Citrus Sinensis ID: 039253

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------20
Protein Sequence
MGWSIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQSRGFGDEFGFCETAVAANNLIPVSSITDGNGEDDNVYD
Secondary Structure (PSIPRED)
ccEEEEEccccccccccHHHHHHHHHHHHcccccccEEEEEccccccccccccccccccccEEEEccccHHHHHHHHHHHHccccccccccHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHccccHHHHHHHHHHccccccHHHHHHHHHHHHHHHHccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccEEccccccccccHHHHHHHHHHHHcccccccccEEEEEEccccccccHHHccccccccEEEEcccccccHHHHHHHHHccccccccccHHHHHcccccccHHHHHHHHHHHHHHHHHHcccccccccEEEcHHHHHHHHHHHHcccHHccEEEcHHHHHHHHHHHcccEEEccccccEEEEEEEccccccEEEccc
Coil and Loop (DISEMBL)
MGWSIVIqrgsgaggaadripnqlltemdglsakKTIFVIGvtnrpdiidpallrpgrldqliyiplpveKSRLQIFKAClrkspvskdvdlEKLAqftqgfsgaDITEICQRACKDATREEIENDIRrrkgkqpeAIEDEVAEIKAEHFEESMKYACKsqsrgfgdefgfcetavaannlipvssitdgngeddnvyd
Flexible Loop (DISEMBL)
MGWSIVIqrgsgaggaadripNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLrkspvskdvdLEKLAQftqgfsgadiTEICQRACKDATreeiendirrrkgkqpeaiEDEVAEIKAEHFEESMKYACKSQSRGFGDEFGFCETAVAAnnlipvssitdgngeddnvyd
Low Complexity Region (SEG)
MGWSIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQSRGFGDEFGFCETAVAANNLIPVSSITDGNGEDDNVYD
Disordered region (IsUnstruct)
****IVI************IPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACK***************************************YACK**SRGFGDEFGFCETAVAANNLIPVS**************
Disordered Region (DISOPRED)
*GWSIVI************IPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIE*******************EIKAEHFE*********************************SSITDGNGED**VY*
Disordered Region (DISEMBL)
MGWSIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQSRGFGDEFGFCETAVAANNLIPVSSITDGNGEDDNVYD
Disordered Region (DISPRO)
**************GAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQSRGFGDEFGFCETAVAANNLIPVSSITDGNGEDDNVYD
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGWSIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQSRGFGDEFGFCETAVAANNLIPVSSITDGNGEDDNVYD
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	199	2.2.26 [Sep-21-2011]
Q96372	805	Cell division cycle prote	N/A	no	0.979	0.242	0.609	5e-66
P54774	807	Cell division cycle prote	no	no	0.979	0.241	0.617	4e-65
Q9LZF6	810	Cell division control pro	yes	no	0.864	0.212	0.663	8e-65
Q9SCN8	815	Cell division control pro	no	no	0.979	0.239	0.582	2e-60
P54609	809	Cell division control pro	yes	no	0.788	0.194	0.655	3e-58
Q7KN62	801	Transitional endoplasmic	yes	no	0.954	0.237	0.560	6e-55
P54812	810	Transitional endoplasmic	yes	no	0.879	0.216	0.580	7e-55
P23787	805	Transitional endoplasmic	N/A	no	0.758	0.187	0.620	2e-53
P54811	809	Transitional endoplasmic	no	no	0.778	0.191	0.582	7e-50
Q7ZU99	806	Transitional endoplasmic	yes	no	0.758	0.187	0.626	4e-49

>sp|Q96372|CDC48_CAPAN Cell division cycle protein 48 homolog OS=Capsicum annuum GN=CAFP PE=2 SV=1

 Score =  250 bits (638), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 134/220 (60%), Positives = 157/220 (71%), Gaps = 25/220 (11%)

Query: 4   SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
           SI  QRGS    AGGAADR+ NQLLTEMDG++AKKT+F+IG TNRPDIIDPALLRPGRLD
Sbjct: 585 SIATQRGSSSGDAGGAADRVLNQLLTEMDGMNAKKTVFIIGATNRPDIIDPALLRPGRLD 644

Query: 61  QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           QLIYIPLP E SR QIFKACLRKSP+SKD+DL  LA+ TQGFSGAD+TEICQRACK A R
Sbjct: 645 QLIYIPLPDEDSRHQIFKACLRKSPLSKDIDLRALAKHTQGFSGADVTEICQRACKYAIR 704

Query: 121 EEIENDIRRRKGKQ--PEAIE---DEVAEIKAEHFEESMKYACKS--------------- 160
           E IE DI R K +Q  P++++   DEV EIK  HFEESMKYA +S               
Sbjct: 705 ENIEKDIEREKRRQENPDSMDEDVDEVPEIKPAHFEESMKYARRSVSDADIRKYQAFAQT 764

Query: 161 --QSRGFGDEFGFCETAVAANNLIPVSSITDGNGEDDNVY 198
             QSRGFG EF F +T+  A       + ++   +DD++Y
Sbjct: 765 LQQSRGFGTEFRFADTSGGATAAADPFATSNAAADDDDLY 804

Probably functions in cell division and growth processes.
Capsicum annuum (taxid: 4072)

>sp|P54774|CDC48_SOYBN Cell division cycle protein 48 homolog OS=Glycine max GN=CDC48 PE=2 SV=1

 Score =  247 bits (630), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 137/222 (61%), Positives = 158/222 (71%), Gaps = 27/222 (12%)

Query: 4   SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
           SI  QRGS    AGGAADR+ NQLLTEMDG+SAKKT+F+IG TNRPDIIDPALLRPGRLD
Sbjct: 585 SIATQRGSSVGDAGGAADRVLNQLLTEMDGMSAKKTVFIIGATNRPDIIDPALLRPGRLD 644

Query: 61  QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           QLIYIPLP E SR QIFKACLRKSP++K+VDL  LA+ TQGFSGADITEICQRACK A R
Sbjct: 645 QLIYIPLPDEDSRHQIFKACLRKSPIAKNVDLRALARHTQGFSGADITEICQRACKYAIR 704

Query: 121 EEIENDI-RRRKGKQ-PEA-----IEDEVAEIKAEHFEESMKYACKS------------- 160
           E IE DI R RK ++ PEA     ++DEVAEIKA HFEESMK+A +S             
Sbjct: 705 ENIEKDIERERKSRENPEAMDEDTVDDEVAEIKAAHFEESMKFARRSVSDADIRKYQAFA 764

Query: 161 ----QSRGFGDEFGFCETAVAANNLIPVSSITDGNGEDDNVY 198
               QSRGFG EF F E+           + + G  ++D++Y
Sbjct: 765 QTLQQSRGFGSEFRFPESGDRTTTGSDPFAASAGGADEDDLY 806

Probably functions in cell division and growth processes.

Glycine max (taxid: 3847)

>sp|Q9LZF6|CD48E_ARATH Cell division control protein 48 homolog E OS=Arabidopsis thaliana GN=CDC48E PE=1 SV=2

 Score =  246 bits (628), Expect = 8e-65,   Method: Compositional matrix adjust.
 Identities = 132/199 (66%), Positives = 148/199 (74%), Gaps = 27/199 (13%)

Query: 4   SIVIQRGSGAG---GAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
           SI  QRG+ AG   GAADR+ NQLLTEMDG++AKKT+F+IG TNRPDIID ALLRPGRLD
Sbjct: 584 SIATQRGNSAGDAGGAADRVLNQLLTEMDGMNAKKTVFIIGATNRPDIIDSALLRPGRLD 643

Query: 61  QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           QLIYIPLP E SRL IFKACLRKSPV+KDVD+  LA++TQGFSGADITEICQRACK A R
Sbjct: 644 QLIYIPLPDEDSRLNIFKACLRKSPVAKDVDVTALAKYTQGFSGADITEICQRACKYAIR 703

Query: 121 EEIENDI--RRRKGKQPEAIE-----DEVAEIKAEHFEESMKYACKS------------- 160
           E IE DI   RR+ + PEA+E     DEV+EI+A HFEESMKYA +S             
Sbjct: 704 ENIEKDIENERRRSQNPEAMEEDMVDDEVSEIRAAHFEESMKYARRSVSDADIRKYQAFA 763

Query: 161 ----QSRGFGDEFGFCETA 175
               QSRGFG EF F  TA
Sbjct: 764 QTLQQSRGFGSEFRFDSTA 782

Probably functions in cell division and growth processes. Interacts with certain SNAREs as part of specialized membrane fusion events where vesicles from the same organelle fuse (homotypic fusion).

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SCN8|CD48D_ARATH Cell division control protein 48 homolog D OS=Arabidopsis thaliana GN=CDC48D PE=1 SV=1

 Score =  231 bits (590), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 134/230 (58%), Positives = 158/230 (68%), Gaps = 35/230 (15%)

Query: 4   SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
           SI  QRG+    AGGAADR+ NQLLTEMDG++AKKT+F+IG TNRPDIIDPALLRPGRLD
Sbjct: 585 SIATQRGNSVGDAGGAADRVLNQLLTEMDGMNAKKTVFIIGATNRPDIIDPALLRPGRLD 644

Query: 61  QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           QLIYIPLP E+SR QIFK+CLRKSPV+KDVDL  LA++TQGFSGADITEICQR+CK A R
Sbjct: 645 QLIYIPLPDEESRYQIFKSCLRKSPVAKDVDLRALAKYTQGFSGADITEICQRSCKYAIR 704

Query: 121 EEIENDI--RRRKGKQP---EAIEDEVAEIKAEHFEESMKYACKS--------------- 160
           E IE DI   R++ + P   E  E+E+AEIKA HFEESMKYA +S               
Sbjct: 705 ENIEKDIEKERKRAESPEAMEEDEEEIAEIKAGHFEESMKYARRSVSDADIRKYQAFAQT 764

Query: 161 --QSRGFGDEFGFCETAVAANNLIPVSSIT----------DGNGEDDNVY 198
             QSRGFG EF F +         P ++ T           G  +DD++Y
Sbjct: 765 LQQSRGFGSEFRFPDAPTGTTGAFPGAAATVGGVDPFATSGGAADDDDLY 814

Probably functions in cell division and growth processes. Interacts with certain SNAREs as part of specialized membrane fusion events where vesicles from the same organelle fuse (homotypic fusion).

Arabidopsis thaliana (taxid: 3702)

>sp|P54609|CD48A_ARATH Cell division control protein 48 homolog A OS=Arabidopsis thaliana GN=CDC48A PE=1 SV=1

 Score =  224 bits (571), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 118/180 (65%), Positives = 135/180 (75%), Gaps = 23/180 (12%)

Query: 19  RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFK 78
           R+ NQLLTEMDG++AKKT+F+IG TNRPDIID ALLRPGRLDQLIYIPLP E SRL IFK
Sbjct: 603 RVLNQLLTEMDGMNAKKTVFIIGATNRPDIIDSALLRPGRLDQLIYIPLPDEDSRLNIFK 662

Query: 79  ACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDI--RRRKGKQPE 136
           A LRKSP++KDVD+  LA++TQGFSGADITEICQRACK A RE IE DI   +R+ + PE
Sbjct: 663 AALRKSPIAKDVDIGALAKYTQGFSGADITEICQRACKYAIRENIEKDIEKEKRRSENPE 722

Query: 137 AIE----DEVAEIKAEHFEESMKYACKS-----------------QSRGFGDEFGFCETA 175
           A+E    DEV+EIKA HFEESMKYA +S                 QSRGFG EF F  +A
Sbjct: 723 AMEEDGVDEVSEIKAAHFEESMKYARRSVSDADIRKYQAFAQTLQQSRGFGSEFRFENSA 782

Probably functions in cell division and growth processes. Interacts with certain SNAREs as part of specialized membrane fusion events where vesicles from the same organelle fuse (homotypic fusion).

Arabidopsis thaliana (taxid: 3702)

>sp|Q7KN62|TERA_DROME Transitional endoplasmic reticulum ATPase TER94 OS=Drosophila melanogaster GN=TER94 PE=1 SV=1

 Score =  213 bits (543), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 125/223 (56%), Positives = 151/223 (67%), Gaps = 33/223 (14%)

Query: 4   SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
           SI   RG     AGGAADR+ NQ+LTEMDG+ AKK +F+IG TNRPDIIDPA+LRPGRLD
Sbjct: 578 SIAKARGGNVGDAGGAADRVINQILTEMDGMGAKKNVFIIGATNRPDIIDPAILRPGRLD 637

Query: 61  QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           QLIYIPLP +KSR  I KA LRKSP++K+VDL  +A+ TQGFSGAD+TEICQRACK A R
Sbjct: 638 QLIYIPLPDDKSREAILKANLRKSPLAKEVDLTYIAKVTQGFSGADLTEICQRACKLAIR 697

Query: 121 EEIENDIRRRKGK---QPEAI----EDEVAEIKAEHFEESMKYACKS------------- 160
           + IE +IRR K +   Q  A+    +D V EI + HFEE+MK+A +S             
Sbjct: 698 QAIEAEIRREKERAENQNSAMDMDEDDPVPEITSAHFEEAMKFARRSVSDNDIRKYEMFA 757

Query: 161 ----QSRGFGDEFGF----CETAVAANNLIPVSSITDGNGEDD 195
               QSRGFG  F F      T+ + NNL PV+S  D NG+DD
Sbjct: 758 QTLQQSRGFGQNFRFPGQTGNTSGSGNNL-PVNSPGD-NGDDD 798

Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process (By similarity). Involved in the ubiquitin-proteasome system. Important for oskar mRNA localization and/or anchoring during oogenesis.

Drosophila melanogaster (taxid: 7227)

>sp|P54812|TERA2_CAEEL Transitional endoplasmic reticulum ATPase homolog 2 OS=Caenorhabditis elegans GN=cdc-48.2 PE=1 SV=2

 Score =  213 bits (542), Expect = 7e-55,   Method: Compositional matrix adjust.
 Identities = 119/205 (58%), Positives = 141/205 (68%), Gaps = 30/205 (14%)

Query: 4   SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
           SI   RG     AGGAADR+ NQ+LTEMDG++AKK +F+IG TNRPDIIDPA+LRPGRLD
Sbjct: 586 SIAKARGGSVGDAGGAADRVINQVLTEMDGMNAKKNVFIIGATNRPDIIDPAVLRPGRLD 645

Query: 61  QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           QLIYIPLP E SRLQIFKA LRK+P+S D+DL  LA+ T GFSGAD+TEICQRACK A R
Sbjct: 646 QLIYIPLPDEASRLQIFKASLRKTPLSADLDLNFLAKNTVGFSGADLTEICQRACKLAIR 705

Query: 121 EEIENDIRRRKGKQ------PEAIEDEVA----EIKAEHFEESMKYACKS---------- 160
           E IE +IR+ K +Q       E +EDE+A    EI   HFEE+MK+A +S          
Sbjct: 706 ESIEREIRQEKERQDRSARGEELMEDELADPVPEITRAHFEEAMKFARRSVTDNDIRKYE 765

Query: 161 -------QSRGFGDEFGFCETAVAA 178
                  QSRGFG+ F F   A +A
Sbjct: 766 MFAQTLQQSRGFGNNFKFPGEAPSA 790

Caenorhabditis elegans (taxid: 6239)

>sp|P23787|TERA_XENLA Transitional endoplasmic reticulum ATPase OS=Xenopus laevis GN=vcp PE=1 SV=3

 Score =  208 bits (529), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 108/174 (62%), Positives = 130/174 (74%), Gaps = 23/174 (13%)

Query: 16  AADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQ 75
           AADR+ NQ+LTEMDG+S KK +F+IG TNRPDIIDPA+LRPGRLDQLIYIPLP EKSR+ 
Sbjct: 596 AADRVINQILTEMDGMSIKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRMA 655

Query: 76  IFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQ- 134
           I KA LRKSPV+KDVD++ LA+ T GFSGAD+TEICQRACK A RE IEN+IRR + +Q 
Sbjct: 656 ILKANLRKSPVAKDVDVDFLAKMTNGFSGADLTEICQRACKLAIRESIENEIRRERDRQT 715

Query: 135 -PEAIE----DEVAEIKAEHFEESMKYACKS-----------------QSRGFG 166
            P A+E    D V EI+ +HFEE+M++A +S                 QSRGFG
Sbjct: 716 NPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFG 769

Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process.

Xenopus laevis (taxid: 8355)

>sp|P54811|TERA1_CAEEL Transitional endoplasmic reticulum ATPase homolog 1 OS=Caenorhabditis elegans GN=cdc-48.1 PE=1 SV=1

 Score =  196 bits (499), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 106/182 (58%), Positives = 127/182 (69%), Gaps = 27/182 (14%)

Query: 17  ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQI 76
           +DR+ NQ+LTEMDG++AKK +F+IG TNRPDIIDPA+LRPGRLDQLIYIPLP E SR QI
Sbjct: 604 SDRVINQVLTEMDGMNAKKNVFIIGATNRPDIIDPAVLRPGRLDQLIYIPLPDEASRHQI 663

Query: 77  FKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQ-- 134
            KA LRK+P+SKD+DL  LA+ T GFSGAD+TEICQRACK A RE IE +IR  K +Q  
Sbjct: 664 LKASLRKTPLSKDLDLTFLAKNTVGFSGADLTEICQRACKLAIRESIEKEIRIEKERQDR 723

Query: 135 ----PEAIEDE----VAEIKAEHFEESMKYACKS-----------------QSRGFGDEF 169
                E +ED+    V EI   HFEE+MK+A +S                 QSRGFG+ F
Sbjct: 724 QARGEELMEDDAVDPVPEITRAHFEEAMKFARRSVTDNDIRKYEMFAQTLQQSRGFGNNF 783

Query: 170 GF 171
            F
Sbjct: 784 KF 785

Caenorhabditis elegans (taxid: 6239)

>sp|Q7ZU99|TERA_DANRE Transitional endoplasmic reticulum ATPase OS=Danio rerio GN=vcp PE=1 SV=1

 Score =  194 bits (492), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 109/174 (62%), Positives = 131/174 (75%), Gaps = 23/174 (13%)

Query: 16  AADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQ 75
           AADR+ NQ+LTEMDG+S+KK +F+IG TNRPDIIDPA+LRPGRLDQLIYIPLP EKSR+ 
Sbjct: 596 AADRVINQILTEMDGMSSKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRIA 655

Query: 76  IFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQ- 134
           I KA LRKSP+SKDVDL+ LA+ T GFSGAD+TEICQRACK A RE IEN+IRR + +Q 
Sbjct: 656 ILKANLRKSPISKDVDLDFLAKMTNGFSGADLTEICQRACKLAIRESIENEIRRERERQT 715

Query: 135 -PEAIE----DEVAEIKAEHFEESMKYACKS-----------------QSRGFG 166
            P A+E    D V EI+ +HFEE+M++A +S                 QSRGFG
Sbjct: 716 NPSAMEVEEDDPVPEIRKDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFG 769

Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process (By similarity). Enhances cell cycle progression and inhibits apoptosis at low temperatures.

Danio rerio (taxid: 7955)

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	199
449440119	804	PREDICTED: cell division cycle protein 4	0.969	0.240	0.645	1e-67
255556938	805	Transitional endoplasmic reticulum ATPas	0.979	0.242	0.644	2e-67
356505246	808	PREDICTED: cell division cycle protein 4	0.984	0.242	0.633	9e-67
255540583	804	Transitional endoplasmic reticulum ATPas	0.979	0.242	0.637	1e-66
356572464	808	PREDICTED: cell division cycle protein 4	0.969	0.238	0.64	3e-66
242039557	810	hypothetical protein SORBIDRAFT_01g02091	0.864	0.212	0.686	7e-66
356518956	814	PREDICTED: cell division cycle protein 4	0.959	0.234	0.65	8e-66
224127332	776	predicted protein [Populus trichocarpa]	0.964	0.247	0.632	8e-66
224133614	813	predicted protein [Populus trichocarpa]	0.964	0.236	0.651	9e-66
226504612	359	uncharacterized protein LOC100274218 [Ze	0.864	0.479	0.686	1e-65

>gi|449440119|ref|XP_004137832.1| PREDICTED: cell division cycle protein 48 homolog [Cucumis sativus] gi|449525650|ref|XP_004169829.1| PREDICTED: cell division cycle protein 48 homolog [Cucumis sativus]

 Score =  261 bits (666), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 144/223 (64%), Positives = 167/223 (74%), Gaps = 30/223 (13%)

Query: 4   SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
           SI  QRGS    AGGAADR+ NQLLTEMDG+SAKKT+F+IG TNRPDIIDPALLRPGRLD
Sbjct: 585 SIATQRGSSVGDAGGAADRVLNQLLTEMDGMSAKKTVFIIGATNRPDIIDPALLRPGRLD 644

Query: 61  QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           QLIYIPLP E+SRLQIFKACLRKSP+SKDV+L  LA++TQGFSGADITEICQRACK A R
Sbjct: 645 QLIYIPLPDEESRLQIFKACLRKSPISKDVELRALAKYTQGFSGADITEICQRACKYAIR 704

Query: 121 EEIENDI--RRRKGKQPEAIE----DEVAEIKAEHFEESMKYACKS-------------- 160
           E IE DI   RRK + PEA+E    DEVAEI+A HFEESMKYA +S              
Sbjct: 705 ENIEKDIEKERRKSENPEAMEEDADDEVAEIRAAHFEESMKYARRSVSDADIRKYQAFAQ 764

Query: 161 ---QSRGFGDEFGFCE-TAVAANNLIPVSSITDGNGEDDNVYD 199
              QSRGFG EF F + +A AA++    S+   G G++D++Y+
Sbjct: 765 TLQQSRGFGAEFRFEQSSAPAASDPFATSA---GGGDEDDLYN 804

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255556938|ref|XP_002519502.1| Transitional endoplasmic reticulum ATPase, putative [Ricinus communis] gi|223541365|gb|EEF42916.1| Transitional endoplasmic reticulum ATPase, putative [Ricinus communis]

 Score =  260 bits (665), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 143/222 (64%), Positives = 161/222 (72%), Gaps = 27/222 (12%)

Query: 4   SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
           SI  QRGS    AGGAADR+ NQLLTEMDG+SAKKT+F+IG TNRPDIIDPALLRPGRLD
Sbjct: 585 SIATQRGSSVGDAGGAADRVLNQLLTEMDGMSAKKTVFIIGATNRPDIIDPALLRPGRLD 644

Query: 61  QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           QLIYIPLP E SR QIFKACLRKSPVSKDVDL  LA++TQGFSGADITEICQRACK A R
Sbjct: 645 QLIYIPLPDEDSRHQIFKACLRKSPVSKDVDLRALAKYTQGFSGADITEICQRACKYAIR 704

Query: 121 EEIENDI--RRRKGKQPEA----IEDEVAEIKAEHFEESMKYACKS-------------- 160
           E IE DI   RR+   PEA    +ED+VAEIKA HFEESMKYA +S              
Sbjct: 705 ENIEKDIERERRQRDNPEAMEEDVEDDVAEIKAAHFEESMKYARRSVSDADIRKYQAFAQ 764

Query: 161 ---QSRGFGDEFGFCETAVAANNLIPVSSITDGNGEDDNVYD 199
              QSRGFG EF F E+   A    P ++ + G  +DD++Y+
Sbjct: 765 TLQQSRGFGSEFRFSESTGGAAGADPFAA-SAGGADDDDLYN 805

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356505246|ref|XP_003521403.1| PREDICTED: cell division cycle protein 48 homolog [Glycine max]

 Score =  258 bits (659), Expect = 9e-67,   Method: Compositional matrix adjust.
 Identities = 142/224 (63%), Positives = 157/224 (70%), Gaps = 28/224 (12%)

Query: 4   SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
           SI  QRGS    AGGAADR+ NQLLTEMDG+SAKKT+F+IG TNRPDIIDPALLRPGRLD
Sbjct: 585 SIATQRGSSVGDAGGAADRVLNQLLTEMDGMSAKKTVFIIGATNRPDIIDPALLRPGRLD 644

Query: 61  QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           QLIYIPLP E SR QIFKACLRKSPVSKDVDL  LA++TQGFSGADITEICQRACK A R
Sbjct: 645 QLIYIPLPDEDSRHQIFKACLRKSPVSKDVDLRALAKYTQGFSGADITEICQRACKYAIR 704

Query: 121 EEIENDI--RRRKGKQPEA-----IEDEVAEIKAEHFEESMKYACKS------------- 160
           E IE DI   RRK   PEA     +EDE+AEIKA HFEESMKYA +S             
Sbjct: 705 ENIEKDIERERRKRDNPEAMEEDDVEDEIAEIKAAHFEESMKYARRSVSDADIRKYQAFA 764

Query: 161 ----QSRGFGDEFGFCETAVAANNLIPVSSITDGNGED-DNVYD 199
               QSRGFG EF F ++  A          +   G D D++Y+
Sbjct: 765 QTLQQSRGFGSEFRFADSTSAGGTAAASDPFSSAGGADEDDLYN 808

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255540583|ref|XP_002511356.1| Transitional endoplasmic reticulum ATPase, putative [Ricinus communis] gi|223550471|gb|EEF51958.1| Transitional endoplasmic reticulum ATPase, putative [Ricinus communis]

 Score =  257 bits (657), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 144/226 (63%), Positives = 161/226 (71%), Gaps = 31/226 (13%)

Query: 4   SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
           SI  QRGS    AGGAADR+ NQLLTEMDG++AKKT+F+IG TNRPDIIDPALLRPGRLD
Sbjct: 580 SIATQRGSSVGDAGGAADRVLNQLLTEMDGMTAKKTVFIIGATNRPDIIDPALLRPGRLD 639

Query: 61  QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           QLIYIPLP E SRLQIFKACLRKSPVS+DV+L  LA++T GFSGADITEICQRACK A R
Sbjct: 640 QLIYIPLPDEASRLQIFKACLRKSPVSRDVELAALARYTHGFSGADITEICQRACKYAIR 699

Query: 121 EEIENDIRRRKGKQ--PEAIE----DEVAEIKAEHFEESMKYACKS-------------- 160
           E IE DI R K KQ  PEA+E    DEV EIK  HFEESMKYA +S              
Sbjct: 700 ENIEKDIEREKRKQENPEAMEEDDVDEVPEIKPAHFEESMKYARRSVSDADIRKYQLFAQ 759

Query: 161 ---QSRGFGDEFGFCE----TAVAANNLIPVSSITDGNGEDDNVYD 199
              QSRGFG EF F +    TA A     P +S T   G+DD++Y+
Sbjct: 760 TLQQSRGFGTEFRFSDRTENTAAAGGASDPFASATTA-GDDDDLYN 804

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356572464|ref|XP_003554388.1| PREDICTED: cell division cycle protein 48 homolog [Glycine max]

 Score =  256 bits (655), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 144/225 (64%), Positives = 160/225 (71%), Gaps = 32/225 (14%)

Query: 4   SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
           SI  QRGS    AGGAADR+ NQLLTEMDG+SAKKT+F+IG TNRPDIIDPALLRPGRLD
Sbjct: 585 SIATQRGSSVGDAGGAADRVLNQLLTEMDGMSAKKTVFIIGATNRPDIIDPALLRPGRLD 644

Query: 61  QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           QLIYIPLP E SR QIFKACLRKSPVSKDVDL  LA++TQGFSGADITEICQRACK A R
Sbjct: 645 QLIYIPLPDEDSRHQIFKACLRKSPVSKDVDLRALAKYTQGFSGADITEICQRACKYAIR 704

Query: 121 EEIENDI--RRRKGKQPEA-----IEDEVAEIKAEHFEESMKYACKS------------- 160
           E IE DI   RRK   PEA     +EDE+AEIKA HFEESMKYA +S             
Sbjct: 705 ENIEKDIERERRKRDNPEAMEEDDVEDEIAEIKAAHFEESMKYARRSVSDADIRKYQAFA 764

Query: 161 ----QSRGFGDEFGFCETAV---AANNLIPVSSITDGNGEDDNVY 198
               QSRGFG EF F ++     AA    P +S   G  ++D++Y
Sbjct: 765 QTLQQSRGFGSEFRFADSTSSGGAATASDPFASA--GGADEDDLY 807

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242039557|ref|XP_002467173.1| hypothetical protein SORBIDRAFT_01g020910 [Sorghum bicolor] gi|241921027|gb|EER94171.1| hypothetical protein SORBIDRAFT_01g020910 [Sorghum bicolor]

 Score =  255 bits (652), Expect = 7e-66,   Method: Compositional matrix adjust.
 Identities = 136/198 (68%), Positives = 150/198 (75%), Gaps = 26/198 (13%)

Query: 4   SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
           SI  QRGS    AGGAADR+ NQLLTEMDG++AKKT+F+IG TNRPDIIDPALLRPGRLD
Sbjct: 588 SIATQRGSSVGDAGGAADRVLNQLLTEMDGMNAKKTVFIIGATNRPDIIDPALLRPGRLD 647

Query: 61  QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           QLIYIPLP E+SRLQIFKACLRKSPV+KDVDL  LA++TQGFSGADITEICQRACK A R
Sbjct: 648 QLIYIPLPDEQSRLQIFKACLRKSPVAKDVDLNALAKYTQGFSGADITEICQRACKYAIR 707

Query: 121 EEIENDI--RRRKGKQPEAIE----DEVAEIKAEHFEESMKYACKS-------------- 160
           E IE DI   RR+   PEA+E    DE+AEIKA HFEESMKYA +S              
Sbjct: 708 ENIEKDIERERRRKDNPEAMEEDEVDEIAEIKAAHFEESMKYARRSVSDADIRKYQAFAQ 767

Query: 161 ---QSRGFGDEFGFCETA 175
              QSRGFG EF F E +
Sbjct: 768 TLQQSRGFGSEFRFSEQS 785

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356518956|ref|XP_003528141.1| PREDICTED: cell division cycle protein 48 homolog [Glycine max]

 Score =  255 bits (651), Expect = 8e-66,   Method: Compositional matrix adjust.
 Identities = 143/220 (65%), Positives = 159/220 (72%), Gaps = 29/220 (13%)

Query: 4   SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
           SI  QRGS    AGGAADR+ NQLLTEMDG++AKKT+F+IG TNRPDIIDPALLRPGRLD
Sbjct: 593 SIATQRGSSVGDAGGAADRVLNQLLTEMDGMTAKKTVFIIGATNRPDIIDPALLRPGRLD 652

Query: 61  QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           QLIYIPLP E SRLQIFKACLRKSP+SKDVDL  LA+FT GFSGADITEICQRACK A R
Sbjct: 653 QLIYIPLPDESSRLQIFKACLRKSPISKDVDLAALARFTHGFSGADITEICQRACKYAIR 712

Query: 121 EEIENDI--RRRKGKQPEAIE----DEVAEIKAEHFEESMKYACKS-------------- 160
           E+IE DI   RRK + PEA+E    DEV EIK  HFEESMK+A +S              
Sbjct: 713 EDIEKDIEKERRKRENPEAMEEDDTDEVPEIKPAHFEESMKFARRSVSDADIRKYQLFAQ 772

Query: 161 ---QSRGFGDEFGFCE--TAVAANNLIPVSSITDGNGEDD 195
              QSRGFG EF F +     AA+   P SS+T   G+DD
Sbjct: 773 TLQQSRGFGSEFRFPDRNENTAADASDPFSSVT-AEGDDD 811

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224127332|ref|XP_002329251.1| predicted protein [Populus trichocarpa] gi|222870705|gb|EEF07836.1| predicted protein [Populus trichocarpa]

 Score =  255 bits (651), Expect = 8e-66,   Method: Compositional matrix adjust.
 Identities = 136/215 (63%), Positives = 159/215 (73%), Gaps = 23/215 (10%)

Query: 4   SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
           SI IQRG+    AGGAADR+ NQLLTEMDGLSAKKT+F+IG TNRPDIIDPAL+RPGRLD
Sbjct: 565 SIAIQRGNSVGDAGGAADRVLNQLLTEMDGLSAKKTVFIIGATNRPDIIDPALMRPGRLD 624

Query: 61  QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           QLIYIPLP E SRLQIFKACLRKSPVSKDVDL+ LA+ T+GFSGADITEICQRACK A R
Sbjct: 625 QLIYIPLPDEGSRLQIFKACLRKSPVSKDVDLQVLAKHTEGFSGADITEICQRACKYAVR 684

Query: 121 EEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKS-----------------QSR 163
           E+IE DI+R+     +++E+ +  +K  HFEESM+YA KS                 QSR
Sbjct: 685 EDIEKDIKRKIEGLEDSMEEGMTWLKVSHFEESMRYARKSVSDSDILKYQMFSQTLQQSR 744

Query: 164 GFGDEFGFCETAVAANNLIPVSSITDGNGEDDNVY 198
           GFG +F F E A +A+ L PV  +T   G DD +Y
Sbjct: 745 GFGSDFKFSEAATSADGLNPV--VTSAGG-DDELY 776

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224133614|ref|XP_002321618.1| predicted protein [Populus trichocarpa] gi|222868614|gb|EEF05745.1| predicted protein [Populus trichocarpa]

 Score =  255 bits (651), Expect = 9e-66,   Method: Compositional matrix adjust.
 Identities = 144/221 (65%), Positives = 155/221 (70%), Gaps = 29/221 (13%)

Query: 4   SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
           SI  QRGS    AGGAADR+ NQLLTEMDG++AKKT+F+IG TNRPDIIDPALLRPGRLD
Sbjct: 590 SIATQRGSSVGDAGGAADRVLNQLLTEMDGMTAKKTVFIIGATNRPDIIDPALLRPGRLD 649

Query: 61  QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           QLIYIPLP E SRLQIFKACLRKSPVSKDVDL  LA++T GFSGADITEICQRACK A R
Sbjct: 650 QLIYIPLPDEASRLQIFKACLRKSPVSKDVDLTALARYTNGFSGADITEICQRACKYAIR 709

Query: 121 EEIENDIRRRKGKQ--PEAIE----DEVAEIKAEHFEESMKYACKS-------------- 160
           E IE DI + K KQ  PEA+E    DEV EIKA HFEESMKYA +S              
Sbjct: 710 ENIEKDIEKEKRKQENPEAMEEDDVDEVPEIKAAHFEESMKYARRSVSDADIRKYQSFAQ 769

Query: 161 ---QSRGFGDEFGF---CETAVAANNLIPVSSITDGNGEDD 195
              QSRGFG EF F    E A       P +S T    EDD
Sbjct: 770 TLQQSRGFGTEFRFPDRPENAADGGAADPFASATTAADEDD 810

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226504612|ref|NP_001142062.1| uncharacterized protein LOC100274218 [Zea mays] gi|194706964|gb|ACF87566.1| unknown [Zea mays]

 Score =  254 bits (649), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 136/198 (68%), Positives = 149/198 (75%), Gaps = 26/198 (13%)

Query: 4   SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
           SI  QRGS    AGGAADR+ NQLLTEMDG++AKKT+F+IG TNRPDIIDPALLRPGRLD
Sbjct: 137 SIATQRGSSVGDAGGAADRVLNQLLTEMDGMNAKKTVFIIGATNRPDIIDPALLRPGRLD 196

Query: 61  QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           QLIYIPLP E+SRLQIFKACLRKSPV+KDVDL  LA++TQGFSGADITEICQRACK A R
Sbjct: 197 QLIYIPLPDEQSRLQIFKACLRKSPVAKDVDLNALAKYTQGFSGADITEICQRACKYAIR 256

Query: 121 EEIENDI--RRRKGKQPEAIE----DEVAEIKAEHFEESMKYACKS-------------- 160
           E IE DI   RR    PEA+E    DE+AEIKA HFEESMKYA +S              
Sbjct: 257 ENIEKDIERERRMKDNPEAMEEDEVDEIAEIKAAHFEESMKYARRSVSDADIRKYQAFAQ 316

Query: 161 ---QSRGFGDEFGFCETA 175
              QSRGFG EF F E +
Sbjct: 317 TLQQSRGFGSEFRFSEQS 334

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

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	199
TAIR|locus:2831844	810	AtCDC48C "cell division cycle	0.798	0.196	0.721	1.1e-60
TAIR|locus:2101933	815	AtCDC48B "AT3G53230" [Arabidop	0.798	0.195	0.724	6.6e-58
TAIR|locus:2085064	809	CDC48 "cell division cycle 48"	0.798	0.196	0.710	4.2e-56
FB|FBgn0261014	801	TER94 "TER94" [Drosophila mela	0.798	0.198	0.627	7.7e-52
ZFIN|ZDB-GENE-030131-5408	806	vcp "valosin containing protei	0.763	0.188	0.679	2.8e-51
UNIPROTKB|Q6GL04	805	vcp "Transitional endoplasmic	0.763	0.188	0.679	6e-51
UNIPROTKB|H9KYT1	538	LOC430766 "Uncharacterized pro	0.763	0.282	0.672	1.1e-50
UNIPROTKB|P23787	805	vcp "Transitional endoplasmic	0.763	0.188	0.672	1.3e-50
UNIPROTKB|G3X757	806	VCP "Transitional endoplasmic	0.763	0.188	0.679	1.3e-50
UNIPROTKB|Q3ZBT1	806	VCP "Transitional endoplasmic	0.763	0.188	0.679	1.3e-50

TAIR|locus:2831844 AtCDC48C "cell division cycle 48C" [Arabidopsis thaliana (taxid:3702)]

 Score = 586 (211.3 bits), Expect = 1.1e-60, Sum P(2) = 1.1e-60
 Identities = 122/169 (72%), Positives = 138/169 (81%)

Query:     4 SIVIQRGSGAG---GAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
             SI  QRG+ AG   GAADR+ NQLLTEMDG++AKKT+F+IG TNRPDIID ALLRPGRLD
Sbjct:   584 SIATQRGNSAGDAGGAADRVLNQLLTEMDGMNAKKTVFIIGATNRPDIIDSALLRPGRLD 643

Query:    61 QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
             QLIYIPLP E SRL IFKACLRKSPV+KDVD+  LA++TQGFSGADITEICQRACK A R
Sbjct:   644 QLIYIPLPDEDSRLNIFKACLRKSPVAKDVDVTALAKYTQGFSGADITEICQRACKYAIR 703

Query:   121 EEIENDIR--RRKGKQPEAIE-----DEVAEIKAEHFEESMKYACKSQS 162
             E IE DI   RR+ + PEA+E     DEV+EI+A HFEESMKYA +S S
Sbjct:   704 ENIEKDIENERRRSQNPEAMEEDMVDDEVSEIRAAHFEESMKYARRSVS 752

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0016787 "hydrolase activity" evidence=IEA

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0005618 "cell wall" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005829 "cytosol" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=IDA

TAIR|locus:2101933 AtCDC48B "AT3G53230" [Arabidopsis thaliana (taxid:3702)]

 Score = 595 (214.5 bits), Expect = 6.6e-58, P = 6.6e-58
 Identities = 121/167 (72%), Positives = 140/167 (83%)

Query:     4 SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
             SI  QRG+    AGGAADR+ NQLLTEMDG++AKKT+F+IG TNRPDIIDPALLRPGRLD
Sbjct:   585 SIATQRGNSVGDAGGAADRVLNQLLTEMDGMNAKKTVFIIGATNRPDIIDPALLRPGRLD 644

Query:    61 QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
             QLIYIPLP E+SR QIFK+CLRKSPV+KDVDL  LA++TQGFSGADITEICQR+CK A R
Sbjct:   645 QLIYIPLPDEESRYQIFKSCLRKSPVAKDVDLRALAKYTQGFSGADITEICQRSCKYAIR 704

Query:   121 EEIENDIR--RRKGKQPEAIED---EVAEIKAEHFEESMKYACKSQS 162
             E IE DI   R++ + PEA+E+   E+AEIKA HFEESMKYA +S S
Sbjct:   705 ENIEKDIEKERKRAESPEAMEEDEEEIAEIKAGHFEESMKYARRSVS 751

GO:0005524 "ATP binding" evidence=ISS

GO:0005730 "nucleolus" evidence=IDA

GO:0046686 "response to cadmium ion" evidence=IEP

GO:0005886 "plasma membrane" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005654 "nucleoplasm" evidence=IDA

GO:0045732 "positive regulation of protein catabolic process" evidence=IDA

TAIR|locus:2085064 CDC48 "cell division cycle 48" [Arabidopsis thaliana (taxid:3702)]

 Score = 578 (208.5 bits), Expect = 4.2e-56, P = 4.2e-56
 Identities = 120/169 (71%), Positives = 137/169 (81%)

Query:     4 SIVIQRGSGAGG----AADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRL 59
             SI  QRG G+GG    AADR+ NQLLTEMDG++AKKT+F+IG TNRPDIID ALLRPGRL
Sbjct:   584 SIATQRGGGSGGDGGGAADRVLNQLLTEMDGMNAKKTVFIIGATNRPDIIDSALLRPGRL 643

Query:    60 DQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDAT 119
             DQLIYIPLP E SRL IFKA LRKSP++KDVD+  LA++TQGFSGADITEICQRACK A 
Sbjct:   644 DQLIYIPLPDEDSRLNIFKAALRKSPIAKDVDIGALAKYTQGFSGADITEICQRACKYAI 703

Query:   120 REEIENDIRR--RKGKQPEAIE----DEVAEIKAEHFEESMKYACKSQS 162
             RE IE DI +  R+ + PEA+E    DEV+EIKA HFEESMKYA +S S
Sbjct:   704 RENIEKDIEKEKRRSENPEAMEEDGVDEVSEIKAAHFEESMKYARRSVS 752

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0042802 "identical protein binding" evidence=IPI

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0005618 "cell wall" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0046686 "response to cadmium ion" evidence=IEP;RCA

GO:0005886 "plasma membrane" evidence=IDA

GO:0005635 "nuclear envelope" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005819 "spindle" evidence=IDA

GO:0009524 "phragmoplast" evidence=IDA

GO:0009846 "pollen germination" evidence=IMP

GO:0009860 "pollen tube growth" evidence=IMP

GO:0051301 "cell division" evidence=IMP

GO:0005829 "cytosol" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

GO:0048046 "apoplast" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=IDA

GO:0006486 "protein glycosylation" evidence=RCA

GO:0016310 "phosphorylation" evidence=RCA

GO:0042742 "defense response to bacterium" evidence=RCA

GO:0005737 "cytoplasm" evidence=IDA

FB|FBgn0261014 TER94 "TER94" [Drosophila melanogaster (taxid:7227)]

 Score = 497 (180.0 bits), Expect = 7.7e-52, Sum P(2) = 7.7e-52
 Identities = 106/169 (62%), Positives = 128/169 (75%)

Query:     4 SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
             SI   RG     AGGAADR+ NQ+LTEMDG+ AKK +F+IG TNRPDIIDPA+LRPGRLD
Sbjct:   578 SIAKARGGNVGDAGGAADRVINQILTEMDGMGAKKNVFIIGATNRPDIIDPAILRPGRLD 637

Query:    61 QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
             QLIYIPLP +KSR  I KA LRKSP++K+VDL  +A+ TQGFSGAD+TEICQRACK A R
Sbjct:   638 QLIYIPLPDDKSREAILKANLRKSPLAKEVDLTYIAKVTQGFSGADLTEICQRACKLAIR 697

Query:   121 EEIENDIRRRKGK---QPEAIE----DEVAEIKAEHFEESMKYACKSQS 162
             + IE +IRR K +   Q  A++    D V EI + HFEE+MK+A +S S
Sbjct:   698 QAIEAEIRREKERAENQNSAMDMDEDDPVPEITSAHFEEAMKFARRSVS 746

GO:0045169 "fusome" evidence=IDA;NAS

GO:0005737 "cytoplasm" evidence=IDA

GO:0016887 "ATPase activity" evidence=NAS

GO:0005783 "endoplasmic reticulum" evidence=NAS

GO:0007030 "Golgi organization" evidence=IMP

GO:0007317 "regulation of pole plasm oskar mRNA localization" evidence=IMP

GO:0016320 "endoplasmic reticulum membrane fusion" evidence=ISS

GO:0000226 "microtubule cytoskeleton organization" evidence=IMP

GO:0007029 "endoplasmic reticulum organization" evidence=IMP

GO:0045451 "pole plasm oskar mRNA localization" evidence=IMP

GO:0008103 "oocyte microtubule cytoskeleton polarization" evidence=IMP

GO:0008104 "protein localization" evidence=IMP

GO:0042052 "rhabdomere development" evidence=IMP

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

GO:0005524 "ATP binding" evidence=IEA

GO:0032436 "positive regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=IMP

GO:0000502 "proteasome complex" evidence=NAS

GO:0006508 "proteolysis" evidence=IMP

GO:0005811 "lipid particle" evidence=IDA

GO:0005875 "microtubule associated complex" evidence=IDA

GO:0030433 "ER-associated protein catabolic process" evidence=IMP

GO:0006200 "ATP catabolic process" evidence=IGI

GO:0048813 "dendrite morphogenesis" evidence=IMP

GO:0043523 "regulation of neuron apoptotic process" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IMP

ZFIN|ZDB-GENE-030131-5408 vcp "valosin containing protein" [Danio rerio (taxid:7955)]

 Score = 536 (193.7 bits), Expect = 2.8e-51, P = 2.8e-51
 Identities = 108/159 (67%), Positives = 130/159 (81%)

Query:    10 GSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPV 69
             G G GGAADR+ NQ+LTEMDG+S+KK +F+IG TNRPDIIDPA+LRPGRLDQLIYIPLP 
Sbjct:   591 GDG-GGAADRVINQILTEMDGMSSKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPD 649

Query:    70 EKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRR 129
             EKSR+ I KA LRKSP+SKDVDL+ LA+ T GFSGAD+TEICQRACK A RE IEN+IRR
Sbjct:   650 EKSRIAILKANLRKSPISKDVDLDFLAKMTNGFSGADLTEICQRACKLAIRESIENEIRR 709

Query:   130 RKGKQ--PEAIE----DEVAEIKAEHFEESMKYACKSQS 162
              + +Q  P A+E    D V EI+ +HFEE+M++A +S S
Sbjct:   710 ERERQTNPSAMEVEEDDPVPEIRKDHFEEAMRFARRSVS 748

GO:0016787 "hydrolase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA;ISS

GO:0016567 "protein ubiquitination" evidence=ISS

GO:0035861 "site of double-strand break" evidence=ISS

GO:0006302 "double-strand break repair" evidence=ISS

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=ISS

GO:0019985 "translesion synthesis" evidence=ISS

GO:0030433 "ER-associated protein catabolic process" evidence=ISS

GO:0009790 "embryo development" evidence=IMP

GO:2000058 "regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process" evidence=IMP

GO:0005634 "nucleus" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0008289 "lipid binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

UNIPROTKB|Q6GL04 vcp "Transitional endoplasmic reticulum ATPase" [Xenopus (Silurana) tropicalis (taxid:8364)]

 Score = 533 (192.7 bits), Expect = 6.0e-51, P = 6.0e-51
 Identities = 108/159 (67%), Positives = 129/159 (81%)

Query:    10 GSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPV 69
             G G GGAADR+ NQ+LTEMDG+S KK +F+IG TNRPDIIDPA+LRPGRLDQLIYIPLP 
Sbjct:   591 GDG-GGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPD 649

Query:    70 EKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRR 129
             EKSR+ I KA LRKSPV+KDVDL+ LA+ T GFSGAD+TEICQRACK A RE IEN+IRR
Sbjct:   650 EKSRIAILKANLRKSPVAKDVDLDFLAKMTNGFSGADLTEICQRACKLAIRESIENEIRR 709

Query:   130 RKGKQ--PEAIE----DEVAEIKAEHFEESMKYACKSQS 162
              + +Q  P A+E    D V EI+ +HFEE+M++A +S S
Sbjct:   710 ERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVS 748

GO:0000785 "chromatin" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0006200 "ATP catabolic process" evidence=ISS

GO:0006302 "double-strand break repair" evidence=ISS

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

GO:0016567 "protein ubiquitination" evidence=ISS

GO:0016887 "ATPase activity" evidence=ISS

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=ISS

GO:0019985 "translesion synthesis" evidence=ISS

GO:0030433 "ER-associated protein catabolic process" evidence=ISS

GO:0032403 "protein complex binding" evidence=ISS

GO:0034214 "protein hexamerization" evidence=ISS

GO:0035861 "site of double-strand break" evidence=ISS

GO:0035101 "FACT complex" evidence=ISS

UNIPROTKB|H9KYT1 LOC430766 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 527 (190.6 bits), Expect = 1.1e-50, P = 1.1e-50
 Identities = 107/159 (67%), Positives = 129/159 (81%)

Query:    10 GSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPV 69
             G G GGAADR+ NQ+LTEMDG+S KK +F+IG TNRPDIIDPA+LRPGRLDQLIYIPLP 
Sbjct:   323 GDG-GGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPD 381

Query:    70 EKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRR 129
             EKSR+ I KA LRKSPV+KDVDL+ LA+ T GFSGAD+TEICQRACK A RE IE++IRR
Sbjct:   382 EKSRVAILKANLRKSPVAKDVDLDFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRR 441

Query:   130 RKGKQ--PEAIE----DEVAEIKAEHFEESMKYACKSQS 162
              + +Q  P A+E    D V EI+ +HFEE+M++A +S S
Sbjct:   442 ERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVS 480

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|P23787 vcp "Transitional endoplasmic reticulum ATPase" [Xenopus laevis (taxid:8355)]

 Score = 530 (191.6 bits), Expect = 1.3e-50, P = 1.3e-50
 Identities = 107/159 (67%), Positives = 129/159 (81%)

Query:    10 GSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPV 69
             G G GGAADR+ NQ+LTEMDG+S KK +F+IG TNRPDIIDPA+LRPGRLDQLIYIPLP 
Sbjct:   591 GDG-GGAADRVINQILTEMDGMSIKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPD 649

Query:    70 EKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRR 129
             EKSR+ I KA LRKSPV+KDVD++ LA+ T GFSGAD+TEICQRACK A RE IEN+IRR
Sbjct:   650 EKSRMAILKANLRKSPVAKDVDVDFLAKMTNGFSGADLTEICQRACKLAIRESIENEIRR 709

Query:   130 RKGKQ--PEAIE----DEVAEIKAEHFEESMKYACKSQS 162
              + +Q  P A+E    D V EI+ +HFEE+M++A +S S
Sbjct:   710 ERDRQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVS 748

GO:0000785 "chromatin" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0006200 "ATP catabolic process" evidence=IDA

GO:0006302 "double-strand break repair" evidence=ISS

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

GO:0016567 "protein ubiquitination" evidence=ISS

GO:0016887 "ATPase activity" evidence=IDA

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=ISS

GO:0019985 "translesion synthesis" evidence=ISS

GO:0030433 "ER-associated protein catabolic process" evidence=ISS

GO:0032403 "protein complex binding" evidence=IPI

GO:0034214 "protein hexamerization" evidence=IDA

GO:0035861 "site of double-strand break" evidence=ISS

GO:0035101 "FACT complex" evidence=IPI

UNIPROTKB|G3X757 VCP "Transitional endoplasmic reticulum ATPase" [Bos taurus (taxid:9913)]

 Score = 530 (191.6 bits), Expect = 1.3e-50, P = 1.3e-50
 Identities = 108/159 (67%), Positives = 129/159 (81%)

Query:    10 GSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPV 69
             G G GGAADR+ NQ+LTEMDG+S KK +F+IG TNRPDIIDPA+LRPGRLDQLIYIPLP 
Sbjct:   591 GDG-GGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPD 649

Query:    70 EKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRR 129
             EKSR+ I KA LRKSPV+KDVDLE LA+ T GFSGAD+TEICQRACK A RE IE++IRR
Sbjct:   650 EKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRR 709

Query:   130 RKGKQ--PEAIE----DEVAEIKAEHFEESMKYACKSQS 162
              + +Q  P A+E    D V EI+ +HFEE+M++A +S S
Sbjct:   710 ERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVS 748

GO:0070842 "aggresome assembly" evidence=IEA

GO:0045732 "positive regulation of protein catabolic process" evidence=IEA

GO:0035861 "site of double-strand break" evidence=IEA

GO:0031593 "polyubiquitin binding" evidence=IEA

GO:0031334 "positive regulation of protein complex assembly" evidence=IEA

GO:0030970 "retrograde protein transport, ER to cytosol" evidence=IEA

GO:0019904 "protein domain specific binding" evidence=IEA

GO:0019903 "protein phosphatase binding" evidence=IEA

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=IEA

GO:0006919 "activation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0006302 "double-strand break repair" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000502 "proteasome complex" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

UNIPROTKB|Q3ZBT1 VCP "Transitional endoplasmic reticulum ATPase" [Bos taurus (taxid:9913)]

 Score = 530 (191.6 bits), Expect = 1.3e-50, P = 1.3e-50
 Identities = 108/159 (67%), Positives = 129/159 (81%)

Query:    10 GSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPV 69
             G G GGAADR+ NQ+LTEMDG+S KK +F+IG TNRPDIIDPA+LRPGRLDQLIYIPLP 
Sbjct:   591 GDG-GGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPD 649

Query:    70 EKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRR 129
             EKSR+ I KA LRKSPV+KDVDLE LA+ T GFSGAD+TEICQRACK A RE IE++IRR
Sbjct:   650 EKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRR 709

Query:   130 RKGKQ--PEAIE----DEVAEIKAEHFEESMKYACKSQS 162
              + +Q  P A+E    D V EI+ +HFEE+M++A +S S
Sbjct:   710 ERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVS 748

GO:0019985 "translesion synthesis" evidence=ISS

GO:0016567 "protein ubiquitination" evidence=ISS

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

GO:0006302 "double-strand break repair" evidence=ISS

GO:0035861 "site of double-strand break" evidence=ISS

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=ISS

GO:0030433 "ER-associated protein catabolic process" evidence=ISS

GO:0005829 "cytosol" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0008289 "lipid binding" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	199
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	2e-41
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	4e-40
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	3e-36
COG1222	406	COG1222, RPT1, ATP-dependent 26S proteasome regula	7e-35
TIGR01242	364	TIGR01242, 26Sp45, 26S proteasome subunit P45 fami	4e-33
TIGR01241	495	TIGR01241, FtsH_fam, ATP-dependent metalloprotease	1e-32
COG0465	596	COG0465, HflB, ATP-dependent Zn proteases [Posttra	1e-31
CHL00176	638	CHL00176, ftsH, cell division protein; Validated	4e-29
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	1e-27
PRK10733	644	PRK10733, hflB, ATP-dependent metalloprotease; Rev	5e-27
PTZ00454	398	PTZ00454, PTZ00454, 26S protease regulatory subuni	1e-25
PTZ00361	438	PTZ00361, PTZ00361, 26 proteosome regulatory subun	1e-19
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	5e-19
COG1223	368	COG1223, COG1223, Predicted ATPase (AAA+ superfami	7e-16
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	1e-15
TIGR03689	512	TIGR03689, pup_AAA, proteasome ATPase	2e-12
CHL00195	489	CHL00195, ycf46, Ycf46; Provisional	8e-12
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	8e-04

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

 Score =  148 bits (374), Expect = 2e-41
 Identities = 70/161 (43%), Positives = 102/161 (63%), Gaps = 2/161 (1%)

Query: 4   SIVIQRGSGAGGA-ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQL 62
           +I   RG+    +  DRI NQLLTEMDG+     + VI  TNRPDI+DPALLRPGR D+L
Sbjct: 557 AIAPARGARFDTSVTDRIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRL 616

Query: 63  IYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREE 122
           I +P P E++R +IFK   R  P+++DVDLE+LA+ T+G++GADI  +C+ A   A RE 
Sbjct: 617 ILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRES 676

Query: 123 IENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQSR 163
           I +  + +     E    ++ +++  HF E++K    S S+
Sbjct: 677 IGSPAKEKLEVGEEEFLKDL-KVEMRHFLEALKKVKPSVSK 716

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

 Score =  141 bits (358), Expect = 4e-40
 Identities = 64/145 (44%), Positives = 90/145 (62%), Gaps = 8/145 (5%)

Query: 4   SIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLI 63
           S+   RG    G+  R+  QLLTE+DG+   + + VI  TNRPD +DPALLRPGR D+LI
Sbjct: 346 SLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLI 405

Query: 64  YIPLPVEKSRLQIFKACLRKS--PVSKDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           Y+PLP  + RL+IFK  LR    P+++DVDLE+LA+ T+G+SGADI  + + A  +A RE
Sbjct: 406 YVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALVREAALEALRE 465

Query: 122 EIENDIRRRKGKQPEAIEDEVAEIK 146
               ++            D + +IK
Sbjct: 466 ARRREVTLD------DFLDALKKIK 484

Length = 494

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

 Score =  129 bits (328), Expect = 3e-36
 Identities = 51/100 (51%), Positives = 69/100 (69%)

Query: 23  QLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR 82
           QLL EMDG   +  + +I  TNR DI+DPA+LRPGR D++I +PLP E+ RL+I K   R
Sbjct: 257 QLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTR 316

Query: 83  KSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREE 122
           K  ++ DVDLE+LA+ T+G SGAD+  IC  A   A R++
Sbjct: 317 KMNLADDVDLEELAELTEGASGADLKAICTEAGMFAIRDD 356

Length = 389

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

 Score =  126 bits (319), Expect = 7e-35
 Identities = 56/114 (49%), Positives = 71/114 (62%), Gaps = 2/114 (1%)

Query: 11  SGAGGAAD--RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLP 68
           SG  G  +  R   +LL ++DG   +  + VI  TNRPDI+DPALLRPGR D+ I  PLP
Sbjct: 263 SGTSGDREVQRTMLELLNQLDGFDPRGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLP 322

Query: 69  VEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREE 122
            E+ R +I K   RK  ++ DVDLE LA+ T+GFSGAD+  IC  A   A RE 
Sbjct: 323 DEEGRAEILKIHTRKMNLADDVDLELLARLTEGFSGADLKAICTEAGMFAIRER 376

Length = 406

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

 Score =  121 bits (304), Expect = 4e-33
 Identities = 53/100 (53%), Positives = 69/100 (69%)

Query: 23  QLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR 82
           QLL E+DG   +  + VI  TNRPDI+DPALLRPGR D++I +PLP  + RL+I K   R
Sbjct: 248 QLLAELDGFDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTR 307

Query: 83  KSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREE 122
           K  +++DVDLE +A+ T+G SGAD+  IC  A   A REE
Sbjct: 308 KMKLAEDVDLEAIAKMTEGASGADLKAICTEAGMFAIREE 347

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

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

 Score =  122 bits (307), Expect = 1e-32
 Identities = 53/117 (45%), Positives = 71/117 (60%), Gaps = 3/117 (2%)

Query: 8   QRGSGAGGAAD---RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIY 64
           QRG+G GG  D   +  NQLL EMDG      + VI  TNRPD++DPALLRPGR D+ + 
Sbjct: 162 QRGAGLGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVV 221

Query: 65  IPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           + LP  K R +I K   +   ++ DVDL+ +A+ T GFSGAD+  +   A   A R+
Sbjct: 222 VDLPDIKGREEILKVHAKNKKLAPDVDLKAVARRTPGFSGADLANLLNEAALLAARK 278

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

 Score =  120 bits (302), Expect = 1e-31
 Identities = 58/133 (43%), Positives = 77/133 (57%), Gaps = 7/133 (5%)

Query: 8   QRGSGAGGAADRIP---NQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIY 64
           QRG+G GG  D      NQLL EMDG    + + VI  TNRPD++DPALLRPGR D+ I 
Sbjct: 257 QRGAGLGGGNDEREQTLNQLLVEMDGFGGNEGVIVIAATNRPDVLDPALLRPGRFDRQIL 316

Query: 65  IPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRA----CKDATR 120
           + LP  K R QI K   +  P+++DVDL+K+A+ T GFSGAD+  +   A     +   +
Sbjct: 317 VELPDIKGREQILKVHAKNKPLAEDVDLKKIARGTPGFSGADLANLLNEAALLAARRNKK 376

Query: 121 EEIENDIRRRKGK 133
           E    DI     +
Sbjct: 377 EITMRDIEEAIDR 389

Length = 596

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

 Score =  112 bits (283), Expect = 4e-29
 Identities = 56/120 (46%), Positives = 69/120 (57%), Gaps = 3/120 (2%)

Query: 8   QRGSGAGGAAD---RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIY 64
           QRG+G GG  D   +  NQLLTEMDG    K + VI  TNR DI+D ALLRPGR D+ I 
Sbjct: 290 QRGAGIGGGNDEREQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQIT 349

Query: 65  IPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIE 124
           + LP  + RL I K   R   +S DV LE +A+ T GFSGAD+  +   A     R +  
Sbjct: 350 VSLPDREGRLDILKVHARNKKLSPDVSLELIARRTPGFSGADLANLLNEAAILTARRKKA 409

Length = 638

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

 Score =  108 bits (272), Expect = 1e-27
 Identities = 61/153 (39%), Positives = 89/153 (58%), Gaps = 2/153 (1%)

Query: 4   SIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLI 63
           +I  +R    G    R+  QLLT MDGL  +  + VIG TNRPD +DPAL RPGR D+ I
Sbjct: 282 AIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREI 341

Query: 64  YIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEI 123
            I +P +++R +I K   R  P+++DVDL+KLA+ T GF GAD+  + + A   A R  I
Sbjct: 342 VIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFI 401

Query: 124 -ENDIRRRKGKQPEAIEDEVAEIKAEHFEESMK 155
            E  I     + P  +  E+ ++  + F E++K
Sbjct: 402 REGKINFEAEEIPAEVLKEL-KVTMKDFMEALK 433

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 =  107 bits (267), Expect = 5e-27
 Identities = 53/116 (45%), Positives = 72/116 (62%), Gaps = 3/116 (2%)

Query: 8   QRGSGAGGAAD---RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIY 64
           QRG+G GG  D   +  NQ+L EMDG    + I VI  TNRPD++DPALLRPGR D+ + 
Sbjct: 259 QRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVV 318

Query: 65  IPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           + LP  + R QI K  +R+ P++ D+D   +A+ T GFSGAD+  +   A   A R
Sbjct: 319 VGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAAR 374

Length = 644

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

 Score =  101 bits (254), Expect = 1e-25
 Identities = 48/111 (43%), Positives = 62/111 (55%)

Query: 11  SGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVE 70
           +GA     RI  +LL +MDG      + VI  TNR D +DPALLRPGRLD+ I  PLP  
Sbjct: 259 TGADREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR 318

Query: 71  KSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           + +  IF+    K  +S++VDLE      +  S ADI  ICQ A   A R+
Sbjct: 319 RQKRLIFQTITSKMNLSEEVDLEDFVSRPEKISAADIAAICQEAGMQAVRK 369

Length = 398

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

 Score = 85.6 bits (212), Expect = 1e-19
 Identities = 48/126 (38%), Positives = 69/126 (54%), Gaps = 12/126 (9%)

Query: 23  QLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR 82
           +LL ++DG  ++  + VI  TNR + +DPAL+RPGR+D+ I  P P EK++ +IF+    
Sbjct: 309 ELLNQLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTS 368

Query: 83  KSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREE------------IENDIRRR 130
           K  +++DVDLE+        SGADI  IC  A   A RE              E  + R+
Sbjct: 369 KMTLAEDVDLEEFIMAKDELSGADIKAICTEAGLLALRERRMKVTQADFRKAKEKVLYRK 428

Query: 131 KGKQPE 136
           KG  PE
Sbjct: 429 KGNIPE 434

Length = 438

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

 Score = 83.7 bits (207), Expect = 5e-19
 Identities = 49/139 (35%), Positives = 65/139 (46%), Gaps = 9/139 (6%)

Query: 9   RGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLP 68
           R S  G    R+  QLL  MDGL   + I VIG TNRPD +DPA  RPGR D+ I + LP
Sbjct: 92  RSSDQGEVERRVVAQLLALMDGLKRGQVI-VIGATNRPDGLDPAKRRPGRFDREIEVNLP 150

Query: 69  VEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIR 128
            E  RL+I +   R   +      + LA  T G SGAD+  +         +E    ++R
Sbjct: 151 DEAGRLEILQIHTRLMFLGPPGTGKTLAARTVGKSGADLGALA--------KEAALRELR 202

Query: 129 RRKGKQPEAIEDEVAEIKA 147
           R      E I     + + 
Sbjct: 203 RAIDLVGEYIGVTEDDFEE 221

Length = 494

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

 Score = 74.1 bits (182), Expect = 7e-16
 Identities = 42/111 (37%), Positives = 62/111 (55%), Gaps = 3/111 (2%)

Query: 15  GAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRL 74
           G    I N LLTE+DG+   + +  I  TNRP+++DPA+    R ++ I   LP ++ RL
Sbjct: 233 GDVSEIVNALLTELDGIKENEGVVTIAATNRPELLDPAI--RSRFEEEIEFKLPNDEERL 290

Query: 75  QIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITE-ICQRACKDATREEIE 124
           +I +   +K P+  D DL  LA  T+G SG DI E + + A   A  E+ E
Sbjct: 291 EILEYYAKKFPLPVDADLRYLAAKTKGMSGRDIKEKVLKTALHRAIAEDRE 341

Length = 368

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

 Score = 69.9 bits (172), Expect = 1e-15
 Identities = 32/65 (49%), Positives = 43/65 (66%), Gaps = 2/65 (3%)

Query: 4   SIVIQRGSGAGGAADRIPNQLLTEMDGLSAKK-TIFVIGVTNRPDIIDPALLRPGRLDQL 62
           ++   RGSG    + R+ NQLLTE+DG ++    + VI  TNRPD +DPALLR GR D++
Sbjct: 68  ALAGSRGSGGDSESRRVVNQLLTELDGFTSSLSKVIVIAATNRPDKLDPALLR-GRFDRI 126

Query: 63  IYIPL 67
           I  PL
Sbjct: 127 IEFPL 131

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

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

 Score = 64.3 bits (157), Expect = 2e-12
 Identities = 55/185 (29%), Positives = 75/185 (40%), Gaps = 47/185 (25%)

Query: 4   SIVIQRGSGAGGAADR-IPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQL 62
           S+   RGSG     +  +  QLL E+DG+ +   + VIG +NR D+IDPA+LRPGRLD  
Sbjct: 300 SLFRTRGSGVSSDVETTVVPQLLAEIDGVESLDNVIVIGASNREDMIDPAILRPGRLDVK 359

Query: 63  IYIPLPVEKSRLQIFKACLRKS-PVSKD---------VDLEKLAQ--------------- 97
           I I  P  ++   IF   L    P+ +D              L Q               
Sbjct: 360 IRIERPDAEAAADIFAKYLTDDLPLPEDLAAHDGDREATAAALIQRVVDALYARSEANRY 419

Query: 98  --------------FTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPE----AIE 139
                         F    SGA +  I  RA K A ++ I      + G + E    A+E
Sbjct: 420 VEVTYANGSTEVLYFADFVSGAMLANIVDRAKKRAIKDHITG---GQVGLRAEHLLAAVE 476

Query: 140 DEVAE 144
           DE  E
Sbjct: 477 DEFRE 481

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|177094 CHL00195, ycf46, Ycf46; Provisional

 Score = 62.7 bits (153), Expect = 8e-12
 Identities = 43/123 (34%), Positives = 68/123 (55%), Gaps = 9/123 (7%)

Query: 11  SGAGGAADRIPNQLLTEMDGLSAKKT-IFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPV 69
            G  G  +R+   L T +  LS KK+ +FV+   N  D++   +LR GR D++ ++ LP 
Sbjct: 337 KGDSGTTNRV---LATFITWLSEKKSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLPS 393

Query: 70  EKSRLQIFKACLRKS-PVS-KDVDLEKLAQFTQGFSGADITEICQRACKDATREEIE--- 124
            + R +IFK  L+K  P S K  D++KL++ +  FSGA+I +    A   A  E+ E   
Sbjct: 394 LEEREKIFKIHLQKFRPKSWKKYDIKKLSKLSNKFSGAEIEQSIIEAMYIAFYEKREFTT 453

Query: 125 NDI 127
           +DI
Sbjct: 454 DDI 456

Length = 489

>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 = 37.9 bits (88), Expect = 8e-04
 Identities = 18/46 (39%), Positives = 22/46 (47%)

Query: 22  NQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPL 67
             L T  D    ++ + VIG TNRP + D       RLD  I IPL
Sbjct: 106 RVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIPL 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	199
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	100.0
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	99.97
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	99.97
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	99.97
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	99.96
KOG0736	953	consensus Peroxisome assembly factor 2 containing	99.95
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	99.95
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.93
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	99.93
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.92
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	99.92
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.92
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	99.92
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	99.92
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	99.91
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	99.91
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	99.91
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	99.91
CHL00195	489	ycf46 Ycf46; Provisional	99.91
PRK03992	389	proteasome-activating nucleotidase; Provisional	99.9
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	99.9
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.9
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.9
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	99.89
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.88
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	99.88
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	99.87
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	99.86
CHL00176	638	ftsH cell division protein; Validated	99.86
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	99.86
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	99.85
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	99.84
CHL00206	2281	ycf2 Ycf2; Provisional	99.84
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	99.83
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.83
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	99.72
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.7
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.4
KOG0736	953	consensus Peroxisome assembly factor 2 containing	99.34
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.34
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	99.24
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	99.18
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	99.05
CHL00181	287	cbbX CbbX; Provisional	98.46
PF00004	132	AAA: ATPase family associated with various cellula	98.42
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	98.21
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.06
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	98.0
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	97.94
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	97.91
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	97.71
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.71
PRK00411	394	cdc6 cell division control protein 6; Reviewed	97.6
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	97.6
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.57
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.47
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	97.34
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	97.3
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	97.28
PRK06893	229	DNA replication initiation factor; Validated	97.27
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.27
PRK09087	226	hypothetical protein; Validated	97.08
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	97.05
PRK07940	394	DNA polymerase III subunit delta'; Validated	97.03
PRK08903	227	DnaA regulatory inactivator Hda; Validated	96.94
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	96.92
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	96.9
PRK12422	445	chromosomal replication initiation protein; Provis	96.87
PRK14088	440	dnaA chromosomal replication initiation protein; P	96.86
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	96.83
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	96.81
PRK14086	617	dnaA chromosomal replication initiation protein; P	96.74
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	96.73
PRK08084	235	DNA replication initiation factor; Provisional	96.7
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	96.67
PRK08727	233	hypothetical protein; Validated	96.63
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	96.57
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	96.52
PRK06620	214	hypothetical protein; Validated	96.51
PRK12402	337	replication factor C small subunit 2; Reviewed	96.46
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	96.43
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	96.41
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	96.41
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	96.4
PRK14087	450	dnaA chromosomal replication initiation protein; P	96.38
PRK00440	319	rfc replication factor C small subunit; Reviewed	96.38
CHL00195	489	ycf46 Ycf46; Provisional	96.35
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	96.34
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	96.34
PRK05642	234	DNA replication initiation factor; Validated	96.31
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	96.22
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	96.2
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	96.19
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	96.14
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	96.12
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	96.09
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	96.0
PRK06964	342	DNA polymerase III subunit delta'; Validated	95.99
PRK10865	857	protein disaggregation chaperone; Provisional	95.93
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	95.93
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	95.93
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	95.87
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	95.84
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	95.84
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	95.64
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	95.64
PRK13342	413	recombination factor protein RarA; Reviewed	95.63
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	95.62
PTZ00112	1164	origin recognition complex 1 protein; Provisional	95.56
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	95.53
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	95.52
PRK04132	846	replication factor C small subunit; Provisional	95.44
PRK04195	482	replication factor C large subunit; Provisional	95.43
PRK05707	328	DNA polymerase III subunit delta'; Validated	95.35
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	95.32
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	95.26
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	95.09
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	95.02
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	95.0
COG0593	408	DnaA ATPase involved in DNA replication initiation	94.97
PRK09112	351	DNA polymerase III subunit delta'; Validated	94.96
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	94.88
PF09336	62	Vps4_C: Vps4 C terminal oligomerisation domain; In	94.81
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	94.6
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	94.29
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	94.23
PHA02544	316	44 clamp loader, small subunit; Provisional	94.2
PLN03025	319	replication factor C subunit; Provisional	94.11
smart00350	509	MCM minichromosome maintenance proteins.	93.82
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	93.74
COG0714	329	MoxR-like ATPases [General function prediction onl	93.68
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	93.59
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	93.31
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	93.28
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	93.27
PRK13341	725	recombination factor protein RarA/unknown domain f	93.26
PRK07993	334	DNA polymerase III subunit delta'; Validated	93.18
PRK08769	319	DNA polymerase III subunit delta'; Validated	93.17
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	92.92
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	92.86
PRK06090	319	DNA polymerase III subunit delta'; Validated	92.82
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	92.53
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	92.5
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	92.44
PRK05564	313	DNA polymerase III subunit delta'; Validated	92.38
PRK07399	314	DNA polymerase III subunit delta'; Validated	91.97
PRK06871	325	DNA polymerase III subunit delta'; Validated	91.89
PRK07471	365	DNA polymerase III subunit delta'; Validated	91.72
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	89.98
CHL00095	821	clpC Clp protease ATP binding subunit	89.33
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	89.3
PRK08058	329	DNA polymerase III subunit delta'; Validated	89.24
PRK06581	263	DNA polymerase III subunit delta'; Validated	88.94
PRK08485	206	DNA polymerase III subunit delta'; Validated	88.81
PRK07276	290	DNA polymerase III subunit delta'; Validated	88.73
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	87.34
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	87.2
PRK10865	857	protein disaggregation chaperone; Provisional	86.68
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	86.44
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	86.27
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	85.45
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	84.82
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	84.43
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	84.32
CHL00095	821	clpC Clp protease ATP binding subunit	83.99
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	83.35
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	82.6
COG1067	647	LonB Predicted ATP-dependent protease [Posttransla	81.81

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

Probab=100.00  E-value=5.5e-33  Score=252.48  Aligned_cols=145  Identities=54%  Similarity=0.847  Sum_probs=138.4

Q ss_pred             cceeeccCCCCCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhc
Q 039253            3 WSIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR   82 (199)
Q Consensus         3 ~sl~~~R~~~~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~   82 (199)
                      +|+++.|++..++.++|++++||++|||+....+|+||||||||+.||+|++||||||+.|+||+||.+.|.+||+.+++
T Consensus       537 Dsi~~~R~g~~~~v~~RVlsqLLtEmDG~e~~k~V~ViAATNRpd~ID~ALlRPGRlD~iiyVplPD~~aR~~Ilk~~~k  616 (693)
T KOG0730|consen  537 DALAGSRGGSSSGVTDRVLSQLLTEMDGLEALKNVLVIAATNRPDMIDPALLRPGRLDRIIYVPLPDLEARLEILKQCAK  616 (693)
T ss_pred             HhHhhccCCCccchHHHHHHHHHHHcccccccCcEEEEeccCChhhcCHHHcCCcccceeEeecCccHHHHHHHHHHHHh
Confidence            57899999888899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcccccc
Q 039253           83 KSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQS  162 (199)
Q Consensus        83 ~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps~~  162 (199)
                      ++++.+++|+..||+.|+|||||||..+|++|++.|+++.+..                 ..|+.+||++|++.++||..
T Consensus       617 kmp~~~~vdl~~La~~T~g~SGAel~~lCq~A~~~a~~e~i~a-----------------~~i~~~hf~~al~~~r~s~~  679 (693)
T KOG0730|consen  617 KMPFSEDVDLEELAQATEGYSGAEIVAVCQEAALLALRESIEA-----------------TEITWQHFEEALKAVRPSLT  679 (693)
T ss_pred             cCCCCccccHHHHHHHhccCChHHHHHHHHHHHHHHHHHhccc-----------------ccccHHHHHHHHHhhcccCC
Confidence            9999999999999999999999999999999999999999753                 56899999999999999987


Q ss_pred             cc
Q 039253          163 RG  164 (199)
Q Consensus       163 r~  164 (199)
                      ..
T Consensus       680 ~~  681 (693)
T KOG0730|consen  680 SE  681 (693)
T ss_pred             HH
Confidence            53

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

Probab=99.97  E-value=7.6e-32  Score=231.32  Aligned_cols=140  Identities=42%  Similarity=0.628  Sum_probs=129.4

Q ss_pred             cceeeccCCCCCc---hhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHH
Q 039253            3 WSIVIQRGSGAGG---AADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKA   79 (199)
Q Consensus         3 ~sl~~~R~~~~~~---~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~   79 (199)
                      +||+.+|....++   ...|+.-+||++||||.+..+|-||+|||+++.||||++||||||++|+||+||.+.|.+||+.
T Consensus       254 DAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~~~nvKVI~ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR~~Il~I  333 (406)
T COG1222         254 DAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKI  333 (406)
T ss_pred             hhhhcccccCCCCchHHHHHHHHHHHHhccCCCCCCCeEEEEecCCccccChhhcCCCcccceeecCCCCHHHHHHHHHH
Confidence            5789999765333   3568899999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccc
Q 039253           80 CLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACK  159 (199)
Q Consensus        80 ~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~P  159 (199)
                      |.+++.+..++||+.||+.|+|+|||||+++|.+|.+.|+|+..                   ..+|++||.+|..++..
T Consensus       334 HtrkM~l~~dvd~e~la~~~~g~sGAdlkaictEAGm~AiR~~R-------------------~~Vt~~DF~~Av~KV~~  394 (406)
T COG1222         334 HTRKMNLADDVDLELLARLTEGFSGADLKAICTEAGMFAIRERR-------------------DEVTMEDFLKAVEKVVK  394 (406)
T ss_pred             HhhhccCccCcCHHHHHHhcCCCchHHHHHHHHHHhHHHHHhcc-------------------CeecHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999885                   67999999999998865


Q ss_pred             cc
Q 039253          160 SQ  161 (199)
Q Consensus       160 s~  161 (199)
                      ..
T Consensus       395 ~~  396 (406)
T COG1222         395 KK  396 (406)
T ss_pred             cc
Confidence            43

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

Probab=99.97  E-value=3.1e-31  Score=239.35  Aligned_cols=158  Identities=39%  Similarity=0.650  Sum_probs=138.9

Q ss_pred             cceeeccCCCCCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhc
Q 039253            3 WSIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR   82 (199)
Q Consensus         3 ~sl~~~R~~~~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~   82 (199)
                      +||+++|+...++.+.|++||||++|||+..+.+|+||+|||||+.||||++||||||+.+++++|+.++|.+||+.+.+
T Consensus       614 DaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDpAiLRPGRlDk~LyV~lPn~~eR~~ILK~~tk  693 (802)
T KOG0733|consen  614 DALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDPAILRPGRLDKLLYVGLPNAEERVAILKTITK  693 (802)
T ss_pred             hhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcccchhhcCCCccCceeeecCCCHHHHHHHHHHHhc
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             --CCCCCCcccHHHHHhhCC--CCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcc
Q 039253           83 --KSPVSKDVDLEKLAQFTQ--GFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYAC  158 (199)
Q Consensus        83 --~~~~~~~~~l~~la~~t~--G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~  158 (199)
                        +.++.++++++.||..+.  |||||||..||++|.+.|+++.+..... ..  ...........+|..||.+|+++++
T Consensus       694 n~k~pl~~dVdl~eia~~~~c~gftGADLaaLvreAsi~AL~~~~~~~~~-~~--~~~~~~~~~~~~t~~hF~eA~~~i~  770 (802)
T KOG0733|consen  694 NTKPPLSSDVDLDEIARNTKCEGFTGADLAALVREASILALRESLFEIDS-SE--DDVTVRSSTIIVTYKHFEEAFQRIR  770 (802)
T ss_pred             cCCCCCCcccCHHHHhhcccccCCchhhHHHHHHHHHHHHHHHHHhhccc-cC--cccceeeeeeeecHHHHHHHHHhcC
Confidence              778889999999999887  9999999999999999999998752211 11  1111111134589999999999999


Q ss_pred             ccccc
Q 039253          159 KSQSR  163 (199)
Q Consensus       159 Ps~~r  163 (199)
                      ||++.
T Consensus       771 pSv~~  775 (802)
T KOG0733|consen  771 PSVSE  775 (802)
T ss_pred             CCccH
Confidence            99985

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

Probab=99.97  E-value=1.7e-31  Score=230.99  Aligned_cols=170  Identities=35%  Similarity=0.495  Sum_probs=140.9

Q ss_pred             cceeeccCCC-CCchhhHHHHHHHHHHhCCCCC-CC---EEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHH
Q 039253            3 WSIVIQRGSG-AGGAADRIPNQLLTEMDGLSAK-KT---IFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIF   77 (199)
Q Consensus         3 ~sl~~~R~~~-~~~~~~r~~~~lL~~ld~~~~~-~~---VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il   77 (199)
                      +|||++|++. +|+.++|+.++||.+|||+... .+   |+|+++||.||+||+||+|  ||+++|+||+|+.+.|..+|
T Consensus       314 Dslcs~RG~s~EHEaSRRvKsELLvQmDG~~~t~e~~k~VmVLAATN~PWdiDEAlrR--RlEKRIyIPLP~~~~R~~Li  391 (491)
T KOG0738|consen  314 DSLCSQRGGSSEHEASRRVKSELLVQMDGVQGTLENSKVVMVLAATNFPWDIDEALRR--RLEKRIYIPLPDAEARSALI  391 (491)
T ss_pred             HHHHhcCCCccchhHHHHHHHHHHHHhhccccccccceeEEEEeccCCCcchHHHHHH--HHhhheeeeCCCHHHHHHHH
Confidence            4799999866 8889999999999999999653 33   9999999999999999999  99999999999999999999


Q ss_pred             HHhhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhc
Q 039253           78 KACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYA  157 (199)
Q Consensus        78 ~~~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~  157 (199)
                      +..++..++.+++++..||+.++||||+||.++|++|.++++||.+.......- ... .......+++++||+.|++++
T Consensus       392 ~~~l~~~~~~~~~~~~~lae~~eGySGaDI~nvCreAsm~~mRR~i~g~~~~ei-~~l-akE~~~~pv~~~Dfe~Al~~v  469 (491)
T KOG0738|consen  392 KILLRSVELDDPVNLEDLAERSEGYSGADITNVCREASMMAMRRKIAGLTPREI-RQL-AKEEPKMPVTNEDFEEALRKV  469 (491)
T ss_pred             HHhhccccCCCCccHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHhcCCcHHh-hhh-hhhccccccchhhHHHHHHHc
Confidence            999999999999999999999999999999999999999999998753211100 000 001112679999999999999


Q ss_pred             cccccc-cCCcccccchhhh
Q 039253          158 CKSQSR-GFGDEFGFCETAV  176 (199)
Q Consensus       158 ~Ps~~r-~~~~~~~~~~~~~  176 (199)
                      +||++. .+...=||+++-+
T Consensus       470 ~pSvs~~d~~k~ekW~~efG  489 (491)
T KOG0738|consen  470 RPSVSAADLEKYEKWMDEFG  489 (491)
T ss_pred             CcCCCHHHHHHHHHHHHHhc
Confidence            999994 4444445555443

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

Probab=99.96  E-value=1.6e-29  Score=228.28  Aligned_cols=168  Identities=35%  Similarity=0.499  Sum_probs=141.9

Q ss_pred             cceeeccCCCCCchhhHHHHHHHHHHhCCCCC----CCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHH
Q 039253            3 WSIVIQRGSGAGGAADRIPNQLLTEMDGLSAK----KTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFK   78 (199)
Q Consensus         3 ~sl~~~R~~~~~~~~~r~~~~lL~~ld~~~~~----~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~   78 (199)
                      +||+++|...+-+.++|+++|||+.||++...    .+|+||+|||||+.||||++|+||||+.|.++.|++.+|++||+
T Consensus       292 DAI~pkRe~aqreMErRiVaQLlt~mD~l~~~~~~g~~VlVIgATnRPDslDpaLRRaGRFdrEI~l~vP~e~aR~~IL~  371 (802)
T KOG0733|consen  292 DAITPKREEAQREMERRIVAQLLTSMDELSNEKTKGDPVLVIGATNRPDSLDPALRRAGRFDREICLGVPSETAREEILR  371 (802)
T ss_pred             cccccchhhHHHHHHHHHHHHHHHhhhcccccccCCCCeEEEecCCCCcccCHHHhccccccceeeecCCchHHHHHHHH
Confidence            58999999988888999999999999999644    67999999999999999999999999999999999999999999


Q ss_pred             HhhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHH--hhcC--CC--------Cc----------
Q 039253           79 ACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIR--RRKG--KQ--------PE----------  136 (199)
Q Consensus        79 ~~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~--~~~~--~~--------~~----------  136 (199)
                      ..++++.+..++++..||+.|+||+||||.+||.+|+..|++|.+.....  ....  +.        ..          
T Consensus       372 ~~~~~lrl~g~~d~~qlA~lTPGfVGADL~AL~~~Aa~vAikR~ld~~~~p~~~~~~~ed~~~~~~~~d~S~i~~~~~~~  451 (802)
T KOG0733|consen  372 IICRGLRLSGDFDFKQLAKLTPGFVGADLMALCREAAFVAIKRILDQSSSPLTKVPISEDSSNKDAEEDQSSIKITSNAE  451 (802)
T ss_pred             HHHhhCCCCCCcCHHHHHhcCCCccchhHHHHHHHHHHHHHHHHhhcccCccccCCccccccCCCccchhhhhhcCCccc
Confidence            99999999999999999999999999999999999999999998753221  0000  00        00          


Q ss_pred             ---------------------chhhccccccHHHHHHHHHhccccccc-cCCcccc
Q 039253          137 ---------------------AIEDEVAEIKAEHFEESMKYACKSQSR-GFGDEFG  170 (199)
Q Consensus       137 ---------------------~~~~~~~~it~~df~~Al~~~~Ps~~r-~~~~~~~  170 (199)
                                           ....+...|+.+||+.|+..++||+.| ||.+.=+
T Consensus       452 ~~~~ld~v~~~~i~~~~d~~S~E~~~~L~i~~eDF~~Al~~iQPSakREGF~tVPd  507 (802)
T KOG0733|consen  452 RPLELDRVVQDAILNNPDPLSKELLEGLSIKFEDFEEALSKIQPSAKREGFATVPD  507 (802)
T ss_pred             ccccHHHHHHHHHHhCCCCcChHHhccceecHHHHHHHHHhcCcchhcccceecCC
Confidence                                 001122458999999999999999998 5665433

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

Probab=99.95  E-value=7.2e-28  Score=221.86  Aligned_cols=159  Identities=38%  Similarity=0.602  Sum_probs=137.7

Q ss_pred             cceeeccCCC--CCchhhHHHHHHHHHHhCCC--CCCCEEEEEeeCCCCCCCccccCCCccceEEEecCC-CHHHHHHHH
Q 039253            3 WSIVIQRGSG--AGGAADRIPNQLLTEMDGLS--AKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLP-VEKSRLQIF   77 (199)
Q Consensus         3 ~sl~~~R~~~--~~~~~~r~~~~lL~~ld~~~--~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P-~~~~R~~il   77 (199)
                      +||+|+|+..  +++.++|+++|||.+|||+.  ....|+||+|||||+.||||++||||||+.++++++ +.+.+..+|
T Consensus       774 DSlAP~RG~sGDSGGVMDRVVSQLLAELDgls~~~s~~VFViGATNRPDLLDpALLRPGRFDKLvyvG~~~d~esk~~vL  853 (953)
T KOG0736|consen  774 DSLAPNRGRSGDSGGVMDRVVSQLLAELDGLSDSSSQDVFVIGATNRPDLLDPALLRPGRFDKLVYVGPNEDAESKLRVL  853 (953)
T ss_pred             cccCccCCCCCCccccHHHHHHHHHHHhhcccCCCCCceEEEecCCCccccChhhcCCCccceeEEecCCccHHHHHHHH
Confidence            5899999854  77789999999999999997  456799999999999999999999999999999998 779999999


Q ss_pred             HHhhcCCCCCCcccHHHHHhhCC-CCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHh
Q 039253           78 KACLRKSPVSKDVDLEKLAQFTQ-GFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKY  156 (199)
Q Consensus        78 ~~~l~~~~~~~~~~l~~la~~t~-G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~  156 (199)
                      +...+++.++.++++..||++++ .|||||+.++|..|++.|++|.+........  ...........|+++||.+|+++
T Consensus       854 ~AlTrkFkLdedVdL~eiAk~cp~~~TGADlYsLCSdA~l~AikR~i~~ie~g~~--~~~e~~~~~v~V~~eDflks~~~  931 (953)
T KOG0736|consen  854 EALTRKFKLDEDVDLVEIAKKCPPNMTGADLYSLCSDAMLAAIKRTIHDIESGTI--SEEEQESSSVRVTMEDFLKSAKR  931 (953)
T ss_pred             HHHHHHccCCCCcCHHHHHhhCCcCCchhHHHHHHHHHHHHHHHHHHHHhhhccc--cccccCCceEEEEHHHHHHHHHh
Confidence            99999999999999999999986 7999999999999999999998765432211  01112223366899999999999


Q ss_pred             ccccccc
Q 039253          157 ACKSQSR  163 (199)
Q Consensus       157 ~~Ps~~r  163 (199)
                      ++||.++
T Consensus       932 l~PSvS~  938 (953)
T KOG0736|consen  932 LQPSVSE  938 (953)
T ss_pred             cCCcccH
Confidence            9999986

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

Probab=99.95  E-value=1.5e-27  Score=212.99  Aligned_cols=137  Identities=36%  Similarity=0.529  Sum_probs=127.9

Q ss_pred             cceeeccCCCCCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhc
Q 039253            3 WSIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR   82 (199)
Q Consensus         3 ~sl~~~R~~~~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~   82 (199)
                      +|++++|........++.+||||.+|||+..+.+||||+|||+|+.||+|+.||||||++|.+|.||...|.+||+.|++
T Consensus       406 DavG~kR~~~~~~y~kqTlNQLLvEmDGF~qNeGiIvigATNfpe~LD~AL~RPGRFD~~v~Vp~PDv~GR~eIL~~yl~  485 (752)
T KOG0734|consen  406 DAVGGKRNPSDQHYAKQTLNQLLVEMDGFKQNEGIIVIGATNFPEALDKALTRPGRFDRHVTVPLPDVRGRTEILKLYLS  485 (752)
T ss_pred             hhhcccCCccHHHHHHHHHHHHHHHhcCcCcCCceEEEeccCChhhhhHHhcCCCccceeEecCCCCcccHHHHHHHHHh
Confidence            57889998776568999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcc
Q 039253           83 KSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYAC  158 (199)
Q Consensus        83 ~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~  158 (199)
                      +.++..++|+.-||+-|.||+||||+++++.|++.|.....                   ..|+++||+-|-.++-
T Consensus       486 ki~~~~~VD~~iiARGT~GFsGAdLaNlVNqAAlkAa~dga-------------------~~VtM~~LE~akDrIl  542 (752)
T KOG0734|consen  486 KIPLDEDVDPKIIARGTPGFSGADLANLVNQAALKAAVDGA-------------------EMVTMKHLEFAKDRIL  542 (752)
T ss_pred             cCCcccCCCHhHhccCCCCCchHHHHHHHHHHHHHHHhcCc-------------------ccccHHHHhhhhhhee
Confidence            99999999999999999999999999999999999887764                   5689999998887764

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.93  E-value=6.3e-26  Score=214.89  Aligned_cols=160  Identities=44%  Similarity=0.686  Sum_probs=135.2

Q ss_pred             ceeeccCCC-CCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhc
Q 039253            4 SIVIQRGSG-AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR   82 (199)
Q Consensus         4 sl~~~R~~~-~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~   82 (199)
                      +|+++|+.. .+...++++++||++||++....+|+||+|||+|+.||+|++||||||++|+|++|+.++|.+||+.+++
T Consensus       557 ~l~~~r~~~~~~~~~~~~~~~lL~~ldg~~~~~~v~vI~aTn~~~~ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~  636 (733)
T TIGR01243       557 AIAPARGARFDTSVTDRIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTR  636 (733)
T ss_pred             hhhccCCCCCCccHHHHHHHHHHHHhhcccCCCCEEEEEeCCChhhCCHhhcCCCccceEEEeCCcCHHHHHHHHHHHhc
Confidence            577888755 4456789999999999999888899999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcccccc
Q 039253           83 KSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQS  162 (199)
Q Consensus        83 ~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps~~  162 (199)
                      +.++..++++..||+.|+||||+||+++|++|++.|+++.......... ............|+++||..|+++++||.+
T Consensus       637 ~~~~~~~~~l~~la~~t~g~sgadi~~~~~~A~~~a~~~~~~~~~~~~~-~~~~~~~~~~~~i~~~~f~~al~~~~ps~~  715 (733)
T TIGR01243       637 SMPLAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRESIGSPAKEKL-EVGEEEFLKDLKVEMRHFLEALKKVKPSVS  715 (733)
T ss_pred             CCCCCccCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHhhhccchhh-hcccccccccCcccHHHHHHHHHHcCCCCC
Confidence            9999889999999999999999999999999999999987643211000 000001112357999999999999999998


Q ss_pred             cc
Q 039253          163 RG  164 (199)
Q Consensus       163 r~  164 (199)
                      ..
T Consensus       716 ~~  717 (733)
T TIGR01243       716 KE  717 (733)
T ss_pred             HH
Confidence            74

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.

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

Probab=99.93  E-value=1.4e-25  Score=193.23  Aligned_cols=157  Identities=32%  Similarity=0.490  Sum_probs=134.2

Q ss_pred             cceeeccCCCCCchhhHHHHHHHHHHhCCCCCCC--EEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHh
Q 039253            3 WSIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKT--IFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKAC   80 (199)
Q Consensus         3 ~sl~~~R~~~~~~~~~r~~~~lL~~ld~~~~~~~--VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~   80 (199)
                      +|+++.|.+++|+....+.++|...+||+.++.+  |+|+||||||.+||.|++|  |+.+++++++|+..+|+.||+.+
T Consensus       196 ds~L~~R~s~dHEa~a~mK~eFM~~WDGl~s~~~~rVlVlgATNRP~DlDeAiiR--R~p~rf~V~lP~~~qR~kILkvi  273 (386)
T KOG0737|consen  196 DSFLGQRRSTDHEATAMMKNEFMALWDGLSSKDSERVLVLGATNRPFDLDEAIIR--RLPRRFHVGLPDAEQRRKILKVI  273 (386)
T ss_pred             HHHHhhcccchHHHHHHHHHHHHHHhccccCCCCceEEEEeCCCCCccHHHHHHH--hCcceeeeCCCchhhHHHHHHHH
Confidence            3567888777999999999999999999987765  9999999999999999999  99999999999999999999999


Q ss_pred             hcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHh---HHhhcCC----CC--cchhhccccccHHHHH
Q 039253           81 LRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIEND---IRRRKGK----QP--EAIEDEVAEIKAEHFE  151 (199)
Q Consensus        81 l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~---~~~~~~~----~~--~~~~~~~~~it~~df~  151 (199)
                      +++..+.+++|+..+|.+|+||||+||+++|..|++.++++.+...   .......    ..  .......++++++||.
T Consensus       274 Lk~e~~e~~vD~~~iA~~t~GySGSDLkelC~~Aa~~~ire~~~~~~~~~d~d~~~~d~~~~~~~~~~~~~r~l~~eDf~  353 (386)
T KOG0737|consen  274 LKKEKLEDDVDLDEIAQMTEGYSGSDLKELCRLAALRPIRELLVSETGLLDLDKAIADLKPTQAAASSCLLRPLEQEDFP  353 (386)
T ss_pred             hcccccCcccCHHHHHHhcCCCcHHHHHHHHHHHhHhHHHHHHHhcccchhhhhhhhhccCCcccccccccCcccHHHHH
Confidence            9999999999999999999999999999999999999999998764   0000000    00  0111225889999999


Q ss_pred             HHHHhccccc
Q 039253          152 ESMKYACKSQ  161 (199)
Q Consensus       152 ~Al~~~~Ps~  161 (199)
                      .|+.++-+++
T Consensus       354 ~a~~~v~~~~  363 (386)
T KOG0737|consen  354 KAINRVSASV  363 (386)
T ss_pred             HHHHhhhhHH
Confidence            9999777764

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

Probab=99.92  E-value=3.7e-25  Score=202.75  Aligned_cols=124  Identities=46%  Similarity=0.722  Sum_probs=119.6

Q ss_pred             cceeeccCCCCCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhc
Q 039253            3 WSIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR   82 (199)
Q Consensus         3 ~sl~~~R~~~~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~   82 (199)
                      +|++|+|+.++.+.++|++||||++|||.++-.+|.|++||.||+.||||++||||+|+.++.++|++.+|.+|++.+..
T Consensus       770 dSiAPkRGhDsTGVTDRVVNQlLTelDG~Egl~GV~i~aaTsRpdliDpALLRpGRlD~~v~C~~P~~~eRl~il~~ls~  849 (952)
T KOG0735|consen  770 DSIAPKRGHDSTGVTDRVVNQLLTELDGAEGLDGVYILAATSRPDLIDPALLRPGRLDKLVYCPLPDEPERLEILQVLSN  849 (952)
T ss_pred             cccCcccCCCCCCchHHHHHHHHHhhccccccceEEEEEecCCccccCHhhcCCCccceeeeCCCCCcHHHHHHHHHHhh
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHh
Q 039253           83 KSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIEND  126 (199)
Q Consensus        83 ~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~  126 (199)
                      ....+.++|++.+|.+|+|||||||..++..|.+.|+++.+...
T Consensus       850 s~~~~~~vdl~~~a~~T~g~tgADlq~ll~~A~l~avh~~l~~~  893 (952)
T KOG0735|consen  850 SLLKDTDVDLECLAQKTDGFTGADLQSLLYNAQLAAVHEILKRE  893 (952)
T ss_pred             ccCCccccchHHHhhhcCCCchhhHHHHHHHHHHHHHHHHHHhc
Confidence            89888999999999999999999999999999999999987543

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

Probab=99.92  E-value=3.2e-26  Score=193.17  Aligned_cols=159  Identities=26%  Similarity=0.429  Sum_probs=137.7

Q ss_pred             cceeeccCCCCCchhhHHHHHHHHHHhCCCCC-CCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhh
Q 039253            3 WSIVIQRGSGAGGAADRIPNQLLTEMDGLSAK-KTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACL   81 (199)
Q Consensus         3 ~sl~~~R~~~~~~~~~r~~~~lL~~ld~~~~~-~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l   81 (199)
                      +|+|++|+.++++.++|+..+||.+|.|+..+ ++|+|+++||-||.||.|++|  ||+++|++|+|+...|..||+.++
T Consensus       235 Dslcg~r~enEseasRRIKTEfLVQMqGVG~d~~gvLVLgATNiPw~LDsAIRR--RFekRIYIPLPe~~AR~~MF~lhl  312 (439)
T KOG0739|consen  235 DSLCGSRSENESEASRRIKTEFLVQMQGVGNDNDGVLVLGATNIPWVLDSAIRR--RFEKRIYIPLPEAHARARMFKLHL  312 (439)
T ss_pred             hhhccCCCCCchHHHHHHHHHHHHhhhccccCCCceEEEecCCCchhHHHHHHH--HhhcceeccCCcHHHhhhhheecc
Confidence            47999999999999999999999999999654 679999999999999999999  999999999999999999999999


Q ss_pred             cCCCCC-CcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCC-----c---c---------------
Q 039253           82 RKSPVS-KDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQP-----E---A---------------  137 (199)
Q Consensus        82 ~~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~-----~---~---------------  137 (199)
                      ...+.. .+.|+..|+++|+||||+||.-+|+.|.++.+|+.+.+.+..++....     .   .               
T Consensus       313 G~tp~~LT~~d~~eL~~kTeGySGsDisivVrDalmePvRkvqsAthFk~v~~~s~~~~~~~lltpcspgd~ga~em~w~  392 (439)
T KOG0739|consen  313 GDTPHVLTEQDFKELARKTEGYSGSDISIVVRDALMEPVRKVQSATHFKKVSGPSNPSEVDDLLTPCSPGDPGAIEMSWM  392 (439)
T ss_pred             CCCccccchhhHHHHHhhcCCCCcCceEEEehhhhhhhHHHhhhhhhhhccCCCCChhhhccccCCCCCCCcchhhhhhc
Confidence            887654 678999999999999999999999999999999987766544321100     0   0               


Q ss_pred             ----hhhccccccHHHHHHHHHhccccccc
Q 039253          138 ----IEDEVAEIKAEHFEESMKYACKSQSR  163 (199)
Q Consensus       138 ----~~~~~~~it~~df~~Al~~~~Ps~~r  163 (199)
                          ...-.+++|+.||..+|...+|++..
T Consensus       393 dv~~dkl~eP~vt~~D~~k~l~~tkPTvn~  422 (439)
T KOG0739|consen  393 DVPADKLLEPPVTMRDFLKSLSRTKPTVNE  422 (439)
T ss_pred             cCCHhhccCCCccHHHHHHHHhhcCCCCCH
Confidence                11123679999999999999999976

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

Probab=99.92  E-value=6.4e-25  Score=199.53  Aligned_cols=142  Identities=45%  Similarity=0.737  Sum_probs=131.6

Q ss_pred             cceeeccCCCCCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhc
Q 039253            3 WSIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR   82 (199)
Q Consensus         3 ~sl~~~R~~~~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~   82 (199)
                      +++++.|+.+.++..+|++++||.+|++++...+|+||+|||+|+.+|+|++||||||+.|+|++|+.++|.+||+.++.
T Consensus       345 Ds~~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~~v~vi~aTN~p~~ld~a~lR~gRfd~~i~v~~pd~~~r~~i~~~~~~  424 (494)
T COG0464         345 DSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLR  424 (494)
T ss_pred             hhhhccCCCCCchHHHHHHHHHHHHhcCCCccCceEEEecCCCccccCHhhcccCccceEeecCCCCHHHHHHHHHHHhc
Confidence            46888998887777799999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC--CCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcccc
Q 039253           83 KSP--VSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKS  160 (199)
Q Consensus        83 ~~~--~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps  160 (199)
                      ...  +..++++..+++.|+||||+||..+|++|++.++++..                  ...+|++||..|++.++||
T Consensus       425 ~~~~~~~~~~~~~~l~~~t~~~sgadi~~i~~ea~~~~~~~~~------------------~~~~~~~~~~~a~~~~~p~  486 (494)
T COG0464         425 DKKPPLAEDVDLEELAEITEGYSGADIAALVREAALEALREAR------------------RREVTLDDFLDALKKIKPS  486 (494)
T ss_pred             ccCCcchhhhhHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHhc------------------cCCccHHHHHHHHHhcCCC
Confidence            543  45789999999999999999999999999999999874                  1579999999999999999


Q ss_pred             cc
Q 039253          161 QS  162 (199)
Q Consensus       161 ~~  162 (199)
                      ..
T Consensus       487 ~~  488 (494)
T COG0464         487 VT  488 (494)
T ss_pred             CC
Confidence            76

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

Probab=99.92  E-value=5.5e-26  Score=202.91  Aligned_cols=156  Identities=37%  Similarity=0.540  Sum_probs=136.9

Q ss_pred             cceeeccCCC--CCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHh
Q 039253            3 WSIVIQRGSG--AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKAC   80 (199)
Q Consensus         3 ~sl~~~R~~~--~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~   80 (199)
                      +|||++|++.  .++..+.++||||+.|||++.-++|+||+.|||++.||+|++|||||+.++++.+||++.|.+||+.|
T Consensus       334 DAICKqRGS~~g~TGVhD~VVNQLLsKmDGVeqLNNILVIGMTNR~DlIDEALLRPGRlEVqmEIsLPDE~gRlQIl~IH  413 (744)
T KOG0741|consen  334 DAICKQRGSMAGSTGVHDTVVNQLLSKMDGVEQLNNILVIGMTNRKDLIDEALLRPGRLEVQMEISLPDEKGRLQILKIH  413 (744)
T ss_pred             HHHHHhcCCCCCCCCccHHHHHHHHHhcccHHhhhcEEEEeccCchhhHHHHhcCCCceEEEEEEeCCCccCceEEEEhh
Confidence            5899999876  56678999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCC----CCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHh
Q 039253           81 LRKS----PVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKY  156 (199)
Q Consensus        81 l~~~----~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~  156 (199)
                      .+++    .+..++|+.+||.+|..||||+|..+|+.|...|+.|.+.....    ........+...|+++||..||..
T Consensus       414 T~rMre~~~l~~dVdl~elA~lTKNfSGAEleglVksA~S~A~nR~vk~~~~----~~~~~~~~e~lkV~r~DFl~aL~d  489 (744)
T KOG0741|consen  414 TKRMRENNKLSADVDLKELAALTKNFSGAELEGLVKSAQSFAMNRHVKAGGK----VEVDPVAIENLKVTRGDFLNALED  489 (744)
T ss_pred             hhhhhhcCCCCCCcCHHHHHHHhcCCchhHHHHHHHHHHHHHHHhhhccCcc----eecCchhhhheeecHHHHHHHHHh
Confidence            9776    45689999999999999999999999999999999988754311    112223344577999999999999


Q ss_pred             cccccc
Q 039253          157 ACKSQS  162 (199)
Q Consensus       157 ~~Ps~~  162 (199)
                      ++|+-.
T Consensus       490 VkPAFG  495 (744)
T KOG0741|consen  490 VKPAFG  495 (744)
T ss_pred             cCcccC
Confidence            999854

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

Probab=99.92  E-value=2.6e-24  Score=190.94  Aligned_cols=138  Identities=38%  Similarity=0.558  Sum_probs=123.9

Q ss_pred             ceeeccCCCC---CchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHh
Q 039253            4 SIVIQRGSGA---GGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKAC   80 (199)
Q Consensus         4 sl~~~R~~~~---~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~   80 (199)
                      +++++|.+..   +....+++.+||++||++....+|+||+|||+|+.||+|++||||||++|+|++|+.++|.+||+.+
T Consensus       249 ~i~~~r~~~~~~~d~~~~r~l~~LL~~ld~~~~~~~v~VI~aTN~~d~LDpAllR~GRfd~~I~~~~P~~~~R~~Il~~~  328 (398)
T PTZ00454        249 SIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTI  328 (398)
T ss_pred             hhccccccccCCccHHHHHHHHHHHHHhhccCCCCCEEEEEecCCchhCCHHHcCCCcccEEEEeCCcCHHHHHHHHHHH
Confidence            4566775432   2345678999999999998888999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcccc
Q 039253           81 LRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKS  160 (199)
Q Consensus        81 l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps  160 (199)
                      +.++.+..++++..+|..|+||||+||+++|++|.+.|+++..                   ..|+++||..|++.+...
T Consensus       329 ~~~~~l~~dvd~~~la~~t~g~sgaDI~~l~~eA~~~A~r~~~-------------------~~i~~~df~~A~~~v~~~  389 (398)
T PTZ00454        329 TSKMNLSEEVDLEDFVSRPEKISAADIAAICQEAGMQAVRKNR-------------------YVILPKDFEKGYKTVVRK  389 (398)
T ss_pred             HhcCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHcCC-------------------CccCHHHHHHHHHHHHhc
Confidence            9999988899999999999999999999999999999998763                   569999999999998654

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

Probab=99.91  E-value=1.9e-24  Score=201.26  Aligned_cols=159  Identities=40%  Similarity=0.605  Sum_probs=136.0

Q ss_pred             cceeeccCC----CCCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHH
Q 039253            3 WSIVIQRGS----GAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFK   78 (199)
Q Consensus         3 ~sl~~~R~~----~~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~   78 (199)
                      ++++++|++    +.++.....+||||.+|||+.....|||+++||+|+-||+|++||||||++|++++|+..+|.+|++
T Consensus       413 da~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~~~~~vi~~a~tnr~d~ld~allrpGRfdr~i~i~~p~~~~r~~i~~  492 (774)
T KOG0731|consen  413 DAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGFETSKGVIVLAATNRPDILDPALLRPGRFDRQIQIDLPDVKGRASILK  492 (774)
T ss_pred             ccccccccccccCCCChHHHHHHHHHHHHhcCCcCCCcEEEEeccCCccccCHHhcCCCccccceeccCCchhhhHHHHH
Confidence            467888842    3445566899999999999999889999999999999999999999999999999999999999999


Q ss_pred             HhhcCCCCC-CcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhc
Q 039253           79 ACLRKSPVS-KDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYA  157 (199)
Q Consensus        79 ~~l~~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~  157 (199)
                      .|+++..+. .++++..||.+|+||+|+||+++|.+|+..|+++..                   ..|+..||+.|++++
T Consensus       493 ~h~~~~~~~~e~~dl~~~a~~t~gf~gadl~n~~neaa~~a~r~~~-------------------~~i~~~~~~~a~~Rv  553 (774)
T KOG0731|consen  493 VHLRKKKLDDEDVDLSKLASLTPGFSGADLANLCNEAALLAARKGL-------------------REIGTKDLEYAIERV  553 (774)
T ss_pred             HHhhccCCCcchhhHHHHHhcCCCCcHHHHHhhhhHHHHHHHHhcc-------------------CccchhhHHHHHHHH
Confidence            999998885 789999999999999999999999999999999875                   679999999999944


Q ss_pred             c------ccccc-cCCcccccchhhhhhcC
Q 039253          158 C------KSQSR-GFGDEFGFCETAVAANN  180 (199)
Q Consensus       158 ~------Ps~~r-~~~~~~~~~~~~~~~~~  180 (199)
                      .      +...+ +-...+-+||.+.|-.+
T Consensus       554 i~G~~~~~~~~~~~~~~~~a~~eagha~~g  583 (774)
T KOG0731|consen  554 IAGMEKKSRVLSLEEKKTVAYHEAGHAVVG  583 (774)
T ss_pred             hccccccchhcCHhhhhhhhhhhccchhhh
Confidence            3      22222 34455667777776555

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

Probab=99.91  E-value=2e-24  Score=179.03  Aligned_cols=138  Identities=38%  Similarity=0.552  Sum_probs=126.3

Q ss_pred             cceeeccCCCC---CchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHH
Q 039253            3 WSIVIQRGSGA---GGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKA   79 (199)
Q Consensus         3 ~sl~~~R~~~~---~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~   79 (199)
                      +||++.|..+.   .+...|..-+||+++||++...++-||++||+.+-||||++||||+|++|+||+|+++.|.+||+.
T Consensus       250 dsigs~r~e~~~ggdsevqrtmlellnqldgfeatknikvimatnridild~allrpgridrkiefp~p~e~ar~~ilki  329 (404)
T KOG0728|consen  250 DSIGSSRVESGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDILDPALLRPGRIDRKIEFPPPNEEARLDILKI  329 (404)
T ss_pred             cccccccccCCCCccHHHHHHHHHHHHhccccccccceEEEEeccccccccHhhcCCCcccccccCCCCCHHHHHHHHHH
Confidence            47888886553   334567888999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccc
Q 039253           80 CLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACK  159 (199)
Q Consensus        80 ~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~P  159 (199)
                      +.+++.+...+++..+|+...|-|||+++.+|.+|.+.|+++..                   ..+|++||+-|..++-.
T Consensus       330 hsrkmnl~rgi~l~kiaekm~gasgaevk~vcteagm~alrerr-------------------vhvtqedfemav~kvm~  390 (404)
T KOG0728|consen  330 HSRKMNLTRGINLRKIAEKMPGASGAEVKGVCTEAGMYALRERR-------------------VHVTQEDFEMAVAKVMQ  390 (404)
T ss_pred             hhhhhchhcccCHHHHHHhCCCCccchhhhhhhhhhHHHHHHhh-------------------ccccHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999875                   67999999999877643

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

Probab=99.91  E-value=1.7e-24  Score=198.05  Aligned_cols=156  Identities=39%  Similarity=0.587  Sum_probs=135.6

Q ss_pred             cceeeccCCC---CCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHH
Q 039253            3 WSIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKA   79 (199)
Q Consensus         3 ~sl~~~R~~~---~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~   79 (199)
                      +|++++|+.+   .+..-++.+||||.+|||+..+.+|+||++||||+-+|+|++||||||+.|.+++||...|++|++.
T Consensus       252 DAvGr~Rg~g~GggnderEQTLNQlLvEmDGF~~~~gviviaaTNRpdVlD~ALlRpgRFDRqI~V~~PDi~gRe~Ilkv  331 (596)
T COG0465         252 DAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGGNEGVIVIAATNRPDVLDPALLRPGRFDRQILVELPDIKGREQILKV  331 (596)
T ss_pred             hhcccccCCCCCCCchHHHHHHHHHHhhhccCCCCCceEEEecCCCcccchHhhcCCCCcceeeecCCcchhhHHHHHHH
Confidence            6788899744   4444567999999999999988999999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccc
Q 039253           80 CLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACK  159 (199)
Q Consensus        80 ~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~P  159 (199)
                      |+++.++..++++..+|+.|.||||+|+.+++.+|++.|+++..                   ..+++.||..|+.++--
T Consensus       332 H~~~~~l~~~Vdl~~iAr~tpGfsGAdL~nl~NEAal~aar~n~-------------------~~i~~~~i~ea~drv~~  392 (596)
T COG0465         332 HAKNKPLAEDVDLKKIARGTPGFSGADLANLLNEAALLAARRNK-------------------KEITMRDIEEAIDRVIA  392 (596)
T ss_pred             HhhcCCCCCcCCHHHHhhhCCCcccchHhhhHHHHHHHHHHhcC-------------------eeEeccchHHHHHHHhc
Confidence            99999999999999999999999999999999999999999875                   67999999999988741


Q ss_pred             c-------ccccCCcccccchhhhh
Q 039253          160 S-------QSRGFGDEFGFCETAVA  177 (199)
Q Consensus       160 s-------~~r~~~~~~~~~~~~~~  177 (199)
                      -       .+..-....-+||-+.|
T Consensus       393 G~erks~vise~ek~~~AYhEagha  417 (596)
T COG0465         393 GPERKSRVISEAEKKITAYHEAGHA  417 (596)
T ss_pred             CcCcCCcccChhhhcchHHHHHHHH
Confidence            1       22234445567777443

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

Probab=99.91  E-value=2e-24  Score=179.89  Aligned_cols=139  Identities=37%  Similarity=0.515  Sum_probs=127.0

Q ss_pred             cceeeccCCCC---CchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHH
Q 039253            3 WSIVIQRGSGA---GGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKA   79 (199)
Q Consensus         3 ~sl~~~R~~~~---~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~   79 (199)
                      +||+.+|..++   .....|..-+||+++||+++..+|-||++||+.+-||||++|+||+|++|+||+|+++.|..|++.
T Consensus       274 DAIGtKRfDSek~GDREVQRTMLELLNQLDGFss~~~vKviAATNRvDiLDPALlRSGRLDRKIEfP~Pne~aRarIlQI  353 (424)
T KOG0652|consen  274 DAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSSDDRVKVIAATNRVDILDPALLRSGRLDRKIEFPHPNEEARARILQI  353 (424)
T ss_pred             hhhccccccccccccHHHHHHHHHHHHhhcCCCCccceEEEeecccccccCHHHhhcccccccccCCCCChHHHHHHHHH
Confidence            46778886652   223567888999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccc
Q 039253           80 CLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACK  159 (199)
Q Consensus        80 ~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~P  159 (199)
                      |.+++...++++|..||+.|++|.|++.+++|-+|.+.|+++..                   ..++++||..+|.+++.
T Consensus       354 HsRKMnv~~DvNfeELaRsTddFNGAQcKAVcVEAGMiALRr~a-------------------tev~heDfmegI~eVqa  414 (424)
T KOG0652|consen  354 HSRKMNVSDDVNFEELARSTDDFNGAQCKAVCVEAGMIALRRGA-------------------TEVTHEDFMEGILEVQA  414 (424)
T ss_pred             hhhhcCCCCCCCHHHHhhcccccCchhheeeehhhhHHHHhccc-------------------ccccHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999875                   56999999999988864


Q ss_pred             c
Q 039253          160 S  160 (199)
Q Consensus       160 s  160 (199)
                      .
T Consensus       415 k  415 (424)
T KOG0652|consen  415 K  415 (424)
T ss_pred             h
Confidence            3

>CHL00195 ycf46 Ycf46; Provisional

Probab=99.91  E-value=1.6e-23  Score=189.85  Aligned_cols=137  Identities=26%  Similarity=0.418  Sum_probs=119.6

Q ss_pred             eeeccC-CCCCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcC
Q 039253            5 IVIQRG-SGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRK   83 (199)
Q Consensus         5 l~~~R~-~~~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~   83 (199)
                      ++..+. .+.++.+.+++++|+++|+.  ...+|+||+|||+++.||++++|+||||+.|+|++|+.++|.+||+.++.+
T Consensus       330 ~~~~~~~~~d~~~~~rvl~~lL~~l~~--~~~~V~vIaTTN~~~~Ld~allR~GRFD~~i~v~lP~~~eR~~Il~~~l~~  407 (489)
T CHL00195        330 AFSNSESKGDSGTTNRVLATFITWLSE--KKSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQK  407 (489)
T ss_pred             hhccccCCCCchHHHHHHHHHHHHHhc--CCCceEEEEecCChhhCCHHHhCCCcCCeEEEeCCcCHHHHHHHHHHHHhh
Confidence            344433 34666788999999999984  456899999999999999999999999999999999999999999999988


Q ss_pred             CCCC--CcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccccc
Q 039253           84 SPVS--KDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQ  161 (199)
Q Consensus        84 ~~~~--~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps~  161 (199)
                      ....  .+.++..||+.|+||||+||+++|.+|+..|+.+.                    .+++.+||..|++.++|++
T Consensus       408 ~~~~~~~~~dl~~La~~T~GfSGAdI~~lv~eA~~~A~~~~--------------------~~lt~~dl~~a~~~~~Pls  467 (489)
T CHL00195        408 FRPKSWKKYDIKKLSKLSNKFSGAEIEQSIIEAMYIAFYEK--------------------REFTTDDILLALKQFIPLA  467 (489)
T ss_pred             cCCCcccccCHHHHHhhcCCCCHHHHHHHHHHHHHHHHHcC--------------------CCcCHHHHHHHHHhcCCCc
Confidence            6432  47899999999999999999999999998887643                    6799999999999999986


Q ss_pred             cc
Q 039253          162 SR  163 (199)
Q Consensus       162 ~r  163 (199)
                      ..
T Consensus       468 ~~  469 (489)
T CHL00195        468 QT  469 (489)
T ss_pred             cc
Confidence            43

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=99.90  E-value=2.6e-23  Score=184.23  Aligned_cols=142  Identities=40%  Similarity=0.658  Sum_probs=126.2

Q ss_pred             ceeeccCCCCC---chhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHh
Q 039253            4 SIVIQRGSGAG---GAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKAC   80 (199)
Q Consensus         4 sl~~~R~~~~~---~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~   80 (199)
                      +++++|+....   ....+.+.+|+.+++++....+|+||+|||+++.+|++++||||||+.|+|++|+.++|.+||+.+
T Consensus       235 ~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~~~~~~~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~  314 (389)
T PRK03992        235 AIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIH  314 (389)
T ss_pred             hhhcccccCCCCccHHHHHHHHHHHHhccccCCCCCEEEEEecCChhhCCHHHcCCccCceEEEECCCCHHHHHHHHHHH
Confidence            45666654422   234577889999999998888999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcccc
Q 039253           81 LRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKS  160 (199)
Q Consensus        81 l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps  160 (199)
                      +++..+..++++..||..|+||||+||+++|++|.+.|+++..                   ..|+.+||.+|++.++|+
T Consensus       315 ~~~~~~~~~~~~~~la~~t~g~sgadl~~l~~eA~~~a~~~~~-------------------~~i~~~d~~~A~~~~~~~  375 (389)
T PRK03992        315 TRKMNLADDVDLEELAELTEGASGADLKAICTEAGMFAIRDDR-------------------TEVTMEDFLKAIEKVMGK  375 (389)
T ss_pred             hccCCCCCcCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHcCC-------------------CCcCHHHHHHHHHHHhcc
Confidence            9999888889999999999999999999999999999988642                   569999999999999998


Q ss_pred             cccc
Q 039253          161 QSRG  164 (199)
Q Consensus       161 ~~r~  164 (199)
                      ....
T Consensus       376 ~~~~  379 (389)
T PRK03992        376 EEKD  379 (389)
T ss_pred             cccc
Confidence            8765

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

Probab=99.90  E-value=6.9e-24  Score=178.68  Aligned_cols=140  Identities=34%  Similarity=0.529  Sum_probs=126.5

Q ss_pred             cceeeccCCCCCch---hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHH
Q 039253            3 WSIVIQRGSGAGGA---ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKA   79 (199)
Q Consensus         3 ~sl~~~R~~~~~~~---~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~   79 (199)
                      +|++.+|=..+++.   ..|..-+||+++|||.++..|-||+|||+.+.||||++||||+|++|+|++||...++.||..
T Consensus       288 dAiGtKRyds~SggerEiQrtmLELLNQldGFdsrgDvKvimATnrie~LDPaLiRPGrIDrKIef~~pDe~TkkkIf~I  367 (440)
T KOG0726|consen  288 DAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKKIFQI  367 (440)
T ss_pred             hhhccccccCCCccHHHHHHHHHHHHHhccCccccCCeEEEEecccccccCHhhcCCCccccccccCCCchhhhceeEEE
Confidence            46778885554443   446677999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccc
Q 039253           80 CLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACK  159 (199)
Q Consensus        80 ~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~P  159 (199)
                      |..++.+..++++..+.-.-+.+|||||+++|.+|.+.|+|+..                   ..++++||.+|.+.+--
T Consensus       368 HTs~Mtl~~dVnle~li~~kddlSGAdIkAictEaGllAlRerR-------------------m~vt~~DF~ka~e~V~~  428 (440)
T KOG0726|consen  368 HTSRMTLAEDVNLEELIMTKDDLSGADIKAICTEAGLLALRERR-------------------MKVTMEDFKKAKEKVLY  428 (440)
T ss_pred             eecccchhccccHHHHhhcccccccccHHHHHHHHhHHHHHHHH-------------------hhccHHHHHHHHHHHHH
Confidence            99999999999999999988999999999999999999999886                   56999999999988765


Q ss_pred             cc
Q 039253          160 SQ  161 (199)
Q Consensus       160 s~  161 (199)
                      +.
T Consensus       429 ~K  430 (440)
T KOG0726|consen  429 KK  430 (440)
T ss_pred             hc
Confidence            54

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.90  E-value=2.3e-23  Score=194.83  Aligned_cols=140  Identities=37%  Similarity=0.607  Sum_probs=125.3

Q ss_pred             ceeeccCCC---CCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHh
Q 039253            4 SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKAC   80 (199)
Q Consensus         4 sl~~~R~~~---~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~   80 (199)
                      +++++|+.+   .+....+++|+||.+||++....+|+||+|||+|+.||+|++||||||++|+|++|+.++|.+||+.+
T Consensus       255 ~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~~~~~vivIaaTN~p~~lD~Al~RpgRfdr~i~v~~Pd~~~R~~Il~~~  334 (644)
T PRK10733        255 AVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVH  334 (644)
T ss_pred             hhhhccCCCCCCCchHHHHHHHHHHHhhhcccCCCCeeEEEecCChhhcCHHHhCCcccceEEEcCCCCHHHHHHHHHHH
Confidence            566777653   33455679999999999999889999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcccc
Q 039253           81 LRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKS  160 (199)
Q Consensus        81 l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps  160 (199)
                      +++.++..++++..+|+.|.||||+||.++|++|+..|+++..                   ..++..||..|+..+.+.
T Consensus       335 ~~~~~l~~~~d~~~la~~t~G~sgadl~~l~~eAa~~a~r~~~-------------------~~i~~~d~~~a~~~v~~g  395 (644)
T PRK10733        335 MRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARGNK-------------------RVVSMVEFEKAKDKIMMG  395 (644)
T ss_pred             hhcCCCCCcCCHHHHHhhCCCCCHHHHHHHHHHHHHHHHHcCC-------------------CcccHHHHHHHHHHHhcc
Confidence            9999988899999999999999999999999999999887542                   569999999999988765


Q ss_pred             cc
Q 039253          161 QS  162 (199)
Q Consensus       161 ~~  162 (199)
                      ..
T Consensus       396 ~~  397 (644)
T PRK10733        396 AE  397 (644)
T ss_pred             cc
Confidence            43

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

Probab=99.90  E-value=2.2e-23  Score=190.11  Aligned_cols=138  Identities=36%  Similarity=0.558  Sum_probs=130.0

Q ss_pred             cceeeccCCCCCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhc
Q 039253            3 WSIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR   82 (199)
Q Consensus         3 ~sl~~~R~~~~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~   82 (199)
                      .+|+++|..... .++|++++|+++||++.+..+|+||++||+|+.||++++| ||||+.++++.|+..+|.+|++.+++
T Consensus       288 d~l~p~r~~~~~-~e~Rv~sqlltL~dg~~~~~~vivl~atnrp~sld~alRR-gRfd~ev~IgiP~~~~RldIl~~l~k  365 (693)
T KOG0730|consen  288 DALCPKREGADD-VESRVVSQLLTLLDGLKPDAKVIVLAATNRPDSLDPALRR-GRFDREVEIGIPGSDGRLDILRVLTK  365 (693)
T ss_pred             hhhCCcccccch-HHHHHHHHHHHHHhhCcCcCcEEEEEecCCccccChhhhc-CCCcceeeecCCCchhHHHHHHHHHH
Confidence            378999988766 8899999999999999988999999999999999999999 99999999999999999999999999


Q ss_pred             CCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcccccc
Q 039253           83 KSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQS  162 (199)
Q Consensus        83 ~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps~~  162 (199)
                      ++++.+++++..+|..|+||+|+||..+|.+|.+++.++                        ++++|+.|+..++||++
T Consensus       366 ~~~~~~~~~l~~iA~~thGyvGaDL~~l~~ea~~~~~r~------------------------~~~~~~~A~~~i~psa~  421 (693)
T KOG0730|consen  366 KMNLLSDVDLEDIAVSTHGYVGADLAALCREASLQATRR------------------------TLEIFQEALMGIRPSAL  421 (693)
T ss_pred             hcCCcchhhHHHHHHHccchhHHHHHHHHHHHHHHHhhh------------------------hHHHHHHHHhcCCchhh
Confidence            999888899999999999999999999999999998886                        47899999999999999


Q ss_pred             ccCC
Q 039253          163 RGFG  166 (199)
Q Consensus       163 r~~~  166 (199)
                      |++.
T Consensus       422 Re~~  425 (693)
T KOG0730|consen  422 REIL  425 (693)
T ss_pred             hhee
Confidence            9763

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

Probab=99.89  E-value=1.7e-22  Score=180.93  Aligned_cols=138  Identities=33%  Similarity=0.497  Sum_probs=122.3

Q ss_pred             ceeeccCCCCC---chhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHh
Q 039253            4 SIVIQRGSGAG---GAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKAC   80 (199)
Q Consensus         4 sl~~~R~~~~~---~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~   80 (199)
                      +++.+|....+   ....+.+.+||.+||++....+|.||+|||+++.||++++||||||++|+|++|+.++|.+||+.+
T Consensus       287 ~l~~kR~~~~sgg~~e~qr~ll~LL~~Ldg~~~~~~V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~  366 (438)
T PTZ00361        287 AIGTKRYDATSGGEKEIQRTMLELLNQLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIH  366 (438)
T ss_pred             HHhccCCCCCCcccHHHHHHHHHHHHHHhhhcccCCeEEEEecCChHHhhHHhccCCeeEEEEEeCCCCHHHHHHHHHHH
Confidence            45566654322   234577889999999998888899999999999999999999999999999999999999999999


Q ss_pred             hcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcccc
Q 039253           81 LRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKS  160 (199)
Q Consensus        81 l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps  160 (199)
                      +.++.+..++++..++..|+||||+||+++|++|.+.|+++..                   ..|+.+||..|+.++...
T Consensus       367 ~~k~~l~~dvdl~~la~~t~g~sgAdI~~i~~eA~~~Alr~~r-------------------~~Vt~~D~~~A~~~v~~~  427 (438)
T PTZ00361        367 TSKMTLAEDVDLEEFIMAKDELSGADIKAICTEAGLLALRERR-------------------MKVTQADFRKAKEKVLYR  427 (438)
T ss_pred             HhcCCCCcCcCHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcC-------------------CccCHHHHHHHHHHHHhh
Confidence            9999888899999999999999999999999999999998763                   569999999999998544

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.88  E-value=1.9e-22  Score=183.61  Aligned_cols=137  Identities=39%  Similarity=0.641  Sum_probs=121.4

Q ss_pred             ceeeccCCC---CCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHh
Q 039253            4 SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKAC   80 (199)
Q Consensus         4 sl~~~R~~~---~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~   80 (199)
                      +++++|+.+   .+....+++++||.+||++....+|+||+|||+|+.||++++||||||++|++++|+.++|.+||+.+
T Consensus       158 ~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~~~~v~vI~aTn~~~~ld~al~r~gRfd~~i~i~~Pd~~~R~~il~~~  237 (495)
T TIGR01241       158 AVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVH  237 (495)
T ss_pred             hhhhccccCcCCccHHHHHHHHHHHhhhccccCCCCeEEEEecCChhhcCHHHhcCCcceEEEEcCCCCHHHHHHHHHHH
Confidence            456666653   23445689999999999998888999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccc
Q 039253           81 LRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACK  159 (199)
Q Consensus        81 l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~P  159 (199)
                      +++.++..++++..+|..|.||||+||.++|++|+..+.++..                   ..++.+||..|+..+.+
T Consensus       238 l~~~~~~~~~~l~~la~~t~G~sgadl~~l~~eA~~~a~~~~~-------------------~~i~~~~l~~a~~~~~~  297 (495)
T TIGR01241       238 AKNKKLAPDVDLKAVARRTPGFSGADLANLLNEAALLAARKNK-------------------TEITMNDIEEAIDRVIA  297 (495)
T ss_pred             HhcCCCCcchhHHHHHHhCCCCCHHHHHHHHHHHHHHHHHcCC-------------------CCCCHHHHHHHHHHHhc
Confidence            9988877788999999999999999999999999888766542                   56999999999998764

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.

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

Probab=99.88  E-value=2.4e-22  Score=166.77  Aligned_cols=137  Identities=39%  Similarity=0.548  Sum_probs=124.0

Q ss_pred             cceeeccCCC---CCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHH
Q 039253            3 WSIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKA   79 (199)
Q Consensus         3 ~sl~~~R~~~---~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~   79 (199)
                      +||+.+|=..   ......|++-+||++|||+....+|-||++||+.+.||||++||||+|++|+||+|++.+++-+|..
T Consensus       258 daiatkrfdaqtgadrevqril~ellnqmdgfdq~~nvkvimatnradtldpallrpgrldrkiefplpdrrqkrlvf~t  337 (408)
T KOG0727|consen  258 DAIATKRFDAQTGADREVQRILIELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFST  337 (408)
T ss_pred             hhHhhhhccccccccHHHHHHHHHHHHhccCcCcccceEEEEecCcccccCHhhcCCccccccccCCCCchhhhhhhHHh
Confidence            3566677544   3334668999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcc
Q 039253           80 CLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYAC  158 (199)
Q Consensus        80 ~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~  158 (199)
                      +..++.+.+++|++.+..+.+..||+||.++|++|.+.|+++..                   ..+...||++|-+...
T Consensus       338 itskm~ls~~vdle~~v~rpdkis~adi~aicqeagm~avr~nr-------------------yvvl~kd~e~ay~~~v  397 (408)
T KOG0727|consen  338 ITSKMNLSDEVDLEDLVARPDKISGADINAICQEAGMLAVRENR-------------------YVVLQKDFEKAYKTVV  397 (408)
T ss_pred             hhhcccCCcccCHHHHhcCccccchhhHHHHHHHHhHHHHHhcc-------------------eeeeHHHHHHHHHhhc
Confidence            99999999999999999999999999999999999999999875                   5688999999987653

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

Probab=99.87  E-value=7.3e-22  Score=164.22  Aligned_cols=125  Identities=34%  Similarity=0.572  Sum_probs=113.8

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCcccHHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLA   96 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~l~~la   96 (199)
                      ...++|.||+.|||+..+.+|+.|++||+|+.||+|+++  ||...|+|.+|+.++|.+|++.+.+++++.-+.++..++
T Consensus       235 VsEiVNALLTelDgi~eneGVvtIaaTN~p~~LD~aiRs--RFEeEIEF~LP~~eEr~~ile~y~k~~Plpv~~~~~~~~  312 (368)
T COG1223         235 VSEIVNALLTELDGIKENEGVVTIAATNRPELLDPAIRS--RFEEEIEFKLPNDEERLEILEYYAKKFPLPVDADLRYLA  312 (368)
T ss_pred             HHHHHHHHHHhccCcccCCceEEEeecCChhhcCHHHHh--hhhheeeeeCCChHHHHHHHHHHHHhCCCccccCHHHHH
Confidence            346899999999999999999999999999999999999  999999999999999999999999999999899999999


Q ss_pred             hhCCCCCHHHHH-HHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcccccc
Q 039253           97 QFTQGFSGADIT-EICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQS  162 (199)
Q Consensus        97 ~~t~G~sgaDI~-~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps~~  162 (199)
                      +.|.||||+||+ .+++.|++.|+.+..                   ..|+.+|++.|+++-++...
T Consensus       313 ~~t~g~SgRdikekvlK~aLh~Ai~ed~-------------------e~v~~edie~al~k~r~~r~  360 (368)
T COG1223         313 AKTKGMSGRDIKEKVLKTALHRAIAEDR-------------------EKVEREDIEKALKKERKRRA  360 (368)
T ss_pred             HHhCCCCchhHHHHHHHHHHHHHHHhch-------------------hhhhHHHHHHHHHhhccccC
Confidence            999999999996 466777888887765                   45889999999998776654

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

Probab=99.86  E-value=5.1e-22  Score=165.92  Aligned_cols=140  Identities=32%  Similarity=0.480  Sum_probs=125.6

Q ss_pred             cceeeccCC---CCCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHH
Q 039253            3 WSIVIQRGS---GAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKA   79 (199)
Q Consensus         3 ~sl~~~R~~---~~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~   79 (199)
                      +|+++.|=.   +..+...|..-+|+++|||+.++.++-|+++||+|+.||||++||||+|++++|.+|+.+.|..||+.
T Consensus       280 daiggarfddg~ggdnevqrtmleli~qldgfdprgnikvlmatnrpdtldpallrpgrldrkvef~lpdlegrt~i~ki  359 (435)
T KOG0729|consen  280 DAIGGARFDDGAGGDNEVQRTMLELINQLDGFDPRGNIKVLMATNRPDTLDPALLRPGRLDRKVEFGLPDLEGRTHIFKI  359 (435)
T ss_pred             ccccCccccCCCCCcHHHHHHHHHHHHhccCCCCCCCeEEEeecCCCCCcCHhhcCCcccccceeccCCcccccceeEEE
Confidence            356777732   24445678888999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccc
Q 039253           80 CLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACK  159 (199)
Q Consensus        80 ~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~P  159 (199)
                      |.+.+.+..++-|+.||..+..-+|++|+.+|.+|.+.|++...                   ...|..||..|+.++..
T Consensus       360 haksmsverdir~ellarlcpnstgaeirsvcteagmfairarr-------------------k~atekdfl~av~kvvk  420 (435)
T KOG0729|consen  360 HAKSMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARR-------------------KVATEKDFLDAVNKVVK  420 (435)
T ss_pred             eccccccccchhHHHHHhhCCCCcchHHHHHHHHhhHHHHHHHh-------------------hhhhHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999998774                   45799999999998754


Q ss_pred             cc
Q 039253          160 SQ  161 (199)
Q Consensus       160 s~  161 (199)
                      ..
T Consensus       421 gy  422 (435)
T KOG0729|consen  421 GY  422 (435)
T ss_pred             HH
Confidence            43

>CHL00176 ftsH cell division protein; Validated

Probab=99.86  E-value=1.8e-21  Score=181.32  Aligned_cols=135  Identities=41%  Similarity=0.629  Sum_probs=120.3

Q ss_pred             ceeeccCCC---CCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHh
Q 039253            4 SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKAC   80 (199)
Q Consensus         4 sl~~~R~~~---~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~   80 (199)
                      +++++|+.+   .+....+++++||.+||++..+.+|+||+|||+++.+|+|++||||||++|+|++|+.++|.+||+.+
T Consensus       286 ~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~~~~~ViVIaaTN~~~~LD~ALlRpGRFd~~I~v~lPd~~~R~~IL~~~  365 (638)
T CHL00176        286 AVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVH  365 (638)
T ss_pred             hhhhcccCCCCCCcHHHHHHHHHHHhhhccccCCCCeeEEEecCchHhhhhhhhccccCceEEEECCCCHHHHHHHHHHH
Confidence            456666543   33445688999999999998888999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhc
Q 039253           81 LRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYA  157 (199)
Q Consensus        81 l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~  157 (199)
                      +++..+..++++..+|..|.||||+||+++|++|+..+.++..                   ..++.+||..|+.++
T Consensus       366 l~~~~~~~d~~l~~lA~~t~G~sgaDL~~lvneAal~a~r~~~-------------------~~It~~dl~~Ai~rv  423 (638)
T CHL00176        366 ARNKKLSPDVSLELIARRTPGFSGADLANLLNEAAILTARRKK-------------------ATITMKEIDTAIDRV  423 (638)
T ss_pred             HhhcccchhHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCC-------------------CCcCHHHHHHHHHHH
Confidence            9987777889999999999999999999999999988876653                   569999999999887

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

Probab=99.86  E-value=4.6e-22  Score=175.96  Aligned_cols=155  Identities=30%  Similarity=0.457  Sum_probs=134.5

Q ss_pred             CcceeeccCCCCCchhhHHHHHHHHHHhCCC--CCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHH
Q 039253            2 GWSIVIQRGSGAGGAADRIPNQLLTEMDGLS--AKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKA   79 (199)
Q Consensus         2 g~sl~~~R~~~~~~~~~r~~~~lL~~ld~~~--~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~   79 (199)
                      +++++.+|+...++.+.|+..+||.++++..  ..++|+||+|||+||.+|.|++|  ||.+++++|+|+.+.|..+|+.
T Consensus       254 idslls~Rs~~e~e~srr~ktefLiq~~~~~s~~~drvlvigaTN~P~e~Dea~~R--rf~kr~yiplPd~etr~~~~~~  331 (428)
T KOG0740|consen  254 IDSLLSKRSDNEHESSRRLKTEFLLQFDGKNSAPDDRVLVIGATNRPWELDEAARR--RFVKRLYIPLPDYETRSLLWKQ  331 (428)
T ss_pred             hHHHHhhcCCcccccchhhhhHHHhhhccccCCCCCeEEEEecCCCchHHHHHHHH--HhhceeeecCCCHHHHHHHHHH
Confidence            3578899988899999999999999999884  45789999999999999999999  9999999999999999999999


Q ss_pred             hhcCCCCC-CcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcc
Q 039253           80 CLRKSPVS-KDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYAC  158 (199)
Q Consensus        80 ~l~~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~  158 (199)
                      ++.+.+.. .+.++..|++.|+||||+||.++|++|++..++......      ..........++++..||..|++.++
T Consensus       332 ll~~~~~~l~~~d~~~l~~~Tegysgsdi~~l~kea~~~p~r~~~~~~------~~~~~~~~~~r~i~~~df~~a~~~i~  405 (428)
T KOG0740|consen  332 LLKEQPNGLSDLDISLLAKVTEGYSGSDITALCKEAAMGPLRELGGTT------DLEFIDADKIRPITYPDFKNAFKNIK  405 (428)
T ss_pred             HHHhCCCCccHHHHHHHHHHhcCcccccHHHHHHHhhcCchhhcccch------hhhhcchhccCCCCcchHHHHHHhhc
Confidence            99887544 678999999999999999999999999999888775320      11122344558899999999999999


Q ss_pred             cccccc
Q 039253          159 KSQSRG  164 (199)
Q Consensus       159 Ps~~r~  164 (199)
                      |+.+.+
T Consensus       406 ~~~s~~  411 (428)
T KOG0740|consen  406 PSVSLE  411 (428)
T ss_pred             cccCcc
Confidence            999874

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=99.85  E-value=1.2e-20  Score=165.80  Aligned_cols=135  Identities=42%  Similarity=0.671  Sum_probs=117.9

Q ss_pred             ceeeccCCCC---CchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHh
Q 039253            4 SIVIQRGSGA---GGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKAC   80 (199)
Q Consensus         4 sl~~~R~~~~---~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~   80 (199)
                      +++.+|....   .....+.+.+++.+++++....+|+||+|||+++.+|++++|||||++.|+|++|+.++|.+||+.+
T Consensus       226 ~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~~~~~~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~  305 (364)
T TIGR01242       226 AIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIH  305 (364)
T ss_pred             hhccccccCCCCccHHHHHHHHHHHHHhhCCCCCCCEEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHHHHHHHHH
Confidence            3455554332   2234567889999999987778899999999999999999999999999999999999999999999


Q ss_pred             hcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhc
Q 039253           81 LRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYA  157 (199)
Q Consensus        81 l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~  157 (199)
                      +.+..+..++++..++..|+||+|+||+++|.+|.+.|+++..                   ..|+.+||..|++.+
T Consensus       306 ~~~~~l~~~~~~~~la~~t~g~sg~dl~~l~~~A~~~a~~~~~-------------------~~i~~~d~~~a~~~~  363 (364)
T TIGR01242       306 TRKMKLAEDVDLEAIAKMTEGASGADLKAICTEAGMFAIREER-------------------DYVTMDDFIKAVEKV  363 (364)
T ss_pred             HhcCCCCccCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhCC-------------------CccCHHHHHHHHHHh
Confidence            9988887789999999999999999999999999999988752                   569999999999875

Many proteins may score above the trusted cutoff because an internal

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

Probab=99.84  E-value=4.2e-21  Score=183.30  Aligned_cols=172  Identities=31%  Similarity=0.387  Sum_probs=139.1

Q ss_pred             cceeeccCCCCCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhc
Q 039253            3 WSIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR   82 (199)
Q Consensus         3 ~sl~~~R~~~~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~   82 (199)
                      ..|++.|++-.......++++||..|||+.++.+|+||+|||||+.+|||++||||||+.++|++|+.+.|.+|+..+.+
T Consensus       373 dGlapvrSskqEqih~SIvSTLLaLmdGldsRgqVvvigATnRpda~dpaLRRPgrfdref~f~lp~~~ar~~Il~Ihtr  452 (1080)
T KOG0732|consen  373 DGLAPVRSSKQEQIHASIVSTLLALMDGLDSRGQVVVIGATNRPDAIDPALRRPGRFDREFYFPLPDVDARAKILDIHTR  452 (1080)
T ss_pred             ccccccccchHHHhhhhHHHHHHHhccCCCCCCceEEEcccCCccccchhhcCCcccceeEeeeCCchHHHHHHHHHhcc
Confidence            45778888776667778999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CCCCC-CcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccccc
Q 039253           83 KSPVS-KDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQ  161 (199)
Q Consensus        83 ~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps~  161 (199)
                      +-... ....+..||+.|.||.|+||+.+|.+|++.++++.............   .......+...||..|+.++.|+.
T Consensus       453 kw~~~i~~~l~~~la~~t~gy~gaDlkaLCTeAal~~~~r~~Pq~y~s~~kl~---~d~~~ikV~~~~f~~A~~~i~ps~  529 (1080)
T KOG0732|consen  453 KWEPPISRELLLWLAEETSGYGGADLKALCTEAALIALRRSFPQIYSSSDKLL---IDVALIKVEVRDFVEAMSRITPSS  529 (1080)
T ss_pred             CCCCCCCHHHHHHHHHhccccchHHHHHHHHHHhhhhhccccCeeeccccccc---ccchhhhhhhHhhhhhhhccCCCC
Confidence            76422 44567889999999999999999999999999886432111110011   111224489999999999999999


Q ss_pred             cccCCcccccchhhhh
Q 039253          162 SRGFGDEFGFCETAVA  177 (199)
Q Consensus       162 ~r~~~~~~~~~~~~~~  177 (199)
                      .|......+.-.+..-
T Consensus       530 ~R~~~~~s~Pl~~~~~  545 (1080)
T KOG0732|consen  530 RRSSVIFSRPLSTYLK  545 (1080)
T ss_pred             CccccCCCCCCCccee
Confidence            9976666665555443

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.84  E-value=9.4e-21  Score=188.01  Aligned_cols=122  Identities=18%  Similarity=0.240  Sum_probs=106.3

Q ss_pred             HHHHHHHHHhCCC---CCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhh--cCCCCCC-cccHH
Q 039253           20 IPNQLLTEMDGLS---AKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACL--RKSPVSK-DVDLE   93 (199)
Q Consensus        20 ~~~~lL~~ld~~~---~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l--~~~~~~~-~~~l~   93 (199)
                      .+++||++||+..   +..+|+||||||+|+.||||++||||||++|++++|+..+|++++..++  ++.++.. .+++.
T Consensus      1753 tL~qLLneLDg~~~~~s~~~VIVIAATNRPD~LDPALLRPGRFDR~I~Ir~Pd~p~R~kiL~ILl~tkg~~L~~~~vdl~ 1832 (2281)
T CHL00206       1753 SLGLLVNSLSRDCERCSTRNILVIASTHIPQKVDPALIAPNKLNTCIKIRRLLIPQQRKHFFTLSYTRGFHLEKKMFHTN 1832 (2281)
T ss_pred             hHHHHHHHhccccccCCCCCEEEEEeCCCcccCCHhHcCCCCCCeEEEeCCCCchhHHHHHHHHHhhcCCCCCcccccHH
Confidence            4899999999874   3567999999999999999999999999999999999999999988654  4555553 36899


Q ss_pred             HHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcccc
Q 039253           94 KLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKS  160 (199)
Q Consensus        94 ~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps  160 (199)
                      .+|+.|.|||||||+++|.+|++.|+++..                   ..|+.++|..|+.+...-
T Consensus      1833 ~LA~~T~GfSGADLanLvNEAaliAirq~k-------------------s~Id~~~I~~Al~Rq~~g 1880 (2281)
T CHL00206       1833 GFGSITMGSNARDLVALTNEALSISITQKK-------------------SIIDTNTIRSALHRQTWD 1880 (2281)
T ss_pred             HHHHhCCCCCHHHHHHHHHHHHHHHHHcCC-------------------CccCHHHHHHHHHHHHhh
Confidence            999999999999999999999999999863                   568999999999877543

>TIGR03689 pup_AAA proteasome ATPase

Probab=99.83  E-value=4.3e-20  Score=167.90  Aligned_cols=139  Identities=37%  Similarity=0.560  Sum_probs=111.0

Q ss_pred             cceeeccCCC-CCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhh
Q 039253            3 WSIVIQRGSG-AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACL   81 (199)
Q Consensus         3 ~sl~~~R~~~-~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l   81 (199)
                      ++++++|+.+ .++...+++++||++||++....+|+||+|||+++.||||++||||||.+|+|++|+.++|++||+.++
T Consensus       299 D~L~~~R~~~~s~d~e~~il~~LL~~LDgl~~~~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r~~Il~~~l  378 (512)
T TIGR03689       299 DSIFRTRGSGVSSDVETTVVPQLLSELDGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFSKYL  378 (512)
T ss_pred             hhhhcccCCCccchHHHHHHHHHHHHhcccccCCceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHHHHHHHHHh
Confidence            3567788765 445567899999999999988889999999999999999999999999999999999999999999998


Q ss_pred             cC-CCCC---------CcccHHHHHh-----------------------------hCCCCCHHHHHHHHHHHHHHHHHHH
Q 039253           82 RK-SPVS---------KDVDLEKLAQ-----------------------------FTQGFSGADITEICQRACKDATREE  122 (199)
Q Consensus        82 ~~-~~~~---------~~~~l~~la~-----------------------------~t~G~sgaDI~~lv~~A~~~a~~~~  122 (199)
                      .. .++.         ...++..+++                             .++.+||++|+++|.+|...|+.+.
T Consensus       379 ~~~l~l~~~l~~~~g~~~a~~~al~~~av~~~~a~~~~~~~l~~~~~~g~~~~l~~~d~~sGa~i~~iv~~a~~~ai~~~  458 (512)
T TIGR03689       379 TDSLPLDADLAEFDGDREATAAALIQRAVDHLYATSEENRYVEVTYANGSTEVLYFKDFVSGAMIANIVDRAKKRAIKDH  458 (512)
T ss_pred             hccCCchHHHHHhcCCCHHHHHHHHHHHHHHHhhhhcccceeEEEecCCceeeEeecccccHHHHHHHHHHHHHHHHHHH
Confidence            64 3431         1122222222                             2577889999999999999998887


Q ss_pred             HHHhHHhhcCCCCcchhhccccccHHHHHHHHHh
Q 039253          123 IENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKY  156 (199)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~  156 (199)
                      +...               ...++.+|+..|+..
T Consensus       459 ~~~~---------------~~~~~~~~l~~a~~~  477 (512)
T TIGR03689       459 ITGG---------------QVGLRIEHLLAAVLD  477 (512)
T ss_pred             HhcC---------------CcCcCHHHHHHHHHH
Confidence            6321               146899999999875

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.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.83  E-value=8.7e-20  Score=173.13  Aligned_cols=162  Identities=37%  Similarity=0.554  Sum_probs=134.2

Q ss_pred             ceeeccCCCCCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcC
Q 039253            4 SIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRK   83 (199)
Q Consensus         4 sl~~~R~~~~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~   83 (199)
                      +++++|+...++...+++++|++.|+++....+|+||++||+++.||++++|+|||+..+++++|+.++|.+||+.+.+.
T Consensus       282 ~l~~~r~~~~~~~~~~~~~~Ll~~ld~l~~~~~vivI~atn~~~~ld~al~r~gRfd~~i~i~~P~~~~R~~Il~~~~~~  361 (733)
T TIGR01243       282 AIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRN  361 (733)
T ss_pred             hhcccccCCcchHHHHHHHHHHHHhhccccCCCEEEEeecCChhhcCHHHhCchhccEEEEeCCcCHHHHHHHHHHHhcC
Confidence            46777776666667899999999999998888999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccccccc
Q 039253           84 SPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQSR  163 (199)
Q Consensus        84 ~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps~~r  163 (199)
                      .++..+.++..+++.|+||+|+||..+|+.|++.++++.......................++.+||..|++.++|+.++
T Consensus       362 ~~l~~d~~l~~la~~t~G~~gadl~~l~~~a~~~al~r~~~~~~~~~~~~~i~~~~~~~~~v~~~df~~Al~~v~ps~~~  441 (733)
T TIGR01243       362 MPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFIREGKINFEAEEIPAEVLKELKVTMKDFMEALKMVEPSAIR  441 (733)
T ss_pred             CCCccccCHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHhhccccccccccccchhcccccccHHHHHHHHhhccccccc
Confidence            88888899999999999999999999999999999988754210000000000011123568999999999999999987


Q ss_pred             cC
Q 039253          164 GF  165 (199)
Q Consensus       164 ~~  165 (199)
                      ++
T Consensus       442 ~~  443 (733)
T TIGR01243       442 EV  443 (733)
T ss_pred             hh
Confidence            54

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.

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

Probab=99.72  E-value=2.7e-18  Score=145.78  Aligned_cols=137  Identities=36%  Similarity=0.539  Sum_probs=117.7

Q ss_pred             cceeeccCCCC---CchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHH
Q 039253            3 WSIVIQRGSGA---GGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKA   79 (199)
Q Consensus         3 ~sl~~~R~~~~---~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~   79 (199)
                      +|+++.|.+..   .....+.+=+|+++||++....+|-+|+|||+|+.|||+++||||+|+.+++|+|++..|..|++.
T Consensus       235 DAigGRr~se~Ts~dreiqrTLMeLlnqmdgfd~l~rVk~ImatNrpdtLdpaLlRpGRldrk~~iPlpne~~r~~I~Ki  314 (388)
T KOG0651|consen  235 DAIGGRRFSEGTSSDREIQRTLMELLNQMDGFDTLHRVKTIMATNRPDTLDPALLRPGRLDRKVEIPLPNEQARLGILKI  314 (388)
T ss_pred             hhhccEEeccccchhHHHHHHHHHHHHhhccchhcccccEEEecCCccccchhhcCCccccceeccCCcchhhceeeEee
Confidence            36677774432   223445666888999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcc
Q 039253           80 CLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYAC  158 (199)
Q Consensus        80 ~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~  158 (199)
                      +........+++.+.+.+.++||.|+|+.+.|++|-+.++++..                   ..+-++||..++.+..
T Consensus       315 h~~~i~~~Geid~eaivK~~d~f~gad~rn~~tEag~Fa~~~~~-------------------~~vl~Ed~~k~vrk~~  374 (388)
T KOG0651|consen  315 HVQPIDFHGEIDDEAILKLVDGFNGADLRNVCTEAGMFAIPEER-------------------DEVLHEDFMKLVRKQA  374 (388)
T ss_pred             ccccccccccccHHHHHHHHhccChHHHhhhcccccccccchhh-------------------HHHhHHHHHHHHHHHH
Confidence            99888777789999999999999999999999999988877664                   3467899998887764

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

Probab=99.70  E-value=4.3e-16  Score=136.01  Aligned_cols=117  Identities=19%  Similarity=0.221  Sum_probs=99.4

Q ss_pred             cceeeccCCCCCchhhHHH-HHHHHHHhCC------------CCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCC
Q 039253            3 WSIVIQRGSGAGGAADRIP-NQLLTEMDGL------------SAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPV   69 (199)
Q Consensus         3 ~sl~~~R~~~~~~~~~r~~-~~lL~~ld~~------------~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~   69 (199)
                      +|++++|++..+....+++ .+||++||+.            ....+|+||+|||+|+.|||+|+||||||+.+  .+|+
T Consensus       222 DA~~g~r~~~~~tv~~qiV~~tLLnl~D~p~~v~l~G~w~~~~~~~~V~VIaTTNrpd~LDpALlRpGRfDk~i--~lPd  299 (413)
T PLN00020        222 DAGAGRFGTTQYTVNNQMVNGTLMNIADNPTNVSLGGDWREKEEIPRVPIIVTGNDFSTLYAPLIRDGRMEKFY--WAPT  299 (413)
T ss_pred             hhcCCCCCCCCcchHHHHHHHHHHHHhcCCccccccccccccccCCCceEEEeCCCcccCCHhHcCCCCCCcee--CCCC
Confidence            4688999866666667776 8999999863            23567999999999999999999999999975  5899


Q ss_pred             HHHHHHHHHHhhcCCCCCCcccHHHHHhhCCC----CCHHHHHHHHHHHHHHHHHHH
Q 039253           70 EKSRLQIFKACLRKSPVSKDVDLEKLAQFTQG----FSGADITEICQRACKDATREE  122 (199)
Q Consensus        70 ~~~R~~il~~~l~~~~~~~~~~l~~la~~t~G----~sgaDI~~lv~~A~~~a~~~~  122 (199)
                      .++|.+||+.++++..+. ..++..|+..+.|    |+||--..+..++....+.+.
T Consensus       300 ~e~R~eIL~~~~r~~~l~-~~dv~~Lv~~f~gq~~Df~GAlrar~yd~~v~~~i~~~  355 (413)
T PLN00020        300 REDRIGVVHGIFRDDGVS-REDVVKLVDTFPGQPLDFFGALRARVYDDEVRKWIAEV  355 (413)
T ss_pred             HHHHHHHHHHHhccCCCC-HHHHHHHHHcCCCCCchhhhHHHHHHHHHHHHHHHHHh
Confidence            999999999999998776 6889999998877    788888888888877777665

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

Probab=99.40  E-value=4.8e-12  Score=115.30  Aligned_cols=144  Identities=36%  Similarity=0.497  Sum_probs=126.5

Q ss_pred             cceeeccCCCCCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhc
Q 039253            3 WSIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR   82 (199)
Q Consensus         3 ~sl~~~R~~~~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~   82 (199)
                      .+++++|.........+++++|+..|+++.... |++++.||++..+|++++++|||+..+++..|+...|.+|+..+..
T Consensus        86 ~~~~~~~~~~~~~~~~~v~~~l~~~~d~~~~~~-v~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ei~~~~~~  164 (494)
T COG0464          86 DALAPKRSSDQGEVERRVVAQLLALMDGLKRGQ-VIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGRLEILQIHTR  164 (494)
T ss_pred             hhcccCccccccchhhHHHHHHHHhcccccCCc-eEEEeecCCccccChhHhCccccceeeecCCCCHHHHHHHHHHHHh
Confidence            356777777666678899999999999999444 9999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcccc
Q 039253           83 KSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKS  160 (199)
Q Consensus        83 ~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps  160 (199)
                      .+....+.++..++..+.||+++|+..+|.++...++++...             .......++.++|.++++.+.|+
T Consensus       165 ~~~~~~~~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~r~~~-------------~~~~~~~~~~~~~~~~l~~~~~~  229 (494)
T COG0464         165 LMFLGPPGTGKTLAARTVGKSGADLGALAKEAALRELRRAID-------------LVGEYIGVTEDDFEEALKKVLPS  229 (494)
T ss_pred             cCCCcccccHHHHHHhcCCccHHHHHHHHHHHHHHHHHhhhc-------------cCcccccccHHHHHHHHHhcCcc
Confidence            888887899999999999999999999999999999888630             01111568999999999999998

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

Probab=99.34  E-value=4.9e-12  Score=117.97  Aligned_cols=161  Identities=17%  Similarity=0.265  Sum_probs=124.5

Q ss_pred             chhhHHHHHHHHHH--hCCC-CCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCccc
Q 039253           15 GAADRIPNQLLTEM--DGLS-AKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVD   91 (199)
Q Consensus        15 ~~~~r~~~~lL~~l--d~~~-~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~   91 (199)
                      +...++...+-.+|  |.+. +..+++||++|+..+.|++.+++  -|-++|.++.|++++|.+||+.|+....+..++.
T Consensus       509 ged~rl~~~i~~~ls~e~~~~~~~~~ivv~t~~s~~~lp~~i~~--~f~~ei~~~~lse~qRl~iLq~y~~~~~~n~~v~  586 (953)
T KOG0736|consen  509 GEDARLLKVIRHLLSNEDFKFSCPPVIVVATTSSIEDLPADIQS--LFLHEIEVPALSEEQRLEILQWYLNHLPLNQDVN  586 (953)
T ss_pred             chhHHHHHHHHHHHhcccccCCCCceEEEEeccccccCCHHHHH--hhhhhccCCCCCHHHHHHHHHHHHhccccchHHH
Confidence            44445544443333  3333 55779999999999999999999  9999999999999999999999999999999999


Q ss_pred             HHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhh-cCCCCcchhhccccccHHHHHHHHHhccccccccCCc---
Q 039253           92 LEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRR-KGKQPEAIEDEVAEIKAEHFEESMKYACKSQSRGFGD---  167 (199)
Q Consensus        92 l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~-~~~~~~~~~~~~~~it~~df~~Al~~~~Ps~~r~~~~---  167 (199)
                      .+.+|++|.|||.+|+.+++......+..+..++..... ..+...........++++||.+|+.+++...+..+|.   
T Consensus       587 ~k~~a~~t~gfs~~~L~~l~~~~s~~~~~~i~~~~l~g~~~~~~~~~~~~~~~~l~~edf~kals~~~~~fs~aiGAPKI  666 (953)
T KOG0736|consen  587 LKQLARKTSGFSFGDLEALVAHSSLAAKTRIKNKGLAGGLQEEDEGELCAAGFLLTEEDFDKALSRLQKEFSDAIGAPKI  666 (953)
T ss_pred             HHHHHHhcCCCCHHHHHHHhcCchHHHHHHHHhhcccccchhccccccccccceecHHHHHHHHHHHHHhhhhhcCCCCC
Confidence            999999999999999999999885555555443331110 1122233555567899999999999999888877666   


Q ss_pred             -ccccchhhhh
Q 039253          168 -EFGFCETAVA  177 (199)
Q Consensus       168 -~~~~~~~~~~  177 (199)
                       ...|.+.+|-
T Consensus       667 PnV~WdDVGGL  677 (953)
T KOG0736|consen  667 PNVSWDDVGGL  677 (953)
T ss_pred             CccchhcccCH
Confidence             6677777664

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

Probab=99.34  E-value=6.6e-12  Score=116.37  Aligned_cols=146  Identities=22%  Similarity=0.283  Sum_probs=116.3

Q ss_pred             hHHHHHHHHH-HhCC-CCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHH
Q 039253           18 DRIPNQLLTE-MDGL-SAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEK   94 (199)
Q Consensus        18 ~r~~~~lL~~-ld~~-~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~   94 (199)
                      ....+.||++ ++.+ ..+..+.||++.+....|+|-+..|++|+.++.++.|+..+|.+||+..+++.... ..-+++-
T Consensus       521 ~~rla~flnqvi~~y~~~~~~ia~Iat~qe~qtl~~~L~s~~~Fq~~~~L~ap~~~~R~~IL~~~~s~~~~~~~~~dLd~  600 (952)
T KOG0735|consen  521 SERLAAFLNQVIKIYLKRNRKIAVIATGQELQTLNPLLVSPLLFQIVIALPAPAVTRRKEILTTIFSKNLSDITMDDLDF  600 (952)
T ss_pred             HHHHHHHHHHHHHHHHccCcEEEEEEechhhhhcChhhcCccceEEEEecCCcchhHHHHHHHHHHHhhhhhhhhHHHHH
Confidence            3445555544 3333 33455799999999999999999999999999999999999999999999876533 3335555


Q ss_pred             HHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccccccccCC----cccc
Q 039253           95 LAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQSRGFG----DEFG  170 (199)
Q Consensus        95 la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps~~r~~~----~~~~  170 (199)
                      ++..|+||...|+..++++|.+.|+.+.+....               ..+|.++|.++|+.+.|.++|++.    +-+|
T Consensus       601 ls~~TEGy~~~DL~ifVeRai~~a~leris~~~---------------klltke~f~ksL~~F~P~aLR~ik~~k~tgi~  665 (952)
T KOG0735|consen  601 LSVKTEGYLATDLVIFVERAIHEAFLERISNGP---------------KLLTKELFEKSLKDFVPLALRGIKLVKSTGIR  665 (952)
T ss_pred             HHHhcCCccchhHHHHHHHHHHHHHHHHhccCc---------------ccchHHHHHHHHHhcChHHhhhccccccCCCC
Confidence            999999999999999999999999966653321               368999999999999999999753    2377


Q ss_pred             cchhhhhh
Q 039253          171 FCETAVAA  178 (199)
Q Consensus       171 ~~~~~~~~  178 (199)
                      |-+.++-.
T Consensus       666 w~digg~~  673 (952)
T KOG0735|consen  666 WEDIGGLF  673 (952)
T ss_pred             ceecccHH
Confidence            87776643

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

Probab=99.24  E-value=3.3e-11  Score=106.23  Aligned_cols=107  Identities=26%  Similarity=0.411  Sum_probs=85.1

Q ss_pred             cceeeccCCC-CCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhh
Q 039253            3 WSIVIQRGSG-AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACL   81 (199)
Q Consensus         3 ~sl~~~R~~~-~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l   81 (199)
                      +|+++.|... .++..+..+|.||-.--  .....++++.+||+|.++|.|+-.  |||..|+||+|.+++|..||..|+
T Consensus       453 DAFLceRnktymSEaqRsaLNAlLfRTG--dqSrdivLvlAtNrpgdlDsAV~D--Ride~veFpLPGeEERfkll~lYl  528 (630)
T KOG0742|consen  453 DAFLCERNKTYMSEAQRSALNALLFRTG--DQSRDIVLVLATNRPGDLDSAVND--RIDEVVEFPLPGEEERFKLLNLYL  528 (630)
T ss_pred             HHHHHHhchhhhcHHHHHHHHHHHHHhc--ccccceEEEeccCCccchhHHHHh--hhhheeecCCCChHHHHHHHHHHH
Confidence            4667777655 77777788999885543  234568999999999999999999  999999999999999999999999


Q ss_pred             cCCCCC---C------------------------cccHHHHHhhCCCCCHHHHHHHHHH
Q 039253           82 RKSPVS---K------------------------DVDLEKLAQFTQGFSGADITEICQR  113 (199)
Q Consensus        82 ~~~~~~---~------------------------~~~l~~la~~t~G~sgaDI~~lv~~  113 (199)
                      .++...   .                        +--+...|+.|+||||++|..|+-.
T Consensus       529 nkyi~~~~~~~~~~~~~~lfkk~sQ~i~l~~~~t~~~~~EaAkkTeGfSGREiakLva~  587 (630)
T KOG0742|consen  529 NKYILKPATSGKPGKWSHLFKKESQRIKLAGFDTGRKCSEAAKKTEGFSGREIAKLVAS  587 (630)
T ss_pred             HHHhcCcCCCCCCchhhHHHhhhhheeeeccchHHHHHHHHHHhccCCcHHHHHHHHHH
Confidence            654211   0                        1125678899999999999999764

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

Probab=99.18  E-value=7.6e-11  Score=104.80  Aligned_cols=93  Identities=27%  Similarity=0.312  Sum_probs=74.8

Q ss_pred             HHHHHHHHHHhCCCCCC--CEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCC-CCCcccHHHH
Q 039253           19 RIPNQLLTEMDGLSAKK--TIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSP-VSKDVDLEKL   95 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~--~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~-~~~~~~l~~l   95 (199)
                      -.++.||+.+||+.+..  --|||+|||+++.||||++||||+|.+|+++..+.++-..+++.|+.-.. ..---++..+
T Consensus       319 VTlSGLLNfiDGlwSscg~ERIivFTTNh~EkLDPALlRpGRmDmhI~mgyCtf~~fK~La~nYL~~~~~h~L~~eie~l  398 (457)
T KOG0743|consen  319 VTLSGLLNFLDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDMHIYMGYCTFEAFKTLASNYLGIEEDHRLFDEIERL  398 (457)
T ss_pred             eehHHhhhhhccccccCCCceEEEEecCChhhcCHhhcCCCcceeEEEcCCCCHHHHHHHHHHhcCCCCCcchhHHHHHH
Confidence            45899999999998765  46899999999999999999999999999999999999999999997532 2111234444


Q ss_pred             HhhCCCCCHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQ  112 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~  112 (199)
                      .+.++ .|+||+...+-
T Consensus       399 ~~~~~-~tPA~V~e~lm  414 (457)
T KOG0743|consen  399 IEETE-VTPAQVAEELM  414 (457)
T ss_pred             hhcCc-cCHHHHHHHHh
Confidence            44444 79999976543

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

Probab=99.05  E-value=3.5e-10  Score=97.21  Aligned_cols=124  Identities=24%  Similarity=0.357  Sum_probs=95.4

Q ss_pred             CCCCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC---
Q 039253           11 SGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS---   87 (199)
Q Consensus        11 ~~~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~---   87 (199)
                      +.+.+..-|++|.+|+|||.+...++|++++|+|-.+.||.||..  |-|.+.+++.|+.+.|++|++.++..+.-.   
T Consensus       272 ~~EpsDaIRvVNalLTQlDrlK~~~NvliL~TSNl~~siD~AfVD--RADi~~yVG~Pt~~ai~~IlkscieEL~~~gIi  349 (423)
T KOG0744|consen  272 RNEPSDAIRVVNALLTQLDRLKRYPNVLILATSNLTDSIDVAFVD--RADIVFYVGPPTAEAIYEILKSCIEELISSGII  349 (423)
T ss_pred             CCCCchHHHHHHHHHHHHHHhccCCCEEEEeccchHHHHHHHhhh--HhhheeecCCccHHHHHHHHHHHHHHHHhcCee
Confidence            335555679999999999999999999999999999999999999  999999999999999999999998643100   


Q ss_pred             ---------------CcccHHHHHhh-CCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHH
Q 039253           88 ---------------KDVDLEKLAQF-TQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFE  151 (199)
Q Consensus        88 ---------------~~~~l~~la~~-t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~  151 (199)
                                     .+.....+++. +.|+||+-|+.+--.|...-.+.                     .+++.++|.
T Consensus       350 ~~~~~s~~~~~~i~~~~~~~~~~~~~~~~gLSGRtlrkLP~Laha~y~~~---------------------~~v~~~~fl  408 (423)
T KOG0744|consen  350 LFHQRSTGVKEFIKYQKALRNILIELSTVGLSGRTLRKLPLLAHAEYFRT---------------------FTVDLSNFL  408 (423)
T ss_pred             eeeccchhhhHHhHhhHhHHHHHHHHhhcCCccchHhhhhHHHHHhccCC---------------------CccChHHHH
Confidence                           01112333333 48999999988866553221111                     578999999


Q ss_pred             HHHHhc
Q 039253          152 ESMKYA  157 (199)
Q Consensus       152 ~Al~~~  157 (199)
                      .|+...
T Consensus       409 ~al~ea  414 (423)
T KOG0744|consen  409 LALLEA  414 (423)
T ss_pred             HHHHHH
Confidence            888654

>CHL00181 cbbX CbbX; Provisional

Probab=98.46  E-value=3.1e-06  Score=72.49  Aligned_cols=125  Identities=18%  Similarity=0.169  Sum_probs=86.6

Q ss_pred             hhhHHHHHHHHHHhCCCCCCCEEEEEeeCCC-----CCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCC--CC
Q 039253           16 AADRIPNQLLTEMDGLSAKKTIFVIGVTNRP-----DIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPV--SK   88 (199)
Q Consensus        16 ~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~-----~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~--~~   88 (199)
                      ....+...|+..|+..  ..+++||++++..     ..++|++++  ||+.+|+|+.++.+++.+|++.++.+...  .+
T Consensus       143 ~~~e~~~~L~~~me~~--~~~~~vI~ag~~~~~~~~~~~np~L~s--R~~~~i~F~~~t~~el~~I~~~~l~~~~~~l~~  218 (287)
T CHL00181        143 YGSEAIEILLQVMENQ--RDDLVVIFAGYKDRMDKFYESNPGLSS--RIANHVDFPDYTPEELLQIAKIMLEEQQYQLTP  218 (287)
T ss_pred             hHHHHHHHHHHHHhcC--CCCEEEEEeCCcHHHHHHHhcCHHHHH--hCCceEEcCCcCHHHHHHHHHHHHHHhcCCCCh
Confidence            4567889999999853  4567788887632     244699999  99999999999999999999999976533  32


Q ss_pred             cccHHHHHh----h--CCCCC-HHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHH
Q 039253           89 DVDLEKLAQ----F--TQGFS-GADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEE  152 (199)
Q Consensus        89 ~~~l~~la~----~--t~G~s-gaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~  152 (199)
                      + ....+..    .  .+.|. ++++++++++|...-..|......       .....+....++.+|+.+
T Consensus       219 ~-~~~~L~~~i~~~~~~~~~GNaR~vrn~ve~~~~~~~~r~~~~~~-------~~~~~~~l~~~~~~d~~~  281 (287)
T CHL00181        219 E-AEKALLDYIKKRMEQPLFANARSVRNALDRARMRQANRIFESGG-------RVLTKADLVTIEAEDILK  281 (287)
T ss_pred             h-HHHHHHHHHHHhCCCCCCccHHHHHHHHHHHHHHHHHHHHcCCC-------CCCCHHHHhCCCHHHHhH
Confidence            2 2222222    2  24566 899999999998887777654311       111233446677777754

>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=98.42  E-value=5e-07  Score=66.88  Aligned_cols=62  Identities=42%  Similarity=0.629  Sum_probs=50.5

Q ss_pred             eeeccCCCCCchhhHHHHHHHHHHhCCCCC-CCEEEEEeeCCCCCCCccccCCCccceEEEecC
Q 039253            5 IVIQRGSGAGGAADRIPNQLLTEMDGLSAK-KTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPL   67 (199)
Q Consensus         5 l~~~R~~~~~~~~~r~~~~lL~~ld~~~~~-~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~   67 (199)
                      ++++.....+....+++++|+..|+..... .+++||+|||.++.+|++++| +||+++|++++
T Consensus        70 l~~~~~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~~~~i~~~l~~-~rf~~~i~~~~  132 (132)
T PF00004_consen   70 LFPKSQPSSSSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNSPDKIDPALLR-SRFDRRIEFPL  132 (132)
T ss_dssp             TSHHCSTSSSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESSGGGSCHHHHS-TTSEEEEEE-S
T ss_pred             cccccccccccccccccceeeecccccccccccceeEEeeCChhhCCHhHHh-CCCcEEEEcCC
Confidence            334443335556778999999999998766 669999999999999999998 89999999974

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 ....

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=98.21  E-value=1.9e-05  Score=67.51  Aligned_cols=127  Identities=17%  Similarity=0.178  Sum_probs=85.8

Q ss_pred             hhhHHHHHHHHHHhCCCCCCCEEEEEeeCC--CCC---CCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-Cc
Q 039253           16 AADRIPNQLLTEMDGLSAKKTIFVIGVTNR--PDI---IDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KD   89 (199)
Q Consensus        16 ~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~--~~~---lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~   89 (199)
                      ....+.+.|++.|+.  ...+++||++++.  ++.   ++|+|.+  ||+..|+||.++.+++..|++.++.+.... ..
T Consensus       142 ~~~~~~~~Ll~~le~--~~~~~~vI~a~~~~~~~~~~~~np~L~s--R~~~~i~fp~l~~edl~~I~~~~l~~~~~~l~~  217 (284)
T TIGR02880       142 YGQEAIEILLQVMEN--QRDDLVVILAGYKDRMDSFFESNPGFSS--RVAHHVDFPDYSEAELLVIAGLMLKEQQYRFSA  217 (284)
T ss_pred             hHHHHHHHHHHHHhc--CCCCEEEEEeCCcHHHHHHHhhCHHHHh--hCCcEEEeCCcCHHHHHHHHHHHHHHhccccCH
Confidence            455678899999984  3456788888764  232   4899999  999999999999999999999999875432 12


Q ss_pred             ccHHHHHhh------CCCC-CHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHH
Q 039253           90 VDLEKLAQF------TQGF-SGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEES  153 (199)
Q Consensus        90 ~~l~~la~~------t~G~-sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~A  153 (199)
                      ..+..+...      -+.+ .+++++++++.|......|.....       ...........++.+|+..+
T Consensus       218 ~a~~~L~~~l~~~~~~~~~GN~R~lrn~ve~~~~~~~~r~~~~~-------~~~~~~~~~~~~~~~d~~~~  281 (284)
T TIGR02880       218 EAEEAFADYIALRRTQPHFANARSIRNAIDRARLRQANRLFCDL-------DRVLDKSDLETIDPEDLLAS  281 (284)
T ss_pred             HHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHhcCc-------CCCCCHHHHhCCCHHHHhhc
Confidence            223333332      1333 379999999999777766664321       11112334466777887543

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.

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.06  E-value=4.9e-05  Score=64.89  Aligned_cols=81  Identities=14%  Similarity=0.165  Sum_probs=65.6

Q ss_pred             CCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhhCCCCCHHHHHHHHHH
Q 039253           35 KTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSGADITEICQR  113 (199)
Q Consensus        35 ~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~~  113 (199)
                      .++++|++||++..+++++++  ||...+.|+.|+.++..++++......... ++..+..|++.+.|+. +.+..++..
T Consensus       128 ~~~~li~~t~~~~~l~~~l~s--R~~~~~~l~~l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~p-R~~~~ll~~  204 (305)
T TIGR00635       128 PPFTLVGATTRAGMLTSPLRD--RFGIILRLEFYTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTP-RIANRLLRR  204 (305)
T ss_pred             CCeEEEEecCCccccCHHHHh--hcceEEEeCCCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCc-chHHHHHHH
Confidence            348899999999999999999  999999999999999999999888755443 3445778999998865 666777776


Q ss_pred             HHHHH
Q 039253          114 ACKDA  118 (199)
Q Consensus       114 A~~~a  118 (199)
                      +...+
T Consensus       205 ~~~~a  209 (305)
T TIGR00635       205 VRDFA  209 (305)
T ss_pred             HHHHH
Confidence            65444

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=98.00  E-value=0.00011  Score=61.75  Aligned_cols=103  Identities=13%  Similarity=0.133  Sum_probs=70.9

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCC-----CCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-Ccc
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRP-----DIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDV   90 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~-----~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~   90 (199)
                      ....++.|+..|+..  ..++++|+++...     ..++|++++  ||+.+|+|+.++.+++.+|++.++...... ++.
T Consensus       126 ~~~~i~~Ll~~~e~~--~~~~~vila~~~~~~~~~~~~~p~L~s--Rf~~~i~f~~~~~~el~~Il~~~~~~~~~~l~~~  201 (261)
T TIGR02881       126 GKEAIDTLVKGMEDN--RNEFVLILAGYSDEMDYFLSLNPGLRS--RFPISIDFPDYTVEELMEIAERMVKEREYKLTEE  201 (261)
T ss_pred             HHHHHHHHHHHHhcc--CCCEEEEecCCcchhHHHHhcChHHHh--ccceEEEECCCCHHHHHHHHHHHHHHcCCccCHH
Confidence            345778899999864  3445666555322     247899999  999999999999999999999999765433 222


Q ss_pred             cHHHHHhh---------CCCCCHHHHHHHHHHHHHHHHHHHH
Q 039253           91 DLEKLAQF---------TQGFSGADITEICQRACKDATREEI  123 (199)
Q Consensus        91 ~l~~la~~---------t~G~sgaDI~~lv~~A~~~a~~~~~  123 (199)
                      -+..|++.         ...-.++.+.++++.|......+..
T Consensus       202 a~~~l~~~~~~~~~~~~~~~gn~R~~~n~~e~a~~~~~~r~~  243 (261)
T TIGR02881       202 AKWKLREHLYKVDQLSSREFSNARYVRNIIEKAIRRQAVRLL  243 (261)
T ss_pred             HHHHHHHHHHHHHhccCCCCchHHHHHHHHHHHHHHHHHHHh
Confidence            23334321         1124578888888888766665554

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.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=97.94  E-value=5.5e-05  Score=65.64  Aligned_cols=83  Identities=17%  Similarity=0.172  Sum_probs=67.1

Q ss_pred             CCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhhCCCCCHHHHHHHHHH
Q 039253           35 KTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSGADITEICQR  113 (199)
Q Consensus        35 ~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~~  113 (199)
                      .++.+|++||++..+++++++  ||...+.|+.|+.+++.+|++.......+. ++..+..|++.+.|.. +.+..+++.
T Consensus       149 ~~~~li~at~~~~~l~~~L~s--Rf~~~~~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~p-R~a~~~l~~  225 (328)
T PRK00080        149 PPFTLIGATTRAGLLTSPLRD--RFGIVQRLEFYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTP-RIANRLLRR  225 (328)
T ss_pred             CCceEEeecCCcccCCHHHHH--hcCeeeecCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCc-hHHHHHHHH
Confidence            347899999999999999999  999999999999999999999998766544 3445788999998854 777777776


Q ss_pred             HHHHHHH
Q 039253          114 ACKDATR  120 (199)
Q Consensus       114 A~~~a~~  120 (199)
                      +...+..
T Consensus       226 ~~~~a~~  232 (328)
T PRK00080        226 VRDFAQV  232 (328)
T ss_pred             HHHHHHH
Confidence            6555443

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=97.91  E-value=3.4e-05  Score=71.39  Aligned_cols=95  Identities=24%  Similarity=0.249  Sum_probs=73.8

Q ss_pred             EEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhhCCCCCHHHHHHHHHHHH
Q 039253           37 IFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSGADITEICQRAC  115 (199)
Q Consensus        37 VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~~A~  115 (199)
                      .++++|||.|+.|++++++  |+. .|.|+.++.+++.+|++..+++..+. ++..++.|+..+  ++++++.++++.|+
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-EIFFRPLLDEEIKEIAKNAAEKIGINLEKHALELIVKYA--SNGREAVNIVQLAA  309 (531)
T ss_pred             EEEEEecCCcccCChHHhh--hhh-eeeCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhh--hhHHHHHHHHHHHH
Confidence            4556667779999999999  985 67888888999999999999876543 333466666655  48999999999998


Q ss_pred             HHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHH
Q 039253          116 KDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMK  155 (199)
Q Consensus       116 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~  155 (199)
                      ..|..+..                   ..|+.+|+..++.
T Consensus       310 ~~A~~~~~-------------------~~It~~dI~~vl~  330 (531)
T TIGR02902       310 GIALGEGR-------------------KRILAEDIEWVAE  330 (531)
T ss_pred             HHHhhCCC-------------------cEEcHHHHHHHhC
Confidence            77654321                   4689999999986

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.

>TIGR00763 lon ATP-dependent protease La

Probab=97.71  E-value=0.00013  Score=70.41  Aligned_cols=86  Identities=22%  Similarity=0.333  Sum_probs=64.3

Q ss_pred             CCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhc-----CCCCC------CcccHHHHHh-hCCCC
Q 039253           35 KTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR-----KSPVS------KDVDLEKLAQ-FTQGF  102 (199)
Q Consensus        35 ~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~-----~~~~~------~~~~l~~la~-~t~G~  102 (199)
                      .++++|+|||.++.||+++++  ||+ .|+|+.|+.+++.+|++.++.     ...+.      .+..+..|++ .|..+
T Consensus       462 s~v~~I~TtN~~~~i~~~L~~--R~~-vi~~~~~~~~e~~~I~~~~l~~~~~~~~~l~~~~~~~~~~~l~~i~~~~~~e~  538 (775)
T TIGR00763       462 SKVIFIATANSIDTIPRPLLD--RME-VIELSGYTEEEKLEIAKKYLIPKALEDHGLKPDELKITDEALLLLIKYYTREA  538 (775)
T ss_pred             CCEEEEEecCCchhCCHHHhC--Cee-EEecCCCCHHHHHHHHHHHHHHHHHHHcCCCcceEEECHHHHHHHHHhcChhc
Confidence            468999999999999999999  995 789999999999999998872     12221      2223555554 44567


Q ss_pred             CHHHHHHHHHHHHHHHHHHHH
Q 039253          103 SGADITEICQRACKDATREEI  123 (199)
Q Consensus       103 sgaDI~~lv~~A~~~a~~~~~  123 (199)
                      ..++|+..+...+..+.++..
T Consensus       539 g~R~l~r~i~~~~~~~~~~~~  559 (775)
T TIGR00763       539 GVRNLERQIEKICRKAAVKLV  559 (775)
T ss_pred             CChHHHHHHHHHHHHHHHHHH
Confidence            778888888777766655544

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.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.71  E-value=0.00029  Score=62.83  Aligned_cols=94  Identities=17%  Similarity=0.236  Sum_probs=66.3

Q ss_pred             HHHHHHHhCCCCCCCEEEEEeeCCCCC---CCccccCCCccce--EEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           22 NQLLTEMDGLSAKKTIFVIGVTNRPDI---IDPALLRPGRLDQ--LIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        22 ~~lL~~ld~~~~~~~VvvI~aTN~~~~---lD~al~R~gRfd~--~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      .+|+..++.+......+||.+++.|..   +++.+++  ||..  .++|+.|+.++|..|++..+....+. ++..+..|
T Consensus       219 ~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~S--Rl~~g~~v~i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~i  296 (405)
T TIGR00362       219 EEFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRS--RFEWGLVVDIEPPDLETRLAILQKKAEEEGLELPDEVLEFI  296 (405)
T ss_pred             HHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhh--hccCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            345555554433344456655555655   5688888  9974  79999999999999999999766544 45557888


Q ss_pred             HhhCCCCCHHHHHHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQRACKDA  118 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A~~~a  118 (199)
                      |++..| +.++|..++......+
T Consensus       297 a~~~~~-~~r~l~~~l~~l~~~a  318 (405)
T TIGR00362       297 AKNIRS-NVRELEGALNRLLAYA  318 (405)
T ss_pred             HHhcCC-CHHHHHHHHHHHHHHH
Confidence            987764 6788888877765444

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).

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=97.60  E-value=0.0003  Score=62.06  Aligned_cols=123  Identities=21%  Similarity=0.258  Sum_probs=79.8

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCC---CCCCccccCCCccc-eEEEecCCCHHHHHHHHHHhhcCC--C-CCCccc
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRP---DIIDPALLRPGRLD-QLIYIPLPVEKSRLQIFKACLRKS--P-VSKDVD   91 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~---~~lD~al~R~gRfd-~~i~~~~P~~~~R~~il~~~l~~~--~-~~~~~~   91 (199)
                      .++..|+..++... ..++.+|+++|.+   +.+++.+.+  ||. ..|.|++++.++..+|++..+...  . .-++..
T Consensus       157 ~~l~~l~~~~~~~~-~~~v~vI~i~~~~~~~~~l~~~~~s--~~~~~~i~f~py~~~e~~~il~~r~~~~~~~~~~~~~~  233 (394)
T PRK00411        157 DVLYSLLRAHEEYP-GARIGVIGISSDLTFLYILDPRVKS--VFRPEEIYFPPYTADEIFDILKDRVEEGFYPGVVDDEV  233 (394)
T ss_pred             hHHHHHHHhhhccC-CCeEEEEEEECCcchhhhcCHHHHh--cCCcceeecCCCCHHHHHHHHHHHHHhhcccCCCCHhH
Confidence            35566666666543 2378889998875   457777776  664 678999999999999999887532  1 112334


Q ss_pred             HHHHHhhCCCCC--HHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccccccc
Q 039253           92 LEKLAQFTQGFS--GADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQSR  163 (199)
Q Consensus        92 l~~la~~t~G~s--gaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps~~r  163 (199)
                      +..+++.+.+.+  .+.+..+|..|...|..+..                   ..|+.+|+..|+..+.++..+
T Consensus       234 l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~-------------------~~I~~~~v~~a~~~~~~~~~~  288 (394)
T PRK00411        234 LDLIADLTAREHGDARVAIDLLRRAGLIAEREGS-------------------RKVTEEDVRKAYEKSEIVHLS  288 (394)
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCC-------------------CCcCHHHHHHHHHHHHHHHHH
Confidence            667777774432  33344666666655544321                   457888888888877655443

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=97.60  E-value=0.00053  Score=59.81  Aligned_cols=103  Identities=21%  Similarity=0.215  Sum_probs=66.6

Q ss_pred             CCEEEEEeeCCCC---CCCccccCCCccc-eEEEecCCCHHHHHHHHHHhhcC-C---CCCCcccHHH---HHhhCCCCC
Q 039253           35 KTIFVIGVTNRPD---IIDPALLRPGRLD-QLIYIPLPVEKSRLQIFKACLRK-S---PVSKDVDLEK---LAQFTQGFS  103 (199)
Q Consensus        35 ~~VvvI~aTN~~~---~lD~al~R~gRfd-~~i~~~~P~~~~R~~il~~~l~~-~---~~~~~~~l~~---la~~t~G~s  103 (199)
                      .++.+|++||.++   .+++.+.+  ||. ..++|++++.++..+|++..+.. .   .+. +..+..   ++..+.|. 
T Consensus       164 ~~v~lI~i~n~~~~~~~l~~~~~s--~~~~~~i~f~p~~~~e~~~il~~r~~~~~~~~~~~-~~~l~~i~~~~~~~~Gd-  239 (365)
T TIGR02928       164 AKVGVIGISNDLKFRENLDPRVKS--SLCEEEIIFPPYDAEELRDILENRAEKAFYDGVLD-DGVIPLCAALAAQEHGD-  239 (365)
T ss_pred             CeEEEEEEECCcchHhhcCHHHhc--cCCcceeeeCCCCHHHHHHHHHHHHHhhccCCCCC-hhHHHHHHHHHHHhcCC-
Confidence            5689999999886   58888888  885 78999999999999999998852 1   122 222333   34444453 


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcccc
Q 039253          104 GADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKS  160 (199)
Q Consensus       104 gaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps  160 (199)
                      .+.+..+|+.|...|..+..                   ..|+.+|+..|+..+..+
T Consensus       240 ~R~al~~l~~a~~~a~~~~~-------------------~~it~~~v~~a~~~~~~~  277 (365)
T TIGR02928       240 ARKAIDLLRVAGEIAEREGA-------------------ERVTEDHVEKAQEKIEKD  277 (365)
T ss_pred             HHHHHHHHHHHHHHHHHcCC-------------------CCCCHHHHHHHHHHHHHH
Confidence            33444567777666654321                   346666666666555433

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.

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.57  E-value=0.00043  Score=62.69  Aligned_cols=113  Identities=18%  Similarity=0.213  Sum_probs=76.4

Q ss_pred             HHHHHHHhCCCCCCCEEEEEeeCCCCC---CCccccCCCccc--eEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           22 NQLLTEMDGLSAKKTIFVIGVTNRPDI---IDPALLRPGRLD--QLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        22 ~~lL~~ld~~~~~~~VvvI~aTN~~~~---lD~al~R~gRfd--~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      .+|+..++.+......+||+++..|..   +++.+++  ||.  ..+++..|+.++|..|++..+....+. ++.-+..|
T Consensus       231 ~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~l~S--Rl~~gl~v~i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~i  308 (450)
T PRK00149        231 EEFFHTFNALHEAGKQIVLTSDRPPKELPGLEERLRS--RFEWGLTVDIEPPDLETRIAILKKKAEEEGIDLPDEVLEFI  308 (450)
T ss_pred             HHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHh--HhcCCeeEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            345555555433344456655555655   6789998  997  589999999999999999999765433 34458888


Q ss_pred             HhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhc
Q 039253           96 AQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYA  157 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~  157 (199)
                      |+.+.| +.++|..++......+....                    .++|.+.+.++|..+
T Consensus       309 a~~~~~-~~R~l~~~l~~l~~~~~~~~--------------------~~it~~~~~~~l~~~  349 (450)
T PRK00149        309 AKNITS-NVRELEGALNRLIAYASLTG--------------------KPITLELAKEALKDL  349 (450)
T ss_pred             HcCcCC-CHHHHHHHHHHHHHHHHhhC--------------------CCCCHHHHHHHHHHh
Confidence            888765 67777777776644433221                    446666666666654

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

Probab=97.47  E-value=0.00023  Score=68.46  Aligned_cols=82  Identities=23%  Similarity=0.248  Sum_probs=60.3

Q ss_pred             CCCCEEEEEeeCCCC-----CCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCccc-----HHHHHhhC---
Q 039253           33 AKKTIFVIGVTNRPD-----IIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVD-----LEKLAQFT---   99 (199)
Q Consensus        33 ~~~~VvvI~aTN~~~-----~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~-----l~~la~~t---   99 (199)
                      .+..+.+|++||.++     ..|+||.|  ||+ .|+++.|+.+++..||+.+..++....++.     +..++..+   
T Consensus       312 ~~g~i~vIgATt~~E~~~~~~~D~AL~r--RFq-~I~v~ePs~~~~~~IL~~~~~~ye~~h~v~i~~~al~~a~~ls~ry  388 (758)
T PRK11034        312 SSGKIRVIGSTTYQEFSNIFEKDRALAR--RFQ-KIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKY  388 (758)
T ss_pred             hCCCeEEEecCChHHHHHHhhccHHHHh--hCc-EEEeCCCCHHHHHHHHHHHHHHhhhccCCCcCHHHHHHHHHHhhcc
Confidence            356799999999865     68999999  996 799999999999999998876553333333     33333333   


Q ss_pred             --CCCCHHHHHHHHHHHHHH
Q 039253          100 --QGFSGADITEICQRACKD  117 (199)
Q Consensus       100 --~G~sgaDI~~lv~~A~~~  117 (199)
                        ..+-+.....++++|+..
T Consensus       389 i~~r~lPdKaidlldea~a~  408 (758)
T PRK11034        389 INDRHLPDKAIDVIDEAGAR  408 (758)
T ss_pred             ccCccChHHHHHHHHHHHHh
Confidence              334556778888888643

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=97.34  E-value=0.0014  Score=60.43  Aligned_cols=94  Identities=17%  Similarity=0.158  Sum_probs=74.8

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHH
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLA   96 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la   96 (199)
                      ....+.|+..|+.  +...+++|++|+.++.+++++++  |. ..++|..++.++...+++..+.+.... .+..+..|+
T Consensus       142 ~~a~naLLk~LEe--pp~~~vfI~aTte~~kI~~tI~S--Rc-~~~ef~~ls~~el~~~L~~i~~~egi~ie~eAL~~Ia  216 (507)
T PRK06645        142 KGAFNALLKTLEE--PPPHIIFIFATTEVQKIPATIIS--RC-QRYDLRRLSFEEIFKLLEYITKQENLKTDIEALRIIA  216 (507)
T ss_pred             HHHHHHHHHHHhh--cCCCEEEEEEeCChHHhhHHHHh--cc-eEEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            3457788888873  44567888888999999999998  88 578999999999999999999766544 334577889


Q ss_pred             hhCCCCCHHHHHHHHHHHHHH
Q 039253           97 QFTQGFSGADITEICQRACKD  117 (199)
Q Consensus        97 ~~t~G~sgaDI~~lv~~A~~~  117 (199)
                      +.+.| +.+++.++++.+...
T Consensus       217 ~~s~G-slR~al~~Ldkai~~  236 (507)
T PRK06645        217 YKSEG-SARDAVSILDQAASM  236 (507)
T ss_pred             HHcCC-CHHHHHHHHHHHHHh
Confidence            88876 889988888887544

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=97.30  E-value=0.0015  Score=56.76  Aligned_cols=92  Identities=22%  Similarity=0.225  Sum_probs=68.6

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHh
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQ   97 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~   97 (199)
                      ...+.|+..|+..  ...+++|++|+.++.+.+++++  |+ ..++|+.|+.++...+++..+++.... ++..+..|++
T Consensus       132 ~~~~~Ll~~le~~--~~~~~lIl~~~~~~~l~~~l~s--r~-~~~~~~~~~~~~l~~~l~~~~~~~g~~i~~~a~~~l~~  206 (355)
T TIGR02397       132 SAFNALLKTLEEP--PEHVVFILATTEPHKIPATILS--RC-QRFDFKRIPLEDIVERLKKILDKEGIKIEDEALELIAR  206 (355)
T ss_pred             HHHHHHHHHHhCC--ccceeEEEEeCCHHHHHHHHHh--he-eEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            4567788888753  3467788888999999999998  87 578999999999999999988766543 3445677787


Q ss_pred             hCCCCCHHHHHHHHHHHHH
Q 039253           98 FTQGFSGADITEICQRACK  116 (199)
Q Consensus        98 ~t~G~sgaDI~~lv~~A~~  116 (199)
                      .+.| +++.+.+.++.+..
T Consensus       207 ~~~g-~~~~a~~~lekl~~  224 (355)
T TIGR02397       207 AADG-SLRDALSLLDQLIS  224 (355)
T ss_pred             HcCC-ChHHHHHHHHHHHh
Confidence            7765 66666666665543

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.

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.28  E-value=0.0023  Score=56.43  Aligned_cols=91  Identities=21%  Similarity=0.239  Sum_probs=70.0

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHh
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQ   97 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~   97 (199)
                      ...+.||..|+.  +...+.+|++|+.++.+.+.+++  |+ ..++|++|+.++...+++..+++.... ++..+..++.
T Consensus       134 ~a~naLLk~lEe--~~~~~~fIl~t~~~~~l~~tI~S--Rc-~~~~~~~l~~~el~~~L~~~~~~~g~~i~~~al~~ia~  208 (363)
T PRK14961        134 HSFNALLKTLEE--PPQHIKFILATTDVEKIPKTILS--RC-LQFKLKIISEEKIFNFLKYILIKESIDTDEYALKLIAY  208 (363)
T ss_pred             HHHHHHHHHHhc--CCCCeEEEEEcCChHhhhHHHHh--hc-eEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            456778888885  33456777888889999999998  87 678999999999999999988765533 3445777888


Q ss_pred             hCCCCCHHHHHHHHHHHH
Q 039253           98 FTQGFSGADITEICQRAC  115 (199)
Q Consensus        98 ~t~G~sgaDI~~lv~~A~  115 (199)
                      .+.| +++++.++++.+.
T Consensus       209 ~s~G-~~R~al~~l~~~~  225 (363)
T PRK14961        209 HAHG-SMRDALNLLEHAI  225 (363)
T ss_pred             HcCC-CHHHHHHHHHHHH
Confidence            8876 6777777777654

>PRK06893 DNA replication initiation factor; Validated

Probab=97.27  E-value=0.0012  Score=54.42  Aligned_cols=91  Identities=8%  Similarity=0.127  Sum_probs=60.3

Q ss_pred             HHHHHHhCCCCCC-CEEEEEeeCCCCCCC---ccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHh
Q 039253           23 QLLTEMDGLSAKK-TIFVIGVTNRPDIID---PALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQ   97 (199)
Q Consensus        23 ~lL~~ld~~~~~~-~VvvI~aTN~~~~lD---~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~   97 (199)
                      .|...++...... .++|+.++..|..++   +.+.+..++...+.++.|+.++|.+|++.......+. ++.-+..|++
T Consensus       112 ~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~~~iL~~~a~~~~l~l~~~v~~~L~~  191 (229)
T PRK06893        112 AIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQLNDLTDEQKIIVLQRNAYQRGIELSDEVANFLLK  191 (229)
T ss_pred             HHHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHHHHhcCCeeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            3444455443333 345555666677776   8899834456799999999999999999888644443 3455778888


Q ss_pred             hCCCCCHHHHHHHHHHH
Q 039253           98 FTQGFSGADITEICQRA  114 (199)
Q Consensus        98 ~t~G~sgaDI~~lv~~A  114 (199)
                      +.+| +.+.+..++...
T Consensus       192 ~~~~-d~r~l~~~l~~l  207 (229)
T PRK06893        192 RLDR-DMHTLFDALDLL  207 (229)
T ss_pred             hccC-CHHHHHHHHHHH
Confidence            7764 555555555543

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

Probab=97.27  E-value=0.00077  Score=64.72  Aligned_cols=69  Identities=25%  Similarity=0.256  Sum_probs=52.1

Q ss_pred             CCCEEEEEeeCCC-----CCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCC----CCC-CcccHHHHHhhCCCCC
Q 039253           34 KKTIFVIGVTNRP-----DIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKS----PVS-KDVDLEKLAQFTQGFS  103 (199)
Q Consensus        34 ~~~VvvI~aTN~~-----~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~----~~~-~~~~l~~la~~t~G~s  103 (199)
                      +..+.+|++||..     ..+|+|+.|  ||. .|+|+.|+.+++.+||+.+...+    .+. .+..+..++..+..|-
T Consensus       309 ~g~i~~IgaTt~~e~~~~~~~d~al~r--Rf~-~i~v~~p~~~~~~~il~~~~~~~e~~~~v~i~~~al~~~~~ls~ryi  385 (731)
T TIGR02639       309 SGKLRCIGSTTYEEYKNHFEKDRALSR--RFQ-KIDVGEPSIEETVKILKGLKEKYEEFHHVKYSDEALEAAVELSARYI  385 (731)
T ss_pred             CCCeEEEEecCHHHHHHHhhhhHHHHH--hCc-eEEeCCCCHHHHHHHHHHHHHHHHhccCcccCHHHHHHHHHhhhccc
Confidence            4678999999963     468999999  997 79999999999999999777542    111 3445666777776664


Q ss_pred             HH
Q 039253          104 GA  105 (199)
Q Consensus       104 ga  105 (199)
                      +.
T Consensus       386 ~~  387 (731)
T TIGR02639       386 ND  387 (731)
T ss_pred             cc
Confidence            43

>PRK09087 hypothetical protein; Validated

Probab=97.08  E-value=0.0031  Score=52.10  Aligned_cols=112  Identities=15%  Similarity=0.089  Sum_probs=71.9

Q ss_pred             HHHHHHhCCCCCCCEEEEEeeCCCCCC---CccccCCCccc--eEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHH
Q 039253           23 QLLTEMDGLSAKKTIFVIGVTNRPDII---DPALLRPGRLD--QLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLA   96 (199)
Q Consensus        23 ~lL~~ld~~~~~~~VvvI~aTN~~~~l---D~al~R~gRfd--~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la   96 (199)
                      +|...++.+....+.+||+++..|..+   .+.++.  ||.  ..+++..|+.+.|.++++..+....+. ++.-+..|+
T Consensus       105 ~lf~l~n~~~~~g~~ilits~~~p~~~~~~~~dL~S--Rl~~gl~~~l~~pd~e~~~~iL~~~~~~~~~~l~~ev~~~La  182 (226)
T PRK09087        105 GLFHLINSVRQAGTSLLMTSRLWPSSWNVKLPDLKS--RLKAATVVEIGEPDDALLSQVIFKLFADRQLYVDPHVVYYLV  182 (226)
T ss_pred             HHHHHHHHHHhCCCeEEEECCCChHHhccccccHHH--HHhCCceeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            355555544444455666666555433   678998  986  889999999999999999999765443 455577888


Q ss_pred             hhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhc
Q 039253           97 QFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYA  157 (199)
Q Consensus        97 ~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~  157 (199)
                      ++..| +.+.+..++......+....                    .++|..-+.++++.+
T Consensus       183 ~~~~r-~~~~l~~~l~~L~~~~~~~~--------------------~~it~~~~~~~l~~~  222 (226)
T PRK09087        183 SRMER-SLFAAQTIVDRLDRLALERK--------------------SRITRALAAEVLNEM  222 (226)
T ss_pred             HHhhh-hHHHHHHHHHHHHHHHHHhC--------------------CCCCHHHHHHHHHhh
Confidence            87762 23333333333322222211                    568888888888764

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=97.05  E-value=0.0051  Score=57.43  Aligned_cols=94  Identities=20%  Similarity=0.227  Sum_probs=72.2

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      +....|.||..|+.  +...+++|++|+.++.|++.+++  |+. .+.|..|+.++-...++..+.+..+. .+..+..+
T Consensus       132 t~~a~naLLKtLEe--pp~~~ifIlatt~~~ki~~tI~S--Rc~-~~~f~~~~~~ei~~~L~~i~~~egi~i~~~al~~i  206 (559)
T PRK05563        132 STGAFNALLKTLEE--PPAHVIFILATTEPHKIPATILS--RCQ-RFDFKRISVEDIVERLKYILDKEGIEYEDEALRLI  206 (559)
T ss_pred             CHHHHHHHHHHhcC--CCCCeEEEEEeCChhhCcHHHHh--Hhe-EEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            34467889988884  34567778788889999999998  875 68899999999999999888766543 34457778


Q ss_pred             HhhCCCCCHHHHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQRACK  116 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A~~  116 (199)
                      +..+.| +.++..++++.+..
T Consensus       207 a~~s~G-~~R~al~~Ldq~~~  226 (559)
T PRK05563        207 ARAAEG-GMRDALSILDQAIS  226 (559)
T ss_pred             HHHcCC-CHHHHHHHHHHHHH
Confidence            888876 78888777776643

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=97.03  E-value=0.0036  Score=56.02  Aligned_cols=85  Identities=15%  Similarity=0.176  Sum_probs=63.0

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCcccHHHHHhh
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQF   98 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~l~~la~~   98 (199)
                      ...|.||+.|+.  +..++++|.+|++++.|.|++++  |. ..+.|+.|+.++...+|....   ... ......++..
T Consensus       132 ~aanaLLk~LEe--p~~~~~fIL~a~~~~~llpTIrS--Rc-~~i~f~~~~~~~i~~~L~~~~---~~~-~~~a~~la~~  202 (394)
T PRK07940        132 RAANALLKAVEE--PPPRTVWLLCAPSPEDVLPTIRS--RC-RHVALRTPSVEAVAEVLVRRD---GVD-PETARRAARA  202 (394)
T ss_pred             HHHHHHHHHhhc--CCCCCeEEEEECChHHChHHHHh--hC-eEEECCCCCHHHHHHHHHHhc---CCC-HHHHHHHHHH
Confidence            456889999984  34456666677779999999999  87 699999999998887776322   232 3446778999


Q ss_pred             CCCCCHHHHHHHHH
Q 039253           99 TQGFSGADITEICQ  112 (199)
Q Consensus        99 t~G~sgaDI~~lv~  112 (199)
                      +.|..+.-+..+..
T Consensus       203 s~G~~~~A~~l~~~  216 (394)
T PRK07940        203 SQGHIGRARRLATD  216 (394)
T ss_pred             cCCCHHHHHHHhcC
Confidence            99988877665543

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=96.94  E-value=0.0078  Score=49.18  Aligned_cols=111  Identities=9%  Similarity=0.059  Sum_probs=70.4

Q ss_pred             HHHHHHHhCCCCCCCEEEEEeeCCCC---CCCccccCCCcc--ceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           22 NQLLTEMDGLSAKKTIFVIGVTNRPD---IIDPALLRPGRL--DQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        22 ~~lL~~ld~~~~~~~VvvI~aTN~~~---~lD~al~R~gRf--d~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      ..|...++........++|.+++.+.   .+.+.+++  ||  ...+++++|+.+++..+++.+.....+. ++.-+..|
T Consensus       108 ~~L~~~~~~~~~~~~~~vl~~~~~~~~~~~l~~~L~s--r~~~~~~i~l~pl~~~~~~~~l~~~~~~~~v~l~~~al~~L  185 (227)
T PRK08903        108 IALFNLFNRVRAHGQGALLVAGPAAPLALPLREDLRT--RLGWGLVYELKPLSDADKIAALKAAAAERGLQLADEVPDYL  185 (227)
T ss_pred             HHHHHHHHHHHHcCCcEEEEeCCCCHHhCCCCHHHHH--HHhcCeEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            44555555544444444455555422   35577776  77  4799999999999999999887655443 34456777


Q ss_pred             HhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMK  155 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~  155 (199)
                      +...+ =+.+++..+++.-...+....                    .+||.....+++.
T Consensus       186 ~~~~~-gn~~~l~~~l~~l~~~~~~~~--------------------~~i~~~~~~~~l~  224 (227)
T PRK08903        186 LTHFR-RDMPSLMALLDALDRYSLEQK--------------------RPVTLPLLREMLA  224 (227)
T ss_pred             HHhcc-CCHHHHHHHHHHHHHHHHHhC--------------------CCCCHHHHHHHHh
Confidence            77544 367777777776433332222                    5688888877765

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=96.92  E-value=0.0046  Score=50.11  Aligned_cols=95  Identities=11%  Similarity=0.156  Sum_probs=60.9

Q ss_pred             HHHHHHhCCCCCCCEEEEEeeCCCCCCC---ccccCCCcc--ceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHH
Q 039253           23 QLLTEMDGLSAKKTIFVIGVTNRPDIID---PALLRPGRL--DQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLA   96 (199)
Q Consensus        23 ~lL~~ld~~~~~~~VvvI~aTN~~~~lD---~al~R~gRf--d~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la   96 (199)
                      .|...++........+|+.++..+..++   +.+.+  |+  ...+.++.|+.+++..+++.+..+.... ++.-+..|+
T Consensus       111 ~L~~~l~~~~~~~~~iIits~~~~~~~~~~~~~L~~--r~~~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~l~~L~  188 (226)
T TIGR03420       111 ALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPDLRT--RLAWGLVFQLPPLSDEEKIAALQSRAARRGLQLPDEVADYLL  188 (226)
T ss_pred             HHHHHHHHHHHcCCeEEEECCCChHHCCcccHHHHH--HHhcCeeEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            3444444332223334444443454443   67777  76  4789999999999999999887654433 344567788


Q ss_pred             hhCCCCCHHHHHHHHHHHHHHHHH
Q 039253           97 QFTQGFSGADITEICQRACKDATR  120 (199)
Q Consensus        97 ~~t~G~sgaDI~~lv~~A~~~a~~  120 (199)
                      .. -+-+.+++.++++.+-..+..
T Consensus       189 ~~-~~gn~r~L~~~l~~~~~~~~~  211 (226)
T TIGR03420       189 RH-GSRDMGSLMALLDALDRASLA  211 (226)
T ss_pred             Hh-ccCCHHHHHHHHHHHHHHHHH
Confidence            85 456889999998886544333

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.

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.90  E-value=0.0057  Score=55.99  Aligned_cols=88  Identities=13%  Similarity=0.178  Sum_probs=63.4

Q ss_pred             HHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhh
Q 039253           20 IPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQF   98 (199)
Q Consensus        20 ~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~   98 (199)
                      ..+.||..|+..  ...+++|++|+.+..+++++++  |+. .++|..|+.++...+++..+...... ++..+..|++.
T Consensus       133 a~~~LLk~LE~p--~~~vv~Ilattn~~kl~~~L~S--R~~-vv~f~~l~~~el~~~L~~i~~~egi~i~~eal~~Ia~~  207 (472)
T PRK14962        133 AFNALLKTLEEP--PSHVVFVLATTNLEKVPPTIIS--RCQ-VIEFRNISDELIIKRLQEVAEAEGIEIDREALSFIAKR  207 (472)
T ss_pred             HHHHHHHHHHhC--CCcEEEEEEeCChHhhhHHHhc--CcE-EEEECCccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            446677777743  3467788888889999999999  884 89999999999999999888654432 34457778886


Q ss_pred             CCCCCHHHHHHHHHH
Q 039253           99 TQGFSGADITEICQR  113 (199)
Q Consensus        99 t~G~sgaDI~~lv~~  113 (199)
                      +.| ..+++-+.++.
T Consensus       208 s~G-dlR~aln~Le~  221 (472)
T PRK14962        208 ASG-GLRDALTMLEQ  221 (472)
T ss_pred             hCC-CHHHHHHHHHH
Confidence            654 44444444443

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=96.87  E-value=0.0075  Score=54.80  Aligned_cols=102  Identities=10%  Similarity=0.152  Sum_probs=64.9

Q ss_pred             CEEEEEeeCCC---CCCCccccCCCccc--eEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhhCCCCCHHHHHH
Q 039253           36 TIFVIGVTNRP---DIIDPALLRPGRLD--QLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSGADITE  109 (199)
Q Consensus        36 ~VvvI~aTN~~---~~lD~al~R~gRfd--~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~t~G~sgaDI~~  109 (199)
                      ..+|+.+++.|   ..+++.+++  ||.  ..+.+..|+.++|..||+..+....+. ++.-+..||....+ ..+.|..
T Consensus       236 k~IIlts~~~p~~l~~l~~rL~S--R~~~Gl~~~l~~pd~e~r~~iL~~k~~~~~~~l~~evl~~la~~~~~-dir~L~g  312 (445)
T PRK12422        236 KLIVISSTCAPQDLKAMEERLIS--RFEWGIAIPLHPLTKEGLRSFLERKAEALSIRIEETALDFLIEALSS-NVKSLLH  312 (445)
T ss_pred             CcEEEecCCCHHHHhhhHHHHHh--hhcCCeEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-CHHHHHH
Confidence            34444444445   356789999  996  788899999999999999998766543 34446667776653 4556665


Q ss_pred             HHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhc
Q 039253          110 ICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYA  157 (199)
Q Consensus       110 lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~  157 (199)
                      .+...+..........                 .++|.+...++++.+
T Consensus       313 ~l~~l~~~~a~~~~~~-----------------~~i~~~~~~~~l~~~  343 (445)
T PRK12422        313 ALTLLAKRVAYKKLSH-----------------QLLYVDDIKALLHDV  343 (445)
T ss_pred             HHHHHHHHHHHHHhhC-----------------CCCCHHHHHHHHHHh
Confidence            5555432222111110                 457777777777654

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=96.86  E-value=0.0051  Score=55.77  Aligned_cols=93  Identities=15%  Similarity=0.154  Sum_probs=62.5

Q ss_pred             HHHHHHhCCCCCCCEEEEEeeCCCCC---CCccccCCCccc--eEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHH
Q 039253           23 QLLTEMDGLSAKKTIFVIGVTNRPDI---IDPALLRPGRLD--QLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLA   96 (199)
Q Consensus        23 ~lL~~ld~~~~~~~VvvI~aTN~~~~---lD~al~R~gRfd--~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la   96 (199)
                      +|...++.+......+||++.+.|..   +++.+++  ||.  ..+.+..|+.+.|..|++..+....+. ++.-+..||
T Consensus       215 elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~rL~S--R~~~gl~v~i~~pd~e~r~~IL~~~~~~~~~~l~~ev~~~Ia  292 (440)
T PRK14088        215 ELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVS--RFQMGLVAKLEPPDEETRKKIARKMLEIEHGELPEEVLNFVA  292 (440)
T ss_pred             HHHHHHHHHHHcCCeEEEECCCCHHHHHHHHHHHhh--HHhcCceEeeCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHH
Confidence            45455554434444556655566666   4567888  875  577899999999999999998754333 344578888


Q ss_pred             hhCCCCCHHHHHHHHHHHHHHH
Q 039253           97 QFTQGFSGADITEICQRACKDA  118 (199)
Q Consensus        97 ~~t~G~sgaDI~~lv~~A~~~a  118 (199)
                      +...| +.++|..++.+....+
T Consensus       293 ~~~~~-~~R~L~g~l~~l~~~~  313 (440)
T PRK14088        293 ENVDD-NLRRLRGAIIKLLVYK  313 (440)
T ss_pred             hcccc-CHHHHHHHHHHHHHHH
Confidence            87765 6777777777654333

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=96.83  E-value=0.0097  Score=55.26  Aligned_cols=96  Identities=24%  Similarity=0.193  Sum_probs=74.3

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      +....+.||..|+..  ...+.+|++|+.+..|.+++++  |. .+++|..++.++-...++..+...... .+..+..|
T Consensus       130 t~~A~NALLK~LEEp--p~~t~FIL~ttd~~kL~~tI~S--Rc-~~~~F~~Ls~~ei~~~L~~Il~~EGi~i~~~Al~~I  204 (535)
T PRK08451        130 TKEAFNALLKTLEEP--PSYVKFILATTDPLKLPATILS--RT-QHFRFKQIPQNSIISHLKTILEKEGVSYEPEALEIL  204 (535)
T ss_pred             CHHHHHHHHHHHhhc--CCceEEEEEECChhhCchHHHh--hc-eeEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            445678899999854  3456777788889999999999  85 689999999999888888888765443 34567788


Q ss_pred             HhhCCCCCHHHHHHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQRACKDA  118 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A~~~a  118 (199)
                      +..+.| +.+++.++++.+...+
T Consensus       205 a~~s~G-dlR~alnlLdqai~~~  226 (535)
T PRK08451        205 ARSGNG-SLRDTLTLLDQAIIYC  226 (535)
T ss_pred             HHHcCC-cHHHHHHHHHHHHHhc
Confidence            888776 8888888888776543

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=96.81  E-value=0.0078  Score=57.87  Aligned_cols=93  Identities=18%  Similarity=0.195  Sum_probs=71.4

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      +....|.||+.|+.  ....+.+|++||.++.|.+.+++  |+ .++.|..++.++-.+.|+..+.+..+. .+..+..|
T Consensus       132 T~~A~NALLKtLEE--PP~~v~FILaTtd~~KIp~TIrS--RC-q~f~Fk~Ls~eeIv~~L~~Il~~EgI~id~eAL~lI  206 (830)
T PRK07003        132 TNHAFNAMLKTLEE--PPPHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPAGHIVSHLERILGEERIAFEPQALRLL  206 (830)
T ss_pred             CHHHHHHHHHHHHh--cCCCeEEEEEECChhhccchhhh--he-EEEecCCcCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            33457888888884  34578999999999999999999  88 788999999999999999988765543 34457778


Q ss_pred             HhhCCCCCHHHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQRAC  115 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A~  115 (199)
                      ++.+.| +.+|.-+++..+.
T Consensus       207 A~~A~G-smRdALsLLdQAi  225 (830)
T PRK07003        207 ARAAQG-SMRDALSLTDQAI  225 (830)
T ss_pred             HHHcCC-CHHHHHHHHHHHH
Confidence            888876 4566666665554

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=96.74  E-value=0.0078  Score=56.61  Aligned_cols=92  Identities=15%  Similarity=0.191  Sum_probs=60.8

Q ss_pred             HHHHHHhCCCCCCCEEEEEeeCCC----CCCCccccCCCccc--eEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           23 QLLTEMDGLSAKKTIFVIGVTNRP----DIIDPALLRPGRLD--QLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        23 ~lL~~ld~~~~~~~VvvI~aTN~~----~~lD~al~R~gRfd--~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      .|...++.+....+-+| .|+|.+    ..+++.|++  ||.  ..+++..|+.+.|..||+..+....+. ++.-+..|
T Consensus       398 eLF~l~N~l~e~gk~II-ITSd~~P~eL~~l~~rL~S--Rf~~GLvv~I~~PD~EtR~aIL~kka~~r~l~l~~eVi~yL  474 (617)
T PRK14086        398 EFFHTFNTLHNANKQIV-LSSDRPPKQLVTLEDRLRN--RFEWGLITDVQPPELETRIAILRKKAVQEQLNAPPEVLEFI  474 (617)
T ss_pred             HHHHHHHHHHhcCCCEE-EecCCChHhhhhccHHHHh--hhhcCceEEcCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHH
Confidence            34444444333333334 466663    357889999  985  566888899999999999999766554 34457778


Q ss_pred             HhhCCCCCHHHHHHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQRACKDA  118 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A~~~a  118 (199)
                      +.+..+ +.++|..++.+....+
T Consensus       475 a~r~~r-nvR~LegaL~rL~a~a  496 (617)
T PRK14086        475 ASRISR-NIRELEGALIRVTAFA  496 (617)
T ss_pred             HHhccC-CHHHHHHHHHHHHHHH
Confidence            887653 5777777777654333

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.73  E-value=0.008  Score=55.06  Aligned_cols=92  Identities=20%  Similarity=0.120  Sum_probs=67.2

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      +....|.||..|+.  +...+++|++|+.++.|.+++++  |. .++.|..++.++-.+.++..+....+. .+..+..|
T Consensus       134 s~~A~NALLKtLEE--Pp~~viFILaTte~~kI~~TI~S--RC-q~~~f~~ls~~~i~~~L~~i~~~Egi~~e~eAL~~I  208 (484)
T PRK14956        134 TDQSFNALLKTLEE--PPAHIVFILATTEFHKIPETILS--RC-QDFIFKKVPLSVLQDYSEKLCKIENVQYDQEGLFWI  208 (484)
T ss_pred             CHHHHHHHHHHhhc--CCCceEEEeecCChhhccHHHHh--hh-heeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            34567888888874  44678999999999999999999  88 468888888888888888888765443 34456777


Q ss_pred             HhhCCCCCHHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQRA  114 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A  114 (199)
                      |+.++| +.+|.-++++.+
T Consensus       209 a~~S~G-d~RdAL~lLeq~  226 (484)
T PRK14956        209 AKKGDG-SVRDMLSFMEQA  226 (484)
T ss_pred             HHHcCC-hHHHHHHHHHHH
Confidence            776665 355555555443

>PRK08084 DNA replication initiation factor; Provisional

Probab=96.70  E-value=0.007  Score=50.15  Aligned_cols=74  Identities=16%  Similarity=0.083  Sum_probs=53.9

Q ss_pred             EEEEeeCCCCC---CCccccCCCccc--eEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhhCCCCCHHHHHHHH
Q 039253           38 FVIGVTNRPDI---IDPALLRPGRLD--QLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSGADITEIC  111 (199)
Q Consensus        38 vvI~aTN~~~~---lD~al~R~gRfd--~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~t~G~sgaDI~~lv  111 (199)
                      +++.+++.|..   +.|.+++  |+.  ..+.+..|+.++|.++++.......+. ++.-+..|+++.+| +.+.+..++
T Consensus       134 li~ts~~~p~~l~~~~~~L~S--Rl~~g~~~~l~~~~~~~~~~~l~~~a~~~~~~l~~~v~~~L~~~~~~-d~r~l~~~l  210 (235)
T PRK08084        134 LLITGDRPPRQLNLGLPDLAS--RLDWGQIYKLQPLSDEEKLQALQLRARLRGFELPEDVGRFLLKRLDR-EMRTLFMTL  210 (235)
T ss_pred             EEEeCCCChHHcCcccHHHHH--HHhCCceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhhcC-CHHHHHHHH
Confidence            55555555666   6899999  987  899999999999999999866544333 34457778887764 666666666


Q ss_pred             HHH
Q 039253          112 QRA  114 (199)
Q Consensus       112 ~~A  114 (199)
                      +..
T Consensus       211 ~~l  213 (235)
T PRK08084        211 DQL  213 (235)
T ss_pred             HHH
Confidence            653

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.67  E-value=0.0045  Score=58.63  Aligned_cols=93  Identities=20%  Similarity=0.199  Sum_probs=70.3

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      +....|.||+.|+.  ....+++|++||.++.|.+.+++  |+ .++.|..++.++-.+.|+..+....+. .+..+..|
T Consensus       137 s~~AaNALLKTLEE--PP~~v~FILaTtep~kLlpTIrS--RC-q~f~f~~ls~eei~~~L~~Il~~Egi~~d~eAL~~I  211 (700)
T PRK12323        137 TNHAFNAMLKTLEE--PPEHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPPGHIVSHLDAILGEEGIAHEVNALRLL  211 (700)
T ss_pred             CHHHHHHHHHhhcc--CCCCceEEEEeCChHhhhhHHHH--HH-HhcccCCCChHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            34567888888884  44678999999999999999999  87 788999999999999998888655443 22336677


Q ss_pred             HhhCCCCCHHHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQRAC  115 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A~  115 (199)
                      ++.+.| +.++..+++..+.
T Consensus       212 A~~A~G-s~RdALsLLdQai  230 (700)
T PRK12323        212 AQAAQG-SMRDALSLTDQAI  230 (700)
T ss_pred             HHHcCC-CHHHHHHHHHHHH
Confidence            777765 5666666666543

>PRK08727 hypothetical protein; Validated

Probab=96.63  E-value=0.012  Score=48.65  Aligned_cols=66  Identities=15%  Similarity=0.277  Sum_probs=47.0

Q ss_pred             EEEeeC-CCCCC---CccccCCCcc--ceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhhCCCCCHHHHHHH
Q 039253           39 VIGVTN-RPDII---DPALLRPGRL--DQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSGADITEI  110 (199)
Q Consensus        39 vI~aTN-~~~~l---D~al~R~gRf--d~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~t~G~sgaDI~~l  110 (199)
                      ||+|+| .|..+   ++++++  ||  ...+.++.|+.++|..|++.......+. ++..+..|++.+.    +|+..+
T Consensus       129 vI~ts~~~p~~l~~~~~dL~S--Rl~~~~~~~l~~~~~e~~~~iL~~~a~~~~l~l~~e~~~~La~~~~----rd~r~~  201 (233)
T PRK08727        129 LLYTARQMPDGLALVLPDLRS--RLAQCIRIGLPVLDDVARAAVLRERAQRRGLALDEAAIDWLLTHGE----RELAGL  201 (233)
T ss_pred             EEEECCCChhhhhhhhHHHHH--HHhcCceEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCC----CCHHHH
Confidence            444444 57766   789999  97  5678999999999999999876543332 3455778888766    444444

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.57  E-value=0.016  Score=53.19  Aligned_cols=92  Identities=21%  Similarity=0.273  Sum_probs=67.5

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHH
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLA   96 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la   96 (199)
                      ....+.||..|+..  ...+++|++|+.++.+++++.+  |+. .+.|..|+.++...+++..+....+. .+..+..|+
T Consensus       133 ~~a~naLLk~LEep--p~~~v~Il~tt~~~kl~~tI~S--Rc~-~i~f~~ls~~el~~~L~~i~k~egi~id~~al~~La  207 (486)
T PRK14953        133 KEAFNALLKTLEEP--PPRTIFILCTTEYDKIPPTILS--RCQ-RFIFSKPTKEQIKEYLKRICNEEKIEYEEKALDLLA  207 (486)
T ss_pred             HHHHHHHHHHHhcC--CCCeEEEEEECCHHHHHHHHHH--hce-EEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            34567788888743  3456677778889999999998  775 79999999999999999988766544 234467778


Q ss_pred             hhCCCCCHHHHHHHHHHHH
Q 039253           97 QFTQGFSGADITEICQRAC  115 (199)
Q Consensus        97 ~~t~G~sgaDI~~lv~~A~  115 (199)
                      ..+.| +.+++.++++.+.
T Consensus       208 ~~s~G-~lr~al~~Ldkl~  225 (486)
T PRK14953        208 QASEG-GMRDAASLLDQAS  225 (486)
T ss_pred             HHcCC-CHHHHHHHHHHHH
Confidence            77664 5666666666654

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=96.52  E-value=0.016  Score=54.93  Aligned_cols=91  Identities=16%  Similarity=0.181  Sum_probs=67.3

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      +....|.||+.|+.  +...+++|++|+.++.|.+.+++  |. ..+.|..++.++-...|+..+....+. .+..+..|
T Consensus       132 s~~a~NALLKtLEE--Pp~~v~FIL~Tt~~~kLl~TI~S--RC-~~~~f~~Ls~~ei~~~L~~il~~e~i~~e~~aL~~I  206 (647)
T PRK07994        132 SRHSFNALLKTLEE--PPEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRQQLEHILQAEQIPFEPRALQLL  206 (647)
T ss_pred             CHHHHHHHHHHHHc--CCCCeEEEEecCCccccchHHHh--hh-eEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            34567888888884  44567888889999999999999  85 889999999999999999888654443 33456677


Q ss_pred             HhhCCCCCHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQR  113 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~  113 (199)
                      +..+.| +.++.-.++..
T Consensus       207 a~~s~G-s~R~Al~lldq  223 (647)
T PRK07994        207 ARAADG-SMRDALSLTDQ  223 (647)
T ss_pred             HHHcCC-CHHHHHHHHHH
Confidence            777665 44444444443

>PRK06620 hypothetical protein; Validated

Probab=96.51  E-value=0.016  Score=47.47  Aligned_cols=86  Identities=16%  Similarity=0.188  Sum_probs=59.5

Q ss_pred             HHHHHhCCCCCCCEEEEEeeCCCCC--CCccccCCCccc--eEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhh
Q 039253           24 LLTEMDGLSAKKTIFVIGVTNRPDI--IDPALLRPGRLD--QLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQF   98 (199)
Q Consensus        24 lL~~ld~~~~~~~VvvI~aTN~~~~--lD~al~R~gRfd--~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~   98 (199)
                      |...++.+....+.++|+++..|..  + +++++  |+.  ..+.+..|+.+.+..+++.......+. ++.-+..|+++
T Consensus       102 lf~l~N~~~e~g~~ilits~~~p~~l~l-~~L~S--Rl~~gl~~~l~~pd~~~~~~~l~k~~~~~~l~l~~ev~~~L~~~  178 (214)
T PRK06620        102 LLHIFNIINEKQKYLLLTSSDKSRNFTL-PDLSS--RIKSVLSILLNSPDDELIKILIFKHFSISSVTISRQIIDFLLVN  178 (214)
T ss_pred             HHHHHHHHHhcCCEEEEEcCCCccccch-HHHHH--HHhCCceEeeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            3334444434456778888777665  5 78888  986  368999999999999999988754433 34457778887


Q ss_pred             CCCCCHHHHHHHHHH
Q 039253           99 TQGFSGADITEICQR  113 (199)
Q Consensus        99 t~G~sgaDI~~lv~~  113 (199)
                      ..| +.+.+..++..
T Consensus       179 ~~~-d~r~l~~~l~~  192 (214)
T PRK06620        179 LPR-EYSKIIEILEN  192 (214)
T ss_pred             ccC-CHHHHHHHHHH
Confidence            753 56666666665

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=96.46  E-value=0.043  Score=47.09  Aligned_cols=86  Identities=20%  Similarity=0.290  Sum_probs=59.3

Q ss_pred             HHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhh
Q 039253           20 IPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQF   98 (199)
Q Consensus        20 ~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~   98 (199)
                      ..+.|+..|+....  ...+|++|+.+..+.+.+.+  |+ ..+++.+|+.++...+++..+.+..+. ++..+..|+..
T Consensus       141 ~~~~L~~~le~~~~--~~~~Il~~~~~~~~~~~L~s--r~-~~v~~~~~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~  215 (337)
T PRK12402        141 AQQALRRIMEQYSR--TCRFIIATRQPSKLIPPIRS--RC-LPLFFRAPTDDELVDVLESIAEAEGVDYDDDGLELIAYY  215 (337)
T ss_pred             HHHHHHHHHHhccC--CCeEEEEeCChhhCchhhcC--Cc-eEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            34556666665432  34566677778888888887  76 578999999999999999988766544 44567778876


Q ss_pred             CCCCCHHHHHHHHHHH
Q 039253           99 TQGFSGADITEICQRA  114 (199)
Q Consensus        99 t~G~sgaDI~~lv~~A  114 (199)
                      +    ++|+..++...
T Consensus       216 ~----~gdlr~l~~~l  227 (337)
T PRK12402        216 A----GGDLRKAILTL  227 (337)
T ss_pred             c----CCCHHHHHHHH
Confidence            6    34555554443

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=96.43  E-value=0.0047  Score=60.35  Aligned_cols=68  Identities=19%  Similarity=0.277  Sum_probs=52.5

Q ss_pred             CCCCEEEEEeeCCC-----CCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCC----CC-CcccHHHHHhhCCCC
Q 039253           33 AKKTIFVIGVTNRP-----DIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSP----VS-KDVDLEKLAQFTQGF  102 (199)
Q Consensus        33 ~~~~VvvI~aTN~~-----~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~----~~-~~~~l~~la~~t~G~  102 (199)
                      .+..+.+|+||+..     ..+|+||.|  ||. .|.|+.|+.+++..||+.+...+.    +. .+..+..++..+.+|
T Consensus       313 ~~G~l~~IgaTT~~e~~~~~~~d~AL~r--Rf~-~i~v~eps~~~~~~iL~~~~~~~e~~~~v~i~d~al~~~~~ls~ry  389 (852)
T TIGR03345       313 ARGELRTIAATTWAEYKKYFEKDPALTR--RFQ-VVKVEEPDEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVELSHRY  389 (852)
T ss_pred             hCCCeEEEEecCHHHHhhhhhccHHHHH--hCe-EEEeCCCCHHHHHHHHHHHHHhhhhcCCCeeCHHHHHHHHHHcccc
Confidence            35678999999964     359999999  995 799999999999999876665432    21 355677788888776


Q ss_pred             C
Q 039253          103 S  103 (199)
Q Consensus       103 s  103 (199)
                      -
T Consensus       390 i  390 (852)
T TIGR03345       390 I  390 (852)
T ss_pred             c
Confidence            3

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.

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.41  E-value=0.024  Score=53.52  Aligned_cols=94  Identities=17%  Similarity=0.203  Sum_probs=71.3

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      +....|.||..|+.  ....+++|++|+.++.+.+.+++  |. ..++|..++.++....++..+.+..+. .+..+..|
T Consensus       137 s~~a~NaLLKtLEE--PP~~~~fIL~Ttd~~kil~TIlS--Rc-~~~~f~~Ls~eei~~~L~~i~~~egi~ie~~AL~~L  211 (618)
T PRK14951        137 TNTAFNAMLKTLEE--PPEYLKFVLATTDPQKVPVTVLS--RC-LQFNLRPMAPETVLEHLTQVLAAENVPAEPQALRLL  211 (618)
T ss_pred             CHHHHHHHHHhccc--CCCCeEEEEEECCchhhhHHHHH--hc-eeeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            34457778888774  34567788888899999999988  77 789999999999999999888765544 34457888


Q ss_pred             HhhCCCCCHHHHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQRACK  116 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A~~  116 (199)
                      ++.+.| +.+++.+++..+..
T Consensus       212 a~~s~G-slR~al~lLdq~ia  231 (618)
T PRK14951        212 ARAARG-SMRDALSLTDQAIA  231 (618)
T ss_pred             HHHcCC-CHHHHHHHHHHHHH
Confidence            888876 77887777766543

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.41  E-value=0.038  Score=51.07  Aligned_cols=92  Identities=17%  Similarity=0.255  Sum_probs=68.3

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      +....+.|+..|+.  ....+++|++|+.++.+.+.+.+  |+. .++|..|+.++-...++..+.+..+. ++..+..|
T Consensus       129 s~~a~naLLk~LEe--p~~~t~~Il~t~~~~kl~~~I~S--Rc~-~~~f~~ls~~el~~~L~~i~~~egi~i~~~Al~~i  203 (504)
T PRK14963        129 SKSAFNALLKTLEE--PPEHVIFILATTEPEKMPPTILS--RTQ-HFRFRRLTEEEIAGKLRRLLEAEGREAEPEALQLV  203 (504)
T ss_pred             CHHHHHHHHHHHHh--CCCCEEEEEEcCChhhCChHHhc--ceE-EEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            34567788888874  33467888889999999999998  875 79999999999999999988766543 34457778


Q ss_pred             HhhCCCCCHHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQRA  114 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A  114 (199)
                      ++.+.| ..+++.++++.+
T Consensus       204 a~~s~G-dlR~aln~Lekl  221 (504)
T PRK14963        204 ARLADG-AMRDAESLLERL  221 (504)
T ss_pred             HHHcCC-CHHHHHHHHHHH
Confidence            887764 455555555554

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.40  E-value=0.015  Score=53.70  Aligned_cols=94  Identities=16%  Similarity=0.137  Sum_probs=71.6

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      +....|.||..|+..  ...+++|++|+.++.+.+.+++  |. ..++|..++.++-...++..+.+.... .+..+..|
T Consensus       132 s~~a~naLLk~LEep--p~~~~fIlattd~~kl~~tI~S--Rc-~~~~f~~l~~~~i~~~l~~il~~egi~~~~~al~~i  206 (509)
T PRK14958        132 SGHSFNALLKTLEEP--PSHVKFILATTDHHKLPVTVLS--RC-LQFHLAQLPPLQIAAHCQHLLKEENVEFENAALDLL  206 (509)
T ss_pred             CHHHHHHHHHHHhcc--CCCeEEEEEECChHhchHHHHH--Hh-hhhhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            345678899999853  3457888888999999999988  77 667888888888888888888765443 34457778


Q ss_pred             HhhCCCCCHHHHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQRACK  116 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A~~  116 (199)
                      ++.+.| +.+++.++++.+..
T Consensus       207 a~~s~G-slR~al~lLdq~ia  226 (509)
T PRK14958        207 ARAANG-SVRDALSLLDQSIA  226 (509)
T ss_pred             HHHcCC-cHHHHHHHHHHHHh
Confidence            888765 78888888877643

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=96.38  E-value=0.018  Score=52.44  Aligned_cols=114  Identities=12%  Similarity=0.165  Sum_probs=72.4

Q ss_pred             HHHHHHHhCCCCCCCEEEEEeeCC-CCC---CCccccCCCccc--eEEEecCCCHHHHHHHHHHhhcCCCC---CCcccH
Q 039253           22 NQLLTEMDGLSAKKTIFVIGVTNR-PDI---IDPALLRPGRLD--QLIYIPLPVEKSRLQIFKACLRKSPV---SKDVDL   92 (199)
Q Consensus        22 ~~lL~~ld~~~~~~~VvvI~aTN~-~~~---lD~al~R~gRfd--~~i~~~~P~~~~R~~il~~~l~~~~~---~~~~~l   92 (199)
                      ..|...++.+....+- +|.|+|. |..   +++.+++  ||.  -.+.+..|+.++|.+|+++.+....+   -++.-+
T Consensus       226 e~lf~l~N~~~~~~k~-iIltsd~~P~~l~~l~~rL~S--R~~~Gl~~~L~~pd~e~r~~iL~~~~~~~gl~~~l~~evl  302 (450)
T PRK14087        226 EIFFTIFNNFIENDKQ-LFFSSDKSPELLNGFDNRLIT--RFNMGLSIAIQKLDNKTATAIIKKEIKNQNIKQEVTEEAI  302 (450)
T ss_pred             HHHHHHHHHHHHcCCc-EEEECCCCHHHHhhccHHHHH--HHhCCceeccCCcCHHHHHHHHHHHHHhcCCCCCCCHHHH
Confidence            3444444444333333 4555554 444   4788888  885  67778889999999999999976432   234456


Q ss_pred             HHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhc
Q 039253           93 EKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYA  157 (199)
Q Consensus        93 ~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~  157 (199)
                      ..|+..+.| +.+.|..+|.++...+.....                  ..++|.+...++++.+
T Consensus       303 ~~Ia~~~~g-d~R~L~gaL~~l~~~a~~~~~------------------~~~it~~~v~~~l~~~  348 (450)
T PRK14087        303 NFISNYYSD-DVRKIKGSVSRLNFWSQQNPE------------------EKIITIEIVSDLFRDI  348 (450)
T ss_pred             HHHHHccCC-CHHHHHHHHHHHHHHHhcccC------------------CCCCCHHHHHHHHhhc
Confidence            778887775 778888888876544433210                  0346666666666654

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=96.38  E-value=0.028  Score=47.79  Aligned_cols=89  Identities=15%  Similarity=0.081  Sum_probs=61.9

Q ss_pred             HHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhh
Q 039253           20 IPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQF   98 (199)
Q Consensus        20 ~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~   98 (199)
                      ..+.|+..++....  ++.+|+++|.+..+.+++.+  |+. .++|+.|+.++...+++.++.+..+. ++..+..|++.
T Consensus       118 ~~~~L~~~le~~~~--~~~lIl~~~~~~~l~~~l~s--r~~-~~~~~~l~~~ei~~~l~~~~~~~~~~i~~~al~~l~~~  192 (319)
T PRK00440        118 AQQALRRTMEMYSQ--NTRFILSCNYSSKIIDPIQS--RCA-VFRFSPLKKEAVAERLRYIAENEGIEITDDALEAIYYV  192 (319)
T ss_pred             HHHHHHHHHhcCCC--CCeEEEEeCCccccchhHHH--Hhh-eeeeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            34567777775433  34566778888888888888  776 58999999999999999998766543 34457778887


Q ss_pred             CCCCCHHHHHHHHHHH
Q 039253           99 TQGFSGADITEICQRA  114 (199)
Q Consensus        99 t~G~sgaDI~~lv~~A  114 (199)
                      +.| ..+.+.+.++.+
T Consensus       193 ~~g-d~r~~~~~l~~~  207 (319)
T PRK00440        193 SEG-DMRKAINALQAA  207 (319)
T ss_pred             cCC-CHHHHHHHHHHH
Confidence            654 344444444433

>CHL00195 ycf46 Ycf46; Provisional

Probab=96.35  E-value=0.023  Score=52.28  Aligned_cols=77  Identities=19%  Similarity=0.230  Sum_probs=59.7

Q ss_pred             CCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhhCCCCCHHHHHHHHH
Q 039253           34 KKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSGADITEICQ  112 (199)
Q Consensus        34 ~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~  112 (199)
                      ..+.+||.+.+  ..+|+.+.+   +-..+.+++|+.++...+++.+....... ++.++..+++.+.|+|-.+++.++.
T Consensus       113 ~~~~~i~~~~~--~~~p~el~~---~~~~~~~~lP~~~ei~~~l~~~~~~~~~~~~~~~~~~l~~~~~gls~~~~~~~~~  187 (489)
T CHL00195        113 QPKTIIIIASE--LNIPKELKD---LITVLEFPLPTESEIKKELTRLIKSLNIKIDSELLENLTRACQGLSLERIRRVLS  187 (489)
T ss_pred             CCCEEEEEcCC--CCCCHHHHh---ceeEEeecCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            34455555543  567777775   45788999999999999998887654332 4667899999999999999999998


Q ss_pred             HHH
Q 039253          113 RAC  115 (199)
Q Consensus       113 ~A~  115 (199)
                      .+.
T Consensus       188 ~~~  190 (489)
T CHL00195        188 KII  190 (489)
T ss_pred             HHH
Confidence            764

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

Probab=96.34  E-value=0.015  Score=56.39  Aligned_cols=141  Identities=16%  Similarity=0.226  Sum_probs=91.6

Q ss_pred             HHHHHHHHhCC-------------CCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcC----
Q 039253           21 PNQLLTEMDGL-------------SAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRK----   83 (199)
Q Consensus        21 ~~~lL~~ld~~-------------~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~----   83 (199)
                      .+.|+..||.=             -..++|++|+|||.. .|+++|+.  |++ .|.|..++.++..+|.+.++-.    
T Consensus       437 ~~aLlevld~~~~~~~~d~~~~~~~dls~v~~i~TaN~~-~i~~aLl~--R~~-ii~~~~~t~eek~~Ia~~~L~~k~~~  512 (784)
T PRK10787        437 ASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNSM-NIPAPLLD--RME-VIRLSGYTEDEKLNIAKRHLLPKQIE  512 (784)
T ss_pred             HHHHHHHhccccEEEEecccccccccCCceEEEEcCCCC-CCCHHHhc--cee-eeecCCCCHHHHHHHHHHhhhHHHHH
Confidence            46777777731             122679999999987 59999999  995 7889999999999999998841    


Q ss_pred             -CCCC------CcccHHHHHh-hCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHH
Q 039253           84 -SPVS------KDVDLEKLAQ-FTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMK  155 (199)
Q Consensus        84 -~~~~------~~~~l~~la~-~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~  155 (199)
                       ..+.      .+--+..|++ .+..+-.+.|+.+++..+..++.+......            .....|+.+++...|-
T Consensus       513 ~~~l~~~~l~i~~~ai~~ii~~yt~e~GaR~LeR~I~~i~r~~l~~~~~~~~------------~~~v~v~~~~~~~~lg  580 (784)
T PRK10787        513 RNALKKGELTVDDSAIIGIIRYYTREAGVRSLEREISKLCRKAVKQLLLDKS------------LKHIEINGDNLHDYLG  580 (784)
T ss_pred             HhCCCCCeEEECHHHHHHHHHhCCcccCCcHHHHHHHHHHHHHHHHHHhcCC------------CceeeecHHHHHHHhC
Confidence             1111      1222444543 445677788888888877666666542110            0114578888887775


Q ss_pred             hcccc-------ccccCCcccccchhhhh
Q 039253          156 YACKS-------QSRGFGDEFGFCETAVA  177 (199)
Q Consensus       156 ~~~Ps-------~~r~~~~~~~~~~~~~~  177 (199)
                      .-+-.       ..-|+.+=+.|+..+|.
T Consensus       581 ~~~~~~~~~~~~~~~G~~~gla~t~~gg~  609 (784)
T PRK10787        581 VQRFDYGRADNENRVGQVTGLAWTEVGGD  609 (784)
T ss_pred             CCccccchhhcCCCceEEEEeEEeCCCeE
Confidence            33211       12266666667766654

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.34  E-value=0.016  Score=53.26  Aligned_cols=95  Identities=15%  Similarity=0.137  Sum_probs=73.8

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      +....|.||..|+.  +...+++|++|+.++.|.+.+++  |+ ..++|..++.++....++..+.+.... ++..+..|
T Consensus       129 s~~A~NaLLK~LEe--Pp~~v~fIlatte~~Kl~~tI~S--Rc-~~~~f~~l~~~el~~~L~~ia~~Egi~i~~eAL~lI  203 (491)
T PRK14964        129 SNSAFNALLKTLEE--PAPHVKFILATTEVKKIPVTIIS--RC-QRFDLQKIPTDKLVEHLVDIAKKENIEHDEESLKLI  203 (491)
T ss_pred             CHHHHHHHHHHHhC--CCCCeEEEEEeCChHHHHHHHHH--hh-eeeecccccHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            34567889999985  34567888888999999999998  87 568999999999999999988766544 34557788


Q ss_pred             HhhCCCCCHHHHHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQRACKD  117 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A~~~  117 (199)
                      ++.+.| +.+++.++++.+...
T Consensus       204 a~~s~G-slR~alslLdqli~y  224 (491)
T PRK14964        204 AENSSG-SMRNALFLLEQAAIY  224 (491)
T ss_pred             HHHcCC-CHHHHHHHHHHHHHh
Confidence            888865 888888888776543

>PRK05642 DNA replication initiation factor; Validated

Probab=96.31  E-value=0.025  Score=46.87  Aligned_cols=91  Identities=12%  Similarity=0.134  Sum_probs=61.4

Q ss_pred             HHHHHHHhCCCCCCCEEEEEeeCCCCCC---CccccCCCccc--eEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           22 NQLLTEMDGLSAKKTIFVIGVTNRPDII---DPALLRPGRLD--QLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        22 ~~lL~~ld~~~~~~~VvvI~aTN~~~~l---D~al~R~gRfd--~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      .+|...++.+....+.++|+++..|..+   .+.+++  ||.  ..+.+..|+.++|..+++.......+. ++.-+..|
T Consensus       117 ~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~S--Rl~~gl~~~l~~~~~e~~~~il~~ka~~~~~~l~~ev~~~L  194 (234)
T PRK05642        117 EALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKS--RLTLALVFQMRGLSDEDKLRALQLRASRRGLHLTDEVGHFI  194 (234)
T ss_pred             HHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHH--HHhcCeeeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            3455666655455566777777666444   688999  985  677788999999999999655443332 34456777


Q ss_pred             HhhCCCCCHHHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQRAC  115 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A~  115 (199)
                      +++.+ =+++.+..+++.-.
T Consensus       195 ~~~~~-~d~r~l~~~l~~l~  213 (234)
T PRK05642        195 LTRGT-RSMSALFDLLERLD  213 (234)
T ss_pred             HHhcC-CCHHHHHHHHHHHH
Confidence            88766 36677766666543

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.22  E-value=0.021  Score=54.28  Aligned_cols=93  Identities=16%  Similarity=0.172  Sum_probs=71.7

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      +....+.||..|+.  ....+.+|++|+.+..+++.+++  |+ .++.|..++.++-...++..+.+.... .+..+..|
T Consensus       131 S~~A~NALLKtLEE--PP~~v~FILaTtd~~kIp~TIlS--RC-q~feFkpLs~eEI~k~L~~Il~kEgI~id~eAL~~I  205 (702)
T PRK14960        131 STHSFNALLKTLEE--PPEHVKFLFATTDPQKLPITVIS--RC-LQFTLRPLAVDEITKHLGAILEKEQIAADQDAIWQI  205 (702)
T ss_pred             CHHHHHHHHHHHhc--CCCCcEEEEEECChHhhhHHHHH--hh-heeeccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            34567888888884  34567888888999999999987  87 688999999999999999888765543 34457778


Q ss_pred             HhhCCCCCHHHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQRAC  115 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A~  115 (199)
                      ++.+.| +.+++.+++..+.
T Consensus       206 A~~S~G-dLRdALnLLDQaI  224 (702)
T PRK14960        206 AESAQG-SLRDALSLTDQAI  224 (702)
T ss_pred             HHHcCC-CHHHHHHHHHHHH
Confidence            887766 7777777776654

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=96.20  E-value=0.02  Score=45.44  Aligned_cols=73  Identities=23%  Similarity=0.296  Sum_probs=54.2

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCcccHHHHHhh
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQF   98 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~l~~la~~   98 (199)
                      ...+.||..|+..  ...+++|++||.+..+.+++++  |. ..++|+.|+.++...+++..    .+. +..+..+++.
T Consensus       111 ~~~~~Ll~~le~~--~~~~~~il~~~~~~~l~~~i~s--r~-~~~~~~~~~~~~~~~~l~~~----gi~-~~~~~~i~~~  180 (188)
T TIGR00678       111 AAANALLKTLEEP--PPNTLFILITPSPEKLLPTIRS--RC-QVLPFPPLSEEALLQWLIRQ----GIS-EEAAELLLAL  180 (188)
T ss_pred             HHHHHHHHHhcCC--CCCeEEEEEECChHhChHHHHh--hc-EEeeCCCCCHHHHHHHHHHc----CCC-HHHHHHHHHH
Confidence            3467788888752  3456677778888999999998  77 48999999999999888876    233 3346666666


Q ss_pred             CCC
Q 039253           99 TQG  101 (199)
Q Consensus        99 t~G  101 (199)
                      +.|
T Consensus       181 ~~g  183 (188)
T TIGR00678       181 AGG  183 (188)
T ss_pred             cCC
Confidence            655

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.

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

Probab=96.19  E-value=0.058  Score=44.81  Aligned_cols=85  Identities=18%  Similarity=0.191  Sum_probs=67.6

Q ss_pred             cccCCCccceEEEecCCCHHHHHHHHHHhhcCCCC-----CCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHh
Q 039253           52 ALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPV-----SKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIEND  126 (199)
Q Consensus        52 al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~-----~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~  126 (199)
                      .+.+  |+...+++++.+.++-.+++...+.....     -.+..+..|++.|.|+... |..+|..+...+..+..   
T Consensus       178 ~l~~--r~~~~~~l~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~-i~~l~~~~~~~a~~~~~---  251 (269)
T TIGR03015       178 QLRQ--RIIASCHLGPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRL-INILCDRLLLSAFLEEK---  251 (269)
T ss_pred             HHHh--heeeeeeCCCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccH-HHHHHHHHHHHHHHcCC---
Confidence            3556  88889999999999999999988864321     1345688899999999655 99999999888776542   


Q ss_pred             HHhhcCCCCcchhhccccccHHHHHHHHHhcc
Q 039253          127 IRRRKGKQPEAIEDEVAEIKAEHFEESMKYAC  158 (199)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~  158 (199)
                                      ..|+.+++..++..++
T Consensus       252 ----------------~~i~~~~v~~~~~~~~  267 (269)
T TIGR03015       252 ----------------REIGGEEVREVIAEID  267 (269)
T ss_pred             ----------------CCCCHHHHHHHHHHhh
Confidence                            5699999999998875

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.

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=96.14  E-value=0.047  Score=51.48  Aligned_cols=92  Identities=18%  Similarity=0.101  Sum_probs=69.8

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHH
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLA   96 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la   96 (199)
                      ....|.||..|+..  ...+++|++|+.++.+.+.+++  |. ..+.|..|+.++-...++..+.+.... .+..+..|+
T Consensus       146 ~~a~naLLKtLEeP--p~~~~fIl~tte~~kll~tI~S--Rc-q~~~f~~l~~~el~~~L~~i~~kegi~i~~eAl~lIa  220 (598)
T PRK09111        146 TAAFNALLKTLEEP--PPHVKFIFATTEIRKVPVTVLS--RC-QRFDLRRIEADVLAAHLSRIAAKEGVEVEDEALALIA  220 (598)
T ss_pred             HHHHHHHHHHHHhC--CCCeEEEEEeCChhhhhHHHHh--he-eEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            34577888888843  3457777788888899999988  87 579999999999999999988766544 334567778


Q ss_pred             hhCCCCCHHHHHHHHHHHH
Q 039253           97 QFTQGFSGADITEICQRAC  115 (199)
Q Consensus        97 ~~t~G~sgaDI~~lv~~A~  115 (199)
                      ..+.| +.+++.++++.+.
T Consensus       221 ~~a~G-dlr~al~~Ldkli  238 (598)
T PRK09111        221 RAAEG-SVRDGLSLLDQAI  238 (598)
T ss_pred             HHcCC-CHHHHHHHHHHHH
Confidence            87765 7788877777654

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=96.12  E-value=0.035  Score=52.48  Aligned_cols=106  Identities=22%  Similarity=0.253  Sum_probs=68.8

Q ss_pred             EEEEE-eeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhhCCCCCHHHHHHHHHHH
Q 039253           37 IFVIG-VTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSGADITEICQRA  114 (199)
Q Consensus        37 VvvI~-aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~~A  114 (199)
                      +++|+ ||+.++.+++++++  ||. .++|++.+.++...|++..+.+.... ++.-+..|++.+  +.|+...+++..+
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-EVFFEPLTPEDIALIVLNAAEKINVHLAAGVEELIARYT--IEGRKAVNILADV  398 (615)
T ss_pred             EEEEEeccccccccCHHHHh--cee-EEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHCC--CcHHHHHHHHHHH
Confidence            45555 55669999999998  997 56888889999999999998865432 233455566654  3566555555555


Q ss_pred             HHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcc
Q 039253          115 CKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYAC  158 (199)
Q Consensus       115 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~  158 (199)
                      ...++.+.....      +     ......|+.+|+.+++..-+
T Consensus       399 ~~~~~~~~~~~~------~-----~~~~~~I~~edv~~~l~~~r  431 (615)
T TIGR02903       399 YGYALYRAAEAG------K-----ENDKVTITQDDVYEVIQISR  431 (615)
T ss_pred             HHHHHHHHHHhc------c-----CCCCeeECHHHHHHHhCCCc
Confidence            444333321000      0     00125689999999998665

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.

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=96.09  E-value=0.025  Score=52.91  Aligned_cols=92  Identities=16%  Similarity=0.163  Sum_probs=67.6

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      +....+.||..|+.  +...+++|++|+.++.|.+++++  |+. .++|..|+.++...+++..+...... .+..+..|
T Consensus       132 s~~a~naLLK~LEe--pp~~~vfI~~tte~~kL~~tI~S--Rc~-~~~f~~l~~~el~~~L~~i~~~egi~id~eAl~lL  206 (563)
T PRK06647        132 SNSAFNALLKTIEE--PPPYIVFIFATTEVHKLPATIKS--RCQ-HFNFRLLSLEKIYNMLKKVCLEDQIKYEDEALKWI  206 (563)
T ss_pred             CHHHHHHHHHhhcc--CCCCEEEEEecCChHHhHHHHHH--hce-EEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            34467788888874  44567888888889999999998  876 68999999999999998888655433 34456667


Q ss_pred             HhhCCCCCHHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQRA  114 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A  114 (199)
                      +..+.| +.+++.++++.+
T Consensus       207 a~~s~G-dlR~alslLdkl  224 (563)
T PRK06647        207 AYKSTG-SVRDAYTLFDQV  224 (563)
T ss_pred             HHHcCC-CHHHHHHHHHHH
Confidence            777766 566666666543

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=96.00  E-value=0.035  Score=53.01  Aligned_cols=94  Identities=14%  Similarity=0.129  Sum_probs=72.8

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      +....+.||+.|+.  ....+.+|++|+.+..+.+.+++  |+ ..+.|..++.++-...|+..+.+..+. .+..+..|
T Consensus       132 s~~A~NALLKtLEE--Pp~~v~fILaTtd~~kL~~TIrS--RC-~~f~f~~Ls~eeI~~~L~~Il~kEgi~id~eAL~~I  206 (709)
T PRK08691        132 SKSAFNAMLKTLEE--PPEHVKFILATTDPHKVPVTVLS--RC-LQFVLRNMTAQQVADHLAHVLDSEKIAYEPPALQLL  206 (709)
T ss_pred             CHHHHHHHHHHHHh--CCCCcEEEEEeCCccccchHHHH--HH-hhhhcCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHH
Confidence            34467788888885  34567888899999999999987  87 667888899999999999998876544 34457788


Q ss_pred             HhhCCCCCHHHHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQRACK  116 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A~~  116 (199)
                      ++.+. -+.+++.++++.+..
T Consensus       207 a~~A~-GslRdAlnLLDqaia  226 (709)
T PRK08691        207 GRAAA-GSMRDALSLLDQAIA  226 (709)
T ss_pred             HHHhC-CCHHHHHHHHHHHHH
Confidence            88775 478888888877654

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=95.99  E-value=0.015  Score=51.12  Aligned_cols=56  Identities=20%  Similarity=0.288  Sum_probs=49.4

Q ss_pred             HHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHh
Q 039253           20 IPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKAC   80 (199)
Q Consensus        20 ~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~   80 (199)
                      ..|.||+.|+  ++..++++|.+|++++.|.|.+++  |. ..+.|++|+.++..+.|...
T Consensus       148 AaNaLLKtLE--EPp~~t~fiL~t~~~~~LLpTI~S--Rc-q~i~~~~~~~~~~~~~L~~~  203 (342)
T PRK06964        148 AANALLKTLE--EPPPGTVFLLVSARIDRLLPTILS--RC-RQFPMTVPAPEAAAAWLAAQ  203 (342)
T ss_pred             HHHHHHHHhc--CCCcCcEEEEEECChhhCcHHHHh--cC-EEEEecCCCHHHHHHHHHHc
Confidence            4599999999  567789999999999999999999  98 68999999999998888764

>PRK10865 protein disaggregation chaperone; Provisional

Probab=95.93  E-value=0.011  Score=57.85  Aligned_cols=49  Identities=20%  Similarity=0.393  Sum_probs=42.3

Q ss_pred             CCCCEEEEEeeCCCC-----CCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCC
Q 039253           33 AKKTIFVIGVTNRPD-----IIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKS   84 (199)
Q Consensus        33 ~~~~VvvI~aTN~~~-----~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~   84 (199)
                      .+..+.+|+||+..+     .+|+|+.|  ||+ .|.++.|+.+++..||+.+...+
T Consensus       304 ~~g~l~~IgaTt~~e~r~~~~~d~al~r--Rf~-~i~v~eP~~~~~~~iL~~l~~~~  357 (857)
T PRK10865        304 ARGELHCVGATTLDEYRQYIEKDAALER--RFQ-KVFVAEPSVEDTIAILRGLKERY  357 (857)
T ss_pred             hcCCCeEEEcCCCHHHHHHhhhcHHHHh--hCC-EEEeCCCCHHHHHHHHHHHhhhh
Confidence            356789999999976     59999999  998 58899999999999998877553

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=95.93  E-value=0.028  Score=52.85  Aligned_cols=89  Identities=19%  Similarity=0.220  Sum_probs=66.5

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHh
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQ   97 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~   97 (199)
                      ...+.||..|+.  +...+++|++|+.+..|.+++++  |+. .++|+.|+.++....++..+.+.... ++..+..++.
T Consensus       134 ~A~NaLLKtLEE--Pp~~tvfIL~Tt~~~KLl~TI~S--Rcq-~ieF~~Ls~~eL~~~L~~il~kegi~Is~eal~~La~  208 (605)
T PRK05896        134 SAWNALLKTLEE--PPKHVVFIFATTEFQKIPLTIIS--RCQ-RYNFKKLNNSELQELLKSIAKKEKIKIEDNAIDKIAD  208 (605)
T ss_pred             HHHHHHHHHHHh--CCCcEEEEEECCChHhhhHHHHh--hhh-hcccCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            356788888884  34567888888899999999998  875 78999999999999999888665432 2344667777


Q ss_pred             hCCCCCHHHHHHHHHH
Q 039253           98 FTQGFSGADITEICQR  113 (199)
Q Consensus        98 ~t~G~sgaDI~~lv~~  113 (199)
                      .+.| +.+++.++++.
T Consensus       209 lS~G-dlR~AlnlLek  223 (605)
T PRK05896        209 LADG-SLRDGLSILDQ  223 (605)
T ss_pred             HcCC-cHHHHHHHHHH
Confidence            7765 55665555555

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.93  E-value=0.026  Score=52.97  Aligned_cols=89  Identities=18%  Similarity=0.142  Sum_probs=64.2

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHH
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLA   96 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la   96 (199)
                      ....|.||..|+.  +...+++|++|+.++.|.+.+++  |. ..++|..++.++-...++..+.+..+. .+..+..|+
T Consensus       133 ~~a~naLLk~LEe--pp~~~~fIl~t~~~~kl~~tI~S--Rc-~~~~f~~l~~~~i~~~L~~i~~~egi~i~~~al~~la  207 (576)
T PRK14965        133 TNAFNALLKTLEE--PPPHVKFIFATTEPHKVPITILS--RC-QRFDFRRIPLQKIVDRLRYIADQEGISISDAALALVA  207 (576)
T ss_pred             HHHHHHHHHHHHc--CCCCeEEEEEeCChhhhhHHHHH--hh-hhhhcCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Confidence            3457889999984  44568888899999999999998  76 478899899988888888877665443 334466667


Q ss_pred             hhCCCCCHHHHHHHHH
Q 039253           97 QFTQGFSGADITEICQ  112 (199)
Q Consensus        97 ~~t~G~sgaDI~~lv~  112 (199)
                      ..+.| +.+++.++++
T Consensus       208 ~~a~G-~lr~al~~Ld  222 (576)
T PRK14965        208 RKGDG-SMRDSLSTLD  222 (576)
T ss_pred             HHcCC-CHHHHHHHHH
Confidence            66665 4444444443

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.87  E-value=0.027  Score=53.16  Aligned_cols=89  Identities=15%  Similarity=0.150  Sum_probs=63.9

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHh
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQ   97 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~   97 (199)
                      ...+.||..|+.  ....+++|++||.++.+.+.+++  |+. +|+|+.++.++-..+|+..+.+.... ++..+..|++
T Consensus       134 ~a~naLLk~LEE--P~~~~ifILaTt~~~kll~TI~S--Rcq-~i~F~pLs~~eL~~~L~~il~~egi~id~eal~lIA~  208 (624)
T PRK14959        134 EAFNALLKTLEE--PPARVTFVLATTEPHKFPVTIVS--RCQ-HFTFTRLSEAGLEAHLTKVLGREGVDYDPAAVRLIAR  208 (624)
T ss_pred             HHHHHHHHHhhc--cCCCEEEEEecCChhhhhHHHHh--hhh-ccccCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            446788888874  33568888899999999999998  874 68899999999999998888665432 3445677787


Q ss_pred             hCCCCCHHHHHHHHHH
Q 039253           98 FTQGFSGADITEICQR  113 (199)
Q Consensus        98 ~t~G~sgaDI~~lv~~  113 (199)
                      .+.| +.+++.+++++
T Consensus       209 ~s~G-dlR~Al~lLeq  223 (624)
T PRK14959        209 RAAG-SVRDSMSLLGQ  223 (624)
T ss_pred             HcCC-CHHHHHHHHHH
Confidence            6653 33444444443

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.84  E-value=0.078  Score=46.54  Aligned_cols=91  Identities=20%  Similarity=0.182  Sum_probs=63.4

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHh
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQ   97 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~   97 (199)
                      ...+.|+..|+.  +....++|++|+.+..+.+++.+  |+. .++|+.|+.++...++...+.+.... ++..+..|+.
T Consensus       123 ~~~~~ll~~le~--~~~~~~~Il~~~~~~kl~~~l~s--r~~-~v~~~~~~~~~l~~~l~~~~~~~g~~i~~~al~~l~~  197 (367)
T PRK14970        123 AAFNAFLKTLEE--PPAHAIFILATTEKHKIIPTILS--RCQ-IFDFKRITIKDIKEHLAGIAVKEGIKFEDDALHIIAQ  197 (367)
T ss_pred             HHHHHHHHHHhC--CCCceEEEEEeCCcccCCHHHHh--cce-eEecCCccHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            345677777764  23345677778888999999998  764 68999999999999998888765543 3445677777


Q ss_pred             hCCCCCHHHHHHHHHHHH
Q 039253           98 FTQGFSGADITEICQRAC  115 (199)
Q Consensus        98 ~t~G~sgaDI~~lv~~A~  115 (199)
                      .+.| +.+.+.+.++...
T Consensus       198 ~~~g-dlr~~~~~lekl~  214 (367)
T PRK14970        198 KADG-ALRDALSIFDRVV  214 (367)
T ss_pred             hCCC-CHHHHHHHHHHHH
Confidence            6654 5555555555443

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.84  E-value=0.053  Score=53.19  Aligned_cols=93  Identities=16%  Similarity=0.168  Sum_probs=68.5

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      .....|.||..|+.  +...+++|++|+.+..|.+.+++  |. .++.|..++.++-..+|++.+....+. .+..+..|
T Consensus       132 T~eAqNALLKtLEE--PP~~vrFILaTTe~~kLl~TIlS--RC-q~f~fkpLs~eEI~~~L~~il~~EgI~~edeAL~lI  206 (944)
T PRK14949        132 SRSSFNALLKTLEE--PPEHVKFLLATTDPQKLPVTVLS--RC-LQFNLKSLTQDEIGTQLNHILTQEQLPFEAEALTLL  206 (944)
T ss_pred             CHHHHHHHHHHHhc--cCCCeEEEEECCCchhchHHHHH--hh-eEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            34567888888884  34567788889999999999998  87 778999999999999999888654433 23346778


Q ss_pred             HhhCCCCCHHHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQRAC  115 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A~  115 (199)
                      ++.+.| +.+++-+++..+.
T Consensus       207 A~~S~G-d~R~ALnLLdQal  225 (944)
T PRK14949        207 AKAANG-SMRDALSLTDQAI  225 (944)
T ss_pred             HHHcCC-CHHHHHHHHHHHH
Confidence            887766 4566666665443

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

Probab=95.64  E-value=0.06  Score=49.76  Aligned_cols=96  Identities=20%  Similarity=0.179  Sum_probs=75.1

Q ss_pred             hhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHH
Q 039253           16 AADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEK   94 (199)
Q Consensus        16 ~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~   94 (199)
                      -+....|.||+.++  ++...|++|.||..+..|++.+++  |. .++.|..-+.++-...|...+.+..+. .+--+..
T Consensus       131 LS~~afNALLKTLE--EPP~hV~FIlATTe~~Kip~TIlS--Rc-q~f~fkri~~~~I~~~L~~i~~~E~I~~e~~aL~~  205 (515)
T COG2812         131 LSKQAFNALLKTLE--EPPSHVKFILATTEPQKIPNTILS--RC-QRFDFKRLDLEEIAKHLAAILDKEGINIEEDALSL  205 (515)
T ss_pred             hhHHHHHHHhcccc--cCccCeEEEEecCCcCcCchhhhh--cc-ccccccCCCHHHHHHHHHHHHHhcCCccCHHHHHH
Confidence            36678899999998  566779999999999999999998  76 346677778889999999999877665 3334666


Q ss_pred             HHhhCCCCCHHHHHHHHHHHHHH
Q 039253           95 LAQFTQGFSGADITEICQRACKD  117 (199)
Q Consensus        95 la~~t~G~sgaDI~~lv~~A~~~  117 (199)
                      +|+.++| |.+|-..+++.|...
T Consensus       206 ia~~a~G-s~RDalslLDq~i~~  227 (515)
T COG2812         206 IARAAEG-SLRDALSLLDQAIAF  227 (515)
T ss_pred             HHHHcCC-ChhhHHHHHHHHHHc
Confidence            7777776 677777777776554

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=95.64  E-value=0.066  Score=52.30  Aligned_cols=91  Identities=15%  Similarity=0.060  Sum_probs=64.7

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      +....|.||+.|+..  ...+++|++|+.++.|-+.+++  |. .+++|..++.++-..+|+..+.+..+. .+..+..|
T Consensus       133 t~~a~NaLLK~LEEp--P~~~~fIl~tt~~~kLl~TIrS--Rc-~~v~F~~l~~~~l~~~L~~il~~EGv~id~eal~lL  207 (824)
T PRK07764        133 TPQGFNALLKIVEEP--PEHLKFIFATTEPDKVIGTIRS--RT-HHYPFRLVPPEVMRGYLERICAQEGVPVEPGVLPLV  207 (824)
T ss_pred             CHHHHHHHHHHHhCC--CCCeEEEEEeCChhhhhHHHHh--he-eEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            345678888888853  3467888888999999999998  76 678999999999999998888665543 23345556


Q ss_pred             HhhCCCCCHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQR  113 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~  113 (199)
                      ++.+.| +.+++.+++++
T Consensus       208 a~~sgG-dlR~Al~eLEK  224 (824)
T PRK07764        208 IRAGGG-SVRDSLSVLDQ  224 (824)
T ss_pred             HHHcCC-CHHHHHHHHHH
Confidence            666554 55555555544

>PRK13342 recombination factor protein RarA; Reviewed

Probab=95.63  E-value=0.091  Score=47.12  Aligned_cols=85  Identities=27%  Similarity=0.387  Sum_probs=56.9

Q ss_pred             HHHHHHHHhCCCCCCCEEEEEeeC--CCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCC-----CCCCcccHH
Q 039253           21 PNQLLTEMDGLSAKKTIFVIGVTN--RPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKS-----PVSKDVDLE   93 (199)
Q Consensus        21 ~~~lL~~ld~~~~~~~VvvI~aTN--~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~-----~~~~~~~l~   93 (199)
                      .+.|+..|+    ...+++|++|+  ....+++++++  |+ ..+.|+.|+.++...+++..+...     .+. +..+.
T Consensus       109 q~~LL~~le----~~~iilI~att~n~~~~l~~aL~S--R~-~~~~~~~ls~e~i~~lL~~~l~~~~~~~i~i~-~~al~  180 (413)
T PRK13342        109 QDALLPHVE----DGTITLIGATTENPSFEVNPALLS--RA-QVFELKPLSEEDIEQLLKRALEDKERGLVELD-DEALD  180 (413)
T ss_pred             HHHHHHHhh----cCcEEEEEeCCCChhhhccHHHhc--cc-eeeEeCCCCHHHHHHHHHHHHHHhhcCCCCCC-HHHHH
Confidence            345555554    24566776653  34589999999  98 789999999999999999887542     222 33466


Q ss_pred             HHHhhCCCCCHHHHHHHHHHH
Q 039253           94 KLAQFTQGFSGADITEICQRA  114 (199)
Q Consensus        94 ~la~~t~G~sgaDI~~lv~~A  114 (199)
                      .|++.+.| ..+.+.++++.+
T Consensus       181 ~l~~~s~G-d~R~aln~Le~~  200 (413)
T PRK13342        181 ALARLANG-DARRALNLLELA  200 (413)
T ss_pred             HHHHhCCC-CHHHHHHHHHHH
Confidence            77776644 455555555554

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=95.62  E-value=0.063  Score=51.55  Aligned_cols=90  Identities=21%  Similarity=0.245  Sum_probs=66.4

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHh
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQ   97 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~   97 (199)
                      ...+.||..|+.  +...+++|++|+.++.|.+.+++  |+. ++.|..|+.++-...++..+.+..+. .+..+..+|.
T Consensus       133 ~A~NALLKtLEE--PP~~tifILaTte~~KLl~TI~S--Rcq-~ieF~~L~~eeI~~~L~~il~kegI~id~eAl~~LA~  207 (725)
T PRK07133        133 SAFNALLKTLEE--PPKHVIFILATTEVHKIPLTILS--RVQ-RFNFRRISEDEIVSRLEFILEKENISYEKNALKLIAK  207 (725)
T ss_pred             HHHHHHHHHhhc--CCCceEEEEEcCChhhhhHHHHh--hce-eEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            457788888884  44567888888999999999998  885 89999999999999998887665543 2333666777


Q ss_pred             hCCCCCHHHHHHHHHHH
Q 039253           98 FTQGFSGADITEICQRA  114 (199)
Q Consensus        98 ~t~G~sgaDI~~lv~~A  114 (199)
                      .+.| +.+++..+++.+
T Consensus       208 lS~G-slR~AlslLekl  223 (725)
T PRK07133        208 LSSG-SLRDALSIAEQV  223 (725)
T ss_pred             HcCC-CHHHHHHHHHHH
Confidence            6664 445555555543

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=95.56  E-value=0.041  Score=53.98  Aligned_cols=76  Identities=17%  Similarity=0.199  Sum_probs=54.0

Q ss_pred             CCCEEEEEeeCC---CCCCCccccCCCccce-EEEecCCCHHHHHHHHHHhhcCCC-CCCcccHHHHHhhCCCCCHHHHH
Q 039253           34 KKTIFVIGVTNR---PDIIDPALLRPGRLDQ-LIYIPLPVEKSRLQIFKACLRKSP-VSKDVDLEKLAQFTQGFSGADIT  108 (199)
Q Consensus        34 ~~~VvvI~aTN~---~~~lD~al~R~gRfd~-~i~~~~P~~~~R~~il~~~l~~~~-~~~~~~l~~la~~t~G~sgaDI~  108 (199)
                      ..+|+||+.+|.   ++.+++.+..  ||.. +|.|++++.++..+||+..+.... .-.+.-+..+|+.+. ...+|++
T Consensus       900 ~SKLiLIGISNdlDLperLdPRLRS--RLg~eeIvF~PYTaEQL~dILk~RAe~A~gVLdDdAIELIArkVA-q~SGDAR  976 (1164)
T PTZ00112        900 NSKLVLIAISNTMDLPERLIPRCRS--RLAFGRLVFSPYKGDEIEKIIKERLENCKEIIDHTAIQLCARKVA-NVSGDIR  976 (1164)
T ss_pred             CCeEEEEEecCchhcchhhhhhhhh--ccccccccCCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhh-hcCCHHH
Confidence            456999999986   7778888888  7764 488899999999999999887542 112334666666544 3346766


Q ss_pred             HHHH
Q 039253          109 EICQ  112 (199)
Q Consensus       109 ~lv~  112 (199)
                      .++.
T Consensus       977 KALD  980 (1164)
T PTZ00112        977 KALQ  980 (1164)
T ss_pred             HHHH
Confidence            5543

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=95.53  E-value=0.02  Score=55.99  Aligned_cols=69  Identities=20%  Similarity=0.316  Sum_probs=53.0

Q ss_pred             CCCCEEEEEeeCCC-----CCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-----CcccHHHHHhhCCCC
Q 039253           33 AKKTIFVIGVTNRP-----DIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-----KDVDLEKLAQFTQGF  102 (199)
Q Consensus        33 ~~~~VvvI~aTN~~-----~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-----~~~~l~~la~~t~G~  102 (199)
                      .+..+.+|++|+..     ..+|+++.|  ||. .|.++.|+.+++..||+.+...+...     .+..+..++..+.+|
T Consensus       299 ~~g~i~~IgaTt~~e~r~~~~~d~al~r--Rf~-~i~v~~p~~~~~~~iL~~~~~~~e~~~~v~~~d~~i~~~~~ls~~y  375 (852)
T TIGR03346       299 ARGELHCIGATTLDEYRKYIEKDAALER--RFQ-PVFVDEPTVEDTISILRGLKERYEVHHGVRITDPAIVAAATLSHRY  375 (852)
T ss_pred             hcCceEEEEeCcHHHHHHHhhcCHHHHh--cCC-EEEeCCCCHHHHHHHHHHHHHHhccccCCCCCHHHHHHHHHhcccc
Confidence            35678999999986     458999999  996 58999999999999999887665332     233466667777766


Q ss_pred             CH
Q 039253          103 SG  104 (199)
Q Consensus       103 sg  104 (199)
                      -.
T Consensus       376 i~  377 (852)
T TIGR03346       376 IT  377 (852)
T ss_pred             cc
Confidence            43

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.

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=95.52  E-value=0.09  Score=47.89  Aligned_cols=89  Identities=16%  Similarity=0.154  Sum_probs=64.3

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHh
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQ   97 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~   97 (199)
                      ...+.|+..|+.  +...+++|++||.+..|.+++++  |+. .++|..|+.++-...++..+.+.... ++..+..|+.
T Consensus       136 ~~~n~LLk~lEe--p~~~~~~Il~t~~~~kl~~tI~s--Rc~-~v~f~~l~~~el~~~L~~~~~~eg~~i~~~al~~L~~  210 (451)
T PRK06305        136 EAFNSLLKTLEE--PPQHVKFFLATTEIHKIPGTILS--RCQ-KMHLKRIPEETIIDKLALIAKQEGIETSREALLPIAR  210 (451)
T ss_pred             HHHHHHHHHhhc--CCCCceEEEEeCChHhcchHHHH--hce-EEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            346778888885  33467788888999999999998  874 68999999999888888887665433 3445677787


Q ss_pred             hCCCCCHHHHHHHHHH
Q 039253           98 FTQGFSGADITEICQR  113 (199)
Q Consensus        98 ~t~G~sgaDI~~lv~~  113 (199)
                      .+.| +.+++.+.++.
T Consensus       211 ~s~g-dlr~a~~~Lek  225 (451)
T PRK06305        211 AAQG-SLRDAESLYDY  225 (451)
T ss_pred             HcCC-CHHHHHHHHHH
Confidence            7654 44555455444

>PRK04132 replication factor C small subunit; Provisional

Probab=95.44  E-value=0.16  Score=49.72  Aligned_cols=79  Identities=10%  Similarity=0.086  Sum_probs=62.0

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHH
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLA   96 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la   96 (199)
                      ....+.|+..|+.  +...+.+|++||.++.+.+++++  |. ..+.|+.|+.++-...++..+.+..+. ++..+..|+
T Consensus       644 ~~AQnALLk~lEe--p~~~~~FILi~N~~~kIi~tIrS--RC-~~i~F~~ls~~~i~~~L~~I~~~Egi~i~~e~L~~Ia  718 (846)
T PRK04132        644 QDAQQALRRTMEM--FSSNVRFILSCNYSSKIIEPIQS--RC-AIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAIL  718 (846)
T ss_pred             HHHHHHHHHHhhC--CCCCeEEEEEeCChhhCchHHhh--hc-eEEeCCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHH
Confidence            3456788888884  34567899999999999999998  86 788999999998888888887654433 345678888


Q ss_pred             hhCCC
Q 039253           97 QFTQG  101 (199)
Q Consensus        97 ~~t~G  101 (199)
                      ..+.|
T Consensus       719 ~~s~G  723 (846)
T PRK04132        719 YIAEG  723 (846)
T ss_pred             HHcCC
Confidence            87765

>PRK04195 replication factor C large subunit; Provisional

Probab=95.43  E-value=0.082  Score=48.40  Aligned_cols=87  Identities=17%  Similarity=0.125  Sum_probs=61.7

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHh
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQ   97 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~   97 (199)
                      ..++.|+..++.    .+..+|++||.+..+++..+|  +....|.|+.|+..+...+++..+....+. ++..+..|++
T Consensus       117 ~~~~aL~~~l~~----~~~~iIli~n~~~~~~~k~Lr--sr~~~I~f~~~~~~~i~~~L~~i~~~egi~i~~eaL~~Ia~  190 (482)
T PRK04195        117 GGARAILELIKK----AKQPIILTANDPYDPSLRELR--NACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAE  190 (482)
T ss_pred             hHHHHHHHHHHc----CCCCEEEeccCccccchhhHh--ccceEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            346777777763    233567788999999884444  455789999999999999999998765543 3445777888


Q ss_pred             hCCCCCHHHHHHHHHHHH
Q 039253           98 FTQGFSGADITEICQRAC  115 (199)
Q Consensus        98 ~t~G~sgaDI~~lv~~A~  115 (199)
                      .+.    +||..++....
T Consensus       191 ~s~----GDlR~ain~Lq  204 (482)
T PRK04195        191 RSG----GDLRSAINDLQ  204 (482)
T ss_pred             HcC----CCHHHHHHHHH
Confidence            654    47776666543

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=95.35  E-value=0.063  Score=46.91  Aligned_cols=80  Identities=20%  Similarity=0.321  Sum_probs=58.9

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCcccHHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLA   96 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~l~~la   96 (199)
                      .....|.||+.|+.  +..++++|.+|+.++.|.|.+++  |... +.|++|+.++-.+.|+.....   ..+.....++
T Consensus       119 ~~~aaNaLLK~LEE--Pp~~~~fiL~t~~~~~ll~TI~S--Rc~~-~~~~~~~~~~~~~~L~~~~~~---~~~~~~~~~l  190 (328)
T PRK05707        119 NRNAANALLKSLEE--PSGDTVLLLISHQPSRLLPTIKS--RCQQ-QACPLPSNEESLQWLQQALPE---SDERERIELL  190 (328)
T ss_pred             CHHHHHHHHHHHhC--CCCCeEEEEEECChhhCcHHHHh--hcee-eeCCCcCHHHHHHHHHHhccc---CChHHHHHHH
Confidence            34578999999984  44678999999999999999999  9866 899999999888888765421   1222344556


Q ss_pred             hhCCCCCH
Q 039253           97 QFTQGFSG  104 (199)
Q Consensus        97 ~~t~G~sg  104 (199)
                      ..+.|-.+
T Consensus       191 ~la~Gsp~  198 (328)
T PRK05707        191 TLAGGSPL  198 (328)
T ss_pred             HHcCCCHH
Confidence            66665433

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.32  E-value=0.099  Score=48.55  Aligned_cols=94  Identities=16%  Similarity=0.141  Sum_probs=70.3

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      +....|.||+.|+.  ....+++|++|+.++.+.+.+++  |. ..++|..|+.++-...++..+.+..+. .+..+..|
T Consensus       132 s~~a~naLLK~LEe--pp~~~~fIL~t~d~~kil~tI~S--Rc-~~~~f~~l~~~~i~~~L~~il~~egi~~~~~al~~l  206 (527)
T PRK14969        132 SKSAFNAMLKTLEE--PPEHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPPPLIVSHLQHILEQENIPFDATALQLL  206 (527)
T ss_pred             CHHHHHHHHHHHhC--CCCCEEEEEEeCChhhCchhHHH--HH-HHHhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            44567889999985  34567888888889999998887  76 789999999999998888888655443 23446777


Q ss_pred             HhhCCCCCHHHHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQRACK  116 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A~~  116 (199)
                      ++.+. -+.+++.++++.+..
T Consensus       207 a~~s~-Gslr~al~lldqai~  226 (527)
T PRK14969        207 ARAAA-GSMRDALSLLDQAIA  226 (527)
T ss_pred             HHHcC-CCHHHHHHHHHHHHH
Confidence            87765 467777777776643

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=95.26  E-value=0.3  Score=42.83  Aligned_cols=63  Identities=19%  Similarity=0.329  Sum_probs=48.8

Q ss_pred             hhHHHHHHHHHHhCCC-----------CCCCEEEEEeeCCCC-CCCccccCCCccceEEEecCCCH-HHHHHHHHHhh
Q 039253           17 ADRIPNQLLTEMDGLS-----------AKKTIFVIGVTNRPD-IIDPALLRPGRLDQLIYIPLPVE-KSRLQIFKACL   81 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~-----------~~~~VvvI~aTN~~~-~lD~al~R~gRfd~~i~~~~P~~-~~R~~il~~~l   81 (199)
                      ..++.+.|+..|+.-.           ...++++|+|+|-.+ .++++++.  ||...+.++.|.. ++|.+|++...
T Consensus       141 ~~~~q~~Lle~mee~~v~v~r~G~~~~~p~rfiviAt~NP~e~~l~~aLld--RF~~~v~v~~~~~~~e~~~il~~~~  216 (334)
T PRK13407        141 EDHIVDLLLDVAQSGENVVEREGLSIRHPARFVLVGSGNPEEGELRPQLLD--RFGLSVEVRSPRDVETRVEVIRRRD  216 (334)
T ss_pred             CHHHHHHHHHHHHcCCeEEEECCeEEecCCCEEEEecCCcccCCCCHHHHh--hcceEEEcCCCCcHHHHHHHHHHhh
Confidence            4467788888886321           124688888888544 58999999  9999999999866 99999998854

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=95.09  E-value=0.27  Score=43.19  Aligned_cols=63  Identities=19%  Similarity=0.226  Sum_probs=47.6

Q ss_pred             hhHHHHHHHHHHhCCC-----------CCCCEEEEEeeCCCC-CCCccccCCCccceEEEecCCCH-HHHHHHHHHhh
Q 039253           17 ADRIPNQLLTEMDGLS-----------AKKTIFVIGVTNRPD-IIDPALLRPGRLDQLIYIPLPVE-KSRLQIFKACL   81 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~-----------~~~~VvvI~aTN~~~-~lD~al~R~gRfd~~i~~~~P~~-~~R~~il~~~l   81 (199)
                      ...+.+.|+..|+.=.           ...++++|+|+|-.+ .++++++.  ||..++.++.|.. ++|.+|++...
T Consensus       144 ~~~~Q~~Ll~~l~~g~~~v~r~G~~~~~~~r~iviat~np~eg~l~~~Lld--Rf~l~i~l~~p~~~eer~eIL~~~~  219 (337)
T TIGR02030       144 EDHLVDVLLDVAASGWNVVEREGISIRHPARFVLVGSGNPEEGELRPQLLD--RFGLHAEIRTVRDVELRVEIVERRT  219 (337)
T ss_pred             CHHHHHHHHHHHHhCCeEEEECCEEEEcCCCEEEEeccccccCCCCHHHHh--hcceEEECCCCCCHHHHHHHHHhhh
Confidence            3456677888775310           124578888887544 69999999  9999999999976 89999998854

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.

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.02  E-value=0.15  Score=47.99  Aligned_cols=91  Identities=15%  Similarity=0.149  Sum_probs=63.9

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      +....|.||..|+.  ....+++|++|+.++.|.+.+++  |. .+++|..++.++-...++.++.+.... .+..+..+
T Consensus       131 t~~A~NALLK~LEE--pp~~~~fIL~tte~~kll~TI~S--Rc-~~~~F~~l~~~~i~~~L~~i~~~egi~i~~~al~~I  205 (584)
T PRK14952        131 TTAGFNALLKIVEE--PPEHLIFIFATTEPEKVLPTIRS--RT-HHYPFRLLPPRTMRALIARICEQEGVVVDDAVYPLV  205 (584)
T ss_pred             CHHHHHHHHHHHhc--CCCCeEEEEEeCChHhhHHHHHH--hc-eEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            33467888888884  34578888888999999999998  84 689999999999998998888765443 23334555


Q ss_pred             HhhCCCCCHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQR  113 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~  113 (199)
                      ++.+.| +.+++.++++.
T Consensus       206 a~~s~G-dlR~aln~Ldq  222 (584)
T PRK14952        206 IRAGGG-SPRDTLSVLDQ  222 (584)
T ss_pred             HHHcCC-CHHHHHHHHHH
Confidence            554443 44444444433

>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=95.00  E-value=0.092  Score=43.07  Aligned_cols=92  Identities=15%  Similarity=0.214  Sum_probs=57.3

Q ss_pred             HHHHHHHHhCCCCCCCEEEEEeeCCCCC---CCccccCCCccce--EEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHH
Q 039253           21 PNQLLTEMDGLSAKKTIFVIGVTNRPDI---IDPALLRPGRLDQ--LIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEK   94 (199)
Q Consensus        21 ~~~lL~~ld~~~~~~~VvvI~aTN~~~~---lD~al~R~gRfd~--~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~   94 (199)
                      -..|...++.+....+-+||.+-..|..   +++.+.+  ||..  .+.+..|+.+.|..|++.......+. ++.-+..
T Consensus       116 q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~~~~L~S--Rl~~Gl~~~l~~pd~~~r~~il~~~a~~~~~~l~~~v~~~  193 (219)
T PF00308_consen  116 QEELFHLFNRLIESGKQLILTSDRPPSELSGLLPDLRS--RLSWGLVVELQPPDDEDRRRILQKKAKERGIELPEEVIEY  193 (219)
T ss_dssp             HHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS-HHHHH--HHHCSEEEEE----HHHHHHHHHHHHHHTT--S-HHHHHH
T ss_pred             HHHHHHHHHHHHhhCCeEEEEeCCCCccccccChhhhh--hHhhcchhhcCCCCHHHHHHHHHHHHHHhCCCCcHHHHHH
Confidence            3455555555544455556655555665   4677888  8775  88889999999999999999766554 3444667


Q ss_pred             HHhhCCCCCHHHHHHHHHHHH
Q 039253           95 LAQFTQGFSGADITEICQRAC  115 (199)
Q Consensus        95 la~~t~G~sgaDI~~lv~~A~  115 (199)
                      |++... -+.++|..++.+-.
T Consensus       194 l~~~~~-~~~r~L~~~l~~l~  213 (219)
T PF00308_consen  194 LARRFR-RDVRELEGALNRLD  213 (219)
T ss_dssp             HHHHTT-SSHHHHHHHHHHHH
T ss_pred             HHHhhc-CCHHHHHHHHHHHH
Confidence            788765 47777777777643

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.

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

Probab=94.97  E-value=0.16  Score=45.78  Aligned_cols=84  Identities=20%  Similarity=0.195  Sum_probs=58.1

Q ss_pred             CCEEEEEeeCCCCCCC---ccccCCCccc--eEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhhCCCCCHHHHH
Q 039253           35 KTIFVIGVTNRPDIID---PALLRPGRLD--QLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSGADIT  108 (199)
Q Consensus        35 ~~VvvI~aTN~~~~lD---~al~R~gRfd--~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~t~G~sgaDI~  108 (199)
                      .+-+|+.+-..|..+.   +.+++  ||.  ..+.+.+|+.+.|..||+.......+. ++.-+..+|.... =+.++|.
T Consensus       208 ~kqIvltsdr~P~~l~~~~~rL~S--R~~~Gl~~~I~~Pd~e~r~aiL~kka~~~~~~i~~ev~~~la~~~~-~nvReLe  284 (408)
T COG0593         208 GKQIVLTSDRPPKELNGLEDRLRS--RLEWGLVVEIEPPDDETRLAILRKKAEDRGIEIPDEVLEFLAKRLD-RNVRELE  284 (408)
T ss_pred             CCEEEEEcCCCchhhccccHHHHH--HHhceeEEeeCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhh-ccHHHHH
Confidence            3345665555577666   88888  987  567778899999999999977665554 3444666777654 4677777


Q ss_pred             HHHHHHHHHHHHH
Q 039253          109 EICQRACKDATRE  121 (199)
Q Consensus       109 ~lv~~A~~~a~~~  121 (199)
                      .++......+...
T Consensus       285 gaL~~l~~~a~~~  297 (408)
T COG0593         285 GALNRLDAFALFT  297 (408)
T ss_pred             HHHHHHHHHHHhc
Confidence            7776665555433

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=94.96  E-value=0.15  Score=44.94  Aligned_cols=80  Identities=14%  Similarity=0.098  Sum_probs=57.6

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCcccHHHHHhh
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQF   98 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~l~~la~~   98 (199)
                      ...|.||+.|+.  +..++++|..|+.|+.+.|.++.  |+ ..+.|++|+.++-..+++.......+. +..+..++..
T Consensus       156 ~aanaLLk~LEE--pp~~~~fiLit~~~~~llptIrS--Rc-~~i~l~pl~~~~~~~~L~~~~~~~~~~-~~~~~~i~~~  229 (351)
T PRK09112        156 NAANAILKTLEE--PPARALFILISHSSGRLLPTIRS--RC-QPISLKPLDDDELKKALSHLGSSQGSD-GEITEALLQR  229 (351)
T ss_pred             HHHHHHHHHHhc--CCCCceEEEEECChhhccHHHHh--hc-cEEEecCCCHHHHHHHHHHhhcccCCC-HHHHHHHHHH
Confidence            456778888885  33456777778889999999998  88 699999999999999998753322222 2335667777


Q ss_pred             CCCCCH
Q 039253           99 TQGFSG  104 (199)
Q Consensus        99 t~G~sg  104 (199)
                      +.|-..
T Consensus       230 s~G~pr  235 (351)
T PRK09112        230 SKGSVR  235 (351)
T ss_pred             cCCCHH
Confidence            765433

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.88  E-value=0.17  Score=47.22  Aligned_cols=92  Identities=18%  Similarity=0.145  Sum_probs=65.8

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      +....+.||..|+.  +...+++|++|+.+..+.+.+++  |. ..++|..++.++-...++..+.+..+. .+..+..|
T Consensus       132 s~~a~naLLK~LEe--pp~~v~fIL~Ttd~~kil~tI~S--Rc-~~~~f~~Ls~~eI~~~L~~il~~egi~~e~~Al~~I  206 (546)
T PRK14957        132 SKQSFNALLKTLEE--PPEYVKFILATTDYHKIPVTILS--RC-IQLHLKHISQADIKDQLKIILAKENINSDEQSLEYI  206 (546)
T ss_pred             cHHHHHHHHHHHhc--CCCCceEEEEECChhhhhhhHHH--he-eeEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            34467788888884  33556777788889999999888  77 889999999999888888887765443 34446667


Q ss_pred             HhhCCCCCHHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQRA  114 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A  114 (199)
                      +..+. -+.+++-++++.+
T Consensus       207 a~~s~-GdlR~alnlLek~  224 (546)
T PRK14957        207 AYHAK-GSLRDALSLLDQA  224 (546)
T ss_pred             HHHcC-CCHHHHHHHHHHH
Confidence            77664 3555555555543

>PF09336 Vps4_C: Vps4 C terminal oligomerisation domain; InterPro: IPR015415 This domain is found at the C-terminal of ATPase proteins involved in vacuolar sorting

Probab=94.81  E-value=0.009  Score=39.54  Aligned_cols=21  Identities=38%  Similarity=0.438  Sum_probs=18.7

Q ss_pred             ccccHHHHHHHHHhccccccc
Q 039253          143 AEIKAEHFEESMKYACKSQSR  163 (199)
Q Consensus       143 ~~it~~df~~Al~~~~Ps~~r  163 (199)
                      .+|+++||..||+.++||++.
T Consensus        28 p~it~~DF~~Al~~~kpSVs~   48 (62)
T PF09336_consen   28 PPITMEDFEEALKKVKPSVSQ   48 (62)
T ss_dssp             HHBCHHHHHHHHHTCGGSS-H
T ss_pred             CCCCHHHHHHHHHHcCCCCCH
Confidence            479999999999999999986

It forms an alpha helix structure and is required for oligomerisation []. ; PDB: 1XWI_A 3EIH_C 2QPA_C 3EIE_A 2RKO_A 2QP9_X 3MHV_C 3CF3_C 3CF1_A 3CF2_A ....

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.60  E-value=0.3  Score=45.92  Aligned_cols=90  Identities=16%  Similarity=0.121  Sum_probs=66.0

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHh
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQ   97 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~   97 (199)
                      ...+.||..|+..  ...+++|++|+.++.+.+.+++  |.. .++|..++..+-..+++..+....+. ++..+..|+.
T Consensus       135 ~a~naLLk~LEep--p~~tv~Il~t~~~~kll~tI~S--R~~-~i~f~~l~~~el~~~L~~~a~~egl~i~~eal~~La~  209 (585)
T PRK14950        135 AAFNALLKTLEEP--PPHAIFILATTEVHKVPATILS--RCQ-RFDFHRHSVADMAAHLRKIAAAEGINLEPGALEAIAR  209 (585)
T ss_pred             HHHHHHHHHHhcC--CCCeEEEEEeCChhhhhHHHHh--ccc-eeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            4567788888753  3456777778888889999887  764 68899999999998888887665443 3344777888


Q ss_pred             hCCCCCHHHHHHHHHHH
Q 039253           98 FTQGFSGADITEICQRA  114 (199)
Q Consensus        98 ~t~G~sgaDI~~lv~~A  114 (199)
                      .+.| +.+++.+.++..
T Consensus       210 ~s~G-dlr~al~~LekL  225 (585)
T PRK14950        210 AATG-SMRDAENLLQQL  225 (585)
T ss_pred             HcCC-CHHHHHHHHHHH
Confidence            7776 777777776653

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=94.29  E-value=0.083  Score=49.92  Aligned_cols=103  Identities=17%  Similarity=0.223  Sum_probs=63.3

Q ss_pred             CEEEEEeeCCC--CCCCccccCCCccc---eEEEec--CC-CHHHHHHHHHHhhc---CCCCC---CcccHHHHHh----
Q 039253           36 TIFVIGVTNRP--DIIDPALLRPGRLD---QLIYIP--LP-VEKSRLQIFKACLR---KSPVS---KDVDLEKLAQ----   97 (199)
Q Consensus        36 ~VvvI~aTN~~--~~lD~al~R~gRfd---~~i~~~--~P-~~~~R~~il~~~l~---~~~~~---~~~~l~~la~----   97 (199)
                      ++.||+++|..  ..+|+.|+.  ||+   .+++|+  +| +.+.|..+.+.+.+   +....   ++--+.+|.+    
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            57889999863  689999999  999   667664  35 45666666554332   22111   1222333322    


Q ss_pred             h---CC--CCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccc
Q 039253           98 F---TQ--GFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACK  159 (199)
Q Consensus        98 ~---t~--G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~P  159 (199)
                      .   -.  -.+.++|..++++|...|..+.                   ...|+.+|+.+|++..+.
T Consensus       346 ~ag~r~~lsl~~R~L~~llR~A~~iA~~~~-------------------~~~I~~ehV~~Ai~~~~~  393 (608)
T TIGR00764       346 RAGRKDHLTLRLRELGGLVRAAGDIAKSSG-------------------KVYVTAEHVLKAKKLAKT  393 (608)
T ss_pred             HHhcccccCCCHHHHHHHHHHHHHHHHhcC-------------------CceecHHHHHHHHHHHHH
Confidence            1   11  2457889999998854443221                   156999999999876543

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

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=94.23  E-value=0.24  Score=41.67  Aligned_cols=43  Identities=28%  Similarity=0.282  Sum_probs=36.8

Q ss_pred             CEEEEEeeCCC-----CCCCccccCCCccceEEEecCCCHHHHHHHHHHhh
Q 039253           36 TIFVIGVTNRP-----DIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACL   81 (199)
Q Consensus        36 ~VvvI~aTN~~-----~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l   81 (199)
                      +..||+|+|..     ..+++++++  || ..+.++.|+.++-.+|++.++
T Consensus       151 ~frvIaTsN~~~~~g~~~l~~aL~~--R~-~~i~i~~P~~~~e~~Il~~~~  198 (262)
T TIGR02640       151 EFRVIFTSNPVEYAGVHETQDALLD--RL-ITIFMDYPDIDTETAILRAKT  198 (262)
T ss_pred             CCEEEEeeCCccccceecccHHHHh--hc-EEEECCCCCHHHHHHHHHHhh
Confidence            56789999975     367999999  99 689999999999999999875

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).

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=94.20  E-value=0.11  Score=44.38  Aligned_cols=55  Identities=22%  Similarity=0.279  Sum_probs=43.2

Q ss_pred             HHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhh
Q 039253           22 NQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACL   81 (199)
Q Consensus        22 ~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l   81 (199)
                      +.|...|+...  .++.+|++||.++.+++++++  ||. .+.|+.|+.+++..+++.++
T Consensus       119 ~~L~~~le~~~--~~~~~Ilt~n~~~~l~~~l~s--R~~-~i~~~~p~~~~~~~il~~~~  173 (316)
T PHA02544        119 RHLRSFMEAYS--KNCSFIITANNKNGIIEPLRS--RCR-VIDFGVPTKEEQIEMMKQMI  173 (316)
T ss_pred             HHHHHHHHhcC--CCceEEEEcCChhhchHHHHh--hce-EEEeCCCCHHHHHHHHHHHH
Confidence            44555566543  456788899999999999999  995 78999999999998877654

>PLN03025 replication factor C subunit; Provisional

Probab=94.11  E-value=0.29  Score=42.20  Aligned_cols=77  Identities=16%  Similarity=0.099  Sum_probs=56.6

Q ss_pred             HHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhh
Q 039253           20 IPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQF   98 (199)
Q Consensus        20 ~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~   98 (199)
                      .-+.|+..|+...  ..+.+|.+||.++.+.+++++  |. ..+.|+.|+.++....++..+.+..+. ++..+..++..
T Consensus       115 aq~aL~~~lE~~~--~~t~~il~~n~~~~i~~~L~S--Rc-~~i~f~~l~~~~l~~~L~~i~~~egi~i~~~~l~~i~~~  189 (319)
T PLN03025        115 AQQALRRTMEIYS--NTTRFALACNTSSKIIEPIQS--RC-AIVRFSRLSDQEILGRLMKVVEAEKVPYVPEGLEAIIFT  189 (319)
T ss_pred             HHHHHHHHHhccc--CCceEEEEeCCccccchhHHH--hh-hcccCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            3466777776433  234577789999999999998  86 579999999999999999888765443 34457777776


Q ss_pred             CCC
Q 039253           99 TQG  101 (199)
Q Consensus        99 t~G  101 (199)
                      +.|
T Consensus       190 ~~g  192 (319)
T PLN03025        190 ADG  192 (319)
T ss_pred             cCC
Confidence            543

>smart00350 MCM minichromosome maintenance proteins

Probab=93.82  E-value=0.57  Score=43.30  Aligned_cols=62  Identities=15%  Similarity=0.149  Sum_probs=45.7

Q ss_pred             HHHHHHHHHHhCCC-----------CCCCEEEEEeeCCCC-------------CCCccccCCCccceEEEe-cCCCHHHH
Q 039253           19 RIPNQLLTEMDGLS-----------AKKTIFVIGVTNRPD-------------IIDPALLRPGRLDQLIYI-PLPVEKSR   73 (199)
Q Consensus        19 r~~~~lL~~ld~~~-----------~~~~VvvI~aTN~~~-------------~lD~al~R~gRfd~~i~~-~~P~~~~R   73 (199)
                      ...+.|+..|+.=.           -..+..||+|+|-.+             .|++++++  |||-.+.+ ..|+.+..
T Consensus       315 ~~q~~L~e~me~~~i~i~k~G~~~~l~~~~~viAa~NP~~g~y~~~~~~~~n~~l~~~lLs--RFdLi~~~~d~~~~~~d  392 (509)
T smart00350      315 SDRTAIHEAMEQQTISIAKAGITTTLNARCSVLAAANPIGGRYDPKLTPEENIDLPAPILS--RFDLLFVVLDEVDEERD  392 (509)
T ss_pred             HHHHHHHHHHhcCEEEEEeCCEEEEecCCcEEEEEeCCCCcccCCCcChhhccCCChHHhC--ceeeEEEecCCCChHHH
Confidence            45566777775311           124578999999542             69999999  99986555 68999999


Q ss_pred             HHHHHHhhc
Q 039253           74 LQIFKACLR   82 (199)
Q Consensus        74 ~~il~~~l~   82 (199)
                      .+|.++.+.
T Consensus       393 ~~i~~~i~~  401 (509)
T smart00350      393 RELAKHVVD  401 (509)
T ss_pred             HHHHHHHHH
Confidence            999988664

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.74  E-value=0.44  Score=45.16  Aligned_cols=91  Identities=18%  Similarity=0.161  Sum_probs=65.0

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHH
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLA   96 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la   96 (199)
                      ....+.||..|+..  ...+++|++|+.+..|-+++++  |. ..++|..++.++-...++..+.+..+. ....+..|+
T Consensus       135 ~~a~naLLK~LEep--p~~tifIL~tt~~~kIl~tI~S--Rc-~iv~f~~ls~~ei~~~L~~ia~~egi~i~~~al~~La  209 (614)
T PRK14971        135 QAAFNAFLKTLEEP--PSYAIFILATTEKHKILPTILS--RC-QIFDFNRIQVADIVNHLQYVASKEGITAEPEALNVIA  209 (614)
T ss_pred             HHHHHHHHHHHhCC--CCCeEEEEEeCCchhchHHHHh--hh-heeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            34567888888853  3456677777788999999998  76 459999999999888888888766554 233467778


Q ss_pred             hhCCCCCHHHHHHHHHHH
Q 039253           97 QFTQGFSGADITEICQRA  114 (199)
Q Consensus        97 ~~t~G~sgaDI~~lv~~A  114 (199)
                      ..+.| +.+++.+.++..
T Consensus       210 ~~s~g-dlr~al~~Lekl  226 (614)
T PRK14971        210 QKADG-GMRDALSIFDQV  226 (614)
T ss_pred             HHcCC-CHHHHHHHHHHH
Confidence            77754 566655555443

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=93.68  E-value=0.19  Score=43.52  Aligned_cols=63  Identities=24%  Similarity=0.286  Sum_probs=48.0

Q ss_pred             hHHHHHHHHHHhCC----------CCCCCEEEEEeeC-----CCCCCCccccCCCccceEEEecCC-CHHHHHHHHHHhh
Q 039253           18 DRIPNQLLTEMDGL----------SAKKTIFVIGVTN-----RPDIIDPALLRPGRLDQLIYIPLP-VEKSRLQIFKACL   81 (199)
Q Consensus        18 ~r~~~~lL~~ld~~----------~~~~~VvvI~aTN-----~~~~lD~al~R~gRfd~~i~~~~P-~~~~R~~il~~~l   81 (199)
                      ..+-+.||..|+.-          .-..+.+||+|+|     .-..+++|+++  ||...++++.| ...+...++....
T Consensus       126 p~~q~aLl~~l~e~~vtv~~~~~~~~~~~f~viaT~Np~e~~g~~~l~eA~ld--Rf~~~~~v~yp~~~~e~~~i~~~~~  203 (329)
T COG0714         126 PEVQNALLEALEERQVTVPGLTTIRLPPPFIVIATQNPGEYEGTYPLPEALLD--RFLLRIYVDYPDSEEEERIILARVG  203 (329)
T ss_pred             HHHHHHHHHHHhCcEEEECCcCCcCCCCCCEEEEccCccccCCCcCCCHHHHh--hEEEEEecCCCCchHHHHHHHHhCc
Confidence            45778888888862          2235688898889     78889999999  99999999999 5555555555554


Q ss_pred             c
Q 039253           82 R   82 (199)
Q Consensus        82 ~   82 (199)
                      .
T Consensus       204 ~  204 (329)
T COG0714         204 G  204 (329)
T ss_pred             c
Confidence            3

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.59  E-value=0.2  Score=44.68  Aligned_cols=90  Identities=16%  Similarity=0.101  Sum_probs=61.7

Q ss_pred             HHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhh
Q 039253           20 IPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQF   98 (199)
Q Consensus        20 ~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~   98 (199)
                      -.+.|+..|+.  +...+++|++|+.+..+-+++.+  |.. .++|..++.++-...++..+...... ++..+..|+..
T Consensus       143 ~~~~LLk~LEe--p~~~t~~Il~t~~~~kl~~tl~s--R~~-~v~f~~l~~~ei~~~l~~~~~~~g~~i~~~al~~l~~~  217 (397)
T PRK14955        143 AFNAFLKTLEE--PPPHAIFIFATTELHKIPATIAS--RCQ-RFNFKRIPLEEIQQQLQGICEAEGISVDADALQLIGRK  217 (397)
T ss_pred             HHHHHHHHHhc--CCCCeEEEEEeCChHHhHHHHHH--HHH-HhhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            34566666663  33455666777788899999988  775 78899999988888888887655432 34457778887


Q ss_pred             CCCCCHHHHHHHHHHHH
Q 039253           99 TQGFSGADITEICQRAC  115 (199)
Q Consensus        99 t~G~sgaDI~~lv~~A~  115 (199)
                      +.| +.+.+.+.++.+.
T Consensus       218 s~g-~lr~a~~~L~kl~  233 (397)
T PRK14955        218 AQG-SMRDAQSILDQVI  233 (397)
T ss_pred             cCC-CHHHHHHHHHHHH
Confidence            765 5556656555543

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

Probab=93.31  E-value=0.68  Score=44.97  Aligned_cols=104  Identities=18%  Similarity=0.244  Sum_probs=74.4

Q ss_pred             hHHHHHHHHHHhCC---CC------CCCEEEEEeeCCC-------------------------CCCCccccCCCccceEE
Q 039253           18 DRIPNQLLTEMDGL---SA------KKTIFVIGVTNRP-------------------------DIIDPALLRPGRLDQLI   63 (199)
Q Consensus        18 ~r~~~~lL~~ld~~---~~------~~~VvvI~aTN~~-------------------------~~lD~al~R~gRfd~~i   63 (199)
                      ..+.+.||+.||.-   ..      -.++++|+|||.-                         ..+.|.|+.  |+|.+|
T Consensus       571 ~~v~~~LLq~ld~G~ltd~~g~~vd~rn~iiI~TsN~g~~~~~~~~~g~~~~~~~~~~~~~~~~~f~pefl~--Rid~ii  648 (758)
T PRK11034        571 PDVFNLLLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNII  648 (758)
T ss_pred             HHHHHHHHHHHhcCeeecCCCceecCCCcEEEEeCCcCHHHHhhcccCcccchhhHHHHHHHHHhcCHHHHc--cCCEEE
Confidence            35788899999832   11      1468899999932                         236688888  999999


Q ss_pred             EecCCCHHHHHHHHHHhhcC---------CCCC-CcccHHHHHhhC--CCCCHHHHHHHHHHHHHHHHHHHH
Q 039253           64 YIPLPVEKSRLQIFKACLRK---------SPVS-KDVDLEKLAQFT--QGFSGADITEICQRACKDATREEI  123 (199)
Q Consensus        64 ~~~~P~~~~R~~il~~~l~~---------~~~~-~~~~l~~la~~t--~G~sgaDI~~lv~~A~~~a~~~~~  123 (199)
                      .|++.+.++...|+..++..         ..+. ++--++.|++..  ..|-.+.|+.++++-...++.+.+
T Consensus       649 ~f~~L~~~~l~~I~~~~l~~~~~~l~~~~i~l~~~~~~~~~l~~~~~~~~~GAR~l~r~i~~~l~~~la~~i  720 (758)
T PRK11034        649 WFDHLSTDVIHQVVDKFIVELQAQLDQKGVSLEVSQEARDWLAEKGYDRAMGARPMARVIQDNLKKPLANEL  720 (758)
T ss_pred             EcCCCCHHHHHHHHHHHHHHHHHHHHHCCCCceECHHHHHHHHHhCCCCCCCCchHHHHHHHHHHHHHHHHH
Confidence            99999999999999888742         2222 233355666543  457788899999888877777664

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=93.28  E-value=1  Score=39.83  Aligned_cols=63  Identities=21%  Similarity=0.251  Sum_probs=47.8

Q ss_pred             hhHHHHHHHHHHhCC---------C--CCCCEEEEEeeCCCC-CCCccccCCCccceEEEecCCC-HHHHHHHHHHhh
Q 039253           17 ADRIPNQLLTEMDGL---------S--AKKTIFVIGVTNRPD-IIDPALLRPGRLDQLIYIPLPV-EKSRLQIFKACL   81 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~---------~--~~~~VvvI~aTN~~~-~lD~al~R~gRfd~~i~~~~P~-~~~R~~il~~~l   81 (199)
                      ...+.+.|+..|+.-         .  ...++++|+|.|-.+ .++++++.  ||..++.+..|+ .+.|.+|++...
T Consensus       157 ~~~~Q~~LLeam~e~~~~ier~G~s~~~p~rfiviaT~np~eg~l~~~Lld--Rf~l~i~l~~~~~~~~e~~il~~~~  232 (350)
T CHL00081        157 DDHLVDILLDSAASGWNTVEREGISIRHPARFVLVGSGNPEEGELRPQLLD--RFGMHAEIRTVKDPELRVKIVEQRT  232 (350)
T ss_pred             CHHHHHHHHHHHHhCCeEEeeCCeeeecCCCEEEEeccCcccCCCCHHHHH--HhCceeecCCCCChHHHHHHHHhhh
Confidence            345667788887541         0  124578888777544 59999999  999999999997 599999998864

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

Probab=93.27  E-value=0.81  Score=38.52  Aligned_cols=67  Identities=12%  Similarity=0.219  Sum_probs=53.4

Q ss_pred             HHHHHHHHhCCC--CCCCEEEEEeeCCCCCCCccccC-C--------------------CccceEEEecCCCHHHHHHHH
Q 039253           21 PNQLLTEMDGLS--AKKTIFVIGVTNRPDIIDPALLR-P--------------------GRLDQLIYIPLPVEKSRLQIF   77 (199)
Q Consensus        21 ~~~lL~~ld~~~--~~~~VvvI~aTN~~~~lD~al~R-~--------------------gRfd~~i~~~~P~~~~R~~il   77 (199)
                      -+.|...|||--  ...+|++.+|+|+-..+++.+.. .                    .||.-.|.|..|+.++-.+|+
T Consensus       124 yk~LKs~LeGgle~~P~NvliyATSNRRHLv~E~~~d~~~~~~~eih~~d~~eEklSLsDRFGL~l~F~~~~q~~YL~IV  203 (249)
T PF05673_consen  124 YKALKSVLEGGLEARPDNVLIYATSNRRHLVPESFSDREDIQDDEIHPSDTIEEKLSLSDRFGLWLSFYPPDQEEYLAIV  203 (249)
T ss_pred             HHHHHHHhcCccccCCCcEEEEEecchhhccchhhhhccCCCccccCcchHHHHHHhHHHhCCcEEEecCCCHHHHHHHH
Confidence            467777788742  34679999999998877775542 2                    389999999999999999999


Q ss_pred             HHhhcCCCCC
Q 039253           78 KACLRKSPVS   87 (199)
Q Consensus        78 ~~~l~~~~~~   87 (199)
                      +.++....+.
T Consensus       204 ~~~~~~~g~~  213 (249)
T PF05673_consen  204 RHYAERYGLE  213 (249)
T ss_pred             HHHHHHcCCC
Confidence            9999877655

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

Probab=93.26  E-value=0.37  Score=46.51  Aligned_cols=77  Identities=21%  Similarity=0.256  Sum_probs=52.4

Q ss_pred             CCEEEEEeeCC--CCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcC-------CCCC-CcccHHHHHhhCCCCCH
Q 039253           35 KTIFVIGVTNR--PDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRK-------SPVS-KDVDLEKLAQFTQGFSG  104 (199)
Q Consensus        35 ~~VvvI~aTN~--~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~-------~~~~-~~~~l~~la~~t~G~sg  104 (199)
                      ..+++|++|..  ...+++++++  |. ..+.|+.++.+++..+++..+..       ..+. ++.-+..|++.+.| ..
T Consensus       136 g~IiLI~aTTenp~~~l~~aL~S--R~-~v~~l~pLs~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La~~s~G-D~  211 (725)
T PRK13341        136 GTITLIGATTENPYFEVNKALVS--RS-RLFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVANG-DA  211 (725)
T ss_pred             ceEEEEEecCCChHhhhhhHhhc--cc-cceecCCCCHHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHHHhCCC-CH
Confidence            45677776643  3578999998  74 46899999999999999998862       2222 23346777876643 45


Q ss_pred             HHHHHHHHHHH
Q 039253          105 ADITEICQRAC  115 (199)
Q Consensus       105 aDI~~lv~~A~  115 (199)
                      +.+.++++.+.
T Consensus       212 R~lln~Le~a~  222 (725)
T PRK13341        212 RSLLNALELAV  222 (725)
T ss_pred             HHHHHHHHHHH
Confidence            55666666554

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=93.18  E-value=0.34  Score=42.44  Aligned_cols=78  Identities=21%  Similarity=0.296  Sum_probs=57.1

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCcccHHHHHh
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQ   97 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~l~~la~   97 (199)
                      ....|.||+.|+  ++..++++|..|++++.|.|.+++  |.. .+.|+.|+.++-.+.|....   ... ......++.
T Consensus       122 ~~AaNaLLKtLE--EPp~~t~fiL~t~~~~~lLpTIrS--RCq-~~~~~~~~~~~~~~~L~~~~---~~~-~~~a~~~~~  192 (334)
T PRK07993        122 DAAANALLKTLE--EPPENTWFFLACREPARLLATLRS--RCR-LHYLAPPPEQYALTWLSREV---TMS-QDALLAALR  192 (334)
T ss_pred             HHHHHHHHHHhc--CCCCCeEEEEEECChhhChHHHHh--ccc-cccCCCCCHHHHHHHHHHcc---CCC-HHHHHHHHH
Confidence            356899999999  466788999999999999999999  887 57999999888877775432   222 222445555


Q ss_pred             hCCCCCH
Q 039253           98 FTQGFSG  104 (199)
Q Consensus        98 ~t~G~sg  104 (199)
                      .+.|-.+
T Consensus       193 la~G~~~  199 (334)
T PRK07993        193 LSAGAPG  199 (334)
T ss_pred             HcCCCHH
Confidence            5655433

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=93.17  E-value=0.46  Score=41.41  Aligned_cols=81  Identities=17%  Similarity=0.225  Sum_probs=58.1

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCcccHHHHHh
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQ   97 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~l~~la~   97 (199)
                      ....|.||+.|+.  +..++++|.+|+.++.|.|.+++  |. ..+.|+.|+.++-...|...    ... ..+...++.
T Consensus       127 ~~AaNaLLKtLEE--Pp~~~~fiL~~~~~~~lLpTIrS--RC-q~i~~~~~~~~~~~~~L~~~----~~~-~~~a~~~~~  196 (319)
T PRK08769        127 RAACNALLKTLEE--PSPGRYLWLISAQPARLPATIRS--RC-QRLEFKLPPAHEALAWLLAQ----GVS-ERAAQEALD  196 (319)
T ss_pred             HHHHHHHHHHhhC--CCCCCeEEEEECChhhCchHHHh--hh-eEeeCCCcCHHHHHHHHHHc----CCC-hHHHHHHHH
Confidence            3567899999984  55678899999999999999999  87 45678889888777777642    222 223446677


Q ss_pred             hCCCCCHHHHH
Q 039253           98 FTQGFSGADIT  108 (199)
Q Consensus        98 ~t~G~sgaDI~  108 (199)
                      .+.|-.+.-+.
T Consensus       197 l~~G~p~~A~~  207 (319)
T PRK08769        197 AARGHPGLAAQ  207 (319)
T ss_pred             HcCCCHHHHHH
Confidence            77776554443

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.92  E-value=0.56  Score=44.51  Aligned_cols=89  Identities=18%  Similarity=0.178  Sum_probs=60.5

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHH
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLA   96 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la   96 (199)
                      ....+.||..|+.  ....+++|++|++++.+-+.+++  |. ..++|..|+.++-...+.....+.... ....+..|+
T Consensus       135 ~~a~naLLK~LEe--Pp~~tvfIL~t~~~~~llpTIrS--Rc-~~~~f~~l~~~ei~~~L~~ia~kegi~is~~al~~La  209 (620)
T PRK14948        135 TAAFNALLKTLEE--PPPRVVFVLATTDPQRVLPTIIS--RC-QRFDFRRIPLEAMVQHLSEIAEKESIEIEPEALTLVA  209 (620)
T ss_pred             HHHHHHHHHHHhc--CCcCeEEEEEeCChhhhhHHHHh--he-eEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Confidence            3467888999984  44567888888899999999998  77 567888888877777777666554332 233466777


Q ss_pred             hhCCCCCHHHHHHHHH
Q 039253           97 QFTQGFSGADITEICQ  112 (199)
Q Consensus        97 ~~t~G~sgaDI~~lv~  112 (199)
                      +.+.|- .+++.++++
T Consensus       210 ~~s~G~-lr~A~~lLe  224 (620)
T PRK14948        210 QRSQGG-LRDAESLLD  224 (620)
T ss_pred             HHcCCC-HHHHHHHHH
Confidence            777652 244433333

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=92.86  E-value=1.1  Score=44.18  Aligned_cols=104  Identities=18%  Similarity=0.245  Sum_probs=73.9

Q ss_pred             hHHHHHHHHHHhCCC---C------CCCEEEEEeeCCCCC-------------------------CCccccCCCccceEE
Q 039253           18 DRIPNQLLTEMDGLS---A------KKTIFVIGVTNRPDI-------------------------IDPALLRPGRLDQLI   63 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~---~------~~~VvvI~aTN~~~~-------------------------lD~al~R~gRfd~~i   63 (199)
                      ..+.+.||+.|+.=.   .      -.+.+||+|||....                         +.|.|+.  |+|..+
T Consensus       681 ~~v~~~Ll~~l~~g~l~d~~g~~vd~rn~iiI~TSn~g~~~~~~~~~~~~~~~~~~~~~~~~~~~F~pel~~--Rid~Ii  758 (852)
T TIGR03346       681 PDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNLGSQFIQELAGGDDYEEMREAVMEVLRAHFRPEFLN--RIDEIV  758 (852)
T ss_pred             HHHHHHHHHHHhcCceecCCCeEEecCCcEEEEeCCcchHhHhhhcccccHHHHHHHHHHHHHhhcCHHHhc--CcCeEE
Confidence            456788888886321   1      145789999998322                         3466776  999999


Q ss_pred             EecCCCHHHHHHHHHHhhcCC---------CCC-CcccHHHHHhhC--CCCCHHHHHHHHHHHHHHHHHHHH
Q 039253           64 YIPLPVEKSRLQIFKACLRKS---------PVS-KDVDLEKLAQFT--QGFSGADITEICQRACKDATREEI  123 (199)
Q Consensus        64 ~~~~P~~~~R~~il~~~l~~~---------~~~-~~~~l~~la~~t--~G~sgaDI~~lv~~A~~~a~~~~~  123 (199)
                      .|.+++.+....|+...+...         .+. ++-.+..|++..  ..+..+.|+.++++.....+.+.+
T Consensus       759 vF~PL~~e~l~~I~~l~L~~l~~~l~~~~~~l~i~~~a~~~L~~~~~~~~~gaR~L~~~i~~~i~~~l~~~~  830 (852)
T TIGR03346       759 VFHPLGREQIARIVEIQLGRLRKRLAERKITLELSDAALDFLAEAGYDPVYGARPLKRAIQREIENPLAKKI  830 (852)
T ss_pred             ecCCcCHHHHHHHHHHHHHHHHHHHHHCCCeecCCHHHHHHHHHhCCCCCCCchhHHHHHHHHHHHHHHHHH
Confidence            999999999999998887521         111 233356677653  367889999999998888777765

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.

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=92.82  E-value=0.25  Score=43.10  Aligned_cols=57  Identities=18%  Similarity=0.299  Sum_probs=48.3

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHH
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKA   79 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~   79 (199)
                      ....|.||+.|+  ++..++++|..|++++.|-|.+++  |.. .+.|+.|+.++..+.+..
T Consensus       122 ~~AaNaLLKtLE--EPp~~t~fiL~t~~~~~lLpTI~S--RCq-~~~~~~~~~~~~~~~L~~  178 (319)
T PRK06090        122 ESASNALLKTLE--EPAPNCLFLLVTHNQKRLLPTIVS--RCQ-QWVVTPPSTAQAMQWLKG  178 (319)
T ss_pred             HHHHHHHHHHhc--CCCCCeEEEEEECChhhChHHHHh--cce-eEeCCCCCHHHHHHHHHH
Confidence            356789999999  466778999999999999999999  875 788999999888877764

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.53  E-value=0.7  Score=43.87  Aligned_cols=87  Identities=17%  Similarity=0.099  Sum_probs=59.8

Q ss_pred             HHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhh
Q 039253           20 IPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQF   98 (199)
Q Consensus        20 ~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~   98 (199)
                      -.+.||..|+..  ...+++|++|+.+..|-+.+++  |. ..++|..|+.++-...++..+...... ++..+..|+..
T Consensus       143 a~naLLK~LEeP--p~~tv~IL~t~~~~kLl~TI~S--Rc-~~vef~~l~~~ei~~~L~~i~~~egi~I~~eal~~La~~  217 (620)
T PRK14954        143 AFNAFLKTLEEP--PPHAIFIFATTELHKIPATIAS--RC-QRFNFKRIPLDEIQSQLQMICRAEGIQIDADALQLIARK  217 (620)
T ss_pred             HHHHHHHHHhCC--CCCeEEEEEeCChhhhhHHHHh--hc-eEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            356777777743  3346667777888999999987  66 589999999998888888877655432 34456777777


Q ss_pred             CCCCCHHHHHHHHH
Q 039253           99 TQGFSGADITEICQ  112 (199)
Q Consensus        99 t~G~sgaDI~~lv~  112 (199)
                      +.| +.+++.+.++
T Consensus       218 s~G-dlr~al~eLe  230 (620)
T PRK14954        218 AQG-SMRDAQSILD  230 (620)
T ss_pred             hCC-CHHHHHHHHH
Confidence            765 4444444443

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=92.50  E-value=1.4  Score=41.61  Aligned_cols=64  Identities=19%  Similarity=0.218  Sum_probs=48.7

Q ss_pred             hhHHHHHHHHHHhCCC-----------CCCCEEEEEeeCCCC---CCCccccCCCccceEEEecC-CCHHHHHHHHHHhh
Q 039253           17 ADRIPNQLLTEMDGLS-----------AKKTIFVIGVTNRPD---IIDPALLRPGRLDQLIYIPL-PVEKSRLQIFKACL   81 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~-----------~~~~VvvI~aTN~~~---~lD~al~R~gRfd~~i~~~~-P~~~~R~~il~~~l   81 (199)
                      ...+.+.|+..|+.=.           ...++.||+|+|..+   .++++++.  ||..++.+.. |+.++|.+|++.++
T Consensus        97 ~~~~q~~Ll~al~~g~v~i~r~G~~~~~p~~f~lIAt~np~e~~g~L~~~Lld--Rf~l~v~~~~~~~~~er~eil~~~~  174 (589)
T TIGR02031        97 DDGLSNRLLQALDEGVVIVEREGISVVHPAKFALIATYDPAEGGGGLPDHLLD--RLALHVSLEDVASQDLRVEIVRRER  174 (589)
T ss_pred             CHHHHHHHHHHHHcCCeEEEECCCceeecCceEEEEecCCccccCCCCHHHHH--hccCeeecCCCCCHHHHHHHHHHHH
Confidence            3467788888886311           013578888888765   79999999  9999988875 57788999999877


Q ss_pred             c
Q 039253           82 R   82 (199)
Q Consensus        82 ~   82 (199)
                      .
T Consensus       175 ~  175 (589)
T TIGR02031       175 C  175 (589)
T ss_pred             H
Confidence            4

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.

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

Probab=92.44  E-value=0.95  Score=43.71  Aligned_cols=104  Identities=22%  Similarity=0.272  Sum_probs=75.6

Q ss_pred             hHHHHHHHHHHhCCC---------CCCCEEEEEeeCCCC-------------------------CCCccccCCCccceEE
Q 039253           18 DRIPNQLLTEMDGLS---------AKKTIFVIGVTNRPD-------------------------IIDPALLRPGRLDQLI   63 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~---------~~~~VvvI~aTN~~~-------------------------~lD~al~R~gRfd~~i   63 (199)
                      ..+.+.|++.||.-.         .-.++++|+|||...                         .+.|.|+.  |||.+|
T Consensus       567 ~~~~~~Ll~~ld~g~~~d~~g~~vd~~~~iii~Tsn~g~~~~~~~~~~f~~~~~~~~~~~~~~~~f~pef~~--Rid~Vi  644 (731)
T TIGR02639       567 PDIYNILLQVMDYATLTDNNGRKADFRNVILIMTSNAGASEMSKPPIGFGSENVESKSDKAIKKLFSPEFRN--RLDAII  644 (731)
T ss_pred             HHHHHHHHHhhccCeeecCCCcccCCCCCEEEECCCcchhhhhhccCCcchhhhHHHHHHHHHhhcChHHHh--cCCeEE
Confidence            457788898888531         113578999998742                         25677877  999999


Q ss_pred             EecCCCHHHHHHHHHHhhcCC---------CCC-CcccHHHHHhh--CCCCCHHHHHHHHHHHHHHHHHHHH
Q 039253           64 YIPLPVEKSRLQIFKACLRKS---------PVS-KDVDLEKLAQF--TQGFSGADITEICQRACKDATREEI  123 (199)
Q Consensus        64 ~~~~P~~~~R~~il~~~l~~~---------~~~-~~~~l~~la~~--t~G~sgaDI~~lv~~A~~~a~~~~~  123 (199)
                      .|.+.+.++..+|++..+...         .+. ++..+..|++.  ...|-.+.|+.+++.....++.+.+
T Consensus       645 ~F~pLs~e~l~~Iv~~~L~~l~~~l~~~~~~l~i~~~a~~~La~~~~~~~~GaR~l~r~i~~~~~~~l~~~~  716 (731)
T TIGR02639       645 HFNPLSEEVLEKIVQKFVDELSKQLNEKNIKLELTDDAKKYLAEKGYDEEFGARPLARVIQEEIKKPLSDEI  716 (731)
T ss_pred             EcCCCCHHHHHHHHHHHHHHHHHHHHhCCCeEEeCHHHHHHHHHhCCCcccCchHHHHHHHHHhHHHHHHHH
Confidence            999999999999999988532         111 23335667764  4567888999999888877776664

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=92.38  E-value=0.91  Score=39.00  Aligned_cols=78  Identities=14%  Similarity=0.222  Sum_probs=56.0

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCcccHHHHHh
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQ   97 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~l~~la~   97 (199)
                      ....|.||..|+.  +...+++|.+|+.++.+.+.+++  |. ..++|..|+.++-...++..+...   +...+..++.
T Consensus       107 ~~a~naLLK~LEe--pp~~t~~il~~~~~~~ll~TI~S--Rc-~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~~~l~~  178 (313)
T PRK05564        107 EQAQNAFLKTIEE--PPKGVFIILLCENLEQILDTIKS--RC-QIYKLNRLSKEEIEKFISYKYNDI---KEEEKKSAIA  178 (313)
T ss_pred             HHHHHHHHHHhcC--CCCCeEEEEEeCChHhCcHHHHh--hc-eeeeCCCcCHHHHHHHHHHHhcCC---CHHHHHHHHH
Confidence            3457889999984  45567777788889999999998  77 489999999988877777654321   1233556666


Q ss_pred             hCCCCC
Q 039253           98 FTQGFS  103 (199)
Q Consensus        98 ~t~G~s  103 (199)
                      .+.|-.
T Consensus       179 ~~~g~~  184 (313)
T PRK05564        179 FSDGIP  184 (313)
T ss_pred             HcCCCH
Confidence            666543

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=91.97  E-value=0.72  Score=40.03  Aligned_cols=81  Identities=21%  Similarity=0.297  Sum_probs=58.4

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCcccHHHHHhh
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQF   98 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~l~~la~~   98 (199)
                      ...|.||+.|+.-.   +.++|..|+.++.|-|.+++  |. ..+.|+.|+.++-.++|+........  +.+...++..
T Consensus       139 ~aaNaLLK~LEEPp---~~~fILi~~~~~~Ll~TI~S--Rc-q~i~f~~l~~~~~~~~L~~~~~~~~~--~~~~~~l~~~  210 (314)
T PRK07399        139 AAANALLKTLEEPG---NGTLILIAPSPESLLPTIVS--RC-QIIPFYRLSDEQLEQVLKRLGDEEIL--NINFPELLAL  210 (314)
T ss_pred             HHHHHHHHHHhCCC---CCeEEEEECChHhCcHHHHh--hc-eEEecCCCCHHHHHHHHHHhhccccc--hhHHHHHHHH
Confidence            45678999998643   44677888899999999999  86 78899999999999988876432211  2234677777


Q ss_pred             CCCCCHHHH
Q 039253           99 TQGFSGADI  107 (199)
Q Consensus        99 t~G~sgaDI  107 (199)
                      +.|-.+.-+
T Consensus       211 a~Gs~~~al  219 (314)
T PRK07399        211 AQGSPGAAI  219 (314)
T ss_pred             cCCCHHHHH
Confidence            766444333

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=91.89  E-value=0.97  Score=39.50  Aligned_cols=59  Identities=19%  Similarity=0.305  Sum_probs=48.7

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHh
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKAC   80 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~   80 (199)
                      .....|.||+.|+  ++..++++|.+|+.++.|.|.+++  |. ..+.|++|+.++-.+.|...
T Consensus       120 ~~~AaNaLLKtLE--EPp~~~~fiL~t~~~~~llpTI~S--RC-~~~~~~~~~~~~~~~~L~~~  178 (325)
T PRK06871        120 TEAAANALLKTLE--EPRPNTYFLLQADLSAALLPTIYS--RC-QTWLIHPPEEQQALDWLQAQ  178 (325)
T ss_pred             CHHHHHHHHHHhc--CCCCCeEEEEEECChHhCchHHHh--hc-eEEeCCCCCHHHHHHHHHHH
Confidence            3456789999999  466778999999999999999998  86 45688899888888777764

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=91.72  E-value=1.2  Score=39.41  Aligned_cols=80  Identities=16%  Similarity=0.201  Sum_probs=57.0

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCcccHHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLA   96 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~l~~la   96 (199)
                      .....|.||+.++.  +..++++|.+|+.++.+.+.+++  |. ..+.|+.|+.++-.+++.......   .+..+..++
T Consensus       154 ~~~aanaLLK~LEe--pp~~~~~IL~t~~~~~llpti~S--Rc-~~i~l~~l~~~~i~~~L~~~~~~~---~~~~~~~l~  225 (365)
T PRK07471        154 NANAANALLKVLEE--PPARSLFLLVSHAPARLLPTIRS--RC-RKLRLRPLAPEDVIDALAAAGPDL---PDDPRAALA  225 (365)
T ss_pred             CHHHHHHHHHHHhc--CCCCeEEEEEECCchhchHHhhc--cc-eEEECCCCCHHHHHHHHHHhcccC---CHHHHHHHH
Confidence            34567888888884  34566888899999999999887  76 678999999999988888764221   122235666


Q ss_pred             hhCCCCCH
Q 039253           97 QFTQGFSG  104 (199)
Q Consensus        97 ~~t~G~sg  104 (199)
                      ..+.|-.+
T Consensus       226 ~~s~Gsp~  233 (365)
T PRK07471        226 ALAEGSVG  233 (365)
T ss_pred             HHcCCCHH
Confidence            66665433

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=89.98  E-value=3.1  Score=39.55  Aligned_cols=63  Identities=22%  Similarity=0.330  Sum_probs=46.5

Q ss_pred             hhHHHHHHHHHHhCC----C-------CCCCEEEEEeeCCC-CCCCccccCCCccceEEEecCC-CHHHHHHHHHHhh
Q 039253           17 ADRIPNQLLTEMDGL----S-------AKKTIFVIGVTNRP-DIIDPALLRPGRLDQLIYIPLP-VEKSRLQIFKACL   81 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~----~-------~~~~VvvI~aTN~~-~~lD~al~R~gRfd~~i~~~~P-~~~~R~~il~~~l   81 (199)
                      ...+.+.|+..|+.=    .       ...++++|+|+|-. ..+.++++.  ||+.+|.++.| +.++|.++++..+
T Consensus       139 ~~~~q~~Ll~~le~g~~~v~r~g~~~~~~~~~~lIat~np~eg~l~~~L~d--R~~l~i~v~~~~~~~~~~~il~~~~  214 (633)
T TIGR02442       139 DDHLVDVLLDAAAMGVNRVEREGLSVSHPARFVLIGTMNPEEGDLRPQLLD--RFGLCVDVAAPRDPEERVEIIRRRL  214 (633)
T ss_pred             CHHHHHHHHHHHhcCCEEEEECCceeeecCCeEEEEecCCCCCCCCHHHHh--hcceEEEccCCCchHHHHHHHHHHH
Confidence            345678888888621    0       12358899988853 368899999  99999999987 4688889987654

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.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=89.33  E-value=0.53  Score=46.05  Aligned_cols=68  Identities=25%  Similarity=0.409  Sum_probs=50.8

Q ss_pred             CCCEEEEEeeCCCC-----CCCccccCCCccceEEEecCCCHHHHHHHHHHhhcC----CCCC-CcccHHHHHhhCCCCC
Q 039253           34 KKTIFVIGVTNRPD-----IIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRK----SPVS-KDVDLEKLAQFTQGFS  103 (199)
Q Consensus        34 ~~~VvvI~aTN~~~-----~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~----~~~~-~~~~l~~la~~t~G~s  103 (199)
                      +..+.+|++|+..+     ..|+++.|  ||.. |.++.|+.++...|++.....    ..+. ++..+..++..+.+|.
T Consensus       305 rg~l~~IgaTt~~ey~~~ie~D~aL~r--Rf~~-I~v~ep~~~e~~aILr~l~~~~e~~~~v~i~deal~~i~~ls~~yi  381 (821)
T CHL00095        305 RGELQCIGATTLDEYRKHIEKDPALER--RFQP-VYVGEPSVEETIEILFGLRSRYEKHHNLSISDKALEAAAKLSDQYI  381 (821)
T ss_pred             CCCcEEEEeCCHHHHHHHHhcCHHHHh--cceE-EecCCCCHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhccC
Confidence            56688999999764     58999999  9975 799999999999999866532    2221 3444777788887775


Q ss_pred             H
Q 039253          104 G  104 (199)
Q Consensus       104 g  104 (199)
                      +
T Consensus       382 ~  382 (821)
T CHL00095        382 A  382 (821)
T ss_pred             c
Confidence            4

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

Probab=89.30  E-value=1.5  Score=42.17  Aligned_cols=44  Identities=30%  Similarity=0.431  Sum_probs=38.4

Q ss_pred             CCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhh
Q 039253           35 KTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACL   81 (199)
Q Consensus        35 ~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l   81 (199)
                      ++|++|+|+|..+.||..++.  |++ .|+++==+..+..+|-+.||
T Consensus       465 S~VmFiaTANsl~tIP~PLlD--RME-iI~lsgYt~~EKl~IAk~~L  508 (782)
T COG0466         465 SKVMFIATANSLDTIPAPLLD--RME-VIRLSGYTEDEKLEIAKRHL  508 (782)
T ss_pred             hheEEEeecCccccCChHHhc--cee-eeeecCCChHHHHHHHHHhc
Confidence            579999999999999999999  884 56666668899999999988

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=89.24  E-value=0.91  Score=39.52  Aligned_cols=58  Identities=21%  Similarity=0.202  Sum_probs=45.8

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKA   79 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~   79 (199)
                      .....|.||+.|+.  +...+++|.+|+.+..|.+.+++  |. ..++|..|+.++-...|+.
T Consensus       123 ~~~a~NaLLK~LEE--Pp~~~~~Il~t~~~~~ll~TIrS--Rc-~~i~~~~~~~~~~~~~L~~  180 (329)
T PRK08058        123 TASAANSLLKFLEE--PSGGTTAILLTENKHQILPTILS--RC-QVVEFRPLPPESLIQRLQE  180 (329)
T ss_pred             CHHHHHHHHHHhcC--CCCCceEEEEeCChHhCcHHHHh--hc-eeeeCCCCCHHHHHHHHHH
Confidence            34467889999984  45567788899999999999998  76 5688888988887777754

>PRK06581 DNA polymerase III subunit delta'; Validated

Probab=88.94  E-value=1.2  Score=37.56  Aligned_cols=73  Identities=14%  Similarity=0.178  Sum_probs=55.0

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCcccHHHHHh
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQ   97 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~l~~la~   97 (199)
                      ....|.||+.|+  ++..++++|..|.+++.|.|.+++  |. ..+.|+.|....-.+.+..++......  ..+.-|.+
T Consensus       103 ~~AANALLKtLE--EPP~~t~fILit~~~~~LLpTIrS--RC-q~i~~~~p~~~~~~e~~~~~~~p~~~~--~~l~~i~~  175 (263)
T PRK06581        103 LNAANSCLKILE--DAPKNSYIFLITSRAASIISTIRS--RC-FKINVRSSILHAYNELYSQFIQPIADN--KTLDFINR  175 (263)
T ss_pred             HHHHHHHHHhhc--CCCCCeEEEEEeCChhhCchhHhh--ce-EEEeCCCCCHHHHHHHHHHhccccccc--HHHHHHHH
Confidence            356789999998  466778899999999999999998  86 567788898887778777777655432  33444444

>PRK08485 DNA polymerase III subunit delta'; Validated

Probab=88.81  E-value=0.93  Score=37.06  Aligned_cols=59  Identities=20%  Similarity=0.192  Sum_probs=46.7

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccce------------EEEecCCCHHHHHHHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQ------------LIYIPLPVEKSRLQIFKA   79 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~------------~i~~~~P~~~~R~~il~~   79 (199)
                      .....|.||..|+  ++..++++|..|..+..+.|.+++  |...            .+.+...+.++-.+.++.
T Consensus        67 ~~~A~NaLLK~LE--EPp~~~~fiL~t~~~~~llpTI~S--Rc~~~~~~~~~~~~~l~l~l~~l~~~~i~~~L~~  137 (206)
T PRK08485         67 GIEAQNALLKILE--EPPKNICFIIVAKSKNLLLPTIRS--RLIIEKRKQKKPVKPLDLDLKKLDLKDIYEFLKE  137 (206)
T ss_pred             CHHHHHHHHHHhc--CCCCCeEEEEEeCChHhCchHHHh--hheeccccccccccccccccCCCCHHHHHHHHHH
Confidence            3457899999999  466778899999999999999998  7654            466666777777777776

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=88.73  E-value=4  Score=35.15  Aligned_cols=55  Identities=22%  Similarity=0.370  Sum_probs=40.9

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHH
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFK   78 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~   78 (199)
                      ....|.||+.|+  ++..++++|..|+.++.|-|.+++  |. ..|.|+. +.+.-.+++.
T Consensus       118 ~~AaNaLLKtLE--EPp~~t~~iL~t~~~~~lLpTI~S--Rc-q~i~f~~-~~~~~~~~L~  172 (290)
T PRK07276        118 VNAANSLLKVIE--EPQSEIYIFLLTNDENKVLPTIKS--RT-QIFHFPK-NEAYLIQLLE  172 (290)
T ss_pred             HHHHHHHHHHhc--CCCCCeEEEEEECChhhCchHHHH--cc-eeeeCCC-cHHHHHHHHH
Confidence            356789999998  456678999999999999999999  87 4566654 4444444443

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=87.34  E-value=2.6  Score=36.91  Aligned_cols=79  Identities=11%  Similarity=0.057  Sum_probs=52.8

Q ss_pred             CCEEEEEeeCCCC------------CCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-Cccc---HHHHHhh
Q 039253           35 KTIFVIGVTNRPD------------IIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVD---LEKLAQF   98 (199)
Q Consensus        35 ~~VvvI~aTN~~~------------~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~---l~~la~~   98 (199)
                      ....||+|+|-.+            .+++|++.  ||-..+.+..|+.+.-.+|+.......... .+.-   +-.+|..
T Consensus       177 p~FrviAT~Np~g~Gd~~G~y~Gt~~l~~A~lD--RF~i~~~~~Yp~~e~E~~Il~~~~~~~~~~~~~~i~~~mV~la~~  254 (327)
T TIGR01650       177 PAFRLFATANTIGLGDTTGLYHGTQQINQAQMD--RWSIVTTLNYLEHDNEAAIVLAKAKGFDDTEGKDIINAMVRVADM  254 (327)
T ss_pred             CCeEEEEeeCCCCcCCCCcceeeeecCCHHHHh--heeeEeeCCCCCHHHHHHHHHhhccCCCccchHHHHHHHHHHHHH
Confidence            3577899999755            46899999  999999999999999999988765433210 0111   1222222


Q ss_pred             ----------CCCCCHHHHHHHHHHHH
Q 039253           99 ----------TQGFSGADITEICQRAC  115 (199)
Q Consensus        99 ----------t~G~sgaDI~~lv~~A~  115 (199)
                                +.|+|++.+....+.+.
T Consensus       255 tR~~~~~~~i~~~~SpR~li~w~~~~~  281 (327)
T TIGR01650       255 TRNAFINGDISTVMSPRTVITWAENAE  281 (327)
T ss_pred             HHhhhccCCccccccHHHHHHHHHHHH
Confidence                      34567777777766543

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=87.20  E-value=4.6  Score=39.83  Aligned_cols=103  Identities=14%  Similarity=0.134  Sum_probs=71.7

Q ss_pred             hHHHHHHHHHHhCCC---C------CCCEEEEEeeCCCC-----------------------------CCCccccCCCcc
Q 039253           18 DRIPNQLLTEMDGLS---A------KKTIFVIGVTNRPD-----------------------------IIDPALLRPGRL   59 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~---~------~~~VvvI~aTN~~~-----------------------------~lD~al~R~gRf   59 (199)
                      ..+.+.|++.||.-.   +      -.+.++|+|||...                             .+.|+|+.  |+
T Consensus       682 ~~v~~~Llq~ld~g~l~d~~Gr~vd~~n~iiI~TSNlg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PEfln--Ri  759 (852)
T TIGR03345       682 PDVLELFYQVFDKGVMEDGEGREIDFKNTVILLTSNAGSDLIMALCADPETAPDPEALLEALRPELLKVFKPAFLG--RM  759 (852)
T ss_pred             HHHHHHHHHHhhcceeecCCCcEEeccccEEEEeCCCchHHHHHhccCcccCcchHHHHHHHHHHHHHhccHHHhc--ce
Confidence            356778888887431   0      14689999999521                             15677787  99


Q ss_pred             ceEEEecCCCHHHHHHHHHHhhcCC--------CCC---CcccHHHHHhhCCC--CCHHHHHHHHHHHHHHHHHHHH
Q 039253           60 DQLIYIPLPVEKSRLQIFKACLRKS--------PVS---KDVDLEKLAQFTQG--FSGADITEICQRACKDATREEI  123 (199)
Q Consensus        60 d~~i~~~~P~~~~R~~il~~~l~~~--------~~~---~~~~l~~la~~t~G--~sgaDI~~lv~~A~~~a~~~~~  123 (199)
                      + .|.|.+.+.++-..|+...+...        .+.   ++.-+..|++...+  |-++.|+.+++.-...++.+.+
T Consensus       760 ~-iI~F~pLs~e~l~~Iv~~~L~~l~~rl~~~~gi~l~i~d~a~~~La~~g~~~~~GAR~L~r~Ie~~i~~~la~~~  835 (852)
T TIGR03345       760 T-VIPYLPLDDDVLAAIVRLKLDRIARRLKENHGAELVYSEALVEHIVARCTEVESGARNIDAILNQTLLPELSRQI  835 (852)
T ss_pred             e-EEEeCCCCHHHHHHHHHHHHHHHHHHHHHhcCceEEECHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence            7 88999999999999998887532        221   22335667776643  6788899998887777766654

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=86.68  E-value=4.8  Score=39.74  Aligned_cols=104  Identities=17%  Similarity=0.210  Sum_probs=69.4

Q ss_pred             hHHHHHHHHHHhCC--C-C------CCCEEEEEeeCCC-------------------------CCCCccccCCCccceEE
Q 039253           18 DRIPNQLLTEMDGL--S-A------KKTIFVIGVTNRP-------------------------DIIDPALLRPGRLDQLI   63 (199)
Q Consensus        18 ~r~~~~lL~~ld~~--~-~------~~~VvvI~aTN~~-------------------------~~lD~al~R~gRfd~~i   63 (199)
                      ..+.+.|++.|+.-  . +      -.+.++|+|||..                         ..+.|+|+.  |+|..+
T Consensus       684 ~~v~~~Ll~ile~g~l~d~~gr~vd~rn~iiI~TSN~g~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PELln--Rld~ii  761 (857)
T PRK10865        684 PDVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNLGSDLIQERFGELDYAHMKELVLGVVSHNFRPEFIN--RIDEVV  761 (857)
T ss_pred             HHHHHHHHHHHhhCceecCCceEEeecccEEEEeCCcchHHHHHhccccchHHHHHHHHHHHcccccHHHHH--hCCeeE
Confidence            35677888888632  1 1      1346889999973                         134578888  999999


Q ss_pred             EecCCCHHHHHHHHHHhhcCC-------CCC---CcccHHHHHhhC--CCCCHHHHHHHHHHHHHHHHHHHH
Q 039253           64 YIPLPVEKSRLQIFKACLRKS-------PVS---KDVDLEKLAQFT--QGFSGADITEICQRACKDATREEI  123 (199)
Q Consensus        64 ~~~~P~~~~R~~il~~~l~~~-------~~~---~~~~l~~la~~t--~G~sgaDI~~lv~~A~~~a~~~~~  123 (199)
                      .|.+++.+.-..|++.++...       ...   ++--+..|+...  .-|-.+.|+.+++.-....+.+.+
T Consensus       762 vF~PL~~edl~~Iv~~~L~~l~~rl~~~gi~l~is~~al~~L~~~gy~~~~GARpL~r~I~~~i~~~la~~i  833 (857)
T PRK10865        762 VFHPLGEQHIASIAQIQLQRLYKRLEERGYEIHISDEALKLLSENGYDPVYGARPLKRAIQQQIENPLAQQI  833 (857)
T ss_pred             ecCCCCHHHHHHHHHHHHHHHHHHHHhCCCcCcCCHHHHHHHHHcCCCccCChHHHHHHHHHHHHHHHHHHH
Confidence            999999999999998888542       111   222244455432  234467888888887777666554

>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=86.44  E-value=1.7  Score=36.25  Aligned_cols=93  Identities=17%  Similarity=0.244  Sum_probs=62.7

Q ss_pred             hhHHHHHHHHHHhCCC-----C-----------CCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHh
Q 039253           17 ADRIPNQLLTEMDGLS-----A-----------KKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKAC   80 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~-----~-----------~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~   80 (199)
                      .+..-..|+..|++..     +           -.+.-+|+||++...|.+.++.  ||.....+..=+.++-..|++..
T Consensus       114 nk~~qe~LlpamEd~~idiiiG~g~~ar~~~~~l~~FTligATTr~g~ls~pLrd--RFgi~~~l~~Y~~~el~~Iv~r~  191 (233)
T PF05496_consen  114 NKAQQEILLPAMEDGKIDIIIGKGPNARSIRINLPPFTLIGATTRAGLLSSPLRD--RFGIVLRLEFYSEEELAKIVKRS  191 (233)
T ss_dssp             -HHHHHHHHHHHHCSEEEEEBSSSSS-BEEEEE----EEEEEESSGCCTSHCCCT--TSSEEEE----THHHHHHHHHHC
T ss_pred             cHHHHHHHHHHhccCeEEEEeccccccceeeccCCCceEeeeeccccccchhHHh--hcceecchhcCCHHHHHHHHHHH
Confidence            3344556777787651     1           1346899999999999999999  99999999988999999999988


Q ss_pred             hcCCCCC-CcccHHHHHhhCCCCCHHHHHHHHH
Q 039253           81 LRKSPVS-KDVDLEKLAQFTQGFSGADITEICQ  112 (199)
Q Consensus        81 l~~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~  112 (199)
                      ...+.+. .+.....||.++.| +++--..+++
T Consensus       192 a~~l~i~i~~~~~~~Ia~rsrG-tPRiAnrll~  223 (233)
T PF05496_consen  192 ARILNIEIDEDAAEEIARRSRG-TPRIANRLLR  223 (233)
T ss_dssp             CHCTT-EE-HHHHHHHHHCTTT-SHHHHHHHHH
T ss_pred             HHHhCCCcCHHHHHHHHHhcCC-ChHHHHHHHH
Confidence            8777665 34457788998887 4544444433

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.

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

Probab=86.27  E-value=5.2  Score=35.51  Aligned_cols=107  Identities=22%  Similarity=0.290  Sum_probs=66.2

Q ss_pred             CCCEEEEEeeCCC---CCCCccccCCCccc-eEEEecCCCHHHHHHHHHHhhcCC---CCCCcccHHHHHh---hCCCCC
Q 039253           34 KKTIFVIGVTNRP---DIIDPALLRPGRLD-QLIYIPLPVEKSRLQIFKACLRKS---PVSKDVDLEKLAQ---FTQGFS  103 (199)
Q Consensus        34 ~~~VvvI~aTN~~---~~lD~al~R~gRfd-~~i~~~~P~~~~R~~il~~~l~~~---~~~~~~~l~~la~---~t~G~s  103 (199)
                      ..+|.+|+.+|..   +.+|+-+.+  +|. .+|.|++=+.+|-..|++......   ..-.+--++.+|.   ...| .
T Consensus       154 ~~~v~vi~i~n~~~~~~~ld~rv~s--~l~~~~I~F~pY~a~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~G-D  230 (366)
T COG1474         154 KVKVSIIAVSNDDKFLDYLDPRVKS--SLGPSEIVFPPYTAEELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESG-D  230 (366)
T ss_pred             ceeEEEEEEeccHHHHHHhhhhhhh--ccCcceeeeCCCCHHHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCc-c
Confidence            4568999999985   588999987  554 346777779999999998887532   1112223444443   3333 3


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcccccc
Q 039253          104 GADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQS  162 (199)
Q Consensus       104 gaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps~~  162 (199)
                      .+---.+|+.|+..|-++..                   ..++.++...|...+.+...
T Consensus       231 AR~aidilr~A~eiAe~~~~-------------------~~v~~~~v~~a~~~~~~~~~  270 (366)
T COG1474         231 ARKAIDILRRAGEIAEREGS-------------------RKVSEDHVREAQEEIERDVL  270 (366)
T ss_pred             HHHHHHHHHHHHHHHHhhCC-------------------CCcCHHHHHHHHHHhhHHHH
Confidence            33444567777777665542                   44566666666554444433

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

Probab=85.45  E-value=1.8  Score=39.64  Aligned_cols=30  Identities=37%  Similarity=0.635  Sum_probs=25.0

Q ss_pred             CCEEEEEeeCCCC----CCCccccCCCccceEEEecC
Q 039253           35 KTIFVIGVTNRPD----IIDPALLRPGRLDQLIYIPL   67 (199)
Q Consensus        35 ~~VvvI~aTN~~~----~lD~al~R~gRfd~~i~~~~   67 (199)
                      .++.||+|+|..+    .+|.|++|  ||.. |++.+
T Consensus       324 ~Nl~IIgTMNt~Drs~~~lD~AlrR--RF~f-i~i~p  357 (459)
T PRK11331        324 ENVYIIGLMNTADRSLAVVDYALRR--RFSF-IDIEP  357 (459)
T ss_pred             CCeEEEEecCccccchhhccHHHHh--hhhe-EEecC
Confidence            5799999999988    89999999  9955 55543

>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=84.82  E-value=2.1  Score=30.70  Aligned_cols=45  Identities=44%  Similarity=0.617  Sum_probs=34.1

Q ss_pred             HHHHHHHHHhCCCC----CCCEEEEEeeCCCC--CCCccccCCCccceEEEec
Q 039253           20 IPNQLLTEMDGLSA----KKTIFVIGVTNRPD--IIDPALLRPGRLDQLIYIP   66 (199)
Q Consensus        20 ~~~~lL~~ld~~~~----~~~VvvI~aTN~~~--~lD~al~R~gRfd~~i~~~   66 (199)
                      ....++..|..+..    ..++.+|++||...  .+++.+..  ||+.+++++
T Consensus       100 ~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~~~~~~~~~~~--r~~~~i~~~  150 (151)
T cd00009         100 AQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYD--RLDIRIVIP  150 (151)
T ss_pred             HHHHHHHHHHhcCceeccCCCeEEEEecCccccCCcChhHHh--hhccEeecC
Confidence            44566666766543    36788999999877  78888888  999888776

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.

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

Probab=84.43  E-value=5.4  Score=35.71  Aligned_cols=98  Identities=22%  Similarity=0.196  Sum_probs=66.2

Q ss_pred             EEEEeeCC------------CCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhhCCCCCH
Q 039253           38 FVIGVTNR------------PDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSG  104 (199)
Q Consensus        38 vvI~aTN~------------~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~t~G~sg  104 (199)
                      ++|+|||+            |.-||..++.  |+- .|...+=+.++-++|++.-.+...+. ++-.++.|+....--|-
T Consensus       322 Iii~AtNRG~~kiRGTd~~sPhGIP~DlLD--Rll-II~t~py~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSL  398 (450)
T COG1224         322 IIILATNRGMTKIRGTDIESPHGIPLDLLD--RLL-IISTRPYSREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSL  398 (450)
T ss_pred             EEEEEcCCceeeecccCCcCCCCCCHhhhh--hee-EEecCCCCHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhH
Confidence            67788884            7778888887  652 22222337889999999888765444 45567788887776666


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhc
Q 039253          105 ADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYA  157 (199)
Q Consensus       105 aDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~  157 (199)
                      +---+|+.-|...|.++..                   ..|..+|++.|-.-+
T Consensus       399 RYa~qLL~pa~iiA~~rg~-------------------~~V~~~dVe~a~~lF  432 (450)
T COG1224         399 RYAVQLLTPASIIAKRRGS-------------------KRVEVEDVERAKELF  432 (450)
T ss_pred             HHHHHhccHHHHHHHHhCC-------------------CeeehhHHHHHHHHH
Confidence            6666777777666666542                   457777777776554

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

Probab=84.32  E-value=1.7  Score=42.02  Aligned_cols=45  Identities=27%  Similarity=0.397  Sum_probs=36.8

Q ss_pred             CCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhc
Q 039253           35 KTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR   82 (199)
Q Consensus        35 ~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~   82 (199)
                      ++|++|+|+|..+.||++++.  |+. .|+++==..++...|-+.||-
T Consensus       553 SkVLFicTAN~idtIP~pLlD--RME-vIelsGYv~eEKv~IA~~yLi  597 (906)
T KOG2004|consen  553 SKVLFICTANVIDTIPPPLLD--RME-VIELSGYVAEEKVKIAERYLI  597 (906)
T ss_pred             hheEEEEeccccccCChhhhh--hhh-eeeccCccHHHHHHHHHHhhh
Confidence            579999999999999999998  874 455544466888999988883

>CHL00095 clpC Clp protease ATP binding subunit

Probab=83.99  E-value=11  Score=37.03  Aligned_cols=105  Identities=20%  Similarity=0.208  Sum_probs=72.2

Q ss_pred             hhHHHHHHHHHHhCCC---------CCCCEEEEEeeCCCCC-------------------------------------CC
Q 039253           17 ADRIPNQLLTEMDGLS---------AKKTIFVIGVTNRPDI-------------------------------------ID   50 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~---------~~~~VvvI~aTN~~~~-------------------------------------lD   50 (199)
                      ...+.+.|++.|+.-.         .-.++++|+|||....                                     +.
T Consensus       624 ~~~v~~~Llq~le~g~~~d~~g~~v~~~~~i~I~Tsn~g~~~i~~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~f~  703 (821)
T CHL00095        624 HPDIFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTSNLGSKVIETNSGGLGFELSENQLSEKQYKRLSNLVNEELKQFFR  703 (821)
T ss_pred             CHHHHHHHHHHhccCceecCCCcEEecCceEEEEeCCcchHHHHhhccccCCcccccccccccHHHHHHHHHHHHHHhcC
Confidence            3457888998888521         1246899999996421                                     23


Q ss_pred             ccccCCCccceEEEecCCCHHHHHHHHHHhhcCC-------C--CC-CcccHHHHHhh--CCCCCHHHHHHHHHHHHHHH
Q 039253           51 PALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKS-------P--VS-KDVDLEKLAQF--TQGFSGADITEICQRACKDA  118 (199)
Q Consensus        51 ~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~-------~--~~-~~~~l~~la~~--t~G~sgaDI~~lv~~A~~~a  118 (199)
                      |.|+.  |+|.+|.|.+.+.++-..|++..+...       .  +. .+--...|++.  ...|-++-|+.+++.-...+
T Consensus       704 pefln--Rid~ii~F~pL~~~~l~~Iv~~~l~~l~~rl~~~~i~l~~~~~~~~~La~~~~~~~~GAR~l~r~i~~~i~~~  781 (821)
T CHL00095        704 PEFLN--RLDEIIVFRQLTKNDVWEIAEIMLKNLFKRLNEQGIQLEVTERIKTLLIEEGYNPLYGARPLRRAIMRLLEDP  781 (821)
T ss_pred             HHHhc--cCCeEEEeCCCCHHHHHHHHHHHHHHHHHHHHHCCcEEEECHHHHHHHHHhcCCCCCChhhHHHHHHHHHHHH
Confidence            56777  999999999999999999998887532       1  11 22235567765  23566788888888777666


Q ss_pred             HHHHH
Q 039253          119 TREEI  123 (199)
Q Consensus       119 ~~~~~  123 (199)
                      +.+.+
T Consensus       782 l~~~~  786 (821)
T CHL00095        782 LAEEV  786 (821)
T ss_pred             HHHHH
Confidence            66554

>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=83.35  E-value=2.3  Score=33.00  Aligned_cols=39  Identities=26%  Similarity=0.455  Sum_probs=31.4

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCcc
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRL   59 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRf   59 (199)
                      .....|.||..|+  ++..++++|.+|+.++.|-+.+++  |.
T Consensus       115 ~~~a~NaLLK~LE--epp~~~~fiL~t~~~~~il~TI~S--Rc  153 (162)
T PF13177_consen  115 TEEAQNALLKTLE--EPPENTYFILITNNPSKILPTIRS--RC  153 (162)
T ss_dssp             -HHHHHHHHHHHH--STTTTEEEEEEES-GGGS-HHHHT--TS
T ss_pred             hHHHHHHHHHHhc--CCCCCEEEEEEECChHHChHHHHh--hc
Confidence            4567899999999  455788999999999999999998  76

...

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

Probab=82.60  E-value=6.5  Score=33.37  Aligned_cols=67  Identities=10%  Similarity=0.162  Sum_probs=51.9

Q ss_pred             HHHHHHHHhCC-C-CCCCEEEEEeeCCCCCCCcccc-C-------------------CCccceEEEecCCCHHHHHHHHH
Q 039253           21 PNQLLTEMDGL-S-AKKTIFVIGVTNRPDIIDPALL-R-------------------PGRLDQLIYIPLPVEKSRLQIFK   78 (199)
Q Consensus        21 ~~~lL~~ld~~-~-~~~~VvvI~aTN~~~~lD~al~-R-------------------~gRfd~~i~~~~P~~~~R~~il~   78 (199)
                      -..|...|||= . ...+|++-+|+|+-..|+.-+. +                   +.||.-.+.|..|+.++-..|+.
T Consensus       157 yK~LKs~LeG~ve~rP~NVl~YATSNRRHLl~e~~~dn~~~~~eih~~eaveEKlSlSDRFGLwL~F~~~~Q~~YL~~V~  236 (287)
T COG2607         157 YKALKSALEGGVEGRPANVLFYATSNRRHLLPEDMKDNEGSTGEIHPSEAVEEKLSLSDRFGLWLSFYPCDQDEYLKIVD  236 (287)
T ss_pred             HHHHHHHhcCCcccCCCeEEEEEecCCcccccHhhhhCCCcccccChhHHHHHhhchhhhcceeecccCCCHHHHHHHHH
Confidence            34555666654 2 2357999999999888885433 1                   34899999999999999999999


Q ss_pred             HhhcCCCCC
Q 039253           79 ACLRKSPVS   87 (199)
Q Consensus        79 ~~l~~~~~~   87 (199)
                      ++.+++.+.
T Consensus       237 ~~a~~~~l~  245 (287)
T COG2607         237 HYAKHFGLD  245 (287)
T ss_pred             HHHHHcCCC
Confidence            999988776

>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]

Probab=81.81  E-value=4.7  Score=38.55  Aligned_cols=104  Identities=17%  Similarity=0.165  Sum_probs=67.5

Q ss_pred             CEEEEEeeCC-----CCCCCccccCCCccceEEEe--cCC-CHHHHHHHHHHhhcCC------CCCCcccHHHHH----h
Q 039253           36 TIFVIGVTNR-----PDIIDPALLRPGRLDQLIYI--PLP-VEKSRLQIFKACLRKS------PVSKDVDLEKLA----Q   97 (199)
Q Consensus        36 ~VvvI~aTN~-----~~~lD~al~R~gRfd~~i~~--~~P-~~~~R~~il~~~l~~~------~~~~~~~l~~la----~   97 (199)
                      ...+|++.|+     ...+|+.++.  -|....++  ++| +.+.|..+|+.+.+..      +.-..--+.+|.    +
T Consensus       276 d~klI~~Gn~~~l~~l~~~~~~r~~--g~~y~ae~~~~m~~~~~nr~k~~~~~~q~v~~d~~ip~~~~~Av~~li~~a~R  353 (647)
T COG1067         276 DLKLILAGNREDLEDLHEPDRSRIE--GFGYEAEFEDTMPITDANRSKLVQFYVQELARDGNIPHLDKDAVEELIREAAR  353 (647)
T ss_pred             ceEEEeeCCHHHHHhhcccCHHHHh--hcceEEEEcCCCCCChHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            4677777775     3445555555  45444555  467 7799999999988643      221112233322    2


Q ss_pred             hC-----CCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcccc
Q 039253           98 FT-----QGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKS  160 (199)
Q Consensus        98 ~t-----~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps  160 (199)
                      .+     --.+++||.++++.|...|..+..                   ..++.+|++.|++..++.
T Consensus       354 ~Ag~~~~Ltl~~rdl~~lv~~A~~ia~~~~~-------------------~~I~ae~Ve~a~~~~~~~  402 (647)
T COG1067         354 RAGDQNKLTLRLRDLGNLVREAGDIAVSEGR-------------------KLITAEDVEEALQKRELR  402 (647)
T ss_pred             hccccceeccCHHHHHHHHHHhhHHHhcCCc-------------------ccCcHHHHHHHHHhhhhH
Confidence            22     126899999999998887766532                   458999999999986654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	199
1r7r_A	816	The Crystal Structure Of Murine P97VCP AT 3.6A Leng		1e-48
3cf1_A	806	Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Len		1e-48
3cf0_A	301	Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH		6e-48
3h4m_A	285	Aaa Atpase Domain Of The Proteasome- Activating Nuc		1e-24
2x8a_A	274	Human Nuclear Valosin Containing Protein Like (Nvl)		4e-24
1lv7_A	257	Crystal Structure Of The Aaa Domain Of Ftsh Length		4e-24
2ce7_A	476	Edta Treated Length = 476		6e-23
3kds_E	465	Apo-ftsh Crystal Structure Length = 465		7e-23
2dhr_A	499	Whole Cytosolic Region Of Atp-Dependent Metalloprot		6e-22
4eiw_A	508	Whole Cytosolic Region Of Atp-Dependent Metalloprot		7e-22
1iy2_A	278	Crystal Structure Of The Ftsh Atpase Domain From Th		1e-21
1ixz_A	254	Crystal Structure Of The Ftsh Atpase Domain From Th		1e-21
2qz4_A	262	Human Paraplegin, Aaa Domain In Complex With Adp Le		3e-20
2r62_A	268	Crystal Structure Of Helicobacter Pylori Atp Depend		2e-18
3hu3_A	489	Structure Of P97 N-D1 R155h Mutant In Complex With		3e-18
3hu2_A	489	Structure Of P97 N-D1 R86a Mutant In Complex With A		3e-18
3hu1_A	489	Structure Of P97 N-D1 R95g Mutant In Complex With A		3e-18
1e32_A	458	Structure Of The N-Terminal Domain And The D1 Aaa D		3e-18
4b4t_J	405	Near-Atomic Resolution Structural Model Of The Yeas		6e-18
4b4t_L	437	Near-Atomic Resolution Structural Model Of The Yeas		6e-18
4b4t_M	434	Near-Atomic Resolution Structural Model Of The Yeas		6e-16
4b4t_K	428	Near-Atomic Resolution Structural Model Of The Yeas		3e-13
4b4t_H	467	Near-Atomic Resolution Structural Model Of The Yeas		4e-13
3d8b_A	357	Crystal Structure Of Human Fidgetin-Like Protein 1		4e-13
3vfd_A	389	Human Spastin Aaa Domain Length = 389		2e-12
4b4t_I	437	Near-Atomic Resolution Structural Model Of The Yeas		1e-11
2zam_A	444	Crystal Structure Of Mouse Skd1VPS4B APO-Form Lengt		6e-11
2qp9_X	355	Crystal Structure Of S.Cerevisiae Vps4 Length = 355		9e-11
1xwi_A	322	Crystal Structure Of Vps4b Length = 322		1e-10
3eih_A	340	Crystal Structure Of S.Cerevisiae Vps4 In The Prese		1e-10
2rko_A	331	Crystal Structure Of The Vps4p-Dimer Length = 331		1e-10
3eie_A	322	Crystal Structure Of S.Cerevisiae Vps4 In The So4-B		1e-10
3b9p_A	297	Spastin Length = 297		3e-10
3kw6_A	78	Crystal Structure Of A Domain Of 26s Proteasome Reg		1e-04
2krk_A	86	Solution Nmr Structure Of 26s Protease Regulatory S		3e-04

>pdb|1R7R|A Chain A, The Crystal Structure Of Murine P97VCP AT 3.6A Length = 816

Iteration: 1
 Score =  189 bits (479), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 109/174 (62%), Positives = 130/174 (74%), Gaps = 23/174 (13%)
Query: 16  AADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQ 75
           AADR+ NQ+LTEMDG+S KK +F+IG TNRPDIIDPA+LRPGRLDQLIYIPLP EKSR+ 
Sbjct: 596 AADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVA 655
Query: 76  IFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQ- 134
           I KA LRKSPV+KDVDLE LA+ T GFSGAD+TEICQRACK A RE IE++IRR + +Q 
Sbjct: 656 ILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQT 715
Query: 135 -PEAIE----DEVAEIKAEHFEESMKYACKS-----------------QSRGFG 166
            P A+E    D V EI+ +HFEE+M++A +S                 QSRGFG
Sbjct: 716 NPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFG 769

>pdb|3CF1|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Length = 806

Iteration: 1
 Score =  188 bits (478), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 109/174 (62%), Positives = 130/174 (74%), Gaps = 23/174 (13%)
Query: 16  AADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQ 75
           AADR+ NQ+LTEMDG+S KK +F+IG TNRPDIIDPA+LRPGRLDQLIYIPLP EKSR+ 
Sbjct: 596 AADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVA 655
Query: 76  IFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQ- 134
           I KA LRKSPV+KDVDLE LA+ T GFSGAD+TEICQRACK A RE IE++IRR + +Q 
Sbjct: 656 ILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQT 715
Query: 135 -PEAIE----DEVAEIKAEHFEESMKYACKS-----------------QSRGFG 166
            P A+E    D V EI+ +HFEE+M++A +S                 QSRGFG
Sbjct: 716 NPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFG 769

>pdb|3CF0|A Chain A, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP Length = 301

Iteration: 1
 Score =  186 bits (473), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 104/153 (67%), Positives = 125/153 (81%), Gaps = 6/153 (3%)
Query: 16  AADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQ 75
           AADR+ NQ+LTEMDG+S KK +F+IG TNRPDIIDPA+LRPGRLDQLIYIPLP EKSR+ 
Sbjct: 134 AADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVA 193
Query: 76  IFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQ- 134
           I KA LRKSPV+KDVDLE LA+ T GFSGAD+TEICQRACK A RE IE++IRR + +Q 
Sbjct: 194 ILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQT 253
Query: 135 -PEAIE----DEVAEIKAEHFEESMKYACKSQS 162
            P A+E    D V EI+ +HFEE+M++A +S S
Sbjct: 254 NPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVS 286

>pdb|3H4M|A Chain A, Aaa Atpase Domain Of The Proteasome- Activating Nucleotidase Length = 285

Iteration: 1
 Score =  108 bits (271), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 53/111 (47%), Positives = 74/111 (66%)
Query: 11  SGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVE 70
           +G      R   QLL EMDG  A+  + +IG TNRPDI+DPA+LRPGR D++I +P P E
Sbjct: 131 TGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDE 190
Query: 71  KSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           K RL+I K   RK  +++DV+LE++A+ T+G  GA++  IC  A  +A RE
Sbjct: 191 KGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAELKAICTEAGMNAIRE 241

>pdb|2X8A|A Chain A, Human Nuclear Valosin Containing Protein Like (Nvl), C- Terminal Aaa-Atpase Domain Length = 274

Iteration: 1
 Score =  107 bits (268), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 64/156 (41%), Positives = 96/156 (61%), Gaps = 17/156 (10%)
Query: 15  GAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRL 74
           GA+ R+ NQLLTEMDGL A++ +F++  TNRPDIIDPA+LRPGRLD+ +++ LP    RL
Sbjct: 125 GASVRVVNQLLTEMDGLEARQQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRL 184
Query: 75  QIFKACLR---KSPVSKDVDLEKLAQFTQ--GFSGADITEICQRACKDATREEIENDIRR 129
            I K   +   K P+  DV+LE +A   +   ++GAD++ + + A   A R+E+    R+
Sbjct: 185 AILKTITKNGTKPPLDADVNLEAIAGDLRCDCYTGADLSALVREASICALRQEMA---RQ 241
Query: 130 RKGKQPEAIEDEVAEIKA--EHFEESMKYACKSQSR 163
           + G       +E  E+K   +HFEE+ K    S S+
Sbjct: 242 KSG-------NEKGELKVSHKHFEEAFKKVRSSISK 270

>pdb|1LV7|A Chain A, Crystal Structure Of The Aaa Domain Of Ftsh Length = 257

Iteration: 1
 Score =  107 bits (267), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 53/116 (45%), Positives = 72/116 (62%), Gaps = 3/116 (2%)
Query: 8   QRGSGAGGAAD---RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIY 64
           QRG+G GG  D   +  NQ+L EMDG    + I VI  TNRPD++DPALLRPGR D+ + 
Sbjct: 119 QRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVV 178
Query: 65  IPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           + LP  + R QI K  +R+ P++ D+D   +A+ T GFSGAD+  +   A   A R
Sbjct: 179 VGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAAR 234

>pdb|2CE7|A Chain A, Edta Treated Length = 476

Iteration: 1
 Score =  103 bits (257), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 54/117 (46%), Positives = 72/117 (61%), Gaps = 3/117 (2%)
Query: 8   QRGSGAGGAAD---RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIY 64
            RG+G GG  D   +  NQLL EMDG  +K+ I V+  TNRPDI+DPALLRPGR D+ I 
Sbjct: 123 HRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPGRFDKKIV 182
Query: 65  IPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           +  P    R +I +   R  P+++DV+LE +A+ T GF GAD+  +   A   A RE
Sbjct: 183 VDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAKRTPGFVGADLENLVNEAALLAARE 239

>pdb|3KDS|E Chain E, Apo-ftsh Crystal Structure Length = 465

Iteration: 1
 Score =  103 bits (257), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 54/117 (46%), Positives = 72/117 (61%), Gaps = 3/117 (2%)
Query: 8   QRGSGAGGAAD---RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIY 64
            RG+G GG  D   +  NQLL EMDG  +K+ I V+  TNRPDI+DPALLRPGR D+ I 
Sbjct: 123 HRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPGRFDKKIV 182
Query: 65  IPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           +  P    R +I +   R  P+++DV+LE +A+ T GF GAD+  +   A   A RE
Sbjct: 183 VDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAKRTPGFVGADLENLVNEAALLAARE 239

>pdb|2DHR|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 499

Iteration: 1
 Score =  100 bits (248), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 54/102 (52%), Positives = 64/102 (62%), Gaps = 3/102 (2%)
Query: 8   QRGSGAGGAAD---RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIY 64
           +RGSG GG  D   +  NQLL EMDG      I V+  TNRPDI+DPALLRPGR D+ I 
Sbjct: 138 KRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIA 197
Query: 65  IPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGAD 106
           I  P  K R QI +   R  P+++DVDL  LA+ T GF GAD
Sbjct: 198 IDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGAD 239

>pdb|4EIW|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 508

Iteration: 1
 Score =  100 bits (248), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 54/102 (52%), Positives = 64/102 (62%), Gaps = 3/102 (2%)
Query: 8   QRGSGAGGAAD---RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIY 64
           +RGSG GG  D   +  NQLL EMDG      I V+  TNRPDI+DPALLRPGR D+ I 
Sbjct: 147 KRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIA 206
Query: 65  IPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGAD 106
           I  P  K R QI +   R  P+++DVDL  LA+ T GF GAD
Sbjct: 207 IDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGAD 248

>pdb|1IY2|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 278

Iteration: 1
 Score = 99.4 bits (246), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 54/102 (52%), Positives = 64/102 (62%), Gaps = 3/102 (2%)
Query: 8   QRGSGAGGAAD---RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIY 64
           +RGSG GG  D   +  NQLL EMDG      I V+  TNRPDI+DPALLRPGR D+ I 
Sbjct: 147 KRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIA 206
Query: 65  IPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGAD 106
           I  P  K R QI +   R  P+++DVDL  LA+ T GF GAD
Sbjct: 207 IDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGAD 248

>pdb|1IXZ|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 254

Iteration: 1
 Score = 99.4 bits (246), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 54/102 (52%), Positives = 64/102 (62%), Gaps = 3/102 (2%)
Query: 8   QRGSGAGGAAD---RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIY 64
           +RGSG GG  D   +  NQLL EMDG      I V+  TNRPDI+DPALLRPGR D+ I 
Sbjct: 123 KRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIA 182
Query: 65  IPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGAD 106
           I  P  K R QI +   R  P+++DVDL  LA+ T GF GAD
Sbjct: 183 IDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGAD 224

>pdb|2QZ4|A Chain A, Human Paraplegin, Aaa Domain In Complex With Adp Length = 262

Iteration: 1
 Score = 94.7 bits (234), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 46/102 (45%), Positives = 64/102 (62%), Gaps = 2/102 (1%)
Query: 22  NQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACL 81
           NQLL EMDG+     + V+  TNR DI+D AL+RPGRLD+ ++I LP  + R +IF+  L
Sbjct: 131 NQLLVEMDGMGTTDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHL 190
Query: 82  RKSPVSKDVDL--EKLAQFTQGFSGADITEICQRACKDATRE 121
           +   +++      ++LA+ T GFSGADI  IC  A   A RE
Sbjct: 191 KSLKLTQSSTFYSQRLAELTPGFSGADIANICNEAALHAARE 232

>pdb|2R62|A Chain A, Crystal Structure Of Helicobacter Pylori Atp Dependent Protease, Ftsh Length = 268

Iteration: 1
 Score = 89.0 bits (219), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 46/123 (37%), Positives = 76/123 (61%), Gaps = 4/123 (3%)
Query: 22  NQLLTEMDGLSAKKT-IFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKAC 80
           NQLL EMDG  ++   + V+  TNRP+I+DPAL+RPGR D+ + +  P    R++I K  
Sbjct: 136 NQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVH 195
Query: 81  LRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIED 140
           ++   ++ DV+L+++A+ T G +GAD+  I   A   A R   + ++R++  K  EA+E 
Sbjct: 196 IKGVKLANDVNLQEVAKLTAGLAGADLANIINEAALLAGRNN-QKEVRQQHLK--EAVER 252
Query: 141 EVA 143
            +A
Sbjct: 253 GIA 255

>pdb|3HU3|A Chain A, Structure Of P97 N-D1 R155h Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score = 88.2 bits (217), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 47/121 (38%), Positives = 70/121 (57%)
Query: 4   SIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLI 63
           +I  +R    G    RI +QLLT MDGL  +  + V+  TNRP+ IDPAL R GR D+ +
Sbjct: 308 AIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREV 367
Query: 64  YIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEI 123
            I +P    RL+I +   +   ++ DVDLE++A  T G  GAD+  +C  A   A R+++
Sbjct: 368 DIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKM 427
Query: 124 E 124
           +
Sbjct: 428 D 428

>pdb|3HU2|A Chain A, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score = 88.2 bits (217), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 47/121 (38%), Positives = 70/121 (57%)
Query: 4   SIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLI 63
           +I  +R    G    RI +QLLT MDGL  +  + V+  TNRP+ IDPAL R GR D+ +
Sbjct: 308 AIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREV 367
Query: 64  YIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEI 123
            I +P    RL+I +   +   ++ DVDLE++A  T G  GAD+  +C  A   A R+++
Sbjct: 368 DIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKM 427
Query: 124 E 124
           +
Sbjct: 428 D 428

>pdb|3HU1|A Chain A, Structure Of P97 N-D1 R95g Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score = 88.2 bits (217), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 47/121 (38%), Positives = 70/121 (57%)
Query: 4   SIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLI 63
           +I  +R    G    RI +QLLT MDGL  +  + V+  TNRP+ IDPAL R GR D+ +
Sbjct: 308 AIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREV 367
Query: 64  YIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEI 123
            I +P    RL+I +   +   ++ DVDLE++A  T G  GAD+  +C  A   A R+++
Sbjct: 368 DIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKM 427
Query: 124 E 124
           +
Sbjct: 428 D 428

>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 = 88.2 bits (217), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 47/121 (38%), Positives = 70/121 (57%)
Query: 4   SIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLI 63
           +I  +R    G    RI +QLLT MDGL  +  + V+  TNRP+ IDPAL R GR D+ +
Sbjct: 308 AIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREV 367
Query: 64  YIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEI 123
            I +P    RL+I +   +   ++ DVDLE++A  T G  GAD+  +C  A   A R+++
Sbjct: 368 DIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKM 427
Query: 124 E 124
           +
Sbjct: 428 D 428

>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 405

Iteration: 1
 Score = 87.0 bits (214), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 47/113 (41%), Positives = 67/113 (59%), Gaps = 1/113 (0%)
Query: 10  GSGAGGA-ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLP 68
           GSG G +   R   +LL ++DG    K I +I  TNR DI+DPALLRPGR+D+ I  P P
Sbjct: 260 GSGGGDSEVQRTMLELLNQLDGFETSKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPP 319
Query: 69  VEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
              +R +I +   RK  +++ ++L K+A+   G SGAD+  +C  A   A RE
Sbjct: 320 SVAARAEILRIHSRKMNLTRGINLRKVAEKMNGCSGADVKGVCTEAGMYALRE 372

>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score = 87.0 bits (214), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 48/113 (42%), Positives = 63/113 (55%)
Query: 10  GSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPV 69
           G+ A     R   +LLT+MDG        +I  TNRPD +DPALLRPGRLD+ + IPLP 
Sbjct: 294 GTSADREIQRTLMELLTQMDGFDNLGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPN 353
Query: 70  EKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREE 122
           E  RL+IFK    K   + + D E   + + GF+GADI      A   A R++
Sbjct: 354 EAGRLEIFKIHTAKVKKTGEFDFEAAVKMSDGFNGADIRNCATEAGFFAIRDD 406

>pdb|4B4T|M Chain M, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 434

Iteration: 1
 Score = 80.5 bits (197), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 41/98 (41%), Positives = 59/98 (60%)
Query: 23  QLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR 82
           +LL ++DG S+   + V+  TNR D++DPALLR GRLD+ I  PLP E SR QI +   R
Sbjct: 307 ELLNQLDGFSSDDRVKVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSR 366
Query: 83  KSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           K     D++ ++LA+ T  F+GA +  +   A   A R
Sbjct: 367 KMTTDDDINWQELARSTDEFNGAQLKAVTVEAGMIALR 404

>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 428

Iteration: 1
 Score = 71.2 bits (173), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 45/112 (40%), Positives = 58/112 (51%), Gaps = 1/112 (0%)
Query: 11  SGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIP-LPV 69
           +G+     RI  +LLT+MDG      + VI  TNR D +DPALLRPGRLD+ I  P L  
Sbjct: 286 TGSDREVQRILIELLTQMDGFDQSTNVKVIMATNRADTLDPALLRPGRLDRKIEFPSLRD 345
Query: 70  EKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
            + R  IF     K  ++ + DL+ L       SGA I  I Q A   A R+
Sbjct: 346 RRERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQEAGLRAVRK 397

>pdb|4B4T|H Chain H, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 467

Iteration: 1
 Score = 71.2 bits (173), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 36/111 (32%), Positives = 60/111 (54%)
Query: 10  GSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPV 69
           G+G      R   +L+T++DG   +  I V+  TNRP+ +DPALLRPGR+D+ +   LP 
Sbjct: 322 GAGGDNEVQRTMLELITQLDGFDPRGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPD 381
Query: 70  EKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
            + R  IF+   +   V + +  E +++     +GA++  +C  A   A R
Sbjct: 382 LEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTEAGMFAIR 432

>pdb|3D8B|A Chain A, Crystal Structure Of Human Fidgetin-Like Protein 1 In Complex With Adp Length = 357

Iteration: 1
 Score = 71.2 bits (173), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 46/127 (36%), Positives = 70/127 (55%), Gaps = 5/127 (3%)
Query: 4   SIVIQRGSGAGGAADRIPNQLLTEMDG--LSAKKTIFVIGVTNRPDIIDPALLRPGRLDQ 61
           S++ QRG G   ++ RI  + L ++DG   S++  I V+G TNRP  ID A  R  RL +
Sbjct: 187 SLLSQRGDGEHESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAARR--RLVK 244
Query: 62  LIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
            +YIPLP   +R QI    + K      + ++E++ Q +  FSGAD+T++C+ A     R
Sbjct: 245 RLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQIVQQSDAFSGADMTQLCREASLGPIR 304
Query: 121 EEIENDI 127
                DI
Sbjct: 305 SLQTADI 311

>pdb|3VFD|A Chain A, Human Spastin Aaa Domain Length = 389

Iteration: 1
 Score = 68.9 bits (167), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/167 (31%), Positives = 90/167 (53%), Gaps = 22/167 (13%)
Query: 4   SIVIQRGSGAGGAADRIPNQLLTEMDGLSAK--KTIFVIGVTNRPDIIDPALLRPGRLDQ 61
           S++ +R  G   A+ R+  + L E DG+ +     + V+G TNRP  +D A+LR  R  +
Sbjct: 218 SLLCERREGEHDASRRLKTEFLIEFDGVQSAGDDRVLVMGATNRPQELDEAVLR--RFIK 275
Query: 62  LIYIPLPVEKSRLQIFKA--CLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDAT 119
            +Y+ LP E++RL + K   C + SP+++  +L +LA+ T G+SG+D+T + + A     
Sbjct: 276 RVYVSLPNEETRLLLLKNLLCKQGSPLTQK-ELAQLARMTDGYSGSDLTALAKDAALGPI 334
Query: 120 REEIENDIRRRKGKQPEAIED----EVAEIKAEHFEESMKYACKSQS 162
           RE            +PE +++    E+  I+   F ES+K   +S S
Sbjct: 335 RE-----------LKPEQVKNMSASEMRNIRLSDFTESLKKIKRSVS 370

>pdb|4B4T|I Chain I, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score = 66.2 bits (160), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 41/113 (36%), Positives = 61/113 (53%), Gaps = 2/113 (1%)
Query: 11  SGAGGAAD--RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLP 68
           S +GG  +  R   +LL ++DG   +  + VI  TN+ + +DPAL+RPGR+D+ I    P
Sbjct: 294 SNSGGEREIQRTMLELLNQLDGFDDRGDVKVIMATNKIETLDPALIRPGRIDRKILFENP 353
Query: 69  VEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
              ++ +I      K  +S+DV+LE L       SGADI  +C  A   A RE
Sbjct: 354 DLSTKKKILGIHTSKMNLSEDVNLETLVTTKDDLSGADIQAMCTEAGLLALRE 406

>pdb|2ZAM|A Chain A, Crystal Structure Of Mouse Skd1VPS4B APO-Form Length = 444

Iteration: 1
 Score = 63.9 bits (154), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 41/120 (34%), Positives = 63/120 (52%), Gaps = 4/120 (3%)
Query: 4   SIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKT-IFVIGVTNRPDIIDPALLRPGRLDQL 62
           S+   R      AA RI  + L +M G+      I V+G TN P ++D A+ R  R ++ 
Sbjct: 238 SLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFEKR 295
Query: 63  IYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           IYIPLP   +R  +F+  L  +  S  + D ++L + T G+SGADI+ I + A     R+
Sbjct: 296 IYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRKTDGYSGADISIIVRDALMQPVRK 355

>pdb|2QP9|X Chain X, Crystal Structure Of S.Cerevisiae Vps4 Length = 355

Iteration: 1
 Score = 63.2 bits (152), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 39/115 (33%), Positives = 63/115 (54%), Gaps = 4/115 (3%)
Query: 9   RGSGAGGAADRIPNQLLTEMDGL-SAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPL 67
           RG G   A+ RI  +LL +M+G+ +  + + V+G TN P  +D A+ R  R ++ IYIPL
Sbjct: 159 RGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERRIYIPL 216
Query: 68  PVEKSRLQIFKACLRKSP-VSKDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           P   +R  +F+  +  +P V    D   L   T+G+SG+DI  + + A     R+
Sbjct: 217 PDLAARTTMFEINVGDTPSVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIRK 271

>pdb|1XWI|A Chain A, Crystal Structure Of Vps4b Length = 322

Iteration: 1
 Score = 62.8 bits (151), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 42/120 (35%), Positives = 62/120 (51%), Gaps = 4/120 (3%)
Query: 4   SIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKT-IFVIGVTNRPDIIDPALLRPGRLDQL 62
           S+   R      AA RI  + L +M G+      I V+G TN P ++D A+ R  R ++ 
Sbjct: 116 SLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFEKR 173
Query: 63  IYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           IYIPLP   +R  +FK  L  +  S  + D  +L + T G+SGADI+ I + A     R+
Sbjct: 174 IYIPLPEPHARAAMFKLHLGTTQNSLTEADFRELGRKTDGYSGADISIIVRDALMQPVRK 233

>pdb|3EIH|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The Presence Of Atpgammas Length = 340

Iteration: 1
 Score = 62.8 bits (151), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 39/115 (33%), Positives = 63/115 (54%), Gaps = 4/115 (3%)
Query: 9   RGSGAGGAADRIPNQLLTEMDGL-SAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPL 67
           RG G   A+ RI  +LL +M+G+ +  + + V+G TN P  +D A+ R  R ++ IYIPL
Sbjct: 144 RGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERRIYIPL 201
Query: 68  PVEKSRLQIFKACLRKSP-VSKDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           P   +R  +F+  +  +P V    D   L   T+G+SG+DI  + + A     R+
Sbjct: 202 PDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIRK 256

>pdb|2RKO|A Chain A, Crystal Structure Of The Vps4p-Dimer Length = 331

Iteration: 1
 Score = 62.8 bits (151), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 39/115 (33%), Positives = 63/115 (54%), Gaps = 4/115 (3%)
Query: 9   RGSGAGGAADRIPNQLLTEMDGL-SAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPL 67
           RG G   A+ RI  +LL +M+G+ +  + + V+G TN P  +D A+ R  R ++ IYIPL
Sbjct: 135 RGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERRIYIPL 192
Query: 68  PVEKSRLQIFKACLRKSP-VSKDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           P   +R  +F+  +  +P V    D   L   T+G+SG+DI  + + A     R+
Sbjct: 193 PDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIRK 247

>pdb|3EIE|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The So4-Bound State Length = 322

Iteration: 1
 Score = 62.8 bits (151), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 39/115 (33%), Positives = 63/115 (54%), Gaps = 4/115 (3%)
Query: 9   RGSGAGGAADRIPNQLLTEMDGL-SAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPL 67
           RG G   A+ RI  +LL +M+G+ +  + + V+G TN P  +D A+ R  R ++ IYIPL
Sbjct: 126 RGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERRIYIPL 183
Query: 68  PVEKSRLQIFKACLRKSP-VSKDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           P   +R  +F+  +  +P V    D   L   T+G+SG+DI  + + A     R+
Sbjct: 184 PDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIRK 238

>pdb|3B9P|A Chain A, Spastin Length = 297

Iteration: 1
 Score = 61.2 bits (147), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 39/111 (35%), Positives = 61/111 (54%), Gaps = 8/111 (7%)
Query: 16  AADRIPNQLLTEMDGLSAKK---TIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKS 72
           A+ R+  + L E DGL        I V+  TNRP  +D A LR  R  + +Y+ LP E++
Sbjct: 136 ASRRLKTEFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALR--RFTKRVYVSLPDEQT 193
Query: 73  RLQIFKACLRK--SPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           R  +    L+K  SP+  +  L +LA+ T G+SG+D+T + + A  +  RE
Sbjct: 194 RELLLNRLLQKQGSPLDTEA-LRRLAKITDGYSGSDLTALAKDAALEPIRE 243

>pdb|3KW6|A Chain A, Crystal Structure Of A Domain Of 26s Proteasome Regulatory Subunit 8 From Homo Sapiens. Northeast Structural Genomics Consortium Target Id Hr3102a Length = 78

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 33/56 (58%)
Query: 66  PLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           P P E++RL I K   RK  +++ ++L K+A+   G SGA++  +C  A   A RE
Sbjct: 1   PPPNEEARLDILKIHSRKXNLTRGINLRKIAELXPGASGAEVKGVCTEAGXYALRE 56

>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 = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/54 (37%), Positives = 32/54 (59%)
Query: 68  PVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           P E++RL I K   RK  +++ ++L K+A+   G SGA++  +C  A   A RE
Sbjct: 11  PNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRE 64

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	199
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	2e-71
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	5e-70
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	3e-65
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	1e-37
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	3e-52
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	2e-50
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	4e-50
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	3e-46
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	1e-44
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	4e-42
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	6e-42
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	9e-42
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	1e-40
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	1e-35
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	2e-35
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	2e-35
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	3e-35
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	1e-34
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	3e-34
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	5e-34
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	6e-33
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	2e-15
2krk_A	86	26S protease regulatory subunit 8; structural geno	3e-15
3aji_B	83	S6C, proteasome (prosome, macropain) 26S subunit,	3e-13
3kw6_A	78	26S protease regulatory subunit 8; structural geno	3e-13
2dzn_B	82	26S protease regulatory subunit 6B homolog; ankyri	1e-12
3vlf_B	88	26S protease regulatory subunit 7 homolog; heat re	1e-10

>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 =  217 bits (556), Expect = 2e-71
 Identities = 107/168 (63%), Positives = 128/168 (76%), Gaps = 9/168 (5%)

Query: 4   SIVIQRGSGAG---GAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
           SI   RG   G   GAADR+ NQ+LTEMDG+S KK +F+IG TNRPDIIDPA+LRPGRLD
Sbjct: 119 SIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLD 178

Query: 61  QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           QLIYIPLP EKSR+ I KA LRKSPV+KDVDLE LA+ T GFSGAD+TEICQRACK A R
Sbjct: 179 QLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIR 238

Query: 121 EEIENDIRRRKGKQP------EAIEDEVAEIKAEHFEESMKYACKSQS 162
           E IE++IRR + +Q          +D V EI+ +HFEE+M++A +S S
Sbjct: 239 ESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVS 286

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens} Length = 274

 Score =  213 bits (544), Expect = 5e-70
 Identities = 62/165 (37%), Positives = 95/165 (57%), Gaps = 13/165 (7%)

Query: 4   SIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLI 63
           ++  +R     GA+ R+ NQLLTEMDGL A++ +F++  TNRPDIIDPA+LRPGRLD+ +
Sbjct: 114 ALCPRRSDRETGASVRVVNQLLTEMDGLEARQQVFIMAATNRPDIIDPAILRPGRLDKTL 173

Query: 64  YIPLPVEKSRLQIFKACLR---KSPVSKDVDLEKLAQF--TQGFSGADITEICQRACKDA 118
           ++ LP    RL I K   +   K P+  DV+LE +A       ++GAD++ + + A   A
Sbjct: 174 FVGLPPPADRLAILKTITKNGTKPPLDADVNLEAIAGDLRCDCYTGADLSALVREASICA 233

Query: 119 TREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQSR 163
            R+E+         +Q    E    ++  +HFEE+ K    S S+
Sbjct: 234 LRQEMA--------RQKSGNEKGELKVSHKHFEEAFKKVRSSISK 270

>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 =  169 bits (430), Expect = 3e-52
 Identities = 46/200 (23%), Positives = 84/200 (42%), Gaps = 35/200 (17%)

Query: 4   SIVIQRGSGAGGAADRIPNQLLTEMDGL-SAKKTIFVIGVTNRPDIIDPALLRPGRLDQL 62
           ++   RG G   A+ RI  +LL +M+G+ +  + + V+G TN P  +D A+ R  R ++ 
Sbjct: 121 ALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERR 178

Query: 63  IYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           IYIPLP   +R  +F+  +  +P      D   L   T+G+SG+DI  + + A     R+
Sbjct: 179 IYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIRK 238

Query: 122 EIENDIRRRKGKQP------------------------EAIEDEVAEIKAEHFEESMKYA 157
                  +    +                         EA E +  ++  + F +++K  
Sbjct: 239 IQSATHFKDVSTEDDETRKLTPCSPGDDGAIEMSWTDIEADELKEPDLTIKDFLKAIKST 298

Query: 158 CKSQSRG-------FGDEFG 170
             + +         F  +FG
Sbjct: 299 RPTVNEDDLLKQEQFTRDFG 318

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens} Length = 322

 Score =  164 bits (418), Expect = 2e-50
 Identities = 50/206 (24%), Positives = 79/206 (38%), Gaps = 41/206 (19%)

Query: 4   SIVIQRGSGAGGAADRIPNQLLTEMDGLSA-KKTIFVIGVTNRPDIIDPALLRPGRLDQL 62
           S+   R      AA RI  + L +M G+      I V+G TN P ++D A+ R  R ++ 
Sbjct: 116 SLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFEKR 173

Query: 63  IYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           IYIPLP   +R  +FK  L  +  S  + D  +L + T G+SGADI+ I + A     R+
Sbjct: 174 IYIPLPEPHARAAMFKLHLGTTQNSLTEADFRELGRKTDGYSGADISIIVRDALMQPVRK 233

Query: 122 EIENDIRRR--------------------KGKQPEAIEDEVAEIKA----------EHFE 151
                  ++                        P AIE    ++                
Sbjct: 234 VQSATHFKKVRGPSRADPNHLVDDLLTPCSPGDPGAIEMTWMDVPGDKLLEPVVSMSDML 293

Query: 152 ESMKYACKSQSRG-------FGDEFG 170
            S+     + +         F ++FG
Sbjct: 294 RSLSNTKPTVNEHDLLKLKKFTEDFG 319

>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 =  165 bits (418), Expect = 4e-50
 Identities = 45/200 (22%), Positives = 84/200 (42%), Gaps = 35/200 (17%)

Query: 4   SIVIQRGSGAGGAADRIPNQLLTEMDGL-SAKKTIFVIGVTNRPDIIDPALLRPGRLDQL 62
           ++   RG G   A+ RI  +LL +M+G+ +  + + V+G TN P  +D A+ R  R ++ 
Sbjct: 154 ALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERR 211

Query: 63  IYIPLPVEKSRLQIFKACLRKSP-VSKDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           IYIPLP   +R  +F+  +  +P V    D   L   T+G+SG+DI  + + A     R+
Sbjct: 212 IYIPLPDLAARTTMFEINVGDTPSVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIRK 271

Query: 122 EIENDIRRRKGKQPEAI------------------------EDEVAEIKAEHFEESMKYA 157
                  +    + +                          E +  ++  + F +++K  
Sbjct: 272 IQSATHFKDVSTEDDETRKLTPSSPGDDGAIEMSWTDIEADELKEPDLTIKDFLKAIKST 331

Query: 158 CKSQSRG-------FGDEFG 170
             + +         F  +FG
Sbjct: 332 RPTVNEDDLLKQEQFTRDFG 351

>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 =  157 bits (397), Expect = 3e-46
 Identities = 49/206 (23%), Positives = 80/206 (38%), Gaps = 41/206 (19%)

Query: 4   SIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKT-IFVIGVTNRPDIIDPALLRPGRLDQL 62
           S+   R      AA RI  + L +M G+      I V+G TN P ++D A+ R  R ++ 
Sbjct: 238 SLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFEKR 295

Query: 63  IYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           IYIPLP   +R  +F+  L  +  S  + D ++L + T G+SGADI+ I + A     R+
Sbjct: 296 IYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRKTDGYSGADISIIVRDALMQPVRK 355

Query: 122 EIENDIRRR--------------------KGKQPEAIEDEVAEIKA----------EHFE 151
                  ++                        P AIE    ++                
Sbjct: 356 VQSATHFKKVRGPSRADPNCIVNDLLTPCSPGDPGAIEMTWMDVPGDKLLEPVVSMWDML 415

Query: 152 ESMKYACKSQSRG-------FGDEFG 170
            S+     + +         F ++FG
Sbjct: 416 RSLSSTKPTVNEQDLLKLKKFTEDFG 441

>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 =  153 bits (388), Expect = 1e-44
 Identities = 49/152 (32%), Positives = 78/152 (51%), Gaps = 2/152 (1%)

Query: 4   SIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLI 63
           +I  +R    G    RI +QLLT MDGL  +  + V+  TNRP+ IDPAL R GR D+ +
Sbjct: 308 AIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREV 367

Query: 64  YIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEI 123
            I +P    RL+I +   +   ++ DVDLE++A  T G  GAD+  +C  A   A R+++
Sbjct: 368 DIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKM 427

Query: 124 ENDIRRRKGKQPEAIEDEVAEIKAEHFEESMK 155
           +      +    E +      +  + F  ++ 
Sbjct: 428 DLIDLEDETIDAEVMNS--LAVTMDDFRWALS 457

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster} Length = 297

 Score =  142 bits (360), Expect = 4e-42
 Identities = 48/178 (26%), Positives = 80/178 (44%), Gaps = 20/178 (11%)

Query: 4   SIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKT---IFVIGVTNRPDIIDPALLRPGRLD 60
           S++ +R S    A+ R+  + L E DGL        I V+  TNRP  +D A LR  R  
Sbjct: 124 SLLSERSSSEHEASRRLKTEFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALR--RFT 181

Query: 61  QLIYIPLPVEKSRLQIFKACLRKSPVSKDV-DLEKLAQFTQGFSGADITEICQRACKDAT 119
           + +Y+ LP E++R  +    L+K     D   L +LA+ T G+SG+D+T + + A  +  
Sbjct: 182 KRVYVSLPDEQTRELLLNRLLQKQGSPLDTEALRRLAKITDGYSGSDLTALAKDAALEPI 241

Query: 120 REEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQSRG-------FGDEFG 170
           RE     ++        AI         + F  S+K   +S +         +  ++G
Sbjct: 242 RELNVEQVKCLDISAMRAIT-------EQDFHSSLKRIRRSVAPQSLNSYEKWSQDYG 292

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii} Length = 285

 Score =  141 bits (358), Expect = 6e-42
 Identities = 61/164 (37%), Positives = 88/164 (53%), Gaps = 15/164 (9%)

Query: 4   SIVIQRGSGAGGA---ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
           +I  +R     G      R   QLL EMDG  A+  + +IG TNRPDI+DPA+LRPGR D
Sbjct: 121 AIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFD 180

Query: 61  QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           ++I +P P EK RL+I K   RK  +++DV+LE++A+ T+G  GA++  IC  A  +A R
Sbjct: 181 RIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAELKAICTEAGMNAIR 240

Query: 121 EE------------IENDIRRRKGKQPEAIEDEVAEIKAEHFEE 152
           E             +E  + ++K K  E    +V      H   
Sbjct: 241 ELRDYVTMDDFRKAVEKIMEKKKVKVKEPAHLDVLYRLEHHHHH 284

>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 =  142 bits (361), Expect = 9e-42
 Identities = 55/177 (31%), Positives = 83/177 (46%), Gaps = 19/177 (10%)

Query: 4   SIVIQRGSGAGGAADRIPNQLLTEMDGL--SAKKTIFVIGVTNRPDIIDPALLRPGRLDQ 61
           S++ QRG G   ++ RI  + L ++DG   S++  I V+G TNRP  ID A  R  RL +
Sbjct: 187 SLLSQRGDGEHESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAARR--RLVK 244

Query: 62  LIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
            +YIPLP   +R QI    + K      + ++E++ Q +  FSGAD+T++C+ A     R
Sbjct: 245 RLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQIVQQSDAFSGADMTQLCREASLGPIR 304

Query: 121 EEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQSRG-------FGDEFG 170
                DI            D+V  I    FE + +    S S         +   FG
Sbjct: 305 SLQTADIATIT-------PDQVRPIAYIDFENAFRTVRPSVSPKDLELYENWNKTFG 354

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens} Length = 389

 Score =  141 bits (356), Expect = 1e-40
 Identities = 51/177 (28%), Positives = 85/177 (48%), Gaps = 19/177 (10%)

Query: 4   SIVIQRGSGAGGAADRIPNQLLTEMDGL--SAKKTIFVIGVTNRPDIIDPALLRPGRLDQ 61
           S++ +R  G   A+ R+  + L E DG+  +    + V+G TNRP  +D A+LR  R  +
Sbjct: 218 SLLCERREGEHDASRRLKTEFLIEFDGVQSAGDDRVLVMGATNRPQELDEAVLR--RFIK 275

Query: 62  LIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
            +Y+ LP E++RL + K  L K        +L +LA+ T G+SG+D+T + + A     R
Sbjct: 276 RVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQLARMTDGYSGSDLTALAKDAALGPIR 335

Query: 121 EEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQSRG-------FGDEFG 170
           E     ++            E+  I+   F ES+K   +S S         +  +FG
Sbjct: 336 ELKPEQVKNMS-------ASEMRNIRLSDFTESLKKIKRSVSPQTLEAYIRWNKDFG 385

>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 =  125 bits (315), Expect = 1e-35
 Identities = 48/121 (39%), Positives = 71/121 (58%), Gaps = 6/121 (4%)

Query: 8   QRGSGAGGAA----DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLI 63
           +R +   G +    ++  NQLL EMDG+     + V+  TNR DI+D AL+RPGRLD+ +
Sbjct: 113 KRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTDHVIVLASTNRADILDGALMRPGRLDRHV 172

Query: 64  YIPLPVEKSRLQIFKACLRKSPVSKDVDL--EKLAQFTQGFSGADITEICQRACKDATRE 121
           +I LP  + R +IF+  L+   +++      ++LA+ T GFSGADI  IC  A   A RE
Sbjct: 173 FIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANICNEAALHAARE 232

Query: 122 E 122
            
Sbjct: 233 G 233

>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 =  123 bits (312), Expect = 2e-35
 Identities = 58/117 (49%), Positives = 70/117 (59%), Gaps = 3/117 (2%)

Query: 8   QRGSGAGGAAD---RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIY 64
           +RGSG GG  D   +  NQLL EMDG      I V+  TNRPDI+DPALLRPGR D+ I 
Sbjct: 123 KRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIA 182

Query: 65  IPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           I  P  K R QI +   R  P+++DVDL  LA+ T GF GAD+  +   A   A RE
Sbjct: 183 IDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAARE 239

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20 Length = 278

 Score =  124 bits (313), Expect = 2e-35
 Identities = 58/117 (49%), Positives = 70/117 (59%), Gaps = 3/117 (2%)

Query: 8   QRGSGAGGAAD---RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIY 64
           +RGSG GG  D   +  NQLL EMDG      I V+  TNRPDI+DPALLRPGR D+ I 
Sbjct: 147 KRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIA 206

Query: 65  IPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           I  P  K R QI +   R  P+++DVDL  LA+ T GF GAD+  +   A   A RE
Sbjct: 207 IDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAARE 263

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20 Length = 257

 Score =  123 bits (312), Expect = 3e-35
 Identities = 53/117 (45%), Positives = 72/117 (61%), Gaps = 3/117 (2%)

Query: 8   QRGSGAGGAAD---RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIY 64
           QRG+G GG  D   +  NQ+L EMDG    + I VI  TNRPD++DPALLRPGR D+ + 
Sbjct: 119 QRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVV 178

Query: 65  IPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           + LP  + R QI K  +R+ P++ D+D   +A+ T GFSGAD+  +   A   A R 
Sbjct: 179 VGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARG 235

>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 =  126 bits (319), Expect = 1e-34
 Identities = 50/103 (48%), Positives = 67/103 (65%), Gaps = 3/103 (2%)

Query: 8   QRGSGAGGAAD---RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIY 64
            RG+G GG  D   +  NQLL EMDG  +K+ I V+  TNRPDI+DPALLRPGR D+ I 
Sbjct: 123 HRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPGRFDKKIV 182

Query: 65  IPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADI 107
           +  P    R +I +   R  P+++DV+LE +A+ T GF GAD+
Sbjct: 183 VDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAKRTPGFVGADL 225

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus} Length = 499

 Score =  125 bits (316), Expect = 3e-34
 Identities = 54/103 (52%), Positives = 65/103 (63%), Gaps = 3/103 (2%)

Query: 8   QRGSGAGGAAD---RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIY 64
           +RGSG GG  D   +  NQLL EMDG      I V+  TNRPDI+DPALLRPGR D+ I 
Sbjct: 138 KRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIA 197

Query: 65  IPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADI 107
           I  P  K R QI +   R  P+++DVDL  LA+ T GF GAD+
Sbjct: 198 IDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADL 240

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A Length = 293

 Score =  121 bits (305), Expect = 5e-34
 Identities = 26/181 (14%), Positives = 54/181 (29%), Gaps = 27/181 (14%)

Query: 4   SIVIQRG-SGAGGAADRIPNQLLTE------------MDGLSAKKTIFVIGVTNRPDIID 50
           +   + G +      +++ N  L              M        + +I   N    + 
Sbjct: 110 AGAGRMGGTTQYTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLY 169

Query: 51  PALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEI 110
             L+R GR+++  + P   +  R+ +     R    + +V  E + +    F G  I   
Sbjct: 170 APLIRDGRMEKFYWAPTRED--RIGVCTGIFR----TDNVPAEDVVKIVDNFPGQSIDFF 223

Query: 111 C---QRACKDATREEIENDIRRRKGKQPE-----AIEDEVAEIKAEHFEESMKYACKSQS 162
                R   D  R+ +      + G +           E  ++  E   E      + Q 
Sbjct: 224 GALRARVYDDEVRKWVSGTGIEKIGDKLLNSFDGPPTFEQPKMTIEKLLEYGNMLVQEQE 283

Query: 163 R 163
            
Sbjct: 284 N 284

>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 =  117 bits (296), Expect = 6e-33
 Identities = 43/119 (36%), Positives = 68/119 (57%), Gaps = 5/119 (4%)

Query: 8   QRGS-GAGGAAD---RIPNQLLTEMDGLSAKKT-IFVIGVTNRPDIIDPALLRPGRLDQL 62
            R + G     D   +  NQLL EMDG  ++   + V+  TNRP+I+DPAL+RPGR D+ 
Sbjct: 118 SRAAGGVVSGNDEREQTLNQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQ 177

Query: 63  IYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATRE 121
           + +  P    R++I K  ++   ++ DV+L+++A+ T G +GAD+  I   A   A R 
Sbjct: 178 VLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAKLTAGLAGADLANIINEAALLAGRN 236

>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 = 71.3 bits (175), Expect = 2e-15
 Identities = 17/97 (17%), Positives = 39/97 (40%), Gaps = 5/97 (5%)

Query: 6   VIQRGSGAGGAADRIPNQLLTEMDGLSAK-KTIFVIGVTNRPDIIDPALLRPGRLDQLIY 64
           ++         ++ +   LL  +     + + + +IG T+R D++   +         I+
Sbjct: 136 LLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQ-EMEMLNAFSTTIH 194

Query: 65  IPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQG 101
           +P     +  Q+ +A L      KD +   +AQ  +G
Sbjct: 195 VPN--IATGEQLLEA-LELLGNFKDKERTTIAQQVKG 228

>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast structural genomics consortium (NESG), target HR3102A, PSI-2; NMR {Homo sapiens} Length = 86

 Score = 66.8 bits (164), Expect = 3e-15
 Identities = 20/60 (33%), Positives = 33/60 (55%)

Query: 63  IYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREE 122
            +   P E++RL I K   RK  +++ ++L K+A+   G SGA++  +C  A   A RE 
Sbjct: 6   HHHSHPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRER 65

>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 = 61.6 bits (150), Expect = 3e-13
 Identities = 24/86 (27%), Positives = 34/86 (39%), Gaps = 19/86 (22%)

Query: 70  EKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRR 129
            + +  IF     K  +S++VDLE         SGADI  ICQ +   A RE        
Sbjct: 3   RRQKRLIFSTITSKMNLSEEVDLEDYVARPDKISGADINSICQESGMLAVRE-------N 55

Query: 130 RKGKQPEAIEDEVAEIKAEHFEESMK 155
           R              + A+ FE++ K
Sbjct: 56  RY------------IVLAKDFEKAYK 69

>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 = 61.3 bits (150), Expect = 3e-13
 Identities = 21/57 (36%), Positives = 33/57 (57%)

Query: 66  PLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREE 122
           P P E++RL I K   RK  +++ ++L K+A+   G SGA++  +C  A   A RE 
Sbjct: 1   PPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRER 57

>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 = 60.1 bits (146), Expect = 1e-12
 Identities = 24/99 (24%), Positives = 33/99 (33%), Gaps = 21/99 (21%)

Query: 73  RLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKG 132
           R  IF     K  ++ + DL+ L       SGA I  I Q A   A R+        R  
Sbjct: 3   RRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQEAGLRAVRK-------NRY- 54

Query: 133 KQPEAIEDEVAEIKAEHFEESMKYACKSQSRGFGDEFGF 171
                       I     EE+     K+ +    D+F F
Sbjct: 55  -----------VILQSDLEEAYATQVKTDNT--VDKFDF 80

>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 = 54.9 bits (133), Expect = 1e-10
 Identities = 17/89 (19%), Positives = 35/89 (39%), Gaps = 9/89 (10%)

Query: 70  EKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRR 129
            + R  IF+   +   V + +  E +++     +GA++  +C  A   A R        R
Sbjct: 3   LEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTEAGMFAIR-------AR 55

Query: 130 RKGKQPEAIEDEVAEI--KAEHFEESMKY 156
           RK    +     V ++    + F  + +Y
Sbjct: 56  RKVATEKDFLKAVDKVISGYKKFSSTSRY 84

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	199
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	99.97
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.97
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	99.97
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	99.97
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	99.97
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	99.96
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	99.96
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.94
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	99.93
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.89
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	99.89
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.87
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.87
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.86
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.86
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.85
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.83
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.83
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.83
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.81
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.78
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.78
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.77
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.76
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.74
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.7
2krk_A	86	26S protease regulatory subunit 8; structural geno	99.69
3kw6_A	78	26S protease regulatory subunit 8; structural geno	99.68
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.68
3aji_B	83	S6C, proteasome (prosome, macropain) 26S subunit,	99.65
3vlf_B	88	26S protease regulatory subunit 7 homolog; heat re	99.64
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.6
2dzn_B	82	26S protease regulatory subunit 6B homolog; ankyri	99.51
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.35
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	98.76
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	98.7
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	98.58
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	98.57
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	98.5
3bos_A	242	Putative DNA replication factor; P-loop containing	98.33
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.31
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	98.31
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	98.31
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.19
2r44_A	331	Uncharacterized protein; putative ATPase, structur	98.19
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	98.17
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	98.13
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	98.13
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.09
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	98.07
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	97.87
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	97.86
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	97.78
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	97.77
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	97.71
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	97.71
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	97.7
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.68
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	97.66
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	97.62
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	97.6
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.52
2chq_A	319	Replication factor C small subunit; DNA-binding pr	97.52
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	97.45
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.42
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	97.38
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.38
3pvs_A	447	Replication-associated recombination protein A; ma	97.28
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.28
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	97.22
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	97.19
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	97.1
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	96.75
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	96.73
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	96.6
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	96.49
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	96.42
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	96.37
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	96.13
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	96.1
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	95.89
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	95.86
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	95.65
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	95.39
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	95.27
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	94.66
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	93.69
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	92.98
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	91.81
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	91.15
3f8t_A	506	Predicted ATPase involved in replication control,	85.82

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.97  E-value=1.1e-31  Score=236.75  Aligned_cols=143  Identities=36%  Similarity=0.549  Sum_probs=130.3

Q ss_pred             cceeeccCCCCCc---hhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHH
Q 039253            3 WSIVIQRGSGAGG---AADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKA   79 (199)
Q Consensus         3 ~sl~~~R~~~~~~---~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~   79 (199)
                      ++++++|+.+.++   ...+++++||++||++....+|+||+|||+|+.||||++||||||++|+|++|+.++|.+||+.
T Consensus       251 Dai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~  330 (405)
T 4b4t_J          251 DSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFETSKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRI  330 (405)
T ss_dssp             SCCTTSCSCSSSGGGGHHHHHHHHHHHHHHTTTCCCCEEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHH
T ss_pred             hhhccCCCCCCCCCcHHHHHHHHHHHHhhhccCCCCCeEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHHHHHHHH
Confidence            4788888765433   4568999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccc
Q 039253           80 CLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACK  159 (199)
Q Consensus        80 ~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~P  159 (199)
                      +++++++..++++..||+.|+|||||||+++|++|++.|+++..                   ..|+++||..|++++.|
T Consensus       331 ~~~~~~l~~dvdl~~lA~~t~G~SGADi~~l~~eA~~~Air~~~-------------------~~vt~~Df~~Al~~v~~  391 (405)
T 4b4t_J          331 HSRKMNLTRGINLRKVAEKMNGCSGADVKGVCTEAGMYALRERR-------------------IHVTQEDFELAVGKVMN  391 (405)
T ss_dssp             HHTTSBCCSSCCHHHHHHHCCSCCHHHHHHHHHHHHHHHHHTTC-------------------SBCCHHHHHHHHHHHHH
T ss_pred             HhcCCCCCccCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHcCC-------------------CCcCHHHHHHHHHHHhC
Confidence            99999998899999999999999999999999999999988642                   56999999999999988


Q ss_pred             ccccc
Q 039253          160 SQSRG  164 (199)
Q Consensus       160 s~~r~  164 (199)
                      +..+.
T Consensus       392 ~~~~~  396 (405)
T 4b4t_J          392 KNQET  396 (405)
T ss_dssp             HHTCC
T ss_pred             ccccc
Confidence            76653

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=99.97  E-value=3e-33  Score=264.46  Aligned_cols=170  Identities=64%  Similarity=0.972  Sum_probs=93.1

Q ss_pred             cceeeccCCC---CCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHH
Q 039253            3 WSIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKA   79 (199)
Q Consensus         3 ~sl~~~R~~~---~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~   79 (199)
                      ++++++|+..   .++..+|++++||++||++.+..+|+||+|||+|+.||+|++||||||++|+|++|+.++|.+||+.
T Consensus       580 Dsl~~~R~~~~~~~~~~~~rv~~~lL~~mdg~~~~~~V~vi~aTN~p~~lD~AllRpgRfd~~i~v~lPd~~~R~~il~~  659 (806)
T 3cf2_A          580 DSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKA  659 (806)
T ss_dssp             GGCC--------------CHHHHHHHHHHHSSCSSSSEEEECC-CCSSSSCHHHHSTTTSCCEEEC-----CHHHHTTTT
T ss_pred             hHHhhccCCCCCCCchHHHHHHHHHHHHHhCCCCCCCEEEEEeCCCchhCCHhHcCCCcceEEEEECCcCHHHHHHHHHH
Confidence            4788999743   4556889999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCC------CcchhhccccccHHHHHHH
Q 039253           80 CLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQ------PEAIEDEVAEIKAEHFEES  153 (199)
Q Consensus        80 ~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~------~~~~~~~~~~it~~df~~A  153 (199)
                      ++++.++..++++..||+.|+||||+||+++|++|++.|+++.+.+.........      .....+...+|+++||..|
T Consensus       660 ~l~~~~~~~~~dl~~la~~t~g~SGadi~~l~~~A~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~df~~a  739 (806)
T 3cf2_A          660 NLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEA  739 (806)
T ss_dssp             TSSCC--CCC----------------CHHHHHHHHHHHHHHHHHC-----------------------CCC----CCTTT
T ss_pred             HhcCCCCCCCCCHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccccccccccCccCHHHHHHH
Confidence            9999999889999999999999999999999999999999998764332211100      0112233467999999999


Q ss_pred             HHhccccccc-------cCCcccccc
Q 039253          154 MKYACKSQSR-------GFGDEFGFC  172 (199)
Q Consensus       154 l~~~~Ps~~r-------~~~~~~~~~  172 (199)
                      ++.++||++.       .|.++|+++
T Consensus       740 l~~~~pSvs~~~l~~y~~~~~~f~~~  765 (806)
T 3cf2_A          740 MRFARRSVSDNDIRKYEMFAQTLQQS  765 (806)
T ss_dssp             C---------------CCCC------
T ss_pred             HHhCCCCCCHHHHHHHHHHHHHHhcc
Confidence            9999999874       355555544

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.97  E-value=4.5e-31  Score=235.06  Aligned_cols=144  Identities=34%  Similarity=0.491  Sum_probs=131.6

Q ss_pred             cceeeccCCCCCc---hhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHH
Q 039253            3 WSIVIQRGSGAGG---AADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKA   79 (199)
Q Consensus         3 ~sl~~~R~~~~~~---~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~   79 (199)
                      ++|+++|..+.++   ...+++++||++||++.+..+|+||+|||+|+.||||++||||||++|+|++|+.++|.+||+.
T Consensus       284 Dal~~~R~~~~~~~~~~~~~~~~~lL~~ldg~~~~~~ViVIaaTNrp~~LD~AllRpGRfD~~I~i~lPd~~~R~~Il~~  363 (434)
T 4b4t_M          284 DAIGTKRFDSEKSGDREVQRTMLELLNQLDGFSSDDRVKVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQI  363 (434)
T ss_dssp             HHHHCCCSSGGGGTTHHHHHHHHHHHHHHTTSCSSCSSEEEEECSSCCCCCTTTCSTTSEEEEEECCCCCHHHHHHHHHH
T ss_pred             hhhhhccCCCCCCCchHHHHHHHHHHHHhhccCCCCCEEEEEeCCCchhcCHhHhcCCceeEEEEeCCcCHHHHHHHHHH
Confidence            4678888765333   3567899999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccc
Q 039253           80 CLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACK  159 (199)
Q Consensus        80 ~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~P  159 (199)
                      +++++++..++++..||+.|+|||||||+++|++|++.|+++..                   ..|+++||..|+++++|
T Consensus       364 ~~~~~~~~~dvdl~~lA~~t~G~sGADi~~l~~eA~~~a~r~~~-------------------~~i~~~Df~~Al~~v~~  424 (434)
T 4b4t_M          364 HSRKMTTDDDINWQELARSTDEFNGAQLKAVTVEAGMIALRNGQ-------------------SSVKHEDFVEGISEVQA  424 (434)
T ss_dssp             HHHHSCBCSCCCHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTC-------------------SSBCHHHHHHHHHSCSS
T ss_pred             HhcCCCCCCcCCHHHHHHhCCCCCHHHHHHHHHHHHHHHHHcCC-------------------CCcCHHHHHHHHHHHhC
Confidence            99999988899999999999999999999999999999988752                   56999999999999999


Q ss_pred             cccccC
Q 039253          160 SQSRGF  165 (199)
Q Consensus       160 s~~r~~  165 (199)
                      +.++.+
T Consensus       425 ~~~~~i  430 (434)
T 4b4t_M          425 RKSKSV  430 (434)
T ss_dssp             SCCCCC
T ss_pred             CCCcCc
Confidence            988765

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.97  E-value=6.9e-31  Score=232.73  Aligned_cols=144  Identities=31%  Similarity=0.432  Sum_probs=131.3

Q ss_pred             cceeeccCCCC---CchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHH
Q 039253            3 WSIVIQRGSGA---GGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKA   79 (199)
Q Consensus         3 ~sl~~~R~~~~---~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~   79 (199)
                      ++++++|+.+.   +....+++++||++||++....+|+||+|||+|+.||||++||||||++|+|++|+.++|.+||+.
T Consensus       285 Dai~~~R~~~~~~~~~~~~~~l~~LL~~lDg~~~~~~ViVIaATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~~  364 (437)
T 4b4t_I          285 DAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDDRGDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGI  364 (437)
T ss_dssp             SSSSCCCSCSSCSSCCHHHHHHHHHHHHHHHCCCSSSEEEEEEESCSTTCCTTSSCTTTEEEEECCCCCCHHHHHHHHHH
T ss_pred             hhhcccCCCCCCCccHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCChhhcCHHHhcCCceeEEEEcCCcCHHHHHHHHHH
Confidence            47888996553   334578899999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccc
Q 039253           80 CLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACK  159 (199)
Q Consensus        80 ~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~P  159 (199)
                      +++++++..++++..||+.|+|||||||+++|++|++.|+++..                   ..|+++||..|++++.|
T Consensus       365 ~l~~~~l~~dvdl~~LA~~T~GfSGADI~~l~~eA~~~Air~~~-------------------~~It~eDf~~Al~rv~~  425 (437)
T 4b4t_I          365 HTSKMNLSEDVNLETLVTTKDDLSGADIQAMCTEAGLLALRERR-------------------MQVTAEDFKQAKERVMK  425 (437)
T ss_dssp             HHTTSCBCSCCCHHHHHHHCCSCCHHHHHHHHHHHHHHHHHTTC-------------------SCBCHHHHHHHHHHHHH
T ss_pred             HhcCCCCCCcCCHHHHHHhCCCCCHHHHHHHHHHHHHHHHHcCC-------------------CccCHHHHHHHHHHHhC
Confidence            99999998899999999999999999999999999999988642                   56999999999999999


Q ss_pred             cccccC
Q 039253          160 SQSRGF  165 (199)
Q Consensus       160 s~~r~~  165 (199)
                      +..++-
T Consensus       426 ~~~~e~  431 (437)
T 4b4t_I          426 NKVEEN  431 (437)
T ss_dssp             HHCCCS
T ss_pred             CCChhh
Confidence            887653

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.97  E-value=9.4e-31  Score=233.17  Aligned_cols=148  Identities=34%  Similarity=0.475  Sum_probs=129.2

Q ss_pred             cceeeccCCCC---CchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHH
Q 039253            3 WSIVIQRGSGA---GGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKA   79 (199)
Q Consensus         3 ~sl~~~R~~~~---~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~   79 (199)
                      ++++++|++..   +....+++++||++||++.+..+|+||+|||+|+.||||++||||||++|+|++|+.++|.+||+.
T Consensus       284 Dai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~vivI~ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~  363 (437)
T 4b4t_L          284 DAIGGRRFSEGTSADREIQRTLMELLTQMDGFDNLGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKI  363 (437)
T ss_dssp             CSSSCCCSSSCCSSTTHHHHHHHHHHHHHHSSSCTTSSEEEEEESSTTSSCTTTTSTTSEEEEECCCCCCHHHHHHHHHH
T ss_pred             cccccccccCCCCcchHHHHHHHHHHHHhhcccCCCCeEEEEecCCchhhCHHHhCCCccceeeecCCcCHHHHHHHHHH
Confidence            47888886543   334568899999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccc
Q 039253           80 CLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACK  159 (199)
Q Consensus        80 ~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~P  159 (199)
                      |++++++..++++..||+.|+|||||||+++|++|++.|+++..                   ..|+++||..|++++.|
T Consensus       364 ~~~~~~~~~d~dl~~lA~~t~G~sGADi~~l~~eA~~~air~~~-------------------~~i~~~d~~~Al~~v~~  424 (437)
T 4b4t_L          364 HTAKVKKTGEFDFEAAVKMSDGFNGADIRNCATEAGFFAIRDDR-------------------DHINPDDLMKAVRKVAE  424 (437)
T ss_dssp             HHHTSCBCSCCCHHHHHHTCCSCCHHHHHHHHHHHHHHHHHTTC-------------------SSBCHHHHHHHHHHHHH
T ss_pred             HhcCCCCCcccCHHHHHHhCCCCCHHHHHHHHHHHHHHHHHcCC-------------------CCCCHHHHHHHHHHHHh
Confidence            99999988899999999999999999999999999999987642                   56999999999999999


Q ss_pred             cccccCCccc
Q 039253          160 SQSRGFGDEF  169 (199)
Q Consensus       160 s~~r~~~~~~  169 (199)
                      +...+-..+|
T Consensus       425 ~~k~e~~~e~  434 (437)
T 4b4t_L          425 VKKLEGTIEY  434 (437)
T ss_dssp             TCC-------
T ss_pred             ccCcccchhh
Confidence            8766544333

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.96  E-value=1.1e-29  Score=225.88  Aligned_cols=142  Identities=35%  Similarity=0.441  Sum_probs=126.7

Q ss_pred             cceeeccCCC---CCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEec-CCCHHHHHHHHH
Q 039253            3 WSIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIP-LPVEKSRLQIFK   78 (199)
Q Consensus         3 ~sl~~~R~~~---~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~-~P~~~~R~~il~   78 (199)
                      ++++++|...   .+....+++++||++|||+.+..+|+||+|||+|+.||||++||||||++|+|| +|+.++|..||+
T Consensus       275 D~i~~~R~~~~~~~~~~~~r~l~~lL~~ldg~~~~~~v~vI~aTN~~~~LD~AllRpGRfd~~I~~p~lPd~~~R~~Il~  354 (428)
T 4b4t_K          275 DSIATKRFDAQTGSDREVQRILIELLTQMDGFDQSTNVKVIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFG  354 (428)
T ss_dssp             HHHHCSCSSSCSCCCCHHHHHHHHHHHHHHHSCSSCSEEEEEEESCSSSCCHHHHSSSSEEEEEECCSSCCHHHHHHHHH
T ss_pred             hhhhccccCCCCCCChHHHHHHHHHHHHhhCCCCCCCEEEEEecCChhhcChhhhcCCcceEEEEcCCCCCHHHHHHHHH
Confidence            3677888544   344567899999999999999999999999999999999999999999999996 899999999999


Q ss_pred             HhhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHh-c
Q 039253           79 ACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKY-A  157 (199)
Q Consensus        79 ~~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~-~  157 (199)
                      .+++++++..++++..||+.|+|||||||+++|++|++.|+++..                   ..|+++||..|+.. +
T Consensus       355 ~~~~~~~l~~~~dl~~lA~~t~G~sgadi~~l~~eA~~~a~r~~~-------------------~~i~~~d~~~A~~~~~  415 (428)
T 4b4t_K          355 TIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQEAGLRAVRKNR-------------------YVILQSDLEEAYATQV  415 (428)
T ss_dssp             HHHHSSCBCTTCCHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTC-------------------SSBCHHHHHHHHHHHS
T ss_pred             HHhcCCCCCcccCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCC-------------------CCCCHHHHHHHHHHhh
Confidence            999999988899999999999999999999999999999988652                   56999999999976 5


Q ss_pred             cccccc
Q 039253          158 CKSQSR  163 (199)
Q Consensus       158 ~Ps~~r  163 (199)
                      +++...
T Consensus       416 ~~~~~~  421 (428)
T 4b4t_K          416 KTDNTV  421 (428)
T ss_dssp             CSCCCS
T ss_pred             CccCCc
Confidence            555543

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.96  E-value=1.4e-29  Score=226.20  Aligned_cols=142  Identities=26%  Similarity=0.430  Sum_probs=128.5

Q ss_pred             cceeeccCCCCCc---hhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHH
Q 039253            3 WSIVIQRGSGAGG---AADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKA   79 (199)
Q Consensus         3 ~sl~~~R~~~~~~---~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~   79 (199)
                      ++++++|+...++   ...+++++||++||++....+|+||+|||+|+.||+|++||||||++|+|++|+.++|.+||+.
T Consensus       312 Dai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~  391 (467)
T 4b4t_H          312 DAVGGARFDDGAGGDNEVQRTMLELITQLDGFDPRGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRI  391 (467)
T ss_dssp             TTTSBCCSSSSCGGGGHHHHHHHHHHHHHHSSCCTTTEEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHHHHHHHH
T ss_pred             ccccccccCcCCCccHHHHHHHHHHHHHhhccCCCCcEEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHHHHHHHH
Confidence            4688888765433   3557899999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccc
Q 039253           80 CLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACK  159 (199)
Q Consensus        80 ~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~P  159 (199)
                      +++++++..++++..||+.|+|||||||+++|++|++.|+++..                   ..++++||..|++++.+
T Consensus       392 ~l~~~~l~~dvdl~~LA~~T~GfSGADI~~l~~eAa~~Air~~~-------------------~~it~~Df~~Al~kV~~  452 (467)
T 4b4t_H          392 HSKSMSVERGIRWELISRLCPNSTGAELRSVCTEAGMFAIRARR-------------------KVATEKDFLKAVDKVIS  452 (467)
T ss_dssp             HHTTSCBCSSCCHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHTC-------------------SSBCHHHHHHHHHHHHH
T ss_pred             HhcCCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHcCC-------------------CccCHHHHHHHHHHHhc
Confidence            99999998899999999999999999999999999999988752                   56899999999999877


Q ss_pred             cccc
Q 039253          160 SQSR  163 (199)
Q Consensus       160 s~~r  163 (199)
                      +..+
T Consensus       453 g~~k  456 (467)
T 4b4t_H          453 GYKK  456 (467)
T ss_dssp             HHCC
T ss_pred             Cccc
Confidence            6543

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=99.94  E-value=4.6e-27  Score=222.31  Aligned_cols=162  Identities=31%  Similarity=0.442  Sum_probs=141.6

Q ss_pred             cceeeccCCCCCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhc
Q 039253            3 WSIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR   82 (199)
Q Consensus         3 ~sl~~~R~~~~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~   82 (199)
                      ++|+++|++..++..++++++||++||++....+|+||+|||+|+.||+|++||||||++|++++|+.++|.+||+.+++
T Consensus       307 Dal~~~r~~~~~~~~~riv~~LL~~mdg~~~~~~V~VIaaTN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~  386 (806)
T 3cf2_A          307 DAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTK  386 (806)
T ss_dssp             GGTCCTTTTCCCTTHHHHHHHHHTHHHHCCGGGCEEEEEECSSTTTSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCS
T ss_pred             cccccccCCCCChHHHHHHHHHHHHHhcccccCCEEEEEecCChhhcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhc
Confidence            47899999888888999999999999999988899999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcccccc
Q 039253           83 KSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQS  162 (199)
Q Consensus        83 ~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps~~  162 (199)
                      +.++..++++..||.+|+||+|+||+.+|++|++.|+++........  .............++.+||..|++.++|+++
T Consensus       387 ~~~~~~dvdl~~lA~~T~GfsgaDL~~Lv~eA~~~A~~r~~~~i~~~--~~~~~~e~~~~~~v~~~Df~~Al~~~~ps~~  464 (806)
T 3cf2_A          387 NMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLE--DETIDAEVMNSLAVTMDDFRWALSQSNPSAL  464 (806)
T ss_dssp             SSEECTTCCHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHHHHHGGGT--CCCCSHHHHHHCEECTTHHHHHHSSSSCCCC
T ss_pred             CCCCCcccCHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcccccccc--ccccchhhhccceeeHHHHHHHHHhCCCccc
Confidence            99888899999999999999999999999999999999876432111  1111112223466899999999999999999


Q ss_pred             ccCC
Q 039253          163 RGFG  166 (199)
Q Consensus       163 r~~~  166 (199)
                      ++..
T Consensus       465 r~~~  468 (806)
T 3cf2_A          465 RETV  468 (806)
T ss_dssp             CCCC
T ss_pred             cccc
Confidence            8653

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=99.93  E-value=1.2e-25  Score=189.06  Aligned_cols=152  Identities=39%  Similarity=0.653  Sum_probs=117.4

Q ss_pred             eeeccCCCCCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcC-
Q 039253            5 IVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRK-   83 (199)
Q Consensus         5 l~~~R~~~~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~-   83 (199)
                      +++.|+....+...+++++++.+|++......++++++||+|+.||++++||||||+.|++++|+.++|.+||+.+++. 
T Consensus       115 ~~~~r~~~~~~~~~~~~~~~l~~Lsgg~~~~~~i~ia~tn~p~~LD~al~r~gRfd~~i~~~~P~~~~r~~il~~~~~~~  194 (274)
T 2x8a_A          115 LCPRRSDRETGASVRVVNQLLTEMDGLEARQQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTITKNG  194 (274)
T ss_dssp             TCC---------CTTHHHHHHHHHHTCCSTTCEEEEEEESCGGGSCHHHHSTTSSCEEEECCSCCHHHHHHHHHHHTTTT
T ss_pred             hhcccCCCcchHHHHHHHHHHHhhhcccccCCEEEEeecCChhhCCHhhcCcccCCeEEEeCCcCHHHHHHHHHHHHhcc
Confidence            3444544333445688999999999998888899999999999999999999999999999999999999999999954 


Q ss_pred             --CCCCCcccHHHHHhhC--CCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccc
Q 039253           84 --SPVSKDVDLEKLAQFT--QGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACK  159 (199)
Q Consensus        84 --~~~~~~~~l~~la~~t--~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~P  159 (199)
                        .++..++++..+|..|  +||||+||.++|++|++.|+++.......        ........|+++||+.|++.++|
T Consensus       195 ~~~~~~~~~~~~~la~~~~~~g~sgadl~~l~~~a~~~a~~~~~~~~~~--------~~~~~~~~i~~~df~~al~~~~p  266 (274)
T 2x8a_A          195 TKPPLDADVNLEAIAGDLRCDCYTGADLSALVREASICALRQEMARQKS--------GNEKGELKVSHKHFEEAFKKVRS  266 (274)
T ss_dssp             BTTBBCTTCCHHHHHTCSGGGSCCHHHHHHHHHHHHHHHHHHHC-------------------CCBCHHHHHHHHTTCCC
T ss_pred             cCCCCccccCHHHHHHhhccCCcCHHHHHHHHHHHHHHHHHHHHhhccc--------cccccCCeecHHHHHHHHHHhcC
Confidence              3455789999999975  49999999999999999999876432110        00112257999999999999999


Q ss_pred             ccccc
Q 039253          160 SQSRG  164 (199)
Q Consensus       160 s~~r~  164 (199)
                      |.+++
T Consensus       267 s~~~~  271 (274)
T 2x8a_A          267 SISKK  271 (274)
T ss_dssp             CC---
T ss_pred             CCChh
Confidence            98764

>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=99.89  E-value=1.3e-22  Score=171.93  Aligned_cols=150  Identities=69%  Similarity=1.077  Sum_probs=124.5

Q ss_pred             chhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCcccHHH
Q 039253           15 GAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEK   94 (199)
Q Consensus        15 ~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~l~~   94 (199)
                      +...+++++||..|+++....+|+||+|||+++.||++++|+|||+..|+|++|+.++|.+||+.++++.++..++++..
T Consensus       133 ~~~~~~~~~lL~~l~~~~~~~~v~vi~atn~~~~ld~al~r~gRf~~~i~i~~p~~~~r~~il~~~l~~~~~~~~~~~~~  212 (301)
T 3cf0_A          133 GAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEF  212 (301)
T ss_dssp             CSCCHHHHHHHHHHHSSCTTSSEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCSSCCHHH
T ss_pred             hHHHHHHHHHHHHhhcccCCCCEEEEEecCCccccChHHhcCCccceEEecCCcCHHHHHHHHHHHHccCCCCccchHHH
Confidence            45678999999999999888889999999999999999999999999999999999999999999999888777899999


Q ss_pred             HHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCC--Cc----chhhccccccHHHHHHHHHhcccccccc
Q 039253           95 LAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQ--PE----AIEDEVAEIKAEHFEESMKYACKSQSRG  164 (199)
Q Consensus        95 la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~--~~----~~~~~~~~it~~df~~Al~~~~Ps~~r~  164 (199)
                      ++..|+||+|+||+++|++|++.|+++.+...........  ..    ........|+.+||..||+.++||.+..
T Consensus       213 la~~~~g~sg~dl~~l~~~a~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~al~~~~~s~~~~  288 (301)
T 3cf0_A          213 LAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDN  288 (301)
T ss_dssp             HHHTCSSCCHHHHHHHHHHHHHHHHHHHHHHHC--------------------CCCBCHHHHHHHHTTCCCSSCHH
T ss_pred             HHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccccccccccccccCCccCHHHHHHHHHHcCCCCCHH
Confidence            9999999999999999999999999887643221100000  00    0012235799999999999999998863

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=99.89  E-value=6.6e-23  Score=175.72  Aligned_cols=159  Identities=27%  Similarity=0.384  Sum_probs=130.5

Q ss_pred             ceeeccCCCCCchhhHHHHHHHHHHhCCC-CCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhc
Q 039253            4 SIVIQRGSGAGGAADRIPNQLLTEMDGLS-AKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR   82 (199)
Q Consensus         4 sl~~~R~~~~~~~~~r~~~~lL~~ld~~~-~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~   82 (199)
                      +++++|+...++...+++++|+.+|+++. ...+|+||+|||+|+.+|++++|  ||+..+++++|+.++|.+||+.+++
T Consensus       116 ~l~~~~~~~~~~~~~~~~~~ll~~ld~~~~~~~~v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~  193 (322)
T 1xwi_A          116 SLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEPHARAAMFKLHLG  193 (322)
T ss_dssp             GGGCCSSSCCTTHHHHHHHHHHHHHHCSSSCCTTEEEEEEESCTTTSCHHHHH--TCCEEEECCCCCHHHHHHHHHHHHT
T ss_pred             HhccccccccchHHHHHHHHHHHHHhcccccCCCEEEEEecCCcccCCHHHHh--hcCeEEEeCCcCHHHHHHHHHHHHh
Confidence            56777877777788999999999999986 35789999999999999999999  9999999999999999999999998


Q ss_pred             CCCCC-CcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhc----CC-----------------------C
Q 039253           83 KSPVS-KDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRK----GK-----------------------Q  134 (199)
Q Consensus        83 ~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~----~~-----------------------~  134 (199)
                      +.+.. .+.++..||+.|+||||+||..+|++|++.++++..........    ..                       .
T Consensus       194 ~~~~~l~~~~l~~la~~t~G~sgadl~~l~~~A~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  273 (322)
T 1xwi_A          194 TTQNSLTEADFRELGRKTDGYSGADISIIVRDALMQPVRKVQSATHFKKVRGPSRADPNHLVDDLLTPCSPGDPGAIEMT  273 (322)
T ss_dssp             TCCBCCCHHHHHHHHHTCTTCCHHHHHHHHHHHHTHHHHHHHHCSEEEEEEEECSSCTTSEEEEEEEECCSSSTTEEECC
T ss_pred             cCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccccccccccccccccccccccchhhcc
Confidence            87654 67889999999999999999999999999999987643211000    00                       0


Q ss_pred             Ccc---hhhccccccHHHHHHHHHhcccccccc
Q 039253          135 PEA---IEDEVAEIKAEHFEESMKYACKSQSRG  164 (199)
Q Consensus       135 ~~~---~~~~~~~it~~df~~Al~~~~Ps~~r~  164 (199)
                      ...   ......+|+++||..||+.++||.+.+
T Consensus       274 ~~~~~~~~~~~~~v~~~df~~al~~~~ps~~~~  306 (322)
T 1xwi_A          274 WMDVPGDKLLEPVVSMSDMLRSLSNTKPTVNEH  306 (322)
T ss_dssp             GGGSCGGGBCCCCBCHHHHHHHHHTCCCSCCHH
T ss_pred             ccccccccccCCCcCHHHHHHHHHhCCCCCCHH
Confidence            000   001125799999999999999998863

>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=99.87  E-value=5.2e-22  Score=172.25  Aligned_cols=159  Identities=26%  Similarity=0.423  Sum_probs=124.0

Q ss_pred             ceeeccCCCCCchhhHHHHHHHHHHhCCCC-CCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhc
Q 039253            4 SIVIQRGSGAGGAADRIPNQLLTEMDGLSA-KKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR   82 (199)
Q Consensus         4 sl~~~R~~~~~~~~~r~~~~lL~~ld~~~~-~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~   82 (199)
                      ++.++|+...+....++.++||.+|+++.. ..+|+||+|||+|+.||++++|  ||+..+++++|+.++|.+||+.++.
T Consensus       154 ~l~~~r~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~  231 (355)
T 2qp9_X          154 ALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVG  231 (355)
T ss_dssp             GGTC------CTHHHHHHHHHHHHHHHCC---CCEEEEEEESCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHHHHT
T ss_pred             hhcccCCCCcchHHHHHHHHHHHHhhcccccCCCeEEEeecCCcccCCHHHHc--ccCEEEEeCCcCHHHHHHHHHHHHh
Confidence            456677776777888999999999999864 5679999999999999999999  9999999999999999999999998


Q ss_pred             CCCCC-CcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcC---------------------CCCcc---
Q 039253           83 KSPVS-KDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKG---------------------KQPEA---  137 (199)
Q Consensus        83 ~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~---------------------~~~~~---  137 (199)
                      ..+.. .+.++..||+.|+||+|+||..+|++|++.|+++...........                     ..+..   
T Consensus       232 ~~~~~~~~~~l~~la~~t~G~sg~dl~~l~~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  311 (355)
T 2qp9_X          232 DTPSVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIRKIQSATHFKDVSTEDDETRKLTPSSPGDDGAIEMSWTDIEA  311 (355)
T ss_dssp             TSCBCCCHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHHHCSEEEECCC-----CCEEEECTTSSSEEECCGGGSCG
T ss_pred             hCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccCcCCccccchhhcccccccc
Confidence            87653 578899999999999999999999999999999875431100000                     00000   


Q ss_pred             hhhccccccHHHHHHHHHhcccccccc
Q 039253          138 IEDEVAEIKAEHFEESMKYACKSQSRG  164 (199)
Q Consensus       138 ~~~~~~~it~~df~~Al~~~~Ps~~r~  164 (199)
                      ......+|+++||..||+.++||++++
T Consensus       312 ~~~~~~~v~~~df~~Al~~~~ps~~~~  338 (355)
T 2qp9_X          312 DELKEPDLTIKDFLKAIKSTRPTVNED  338 (355)
T ss_dssp             GGBCCCCBCHHHHHHHHHHSCCSSCHH
T ss_pred             cccccCCccHHHHHHHHHHcCCCCCHH
Confidence            011235699999999999999999864

>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=99.87  E-value=5.4e-22  Score=169.54  Aligned_cols=159  Identities=27%  Similarity=0.452  Sum_probs=125.9

Q ss_pred             ceeeccCCCCCchhhHHHHHHHHHHhCCC-CCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhc
Q 039253            4 SIVIQRGSGAGGAADRIPNQLLTEMDGLS-AKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR   82 (199)
Q Consensus         4 sl~~~R~~~~~~~~~r~~~~lL~~ld~~~-~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~   82 (199)
                      ++.++|+...+....++.++|+..|+++. ...+|+||+|||+|+.||++++|  ||+..+++++|+.++|.+||+.++.
T Consensus       121 ~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~atn~~~~ld~al~~--Rf~~~i~~~~p~~~~r~~il~~~~~  198 (322)
T 3eie_A          121 ALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVG  198 (322)
T ss_dssp             GGSCC------CCTHHHHHHHHHHHGGGGTSCCCEEEEEEESCGGGSCHHHHH--HCCEEEECCCCCHHHHHHHHHHHHT
T ss_pred             hhhccCCCCcchHHHHHHHHHHHHhccccccCCceEEEEecCChhhCCHHHHc--ccCeEEEeCCCCHHHHHHHHHHHhc
Confidence            46677776677778899999999999985 55779999999999999999999  9999999999999999999999998


Q ss_pred             CCCCC-CcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcC----C--C------------------Ccc
Q 039253           83 KSPVS-KDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKG----K--Q------------------PEA  137 (199)
Q Consensus        83 ~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~----~--~------------------~~~  137 (199)
                      +.+.. .+.++..|++.|+||+|+||..+|++|++.++++...........    .  .                  ...
T Consensus       199 ~~~~~~~~~~l~~la~~t~g~sg~di~~l~~~a~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  278 (322)
T 3eie_A          199 DTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIRKIQSATHFKDVSTEDDETRKLTPCSPGDDGAIEMSWTDIEA  278 (322)
T ss_dssp             TCCCCCCHHHHHHHHHTTTTCCHHHHHHHHHHHTTHHHHHHHHCEEEEECC----CCCCEEECCSSCTTEEEEEGGGSCS
T ss_pred             cCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHhhhhhhhhhcccccccccccccccccccccccccccccc
Confidence            87654 678899999999999999999999999999999986532110000    0  0                  000


Q ss_pred             hhhccccccHHHHHHHHHhcccccccc
Q 039253          138 IEDEVAEIKAEHFEESMKYACKSQSRG  164 (199)
Q Consensus       138 ~~~~~~~it~~df~~Al~~~~Ps~~r~  164 (199)
                      ......+||++||..|++.++||++.+
T Consensus       279 ~~~~~~~it~~df~~al~~~~ps~~~~  305 (322)
T 3eie_A          279 DELKEPDLTIKDFLKAIKSTRPTVNED  305 (322)
T ss_dssp             SCBCCCCCCHHHHHHHHHHSCCSSCTT
T ss_pred             ccccCCCCCHHHHHHHHHhcCCCCCHH
Confidence            011225799999999999999999864

>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=99.86  E-value=8.8e-22  Score=175.60  Aligned_cols=158  Identities=27%  Similarity=0.381  Sum_probs=129.5

Q ss_pred             ceeeccCCCCCchhhHHHHHHHHHHhCCCC-CCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhc
Q 039253            4 SIVIQRGSGAGGAADRIPNQLLTEMDGLSA-KKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR   82 (199)
Q Consensus         4 sl~~~R~~~~~~~~~r~~~~lL~~ld~~~~-~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~   82 (199)
                      +++++|+...++...+++++||..|+++.. ..+|+||+|||+|+.||++++|  ||+..+++++|+.++|..||+.++.
T Consensus       238 ~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~v~vI~atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~  315 (444)
T 2zan_A          238 SLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEAHARAAMFRLHLG  315 (444)
T ss_dssp             TTCCCSSCCCCGGGHHHHHHHHTTTTCSSCCCSSCEEEEEESCGGGSCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHT
T ss_pred             hhccCCCCccccHHHHHHHHHHHHHhCcccCCCCEEEEecCCCccccCHHHHh--hcceEEEeCCcCHHHHHHHHHHHHh
Confidence            466777777777888999999999999864 5779999999999999999999  9999999999999999999999998


Q ss_pred             CCCCC-CcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCC---------------------------C
Q 039253           83 KSPVS-KDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGK---------------------------Q  134 (199)
Q Consensus        83 ~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~---------------------------~  134 (199)
                      ..+.. .+.++..||..|+||||+||..+|++|++.|+++............                           .
T Consensus       316 ~~~~~l~~~~l~~la~~t~G~sgadl~~l~~~a~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  395 (444)
T 2zan_A          316 STQNSLTEADFQELGRKTDGYSGADISIIVRDALMQPVRKVQSATHFKKVRGPSRADPNCIVNDLLTPCSPGDPGAIEMT  395 (444)
T ss_dssp             TSCEECCHHHHHHHHHHTTTCCHHHHHHHHHHHHTHHHHHHHHCSEEEEECCBCSSCTTSBCSCEEEEECTTSTTEEECC
T ss_pred             cCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccccccccccccccccCCCCcccchhcc
Confidence            87653 6788999999999999999999999999999999865321110000                           0


Q ss_pred             Ccc---hhhccccccHHHHHHHHHhccccccc
Q 039253          135 PEA---IEDEVAEIKAEHFEESMKYACKSQSR  163 (199)
Q Consensus       135 ~~~---~~~~~~~it~~df~~Al~~~~Ps~~r  163 (199)
                      +..   ......+||++||..||+.++||++.
T Consensus       396 ~~~~~~~~~~~~~v~~~df~~a~~~~~ps~~~  427 (444)
T 2zan_A          396 WMDVPGDKLLEPVVSMWDMLRSLSSTKPTVNE  427 (444)
T ss_dssp             TTTSCTTCBCCCCEEHHHHHHHHHTCCCSCCH
T ss_pred             cccCchhhccCCccCHHHHHHHHHhCCCCCCH
Confidence            000   00112579999999999999999875

>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=99.86  E-value=1.4e-21  Score=176.50  Aligned_cols=173  Identities=30%  Similarity=0.425  Sum_probs=136.0

Q ss_pred             ceeeccCCCCCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcC
Q 039253            4 SIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRK   83 (199)
Q Consensus         4 sl~~~R~~~~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~   83 (199)
                      +++++|+...++...++.++||..|+++....+|+||+|||+++.||++++|+|||+..|+|++|+.++|.+||+.+++.
T Consensus       308 ~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~v~vIaaTn~~~~Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~~  387 (489)
T 3hu3_A          308 AIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKN  387 (489)
T ss_dssp             HHCBCTTSCCCHHHHHHHHHHHHHHHHSCTTSCEEEEEEESCGGGBCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHTTT
T ss_pred             hhccccccccchHHHHHHHHHHHHhhccccCCceEEEEecCCccccCHHHhCCCcCceEEEeCCCCHHHHHHHHHHHHhc
Confidence            45677776667778899999999999998888999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccccccc
Q 039253           84 SPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQSR  163 (199)
Q Consensus        84 ~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps~~r  163 (199)
                      .++..+.++..++..+.||+|+||..+|++|++.++++........  .............++++||..|++.++||++|
T Consensus       388 ~~l~~~~~l~~la~~t~g~s~~dL~~L~~~A~~~a~r~~~~~i~~~--~~~~~~~~~~~~~vt~edf~~Al~~~~ps~~r  465 (489)
T 3hu3_A          388 MKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLE--DETIDAEVMNSLAVTMDDFRWALSQSNPSALR  465 (489)
T ss_dssp             SCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTTTTCCTT--CSSCCHHHHHHCCBCHHHHHHHHTSHHHHHHH
T ss_pred             CCCcchhhHHHHHHHccCCcHHHHHHHHHHHHHHHHHhcccccccc--ccccchhhcccCcCCHHHHHHHHHhCCchhhh
Confidence            8888888999999999999999999999999999988764211000  00001112233579999999999999999999


Q ss_pred             cCCcc---cccchhhhhh
Q 039253          164 GFGDE---FGFCETAVAA  178 (199)
Q Consensus       164 ~~~~~---~~~~~~~~~~  178 (199)
                      ++.-+   ..|.+.+|-.
T Consensus       466 e~~~e~p~v~W~dig~~~  483 (489)
T 3hu3_A          466 ETVVEVPQVTWEDIGGRS  483 (489)
T ss_dssp             GGGC--------------
T ss_pred             cccccCCCCCHHHcCCCc
Confidence            76443   6677776643

>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=99.85  E-value=6.6e-21  Score=171.52  Aligned_cols=140  Identities=39%  Similarity=0.631  Sum_probs=117.8

Q ss_pred             ceeeccCCC---CCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHh
Q 039253            4 SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKAC   80 (199)
Q Consensus         4 sl~~~R~~~---~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~   80 (199)
                      +++++|+.+   .+....+++++||..||++....+|+||+|||+++.||++++|||||++.|+|++|+.++|.+||+.+
T Consensus       119 ~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~~~~~~~viVIaaTn~~~~Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~  198 (476)
T 2ce7_A          119 AVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIH  198 (476)
T ss_dssp             GTCCC---------CHHHHHHHHHHHHHHHSCGGGTEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHH
T ss_pred             hhhhhcccccCcCcHHHHHHHHHHHHHHhccCCCCCEEEEEecCChhhhchhhcccCcceeEeecCCCCHHHHHHHHHHH
Confidence            455666532   33445688999999999988778899999999999999999999999999999999999999999999


Q ss_pred             hcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcccc
Q 039253           81 LRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKS  160 (199)
Q Consensus        81 l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps  160 (199)
                      +++.++..++++..+|..|+||+|+||.++|++|+..|.++..                   ..|+.+||..|+.++.+.
T Consensus       199 ~~~~~l~~~v~l~~la~~t~G~sgadL~~lv~~Aal~A~~~~~-------------------~~I~~~dl~~al~~v~~~  259 (476)
T 2ce7_A          199 TRNKPLAEDVNLEIIAKRTPGFVGADLENLVNEAALLAAREGR-------------------DKITMKDFEEAIDRVIAG  259 (476)
T ss_dssp             HTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTC-------------------SSBCHHHHHHHHHHHC--
T ss_pred             HHhCCCcchhhHHHHHHhcCCCcHHHHHHHHHHHHHHHHHcCC-------------------CeecHHHHHHHHHHHhcC
Confidence            9998888889999999999999999999999999988875431                   569999999999998765


Q ss_pred             cc
Q 039253          161 QS  162 (199)
Q Consensus       161 ~~  162 (199)
                      ..
T Consensus       260 ~~  261 (476)
T 2ce7_A          260 PA  261 (476)
T ss_dssp             --
T ss_pred             cc
Confidence            43

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=99.83  E-value=1.5e-19  Score=149.03  Aligned_cols=125  Identities=38%  Similarity=0.627  Sum_probs=114.1

Q ss_pred             hhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCcccHHHH
Q 039253           16 AADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKL   95 (199)
Q Consensus        16 ~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~l~~l   95 (199)
                      ...++++++|..|+++....+++||+|||+++.+|++++|+|||++.+++++|+.++|.+||+.++++.++..+.++..+
T Consensus       130 ~~~~~~~~ll~~l~~~~~~~~~~vI~~tn~~~~l~~~l~r~~rf~~~i~i~~P~~~~r~~il~~~~~~~~l~~~~~~~~l  209 (257)
T 1lv7_A          130 EREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAII  209 (257)
T ss_dssp             HHHHHHHHHHHHHHTCCSSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHH
T ss_pred             HHHHHHHHHHHHhhCcccCCCEEEEEeeCCchhCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhcCCCCccccHHHH
Confidence            34578999999999998888899999999999999999999999999999999999999999999998888888899999


Q ss_pred             HhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccc
Q 039253           96 AQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACK  159 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~P  159 (199)
                      +..++||+++||.++|++|+..|.++..                   ..|+.+||..|++.+..
T Consensus       210 a~~~~G~~~~dl~~l~~~a~~~a~~~~~-------------------~~i~~~~~~~a~~~~~~  254 (257)
T 1lv7_A          210 ARGTPGFSGADLANLVNEAALFAARGNK-------------------RVVSMVEFEKAKDKIMM  254 (257)
T ss_dssp             HHTCTTCCHHHHHHHHHHHHHHHHHTTC-------------------SSBCHHHHHHHHHHHTT
T ss_pred             HHHcCCCCHHHHHHHHHHHHHHHHHhCC-------------------CcccHHHHHHHHHHHhc
Confidence            9999999999999999999988876532                   56999999999998753

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=99.83  E-value=1.8e-20  Score=169.57  Aligned_cols=154  Identities=39%  Similarity=0.573  Sum_probs=128.1

Q ss_pred             eeeccCCC---CCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhh
Q 039253            5 IVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACL   81 (199)
Q Consensus         5 l~~~R~~~---~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l   81 (199)
                      +.++|...   .+....+.+++||.+|++......+++|++||+|+.||++++|+|||++.|+|++|+.++|.+||+.++
T Consensus       135 l~~~r~~~~~~~~~e~~~~l~~LL~~Ldg~~~~~~viviAatn~p~~LD~aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~  214 (499)
T 2dhr_A          135 VGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHA  214 (499)
T ss_dssp             TCCCSSSSTTTSSHHHHHHHHHHHHHGGGCCSSCCCEEEECCSCGGGSCTTTSSTTSSCCEEECCCCCHHHHHHHHHHTT
T ss_pred             HHHhhccCcCCCcHHHHHHHHHHHHHhcccccCccEEEEEecCChhhcCcccccccccceEEecCCCCHHHHHHHHHHHH
Confidence            44555432   234456789999999999988788999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccccc
Q 039253           82 RKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQ  161 (199)
Q Consensus        82 ~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps~  161 (199)
                      ++.++..++++..+|..|+||+|+||+++|++|+..|.++..                   ..|+.+||..|+..+.+..
T Consensus       215 ~~~~l~~dv~l~~lA~~t~G~~gadL~~lv~~Aa~~A~~~~~-------------------~~It~~dl~~al~~v~~~~  275 (499)
T 2dhr_A          215 RGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREGR-------------------RKITMKDLEEAADRVMMLP  275 (499)
T ss_dssp             SSSCCCCSSTTHHHHTTSCSCCHHHHHHHHHHHHHHHTTTCC-------------------SSCCSHHHHHHHHHHTTCS
T ss_pred             hcCCCChHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhCC-------------------CccCHHHHHHHHHHHhccc
Confidence            988888889999999999999999999999999888765431                   4699999999999998775


Q ss_pred             ccc---CC----cccccchhhhh
Q 039253          162 SRG---FG----DEFGFCETAVA  177 (199)
Q Consensus       162 ~r~---~~----~~~~~~~~~~~  177 (199)
                      .+.   +.    ...-|+|.+.+
T Consensus       276 ~~~~~~~~~~e~~~~a~~e~g~a  298 (499)
T 2dhr_A          276 AKKSLVLSPRDRRITAYHEAGHA  298 (499)
T ss_dssp             SSSCCCCCTTHHHHHHHHHHHHH
T ss_pred             ccccchhhHHHHhhhHHHHHHHH
Confidence            432   11    23456666554

>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=99.81  E-value=2.4e-19  Score=147.50  Aligned_cols=121  Identities=45%  Similarity=0.664  Sum_probs=109.7

Q ss_pred             chhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCcccHHH
Q 039253           15 GAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEK   94 (199)
Q Consensus        15 ~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~l~~   94 (199)
                      ....+++++++..|++......++++++||+|+.||++++|+|||++.+++++|+.++|.+||+.+++..++..++++..
T Consensus       133 ~~~~~~~~~ll~~l~g~~~~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~  212 (254)
T 1ixz_A          133 DEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLAL  212 (254)
T ss_dssp             HHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHH
T ss_pred             hHHHHHHHHHHHHHhCCCCCCCEEEEEccCCchhCCHHHcCCCcCCeEEeeCCcCHHHHHHHHHHHHcCCCCCcccCHHH
Confidence            34567899999999998877789999999999999999999999999999999999999999999998888878889999


Q ss_pred             HHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHH
Q 039253           95 LAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESM  154 (199)
Q Consensus        95 la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al  154 (199)
                      +|..|+||+|+||+++|++|+..|.++..                   ..|+.+||.+|+
T Consensus       213 la~~~~G~~~~dl~~~~~~a~~~a~~~~~-------------------~~I~~~dl~~a~  253 (254)
T 1ixz_A          213 LAKRTPGFVGADLENLLNEAALLAAREGR-------------------RKITMKDLEEAA  253 (254)
T ss_dssp             HHHTCTTCCHHHHHHHHHHHHHHHHHTTC-------------------SSBCHHHHHHHT
T ss_pred             HHHHcCCCCHHHHHHHHHHHHHHHHHhcC-------------------CCcCHHHHHHHh
Confidence            99999999999999999999888865431                   469999999886

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=99.78  E-value=1.4e-18  Score=144.76  Aligned_cols=128  Identities=41%  Similarity=0.706  Sum_probs=115.7

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCcccHHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLA   96 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~l~~la   96 (199)
                      ..+.+..++..++++....+++||+|||.++.+|++++|+|||+..++++.|+.++|.+||+.++....+..+.++..++
T Consensus       137 ~~~~l~~ll~~~~~~~~~~~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~l~  216 (285)
T 3h4m_A          137 VQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIA  216 (285)
T ss_dssp             HHHHHHHHHHHHHTTCSSSSEEEEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHH
T ss_pred             HHHHHHHHHHHhhCCCCCCCEEEEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCCCcCCHHHHH
Confidence            45678888999998888889999999999999999999999999999999999999999999999988877788999999


Q ss_pred             hhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccccccc
Q 039253           97 QFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQSR  163 (199)
Q Consensus        97 ~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps~~r  163 (199)
                      ..+.||+|+||..+|+.|...|+.+..                   ..|+.+||..|++.+.+....
T Consensus       217 ~~~~g~~~~~i~~l~~~a~~~a~~~~~-------------------~~I~~~d~~~al~~~~~~~~~  264 (285)
T 3h4m_A          217 KMTEGCVGAELKAICTEAGMNAIRELR-------------------DYVTMDDFRKAVEKIMEKKKV  264 (285)
T ss_dssp             HHCTTCCHHHHHHHHHHHHHHHHHTTC-------------------SSBCHHHHHHHHHHHHHHHCC
T ss_pred             HHcCCCCHHHHHHHHHHHHHHHHHhcc-------------------CcCCHHHHHHHHHHHHhcccc
Confidence            999999999999999999999877642                   569999999999998765443

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=99.78  E-value=2.5e-18  Score=143.51  Aligned_cols=121  Identities=45%  Similarity=0.664  Sum_probs=108.9

Q ss_pred             chhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCcccHHH
Q 039253           15 GAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEK   94 (199)
Q Consensus        15 ~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~l~~   94 (199)
                      ....+.+++++..|++......++++++||+|+.||++++|++||++.|+|++|+.++|.+||+.+++...+..++++..
T Consensus       157 ~~~~~~~~~ll~~lsgg~~~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~  236 (278)
T 1iy2_A          157 DEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLAL  236 (278)
T ss_dssp             HHHHHHHHHHHHHHTTCCTTCCEEEEEEESCTTSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHH
T ss_pred             hHHHHHHHHHHHHHhCCCCCCCEEEEEecCCchhCCHhHcCCCcCCeEEEeCCcCHHHHHHHHHHHHccCCCCcccCHHH
Confidence            34567889999999998777779999999999999999999999999999999999999999999998888778889999


Q ss_pred             HHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHH
Q 039253           95 LAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESM  154 (199)
Q Consensus        95 la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al  154 (199)
                      +|..++||+|+||+++|++|+..|.++..                   ..|+.+||.+|+
T Consensus       237 la~~~~G~~~~dl~~l~~~a~~~a~~~~~-------------------~~I~~~dl~~a~  277 (278)
T 1iy2_A          237 LAKRTPGFVGADLENLLNEAALLAAREGR-------------------RKITMKDLEEAA  277 (278)
T ss_dssp             HHHTCTTCCHHHHHHHHHHHHHHHHHTTC-------------------CSBCHHHHHHHT
T ss_pred             HHHHcCCCCHHHHHHHHHHHHHHHHHhCC-------------------CCcCHHHHHHHh
Confidence            99999999999999999999888765431                   469999999886

>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=99.77  E-value=4.8e-19  Score=145.30  Aligned_cols=130  Identities=37%  Similarity=0.639  Sum_probs=107.8

Q ss_pred             chhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCcc--cH
Q 039253           15 GAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDV--DL   92 (199)
Q Consensus        15 ~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~--~l   92 (199)
                      ....+.++.|+..++++....+++||+|||.++.+|++++|+|||+..++|++|+.++|.+||+.++....+....  .+
T Consensus       124 ~~~~~~l~~ll~~~~~~~~~~~~~vi~~tn~~~~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~  203 (262)
T 2qz4_A          124 TEEEQTLNQLLVEMDGMGTTDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYS  203 (262)
T ss_dssp             ---CHHHHHHHHHHHTCCTTCCEEEEEEESCGGGGGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHTTCCBTHHHHH
T ss_pred             hhHHHHHHHHHHHhhCcCCCCCEEEEecCCChhhcCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhCCCCcchhhHH
Confidence            3455788999999999877788999999999999999999999999999999999999999999999877665333  35


Q ss_pred             HHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccccccc
Q 039253           93 EKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQSR  163 (199)
Q Consensus        93 ~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps~~r  163 (199)
                      ..++..+.||+|+||..+|++|+..|.++..                   ..|+.+||..|++.+.|+..+
T Consensus       204 ~~l~~~~~g~~~~~l~~l~~~a~~~a~~~~~-------------------~~i~~~d~~~a~~~~~~~~~~  255 (262)
T 2qz4_A          204 QRLAELTPGFSGADIANICNEAALHAAREGH-------------------TSVHTLNFEYAVERVLAGTAK  255 (262)
T ss_dssp             HHHHHTCTTCCHHHHHHHHHHHHTC---------------------------CCBCCHHHHHHHHHHHHHC
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHcCC-------------------CCCCHHHHHHHHHHhccChhh
Confidence            7899999999999999999999988876643                   569999999999999887654

>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=99.76  E-value=2.3e-18  Score=149.22  Aligned_cols=151  Identities=34%  Similarity=0.546  Sum_probs=116.5

Q ss_pred             eeeccCCCCCchhhHHHHHHHHHHhCCCC--CCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhc
Q 039253            5 IVIQRGSGAGGAADRIPNQLLTEMDGLSA--KKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR   82 (199)
Q Consensus         5 l~~~R~~~~~~~~~r~~~~lL~~ld~~~~--~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~   82 (199)
                      ++++|+.+.+....++.++||..|+++..  ..+|+||+|||+++.+|++++|  ||+..+++++|+.++|.+||+.++.
T Consensus       188 l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~--Rf~~~i~i~~p~~~~r~~il~~~~~  265 (357)
T 3d8b_A          188 LLSQRGDGEHESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAARR--RLVKRLYIPLPEASARKQIVINLMS  265 (357)
T ss_dssp             HTBC------CHHHHHHHHHHHHHHC----CCCCEEEEEEESCGGGBCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHH
T ss_pred             hhccCCCCcchHHHHHHHHHHHHHhcccccCCCCEEEEEecCChhhCCHHHHh--hCceEEEeCCcCHHHHHHHHHHHHh
Confidence            45566665666788999999999998753  4679999999999999999999  9999999999999999999999997


Q ss_pred             CCCCC-CcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccccc
Q 039253           83 KSPVS-KDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQ  161 (199)
Q Consensus        83 ~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps~  161 (199)
                      ..... .+.++..|++.|.||+|+||..+|++|+..++++......       .........+|+.+||..|++.++||.
T Consensus       266 ~~~~~l~~~~l~~la~~t~G~s~~dl~~l~~~a~~~~ir~l~~~~~-------~~~~~~~~~~i~~~d~~~al~~~~ps~  338 (357)
T 3d8b_A          266 KEQCCLSEEEIEQIVQQSDAFSGADMTQLCREASLGPIRSLQTADI-------ATITPDQVRPIAYIDFENAFRTVRPSV  338 (357)
T ss_dssp             TSCBCCCHHHHHHHHHHTTTCCHHHHHHHHHHHHTHHHHHCCC-----------------CCCBCHHHHHHHHHHHGGGC
T ss_pred             hcCCCccHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHhhhhhh-------ccccccccCCcCHHHHHHHHHhcCCCC
Confidence            76443 4667999999999999999999999999998875421100       001112236799999999999999998


Q ss_pred             ccc
Q 039253          162 SRG  164 (199)
Q Consensus       162 ~r~  164 (199)
                      +..
T Consensus       339 ~~~  341 (357)
T 3d8b_A          339 SPK  341 (357)
T ss_dssp             CCC
T ss_pred             CHH
Confidence            764

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=99.74  E-value=1.6e-18  Score=145.34  Aligned_cols=151  Identities=29%  Similarity=0.481  Sum_probs=115.9

Q ss_pred             eeeccCCCCCchhhHHHHHHHHHHhCCCCC---CCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhh
Q 039253            5 IVIQRGSGAGGAADRIPNQLLTEMDGLSAK---KTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACL   81 (199)
Q Consensus         5 l~~~R~~~~~~~~~r~~~~lL~~ld~~~~~---~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l   81 (199)
                      +...|....+....++.++|+..++++...   .+++||++||+++.+|++++|  ||+..+++++|+.++|..||+.++
T Consensus       125 l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~v~vi~~tn~~~~l~~~l~~--R~~~~i~~~~p~~~~r~~il~~~~  202 (297)
T 3b9p_A          125 LLSERSSSEHEASRRLKTEFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALR--RFTKRVYVSLPDEQTRELLLNRLL  202 (297)
T ss_dssp             TSBCC-----CCSHHHHHHHHHHHHHCC------CEEEEEEESCGGGBCHHHHH--HCCEEEECCCCCHHHHHHHHHHHH
T ss_pred             hccccccCcchHHHHHHHHHHHHHhcccccCCCCcEEEEeecCChhhCCHHHHh--hCCeEEEeCCcCHHHHHHHHHHHH
Confidence            445555444555678899999999988653   579999999999999999999  999999999999999999999999


Q ss_pred             cCCCCC-CcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcccc
Q 039253           82 RKSPVS-KDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKS  160 (199)
Q Consensus        82 ~~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps  160 (199)
                      .+.... .+..+..+++.|.||+|+||..+|++|+..++++.......       .........|+.+||..|++.++||
T Consensus       203 ~~~~~~~~~~~~~~la~~~~g~~~~~l~~l~~~a~~~a~r~~~~~~~~-------~~~~~~~~~i~~~d~~~a~~~~~~s  275 (297)
T 3b9p_A          203 QKQGSPLDTEALRRLAKITDGYSGSDLTALAKDAALEPIRELNVEQVK-------CLDISAMRAITEQDFHSSLKRIRRS  275 (297)
T ss_dssp             GGGSCCSCHHHHHHHHHHTTTCCHHHHHHHHHHHTTHHHHTCC---------------CCCCCCCCHHHHHHHTTSCCCS
T ss_pred             HhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHhhhhcc-------cccccccCCcCHHHHHHHHHHcCCC
Confidence            876443 45678999999999999999999999999988764211000       0011122579999999999999999


Q ss_pred             cccc
Q 039253          161 QSRG  164 (199)
Q Consensus       161 ~~r~  164 (199)
                      ...+
T Consensus       276 ~~~~  279 (297)
T 3b9p_A          276 VAPQ  279 (297)
T ss_dssp             SCHH
T ss_pred             CCHH
Confidence            8653

>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=99.70  E-value=6.9e-19  Score=145.51  Aligned_cols=128  Identities=34%  Similarity=0.640  Sum_probs=111.6

Q ss_pred             hHHHHHHHHHHhCCCCC-CCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCcccHHHHH
Q 039253           18 DRIPNQLLTEMDGLSAK-KTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLA   96 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~-~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~l~~la   96 (199)
                      .+++++|+..|+++... .+|+||+|||.++.+|++++|+|||+..++|++|+.++|.+||+.+++...+..++++..++
T Consensus       132 ~~~~~~ll~~l~~~~~~~~~v~vi~ttn~~~~ld~~l~r~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la  211 (268)
T 2r62_A          132 EQTLNQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVA  211 (268)
T ss_dssp             CSSTTTTTTTTTCSSCSCSCCEEEECBSCCTTSCGGGGSSSSSCCCCBCCCCCTTTHHHHHHHHTSSSCCCSSCCTTTTT
T ss_pred             HHHHHHHHHHhhCcccCCCCEEEEEecCCchhcCHhHcCCCCCCeEEEecCcCHHHHHHHHHHHHhcCCCCCccCHHHHH
Confidence            45678899999887643 45999999999999999999999999999999999999999999999988877788899999


Q ss_pred             hhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcccccccc
Q 039253           97 QFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQSRG  164 (199)
Q Consensus        97 ~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps~~r~  164 (199)
                      ..+.||+|+||.++|++|+..|..+.                   ...|+.+||..|++.+.|+..+.
T Consensus       212 ~~~~g~~g~dl~~l~~~a~~~a~~~~-------------------~~~i~~~~~~~a~~~~~~~~~~~  260 (268)
T 2r62_A          212 KLTAGLAGADLANIINEAALLAGRNN-------------------QKEVRQQHLKEAVERGIAGLEKK  260 (268)
T ss_dssp             SSSCSSCHHHHHHHHHHHHHTTSSSC-------------------CCSCCHHHHHTSCTTCCCCCC--
T ss_pred             HHcCCCCHHHHHHHHHHHHHHHHHhc-------------------cCCcCHHHHHHHHHHHhhcchhh
Confidence            99999999999999999987764432                   15699999999999999988764

>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast structural genomics consortium (NESG), target HR3102A, PSI-2; NMR {Homo sapiens}

Probab=99.69  E-value=3.1e-17  Score=115.22  Aligned_cols=78  Identities=29%  Similarity=0.467  Sum_probs=71.9

Q ss_pred             EecCCCHHHHHHHHHHhhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccc
Q 039253           64 YIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVA  143 (199)
Q Consensus        64 ~~~~P~~~~R~~il~~~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  143 (199)
                      .-.+|+.++|++||+.++++.++..++++..||+.|+|||||||+++|++|++.|+++..                   .
T Consensus         7 ~~~~Pd~~~R~~IL~~~l~~~~l~~dvdl~~LA~~T~G~SGADL~~l~~eAa~~alr~~~-------------------~   67 (86)
T 2krk_A            7 HHSHPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRERR-------------------V   67 (86)
T ss_dssp             CCCCCCHHHHHHHHHHHTTTSEECTTCCCHHHHHTCSSCCHHHHHHHHHHHHHHHHHTTC-------------------S
T ss_pred             CCCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHcC-------------------C
Confidence            346899999999999999999888899999999999999999999999999999998752                   6


Q ss_pred             cccHHHHHHHHHhcccc
Q 039253          144 EIKAEHFEESMKYACKS  160 (199)
Q Consensus       144 ~it~~df~~Al~~~~Ps  160 (199)
                      .|+++||..|+++++|.
T Consensus        68 ~I~~~df~~Al~~v~p~   84 (86)
T 2krk_A           68 HVTQEDFEMAVAKVMQK   84 (86)
T ss_dssp             EECHHHHHHHHHHHHCC
T ss_pred             CCCHHHHHHHHHHHccC
Confidence            79999999999999885

>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Homo sapiens}

Probab=99.68  E-value=5e-17  Score=111.79  Aligned_cols=76  Identities=32%  Similarity=0.528  Sum_probs=69.6

Q ss_pred             cCCCHHHHHHHHHHhhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccc
Q 039253           66 PLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEI  145 (199)
Q Consensus        66 ~~P~~~~R~~il~~~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~i  145 (199)
                      |+|+.++|.+||+.+++++++..++++..||+.|+||||+||.++|++|++.|+++..                   ..|
T Consensus         1 plPd~~~R~~Il~~~l~~~~~~~~~dl~~la~~t~G~SGADi~~l~~eA~~~a~~~~~-------------------~~i   61 (78)
T 3kw6_A            1 PPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRERR-------------------VHV   61 (78)
T ss_dssp             CCCCHHHHHHHHHHHHTTSEECTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTC-------------------SEE
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCCccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhCC-------------------CCC
Confidence            6899999999999999999888899999999999999999999999999999998752                   579


Q ss_pred             cHHHHHHHHHhcccc
Q 039253          146 KAEHFEESMKYACKS  160 (199)
Q Consensus       146 t~~df~~Al~~~~Ps  160 (199)
                      +++||..|++++..+
T Consensus        62 ~~~d~~~Al~~v~~~   76 (78)
T 3kw6_A           62 TQEDFEMAVAKVMQK   76 (78)
T ss_dssp             CHHHHHHHHHHHHC-
T ss_pred             CHHHHHHHHHHHHhc
Confidence            999999999988653

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=99.68  E-value=2e-16  Score=138.17  Aligned_cols=150  Identities=32%  Similarity=0.552  Sum_probs=115.7

Q ss_pred             eeeccCCCCCchhhHHHHHHHHHHhCCCC--CCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhc
Q 039253            5 IVIQRGSGAGGAADRIPNQLLTEMDGLSA--KKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR   82 (199)
Q Consensus         5 l~~~R~~~~~~~~~r~~~~lL~~ld~~~~--~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~   82 (199)
                      ++..|....+....++.++|+..|+++..  ..+|+||+|||+++.||++++|  ||+..++|++|+.++|.+||+.++.
T Consensus       219 l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~--R~~~~i~i~~p~~~~r~~il~~~~~  296 (389)
T 3vfd_A          219 LLCERREGEHDASRRLKTEFLIEFDGVQSAGDDRVLVMGATNRPQELDEAVLR--RFIKRVYVSLPNEETRLLLLKNLLC  296 (389)
T ss_dssp             GC--------CTHHHHHHHHHHHHHHHC-----CEEEEEEESCGGGCCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHT
T ss_pred             hcccCCCccchHHHHHHHHHHHHhhcccccCCCCEEEEEecCCchhcCHHHHc--CcceEEEcCCcCHHHHHHHHHHHHH
Confidence            45566666666788999999999998865  4679999999999999999999  9999999999999999999999997


Q ss_pred             CCCCC-CcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccccc
Q 039253           83 KSPVS-KDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQ  161 (199)
Q Consensus        83 ~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps~  161 (199)
                      ..... .+.++..|+..+.||++++|..+|+.|+..++++......       ..........|+.+||..+++.++|+.
T Consensus       297 ~~~~~l~~~~~~~la~~~~g~~~~~l~~L~~~a~~~~~rel~~~~~-------~~~~~~~~~~i~~~d~~~al~~~~~s~  369 (389)
T 3vfd_A          297 KQGSPLTQKELAQLARMTDGYSGSDLTALAKDAALGPIRELKPEQV-------KNMSASEMRNIRLSDFTESLKKIKRSV  369 (389)
T ss_dssp             TSCCCSCHHHHHHHHHHTTTCCHHHHHHHHHHHTTHHHHTSCCC----------CCSSSCCCCCCHHHHHHHHHHCCCSS
T ss_pred             hcCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhhhhhhh-------hccchhhcCCcCHHHHHHHHHHcCCCC
Confidence            75443 4567899999999999999999999999998876421100       001112235799999999999999997


Q ss_pred             cc
Q 039253          162 SR  163 (199)
Q Consensus       162 ~r  163 (199)
                      ..
T Consensus       370 ~~  371 (389)
T 3vfd_A          370 SP  371 (389)
T ss_dssp             CH
T ss_pred             CH
Confidence            65

>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=99.65  E-value=1.2e-16  Score=111.08  Aligned_cols=75  Identities=32%  Similarity=0.404  Sum_probs=67.3

Q ss_pred             CHHHHHHHHHHhhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHH
Q 039253           69 VEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAE  148 (199)
Q Consensus        69 ~~~~R~~il~~~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~  148 (199)
                      |.++|.+||+.+++++++..++++..||+.|+|||||||.++|++|++.|+++..                   ..|+++
T Consensus         2 d~~~R~~Il~~~l~~~~~~~~vdl~~la~~t~G~SGADi~~l~~eA~~~a~~~~~-------------------~~i~~~   62 (83)
T 3aji_B            2 DRRQKRLIFSTITSKMNLSEEVDLEDYVARPDKISGADINSICQESGMLAVRENR-------------------YIVLAK   62 (83)
T ss_dssp             CHHHHHHHHHHHHTTSCBCTTCCTHHHHTSSCCCCHHHHHHHHHHHHHGGGTSCC-------------------SSBCHH
T ss_pred             CHHHHHHHHHHHhCCCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcc-------------------CCcCHH
Confidence            6789999999999999988899999999999999999999999999999987652                   679999


Q ss_pred             HHHHHHHhcccccc
Q 039253          149 HFEESMKYACKSQS  162 (199)
Q Consensus       149 df~~Al~~~~Ps~~  162 (199)
                      ||..|+++++|+.+
T Consensus        63 df~~Al~~~~ps~~   76 (83)
T 3aji_B           63 DFEKAYKTVIKKDE   76 (83)
T ss_dssp             HHHHHHHHHCC---
T ss_pred             HHHHHHHHHccCch
Confidence            99999999999987

>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=99.64  E-value=2.9e-16  Score=110.64  Aligned_cols=76  Identities=16%  Similarity=0.271  Sum_probs=67.5

Q ss_pred             CHHHHHHHHHHhhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHH
Q 039253           69 VEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAE  148 (199)
Q Consensus        69 ~~~~R~~il~~~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~  148 (199)
                      |.++|.+||+.++++.++..++++..||+.|+|||||||.++|++|++.|+++..                   ..|+++
T Consensus         2 d~~~R~~Il~~~~~~~~~~~dvdl~~lA~~t~G~SGADl~~l~~eAa~~a~r~~~-------------------~~i~~~   62 (88)
T 3vlf_B            2 DLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTEAGMFAIRARR-------------------KVATEK   62 (88)
T ss_dssp             CSSHHHHHHHHHHTTSCBCSCCCHHHHHHTCSSCCHHHHHHHHHHHHHHHHHHSC-------------------SSBCHH
T ss_pred             CHHHHHHHHHHHHCCCCCCCccCHHHHHHHcCCCcHHHHHHHHHHHHHHHHHhcc-------------------ccCCHH
Confidence            5679999999999999998899999999999999999999999999999998853                   569999


Q ss_pred             HHHHHHHhccccccc
Q 039253          149 HFEESMKYACKSQSR  163 (199)
Q Consensus       149 df~~Al~~~~Ps~~r  163 (199)
                      ||..|++++.|+..+
T Consensus        63 df~~Al~~v~~~~~~   77 (88)
T 3vlf_B           63 DFLKAVDKVISGYKK   77 (88)
T ss_dssp             HHHHHHHHHTC----
T ss_pred             HHHHHHHHHhcCccc
Confidence            999999999998765

>2dzn_B 26S protease regulatory subunit 6B homolog; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} PDB: 2dzo_B

Probab=99.51  E-value=3.7e-15  Score=103.42  Aligned_cols=75  Identities=25%  Similarity=0.264  Sum_probs=51.6

Q ss_pred             HHHHHHHHHhhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHH
Q 039253           71 KSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHF  150 (199)
Q Consensus        71 ~~R~~il~~~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df  150 (199)
                      ++|.+||+.+++++++..++++..||+.|+|||||||.++|++|++.|+++..                   ..|+++||
T Consensus         1 ~~R~~Il~~~l~~~~~~~~vdl~~lA~~t~G~SGADi~~l~~eAa~~ai~~~~-------------------~~i~~~df   61 (82)
T 2dzn_B            1 MERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQEAGLRAVRKNR-------------------YVILQSDL   61 (82)
T ss_dssp             -------------CEECTTCCSTTTTTSSCCCCHHHHHHHHHHHHHHHHHTTC-------------------SEECHHHH
T ss_pred             CHHHHHHHHHHcCCCCCCcCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcc-------------------CCcCHHHH
Confidence            47999999999999888889999999999999999999999999999998752                   56999999


Q ss_pred             HHHHHhcc-cccccc
Q 039253          151 EESMKYAC-KSQSRG  164 (199)
Q Consensus       151 ~~Al~~~~-Ps~~r~  164 (199)
                      ..|++++. |+....
T Consensus        62 ~~Al~~v~~~~~~~~   76 (82)
T 2dzn_B           62 EEAYATQVKTDNTVD   76 (82)
T ss_dssp             HHHHHTTCC------
T ss_pred             HHHHHHHHcCcCChH
Confidence            99999984 665543

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=99.35  E-value=1e-12  Score=110.75  Aligned_cols=88  Identities=18%  Similarity=0.371  Sum_probs=74.2

Q ss_pred             hhhHHHHHHHHHHhCCC-----------CCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCC
Q 039253           16 AADRIPNQLLTEMDGLS-----------AKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKS   84 (199)
Q Consensus        16 ~~~r~~~~lL~~ld~~~-----------~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~   84 (199)
                      ...++.+.|++.||+..           ...+|+||+|||+++.||++++|+|||++.|+  +|+.++|.+|++.++...
T Consensus       124 ~~~~v~~~Ll~~ld~~~~~~~~~~~~~~~~~~v~vI~ttN~~~~ld~al~R~~R~d~~i~--~P~~~~r~~Il~~~~~~~  201 (293)
T 3t15_A          124 NNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEKFYW--APTREDRIGVCTGIFRTD  201 (293)
T ss_dssp             CHHHHHHHHHHHHHCCC-----------CCCCCCEEEECSSCCC--CHHHHHHHEEEEEE--CCCHHHHHHHHHHHHGGG
T ss_pred             hHHHHHHHHHHHhccccccccccccccccCCCcEEEEecCCcccCCHHHhCCCCCceeEe--CcCHHHHHHHHHHhccCC
Confidence            34567899999998553           45679999999999999999999999999997  579999999999888643


Q ss_pred             CCCCcccHHHHHhhCCCCCHHHHHH
Q 039253           85 PVSKDVDLEKLAQFTQGFSGADITE  109 (199)
Q Consensus        85 ~~~~~~~l~~la~~t~G~sgaDI~~  109 (199)
                          ++++..+++.++||++++|..
T Consensus       202 ----~~~~~~l~~~~~~~~~~~l~~  222 (293)
T 3t15_A          202 ----NVPAEDVVKIVDNFPGQSIDF  222 (293)
T ss_dssp             ----CCCHHHHHHHHHHSCSCCHHH
T ss_pred             ----CCCHHHHHHHhCCCCcccHHH
Confidence                567899999999999999964

>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=98.76  E-value=3.5e-11  Score=107.18  Aligned_cols=86  Identities=17%  Similarity=0.278  Sum_probs=55.5

Q ss_pred             HHHHHHHHHHh--CCCCCCCEEEEEeeCCCCCCCccccCCCccce--EEEecCCC--HHHHHHHHHHhhcCCCCCCcccH
Q 039253           19 RIPNQLLTEMD--GLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQ--LIYIPLPV--EKSRLQIFKACLRKSPVSKDVDL   92 (199)
Q Consensus        19 r~~~~lL~~ld--~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~--~i~~~~P~--~~~R~~il~~~l~~~~~~~~~~l   92 (199)
                      ++.++++.+|+  ++...+.|+|++|||+++.+|++++|+||||+  .++++.|+  .++|.+|++.+..       .++
T Consensus       171 ~~~~~ll~~l~~~~~~~~~~v~i~attn~~~~ld~a~~r~~rfd~~~~~~v~~p~~~~~~R~~il~~~~~-------~dl  243 (456)
T 2c9o_A          171 KLDPSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQDVTL-------HDL  243 (456)
T ss_dssp             EECHHHHHHHHHTTCCTTEEEEEETTTCCEEEEEEETTSCCTTSCSSSSEECCCCSCSEEEEEEEEEEEH-------HHH
T ss_pred             hhhHHHHHHHhhccCCCCCEEEEEcCCCCcccCChhhcCCcccCcceeEecCCCchhHHHHHHHHHHHHH-------HHH
Confidence            44556777776  44444557777999999999999999999999  67778884  4788888876653       278


Q ss_pred             HHHHhhCCCCCHHHHHHHHHH
Q 039253           93 EKLAQFTQGFSGADITEICQR  113 (199)
Q Consensus        93 ~~la~~t~G~sgaDI~~lv~~  113 (199)
                      +.++..|+|  |+||.++|..
T Consensus       244 ~~~a~~t~g--gadl~~l~~~  262 (456)
T 2c9o_A          244 DVANARPQG--GQDILSMMGQ  262 (456)
T ss_dssp             HHTC-----------------
T ss_pred             HHHHHhCCC--hhHHHHHHhh
Confidence            999999999  9999999954

>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=98.70  E-value=1.6e-09  Score=96.61  Aligned_cols=67  Identities=16%  Similarity=0.110  Sum_probs=0.4

Q ss_pred             cCCCCCchhhHHHHHHHHHHhCCCCCCCEEEEEe-eCCCCCCCccccCCCccceEEEecCCCHH-HHHHHH
Q 039253            9 RGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGV-TNRPDIIDPALLRPGRLDQLIYIPLPVEK-SRLQIF   77 (199)
Q Consensus         9 R~~~~~~~~~r~~~~lL~~ld~~~~~~~VvvI~a-TN~~~~lD~al~R~gRfd~~i~~~~P~~~-~R~~il   77 (199)
                      ++...+...++++++||.+||++.+...|  +++ ||+|+.||+|++||||||++|++++|+.. .|.+|+
T Consensus       120 ~~~~~~~~e~rvl~~LL~~~dg~~~~~~v--~a~~TN~~~~ld~aL~rggr~D~~i~i~lP~~~~~~~ei~  188 (444)
T 1g41_A          120 RARAEDVAEERILDALLPPAKNQWGEVEN--HDSHSSTRQAFRKKLREGQLDDKEIEIDVSAGVSMGVEIM  188 (444)
T ss_dssp             C----------------------------------------------------------------------
T ss_pred             hccchhhHHHHHHHHHHHHhhcccccccc--ccccccCHHHHHHHHHcCCCcceEEEEcCCCCccchhhhh
Confidence            44445566789999999999999776655  455 99999999999999999999999999987 788875

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=98.58  E-value=1.5e-07  Score=80.22  Aligned_cols=115  Identities=14%  Similarity=0.105  Sum_probs=88.0

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEee-----------CCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVT-----------NRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS   87 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aT-----------N~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~   87 (199)
                      ...+.|+..++..  ..+++++++.           |.++.+++++++  ||.. ++|++|+.+++.+|++..+......
T Consensus       204 ~~~~~L~~~le~~--~~~~~ii~t~~~~~~i~~t~~~~~~~l~~~l~s--R~~~-i~~~~~~~~e~~~il~~~~~~~~~~  278 (368)
T 3uk6_A          204 ESFSFLNRALESD--MAPVLIMATNRGITRIRGTSYQSPHGIPIDLLD--RLLI-VSTTPYSEKDTKQILRIRCEEEDVE  278 (368)
T ss_dssp             HHHHHHHHHTTCT--TCCEEEEEESCSEEECBTSSCEEETTCCHHHHT--TEEE-EEECCCCHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHhhCc--CCCeeeeecccceeeeeccCCCCcccCCHHHHh--hccE-EEecCCCHHHHHHHHHHHHHHcCCC
Confidence            3455566666532  3345555443           358899999999  9977 8999999999999999988764433


Q ss_pred             -CcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhc
Q 039253           88 -KDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYA  157 (199)
Q Consensus        88 -~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~  157 (199)
                       ++..+..|++.+.|.+++++.++|+.|...|..+..                   ..|+.+|+..|+..+
T Consensus       279 ~~~~~l~~l~~~~~~G~~r~~~~ll~~a~~~A~~~~~-------------------~~It~~~v~~a~~~~  330 (368)
T 3uk6_A          279 MSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKG-------------------TEVQVDDIKRVYSLF  330 (368)
T ss_dssp             BCHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTC-------------------SSBCHHHHHHHHHHS
T ss_pred             CCHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCC-------------------CCCCHHHHHHHHHHh
Confidence             344578899999878999999999999888765432                   579999999999884

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=98.57  E-value=7.5e-08  Score=80.27  Aligned_cols=105  Identities=14%  Similarity=0.121  Sum_probs=81.7

Q ss_pred             hhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCC-----CCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-Cc
Q 039253           16 AADRIPNQLLTEMDGLSAKKTIFVIGVTNRPD-----IIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KD   89 (199)
Q Consensus        16 ~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~-----~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~   89 (199)
                      ....+.+.|+..|+.  ...++++|++||.++     .++|++++  ||+..++|+.|+.+++..|++.++...... ++
T Consensus       151 ~~~~~~~~Ll~~l~~--~~~~~~~i~~~~~~~~~~~~~~~~~l~~--R~~~~i~~~~~~~~~~~~il~~~l~~~~~~~~~  226 (309)
T 3syl_A          151 YGQEAIEILLQVMEN--NRDDLVVILAGYADRMENFFQSNPGFRS--RIAHHIEFPDYSDEELFEIAGHMLDDQNYQMTP  226 (309)
T ss_dssp             CTHHHHHHHHHHHHH--CTTTCEEEEEECHHHHHHHHHHSTTHHH--HEEEEEEECCCCHHHHHHHHHHHHHHTTCEECH
T ss_pred             ccHHHHHHHHHHHhc--CCCCEEEEEeCChHHHHHHHhhCHHHHH--hCCeEEEcCCcCHHHHHHHHHHHHHHcCCCCCH
Confidence            345788999999985  345788999998654     36899999  999999999999999999999999866543 23


Q ss_pred             ccHHHHHhh-------CCCCCHHHHHHHHHHHHHHHHHHHHH
Q 039253           90 VDLEKLAQF-------TQGFSGADITEICQRACKDATREEIE  124 (199)
Q Consensus        90 ~~l~~la~~-------t~G~sgaDI~~lv~~A~~~a~~~~~~  124 (199)
                      ..+..++..       ...-.++++.++++.|...+..+...
T Consensus       227 ~~~~~l~~~~~~~~~~~~~gn~r~l~~~l~~a~~~~~~r~~~  268 (309)
T 3syl_A          227 EAETALRAYIGLRRNQPHFANARSIRNALDRARLRQANRLFT  268 (309)
T ss_dssp             HHHHHHHHHHHHHTTSSSCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHHHHHHHHHHh
Confidence            345556554       22234899999999999888777654

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=98.50  E-value=7.7e-07  Score=75.18  Aligned_cols=99  Identities=14%  Similarity=0.149  Sum_probs=77.3

Q ss_pred             hHHHHHHHHHHhCCCC----------------CCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhh
Q 039253           18 DRIPNQLLTEMDGLSA----------------KKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACL   81 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~----------------~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l   81 (199)
                      ..+.+.|+..|+...-                ..++++|++||+...+++++++  ||+..++|+.|+.+++..+++.++
T Consensus       120 ~~~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~i~atn~~~~l~~~L~~--R~~~~i~l~~~~~~e~~~il~~~~  197 (338)
T 3pfi_A          120 PAIEEVLYPAMEDYRLDIIIGSGPAAQTIKIDLPKFTLIGATTRAGMLSNPLRD--RFGMQFRLEFYKDSELALILQKAA  197 (338)
T ss_dssp             HHHHHHHHHHHHTSCC---------CCCCCCCCCCCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccchhhcccCccccceecCCCCeEEEEeCCCccccCHHHHh--hcCEEeeCCCcCHHHHHHHHHHHH
Confidence            3566777877775421                1248999999999999999999  999999999999999999999998


Q ss_pred             cCCCCC-CcccHHHHHhhCCCCCHHHHHHHHHHHHHHHH
Q 039253           82 RKSPVS-KDVDLEKLAQFTQGFSGADITEICQRACKDAT  119 (199)
Q Consensus        82 ~~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~  119 (199)
                      ...... ++..+..|+..+.| ..+++.++++.+...+.
T Consensus       198 ~~~~~~~~~~~~~~l~~~~~G-~~r~l~~~l~~~~~~a~  235 (338)
T 3pfi_A          198 LKLNKTCEEKAALEIAKRSRS-TPRIALRLLKRVRDFAD  235 (338)
T ss_dssp             HHTTCEECHHHHHHHHHTTTT-CHHHHHHHHHHHHHHHH
T ss_pred             HhcCCCCCHHHHHHHHHHHCc-CHHHHHHHHHHHHHHHH
Confidence            766543 34457778886665 56888888888765543

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=98.33  E-value=9.7e-07  Score=70.05  Aligned_cols=112  Identities=9%  Similarity=0.139  Sum_probs=79.5

Q ss_pred             HHHHHHHHhCCCCCCCE-EEEEeeCCCC---CCCccccCCCccc--eEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHH
Q 039253           21 PNQLLTEMDGLSAKKTI-FVIGVTNRPD---IIDPALLRPGRLD--QLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLE   93 (199)
Q Consensus        21 ~~~lL~~ld~~~~~~~V-vvI~aTN~~~---~lD~al~R~gRfd--~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~   93 (199)
                      ...|+..++.......+ +|+.++..+.   .+++++.+  ||.  ..++++.|+.+++.++++.++...... ++..+.
T Consensus       123 ~~~l~~~l~~~~~~~~~~ii~~~~~~~~~~~~~~~~l~~--r~~~~~~i~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~~  200 (242)
T 3bos_A          123 EEAIFDLYNRVAEQKRGSLIVSASASPMEAGFVLPDLVS--RMHWGLTYQLQPMMDDEKLAALQRRAAMRGLQLPEDVGR  200 (242)
T ss_dssp             HHHHHHHHHHHHHHCSCEEEEEESSCTTTTTCCCHHHHH--HHHHSEEEECCCCCGGGHHHHHHHHHHHTTCCCCHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCeEEEEcCCCHHHHHHhhhhhhh--HhhcCceEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            34455555544333344 4444444454   56688998  887  999999999999999999998754432 344577


Q ss_pred             HHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHH
Q 039253           94 KLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMK  155 (199)
Q Consensus        94 ~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~  155 (199)
                      .+++.+.| +.+++.++++.+...+..+.                    ..|+.+++.++++
T Consensus       201 ~l~~~~~g-~~r~l~~~l~~~~~~a~~~~--------------------~~It~~~v~~~l~  241 (242)
T 3bos_A          201 FLLNRMAR-DLRTLFDVLDRLDKASMVHQ--------------------RKLTIPFVKEMLR  241 (242)
T ss_dssp             HHHHHTTT-CHHHHHHHHHHHHHHHHHHT--------------------CCCCHHHHHHHHT
T ss_pred             HHHHHccC-CHHHHHHHHHHHHHHHHHhC--------------------CCCcHHHHHHHhh
Confidence            88888866 78899999998877664332                    5699999988874

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=98.31  E-value=3e-06  Score=66.48  Aligned_cols=108  Identities=14%  Similarity=0.161  Sum_probs=84.0

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHH
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLA   96 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la   96 (199)
                      ....+.|+..++..  ..++.+|++||.++.+++++++  |+ ..++++.|+.++..++++.++...... ++..+..++
T Consensus       140 ~~~~~~l~~~l~~~--~~~~~~i~~t~~~~~~~~~l~~--r~-~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~~~~l~  214 (250)
T 1njg_A          140 RHSFNALLKTLEEP--PEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLA  214 (250)
T ss_dssp             HHHHHHHHHHHHSC--CTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHH
T ss_pred             HHHHHHHHHHHhcC--CCceEEEEEeCChHhCCHHHHH--Hh-hhccCCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHH
Confidence            35667788888743  4578999999999999999998  75 789999999999999999988654332 344578899


Q ss_pred             hhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHH
Q 039253           97 QFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESM  154 (199)
Q Consensus        97 ~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al  154 (199)
                      +.+.| .++.+.++++.|...+                       ...|+.+++.+++
T Consensus       215 ~~~~G-~~~~~~~~~~~~~~~~-----------------------~~~i~~~~v~~~~  248 (250)
T 1njg_A          215 RAAEG-SLRDALSLTDQAIASG-----------------------DGQVSTQAVSAML  248 (250)
T ss_dssp             HHHTT-CHHHHHHHHHHHHTTT-----------------------TSSBCHHHHHHHS
T ss_pred             HHcCC-CHHHHHHHHHHHHhcc-----------------------CceecHHHHHHHh
Confidence            99987 7888888888773221                       0368999998875

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=98.31  E-value=1.3e-06  Score=73.02  Aligned_cols=80  Identities=19%  Similarity=0.161  Sum_probs=66.2

Q ss_pred             CEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhhCCCCCHHHHHHHHHHH
Q 039253           36 TIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSGADITEICQRA  114 (199)
Q Consensus        36 ~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~~A  114 (199)
                      ++++|++||.+..+++++++  ||+..+.++.|+.+++..+++.++...... ++..+..|+..+.|+ ++.+.++++.+
T Consensus       138 ~~~~i~~t~~~~~~~~~l~~--R~~~~i~l~~~~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~-~r~l~~~l~~~  214 (324)
T 1hqc_A          138 RFTLIGATTRPGLITAPLLS--RFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGT-MRVAKRLFRRV  214 (324)
T ss_dssp             CCEEEEEESCCSSCSCSTTT--TCSCEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHSCSC-HHHHHHHHHHH
T ss_pred             CEEEEEeCCCcccCCHHHHh--cccEEEecCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHccCC-HHHHHHHHHHH
Confidence            58899999999999999999  999999999999999999999998765443 344578888888765 57888888776


Q ss_pred             HHHH
Q 039253          115 CKDA  118 (199)
Q Consensus       115 ~~~a  118 (199)
                      ...+
T Consensus       215 ~~~a  218 (324)
T 1hqc_A          215 RDFA  218 (324)
T ss_dssp             TTTS
T ss_pred             HHHH
Confidence            5443

>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=98.31  E-value=3e-07  Score=83.66  Aligned_cols=123  Identities=14%  Similarity=0.230  Sum_probs=81.8

Q ss_pred             HHHHHHHHHhCCCC-------------CCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhc----
Q 039253           20 IPNQLLTEMDGLSA-------------KKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR----   82 (199)
Q Consensus        20 ~~~~lL~~ld~~~~-------------~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~----   82 (199)
                      ..+.||..||....             ..++++|+|||.++.+|++|++  ||+ .|+|+.|+.++|..|++.++.    
T Consensus       195 ~~~~LL~~ld~~~~~~~~~~~~~~~~~~~~v~iI~ttN~~~~l~~aL~~--R~~-vi~~~~~~~~e~~~Il~~~l~~~~~  271 (543)
T 3m6a_A          195 PSSAMLEVLDPEQNSSFSDHYIEETFDLSKVLFIATANNLATIPGPLRD--RME-IINIAGYTEIEKLEIVKDHLLPKQI  271 (543)
T ss_dssp             ---CCGGGTCTTTTTBCCCSSSCCCCBCSSCEEEEECSSTTTSCHHHHH--HEE-EEECCCCCHHHHHHHHHHTHHHHHH
T ss_pred             HHHHHHHHHhhhhcceeecccCCeeecccceEEEeccCccccCCHHHHh--hcc-eeeeCCCCHHHHHHHHHHHHHHHHH
Confidence            44667777764321             1568999999999999999999  995 799999999999999999872    


Q ss_pred             -CCCCC------CcccHHHHHhhCCC-CCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHH
Q 039253           83 -KSPVS------KDVDLEKLAQFTQG-FSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESM  154 (199)
Q Consensus        83 -~~~~~------~~~~l~~la~~t~G-~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al  154 (199)
                       ...+.      ++..+..++....+ ...++|++.+..++..+..+.....             .....|+.+++..++
T Consensus       272 ~~~~~~~~~i~i~~~~l~~l~~~~~~~~~vR~L~~~i~~~~~~aa~~~~~~~-------------~~~~~It~~~l~~~L  338 (543)
T 3m6a_A          272 KEHGLKKSNLQLRDQAILDIIRYYTREAGVRSLERQLAAICRKAAKAIVAEE-------------RKRITVTEKNLQDFI  338 (543)
T ss_dssp             HHTTCCGGGCEECHHHHHHHHHHHCCCSSSHHHHHHHHHHHHHHHHHHHTTC-------------CSCCEECTTTTHHHH
T ss_pred             HHcCCCcccccCCHHHHHHHHHhCChhhchhHHHHHHHHHHHHHHHHHHhcC-------------CcceecCHHHHHHHh
Confidence             22221      12234555553333 4557777777766666555543211             112468999999988


Q ss_pred             Hhcc
Q 039253          155 KYAC  158 (199)
Q Consensus       155 ~~~~  158 (199)
                      ..-+
T Consensus       339 g~~~  342 (543)
T 3m6a_A          339 GKRI  342 (543)
T ss_dssp             CSCC
T ss_pred             CCcc
Confidence            6544

>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=98.19  E-value=6.9e-06  Score=63.76  Aligned_cols=107  Identities=15%  Similarity=0.050  Sum_probs=78.1

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHh
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQ   97 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~   97 (199)
                      ...+.|+..++..  ..++.+|++||.++.+++++.+  ||. .++++.|+.++...+++.++...... ++..+..+++
T Consensus       117 ~~~~~l~~~l~~~--~~~~~~i~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  191 (226)
T 2chg_A          117 DAQAALRRTMEMY--SKSCRFILSCNYVSRIIEPIQS--RCA-VFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIY  191 (226)
T ss_dssp             HHHHHHHHHHHHT--TTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhc--CCCCeEEEEeCChhhcCHHHHH--hCc-eeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            3456677777753  4567889999999999999999  998 89999999999999999988644332 3445677887


Q ss_pred             hCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHH
Q 039253           98 FTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMK  155 (199)
Q Consensus        98 ~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~  155 (199)
                      .+.| ..+.+.++++.++..+                        ..|+.+|+.+++.
T Consensus       192 ~~~g-~~r~l~~~l~~~~~~~------------------------~~I~~~~v~~~~~  224 (226)
T 2chg_A          192 ISGG-DFRKAINALQGAAAIG------------------------EVVDADTIYQITA  224 (226)
T ss_dssp             HHTT-CHHHHHHHHHHHHHTC------------------------SCBCHHHHHHHHH
T ss_pred             HcCC-CHHHHHHHHHHHHhcC------------------------ceecHHHHHHHhc
Confidence            7765 4555555555443221                        3589999998875

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=98.19  E-value=1.2e-05  Score=67.81  Aligned_cols=65  Identities=15%  Similarity=0.227  Sum_probs=50.5

Q ss_pred             hHHHHHHHHHHhCC---------CCCCCEEEEEeeCCCC-----CCCccccCCCccceEEEecCCCHHHHHHHHHHhhcC
Q 039253           18 DRIPNQLLTEMDGL---------SAKKTIFVIGVTNRPD-----IIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRK   83 (199)
Q Consensus        18 ~r~~~~lL~~ld~~---------~~~~~VvvI~aTN~~~-----~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~   83 (199)
                      ....+.|+..|+.-         ....+++||+|+|..+     .+++++++  ||+.+++++.|+.++|.+||+..+..
T Consensus       123 ~~~~~~Ll~~l~~~~~~~~g~~~~~~~~~~viat~np~~~~~~~~l~~~l~~--Rf~~~i~i~~p~~~~~~~il~~~~~~  200 (331)
T 2r44_A          123 AKVQSALLECMQEKQVTIGDTTYPLDNPFLVLATQNPVEQEGTYPLPEAQVD--RFMMKIHLTYLDKESELEVMRRVSNM  200 (331)
T ss_dssp             HHHHHHHHHHHHHSEEEETTEEEECCSSCEEEEEECTTCCSCCCCCCHHHHT--TSSEEEECCCCCHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHhcCceeeCCEEEECCCCEEEEEecCCCcccCcccCCHHHHh--heeEEEEcCCCCHHHHHHHHHhcccc
Confidence            45677788877742         1234578888888433     39999999  99999999999999999999998865


Q ss_pred             C
Q 039253           84 S   84 (199)
Q Consensus        84 ~   84 (199)
                      .
T Consensus       201 ~  201 (331)
T 2r44_A          201 N  201 (331)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=98.17  E-value=2e-06  Score=71.20  Aligned_cols=125  Identities=14%  Similarity=0.205  Sum_probs=86.6

Q ss_pred             HHHHHHHHHHhCCC--------CCCCEEEEEe----eCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhh-----
Q 039253           19 RIPNQLLTEMDGLS--------AKKTIFVIGV----TNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACL-----   81 (199)
Q Consensus        19 r~~~~lL~~ld~~~--------~~~~VvvI~a----TN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l-----   81 (199)
                      .+.+.|+..|++..        ...++++|++    ++.+..+++++++  ||+..++|+.|+.+++.+|++...     
T Consensus       143 ~~~~~Ll~~le~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~l~~~l~~--R~~~~i~~~~~~~~~~~~il~~~~~~~~~  220 (310)
T 1ofh_A          143 GVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG--RLPIRVELTALSAADFERILTEPHASLTE  220 (310)
T ss_dssp             HHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSSCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHSSTTCHHH
T ss_pred             HHHHHHHHHhcCCeEecccccccCCcEEEEEcCCcccCCcccCCHHHHh--hCCceEEcCCcCHHHHHHHHHhhHHHHHH
Confidence            35788999998641        2346788888    5688999999999  999999999999999999999422     


Q ss_pred             ------cCCCC--C-CcccHHHHHhhC-------CCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccc
Q 039253           82 ------RKSPV--S-KDVDLEKLAQFT-------QGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEI  145 (199)
Q Consensus        82 ------~~~~~--~-~~~~l~~la~~t-------~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~i  145 (199)
                            .....  . ++..+..|++.+       ++...+.+.++++.+...+..+....             ......|
T Consensus       221 ~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~~g~~R~l~~~l~~~~~~~~~~~~~~-------------~~~~~~i  287 (310)
T 1ofh_A          221 QYKALMATEGVNIAFTTDAVKKIAEAAFRVNEKTENIGARRLHTVMERLMDKISFSASDM-------------NGQTVNI  287 (310)
T ss_dssp             HHHHHHHHTTCEEEECHHHHHHHHHHHHHHHHHSCCCTTHHHHHHHHHHSHHHHHHGGGC-------------TTCEEEE
T ss_pred             HHHHHHHhcCCeeccCHHHHHHHHHHhhhhcccccccCcHHHHHHHHHHHHhhhcCCccc-------------cCCEEEE
Confidence                  11111  1 233466677665       25788999999988765544322100             0011359


Q ss_pred             cHHHHHHHHHhcc
Q 039253          146 KAEHFEESMKYAC  158 (199)
Q Consensus       146 t~~df~~Al~~~~  158 (199)
                      +.+++..++....
T Consensus       288 ~~~~v~~~l~~~~  300 (310)
T 1ofh_A          288 DAAYVADALGEVV  300 (310)
T ss_dssp             CHHHHHHHTCSSS
T ss_pred             eeHHHHHHHHhhh
Confidence            9999999988653

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=98.13  E-value=9.7e-06  Score=68.75  Aligned_cols=117  Identities=13%  Similarity=0.152  Sum_probs=78.9

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCC---CCCCccccCCCccce-EEEecCCCHHHHHHHHHHhhcC----CCCCCcc
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRP---DIIDPALLRPGRLDQ-LIYIPLPVEKSRLQIFKACLRK----SPVSKDV   90 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~---~~lD~al~R~gRfd~-~i~~~~P~~~~R~~il~~~l~~----~~~~~~~   90 (199)
                      .++..++.+++......++.+|++||.+   +.+++++.+  ||.. .+.|++|+.+++.+|++..+..    ..+ ++.
T Consensus       150 ~~l~~l~~~~~~~~~~~~~~~I~~t~~~~~~~~l~~~l~~--r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~-~~~  226 (387)
T 2v1u_A          150 DLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKS--SLGEVELVFPPYTAPQLRDILETRAEEAFNPGVL-DPD  226 (387)
T ss_dssp             HHHHHHHHGGGCC-----CEEEEECSCSTTSSSSCHHHHT--TTTSEECCBCCCCHHHHHHHHHHHHHHHBCTTTB-CSS
T ss_pred             hHHHhHhhchhhcCCCceEEEEEEECCCchHhhhCHHHHh--cCCCeEEeeCCCCHHHHHHHHHHHHHhhccCCCC-CHH
Confidence            3444555555443215678999999998   889999999  9986 8999999999999999988763    222 234


Q ss_pred             cHHHHHhhCC---CCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcc
Q 039253           91 DLEKLAQFTQ---GFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYAC  158 (199)
Q Consensus        91 ~l~~la~~t~---G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~  158 (199)
                      .+..+++.+.   | .++.+.++|+.|...+..+.                   ...|+.+++..|+....
T Consensus       227 ~~~~l~~~~~~~~G-~~r~~~~~l~~a~~~a~~~~-------------------~~~i~~~~v~~a~~~~~  277 (387)
T 2v1u_A          227 VVPLCAALAAREHG-DARRALDLLRVAGEIAERRR-------------------EERVRREHVYSARAEIE  277 (387)
T ss_dssp             HHHHHHHHHHSSSC-CHHHHHHHHHHHHHHHHHTT-------------------CSCBCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcc-CHHHHHHHHHHHHHHHHHcC-------------------CCCcCHHHHHHHHHHHh
Confidence            4677777776   5 46677788888765553321                   03466777766666554

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=98.13  E-value=1.6e-06  Score=71.29  Aligned_cols=115  Identities=17%  Similarity=0.246  Sum_probs=76.8

Q ss_pred             hhHHHHHHHHHHhCCCC-CCCEEEEEeeCCCCCCCc-cccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCcccHHH
Q 039253           17 ADRIPNQLLTEMDGLSA-KKTIFVIGVTNRPDIIDP-ALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEK   94 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~-~~~VvvI~aTN~~~~lD~-al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~l~~   94 (199)
                      ...+.+.|+..+++... ..+++||+|||.++.+|+ .+++  ||+..|++|.++.  |.+|.+.+.....+ .+..+..
T Consensus       147 ~~~~l~~L~~~~~~~~~~~~~~~ii~ttn~~~~l~~~~l~~--rf~~~i~~p~l~~--r~~i~~i~~~~~~~-~~~~~~~  221 (272)
T 1d2n_A          147 SNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEMLN--AFSTTIHVPNIAT--GEQLLEALELLGNF-KDKERTT  221 (272)
T ss_dssp             CHHHHHHHHHHTTCCCSTTCEEEEEEEESCHHHHHHTTCTT--TSSEEEECCCEEE--HHHHHHHHHHHTCS-CHHHHHH
T ss_pred             HHHHHHHHHHHhcCccCCCCCEEEEEecCChhhcchhhhhc--ccceEEcCCCccH--HHHHHHHHHhcCCC-CHHHHHH
Confidence            45677788888887643 456899999999999999 5666  9999988865544  33344333332333 3556888


Q ss_pred             HHhhCCCC----CHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcccc
Q 039253           95 LAQFTQGF----SGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKS  160 (199)
Q Consensus        95 la~~t~G~----sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps  160 (199)
                      +++.+.||    ..+++.++++.|...+                        .....++|..++.....+
T Consensus       222 l~~~~~g~~~~g~ir~l~~~l~~a~~~~------------------------~~~~~~~~~~~l~~~~~~  267 (272)
T 1d2n_A          222 IAQQVKGKKVWIGIKKLLMLIEMSLQMD------------------------PEYRVRKFLALLREEGAS  267 (272)
T ss_dssp             HHHHHTTSEEEECHHHHHHHHHHHTTSC------------------------GGGHHHHHHHHHHHTSCC
T ss_pred             HHHHhcCCCccccHHHHHHHHHHHhhhc------------------------hHHHHHHHHHHHHHcCCc
Confidence            99999998    5666666666553211                        224567777777776554

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=98.09  E-value=4e-06  Score=74.29  Aligned_cols=115  Identities=15%  Similarity=0.139  Sum_probs=83.2

Q ss_pred             HHHHHHHHhCCCCCCCEEEEEeeCCCCC---CCccccCCCccc--eEEEecCCCHHHHHHHHHHhhcCC--CCCCcccHH
Q 039253           21 PNQLLTEMDGLSAKKTIFVIGVTNRPDI---IDPALLRPGRLD--QLIYIPLPVEKSRLQIFKACLRKS--PVSKDVDLE   93 (199)
Q Consensus        21 ~~~lL~~ld~~~~~~~VvvI~aTN~~~~---lD~al~R~gRfd--~~i~~~~P~~~~R~~il~~~l~~~--~~~~~~~l~   93 (199)
                      ...|+..++.+......+||++.+.+..   +++++++  ||.  ..+.++.|+.++|..||+..+...  .+. +..+.
T Consensus       213 q~~l~~~l~~l~~~~~~iIitt~~~~~~l~~l~~~L~s--R~~~g~~i~l~~p~~e~r~~iL~~~~~~~~~~i~-~e~l~  289 (440)
T 2z4s_A          213 QTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVS--RFQMGLVAKLEPPDEETRKSIARKMLEIEHGELP-EEVLN  289 (440)
T ss_dssp             HHHHHHHHHHHHTTTCEEEEEESSCGGGCSSCCHHHHH--HHHSSBCCBCCCCCHHHHHHHHHHHHHHHTCCCC-TTHHH
T ss_pred             HHHHHHHHHHHHHCCCeEEEEECCCHHHHHHHHHHHHh--hccCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCC-HHHHH
Confidence            3455555554434444555555554554   8899999  997  889999999999999999988643  333 33478


Q ss_pred             HHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccc
Q 039253           94 KLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACK  159 (199)
Q Consensus        94 ~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~P  159 (199)
                      .|+..+.| +.+++..+++.+...+....                    ..|+.+++.++++...+
T Consensus       290 ~la~~~~g-n~R~l~~~L~~~~~~a~~~~--------------------~~It~~~~~~~l~~~~~  334 (440)
T 2z4s_A          290 FVAENVDD-NLRRLRGAIIKLLVYKETTG--------------------KEVDLKEAILLLKDFIK  334 (440)
T ss_dssp             HHHHHCCS-CHHHHHHHHHHHHHHHHHSS--------------------SCCCHHHHHHHTSTTTC
T ss_pred             HHHHhcCC-CHHHHHHHHHHHHHHHHHhC--------------------CCCCHHHHHHHHHHHhh
Confidence            89998875 88999999998866654221                    45888888888887763

>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=98.07  E-value=1.9e-05  Score=66.52  Aligned_cols=122  Identities=16%  Similarity=0.174  Sum_probs=81.2

Q ss_pred             HHHHHHHHHHhC----CCC-------CCCEEEEEeeCCCC-CCCccccCCCccceEEEecCC-CHHHHHHHHHHhhc---
Q 039253           19 RIPNQLLTEMDG----LSA-------KKTIFVIGVTNRPD-IIDPALLRPGRLDQLIYIPLP-VEKSRLQIFKACLR---   82 (199)
Q Consensus        19 r~~~~lL~~ld~----~~~-------~~~VvvI~aTN~~~-~lD~al~R~gRfd~~i~~~~P-~~~~R~~il~~~l~---   82 (199)
                      ...+.|+..|+.    +..       ..++++|+|||..+ .+++++++  ||+.+++++.| +.++|.+|++..+.   
T Consensus       159 ~~~~~Ll~~le~~~~~~~~~g~~~~~~~~~~li~~~n~~~~~l~~~L~~--R~~~~~~l~~~~~~~~~~~il~~~~~~~~  236 (350)
T 1g8p_A          159 HIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLD--RFGLSVEVLSPRDVETRVEVIRRRDTYDA  236 (350)
T ss_dssp             HHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHT--TCSEEEECCCCCSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCceEEEecceEEeeCCceEEEEEeCCCCCCCCHHHHh--hcceEEEcCCCCcHHHHHHHHHHHHhccc
Confidence            456677777764    111       13689999999744 89999999  99999999999 67888888876321   


Q ss_pred             ----------------------------CCCCCCcccHHHHHhhCCC---CCHHHHHHHHHHHHHHHHHHHHHHhHHhhc
Q 039253           83 ----------------------------KSPVSKDVDLEKLAQFTQG---FSGADITEICQRACKDATREEIENDIRRRK  131 (199)
Q Consensus        83 ----------------------------~~~~~~~~~l~~la~~t~G---~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~  131 (199)
                                                  ...+. +..+..|+..+.+   -+.+.+.++++.|...|..+..        
T Consensus       237 ~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ls-~~~~~~l~~~~~~~~~~~~R~~~~ll~~a~~~A~~~~~--------  307 (350)
T 1g8p_A          237 DPKAFLEEWRPKDMDIRNQILEARERLPKVEAP-NTALYDCAALCIALGSDGLRGELTLLRSARALAALEGA--------  307 (350)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHGGGCBCC-HHHHHHHHHHHHHSSSCSHHHHHHHHHHHHHHHHHTTC--------
T ss_pred             CchhhccccccchHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCC--------
Confidence                                        11222 2223444443332   2567777777777665543321        


Q ss_pred             CCCCcchhhccccccHHHHHHHHHhcccccc
Q 039253          132 GKQPEAIEDEVAEIKAEHFEESMKYACKSQS  162 (199)
Q Consensus       132 ~~~~~~~~~~~~~it~~df~~Al~~~~Ps~~  162 (199)
                                 ..|+.+|+..|+..+-+...
T Consensus       308 -----------~~v~~~~v~~a~~~~l~~r~  327 (350)
T 1g8p_A          308 -----------TAVGRDHLKRVATMALSHRL  327 (350)
T ss_dssp             -----------SBCCHHHHHHHHHHHHGGGC
T ss_pred             -----------CcCCHHHHHHHHHHHHhhcc
Confidence                       45899999999988765544

>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=97.87  E-value=6.7e-05  Score=63.71  Aligned_cols=101  Identities=17%  Similarity=0.214  Sum_probs=78.1

Q ss_pred             CEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhhCCCCCHHHHHHHHHHH
Q 039253           36 TIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSGADITEICQRA  114 (199)
Q Consensus        36 ~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~~A  114 (199)
                      .+.++++|+++..|++++++  ||...+.+.+|+.++..+|++......... ++..+..||.++.| +++++..+++.+
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  999999999999999999999887655443 33447889999887 468888888887


Q ss_pred             HHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcc
Q 039253          115 CKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYAC  158 (199)
Q Consensus       115 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~  158 (199)
                      ...|..+..                   ..||.+++.+|+....
T Consensus       227 ~~~a~~~~~-------------------~~It~~~v~~al~~~~  251 (334)
T 1in4_A          227 RDMLTVVKA-------------------DRINTDIVLKTMEVLN  251 (334)
T ss_dssp             HHHHHHHTC-------------------SSBCHHHHHHHHHHHT
T ss_pred             HHHHHHcCC-------------------CCcCHHHHHHHHHHhC
Confidence            666543321                   3577777777776653

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=97.86  E-value=1.2e-05  Score=66.63  Aligned_cols=105  Identities=18%  Similarity=0.215  Sum_probs=80.9

Q ss_pred             hHHHHHHHHHHhCCC--C-------CCCEEEEEeeCC--------------------------CCCCCccccCCCccceE
Q 039253           18 DRIPNQLLTEMDGLS--A-------KKTIFVIGVTNR--------------------------PDIIDPALLRPGRLDQL   62 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~--~-------~~~VvvI~aTN~--------------------------~~~lD~al~R~gRfd~~   62 (199)
                      ..+.+.|+..|+.-.  .       -.++++|+|||.                          ...++++|+.  ||+..
T Consensus       133 ~~~~~~Ll~~le~~~~~~~~~~~~~~~~~iiI~ttn~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~--R~~~~  210 (311)
T 4fcw_A          133 PDVFNILLQMLDDGRLTDSHGRTVDFRNTVIIMTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEI  210 (311)
T ss_dssp             HHHHHHHHHHHHHSEEECTTSCEEECTTEEEEEEESTTHHHHHTTTTSCCCSSTHHHHTHHHHHHHSCHHHHT--TCSEE
T ss_pred             HHHHHHHHHHHhcCEEEcCCCCEEECCCcEEEEecccCHHHHHhhhcccccHHHHHHHHHHHHHHhCCHHHHh--cCCeE
Confidence            356778888887532  0       136889999998                          5578999998  99999


Q ss_pred             EEecCCCHHHHHHHHHHhhcCC---------CCC-CcccHHHHHhhCC--CCCHHHHHHHHHHHHHHHHHHHHH
Q 039253           63 IYIPLPVEKSRLQIFKACLRKS---------PVS-KDVDLEKLAQFTQ--GFSGADITEICQRACKDATREEIE  124 (199)
Q Consensus        63 i~~~~P~~~~R~~il~~~l~~~---------~~~-~~~~l~~la~~t~--G~sgaDI~~lv~~A~~~a~~~~~~  124 (199)
                      +.+++|+.+++..|++.++...         ... ++..+..|++..-  ....++|+++++.+...++.+.+.
T Consensus       211 ~~~~p~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~gn~R~L~~~i~~~~~~~~~~~i~  284 (311)
T 4fcw_A          211 VVFRPLTKEQIRQIVEIQMSYLRARLAEKRISLELTEAAKDFLAERGYDPVFGARPLRRVIQRELETPLAQKIL  284 (311)
T ss_dssp             EECCCCCHHHHHHHHHHHTHHHHHHHHTTTCEEEECHHHHHHHHHHSCBTTTBTTTHHHHHHHHTHHHHHHHHH
T ss_pred             EEeCCCCHHHHHHHHHHHHHHHHHHHHhCCcEEEeCHHHHHHHHHhCCCccCCchhHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999988642         111 2334667777654  678999999999998888777654

>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=97.78  E-value=6.7e-05  Score=63.82  Aligned_cols=81  Identities=19%  Similarity=0.150  Sum_probs=60.5

Q ss_pred             CCEEEEEeeCCC---CCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcC----CCCCCcccHHHHHhhCCCC--CHH
Q 039253           35 KTIFVIGVTNRP---DIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRK----SPVSKDVDLEKLAQFTQGF--SGA  105 (199)
Q Consensus        35 ~~VvvI~aTN~~---~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~----~~~~~~~~l~~la~~t~G~--sga  105 (199)
                      .++.+|++||.+   +.+++++++  ||...++|++|+.++..+|++..+..    ..+. +..+..+++.+.+.  ...
T Consensus       163 ~~~~iI~~t~~~~~~~~l~~~l~s--r~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~-~~~~~~i~~~~~~~~G~~r  239 (384)
T 2qby_B          163 ANISVIMISNDINVRDYMEPRVLS--SLGPSVIFKPYDAEQLKFILSKYAEYGLIKGTYD-DEILSYIAAISAKEHGDAR  239 (384)
T ss_dssp             SCEEEEEECSSTTTTTTSCHHHHH--TCCCEEEECCCCHHHHHHHHHHHHHHTSCTTSCC-SHHHHHHHHHHHTTCCCHH
T ss_pred             cceEEEEEECCCchHhhhCHHHHh--cCCCeEEECCCCHHHHHHHHHHHHHhhcccCCcC-HHHHHHHHHHHHhccCCHH
Confidence            678999999987   789999999  99889999999999999999998763    2222 33467777777532  234


Q ss_pred             HHHHHHHHHHHHH
Q 039253          106 DITEICQRACKDA  118 (199)
Q Consensus       106 DI~~lv~~A~~~a  118 (199)
                      .+.++|+.|...+
T Consensus       240 ~a~~~l~~a~~~a  252 (384)
T 2qby_B          240 KAVNLLFRAAQLA  252 (384)
T ss_dssp             HHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHh
Confidence            4556666665443

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=97.77  E-value=4.3e-05  Score=68.06  Aligned_cols=82  Identities=21%  Similarity=0.298  Sum_probs=62.6

Q ss_pred             CCCEEEEEeeCCCC-----CCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCC----CCC-CcccHHHHHhhCCCC-
Q 039253           34 KKTIFVIGVTNRPD-----IIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKS----PVS-KDVDLEKLAQFTQGF-  102 (199)
Q Consensus        34 ~~~VvvI~aTN~~~-----~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~----~~~-~~~~l~~la~~t~G~-  102 (199)
                      ...+.+|++||.++     .+|++++|  ||.. |.|+.|+.+++..||+.++..+    ... .+..+..++..+.+| 
T Consensus       289 ~g~v~vI~at~~~e~~~~~~~~~al~~--Rf~~-i~v~~p~~e~~~~iL~~~~~~~~~~~~~~i~~~al~~l~~~s~~~~  365 (468)
T 3pxg_A          289 RGELQCIGATTLDEYRKYIEKDAALER--RFQP-IQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYI  365 (468)
T ss_dssp             SSSCEEEEECCTTTTHHHHTTCSHHHH--SEEE-EECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHHHHHHHHHHHHHSS
T ss_pred             CCCEEEEecCCHHHHHHHhhcCHHHHH--hCcc-ceeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHh
Confidence            45689999999987     79999999  9985 9999999999999999988763    222 334466666665544 


Q ss_pred             ----CHHHHHHHHHHHHHHH
Q 039253          103 ----SGADITEICQRACKDA  118 (199)
Q Consensus       103 ----sgaDI~~lv~~A~~~a  118 (199)
                          .+.....+++.|...+
T Consensus       366 ~~~~lp~~ai~ll~~a~~~~  385 (468)
T 3pxg_A          366 SDRFLPDKAIDLIDEAGSKV  385 (468)
T ss_dssp             CCSCTTHHHHHHHHHHHHHH
T ss_pred             ccCcCCcHHHHHHHHHHHHH
Confidence                4557778888776443

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=97.71  E-value=6e-05  Score=69.28  Aligned_cols=121  Identities=15%  Similarity=0.101  Sum_probs=80.8

Q ss_pred             HHHHHHHHHHhCCC-----------CCCCEEEEEeeCCCC-------------CCCccccCCCccc-eEEEecCCCHHHH
Q 039253           19 RIPNQLLTEMDGLS-----------AKKTIFVIGVTNRPD-------------IIDPALLRPGRLD-QLIYIPLPVEKSR   73 (199)
Q Consensus        19 r~~~~lL~~ld~~~-----------~~~~VvvI~aTN~~~-------------~lD~al~R~gRfd-~~i~~~~P~~~~R   73 (199)
                      ...+.|+..|+.-.           -..++.||+|||.++             .|++++++  ||| ..+..+.|+.+ .
T Consensus       406 ~~q~~Ll~~le~~~i~i~~~g~~~~~~~~~~vIaatNp~~G~~~~~~~~~~ni~l~~aLl~--RFDl~~~~~~~~~~e-~  482 (595)
T 3f9v_A          406 EDRVAIHEAMEQQTVSIAKAGIVAKLNARAAVIAAGNPKFGRYISERPVSDNINLPPTILS--RFDLIFILKDQPGEQ-D  482 (595)
T ss_dssp             HHHHHHHHHHHSSSEEEESSSSEEEECCCCEEEEEECCTTCCSCTTSCSCTTTCSCSSSGG--GCSCCEEECCTTHHH-H
T ss_pred             hHhhhhHHHHhCCEEEEecCCcEEEecCceEEEEEcCCcCCccCcccCchhccCCCHHHHh--hCeEEEEeCCCCCHH-H
Confidence            46678888887421           124678999999987             99999999  998 56666778888 8


Q ss_pred             HHHHHHhhcCCCCC--------------------------CcccHHHHHhh--------------CCCCCHHHHHHHHHH
Q 039253           74 LQIFKACLRKSPVS--------------------------KDVDLEKLAQF--------------TQGFSGADITEICQR  113 (199)
Q Consensus        74 ~~il~~~l~~~~~~--------------------------~~~~l~~la~~--------------t~G~sgaDI~~lv~~  113 (199)
                      ..|.++.+......                          ++.....|...              +.+.|.+.+..+++.
T Consensus       483 ~~i~~~il~~~~~~~~~~~l~~~~l~~~i~~ar~~~~p~ls~ea~~~l~~~y~~lR~~~~~~~~~~~~~s~R~l~~lirl  562 (595)
T 3f9v_A          483 RELANYILDVHSGKSTKNIIDIDTLRKYIAYARKYVTPKITSEAKNLITDFFVEMRKKSSETPDSPILITPRQLEALIRI  562 (595)
T ss_dssp             HHHHHHHHTTTCCCSSSSTTCCTTTHHHHHHHHHHHCCCCCCCTHHHHHHHHTTSSCSCCBCSSSCBCSSTTTTTHHHHH
T ss_pred             HHHHHHHHHHhhccccccCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHhhccCCCccccccHHHHHHHHHH
Confidence            88888877643210                          01111222221              346677777777776


Q ss_pred             HHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccccc
Q 039253          114 ACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQ  161 (199)
Q Consensus       114 A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps~  161 (199)
                      |...|..+..                   ..|+.+|+..|+.-++.|.
T Consensus       563 a~a~A~l~~~-------------------~~V~~~dv~~Ai~l~~~sl  591 (595)
T 3f9v_A          563 SEAYAKMALK-------------------AEVTREDAERAINIMRLFL  591 (595)
T ss_dssp             HHHHHHTTSS-------------------CCSSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCc-------------------CCCCHHHHHHHHHHHHHHH
Confidence            6555433321                   5699999999998876654

>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=97.71  E-value=8.1e-05  Score=63.23  Aligned_cols=100  Identities=13%  Similarity=0.095  Sum_probs=72.8

Q ss_pred             HHHHHHHHHHhCCCC--CCCEEEEEeeCCC---CCCCccccCCCccce-EEEecCCCHHHHHHHHHHhhcC---CCCCCc
Q 039253           19 RIPNQLLTEMDGLSA--KKTIFVIGVTNRP---DIIDPALLRPGRLDQ-LIYIPLPVEKSRLQIFKACLRK---SPVSKD   89 (199)
Q Consensus        19 r~~~~lL~~ld~~~~--~~~VvvI~aTN~~---~~lD~al~R~gRfd~-~i~~~~P~~~~R~~il~~~l~~---~~~~~~   89 (199)
                      .....|+..++.+..  ..++.+|++||.+   +.+++.+.+  ||.. .+.|++++.++..++++..+..   ...-++
T Consensus       140 ~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~~~~~l~~~~~~--r~~~~~i~~~pl~~~~~~~~l~~~~~~~~~~~~~~~  217 (389)
T 1fnn_A          140 DILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRG--IMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSE  217 (389)
T ss_dssp             HHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSCHHHHH--HHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCH
T ss_pred             HHHHHHHHHHHhCCCCCcCCEEEEEEECCchHHHHhCHHhhh--cCCCceEEeCCCCHHHHHHHHHHHHHhhcCCCCCCH
Confidence            456666666665432  2578999999988   788999988  8886 8999999999999999988754   111234


Q ss_pred             ccHHHHHhhCCCC--------CHHHHHHHHHHHHHHHHH
Q 039253           90 VDLEKLAQFTQGF--------SGADITEICQRACKDATR  120 (199)
Q Consensus        90 ~~l~~la~~t~G~--------sgaDI~~lv~~A~~~a~~  120 (199)
                      ..+..+++.+.+.        .+..+..+|+.|...+..
T Consensus       218 ~~~~~l~~~~~~~~~~~~~~G~~r~~~~~l~~a~~~a~~  256 (389)
T 1fnn_A          218 DILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQ  256 (389)
T ss_dssp             HHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcccCCCCCCcHHHHHHHHHHHHHHHHH
Confidence            4577788888422        467778888888766644

>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=97.70  E-value=0.0001  Score=62.22  Aligned_cols=96  Identities=20%  Similarity=0.217  Sum_probs=67.5

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCC---CCCCccccCCCccc-eEEEecCCCHHHHHHHHHHhhcC----CCCCCcc
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRP---DIIDPALLRPGRLD-QLIYIPLPVEKSRLQIFKACLRK----SPVSKDV   90 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~---~~lD~al~R~gRfd-~~i~~~~P~~~~R~~il~~~l~~----~~~~~~~   90 (199)
                      .+...|+..++.+ ...++.+|++||.+   +.+++.+.+  ||. ..++|++|+.++..+|++..+..    ..+ .+.
T Consensus       147 ~~l~~l~~~~~~~-~~~~~~~I~~~~~~~~~~~~~~~~~~--r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~-~~~  222 (386)
T 2qby_A          147 DILYKLSRINSEV-NKSKISFIGITNDVKFVDLLDPRVKS--SLSEEEIIFPPYNAEELEDILTKRAQMAFKPGVL-PDN  222 (386)
T ss_dssp             THHHHHHHHHHSC-CC--EEEEEEESCGGGGGGCTTHHHH--TTTTEEEEECCCCHHHHHHHHHHHHHHHBCSSCS-CHH
T ss_pred             HHHHHHhhchhhc-CCCeEEEEEEECCCChHhhhCHHHhc--cCCCeeEEeCCCCHHHHHHHHHHHHHhhccCCCC-CHH
Confidence            4566777777765 45678999999987   578888888  876 59999999999999999987752    222 233


Q ss_pred             cHHHHHhhCC---CCCHHHHHHHHHHHHHHHH
Q 039253           91 DLEKLAQFTQ---GFSGADITEICQRACKDAT  119 (199)
Q Consensus        91 ~l~~la~~t~---G~sgaDI~~lv~~A~~~a~  119 (199)
                      .+..++..+.   | .+..+..+|+.|...+.
T Consensus       223 ~~~~l~~~~~~~~G-~~r~~~~ll~~a~~~a~  253 (386)
T 2qby_A          223 VIKLCAALAAREHG-DARRALDLLRVSGEIAE  253 (386)
T ss_dssp             HHHHHHHHHHHTTC-CHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcC-CHHHHHHHHHHHHHHHH
Confidence            4566777665   4 45566667777765553

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=97.68  E-value=0.00013  Score=61.14  Aligned_cols=91  Identities=16%  Similarity=0.214  Sum_probs=66.6

Q ss_pred             HHHHHHHhCCCCCCCEEEEEeeCCCC---CCCccccCCCccc--eEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHH
Q 039253           22 NQLLTEMDGLSAKKTIFVIGVTNRPD---IIDPALLRPGRLD--QLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKL   95 (199)
Q Consensus        22 ~~lL~~ld~~~~~~~VvvI~aTN~~~---~lD~al~R~gRfd--~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~l   95 (199)
                      ..|+..++.+......+|+++++.+.   .+++++++  ||.  ..+++++ +.++|..|++.++...... ++..+..|
T Consensus       118 ~~l~~~l~~~~~~~~~iii~~~~~~~~l~~l~~~L~s--R~~~~~~i~l~~-~~~e~~~il~~~~~~~~~~l~~~~l~~l  194 (324)
T 1l8q_A          118 IEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVS--RFEGGILVEIEL-DNKTRFKIIKEKLKEFNLELRKEVIDYL  194 (324)
T ss_dssp             HHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHH--HHHTSEEEECCC-CHHHHHHHHHHHHHHTTCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCeEEEEecCChHHHHHhhhHhhh--cccCceEEEeCC-CHHHHHHHHHHHHHhcCCCCCHHHHHHH
Confidence            44444544433344567777777766   68999999  997  7789998 9999999999998754433 34457889


Q ss_pred             HhhCCCCCHHHHHHHHHHHHHH
Q 039253           96 AQFTQGFSGADITEICQRACKD  117 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv~~A~~~  117 (199)
                      +..+  -..+++..++..+...
T Consensus       195 ~~~~--g~~r~l~~~l~~~~~~  214 (324)
T 1l8q_A          195 LENT--KNVREIEGKIKLIKLK  214 (324)
T ss_dssp             HHHC--SSHHHHHHHHHHHHHH
T ss_pred             HHhC--CCHHHHHHHHHHHHHc
Confidence            9988  4678888888877654

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=97.66  E-value=0.0003  Score=59.50  Aligned_cols=92  Identities=16%  Similarity=0.175  Sum_probs=72.7

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHH
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLA   96 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la   96 (199)
                      ....+.|+..++.  ...++++|++|+.+..+++++++  |+ ..+.|+.|+.++...+++.++...... ++..+..++
T Consensus       133 ~~~~~~Ll~~le~--~~~~~~~Il~~~~~~~l~~~l~s--r~-~~i~~~~l~~~~~~~~l~~~~~~~~~~~~~~a~~~l~  207 (373)
T 1jr3_A          133 RHSFNALLKTLEE--PPEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLA  207 (373)
T ss_dssp             HHHHHHHHHHHHS--CCSSEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHH
T ss_pred             HHHHHHHHHHHhc--CCCceEEEEEeCChHhCcHHHHh--he-eEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            3456788888875  34578899999999999999998  87 789999999999999999988654433 233477889


Q ss_pred             hhCCCCCHHHHHHHHHHHH
Q 039253           97 QFTQGFSGADITEICQRAC  115 (199)
Q Consensus        97 ~~t~G~sgaDI~~lv~~A~  115 (199)
                      +.+.| ..+++.++++.+.
T Consensus       208 ~~~~G-~~r~~~~~l~~~~  225 (373)
T 1jr3_A          208 RAAEG-SLRDALSLTDQAI  225 (373)
T ss_dssp             HHSSS-CHHHHHHHHHHHH
T ss_pred             HHCCC-CHHHHHHHHHHHH
Confidence            98877 6778888887764

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.62  E-value=0.00029  Score=59.08  Aligned_cols=92  Identities=15%  Similarity=0.053  Sum_probs=68.7

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHh
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQ   97 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~   97 (199)
                      ...+.|+..|+...  ..+.+|++||.++.+++++++  |+. .+.|+.|+.++...+++..+....+. ++..+..|++
T Consensus       148 ~~~~~Ll~~le~~~--~~~~~il~~~~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~l~~l~~  222 (353)
T 1sxj_D          148 DAQSALRRTMETYS--GVTRFCLICNYVTRIIDPLAS--QCS-KFRFKALDASNAIDRLRFISEQENVKCDDGVLERILD  222 (353)
T ss_dssp             HHHHHHHHHHHHTT--TTEEEEEEESCGGGSCHHHHH--HSE-EEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcC--CCceEEEEeCchhhCcchhhc--cCc-eEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence            45677888888543  356777889999999999999  986 89999999999999999988654432 3445788888


Q ss_pred             hCCCCCHHHHHHHHHHHHH
Q 039253           98 FTQGFSGADITEICQRACK  116 (199)
Q Consensus        98 ~t~G~sgaDI~~lv~~A~~  116 (199)
                      .+.|. .+.+.++++.+..
T Consensus       223 ~~~G~-~r~~~~~l~~~~~  240 (353)
T 1sxj_D          223 ISAGD-LRRGITLLQSASK  240 (353)
T ss_dssp             HTSSC-HHHHHHHHHHTHH
T ss_pred             HcCCC-HHHHHHHHHHHHH
Confidence            88764 4555555555443

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=97.60  E-value=0.00016  Score=64.06  Aligned_cols=115  Identities=19%  Similarity=0.127  Sum_probs=83.3

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEe---------eC---CCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCC
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGV---------TN---RPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSP   85 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~a---------TN---~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~   85 (199)
                      ....+.|+..|+.-  ..+++++++         |+   .|..|++.+++  ||.. +.|+.|+.++..++|+..+....
T Consensus       309 ~~a~~aLlk~lEe~--~~~~~il~tn~~~~~i~~~~~~~~~~~l~~~i~s--R~~~-~~~~~~~~~e~~~iL~~~~~~~~  383 (456)
T 2c9o_A          309 IECFTYLHRALESS--IAPIVIFASNRGNCVIRGTEDITSPHGIPLDLLD--RVMI-IRTMLYTPQEMKQIIKIRAQTEG  383 (456)
T ss_dssp             HHHHHHHHHHTTST--TCCEEEEEECCSEEECBTTSSCEEETTCCHHHHT--TEEE-EECCCCCHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhhcc--CCCEEEEecCCccccccccccccccccCChhHHh--hcce-eeCCCCCHHHHHHHHHHHHHHhC
Confidence            45788888888853  334544444         22   28899999999  9988 59999999999999998875333


Q ss_pred             CC-CcccHHHHHhhC-CCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhc
Q 039253           86 VS-KDVDLEKLAQFT-QGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYA  157 (199)
Q Consensus        86 ~~-~~~~l~~la~~t-~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~  157 (199)
                      .. ++..+..++..+ .| +++..-.+++.|...|..+..                   ..|+.+|+..|+.-+
T Consensus       384 ~~~~~~~~~~i~~~a~~g-~~r~a~~ll~~a~~~A~~~~~-------------------~~v~~~~v~~~~~~~  437 (456)
T 2c9o_A          384 INISEEALNHLGEIGTKT-TLRYSVQLLTPANLLAKINGK-------------------DSIEKEHVEEISELF  437 (456)
T ss_dssp             CCBCHHHHHHHHHHHHHS-CHHHHHHTHHHHHHHHHHTTC-------------------SSBCHHHHHHHHHHS
T ss_pred             CCCCHHHHHHHHHHccCC-CHHHHHHHHHHHHHHHhhcCC-------------------CccCHHHHHHHHHHh
Confidence            22 233466777777 55 788888888887666654331                   569999999998775

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=97.52  E-value=0.0002  Score=67.25  Aligned_cols=83  Identities=22%  Similarity=0.288  Sum_probs=63.2

Q ss_pred             CCCEEEEEeeCCCC-----CCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCC----C-CcccHHHHHhh-----
Q 039253           34 KKTIFVIGVTNRPD-----IIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPV----S-KDVDLEKLAQF-----   98 (199)
Q Consensus        34 ~~~VvvI~aTN~~~-----~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~----~-~~~~l~~la~~-----   98 (199)
                      ...+.+|+|||..+     .+|++++|  || ..|.|+.|+.+++.+||+.+...+..    . .+..+..++..     
T Consensus       289 ~~~v~~I~at~~~~~~~~~~~d~al~r--Rf-~~i~v~~p~~~~~~~il~~~~~~~~~~~~~~i~~~al~~~~~~s~~~i  365 (758)
T 3pxi_A          289 RGELQCIGATTLDEYRKYIEKDAALER--RF-QPIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYI  365 (758)
T ss_dssp             SSSCEEEEECCTTTTHHHHTTCSHHHH--SE-EEEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHHHHHHHHHHHHHSS
T ss_pred             cCCEEEEeCCChHHHHHHhhccHHHHh--hC-cEEEeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccc
Confidence            55789999999988     79999999  99 56999999999999999988876422    1 22334455543     


Q ss_pred             CCCCCHHHHHHHHHHHHHHHH
Q 039253           99 TQGFSGADITEICQRACKDAT  119 (199)
Q Consensus        99 t~G~sgaDI~~lv~~A~~~a~  119 (199)
                      ++++.+.+...++..|+..+.
T Consensus       366 ~~~~~p~~ai~ll~~a~~~~~  386 (758)
T 3pxi_A          366 SDRFLPDKAIDLIDEAGSKVR  386 (758)
T ss_dssp             CCSCTTHHHHHHHHHHHHHHH
T ss_pred             ccCcCCcHHHHHHHHHHHHHH
Confidence            356778888888888765543

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=97.52  E-value=0.00024  Score=58.55  Aligned_cols=89  Identities=17%  Similarity=0.050  Sum_probs=64.4

Q ss_pred             HHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhh
Q 039253           20 IPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQF   98 (199)
Q Consensus        20 ~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~   98 (199)
                      ..+.|+..|+.  ...++++|++||.+..+++++.+  |+. .+.|++|+.+++..+++..+...... ++..+..|+..
T Consensus       118 ~~~~L~~~le~--~~~~~~~i~~~~~~~~l~~~l~s--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~  192 (319)
T 2chq_A          118 AQAALRRTMEM--YSKSCRFILSCNYVSRIIEPIQS--RCA-VFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYI  192 (319)
T ss_dssp             HHHTTGGGTSS--SSSSEEEEEEESCGGGSCHHHHT--TCE-EEECCCCCHHHHHHHHHHHHHTTCCCBCHHHHHHHHHT
T ss_pred             HHHHHHHHHHh--cCCCCeEEEEeCChhhcchHHHh--hCe-EEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            34555555553  23568899999999999999999  886 89999999999999999998766543 34456778876


Q ss_pred             CCCCCHHHHHHHHHHH
Q 039253           99 TQGFSGADITEICQRA  114 (199)
Q Consensus        99 t~G~sgaDI~~lv~~A  114 (199)
                      +.| ..+.+.++++.+
T Consensus       193 ~~G-~~r~~~~~l~~~  207 (319)
T 2chq_A          193 SGG-DFRKAINALQGA  207 (319)
T ss_dssp             TTT-CHHHHHHHHHHH
T ss_pred             cCC-CHHHHHHHHHHH
Confidence            655 344444444443

>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=97.45  E-value=0.00028  Score=58.40  Aligned_cols=91  Identities=12%  Similarity=0.099  Sum_probs=68.5

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHh
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQ   97 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~   97 (199)
                      ...+.|+..|+..  ..++.+|++||.++.+++++.+  |+. .+.|++|+.++...+++..+...... ++..+..|+.
T Consensus       125 ~~~~~L~~~le~~--~~~~~~i~~~~~~~~l~~~l~s--r~~-~~~~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  199 (327)
T 1iqp_A          125 DAQQALRRTMEMF--SSNVRFILSCNYSSKIIEPIQS--RCA-IFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILY  199 (327)
T ss_dssp             HHHHHHHHHHHHT--TTTEEEEEEESCGGGSCHHHHH--TEE-EEECCCCCHHHHHHHHHHHHHTTTCEECHHHHHHHHH
T ss_pred             HHHHHHHHHHHhc--CCCCeEEEEeCCccccCHHHHh--hCc-EEEecCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Confidence            4567788888753  4567888899999999999998  887 78999999999999999988765543 3445677888


Q ss_pred             hCCCCCHHHHHHHHHHHH
Q 039253           98 FTQGFSGADITEICQRAC  115 (199)
Q Consensus        98 ~t~G~sgaDI~~lv~~A~  115 (199)
                      .+.| +.+.+.++++.+.
T Consensus       200 ~~~g-~~r~~~~~l~~~~  216 (327)
T 1iqp_A          200 IAEG-DMRRAINILQAAA  216 (327)
T ss_dssp             HHTT-CHHHHHHHHHHHH
T ss_pred             HCCC-CHHHHHHHHHHHH
Confidence            7765 4555555555543

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=97.42  E-value=0.00021  Score=66.91  Aligned_cols=114  Identities=18%  Similarity=0.151  Sum_probs=76.5

Q ss_pred             HHhCCCCCCCEEEEEeeCCC-----CCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCC----CCC-CcccHHHHH
Q 039253           27 EMDGLSAKKTIFVIGVTNRP-----DIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKS----PVS-KDVDLEKLA   96 (199)
Q Consensus        27 ~ld~~~~~~~VvvI~aTN~~-----~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~----~~~-~~~~l~~la   96 (199)
                      .+..+.....+.+|++||.+     ..+|+++.|  ||+ .+.|+.|+.++|.+||+.+...+    .+. .+..+..++
T Consensus       306 ~L~~~l~~~~~~~I~at~~~~~~~~~~~d~aL~~--Rf~-~i~v~~p~~~e~~~il~~l~~~~~~~~~v~~~~~al~~~~  382 (758)
T 1r6b_X          306 LIKPLLSSGKIRVIGSTTYQEFSNIFEKDRALAR--RFQ-KIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAV  382 (758)
T ss_dssp             HHSSCSSSCCCEEEEEECHHHHHCCCCCTTSSGG--GEE-EEECCCCCHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHH
T ss_pred             HHHHHHhCCCeEEEEEeCchHHhhhhhcCHHHHh--Cce-EEEcCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHH
Confidence            34444455678999999964     468999999  998 69999999999999999887542    111 233456666


Q ss_pred             hhCCC-----CCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcc
Q 039253           97 QFTQG-----FSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYAC  158 (199)
Q Consensus        97 ~~t~G-----~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~  158 (199)
                      ..+.|     +.+..+..++.+|+..+....               .......++.+|+..++..+.
T Consensus       383 ~~s~~~i~~~~lp~~~i~lld~a~~~~~~~~---------------~~~~~~~v~~~di~~~~~~~~  434 (758)
T 1r6b_X          383 ELAVKYINDRHLPDKAIDVIDEAGARARLMP---------------VSKRKKTVNVADIESVVARIA  434 (758)
T ss_dssp             HHHHHHCTTSCTTHHHHHHHHHHHHHHHHSS---------------SCCCCCSCCHHHHHHHHHHHS
T ss_pred             HHhhhhcccccCchHHHHHHHHHHHHHhccc---------------ccccCCccCHHHHHHHHHHhc
Confidence            65544     566778888887754332100               001124588888888887764

>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=97.38  E-value=0.00066  Score=56.01  Aligned_cols=90  Identities=12%  Similarity=0.048  Sum_probs=65.1

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHh
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQ   97 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~   97 (199)
                      ...+.|+..++.  ...++.+|++||.+..+++++.+  |+. .+.|+.|+.++..++++..+...... ++..+..+++
T Consensus       122 ~~~~~L~~~le~--~~~~~~~il~~~~~~~l~~~l~s--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~  196 (323)
T 1sxj_B          122 GAQQALRRTMEL--YSNSTRFAFACNQSNKIIEPLQS--QCA-ILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIF  196 (323)
T ss_dssp             HHHHTTHHHHHH--TTTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHH
T ss_pred             HHHHHHHHHHhc--cCCCceEEEEeCChhhchhHHHh--hce-EEeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            345667777774  34567888899999999999999  876 89999999999999999887643332 2445677888


Q ss_pred             hCCCCCHHHHHHHHHHH
Q 039253           98 FTQGFSGADITEICQRA  114 (199)
Q Consensus        98 ~t~G~sgaDI~~lv~~A  114 (199)
                      .+.|- .+.+.++++.+
T Consensus       197 ~~~G~-~r~a~~~l~~~  212 (323)
T 1sxj_B          197 TAEGD-MRQAINNLQST  212 (323)
T ss_dssp             HHTTC-HHHHHHHHHHH
T ss_pred             HcCCC-HHHHHHHHHHH
Confidence            77653 44444444443

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=97.38  E-value=0.00037  Score=65.38  Aligned_cols=105  Identities=18%  Similarity=0.222  Sum_probs=77.5

Q ss_pred             hhHHHHHHHHHHhCCC---------CCCCEEEEEeeCCCCC------------CCccccCCCccceEEEecCCCHHHHHH
Q 039253           17 ADRIPNQLLTEMDGLS---------AKKTIFVIGVTNRPDI------------IDPALLRPGRLDQLIYIPLPVEKSRLQ   75 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~---------~~~~VvvI~aTN~~~~------------lD~al~R~gRfd~~i~~~~P~~~~R~~   75 (199)
                      ...+.+.|++.|+.-.         ...++++|+|||.+..            ++|+|+.  ||+..|.|++|+.+++..
T Consensus       592 ~~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn~~~~~~~~~~~~~~~~f~p~l~~--Rl~~~i~~~~l~~~~~~~  669 (758)
T 3pxi_A          592 HPDVFNILLQVLEDGRLTDSKGRTVDFRNTILIMTSNVGASEKDKVMGELKRAFRPEFIN--RIDEIIVFHSLEKKHLTE  669 (758)
T ss_dssp             CHHHHHHHHHHHHHSBCC-----CCBCTTCEEEEEESSSTTCCHHHHHHHHHHSCHHHHT--TSSEEEECC--CHHHHHH
T ss_pred             CHHHHHHHHHHhccCeEEcCCCCEeccCCeEEEEeCCCChhhHHHHHHHHHhhCCHHHHh--hCCeEEecCCCCHHHHHH
Confidence            3467889999998621         1245799999998665            7899998  999999999999999999


Q ss_pred             HHHHhhcCC-------CCC---CcccHHHHHhh--CCCCCHHHHHHHHHHHHHHHHHHHH
Q 039253           76 IFKACLRKS-------PVS---KDVDLEKLAQF--TQGFSGADITEICQRACKDATREEI  123 (199)
Q Consensus        76 il~~~l~~~-------~~~---~~~~l~~la~~--t~G~sgaDI~~lv~~A~~~a~~~~~  123 (199)
                      |++.++..+       ...   ++.-+..|++.  ...+..++|+++++++...++.+.+
T Consensus       670 i~~~~l~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~R~L~~~i~~~v~~~l~~~~  729 (758)
T 3pxi_A          670 IVSLMSDQLTKRLKEQDLSIELTDAAKAKVAEEGVDLEYGARPLRRAIQKHVEDRLSEEL  729 (758)
T ss_dssp             HHHHHHHHHHHHHHTTTCEEEECHHHHHHHHGGGCCTTTTTTTHHHHHHHHTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCeEEECHHHHHHHHHhCCCCCCCChHHHHHHHHHHHHHHHHHH
Confidence            999888542       111   23346667664  3457788999999998887776665

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=97.28  E-value=0.00016  Score=64.24  Aligned_cols=114  Identities=17%  Similarity=0.210  Sum_probs=75.2

Q ss_pred             HHHHHHHHhCCCCCCCEEEEEee--CCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCC-------CC-Ccc
Q 039253           21 PNQLLTEMDGLSAKKTIFVIGVT--NRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSP-------VS-KDV   90 (199)
Q Consensus        21 ~~~lL~~ld~~~~~~~VvvI~aT--N~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~-------~~-~~~   90 (199)
                      .+.||..|+.    ..+++|++|  |....+++++++  |+. .+.|+.|+.+++..+++..+....       .. ++.
T Consensus       123 q~~LL~~le~----~~v~lI~att~n~~~~l~~aL~s--R~~-v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~  195 (447)
T 3pvs_A          123 QDAFLPHIED----GTITFIGATTENPSFELNSALLS--RAR-VYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDE  195 (447)
T ss_dssp             --CCHHHHHT----TSCEEEEEESSCGGGSSCHHHHT--TEE-EEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEECCHH
T ss_pred             HHHHHHHHhc----CceEEEecCCCCcccccCHHHhC--cee-EEeeCCcCHHHHHHHHHHHHHHHhhhhccccCcCCHH
Confidence            3456666663    456777777  445689999999  987 677999999999999999987521       11 233


Q ss_pred             cHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhccc
Q 039253           91 DLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACK  159 (199)
Q Consensus        91 ~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~P  159 (199)
                      .+..|+..+.| ..+.+.++++.+...+...                 ......||.+++.+++....+
T Consensus       196 al~~L~~~~~G-d~R~lln~Le~a~~~a~~~-----------------~~~~~~It~e~v~~~l~~~~~  246 (447)
T 3pvs_A          196 TRRAIAELVNG-DARRALNTLEMMADMAEVD-----------------DSGKRVLKPELLTEIAGERSA  246 (447)
T ss_dssp             HHHHHHHHHCS-CHHHHHHHHHHHHHHSCBC-----------------TTSCEECCHHHHHHHHTCCCC
T ss_pred             HHHHHHHHCCC-CHHHHHHHHHHHHHhcccc-----------------cCCCCccCHHHHHHHHhhhhh
Confidence            46778887655 5677777777665443110                 001145788888877766543

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=97.28  E-value=0.00031  Score=65.76  Aligned_cols=106  Identities=18%  Similarity=0.211  Sum_probs=79.5

Q ss_pred             hhHHHHHHHHHHhCCC----C-----CCCEEEEEeeCCCC-------------------------CCCccccCCCccceE
Q 039253           17 ADRIPNQLLTEMDGLS----A-----KKTIFVIGVTNRPD-------------------------IIDPALLRPGRLDQL   62 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~----~-----~~~VvvI~aTN~~~-------------------------~lD~al~R~gRfd~~   62 (199)
                      ...+.+.|++.|+.-.    .     -.+++||+|||.+.                         .++|+|+.  ||+..
T Consensus       570 ~~~~~~~Ll~~le~~~~~~~~g~~~~~~~~~iI~tsN~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~--R~~~~  647 (758)
T 1r6b_X          570 HPDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNI  647 (758)
T ss_dssp             CHHHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEECSSCC-----------------CHHHHHHHSCHHHHT--TCSEE
T ss_pred             CHHHHHHHHHHhcCcEEEcCCCCEEecCCeEEEEecCcchhhhhhcccCccccchHHHHHHHHHHhcCHHHHh--hCCcc
Confidence            3468889999998421    0     14688999999854                         68899999  99999


Q ss_pred             EEecCCCHHHHHHHHHHhhcCC---------CCC-CcccHHHHHhhC--CCCCHHHHHHHHHHHHHHHHHHHHH
Q 039253           63 IYIPLPVEKSRLQIFKACLRKS---------PVS-KDVDLEKLAQFT--QGFSGADITEICQRACKDATREEIE  124 (199)
Q Consensus        63 i~~~~P~~~~R~~il~~~l~~~---------~~~-~~~~l~~la~~t--~G~sgaDI~~lv~~A~~~a~~~~~~  124 (199)
                      |.|++|+.+++..|++.++...         .+. ++.-+..|++..  ..+..++|..+++.+...++.+.+-
T Consensus       648 i~~~~l~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~g~R~l~~~i~~~~~~~l~~~~l  721 (758)
T 1r6b_X          648 IWFDHLSTDVIHQVVDKFIVELQVQLDQKGVSLEVSQEARNWLAEKGYDRAMGARPMARVIQDNLKKPLANELL  721 (758)
T ss_dssp             EECCCCCHHHHHHHHHHHHHHHHHHHHHTTEEEEECHHHHHHHHHHHCBTTTBTTTHHHHHHHHHTHHHHHHHH
T ss_pred             eeeCCCCHHHHHHHHHHHHHHHHHHHHHCCcEEEeCHHHHHHHHHhCCCcCCCchHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999988632         111 233456666543  4677899999999998887766543

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.22  E-value=0.001  Score=56.01  Aligned_cols=91  Identities=19%  Similarity=0.181  Sum_probs=68.5

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-C-cccHHHHH
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-K-DVDLEKLA   96 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~-~~~l~~la   96 (199)
                      ...+.|+..|+...  .++.+|.+||.++.+.+++++  |+ ..+.|++|+.++...+++..+....+. + +..+..|+
T Consensus       149 ~~~~~L~~~le~~~--~~~~~Il~t~~~~~l~~~l~s--R~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~i~  223 (354)
T 1sxj_E          149 DAQAALRRTMEKYS--KNIRLIMVCDSMSPIIAPIKS--QC-LLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIA  223 (354)
T ss_dssp             HHHHHHHHHHHHST--TTEEEEEEESCSCSSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCEECCSHHHHHHH
T ss_pred             HHHHHHHHHHHhhc--CCCEEEEEeCCHHHHHHHHHh--hc-eEEecCCcCHHHHHHHHHHHHHHcCCCCCcHHHHHHHH
Confidence            45677888887643  357888999999999999999  88 889999999999999999988654433 2 44577888


Q ss_pred             hhCCCCCHHHHHHHHHHHH
Q 039253           97 QFTQGFSGADITEICQRAC  115 (199)
Q Consensus        97 ~~t~G~sgaDI~~lv~~A~  115 (199)
                      +.+.| +.+++.++++.+.
T Consensus       224 ~~~~G-~~r~a~~~l~~~~  241 (354)
T 1sxj_E          224 QASNG-NLRVSLLMLESMA  241 (354)
T ss_dssp             HHHTT-CHHHHHHHHTHHH
T ss_pred             HHcCC-CHHHHHHHHHHHH
Confidence            87755 4555555555443

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=97.19  E-value=0.00049  Score=62.00  Aligned_cols=103  Identities=13%  Similarity=0.059  Sum_probs=66.3

Q ss_pred             hhHHHHHHHHHHhCCC--------CCCCEEEEEeeCCCCC---CCccccCCCccceEEEecCCCH-HHHHHHHHHhhcCC
Q 039253           17 ADRIPNQLLTEMDGLS--------AKKTIFVIGVTNRPDI---IDPALLRPGRLDQLIYIPLPVE-KSRLQIFKACLRKS   84 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~--------~~~~VvvI~aTN~~~~---lD~al~R~gRfd~~i~~~~P~~-~~R~~il~~~l~~~   84 (199)
                      ...+.+.|+..|+.-.        .....++|+|||.+..   ..+++++  ||...+++++|+. ++|..|++......
T Consensus       122 ~~~~q~~LL~~lee~~v~i~G~~~~~~~~~iI~ATN~lpe~~~~~~aLld--RF~~~i~v~~p~~~ee~~~IL~~~~~~~  199 (500)
T 3nbx_X          122 GPAILNTLLTAINERQFRNGAHVEKIPMRLLVAASNELPEADSSLEALYD--RMLIRLWLDKVQDKANFRSMLTSQQDEN  199 (500)
T ss_dssp             CHHHHHHHHHHHHSSEEECSSSEEECCCCEEEEEESSCCCTTCTTHHHHT--TCCEEEECCSCCCHHHHHHHHTCCCCTT
T ss_pred             cHHHHHHHHHHHHHHhccCCCCcCCcchhhhhhccccCCCccccHHHHHH--HHHHHHHHHHhhhhhhHHHHHhcccccC
Confidence            3467788999987320        1122357888886332   3459999  9999999999987 78999998765321


Q ss_pred             -------------------------CCCCcccHHHHHhh---------CCCCCHHHHHHHHHHHHHHHHHHH
Q 039253           85 -------------------------PVSKDVDLEKLAQF---------TQGFSGADITEICQRACKDATREE  122 (199)
Q Consensus        85 -------------------------~~~~~~~l~~la~~---------t~G~sgaDI~~lv~~A~~~a~~~~  122 (199)
                                               .+. +.-+..++..         ..|.|++.+..+++.|...|..+.
T Consensus       200 ~~~~~~~~~~~~e~l~~~~~~~~~v~v~-d~v~e~i~~l~~~lr~~r~~~~iS~R~~~~llr~A~A~A~l~g  270 (500)
T 3nbx_X          200 DNPVPDALQVTDEEYERWQKEIGEITLP-DHVFELIFMLRQQLDKLPDAPYVSDRRWKKAIRLLQASAFFSG  270 (500)
T ss_dssp             SCCSCTTTSBCHHHHHHHHHHHTTCBCC-HHHHHHHHHHHHHHHHCSSSCCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCccceecHHHHHHHHhcCCcccCc-hHHHHHHHHHHHHhhcCCCCCccchhHHHHHHHHHHHHHhhcC
Confidence                                     111 1112233322         358899998888887766665443

>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=97.10  E-value=0.0022  Score=54.60  Aligned_cols=72  Identities=19%  Similarity=0.252  Sum_probs=52.2

Q ss_pred             CCccccCCCccceEEEecCCCHHHHHHHHHH----hhc-------CCCCC---CcccHHHHHhh--CCCCCHHHHHHHHH
Q 039253           49 IDPALLRPGRLDQLIYIPLPVEKSRLQIFKA----CLR-------KSPVS---KDVDLEKLAQF--TQGFSGADITEICQ  112 (199)
Q Consensus        49 lD~al~R~gRfd~~i~~~~P~~~~R~~il~~----~l~-------~~~~~---~~~~l~~la~~--t~G~sgaDI~~lv~  112 (199)
                      +.|+|+.  ||+..+.|.+|+.+++.+|+..    ++.       .....   ++.-+..|++.  ...+.+++|+++++
T Consensus       239 ~~~~l~~--R~~~~~~~~pl~~~~~~~I~~~~~~~l~~~~~~~~~~~~~~l~~~~~a~~~L~~~~~~~~~gaR~L~~~ie  316 (363)
T 3hws_A          239 LIPEFIG--RLPVVATLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVE  316 (363)
T ss_dssp             CCHHHHT--TCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHTTCTTTTHHHHHH
T ss_pred             CCHHHhc--ccCeeeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCceEEECHHHHHHHHHhhcCCccCchHHHHHHH
Confidence            7888888  9999999999999999999987    221       11211   23335666653  34566789999999


Q ss_pred             HHHHHHHHHH
Q 039253          113 RACKDATREE  122 (199)
Q Consensus       113 ~A~~~a~~~~  122 (199)
                      ++...++.+.
T Consensus       317 ~~~~~~l~~~  326 (363)
T 3hws_A          317 AALLDTMYDL  326 (363)
T ss_dssp             HHHHHHHHST
T ss_pred             HHHHHHHHhc
Confidence            9887776544

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=96.75  E-value=0.0042  Score=52.47  Aligned_cols=86  Identities=20%  Similarity=0.262  Sum_probs=64.4

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCcccHHHHHh
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQ   97 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~l~~la~   97 (199)
                      ....|.||+.|+.  +..++++|++||.++.+++++++  |.. .+.|+.|+.++...+++...   .+. +..+..++.
T Consensus       122 ~~a~naLLk~lEe--p~~~~~~Il~t~~~~~l~~ti~S--Rc~-~~~~~~~~~~~~~~~L~~~~---~~~-~~~~~~l~~  192 (334)
T 1a5t_A          122 DAAANALLKTLEE--PPAETWFFLATREPERLLATLRS--RCR-LHYLAPPPEQYAVTWLSREV---TMS-QDALLAALR  192 (334)
T ss_dssp             HHHHHHHHHHHTS--CCTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHHHC---CCC-HHHHHHHHH
T ss_pred             HHHHHHHHHHhcC--CCCCeEEEEEeCChHhCcHHHhh--cce-eeeCCCCCHHHHHHHHHHhc---CCC-HHHHHHHHH
Confidence            3457889999984  45578899999999999999999  874 79999999999999998876   222 344667787


Q ss_pred             hCCCCCHHHHHHHHHH
Q 039253           98 FTQGFSGADITEICQR  113 (199)
Q Consensus        98 ~t~G~sgaDI~~lv~~  113 (199)
                      .+.| +.+.+.++++.
T Consensus       193 ~s~G-~~r~a~~~l~~  207 (334)
T 1a5t_A          193 LSAG-SPGAALALFQG  207 (334)
T ss_dssp             HTTT-CHHHHHHTTSS
T ss_pred             HcCC-CHHHHHHHhcc
Confidence            7765 44444444443

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=96.73  E-value=0.0027  Score=52.90  Aligned_cols=79  Identities=18%  Similarity=0.225  Sum_probs=57.7

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcC-------CCCC-Cc
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRK-------SPVS-KD   89 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~-------~~~~-~~   89 (199)
                      ....+.|+..|+..  ..++.+|++||.+..+++++++  ||. .+.|+.|+.++|.+|++.++..       ..+. ++
T Consensus       120 ~~~~~~L~~~le~~--~~~~~iI~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~e~~~il~~~~~~l~~~~~~~~~~~~~  194 (324)
T 3u61_B          120 AESQRHLRSFMEAY--SSNCSIIITANNIDGIIKPLQS--RCR-VITFGQPTDEDKIEMMKQMIRRLTEICKHEGIAIAD  194 (324)
T ss_dssp             HHHHHHHHHHHHHH--GGGCEEEEEESSGGGSCTTHHH--HSE-EEECCCCCHHHHHHHHHHHHHHHHHHHHHHTCCBSC
T ss_pred             HHHHHHHHHHHHhC--CCCcEEEEEeCCccccCHHHHh--hCc-EEEeCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCCc
Confidence            44567788888754  2457889999999999999999  995 6999999999988776665432       1222 23


Q ss_pred             -ccHHHHHhhCCC
Q 039253           90 -VDLEKLAQFTQG  101 (199)
Q Consensus        90 -~~l~~la~~t~G  101 (199)
                       ..+..+++.+.|
T Consensus       195 ~~~~~~l~~~~~g  207 (324)
T 3u61_B          195 MKVVAALVKKNFP  207 (324)
T ss_dssp             HHHHHHHHHHTCS
T ss_pred             HHHHHHHHHhCCC
Confidence             446777877655

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=96.60  E-value=0.002  Score=61.33  Aligned_cols=106  Identities=19%  Similarity=0.209  Sum_probs=79.6

Q ss_pred             hhHHHHHHHHHHhCCC---------CCCCEEEEEeeCC--------------------------CCCCCccccCCCccce
Q 039253           17 ADRIPNQLLTEMDGLS---------AKKTIFVIGVTNR--------------------------PDIIDPALLRPGRLDQ   61 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~---------~~~~VvvI~aTN~--------------------------~~~lD~al~R~gRfd~   61 (199)
                      ...+.+.|++.|+.-.         .-.+++||+|||.                          ...+.|+|+.  ||+.
T Consensus       673 ~~~~~~~Ll~~l~~~~~~~~~g~~vd~~~~iiI~tsn~~~~~~~~~~~~~~~~~~l~~~v~~~~~~~f~~~l~~--Rl~~  750 (854)
T 1qvr_A          673 HPDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDE  750 (854)
T ss_dssp             CHHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHH--TCSB
T ss_pred             CHHHHHHHHHHhccCceECCCCCEeccCCeEEEEecCcChHHHhhhcccccchHHHHHHHHHHHHhhCCHHHHH--hcCe
Confidence            3468889999998431         0136889999997                          2356778887  9999


Q ss_pred             EEEecCCCHHHHHHHHHHhhcCC---------CCC-CcccHHHHHhhCC--CCCHHHHHHHHHHHHHHHHHHHHH
Q 039253           62 LIYIPLPVEKSRLQIFKACLRKS---------PVS-KDVDLEKLAQFTQ--GFSGADITEICQRACKDATREEIE  124 (199)
Q Consensus        62 ~i~~~~P~~~~R~~il~~~l~~~---------~~~-~~~~l~~la~~t~--G~sgaDI~~lv~~A~~~a~~~~~~  124 (199)
                      .+.|.+|+.++...|++.++...         .+. ++.-+..|++..-  .+..++|+++++++...++.+.+.
T Consensus       751 ~i~~~pl~~edi~~i~~~~l~~~~~~~~~~~~~~~~~~~a~~~L~~~~~~~~gn~R~L~~~i~~~~~~~~~~~i~  825 (854)
T 1qvr_A          751 IVVFRPLTKEQIRQIVEIQLSYLRARLAEKRISLELTEAAKDFLAERGYDPVFGARPLRRVIQRELETPLAQKIL  825 (854)
T ss_dssp             CCBCCCCCHHHHHHHHHHHHHHHHHHHHTTTCEEEECHHHHHHHHHHHCBTTTBTSTHHHHHHHHTHHHHHHHHH
T ss_pred             EEeCCCCCHHHHHHHHHHHHHHHHHHHHhCCceEEECHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999888631         111 2334666777654  678999999999998888777654

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=96.49  E-value=0.0038  Score=59.38  Aligned_cols=93  Identities=22%  Similarity=0.295  Sum_probs=63.8

Q ss_pred             HHHHHHHHHhCCCCCCCEEEEEeeCCCC----CCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCC----CCC-Ccc
Q 039253           20 IPNQLLTEMDGLSAKKTIFVIGVTNRPD----IIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKS----PVS-KDV   90 (199)
Q Consensus        20 ~~~~lL~~ld~~~~~~~VvvI~aTN~~~----~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~----~~~-~~~   90 (199)
                      +.+.|...++    ..++.+|++||.++    .+|+++.|  ||+. |.|+.|+.+++.+||+.++...    ... .+.
T Consensus       287 ~~~~L~~~l~----~~~i~~I~at~~~~~~~~~~d~aL~r--Rf~~-i~l~~p~~~e~~~iL~~~~~~~~~~~~~~i~~~  359 (854)
T 1qvr_A          287 AGNMLKPALA----RGELRLIGATTLDEYREIEKDPALER--RFQP-VYVDEPTVEETISILRGLKEKYEVHHGVRISDS  359 (854)
T ss_dssp             -----HHHHH----TTCCCEEEEECHHHHHHHTTCTTTCS--CCCC-EEECCCCHHHHHHHHHHHHHHHHHHTTCEECHH
T ss_pred             HHHHHHHHHh----CCCeEEEEecCchHHhhhccCHHHHh--CCce-EEeCCCCHHHHHHHHHhhhhhhhhhcCCCCCHH
Confidence            3344454554    35678999999875    58999999  9996 9999999999999999877533    221 233


Q ss_pred             cHHHHHhh-----CCCCCHHHHHHHHHHHHHHHH
Q 039253           91 DLEKLAQF-----TQGFSGADITEICQRACKDAT  119 (199)
Q Consensus        91 ~l~~la~~-----t~G~sgaDI~~lv~~A~~~a~  119 (199)
                      .+..++..     +.+|.+.....++.+|+..+.
T Consensus       360 al~~~~~ls~r~i~~~~lp~kai~lldea~a~~~  393 (854)
T 1qvr_A          360 AIIAAATLSHRYITERRLPDKAIDLIDEAAARLR  393 (854)
T ss_dssp             HHHHHHHHHHHHCCSSCTHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhcccccChHHHHHHHHHHHHHHH
Confidence            45555554     356778888888888765544

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=96.42  E-value=0.00023  Score=53.69  Aligned_cols=40  Identities=23%  Similarity=0.432  Sum_probs=35.6

Q ss_pred             CCEEEEEeeCCCC-----CCCccccCCCccceEEEecCCCHHHHHHHH
Q 039253           35 KTIFVIGVTNRPD-----IIDPALLRPGRLDQLIYIPLPVEKSRLQIF   77 (199)
Q Consensus        35 ~~VvvI~aTN~~~-----~lD~al~R~gRfd~~i~~~~P~~~~R~~il   77 (199)
                      .++.+|++||.++     .+|+++++  ||+ .++++.|+.++|.+||
T Consensus       150 ~~~~~i~~~~~~~~~~~~~~~~~l~~--r~~-~i~~~~p~~~~~~~il  194 (195)
T 1jbk_A          150 GELHCVGATTLDEYRQYIEKDAALER--RFQ-KVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             TSCCEEEEECHHHHHHHTTTCHHHHT--TEE-EEECCCCCHHHHHTTC
T ss_pred             CCeEEEEeCCHHHHHHHHhcCHHHHH--Hhc-eeecCCCCHHHHHHHh
Confidence            4678899999887     89999999  999 6999999999999876

>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=96.37  E-value=0.011  Score=50.40  Aligned_cols=98  Identities=14%  Similarity=0.134  Sum_probs=65.8

Q ss_pred             HHHHHHHHHHhCCCC-C--CCEEEEEeeCCCC---CCC---ccccCCCccceEEEecCCCHHHHHHHHHHhhcCC---CC
Q 039253           19 RIPNQLLTEMDGLSA-K--KTIFVIGVTNRPD---IID---PALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKS---PV   86 (199)
Q Consensus        19 r~~~~lL~~ld~~~~-~--~~VvvI~aTN~~~---~lD---~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~---~~   86 (199)
                      .+...|+..++.+.. .  .++.+|++||.++   .++   +.+.+  ||...+.+++++.++..++++..+...   ..
T Consensus       159 ~~l~~l~~~~~~~~~~~~~~~v~lI~~~~~~~~~~~l~~~~~~~~~--~~~~~i~l~~l~~~e~~~ll~~~~~~~~~~~~  236 (412)
T 1w5s_A          159 EDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVES--QIGFKLHLPAYKSRELYTILEQRAELGLRDTV  236 (412)
T ss_dssp             HHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHHBCTTS
T ss_pred             HHHHHHHHHHHhcccCCCCceEEEEEEeccccHHHHHhhhcchhhh--hcCCeeeeCCCCHHHHHHHHHHHHHhcCCCCC
Confidence            345555566654431 3  6788999998765   344   66667  676679999999999999998776421   11


Q ss_pred             CCcccHHHHHhhCC------CCCHHHHHHHHHHHHHHHH
Q 039253           87 SKDVDLEKLAQFTQ------GFSGADITEICQRACKDAT  119 (199)
Q Consensus        87 ~~~~~l~~la~~t~------G~sgaDI~~lv~~A~~~a~  119 (199)
                      .++..+..+++.+.      |. +..+..++..|...+.
T Consensus       237 ~~~~~~~~i~~~~~~~~~~~G~-p~~~~~l~~~a~~~a~  274 (412)
T 1w5s_A          237 WEPRHLELISDVYGEDKGGDGS-ARRAIVALKMACEMAE  274 (412)
T ss_dssp             CCHHHHHHHHHHHCGGGTSCCC-HHHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHhccCCCc-HHHHHHHHHHHHHHHH
Confidence            12345677888887      64 5677778877765553

>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=96.13  E-value=0.022  Score=51.05  Aligned_cols=84  Identities=17%  Similarity=0.120  Sum_probs=54.6

Q ss_pred             HHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcC--CCCCCcccHHHHHh
Q 039253           20 IPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRK--SPVSKDVDLEKLAQ   97 (199)
Q Consensus        20 ~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~--~~~~~~~~l~~la~   97 (199)
                      .++.|+..++.  ...++++|+++.....+++ + +  |+...+.|+.|+.+++.++|+..+..  ..+. +..+..|++
T Consensus       167 ~l~~L~~~l~~--~~~~iIli~~~~~~~~l~~-l-~--~r~~~i~f~~~~~~~~~~~L~~i~~~~~~~i~-~~~l~~la~  239 (516)
T 1sxj_A          167 GVGQLAQFCRK--TSTPLILICNERNLPKMRP-F-D--RVCLDIQFRRPDANSIKSRLMTIAIREKFKLD-PNVIDRLIQ  239 (516)
T ss_dssp             HHHHHHHHHHH--CSSCEEEEESCTTSSTTGG-G-T--TTSEEEECCCCCHHHHHHHHHHHHHHHTCCCC-TTHHHHHHH
T ss_pred             HHHHHHHHHHh--cCCCEEEEEcCCCCccchh-h-H--hceEEEEeCCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHH
Confidence            45677777764  3344555555544445544 4 3  56679999999999999999887754  3344 334888888


Q ss_pred             hCCCCCHHHHHHHHHHH
Q 039253           98 FTQGFSGADITEICQRA  114 (199)
Q Consensus        98 ~t~G~sgaDI~~lv~~A  114 (199)
                      .+.|    |+..+++..
T Consensus       240 ~s~G----diR~~i~~L  252 (516)
T 1sxj_A          240 TTRG----DIRQVINLL  252 (516)
T ss_dssp             HTTT----CHHHHHHHH
T ss_pred             HcCC----cHHHHHHHH
Confidence            7754    555555543

>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=96.10  E-value=0.015  Score=61.54  Aligned_cols=78  Identities=21%  Similarity=0.350  Sum_probs=57.0

Q ss_pred             CEEEEEeeCCCC-----CCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCC-CCCCccc--HHHHH-----------
Q 039253           36 TIFVIGVTNRPD-----IIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKS-PVSKDVD--LEKLA-----------   96 (199)
Q Consensus        36 ~VvvI~aTN~~~-----~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~-~~~~~~~--l~~la-----------   96 (199)
                      ++.+|+|||.|.     .||++|+|  || ..++++.|+.+++..|+..++... ...+++.  ...|+           
T Consensus      1384 ~i~lIaA~Npp~~gGR~~l~~rllR--rf-~vi~i~~P~~~~l~~I~~~il~~~l~~~~~v~~~~~~lv~ati~~y~~v~ 1460 (2695)
T 4akg_A         1384 RIHIVGACNPPTDPGRIPMSERFTR--HA-AILYLGYPSGKSLSQIYEIYYKAIFKLVPEFRSYTEPFARASVHLYNECK 1460 (2695)
T ss_dssp             SEEEEEEECCTTSTTCCCCCHHHHT--TE-EEEECCCCTTTHHHHHHHHHHHHHTTSSGGGGGGHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEecCCCccCCCccCChhhhh--ee-eEEEeCCCCHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHHHHHHHH
Confidence            589999999994     89999999  99 889999999999999999888543 2221111  11111           


Q ss_pred             h------h-CCCCCHHHHHHHHHHHHH
Q 039253           97 Q------F-TQGFSGADITEICQRACK  116 (199)
Q Consensus        97 ~------~-t~G~sgaDI~~lv~~A~~  116 (199)
                      +      + ---|+.+||..+++....
T Consensus      1461 ~~~~~~~k~HY~FnlRDLsrv~qGll~ 1487 (2695)
T 4akg_A         1461 ARYSTGLQSHYLFSPRELTRLVRGVYT 1487 (2695)
T ss_dssp             HHSCTTTCTTCCCCHHHHHHHHHHHHH
T ss_pred             HHcCCccCCCcccCHHHHHHHHHHHHh
Confidence            1      1 125899999998876543

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=95.89  E-value=0.014  Score=53.40  Aligned_cols=100  Identities=19%  Similarity=0.269  Sum_probs=64.7

Q ss_pred             CEEEEEeeCCC--CCCCccccCCCccc---eEEEecC--C-CHHHHHHHHHHhhcCC------CCCCcccHHHHHhhC--
Q 039253           36 TIFVIGVTNRP--DIIDPALLRPGRLD---QLIYIPL--P-VEKSRLQIFKACLRKS------PVSKDVDLEKLAQFT--   99 (199)
Q Consensus        36 ~VvvI~aTN~~--~~lD~al~R~gRfd---~~i~~~~--P-~~~~R~~il~~~l~~~------~~~~~~~l~~la~~t--   99 (199)
                      ++.||+|||+.  +.++++|++  ||+   ..+.|+.  | ..+....+++.+.+..      ..-.+..+..|.+..  
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  789999999  997   5665543  2 3455666665544321      111233355555433  


Q ss_pred             -CCC------CHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHh
Q 039253          100 -QGF------SGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKY  156 (199)
Q Consensus       100 -~G~------sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~  156 (199)
                       .|-      +.++|.++++.|...|..+..                   ..|+.+|+..|++.
T Consensus       330 ~~g~r~~l~~~~R~l~~llr~A~~~A~~~~~-------------------~~I~~edv~~A~~~  374 (604)
T 3k1j_A          330 RAGRKGHLTLRLRDLGGIVRAAGDIAVKKGK-------------------KYVEREDVIEAVKM  374 (604)
T ss_dssp             TTCSTTEEECCHHHHHHHHHHHHHHHHHTTC-------------------SSBCHHHHHHHHHH
T ss_pred             hhccccccccCHHHHHHHHHHHHHHHHhcCc-------------------ccccHHHHHHHHHh
Confidence             553      789999999998666543221                   45788888888754

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=95.86  E-value=0.011  Score=50.54  Aligned_cols=91  Identities=13%  Similarity=0.191  Sum_probs=58.4

Q ss_pred             CCccccCCCccceEEEecCCCHHHHHHHHHH----hhc---------CCCCC-CcccHHHHHhhCC--CCCHHHHHHHHH
Q 039253           49 IDPALLRPGRLDQLIYIPLPVEKSRLQIFKA----CLR---------KSPVS-KDVDLEKLAQFTQ--GFSGADITEICQ  112 (199)
Q Consensus        49 lD~al~R~gRfd~~i~~~~P~~~~R~~il~~----~l~---------~~~~~-~~~~l~~la~~t~--G~sgaDI~~lv~  112 (199)
                      +.|+|+.  ||+..+.|+.++.++...|+..    ++.         ...+. ++.-+..|++...  ....+.|.++++
T Consensus       256 ~~p~l~~--R~~~~i~~~~l~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~R~L~~~le  333 (376)
T 1um8_A          256 LIPELIG--RLPVLSTLDSISLEAMVDILQKPKNALIKQYQQLFKMDEVDLIFEEEAIKEIAQLALERKTGARGLRAIIE  333 (376)
T ss_dssp             CCHHHHT--TCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHTTCTGGGHHHHHH
T ss_pred             CChHHhc--CCCceeeccCCCHHHHHHHHhhhHHHHHHHHHHHHhhcCceEEECHHHHHHHHHHhcccccCcHHHHHHHH
Confidence            5677777  8989999999999999999973    211         11111 2333566666543  467899999999


Q ss_pred             HHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHH
Q 039253          113 RACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESM  154 (199)
Q Consensus       113 ~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al  154 (199)
                      .+...++.+.....             .....|+.+++..+.
T Consensus       334 ~~~~~~~~~~~~~~-------------~~~~~i~~~~v~~~~  362 (376)
T 1um8_A          334 DFCLDIMFDLPKLK-------------GSEVRITKDCVLKQA  362 (376)
T ss_dssp             HHHHHHHHTGGGGT-------------TSEEEECHHHHTTSS
T ss_pred             HHHHHHHhhccCCC-------------CCEEEEeHHHhcCCC
Confidence            88777766543110             111457888876543

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=95.65  E-value=0.064  Score=47.49  Aligned_cols=121  Identities=17%  Similarity=0.252  Sum_probs=78.7

Q ss_pred             HHHHHHHHHhCCC--------CCCCEEEEEee----CCCCCCCccccCCCccceEEEecCCCHHHHHHHHH---Hhh---
Q 039253           20 IPNQLLTEMDGLS--------AKKTIFVIGVT----NRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFK---ACL---   81 (199)
Q Consensus        20 ~~~~lL~~ld~~~--------~~~~VvvI~aT----N~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~---~~l---   81 (199)
                      +-..||..|++-.        ..++|++|+|.    ++|.++-|.|+.  ||+.+|+|+..+.++...|+.   .++   
T Consensus       278 vq~aLL~~le~~~~~~~~~~~d~~~ilfI~~gaf~~~~~~dlipel~~--R~~i~i~l~~lt~~e~~~Il~~~~~~l~~q  355 (444)
T 1g41_A          278 VQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG--RLPIRVELTALSAADFERILTEPHASLTEQ  355 (444)
T ss_dssp             HHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSCCGGGSCHHHHT--TCCEEEECCCCCHHHHHHHHHSSTTCHHHH
T ss_pred             HHHHHHHHhcccccccccceecCCcEEEEeccccccCChhhcchHHhc--ccceeeeCCCCCHHHHHHHHHHHHHhHHHH
Confidence            6678999999741        34678999887    356666688988  999999999999999999993   222   


Q ss_pred             -----cCCCCC---CcccHHHHHh-------hCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhcccccc
Q 039253           82 -----RKSPVS---KDVDLEKLAQ-------FTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIK  146 (199)
Q Consensus        82 -----~~~~~~---~~~~l~~la~-------~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it  146 (199)
                           ......   .+--+..|++       .|...-++-|+.++..++.....+....             ......|+
T Consensus       356 ~~~~~~~~~~~l~~~~~al~~i~~~a~~~~~~t~~~GaR~L~~~ie~~~~~~~~~~~~~-------------~~~~~~i~  422 (444)
T 1g41_A          356 YKALMATEGVNIAFTTDAVKKIAEAAFRVNEKTENIGARRLHTVMERLMDKISFSASDM-------------NGQTVNID  422 (444)
T ss_dssp             HHHHHHTTTCEEEECHHHHHHHHHHHHHHHHHSCCCGGGHHHHHHHHHHHHHHHHGGGC-------------TTCEEEEC
T ss_pred             HHHHhcccCceEEECHHHHHHHHHHHHHhccCCccCCchHHHHHHHHHHHHHHhhcccc-------------CCCeEEEe
Confidence                 111111   2233555555       3566777778877777766655443210             01124578


Q ss_pred             HHHHHHHHH
Q 039253          147 AEHFEESMK  155 (199)
Q Consensus       147 ~~df~~Al~  155 (199)
                      .+.+...+.
T Consensus       423 ~~~v~~~l~  431 (444)
T 1g41_A          423 AAYVADALG  431 (444)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHhcC
Confidence            777776554

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=95.39  E-value=0.053  Score=45.92  Aligned_cols=62  Identities=13%  Similarity=0.062  Sum_probs=47.7

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCC----CCccccCCCccc-eEEEecCCCHHHHHHHHHHhhcC
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDI----IDPALLRPGRLD-QLIYIPLPVEKSRLQIFKACLRK   83 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~----lD~al~R~gRfd-~~i~~~~P~~~~R~~il~~~l~~   83 (199)
                      ..++..|+.+..  ....+++||+.+|..+.    |++++++  ||. .+|.|++++.++-.+|++..+..
T Consensus       147 q~~L~~l~~~~~--~~~s~~~vI~i~n~~d~~~~~L~~~v~S--R~~~~~i~F~pYt~~el~~Il~~Rl~~  213 (318)
T 3te6_A          147 EKILQYFEKWIS--SKNSKLSIICVGGHNVTIREQINIMPSL--KAHFTEIKLNKVDKNELQQMIITRLKS  213 (318)
T ss_dssp             THHHHHHHHHHH--CSSCCEEEEEECCSSCCCHHHHHTCHHH--HTTEEEEECCCCCHHHHHHHHHHHHHH
T ss_pred             chHHHHHHhccc--ccCCcEEEEEEecCcccchhhcchhhhc--cCCceEEEeCCCCHHHHHHHHHHHHHh
Confidence            345666666554  24567999999999865    4556677  887 68999999999999999998865

>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=95.27  E-value=0.034  Score=46.65  Aligned_cols=77  Identities=13%  Similarity=0.101  Sum_probs=54.9

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHh
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQ   97 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~   97 (199)
                      ...+.|+..|+..  ...+.+|++||.+..+.+++++  |+. .+.|+.++.++...++...+....+. ++..+..++.
T Consensus       125 ~~~~~L~~~le~~--~~~~~~il~~n~~~~i~~~i~s--R~~-~~~~~~l~~~~~~~~l~~~~~~~~~~i~~~~~~~i~~  199 (340)
T 1sxj_C          125 AAQNALRRVIERY--TKNTRFCVLANYAHKLTPALLS--QCT-RFRFQPLPQEAIERRIANVLVHEKLKLSPNAEKALIE  199 (340)
T ss_dssp             HHHHHHHHHHHHT--TTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHHHHHTTTCCBCHHHHHHHHH
T ss_pred             HHHHHHHHHHhcC--CCCeEEEEEecCccccchhHHh--hce-eEeccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            3456777777753  3456778889999999999999  886 78899899999999998888543322 2333455555


Q ss_pred             hCC
Q 039253           98 FTQ  100 (199)
Q Consensus        98 ~t~  100 (199)
                      .+.
T Consensus       200 ~s~  202 (340)
T 1sxj_C          200 LSN  202 (340)
T ss_dssp             HHT
T ss_pred             HcC
Confidence            443

>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=94.66  E-value=0.035  Score=46.51  Aligned_cols=57  Identities=16%  Similarity=0.234  Sum_probs=48.9

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhh
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACL   81 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l   81 (199)
                      ....|.||..|+.  +...+++|++|+.++.|.+++++  |   .+.|+.|+.++-..+++..+
T Consensus        96 ~~a~naLLk~LEe--p~~~t~fIl~t~~~~kl~~tI~S--R---~~~f~~l~~~~i~~~L~~~~  152 (305)
T 2gno_A           96 QQAANAFLKALEE--PPEYAVIVLNTRRWHYLLPTIKS--R---VFRVVVNVPKEFRDLVKEKI  152 (305)
T ss_dssp             HHHHHHTHHHHHS--CCTTEEEEEEESCGGGSCHHHHT--T---SEEEECCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC--CCCCeEEEEEECChHhChHHHHc--e---eEeCCCCCHHHHHHHHHHHh
Confidence            3457889999984  45677888889999999999999  8   89999999999999998876

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=93.69  E-value=0.058  Score=44.93  Aligned_cols=97  Identities=15%  Similarity=0.169  Sum_probs=55.9

Q ss_pred             HHHHHHHHHHhCCC---------CCCCEEEEEeeCCC-------CCCCccccCCCccceEEEecCCCHHH----HHHHHH
Q 039253           19 RIPNQLLTEMDGLS---------AKKTIFVIGVTNRP-------DIIDPALLRPGRLDQLIYIPLPVEKS----RLQIFK   78 (199)
Q Consensus        19 r~~~~lL~~ld~~~---------~~~~VvvI~aTN~~-------~~lD~al~R~gRfd~~i~~~~P~~~~----R~~il~   78 (199)
                      .+...|+..|+.-.         ...++.||+|||.+       ..+++++..  ||. .+.+.+|...+    ...+++
T Consensus       111 ~~q~~Ll~~l~~~~~~~~g~~~~~~~~~riI~atn~~l~~~v~~g~fr~~L~~--Rl~-~~~i~lPpL~eR~edi~~l~~  187 (304)
T 1ojl_A          111 LMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYY--RLN-VVAIEMPSLRQRREDIPLLAD  187 (304)
T ss_dssp             HHHHHHHHHHHSSBCCBTTBCCCCBCCCEEEEEESSCHHHHHHHTSSCHHHHH--HHS-SEEEECCCSGGGGGGHHHHHH
T ss_pred             HHHHHHHHHHhcCEeeecCCcccccCCeEEEEecCccHHHHHHhCCcHHHHHh--hcC-eeEEeccCHHHhHhhHHHHHH
Confidence            45667888887542         12358899999985       235566666  765 55555565444    444666


Q ss_pred             HhhcCC----C---CC-CcccHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 039253           79 ACLRKS----P---VS-KDVDLEKLAQFTQGFSGADITEICQRACKDA  118 (199)
Q Consensus        79 ~~l~~~----~---~~-~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a  118 (199)
                      +++...    .   .. ++..+..|....-.-..++|.++++.|...+
T Consensus       188 ~~l~~~~~~~~~~~~~~s~~a~~~L~~~~wpGnvReL~~~l~~~~~~~  235 (304)
T 1ojl_A          188 HFLRRFAERNRKVVKGFTPQAMDLLIHYDWPGNIRELENAIERAVVLL  235 (304)
T ss_dssp             HHHHHHHHHTTCCCCCBCHHHHHHHHHCCCSSHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHhccCccCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhC
Confidence            665421    1   11 2223555665542224568888888876543

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=92.98  E-value=0.0083  Score=44.86  Aligned_cols=43  Identities=30%  Similarity=0.369  Sum_probs=33.0

Q ss_pred             HHHHHHHHHhCCCCCCCEEEEEeeCCCC-----CCCccccCCCccceEEEecCCC
Q 039253           20 IPNQLLTEMDGLSAKKTIFVIGVTNRPD-----IIDPALLRPGRLDQLIYIPLPV   69 (199)
Q Consensus        20 ~~~~lL~~ld~~~~~~~VvvI~aTN~~~-----~lD~al~R~gRfd~~i~~~~P~   69 (199)
                      +.+.|+..++    ..++++|++||.++     .+|+++++  ||+. ++++.|+
T Consensus       140 ~~~~l~~~~~----~~~~~ii~~~~~~~~~~~~~~~~~l~~--R~~~-i~i~~p~  187 (187)
T 2p65_A          140 AGNILKPMLA----RGELRCIGATTVSEYRQFIEKDKALER--RFQQ-ILVEQPS  187 (187)
T ss_dssp             THHHHHHHHH----TTCSCEEEEECHHHHHHHTTTCHHHHH--HEEE-EECCSCC
T ss_pred             HHHHHHHHHh----cCCeeEEEecCHHHHHHHHhccHHHHH--hcCc-ccCCCCC
Confidence            4445555554    35678999999875     79999999  9995 9999986

>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=91.81  E-value=0.31  Score=38.98  Aligned_cols=96  Identities=13%  Similarity=0.119  Sum_probs=54.0

Q ss_pred             HHHHHHHHHHhCCC---------CCCCEEEEEeeCCC-------CCCCccccCCCccceEEEecCCCH----HHHHHHHH
Q 039253           19 RIPNQLLTEMDGLS---------AKKTIFVIGVTNRP-------DIIDPALLRPGRLDQLIYIPLPVE----KSRLQIFK   78 (199)
Q Consensus        19 r~~~~lL~~ld~~~---------~~~~VvvI~aTN~~-------~~lD~al~R~gRfd~~i~~~~P~~----~~R~~il~   78 (199)
                      .+...|+..|+.-.         ...++.+|+|||.+       ..+++++..  ||.. +.+.+|..    ++...+++
T Consensus       115 ~~q~~Ll~~l~~~~~~~~g~~~~~~~~~~iI~atn~~~~~~~~~~~~~~~L~~--Rl~~-~~i~lp~L~~R~~di~~l~~  191 (265)
T 2bjv_A          115 MVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVNEGTFRADLLD--ALAF-DVVQLPPLRERESDIMLMAE  191 (265)
T ss_dssp             HHHHHHHHHHHHCEECCCCC--CEECCCEEEEEESSCHHHHHHHTSSCHHHHH--HHCS-EEEECCCGGGCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCeecCCCcccccCCeEEEEecCcCHHHHHHcCCccHHHHH--hhcC-cEEeCCChhhhhHHHHHHHH
Confidence            45567777777421         12357899999984       257888988  9864 34445544    34445555


Q ss_pred             HhhcC----CCCC-----CcccHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 039253           79 ACLRK----SPVS-----KDVDLEKLAQFTQGFSGADITEICQRACKD  117 (199)
Q Consensus        79 ~~l~~----~~~~-----~~~~l~~la~~t~G~sgaDI~~lv~~A~~~  117 (199)
                      +++..    ....     ++..+..|....-.-..++|.++++.+...
T Consensus       192 ~~l~~~~~~~~~~~~~~~~~~a~~~L~~~~~~gn~reL~~~l~~~~~~  239 (265)
T 2bjv_A          192 YFAIQMCREIKLPLFPGFTERARETLLNYRWPGNIRELKNVVERSVYR  239 (265)
T ss_dssp             HHHHHHHHHTTCSSCCCBCHHHHHHHHHSCCTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCcccCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHh
Confidence            55432    2211     122234444433223456888888877544

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*

Probab=91.15  E-value=0.63  Score=38.74  Aligned_cols=91  Identities=19%  Similarity=0.134  Sum_probs=59.5

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCC------CCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-Ccc
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRP------DIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDV   90 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~------~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~   90 (199)
                      ....+.|+..++..  ...+++|.+|+.+      ..+-+++.+  |. ..+.|..|+..+....++..+....+. +..
T Consensus        91 ~~~~~aLl~~le~p--~~~~~~il~~~~~~~~~~~~k~~~~i~s--r~-~~~~~~~l~~~~l~~~l~~~~~~~g~~i~~~  165 (343)
T 1jr3_D           91 AAINEQLLTLTGLL--HDDLLLIVRGNKLSKAQENAAWFTALAN--RS-VQVTCQTPEQAQLPRWVAARAKQLNLELDDA  165 (343)
T ss_dssp             TTHHHHHHHHHTTC--BTTEEEEEEESCCCTTTTTSHHHHHHTT--TC-EEEEECCCCTTHHHHHHHHHHHHTTCEECHH
T ss_pred             hHHHHHHHHHHhcC--CCCeEEEEEcCCCChhhHhhHHHHHHHh--Cc-eEEEeeCCCHHHHHHHHHHHHHHcCCCCCHH
Confidence            34667888888853  3345555555553      346677776  54 578999999999998998888766544 334


Q ss_pred             cHHHHHhhCCCCCHHHHHHHHHHH
Q 039253           91 DLEKLAQFTQGFSGADITEICQRA  114 (199)
Q Consensus        91 ~l~~la~~t~G~sgaDI~~lv~~A  114 (199)
                      .+..|++.+.| +.+++.+.++..
T Consensus       166 a~~~l~~~~~g-dl~~~~~elekl  188 (343)
T 1jr3_D          166 ANQVLCYCYEG-NLLALAQALERL  188 (343)
T ss_dssp             HHHHHHHSSTT-CHHHHHHHHHHH
T ss_pred             HHHHHHHHhch-HHHHHHHHHHHH
Confidence            46677776654 455555555544

>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=85.82  E-value=3.5  Score=36.95  Aligned_cols=126  Identities=13%  Similarity=0.112  Sum_probs=71.8

Q ss_pred             hhHHHHHHHHHHhCC----C---CCCCEEEEEeeCCCC-----------CCCccccCCCccceEEE-ecCCCHHHHH---
Q 039253           17 ADRIPNQLLTEMDGL----S---AKKTIFVIGVTNRPD-----------IIDPALLRPGRLDQLIY-IPLPVEKSRL---   74 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~----~---~~~~VvvI~aTN~~~-----------~lD~al~R~gRfd~~i~-~~~P~~~~R~---   74 (199)
                      ..++...|+..|+.=    .   -..++.||+|+|..+           .|+++++.  |||-.+. +..|+.+.-.   
T Consensus       313 ~~~~qsaLlEaMEe~~VtI~G~~lparf~VIAA~NP~~~yd~~~s~~~~~Lp~alLD--RFDLi~i~~d~pd~e~d~e~~  390 (506)
T 3f8t_A          313 PEPHRWALMEAMDKGTVTVDGIALNARCAVLAAINPGEQWPSDPPIARIDLDQDFLS--HFDLIAFLGVDPRPGEPEEQD  390 (506)
T ss_dssp             CHHHHHHHHHHHHHSEEEETTEEEECCCEEEEEECCCC--CCSCGGGGCCSCHHHHT--TCSEEEETTC-----------
T ss_pred             CHHHHHHHHHHHhCCcEEECCEEcCCCeEEEEEeCcccccCCCCCccccCCChHHhh--heeeEEEecCCCChhHhhccc
Confidence            345667788777731    1   124578999999865           88999999  9987554 4566654311   


Q ss_pred             ------HHHHHhh---c--CC-CCCCcccHHHHH-----------h------hCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 039253           75 ------QIFKACL---R--KS-PVSKDVDLEKLA-----------Q------FTQGFSGADITEICQRACKDATREEIEN  125 (199)
Q Consensus        75 ------~il~~~l---~--~~-~~~~~~~l~~la-----------~------~t~G~sgaDI~~lv~~A~~~a~~~~~~~  125 (199)
                            +.++.|.   +  .. +.-++...+.|.           .      ..-|.|++.+..+++-|.-.|..+..  
T Consensus       391 ~~~ls~e~L~~yi~~ar~~~~~p~ls~ea~~yI~~~y~~tR~~~~~~~~~~~~~~giSpR~leaLiRlA~A~A~L~gR--  468 (506)
T 3f8t_A          391 TEVPSYTLLRRYLLYAIREHPAPELTEEARKRLEHWYETRREEVEERLGMGLPTLPVTRRQLESVERLAKAHARMRLS--  468 (506)
T ss_dssp             ---CCHHHHHHHHHHHHHHCSCCEECHHHHHHHHHHHHHHHHHHHHHHHTTCCCCCCCHHHHHHHHHHHHHHHHHTTC--
T ss_pred             CCCCCHHHHHHHHHHHHhcCCCceeCHHHHHHHHHHHHHHhcCcccccccccccccccHHHHHHHHHHHHHHHHHcCc--
Confidence                  2222222   2  11 111111111111           0      24478888888888877666655442  


Q ss_pred             hHHhhcCCCCcchhhccccccHHHHHHHHHhccccccc
Q 039253          126 DIRRRKGKQPEAIEDEVAEIKAEHFEESMKYACKSQSR  163 (199)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~Ps~~r  163 (199)
                                       ..++.+|+..|+.-+.-|...
T Consensus       469 -----------------~~V~~eDV~~Ai~L~~~Sl~~  489 (506)
T 3f8t_A          469 -----------------DDVEPEDVDIAAELVDWYLET  489 (506)
T ss_dssp             -----------------SEECHHHHHHHHHHHHHHHHH
T ss_pred             -----------------CCCCHHHHHHHHHHHHHHHHH
Confidence                             568999999999888766443

---

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	199
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	3e-43
d1lv7a_	256	c.37.1.20 (A:) AAA domain of cell division protein	3e-42
d1r7ra3	265	c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p	5e-39
d1e32a2	258	c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p	6e-21
d1w44a_	321	c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [Ta	1e-16
d1gvnb_	273	c.37.1.21 (B:) Plasmid maintenance system epsilon/	6e-13
d1d2na_	246	c.37.1.20 (A:) Hexamerization domain of N-ethylmal	1e-10
d1svma_	362	c.37.1.20 (A:) Papillomavirus large T antigen heli	1e-10

>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 =  143 bits (361), Expect = 3e-43
 Identities = 57/124 (45%), Positives = 72/124 (58%), Gaps = 3/124 (2%)

Query: 4   SIVIQRGSGAGG---AADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
           ++  +RGSG GG     ++  NQLL EMDG      I V+  TNRPDI+DPALLRPGR D
Sbjct: 112 AVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFD 171

Query: 61  QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           + I I  P  K R QI +   R  P+++DVDL  LA+ T GF GAD+  +   A   A R
Sbjct: 172 RQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAR 231

Query: 121 EEIE 124
           E   
Sbjct: 232 EGRR 235

>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 =  140 bits (355), Expect = 3e-42
 Identities = 54/155 (34%), Positives = 79/155 (50%), Gaps = 22/155 (14%)

Query: 4   SIVIQRGSGAGG---AADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLD 60
           ++  QRG+G GG     ++  NQ+L EMDG    + I VI  TNRPD++DPALLRPGR D
Sbjct: 115 AVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFD 174

Query: 61  QLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
           + + + LP  + R QI K  +R+ P++ D+D   +A+ T GFSGAD+  +   A   A R
Sbjct: 175 RQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAAR 234

Query: 121 EEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMK 155
                                   +    FE++  
Sbjct: 235 GNKR-------------------VVSMVEFEKAKD 250

>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 =  132 bits (333), Expect = 5e-39
 Identities = 98/148 (66%), Positives = 114/148 (77%), Gaps = 6/148 (4%)

Query: 8   QRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPL 67
                 GGAADR+ NQ+LTEMDG+S KK +F+IG TNRPDIIDPA+LRPGRLDQLIYIPL
Sbjct: 118 GNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPL 177

Query: 68  PVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDI 127
           P EKSR+ I KA LRKSPV+KDVDLE LA+ T GFSGAD+TEICQRACK A RE IE++I
Sbjct: 178 PDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEI 237

Query: 128 RR--RKGKQPEAIE----DEVAEIKAEH 149
           RR   +   P A+E    D V EI+ +H
Sbjct: 238 RRERERQTNPSAMEVEEDDPVPEIRRDH 265

>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 = 85.1 bits (209), Expect = 6e-21
 Identities = 52/154 (33%), Positives = 80/154 (51%), Gaps = 8/154 (5%)

Query: 5   IVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIY 64
           I  +R    G    RI +QLLT MDGL  +  + V+  TNRP+ IDPAL R GR D+ + 
Sbjct: 109 IAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVD 168

Query: 65  IPLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIE 124
           I +P    RL+I +   +   ++ DVDLE++A  T G  GAD+  +C  A   A R++++
Sbjct: 169 IGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMD 228

Query: 125 NDIRRRKGKQPEAIEDEVAE---IKAEHFEESMK 155
                    + E I+ EV     +  + F  ++ 
Sbjct: 229 -----LIDLEDETIDAEVMNSLAVTMDDFRWALS 257

>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 = 74.3 bits (182), Expect = 1e-16
 Identities = 18/121 (14%), Positives = 35/121 (28%), Gaps = 3/121 (2%)

Query: 9   RGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNR---PDIIDPALLRPGRLDQLIYI 65
            G+   G   R    LL+++  ++A +   VI   N     D I   +    R +    +
Sbjct: 199 GGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLV 258

Query: 66  PLPVEKSRLQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIEN 125
                    Q+                    + +            ++A   A +  I+N
Sbjct: 259 ISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEHSVLTIHTSKQSGGKQASGKAIQTVIKN 318

Query: 126 D 126
           D
Sbjct: 319 D 319

>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 = 63.4 bits (153), Expect = 6e-13
 Identities = 17/132 (12%), Positives = 38/132 (28%), Gaps = 9/132 (6%)

Query: 22  NQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACL 81
               T+M  ++  K    +G   R + +        R        + V+     +     
Sbjct: 134 KGYETKMYVMAVPKINSYLGTIERYETMYADDPMTARATPKQAHDIVVKNLPTNLETLHK 193

Query: 82  RKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDA------TREEIENDIRRRKGKQP 135
                   +   +     + +S  +   I  +   +       + +EI+  + R + K  
Sbjct: 194 TGLFSDIRLYNREG---VKLYSSLETPSISPKETLEKELNRKVSGKEIQPTLERIEQKMV 250

Query: 136 EAIEDEVAEIKA 147
                E  E KA
Sbjct: 251 LNKHQETPEFKA 262

>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 = 56.9 bits (136), Expect = 1e-10
 Identities = 17/87 (19%), Positives = 35/87 (40%), Gaps = 5/87 (5%)

Query: 19  RIPNQLLTEMDGLSAK-KTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIF 77
            +   LL  +     + + + +IG T+R D++    +        I++P     +  Q+ 
Sbjct: 125 LVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEML-NAFSTTIHVPN--IATGEQLL 181

Query: 78  KACLRKSPVSKDVDLEKLAQFTQGFSG 104
           +A L      KD +   +AQ  +G   
Sbjct: 182 EA-LELLGNFKDKERTTIAQQVKGKKV 207

>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 = 57.0 bits (137), Expect = 1e-10
 Identities = 15/109 (13%), Positives = 27/109 (24%), Gaps = 12/109 (11%)

Query: 22  NQLLTEMDGLSA----KKTIFVIGVTNRPDII-----DPALLRPGRLDQLIYIPLPVEKS 72
           + L   +DG       KK +        P I+             R  + I         
Sbjct: 230 DNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEYSVPKTLQARFVKQIDFRPKDYLK 289

Query: 73  R-LQIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATR 120
             L+  +  L K  +     +  L         A+  +  Q    +   
Sbjct: 290 HCLERSEFLLEKRII--QSGIALLLMLIWYRPVAEFAQSIQSRIVEWKE 336

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	199
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.95
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	99.95
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	99.94
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.91
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.1
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	98.7
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	98.51
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	98.06
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.01
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	97.98
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	97.79
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	97.73
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	97.7
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	97.61
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	97.46
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	97.44
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	97.4
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	97.24
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	96.87
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	96.34
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	95.38
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	94.95
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	92.27
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	89.66
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	88.15
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	84.16

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.95  E-value=4.2e-28  Score=200.39  Aligned_cols=152  Identities=32%  Similarity=0.480  Sum_probs=130.0

Q ss_pred             cceeeccCCCCCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhc
Q 039253            3 WSIVIQRGSGAGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLR   82 (199)
Q Consensus         3 ~sl~~~R~~~~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~   82 (199)
                      ++++++|+++.++...++++.++..+++.....+|+||+|||+|+.||+|++||||||++|+|++|+.++|.+||+.+++
T Consensus       107 d~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~vlvi~tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~  186 (258)
T d1e32a2         107 DAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTK  186 (258)
T ss_dssp             GGTCCHHHHCCCTTHHHHHHHHHHHHHTCCCSSCEEEEEEESCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTT
T ss_pred             hhhccCCCCCCCchHHHHHHHhccccccccccCCccEEEeCCCccccchhhhhcccccceeECCCCCHHHHHHHhhhhcc
Confidence            35778888888888889999999999999998999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHh
Q 039253           83 KSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKY  156 (199)
Q Consensus        83 ~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~  156 (199)
                      +.++..++++..||++|+||||+||+++|++|++.|+++.......  ..+..........++|++||..||++
T Consensus       187 ~~~~~~~~~~~~la~~t~G~s~adl~~lv~~A~~~a~~~~~~~~~~--~~~~~~~~~~~~~~it~~Df~~AL~~  258 (258)
T d1e32a2         187 NMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDL--EDETIDAEVMNSLAVTMDDFRWALSQ  258 (258)
T ss_dssp             TSCBCTTCCHHHHHHHCTTCCHHHHHHHHHHHHHHHHHHHHHHHCC--CSSCCBHHHHHHCCBCHHHHHHHHTC
T ss_pred             CcccccccchhhhhhcccCCCHHHHHHHHHHHHHHHHHhhccccch--hhhhhhhhhhccCccCHHHHHHHhCc
Confidence            9988888999999999999999999999999999999887533110  01111112233467999999999863

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=99.95  E-value=5.7e-28  Score=199.84  Aligned_cols=136  Identities=38%  Similarity=0.623  Sum_probs=122.8

Q ss_pred             ceeeccCCCC---CchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHh
Q 039253            4 SIVIQRGSGA---GGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKAC   80 (199)
Q Consensus         4 sl~~~R~~~~---~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~   80 (199)
                      +++++|++..   +....+++++||++||++....+|+||+|||+|+.||++++||||||++|+|++|+.++|.+||+.+
T Consensus       115 ~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~v~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~  194 (256)
T d1lv7a_         115 AVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVH  194 (256)
T ss_dssp             HHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHH
T ss_pred             hhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCcccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHh
Confidence            5677776553   3456789999999999998889999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhcc
Q 039253           81 LRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYAC  158 (199)
Q Consensus        81 l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~~  158 (199)
                      +++.++..++++..|++.|+||||+||+++|++|++.|+++..                   ..++++||..|++++-
T Consensus       195 l~~~~~~~~~~~~~la~~t~G~s~adi~~l~~~A~~~a~~~~~-------------------~~i~~~d~~~Al~rv~  253 (256)
T d1lv7a_         195 MRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARGNK-------------------RVVSMVEFEKAKDKIM  253 (256)
T ss_dssp             HTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTC-------------------SSBCHHHHHHHHHHHT
T ss_pred             ccCCCcCcccCHHHHHHhCCCCCHHHHHHHHHHHHHHHHHcCC-------------------CccCHHHHHHHHHHHh
Confidence            9999988899999999999999999999999999988876542                   5689999999998863

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=99.94  E-value=3e-27  Score=194.50  Aligned_cols=132  Identities=44%  Similarity=0.662  Sum_probs=115.9

Q ss_pred             ceeeccCCC---CCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHh
Q 039253            4 SIVIQRGSG---AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKAC   80 (199)
Q Consensus         4 sl~~~R~~~---~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~   80 (199)
                      +|+++|+..   .+....+++++||++||++..+.+|+||+|||+|+.||++++|+|||+++|+|++|+.++|.+||+.+
T Consensus       112 ~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~  191 (247)
T d1ixza_         112 AVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIH  191 (247)
T ss_dssp             HHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHH
T ss_pred             hhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCccccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHH
Confidence            567777654   33456789999999999998889999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHH
Q 039253           81 LRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESM  154 (199)
Q Consensus        81 l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al  154 (199)
                      +.+.++..++++..||+.|+||||+||.++|++|++.|+++..                   ..|+++||.+|+
T Consensus       192 l~~~~~~~~~~~~~la~~t~g~s~~di~~lv~~A~l~a~~~~~-------------------~~i~~~d~~~A~  246 (247)
T d1ixza_         192 ARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREGR-------------------RKITMKDLEEAA  246 (247)
T ss_dssp             HTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTC-------------------SSBCHHHHHHHT
T ss_pred             hcccCCccccCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHcCC-------------------CCcCHHHHHHhh
Confidence            9998888899999999999999999999999999998877542                   569999999986

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.91  E-value=1.7e-25  Score=185.39  Aligned_cols=150  Identities=63%  Similarity=0.983  Sum_probs=104.5

Q ss_pred             ceeeccCCCC---CchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHh
Q 039253            4 SIVIQRGSGA---GGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKAC   80 (199)
Q Consensus         4 sl~~~R~~~~---~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~   80 (199)
                      +++.+|+...   ....+++++.|+++|+++..+.+|+||+|||+|+.||++++|+|||+++|+|++|+.++|++||+.+
T Consensus       111 ~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gRf~~~i~~~~p~~~~R~~il~~~  190 (265)
T d1r7ra3         111 SIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKAN  190 (265)
T ss_dssp             GTCCHHHHCCCTTHHHHHHHHHHHHHTCC------CCEEEECCBSCTTTSCGGGSSTTSEEEEECCCCCCHHHHHHHHHH
T ss_pred             hccccCCCcCCCCcHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCCchhCCHHHhCCCCccEEEEecchHHHHHHHHHHHH
Confidence            4566665432   2345679999999999998888999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHh
Q 039253           81 LRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKY  156 (199)
Q Consensus        81 l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~  156 (199)
                      +++.....++++..||++|+||||+||..+|++|.+.|+++..........   .....+...+++.+|+..+|++
T Consensus       191 l~~~~~~~~~~l~~la~~t~g~s~~di~~lv~~A~~~A~~~~~~~~~~~~~---~~~~~~~~~~~~~~d~v~~i~~  263 (265)
T d1r7ra3         191 LRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRER---ERQTNPSAMEVEEDDPVPEIRR  263 (265)
T ss_dssp             TTCC----CCCCHHHHHHHCSSCCHHHHHHHHHHHHHHHHHC---------------------------CHHHHHH
T ss_pred             hccCCchhhhhHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HhccCccccccccccchHHHcc
Confidence            999888888999999999999999999999999999999887654322111   1111222345677888888764

>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=99.10  E-value=1.2e-13  Score=116.47  Aligned_cols=82  Identities=16%  Similarity=0.185  Sum_probs=62.8

Q ss_pred             cceeeccCCC-CCchhhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCC----CCccccCCCccceEEEecCCCHHHHHHHH
Q 039253            3 WSIVIQRGSG-AGGAADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDI----IDPALLRPGRLDQLIYIPLPVEKSRLQIF   77 (199)
Q Consensus         3 ~sl~~~R~~~-~~~~~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~----lD~al~R~gRfd~~i~~~~P~~~~R~~il   77 (199)
                      .+++++|+++ .++..+|++|+||++||++....+|+||+||| |+.    ||+++.|+|||+++++++.|+.+.|.+||
T Consensus       192 d~~~~~r~~~~~~~~~~r~v~~lL~e~dg~~~~~~v~viaatN-~~~~~~~i~~~~~r~~Rf~~~v~v~~pd~~~r~~il  270 (321)
T d1w44a_         192 KNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLN-PTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVL  270 (321)
T ss_dssp             TTTC-----------CCHHHHHHHHHHHHHHHHHTCEEEEECC-CCCCCHHHHHHHHHHHHHSCSEEEEECSSTTEEEEE
T ss_pred             hhhccccccCCCCCcchhhhhhhhhhccccccCCCeEEEEeCC-CcccccchhhhhhccCcccceeecCCCChHHHHHHH
Confidence            3677888655 44556799999999999998888999999999 444    55566899999999999999999999999


Q ss_pred             HHhhcCCC
Q 039253           78 KACLRKSP   85 (199)
Q Consensus        78 ~~~l~~~~   85 (199)
                      +.+...+.
T Consensus       271 ~~~~~~~~  278 (321)
T d1w44a_         271 TRTGEGLQ  278 (321)
T ss_dssp             EECBTTCC
T ss_pred             HHhccCcc
Confidence            98887664

>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=98.70  E-value=3.4e-09  Score=85.33  Aligned_cols=94  Identities=18%  Similarity=0.243  Sum_probs=65.5

Q ss_pred             eeeccCCCCCchhhHHHHHHHHHHhCCCCC-CCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcC
Q 039253            5 IVIQRGSGAGGAADRIPNQLLTEMDGLSAK-KTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRK   83 (199)
Q Consensus         5 l~~~R~~~~~~~~~r~~~~lL~~ld~~~~~-~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~   83 (199)
                      +++.+..+ +...++++++|+++|++.... .+|+||+|||+|+.+|++.++ +||+.+|++  |+..+|.+|++.+...
T Consensus       112 l~~~~~~~-~~~~~~~~~~ll~~l~~~~~~~~~v~vi~tTn~~~~ld~~~~~-~rF~~~i~~--P~~~~r~~il~~l~~~  187 (246)
T d1d2na_         112 LLDYVPIG-PRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEML-NAFSTTIHV--PNIATGEQLLEALELL  187 (246)
T ss_dssp             HTTCBTTT-TBCCHHHHHHHHHHTTCCCSTTCEEEEEEEESCHHHHHHTTCT-TTSSEEEEC--CCEEEHHHHHHHHHHH
T ss_pred             Hhhhcccc-cchhHHHHHHHHHHhcCCCccccceeeeeccCChhhccchhhc-CccceEEec--CCchhHHHHHHHHHhc
Confidence            34444443 233568899999999988644 569999999999999986443 599999987  4444555666544332


Q ss_pred             CCCCCcccHHHHHhhCCCCC
Q 039253           84 SPVSKDVDLEKLAQFTQGFS  103 (199)
Q Consensus        84 ~~~~~~~~l~~la~~t~G~s  103 (199)
                      ..+ .+.++..+++.+.|.+
T Consensus       188 ~~~-~~~~~~~i~~~~~g~~  206 (246)
T d1d2na_         188 GNF-KDKERTTIAQQVKGKK  206 (246)
T ss_dssp             TCS-CHHHHHHHHHHHTTSE
T ss_pred             cCC-ChHHHHHHHHHcCCCc
Confidence            232 3567788888888854

>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=98.51  E-value=2.4e-07  Score=72.64  Aligned_cols=101  Identities=17%  Similarity=0.225  Sum_probs=81.2

Q ss_pred             CCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhhCCCCCHHHHHHHHHH
Q 039253           35 KTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSGADITEICQR  113 (199)
Q Consensus        35 ~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~~  113 (199)
                      .++++|++||++..+++++++  ||...+.++.|+.+++..+++......... .+..+..+++.+.| +++.+.++++.
T Consensus       133 ~~~~~I~at~~~~~~~~~~~~--r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~i~~~s~g-d~R~ai~~l~~  209 (238)
T d1in4a2         133 QPFTLVGATTRSGLLSSPLRS--RFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRG-TPRIAIRLTKR  209 (238)
T ss_dssp             CCCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTT-CHHHHHHHHHH
T ss_pred             CCeEEEEecCCCcccccccee--eeeEEEEecCCCHHHHHHHHHHhhhhccchhhHHHHHHHHHhCCC-CHHHHHHHHHH
Confidence            478999999999999999999  999999999999999999999999776655 34458888888876 67877777777


Q ss_pred             HHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhc
Q 039253          114 ACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYA  157 (199)
Q Consensus       114 A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~  157 (199)
                      +...+.....                   ..+|.+...+|++.+
T Consensus       210 ~~~~~~~~~~-------------------~~it~~~~~~al~~l  234 (238)
T d1in4a2         210 VRDMLTVVKA-------------------DRINTDIVLKTMEVL  234 (238)
T ss_dssp             HHHHHHHHTC-------------------SSBCHHHHHHHHHHH
T ss_pred             HHHHHHHhcC-------------------CccCHHHHHHHHHhh
Confidence            6554433221                   458899998888754

>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=98.06  E-value=5.9e-07  Score=75.92  Aligned_cols=79  Identities=11%  Similarity=-0.075  Sum_probs=64.0

Q ss_pred             EEEeeCCCCCCCccccCCCccceEEEecCCCHHHHH-HHHHHhhcCCCCCCcccHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 039253           39 VIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRL-QIFKACLRKSPVSKDVDLEKLAQFTQGFSGADITEICQRACKD  117 (199)
Q Consensus        39 vI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~-~il~~~l~~~~~~~~~~l~~la~~t~G~sgaDI~~lv~~A~~~  117 (199)
                      +|+|||.   ++.++.|||||+..+++..|+...|. +++..++++..+.  .+...|+..+.|++|+||.++++.+...
T Consensus       259 ~i~ttN~---~~~~~~r~~Rf~~~i~~~~~~~~~~~~~~l~~i~~~~~l~--~~~~~L~~li~~~s~~D~~~~i~~~~~~  333 (362)
T d1svma_         259 GIVTMNE---YSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRIIQ--SGIALLLMLIWYRPVAEFAQSIQSRIVE  333 (362)
T ss_dssp             EEEEECS---CCCCHHHHTTEEEEEECCCCHHHHHHHHTCTHHHHTTCTT--CHHHHHHHHHHHSCGGGSCGGGHHHHHH
T ss_pred             ceeeccc---ccccccccccCceEEeecCCCcHHHHHHHHHHHhcccCCC--CCHHHHHHHccCCCHHHHHHHHHHHHHH
Confidence            7889994   67888899999999999999877664 5556666666654  4567788999999999999999999887


Q ss_pred             HHHHH
Q 039253          118 ATREE  122 (199)
Q Consensus       118 a~~~~  122 (199)
                      +.++.
T Consensus       334 ~~~~l  338 (362)
T d1svma_         334 WKERL  338 (362)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76654

>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=98.01  E-value=8.1e-06  Score=64.08  Aligned_cols=113  Identities=11%  Similarity=0.074  Sum_probs=78.7

Q ss_pred             HHHHHHhCCCCCCCEEEEEeeCCCCCC------CccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC---CcccHH
Q 039253           23 QLLTEMDGLSAKKTIFVIGVTNRPDII------DPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS---KDVDLE   93 (199)
Q Consensus        23 ~lL~~ld~~~~~~~VvvI~aTN~~~~l------D~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~---~~~~l~   93 (199)
                      .+.+.+........+.+|+.+|.++..      ++.+.+  ||..+++|+.++.++..+|++..++.....   .+..+.
T Consensus       160 ~l~~~l~~~~~~~~~~~i~i~~~~~~~~~~~~~~~~~~~--r~~~~i~f~~y~~~el~~Il~~r~~~~~~~~~~~~~al~  237 (287)
T d1w5sa2         160 RVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVES--QIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLE  237 (287)
T ss_dssp             THHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHH
T ss_pred             HHHHhcchhhcccceeEEeecccHHHHHHHHhhccchhc--ccceeeeccCCcHHHHHHHHhhhHHHhhccCCCCHHHHH
Confidence            344444455555677777777766543      467777  999999999999999999999887532111   233477


Q ss_pred             HHHhhCCCC-----CHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHh
Q 039253           94 KLAQFTQGF-----SGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKY  156 (199)
Q Consensus        94 ~la~~t~G~-----sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~  156 (199)
                      .+|+.+..+     .++....+|+.|+..|..+..                   ..||.+|+.+|+.+
T Consensus       238 ~ia~~~~~~~~~~gd~R~ai~~l~~a~~~A~~~~~-------------------~~It~~~V~~A~~e  286 (287)
T d1w5sa2         238 LISDVYGEDKGGDGSARRAIVALKMACEMAEAMGR-------------------DSLSEDLVRKAVSE  286 (287)
T ss_dssp             HHHHHHCGGGTSCCCHHHHHHHHHHHHHHHHHTTC-------------------SSCCHHHHHHHHHH
T ss_pred             HHHHHHhccccCCCCHHHHHHHHHHHHHHHHHcCC-------------------CCCCHHHHHHHHhc
Confidence            788776432     456666778888766654432                   57999999999875

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=97.98  E-value=1.7e-05  Score=61.85  Aligned_cols=102  Identities=18%  Similarity=0.128  Sum_probs=76.5

Q ss_pred             CCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHhhCCCCCHHHHHHHHH
Q 039253           34 KKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQFTQGFSGADITEICQ  112 (199)
Q Consensus        34 ~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~~t~G~sgaDI~~lv~  112 (199)
                      ..++++|++||++...+++.++  |+...+.+..|+.+++..+++..+....+. ....+..++..+.| ..+...++++
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            3468899999999999999999  999999999999999999999988776554 34467889999988 4555555555


Q ss_pred             HHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhc
Q 039253          113 RACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYA  157 (199)
Q Consensus       113 ~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~  157 (199)
                      .+...+..                   .....||.++..+++..+
T Consensus       210 ~~~~~a~~-------------------~~~~~It~~~~~~~l~~l  235 (239)
T d1ixsb2         210 RVRDFAQV-------------------AGEEVITRERALEALAAL  235 (239)
T ss_dssp             HHHHHHTT-------------------SCCSCBCHHHHHHHHHHH
T ss_pred             HHHHHHHH-------------------hCCCCcCHHHHHHHHhhh
Confidence            44222110                   011558999999988654

>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=97.79  E-value=1.4e-05  Score=65.53  Aligned_cols=76  Identities=17%  Similarity=0.219  Sum_probs=58.6

Q ss_pred             ceeeccCCCCCchh-hHHHHHHHHHHhCCC--------CCCCEEEEEe----eCCCCCCCccccCCCccceEEEecCCCH
Q 039253            4 SIVIQRGSGAGGAA-DRIPNQLLTEMDGLS--------AKKTIFVIGV----TNRPDIIDPALLRPGRLDQLIYIPLPVE   70 (199)
Q Consensus         4 sl~~~R~~~~~~~~-~r~~~~lL~~ld~~~--------~~~~VvvI~a----TN~~~~lD~al~R~gRfd~~i~~~~P~~   70 (199)
                      ++++++.....+.. +.+.++||+.||+..        ..++|++|++    +|+++.++|++++  ||+.++.|+.|+.
T Consensus       126 ki~~~~~~~~~~~~~~gv~~~LL~~~dg~~~~~~~~~i~~s~ilfi~~ga~~~~~~~~~~p~l~~--R~~~~i~~~~~~~  203 (309)
T d1ofha_         126 KICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG--RLPIRVELTALSA  203 (309)
T ss_dssp             GGSCCSSCCSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSSCGGGSCHHHHH--TCCEEEECCCCCH
T ss_pred             hhhhhccCcccchhhhHHHHHhhHHhcCCEEecCCeEEEccceeEEeccchhhcCcccchhhhhh--hhheeeeccCCCH
Confidence            45666655554444 348899999999852        1335677766    6789999999986  9999999999999


Q ss_pred             HHHHHHHHHhh
Q 039253           71 KSRLQIFKACL   81 (199)
Q Consensus        71 ~~R~~il~~~l   81 (199)
                      .++.+|++.+.
T Consensus       204 ~~~~~Il~~~~  214 (309)
T d1ofha_         204 ADFERILTEPH  214 (309)
T ss_dssp             HHHHHHHHSST
T ss_pred             HHHHHHHHHHH
Confidence            99999987654

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.73  E-value=9.1e-05  Score=57.92  Aligned_cols=79  Identities=15%  Similarity=0.178  Sum_probs=63.0

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHH
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLA   96 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la   96 (199)
                      ....+.|+..|+.  ...++.+|++||+++.+.+++++  |+ ..+.|+.|+.++-..++...+...... ++..+..|+
T Consensus       129 ~~~q~~Llk~lE~--~~~~~~~il~tn~~~~i~~~i~S--Rc-~~i~~~~~~~~~i~~~l~~i~~~e~~~~~~~~l~~i~  203 (239)
T d1njfa_         129 RHSFNALLKTLEE--PPEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLA  203 (239)
T ss_dssp             HHHHHHHHHHHHS--CCTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHH
T ss_pred             HHHHHHHHHHHhc--CCCCeEEEEEcCCccccChhHhh--hh-cccccccCcHHHhhhHHHHHHhhhccCCCHHHHHHHH
Confidence            4566889999984  44667899999999999999999  88 689999999999888888887644332 345678888


Q ss_pred             hhCCC
Q 039253           97 QFTQG  101 (199)
Q Consensus        97 ~~t~G  101 (199)
                      ..+.|
T Consensus       204 ~~s~G  208 (239)
T d1njfa_         204 RAAEG  208 (239)
T ss_dssp             HHTTT
T ss_pred             HHcCC
Confidence            87776

>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=97.70  E-value=4.1e-05  Score=59.50  Aligned_cols=103  Identities=16%  Similarity=0.106  Sum_probs=73.0

Q ss_pred             CCCEEEEEeeCC---CCCCCccccCCCcc-ceEEEecCCCHHHHHHHHHHhhcCC---CCCCcccHHHHHhhCCC-----
Q 039253           34 KKTIFVIGVTNR---PDIIDPALLRPGRL-DQLIYIPLPVEKSRLQIFKACLRKS---PVSKDVDLEKLAQFTQG-----  101 (199)
Q Consensus        34 ~~~VvvI~aTN~---~~~lD~al~R~gRf-d~~i~~~~P~~~~R~~il~~~l~~~---~~~~~~~l~~la~~t~G-----  101 (199)
                      ..++++|+++|.   .+.+++.+.+  |+ ...|.|+.|+.+++.+|++..+...   ..-++..++.+++.+..     
T Consensus       156 ~~~~~~i~~~~~~~~~~~~~~~~~~--r~~~~~i~~~~~~~~e~~~il~~r~~~~~~~~~~~~~~l~~ia~~~~~~~~~~  233 (276)
T d1fnna2         156 AFRIALVIVGHNDAVLNNLDPSTRG--IMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLD  233 (276)
T ss_dssp             SCCEEEEEEESSTHHHHTSCHHHHH--HHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTC
T ss_pred             ccceEEeecCCchhhhhhcchhhhh--hhcchhccccchhHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhhhhhhhh
Confidence            456788888887   4578888887  65 3578999999999999999877532   11234446667765421     


Q ss_pred             -C--CHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhc
Q 039253          102 -F--SGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYA  157 (199)
Q Consensus       102 -~--sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~  157 (199)
                       +  +++.+.++|+.|+..|..+..                   ..|+.+|+.+|++++
T Consensus       234 ~~~G~~R~a~~ll~~a~~~A~~~~~-------------------~~I~~edv~~A~~~~  273 (276)
T d1fnna2         234 TNRGDARLAIDILYRSAYAAQQNGR-------------------KHIAPEDVRKSSKEV  273 (276)
T ss_dssp             TTSCCHHHHHHHHHHHHHHHHHTTC-------------------SSCCHHHHHHHHHHH
T ss_pred             hcCCCHHHHHHHHHHHHHHHHHcCC-------------------CCcCHHHHHHHHHHH
Confidence             1  456677788888766655432                   579999999999875

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.61  E-value=9.7e-05  Score=57.35  Aligned_cols=85  Identities=19%  Similarity=0.209  Sum_probs=64.9

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCC--CCCcccHHHH
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSP--VSKDVDLEKL   95 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~--~~~~~~l~~l   95 (199)
                      ....+.|+..++.  ...++.+|++||.++.+++++++  |+ ..|+|+.|+.++..++++..+....  ...+.-+..|
T Consensus       145 ~~~~~~l~~~~e~--~~~~~~~Il~tn~~~~i~~~l~s--R~-~~i~~~~~~~~~~~~~l~~i~~~e~~~~~~~~~l~~i  219 (252)
T d1sxje2         145 KDAQAALRRTMEK--YSKNIRLIMVCDSMSPIIAPIKS--QC-LLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRI  219 (252)
T ss_dssp             HHHHHHHHHHHHH--STTTEEEEEEESCSCSSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCEECCSHHHHHH
T ss_pred             cccchhhhccccc--ccccccceeeeccccchhhhhhc--ch-heeeecccchhhHHHHHHHHHHHcCCCCCcHHHHHHH
Confidence            3455677777774  34567889999999999999998  98 5899999999999999998886543  3334446788


Q ss_pred             HhhCCCCCHHHHHHHH
Q 039253           96 AQFTQGFSGADITEIC  111 (199)
Q Consensus        96 a~~t~G~sgaDI~~lv  111 (199)
                      +..+.|    |++.++
T Consensus       220 ~~~s~G----d~R~ai  231 (252)
T d1sxje2         220 AQASNG----NLRVSL  231 (252)
T ss_dssp             HHHHTT----CHHHHH
T ss_pred             HHHcCC----cHHHHH
Confidence            887766    665544

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=97.46  E-value=0.00019  Score=55.29  Aligned_cols=82  Identities=10%  Similarity=0.064  Sum_probs=65.2

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHh
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQ   97 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~   97 (199)
                      ...+.|+..|+.  ...++++|++||.+..+++++++  |+ ..+.++.|+..+...+++..+.+..+. ++..+..+++
T Consensus       124 ~~~~~ll~~l~~--~~~~~~~i~~~n~~~~i~~~l~s--R~-~~i~~~~~~~~~~~~~l~~~~~~e~i~i~~~~l~~I~~  198 (231)
T d1iqpa2         124 DAQQALRRTMEM--FSSNVRFILSCNYSSKIIEPIQS--RC-AIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILY  198 (231)
T ss_dssp             HHHHHHHHHHHH--TTTTEEEEEEESCGGGSCHHHHH--TE-EEEECCCCCHHHHHHHHHHHHHTTTCEECHHHHHHHHH
T ss_pred             hHHHHHhhhccc--CCcceEEEeccCChhhchHhHhC--cc-ccccccccchhhHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence            445667777763  45678999999999999999998  88 469999999999999999999877664 4556788888


Q ss_pred             hCCCCCHHH
Q 039253           98 FTQGFSGAD  106 (199)
Q Consensus        98 ~t~G~sgaD  106 (199)
                      .+.| ..++
T Consensus       199 ~~~g-diR~  206 (231)
T d1iqpa2         199 IAEG-DMRR  206 (231)
T ss_dssp             HHTT-CHHH
T ss_pred             HcCC-CHHH
Confidence            7765 4443

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.44  E-value=0.00038  Score=53.31  Aligned_cols=78  Identities=13%  Similarity=0.066  Sum_probs=61.7

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHh
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQ   97 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~   97 (199)
                      ...+.|+..++.  ......+|.+++.+..+.+++++  |+ ..+.|+.|+..+...+|+..+.+..+. ++..+..||+
T Consensus       123 ~~~~~l~~~~~~--~~~~~~~i~~~~~~~~~~~~l~s--r~-~~i~f~~~~~~~~~~~L~~i~~~e~i~i~~~~l~~ia~  197 (237)
T d1sxjd2         123 DAQSALRRTMET--YSGVTRFCLICNYVTRIIDPLAS--QC-SKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILD  197 (237)
T ss_dssp             HHHHHHHHHHHH--TTTTEEEEEEESCGGGSCHHHHH--HS-EEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHH
T ss_pred             HHHHHHhhcccc--ccccccccccccccccccccccc--hh-hhhccccccccccchhhhhhhhhhcCcCCHHHHHHHHH
Confidence            345666666663  34566788899999999999999  98 688999999999999999998876553 4455788999


Q ss_pred             hCCC
Q 039253           98 FTQG  101 (199)
Q Consensus        98 ~t~G  101 (199)
                      .+.|
T Consensus       198 ~s~g  201 (237)
T d1sxjd2         198 ISAG  201 (237)
T ss_dssp             HTSS
T ss_pred             HcCC
Confidence            8866

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.40  E-value=5.3e-05  Score=58.29  Aligned_cols=79  Identities=14%  Similarity=0.136  Sum_probs=63.6

Q ss_pred             hHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHH
Q 039253           18 DRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLA   96 (199)
Q Consensus        18 ~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la   96 (199)
                      ....+.|+..|+..  ...++++++||.+..+++++++  |+ ..+.|+.|+..+-..++...+....+. ++..++.|+
T Consensus       113 ~~~~~~Ll~~le~~--~~~~~~~~~~~~~~~i~~~i~s--r~-~~i~~~~~~~~~i~~~l~~I~~~e~i~i~~~~l~~i~  187 (227)
T d1sxjc2         113 NAAQNALRRVIERY--TKNTRFCVLANYAHKLTPALLS--QC-TRFRFQPLPQEAIERRIANVLVHEKLKLSPNAEKALI  187 (227)
T ss_dssp             HHHHHHHHHHHHHT--TTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHTTTCCBCHHHHHHHH
T ss_pred             hhHHHHHHHHhhhc--ccceeeccccCcHHHhHHHHHH--HH-hhhccccccccccccccccccccccccCCHHHHHHHH
Confidence            34567788888754  4567899999999999999998  87 578999999999999999988776554 455578888


Q ss_pred             hhCCC
Q 039253           97 QFTQG  101 (199)
Q Consensus        97 ~~t~G  101 (199)
                      +.+.|
T Consensus       188 ~~s~G  192 (227)
T d1sxjc2         188 ELSNG  192 (227)
T ss_dssp             HHHTT
T ss_pred             HHcCC
Confidence            88766

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.24  E-value=0.00074  Score=52.20  Aligned_cols=82  Identities=17%  Similarity=0.137  Sum_probs=57.6

Q ss_pred             HHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcC--CCCCCcccHHHHHh
Q 039253           20 IPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRK--SPVSKDVDLEKLAQ   97 (199)
Q Consensus        20 ~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~--~~~~~~~~l~~la~   97 (199)
                      ....++..+..  ...+++++++++....+++  +|  |+...|+|+.|+.+++..+++..+..  ..+. +-.+..|++
T Consensus       142 ~~~~~~~~~~~--~~~~ii~i~~~~~~~~~~~--l~--~~~~~i~f~~~~~~~i~~~l~~i~~~e~i~i~-~~~l~~i~~  214 (253)
T d1sxja2         142 GVGQLAQFCRK--TSTPLILICNERNLPKMRP--FD--RVCLDIQFRRPDANSIKSRLMTIAIREKFKLD-PNVIDRLIQ  214 (253)
T ss_dssp             HHHHHHHHHHH--CSSCEEEEESCTTSSTTGG--GT--TTSEEEECCCCCHHHHHHHHHHHHHHHTCCCC-TTHHHHHHH
T ss_pred             hhHHHhhhhcc--ccccccccccccccccccc--cc--ceeeeeeccccchhHHHHHHHHHHHHhCCCCC-HHHHHHHHH
Confidence            44555555543  2345666666666666664  45  77899999999999999999998864  3444 346889999


Q ss_pred             hCCCCCHHHHHHHHH
Q 039253           98 FTQGFSGADITEICQ  112 (199)
Q Consensus        98 ~t~G~sgaDI~~lv~  112 (199)
                      .+.|    ||+.++.
T Consensus       215 ~s~G----DiR~ai~  225 (253)
T d1sxja2         215 TTRG----DIRQVIN  225 (253)
T ss_dssp             HTTT----CHHHHHH
T ss_pred             hCCC----cHHHHHH
Confidence            8765    8877654

>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=96.87  E-value=0.0016  Score=49.71  Aligned_cols=76  Identities=18%  Similarity=0.287  Sum_probs=59.6

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCCCcccHHHHH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVSKDVDLEKLA   96 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~l~~la   96 (199)
                      .....+.||..|+.  +..++++|++||+++.|.+++++  |+ ..+.|+.|+.++-..+|+...   .+ ++-.+..++
T Consensus       121 ~~~a~n~Llk~lEe--p~~~~~fIl~t~~~~~ll~tI~S--Rc-~~i~~~~~~~~~~~~~L~~~~---~~-~~~~~~~i~  191 (207)
T d1a5ta2         121 TDAAANALLKTLEE--PPAETWFFLATREPERLLATLRS--RC-RLHYLAPPPEQYAVTWLSREV---TM-SQDALLAAL  191 (207)
T ss_dssp             CHHHHHHHHHHHTS--CCTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHC---CC-CHHHHHHHH
T ss_pred             hhhhhHHHHHHHHh--hcccceeeeeecChhhhhhhhcc--ee-EEEecCCCCHHHHHHHHHHcC---CC-CHHHHHHHH
Confidence            34567899999984  45678999999999999999999  98 899999999998888886543   22 234566677


Q ss_pred             hhCCC
Q 039253           97 QFTQG  101 (199)
Q Consensus        97 ~~t~G  101 (199)
                      +.+.|
T Consensus       192 ~~s~G  196 (207)
T d1a5ta2         192 RLSAG  196 (207)
T ss_dssp             HHTTT
T ss_pred             HHcCC
Confidence            76665

>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=96.34  E-value=0.0083  Score=45.43  Aligned_cols=85  Identities=13%  Similarity=0.117  Sum_probs=63.1

Q ss_pred             HHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHh
Q 039253           19 RIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQ   97 (199)
Q Consensus        19 r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~   97 (199)
                      ..-+.|+..|+.  ......++.+|+..+.+.+++++  |+ ..|.|+.|+.++...++...+.+..+. ++-.+..++.
T Consensus       116 ~~~~~ll~~~e~--~~~~~~~i~~~~~~~~i~~~l~s--r~-~~i~~~~~~~~~i~~~l~~i~~~e~~~i~~~~l~~I~~  190 (224)
T d1sxjb2         116 GAQQALRRTMEL--YSNSTRFAFACNQSNKIIEPLQS--QC-AILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIF  190 (224)
T ss_dssp             HHHHTTHHHHHH--TTTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHH
T ss_pred             hHHHHHhhhccc--cccceeeeeccCchhhhhhHHHH--HH-HHhhhcccchhhhHHHHHHHHHhcccCCCHHHHHHHHH
Confidence            344566666663  34567889999999999999999  88 469999999999999999988755443 3445777888


Q ss_pred             hCCCCCHHHHHHHHH
Q 039253           98 FTQGFSGADITEICQ  112 (199)
Q Consensus        98 ~t~G~sgaDI~~lv~  112 (199)
                      .+.|    |++.++.
T Consensus       191 ~s~G----d~R~ai~  201 (224)
T d1sxjb2         191 TAEG----DMRQAIN  201 (224)
T ss_dssp             HHTT----CHHHHHH
T ss_pred             HcCC----cHHHHHH
Confidence            6654    5544443

>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=95.38  E-value=0.074  Score=42.47  Aligned_cols=61  Identities=20%  Similarity=0.318  Sum_probs=45.5

Q ss_pred             hhHHHHHHHHHHhCCC-----C------CCCEEEEEeeCC-CCCCCccccCCCccceEEEecCC-CHHHHHHHHHH
Q 039253           17 ADRIPNQLLTEMDGLS-----A------KKTIFVIGVTNR-PDIIDPALLRPGRLDQLIYIPLP-VEKSRLQIFKA   79 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~-----~------~~~VvvI~aTN~-~~~lD~al~R~gRfd~~i~~~~P-~~~~R~~il~~   79 (199)
                      ..++.+.|++-|+.-.     .      ..+.++|+|+|- +..++++++.  ||+..+.++.| +...|.++...
T Consensus       140 ~~~~~~aLl~~me~~~v~i~r~g~~~~~p~~f~liaa~Np~~~~l~~~llD--Rf~~~i~v~~~~~~~~~~~~~~~  213 (333)
T d1g8pa_         140 EDHIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLD--RFGLSVEVLSPRDVETRVEVIRR  213 (333)
T ss_dssp             CHHHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHT--TCSEEEECCCCCSHHHHHHHHHH
T ss_pred             HHHHHHHHhhhhcCCeEEecccCceecCCCCEEEEEecCccccccccchhh--hhcceeeccCcchhhHHHHHHHh
Confidence            4578899999997321     0      134688888887 6779999999  99999999987 55666665543

>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=94.95  E-value=0.02  Score=43.54  Aligned_cols=86  Identities=17%  Similarity=0.270  Sum_probs=59.2

Q ss_pred             HHHHHhCCCCCCCEEEEEeeCCCCCCC---ccccCCCccce--EEEecCCCHHHHHHHHHHhhcCCCCC-CcccHHHHHh
Q 039253           24 LLTEMDGLSAKKTIFVIGVTNRPDIID---PALLRPGRLDQ--LIYIPLPVEKSRLQIFKACLRKSPVS-KDVDLEKLAQ   97 (199)
Q Consensus        24 lL~~ld~~~~~~~VvvI~aTN~~~~lD---~al~R~gRfd~--~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~l~~la~   97 (199)
                      |...++.+....+-+||.+...|..++   +.+.+  |+..  .+.++ |+.+.|.++++.+.....+. ++.-+..|++
T Consensus       119 lf~lin~~~~~~~~iiits~~~p~~l~~~~~dL~S--RL~~g~~~~i~-p~d~~~~~iL~~~a~~rgl~l~~~v~~yl~~  195 (213)
T d1l8qa2         119 FFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVS--RFEGGILVEIE-LDNKTRFKIIKEKLKEFNLELRKEVIDYLLE  195 (213)
T ss_dssp             HHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHH--HHHTSEEEECC-CCHHHHHHHHHHHHHHTTCCCCHHHHHHHHH
T ss_pred             HHHHHHHHhhccceEEEecCCcchhccccchHHHH--HhhCceEEEEC-CCcHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            444444444455567777777776554   67888  8764  45555 67789999999999766554 4556788898


Q ss_pred             hCCCCCHHHHHHHHHHH
Q 039253           98 FTQGFSGADITEICQRA  114 (199)
Q Consensus        98 ~t~G~sgaDI~~lv~~A  114 (199)
                      ++.  +.+||..+++..
T Consensus       196 ~~~--~~R~L~~~l~~l  210 (213)
T d1l8qa2         196 NTK--NVREIEGKIKLI  210 (213)
T ss_dssp             HCS--SHHHHHHHHHHH
T ss_pred             hcC--cHHHHHHHHHHh
Confidence            874  578888887654

>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=92.27  E-value=0.086  Score=39.41  Aligned_cols=49  Identities=16%  Similarity=0.292  Sum_probs=40.5

Q ss_pred             hhHHHHHHHHHHhCCCCCCCEEEEEeeCCCCCCCccccCCCccceEEEecCCCH
Q 039253           17 ADRIPNQLLTEMDGLSAKKTIFVIGVTNRPDIIDPALLRPGRLDQLIYIPLPVE   70 (199)
Q Consensus        17 ~~r~~~~lL~~ld~~~~~~~VvvI~aTN~~~~lD~al~R~gRfd~~i~~~~P~~   70 (199)
                      ....-|.||..|+  ++..++++|.+|++++.|.|.+++  |. ..+.|+.|..
T Consensus        92 ~~~aqNaLLK~LE--EPp~~t~fiLit~~~~~ll~TI~S--RC-~~i~~~~p~~  140 (198)
T d2gnoa2          92 TQQAANAFLKALE--EPPEYAVIVLNTRRWHYLLPTIKS--RV-FRVVVNVPKE  140 (198)
T ss_dssp             CHHHHHHTHHHHH--SCCTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCHH
T ss_pred             chhhhhHHHHHHh--CCCCCceeeeccCChhhCHHHHhc--ce-EEEeCCCchH
Confidence            4456789999999  456678999999999999999999  87 6778887754

>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=89.66  E-value=0.84  Score=35.55  Aligned_cols=109  Identities=20%  Similarity=0.188  Sum_probs=66.1

Q ss_pred             hCCCCCCCEEEEEeeC-----CCCCCCccccCCCccceEEEecCCCHHHHHHHHHHhhcC------CCCCCcccHHHHHh
Q 039253           29 DGLSAKKTIFVIGVTN-----RPDIIDPALLRPGRLDQLIYIPLPVEKSRLQIFKACLRK------SPVSKDVDLEKLAQ   97 (199)
Q Consensus        29 d~~~~~~~VvvI~aTN-----~~~~lD~al~R~gRfd~~i~~~~P~~~~R~~il~~~l~~------~~~~~~~~l~~la~   97 (199)
                      ..+-.+..+-+|++|.     ....-|++|.|  || .+|.+.-|+.++-..|++.+...      ..+. +.-+..+..
T Consensus       140 kp~L~rg~i~vIgatT~eey~~~~e~d~al~r--rF-~~I~V~Eps~e~t~~IL~~~~~~~e~~h~v~~~-~~al~~~v~  215 (268)
T d1r6bx2         140 KPLLSSGKIRVIGSTTYQEFSNIFEKDRALAR--RF-QKIDITEPSIEETVQIINGLKPKYEAHHDVRYT-AKAVRAAVE  215 (268)
T ss_dssp             SSCSSSCCCEEEEEECHHHHHCCCCCTTSSGG--GE-EEEECCCCCHHHHHHHHHHHHHHHHHHHTCCCC-HHHHHHHHH
T ss_pred             hHHHhCCCCeEEEeCCHHHHHHHHhhcHHHHh--hh-cccccCCCCHHHHHHHHHHhhHHHhccCCEEeC-hHHHHHHHH
Confidence            3333466788888887     35567999999  99 56889999999999999775532      2222 223333333


Q ss_pred             hC------CCCCHHHHHHHHHHHHHHHHHHHHHHhHHhhcCCCCcchhhccccccHHHHHHHHHhc
Q 039253           98 FT------QGFSGADITEICQRACKDATREEIENDIRRRKGKQPEAIEDEVAEIKAEHFEESMKYA  157 (199)
Q Consensus        98 ~t------~G~sgaDI~~lv~~A~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~Al~~~  157 (199)
                      .+      ..|.+.-|. ++++|+..+.....               ......+..+|++..+.++
T Consensus       216 ls~ryi~~~~~PdKAId-llDea~a~~~~~~~---------------~~~~~~i~~~di~~~i~~~  265 (268)
T d1r6bx2         216 LAVKYINDRHLPDKAID-VIDEAGARARLMPV---------------SKRKKTVNVADIESVVARI  265 (268)
T ss_dssp             HHHHHCTTSCTTHHHHH-HHHHHHHHHHHSSS---------------CCCCCSCCHHHHHHHHHHH
T ss_pred             HHHhhccCCCCCcHHHH-HHHHHHHHHHhhcc---------------ccCcccCCHHHHHHHHHHH
Confidence            22      234444444 66776443322110               0111457888888777665

>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=88.15  E-value=0.42  Score=38.02  Aligned_cols=104  Identities=20%  Similarity=0.246  Sum_probs=74.8

Q ss_pred             hHHHHHHHHHHhCC---CC------CCCEEEEEeeCC--------------------------CCCCCccccCCCccceE
Q 039253           18 DRIPNQLLTEMDGL---SA------KKTIFVIGVTNR--------------------------PDIIDPALLRPGRLDQL   62 (199)
Q Consensus        18 ~r~~~~lL~~ld~~---~~------~~~VvvI~aTN~--------------------------~~~lD~al~R~gRfd~~   62 (199)
                      ..+.+.|++.|+.=   ..      -.+.++|+|||-                          .+.+.|.|+.  |||..
T Consensus       139 ~~v~~~ll~~l~~g~~~~~~gr~v~~~~~i~i~tsnlG~~~i~~~~~~~~~~~~~~~~~~~~l~~~f~pEfln--Rid~I  216 (315)
T d1qvra3         139 PDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEI  216 (315)
T ss_dssp             HHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHH--TCSBC
T ss_pred             HHHHHHHHHHhccCceeCCCCcEecCcceEEEEecccChHHHhhhcccccchhhhhHHHHHHHHhhcCHHHHh--cCCee
Confidence            35677788777652   11      245899999995                          3569999999  99999


Q ss_pred             EEecCCCHHHHHHHHHHhhcCC-------CCC---CcccHHHHHhh--CCCCCHHHHHHHHHHHHHHHHHHHH
Q 039253           63 IYIPLPVEKSRLQIFKACLRKS-------PVS---KDVDLEKLAQF--TQGFSGADITEICQRACKDATREEI  123 (199)
Q Consensus        63 i~~~~P~~~~R~~il~~~l~~~-------~~~---~~~~l~~la~~--t~G~sgaDI~~lv~~A~~~a~~~~~  123 (199)
                      +.|.+.+.++-..|+...+...       ...   .+..++.|++.  ...|-++.|+.++++.....+.+.+
T Consensus       217 i~F~~L~~~~~~~I~~~~l~~l~~rl~~~~i~l~i~~~~~~~L~~~~y~~~~GAR~L~r~Ie~~i~~~La~~i  289 (315)
T d1qvra3         217 VVFRPLTKEQIRQIVEIQLSYLRARLAEKRISLELTEAAKDFLAERGYDPVFGARPLRRVIQRELETPLAQKI  289 (315)
T ss_dssp             CBCCCCCHHHHHHHHHHHHHHHHHHHHTTTCEEEECHHHHHHHHHHHCBTTTBTSTHHHHHHHHTHHHHHHHH
T ss_pred             eeccchhhhhhHHHHHHHHHHHHHHHHhccccccccHHHHHHHHHhCCCCCCCcchHHHHHHHHHHHHHHHHH
Confidence            9999999999999987666421       111   23335667764  4567778999888887777766654

>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=84.16  E-value=1.7  Score=34.25  Aligned_cols=104  Identities=20%  Similarity=0.260  Sum_probs=71.6

Q ss_pred             hHHHHHHHHHHhCC---------CCCCCEEEEEeeCCCC-------------------------CCCccccCCCccceEE
Q 039253           18 DRIPNQLLTEMDGL---------SAKKTIFVIGVTNRPD-------------------------IIDPALLRPGRLDQLI   63 (199)
Q Consensus        18 ~r~~~~lL~~ld~~---------~~~~~VvvI~aTN~~~-------------------------~lD~al~R~gRfd~~i   63 (199)
                      ..+.+.||+.||.=         -.-.+.++|+|||-..                         .+.|.|+.  |||..+
T Consensus       135 ~~V~~~lLqild~G~ltd~~Gr~vdf~n~iiI~Tsnig~~~i~~~~~~~~~~~~~~~~~~~l~~~f~pEfln--Rid~ii  212 (315)
T d1r6bx3         135 PDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNII  212 (315)
T ss_dssp             HHHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEECSSCC-----------------CHHHHHHHSCHHHHT--TCSEEE
T ss_pred             chHhhhhHHhhccceecCCCCCccCccceEEEeccchhhHHHHhhhccchhhhhhHhHHHHHHHhcCHHHHh--hhhhhh
Confidence            35778888888631         1234688999999521                         36788888  999999


Q ss_pred             EecCCCHHHHHHHHHHhhcCC-------CCC---CcccHHHHHh--hCCCCCHHHHHHHHHHHHHHHHHHHH
Q 039253           64 YIPLPVEKSRLQIFKACLRKS-------PVS---KDVDLEKLAQ--FTQGFSGADITEICQRACKDATREEI  123 (199)
Q Consensus        64 ~~~~P~~~~R~~il~~~l~~~-------~~~---~~~~l~~la~--~t~G~sgaDI~~lv~~A~~~a~~~~~  123 (199)
                      .|.+.+.++-..|+..++...       ...   .+-.+..|++  ....+-++.|+.++++-....+.+.+
T Consensus       213 ~f~~l~~~~~~~I~~~~l~~~~~~l~~~~i~l~~~~~a~~~l~~~~yd~~~GaR~L~r~Ie~~i~~~la~~i  284 (315)
T d1r6bx3         213 WFDHLSTDVIHQVVDKFIVELQVQLDQKGVSLEVSQEARNWLAEKGYDRAMGARPMARVIQDNLKKPLANEL  284 (315)
T ss_dssp             ECCCCCHHHHHHHHHHHHHHHHHHHHHTTEEEEECHHHHHHHHHHHCBTTTBTTTHHHHHHHHHTHHHHHHH
T ss_pred             cccchhhhHHHHHHHHHHHHHHHHHHhcCcchhhHHHHHHHHHHhCCCCCCChhhHHHHHHHHHHHHHHHHH
Confidence            999999999999887777432       111   2233556665  34567778888888877666665543