271

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
           K+I ATNR D LDPA+LRPGR DR IE PLPD   +  + +     MNL+D+VDLE+   
Sbjct: 272 KIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVDLEELAE 331

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDF 164
             +  S A++ AIC EAGM A+R +R  +  +DF K     + K + D 
Sbjct: 332 LTEGASGADLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKVMGKEEKDS 380

Length = 389

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

 Score =  177 bits (451), Expect = 3e-55
 Identities = 85/156 (54%), Positives = 106/156 (67%), Gaps = 5/156 (3%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           +VR++F LAKE AP+IIFIDE+DAIA  R D+ T  DREVQR LM+LL ++DGFD   NV
Sbjct: 203 LVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRGNV 262

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
           KVI ATNR D LDPALLRPGR DR IE PLPD   +  + +     M L+++VDLE    
Sbjct: 263 KVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVDLEAIAK 322

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
             +  S A++ AIC EAGM A+R+ R  +   DF K
Sbjct: 323 MTEGASGADLKAICTEAGMFAIREERDYVTMDDFIK 358

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

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

 Score =  142 bits (361), Expect = 6e-41
 Identities = 67/155 (43%), Positives = 92/155 (59%), Gaps = 5/155 (3%)

Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           VRD+F  AK+NAP IIFIDE+DA+   R     G + E ++ L +LL +MDGF     V 
Sbjct: 136 VRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTNTGVI 195

Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQM-----NLSDEVDLEDYVSR 116
           VI ATNR D LDPALLRPGR DR++   LPD + +  + ++      L+ +VDL+    R
Sbjct: 196 VIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAPDVDLKAVARR 255

Query: 117 PDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
               S A++A +  EA + A RKN+  I   D E+
Sbjct: 256 TPGFSGADLANLLNEAALLAARKNKTEITMNDIEE 290

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

 Score =  134 bits (339), Expect = 9e-38
 Identities = 68/175 (38%), Positives = 105/175 (60%), Gaps = 13/175 (7%)

Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           +R++F  A++ AP+IIFIDE+D++A+ R       D   +R++ +LL ++DG ++   V 
Sbjct: 324 IRELFEKARKLAPSIIFIDEIDSLASGR---GPSEDGSGRRVVGQLLTELDGIEKAEGVL 380

Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD-------EVDLEDYV 114
           VI ATNR D LDPALLRPGR DR I  PLPD  ++  +F+++L D       +VDLE+  
Sbjct: 381 VIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELA 440

Query: 115 SRPDKISAAEIAAICQEAGMHAVRKN-RYVILPKDFEKGYRTNVKKPDTDFEFYK 168
              +  S A+IAA+ +EA + A+R+  R  +   DF    +    KP   +E +K
Sbjct: 441 EITEGYSGADIAALVREAALEALREARRREVTLDDFLDALKKI--KPSVTYEEWK 493

Length = 494

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

 Score =  129 bits (326), Expect = 2e-35
 Identities = 69/163 (42%), Positives = 97/163 (59%), Gaps = 7/163 (4%)

Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           +R++FR A++ APAIIF DE+DAIA AR            RI+ +LL +MDG  +  NV 
Sbjct: 535 IREIFRKARQAAPAIIFFDEIDAIAPAR--GARFDTSVTDRIVNQLLTEMDGIQELSNVV 592

Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVSR 116
           VI ATNR D LDPALLRPGR DR I  P PD   ++ +F+     M L+++VDLE+    
Sbjct: 593 VIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEM 652

Query: 117 PDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKK 159
            +  + A+I A+C+EA M A+R++      +  E G    +K 
Sbjct: 653 TEGYTGADIEAVCREAAMAALRESIGSPAKEKLEVGEEEFLKD 695

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|214386 CHL00176, ftsH, cell division protein; Validated

 Score =  127 bits (322), Expect = 8e-35
 Identities = 68/156 (43%), Positives = 89/156 (57%), Gaps = 7/156 (4%)

Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           VRD+F+ AKEN+P I+FIDE+DA+   R     G + E ++ L +LL +MDGF     V 
Sbjct: 264 VRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNKGVI 323

Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRL----VFQMN--LSDEVDLEDYVS 115
           VI ATNR D LD ALLRPGR DR+I   LPDR   RL    V   N  LS +V LE    
Sbjct: 324 VIAATNRVDILDAALLRPGRFDRQITVSLPDREG-RLDILKVHARNKKLSPDVSLELIAR 382

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
           R    S A++A +  EA +   R+ +  I  K+ + 
Sbjct: 383 RTPGFSGADLANLLNEAAILTARRKKATITMKEIDT 418

Length = 638

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

 Score =  123 bits (310), Expect = 3e-33
 Identities = 66/155 (42%), Positives = 93/155 (60%), Gaps = 5/155 (3%)

Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           VRD+F  AK+NAP IIFIDE+DA+   R     G + E ++ L +LL +MDGF     V 
Sbjct: 231 VRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGGNEGVI 290

Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQM-----NLSDEVDLEDYVSR 116
           VI ATNR D LDPALLRPGR DR+I   LPD + +  + ++      L+++VDL+     
Sbjct: 291 VIAATNRPDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLAEDVDLKKIARG 350

Query: 117 PDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
               S A++A +  EA + A R+N+  I  +D E+
Sbjct: 351 TPGFSGADLANLLNEAALLAARRNKKEITMRDIEE 385

Length = 596

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

 Score =  106 bits (267), Expect = 3e-30
 Identities = 48/90 (53%), Positives = 64/90 (71%), Gaps = 5/90 (5%)

Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTV-NV 60
           +R++F  AK+ AP +IFIDE+DA+A +R     G D E +R++ +LL ++DGF  ++  V
Sbjct: 46  LRELFEAAKKLAPCVIFIDEIDALAGSRGS---GGDSESRRVVNQLLTELDGFTSSLSKV 102

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPL 90
            VI ATNR D LDPALLR GR DR IEFPL
Sbjct: 103 IVIAATNRPDKLDPALLR-GRFDRIIEFPL 131

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

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

 Score =  113 bits (284), Expect = 1e-29
 Identities = 60/143 (41%), Positives = 90/143 (62%), Gaps = 8/143 (5%)

Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           +R++F+ A+ENAP+IIFIDE+DAIA  R +     ++   R++ +LL  MDG      V 
Sbjct: 260 LREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEK---RVVAQLLTLMDGLKGRGRVI 316

Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVSR 116
           VI ATNR D LDPAL RPGR DR+I   +PD+R ++ + +     M L+++VDL+     
Sbjct: 317 VIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEV 376

Query: 117 PDKISAAEIAAICQEAGMHAVRK 139
                 A++AA+ +EA M A+R+
Sbjct: 377 THGFVGADLAALAKEAAMAALRR 399

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|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed

 Score =  112 bits (281), Expect = 2e-29
 Identities = 62/156 (39%), Positives = 90/156 (57%), Gaps = 5/156 (3%)

Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           VRD+F  AK+ AP IIFIDE+DA+   R     G   E ++ L ++L +MDGF+    + 
Sbjct: 233 VRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGII 292

Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMN-----LSDEVDLEDYVSR 116
           VI ATNR D LDPALLRPGR DR++   LPD R +  + +++     L+ ++D       
Sbjct: 293 VIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARG 352

Query: 117 PDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKG 152
               S A++A +  EA + A R N+ V+   +FEK 
Sbjct: 353 TPGFSGADLANLVNEAALFAARGNKRVVSMVEFEKA 388

Length = 644

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

 Score = 86.3 bits (214), Expect = 3e-20
 Identities = 54/150 (36%), Positives = 85/150 (56%), Gaps = 11/150 (7%)

Query: 2   VRDVFRLAKENA----PAIIFIDEVDAIATARFDAQTGADREVQR-ILMELLNQMDGFDQ 56
           +R +F+ A+E A    P I+F DE+D++   R    +G   +V+  ++ +LL ++DG + 
Sbjct: 274 IRLIFQRAREKASEGRPVIVFFDEMDSLFRTR---GSGVSSDVETTVVPQLLAEIDGVES 330

Query: 57  TVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSDEVDLEDYVSR 116
             NV VI A+NR D +DPA+LRPGRLD KI    PD      +F   L+D++ L + ++ 
Sbjct: 331 LDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFAKYLTDDLPLPEDLAA 390

Query: 117 PDKISAAEIAAICQEA--GMHAVRK-NRYV 143
            D    A  AA+ Q     ++A  + NRYV
Sbjct: 391 HDGDREATAAALIQRVVDALYARSEANRYV 420

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 = 82.9 bits (205), Expect = 3e-19
 Identities = 56/150 (37%), Positives = 80/150 (53%), Gaps = 9/150 (6%)

Query: 3   RDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKV 62
           R++F  A++ AP+IIFIDE+DA+A  R   Q   +R V     +LL  MDG  +   V V
Sbjct: 66  RELFEEAEKLAPSIIFIDEIDALAPKRSSDQGEVERRVVA---QLLALMDGLKR-GQVIV 121

Query: 63  IMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVSRP 117
           I ATNR D LDPA  RPGR DR+IE  LPD   +  + Q     M L      +   +R 
Sbjct: 122 IGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGRLEILQIHTRLMFLGPPGTGKTLAART 181

Query: 118 DKISAAEIAAICQEAGMHAVRKNRYVILPK 147
              S A++ A+ +EA +  +R+   ++   
Sbjct: 182 VGKSGADLGALAKEAALRELRRAIDLVGEY 211

Length = 494

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

 Score = 78.3 bits (193), Expect = 1e-17
 Identities = 46/157 (29%), Positives = 80/157 (50%), Gaps = 10/157 (6%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
            + +++  A++ AP I+FIDE+DAIA  R   +   D  V  I+  LL ++DG  +   V
Sbjct: 198 RIHELYERARKAAPCIVFIDELDAIALDRRYQELRGD--VSEIVNALLTELDGIKENEGV 255

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD-----EVDLEDYVS 115
             I ATNR + LDPA+    R + +IEF LP+  ++  + +          + DL    +
Sbjct: 256 VTIAATNRPELLDPAI--RSRFEEEIEFKLPNDEERLEILEYYAKKFPLPVDADLRYLAA 313

Query: 116 RPDKISAAEIAAICQEAGMH-AVRKNRYVILPKDFEK 151
           +   +S  +I     +  +H A+ ++R  +  +D EK
Sbjct: 314 KTKGMSGRDIKEKVLKTALHRAIAEDREKVEREDIEK 350

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 = 55.6 bits (134), Expect = 2e-10
 Identities = 31/90 (34%), Positives = 44/90 (48%), Gaps = 12/90 (13%)

Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQ-MDGFDQTVNV 60
           VR +F LA++  P ++FIDE+D+++           R  Q  L+ +L    D      NV
Sbjct: 73  VRLLFELAEKAKPGVLFIDEIDSLS-----------RGAQNALLRVLETLNDLRIDRENV 121

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPL 90
           +VI ATNR    D       RLD +I  PL
Sbjct: 122 RVIGATNRPLLGDLDRALYDRLDIRIVIPL 151

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

 Score = 53.5 bits (128), Expect = 1e-09
 Identities = 27/92 (29%), Positives = 44/92 (47%), Gaps = 9/92 (9%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
            +R    LA++  P ++ +DE+ ++          A++E   +L+E L  +       N+
Sbjct: 66  RLRLALALARKLKPDVLILDEITSLL--------DAEQEALLLLLEELRLLLLLKSEKNL 117

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPD 92
            VI+ TN    L PALLR  R DR+I   L  
Sbjct: 118 TVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148

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|177094 CHL00195, ycf46, Ycf46; Provisional

 Score = 48.9 bits (117), Expect = 2e-07
 Identities = 37/148 (25%), Positives = 65/148 (43%), Gaps = 13/148 (8%)

Query: 2   VRDVFRLAKENAPAIIFIDEVD-AIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           +R + R+A+  +P I++IDE+D A + +     +G    V    +  L++     +   V
Sbjct: 307 MRQMIRIAEALSPCILWIDEIDKAFSNSESKGDSGTTNRVLATFITWLSE-----KKSPV 361

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLS-------DEVDLEDY 113
            V+   N  D L   +LR GR D      LP   ++  +F+++L         + D++  
Sbjct: 362 FVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYDIKKL 421

Query: 114 VSRPDKISAAEIAAICQEAGMHAVRKNR 141
               +K S AEI     EA   A  + R
Sbjct: 422 SKLSNKFSGAEIEQSIIEAMYIAFYEKR 449

Length = 489

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	168
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	100.0
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	100.0
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	100.0
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	100.0
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	100.0
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	100.0
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	100.0
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	100.0
KOG0736	953	consensus Peroxisome assembly factor 2 containing	100.0
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	100.0
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	100.0
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	100.0
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	100.0
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	100.0
CHL00195	489	ycf46 Ycf46; Provisional	100.0
PRK03992	389	proteasome-activating nucleotidase; Provisional	100.0
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.98
CHL00206	2281	ycf2 Ycf2; Provisional	99.98
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	99.97
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.97
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.97
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.97
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	99.97
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.97
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	99.97
CHL00176	638	ftsH cell division protein; Validated	99.97
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	99.97
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	99.96
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	99.96
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.94
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	99.94
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	99.94
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	99.93
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	99.93
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	99.93
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.91
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.89
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.8
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	99.75
KOG0736	953	consensus Peroxisome assembly factor 2 containing	99.65
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.63
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	99.55
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	99.55
PF00004	132	AAA: ATPase family associated with various cellula	99.54
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.08
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.07
CHL00181	287	cbbX CbbX; Provisional	99.03
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	98.97
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.95
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.86
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	98.86
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.85
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.84
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	98.83
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	98.77
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	98.75
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	98.75
PRK00149	450	dnaA chromosomal replication initiation protein; R	98.7
PRK06893	229	DNA replication initiation factor; Validated	98.52
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.51
PRK14088	440	dnaA chromosomal replication initiation protein; P	98.47
PRK07940	394	DNA polymerase III subunit delta'; Validated	98.43
PRK10865	857	protein disaggregation chaperone; Provisional	98.42
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	98.41
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	98.41
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	98.35
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	98.34
PRK14087	450	dnaA chromosomal replication initiation protein; P	98.33
CHL00095	821	clpC Clp protease ATP binding subunit	98.32
PRK14086	617	dnaA chromosomal replication initiation protein; P	98.31
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	98.28
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	98.28
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.25
PRK12422	445	chromosomal replication initiation protein; Provis	98.24
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.22
PRK08727	233	hypothetical protein; Validated	98.22
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	98.19
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	98.17
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	98.17
PRK13342	413	recombination factor protein RarA; Reviewed	98.16
PRK08084	235	DNA replication initiation factor; Provisional	98.14
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	98.1
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	98.09
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	98.06
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	98.06
PRK12402	337	replication factor C small subunit 2; Reviewed	98.02
PRK05642	234	DNA replication initiation factor; Validated	98.02
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	98.01
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	98.0
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	98.0
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	97.99
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.98
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	97.96
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	97.96
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	97.94
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	97.94
PRK04195	482	replication factor C large subunit; Provisional	97.91
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.89
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	97.87
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.86
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.85
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	97.84
COG2256	436	MGS1 ATPase related to the helicase subunit of the	97.81
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	97.8
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	97.79
PRK04132	846	replication factor C small subunit; Provisional	97.79
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.79
PRK09087	226	hypothetical protein; Validated	97.79
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	97.78
PRK06620	214	hypothetical protein; Validated	97.77
KOG1514	767	consensus Origin recognition complex, subunit 1, a	97.77
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	97.76
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	97.74
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.74
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.74
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	97.7
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	97.68
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	97.67
COG0593	408	DnaA ATPase involved in DNA replication initiation	97.67
smart00350	509	MCM minichromosome maintenance proteins.	97.66
CHL00195	489	ycf46 Ycf46; Provisional	97.66
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	97.64
PRK06964	342	DNA polymerase III subunit delta'; Validated	97.63
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.62
PRK05707	328	DNA polymerase III subunit delta'; Validated	97.62
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	97.61
PLN03025	319	replication factor C subunit; Provisional	97.59
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	97.58
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	97.57
PRK13341	725	recombination factor protein RarA/unknown domain f	97.56
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.56
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	97.5
PHA02544	316	44 clamp loader, small subunit; Provisional	97.44
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	97.4
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	97.4
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	97.39
PRK09112	351	DNA polymerase III subunit delta'; Validated	97.36
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	97.34
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	97.33
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.32
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	97.32
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	97.28
PRK07471	365	DNA polymerase III subunit delta'; Validated	97.24
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	97.24
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	97.22
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	97.21
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	97.2
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	97.18
PRK08769	319	DNA polymerase III subunit delta'; Validated	97.17
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	97.16
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	97.16
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.16
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.15
COG0714	329	MoxR-like ATPases [General function prediction onl	97.14
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	97.11
PRK07993	334	DNA polymerase III subunit delta'; Validated	97.11
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	97.1
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	97.09
KOG2028	554	consensus ATPase related to the helicase subunit o	97.08
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	97.07
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	97.07
CHL00095	821	clpC Clp protease ATP binding subunit	97.03
PRK06871	325	DNA polymerase III subunit delta'; Validated	97.02
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	96.94
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	96.92
PRK06090	319	DNA polymerase III subunit delta'; Validated	96.88
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	96.85
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	96.83
KOG2680	454	consensus DNA helicase TIP49, TBP-interacting prot	96.82
smart00382	148	AAA ATPases associated with a variety of cellular	96.76
PRK07276	290	DNA polymerase III subunit delta'; Validated	96.75
PRK09862	506	putative ATP-dependent protease; Provisional	96.7
PRK08058	329	DNA polymerase III subunit delta'; Validated	96.62
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	96.55
PRK05564	313	DNA polymerase III subunit delta'; Validated	96.54
PRK07399	314	DNA polymerase III subunit delta'; Validated	96.44
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	96.35
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	96.28
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	96.23
PRK13531	498	regulatory ATPase RavA; Provisional	96.23
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	96.17
PRK10865	857	protein disaggregation chaperone; Provisional	96.14
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	96.01
PRK06581	263	DNA polymerase III subunit delta'; Validated	96.01
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	95.94
COG1067	647	LonB Predicted ATP-dependent protease [Posttransla	95.92
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	95.65
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	95.62
PF05729	166	NACHT: NACHT domain	95.6
KOG1942	456	consensus DNA helicase, TBP-interacting protein [R	95.56
PHA02244	383	ATPase-like protein	95.53
PRK07132	299	DNA polymerase III subunit delta'; Validated	95.52
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	95.48
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	95.36
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	95.28
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	95.28
PRK05917	290	DNA polymerase III subunit delta'; Validated	95.22
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	95.0
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	94.99
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	94.98
PRK05818	261	DNA polymerase III subunit delta'; Validated	94.79
PRK08699	325	DNA polymerase III subunit delta'; Validated	94.59
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	94.48
PRK14700	300	recombination factor protein RarA; Provisional	94.46
PF05872	502	DUF853: Bacterial protein of unknown function (DUF	94.13
PRK08485	206	DNA polymerase III subunit delta'; Validated	94.1
PF14516	331	AAA_35: AAA-like domain	93.93
PRK13765	637	ATP-dependent protease Lon; Provisional	93.93
PF00493	331	MCM: MCM2/3/5 family This family extends the MCM d	93.88
PF12846	304	AAA_10: AAA-like domain	93.54
KOG1969	877	consensus DNA replication checkpoint protein CHL12	93.03
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	91.99
TIGR01128	302	holA DNA polymerase III, delta subunit. subunit ar	91.61
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	91.54
PRK05574	340	holA DNA polymerase III subunit delta; Reviewed	91.12
PRK10365	441	transcriptional regulatory protein ZraR; Provision	90.79
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	90.5
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	89.87
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	89.54
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	89.48
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	89.05
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	88.25
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	87.93
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	87.85
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	87.71
PRK04841	903	transcriptional regulator MalT; Provisional	87.67
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	86.74
TIGR02237	209	recomb_radB DNA repair and recombination protein R	86.65
KOG0478	804	consensus DNA replication licensing factor, MCM4 c	86.51
KOG1968	871	consensus Replication factor C, subunit RFC1 (larg	86.26
PHA00012	361	I assembly protein	85.92
PRK07452	326	DNA polymerase III subunit delta; Validated	85.78
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	84.56
PF13304	303	AAA_21: AAA domain; PDB: 3QKS_B 1US8_B 1F2U_B 1F2T	84.35
PRK15115	444	response regulator GlrR; Provisional	83.99
PRK11608	326	pspF phage shock protein operon transcriptional ac	83.37
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	83.2
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	82.87
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	82.47
PF07726	131	AAA_3: ATPase family associated with various cellu	82.43
PF02969	66	TAF: TATA box binding protein associated factor (T	82.31
PLN03210	1153	Resistant to P. syringae 6; Provisional	82.25
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	81.96
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	81.15
PF00808	65	CBFD_NFYB_HMF: Histone-like transcription factor (	80.53
COG1485	367	Predicted ATPase [General function prediction only	80.29
PF13173	128	AAA_14: AAA domain	80.07
PRK05022	509	anaerobic nitric oxide reductase transcription reg	80.04

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

Probab=100.00  E-value=2.9e-43  Score=274.99  Aligned_cols=160  Identities=58%  Similarity=0.905  Sum_probs=153.4

Q ss_pred             CHHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCC
Q 030960            1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPG   80 (168)
Q Consensus         1 ~l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~g   80 (168)
                      |+|++|+.|+.++||||||||+|+++.+|.+.+.+.+..+++.+-+||++||||....+|-||++||+++-|||||+|||
T Consensus       232 lVRelF~lArekaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~~~nvKVI~ATNR~D~LDPALLRPG  311 (406)
T COG1222         232 LVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRGNVKVIMATNRPDILDPALLRPG  311 (406)
T ss_pred             HHHHHHHHHhhcCCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCCCCCCeEEEEecCCccccChhhcCCC
Confidence            58999999999999999999999999999998888999999999999999999999999999999999999999999999


Q ss_pred             CcceEEecCCCCHHHHHHHHHh-----hcCCCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQM-----NLSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~~-----~l~~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      |||+.|+||+|+.+.|.+||+.     .+.+++||+.+|..|+|+||+||+++|.+|.+.|+|+.+..+|++||..|+++
T Consensus       312 R~DRkIEfplPd~~gR~~Il~IHtrkM~l~~dvd~e~la~~~~g~sGAdlkaictEAGm~AiR~~R~~Vt~~DF~~Av~K  391 (406)
T COG1222         312 RFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLARLTEGFSGADLKAICTEAGMFAIRERRDEVTMEDFLKAVEK  391 (406)
T ss_pred             cccceeecCCCCHHHHHHHHHHHhhhccCccCcCHHHHHHhcCCCchHHHHHHHHHHhHHHHHhccCeecHHHHHHHHHH
Confidence            9999999999999999999984     45579999999999999999999999999999999999999999999999999


Q ss_pred             hcCCC
Q 030960          156 NVKKP  160 (168)
Q Consensus       156 ~~p~~  160 (168)
                      +....
T Consensus       392 V~~~~  396 (406)
T COG1222         392 VVKKK  396 (406)
T ss_pred             HHhcc
Confidence            87754

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

Probab=100.00  E-value=2.7e-39  Score=268.04  Aligned_cols=156  Identities=43%  Similarity=0.665  Sum_probs=144.9

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      |+++|++|++.+||||||||+|+++..|++..+   ....++++++|++|||+...++|+|||+||+|+.||+|++||||
T Consensus       516 ir~iF~kAR~~aP~IiFfDEiDsi~~~R~g~~~---~v~~RVlsqLLtEmDG~e~~k~V~ViAATNRpd~ID~ALlRPGR  592 (693)
T KOG0730|consen  516 IREVFRKARQVAPCIIFFDEIDALAGSRGGSSS---GVTDRVLSQLLTEMDGLEALKNVLVIAATNRPDMIDPALLRPGR  592 (693)
T ss_pred             HHHHHHHHhhcCCeEEehhhHHhHhhccCCCcc---chHHHHHHHHHHHcccccccCcEEEEeccCChhhcCHHHcCCcc
Confidence            789999999999999999999999999974443   45679999999999999999999999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC--CCccCHHHHHHHHH
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN--RYVILPKDFEKGYR  154 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~--~~~i~~~d~~~al~  154 (168)
                      ||+.||||+|+.+.|.+||+.+..     +++++.+||+.|+||||+||..+|++|+..|++++  -..|+++||++|++
T Consensus       593 lD~iiyVplPD~~aR~~Ilk~~~kkmp~~~~vdl~~La~~T~g~SGAel~~lCq~A~~~a~~e~i~a~~i~~~hf~~al~  672 (693)
T KOG0730|consen  593 LDRIIYVPLPDLEARLEILKQCAKKMPFSEDVDLEELAQATEGYSGAEIVAVCQEAALLALRESIEATEITWQHFEEALK  672 (693)
T ss_pred             cceeEeecCccHHHHHHHHHHHHhcCCCCccccHHHHHHHhccCChHHHHHHHHHHHHHHHHHhcccccccHHHHHHHHH
Confidence            999999999999999999996665     68899999999999999999999999999999986  35699999999999


Q ss_pred             hhcCCC
Q 030960          155 TNVKKP  160 (168)
Q Consensus       155 ~~~p~~  160 (168)
                      ..+|+-
T Consensus       673 ~~r~s~  678 (693)
T KOG0730|consen  673 AVRPSL  678 (693)
T ss_pred             hhcccC
Confidence            998865

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

Probab=100.00  E-value=2.9e-37  Score=254.08  Aligned_cols=156  Identities=35%  Similarity=0.616  Sum_probs=141.4

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      +|.+|++|+..+||||||||+|+|++.|+...+.   ...+++|+||++|||+....+|+|||+||+|+-||||++||||
T Consensus       593 VR~vFqRAR~saPCVIFFDEiDaL~p~R~~~~s~---~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDpAiLRPGR  669 (802)
T KOG0733|consen  593 VRQVFQRARASAPCVIFFDEIDALVPRRSDEGSS---VSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDPAILRPGR  669 (802)
T ss_pred             HHHHHHHhhcCCCeEEEecchhhcCcccCCCCch---hHHHHHHHHHHHhcccccccceEEEeecCCCcccchhhcCCCc
Confidence            6899999999999999999999999999766543   3459999999999999999999999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhc-------CCCCCHHHHHhCCC--CCCHHHHHHHHHHHHHHHHHhC------------
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNL-------SDEVDLEDYVSRPD--KISAAEIAAICQEAGMHAVRKN------------  140 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l-------~~~~~~~~la~~t~--g~s~~di~~l~~~a~~~a~~~~------------  140 (168)
                      ||+.+++++|+.++|.+||+...       ..++++++||..+.  ||||+||..+|++|.+.|+++.            
T Consensus       670 lDk~LyV~lPn~~eR~~ILK~~tkn~k~pl~~dVdl~eia~~~~c~gftGADLaaLvreAsi~AL~~~~~~~~~~~~~~~  749 (802)
T KOG0733|consen  670 LDKLLYVGLPNAEERVAILKTITKNTKPPLSSDVDLDEIARNTKCEGFTGADLAALVREASILALRESLFEIDSSEDDVT  749 (802)
T ss_pred             cCceeeecCCCHHHHHHHHHHHhccCCCCCCcccCHHHHhhcccccCCchhhHHHHHHHHHHHHHHHHHhhccccCcccc
Confidence            99999999999999999998544       47899999998876  9999999999999999999873            


Q ss_pred             ----CCccCHHHHHHHHHhhcCCC
Q 030960          141 ----RYVILPKDFEKGYRTNVKKP  160 (168)
Q Consensus       141 ----~~~i~~~d~~~al~~~~p~~  160 (168)
                          ...++..||++|+++++|+-
T Consensus       750 ~~~~~~~~t~~hF~eA~~~i~pSv  773 (802)
T KOG0733|consen  750 VRSSTIIVTYKHFEEAFQRIRPSV  773 (802)
T ss_pred             eeeeeeeecHHHHHHHHHhcCCCc
Confidence                12478889999999999975

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

Probab=100.00  E-value=1.4e-36  Score=247.15  Aligned_cols=154  Identities=36%  Similarity=0.540  Sum_probs=143.4

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      +|++|+.|++.+||||||||+|+++++|......   ..++.++++|.+||++.++.+|+||++||.|+.||+||.||||
T Consensus       385 VRdLF~aAk~~APcIIFIDEiDavG~kR~~~~~~---y~kqTlNQLLvEmDGF~qNeGiIvigATNfpe~LD~AL~RPGR  461 (752)
T KOG0734|consen  385 VRDLFAAAKARAPCIIFIDEIDAVGGKRNPSDQH---YAKQTLNQLLVEMDGFKQNEGIIVIGATNFPEALDKALTRPGR  461 (752)
T ss_pred             HHHHHHHHHhcCCeEEEEechhhhcccCCccHHH---HHHHHHHHHHHHhcCcCcCCceEEEeccCChhhhhHHhcCCCc
Confidence            6899999999999999999999999998443322   5679999999999999999999999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      ||+.|.+|.||...|.+||+.|+.     +++|+.-||.-|.||||+||+|+++.|+..|...+...++.++|+-|-.++
T Consensus       462 FD~~v~Vp~PDv~GR~eIL~~yl~ki~~~~~VD~~iiARGT~GFsGAdLaNlVNqAAlkAa~dga~~VtM~~LE~akDrI  541 (752)
T KOG0734|consen  462 FDRHVTVPLPDVRGRTEILKLYLSKIPLDEDVDPKIIARGTPGFSGADLANLVNQAALKAAVDGAEMVTMKHLEFAKDRI  541 (752)
T ss_pred             cceeEecCCCCcccHHHHHHHHHhcCCcccCCCHhHhccCCCCCchHHHHHHHHHHHHHHHhcCcccccHHHHhhhhhhe
Confidence            999999999999999999998876     589999999999999999999999999999999999999999999998776


Q ss_pred             cC
Q 030960          157 VK  158 (168)
Q Consensus       157 ~p  158 (168)
                      .-
T Consensus       542 lM  543 (752)
T KOG0734|consen  542 LM  543 (752)
T ss_pred             ee
Confidence            53

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

Probab=100.00  E-value=6.9e-36  Score=225.28  Aligned_cols=168  Identities=88%  Similarity=1.274  Sum_probs=162.3

Q ss_pred             CHHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCC
Q 030960            1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPG   80 (168)
Q Consensus         1 ~l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~g   80 (168)
                      |++++|..|++++|+||||||+|+++.+|-+...+.+...++++-++|++||++.+..+|-||++||+.+.+|||++|||
T Consensus       236 mvrdvfrlakenapsiifideidaiatkrfdaqtgadrevqril~ellnqmdgfdq~~nvkvimatnradtldpallrpg  315 (408)
T KOG0727|consen  236 MVRDVFRLAKENAPSIIFIDEIDAIATKRFDAQTGADREVQRILIELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPG  315 (408)
T ss_pred             HHHHHHHHHhccCCcEEEeehhhhHhhhhccccccccHHHHHHHHHHHHhccCcCcccceEEEEecCcccccCHhhcCCc
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcceEEecCCCCHHHHHHHHH-----hhcCCCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~-----~~l~~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      |+|++|+||+|+.-++.-+|.     +.+.+++|++.+..+.+..|++||.++|++|.+.|++.++..+.+.||+++++.
T Consensus       316 rldrkiefplpdrrqkrlvf~titskm~ls~~vdle~~v~rpdkis~adi~aicqeagm~avr~nryvvl~kd~e~ay~~  395 (408)
T KOG0727|consen  316 RLDRKIEFPLPDRRQKRLVFSTITSKMNLSDEVDLEDLVARPDKISGADINAICQEAGMLAVRENRYVVLQKDFEKAYKT  395 (408)
T ss_pred             cccccccCCCCchhhhhhhHHhhhhcccCCcccCHHHHhcCccccchhhHHHHHHHHhHHHHHhcceeeeHHHHHHHHHh
Confidence            999999999999999998886     667789999999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCCcccccC
Q 030960          156 NVKKPDTDFEFYK  168 (168)
Q Consensus       156 ~~p~~~~~~~~~k  168 (168)
                      .......++++||
T Consensus       396 ~vk~~~~~~~fyk  408 (408)
T KOG0727|consen  396 VVKKDETQFEFYK  408 (408)
T ss_pred             hcCCcccchhccC
Confidence            9999999999997

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

Probab=100.00  E-value=3.3e-36  Score=237.32  Aligned_cols=163  Identities=37%  Similarity=0.587  Sum_probs=145.5

Q ss_pred             CHHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCC----CCeEEEEecCCCCCCCccc
Q 030960            1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQT----VNVKVIMATNRADTLDPAL   76 (168)
Q Consensus         1 ~l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~----~~v~vi~ttn~~~~ld~al   76 (168)
                      |+|-+|+.|+.++|++|||||||+|+..|++.  +.+...+++.++||.+|||+..+    +-|+|+|+||.||+||.|+
T Consensus       292 lvRlLFemARfyAPStIFiDEIDslcs~RG~s--~EHEaSRRvKsELLvQmDG~~~t~e~~k~VmVLAATN~PWdiDEAl  369 (491)
T KOG0738|consen  292 LVRLLFEMARFYAPSTIFIDEIDSLCSQRGGS--SEHEASRRVKSELLVQMDGVQGTLENSKVVMVLAATNFPWDIDEAL  369 (491)
T ss_pred             HHHHHHHHHHHhCCceeehhhHHHHHhcCCCc--cchhHHHHHHHHHHHHhhccccccccceeEEEEeccCCCcchHHHH
Confidence            57899999999999999999999999999655  45666789999999999998532    2399999999999999999


Q ss_pred             cCCCCcceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC-----------
Q 030960           77 LRPGRLDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN-----------  140 (168)
Q Consensus        77 ~r~grf~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~-----------  140 (168)
                      +|  ||.+.|+||+|+.+.|..+++.++.     ++++++.+|+.++||||+||.++|++|.+.+.|+.           
T Consensus       370 rR--RlEKRIyIPLP~~~~R~~Li~~~l~~~~~~~~~~~~~lae~~eGySGaDI~nvCreAsm~~mRR~i~g~~~~ei~~  447 (491)
T KOG0738|consen  370 RR--RLEKRIYIPLPDAEARSALIKILLRSVELDDPVNLEDLAERSEGYSGADITNVCREASMMAMRRKIAGLTPREIRQ  447 (491)
T ss_pred             HH--HHhhheeeeCCCHHHHHHHHHHhhccccCCCCccHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHhcCCcHHhhh
Confidence            99  9999999999999999999998776     58899999999999999999999999999999862           


Q ss_pred             ------CCccCHHHHHHHHHhhcCCCC-Cccccc
Q 030960          141 ------RYVILPKDFEKGYRTNVKKPD-TDFEFY  167 (168)
Q Consensus       141 ------~~~i~~~d~~~al~~~~p~~~-~~~~~~  167 (168)
                            +.+++..||+.|++++.|+.. ..++.|
T Consensus       448 lakE~~~~pv~~~Dfe~Al~~v~pSvs~~d~~k~  481 (491)
T KOG0738|consen  448 LAKEEPKMPVTNEDFEEALRKVRPSVSAADLEKY  481 (491)
T ss_pred             hhhhccccccchhhHHHHHHHcCcCCCHHHHHHH
Confidence                  247999999999999999876 455444

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

Probab=100.00  E-value=1.2e-34  Score=218.39  Aligned_cols=159  Identities=48%  Similarity=0.830  Sum_probs=149.9

Q ss_pred             CHHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCC
Q 030960            1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPG   80 (168)
Q Consensus         1 ~l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~g   80 (168)
                      |++++|-.|+.++|+|||+||+|+++..|...+++.++..++..-++|+++|++..++++-||++||+++-+|||++|||
T Consensus       228 mvrelfvmarehapsiifmdeidsigs~r~e~~~ggdsevqrtmlellnqldgfeatknikvimatnridild~allrpg  307 (404)
T KOG0728|consen  228 MVRELFVMAREHAPSIIFMDEIDSIGSSRVESGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDILDPALLRPG  307 (404)
T ss_pred             HHHHHHHHHHhcCCceEeeecccccccccccCCCCccHHHHHHHHHHHHhccccccccceEEEEeccccccccHhhcCCC
Confidence            57999999999999999999999999999888888888999999999999999999999999999999999999999999


Q ss_pred             CcceEEecCCCCHHHHHHHHHhh-----cCCCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQMN-----LSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~~~-----l~~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      |+|+.|+||+|+.+.|.+|++.+     +...+++..+|+..+|.||++++.+|.+|.+.|+++.+..+|++||+-|..+
T Consensus       308 ridrkiefp~p~e~ar~~ilkihsrkmnl~rgi~l~kiaekm~gasgaevk~vcteagm~alrerrvhvtqedfemav~k  387 (404)
T KOG0728|consen  308 RIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAEKMPGASGAEVKGVCTEAGMYALRERRVHVTQEDFEMAVAK  387 (404)
T ss_pred             cccccccCCCCCHHHHHHHHHHhhhhhchhcccCHHHHHHhCCCCccchhhhhhhhhhHHHHHHhhccccHHHHHHHHHH
Confidence            99999999999999999999844     4468999999999999999999999999999999999999999999999987


Q ss_pred             hcCC
Q 030960          156 NVKK  159 (168)
Q Consensus       156 ~~p~  159 (168)
                      +...
T Consensus       388 vm~k  391 (404)
T KOG0728|consen  388 VMQK  391 (404)
T ss_pred             HHhc
Confidence            6653

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

Probab=100.00  E-value=4e-34  Score=232.31  Aligned_cols=166  Identities=87%  Similarity=1.298  Sum_probs=152.6

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++++|..|+..+||||||||+|.++..|.+...+.+....+++..++++++++....+++||++||+++.||++++||||
T Consensus       227 lr~lf~~A~~~~P~ILfIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~~ld~~~~~~~v~VI~aTN~~d~LDpAllR~GR  306 (398)
T PTZ00454        227 VRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGR  306 (398)
T ss_pred             HHHHHHHHHhcCCeEEEEECHhhhccccccccCCccHHHHHHHHHHHHHhhccCCCCCEEEEEecCCchhCCHHHcCCCc
Confidence            67899999999999999999999998886555555666778999999999999888899999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      ||+.|+|++|+.++|..||+.++.     .++++.+++..|+||||+||.++|++|.+.|++++...|+.+||.+|++++
T Consensus       307 fd~~I~~~~P~~~~R~~Il~~~~~~~~l~~dvd~~~la~~t~g~sgaDI~~l~~eA~~~A~r~~~~~i~~~df~~A~~~v  386 (398)
T PTZ00454        307 LDRKIEFPLPDRRQKRLIFQTITSKMNLSEEVDLEDFVSRPEKISAADIAAICQEAGMQAVRKNRYVILPKDFEKGYKTV  386 (398)
T ss_pred             ccEEEEeCCcCHHHHHHHHHHHHhcCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHH
Confidence            999999999999999999996655     578999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCccccc
Q 030960          157 VKKPDTDFEFY  167 (168)
Q Consensus       157 ~p~~~~~~~~~  167 (168)
                      .......+.||
T Consensus       387 ~~~~~~~~~~~  397 (398)
T PTZ00454        387 VRKTDRDYDFY  397 (398)
T ss_pred             Hhccccchhcc
Confidence            88777778777

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

Probab=100.00  E-value=2e-34  Score=242.11  Aligned_cols=158  Identities=33%  Similarity=0.555  Sum_probs=141.4

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC--CCCCeEEEEecCCCCCCCccccCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD--QTVNVKVIMATNRADTLDPALLRP   79 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~--~~~~v~vi~ttn~~~~ld~al~r~   79 (168)
                      +|++|++||..+||||||||+|+++++|+.++ .+...+.++++++|.+||++.  ....|+|||+||+|+.|||||+||
T Consensus       753 VR~VFerAR~A~PCVIFFDELDSlAP~RG~sG-DSGGVMDRVVSQLLAELDgls~~~s~~VFViGATNRPDLLDpALLRP  831 (953)
T KOG0736|consen  753 VREVFERARSAAPCVIFFDELDSLAPNRGRSG-DSGGVMDRVVSQLLAELDGLSDSSSQDVFVIGATNRPDLLDPALLRP  831 (953)
T ss_pred             HHHHHHHhhccCCeEEEeccccccCccCCCCC-CccccHHHHHHHHHHHhhcccCCCCCceEEEecCCCccccChhhcCC
Confidence            79999999999999999999999999996544 556678899999999999996  466899999999999999999999


Q ss_pred             CCcceEEecCCC-CHHHHHHHHH-----hhcCCCCCHHHHHhCC-CCCCHHHHHHHHHHHHHHHHHhC------------
Q 030960           80 GRLDRKIEFPLP-DRRQKRLVFQ-----MNLSDEVDLEDYVSRP-DKISAAEIAAICQEAGMHAVRKN------------  140 (168)
Q Consensus        80 grf~~~i~~~~P-~~~~R~~il~-----~~l~~~~~~~~la~~t-~g~s~~di~~l~~~a~~~a~~~~------------  140 (168)
                      ||||+.+|++++ +.+.+..+++     ..+++++++.++|+.+ +.|||+|+.++|.+|.+.|++|.            
T Consensus       832 GRFDKLvyvG~~~d~esk~~vL~AlTrkFkLdedVdL~eiAk~cp~~~TGADlYsLCSdA~l~AikR~i~~ie~g~~~~~  911 (953)
T KOG0736|consen  832 GRFDKLVYVGPNEDAESKLRVLEALTRKFKLDEDVDLVEIAKKCPPNMTGADLYSLCSDAMLAAIKRTIHDIESGTISEE  911 (953)
T ss_pred             CccceeEEecCCccHHHHHHHHHHHHHHccCCCCcCHHHHHhhCCcCCchhHHHHHHHHHHHHHHHHHHHHhhhcccccc
Confidence            999999999988 5566778886     5667899999999998 46999999999999999999883            


Q ss_pred             -----CCccCHHHHHHHHHhhcCCC
Q 030960          141 -----RYVILPKDFEKGYRTNVKKP  160 (168)
Q Consensus       141 -----~~~i~~~d~~~al~~~~p~~  160 (168)
                           .-.++++||.+++++.+|+-
T Consensus       912 e~~~~~v~V~~eDflks~~~l~PSv  936 (953)
T KOG0736|consen  912 EQESSSVRVTMEDFLKSAKRLQPSV  936 (953)
T ss_pred             ccCCceEEEEHHHHHHHHHhcCCcc
Confidence                 13689999999999999975

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

Probab=100.00  E-value=9.3e-34  Score=214.63  Aligned_cols=167  Identities=50%  Similarity=0.826  Sum_probs=158.0

Q ss_pred             CHHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCC
Q 030960            1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPG   80 (168)
Q Consensus         1 ~l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~g   80 (168)
                      ++|..|..|+..+|+||||||+|+++.+|-++....+..+++..-++|+++|++.++..|-||++||+.+-+|||++|.|
T Consensus       252 LVRDAFaLAKEkaP~IIFIDElDAIGtKRfDSek~GDREVQRTMLELLNQLDGFss~~~vKviAATNRvDiLDPALlRSG  331 (424)
T KOG0652|consen  252 LVRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSSDDRVKVIAATNRVDILDPALLRSG  331 (424)
T ss_pred             HHHHHHHHhhccCCeEEEEechhhhccccccccccccHHHHHHHHHHHHhhcCCCCccceEEEeecccccccCHHHhhcc
Confidence            57899999999999999999999999999888888889999999999999999999999999999999999999999999


Q ss_pred             CcceEEecCCCCHHHHHHHHHhh-----cCCCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQMN-----LSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~~~-----l~~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      |+|++|+||.|+.+.|.+|++.+     ..++++|+++|..|++|.|++++.+|-+|.+.|++++...++.+||.++|.+
T Consensus       332 RLDRKIEfP~Pne~aRarIlQIHsRKMnv~~DvNfeELaRsTddFNGAQcKAVcVEAGMiALRr~atev~heDfmegI~e  411 (424)
T KOG0652|consen  332 RLDRKIEFPHPNEEARARILQIHSRKMNVSDDVNFEELARSTDDFNGAQCKAVCVEAGMIALRRGATEVTHEDFMEGILE  411 (424)
T ss_pred             cccccccCCCCChHHHHHHHHHhhhhcCCCCCCCHHHHhhcccccCchhheeeehhhhHHHHhcccccccHHHHHHHHHH
Confidence            99999999999999999999844     4479999999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCCccccc
Q 030960          156 NVKKPDTDFEFY  167 (168)
Q Consensus       156 ~~p~~~~~~~~~  167 (168)
                      ++...+..+.+|
T Consensus       412 VqakKka~l~yy  423 (424)
T KOG0652|consen  412 VQAKKKASLNYY  423 (424)
T ss_pred             HHHhhhhccccc
Confidence            888777777766

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

Probab=100.00  E-value=2.8e-33  Score=237.50  Aligned_cols=156  Identities=44%  Similarity=0.698  Sum_probs=143.7

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccC-CCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFD-AQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPG   80 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~-~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~g   80 (168)
                      ++++|..|+.++||||||||+|+++..|++ .....+...+..++++|.+||++..+.+|+|+|+||+++.+|+|++|||
T Consensus       392 vr~lf~~ar~~aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~~~~~vi~~a~tnr~d~ld~allrpG  471 (774)
T KOG0731|consen  392 VRDLFPLARKNAPSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGFETSKGVIVLAATNRPDILDPALLRPG  471 (774)
T ss_pred             HHHHHHHhhccCCeEEEecccccccccccccccCCCChHHHHHHHHHHHHhcCCcCCCcEEEEeccCCccccCHHhcCCC
Confidence            689999999999999999999999999942 3334555667999999999999998889999999999999999999999


Q ss_pred             CcceEEecCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      |||+.|++++|+..+|.+|++.|+.      +++++..+|.+|+||||+||.++|++|+..|++++...|+..||+.|++
T Consensus       472 Rfdr~i~i~~p~~~~r~~i~~~h~~~~~~~~e~~dl~~~a~~t~gf~gadl~n~~neaa~~a~r~~~~~i~~~~~~~a~~  551 (774)
T KOG0731|consen  472 RFDRQIQIDLPDVKGRASILKVHLRKKKLDDEDVDLSKLASLTPGFSGADLANLCNEAALLAARKGLREIGTKDLEYAIE  551 (774)
T ss_pred             ccccceeccCCchhhhHHHHHHHhhccCCCcchhhHHHHHhcCCCCcHHHHHhhhhHHHHHHHHhccCccchhhHHHHHH
Confidence            9999999999999999999997776      4678888999999999999999999999999999999999999999999


Q ss_pred             hhc
Q 030960          155 TNV  157 (168)
Q Consensus       155 ~~~  157 (168)
                      +..
T Consensus       552 Rvi  554 (774)
T KOG0731|consen  552 RVI  554 (774)
T ss_pred             HHh
Confidence            654

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

Probab=100.00  E-value=1.7e-33  Score=215.65  Aligned_cols=161  Identities=54%  Similarity=0.945  Sum_probs=151.6

Q ss_pred             CHHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCC
Q 030960            1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPG   80 (168)
Q Consensus         1 ~l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~g   80 (168)
                      ++|++|+.|..++|+|+||||||+++.+|-+++++....+++..-++|+++|+|.....|-||++||+++.|||||+|||
T Consensus       266 lvRqlF~vA~e~apSIvFiDEIdAiGtKRyds~SggerEiQrtmLELLNQldGFdsrgDvKvimATnrie~LDPaLiRPG  345 (440)
T KOG0726|consen  266 LVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPG  345 (440)
T ss_pred             HHHHHHHHHHhcCCceEEeehhhhhccccccCCCccHHHHHHHHHHHHHhccCccccCCeEEEEecccccccCHhhcCCC
Confidence            57999999999999999999999999999888888999999999999999999999989999999999999999999999


Q ss_pred             CcceEEecCCCCHHHHHHHHH-----hhcCCCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~-----~~l~~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      |+|+.|+|+.|+...+..||.     +-+.++++++++...-+.+||+||+++|.+|.+.|+|+.+..++.+||..|.++
T Consensus       346 rIDrKIef~~pDe~TkkkIf~IHTs~Mtl~~dVnle~li~~kddlSGAdIkAictEaGllAlRerRm~vt~~DF~ka~e~  425 (440)
T KOG0726|consen  346 RIDRKIEFPLPDEKTKKKIFQIHTSRMTLAEDVNLEELIMTKDDLSGADIKAICTEAGLLALRERRMKVTMEDFKKAKEK  425 (440)
T ss_pred             ccccccccCCCchhhhceeEEEeecccchhccccHHHHhhcccccccccHHHHHHHHhHHHHHHHHhhccHHHHHHHHHH
Confidence            999999999999999999997     556689999999999999999999999999999999999999999999999998


Q ss_pred             hcCCCC
Q 030960          156 NVKKPD  161 (168)
Q Consensus       156 ~~p~~~  161 (168)
                      +.-+.+
T Consensus       426 V~~~K~  431 (440)
T KOG0726|consen  426 VLYKKK  431 (440)
T ss_pred             HHHhcc
Confidence            765443

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

Probab=100.00  E-value=4.2e-33  Score=232.53  Aligned_cols=157  Identities=41%  Similarity=0.647  Sum_probs=146.8

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      +|++|..|++++||||||||+|+++..|+....+.+...++.++++|.+||++..+.+|+||++||+|+-+|+||+||||
T Consensus       231 VRdLF~qAkk~aP~IIFIDEiDAvGr~Rg~g~GggnderEQTLNQlLvEmDGF~~~~gviviaaTNRpdVlD~ALlRpgR  310 (596)
T COG0465         231 VRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGGNEGVIVIAATNRPDVLDPALLRPGR  310 (596)
T ss_pred             HHHHHHHhhccCCCeEEEehhhhcccccCCCCCCCchHHHHHHHHHHhhhccCCCCCceEEEecCCCcccchHhhcCCCC
Confidence            68999999999999999999999999997666666667789999999999999988899999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      ||+.|.++.||...|++|++.+..     +++++..+|..|+||||+|+++++++|+..++++++..++..||.+|+.++
T Consensus       311 FDRqI~V~~PDi~gRe~IlkvH~~~~~l~~~Vdl~~iAr~tpGfsGAdL~nl~NEAal~aar~n~~~i~~~~i~ea~drv  390 (596)
T COG0465         311 FDRQILVELPDIKGREQILKVHAKNKPLAEDVDLKKIARGTPGFSGADLANLLNEAALLAARRNKKEITMRDIEEAIDRV  390 (596)
T ss_pred             cceeeecCCcchhhHHHHHHHHhhcCCCCCcCCHHHHhhhCCCcccchHhhhHHHHHHHHHHhcCeeEeccchHHHHHHH
Confidence            999999999999999999994443     689999999999999999999999999999999999999999999999987


Q ss_pred             cC
Q 030960          157 VK  158 (168)
Q Consensus       157 ~p  158 (168)
                      .-
T Consensus       391 ~~  392 (596)
T COG0465         391 IA  392 (596)
T ss_pred             hc
Confidence            63

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

Probab=100.00  E-value=3e-33  Score=230.54  Aligned_cols=135  Identities=39%  Similarity=0.655  Sum_probs=122.7

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCC----CCeEEEEecCCCCCCCcccc
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQT----VNVKVIMATNRADTLDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~----~~v~vi~ttn~~~~ld~al~   77 (168)
                      |+++|+.|+.++|||+||||||++.++|...+...   .++++.+||+.||++...    .+|+|||+||+|+.|||+|+
T Consensus       271 iRelF~~A~~~aPcivFiDeIDAI~pkRe~aqreM---ErRiVaQLlt~mD~l~~~~~~g~~VlVIgATnRPDslDpaLR  347 (802)
T KOG0733|consen  271 IRELFDQAKSNAPCIVFIDEIDAITPKREEAQREM---ERRIVAQLLTSMDELSNEKTKGDPVLVIGATNRPDSLDPALR  347 (802)
T ss_pred             HHHHHHHHhccCCeEEEeecccccccchhhHHHHH---HHHHHHHHHHhhhcccccccCCCCeEEEecCCCCcccCHHHh
Confidence            78999999999999999999999999996544333   349999999999998433    57999999999999999999


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHh-----hcCCCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHh
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQM-----NLSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRK  139 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~-----~l~~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~  139 (168)
                      |+||||+.|.++.|+..+|.+||+.     .+..++++.+||..|+||.|+||.++|.+|+..|+++
T Consensus       348 RaGRFdrEI~l~vP~e~aR~~IL~~~~~~lrl~g~~d~~qlA~lTPGfVGADL~AL~~~Aa~vAikR  414 (802)
T KOG0733|consen  348 RAGRFDREICLGVPSETAREEILRIICRGLRLSGDFDFKQLAKLTPGFVGADLMALCREAAFVAIKR  414 (802)
T ss_pred             ccccccceeeecCCchHHHHHHHHHHHhhCCCCCCcCHHHHHhcCCCccchhHHHHHHHHHHHHHHH
Confidence            9999999999999999999999984     3447899999999999999999999999999999988

>CHL00195 ycf46 Ycf46; Provisional

Probab=100.00  E-value=6e-32  Score=224.05  Aligned_cols=159  Identities=24%  Similarity=0.368  Sum_probs=139.7

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++++|+.|+..+||||||||+|.++.++...  +.+....++++.|++++++  ...+|+||||||+++.||++++||||
T Consensus       307 l~~~f~~A~~~~P~IL~IDEID~~~~~~~~~--~d~~~~~rvl~~lL~~l~~--~~~~V~vIaTTN~~~~Ld~allR~GR  382 (489)
T CHL00195        307 MRQMIRIAEALSPCILWIDEIDKAFSNSESK--GDSGTTNRVLATFITWLSE--KKSPVFVVATANNIDLLPLEILRKGR  382 (489)
T ss_pred             HHHHHHHHHhcCCcEEEehhhhhhhccccCC--CCchHHHHHHHHHHHHHhc--CCCceEEEEecCChhhCCHHHhCCCc
Confidence            6889999999999999999999998765322  2334556899999999984  55689999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcCC-------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLSD-------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~~-------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      ||..+++++|+.++|.+||+.++..       +.+++.+|+.|+||||+||+++|.+|+..|..++ ..++.+||..|++
T Consensus       383 FD~~i~v~lP~~~eR~~Il~~~l~~~~~~~~~~~dl~~La~~T~GfSGAdI~~lv~eA~~~A~~~~-~~lt~~dl~~a~~  461 (489)
T CHL00195        383 FDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYDIKKLSKLSNKFSGAEIEQSIIEAMYIAFYEK-REFTTDDILLALK  461 (489)
T ss_pred             CCeEEEeCCcCHHHHHHHHHHHHhhcCCCcccccCHHHHHhhcCCCCHHHHHHHHHHHHHHHHHcC-CCcCHHHHHHHHH
Confidence            9999999999999999999977752       6789999999999999999999999999998875 4689999999999


Q ss_pred             hhcCCCCCccc
Q 030960          155 TNVKKPDTDFE  165 (168)
Q Consensus       155 ~~~p~~~~~~~  165 (168)
                      ++.|.+..+.+
T Consensus       462 ~~~Pls~~~~e  472 (489)
T CHL00195        462 QFIPLAQTEKE  472 (489)
T ss_pred             hcCCCcccCHH
Confidence            99998765543

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=100.00  E-value=1.1e-31  Score=218.20  Aligned_cols=162  Identities=52%  Similarity=0.824  Sum_probs=147.6

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|+.|+..+||||||||+|.++..+.+.....+....+.+..++..++++....++.||+|||+++.+|++++||||
T Consensus       213 i~~~f~~a~~~~p~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~~~~~~~v~VI~aTn~~~~ld~allRpgR  292 (389)
T PRK03992        213 VRELFELAREKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGR  292 (389)
T ss_pred             HHHHHHHHHhcCCeEEEEechhhhhcccccCCCCccHHHHHHHHHHHHhccccCCCCCEEEEEecCChhhCCHHHcCCcc
Confidence            67899999999999999999999998886655555566778888999999998887899999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      ||..|+|++|+.++|.+||+.++.     .++++..+|..|+||||+||.++|++|++.|++++...|+.+||.+|++.+
T Consensus       293 fd~~I~v~~P~~~~R~~Il~~~~~~~~~~~~~~~~~la~~t~g~sgadl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~  372 (389)
T PRK03992        293 FDRIIEVPLPDEEGRLEILKIHTRKMNLADDVDLEELAELTEGASGADLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKV  372 (389)
T ss_pred             CceEEEECCCCHHHHHHHHHHHhccCCCCCcCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence            999999999999999999997655     468999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCc
Q 030960          157 VKKPDTD  163 (168)
Q Consensus       157 ~p~~~~~  163 (168)
                      +++..+.
T Consensus       373 ~~~~~~~  379 (389)
T PRK03992        373 MGKEEKD  379 (389)
T ss_pred             hcccccc
Confidence            9876554

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

Probab=99.98  E-value=6.9e-32  Score=225.62  Aligned_cols=157  Identities=40%  Similarity=0.681  Sum_probs=145.5

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      |+.+|..|++.+||||||||+|++++.|+....+..   .+++++++.+++++....+|+||++||+|+.+|+|++||||
T Consensus       324 ir~~F~~A~~~~p~iiFiDEiDs~~~~r~~~~~~~~---~r~~~~lL~~~d~~e~~~~v~vi~aTN~p~~ld~a~lR~gR  400 (494)
T COG0464         324 IRELFEKARKLAPSIIFIDEIDSLASGRGPSEDGSG---RRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGR  400 (494)
T ss_pred             HHHHHHHHHcCCCcEEEEEchhhhhccCCCCCchHH---HHHHHHHHHHhcCCCccCceEEEecCCCccccCHhhcccCc
Confidence            789999999999999999999999999865554433   59999999999999999999999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC-CCccCHHHHHHHH
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN-RYVILPKDFEKGY  153 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~-~~~i~~~d~~~al  153 (168)
                      ||..++|++|+.++|.+||+.++.       .++++..+++.|+||||+||..+|++|++.++++. ...++.+||..|+
T Consensus       401 fd~~i~v~~pd~~~r~~i~~~~~~~~~~~~~~~~~~~~l~~~t~~~sgadi~~i~~ea~~~~~~~~~~~~~~~~~~~~a~  480 (494)
T COG0464         401 FDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALVREAALEALREARRREVTLDDFLDAL  480 (494)
T ss_pred             cceEeecCCCCHHHHHHHHHHHhcccCCcchhhhhHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHhccCCccHHHHHHHH
Confidence            999999999999999999998877       36889999999999999999999999999999998 7789999999999


Q ss_pred             HhhcCCCC
Q 030960          154 RTNVKKPD  161 (168)
Q Consensus       154 ~~~~p~~~  161 (168)
                      ++..|+-.
T Consensus       481 ~~~~p~~~  488 (494)
T COG0464         481 KKIKPSVT  488 (494)
T ss_pred             HhcCCCCC
Confidence            99888754

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.98  E-value=1e-31  Score=242.13  Aligned_cols=150  Identities=22%  Similarity=0.263  Sum_probs=131.3

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC---CCCCeEEEEecCCCCCCCccccC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD---QTVNVKVIMATNRADTLDPALLR   78 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~---~~~~v~vi~ttn~~~~ld~al~r   78 (168)
                      |+.+|+.|++++||||||||||+++.+.      ..   ...++.+++.|++..   ...+|+||||||+|+.|||||+|
T Consensus      1721 Ir~lFelARk~SPCIIFIDEIDaL~~~d------s~---~ltL~qLLneLDg~~~~~s~~~VIVIAATNRPD~LDPALLR 1791 (2281)
T CHL00206       1721 ITLQFELAKAMSPCIIWIPNIHDLNVNE------SN---YLSLGLLVNSLSRDCERCSTRNILVIASTHIPQKVDPALIA 1791 (2281)
T ss_pred             HHHHHHHHHHCCCeEEEEEchhhcCCCc------cc---eehHHHHHHHhccccccCCCCCEEEEEeCCCcccCCHhHcC
Confidence            6789999999999999999999998652      00   134788899998763   45689999999999999999999


Q ss_pred             CCCcceEEecCCCCHHHHHHHHHh-------hcCC-CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHH
Q 030960           79 PGRLDRKIEFPLPDRRQKRLVFQM-------NLSD-EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFE  150 (168)
Q Consensus        79 ~grf~~~i~~~~P~~~~R~~il~~-------~l~~-~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~  150 (168)
                      |||||+.|+|+.|+..+|++++..       ++.+ .++++.+|..|.|||||||+++|++|+..|+++++..|+.++|.
T Consensus      1792 PGRFDR~I~Ir~Pd~p~R~kiL~ILl~tkg~~L~~~~vdl~~LA~~T~GfSGADLanLvNEAaliAirq~ks~Id~~~I~ 1871 (2281)
T CHL00206       1792 PNKLNTCIKIRRLLIPQQRKHFFTLSYTRGFHLEKKMFHTNGFGSITMGSNARDLVALTNEALSISITQKKSIIDTNTIR 1871 (2281)
T ss_pred             CCCCCeEEEeCCCCchhHHHHHHHHHhhcCCCCCcccccHHHHHHhCCCCCHHHHHHHHHHHHHHHHHcCCCccCHHHHH
Confidence            999999999999999999998863       2333 36899999999999999999999999999999999999999999


Q ss_pred             HHHHhhcCCC
Q 030960          151 KGYRTNVKKP  160 (168)
Q Consensus       151 ~al~~~~p~~  160 (168)
                      .|+.++.+..
T Consensus      1872 ~Al~Rq~~g~ 1881 (2281)
T CHL00206       1872 SALHRQTWDL 1881 (2281)
T ss_pred             HHHHHHHhhh
Confidence            9999887644

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

Probab=99.97  E-value=1.1e-32  Score=211.61  Aligned_cols=155  Identities=33%  Similarity=0.557  Sum_probs=140.5

Q ss_pred             CHHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC-CCCCCeEEEEecCCCCCCCccccCC
Q 030960            1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF-DQTVNVKVIMATNRADTLDPALLRP   79 (168)
Q Consensus         1 ~l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~-~~~~~v~vi~ttn~~~~ld~al~r~   79 (168)
                      |++.+|+.|+++.|+||||||+|++++.|+.+++..   .+++..+||.+|+++ ..+.+|+|+++||.||.||.|++| 
T Consensus       213 LVknLFemARe~kPSIIFiDEiDslcg~r~enEsea---sRRIKTEfLVQMqGVG~d~~gvLVLgATNiPw~LDsAIRR-  288 (439)
T KOG0739|consen  213 LVKNLFEMARENKPSIIFIDEIDSLCGSRSENESEA---SRRIKTEFLVQMQGVGNDNDGVLVLGATNIPWVLDSAIRR-  288 (439)
T ss_pred             HHHHHHHHHHhcCCcEEEeehhhhhccCCCCCchHH---HHHHHHHHHHhhhccccCCCceEEEecCCCchhHHHHHHH-
Confidence            578999999999999999999999999886655544   459999999999998 556789999999999999999999 


Q ss_pred             CCcceEEecCCCCHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC-------------
Q 030960           80 GRLDRKIEFPLPDRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN-------------  140 (168)
Q Consensus        80 grf~~~i~~~~P~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~-------------  140 (168)
                       ||++.||+|+|+...|..||+.++.+      +.|+.+|+.+|+||||+||.-++++|.+..+|..             
T Consensus       289 -RFekRIYIPLPe~~AR~~MF~lhlG~tp~~LT~~d~~eL~~kTeGySGsDisivVrDalmePvRkvqsAthFk~v~~~s  367 (439)
T KOG0739|consen  289 -RFEKRIYIPLPEAHARARMFKLHLGDTPHVLTEQDFKELARKTEGYSGSDISIVVRDALMEPVRKVQSATHFKKVSGPS  367 (439)
T ss_pred             -HhhcceeccCCcHHHhhhhheeccCCCccccchhhHHHHHhhcCCCCcCceEEEehhhhhhhHHHhhhhhhhhccCCCC
Confidence             99999999999999999999988873      5689999999999999999999999999998872             


Q ss_pred             ---------------------------------CCccCHHHHHHHHHhhcCCC
Q 030960          141 ---------------------------------RYVILPKDFEKGYRTNVKKP  160 (168)
Q Consensus       141 ---------------------------------~~~i~~~d~~~al~~~~p~~  160 (168)
                                                       .+++|..||..++.+.+|.-
T Consensus       368 ~~~~~~~lltpcspgd~ga~em~w~dv~~dkl~eP~vt~~D~~k~l~~tkPTv  420 (439)
T KOG0739|consen  368 NPSEVDDLLTPCSPGDPGAIEMSWMDVPADKLLEPPVTMRDFLKSLSRTKPTV  420 (439)
T ss_pred             ChhhhccccCCCCCCCcchhhhhhccCCHhhccCCCccHHHHHHHHhhcCCCC
Confidence                                             14799999999999999965

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.97  E-value=9.8e-31  Score=218.64  Aligned_cols=157  Identities=42%  Similarity=0.650  Sum_probs=142.6

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|+.|+..+||||||||+|.++..+.....+.+....++++.|+..|+++.+..+++||+|||+|+.||++++||||
T Consensus       136 l~~~f~~a~~~~p~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~~~~v~vI~aTn~~~~ld~al~r~gR  215 (495)
T TIGR01241       136 VRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAATNRPDVLDPALLRPGR  215 (495)
T ss_pred             HHHHHHHHHhcCCCEEEEechhhhhhccccCcCCccHHHHHHHHHHHhhhccccCCCCeEEEEecCChhhcCHHHhcCCc
Confidence            67899999999999999999999998875543344445568999999999999888899999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      ||+.+++++|+.++|.+||+.++.     .+.++..+|..|.|||++||.++|++|+..+.++++..|+.+||.+|+.++
T Consensus       216 fd~~i~i~~Pd~~~R~~il~~~l~~~~~~~~~~l~~la~~t~G~sgadl~~l~~eA~~~a~~~~~~~i~~~~l~~a~~~~  295 (495)
T TIGR01241       216 FDRQVVVDLPDIKGREEILKVHAKNKKLAPDVDLKAVARRTPGFSGADLANLLNEAALLAARKNKTEITMNDIEEAIDRV  295 (495)
T ss_pred             ceEEEEcCCCCHHHHHHHHHHHHhcCCCCcchhHHHHHHhCCCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            999999999999999999997765     367899999999999999999999999999999999999999999999987


Q ss_pred             cC
Q 030960          157 VK  158 (168)
Q Consensus       157 ~p  158 (168)
                      ..
T Consensus       296 ~~  297 (495)
T TIGR01241       296 IA  297 (495)
T ss_pred             hc
Confidence            64

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.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.97  E-value=1.2e-30  Score=226.84  Aligned_cols=158  Identities=41%  Similarity=0.673  Sum_probs=141.1

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|+.|+..+||||||||+|.+++.|+....  .....+++++|+..|+++....+++||+|||+|+.||++++||||
T Consensus       535 i~~~f~~A~~~~p~iifiDEid~l~~~r~~~~~--~~~~~~~~~~lL~~ldg~~~~~~v~vI~aTn~~~~ld~allRpgR  612 (733)
T TIGR01243       535 IREIFRKARQAAPAIIFFDEIDAIAPARGARFD--TSVTDRIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGR  612 (733)
T ss_pred             HHHHHHHHHhcCCEEEEEEChhhhhccCCCCCC--ccHHHHHHHHHHHHhhcccCCCCEEEEEeCCChhhCCHhhcCCCc
Confidence            688999999999999999999999998854322  224568999999999999888899999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC----------------
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN----------------  140 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~----------------  140 (168)
                      ||+.+++++|+.++|.+||+.+..     ++++++.+|+.|+||||+||.++|++|+..++++.                
T Consensus       613 fd~~i~v~~Pd~~~R~~i~~~~~~~~~~~~~~~l~~la~~t~g~sgadi~~~~~~A~~~a~~~~~~~~~~~~~~~~~~~~  692 (733)
T TIGR01243       613 FDRLILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRESIGSPAKEKLEVGEEEF  692 (733)
T ss_pred             cceEEEeCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHhhhccchhhhcccccc
Confidence            999999999999999999986544     57899999999999999999999999999998852                


Q ss_pred             --CCccCHHHHHHHHHhhcCCCC
Q 030960          141 --RYVILPKDFEKGYRTNVKKPD  161 (168)
Q Consensus       141 --~~~i~~~d~~~al~~~~p~~~  161 (168)
                        ...|+.+||.+|+++++|+..
T Consensus       693 ~~~~~i~~~~f~~al~~~~ps~~  715 (733)
T TIGR01243       693 LKDLKVEMRHFLEALKKVKPSVS  715 (733)
T ss_pred             cccCcccHHHHHHHHHHcCCCCC
Confidence              126999999999999999763

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.

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.97  E-value=1.1e-30  Score=223.61  Aligned_cols=158  Identities=39%  Similarity=0.612  Sum_probs=144.4

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|+.|+..+||||||||+|.++..|+....+.+....++++.+|..|+++....+++||+|||+|+.||++++||||
T Consensus       233 ~~~~f~~a~~~~P~IifIDEiD~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~~~~~vivIaaTN~p~~lD~Al~RpgR  312 (644)
T PRK10733        233 VRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGR  312 (644)
T ss_pred             HHHHHHHHHhcCCcEEEehhHhhhhhccCCCCCCCchHHHHHHHHHHHhhhcccCCCCeeEEEecCChhhcCHHHhCCcc
Confidence            57899999999999999999999998886554445555678999999999999888899999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      ||+.++|++|+.++|.+||+.++.     .++++..+|..|.||||+||.++|++|+..|++.++..|+..||+.|+.++
T Consensus       313 fdr~i~v~~Pd~~~R~~Il~~~~~~~~l~~~~d~~~la~~t~G~sgadl~~l~~eAa~~a~r~~~~~i~~~d~~~a~~~v  392 (644)
T PRK10733        313 FDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARGNKRVVSMVEFEKAKDKI  392 (644)
T ss_pred             cceEEEcCCCCHHHHHHHHHHHhhcCCCCCcCCHHHHHhhCCCCCHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHH
Confidence            999999999999999999997765     478899999999999999999999999999999999999999999999887


Q ss_pred             cCC
Q 030960          157 VKK  159 (168)
Q Consensus       157 ~p~  159 (168)
                      .+.
T Consensus       393 ~~g  395 (644)
T PRK10733        393 MMG  395 (644)
T ss_pred             hcc
Confidence            653

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

Probab=99.97  E-value=6.2e-31  Score=215.30  Aligned_cols=157  Identities=54%  Similarity=0.949  Sum_probs=144.1

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|..|+.++||||||||+|.++..+....++.+....+.+.+++..++++....++.||++||+++.+|++++||||
T Consensus       265 vr~lF~~A~~~~P~ILfIDEID~l~~kR~~~~sgg~~e~qr~ll~LL~~Ldg~~~~~~V~VI~ATNr~d~LDpaLlRpGR  344 (438)
T PTZ00361        265 VRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGFDSRGDVKVIMATNRIESLDPALIRPGR  344 (438)
T ss_pred             HHHHHHHHHhCCCcEEeHHHHHHHhccCCCCCCcccHHHHHHHHHHHHHHhhhcccCCeEEEEecCChHHhhHHhccCCe
Confidence            68899999999999999999999998886655555666778888999999998877789999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      ||..|+|++|+.++|.+||+.++.     .++++..++..|+||||+||.++|++|++.|++++...|+.+||..|++++
T Consensus       345 fd~~I~~~~Pd~~~R~~Il~~~~~k~~l~~dvdl~~la~~t~g~sgAdI~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~v  424 (438)
T PTZ00361        345 IDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDVDLEEFIMAKDELSGADIKAICTEAGLLALRERRMKVTQADFRKAKEKV  424 (438)
T ss_pred             eEEEEEeCCCCHHHHHHHHHHHHhcCCCCcCcCHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHH
Confidence            999999999999999999997654     578999999999999999999999999999999999999999999999987


Q ss_pred             cC
Q 030960          157 VK  158 (168)
Q Consensus       157 ~p  158 (168)
                      ..
T Consensus       425 ~~  426 (438)
T PTZ00361        425 LY  426 (438)
T ss_pred             Hh
Confidence            54

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

Probab=99.97  E-value=7.2e-31  Score=219.35  Aligned_cols=135  Identities=38%  Similarity=0.637  Sum_probs=125.2

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      +|.+|++|+..+|||+||||+|+++++|+-.+.+-.   .++++++|++|||.+.-.+|.|+|+|++|+-|||||+||||
T Consensus       749 vR~lF~rA~~a~PCiLFFDEfdSiAPkRGhDsTGVT---DRVVNQlLTelDG~Egl~GV~i~aaTsRpdliDpALLRpGR  825 (952)
T KOG0735|consen  749 VRDLFERAQSAKPCILFFDEFDSIAPKRGHDSTGVT---DRVVNQLLTELDGAEGLDGVYILAATSRPDLIDPALLRPGR  825 (952)
T ss_pred             HHHHHHHhhccCCeEEEeccccccCcccCCCCCCch---HHHHHHHHHhhccccccceEEEEEecCCccccCHhhcCCCc
Confidence            689999999999999999999999999976555443   49999999999999999999999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHH-----hhcCCCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRK  139 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~-----~~l~~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~  139 (168)
                      +|+.++.++|+..+|.+|++     ...+.++|++.+|..|+||||+||..++-+|.+.|+++
T Consensus       826 lD~~v~C~~P~~~eRl~il~~ls~s~~~~~~vdl~~~a~~T~g~tgADlq~ll~~A~l~avh~  888 (952)
T KOG0735|consen  826 LDKLVYCPLPDEPERLEILQVLSNSLLKDTDVDLECLAQKTDGFTGADLQSLLYNAQLAAVHE  888 (952)
T ss_pred             cceeeeCCCCCcHHHHHHHHHHhhccCCccccchHHHhhhcCCCchhhHHHHHHHHHHHHHHH
Confidence            99999999999999999998     34457899999999999999999999999999888876

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

Probab=99.97  E-value=6e-31  Score=199.92  Aligned_cols=160  Identities=49%  Similarity=0.794  Sum_probs=149.4

Q ss_pred             CHHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCC
Q 030960            1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPG   80 (168)
Q Consensus         1 ~l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~g   80 (168)
                      |++++|+.|+....|||||||+|++++.|-+...+.+..+++...++++++|++....++-|+++||+|+.|||||+|||
T Consensus       258 mvrelf~martkkaciiffdeidaiggarfddg~ggdnevqrtmleli~qldgfdprgnikvlmatnrpdtldpallrpg  337 (435)
T KOG0729|consen  258 MVRELFEMARTKKACIIFFDEIDAIGGARFDDGAGGDNEVQRTMLELINQLDGFDPRGNIKVLMATNRPDTLDPALLRPG  337 (435)
T ss_pred             HHHHHHHHhcccceEEEEeeccccccCccccCCCCCcHHHHHHHHHHHHhccCCCCCCCeEEEeecCCCCCcCHhhcCCc
Confidence            58999999999999999999999999999777777778889999999999999999999999999999999999999999


Q ss_pred             CcceEEecCCCCHHHHHHHHHhh-----cCCCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQMN-----LSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~~~-----l~~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      |+|++++|++|+.+.|..||+.+     ...++-|+.+|..|+.-||++|.++|.+|.+.|++..++..|++||..|+++
T Consensus       338 rldrkvef~lpdlegrt~i~kihaksmsverdir~ellarlcpnstgaeirsvcteagmfairarrk~atekdfl~av~k  417 (435)
T KOG0729|consen  338 RLDRKVEFGLPDLEGRTHIFKIHAKSMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKVATEKDFLDAVNK  417 (435)
T ss_pred             ccccceeccCCcccccceeEEEeccccccccchhHHHHHhhCCCCcchHHHHHHHHhhHHHHHHHhhhhhHHHHHHHHHH
Confidence            99999999999999999999844     4467889999999999999999999999999999999999999999999998


Q ss_pred             hcCCC
Q 030960          156 NVKKP  160 (168)
Q Consensus       156 ~~p~~  160 (168)
                      +.+..
T Consensus       418 vvkgy  422 (435)
T KOG0729|consen  418 VVKGY  422 (435)
T ss_pred             HHHHH
Confidence            87644

>CHL00176 ftsH cell division protein; Validated

Probab=99.97  E-value=6.2e-30  Score=217.74  Aligned_cols=156  Identities=40%  Similarity=0.629  Sum_probs=142.7

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|+.|+..+||||||||+|.++..|+....+.+....+.++.++..++++....+++||++||+++.+|++++||||
T Consensus       264 vr~lF~~A~~~~P~ILfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~~~~~ViVIaaTN~~~~LD~ALlRpGR  343 (638)
T CHL00176        264 VRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGR  343 (638)
T ss_pred             HHHHHHHHhcCCCcEEEEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhccccCCCCeeEEEecCchHhhhhhhhcccc
Confidence            57899999999999999999999998876555555566678999999999999888899999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      ||+.+++++|+.++|.+||+.++.     .+.++..+|..|.|||++||.++|++|+..+.+++...|+.+||++|+.++
T Consensus       344 Fd~~I~v~lPd~~~R~~IL~~~l~~~~~~~d~~l~~lA~~t~G~sgaDL~~lvneAal~a~r~~~~~It~~dl~~Ai~rv  423 (638)
T CHL00176        344 FDRQITVSLPDREGRLDILKVHARNKKLSPDVSLELIARRTPGFSGADLANLLNEAAILTARRKKATITMKEIDTAIDRV  423 (638)
T ss_pred             CceEEEECCCCHHHHHHHHHHHHhhcccchhHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHH
Confidence            999999999999999999997765     466889999999999999999999999999999999999999999999987


Q ss_pred             c
Q 030960          157 V  157 (168)
Q Consensus       157 ~  157 (168)
                      .
T Consensus       424 ~  424 (638)
T CHL00176        424 I  424 (638)
T ss_pred             H
Confidence            3

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

Probab=99.97  E-value=5.2e-30  Score=193.82  Aligned_cols=156  Identities=29%  Similarity=0.500  Sum_probs=139.7

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      |+++|+.|++.+|||+||||+|+++-.|.-.+-  -..+..++|.+|+.||++.++.+|+.||+||+|+.||+|+++  |
T Consensus       199 Ihely~rA~~~aPcivFiDE~DAiaLdRryQel--RGDVsEiVNALLTelDgi~eneGVvtIaaTN~p~~LD~aiRs--R  274 (368)
T COG1223         199 IHELYERARKAAPCIVFIDELDAIALDRRYQEL--RGDVSEIVNALLTELDGIKENEGVVTIAATNRPELLDPAIRS--R  274 (368)
T ss_pred             HHHHHHHHHhcCCeEEEehhhhhhhhhhhHHHh--cccHHHHHHHHHHhccCcccCCceEEEeecCChhhcCHHHHh--h
Confidence            789999999999999999999999987744321  112348999999999999999999999999999999999999  9


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHH-HHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAA-ICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~-l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      |...|+|.+|+.++|.+|++.+..     -+.++..+++.|.||||+||.. ++..|.+.|+.+++..|+.+||+.|+++
T Consensus       275 FEeEIEF~LP~~eEr~~ile~y~k~~Plpv~~~~~~~~~~t~g~SgRdikekvlK~aLh~Ai~ed~e~v~~edie~al~k  354 (368)
T COG1223         275 FEEEIEFKLPNDEERLEILEYYAKKFPLPVDADLRYLAAKTKGMSGRDIKEKVLKTALHRAIAEDREKVEREDIEKALKK  354 (368)
T ss_pred             hhheeeeeCCChHHHHHHHHHHHHhCCCccccCHHHHHHHhCCCCchhHHHHHHHHHHHHHHHhchhhhhHHHHHHHHHh
Confidence            999999999999999999997766     3678999999999999999986 7888999999999999999999999998


Q ss_pred             hcCCCC
Q 030960          156 NVKKPD  161 (168)
Q Consensus       156 ~~p~~~  161 (168)
                      ..+...
T Consensus       355 ~r~~r~  360 (368)
T COG1223         355 ERKRRA  360 (368)
T ss_pred             hccccC
Confidence            776543

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=99.96  E-value=1.4e-28  Score=198.69  Aligned_cols=155  Identities=54%  Similarity=0.821  Sum_probs=140.5

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|+.|+..+|+||||||+|.++..+.+...+.+....+.+..++..++++...+++.||+|||+++.+|++++||||
T Consensus       204 i~~~f~~a~~~~p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~~~~~~v~vI~ttn~~~~ld~al~r~gr  283 (364)
T TIGR01242       204 VREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPDILDPALLRPGR  283 (364)
T ss_pred             HHHHHHHHHhcCCcEEEhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhCCCCCCCEEEEEecCChhhCChhhcCccc
Confidence            57899999999999999999999998776555455556678888999999988777799999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      ||+.|+|++|+.++|.+||+.+..     .++++..++..|+||||+||.++|++|++.|++++...|+.+||..|+.++
T Consensus       284 fd~~i~v~~P~~~~r~~Il~~~~~~~~l~~~~~~~~la~~t~g~sg~dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~~  363 (364)
T TIGR01242       284 FDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVDLEAIAKMTEGASGADLKAICTEAGMFAIREERDYVTMDDFIKAVEKV  363 (364)
T ss_pred             CceEEEeCCcCHHHHHHHHHHHHhcCCCCccCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHh
Confidence            999999999999999999986654     457899999999999999999999999999999999999999999999875

Many proteins may score above the trusted cutoff because an internal

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

Probab=99.96  E-value=4.9e-29  Score=195.86  Aligned_cols=153  Identities=31%  Similarity=0.503  Sum_probs=135.1

Q ss_pred             CHHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCC--eEEEEecCCCCCCCccccC
Q 030960            1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVN--VKVIMATNRADTLDPALLR   78 (168)
Q Consensus         1 ~l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~--v~vi~ttn~~~~ld~al~r   78 (168)
                      +++.+|..|...+||||||||+|++++.|.   ++.+..+..+.++|+..+||+..+.+  |+|+|+||+|.++|.|++|
T Consensus       174 lv~AvFslAsKl~P~iIFIDEvds~L~~R~---s~dHEa~a~mK~eFM~~WDGl~s~~~~rVlVlgATNRP~DlDeAiiR  250 (386)
T KOG0737|consen  174 LVKAVFSLASKLQPSIIFIDEVDSFLGQRR---STDHEATAMMKNEFMALWDGLSSKDSERVLVLGATNRPFDLDEAIIR  250 (386)
T ss_pred             HHHHHHhhhhhcCcceeehhhHHHHHhhcc---cchHHHHHHHHHHHHHHhccccCCCCceEEEEeCCCCCccHHHHHHH
Confidence            468899999999999999999999999882   45666777999999999999966554  9999999999999999999


Q ss_pred             CCCcceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC-------------
Q 030960           79 PGRLDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN-------------  140 (168)
Q Consensus        79 ~grf~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~-------------  140 (168)
                        |+.+.++|+.|+..+|.+|++..+.     +++|+.++|..|+||||+||.++|..|+..++++-             
T Consensus       251 --R~p~rf~V~lP~~~qR~kILkviLk~e~~e~~vD~~~iA~~t~GySGSDLkelC~~Aa~~~ire~~~~~~~~~d~d~~  328 (386)
T KOG0737|consen  251 --RLPRRFHVGLPDAEQRRKILKVILKKEKLEDDVDLDEIAQMTEGYSGSDLKELCRLAALRPIRELLVSETGLLDLDKA  328 (386)
T ss_pred             --hCcceeeeCCCchhhHHHHHHHHhcccccCcccCHHHHHHhcCCCcHHHHHHHHHHHhHhHHHHHHHhcccchhhhhh
Confidence              9999999999999999999997766     68999999999999999999999999999888751             


Q ss_pred             ---------------CCccCHHHHHHHHHhhcC
Q 030960          141 ---------------RYVILPKDFEKGYRTNVK  158 (168)
Q Consensus       141 ---------------~~~i~~~d~~~al~~~~p  158 (168)
                                     ..++.++||..+++++-+
T Consensus       329 ~~d~~~~~~~~~~~~~r~l~~eDf~~a~~~v~~  361 (386)
T KOG0737|consen  329 IADLKPTQAAASSCLLRPLEQEDFPKAINRVSA  361 (386)
T ss_pred             hhhccCCcccccccccCcccHHHHHHHHHhhhh
Confidence                           146778888888875444

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

Probab=99.94  E-value=8.1e-27  Score=194.06  Aligned_cols=151  Identities=34%  Similarity=0.539  Sum_probs=138.1

Q ss_pred             HHHHHHHHHHcC-CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCC
Q 030960            2 VRDVFRLAKENA-PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPG   80 (168)
Q Consensus         2 l~~iF~~a~~~~-p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~g   80 (168)
                      +|++|+.|..++ |++|||||+|+++++|.....    ...++++++++.++++....+++|+++||+|+.||++++| |
T Consensus       266 LR~~f~~a~k~~~psii~IdEld~l~p~r~~~~~----~e~Rv~sqlltL~dg~~~~~~vivl~atnrp~sld~alRR-g  340 (693)
T KOG0730|consen  266 LRKAFAEALKFQVPSIIFIDELDALCPKREGADD----VESRVVSQLLTLLDGLKPDAKVIVLAATNRPDSLDPALRR-G  340 (693)
T ss_pred             HHHHHHHHhccCCCeeEeHHhHhhhCCcccccch----HHHHHHHHHHHHHhhCcCcCcEEEEEecCCccccChhhhc-C
Confidence            789999999999 999999999999999855443    3459999999999999988899999999999999999999 9


Q ss_pred             CcceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      |||+.+.++.|+..+|.+|++.+..     ++.++.++|..|.||+|+||..+|.+|++.+.++     +.++|..|+..
T Consensus       341 Rfd~ev~IgiP~~~~RldIl~~l~k~~~~~~~~~l~~iA~~thGyvGaDL~~l~~ea~~~~~r~-----~~~~~~~A~~~  415 (693)
T KOG0730|consen  341 RFDREVEIGIPGSDGRLDILRVLTKKMNLLSDVDLEDIAVSTHGYVGADLAALCREASLQATRR-----TLEIFQEALMG  415 (693)
T ss_pred             CCcceeeecCCCchhHHHHHHHHHHhcCCcchhhHHHHHHHccchhHHHHHHHHHHHHHHHhhh-----hHHHHHHHHhc
Confidence            9999999999999999999985444     4689999999999999999999999999999998     78999999999


Q ss_pred             hcCCCCC
Q 030960          156 NVKKPDT  162 (168)
Q Consensus       156 ~~p~~~~  162 (168)
                      +.|+...
T Consensus       416 i~psa~R  422 (693)
T KOG0730|consen  416 IRPSALR  422 (693)
T ss_pred             CCchhhh
Confidence            9987644

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

Probab=99.94  E-value=4.6e-27  Score=189.74  Aligned_cols=155  Identities=32%  Similarity=0.517  Sum_probs=136.0

Q ss_pred             CHHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC--CCCCeEEEEecCCCCCCCccccC
Q 030960            1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD--QTVNVKVIMATNRADTLDPALLR   78 (168)
Q Consensus         1 ~l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~--~~~~v~vi~ttn~~~~ld~al~r   78 (168)
                      +||.+|..|+..+|+||||||+|.++..|.+.....+   .++..+++.++++..  ..++|+||||||.||.+|.+++|
T Consensus       233 ~vralf~vAr~~qPsvifidEidslls~Rs~~e~e~s---rr~ktefLiq~~~~~s~~~drvlvigaTN~P~e~Dea~~R  309 (428)
T KOG0740|consen  233 LVRALFKVARSLQPSVIFIDEIDSLLSKRSDNEHESS---RRLKTEFLLQFDGKNSAPDDRVLVIGATNRPWELDEAARR  309 (428)
T ss_pred             HHHHHHHHHHhcCCeEEEechhHHHHhhcCCcccccc---hhhhhHHHhhhccccCCCCCeEEEEecCCCchHHHHHHHH
Confidence            5899999999999999999999999999955554444   488899999988773  45589999999999999999999


Q ss_pred             CCCcceEEecCCCCHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC------------
Q 030960           79 PGRLDRKIEFPLPDRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN------------  140 (168)
Q Consensus        79 ~grf~~~i~~~~P~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~------------  140 (168)
                        ||.+.+++|+|+.+.|..+|...+.+      +.+++.+++.|+|||++||.++|.+|++-.++..            
T Consensus       310 --rf~kr~yiplPd~etr~~~~~~ll~~~~~~l~~~d~~~l~~~Tegysgsdi~~l~kea~~~p~r~~~~~~~~~~~~~~  387 (428)
T KOG0740|consen  310 --RFVKRLYIPLPDYETRSLLWKQLLKEQPNGLSDLDISLLAKVTEGYSGSDITALCKEAAMGPLRELGGTTDLEFIDAD  387 (428)
T ss_pred             --HhhceeeecCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCcccccHHHHHHHhhcCchhhcccchhhhhcchh
Confidence              99999999999999999999977764      3678899999999999999999999987776653            


Q ss_pred             -CCccCHHHHHHHHHhhcCCC
Q 030960          141 -RYVILPKDFEKGYRTNVKKP  160 (168)
Q Consensus       141 -~~~i~~~d~~~al~~~~p~~  160 (168)
                       .+.++..||..+++.++|+-
T Consensus       388 ~~r~i~~~df~~a~~~i~~~~  408 (428)
T KOG0740|consen  388 KIRPITYPDFKNAFKNIKPSV  408 (428)
T ss_pred             ccCCCCcchHHHHHHhhcccc
Confidence             25789999999999999854

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

Probab=99.94  E-value=3.1e-27  Score=182.18  Aligned_cols=157  Identities=51%  Similarity=0.830  Sum_probs=145.6

Q ss_pred             CHHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCC
Q 030960            1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPG   80 (168)
Q Consensus         1 ~l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~g   80 (168)
                      +||+.|..|+.+.|||||+||+|++++.+.......+..+++.+-.++++|+++..-.+|-+|+|||+|+.|||+|+|||
T Consensus       213 lIRemf~yA~~~~pciifmdeiDAigGRr~se~Ts~dreiqrTLMeLlnqmdgfd~l~rVk~ImatNrpdtLdpaLlRpG  292 (388)
T KOG0651|consen  213 LIRDMFRYAREVIPCIIFMDEIDAIGGRRFSEGTSSDREIQRTLMELLNQMDGFDTLHRVKTIMATNRPDTLDPALLRPG  292 (388)
T ss_pred             HHHHHHHHHhhhCceEEeehhhhhhccEEeccccchhHHHHHHHHHHHHhhccchhcccccEEEecCCccccchhhcCCc
Confidence            58999999999999999999999999999777777778888999999999999999999999999999999999999999


Q ss_pred             CcceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      |.|+.+++|.|+...|..|++.+-.     ..++.+.+.+..+||.|+|+.+.|.+|.+-+++.....+-.+||..++.+
T Consensus       293 Rldrk~~iPlpne~~r~~I~Kih~~~i~~~Geid~eaivK~~d~f~gad~rn~~tEag~Fa~~~~~~~vl~Ed~~k~vrk  372 (388)
T KOG0651|consen  293 RLDRKVEIPLPNEQARLGILKIHVQPIDFHGEIDDEAILKLVDGFNGADLRNVCTEAGMFAIPEERDEVLHEDFMKLVRK  372 (388)
T ss_pred             cccceeccCCcchhhceeeEeeccccccccccccHHHHHHHHhccChHHHhhhcccccccccchhhHHHhHHHHHHHHHH
Confidence            9999999999999999999985444     57889999999999999999999999999999988888999999999987


Q ss_pred             hc
Q 030960          156 NV  157 (168)
Q Consensus       156 ~~  157 (168)
                      +.
T Consensus       373 ~~  374 (388)
T KOG0651|consen  373 QA  374 (388)
T ss_pred             HH
Confidence            64

>TIGR03689 pup_AAA proteasome ATPase

Probab=99.93  E-value=2.6e-25  Score=184.75  Aligned_cols=155  Identities=32%  Similarity=0.485  Sum_probs=127.1

Q ss_pred             HHHHHHHHHHc----CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcccc
Q 030960            2 VRDVFRLAKEN----APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~~----~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~   77 (168)
                      ++.+|+.|+..    .||||||||+|.++..|+...+  +....+++++|++.|+++...++++||+|||+++.||||++
T Consensus       274 ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~~~s--~d~e~~il~~LL~~LDgl~~~~~ViVI~ATN~~d~LDpALl  351 (512)
T TIGR03689       274 IRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGSGVS--SDVETTVVPQLLSELDGVESLDNVIVIGASNREDMIDPAIL  351 (512)
T ss_pred             HHHHHHHHHHHhhcCCCceEEEehhhhhhcccCCCcc--chHHHHHHHHHHHHhcccccCCceEEEeccCChhhCCHhhc
Confidence            57889988864    6999999999999988743222  22235788999999999988889999999999999999999


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhcCCCCCH---------------HHHH----------------------------
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNLSDEVDL---------------EDYV----------------------------  114 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l~~~~~~---------------~~la----------------------------  114 (168)
                      ||||||.+|+|++|+.++|.+||+.++.+...+               ..++                            
T Consensus       352 RpGRfD~~I~~~~Pd~e~r~~Il~~~l~~~l~l~~~l~~~~g~~~a~~~al~~~av~~~~a~~~~~~~l~~~~~~g~~~~  431 (512)
T TIGR03689       352 RPGRLDVKIRIERPDAEAAADIFSKYLTDSLPLDADLAEFDGDREATAAALIQRAVDHLYATSEENRYVEVTYANGSTEV  431 (512)
T ss_pred             CccccceEEEeCCCCHHHHHHHHHHHhhccCCchHHHHHhcCCCHHHHHHHHHHHHHHHhhhhcccceeEEEecCCceee
Confidence            999999999999999999999999888753332               1111                            


Q ss_pred             -hCCCCCCHHHHHHHHHHHHHHHHHh----CCCccCHHHHHHHHHhhcC
Q 030960          115 -SRPDKISAAEIAAICQEAGMHAVRK----NRYVILPKDFEKGYRTNVK  158 (168)
Q Consensus       115 -~~t~g~s~~di~~l~~~a~~~a~~~----~~~~i~~~d~~~al~~~~p  158 (168)
                       ..++++||++|+++|..|...|+++    +...++.+|+..|+.....
T Consensus       432 l~~~d~~sGa~i~~iv~~a~~~ai~~~~~~~~~~~~~~~l~~a~~~e~~  480 (512)
T TIGR03689       432 LYFKDFVSGAMIANIVDRAKKRAIKDHITGGQVGLRIEHLLAAVLDEFR  480 (512)
T ss_pred             EeecccccHHHHHHHHHHHHHHHHHHHHhcCCcCcCHHHHHHHHHHhhc
Confidence             1256789999999999998888876    3468999999999987654

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.

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

Probab=99.93  E-value=1.2e-26  Score=189.20  Aligned_cols=158  Identities=32%  Similarity=0.483  Sum_probs=139.5

Q ss_pred             HHHHHHHHHH--------cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCC
Q 030960            2 VRDVFRLAKE--------NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLD   73 (168)
Q Consensus         2 l~~iF~~a~~--------~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld   73 (168)
                      +|++|.-|.+        ..-.||+|||+|++|.+|++... .+.....+++++|+.||++.+-++++||+.||+.+-||
T Consensus       305 vR~LFaDAEeE~r~~g~~SgLHIIIFDEiDAICKqRGS~~g-~TGVhD~VVNQLLsKmDGVeqLNNILVIGMTNR~DlID  383 (744)
T KOG0741|consen  305 VRKLFADAEEEQRRLGANSGLHIIIFDEIDAICKQRGSMAG-STGVHDTVVNQLLSKMDGVEQLNNILVIGMTNRKDLID  383 (744)
T ss_pred             HHHHHHhHHHHHHhhCccCCceEEEehhhHHHHHhcCCCCC-CCCccHHHHHHHHHhcccHHhhhcEEEEeccCchhhHH
Confidence            6889988863        23689999999999999866543 33455699999999999999999999999999999999


Q ss_pred             ccccCCCCcceEEecCCCCHHHHHHHHH---------hhcCCCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC----
Q 030960           74 PALLRPGRLDRKIEFPLPDRRQKRLVFQ---------MNLSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN----  140 (168)
Q Consensus        74 ~al~r~grf~~~i~~~~P~~~~R~~il~---------~~l~~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~----  140 (168)
                      +||+|||||...+++.+||.+.|.+|++         .++..++|+.++|..|..|||++|+-+++.|...|+.+.    
T Consensus       384 EALLRPGRlEVqmEIsLPDE~gRlQIl~IHT~rMre~~~l~~dVdl~elA~lTKNfSGAEleglVksA~S~A~nR~vk~~  463 (744)
T KOG0741|consen  384 EALLRPGRLEVQMEISLPDEKGRLQILKIHTKRMRENNKLSADVDLKELAALTKNFSGAELEGLVKSAQSFAMNRHVKAG  463 (744)
T ss_pred             HHhcCCCceEEEEEEeCCCccCceEEEEhhhhhhhhcCCCCCCcCHHHHHHHhcCCchhHHHHHHHHHHHHHHHhhhccC
Confidence            9999999999999999999999999997         455689999999999999999999999999988888763    


Q ss_pred             -----------CCccCHHHHHHHHHhhcCCC
Q 030960          141 -----------RYVILPKDFEKGYRTNVKKP  160 (168)
Q Consensus       141 -----------~~~i~~~d~~~al~~~~p~~  160 (168)
                                 +-.|+.+||..|+++++|.-
T Consensus       464 ~~~~~~~~~~e~lkV~r~DFl~aL~dVkPAF  494 (744)
T KOG0741|consen  464 GKVEVDPVAIENLKVTRGDFLNALEDVKPAF  494 (744)
T ss_pred             cceecCchhhhheeecHHHHHHHHHhcCccc
Confidence                       12599999999999999964

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

Probab=99.93  E-value=1.2e-25  Score=195.79  Aligned_cols=158  Identities=34%  Similarity=0.522  Sum_probs=138.6

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|+.|+..+|+|||+||||-+++.|+......+   .++++.+|..|+|+...+.|+||++||+|+.+|||++||||
T Consensus       352 lrllFeeA~k~qPSIIffdeIdGlapvrSskqEqih---~SIvSTLLaLmdGldsRgqVvvigATnRpda~dpaLRRPgr  428 (1080)
T KOG0732|consen  352 LRLLFEEAQKTQPSIIFFDEIDGLAPVRSSKQEQIH---ASIVSTLLALMDGLDSRGQVVVIGATNRPDAIDPALRRPGR  428 (1080)
T ss_pred             HHHHHHHHhccCceEEeccccccccccccchHHHhh---hhHHHHHHHhccCCCCCCceEEEcccCCccccchhhcCCcc
Confidence            678999999999999999999999999854443333   38999999999999999999999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCC--------------
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNR--------------  141 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~--------------  141 (168)
                      ||+.++|++|+.+.|.+|+...-.+      .--+..+|+.|.||-|+||+.+|.+|+..++++.-              
T Consensus       429 fdref~f~lp~~~ar~~Il~Ihtrkw~~~i~~~l~~~la~~t~gy~gaDlkaLCTeAal~~~~r~~Pq~y~s~~kl~~d~  508 (1080)
T KOG0732|consen  429 FDREFYFPLPDVDARAKILDIHTRKWEPPISRELLLWLAEETSGYGGADLKALCTEAALIALRRSFPQIYSSSDKLLIDV  508 (1080)
T ss_pred             cceeEeeeCCchHHHHHHHHHhccCCCCCCCHHHHHHHHHhccccchHHHHHHHHHHhhhhhccccCeeecccccccccc
Confidence            9999999999999999999854442      22456799999999999999999999999998841              


Q ss_pred             --CccCHHHHHHHHHhhcCCCCC
Q 030960          142 --YVILPKDFEKGYRTNVKKPDT  162 (168)
Q Consensus       142 --~~i~~~d~~~al~~~~p~~~~  162 (168)
                        ..+...||..|+.+..|+...
T Consensus       509 ~~ikV~~~~f~~A~~~i~ps~~R  531 (1080)
T KOG0732|consen  509 ALIKVEVRDFVEAMSRITPSSRR  531 (1080)
T ss_pred             hhhhhhhHhhhhhhhccCCCCCc
Confidence              248899999999999987644

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.91  E-value=2.1e-23  Score=181.66  Aligned_cols=157  Identities=39%  Similarity=0.621  Sum_probs=136.9

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|+.|...+|+||||||+|.+++.++.....   ...++++.|++.++++....+++||++||.++.+|++++||||
T Consensus       260 l~~lf~~a~~~~p~il~iDEid~l~~~r~~~~~~---~~~~~~~~Ll~~ld~l~~~~~vivI~atn~~~~ld~al~r~gR  336 (733)
T TIGR01243       260 LREIFKEAEENAPSIIFIDEIDAIAPKREEVTGE---VEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGR  336 (733)
T ss_pred             HHHHHHHHHhcCCcEEEeehhhhhcccccCCcch---HHHHHHHHHHHHhhccccCCCEEEEeecCChhhcCHHHhCchh
Confidence            6789999999999999999999999887443322   2247888999999998888899999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC----------------
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN----------------  140 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~----------------  140 (168)
                      |+..+++++|+.++|.+||+.+..     .+.+++.+++.|+||+++||..+|+.|+..++++.                
T Consensus       337 fd~~i~i~~P~~~~R~~Il~~~~~~~~l~~d~~l~~la~~t~G~~gadl~~l~~~a~~~al~r~~~~~~~~~~~~~i~~~  416 (733)
T TIGR01243       337 FDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFIREGKINFEAEEIPAE  416 (733)
T ss_pred             ccEEEEeCCcCHHHHHHHHHHHhcCCCCccccCHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHhhccccccccccccch
Confidence            999999999999999999996544     46789999999999999999999999999888752                


Q ss_pred             ---CCccCHHHHHHHHHhhcCCCC
Q 030960          141 ---RYVILPKDFEKGYRTNVKKPD  161 (168)
Q Consensus       141 ---~~~i~~~d~~~al~~~~p~~~  161 (168)
                         ...++.+||..|++...|+..
T Consensus       417 ~~~~~~v~~~df~~Al~~v~ps~~  440 (733)
T TIGR01243       417 VLKELKVTMKDFMEALKMVEPSAI  440 (733)
T ss_pred             hcccccccHHHHHHHHhhcccccc
Confidence               124788999999999998763

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.

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

Probab=99.89  E-value=7.1e-23  Score=162.71  Aligned_cols=134  Identities=22%  Similarity=0.237  Sum_probs=106.5

Q ss_pred             CHHHHHHHHHHc-----CCeEEEEcccccccccccCCCCCcchHHHHHH-HHHHHhccCC------------CCCCCeEE
Q 030960            1 MVRDVFRLAKEN-----APAIIFIDEVDAIATARFDAQTGADREVQRIL-MELLNQMDGF------------DQTVNVKV   62 (168)
Q Consensus         1 ~l~~iF~~a~~~-----~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~-~~ll~~l~~~------------~~~~~v~v   62 (168)
                      +|+++|..|++.     +||||||||||++++.+++....   ...+++ .+|++.+|+.            ....+|+|
T Consensus       195 ~IR~~F~~A~~~a~~~~aPcVLFIDEIDA~~g~r~~~~~t---v~~qiV~~tLLnl~D~p~~v~l~G~w~~~~~~~~V~V  271 (413)
T PLN00020        195 LIRQRYREAADIIKKKGKMSCLFINDLDAGAGRFGTTQYT---VNNQMVNGTLMNIADNPTNVSLGGDWREKEEIPRVPI  271 (413)
T ss_pred             HHHHHHHHHHHHhhccCCCeEEEEehhhhcCCCCCCCCcc---hHHHHHHHHHHHHhcCCccccccccccccccCCCceE
Confidence            489999999864     69999999999999988532221   223554 7999998863            23567999


Q ss_pred             EEecCCCCCCCccccCCCCcceEEecCCCCHHHHHHHHHhhcCC----CCCHHHHHhCCCC----CCHHHHHHHHHHHHH
Q 030960           63 IMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD----EVDLEDYVSRPDK----ISAAEIAAICQEAGM  134 (168)
Q Consensus        63 i~ttn~~~~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~~----~~~~~~la~~t~g----~s~~di~~l~~~a~~  134 (168)
                      |+|||+|+.||++|+||||||+.+  ..|+.++|.+||+.++..    ..++..|+..++|    |+|+--..+..++..
T Consensus       272 IaTTNrpd~LDpALlRpGRfDk~i--~lPd~e~R~eIL~~~~r~~~l~~~dv~~Lv~~f~gq~~Df~GAlrar~yd~~v~  349 (413)
T PLN00020        272 IVTGNDFSTLYAPLIRDGRMEKFY--WAPTREDRIGVVHGIFRDDGVSREDVVKLVDTFPGQPLDFFGALRARVYDDEVR  349 (413)
T ss_pred             EEeCCCcccCCHhHcCCCCCCcee--CCCCHHHHHHHHHHHhccCCCCHHHHHHHHHcCCCCCchhhhHHHHHHHHHHHH
Confidence            999999999999999999999975  589999999999977763    3467778888877    677777778887776


Q ss_pred             HHHHh
Q 030960          135 HAVRK  139 (168)
Q Consensus       135 ~a~~~  139 (168)
                      ..+.+
T Consensus       350 ~~i~~  354 (413)
T PLN00020        350 KWIAE  354 (413)
T ss_pred             HHHHH
Confidence            66654

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

Probab=99.80  E-value=4.1e-19  Score=149.44  Aligned_cols=165  Identities=23%  Similarity=0.336  Sum_probs=134.0

Q ss_pred             CHHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhc-cCC-CCCCCeEEEEecCCCCCCCccccC
Q 030960            1 MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQM-DGF-DQTVNVKVIMATNRADTLDPALLR   78 (168)
Q Consensus         1 ~l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l-~~~-~~~~~v~vi~ttn~~~~ld~al~r   78 (168)
                      +++.+|..|-+++|+||++|++|.|++..+. +++........+..+++++ ..+ .....+.+||+.+....+++.|..
T Consensus       482 ~l~~vfse~~~~~PSiIvLDdld~l~~~s~~-e~~q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~qtl~~~L~s  560 (952)
T KOG0735|consen  482 FLNNVFSEALWYAPSIIVLDDLDCLASASSN-ENGQDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQELQTLNPLLVS  560 (952)
T ss_pred             HHHHHHHHHHhhCCcEEEEcchhhhhccCcc-cCCcchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhhhhcChhhcC
Confidence            3788999999999999999999999984433 3334444445556666543 333 445568999999999999999999


Q ss_pred             CCCcceEEecCCCCHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHh----CCCccCHHH
Q 030960           79 PGRLDRKIEFPLPDRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRK----NRYVILPKD  148 (168)
Q Consensus        79 ~grf~~~i~~~~P~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~----~~~~i~~~d  148 (168)
                      |++|+.++.+++|+..+|.+|++..+.+      ..+++-++..|+||.+.|++-++.+|.+.+..+    +.+.+|.++
T Consensus       561 ~~~Fq~~~~L~ap~~~~R~~IL~~~~s~~~~~~~~~dLd~ls~~TEGy~~~DL~ifVeRai~~a~leris~~~klltke~  640 (952)
T KOG0735|consen  561 PLLFQIVIALPAPAVTRRKEILTTIFSKNLSDITMDDLDFLSVKTEGYLATDLVIFVERAIHEAFLERISNGPKLLTKEL  640 (952)
T ss_pred             ccceEEEEecCCcchhHHHHHHHHHHHhhhhhhhhHHHHHHHHhcCCccchhHHHHHHHHHHHHHHHHhccCcccchHHH
Confidence            9999999999999999999999976663      235666999999999999999999999998833    345899999


Q ss_pred             HHHHHHhhcCCCCCcccc
Q 030960          149 FEKGYRTNVKKPDTDFEF  166 (168)
Q Consensus       149 ~~~al~~~~p~~~~~~~~  166 (168)
                      |.++++.+.|....++.+
T Consensus       641 f~ksL~~F~P~aLR~ik~  658 (952)
T KOG0735|consen  641 FEKSLKDFVPLALRGIKL  658 (952)
T ss_pred             HHHHHHhcChHHhhhccc
Confidence            999999999977665543

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

Probab=99.75  E-value=7.1e-18  Score=135.03  Aligned_cols=148  Identities=25%  Similarity=0.387  Sum_probs=119.7

Q ss_pred             HHHHHHHHHHcC-CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCC
Q 030960            2 VRDVFRLAKENA-PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPG   80 (168)
Q Consensus         2 l~~iF~~a~~~~-p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~g   80 (168)
                      |+++|++|+... .-++||||+|.++..|+.  ...+......+|.||-.-.  .++..++++.+||+|.++|.|+..  
T Consensus       431 iH~lFDWakkS~rGLllFIDEADAFLceRnk--tymSEaqRsaLNAlLfRTG--dqSrdivLvlAtNrpgdlDsAV~D--  504 (630)
T KOG0742|consen  431 IHKLFDWAKKSRRGLLLFIDEADAFLCERNK--TYMSEAQRSALNALLFRTG--DQSRDIVLVLATNRPGDLDSAVND--  504 (630)
T ss_pred             HHHHHHHHhhcccceEEEehhhHHHHHHhch--hhhcHHHHHHHHHHHHHhc--ccccceEEEeccCCccchhHHHHh--
Confidence            789999999766 567889999999988843  3455556688888887765  466689999999999999999999  


Q ss_pred             CcceEEecCCCCHHHHHHHHHhhcCC----------------------------CC----CHHHHHhCCCCCCHHHHHHH
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQMNLSD----------------------------EV----DLEDYVSRPDKISAAEIAAI  128 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~~~l~~----------------------------~~----~~~~la~~t~g~s~~di~~l  128 (168)
                      |||.+++||+|..++|..++..|+.+                            ..    -+.+.|..|+||||++|..|
T Consensus       505 Ride~veFpLPGeEERfkll~lYlnkyi~~~~~~~~~~~~~~lfkk~sQ~i~l~~~~t~~~~~EaAkkTeGfSGREiakL  584 (630)
T KOG0742|consen  505 RIDEVVEFPLPGEEERFKLLNLYLNKYILKPATSGKPGKWSHLFKKESQRIKLAGFDTGRKCSEAAKKTEGFSGREIAKL  584 (630)
T ss_pred             hhhheeecCCCChHHHHHHHHHHHHHHhcCcCCCCCCchhhHHHhhhhheeeeccchHHHHHHHHHHhccCCcHHHHHHH
Confidence            99999999999999999999866651                            11    24568899999999999999


Q ss_pred             HHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960          129 CQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus       129 ~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      +......+.-+...+++..-|.+.+..
T Consensus       585 va~vQAavYgsedcvLd~~lf~e~v~y  611 (630)
T KOG0742|consen  585 VASVQAAVYGSEDCVLDEALFDERVDY  611 (630)
T ss_pred             HHHHHHHHhcccchhhHHHHHHHHHHH
Confidence            987666666666667777777776653

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

Probab=99.65  E-value=9.1e-16  Score=130.39  Aligned_cols=152  Identities=19%  Similarity=0.398  Sum_probs=122.8

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC-CCCCeEEEEecCCCCCCCccccCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD-QTVNVKVIMATNRADTLDPALLRPG   80 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-~~~~v~vi~ttn~~~~ld~al~r~g   80 (168)
                      +..+|++|+..+|+|||+-++|.+..++.+   +.+.+..+.+..++. ++.+. +..+++||++|++.+.+|+.+++  
T Consensus       479 l~~~f~~a~~~~pavifl~~~dvl~id~dg---ged~rl~~~i~~~ls-~e~~~~~~~~~ivv~t~~s~~~lp~~i~~--  552 (953)
T KOG0736|consen  479 LQAIFSRARRCSPAVLFLRNLDVLGIDQDG---GEDARLLKVIRHLLS-NEDFKFSCPPVIVVATTSSIEDLPADIQS--  552 (953)
T ss_pred             HHHHHHHHhhcCceEEEEeccceeeecCCC---chhHHHHHHHHHHHh-cccccCCCCceEEEEeccccccCCHHHHH--
Confidence            568999999999999999999999965533   444445555665555 34333 56789999999999999999999  


Q ss_pred             CcceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHH---HHHHHhC------------
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAG---MHAVRKN------------  140 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~---~~a~~~~------------  140 (168)
                      .|-+.|.++.|+++||.+||++|+.     .++.+..++.+|.|||.+|++.++....   ..-+++.            
T Consensus       553 ~f~~ei~~~~lse~qRl~iLq~y~~~~~~n~~v~~k~~a~~t~gfs~~~L~~l~~~~s~~~~~~i~~~~l~g~~~~~~~~  632 (953)
T KOG0736|consen  553 LFLHEIEVPALSEEQRLEILQWYLNHLPLNQDVNLKQLARKTSGFSFGDLEALVAHSSLAAKTRIKNKGLAGGLQEEDEG  632 (953)
T ss_pred             hhhhhccCCCCCHHHHHHHHHHHHhccccchHHHHHHHHHhcCCCCHHHHHHHhcCchHHHHHHHHhhcccccchhcccc
Confidence            9999999999999999999998876     4667889999999999999999998872   2222221            


Q ss_pred             -----CCccCHHHHHHHHHhhcCC
Q 030960          141 -----RYVILPKDFEKGYRTNVKK  159 (168)
Q Consensus       141 -----~~~i~~~d~~~al~~~~p~  159 (168)
                           ...++++||..++.+.+..
T Consensus       633 ~~~~~~~~l~~edf~kals~~~~~  656 (953)
T KOG0736|consen  633 ELCAAGFLLTEEDFDKALSRLQKE  656 (953)
T ss_pred             ccccccceecHHHHHHHHHHHHHh
Confidence                 1579999999999977653

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

Probab=99.63  E-value=1.5e-14  Score=121.40  Aligned_cols=154  Identities=36%  Similarity=0.559  Sum_probs=135.0

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|+.|+..+|+++++|++|.+.+.+..   .......+++.+++..++++.... +++++.||.+..+++++++|||
T Consensus        65 ~~~~~~~a~~~~~~ii~~d~~~~~~~~~~~---~~~~~~~~v~~~l~~~~d~~~~~~-v~~~~~~~~~~~~~~a~~~~~~  140 (494)
T COG0464          65 LRELFEEAEKLAPSIIFIDEIDALAPKRSS---DQGEVERRVVAQLLALMDGLKRGQ-VIVIGATNRPDGLDPAKRRPGR  140 (494)
T ss_pred             HHHHHHHHHHhCCCeEeechhhhcccCccc---cccchhhHHHHHHHHhcccccCCc-eEEEeecCCccccChhHhCccc
Confidence            468999999999999999999999998866   233344589999999999988444 9999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhh-----cCCCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC------CCccCHHHHH
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMN-----LSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN------RYVILPKDFE  150 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~-----l~~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~------~~~i~~~d~~  150 (168)
                      |+..++++.|+...|.++++..     +..+.++..++..+.||+++|+..++..+...+.++.      ...++.+++.
T Consensus       141 ~~~~~~~~~~~~~~~~ei~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~r~~~~~~~~~~~~~~~~~  220 (494)
T COG0464         141 FDREIEVNLPDEAGRLEILQIHTRLMFLGPPGTGKTLAARTVGKSGADLGALAKEAALRELRRAIDLVGEYIGVTEDDFE  220 (494)
T ss_pred             cceeeecCCCCHHHHHHHHHHHHhcCCCcccccHHHHHHhcCCccHHHHHHHHHHHHHHHHHhhhccCcccccccHHHHH
Confidence            9999999999999999998733     3346789999999999999999999999999888885      3458999999


Q ss_pred             HHHHhhcCC
Q 030960          151 KGYRTNVKK  159 (168)
Q Consensus       151 ~al~~~~p~  159 (168)
                      ++++++.|+
T Consensus       221 ~~l~~~~~~  229 (494)
T COG0464         221 EALKKVLPS  229 (494)
T ss_pred             HHHHhcCcc
Confidence            999999885

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

Probab=99.55  E-value=2e-14  Score=116.38  Aligned_cols=117  Identities=23%  Similarity=0.321  Sum_probs=92.1

Q ss_pred             cCCeEEEEcccccccccccCCCC---Ccc-hHHHHHHHHHHHhccCCCCCC--CeEEEEecCCCCCCCccccCCCCcceE
Q 030960           12 NAPAIIFIDEVDAIATARFDAQT---GAD-REVQRILMELLNQMDGFDQTV--NVKVIMATNRADTLDPALLRPGRLDRK   85 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~---~~~-~~~~~~~~~ll~~l~~~~~~~--~v~vi~ttn~~~~ld~al~r~grf~~~   85 (168)
                      ...+||+|+|||.-+.-++....   +.+ ....-.++.||+.+||+.+..  ..++|+|||+++.|||||+||||.|.+
T Consensus       285 ~~kSIivIEDIDcs~~l~~~~~~~~~~~~~~~~~VTlSGLLNfiDGlwSscg~ERIivFTTNh~EkLDPALlRpGRmDmh  364 (457)
T KOG0743|consen  285 PNKSILLIEDIDCSFDLRERRKKKKENFEGDLSRVTLSGLLNFLDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDMH  364 (457)
T ss_pred             CCCcEEEEeecccccccccccccccccccCCcceeehHHhhhhhccccccCCCceEEEEecCChhhcCHhhcCCCcceeE
Confidence            34699999999998754322221   111 112356788999999998766  688999999999999999999999999


Q ss_pred             EecCCCCHHHHHHHHHhhcCC---CCCHHHHHhCCCC--CCHHHHHHH
Q 030960           86 IEFPLPDRRQKRLVFQMNLSD---EVDLEDYVSRPDK--ISAAEIAAI  128 (168)
Q Consensus        86 i~~~~P~~~~R~~il~~~l~~---~~~~~~la~~t~g--~s~~di~~l  128 (168)
                      |+++..+.++-..++..|++-   ..-++++....+|  .||||+...
T Consensus       365 I~mgyCtf~~fK~La~nYL~~~~~h~L~~eie~l~~~~~~tPA~V~e~  412 (457)
T KOG0743|consen  365 IYMGYCTFEAFKTLASNYLGIEEDHRLFDEIERLIEETEVTPAQVAEE  412 (457)
T ss_pred             EEcCCCCHHHHHHHHHHhcCCCCCcchhHHHHHHhhcCccCHHHHHHH
Confidence            999999999999999999984   3345667766555  699999763

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

Probab=99.55  E-value=1e-14  Score=113.87  Aligned_cols=152  Identities=18%  Similarity=0.243  Sum_probs=116.6

Q ss_pred             HHHHHHHHHHc-----CCeEEEEcccccccccccCCC-CCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcc
Q 030960            2 VRDVFRLAKEN-----APAIIFIDEVDAIATARFDAQ-TGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPA   75 (168)
Q Consensus         2 l~~iF~~a~~~-----~p~ii~iDe~D~l~~~~~~~~-~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~a   75 (168)
                      +.++|++....     .-..++|||+|+++..|.+.. .......-++++.+|++||++++.++|++++|+|-.+.||.|
T Consensus       234 V~kmF~kI~ELv~d~~~lVfvLIDEVESLa~aR~s~~S~~EpsDaIRvVNalLTQlDrlK~~~NvliL~TSNl~~siD~A  313 (423)
T KOG0744|consen  234 VAKMFQKIQELVEDRGNLVFVLIDEVESLAAARTSASSRNEPSDAIRVVNALLTQLDRLKRYPNVLILATSNLTDSIDVA  313 (423)
T ss_pred             HHHHHHHHHHHHhCCCcEEEEEeHHHHHHHHHHHhhhcCCCCchHHHHHHHHHHHHHHhccCCCEEEEeccchHHHHHHH
Confidence            55666666533     235667999999998885433 333344569999999999999999999999999999999999


Q ss_pred             ccCCCCcceEEecCCCCHHHHHHHHHhhcCC-----------------------CCCHHHHHhC-CCCCCHHHHHHHHHH
Q 030960           76 LLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD-----------------------EVDLEDYVSR-PDKISAAEIAAICQE  131 (168)
Q Consensus        76 l~r~grf~~~i~~~~P~~~~R~~il~~~l~~-----------------------~~~~~~la~~-t~g~s~~di~~l~~~  131 (168)
                      +..  |-|-+.++++|+...|.+|++.|+.+                       +.....+.+. +.|+||+-|..+--.
T Consensus       314 fVD--RADi~~yVG~Pt~~ai~~IlkscieEL~~~gIi~~~~~s~~~~~~i~~~~~~~~~~~~~~~~gLSGRtlrkLP~L  391 (423)
T KOG0744|consen  314 FVD--RADIVFYVGPPTAEAIYEILKSCIEELISSGIILFHQRSTGVKEFIKYQKALRNILIELSTVGLSGRTLRKLPLL  391 (423)
T ss_pred             hhh--HhhheeecCCccHHHHHHHHHHHHHHHHhcCeeeeeccchhhhHHhHhhHhHHHHHHHHhhcCCccchHhhhhHH
Confidence            999  99999999999999999999977661                       1122233333 489999999998776


Q ss_pred             HHHHHHHhCCCccCHHHHHHHHHhhc
Q 030960          132 AGMHAVRKNRYVILPKDFEKGYRTNV  157 (168)
Q Consensus       132 a~~~a~~~~~~~i~~~d~~~al~~~~  157 (168)
                      |-..-.  ...+++.++|..|+-...
T Consensus       392 aha~y~--~~~~v~~~~fl~al~ea~  415 (423)
T KOG0744|consen  392 AHAEYF--RTFTVDLSNFLLALLEAA  415 (423)
T ss_pred             HHHhcc--CCCccChHHHHHHHHHHH
Confidence            533222  235799999999886543

>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=99.54  E-value=3.4e-14  Score=98.29  Aligned_cols=85  Identities=46%  Similarity=0.747  Sum_probs=72.1

Q ss_pred             HHHHHHHHHHcC-CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCC-CCeEEEEecCCCCCCCccccCC
Q 030960            2 VRDVFRLAKENA-PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQT-VNVKVIMATNRADTLDPALLRP   79 (168)
Q Consensus         2 l~~iF~~a~~~~-p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~-~~v~vi~ttn~~~~ld~al~r~   79 (168)
                      ++.+|+.|+..+ ||||+|||+|.+++..   ..........++..++..++..... +++++|+|||.++.++++++| 
T Consensus        46 i~~~~~~~~~~~~~~vl~iDe~d~l~~~~---~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~~~~i~~~l~~-  121 (132)
T PF00004_consen   46 IRDFFKKAKKSAKPCVLFIDEIDKLFPKS---QPSSSSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNSPDKIDPALLR-  121 (132)
T ss_dssp             HHHHHHHHHHTSTSEEEEEETGGGTSHHC---STSSSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESSGGGSCHHHHS-
T ss_pred             cccccccccccccceeeeeccchhccccc---ccccccccccccceeeecccccccccccceeEEeeCChhhCCHhHHh-
Confidence            678999999998 9999999999999877   2234445568888999999987554 679999999999999999998 


Q ss_pred             CCcceEEecCC
Q 030960           80 GRLDRKIEFPL   90 (168)
Q Consensus        80 grf~~~i~~~~   90 (168)
                      |||+..+++++
T Consensus       122 ~rf~~~i~~~~  132 (132)
T PF00004_consen  122 SRFDRRIEFPL  132 (132)
T ss_dssp             TTSEEEEEE-S
T ss_pred             CCCcEEEEcCC
Confidence            89999999874

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 ....

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

Probab=99.08  E-value=5.4e-10  Score=97.94  Aligned_cols=145  Identities=20%  Similarity=0.204  Sum_probs=97.6

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCC-----CCCCccc
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRA-----DTLDPAL   76 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~-----~~ld~al   76 (168)
                      ++.+|+.++...|+||||||+|.+++.+...++  +..   ..+.+...+.    ...+.+|++||..     ...|+++
T Consensus       263 l~~i~~~~~~~~~~ILfiDEih~l~~~g~~~~~--~~~---~~~~L~~~l~----~g~i~~IgaTt~~e~~~~~~~d~al  333 (731)
T TIGR02639       263 LKAVVSEIEKEPNAILFIDEIHTIVGAGATSGG--SMD---ASNLLKPALS----SGKLRCIGSTTYEEYKNHFEKDRAL  333 (731)
T ss_pred             HHHHHHHHhccCCeEEEEecHHHHhccCCCCCc--cHH---HHHHHHHHHh----CCCeEEEEecCHHHHHHHhhhhHHH
Confidence            678999998888999999999999876532221  111   1223333332    4579999999963     3689999


Q ss_pred             cCCCCcceEEecCCCCHHHHHHHHHhhcC----------CCCCHHHHHhCCCCCCH-----HHHHHHHHHHHHHHHHh--
Q 030960           77 LRPGRLDRKIEFPLPDRRQKRLVFQMNLS----------DEVDLEDYVSRPDKISA-----AEIAAICQEAGMHAVRK--  139 (168)
Q Consensus        77 ~r~grf~~~i~~~~P~~~~R~~il~~~l~----------~~~~~~~la~~t~g~s~-----~di~~l~~~a~~~a~~~--  139 (168)
                      .|  ||. .|+++.|+.+++.+|++....          .+-.+..++..+..|-+     .---.++.+|+.....+  
T Consensus       334 ~r--Rf~-~i~v~~p~~~~~~~il~~~~~~~e~~~~v~i~~~al~~~~~ls~ryi~~r~~P~kai~lld~a~a~~~~~~~  410 (731)
T TIGR02639       334 SR--RFQ-KIDVGEPSIEETVKILKGLKEKYEEFHHVKYSDEALEAAVELSARYINDRFLPDKAIDVIDEAGASFRLRPK  410 (731)
T ss_pred             HH--hCc-eEEeCCCCHHHHHHHHHHHHHHHHhccCcccCHHHHHHHHHhhhcccccccCCHHHHHHHHHhhhhhhcCcc
Confidence            99  997 799999999999999984332          12234556666655543     33344555554322211  


Q ss_pred             --CCCccCHHHHHHHHHhhcC
Q 030960          140 --NRYVILPKDFEKGYRTNVK  158 (168)
Q Consensus       140 --~~~~i~~~d~~~al~~~~p  158 (168)
                        .+..|+.+|+..++.....
T Consensus       411 ~~~~~~v~~~~i~~~i~~~tg  431 (731)
T TIGR02639       411 AKKKANVSVKDIENVVAKMAH  431 (731)
T ss_pred             cccccccCHHHHHHHHHHHhC
Confidence              1346999999999998753

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

Probab=99.07  E-value=4.3e-10  Score=98.36  Aligned_cols=145  Identities=19%  Similarity=0.287  Sum_probs=100.2

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC-----CCCccc
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD-----TLDPAL   76 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~-----~ld~al   76 (168)
                      ++.+|..++..+|+||||||+|.+++.++....  .....+++..   .+    ....+.+|++|+.++     ..|+++
T Consensus       267 l~~l~~~l~~~~~~ILfIDEIh~L~g~g~~~~g--~~d~~nlLkp---~L----~~g~i~vIgATt~~E~~~~~~~D~AL  337 (758)
T PRK11034        267 FKALLKQLEQDTNSILFIDEIHTIIGAGAASGG--QVDAANLIKP---LL----SSGKIRVIGSTTYQEFSNIFEKDRAL  337 (758)
T ss_pred             HHHHHHHHHhcCCCEEEeccHHHHhccCCCCCc--HHHHHHHHHH---HH----hCCCeEEEecCChHHHHHHhhccHHH
Confidence            467888888888999999999999876632221  1111222222   22    345799999999865     579999


Q ss_pred             cCCCCcceEEecCCCCHHHHHHHHHhhcC-----CCCCHHH-----HHh---C--CCCCCHHHHHHHHHHHHHHHH----
Q 030960           77 LRPGRLDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLED-----YVS---R--PDKISAAEIAAICQEAGMHAV----  137 (168)
Q Consensus        77 ~r~grf~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~-----la~---~--t~g~s~~di~~l~~~a~~~a~----  137 (168)
                      .|  ||+ .|.++.|+.+++.+|++....     .++.+.+     .+.   +  +..+.|.....++.+|+....    
T Consensus       338 ~r--RFq-~I~v~ePs~~~~~~IL~~~~~~ye~~h~v~i~~~al~~a~~ls~ryi~~r~lPdKaidlldea~a~~~~~~~  414 (758)
T PRK11034        338 AR--RFQ-KIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGARARLMPV  414 (758)
T ss_pred             Hh--hCc-EEEeCCCCHHHHHHHHHHHHHHhhhccCCCcCHHHHHHHHHHhhccccCccChHHHHHHHHHHHHhhccCcc
Confidence            99  996 799999999999999984332     2333322     222   2  345677788889988875432    


Q ss_pred             HhCCCccCHHHHHHHHHhhcC
Q 030960          138 RKNRYVILPKDFEKGYRTNVK  158 (168)
Q Consensus       138 ~~~~~~i~~~d~~~al~~~~p  158 (168)
                      ...+..++.+|+.+.+.+...
T Consensus       415 ~~~~~~v~~~~i~~v~~~~tg  435 (758)
T PRK11034        415 SKRKKTVNVADIESVVARIAR  435 (758)
T ss_pred             cccccccChhhHHHHHHHHhC
Confidence            223456888999999887654

>CHL00181 cbbX CbbX; Provisional

Probab=99.03  E-value=6.7e-09  Score=81.66  Aligned_cols=118  Identities=18%  Similarity=0.254  Sum_probs=80.5

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC-----CCCccccCCCCcceEEe
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD-----TLDPALLRPGRLDRKIE   87 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~-----~ld~al~r~grf~~~i~   87 (168)
                      .++||||||+|.++..++.  ..   ........++..|+.  ...+++||++++...     .++|++.+  ||+..|+
T Consensus       122 ~ggVLfIDE~~~l~~~~~~--~~---~~~e~~~~L~~~me~--~~~~~~vI~ag~~~~~~~~~~~np~L~s--R~~~~i~  192 (287)
T CHL00181        122 MGGVLFIDEAYYLYKPDNE--RD---YGSEAIEILLQVMEN--QRDDLVVIFAGYKDRMDKFYESNPGLSS--RIANHVD  192 (287)
T ss_pred             cCCEEEEEccchhccCCCc--cc---hHHHHHHHHHHHHhc--CCCCEEEEEeCCcHHHHHHHhcCHHHHH--hCCceEE
Confidence            4689999999999754321  11   123667778888874  334677777764311     34689999  9999999


Q ss_pred             cCCCCHHHHHHHHHhhcCC---CC---CHHH----HHhC--CCCCC-HHHHHHHHHHHHHHHHHh
Q 030960           88 FPLPDRRQKRLVFQMNLSD---EV---DLED----YVSR--PDKIS-AAEIAAICQEAGMHAVRK  139 (168)
Q Consensus        88 ~~~P~~~~R~~il~~~l~~---~~---~~~~----la~~--t~g~s-~~di~~l~~~a~~~a~~~  139 (168)
                      |++++.+++.+|++.++..   .+   ....    +...  .+.|. ++++.++++.+...-..+
T Consensus       193 F~~~t~~el~~I~~~~l~~~~~~l~~~~~~~L~~~i~~~~~~~~~GNaR~vrn~ve~~~~~~~~r  257 (287)
T CHL00181        193 FPDYTPEELLQIAKIMLEEQQYQLTPEAEKALLDYIKKRMEQPLFANARSVRNALDRARMRQANR  257 (287)
T ss_pred             cCCcCHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHhCCCCCCccHHHHHHHHHHHHHHHHHH
Confidence            9999999999999977652   11   1222    2222  34566 899999999986554443

>TIGR00763 lon ATP-dependent protease La

Probab=98.97  E-value=6.6e-09  Score=91.67  Aligned_cols=138  Identities=25%  Similarity=0.354  Sum_probs=88.6

Q ss_pred             HHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC-----CC--------CCCCeEEEEecCCC
Q 030960            3 RDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG-----FD--------QTVNVKVIMATNRA   69 (168)
Q Consensus         3 ~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~-----~~--------~~~~v~vi~ttn~~   69 (168)
                      ...|..|....| ||+|||+|.+.+...+    .      ..+.|+..+|.     +.        ..+++++|+|||.+
T Consensus       405 ~~~l~~~~~~~~-villDEidk~~~~~~~----~------~~~aLl~~ld~~~~~~f~d~~~~~~~d~s~v~~I~TtN~~  473 (775)
T TIGR00763       405 IQGLKKAKTKNP-LFLLDEIDKIGSSFRG----D------PASALLEVLDPEQNNAFSDHYLDVPFDLSKVIFIATANSI  473 (775)
T ss_pred             HHHHHHhCcCCC-EEEEechhhcCCccCC----C------HHHHHHHhcCHHhcCccccccCCceeccCCEEEEEecCCc
Confidence            456777766655 8899999999853211    1      12344554442     11        12578999999999


Q ss_pred             CCCCccccCCCCcceEEecCCCCHHHHHHHHHhhcC-----------CCC-----CHHHHHh-CCCCCCHHHHHH----H
Q 030960           70 DTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLS-----------DEV-----DLEDYVS-RPDKISAAEIAA----I  128 (168)
Q Consensus        70 ~~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~-----------~~~-----~~~~la~-~t~g~s~~di~~----l  128 (168)
                      +.+|+++++  ||+ .|+|+.|+.+++.+|++.++.           ..+     .+..+++ .|..+..++|+.    +
T Consensus       474 ~~i~~~L~~--R~~-vi~~~~~~~~e~~~I~~~~l~~~~~~~~~l~~~~~~~~~~~l~~i~~~~~~e~g~R~l~r~i~~~  550 (775)
T TIGR00763       474 DTIPRPLLD--RME-VIELSGYTEEEKLEIAKKYLIPKALEDHGLKPDELKITDEALLLLIKYYTREAGVRNLERQIEKI  550 (775)
T ss_pred             hhCCHHHhC--Cee-EEecCCCCHHHHHHHHHHHHHHHHHHHcCCCcceEEECHHHHHHHHHhcChhcCChHHHHHHHHH
Confidence            999999999  995 789999999999999986652           111     2334444 344455555555    4


Q ss_pred             HHHHHHHHHHhCC--------CccCHHHHHHHHH
Q 030960          129 CQEAGMHAVRKNR--------YVILPKDFEKGYR  154 (168)
Q Consensus       129 ~~~a~~~a~~~~~--------~~i~~~d~~~al~  154 (168)
                      |+.++...+..+.        ..++.+++...+.
T Consensus       551 ~~~~~~~~~~~~~~~~~~~~~v~i~~~~~~~~lg  584 (775)
T TIGR00763       551 CRKAAVKLVEQGEKKKSEAESVVITPDNLKKYLG  584 (775)
T ss_pred             HHHHHHHHHhccCcccCCcccccCCHHHHHHhcC
Confidence            5444443332221        3678887776654

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.

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.95  E-value=1.5e-08  Score=81.82  Aligned_cols=141  Identities=22%  Similarity=0.266  Sum_probs=96.5

Q ss_pred             HHHHHHHH-HcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC-CCCCCeEEEEecCCCC---CCCcccc
Q 030960            3 RDVFRLAK-ENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF-DQTVNVKVIMATNRAD---TLDPALL   77 (168)
Q Consensus         3 ~~iF~~a~-~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~-~~~~~v~vi~ttn~~~---~ld~al~   77 (168)
                      +.+++... ...|.||+|||+|.+....       .    .++..++...+.. ....++.+|+++|.++   .+++.+.
T Consensus       118 ~~l~~~l~~~~~~~vlvIDE~d~L~~~~-------~----~~L~~l~~~~~~~~~~~~~v~lI~i~n~~~~~~~l~~~~~  186 (365)
T TIGR02928       118 RRLYKELNERGDSLIIVLDEIDYLVGDD-------D----DLLYQLSRARSNGDLDNAKVGVIGISNDLKFRENLDPRVK  186 (365)
T ss_pred             HHHHHHHHhcCCeEEEEECchhhhccCC-------c----HHHHhHhccccccCCCCCeEEEEEEECCcchHhhcCHHHh
Confidence            34555444 3457899999999997211       0    2444555442211 2235788999999886   5888888


Q ss_pred             CCCCcc-eEEecCCCCHHHHHHHHHhhcC----C-CCC---HHH---HHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccC
Q 030960           78 RPGRLD-RKIEFPLPDRRQKRLVFQMNLS----D-EVD---LED---YVSRPDKISAAEIAAICQEAGMHAVRKNRYVIL  145 (168)
Q Consensus        78 r~grf~-~~i~~~~P~~~~R~~il~~~l~----~-~~~---~~~---la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~  145 (168)
                      +  ||. ..++|++++.++..+|++..+.    + .++   ++.   ++..+.| .++..-.+|..|+..|..++...|+
T Consensus       187 s--~~~~~~i~f~p~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~G-d~R~al~~l~~a~~~a~~~~~~~it  263 (365)
T TIGR02928       187 S--SLCEEEIIFPPYDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHG-DARKAIDLLRVAGEIAEREGAERVT  263 (365)
T ss_pred             c--cCCcceeeeCCCCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcC-CHHHHHHHHHHHHHHHHHcCCCCCC
Confidence            7  775 6799999999999999986553    1 111   222   3334445 3455566888899889888888999


Q ss_pred             HHHHHHHHHhhc
Q 030960          146 PKDFEKGYRTNV  157 (168)
Q Consensus       146 ~~d~~~al~~~~  157 (168)
                      .+|+..|+....
T Consensus       264 ~~~v~~a~~~~~  275 (365)
T TIGR02928       264 EDHVEKAQEKIE  275 (365)
T ss_pred             HHHHHHHHHHHH
Confidence            999999987653

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

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.86  E-value=3.7e-08  Score=80.35  Aligned_cols=132  Identities=17%  Similarity=0.267  Sum_probs=94.1

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC---CCCccccCCCCcc-eEEec
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD---TLDPALLRPGRLD-RKIEF   88 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~---~ld~al~r~grf~-~~i~~   88 (168)
                      .+.||+|||+|.+....     .     ...+..++..++.... .++.+|+++|.++   .+++.+.+  ||. ..+.|
T Consensus       138 ~~~viviDE~d~l~~~~-----~-----~~~l~~l~~~~~~~~~-~~v~vI~i~~~~~~~~~l~~~~~s--~~~~~~i~f  204 (394)
T PRK00411        138 RVLIVALDDINYLFEKE-----G-----NDVLYSLLRAHEEYPG-ARIGVIGISSDLTFLYILDPRVKS--VFRPEEIYF  204 (394)
T ss_pred             CEEEEEECCHhHhhccC-----C-----chHHHHHHHhhhccCC-CeEEEEEEECCcchhhhcCHHHHh--cCCcceeec
Confidence            47899999999997211     0     1456666666655433 3788888888764   46777766  664 57899


Q ss_pred             CCCCHHHHHHHHHhhcCC--------CCCHHHHHhCCCCC--CHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhc
Q 030960           89 PLPDRRQKRLVFQMNLSD--------EVDLEDYVSRPDKI--SAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNV  157 (168)
Q Consensus        89 ~~P~~~~R~~il~~~l~~--------~~~~~~la~~t~g~--s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~  157 (168)
                      ++++.++..+|++..+..        +..++.+++.+.+.  ..+..-.+|..|+..|..++...|+.+|+.+|+....
T Consensus       205 ~py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~  283 (394)
T PRK00411        205 PPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSE  283 (394)
T ss_pred             CCCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHH
Confidence            999999999999865431        12345566666332  3455567888888888888888999999999998764

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=98.86  E-value=3.9e-08  Score=77.23  Aligned_cols=125  Identities=18%  Similarity=0.306  Sum_probs=83.8

Q ss_pred             HHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCC--CC---CCCcccc
Q 030960            3 RDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNR--AD---TLDPALL   77 (168)
Q Consensus         3 ~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~--~~---~ld~al~   77 (168)
                      +.+|+.|   .+++|||||+|.+...+..  ..   ....+.+.++..|+.  ...+++||++++.  ++   .++|++.
T Consensus       114 ~~~~~~a---~~gvL~iDEi~~L~~~~~~--~~---~~~~~~~~Ll~~le~--~~~~~~vI~a~~~~~~~~~~~~np~L~  183 (284)
T TIGR02880       114 KEILKRA---MGGVLFIDEAYYLYRPDNE--RD---YGQEAIEILLQVMEN--QRDDLVVILAGYKDRMDSFFESNPGFS  183 (284)
T ss_pred             HHHHHHc---cCcEEEEechhhhccCCCc--cc---hHHHHHHHHHHHHhc--CCCCEEEEEeCCcHHHHHHHhhCHHHH
Confidence            3455554   4699999999998644311  11   223566778888874  3456777777653  23   2479999


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhcCC---CCC---HHHHHhC------CCCCC-HHHHHHHHHHHHHHHHHh
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNLSD---EVD---LEDYVSR------PDKIS-AAEIAAICQEAGMHAVRK  139 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l~~---~~~---~~~la~~------t~g~s-~~di~~l~~~a~~~a~~~  139 (168)
                      +  ||+..|+||+++.+++..|++.++..   .++   +..+..+      -+.+. ++++.++++.+...-..+
T Consensus       184 s--R~~~~i~fp~l~~edl~~I~~~~l~~~~~~l~~~a~~~L~~~l~~~~~~~~~GN~R~lrn~ve~~~~~~~~r  256 (284)
T TIGR02880       184 S--RVAHHVDFPDYSEAELLVIAGLMLKEQQYRFSAEAEEAFADYIALRRTQPHFANARSIRNAIDRARLRQANR  256 (284)
T ss_pred             h--hCCcEEEeCCcCHHHHHHHHHHHHHHhccccCHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHH
Confidence            9  99999999999999999999987763   111   1222222      13333 799999999986555443

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.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=98.85  E-value=3.2e-08  Score=79.15  Aligned_cols=98  Identities=16%  Similarity=0.064  Sum_probs=80.1

Q ss_pred             CCeEEEEecCCCCCCCccccCCCCcceEEecCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHH
Q 030960           58 VNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQE  131 (168)
Q Consensus        58 ~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~  131 (168)
                      +++.+|++||.+..+++++++  ||+..+.+++|+.+++.++++....      ++-.+..+++.+.| +++.+..+++.
T Consensus       149 ~~~~li~at~~~~~l~~~L~s--Rf~~~~~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G-~pR~a~~~l~~  225 (328)
T PRK00080        149 PPFTLIGATTRAGLLTSPLRD--RFGIVQRLEFYTVEELEKIVKRSARILGVEIDEEGALEIARRSRG-TPRIANRLLRR  225 (328)
T ss_pred             CCceEEeecCCcccCCHHHHH--hcCeeeecCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCC-CchHHHHHHHH
Confidence            347889999999999999998  9999999999999999999985544      12236778888887 45888888888


Q ss_pred             HHHHHHHhCCCccCHHHHHHHHHhhcC
Q 030960          132 AGMHAVRKNRYVILPKDFEKGYRTNVK  158 (168)
Q Consensus       132 a~~~a~~~~~~~i~~~d~~~al~~~~p  158 (168)
                      +...+...+...|+.+++..++.....
T Consensus       226 ~~~~a~~~~~~~I~~~~v~~~l~~~~~  252 (328)
T PRK00080        226 VRDFAQVKGDGVITKEIADKALDMLGV  252 (328)
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHhCC
Confidence            877777666678999999999976543

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.84  E-value=3.4e-08  Score=77.96  Aligned_cols=96  Identities=11%  Similarity=0.043  Sum_probs=77.7

Q ss_pred             CCeEEEEecCCCCCCCccccCCCCcceEEecCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHH
Q 030960           58 VNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQE  131 (168)
Q Consensus        58 ~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~  131 (168)
                      +++.+|++||++..+++++++  ||...+.+++|+.+++.++++....      ++-.++.+++.+.|+ ++.+..++..
T Consensus       128 ~~~~li~~t~~~~~l~~~l~s--R~~~~~~l~~l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~-pR~~~~ll~~  204 (305)
T TIGR00635       128 PPFTLVGATTRAGMLTSPLRD--RFGIILRLEFYTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGT-PRIANRLLRR  204 (305)
T ss_pred             CCeEEEEecCCccccCHHHHh--hcceEEEeCCCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCC-cchHHHHHHH
Confidence            348899999999999999999  9999999999999999999985543      122456788888884 4777888888


Q ss_pred             HHHHHHHhCCCccCHHHHHHHHHhh
Q 030960          132 AGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus       132 a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      +...+...+...++.+++..++...
T Consensus       205 ~~~~a~~~~~~~it~~~v~~~l~~l  229 (305)
T TIGR00635       205 VRDFAQVRGQKIINRDIALKALEML  229 (305)
T ss_pred             HHHHHHHcCCCCcCHHHHHHHHHHh
Confidence            7766666666779999999888763

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.

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=98.83  E-value=1.1e-07  Score=73.85  Aligned_cols=124  Identities=18%  Similarity=0.193  Sum_probs=80.1

Q ss_pred             HHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCC-----CCCCcccc
Q 030960            3 RDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRA-----DTLDPALL   77 (168)
Q Consensus         3 ~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~-----~~ld~al~   77 (168)
                      +++|+.|   .++||||||+|.+....      ........+..++..++..  ...+++|+++...     ..++|++.
T Consensus        98 ~~~~~~a---~~~VL~IDE~~~L~~~~------~~~~~~~~i~~Ll~~~e~~--~~~~~vila~~~~~~~~~~~~~p~L~  166 (261)
T TIGR02881        98 REVIKKA---LGGVLFIDEAYSLARGG------EKDFGKEAIDTLVKGMEDN--RNEFVLILAGYSDEMDYFLSLNPGLR  166 (261)
T ss_pred             HHHHHhc---cCCEEEEechhhhccCC------ccchHHHHHHHHHHHHhcc--CCCEEEEecCCcchhHHHHhcChHHH
Confidence            4566555   36899999999996311      1112235677788888753  3445555544321     24688999


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhcCCC-C-----CHHHHHhC---------CCCCCHHHHHHHHHHHHHHHHHh
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNLSDE-V-----DLEDYVSR---------PDKISAAEIAAICQEAGMHAVRK  139 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l~~~-~-----~~~~la~~---------t~g~s~~di~~l~~~a~~~a~~~  139 (168)
                      +  ||+..++|+.++.+++.+|++.++... .     .+..+++.         ...-.++.+.+++..|......+
T Consensus       167 s--Rf~~~i~f~~~~~~el~~Il~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~~~~gn~R~~~n~~e~a~~~~~~r  241 (261)
T TIGR02881       167 S--RFPISIDFPDYTVEELMEIAERMVKEREYKLTEEAKWKLREHLYKVDQLSSREFSNARYVRNIIEKAIRRQAVR  241 (261)
T ss_pred             h--ccceEEEECCCCHHHHHHHHHHHHHHcCCccCHHHHHHHHHHHHHHHhccCCCCchHHHHHHHHHHHHHHHHHH
Confidence            9  999999999999999999999776521 1     12233221         12245788888888876555443

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.

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=98.77  E-value=4.8e-08  Score=82.90  Aligned_cols=91  Identities=22%  Similarity=0.138  Sum_probs=74.3

Q ss_pred             eEEEEecCCCCCCCccccCCCCcceEEecCCCCHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHH
Q 030960           60 VKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAG  133 (168)
Q Consensus        60 v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~  133 (168)
                      .++++||+.|+.+++++++  |+. .+.+++++.+++.++++..+..      +..++.++.++.  +++++.++++.|+
T Consensus       235 rlI~ATt~~p~~L~paLrs--R~~-~I~f~pL~~eei~~Il~~~a~k~~i~is~~al~~I~~y~~--n~Rel~nll~~Aa  309 (531)
T TIGR02902       235 RLIGATTRNPEEIPPALRS--RCV-EIFFRPLLDEEIKEIAKNAAEKIGINLEKHALELIVKYAS--NGREAVNIVQLAA  309 (531)
T ss_pred             EEEEEecCCcccCChHHhh--hhh-eeeCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhh--hHHHHHHHHHHHH
Confidence            4566788899999999999  884 6889999999999999976652      122445666553  7899999999999


Q ss_pred             HHHHHhCCCccCHHHHHHHHHh
Q 030960          134 MHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus       134 ~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      ..+..+++..|+.+|+..++..
T Consensus       310 ~~A~~~~~~~It~~dI~~vl~~  331 (531)
T TIGR02902       310 GIALGEGRKRILAEDIEWVAEN  331 (531)
T ss_pred             HHHhhCCCcEEcHHHHHHHhCC
Confidence            9888888888999999999973

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=98.75  E-value=5.7e-08  Score=86.40  Aligned_cols=139  Identities=21%  Similarity=0.252  Sum_probs=88.6

Q ss_pred             HHHHHHHHHH-cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC-----CCCcc
Q 030960            2 VRDVFRLAKE-NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD-----TLDPA   75 (168)
Q Consensus         2 l~~iF~~a~~-~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~-----~ld~a   75 (168)
                      ++.+|+.++. ..++||||||++.+.+.++.....+      ..+.|+..+    ..+.+.+||+|+..+     .+|+|
T Consensus       268 lk~ii~e~~~~~~~~ILfIDEih~l~~~g~~~~~~d------~~n~Lkp~l----~~G~l~~IgaTT~~e~~~~~~~d~A  337 (852)
T TIGR03345       268 LKSVIDEVKASPQPIILFIDEAHTLIGAGGQAGQGD------AANLLKPAL----ARGELRTIAATTWAEYKKYFEKDPA  337 (852)
T ss_pred             HHHHHHHHHhcCCCeEEEEeChHHhccCCCcccccc------HHHHhhHHh----hCCCeEEEEecCHHHHhhhhhccHH
Confidence            5778888875 4689999999999987653322111      112233333    355799999998643     48999


Q ss_pred             ccCCCCcceEEecCCCCHHHHHHHHHhh---cC-------CCCCHHHHHhCCCCCC-----HHHHHHHHHHHHHHH-HHh
Q 030960           76 LLRPGRLDRKIEFPLPDRRQKRLVFQMN---LS-------DEVDLEDYVSRPDKIS-----AAEIAAICQEAGMHA-VRK  139 (168)
Q Consensus        76 l~r~grf~~~i~~~~P~~~~R~~il~~~---l~-------~~~~~~~la~~t~g~s-----~~di~~l~~~a~~~a-~~~  139 (168)
                      |.|  ||. .|.++.|+.+++.+||+..   +.       .+..+..++..+.+|-     |.---.++.+|+... +..
T Consensus       338 L~r--Rf~-~i~v~eps~~~~~~iL~~~~~~~e~~~~v~i~d~al~~~~~ls~ryi~~r~LPDKAIdlldea~a~~~~~~  414 (852)
T TIGR03345       338 LTR--RFQ-VVKVEEPDEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVELSHRYIPGRQLPDKAVSLLDTACARVALSQ  414 (852)
T ss_pred             HHH--hCe-EEEeCCCCHHHHHHHHHHHHHhhhhcCCCeeCHHHHHHHHHHcccccccccCccHHHHHHHHHHHHHHHhc
Confidence            999  996 7999999999999997622   22       1334556677776654     333444556654333 333


Q ss_pred             CCCccCHHHHHHHH
Q 030960          140 NRYVILPKDFEKGY  153 (168)
Q Consensus       140 ~~~~i~~~d~~~al  153 (168)
                      ...+...+++.+.+
T Consensus       415 ~~~p~~~~~~~~~~  428 (852)
T TIGR03345       415 NATPAALEDLRRRI  428 (852)
T ss_pred             cCCchhHHHHHHHH
Confidence            34444444444443

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.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=98.75  E-value=1.2e-07  Score=78.01  Aligned_cols=129  Identities=13%  Similarity=0.168  Sum_probs=87.1

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCC---CCccccCCCCcc--eEEe
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADT---LDPALLRPGRLD--RKIE   87 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~---ld~al~r~grf~--~~i~   87 (168)
                      .+.+|+|||+|.+.+.+            .....++..++.+...+..+||+++..|..   +++.+.+  ||.  ..+.
T Consensus       199 ~~dlLiiDDi~~l~~~~------------~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~S--Rl~~g~~v~  264 (405)
T TIGR00362       199 SVDLLLIDDIQFLAGKE------------RTQEEFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRS--RFEWGLVVD  264 (405)
T ss_pred             hCCEEEEehhhhhcCCH------------HHHHHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhh--hccCCeEEE
Confidence            36899999999986432            111123333333222334556666666665   5578888  996  4799


Q ss_pred             cCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhc
Q 030960           88 FPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNV  157 (168)
Q Consensus        88 ~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~  157 (168)
                      +++|+.++|..|++....      ++-.++.+|++..| +.++|+.+++.....+... +..||.+.+.+++....
T Consensus       265 i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~-~~r~l~~~l~~l~~~a~~~-~~~it~~~~~~~L~~~~  338 (405)
T TIGR00362       265 IEPPDLETRLAILQKKAEEEGLELPDEVLEFIAKNIRS-NVRELEGALNRLLAYASLT-GKPITLELAKEALKDLL  338 (405)
T ss_pred             eCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-CHHHHHHHHHHHHHHHHHh-CCCCCHHHHHHHHHHhc
Confidence            999999999999996654      23345668877654 7788998888876666543 35688888888887653

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).

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=98.70  E-value=1.2e-07  Score=78.94  Aligned_cols=129  Identities=12%  Similarity=0.175  Sum_probs=89.3

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCC---CCccccCCCCcc--eEEe
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADT---LDPALLRPGRLD--RKIE   87 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~---ld~al~r~grf~--~~i~   87 (168)
                      .+.+|+|||+|.+.+++            .....++..++.+....+.++|+++..|..   +++.+.+  ||.  ..+.
T Consensus       211 ~~dlLiiDDi~~l~~~~------------~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~l~S--Rl~~gl~v~  276 (450)
T PRK00149        211 SVDVLLIDDIQFLAGKE------------RTQEEFFHTFNALHEAGKQIVLTSDRPPKELPGLEERLRS--RFEWGLTVD  276 (450)
T ss_pred             cCCEEEEehhhhhcCCH------------HHHHHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHh--HhcCCeeEE
Confidence            47899999999985432            111223333333222334456666666655   6788988  996  5899


Q ss_pred             cCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhc
Q 030960           88 FPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNV  157 (168)
Q Consensus        88 ~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~  157 (168)
                      +.+|+.++|..|++....      ++..++.+|..+.| +.++|..+++.....+...+ ..||.+.+.++++...
T Consensus       277 i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~-~~R~l~~~l~~l~~~~~~~~-~~it~~~~~~~l~~~~  350 (450)
T PRK00149        277 IEPPDLETRIAILKKKAEEEGIDLPDEVLEFIAKNITS-NVRELEGALNRLIAYASLTG-KPITLELAKEALKDLL  350 (450)
T ss_pred             ecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHcCcCC-CHHHHHHHHHHHHHHHHhhC-CCCCHHHHHHHHHHhh
Confidence            999999999999996654      22346677877755 78888888888766665443 4689999999988763

>PRK06893 DNA replication initiation factor; Validated

Probab=98.52  E-value=4.3e-07  Score=69.16  Aligned_cols=128  Identities=13%  Similarity=0.125  Sum_probs=83.5

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCC-CeEEEEecCCCCCCC---ccccCCCCcceEEec
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTV-NVKVIMATNRADTLD---PALLRPGRLDRKIEF   88 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~-~v~vi~ttn~~~~ld---~al~r~grf~~~i~~   88 (168)
                      ++.+|+|||++.+.+++     .    .+..+-.+++.+   ...+ .+++++++..|..++   +.+.+..+++..+.+
T Consensus        91 ~~dlLilDDi~~~~~~~-----~----~~~~l~~l~n~~---~~~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l  158 (229)
T PRK06893         91 QQDLVCLDDLQAVIGNE-----E----WELAIFDLFNRI---KEQGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQL  158 (229)
T ss_pred             cCCEEEEeChhhhcCCh-----H----HHHHHHHHHHHH---HHcCCcEEEEeCCCChHHccccchhHHHHHhcCCeeeC
Confidence            46899999999886432     1    112233333333   2233 355666667787776   788884456689999


Q ss_pred             CCCCHHHHHHHHHhhcC-C-----CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960           89 PLPDRRQKRLVFQMNLS-D-----EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus        89 ~~P~~~~R~~il~~~l~-~-----~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      ++|+.++|.++++.... .     +..++.|+.+.+| +.+.+..+++.-...+.. .++.||...+.+++.
T Consensus       159 ~~pd~e~~~~iL~~~a~~~~l~l~~~v~~~L~~~~~~-d~r~l~~~l~~l~~~~~~-~~~~it~~~v~~~L~  228 (229)
T PRK06893        159 NDLTDEQKIIVLQRNAYQRGIELSDEVANFLLKRLDR-DMHTLFDALDLLDKASLQ-AQRKLTIPFVKEILG  228 (229)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccC-CHHHHHHHHHHHHHHHHh-cCCCCCHHHHHHHhc
Confidence            99999999999985543 2     2334567777754 677777777765434443 334799888887763

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.51  E-value=9.1e-07  Score=78.07  Aligned_cols=137  Identities=18%  Similarity=0.269  Sum_probs=88.7

Q ss_pred             HHHHHHHHH--HcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCC---CCCCCccc
Q 030960            2 VRDVFRLAK--ENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNR---ADTLDPAL   76 (168)
Q Consensus         2 l~~iF~~a~--~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~---~~~ld~al   76 (168)
                      +..+|....  ...++||+|||+|.|....           +.++-.|..+..  ....++.|||++|.   +..+++.+
T Consensus       856 LerLF~~L~k~~r~v~IIILDEID~L~kK~-----------QDVLYnLFR~~~--~s~SKLiLIGISNdlDLperLdPRL  922 (1164)
T PTZ00112        856 LDRLFNQNKKDNRNVSILIIDEIDYLITKT-----------QKVLFTLFDWPT--KINSKLVLIAISNTMDLPERLIPRC  922 (1164)
T ss_pred             HHHHHhhhhcccccceEEEeehHhhhCccH-----------HHHHHHHHHHhh--ccCCeEEEEEecCchhcchhhhhhh
Confidence            455666552  2236799999999997421           244555555443  23457999999986   66778888


Q ss_pred             cCCCCcce-EEecCCCCHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHH---HHHHHHHHHhCCCccCH
Q 030960           77 LRPGRLDR-KIEFPLPDRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAIC---QEAGMHAVRKNRYVILP  146 (168)
Q Consensus        77 ~r~grf~~-~i~~~~P~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~---~~a~~~a~~~~~~~i~~  146 (168)
                      .+  ||.. .+.|++++.++..+||+..+..      +..+..+|.... -..+|+..++   +.|+..   .+...|+.
T Consensus       923 RS--RLg~eeIvF~PYTaEQL~dILk~RAe~A~gVLdDdAIELIArkVA-q~SGDARKALDILRrAgEi---kegskVT~  996 (1164)
T PTZ00112        923 RS--RLAFGRLVFSPYKGDEIEKIIKERLENCKEIIDHTAIQLCARKVA-NVSGDIRKALQICRKAFEN---KRGQKIVP  996 (1164)
T ss_pred             hh--ccccccccCCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhh-hcCCHHHHHHHHHHHHHhh---cCCCccCH
Confidence            88  7764 4888999999999999865542      222444555333 2335665544   444432   23447999


Q ss_pred             HHHHHHHHhhc
Q 030960          147 KDFEKGYRTNV  157 (168)
Q Consensus       147 ~d~~~al~~~~  157 (168)
                      +|+.+|+.+..
T Consensus       997 eHVrkAleeiE 1007 (1164)
T PTZ00112        997 RDITEATNQLF 1007 (1164)
T ss_pred             HHHHHHHHHHH
Confidence            99999987653

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=98.47  E-value=7.6e-07  Score=74.02  Aligned_cols=129  Identities=12%  Similarity=0.128  Sum_probs=85.7

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCC---CCccccCCCCcc--eEEe
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADT---LDPALLRPGRLD--RKIE   87 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~---ld~al~r~grf~--~~i~   87 (168)
                      +|.+|+|||++.+.+...            ....+...++.+...++.+||++...|..   +.+.+.+  ||.  ..+.
T Consensus       194 ~~dvLlIDDi~~l~~~~~------------~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~rL~S--R~~~gl~v~  259 (440)
T PRK14088        194 KVDVLLIDDVQFLIGKTG------------VQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVS--RFQMGLVAK  259 (440)
T ss_pred             cCCEEEEechhhhcCcHH------------HHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHHHHhh--HHhcCceEe
Confidence            689999999998864320            11122222332223334556666667765   4567887  774  6778


Q ss_pred             cCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhc
Q 030960           88 FPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNV  157 (168)
Q Consensus        88 ~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~  157 (168)
                      +.+|+.+.|.+|++....      ++..++.||+...| +.++|+.++..-...+...+ .++|.+...++++...
T Consensus       260 i~~pd~e~r~~IL~~~~~~~~~~l~~ev~~~Ia~~~~~-~~R~L~g~l~~l~~~~~~~~-~~it~~~a~~~L~~~~  333 (440)
T PRK14088        260 LEPPDEETRKKIARKMLEIEHGELPEEVLNFVAENVDD-NLRRLRGAIIKLLVYKETTG-EEVDLKEAILLLKDFI  333 (440)
T ss_pred             eCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHhcccc-CHHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHHHHHh
Confidence            999999999999986654      12345667887765 78888888887655554443 4688888888887653

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=98.43  E-value=1.6e-06  Score=71.04  Aligned_cols=108  Identities=14%  Similarity=0.183  Sum_probs=77.1

Q ss_pred             HHHHHHHHHHc----CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcccc
Q 030960            2 VRDVFRLAKEN----APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~~----~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~   77 (168)
                      |+++++.+...    ...|++|||+|.+..              ...+.|+..|+.  ..+++++|.+|++++.++|+++
T Consensus       102 iR~l~~~~~~~p~~~~~kViiIDead~m~~--------------~aanaLLk~LEe--p~~~~~fIL~a~~~~~llpTIr  165 (394)
T PRK07940        102 VRELVTIAARRPSTGRWRIVVIEDADRLTE--------------RAANALLKAVEE--PPPRTVWLLCAPSPEDVLPTIR  165 (394)
T ss_pred             HHHHHHHHHhCcccCCcEEEEEechhhcCH--------------HHHHHHHHHhhc--CCCCCeEEEEECChHHChHHHH
Confidence            57788777643    245999999999832              234667888874  3445556666666999999999


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhcC-CCCCHHHHHhCCCCCCHHHHHHH
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNLS-DEVDLEDYVSRPDKISAAEIAAI  128 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l~-~~~~~~~la~~t~g~s~~di~~l  128 (168)
                      +  |+ ..+.|++|+.++..+.+..... +......++..+.|..+..+.-+
T Consensus       166 S--Rc-~~i~f~~~~~~~i~~~L~~~~~~~~~~a~~la~~s~G~~~~A~~l~  214 (394)
T PRK07940        166 S--RC-RHVALRTPSVEAVAEVLVRRDGVDPETARRAARASQGHIGRARRLA  214 (394)
T ss_pred             h--hC-eEEECCCCCHHHHHHHHHHhcCCCHHHHHHHHHHcCCCHHHHHHHh
Confidence            9  87 6999999999999888864322 22335568888889877665443

>PRK10865 protein disaggregation chaperone; Provisional

Probab=98.42  E-value=5.7e-07  Score=80.27  Aligned_cols=88  Identities=19%  Similarity=0.251  Sum_probs=64.5

Q ss_pred             HHHHHHHHH-HcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC-----CCCcc
Q 030960            2 VRDVFRLAK-ENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD-----TLDPA   75 (168)
Q Consensus         2 l~~iF~~a~-~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~-----~ld~a   75 (168)
                      ++.+|+.+. ...|+||||||++.+.+.+++.++ .  ....+   |...    -..+.+.+||+|+..+     .+|++
T Consensus       259 lk~~~~~~~~~~~~~ILfIDEih~l~~~~~~~~~-~--d~~~~---lkp~----l~~g~l~~IgaTt~~e~r~~~~~d~a  328 (857)
T PRK10865        259 LKGVLNDLAKQEGNVILFIDELHTMVGAGKADGA-M--DAGNM---LKPA----LARGELHCVGATTLDEYRQYIEKDAA  328 (857)
T ss_pred             HHHHHHHHHHcCCCeEEEEecHHHhccCCCCccc-h--hHHHH---hcch----hhcCCCeEEEcCCCHHHHHHhhhcHH
Confidence            567887754 356999999999999876532221 1  11122   2222    2456899999999877     48999


Q ss_pred             ccCCCCcceEEecCCCCHHHHHHHHHh
Q 030960           76 LLRPGRLDRKIEFPLPDRRQKRLVFQM  102 (168)
Q Consensus        76 l~r~grf~~~i~~~~P~~~~R~~il~~  102 (168)
                      +.|  ||+ .|.++.|+.+++..|++.
T Consensus       329 l~r--Rf~-~i~v~eP~~~~~~~iL~~  352 (857)
T PRK10865        329 LER--RFQ-KVFVAEPSVEDTIAILRG  352 (857)
T ss_pred             HHh--hCC-EEEeCCCCHHHHHHHHHH
Confidence            999  998 588999999999999973

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=98.41  E-value=5.1e-07  Score=80.61  Aligned_cols=88  Identities=19%  Similarity=0.182  Sum_probs=63.6

Q ss_pred             HHHHHHHHHHc-CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC-----CCCcc
Q 030960            2 VRDVFRLAKEN-APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD-----TLDPA   75 (168)
Q Consensus         2 l~~iF~~a~~~-~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~-----~ld~a   75 (168)
                      ++.+|+.+... .|+||||||++.+++.+...+.   .   ...+.+...    .....+.+||+|+..+     .+|++
T Consensus       254 l~~~l~~~~~~~~~~ILfIDEih~l~~~g~~~~~---~---d~~~~Lk~~----l~~g~i~~IgaTt~~e~r~~~~~d~a  323 (852)
T TIGR03346       254 LKAVLNEVTKSEGQIILFIDELHTLVGAGKAEGA---M---DAGNMLKPA----LARGELHCIGATTLDEYRKYIEKDAA  323 (852)
T ss_pred             HHHHHHHHHhcCCCeEEEeccHHHhhcCCCCcch---h---HHHHHhchh----hhcCceEEEEeCcHHHHHHHhhcCHH
Confidence            56778877654 5999999999999865422211   1   122222222    2455799999999874     58999


Q ss_pred             ccCCCCcceEEecCCCCHHHHHHHHHh
Q 030960           76 LLRPGRLDRKIEFPLPDRRQKRLVFQM  102 (168)
Q Consensus        76 l~r~grf~~~i~~~~P~~~~R~~il~~  102 (168)
                      +.|  ||. .|.++.|+.+++..|++.
T Consensus       324 l~r--Rf~-~i~v~~p~~~~~~~iL~~  347 (852)
T TIGR03346       324 LER--RFQ-PVFVDEPTVEDTISILRG  347 (852)
T ss_pred             HHh--cCC-EEEeCCCCHHHHHHHHHH
Confidence            999  996 589999999999999984

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.

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.41  E-value=4.7e-06  Score=67.67  Aligned_cols=117  Identities=16%  Similarity=0.177  Sum_probs=84.8

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      ..|++|||+|.+-.              ...+.++..++.  ....+.+|.+|+.++.+++++++  |+ ..+.+++|+.
T Consensus       120 ~kviIIDEa~~l~~--------------~a~naLLk~lEe--~~~~~~fIl~t~~~~~l~~tI~S--Rc-~~~~~~~l~~  180 (363)
T PRK14961        120 FKVYLIDEVHMLSR--------------HSFNALLKTLEE--PPQHIKFILATTDVEKIPKTILS--RC-LQFKLKIISE  180 (363)
T ss_pred             ceEEEEEChhhcCH--------------HHHHHHHHHHhc--CCCCeEEEEEcCChHhhhHHHHh--hc-eEEeCCCCCH
Confidence            45999999998731              334567777764  34466677778889999999988  87 6789999999


Q ss_pred             HHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960           94 RQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus        94 ~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      ++..++++..+..      +..+..++..+.| +++++.+++..+...    +...++.+++.+++.
T Consensus       181 ~el~~~L~~~~~~~g~~i~~~al~~ia~~s~G-~~R~al~~l~~~~~~----~~~~It~~~v~~~l~  242 (363)
T PRK14961        181 EKIFNFLKYILIKESIDTDEYALKLIAYHAHG-SMRDALNLLEHAINL----GKGNINIKNVTDMLG  242 (363)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHHh----cCCCCCHHHHHHHHC
Confidence            9999988864432      2234557777766 788888888776533    345688888877664

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=98.35  E-value=6.3e-06  Score=69.56  Aligned_cols=132  Identities=15%  Similarity=0.246  Sum_probs=95.0

Q ss_pred             HHHHHHHHHHc----CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcccc
Q 030960            2 VRDVFRLAKEN----APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~~----~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~   77 (168)
                      ++.+.+.+...    ..-|++|||+|.+..              ...+.|+..++.  ....+++|.+|+.++.+++.++
T Consensus       113 Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~--------------~a~naLLk~LEe--pp~~~vfI~aTte~~kI~~tI~  176 (507)
T PRK06645        113 IRRIIESAEYKPLQGKHKIFIIDEVHMLSK--------------GAFNALLKTLEE--PPPHIIFIFATTEVQKIPATII  176 (507)
T ss_pred             HHHHHHHHHhccccCCcEEEEEEChhhcCH--------------HHHHHHHHHHhh--cCCCEEEEEEeCChHHhhHHHH
Confidence            45666666533    246999999998731              345667777763  4456777777888999999999


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhcCC---CC---CHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHH
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNLSD---EV---DLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK  151 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l~~---~~---~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~  151 (168)
                      +  |+ ..+.|.+++.++...+++..+..   .+   .+..++..++| +.+++.+++..++..+-.. ...||.+++.+
T Consensus       177 S--Rc-~~~ef~~ls~~el~~~L~~i~~~egi~ie~eAL~~Ia~~s~G-slR~al~~Ldkai~~~~~~-~~~It~~~V~~  251 (507)
T PRK06645        177 S--RC-QRYDLRRLSFEEIFKLLEYITKQENLKTDIEALRIIAYKSEG-SARDAVSILDQAASMSAKS-DNIISPQVINQ  251 (507)
T ss_pred             h--cc-eEEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHHhhccC-CCCcCHHHHHH
Confidence            8  77 57899999999999999866642   12   35678888876 8999999998886554321 23578777776


Q ss_pred             HHH
Q 030960          152 GYR  154 (168)
Q Consensus       152 al~  154 (168)
                      .+.
T Consensus       252 llg  254 (507)
T PRK06645        252 MLG  254 (507)
T ss_pred             HHC
Confidence            654

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=98.34  E-value=5.5e-06  Score=66.64  Aligned_cols=129  Identities=17%  Similarity=0.209  Sum_probs=87.9

Q ss_pred             HHHHHHHHHHc----CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcccc
Q 030960            2 VRDVFRLAKEN----APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~~----~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~   77 (168)
                      ++.+++.+...    ..-||+|||+|.+..              ...+.++..++.  ....+++|.+|++++.+.++++
T Consensus       102 ~~~l~~~~~~~p~~~~~~vviidea~~l~~--------------~~~~~Ll~~le~--~~~~~~lIl~~~~~~~l~~~l~  165 (355)
T TIGR02397       102 IREILDNVKYAPSSGKYKVYIIDEVHMLSK--------------SAFNALLKTLEE--PPEHVVFILATTEPHKIPATIL  165 (355)
T ss_pred             HHHHHHHHhcCcccCCceEEEEeChhhcCH--------------HHHHHHHHHHhC--CccceeEEEEeCCHHHHHHHHH
Confidence            45667666533    135999999998731              345667777764  3346777778889999999999


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhcCC---CC---CHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHH
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNLSD---EV---DLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK  151 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l~~---~~---~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~  151 (168)
                      +  |+ ..+++++|+..+...+++..+..   .+   .+..+++.+.| +++.+.+.++.+...+    ...|+.+++.+
T Consensus       166 s--r~-~~~~~~~~~~~~l~~~l~~~~~~~g~~i~~~a~~~l~~~~~g-~~~~a~~~lekl~~~~----~~~it~~~v~~  237 (355)
T TIGR02397       166 S--RC-QRFDFKRIPLEDIVERLKKILDKEGIKIEDEALELIARAADG-SLRDALSLLDQLISFG----NGNITYEDVNE  237 (355)
T ss_pred             h--he-eEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-ChHHHHHHHHHHHhhc----CCCCCHHHHHH
Confidence            8  87 47899999999999999865542   12   34456666655 7777777776655432    23477777766


Q ss_pred             HHH
Q 030960          152 GYR  154 (168)
Q Consensus       152 al~  154 (168)
                      ++.
T Consensus       238 ~~~  240 (355)
T TIGR02397       238 LLG  240 (355)
T ss_pred             HhC
Confidence            553

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.

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=98.33  E-value=3.1e-06  Score=70.57  Aligned_cols=131  Identities=11%  Similarity=0.186  Sum_probs=87.1

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCC---CCccccCCCCcc--eEE
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADT---LDPALLRPGRLD--RKI   86 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~---ld~al~r~grf~--~~i   86 (168)
                      ..+.+|+|||++.+.++.         .....+-.+++.+.   ...+.+|+.+...|..   +++.+.+  ||.  ..+
T Consensus       205 ~~~dvLiIDDiq~l~~k~---------~~~e~lf~l~N~~~---~~~k~iIltsd~~P~~l~~l~~rL~S--R~~~Gl~~  270 (450)
T PRK14087        205 CQNDVLIIDDVQFLSYKE---------KTNEIFFTIFNNFI---ENDKQLFFSSDKSPELLNGFDNRLIT--RFNMGLSI  270 (450)
T ss_pred             ccCCEEEEeccccccCCH---------HHHHHHHHHHHHHH---HcCCcEEEECCCCHHHHhhccHHHHH--HHhCCcee
Confidence            357899999999885332         11123333333332   2323334443334443   4678888  885  677


Q ss_pred             ecCCCCHHHHHHHHHhhcCC--------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC-CCccCHHHHHHHHHhhc
Q 030960           87 EFPLPDRRQKRLVFQMNLSD--------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN-RYVILPKDFEKGYRTNV  157 (168)
Q Consensus        87 ~~~~P~~~~R~~il~~~l~~--------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~-~~~i~~~d~~~al~~~~  157 (168)
                      .+.+|+.++|.+|++..+..        +-.+..|+..+.| +++.+..+++.....+.... ...|+.+.+.++++...
T Consensus       271 ~L~~pd~e~r~~iL~~~~~~~gl~~~l~~evl~~Ia~~~~g-d~R~L~gaL~~l~~~a~~~~~~~~it~~~v~~~l~~~~  349 (450)
T PRK14087        271 AIQKLDNKTATAIIKKEIKNQNIKQEVTEEAINFISNYYSD-DVRKIKGSVSRLNFWSQQNPEEKIITIEIVSDLFRDIP  349 (450)
T ss_pred             ccCCcCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHccCC-CHHHHHHHHHHHHHHHhcccCCCCCCHHHHHHHHhhcc
Confidence            88999999999999866542        1234457777766 88999999998876665542 36799999999998764

>CHL00095 clpC Clp protease ATP binding subunit

Probab=98.32  E-value=4.4e-06  Score=74.45  Aligned_cols=121  Identities=22%  Similarity=0.236  Sum_probs=80.6

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC-----CCCccc
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD-----TLDPAL   76 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~-----~ld~al   76 (168)
                      |+.+|+.++...|+||||||+|.+++..+..+. .     .+.+.|...+    ..+.+.+||+|+..+     ..|+++
T Consensus       260 l~~i~~~~~~~~~~ILfiDEih~l~~~g~~~g~-~-----~~a~lLkp~l----~rg~l~~IgaTt~~ey~~~ie~D~aL  329 (821)
T CHL00095        260 LKRIFDEIQENNNIILVIDEVHTLIGAGAAEGA-I-----DAANILKPAL----ARGELQCIGATTLDEYRKHIEKDPAL  329 (821)
T ss_pred             HHHHHHHHHhcCCeEEEEecHHHHhcCCCCCCc-c-----cHHHHhHHHH----hCCCcEEEEeCCHHHHHHHHhcCHHH
Confidence            578999998888999999999999876532221 1     1122222223    245788999998764     589999


Q ss_pred             cCCCCcceEEecCCCCHHHHHHHHHhhc-------C---CCCCHHHHHhCCCCCCH-----HHHHHHHHHHHHH
Q 030960           77 LRPGRLDRKIEFPLPDRRQKRLVFQMNL-------S---DEVDLEDYVSRPDKISA-----AEIAAICQEAGMH  135 (168)
Q Consensus        77 ~r~grf~~~i~~~~P~~~~R~~il~~~l-------~---~~~~~~~la~~t~g~s~-----~di~~l~~~a~~~  135 (168)
                      .+  ||.. +.++.|+.++...|++...       .   ++-.+..++..+.||.+     .---.++.+|+..
T Consensus       330 ~r--Rf~~-I~v~ep~~~e~~aILr~l~~~~e~~~~v~i~deal~~i~~ls~~yi~~r~lPdkaidlld~a~a~  400 (821)
T CHL00095        330 ER--RFQP-VYVGEPSVEETIEILFGLRSRYEKHHNLSISDKALEAAAKLSDQYIADRFLPDKAIDLLDEAGSR  400 (821)
T ss_pred             Hh--cceE-EecCCCCHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhccCccccCchHHHHHHHHHHHH
Confidence            99  9974 7999999999999987322       1   12234556666666543     4344555665443

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=98.31  E-value=5.6e-06  Score=70.92  Aligned_cols=129  Identities=16%  Similarity=0.181  Sum_probs=83.8

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCC-C---CCCCccccCCCCcc--eEE
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNR-A---DTLDPALLRPGRLD--RKI   86 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~-~---~~ld~al~r~grf~--~~i   86 (168)
                      ++.+|+|||++.+.++.     ..    +..+-++++.+   ...++-+|| |+|. |   ..+++.|++  ||.  ..+
T Consensus       377 ~~DLLlIDDIq~l~gke-----~t----qeeLF~l~N~l---~e~gk~III-TSd~~P~eL~~l~~rL~S--Rf~~GLvv  441 (617)
T PRK14086        377 EMDILLVDDIQFLEDKE-----ST----QEEFFHTFNTL---HNANKQIVL-SSDRPPKQLVTLEDRLRN--RFEWGLIT  441 (617)
T ss_pred             cCCEEEEehhccccCCH-----HH----HHHHHHHHHHH---HhcCCCEEE-ecCCChHhhhhccHHHHh--hhhcCceE
Confidence            47999999999986433     11    12222333333   222333344 5554 3   357888999  884  666


Q ss_pred             ecCCCCHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhcC
Q 030960           87 EFPLPDRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVK  158 (168)
Q Consensus        87 ~~~~P~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~p  158 (168)
                      .+..|+.+.|.+||+.....      +-.+..|+.+..+ +.++|+.++..-...+... ...|+.+...+.++.+.+
T Consensus       442 ~I~~PD~EtR~aIL~kka~~r~l~l~~eVi~yLa~r~~r-nvR~LegaL~rL~a~a~~~-~~~itl~la~~vL~~~~~  517 (617)
T PRK14086        442 DVQPPELETRIAILRKKAVQEQLNAPPEVLEFIASRISR-NIRELEGALIRVTAFASLN-RQPVDLGLTEIVLRDLIP  517 (617)
T ss_pred             EcCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhccC-CHHHHHHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhhc
Confidence            99999999999999966552      2235567777654 6788888888765555443 345788888888876654

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

Probab=98.28  E-value=1.1e-05  Score=71.51  Aligned_cols=127  Identities=14%  Similarity=0.203  Sum_probs=83.5

Q ss_pred             eEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC---------C----CCCCCeEEEEecCCCCCCCccccCCCC
Q 030960           15 AIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG---------F----DQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus        15 ~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~---------~----~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      .||+|||+|.+.....+          ...+.|+..+|.         +    -.-++|++|+|||.. .||++++.  |
T Consensus       418 ~villDEidk~~~~~~g----------~~~~aLlevld~~~~~~~~d~~~~~~~dls~v~~i~TaN~~-~i~~aLl~--R  484 (784)
T PRK10787        418 PLFLLDEIDKMSSDMRG----------DPASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNSM-NIPAPLLD--R  484 (784)
T ss_pred             CEEEEEChhhcccccCC----------CHHHHHHHHhccccEEEEecccccccccCCceEEEEcCCCC-CCCHHHhc--c
Confidence            48999999998643211          112345555552         1    122679999999988 59999999  9


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcCC-----------CC-----CHHHHHh-CCCCCCHHHHHHHHHHHHHHHHHh----C
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLSD-----------EV-----DLEDYVS-RPDKISAAEIAAICQEAGMHAVRK----N  140 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~~-----------~~-----~~~~la~-~t~g~s~~di~~l~~~a~~~a~~~----~  140 (168)
                      +. .|.+..++.++..+|.+.++.+           .+     -+..+++ .+..+-.+.|++.++..+..++.+    +
T Consensus       485 ~~-ii~~~~~t~eek~~Ia~~~L~~k~~~~~~l~~~~l~i~~~ai~~ii~~yt~e~GaR~LeR~I~~i~r~~l~~~~~~~  563 (784)
T PRK10787        485 ME-VIRLSGYTEDEKLNIAKRHLLPKQIERNALKKGELTVDDSAIIGIIRYYTREAGVRSLEREISKLCRKAVKQLLLDK  563 (784)
T ss_pred             ee-eeecCCCCHHHHHHHHHHhhhHHHHHHhCCCCCeEEECHHHHHHHHHhCCcccCCcHHHHHHHHHHHHHHHHHHhcC
Confidence            95 7899999999999999877741           11     1333443 344555577777666655444433    1


Q ss_pred             ---CCccCHHHHHHHHHh
Q 030960          141 ---RYVILPKDFEKGYRT  155 (168)
Q Consensus       141 ---~~~i~~~d~~~al~~  155 (168)
                         +..|+.+++.+.+..
T Consensus       564 ~~~~v~v~~~~~~~~lg~  581 (784)
T PRK10787        564 SLKHIEINGDNLHDYLGV  581 (784)
T ss_pred             CCceeeecHHHHHHHhCC
Confidence               236888888887753

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.28  E-value=1.2e-05  Score=67.36  Aligned_cols=130  Identities=15%  Similarity=0.162  Sum_probs=88.0

Q ss_pred             HHHHHHHHHHc----CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcccc
Q 030960            2 VRDVFRLAKEN----APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~~----~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~   77 (168)
                      ++.+.+.+...    ...||+|||+|.+..              ...+.|+..++.  ..+.+++|++|+++..++++++
T Consensus       102 iR~i~~~~~~~p~~~~~kVvIIDE~h~Lt~--------------~a~~~LLk~LE~--p~~~vv~Ilattn~~kl~~~L~  165 (472)
T PRK14962        102 IRKIRDAVGYRPMEGKYKVYIIDEVHMLTK--------------EAFNALLKTLEE--PPSHVVFVLATTNLEKVPPTII  165 (472)
T ss_pred             HHHHHHHHhhChhcCCeEEEEEEChHHhHH--------------HHHHHHHHHHHh--CCCcEEEEEEeCChHhhhHHHh
Confidence            35555555432    246999999998831              234567777764  3346777777778999999999


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHH
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK  151 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~  151 (168)
                      +  |+. .+.|.+|+.++...+++.....      +..++.|+..+.| +.+++.+.+..+...    ....|+.+++.+
T Consensus       166 S--R~~-vv~f~~l~~~el~~~L~~i~~~egi~i~~eal~~Ia~~s~G-dlR~aln~Le~l~~~----~~~~It~e~V~~  237 (472)
T PRK14962        166 S--RCQ-VIEFRNISDELIIKRLQEVAEAEGIEIDREALSFIAKRASG-GLRDALTMLEQVWKF----SEGKITLETVHE  237 (472)
T ss_pred             c--CcE-EEEECCccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCC-CHHHHHHHHHHHHHh----cCCCCCHHHHHH
Confidence            9  874 8999999999998888765431      2235667776654 556666666554332    122488888888


Q ss_pred             HHHh
Q 030960          152 GYRT  155 (168)
Q Consensus       152 al~~  155 (168)
                      ++..
T Consensus       238 ~l~~  241 (472)
T PRK14962        238 ALGL  241 (472)
T ss_pred             HHcC
Confidence            7754

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.25  E-value=4.6e-06  Score=62.88  Aligned_cols=124  Identities=16%  Similarity=0.181  Sum_probs=79.9

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCC---ccccCCCCc--ceEEec
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLD---PALLRPGRL--DRKIEF   88 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld---~al~r~grf--~~~i~~   88 (168)
                      +.+|+|||+|.+....     .    ....+..++..+.   ..+..+|+.++..+..++   +.+.+  |+  ...+.+
T Consensus        91 ~~lLvIDdi~~l~~~~-----~----~~~~L~~~l~~~~---~~~~~iIits~~~~~~~~~~~~~L~~--r~~~~~~i~l  156 (226)
T TIGR03420        91 ADLVCLDDVEAIAGQP-----E----WQEALFHLYNRVR---EAGGRLLIAGRAAPAQLPLRLPDLRT--RLAWGLVFQL  156 (226)
T ss_pred             CCEEEEeChhhhcCCh-----H----HHHHHHHHHHHHH---HcCCeEEEECCCChHHCCcccHHHHH--HHhcCeeEec
Confidence            5699999999874221     0    0122333333332   222344554444554443   66776  66  578999


Q ss_pred             CCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           89 PLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        89 ~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      ++|+.+++..+++.+..      ++-.+..+++. -+-+++++.++++.+...+.+.+ ..|+.+...+.+
T Consensus       157 ~~l~~~e~~~~l~~~~~~~~~~~~~~~l~~L~~~-~~gn~r~L~~~l~~~~~~~~~~~-~~i~~~~~~~~~  225 (226)
T TIGR03420       157 PPLSDEEKIAALQSRAARRGLQLPDEVADYLLRH-GSRDMGSLMALLDALDRASLAAK-RKITIPFVKEVL  225 (226)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHh-ccCCHHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHh
Confidence            99999999999986543      12235567774 56689999999998876665544 579888887765

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.

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=98.24  E-value=6.1e-06  Score=68.73  Aligned_cols=130  Identities=12%  Similarity=0.199  Sum_probs=80.6

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC---CCCccccCCCCcc--eEEe
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD---TLDPALLRPGRLD--RKIE   87 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~---~ld~al~r~grf~--~~i~   87 (168)
                      ++.+|+|||++.+.+..     ..    +..+-.+++.+   ....+.+|++++..|.   .+++.+++  ||.  ..+.
T Consensus       202 ~~dvLiIDDiq~l~~k~-----~~----qeelf~l~N~l---~~~~k~IIlts~~~p~~l~~l~~rL~S--R~~~Gl~~~  267 (445)
T PRK12422        202 NVDALFIEDIEVFSGKG-----AT----QEEFFHTFNSL---HTEGKLIVISSTCAPQDLKAMEERLIS--RFEWGIAIP  267 (445)
T ss_pred             cCCEEEEcchhhhcCCh-----hh----HHHHHHHHHHH---HHCCCcEEEecCCCHHHHhhhHHHHHh--hhcCCeEEe
Confidence            57899999999875322     11    12222233222   1223444555544454   56789999  995  8899


Q ss_pred             cCCCCHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHH-HHHh-CCCccCHHHHHHHHHhhc
Q 030960           88 FPLPDRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMH-AVRK-NRYVILPKDFEKGYRTNV  157 (168)
Q Consensus        88 ~~~P~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~-a~~~-~~~~i~~~d~~~al~~~~  157 (168)
                      +.+|+.++|..|++.....      +-.++.++....| ..+.|...++..+.. +... ...+++.++..++++...
T Consensus       268 l~~pd~e~r~~iL~~k~~~~~~~l~~evl~~la~~~~~-dir~L~g~l~~l~~~~a~~~~~~~~i~~~~~~~~l~~~~  344 (445)
T PRK12422        268 LHPLTKEGLRSFLERKAEALSIRIEETALDFLIEALSS-NVKSLLHALTLLAKRVAYKKLSHQLLYVDDIKALLHDVL  344 (445)
T ss_pred             cCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-CHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHhh
Confidence            9999999999999865542      2234456665543 566777766665322 2221 234688899999888753

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

Probab=98.22  E-value=3e-05  Score=59.96  Aligned_cols=132  Identities=16%  Similarity=0.169  Sum_probs=87.6

Q ss_pred             HHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC---CCC----ccccCCCC
Q 030960            9 AKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD---TLD----PALLRPGR   81 (168)
Q Consensus         9 a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~---~ld----~al~r~gr   81 (168)
                      .....+.+|+|||++.+-..           ....+..+....   ......+.|..+..++   .+.    ..+.+  |
T Consensus       119 ~~~~~~~vliiDe~~~l~~~-----------~~~~l~~l~~~~---~~~~~~~~vvl~g~~~~~~~l~~~~~~~l~~--r  182 (269)
T TIGR03015       119 FAAGKRALLVVDEAQNLTPE-----------LLEELRMLSNFQ---TDNAKLLQIFLVGQPEFRETLQSPQLQQLRQ--R  182 (269)
T ss_pred             HhCCCCeEEEEECcccCCHH-----------HHHHHHHHhCcc---cCCCCeEEEEEcCCHHHHHHHcCchhHHHHh--h
Confidence            34566899999999987311           112222222111   1122222223333333   111    13445  7


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC----------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHH
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS----------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK  151 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~----------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~  151 (168)
                      +...+++++.+.++-.+++...+.          .+..++.+.+.|.|.. +.|..+|..+...+..++...|+.+++.+
T Consensus       183 ~~~~~~l~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p-~~i~~l~~~~~~~a~~~~~~~i~~~~v~~  261 (269)
T TIGR03015       183 IIASCHLGPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIP-RLINILCDRLLLSAFLEEKREIGGEEVRE  261 (269)
T ss_pred             eeeeeeCCCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcc-cHHHHHHHHHHHHHHHcCCCCCCHHHHHH
Confidence            888999999999999999885543          1124566888999985 55999999999999999999999999999


Q ss_pred             HHHhhc
Q 030960          152 GYRTNV  157 (168)
Q Consensus       152 al~~~~  157 (168)
                      ++....
T Consensus       262 ~~~~~~  267 (269)
T TIGR03015       262 VIAEID  267 (269)
T ss_pred             HHHHhh
Confidence            998754

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.

>PRK08727 hypothetical protein; Validated

Probab=98.22  E-value=9e-06  Score=62.09  Aligned_cols=128  Identities=16%  Similarity=0.218  Sum_probs=80.1

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCC---CccccCCCCc--ceEEe
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTL---DPALLRPGRL--DRKIE   87 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~l---d~al~r~grf--~~~i~   87 (168)
                      +..+|+|||+|.+....     ..    ...+-.+++...   ..+.-+++.+...|..+   ++.+++  ||  ...+.
T Consensus        93 ~~dlLiIDDi~~l~~~~-----~~----~~~lf~l~n~~~---~~~~~vI~ts~~~p~~l~~~~~dL~S--Rl~~~~~~~  158 (233)
T PRK08727         93 GRSLVALDGLESIAGQR-----ED----EVALFDFHNRAR---AAGITLLYTARQMPDGLALVLPDLRS--RLAQCIRIG  158 (233)
T ss_pred             cCCEEEEeCcccccCCh-----HH----HHHHHHHHHHHH---HcCCeEEEECCCChhhhhhhhHHHHH--HHhcCceEE
Confidence            46799999999886433     11    122223444432   22233444455567766   689998  87  56789


Q ss_pred             cCCCCHHHHHHHHHh-hcCC-----CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           88 FPLPDRRQKRLVFQM-NLSD-----EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        88 ~~~P~~~~R~~il~~-~l~~-----~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      +++|+.++|.++++. +...     +..++.++++++| +.+.+.++++.....+... ++.||...+.+.+...
T Consensus       159 l~~~~~e~~~~iL~~~a~~~~l~l~~e~~~~La~~~~r-d~r~~l~~L~~l~~~~~~~-~~~it~~~~~~~l~~~  231 (233)
T PRK08727        159 LPVLDDVARAAVLRERAQRRGLALDEAAIDWLLTHGER-ELAGLVALLDRLDRESLAA-KRRVTVPFLRRVLEEG  231 (233)
T ss_pred             ecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHHh-CCCCCHHHHHHHHhhc
Confidence            999999999999996 3322     2345667877663 3444444455544434443 3479999999888654

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.19  E-value=2.1e-05  Score=65.73  Aligned_cols=117  Identities=15%  Similarity=0.141  Sum_probs=81.6

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      ..-|++|||+|.+-.              ...+.||..++.  ...++++|++|+.++.|++++++  |+. .+.|.+++
T Consensus       121 ~~KV~IIDEah~Ls~--------------~A~NALLKtLEE--Pp~~viFILaTte~~kI~~TI~S--RCq-~~~f~~ls  181 (484)
T PRK14956        121 KYKVYIIDEVHMLTD--------------QSFNALLKTLEE--PPAHIVFILATTEFHKIPETILS--RCQ-DFIFKKVP  181 (484)
T ss_pred             CCEEEEEechhhcCH--------------HHHHHHHHHhhc--CCCceEEEeecCChhhccHHHHh--hhh-eeeecCCC
Confidence            457999999998831              456778888873  44578888999999999999999  874 68888888


Q ss_pred             HHHHHHHHHhhcC-C-----CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           93 RRQKRLVFQMNLS-D-----EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        93 ~~~R~~il~~~l~-~-----~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      .++-.+.++..+. .     +..+..|+..++| +++|.-+++..+...    ....|+.+++.+.+
T Consensus       182 ~~~i~~~L~~i~~~Egi~~e~eAL~~Ia~~S~G-d~RdAL~lLeq~i~~----~~~~it~~~V~~~l  243 (484)
T PRK14956        182 LSVLQDYSEKLCKIENVQYDQEGLFWIAKKGDG-SVRDMLSFMEQAIVF----TDSKLTGVKIRKMI  243 (484)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-hHHHHHHHHHHHHHh----CCCCcCHHHHHHHh
Confidence            8777777775543 1     2235567777766 577777777665432    12246666665544

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=98.17  E-value=3.2e-05  Score=66.23  Aligned_cols=128  Identities=17%  Similarity=0.187  Sum_probs=88.7

Q ss_pred             HHHHHHHHHHc----CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcccc
Q 030960            2 VRDVFRLAKEN----APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~~----~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~   77 (168)
                      ++++.+.+...    ..-|++|||+|.+..              ...+.|+..++.  ...++++|.+|+.++.+++.++
T Consensus       104 ir~i~~~v~~~p~~~~~kViIIDE~~~Lt~--------------~a~naLLKtLEe--pp~~~ifIlatt~~~ki~~tI~  167 (559)
T PRK05563        104 IRDIRDKVKYAPSEAKYKVYIIDEVHMLST--------------GAFNALLKTLEE--PPAHVIFILATTEPHKIPATIL  167 (559)
T ss_pred             HHHHHHHHhhCcccCCeEEEEEECcccCCH--------------HHHHHHHHHhcC--CCCCeEEEEEeCChhhCcHHHH
Confidence            45666665532    256999999998731              346677877774  3446667777788999999999


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHH
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK  151 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~  151 (168)
                      +  |+. .+.|.+|+..+-...++..+..      +..+..++..+.| +.++..+++..+....    ...|+.+++..
T Consensus       168 S--Rc~-~~~f~~~~~~ei~~~L~~i~~~egi~i~~~al~~ia~~s~G-~~R~al~~Ldq~~~~~----~~~It~~~V~~  239 (559)
T PRK05563        168 S--RCQ-RFDFKRISVEDIVERLKYILDKEGIEYEDEALRLIARAAEG-GMRDALSILDQAISFG----DGKVTYEDALE  239 (559)
T ss_pred             h--Hhe-EEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHHhc----cCCCCHHHHHH
Confidence            8  875 5789999999988888765432      2235567777776 8888888887765432    33467666555


Q ss_pred             HH
Q 030960          152 GY  153 (168)
Q Consensus       152 al  153 (168)
                      .+
T Consensus       240 vl  241 (559)
T PRK05563        240 VT  241 (559)
T ss_pred             Hh
Confidence            43

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.17  E-value=9.6e-06  Score=69.87  Aligned_cols=101  Identities=16%  Similarity=0.208  Sum_probs=75.7

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      ...|++|||+|.+-.              ...|.||..|+.  ...++.+|.+||+++.|.+.+++  |+ ..+.|..++
T Consensus       124 r~KViIIDEah~Ls~--------------~AaNALLKTLEE--PP~~v~FILaTtep~kLlpTIrS--RC-q~f~f~~ls  184 (700)
T PRK12323        124 RFKVYMIDEVHMLTN--------------HAFNAMLKTLEE--PPEHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMP  184 (700)
T ss_pred             CceEEEEEChHhcCH--------------HHHHHHHHhhcc--CCCCceEEEEeCChHhhhhHHHH--HH-HhcccCCCC
Confidence            357999999998831              456778888873  45578899999999999999999  87 788999999


Q ss_pred             HHHHHHHHHhhcC-CCCC-----HHHHHhCCCCCCHHHHHHHHHHHH
Q 030960           93 RRQKRLVFQMNLS-DEVD-----LEDYVSRPDKISAAEIAAICQEAG  133 (168)
Q Consensus        93 ~~~R~~il~~~l~-~~~~-----~~~la~~t~g~s~~di~~l~~~a~  133 (168)
                      .++..+.++..+. ..+.     +..|+..++| ++++.-+++..+.
T Consensus       185 ~eei~~~L~~Il~~Egi~~d~eAL~~IA~~A~G-s~RdALsLLdQai  230 (700)
T PRK12323        185 PGHIVSHLDAILGEEGIAHEVNALRLLAQAAQG-SMRDALSLTDQAI  230 (700)
T ss_pred             hHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHH
Confidence            9988888875543 2222     3456666654 7777777776554

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.16  E-value=7.7e-05  Score=61.62  Aligned_cols=129  Identities=22%  Similarity=0.304  Sum_probs=85.3

Q ss_pred             HHHHHHHHHH----cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecC-C-CCCCCcc
Q 030960            2 VRDVFRLAKE----NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATN-R-ADTLDPA   75 (168)
Q Consensus         2 l~~iF~~a~~----~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn-~-~~~ld~a   75 (168)
                      ++.+++.++.    ....||+|||+|.+..              ...+.++..++    ...+++|++|+ + ...++++
T Consensus        77 ir~ii~~~~~~~~~g~~~vL~IDEi~~l~~--------------~~q~~LL~~le----~~~iilI~att~n~~~~l~~a  138 (413)
T PRK13342         77 LREVIEEARQRRSAGRRTILFIDEIHRFNK--------------AQQDALLPHVE----DGTITLIGATTENPSFEVNPA  138 (413)
T ss_pred             HHHHHHHHHHhhhcCCceEEEEechhhhCH--------------HHHHHHHHHhh----cCcEEEEEeCCCChhhhccHH
Confidence            4556666642    2578999999998741              12234555554    24566666543 3 4589999


Q ss_pred             ccCCCCcceEEecCCCCHHHHHHHHHhhcCC------CCC---HHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCH
Q 030960           76 LLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD------EVD---LEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILP  146 (168)
Q Consensus        76 l~r~grf~~~i~~~~P~~~~R~~il~~~l~~------~~~---~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~  146 (168)
                      +++  |+ ..+.+++|+.++...+++..+..      .++   +..+++.+.| .++.+.++++.+...     ...|+.
T Consensus       139 L~S--R~-~~~~~~~ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s~G-d~R~aln~Le~~~~~-----~~~It~  209 (413)
T PRK13342        139 LLS--RA-QVFELKPLSEEDIEQLLKRALEDKERGLVELDDEALDALARLANG-DARRALNLLELAALG-----VDSITL  209 (413)
T ss_pred             Hhc--cc-eeeEeCCCCHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhCCC-CHHHHHHHHHHHHHc-----cCCCCH
Confidence            999  88 78999999999999999865432      122   3456666643 566666666655433     446899


Q ss_pred             HHHHHHHHhhc
Q 030960          147 KDFEKGYRTNV  157 (168)
Q Consensus       147 ~d~~~al~~~~  157 (168)
                      +++.+++....
T Consensus       210 ~~v~~~~~~~~  220 (413)
T PRK13342        210 ELLEEALQKRA  220 (413)
T ss_pred             HHHHHHHhhhh
Confidence            99988887643

>PRK08084 DNA replication initiation factor; Provisional

Probab=98.14  E-value=8.5e-06  Score=62.32  Aligned_cols=124  Identities=14%  Similarity=0.130  Sum_probs=79.0

Q ss_pred             eEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCC-eEEEEecCCCCC---CCccccCCCCcc--eEEec
Q 030960           15 AIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVN-VKVIMATNRADT---LDPALLRPGRLD--RKIEF   88 (168)
Q Consensus        15 ~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~-v~vi~ttn~~~~---ld~al~r~grf~--~~i~~   88 (168)
                      .+|+|||++.+.++.     .+    +..+-++++.+   ...++ .+++.+++.|..   +.+.+++  |+.  ..+.+
T Consensus        99 dlliiDdi~~~~~~~-----~~----~~~lf~l~n~~---~e~g~~~li~ts~~~p~~l~~~~~~L~S--Rl~~g~~~~l  164 (235)
T PRK08084         99 SLVCIDNIECIAGDE-----LW----EMAIFDLYNRI---LESGRTRLLITGDRPPRQLNLGLPDLAS--RLDWGQIYKL  164 (235)
T ss_pred             CEEEEeChhhhcCCH-----HH----HHHHHHHHHHH---HHcCCCeEEEeCCCChHHcCcccHHHHH--HHhCCceeee
Confidence            589999999874322     11    12232333332   22333 355555555555   5789999  986  88999


Q ss_pred             CCCCHHHHHHHHHhhcC-C-----CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960           89 PLPDRRQKRLVFQMNLS-D-----EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus        89 ~~P~~~~R~~il~~~l~-~-----~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      .+|+.++|.++++.... .     +..++.++.+.+| +.+.+..+++.....+.. .+..||...+.+++.
T Consensus       165 ~~~~~~~~~~~l~~~a~~~~~~l~~~v~~~L~~~~~~-d~r~l~~~l~~l~~~~l~-~~~~it~~~~k~~l~  234 (235)
T PRK08084        165 QPLSDEEKLQALQLRARLRGFELPEDVGRFLLKRLDR-EMRTLFMTLDQLDRASIT-AQRKLTIPFVKEILK  234 (235)
T ss_pred             cCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhhcC-CHHHHHHHHHHHHHHHHh-cCCCCCHHHHHHHHc
Confidence            99999999999986332 2     2235567777654 777888888775433333 345688888887763

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=98.10  E-value=4.6e-05  Score=65.97  Aligned_cols=117  Identities=19%  Similarity=0.211  Sum_probs=82.1

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      ..-|++|||+|.+-.              ...+.||..|+.  ...++.+|.+|+.++.|.+.+++  |+ ..+.|.+++
T Consensus       119 ~~KV~IIDEah~Ls~--------------~a~NALLKtLEE--Pp~~v~FIL~Tt~~~kLl~TI~S--RC-~~~~f~~Ls  179 (647)
T PRK07994        119 RFKVYLIDEVHMLSR--------------HSFNALLKTLEE--PPEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALD  179 (647)
T ss_pred             CCEEEEEechHhCCH--------------HHHHHHHHHHHc--CCCCeEEEEecCCccccchHHHh--hh-eEeeCCCCC
Confidence            356999999998731              456788888873  45577788888899999999999  85 889999999


Q ss_pred             HHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           93 RRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        93 ~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      .++-...++..+..      +..+..++..+.| ++++.-+++..+...    +...|+.+++...+
T Consensus       180 ~~ei~~~L~~il~~e~i~~e~~aL~~Ia~~s~G-s~R~Al~lldqaia~----~~~~it~~~v~~~l  241 (647)
T PRK07994        180 VEQIRQQLEHILQAEQIPFEPRALQLLARAADG-SMRDALSLTDQAIAS----GNGQVTTDDVSAML  241 (647)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHHh----cCCCcCHHHHHHHH
Confidence            99999888865531      2234456666555 667777777655322    22335555555443

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=98.09  E-value=3.8e-05  Score=67.26  Aligned_cols=112  Identities=15%  Similarity=0.178  Sum_probs=80.3

Q ss_pred             HHHHHHHHHH----cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcccc
Q 030960            2 VRDVFRLAKE----NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~----~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~   77 (168)
                      ++++.+.+..    ...-|++|||+|.+-.              ...+.||..|+.  ...++.+|.+||+++.|.+.++
T Consensus       104 IReLIe~a~~~P~~gr~KVIIIDEah~LT~--------------~A~NALLKtLEE--PP~~v~FILaTtd~~KIp~TIr  167 (830)
T PRK07003        104 MAALLERAVYAPVDARFKVYMIDEVHMLTN--------------HAFNAMLKTLEE--PPPHVKFILATTDPQKIPVTVL  167 (830)
T ss_pred             HHHHHHHHHhccccCCceEEEEeChhhCCH--------------HHHHHHHHHHHh--cCCCeEEEEEECChhhccchhh
Confidence            3455555432    2357999999998831              345677887873  4557889999999999999999


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhcCC-C-----CCHHHHHhCCCCCCHHHHHHHHHHHH
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNLSD-E-----VDLEDYVSRPDKISAAEIAAICQEAG  133 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l~~-~-----~~~~~la~~t~g~s~~di~~l~~~a~  133 (168)
                      +  |+ ..+.|..++.++-.+.|+..+.. .     ..+..|+..++| +.+|.-+++..+.
T Consensus       168 S--RC-q~f~Fk~Ls~eeIv~~L~~Il~~EgI~id~eAL~lIA~~A~G-smRdALsLLdQAi  225 (830)
T PRK07003        168 S--RC-LQFNLKQMPAGHIVSHLERILGEERIAFEPQALRLLARAAQG-SMRDALSLTDQAI  225 (830)
T ss_pred             h--he-EEEecCCcCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHH
Confidence            9  88 78999999999998888765542 2     234567777766 4566666666554

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=98.06  E-value=2.7e-05  Score=57.27  Aligned_cols=82  Identities=15%  Similarity=0.272  Sum_probs=60.4

Q ss_pred             HHHHHHHHH----cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccC
Q 030960            3 RDVFRLAKE----NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLR   78 (168)
Q Consensus         3 ~~iF~~a~~----~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r   78 (168)
                      +.+.+.+..    ..+-||+|||+|.+..              ...+.|+..++.  ..+...+|.+|+++..+++++++
T Consensus        82 ~~i~~~~~~~~~~~~~kviiide~~~l~~--------------~~~~~Ll~~le~--~~~~~~~il~~~~~~~l~~~i~s  145 (188)
T TIGR00678        82 RELVEFLSRTPQESGRRVVIIEDAERMNE--------------AAANALLKTLEE--PPPNTLFILITPSPEKLLPTIRS  145 (188)
T ss_pred             HHHHHHHccCcccCCeEEEEEechhhhCH--------------HHHHHHHHHhcC--CCCCeEEEEEECChHhChHHHHh
Confidence            344555543    3467999999998742              234567777775  33456677777888999999998


Q ss_pred             CCCcceEEecCCCCHHHHHHHHHhh
Q 030960           79 PGRLDRKIEFPLPDRRQKRLVFQMN  103 (168)
Q Consensus        79 ~grf~~~i~~~~P~~~~R~~il~~~  103 (168)
                        |+ ..+.+++|+.++..++++..
T Consensus       146 --r~-~~~~~~~~~~~~~~~~l~~~  167 (188)
T TIGR00678       146 --RC-QVLPFPPLSEEALLQWLIRQ  167 (188)
T ss_pred             --hc-EEeeCCCCCHHHHHHHHHHc
Confidence              77 48999999999999888765

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.

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.06  E-value=6.8e-05  Score=64.74  Aligned_cols=116  Identities=12%  Similarity=0.123  Sum_probs=83.4

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      .-|++|||+|.+..              ...+.|+..++.  ....+.+|.+|+.++.+.+.+++  |+ ..+.|..++.
T Consensus       125 ~KV~IIDEvh~Ls~--------------~a~NaLLKtLEE--PP~~~~fIL~Ttd~~kil~TIlS--Rc-~~~~f~~Ls~  185 (618)
T PRK14951        125 FKVFMIDEVHMLTN--------------TAFNAMLKTLEE--PPEYLKFVLATTDPQKVPVTVLS--RC-LQFNLRPMAP  185 (618)
T ss_pred             ceEEEEEChhhCCH--------------HHHHHHHHhccc--CCCCeEEEEEECCchhhhHHHHH--hc-eeeecCCCCH
Confidence            35999999998732              336678888873  44567777788889999999988  76 7899999999


Q ss_pred             HHHHHHHHhhcCC-C-----CCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           94 RQKRLVFQMNLSD-E-----VDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        94 ~~R~~il~~~l~~-~-----~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      ++....++..+.. .     ..+..|+..+.| +.+++.+++..+...    +...|+.+++.+.+
T Consensus       186 eei~~~L~~i~~~egi~ie~~AL~~La~~s~G-slR~al~lLdq~ia~----~~~~It~~~V~~~L  246 (618)
T PRK14951        186 ETVLEHLTQVLAAENVPAEPQALRLLARAARG-SMRDALSLTDQAIAF----GSGQLQEAAVRQML  246 (618)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHHh----cCCCcCHHHHHHHH
Confidence            9988888755431 2     235667887776 888888887665543    23457766666554

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.02  E-value=0.00013  Score=58.08  Aligned_cols=117  Identities=15%  Similarity=0.149  Sum_probs=72.6

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      +.+|+|||+|.+..              ...+.+...++....  ...+|.+|+.+..+.+.+.+  |+ ..+.+.+|+.
T Consensus       126 ~~vlilDe~~~l~~--------------~~~~~L~~~le~~~~--~~~~Il~~~~~~~~~~~L~s--r~-~~v~~~~~~~  186 (337)
T PRK12402        126 YKTILLDNAEALRE--------------DAQQALRRIMEQYSR--TCRFIIATRQPSKLIPPIRS--RC-LPLFFRAPTD  186 (337)
T ss_pred             CcEEEEeCcccCCH--------------HHHHHHHHHHHhccC--CCeEEEEeCChhhCchhhcC--Cc-eEEEecCCCH
Confidence            46999999997731              112234444443222  23455566677788888887  75 5789999999


Q ss_pred             HHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960           94 RQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus        94 ~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      ++...+++..+..      +..+..++..+    ++|+..+++.....+.  ....||.+++.+++..
T Consensus       187 ~~~~~~l~~~~~~~~~~~~~~al~~l~~~~----~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~  248 (337)
T PRK12402        187 DELVDVLESIAEAEGVDYDDDGLELIAYYA----GGDLRKAILTLQTAAL--AAGEITMEAAYEALGD  248 (337)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHc----CCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCC
Confidence            9999999865442      22345566665    3344444443333332  2236888888887654

>PRK05642 DNA replication initiation factor; Validated

Probab=98.02  E-value=3.6e-05  Score=58.83  Aligned_cols=125  Identities=12%  Similarity=0.136  Sum_probs=79.9

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCC---CccccCCCCcc--eEEec
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTL---DPALLRPGRLD--RKIEF   88 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~l---d~al~r~grf~--~~i~~   88 (168)
                      ..+|+|||++.+.+..     ..    +.   .+...++.+...++.++|+++..|..+   .+.+++  ||.  ..+.+
T Consensus        98 ~d~LiiDDi~~~~~~~-----~~----~~---~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~S--Rl~~gl~~~l  163 (234)
T PRK05642         98 YELVCLDDLDVIAGKA-----DW----EE---ALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKS--RLTLALVFQM  163 (234)
T ss_pred             CCEEEEechhhhcCCh-----HH----HH---HHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHH--HHhcCeeeec
Confidence            3588999999875332     11    12   233333333445567777777666544   578888  884  77788


Q ss_pred             CCCCHHHHHHHHHh-hcCC-----CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960           89 PLPDRRQKRLVFQM-NLSD-----EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus        89 ~~P~~~~R~~il~~-~l~~-----~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      .+|+.++|.++++. +...     +-.++.++.+.+| +++.+..+++.-...++. .+++||..-+.+++.
T Consensus       164 ~~~~~e~~~~il~~ka~~~~~~l~~ev~~~L~~~~~~-d~r~l~~~l~~l~~~~l~-~~~~it~~~~~~~L~  233 (234)
T PRK05642        164 RGLSDEDKLRALQLRASRRGLHLTDEVGHFILTRGTR-SMSALFDLLERLDQASLQ-AQRKLTIPFLKETLG  233 (234)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-CHHHHHHHHHHHHHHHHH-cCCcCCHHHHHHHhc
Confidence            99999999999983 2222     2234456666543 778888887766554444 345688877777664

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.01  E-value=2.7e-05  Score=65.96  Aligned_cols=118  Identities=19%  Similarity=0.185  Sum_probs=83.7

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      .-|++|||+|.+-.              ...+.++..|+.  ...++.+|.+|+.++.+++.+++  |+ ..++|.+++.
T Consensus       120 ~kV~iIDE~~~ls~--------------~a~naLLk~LEe--pp~~~~fIlattd~~kl~~tI~S--Rc-~~~~f~~l~~  180 (509)
T PRK14958        120 FKVYLIDEVHMLSG--------------HSFNALLKTLEE--PPSHVKFILATTDHHKLPVTVLS--RC-LQFHLAQLPP  180 (509)
T ss_pred             cEEEEEEChHhcCH--------------HHHHHHHHHHhc--cCCCeEEEEEECChHhchHHHHH--Hh-hhhhcCCCCH
Confidence            46999999998841              345678888874  34467777788889999999988  76 6678888888


Q ss_pred             HHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960           94 RQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus        94 ~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      ++-...++..+..      +..+..++..+.| +.+++.+++..+...    +...|+.+++.+.+..
T Consensus       181 ~~i~~~l~~il~~egi~~~~~al~~ia~~s~G-slR~al~lLdq~ia~----~~~~It~~~V~~~lg~  243 (509)
T PRK14958        181 LQIAAHCQHLLKEENVEFENAALDLLARAANG-SVRDALSLLDQSIAY----GNGKVLIADVKTMLGT  243 (509)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-cHHHHHHHHHHHHhc----CCCCcCHHHHHHHHCC
Confidence            8777666544431      2235567777765 889999998876433    2345888877776643

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.00  E-value=5e-05  Score=65.66  Aligned_cols=118  Identities=14%  Similarity=0.150  Sum_probs=85.0

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      ..-|++|||+|.+-.              ...+.|+..++.  ...++.+|++|+.+..+++.+++  |+ ..+.|.+++
T Consensus       118 k~KV~IIDEVh~LS~--------------~A~NALLKtLEE--PP~~v~FILaTtd~~kIp~TIlS--RC-q~feFkpLs  178 (702)
T PRK14960        118 RFKVYLIDEVHMLST--------------HSFNALLKTLEE--PPEHVKFLFATTDPQKLPITVIS--RC-LQFTLRPLA  178 (702)
T ss_pred             CcEEEEEechHhcCH--------------HHHHHHHHHHhc--CCCCcEEEEEECChHhhhHHHHH--hh-heeeccCCC
Confidence            357999999998731              345667777774  34567778888889999999887  77 688999999


Q ss_pred             HHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960           93 RRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus        93 ~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      ..+-.+.++..+..      +..+..++..+.| +.+++.+++..+...    +...|+.+++...+.
T Consensus       179 ~eEI~k~L~~Il~kEgI~id~eAL~~IA~~S~G-dLRdALnLLDQaIay----g~g~IT~edV~~lLG  241 (702)
T PRK14960        179 VDEITKHLGAILEKEQIAADQDAIWQIAESAQG-SLRDALSLTDQAIAY----GQGAVHHQDVKEMLG  241 (702)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHHh----cCCCcCHHHHHHHhc
Confidence            99988888765542      2235567777766 888888887766532    344577777766543

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.00  E-value=6.2e-05  Score=63.30  Aligned_cols=128  Identities=14%  Similarity=0.151  Sum_probs=91.8

Q ss_pred             HHHHHHHHHHc----CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcccc
Q 030960            2 VRDVFRLAKEN----APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~~----~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~   77 (168)
                      ++++.+.+...    ..-|++|||+|.+-.              ...+.|+..++.  ..+.+.+|.+|+.++.+++.++
T Consensus       101 IR~Iie~~~~~P~~~~~KVvIIDEah~Ls~--------------~A~NaLLK~LEe--Pp~~v~fIlatte~~Kl~~tI~  164 (491)
T PRK14964        101 IKVILENSCYLPISSKFKVYIIDEVHMLSN--------------SAFNALLKTLEE--PAPHVKFILATTEVKKIPVTII  164 (491)
T ss_pred             HHHHHHHHHhccccCCceEEEEeChHhCCH--------------HHHHHHHHHHhC--CCCCeEEEEEeCChHHHHHHHH
Confidence            45566665433    256999999987731              346778888874  4456777778888999999999


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHH
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK  151 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~  151 (168)
                      +  |+ ..+.|.+++.++....++.....      +..+..++..++| +.+++.+++..+...+    ...||.+++.+
T Consensus       165 S--Rc-~~~~f~~l~~~el~~~L~~ia~~Egi~i~~eAL~lIa~~s~G-slR~alslLdqli~y~----~~~It~e~V~~  236 (491)
T PRK14964        165 S--RC-QRFDLQKIPTDKLVEHLVDIAKKENIEHDEESLKLIAENSSG-SMRNALFLLEQAAIYS----NNKISEKSVRD  236 (491)
T ss_pred             H--hh-eeeecccccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHHhc----CCCCCHHHHHH
Confidence            8  77 56899999999988888764432      2235567888865 8889988888776543    23588888776


Q ss_pred             HH
Q 030960          152 GY  153 (168)
Q Consensus       152 al  153 (168)
                      .+
T Consensus       237 ll  238 (491)
T PRK14964        237 LL  238 (491)
T ss_pred             HH
Confidence            64

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.99  E-value=0.0001  Score=62.16  Aligned_cols=116  Identities=16%  Similarity=0.240  Sum_probs=80.2

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      +-|++|||+|.+..              ...+.|+..++.  ....+++|.+|+.++.+++++.+  |+. .+.|.+|+.
T Consensus       120 ~KVvIIDEad~Lt~--------------~a~naLLk~LEe--pp~~~v~Il~tt~~~kl~~tI~S--Rc~-~i~f~~ls~  180 (486)
T PRK14953        120 YKVYIIDEAHMLTK--------------EAFNALLKTLEE--PPPRTIFILCTTEYDKIPPTILS--RCQ-RFIFSKPTK  180 (486)
T ss_pred             eeEEEEEChhhcCH--------------HHHHHHHHHHhc--CCCCeEEEEEECCHHHHHHHHHH--hce-EEEcCCCCH
Confidence            57999999997731              234667777764  33456666667778999999988  765 699999999


Q ss_pred             HHHHHHHHhhcCC-C-----CCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           94 RQKRLVFQMNLSD-E-----VDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        94 ~~R~~il~~~l~~-~-----~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      ++....++..+.. .     ..+..+++.+.| +.+++.++++.+...    +...+|.+++.+.+
T Consensus       181 ~el~~~L~~i~k~egi~id~~al~~La~~s~G-~lr~al~~Ldkl~~~----~~~~It~~~V~~~l  241 (486)
T PRK14953        181 EQIKEYLKRICNEEKIEYEEKALDLLAQASEG-GMRDAASLLDQASTY----GEGKVTIKVVEEFL  241 (486)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHHh----cCCCcCHHHHHHHh
Confidence            9999888864432 1     234556766654 677887877776533    23357777776654

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.98  E-value=0.00011  Score=59.66  Aligned_cols=128  Identities=14%  Similarity=0.208  Sum_probs=81.9

Q ss_pred             HHHHHHHHHc----CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccC
Q 030960            3 RDVFRLAKEN----APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLR   78 (168)
Q Consensus         3 ~~iF~~a~~~----~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r   78 (168)
                      +.+++.+...    .+.||+|||+|.+..              ...+.++..++.  .....++|.+|+.+..+.+++.+
T Consensus        94 ~~l~~~~~~~p~~~~~kiviIDE~~~l~~--------------~~~~~ll~~le~--~~~~~~~Il~~~~~~kl~~~l~s  157 (367)
T PRK14970         94 RNLIDQVRIPPQTGKYKIYIIDEVHMLSS--------------AAFNAFLKTLEE--PPAHAIFILATTEKHKIIPTILS  157 (367)
T ss_pred             HHHHHHHhhccccCCcEEEEEeChhhcCH--------------HHHHHHHHHHhC--CCCceEEEEEeCCcccCCHHHHh
Confidence            4555555432    257999999997632              234567666664  23345666677788999999988


Q ss_pred             CCCcceEEecCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHH
Q 030960           79 PGRLDRKIEFPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKG  152 (168)
Q Consensus        79 ~grf~~~i~~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~a  152 (168)
                        |+. .+.+++|+.++...++.....      ++..++.+++.+.| +.+.+.+.++.....+   ++. |+.+++...
T Consensus       158 --r~~-~v~~~~~~~~~l~~~l~~~~~~~g~~i~~~al~~l~~~~~g-dlr~~~~~lekl~~y~---~~~-it~~~v~~~  229 (367)
T PRK14970        158 --RCQ-IFDFKRITIKDIKEHLAGIAVKEGIKFEDDALHIIAQKADG-ALRDALSIFDRVVTFC---GKN-ITRQAVTEN  229 (367)
T ss_pred             --cce-eEecCCccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCC-CHHHHHHHHHHHHHhc---CCC-CCHHHHHHH
Confidence              664 689999999998888875333      12234567776654 6676666666554332   222 666666655


Q ss_pred             HH
Q 030960          153 YR  154 (168)
Q Consensus       153 l~  154 (168)
                      +.
T Consensus       230 ~~  231 (367)
T PRK14970        230 LN  231 (367)
T ss_pred             hC
Confidence            43

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=97.96  E-value=7.8e-05  Score=63.30  Aligned_cols=115  Identities=19%  Similarity=0.204  Sum_probs=81.8

Q ss_pred             eEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCHH
Q 030960           15 AIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRR   94 (168)
Q Consensus        15 ~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~~   94 (168)
                      -|++|||+|.+-.              ...+.|+..++..  .+.+.+|.+|+.+..|++++++  |. ..++|.+++.+
T Consensus       119 KVvIIDEad~Lt~--------------~A~NALLK~LEEp--p~~t~FIL~ttd~~kL~~tI~S--Rc-~~~~F~~Ls~~  179 (535)
T PRK08451        119 KIFIIDEVHMLTK--------------EAFNALLKTLEEP--PSYVKFILATTDPLKLPATILS--RT-QHFRFKQIPQN  179 (535)
T ss_pred             EEEEEECcccCCH--------------HHHHHHHHHHhhc--CCceEEEEEECChhhCchHHHh--hc-eeEEcCCCCHH
Confidence            5899999987731              4456788888753  4456677777889999999999  85 58899999998


Q ss_pred             HHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           95 QKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        95 ~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      +-...++..+..      +..+..++..+.| +.+++.+++..+...+    ...||.+++.+.+
T Consensus       180 ei~~~L~~Il~~EGi~i~~~Al~~Ia~~s~G-dlR~alnlLdqai~~~----~~~It~~~V~~~l  239 (535)
T PRK08451        180 SIISHLKTILEKEGVSYEPEALEILARSGNG-SLRDTLTLLDQAIIYC----KNAITESKVADML  239 (535)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-cHHHHHHHHHHHHHhc----CCCCCHHHHHHHh
Confidence            888877754432      2235567777766 8889988888776544    2236666555443

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.96  E-value=0.00018  Score=60.93  Aligned_cols=117  Identities=15%  Similarity=0.202  Sum_probs=82.3

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      .+.||+|||+|.+.              ....+.++..++.  ...++++|.+|+.++.+++.+.+  |+. .+.|.+|+
T Consensus       116 ~~kVVIIDEad~ls--------------~~a~naLLk~LEe--p~~~t~~Il~t~~~~kl~~~I~S--Rc~-~~~f~~ls  176 (504)
T PRK14963        116 GRKVYILDEAHMMS--------------KSAFNALLKTLEE--PPEHVIFILATTEPEKMPPTILS--RTQ-HFRFRRLT  176 (504)
T ss_pred             CCeEEEEECccccC--------------HHHHHHHHHHHHh--CCCCEEEEEEcCChhhCChHHhc--ceE-EEEecCCC
Confidence            46799999998652              1446677777764  34467777888999999999998  765 79999999


Q ss_pred             HHHHHHHHHhhcCC-CC-----CHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960           93 RRQKRLVFQMNLSD-EV-----DLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus        93 ~~~R~~il~~~l~~-~~-----~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      .++-...++..+.. .+     .+..+++.+.| +.+++.++++.+...     ...||.+++.+.+.
T Consensus       177 ~~el~~~L~~i~~~egi~i~~~Al~~ia~~s~G-dlR~aln~Lekl~~~-----~~~It~~~V~~~l~  238 (504)
T PRK14963        177 EEEIAGKLRRLLEAEGREAEPEALQLVARLADG-AMRDAESLLERLLAL-----GTPVTRKQVEEALG  238 (504)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHhc-----CCCCCHHHHHHHHC
Confidence            99999888765542 22     34556766654 666676666665331     23588887776654

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

Probab=97.94  E-value=0.00027  Score=57.58  Aligned_cols=129  Identities=21%  Similarity=0.249  Sum_probs=93.0

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC---CCCccccCCCCcc-eEEe
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD---TLDPALLRPGRLD-RKIE   87 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~---~ld~al~r~grf~-~~i~   87 (168)
                      ..+.||++||+|.|....+           .++-.++..-+..  ..+|.+|+.+|..+   .+|+.+.+  +|. ..|.
T Consensus       122 ~~~~IvvLDEid~L~~~~~-----------~~LY~L~r~~~~~--~~~v~vi~i~n~~~~~~~ld~rv~s--~l~~~~I~  186 (366)
T COG1474         122 GKTVIVILDEVDALVDKDG-----------EVLYSLLRAPGEN--KVKVSIIAVSNDDKFLDYLDPRVKS--SLGPSEIV  186 (366)
T ss_pred             CCeEEEEEcchhhhccccc-----------hHHHHHHhhcccc--ceeEEEEEEeccHHHHHHhhhhhhh--ccCcceee
Confidence            4578999999999985542           3444555555433  56789999999874   88898887  655 4589


Q ss_pred             cCCCCHHHHHHHHHhhcC----C----CCCHHHHH---hCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           88 FPLPDRRQKRLVFQMNLS----D----EVDLEDYV---SRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        88 ~~~P~~~~R~~il~~~l~----~----~~~~~~la---~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      |++=+.+|-..|++....    +    +..++.+|   ....| ..+---.+|+.|+..|-+++...++.++...|....
T Consensus       187 F~pY~a~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~G-DAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~  265 (366)
T COG1474         187 FPPYTAEELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESG-DARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEI  265 (366)
T ss_pred             eCCCCHHHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCc-cHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHh
Confidence            999999999999984443    1    22233333   33444 445555688999999999999999999999995443

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=97.94  E-value=0.00014  Score=63.69  Aligned_cols=127  Identities=18%  Similarity=0.252  Sum_probs=86.0

Q ss_pred             HHHHHHHHHHc----CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcccc
Q 030960            2 VRDVFRLAKEN----APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~~----~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~   77 (168)
                      ++.+.+.+...    ...|++|||+|.+-.              ...+.|+..|+.  ....+++|.+|+.++.|++.++
T Consensus       103 IReLie~~~~~P~~g~~KV~IIDEa~~LT~--------------~A~NALLKtLEE--PP~~tifILaTte~~KLl~TI~  166 (725)
T PRK07133        103 IRELIENVKNLPTQSKYKIYIIDEVHMLSK--------------SAFNALLKTLEE--PPKHVIFILATTEVHKIPLTIL  166 (725)
T ss_pred             HHHHHHHHHhchhcCCCEEEEEEChhhCCH--------------HHHHHHHHHhhc--CCCceEEEEEcCChhhhhHHHH
Confidence            45666666533    356999999998731              346678888874  4456778888889999999999


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhcCC-CC-----CHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHH
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNLSD-EV-----DLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK  151 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l~~-~~-----~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~  151 (168)
                      +  |+. .+.|.+|+.++....++..+.. .+     .+..+|..+. -+.+++.+++.......    ...|+.+++.+
T Consensus       167 S--Rcq-~ieF~~L~~eeI~~~L~~il~kegI~id~eAl~~LA~lS~-GslR~AlslLekl~~y~----~~~It~e~V~e  238 (725)
T PRK07133        167 S--RVQ-RFNFRRISEDEIVSRLEFILEKENISYEKNALKLIAKLSS-GSLRDALSIAEQVSIFG----NNKITLKNVEE  238 (725)
T ss_pred             h--hce-eEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcC-CCHHHHHHHHHHHHHhc----cCCCCHHHHHH
Confidence            8  885 8999999999988888754431 12     2445666665 46677777777654322    22366666554


Q ss_pred             H
Q 030960          152 G  152 (168)
Q Consensus       152 a  152 (168)
                      .
T Consensus       239 l  239 (725)
T PRK07133        239 L  239 (725)
T ss_pred             H
Confidence            4

>PRK04195 replication factor C large subunit; Provisional

Probab=97.91  E-value=0.00011  Score=61.99  Aligned_cols=118  Identities=15%  Similarity=0.147  Sum_probs=77.2

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCc-cccCCCCcceEEecCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDP-ALLRPGRLDRKIEFPLP   91 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~-al~r~grf~~~i~~~~P   91 (168)
                      .+.||+|||+|.+..+.      ..    ..+..++..++.    .+..+|+++|.+..+++ .+++   ....+.|++|
T Consensus        98 ~~kvIiIDEaD~L~~~~------d~----~~~~aL~~~l~~----~~~~iIli~n~~~~~~~k~Lrs---r~~~I~f~~~  160 (482)
T PRK04195         98 RRKLILLDEVDGIHGNE------DR----GGARAILELIKK----AKQPIILTANDPYDPSLRELRN---ACLMIEFKRL  160 (482)
T ss_pred             CCeEEEEecCccccccc------ch----hHHHHHHHHHHc----CCCCEEEeccCccccchhhHhc---cceEEEecCC
Confidence            47899999999986421      11    223445555542    23447778899998887 5544   4568999999


Q ss_pred             CHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           92 DRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        92 ~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      +..+...+++..+..      +..+..|++.+.    +|+..+++....  +..+...++.+++....
T Consensus       161 ~~~~i~~~L~~i~~~egi~i~~eaL~~Ia~~s~----GDlR~ain~Lq~--~a~~~~~it~~~v~~~~  222 (482)
T PRK04195        161 STRSIVPVLKRICRKEGIECDDEALKEIAERSG----GDLRSAINDLQA--IAEGYGKLTLEDVKTLG  222 (482)
T ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcC----CCHHHHHHHHHH--HhcCCCCCcHHHHHHhh
Confidence            999999999865531      223556777654    477777776544  33344567777776554

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.89  E-value=9.9e-05  Score=64.21  Aligned_cols=130  Identities=16%  Similarity=0.166  Sum_probs=90.6

Q ss_pred             HHHHHHHHHH----cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcccc
Q 030960            2 VRDVFRLAKE----NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~----~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~   77 (168)
                      |+++.+.+..    ....|++|||+|.+-              ....+.|+..|+.  ....+.+|++|+.+..+.+.++
T Consensus       104 IRelle~a~~~P~~gk~KVIIIDEad~Ls--------------~~A~NALLKtLEE--Pp~~v~fILaTtd~~kL~~TIr  167 (709)
T PRK08691        104 IREVLENAQYAPTAGKYKVYIIDEVHMLS--------------KSAFNAMLKTLEE--PPEHVKFILATTDPHKVPVTVL  167 (709)
T ss_pred             HHHHHHHHHhhhhhCCcEEEEEECccccC--------------HHHHHHHHHHHHh--CCCCcEEEEEeCCccccchHHH
Confidence            4566665532    234699999999762              1345678888874  3446777888889999999998


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhcCC-CC-----CHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHH
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNLSD-EV-----DLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK  151 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l~~-~~-----~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~  151 (168)
                      +  |+ ..+.|++++.++-...++..+.. .+     .+..|+..+. -+.+++.+++..+...    +...|+.+++..
T Consensus       168 S--RC-~~f~f~~Ls~eeI~~~L~~Il~kEgi~id~eAL~~Ia~~A~-GslRdAlnLLDqaia~----g~g~It~e~V~~  239 (709)
T PRK08691        168 S--RC-LQFVLRNMTAQQVADHLAHVLDSEKIAYEPPALQLLGRAAA-GSMRDALSLLDQAIAL----GSGKVAENDVRQ  239 (709)
T ss_pred             H--HH-hhhhcCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHhC-CCHHHHHHHHHHHHHh----cCCCcCHHHHHH
Confidence            7  87 56788899999988888766653 22     2566777774 5788888888776553    233577777666


Q ss_pred             HHHh
Q 030960          152 GYRT  155 (168)
Q Consensus       152 al~~  155 (168)
                      .+..
T Consensus       240 lLG~  243 (709)
T PRK08691        240 MIGA  243 (709)
T ss_pred             HHcc
Confidence            6543

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=97.87  E-value=0.00023  Score=61.41  Aligned_cols=129  Identities=16%  Similarity=0.197  Sum_probs=90.1

Q ss_pred             HHHHHHHHHHc----CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcccc
Q 030960            2 VRDVFRLAKEN----APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~~----~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~   77 (168)
                      |+++.+.++..    ..-|++|||+|.+-.              ...+.|+..|+.  ....+.+|.+|+.++.+.+.++
T Consensus       117 IReIie~~~~~P~~a~~KVvIIDEad~Ls~--------------~a~naLLKtLEe--Pp~~~~fIl~tte~~kll~tI~  180 (598)
T PRK09111        117 IREIIESVRYRPVSARYKVYIIDEVHMLST--------------AAFNALLKTLEE--PPPHVKFIFATTEIRKVPVTVL  180 (598)
T ss_pred             HHHHHHHHHhchhcCCcEEEEEEChHhCCH--------------HHHHHHHHHHHh--CCCCeEEEEEeCChhhhhHHHH
Confidence            46666666533    256999999998731              346677777774  3345667777788888999998


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhcCC---CC---CHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHH
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNLSD---EV---DLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK  151 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l~~---~~---~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~  151 (168)
                      +  |+ ..+.|..|+.++-...++..+..   .+   .+..++..+.| +.+++.+++..+....    ...|+.+++..
T Consensus       181 S--Rc-q~~~f~~l~~~el~~~L~~i~~kegi~i~~eAl~lIa~~a~G-dlr~al~~Ldkli~~g----~g~It~e~V~~  252 (598)
T PRK09111        181 S--RC-QRFDLRRIEADVLAAHLSRIAAKEGVEVEDEALALIARAAEG-SVRDGLSLLDQAIAHG----AGEVTAEAVRD  252 (598)
T ss_pred             h--he-eEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHhhc----CCCcCHHHHHH
Confidence            8  77 57999999999988888765442   12   34456777765 7888888887765432    33588888777


Q ss_pred             HHH
Q 030960          152 GYR  154 (168)
Q Consensus       152 al~  154 (168)
                      .+.
T Consensus       253 llg  255 (598)
T PRK09111        253 MLG  255 (598)
T ss_pred             HhC
Confidence            654

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.86  E-value=0.00015  Score=64.61  Aligned_cols=102  Identities=18%  Similarity=0.170  Sum_probs=72.9

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCC
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLP   91 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P   91 (168)
                      ...-|++|||+|.|-.              ...+.||+.|+.  ...++++|++|+.++.|.+.+++  |+ ..+.|..+
T Consensus       119 ~~~KV~IIDEad~lt~--------------~a~NaLLK~LEE--pP~~~~fIl~tt~~~kLl~TIrS--Rc-~~v~F~~l  179 (824)
T PRK07764        119 SRYKIFIIDEAHMVTP--------------QGFNALLKIVEE--PPEHLKFIFATTEPDKVIGTIRS--RT-HHYPFRLV  179 (824)
T ss_pred             CCceEEEEechhhcCH--------------HHHHHHHHHHhC--CCCCeEEEEEeCChhhhhHHHHh--he-eEEEeeCC
Confidence            3457999999999841              446678888874  34467777778888999999998  75 57899999


Q ss_pred             CHHHHHHHHHhhcC-CCC-----CHHHHHhCCCCCCHHHHHHHHHHHH
Q 030960           92 DRRQKRLVFQMNLS-DEV-----DLEDYVSRPDKISAAEIAAICQEAG  133 (168)
Q Consensus        92 ~~~~R~~il~~~l~-~~~-----~~~~la~~t~g~s~~di~~l~~~a~  133 (168)
                      +.++-.++++..+. ..+     .+..++..+.| +.+++.++++..+
T Consensus       180 ~~~~l~~~L~~il~~EGv~id~eal~lLa~~sgG-dlR~Al~eLEKLi  226 (824)
T PRK07764        180 PPEVMRGYLERICAQEGVPVEPGVLPLVIRAGGG-SVRDSLSVLDQLL  226 (824)
T ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHH
Confidence            98888888876553 122     23456666655 7777777776644

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.85  E-value=0.00028  Score=60.09  Aligned_cols=129  Identities=15%  Similarity=0.145  Sum_probs=88.1

Q ss_pred             HHHHHHHHHHc----CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcccc
Q 030960            2 VRDVFRLAKEN----APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~~----~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~   77 (168)
                      ++++.+.+...    ...|++|||+|.+..              ...+.|+..++.  ....+.+|.+|++++.+.+.++
T Consensus       104 ir~l~~~~~~~p~~~~~kVvIIDEad~ls~--------------~a~naLLK~LEe--pp~~~~fIL~t~d~~kil~tI~  167 (527)
T PRK14969        104 MRELLDNAQYAPTRGRFKVYIIDEVHMLSK--------------SAFNAMLKTLEE--PPEHVKFILATTDPQKIPVTVL  167 (527)
T ss_pred             HHHHHHHHhhCcccCCceEEEEcCcccCCH--------------HHHHHHHHHHhC--CCCCEEEEEEeCChhhCchhHH
Confidence            45566655422    245999999997731              345678888874  4456777777888999998888


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhcCC-CC-----CHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHH
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNLSD-EV-----DLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK  151 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l~~-~~-----~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~  151 (168)
                      +  |+ ..+.|.+|+.++-...+...+.. .+     .+..++..+. -++++..+++..+...    +...|+.+++..
T Consensus       168 S--Rc-~~~~f~~l~~~~i~~~L~~il~~egi~~~~~al~~la~~s~-Gslr~al~lldqai~~----~~~~I~~~~v~~  239 (527)
T PRK14969        168 S--RC-LQFNLKQMPPPLIVSHLQHILEQENIPFDATALQLLARAAA-GSMRDALSLLDQAIAY----GGGTVNESEVRA  239 (527)
T ss_pred             H--HH-HHHhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcC-CCHHHHHHHHHHHHHh----cCCCcCHHHHHH
Confidence            7  76 78999999999988877755431 12     2345666654 4678888888776543    344577777766


Q ss_pred             HHH
Q 030960          152 GYR  154 (168)
Q Consensus       152 al~  154 (168)
                      .+.
T Consensus       240 ~~~  242 (527)
T PRK14969        240 MLG  242 (527)
T ss_pred             HHC
Confidence            553

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=97.84  E-value=0.00034  Score=56.34  Aligned_cols=128  Identities=16%  Similarity=0.200  Sum_probs=86.3

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC---------C--CCCCCeEEEEecCCCC-CCCccccCCCC
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG---------F--DQTVNVKVIMATNRAD-TLDPALLRPGR   81 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~---------~--~~~~~v~vi~ttn~~~-~ld~al~r~gr   81 (168)
                      ..++|+||++.+-.              .+.+.++..|+.         .  ....++++|+|+|-.+ .++++++.  |
T Consensus       132 ~GvL~lDEi~~L~~--------------~~Q~~Ll~~l~~g~~~v~r~G~~~~~~~r~iviat~np~eg~l~~~Lld--R  195 (337)
T TIGR02030       132 RGILYIDEVNLLED--------------HLVDVLLDVAASGWNVVEREGISIRHPARFVLVGSGNPEEGELRPQLLD--R  195 (337)
T ss_pred             CCEEEecChHhCCH--------------HHHHHHHHHHHhCCeEEEECCEEEEcCCCEEEEeccccccCCCCHHHHh--h
Confidence            47999999998621              233344444421         1  1223577788877544 68999999  9


Q ss_pred             cceEEecCCCCH-HHHHHHHHhhcC------------------------------CCCC--------HHHHHhCCCCCCH
Q 030960           82 LDRKIEFPLPDR-RQKRLVFQMNLS------------------------------DEVD--------LEDYVSRPDKISA  122 (168)
Q Consensus        82 f~~~i~~~~P~~-~~R~~il~~~l~------------------------------~~~~--------~~~la~~t~g~s~  122 (168)
                      |...+.++.|.. ++|.+|++....                              ..+.        +.+++..+..-|+
T Consensus       196 f~l~i~l~~p~~~eer~eIL~~~~~~~~~~~~~~~~~~~e~~~~~~~I~~a~~~~~~V~v~d~~~~~i~~l~~~~~~~s~  275 (337)
T TIGR02030       196 FGLHAEIRTVRDVELRVEIVERRTEYDADPHAFCEKWQTEQEALQAKIVNAQNLLPQVTIPYDVLVKVAELCAELDVDGL  275 (337)
T ss_pred             cceEEECCCCCCHHHHHHHHHhhhhcccCchhhhhhhhhhhhcCHHHHHHHHHHhccCcCCHHHHHHHHHHHHHHCCCCC
Confidence            999999999976 889999875211                              0111        1123333433356


Q ss_pred             HHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhc
Q 030960          123 AEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNV  157 (168)
Q Consensus       123 ~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~  157 (168)
                      +--..+++-|...|+.+++..++.+|+..+..-+.
T Consensus       276 Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~~vL  310 (337)
T TIGR02030       276 RGELTLNRAAKALAAFEGRTEVTVDDIRRVAVLAL  310 (337)
T ss_pred             cHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence            66667778888888889999999999998876443

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.

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

Probab=97.81  E-value=0.00014  Score=59.09  Aligned_cols=138  Identities=18%  Similarity=0.270  Sum_probs=85.7

Q ss_pred             HHHHHHHHHHcC----CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEE-ecCCCC-CCCcc
Q 030960            2 VRDVFRLAKENA----PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIM-ATNRAD-TLDPA   75 (168)
Q Consensus         2 l~~iF~~a~~~~----p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~-ttn~~~-~ld~a   75 (168)
                      |+++|+.|+...    ..|||+||++.+-.              .....||-.++    +..|++|| ||.+|. .|.+|
T Consensus        89 lr~i~e~a~~~~~~gr~tiLflDEIHRfnK--------------~QQD~lLp~vE----~G~iilIGATTENPsF~ln~A  150 (436)
T COG2256          89 LREIIEEARKNRLLGRRTILFLDEIHRFNK--------------AQQDALLPHVE----NGTIILIGATTENPSFELNPA  150 (436)
T ss_pred             HHHHHHHHHHHHhcCCceEEEEehhhhcCh--------------hhhhhhhhhhc----CCeEEEEeccCCCCCeeecHH
Confidence            688999996544    59999999998831              11223666664    45677777 555565 89999


Q ss_pred             ccCCCCcceEEecCCCCHHHHHHHHHhhcC-C-------CCCHHH-HHhCCCCCCHHHHHHHHHHHHHHHHHhC-CCccC
Q 030960           76 LLRPGRLDRKIEFPLPDRRQKRLVFQMNLS-D-------EVDLED-YVSRPDKISAAEIAAICQEAGMHAVRKN-RYVIL  145 (168)
Q Consensus        76 l~r~grf~~~i~~~~P~~~~R~~il~~~l~-~-------~~~~~~-la~~t~g~s~~di~~l~~~a~~~a~~~~-~~~i~  145 (168)
                      +++  |. .++++.+.+.++-.++++..+. .       .+.+++ .-...-..+.+|...+++..-+.+.... ...++
T Consensus       151 LlS--R~-~vf~lk~L~~~di~~~l~ra~~~~~rgl~~~~~~i~~~a~~~l~~~s~GD~R~aLN~LE~~~~~~~~~~~~~  227 (436)
T COG2256         151 LLS--RA-RVFELKPLSSEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVRLSNGDARRALNLLELAALSAEPDEVLI  227 (436)
T ss_pred             Hhh--hh-heeeeecCCHHHHHHHHHHHHhhhhcCCCcccccCCHHHHHHHHHhcCchHHHHHHHHHHHHHhcCCCcccC
Confidence            998  64 5688999999999999986222 1       111222 2222223445577776664422222211 12455


Q ss_pred             HHHHHHHHHhhcCCC
Q 030960          146 PKDFEKGYRTNVKKP  160 (168)
Q Consensus       146 ~~d~~~al~~~~p~~  160 (168)
                      .+++.+.+.+..+..
T Consensus       228 ~~~l~~~l~~~~~~~  242 (436)
T COG2256         228 LELLEEILQRRSARF  242 (436)
T ss_pred             HHHHHHHHhhhhhcc
Confidence            788888887766544

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=97.80  E-value=0.00047  Score=55.45  Aligned_cols=123  Identities=17%  Similarity=0.200  Sum_probs=83.2

Q ss_pred             eEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC-----------CCCCCeEEEEecCCCC-CCCccccCCCCc
Q 030960           15 AIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF-----------DQTVNVKVIMATNRAD-TLDPALLRPGRL   82 (168)
Q Consensus        15 ~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~-----------~~~~~v~vi~ttn~~~-~ld~al~r~grf   82 (168)
                      .+|++||++.+-.              .+.+.++..|+.-           ....++++++|+|-.+ .++++++.  ||
T Consensus       130 GiL~lDEInrl~~--------------~~q~~Lle~mee~~v~v~r~G~~~~~p~rfiviAt~NP~e~~l~~aLld--RF  193 (334)
T PRK13407        130 GYLYIDEVNLLED--------------HIVDLLLDVAQSGENVVEREGLSIRHPARFVLVGSGNPEEGELRPQLLD--RF  193 (334)
T ss_pred             CeEEecChHhCCH--------------HHHHHHHHHHHcCCeEEEECCeEEecCCCEEEEecCCcccCCCCHHHHh--hc
Confidence            5899999998631              3444455555321           1234678888877544 58899999  99


Q ss_pred             ceEEecCCCCH-HHHHHHHHhhcCCC------------------------------C-----CHH---HHHhCC--CCCC
Q 030960           83 DRKIEFPLPDR-RQKRLVFQMNLSDE------------------------------V-----DLE---DYVSRP--DKIS  121 (168)
Q Consensus        83 ~~~i~~~~P~~-~~R~~il~~~l~~~------------------------------~-----~~~---~la~~t--~g~s  121 (168)
                      ...+.+++|.. ++|.+|++.....+                              +     .+.   +++..+  +| .
T Consensus       194 ~~~v~v~~~~~~~e~~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~a~~~~~~V~v~~~~~~yi~~l~~~~~~~s-~  272 (334)
T PRK13407        194 GLSVEVRSPRDVETRVEVIRRRDAYDADHDAFMAKWGAEDMQLRGRILGARARLPQLKTPNTVLHDCAALCIALGSDG-L  272 (334)
T ss_pred             ceEEEcCCCCcHHHHHHHHHHhhcccccchhhhccccccccCCHHHHHHHHHhcCCcccCHHHHHHHHHHHHHHCCCC-c
Confidence            99999998877 99999997532110                              0     011   122222  23 3


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960          122 AAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus       122 ~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      -++|. +++.|...|+..++..|+.+|+..+..-
T Consensus       273 Ra~i~-l~~aA~a~A~l~Gr~~V~~~Di~~~~~~  305 (334)
T PRK13407        273 RGELT-LLRAARALAAFEGAEAVGRSHLRSVATM  305 (334)
T ss_pred             hHHHH-HHHHHHHHHHHcCCCeeCHHHHHHHHHH
Confidence            35565 8888899999999999999999887743

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.79  E-value=0.0003  Score=62.74  Aligned_cols=100  Identities=17%  Similarity=0.238  Sum_probs=75.4

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      .-|++|||+|.+-              ....+.||..|+.  ...++.+|++|+.+..|.+.+++  |+ ..+.|++++.
T Consensus       120 ~KViIIDEAh~LT--------------~eAqNALLKtLEE--PP~~vrFILaTTe~~kLl~TIlS--RC-q~f~fkpLs~  180 (944)
T PRK14949        120 FKVYLIDEVHMLS--------------RSSFNALLKTLEE--PPEHVKFLLATTDPQKLPVTVLS--RC-LQFNLKSLTQ  180 (944)
T ss_pred             cEEEEEechHhcC--------------HHHHHHHHHHHhc--cCCCeEEEEECCCchhchHHHHH--hh-eEEeCCCCCH
Confidence            4699999999883              1567788888874  44567777788899999999998  77 6799999999


Q ss_pred             HHHHHHHHhhcCC-CC-----CHHHHHhCCCCCCHHHHHHHHHHHH
Q 030960           94 RQKRLVFQMNLSD-EV-----DLEDYVSRPDKISAAEIAAICQEAG  133 (168)
Q Consensus        94 ~~R~~il~~~l~~-~~-----~~~~la~~t~g~s~~di~~l~~~a~  133 (168)
                      ++-.+.++..+.. .+     .+..|+..+.| +++++-+++..+.
T Consensus       181 eEI~~~L~~il~~EgI~~edeAL~lIA~~S~G-d~R~ALnLLdQal  225 (944)
T PRK14949        181 DEIGTQLNHILTQEQLPFEAEALTLLAKAANG-SMRDALSLTDQAI  225 (944)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHH
Confidence            9999888865532 22     34556766655 6778888877655

>PRK04132 replication factor C small subunit; Provisional

Probab=97.79  E-value=0.0004  Score=61.88  Aligned_cols=86  Identities=20%  Similarity=0.233  Sum_probs=63.8

Q ss_pred             eEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCHH
Q 030960           15 AIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRR   94 (168)
Q Consensus        15 ~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~~   94 (168)
                      -|++|||+|.+-.              ...+.|+..|+.  ...++.+|++||+++.+.+++++  |+ ..+.|++|+.+
T Consensus       632 KVvIIDEaD~Lt~--------------~AQnALLk~lEe--p~~~~~FILi~N~~~kIi~tIrS--RC-~~i~F~~ls~~  692 (846)
T PRK04132        632 KIIFLDEADALTQ--------------DAQQALRRTMEM--FSSNVRFILSCNYSSKIIEPIQS--RC-AIFRFRPLRDE  692 (846)
T ss_pred             EEEEEECcccCCH--------------HHHHHHHHHhhC--CCCCeEEEEEeCChhhCchHHhh--hc-eEEeCCCCCHH
Confidence            5999999998831              334567777773  34578899999999999999998  86 77899999988


Q ss_pred             HHHHHHHhhcC------CCCCHHHHHhCCCC
Q 030960           95 QKRLVFQMNLS------DEVDLEDYVSRPDK  119 (168)
Q Consensus        95 ~R~~il~~~l~------~~~~~~~la~~t~g  119 (168)
                      +-...++....      ++..+..++..++|
T Consensus       693 ~i~~~L~~I~~~Egi~i~~e~L~~Ia~~s~G  723 (846)
T PRK04132        693 DIAKRLRYIAENEGLELTEEGLQAILYIAEG  723 (846)
T ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHHHcCC
Confidence            88877764433      12245566666655

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.79  E-value=0.00019  Score=56.68  Aligned_cols=118  Identities=17%  Similarity=0.168  Sum_probs=77.1

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      +.+|+|||+|.+...              ....++..++....  ...+|.++|.+..+.+++.+  |+. .+++++|+.
T Consensus       103 ~~vviiDe~~~l~~~--------------~~~~L~~~le~~~~--~~~lIl~~~~~~~l~~~l~s--r~~-~~~~~~l~~  163 (319)
T PRK00440        103 FKIIFLDEADNLTSD--------------AQQALRRTMEMYSQ--NTRFILSCNYSSKIIDPIQS--RCA-VFRFSPLKK  163 (319)
T ss_pred             ceEEEEeCcccCCHH--------------HHHHHHHHHhcCCC--CCeEEEEeCCccccchhHHH--Hhh-eeeeCCCCH
Confidence            569999999988421              12334445554332  34566677888888888888  765 589999999


Q ss_pred             HHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           94 RQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        94 ~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      ++...+++..+..      ...+..++..+.| +.+.+.+.++.++..     ...||.+++..++...
T Consensus       164 ~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~g-d~r~~~~~l~~~~~~-----~~~it~~~v~~~~~~~  226 (319)
T PRK00440        164 EAVAERLRYIAENEGIEITDDALEAIYYVSEG-DMRKAINALQAAAAT-----GKEVTEEAVYKITGTA  226 (319)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHHc-----CCCCCHHHHHHHhCCC
Confidence            9999888865542      2245667777655 555555555544432     3468888887776443

>PRK09087 hypothetical protein; Validated

Probab=97.79  E-value=0.0001  Score=56.09  Aligned_cols=123  Identities=17%  Similarity=0.131  Sum_probs=79.0

Q ss_pred             eEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCC---CccccCCCCcc--eEEecC
Q 030960           15 AIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTL---DPALLRPGRLD--RKIEFP   89 (168)
Q Consensus        15 ~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~l---d~al~r~grf~--~~i~~~   89 (168)
                      .+|+|||+|.+.        ...    .-   +...++.+....+.+||+++..|..+   .+.+++  ||.  ..+++.
T Consensus        89 ~~l~iDDi~~~~--------~~~----~~---lf~l~n~~~~~g~~ilits~~~p~~~~~~~~dL~S--Rl~~gl~~~l~  151 (226)
T PRK09087         89 GPVLIEDIDAGG--------FDE----TG---LFHLINSVRQAGTSLLMTSRLWPSSWNVKLPDLKS--RLKAATVVEIG  151 (226)
T ss_pred             CeEEEECCCCCC--------CCH----HH---HHHHHHHHHhCCCeEEEECCCChHHhccccccHHH--HHhCCceeecC
Confidence            578899999762        111    11   22333332344456666666555533   677888  886  888999


Q ss_pred             CCCHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           90 LPDRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        90 ~P~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      +|+.+.|.++++..+..      +-.++.|+++.+| +.+.+..+++.-...+... +..+|...+.++++..
T Consensus       152 ~pd~e~~~~iL~~~~~~~~~~l~~ev~~~La~~~~r-~~~~l~~~l~~L~~~~~~~-~~~it~~~~~~~l~~~  222 (226)
T PRK09087        152 EPDDALLSQVIFKLFADRQLYVDPHVVYYLVSRMER-SLFAAQTIVDRLDRLALER-KSRITRALAAEVLNEM  222 (226)
T ss_pred             CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhh-hHHHHHHHHHHHHHHHHHh-CCCCCHHHHHHHHHhh
Confidence            99999999999976652      2245567776652 4455555555554444443 4568999999998765

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.78  E-value=0.00018  Score=61.95  Aligned_cols=127  Identities=17%  Similarity=0.173  Sum_probs=85.2

Q ss_pred             HHHHHHHHHHc----CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcccc
Q 030960            2 VRDVFRLAKEN----APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~~----~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~   77 (168)
                      ++++.+.++..    ..-|++|||+|.+..              ...+.|+..|+.  ...++++|.+|+.++.|++.++
T Consensus       104 ir~l~~~~~~~p~~~~~KVvIIdev~~Lt~--------------~a~naLLk~LEe--pp~~~~fIl~t~~~~kl~~tI~  167 (576)
T PRK14965        104 IRELRENVKYLPSRSRYKIFIIDEVHMLST--------------NAFNALLKTLEE--PPPHVKFIFATTEPHKVPITIL  167 (576)
T ss_pred             HHHHHHHHHhccccCCceEEEEEChhhCCH--------------HHHHHHHHHHHc--CCCCeEEEEEeCChhhhhHHHH
Confidence            35555555432    135999999997731              345678888873  4457788888899999999999


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHH
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK  151 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~  151 (168)
                      +  |+ ..+.|..++.++-...++..+..      ...+..++..+.| +.++..+++..+...+-    ..|+.+++..
T Consensus       168 S--Rc-~~~~f~~l~~~~i~~~L~~i~~~egi~i~~~al~~la~~a~G-~lr~al~~Ldqliay~g----~~It~edV~~  239 (576)
T PRK14965        168 S--RC-QRFDFRRIPLQKIVDRLRYIADQEGISISDAALALVARKGDG-SMRDSLSTLDQVLAFCG----DAVGDDDVAE  239 (576)
T ss_pred             H--hh-hhhhcCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHHhcc----CCCCHHHHHH
Confidence            8  76 47889889888877777654431      2235567777765 77777777765543321    2366666554


Q ss_pred             H
Q 030960          152 G  152 (168)
Q Consensus       152 a  152 (168)
                      .
T Consensus       240 l  240 (576)
T PRK14965        240 L  240 (576)
T ss_pred             H
Confidence            4

>PRK06620 hypothetical protein; Validated

Probab=97.77  E-value=7.6e-05  Score=56.34  Aligned_cols=118  Identities=13%  Similarity=0.231  Sum_probs=77.9

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCC--CCccccCCCCcc--eEEecC
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADT--LDPALLRPGRLD--RKIEFP   89 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~--ld~al~r~grf~--~~i~~~   89 (168)
                      ..+++|||+|.+          ..    ..+-.+++.+   ...++.++|+++..|..  + +++++  |+.  ..+.+.
T Consensus        86 ~d~lliDdi~~~----------~~----~~lf~l~N~~---~e~g~~ilits~~~p~~l~l-~~L~S--Rl~~gl~~~l~  145 (214)
T PRK06620         86 YNAFIIEDIENW----------QE----PALLHIFNII---NEKQKYLLLTSSDKSRNFTL-PDLSS--RIKSVLSILLN  145 (214)
T ss_pred             CCEEEEeccccc----------hH----HHHHHHHHHH---HhcCCEEEEEcCCCccccch-HHHHH--HHhCCceEeeC
Confidence            478999999943          00    1222343333   34556778887777765  5 67888  876  468999


Q ss_pred             CCCHHHHHHHHHhhcC-C-----CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           90 LPDRRQKRLVFQMNLS-D-----EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        90 ~P~~~~R~~il~~~l~-~-----~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      +|+.+.|..+++.... .     +..++.++++.+| +.+.+..+++.....+.. .+..||...+.+++
T Consensus       146 ~pd~~~~~~~l~k~~~~~~l~l~~ev~~~L~~~~~~-d~r~l~~~l~~l~~~~~~-~~~~it~~~~~~~l  213 (214)
T PRK06620        146 SPDDELIKILIFKHFSISSVTISRQIIDFLLVNLPR-EYSKIIEILENINYFALI-SKRKITISLVKEVL  213 (214)
T ss_pred             CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHccC-CHHHHHHHHHHHHHHHHH-cCCCCCHHHHHHHh
Confidence            9999999999986554 2     2234556776643 677777777765433333 34578888887765

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

Probab=97.77  E-value=0.00031  Score=60.67  Aligned_cols=134  Identities=20%  Similarity=0.269  Sum_probs=91.1

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccC---CCCcc-eEEec
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLR---PGRLD-RKIEF   88 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r---~grf~-~~i~~   88 (168)
                      .|+||+|||+|.|+..+           +.++-.|..|-.  .+..+++||+.+|..+ +|..++-   .-|++ ..|.|
T Consensus       508 ~~~VvLiDElD~Lvtr~-----------QdVlYn~fdWpt--~~~sKLvvi~IaNTmd-lPEr~l~nrvsSRlg~tRi~F  573 (767)
T KOG1514|consen  508 STTVVLIDELDILVTRS-----------QDVLYNIFDWPT--LKNSKLVVIAIANTMD-LPERLLMNRVSSRLGLTRICF  573 (767)
T ss_pred             CCEEEEeccHHHHhccc-----------HHHHHHHhcCCc--CCCCceEEEEeccccc-CHHHHhccchhhhccceeeec
Confidence            49999999999998533           356666666654  4566788888777655 4444432   11555 56888


Q ss_pred             CCCCHHHHHHHHHhhcCCCC----CHHHH-HhCCCCCCH--HHHHHHHHHHHHHHHHhCC-------CccCHHHHHHHHH
Q 030960           89 PLPDRRQKRLVFQMNLSDEV----DLEDY-VSRPDKISA--AEIAAICQEAGMHAVRKNR-------YVILPKDFEKGYR  154 (168)
Q Consensus        89 ~~P~~~~R~~il~~~l~~~~----~~~~l-a~~t~g~s~--~di~~l~~~a~~~a~~~~~-------~~i~~~d~~~al~  154 (168)
                      .+-+..|-++|+...|..-.    +.-+| |..-...||  +--..+|++|+..|-.+..       ..++..|+.+|++
T Consensus       574 ~pYth~qLq~Ii~~RL~~~~~f~~~aielvarkVAavSGDaRraldic~RA~Eia~~~~~~~k~~~~q~v~~~~v~~Ai~  653 (767)
T KOG1514|consen  574 QPYTHEQLQEIISARLKGLDAFENKAIELVARKVAAVSGDARRALDICRRAAEIAEERNVKGKLAVSQLVGILHVMEAIN  653 (767)
T ss_pred             CCCCHHHHHHHHHHhhcchhhcchhHHHHHHHHHHhccccHHHHHHHHHHHHHHhhhhcccccccccceeehHHHHHHHH
Confidence            89999999999998887431    22233 333333333  3344588888888877754       5689999999999


Q ss_pred             hhcCCC
Q 030960          155 TNVKKP  160 (168)
Q Consensus       155 ~~~p~~  160 (168)
                      .+..+.
T Consensus       654 em~~~~  659 (767)
T KOG1514|consen  654 EMLASP  659 (767)
T ss_pred             HHhhhh
Confidence            876543

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=97.76  E-value=0.00039  Score=59.67  Aligned_cols=117  Identities=14%  Similarity=0.158  Sum_probs=83.1

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      ..-|++|||+|.+-.              ...+.|+..++.  ....+++|++|+.++.+.+++++  |+. .+.|.+|+
T Consensus       119 ~~KVvIIDEa~~Ls~--------------~a~naLLK~LEe--pp~~~vfI~~tte~~kL~~tI~S--Rc~-~~~f~~l~  179 (563)
T PRK06647        119 RYRVYIIDEVHMLSN--------------SAFNALLKTIEE--PPPYIVFIFATTEVHKLPATIKS--RCQ-HFNFRLLS  179 (563)
T ss_pred             CCEEEEEEChhhcCH--------------HHHHHHHHhhcc--CCCCEEEEEecCChHHhHHHHHH--hce-EEEecCCC
Confidence            356999999998731              345678888873  44567777788889999999998  876 68999999


Q ss_pred             HHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           93 RRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        93 ~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      .++....++....      +...+..++..+.| +.+++.+++..+...+    ...++.+++.+.+
T Consensus       180 ~~el~~~L~~i~~~egi~id~eAl~lLa~~s~G-dlR~alslLdklis~~----~~~It~e~V~~ll  241 (563)
T PRK06647        180 LEKIYNMLKKVCLEDQIKYEDEALKWIAYKSTG-SVRDAYTLFDQVVSFS----DSDITLEQIRSKM  241 (563)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHhhc----CCCCCHHHHHHHh
Confidence            9999888875442      12345567777766 7888888887664332    2346766666544

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=97.74  E-value=0.00017  Score=61.88  Aligned_cols=127  Identities=16%  Similarity=0.208  Sum_probs=84.8

Q ss_pred             HHHHHHHHHHc----CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcccc
Q 030960            2 VRDVFRLAKEN----APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~~----~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~   77 (168)
                      ++.+.+.+...    ..-|++|||+|.+-.              ...+.|+..|+.  ....+++|++|+.+..|.++++
T Consensus       104 IReIi~~~~~~P~~~~~KVIIIDEad~Lt~--------------~A~NaLLKtLEE--Pp~~tvfIL~Tt~~~KLl~TI~  167 (605)
T PRK05896        104 IRNIIDNINYLPTTFKYKVYIIDEAHMLST--------------SAWNALLKTLEE--PPKHVVFIFATTEFQKIPLTII  167 (605)
T ss_pred             HHHHHHHHHhchhhCCcEEEEEechHhCCH--------------HHHHHHHHHHHh--CCCcEEEEEECCChHhhhHHHH
Confidence            45555555433    235999999998731              234667777773  4446778888888999999999


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHH
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK  151 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~  151 (168)
                      +  |+. .+.|++|+..+....++..+..      ...+..++..+.| +++++.++++......   +. .|+.+++.+
T Consensus       168 S--Rcq-~ieF~~Ls~~eL~~~L~~il~kegi~Is~eal~~La~lS~G-dlR~AlnlLekL~~y~---~~-~It~e~V~e  239 (605)
T PRK05896        168 S--RCQ-RYNFKKLNNSELQELLKSIAKKEKIKIEDNAIDKIADLADG-SLRDGLSILDQLSTFK---NS-EIDIEDINK  239 (605)
T ss_pred             h--hhh-hcccCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-cHHHHHHHHHHHHhhc---CC-CCCHHHHHH
Confidence            8  875 7899999999988888764431      1234566667665 6777777777643322   21 266665555


Q ss_pred             H
Q 030960          152 G  152 (168)
Q Consensus       152 a  152 (168)
                      .
T Consensus       240 l  240 (605)
T PRK05896        240 T  240 (605)
T ss_pred             H
Confidence            3

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.74  E-value=0.00023  Score=53.86  Aligned_cols=124  Identities=13%  Similarity=0.125  Sum_probs=76.4

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC---CCCccccCCCCc--ceEEe
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD---TLDPALLRPGRL--DRKIE   87 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~---~ld~al~r~grf--~~~i~   87 (168)
                      .+.+|+|||+|.+-..           ....+..+++.+   ......+++.+++.+.   .+.+.+.+  ||  ...+.
T Consensus        90 ~~~~liiDdi~~l~~~-----------~~~~L~~~~~~~---~~~~~~~vl~~~~~~~~~~~l~~~L~s--r~~~~~~i~  153 (227)
T PRK08903         90 EAELYAVDDVERLDDA-----------QQIALFNLFNRV---RAHGQGALLVAGPAAPLALPLREDLRT--RLGWGLVYE  153 (227)
T ss_pred             cCCEEEEeChhhcCch-----------HHHHHHHHHHHH---HHcCCcEEEEeCCCCHHhCCCCHHHHH--HHhcCeEEE
Confidence            3678999999976211           112223333332   3333433444444322   34466666  77  57999


Q ss_pred             cCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960           88 FPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus        88 ~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      +++|+..++..+++....      ++.-++.++... +=+.+++.++++.-...+.. .+..||...+.+++.
T Consensus       154 l~pl~~~~~~~~l~~~~~~~~v~l~~~al~~L~~~~-~gn~~~l~~~l~~l~~~~~~-~~~~i~~~~~~~~l~  224 (227)
T PRK08903        154 LKPLSDADKIAALKAAAAERGLQLADEVPDYLLTHF-RRDMPSLMALLDALDRYSLE-QKRPVTLPLLREMLA  224 (227)
T ss_pred             ecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhc-cCCHHHHHHHHHHHHHHHHH-hCCCCCHHHHHHHHh
Confidence            999999999999886433      122345567643 34788888888875444434 346899998888875

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=97.74  E-value=3.4e-05  Score=58.45  Aligned_cols=107  Identities=20%  Similarity=0.327  Sum_probs=64.9

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCC---CccccCCCCcce--EEe
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTL---DPALLRPGRLDR--KIE   87 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~l---d~al~r~grf~~--~i~   87 (168)
                      ...+|+|||++.+.++.         ..+..+-.+++.+   ...++.+|+++...|..+   ++.+.+  ||..  .+.
T Consensus        97 ~~DlL~iDDi~~l~~~~---------~~q~~lf~l~n~~---~~~~k~li~ts~~~P~~l~~~~~~L~S--Rl~~Gl~~~  162 (219)
T PF00308_consen   97 SADLLIIDDIQFLAGKQ---------RTQEELFHLFNRL---IESGKQLILTSDRPPSELSGLLPDLRS--RLSWGLVVE  162 (219)
T ss_dssp             TSSEEEEETGGGGTTHH---------HHHHHHHHHHHHH---HHTTSEEEEEESS-TTTTTTS-HHHHH--HHHCSEEEE
T ss_pred             cCCEEEEecchhhcCch---------HHHHHHHHHHHHH---HhhCCeEEEEeCCCCccccccChhhhh--hHhhcchhh
Confidence            47899999999986332         1123333333333   344556677766666654   567777  8765  888


Q ss_pred             cCCCCHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHH
Q 030960           88 FPLPDRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGM  134 (168)
Q Consensus        88 ~~~P~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~  134 (168)
                      +.+|+.+.|.++++.....      +..+..++++.++ +.++|..+++.-..
T Consensus       163 l~~pd~~~r~~il~~~a~~~~~~l~~~v~~~l~~~~~~-~~r~L~~~l~~l~~  214 (219)
T PF00308_consen  163 LQPPDDEDRRRILQKKAKERGIELPEEVIEYLARRFRR-DVRELEGALNRLDA  214 (219)
T ss_dssp             E----HHHHHHHHHHHHHHTT--S-HHHHHHHHHHTTS-SHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHHHHhCCCCcHHHHHHHHHhhcC-CHHHHHHHHHHHHH
Confidence            9999999999999865541      2234456666543 77888887776543

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.

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

Probab=97.70  E-value=0.00021  Score=56.40  Aligned_cols=135  Identities=19%  Similarity=0.291  Sum_probs=82.1

Q ss_pred             HHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC--CCCccccCCCC
Q 030960            4 DVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD--TLDPALLRPGR   81 (168)
Q Consensus         4 ~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~--~ld~al~r~gr   81 (168)
                      .+....+..++-+|+|||++.++..+       ... ++.+..++..+.+ .-.-+++.+||-.-..  .-|+-+-+  |
T Consensus       136 ~~~~llr~~~vrmLIIDE~H~lLaGs-------~~~-qr~~Ln~LK~L~N-eL~ipiV~vGt~~A~~al~~D~QLa~--R  204 (302)
T PF05621_consen  136 QVLRLLRRLGVRMLIIDEFHNLLAGS-------YRK-QREFLNALKFLGN-ELQIPIVGVGTREAYRALRTDPQLAS--R  204 (302)
T ss_pred             HHHHHHHHcCCcEEEeechHHHhccc-------HHH-HHHHHHHHHHHhh-ccCCCeEEeccHHHHHHhccCHHHHh--c
Confidence            35566788899999999999987432       111 2333334444432 1122566666544333  33555656  8


Q ss_pred             cceEEecCCCC-HHHHHHHHH---hhc--CC--CCCH----HHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHH
Q 030960           82 LDRKIEFPLPD-RRQKRLVFQ---MNL--SD--EVDL----EDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDF  149 (168)
Q Consensus        82 f~~~i~~~~P~-~~~R~~il~---~~l--~~--~~~~----~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~  149 (168)
                      |+.. .+|... .++...++.   ..+  ..  ...-    ..+-..|+|.+| +|.++++.|+..|++.+...||.+.+
T Consensus       205 F~~~-~Lp~W~~d~ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~~s~G~iG-~l~~ll~~aA~~AI~sG~E~It~~~l  282 (302)
T PF05621_consen  205 FEPF-ELPRWELDEEFRRLLASFERALPLRKPSNLASPELARRIHERSEGLIG-ELSRLLNAAAIAAIRSGEERITREIL  282 (302)
T ss_pred             cCCc-cCCCCCCCcHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHcCCchH-HHHHHHHHHHHHHHhcCCceecHHHH
Confidence            8643 445443 233344443   222  22  2222    345566777665 89999999999999999999999988


Q ss_pred             HH
Q 030960          150 EK  151 (168)
Q Consensus       150 ~~  151 (168)
                      ..
T Consensus       283 ~~  284 (302)
T PF05621_consen  283 DK  284 (302)
T ss_pred             hh
Confidence            76

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

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=97.68  E-value=0.00074  Score=54.61  Aligned_cols=128  Identities=19%  Similarity=0.224  Sum_probs=83.5

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC---------C--CCCCCeEEEEecCCCC-CCCccccCCCC
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG---------F--DQTVNVKVIMATNRAD-TLDPALLRPGR   81 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~---------~--~~~~~v~vi~ttn~~~-~ld~al~r~gr   81 (168)
                      ..+||+||++.+-+              .+.+.++..|+.         .  ....++++|+|.|-.+ .+++++..  |
T Consensus       145 ~GiL~lDEInrL~~--------------~~Q~~LLeam~e~~~~ier~G~s~~~p~rfiviaT~np~eg~l~~~Lld--R  208 (350)
T CHL00081        145 RGILYVDEVNLLDD--------------HLVDILLDSAASGWNTVEREGISIRHPARFVLVGSGNPEEGELRPQLLD--R  208 (350)
T ss_pred             CCEEEecChHhCCH--------------HHHHHHHHHHHhCCeEEeeCCeeeecCCCEEEEeccCcccCCCCHHHHH--H
Confidence            47999999998742              223334444422         1  1233577777666444 59999999  9


Q ss_pred             cceEEecCCCC-HHHHHHHHHhhcCCC------------------------------CC--------HHHHHhCCCCCCH
Q 030960           82 LDRKIEFPLPD-RRQKRLVFQMNLSDE------------------------------VD--------LEDYVSRPDKISA  122 (168)
Q Consensus        82 f~~~i~~~~P~-~~~R~~il~~~l~~~------------------------------~~--------~~~la~~t~g~s~  122 (168)
                      |...+.++.|+ .+.|.+|++......                              +.        +.+++..+.--|+
T Consensus       209 f~l~i~l~~~~~~~~e~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~ar~~~~~V~v~~~~~~yi~~l~~~~~~~s~  288 (350)
T CHL00081        209 FGMHAEIRTVKDPELRVKIVEQRTSFDKNPQEFREKYEESQEELRSKIVAAQNLLPKVEIDYDLRVKISQICSELDVDGL  288 (350)
T ss_pred             hCceeecCCCCChHHHHHHHHhhhccccChhhhhhhhccccccCHHHHHHHHHhcCCCccCHHHHHHHHHHHHHHCCCCC
Confidence            99999999997 699999998533210                              00        1112223322355


Q ss_pred             HHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhc
Q 030960          123 AEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNV  157 (168)
Q Consensus       123 ~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~  157 (168)
                      +---.+++-|...|+-+++..++.+|+..+..-+.
T Consensus       289 Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~~vL  323 (350)
T CHL00081        289 RGDIVTNRAAKALAAFEGRTEVTPKDIFKVITLCL  323 (350)
T ss_pred             hHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence            55556667677777778889999999999886543

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.67  E-value=0.00015  Score=62.49  Aligned_cols=117  Identities=11%  Similarity=0.122  Sum_probs=78.5

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      ...||+|||+|.+-.              ...+.|+..++.  ...++++|++|+.++.+.+.+++  |+. .+.|++++
T Consensus       119 ~~kVIIIDEad~Lt~--------------~a~naLLk~LEE--P~~~~ifILaTt~~~kll~TI~S--Rcq-~i~F~pLs  179 (624)
T PRK14959        119 RYKVFIIDEAHMLTR--------------EAFNALLKTLEE--PPARVTFVLATTEPHKFPVTIVS--RCQ-HFTFTRLS  179 (624)
T ss_pred             CceEEEEEChHhCCH--------------HHHHHHHHHhhc--cCCCEEEEEecCChhhhhHHHHh--hhh-ccccCCCC
Confidence            357999999998831              345677877774  34578888889999999999988  874 67999999


Q ss_pred             HHHHHHHHHhhcCC-C--C---CHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           93 RRQKRLVFQMNLSD-E--V---DLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        93 ~~~R~~il~~~l~~-~--~---~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      .++-..+++..+.. .  +   .+..+++.+.| +.++..+++..++    ..+...|+.+++..++
T Consensus       180 ~~eL~~~L~~il~~egi~id~eal~lIA~~s~G-dlR~Al~lLeqll----~~g~~~It~d~V~~~l  241 (624)
T PRK14959        180 EAGLEAHLTKVLGREGVDYDPAAVRLIARRAAG-SVRDSMSLLGQVL----ALGESRLTIDGARGVL  241 (624)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHH----HhcCCCcCHHHHHHHh
Confidence            99999888764432 2  2   24456665543 4455555555432    2234467777655544

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

Probab=97.67  E-value=0.00036  Score=57.33  Aligned_cols=132  Identities=16%  Similarity=0.221  Sum_probs=86.9

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCC---ccccCCCCcce--EEe
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLD---PALLRPGRLDR--KIE   87 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld---~al~r~grf~~--~i~   87 (168)
                      +-.+++|||++.+.++.            +.-..|...+..+...++-+|+.+-..|..++   +.|++  ||.+  .+.
T Consensus       175 ~~dlllIDDiq~l~gk~------------~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~S--R~~~Gl~~~  240 (408)
T COG0593         175 SLDLLLIDDIQFLAGKE------------RTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLRS--RLEWGLVVE  240 (408)
T ss_pred             ccCeeeechHhHhcCCh------------hHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHHH--HHhceeEEe
Confidence            45799999999997654            11222333333334444556666666677665   78888  9874  567


Q ss_pred             cCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhcCCC
Q 030960           88 FPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKP  160 (168)
Q Consensus        88 ~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~p~~  160 (168)
                      +.+|+.+.|..|++....      ++-....+|.+.. =+.++|+.+++.....+...+. .||.....++++......
T Consensus       241 I~~Pd~e~r~aiL~kka~~~~~~i~~ev~~~la~~~~-~nvReLegaL~~l~~~a~~~~~-~iTi~~v~e~L~~~~~~~  317 (408)
T COG0593         241 IEPPDDETRLAILRKKAEDRGIEIPDEVLEFLAKRLD-RNVRELEGALNRLDAFALFTKR-AITIDLVKEILKDLLRAG  317 (408)
T ss_pred             eCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhh-ccHHHHHHHHHHHHHHHHhcCc-cCcHHHHHHHHHHhhccc
Confidence            799999999999986443      2223445665543 3678888888777666655543 678888888777665543

>smart00350 MCM minichromosome maintenance proteins

Probab=97.66  E-value=0.0014  Score=55.70  Aligned_cols=128  Identities=20%  Similarity=0.226  Sum_probs=87.5

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC---------C--CCCCCeEEEEecCCCC------------
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG---------F--DQTVNVKVIMATNRAD------------   70 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~---------~--~~~~~v~vi~ttn~~~------------   70 (168)
                      ..+++|||+|.+-.              .....++..|+.         .  .-..+..||||+|-..            
T Consensus       301 ~Gil~iDEi~~l~~--------------~~q~~L~e~me~~~i~i~k~G~~~~l~~~~~viAa~NP~~g~y~~~~~~~~n  366 (509)
T smart00350      301 NGVCCIDEFDKMDD--------------SDRTAIHEAMEQQTISIAKAGITTTLNARCSVLAAANPIGGRYDPKLTPEEN  366 (509)
T ss_pred             CCEEEEechhhCCH--------------HHHHHHHHHHhcCEEEEEeCCEEEEecCCcEEEEEeCCCCcccCCCcChhhc
Confidence            46899999998731              222334444432         1  1124678999999542            


Q ss_pred             -CCCccccCCCCcceEEec-CCCCHHHHHHHHHhhcC----------C----CCC------------------H-----H
Q 030960           71 -TLDPALLRPGRLDRKIEF-PLPDRRQKRLVFQMNLS----------D----EVD------------------L-----E  111 (168)
Q Consensus        71 -~ld~al~r~grf~~~i~~-~~P~~~~R~~il~~~l~----------~----~~~------------------~-----~  111 (168)
                       .+++++++  |||..+.+ +.|+.+.+.+|.++.+.          .    ..+                  +     +
T Consensus       367 ~~l~~~lLs--RFdLi~~~~d~~~~~~d~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~l~~yi~~ar~~~~P~ls~~~~~  444 (509)
T smart00350      367 IDLPAPILS--RFDLLFVVLDEVDEERDRELAKHVVDLHRYSHPEPDEADEVPISQEFLRKYIAYAREKIKPKLSEEAAE  444 (509)
T ss_pred             cCCChHHhC--ceeeEEEecCCCChHHHHHHHHHHHHhhcccCccccccccccCCHHHHHHHHHHHHhcCCCCCCHHHHH
Confidence             69999999  99987655 89999999888875211          0    000                  0     0


Q ss_pred             HH-----HhC----------CCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhc
Q 030960          112 DY-----VSR----------PDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNV  157 (168)
Q Consensus       112 ~l-----a~~----------t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~  157 (168)
                      .+     .-+          .-|.|++.+..+++-|...|.-+.+..++.+|+..|++-+.
T Consensus       445 ~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V~~~Dv~~ai~l~~  505 (509)
T smart00350      445 KLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVVEEADVEEAIRLLR  505 (509)
T ss_pred             HHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHHH
Confidence            01     001          12579999999999999999999999999999999987553

>CHL00195 ycf46 Ycf46; Provisional

Probab=97.66  E-value=0.00063  Score=57.42  Aligned_cols=119  Identities=17%  Similarity=0.208  Sum_probs=80.7

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      |+|+++.|++.++..         ....+.+..+...+.   ..++.+|+.+.  ...+|+.|.   ++-..+.+++|+.
T Consensus        82 ~~~~vl~d~h~~~~~---------~~~~r~l~~l~~~~~---~~~~~~i~~~~--~~~~p~el~---~~~~~~~~~lP~~  144 (489)
T CHL00195         82 PALFLLKDFNRFLND---------ISISRKLRNLSRILK---TQPKTIIIIAS--ELNIPKELK---DLITVLEFPLPTE  144 (489)
T ss_pred             CcEEEEecchhhhcc---------hHHHHHHHHHHHHHH---hCCCEEEEEcC--CCCCCHHHH---hceeEEeecCcCH
Confidence            799999999999822         123344555544443   34445555544  356777776   4557889999999


Q ss_pred             HHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960           94 RQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus        94 ~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      +++.++++....      ++.+++.++..+.|+|..++.+++..+..    . ...++.+++...++
T Consensus       145 ~ei~~~l~~~~~~~~~~~~~~~~~~l~~~~~gls~~~~~~~~~~~~~----~-~~~~~~~~~~~i~~  206 (489)
T CHL00195        145 SEIKKELTRLIKSLNIKIDSELLENLTRACQGLSLERIRRVLSKIIA----T-YKTIDENSIPLILE  206 (489)
T ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCHHHHHHHHHHHHH----H-cCCCChhhHHHHHH
Confidence            999999976543      24467889999999999999999887532    1 22355555444443

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.64  E-value=0.00058  Score=58.31  Aligned_cols=117  Identities=17%  Similarity=0.183  Sum_probs=81.0

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      .-|++|||+|.+-.              ...+.|+..|+.  ....+.+|++|+.+..+.+.+++  |+ ..++|.+++.
T Consensus       120 ~kViIIDEa~~ls~--------------~a~naLLK~LEe--pp~~v~fIL~Ttd~~kil~tI~S--Rc-~~~~f~~Ls~  180 (546)
T PRK14957        120 YKVYLIDEVHMLSK--------------QSFNALLKTLEE--PPEYVKFILATTDYHKIPVTILS--RC-IQLHLKHISQ  180 (546)
T ss_pred             cEEEEEechhhccH--------------HHHHHHHHHHhc--CCCCceEEEEECChhhhhhhHHH--he-eeEEeCCCCH
Confidence            56999999998731              355678888874  34466677777779999989888  77 7899999999


Q ss_pred             HHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960           94 RQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus        94 ~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      ++-...++..+..      +..+..++..+ |-+.+++.+++..+...+    ...|+.+++.+++.
T Consensus       181 ~eI~~~L~~il~~egi~~e~~Al~~Ia~~s-~GdlR~alnlLek~i~~~----~~~It~~~V~~~l~  242 (546)
T PRK14957        181 ADIKDQLKIILAKENINSDEQSLEYIAYHA-KGSLRDALSLLDQAISFC----GGELKQAQIKQMLG  242 (546)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-CCCHHHHHHHHHHHHHhc----cCCCCHHHHHHHHc
Confidence            9888777754331      22344566666 457777777777665432    13477777776543

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=97.63  E-value=0.00035  Score=56.37  Aligned_cols=71  Identities=15%  Similarity=0.320  Sum_probs=58.9

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      .-|++||++|.+-              ....|.||..++  +..+++++|.+|++++.|.|.+++  |+ ..+.|++|+.
T Consensus       133 ~kV~iI~~ae~m~--------------~~AaNaLLKtLE--EPp~~t~fiL~t~~~~~LLpTI~S--Rc-q~i~~~~~~~  193 (342)
T PRK06964        133 ARVVVLYPAEALN--------------VAAANALLKTLE--EPPPGTVFLLVSARIDRLLPTILS--RC-RQFPMTVPAP  193 (342)
T ss_pred             ceEEEEechhhcC--------------HHHHHHHHHHhc--CCCcCcEEEEEECChhhCcHHHHh--cC-EEEEecCCCH
Confidence            4578888888763              155678899998  566789999999999999999999  88 6899999999


Q ss_pred             HHHHHHHHhh
Q 030960           94 RQKRLVFQMN  103 (168)
Q Consensus        94 ~~R~~il~~~  103 (168)
                      ++..+.+...
T Consensus       194 ~~~~~~L~~~  203 (342)
T PRK06964        194 EAAAAWLAAQ  203 (342)
T ss_pred             HHHHHHHHHc
Confidence            9999888753

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

Probab=97.62  E-value=0.00063  Score=60.17  Aligned_cols=118  Identities=19%  Similarity=0.269  Sum_probs=80.7

Q ss_pred             HHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC---------CCCCeEEEEecCCCC-----
Q 030960            5 VFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD---------QTVNVKVIMATNRAD-----   70 (168)
Q Consensus         5 iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~---------~~~~v~vi~ttn~~~-----   70 (168)
                      +.+..+....+||+|||+|.+-+              .+.+.|+..++.-.         ...++++|+|||...     
T Consensus       545 l~~~~~~~p~~VvllDEieka~~--------------~~~~~Ll~~ld~g~~~d~~g~~vd~~~~iii~Tsn~g~~~~~~  610 (731)
T TIGR02639       545 LTEAVRKHPHCVLLLDEIEKAHP--------------DIYNILLQVMDYATLTDNNGRKADFRNVILIMTSNAGASEMSK  610 (731)
T ss_pred             HHHHHHhCCCeEEEEechhhcCH--------------HHHHHHHHhhccCeeecCCCcccCCCCCEEEECCCcchhhhhh
Confidence            44555667789999999997631              45566666666421         124578999998742     


Q ss_pred             --------------------CCCccccCCCCcceEEecCCCCHHHHHHHHHhhcCC---------------CCCHHHHHh
Q 030960           71 --------------------TLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD---------------EVDLEDYVS  115 (168)
Q Consensus        71 --------------------~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~~---------------~~~~~~la~  115 (168)
                                          .+.|.++.  |||.++.|.+.+.++..+|++..+..               +-.++.+++
T Consensus       611 ~~~~f~~~~~~~~~~~~~~~~f~pef~~--Rid~Vi~F~pLs~e~l~~Iv~~~L~~l~~~l~~~~~~l~i~~~a~~~La~  688 (731)
T TIGR02639       611 PPIGFGSENVESKSDKAIKKLFSPEFRN--RLDAIIHFNPLSEEVLEKIVQKFVDELSKQLNEKNIKLELTDDAKKYLAE  688 (731)
T ss_pred             ccCCcchhhhHHHHHHHHHhhcChHHHh--cCCeEEEcCCCCHHHHHHHHHHHHHHHHHHHHhCCCeEEeCHHHHHHHHH
Confidence                                24566665  99999999999999999999866541               112344555


Q ss_pred             C--CCCCCHHHHHHHHHHHHHHHHH
Q 030960          116 R--PDKISAAEIAAICQEAGMHAVR  138 (168)
Q Consensus       116 ~--t~g~s~~di~~l~~~a~~~a~~  138 (168)
                      .  ...|..+.|.++++.....++.
T Consensus       689 ~~~~~~~GaR~l~r~i~~~~~~~l~  713 (731)
T TIGR02639       689 KGYDEEFGARPLARVIQEEIKKPLS  713 (731)
T ss_pred             hCCCcccCchHHHHHHHHHhHHHHH
Confidence            3  4567778888888776655543

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=97.62  E-value=0.00023  Score=57.11  Aligned_cols=74  Identities=16%  Similarity=0.342  Sum_probs=60.6

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCC
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLP   91 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P   91 (168)
                      ...-|++||++|.+-.              ...+.||..++.  ...++++|.+|++++.|.|.+++  |+.. +.|++|
T Consensus       105 ~~~kv~iI~~a~~m~~--------------~aaNaLLK~LEE--Pp~~~~fiL~t~~~~~ll~TI~S--Rc~~-~~~~~~  165 (328)
T PRK05707        105 GGRKVVLIEPAEAMNR--------------NAANALLKSLEE--PSGDTVLLLISHQPSRLLPTIKS--RCQQ-QACPLP  165 (328)
T ss_pred             CCCeEEEECChhhCCH--------------HHHHHHHHHHhC--CCCCeEEEEEECChhhCcHHHHh--hcee-eeCCCc
Confidence            3467889999998741              556788888884  44678899999999999999999  8866 899999


Q ss_pred             CHHHHHHHHHhhc
Q 030960           92 DRRQKRLVFQMNL  104 (168)
Q Consensus        92 ~~~~R~~il~~~l  104 (168)
                      +.++-.+.+....
T Consensus       166 ~~~~~~~~L~~~~  178 (328)
T PRK05707        166 SNEESLQWLQQAL  178 (328)
T ss_pred             CHHHHHHHHHHhc
Confidence            9999988887654

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=97.61  E-value=0.00086  Score=56.12  Aligned_cols=118  Identities=16%  Similarity=0.161  Sum_probs=79.1

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCC
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLP   91 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P   91 (168)
                      ....||+|||+|.+..              ...+.|+..++.  ....+++|++|+.++.|.+++++  |+. .++|.++
T Consensus       120 ~~~kvvIIdead~lt~--------------~~~n~LLk~lEe--p~~~~~~Il~t~~~~kl~~tI~s--Rc~-~v~f~~l  180 (451)
T PRK06305        120 SRYKIYIIDEVHMLTK--------------EAFNSLLKTLEE--PPQHVKFFLATTEIHKIPGTILS--RCQ-KMHLKRI  180 (451)
T ss_pred             CCCEEEEEecHHhhCH--------------HHHHHHHHHhhc--CCCCceEEEEeCChHhcchHHHH--hce-EEeCCCC
Confidence            3478999999998731              235677888875  34467777788889999999998  774 6899999


Q ss_pred             CHHHHHHHHHhhcCC---CC---CHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           92 DRRQKRLVFQMNLSD---EV---DLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        92 ~~~~R~~il~~~l~~---~~---~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      +.++-...++..+..   .+   .+..++..+.| +.+++.+.++.....   .+ ..|+.+++.+.+
T Consensus       181 ~~~el~~~L~~~~~~eg~~i~~~al~~L~~~s~g-dlr~a~~~Lekl~~~---~~-~~It~~~V~~l~  243 (451)
T PRK06305        181 PEETIIDKLALIAKQEGIETSREALLPIARAAQG-SLRDAESLYDYVVGL---FP-KSLDPDSVAKAL  243 (451)
T ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHHh---cc-CCcCHHHHHHHH
Confidence            999988877754431   12   34567776654 666666666654322   11 236666554443

>PLN03025 replication factor C subunit; Provisional

Probab=97.59  E-value=0.00041  Score=55.35  Aligned_cols=114  Identities=13%  Similarity=0.132  Sum_probs=70.9

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      .+.||+|||+|.+...              ..+.++..++...  ....+|.+||.++.+.+++++  |+ ..+.|++|+
T Consensus        99 ~~kviiiDE~d~lt~~--------------aq~aL~~~lE~~~--~~t~~il~~n~~~~i~~~L~S--Rc-~~i~f~~l~  159 (319)
T PLN03025         99 RHKIVILDEADSMTSG--------------AQQALRRTMEIYS--NTTRFALACNTSSKIIEPIQS--RC-AIVRFSRLS  159 (319)
T ss_pred             CeEEEEEechhhcCHH--------------HHHHHHHHHhccc--CCceEEEEeCCccccchhHHH--hh-hcccCCCCC
Confidence            3679999999988421              1233444454322  234466788888999999998  76 579999999


Q ss_pred             HHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHH
Q 030960           93 RRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK  151 (168)
Q Consensus        93 ~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~  151 (168)
                      .++....++.....      +..+..++..+.| ..+.+.+.++.+.     .+...++.+++.+
T Consensus       160 ~~~l~~~L~~i~~~egi~i~~~~l~~i~~~~~g-DlR~aln~Lq~~~-----~~~~~i~~~~v~~  218 (319)
T PLN03025        160 DQEILGRLMKVVEAEKVPYVPEGLEAIIFTADG-DMRQALNNLQATH-----SGFGFVNQENVFK  218 (319)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHH-----hcCCCCCHHHHHH
Confidence            99998888754431      2235566666543 4445544444221     1223466666544

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

Probab=97.58  E-value=0.00063  Score=56.24  Aligned_cols=138  Identities=20%  Similarity=0.212  Sum_probs=85.3

Q ss_pred             HcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC-----------CCCCeEEEEecCCCC---------
Q 030960           11 ENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD-----------QTVNVKVIMATNRAD---------   70 (168)
Q Consensus        11 ~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-----------~~~~v~vi~ttn~~~---------   70 (168)
                      ...++||||||+|.+...+.+.+...+-....+.+.||..|++-.           .....++|.|+|-..         
T Consensus       171 ~a~~gIi~iDEIdkl~~~~~~~~~~~d~s~~~vQ~~LL~~Leg~~~~v~~~gg~~~~~~~~~~i~t~nilfi~~Gaf~g~  250 (412)
T PRK05342        171 KAQRGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRKHPQQEFIQVDTTNILFICGGAFDGL  250 (412)
T ss_pred             HcCCcEEEEechhhhccccCCCCcCCCcccHHHHHHHHHHHhcCeEEeCCCCCcCcCCCCeEEeccCCceeeecccccCc
Confidence            346899999999999876433222221112246667777776420           112355666666511         


Q ss_pred             -------------------------------------------CCCccccCCCCcceEEecCCCCHHHHHHHHHh----h
Q 030960           71 -------------------------------------------TLDPALLRPGRLDRKIEFPLPDRRQKRLVFQM----N  103 (168)
Q Consensus        71 -------------------------------------------~ld~al~r~grf~~~i~~~~P~~~~R~~il~~----~  103 (168)
                                                                 -+.|+++  ||+|..+.|.+.+.++..+|+..    .
T Consensus       251 ~~~~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~dL~~~gf~PEfl--gRld~iv~f~~L~~~~L~~Il~~~~~~l  328 (412)
T PRK05342        251 EKIIKQRLGKKGIGFGAEVKSKKEKRTEGELLKQVEPEDLIKFGLIPEFI--GRLPVVATLEELDEEALVRILTEPKNAL  328 (412)
T ss_pred             HHHHHHHHhhcccCCccccccccccchhHHHHHhcCHHHHHHHhhhHHHh--CCCCeeeecCCCCHHHHHHHHHHHHHHH
Confidence                                                       0234454  49999999999999999999962    1


Q ss_pred             cC---------------CCCCHHHHHhC--CCCCCHHHHHHHHHHHHHHHHHhCC-------CccCHHHHH
Q 030960          104 LS---------------DEVDLEDYVSR--PDKISAAEIAAICQEAGMHAVRKNR-------YVILPKDFE  150 (168)
Q Consensus       104 l~---------------~~~~~~~la~~--t~g~s~~di~~l~~~a~~~a~~~~~-------~~i~~~d~~  150 (168)
                      +.               ++--+..|++.  ..++-.+-|..++++...-.+.+-.       ..|+.+.+.
T Consensus       329 ~~q~~~~l~~~~i~L~~t~~al~~Ia~~~~~~~~GAR~Lrriie~~l~~~~~~~p~~~~~~~v~I~~~~v~  399 (412)
T PRK05342        329 VKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLRSILEEILLDVMFELPSREDVEKVVITKEVVE  399 (412)
T ss_pred             HHHHHHHHHhCCcEEEECHHHHHHHHHhCCCCCCCCchHHHHHHHHhHHHHHhccccCCCceEEECHHHhc
Confidence            11               12235567764  5677888888888887666655421       236666654

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

Probab=97.57  E-value=0.00044  Score=57.09  Aligned_cols=127  Identities=18%  Similarity=0.210  Sum_probs=81.8

Q ss_pred             HcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC-----------CCCCeEEEEecCCC----------
Q 030960           11 ENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD-----------QTVNVKVIMATNRA----------   69 (168)
Q Consensus        11 ~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-----------~~~~v~vi~ttn~~----------   69 (168)
                      ..+|+||||||+|.+...+.+.+...+-....+.+.||..|++..           ...+.++|.|+|-.          
T Consensus       179 ~a~~gIV~lDEIdkl~~~~~~~s~~~dvsg~~vq~~LL~iLeG~~~~v~~~~gr~~~~~~~i~i~TsNilfi~~Gaf~g~  258 (413)
T TIGR00382       179 KAQKGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKIIEGTVANVPPQGGRKHPYQEFIQIDTSNILFICGGAFVGL  258 (413)
T ss_pred             hcccceEEecccchhchhhccccccccccchhHHHHHHHHhhccceecccCCCccccCCCeEEEEcCCceeeecccccCh
Confidence            346889999999999876533222211111245566666665431           12346778887761          


Q ss_pred             -----------------C-----------------------CCCccccCCCCcceEEecCCCCHHHHHHHHHhhcC----
Q 030960           70 -----------------D-----------------------TLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLS----  105 (168)
Q Consensus        70 -----------------~-----------------------~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~----  105 (168)
                                       +                       .+.|+++-  |+|..+.|.+.+.++..+|+...+.    
T Consensus       259 ~~i~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~dl~~~g~~PEflg--Rld~Iv~f~pL~~~~L~~Il~~~~n~l~k  336 (413)
T TIGR00382       259 EKIIKKRTGKSSIGFGAEVKKKSKEKADLLRQVEPEDLVKFGLIPEFIG--RLPVIATLEKLDEEALIAILTKPKNALVK  336 (413)
T ss_pred             HHHHHHHhhhccccccccccccchhhHHHHHHHHHHHHHHHhhHHHHhC--CCCeEeecCCCCHHHHHHHHHHHHHHHHH
Confidence                             0                       03355554  9999999999999999999874211    


Q ss_pred             ---------------CCCCHHHHHhC--CCCCCHHHHHHHHHHHHHHHHHh
Q 030960          106 ---------------DEVDLEDYVSR--PDKISAAEIAAICQEAGMHAVRK  139 (168)
Q Consensus       106 ---------------~~~~~~~la~~--t~g~s~~di~~l~~~a~~~a~~~  139 (168)
                                     ++--++.|++.  ..++-.+-|..+++........+
T Consensus       337 q~~~~l~~~gi~L~~t~~a~~~Ia~~~~~~~~GAR~Lr~iie~~l~~~m~e  387 (413)
T TIGR00382       337 QYQALFKMDNVELDFEEEALKAIAKKALERKTGARGLRSIVEGLLLDVMFD  387 (413)
T ss_pred             HHHHHhccCCeEEEECHHHHHHHHHhCCCCCCCchHHHHHHHHhhHHHHhh
Confidence                           12235567765  46788888988888877666654

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.

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

Probab=97.56  E-value=0.0011  Score=58.46  Aligned_cols=122  Identities=18%  Similarity=0.154  Sum_probs=77.9

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecC-CC-CCCCccccCCCCcceEEecCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATN-RA-DTLDPALLRPGRLDRKIEFPL   90 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn-~~-~~ld~al~r~grf~~~i~~~~   90 (168)
                      ...+|+|||+|.+..              .....++..++    ...+++|++|+ ++ ..+++++++  |. ..+.+++
T Consensus       109 ~~~IL~IDEIh~Ln~--------------~qQdaLL~~lE----~g~IiLI~aTTenp~~~l~~aL~S--R~-~v~~l~p  167 (725)
T PRK13341        109 KRTILFIDEVHRFNK--------------AQQDALLPWVE----NGTITLIGATTENPYFEVNKALVS--RS-RLFRLKS  167 (725)
T ss_pred             CceEEEEeChhhCCH--------------HHHHHHHHHhc----CceEEEEEecCCChHhhhhhHhhc--cc-cceecCC
Confidence            467999999998731              11233444443    24566666553 33 468999998  64 4689999


Q ss_pred             CCHHHHHHHHHhhcC--------CCC-----CHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCC--CccCHHHHHHHHHh
Q 030960           91 PDRRQKRLVFQMNLS--------DEV-----DLEDYVSRPDKISAAEIAAICQEAGMHAVRKNR--YVILPKDFEKGYRT  155 (168)
Q Consensus        91 P~~~~R~~il~~~l~--------~~~-----~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~--~~i~~~d~~~al~~  155 (168)
                      ++.+++..+++..+.        ..+     .++.|+..+.| ..+.+.++++.++..+.....  ..|+.+++.+++.+
T Consensus       168 Ls~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La~~s~G-D~R~lln~Le~a~~~~~~~~~~~i~It~~~~~e~l~~  246 (725)
T PRK13341        168 LSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVANG-DARSLLNALELAVESTPPDEDGLIDITLAIAEESIQQ  246 (725)
T ss_pred             CCHHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcccCCCCceeccHHHHHHHHHH
Confidence            999999999986654        112     24567776643 567777777766543322211  23777888887765


Q ss_pred             h
Q 030960          156 N  156 (168)
Q Consensus       156 ~  156 (168)
                      .
T Consensus       247 ~  247 (725)
T PRK13341        247 R  247 (725)
T ss_pred             h
Confidence            3

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

Probab=97.56  E-value=0.00053  Score=60.69  Aligned_cols=116  Identities=19%  Similarity=0.243  Sum_probs=77.3

Q ss_pred             HHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC--C-------CCCCeEEEEecCCC--------
Q 030960            7 RLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF--D-------QTVNVKVIMATNRA--------   69 (168)
Q Consensus         7 ~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~--~-------~~~~v~vi~ttn~~--------   69 (168)
                      +..+....+||||||+|.+-+              .+.+.|+..|+.-  .       ...++++|+|||.-        
T Consensus       551 ~~v~~~p~sVlllDEieka~~--------------~v~~~LLq~ld~G~ltd~~g~~vd~rn~iiI~TsN~g~~~~~~~~  616 (758)
T PRK11034        551 DAVIKHPHAVLLLDEIEKAHP--------------DVFNLLLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKS  616 (758)
T ss_pred             HHHHhCCCcEEEeccHhhhhH--------------HHHHHHHHHHhcCeeecCCCceecCCCcEEEEeCCcCHHHHhhcc
Confidence            344556679999999998731              4556666666521  1       12468899999932        


Q ss_pred             -----------------CCCCccccCCCCcceEEecCCCCHHHHHHHHHhhcCC---------------CCCHHHHHhC-
Q 030960           70 -----------------DTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD---------------EVDLEDYVSR-  116 (168)
Q Consensus        70 -----------------~~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~~---------------~~~~~~la~~-  116 (168)
                                       ..+.|.++.  |+|..+.|++.+.++..+|+...+..               +--++.|++. 
T Consensus       617 ~g~~~~~~~~~~~~~~~~~f~pefl~--Rid~ii~f~~L~~~~l~~I~~~~l~~~~~~l~~~~i~l~~~~~~~~~l~~~~  694 (758)
T PRK11034        617 IGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTDVIHQVVDKFIVELQAQLDQKGVSLEVSQEARDWLAEKG  694 (758)
T ss_pred             cCcccchhhHHHHHHHHHhcCHHHHc--cCCEEEEcCCCCHHHHHHHHHHHHHHHHHHHHHCCCCceECHHHHHHHHHhC
Confidence                             125566766  99999999999999999999865541               1123445543 


Q ss_pred             -CCCCCHHHHHHHHHHHHHHHHH
Q 030960          117 -PDKISAAEIAAICQEAGMHAVR  138 (168)
Q Consensus       117 -t~g~s~~di~~l~~~a~~~a~~  138 (168)
                       ..+|-.+.|.+++++-....+.
T Consensus       695 ~~~~~GAR~l~r~i~~~l~~~la  717 (758)
T PRK11034        695 YDRAMGARPMARVIQDNLKKPLA  717 (758)
T ss_pred             CCCCCCCchHHHHHHHHHHHHHH
Confidence             2456667787777776554443

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.50  E-value=0.0017  Score=56.15  Aligned_cols=116  Identities=16%  Similarity=0.162  Sum_probs=80.1

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      .-||+|||+|.+..              ...+.|+..++.  ....+++|.+|+.++.+.+.+++  |+. .+.|..++.
T Consensus       121 ~kVvIIDEa~~L~~--------------~a~naLLk~LEe--pp~~tv~Il~t~~~~kll~tI~S--R~~-~i~f~~l~~  181 (585)
T PRK14950        121 YKVYIIDEVHMLST--------------AAFNALLKTLEE--PPPHAIFILATTEVHKVPATILS--RCQ-RFDFHRHSV  181 (585)
T ss_pred             eEEEEEeChHhCCH--------------HHHHHHHHHHhc--CCCCeEEEEEeCChhhhhHHHHh--ccc-eeeCCCCCH
Confidence            56999999997731              345667777774  23456677777888889888887  764 688999999


Q ss_pred             HHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           94 RQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        94 ~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      .+...+++.....      ...+..++..+.| +.+++.+.++.....    ....|+.+++...+
T Consensus       182 ~el~~~L~~~a~~egl~i~~eal~~La~~s~G-dlr~al~~LekL~~y----~~~~It~e~V~~ll  242 (585)
T PRK14950        182 ADMAAHLRKIAAAEGINLEPGALEAIARAATG-SMRDAENLLQQLATT----YGGEISLSQVQSLL  242 (585)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHHh----cCCCCCHHHHHHHh
Confidence            9888888755432      1235567777766 888888887764332    23457777766544

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=97.44  E-value=0.00033  Score=55.53  Aligned_cols=72  Identities=25%  Similarity=0.400  Sum_probs=52.0

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      .+.+|+|||+|.+...          .....+.   ..++.  ...++.+|++||.++.+++++++  ||. .+.++.|+
T Consensus       100 ~~~vliiDe~d~l~~~----------~~~~~L~---~~le~--~~~~~~~Ilt~n~~~~l~~~l~s--R~~-~i~~~~p~  161 (316)
T PHA02544        100 GGKVIIIDEFDRLGLA----------DAQRHLR---SFMEA--YSKNCSFIITANNKNGIIEPLRS--RCR-VIDFGVPT  161 (316)
T ss_pred             CCeEEEEECcccccCH----------HHHHHHH---HHHHh--cCCCceEEEEcCChhhchHHHHh--hce-EEEeCCCC
Confidence            5789999999977211          1112233   33443  23456788899999999999999  885 78999999


Q ss_pred             HHHHHHHHHh
Q 030960           93 RRQKRLVFQM  102 (168)
Q Consensus        93 ~~~R~~il~~  102 (168)
                      .+++..+++.
T Consensus       162 ~~~~~~il~~  171 (316)
T PHA02544        162 KEEQIEMMKQ  171 (316)
T ss_pred             HHHHHHHHHH
Confidence            9999877663

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=97.40  E-value=0.0012  Score=57.11  Aligned_cols=127  Identities=16%  Similarity=0.239  Sum_probs=83.0

Q ss_pred             eEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC---------CC--CCCCeEEEEecCCCC---CCCccccCCC
Q 030960           15 AIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG---------FD--QTVNVKVIMATNRAD---TLDPALLRPG   80 (168)
Q Consensus        15 ~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~---------~~--~~~~v~vi~ttn~~~---~ld~al~r~g   80 (168)
                      .+||+||++.+-+              .+.+.|+..|+.         ..  ...++.||+|+|..+   .+++++..  
T Consensus        86 GvL~lDEi~rl~~--------------~~q~~Ll~al~~g~v~i~r~G~~~~~p~~f~lIAt~np~e~~g~L~~~Lld--  149 (589)
T TIGR02031        86 GVLYVDMANLLDD--------------GLSNRLLQALDEGVVIVEREGISVVHPAKFALIATYDPAEGGGGLPDHLLD--  149 (589)
T ss_pred             CcEeccchhhCCH--------------HHHHHHHHHHHcCCeEEEECCCceeecCceEEEEecCCccccCCCCHHHHH--
Confidence            5899999998732              344455555532         11  123578888888765   79999999  


Q ss_pred             CcceEEecC-CCCHHHHHHHHHhhcC------------------------CCC-----CHHHHHhCC--CCCC-HHHHHH
Q 030960           81 RLDRKIEFP-LPDRRQKRLVFQMNLS------------------------DEV-----DLEDYVSRP--DKIS-AAEIAA  127 (168)
Q Consensus        81 rf~~~i~~~-~P~~~~R~~il~~~l~------------------------~~~-----~~~~la~~t--~g~s-~~di~~  127 (168)
                      ||+..+.+. +|...+|.+|++..+.                        ..+     .+..+++.+  -|.+ .+--..
T Consensus       150 Rf~l~v~~~~~~~~~er~eil~~~~~~~~~~~~~~~~~~~~~i~~ar~~~~~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~  229 (589)
T TIGR02031       150 RLALHVSLEDVASQDLRVEIVRRERCNEVFRMNDELELLRGQIEAARELLPQVTISAEQVKELVLTAASLGISGHRADLF  229 (589)
T ss_pred             hccCeeecCCCCCHHHHHHHHHHHHHhhhhhcchhhHHHHHHHHHHHHhcCCccCCHHHHHHHHHHHHHcCCCCccHHHH
Confidence            999988885 5677889998876441                        011     111222211  2333 444445


Q ss_pred             HHHHHHHHHHHhCCCccCHHHHHHHHHhhc
Q 030960          128 ICQEAGMHAVRKNRYVILPKDFEKGYRTNV  157 (168)
Q Consensus       128 l~~~a~~~a~~~~~~~i~~~d~~~al~~~~  157 (168)
                      +++-|...|.-+++..|+.+|+..+..-+.
T Consensus       230 ~~r~ArA~Aal~gr~~V~~~Dv~~a~~lvl  259 (589)
T TIGR02031       230 AVRAAKAHAALHGRTEVTEEDLKLAVELVL  259 (589)
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHHh
Confidence            566677777778889999999999997654

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.

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.40  E-value=0.0016  Score=56.11  Aligned_cols=117  Identities=16%  Similarity=0.130  Sum_probs=79.1

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      .-|++|||+|.+-.              ...+.|+..|+.  ...++++|.+|+.++.|.+.+++  |. ..+.|.+++.
T Consensus       119 ~KVvIIDEah~Lt~--------------~A~NALLK~LEE--pp~~~~fIL~tte~~kll~TI~S--Rc-~~~~F~~l~~  179 (584)
T PRK14952        119 YRIFIVDEAHMVTT--------------AGFNALLKIVEE--PPEHLIFIFATTEPEKVLPTIRS--RT-HHYPFRLLPP  179 (584)
T ss_pred             ceEEEEECCCcCCH--------------HHHHHHHHHHhc--CCCCeEEEEEeCChHhhHHHHHH--hc-eEEEeeCCCH
Confidence            46999999998831              356678888873  44577788888889999999998  74 6899999999


Q ss_pred             HHHHHHHHhhcCC-C--CC---HHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           94 RQKRLVFQMNLSD-E--VD---LEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        94 ~~R~~il~~~l~~-~--~~---~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      ++-.+.++..+.. .  ++   +..++.. .|-+.++..+++...+...   +...|+.+++...+
T Consensus       180 ~~i~~~L~~i~~~egi~i~~~al~~Ia~~-s~GdlR~aln~Ldql~~~~---~~~~It~~~v~~ll  241 (584)
T PRK14952        180 RTMRALIARICEQEGVVVDDAVYPLVIRA-GGGSPRDTLSVLDQLLAGA---ADTHVTYQRALGLL  241 (584)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHH-cCCCHHHHHHHHHHHHhcc---CCCCcCHHHHHHHH
Confidence            8888887754442 2  22   2334443 4557778888777654322   12345555555443

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=97.39  E-value=0.0023  Score=49.71  Aligned_cols=123  Identities=16%  Similarity=0.092  Sum_probs=74.8

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC-------C-------CCCCeEEEEecCCC-----CCCCc
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF-------D-------QTVNVKVIMATNRA-----DTLDP   74 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~-------~-------~~~~v~vi~ttn~~-----~~ld~   74 (168)
                      +.+|+|||+|.+-+              .+.+.|+..++.-       .       ..+++.||+|+|..     ..+++
T Consensus       106 g~~lllDEi~r~~~--------------~~q~~Ll~~Le~~~~~i~~~~~~~~~i~~~~~frvIaTsN~~~~~g~~~l~~  171 (262)
T TIGR02640       106 GFTLVYDEFTRSKP--------------ETNNVLLSVFEEGVLELPGKRGTSRYVDVHPEFRVIFTSNPVEYAGVHETQD  171 (262)
T ss_pred             CCEEEEcchhhCCH--------------HHHHHHHHHhcCCeEEccCCCCCCceEecCCCCEEEEeeCCccccceecccH
Confidence            57999999997521              2333344444321       0       12356799999975     36789


Q ss_pred             cccCCCCcceEEecCCCCHHHHHHHHHhhcCCCC-CHHH---HHhC------CCCCCHHHHHHHHHHHHHHHHHhCCCcc
Q 030960           75 ALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSDEV-DLED---YVSR------PDKISAAEIAAICQEAGMHAVRKNRYVI  144 (168)
Q Consensus        75 al~r~grf~~~i~~~~P~~~~R~~il~~~l~~~~-~~~~---la~~------t~g~s~~di~~l~~~a~~~a~~~~~~~i  144 (168)
                      ++++  || ..++++.|+.++-.+|++....-+. ..+.   ++..      ...++.+..-.+++.+...   .....+
T Consensus       172 aL~~--R~-~~i~i~~P~~~~e~~Il~~~~~~~~~~~~~iv~~~~~~R~~~~~~~~~~r~~i~~~~~~~~~---~~~~~~  245 (262)
T TIGR02640       172 ALLD--RL-ITIFMDYPDIDTETAILRAKTDVAEDSAATIVRLVREFRASGDEITSGLRASLMIAEVATQQ---DIPVDV  245 (262)
T ss_pred             HHHh--hc-EEEECCCCCHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHhhCCccCCcHHHHHHHHHHHHHc---CCCCCC
Confidence            9999  98 6899999999999999987654111 1111   1111      1234444444444444333   335567


Q ss_pred             CHHHHHHHHHhh
Q 030960          145 LPKDFEKGYRTN  156 (168)
Q Consensus       145 ~~~d~~~al~~~  156 (168)
                      +.+||.+....+
T Consensus       246 ~~~~~~~~~~~~  257 (262)
T TIGR02640       246 DDEDFVDLCIDI  257 (262)
T ss_pred             CcHHHHHHHHHH
Confidence            888888776554

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).

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=97.36  E-value=0.0015  Score=53.02  Aligned_cols=89  Identities=16%  Similarity=0.192  Sum_probs=64.2

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCC
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLP   91 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P   91 (168)
                      ...-|++|||+|.+-.              ...+.+|..++.  ...+.++|..|+.++.+.+.+++  |+ ..+.+++|
T Consensus       140 g~~rVviIDeAd~l~~--------------~aanaLLk~LEE--pp~~~~fiLit~~~~~llptIrS--Rc-~~i~l~pl  200 (351)
T PRK09112        140 GNWRIVIIDPADDMNR--------------NAANAILKTLEE--PPARALFILISHSSGRLLPTIRS--RC-QPISLKPL  200 (351)
T ss_pred             CCceEEEEEchhhcCH--------------HHHHHHHHHHhc--CCCCceEEEEECChhhccHHHHh--hc-cEEEecCC
Confidence            3467999999998831              345667888875  33456666667889999999998  88 69999999


Q ss_pred             CHHHHHHHHHhhcCC-CC---CHHHHHhCCCC
Q 030960           92 DRRQKRLVFQMNLSD-EV---DLEDYVSRPDK  119 (168)
Q Consensus        92 ~~~~R~~il~~~l~~-~~---~~~~la~~t~g  119 (168)
                      +.++-.++++..... .+   .+..++..+.|
T Consensus       201 ~~~~~~~~L~~~~~~~~~~~~~~~~i~~~s~G  232 (351)
T PRK09112        201 DDDELKKALSHLGSSQGSDGEITEALLQRSKG  232 (351)
T ss_pred             CHHHHHHHHHHhhcccCCCHHHHHHHHHHcCC
Confidence            999999999863221 11   24456665655

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=97.34  E-value=0.004  Score=54.10  Aligned_cols=93  Identities=14%  Similarity=0.095  Sum_probs=62.2

Q ss_pred             eEEEE-ecCCCCCCCccccCCCCcceEEecCCCCHHHHHHHHHhhcCC-C--C---CHHHHHhCCCCCCHHHHHHHHHHH
Q 030960           60 VKVIM-ATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD-E--V---DLEDYVSRPDKISAAEIAAICQEA  132 (168)
Q Consensus        60 v~vi~-ttn~~~~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~~-~--~---~~~~la~~t~g~s~~di~~l~~~a  132 (168)
                      +++|+ ||+.++.+++++++  ||. .+.+++++.++...|++..+.. .  +   .+..++..+.  .++..-+.+.++
T Consensus       324 ~VLI~aTt~~~~~l~~aLrS--R~~-~i~~~pls~edi~~Il~~~a~~~~v~ls~eal~~L~~ys~--~gRraln~L~~~  398 (615)
T TIGR02903       324 FVLIGATTRDPEEINPALRS--RCA-EVFFEPLTPEDIALIVLNAAEKINVHLAAGVEELIARYTI--EGRKAVNILADV  398 (615)
T ss_pred             EEEEEeccccccccCHHHHh--cee-EEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCC--cHHHHHHHHHHH
Confidence            45554 66779999999998  987 5688999999999999976552 1  1   2334555442  455555555555


Q ss_pred             HHHHHHh--------CCCccCHHHHHHHHHhhc
Q 030960          133 GMHAVRK--------NRYVILPKDFEKGYRTNV  157 (168)
Q Consensus       133 ~~~a~~~--------~~~~i~~~d~~~al~~~~  157 (168)
                      ...++.+        ....|+.+|+.+++..-+
T Consensus       399 ~~~~~~~~~~~~~~~~~~~I~~edv~~~l~~~r  431 (615)
T TIGR02903       399 YGYALYRAAEAGKENDKVTITQDDVYEVIQISR  431 (615)
T ss_pred             HHHHHHHHHHhccCCCCeeECHHHHHHHhCCCc
Confidence            4443222        223699999999998544

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.

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

Probab=97.33  E-value=0.00063  Score=59.09  Aligned_cols=84  Identities=29%  Similarity=0.349  Sum_probs=57.9

Q ss_pred             HHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC---------CC----CCCCeEEEEecCCCCCCCc
Q 030960            8 LAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG---------FD----QTVNVKVIMATNRADTLDP   74 (168)
Q Consensus         8 ~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~---------~~----~~~~v~vi~ttn~~~~ld~   74 (168)
                      +.+.. .-+++|||+|.++..-  .+...        +.+|+.||-         +-    .-++|++|+|+|.++.||+
T Consensus       501 ~v~t~-NPliLiDEvDKlG~g~--qGDPa--------sALLElLDPEQNanFlDHYLdVp~DLSkVLFicTAN~idtIP~  569 (906)
T KOG2004|consen  501 KVKTE-NPLILIDEVDKLGSGH--QGDPA--------SALLELLDPEQNANFLDHYLDVPVDLSKVLFICTANVIDTIPP  569 (906)
T ss_pred             hhCCC-CceEEeehhhhhCCCC--CCChH--------HHHHHhcChhhccchhhhccccccchhheEEEEeccccccCCh
Confidence            33333 4578999999998322  22111        234444442         11    2346999999999999999


Q ss_pred             cccCCCCcceEEecCCCCHHHHHHHHHhhcC
Q 030960           75 ALLRPGRLDRKIEFPLPDRRQKRLVFQMNLS  105 (168)
Q Consensus        75 al~r~grf~~~i~~~~P~~~~R~~il~~~l~  105 (168)
                      .|+.  |. ..|+++=-..++...|-+.||-
T Consensus       570 pLlD--RM-EvIelsGYv~eEKv~IA~~yLi  597 (906)
T KOG2004|consen  570 PLLD--RM-EVIELSGYVAEEKVKIAERYLI  597 (906)
T ss_pred             hhhh--hh-heeeccCccHHHHHHHHHHhhh
Confidence            9998  87 4677777788899999887765

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.32  E-value=0.0025  Score=57.38  Aligned_cols=117  Identities=19%  Similarity=0.275  Sum_probs=77.5

Q ss_pred             HHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC--C-------CCCCeEEEEecCCCCC------
Q 030960            7 RLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF--D-------QTVNVKVIMATNRADT------   71 (168)
Q Consensus         7 ~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~--~-------~~~~v~vi~ttn~~~~------   71 (168)
                      ...+....+||+|||+|.+-           .   .+.+.|+..++.=  .       ...+.+||+|||....      
T Consensus       661 ~~v~~~p~~vlllDeieka~-----------~---~v~~~Ll~~l~~g~l~d~~g~~vd~rn~iiI~TSn~g~~~~~~~~  726 (852)
T TIGR03346       661 EAVRRKPYSVVLFDEVEKAH-----------P---DVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNLGSQFIQELA  726 (852)
T ss_pred             HHHHcCCCcEEEEeccccCC-----------H---HHHHHHHHHHhcCceecCCCeEEecCCcEEEEeCCcchHhHhhhc
Confidence            34455566899999999652           1   4555666666421  1       1346789999998332      


Q ss_pred             -------------------CCccccCCCCcceEEecCCCCHHHHHHHHHhhcCC---------------CCCHHHHHhC-
Q 030960           72 -------------------LDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD---------------EVDLEDYVSR-  116 (168)
Q Consensus        72 -------------------ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~~---------------~~~~~~la~~-  116 (168)
                                         +.|.++.  |+|..+.|.+++.++..+|+...+..               +-.++.|++. 
T Consensus       727 ~~~~~~~~~~~~~~~~~~~F~pel~~--Rid~IivF~PL~~e~l~~I~~l~L~~l~~~l~~~~~~l~i~~~a~~~L~~~~  804 (852)
T TIGR03346       727 GGDDYEEMREAVMEVLRAHFRPEFLN--RIDEIVVFHPLGREQIARIVEIQLGRLRKRLAERKITLELSDAALDFLAEAG  804 (852)
T ss_pred             ccccHHHHHHHHHHHHHhhcCHHHhc--CcCeEEecCCcCHHHHHHHHHHHHHHHHHHHHHCCCeecCCHHHHHHHHHhC
Confidence                               3355665  99999999999999999999754431               1123345554 


Q ss_pred             -CCCCCHHHHHHHHHHHHHHHHHh
Q 030960          117 -PDKISAAEIAAICQEAGMHAVRK  139 (168)
Q Consensus       117 -t~g~s~~di~~l~~~a~~~a~~~  139 (168)
                       ...+..+.|.+++++.....+.+
T Consensus       805 ~~~~~gaR~L~~~i~~~i~~~l~~  828 (852)
T TIGR03346       805 YDPVYGARPLKRAIQREIENPLAK  828 (852)
T ss_pred             CCCCCCchhHHHHHHHHHHHHHHH
Confidence             23567788888888876665543

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.

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.32  E-value=0.0037  Score=54.37  Aligned_cols=110  Identities=15%  Similarity=0.220  Sum_probs=73.0

Q ss_pred             HHHHHHHHHHc----CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcccc
Q 030960            2 VRDVFRLAKEN----APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~~----~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~   77 (168)
                      ++++.+.+...    ..-|++|||+|.+-.              ...+.|+..++.  ....+++|++|++++.+.+.++
T Consensus       106 IReii~~a~~~p~~~~~KViIIDEad~Lt~--------------~a~naLLK~LEe--Pp~~tvfIL~t~~~~~llpTIr  169 (620)
T PRK14948        106 IRELIERAQFAPVQARWKVYVIDECHMLST--------------AAFNALLKTLEE--PPPRVVFVLATTDPQRVLPTII  169 (620)
T ss_pred             HHHHHHHHhhChhcCCceEEEEECccccCH--------------HHHHHHHHHHhc--CCcCeEEEEEeCChhhhhHHHH
Confidence            46666666432    246999999998731              345678888873  4456777778888999999999


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhcCC---C---CCHHHHHhCCCCCCHHHHHHHHHH
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNLSD---E---VDLEDYVSRPDKISAAEIAAICQE  131 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l~~---~---~~~~~la~~t~g~s~~di~~l~~~  131 (168)
                      +  |+ ..+.|..++.++-...+......   .   ..+..+++.+.| +.++..++++.
T Consensus       170 S--Rc-~~~~f~~l~~~ei~~~L~~ia~kegi~is~~al~~La~~s~G-~lr~A~~lLek  225 (620)
T PRK14948        170 S--RC-QRFDFRRIPLEAMVQHLSEIAEKESIEIEPEALTLVAQRSQG-GLRDAESLLDQ  225 (620)
T ss_pred             h--he-eEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC-CHHHHHHHHHH
Confidence            8  76 56788888877766655543321   1   235566667665 34666666654

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

Probab=97.28  E-value=0.0019  Score=53.76  Aligned_cols=71  Identities=30%  Similarity=0.392  Sum_probs=47.7

Q ss_pred             HHHHHHHHc--CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhcc--------------------CCCCCCCeE
Q 030960            4 DVFRLAKEN--APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMD--------------------GFDQTVNVK   61 (168)
Q Consensus         4 ~iF~~a~~~--~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~--------------------~~~~~~~v~   61 (168)
                      ++...|+..  .|++|+|||++.--..             ++...+++.|+                    .+.-..++.
T Consensus       261 ~~~~~A~~~p~~~~vliIDEINRani~-------------kiFGel~~lLE~~~rg~~~~v~l~y~e~d~e~f~iP~Nl~  327 (459)
T PRK11331        261 NFCQQAKEQPEKKYVFIIDEINRANLS-------------KVFGEVMMLMEHDKRGENWSVPLTYSENDEERFYVPENVY  327 (459)
T ss_pred             HHHHHHHhcccCCcEEEEehhhccCHH-------------HhhhhhhhhccccccccccceeeeccccccccccCCCCeE
Confidence            345666654  4899999999964322             23333333332                    234456799


Q ss_pred             EEEecCCCC----CCCccccCCCCcceEEecCC
Q 030960           62 VIMATNRAD----TLDPALLRPGRLDRKIEFPL   90 (168)
Q Consensus        62 vi~ttn~~~----~ld~al~r~grf~~~i~~~~   90 (168)
                      +|||+|..+    .+|.|++|  ||.. +++.+
T Consensus       328 IIgTMNt~Drs~~~lD~AlrR--RF~f-i~i~p  357 (459)
T PRK11331        328 IIGLMNTADRSLAVVDYALRR--RFSF-IDIEP  357 (459)
T ss_pred             EEEecCccccchhhccHHHHh--hhhe-EEecC
Confidence            999999988    89999999  9965 55543

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=97.24  E-value=0.0023  Score=52.11  Aligned_cols=90  Identities=13%  Similarity=0.169  Sum_probs=66.1

Q ss_pred             HcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCC
Q 030960           11 ENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPL   90 (168)
Q Consensus        11 ~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~   90 (168)
                      ...|-|++|||+|.+-              ....+.++..++.  ...++++|.+|++++.+.+.+++  |+ ..+.|++
T Consensus       139 ~~~~kVviIDead~m~--------------~~aanaLLK~LEe--pp~~~~~IL~t~~~~~llpti~S--Rc-~~i~l~~  199 (365)
T PRK07471        139 EGGWRVVIVDTADEMN--------------ANAANALLKVLEE--PPARSLFLLVSHAPARLLPTIRS--RC-RKLRLRP  199 (365)
T ss_pred             cCCCEEEEEechHhcC--------------HHHHHHHHHHHhc--CCCCeEEEEEECCchhchHHhhc--cc-eEEECCC
Confidence            3458899999999772              1456678888873  44467788899999999999887  75 5789999


Q ss_pred             CCHHHHHHHHHhhcCCCCC--HHHHHhCCCC
Q 030960           91 PDRRQKRLVFQMNLSDEVD--LEDYVSRPDK  119 (168)
Q Consensus        91 P~~~~R~~il~~~l~~~~~--~~~la~~t~g  119 (168)
                      |+.++-.+++........+  +..++..+.|
T Consensus       200 l~~~~i~~~L~~~~~~~~~~~~~~l~~~s~G  230 (365)
T PRK07471        200 LAPEDVIDALAAAGPDLPDDPRAALAALAEG  230 (365)
T ss_pred             CCHHHHHHHHHHhcccCCHHHHHHHHHHcCC
Confidence            9999999999876542221  2456666655

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

Probab=97.24  E-value=0.0081  Score=46.18  Aligned_cols=91  Identities=18%  Similarity=0.276  Sum_probs=64.3

Q ss_pred             HHHHHHHHH-HcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC--CCCCCeEEEEecCCCCCCCccccC
Q 030960            2 VRDVFRLAK-ENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF--DQTVNVKVIMATNRADTLDPALLR   78 (168)
Q Consensus         2 l~~iF~~a~-~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~--~~~~~v~vi~ttn~~~~ld~al~r   78 (168)
                      |-.+++..+ ...+.|||+||+-  |...       +    .-...|...|+|-  ....+|++.||+|+-+-++.....
T Consensus        94 l~~l~~~l~~~~~kFIlf~DDLs--Fe~~-------d----~~yk~LKs~LeGgle~~P~NvliyATSNRRHLv~E~~~d  160 (249)
T PF05673_consen   94 LPELLDLLRDRPYKFILFCDDLS--FEEG-------D----TEYKALKSVLEGGLEARPDNVLIYATSNRRHLVPESFSD  160 (249)
T ss_pred             HHHHHHHHhcCCCCEEEEecCCC--CCCC-------c----HHHHHHHHHhcCccccCCCcEEEEEecchhhccchhhhh
Confidence            345666655 3458999999854  3211       1    1223455555543  345689999999998888775442


Q ss_pred             ----------C-----------CCcceEEecCCCCHHHHHHHHHhhcC
Q 030960           79 ----------P-----------GRLDRKIEFPLPDRRQKRLVFQMNLS  105 (168)
Q Consensus        79 ----------~-----------grf~~~i~~~~P~~~~R~~il~~~l~  105 (168)
                                |           .||...|.|.+|+.++-.+|++.+..
T Consensus       161 ~~~~~~~eih~~d~~eEklSLsDRFGL~l~F~~~~q~~YL~IV~~~~~  208 (249)
T PF05673_consen  161 REDIQDDEIHPSDTIEEKLSLSDRFGLWLSFYPPDQEEYLAIVRHYAE  208 (249)
T ss_pred             ccCCCccccCcchHHHHHHhHHHhCCcEEEecCCCHHHHHHHHHHHHH
Confidence                      1           18999999999999999999998885

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.22  E-value=0.0011  Score=54.67  Aligned_cols=120  Identities=13%  Similarity=0.120  Sum_probs=78.5

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      .-|++|||+|.+..              ...+.++..++.  ..+..++|.+|+.+..+.+++.+  |+. .++|.+++.
T Consensus       128 ~kvvIIdea~~l~~--------------~~~~~LLk~LEe--p~~~t~~Il~t~~~~kl~~tl~s--R~~-~v~f~~l~~  188 (397)
T PRK14955        128 YRVYIIDEVHMLSI--------------AAFNAFLKTLEE--PPPHAIFIFATTELHKIPATIAS--RCQ-RFNFKRIPL  188 (397)
T ss_pred             eEEEEEeChhhCCH--------------HHHHHHHHHHhc--CCCCeEEEEEeCChHHhHHHHHH--HHH-HhhcCCCCH
Confidence            45999999998741              234556777763  33455566666778889888887  764 788999998


Q ss_pred             HHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHH-hCCCccCHHHHHHHH
Q 030960           94 RQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVR-KNRYVILPKDFEKGY  153 (168)
Q Consensus        94 ~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~-~~~~~i~~~d~~~al  153 (168)
                      ++-...++..+..      +..++.++..+.| +.+.+.+.++.....+-. .....|+.+++.+.+
T Consensus       189 ~ei~~~l~~~~~~~g~~i~~~al~~l~~~s~g-~lr~a~~~L~kl~~~~~~~~~~~~It~~~v~~~v  254 (397)
T PRK14955        189 EEIQQQLQGICEAEGISVDADALQLIGRKAQG-SMRDAQSILDQVIAFSVESEGEGSIRYDKVAELL  254 (397)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHHhccccCCCCccCHHHHHHHH
Confidence            8888777765431      1234556666654 677777777765544321 123467777776655

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

Probab=97.21  E-value=0.002  Score=56.05  Aligned_cols=135  Identities=22%  Similarity=0.308  Sum_probs=85.7

Q ss_pred             HHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC---------C----CCCCCeEEEEecCCCCCCC
Q 030960            7 RLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG---------F----DQTVNVKVIMATNRADTLD   73 (168)
Q Consensus         7 ~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~---------~----~~~~~v~vi~ttn~~~~ld   73 (168)
                      .+|+... -++++||+|.+...-.+.   ..       +.||+-||-         +    -.=++|++|+|+|+.+.||
T Consensus       412 kka~~~N-Pv~LLDEIDKm~ss~rGD---Pa-------SALLEVLDPEQN~~F~DhYLev~yDLS~VmFiaTANsl~tIP  480 (782)
T COG0466         412 KKAGVKN-PVFLLDEIDKMGSSFRGD---PA-------SALLEVLDPEQNNTFSDHYLEVPYDLSKVMFIATANSLDTIP  480 (782)
T ss_pred             HHhCCcC-CeEEeechhhccCCCCCC---hH-------HHHHhhcCHhhcCchhhccccCccchhheEEEeecCccccCC
Confidence            3444444 578899999997542111   11       234444441         1    1123699999999999999


Q ss_pred             ccccCCCCcceEEecCCCCHHHHHHHHHhhcCC-----------CCC-----HHHHHh-CC--CCCCH--HHHHHHHHHH
Q 030960           74 PALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD-----------EVD-----LEDYVS-RP--DKISA--AEIAAICQEA  132 (168)
Q Consensus        74 ~al~r~grf~~~i~~~~P~~~~R~~il~~~l~~-----------~~~-----~~~la~-~t--~g~s~--~di~~l~~~a  132 (168)
                      ..|+.  |. ..|.++--+..+..+|-+.||-+           ++.     +..+.. +|  .|.-+  +.|..+|+.+
T Consensus       481 ~PLlD--RM-EiI~lsgYt~~EKl~IAk~~LiPk~~~~~gL~~~el~i~d~ai~~iI~~YTREAGVR~LeR~i~ki~RK~  557 (782)
T COG0466         481 APLLD--RM-EVIRLSGYTEDEKLEIAKRHLIPKQLKEHGLKKGELTITDEAIKDIIRYYTREAGVRNLEREIAKICRKA  557 (782)
T ss_pred             hHHhc--ce-eeeeecCCChHHHHHHHHHhcchHHHHHcCCCccceeecHHHHHHHHHHHhHhhhhhHHHHHHHHHHHHH
Confidence            99998  87 46888888999999999866642           121     222222 22  23322  6788888887


Q ss_pred             HHHHHHhCCC---ccCHHHHHHHHHh
Q 030960          133 GMHAVRKNRY---VILPKDFEKGYRT  155 (168)
Q Consensus       133 ~~~a~~~~~~---~i~~~d~~~al~~  155 (168)
                      +..-+.....   .++..++..-+..
T Consensus       558 ~~~i~~~~~k~~~~i~~~~l~~yLG~  583 (782)
T COG0466         558 AKKILLKKEKSIVKIDEKNLKKYLGV  583 (782)
T ss_pred             HHHHHhcCcccceeeCHHHHHHHhCC
Confidence            7666654332   4777777777653

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

Probab=97.20  E-value=0.0065  Score=47.71  Aligned_cols=126  Identities=18%  Similarity=0.143  Sum_probs=92.2

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC----------------CCCCeEEEEecCCCCCCCcccc
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD----------------QTVNVKVIMATNRADTLDPALL   77 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~----------------~~~~v~vi~ttn~~~~ld~al~   77 (168)
                      ..|+|||||+.+.+.              +-..+...|+++.                .-++..+|++|.+.-.|..-|+
T Consensus       104 ~DVLFIDEIHrl~~~--------------vEE~LYpaMEDf~lDI~IG~gp~Arsv~ldLppFTLIGATTr~G~lt~PLr  169 (332)
T COG2255         104 GDVLFIDEIHRLSPA--------------VEEVLYPAMEDFRLDIIIGKGPAARSIRLDLPPFTLIGATTRAGMLTNPLR  169 (332)
T ss_pred             CCeEEEehhhhcChh--------------HHHHhhhhhhheeEEEEEccCCccceEeccCCCeeEeeeccccccccchhH
Confidence            589999999998532              2223444455441                1235889999999999999999


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHH---hhcCC---CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHH
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQ---MNLSD---EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK  151 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~---~~l~~---~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~  151 (168)
                      .  ||.....+..-+.++-.+|+.   ..+.-   +....++|.++.| ||+==-+++++..-.|.-.+...|+.+--.+
T Consensus       170 d--RFGi~~rlefY~~~eL~~Iv~r~a~~l~i~i~~~~a~eIA~rSRG-TPRIAnRLLrRVRDfa~V~~~~~I~~~ia~~  246 (332)
T COG2255         170 D--RFGIIQRLEFYTVEELEEIVKRSAKILGIEIDEEAALEIARRSRG-TPRIANRLLRRVRDFAQVKGDGDIDRDIADK  246 (332)
T ss_pred             H--hcCCeeeeecCCHHHHHHHHHHHHHHhCCCCChHHHHHHHHhccC-CcHHHHHHHHHHHHHHHHhcCCcccHHHHHH
Confidence            9  999999999999999999997   34442   2335578888876 5665556777777777767777777777777


Q ss_pred             HHHhh
Q 030960          152 GYRTN  156 (168)
Q Consensus       152 al~~~  156 (168)
                      |++..
T Consensus       247 aL~~L  251 (332)
T COG2255         247 ALKML  251 (332)
T ss_pred             HHHHh
Confidence            77653

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

Probab=97.18  E-value=0.004  Score=50.04  Aligned_cols=91  Identities=22%  Similarity=0.323  Sum_probs=66.1

Q ss_pred             HHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC--------CCCCCeEEEEe----cCCCCCC
Q 030960            5 VFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF--------DQTVNVKVIMA----TNRADTL   72 (168)
Q Consensus         5 iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~--------~~~~~v~vi~t----tn~~~~l   72 (168)
                      ..+.|..  -.||||||||.++...+....  +-.-+.+...+|-.++|-        -+++++++||+    ...|++|
T Consensus       244 Ai~~aE~--~GIvFIDEIDKIa~~~~~g~~--dvSREGVQRDlLPlvEGstV~TKyG~VkTdHILFIasGAFh~sKPSDL  319 (444)
T COG1220         244 AIDAAEQ--NGIVFIDEIDKIAKRGGSGGP--DVSREGVQRDLLPLVEGSTVSTKYGPVKTDHILFIASGAFHVAKPSDL  319 (444)
T ss_pred             HHHHHHh--cCeEEEehhhHHHhcCCCCCC--CcchhhhcccccccccCceeeccccccccceEEEEecCceecCChhhc
Confidence            3344444  479999999999976542221  222245666777777764        24556888885    4668888


Q ss_pred             CccccCCCCcceEEecCCCCHHHHHHHHH
Q 030960           73 DPALLRPGRLDRKIEFPLPDRRQKRLVFQ  101 (168)
Q Consensus        73 d~al~r~grf~~~i~~~~P~~~~R~~il~  101 (168)
                      =|.|..  ||...+++...+.+.-.+||.
T Consensus       320 iPELQG--RfPIRVEL~~Lt~~Df~rILt  346 (444)
T COG1220         320 IPELQG--RFPIRVELDALTKEDFERILT  346 (444)
T ss_pred             ChhhcC--CCceEEEcccCCHHHHHHHHc
Confidence            889975  999999999999999998886

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=97.17  E-value=0.0018  Score=51.83  Aligned_cols=90  Identities=14%  Similarity=0.249  Sum_probs=64.6

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      --|++||++|.+-              ....|.+|..++  +...++++|.+|++++.|.|.+++  |+. .+.|++|+.
T Consensus       114 ~kV~iI~~ae~m~--------------~~AaNaLLKtLE--EPp~~~~fiL~~~~~~~lLpTIrS--RCq-~i~~~~~~~  174 (319)
T PRK08769        114 AQVVIVDPADAIN--------------RAACNALLKTLE--EPSPGRYLWLISAQPARLPATIRS--RCQ-RLEFKLPPA  174 (319)
T ss_pred             cEEEEeccHhhhC--------------HHHHHHHHHHhh--CCCCCCeEEEEECChhhCchHHHh--hhe-EeeCCCcCH
Confidence            4699999999883              145677888888  455678888899999999999999  864 567889999


Q ss_pred             HHHHHHHHhhcCCCCCHHHHHhCCCCCCH
Q 030960           94 RQKRLVFQMNLSDEVDLEDYVSRPDKISA  122 (168)
Q Consensus        94 ~~R~~il~~~l~~~~~~~~la~~t~g~s~  122 (168)
                      ++-.+.+...-.+..+...++..+.|--+
T Consensus       175 ~~~~~~L~~~~~~~~~a~~~~~l~~G~p~  203 (319)
T PRK08769        175 HEALAWLLAQGVSERAAQEALDAARGHPG  203 (319)
T ss_pred             HHHHHHHHHcCCChHHHHHHHHHcCCCHH
Confidence            88887776432122223345555555444

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

Probab=97.16  E-value=0.0011  Score=54.83  Aligned_cols=85  Identities=24%  Similarity=0.347  Sum_probs=63.0

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC--------CCCCCeEEEEe----cCCCCCCCccccCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF--------DQTVNVKVIMA----TNRADTLDPALLRPG   80 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~--------~~~~~v~vi~t----tn~~~~ld~al~r~g   80 (168)
                      +-.||||||+|.++...++.  +.+-....+-..||..++|-        -.+.++++|++    ...|+++=|.+..  
T Consensus       249 ~~GIVfiDEiDKIa~~~~~~--~~DvS~eGVQ~~LLki~EG~~v~~k~~~i~T~~ILFI~~GAF~~~kp~DlIPEl~G--  324 (443)
T PRK05201        249 QNGIVFIDEIDKIAARGGSS--GPDVSREGVQRDLLPLVEGSTVSTKYGMVKTDHILFIASGAFHVSKPSDLIPELQG--  324 (443)
T ss_pred             cCCEEEEEcchhhcccCCCC--CCCCCccchhcccccccccceeeecceeEECCceeEEecCCcCCCChhhccHHHhC--
Confidence            46899999999999765322  22222246777888888873        13456777774    2457788888886  


Q ss_pred             CcceEEecCCCCHHHHHHHHH
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQ  101 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~  101 (168)
                      ||...+.+.+++.++-.+||.
T Consensus       325 R~Pi~v~L~~L~~~dL~~ILt  345 (443)
T PRK05201        325 RFPIRVELDALTEEDFVRILT  345 (443)
T ss_pred             ccceEEECCCCCHHHHHHHhc
Confidence            999999999999999999985

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.16  E-value=0.0056  Score=53.20  Aligned_cols=101  Identities=18%  Similarity=0.219  Sum_probs=70.1

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      .-|++|||+|.+-.              ...+.|+..|+.  .....++|.+|+.+..|-+.+++  |+ ..+.|.+++.
T Consensus       122 ~KVvIIdea~~Ls~--------------~a~naLLK~LEe--pp~~tifIL~tt~~~kIl~tI~S--Rc-~iv~f~~ls~  182 (614)
T PRK14971        122 YKIYIIDEVHMLSQ--------------AAFNAFLKTLEE--PPSYAIFILATTEKHKILPTILS--RC-QIFDFNRIQV  182 (614)
T ss_pred             cEEEEEECcccCCH--------------HHHHHHHHHHhC--CCCCeEEEEEeCCchhchHHHHh--hh-heeecCCCCH
Confidence            34999999998831              345678888874  33356666677778899999998  76 4599999999


Q ss_pred             HHHHHHHHhhcCC-CC-----CHHHHHhCCCCCCHHHHHHHHHHHHH
Q 030960           94 RQKRLVFQMNLSD-EV-----DLEDYVSRPDKISAAEIAAICQEAGM  134 (168)
Q Consensus        94 ~~R~~il~~~l~~-~~-----~~~~la~~t~g~s~~di~~l~~~a~~  134 (168)
                      ++-...++..+.. .+     .+..+++.+.| +.+++.+.+.....
T Consensus       183 ~ei~~~L~~ia~~egi~i~~~al~~La~~s~g-dlr~al~~Lekl~~  228 (614)
T PRK14971        183 ADIVNHLQYVASKEGITAEPEALNVIAQKADG-GMRDALSIFDQVVS  228 (614)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHH
Confidence            8888777754331 12     35567777744 77777777766543

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

Probab=97.16  E-value=0.0018  Score=44.23  Aligned_cols=68  Identities=41%  Similarity=0.632  Sum_probs=45.3

Q ss_pred             HHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC----CCCCeEEEEecCCCC--CCCccccCCC
Q 030960            7 RLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD----QTVNVKVIMATNRAD--TLDPALLRPG   80 (168)
Q Consensus         7 ~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~----~~~~v~vi~ttn~~~--~ld~al~r~g   80 (168)
                      ..+....+.+|++||++.+..              .....++..+....    ...++.+|+++|...  .+++.+..  
T Consensus        78 ~~~~~~~~~~lilDe~~~~~~--------------~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~~~~~~~~~~~--  141 (151)
T cd00009          78 ELAEKAKPGVLFIDEIDSLSR--------------GAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYD--  141 (151)
T ss_pred             HhhccCCCeEEEEeChhhhhH--------------HHHHHHHHHHHhcCceeccCCCeEEEEecCccccCCcChhHHh--
Confidence            344455699999999998721              11223333333322    245788899998887  78888887  


Q ss_pred             CcceEEecCC
Q 030960           81 RLDRKIEFPL   90 (168)
Q Consensus        81 rf~~~i~~~~   90 (168)
                      ||+..+.+++
T Consensus       142 r~~~~i~~~~  151 (151)
T cd00009         142 RLDIRIVIPL  151 (151)
T ss_pred             hhccEeecCC
Confidence            9998888763

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.15  E-value=0.0042  Score=55.92  Aligned_cols=116  Identities=19%  Similarity=0.278  Sum_probs=75.8

Q ss_pred             HHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC---------CCCCeEEEEecCCCC------
Q 030960            6 FRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD---------QTVNVKVIMATNRAD------   70 (168)
Q Consensus         6 F~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~---------~~~~v~vi~ttn~~~------   70 (168)
                      .+..+++.++||+|||+|..-           .   .+.+.|+..++.-.         ...+.++|+|||...      
T Consensus       661 ~~~v~~~p~svvllDEieka~-----------~---~v~~~Llq~ld~g~l~d~~Gr~vd~~n~iiI~TSNlg~~~~~~~  726 (852)
T TIGR03345       661 TEAVRRKPYSVVLLDEVEKAH-----------P---DVLELFYQVFDKGVMEDGEGREIDFKNTVILLTSNAGSDLIMAL  726 (852)
T ss_pred             HHHHHhCCCcEEEEechhhcC-----------H---HHHHHHHHHhhcceeecCCCcEEeccccEEEEeCCCchHHHHHh
Confidence            455567788999999998542           1   45556666665321         124688999998522      


Q ss_pred             -----------------------CCCccccCCCCcceEEecCCCCHHHHHHHHHhhcCC----------------CCCHH
Q 030960           71 -----------------------TLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD----------------EVDLE  111 (168)
Q Consensus        71 -----------------------~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~~----------------~~~~~  111 (168)
                                             .+.|+++.  |++ .|.|.+.+.++-.+|+...+..                +..++
T Consensus       727 ~~~~~~~~~~~~~~~~~~~~~~~~f~PEfln--Ri~-iI~F~pLs~e~l~~Iv~~~L~~l~~rl~~~~gi~l~i~d~a~~  803 (852)
T TIGR03345       727 CADPETAPDPEALLEALRPELLKVFKPAFLG--RMT-VIPYLPLDDDVLAAIVRLKLDRIARRLKENHGAELVYSEALVE  803 (852)
T ss_pred             ccCcccCcchHHHHHHHHHHHHHhccHHHhc--cee-EEEeCCCCHHHHHHHHHHHHHHHHHHHHHhcCceEEECHHHHH
Confidence                                   14566666  887 8899999999999999755431                11234


Q ss_pred             HHHhCCC--CCCHHHHHHHHHHHHHHHHH
Q 030960          112 DYVSRPD--KISAAEIAAICQEAGMHAVR  138 (168)
Q Consensus       112 ~la~~t~--g~s~~di~~l~~~a~~~a~~  138 (168)
                      .|++...  .|-.+.|.++++.-...++.
T Consensus       804 ~La~~g~~~~~GAR~L~r~Ie~~i~~~la  832 (852)
T TIGR03345       804 HIVARCTEVESGARNIDAILNQTLLPELS  832 (852)
T ss_pred             HHHHHcCCCCCChHHHHHHHHHHHHHHHH
Confidence            4665543  36678888887775554443

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.

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=97.14  E-value=0.0016  Score=52.25  Aligned_cols=71  Identities=23%  Similarity=0.376  Sum_probs=51.3

Q ss_pred             eEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC----------CCCCCCeEEEEecC-----CCCCCCccccCC
Q 030960           15 AIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG----------FDQTVNVKVIMATN-----RADTLDPALLRP   79 (168)
Q Consensus        15 ~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~----------~~~~~~v~vi~ttn-----~~~~ld~al~r~   79 (168)
                      +|+++|||+..-           .   .+.+.++..|+.          +.-....+||+|+|     ....+++|+++ 
T Consensus       114 ~ill~DEInra~-----------p---~~q~aLl~~l~e~~vtv~~~~~~~~~~~f~viaT~Np~e~~g~~~l~eA~ld-  178 (329)
T COG0714         114 VILLLDEINRAP-----------P---EVQNALLEALEERQVTVPGLTTIRLPPPFIVIATQNPGEYEGTYPLPEALLD-  178 (329)
T ss_pred             eEEEEeccccCC-----------H---HHHHHHHHHHhCcEEEECCcCCcCCCCCCEEEEccCccccCCCcCCCHHHHh-
Confidence            599999999642           2   444555555554          22335688999989     77789999999 


Q ss_pred             CCcceEEecCCC-CHHHHHHHHH
Q 030960           80 GRLDRKIEFPLP-DRRQKRLVFQ  101 (168)
Q Consensus        80 grf~~~i~~~~P-~~~~R~~il~  101 (168)
                       ||-..+++++| ...+...+..
T Consensus       179 -Rf~~~~~v~yp~~~~e~~~i~~  200 (329)
T COG0714         179 -RFLLRIYVDYPDSEEEERIILA  200 (329)
T ss_pred             -hEEEEEecCCCCchHHHHHHHH
Confidence             99999999999 5555555554

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=97.11  E-value=0.0018  Score=56.11  Aligned_cols=97  Identities=13%  Similarity=0.222  Sum_probs=65.7

Q ss_pred             CeEEEEecCCC--CCCCccccCCCCcc---eEEecC---CCCHHHHHHHHHh---hc-----CCCCCHH---HHH---hC
Q 030960           59 NVKVIMATNRA--DTLDPALLRPGRLD---RKIEFP---LPDRRQKRLVFQM---NL-----SDEVDLE---DYV---SR  116 (168)
Q Consensus        59 ~v~vi~ttn~~--~~ld~al~r~grf~---~~i~~~---~P~~~~R~~il~~---~l-----~~~~~~~---~la---~~  116 (168)
                      .+.+|+++|..  ..+++.++.  ||+   ..+.++   +++.+.|..+.+.   .+     .+.++-+   .+.   .+
T Consensus       268 dvrvIa~~~~~~l~~l~~~l~~--rf~~y~v~v~~~~~~~~~~e~~~~~~~~i~~~~~r~G~l~~~s~~Av~~Li~~~~R  345 (608)
T TIGR00764       268 DFILVASGNLDDLEGMHPALRS--RIRGYGYEVYMKDTMPDTPENRDKLVQFVAQEVKKDGRIPHFTRDAVEEIVREAQR  345 (608)
T ss_pred             ceEEEEECCHHHHhhcCHHHHH--HhcCCeEEEEeeccCCCCHHHHHHHHHHHHHHHHHhCCCCcCCHHHHHHHHHHHHH
Confidence            57788888863  689999999  999   666664   3355666555441   11     1122222   222   11


Q ss_pred             CC------CCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhc
Q 030960          117 PD------KISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNV  157 (168)
Q Consensus       117 t~------g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~  157 (168)
                      ..      ..+.++|.++++.|...|..++...|+.+|+.+|++...
T Consensus       346 ~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~~  392 (608)
T TIGR00764       346 RAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLAK  392 (608)
T ss_pred             HHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHHH
Confidence            11      256799999999998777777888999999999987554

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

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=97.11  E-value=0.0024  Score=51.43  Aligned_cols=76  Identities=12%  Similarity=0.168  Sum_probs=61.7

Q ss_pred             HHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEec
Q 030960            9 AKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEF   88 (168)
Q Consensus         9 a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~   88 (168)
                      ......-|++||++|.+-              ....|.||..|+  +...++++|.+|++++.|.|.+++  |.. .+.|
T Consensus       104 ~~~g~~kV~iI~~ae~m~--------------~~AaNaLLKtLE--EPp~~t~fiL~t~~~~~lLpTIrS--RCq-~~~~  164 (334)
T PRK07993        104 ARLGGAKVVWLPDAALLT--------------DAAANALLKTLE--EPPENTWFFLACREPARLLATLRS--RCR-LHYL  164 (334)
T ss_pred             cccCCceEEEEcchHhhC--------------HHHHHHHHHHhc--CCCCCeEEEEEECChhhChHHHHh--ccc-cccC
Confidence            334456799999999874              155678999998  466689999999999999999999  887 5799


Q ss_pred             CCCCHHHHHHHHHhh
Q 030960           89 PLPDRRQKRLVFQMN  103 (168)
Q Consensus        89 ~~P~~~~R~~il~~~  103 (168)
                      ++|+.++-.+.+...
T Consensus       165 ~~~~~~~~~~~L~~~  179 (334)
T PRK07993        165 APPPEQYALTWLSRE  179 (334)
T ss_pred             CCCCHHHHHHHHHHc
Confidence            999999988887643

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=97.10  E-value=0.0048  Score=53.80  Aligned_cols=127  Identities=17%  Similarity=0.206  Sum_probs=82.0

Q ss_pred             eEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC---------C--CCCCCeEEEEecCCC-CCCCccccCCCCc
Q 030960           15 AIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG---------F--DQTVNVKVIMATNRA-DTLDPALLRPGRL   82 (168)
Q Consensus        15 ~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~---------~--~~~~~v~vi~ttn~~-~~ld~al~r~grf   82 (168)
                      .||||||++.+-.              .+.+.|+..|+.         .  ....++.+|+|+|-- ..++++|+.  ||
T Consensus       128 GiL~lDEi~~l~~--------------~~q~~Ll~~le~g~~~v~r~g~~~~~~~~~~lIat~np~eg~l~~~L~d--R~  191 (633)
T TIGR02442       128 GILYIDEVNLLDD--------------HLVDVLLDAAAMGVNRVEREGLSVSHPARFVLIGTMNPEEGDLRPQLLD--RF  191 (633)
T ss_pred             CeEEeChhhhCCH--------------HHHHHHHHHHhcCCEEEEECCceeeecCCeEEEEecCCCCCCCCHHHHh--hc
Confidence            5999999998731              344455555531         1  112358889988843 358889999  99


Q ss_pred             ceEEecCCCC-HHHHHHHHHhhcCC------------------------------CC-----CHHHHHhCC--CCC-CHH
Q 030960           83 DRKIEFPLPD-RRQKRLVFQMNLSD------------------------------EV-----DLEDYVSRP--DKI-SAA  123 (168)
Q Consensus        83 ~~~i~~~~P~-~~~R~~il~~~l~~------------------------------~~-----~~~~la~~t--~g~-s~~  123 (168)
                      +..+.++.|. .++|.++++..+..                              .+     .+..++..+  -|. +.+
T Consensus       192 ~l~i~v~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~ar~~~~~V~is~~~~~~l~~~~~~~~i~s~R  271 (633)
T TIGR02442       192 GLCVDVAAPRDPEERVEIIRRRLAFDADPEAFAARWAAEQEELRNRIARARSLLPSVRISDSLIRFISELCIEFGVDGHR  271 (633)
T ss_pred             ceEEEccCCCchHHHHHHHHHHHhhccCcHHHHHHhhhhHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHhCCCCcc
Confidence            9999998774 67788887643220                              01     011122211  234 345


Q ss_pred             HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhc
Q 030960          124 EIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNV  157 (168)
Q Consensus       124 di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~  157 (168)
                      -...+++-|...|.-++...|+.+|+.+|+.-+.
T Consensus       272 a~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~lvL  305 (633)
T TIGR02442       272 ADIVMARAARALAALDGRRRVTAEDVREAAELVL  305 (633)
T ss_pred             HHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHHh
Confidence            5555667777777788889999999999987654

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.

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

Probab=97.09  E-value=0.0086  Score=50.77  Aligned_cols=103  Identities=18%  Similarity=0.280  Sum_probs=77.9

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      ..-|.+|||++-+-              ....|.||..++  +...+|.+|.+|..++.+|+.+++  |+. .+.|..-+
T Consensus       119 ryKVyiIDEvHMLS--------------~~afNALLKTLE--EPP~hV~FIlATTe~~Kip~TIlS--Rcq-~f~fkri~  179 (515)
T COG2812         119 RYKVYIIDEVHMLS--------------KQAFNALLKTLE--EPPSHVKFILATTEPQKIPNTILS--RCQ-RFDFKRLD  179 (515)
T ss_pred             cceEEEEecHHhhh--------------HHHHHHHhcccc--cCccCeEEEEecCCcCcCchhhhh--ccc-cccccCCC
Confidence            36799999998763              267888998888  566689999999999999999998  753 46777788


Q ss_pred             HHHHHHHHHhhcCC-CC-----CHHHHHhCCCCCCHHHHHHHHHHHHHH
Q 030960           93 RRQKRLVFQMNLSD-EV-----DLEDYVSRPDKISAAEIAAICQEAGMH  135 (168)
Q Consensus        93 ~~~R~~il~~~l~~-~~-----~~~~la~~t~g~s~~di~~l~~~a~~~  135 (168)
                      .++-...+...+.. .+     .+.-+|...+| |.+|-.+++..+...
T Consensus       180 ~~~I~~~L~~i~~~E~I~~e~~aL~~ia~~a~G-s~RDalslLDq~i~~  227 (515)
T COG2812         180 LEEIAKHLAAILDKEGINIEEDALSLIARAAEG-SLRDALSLLDQAIAF  227 (515)
T ss_pred             HHHHHHHHHHHHHhcCCccCHHHHHHHHHHcCC-ChhhHHHHHHHHHHc
Confidence            88888888766652 22     34456666666 778888888877544

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

Probab=97.08  E-value=0.0053  Score=49.92  Aligned_cols=135  Identities=20%  Similarity=0.303  Sum_probs=85.3

Q ss_pred             HHHHHHHHHHc-----CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEE-ecCCCC-CCCc
Q 030960            2 VRDVFRLAKEN-----APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIM-ATNRAD-TLDP   74 (168)
Q Consensus         2 l~~iF~~a~~~-----~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~-ttn~~~-~ld~   74 (168)
                      +|.+|+.|+..     ...||||||++.+-..              ....||-.++    ...|.+|+ ||.+|. .+..
T Consensus       206 vR~ife~aq~~~~l~krkTilFiDEiHRFNks--------------QQD~fLP~VE----~G~I~lIGATTENPSFqln~  267 (554)
T KOG2028|consen  206 VRDIFEQAQNEKSLTKRKTILFIDEIHRFNKS--------------QQDTFLPHVE----NGDITLIGATTENPSFQLNA  267 (554)
T ss_pred             HHHHHHHHHHHHhhhcceeEEEeHHhhhhhhh--------------hhhcccceec----cCceEEEecccCCCccchhH
Confidence            58899999843     3899999999987311              1123444443    45677887 445554 7888


Q ss_pred             cccCCCCcceEEecCCCCHHHHHHHHHhhcC-------------C------CCCHHHHHhCCCCCCHHHHHHHHHHHHHH
Q 030960           75 ALLRPGRLDRKIEFPLPDRRQKRLVFQMNLS-------------D------EVDLEDYVSRPDKISAAEIAAICQEAGMH  135 (168)
Q Consensus        75 al~r~grf~~~i~~~~P~~~~R~~il~~~l~-------------~------~~~~~~la~~t~g~s~~di~~l~~~a~~~  135 (168)
                      +|++  |+ .++.+.......-..|+...+.             .      +..++.++..++|=.-+-|..+=-.+.+.
T Consensus       268 aLlS--RC-~VfvLekL~~n~v~~iL~raia~l~dser~~~~l~n~s~~ve~siidyla~lsdGDaR~aLN~Lems~~m~  344 (554)
T KOG2028|consen  268 ALLS--RC-RVFVLEKLPVNAVVTILMRAIASLGDSERPTDPLPNSSMFVEDSIIDYLAYLSDGDARAALNALEMSLSMF  344 (554)
T ss_pred             HHHh--cc-ceeEeccCCHHHHHHHHHHHHHhhccccccCCCCCCcchhhhHHHHHHHHHhcCchHHHHHHHHHHHHHHH
Confidence            9998  54 3566677777777777764222             1      12356788888875555554332222333


Q ss_pred             HHHhC---CCccCHHHHHHHHHhhc
Q 030960          136 AVRKN---RYVILPKDFEKGYRTNV  157 (168)
Q Consensus       136 a~~~~---~~~i~~~d~~~al~~~~  157 (168)
                      +.+.+   +..++.+|+.+.+.+..
T Consensus       345 ~tr~g~~~~~~lSidDvke~lq~s~  369 (554)
T KOG2028|consen  345 CTRSGQSSRVLLSIDDVKEGLQRSH  369 (554)
T ss_pred             HhhcCCcccceecHHHHHHHHhhcc
Confidence            44444   35789999999987643

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.07  E-value=0.0082  Score=52.18  Aligned_cols=120  Identities=16%  Similarity=0.173  Sum_probs=78.8

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      .-|++|||+|.+..              ...+.|+..|+.  ....+++|.+|+.+..|.+.+++  |. ..++|.+++.
T Consensus       128 ~KVvIIdEad~Lt~--------------~a~naLLK~LEe--Pp~~tv~IL~t~~~~kLl~TI~S--Rc-~~vef~~l~~  188 (620)
T PRK14954        128 YRVYIIDEVHMLST--------------AAFNAFLKTLEE--PPPHAIFIFATTELHKIPATIAS--RC-QRFNFKRIPL  188 (620)
T ss_pred             CEEEEEeChhhcCH--------------HHHHHHHHHHhC--CCCCeEEEEEeCChhhhhHHHHh--hc-eEEecCCCCH
Confidence            46999999998731              235668888874  33356666666778999999887  65 5899999999


Q ss_pred             HHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHH-hCCCccCHHHHHHHH
Q 030960           94 RQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVR-KNRYVILPKDFEKGY  153 (168)
Q Consensus        94 ~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~-~~~~~i~~~d~~~al  153 (168)
                      ++-...++..+..      +..++.++..+.| +.+++.+.++.....+.. .....|+.+++.+.+
T Consensus       189 ~ei~~~L~~i~~~egi~I~~eal~~La~~s~G-dlr~al~eLeKL~~y~~~~~~~~~It~~~V~~lv  254 (620)
T PRK14954        189 DEIQSQLQMICRAEGIQIDADALQLIARKAQG-SMRDAQSILDQVIAFSVGSEAEKVIAYQGVAELL  254 (620)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCC-CHHHHHHHHHHHHHhccccccCCccCHHHHHHHH
Confidence            8887777654431      2235567777755 667777766655444321 123457776666554

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

Probab=97.07  E-value=0.0021  Score=48.79  Aligned_cols=102  Identities=20%  Similarity=0.217  Sum_probs=65.7

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC-----C-----------CCCeEEEEecCCCCCCCccc
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD-----Q-----------TVNVKVIMATNRADTLDPAL   76 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-----~-----------~~~v~vi~ttn~~~~ld~al   76 (168)
                      ...||||||++.+-.              .+-..|+..|++..     +           -++..+|++|++...|.+.+
T Consensus       101 ~~~ILFIDEIHRlnk--------------~~qe~LlpamEd~~idiiiG~g~~ar~~~~~l~~FTligATTr~g~ls~pL  166 (233)
T PF05496_consen  101 EGDILFIDEIHRLNK--------------AQQEILLPAMEDGKIDIIIGKGPNARSIRINLPPFTLIGATTRAGLLSSPL  166 (233)
T ss_dssp             TT-EEEECTCCC--H--------------HHHHHHHHHHHCSEEEEEBSSSSS-BEEEEE----EEEEEESSGCCTSHCC
T ss_pred             CCcEEEEechhhccH--------------HHHHHHHHHhccCeEEEEeccccccceeeccCCCceEeeeeccccccchhH
Confidence            468999999998831              23334566665431     1           13488999999999999999


Q ss_pred             cCCCCcceEEecCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHH
Q 030960           77 LRPGRLDRKIEFPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQE  131 (168)
Q Consensus        77 ~r~grf~~~i~~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~  131 (168)
                      +.  ||.....+..-+.++-.+|++..-.      ++....++|.++.| ||+=--++++.
T Consensus       167 rd--RFgi~~~l~~Y~~~el~~Iv~r~a~~l~i~i~~~~~~~Ia~rsrG-tPRiAnrll~r  224 (233)
T PF05496_consen  167 RD--RFGIVLRLEFYSEEELAKIVKRSARILNIEIDEDAAEEIARRSRG-TPRIANRLLRR  224 (233)
T ss_dssp             CT--TSSEEEE----THHHHHHHHHHCCHCTT-EE-HHHHHHHHHCTTT-SHHHHHHHHHH
T ss_pred             Hh--hcceecchhcCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHhcCC-ChHHHHHHHHH
Confidence            99  9999999999999999999973322      22335578888876 55544445443

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.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.03  E-value=0.0091  Score=53.63  Aligned_cols=118  Identities=17%  Similarity=0.202  Sum_probs=77.5

Q ss_pred             HHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC---------CCCCeEEEEecCCCCC----
Q 030960            5 VFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD---------QTVNVKVIMATNRADT----   71 (168)
Q Consensus         5 iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~---------~~~~v~vi~ttn~~~~----   71 (168)
                      +.+..+....+||+|||+|..-           +   .+.+.|+..++.-.         ..++.++|+|||....    
T Consensus       603 l~~~~~~~p~~VvllDeieka~-----------~---~v~~~Llq~le~g~~~d~~g~~v~~~~~i~I~Tsn~g~~~i~~  668 (821)
T CHL00095        603 LTEAVRKKPYTVVLFDEIEKAH-----------P---DIFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTSNLGSKVIET  668 (821)
T ss_pred             HHHHHHhCCCeEEEECChhhCC-----------H---HHHHHHHHHhccCceecCCCcEEecCceEEEEeCCcchHHHHh
Confidence            4555666666999999999752           1   45666776666311         1346889999996432    


Q ss_pred             ---------------------------------CCccccCCCCcceEEecCCCCHHHHHHHHHhhcCC------------
Q 030960           72 ---------------------------------LDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD------------  106 (168)
Q Consensus        72 ---------------------------------ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~~------------  106 (168)
                                                       +.|.++.  |+|.++.|.+.+.++-.+|++..+..            
T Consensus       669 ~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~f~pefln--Rid~ii~F~pL~~~~l~~Iv~~~l~~l~~rl~~~~i~l  746 (821)
T CHL00095        669 NSGGLGFELSENQLSEKQYKRLSNLVNEELKQFFRPEFLN--RLDEIIVFRQLTKNDVWEIAEIMLKNLFKRLNEQGIQL  746 (821)
T ss_pred             hccccCCcccccccccccHHHHHHHHHHHHHHhcCHHHhc--cCCeEEEeCCCCHHHHHHHHHHHHHHHHHHHHHCCcEE
Confidence                                             1244565  99999999999999999998755541            


Q ss_pred             ---CCCHHHHHhC--CCCCCHHHHHHHHHHHHHHHHH
Q 030960          107 ---EVDLEDYVSR--PDKISAAEIAAICQEAGMHAVR  138 (168)
Q Consensus       107 ---~~~~~~la~~--t~g~s~~di~~l~~~a~~~a~~  138 (168)
                         +-..+.+++.  ...|-.+-|.++++.-...++.
T Consensus       747 ~~~~~~~~~La~~~~~~~~GAR~l~r~i~~~i~~~l~  783 (821)
T CHL00095        747 EVTERIKTLLIEEGYNPLYGARPLRRAIMRLLEDPLA  783 (821)
T ss_pred             EECHHHHHHHHHhcCCCCCChhhHHHHHHHHHHHHHH
Confidence               1123445654  2456677777777765544443

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=97.02  E-value=0.0072  Score=48.49  Aligned_cols=73  Identities=14%  Similarity=0.270  Sum_probs=58.8

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCC
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLP   91 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P   91 (168)
                      ...-|++||++|.+-.              ...|.||..++  +...++++|.+|++++.|.|.+++  |. ..+.|++|
T Consensus       106 g~~KV~iI~~a~~m~~--------------~AaNaLLKtLE--EPp~~~~fiL~t~~~~~llpTI~S--RC-~~~~~~~~  166 (325)
T PRK06871        106 GGNKVVYIQGAERLTE--------------AAANALLKTLE--EPRPNTYFLLQADLSAALLPTIYS--RC-QTWLIHPP  166 (325)
T ss_pred             CCceEEEEechhhhCH--------------HHHHHHHHHhc--CCCCCeEEEEEECChHhCchHHHh--hc-eEEeCCCC
Confidence            3456899999998731              45678899998  466688999999999999999998  76 45789999


Q ss_pred             CHHHHHHHHHhh
Q 030960           92 DRRQKRLVFQMN  103 (168)
Q Consensus        92 ~~~~R~~il~~~  103 (168)
                      +.++-.+.+...
T Consensus       167 ~~~~~~~~L~~~  178 (325)
T PRK06871        167 EEQQALDWLQAQ  178 (325)
T ss_pred             CHHHHHHHHHHH
Confidence            999888887754

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

Probab=96.94  E-value=0.01  Score=48.07  Aligned_cols=126  Identities=21%  Similarity=0.283  Sum_probs=86.6

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCC------------CCCCCccccCCCC
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNR------------ADTLDPALLRPGR   81 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~------------~~~ld~al~r~gr   81 (168)
                      |.|+||||++-|=-              ..++-|-..|+  ..-.++ +|.+||+            |+-||..++.  |
T Consensus       292 pGVLFIDEvHmLDI--------------E~FsFlnrAlE--se~aPI-ii~AtNRG~~kiRGTd~~sPhGIP~DlLD--R  352 (450)
T COG1224         292 PGVLFIDEVHMLDI--------------ECFSFLNRALE--SELAPI-IILATNRGMTKIRGTDIESPHGIPLDLLD--R  352 (450)
T ss_pred             cceEEEechhhhhH--------------HHHHHHHHHhh--cccCcE-EEEEcCCceeeecccCCcCCCCCCHhhhh--h
Confidence            99999999987621              23333333343  122234 5555653            5667766665  5


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-C-----CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-D-----EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-~-----~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      . ..|...+-+.++..+|++.-.. .     +-.++.|+..-..-|-+--.+|+.-|...|-+++...+..+|+++|.+-
T Consensus       353 l-lII~t~py~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~l  431 (450)
T COG1224         353 L-LIISTRPYSREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKEL  431 (450)
T ss_pred             e-eEEecCCCCHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHHH
Confidence            3 3455567788889999984443 2     3345667777777788888888888999999999999999999999887


Q ss_pred             hcCC
Q 030960          156 NVKK  159 (168)
Q Consensus       156 ~~p~  159 (168)
                      +.-.
T Consensus       432 F~D~  435 (450)
T COG1224         432 FLDV  435 (450)
T ss_pred             HhhH
Confidence            6543

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

Probab=96.92  E-value=0.0099  Score=50.45  Aligned_cols=94  Identities=18%  Similarity=0.244  Sum_probs=66.9

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCC-CCCeEEEEecCCCCCCCc-cccCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQ-TVNVKVIMATNRADTLDP-ALLRP   79 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~-~~~v~vi~ttn~~~~ld~-al~r~   79 (168)
                      |+.+|+-|.+..-+||++|++|.|..--    .-.....+.++..++..+..... ..+.+|++||+..+-+-. .+.. 
T Consensus       587 i~k~F~DAYkS~lsiivvDdiErLiD~v----pIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~i~~-  661 (744)
T KOG0741|consen  587 IKKIFEDAYKSPLSIIVVDDIERLLDYV----PIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMGILD-  661 (744)
T ss_pred             HHHHHHHhhcCcceEEEEcchhhhhccc----ccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcCHHH-
Confidence            6899999999999999999999987321    11112334666677777776543 346888888887665554 3444 


Q ss_pred             CCcceEEecCCCCH-HHHHHHHH
Q 030960           80 GRLDRKIEFPLPDR-RQKRLVFQ  101 (168)
Q Consensus        80 grf~~~i~~~~P~~-~~R~~il~  101 (168)
                       .|+..+++|..+. ++-.+++.
T Consensus       662 -~F~~~i~Vpnl~~~~~~~~vl~  683 (744)
T KOG0741|consen  662 -CFSSTIHVPNLTTGEQLLEVLE  683 (744)
T ss_pred             -hhhheeecCccCchHHHHHHHH
Confidence             7999999998766 56666665

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=96.88  E-value=0.0038  Score=49.93  Aligned_cols=71  Identities=17%  Similarity=0.265  Sum_probs=58.9

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      ..-|++||++|.+-              ....|.||..++  +...++++|.+|++++.|.|.+++  |.. .+.|++|+
T Consensus       108 ~~kV~iI~~ae~m~--------------~~AaNaLLKtLE--EPp~~t~fiL~t~~~~~lLpTI~S--RCq-~~~~~~~~  168 (319)
T PRK06090        108 GYRLFVIEPADAMN--------------ESASNALLKTLE--EPAPNCLFLLVTHNQKRLLPTIVS--RCQ-QWVVTPPS  168 (319)
T ss_pred             CceEEEecchhhhC--------------HHHHHHHHHHhc--CCCCCeEEEEEECChhhChHHHHh--cce-eEeCCCCC
Confidence            35799999999873              155678999998  466679999999999999999999  875 78999999


Q ss_pred             HHHHHHHHHh
Q 030960           93 RRQKRLVFQM  102 (168)
Q Consensus        93 ~~~R~~il~~  102 (168)
                      .++..+.+..
T Consensus       169 ~~~~~~~L~~  178 (319)
T PRK06090        169 TAQAMQWLKG  178 (319)
T ss_pred             HHHHHHHHHH
Confidence            9998888764

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=96.85  E-value=0.0052  Score=50.85  Aligned_cols=85  Identities=26%  Similarity=0.339  Sum_probs=62.1

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC--------CCCCCeEEEEec----CCCCCCCccccCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF--------DQTVNVKVIMAT----NRADTLDPALLRPG   80 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~--------~~~~~v~vi~tt----n~~~~ld~al~r~g   80 (168)
                      +-.||||||+|.++.......  .+-....+...||..+++-        -.+.++++|++-    ..|.++=|.+..  
T Consensus       247 ~~GIVfiDEiDKIa~~~~~~~--~DvS~eGVQ~~LLkilEGt~v~~k~~~v~T~~ILFI~~GAF~~~kp~DlIPEl~G--  322 (441)
T TIGR00390       247 QSGIIFIDEIDKIAKKGESSG--ADVSREGVQRDLLPIVEGSTVNTKYGMVKTDHILFIAAGAFQLAKPSDLIPELQG--  322 (441)
T ss_pred             cCCEEEEEchhhhcccCCCCC--CCCCccchhccccccccCceeeecceeEECCceeEEecCCcCCCChhhccHHHhC--
Confidence            468999999999996652221  1222235677888888773        134568777743    357777778875  


Q ss_pred             CcceEEecCCCCHHHHHHHHH
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQ  101 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~  101 (168)
                      ||...+.+.+++.++-..||.
T Consensus       323 R~Pi~v~L~~L~~edL~rILt  343 (441)
T TIGR00390       323 RFPIRVELQALTTDDFERILT  343 (441)
T ss_pred             ccceEEECCCCCHHHHHHHhc
Confidence            999999999999999999985

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.

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=96.83  E-value=0.0067  Score=48.63  Aligned_cols=112  Identities=11%  Similarity=0.122  Sum_probs=71.9

Q ss_pred             HHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHh-----ccC----CCCCCCeEEEEecCCCC--------
Q 030960            8 LAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQ-----MDG----FDQTVNVKVIMATNRAD--------   70 (168)
Q Consensus         8 ~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~-----l~~----~~~~~~v~vi~ttn~~~--------   70 (168)
                      .|.. .++++++||+|..-           ......++.+|..     +.+    +...+...||||+|...        
T Consensus       130 ~A~~-~g~illlDEin~a~-----------p~~~~~L~~lLE~~~~l~i~~~~~~i~~hp~FrviAT~Np~g~Gd~~G~y  197 (327)
T TIGR01650       130 WALQ-HNVALCFDEYDAGR-----------PDVMFVIQRVLEAGGKLTLLDQNRVIRAHPAFRLFATANTIGLGDTTGLY  197 (327)
T ss_pred             hHHh-CCeEEEechhhccC-----------HHHHHHHHHHhccCCeEEECCCceEecCCCCeEEEEeeCCCCcCCCCcce
Confidence            3433 47999999999762           1222444445442     111    12344688999999755        


Q ss_pred             ----CCCccccCCCCcceEEecCCCCHHHHHHHHHhhcCCCC---------CHHHHHhC----------CCCCCHHHHHH
Q 030960           71 ----TLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSDEV---------DLEDYVSR----------PDKISAAEIAA  127 (168)
Q Consensus        71 ----~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~~~~---------~~~~la~~----------t~g~s~~di~~  127 (168)
                          .++.|++.  ||-.++.+++|+.++-.+|+......-.         .+-++|..          ..|+|++.+..
T Consensus       198 ~Gt~~l~~A~lD--RF~i~~~~~Yp~~e~E~~Il~~~~~~~~~~~~~~i~~~mV~la~~tR~~~~~~~i~~~~SpR~li~  275 (327)
T TIGR01650       198 HGTQQINQAQMD--RWSIVTTLNYLEHDNEAAIVLAKAKGFDDTEGKDIINAMVRVADMTRNAFINGDISTVMSPRTVIT  275 (327)
T ss_pred             eeeecCCHHHHh--heeeEeeCCCCCHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhccCCccccccHHHHHH
Confidence                45889998  9999999999999999999875432100         01112222          34678888888


Q ss_pred             HHHHHH
Q 030960          128 ICQEAG  133 (168)
Q Consensus       128 l~~~a~  133 (168)
                      ..+.+.
T Consensus       276 w~~~~~  281 (327)
T TIGR01650       276 WAENAE  281 (327)
T ss_pred             HHHHHH
Confidence            777654

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.

>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=96.82  E-value=0.024  Score=45.13  Aligned_cols=89  Identities=15%  Similarity=0.198  Sum_probs=63.8

Q ss_pred             CCCCCccccCCCCcceEEecCCCCHHHHHHHHHh-hcCCCCC-----HHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCC
Q 030960           69 ADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQM-NLSDEVD-----LEDYVSRPDKISAAEIAAICQEAGMHAVRKNRY  142 (168)
Q Consensus        69 ~~~ld~al~r~grf~~~i~~~~P~~~~R~~il~~-~l~~~~~-----~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~  142 (168)
                      |.-||-.++.  |. ..|...+-+.++-.+||+. |..+++.     ++.|......-|.+---+++..|...|.++...
T Consensus       339 phGiP~D~lD--R~-lII~t~py~~~d~~~IL~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~  415 (454)
T KOG2680|consen  339 PHGIPIDLLD--RM-LIISTQPYTEEDIKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGK  415 (454)
T ss_pred             CCCCcHHHhh--hh-heeecccCcHHHHHHHHHhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCc
Confidence            5667766665  53 3455566788888999984 4454443     333444444557777778889999999999999


Q ss_pred             ccCHHHHHHHHHhhcCCC
Q 030960          143 VILPKDFEKGYRTNVKKP  160 (168)
Q Consensus       143 ~i~~~d~~~al~~~~p~~  160 (168)
                      .+..+|+..+++-+.-..
T Consensus       416 ~v~~~di~r~y~LFlD~~  433 (454)
T KOG2680|consen  416 VVEVDDIERVYRLFLDEK  433 (454)
T ss_pred             eeehhHHHHHHHHHhhhh
Confidence            999999999998776544

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=96.76  E-value=0.0063  Score=41.05  Aligned_cols=80  Identities=30%  Similarity=0.417  Sum_probs=47.9

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCC-CCCCCccccCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNR-ADTLDPALLRPG   80 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~-~~~ld~al~r~g   80 (168)
                      ++.+++.|+...|.+|++||++.+........        .................+..+|+++|. ....+..+.+  
T Consensus        67 ~~~~~~~~~~~~~~viiiDei~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~--  136 (148)
T smart00382       67 LRLALALARKLKPDVLILDEITSLLDAEQEAL--------LLLLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR--  136 (148)
T ss_pred             HHHHHHHHHhcCCCEEEEECCcccCCHHHHHH--------HHhhhhhHHHHHHHhcCCCEEEEEeCCCccCchhhhhh--
Confidence            35678888888889999999999864331100        000000000111123446778888886 4555555655  


Q ss_pred             CcceEEecCCC
Q 030960           81 RLDRKIEFPLP   91 (168)
Q Consensus        81 rf~~~i~~~~P   91 (168)
                      |++..+.++.+
T Consensus       137 ~~~~~~~~~~~  147 (148)
T smart00382      137 RFDRRIVLLLI  147 (148)
T ss_pred             ccceEEEecCC
Confidence            89999888665

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.

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=96.75  E-value=0.016  Score=45.82  Aligned_cols=94  Identities=13%  Similarity=0.264  Sum_probs=61.8

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      .-|++||++|.+..              ...|.||..++  +...++++|.+|++++.|.|.+++  |. ..+.|+. +.
T Consensus       105 ~kV~II~~ad~m~~--------------~AaNaLLKtLE--EPp~~t~~iL~t~~~~~lLpTI~S--Rc-q~i~f~~-~~  164 (290)
T PRK07276        105 QQVFIIKDADKMHV--------------NAANSLLKVIE--EPQSEIYIFLLTNDENKVLPTIKS--RT-QIFHFPK-NE  164 (290)
T ss_pred             cEEEEeehhhhcCH--------------HHHHHHHHHhc--CCCCCeEEEEEECChhhCchHHHH--cc-eeeeCCC-cH
Confidence            57999999998741              45677888888  455678899999999999999999  86 4566655 55


Q ss_pred             HHHHHHHHhhcCCCCCHHHHHhCCCCCCHHHHHHHH
Q 030960           94 RQKRLVFQMNLSDEVDLEDYVSRPDKISAAEIAAIC  129 (168)
Q Consensus        94 ~~R~~il~~~l~~~~~~~~la~~t~g~s~~di~~l~  129 (168)
                      ++-.+++... +-+.+...++....| +++....+.
T Consensus       165 ~~~~~~L~~~-g~~~~~a~~la~~~~-s~~~A~~l~  198 (290)
T PRK07276        165 AYLIQLLEQK-GLLKTQAELLAKLAQ-STSEAEKLA  198 (290)
T ss_pred             HHHHHHHHHc-CCChHHHHHHHHHCC-CHHHHHHHh
Confidence            5555555422 111122233334445 566555555

>PRK09862 putative ATP-dependent protease; Provisional

Probab=96.70  E-value=0.051  Score=46.21  Aligned_cols=125  Identities=19%  Similarity=0.237  Sum_probs=81.2

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC-------C----CCCCCeEEEEecCCCC------------
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG-------F----DQTVNVKVIMATNRAD------------   70 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~-------~----~~~~~v~vi~ttn~~~------------   70 (168)
                      ..++|+||++.+-.              .+...+++.|+.       .    ....++.+|+|+|-..            
T Consensus       295 gGvLfLDEi~e~~~--------------~~~~~L~~~LE~g~v~I~r~g~~~~~pa~f~lIAa~NP~pcG~~~~~~c~c~  360 (506)
T PRK09862        295 NGVLFLDELPEFER--------------RTLDALREPIESGQIHLSRTRAKITYPARFQLVAAMNPSPTGHYQGNHNRCT  360 (506)
T ss_pred             CCEEecCCchhCCH--------------HHHHHHHHHHHcCcEEEecCCcceeccCCEEEEEeecCccceecCCCCCCcC
Confidence            47999999986521              344444444421       1    1133588999998742            


Q ss_pred             ---------CCCccccCCCCcceEEecCCCCHHH----------HHHHHH-------------hhcCCCCCHHHH-----
Q 030960           71 ---------TLDPALLRPGRLDRKIEFPLPDRRQ----------KRLVFQ-------------MNLSDEVDLEDY-----  113 (168)
Q Consensus        71 ---------~ld~al~r~grf~~~i~~~~P~~~~----------R~~il~-------------~~l~~~~~~~~l-----  113 (168)
                               .++..++.  |||..+.++.|+.++          +.++-+             ..+.....-..+     
T Consensus       361 ~~~~~~Y~~~ls~plLD--RfdL~v~v~~~~~~~l~~~~~~~ess~~i~~rV~~ar~~q~~r~~~~n~~l~~~~l~~~~~  438 (506)
T PRK09862        361 PEQTLRYLNRLSGPFLD--RFDLSLEIPLPPPGILSKTVVPGESSATVKQRVMAARERQFKRQNKLNAWLDSPEIRQFCK  438 (506)
T ss_pred             HHHHHHHHhhCCHhHHh--hccEEEEeCCCCHHHHhcccCCCCChHHHHHHHhhHHHHHHHHHHHHhcccCHHHHHHHhC
Confidence                     46778888  999999999885321          111211             011111111111     


Q ss_pred             -----------HhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960          114 -----------VSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus       114 -----------a~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                                 +...-|+|++....+++-|...|.-++...|+.+|+.+|+.
T Consensus       439 l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~  490 (506)
T PRK09862        439 LESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVS  490 (506)
T ss_pred             CCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence                       11234789999999999999999999999999999999986

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=96.62  E-value=0.014  Score=46.82  Aligned_cols=70  Identities=17%  Similarity=0.239  Sum_probs=54.8

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      .-|++|||+|.+-              ....+.|+..++.  ..+++++|.+|+.+..|.+.+++  |. ..++|.+|+.
T Consensus       111 ~kvviI~~a~~~~--------------~~a~NaLLK~LEE--Pp~~~~~Il~t~~~~~ll~TIrS--Rc-~~i~~~~~~~  171 (329)
T PRK08058        111 KKVYIIEHADKMT--------------ASAANSLLKFLEE--PSGGTTAILLTENKHQILPTILS--RC-QVVEFRPLPP  171 (329)
T ss_pred             ceEEEeehHhhhC--------------HHHHHHHHHHhcC--CCCCceEEEEeCChHhCcHHHHh--hc-eeeeCCCCCH
Confidence            4599999998773              1455678888884  45577777888899999999998  65 5788999999


Q ss_pred             HHHHHHHHh
Q 030960           94 RQKRLVFQM  102 (168)
Q Consensus        94 ~~R~~il~~  102 (168)
                      ++-.+.++.
T Consensus       172 ~~~~~~L~~  180 (329)
T PRK08058        172 ESLIQRLQE  180 (329)
T ss_pred             HHHHHHHHH
Confidence            888777764

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

Probab=96.55  E-value=0.0082  Score=53.12  Aligned_cols=88  Identities=22%  Similarity=0.329  Sum_probs=63.3

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC-----CCCccc
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD-----TLDPAL   76 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~-----~ld~al   76 (168)
                      ++.+.+..+...+.|+||||++.+.+..+..+.  .....+++.-.   +    ....+-+||+|+.-+     .=|+||
T Consensus       251 lk~vl~ev~~~~~vILFIDEiHtiVGAG~~~G~--a~DAaNiLKPa---L----ARGeL~~IGATT~~EYRk~iEKD~AL  321 (786)
T COG0542         251 LKAVLKEVEKSKNVILFIDEIHTIVGAGATEGG--AMDAANLLKPA---L----ARGELRCIGATTLDEYRKYIEKDAAL  321 (786)
T ss_pred             HHHHHHHHhcCCCeEEEEechhhhcCCCccccc--ccchhhhhHHH---H----hcCCeEEEEeccHHHHHHHhhhchHH
Confidence            567778888888999999999999977644331  11112333322   2    244566888887544     458899


Q ss_pred             cCCCCcceEEecCCCCHHHHHHHHH
Q 030960           77 LRPGRLDRKIEFPLPDRRQKRLVFQ  101 (168)
Q Consensus        77 ~r~grf~~~i~~~~P~~~~R~~il~  101 (168)
                      -|  ||. .|.+..|+.++-..|++
T Consensus       322 ~R--RFQ-~V~V~EPs~e~ti~ILr  343 (786)
T COG0542         322 ER--RFQ-KVLVDEPSVEDTIAILR  343 (786)
T ss_pred             Hh--cCc-eeeCCCCCHHHHHHHHH
Confidence            99  996 58899999999999997

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=96.54  E-value=0.012  Score=46.89  Aligned_cols=88  Identities=9%  Similarity=0.166  Sum_probs=62.9

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      +.-|++||++|.+-              ....+.++..++.  ..+++++|.+|++++.+.+.+++  |. ..++|++|+
T Consensus        93 ~~kv~iI~~ad~m~--------------~~a~naLLK~LEe--pp~~t~~il~~~~~~~ll~TI~S--Rc-~~~~~~~~~  153 (313)
T PRK05564         93 DKKVIIIYNSEKMT--------------EQAQNAFLKTIEE--PPKGVFIILLCENLEQILDTIKS--RC-QIYKLNRLS  153 (313)
T ss_pred             CceEEEEechhhcC--------------HHHHHHHHHHhcC--CCCCeEEEEEeCChHhCcHHHHh--hc-eeeeCCCcC
Confidence            35699999998762              1345678888884  44567777777889999999998  77 489999999


Q ss_pred             HHHHHHHHHhhcC--CCCCHHHHHhCCCC
Q 030960           93 RRQKRLVFQMNLS--DEVDLEDYVSRPDK  119 (168)
Q Consensus        93 ~~~R~~il~~~l~--~~~~~~~la~~t~g  119 (168)
                      .++-...++..+.  +...+..++..+.|
T Consensus       154 ~~~~~~~l~~~~~~~~~~~~~~l~~~~~g  182 (313)
T PRK05564        154 KEEIEKFISYKYNDIKEEEKKSAIAFSDG  182 (313)
T ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHcCC
Confidence            9998888875542  12223445555555

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=96.44  E-value=0.038  Score=44.15  Aligned_cols=97  Identities=14%  Similarity=0.224  Sum_probs=68.0

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      ..-|++||++|.+-.              ...+.||..|+...   +.++|.+|++++.|.|.+++  |. ..+.|++|+
T Consensus       124 ~~kVvII~~ae~m~~--------------~aaNaLLK~LEEPp---~~~fILi~~~~~~Ll~TI~S--Rc-q~i~f~~l~  183 (314)
T PRK07399        124 PRKVVVIEDAETMNE--------------AAANALLKTLEEPG---NGTLILIAPSPESLLPTIVS--RC-QIIPFYRLS  183 (314)
T ss_pred             CceEEEEEchhhcCH--------------HHHHHHHHHHhCCC---CCeEEEEECChHhCcHHHHh--hc-eEEecCCCC
Confidence            468999999987731              45567888887533   44567777899999999999  86 688999999


Q ss_pred             HHHHHHHHHhhcC-CCCC--HHHHHhCCCCCCHHHHHHHHH
Q 030960           93 RRQKRLVFQMNLS-DEVD--LEDYVSRPDKISAAEIAAICQ  130 (168)
Q Consensus        93 ~~~R~~il~~~l~-~~~~--~~~la~~t~g~s~~di~~l~~  130 (168)
                      .++-.+++..... +..+  ...++....| +++...++++
T Consensus       184 ~~~~~~~L~~~~~~~~~~~~~~~l~~~a~G-s~~~al~~l~  223 (314)
T PRK07399        184 DEQLEQVLKRLGDEEILNINFPELLALAQG-SPGAAIANIE  223 (314)
T ss_pred             HHHHHHHHHHhhccccchhHHHHHHHHcCC-CHHHHHHHHH
Confidence            9999999986543 2222  3566666655 4434333333

>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=96.35  E-value=0.0048  Score=46.00  Aligned_cols=92  Identities=21%  Similarity=0.348  Sum_probs=49.5

Q ss_pred             HHHHHHHHHHcC-CeEEEEccccccc-ccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC------CCC
Q 030960            2 VRDVFRLAKENA-PAIIFIDEVDAIA-TARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD------TLD   73 (168)
Q Consensus         2 l~~iF~~a~~~~-p~ii~iDe~D~l~-~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~------~ld   73 (168)
                      +..+++...... ..||+|||+|.+. ..+      ..   ...+..+.+.++......++.+|.+++...      .-.
T Consensus       106 l~~~~~~l~~~~~~~iiviDe~~~~~~~~~------~~---~~~~~~l~~~~~~~~~~~~~~~v~~~S~~~~~~~~~~~~  176 (234)
T PF01637_consen  106 LERLLEKLKKKGKKVIIVIDEFQYLAIASE------ED---KDFLKSLRSLLDSLLSQQNVSIVITGSSDSLMEEFLDDK  176 (234)
T ss_dssp             HHHHHHHHHHCHCCEEEEEETGGGGGBCTT------TT---HHHHHHHHHHHHH----TTEEEEEEESSHHHHHHTT-TT
T ss_pred             HHHHHHHHHhcCCcEEEEEecHHHHhhccc------ch---HHHHHHHHHHHhhccccCCceEEEECCchHHHHHhhccc
Confidence            456666666554 5999999999997 111      11   255556666666544445554444443321      122


Q ss_pred             ccccCCCCcceEEecCCCCHHHHHHHHHhhcC
Q 030960           74 PALLRPGRLDRKIEFPLPDRRQKRLVFQMNLS  105 (168)
Q Consensus        74 ~al~r~grf~~~i~~~~P~~~~R~~il~~~l~  105 (168)
                      ..+.  ||+.. +++++.+.++-.++++..+.
T Consensus       177 ~~~~--~~~~~-~~l~~l~~~e~~~~~~~~~~  205 (234)
T PF01637_consen  177 SPLF--GRFSH-IELKPLSKEEAREFLKELFK  205 (234)
T ss_dssp             STTT--T---E-EEE----HHHHHHHHHHHHH
T ss_pred             Cccc--cccce-EEEeeCCHHHHHHHHHHHHH
Confidence            2333  38888 99999999999999987643

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

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

Probab=96.28  E-value=0.028  Score=49.84  Aligned_cols=116  Identities=16%  Similarity=0.265  Sum_probs=79.1

Q ss_pred             HHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC--C-------CCCCeEEEEecCCCCC------
Q 030960            7 RLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF--D-------QTVNVKVIMATNRADT------   71 (168)
Q Consensus         7 ~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~--~-------~~~~v~vi~ttn~~~~------   71 (168)
                      +..++...|||+|||+|.-           ++   .+++.||.-+|.=  .       .-++.++|+|||--..      
T Consensus       587 EaVRr~PySViLlDEIEKA-----------Hp---dV~nilLQVlDdGrLTD~~Gr~VdFrNtiIImTSN~Gs~~i~~~~  652 (786)
T COG0542         587 EAVRRKPYSVILLDEIEKA-----------HP---DVFNLLLQVLDDGRLTDGQGRTVDFRNTIIIMTSNAGSEEILRDA  652 (786)
T ss_pred             HhhhcCCCeEEEechhhhc-----------CH---HHHHHHHHHhcCCeeecCCCCEEecceeEEEEecccchHHHHhhc
Confidence            4556677899999999953           22   7888888888742  1       1235899999986422      


Q ss_pred             ----------------------CCccccCCCCcceEEecCCCCHHHHHHHHHhhcCC---------------CCCHHHHH
Q 030960           72 ----------------------LDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD---------------EVDLEDYV  114 (168)
Q Consensus        72 ----------------------ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~~---------------~~~~~~la  114 (168)
                                            ..|+++.  |+|.+|.|.+.+.+.-.+|+...+..               +.-.+.++
T Consensus       653 ~~~~~~~~~~~~~~v~~~l~~~F~PEFLN--Rid~II~F~~L~~~~l~~Iv~~~L~~l~~~L~~~~i~l~~s~~a~~~l~  730 (786)
T COG0542         653 DGDDFADKEALKEAVMEELKKHFRPEFLN--RIDEIIPFNPLSKEVLERIVDLQLNRLAKRLAERGITLELSDEAKDFLA  730 (786)
T ss_pred             cccccchhhhHHHHHHHHHHhhCCHHHHh--hcccEEeccCCCHHHHHHHHHHHHHHHHHHHHhCCceEEECHHHHHHHH
Confidence                                  2344555  99999999999999999999855541               11233455


Q ss_pred             hCC--CCCCHHHHHHHHHHHHHHHHH
Q 030960          115 SRP--DKISAAEIAAICQEAGMHAVR  138 (168)
Q Consensus       115 ~~t--~g~s~~di~~l~~~a~~~a~~  138 (168)
                      +..  +.|-.+-|.+++++-....+.
T Consensus       731 ~~gyd~~~GARpL~R~Iq~~i~~~La  756 (786)
T COG0542         731 EKGYDPEYGARPLRRAIQQEIEDPLA  756 (786)
T ss_pred             HhccCCCcCchHHHHHHHHHHHHHHH
Confidence            543  457778888777766544443

>TIGR00368 Mg chelatase-related protein

Probab=96.23  E-value=0.14  Score=43.61  Aligned_cols=37  Identities=16%  Similarity=0.026  Sum_probs=32.9

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960          118 DKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus       118 ~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      -++|.+-...+++-|...|--++...++.+|+.+|+.
T Consensus       461 ~~lS~R~~~rilrvArTiAdL~g~~~i~~~hv~eA~~  497 (499)
T TIGR00368       461 LGLSSRATHRILKVARTIADLKEEKNISREHLAEAIE  497 (499)
T ss_pred             cCCCchHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHh
Confidence            3689999999999998888888899999999999985

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>PRK13531 regulatory ATPase RavA; Provisional

Probab=96.23  E-value=0.045  Score=46.20  Aligned_cols=125  Identities=17%  Similarity=0.160  Sum_probs=80.4

Q ss_pred             eEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC-C-------CCCCCeEEEEecCCCCCCCc------cccCCC
Q 030960           15 AIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG-F-------DQTVNVKVIMATNRADTLDP------ALLRPG   80 (168)
Q Consensus        15 ~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~-~-------~~~~~v~vi~ttn~~~~ld~------al~r~g   80 (168)
                      .++|+||+...-              ..+.+.|+..|+. .       .+-+..+++++||   .+|.      ++..  
T Consensus       109 ~lLfLDEI~ras--------------p~~QsaLLeam~Er~~t~g~~~~~lp~rfiv~ATN---~LPE~g~~leAL~D--  169 (498)
T PRK13531        109 EIVFLDEIWKAG--------------PAILNTLLTAINERRFRNGAHEEKIPMRLLVTASN---ELPEADSSLEALYD--  169 (498)
T ss_pred             cEEeecccccCC--------------HHHHHHHHHHHHhCeEecCCeEEeCCCcEEEEECC---CCcccCCchHHhHh--
Confidence            489999996331              1556667777732 1       1112245556666   3554      8888  


Q ss_pred             CcceEEecCCCC-HHHHHHHHHhhcC-------C--CCC-----------------------HHHHHh---CC---CCCC
Q 030960           81 RLDRKIEFPLPD-RRQKRLVFQMNLS-------D--EVD-----------------------LEDYVS---RP---DKIS  121 (168)
Q Consensus        81 rf~~~i~~~~P~-~~~R~~il~~~l~-------~--~~~-----------------------~~~la~---~t---~g~s  121 (168)
                      ||-..+.+|+|+ .++-.+|+.....       .  -+.                       +-.+..   .+   ...|
T Consensus       170 RFliri~vp~l~~~~~e~~lL~~~~~~~~~~~~~~~vis~eel~~lq~~v~~V~v~d~v~eyI~~L~~~lr~~r~~~~~S  249 (498)
T PRK13531        170 RMLIRLWLDKVQDKANFRSMLTSQQDENDNPVPASLQITDEEYQQWQKEIGKITLPDHVFELIFQLRQQLDALPNAPYVS  249 (498)
T ss_pred             hEEEEEECCCCCchHHHHHHHHcccccccCCCcccCCCCHHHHHHHHHHhcceeCCHHHHHHHHHHHHHHhcCCCCCCcC
Confidence            998899999997 4665777753211       0  011                       112332   12   2378


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhcCC
Q 030960          122 AAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKK  159 (168)
Q Consensus       122 ~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~p~  159 (168)
                      ++--..+++-+...|+-.++..++.+|+. .+....+.
T Consensus       250 pR~~~~l~~~akA~A~l~GR~~V~p~Dv~-ll~~vL~H  286 (498)
T PRK13531        250 DRRWKKAIRLLQASAFFSGRDAIAPIDLI-LLKDCLWH  286 (498)
T ss_pred             cHHHHHHHHHHHHHHHHCCCCCCCHHHHH-HhHHHhcc
Confidence            88888999988899999999999999999 66555443

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

Probab=96.17  E-value=0.1  Score=40.40  Aligned_cols=130  Identities=18%  Similarity=0.214  Sum_probs=85.0

Q ss_pred             HHHHHHHcC-CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCC---
Q 030960            5 VFRLAKENA-PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPG---   80 (168)
Q Consensus         5 iF~~a~~~~-p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~g---   80 (168)
                      +.+..++.+ |.++++||++.+....        -   ..+.-|.+.-.+..+.-++++||-..    |.+.++.|.   
T Consensus       122 L~al~~~g~r~v~l~vdEah~L~~~~--------l---e~Lrll~nl~~~~~~~l~ivL~Gqp~----L~~~lr~~~l~e  186 (269)
T COG3267         122 LAALVKKGKRPVVLMVDEAHDLNDSA--------L---EALRLLTNLEEDSSKLLSIVLIGQPK----LRPRLRLPVLRE  186 (269)
T ss_pred             HHHHHHhCCCCeEEeehhHhhhChhH--------H---HHHHHHHhhcccccCceeeeecCCcc----cchhhchHHHHh
Confidence            334444444 7999999999885221        1   22222322222222222466666422    333333222   


Q ss_pred             ---CcceEEecCCCCHHHHHHHHHhhcC---------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHH
Q 030960           81 ---RLDRKIEFPLPDRRQKRLVFQMNLS---------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKD  148 (168)
Q Consensus        81 ---rf~~~i~~~~P~~~~R~~il~~~l~---------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d  148 (168)
                         |++..|++++.+.++-..++++.+.         .+..+..+...+.| .|+-|.++|..|...|...+++.|+...
T Consensus       187 ~~~R~~ir~~l~P~~~~~t~~yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg-~P~lin~~~~~Al~~a~~a~~~~v~~a~  265 (269)
T COG3267         187 LEQRIDIRIELPPLTEAETGLYLRHRLEGAGLPEPLFSDDALLLIHEASQG-IPRLINNLATLALDAAYSAGEDGVSEAE  265 (269)
T ss_pred             hhheEEEEEecCCcChHHHHHHHHHHHhccCCCcccCChhHHHHHHHHhcc-chHHHHHHHHHHHHHHHHcCCCccchhh
Confidence               7888899999999988888887666         23456678888888 8999999999999999999988888766


Q ss_pred             HH
Q 030960          149 FE  150 (168)
Q Consensus       149 ~~  150 (168)
                      ..
T Consensus       266 ~~  267 (269)
T COG3267         266 IK  267 (269)
T ss_pred             cc
Confidence            54

>PRK10865 protein disaggregation chaperone; Provisional

Probab=96.14  E-value=0.051  Score=49.17  Aligned_cols=80  Identities=23%  Similarity=0.365  Sum_probs=55.0

Q ss_pred             HHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC--C-------CCCCeEEEEecCCCC----------
Q 030960           10 KENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF--D-------QTVNVKVIMATNRAD----------   70 (168)
Q Consensus        10 ~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~--~-------~~~~v~vi~ttn~~~----------   70 (168)
                      +....+||+|||+|.+-           .   .+.+.|+..++.-  .       ...+.++|+|||...          
T Consensus       667 ~~~p~~vLllDEieka~-----------~---~v~~~Ll~ile~g~l~d~~gr~vd~rn~iiI~TSN~g~~~~~~~~~~~  732 (857)
T PRK10865        667 RRRPYSVILLDEVEKAH-----------P---DVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNLGSDLIQERFGEL  732 (857)
T ss_pred             HhCCCCeEEEeehhhCC-----------H---HHHHHHHHHHhhCceecCCceEEeecccEEEEeCCcchHHHHHhcccc
Confidence            33344999999998652           1   3445555555421  1       123567899999731          


Q ss_pred             ---------------CCCccccCCCCcceEEecCCCCHHHHHHHHHhhcC
Q 030960           71 ---------------TLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLS  105 (168)
Q Consensus        71 ---------------~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~  105 (168)
                                     .+.|+++.  |+|..+.|.+++.+...+|++.++.
T Consensus       733 ~~~~~~~~~~~~~~~~f~PELln--Rld~iivF~PL~~edl~~Iv~~~L~  780 (857)
T PRK10865        733 DYAHMKELVLGVVSHNFRPEFIN--RIDEVVVFHPLGEQHIASIAQIQLQ  780 (857)
T ss_pred             chHHHHHHHHHHHcccccHHHHH--hCCeeEecCCCCHHHHHHHHHHHHH
Confidence                           24467777  9999999999999999999886554

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

Probab=96.01  E-value=0.025  Score=44.90  Aligned_cols=87  Identities=18%  Similarity=0.190  Sum_probs=55.6

Q ss_pred             eEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCHH
Q 030960           15 AIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRR   94 (168)
Q Consensus        15 ~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~~   94 (168)
                      -||+|||+|++..              ..-+.|..-|+.  ....+.+|..||+++.|+.-+.+  |..+--.=++++..
T Consensus       131 KiiIlDEcdsmts--------------daq~aLrr~mE~--~s~~trFiLIcnylsrii~pi~S--RC~KfrFk~L~d~~  192 (346)
T KOG0989|consen  131 KIIILDECDSMTS--------------DAQAALRRTMED--FSRTTRFILICNYLSRIIRPLVS--RCQKFRFKKLKDED  192 (346)
T ss_pred             eEEEEechhhhhH--------------HHHHHHHHHHhc--cccceEEEEEcCChhhCChHHHh--hHHHhcCCCcchHH
Confidence            7999999999852              223445566664  34467888899999999999999  87654433444444


Q ss_pred             HHHHHHHhhcCCCC-----CHHHHHhCCCC
Q 030960           95 QKRLVFQMNLSDEV-----DLEDYVSRPDK  119 (168)
Q Consensus        95 ~R~~il~~~l~~~~-----~~~~la~~t~g  119 (168)
                      .-..+-..+-.+.+     .++.+++.++|
T Consensus       193 iv~rL~~Ia~~E~v~~d~~al~~I~~~S~G  222 (346)
T KOG0989|consen  193 IVDRLEKIASKEGVDIDDDALKLIAKISDG  222 (346)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHcCC
Confidence            43333333433333     34556776554

>PRK06581 DNA polymerase III subunit delta'; Validated

Probab=96.01  E-value=0.048  Score=42.07  Aligned_cols=76  Identities=13%  Similarity=0.137  Sum_probs=59.8

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCC
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLP   91 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P   91 (168)
                      ...-|++|+++|.+-.              ...+.+|..++  +...++++|..|+++..+.|.+++  |+ ..+.++.|
T Consensus        88 g~~KViII~~ae~mt~--------------~AANALLKtLE--EPP~~t~fILit~~~~~LLpTIrS--RC-q~i~~~~p  148 (263)
T PRK06581         88 SGYKVAIIYSAELMNL--------------NAANSCLKILE--DAPKNSYIFLITSRAASIISTIRS--RC-FKINVRSS  148 (263)
T ss_pred             CCcEEEEEechHHhCH--------------HHHHHHHHhhc--CCCCCeEEEEEeCChhhCchhHhh--ce-EEEeCCCC
Confidence            3467999999998742              45678888888  456678888889999999999998  76 46778999


Q ss_pred             CHHHHHHHHHhhcCC
Q 030960           92 DRRQKRLVFQMNLSD  106 (168)
Q Consensus        92 ~~~~R~~il~~~l~~  106 (168)
                      +...-.+.+...+.+
T Consensus       149 ~~~~~~e~~~~~~~p  163 (263)
T PRK06581        149 ILHAYNELYSQFIQP  163 (263)
T ss_pred             CHHHHHHHHHHhccc
Confidence            888777777765553

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

Probab=95.94  E-value=0.015  Score=41.88  Aligned_cols=52  Identities=25%  Similarity=0.403  Sum_probs=40.9

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCc
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRL   82 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf   82 (168)
                      ..-|++|||+|.+-              ....+.||..|+  +...++.+|.+|++++.|.+.+++  |.
T Consensus       102 ~~KviiI~~ad~l~--------------~~a~NaLLK~LE--epp~~~~fiL~t~~~~~il~TI~S--Rc  153 (162)
T PF13177_consen  102 KYKVIIIDEADKLT--------------EEAQNALLKTLE--EPPENTYFILITNNPSKILPTIRS--RC  153 (162)
T ss_dssp             SSEEEEEETGGGS---------------HHHHHHHHHHHH--STTTTEEEEEEES-GGGS-HHHHT--TS
T ss_pred             CceEEEeehHhhhh--------------HHHHHHHHHHhc--CCCCCEEEEEEECChHHChHHHHh--hc
Confidence            46799999999874              256678899998  455689999999999999999999  75

...

>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]

Probab=95.92  E-value=0.014  Score=50.95  Aligned_cols=87  Identities=18%  Similarity=0.332  Sum_probs=61.0

Q ss_pred             CCCccccCCCCcceEEec--CCC-CHHHHHHHHHhhcC--------CCCCHH---H---HHhCCCC------CCHHHHHH
Q 030960           71 TLDPALLRPGRLDRKIEF--PLP-DRRQKRLVFQMNLS--------DEVDLE---D---YVSRPDK------ISAAEIAA  127 (168)
Q Consensus        71 ~ld~al~r~grf~~~i~~--~~P-~~~~R~~il~~~l~--------~~~~~~---~---la~~t~g------~s~~di~~  127 (168)
                      ..++.++.  -|+...++  +.| +.+.|.++|+.+..        +.++.+   +   .|.+..|      .+++||.+
T Consensus       293 ~~~~~r~~--g~~y~ae~~~~m~~~~~nr~k~~~~~~q~v~~d~~ip~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~  370 (647)
T COG1067         293 EPDRSRIE--GFGYEAEFEDTMPITDANRSKLVQFYVQELARDGNIPHLDKDAVEELIREAARRAGDQNKLTLRLRDLGN  370 (647)
T ss_pred             ccCHHHHh--hcceEEEEcCCCCCChHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhccccceeccCHHHHHH
Confidence            34444444  46666666  566 77899999885544        122222   1   2222222      68999999


Q ss_pred             HHHHHHHHHHHhCCCccCHHHHHHHHHhhcCC
Q 030960          128 ICQEAGMHAVRKNRYVILPKDFEKGYRTNVKK  159 (168)
Q Consensus       128 l~~~a~~~a~~~~~~~i~~~d~~~al~~~~p~  159 (168)
                      +++.|...|...+...|+.+|+++|++...+.
T Consensus       371 lv~~A~~ia~~~~~~~I~ae~Ve~a~~~~~~~  402 (647)
T COG1067         371 LVREAGDIAVSEGRKLITAEDVEEALQKRELR  402 (647)
T ss_pred             HHHHhhHHHhcCCcccCcHHHHHHHHHhhhhH
Confidence            99999999999999999999999999986553

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

Probab=95.65  E-value=0.042  Score=43.33  Aligned_cols=70  Identities=23%  Similarity=0.416  Sum_probs=52.5

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      ..-||+|||+|.+..              ...+.++..++  ....+..+|.+||+++.+-+.+++  |. ..+.|++|+
T Consensus       109 ~~kviiidead~mt~--------------~A~nallk~lE--ep~~~~~~il~~n~~~~il~tI~S--Rc-~~i~f~~~~  169 (325)
T COG0470         109 GYKVVIIDEADKLTE--------------DAANALLKTLE--EPPKNTRFILITNDPSKILPTIRS--RC-QRIRFKPPS  169 (325)
T ss_pred             CceEEEeCcHHHHhH--------------HHHHHHHHHhc--cCCCCeEEEEEcCChhhccchhhh--cc-eeeecCCch
Confidence            368999999998853              34556777776  456678899999999999999998  65 467777766


Q ss_pred             HHHHHHHHH
Q 030960           93 RRQKRLVFQ  101 (168)
Q Consensus        93 ~~~R~~il~  101 (168)
                      ...+....+
T Consensus       170 ~~~~i~~~e  178 (325)
T COG0470         170 RLEAIAWLE  178 (325)
T ss_pred             HHHHHHHhh
Confidence            666665555

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

Probab=95.62  E-value=0.072  Score=44.62  Aligned_cols=133  Identities=18%  Similarity=0.164  Sum_probs=85.6

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccC----CCCcceEEecC
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLR----PGRLDRKIEFP   89 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r----~grf~~~i~~~   89 (168)
                      +-++++||.|.|+..+.           .++- -+-++.. ..+.++++||.+|..+-=|..|-|    -+.-...+.|+
T Consensus       257 ~~llVlDEmD~L~tr~~-----------~vLy-~lFewp~-lp~sr~iLiGiANslDlTdR~LprL~~~~~~~P~~l~F~  323 (529)
T KOG2227|consen  257 MLLLVLDEMDHLITRSQ-----------TVLY-TLFEWPK-LPNSRIILIGIANSLDLTDRFLPRLNLDLTIKPKLLVFP  323 (529)
T ss_pred             eEEEEechhhHHhhccc-----------ceee-eehhccc-CCcceeeeeeehhhhhHHHHHhhhhhhccCCCCceeeec
Confidence            88999999999983221           1111 2223333 244588999999998876665542    23345688999


Q ss_pred             CCCHHHHHHHHHhhcCC-------CCCHHHHHhCCCCCCHHHHHH---HHHHHHHHHHHhC----------------CCc
Q 030960           90 LPDRRQKRLVFQMNLSD-------EVDLEDYVSRPDKISAAEIAA---ICQEAGMHAVRKN----------------RYV  143 (168)
Q Consensus        90 ~P~~~~R~~il~~~l~~-------~~~~~~la~~t~g~s~~di~~---l~~~a~~~a~~~~----------------~~~  143 (168)
                      +-+.++..+|++.-+..       +..+.-.|....|.|| |+..   +|+.|...+-.+.                +..
T Consensus       324 PYTk~qI~~Il~~rl~~~~t~~~~~~Aie~~ArKvaa~SG-DlRkaLdv~R~aiEI~E~e~r~~~~~~l~~~~~p~~~~~  402 (529)
T KOG2227|consen  324 PYTKDQIVEILQQRLSEESTSIFLNAAIELCARKVAAPSG-DLRKALDVCRRAIEIAEIEKRKILDDPLSPGTSPEKKKK  402 (529)
T ss_pred             CCCHHHHHHHHHHHHhcccccccchHHHHHHHHHhccCch-hHHHHHHHHHHHHHHHHHHHhhccccCCCCCCCcccccc
Confidence            99999999999976652       1234456777778776 4544   5565554443332                134


Q ss_pred             cCHHHHHHHHHhhcCCC
Q 030960          144 ILPKDFEKGYRTNVKKP  160 (168)
Q Consensus       144 i~~~d~~~al~~~~p~~  160 (168)
                      |.-+++..++..+..++
T Consensus       403 v~~~~va~viSk~~~s~  419 (529)
T KOG2227|consen  403 VGVEHVAAVISKVDGSP  419 (529)
T ss_pred             cchHHHHHHhhhhccCh
Confidence            55778888887766544

>PF05729 NACHT: NACHT domain

Probab=95.60  E-value=0.06  Score=37.84  Aligned_cols=87  Identities=18%  Similarity=0.244  Sum_probs=48.1

Q ss_pred             HHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecC--CCCCCCccccCCCCcceE
Q 030960            8 LAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATN--RADTLDPALLRPGRLDRK   85 (168)
Q Consensus         8 ~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn--~~~~ld~al~r~grf~~~   85 (168)
                      .+....+.+|+||.+|.+......      .........+...+.. ...+++-++.|++  ....+...+..    ...
T Consensus        76 ~~~~~~~~llilDglDE~~~~~~~------~~~~~~~~~l~~l~~~-~~~~~~~liit~r~~~~~~~~~~~~~----~~~  144 (166)
T PF05729_consen   76 LLEKNKRVLLILDGLDELEEQDQS------QERQRLLDLLSQLLPQ-ALPPGVKLIITSRPRAFPDLRRRLKQ----AQI  144 (166)
T ss_pred             HHHcCCceEEEEechHhcccchhh------hHHHHHHHHHHHHhhh-ccCCCCeEEEEEcCChHHHHHHhcCC----CcE
Confidence            345667899999999999754321      0111222222223332 1122333333333  22223333332    167


Q ss_pred             EecCCCCHHHHHHHHHhhcC
Q 030960           86 IEFPLPDRRQKRLVFQMNLS  105 (168)
Q Consensus        86 i~~~~P~~~~R~~il~~~l~  105 (168)
                      +.+.+.+.+++.++++.++.
T Consensus       145 ~~l~~~~~~~~~~~~~~~f~  164 (166)
T PF05729_consen  145 LELEPFSEEDIKQYLRKYFS  164 (166)
T ss_pred             EEECCCCHHHHHHHHHHHhh
Confidence            89999999999999998875

>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]

Probab=95.56  E-value=0.14  Score=40.70  Aligned_cols=125  Identities=22%  Similarity=0.302  Sum_probs=76.6

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCC-------------CCCCCccccCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNR-------------ADTLDPALLRP   79 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~-------------~~~ld~al~r~   79 (168)
                      -|.|+||||++-|-              ...++.+-..++  ..-.++ ||.+||+             |..+|+.++. 
T Consensus       296 vPGVLFIDEVhMLD--------------iEcFTyL~kalE--S~iaPi-vifAsNrG~~~irGt~d~~sPhGip~dllD-  357 (456)
T KOG1942|consen  296 VPGVLFIDEVHMLD--------------IECFTYLHKALE--SPIAPI-VIFASNRGMCTIRGTEDILSPHGIPPDLLD-  357 (456)
T ss_pred             cCcceEeeehhhhh--------------hHHHHHHHHHhc--CCCCce-EEEecCCcceeecCCcCCCCCCCCCHHHhh-
Confidence            49999999998662              145555655564  222334 5555553             4556666665 


Q ss_pred             CCcceEEecCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           80 GRLDRKIEFPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        80 grf~~~i~~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                       |+-..=..++++ ++-.+|++.--.      ++-.++.+++....-|-+--..++.-|...|-..++..|+.+|++++-
T Consensus       358 -Rl~Iirt~~y~~-~e~r~Ii~~Ra~~E~l~~~e~a~~~l~~~gt~tsLRy~vqLl~p~~~~ak~~g~~~i~v~dvee~~  435 (456)
T KOG1942|consen  358 -RLLIIRTLPYDE-EEIRQIIKIRAQVEGLQVEEEALDLLAEIGTSTSLRYAVQLLTPASILAKTNGRKEISVEDVEEVT  435 (456)
T ss_pred             -heeEEeeccCCH-HHHHHHHHHHHhhhcceecHHHHHHHHhhccchhHHHHHHhcCHHHHHHHHcCCceeecccHHHHH
Confidence             543333444544 444555543222      233455677766666777777777777777777788889999998887


Q ss_pred             Hhhc
Q 030960          154 RTNV  157 (168)
Q Consensus       154 ~~~~  157 (168)
                      +-+.
T Consensus       436 ~Lf~  439 (456)
T KOG1942|consen  436 ELFL  439 (456)
T ss_pred             HHHH
Confidence            6554

>PHA02244 ATPase-like protein

Probab=95.53  E-value=0.054  Score=44.26  Aligned_cols=73  Identities=27%  Similarity=0.379  Sum_probs=46.6

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHH-----hccCC-CCCCCeEEEEecCCC-----------CCCCcc
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLN-----QMDGF-DQTVNVKVIMATNRA-----------DTLDPA   75 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~-----~l~~~-~~~~~v~vi~ttn~~-----------~~ld~a   75 (168)
                      .+.+++|||++.+-+.           ....++.++.     ..++. ....++.+|+|+|.+           ..+++|
T Consensus       180 ~GgvLiLDEId~a~p~-----------vq~~L~~lLd~r~l~l~g~~i~~h~~FRlIATsN~~~~G~~~~y~G~k~L~~A  248 (383)
T PHA02244        180 KGGLFFIDEIDASIPE-----------ALIIINSAIANKFFDFADERVTAHEDFRVISAGNTLGKGADHIYVARNKIDGA  248 (383)
T ss_pred             cCCEEEEeCcCcCCHH-----------HHHHHHHHhccCeEEecCcEEecCCCEEEEEeeCCCccCcccccCCCcccCHH
Confidence            4689999999976321           1122333322     11111 234578999999973           688999


Q ss_pred             ccCCCCcceEEecCCCCHHHHHHHH
Q 030960           76 LLRPGRLDRKIEFPLPDRRQKRLVF  100 (168)
Q Consensus        76 l~r~grf~~~i~~~~P~~~~R~~il  100 (168)
                      ++.  ||- .++++.|+. ....|.
T Consensus       249 llD--RFv-~I~~dyp~~-~E~~i~  269 (383)
T PHA02244        249 TLD--RFA-PIEFDYDEK-IEHLIS  269 (383)
T ss_pred             HHh--hcE-EeeCCCCcH-HHHHHh
Confidence            999  995 699999984 333444

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=95.52  E-value=0.11  Score=41.21  Aligned_cols=71  Identities=14%  Similarity=0.314  Sum_probs=52.4

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      ..-|++||++|.+.              ....+.++..++.  ..+.+++|.+|+.++.+-+.+++  |. ..++|.+|+
T Consensus        90 ~~KvvII~~~e~m~--------------~~a~NaLLK~LEE--Pp~~t~~il~~~~~~kll~TI~S--Rc-~~~~f~~l~  150 (299)
T PRK07132         90 QKKILIIKNIEKTS--------------NSLLNALLKTIEE--PPKDTYFLLTTKNINKVLPTIVS--RC-QVFNVKEPD  150 (299)
T ss_pred             CceEEEEecccccC--------------HHHHHHHHHHhhC--CCCCeEEEEEeCChHhChHHHHh--Ce-EEEECCCCC
Confidence            45677777776552              2456678888884  45567777777789999999988  64 458999999


Q ss_pred             HHHHHHHHHh
Q 030960           93 RRQKRLVFQM  102 (168)
Q Consensus        93 ~~~R~~il~~  102 (168)
                      .++-.+.+..
T Consensus       151 ~~~l~~~l~~  160 (299)
T PRK07132        151 QQKILAKLLS  160 (299)
T ss_pred             HHHHHHHHHH
Confidence            8888877764

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=95.48  E-value=0.013  Score=40.70  Aligned_cols=54  Identities=30%  Similarity=0.514  Sum_probs=35.4

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC-----------CCCC------CeEEEEecCCCC----C
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF-----------DQTV------NVKVIMATNRAD----T   71 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~-----------~~~~------~v~vi~ttn~~~----~   71 (168)
                      .+++++|||++..-           .   .++..++..+++-           ....      ++.+|+|+|...    .
T Consensus        65 ~~~il~lDEin~a~-----------~---~v~~~L~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~t~N~~~~~~~~  130 (139)
T PF07728_consen   65 KGGILVLDEINRAP-----------P---EVLESLLSLLEERRIQLPEGGEEIKEPNNDLASPNFRIIATMNPRDKGRKE  130 (139)
T ss_dssp             EEEEEEESSCGG-------------H---HHHHTTHHHHSSSEEEE-TSSSEEE--TT------EEEEEEESSST--TTT
T ss_pred             ceeEEEECCcccCC-----------H---HHHHHHHHHHhhCcccccCCCcEEecCcccccccceEEEEEEcCCCCCcCc
Confidence            47999999999642           1   3444444444421           0111      389999999999    9


Q ss_pred             CCccccCCCCc
Q 030960           72 LDPALLRPGRL   82 (168)
Q Consensus        72 ld~al~r~grf   82 (168)
                      +++++++  ||
T Consensus       131 l~~al~~--Rf  139 (139)
T PF07728_consen  131 LSPALLD--RF  139 (139)
T ss_dssp             TCHHHHT--T-
T ss_pred             CCHHHHh--hC
Confidence            9999999  87

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.

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

Probab=95.36  E-value=0.078  Score=41.97  Aligned_cols=78  Identities=21%  Similarity=0.331  Sum_probs=48.2

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccC---------CC--
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLR---------PG--   80 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r---------~g--   80 (168)
                      ..|-||+|||+|.+-+.              .+..++..+..+-..+++++|.+.+ ++.+-.++..         .|  
T Consensus       171 ~~~iViiIDdLDR~~~~--------------~i~~~l~~ik~~~~~~~i~~Il~~D-~~~l~~ai~~~~~~~~~~~~~~~  235 (325)
T PF07693_consen  171 KKRIVIIIDDLDRCSPE--------------EIVELLEAIKLLLDFPNIIFILAFD-PEILEKAIEKNYGEGFDEIDGRE  235 (325)
T ss_pred             CceEEEEEcchhcCCcH--------------HHHHHHHHHHHhcCCCCeEEEEEec-HHHHHHHHHhhcCcccccccHHH
Confidence            45899999999987321              1223333333333446777776654 2222222221         11  


Q ss_pred             ----CcceEEecCCCCHHHHHHHHHhhc
Q 030960           81 ----RLDRKIEFPLPDRRQKRLVFQMNL  104 (168)
Q Consensus        81 ----rf~~~i~~~~P~~~~R~~il~~~l  104 (168)
                          -|+..+.+|+|+..+...++...+
T Consensus       236 yLeKiiq~~~~lP~~~~~~~~~~~~~~~  263 (325)
T PF07693_consen  236 YLEKIIQVPFSLPPPSPSDLERYLNELL  263 (325)
T ss_pred             HHHhhcCeEEEeCCCCHHHHHHHHHHHH
Confidence                388899999999999888887554

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

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=95.28  E-value=0.19  Score=43.52  Aligned_cols=128  Identities=13%  Similarity=0.122  Sum_probs=83.7

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC---------C--CCCCCeEEEEecCCC---CCCCccccCC
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG---------F--DQTVNVKVIMATNRA---DTLDPALLRP   79 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~---------~--~~~~~v~vi~ttn~~---~~ld~al~r~   79 (168)
                      ..|||+||+..+-              .+++..|+.-|+.         .  ....+.++|++-|..   ..|+++++. 
T Consensus        94 ~GvL~lDe~n~~~--------------~~~~~aLleame~G~vtIeR~G~s~~~Pa~F~LIat~~~~~~~~~L~~~lLD-  158 (584)
T PRK13406         94 GGVLVLAMAERLE--------------PGTAARLAAALDTGEVRLERDGLALRLPARFGLVALDEGAEEDERAPAALAD-  158 (584)
T ss_pred             CCEEEecCcccCC--------------HHHHHHHHHHHhCCcEEEEECCcEEecCCCcEEEecCCChhcccCCCHHhHh-
Confidence            3799999998762              1667777777752         1  112357778863322   358889999 


Q ss_pred             CCcceEEecCCCCHHHHH-------HHH--HhhcCC----CCCHHHHHhC--CCCC-CHHHHHHHHHHHHHHHHHhCCCc
Q 030960           80 GRLDRKIEFPLPDRRQKR-------LVF--QMNLSD----EVDLEDYVSR--PDKI-SAAEIAAICQEAGMHAVRKNRYV  143 (168)
Q Consensus        80 grf~~~i~~~~P~~~~R~-------~il--~~~l~~----~~~~~~la~~--t~g~-s~~di~~l~~~a~~~a~~~~~~~  143 (168)
                       ||+..+.++.|+..+-.       +|.  +..+..    +..+..++..  .-|. |.+--..+++-|...|.-++...
T Consensus       159 -Rf~l~v~v~~~~~~~~~~~~~~~~~I~~AR~rl~~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~  237 (584)
T PRK13406        159 -RLAFHLDLDGLALRDAREIPIDADDIAAARARLPAVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTA  237 (584)
T ss_pred             -heEEEEEcCCCChHHhcccCCCHHHHHHHHHHHccCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCC
Confidence             99999999988765421       122  122221    1112222222  1355 77777788888888888889999


Q ss_pred             cCHHHHHHHHHhhc
Q 030960          144 ILPKDFEKGYRTNV  157 (168)
Q Consensus       144 i~~~d~~~al~~~~  157 (168)
                      |+.+|+.+|+.-+.
T Consensus       238 V~~~dv~~Aa~lvL  251 (584)
T PRK13406        238 VEEEDLALAARLVL  251 (584)
T ss_pred             CCHHHHHHHHHHHH
Confidence            99999999997543

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=95.28  E-value=0.16  Score=45.93  Aligned_cols=38  Identities=18%  Similarity=0.111  Sum_probs=33.6

Q ss_pred             CCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhc
Q 030960          120 ISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNV  157 (168)
Q Consensus       120 ~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~  157 (168)
                      .|.+.|+++++-|-..|-.+-+..++.+|...|++-+.
T Consensus       768 iT~RqLEsLIRLsEA~AK~rLs~~Vt~~Dv~~Ai~L~~  805 (915)
T PTZ00111        768 VSSRMISSIIRISVSLARMRLSTVVTPADALQAVQIVK  805 (915)
T ss_pred             ccHHHHHHHHHHHHHHhhhcCcCcccHHHHHHHHHHHH
Confidence            68999999999998888888888999999999987654

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=95.22  E-value=0.26  Score=38.95  Aligned_cols=59  Identities=20%  Similarity=0.377  Sum_probs=45.1

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCC
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLP   91 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P   91 (168)
                      .-|++||++|.+-.              ...|.+|..++  +...++++|..|++++.+.|.+++  |+. .+.|+++
T Consensus        96 ~kv~ii~~ad~mt~--------------~AaNaLLK~LE--EPp~~~~fiL~~~~~~~ll~TI~S--Rcq-~~~~~~~  154 (290)
T PRK05917         96 YKIYIIHEADRMTL--------------DAISAFLKVLE--DPPQHGVIILTSAKPQRLPPTIRS--RSL-SIHIPME  154 (290)
T ss_pred             ceEEEEechhhcCH--------------HHHHHHHHHhh--cCCCCeEEEEEeCChhhCcHHHHh--cce-EEEccch
Confidence            46889999998742              45677888888  466688999999999999999998  764 3445544

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=95.00  E-value=0.03  Score=41.40  Aligned_cols=68  Identities=13%  Similarity=0.156  Sum_probs=41.2

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLP   91 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P   91 (168)
                      ..++|+|||+..+++.+.......    ...+    ..+.. ....+.-+|.+|.++..||+.++.  +.+..+.+..+
T Consensus        79 ~~~liviDEa~~~~~~r~~~~~~~----~~~~----~~l~~-hRh~g~diiliTQ~~~~id~~ir~--lve~~~~~~k~  146 (193)
T PF05707_consen   79 KGSLIVIDEAQNFFPSRSWKGKKV----PEII----EFLAQ-HRHYGWDIILITQSPSQIDKFIRD--LVEYHYHCRKL  146 (193)
T ss_dssp             TT-EEEETTGGGTSB---T-T--------HHH----HGGGG-CCCTT-EEEEEES-GGGB-HHHHC--CEEEEEEEEE-
T ss_pred             CCcEEEEECChhhcCCCccccccc----hHHH----HHHHH-hCcCCcEEEEEeCCHHHHhHHHHH--HHheEEEEEee
Confidence            579999999999998874421111    1223    33322 234467899999999999999987  88888877654

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=94.99  E-value=0.039  Score=40.15  Aligned_cols=56  Identities=25%  Similarity=0.343  Sum_probs=37.2

Q ss_pred             eEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC---------CCCCCeEEEEecCCCCCCC
Q 030960           15 AIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF---------DQTVNVKVIMATNRADTLD   73 (168)
Q Consensus        15 ~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~---------~~~~~v~vi~ttn~~~~ld   73 (168)
                      .||+|||+|...+.   .+.+.+-....+.+.||..+++-         -..+++++|+|+|.-....
T Consensus        70 gVVllDEidKa~~~---~~~~~~v~~~~V~~~LL~~le~g~~~d~~g~~vd~~n~ifI~Tsn~~~~~~  134 (171)
T PF07724_consen   70 GVVLLDEIDKAHPS---NSGGADVSGEGVQNSLLQLLEGGTLTDSYGRTVDTSNIIFIMTSNFGAEEI  134 (171)
T ss_dssp             TEEEEETGGGCSHT---TTTCSHHHHHHHHHHHHHHHHHSEEEETTCCEEEGTTEEEEEEESSSTHHH
T ss_pred             hhhhhHHHhhcccc---ccccchhhHHHHHHHHHHHhcccceecccceEEEeCCceEEEecccccchh
Confidence            49999999999875   22233333447777788877532         1234699999999765433

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

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

Probab=94.98  E-value=0.34  Score=37.44  Aligned_cols=89  Identities=18%  Similarity=0.271  Sum_probs=59.4

Q ss_pred             HHHHHHHH-cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC-C-CCCCCeEEEEecCCCCCCCcccc-C-
Q 030960            4 DVFRLAKE-NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG-F-DQTVNVKVIMATNRADTLDPALL-R-   78 (168)
Q Consensus         4 ~iF~~a~~-~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~-~-~~~~~v~vi~ttn~~~~ld~al~-r-   78 (168)
                      .+++..+. .++.|||.|++-.        +.+.     .-...+...++| + ....+|++-||+|+-+.|+.... + 
T Consensus       129 ~l~~~Lr~~~~kFIlFcDDLSF--------e~gd-----~~yK~LKs~LeG~ve~rP~NVl~YATSNRRHLl~e~~~dn~  195 (287)
T COG2607         129 DLVELLRARPEKFILFCDDLSF--------EEGD-----DAYKALKSALEGGVEGRPANVLFYATSNRRHLLPEDMKDNE  195 (287)
T ss_pred             HHHHHHhcCCceEEEEecCCCC--------CCCc-----hHHHHHHHHhcCCcccCCCeEEEEEecCCcccccHhhhhCC
Confidence            45555553 3488999998642        1111     112233344443 2 34558999999999988884332 1 


Q ss_pred             ------------------CCCcceEEecCCCCHHHHHHHHHhhcC
Q 030960           79 ------------------PGRLDRKIEFPLPDRRQKRLVFQMNLS  105 (168)
Q Consensus        79 ------------------~grf~~~i~~~~P~~~~R~~il~~~l~  105 (168)
                                        ..||+..+.|.+|+.++-..|+..+..
T Consensus       196 ~~~~eih~~eaveEKlSlSDRFGLwL~F~~~~Q~~YL~~V~~~a~  240 (287)
T COG2607         196 GSTGEIHPSEAVEEKLSLSDRFGLWLSFYPCDQDEYLKIVDHYAK  240 (287)
T ss_pred             CcccccChhHHHHHhhchhhhcceeecccCCCHHHHHHHHHHHHH
Confidence                              128999999999999999999998774

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=94.79  E-value=0.24  Score=38.58  Aligned_cols=59  Identities=15%  Similarity=0.187  Sum_probs=46.7

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCC
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLP   91 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P   91 (168)
                      .-|++|+++|.+-              ....+.||..++  +...++++|.+|++++.+.|.+++  |... +.++.+
T Consensus        89 ~KV~II~~ae~m~--------------~~AaNaLLK~LE--EPp~~t~fiLit~~~~~lLpTI~S--RCq~-~~~~~~  147 (261)
T PRK05818         89 KKIYIIYGIEKLN--------------KQSANSLLKLIE--EPPKNTYGIFTTRNENNILNTILS--RCVQ-YVVLSK  147 (261)
T ss_pred             CEEEEeccHhhhC--------------HHHHHHHHHhhc--CCCCCeEEEEEECChHhCchHhhh--heee-eecCCh
Confidence            5788888888773              256678999998  466789999999999999999999  8644 555555

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=94.59  E-value=0.061  Score=43.22  Aligned_cols=82  Identities=18%  Similarity=0.316  Sum_probs=58.0

Q ss_pred             HHHHHHHHHH----cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcccc
Q 030960            2 VRDVFRLAKE----NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~----~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~   77 (168)
                      ||++-+.+..    ...-|++||++|.+-.              ...+.++..++...  .++.+|.+|++++.+.+.++
T Consensus        98 iR~l~~~~~~~p~~~~~kV~iiEp~~~Ld~--------------~a~naLLk~LEep~--~~~~~Ilvth~~~~ll~ti~  161 (325)
T PRK08699         98 VREIIDNVYLTSVRGGLRVILIHPAESMNL--------------QAANSLLKVLEEPP--PQVVFLLVSHAADKVLPTIK  161 (325)
T ss_pred             HHHHHHHHhhCcccCCceEEEEechhhCCH--------------HHHHHHHHHHHhCc--CCCEEEEEeCChHhChHHHH
Confidence            3555555543    3356889999998731              34455677776543  34667779999999999998


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHh
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQM  102 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~  102 (168)
                      +  |+ ..+.|++|+.++-.+.+..
T Consensus       162 S--Rc-~~~~~~~~~~~~~~~~L~~  183 (325)
T PRK08699        162 S--RC-RKMVLPAPSHEEALAYLRE  183 (325)
T ss_pred             H--Hh-hhhcCCCCCHHHHHHHHHh
Confidence            7  65 5678899999988877753

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=94.48  E-value=0.65  Score=38.48  Aligned_cols=80  Identities=24%  Similarity=0.452  Sum_probs=55.3

Q ss_pred             HHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhcc---------CC--CCCCCeEEEEecCCC-CCCCccc
Q 030960            9 AKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMD---------GF--DQTVNVKVIMATNRA-DTLDPAL   76 (168)
Q Consensus         9 a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~---------~~--~~~~~v~vi~ttn~~-~~ld~al   76 (168)
                      |+++ ..|+++||+-.|-              .++++.||+.+.         |+  ...-++++|||+|-- -.|=|-|
T Consensus       141 a~An-RGIlYvDEvnlL~--------------d~lvd~LLd~aaeG~n~vereGisi~hpa~fvligTmNPEeGeLrpqL  205 (423)
T COG1239         141 ARAN-RGILYVDEVNLLD--------------DHLVDALLDVAAEGVNDVEREGISIRHPARFLLIGTMNPEEGELRPQL  205 (423)
T ss_pred             hhcc-CCEEEEecccccc--------------HHHHHHHHHHHHhCCceeeeCceeeccCccEEEEeecCccccccchhh
Confidence            4455 4899999998773              145555555543         22  233468899998842 2566677


Q ss_pred             cCCCCcceEEecCCC-CHHHHHHHHHhhcC
Q 030960           77 LRPGRLDRKIEFPLP-DRRQKRLVFQMNLS  105 (168)
Q Consensus        77 ~r~grf~~~i~~~~P-~~~~R~~il~~~l~  105 (168)
                      +.  ||+..+.+..| +.++|.+|.+.-..
T Consensus       206 lD--Rfg~~v~~~~~~~~~~rv~Ii~r~~~  233 (423)
T COG1239         206 LD--RFGLEVDTHYPLDLEERVEIIRRRLA  233 (423)
T ss_pred             Hh--hhcceeeccCCCCHHHHHHHHHHHHH
Confidence            77  99999999655 78999999984443

>PRK14700 recombination factor protein RarA; Provisional

Probab=94.46  E-value=0.24  Score=39.27  Aligned_cols=99  Identities=11%  Similarity=0.132  Sum_probs=63.7

Q ss_pred             CCCeEEEE-ecCCCC-CCCccccCCCCcceEEecCCCCHHHHHHHHHhhcCC-------CCCH-HHHHhCCCCCCHHHHH
Q 030960           57 TVNVKVIM-ATNRAD-TLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD-------EVDL-EDYVSRPDKISAAEIA  126 (168)
Q Consensus        57 ~~~v~vi~-ttn~~~-~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~~-------~~~~-~~la~~t~g~s~~di~  126 (168)
                      ++.+.+|| ||.+|. .+.+||++  |. +++.+.+++.++-..+++..+..       ++.+ ++.......++.+|..
T Consensus         6 ~G~i~LIGATTENP~f~vn~ALlS--R~-~v~~l~~L~~~di~~il~ral~~~~~~~~~~~~i~~~al~~ia~~a~GDaR   82 (300)
T PRK14700          6 SGKIILIGATTENPTYYLNDALVS--RL-FILRLKRLSLVATQKLIEKALSQDEVLAKHKFKIDDGLYNAMHNYNEGDCR   82 (300)
T ss_pred             CCcEEEEeecCCCccceecHhhhh--hh-heeeecCCCHHHHHHHHHHHHHhhhccCCcCCCcCHHHHHHHHHhcCCHHH
Confidence            45677887 444554 89999999  87 78999999999999999876642       1222 2222333345566777


Q ss_pred             HHHHHHHHHHHH----hCCCccCHHHHHHHHHhhcCC
Q 030960          127 AICQEAGMHAVR----KNRYVILPKDFEKGYRTNVKK  159 (168)
Q Consensus       127 ~l~~~a~~~a~~----~~~~~i~~~d~~~al~~~~p~  159 (168)
                      ..++.-- .++.    .....||.+++.+.+.+....
T Consensus        83 ~aLN~LE-~a~~~~~~~~~~~it~~~~~~~~~~~~~~  118 (300)
T PRK14700         83 KILNLLE-RMFLISTRGDEIYLNKELFDQAVGETSRD  118 (300)
T ss_pred             HHHHHHH-HHHhhccccCCCccCHHHHHHHHhHHHhc
Confidence            7666332 2221    112248999999988765443

>PF05872 DUF853: Bacterial protein of unknown function (DUF853); InterPro: IPR008571 Members of this family have a P-loop containing nucleotide triphosphate hydrolases fold

Probab=94.13  E-value=0.081  Score=44.24  Aligned_cols=73  Identities=16%  Similarity=0.347  Sum_probs=47.9

Q ss_pred             CHHHHHHHHHHcC----Ce-EEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcc
Q 030960            1 MVRDVFRLAKENA----PA-IIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPA   75 (168)
Q Consensus         1 ~l~~iF~~a~~~~----p~-ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~a   75 (168)
                      ||.++|+..-+-.    |- |+||||++.||.+.       .+....-+.+..    ++-.+++|-|+..|.+|.+||..
T Consensus       238 LLsELfe~LPEvGD~dkPklVfFfDEAHLLF~da-------~kall~~ieqvv----rLIRSKGVGv~fvTQ~P~DiP~~  306 (502)
T PF05872_consen  238 LLSELFEQLPEVGDLDKPKLVFFFDEAHLLFNDA-------PKALLDKIEQVV----RLIRSKGVGVYFVTQNPTDIPDD  306 (502)
T ss_pred             HHHHHHHhCccCCCCCCceEEEEEechhhhhcCC-------CHHHHHHHHHHH----HHhhccCceEEEEeCCCCCCCHH
Confidence            4667777765432    54 46699999999432       222222233333    33357789999999999999999


Q ss_pred             ccCCCCcceEE
Q 030960           76 LLRPGRLDRKI   86 (168)
Q Consensus        76 l~r~grf~~~i   86 (168)
                      ++.  -+...|
T Consensus       307 VL~--QLGnrI  315 (502)
T PF05872_consen  307 VLG--QLGNRI  315 (502)
T ss_pred             HHH--hhhhHH
Confidence            986  555555

This family is restricted to bacterial proteins, none of which have currently been characterised.

>PRK08485 DNA polymerase III subunit delta'; Validated

Probab=94.10  E-value=0.39  Score=35.93  Aligned_cols=83  Identities=14%  Similarity=0.165  Sum_probs=58.5

Q ss_pred             HHHHHHHHHHcC-CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCC
Q 030960            2 VRDVFRLAKENA-PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPG   80 (168)
Q Consensus         2 l~~iF~~a~~~~-p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~g   80 (168)
                      +|++.+.+...+ ...++|+++|.+.              ....|.+|..++  ....++++|..|+.+..+.|.+++  
T Consensus        42 iReii~~~~~~~~~~k~iI~~a~~l~--------------~~A~NaLLK~LE--EPp~~~~fiL~t~~~~~llpTI~S--  103 (206)
T PRK08485         42 AKEVIAEAYIAESEEKIIVIAAPSYG--------------IEAQNALLKILE--EPPKNICFIIVAKSKNLLLPTIRS--  103 (206)
T ss_pred             HHHHHHHHhhCCCCcEEEEEchHhhC--------------HHHHHHHHHHhc--CCCCCeEEEEEeCChHhCchHHHh--
Confidence            344555443221 2334577787663              255678898898  466678888888899999999998  


Q ss_pred             Ccce------------EEecCCCCHHHHHHHHHh
Q 030960           81 RLDR------------KIEFPLPDRRQKRLVFQM  102 (168)
Q Consensus        81 rf~~------------~i~~~~P~~~~R~~il~~  102 (168)
                      |+..            .+.+...+.++-.+.++.
T Consensus       104 Rc~~~~~~~~~~~~~l~l~l~~l~~~~i~~~L~~  137 (206)
T PRK08485        104 RLIIEKRKQKKPVKPLDLDLKKLDLKDIYEFLKE  137 (206)
T ss_pred             hheeccccccccccccccccCCCCHHHHHHHHHH
Confidence            7653            567788888888888876

>PF14516 AAA_35: AAA-like domain

Probab=93.93  E-value=0.64  Score=37.40  Aligned_cols=101  Identities=14%  Similarity=0.118  Sum_probs=54.0

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC---CCCC-eEEEEecCCCCCCCccccCCCCcceEEe
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD---QTVN-VKVIMATNRADTLDPALLRPGRLDRKIE   87 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~---~~~~-v~vi~ttn~~~~ld~al~r~grf~~~i~   87 (168)
                      ..|-||+|||+|.++...     ..   ....+..+-.+.+.-.   .-.+ +++++.+..+......-.+|=.+...+.
T Consensus       126 ~~~lVL~iDEiD~l~~~~-----~~---~~dF~~~LR~~~~~~~~~~~~~~L~li~~~~t~~~~~~~~~~SPFNIg~~i~  197 (331)
T PF14516_consen  126 DKPLVLFIDEIDRLFEYP-----QI---ADDFFGLLRSWYEQRKNNPIWQKLRLILAGSTEDYIILDINQSPFNIGQPIE  197 (331)
T ss_pred             CCCEEEEEechhhhccCc-----ch---HHHHHHHHHHHHHhcccCcccceEEEEEecCcccccccCCCCCCccccccee
Confidence            469999999999998432     11   0122221111111111   1112 3344433322222222234434667888


Q ss_pred             cCCCCHHHHHHHHHhhcCC--CCCHHHHHhCCCCC
Q 030960           88 FPLPDRRQKRLVFQMNLSD--EVDLEDYVSRPDKI  120 (168)
Q Consensus        88 ~~~P~~~~R~~il~~~l~~--~~~~~~la~~t~g~  120 (168)
                      ++.-+.++-..+++.+-..  ...++.+-..|.|.
T Consensus       198 L~~Ft~~ev~~L~~~~~~~~~~~~~~~l~~~tgGh  232 (331)
T PF14516_consen  198 LPDFTPEEVQELAQRYGLEFSQEQLEQLMDWTGGH  232 (331)
T ss_pred             CCCCCHHHHHHHHHhhhccCCHHHHHHHHHHHCCC
Confidence            8888999999998865432  22367777777773

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=93.93  E-value=0.21  Score=43.69  Aligned_cols=95  Identities=13%  Similarity=0.252  Sum_probs=62.4

Q ss_pred             CeEEEEecCCC--CCCCccccCCCCcc---eEEecC--CC-CHHHHHHHHHh---hcC-----CCCCHHH---HHh---C
Q 030960           59 NVKVIMATNRA--DTLDPALLRPGRLD---RKIEFP--LP-DRRQKRLVFQM---NLS-----DEVDLED---YVS---R  116 (168)
Q Consensus        59 ~v~vi~ttn~~--~~ld~al~r~grf~---~~i~~~--~P-~~~~R~~il~~---~l~-----~~~~~~~---la~---~  116 (168)
                      .+.||+++|..  ..+||++..  ||.   ..+++.  .| +.+.+..+++.   ...     ..++-+.   +.+   +
T Consensus       277 dvrvI~a~~~~ll~~~dpdL~~--rfk~~~v~v~f~~~~~d~~e~~~~~~~~iaqe~~~~G~l~~f~~eAVa~LI~~~~R  354 (637)
T PRK13765        277 DFIMVAAGNLDALENMHPALRS--RIKGYGYEVYMRDTMEDTPENRRKLVRFVAQEVKRDGKIPHFDRDAVEEIIREAKR  354 (637)
T ss_pred             eeEEEEecCcCHHHhhhHHHHH--HhccCeEEEEcccccCCCHHHHHHHHHHHHHHhhhccCCCCCCHHHHHHHHHHHHH
Confidence            46788888874  677999988  886   566664  22 34555555541   111     1233222   211   1


Q ss_pred             CCC------CCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960          117 PDK------ISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus       117 t~g------~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      ..|      +..++|..+++.|...|..++...++.+|..+|+..
T Consensus       355 ~ag~r~~lsl~~~~l~~l~r~a~~~a~~~~~~~i~~~~v~~a~~~  399 (637)
T PRK13765        355 RAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTTAEHVLEAKKI  399 (637)
T ss_pred             HhCCccccccCHHHHHHHHHHHHHHHHhhccceecHHHHHHHHHh
Confidence            122      457999999999999999998889999999888754

>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite

Probab=93.88  E-value=0.13  Score=41.33  Aligned_cols=127  Identities=21%  Similarity=0.234  Sum_probs=74.2

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC----CC-------CCCeEEEEecCCCC------------
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF----DQ-------TVNVKVIMATNRAD------------   70 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~----~~-------~~~v~vi~ttn~~~------------   70 (168)
                      ..|++|||+|.+-.              .....+++.|+.-    .+       ..+.-|+|++|-..            
T Consensus       122 ~GiccIDe~dk~~~--------------~~~~~l~eaMEqq~isi~kagi~~~l~ar~svlaa~NP~~g~~~~~~~~~~n  187 (331)
T PF00493_consen  122 GGICCIDEFDKMKE--------------DDRDALHEAMEQQTISIAKAGIVTTLNARCSVLAAANPKFGRYDPNKSLSEN  187 (331)
T ss_dssp             TSEEEECTTTT--C--------------HHHHHHHHHHHCSCEEECTSSSEEEEE---EEEEEE--TT--S-TTS-CGCC
T ss_pred             Cceeeecccccccc--------------hHHHHHHHHHHcCeeccchhhhcccccchhhhHHHHhhhhhhcchhhhhHHh
Confidence            58999999998732              1233444555431    11       23477899988666            


Q ss_pred             -CCCccccCCCCcceEEec-CCCCHHHHHHHHHhhcC----C-------------CC-----------------------
Q 030960           71 -TLDPALLRPGRLDRKIEF-PLPDRRQKRLVFQMNLS----D-------------EV-----------------------  108 (168)
Q Consensus        71 -~ld~al~r~grf~~~i~~-~~P~~~~R~~il~~~l~----~-------------~~-----------------------  108 (168)
                       .+++.+++  |||..+.+ ..|+.+.=..+.++.+.    .             ..                       
T Consensus       188 i~l~~~LLS--RFDLif~l~D~~d~~~D~~la~~il~~~~~~~~~~~~~~~~~~~~~~~~~lr~yI~yar~~~~P~ls~e  265 (331)
T PF00493_consen  188 INLPPPLLS--RFDLIFLLRDKPDEEEDERLAEHILDSHRNGKKSKEKKIKKNDKPISEDLLRKYIAYARQNIHPVLSEE  265 (331)
T ss_dssp             T-S-CCCHC--C-SEEECC--TTT-HHHHHHHHHHHTTT---S--------SSS-TT-HCCCHHHHHHHHHHC--EE-HH
T ss_pred             cccchhhHh--hcCEEEEeccccccccccccceEEEeccccccccccccccccCCccCHHHHHHHHHHHHhhcccccCHH
Confidence             58999999  99999876 67775554444432221    0             00                       


Q ss_pred             CHHHH----------H---hCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960          109 DLEDY----------V---SRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus       109 ~~~~l----------a---~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      ..+.|          .   ......|.+.|+.+++-|...|--+-+..|+.+|+..|+.-+
T Consensus       266 a~~~I~~~Yv~lR~~~~~~~~~~~iT~R~LeSLIRLseA~AKl~lr~~V~~~Dv~~Ai~L~  326 (331)
T PF00493_consen  266 AKELIINYYVELRKESKSNNKSIPITIRQLESLIRLSEAHAKLRLRDEVTEEDVEEAIRLF  326 (331)
T ss_dssp             CHHHHHHHHCCCCHCHHCHSS-B-SSCCCCCHHHHHHHHHHHCTTSSECSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcccccccccccccchhhHHHHHHHHHHHHHHhccCceeHHHHHHHHHHH
Confidence            00011          0   112246788899999999888888888899999999998754

; InterPro: IPR001208 MCM proteins are DNA-dependent ATPases required for the initiation of eukaryotic DNA replication [, , ]. In eukaryotes there is a family of six proteins, MCM2 to MCM7. They were first identified in yeast where most of them have a direct role in the initiation of chromosomal DNA replication by interacting directly with autonomously replicating sequences (ARS). They were thus called minichromosome maintenance proteins, MCM proteins []. This family is also present in the archebacteria in 1 to 4 copies. Methanocaldococcus jannaschii (Methanococcus jannaschii) has four members, MJ0363, MJ0961, MJ1489 and MJECL13. The "MCM motif" contains Walker-A and Walker-B type nucleotide binding motifs. The diagnostic sequence defining the MCMs is IDEFDKM. Only Mcm2 (aka Cdc19 or Nda1) has been subjected to mutational analysis in this region, and most mutations abolish its activity []. The presence of a putative ATP-binding domain implies that these proteins may be involved in an ATP-consuming step in the initiation of DNA replication in eukaryotes. The MCM proteins bind together in a large complex []. Within this complex, individual subunits associate with different affinities, and there is a tightly associated core of Mcm4 (Cdc21), Mcm6 (Mis5) and Mcm7 []. This core complex in human MCMs has been associated with helicase activity in vitro [], leading to the suggestion that the MCM proteins are the eukaryotic replicative helicase. Schizosaccharomyces pombe (Fission yeast) MCMs, like those in metazoans, are found in the nucleus throughout the cell cycle. This is in contrast to the Saccharomyces cerevisiae (Baker's yeast) in which MCM proteins move in and out of the nucleus during each cell cycle. The assembly of the MCM complex in S. pombe is required for MCM localisation, ensuring that only intact MCM complexes remain in the nucleus [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 3F8T_A 3F9V_A.

>PF12846 AAA_10: AAA-like domain

Probab=93.54  E-value=0.066  Score=41.50  Aligned_cols=71  Identities=31%  Similarity=0.405  Sum_probs=52.5

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCC-----ccccCCCCcceEE
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLD-----PALLRPGRLDRKI   86 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld-----~al~r~grf~~~i   86 (168)
                      ..|.++++||+..+....         .....+..++...    ...++.++.+|..|.+++     ++++.  -+...+
T Consensus       219 ~~~~~i~iDEa~~~~~~~---------~~~~~~~~~~~~~----Rk~g~~~~l~tQ~~~~l~~~~~~~~i~~--n~~~~i  283 (304)
T PF12846_consen  219 GRPKIIVIDEAHNFLSNP---------SGAEFLDELLREG----RKYGVGLILATQSPSDLPKSPIEDAILA--NCNTKI  283 (304)
T ss_pred             CceEEEEeCCcccccccc---------chhhhhhHHHHHH----HhcCCEEEEeeCCHHHHhccchHHHHHH--hCCcEE
Confidence            569999999999887542         1123344444443    344788999999999999     78887  788888


Q ss_pred             ecCCCCHHHHH
Q 030960           87 EFPLPDRRQKR   97 (168)
Q Consensus        87 ~~~~P~~~~R~   97 (168)
                      .+..++.+...
T Consensus       284 ~~~~~~~~~~~  294 (304)
T PF12846_consen  284 IFRLEDSDDAE  294 (304)
T ss_pred             EecCChHHHHH
Confidence            88888877766

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

Probab=93.03  E-value=0.8  Score=40.65  Aligned_cols=104  Identities=15%  Similarity=0.126  Sum_probs=61.1

Q ss_pred             eEEEEecCCCCCCCccccCCCCcceEEecCCCCHHHHHHHHH-hhcCC--CCCHHHHHhCCCCCCHHHHHHHHHHHHHHH
Q 030960           60 VKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-MNLSD--EVDLEDYVSRPDKISAAEIAAICQEAGMHA  136 (168)
Q Consensus        60 v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~~~R~~il~-~~l~~--~~~~~~la~~t~g~s~~di~~l~~~a~~~a  136 (168)
                      .-||+.+|+.  --|||+.=--|-..++|.+|....-.+=|+ .|..+  ..+...|+..|+ ++..||.+.++.-.+.+
T Consensus       439 RPIICICNdL--YaPaLR~Lr~~A~ii~f~~p~~s~Lv~RL~~IC~rE~mr~d~~aL~~L~e-l~~~DIRsCINtLQfLa  515 (877)
T KOG1969|consen  439 RPIICICNDL--YAPALRPLRPFAEIIAFVPPSQSRLVERLNEICHRENMRADSKALNALCE-LTQNDIRSCINTLQFLA  515 (877)
T ss_pred             CCEEEEecCc--cchhhhhcccceEEEEecCCChhHHHHHHHHHHhhhcCCCCHHHHHHHHH-HhcchHHHHHHHHHHHH
Confidence            4588888854  456665322489999999998776555444 34433  234444444443 55679999999877766


Q ss_pred             HHhCC--CccCHHHHHHHHHhhcCCCCCcccc
Q 030960          137 VRKNR--YVILPKDFEKGYRTNVKKPDTDFEF  166 (168)
Q Consensus       137 ~~~~~--~~i~~~d~~~al~~~~p~~~~~~~~  166 (168)
                      .+..+  ..+...++-+.....+.++.+-++|
T Consensus       516 ~~~~r~ds~i~~~~i~a~~~~~k~~~~slf~~  547 (877)
T KOG1969|consen  516 SNVDRRDSSISVKLICAKNVGAKSNSDSLFSW  547 (877)
T ss_pred             HhcccccccchhhhhhhhhhcccccccchHHH
Confidence            65322  2344455544444444444444444

>TIGR00602 rad24 checkpoint protein rad24

Probab=91.99  E-value=1.5  Score=38.52  Aligned_cols=107  Identities=12%  Similarity=0.177  Sum_probs=58.4

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHH-hccCCCCCCCeEEEE-ecCCCC--------C------CCccc
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLN-QMDGFDQTVNVKVIM-ATNRAD--------T------LDPAL   76 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~-~l~~~~~~~~v~vi~-ttn~~~--------~------ld~al   76 (168)
                      ...||+|||+|.++...       .    +.+..++. ...   ....+.+|+ +|..+.        .      |.+++
T Consensus       195 ~~~IILIDEiPn~~~r~-------~----~~lq~lLr~~~~---e~~~~pLI~I~TE~~~~~~~~~~~~f~~~~lL~~eL  260 (637)
T TIGR00602       195 DKKIILVEDLPNQFYRD-------T----RALHEILRWKYV---SIGRCPLVFIITESLEGDNNQRRLLFPAETIMNKEI  260 (637)
T ss_pred             ceeEEEeecchhhchhh-------H----HHHHHHHHHHhh---cCCCceEEEEecCCccccccccccccchhcccCHhH
Confidence            46899999999876321       1    22333443 221   233443444 442332        0      22566


Q ss_pred             cCCCCcceEEecCCCCHHHHHHHHHhhcCC-------C------CCHHHHHhCCCCCCHHHHHHHHHHHHHHHHH
Q 030960           77 LRPGRLDRKIEFPLPDRRQKRLVFQMNLSD-------E------VDLEDYVSRPDKISAAEIAAICQEAGMHAVR  138 (168)
Q Consensus        77 ~r~grf~~~i~~~~P~~~~R~~il~~~l~~-------~------~~~~~la~~t~g~s~~di~~l~~~a~~~a~~  138 (168)
                      +...|. ..|.|.+.+...-.+.|+..+..       +      ..+..|+.    .+.+||..+++.-.+.+.+
T Consensus       261 ls~~rv-~~I~FnPia~t~l~K~L~rIl~~E~~~~~~~~~~p~~~~l~~I~~----~s~GDiRsAIn~LQf~~~~  330 (637)
T TIGR00602       261 LEEPRV-SNISFNPIAPTIMKKFLNRIVTIEAKKNGEKIKVPKKTSVELLCQ----GCSGDIRSAINSLQFSSSK  330 (637)
T ss_pred             hcccce-eEEEeCCCCHHHHHHHHHHHHHhhhhccccccccCCHHHHHHHHH----hCCChHHHHHHHHHHHHhc
Confidence            542233 37899999998866666533331       1      13444555    5667998888865555443

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

>TIGR01128 holA DNA polymerase III, delta subunit

Probab=91.61  E-value=5.3  Score=31.10  Aligned_cols=123  Identities=14%  Similarity=0.097  Sum_probs=67.5

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCC---ccccCCCCcceEEecCC
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLD---PALLRPGRLDRKIEFPL   90 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld---~al~r~grf~~~i~~~~   90 (168)
                      .-+|+|++++.+...             ...+.++..+...  .+..++|..++.++.-.   ..+..- .-...+.+..
T Consensus        47 ~kliii~~~~~~~~~-------------~~~~~L~~~l~~~--~~~~~~i~~~~~~~~~~~~~k~~~~~-~~~~~i~~~~  110 (302)
T TIGR01128        47 RRLVELRNPEGKPGA-------------KGLKALEEYLANP--PPDTLLLIEAPKLDKRKKLTKWLKAL-KNAQIVECKT  110 (302)
T ss_pred             CeEEEEECCCCCCCH-------------HHHHHHHHHHhcC--CCCEEEEEecCCCCHhHHHHHHHHHh-cCeeEEEecC
Confidence            568888888865311             1244566666643  23444555555332111   111110 1245778889


Q ss_pred             CCHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           91 PDRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        91 P~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      |+..+...+++..+..      .-.+..+++.++|    |+..+.++.-..+.-.+...||.+|+...+...
T Consensus       111 ~~~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~----d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~~  178 (302)
T TIGR01128       111 PKEQELPRWIQARLKKLGLRIDPDAVQLLAELVEG----NLLAIAQELEKLALYAPDGKITLEDVEEAVSDS  178 (302)
T ss_pred             CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCc----HHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhhh
Confidence            9999999888765542      2234455555543    555554444444443333468888888877644

subunit around DNA forming a DNA sliding clamp.

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

Probab=91.54  E-value=0.3  Score=39.30  Aligned_cols=42  Identities=29%  Similarity=0.412  Sum_probs=30.7

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF   54 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~   54 (168)
                      +..||+|||+|.+..+..+.+-..+-..+.+...+|..++|-
T Consensus       162 erGIIyIDEIDKIarkSeN~SITRDVSGEGVQQALLKiiEGT  203 (408)
T COG1219         162 ERGIIYIDEIDKIARKSENPSITRDVSGEGVQQALLKIIEGT  203 (408)
T ss_pred             hCCeEEEechhhhhccCCCCCcccccCchHHHHHHHHHHcCc
Confidence            469999999999998775554443333456777888888764

>PRK05574 holA DNA polymerase III subunit delta; Reviewed

Probab=91.12  E-value=6.5  Score=31.20  Aligned_cols=126  Identities=16%  Similarity=0.120  Sum_probs=68.3

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCC------CccccCCCCcceEEe
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTL------DPALLRPGRLDRKIE   87 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~l------d~al~r~grf~~~i~   87 (168)
                      .-+|++++.+.+-...          ....+..+...+ .....+.++++..++..+.-      -+++.   .....+.
T Consensus        77 ~klvii~~~~~l~~~~----------~~~~l~~l~~~l-~~~~~~~~~li~~~~~~~~~~k~~k~~k~~~---~~~~~~~  142 (340)
T PRK05574         77 RKLVELRLPEFLTGAK----------GEKALKRLEAYL-NPLPHPDLLLIVRLPKLDKAKKKSAWFKALK---KKAVVVE  142 (340)
T ss_pred             CeEEEEECCCCCCchh----------HHHHHHHHHHhc-cCCCCCcEEEEEECCcCCHHHHhhHHHHHHH---hCceEEE
Confidence            5677788877653211          123344455545 33334345555555543321      11222   2346788


Q ss_pred             cCCCCHHHHHHHHHhhcCC---CC---CHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhc
Q 030960           88 FPLPDRRQKRLVFQMNLSD---EV---DLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNV  157 (168)
Q Consensus        88 ~~~P~~~~R~~il~~~l~~---~~---~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~  157 (168)
                      ++.|+..+....++..+..   .+   .++.+++.+    +.|+..+.++.-..+.-.+...||.+++.+.+....
T Consensus       143 ~~~~~~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~----~~d~~~l~~El~KL~l~~~~~~It~~~I~~~i~~~~  214 (340)
T PRK05574        143 AQPPKEAELPQWIQQRLKQQGLQIDAAALQLLAERV----EGNLLALAQELEKLALLYPDGKITLEDVEEAVPDSA  214 (340)
T ss_pred             cCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHh----CchHHHHHHHHHHHHhhcCCCCCCHHHHHHHHhhhh
Confidence            8899999988888766642   22   233444443    346666666555555443222388888887776543

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=90.79  E-value=0.92  Score=37.50  Aligned_cols=121  Identities=19%  Similarity=0.245  Sum_probs=58.9

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC-----CC----CCCeEEEEecCCCCCCCccccCCCCcc
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF-----DQ----TVNVKVIMATNRADTLDPALLRPGRLD   83 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~-----~~----~~~v~vi~ttn~~~~ld~al~r~grf~   83 (168)
                      .+..|||||+|.+-..              ....++..++.-     ..    ...+-+|++|+..-   .....+|+|.
T Consensus       233 ~~gtl~ldei~~l~~~--------------~q~~l~~~l~~~~~~~~~~~~~~~~~~rii~~t~~~~---~~~~~~~~~~  295 (441)
T PRK10365        233 DGGTLFLDEIGDISPM--------------MQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDL---AAEVNAGRFR  295 (441)
T ss_pred             CCCEEEEeccccCCHH--------------HHHHHHHHHccCcEEeCCCCceeeeceEEEEeCCCCH---HHHHHcCCch
Confidence            3688999999998521              122333333321     11    12456777776532   2334566774


Q ss_pred             e-------EEecCCCCHHHHHH----HHHhhcCC----------CCCHH---HHHhCCCCCCHHHHHHHHHHHHHHHHHh
Q 030960           84 R-------KIEFPLPDRRQKRL----VFQMNLSD----------EVDLE---DYVSRPDKISAAEIAAICQEAGMHAVRK  139 (168)
Q Consensus        84 ~-------~i~~~~P~~~~R~~----il~~~l~~----------~~~~~---~la~~t~g~s~~di~~l~~~a~~~a~~~  139 (168)
                      .       .+.+..|...+|.+    ++++++..          .++-+   .|..+.=--..++|.++++.++..   .
T Consensus       296 ~~l~~~l~~~~i~~ppLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgN~reL~~~~~~~~~~---~  372 (441)
T PRK10365        296 QDLYYRLNVVAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAVERAVVL---L  372 (441)
T ss_pred             HHHHHHhccceecCCChhhcchhHHHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHhCCCCCHHHHHHHHHHHHHHh---C
Confidence            3       34555555555543    33444331          01111   122221111346666666666543   2


Q ss_pred             CCCccCHHHHHHHH
Q 030960          140 NRYVILPKDFEKGY  153 (168)
Q Consensus       140 ~~~~i~~~d~~~al  153 (168)
                      ....|+.+++...+
T Consensus       373 ~~~~i~~~~l~~~~  386 (441)
T PRK10365        373 TGEYISERELPLAI  386 (441)
T ss_pred             CCCccchHhCchhh
Confidence            33457777765444

>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=90.50  E-value=0.61  Score=38.24  Aligned_cols=72  Identities=22%  Similarity=0.344  Sum_probs=40.7

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecC------------CCCCCCccccCCCC
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATN------------RADTLDPALLRPGR   81 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn------------~~~~ld~al~r~gr   81 (168)
                      |.|+||||++-|=           .   ..++.|-..++   ..-..+||.+||            .|.-+|..++.  |
T Consensus       279 pGVLFIDEvHmLD-----------i---EcFsfLnralE---s~~sPiiIlATNRg~~~irGt~~~sphGiP~DlLD--R  339 (398)
T PF06068_consen  279 PGVLFIDEVHMLD-----------I---ECFSFLNRALE---SELSPIIILATNRGITKIRGTDIISPHGIPLDLLD--R  339 (398)
T ss_dssp             E-EEEEESGGGSB-----------H---HHHHHHHHHHT---STT--EEEEEES-SEEE-BTTS-EEETT--HHHHT--T
T ss_pred             cceEEecchhhcc-----------H---HHHHHHHHHhc---CCCCcEEEEecCceeeeccCccCcCCCCCCcchHh--h
Confidence            9999999999762           1   33444444443   333445666777            46667767766  5


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS  105 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~  105 (168)
                      + ..|...+.+.++-.+|++.-..
T Consensus       340 l-lII~t~py~~~ei~~Il~iR~~  362 (398)
T PF06068_consen  340 L-LIIRTKPYSEEEIKQILKIRAK  362 (398)
T ss_dssp             E-EEEEE----HHHHHHHHHHHHH
T ss_pred             c-EEEECCCCCHHHHHHHHHhhhh
Confidence            4 4566678899999999985443

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.

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

Probab=89.87  E-value=0.81  Score=30.86  Aligned_cols=49  Identities=14%  Similarity=0.247  Sum_probs=30.1

Q ss_pred             HHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEec
Q 030960            3 RDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMAT   66 (168)
Q Consensus         3 ~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~tt   66 (168)
                      +.+.+..+.....+|+|||+|.+. +            ...++.+...++  ...-+++++++.
T Consensus        77 ~~~~~~l~~~~~~~lviDe~~~l~-~------------~~~l~~l~~l~~--~~~~~vvl~G~~  125 (131)
T PF13401_consen   77 SLLIDALDRRRVVLLVIDEADHLF-S------------DEFLEFLRSLLN--ESNIKVVLVGTP  125 (131)
T ss_dssp             HHHHHHHHHCTEEEEEEETTHHHH-T------------HHHHHHHHHHTC--SCBEEEEEEESS
T ss_pred             HHHHHHHHhcCCeEEEEeChHhcC-C------------HHHHHHHHHHHh--CCCCeEEEEECh
Confidence            445556666666799999999975 1            255666655555  233345555554

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=89.54  E-value=1.3  Score=36.73  Aligned_cols=120  Identities=19%  Similarity=0.311  Sum_probs=61.5

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC-----CCC----CCCeEEEEecCCCCCCCccccCCCCcce
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG-----FDQ----TVNVKVIMATNRADTLDPALLRPGRLDR   84 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~-----~~~----~~~v~vi~ttn~~~~ld~al~r~grf~~   84 (168)
                      ..+|||||+|.+-.              .+...++..++.     +..    ...+.+|+||+..-  . .+.+.|+|..
T Consensus       238 ~gtl~ld~i~~l~~--------------~~q~~L~~~l~~~~~~~~~~~~~~~~~~rii~~t~~~l--~-~~~~~g~~~~  300 (457)
T PRK11361        238 EGTLLLDEIGEMPL--------------VLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDL--Q-AMVKEGTFRE  300 (457)
T ss_pred             CCEEEEechhhCCH--------------HHHHHHHHHHhcCcEEeCCCCceeeeceEEEEeCCCCH--H-HHHHcCCchH
Confidence            46899999998842              122333443332     111    12478888887532  1 3334455554


Q ss_pred             -------EEecCCCCHHHHHH----HHHhhcCC----------CCCH---HHHHhCCCCCCHHHHHHHHHHHHHHHHHhC
Q 030960           85 -------KIEFPLPDRRQKRL----VFQMNLSD----------EVDL---EDYVSRPDKISAAEIAAICQEAGMHAVRKN  140 (168)
Q Consensus        85 -------~i~~~~P~~~~R~~----il~~~l~~----------~~~~---~~la~~t~g~s~~di~~l~~~a~~~a~~~~  140 (168)
                             .+.+..|...+|.+    +.+.++..          .++-   ..+..+.=--..++|+++++.|+..+   .
T Consensus       301 ~l~~~l~~~~i~~ppLreR~~di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~wpgNv~eL~~~~~~~~~~~---~  377 (457)
T PRK11361        301 DLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWPGNIRELSNVIERAVVMN---S  377 (457)
T ss_pred             HHHHHhccceecCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHcCCCCCcHHHHHHHHHHHHHhC---C
Confidence                   35566666666653    33333321          1111   12222221124578888887776532   3


Q ss_pred             CCccCHHHHHHHH
Q 030960          141 RYVILPKDFEKGY  153 (168)
Q Consensus       141 ~~~i~~~d~~~al  153 (168)
                      ...|+.+|+...+
T Consensus       378 ~~~i~~~~l~~~~  390 (457)
T PRK11361        378 GPIIFSEDLPPQI  390 (457)
T ss_pred             CCcccHHHChHhh
Confidence            3467777776544

>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=89.48  E-value=0.99  Score=34.89  Aligned_cols=100  Identities=16%  Similarity=0.171  Sum_probs=53.0

Q ss_pred             HHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcce
Q 030960            5 VFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDR   84 (168)
Q Consensus         5 iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~   84 (168)
                      +.+..+. .+++|+||+++...                .+..+...+.  ....+.-||.||.... +-....   .-..
T Consensus        94 l~~~L~~-~~~LlVlDdv~~~~----------------~~~~l~~~~~--~~~~~~kilvTTR~~~-v~~~~~---~~~~  150 (287)
T PF00931_consen   94 LRELLKD-KRCLLVLDDVWDEE----------------DLEELREPLP--SFSSGSKILVTTRDRS-VAGSLG---GTDK  150 (287)
T ss_dssp             HHHHHCC-TSEEEEEEEE-SHH----------------HH-------H--CHHSS-EEEEEESCGG-GGTTHH---SCEE
T ss_pred             chhhhcc-ccceeeeeeecccc----------------cccccccccc--cccccccccccccccc-cccccc---cccc
Confidence            3343333 49999999988642                1112222221  1222455677777643 222221   1267


Q ss_pred             EEecCCCCHHHHHHHHHhhcCCC---------CCHHHHHhCCCCCCHHHHHHH
Q 030960           85 KIEFPLPDRRQKRLVFQMNLSDE---------VDLEDYVSRPDKISAAEIAAI  128 (168)
Q Consensus        85 ~i~~~~P~~~~R~~il~~~l~~~---------~~~~~la~~t~g~s~~di~~l  128 (168)
                      .++++..+.++-.++|.......         ....++++.+.| .|--|..+
T Consensus       151 ~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~g-lPLal~~~  202 (287)
T PF00931_consen  151 VIELEPLSEEEALELFKKRAGRKESESPEDLEDLAKEIVEKCGG-LPLALKLI  202 (287)
T ss_dssp             EEECSS--HHHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT--HHHHHHH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccc-cccccccc
Confidence            89999999999999998665421         124568888865 45555544

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.

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=89.05  E-value=1.1  Score=36.04  Aligned_cols=14  Identities=21%  Similarity=0.508  Sum_probs=11.6

Q ss_pred             CCeEEEEccccccc
Q 030960           13 APAIIFIDEVDAIA   26 (168)
Q Consensus        13 ~p~ii~iDe~D~l~   26 (168)
                      ....|||||+|.+-
T Consensus        93 ~gGtL~Ldei~~L~  106 (329)
T TIGR02974        93 DGGTLFLDELATAS  106 (329)
T ss_pred             CCCEEEeCChHhCC
Confidence            36889999999873

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

>TIGR01817 nifA Nif-specific regulatory protein

Probab=88.25  E-value=2.1  Score=36.65  Aligned_cols=117  Identities=21%  Similarity=0.302  Sum_probs=59.6

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC--C---CC----CCCeEEEEecCCCCCCCccccCCCCcc-
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG--F---DQ----TVNVKVIMATNRADTLDPALLRPGRLD-   83 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~--~---~~----~~~v~vi~ttn~~~~ld~al~r~grf~-   83 (168)
                      ...|||||+|.+-.              .....++..++.  +   ..    ...+-+|++|+..  +.. +...|+|. 
T Consensus       291 ~GtL~ldei~~L~~--------------~~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~~s~~~--l~~-~~~~~~f~~  353 (534)
T TIGR01817       291 GGTLFLDEIGEISP--------------AFQAKLLRVLQEGEFERVGGNRTLKVDVRLVAATNRD--LEE-AVAKGEFRA  353 (534)
T ss_pred             CCeEEEechhhCCH--------------HHHHHHHHHHhcCcEEECCCCceEeecEEEEEeCCCC--HHH-HHHcCCCCH
Confidence            57899999998732              222334444432  1   11    1246788887643  111 22345552 


Q ss_pred             --------eEEecCCCC--HHHHHHHHHhhcCC-------CC--C---HHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCC
Q 030960           84 --------RKIEFPLPD--RRQKRLVFQMNLSD-------EV--D---LEDYVSRPDKISAAEIAAICQEAGMHAVRKNR  141 (168)
Q Consensus        84 --------~~i~~~~P~--~~~R~~il~~~l~~-------~~--~---~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~  141 (168)
                              ..|.+|+..  .++...++++++..       ..  +   +..|..+.=--..++|+++++.++..+   ..
T Consensus       354 ~L~~rl~~~~i~lPpLreR~eDi~~L~~~~l~~~~~~~~~~~~~s~~a~~~L~~~~WPGNvrEL~~v~~~a~~~~---~~  430 (534)
T TIGR01817       354 DLYYRINVVPIFLPPLRERREDIPLLAEAFLEKFNRENGRPLTITPSAIRVLMSCKWPGNVRELENCLERTATLS---RS  430 (534)
T ss_pred             HHHHHhcCCeeeCCCcccccccHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhCCCCChHHHHHHHHHHHHHhC---CC
Confidence                    345555443  34444555555431       11  1   122233221124578888888776543   34


Q ss_pred             CccCHHHHH
Q 030960          142 YVILPKDFE  150 (168)
Q Consensus       142 ~~i~~~d~~  150 (168)
                      ..|+.+|+.
T Consensus       431 ~~I~~~~l~  439 (534)
T TIGR01817       431 GTITRSDFS  439 (534)
T ss_pred             CcccHHHCc
Confidence            568888875

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.

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=87.93  E-value=2.7  Score=36.78  Aligned_cols=121  Identities=21%  Similarity=0.328  Sum_probs=61.5

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC-----CCCC----CCeEEEEecCCCCCCCccccCCCCcce
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG-----FDQT----VNVKVIMATNRADTLDPALLRPGRLDR   84 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~-----~~~~----~~v~vi~ttn~~~~ld~al~r~grf~~   84 (168)
                      ...|||||+|.+-.              .+...++..++.     +...    ..+-+|+||+..-   ..+...|+|..
T Consensus       417 ~GtL~ldei~~l~~--------------~~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~~t~~~l---~~~~~~~~f~~  479 (638)
T PRK11388        417 GGTLFLEKVEYLSP--------------ELQSALLQVLKTGVITRLDSRRLIPVDVRVIATTTADL---AMLVEQNRFSR  479 (638)
T ss_pred             CCEEEEcChhhCCH--------------HHHHHHHHHHhcCcEEeCCCCceEEeeEEEEEeccCCH---HHHHhcCCChH
Confidence            57899999998732              222233333321     1111    1467888887542   23333456532


Q ss_pred             -------EEecCCCCHHHHH----HHHHhhcCC-------C--CC---HHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCC
Q 030960           85 -------KIEFPLPDRRQKR----LVFQMNLSD-------E--VD---LEDYVSRPDKISAAEIAAICQEAGMHAVRKNR  141 (168)
Q Consensus        85 -------~i~~~~P~~~~R~----~il~~~l~~-------~--~~---~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~  141 (168)
                             .+.+..|...+|.    .+++.++..       .  +.   +..|..+.=--..++|.++++.++..+   ..
T Consensus       480 dL~~~l~~~~i~lPpLreR~~Di~~L~~~~l~~~~~~~~~~~~~s~~a~~~L~~y~WPGNvreL~~~l~~~~~~~---~~  556 (638)
T PRK11388        480 QLYYALHAFEITIPPLRMRREDIPALVNNKLRSLEKRFSTRLKIDDDALARLVSYRWPGNDFELRSVIENLALSS---DN  556 (638)
T ss_pred             HHhhhhceeEEeCCChhhhhhHHHHHHHHHHHHHHHHhCCCCCcCHHHHHHHHcCCCCChHHHHHHHHHHHHHhC---CC
Confidence                   3455566666663    333333321       1  11   122222221124588888888776543   33


Q ss_pred             CccCHHHHHHHHH
Q 030960          142 YVILPKDFEKGYR  154 (168)
Q Consensus       142 ~~i~~~d~~~al~  154 (168)
                      ..|+.+|+...+.
T Consensus       557 ~~i~~~~lp~~~~  569 (638)
T PRK11388        557 GRIRLSDLPEHLF  569 (638)
T ss_pred             CeecHHHCchhhh
Confidence            4678888776664

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=87.85  E-value=1.4  Score=35.87  Aligned_cols=76  Identities=21%  Similarity=0.227  Sum_probs=50.4

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC-CCCCCeEEEEecCCCCC---CCccccCCCCcceE-Eec
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF-DQTVNVKVIMATNRADT---LDPALLRPGRLDRK-IEF   88 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~-~~~~~v~vi~ttn~~~~---ld~al~r~grf~~~-i~~   88 (168)
                      |.|.++||+|.+++-.           +++  .+.+.+|-. ....++.|||.|.+.+.   +.+.+.+  ||.+. |++
T Consensus       138 ~ViFIldEfDlf~~h~-----------rQt--llYnlfDisqs~r~Piciig~Ttrld~lE~LEKRVKS--RFshr~I~m  202 (408)
T KOG2228|consen  138 KVIFILDEFDLFAPHS-----------RQT--LLYNLFDISQSARAPICIIGVTTRLDILELLEKRVKS--RFSHRVIFM  202 (408)
T ss_pred             eEEEEeehhhccccch-----------hhH--HHHHHHHHHhhcCCCeEEEEeeccccHHHHHHHHHHh--hcccceeec
Confidence            5677788999987432           011  123333322 23558999998888765   4567888  99987 666


Q ss_pred             CCC-CHHHHHHHHHhhc
Q 030960           89 PLP-DRRQKRLVFQMNL  104 (168)
Q Consensus        89 ~~P-~~~~R~~il~~~l  104 (168)
                      .+| ..++-..+++..+
T Consensus       203 ~~~~~l~~yv~l~r~ll  219 (408)
T KOG2228|consen  203 LPSLPLGDYVDLYRKLL  219 (408)
T ss_pred             cCCCChHHHHHHHHHHh
Confidence            443 6788888888655

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=87.71  E-value=2.2  Score=29.43  Aligned_cols=64  Identities=23%  Similarity=0.284  Sum_probs=36.1

Q ss_pred             HHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCC
Q 030960            5 VFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTL   72 (168)
Q Consensus         5 iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~l   72 (168)
                      ++..+....|.+++|||+..+..................+..++..+.    ..++.+|++++.....
T Consensus        77 ~~~~~~~~~~~~lviDe~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~----~~~~~vv~~~~~~~~~  140 (165)
T cd01120          77 AERLRERGGDDLIILDELTRLVRALREIREGYPGELDEELRELLERAR----KGGVTVIFTLQVPSGD  140 (165)
T ss_pred             HHHHHhCCCCEEEEEEcHHHHHHHHHHHHhcCChHHHHHHHHHHHHHh----cCCceEEEEEecCCcc
Confidence            455667778999999999998754321111222223344444444443    2356666666655544

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=87.67  E-value=3.8  Score=37.05  Aligned_cols=94  Identities=18%  Similarity=0.272  Sum_probs=52.4

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecC--
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFP--   89 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~--   89 (168)
                      ..|.+|+|||++.+-.          ......+..++...     .+++.+|.+|.....++-.-++  .-+..+.++  
T Consensus       120 ~~~~~lvlDD~h~~~~----------~~~~~~l~~l~~~~-----~~~~~lv~~sR~~~~~~~~~l~--~~~~~~~l~~~  182 (903)
T PRK04841        120 HQPLYLVIDDYHLITN----------PEIHEAMRFFLRHQ-----PENLTLVVLSRNLPPLGIANLR--VRDQLLEIGSQ  182 (903)
T ss_pred             CCCEEEEEeCcCcCCC----------hHHHHHHHHHHHhC-----CCCeEEEEEeCCCCCCchHhHH--hcCcceecCHH
Confidence            5699999999998721          11224455554433     2234344455442222211111  112345555  


Q ss_pred             --CCCHHHHHHHHHhhcCCC---CCHHHHHhCCCCCCH
Q 030960           90 --LPDRRQKRLVFQMNLSDE---VDLEDYVSRPDKISA  122 (168)
Q Consensus        90 --~P~~~~R~~il~~~l~~~---~~~~~la~~t~g~s~  122 (168)
                        +.+.++-.+++...+...   .+...+.+.|+|+-.
T Consensus       183 ~l~f~~~e~~~ll~~~~~~~~~~~~~~~l~~~t~Gwp~  220 (903)
T PRK04841        183 QLAFDHQEAQQFFDQRLSSPIEAAESSRLCDDVEGWAT  220 (903)
T ss_pred             hCCCCHHHHHHHHHhccCCCCCHHHHHHHHHHhCChHH
Confidence              668899999998666533   345667788888754

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

Probab=86.74  E-value=1.6  Score=39.78  Aligned_cols=51  Identities=20%  Similarity=0.281  Sum_probs=36.3

Q ss_pred             HHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC---------CCCCeEEEEecCC
Q 030960            4 DVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD---------QTVNVKVIMATNR   68 (168)
Q Consensus         4 ~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~---------~~~~v~vi~ttn~   68 (168)
                      .+.+..++..-+||||||+|.-           +.   .+.+.|+..+|.-.         .-++++||+|+|.
T Consensus       651 ~LteavrrrP~sVVLfdeIEkA-----------h~---~v~n~llq~lD~GrltDs~Gr~Vd~kN~I~IMTsn~  710 (898)
T KOG1051|consen  651 QLTEAVKRRPYSVVLFEEIEKA-----------HP---DVLNILLQLLDRGRLTDSHGREVDFKNAIFIMTSNV  710 (898)
T ss_pred             HHHHHHhcCCceEEEEechhhc-----------CH---HHHHHHHHHHhcCccccCCCcEeeccceEEEEeccc
Confidence            5677778888999999999953           22   56666677676432         2335899999876

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=86.65  E-value=0.99  Score=33.38  Aligned_cols=68  Identities=10%  Similarity=0.227  Sum_probs=38.1

Q ss_pred             HHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCC
Q 030960            3 RDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLD   73 (168)
Q Consensus         3 ~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld   73 (168)
                      ..+.+.+....|.+|+||-+..++.......  .. ...+.+..++..+..+.+..++.+|.|+......+
T Consensus        87 ~~l~~~~~~~~~~lvVIDSis~l~~~~~~~~--~~-~~~~~l~~~~~~L~~~~~~~~v~vl~t~~~~~~~~  154 (209)
T TIGR02237        87 QKTSKFIDRDSASLVVVDSFTALYRLELSDD--RI-SRNRELARQLTLLLSLARKKNLAVVITNQVYTDVN  154 (209)
T ss_pred             HHHHHHHhhcCccEEEEeCcHHHhHHHhCCc--cH-HHHHHHHHHHHHHHHHHHHcCCEEEEEcccEEecC
Confidence            3445556666899999999999874321111  11 11223333444444444566777887765444443

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

>KOG0478 consensus DNA replication licensing factor, MCM4 component [Replication, recombination and repair]

Probab=86.51  E-value=7.4  Score=34.56  Aligned_cols=36  Identities=14%  Similarity=0.161  Sum_probs=29.3

Q ss_pred             CCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960          120 ISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus       120 ~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      -+++.++.+.+.+...|-.+....+...|+++|+.-
T Consensus       688 at~rQlesLiRlsEahak~r~s~~ve~~dV~eA~~l  723 (804)
T KOG0478|consen  688 ATPRQLESLIRLSEAHAKMRLSNRVEEIDVEEAVRL  723 (804)
T ss_pred             hhHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHH
Confidence            467889999888887777777788888999988854

>KOG1968 consensus Replication factor C, subunit RFC1 (large subunit) [Replication, recombination and repair]

Probab=86.26  E-value=3.4  Score=37.66  Aligned_cols=99  Identities=17%  Similarity=0.192  Sum_probs=64.9

Q ss_pred             eEEEEcccccccc-cccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           15 AIIFIDEVDAIAT-ARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        15 ~ii~iDe~D~l~~-~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      .||++||+|.++. .|            ..+..+...+.    ...+-+|.++|..+--+.....  |-..-++|+.|+.
T Consensus       430 ~vil~devD~~~~~dR------------g~v~~l~~l~~----ks~~Piv~~cndr~~p~sr~~~--~~~~~l~f~kP~~  491 (871)
T KOG1968|consen  430 FLILMDEVDGMFGEDR------------GGVSKLSSLCK----KSSRPLVCTCNDRNLPKSRALS--RACSDLRFSKPSS  491 (871)
T ss_pred             eEEEEeccccccchhh------------hhHHHHHHHHH----hccCCeEEEecCCCCccccchh--hhcceeeecCCcH
Confidence            3999999999874 11            22222222232    2344588888888877775555  6668899999999


Q ss_pred             HHHHHHHHhhcC-C-----CCCHHHHHhCCCCCCHHHHHHHHHHHHHH
Q 030960           94 RQKRLVFQMNLS-D-----EVDLEDYVSRPDKISAAEIAAICQEAGMH  135 (168)
Q Consensus        94 ~~R~~il~~~l~-~-----~~~~~~la~~t~g~s~~di~~l~~~a~~~  135 (168)
                      ..+..-+..... +     +-.++++.+.+    ++||...+..-.+.
T Consensus       492 ~~i~~ri~si~~se~~ki~~~~l~~~s~~~----~~DiR~~i~~lq~~  535 (871)
T KOG1968|consen  492 ELIRSRIMSICKSEGIKISDDVLEEISKLS----GGDIRQIIMQLQFW  535 (871)
T ss_pred             HHHHhhhhhhhcccceecCcHHHHHHHHhc----ccCHHHHHHHHhhh
Confidence            998876654333 2     33456666655    78888877765554

>PHA00012 I assembly protein

Probab=85.92  E-value=0.59  Score=37.72  Aligned_cols=80  Identities=10%  Similarity=0.120  Sum_probs=50.4

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCC-C----CcceEE
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRP-G----RLDRKI   86 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~-g----rf~~~i   86 (168)
                      ..-+++++||+...++.|.......     .-+.+++...    ...+.-+|.+|.+|..+|+.++.. +    |+-+.-
T Consensus        80 p~gsLlVlDEaq~~fp~R~~~sk~p-----~~vie~l~~h----Rh~G~DvilITQ~ps~VDs~IR~ll~eH~v~cRRld  150 (361)
T PHA00012         80 SKNGLLVLDECGTWFNSRSWNDKER-----QPVIDWFLHA----RKLGWDIIFIIQDISIMDKQAREALAEHVVYCRRLD  150 (361)
T ss_pred             CCCcEEEEECcccccCCCCcCcCCc-----HHHHHHHHHh----ccCCceEEEEcCCHHHHhHHHHHhhhheEEEEEecc
Confidence            3468999999999999985544322     2122333322    344677999999999999998731 1    122222


Q ss_pred             ecCCCCHHHHHHHH
Q 030960           87 EFPLPDRRQKRLVF  100 (168)
Q Consensus        87 ~~~~P~~~~R~~il  100 (168)
                      .+..|-...-..++
T Consensus       151 ~~~iP~i~~~~~~~  164 (361)
T PHA00012        151 KITIPFIGTLYSVL  164 (361)
T ss_pred             ccccceehhHHHHh
Confidence            45566656655555

>PRK07452 DNA polymerase III subunit delta; Validated

Probab=85.78  E-value=12  Score=29.76  Aligned_cols=123  Identities=12%  Similarity=0.150  Sum_probs=63.2

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC---CCCccccCCCCcceEEecCC
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD---TLDPALLRPGRLDRKIEFPL   90 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~---~ld~al~r~grf~~~i~~~~   90 (168)
                      +-+|++++.+.+-.        ..   ......+...+++... ..++|+.+++.++   .+...+..   +.....+.+
T Consensus        62 ~rlVvv~~~~~~~~--------~~---~~~~~~L~~~l~~~~~-~~~li~~~~~~~d~r~k~~k~l~k---~~~~~~~~~  126 (326)
T PRK07452         62 GRLVWLKNSPLCQG--------CS---EELLAELERTLPLIPE-NTHLLLTNTKKPDGRLKSTKLLQK---LAEEKEFSL  126 (326)
T ss_pred             ceEEEEeCchhhcc--------CC---HHHHHHHHHHHcCCCC-CcEEEEEeCCCcchHHHHHHHHHH---ceeEEEecC
Confidence            56677777654311        11   1344566666765433 3455655544332   12223332   344555544


Q ss_pred             C---CHHHHHHHHHhhcCC---CC---CHHHHHhCCCCCCHHHHHHHHHHHHHHHHH--hCCCccCHHHHHHHHHh
Q 030960           91 P---DRRQKRLVFQMNLSD---EV---DLEDYVSRPDKISAAEIAAICQEAGMHAVR--KNRYVILPKDFEKGYRT  155 (168)
Q Consensus        91 P---~~~~R~~il~~~l~~---~~---~~~~la~~t~g~s~~di~~l~~~a~~~a~~--~~~~~i~~~d~~~al~~  155 (168)
                      |   +.++...+++..+..   .+   .+..+++.+.    .|+..+.++.-..+.-  .....||.+|+.+.+..
T Consensus       127 ~~~~~~~~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g----~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~  198 (326)
T PRK07452        127 IPPWDTEGLKQLVERTAQELGVKLTPEAAELLAEAVG----NDSRRLYNELEKLALYAENSTKPISAEEVKALVSN  198 (326)
T ss_pred             CCcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhC----ccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhcc
Confidence            4   445555666544431   22   2344555443    4555555555555444  23457999999988764

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=84.56  E-value=1.8  Score=36.43  Aligned_cols=79  Identities=28%  Similarity=0.402  Sum_probs=44.5

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC-----CC------CCCeEEEE-------ecCCCCCCCc
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF-----DQ------TVNVKVIM-------ATNRADTLDP   74 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~-----~~------~~~v~vi~-------ttn~~~~ld~   74 (168)
                      +-.||||||+|.+...........+-..+.+...||..+++-     .+      ....+.|-       ++..-..||.
T Consensus       291 QqGIVflDEvDKi~~~~~~i~~~RDVsGEGVQQaLLKllEGtvVnVpeK~~~~~~rgd~vqiDTtnILFiasGAF~~Ldk  370 (564)
T KOG0745|consen  291 QQGIVFLDEVDKITKKAESIHTSRDVSGEGVQQALLKLLEGTVVNVPEKGSRRKPRGDTVQIDTTNILFIASGAFVGLDK  370 (564)
T ss_pred             hcCeEEEehhhhhcccCccccccccccchhHHHHHHHHhcccEEcccCCCCCCCCCCCeEEEeccceEEEecccccchHH
Confidence            459999999999984432222111112235666677777653     01      11122333       3334456787


Q ss_pred             cccCCCCcc-eEEecCCCCH
Q 030960           75 ALLRPGRLD-RKIEFPLPDR   93 (168)
Q Consensus        75 al~r~grf~-~~i~~~~P~~   93 (168)
                      -+-|  |.+ ..+-|+.|+.
T Consensus       371 ~I~r--R~~d~slGFg~~s~  388 (564)
T KOG0745|consen  371 IISR--RLDDKSLGFGAPSS  388 (564)
T ss_pred             HHHH--hhcchhcccCCCCC
Confidence            7776  654 6677888833

>PF13304 AAA_21: AAA domain; PDB: 3QKS_B 1US8_B 1F2U_B 1F2T_B 3QKT_A 1II8_B 3QKR_B 3QKU_A

Probab=84.35  E-value=3  Score=30.62  Aligned_cols=45  Identities=36%  Similarity=0.536  Sum_probs=25.8

Q ss_pred             eEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCC
Q 030960           15 AIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLD   73 (168)
Q Consensus        15 ~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld   73 (168)
                      .+++|||.|.-+..          ...+.+-.++..+.   . .++=||.||++|.-||
T Consensus       259 ~illiDEpE~~LHp----------~~q~~l~~~l~~~~---~-~~~QviitTHSp~ild  303 (303)
T PF13304_consen  259 SILLIDEPENHLHP----------SWQRKLIELLKELS---K-KNIQVIITTHSPFILD  303 (303)
T ss_dssp             SEEEEESSSTTSSH----------HHHHHHHHHHHHTG---G-GSSEEEEEES-GGG--
T ss_pred             eEEEecCCcCCCCH----------HHHHHHHHHHHhhC---c-cCCEEEEeCccchhcC
Confidence            99999999986532          22222223443332   2 3555899999987654

>PRK15115 response regulator GlrR; Provisional

Probab=83.99  E-value=6.6  Score=32.56  Aligned_cols=120  Identities=15%  Similarity=0.274  Sum_probs=61.1

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC-----CCC----CCCeEEEEecCCCCCCCccccCCCCcce
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG-----FDQ----TVNVKVIMATNRADTLDPALLRPGRLDR   84 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~-----~~~----~~~v~vi~ttn~~~~ld~al~r~grf~~   84 (168)
                      ...|||||+|.+-..              ....++..++.     +..    ...+.+|+||+.  +++..+. .|+|..
T Consensus       229 ~gtl~l~~i~~l~~~--------------~q~~L~~~l~~~~~~~~g~~~~~~~~~rii~~~~~--~l~~~~~-~~~f~~  291 (444)
T PRK15115        229 GGTLFLDEIGDMPAP--------------LQVKLLRVLQERKVRPLGSNRDIDIDVRIISATHR--DLPKAMA-RGEFRE  291 (444)
T ss_pred             CCEEEEEccccCCHH--------------HHHHHHHHHhhCCEEeCCCCceeeeeEEEEEeCCC--CHHHHHH-cCCccH
Confidence            578999999987421              22223333321     111    125788888885  3444443 366632


Q ss_pred             -------EEecCCCCHHHHHH----HHHhhcCC-------C---CC---HHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC
Q 030960           85 -------KIEFPLPDRRQKRL----VFQMNLSD-------E---VD---LEDYVSRPDKISAAEIAAICQEAGMHAVRKN  140 (168)
Q Consensus        85 -------~i~~~~P~~~~R~~----il~~~l~~-------~---~~---~~~la~~t~g~s~~di~~l~~~a~~~a~~~~  140 (168)
                             .+.+..|...+|.+    ++++++..       .   ++   +..|..+.=--..++|.++++.++..   ..
T Consensus       292 ~l~~~l~~~~i~lPpLr~R~eDi~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~WpgNvreL~~~i~~~~~~---~~  368 (444)
T PRK15115        292 DLYYRLNVVSLKIPALAERTEDIPLLANHLLRQAAERHKPFVRAFSTDAMKRLMTASWPGNVRQLVNVIEQCVAL---TS  368 (444)
T ss_pred             HHHHhhceeeecCCChHhccccHHHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHhCCCCChHHHHHHHHHHHHHh---CC
Confidence                   23455566666642    33333321       1   11   22233332122457777777776543   23


Q ss_pred             CCccCHHHHHHHH
Q 030960          141 RYVILPKDFEKGY  153 (168)
Q Consensus       141 ~~~i~~~d~~~al  153 (168)
                      ...|+.+++...+
T Consensus       369 ~~~i~~~~l~~~~  381 (444)
T PRK15115        369 SPVISDALVEQAL  381 (444)
T ss_pred             CCccChhhhhhhh
Confidence            4457777765444

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=83.37  E-value=5.8  Score=31.81  Aligned_cols=13  Identities=23%  Similarity=0.534  Sum_probs=11.0

Q ss_pred             CeEEEEccccccc
Q 030960           14 PAIIFIDEVDAIA   26 (168)
Q Consensus        14 p~ii~iDe~D~l~   26 (168)
                      ...|||||+|.+-
T Consensus       101 gGtL~l~~i~~L~  113 (326)
T PRK11608        101 GGTLFLDELATAP  113 (326)
T ss_pred             CCeEEeCChhhCC
Confidence            5789999999874

>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=83.20  E-value=1.5  Score=34.32  Aligned_cols=85  Identities=19%  Similarity=0.419  Sum_probs=44.7

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhc---cC--C--CCCCCeEEEEecCCCC---CCCccccCCCCc
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQM---DG--F--DQTVNVKVIMATNRAD---TLDPALLRPGRL   82 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l---~~--~--~~~~~v~vi~ttn~~~---~ld~al~r~grf   82 (168)
                      ..+|+||||+..-..+.    .+.. ....++.++++.=   |.  +  ..-..+-+||+.+.+.   .+++.++|  .|
T Consensus       100 k~lv~fiDDlN~p~~d~----ygtq-~~iElLRQ~i~~~g~yd~~~~~~~~i~~i~~vaa~~p~~Gr~~is~R~~r--~f  172 (272)
T PF12775_consen  100 KKLVLFIDDLNMPQPDK----YGTQ-PPIELLRQLIDYGGFYDRKKLEWKSIEDIQFVAAMNPTGGRNPISPRFLR--HF  172 (272)
T ss_dssp             SEEEEEEETTT-S---T----TS---HHHHHHHHHHHCSEEECTTTTEEEEECSEEEEEEESSTTT--SHHHHHHT--TE
T ss_pred             cEEEEEecccCCCCCCC----CCCc-CHHHHHHHHHHhcCcccCCCcEEEEEeeeEEEEecCCCCCCCCCChHHhh--he
Confidence            46899999998654333    1111 1224444444331   11  0  1122477888876422   47777776  55


Q ss_pred             ceEEecCCCCHHHHHHHHHhhcC
Q 030960           83 DRKIEFPLPDRRQKRLVFQMNLS  105 (168)
Q Consensus        83 ~~~i~~~~P~~~~R~~il~~~l~  105 (168)
                       ..+.++.|+.+.-..|+...+.
T Consensus       173 -~i~~~~~p~~~sl~~If~~il~  194 (272)
T PF12775_consen  173 -NILNIPYPSDESLNTIFSSILQ  194 (272)
T ss_dssp             -EEEE----TCCHHHHHHHHHHH
T ss_pred             -EEEEecCCChHHHHHHHHHHHh
Confidence             4789999999988888774443

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=82.87  E-value=3.6  Score=34.10  Aligned_cols=13  Identities=23%  Similarity=0.646  Sum_probs=11.1

Q ss_pred             CeEEEEccccccc
Q 030960           14 PAIIFIDEVDAIA   26 (168)
Q Consensus        14 p~ii~iDe~D~l~   26 (168)
                      ...|||||+|.+-
T Consensus       234 ~gtl~l~~i~~l~  246 (445)
T TIGR02915       234 GGTLFLDEIGDLP  246 (445)
T ss_pred             CCEEEEechhhCC
Confidence            5789999999874

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).

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=82.47  E-value=7.8  Score=32.27  Aligned_cols=119  Identities=20%  Similarity=0.318  Sum_probs=61.3

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC-----CC----CCCCeEEEEecCCCCCCCccccCCCCcc-
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG-----FD----QTVNVKVIMATNRADTLDPALLRPGRLD-   83 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~-----~~----~~~~v~vi~ttn~~~~ld~al~r~grf~-   83 (168)
                      ...|||||+|.+-..              +...++..++.     ..    ....+-+|++|+..-  + .+...|+|. 
T Consensus       229 ~gtl~l~ei~~l~~~--------------~q~~ll~~l~~~~~~~~~~~~~~~~~~rii~~~~~~l--~-~~~~~~~f~~  291 (463)
T TIGR01818       229 GGTLFLDEIGDMPLD--------------AQTRLLRVLADGEFYRVGGRTPIKVDVRIVAATHQNL--E-ALVRQGKFRE  291 (463)
T ss_pred             CCeEEEEchhhCCHH--------------HHHHHHHHHhcCcEEECCCCceeeeeeEEEEeCCCCH--H-HHHHcCCcHH
Confidence            678999999987421              12223333321     11    112466788776432  1 222334443 


Q ss_pred             --------eEEecCCCC--HHHHHHHHHhhcCC----------CCC---HHHHHhCCCCC--CHHHHHHHHHHHHHHHHH
Q 030960           84 --------RKIEFPLPD--RRQKRLVFQMNLSD----------EVD---LEDYVSRPDKI--SAAEIAAICQEAGMHAVR  138 (168)
Q Consensus        84 --------~~i~~~~P~--~~~R~~il~~~l~~----------~~~---~~~la~~t~g~--s~~di~~l~~~a~~~a~~  138 (168)
                              ..|++|+..  .++...++++++..          .++   +..|..+  +|  ..++|++++..++..+  
T Consensus       292 ~L~~rl~~~~i~lPpLr~R~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~--~wpgNvreL~~~~~~~~~~~--  367 (463)
T TIGR01818       292 DLFHRLNVIRIHLPPLRERREDIPRLARHFLALAARELDVEPKLLDPEALERLKQL--RWPGNVRQLENLCRWLTVMA--  367 (463)
T ss_pred             HHHHHhCcceecCCCcccchhhHHHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHhC--CCCChHHHHHHHHHHHHHhC--
Confidence                    355565554  44555555555431          111   1122222  33  2378888888776544  


Q ss_pred             hCCCccCHHHHHHHHH
Q 030960          139 KNRYVILPKDFEKGYR  154 (168)
Q Consensus       139 ~~~~~i~~~d~~~al~  154 (168)
                       ....|+.+|+...+.
T Consensus       368 -~~~~i~~~~l~~~~~  382 (463)
T TIGR01818       368 -SGDEVLVSDLPAELA  382 (463)
T ss_pred             -CCCcccHHhchHHHh
Confidence             234688888866553

This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.

>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=82.43  E-value=1.5  Score=30.57  Aligned_cols=52  Identities=25%  Similarity=0.309  Sum_probs=28.1

Q ss_pred             eEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC---------CCCCCeEEEEecCCCC-----CCCccccCCC
Q 030960           15 AIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF---------DQTVNVKVIMATNRAD-----TLDPALLRPG   80 (168)
Q Consensus        15 ~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~---------~~~~~v~vi~ttn~~~-----~ld~al~r~g   80 (168)
                      .|+++||+...-           .   ++.+.+|+.|..-         .-..+.+||||-|..+     .||.+++.  
T Consensus        64 ~ill~DEiNrap-----------p---ktQsAlLeam~Er~Vt~~g~~~~lp~pf~ViATqNp~e~~Gty~Lpea~~D--  127 (131)
T PF07726_consen   64 NILLADEINRAP-----------P---KTQSALLEAMEERQVTIDGQTYPLPDPFFVIATQNPVEQEGTYPLPEAQLD--  127 (131)
T ss_dssp             SEEEEETGGGS------------H---HHHHHHHHHHHHSEEEETTEEEE--SS-EEEEEE-TT--S------HHHHT--
T ss_pred             ceeeecccccCC-----------H---HHHHHHHHHHHcCeEEeCCEEEECCCcEEEEEecCccccCceecCCHHHhc--
Confidence            589999987532           1   4445556555421         1233588888988766     67777776  


Q ss_pred             Cc
Q 030960           81 RL   82 (168)
Q Consensus        81 rf   82 (168)
                      ||
T Consensus       128 RF  129 (131)
T PF07726_consen  128 RF  129 (131)
T ss_dssp             TS
T ss_pred             cc
Confidence            76

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.

>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex

Probab=82.31  E-value=3.6  Score=25.05  Aligned_cols=31  Identities=23%  Similarity=0.240  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960          124 EIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus       124 di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      -|..++++|...+....+..+|.+|+..||+
T Consensus        36 rlreiiq~a~kfm~hskR~~Lt~~Di~~ALr   66 (66)
T PF02969_consen   36 RLREIIQEALKFMRHSKRTKLTTDDINSALR   66 (66)
T ss_dssp             HHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred             HHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence            4566777787777777778899999999985

TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.

>PLN03210 Resistant to P

Probab=82.25  E-value=13  Score=35.13  Aligned_cols=71  Identities=25%  Similarity=0.373  Sum_probs=44.5

Q ss_pred             HcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCC
Q 030960           11 ENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPL   90 (168)
Q Consensus        11 ~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~   90 (168)
                      ...+.+|++||+|..                ..+..+....+.+  ..+..||.||.+..     +.+....++.++++.
T Consensus       294 ~~krvLLVLDdv~~~----------------~~l~~L~~~~~~~--~~GsrIIiTTrd~~-----vl~~~~~~~~~~v~~  350 (1153)
T PLN03210        294 KHRKVLIFIDDLDDQ----------------DVLDALAGQTQWF--GSGSRIIVITKDKH-----FLRAHGIDHIYEVCL  350 (1153)
T ss_pred             hCCeEEEEEeCCCCH----------------HHHHHHHhhCccC--CCCcEEEEEeCcHH-----HHHhcCCCeEEEecC
Confidence            346889999998742                2233333322211  22344666777543     333345788999999


Q ss_pred             CCHHHHHHHHHhhc
Q 030960           91 PDRRQKRLVFQMNL  104 (168)
Q Consensus        91 P~~~~R~~il~~~l  104 (168)
                      |+.++..++|..+.
T Consensus       351 l~~~ea~~LF~~~A  364 (1153)
T PLN03210        351 PSNELALEMFCRSA  364 (1153)
T ss_pred             CCHHHHHHHHHHHh
Confidence            99999999997543

syringae 6; Provisional

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

Probab=81.96  E-value=3.5  Score=32.78  Aligned_cols=87  Identities=17%  Similarity=0.279  Sum_probs=58.4

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      --+|+|.|+|.|..+.       .       ..+-.-|+.  ..++.-+|..+|+...+=+++++  |. ..+.++.|+.
T Consensus       128 fKvvvi~ead~LT~dA-------Q-------~aLRRTMEk--Ys~~~RlIl~cns~SriIepIrS--RC-l~iRvpaps~  188 (351)
T KOG2035|consen  128 FKVVVINEADELTRDA-------Q-------HALRRTMEK--YSSNCRLILVCNSTSRIIEPIRS--RC-LFIRVPAPSD  188 (351)
T ss_pred             eEEEEEechHhhhHHH-------H-------HHHHHHHHH--HhcCceEEEEecCcccchhHHhh--he-eEEeCCCCCH
Confidence            3588999999885321       1       112223332  23356678888999999999998  64 4688999999


Q ss_pred             HHHHHHHHhhcCC------CCCHHHHHhCCCC
Q 030960           94 RQKRLVFQMNLSD------EVDLEDYVSRPDK  119 (168)
Q Consensus        94 ~~R~~il~~~l~~------~~~~~~la~~t~g  119 (168)
                      ++...++..-+..      +--+.++|+.++|
T Consensus       189 eeI~~vl~~v~~kE~l~lp~~~l~rIa~kS~~  220 (351)
T KOG2035|consen  189 EEITSVLSKVLKKEGLQLPKELLKRIAEKSNR  220 (351)
T ss_pred             HHHHHHHHHHHHHhcccCcHHHHHHHHHHhcc
Confidence            9999999855542      2335566666654

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=81.15  E-value=10  Score=31.09  Aligned_cols=28  Identities=18%  Similarity=0.495  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccc
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATAR   29 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~   29 (168)
                      +..+++.++...|.+|+||.+-.++...
T Consensus       147 le~I~~~i~~~~~~lVVIDSIq~l~~~~  174 (372)
T cd01121         147 LEDILASIEELKPDLVIIDSIQTVYSSE  174 (372)
T ss_pred             HHHHHHHHHhcCCcEEEEcchHHhhccc
Confidence            4567778888899999999999987443

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.

>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin

Probab=80.53  E-value=3.9  Score=24.44  Aligned_cols=30  Identities=30%  Similarity=0.251  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960          124 EIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus       124 di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      =|..++.+|...+...+++.|+.+|+..|+
T Consensus        36 Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av   65 (65)
T PF00808_consen   36 FIQYLAKEANEIAQRDKRKTITYEDVAKAV   65 (65)
T ss_dssp             HHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence            466678888888888889999999999885

The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....

>COG1485 Predicted ATPase [General function prediction only]

Probab=80.29  E-value=1.9  Score=35.08  Aligned_cols=46  Identities=24%  Similarity=0.308  Sum_probs=30.2

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCC-CCCCCc
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNR-ADTLDP   74 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~-~~~ld~   74 (168)
                      --||.|||+..-           +..-.-+++.|++.|-    ..+|++|+|+|. |++|-+
T Consensus       131 ~~vLCfDEF~Vt-----------DI~DAMiL~rL~~~Lf----~~GV~lvaTSN~~P~~LY~  177 (367)
T COG1485         131 TRVLCFDEFEVT-----------DIADAMILGRLLEALF----ARGVVLVATSNTAPDNLYK  177 (367)
T ss_pred             CCEEEeeeeeec-----------ChHHHHHHHHHHHHHH----HCCcEEEEeCCCChHHhcc
Confidence            468999998742           1122356667777663    338999999997 555544

>PF13173 AAA_14: AAA domain

Probab=80.07  E-value=4.4  Score=27.51  Aligned_cols=64  Identities=28%  Similarity=0.350  Sum_probs=34.4

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCc--cccCCCCcceEEecCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDP--ALLRPGRLDRKIEFPL   90 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~--al~r~grf~~~i~~~~   90 (168)
                      ++.+|+|||+..+-        ..    ...+..+.   +.   ..++-+|.|++....+..  +-.-+||.. .+++.|
T Consensus        61 ~~~~i~iDEiq~~~--------~~----~~~lk~l~---d~---~~~~~ii~tgS~~~~l~~~~~~~l~gr~~-~~~l~P  121 (128)
T PF13173_consen   61 GKKYIFIDEIQYLP--------DW----EDALKFLV---DN---GPNIKIILTGSSSSLLSKDIAESLAGRVI-EIELYP  121 (128)
T ss_pred             CCcEEEEehhhhhc--------cH----HHHHHHHH---Hh---ccCceEEEEccchHHHhhcccccCCCeEE-EEEECC
Confidence            67999999998761        11    13333332   21   124445555554444422  222345765 677888


Q ss_pred             CCHHH
Q 030960           91 PDRRQ   95 (168)
Q Consensus        91 P~~~~   95 (168)
                      .+..|
T Consensus       122 lsf~E  126 (128)
T PF13173_consen  122 LSFRE  126 (128)
T ss_pred             CCHHH
Confidence            77765

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=80.04  E-value=6  Score=33.77  Aligned_cols=18  Identities=17%  Similarity=0.228  Sum_probs=13.9

Q ss_pred             CHHHHHHHHHHHHHHHHH
Q 030960          121 SAAEIAAICQEAGMHAVR  138 (168)
Q Consensus       121 s~~di~~l~~~a~~~a~~  138 (168)
                      ..++|+++++.|+..+..
T Consensus       405 NvrEL~~~i~ra~~~~~~  422 (509)
T PRK05022        405 NVRELEHVISRAALLARA  422 (509)
T ss_pred             cHHHHHHHHHHHHHhcCC
Confidence            558999999988876643

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	168
4b4t_K	428	Near-Atomic Resolution Structural Model Of The Yeas		7e-65
4b4t_I	437	Near-Atomic Resolution Structural Model Of The Yeas		7e-44
3h4m_A	285	Aaa Atpase Domain Of The Proteasome- Activating Nuc		7e-42
4b4t_J	405	Near-Atomic Resolution Structural Model Of The Yeas		4e-41
4b4t_M	434	Near-Atomic Resolution Structural Model Of The Yeas		4e-40
4b4t_L	437	Near-Atomic Resolution Structural Model Of The Yeas		2e-39
4b4t_H	467	Near-Atomic Resolution Structural Model Of The Yeas		3e-36
2dvw_B	83	Structure Of The Oncoprotein Gankyrin In Complex Wi		1e-26
1lv7_A	257	Crystal Structure Of The Aaa Domain Of Ftsh Length		6e-26
3kds_E	465	Apo-ftsh Crystal Structure Length = 465		1e-25
2ce7_A	476	Edta Treated Length = 476		1e-25
3hu3_A	489	Structure Of P97 N-D1 R155h Mutant In Complex With		1e-24
3hu2_A	489	Structure Of P97 N-D1 R86a Mutant In Complex With A		1e-24
3hu1_A	489	Structure Of P97 N-D1 R95g Mutant In Complex With A		2e-24
1e32_A	458	Structure Of The N-Terminal Domain And The D1 Aaa D		2e-24
3cf1_A	806	Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Len		2e-24
1r7r_A	816	The Crystal Structure Of Murine P97VCP AT 3.6A Leng		2e-24
2qz4_A	262	Human Paraplegin, Aaa Domain In Complex With Adp Le		2e-24
3cf0_A	301	Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH		2e-23
1iy2_A	278	Crystal Structure Of The Ftsh Atpase Domain From Th		8e-23
4eiw_A	508	Whole Cytosolic Region Of Atp-Dependent Metalloprot		8e-23
2dhr_A	499	Whole Cytosolic Region Of Atp-Dependent Metalloprot		8e-23
1ixz_A	254	Crystal Structure Of The Ftsh Atpase Domain From Th		9e-23
2r62_A	268	Crystal Structure Of Helicobacter Pylori Atp Depend		6e-21
2x8a_A	274	Human Nuclear Valosin Containing Protein Like (Nvl)		6e-20
2rko_A	331	Crystal Structure Of The Vps4p-Dimer Length = 331		2e-17
2qp9_X	355	Crystal Structure Of S.Cerevisiae Vps4 Length = 355		3e-17
3eih_A	340	Crystal Structure Of S.Cerevisiae Vps4 In The Prese		5e-17
3eie_A	322	Crystal Structure Of S.Cerevisiae Vps4 In The So4-B		6e-17
2zam_A	444	Crystal Structure Of Mouse Skd1VPS4B APO-Form Lengt		3e-16
1xwi_A	322	Crystal Structure Of Vps4b Length = 322		8e-16
2dzn_B	82	Crystal Structure Analysis Of Yeast Nas6p Complexed		4e-15
3d8b_A	357	Crystal Structure Of Human Fidgetin-Like Protein 1		7e-15
3vfd_A	389	Human Spastin Aaa Domain Length = 389		2e-08
3b9p_A	297	Spastin Length = 297		5e-08
2krk_A	86	Solution Nmr Structure Of 26s Protease Regulatory S		3e-04

>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 428

Iteration: 1
 Score =  242 bits (618), Expect = 7e-65,   Method: Compositional matrix adjust.
 Identities = 125/176 (71%), Positives = 144/176 (81%), Gaps = 8/176 (4%)
Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVRDVFRLA+ENAP+IIFIDEVD+IAT RFDAQTG+DREVQRIL+ELL QMDGFDQ+ NV
Sbjct: 253 MVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQSTNV 312
Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFP-LPDRRQKRLVF-----QMNLSDEVDLEDYV 114
           KVIMATNRADTLDPALLRPGRLDRKIEFP L DRR++RL+F     +M+L+ E DL+  +
Sbjct: 313 KVIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLAPEADLDSLI 372
Query: 115 SRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDT--DFEFYK 168
            R D +S A IAAI QEAG+ AVRKNRYVIL  D E+ Y T VK  +T   F+FYK
Sbjct: 373 IRNDSLSGAVIAAIMQEAGLRAVRKNRYVILQSDLEEAYATQVKTDNTVDKFDFYK 428

>pdb|4B4T|I Chain I, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score =  172 bits (437), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 80/156 (51%), Positives = 117/156 (75%), Gaps = 5/156 (3%)
Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           + R +F++A ENAP+I+FIDE+DAI T R+D+ +G +RE+QR ++ELLNQ+DGFD   +V
Sbjct: 263 LCRQIFKVAGENAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDDRGDV 322
Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVF-----QMNLSDEVDLEDYVS 115
           KVIMATN+ +TLDPAL+RPGR+DRKI F  PD   K+ +      +MNLS++V+LE  V+
Sbjct: 323 KVIMATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLSEDVNLETLVT 382
Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
             D +S A+I A+C EAG+ A+R+ R  +  +DF++
Sbjct: 383 TKDDLSGADIQAMCTEAGLLALRERRMQVTAEDFKQ 418

>pdb|3H4M|A Chain A, Aaa Atpase Domain Of The Proteasome- Activating Nucleotidase Length = 285

Iteration: 1
 Score =  166 bits (419), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 84/156 (53%), Positives = 110/156 (70%), Gaps = 5/156 (3%)
Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           +V+D+F+LAKE AP+IIFIDE+DAIA  R DA TG DREVQR LM+LL +MDGFD   +V
Sbjct: 98  LVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDV 157
Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVF-----QMNLSDEVDLEDYVS 115
           K+I ATNR D LDPA+LRPGR DR IE P PD + +  +      +MNL+++V+LE+   
Sbjct: 158 KIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAK 217
Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
             +    AE+ AIC EAGM+A+R+ R  +   DF K
Sbjct: 218 MTEGCVGAELKAICTEAGMNAIRELRDYVTMDDFRK 253

>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 405

Iteration: 1
 Score =  163 bits (413), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 74/155 (47%), Positives = 109/155 (70%), Gaps = 5/155 (3%)
Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVR++F +A+E+AP+IIF+DE+D+I + R +   G D EVQR ++ELLNQ+DGF+ + N+
Sbjct: 229 MVRELFVMAREHAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFETSKNI 288
Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVF-----QMNLSDEVDLEDYVS 115
           K+IMATNR D LDPALLRPGR+DRKIEFP P    +  +      +MNL+  ++L     
Sbjct: 289 KIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGINLRKVAE 348
Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFE 150
           + +  S A++  +C EAGM+A+R+ R  +  +DFE
Sbjct: 349 KMNGCSGADVKGVCTEAGMYALRERRIHVTQEDFE 383

>pdb|4B4T|M Chain M, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 434

Iteration: 1
 Score =  160 bits (404), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 81/172 (47%), Positives = 107/172 (62%), Gaps = 5/172 (2%)
Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           +VRD F LAKE AP IIFIDE+DAI T RFD++   DREVQR ++ELLNQ+DGF     V
Sbjct: 262 LVRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQLDGFSSDDRV 321
Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
           KV+ ATNR D LDPALLR GRLDRKIEFPLP    +  + Q     M   D+++ ++   
Sbjct: 322 KVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTDDDINWQELAR 381
Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEFY 167
             D+ + A++ A+  EAGM A+R  +  +  +DF +G      +      FY
Sbjct: 382 STDEFNGAQLKAVTVEAGMIALRNGQSSVKHEDFVEGISEVQARKSKSVSFY 433

>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score =  157 bits (398), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 86/175 (49%), Positives = 108/175 (61%), Gaps = 7/175 (4%)
Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           ++R++F  AKE+ P IIF+DEVDAI   RF   T ADRE+QR LMELL QMDGFD     
Sbjct: 262 IIREMFAYAKEHEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFDNLGQT 321
Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNL-----SDEVDLEDYVS 115
           K+IMATNR DTLDPALLRPGRLDRK+E PLP+   +  +F+++      + E D E  V 
Sbjct: 322 KIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEFDFEAAVK 381
Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR--TNVKKPDTDFEFYK 168
             D  + A+I     EAG  A+R +R  I P D  K  R    VKK +   E+ K
Sbjct: 382 MSDGFNGADIRNCATEAGFFAIRDDRDHINPDDLMKAVRKVAEVKKLEGTIEYQK 436

>pdb|4B4T|H Chain H, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 467

Iteration: 1
 Score =  147 bits (370), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 76/158 (48%), Positives = 106/158 (67%), Gaps = 9/158 (5%)
Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           MVR++F +A+     IIF DE+DA+  ARFD   G D EVQR ++EL+ Q+DGFD   N+
Sbjct: 290 MVRELFEMARTKKACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDPRGNI 349
Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSDEVDLE-----DYVS 115
           KV+ ATNR +TLDPALLRPGR+DRK+EF LPD   +  +F+++ S  + +E     + +S
Sbjct: 350 KVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIH-SKSMSVERGIRWELIS 408
Query: 116 R--PDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
           R  P+  + AE+ ++C EAGM A+R  R V   KDF K
Sbjct: 409 RLCPNS-TGAELRSVCTEAGMFAIRARRKVATEKDFLK 445

>pdb|2DVW|B Chain B, Structure Of The Oncoprotein Gankyrin In Complex With S6 Atpase Of The 26s Proteasome Length = 83

Iteration: 1
 Score =  115 bits (289), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 54/82 (65%), Positives = 68/82 (82%), Gaps = 5/82 (6%)
Query: 92  DRRQKRLVF-----QMNLSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILP 146
           DRRQKRL+F     +MNLS+EVDLEDYV+RPDKIS A+I +ICQE+GM AVR+NRY++L 
Sbjct: 2   DRRQKRLIFSTITSKMNLSEEVDLEDYVARPDKISGADINSICQESGMLAVRENRYIVLA 61
Query: 147 KDFEKGYRTNVKKPDTDFEFYK 168
           KDFEK Y+T +KK + + EFYK
Sbjct: 62  KDFEKAYKTVIKKDEQEHEFYK 83

>pdb|1LV7|A Chain A, Crystal Structure Of The Aaa Domain Of Ftsh Length = 257

Iteration: 1
 Score =  113 bits (282), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 62/155 (40%), Positives = 90/155 (58%), Gaps = 5/155 (3%)
Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           VRD+F  AK+ AP IIFIDE+DA+   R     G   E ++ L ++L +MDGF+    + 
Sbjct: 93  VRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGII 152
Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMN-----LSDEVDLEDYVSR 116
           VI ATNR D LDPALLRPGR DR++   LPD R +  + +++     L+ ++D       
Sbjct: 153 VIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARG 212
Query: 117 PDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
               S A++A +  EA + A R N+ V+   +FEK
Sbjct: 213 TPGFSGADLANLVNEAALFAARGNKRVVSMVEFEK 247

>pdb|3KDS|E Chain E, Apo-ftsh Crystal Structure Length = 465

Iteration: 1
 Score =  112 bits (280), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 63/155 (40%), Positives = 91/155 (58%), Gaps = 5/155 (3%)
Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           VRD+F  AK +AP I+FIDE+DA+   R     G   E ++ L +LL +MDGFD    + 
Sbjct: 97  VRDLFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGII 156
Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMN-----LSDEVDLEDYVSR 116
           V+ ATNR D LDPALLRPGR D+KI    PD   ++ + +++     L+++V+LE    R
Sbjct: 157 VMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAKR 216
Query: 117 PDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
                 A++  +  EA + A R+ R  I  KDFE+
Sbjct: 217 TPGFVGADLENLVNEAALLAAREGRDKITMKDFEE 251

>pdb|2CE7|A Chain A, Edta Treated Length = 476

Iteration: 1
 Score =  112 bits (280), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 63/155 (40%), Positives = 91/155 (58%), Gaps = 5/155 (3%)
Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           VRD+F  AK +AP I+FIDE+DA+   R     G   E ++ L +LL +MDGFD    + 
Sbjct: 97  VRDLFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGII 156
Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMN-----LSDEVDLEDYVSR 116
           V+ ATNR D LDPALLRPGR D+KI    PD   ++ + +++     L+++V+LE    R
Sbjct: 157 VMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAKR 216
Query: 117 PDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
                 A++  +  EA + A R+ R  I  KDFE+
Sbjct: 217 TPGFVGADLENLVNEAALLAAREGRDKITMKDFEE 251

>pdb|3HU3|A Chain A, Structure Of P97 N-D1 R155h Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  108 bits (270), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 61/143 (42%), Positives = 87/143 (60%), Gaps = 8/143 (5%)
Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           +R  F  A++NAPAIIFIDE+DAIA  R       +R   RI+ +LL  MDG  Q  +V 
Sbjct: 286 LRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVER---RIVSQLLTLMDGLKQRAHVI 342
Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVSR 116
           V+ ATNR +++DPAL R GR DR+++  +PD   +  + Q     M L+D+VDLE   + 
Sbjct: 343 VMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANE 402
Query: 117 PDKISAAEIAAICQEAGMHAVRK 139
                 A++AA+C EA + A+RK
Sbjct: 403 THGHVGADLAALCSEAALQAIRK 425

>pdb|3HU2|A Chain A, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  108 bits (270), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 61/143 (42%), Positives = 87/143 (60%), Gaps = 8/143 (5%)
Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           +R  F  A++NAPAIIFIDE+DAIA  R       +R   RI+ +LL  MDG  Q  +V 
Sbjct: 286 LRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVER---RIVSQLLTLMDGLKQRAHVI 342
Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVSR 116
           V+ ATNR +++DPAL R GR DR+++  +PD   +  + Q     M L+D+VDLE   + 
Sbjct: 343 VMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANE 402
Query: 117 PDKISAAEIAAICQEAGMHAVRK 139
                 A++AA+C EA + A+RK
Sbjct: 403 THGHVGADLAALCSEAALQAIRK 425

>pdb|3HU1|A Chain A, Structure Of P97 N-D1 R95g Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  108 bits (270), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 61/143 (42%), Positives = 87/143 (60%), Gaps = 8/143 (5%)
Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           +R  F  A++NAPAIIFIDE+DAIA  R       +R   RI+ +LL  MDG  Q  +V 
Sbjct: 286 LRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVER---RIVSQLLTLMDGLKQRAHVI 342
Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVSR 116
           V+ ATNR +++DPAL R GR DR+++  +PD   +  + Q     M L+D+VDLE   + 
Sbjct: 343 VMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANE 402
Query: 117 PDKISAAEIAAICQEAGMHAVRK 139
                 A++AA+C EA + A+RK
Sbjct: 403 THGHVGADLAALCSEAALQAIRK 425

>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 =  108 bits (270), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 61/143 (42%), Positives = 87/143 (60%), Gaps = 8/143 (5%)
Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           +R  F  A++NAPAIIFIDE+DAIA  R       +R   RI+ +LL  MDG  Q  +V 
Sbjct: 286 LRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVER---RIVSQLLTLMDGLKQRAHVI 342
Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVSR 116
           V+ ATNR +++DPAL R GR DR+++  +PD   +  + Q     M L+D+VDLE   + 
Sbjct: 343 VMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANE 402
Query: 117 PDKISAAEIAAICQEAGMHAVRK 139
                 A++AA+C EA + A+RK
Sbjct: 403 THGHVGADLAALCSEAALQAIRK 425

>pdb|3CF1|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Length = 806

Iteration: 1
 Score =  108 bits (269), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 61/143 (42%), Positives = 87/143 (60%), Gaps = 8/143 (5%)
Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           +R  F  A++NAPAIIFIDE+DAIA  R       +R   RI+ +LL  MDG  Q  +V 
Sbjct: 286 LRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVER---RIVSQLLTLMDGLKQRAHVI 342
Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVSR 116
           V+ ATNR +++DPAL R GR DR+++  +PD   +  + Q     M L+D+VDLE   + 
Sbjct: 343 VMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANE 402
Query: 117 PDKISAAEIAAICQEAGMHAVRK 139
                 A++AA+C EA + A+RK
Sbjct: 403 THGHVGADLAALCSEAALQAIRK 425

>pdb|1R7R|A Chain A, The Crystal Structure Of Murine P97VCP AT 3.6A Length = 816

Iteration: 1
 Score =  108 bits (269), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 61/143 (42%), Positives = 87/143 (60%), Gaps = 8/143 (5%)
Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           +R  F  A++NAPAIIFIDE+DAIA  R       +R   RI+ +LL  MDG  Q  +V 
Sbjct: 286 LRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVER---RIVSQLLTLMDGLKQRAHVI 342
Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVSR 116
           V+ ATNR +++DPAL R GR DR+++  +PD   +  + Q     M L+D+VDLE   + 
Sbjct: 343 VMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANE 402
Query: 117 PDKISAAEIAAICQEAGMHAVRK 139
                 A++AA+C EA + A+RK
Sbjct: 403 THGHVGADLAALCSEAALQAIRK 425

>pdb|2QZ4|A Chain A, Human Paraplegin, Aaa Domain In Complex With Adp Length = 262

Iteration: 1
 Score =  107 bits (268), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 59/157 (37%), Positives = 90/157 (57%), Gaps = 8/157 (5%)
Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTG-ADREVQRILMELLNQMDGFDQTVNV 60
           VR +F+ A+  AP I++IDE+DA+   R    +G ++ E ++ L +LL +MDG   T +V
Sbjct: 87  VRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTDHV 146
Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNL-------SDEVDLEDY 113
            V+ +TNRAD LD AL+RPGRLDR +   LP  +++R +F+ +L       S     +  
Sbjct: 147 IVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRL 206
Query: 114 VSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFE 150
                  S A+IA IC EA +HA R+    +   +FE
Sbjct: 207 AELTPGFSGADIANICNEAALHAAREGHTSVHTLNFE 243

>pdb|3CF0|A Chain A, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP Length = 301

Iteration: 1
 Score =  104 bits (259), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 54/136 (39%), Positives = 80/136 (58%), Gaps = 5/136 (3%)
Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           VR++F  A++ AP ++F DE+D+IA AR            R++ ++L +MDG     NV 
Sbjct: 97  VREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVF 156
Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNL-----SDEVDLEDYVSR 116
           +I ATNR D +DPA+LRPGRLD+ I  PLPD + +  + + NL     + +VDLE     
Sbjct: 157 IIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKM 216
Query: 117 PDKISAAEIAAICQEA 132
            +  S A++  ICQ A
Sbjct: 217 TNGFSGADLTEICQRA 232

>pdb|1IY2|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 278

Iteration: 1
 Score =  102 bits (255), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 61/155 (39%), Positives = 91/155 (58%), Gaps = 5/155 (3%)
Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           VRD+F  AK +AP I+FIDE+DA+   R     G + E ++ L +LL +MDGF++   + 
Sbjct: 121 VRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIV 180
Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMN-----LSDEVDLEDYVSR 116
           V+ ATNR D LDPALLRPGR DR+I    PD + +  + +++     L+++VDL     R
Sbjct: 181 VMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKR 240
Query: 117 PDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
                 A++  +  EA + A R+ R  I  KD E+
Sbjct: 241 TPGFVGADLENLLNEAALLAAREGRRKITMKDLEE 275

>pdb|4EIW|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 508

Iteration: 1
 Score =  102 bits (255), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 61/155 (39%), Positives = 91/155 (58%), Gaps = 5/155 (3%)
Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           VRD+F  AK +AP I+FIDE+DA+   R     G + E ++ L +LL +MDGF++   + 
Sbjct: 121 VRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIV 180
Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMN-----LSDEVDLEDYVSR 116
           V+ ATNR D LDPALLRPGR DR+I    PD + +  + +++     L+++VDL     R
Sbjct: 181 VMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKR 240
Query: 117 PDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
                 A++  +  EA + A R+ R  I  KD E+
Sbjct: 241 TPGFVGADLENLLNEAALLAAREGRRKITMKDLEE 275

>pdb|2DHR|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 499

Iteration: 1
 Score =  102 bits (255), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 61/155 (39%), Positives = 91/155 (58%), Gaps = 5/155 (3%)
Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           VRD+F  AK +AP I+FIDE+DA+   R     G + E ++ L +LL +MDGF++   + 
Sbjct: 112 VRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIV 171
Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMN-----LSDEVDLEDYVSR 116
           V+ ATNR D LDPALLRPGR DR+I    PD + +  + +++     L+++VDL     R
Sbjct: 172 VMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKR 231
Query: 117 PDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
                 A++  +  EA + A R+ R  I  KD E+
Sbjct: 232 TPGFVGADLENLLNEAALLAAREGRRKITMKDLEE 266

>pdb|1IXZ|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 254

Iteration: 1
 Score =  102 bits (254), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 61/155 (39%), Positives = 91/155 (58%), Gaps = 5/155 (3%)
Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           VRD+F  AK +AP I+FIDE+DA+   R     G + E ++ L +LL +MDGF++   + 
Sbjct: 97  VRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIV 156
Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMN-----LSDEVDLEDYVSR 116
           V+ ATNR D LDPALLRPGR DR+I    PD + +  + +++     L+++VDL     R
Sbjct: 157 VMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKR 216
Query: 117 PDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
                 A++  +  EA + A R+ R  I  KD E+
Sbjct: 217 TPGFVGADLENLLNEAALLAAREGRRKITMKDLEE 251

>pdb|2R62|A Chain A, Crystal Structure Of Helicobacter Pylori Atp Dependent Protease, Ftsh Length = 268

Iteration: 1
 Score = 96.7 bits (239), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 56/147 (38%), Positives = 89/147 (60%), Gaps = 7/147 (4%)
Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQT-GADREVQRILMELLNQMDGF-DQTVN 59
           VRD+F  AK+ AP+IIFIDE+DAI  +R        + E ++ L +LL +MDGF  +   
Sbjct: 92  VRDLFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSENAP 151
Query: 60  VKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMN-----LSDEVDLEDYV 114
           V V+ ATNR + LDPAL+RPGR DR++    PD   +  + +++     L+++V+L++  
Sbjct: 152 VIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVA 211
Query: 115 SRPDKISAAEIAAICQEAGMHAVRKNR 141
                ++ A++A I  EA + A R N+
Sbjct: 212 KLTAGLAGADLANIINEAALLAGRNNQ 238

>pdb|2X8A|A Chain A, Human Nuclear Valosin Containing Protein Like (Nvl), C- Terminal Aaa-Atpase Domain Length = 274

Iteration: 1
 Score = 93.2 bits (230), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 63/184 (34%), Positives = 98/184 (53%), Gaps = 27/184 (14%)
Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           VR VF+ AK +AP +IF DEVDA+   R D +TGA     R++ +LL +MDG +    V 
Sbjct: 92  VRQVFQRAKNSAPCVIFFDEVDALCPRRSDRETGAS---VRVVNQLLTEMDGLEARQQVF 148
Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQM--------NLSDEVDLEDY 113
           ++ ATNR D +DPA+LRPGRLD+ +   LP    +  + +          L  +V+LE  
Sbjct: 149 IMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTITKNGTKPPLDADVNLEAI 208
Query: 114 VS--RPDKISAAEIAAICQEAGMHAVR-----------KNRYVILPKDFEKGY---RTNV 157
               R D  + A+++A+ +EA + A+R           K    +  K FE+ +   R+++
Sbjct: 209 AGDLRCDCYTGADLSALVREASICALRQEMARQKSGNEKGELKVSHKHFEEAFKKVRSSI 268
Query: 158 KKPD 161
            K D
Sbjct: 269 SKKD 272

>pdb|2RKO|A Chain A, Crystal Structure Of The Vps4p-Dimer Length = 331

Iteration: 1
 Score = 84.7 bits (208), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 55/146 (37%), Positives = 86/146 (58%), Gaps = 12/146 (8%)
Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF-DQTVN 59
           +V+ +F +A+EN P+IIFIDEVDA+   R + ++ A R   RI  ELL QM+G  + +  
Sbjct: 107 LVKQLFAMARENKPSIIFIDEVDALTGTRGEGESEASR---RIKTELLVQMNGVGNDSQG 163
Query: 60  VKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSDE---VDLEDY--- 113
           V V+ ATN    LD A+ R  R +R+I  PLPD   +  +F++N+ D    +  EDY   
Sbjct: 164 VLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTL 221
Query: 114 VSRPDKISAAEIAAICQEAGMHAVRK 139
            +  +  S ++IA + ++A M  +RK
Sbjct: 222 GAMTEGYSGSDIAVVVKDALMQPIRK 247

>pdb|2QP9|X Chain X, Crystal Structure Of S.Cerevisiae Vps4 Length = 355

Iteration: 1
 Score = 84.3 bits (207), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 54/146 (36%), Positives = 86/146 (58%), Gaps = 12/146 (8%)
Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF-DQTVN 59
           +V+ +F +A+EN P+IIFID+VDA+   R + ++ A R   RI  ELL QM+G  + +  
Sbjct: 131 LVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASR---RIKTELLVQMNGVGNDSQG 187
Query: 60  VKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSDEVDL---EDY--- 113
           V V+ ATN    LD A+ R  R +R+I  PLPD   +  +F++N+ D   +   EDY   
Sbjct: 188 VLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPSVLTKEDYRTL 245
Query: 114 VSRPDKISAAEIAAICQEAGMHAVRK 139
            +  +  S ++IA + ++A M  +RK
Sbjct: 246 GAMTEGYSGSDIAVVVKDALMQPIRK 271

>pdb|3EIH|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The Presence Of Atpgammas Length = 340

Iteration: 1
 Score = 83.6 bits (205), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 54/146 (36%), Positives = 86/146 (58%), Gaps = 12/146 (8%)
Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF-DQTVN 59
           +V+ +F +A+EN P+IIFID+VDA+   R + ++ A R   RI  ELL QM+G  + +  
Sbjct: 116 LVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASR---RIKTELLVQMNGVGNDSQG 172
Query: 60  VKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSDE---VDLEDY--- 113
           V V+ ATN    LD A+ R  R +R+I  PLPD   +  +F++N+ D    +  EDY   
Sbjct: 173 VLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTL 230
Query: 114 VSRPDKISAAEIAAICQEAGMHAVRK 139
            +  +  S ++IA + ++A M  +RK
Sbjct: 231 GAMTEGYSGSDIAVVVKDALMQPIRK 256

>pdb|3EIE|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The So4-Bound State Length = 322

Iteration: 1
 Score = 83.2 bits (204), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 54/146 (36%), Positives = 86/146 (58%), Gaps = 12/146 (8%)
Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF-DQTVN 59
           +V+ +F +A+EN P+IIFID+VDA+   R + ++ A R   RI  ELL QM+G  + +  
Sbjct: 98  LVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASR---RIKTELLVQMNGVGNDSQG 154
Query: 60  VKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSDE---VDLEDY--- 113
           V V+ ATN    LD A+ R  R +R+I  PLPD   +  +F++N+ D    +  EDY   
Sbjct: 155 VLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTL 212
Query: 114 VSRPDKISAAEIAAICQEAGMHAVRK 139
            +  +  S ++IA + ++A M  +RK
Sbjct: 213 GAMTEGYSGSDIAVVVKDALMQPIRK 238

>pdb|2ZAM|A Chain A, Crystal Structure Of Mouse Skd1VPS4B APO-Form Length = 444

Iteration: 1
 Score = 80.9 bits (198), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 51/146 (34%), Positives = 84/146 (57%), Gaps = 12/146 (8%)
Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD-QTVN 59
           +V+++F+LA+EN P+IIFIDE+D++  +R + ++ A R   RI  E L QM G       
Sbjct: 215 LVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAAR---RIKTEFLVQMQGVGVDNDG 271
Query: 60  VKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD------EVDLEDY 113
           + V+ ATN    LD A+ R  R +++I  PLP+   +  +F+++L        E D ++ 
Sbjct: 272 ILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQEL 329
Query: 114 VSRPDKISAAEIAAICQEAGMHAVRK 139
             + D  S A+I+ I ++A M  VRK
Sbjct: 330 GRKTDGYSGADISIIVRDALMQPVRK 355

>pdb|1XWI|A Chain A, Crystal Structure Of Vps4b Length = 322

Iteration: 1
 Score = 79.3 bits (194), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 51/146 (34%), Positives = 83/146 (56%), Gaps = 12/146 (8%)
Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD-QTVN 59
           +V+++F+LA+EN P+IIFIDE+D++  +R + ++ A R   RI  E L QM G       
Sbjct: 93  LVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAAR---RIKTEFLVQMQGVGVDNDG 149
Query: 60  VKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLS------DEVDLEDY 113
           + V+ ATN    LD A+ R  R +++I  PLP+   +  +F+++L        E D  + 
Sbjct: 150 ILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEPHARAAMFKLHLGTTQNSLTEADFREL 207
Query: 114 VSRPDKISAAEIAAICQEAGMHAVRK 139
             + D  S A+I+ I ++A M  VRK
Sbjct: 208 GRKTDGYSGADISIIVRDALMQPVRK 233

>pdb|2DZN|B Chain B, Crystal Structure Analysis Of Yeast Nas6p Complexed With The Proteasome Subunit, Rpt3 Length = 82

Iteration: 1
 Score = 77.0 bits (188), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 41/81 (50%), Positives = 54/81 (66%), Gaps = 7/81 (8%)
Query: 95  QKRLVF-----QMNLSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDF 149
           ++RL+F     +M+L+ E DL+  + R D +S A IAAI QEAG+ AVRKNRYVIL  D 
Sbjct: 2   ERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQEAGLRAVRKNRYVILQSDL 61
Query: 150 EKGYRTNVKKPDT--DFEFYK 168
           E+ Y T VK  +T   F+FYK
Sbjct: 62  EEAYATQVKTDNTVDKFDFYK 82

>pdb|3D8B|A Chain A, Crystal Structure Of Human Fidgetin-Like Protein 1 In Complex With Adp Length = 357

Iteration: 1
 Score = 76.3 bits (186), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 60/192 (31%), Positives = 96/192 (50%), Gaps = 32/192 (16%)
Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVN- 59
           MVR +F +A+   PA+IFIDE+D++ + R D +  + R   RI  E L Q+DG   +   
Sbjct: 164 MVRALFAVARCQQPAVIFIDEIDSLLSQRGDGEHESSR---RIKTEFLVQLDGATTSSED 220
Query: 60  -VKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVF-------QMNLSDEVDLE 111
            + V+ ATNR   +D A  R  RL +++  PLP+   ++ +        Q  LS+E ++E
Sbjct: 221 RILVVGATNRPQEIDEAARR--RLVKRLYIPLPEASARKQIVINLMSKEQCCLSEE-EIE 277
Query: 112 DYVSRPDKISAAEIAAICQEAGMHAVRKNRY----VILPK--------DFEKGYRTNVKK 159
             V + D  S A++  +C+EA +  +R  +      I P         DFE  +RT   +
Sbjct: 278 QIVQQSDAFSGADMTQLCREASLGPIRSLQTADIATITPDQVRPIAYIDFENAFRT--VR 335
Query: 160 PDT---DFEFYK 168
           P     D E Y+
Sbjct: 336 PSVSPKDLELYE 347

>pdb|3VFD|A Chain A, Human Spastin Aaa Domain Length = 389

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 43/147 (29%), Positives = 76/147 (51%), Gaps = 13/147 (8%)
Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVN- 59
           +VR +F +A+E  P+IIFID+VD++   R + +  A R   R+  E L + DG     + 
Sbjct: 195 LVRALFAVARELQPSIIFIDQVDSLLCERREGEHDASR---RLKTEFLIEFDGVQSAGDD 251
Query: 60  -VKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVF------QMNLSDEVDLED 112
            V V+ ATNR   LD A+LR  R  +++   LP+   + L+       Q +   + +L  
Sbjct: 252 RVLVMGATNRPQELDEAVLR--RFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQ 309
Query: 113 YVSRPDKISAAEIAAICQEAGMHAVRK 139
                D  S +++ A+ ++A +  +R+
Sbjct: 310 LARMTDGYSGSDLTALAKDAALGPIRE 336

>pdb|3B9P|A Chain A, Spastin Length = 297

Iteration: 1
 Score = 53.5 bits (127), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 44/148 (29%), Positives = 75/148 (50%), Gaps = 14/148 (9%)
Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVN- 59
           +VR +F +A+   P+IIFIDEVD++ + R  ++  A R   R+  E L + DG     + 
Sbjct: 101 LVRALFAVARHMQPSIIFIDEVDSLLSERSSSEHEASR---RLKTEFLVEFDGLPGNPDG 157
Query: 60  --VKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVF------QMNLSDEVDLE 111
             + V+ ATNR   LD A LR  R  +++   LPD + + L+       Q +  D   L 
Sbjct: 158 DRIVVLAATNRPQELDEAALR--RFTKRVYVSLPDEQTRELLLNRLLQKQGSPLDTEALR 215
Query: 112 DYVSRPDKISAAEIAAICQEAGMHAVRK 139
                 D  S +++ A+ ++A +  +R+
Sbjct: 216 RLAKITDGYSGSDLTALAKDAALEPIRE 243

>pdb|2KRK|A Chain A, Solution Nmr Structure Of 26s Protease Regulatory Subunit 8 From H.Sapiens, Northeast Structural Genomics Consortium Target Target Hr3102a Length = 86

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/50 (36%), Positives = 29/50 (58%)
Query: 101 QMNLSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFE 150
           +MNL+  ++L          S AE+  +C EAGM+A+R+ R  +  +DFE
Sbjct: 26  KMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRERRVHVTQEDFE 75

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	168
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	1e-90
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	2e-50
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	4e-48
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	7e-48
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	9e-34
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	2e-47
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	3e-46
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	5e-41
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	6e-40
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	7e-40
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	8e-40
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	1e-39
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	2e-39
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	2e-38
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	7e-38
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	2e-37
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	3e-37
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	1e-36
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	2e-36
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	3e-36
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	5e-36
3aji_B	83	S6C, proteasome (prosome, macropain) 26S subunit,	3e-31
2dzn_B	82	26S protease regulatory subunit 6B homolog; ankyri	2e-28
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	1e-20
2krk_A	86	26S protease regulatory subunit 8; structural geno	2e-16
3kw6_A	78	26S protease regulatory subunit 8; structural geno	9e-14
3vlf_B	88	26S protease regulatory subunit 7 homolog; heat re	6e-08

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii} Length = 285

 Score =  264 bits (677), Expect = 1e-90
 Identities = 85/164 (51%), Positives = 113/164 (68%), Gaps = 5/164 (3%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
           +V+D+F+LAKE AP+IIFIDE+DAIA  R DA TG DREVQR LM+LL +MDGFD   +V
Sbjct: 98  LVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDV 157

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
           K+I ATNR D LDPA+LRPGR DR IE P PD + +  + +     MNL+++V+LE+   
Sbjct: 158 KIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAK 217

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKK 159
             +    AE+ AIC EAGM+A+R+ R  +   DF K     ++K
Sbjct: 218 MTEGCVGAELKAICTEAGMNAIRELRDYVTMDDFRKAVEKIMEK 261

>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 =  162 bits (413), Expect = 2e-50
 Identities = 56/167 (33%), Positives = 93/167 (55%), Gaps = 5/167 (2%)

Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           VR++F  A++ AP ++F DE+D+IA AR            R++ ++L +MDG     NV 
Sbjct: 97  VREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVF 156

Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVSR 116
           +I ATNR D +DPA+LRPGRLD+ I  PLPD + +  + +       ++ +VDLE     
Sbjct: 157 IIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKM 216

Query: 117 PDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTD 163
            +  S A++  ICQ A   A+R++    + ++ E+    +  + + D
Sbjct: 217 TNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEED 263

>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 =  161 bits (409), Expect = 4e-48
 Identities = 63/153 (41%), Positives = 91/153 (59%), Gaps = 8/153 (5%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
            +R  F  A++NAPAIIFIDE+DAIA  R       +R   RI+ +LL  MDG  Q  +V
Sbjct: 285 NLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVER---RIVSQLLTLMDGLKQRAHV 341

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
            V+ ATNR +++DPAL R GR DR+++  +PD   +  + Q     M L+D+VDLE   +
Sbjct: 342 IVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVAN 401

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKD 148
                  A++AA+C EA + A+RK   +I  +D
Sbjct: 402 ETHGHVGADLAALCSEAALQAIRKKMDLIDLED 434

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens} Length = 274

 Score =  154 bits (392), Expect = 2e-47
 Identities = 56/149 (37%), Positives = 86/149 (57%), Gaps = 13/149 (8%)

Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           VR VF+ AK +AP +IF DEVDA+   R D +TGA     R++ +LL +MDG +    V 
Sbjct: 92  VRQVFQRAKNSAPCVIFFDEVDALCPRRSDRETGA---SVRVVNQLLTEMDGLEARQQVF 148

Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ--------MNLSDEVDLEDY 113
           ++ ATNR D +DPA+LRPGRLD+ +   LP    +  + +          L  +V+LE  
Sbjct: 149 IMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTITKNGTKPPLDADVNLEAI 208

Query: 114 V--SRPDKISAAEIAAICQEAGMHAVRKN 140
               R D  + A+++A+ +EA + A+R+ 
Sbjct: 209 AGDLRCDCYTGADLSALVREASICALRQE 237

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A Length = 293

 Score =  151 bits (384), Expect = 3e-46
 Identities = 37/182 (20%), Positives = 65/182 (35%), Gaps = 15/182 (8%)

Query: 1   MVRDVFRLA----KENAPAIIFIDEVDAIATAR--FDAQTGADREVQRILMELLN----- 49
           ++R  +R A    ++     +FI+++DA A         T  ++ V   LM + +     
Sbjct: 83  LIRQRYREAAEIIRKGNMCCLFINDLDAGAGRMGGTTQYTVNNQMVNATLMNIADNPTNV 142

Query: 50  QMDGFD---QTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD 106
           Q+ G     +   V +I+  N   TL   L+R GR+++    P  + R       +  +D
Sbjct: 143 QLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEKFYWAPTREDRIGVCTG-IFRTD 201

Query: 107 EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEF 166
            V  ED V   D      I             + R  +     EK     +   D    F
Sbjct: 202 NVPAEDVVKIVDNFPGQSIDFFGALRARVYDDEVRKWVSGTGIEKIGDKLLNSFDGPPTF 261

Query: 167 YK 168
            +
Sbjct: 262 EQ 263

>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 =  137 bits (347), Expect = 5e-41
 Identities = 58/160 (36%), Positives = 87/160 (54%), Gaps = 12/160 (7%)

Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGA---DREVQRILMELLNQMDGFDQTV 58
           VR +F+ A+  AP I++IDE+DA+   R    +G    + E  + L +LL +MDG   T 
Sbjct: 87  VRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEE--QTLNQLLVEMDGMGTTD 144

Query: 59  NVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDY 113
           +V V+ +TNRAD LD AL+RPGRLDR +   LP  +++R +F+     + L+        
Sbjct: 145 HVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQ 204

Query: 114 V--SRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
                    S A+IA IC EA +HA R+    +   +FE 
Sbjct: 205 RLAELTPGFSGADIANICNEAALHAAREGHTSVHTLNFEY 244

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20 Length = 278

 Score =  135 bits (341), Expect = 6e-40
 Identities = 61/155 (39%), Positives = 91/155 (58%), Gaps = 5/155 (3%)

Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           VRD+F  AK +AP I+FIDE+DA+   R     G + E ++ L +LL +MDGF++   + 
Sbjct: 121 VRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIV 180

Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMN-----LSDEVDLEDYVSR 116
           V+ ATNR D LDPALLRPGR DR+I    PD + +  + +++     L+++VDL     R
Sbjct: 181 VMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKR 240

Query: 117 PDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
                 A++  +  EA + A R+ R  I  KD E+
Sbjct: 241 TPGFVGADLENLLNEAALLAAREGRRKITMKDLEE 275

>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 =  136 bits (344), Expect = 7e-40
 Identities = 52/146 (35%), Positives = 82/146 (56%), Gaps = 12/146 (8%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTV-N 59
           +V+ +F +A+EN P+IIFID+VDA+   R + ++ A R   RI  ELL QM+G       
Sbjct: 98  LVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASR---RIKTELLVQMNGVGNDSQG 154

Query: 60  VKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD------EVDLEDY 113
           V V+ ATN    LD A+ R  R +R+I  PLPD   +  +F++N+ D      + D    
Sbjct: 155 VLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTL 212

Query: 114 VSRPDKISAAEIAAICQEAGMHAVRK 139
            +  +  S ++IA + ++A M  +RK
Sbjct: 213 GAMTEGYSGSDIAVVVKDALMQPIRK 238

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens} Length = 322

 Score =  135 bits (343), Expect = 8e-40
 Identities = 54/171 (31%), Positives = 88/171 (51%), Gaps = 12/171 (7%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTV-N 59
           +V+++F+LA+EN P+IIFIDE+D++  +R + ++ A R   RI  E L QM G       
Sbjct: 93  LVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAAR---RIKTEFLVQMQGVGVDNDG 149

Query: 60  VKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD------EVDLEDY 113
           + V+ ATN    LD A+ R  R +++I  PLP+   +  +F+++L        E D  + 
Sbjct: 150 ILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEPHARAAMFKLHLGTTQNSLTEADFREL 207

Query: 114 VSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDF 164
             + D  S A+I+ I ++A M  VRK +     K      R +      D 
Sbjct: 208 GRKTDGYSGADISIIVRDALMQPVRKVQSATHFKKVRGPSRADPNHLVDDL 258

>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 =  133 bits (337), Expect = 1e-39
 Identities = 61/155 (39%), Positives = 91/155 (58%), Gaps = 5/155 (3%)

Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           VRD+F  AK +AP I+FIDE+DA+   R     G + E ++ L +LL +MDGF++   + 
Sbjct: 97  VRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIV 156

Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMN-----LSDEVDLEDYVSR 116
           V+ ATNR D LDPALLRPGR DR+I    PD + +  + +++     L+++VDL     R
Sbjct: 157 VMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKR 216

Query: 117 PDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
                 A++  +  EA + A R+ R  I  KD E+
Sbjct: 217 TPGFVGADLENLLNEAALLAAREGRRKITMKDLEE 251

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20 Length = 257

 Score =  133 bits (336), Expect = 2e-39
 Identities = 62/155 (40%), Positives = 90/155 (58%), Gaps = 5/155 (3%)

Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           VRD+F  AK+ AP IIFIDE+DA+   R     G   E ++ L ++L +MDGF+    + 
Sbjct: 93  VRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGII 152

Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMN-----LSDEVDLEDYVSR 116
           VI ATNR D LDPALLRPGR DR++   LPD R +  + +++     L+ ++D       
Sbjct: 153 VIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARG 212

Query: 117 PDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
               S A++A +  EA + A R N+ V+   +FEK
Sbjct: 213 TPGFSGADLANLVNEAALFAARGNKRVVSMVEFEK 247

>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 =  133 bits (335), Expect = 2e-38
 Identities = 52/146 (35%), Positives = 82/146 (56%), Gaps = 12/146 (8%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTV-N 59
           +V+ +F +A+EN P+IIFID+VDA+   R + ++ A R   RI  ELL QM+G       
Sbjct: 131 LVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASR---RIKTELLVQMNGVGNDSQG 187

Query: 60  VKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD------EVDLEDY 113
           V V+ ATN    LD A+ R  R +R+I  PLPD   +  +F++N+ D      + D    
Sbjct: 188 VLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPSVLTKEDYRTL 245

Query: 114 VSRPDKISAAEIAAICQEAGMHAVRK 139
            +  +  S ++IA + ++A M  +RK
Sbjct: 246 GAMTEGYSGSDIAVVVKDALMQPIRK 271

>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 =  129 bits (327), Expect = 7e-38
 Identities = 56/157 (35%), Positives = 93/157 (59%), Gaps = 7/157 (4%)

Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATAR-FDAQTGADREVQRILMELLNQMDGFD-QTVN 59
           VRD+F  AK+ AP+IIFIDE+DAI  +R        + E ++ L +LL +MDGF  +   
Sbjct: 92  VRDLFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSENAP 151

Query: 60  VKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMN-----LSDEVDLEDYV 114
           V V+ ATNR + LDPAL+RPGR DR++    PD   +  + +++     L+++V+L++  
Sbjct: 152 VIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVA 211

Query: 115 SRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
                ++ A++A I  EA + A R N+  +  +  ++
Sbjct: 212 KLTAGLAGADLANIINEAALLAGRNNQKEVRQQHLKE 248

>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 =  132 bits (333), Expect = 2e-37
 Identities = 54/171 (31%), Positives = 89/171 (52%), Gaps = 12/171 (7%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTV-N 59
           +V+++F+LA+EN P+IIFIDE+D++  +R + ++ A R   RI  E L QM G       
Sbjct: 215 LVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAAR---RIKTEFLVQMQGVGVDNDG 271

Query: 60  VKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD------EVDLEDY 113
           + V+ ATN    LD A+ R  R +++I  PLP+   +  +F+++L        E D ++ 
Sbjct: 272 ILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQEL 329

Query: 114 VSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDF 164
             + D  S A+I+ I ++A M  VRK +     K      R +      D 
Sbjct: 330 GRKTDGYSGADISIIVRDALMQPVRKVQSATHFKKVRGPSRADPNCIVNDL 380

>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 =  130 bits (328), Expect = 3e-37
 Identities = 47/147 (31%), Positives = 78/147 (53%), Gaps = 13/147 (8%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF--DQTV 58
           MVR +F +A+   PA+IFIDE+D++ + R D +  + R   RI  E L Q+DG       
Sbjct: 164 MVRALFAVARCQQPAVIFIDEIDSLLSQRGDGEHESSR---RIKTEFLVQLDGATTSSED 220

Query: 59  NVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD------EVDLED 112
            + V+ ATNR   +D A  R  RL +++  PLP+   ++ +    +S       E ++E 
Sbjct: 221 RILVVGATNRPQEIDEAARR--RLVKRLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQ 278

Query: 113 YVSRPDKISAAEIAAICQEAGMHAVRK 139
            V + D  S A++  +C+EA +  +R 
Sbjct: 279 IVQQSDAFSGADMTQLCREASLGPIRS 305

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster} Length = 297

 Score =  127 bits (320), Expect = 1e-36
 Identities = 44/148 (29%), Positives = 73/148 (49%), Gaps = 14/148 (9%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF---DQT 57
           +VR +F +A+   P+IIFIDEVD++ + R  ++  A R   R+  E L + DG       
Sbjct: 101 LVRALFAVARHMQPSIIFIDEVDSLLSERSSSEHEASR---RLKTEFLVEFDGLPGNPDG 157

Query: 58  VNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLS------DEVDLE 111
             + V+ ATNR   LD A LR  R  +++   LPD + + L+    L       D   L 
Sbjct: 158 DRIVVLAATNRPQELDEAALR--RFTKRVYVSLPDEQTRELLLNRLLQKQGSPLDTEALR 215

Query: 112 DYVSRPDKISAAEIAAICQEAGMHAVRK 139
                 D  S +++ A+ ++A +  +R+
Sbjct: 216 RLAKITDGYSGSDLTALAKDAALEPIRE 243

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus} Length = 499

 Score =  130 bits (329), Expect = 2e-36
 Identities = 61/155 (39%), Positives = 91/155 (58%), Gaps = 5/155 (3%)

Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           VRD+F  AK +AP I+FIDE+DA+   R     G + E ++ L +LL +MDGF++   + 
Sbjct: 112 VRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIV 171

Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMN-----LSDEVDLEDYVSR 116
           V+ ATNR D LDPALLRPGR DR+I    PD + +  + +++     L+++VDL     R
Sbjct: 172 VMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKR 231

Query: 117 PDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
                 A++  +  EA + A R+ R  I  KD E+
Sbjct: 232 TPGFVGADLENLLNEAALLAAREGRRKITMKDLEE 266

>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 =  129 bits (327), Expect = 3e-36
 Identities = 63/155 (40%), Positives = 91/155 (58%), Gaps = 5/155 (3%)

Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           VRD+F  AK +AP I+FIDE+DA+   R     G   E ++ L +LL +MDGFD    + 
Sbjct: 97  VRDLFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGII 156

Query: 62  VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMN-----LSDEVDLEDYVSR 116
           V+ ATNR D LDPALLRPGR D+KI    PD   ++ + +++     L+++V+LE    R
Sbjct: 157 VMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAKR 216

Query: 117 PDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
                 A++  +  EA + A R+ R  I  KDFE+
Sbjct: 217 TPGFVGADLENLVNEAALLAAREGRDKITMKDFEE 251

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens} Length = 389

 Score =  127 bits (321), Expect = 5e-36
 Identities = 43/147 (29%), Positives = 75/147 (51%), Gaps = 13/147 (8%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF--DQTV 58
           +VR +F +A+E  P+IIFID+VD++   R + +  A R   R+  E L + DG       
Sbjct: 195 LVRALFAVARELQPSIIFIDQVDSLLCERREGEHDASR---RLKTEFLIEFDGVQSAGDD 251

Query: 59  NVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD------EVDLED 112
            V V+ ATNR   LD A+LR  R  +++   LP+   + L+ +  L        + +L  
Sbjct: 252 RVLVMGATNRPQELDEAVLR--RFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQ 309

Query: 113 YVSRPDKISAAEIAAICQEAGMHAVRK 139
                D  S +++ A+ ++A +  +R+
Sbjct: 310 LARMTDGYSGSDLTALAKDAALGPIRE 336

>3aji_B S6C, proteasome (prosome, macropain) 26S subunit, ATPA; gankyrin, S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber suppression; HET: PBF; 2.05A {Mus musculus} PDB: 2dwz_B* 2dvw_B* Length = 83

 Score =  107 bits (268), Expect = 3e-31
 Identities = 54/82 (65%), Positives = 67/82 (81%), Gaps = 5/82 (6%)

Query: 92  DRRQKRLVFQ-----MNLSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILP 146
           DRRQKRL+F      MNLS+EVDLEDYV+RPDKIS A+I +ICQE+GM AVR+NRY++L 
Sbjct: 2   DRRQKRLIFSTITSKMNLSEEVDLEDYVARPDKISGADINSICQESGMLAVRENRYIVLA 61

Query: 147 KDFEKGYRTNVKKPDTDFEFYK 168
           KDFEK Y+T +KK + + EFYK
Sbjct: 62  KDFEKAYKTVIKKDEQEHEFYK 83

>2dzn_B 26S protease regulatory subunit 6B homolog; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} PDB: 2dzo_B Length = 82

 Score = 99.7 bits (249), Expect = 2e-28
 Identities = 41/81 (50%), Positives = 53/81 (65%), Gaps = 7/81 (8%)

Query: 95  QKRLVFQ-----MNLSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDF 149
           ++RL+F      M+L+ E DL+  + R D +S A IAAI QEAG+ AVRKNRYVIL  D 
Sbjct: 2   ERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQEAGLRAVRKNRYVILQSDL 61

Query: 150 EKGYRTNVKKPDT--DFEFYK 168
           E+ Y T VK  +T   F+FYK
Sbjct: 62  EEAYATQVKTDNTVDKFDFYK 82

>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 = 84.8 bits (210), Expect = 1e-20
 Identities = 17/147 (11%), Positives = 46/147 (31%), Gaps = 11/147 (7%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD-QTVN 59
            ++ +F  A ++  + + +D+++ +            R    +L  LL  +     Q   
Sbjct: 112 AMKKIFDDAYKSQLSCVVVDDIERLLDYV----PIGPRFSNLVLQALLVLLKKAPPQGRK 167

Query: 60  VKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQK--RLVFQMNLSDEVDLEDYVSR- 116
           + +I  T+R D L   +         I  P     ++    +  +    + +      + 
Sbjct: 168 LLIIGTTSRKDVLQ-EMEMLNAFSTTIHVPNIATGEQLLEALELLGNFKDKERTTIAQQV 226

Query: 117 --PDKISAAEIAAICQEAGMHAVRKNR 141
                    +   +  E  +    + R
Sbjct: 227 KGKKVWIGIKKLLMLIEMSLQMDPEYR 253

>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast structural genomics consortium (NESG), target HR3102A, PSI-2; NMR {Homo sapiens} Length = 86

 Score = 69.1 bits (170), Expect = 2e-16
 Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 5/72 (6%)

Query: 86  IEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN 140
                P+   +  + +     MNL+  ++L          S AE+  +C EAGM+A+R+ 
Sbjct: 6   HHHSHPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRER 65

Query: 141 RYVILPKDFEKG 152
           R  +  +DFE  
Sbjct: 66  RVHVTQEDFEMA 77

>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Homo sapiens} Length = 78

 Score = 62.1 bits (152), Expect = 9e-14
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 5/69 (7%)

Query: 89  PLPDRRQKRLVFQ-----MNLSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYV 143
           P P+   +  + +     MNL+  ++L          S AE+  +C EAGM+A+R+ R  
Sbjct: 1   PPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRERRVH 60

Query: 144 ILPKDFEKG 152
           +  +DFE  
Sbjct: 61  VTQEDFEMA 69

>3vlf_B 26S protease regulatory subunit 7 homolog; heat repeat, chaperone, chaperone-protein binding complex; HET: DNA; 3.80A {Saccharomyces cerevisiae} PDB: 4a3v_B* Length = 88

 Score = 46.8 bits (112), Expect = 6e-08
 Identities = 17/50 (34%), Positives = 25/50 (50%)

Query: 102 MNLSDEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
           M++   +  E         + AE+ ++C EAGM A+R  R V   KDF K
Sbjct: 17  MSVERGIRWELISRLCPNSTGAELRSVCTEAGMFAIRARRKVATEKDFLK 66

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	168
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	100.0
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	100.0
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	100.0
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	100.0
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	100.0
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	100.0
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	100.0
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	100.0
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	99.97
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.96
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.96
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.95
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	99.95
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.94
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.94
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.94
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.94
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.94
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.93
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.93
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.93
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.92
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.92
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.91
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.89
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.88
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.87
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.81
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.78
2krk_A	86	26S protease regulatory subunit 8; structural geno	99.71
3kw6_A	78	26S protease regulatory subunit 8; structural geno	99.7
3aji_B	83	S6C, proteasome (prosome, macropain) 26S subunit,	99.68
3vlf_B	88	26S protease regulatory subunit 7 homolog; heat re	99.61
2dzn_B	82	26S protease regulatory subunit 6B homolog; ankyri	99.57
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.5
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	99.34
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	99.31
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	99.29
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.23
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.21
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.17
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	99.14
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	99.08
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.08
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.07
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.04
3bos_A	242	Putative DNA replication factor; P-loop containing	99.01
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.98
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.97
2r44_A	331	Uncharacterized protein; putative ATPase, structur	98.96
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	98.94
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	98.92
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	98.9
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	98.88
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	98.88
3pvs_A	447	Replication-associated recombination protein A; ma	98.74
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	98.71
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	98.7
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	98.69
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.68
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	98.68
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	98.66
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	98.66
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	98.65
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	98.63
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	98.61
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	98.6
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	98.58
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	98.57
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	98.54
2chq_A	319	Replication factor C small subunit; DNA-binding pr	98.51
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.48
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	98.47
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	98.47
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	98.46
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.39
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.32
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	98.28
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	98.21
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	98.21
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	98.2
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	98.05
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	98.05
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	97.93
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	97.85
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	97.74
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	97.66
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	97.42
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	97.35
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	97.19
3f8t_A	506	Predicted ATPase involved in replication control,	97.18
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	97.13
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	96.68
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	96.18
2fna_A	357	Conserved hypothetical protein; structural genomic	96.17
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	94.89
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	94.62
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	93.73
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	93.69
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	93.42
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	93.27
3co5_A	143	Putative two-component system transcriptional RES	93.08
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	92.4
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	90.77
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	88.84
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	88.76
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	87.97
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	85.43
1taf_B	70	TFIID TBP associated factor 62; transcription init	81.78
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	81.02
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	80.23

>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=3.2e-41  Score=272.21  Aligned_cols=158  Identities=45%  Similarity=0.797  Sum_probs=148.7

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      |+.+|+.|+.++||||||||+|++++.|....++.+....+++++||++||++....+|+||||||+|+.||||++||||
T Consensus       230 vr~lF~~Ar~~aP~IIFiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~V~vIaATNrpd~LDpAllRpGR  309 (405)
T 4b4t_J          230 VRELFVMAREHAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFETSKNIKIIMATNRLDILDPALLRPGR  309 (405)
T ss_dssp             HHHHHHHHHHTCSEEEEEESSSCCTTSCSCSSSGGGGHHHHHHHHHHHHHHTTTCCCCEEEEEEESCSSSSCHHHHSTTS
T ss_pred             HHHHHHHHHHhCCceEeeecchhhccCCCCCCCCCcHHHHHHHHHHHHhhhccCCCCCeEEEeccCChhhCCHhHcCCCc
Confidence            78999999999999999999999999987777666777889999999999999999999999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      ||+.|+|++|+.++|.+||+.++.     .+++++.+|+.|+||||+||+++|++|++.|++++...|+.+||+.|++++
T Consensus       310 fD~~I~i~lPd~~~R~~Il~~~~~~~~l~~dvdl~~lA~~t~G~SGADi~~l~~eA~~~Air~~~~~vt~~Df~~Al~~v  389 (405)
T 4b4t_J          310 IDRKIEFPPPSVAARAEILRIHSRKMNLTRGINLRKVAEKMNGCSGADVKGVCTEAGMYALRERRIHVTQEDFELAVGKV  389 (405)
T ss_dssp             SCCEEECCCCCHHHHHHHHHHHHTTSBCCSSCCHHHHHHHCCSCCHHHHHHHHHHHHHHHHHTTCSBCCHHHHHHHHHHH
T ss_pred             CceEEEcCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence            999999999999999999997665     578999999999999999999999999999999999999999999999988


Q ss_pred             cCC
Q 030960          157 VKK  159 (168)
Q Consensus       157 ~p~  159 (168)
                      .++
T Consensus       390 ~~~  392 (405)
T 4b4t_J          390 MNK  392 (405)
T ss_dssp             HHH
T ss_pred             hCc
Confidence            764

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=9.8e-41  Score=272.38  Aligned_cols=166  Identities=48%  Similarity=0.797  Sum_probs=156.5

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|..|+.++||||||||+|++++.|.....+.+....++++.||++|+++....+|+||||||+|+.||||++||||
T Consensus       263 ir~lF~~A~~~aP~IifiDEiDal~~~R~~~~~~~~~~~~~~~~~lL~~ldg~~~~~~ViVIaaTNrp~~LD~AllRpGR  342 (434)
T 4b4t_M          263 VRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQLDGFSSDDRVKVLAATNRVDVLDPALLRSGR  342 (434)
T ss_dssp             HHHHHHHHHHHCSEEEEEECTHHHHCCCSSGGGGTTHHHHHHHHHHHHHHTTSCSSCSSEEEEECSSCCCCCTTTCSTTS
T ss_pred             HHHHHHHHHhcCCeEEeecchhhhhhccCCCCCCCchHHHHHHHHHHHHhhccCCCCCEEEEEeCCCchhcCHhHhcCCc
Confidence            78999999999999999999999999997766666667788999999999999988899999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      ||+.|+|++|+.++|.+||+.++.     ++++++.+|+.|+||||+||.++|++|++.|++++...|+.+||.+|++++
T Consensus       343 fD~~I~i~lPd~~~R~~Il~~~~~~~~~~~dvdl~~lA~~t~G~sGADi~~l~~eA~~~a~r~~~~~i~~~Df~~Al~~v  422 (434)
T 4b4t_M          343 LDRKIEFPLPSEDSRAQILQIHSRKMTTDDDINWQELARSTDEFNGAQLKAVTVEAGMIALRNGQSSVKHEDFVEGISEV  422 (434)
T ss_dssp             EEEEEECCCCCHHHHHHHHHHHHHHSCBCSCCCHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTCSSBCHHHHHHHHHSC
T ss_pred             eeEEEEeCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHHhCCCCCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence            999999999999999999986554     678999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCccccc
Q 030960          157 VKKPDTDFEFY  167 (168)
Q Consensus       157 ~p~~~~~~~~~  167 (168)
                      +|+..+.+.+|
T Consensus       423 ~~~~~~~i~~Y  433 (434)
T 4b4t_M          423 QARKSKSVSFY  433 (434)
T ss_dssp             SSSCCCCCCCC
T ss_pred             hCCCCcCcccc
Confidence            99998999988

>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=5.7e-40  Score=266.00  Aligned_cols=164  Identities=48%  Similarity=0.851  Sum_probs=151.3

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|..|+..+||||||||+|+++..|.......+....++++++|+++|++....+|+||||||+|+.||+|++||||
T Consensus       264 ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~LL~~lDg~~~~~~ViVIaATNrpd~LDpALlRpGR  343 (437)
T 4b4t_I          264 CRQIFKVAGENAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDDRGDVKVIMATNKIETLDPALIRPGR  343 (437)
T ss_dssp             HHHHHHHHHHTCSEEEEEEEESSSSCCCSCSSCSSCCHHHHHHHHHHHHHHHCCCSSSEEEEEEESCSTTCCTTSSCTTT
T ss_pred             HHHHHHHHHhcCCcEEEEehhhhhcccCCCCCCCccHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCChhhcCHHHhcCCc
Confidence            78999999999999999999999999997777666777789999999999999888899999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      ||+.|+|++|+.++|.+||+.++.     .+++++.+|+.|+||||+||+++|++|++.|++++...|+.+||..|++++
T Consensus       344 fD~~I~v~lPd~~~R~~Il~~~l~~~~l~~dvdl~~LA~~T~GfSGADI~~l~~eA~~~Air~~~~~It~eDf~~Al~rv  423 (437)
T 4b4t_I          344 IDRKILFENPDLSTKKKILGIHTSKMNLSEDVNLETLVTTKDDLSGADIQAMCTEAGLLALRERRMQVTAEDFKQAKERV  423 (437)
T ss_dssp             EEEEECCCCCCHHHHHHHHHHHHTTSCBCSCCCHHHHHHHCCSCCHHHHHHHHHHHHHHHHHTTCSCBCHHHHHHHHHHH
T ss_pred             eeEEEEcCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHHhCCCCCHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHH
Confidence            999999999999999999997765     578999999999999999999999999999999999999999999999988


Q ss_pred             cCCC-CCccc
Q 030960          157 VKKP-DTDFE  165 (168)
Q Consensus       157 ~p~~-~~~~~  165 (168)
                      .|+. .+.++
T Consensus       424 ~~~~~~e~le  433 (437)
T 4b4t_I          424 MKNKVEENLE  433 (437)
T ss_dssp             HHHHCCCSSS
T ss_pred             hCCCChhhHH
Confidence            7643 34444

>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=265.07  Aligned_cols=167  Identities=50%  Similarity=0.780  Sum_probs=149.1

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|..|+.++||||||||+|++++.|.......+....+++++||++||++....+|+||+|||+|+.||||++||||
T Consensus       263 ir~~F~~A~~~~P~IifiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~vivI~ATNrp~~LDpAllRpGR  342 (437)
T 4b4t_L          263 IREMFAYAKEHEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFDNLGQTKIIMATNRPDTLDPALLRPGR  342 (437)
T ss_dssp             HHHHHHHHHHSCSEEEEEECCCSSSCCCSSSCCSSTTHHHHHHHHHHHHHHSSSCTTSSEEEEEESSTTSSCTTTTSTTS
T ss_pred             HHHHHHHHHhcCCceeeeecccccccccccCCCCcchHHHHHHHHHHHHhhcccCCCCeEEEEecCCchhhCHHHhCCCc
Confidence            78999999999999999999999999997776667777789999999999999988899999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      ||+.|+|++|+.++|.+||+.++.     .+++++.+|+.|+||||+||.++|++|++.|++++...|+.+||..|++++
T Consensus       343 fD~~I~i~lPd~~~R~~Il~~~~~~~~~~~d~dl~~lA~~t~G~sGADi~~l~~eA~~~air~~~~~i~~~d~~~Al~~v  422 (437)
T 4b4t_L          343 LDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEFDFEAAVKMSDGFNGADIRNCATEAGFFAIRDDRDHINPDDLMKAVRKV  422 (437)
T ss_dssp             EEEEECCCCCCHHHHHHHHHHHHHTSCBCSCCCHHHHHHTCCSCCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             cceeeecCCcCHHHHHHHHHHHhcCCCCCcccCHHHHHHhCCCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            999999999999999999997664     578999999999999999999999999999999999999999999999998


Q ss_pred             cCCC--CCcccccC
Q 030960          157 VKKP--DTDFEFYK  168 (168)
Q Consensus       157 ~p~~--~~~~~~~k  168 (168)
                      .|..  ....+|.|
T Consensus       423 ~~~~k~e~~~e~~K  436 (437)
T 4b4t_L          423 AEVKKLEGTIEYQK  436 (437)
T ss_dssp             HHTCC---------
T ss_pred             HhccCcccchhhhc
Confidence            8754  23445544

>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=1.8e-39  Score=264.68  Aligned_cols=167  Identities=73%  Similarity=1.078  Sum_probs=153.5

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      |+.+|..|+.++||||||||+|++++.|.......+....+++++||++||++....+|+||||||+|+.||||++||||
T Consensus       254 ir~lF~~A~~~aP~IifiDEiD~i~~~R~~~~~~~~~~~~r~l~~lL~~ldg~~~~~~v~vI~aTN~~~~LD~AllRpGR  333 (428)
T 4b4t_K          254 VRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQSTNVKVIMATNRADTLDPALLRPGR  333 (428)
T ss_dssp             HHHHHHHHHHTCSEEEEEECTHHHHCSCSSSCSCCCCHHHHHHHHHHHHHHHSCSSCSEEEEEEESCSSSCCHHHHSSSS
T ss_pred             HHHHHHHHHHcCCCeeechhhhhhhccccCCCCCCChHHHHHHHHHHHHhhCCCCCCCEEEEEecCChhhcChhhhcCCc
Confidence            78999999999999999999999999997777666777789999999999999988899999999999999999999999


Q ss_pred             cceEEecC-CCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960           82 LDRKIEFP-LPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus        82 f~~~i~~~-~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      ||+.|+|| +|+.++|..||+.++.     .+++++.+|..|+||||+||.++|++|++.|+++++..|+.+||++|+.+
T Consensus       334 fd~~I~~p~lPd~~~R~~Il~~~~~~~~l~~~~dl~~lA~~t~G~sgadi~~l~~eA~~~a~r~~~~~i~~~d~~~A~~~  413 (428)
T 4b4t_K          334 LDRKIEFPSLRDRRERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQEAGLRAVRKNRYVILQSDLEEAYAT  413 (428)
T ss_dssp             EEEEEECCSSCCHHHHHHHHHHHHHSSCBCTTCCHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH
Confidence            99999996 8999999999986654     57899999999999999999999999999999999999999999999988


Q ss_pred             hcCCC--CCcccccC
Q 030960          156 NVKKP--DTDFEFYK  168 (168)
Q Consensus       156 ~~p~~--~~~~~~~k  168 (168)
                      ..+.+  ...+++||
T Consensus       414 ~~~~~~~~~~~d~yk  428 (428)
T 4b4t_K          414 QVKTDNTVDKFDFYK  428 (428)
T ss_dssp             HSCSCCCSSCCCSCC
T ss_pred             hhCccCCccHhhhhC
Confidence            65543  56788887

>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=1.5e-38  Score=259.72  Aligned_cols=157  Identities=45%  Similarity=0.757  Sum_probs=147.9

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|..|+..+||||||||+|+++..|.....+......++++++|++|+++....+|+||||||+|+.||+|++||||
T Consensus       291 ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~ViVIaATNrpd~LDpALlRpGR  370 (467)
T 4b4t_H          291 VRELFEMARTKKACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDPRGNIKVMFATNRPNTLDPALLRPGR  370 (467)
T ss_dssp             HHHHHHHHHHTCSEEEEEECCTTTSBCCSSSSCGGGGHHHHHHHHHHHHHHSSCCTTTEEEEEECSCTTSBCHHHHSTTT
T ss_pred             HHHHHHHHHhcCCceEeecccccccccccCcCCCccHHHHHHHHHHHHHhhccCCCCcEEEEeCCCCcccCChhhhcccc
Confidence            78999999999999999999999999997777677777789999999999999888999999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      ||+.|+|++|+.++|.+||+.++.     .+++++.+|+.|+||||+||+++|++|++.|++++...++.+||..|++++
T Consensus       371 FD~~I~i~lPd~~~R~~Ilk~~l~~~~l~~dvdl~~LA~~T~GfSGADI~~l~~eAa~~Air~~~~~it~~Df~~Al~kV  450 (467)
T 4b4t_H          371 IDRKVEFSLPDLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTEAGMFAIRARRKVATEKDFLKAVDKV  450 (467)
T ss_dssp             CCEEECCCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHTCSSBCHHHHHHHHHHH
T ss_pred             ccEEEEeCCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHH
Confidence            999999999999999999997765     578999999999999999999999999999999999999999999999987


Q ss_pred             cC
Q 030960          157 VK  158 (168)
Q Consensus       157 ~p  158 (168)
                      .+
T Consensus       451 ~~  452 (467)
T 4b4t_H          451 IS  452 (467)
T ss_dssp             HH
T ss_pred             hc
Confidence            64

>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=100.00  E-value=1e-37  Score=270.03  Aligned_cols=166  Identities=38%  Similarity=0.620  Sum_probs=104.9

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      |+.+|+.|++.+||||||||+|++++.|+......+....+++++||++||++....+|+||||||+|+.||+|++||||
T Consensus       559 vr~lF~~Ar~~~P~IifiDEiDsl~~~R~~~~~~~~~~~~rv~~~lL~~mdg~~~~~~V~vi~aTN~p~~lD~AllRpgR  638 (806)
T 3cf2_A          559 VREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGR  638 (806)
T ss_dssp             HHHHHHHHHTTCSEEEECSCGGGCC--------------CHHHHHHHHHHHSSCSSSSEEEECC-CCSSSSCHHHHSTTT
T ss_pred             HHHHHHHHHHcCCceeechhhhHHhhccCCCCCCCchHHHHHHHHHHHHHhCCCCCCCEEEEEeCCCchhCCHhHcCCCc
Confidence            78999999999999999999999999986554444555669999999999999988899999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC----------------
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN----------------  140 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~----------------  140 (168)
                      ||+.|+|++|+.++|.+||+.++.     .+++++.||+.|+||||+||+++|++|++.|+++.                
T Consensus       639 fd~~i~v~lPd~~~R~~il~~~l~~~~~~~~~dl~~la~~t~g~SGadi~~l~~~A~~~a~r~~~~~~~~~~~~~~~~~~  718 (806)
T 3cf2_A          639 LDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPS  718 (806)
T ss_dssp             SCCEEEC-----CHHHHTTTTTSSCC--CCC----------------CHHHHHHHHHHHHHHHHHC--------------
T ss_pred             ceEEEEECCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhccCcc
Confidence            999999999999999999997776     47899999999999999999999999999999873                


Q ss_pred             ---------CCccCHHHHHHHHHhhcCCC-CCccccc
Q 030960          141 ---------RYVILPKDFEKGYRTNVKKP-DTDFEFY  167 (168)
Q Consensus       141 ---------~~~i~~~d~~~al~~~~p~~-~~~~~~~  167 (168)
                               ...|+.+||++|+++++|+- .++++.|
T Consensus       719 ~~~~~~~~~~~~i~~~df~~al~~~~pSvs~~~l~~y  755 (806)
T 3cf2_A          719 AMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKY  755 (806)
T ss_dssp             ---------CCC----CCTTTC---------------
T ss_pred             ccccccccccCccCHHHHHHHHHhCCCCCCHHHHHHH
Confidence                     13699999999999999963 5566655

>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=100.00  E-value=2.1e-32  Score=236.87  Aligned_cols=158  Identities=38%  Similarity=0.604  Sum_probs=143.0

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|+.|++++||||||||+|++++.|++..+..   ..+++++|+++|+++....+|+|||+||+++.||++++||||
T Consensus       286 lr~lF~~A~~~~PsIIfIDEiDal~~~r~~~~~~~---~~riv~~LL~~mdg~~~~~~V~VIaaTN~~d~LD~ALrR~GR  362 (806)
T 3cf2_A          286 LRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEV---ERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGR  362 (806)
T ss_dssp             HHHHHHHHTTSCSEEEEEESGGGTCCTTTTCCCTT---HHHHHHHHHTHHHHCCGGGCEEEEEECSSTTTSCTTTTSTTS
T ss_pred             HHHHHHHHHHcCCeEEEEehhcccccccCCCCChH---HHHHHHHHHHHHhcccccCCEEEEEecCChhhcCHHHhCCcc
Confidence            68999999999999999999999999886554433   358999999999999888899999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC----------------
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN----------------  140 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~----------------  140 (168)
                      ||+.|++++|+.++|.+||+.++.     .++++..+|..|+||+|+||.++|++|++.|+++.                
T Consensus       363 Fd~~I~i~~Pd~~~R~~IL~~~l~~~~~~~dvdl~~lA~~T~GfsgaDL~~Lv~eA~~~A~~r~~~~i~~~~~~~~~e~~  442 (806)
T 3cf2_A          363 FDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVM  442 (806)
T ss_dssp             SCEEEECCCCCHHHHHHHHHHTCSSSEECTTCCHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHHHHHGGGTCCCCSHHHH
T ss_pred             cceEEecCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhccccccccccccchhhh
Confidence            999999999999999999997775     57899999999999999999999999999998773                


Q ss_pred             -CCccCHHHHHHHHHhhcCCCCC
Q 030960          141 -RYVILPKDFEKGYRTNVKKPDT  162 (168)
Q Consensus       141 -~~~i~~~d~~~al~~~~p~~~~  162 (168)
                       ...++.+||..|++..+|+...
T Consensus       443 ~~~~v~~~Df~~Al~~~~ps~~r  465 (806)
T 3cf2_A          443 NSLAVTMDDFRWALSQSNPSALR  465 (806)
T ss_dssp             HHCEECTTHHHHHHSSSSCCCCC
T ss_pred             ccceeeHHHHHHHHHhCCCcccc
Confidence             1358899999999999997643

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=99.97  E-value=1.3e-29  Score=196.49  Aligned_cols=157  Identities=36%  Similarity=0.603  Sum_probs=132.4

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|+.|+...||++++||+|.++..++.....   ...++++.++..|++......++++++||+|+.||++++||||
T Consensus        92 i~~vf~~a~~~~p~i~~~Deid~~~~~r~~~~~~---~~~~~~~~~l~~Lsgg~~~~~~i~ia~tn~p~~LD~al~r~gR  168 (274)
T 2x8a_A           92 VRQVFQRAKNSAPCVIFFDEVDALCPRRSDRETG---ASVRVVNQLLTEMDGLEARQQVFIMAATNRPDIIDPAILRPGR  168 (274)
T ss_dssp             HHHHHHHHHHTCSEEEEEETCTTTCC------------CTTHHHHHHHHHHTCCSTTCEEEEEEESCGGGSCHHHHSTTS
T ss_pred             HHHHHHHHHhcCCCeEeeehhhhhhcccCCCcch---HHHHHHHHHHHhhhcccccCCEEEEeecCChhhCCHhhcCccc
Confidence            5789999999999999999999998765432211   1236788999999998888889999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC--------CCCCHHHHHhCC--CCCCHHHHHHHHHHHHHHHHHhC-----------
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS--------DEVDLEDYVSRP--DKISAAEIAAICQEAGMHAVRKN-----------  140 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~--------~~~~~~~la~~t--~g~s~~di~~l~~~a~~~a~~~~-----------  140 (168)
                      ||+.|++++|+.++|.+||+.++.        .++++..+|..|  +||||+||.++|++|++.|+++.           
T Consensus       169 fd~~i~~~~P~~~~r~~il~~~~~~~~~~~~~~~~~~~~la~~~~~~g~sgadl~~l~~~a~~~a~~~~~~~~~~~~~~~  248 (274)
T 2x8a_A          169 LDKTLFVGLPPPADRLAILKTITKNGTKPPLDADVNLEAIAGDLRCDCYTGADLSALVREASICALRQEMARQKSGNEKG  248 (274)
T ss_dssp             SCEEEECCSCCHHHHHHHHHHHTTTTBTTBBCTTCCHHHHHTCSGGGSCCHHHHHHHHHHHHHHHHHHHC----------
T ss_pred             CCeEEEeCCcCHHHHHHHHHHHHhcccCCCCccccCHHHHHHhhccCCcCHHHHHHHHHHHHHHHHHHHHhhcccccccc
Confidence            999999999999999999997663        478899999985  59999999999999999998762           


Q ss_pred             CCccCHHHHHHHHHhhcCCCC
Q 030960          141 RYVILPKDFEKGYRTNVKKPD  161 (168)
Q Consensus       141 ~~~i~~~d~~~al~~~~p~~~  161 (168)
                      ...|+.+||++|+++++|+..
T Consensus       249 ~~~i~~~df~~al~~~~ps~~  269 (274)
T 2x8a_A          249 ELKVSHKHFEEAFKKVRSSIS  269 (274)
T ss_dssp             -CCBCHHHHHHHHTTCCCCC-
T ss_pred             CCeecHHHHHHHHHHhcCCCC
Confidence            346999999999999999653

>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=99.96  E-value=2.5e-28  Score=201.65  Aligned_cols=158  Identities=39%  Similarity=0.615  Sum_probs=136.4

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|+.|+..+||||||||+|.+...++....+.+....++++.++..++++....+++||++||+++.+|++++||||
T Consensus        97 ~r~lf~~A~~~~p~ILfIDEid~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~~~~~~~viVIaaTn~~~~Ld~allR~gR  176 (476)
T 2ce7_A           97 VRDLFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPGR  176 (476)
T ss_dssp             HHHHHHHHHHTCSEEEEEETGGGTCCC---------CHHHHHHHHHHHHHHHSCGGGTEEEEEEESCGGGSCGGGGSTTS
T ss_pred             HHHHHHHHHhcCCCEEEEechhhhhhhcccccCcCcHHHHHHHHHHHHHHhccCCCCCEEEEEecCChhhhchhhcccCc
Confidence            57899999999999999999999998875443344445568899999999988777799999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      |+..+.+++|+.++|.+|++.++.     +++++..++..|+||+|+||.++|++|+..|.+++...|+.+||..|+.++
T Consensus       177 Fd~~i~i~~Pd~~~R~~Il~~~~~~~~l~~~v~l~~la~~t~G~sgadL~~lv~~Aal~A~~~~~~~I~~~dl~~al~~v  256 (476)
T 2ce7_A          177 FDKKIVVDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAKRTPGFVGADLENLVNEAALLAAREGRDKITMKDFEEAIDRV  256 (476)
T ss_dssp             SCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             ceeEeecCCCCHHHHHHHHHHHHHhCCCcchhhHHHHHHhcCCCcHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHH
Confidence            999999999999999999986655     467899999999999999999999999999999888899999999999998


Q ss_pred             cCC
Q 030960          157 VKK  159 (168)
Q Consensus       157 ~p~  159 (168)
                      .+.
T Consensus       257 ~~~  259 (476)
T 2ce7_A          257 IAG  259 (476)
T ss_dssp             C--
T ss_pred             hcC
Confidence            764

>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=99.96  E-value=3e-28  Score=190.84  Aligned_cols=159  Identities=38%  Similarity=0.614  Sum_probs=137.1

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|+.|+..+|+||||||+|.+...++...........++++.++..++++....+++||+|||+++.+|++++||||
T Consensus        97 ~~~~f~~a~~~~p~il~iDEid~l~~~~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~v~vi~atn~~~~ld~al~r~gR  176 (301)
T 3cf0_A           97 VREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGR  176 (301)
T ss_dssp             HHHHHHHHHHTCSEEEEECSTTHHHHHHTTTTCCSSCSCCHHHHHHHHHHHSSCTTSSEEEEEEESCGGGSCGGGGSTTS
T ss_pred             HHHHHHHHHhcCCeEEEEEChHHHhhccCCCcCCcchHHHHHHHHHHHHhhcccCCCCEEEEEecCCccccChHHhcCCc
Confidence            57899999999999999999999998764432222222237788899999988777789999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC----------------
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN----------------  140 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~----------------  140 (168)
                      |+..+++++|+.++|.+|++.++.     .++++..++..|.||+|+||.++|++|+..|.++.                
T Consensus       177 f~~~i~i~~p~~~~r~~il~~~l~~~~~~~~~~~~~la~~~~g~sg~dl~~l~~~a~~~a~~~~~~~~~~~~~~~~~~~~  256 (301)
T 3cf0_A          177 LDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPS  256 (301)
T ss_dssp             SCEEEECCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHHTCSSCCHHHHHHHHHHHHHHHHHHHHHHHC-----------
T ss_pred             cceEEecCCcCHHHHHHHHHHHHccCCCCccchHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccccc
Confidence            999999999999999999997775     46889999999999999999999999998887652                


Q ss_pred             ---------CCccCHHHHHHHHHhhcCCC
Q 030960          141 ---------RYVILPKDFEKGYRTNVKKP  160 (168)
Q Consensus       141 ---------~~~i~~~d~~~al~~~~p~~  160 (168)
                               ...|+.+||.+|+++.+|+.
T Consensus       257 ~~~~~~~~~~~~v~~~~~~~al~~~~~s~  285 (301)
T 3cf0_A          257 AMEVEEDDPVPEIRRDHFEEAMRFARRSV  285 (301)
T ss_dssp             ---------CCCBCHHHHHHHHTTCCCSS
T ss_pred             cccccccccCCccCHHHHHHHHHHcCCCC
Confidence                     13689999999999999865

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=99.95  E-value=1.2e-26  Score=177.52  Aligned_cols=158  Identities=39%  Similarity=0.612  Sum_probs=139.7

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|+.|+...|++++|||+|.+...+............+.++.++..++++....+++||++||.++.+|++++||||
T Consensus        93 ~~~~~~~a~~~~~~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~vI~~tn~~~~l~~~l~r~~r  172 (257)
T 1lv7_A           93 VRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGR  172 (257)
T ss_dssp             HHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEEESCTTTSCGGGGSTTS
T ss_pred             HHHHHHHHHHcCCeeehhhhhhhhccCCCCCcCCCchHHHHHHHHHHHHhhCcccCCCEEEEEeeCCchhCCHHHcCCCc
Confidence            56889999998999999999999998765433333334457888999999988777889999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      |+..+++++|+.++|.+|++.++.     ++.++..++..++||+++||.++|++|+..|.+++...|+.+||.+|++.+
T Consensus       173 f~~~i~i~~P~~~~r~~il~~~~~~~~l~~~~~~~~la~~~~G~~~~dl~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~  252 (257)
T 1lv7_A          173 FDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARGNKRVVSMVEFEKAKDKI  252 (257)
T ss_dssp             SCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             CCeEEEeCCCCHHHHHHHHHHHHhcCCCCccccHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHH
Confidence            999999999999999999987654     467889999999999999999999999999999988999999999999987


Q ss_pred             cCC
Q 030960          157 VKK  159 (168)
Q Consensus       157 ~p~  159 (168)
                      ...
T Consensus       253 ~~~  255 (257)
T 1lv7_A          253 MMG  255 (257)
T ss_dssp             TTC
T ss_pred             hcC
Confidence            654

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=99.95  E-value=5.3e-27  Score=185.51  Aligned_cols=154  Identities=33%  Similarity=0.542  Sum_probs=135.2

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC-CCCCeEEEEecCCCCCCCccccCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD-QTVNVKVIMATNRADTLDPALLRPG   80 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-~~~~v~vi~ttn~~~~ld~al~r~g   80 (168)
                      ++.+|..|+..+|+||||||+|.+++.+....   .....+++++++..++++. ...+++||++||.|+.+|++++|  
T Consensus        94 ~~~lf~~a~~~~~~vl~iDEid~l~~~~~~~~---~~~~~~~~~~ll~~ld~~~~~~~~v~vI~atn~~~~ld~al~r--  168 (322)
T 1xwi_A           94 VKNLFQLARENKPSIIFIDEIDSLCGSRSENE---SEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--  168 (322)
T ss_dssp             HHHHHHHHHHTSSEEEEEETTTGGGCCSSSCC---TTHHHHHHHHHHHHHHCSSSCCTTEEEEEEESCTTTSCHHHHH--
T ss_pred             HHHHHHHHHhcCCcEEEeecHHHhcccccccc---chHHHHHHHHHHHHHhcccccCCCEEEEEecCCcccCCHHHHh--
Confidence            67899999999999999999999998775433   2345688999999999885 45789999999999999999999  


Q ss_pred             CcceEEecCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC--------------
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN--------------  140 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~--------------  140 (168)
                      ||+..+++++|+.++|.+||+.++.      .+.++..++..|+||||+||..+|++|++.++++.              
T Consensus       169 Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~~~A~~~a~r~~~~~~~~~~~~~~~~  248 (322)
T 1xwi_A          169 RFEKRIYIPLPEPHARAAMFKLHLGTTQNSLTEADFRELGRKTDGYSGADISIIVRDALMQPVRKVQSATHFKKVRGPSR  248 (322)
T ss_dssp             TCCEEEECCCCCHHHHHHHHHHHHTTCCBCCCHHHHHHHHHTCTTCCHHHHHHHHHHHHTHHHHHHHHCSEEEEEEEECS
T ss_pred             hcCeEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccc
Confidence            9999999999999999999998765      34568899999999999999999999999988762              


Q ss_pred             -----------------------------------CCccCHHHHHHHHHhhcCCC
Q 030960          141 -----------------------------------RYVILPKDFEKGYRTNVKKP  160 (168)
Q Consensus       141 -----------------------------------~~~i~~~d~~~al~~~~p~~  160 (168)
                                                         ..+|+.+||..|++.++|+.
T Consensus       249 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~al~~~~ps~  303 (322)
T 1xwi_A          249 ADPNHLVDDLLTPCSPGDPGAIEMTWMDVPGDKLLEPVVSMSDMLRSLSNTKPTV  303 (322)
T ss_dssp             SCTTSEEEEEEEECCSSSTTEEECCGGGSCGGGBCCCCBCHHHHHHHHHTCCCSC
T ss_pred             cccccccccccccccccccchhhccccccccccccCCCcCHHHHHHHHHhCCCCC
Confidence                                               13699999999999999975

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=99.94  E-value=3.6e-26  Score=176.88  Aligned_cols=166  Identities=50%  Similarity=0.794  Sum_probs=142.2

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|..++...|+||+|||+|.+++++.+...+........+..++..++++....++++|+|||.++.+|++++|+||
T Consensus        99 ~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~~vI~ttn~~~~l~~~l~~~~R  178 (285)
T 3h4m_A           99 VKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGR  178 (285)
T ss_dssp             HHHHHHHHHHTCSEEEEEETTHHHHBCCSSSCCGGGGHHHHHHHHHHHHHHTTCSSSSEEEEEECSCGGGBCHHHHSTTS
T ss_pred             HHHHHHHHHHcCCeEEEEECHHHhcccCccccCCccHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCchhcCHHHcCCCc
Confidence            56889999999999999999999998876665555666778888999999888777899999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      |+..+++++|+.++|.+|++.++.     .+.++..++..+.||+++||..+|+.|...|+.++...|+.+||.+|++++
T Consensus       179 f~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~l~~~~~g~~~~~i~~l~~~a~~~a~~~~~~~I~~~d~~~al~~~  258 (285)
T 3h4m_A          179 FDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAELKAICTEAGMNAIRELRDYVTMDDFRKAVEKI  258 (285)
T ss_dssp             EEEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHHCTTCCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             CCeEEEECCCCHHHHHHHHHHHHhcCCCCCcCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhccCcCCHHHHHHHHHHH
Confidence            999999999999999999997665     467899999999999999999999999999999999999999999999876


Q ss_pred             cC-------CCCCccccc
Q 030960          157 VK-------KPDTDFEFY  167 (168)
Q Consensus       157 ~p-------~~~~~~~~~  167 (168)
                      .+       .+.....||
T Consensus       259 ~~~~~~~~~~~~~~~~~~  276 (285)
T 3h4m_A          259 MEKKKVKVKEPAHLDVLY  276 (285)
T ss_dssp             HHHHCCC-----------
T ss_pred             HhccccccCCchHHHHHH
Confidence            53       234555555

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=99.94  E-value=2.3e-26  Score=190.91  Aligned_cols=159  Identities=38%  Similarity=0.630  Sum_probs=140.3

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|+.|+...|||+||||+|.+...+............+.+++++..|++......++++++||+|+.+|++++||||
T Consensus       112 v~~lfq~a~~~~p~il~IDEId~l~~~r~~~~~~~~~e~~~~l~~LL~~Ldg~~~~~~viviAatn~p~~LD~aLlr~gR  191 (499)
T 2dhr_A          112 VRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGR  191 (499)
T ss_dssp             HHHHTTTSSSSSSCEEEEECGGGTCCCSSSSTTTSSHHHHHHHHHHHHHGGGCCSSCCCEEEECCSCGGGSCTTTSSTTS
T ss_pred             HHHHHHHHHhcCCCEEEEehHHHHHHhhccCcCCCcHHHHHHHHHHHHHhcccccCccEEEEEecCChhhcCcccccccc
Confidence            46788888888899999999999987764322233445568889999999998887889999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      ||+.+++++|+..+|.+||+.++.     +++++..+|..|+||+|+||+++|++|+..|.+++...|+.+||.+++.++
T Consensus       192 fdr~i~i~~Pd~~~R~~IL~~~~~~~~l~~dv~l~~lA~~t~G~~gadL~~lv~~Aa~~A~~~~~~~It~~dl~~al~~v  271 (499)
T 2dhr_A          192 FDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREGRRKITMKDLEEAADRV  271 (499)
T ss_dssp             SCCEEECCCCCHHHHHHHHHHTTSSSCCCCSSTTHHHHTTSCSCCHHHHHHHHHHHHHHHTTTCCSSCCSHHHHHHHHHH
T ss_pred             cceEEecCCCCHHHHHHHHHHHHhcCCCChHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHH
Confidence            999999999999999999997654     577899999999999999999999999999998888899999999999998


Q ss_pred             cCCC
Q 030960          157 VKKP  160 (168)
Q Consensus       157 ~p~~  160 (168)
                      .+..
T Consensus       272 ~~~~  275 (499)
T 2dhr_A          272 MMLP  275 (499)
T ss_dssp             TTCS
T ss_pred             hccc
Confidence            7653

>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=99.94  E-value=5.9e-27  Score=185.02  Aligned_cols=159  Identities=35%  Similarity=0.527  Sum_probs=133.3

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC-CCCCeEEEEecCCCCCCCccccCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD-QTVNVKVIMATNRADTLDPALLRPG   80 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-~~~~v~vi~ttn~~~~ld~al~r~g   80 (168)
                      ++.+|..|+..+|+||||||+|.+.+.++......   ..++.+.++..++++. ...+++||+|||.++.+|++++|  
T Consensus        99 ~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~---~~~~~~~ll~~l~~~~~~~~~v~vi~atn~~~~ld~al~~--  173 (322)
T 3eie_A           99 VKQLFAMARENKPSIIFIDQVDALTGTRGEGESEA---SRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--  173 (322)
T ss_dssp             HHHHHHHHHHTSSEEEEEECGGGGSCC------CC---THHHHHHHHHHHGGGGTSCCCEEEEEEESCGGGSCHHHHH--
T ss_pred             HHHHHHHHHhcCCeEEEechhhhhhccCCCCcchH---HHHHHHHHHHHhccccccCCceEEEEecCChhhCCHHHHc--
Confidence            67899999999999999999999998775443332   3478889999998874 55689999999999999999999  


Q ss_pred             CcceEEecCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCC-------------
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNR-------------  141 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~-------------  141 (168)
                      ||+..+++++|+.++|.+||+.++.      .+.++..++..|+|||++||.++|++|+..++++..             
T Consensus       174 Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~l~~la~~t~g~sg~di~~l~~~a~~~a~r~~~~~~~~~~~~~~~~  253 (322)
T 3eie_A          174 RFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIRKIQSATHFKDVSTEDD  253 (322)
T ss_dssp             HCCEEEECCCCCHHHHHHHHHHHHTTCCCCCCHHHHHHHHHTTTTCCHHHHHHHHHHHTTHHHHHHHHCEEEEECC----
T ss_pred             ccCeEEEeCCCCHHHHHHHHHHHhccCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHhhhhhhhhhccccc
Confidence            9999999999999999999998765      344688999999999999999999999999888631             


Q ss_pred             ------------------------------CccCHHHHHHHHHhhcCCC-CCccc
Q 030960          142 ------------------------------YVILPKDFEKGYRTNVKKP-DTDFE  165 (168)
Q Consensus       142 ------------------------------~~i~~~d~~~al~~~~p~~-~~~~~  165 (168)
                                                    ..|+.+||.+|++.++|+. .+.++
T Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~al~~~~ps~~~~~~~  308 (322)
T 3eie_A          254 ETRKLTPCSPGDDGAIEMSWTDIEADELKEPDLTIKDFLKAIKSTRPTVNEDDLL  308 (322)
T ss_dssp             CCCCEEECCSSCTTEEEEEGGGSCSSCBCCCCCCHHHHHHHHHHSCCSSCTTHHH
T ss_pred             cccccccccccccccccccccccccccccCCCCCHHHHHHHHHhcCCCCCHHHHH
Confidence                                          3599999999999999975 33443

>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=99.94  E-value=1.2e-25  Score=171.60  Aligned_cols=152  Identities=39%  Similarity=0.652  Sum_probs=129.4

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|+.+....|+++++||+|.++..+............+.++.++..+++......++++++||.|+.+|++++|+||
T Consensus        97 i~~~~~~~~~~~~~i~~~Deid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~g~~~~~~~i~~a~t~~p~~ld~~l~r~~r  176 (254)
T 1ixz_A           97 VRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGR  176 (254)
T ss_dssp             HHHHHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGGGSCGGGGSTTS
T ss_pred             HHHHHHHHHhcCCeEEEehhhhhhhcccCccccccchHHHHHHHHHHHHHhCCCCCCCEEEEEccCCchhCCHHHcCCCc
Confidence            46789998888899999999999987664322223344567888999999988777789999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      |+..+++++|+.++|.+||+.+..     ++.++..++..++||+++||.++|++|+..|.+++...|+.+||.+++
T Consensus       177 f~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~G~~~~dl~~~~~~a~~~a~~~~~~~I~~~dl~~a~  253 (254)
T 1ixz_A          177 FDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREGRRKITMKDLEEAA  253 (254)
T ss_dssp             SCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHT
T ss_pred             CCeEEeeCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCCcCHHHHHHHh
Confidence            999999999999999999986543     577899999999999999999999999999999888899999999986

>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=99.94  E-value=4.6e-26  Score=182.29  Aligned_cols=155  Identities=34%  Similarity=0.523  Sum_probs=130.4

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCC-CCCeEEEEecCCCCCCCccccCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQ-TVNVKVIMATNRADTLDPALLRPG   80 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~-~~~v~vi~ttn~~~~ld~al~r~g   80 (168)
                      ++.+|..|+..+|+||||||+|.+.+.++...   .....++.+.++..++++.. ..+++||++||.++.+|++++|  
T Consensus       132 ~~~~f~~a~~~~~~vl~iDEid~l~~~r~~~~---~~~~~~~~~~ll~~l~~~~~~~~~v~vI~atn~~~~ld~al~r--  206 (355)
T 2qp9_X          132 VKQLFAMARENKPSIIFIDQVDALTGTRGEGE---SEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--  206 (355)
T ss_dssp             HHHHHHHHHHTSSEEEEEECGGGGTC---------CTHHHHHHHHHHHHHHHCC---CCEEEEEEESCGGGSCHHHHH--
T ss_pred             HHHHHHHHHHcCCeEEEEechHhhcccCCCCc---chHHHHHHHHHHHHhhcccccCCCeEEEeecCCcccCCHHHHc--
Confidence            57899999999999999999999998774432   23445788899999988753 5689999999999999999999  


Q ss_pred             CcceEEecCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC--------------
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN--------------  140 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~--------------  140 (168)
                      ||+..+++++|+.++|.+||+.++.      .+.++..|+..|+||+|+||.++|++|++.|+++.              
T Consensus       207 Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~~~~~~l~~la~~t~G~sg~dl~~l~~~A~~~a~~~~~~~~~~~~~~~~~~  286 (355)
T 2qp9_X          207 RFERRIYIPLPDLAARTTMFEINVGDTPSVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIRKIQSATHFKDVSTEDD  286 (355)
T ss_dssp             TCCEEEECCCCCHHHHHHHHHHHHTTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHHHCSEEEECCC---
T ss_pred             ccCEEEEeCCcCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhhccccc
Confidence            9999999999999999999998775      24568899999999999999999999999999862              


Q ss_pred             -----------------------------CCccCHHHHHHHHHhhcCCCC
Q 030960          141 -----------------------------RYVILPKDFEKGYRTNVKKPD  161 (168)
Q Consensus       141 -----------------------------~~~i~~~d~~~al~~~~p~~~  161 (168)
                                                   ...|+.+||..|++.++|+..
T Consensus       287 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~Al~~~~ps~~  336 (355)
T 2qp9_X          287 ETRKLTPSSPGDDGAIEMSWTDIEADELKEPDLTIKDFLKAIKSTRPTVN  336 (355)
T ss_dssp             --CCEEEECTTSSSEEECCGGGSCGGGBCCCCBCHHHHHHHHHHSCCSSC
T ss_pred             cccccCcCCccccchhhcccccccccccccCCccHHHHHHHHHHcCCCCC
Confidence                                         135999999999999999753

>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=99.93  E-value=1.8e-25  Score=183.60  Aligned_cols=154  Identities=33%  Similarity=0.542  Sum_probs=134.7

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC-CCCCeEEEEecCCCCCCCccccCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD-QTVNVKVIMATNRADTLDPALLRPG   80 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-~~~~v~vi~ttn~~~~ld~al~r~g   80 (168)
                      ++.+|..|+..+|+||||||+|.+++.+.....   ....++++.|+..++++. ...+++||+|||.|+.+|++++|  
T Consensus       216 ~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~---~~~~~~~~~lL~~l~~~~~~~~~v~vI~atn~~~~ld~al~r--  290 (444)
T 2zan_A          216 VKNLFQLARENKPSIIFIDEIDSLCGSRSENES---EAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--  290 (444)
T ss_dssp             HHHHHHHHHHSCSEEEEESCTTTTCCCSSCCCC---GGGHHHHHHHHTTTTCSSCCCSSCEEEEEESCGGGSCHHHHT--
T ss_pred             HHHHHHHHHHcCCeEEEEechHhhccCCCCccc---cHHHHHHHHHHHHHhCcccCCCCEEEEecCCCccccCHHHHh--
Confidence            688999999999999999999999987754432   234588999999999875 35689999999999999999999  


Q ss_pred             CcceEEecCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC--------------
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN--------------  140 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~--------------  140 (168)
                      ||+..+++++|+.++|..||+.++.      .+.++..++..|+||||+||..+|++|++.++++.              
T Consensus       291 Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~~~a~~~a~r~~~~~~~~~~~~~~~~  370 (444)
T 2zan_A          291 RFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRKTDGYSGADISIIVRDALMQPVRKVQSATHFKKVRGPSR  370 (444)
T ss_dssp             TCCEEEECCCCCHHHHHHHHHHHHTTSCEECCHHHHHHHHHHTTTCCHHHHHHHHHHHHTHHHHHHHHCSEEEEECCBCS
T ss_pred             hcceEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccc
Confidence            9999999999999999999998765      34578899999999999999999999999888752              


Q ss_pred             -----------------------------------CCccCHHHHHHHHHhhcCCC
Q 030960          141 -----------------------------------RYVILPKDFEKGYRTNVKKP  160 (168)
Q Consensus       141 -----------------------------------~~~i~~~d~~~al~~~~p~~  160 (168)
                                                         ..+|+.+||..|++.++|+.
T Consensus       371 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~a~~~~~ps~  425 (444)
T 2zan_A          371 ADPNCIVNDLLTPCSPGDPGAIEMTWMDVPGDKLLEPVVSMWDMLRSLSSTKPTV  425 (444)
T ss_dssp             SCTTSBCSCEEEEECTTSTTEEECCTTTSCTTCBCCCCEEHHHHHHHHHTCCCSC
T ss_pred             cccccccccccccCCCCcccchhcccccCchhhccCCccCHHHHHHHHHhCCCCC
Confidence                                               13689999999999999975

>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=99.93  E-value=3.2e-25  Score=183.96  Aligned_cols=156  Identities=38%  Similarity=0.612  Sum_probs=138.1

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|..|...+|++|||||+|.+.+.+....   .....++++.|+..|+++....+++||+|||+++.||++++++||
T Consensus       286 ~~~~f~~A~~~~p~iLfLDEId~l~~~~~~~~---~~~~~~~~~~LL~~ld~~~~~~~v~vIaaTn~~~~Ld~al~r~gR  362 (489)
T 3hu3_A          286 LRKAFEEAEKNAPAIIFIDELDAIAPKREKTH---GEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGR  362 (489)
T ss_dssp             HHHHHHHHHHTCSEEEEEESHHHHCBCTTSCC---CHHHHHHHHHHHHHHHHSCTTSCEEEEEEESCGGGBCGGGGSTTS
T ss_pred             HHHHHHHHHhcCCcEEEecchhhhcccccccc---chHHHHHHHHHHHHhhccccCCceEEEEecCCccccCHHHhCCCc
Confidence            57899999999999999999999998774332   234458888999999988778899999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCC--------------
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRY--------------  142 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~--------------  142 (168)
                      |+..+++++|+.++|.+||+.++.     .+.++..++..+.||+++||.++|++|+..++++...              
T Consensus       363 f~~~i~i~~P~~~eR~~IL~~~~~~~~l~~~~~l~~la~~t~g~s~~dL~~L~~~A~~~a~r~~~~~i~~~~~~~~~~~~  442 (489)
T 3hu3_A          363 FDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVM  442 (489)
T ss_dssp             SCEEEECCCCCHHHHHHHHHHHTTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTTTTCCTTCSSCCHHHH
T ss_pred             CceEEEeCCCCHHHHHHHHHHHHhcCCCcchhhHHHHHHHccCCcHHHHHHHHHHHHHHHHHhccccccccccccchhhc
Confidence            999999999999999999997665     4678999999999999999999999999999987532              


Q ss_pred             ---ccCHHHHHHHHHhhcCCC
Q 030960          143 ---VILPKDFEKGYRTNVKKP  160 (168)
Q Consensus       143 ---~i~~~d~~~al~~~~p~~  160 (168)
                         .++.+||..|++.+.|+.
T Consensus       443 ~~~~vt~edf~~Al~~~~ps~  463 (489)
T 3hu3_A          443 NSLAVTMDDFRWALSQSNPSA  463 (489)
T ss_dssp             HHCCBCHHHHHHHHTSHHHHH
T ss_pred             ccCcCCHHHHHHHHHhCCchh
Confidence               589999999999998865

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=99.93  E-value=1.8e-24  Score=167.41  Aligned_cols=152  Identities=39%  Similarity=0.652  Sum_probs=129.7

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|+.+....|+++++||+|.+...+..............++.++..+++......++++++||.|+.+|++++|+||
T Consensus       121 i~~~~~~~~~~~~~i~~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~lsgg~~~~~~i~~a~t~~p~~ld~~l~r~~r  200 (278)
T 1iy2_A          121 VRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGR  200 (278)
T ss_dssp             HHHHHHHHHTSCSEEEEEETHHHHHCC--------CHHHHHHHHHHHHHHTTCCTTCCEEEEEEESCTTSSCHHHHSTTS
T ss_pred             HHHHHHHHHhcCCcEEehhhhHhhhcccccccCCcchHHHHHHHHHHHHHhCCCCCCCEEEEEecCCchhCCHhHcCCCc
Confidence            46789999888899999999999986653322222334567888999999988777789999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      |+..+++++|+.++|.+||+.+..     ++.++..++..++||+++||.++|++|+..|.+++...|+.+||.+|+
T Consensus       201 f~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~G~~~~dl~~l~~~a~~~a~~~~~~~I~~~dl~~a~  277 (278)
T 1iy2_A          201 FDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREGRRKITMKDLEEAA  277 (278)
T ss_dssp             SCCEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTCCSBCHHHHHHHT
T ss_pred             CCeEEEeCCcCHHHHHHHHHHHHccCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhCCCCcCHHHHHHHh
Confidence            999999999999999999986553     567899999999999999999999999999998888889999999986

>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=99.92  E-value=2.2e-25  Score=170.15  Aligned_cols=159  Identities=36%  Similarity=0.595  Sum_probs=118.9

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCC-cchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTG-ADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPG   80 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~-~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~g   80 (168)
                      ++.+|..|...+|+||+|||+|.++..+...... ........++.++..++++....++++|+|||.++.+|++++|||
T Consensus        87 ~~~~~~~a~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~~vi~~tn~~~~ld~~l~~~~  166 (262)
T 2qz4_A           87 VRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTDHVIVLASTNRADILDGALMRPG  166 (262)
T ss_dssp             HHHHHHHHHHTCSEEEEEECC-------------------CHHHHHHHHHHHTCCTTCCEEEEEEESCGGGGGSGGGSTT
T ss_pred             HHHHHHHHHhcCCeEEEEeCcchhhccccccccCccchhHHHHHHHHHHHhhCcCCCCCEEEEecCCChhhcCHHHhcCC
Confidence            5678999999999999999999998776432211 122334678889999988777778999999999999999999999


Q ss_pred             CcceEEecCCCCHHHHHHHHHhhcCC-------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQMNLSD-------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~~~l~~-------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      ||+..+++++|+.++|.+|++.++..       +..+..++..+.||+++||.++|+.|+..|.+++...|+.+||..|+
T Consensus       167 R~~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~~~l~~~~~g~~~~~l~~l~~~a~~~a~~~~~~~i~~~d~~~a~  246 (262)
T 2qz4_A          167 RLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANICNEAALHAAREGHTSVHTLNFEYAV  246 (262)
T ss_dssp             SCCEEEECCSCCHHHHHHHHHHHHHHTTCCBTHHHHHHHHHHTCTTCCHHHHHHHHHHHHTC--------CCBCCHHHHH
T ss_pred             cCCeEEEeCCcCHHHHHHHHHHHHHhCCCCcchhhHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence            99999999999999999999976652       11347899999999999999999999999999888899999999999


Q ss_pred             HhhcCCC
Q 030960          154 RTNVKKP  160 (168)
Q Consensus       154 ~~~~p~~  160 (168)
                      ++..+..
T Consensus       247 ~~~~~~~  253 (262)
T 2qz4_A          247 ERVLAGT  253 (262)
T ss_dssp             HHHHHHH
T ss_pred             HHhccCh
Confidence            9877643

>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=99.91  E-value=1.2e-25  Score=172.66  Aligned_cols=163  Identities=34%  Similarity=0.583  Sum_probs=130.1

Q ss_pred             HHHHHHHHHcCCeEEEEcccccccccccCCCC-CcchHHHHHHHHHHHhccCCCC-CCCeEEEEecCCCCCCCccccCCC
Q 030960            3 RDVFRLAKENAPAIIFIDEVDAIATARFDAQT-GADREVQRILMELLNQMDGFDQ-TVNVKVIMATNRADTLDPALLRPG   80 (168)
Q Consensus         3 ~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~-~~~~~~~~~~~~ll~~l~~~~~-~~~v~vi~ttn~~~~ld~al~r~g   80 (168)
                      +.+|+.|...+|+||+|||+|.+...+..... ..+....+.++.++..+++... ..+++||+|||.++.+|++++|+|
T Consensus        93 ~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~ttn~~~~ld~~l~r~~  172 (268)
T 2r62_A           93 RDLFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPG  172 (268)
T ss_dssp             STTHHHHHHSCSCEEEESCGGGTTC----------CCCSCSSTTTTTTTTTCSSCSCSCCEEEECBSCCTTSCGGGGSSS
T ss_pred             HHHHHHHHhcCCeEEEEeChhhhcccccccccCCCchhHHHHHHHHHHHhhCcccCCCCEEEEEecCCchhcCHhHcCCC
Confidence            46789999999999999999999876522110 0011112455667788877643 345999999999999999999999


Q ss_pred             CcceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      ||+..+++++|+.++|.++|+.++.     .+.++..++..+.||+|+||.++|+.|+..|..++...|+.+|+.++++.
T Consensus       173 Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~g~~g~dl~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~  252 (268)
T 2r62_A          173 RFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAKLTAGLAGADLANIINEAALLAGRNNQKEVRQQHLKEAVER  252 (268)
T ss_dssp             SSCCCCBCCCCCTTTHHHHHHHHTSSSCCCSSCCTTTTTSSSCSSCHHHHHHHHHHHHHTTSSSCCCSCCHHHHHTSCTT
T ss_pred             CCCeEEEecCcCHHHHHHHHHHHHhcCCCCCccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhccCCcCHHHHHHHHHH
Confidence            9999999999999999999997765     45678899999999999999999999999998887889999999999999


Q ss_pred             hcCCCCCccc
Q 030960          156 NVKKPDTDFE  165 (168)
Q Consensus       156 ~~p~~~~~~~  165 (168)
                      ..|......+
T Consensus       253 ~~~~~~~~~~  262 (268)
T 2r62_A          253 GIAGLEKKLE  262 (268)
T ss_dssp             CCCCCC----
T ss_pred             Hhhcchhhhh
Confidence            9988765543

>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=99.89  E-value=1.1e-22  Score=162.79  Aligned_cols=154  Identities=33%  Similarity=0.532  Sum_probs=128.2

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC--CCCCeEEEEecCCCCCCCccccCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD--QTVNVKVIMATNRADTLDPALLRP   79 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~--~~~~v~vi~ttn~~~~ld~al~r~   79 (168)
                      ++.+|..|+..+|+||||||+|.++..+....   .....++++.++..+++..  ...+++||++||.++.+|+++++ 
T Consensus       165 ~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~---~~~~~~~~~~lL~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~-  240 (357)
T 3d8b_A          165 VRALFAVARCQQPAVIFIDEIDSLLSQRGDGE---HESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAARR-  240 (357)
T ss_dssp             HHHHHHHHHHTCSEEEEEETHHHHTBC---------CHHHHHHHHHHHHHHC----CCCCEEEEEEESCGGGBCHHHHT-
T ss_pred             HHHHHHHHHhcCCeEEEEeCchhhhccCCCCc---chHHHHHHHHHHHHHhcccccCCCCEEEEEecCChhhCCHHHHh-
Confidence            57889999999999999999999998764322   2234578889999998764  34579999999999999999999 


Q ss_pred             CCcceEEecCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC------------C
Q 030960           80 GRLDRKIEFPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN------------R  141 (168)
Q Consensus        80 grf~~~i~~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~------------~  141 (168)
                       ||+..+++++|+.++|.++++.++.      .+.++..++..++||+++||..+|+.|...++++.            .
T Consensus       241 -Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~l~~la~~t~G~s~~dl~~l~~~a~~~~ir~l~~~~~~~~~~~~~  319 (357)
T 3d8b_A          241 -RLVKRLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQIVQQSDAFSGADMTQLCREASLGPIRSLQTADIATITPDQV  319 (357)
T ss_dssp             -TCCEEEECCCCCHHHHHHHHHHHHHTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHHHHHTHHHHHCCC----------C
T ss_pred             -hCceEEEeCCcCHHHHHHHHHHHHhhcCCCccHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHhhhhhhcccccccc
Confidence             9999999999999999999987653      23457789999999999999999999999998853            2


Q ss_pred             CccCHHHHHHHHHhhcCCC
Q 030960          142 YVILPKDFEKGYRTNVKKP  160 (168)
Q Consensus       142 ~~i~~~d~~~al~~~~p~~  160 (168)
                      ..|+.+||..|+..++|+.
T Consensus       320 ~~i~~~d~~~al~~~~ps~  338 (357)
T 3d8b_A          320 RPIAYIDFENAFRTVRPSV  338 (357)
T ss_dssp             CCBCHHHHHHHHHHHGGGC
T ss_pred             CCcCHHHHHHHHHhcCCCC
Confidence            5799999999999999854

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=99.88  E-value=1.2e-22  Score=157.95  Aligned_cols=154  Identities=29%  Similarity=0.502  Sum_probs=126.7

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCC---CCeEEEEecCCCCCCCccccC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQT---VNVKVIMATNRADTLDPALLR   78 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~---~~v~vi~ttn~~~~ld~al~r   78 (168)
                      ++.+|..+...+|+||||||+|.++..+........   .++.+.++..++++...   .+++||++||+++.+|+++++
T Consensus       102 ~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~---~~~~~~ll~~l~~~~~~~~~~~v~vi~~tn~~~~l~~~l~~  178 (297)
T 3b9p_A          102 VRALFAVARHMQPSIIFIDEVDSLLSERSSSEHEAS---RRLKTEFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALR  178 (297)
T ss_dssp             HHHHHHHHHHTCSEEEEEETGGGTSBCC-----CCS---HHHHHHHHHHHHHCC------CEEEEEEESCGGGBCHHHHH
T ss_pred             HHHHHHHHHHcCCcEEEeccHHHhccccccCcchHH---HHHHHHHHHHHhcccccCCCCcEEEEeecCChhhCCHHHHh
Confidence            567899999999999999999999987644332222   36677788888876433   579999999999999999999


Q ss_pred             CCCcceEEecCCCCHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC------------
Q 030960           79 PGRLDRKIEFPLPDRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN------------  140 (168)
Q Consensus        79 ~grf~~~i~~~~P~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~------------  140 (168)
                        ||+..+++++|+.++|..|++.++..      +.++..++..+.||+++||..+|+.|+..++++.            
T Consensus       179 --R~~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~~la~~~~g~~~~~l~~l~~~a~~~a~r~~~~~~~~~~~~~~  256 (297)
T 3b9p_A          179 --RFTKRVYVSLPDEQTRELLLNRLLQKQGSPLDTEALRRLAKITDGYSGSDLTALAKDAALEPIRELNVEQVKCLDISA  256 (297)
T ss_dssp             --HCCEEEECCCCCHHHHHHHHHHHHGGGSCCSCHHHHHHHHHHTTTCCHHHHHHHHHHHTTHHHHTCC--------CCC
T ss_pred             --hCCeEEEeCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHhhhhcccccccc
Confidence              99999999999999999999876542      3357789999999999999999999999999874            


Q ss_pred             CCccCHHHHHHHHHhhcCCC
Q 030960          141 RYVILPKDFEKGYRTNVKKP  160 (168)
Q Consensus       141 ~~~i~~~d~~~al~~~~p~~  160 (168)
                      ...|+.+||..|+...+|+.
T Consensus       257 ~~~i~~~d~~~a~~~~~~s~  276 (297)
T 3b9p_A          257 MRAITEQDFHSSLKRIRRSV  276 (297)
T ss_dssp             CCCCCHHHHHHHTTSCCCSS
T ss_pred             cCCcCHHHHHHHHHHcCCCC
Confidence            25799999999999998864

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=99.87  E-value=1.2e-21  Score=158.22  Aligned_cols=154  Identities=29%  Similarity=0.471  Sum_probs=125.7

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCC--CCCeEEEEecCCCCCCCccccCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQ--TVNVKVIMATNRADTLDPALLRP   79 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~--~~~v~vi~ttn~~~~ld~al~r~   79 (168)
                      ++.+|..|+..+|+||||||+|.++..+......   ...++.+.++..++++..  ..+++||+|||.++.+|+++++ 
T Consensus       196 ~~~~~~~a~~~~~~il~iDEid~l~~~~~~~~~~---~~~~~~~~ll~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~-  271 (389)
T 3vfd_A          196 VRALFAVARELQPSIIFIDQVDSLLCERREGEHD---ASRRLKTEFLIEFDGVQSAGDDRVLVMGATNRPQELDEAVLR-  271 (389)
T ss_dssp             HHHHHHHHHHSSSEEEEEETGGGGC--------C---THHHHHHHHHHHHHHHC-----CEEEEEEESCGGGCCHHHHT-
T ss_pred             HHHHHHHHHhcCCeEEEEECchhhcccCCCccch---HHHHHHHHHHHHhhcccccCCCCEEEEEecCCchhcCHHHHc-
Confidence            5789999999999999999999998776433222   234777888888887644  4579999999999999999999 


Q ss_pred             CCcceEEecCCCCHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC------------C
Q 030960           80 GRLDRKIEFPLPDRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN------------R  141 (168)
Q Consensus        80 grf~~~i~~~~P~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~------------~  141 (168)
                       ||+..+++++|+.++|.+||+.++..      +.++..++..+.||+++||..+|+.|...++++.            .
T Consensus       272 -R~~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~~~~la~~~~g~~~~~l~~L~~~a~~~~~rel~~~~~~~~~~~~~  350 (389)
T 3vfd_A          272 -RFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQLARMTDGYSGSDLTALAKDAALGPIRELKPEQVKNMSASEM  350 (389)
T ss_dssp             -TCCEEEECCCCCHHHHHHHHHHHHTTSCCCSCHHHHHHHHHHTTTCCHHHHHHHHHHHTTHHHHTSCCC---CCSSSCC
T ss_pred             -CcceEEEcCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhhhhhhhhccchhhc
Confidence             99999999999999999999977652      2357789999999999999999999999999872            3


Q ss_pred             CccCHHHHHHHHHhhcCCC
Q 030960          142 YVILPKDFEKGYRTNVKKP  160 (168)
Q Consensus       142 ~~i~~~d~~~al~~~~p~~  160 (168)
                      ..|+.+||..+++...|+.
T Consensus       351 ~~i~~~d~~~al~~~~~s~  369 (389)
T 3vfd_A          351 RNIRLSDFTESLKKIKRSV  369 (389)
T ss_dssp             CCCCHHHHHHHHHHCCCSS
T ss_pred             CCcCHHHHHHHHHHcCCCC
Confidence            4799999999999988864

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=99.78  E-value=1.2e-19  Score=141.61  Aligned_cols=123  Identities=25%  Similarity=0.297  Sum_probs=90.7

Q ss_pred             HHHHHHHH----HHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC-----------CCCCeEEEEec
Q 030960            2 VRDVFRLA----KENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD-----------QTVNVKVIMAT   66 (168)
Q Consensus         2 l~~iF~~a----~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-----------~~~~v~vi~tt   66 (168)
                      ++.+|..|    +..+||||||||+|.+++.+++... .......+.+.|++.+|+..           ...+++||+||
T Consensus        84 i~~~f~~a~~~~~~~~~~vl~iDEiD~~~~~~~~~~~-~~~~~~~v~~~Ll~~ld~~~~~~~~~~~~~~~~~~v~vI~tt  162 (293)
T 3t15_A           84 IRQRYREAAEIIRKGNMCCLFINDLDAGAGRMGGTTQ-YTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTG  162 (293)
T ss_dssp             HHHHHHHHHHHHTTSSCCCEEEECCC---------------CHHHHHHHHHHHHHCCC-----------CCCCCCEEEEC
T ss_pred             HHHHHHHHHHHHhcCCCeEEEEechhhhcCCCCCCcc-ccchHHHHHHHHHHHhccccccccccccccccCCCcEEEEec
Confidence            56788888    5778999999999999985533221 11123356677888877432           45679999999


Q ss_pred             CCCCCCCccccCCCCcceEEecCCCCHHHHHHHHHhhcC-CCCCHHHHHhCCCCCCHHHHHH
Q 030960           67 NRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLS-DEVDLEDYVSRPDKISAAEIAA  127 (168)
Q Consensus        67 n~~~~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~-~~~~~~~la~~t~g~s~~di~~  127 (168)
                      |+++.+|++++|||||+..++  .|+.++|.+|++.++. ..++++.++..++||+++||..
T Consensus       163 N~~~~ld~al~R~~R~d~~i~--~P~~~~r~~Il~~~~~~~~~~~~~l~~~~~~~~~~~l~~  222 (293)
T 3t15_A          163 NDFSTLYAPLIRDGRMEKFYW--APTREDRIGVCTGIFRTDNVPAEDVVKIVDNFPGQSIDF  222 (293)
T ss_dssp             SSCCC--CHHHHHHHEEEEEE--CCCHHHHHHHHHHHHGGGCCCHHHHHHHHHHSCSCCHHH
T ss_pred             CCcccCCHHHhCCCCCceeEe--CcCHHHHHHHHHHhccCCCCCHHHHHHHhCCCCcccHHH
Confidence            999999999999999999997  5799999999997665 5789999999999999999974

>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast structural genomics consortium (NESG), target HR3102A, PSI-2; NMR {Homo sapiens}

Probab=99.71  E-value=4.9e-17  Score=104.74  Aligned_cols=74  Identities=23%  Similarity=0.395  Sum_probs=68.4

Q ss_pred             ecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhcCCC
Q 030960           87 EFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKP  160 (168)
Q Consensus        87 ~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~p~~  160 (168)
                      .-.+|+.++|.+||+.++.     .+++++.||+.|+||||+||+++|++|++.|+++....|+.+||..|+++++|..
T Consensus         7 ~~~~Pd~~~R~~IL~~~l~~~~l~~dvdl~~LA~~T~G~SGADL~~l~~eAa~~alr~~~~~I~~~df~~Al~~v~p~~   85 (86)
T 2krk_A            7 HHSHPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRERRVHVTQEDFEMAVAKVMQKD   85 (86)
T ss_dssp             CCCCCCHHHHHHHHHHHTTTSEECTTCCCHHHHHTCSSCCHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHHCCC
T ss_pred             CCCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHccCC
Confidence            3479999999999997776     4789999999999999999999999999999999999999999999999998853

>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Homo sapiens}

Probab=99.70  E-value=8.4e-17  Score=101.81  Aligned_cols=71  Identities=25%  Similarity=0.445  Sum_probs=66.0

Q ss_pred             CCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhcCC
Q 030960           89 PLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKK  159 (168)
Q Consensus        89 ~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~p~  159 (168)
                      |+|+.++|.+||+.++.     ++++++.+|+.|+||||+||.++|++|++.|++++...|+.+||..|++++..+
T Consensus         1 plPd~~~R~~Il~~~l~~~~~~~~~dl~~la~~t~G~SGADi~~l~~eA~~~a~~~~~~~i~~~d~~~Al~~v~~~   76 (78)
T 3kw6_A            1 PPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRERRVHVTQEDFEMAVAKVMQK   76 (78)
T ss_dssp             CCCCHHHHHHHHHHHHTTSEECTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHHC-
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCCccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc
Confidence            68999999999997776     578999999999999999999999999999999999999999999999988764

>3aji_B S6C, proteasome (prosome, macropain) 26S subunit, ATPA; gankyrin, S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber suppression; HET: PBF; 2.05A {Mus musculus} PDB: 2dwz_B* 2dvw_B*

Probab=99.68  E-value=1e-16  Score=102.58  Aligned_cols=77  Identities=66%  Similarity=1.087  Sum_probs=63.1

Q ss_pred             CHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhcCCCCCcccc
Q 030960           92 DRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDTDFEF  166 (168)
Q Consensus        92 ~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~p~~~~~~~~  166 (168)
                      +.++|.+||+.++.     +++++..+|+.|+||||+||.++|++|++.|++++...|+.+||..|+++++|+...++++
T Consensus         2 d~~~R~~Il~~~l~~~~~~~~vdl~~la~~t~G~SGADi~~l~~eA~~~a~~~~~~~i~~~df~~Al~~~~ps~~~~l~~   81 (83)
T 3aji_B            2 DRRQKRLIFSTITSKMNLSEEVDLEDYVARPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEF   81 (83)
T ss_dssp             CHHHHHHHHHHHHTTSCBCTTCCTHHHHTSSCCCCHHHHHHHHHHHHHGGGTSCCSSBCHHHHHHHHHHHCC--------
T ss_pred             CHHHHHHHHHHHhCCCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhccCCcCHHHHHHHHHHHccCchHHHHh
Confidence            67899999997665     5789999999999999999999999999999999989999999999999999987777888


Q ss_pred             cC
Q 030960          167 YK  168 (168)
Q Consensus       167 ~k  168 (168)
                      |+
T Consensus        82 y~   83 (83)
T 3aji_B           82 YK   83 (83)
T ss_dssp             --
T ss_pred             cC
Confidence            75

>3vlf_B 26S protease regulatory subunit 7 homolog; heat repeat, chaperone, chaperone-protein binding complex; HET: DNA; 3.80A {Saccharomyces cerevisiae} PDB: 4a3v_B*

Probab=99.61  E-value=2.5e-15  Score=97.12  Aligned_cols=69  Identities=26%  Similarity=0.356  Sum_probs=62.5

Q ss_pred             CHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhcCCC
Q 030960           92 DRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKP  160 (168)
Q Consensus        92 ~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~p~~  160 (168)
                      |.++|.+||+.++.     ++++++.||+.|+||||+||.++|++|++.|++++...|+.+||..|++++.+..
T Consensus         2 d~~~R~~Il~~~~~~~~~~~dvdl~~lA~~t~G~SGADl~~l~~eAa~~a~r~~~~~i~~~df~~Al~~v~~~~   75 (88)
T 3vlf_B            2 DLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTEAGMFAIRARRKVATEKDFLKAVDKVISGY   75 (88)
T ss_dssp             CSSHHHHHHHHHHTTSCBCSCCCHHHHHHTCSSCCHHHHHHHHHHHHHHHHHHSCSSBCHHHHHHHHHHHTC--
T ss_pred             CHHHHHHHHHHHHCCCCCCCccCHHHHHHHcCCCcHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHhcCc
Confidence            56789999996665     5789999999999999999999999999999999999999999999999998865

>2dzn_B 26S protease regulatory subunit 6B homolog; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} PDB: 2dzo_B

Probab=99.57  E-value=2.7e-15  Score=95.70  Aligned_cols=75  Identities=52%  Similarity=0.782  Sum_probs=50.3

Q ss_pred             HHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhcC--CCCCcccc
Q 030960           94 RQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVK--KPDTDFEF  166 (168)
Q Consensus        94 ~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~p--~~~~~~~~  166 (168)
                      ++|.+||+.++.     ++++++.+|+.|+||||+||.++|++|++.|++++...|+.+||..|++++.+  ....++++
T Consensus         1 ~~R~~Il~~~l~~~~~~~~vdl~~lA~~t~G~SGADi~~l~~eAa~~ai~~~~~~i~~~df~~Al~~v~~~~~~~~~~~~   80 (82)
T 2dzn_B            1 MERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQEAGLRAVRKNRYVILQSDLEEAYATQVKTDNTVDKFDF   80 (82)
T ss_dssp             -------------CEECTTCCSTTTTTSSCCCCHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHTTCC----------
T ss_pred             CHHHHHHHHHHcCCCCCCcCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhccCCcCHHHHHHHHHHHHcCcCChHHHHh
Confidence            468899986664     57899999999999999999999999999999999999999999999999853  33567788


Q ss_pred             cC
Q 030960          167 YK  168 (168)
Q Consensus       167 ~k  168 (168)
                      |+
T Consensus        81 y~   82 (82)
T 2dzn_B           81 YK   82 (82)
T ss_dssp             --
T ss_pred             hC
Confidence            75

>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=99.50  E-value=3.2e-17  Score=134.89  Aligned_cols=126  Identities=13%  Similarity=0.203  Sum_probs=76.5

Q ss_pred             HHHHHHHH---HHcCCeEEEEcccccccccccCCCCCcch-HHH---------------HHHHHHHHhcc--CCCCCCCe
Q 030960            2 VRDVFRLA---KENAPAIIFIDEVDAIATARFDAQTGADR-EVQ---------------RILMELLNQMD--GFDQTVNV   60 (168)
Q Consensus         2 l~~iF~~a---~~~~p~ii~iDe~D~l~~~~~~~~~~~~~-~~~---------------~~~~~ll~~l~--~~~~~~~v   60 (168)
                      ++.+|..|   +..+||||||||+|.++++++....+... ...               ++.+.++..++  ++...+.+
T Consensus       112 ~~~~f~~a~~~~~~~~~il~iDEid~l~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ll~~l~~~~~~~~~~v  191 (456)
T 2c9o_A          112 LMENFRRAIGLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFESLQKERVEAGDVI  191 (456)
T ss_dssp             HHHHHHHTEEEEEEEEEEEEEEEEEEEEEC--------------CEEEEEEETTEEEEEEECHHHHHHHHHTTCCTTEEE
T ss_pred             HHHHHHHHHhhhhcCCcEEEEechhhcccccCCCCCCCcchHHHHHHHHHhccccchhHhhhHHHHHHHhhccCCCCCEE
Confidence            46789998   78889999999999999888544221111 001               12233555554  33445557


Q ss_pred             EEEEecCCCCCCCccccCCCCcce--EEecCCCC--HHHHHHHHHhhcCCCCCHHHHHhCCCCCCHHHHHHHHHH
Q 030960           61 KVIMATNRADTLDPALLRPGRLDR--KIEFPLPD--RRQKRLVFQMNLSDEVDLEDYVSRPDKISAAEIAAICQE  131 (168)
Q Consensus        61 ~vi~ttn~~~~ld~al~r~grf~~--~i~~~~P~--~~~R~~il~~~l~~~~~~~~la~~t~g~s~~di~~l~~~  131 (168)
                      +|++|||+++.+|+++.||||||.  .++++.|+  ..+|.+|++.+..  .+++.++..|+|  |+||.++|..
T Consensus       192 ~i~attn~~~~ld~a~~r~~rfd~~~~~~v~~p~~~~~~R~~il~~~~~--~dl~~~a~~t~g--gadl~~l~~~  262 (456)
T 2c9o_A          192 YIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQDVTL--HDLDVANARPQG--GQDILSMMGQ  262 (456)
T ss_dssp             EEETTTCCEEEEEEETTSCCTTSCSSSSEECCCCSCSEEEEEEEEEEEH--HHHHHTC-----------------
T ss_pred             EEEcCCCCcccCChhhcCCcccCcceeEecCCCchhHHHHHHHHHHHHH--HHHHHHHHhCCC--hhHHHHHHhh
Confidence            777999999999999999999999  66777774  5788888875553  378999999999  9999999964

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=99.34  E-value=4.1e-12  Score=100.98  Aligned_cols=125  Identities=14%  Similarity=0.186  Sum_probs=99.5

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEec-----------CCCCCCCccccCCCCc
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMAT-----------NRADTLDPALLRPGRL   82 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~tt-----------n~~~~ld~al~r~grf   82 (168)
                      |+||||||+|.+..              ...+.++..++.  ...+++++++.           |.+..+++++++  ||
T Consensus       190 ~~vl~IDEi~~l~~--------------~~~~~L~~~le~--~~~~~~ii~t~~~~~~i~~t~~~~~~~l~~~l~s--R~  251 (368)
T 3uk6_A          190 PGVLFIDEVHMLDI--------------ESFSFLNRALES--DMAPVLIMATNRGITRIRGTSYQSPHGIPIDLLD--RL  251 (368)
T ss_dssp             BCEEEEESGGGSBH--------------HHHHHHHHHTTC--TTCCEEEEEESCSEEECBTSSCEEETTCCHHHHT--TE
T ss_pred             CceEEEhhccccCh--------------HHHHHHHHHhhC--cCCCeeeeecccceeeeeccCCCCcccCCHHHHh--hc
Confidence            78999999998741              445566666664  23345555554           358899999999  99


Q ss_pred             ceEEecCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           83 DRKIEFPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        83 ~~~i~~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      .. +.|++|+.+++.++++..+.      ++..+..++..+.|.+++++.++++.|...|..++...|+.+++.+++..+
T Consensus       252 ~~-i~~~~~~~~e~~~il~~~~~~~~~~~~~~~l~~l~~~~~~G~~r~~~~ll~~a~~~A~~~~~~~It~~~v~~a~~~~  330 (368)
T 3uk6_A          252 LI-VSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSLF  330 (368)
T ss_dssp             EE-EEECCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHS
T ss_pred             cE-EEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHh
Confidence            77 79999999999999996553      122466788888878999999999999999999888999999999999874


Q ss_pred             c
Q 030960          157 V  157 (168)
Q Consensus       157 ~  157 (168)
                      .
T Consensus       331 ~  331 (368)
T 3uk6_A          331 L  331 (368)
T ss_dssp             B
T ss_pred             c
Confidence            4

>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=99.31  E-value=6.7e-12  Score=96.17  Aligned_cols=148  Identities=13%  Similarity=0.127  Sum_probs=104.3

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC-CCCCeEEEEecCCCCCCCc-cccCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD-QTVNVKVIMATNRADTLDP-ALLRP   79 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-~~~~v~vi~ttn~~~~ld~-al~r~   79 (168)
                      ++.+|+.+....|++|+|||+|.+++.+..... ..   ..++..+...+++.. ...++++|+|||.++.+++ .+.+ 
T Consensus       113 ~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~-~~---~~~l~~L~~~~~~~~~~~~~~~ii~ttn~~~~l~~~~l~~-  187 (272)
T 1d2n_A          113 MKKIFDDAYKSQLSCVVVDDIERLLDYVPIGPR-FS---NLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEMLN-  187 (272)
T ss_dssp             HHHHHHHHHTSSEEEEEECCHHHHTTCBTTTTB-CC---HHHHHHHHHHTTCCCSTTCEEEEEEEESCHHHHHHTTCTT-
T ss_pred             HHHHHHHHHhcCCcEEEEEChhhhhccCCCChh-HH---HHHHHHHHHHhcCccCCCCCEEEEEecCChhhcchhhhhc-
Confidence            467888888888999999999999876532221 12   255666666777654 3446889999999999998 5665 


Q ss_pred             CCcceEEecCCCCH-HHHHHHHHhhcC-CCCCHHHHHhCCCCC----CHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           80 GRLDRKIEFPLPDR-RQKRLVFQMNLS-DEVDLEDYVSRPDKI----SAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        80 grf~~~i~~~~P~~-~~R~~il~~~l~-~~~~~~~la~~t~g~----s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                       ||+..+++|+++. ++...++..... .+..+..++..+.||    ..+++.++++.|...     ......+++.+++
T Consensus       188 -rf~~~i~~p~l~~r~~i~~i~~~~~~~~~~~~~~l~~~~~g~~~~g~ir~l~~~l~~a~~~-----~~~~~~~~~~~~l  261 (272)
T 1d2n_A          188 -AFSTTIHVPNIATGEQLLEALELLGNFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMSLQM-----DPEYRVRKFLALL  261 (272)
T ss_dssp             -TSSEEEECCCEEEHHHHHHHHHHHTCSCHHHHHHHHHHHTTSEEEECHHHHHHHHHHHTTS-----CGGGHHHHHHHHH
T ss_pred             -ccceEEcCCCccHHHHHHHHHHhcCCCCHHHHHHHHHHhcCCCccccHHHHHHHHHHHhhh-----chHHHHHHHHHHH
Confidence             9999999987765 555566554321 344577889999998    677777777766432     2335667788888


Q ss_pred             HhhcCCC
Q 030960          154 RTNVKKP  160 (168)
Q Consensus       154 ~~~~p~~  160 (168)
                      ......+
T Consensus       262 ~~~~~~~  268 (272)
T 1d2n_A          262 REEGASP  268 (272)
T ss_dssp             HHTSCCS
T ss_pred             HHcCCcc
Confidence            7766543

>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=99.29  E-value=1.2e-12  Score=109.75  Aligned_cols=142  Identities=18%  Similarity=0.232  Sum_probs=93.8

Q ss_pred             HHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCC-------------CCCeEEEEecCCC
Q 030960            3 RDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQ-------------TVNVKVIMATNRA   69 (168)
Q Consensus         3 ~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~-------------~~~v~vi~ttn~~   69 (168)
                      ...|..|....| |+||||+|.+...+.+          ...+.++..++....             ..++++|+|||.+
T Consensus       166 ~~~~~~a~~~~~-vl~lDEid~l~~~~~~----------~~~~~LL~~ld~~~~~~~~~~~~~~~~~~~~v~iI~ttN~~  234 (543)
T 3m6a_A          166 IQGMKKAGKLNP-VFLLDEIDKMSSDFRG----------DPSSAMLEVLDPEQNSSFSDHYIEETFDLSKVLFIATANNL  234 (543)
T ss_dssp             HHHHHTTCSSSE-EEEEEESSSCC-------------------CCGGGTCTTTTTBCCCSSSCCCCBCSSCEEEEECSST
T ss_pred             HHHHHHhhccCC-EEEEhhhhhhhhhhcc----------CHHHHHHHHHhhhhcceeecccCCeeecccceEEEeccCcc
Confidence            456666666666 9999999999765421          123456666654321             1568999999999


Q ss_pred             CCCCccccCCCCcceEEecCCCCHHHHHHHHHhhcCC-----------C--C---CHHHHHhCCCC-CCH----HHHHHH
Q 030960           70 DTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD-----------E--V---DLEDYVSRPDK-ISA----AEIAAI  128 (168)
Q Consensus        70 ~~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~~-----------~--~---~~~~la~~t~g-~s~----~di~~l  128 (168)
                      +.+|+++++  ||+ .|+++.|+.++|.+|++.++-+           .  +   .+..++....+ ...    +.|+++
T Consensus       235 ~~l~~aL~~--R~~-vi~~~~~~~~e~~~Il~~~l~~~~~~~~~~~~~~i~i~~~~l~~l~~~~~~~~~vR~L~~~i~~~  311 (543)
T 3m6a_A          235 ATIPGPLRD--RME-IINIAGYTEIEKLEIVKDHLLPKQIKEHGLKKSNLQLRDQAILDIIRYYTREAGVRSLERQLAAI  311 (543)
T ss_dssp             TTSCHHHHH--HEE-EEECCCCCHHHHHHHHHHTHHHHHHHHTTCCGGGCEECHHHHHHHHHHHCCCSSSHHHHHHHHHH
T ss_pred             ccCCHHHHh--hcc-eeeeCCCCHHHHHHHHHHHHHHHHHHHcCCCcccccCCHHHHHHHHHhCChhhchhHHHHHHHHH
Confidence            999999999  995 7999999999999999876521           1  1   23344443332 233    455556


Q ss_pred             HHHHHHHHHHh--CCCccCHHHHHHHHHhhcC
Q 030960          129 CQEAGMHAVRK--NRYVILPKDFEKGYRTNVK  158 (168)
Q Consensus       129 ~~~a~~~a~~~--~~~~i~~~d~~~al~~~~p  158 (168)
                      |+.++..+++.  ....|+.+++.+++.....
T Consensus       312 ~~~aa~~~~~~~~~~~~It~~~l~~~Lg~~~~  343 (543)
T 3m6a_A          312 CRKAAKAIVAEERKRITVTEKNLQDFIGKRIF  343 (543)
T ss_dssp             HHHHHHHHHTTCCSCCEECTTTTHHHHCSCCS
T ss_pred             HHHHHHHHHhcCCcceecCHHHHHHHhCCccc
Confidence            66666655554  2447999999999975443

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=99.23  E-value=1.3e-11  Score=95.90  Aligned_cols=125  Identities=19%  Similarity=0.235  Sum_probs=88.9

Q ss_pred             HHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC-----CCCcccc
Q 030960            3 RDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD-----TLDPALL   77 (168)
Q Consensus         3 ~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~-----~ld~al~   77 (168)
                      +.+|..+   .++||+|||+|.++..+++.  ..+   ...++.|+..++.  ...++.+|++||.+.     .++|+++
T Consensus       123 ~~~~~~~---~~~vl~iDEid~l~~~~~~~--~~~---~~~~~~Ll~~l~~--~~~~~~~i~~~~~~~~~~~~~~~~~l~  192 (309)
T 3syl_A          123 KEVLKRA---MGGVLFIDEAYYLYRPDNER--DYG---QEAIEILLQVMEN--NRDDLVVILAGYADRMENFFQSNPGFR  192 (309)
T ss_dssp             HHHHHHH---TTSEEEEETGGGSCCCC-----CCT---HHHHHHHHHHHHH--CTTTCEEEEEECHHHHHHHHHHSTTHH
T ss_pred             HHHHHhc---CCCEEEEEChhhhccCCCcc--ccc---HHHHHHHHHHHhc--CCCCEEEEEeCChHHHHHHHhhCHHHH
Confidence            4556655   57999999999998655321  112   2667777777773  345788889887654     3679999


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhcCC------CCCHHHHHhC------CCC-CCHHHHHHHHHHHHHHHHHh
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNLSD------EVDLEDYVSR------PDK-ISAAEIAAICQEAGMHAVRK  139 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l~~------~~~~~~la~~------t~g-~s~~di~~l~~~a~~~a~~~  139 (168)
                      +  ||+..++|++|+.+++.+|++.++..      +..+..++..      +.+ -+++++.++++.|...+..+
T Consensus       193 ~--R~~~~i~~~~~~~~~~~~il~~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~gn~r~l~~~l~~a~~~~~~r  265 (309)
T 3syl_A          193 S--RIAHHIEFPDYSDEELFEIAGHMLDDQNYQMTPEAETALRAYIGLRRNQPHFANARSIRNALDRARLRQANR  265 (309)
T ss_dssp             H--HEEEEEEECCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHTTSSSCCHHHHHHHHHHHHHHHHHHH
T ss_pred             H--hCCeEEEcCCcCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence            9  99999999999999999999876652      1223444443      123 34899999999998765544

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.21  E-value=1e-10  Score=92.77  Aligned_cols=142  Identities=17%  Similarity=0.162  Sum_probs=104.0

Q ss_pred             HHHHHHHHc-CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCC---CCCCccccCC
Q 030960            4 DVFRLAKEN-APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRA---DTLDPALLRP   79 (168)
Q Consensus         4 ~iF~~a~~~-~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~---~~ld~al~r~   79 (168)
                      .+++.+... .|+||+|||+|.+...+         .....+..++..++......++.+|++||.+   +.+++.+.+ 
T Consensus       120 ~l~~~l~~~~~~~vlilDEi~~l~~~~---------~~~~~l~~l~~~~~~~~~~~~~~~I~~t~~~~~~~~l~~~l~~-  189 (387)
T 2v1u_A          120 RLVKRLSRLRGIYIIVLDEIDFLPKRP---------GGQDLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKS-  189 (387)
T ss_dssp             HHHHHHTTSCSEEEEEEETTTHHHHST---------THHHHHHHHHHGGGCC-----CEEEEECSCSTTSSSSCHHHHT-
T ss_pred             HHHHHHhccCCeEEEEEccHhhhcccC---------CCChHHHhHhhchhhcCCCceEEEEEEECCCchHhhhCHHHHh-
Confidence            344444433 38999999999986432         1235666777777654325578899999988   789999998 


Q ss_pred             CCcce-EEecCCCCHHHHHHHHHhhcC--------CCCCHHHHHhCCC---CCCHHHHHHHHHHHHHHHHHhCCCccCHH
Q 030960           80 GRLDR-KIEFPLPDRRQKRLVFQMNLS--------DEVDLEDYVSRPD---KISAAEIAAICQEAGMHAVRKNRYVILPK  147 (168)
Q Consensus        80 grf~~-~i~~~~P~~~~R~~il~~~l~--------~~~~~~~la~~t~---g~s~~di~~l~~~a~~~a~~~~~~~i~~~  147 (168)
                       ||.. .+.+++|+.+++.++++..+.        ++..+..++..+.   | .++.+.++++.|...+...+...|+.+
T Consensus       190 -r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G-~~r~~~~~l~~a~~~a~~~~~~~i~~~  267 (387)
T 2v1u_A          190 -SLGEVELVFPPYTAPQLRDILETRAEEAFNPGVLDPDVVPLCAALAAREHG-DARRALDLLRVAGEIAERRREERVRRE  267 (387)
T ss_dssp             -TTTSEECCBCCCCHHHHHHHHHHHHHHHBCTTTBCSSHHHHHHHHHHSSSC-CHHHHHHHHHHHHHHHHHTTCSCBCHH
T ss_pred             -cCCCeEEeeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhcc-CHHHHHHHHHHHHHHHHHcCCCCcCHH
Confidence             9986 899999999999999985543        1223556666665   5 678888999999888887788889999


Q ss_pred             HHHHHHHhhc
Q 030960          148 DFEKGYRTNV  157 (168)
Q Consensus       148 d~~~al~~~~  157 (168)
                      ++.+++....
T Consensus       268 ~v~~a~~~~~  277 (387)
T 2v1u_A          268 HVYSARAEIE  277 (387)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            9999987653

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=99.17  E-value=3.6e-10  Score=88.84  Aligned_cols=130  Identities=18%  Similarity=0.205  Sum_probs=100.2

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC----------------CCCCeEEEEecCCCCCCCcc
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD----------------QTVNVKVIMATNRADTLDPA   75 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~----------------~~~~v~vi~ttn~~~~ld~a   75 (168)
                      ..+++|||||+|.+..              .....++..++...                ..+++.+|++||....++++
T Consensus       105 ~~~~vl~lDEi~~l~~--------------~~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~i~atn~~~~l~~~  170 (338)
T 3pfi_A          105 SEGDILFIDEIHRLSP--------------AIEEVLYPAMEDYRLDIIIGSGPAAQTIKIDLPKFTLIGATTRAGMLSNP  170 (338)
T ss_dssp             CTTCEEEEETGGGCCH--------------HHHHHHHHHHHTSCC---------CCCCCCCCCCCEEEEEESCGGGSCHH
T ss_pred             cCCCEEEEechhhcCH--------------HHHHHHHHHHHhccchhhcccCccccceecCCCCeEEEEeCCCccccCHH
Confidence            4589999999998841              23334444444321                11248999999999999999


Q ss_pred             ccCCCCcceEEecCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHH
Q 030960           76 LLRPGRLDRKIEFPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDF  149 (168)
Q Consensus        76 l~r~grf~~~i~~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~  149 (168)
                      +++  ||+..+.+++|+.+++..+++....      ++..+..++..+.| +++++.++++.+...+...+...|+.+++
T Consensus       171 L~~--R~~~~i~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~l~~~~~G-~~r~l~~~l~~~~~~a~~~~~~~i~~~~~  247 (338)
T 3pfi_A          171 LRD--RFGMQFRLEFYKDSELALILQKAALKLNKTCEEKAALEIAKRSRS-TPRIALRLLKRVRDFADVNDEEIITEKRA  247 (338)
T ss_dssp             HHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHHTTTT-CHHHHHHHHHHHHHHHHHTTCSEECHHHH
T ss_pred             HHh--hcCEEeeCCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCc-CHHHHHHHHHHHHHHHHhhcCCccCHHHH
Confidence            999  9999999999999999999986654      22345677886655 67899999999988887777788999999


Q ss_pred             HHHHHhhcC
Q 030960          150 EKGYRTNVK  158 (168)
Q Consensus       150 ~~al~~~~p  158 (168)
                      ..++.....
T Consensus       248 ~~~~~~~~~  256 (338)
T 3pfi_A          248 NEALNSLGV  256 (338)
T ss_dssp             HHHHHHHTC
T ss_pred             HHHHHHhCC
Confidence            999887543

>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=99.14  E-value=1.2e-10  Score=90.05  Aligned_cols=142  Identities=18%  Similarity=0.213  Sum_probs=100.0

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC--------CCCCeEEEEe----cCCCCCCCccccCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD--------QTVNVKVIMA----TNRADTLDPALLRPG   80 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~--------~~~~v~vi~t----tn~~~~ld~al~r~g   80 (168)
                      .++||+|||+|.+.......  ..+.....+.+.|+..+++..        ...++++|++    ++.+..+++++++  
T Consensus       116 ~~~vl~iDEi~~l~~~~~~~--~~~~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~l~~~l~~--  191 (310)
T 1ofh_A          116 QNGIVFIDEIDKICKKGEYS--GADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG--  191 (310)
T ss_dssp             HHCEEEEECGGGGSCCSSCC--SSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSSCGGGSCHHHHH--
T ss_pred             CCCEEEEEChhhcCcccccc--ccchhHHHHHHHHHHHhcCCeEecccccccCCcEEEEEcCCcccCCcccCCHHHHh--
Confidence            47999999999998665322  222223345667777777531        2346788888    5688999999998  


Q ss_pred             CcceEEecCCCCHHHHHHHHHhhc-------------C------CCCCHHHHHhCC-------CCCCHHHHHHHHHHHHH
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQMNL-------------S------DEVDLEDYVSRP-------DKISAAEIAAICQEAGM  134 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~~~l-------------~------~~~~~~~la~~t-------~g~s~~di~~l~~~a~~  134 (168)
                      ||+..++|++|+.+++.+|++...             .      ++..+..+++.+       ++...+.+.++++.+..
T Consensus       192 R~~~~i~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~~g~~R~l~~~l~~~~~  271 (310)
T 1ofh_A          192 RLPIRVELTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKKIAEAAFRVNEKTENIGARRLHTVMERLMD  271 (310)
T ss_dssp             TCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHHTTCEEEECHHHHHHHHHHHHHHHHHSCCCTTHHHHHHHHHHSH
T ss_pred             hCCceEEcCCcCHHHHHHHHHhhHHHHHHHHHHHHHhcCCeeccCHHHHHHHHHHhhhhcccccccCcHHHHHHHHHHHH
Confidence            999999999999999999998421             1      111244556554       36788999999998765


Q ss_pred             HHHHhC-----CC-ccCHHHHHHHHHhhcC
Q 030960          135 HAVRKN-----RY-VILPKDFEKGYRTNVK  158 (168)
Q Consensus       135 ~a~~~~-----~~-~i~~~d~~~al~~~~p  158 (168)
                      .+..+.     .. .|+.+++.+++.....
T Consensus       272 ~~~~~~~~~~~~~~~i~~~~v~~~l~~~~~  301 (310)
T 1ofh_A          272 KISFSASDMNGQTVNIDAAYVADALGEVVE  301 (310)
T ss_dssp             HHHHHGGGCTTCEEEECHHHHHHHTCSSSS
T ss_pred             hhhcCCccccCCEEEEeeHHHHHHHHhhhh
Confidence            443221     11 4999999999987543

>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=99.08  E-value=2.8e-10  Score=93.19  Aligned_cols=130  Identities=14%  Similarity=0.150  Sum_probs=94.6

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCC---CCccccCCCCcc--eEEe
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADT---LDPALLRPGRLD--RKIE   87 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~---ld~al~r~grf~--~~i~   87 (168)
                      .|.||+|||+|.+...+            .....++..++.+...+..+||++.+.+..   +++++++  ||.  ..+.
T Consensus       194 ~~~vL~IDEi~~l~~~~------------~~q~~l~~~l~~l~~~~~~iIitt~~~~~~l~~l~~~L~s--R~~~g~~i~  259 (440)
T 2z4s_A          194 KVDILLIDDVQFLIGKT------------GVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVS--RFQMGLVAK  259 (440)
T ss_dssp             TCSEEEEECGGGGSSCH------------HHHHHHHHHHHHHHTTTCEEEEEESSCGGGCSSCCHHHHH--HHHSSBCCB
T ss_pred             CCCEEEEeCcccccCCh------------HHHHHHHHHHHHHHHCCCeEEEEECCCHHHHHHHHHHHHh--hccCCeEEE
Confidence            69999999999986432            111122222222223345556655555555   8899999  986  8899


Q ss_pred             cCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhcC
Q 030960           88 FPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVK  158 (168)
Q Consensus        88 ~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~p  158 (168)
                      +++|+.++|.++++..+.      ++..+..++..+.| +++++.++++.+...+...+ ..|+.+++.++++...+
T Consensus       260 l~~p~~e~r~~iL~~~~~~~~~~i~~e~l~~la~~~~g-n~R~l~~~L~~~~~~a~~~~-~~It~~~~~~~l~~~~~  334 (440)
T 2z4s_A          260 LEPPDEETRKSIARKMLEIEHGELPEEVLNFVAENVDD-NLRRLRGAIIKLLVYKETTG-KEVDLKEAILLLKDFIK  334 (440)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHSS-SCCCHHHHHHHTSTTTC
T ss_pred             eCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-CHHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHHHHHhh
Confidence            999999999999986543      23346778888865 89999999999988876655 46999999999988763

>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=99.08  E-value=5.6e-10  Score=87.02  Aligned_cols=129  Identities=16%  Similarity=0.100  Sum_probs=96.0

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC----------------CCCCeEEEEecCCCCCCCcc
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD----------------QTVNVKVIMATNRADTLDPA   75 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~----------------~~~~v~vi~ttn~~~~ld~a   75 (168)
                      ..+++|||||+|.+...              ....++..++...                ...++.+|++||.+..++++
T Consensus        89 ~~~~~l~lDEi~~l~~~--------------~~~~L~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~~i~~t~~~~~~~~~  154 (324)
T 1hqc_A           89 EEGDILFIDEIHRLSRQ--------------AEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAP  154 (324)
T ss_dssp             CTTCEEEETTTTSCCHH--------------HHHHHHHHHHHSEEEECCSSSSSCCCEEEECCCCEEEEEESCCSSCSCS
T ss_pred             cCCCEEEEECCcccccc--------------hHHHHHHHHHhhhhHHhccccccccccccCCCCEEEEEeCCCcccCCHH
Confidence            45899999999987421              1222333332210                11358899999999999999


Q ss_pred             ccCCCCcceEEecCCCCHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHH
Q 030960           76 LLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDF  149 (168)
Q Consensus        76 l~r~grf~~~i~~~~P~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~  149 (168)
                      +.+  ||+..+.+++|+.+++..+++.+...      +..+..++..+.| .++++.++++.+...+...+...|+.+++
T Consensus       155 l~~--R~~~~i~l~~~~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G-~~r~l~~~l~~~~~~a~~~~~~~i~~~~~  231 (324)
T 1hqc_A          155 LLS--RFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRG-TMRVAKRLFRRVRDFAQVAGEEVITRERA  231 (324)
T ss_dssp             TTT--TCSCEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHSCS-CHHHHHHHHHHHTTTSTTTSCSCCCHHHH
T ss_pred             HHh--cccEEEecCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHccC-CHHHHHHHHHHHHHHHHHhcCCCCCHHHH
Confidence            998  99999999999999999999866531      2235677888866 56899999998877776666678999999


Q ss_pred             HHHHHhhc
Q 030960          150 EKGYRTNV  157 (168)
Q Consensus       150 ~~al~~~~  157 (168)
                      ..++....
T Consensus       232 ~~~~~~~~  239 (324)
T 1hqc_A          232 LEALAALG  239 (324)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHhc
Confidence            88887654

>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=99.07  E-value=4.2e-10  Score=97.56  Aligned_cols=145  Identities=19%  Similarity=0.225  Sum_probs=102.4

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCC-----CCCCccc
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRA-----DTLDPAL   76 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~-----~~ld~al   76 (168)
                      ++.+|+.+....++||||||+|.+++.++....  ..   ...    +.+..+.....+.+|++||.+     ..+|+++
T Consensus       267 l~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~~~--~~---~~~----~~L~~~l~~~~~~~I~at~~~~~~~~~~~d~aL  337 (758)
T 1r6b_X          267 FKALLKQLEQDTNSILFIDEIHTIIGAGAASGG--QV---DAA----NLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRAL  337 (758)
T ss_dssp             HHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSC--HH---HHH----HHHSSCSSSCCCEEEEEECHHHHHCCCCCTTSS
T ss_pred             HHHHHHHHHhcCCeEEEEechHHHhhcCCCCcc--hH---HHH----HHHHHHHhCCCeEEEEEeCchHHhhhhhcCHHH
Confidence            567888888878999999999999876532211  11   222    223333445678899999864     3688999


Q ss_pred             cCCCCcceEEecCCCCHHHHHHHHHhhcCC----------CCCHHHHHhCC-----CCCCHHHHHHHHHHHHHHHHH---
Q 030960           77 LRPGRLDRKIEFPLPDRRQKRLVFQMNLSD----------EVDLEDYVSRP-----DKISAAEIAAICQEAGMHAVR---  138 (168)
Q Consensus        77 ~r~grf~~~i~~~~P~~~~R~~il~~~l~~----------~~~~~~la~~t-----~g~s~~di~~l~~~a~~~a~~---  138 (168)
                      .+  ||+ .+.|+.|+.++|.+|++.....          +..+..++..+     ..+.+..+..++.+|...+..   
T Consensus       338 ~~--Rf~-~i~v~~p~~~e~~~il~~l~~~~~~~~~v~~~~~al~~~~~~s~~~i~~~~lp~~~i~lld~a~~~~~~~~~  414 (758)
T 1r6b_X          338 AR--RFQ-KIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGARARLMPV  414 (758)
T ss_dssp             GG--GEE-EEECCCCCHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHCTTSCTTHHHHHHHHHHHHHHHHSSS
T ss_pred             Hh--Cce-EEEcCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhcccccCchHHHHHHHHHHHHHhcccc
Confidence            99  998 6999999999999999854321          11234444443     446778888899888765544   


Q ss_pred             -hCCCccCHHHHHHHHHhhcC
Q 030960          139 -KNRYVILPKDFEKGYRTNVK  158 (168)
Q Consensus       139 -~~~~~i~~~d~~~al~~~~p  158 (168)
                       .....++.+|+.+++.....
T Consensus       415 ~~~~~~v~~~di~~~~~~~~~  435 (758)
T 1r6b_X          415 SKRKKTVNVADIESVVARIAR  435 (758)
T ss_dssp             CCCCCSCCHHHHHHHHHHHSC
T ss_pred             cccCCccCHHHHHHHHHHhcC
Confidence             23467999999999988754

>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=99.04  E-value=8.5e-10  Score=81.44  Aligned_cols=117  Identities=17%  Similarity=0.198  Sum_probs=90.4

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      .|.+|+|||+|.+..              ...+.++..++.  ...++.+|++||.+..+++++.+  |+ ..+++++|+
T Consensus       126 ~~~vlviDe~~~l~~--------------~~~~~l~~~l~~--~~~~~~~i~~t~~~~~~~~~l~~--r~-~~i~l~~l~  186 (250)
T 1njg_A          126 RFKVYLIDEVHMLSR--------------HSFNALLKTLEE--PPEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALD  186 (250)
T ss_dssp             SSEEEEEETGGGSCH--------------HHHHHHHHHHHS--CCTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCC
T ss_pred             CceEEEEECcccccH--------------HHHHHHHHHHhc--CCCceEEEEEeCChHhCCHHHHH--Hh-hhccCCCCC
Confidence            489999999998731              234556666653  34578899999999999999988  75 789999999


Q ss_pred             HHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           93 RRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        93 ~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      .++..++++..+.      ++..+..+++.+.| .++.+.++++.+...    +...|+.+++.+++
T Consensus       187 ~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G-~~~~~~~~~~~~~~~----~~~~i~~~~v~~~~  248 (250)
T 1njg_A          187 VEQIRHQLEHILNEEHIAHEPRALQLLARAAEG-SLRDALSLTDQAIAS----GDGQVSTQAVSAML  248 (250)
T ss_dssp             HHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHTT-CHHHHHHHHHHHHTT----TTSSBCHHHHHHHS
T ss_pred             HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHhc----cCceecHHHHHHHh
Confidence            9999999986663      12236678888977 899999999877432    34479999999876

>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=99.01  E-value=3.5e-10  Score=84.08  Aligned_cols=126  Identities=13%  Similarity=0.089  Sum_probs=87.4

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCe-EEEEecCCCC---CCCccccCCCCcc--eEE
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV-KVIMATNRAD---TLDPALLRPGRLD--RKI   86 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v-~vi~ttn~~~---~ld~al~r~grf~--~~i   86 (168)
                      .|.+|+|||+|.+....         .....   ++..++.......+ +|++++..+.   .+++++.+  ||.  ..+
T Consensus       104 ~~~vliiDe~~~~~~~~---------~~~~~---l~~~l~~~~~~~~~~ii~~~~~~~~~~~~~~~~l~~--r~~~~~~i  169 (242)
T 3bos_A          104 QFDLICIDDVDAVAGHP---------LWEEA---IFDLYNRVAEQKRGSLIVSASASPMEAGFVLPDLVS--RMHWGLTY  169 (242)
T ss_dssp             GSSEEEEETGGGGTTCH---------HHHHH---HHHHHHHHHHHCSCEEEEEESSCTTTTTCCCHHHHH--HHHHSEEE
T ss_pred             CCCEEEEeccccccCCH---------HHHHH---HHHHHHHHHHcCCCeEEEEcCCCHHHHHHhhhhhhh--HhhcCceE
Confidence            48999999999885321         01122   22222222223334 5555555554   45678888  886  899


Q ss_pred             ecCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960           87 EFPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus        87 ~~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      ++++|+.+++.++++..+.      ++..++.++..+.| +.+++.++++.+...+...+ ..|+.+++.++++
T Consensus       170 ~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g-~~r~l~~~l~~~~~~a~~~~-~~It~~~v~~~l~  241 (242)
T 3bos_A          170 QLQPMMDDEKLAALQRRAAMRGLQLPEDVGRFLLNRMAR-DLRTLFDVLDRLDKASMVHQ-RKLTIPFVKEMLR  241 (242)
T ss_dssp             ECCCCCGGGHHHHHHHHHHHTTCCCCHHHHHHHHHHTTT-CHHHHHHHHHHHHHHHHHHT-CCCCHHHHHHHHT
T ss_pred             EeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHccC-CHHHHHHHHHHHHHHHHHhC-CCCcHHHHHHHhh
Confidence            9999999999999987653      12235667888866 89999999999988886554 4699999999875

>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=98.98  E-value=1.7e-09  Score=79.00  Aligned_cols=118  Identities=16%  Similarity=0.121  Sum_probs=87.2

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCC
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLP   91 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P   91 (168)
                      ..|.+|+|||+|.+...              ....++..++.  ...++.+|++||.+..+++++.+  ||. .+.+++|
T Consensus       101 ~~~~vliiDe~~~l~~~--------------~~~~l~~~l~~--~~~~~~~i~~~~~~~~~~~~l~~--r~~-~i~~~~~  161 (226)
T 2chg_A          101 APFKIIFLDEADALTAD--------------AQAALRRTMEM--YSKSCRFILSCNYVSRIIEPIQS--RCA-VFRFKPV  161 (226)
T ss_dssp             CSCEEEEEETGGGSCHH--------------HHHHHHHHHHH--TTTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCC
T ss_pred             cCceEEEEeChhhcCHH--------------HHHHHHHHHHh--cCCCCeEEEEeCChhhcCHHHHH--hCc-eeecCCC
Confidence            46899999999987421              12334444442  23467889999999999999999  988 8999999


Q ss_pred             CHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960           92 DRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus        92 ~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      +.++..++++..+.      ++..+..+++.+.| .++.+.++++.++..+     ..|+.+|+.+++.
T Consensus       162 ~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g-~~r~l~~~l~~~~~~~-----~~I~~~~v~~~~~  224 (226)
T 2chg_A          162 PKEAMKKRLLEICEKEGVKITEDGLEALIYISGG-DFRKAINALQGAAAIG-----EVVDADTIYQITA  224 (226)
T ss_dssp             CHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTT-CHHHHHHHHHHHHHTC-----SCBCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHhcC-----ceecHHHHHHHhc
Confidence            99999999986553      12235567776655 6777777777665543     5799999999875

>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=98.97  E-value=1.6e-09  Score=85.77  Aligned_cols=142  Identities=17%  Similarity=0.182  Sum_probs=100.4

Q ss_pred             HHHHHHHHHcC-CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCC---CCCCccccC
Q 030960            3 RDVFRLAKENA-PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRA---DTLDPALLR   78 (168)
Q Consensus         3 ~~iF~~a~~~~-p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~---~~ld~al~r   78 (168)
                      +.+++...... |+||+|||+|.+....+     .     ..+..++..++.+ ...++.+|++|+.+   ..+++.+.+
T Consensus       117 ~~l~~~l~~~~~~~vlilDE~~~l~~~~~-----~-----~~l~~l~~~~~~~-~~~~~~~I~~~~~~~~~~~~~~~~~~  185 (386)
T 2qby_A          117 RRLVKAVRDYGSQVVIVLDEIDAFVKKYN-----D-----DILYKLSRINSEV-NKSKISFIGITNDVKFVDLLDPRVKS  185 (386)
T ss_dssp             HHHHHHHHTCCSCEEEEEETHHHHHHSSC-----S-----THHHHHHHHHHSC-CC--EEEEEEESCGGGGGGCTTHHHH
T ss_pred             HHHHHHHhccCCeEEEEEcChhhhhccCc-----C-----HHHHHHhhchhhc-CCCeEEEEEEECCCChHhhhCHHHhc
Confidence            34445554444 99999999999864321     1     3455666666544 34578889999887   578888888


Q ss_pred             CCCcc-eEEecCCCCHHHHHHHHHhhcC-----CCC---CHHHHHhCCCC--CCHHHHHHHHHHHHHHHHHhCCCccCHH
Q 030960           79 PGRLD-RKIEFPLPDRRQKRLVFQMNLS-----DEV---DLEDYVSRPDK--ISAAEIAAICQEAGMHAVRKNRYVILPK  147 (168)
Q Consensus        79 ~grf~-~~i~~~~P~~~~R~~il~~~l~-----~~~---~~~~la~~t~g--~s~~di~~l~~~a~~~a~~~~~~~i~~~  147 (168)
                        ||. ..+.+++++.++..++++..+.     ..+   .+..++..+..  -.++.+.+++..|...+...+...|+.+
T Consensus       186 --r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~ll~~a~~~a~~~~~~~i~~~  263 (386)
T 2qby_A          186 --SLSEEEIIFPPYNAEELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDLLRVSGEIAERMKDTKVKEE  263 (386)
T ss_dssp             --TTTTEEEEECCCCHHHHHHHHHHHHHHHBCSSCSCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCSSCCHH
T ss_pred             --cCCCeeEEeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhcCCCccCHH
Confidence              776 5899999999999999986443     112   23445555541  3677777899999888887777889999


Q ss_pred             HHHHHHHhhc
Q 030960          148 DFEKGYRTNV  157 (168)
Q Consensus       148 d~~~al~~~~  157 (168)
                      ++..++....
T Consensus       264 ~v~~a~~~~~  273 (386)
T 2qby_A          264 YVYMAKEEIE  273 (386)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            9999887654

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=98.96  E-value=8.9e-09  Score=80.75  Aligned_cols=128  Identities=20%  Similarity=0.161  Sum_probs=92.7

Q ss_pred             eEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC---------CCCCCeEEEEecCCCC-----CCCccccCCC
Q 030960           15 AIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF---------DQTVNVKVIMATNRAD-----TLDPALLRPG   80 (168)
Q Consensus        15 ~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~---------~~~~~v~vi~ttn~~~-----~ld~al~r~g   80 (168)
                      +|++|||+|.+.+              ...+.++..++.-         ....++++|+|+|..+     .+++++++  
T Consensus       111 ~vl~iDEi~~~~~--------------~~~~~Ll~~l~~~~~~~~g~~~~~~~~~~viat~np~~~~~~~~l~~~l~~--  174 (331)
T 2r44_A          111 NFILADEVNRSPA--------------KVQSALLECMQEKQVTIGDTTYPLDNPFLVLATQNPVEQEGTYPLPEAQVD--  174 (331)
T ss_dssp             SEEEEETGGGSCH--------------HHHHHHHHHHHHSEEEETTEEEECCSSCEEEEEECTTCCSCCCCCCHHHHT--
T ss_pred             cEEEEEccccCCH--------------HHHHHHHHHHhcCceeeCCEEEECCCCEEEEEecCCCcccCcccCCHHHHh--
Confidence            7999999998631              2233344444321         1234677888888433     38999999  


Q ss_pred             CcceEEecCCCCHHHHHHHHHhhcCCC-----------------------C-----CHHHHHhC----------------
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQMNLSDE-----------------------V-----DLEDYVSR----------------  116 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~~~l~~~-----------------------~-----~~~~la~~----------------  116 (168)
                      ||+..+.+++|+.++|.+|++......                       +     .++.++..                
T Consensus       175 Rf~~~i~i~~p~~~~~~~il~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~v~~~~~~~~~i~~~~~~~r~~~~~~~~~~~  254 (331)
T 2r44_A          175 RFMMKIHLTYLDKESELEVMRRVSNMNFNYQVQKIVSKNDVLEIRNEINKVTISESLEKYIIELVFATRFPAEYGLEAEA  254 (331)
T ss_dssp             TSSEEEECCCCCHHHHHHHHHHHHCTTCCCCCCCCSCHHHHHHHHHHHHTCBCCHHHHHHHHHHHHHHHSGGGGTCHHHH
T ss_pred             heeEEEEcCCCCHHHHHHHHHhccccCcchhccccCCHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHhccccccccccc
Confidence            999999999999999999998665421                       1     12233221                


Q ss_pred             ---CCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhcC
Q 030960          117 ---PDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVK  158 (168)
Q Consensus       117 ---t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~p  158 (168)
                         ..|.|++.+.++++.|...|...+...++.+|+.+++..+..
T Consensus       255 ~~~~~~~s~R~~~~ll~~a~a~A~l~g~~~v~~~dv~~~~~~vl~  299 (331)
T 2r44_A          255 SYILYGASTRAAINLNRVAKAMAFFNNRDYVLPEDIKEVAYDILN  299 (331)
T ss_dssp             HHEEECCCHHHHHHHHHHHHHHHHHTTCSBCCHHHHHHHHHHHHT
T ss_pred             cccccCcChhHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhH
Confidence               126799999999999988888888888999999999987654

>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=98.94  E-value=9.3e-09  Score=80.82  Aligned_cols=128  Identities=16%  Similarity=0.172  Sum_probs=90.0

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC-------CC----CCCCeEEEEecCCCC-CCCccccCCCC
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG-------FD----QTVNVKVIMATNRAD-TLDPALLRPGR   81 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~-------~~----~~~~v~vi~ttn~~~-~ld~al~r~gr   81 (168)
                      +++|+|||+|.+..              ...+.++..++.       ..    ...++.+|+|||..+ .+++++++  |
T Consensus       145 ~~vl~iDEi~~l~~--------------~~~~~Ll~~le~~~~~~~~~g~~~~~~~~~~li~~~n~~~~~l~~~L~~--R  208 (350)
T 1g8p_A          145 RGYLYIDECNLLED--------------HIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLD--R  208 (350)
T ss_dssp             TEEEEETTGGGSCH--------------HHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHT--T
T ss_pred             CCEEEEeChhhCCH--------------HHHHHHHHHHhcCceEEEecceEEeeCCceEEEEEeCCCCCCCCHHHHh--h
Confidence            78999999998742              122233333321       11    113688999999744 89999999  9


Q ss_pred             cceEEecCCC-CHHHHHHHHHhhcC-----------------------------------CCCCHHHHHhCC---CCCCH
Q 030960           82 LDRKIEFPLP-DRRQKRLVFQMNLS-----------------------------------DEVDLEDYVSRP---DKISA  122 (168)
Q Consensus        82 f~~~i~~~~P-~~~~R~~il~~~l~-----------------------------------~~~~~~~la~~t---~g~s~  122 (168)
                      |+..+.+++| +.++|.+|++..+.                                   ++..+..++...   .+-++
T Consensus       209 ~~~~~~l~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ls~~~~~~l~~~~~~~~~~~~  288 (350)
T 1g8p_A          209 FGLSVEVLSPRDVETRVEVIRRRDTYDADPKAFLEEWRPKDMDIRNQILEARERLPKVEAPNTALYDCAALCIALGSDGL  288 (350)
T ss_dssp             CSEEEECCCCCSHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHGGGCBCCHHHHHHHHHHHHHSSSCSH
T ss_pred             cceEEEcCCCCcHHHHHHHHHHHHhcccCchhhccccccchHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHhCCCCc
Confidence            9999999999 67888788865210                                   111122333333   22378


Q ss_pred             HHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhc
Q 030960          123 AEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNV  157 (168)
Q Consensus       123 ~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~  157 (168)
                      +.+.++++.|...|..++...|+.+|+.+++....
T Consensus       289 R~~~~ll~~a~~~A~~~~~~~v~~~~v~~a~~~~l  323 (350)
T 1g8p_A          289 RGELTLLRSARALAALEGATAVGRDHLKRVATMAL  323 (350)
T ss_dssp             HHHHHHHHHHHHHHHHTTCSBCCHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHHH
Confidence            99999999999988888888899999999998654

>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=98.92  E-value=7.1e-11  Score=96.62  Aligned_cols=87  Identities=17%  Similarity=0.109  Sum_probs=15.6

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEe-cCCCCCCCccccCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMA-TNRADTLDPALLRPG   80 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~t-tn~~~~ld~al~r~g   80 (168)
                      ++.+|+.|....|    +||+|.+....      ......++++.|+.+||++.....+  +++ ||+++.||++|+|||
T Consensus       100 lr~lf~~a~~~~~----~De~d~~~~~~------~~~~e~rvl~~LL~~~dg~~~~~~v--~a~~TN~~~~ld~aL~rgg  167 (444)
T 1g41_A          100 IRDLTDSAMKLVR----QQEIAKNRARA------EDVAEERILDALLPPAKNQWGEVEN--HDSHSSTRQAFRKKLREGQ  167 (444)
T ss_dssp             HHHHHHHHHHHHH----HHHHHSCC-------------------------------------------------------
T ss_pred             HHHHHHHHHhcch----hhhhhhhhccc------hhhHHHHHHHHHHHHhhcccccccc--ccccccCHHHHHHHHHcCC
Confidence            5778888877643    78888765322      1122358999999999998766554  455 999999999999999


Q ss_pred             CcceEEecCCCCHH-HHHHHH
Q 030960           81 RLDRKIEFPLPDRR-QKRLVF  100 (168)
Q Consensus        81 rf~~~i~~~~P~~~-~R~~il  100 (168)
                      |||+.|++++|+.. .|.+|+
T Consensus       168 r~D~~i~i~lP~~~~~~~ei~  188 (444)
T 1g41_A          168 LDDKEIEIDVSAGVSMGVEIM  188 (444)
T ss_dssp             ---------------------
T ss_pred             CcceEEEEcCCCCccchhhhh
Confidence            99999999999998 788876

>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=98.90  E-value=3e-09  Score=84.58  Aligned_cols=133  Identities=25%  Similarity=0.313  Sum_probs=94.0

Q ss_pred             HHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHH-HHHHHHhccCCCCCCCeEEEEecCCC---CCCCccccCC
Q 030960            4 DVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRI-LMELLNQMDGFDQTVNVKVIMATNRA---DTLDPALLRP   79 (168)
Q Consensus         4 ~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~-~~~ll~~l~~~~~~~~v~vi~ttn~~---~~ld~al~r~   79 (168)
                      .++..++... .||+|||+|.+....     . .    .. +..++...      .++.+|++||.+   +.+++++.+ 
T Consensus       125 ~l~~~l~~~~-~vlilDEi~~l~~~~-----~-~----~~~l~~l~~~~------~~~~iI~~t~~~~~~~~l~~~l~s-  186 (384)
T 2qby_B          125 KIKNGTRNIR-AIIYLDEVDTLVKRR-----G-G----DIVLYQLLRSD------ANISVIMISNDINVRDYMEPRVLS-  186 (384)
T ss_dssp             HHHHHHSSSC-EEEEEETTHHHHHST-----T-S----HHHHHHHHTSS------SCEEEEEECSSTTTTTTSCHHHHH-
T ss_pred             HHHHHhccCC-CEEEEECHHHhccCC-----C-C----ceeHHHHhcCC------cceEEEEEECCCchHhhhCHHHHh-
Confidence            3444444444 499999999986432     0 1    23 44443332      688999999987   789999998 


Q ss_pred             CCcceEEecCCCCHHHHHHHHHhhcC--------CCCCHHHHHhCCCC--CCHHHHHHHHHHHHHHHHHhCCCccCHHHH
Q 030960           80 GRLDRKIEFPLPDRRQKRLVFQMNLS--------DEVDLEDYVSRPDK--ISAAEIAAICQEAGMHAVRKNRYVILPKDF  149 (168)
Q Consensus        80 grf~~~i~~~~P~~~~R~~il~~~l~--------~~~~~~~la~~t~g--~s~~di~~l~~~a~~~a~~~~~~~i~~~d~  149 (168)
                       ||...+.+++|+.+++.++++..+.        ++..+..++..+.+  -.++.+.++++.|...+.  +...|+.+++
T Consensus       187 -r~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~i~~~~~~~~G~~r~a~~~l~~a~~~a~--~~~~i~~~~v  263 (384)
T 2qby_B          187 -SLGPSVIFKPYDAEQLKFILSKYAEYGLIKGTYDDEILSYIAAISAKEHGDARKAVNLLFRAAQLAS--GGGIIRKEHV  263 (384)
T ss_dssp             -TCCCEEEECCCCHHHHHHHHHHHHHHTSCTTSCCSHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHTT--SSSCCCHHHH
T ss_pred             -cCCCeEEECCCCHHHHHHHHHHHHHhhcccCCcCHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHhc--CCCccCHHHH
Confidence             9988999999999999999986543        12234556666652  245667778888877665  5567999999


Q ss_pred             HHHHHhhc
Q 030960          150 EKGYRTNV  157 (168)
Q Consensus       150 ~~al~~~~  157 (168)
                      ..++....
T Consensus       264 ~~~~~~~~  271 (384)
T 2qby_B          264 DKAIVDYE  271 (384)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHh
Confidence            99988754

>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=98.88  E-value=5.9e-09  Score=82.82  Aligned_cols=131  Identities=15%  Similarity=0.172  Sum_probs=100.2

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCC--CCCeEEEEecCCC---CCCCccccCCCCcce-E
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQ--TVNVKVIMATNRA---DTLDPALLRPGRLDR-K   85 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~--~~~v~vi~ttn~~---~~ld~al~r~grf~~-~   85 (168)
                      ..|.||+|||+|.+-              ...+..++..++.+..  ..++.+|++||.+   +.+++.+.+  ||.. .
T Consensus       124 ~~~~vlilDE~~~l~--------------~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~~~~~l~~~~~~--r~~~~~  187 (389)
T 1fnn_A          124 DLYMFLVLDDAFNLA--------------PDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRG--IMGKYV  187 (389)
T ss_dssp             TCCEEEEEETGGGSC--------------HHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSCHHHHH--HHTTCE
T ss_pred             CCeEEEEEECccccc--------------hHHHHHHHHHHHhCCCCCcCCEEEEEEECCchHHHHhCHHhhh--cCCCce
Confidence            459999999999881              1455566666654332  2478899999988   778888888  8875 8


Q ss_pred             EecCCCCHHHHHHHHHhhcCC-----CC---CHHHHHhCCC--------CCCHHHHHHHHHHHHHHHHHhCCCccCHHHH
Q 030960           86 IEFPLPDRRQKRLVFQMNLSD-----EV---DLEDYVSRPD--------KISAAEIAAICQEAGMHAVRKNRYVILPKDF  149 (168)
Q Consensus        86 i~~~~P~~~~R~~il~~~l~~-----~~---~~~~la~~t~--------g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~  149 (168)
                      +.+++++.++..++++..+..     .+   .+..++..+.        +-.++.+.++++.|...+..++...++.+++
T Consensus       188 i~~~pl~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~l~~a~~~a~~~~~~~i~~~~v  267 (389)
T 1fnn_A          188 IRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPEDV  267 (389)
T ss_dssp             EECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHHHHHHHTTCSSCCHHHH
T ss_pred             EEeCCCCHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHHHHHHHHHHhCCCCcCHHHH
Confidence            999999999999999855431     22   3456777773        2267889999999999888888888999999


Q ss_pred             HHHHHhhcC
Q 030960          150 EKGYRTNVK  158 (168)
Q Consensus       150 ~~al~~~~p  158 (168)
                      ..++.....
T Consensus       268 ~~~~~~~~~  276 (389)
T 1fnn_A          268 RKSSKEVLF  276 (389)
T ss_dssp             HHHHHHHSC
T ss_pred             HHHHHHHhh
Confidence            999987654

>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=98.88  E-value=5.9e-09  Score=83.00  Aligned_cols=149  Identities=16%  Similarity=0.195  Sum_probs=97.5

Q ss_pred             HHHHHHH----HHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC-------------------CCCC
Q 030960            3 RDVFRLA----KENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD-------------------QTVN   59 (168)
Q Consensus         3 ~~iF~~a----~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-------------------~~~~   59 (168)
                      +.+|..+    ....|+||||||+|.+...+.+...+.......+.+.|+..|++..                   ...+
T Consensus       102 ~~~~~~~~~~~~~~~~~vl~lDEid~l~~~~~~~~~~~~~~~~~~~~~Ll~~leg~~~~~~~~~~~~~~~~~~~~i~tsn  181 (363)
T 3hws_A          102 QKLLQKCDYDVQKAQRGIVYIDQIDKISRKSDNPSITRDVSGEGVQQALLKLIEGTVAAVPPQGGRKHPQQEFLQVDTSK  181 (363)
T ss_dssp             HHHHHHTTTCHHHHHHCEEEEECHHHHCCCSSCC---CHHHHHHHHHHHHHHHHCC----------------CCCCCTTS
T ss_pred             HHHHHHhhhhHHhcCCcEEEEeChhhhcccccccccccccchHHHHHHHHHHhcCceeeccCccccccCCCceEEEECCC
Confidence            4555554    4456899999999999987755544444444568888888888421                   2234


Q ss_pred             eEEEEecCCC----------CC-----------------------------------CCccccCCCCcceEEecCCCCHH
Q 030960           60 VKVIMATNRA----------DT-----------------------------------LDPALLRPGRLDRKIEFPLPDRR   94 (168)
Q Consensus        60 v~vi~ttn~~----------~~-----------------------------------ld~al~r~grf~~~i~~~~P~~~   94 (168)
                      +++|+++|..          ..                                   +.|++..  ||+..+.+.+|+.+
T Consensus       182 ~~~i~~g~~~~l~~~i~~~~~~~~~~gf~~~~~~~~~~~~~~~l~~~v~~~~l~~~~~~~~l~~--R~~~~~~~~pl~~~  259 (363)
T 3hws_A          182 ILFICGGAFAGLDKVISHRVETGSGIGFGATVKAKSDKASEGELLAQVEPEDLIKFGLIPEFIG--RLPVVATLNELSEE  259 (363)
T ss_dssp             SEEEEEECCTTHHHHHHHHHCCCC------------CCSCHHHHHHTCCHHHHHHHTCCHHHHT--TCCEEEECCCCCHH
T ss_pred             ceEEecCCcHHHHHHHHHhhhccccCCccccccccccchhhHHHHHhCCHHHHHHcCCCHHHhc--ccCeeeecCCCCHH
Confidence            4555555532          11                                   6788887  99999999999999


Q ss_pred             HHHHHHHhhcC-------------------CCCCHHHHHh--CCCCCCHHHHHHHHHHHHHHHHHhCC-------CccCH
Q 030960           95 QKRLVFQMNLS-------------------DEVDLEDYVS--RPDKISAAEIAAICQEAGMHAVRKNR-------YVILP  146 (168)
Q Consensus        95 ~R~~il~~~l~-------------------~~~~~~~la~--~t~g~s~~di~~l~~~a~~~a~~~~~-------~~i~~  146 (168)
                      ++.+|++..+.                   .+..++.+++  ....+..++|.++++.+...++.+..       ..|+.
T Consensus       260 ~~~~I~~~~~~~l~~~~~~~~~~~~~~l~~~~~a~~~L~~~~~~~~~gaR~L~~~ie~~~~~~l~~~~~~~~~~~~~I~~  339 (363)
T 3hws_A          260 ALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVEAALLDTMYDLPSMEDVEKVVIDE  339 (363)
T ss_dssp             HHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHTTCTTTTHHHHHHHHHHHHHHSTTTCCCSEEEECHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCceEEECHHHHHHHHHhhcCCccCchHHHHHHHHHHHHHHHhcccccCCceeEEcH
Confidence            99999985211                   1112445654  34556778999999998888776642       14666


Q ss_pred             HHHHHHH
Q 030960          147 KDFEKGY  153 (168)
Q Consensus       147 ~d~~~al  153 (168)
                      +++.+.+
T Consensus       340 ~~v~~~~  346 (363)
T 3hws_A          340 SVIDGQS  346 (363)
T ss_dssp             HHTTCCS
T ss_pred             HHHhCcC
Confidence            6665544

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=98.74  E-value=1.2e-08  Score=83.64  Aligned_cols=136  Identities=17%  Similarity=0.183  Sum_probs=94.1

Q ss_pred             HHHHHHHHHH----cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEec--CCCCCCCcc
Q 030960            2 VRDVFRLAKE----NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMAT--NRADTLDPA   75 (168)
Q Consensus         2 l~~iF~~a~~----~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~tt--n~~~~ld~a   75 (168)
                      ++.+|..+..    ..+.||||||+|.+...              ....|+..++.    ..+.+|++|  |....++++
T Consensus        91 ir~~~~~a~~~~~~~~~~iLfIDEI~~l~~~--------------~q~~LL~~le~----~~v~lI~att~n~~~~l~~a  152 (447)
T 3pvs_A           91 IREAIERARQNRNAGRRTILFVDEVHRFNKS--------------QQDAFLPHIED----GTITFIGATTENPSFELNSA  152 (447)
T ss_dssp             HHHHHHHHHHHHHTTCCEEEEEETTTCC--------------------CCHHHHHT----TSCEEEEEESSCGGGSSCHH
T ss_pred             HHHHHHHHHHhhhcCCCcEEEEeChhhhCHH--------------HHHHHHHHHhc----CceEEEecCCCCcccccCHH
Confidence            4566666653    35899999999988422              12235555552    356666655  334589999


Q ss_pred             ccCCCCcceEEecCCCCHHHHHHHHHhhcCC-------------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHh--C
Q 030960           76 LLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD-------------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRK--N  140 (168)
Q Consensus        76 l~r~grf~~~i~~~~P~~~~R~~il~~~l~~-------------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~--~  140 (168)
                      +++  |+. .+.+++|+.+++..+++..+..             +..++.++..+.| ..+++.++++.++..+...  +
T Consensus       153 L~s--R~~-v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~al~~L~~~~~G-d~R~lln~Le~a~~~a~~~~~~  228 (447)
T 3pvs_A          153 LLS--RAR-VYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNG-DARRALNTLEMMADMAEVDDSG  228 (447)
T ss_dssp             HHT--TEE-EEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEECCHHHHHHHHHHHCS-CHHHHHHHHHHHHHHSCBCTTS
T ss_pred             HhC--cee-EEeeCCcCHHHHHHHHHHHHHHHhhhhccccCcCCHHHHHHHHHHCCC-CHHHHHHHHHHHHHhcccccCC
Confidence            999  886 7789999999999999866542             1125567777554 7788888888887766423  4


Q ss_pred             CCccCHHHHHHHHHhhcCC
Q 030960          141 RYVILPKDFEKGYRTNVKK  159 (168)
Q Consensus       141 ~~~i~~~d~~~al~~~~p~  159 (168)
                      ...|+.+++.+++......
T Consensus       229 ~~~It~e~v~~~l~~~~~~  247 (447)
T 3pvs_A          229 KRVLKPELLTEIAGERSAR  247 (447)
T ss_dssp             CEECCHHHHHHHHTCCCCC
T ss_pred             CCccCHHHHHHHHhhhhhc
Confidence            4679999999999876543

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=98.71  E-value=2.3e-08  Score=77.39  Aligned_cols=115  Identities=19%  Similarity=0.271  Sum_probs=81.5

Q ss_pred             HHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC---------CCCCeEEEEecCC----------
Q 030960            8 LAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD---------QTVNVKVIMATNR----------   68 (168)
Q Consensus         8 ~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~---------~~~~v~vi~ttn~----------   68 (168)
                      ......++||+|||+|.+..              .+.+.++..++.-.         ...++++|+|||.          
T Consensus       114 ~~~~~~~~vl~lDEi~~l~~--------------~~~~~Ll~~le~~~~~~~~~~~~~~~~~iiI~ttn~~~~~i~~~~~  179 (311)
T 4fcw_A          114 AVRRRPYSVILFDAIEKAHP--------------DVFNILLQMLDDGRLTDSHGRTVDFRNTVIIMTSNLGSPLILEGLQ  179 (311)
T ss_dssp             HHHHCSSEEEEEETGGGSCH--------------HHHHHHHHHHHHSEEECTTSCEEECTTEEEEEEESTTHHHHHTTTT
T ss_pred             HHHhCCCeEEEEeChhhcCH--------------HHHHHHHHHHhcCEEEcCCCCEEECCCcEEEEecccCHHHHHhhhc
Confidence            33444569999999998731              34445555554211         1136789999998          


Q ss_pred             ----------------CCCCCccccCCCCcceEEecCCCCHHHHHHHHHhhcCC---------------CCCHHHHHhCC
Q 030960           69 ----------------ADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD---------------EVDLEDYVSRP  117 (168)
Q Consensus        69 ----------------~~~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~~---------------~~~~~~la~~t  117 (168)
                                      ...++++++.  ||+..+.+++|+.+++..|++.++..               +..+..+++..
T Consensus       180 ~~~~~~~l~~~~~~~~~~~~~~~l~~--R~~~~~~~~p~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~  257 (311)
T 4fcw_A          180 KGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRPLTKEQIRQIVEIQMSYLRARLAEKRISLELTEAAKDFLAERG  257 (311)
T ss_dssp             SCCCSSTHHHHTHHHHHHHSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHTHHHHHHHHTTTCEEEECHHHHHHHHHHS
T ss_pred             ccccHHHHHHHHHHHHHHhCCHHHHh--cCCeEEEeCCCCHHHHHHHHHHHHHHHHHHHHhCCcEEEeCHHHHHHHHHhC
Confidence                            5578889998  99999999999999999999876642               11344566544


Q ss_pred             C--CCCHHHHHHHHHHHHHHHHH
Q 030960          118 D--KISAAEIAAICQEAGMHAVR  138 (168)
Q Consensus       118 ~--g~s~~di~~l~~~a~~~a~~  138 (168)
                      -  ....++|.++++.+...+..
T Consensus       258 ~~~~gn~R~L~~~i~~~~~~~~~  280 (311)
T 4fcw_A          258 YDPVFGARPLRRVIQRELETPLA  280 (311)
T ss_dssp             CBTTTBTTTHHHHHHHHTHHHHH
T ss_pred             CCccCCchhHHHHHHHHHHHHHH
Confidence            3  57789999999988766554

>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=98.70  E-value=1e-08  Score=80.24  Aligned_cols=128  Identities=11%  Similarity=0.170  Sum_probs=87.4

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC---CCCccccCCCCcc--eEEe
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD---TLDPALLRPGRLD--RKIE   87 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~---~ld~al~r~grf~--~~i~   87 (168)
                      .|.+|+|||+|.+..++         .....+..+++.+   ...+..+|+++++.+.   .+++++.+  ||+  ..+.
T Consensus        98 ~~~vL~iDEi~~l~~~~---------~~~~~l~~~l~~~---~~~~~~iii~~~~~~~~l~~l~~~L~s--R~~~~~~i~  163 (324)
T 1l8q_A           98 SVDLLLLDDVQFLSGKE---------RTQIEFFHIFNTL---YLLEKQIILASDRHPQKLDGVSDRLVS--RFEGGILVE  163 (324)
T ss_dssp             TCSEEEEECGGGGTTCH---------HHHHHHHHHHHHH---HHTTCEEEEEESSCGGGCTTSCHHHHH--HHHTSEEEE
T ss_pred             CCCEEEEcCcccccCCh---------HHHHHHHHHHHHH---HHCCCeEEEEecCChHHHHHhhhHhhh--cccCceEEE
Confidence            48999999999986432         1112222222222   2334567777777776   68999999  987  7899


Q ss_pred             cCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHH---HHH-hCCCcc-CHHHHHHHHHhh
Q 030960           88 FPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMH---AVR-KNRYVI-LPKDFEKGYRTN  156 (168)
Q Consensus        88 ~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~---a~~-~~~~~i-~~~d~~~al~~~  156 (168)
                      +++ +.++|.++++..+.      ++..++.++..+  -..+++.++++.+...   +++ .....+ +.+++.+++...
T Consensus       164 l~~-~~~e~~~il~~~~~~~~~~l~~~~l~~l~~~~--g~~r~l~~~l~~~~~~~~~~l~~~~~~~i~t~~~i~~~~~~~  240 (324)
T 1l8q_A          164 IEL-DNKTRFKIIKEKLKEFNLELRKEVIDYLLENT--KNVREIEGKIKLIKLKGFEGLERKERKERDKLMQIVEFVANY  240 (324)
T ss_dssp             CCC-CHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHC--SSHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             eCC-CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhC--CCHHHHHHHHHHHHHcCHHHhccccccCCCCHHHHHHHHHHH
Confidence            999 99999999986653      122356788888  4778899988887655   111 223458 889999888764


Q ss_pred             c
Q 030960          157 V  157 (168)
Q Consensus       157 ~  157 (168)
                      .
T Consensus       241 ~  241 (324)
T 1l8q_A          241 Y  241 (324)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=98.69  E-value=6.6e-08  Score=79.34  Aligned_cols=124  Identities=15%  Similarity=0.162  Sum_probs=95.5

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEe---------cC---CCCCCCccccCCCC
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMA---------TN---RADTLDPALLRPGR   81 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~t---------tn---~~~~ld~al~r~gr   81 (168)
                      |.|++|||+|.+-              ....+.|+..++..  ..++++++|         |+   .+..+++.+++  |
T Consensus       296 ~~VliIDEa~~l~--------------~~a~~aLlk~lEe~--~~~~~il~tn~~~~~i~~~~~~~~~~~l~~~i~s--R  357 (456)
T 2c9o_A          296 PGVLFVDEVHMLD--------------IECFTYLHRALESS--IAPIVIFASNRGNCVIRGTEDITSPHGIPLDLLD--R  357 (456)
T ss_dssp             ECEEEEESGGGCB--------------HHHHHHHHHHTTST--TCCEEEEEECCSEEECBTTSSCEEETTCCHHHHT--T
T ss_pred             ceEEEEechhhcC--------------HHHHHHHHHHhhcc--CCCEEEEecCCccccccccccccccccCChhHHh--h
Confidence            4699999999883              15677788888743  334655565         33   28899999999  9


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC------CCCCHHHHHhCC-CCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS------DEVDLEDYVSRP-DKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~------~~~~~~~la~~t-~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      |.. +.+++|+.++..++++....      ++..+..++..+ .| +++..-.+++.|...|..++...|+.+|+.+++.
T Consensus       358 ~~~-~~~~~~~~~e~~~iL~~~~~~~~~~~~~~~~~~i~~~a~~g-~~r~a~~ll~~a~~~A~~~~~~~v~~~~v~~~~~  435 (456)
T 2c9o_A          358 VMI-IRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKT-TLRYSVQLLTPANLLAKINGKDSIEKEHVEEISE  435 (456)
T ss_dssp             EEE-EECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHHHS-CHHHHHHTHHHHHHHHHHTTCSSBCHHHHHHHHH
T ss_pred             cce-eeCCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHccCC-CHHHHHHHHHHHHHHHhhcCCCccCHHHHHHHHH
Confidence            988 59999999999999985432      122345566666 44 8999999999998899888888999999999987


Q ss_pred             hhc
Q 030960          155 TNV  157 (168)
Q Consensus       155 ~~~  157 (168)
                      -+.
T Consensus       436 ~~~  438 (456)
T 2c9o_A          436 LFY  438 (456)
T ss_dssp             HSC
T ss_pred             Hhc
Confidence            653

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.68  E-value=1.3e-08  Score=72.61  Aligned_cols=87  Identities=21%  Similarity=0.275  Sum_probs=58.2

Q ss_pred             HHHHHHHHH-HcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC-----CCCcc
Q 030960            2 VRDVFRLAK-ENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD-----TLDPA   75 (168)
Q Consensus         2 l~~iF~~a~-~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~-----~ld~a   75 (168)
                      ++.+|..+. ...|+||+|||+|.+...+.......   ....+..++   +    ..++.+|++||.+.     .++++
T Consensus       103 ~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~~~~~~---~~~~l~~~~---~----~~~~~~i~~~~~~~~~~~~~~~~~  172 (195)
T 1jbk_A          103 LKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMD---AGNMLKPAL---A----RGELHCVGATTLDEYRQYIEKDAA  172 (195)
T ss_dssp             HHHHHHHHHHSTTTEEEEEETGGGGTT------CCC---CHHHHHHHH---H----TTSCCEEEEECHHHHHHHTTTCHH
T ss_pred             HHHHHHHHhhcCCCeEEEEeCHHHHhccCcccchHH---HHHHHHHhh---c----cCCeEEEEeCCHHHHHHHHhcCHH
Confidence            345566443 45589999999999976542211111   113333332   2    34677899998886     78999


Q ss_pred             ccCCCCcceEEecCCCCHHHHHHHHH
Q 030960           76 LLRPGRLDRKIEFPLPDRRQKRLVFQ  101 (168)
Q Consensus        76 l~r~grf~~~i~~~~P~~~~R~~il~  101 (168)
                      +.+  ||+ .+++++|+.++|.+|++
T Consensus       173 l~~--r~~-~i~~~~p~~~~~~~il~  195 (195)
T 1jbk_A          173 LER--RFQ-KVFVAEPSVEDTIAILR  195 (195)
T ss_dssp             HHT--TEE-EEECCCCCHHHHHTTCC
T ss_pred             HHH--Hhc-eeecCCCCHHHHHHHhC
Confidence            999  999 69999999999998763

>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=98.68  E-value=2.1e-08  Score=78.32  Aligned_cols=117  Identities=16%  Similarity=0.140  Sum_probs=71.5

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      .+.||+|||+|.+.+          .   ...+.|+..++.  ...++.+|++||.+..+++++++  ||. .+.|++|+
T Consensus       105 ~~~vliiDEi~~l~~----------~---~~~~~L~~~le~--~~~~~~iI~~~n~~~~l~~~l~s--R~~-~i~~~~~~  166 (324)
T 3u61_B          105 RQKVIVIDEFDRSGL----------A---ESQRHLRSFMEA--YSSNCSIIITANNIDGIIKPLQS--RCR-VITFGQPT  166 (324)
T ss_dssp             CEEEEEEESCCCGGG----------H---HHHHHHHHHHHH--HGGGCEEEEEESSGGGSCTTHHH--HSE-EEECCCCC
T ss_pred             CCeEEEEECCcccCc----------H---HHHHHHHHHHHh--CCCCcEEEEEeCCccccCHHHHh--hCc-EEEeCCCC
Confidence            579999999999841          1   223344444442  23467889999999999999999  995 79999999


Q ss_pred             HHHHHHHHHhhcC-------------CC-CCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960           93 RRQKRLVFQMNLS-------------DE-VDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus        93 ~~~R~~il~~~l~-------------~~-~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      .++|.++++..+.             ++ ..+..++..+.| ..+++.+.++.++      ....|+.+++.+++.
T Consensus       167 ~~e~~~il~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~g-d~R~a~~~L~~~~------~~~~i~~~~v~~~~~  235 (324)
T 3u61_B          167 DEDKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVKKNFP-DFRKTIGELDSYS------SKGVLDAGILSLVTN  235 (324)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCBSCHHHHHHHHHHTCS-CTTHHHHHHHHHG------GGTCBCC--------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHhCCC-CHHHHHHHHHHHh------ccCCCCHHHHHHHhC
Confidence            9998877653322             12 235567777655 3333444444443      223467776665543

>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=98.66  E-value=2e-07  Score=73.67  Aligned_cols=129  Identities=17%  Similarity=0.203  Sum_probs=92.8

Q ss_pred             HHHHHHHHHH----cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcccc
Q 030960            2 VRDVFRLAKE----NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~----~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~   77 (168)
                      ++.+++.+..    ..+.||+|||+|.+..              ...+.++..++.  ...++++|++|+.+..+++.+.
T Consensus       104 ~~~l~~~~~~~~~~~~~~vliiDe~~~l~~--------------~~~~~Ll~~le~--~~~~~~~Il~~~~~~~l~~~l~  167 (373)
T 1jr3_A          104 TRDLLDNVQYAPARGRFKVYLIDEVHMLSR--------------HSFNALLKTLEE--PPEHVKFLLATTDPQKLPVTIL  167 (373)
T ss_dssp             HHHHHHHTTSCCSSSSSEEEEEECGGGSCH--------------HHHHHHHHHHHS--CCSSEEEEEEESCGGGSCHHHH
T ss_pred             HHHHHHHHhhccccCCeEEEEEECcchhcH--------------HHHHHHHHHHhc--CCCceEEEEEeCChHhCcHHHH
Confidence            3555665542    2378999999998731              234556666663  3457888888999999999999


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhcCC---CC---CHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHH
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNLSD---EV---DLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK  151 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l~~---~~---~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~  151 (168)
                      +  |+ ..+.+++|+.++..++++..+..   .+   .+..++..+.| +++++.++++.+...+    ...|+.+++.+
T Consensus       168 s--r~-~~i~~~~l~~~~~~~~l~~~~~~~~~~~~~~a~~~l~~~~~G-~~r~~~~~l~~~~~~~----~~~i~~~~v~~  239 (373)
T 1jr3_A          168 S--RC-LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEG-SLRDALSLTDQAIASG----DGQVSTQAVSA  239 (373)
T ss_dssp             T--TS-EEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHSSS-CHHHHHHHHHHHHHHT----TTCBCHHHHHH
T ss_pred             h--he-eEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHCCC-CHHHHHHHHHHHHHhc----CCcccHHHHHH
Confidence            8  76 78999999999999999865531   22   25668888877 7888888888775432    34578777766


Q ss_pred             HHH
Q 030960          152 GYR  154 (168)
Q Consensus       152 al~  154 (168)
                      ++.
T Consensus       240 ~~~  242 (373)
T 1jr3_A          240 MLG  242 (373)
T ss_dssp             HTT
T ss_pred             HhC
Confidence            543

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=98.66  E-value=9.4e-08  Score=80.99  Aligned_cols=127  Identities=20%  Similarity=0.166  Sum_probs=91.3

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC-----------CCCCCeEEEEecCCCC------------
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF-----------DQTVNVKVIMATNRAD------------   70 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~-----------~~~~~v~vi~ttn~~~------------   70 (168)
                      .+|+||||+|.+-.              ...+.++..|+.-           ....++.||||||.+.            
T Consensus       392 ~gil~IDEid~l~~--------------~~q~~Ll~~le~~~i~i~~~g~~~~~~~~~~vIaatNp~~G~~~~~~~~~~n  457 (595)
T 3f9v_A          392 GGIAVIDEIDKMRD--------------EDRVAIHEAMEQQTVSIAKAGIVAKLNARAAVIAAGNPKFGRYISERPVSDN  457 (595)
T ss_dssp             SSEECCTTTTCCCS--------------HHHHHHHHHHHSSSEEEESSSSEEEECCCCEEEEEECCTTCCSCTTSCSCTT
T ss_pred             CCcEEeehhhhCCH--------------hHhhhhHHHHhCCEEEEecCCcEEEecCceEEEEEcCCcCCccCcccCchhc
Confidence            58999999998732              2234455555421           1124688999999887            


Q ss_pred             -CCCccccCCCCcce-EEecCCCCHHHHHHHHHhhcCC-------------------------------CCCHHHHHhC-
Q 030960           71 -TLDPALLRPGRLDR-KIEFPLPDRRQKRLVFQMNLSD-------------------------------EVDLEDYVSR-  116 (168)
Q Consensus        71 -~ld~al~r~grf~~-~i~~~~P~~~~R~~il~~~l~~-------------------------------~~~~~~la~~-  116 (168)
                       .+++++++  |||. .+..+.|+.+ ...|.++.+..                               +...+.+... 
T Consensus       458 i~l~~aLl~--RFDl~~~~~~~~~~e-~~~i~~~il~~~~~~~~~~~l~~~~l~~~i~~ar~~~~p~ls~ea~~~l~~~y  534 (595)
T 3f9v_A          458 INLPPTILS--RFDLIFILKDQPGEQ-DRELANYILDVHSGKSTKNIIDIDTLRKYIAYARKYVTPKITSEAKNLITDFF  534 (595)
T ss_dssp             TCSCSSSGG--GCSCCEEECCTTHHH-HHHHHHHHHTTTCCCSSSSTTCCTTTHHHHHHHHHHHCCCCCCCTHHHHHHHH
T ss_pred             cCCCHHHHh--hCeEEEEeCCCCCHH-HHHHHHHHHHHhhccccccCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Confidence             89999999  9985 5566788887 77777644331                               0111222222 


Q ss_pred             -------------CCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhc
Q 030960          117 -------------PDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNV  157 (168)
Q Consensus       117 -------------t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~  157 (168)
                                   +.+.|++.+.++++.|...|..++...++.+|+.+|+.-..
T Consensus       535 ~~lR~~~~~~~~~~~~~s~R~l~~lirla~a~A~l~~~~~V~~~dv~~Ai~l~~  588 (595)
T 3f9v_A          535 VEMRKKSSETPDSPILITPRQLEALIRISEAYAKMALKAEVTREDAERAINIMR  588 (595)
T ss_dssp             TTSSCSCCBCSSSCBCSSTTTTTHHHHHHHHHHHTTSSCCSSHHHHHHHHHHHH
T ss_pred             HHHHHhhccCCCccccccHHHHHHHHHHHHHHHHHhCcCCCCHHHHHHHHHHHH
Confidence                         35789999999999999999989999999999999997654

>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=98.65  E-value=3.5e-07  Score=72.02  Aligned_cols=96  Identities=13%  Similarity=0.061  Sum_probs=80.6

Q ss_pred             CeEEEEecCCCCCCCccccCCCCcceEEecCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHH
Q 030960           59 NVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEA  132 (168)
Q Consensus        59 ~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a  132 (168)
                      .+.++++|+.+..+++.+++  ||...+.+++|+.+++.++++....      ++..+..++..+.| +++++.++++.+
T Consensus       150 ~~~li~at~~~~~Ls~~l~s--R~~l~~~Ld~~~~~~l~~iL~~~~~~~~~~~~~~~~~~ia~~~~G-~~R~a~~ll~~~  226 (334)
T 1in4_A          150 PFTLVGATTRSGLLSSPLRS--RFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRG-TPRIAIRLTKRV  226 (334)
T ss_dssp             CCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTT-CHHHHHHHHHHH
T ss_pred             CeEEEEecCCcccCCHHHHH--hcCceeeCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhcCC-ChHHHHHHHHHH
Confidence            46778899999999999999  9999999999999999999985432      12235678888877 678999999999


Q ss_pred             HHHHHHhCCCccCHHHHHHHHHhhc
Q 030960          133 GMHAVRKNRYVILPKDFEKGYRTNV  157 (168)
Q Consensus       133 ~~~a~~~~~~~i~~~d~~~al~~~~  157 (168)
                      ...|...+...|+.+++.+++....
T Consensus       227 ~~~a~~~~~~~It~~~v~~al~~~~  251 (334)
T 1in4_A          227 RDMLTVVKADRINTDIVLKTMEVLN  251 (334)
T ss_dssp             HHHHHHHTCSSBCHHHHHHHHHHHT
T ss_pred             HHHHHHcCCCCcCHHHHHHHHHHhC
Confidence            8888877778899999999998754

>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=98.63  E-value=7.2e-08  Score=84.74  Aligned_cols=125  Identities=16%  Similarity=0.174  Sum_probs=78.0

Q ss_pred             HHHHHHHHHHc-CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC----CCCccc
Q 030960            2 VRDVFRLAKEN-APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD----TLDPAL   76 (168)
Q Consensus         2 l~~iF~~a~~~-~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~----~ld~al   76 (168)
                      ++.+|..++.. .|+||||||+|.+.+.+.....   .   ...+.+...++    ..++.+|++||.++    .+|+++
T Consensus       251 l~~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~g~---~---~~~~~L~~~l~----~~~i~~I~at~~~~~~~~~~d~aL  320 (854)
T 1qvr_A          251 LKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGA---V---DAGNMLKPALA----RGELRLIGATTLDEYREIEKDPAL  320 (854)
T ss_dssp             HHHHHHHHHTTCSSEEEEECCC-------------------------HHHHH----TTCCCEEEEECHHHHHHHTTCTTT
T ss_pred             HHHHHHHHHhcCCCeEEEEecHHHHhccCCccch---H---HHHHHHHHHHh----CCCeEEEEecCchHHhhhccCHHH
Confidence            56788888765 6999999999999865532211   1   22222333332    34677899998775    489999


Q ss_pred             cCCCCcceEEecCCCCHHHHHHHHHhhcC----------CCCCHHHHHh-----CCCCCCHHHHHHHHHHHHHHHHHh
Q 030960           77 LRPGRLDRKIEFPLPDRRQKRLVFQMNLS----------DEVDLEDYVS-----RPDKISAAEIAAICQEAGMHAVRK  139 (168)
Q Consensus        77 ~r~grf~~~i~~~~P~~~~R~~il~~~l~----------~~~~~~~la~-----~t~g~s~~di~~l~~~a~~~a~~~  139 (168)
                      .+  ||+. +.+++|+.+++.+|++..+.          .+..+..++.     .+++|.+.....++.+|+..+...
T Consensus       321 ~r--Rf~~-i~l~~p~~~e~~~iL~~~~~~~~~~~~~~i~~~al~~~~~ls~r~i~~~~lp~kai~lldea~a~~~~~  395 (854)
T 1qvr_A          321 ER--RFQP-VYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSHRYITERRLPDKAIDLIDEAAARLRMA  395 (854)
T ss_dssp             CS--CCCC-EEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHCCSSCTHHHHHHHHHHHHHHHHHT
T ss_pred             Hh--CCce-EEeCCCCHHHHHHHHHhhhhhhhhhcCCCCCHHHHHHHHHHHhhhcccccChHHHHHHHHHHHHHHHhh
Confidence            99  9996 99999999999999985443          1112333444     356788888889888887665543

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=98.61  E-value=4.4e-07  Score=78.75  Aligned_cols=111  Identities=23%  Similarity=0.271  Sum_probs=78.2

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC-----CCCccc
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD-----TLDPAL   76 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~-----~ld~al   76 (168)
                      ++.+|..+....|+|||||     + .    .        ...+.++..+    ....+.+|++||..+     .+|+++
T Consensus       256 l~~~~~~~~~~~~~iLfiD-----~-~----~--------~~~~~L~~~l----~~~~v~~I~at~~~~~~~~~~~d~al  313 (758)
T 3pxi_A          256 LKKVMDEIRQAGNIILFID-----A-A----I--------DASNILKPSL----ARGELQCIGATTLDEYRKYIEKDAAL  313 (758)
T ss_dssp             HHHHHHHHHTCCCCEEEEC-----C---------------------CCCT----TSSSCEEEEECCTTTTHHHHTTCSHH
T ss_pred             HHHHHHHHHhcCCEEEEEc-----C-c----h--------hHHHHHHHHH----hcCCEEEEeCCChHHHHHHhhccHHH
Confidence            5789999999999999999     1 0    0        1122233223    355799999999988     799999


Q ss_pred             cCCCCcceEEecCCCCHHHHHHHHHhhcCC-----CCC-----HHHHHh-----CCCCCCHHHHHHHHHHHHHHHH
Q 030960           77 LRPGRLDRKIEFPLPDRRQKRLVFQMNLSD-----EVD-----LEDYVS-----RPDKISAAEIAAICQEAGMHAV  137 (168)
Q Consensus        77 ~r~grf~~~i~~~~P~~~~R~~il~~~l~~-----~~~-----~~~la~-----~t~g~s~~di~~l~~~a~~~a~  137 (168)
                      .|  || ..+.|+.|+.+++.+||+.....     .+.     +..++.     .++++.+.+...++..|+..+.
T Consensus       314 ~r--Rf-~~i~v~~p~~~~~~~il~~~~~~~~~~~~~~i~~~al~~~~~~s~~~i~~~~~p~~ai~ll~~a~~~~~  386 (758)
T 3pxi_A          314 ER--RF-QPIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYISDRFLPDKAIDLIDEAGSKVR  386 (758)
T ss_dssp             HH--SE-EEEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHHHHHHHHHHHHHSSCCSCTTHHHHHHHHHHHHHHH
T ss_pred             Hh--hC-cEEEeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhcccccCcCCcHHHHHHHHHHHHHH
Confidence            99  99 56999999999999999965542     122     233333     2467788888888887765443

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=98.60  E-value=1.9e-07  Score=77.61  Aligned_cols=126  Identities=17%  Similarity=0.150  Sum_probs=85.6

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC-------C-CCCCCeEEEEecCCCCC---CCccccCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG-------F-DQTVNVKVIMATNRADT---LDPALLRPGR   81 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~-------~-~~~~~v~vi~ttn~~~~---ld~al~r~gr   81 (168)
                      .++||||||++.+-           .   .+.+.++..|+.       . ...+..++|++||.+..   ..+++++  |
T Consensus       109 ~~~IL~IDEI~r~~-----------~---~~q~~LL~~lee~~v~i~G~~~~~~~~~iI~ATN~lpe~~~~~~aLld--R  172 (500)
T 3nbx_X          109 EAEIVFLDEIWKAG-----------P---AILNTLLTAINERQFRNGAHVEKIPMRLLVAASNELPEADSSLEALYD--R  172 (500)
T ss_dssp             GCSEEEEESGGGCC-----------H---HHHHHHHHHHHSSEEECSSSEEECCCCEEEEEESSCCCTTCTTHHHHT--T
T ss_pred             cceeeeHHhHhhhc-----------H---HHHHHHHHHHHHHhccCCCCcCCcchhhhhhccccCCCccccHHHHHH--H
Confidence            47899999997542           1   344556665542       1 11122356777775322   3348999  9


Q ss_pred             cceEEecCCCCH-HHHHHHHHhhcCC------------------------CC-----CHHHHHhC---------CCCCCH
Q 030960           82 LDRKIEFPLPDR-RQKRLVFQMNLSD------------------------EV-----DLEDYVSR---------PDKISA  122 (168)
Q Consensus        82 f~~~i~~~~P~~-~~R~~il~~~l~~------------------------~~-----~~~~la~~---------t~g~s~  122 (168)
                      |...+.+++|+. ++|.+|++.....                        .+     .++.++..         ..|.|+
T Consensus       173 F~~~i~v~~p~~~ee~~~IL~~~~~~~~~~~~~~~~~~~e~l~~~~~~~~~v~v~d~v~e~i~~l~~~lr~~r~~~~iS~  252 (500)
T 3nbx_X          173 MLIRLWLDKVQDKANFRSMLTSQQDENDNPVPDALQVTDEEYERWQKEIGEITLPDHVFELIFMLRQQLDKLPDAPYVSD  252 (500)
T ss_dssp             CCEEEECCSCCCHHHHHHHHTCCCCTTSCCSCTTTSBCHHHHHHHHHHHTTCBCCHHHHHHHHHHHHHHHHCSSSCCCCH
T ss_pred             HHHHHHHHHhhhhhhHHHHHhcccccCCCCCCccceecHHHHHHHHhcCCcccCchHHHHHHHHHHHHhhcCCCCCccch
Confidence            999999999987 7889999854421                        01     12223222         358999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960          123 AEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus       123 ~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      +.+..+++.|...|...++..++.+|+. ++..
T Consensus       253 R~~~~llr~A~A~A~l~gr~~Vt~eDv~-~a~~  284 (500)
T 3nbx_X          253 RRWKKAIRLLQASAFFSGRSAVAPVDLI-LLKD  284 (500)
T ss_dssp             HHHHHHHHHHHHHHHHTTCSBCCGGGGG-GGGG
T ss_pred             hHHHHHHHHHHHHHhhcCCccccchHHH-HHHh
Confidence            9999999999999999999899999988 4443

>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=98.58  E-value=2.1e-07  Score=72.97  Aligned_cols=122  Identities=16%  Similarity=0.100  Sum_probs=86.9

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      .+.||+|||+|.+...              ..+.++..++..  ..++.+|++||++..+++++++  |+. .+.+++|+
T Consensus       133 ~~~vliiDE~~~l~~~--------------~~~~Ll~~le~~--~~~~~~il~~~~~~~l~~~l~s--R~~-~i~~~~~~  193 (353)
T 1sxj_D          133 PYKIIILDEADSMTAD--------------AQSALRRTMETY--SGVTRFCLICNYVTRIIDPLAS--QCS-KFRFKALD  193 (353)
T ss_dssp             SCEEEEETTGGGSCHH--------------HHHHHHHHHHHT--TTTEEEEEEESCGGGSCHHHHH--HSE-EEECCCCC
T ss_pred             CceEEEEECCCccCHH--------------HHHHHHHHHHhc--CCCceEEEEeCchhhCcchhhc--cCc-eEEeCCCC
Confidence            3579999999988421              223455555532  2356677788999999999999  886 89999999


Q ss_pred             HHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCC-ccCHHHHHHHHH
Q 030960           93 RRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRY-VILPKDFEKGYR  154 (168)
Q Consensus        93 ~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~-~i~~~d~~~al~  154 (168)
                      .++...+++..+..      +..+..++..+.| .++.+.++++.+...+-+.+.. .|+.+++.+++.
T Consensus       194 ~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~~~G-~~r~~~~~l~~~~~~~~~~~~~~~It~~~v~~~~~  261 (353)
T 1sxj_D          194 ASNAIDRLRFISEQENVKCDDGVLERILDISAG-DLRRGITLLQSASKGAQYLGDGKNITSTQVEELAG  261 (353)
T ss_dssp             HHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTSS-CHHHHHHHHHHTHHHHHHHCSCCCCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHHhcCCCccCccccHHHHHHHhC
Confidence            99999999865431      2235677888876 4677777777776655444322 699999888766

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=98.57  E-value=1.6e-07  Score=77.29  Aligned_cols=129  Identities=22%  Similarity=0.232  Sum_probs=84.6

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC-----CCCccc
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD-----TLDPAL   76 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~-----~ld~al   76 (168)
                      ++.+|..++...|+|||||     + ..            ...+.|+..+    ..+.+.+|++||.++     .+|+++
T Consensus       256 ~~~~~~~~~~~~~~iLfiD-----~-~~------------~a~~~L~~~L----~~g~v~vI~at~~~e~~~~~~~~~al  313 (468)
T 3pxg_A          256 LKKVMDEIRQAGNIILFID-----A-AI------------DASNILKPSL----ARGELQCIGATTLDEYRKYIEKDAAL  313 (468)
T ss_dssp             HHHHHHHHHTCCCCEEEEC-----C---------------------CCCT----TSSSCEEEEECCTTTTHHHHTTCSHH
T ss_pred             HHHHHHHHHhcCCeEEEEe-----C-ch------------hHHHHHHHhh----cCCCEEEEecCCHHHHHHHhhcCHHH
Confidence            5788999998899999999     1 00            1122233223    355799999999987     799999


Q ss_pred             cCCCCcceEEecCCCCHHHHHHHHHhhcCC-----CC-----CHHHHHhCC-----CCCCHHHHHHHHHHHHHHHHHhC-
Q 030960           77 LRPGRLDRKIEFPLPDRRQKRLVFQMNLSD-----EV-----DLEDYVSRP-----DKISAAEIAAICQEAGMHAVRKN-  140 (168)
Q Consensus        77 ~r~grf~~~i~~~~P~~~~R~~il~~~l~~-----~~-----~~~~la~~t-----~g~s~~di~~l~~~a~~~a~~~~-  140 (168)
                      .+  ||. .+.|++|+.+++.+|++.+...     .+     .+..++..+     ..+.+.....++..|...+..+. 
T Consensus       314 ~~--Rf~-~i~v~~p~~e~~~~iL~~~~~~~~~~~~~~i~~~al~~l~~~s~~~~~~~~lp~~ai~ll~~a~~~~~~~~~  390 (468)
T 3pxg_A          314 ER--RFQ-PIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYISDRFLPDKAIDLIDEAGSKVRLRSF  390 (468)
T ss_dssp             HH--SEE-EEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHHHHHHHHHHHHHSSCCSCTTHHHHHHHHHHHHHHHHHTT
T ss_pred             HH--hCc-cceeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhccCcCCcHHHHHHHHHHHHHHhccC
Confidence            99  998 4999999999999999966542     11     233444433     34556688888888765554433 


Q ss_pred             CCccCHHHHHHHHHh
Q 030960          141 RYVILPKDFEKGYRT  155 (168)
Q Consensus       141 ~~~i~~~d~~~al~~  155 (168)
                      ..+-.-.++++.++.
T Consensus       391 ~~p~~i~~l~~~i~~  405 (468)
T 3pxg_A          391 TTPPNLKELEQKLDE  405 (468)
T ss_dssp             SCCSSTHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHH
Confidence            223334444444443

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=98.54  E-value=1.5e-07  Score=81.66  Aligned_cols=117  Identities=12%  Similarity=0.198  Sum_probs=81.6

Q ss_pred             HHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC---------CCCCeEEEEecCCCCC-----
Q 030960            6 FRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD---------QTVNVKVIMATNRADT-----   71 (168)
Q Consensus         6 F~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~---------~~~~v~vi~ttn~~~~-----   71 (168)
                      +...+...++||||||+|.+-           .   .+.+.|+..++.-.         ...++++|+|||.+..     
T Consensus       572 ~~~~~~~~~~vl~lDEi~~~~-----------~---~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn~~~~~~~~~  637 (758)
T 3pxi_A          572 TEKVRRKPYSVVLLDAIEKAH-----------P---DVFNILLQVLEDGRLTDSKGRTVDFRNTILIMTSNVGASEKDKV  637 (758)
T ss_dssp             HHHHHHCSSSEEEEECGGGSC-----------H---HHHHHHHHHHHHSBCC-----CCBCTTCEEEEEESSSTTCCHHH
T ss_pred             hHHHHhCCCeEEEEeCccccC-----------H---HHHHHHHHHhccCeEEcCCCCEeccCCeEEEEeCCCChhhHHHH
Confidence            445566678999999999762           1   44555665555311         2346899999997665     


Q ss_pred             -------CCccccCCCCcceEEecCCCCHHHHHHHHHhhcCC---------------CCCHHHHHh--CCCCCCHHHHHH
Q 030960           72 -------LDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD---------------EVDLEDYVS--RPDKISAAEIAA  127 (168)
Q Consensus        72 -------ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~~---------------~~~~~~la~--~t~g~s~~di~~  127 (168)
                             ++|+++.  ||+..+.|++|+.+++..|++.++..               +..++.+++  ....+..++|.+
T Consensus       638 ~~~~~~~f~p~l~~--Rl~~~i~~~~l~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~R~L~~  715 (758)
T 3pxi_A          638 MGELKRAFRPEFIN--RIDEIIVFHSLEKKHLTEIVSLMSDQLTKRLKEQDLSIELTDAAKAKVAEEGVDLEYGARPLRR  715 (758)
T ss_dssp             HHHHHHHSCHHHHT--TSSEEEECC--CHHHHHHHHHHHHHHHHHHHHTTTCEEEECHHHHHHHHGGGCCTTTTTTTHHH
T ss_pred             HHHHHhhCCHHHHh--hCCeEEecCCCCHHHHHHHHHHHHHHHHHHHHhCCCeEEECHHHHHHHHHhCCCCCCCChHHHH
Confidence                   7888888  99999999999999999999865531               113445655  345677889999


Q ss_pred             HHHHHHHHHHH
Q 030960          128 ICQEAGMHAVR  138 (168)
Q Consensus       128 l~~~a~~~a~~  138 (168)
                      +++++...++.
T Consensus       716 ~i~~~v~~~l~  726 (758)
T 3pxi_A          716 AIQKHVEDRLS  726 (758)
T ss_dssp             HHHHHTHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99887665554

>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=98.51  E-value=4.3e-07  Score=70.08  Aligned_cols=118  Identities=16%  Similarity=0.118  Sum_probs=82.5

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCC
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLP   91 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P   91 (168)
                      ..+.||+|||+|.+..              ...+.++..++.  ...++.+|++||.+..+++++.+  |+. .+.+++|
T Consensus       101 ~~~~vliiDe~~~l~~--------------~~~~~L~~~le~--~~~~~~~i~~~~~~~~l~~~l~s--r~~-~i~~~~~  161 (319)
T 2chq_A          101 APFKIIFLDEADALTA--------------DAQAALRRTMEM--YSKSCRFILSCNYVSRIIEPIQS--RCA-VFRFKPV  161 (319)
T ss_dssp             CCCEEEEEETGGGSCH--------------HHHHTTGGGTSS--SSSSEEEEEEESCGGGSCHHHHT--TCE-EEECCCC
T ss_pred             CCceEEEEeCCCcCCH--------------HHHHHHHHHHHh--cCCCCeEEEEeCChhhcchHHHh--hCe-EEEecCC
Confidence            3489999999998842              223445555653  34578889999999999999999  886 8999999


Q ss_pred             CHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960           92 DRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus        92 ~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      +.+++..+++..+..      +..+..++..+.| ..+.+.++++.++..     ...++.+++.+.+.
T Consensus       162 ~~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~~~G-~~r~~~~~l~~~~~~-----~~~i~~~~v~~~~~  224 (319)
T 2chq_A          162 PKEAMKKRLLEICEKEGVKITEDGLEALIYISGG-DFRKAINALQGAAAI-----GEVVDADTIYQITA  224 (319)
T ss_dssp             CHHHHHHHHHHHHHTTCCCBCHHHHHHHHHTTTT-CHHHHHHHHHHHHHS-----SSCBCHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHHc-----CCCCCHHHHHHHHC
Confidence            999999999865542      2235567776655 555555666554431     23577777766544

>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=98.48  E-value=6.9e-07  Score=69.05  Aligned_cols=118  Identities=11%  Similarity=0.092  Sum_probs=81.5

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      .+.||+|||+|.+..              ...+.++..++.  ...++.+|++||.+..+++++.+  |+. .+.+++|+
T Consensus       107 ~~~viiiDe~~~l~~--------------~~~~~L~~~le~--~~~~~~~il~~~~~~~l~~~l~s--r~~-~i~~~~~~  167 (323)
T 1sxj_B          107 KHKIVILDEADSMTA--------------GAQQALRRTMEL--YSNSTRFAFACNQSNKIIEPLQS--QCA-ILRYSKLS  167 (323)
T ss_dssp             CCEEEEEESGGGSCH--------------HHHHTTHHHHHH--TTTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCC
T ss_pred             CceEEEEECcccCCH--------------HHHHHHHHHHhc--cCCCceEEEEeCChhhchhHHHh--hce-EEeecCCC
Confidence            389999999998842              122334444442  33467788888999999999998  776 89999999


Q ss_pred             HHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960           93 RRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus        93 ~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      .++..++++..+.      ++..+..+++.+.| .++.+.++++.+...   .  ..++.+++.+++..
T Consensus       168 ~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G-~~r~a~~~l~~~~~~---~--~~i~~~~v~~~~~~  230 (323)
T 1sxj_B          168 DEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEG-DMRQAINNLQSTVAG---H--GLVNADNVFKIVDS  230 (323)
T ss_dssp             HHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTT-CHHHHHHHHHHHHHH---H--SSBCHHHHHHHHTS
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHhc---C--CCcCHHHHHHHHCC
Confidence            9999999986543      12235567777755 555555655555422   1  35888888777653

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=98.47  E-value=3.6e-07  Score=73.08  Aligned_cols=135  Identities=14%  Similarity=0.138  Sum_probs=93.5

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC-CC--CCeEEEEecCCCC---CCC---ccccCCCCc
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD-QT--VNVKVIMATNRAD---TLD---PALLRPGRL   82 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-~~--~~v~vi~ttn~~~---~ld---~al~r~grf   82 (168)
                      ..|.||+|||+|.+...+.     .+.   ..+..++..+..+. ..  .++.+|++|+.++   .++   +.+.+  +|
T Consensus       137 ~~~~llvlDe~~~l~~~~~-----~~~---~~l~~l~~~~~~~~~~~~~~~v~lI~~~~~~~~~~~l~~~~~~~~~--~~  206 (412)
T 1w5s_A          137 NHYLLVILDEFQSMLSSPR-----IAA---EDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVES--QI  206 (412)
T ss_dssp             TCEEEEEEESTHHHHSCTT-----SCH---HHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHT--TC
T ss_pred             CCeEEEEEeCHHHHhhccC-----cch---HHHHHHHHHHHhcccCCCCceEEEEEEeccccHHHHHhhhcchhhh--hc
Confidence            4599999999999864310     111   34444444444332 12  5788888888765   344   55666  66


Q ss_pred             ceEEecCCCCHHHHHHHHHhhcC--------CCCCHHHHHhCCC------CCCHHHHHHHHHHHHHHHHHhCCCccCHHH
Q 030960           83 DRKIEFPLPDRRQKRLVFQMNLS--------DEVDLEDYVSRPD------KISAAEIAAICQEAGMHAVRKNRYVILPKD  148 (168)
Q Consensus        83 ~~~i~~~~P~~~~R~~il~~~l~--------~~~~~~~la~~t~------g~s~~di~~l~~~a~~~a~~~~~~~i~~~d  148 (168)
                      ...+.+++++.++..++++..+.        ++..+..++..+.      | .++.+..++..|...+..++...++.++
T Consensus       207 ~~~i~l~~l~~~e~~~ll~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~G-~p~~~~~l~~~a~~~a~~~~~~~i~~~~  285 (412)
T 1w5s_A          207 GFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDG-SARRAIVALKMACEMAEAMGRDSLSEDL  285 (412)
T ss_dssp             SEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGTSCC-CHHHHHHHHHHHHHHHHHTTCSSCCHHH
T ss_pred             CCeeeeCCCCHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHhccCCC-cHHHHHHHHHHHHHHHHHcCCCCCCHHH
Confidence            66699999999999999975432        1123456777777      5 5778888999888888877777899999


Q ss_pred             HHHHHHhhc
Q 030960          149 FEKGYRTNV  157 (168)
Q Consensus       149 ~~~al~~~~  157 (168)
                      +..++....
T Consensus       286 v~~~~~~~~  294 (412)
T 1w5s_A          286 VRKAVSENE  294 (412)
T ss_dssp             HHHHHHHC-
T ss_pred             HHHHHHHHh
Confidence            998887653

>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=98.47  E-value=3e-07  Score=79.66  Aligned_cols=118  Identities=19%  Similarity=0.208  Sum_probs=84.4

Q ss_pred             HHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC---------CCCCeEEEEecCCCC-----
Q 030960            5 VFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD---------QTVNVKVIMATNRAD-----   70 (168)
Q Consensus         5 iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~---------~~~~v~vi~ttn~~~-----   70 (168)
                      +....+...++||||||+|.+-           .   .+.+.|+..++.-.         ...++++|+|||.+.     
T Consensus       549 l~~~~~~~~~~vl~lDEi~~~~-----------~---~~~~~Ll~~le~~~~~~~~g~~~~~~~~~iI~tsN~~~~~~~~  614 (758)
T 1r6b_X          549 LTDAVIKHPHAVLLLDEIEKAH-----------P---DVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETER  614 (758)
T ss_dssp             HHHHHHHCSSEEEEEETGGGSC-----------H---HHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEECSSCC----
T ss_pred             HHHHHHhCCCcEEEEeCccccC-----------H---HHHHHHHHHhcCcEEEcCCCCEEecCCeEEEEecCcchhhhhh
Confidence            3455556668999999999762           1   45666666665311         024688999999854     


Q ss_pred             --------------------CCCccccCCCCcceEEecCCCCHHHHHHHHHhhcCC---------------CCCHHHHHh
Q 030960           71 --------------------TLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD---------------EVDLEDYVS  115 (168)
Q Consensus        71 --------------------~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~~---------------~~~~~~la~  115 (168)
                                          .++|+++.  ||+..+.|++|+.+++..|++.++..               +-.+..+++
T Consensus       615 ~~~g~~~~~~~~~~~~~~~~~~~~~l~~--R~~~~i~~~~l~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~a~~~l~~  692 (758)
T 1r6b_X          615 KSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTDVIHQVVDKFIVELQVQLDQKGVSLEVSQEARNWLAE  692 (758)
T ss_dssp             -------------CHHHHHHHSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHHHHHHHHTTEEEEECHHHHHHHHH
T ss_pred             cccCccccchHHHHHHHHHHhcCHHHHh--hCCcceeeCCCCHHHHHHHHHHHHHHHHHHHHHCCcEEEeCHHHHHHHHH
Confidence                                67888888  99999999999999999999866541               112444554


Q ss_pred             --CCCCCCHHHHHHHHHHHHHHHHH
Q 030960          116 --RPDKISAAEIAAICQEAGMHAVR  138 (168)
Q Consensus       116 --~t~g~s~~di~~l~~~a~~~a~~  138 (168)
                        ...++..++|.++++.+...++.
T Consensus       693 ~~~~~~~g~R~l~~~i~~~~~~~l~  717 (758)
T 1r6b_X          693 KGYDRAMGARPMARVIQDNLKKPLA  717 (758)
T ss_dssp             HHCBTTTBTTTHHHHHHHHHTHHHH
T ss_pred             hCCCcCCCchHHHHHHHHHHHHHHH
Confidence              34567789999999888765443

>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=98.46  E-value=2.8e-07  Score=73.54  Aligned_cols=143  Identities=19%  Similarity=0.150  Sum_probs=86.4

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC-------------------CCCCeEEEEecCC----
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD-------------------QTVNVKVIMATNR----   68 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-------------------~~~~v~vi~ttn~----   68 (168)
                      ..++||||||+|.+...+.......+.....+.+.|+..|++..                   ...++++|++||.    
T Consensus       136 ~~~~vl~iDEi~~l~~~~~~~~~~~~~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~~~~~i~t~n~~~I~~~~~~~l~  215 (376)
T 1um8_A          136 AQKGIVFIDEIDKISRLSENRSITRDVSGEGVQQALLKIVEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLA  215 (376)
T ss_dssp             HTTSEEEEETGGGC--------------CHHHHHHHHHHHHCCEEC---------------CEECTTCEEEEEECCTTHH
T ss_pred             cCCeEEEEcCHHHHhhhcCCCceecccchHHHHHHHHHHhhccceecccccccccCCcceEEEecCCeEEEecCCHHHHH
Confidence            36899999999999876533322222222246677777776421                   1245677887762    


Q ss_pred             -------------------------------------CCCCCccccCCCCcceEEecCCCCHHHHHHHHHhhcC------
Q 030960           69 -------------------------------------ADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLS------  105 (168)
Q Consensus        69 -------------------------------------~~~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~------  105 (168)
                                                           ...+.+++..  ||+..+.|++++.++...++...+.      
T Consensus       216 ~~l~~R~~~~~~g~~~~~~~~~~~~~~~~~~~~~~l~~~~~~p~l~~--R~~~~i~~~~l~~~~l~~i~~~~~~~~~~~~  293 (376)
T 1um8_A          216 EIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVTYGLIPELIG--RLPVLSTLDSISLEAMVDILQKPKNALIKQY  293 (376)
T ss_dssp             HHTTTSCSSCCCSCCCSSCCTTTTTTSGGGCCHHHHHHTTCCHHHHT--TCCEEEECCCCCHHHHHHHHHSSTTCHHHHH
T ss_pred             HHHHHHhcccccCCCchhhhccchhHHHhhcCHHHHhhcCCChHHhc--CCCceeeccCCCHHHHHHHHhhhHHHHHHHH
Confidence                                                 0124566666  8989999999999999999963110      


Q ss_pred             -------------CCCCHHHHHhCC--CCCCHHHHHHHHHHHHHHHHHhCC------CccCHHHHHHHHHhh
Q 030960          106 -------------DEVDLEDYVSRP--DKISAAEIAAICQEAGMHAVRKNR------YVILPKDFEKGYRTN  156 (168)
Q Consensus       106 -------------~~~~~~~la~~t--~g~s~~di~~l~~~a~~~a~~~~~------~~i~~~d~~~al~~~  156 (168)
                                   ++-.+..++...  .+...+.|.++++.+...++.+..      ..|+.+++.++.+..
T Consensus       294 ~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~R~L~~~le~~~~~~~~~~~~~~~~~~~i~~~~v~~~~~~~  365 (376)
T 1um8_A          294 QQLFKMDEVDLIFEEEAIKEIAQLALERKTGARGLRAIIEDFCLDIMFDLPKLKGSEVRITKDCVLKQAEPL  365 (376)
T ss_dssp             HHHHHTTTCEEEECHHHHHHHHHHHHHTTCTGGGHHHHHHHHHHHHHHTGGGGTTSEEEECHHHHTTSSCCE
T ss_pred             HHHHhhcCceEEECHHHHHHHHHHhcccccCcHHHHHHHHHHHHHHHhhccCCCCCEEEEeHHHhcCCCCce
Confidence                         111234455543  246789999999998877666432      258999887765543

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.39  E-value=7.8e-07  Score=69.84  Aligned_cols=86  Identities=10%  Similarity=0.172  Sum_probs=64.9

Q ss_pred             HHHHHHHH--HHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCC----CCcc
Q 030960            2 VRDVFRLA--KENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADT----LDPA   75 (168)
Q Consensus         2 l~~iF~~a--~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~----ld~a   75 (168)
                      ++.+|..+  ....|+||+|||+|.+. .            +.++..++.+..  ....++.+|+++|..+.    ++++
T Consensus       119 L~~~f~~~~~~~~~~~ii~lDE~d~l~-~------------q~~L~~l~~~~~--~~~s~~~vI~i~n~~d~~~~~L~~~  183 (318)
T 3te6_A          119 LNFYITNVPKAKKRKTLILIQNPENLL-S------------EKILQYFEKWIS--SKNSKLSIICVGGHNVTIREQINIM  183 (318)
T ss_dssp             HHHHHHHSCGGGSCEEEEEEECCSSSC-C------------THHHHHHHHHHH--CSSCCEEEEEECCSSCCCHHHHHTC
T ss_pred             HHHHHHHhhhccCCceEEEEecHHHhh-c------------chHHHHHHhccc--ccCCcEEEEEEecCcccchhhcchh
Confidence            46677765  35568999999999997 1            155666666543  34567999999998864    5566


Q ss_pred             ccCCCCcc-eEEecCCCCHHHHHHHHHhhc
Q 030960           76 LLRPGRLD-RKIEFPLPDRRQKRLVFQMNL  104 (168)
Q Consensus        76 l~r~grf~-~~i~~~~P~~~~R~~il~~~l  104 (168)
                      +.+  ||+ ..|.|++++.++-.+|++.-+
T Consensus       184 v~S--R~~~~~i~F~pYt~~el~~Il~~Rl  211 (318)
T 3te6_A          184 PSL--KAHFTEIKLNKVDKNELQQMIITRL  211 (318)
T ss_dssp             HHH--HTTEEEEECCCCCHHHHHHHHHHHH
T ss_pred             hhc--cCCceEEEeCCCCHHHHHHHHHHHH
Confidence            677  887 689999999999999998544

>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=98.32  E-value=1e-06  Score=68.16  Aligned_cols=117  Identities=18%  Similarity=0.153  Sum_probs=79.5

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCC
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLP   91 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P   91 (168)
                      ..+.||+|||+|.+..              ...+.++..++.  ...++.+|++||.++.+++++.+  |+. .+.+++|
T Consensus       109 ~~~~vliiDe~~~l~~--------------~~~~~L~~~le~--~~~~~~~i~~~~~~~~l~~~l~s--r~~-~~~~~~l  169 (327)
T 1iqp_A          109 ASFKIIFLDEADALTQ--------------DAQQALRRTMEM--FSSNVRFILSCNYSSKIIEPIQS--RCA-IFRFRPL  169 (327)
T ss_dssp             CSCEEEEEETGGGSCH--------------HHHHHHHHHHHH--TTTTEEEEEEESCGGGSCHHHHH--TEE-EEECCCC
T ss_pred             CCCeEEEEeCCCcCCH--------------HHHHHHHHHHHh--cCCCCeEEEEeCCccccCHHHHh--hCc-EEEecCC
Confidence            3489999999998742              223445555543  24467788899999999999998  887 7899999


Q ss_pred             CHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           92 DRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        92 ~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      +.++...+++..+..      +..+..++..+.| +++.+.++++.+...     ...++.+++...+
T Consensus       170 ~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g-~~r~~~~~l~~~~~~-----~~~i~~~~v~~~~  231 (327)
T 1iqp_A          170 RDEDIAKRLRYIAENEGLELTEEGLQAILYIAEG-DMRRAINILQAAAAL-----DKKITDENVFMVA  231 (327)
T ss_dssp             CHHHHHHHHHHHHHTTTCEECHHHHHHHHHHHTT-CHHHHHHHHHHHHTT-----CSEECHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHCCC-CHHHHHHHHHHHHhc-----CCCCCHHHHHHHH
Confidence            999999999865432      2235567777655 666666666655421     2245555555443

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=98.28  E-value=4e-07  Score=64.59  Aligned_cols=79  Identities=22%  Similarity=0.302  Sum_probs=53.2

Q ss_pred             HHHHHHHHHHc-CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC-----CCCcc
Q 030960            2 VRDVFRLAKEN-APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD-----TLDPA   75 (168)
Q Consensus         2 l~~iF~~a~~~-~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~-----~ld~a   75 (168)
                      ++.+|..+... .|++|+|||+|.+.+.+......  .   .+.+.+...++    ..++.+|++||.+.     .++++
T Consensus       103 ~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~~~~~--~---~~~~~l~~~~~----~~~~~ii~~~~~~~~~~~~~~~~~  173 (187)
T 2p65_A          103 LKSILKEVQDAEGQVVMFIDEIHTVVGAGAVAEGA--L---DAGNILKPMLA----RGELRCIGATTVSEYRQFIEKDKA  173 (187)
T ss_dssp             HHHHHHHHHHTTTSEEEEETTGGGGSSSSSSCTTS--C---CTHHHHHHHHH----TTCSCEEEEECHHHHHHHTTTCHH
T ss_pred             HHHHHHHHHhcCCceEEEEeCHHHhcccccccccc--h---HHHHHHHHHHh----cCCeeEEEecCHHHHHHHHhccHH
Confidence            34566666655 68999999999998654311111  1   12222333332    34678999999875     68999


Q ss_pred             ccCCCCcceEEecCCCC
Q 030960           76 LLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        76 l~r~grf~~~i~~~~P~   92 (168)
                      +.+  ||+. +++++|+
T Consensus       174 l~~--R~~~-i~i~~p~  187 (187)
T 2p65_A          174 LER--RFQQ-ILVEQPS  187 (187)
T ss_dssp             HHH--HEEE-EECCSCC
T ss_pred             HHH--hcCc-ccCCCCC
Confidence            999  9995 9999986

>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=98.21  E-value=5.2e-06  Score=65.29  Aligned_cols=109  Identities=15%  Similarity=0.181  Sum_probs=77.1

Q ss_pred             HHHHHHHHHH----cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcccc
Q 030960            2 VRDVFRLAKE----NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~----~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~   77 (168)
                      ++++.+.+..    ..+.|++|||+|.+..              ...+.|+..++.  ...++++|.+||+++.++++++
T Consensus        93 ir~l~~~~~~~~~~~~~kvviIdead~l~~--------------~a~naLLk~lEe--p~~~~~~Il~t~~~~~l~~ti~  156 (334)
T 1a5t_A           93 VREVTEKLNEHARLGGAKVVWVTDAALLTD--------------AAANALLKTLEE--PPAETWFFLATREPERLLATLR  156 (334)
T ss_dssp             HHHHHHHTTSCCTTSSCEEEEESCGGGBCH--------------HHHHHHHHHHTS--CCTTEEEEEEESCGGGSCHHHH
T ss_pred             HHHHHHHHhhccccCCcEEEEECchhhcCH--------------HHHHHHHHHhcC--CCCCeEEEEEeCChHhCcHHHh
Confidence            4556666543    2378999999998842              235667777873  4557888889999999999999


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhcC-CCCCHHHHHhCCCCCCHHHHHHHHH
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNLS-DEVDLEDYVSRPDKISAAEIAAICQ  130 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l~-~~~~~~~la~~t~g~s~~di~~l~~  130 (168)
                      +  |+. .+.|++|+.++..++++.... ++..+..++..+.| +++...++++
T Consensus       157 S--Rc~-~~~~~~~~~~~~~~~L~~~~~~~~~~~~~l~~~s~G-~~r~a~~~l~  206 (334)
T 1a5t_A          157 S--RCR-LHYLAPPPEQYAVTWLSREVTMSQDALLAALRLSAG-SPGAALALFQ  206 (334)
T ss_dssp             T--TSE-EEECCCCCHHHHHHHHHHHCCCCHHHHHHHHHHTTT-CHHHHHHTTS
T ss_pred             h--cce-eeeCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHcCC-CHHHHHHHhc
Confidence            9  874 799999999999999987652 22234556666655 4444444433

>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=98.21  E-value=9.6e-06  Score=67.47  Aligned_cols=121  Identities=13%  Similarity=0.150  Sum_probs=73.8

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCC
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLP   91 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P   91 (168)
                      ..++||+|||+|.+.....           ..+..++..++.  ....+++++++.....+++ +.   |+...+.|++|
T Consensus       147 ~~~~vliIDEid~l~~~~~-----------~~l~~L~~~l~~--~~~~iIli~~~~~~~~l~~-l~---~r~~~i~f~~~  209 (516)
T 1sxj_A          147 GKHFVIIMDEVDGMSGGDR-----------GGVGQLAQFCRK--TSTPLILICNERNLPKMRP-FD---RVCLDIQFRRP  209 (516)
T ss_dssp             TTSEEEEECSGGGCCTTST-----------THHHHHHHHHHH--CSSCEEEEESCTTSSTTGG-GT---TTSEEEECCCC
T ss_pred             CCCeEEEEECCCccchhhH-----------HHHHHHHHHHHh--cCCCEEEEEcCCCCccchh-hH---hceEEEEeCCC
Confidence            4689999999999974320           123334444432  2234555555444445543 33   56679999999


Q ss_pred             CHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960           92 DRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus        92 ~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      +.+++.++++....      ++..+..+++.+.|    |+..+++.....+.  ....|+.+++.+++..
T Consensus       210 ~~~~~~~~L~~i~~~~~~~i~~~~l~~la~~s~G----diR~~i~~L~~~~~--~~~~It~~~v~~~~~~  273 (516)
T 1sxj_A          210 DANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRG----DIRQVINLLSTIST--TTKTINHENINEISKA  273 (516)
T ss_dssp             CHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHTTT----CHHHHHHHHTHHHH--HSSCCCTTHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC----cHHHHHHHHHHHHh--cCCCCchHHHHHHHHh
Confidence            99999999874332      23347778887754    45444444333232  3456888888877764

>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=98.20  E-value=4.7e-06  Score=65.45  Aligned_cols=103  Identities=11%  Similarity=0.207  Sum_probs=74.1

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      .|.||+|||+|.+-.              ...+.++..++..  ..++.+|.+|+.++.+++.+++  |+ ..+.|++|+
T Consensus       134 ~~~vlilDE~~~L~~--------------~~~~~L~~~le~~--~~~~~~Il~t~~~~~l~~~l~s--R~-~~~~~~~~~  194 (354)
T 1sxj_E          134 RYKCVIINEANSLTK--------------DAQAALRRTMEKY--SKNIRLIMVCDSMSPIIAPIKS--QC-LLIRCPAPS  194 (354)
T ss_dssp             CCEEEEEECTTSSCH--------------HHHHHHHHHHHHS--TTTEEEEEEESCSCSSCHHHHT--TS-EEEECCCCC
T ss_pred             CCeEEEEeCccccCH--------------HHHHHHHHHHHhh--cCCCEEEEEeCCHHHHHHHHHh--hc-eEEecCCcC
Confidence            578999999998521              2233444445432  2357788889999999999999  88 889999999


Q ss_pred             HHHHHHHHHhhcC------C-CCCHHHHHhCCCCCCHHHHHHHHHHHHHH
Q 030960           93 RRQKRLVFQMNLS------D-EVDLEDYVSRPDKISAAEIAAICQEAGMH  135 (168)
Q Consensus        93 ~~~R~~il~~~l~------~-~~~~~~la~~t~g~s~~di~~l~~~a~~~  135 (168)
                      .++..++++....      + +..+..++..+.| +.+++.++++.+...
T Consensus       195 ~~~~~~~l~~~~~~~~~~~~~~~~l~~i~~~~~G-~~r~a~~~l~~~~~~  243 (354)
T 1sxj_E          195 DSEISTILSDVVTNERIQLETKDILKRIAQASNG-NLRVSLLMLESMALN  243 (354)
T ss_dssp             HHHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTT-CHHHHHHHHTHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCC-CHHHHHHHHHHHHHh
Confidence            9999999985543      1 3346677777755 667777777766543

>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=98.05  E-value=5.1e-06  Score=73.04  Aligned_cols=118  Identities=19%  Similarity=0.271  Sum_probs=82.8

Q ss_pred             HHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC---------CCCCeEEEEecCCC-------
Q 030960            6 FRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD---------QTVNVKVIMATNRA-------   69 (168)
Q Consensus         6 F~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~---------~~~~v~vi~ttn~~-------   69 (168)
                      ....+...++||||||+|.+-              ..+.+.|+..++.-.         ...++++|+|||..       
T Consensus       653 ~~~~~~~~~~vl~lDEi~~l~--------------~~~~~~Ll~~l~~~~~~~~~g~~vd~~~~iiI~tsn~~~~~~~~~  718 (854)
T 1qvr_A          653 TEAVRRRPYSVILFDEIEKAH--------------PDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPLILEG  718 (854)
T ss_dssp             HHHHHHCSSEEEEESSGGGSC--------------HHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCTTHHHHHHH
T ss_pred             HHHHHhCCCeEEEEecccccC--------------HHHHHHHHHHhccCceECCCCCEeccCCeEEEEecCcChHHHhhh
Confidence            344455567999999999762              156677777776421         12368899999972       


Q ss_pred             -------------------CCCCccccCCCCcceEEecCCCCHHHHHHHHHhhcCC---------------CCCHHHHHh
Q 030960           70 -------------------DTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD---------------EVDLEDYVS  115 (168)
Q Consensus        70 -------------------~~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~~---------------~~~~~~la~  115 (168)
                                         ..+.|+++.  ||+..+.+.+|+.++...|++.++..               +-.++.+++
T Consensus       719 ~~~~~~~~~l~~~v~~~~~~~f~~~l~~--Rl~~~i~~~pl~~edi~~i~~~~l~~~~~~~~~~~~~~~~~~~a~~~L~~  796 (854)
T 1qvr_A          719 LQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRPLTKEQIRQIVEIQLSYLRARLAEKRISLELTEAAKDFLAE  796 (854)
T ss_dssp             HHTTCCHHHHHHHHHHHHHTTSCHHHHH--TCSBCCBCCCCCHHHHHHHHHHHHHHHHHHHHTTTCEEEECHHHHHHHHH
T ss_pred             cccccchHHHHHHHHHHHHhhCCHHHHH--hcCeEEeCCCCCHHHHHHHHHHHHHHHHHHHHhCCceEEECHHHHHHHHH
Confidence                               245666776  99999999999999999999866541               112345665


Q ss_pred             CCC--CCCHHHHHHHHHHHHHHHHHh
Q 030960          116 RPD--KISAAEIAAICQEAGMHAVRK  139 (168)
Q Consensus       116 ~t~--g~s~~di~~l~~~a~~~a~~~  139 (168)
                      ..-  .+..++|.++++.+...++.+
T Consensus       797 ~~~~~~gn~R~L~~~i~~~~~~~~~~  822 (854)
T 1qvr_A          797 RGYDPVFGARPLRRVIQRELETPLAQ  822 (854)
T ss_dssp             HHCBTTTBTSTHHHHHHHHTHHHHHH
T ss_pred             cCCCCCCChHHHHHHHHHHHHHHHHH
Confidence            433  678899999999887666543

>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=98.05  E-value=5.1e-05  Score=62.05  Aligned_cols=139  Identities=19%  Similarity=0.229  Sum_probs=90.4

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC--------CCCCeEEEEec----CCCCCCCccccCCCC
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD--------QTVNVKVIMAT----NRADTLDPALLRPGR   81 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~--------~~~~v~vi~tt----n~~~~ld~al~r~gr   81 (168)
                      ..|+++||+|.++...++  ...+...+.+...||..+++-.        ..++|++|+|.    ++|.++-|.++.  |
T Consensus       251 ~~il~~DEidki~~~~~~--~~~D~s~egvq~aLL~~le~~~~~~~~~~~d~~~ilfI~~gaf~~~~~~dlipel~~--R  326 (444)
T 1g41_A          251 NGIVFIDEIDKICKKGEY--SGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG--R  326 (444)
T ss_dssp             HCEEEEETGGGGSCCSSC--SSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSCCGGGSCHHHHT--T
T ss_pred             CCeeeHHHHHHHhhccCC--CCCCchHHHHHHHHHHHhcccccccccceecCCcEEEEeccccccCChhhcchHHhc--c
Confidence            368999999999865432  2333333457778888888631        34578888886    356666678887  9


Q ss_pred             cceEEecCCCCHHHHHHHHHh---hc----------C------CCCCHHHHHh-------CCCCCCHHHHHHHHHHHHHH
Q 030960           82 LDRKIEFPLPDRRQKRLVFQM---NL----------S------DEVDLEDYVS-------RPDKISAAEIAAICQEAGMH  135 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~---~l----------~------~~~~~~~la~-------~t~g~s~~di~~l~~~a~~~  135 (168)
                      |...+.++..+.++..+|+..   ++          .      .+-.+..+++       .|.+.-.+-|.+++......
T Consensus       327 ~~i~i~l~~lt~~e~~~Il~~~~~~l~~q~~~~~~~~~~~l~~~~~al~~i~~~a~~~~~~t~~~GaR~L~~~ie~~~~~  406 (444)
T 1g41_A          327 LPIRVELTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKKIAEAAFRVNEKTENIGARRLHTVMERLMDK  406 (444)
T ss_dssp             CCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHHHHHSCCCGGGHHHHHHHHHHHH
T ss_pred             cceeeeCCCCCHHHHHHHHHHHHHhHHHHHHHHhcccCceEEECHHHHHHHHHHHHHhccCCccCCchHHHHHHHHHHHH
Confidence            999999999999999999941   11          1      1112344544       45566666666655555443


Q ss_pred             HHHhC------CCccCHHHHHHHHHhh
Q 030960          136 AVRKN------RYVILPKDFEKGYRTN  156 (168)
Q Consensus       136 a~~~~------~~~i~~~d~~~al~~~  156 (168)
                      ...+.      ...|+.+.+...+...
T Consensus       407 ~~~~~~~~~~~~~~i~~~~v~~~l~~~  433 (444)
T 1g41_A          407 ISFSASDMNGQTVNIDAAYVADALGEV  433 (444)
T ss_dssp             HHHHGGGCTTCEEEECHHHHHHHHTTT
T ss_pred             HHhhccccCCCeEEEeHHHHHHhcCcc
Confidence            33321      2358888888777543

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=97.93  E-value=1.5e-05  Score=67.56  Aligned_cols=95  Identities=20%  Similarity=0.317  Sum_probs=66.9

Q ss_pred             CeEEEEecCCC--CCCCccccCCCCcc---eEEecCC--C-CHHHHHHHHHhhc---C-----CCCC---HHHHHhC---
Q 030960           59 NVKVIMATNRA--DTLDPALLRPGRLD---RKIEFPL--P-DRRQKRLVFQMNL---S-----DEVD---LEDYVSR---  116 (168)
Q Consensus        59 ~v~vi~ttn~~--~~ld~al~r~grf~---~~i~~~~--P-~~~~R~~il~~~l---~-----~~~~---~~~la~~---  116 (168)
                      .+.||++||..  ..+++++++  ||+   ..+.++.  + +.+....+++..-   .     ..++   +..+.+.   
T Consensus       252 ~~~vI~atn~~~~~~l~~~l~~--R~~v~~i~i~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ls~eAl~~Li~~~~r  329 (604)
T 3k1j_A          252 DFVLVAAGNLDTVDKMHPALRS--RIRGYGYEVYMRTTMPDTIENRRKLVQFVAQEVKRDGKIPHFTKEAVEEIVREAQK  329 (604)
T ss_dssp             CCEEEEEECHHHHHHSCHHHHH--HHHHHSEEEECCSEEECCHHHHHHHHHHHHHHHHHHCSSCCBBHHHHHHHHHHHHH
T ss_pred             eEEEEEecCHHHHhhcCHHHHH--HhhccceEeeccccccCCHHHHHHHHHHHHHHHhhccCcccCCHHHHHHHHHHHhh
Confidence            57899999986  689999999  997   5666543  2 3444555553211   1     1222   2333332   


Q ss_pred             CCC------CCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960          117 PDK------ISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus       117 t~g------~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      ..|      .+.+++.++++.|...|..++...|+.+|+.+|+..
T Consensus       330 ~~g~r~~l~~~~R~l~~llr~A~~~A~~~~~~~I~~edv~~A~~~  374 (604)
T 3k1j_A          330 RAGRKGHLTLRLRDLGGIVRAAGDIAVKKGKKYVEREDVIEAVKM  374 (604)
T ss_dssp             TTCSTTEEECCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             hhccccccccCHHHHHHHHHHHHHHHHhcCcccccHHHHHHHHHh
Confidence            255      379999999999998888888889999999999965

>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=97.85  E-value=8.6e-05  Score=71.88  Aligned_cols=82  Identities=15%  Similarity=0.323  Sum_probs=59.1

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC--------CCCCeEEEEecCCC-----CCCCccccCCC
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD--------QTVNVKVIMATNRA-----DTLDPALLRPG   80 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~--------~~~~v~vi~ttn~~-----~~ld~al~r~g   80 (168)
                      ++||||||+|.....+.+     ......++.+++.. .++.        ...++.+|||||.|     ..|+++++|  
T Consensus      1337 ~~VlFiDEinmp~~d~yg-----~q~~lelLRq~le~-gg~yd~~~~~~~~~~~i~lIaA~Npp~~gGR~~l~~rllR-- 1408 (2695)
T 4akg_A         1337 NLVLFCDEINLPKLDKYG-----SQNVVLFLRQLMEK-QGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFTR-- 1408 (2695)
T ss_dssp             CEEEEEETTTCSCCCSSS-----CCHHHHHHHHHHHT-SSEECTTTCCEEEEESEEEEEEECCTTSTTCCCCCHHHHT--
T ss_pred             eEEEEecccccccccccC-----chhHHHHHHHHHhc-CCEEEcCCCcEEEecCEEEEEecCCCccCCCccCChhhhh--
Confidence            589999999974433311     12234566666542 1221        11358999999999     489999999  


Q ss_pred             CcceEEecCCCCHHHHHHHHHhhc
Q 030960           81 RLDRKIEFPLPDRRQKRLVFQMNL  104 (168)
Q Consensus        81 rf~~~i~~~~P~~~~R~~il~~~l  104 (168)
                      || ..++++.|+.+++..|+...+
T Consensus      1409 rf-~vi~i~~P~~~~l~~I~~~il 1431 (2695)
T 4akg_A         1409 HA-AILYLGYPSGKSLSQIYEIYY 1431 (2695)
T ss_dssp             TE-EEEECCCCTTTHHHHHHHHHH
T ss_pred             ee-eEEEeCCCCHHHHHHHHHHHH
Confidence            99 889999999999999998554

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.74  E-value=1.7e-05  Score=62.27  Aligned_cols=122  Identities=16%  Similarity=0.158  Sum_probs=73.2

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      .+.|++|||+|.+..              ...+.++..++.  ....+.+|++||.+..+.+++++  |+. .+.+++++
T Consensus       110 ~~~viiiDe~~~l~~--------------~~~~~L~~~le~--~~~~~~~il~~n~~~~i~~~i~s--R~~-~~~~~~l~  170 (340)
T 1sxj_C          110 GFKLIILDEADAMTN--------------AAQNALRRVIER--YTKNTRFCVLANYAHKLTPALLS--QCT-RFRFQPLP  170 (340)
T ss_dssp             SCEEEEETTGGGSCH--------------HHHHHHHHHHHH--TTTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCC
T ss_pred             CceEEEEeCCCCCCH--------------HHHHHHHHHHhc--CCCCeEEEEEecCccccchhHHh--hce-eEeccCCC
Confidence            378999999998742              123345555553  23456677888999999999999  886 78899999


Q ss_pred             HHHHHHHHHhhcC-CCC-----CHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960           93 RRQKRLVFQMNLS-DEV-----DLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus        93 ~~~R~~il~~~l~-~~~-----~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      .++..+.+...+. ..+     .+..++..+.| ..+.+.++++.+...+...+...++.+++.+++.
T Consensus       171 ~~~~~~~l~~~~~~~~~~i~~~~~~~i~~~s~G-~~r~~~~~l~~~~~~~~~~~~~~it~~~v~~~~~  237 (340)
T 1sxj_C          171 QEAIERRIANVLVHEKLKLSPNAEKALIELSNG-DMRRVLNVLQSCKATLDNPDEDEISDDVIYECCG  237 (340)
T ss_dssp             HHHHHHHHHHHHHTTTCCBCHHHHHHHHHHHTT-CHHHHHHHTTTTTTTTCSSSCCCBCHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHHhcCCcccccccHHHHHHHhC
Confidence            9888888875552 112     23334444433 3333333333332211111122577777665544

>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=97.66  E-value=8.1e-05  Score=57.95  Aligned_cols=82  Identities=10%  Similarity=0.209  Sum_probs=64.3

Q ss_pred             HHHHHHHHHHcC----CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcccc
Q 030960            2 VRDVFRLAKENA----PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~~~----p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~   77 (168)
                      ++++.+.+....    .-|++|||+|.+-.              ...+.|+..|+.  ..+++++|.+|++++.+.++++
T Consensus        67 ir~li~~~~~~p~~~~~kvviIdead~lt~--------------~a~naLLk~LEe--p~~~t~fIl~t~~~~kl~~tI~  130 (305)
T 2gno_A           67 IRTIKDFLNYSPELYTRKYVIVHDCERMTQ--------------QAANAFLKALEE--PPEYAVIVLNTRRWHYLLPTIK  130 (305)
T ss_dssp             HHHHHHHHTSCCSSSSSEEEEETTGGGBCH--------------HHHHHTHHHHHS--CCTTEEEEEEESCGGGSCHHHH
T ss_pred             HHHHHHHHhhccccCCceEEEeccHHHhCH--------------HHHHHHHHHHhC--CCCCeEEEEEECChHhChHHHH
Confidence            567777775432    46999999999831              335668888873  4557778888899999999999


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhc
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNL  104 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l  104 (168)
                      +  |   .+.|++|+.++..+.++..+
T Consensus       131 S--R---~~~f~~l~~~~i~~~L~~~~  152 (305)
T 2gno_A          131 S--R---VFRVVVNVPKEFRDLVKEKI  152 (305)
T ss_dssp             T--T---SEEEECCCCHHHHHHHHHHH
T ss_pred             c--e---eEeCCCCCHHHHHHHHHHHh
Confidence            9  8   89999999999999987665

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=97.42  E-value=0.00025  Score=55.02  Aligned_cols=119  Identities=20%  Similarity=0.261  Sum_probs=64.8

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC---------CCCCeEEEEecCCC-------CCCCcccc
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD---------QTVNVKVIMATNRA-------DTLDPALL   77 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~---------~~~~v~vi~ttn~~-------~~ld~al~   77 (168)
                      +++|||||+|.+..              .....++..++.-.         ....+.+|++||..       ..+++.+.
T Consensus        97 ~g~L~LDEi~~l~~--------------~~q~~Ll~~l~~~~~~~~g~~~~~~~~~riI~atn~~l~~~v~~g~fr~~L~  162 (304)
T 1ojl_A           97 GGTLFLDEIGDISP--------------LMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLY  162 (304)
T ss_dssp             TSEEEEESCTTCCH--------------HHHHHHHHHHHSSBCCBTTBCCCCBCCCEEEEEESSCHHHHHHHTSSCHHHH
T ss_pred             CCEEEEeccccCCH--------------HHHHHHHHHHhcCEeeecCCcccccCCeEEEEecCccHHHHHHhCCcHHHHH
Confidence            58999999998842              12233444444211         12358899999975       12344455


Q ss_pred             CCCCcc-eEEecCCCC--HHHHHHHHHhhcC----------CCCC---HHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCC
Q 030960           78 RPGRLD-RKIEFPLPD--RRQKRLVFQMNLS----------DEVD---LEDYVSRPDKISAAEIAAICQEAGMHAVRKNR  141 (168)
Q Consensus        78 r~grf~-~~i~~~~P~--~~~R~~il~~~l~----------~~~~---~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~  141 (168)
                      .  ||. ..+.+|+..  .++...++++++.          ..++   +..+..+.-.-..++|.+++..++..+   ..
T Consensus       163 ~--Rl~~~~i~lPpL~eR~edi~~l~~~~l~~~~~~~~~~~~~~s~~a~~~L~~~~wpGnvReL~~~l~~~~~~~---~~  237 (304)
T 1ojl_A          163 Y--RLNVVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELENAIERAVVLL---TG  237 (304)
T ss_dssp             H--HHSSEEEECCCSGGGGGGHHHHHHHHHHHHHHHTTCCCCCBCHHHHHHHHHCCCSSHHHHHHHHHHHHHHHC---CS
T ss_pred             h--hcCeeEEeccCHHHhHhhHHHHHHHHHHHHHHHhccCccCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhC---CC
Confidence            4  554 334454444  3344445554332          1122   344555542235678888888876644   23


Q ss_pred             CccCHHHHHH
Q 030960          142 YVILPKDFEK  151 (168)
Q Consensus       142 ~~i~~~d~~~  151 (168)
                      ..|+.+|+..
T Consensus       238 ~~i~~~~l~~  247 (304)
T 1ojl_A          238 EYISERELPL  247 (304)
T ss_dssp             SSBCGGGSCG
T ss_pred             CcccHHhhhh
Confidence            4566666643

>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=97.35  E-value=0.0001  Score=68.81  Aligned_cols=71  Identities=17%  Similarity=0.197  Sum_probs=54.0

Q ss_pred             HHHHHHHHHHcCCeEEEEccccccccccc---CCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCC-CCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARF---DAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRA-DTLD   73 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~---~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~-~~ld   73 (168)
                      |+.+|.+|+..+||+|++|++|+|++.+.   ...........++++++|+.++++....+|+|| +||+. +.+.
T Consensus      1149 l~~~~~~ar~~~~~~i~~d~~~al~~~~~~~g~~~~~~~~~~~r~~~q~l~~~~~~~~~~~v~v~-~~n~~~~~~~ 1223 (1706)
T 3cmw_A         1149 LEICDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNLKQSNTLLI-FINQIRMKIG 1223 (1706)
T ss_dssp             HHHHHHHHHHTCCSEEEESCGGGCCCHHHHHSCTTCCCTTHHHHHHHHHHHHHHHHHHHTTCEEE-EEECEEECTT
T ss_pred             HHHHHHHHHhcCCeEEEeCchHhcCcccccccccccccccHHHHHHHHHHHHHHhhhccCCeEEE-Eeccccccch
Confidence            57889999999999999999999999853   222222245568999999999988777788888 55554 4443

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=97.19  E-value=0.00046  Score=51.95  Aligned_cols=118  Identities=17%  Similarity=0.152  Sum_probs=65.8

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC---------CCCCCeEEEEecCCC-------CCCCccc
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF---------DQTVNVKVIMATNRA-------DTLDPAL   76 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~---------~~~~~v~vi~ttn~~-------~~ld~al   76 (168)
                      .+.+|||||+|.+..              .....++..++.-         ....++.+|+|||.+       ..+++++
T Consensus       100 ~~~~l~lDEi~~l~~--------------~~q~~Ll~~l~~~~~~~~g~~~~~~~~~~iI~atn~~~~~~~~~~~~~~~L  165 (265)
T 2bjv_A          100 DGGTLFLDELATAPM--------------MVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVNEGTFRADL  165 (265)
T ss_dssp             TTSEEEEESGGGSCH--------------HHHHHHHHHHHHCEECCCCC--CEECCCEEEEEESSCHHHHHHHTSSCHHH
T ss_pred             CCcEEEEechHhcCH--------------HHHHHHHHHHHhCCeecCCCcccccCCeEEEEecCcCHHHHHHcCCccHHH
Confidence            368999999998742              1222333333311         112357889999874       2467888


Q ss_pred             cCCCCcc-eEEecCCCCH--HHHHHHHHhhcC-------C----CCCH---HHHHhCCCCCCHHHHHHHHHHHHHHHHHh
Q 030960           77 LRPGRLD-RKIEFPLPDR--RQKRLVFQMNLS-------D----EVDL---EDYVSRPDKISAAEIAAICQEAGMHAVRK  139 (168)
Q Consensus        77 ~r~grf~-~~i~~~~P~~--~~R~~il~~~l~-------~----~~~~---~~la~~t~g~s~~di~~l~~~a~~~a~~~  139 (168)
                      ..  ||+ ..+.+|+...  ++...+++.++.       .    .++-   ..+....-.-..++|.++++.++..+   
T Consensus       166 ~~--Rl~~~~i~lp~L~~R~~di~~l~~~~l~~~~~~~~~~~~~~~~~~a~~~L~~~~~~gn~reL~~~l~~~~~~~---  240 (265)
T 2bjv_A          166 LD--ALAFDVVQLPPLRERESDIMLMAEYFAIQMCREIKLPLFPGFTERARETLLNYRWPGNIRELKNVVERSVYRH---  240 (265)
T ss_dssp             HH--HHCSEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCSSCCCBCHHHHHHHHHSCCTTHHHHHHHHHHHHHHHH---
T ss_pred             HH--hhcCcEEeCCChhhhhHHHHHHHHHHHHHHHHHhCCCcccCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHhC---
Confidence            88  886 3455555543  444445443322       1    2222   23433332235678888888876554   


Q ss_pred             CCCccCHHHH
Q 030960          140 NRYVILPKDF  149 (168)
Q Consensus       140 ~~~~i~~~d~  149 (168)
                      ....|+.+|+
T Consensus       241 ~~~~i~~~~l  250 (265)
T 2bjv_A          241 GTSDYPLDDI  250 (265)
T ss_dssp             CCSSSCBCCC
T ss_pred             CCCcCcHHHc
Confidence            2345666655

>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=97.18  E-value=0.0041  Score=51.27  Aligned_cols=128  Identities=16%  Similarity=0.161  Sum_probs=80.9

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhcc-------CCCCCCCeEEEEecCCCC-----------CCCcc
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMD-------GFDQTVNVKVIMATNRAD-----------TLDPA   75 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~-------~~~~~~~v~vi~ttn~~~-----------~ld~a   75 (168)
                      -.++|+||++.+-.              .....+++.|+       +..-..++.||||+|-..           .|+++
T Consensus       301 gGvl~lDEIn~~~~--------------~~qsaLlEaMEe~~VtI~G~~lparf~VIAA~NP~~~yd~~~s~~~~~Lp~a  366 (506)
T 3f8t_A          301 GGILAVDHLEGAPE--------------PHRWALMEAMDKGTVTVDGIALNARCAVLAAINPGEQWPSDPPIARIDLDQD  366 (506)
T ss_dssp             TSEEEEECCTTCCH--------------HHHHHHHHHHHHSEEEETTEEEECCCEEEEEECCCC--CCSCGGGGCCSCHH
T ss_pred             CCeeehHhhhhCCH--------------HHHHHHHHHHhCCcEEECCEEcCCCeEEEEEeCcccccCCCCCccccCCChH
Confidence            37999999997621              33344444443       211134688999999765           88999


Q ss_pred             ccCCCCcceEEe-cCCCCHHHH-------------HHHHH----hhcCCCCC---HHHH---------H--------hCC
Q 030960           76 LLRPGRLDRKIE-FPLPDRRQK-------------RLVFQ----MNLSDEVD---LEDY---------V--------SRP  117 (168)
Q Consensus        76 l~r~grf~~~i~-~~~P~~~~R-------------~~il~----~~l~~~~~---~~~l---------a--------~~t  117 (168)
                      ++.  |||..+. ++.|+.+.-             .+++.    ..+...++   .+.+         .        ...
T Consensus       367 lLD--RFDLi~i~~d~pd~e~d~e~~~~~ls~e~L~~yi~~ar~~~~~p~ls~ea~~yI~~~y~~tR~~~~~~~~~~~~~  444 (506)
T 3f8t_A          367 FLS--HFDLIAFLGVDPRPGEPEEQDTEVPSYTLLRRYLLYAIREHPAPELTEEARKRLEHWYETRREEVEERLGMGLPT  444 (506)
T ss_dssp             HHT--TCSEEEETTC--------------CCHHHHHHHHHHHHHHCSCCEECHHHHHHHHHHHHHHHHHHHHHHHTTCCC
T ss_pred             Hhh--heeeEEEecCCCChhHhhcccCCCCCHHHHHHHHHHHHhcCCCceeCHHHHHHHHHHHHHHhcCccccccccccc
Confidence            999  9997654 467765431             11111    11121111   0000         0        035


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhc
Q 030960          118 DKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNV  157 (168)
Q Consensus       118 ~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~  157 (168)
                      -|.|++.+..+++-|...|.-+++..++.+|+.+|+.-+.
T Consensus       445 ~giSpR~leaLiRlA~A~A~L~gR~~V~~eDV~~Ai~L~~  484 (506)
T 3f8t_A          445 LPVTRRQLESVERLAKAHARMRLSDDVEPEDVDIAAELVD  484 (506)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHH
T ss_pred             ccccHHHHHHHHHHHHHHHHHcCcCCCCHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999997544

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=97.13  E-value=0.00048  Score=50.33  Aligned_cols=74  Identities=14%  Similarity=0.211  Sum_probs=52.6

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCC
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLP   91 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P   91 (168)
                      ..++||+|||++.+++.+..... . .   +    ++..+.. ....++-+|.+|+.+..|+.+++.  |++..+++++|
T Consensus        86 ~~~~vliIDEAq~l~~~~~~~~e-~-~---r----ll~~l~~-~r~~~~~iil~tq~~~~l~~~lr~--ri~~~~~l~~~  153 (199)
T 2r2a_A           86 NIGSIVIVDEAQDVWPARSAGSK-I-P---E----NVQWLNT-HRHQGIDIFVLTQGPKLLDQNLRT--LVRKHYHIASN  153 (199)
T ss_dssp             GTTCEEEETTGGGTSBCCCTTCC-C-C---H----HHHGGGG-TTTTTCEEEEEESCGGGBCHHHHT--TEEEEEEEEEC
T ss_pred             cCceEEEEEChhhhccCccccch-h-H---H----HHHHHHh-cCcCCeEEEEECCCHHHHhHHHHH--HhheEEEEcCc
Confidence            34899999999999876532211 1 1   2    4445543 334466778888889999999998  99999999887


Q ss_pred             CHHHHH
Q 030960           92 DRRQKR   97 (168)
Q Consensus        92 ~~~~R~   97 (168)
                      ....|.
T Consensus       154 ~~~~~~  159 (199)
T 2r2a_A          154 KMGMRT  159 (199)
T ss_dssp             SSCCEE
T ss_pred             ccCcce
Confidence            655543

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*

Probab=96.68  E-value=0.013  Score=45.58  Aligned_cols=133  Identities=11%  Similarity=0.064  Sum_probs=80.7

Q ss_pred             HHHHHHHHHHc----CCeEEEEccccc-ccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCC------C
Q 030960            2 VRDVFRLAKEN----APAIIFIDEVDA-IATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRA------D   70 (168)
Q Consensus         2 l~~iF~~a~~~----~p~ii~iDe~D~-l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~------~   70 (168)
                      ++++.+.+...    ..-||+|||+|. +..              ...+.++..++..  .+.+++|.+|+.+      .
T Consensus        61 ~~~l~~~~~~~plf~~~kvvii~~~~~kl~~--------------~~~~aLl~~le~p--~~~~~~il~~~~~~~~~~~~  124 (343)
T 1jr3_D           61 WNAIFSLCQAMSLFASRQTLLLLLPENGPNA--------------AINEQLLTLTGLL--HDDLLLIVRGNKLSKAQENA  124 (343)
T ss_dssp             HHHHHHHHHHHHHCCSCEEEEEECCSSCCCT--------------THHHHHHHHHTTC--BTTEEEEEEESCCCTTTTTS
T ss_pred             HHHHHHHhcCcCCccCCeEEEEECCCCCCCh--------------HHHHHHHHHHhcC--CCCeEEEEEcCCCChhhHhh
Confidence            35566665532    367999999987 421              2344566666642  2344444444443      4


Q ss_pred             CCCccccCCCCcceEEecCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCcc
Q 030960           71 TLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVI  144 (168)
Q Consensus        71 ~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i  144 (168)
                      .+.+++.+  |. ..+.+.+|+..+....++..+.      +...+..+++.++| +.+++.+.++.....+   +...|
T Consensus       125 k~~~~i~s--r~-~~~~~~~l~~~~l~~~l~~~~~~~g~~i~~~a~~~l~~~~~g-dl~~~~~elekl~l~~---~~~~I  197 (343)
T 1jr3_D          125 AWFTALAN--RS-VQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEG-NLLALAQALERLSLLW---PDGKL  197 (343)
T ss_dssp             HHHHHHTT--TC-EEEEECCCCTTHHHHHHHHHHHHTTCEECHHHHHHHHHSSTT-CHHHHHHHHHHHHHHC---TTCEE
T ss_pred             HHHHHHHh--Cc-eEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhch-HHHHHHHHHHHHHHhc---CCCCC
Confidence            57777777  54 5788999998888877775543      12234567776655 6666666666554432   34468


Q ss_pred             CHHHHHHHHHhhc
Q 030960          145 LPKDFEKGYRTNV  157 (168)
Q Consensus       145 ~~~d~~~al~~~~  157 (168)
                      |.+++.+.+....
T Consensus       198 t~e~V~~~~~~~~  210 (343)
T 1jr3_D          198 TLPRVEQAVNDAA  210 (343)
T ss_dssp             CHHHHHHHHHHHC
T ss_pred             CHHHHHHHHhhhh
Confidence            8888887766543

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=96.18  E-value=0.019  Score=44.16  Aligned_cols=105  Identities=15%  Similarity=0.220  Sum_probs=59.2

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC---------CCCccccCCCCc
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD---------TLDPALLRPGRL   82 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~---------~ld~al~r~grf   82 (168)
                      ..|.+|+|||++.+....    ...+......+..+....      .++.+|.|++...         .....+  .||+
T Consensus       127 ~~~~vlvlDe~~~~~~~~----~~~~~~~~~~L~~~~~~~------~~~~~il~g~~~~~l~~~l~~~~~~~~l--~~~~  194 (350)
T 2qen_A          127 LGEFIVAFDEAQYLRFYG----SRGGKELLALFAYAYDSL------PNLKIILTGSEVGLLHDFLKITDYESPL--YGRI  194 (350)
T ss_dssp             HSCEEEEEETGGGGGGBT----TTTTHHHHHHHHHHHHHC------TTEEEEEEESSHHHHHHHHCTTCTTSTT--TTCC
T ss_pred             cCCEEEEEeCHHHHhccC----ccchhhHHHHHHHHHHhc------CCeEEEEECCcHHHHHHHHhhcCCCCcc--ccCc
Confidence            359999999999986411    011122223333332221      3565666554321         111222  2477


Q ss_pred             ceEEecCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHH
Q 030960           83 DRKIEFPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAIC  129 (168)
Q Consensus        83 ~~~i~~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~  129 (168)
                      ...+.+++.+.++-.++++..+.      +...+..+...|.|+- .-+..++
T Consensus       195 ~~~i~l~pl~~~e~~~~l~~~~~~~~~~~~~~~~~~i~~~tgG~P-~~l~~~~  246 (350)
T 2qen_A          195 AGEVLVKPFDKDTSVEFLKRGFREVNLDVPENEIEEAVELLDGIP-GWLVVFG  246 (350)
T ss_dssp             CEEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHTTCH-HHHHHHH
T ss_pred             cceeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCH-HHHHHHH
Confidence            78999999999999999986542      1123456677777754 3344443

>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=96.17  E-value=0.032  Score=42.92  Aligned_cols=112  Identities=17%  Similarity=0.187  Sum_probs=65.4

Q ss_pred             HHHHHHHHHc--CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCC--------
Q 030960            3 RDVFRLAKEN--APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTL--------   72 (168)
Q Consensus         3 ~~iF~~a~~~--~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~l--------   72 (168)
                      ..+++.....  .|.+|+|||++.+....    +..   ....+..+....      .++.+|.|++....+        
T Consensus       125 ~~l~~~l~~~~~~~~vlvlDe~~~~~~~~----~~~---~~~~l~~~~~~~------~~~~~i~~g~~~~~l~~~l~~~~  191 (357)
T 2fna_A          125 ANLLESFEQASKDNVIIVLDEAQELVKLR----GVN---LLPALAYAYDNL------KRIKFIMSGSEMGLLYDYLRVED  191 (357)
T ss_dssp             HHHHHHHHHTCSSCEEEEEETGGGGGGCT----TCC---CHHHHHHHHHHC------TTEEEEEEESSHHHHHHHTTTTC
T ss_pred             HHHHHHHHhcCCCCeEEEEECHHHhhccC----chh---HHHHHHHHHHcC------CCeEEEEEcCchHHHHHHHhccC
Confidence            4555555543  49999999999986421    011   113333333221      256566666543211        


Q ss_pred             -CccccCCCCcceEEecCCCCHHHHHHHHHhhcC----CCCCHHHHHhCCCCCCHHHHHHHHH
Q 030960           73 -DPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLS----DEVDLEDYVSRPDKISAAEIAAICQ  130 (168)
Q Consensus        73 -d~al~r~grf~~~i~~~~P~~~~R~~il~~~l~----~~~~~~~la~~t~g~s~~di~~l~~  130 (168)
                       ...+  .||+...+.+++.+.++-.++++..+.    ...+...+...|.|+-. -+..++.
T Consensus       192 ~~~~l--~~r~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~~i~~~t~G~P~-~l~~~~~  251 (357)
T 2fna_A          192 PESPL--FGRAFSTVELKPFSREEAIEFLRRGFQEADIDFKDYEVVYEKIGGIPG-WLTYFGF  251 (357)
T ss_dssp             TTSTT--TTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCCCHHHHHHHHCSCHH-HHHHHHH
T ss_pred             CCCcc--ccCccceeecCCCCHHHHHHHHHHHHHHcCCCCCcHHHHHHHhCCCHH-HHHHHHH
Confidence             1122  347778999999999999999986542    22234778888888643 3444443

>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=94.89  E-value=0.017  Score=45.38  Aligned_cols=69  Identities=20%  Similarity=0.289  Sum_probs=39.0

Q ss_pred             HHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccc
Q 030960            3 RDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPAL   76 (168)
Q Consensus         3 ~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al   76 (168)
                      +.+++......  +|+||+++.+.........  .....+.+.+++..|.++.+..++.+|++|| +...|+++
T Consensus       174 ~~i~~~l~~~~--LLVIDsI~aL~~~~~~~s~--~G~v~~~lrqlL~~L~~~~k~~gvtVIlttn-p~s~deal  242 (331)
T 2vhj_A          174 DDIARAMLQHR--VIVIDSLKNVIGAAGGNTT--SGGISRGAFDLLSDIGAMAASRGCVVIASLN-PTSNDDKI  242 (331)
T ss_dssp             HHHHHHHHHCS--EEEEECCTTTC-------------CCHHHHHHHHHHHHHHHHHTCEEEEECC-CSSCSSSH
T ss_pred             HHHHHHHhhCC--EEEEecccccccccccccc--cchHHHHHHHHHHHHHHHHhhCCCEEEEEeC-CcccchhH
Confidence            44566666654  9999999999754422110  0011244555555555544455777888888 77777765

>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=94.62  E-value=0.12  Score=41.24  Aligned_cols=124  Identities=20%  Similarity=0.264  Sum_probs=62.2

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHh--ccCCCC----CCCeEEEEecCCCCCCCccccCCCCcce---
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQ--MDGFDQ----TVNVKVIMATNRADTLDPALLRPGRLDR---   84 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~--l~~~~~----~~~v~vi~ttn~~~~ld~al~r~grf~~---   84 (168)
                      ..+|||||++.+-.           ..+..+..++..  +..+..    ...+-+|++||..-  . .+...|+|..   
T Consensus       232 ~gtlfldei~~l~~-----------~~q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~at~~~l--~-~~~~~g~fr~dl~  297 (387)
T 1ny5_A          232 GGTLFLDEIGELSL-----------EAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRNI--K-ELVKEGKFREDLY  297 (387)
T ss_dssp             TSEEEEESGGGCCH-----------HHHHHHHHHHHHSEECCBTCCSBEECCCEEEEEESSCH--H-HHHHTTSSCHHHH
T ss_pred             CcEEEEcChhhCCH-----------HHHHHHHHHHhcCcEEeCCCCceeeccEEEEEeCCCCH--H-HHHHcCCccHHHH
Confidence            47999999998831           122223333332  111111    12577999998532  1 2334455532   


Q ss_pred             ----EEecCCCCH----HHHHHHHHhhcC-------C---CCCH---HHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCc
Q 030960           85 ----KIEFPLPDR----RQKRLVFQMNLS-------D---EVDL---EDYVSRPDKISAAEIAAICQEAGMHAVRKNRYV  143 (168)
Q Consensus        85 ----~i~~~~P~~----~~R~~il~~~l~-------~---~~~~---~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~  143 (168)
                          .+.+..|..    ++...++++++.       .   .++-   ..+..+.=--..++|+++++.|+..+   ....
T Consensus       298 ~rl~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~l~~~~wpGNvreL~~~i~~~~~~~---~~~~  374 (387)
T 1ny5_A          298 YRLGVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSYPWYGNVRELKNVIERAVLFS---EGKF  374 (387)
T ss_dssp             HHHTTEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCCCCEECHHHHHHHHHSCCTTHHHHHHHHHHHHHHHC---CSSE
T ss_pred             HhhcCCeecCCcchhccccHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhCCCCcHHHHHHHHHHHHHHhC---CCCc
Confidence                123334444    344444444432       1   1222   22333221113468999988887654   3357


Q ss_pred             cCHHHHHHHHH
Q 030960          144 ILPKDFEKGYR  154 (168)
Q Consensus       144 i~~~d~~~al~  154 (168)
                      |+.+|+...++
T Consensus       375 i~~~~l~~~~~  385 (387)
T 1ny5_A          375 IDRGELSCLVN  385 (387)
T ss_dssp             ECHHHHHHHC-
T ss_pred             CcHHHCcHhhh
Confidence            88888865543

>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=93.73  E-value=0.35  Score=38.26  Aligned_cols=84  Identities=11%  Similarity=0.170  Sum_probs=53.9

Q ss_pred             HHHHHHHHH--cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCc------
Q 030960            3 RDVFRLAKE--NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDP------   74 (168)
Q Consensus         3 ~~iF~~a~~--~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~------   74 (168)
                      ..+|..+..  ..|.++++||+..++...       .......+..++...    ...++.++.+|.++.++..      
T Consensus       250 ~~i~~~~~~~~~~~~~i~iDEa~~~~~~~-------~~~~~~~l~~~~~~~----Rk~g~~~~~~tQ~~~d~~~~~~~~~  318 (392)
T 4ag6_A          250 SFAWNILERDRRERTVLVVDEAWMLVDPQ-------TPQAIAFLRDTSKRI----RKYNGSLIVISQNVIDFLAPEVQRY  318 (392)
T ss_dssp             HHHHHHHHHSCCTTCEEEETTGGGGCCTT-------CTHHHHHHHHHHHHG----GGGTCEEEEEESCGGGGGSTTTHHH
T ss_pred             HHHHHHHHhCCCccEEEEEecHHHHhCcC-------chHHHHHHHHHHHHh----hhhCeEEEEEcCCHHHhhChhhHHH
Confidence            344555544  359999999999998431       122234455555554    2346778889999998875      


Q ss_pred             --cccCCCCcceEEecCCCCHHHHHHHH
Q 030960           75 --ALLRPGRLDRKIEFPLPDRRQKRLVF  100 (168)
Q Consensus        75 --al~r~grf~~~i~~~~P~~~~R~~il  100 (168)
                        +++.  ..+..|.++.+. .++..+-
T Consensus       319 ~~~il~--n~~~~i~l~~~~-~~~~~~~  343 (392)
T 4ag6_A          319 GQALLD--NPTYKLLLAQGE-KDLEAIT  343 (392)
T ss_dssp             HHHHHH--SCSEEEECSCCH-HHHHHHH
T ss_pred             HHHHHH--hhhhhheeCCCh-hhHHHHH
Confidence              4555  678888888764 4444443

>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=93.69  E-value=0.022  Score=45.46  Aligned_cols=71  Identities=17%  Similarity=0.228  Sum_probs=47.0

Q ss_pred             HcCCeEEEEcccccccc-cccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecC
Q 030960           11 ENAPAIIFIDEVDAIAT-ARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFP   89 (168)
Q Consensus        11 ~~~p~ii~iDe~D~l~~-~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~   89 (168)
                      ..+.+++++||++.+.. .+.... +..  . .....+...+++     .+.|+++||+++.+ +++.+|||++..++..
T Consensus       214 ~~q~~~~l~dd~~~~~~~~r~l~~-~~~--~-~~~~~l~~~ldG-----~v~v~~~tn~~~~l-~alf~pg~ld~~~~~l  283 (377)
T 1svm_A          214 AIDQFLVVFEDVKGTGGESRDLPS-GQG--I-NNLDNLRDYLDG-----SVKVNLEKKHLNKR-TQIFPPGIVTMNEYSV  283 (377)
T ss_dssp             GTTCSCEEETTCCCSTTTTTTCCC-CSH--H-HHHHTTHHHHHC-----SSCEEECCSSSCCE-EECCCCEEEEECSCCC
T ss_pred             hcchhHHHHHHHHHHHHHHhhccc-cCc--c-hHHHHHHHHhcC-----CCeEeeccCchhhH-HHhhcCcccChhHHhh
Confidence            34567889999999875 332111 111  0 012334444554     35578899999999 7999999999988886


Q ss_pred             CC
Q 030960           90 LP   91 (168)
Q Consensus        90 ~P   91 (168)
                      ++
T Consensus       284 ~~  285 (377)
T 1svm_A          284 PK  285 (377)
T ss_dssp             CH
T ss_pred             cH
Confidence            63

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=93.42  E-value=0.11  Score=35.13  Aligned_cols=47  Identities=11%  Similarity=0.179  Sum_probs=28.4

Q ss_pred             HHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCC
Q 030960            4 DVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRA   69 (168)
Q Consensus         4 ~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~   69 (168)
                      ..|+.|   .+++|||||+|.+-.              .....++..+..  ...++.+|+|||.+
T Consensus        70 ~~~~~a---~~g~l~ldei~~l~~--------------~~q~~Ll~~l~~--~~~~~~~I~~t~~~  116 (145)
T 3n70_A           70 DFIALA---QGGTLVLSHPEHLTR--------------EQQYHLVQLQSQ--EHRPFRLIGIGDTS  116 (145)
T ss_dssp             HHHHHH---TTSCEEEECGGGSCH--------------HHHHHHHHHHHS--SSCSSCEEEEESSC
T ss_pred             cHHHHc---CCcEEEEcChHHCCH--------------HHHHHHHHHHhh--cCCCEEEEEECCcC
Confidence            445554   468999999998842              122334444432  23356688888864

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=93.27  E-value=0.079  Score=50.63  Aligned_cols=71  Identities=15%  Similarity=0.178  Sum_probs=48.2

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccc---cCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATAR---FDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTL   72 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~---~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~l   72 (168)
                      ++.++..++..+|++|+||+++.+.+..   +...........+++++++..|.++....+++||.|.......
T Consensus      1494 l~~~~~lvr~~~~~lVVIDsi~al~p~~~~~g~~~~~~~~~~~R~lsqlL~~L~~~~~~~~v~VI~tNq~~~~~ 1567 (2050)
T 3cmu_A         1494 LEICDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNLKQSNTLLIFINQIRMKI 1567 (2050)
T ss_dssp             HHHHHHHHHHTCCSEEEESCGGGCCCHHHHHSCTTCCCTTHHHHHHHHHHHHHHHHHHTTTCEEEEEECEEECT
T ss_pred             HHHHHHHHhcCCCCEEEEcChhHhcccccccccccccccchHHHHHHHHHHHHHHHHHhCCcEEEEEccccccc
Confidence            4667888889999999999999999753   2111111111347888888888877666777777765443333

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=93.08  E-value=0.058  Score=36.57  Aligned_cols=49  Identities=12%  Similarity=0.262  Sum_probs=28.5

Q ss_pred             HHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCC
Q 030960            3 RDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRA   69 (168)
Q Consensus         3 ~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~   69 (168)
                      ..+|+.|   .+.+|||||+|.+...              ....++..++.- ...++.+|+|||.+
T Consensus        68 ~~~~~~a---~~~~l~lDei~~l~~~--------------~q~~Ll~~l~~~-~~~~~~iI~~tn~~  116 (143)
T 3co5_A           68 MELLQKA---EGGVLYVGDIAQYSRN--------------IQTGITFIIGKA-ERCRVRVIASCSYA  116 (143)
T ss_dssp             HHHHHHT---TTSEEEEEECTTCCHH--------------HHHHHHHHHHHH-TTTTCEEEEEEEEC
T ss_pred             hhHHHhC---CCCeEEEeChHHCCHH--------------HHHHHHHHHHhC-CCCCEEEEEecCCC
Confidence            3455554   3689999999988421              122233333321 13457788888864

>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=92.40  E-value=2.2  Score=42.25  Aligned_cols=118  Identities=13%  Similarity=0.129  Sum_probs=72.6

Q ss_pred             HHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHH----HHHHhccC-----------CCCCCCeEEEEecC
Q 030960            3 RDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILM----ELLNQMDG-----------FDQTVNVKVIMATN   67 (168)
Q Consensus         3 ~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~----~ll~~l~~-----------~~~~~~v~vi~ttn   67 (168)
                      ..+|.-|.+. ++.+++||++.+-.           ...++++    .++..+..           +.-.++..|++|.|
T Consensus       688 g~~~~g~~~~-Gaw~~~DE~nr~~~-----------evLs~l~~~l~~i~~al~~~~~~i~~~g~~i~l~~~~~vfiT~N  755 (2695)
T 4akg_A          688 SRLLVGITQI-GAWGCFDEFNRLDE-----------KVLSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLN  755 (2695)
T ss_dssp             HHHHHHHHHH-TCEEEEETTTSSCH-----------HHHHHHHHHHHHHHHHHHHTCSEEECSSSEEECCTTCEEEEEEC
T ss_pred             hHHHHHHHhc-CCEeeehhhhhcCh-----------HHHHHHHHHHHHHHHHHHcCCcEEeeCCcEEecCCCceEEEEeC
Confidence            4567766665 59999999997632           1223332    22222211           01234567888888


Q ss_pred             ----CCCCCCccccCCCCcceEEecCCCCHHHHHHHHHhhcC--CCCC--------HHHHHhCCC-----CCCHHHHHHH
Q 030960           68 ----RADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLS--DEVD--------LEDYVSRPD-----KISAAEIAAI  128 (168)
Q Consensus        68 ----~~~~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~--~~~~--------~~~la~~t~-----g~s~~di~~l  128 (168)
                          ....||+++++  || +.+.+..|+.+...+|+-...+  ....        +..+.+...     .|..+.|..+
T Consensus       756 Pgy~g~~eLP~~Lk~--~F-r~v~m~~Pd~~~i~ei~l~s~Gf~~a~~la~kiv~~~~l~~e~ls~q~hydfglRalksv  832 (2695)
T 4akg_A          756 PGYNGRSELPENLKK--SF-REFSMKSPQSGTIAEMILQIMGFEDSKSLASKIVHFLELLSSKCSSMNHYHFGLRTLKGV  832 (2695)
T ss_dssp             CCSSSSCCCCHHHHT--TE-EEEECCCCCHHHHHHHHHHHHHCSSHHHHHHHHHHHHHHHHHHSCCCTTCCCSHHHHHHH
T ss_pred             CCccCcccccHHHHh--he-EEEEeeCCCHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHHHhCcCCcccccHHHHHHH
Confidence                56689999998  88 6899999999999998643221  1111        111222222     3788999998


Q ss_pred             HHHHHHH
Q 030960          129 CQEAGMH  135 (168)
Q Consensus       129 ~~~a~~~  135 (168)
                      +..|...
T Consensus       833 L~~ag~l  839 (2695)
T 4akg_A          833 LRNCSPL  839 (2695)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            8876543

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=90.77  E-value=0.64  Score=46.46  Aligned_cols=81  Identities=14%  Similarity=0.220  Sum_probs=54.8

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhc---cC----CCCCCCeEEEEecCCC-----CCCCccccCCCC
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQM---DG----FDQTVNVKVIMATNRA-----DTLDPALLRPGR   81 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l---~~----~~~~~~v~vi~ttn~~-----~~ld~al~r~gr   81 (168)
                      ..|+||||++---...     ........++.+++..-   +.    ...-.++.+|||.|.|     ..|+++++|  |
T Consensus      1375 ~~VlFiDDiNmp~~D~-----yGtQ~~ielLrqlld~~g~yd~~~~~~~~i~d~~~vaamnPp~~gGr~~l~~Rf~r--~ 1447 (3245)
T 3vkg_A         1375 WLVVFCDEINLPSTDK-----YGTQRVITFIRQMVEKGGFWRTSDHTWIKLDKIQFVGACNPPTDAGRVQLTHRFLR--H 1447 (3245)
T ss_dssp             EEEEEETTTTCCCCCT-----TSCCHHHHHHHHHHHHSEEEETTTTEEEEESSEEEEEEECCTTSTTCCCCCHHHHT--T
T ss_pred             eEEEEecccCCCCccc-----cccccHHHHHHHHHHcCCeEECCCCeEEEecCeEEEEEcCCCCCCCCccCCHHHHh--h
Confidence            4799999998532222     11222335556665431   11    0112357899999987     579999999  9


Q ss_pred             cceEEecCCCCHHHHHHHHHh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQM  102 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~  102 (168)
                      |.. ++++.|+.+.-..|+..
T Consensus      1448 F~v-i~i~~ps~esL~~If~t 1467 (3245)
T 3vkg_A         1448 API-LLVDFPSTSSLTQIYGT 1467 (3245)
T ss_dssp             CCE-EECCCCCHHHHHHHHHH
T ss_pred             ceE-EEeCCCCHHHHHHHHHH
Confidence            976 89999999999999763

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=88.84  E-value=0.53  Score=39.61  Aligned_cols=75  Identities=13%  Similarity=0.365  Sum_probs=54.8

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC--CCCccccCCCCcceEEecCCC
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD--TLDPALLRPGRLDRKIEFPLP   91 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~--~ld~al~r~grf~~~i~~~~P   91 (168)
                      +.+|+|||+..++...       .......+..+.    ..-..-+|.+|.+|.+|.  .|+..++.  -|...|.+...
T Consensus       344 ~ivvVIDE~~~L~~~~-------~~~~~~~L~~Ia----r~GRa~GIhLIlaTQRPs~d~I~~~Ira--n~~~RI~lrv~  410 (574)
T 2iut_A          344 TIVVVVDEFADMMMIV-------GKKVEELIARIA----QKARAAGIHLILATQRPSVDVITGLIKA--NIPTRIAFQVS  410 (574)
T ss_dssp             EEEEEESCCTTHHHHT-------CHHHHHHHHHHH----HHCTTTTEEEEEEESCCCTTTSCHHHHH--TCCEEEEECCS
T ss_pred             cEEEEEeCHHHHhhhh-------hHHHHHHHHHHH----HHHhhCCeEEEEEecCcccccccHHHHh--hhccEEEEEcC
Confidence            3689999999887432       112223333322    223456899999999998  89888887  89999999999


Q ss_pred             CHHHHHHHHH
Q 030960           92 DRRQKRLVFQ  101 (168)
Q Consensus        92 ~~~~R~~il~  101 (168)
                      +..+...++.
T Consensus       411 s~~Dsr~ILd  420 (574)
T 2iut_A          411 SKIDSRTILD  420 (574)
T ss_dssp             CHHHHHHHHS
T ss_pred             CHHHHHHhcC
Confidence            9999888884

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=88.76  E-value=0.14  Score=35.05  Aligned_cols=61  Identities=13%  Similarity=0.280  Sum_probs=32.2

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCC-eEEEEecCCCCCCC--ccccCCCCcceEEecC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVN-VKVIMATNRADTLD--PALLRPGRLDRKIEFP   89 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~-v~vi~ttn~~~~ld--~al~r~grf~~~i~~~   89 (168)
                      .|.+|+|||++.+....           +..+-.+++.+.   .... +++|.+...|..+.  +.+.+  |+..-..+.
T Consensus        83 ~~~lLilDE~~~~~~~~-----------~~~l~~li~~~~---~~g~~~iiits~~~p~~l~~~~~L~S--Rl~~g~~~~  146 (149)
T 2kjq_A           83 EAEYLAVDQVEKLGNEE-----------QALLFSIFNRFR---NSGKGFLLLGSEYTPQQLVIREDLRT--RMAYCLVYE  146 (149)
T ss_dssp             GCSEEEEESTTCCCSHH-----------HHHHHHHHHHHH---HHTCCEEEEEESSCTTTSSCCHHHHH--HGGGSEECC
T ss_pred             CCCEEEEeCccccChHH-----------HHHHHHHHHHHH---HcCCcEEEEECCCCHHHccccHHHHH--HHhcCeeEE
Confidence            58899999998753211           233333444332   2223 34554443565554  66776  766544443

>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=87.97  E-value=0.51  Score=37.25  Aligned_cols=75  Identities=25%  Similarity=0.475  Sum_probs=40.0

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhcc-----CCCCC----CCeEEEEecCCCCCCCccccCCCCcce
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMD-----GFDQT----VNVKVIMATNRADTLDPALLRPGRLDR   84 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~-----~~~~~----~~v~vi~ttn~~~~ld~al~r~grf~~   84 (168)
                      ...||+||++.+-.              .+...++..++     .+...    ..+-+|++||.  ++. .....|+|..
T Consensus       223 ~gtlfldei~~l~~--------------~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~at~~--~l~-~~v~~g~fr~  285 (368)
T 3dzd_A          223 QGTLFLDEVGELDQ--------------RVQAKLLRVLETGSFTRLGGNQKIEVDIRVISATNK--NLE-EEIKKGNFRE  285 (368)
T ss_dssp             TSEEEEETGGGSCH--------------HHHHHHHHHHHHSEECCBTCCCBEECCCEEEEEESS--CHH-HHHHTTSSCH
T ss_pred             CCeEEecChhhCCH--------------HHHHHHHHHHHhCCcccCCCCcceeeeeEEEEecCC--CHH-HHHHcCCccH
Confidence            46899999998831              22223333332     11111    24678888884  232 3334566644


Q ss_pred             ---------EEecCCCCH--HHHHHHHHhhcC
Q 030960           85 ---------KIEFPLPDR--RQKRLVFQMNLS  105 (168)
Q Consensus        85 ---------~i~~~~P~~--~~R~~il~~~l~  105 (168)
                               .|++|+...  ++...++++++.
T Consensus       286 dL~~rl~~~~i~lPpLreR~~Di~~l~~~~l~  317 (368)
T 3dzd_A          286 DLYYRLSVFQIYLPPLRERGKDVILLAEYFLK  317 (368)
T ss_dssp             HHHHHHTSEEEECCCGGGSTTHHHHHHHHHHH
T ss_pred             HHHHHhCCeEEeCCChhhchhhHHHHHHHHHH
Confidence                     456665544  555555555543

>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=85.43  E-value=1.4  Score=30.45  Aligned_cols=45  Identities=9%  Similarity=0.116  Sum_probs=25.5

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD   70 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~   70 (168)
                      .|.+|+|||++....         +......+..++....   . .+..+|.|||.+.
T Consensus       100 ~~~llilDE~~~~~~---------~~~~~~~l~~ll~~~~---~-~~~~ii~tsn~~~  144 (180)
T 3ec2_A          100 NSPVLVLDDLGSERL---------SDWQRELISYIITYRY---N-NLKSTIITTNYSL  144 (180)
T ss_dssp             TCSEEEEETCSSSCC---------CHHHHHHHHHHHHHHH---H-TTCEEEEECCCCS
T ss_pred             CCCEEEEeCCCCCcC---------CHHHHHHHHHHHHHHH---H-cCCCEEEEcCCCh
Confidence            589999999985421         1222344444444432   1 2345777777654

>1taf_B TFIID TBP associated factor 62; transcription initiation, histone fold, complex (TWO transcr factors); 2.00A {Drosophila melanogaster} SCOP: a.22.1.3

Probab=81.78  E-value=2.5  Score=25.23  Aligned_cols=31  Identities=16%  Similarity=0.269  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960          124 EIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus       124 di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      -+..++++|...+...+++.++.+|+..|++
T Consensus        39 r~~eI~qeA~kfmrHakRk~Lt~~DI~~Alk   69 (70)
T 1taf_B           39 KLKRIVQDAAKFMNHAKRQKLSVRDIDMSLK   69 (70)
T ss_dssp             HHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHcCCCeecHHHHHHHHc
Confidence            3556677787777788889999999999985

>1b67_A Protein (histone HMFA); DNA binding protein; 1.48A {Methanothermus fervidus} SCOP: a.22.1.2 PDB: 1hta_A 1a7w_A 1b6w_A 1bfm_A

Probab=81.02  E-value=2.5  Score=24.71  Aligned_cols=34  Identities=24%  Similarity=0.098  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960          123 AEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus       123 ~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      .-|..+..+|...|...+++.|+.+|+..|++..
T Consensus        34 ~fi~~l~~~A~~~a~~~kRkTI~~~Di~~A~~~l   67 (68)
T 1b67_A           34 EMGEEIASEAVKLAKHAGRKTIKAEDIELARKMF   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHTTCSEECHHHHHHHGGGG
T ss_pred             HHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhc
Confidence            4566777888888888899999999999998764

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=80.23  E-value=1.4  Score=36.53  Aligned_cols=75  Identities=15%  Similarity=0.412  Sum_probs=53.3

Q ss_pred             Ce-EEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC--CCCccccCCCCcceEEecCC
Q 030960           14 PA-IIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD--TLDPALLRPGRLDRKIEFPL   90 (168)
Q Consensus        14 p~-ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~--~ld~al~r~grf~~~i~~~~   90 (168)
                      |- +|+|||+..++...       ...    +..++..+-..-..-++.+|.+|.+|.  .++..++.  -|...|.+..
T Consensus       297 P~ivlvIDE~~~ll~~~-------~~~----~~~~l~~Lar~gRa~GI~LIlaTQrp~~dvl~~~i~~--n~~~RI~lrv  363 (512)
T 2ius_A          297 PYIVVLVDEFADLMMTV-------GKK----VEELIARLAQKARAAGIHLVLATQRPSVDVITGLIKA--NIPTRIAFTV  363 (512)
T ss_dssp             CEEEEEEETHHHHHHHH-------HHH----HHHHHHHHHHHCGGGTEEEEEEESCCCTTTSCHHHHH--HCCEEEEECC
T ss_pred             CcEEEEEeCHHHHHhhh-------hHH----HHHHHHHHHHHhhhCCcEEEEEecCCccccccHHHHh--hcCCeEEEEc
Confidence            64 89999998876421       111    223333332223445788999999998  58877877  8999999999


Q ss_pred             CCHHHHHHHHH
Q 030960           91 PDRRQKRLVFQ  101 (168)
Q Consensus        91 P~~~~R~~il~  101 (168)
                      .+..+...++.
T Consensus       364 ~s~~dsr~ilg  374 (512)
T 2ius_A          364 SSKIDSRTILD  374 (512)
T ss_dssp             SSHHHHHHHHS
T ss_pred             CCHHHHHHhcC
Confidence            99999998886

---

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	168
d1lv7a_	256	c.37.1.20 (A:) AAA domain of cell division protein	3e-57
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	3e-57
d1r7ra3	265	c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p	1e-35
d1w44a_	321	c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [Ta	1e-23
d1e32a2	258	c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p	5e-22
d1svma_	362	c.37.1.20 (A:) Papillomavirus large T antigen heli	6e-12
d1gvnb_	273	c.37.1.21 (B:) Plasmid maintenance system epsilon/	4e-10
d1d2na_	246	c.37.1.20 (A:) Hexamerization domain of N-ethylmal	3e-09
d1ofha_	309	c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId	4e-06
d1fnna2	276	c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrob	2e-05
d1w5sa2	287	c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-t	7e-04

>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 =  178 bits (452), Expect = 3e-57
 Identities = 62/156 (39%), Positives = 89/156 (57%), Gaps = 5/156 (3%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
            VRD+F  AK+ AP IIFIDE+DA+   R     G   E ++ L ++L +MDGF+    +
Sbjct: 92  RVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGI 151

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
            VI ATNR D LDPALLRPGR DR++   LPD R +  + +     + L+ ++D      
Sbjct: 152 IVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIAR 211

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
                S A++A +  EA + A R N+ V+   +FEK
Sbjct: 212 GTPGFSGADLANLVNEAALFAARGNKRVVSMVEFEK 247

>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 =  177 bits (450), Expect = 3e-57
 Identities = 61/156 (39%), Positives = 89/156 (57%), Gaps = 5/156 (3%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
            VRD+F  AK +AP I+FIDE+DA+   R     G + E ++ L +LL +MDGF++   +
Sbjct: 89  RVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAI 148

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQ-----MNLSDEVDLEDYVS 115
            V+ ATNR D LDPALLRPGR DR+I    PD + +  + +       L+++VDL     
Sbjct: 149 VVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAK 208

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
           R      A++  +  EA + A R+ R  I  KD E+
Sbjct: 209 RTPGFVGADLENLLNEAALLAAREGRRKITMKDLEE 244

>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 =  123 bits (308), Expect = 1e-35
 Identities = 56/156 (35%), Positives = 88/156 (56%), Gaps = 5/156 (3%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
            VR++F  A++ AP ++F DE+D+IA AR            R++ ++L +MDG     NV
Sbjct: 88  NVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNV 147

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPD-----RRQKRLVFQMNLSDEVDLEDYVS 115
            +I ATNR D +DPA+LRPGRLD+ I  PLPD        K  + +  ++ +VDLE    
Sbjct: 148 FIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAK 207

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
             +  S A++  ICQ A   A+R++    + ++ E+
Sbjct: 208 MTNGFSGADLTEICQRACKLAIRESIESEIRRERER 243

>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 = 92.0 bits (228), Expect = 1e-23
 Identities = 20/153 (13%), Positives = 41/153 (26%), Gaps = 18/153 (11%)

Query: 2   VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVK 61
           V D+ R   +    +I ID +  +  A     T       R   +LL+ +     +    
Sbjct: 173 VDDIARAMLQ--HRVIVIDSLKNVIGAAGGNTTSGGIS--RGAFDLLSDIGAMAASRGCV 228

Query: 62  VIMATNRA---DTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSDEVDLEDYVSRPD 118
           VI + N     D +   +    R +        D   +  V                   
Sbjct: 229 VIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGL----------- 277

Query: 119 KISAAEIAAICQEAGMHAVRKNRYVILPKDFEK 151
           +     +     E  +  +  ++     +   K
Sbjct: 278 QRLTHTLQTSYGEHSVLTIHTSKQSGGKQASGK 310

>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 = 87.0 bits (214), Expect = 5e-22
 Identities = 63/172 (36%), Positives = 93/172 (54%), Gaps = 10/172 (5%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
            +R  F  A++NAPAIIFIDE+DAIA  R       +R   RI+ +LL  MDG  Q  +V
Sbjct: 85  NLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVER---RIVSQLLTLMDGLKQRAHV 141

Query: 61  KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD-----EVDLEDYVS 115
            V+ ATNR +++DPAL R GR DR+++  +PD   +  + Q++  +     +VDLE   +
Sbjct: 142 IVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVAN 201

Query: 116 RPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNVKKPDT--DFE 165
                  A++AA+C EA + A+RK   +I  +D             T  DF 
Sbjct: 202 ETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFR 253

>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 = 60.5 bits (146), Expect = 6e-12
 Identities = 16/147 (10%), Positives = 37/147 (25%), Gaps = 17/147 (11%)

Query: 9   AKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNR 68
              + P+   I+ +D +      +      +        +              I+  N 
Sbjct: 216 ESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPP----------GIVTMNE 265

Query: 69  ADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSD----EVDLEDYVSRPDKISAAE 124
                       R  ++I+F   D  +  L     L +    +  +   +        AE
Sbjct: 266 ---YSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAE 322

Query: 125 IAAICQEAGMHAVRKNRYVILPKDFEK 151
            A   Q   +    +         ++K
Sbjct: 323 FAQSIQSRIVEWKERLDKEFSLSVYQK 349

>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 = 55.0 bits (131), Expect = 4e-10
 Identities = 14/162 (8%), Positives = 37/162 (22%), Gaps = 12/162 (7%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMEL--------LNQMD 52
             +DV +     +  +                  G  R     +             +M 
Sbjct: 82  YEKDVVKHVTPYSNRMTEAIISRLSDQGYNLVIEGTGRTTDVPIQTATMLQAKGYETKMY 141

Query: 53  GFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSDEVDLED 112
                     +    R +T+        R   K    +  +     +  ++ +       
Sbjct: 142 VMAVPKINSYLGTIERYETMYADDPMTARATPKQAHDIVVKNLPTNLETLHKTGLFSDIR 201

Query: 113 YVSRPDKI--SAAEIAAICQEAGMHAVRKNRYVILPKDFEKG 152
             +R      S+ E  +I  +  +      +     K+ +  
Sbjct: 202 LYNREGVKLYSSLETPSISPKETLEKELNRKVS--GKEIQPT 241

>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 = 51.9 bits (123), Expect = 3e-09
 Identities = 21/147 (14%), Positives = 46/147 (31%), Gaps = 11/147 (7%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNV 60
            ++ +F  A ++  + + +D+++ +            R    +L  LL  +         
Sbjct: 88  AMKKIFDDAYKSQLSCVVVDDIERLLDYVPIG----PRFSNLVLQALLVLLKKAPPQGRK 143

Query: 61  KV-IMATNRADTLDPALLRPGRLDRKIEFP-LPDRRQ--KRLVFQMNLSDE--VDLEDYV 114
            + I  T+R D L    +        I  P +    Q  + L    N  D+    +   V
Sbjct: 144 LLIIGTTSRKDVLQEMEML-NAFSTTIHVPNIATGEQLLEALELLGNFKDKERTTIAQQV 202

Query: 115 SRPDKISAAEIAAICQEAGMHAVRKNR 141
                    +   +  E  +    + R
Sbjct: 203 KGKKVWIGIKKLLMLIEMSLQMDPEYR 229

>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 = 43.3 bits (101), Expect = 4e-06
 Identities = 23/142 (16%), Positives = 46/142 (32%), Gaps = 12/142 (8%)

Query: 12  NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATN---- 67
               I+FIDE+D I      +  GAD   + +  +LL  ++G   +    ++   +    
Sbjct: 114 EQNGIVFIDEIDKICKKGEYS--GADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFI 171

Query: 68  ------RADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSDEVDLEDYVSRPDKIS 121
                  A   D      GRL  ++E           +     +   +    +   + ++
Sbjct: 172 ASGAFQVARPSDLIPELQGRLPIRVELTALSAADFERILTEPHASLTEQYKALMATEGVN 231

Query: 122 AAEIAAICQEAGMHAVRKNRYV 143
            A      ++    A R N   
Sbjct: 232 IAFTTDAVKKIAEAAFRVNEKT 253

>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 = 40.9 bits (94), Expect = 2e-05
 Identities = 15/175 (8%), Positives = 35/175 (20%), Gaps = 24/175 (13%)

Query: 1   MVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRI------LMELLNQMDGF 54
                    +       F+  +      R         +   +          L Q    
Sbjct: 94  ARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADK 153

Query: 55  DQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD----------RRQKRLVFQMNL 104
                + +++  +    L+        +  K                   + +       
Sbjct: 154 LGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGS 213

Query: 105 SDEVDLEDYVSRPDKISAAEIAA--------ICQEAGMHAVRKNRYVILPKDFEK 151
             E  L+         +  +           I   +   A +  R  I P+D  K
Sbjct: 214 YSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPEDVRK 268

>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 = 36.7 bits (83), Expect = 7e-04
 Identities = 13/157 (8%), Positives = 39/157 (24%), Gaps = 16/157 (10%)

Query: 9   AKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNR 68
             EN   ++ +DE  ++ ++        D      + E +   DG ++   + V      
Sbjct: 128 YVENHYLLVILDEFQSMLSSPRI--AAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRA 185

Query: 69  ADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLSDEVDLEDYVSRPDKISAAEIAA- 127
              +   + +              + ++        ++    +           +++   
Sbjct: 186 LSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGE 245

Query: 128 -------------ICQEAGMHAVRKNRYVILPKDFEK 151
                          + A   A    R  +      K
Sbjct: 246 DKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRK 282

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	168
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	100.0
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	100.0
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	100.0
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	100.0
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.68
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.67
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.22
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	98.99
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.89
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	98.73
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	98.64
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	98.59
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.4
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.37
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	98.34
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.32
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.3
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.29
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.24
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	98.24
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	97.83
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.74
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	97.65
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.63
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.28
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	97.28
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.24
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	96.79
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	95.93
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	93.44
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	90.44
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	89.72
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	89.39
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	88.98
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	83.98
d1ku5a_	66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	83.23
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	82.01
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	81.59
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	80.68

>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=100.00  E-value=1.1e-37  Score=237.67  Aligned_cols=156  Identities=39%  Similarity=0.625  Sum_probs=145.4

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      |+.+|+.|++++||||||||+|.++++|+......+....+++++|++.++++...++|+||||||+|+.||++++||||
T Consensus        93 l~~~f~~A~~~~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~v~vIatTn~~~~ld~al~R~gR  172 (256)
T d1lv7a_          93 VRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGR  172 (256)
T ss_dssp             HHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEEESCTTTSCGGGGSTTS
T ss_pred             HHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCcccCCHhHcCCCC
Confidence            68999999999999999999999999887666655566678999999999999888899999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      ||+.|+|++|+.++|.+||+.++.     .+.++..+++.|+|||++||.++|++|+..++++++..++.+||+.|++++
T Consensus       173 fd~~i~i~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~G~s~adi~~l~~~A~~~a~~~~~~~i~~~d~~~Al~rv  252 (256)
T d1lv7a_         173 FDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARGNKRVVSMVEFEKAKDKI  252 (256)
T ss_dssp             SCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             CCEEEECCCcCHHHHHHHHHHhccCCCcCcccCHHHHHHhCCCCCHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHH
Confidence            999999999999999999997776     478999999999999999999999999999999999999999999999987


Q ss_pred             c
Q 030960          157 V  157 (168)
Q Consensus       157 ~  157 (168)
                      .
T Consensus       253 ~  253 (256)
T d1lv7a_         253 M  253 (256)
T ss_dssp             T
T ss_pred             h
Confidence            5

>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=100.00  E-value=4.9e-37  Score=233.12  Aligned_cols=152  Identities=39%  Similarity=0.652  Sum_probs=135.9

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      |+++|+.|+.++||||||||+|.++++++......+....++++.|++.|+++...++|+||+|||+|+.+|++++||||
T Consensus        90 l~~~f~~a~~~~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~vivi~tTn~~~~ld~al~R~~R  169 (247)
T d1ixza_          90 VRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGR  169 (247)
T ss_dssp             HHHHHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGGGSCGGGGSTTS
T ss_pred             HHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCccccCHhHcCCCC
Confidence            68999999999999999999999999887766666667778999999999999888899999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      ||+.|+|++|+.++|.+||+.++.     .+.+++.+|+.|+|||++||.++|++|+..|+++++..|+.+||++|+
T Consensus       170 f~~~i~~~~P~~~eR~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~lv~~A~l~a~~~~~~~i~~~d~~~A~  246 (247)
T d1ixza_         170 FDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREGRRKITMKDLEEAA  246 (247)
T ss_dssp             SCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHT
T ss_pred             CcEEEEECCcCHHHHHHHHHHHhcccCCccccCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHhh
Confidence            999999999999999999998775     578899999999999999999999999999999999999999999986

>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=100.00  E-value=4.3e-35  Score=223.68  Aligned_cols=151  Identities=40%  Similarity=0.641  Sum_probs=134.9

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|+.|+.++||||||||+|.++++++...+..   ..++++.++..+++.....+|+||+|||+|+.+|++++||||
T Consensus        86 l~~~f~~A~~~~p~il~iDeid~l~~~r~~~~~~~---~~~~~~~~~~~~~~~~~~~~vlvi~tTn~~~~ld~al~r~gR  162 (258)
T d1e32a2          86 LRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEV---ERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGR  162 (258)
T ss_dssp             HHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTT---HHHHHHHHHHHHHTCCCSSCEEEEEEESCGGGSCGGGTSTTS
T ss_pred             HHHHHHHHHhcCCeEEEehhhhhhccCCCCCCCch---HHHHHHHhccccccccccCCccEEEeCCCccccchhhhhccc
Confidence            67899999999999999999999998885544333   347888888889888888899999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCC---------------
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNR---------------  141 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~---------------  141 (168)
                      ||+.|+|++|+.++|.+||+.++.     .+.++..+|+.|+|||++||.++|++|+..|++++.               
T Consensus       163 fd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~G~s~adl~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~  242 (258)
T d1e32a2         163 FDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVM  242 (258)
T ss_dssp             SCEEEECCCCCHHHHHHHHHHTTTTSCBCTTCCHHHHHHHCTTCCHHHHHHHHHHHHHHHHHHHHHHHCCCSSCCBHHHH
T ss_pred             ccceeECCCCCHHHHHHHhhhhccCcccccccchhhhhhcccCCCHHHHHHHHHHHHHHHHHhhccccchhhhhhhhhhh
Confidence            999999999999999999998876     467899999999999999999999999999988741               


Q ss_pred             --CccCHHHHHHHHHh
Q 030960          142 --YVILPKDFEKGYRT  155 (168)
Q Consensus       142 --~~i~~~d~~~al~~  155 (168)
                        ..++.+||+.|+.+
T Consensus       243 ~~~~it~~Df~~AL~~  258 (258)
T d1e32a2         243 NSLAVTMDDFRWALSQ  258 (258)
T ss_dssp             HHCCBCHHHHHHHHTC
T ss_pred             ccCccCHHHHHHHhCc
Confidence              35899999999863

>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=100.00  E-value=3.3e-33  Score=213.95  Aligned_cols=139  Identities=40%  Similarity=0.682  Sum_probs=123.1

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGR   81 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gr   81 (168)
                      ++.+|..|+.++||||||||+|.++.+++...........++++.+++.++++...++|+||||||+|+.||++++||||
T Consensus        89 l~~~f~~A~~~~p~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gR  168 (265)
T d1r7ra3          89 VREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGR  168 (265)
T ss_dssp             HHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC------CCEEEECCBSCTTTSCGGGSSTT
T ss_pred             HHHHHHHHHhcCCcceeHHhhhhccccCCCcCCCCcHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCCchhCCHHHhCCCC
Confidence            67899999999999999999999999887666666666778999999999999888889999999999999999999999


Q ss_pred             cceEEecCCCCHHHHHHHHHhhcC-----CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhC
Q 030960           82 LDRKIEFPLPDRRQKRLVFQMNLS-----DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKN  140 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~~~l~-----~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~  140 (168)
                      |+++|+|++|+.++|.+||+.++.     .++++..+++.|+|||++||.++|++|...|+++.
T Consensus       169 f~~~i~~~~p~~~~R~~il~~~l~~~~~~~~~~l~~la~~t~g~s~~di~~lv~~A~~~A~~~~  232 (265)
T d1r7ra3         169 LDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRES  232 (265)
T ss_dssp             SEEEEECCCCCCHHHHHHHHHHTTCC----CCCCHHHHHHHCSSCCHHHHHHHHHHHHHHHHHC
T ss_pred             ccEEEEecchHHHHHHHHHHHHhccCCchhhhhHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999998776     47899999999999999999999999999999874

>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=99.68  E-value=2.7e-17  Score=123.58  Aligned_cols=152  Identities=12%  Similarity=0.068  Sum_probs=102.0

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCC-CCCeEEEEecCCCCCCCccccCCC
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQ-TVNVKVIMATNRADTLDPALLRPG   80 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~-~~~v~vi~ttn~~~~ld~al~r~g   80 (168)
                      ++.+|+.|++.+||||||||+|.++..+.......    ..+++.++..+++... ..+|+||||||+++.+|++.++ +
T Consensus        89 i~~if~~A~~~~p~il~iDEid~l~~~~~~~~~~~----~~~~~~ll~~l~~~~~~~~~v~vi~tTn~~~~ld~~~~~-~  163 (246)
T d1d2na_          89 MKKIFDDAYKSQLSCVVVDDIERLLDYVPIGPRFS----NLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEML-N  163 (246)
T ss_dssp             HHHHHHHHHTSSEEEEEECCHHHHTTCBTTTTBCC----HHHHHHHHHHTTCCCSTTCEEEEEEEESCHHHHHHTTCT-T
T ss_pred             hhhhhhhhhhcccceeehhhhhhHhhhcccccchh----HHHHHHHHHHhcCCCccccceeeeeccCChhhccchhhc-C
Confidence            68899999999999999999999987764332222    3778889999988744 4479999999999999976443 6


Q ss_pred             CcceEEecCCC-CHHHHHHHHHhhcC-CCCCHHHHHhCCCCCCHH-HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHhhc
Q 030960           81 RLDRKIEFPLP-DRRQKRLVFQMNLS-DEVDLEDYVSRPDKISAA-EIAAICQEAGMHAVRKNRYVILPKDFEKGYRTNV  157 (168)
Q Consensus        81 rf~~~i~~~~P-~~~~R~~il~~~l~-~~~~~~~la~~t~g~s~~-di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~~~  157 (168)
                      ||+..|++|.| ..+++.++++..-. ...++..+++.+.|.+.. .++.++.. ...+ ....+.....+|...+++..
T Consensus       164 rF~~~i~~P~~~~r~~il~~l~~~~~~~~~~~~~i~~~~~g~~~~~~ik~ll~~-ie~a-~~~~~~~~~~~~l~~l~e~g  241 (246)
T d1d2na_         164 AFSTTIHVPNIATGEQLLEALELLGNFKDKERTTIAQQVKGKKVWIGIKKLLML-IEMS-LQMDPEYRVRKFLALLREEG  241 (246)
T ss_dssp             TSSEEEECCCEEEHHHHHHHHHHHTCSCHHHHHHHHHHHTTSEEEECHHHHHHH-HHHH-TTSCGGGHHHHHHHHHHHTS
T ss_pred             ccceEEecCCchhHHHHHHHHHhccCCChHHHHHHHHHcCCCccchhHHHHHHH-HHHH-HhcCcccHHHHHHHHHHhcC
Confidence            99999999544 34455555554322 344567788888775421 23433321 1111 22333445667777777665


Q ss_pred             CCC
Q 030960          158 KKP  160 (168)
Q Consensus       158 p~~  160 (168)
                      +.+
T Consensus       242 ~~~  244 (246)
T d1d2na_         242 ASP  244 (246)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            543

>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=99.67  E-value=6.8e-20  Score=142.25  Aligned_cols=99  Identities=17%  Similarity=0.174  Sum_probs=76.9

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCC----CCcccc
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADT----LDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~----ld~al~   77 (168)
                      ++++|+.|+.  ||||||||+|.++++|+.....  ....++++++|++||++....+|+|||||| |+.    +|+++.
T Consensus       173 ~~~~f~~a~~--~~ilf~DEid~~~~~r~~~~~~--~~~~r~v~~lL~e~dg~~~~~~v~viaatN-~~~~~~~i~~~~~  247 (321)
T d1w44a_         173 VDDIARAMLQ--HRVIVIDSLKNVIGAAGGNTTS--GGISRGAFDLLSDIGAMAASRGCVVIASLN-PTSNDDKIVELVK  247 (321)
T ss_dssp             HHHHHHHHHH--CSEEEEECCTTTC-------------CCHHHHHHHHHHHHHHHHHTCEEEEECC-CCCCCHHHHHHHH
T ss_pred             HHHHHHHHhh--ccEEEeehhhhhccccccCCCC--CcchhhhhhhhhhccccccCCCeEEEEeCC-Ccccccchhhhhh
Confidence            6899999985  8999999999999988543321  122389999999999998888999999999 544    555668


Q ss_pred             CCCCcceEEecCCCCHHHHHHHHHhhcC
Q 030960           78 RPGRLDRKIEFPLPDRRQKRLVFQMNLS  105 (168)
Q Consensus        78 r~grf~~~i~~~~P~~~~R~~il~~~l~  105 (168)
                      ||||||..+++++|+.++|.+|++.+..
T Consensus       248 r~~Rf~~~v~v~~pd~~~r~~il~~~~~  275 (321)
T d1w44a_         248 EASRSNSTSLVISTDVDGEWQVLTRTGE  275 (321)
T ss_dssp             HHHHHSCSEEEEECSSTTEEEEEEECBT
T ss_pred             ccCcccceeecCCCChHHHHHHHHHhcc
Confidence            9999999999999999999998875543

>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=99.22  E-value=1.3e-11  Score=94.87  Aligned_cols=99  Identities=23%  Similarity=0.306  Sum_probs=74.8

Q ss_pred             HHHHHHHHHH-----cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC--------CCCCeEEEEe---
Q 030960            2 VRDVFRLAKE-----NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD--------QTVNVKVIMA---   65 (168)
Q Consensus         2 l~~iF~~a~~-----~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~--------~~~~v~vi~t---   65 (168)
                      ++.+|..|+.     .+||||||||+|.+++.+.+...  +-....+++.||+.+++..        ..+++++|++   
T Consensus        99 ~~~~f~~a~~~~~~~~~~~IIf~DEIdki~~~~~~~~~--~~~~~gv~~~LL~~~dg~~~~~~~~~i~~s~ilfi~~ga~  176 (309)
T d1ofha_          99 IRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEYSGA--DVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAF  176 (309)
T ss_dssp             HHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSCCSS--HHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECC
T ss_pred             ccccchhhhcccccccCCceEEehhhhhhhhhccCccc--chhhhHHHHHhhHHhcCCEEecCCeEEEccceeEEeccch
Confidence            5678888764     35899999999999976644332  2222357888999998752        2335667766   


Q ss_pred             -cCCCCCCCccccCCCCcceEEecCCCCHHHHHHHHHhhc
Q 030960           66 -TNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNL  104 (168)
Q Consensus        66 -tn~~~~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l  104 (168)
                       ++.++.++|+++.  ||+..+.+++|+..++.+|+..+.
T Consensus       177 ~~~~~~~~~p~l~~--R~~~~i~~~~~~~~~~~~Il~~~~  214 (309)
T d1ofha_         177 QVARPSDLIPELQG--RLPIRVELTALSAADFERILTEPH  214 (309)
T ss_dssp             SSSCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHSST
T ss_pred             hhcCcccchhhhhh--hhheeeeccCCCHHHHHHHHHHHH
Confidence             6778888888886  999999999999999999987443

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=98.99  E-value=3.3e-09  Score=77.60  Aligned_cols=97  Identities=12%  Similarity=0.061  Sum_probs=81.6

Q ss_pred             CCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHH
Q 030960           57 TVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQ  130 (168)
Q Consensus        57 ~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~  130 (168)
                      ..++++|++||++..+++++++  ||...+.+++|+..++..+++....      .+..+..++..+.| +++++.++++
T Consensus       132 ~~~~~~I~at~~~~~~~~~~~~--r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~i~~~s~g-d~R~ai~~l~  208 (238)
T d1in4a2         132 IQPFTLVGATTRSGLLSSPLRS--RFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRG-TPRIAIRLTK  208 (238)
T ss_dssp             -CCCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTT-CHHHHHHHHH
T ss_pred             CCCeEEEEecCCCcccccccee--eeeEEEEecCCCHHHHHHHHHHhhhhccchhhHHHHHHHHHhCCC-CHHHHHHHHH
Confidence            3478999999999999999999  9999999999999999999985444      12236778888876 8999999999


Q ss_pred             HHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960          131 EAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus       131 ~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      .+...+...+...|+.+++.++++..
T Consensus       209 ~~~~~~~~~~~~~it~~~~~~al~~l  234 (238)
T d1in4a2         209 RVRDMLTVVKADRINTDIVLKTMEVL  234 (238)
T ss_dssp             HHHHHHHHHTCSSBCHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCccCHHHHHHHHHhh
Confidence            88888877777789999999998753

>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=98.89  E-value=4.9e-09  Score=77.69  Aligned_cols=138  Identities=14%  Similarity=0.133  Sum_probs=100.7

Q ss_pred             HcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCC------CccccCCCCcce
Q 030960           11 ENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTL------DPALLRPGRLDR   84 (168)
Q Consensus        11 ~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~l------d~al~r~grf~~   84 (168)
                      ...+.++++|++|.+....     .........+..+.+.+........+.+|+.+|.++..      ++.+.+  ||..
T Consensus       130 ~~~~~~~iide~d~l~~~~-----~~~~~~~~~l~~l~~~l~~~~~~~~~~~i~i~~~~~~~~~~~~~~~~~~~--r~~~  202 (287)
T d1w5sa2         130 ENHYLLVILDEFQSMLSSP-----RIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVES--QIGF  202 (287)
T ss_dssp             HTCEEEEEEESTHHHHSCT-----TSCHHHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHT--TCSE
T ss_pred             ccCccccceeEEEEecccc-----ccchhHHHHHHHHHHhcchhhcccceeEEeecccHHHHHHHHhhccchhc--ccce
Confidence            4457888999999997544     12222234444556666666666677777777766543      356777  9999


Q ss_pred             EEecCCCCHHHHHHHHHhhc-----CCCCC---HHHHHhCCCC-----CCHHHHHHHHHHHHHHHHHhCCCccCHHHHHH
Q 030960           85 KIEFPLPDRRQKRLVFQMNL-----SDEVD---LEDYVSRPDK-----ISAAEIAAICQEAGMHAVRKNRYVILPKDFEK  151 (168)
Q Consensus        85 ~i~~~~P~~~~R~~il~~~l-----~~~~~---~~~la~~t~g-----~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~  151 (168)
                      .+++++++.++..+|++..+     ...++   ++.+|+.+.+     -.++..-++|+.|+..|..++...|+.+|+.+
T Consensus       203 ~i~f~~y~~~el~~Il~~r~~~~~~~~~~~~~al~~ia~~~~~~~~~~gd~R~ai~~l~~a~~~A~~~~~~~It~~~V~~  282 (287)
T d1w5sa2         203 KLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRK  282 (287)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGTSCCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHH
T ss_pred             eeeccCCcHHHHHHHHhhhHHHhhccCCCCHHHHHHHHHHHhccccCCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHH
Confidence            99999999999999998433     22333   6667766532     36778888999999999999999999999999


Q ss_pred             HHHh
Q 030960          152 GYRT  155 (168)
Q Consensus       152 al~~  155 (168)
                      |+.+
T Consensus       283 A~~e  286 (287)
T d1w5sa2         283 AVSE  286 (287)
T ss_dssp             HHHH
T ss_pred             HHhc
Confidence            9875

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=98.73  E-value=7e-08  Score=70.41  Aligned_cols=97  Identities=12%  Similarity=-0.001  Sum_probs=79.2

Q ss_pred             CCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCHHHHHHHHHhhcC-C-----CCCHHHHHhCCCCCCHHHHHHHHH
Q 030960           57 TVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLS-D-----EVDLEDYVSRPDKISAAEIAAICQ  130 (168)
Q Consensus        57 ~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~-~-----~~~~~~la~~t~g~s~~di~~l~~  130 (168)
                      .+++++|++|+++...+++.++  |+...+.+..|+.+++..+++.... .     .-.++.++..+.| +.++..++++
T Consensus       133 ~~~~~~i~~~~~~~~~~~~~l~--~~~~~~~~~~~~~~~~~~i~~~~~~~~~i~~~~~~l~~ia~~s~g-d~R~a~~~l~  209 (239)
T d1ixsb2         133 LPRFTLIGATTRPGLITAPLLS--RFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRG-TMRVAKRLFR  209 (239)
T ss_dssp             CCCCEEEEEESCCSSCSCGGGG--GCSEEEECCCCCHHHHHHHHHHHHGGGCCCBCHHHHHHHHHHTTS-SHHHHHHHHH
T ss_pred             CCCEEEEeeccCcccccchhhc--ccceeeEeeccChhhhhHHHHHHHHHhCCccchHHHHHHHHHcCC-CHHHHHHHHH
Confidence            4568889999999999999999  9999999999999999999884443 1     2245678899988 7788888888


Q ss_pred             HHHHHHHHhCCCccCHHHHHHHHHhh
Q 030960          131 EAGMHAVRKNRYVILPKDFEKGYRTN  156 (168)
Q Consensus       131 ~a~~~a~~~~~~~i~~~d~~~al~~~  156 (168)
                      .+...+...+...||.++..+++...
T Consensus       210 ~~~~~a~~~~~~~It~~~~~~~l~~l  235 (239)
T d1ixsb2         210 RVRDFAQVAGEEVITRERALEALAAL  235 (239)
T ss_dssp             HHHHHHTTSCCSCBCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHHhhh
Confidence            88777766777889999999998643

>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=98.64  E-value=1.4e-07  Score=69.12  Aligned_cols=116  Identities=17%  Similarity=0.224  Sum_probs=84.5

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      .-|++|||+|.+-.              ...+.|+..|+.  ...++.+|++||+++.+.+++++  |+ ..+.+++|+.
T Consensus       116 ~kviiIde~d~l~~--------------~~q~~Llk~lE~--~~~~~~~il~tn~~~~i~~~i~S--Rc-~~i~~~~~~~  176 (239)
T d1njfa_         116 FKVYLIDEVHMLSR--------------HSFNALLKTLEE--PPEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDV  176 (239)
T ss_dssp             SEEEEEETGGGSCH--------------HHHHHHHHHHHS--CCTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCH
T ss_pred             CEEEEEECcccCCH--------------HHHHHHHHHHhc--CCCCeEEEEEcCCccccChhHhh--hh-cccccccCcH
Confidence            46999999998731              334567777773  45578899999999999999999  88 6789999999


Q ss_pred             HHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           94 RQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        94 ~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      ++-..++.....      ++..++.++..+.| +.+..-++++.    +...+...|+.+++.+++
T Consensus       177 ~~i~~~l~~i~~~e~~~~~~~~l~~i~~~s~G-d~R~ain~l~~----~~~~~~~~I~~~~v~~~l  237 (239)
T d1njfa_         177 EQIRHQLEHILNEEHIAHEPRALQLLARAAEG-SLRDALSLTDQ----AIASGDGQVSTQAVSAML  237 (239)
T ss_dssp             HHHHHHHHHHHHHHTCCBCHHHHHHHHHHTTT-CHHHHHHHHHH----HHHHTTTSBCHHHHHHHH
T ss_pred             HHhhhHHHHHHhhhccCCCHHHHHHHHHHcCC-CHHHHHHHHHH----HHHhCCCCcCHHHHHHHh
Confidence            888887764332      23346678887766 55555555443    445556679999998876

>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=98.59  E-value=6.9e-09  Score=81.06  Aligned_cols=94  Identities=14%  Similarity=-0.019  Sum_probs=71.6

Q ss_pred             EEEEecCCCCCCCccccCCCCcceEEecCCCCHHHHHH-HHHhhcC---CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHH
Q 030960           61 KVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRL-VFQMNLS---DEVDLEDYVSRPDKISAAEIAAICQEAGMHA  136 (168)
Q Consensus        61 ~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~~~R~~-il~~~l~---~~~~~~~la~~t~g~s~~di~~l~~~a~~~a  136 (168)
                      .+|+|||+   ++.++.+||||+..+++.+|+...|.. ++...+.   -..+.+.++..+.|++++|+.++++.++..+
T Consensus       258 p~i~ttN~---~~~~~~r~~Rf~~~i~~~~~~~~~~~~~~l~~i~~~~~l~~~~~~L~~li~~~s~~D~~~~i~~~~~~~  334 (362)
T d1svma_         258 PGIVTMNE---YSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEW  334 (362)
T ss_dssp             CEEEEECS---CCCCHHHHTTEEEEEECCCCHHHHHHHHTCTHHHHTTCTTCHHHHHHHHHHHSCGGGSCGGGHHHHHHH
T ss_pred             Cceeeccc---ccccccccccCceEEeecCCCcHHHHHHHHHHHhcccCCCCCHHHHHHHccCCCHHHHHHHHHHHHHHH
Confidence            37889994   577788999999999999998877752 2222222   2455677888899999999999999998888


Q ss_pred             HHhCCCccCHHHHHHHHHhhc
Q 030960          137 VRKNRYVILPKDFEKGYRTNV  157 (168)
Q Consensus       137 ~~~~~~~i~~~d~~~al~~~~  157 (168)
                      .++....++...|.....++.
T Consensus       335 ~~~l~~ei~~~~~~~~k~~I~  355 (362)
T d1svma_         335 KERLDKEFSLSVYQKMKFNVA  355 (362)
T ss_dssp             HHHHHHHCCHHHHHHHHHHHH
T ss_pred             HHHHhhhccHHHHHHHHHHHH
Confidence            777666677777777766543

>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=98.40  E-value=9.5e-08  Score=69.10  Aligned_cols=120  Identities=16%  Similarity=0.146  Sum_probs=81.4

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      ..+|+|||+|.+..              ...+.++..++.  ....+.++++||.+..+++++++  |+ ..+.|++|+.
T Consensus       100 ~kiiiiDe~d~~~~--------------~~~~~Ll~~le~--~~~~~~~~~~~~~~~~i~~~i~s--r~-~~i~~~~~~~  160 (227)
T d1sxjc2         100 FKLIILDEADAMTN--------------AAQNALRRVIER--YTKNTRFCVLANYAHKLTPALLS--QC-TRFRFQPLPQ  160 (227)
T ss_dssp             CEEEEETTGGGSCH--------------HHHHHHHHHHHH--TTTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCH
T ss_pred             eEEEEEeccccchh--------------hHHHHHHHHhhh--cccceeeccccCcHHHhHHHHHH--HH-hhhccccccc
Confidence            46999999998742              223345555553  34578889999999999999998  86 5789999999


Q ss_pred             HHHHHHHHhhcC-C-----CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHH
Q 030960           94 RQKRLVFQMNLS-D-----EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGY  153 (168)
Q Consensus        94 ~~R~~il~~~l~-~-----~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al  153 (168)
                      .+...++...+. .     +..++.+++.+.| +.+..-+.++.+...+-..+...|+.+++.+++
T Consensus       161 ~~i~~~l~~I~~~e~i~i~~~~l~~i~~~s~G-d~R~ain~Lq~~~~~~~~~~~~~It~~~v~e~~  225 (227)
T d1sxjc2         161 EAIERRIANVLVHEKLKLSPNAEKALIELSNG-DMRRVLNVLQSCKATLDNPDEDEISDDVIYECC  225 (227)
T ss_dssp             HHHHHHHHHHHHTTTCCBCHHHHHHHHHHHTT-CHHHHHHHTTTTTTTTCSSSCCCBCHHHHHHHT
T ss_pred             cccccccccccccccccCCHHHHHHHHHHcCC-cHHHHHHHHHHHHHhcCCCCCCeeCHHHHHHHh
Confidence            999998875443 2     2235677877766 344433333333222222345678999888775

>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=98.37  E-value=1.3e-06  Score=63.84  Aligned_cols=132  Identities=14%  Similarity=0.139  Sum_probs=88.8

Q ss_pred             HcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCC---CCCCccccCCCCcc-eEE
Q 030960           11 ENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRA---DTLDPALLRPGRLD-RKI   86 (168)
Q Consensus        11 ~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~---~~ld~al~r~grf~-~~i   86 (168)
                      ...+.++++|++|.+....           ......++..+.. ....++.+|++++..   +.+++.+.+  |+. ..+
T Consensus       122 ~~~~~~~~~~~~d~~~~~~-----------~~~~~~~~~~~~~-~~~~~~~~i~~~~~~~~~~~~~~~~~~--r~~~~~i  187 (276)
T d1fnna2         122 RDLYMFLVLDDAFNLAPDI-----------LSTFIRLGQEADK-LGAFRIALVIVGHNDAVLNNLDPSTRG--IMGKYVI  187 (276)
T ss_dssp             TTCCEEEEEETGGGSCHHH-----------HHHHHHHTTCHHH-HSSCCEEEEEEESSTHHHHTSCHHHHH--HHTTCEE
T ss_pred             cccccccchhHHHHhhhhh-----------hhhHHHHHhcccc-ccccceEEeecCCchhhhhhcchhhhh--hhcchhc
Confidence            3357888899999775221           1112222222211 234467788888874   467777776  643 568


Q ss_pred             ecCCCCHHHHHHHHHhhcC-----CCC---CHHHHHhCCC--------CCCHHHHHHHHHHHHHHHHHhCCCccCHHHHH
Q 030960           87 EFPLPDRRQKRLVFQMNLS-----DEV---DLEDYVSRPD--------KISAAEIAAICQEAGMHAVRKNRYVILPKDFE  150 (168)
Q Consensus        87 ~~~~P~~~~R~~il~~~l~-----~~~---~~~~la~~t~--------g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~  150 (168)
                      .|++|+.+++.+|++..+.     ..+   .++.++..+.        +=+++.+.++|+.|+..|..++...|+.+|++
T Consensus       188 ~~~~~~~~e~~~il~~r~~~~~~~~~~~~~~l~~ia~~~~~~~~~~~~~G~~R~a~~ll~~a~~~A~~~~~~~I~~edv~  267 (276)
T d1fnna2         188 RFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPEDVR  267 (276)
T ss_dssp             ECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHH
T ss_pred             cccchhHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhhhhhhhhhcCCCHHHHHHHHHHHHHHHHHcCCCCcCHHHHH
Confidence            9999999999999985433     112   2344554431        12567888899999999999999999999999


Q ss_pred             HHHHhh
Q 030960          151 KGYRTN  156 (168)
Q Consensus       151 ~al~~~  156 (168)
                      +|.++.
T Consensus       268 ~A~~~~  273 (276)
T d1fnna2         268 KSSKEV  273 (276)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            999875

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=98.34  E-value=6.8e-07  Score=64.64  Aligned_cols=115  Identities=18%  Similarity=0.167  Sum_probs=80.8

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCC
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLP   91 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P   91 (168)
                      ..+.|+++||+|.+...              ....++..++  ....++.+|++||.+..+++++++  |+ ..+.+++|
T Consensus       108 ~~~~iilide~d~~~~~--------------~~~~ll~~l~--~~~~~~~~i~~~n~~~~i~~~l~s--R~-~~i~~~~~  168 (231)
T d1iqpa2         108 ASFKIIFLDEADALTQD--------------AQQALRRTME--MFSSNVRFILSCNYSSKIIEPIQS--RC-AIFRFRPL  168 (231)
T ss_dssp             CSCEEEEEETGGGSCHH--------------HHHHHHHHHH--HTTTTEEEEEEESCGGGSCHHHHH--TE-EEEECCCC
T ss_pred             CCceEEeehhhhhcchh--------------HHHHHhhhcc--cCCcceEEEeccCChhhchHhHhC--cc-cccccccc
Confidence            35899999999987532              2223445554  234568899999999999999998  88 46999999


Q ss_pred             CHHHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHH
Q 030960           92 DRRQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEK  151 (168)
Q Consensus        92 ~~~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~  151 (168)
                      +..+...+++..+..      +..++.+++.+.| +.+++-+.++.+     ......++.+++..
T Consensus       169 ~~~~~~~~l~~~~~~e~i~i~~~~l~~I~~~~~g-diR~ai~~Lq~~-----~~~~~~it~e~v~~  228 (231)
T d1iqpa2         169 RDEDIAKRLRYIAENEGLELTEEGLQAILYIAEG-DMRRAINILQAA-----AALDKKITDENVFM  228 (231)
T ss_dssp             CHHHHHHHHHHHHHTTTCEECHHHHHHHHHHHTT-CHHHHHHHHHHH-----HTTCSEECHHHHHH
T ss_pred             chhhHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHH-----HHcCCCcCHHHHHh
Confidence            999999999866542      2345778887766 555555544433     22345688887754

>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=98.32  E-value=1.5e-06  Score=62.71  Aligned_cols=120  Identities=16%  Similarity=0.094  Sum_probs=84.9

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      .-||+|||+|.+...              ..+.++..++  .......+|.+++..+.+.+++++  || ..+.|++|+.
T Consensus       109 ~~viiiDe~d~l~~~--------------~~~~l~~~~~--~~~~~~~~i~~~~~~~~~~~~l~s--r~-~~i~f~~~~~  169 (237)
T d1sxjd2         109 YKIIILDEADSMTAD--------------AQSALRRTME--TYSGVTRFCLICNYVTRIIDPLAS--QC-SKFRFKALDA  169 (237)
T ss_dssp             CEEEEETTGGGSCHH--------------HHHHHHHHHH--HTTTTEEEEEEESCGGGSCHHHHH--HS-EEEECCCCCH
T ss_pred             ceEEEEecccccCHH--------------HHHHHhhccc--cccccccccccccccccccccccc--hh-hhhccccccc
Confidence            458999999988532              1222333333  233456678888999999999998  88 6789999999


Q ss_pred             HHHHHHHHhhcCC------CCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHh-CCCccCHHHHHHHH
Q 030960           94 RQKRLVFQMNLSD------EVDLEDYVSRPDKISAAEIAAICQEAGMHAVRK-NRYVILPKDFEKGY  153 (168)
Q Consensus        94 ~~R~~il~~~l~~------~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~-~~~~i~~~d~~~al  153 (168)
                      ++..++++..+..      +..++.+++.+.| ..+..-+.++.++..+... ....|+.+++.+++
T Consensus       170 ~~~~~~L~~i~~~e~i~i~~~~l~~ia~~s~g-d~R~ai~~L~~~~~~~~~~~~~~~It~~~i~e~~  235 (237)
T d1sxjd2         170 SNAIDRLRFISEQENVKCDDGVLERILDISAG-DLRRGITLLQSASKGAQYLGDGKNITSTQVEELA  235 (237)
T ss_dssp             HHHHHHHHHHHHTTTCCCCHHHHHHHHHHTSS-CHHHHHHHHHHTHHHHHHHCSCCCCCHHHHHHHH
T ss_pred             cccchhhhhhhhhhcCcCCHHHHHHHHHHcCC-CHHHHHHHHHHHHHhchhcCCCCccCHHHHHHhh
Confidence            9999999865442      2235678888876 6666666677766655544 34679999998765

>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=98.30  E-value=1.1e-06  Score=64.08  Aligned_cols=94  Identities=12%  Similarity=0.196  Sum_probs=66.9

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      ..+++|||+|.+..              ...+.++..++  ....++.+|++||+++.+++++++  || ..|+|++|+.
T Consensus       132 ~~iiiide~d~l~~--------------~~~~~l~~~~e--~~~~~~~~Il~tn~~~~i~~~l~s--R~-~~i~~~~~~~  192 (252)
T d1sxje2         132 YKCVIINEANSLTK--------------DAQAALRRTME--KYSKNIRLIMVCDSMSPIIAPIKS--QC-LLIRCPAPSD  192 (252)
T ss_dssp             CEEEEEECTTSSCH--------------HHHHHHHHHHH--HSTTTEEEEEEESCSCSSCHHHHT--TS-EEEECCCCCH
T ss_pred             ceEEEecccccccc--------------ccchhhhcccc--cccccccceeeeccccchhhhhhc--ch-heeeecccch
Confidence            56999999998732              12233444444  234567889999999999999998  98 5899999999


Q ss_pred             HHHHHHHHhhcC-------CCCCHHHHHhCCCCCCHHHHHHHHH
Q 030960           94 RQKRLVFQMNLS-------DEVDLEDYVSRPDKISAAEIAAICQ  130 (168)
Q Consensus        94 ~~R~~il~~~l~-------~~~~~~~la~~t~g~s~~di~~l~~  130 (168)
                      ++..++++..+.       .+..++.++..+.|    |+..+++
T Consensus       193 ~~~~~~l~~i~~~e~~~~~~~~~l~~i~~~s~G----d~R~ai~  232 (252)
T d1sxje2         193 SEISTILSDVVTNERIQLETKDILKRIAQASNG----NLRVSLL  232 (252)
T ss_dssp             HHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTT----CHHHHHH
T ss_pred             hhHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCC----cHHHHHH
Confidence            999999975432       23335677776665    5555443

>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=98.29  E-value=1.8e-06  Score=61.83  Aligned_cols=88  Identities=11%  Similarity=0.172  Sum_probs=67.9

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      ..-|++|||+|.+-.              ...+.++..|+  ....++.+|.+|++++.|.+++++  |+ ..+.|++|+
T Consensus       108 ~~kviIide~d~l~~--------------~a~n~Llk~lE--ep~~~~~fIl~t~~~~~ll~tI~S--Rc-~~i~~~~~~  168 (207)
T d1a5ta2         108 GAKVVWVTDAALLTD--------------AAANALLKTLE--EPPAETWFFLATREPERLLATLRS--RC-RLHYLAPPP  168 (207)
T ss_dssp             SCEEEEESCGGGBCH--------------HHHHHHHHHHT--SCCTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCC
T ss_pred             ccceEEechhhhhhh--------------hhhHHHHHHHH--hhcccceeeeeecChhhhhhhhcc--ee-EEEecCCCC
Confidence            466999999998842              34567888887  345679999999999999999999  98 899999999


Q ss_pred             HHHHHHHHHhhcC-CCCCHHHHHhCCCC
Q 030960           93 RRQKRLVFQMNLS-DEVDLEDYVSRPDK  119 (168)
Q Consensus        93 ~~~R~~il~~~l~-~~~~~~~la~~t~g  119 (168)
                      .++-..+++.... ++..+..++..+.|
T Consensus       169 ~~~~~~~L~~~~~~~~~~~~~i~~~s~G  196 (207)
T d1a5ta2         169 EQYAVTWLSREVTMSQDALLAALRLSAG  196 (207)
T ss_dssp             HHHHHHHHHHHCCCCHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHcCC
Confidence            9999998876553 23334455555543

>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=98.24  E-value=8.6e-06  Score=60.58  Aligned_cols=144  Identities=18%  Similarity=0.211  Sum_probs=92.5

Q ss_pred             HHHHHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCC-----CCCCCccc
Q 030960            2 VRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNR-----ADTLDPAL   76 (168)
Q Consensus         2 l~~iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~-----~~~ld~al   76 (168)
                      ++.+++.+......|+||||++.+++..++.+  .+.   .    +-+.|..+-..+.+-+||+|+.     .-.-|+++
T Consensus        99 ~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g--~~~---d----~a~~Lkp~L~rg~i~vIgatT~eey~~~~e~d~al  169 (268)
T d1r6bx2          99 FKALLKQLEQDTNSILFIDEIHTIIGAGAASG--GQV---D----AANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRAL  169 (268)
T ss_dssp             HHHHHHHHSSSSCEEEEETTTTTTTTSCCSSS--CHH---H----HHHHHSSCSSSCCCEEEEEECHHHHHCCCCCTTSS
T ss_pred             HHHHHHHhhccCCceEEecchHHHhcCCCCCC--ccc---c----HHHHhhHHHhCCCCeEEEeCCHHHHHHHHhhcHHH
Confidence            46788888888889999999999986543222  111   1    2222333345667889998763     33568999


Q ss_pred             cCCCCcceEEecCCCCHHHHHHHHHhhc-------CCCCC---HHH---HHhC--CCCCCHHHHHHHHHHHHHHHHHh--
Q 030960           77 LRPGRLDRKIEFPLPDRRQKRLVFQMNL-------SDEVD---LED---YVSR--PDKISAAEIAAICQEAGMHAVRK--  139 (168)
Q Consensus        77 ~r~grf~~~i~~~~P~~~~R~~il~~~l-------~~~~~---~~~---la~~--t~g~s~~di~~l~~~a~~~a~~~--  139 (168)
                      .|  || ..|.+..|+.++-.+|++...       .-.+.   +..   ++.+  .+.+-|.---.++.+|+..+...  
T Consensus       170 ~r--rF-~~I~V~Eps~e~t~~IL~~~~~~~e~~h~v~~~~~al~~~v~ls~ryi~~~~~PdKAIdllDea~a~~~~~~~  246 (268)
T d1r6bx2         170 AR--RF-QKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGARARLMPV  246 (268)
T ss_dssp             GG--GE-EEEECCCCCHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHCTTSCTTHHHHHHHHHHHHHHHHSSS
T ss_pred             Hh--hh-cccccCCCCHHHHHHHHHHhhHHHhccCCEEeChHHHHHHHHHHHhhccCCCCCcHHHHHHHHHHHHHHhhcc
Confidence            99  99 468999999999999997311       11122   222   2222  23444444445777776555432  


Q ss_pred             --CCCccCHHHHHHHHHhhc
Q 030960          140 --NRYVILPKDFEKGYRTNV  157 (168)
Q Consensus       140 --~~~~i~~~d~~~al~~~~  157 (168)
                        .+..++.+|+...+.+..
T Consensus       247 ~~~~~~i~~~di~~~i~~~~  266 (268)
T d1r6bx2         247 SKRKKTVNVADIESVVARIA  266 (268)
T ss_dssp             CCCCCSCCHHHHHHHHHHHS
T ss_pred             ccCcccCCHHHHHHHHHHHh
Confidence              245689999988887654

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.24  E-value=4e-06  Score=61.02  Aligned_cols=120  Identities=13%  Similarity=0.185  Sum_probs=77.0

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCC
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD   92 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~   92 (168)
                      .+.++++||+|.+....      .     .....++....  .....++++++++....+++ + +  |+...++|++|+
T Consensus       123 ~~~vi~ide~~~~~~~~------~-----~~~~~~~~~~~--~~~~~ii~i~~~~~~~~~~~-l-~--~~~~~i~f~~~~  185 (253)
T d1sxja2         123 KHFVIIMDEVDGMSGGD------R-----GGVGQLAQFCR--KTSTPLILICNERNLPKMRP-F-D--RVCLDIQFRRPD  185 (253)
T ss_dssp             TSEEEEECSGGGCCTTS------T-----THHHHHHHHHH--HCSSCEEEEESCTTSSTTGG-G-T--TTSEEEECCCCC
T ss_pred             cceEEEeeeccccccch------h-----hhhHHHhhhhc--cccccccccccccccccccc-c-c--ceeeeeeccccc
Confidence            47899999999986432      0     12223333332  12335666666666666664 3 4  678899999999


Q ss_pred             HHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960           93 RRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus        93 ~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      .+++..+++..+.      ++-.++.++..+.|    ||..+++.-  .++......++.+++.+..+.
T Consensus       186 ~~~i~~~l~~i~~~e~i~i~~~~l~~i~~~s~G----DiR~ai~~L--~~~~~~~~~i~~~~~~~~~~~  248 (253)
T d1sxja2         186 ANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRG----DIRQVINLL--STISTTTKTINHENINEISKA  248 (253)
T ss_dssp             HHHHHHHHHHHHHHHTCCCCTTHHHHHHHHTTT----CHHHHHHHH--THHHHHSSCCCTTHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhCCCCCHHHHHHHHHhCCC----cHHHHHHHH--HHHHHcCCCCCHHHHHHHhch
Confidence            9999999986443      23457888888765    777766532  223334556888887766654

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.83  E-value=3.3e-05  Score=55.21  Aligned_cols=116  Identities=11%  Similarity=0.111  Sum_probs=77.0

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcceEEecCCCCH
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR   93 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~~i~~~~P~~   93 (168)
                      .-++++||+|.+....              .+.++..++  .......++.+|+..+.+.+++++  |+ ..+.|++|+.
T Consensus       102 ~kviiiDe~d~~~~~~--------------~~~ll~~~e--~~~~~~~~i~~~~~~~~i~~~l~s--r~-~~i~~~~~~~  162 (224)
T d1sxjb2         102 HKIVILDEADSMTAGA--------------QQALRRTME--LYSNSTRFAFACNQSNKIIEPLQS--QC-AILRYSKLSD  162 (224)
T ss_dssp             CEEEEEESGGGSCHHH--------------HHTTHHHHH--HTTTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCH
T ss_pred             eEEEEEecccccchhH--------------HHHHhhhcc--ccccceeeeeccCchhhhhhHHHH--HH-HHhhhcccch
Confidence            5699999999875321              223444444  244567788889999999999999  88 4699999999


Q ss_pred             HHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960           94 RQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus        94 ~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      ++...++...+.      ++-.++.++..+.| +.+..-+.++.+   .  .+...++.+++.+.+.
T Consensus       163 ~~i~~~l~~i~~~e~~~i~~~~l~~I~~~s~G-d~R~ai~~Lq~~---~--~~~~~i~~~~i~~~~d  223 (224)
T d1sxjb2         163 EDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEG-DMRQAINNLQST---V--AGHGLVNADNVFKIVD  223 (224)
T ss_dssp             HHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTT-CHHHHHHHHHHH---H--HHHSSBCHHHHHHHHT
T ss_pred             hhhHHHHHHHHHhcccCCCHHHHHHHHHHcCC-cHHHHHHHHHHH---H--HcCCCcCHHHHHHHhC
Confidence            999999875443      22235567776654 333333333322   1  1234688888776653

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=97.74  E-value=1.3e-05  Score=57.52  Aligned_cols=103  Identities=13%  Similarity=0.242  Sum_probs=69.1

Q ss_pred             CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCC---ccccCCCCcc--eEEe
Q 030960           13 APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLD---PALLRPGRLD--RKIE   87 (168)
Q Consensus        13 ~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld---~al~r~grf~--~~i~   87 (168)
                      +..+|+|||+|.+.++.         ..+..+-.+++.+   ...++.++|++...|..++   +.+.+  |+.  ..+.
T Consensus        97 ~~dll~iDDi~~i~~~~---------~~~~~lf~lin~~---~~~~~~iiits~~~p~~l~~~~~dL~S--RL~~g~~~~  162 (213)
T d1l8qa2          97 SVDLLLLDDVQFLSGKE---------RTQIEFFHIFNTL---YLLEKQIILASDRHPQKLDGVSDRLVS--RFEGGILVE  162 (213)
T ss_dssp             TCSEEEEECGGGGTTCH---------HHHHHHHHHHHHH---HHTTCEEEEEESSCGGGCTTSCHHHHH--HHHTSEEEE
T ss_pred             hccchhhhhhhhhcCch---------HHHHHHHHHHHHH---hhccceEEEecCCcchhccccchHHHH--HhhCceEEE
Confidence            46899999999996433         1223333344443   4455677888888887665   56777  765  5566


Q ss_pred             cCCCCHHHHHHHHHhhcC------CCCCHHHHHhCCCCCCHHHHHHHHHHH
Q 030960           88 FPLPDRRQKRLVFQMNLS------DEVDLEDYVSRPDKISAAEIAAICQEA  132 (168)
Q Consensus        88 ~~~P~~~~R~~il~~~l~------~~~~~~~la~~t~g~s~~di~~l~~~a  132 (168)
                      ++ |+.++|.++++.+..      ++-.++.+++++.  +.+||+.+++.-
T Consensus       163 i~-p~d~~~~~iL~~~a~~rgl~l~~~v~~yl~~~~~--~~R~L~~~l~~l  210 (213)
T d1l8qa2         163 IE-LDNKTRFKIIKEKLKEFNLELRKEVIDYLLENTK--NVREIEGKIKLI  210 (213)
T ss_dssp             CC-CCHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHCS--SHHHHHHHHHHH
T ss_pred             EC-CCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcC--cHHHHHHHHHHh
Confidence            76 667899999986554      2334667888774  689998887754

>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=97.65  E-value=0.00016  Score=54.67  Aligned_cols=126  Identities=16%  Similarity=0.165  Sum_probs=87.2

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC---------C--CCCCeEEEEecCC-CCCCCccccCCCC
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF---------D--QTVNVKVIMATNR-ADTLDPALLRPGR   81 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~---------~--~~~~v~vi~ttn~-~~~ld~al~r~gr   81 (168)
                      ..|+|+||++.+-+              ++.+.+++-|+.-         .  -..+.++++|+|- +..++++++.  |
T Consensus       128 ~gvl~iDEi~~~~~--------------~~~~aLl~~me~~~v~i~r~g~~~~~p~~f~liaa~Np~~~~l~~~llD--R  191 (333)
T d1g8pa_         128 RGYLYIDECNLLED--------------HIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLD--R  191 (333)
T ss_dssp             TEEEEETTGGGSCH--------------HHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHT--T
T ss_pred             ccEeecccHHHHHH--------------HHHHHHhhhhcCCeEEecccCceecCCCCEEEEEecCccccccccchhh--h
Confidence            37999999997631              5666677766521         0  1124678888776 4568999999  9


Q ss_pred             cceEEecCCC-CHHHHHHHHHhhcC------------------------------CCC--------CHHHHHhCCCCCCH
Q 030960           82 LDRKIEFPLP-DRRQKRLVFQMNLS------------------------------DEV--------DLEDYVSRPDKISA  122 (168)
Q Consensus        82 f~~~i~~~~P-~~~~R~~il~~~l~------------------------------~~~--------~~~~la~~t~g~s~  122 (168)
                      |+..+.++.| +...|.++......                              ..+        .+..........|+
T Consensus       192 f~~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~v~~~~~~~~~~~~~~~~~~~~S~  271 (333)
T d1g8pa_         192 FGLSVEVLSPRDVETRVEVIRRRDTYDADPKAFLEEWRPKDMDIRNQILEARERLPKVEAPNTALYDCAALCIALGSDGL  271 (333)
T ss_dssp             CSEEEECCCCCSHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHGGGCBCCHHHHHHHHHHHHHSSSCSH
T ss_pred             hcceeeccCcchhhHHHHHHHhhhhcccChHHHHHHHHHHHHHHHHHHHHHhhcccceecCHHHHHHHHHHHHHcCCCCh
Confidence            9999999877 56666655531000                              001        11123333456689


Q ss_pred             HHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960          123 AEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus       123 ~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      +-...+++-|...|.-++...|+.+|+.+|+.-
T Consensus       272 R~~~~llrvArtiA~L~gr~~V~~~di~~a~~l  304 (333)
T d1g8pa_         272 RGELTLLRSARALAALEGATAVGRDHLKRVATM  304 (333)
T ss_dssp             HHHHHHHHHHHHHHHHTTCSBCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence            999999999999999999999999999997753

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=97.63  E-value=5.8e-05  Score=57.17  Aligned_cols=117  Identities=20%  Similarity=0.284  Sum_probs=80.0

Q ss_pred             HHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCC---------CCCCCeEEEEecCC-------
Q 030960            5 VFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGF---------DQTVNVKVIMATNR-------   68 (168)
Q Consensus         5 iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~---------~~~~~v~vi~ttn~-------   68 (168)
                      +.+..+++.-|||+|||+|...+              .+.+.|+..++.=         -..++.++|+|||-       
T Consensus       117 l~~~~~~~p~~Vvl~DEieK~~~--------------~v~~~ll~~l~~g~~~~~~gr~v~~~~~i~i~tsnlG~~~i~~  182 (315)
T d1qvra3         117 LTEAVRRRPYSVILFDEIEKAHP--------------DVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPLILE  182 (315)
T ss_dssp             HHHHHHHCSSEEEEESSGGGSCH--------------HHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCTTHHHHHH
T ss_pred             HHHHHHhCCCcEEEEehHhhcCH--------------HHHHHHHHHhccCceeCCCCcEecCcceEEEEecccChHHHhh
Confidence            34455666679999999998531              3555555555431         12346899999995       


Q ss_pred             -------------------CCCCCccccCCCCcceEEecCCCCHHHHHHHHHhhcC---------------CCCCHHHHH
Q 030960           69 -------------------ADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLS---------------DEVDLEDYV  114 (168)
Q Consensus        69 -------------------~~~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~---------------~~~~~~~la  114 (168)
                                         .+.+.|.++.  |||..+.|.+.+.++-.+|+...+.               ++..++.|+
T Consensus       183 ~~~~~~~~~~~~~~~~~~l~~~f~pEfln--Rid~Ii~F~~L~~~~~~~I~~~~l~~l~~rl~~~~i~l~i~~~~~~~L~  260 (315)
T d1qvra3         183 GLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRPLTKEQIRQIVEIQLSYLRARLAEKRISLELTEAAKDFLA  260 (315)
T ss_dssp             HHHTTCCHHHHHHHHHHHHHTTSCHHHHH--TCSBCCBCCCCCHHHHHHHHHHHHHHHHHHHHTTTCEEEECHHHHHHHH
T ss_pred             hcccccchhhhhHHHHHHHHhhcCHHHHh--cCCeeeeccchhhhhhHHHHHHHHHHHHHHHHhccccccccHHHHHHHH
Confidence                               3558889988  9999999999999999999874433               122344565


Q ss_pred             hC--CCCCCHHHHHHHHHHHHHHHH
Q 030960          115 SR--PDKISAAEIAAICQEAGMHAV  137 (168)
Q Consensus       115 ~~--t~g~s~~di~~l~~~a~~~a~  137 (168)
                      +.  ...|-++.|.+.+++.....+
T Consensus       261 ~~~y~~~~GAR~L~r~Ie~~i~~~L  285 (315)
T d1qvra3         261 ERGYDPVFGARPLRRVIQRELETPL  285 (315)
T ss_dssp             HHHCBTTTBTSTHHHHHHHHTHHHH
T ss_pred             HhCCCCCCCcchHHHHHHHHHHHHH
Confidence            53  466666778777776554443

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.28  E-value=0.00045  Score=52.04  Aligned_cols=116  Identities=19%  Similarity=0.207  Sum_probs=77.7

Q ss_pred             HHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccC------C---CCCCCeEEEEecCCCC-----
Q 030960            5 VFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDG------F---DQTVNVKVIMATNRAD-----   70 (168)
Q Consensus         5 iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~------~---~~~~~v~vi~ttn~~~-----   70 (168)
                      +....+....+|+++||+|...           +   .+.+.|+..++.      .   -..++.++|+|||.-.     
T Consensus       113 l~~~~~~~~~~vvl~DeieKa~-----------~---~V~~~lLqild~G~ltd~~Gr~vdf~n~iiI~Tsnig~~~i~~  178 (315)
T d1r6bx3         113 LTDAVIKHPHAVLLLDEIEKAH-----------P---DVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETER  178 (315)
T ss_dssp             HHHHHHHCSSEEEEEETGGGSC-----------H---HHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEECSSCC----
T ss_pred             hhHHHHhCccchhhhccccccc-----------c---hHhhhhHHhhccceecCCCCCccCccceEEEeccchhhHHHHh
Confidence            3445567778999999999753           1   345556665532      1   1344688999999532     


Q ss_pred             --------------------CCCccccCCCCcceEEecCCCCHHHHHHHHHhhcC---------------CCCCHHHHHh
Q 030960           71 --------------------TLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMNLS---------------DEVDLEDYVS  115 (168)
Q Consensus        71 --------------------~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~l~---------------~~~~~~~la~  115 (168)
                                          .+.|.++.  |||..+.|.+.+.++-.+|+...+.               .+-.++.+++
T Consensus       179 ~~~~~~~~~~~~~~~~~l~~~f~pEfln--Rid~ii~f~~l~~~~~~~I~~~~l~~~~~~l~~~~i~l~~~~~a~~~l~~  256 (315)
T d1r6bx3         179 KSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTDVIHQVVDKFIVELQVQLDQKGVSLEVSQEARNWLAE  256 (315)
T ss_dssp             -------------CHHHHHHHSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHHHHHHHHTTEEEEECHHHHHHHHH
T ss_pred             hhccchhhhhhHhHHHHHHHhcCHHHHh--hhhhhhcccchhhhHHHHHHHHHHHHHHHHHHhcCcchhhHHHHHHHHHH
Confidence                                36777777  9999999999999999988875443               1223444554


Q ss_pred             --CCCCCCHHHHHHHHHHHHHHH
Q 030960          116 --RPDKISAAEIAAICQEAGMHA  136 (168)
Q Consensus       116 --~t~g~s~~di~~l~~~a~~~a  136 (168)
                        ...++-.+.|.+++++-....
T Consensus       257 ~~yd~~~GaR~L~r~Ie~~i~~~  279 (315)
T d1r6bx3         257 KGYDRAMGARPMARVIQDNLKKP  279 (315)
T ss_dssp             HHCBTTTBTTTHHHHHHHHHTHH
T ss_pred             hCCCCCCChhhHHHHHHHHHHHH
Confidence              346666778887777654443

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.28  E-value=0.00016  Score=50.96  Aligned_cols=86  Identities=21%  Similarity=0.270  Sum_probs=54.0

Q ss_pred             HHHHHHHHHHc-CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCC-----CCCCcc
Q 030960            2 VRDVFRLAKEN-APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRA-----DTLDPA   75 (168)
Q Consensus         2 l~~iF~~a~~~-~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~-----~~ld~a   75 (168)
                      ++.+++.+... .+.|+||||+..+++..+..++ .+  ...++.-.   |.    ...+-+|++|..-     -.-|++
T Consensus       103 l~~il~e~~~~~~~iILfIDeih~l~~~g~~~g~-~d--~~~~Lkp~---L~----rg~l~~IgatT~eey~~~~e~d~a  172 (195)
T d1jbka_         103 LKGVLNDLAKQEGNVILFIDELHTMVGAGKADGA-MD--AGNMLKPA---LA----RGELHCVGATTLDEYRQYIEKDAA  172 (195)
T ss_dssp             HHHHHHHHHHSTTTEEEEEETGGGGTT------C-CC--CHHHHHHH---HH----TTSCCEEEEECHHHHHHHTTTCHH
T ss_pred             HHHHHHHHhcCCCcEEEEcchHHHHhcCCCCCCc-cc--HHHHHHHH---Hh----CCCceEEecCCHHHHHHHHHcCHH
Confidence            45677776555 4789999999999865432211 11  12333333   32    3456688877632     245899


Q ss_pred             ccCCCCcceEEecCCCCHHHHHHHH
Q 030960           76 LLRPGRLDRKIEFPLPDRRQKRLVF  100 (168)
Q Consensus        76 l~r~grf~~~i~~~~P~~~~R~~il  100 (168)
                      |.|  ||. .|.+..|+.++-.+|+
T Consensus       173 L~r--rF~-~I~V~Ep~~e~t~~IL  194 (195)
T d1jbka_         173 LER--RFQ-KVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             HHT--TEE-EEECCCCCHHHHHTTC
T ss_pred             HHh--cCC-EeecCCCCHHHHHHHh
Confidence            999  995 6889999998877665

>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=97.24  E-value=0.0004  Score=48.93  Aligned_cols=73  Identities=11%  Similarity=0.297  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHc----CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCcccc
Q 030960            2 VRDVFRLAKEN----APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALL   77 (168)
Q Consensus         2 l~~iF~~a~~~----~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~   77 (168)
                      +|++.+.+...    +.-|++|||+|.+-.              ...+.||..|+  +...++++|.+|++++.|.|.++
T Consensus        64 IR~i~~~~~~~~~~~~~KviIId~ad~l~~--------------~aqNaLLK~LE--EPp~~t~fiLit~~~~~ll~TI~  127 (198)
T d2gnoa2          64 IRTIKDFLNYSPELYTRKYVIVHDCERMTQ--------------QAANAFLKALE--EPPEYAVIVLNTRRWHYLLPTIK  127 (198)
T ss_dssp             HHHHHHHHTSCCSSSSSEEEEETTGGGBCH--------------HHHHHTHHHHH--SCCTTEEEEEEESCGGGSCHHHH
T ss_pred             HHHHHHHHhhCcccCCCEEEEEeCccccch--------------hhhhHHHHHHh--CCCCCceeeeccCChhhCHHHHh
Confidence            45666666533    245999999998842              44567888887  45567888899999999999999


Q ss_pred             CCCCcceEEecCCCCH
Q 030960           78 RPGRLDRKIEFPLPDR   93 (168)
Q Consensus        78 r~grf~~~i~~~~P~~   93 (168)
                      +  |+ ..+.+++|..
T Consensus       128 S--RC-~~i~~~~p~~  140 (198)
T d2gnoa2         128 S--RV-FRVVVNVPKE  140 (198)
T ss_dssp             T--TS-EEEECCCCHH
T ss_pred             c--ce-EEEeCCCchH
Confidence            9  87 6778887754

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=96.79  E-value=0.00092  Score=51.80  Aligned_cols=86  Identities=21%  Similarity=0.282  Sum_probs=49.3

Q ss_pred             HHHHHHHHHHc-CCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCC-----CCCCCcc
Q 030960            2 VRDVFRLAKEN-APAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNR-----ADTLDPA   75 (168)
Q Consensus         2 l~~iF~~a~~~-~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~-----~~~ld~a   75 (168)
                      ++.+...+... .+.||||||++.+++..+..++   .   ...+.|.-.|.    .+.+-+||+|..     .+. |++
T Consensus       103 ~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g~---~---d~a~~Lkp~L~----rg~~~~I~~tT~~ey~~~e~-d~a  171 (387)
T d1qvra2         103 LKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGA---V---DAGNMLKPALA----RGELRLIGATTLDEYREIEK-DPA  171 (387)
T ss_dssp             HHHHHHHHHTTCSSEEEEECCC-------------------------HHHHH----TTCCCEEEEECHHHHHHHTT-CTT
T ss_pred             HHHHHHHhccCCCceEEEeccHHHHhcCCCCCCc---c---cHHHHHHHHHh----CCCcceeeecCHHHHHHhcc-cHH
Confidence            34566666665 4789999999999865432211   1   22222333332    345668887763     233 899


Q ss_pred             ccCCCCcceEEecCCCCHHHHHHHHH
Q 030960           76 LLRPGRLDRKIEFPLPDRRQKRLVFQ  101 (168)
Q Consensus        76 l~r~grf~~~i~~~~P~~~~R~~il~  101 (168)
                      |.|  ||. .|.+..|+.++-..|++
T Consensus       172 l~r--rF~-~v~v~ep~~~~~~~il~  194 (387)
T d1qvra2         172 LER--RFQ-PVYVDEPTVEETISILR  194 (387)
T ss_dssp             TCS--CCC-CEEECCCCHHHHHHHHH
T ss_pred             HHH--hcc-cccCCCCcHHHHHHHHH
Confidence            999  995 68999999999999997

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=95.93  E-value=0.0085  Score=45.76  Aligned_cols=92  Identities=21%  Similarity=0.190  Sum_probs=53.2

Q ss_pred             HHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC-----------CCCCeEEEEecCC----------
Q 030960           10 KENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD-----------QTVNVKVIMATNR----------   68 (168)
Q Consensus        10 ~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~-----------~~~~v~vi~ttn~----------   68 (168)
                      +....+||++||+|...+.........+.....+.+.||..+++-.           ...+.++|.|+|.          
T Consensus       130 ~~~~~~iv~lDEieK~~~~s~~~~~~~d~a~~~V~~~lLqild~~~~~~~~~~gr~~~~~~~i~i~t~~i~~~~~ga~~~  209 (364)
T d1um8a_         130 QKAQKGIVFIDEIDKISRLSENRSITRDVSGEGVQQALLKIVEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDG  209 (364)
T ss_dssp             HHHTTSEEEEETGGGC--------------CHHHHHHHHHHHHCCEEC---------------CEECTTCEEEEEECCTT
T ss_pred             HHhhcccchhhhhhhhccccccccccccccchHHHHhhhhhhcCceeccCCCCCCcCCcceeEEEeehhhhhhhcccchh
Confidence            4556799999999998865432222211122356666777776310           1224566666665          


Q ss_pred             ---------------------------------------CCCCCccccCCCCcceEEecCCCCHHHHHHHHHhh
Q 030960           69 ---------------------------------------ADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFQMN  103 (168)
Q Consensus        69 ---------------------------------------~~~ld~al~r~grf~~~i~~~~P~~~~R~~il~~~  103 (168)
                                                             ...+.|.++-  ||+..+.|.+.+.++-.+|+...
T Consensus       210 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PEf~g--Ri~~iv~f~~L~~~~l~~Il~~~  281 (364)
T d1um8a_         210 LAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVTYGLIPELIG--RLPVLSTLDSISLEAMVDILQKP  281 (364)
T ss_dssp             HHHHTTTSCSSCCCSCCCSSCCTTTTTTSGGGCCHHHHHHTTCCHHHHT--TCCEEEECCCCCHHHHHHHHHSS
T ss_pred             hhhhhhhhcccccccccccccchhhhhhhhccccHHHHhhhhhHHHHHH--HhcchhhHhhhhHHHHHHHHHHH
Confidence                                                   1235666765  99999999999999999999743

>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=93.44  E-value=0.23  Score=35.24  Aligned_cols=26  Identities=12%  Similarity=0.132  Sum_probs=18.0

Q ss_pred             HHHHHHHHHHHHHHHHhCCCccCHHHHHH
Q 030960          123 AEIAAICQEAGMHAVRKNRYVILPKDFEK  151 (168)
Q Consensus       123 ~di~~l~~~a~~~a~~~~~~~i~~~d~~~  151 (168)
                      ++|+++++.|+..+   ....|+.+|+-.
T Consensus       220 ~EL~~~l~~a~~~~---~~~~I~~~dl~~  245 (247)
T d1ny5a2         220 RELKNVIERAVLFS---EGKFIDRGELSC  245 (247)
T ss_dssp             HHHHHHHHHHHHHC---CSSEECHHHHHH
T ss_pred             HHHHHHHHHHHHhC---CCCeECHHHccc
Confidence            67888888776433   456788888753

>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=90.44  E-value=1.8  Score=29.63  Aligned_cols=107  Identities=20%  Similarity=0.157  Sum_probs=61.9

Q ss_pred             cCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCC-------CCCccccCCCCcce
Q 030960           12 NAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRAD-------TLDPALLRPGRLDR   84 (168)
Q Consensus        12 ~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~-------~ld~al~r~grf~~   84 (168)
                      ..+.++++||++.+......          .+...+...++   ...++..+.+.....       ..+..---.||+..
T Consensus       135 ~~~~~i~id~~~~~~~~~~~----------~~~~~l~~~~~---~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~  201 (283)
T d2fnaa2         135 KDNVIIVLDEAQELVKLRGV----------NLLPALAYAYD---NLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFS  201 (283)
T ss_dssp             SSCEEEEEETGGGGGGCTTC----------CCHHHHHHHHH---HCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCE
T ss_pred             ccccccccchhhhhcccchH----------HHHHHHHHHHH---hhhhhhhhhccccchHHHHHHHhhhhcchhccccee
Confidence            45899999999998643211          11222222222   122343444332211       11111111257778


Q ss_pred             EEecCCCCHHHHHHHHHhhcC----CCCCHHHHHhCCCCCCHHHHHHHHHHH
Q 030960           85 KIEFPLPDRRQKRLVFQMNLS----DEVDLEDYVSRPDKISAAEIAAICQEA  132 (168)
Q Consensus        85 ~i~~~~P~~~~R~~il~~~l~----~~~~~~~la~~t~g~s~~di~~l~~~a  132 (168)
                      .+.+++.+.++..++++..+.    +.-+++.+.+.+.|. |..|..++...
T Consensus       202 ~i~L~~l~~~e~~~~l~~~~~~~~~~~~~~~~i~~~~~G~-P~~L~~~~~~~  252 (283)
T d2fnaa2         202 TVELKPFSREEAIEFLRRGFQEADIDFKDYEVVYEKIGGI-PGWLTYFGFIY  252 (283)
T ss_dssp             EEEECCCCHHHHHHHHHHHHHHHTCCCCCHHHHHHHHCSC-HHHHHHHHHHH
T ss_pred             EEeeCCCCHHHHHHHHHhhhhhcCCCHHHHHHHHHHhCCC-HHHHHHHHHHH
Confidence            899999999999999875443    233577888888886 66777665533

>d1htaa_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanothermus fervidus, histone A [TaxId: 2180]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon Methanothermus fervidus, histone A [TaxId: 2180]

Probab=89.39  E-value=0.31  Score=27.33  Aligned_cols=33  Identities=24%  Similarity=0.132  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHh
Q 030960          123 AEIAAICQEAGMHAVRKNRYVILPKDFEKGYRT  155 (168)
Q Consensus       123 ~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~~  155 (168)
                      -=|..++++|...+...+++.|+.+|+..|+++
T Consensus        35 ~fi~~l~~~a~~~a~~~kRkTi~~~DV~~Alk~   67 (68)
T d1htaa_          35 EMGEEIASEAVKLAKHAGRKTIKAEDIELARKM   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHh
Confidence            346677788888888888999999999999986

>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=83.98  E-value=7.3  Score=29.61  Aligned_cols=84  Identities=25%  Similarity=0.338  Sum_probs=59.1

Q ss_pred             CeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCC--------CCCCeEEEEecCC----CCCCCccccCCCC
Q 030960           14 PAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFD--------QTVNVKVIMATNR----ADTLDPALLRPGR   81 (168)
Q Consensus        14 p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~--------~~~~v~vi~ttn~----~~~ld~al~r~gr   81 (168)
                      ..++++||+|.........  +.+.....+...++..+++..        +...++.|++...    +..+=|.+..  |
T Consensus       250 ~~~~~~dei~k~~~~~~~~--g~d~~~eg~~~~ll~~~e~~~v~~~~~~~~~~~~l~i~~~~~~~~~~~gliPEliG--R  325 (443)
T d1g41a_         250 NGIVFIDEIDKICKKGEYS--GADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG--R  325 (443)
T ss_dssp             HCEEEEETGGGGSCCSSCS--SSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSCCGGGSCHHHHT--T
T ss_pred             cCccccchhhhhhhcccCC--CCCcccchhhhhhhhhccccccccccccccccchhhccccchhhcccccchhhhcc--c
Confidence            6899999999998765432  334444566667777665531        3445666665433    3345567765  9


Q ss_pred             cceEEecCCCCHHHHHHHHH
Q 030960           82 LDRKIEFPLPDRRQKRLVFQ  101 (168)
Q Consensus        82 f~~~i~~~~P~~~~R~~il~  101 (168)
                      |...+.+.+.+.++-.+|+.
T Consensus       326 lPi~v~L~~L~~~dL~rILt  345 (443)
T d1g41a_         326 LPIRVELTALSAADFERILT  345 (443)
T ss_dssp             CCEEEECCCCCHHHHHHHHH
T ss_pred             eEEEEEccCccHHHHHHHHH
Confidence            99999999999999999986

>d1ku5a_ a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococcus horikoshii) [TaxId: 53953]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon (Pyrococcus horikoshii) [TaxId: 53953]

Probab=83.23  E-value=0.73  Score=25.55  Aligned_cols=32  Identities=16%  Similarity=0.119  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Q 030960          123 AEIAAICQEAGMHAVRKNRYVILPKDFEKGYR  154 (168)
Q Consensus       123 ~di~~l~~~a~~~a~~~~~~~i~~~d~~~al~  154 (168)
                      -=|..++.+|...+...+++.|+.+|+..|++
T Consensus        34 ~Fi~~l~~~a~~~a~~~~RKTI~~~Dv~~Al~   65 (66)
T d1ku5a_          34 EYAIEIAKKAVEFARHAGRKTVKVEDIKLAIK   65 (66)
T ss_dssp             HHHHHHHHHHHHHHHTTTCSEECHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHh
Confidence            45677888888888888999999999999986

>d1e69a_ c.37.1.12 (A:) Smc head domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=82.01  E-value=2.4  Score=29.87  Aligned_cols=49  Identities=16%  Similarity=0.233  Sum_probs=29.8

Q ss_pred             HHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCC
Q 030960           10 KENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLD   73 (168)
Q Consensus        10 ~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld   73 (168)
                      ....|.+++|||.|.-+.          +...+.+..++..+.   +  +.=||.||.+|.-++
T Consensus       238 ~~~~~~~~~iDEpe~~Lh----------p~~~~~l~~~l~~~~---~--~~QviitTHsp~~~~  286 (308)
T d1e69a_         238 EIKPSPFYVLDEVDSPLD----------DYNAERFKRLLKENS---K--HTQFIVITHNKIVME  286 (308)
T ss_dssp             TTSCCSEEEEESCCSSCC----------HHHHHHHHHHHHHHT---T--TSEEEEECCCTTGGG
T ss_pred             hhccCchhhhhhccccCC----------HHHHHHHHHHHHHhc---c--CCEEEEEECCHHHHH
Confidence            345589999999997542          222233334444442   1  223778999988776

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=81.59  E-value=2.3  Score=27.22  Aligned_cols=23  Identities=30%  Similarity=0.580  Sum_probs=17.7

Q ss_pred             HHHHHHHHHcCCeEEEEcccccc
Q 030960            3 RDVFRLAKENAPAIIFIDEVDAI   25 (168)
Q Consensus         3 ~~iF~~a~~~~p~ii~iDe~D~l   25 (168)
                      +..+..+....|.++++||+...
T Consensus        89 ~~~l~~~~~~~~~vlllDE~~~~  111 (178)
T d1ye8a1          89 ERAYREAKKDRRKVIIIDEIGKM  111 (178)
T ss_dssp             HHHHHHHHHCTTCEEEECCCSTT
T ss_pred             HHHHHHHHhcCCCceeecCCCcc
Confidence            34566777889999999997543

>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=80.68  E-value=3.2  Score=29.29  Aligned_cols=62  Identities=21%  Similarity=0.366  Sum_probs=34.6

Q ss_pred             HHHHHHHcCCeEEEEcccccccccccCCCCCcchHHHHHHHHHHHhccCCCCCCCeEEEEecCCCCCCCccccCCCCcce
Q 030960            5 VFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPALLRPGRLDR   84 (168)
Q Consensus         5 iF~~a~~~~p~ii~iDe~D~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~grf~~   84 (168)
                      ...+|-...|.|+++||.-+-+          +...+..+...+..+.   +  +..+|..|++++.+.       ++|+
T Consensus       164 ~iARal~~~p~ililDEpts~L----------D~~t~~~i~~~l~~l~---~--~~TvI~itH~~~~~~-------~~D~  221 (255)
T d2hyda1         164 SIARIFLNNPPILILDEATSAL----------DLESESIIQEALDVLS---K--DRTTLIVAHRLSTIT-------HADK  221 (255)
T ss_dssp             HHHHHHHHCCSEEEEESTTTTC----------CHHHHHHHHHHHHHHT---T--TSEEEEECSSGGGTT-------TCSE
T ss_pred             HHHHHHhcCCCEEEEeCccccC----------CHHHHHHHHHHHHHHh---c--CCEEEEEeCCHHHHH-------hCCE
Confidence            3445556689999999966433          2223344444444442   2  224566677665443       5666


Q ss_pred             EEec
Q 030960           85 KIEF   88 (168)
Q Consensus        85 ~i~~   88 (168)
                      ++.+
T Consensus       222 ii~l  225 (255)
T d2hyda1         222 IVVI  225 (255)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            6654