Psyllid ID: psy522

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-
Protein Sequence
LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT
Secondary Structure (PSIPRED)
cHHHHHHccccEEEEEccccccccccccccccHHHHHHHHHHHHHHcccccccccEEEEEcccccccccccccccccccEEEccccccHHHHHHHHHHHHccccccccccHHHHHHHcccccHHHHccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHcccEEEEEEEEccccccccccccccccHHHHHHHHHHHHcccccccccEEEEEEccccccccHHHccccccccEEEEcccccccHHHHHHHHHccccccccccHHHHHcccccccHHcHHHHcc
Coil and Loop (DISEMBL)
lfrvaeehapsivfideidavgtkrydsnsggeREIQRTMLELLNQldgfdsrgdvKVIMATnrietldpalirpgridrkiefplpdektkrRIFNIHTSRMTLAEDVNLQELIMAkddlsgadIKAICT
Flexible Loop (DISEMBL)
lfrvaeehapsivfideidavgtkrydsnsggeREIQRTMLELLNQLDGFDSRGDVKVIMatnrietldpalirpgridrkiefplpdektkrrifNIHTSRMTLAEDVNLQELImakddlsgadIKAICT
Low Complexity Region (SEG)
LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT
Disordered region (IsUnstruct)
**********SIVFIDEIDAVGTK*************RTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKD************
Disordered Region (DISOPRED)
LFRVA*EHAPSIVFIDEIDAVGT**************RTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT
Disordered Region (DISEMBL)
LFRVAEEHAPSIVFIDEIDAVGTK********EREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT
Disordered Region (DISPRO)
LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADI**I*T
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT
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	131	2.2.26 [Sep-21-2011]
P48601	439	26S protease regulatory s	yes	N/A	1.0	0.298	0.984	1e-70
P62193	440	26S protease regulatory s	yes	N/A	1.0	0.297	0.946	3e-68
P62192	440	26S protease regulatory s	yes	N/A	1.0	0.297	0.946	3e-68
P62191	440	26S protease regulatory s	yes	N/A	1.0	0.297	0.946	3e-68
Q90732	440	26S protease regulatory s	yes	N/A	1.0	0.297	0.946	3e-68
O16368	443	Probable 26S protease reg	yes	N/A	1.0	0.295	0.908	1e-65
Q55BV5	439	26S protease regulatory s	yes	N/A	1.0	0.298	0.877	3e-63
Q9SL67	443	26S proteasome regulatory	yes	N/A	1.0	0.295	0.862	7e-63
P46466	448	26S protease regulatory s	yes	N/A	1.0	0.292	0.854	3e-62
Q9SZD4	443	26S proteasome regulatory	yes	N/A	1.0	0.295	0.847	6e-62

>sp|P48601|PRS4_DROME 26S protease regulatory subunit 4 OS=Drosophila melanogaster GN=Pros26.4 PE=2 SV=2

 Score =  264 bits (674), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 129/131 (98%), Positives = 129/131 (98%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct: 269 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 328

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIF IHTSRMTLAEDVNL ELIMAKDD
Sbjct: 329 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFTIHTSRMTLAEDVNLSELIMAKDD 388

Query: 121 LSGADIKAICT 131
           LSGADIKAICT
Sbjct: 389 LSGADIKAICT 399

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.
Drosophila melanogaster (taxid: 7227)

>sp|P62193|PRS4_RAT 26S protease regulatory subunit 4 OS=Rattus norvegicus GN=Psmc1 PE=2 SV=1

 Score =  256 bits (654), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 124/131 (94%), Positives = 128/131 (97%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LFRVAEEHAPSIVFIDEIDA+GTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct: 270 LFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 329

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRIETLDPALIRPGRIDRKIEFPLPDEKTK+RIF IHTSRMTLA+DV L +LIMAKDD
Sbjct: 330 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKRIFQIHTSRMTLADDVTLDDLIMAKDD 389

Query: 121 LSGADIKAICT 131
           LSGADIKAICT
Sbjct: 390 LSGADIKAICT 400

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

Rattus norvegicus (taxid: 10116)

>sp|P62192|PRS4_MOUSE 26S protease regulatory subunit 4 OS=Mus musculus GN=Psmc1 PE=1 SV=1

 Score =  256 bits (654), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 124/131 (94%), Positives = 128/131 (97%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LFRVAEEHAPSIVFIDEIDA+GTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct: 270 LFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 329

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRIETLDPALIRPGRIDRKIEFPLPDEKTK+RIF IHTSRMTLA+DV L +LIMAKDD
Sbjct: 330 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKRIFQIHTSRMTLADDVTLDDLIMAKDD 389

Query: 121 LSGADIKAICT 131
           LSGADIKAICT
Sbjct: 390 LSGADIKAICT 400

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

Mus musculus (taxid: 10090)

>sp|P62191|PRS4_HUMAN 26S protease regulatory subunit 4 OS=Homo sapiens GN=PSMC1 PE=1 SV=1

 Score =  256 bits (654), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 124/131 (94%), Positives = 128/131 (97%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LFRVAEEHAPSIVFIDEIDA+GTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct: 270 LFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 329

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRIETLDPALIRPGRIDRKIEFPLPDEKTK+RIF IHTSRMTLA+DV L +LIMAKDD
Sbjct: 330 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKRIFQIHTSRMTLADDVTLDDLIMAKDD 389

Query: 121 LSGADIKAICT 131
           LSGADIKAICT
Sbjct: 390 LSGADIKAICT 400

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

Homo sapiens (taxid: 9606)

>sp|Q90732|PRS4_CHICK 26S protease regulatory subunit 4 OS=Gallus gallus GN=PSMC1 PE=2 SV=1

 Score =  256 bits (653), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 124/131 (94%), Positives = 127/131 (96%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LFRVAEEH PSIVFIDEIDA+GTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct: 270 LFRVAEEHGPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 329

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRIETLDPALIRPGRIDRKIEFPLPDEKTK+RIF IHTSRMTLA+DV L ELIMAKDD
Sbjct: 330 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKRIFQIHTSRMTLADDVTLDELIMAKDD 389

Query: 121 LSGADIKAICT 131
           LSGADIKAICT
Sbjct: 390 LSGADIKAICT 400

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

Gallus gallus (taxid: 9031)

>sp|O16368|PRS4_CAEEL Probable 26S protease regulatory subunit 4 OS=Caenorhabditis elegans GN=rpt-2 PE=3 SV=1

 Score =  248 bits (632), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 119/131 (90%), Positives = 127/131 (96%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LFRVAEE+APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKV+M
Sbjct: 273 LFRVAEENAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVLM 332

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRIE+LDPALIRPGRIDRKIEFPLPDEKTKRRIF IHTSRMTL ++VNL+E I AKD+
Sbjct: 333 ATNRIESLDPALIRPGRIDRKIEFPLPDEKTKRRIFQIHTSRMTLGKEVNLEEFITAKDE 392

Query: 121 LSGADIKAICT 131
           LSGADIKA+CT
Sbjct: 393 LSGADIKAMCT 403

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

Caenorhabditis elegans (taxid: 6239)

>sp|Q55BV5|PRS4_DICDI 26S protease regulatory subunit 4 homolog OS=Dictyostelium discoideum GN=psmC1 PE=1 SV=1

 Score =  239 bits (611), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 115/131 (87%), Positives = 124/131 (94%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LFRVA+E APSIVFIDEIDAVGTKRYDS SGGEREIQRTMLELLNQLDGFD+R DVKVIM
Sbjct: 269 LFRVADECAPSIVFIDEIDAVGTKRYDSQSGGEREIQRTMLELLNQLDGFDARTDVKVIM 328

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRIETLDPALIRPGRIDRKIEFPLPD KTKR+IF IHT++M L+EDVNL+E +M+KDD
Sbjct: 329 ATNRIETLDPALIRPGRIDRKIEFPLPDIKTKRKIFEIHTAKMNLSEDVNLEEFVMSKDD 388

Query: 121 LSGADIKAICT 131
           LSGADIKAICT
Sbjct: 389 LSGADIKAICT 399

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex (By similarity). Plays an important role in regulating both growth and multicellular development.

Dictyostelium discoideum (taxid: 44689)

>sp|Q9SL67|PRS4B_ARATH 26S proteasome regulatory subunit 4 homolog B OS=Arabidopsis thaliana GN=RPT2B PE=2 SV=1

 Score =  238 bits (608), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 113/131 (86%), Positives = 125/131 (95%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LFRVA++ +PSIVFIDEIDAVGTKRYD+NSGGEREIQRTMLELLNQLDGFDSRGDVKVI+
Sbjct: 273 LFRVADDLSPSIVFIDEIDAVGTKRYDANSGGEREIQRTMLELLNQLDGFDSRGDVKVIL 332

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRIE+LDPAL+RPGRIDRKIEFPLPD KT+RRIF IHTS+MTLAEDVNL+E +M KD+
Sbjct: 333 ATNRIESLDPALLRPGRIDRKIEFPLPDIKTRRRIFQIHTSKMTLAEDVNLEEFVMTKDE 392

Query: 121 LSGADIKAICT 131
            SGADIKAICT
Sbjct: 393 FSGADIKAICT 403

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

Arabidopsis thaliana (taxid: 3702)

>sp|P46466|PRS4_ORYSJ 26S protease regulatory subunit 4 homolog OS=Oryza sativa subsp. japonica GN=TBP2 PE=2 SV=2

 Score =  236 bits (602), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 112/131 (85%), Positives = 125/131 (95%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LFRVA+E +PSIVFIDEIDAVGTKRYD++SGGEREIQRTMLELLNQLDGFDSRGDVKVI+
Sbjct: 278 LFRVADELSPSIVFIDEIDAVGTKRYDAHSGGEREIQRTMLELLNQLDGFDSRGDVKVIL 337

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRIE+LDPAL+RPGRIDRKIEFPLPD KT+RRIF IHTS+MTLA+DVNL+E +M KD+
Sbjct: 338 ATNRIESLDPALLRPGRIDRKIEFPLPDIKTRRRIFQIHTSKMTLADDVNLEEFVMTKDE 397

Query: 121 LSGADIKAICT 131
            SGADIKAICT
Sbjct: 398 FSGADIKAICT 408

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

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9SZD4|PRS4A_ARATH 26S proteasome regulatory subunit 4 homolog A OS=Arabidopsis thaliana GN=RPT2A PE=2 SV=1

 Score =  235 bits (599), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 111/131 (84%), Positives = 125/131 (95%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LFRVA++ +PSIVFIDEIDAVGTKRYD++SGGEREIQRTMLELLNQLDGFDSRGDVKVI+
Sbjct: 273 LFRVADDLSPSIVFIDEIDAVGTKRYDAHSGGEREIQRTMLELLNQLDGFDSRGDVKVIL 332

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRIE+LDPAL+RPGRIDRKIEFPLPD KT+RRIF IHTS+MTL+EDVNL+E +M KD+
Sbjct: 333 ATNRIESLDPALLRPGRIDRKIEFPLPDIKTRRRIFQIHTSKMTLSEDVNLEEFVMTKDE 392

Query: 121 LSGADIKAICT 131
            SGADIKAICT
Sbjct: 393 FSGADIKAICT 403

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex. Is required for the maintenance of postembryonic root and shoot meristems. Has a specific role in the regulation of organs size.

Arabidopsis thaliana (taxid: 3702)

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	131
332375398	438	unknown [Dendroctonus ponderosae]	1.0	0.299	1.0	4e-70
242022643	440	26S protease regulatory subunit, putativ	1.0	0.297	0.992	8e-70
91086399	438	PREDICTED: similar to 26S protease regul	1.0	0.299	0.992	1e-69
289740351	439	26S proteasome regulatory complex ATPase	1.0	0.298	0.992	2e-69
193617698	440	PREDICTED: 26S protease regulatory subun	1.0	0.297	0.984	4e-69
158291405	438	AGAP003215-PA [Anopheles gambiae str. PE	1.0	0.299	0.984	4e-69
170051679	438	26S protease regulatory subunit 4 [Culex	1.0	0.299	0.984	5e-69
312384064	438	hypothetical protein AND_02632 [Anophele	1.0	0.299	0.984	5e-69
1066065	439	P26s4 [Drosophila melanogaster]	1.0	0.298	0.984	9e-69
24649446	439	proteasome 26S subunit subunit 4 ATPase	1.0	0.298	0.984	1e-68

>gi|332375398|gb|AEE62840.1| unknown [Dendroctonus ponderosae]

 Score =  268 bits (686), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 131/131 (100%), Positives = 131/131 (100%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct: 268 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 327

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD
Sbjct: 328 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 387

Query: 121 LSGADIKAICT 131
           LSGADIKAICT
Sbjct: 388 LSGADIKAICT 398

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242022643|ref|XP_002431748.1| 26S protease regulatory subunit, putative [Pediculus humanus corporis] gi|212517073|gb|EEB19010.1| 26S protease regulatory subunit, putative [Pediculus humanus corporis]

 Score =  267 bits (683), Expect = 8e-70,   Method: Compositional matrix adjust.
 Identities = 130/131 (99%), Positives = 131/131 (100%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct: 270 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 329

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRIETLDPALIRPGRIDRKIEFPLPDEKTK+RIFNIHTSRMTLAEDVNLQELIMAKDD
Sbjct: 330 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKRIFNIHTSRMTLAEDVNLQELIMAKDD 389

Query: 121 LSGADIKAICT 131
           LSGADIKAICT
Sbjct: 390 LSGADIKAICT 400

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91086399|ref|XP_974859.1| PREDICTED: similar to 26S protease regulatory subunit 4 [Tribolium castaneum] gi|270010293|gb|EFA06741.1| hypothetical protein TcasGA2_TC009675 [Tribolium castaneum]

 Score =  267 bits (682), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 130/131 (99%), Positives = 131/131 (100%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct: 268 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 327

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRIETLDPALIRPGRIDRKIEFPLPDEKTK+RIFNIHTSRMTLAEDVNLQELIMAKDD
Sbjct: 328 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKRIFNIHTSRMTLAEDVNLQELIMAKDD 387

Query: 121 LSGADIKAICT 131
           LSGADIKAICT
Sbjct: 388 LSGADIKAICT 398

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|289740351|gb|ADD18923.1| 26S proteasome regulatory complex ATPase RPT2 [Glossina morsitans morsitans]

 Score =  266 bits (680), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 130/131 (99%), Positives = 130/131 (99%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct: 269 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 328

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNL ELIMAKDD
Sbjct: 329 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLSELIMAKDD 388

Query: 121 LSGADIKAICT 131
           LSGADIKAICT
Sbjct: 389 LSGADIKAICT 399

Source: Glossina morsitans morsitans

Species: Glossina morsitans

Genus: Glossina

Family: Glossinidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193617698|ref|XP_001948523.1| PREDICTED: 26S protease regulatory subunit 4-like [Acyrthosiphon pisum]

 Score =  265 bits (677), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 129/131 (98%), Positives = 130/131 (99%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKV+M
Sbjct: 270 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVVM 329

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAE VNLQELIMAKDD
Sbjct: 330 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEGVNLQELIMAKDD 389

Query: 121 LSGADIKAICT 131
           LSGADIKAICT
Sbjct: 390 LSGADIKAICT 400

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158291405|ref|XP_312923.4| AGAP003215-PA [Anopheles gambiae str. PEST] gi|158291407|ref|XP_312924.4| AGAP003216-PA [Anopheles gambiae str. PEST] gi|157017759|gb|EAA08386.4| AGAP003215-PA [Anopheles gambiae str. PEST] gi|157017760|gb|EAA08387.4| AGAP003216-PA [Anopheles gambiae str. PEST]

 Score =  265 bits (677), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 129/131 (98%), Positives = 130/131 (99%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct: 268 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 327

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHT+RMTLAEDVNL ELIMAKDD
Sbjct: 328 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTARMTLAEDVNLSELIMAKDD 387

Query: 121 LSGADIKAICT 131
           LSGADIKAICT
Sbjct: 388 LSGADIKAICT 398

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170051679|ref|XP_001861875.1| 26S protease regulatory subunit 4 [Culex quinquefasciatus] gi|167872831|gb|EDS36214.1| 26S protease regulatory subunit 4 [Culex quinquefasciatus]

 Score =  265 bits (676), Expect = 5e-69,   Method: Compositional matrix adjust.
 Identities = 129/131 (98%), Positives = 130/131 (99%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct: 268 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 327

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHT+RMTLAEDVNL ELIMAKDD
Sbjct: 328 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTARMTLAEDVNLSELIMAKDD 387

Query: 121 LSGADIKAICT 131
           LSGADIKAICT
Sbjct: 388 LSGADIKAICT 398

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312384064|gb|EFR28883.1| hypothetical protein AND_02632 [Anopheles darlingi] gi|312384065|gb|EFR28884.1| hypothetical protein AND_02633 [Anopheles darlingi]

 Score =  265 bits (676), Expect = 5e-69,   Method: Compositional matrix adjust.
 Identities = 129/131 (98%), Positives = 130/131 (99%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct: 268 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 327

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHT+RMTLAEDVNL ELIMAKDD
Sbjct: 328 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTARMTLAEDVNLAELIMAKDD 387

Query: 121 LSGADIKAICT 131
           LSGADIKAICT
Sbjct: 388 LSGADIKAICT 398

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|1066065|gb|AAB34134.1| P26s4 [Drosophila melanogaster]

 Score =  264 bits (675), Expect = 9e-69,   Method: Compositional matrix adjust.
 Identities = 129/131 (98%), Positives = 129/131 (98%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct: 269 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 328

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIF IHTSRMTLAEDVNL ELIMAKDD
Sbjct: 329 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFTIHTSRMTLAEDVNLSELIMAKDD 388

Query: 121 LSGADIKAICT 131
           LSGADIKAICT
Sbjct: 389 LSGADIKAICT 399

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|24649446|ref|NP_524469.2| proteasome 26S subunit subunit 4 ATPase [Drosophila melanogaster] gi|195331448|ref|XP_002032413.1| GM23527 [Drosophila sechellia] gi|195573289|ref|XP_002104626.1| GD18337 [Drosophila simulans] gi|30581054|sp|P48601.2|PRS4_DROME RecName: Full=26S protease regulatory subunit 4; Short=P26s4 gi|7301070|gb|AAF56205.1| proteasome 26S subunit subunit 4 ATPase [Drosophila melanogaster] gi|16198307|gb|AAL13988.1| SD02658p [Drosophila melanogaster] gi|194121356|gb|EDW43399.1| GM23527 [Drosophila sechellia] gi|194200553|gb|EDX14129.1| GD18337 [Drosophila simulans] gi|220956224|gb|ACL90655.1| Pros26.4-PA [synthetic construct]

 Score =  264 bits (674), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 129/131 (98%), Positives = 129/131 (98%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct: 269 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 328

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIF IHTSRMTLAEDVNL ELIMAKDD
Sbjct: 329 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFTIHTSRMTLAEDVNLSELIMAKDD 388

Query: 121 LSGADIKAICT 131
           LSGADIKAICT
Sbjct: 389 LSGADIKAICT 399

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	131
FB|FBgn0015282	439	Rpt2 "Regulatory particle trip	1.0	0.298	0.984	1.2e-63
UNIPROTKB|F1NSP7	439	PSMC1 "26S protease regulatory	1.0	0.298	0.954	3e-62
UNIPROTKB|F1NTZ4	438	PSMC1 "26S protease regulatory	1.0	0.299	0.954	3e-62
ZFIN|ZDB-GENE-040625-69	440	psmc1b "proteasome (prosome, m	1.0	0.297	0.946	4.8e-62
UNIPROTKB|A4FUZ3	440	PSMC1 "Proteasome (Prosome, ma	1.0	0.297	0.946	6.2e-62
UNIPROTKB|F1PQ40	440	PSMC1 "Uncharacterized protein	1.0	0.297	0.946	6.2e-62
UNIPROTKB|B4DR63	367	PSMC1 "cDNA FLJ58247, highly s	1.0	0.356	0.946	6.2e-62
UNIPROTKB|P62191	440	PSMC1 "26S protease regulatory	1.0	0.297	0.946	6.2e-62
UNIPROTKB|F2Z5J1	440	PSMC1 "Uncharacterized protein	1.0	0.297	0.946	6.2e-62
MGI|MGI:106054	440	Psmc1 "protease (prosome, macr	1.0	0.297	0.946	6.2e-62

FB|FBgn0015282 Rpt2 "Regulatory particle triple-A ATPase 2" [Drosophila melanogaster (taxid:7227)]

 Score = 649 (233.5 bits), Expect = 1.2e-63, P = 1.2e-63
 Identities = 129/131 (98%), Positives = 129/131 (98%)

Query:     1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
             LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct:   269 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 328

Query:    61 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
             ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIF IHTSRMTLAEDVNL ELIMAKDD
Sbjct:   329 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFTIHTSRMTLAEDVNLSELIMAKDD 388

Query:   121 LSGADIKAICT 131
             LSGADIKAICT
Sbjct:   389 LSGADIKAICT 399

GO:0006508 "proteolysis" evidence=ISS;IDA;NAS

GO:0000502 "proteasome complex" evidence=NAS

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

GO:0016887 "ATPase activity" evidence=NAS

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

GO:0004175 "endopeptidase activity" evidence=IDA

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

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

GO:0005737 "cytoplasm" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0030163 "protein catabolic process" evidence=IEA

GO:0009987 "cellular process" evidence=IMP

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0000022 "mitotic spindle elongation" evidence=IMP

GO:0008283 "cell proliferation" evidence=IMP

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

UNIPROTKB|F1NSP7 PSMC1 "26S protease regulatory subunit 4" [Gallus gallus (taxid:9031)]

 Score = 636 (228.9 bits), Expect = 3.0e-62, P = 3.0e-62
 Identities = 125/131 (95%), Positives = 128/131 (97%)

Query:     1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
             LFRVAEEHAPSIVFIDEIDA+GTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct:   269 LFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 328

Query:    61 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
             ATNRIETLDPALIRPGRIDRKIEFPLPDEKTK+RIF IHTSRMTLA+DV L ELIMAKDD
Sbjct:   329 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKRIFQIHTSRMTLADDVTLDELIMAKDD 388

Query:   121 LSGADIKAICT 131
             LSGADIKAICT
Sbjct:   389 LSGADIKAICT 399

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

GO:0030163 "protein catabolic process" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0022624 "proteasome accessory complex" evidence=IEA

UNIPROTKB|F1NTZ4 PSMC1 "26S protease regulatory subunit 4" [Gallus gallus (taxid:9031)]

 Score = 636 (228.9 bits), Expect = 3.0e-62, P = 3.0e-62
 Identities = 125/131 (95%), Positives = 128/131 (97%)

Query:     1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
             LFRVAEEHAPSIVFIDEIDA+GTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct:   268 LFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 327

Query:    61 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
             ATNRIETLDPALIRPGRIDRKIEFPLPDEKTK+RIF IHTSRMTLA+DV L ELIMAKDD
Sbjct:   328 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKRIFQIHTSRMTLADDVTLDELIMAKDD 387

Query:   121 LSGADIKAICT 131
             LSGADIKAICT
Sbjct:   388 LSGADIKAICT 398

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

GO:0030163 "protein catabolic process" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0022624 "proteasome accessory complex" evidence=IEA

ZFIN|ZDB-GENE-040625-69 psmc1b "proteasome (prosome, macropain) 26S subunit, ATPase, 1b" [Danio rerio (taxid:7955)]

 Score = 634 (228.2 bits), Expect = 4.8e-62, P = 4.8e-62
 Identities = 124/131 (94%), Positives = 129/131 (98%)

Query:     1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
             LFRVAEEHAPSIVFIDEIDA+GTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct:   270 LFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 329

Query:    61 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
             ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIF IHTSRMT+AEDV+L +LI+AKDD
Sbjct:   330 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFQIHTSRMTVAEDVSLDDLILAKDD 389

Query:   121 LSGADIKAICT 131
             LSGADIKAICT
Sbjct:   390 LSGADIKAICT 400

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

GO:0005524 "ATP binding" evidence=IEA

GO:0030163 "protein catabolic process" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0000502 "proteasome complex" evidence=IEA

UNIPROTKB|A4FUZ3 PSMC1 "Proteasome (Prosome, macropain) 26S subunit, ATPase, 1" [Bos taurus (taxid:9913)]

 Score = 633 (227.9 bits), Expect = 6.2e-62, P = 6.2e-62
 Identities = 124/131 (94%), Positives = 128/131 (97%)

Query:     1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
             LFRVAEEHAPSIVFIDEIDA+GTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct:   270 LFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 329

Query:    61 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
             ATNRIETLDPALIRPGRIDRKIEFPLPDEKTK+RIF IHTSRMTLA+DV L +LIMAKDD
Sbjct:   330 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKRIFQIHTSRMTLADDVTLDDLIMAKDD 389

Query:   121 LSGADIKAICT 131
             LSGADIKAICT
Sbjct:   390 LSGADIKAICT 400

GO:0022624 "proteasome accessory complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0030163 "protein catabolic process" evidence=IEA

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

UNIPROTKB|F1PQ40 PSMC1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 633 (227.9 bits), Expect = 6.2e-62, P = 6.2e-62
 Identities = 124/131 (94%), Positives = 128/131 (97%)

Query:     1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
             LFRVAEEHAPSIVFIDEIDA+GTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct:   270 LFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 329

Query:    61 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
             ATNRIETLDPALIRPGRIDRKIEFPLPDEKTK+RIF IHTSRMTLA+DV L +LIMAKDD
Sbjct:   330 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKRIFQIHTSRMTLADDVTLDDLIMAKDD 389

Query:   121 LSGADIKAICT 131
             LSGADIKAICT
Sbjct:   390 LSGADIKAICT 400

GO:0005524 "ATP binding" evidence=IEA

GO:0030163 "protein catabolic process" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|B4DR63 PSMC1 "cDNA FLJ58247, highly similar to 26S protease regulatory subunit 4" [Homo sapiens (taxid:9606)]

 Score = 633 (227.9 bits), Expect = 6.2e-62, P = 6.2e-62
 Identities = 124/131 (94%), Positives = 128/131 (97%)

Query:     1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
             LFRVAEEHAPSIVFIDEIDA+GTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct:   197 LFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 256

Query:    61 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
             ATNRIETLDPALIRPGRIDRKIEFPLPDEKTK+RIF IHTSRMTLA+DV L +LIMAKDD
Sbjct:   257 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKRIFQIHTSRMTLADDVTLDDLIMAKDD 316

Query:   121 LSGADIKAICT 131
             LSGADIKAICT
Sbjct:   317 LSGADIKAICT 327

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

GO:0030163 "protein catabolic process" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006508 "proteolysis" evidence=IEA

GO:0008233 "peptidase activity" evidence=IEA

GO:0022624 "proteasome accessory complex" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|P62191 PSMC1 "26S protease regulatory subunit 4" [Homo sapiens (taxid:9606)]

 Score = 633 (227.9 bits), Expect = 6.2e-62, P = 6.2e-62
 Identities = 124/131 (94%), Positives = 128/131 (97%)

Query:     1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
             LFRVAEEHAPSIVFIDEIDA+GTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct:   270 LFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 329

Query:    61 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
             ATNRIETLDPALIRPGRIDRKIEFPLPDEKTK+RIF IHTSRMTLA+DV L +LIMAKDD
Sbjct:   330 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKRIFQIHTSRMTLADDVTLDDLIMAKDD 389

Query:   121 LSGADIKAICT 131
             LSGADIKAICT
Sbjct:   390 LSGADIKAICT 400

GO:0005524 "ATP binding" evidence=IEA

GO:0022624 "proteasome accessory complex" evidence=ISS

GO:0016887 "ATPase activity" evidence=ISS

GO:0000502 "proteasome complex" evidence=NAS

GO:0000075 "cell cycle checkpoint" evidence=TAS

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

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

GO:0000209 "protein polyubiquitination" evidence=TAS

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

GO:0000278 "mitotic cell cycle" evidence=TAS

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

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

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

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

GO:0006915 "apoptotic process" evidence=TAS

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

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

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

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

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

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

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

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

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0006200 "ATP catabolic process" evidence=ISS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|F2Z5J1 PSMC1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 633 (227.9 bits), Expect = 6.2e-62, P = 6.2e-62
 Identities = 124/131 (94%), Positives = 128/131 (97%)

Query:     1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
             LFRVAEEHAPSIVFIDEIDA+GTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct:   270 LFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 329

Query:    61 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
             ATNRIETLDPALIRPGRIDRKIEFPLPDEKTK+RIF IHTSRMTLA+DV L +LIMAKDD
Sbjct:   330 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKRIFQIHTSRMTLADDVTLDDLIMAKDD 389

Query:   121 LSGADIKAICT 131
             LSGADIKAICT
Sbjct:   390 LSGADIKAICT 400

GO:0022624 "proteasome accessory complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0030163 "protein catabolic process" evidence=IEA

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

MGI|MGI:106054 Psmc1 "protease (prosome, macropain) 26S subunit, ATPase 1" [Mus musculus (taxid:10090)]

 Score = 633 (227.9 bits), Expect = 6.2e-62, P = 6.2e-62
 Identities = 124/131 (94%), Positives = 128/131 (97%)

Query:     1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
             LFRVAEEHAPSIVFIDEIDA+GTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct:   270 LFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 329

Query:    61 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
             ATNRIETLDPALIRPGRIDRKIEFPLPDEKTK+RIF IHTSRMTLA+DV L +LIMAKDD
Sbjct:   330 ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKRIFQIHTSRMTLADDVTLDDLIMAKDD 389

Query:   121 LSGADIKAICT 131
             LSGADIKAICT
Sbjct:   390 LSGADIKAICT 400

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000502 "proteasome complex" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0017025 "TBP-class protein binding" evidence=ISO

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

GO:0022624 "proteasome accessory complex" evidence=IDA

GO:0030163 "protein catabolic process" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P40327	PRS4_YEAST	No assigned EC number	0.8015	1.0	0.2997	yes	N/A
O28303	PAN_ARCFU	No assigned EC number	0.6030	1.0	0.3291	yes	N/A
P46466	PRS4_ORYSJ	No assigned EC number	0.8549	1.0	0.2924	yes	N/A
P36612	PRS4_SCHPO	No assigned EC number	0.7878	1.0	0.2924	yes	N/A
P48601	PRS4_DROME	No assigned EC number	0.9847	1.0	0.2984	yes	N/A
O16368	PRS4_CAEEL	No assigned EC number	0.9083	1.0	0.2957	yes	N/A
Q55BV5	PRS4_DICDI	No assigned EC number	0.8778	1.0	0.2984	yes	N/A
Q9SZD4	PRS4A_ARATH	No assigned EC number	0.8473	1.0	0.2957	yes	N/A
Q8SRH0	PRS4_ENCCU	No assigned EC number	0.7709	1.0	0.3089	yes	N/A
Q9SL67	PRS4B_ARATH	No assigned EC number	0.8625	1.0	0.2957	yes	N/A
P62191	PRS4_HUMAN	No assigned EC number	0.9465	1.0	0.2977	yes	N/A
P62192	PRS4_MOUSE	No assigned EC number	0.9465	1.0	0.2977	yes	N/A
P62193	PRS4_RAT	No assigned EC number	0.9465	1.0	0.2977	yes	N/A
Q58576	PAN_METJA	No assigned EC number	0.5877	1.0	0.3046	yes	N/A
Q90732	PRS4_CHICK	No assigned EC number	0.9465	1.0	0.2977	yes	N/A
O26824	PAN_METTH	No assigned EC number	0.5801	1.0	0.3195	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	131
PTZ00361	438	PTZ00361, PTZ00361, 26 proteosome regulatory subun	7e-96
COG1222	406	COG1222, RPT1, ATP-dependent 26S proteasome regula	7e-83
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	5e-68
PTZ00454	398	PTZ00454, PTZ00454, 26S protease regulatory subuni	2e-63
TIGR01242	364	TIGR01242, 26Sp45, 26S proteasome subunit P45 fami	6e-59
TIGR01241	495	TIGR01241, FtsH_fam, ATP-dependent metalloprotease	2e-38
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	2e-35
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	1e-34
COG0465	596	COG0465, HflB, ATP-dependent Zn proteases [Posttra	1e-32
CHL00176	638	CHL00176, ftsH, cell division protein; Validated	7e-32
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	2e-31
PRK10733	644	PRK10733, hflB, ATP-dependent metalloprotease; Rev	6e-28
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	5e-27
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	3e-20
COG1223	368	COG1223, COG1223, Predicted ATPase (AAA+ superfami	3e-20
TIGR03689	512	TIGR03689, pup_AAA, proteasome ATPase	5e-17
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	1e-10
CHL00195	489	CHL00195, ycf46, Ycf46; Provisional	7e-10
smart00382	148	smart00382, AAA, ATPases associated with a variety	1e-07

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

 Score =  282 bits (722), Expect = 7e-96
 Identities = 118/131 (90%), Positives = 127/131 (96%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LFRVAEE+APSIVFIDEIDA+GTKRYD+ SGGE+EIQRTMLELLNQLDGFDSRGDVKVIM
Sbjct: 268 LFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGFDSRGDVKVIM 327

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRIE+LDPALIRPGRIDRKIEFP PDEKTKRRIF IHTS+MTLAEDV+L+E IMAKD+
Sbjct: 328 ATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDVDLEEFIMAKDE 387

Query: 121 LSGADIKAICT 131
           LSGADIKAICT
Sbjct: 388 LSGADIKAICT 398

Length = 438

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

 Score =  247 bits (634), Expect = 7e-83
 Identities = 89/131 (67%), Positives = 107/131 (81%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LF +A E APSI+FIDEIDA+G KR+DS + G+RE+QRTMLELLNQLDGFD RG+VKVIM
Sbjct: 236 LFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRGNVKVIM 295

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + LDPAL+RPGR DRKIEFPLPDE+ +  I  IHT +M LA+DV+L+ L    + 
Sbjct: 296 ATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLARLTEG 355

Query: 121 LSGADIKAICT 131
            SGAD+KAICT
Sbjct: 356 FSGADLKAICT 366

Length = 406

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

 Score =  209 bits (534), Expect = 5e-68
 Identities = 79/131 (60%), Positives = 103/131 (78%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LF +A E APSI+FIDEIDA+  KR DS + G+RE+QRT+++LL ++DGFD RG+VK+I 
Sbjct: 216 LFELAREKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPRGNVKIIA 275

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNRI+ LDPA++RPGR DR IE PLPDE+ +  I  IHT +M LA+DV+L+EL    + 
Sbjct: 276 ATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVDLEELAELTEG 335

Query: 121 LSGADIKAICT 131
            SGAD+KAICT
Sbjct: 336 ASGADLKAICT 346

Length = 389

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

 Score =  197 bits (503), Expect = 2e-63
 Identities = 79/130 (60%), Positives = 107/130 (82%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           +FR+A E+APSI+FIDE+D++ TKR+D+ +G +RE+QR +LELLNQ+DGFD   +VKVIM
Sbjct: 230 VFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNVKVIM 289

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR +TLDPAL+RPGR+DRKIEFPLPD + KR IF   TS+M L+E+V+L++ +   + 
Sbjct: 290 ATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSEEVDLEDFVSRPEK 349

Query: 121 LSGADIKAIC 130
           +S ADI AIC
Sbjct: 350 ISAADIAAIC 359

Length = 398

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

 Score =  185 bits (471), Expect = 6e-59
 Identities = 78/131 (59%), Positives = 101/131 (77%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           +F +A+E APSI+FIDEIDA+  KR DS + G+RE+QRT+++LL +LDGFD RG+VKVI 
Sbjct: 207 IFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRGNVKVIA 266

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + LDPAL+RPGR DR IE PLPD + +  I  IHT +M LAEDV+L+ +    + 
Sbjct: 267 ATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVDLEAIAKMTEG 326

Query: 121 LSGADIKAICT 131
            SGAD+KAICT
Sbjct: 327 ASGADLKAICT 337

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

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

 Score =  134 bits (340), Expect = 2e-38
 Identities = 58/130 (44%), Positives = 81/130 (62%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LF  A+++AP I+FIDEIDAVG +R     GG  E ++T+ +LL ++DGF +   V VI 
Sbjct: 139 LFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTNTGVIVIA 198

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + LDPAL+RPGR DR++   LPD K +  I  +H     LA DV+L+ +      
Sbjct: 199 ATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAPDVDLKAVARRTPG 258

Query: 121 LSGADIKAIC 130
            SGAD+  + 
Sbjct: 259 FSGADLANLL 268

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH [Cellular processes, Cell division, Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 495

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

 Score =  126 bits (319), Expect = 2e-35
 Identities = 64/132 (48%), Positives = 81/132 (61%), Gaps = 5/132 (3%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LF  A + APSI+FIDEID++ + R  S  G  R   R + +LL +LDG +    V VI 
Sbjct: 327 LFEKARKLAPSIIFIDEIDSLASGRGPSEDGSGR---RVVGQLLTELDGIEKAEGVLVIA 383

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRM--TLAEDVNLQELIMAK 118
           ATNR + LDPAL+RPGR DR I  PLPD + +  IF IH       LAEDV+L+EL    
Sbjct: 384 ATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEIT 443

Query: 119 DDLSGADIKAIC 130
           +  SGADI A+ 
Sbjct: 444 EGYSGADIAALV 455

Length = 494

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

 Score =  125 bits (316), Expect = 1e-34
 Identities = 61/130 (46%), Positives = 82/130 (63%), Gaps = 2/130 (1%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           +FR A + AP+I+F DEIDA+   R            R + +LL ++DG     +V VI 
Sbjct: 538 IFRKARQAAPAIIFFDEIDAIAPAR--GARFDTSVTDRIVNQLLTEMDGIQELSNVVVIA 595

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + LDPAL+RPGR DR I  P PDE+ ++ IF IHT  M LAEDV+L+EL    + 
Sbjct: 596 ATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEMTEG 655

Query: 121 LSGADIKAIC 130
            +GADI+A+C
Sbjct: 656 YTGADIEAVC 665

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

 Score =  119 bits (300), Expect = 1e-32
 Identities = 60/126 (47%), Positives = 82/126 (65%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LF  A+++AP I+FIDEIDAVG +R     GG  E ++T+ +LL ++DGF     V VI 
Sbjct: 234 LFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGGNEGVIVIA 293

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + LDPAL+RPGR DR+I   LPD K + +I  +H     LAEDV+L+++      
Sbjct: 294 ATNRPDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLAEDVDLKKIARGTPG 353

Query: 121 LSGADI 126
            SGAD+
Sbjct: 354 FSGADL 359

Length = 596

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

 Score =  117 bits (296), Expect = 7e-32
 Identities = 57/126 (45%), Positives = 80/126 (63%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LF+ A+E++P IVFIDEIDAVG +R     GG  E ++T+ +LL ++DGF     V VI 
Sbjct: 267 LFKKAKENSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNKGVIVIA 326

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR++ LD AL+RPGR DR+I   LPD + +  I  +H     L+ DV+L+ +      
Sbjct: 327 ATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHARNKKLSPDVSLELIARRTPG 386

Query: 121 LSGADI 126
            SGAD+
Sbjct: 387 FSGADL 392

Length = 638

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

 Score =  116 bits (293), Expect = 2e-31
 Identities = 63/130 (48%), Positives = 85/130 (65%), Gaps = 3/130 (2%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           +F+ AEE+APSI+FIDEIDA+  KR +    GE E +R + +LL  +DG   RG V VI 
Sbjct: 263 IFKEAEENAPSIIFIDEIDAIAPKREEVT--GEVE-KRVVAQLLTLMDGLKGRGRVIVIG 319

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + LDPAL RPGR DR+I   +PD++ ++ I  +HT  M LAEDV+L +L      
Sbjct: 320 ATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEVTHG 379

Query: 121 LSGADIKAIC 130
             GAD+ A+ 
Sbjct: 380 FVGADLAALA 389

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 =  106 bits (266), Expect = 6e-28
 Identities = 53/126 (42%), Positives = 80/126 (63%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           +F  A++ AP I+FIDEIDAVG +R     GG  E ++T+ ++L ++DGF+    + VI 
Sbjct: 236 MFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIA 295

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + LDPAL+RPGR DR++   LPD + + +I  +H  R+ LA D++   +      
Sbjct: 296 ATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPG 355

Query: 121 LSGADI 126
            SGAD+
Sbjct: 356 FSGADL 361

Length = 644

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

 Score = 96.9 bits (242), Expect = 5e-27
 Identities = 47/87 (54%), Positives = 59/87 (67%), Gaps = 5/87 (5%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGD-VKVI 59
           LF  A++ AP ++FIDEIDA+   R    SGG+ E +R + +LL +LDGF S    V VI
Sbjct: 49  LFEAAKKLAPCVIFIDEIDALAGSR---GSGGDSESRRVVNQLLTELDGFTSSLSKVIVI 105

Query: 60  MATNRIETLDPALIRPGRIDRKIEFPL 86
            ATNR + LDPAL+R GR DR IEFPL
Sbjct: 106 AATNRPDKLDPALLR-GRFDRIIEFPL 131

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

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

 Score = 84.5 bits (209), Expect = 3e-20
 Identities = 57/127 (44%), Positives = 70/127 (55%), Gaps = 4/127 (3%)

Query: 5   AEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNR 64
           AE+ APSI+FIDEIDA+  KR       ER +   +L L++ L     RG V VI ATNR
Sbjct: 72  AEKLAPSIIFIDEIDALAPKRSSDQGEVERRVVAQLLALMDGL----KRGQVIVIGATNR 127

Query: 65  IETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGA 124
            + LDPA  RPGR DR+IE  LPDE  +  I  IHT  M L      + L       SGA
Sbjct: 128 PDGLDPAKRRPGRFDREIEVNLPDEAGRLEILQIHTRLMFLGPPGTGKTLAARTVGKSGA 187

Query: 125 DIKAICT 131
           D+ A+  
Sbjct: 188 DLGALAK 194

Length = 494

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

 Score = 84.1 bits (208), Expect = 3e-20
 Identities = 51/128 (39%), Positives = 68/128 (53%), Gaps = 6/128 (4%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVG-TKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVI 59
           L+  A + AP IVFIDE+DA+   +RY    G   EI      LL +LDG      V  I
Sbjct: 202 LYERARKAAPCIVFIDELDAIALDRRYQELRGDVSEIVNA---LLTELDGIKENEGVVTI 258

Query: 60  MATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKD 119
            ATNR E LDPA IR  R + +IEF LP+++ +  I   +  +  L  D +L+ L     
Sbjct: 259 AATNRPELLDPA-IR-SRFEEEIEFKLPNDEERLEILEYYAKKFPLPVDADLRYLAAKTK 316

Query: 120 DLSGADIK 127
            +SG DIK
Sbjct: 317 GMSGRDIK 324

Length = 368

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

 Score = 75.5 bits (186), Expect = 5e-17
 Identities = 46/128 (35%), Positives = 71/128 (55%), Gaps = 9/128 (7%)

Query: 3   RVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTML-ELLNQLDGFDSRGDVKVIMA 61
             A E  P IVF DE+D++   R    SG   +++ T++ +LL ++DG +S  +V VI A
Sbjct: 283 EKASEGRPVIVFFDEMDSLFRTR---GSGVSSDVETTVVPQLLAEIDGVESLDNVIVIGA 339

Query: 62  TNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDL 121
           +NR + +DPA++RPGR+D KI    PD +    IF  +     L +D+ L E + A D  
Sbjct: 340 SNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFAKY-----LTDDLPLPEDLAAHDGD 394

Query: 122 SGADIKAI 129
             A   A+
Sbjct: 395 REATAAAL 402

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

 Score = 55.2 bits (133), Expect = 1e-10
 Identities = 31/87 (35%), Positives = 43/87 (49%), Gaps = 12/87 (13%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQL-DGFDSRGDVKVI 59
           LF +AE+  P ++FIDEID++            R  Q  +L +L  L D    R +V+VI
Sbjct: 76  LFELAEKAKPGVLFIDEIDSLS-----------RGAQNALLRVLETLNDLRIDRENVRVI 124

Query: 60  MATNRIETLDPALIRPGRIDRKIEFPL 86
            ATNR    D       R+D +I  PL
Sbjct: 125 GATNRPLLGDLDRALYDRLDIRIVIPL 151

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

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

 Score = 55.0 bits (133), Expect = 7e-10
 Identities = 35/128 (27%), Positives = 60/128 (46%), Gaps = 8/128 (6%)

Query: 3   RVAEEHAPSIVFIDEIDAVGTKRYDSN-SGGEREIQRTMLELLNQLDGFDSRGDVKVIMA 61
           R+AE  +P I++IDEID   +       SG    +  T +  L++      +  V V+  
Sbjct: 312 RIAEALSPCILWIDEIDKAFSNSESKGDSGTTNRVLATFITWLSE-----KKSPVFVVAT 366

Query: 62  TNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTS--RMTLAEDVNLQELIMAKD 119
            N I+ L   ++R GR D      LP  + + +IF IH    R    +  ++++L    +
Sbjct: 367 ANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYDIKKLSKLSN 426

Query: 120 DLSGADIK 127
             SGA+I+
Sbjct: 427 KFSGAEIE 434

Length = 489

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

 Score = 47.4 bits (112), Expect = 1e-07
 Identities = 26/88 (29%), Positives = 41/88 (46%), Gaps = 9/88 (10%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
              +A +  P ++ +DEI ++           E+E    +LE L  L    S  ++ VI+
Sbjct: 70  ALALARKLKPDVLILDEITSLLDA--------EQEALLLLLEELRLLLLLKSEKNLTVIL 121

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPD 88
            TN  + L PAL+R  R DR+I   L  
Sbjct: 122 TTNDEKDLGPALLRR-RFDRRIVLLLIL 148

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment. Length = 148

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	131
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	100.0
KOG0730|consensus	693		100.0
KOG0734|consensus	752		100.0
KOG0733|consensus	802		100.0
KOG0733|consensus	802		99.98
KOG0738|consensus	491		99.97
KOG0736|consensus	953		99.97
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	99.97
KOG0735|consensus	952		99.96
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	99.96
KOG0728|consensus	404		99.96
KOG0731|consensus	774		99.96
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.96
KOG0739|consensus	439		99.96
PRK03992	389	proteasome-activating nucleotidase; Provisional	99.96
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.96
KOG0652|consensus	424		99.96
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.96
CHL00195	489	ycf46 Ycf46; Provisional	99.95
KOG0726|consensus	440		99.95
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.95
KOG0727|consensus	408		99.95
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	99.95
KOG0737|consensus	386		99.95
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	99.95
CHL00206	2281	ycf2 Ycf2; Provisional	99.95
CHL00176	638	ftsH cell division protein; Validated	99.94
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	99.94
KOG0740|consensus	428		99.92
KOG0730|consensus	693		99.92
KOG0729|consensus	435		99.91
KOG0732|consensus	1080		99.91
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	99.91
KOG0651|consensus	388		99.9
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.89
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.88
KOG0741|consensus	744		99.86
KOG0735|consensus	952		99.71
KOG0742|consensus	630		99.7
KOG0736|consensus	953		99.69
KOG0743|consensus	457		99.64
PF00004	132	AAA: ATPase family associated with various cellula	99.54
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.47
KOG0744|consensus	423		99.2
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.04
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.01
CHL00181	287	cbbX CbbX; Provisional	98.95
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	98.93
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	98.81
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	98.79
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	98.74
PRK10865	857	protein disaggregation chaperone; Provisional	98.68
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.68
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	98.66
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.65
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	98.6
PRK06893	229	DNA replication initiation factor; Validated	98.53
CHL00095	821	clpC Clp protease ATP binding subunit	98.53
PRK00149	450	dnaA chromosomal replication initiation protein; R	98.52
PRK14088	440	dnaA chromosomal replication initiation protein; P	98.45
PRK08727	233	hypothetical protein; Validated	98.4
PRK14086	617	dnaA chromosomal replication initiation protein; P	98.36
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	98.35
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	98.34
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	98.29
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.24
PRK08084	235	DNA replication initiation factor; Provisional	98.23
PRK14087	450	dnaA chromosomal replication initiation protein; P	98.23
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	98.23
PRK07940	394	DNA polymerase III subunit delta'; Validated	98.23
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	98.22
PRK12422	445	chromosomal replication initiation protein; Provis	98.21
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	98.18
PRK05642	234	DNA replication initiation factor; Validated	98.17
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.17
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	98.13
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	98.12
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.1
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	98.09
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	98.08
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	98.08
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	98.08
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	98.06
PHA02544	316	44 clamp loader, small subunit; Provisional	98.03
PRK00411	394	cdc6 cell division control protein 6; Reviewed	97.99
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.98
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.98
PRK04132	846	replication factor C small subunit; Provisional	97.97
PRK04195	482	replication factor C large subunit; Provisional	97.96
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.92
PRK09087	226	hypothetical protein; Validated	97.92
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	97.9
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.9
PLN03025	319	replication factor C subunit; Provisional	97.89
CHL00195	489	ycf46 Ycf46; Provisional	97.89
PRK06620	214	hypothetical protein; Validated	97.89
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	97.88
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	97.87
COG0593	408	DnaA ATPase involved in DNA replication initiation	97.84
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.83
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.82
PRK09112	351	DNA polymerase III subunit delta'; Validated	97.81
PRK06964	342	DNA polymerase III subunit delta'; Validated	97.8
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	97.8
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	97.79
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	97.78
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	97.78
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	97.78
PRK12402	337	replication factor C small subunit 2; Reviewed	97.77
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	97.76
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	97.75
PRK05707	328	DNA polymerase III subunit delta'; Validated	97.72
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	97.72
PRK13342	413	recombination factor protein RarA; Reviewed	97.71
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	97.7
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	97.67
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	97.66
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	97.6
PRK07471	365	DNA polymerase III subunit delta'; Validated	97.6
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.59
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.59
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	97.59
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.58
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	97.57
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	97.56
COG0714	329	MoxR-like ATPases [General function prediction onl	97.54
COG2256	436	MGS1 ATPase related to the helicase subunit of the	97.53
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	97.51
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.51
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	97.5
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	97.5
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	97.49
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	97.49
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	97.47
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.47
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	97.45
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.44
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	97.44
KOG0989|consensus	346		97.43
PRK08769	319	DNA polymerase III subunit delta'; Validated	97.4
KOG2004|consensus	906		97.4
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	97.36
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	97.36
PRK06090	319	DNA polymerase III subunit delta'; Validated	97.34
PRK06871	325	DNA polymerase III subunit delta'; Validated	97.32
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	97.27
PRK07993	334	DNA polymerase III subunit delta'; Validated	97.26
PRK13341	725	recombination factor protein RarA/unknown domain f	97.23
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	97.23
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	97.19
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.11
PRK08058	329	DNA polymerase III subunit delta'; Validated	97.1
smart00382	148	AAA ATPases associated with a variety of cellular	97.09
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	97.08
PRK05564	313	DNA polymerase III subunit delta'; Validated	97.08
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	97.08
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	97.06
PHA02244	383	ATPase-like protein	97.03
PRK07399	314	DNA polymerase III subunit delta'; Validated	97.01
PRK07276	290	DNA polymerase III subunit delta'; Validated	97.01
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	96.99
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	96.96
PRK06581	263	DNA polymerase III subunit delta'; Validated	96.96
CHL00095	821	clpC Clp protease ATP binding subunit	96.94
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.86
KOG0741|consensus	744		96.82
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	96.79
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	96.79
KOG2035|consensus	351		96.78
PF05729	166	NACHT: NACHT domain	96.74
smart00350	509	MCM minichromosome maintenance proteins.	96.73
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	96.72
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	96.65
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	96.63
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	96.56
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	96.53
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	96.42
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	96.34
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	96.33
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	96.31
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	96.27
PRK08699	325	DNA polymerase III subunit delta'; Validated	96.2
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	96.19
PRK10865	857	protein disaggregation chaperone; Provisional	96.19
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	95.92
PRK07132	299	DNA polymerase III subunit delta'; Validated	95.87
KOG2228|consensus	408		95.8
PF14516	331	AAA_35: AAA-like domain	95.72
KOG2028|consensus	554		95.59
PRK13531	498	regulatory ATPase RavA; Provisional	95.53
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	95.38
PRK05818	261	DNA polymerase III subunit delta'; Validated	95.37
KOG1514|consensus	767		95.35
PF05872	502	DUF853: Bacterial protein of unknown function (DUF	95.24
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	95.2
PRK08485	206	DNA polymerase III subunit delta'; Validated	94.98
PRK09862	506	putative ATP-dependent protease; Provisional	94.85
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	94.8
PRK05917	290	DNA polymerase III subunit delta'; Validated	94.78
PF12846	304	AAA_10: AAA-like domain	94.73
KOG1942|consensus	456		94.49
PF00493	331	MCM: MCM2/3/5 family This family extends the MCM d	94.26
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	94.25
KOG0990|consensus	360		93.99
KOG1968|consensus	871		93.9
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	93.61
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	92.94
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	92.88
PRK14700	300	recombination factor protein RarA; Provisional	92.86
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	92.69
KOG2227|consensus	529		92.58
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	92.38
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	92.28
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	91.62
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	91.14
KOG2170|consensus	344		91.01
PF13304	303	AAA_21: AAA domain; PDB: 3QKS_B 1US8_B 1F2U_B 1F2T	90.88
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	90.78
KOG0745|consensus	564		90.42
KOG2383|consensus	467		90.35
PF05272	198	VirE: Virulence-associated protein E; InterPro: IP	90.26
PHA00012	361	I assembly protein	90.23
PF07726	131	AAA_3: ATPase family associated with various cellu	88.48
PLN03210	1153	Resistant to P. syringae 6; Provisional	87.62
PRK05574	340	holA DNA polymerase III subunit delta; Reviewed	87.59
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	87.46
KOG1051|consensus	898		87.4
PRK08116	268	hypothetical protein; Validated	87.28
KOG1051|consensus	898		87.27
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	87.21
PRK13539	207	cytochrome c biogenesis protein CcmA; Provisional	86.46
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	86.11
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	85.98
PF09820	284	AAA-ATPase_like: Predicted AAA-ATPase; InterPro: I	85.86
COG1241	682	MCM2 Predicted ATPase involved in replication cont	85.68
TIGR02237	209	recomb_radB DNA repair and recombination protein R	85.64
COG1131	293	CcmA ABC-type multidrug transport system, ATPase c	85.34
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	84.76
PRK10365	441	transcriptional regulatory protein ZraR; Provision	84.58
KOG1969|consensus	877		84.49
PRK11608	326	pspF phage shock protein operon transcriptional ac	83.87
PF13173	128	AAA_14: AAA domain	83.81
COG4565	224	CitB Response regulator of citrate/malate metaboli	83.45
COG4555	245	NatA ABC-type Na+ transport system, ATPase compone	83.37
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	83.26
PRK13538	204	cytochrome c biogenesis protein CcmA; Provisional	82.45
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	81.87
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	81.82
TIGR01128	302	holA DNA polymerase III, delta subunit. subunit ar	81.58
KOG2680|consensus	454		81.53
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	80.36
KOG0481|consensus	729		80.21
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	80.2

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

Probab=100.00  E-value=1.1e-37  Score=222.73  Aligned_cols=131  Identities=68%  Similarity=1.106  Sum_probs=127.1

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|+.++||||||||+|++..+|...+.+...+.++++.++|++|||+...++|-||++||+++-+|||++||||||+
T Consensus       236 lF~lArekaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~~~nvKVI~ATNR~D~LDPALLRPGR~DR  315 (406)
T COG1222         236 LFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRGNVKVIMATNRPDILDPALLRPGRFDR  315 (406)
T ss_pred             HHHHHhhcCCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCCCCCCeEEEEecCCccccChhhcCCCcccc
Confidence            59999999999999999999999998888888889999999999999999999999999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .|+||+|+.+.|.+||+.+.+.+.+..++||..+|..|+|+|||||+++|+
T Consensus       316 kIEfplPd~~gR~~Il~IHtrkM~l~~dvd~e~la~~~~g~sGAdlkaict  366 (406)
T COG1222         316 KIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLARLTEGFSGADLKAICT  366 (406)
T ss_pred             eeecCCCCHHHHHHHHHHHhhhccCccCcCHHHHHHhcCCCchHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999984

>KOG0730|consensus

Probab=100.00  E-value=1.7e-35  Score=224.02  Aligned_cols=128  Identities=45%  Similarity=0.735  Sum_probs=120.5

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|++|++.+||||||||+|++...|+..+.   ....++++++|++|||+....+|+|||+||+|+.||+|++||||||+
T Consensus       519 iF~kAR~~aP~IiFfDEiDsi~~~R~g~~~---~v~~RVlsqLLtEmDG~e~~k~V~ViAATNRpd~ID~ALlRPGRlD~  595 (693)
T KOG0730|consen  519 VFRKARQVAPCIIFFDEIDALAGSRGGSSS---GVTDRVLSQLLTEMDGLEALKNVLVIAATNRPDMIDPALLRPGRLDR  595 (693)
T ss_pred             HHHHHhhcCCeEEehhhHHhHhhccCCCcc---chHHHHHHHHHHHcccccccCcEEEEeccCChhhcCHHHcCCcccce
Confidence            599999999999999999999999963333   44568999999999999888999999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .|++|+|+.+.|.+||+.++++.++.+++|+..||+.|+||||+||..+|+
T Consensus       596 iiyVplPD~~aR~~Ilk~~~kkmp~~~~vdl~~La~~T~g~SGAel~~lCq  646 (693)
T KOG0730|consen  596 IIYVPLPDLEARLEILKQCAKKMPFSEDVDLEELAQATEGYSGAEIVAVCQ  646 (693)
T ss_pred             eEeecCccHHHHHHHHHHHHhcCCCCccccHHHHHHHhccCChHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999995

>KOG0734|consensus

Probab=100.00  E-value=1.4e-34  Score=215.44  Aligned_cols=128  Identities=41%  Similarity=0.655  Sum_probs=119.9

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|..|++++||||||||+|++..+|.+ .+ .. ...++++++|.+||++..+.+|+|||+||.|+.+|+++.||||||+
T Consensus       388 LF~aAk~~APcIIFIDEiDavG~kR~~-~~-~~-y~kqTlNQLLvEmDGF~qNeGiIvigATNfpe~LD~AL~RPGRFD~  464 (752)
T KOG0734|consen  388 LFAAAKARAPCIIFIDEIDAVGGKRNP-SD-QH-YAKQTLNQLLVEMDGFKQNEGIIVIGATNFPEALDKALTRPGRFDR  464 (752)
T ss_pred             HHHHHHhcCCeEEEEechhhhcccCCc-cH-HH-HHHHHHHHHHHHhcCcCcCCceEEEeccCChhhhhHHhcCCCccce
Confidence            599999999999999999999998832 22 22 7789999999999999999999999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      +|.+|.||...|.+||++|+++.....++|+.-+|.-|.||+|+||+.|+|
T Consensus       465 ~v~Vp~PDv~GR~eIL~~yl~ki~~~~~VD~~iiARGT~GFsGAdLaNlVN  515 (752)
T KOG0734|consen  465 HVTVPLPDVRGRTEILKLYLSKIPLDEDVDPKIIARGTPGFSGADLANLVN  515 (752)
T ss_pred             eEecCCCCcccHHHHHHHHHhcCCcccCCCHhHhccCCCCCchHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999985

>KOG0733|consensus

Probab=100.00  E-value=4.1e-34  Score=215.29  Aligned_cols=128  Identities=37%  Similarity=0.639  Sum_probs=118.3

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|++||.++||||||||+|+|++.|+...   .....++++++|.+|||+....+|+|||+||+|+-||||++||||||+
T Consensus       596 vFqRAR~saPCVIFFDEiDaL~p~R~~~~---s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDpAiLRPGRlDk  672 (802)
T KOG0733|consen  596 VFQRARASAPCVIFFDEIDALVPRRSDEG---SSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDPAILRPGRLDK  672 (802)
T ss_pred             HHHHhhcCCCeEEEecchhhcCcccCCCC---chhHHHHHHHHHHHhcccccccceEEEeecCCCcccchhhcCCCccCc
Confidence            69999999999999999999999996544   334568999999999999888999999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhc--CCCCCCcccHHHHHHHcC--CCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTS--RMTLAEDVNLQELIMAKD--DLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~--~~~~~~~~~~~~la~~t~--g~s~~di~~l~~  131 (131)
                      .+++++|+.++|.+||+..++  +.++..++|++++|..+.  ||||+||..||+
T Consensus       673 ~LyV~lPn~~eR~~ILK~~tkn~k~pl~~dVdl~eia~~~~c~gftGADLaaLvr  727 (802)
T KOG0733|consen  673 LLYVGLPNAEERVAILKTITKNTKPPLSSDVDLDEIARNTKCEGFTGADLAALVR  727 (802)
T ss_pred             eeeecCCCHHHHHHHHHHHhccCCCCCCcccCHHHHhhcccccCCchhhHHHHHH
Confidence            999999999999999999999  667779999999999976  999999999984

>KOG0733|consensus

Probab=99.98  E-value=2.9e-32  Score=205.40  Aligned_cols=128  Identities=40%  Similarity=0.638  Sum_probs=116.9

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCC----CCeEEEeeCCCCCcccccccCCC
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSR----GDVKVIMATNRIETLDPALIRPG   76 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----~~v~vi~ttn~~~~id~~l~~~g   76 (131)
                      +|+.|+.++|||+||||+|++.++|...+...+   .+++.++++.||++...    .+|+|||+||+|+++|++++|+|
T Consensus       274 lF~~A~~~aPcivFiDeIDAI~pkRe~aqreME---rRiVaQLlt~mD~l~~~~~~g~~VlVIgATnRPDslDpaLRRaG  350 (802)
T KOG0733|consen  274 LFDQAKSNAPCIVFIDEIDAITPKREEAQREME---RRIVAQLLTSMDELSNEKTKGDPVLVIGATNRPDSLDPALRRAG  350 (802)
T ss_pred             HHHHHhccCCeEEEeecccccccchhhHHHHHH---HHHHHHHHHhhhcccccccCCCCeEEEecCCCCcccCHHHhccc
Confidence            699999999999999999999999966555444   46777888888887554    57999999999999999999999


Q ss_pred             ccceEEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           77 RIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        77 rf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      |||+.|.++.|++.+|.+||+..+++..+..++|+..||..|.||.|+||.+||.
T Consensus       351 RFdrEI~l~vP~e~aR~~IL~~~~~~lrl~g~~d~~qlA~lTPGfVGADL~AL~~  405 (802)
T KOG0733|consen  351 RFDREICLGVPSETAREEILRIICRGLRLSGDFDFKQLAKLTPGFVGADLMALCR  405 (802)
T ss_pred             cccceeeecCCchHHHHHHHHHHHhhCCCCCCcCHHHHHhcCCCccchhHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999983

>KOG0738|consensus

Probab=99.97  E-value=3.4e-32  Score=196.39  Aligned_cols=127  Identities=38%  Similarity=0.584  Sum_probs=117.1

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCC-CC---eEEEeeCCCCCcccccccCCC
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSR-GD---VKVIMATNRIETLDPALIRPG   76 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~---v~vi~ttn~~~~id~~l~~~g   76 (131)
                      +|+.|+.++|++|||||||+|+..|++.  ..+....++.+++|.+||++... ..   |+|+|+||.||.||++++|  
T Consensus       296 LFemARfyAPStIFiDEIDslcs~RG~s--~EHEaSRRvKsELLvQmDG~~~t~e~~k~VmVLAATN~PWdiDEAlrR--  371 (491)
T KOG0738|consen  296 LFEMARFYAPSTIFIDEIDSLCSQRGGS--SEHEASRRVKSELLVQMDGVQGTLENSKVVMVLAATNFPWDIDEALRR--  371 (491)
T ss_pred             HHHHHHHhCCceeehhhHHHHHhcCCCc--cchhHHHHHHHHHHHHhhccccccccceeEEEEeccCCCcchHHHHHH--
Confidence            5999999999999999999999999543  44555678999999999998665 33   9999999999999999999  


Q ss_pred             ccceEEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           77 RIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        77 rf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      ||+++|++|+|+.+.|..+++..++.....+++++..+++.++||||+||..+|+
T Consensus       372 RlEKRIyIPLP~~~~R~~Li~~~l~~~~~~~~~~~~~lae~~eGySGaDI~nvCr  426 (491)
T KOG0738|consen  372 RLEKRIYIPLPDAEARSALIKILLRSVELDDPVNLEDLAERSEGYSGADITNVCR  426 (491)
T ss_pred             HHhhheeeeCCCHHHHHHHHHHhhccccCCCCccHHHHHHHhcCCChHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999985

>KOG0736|consensus

Probab=99.97  E-value=4.7e-31  Score=202.67  Aligned_cols=130  Identities=38%  Similarity=0.643  Sum_probs=119.9

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCC--CCCeEEEeeCCCCCcccccccCCCcc
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDS--RGDVKVIMATNRIETLDPALIRPGRI   78 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~v~vi~ttn~~~~id~~l~~~grf   78 (131)
                      ||++||..+|||||+||+|++.++|+..++... -+.++++++|.++|++..  ..+|+|||+||+|+.|||+++|||||
T Consensus       756 VFerAR~A~PCVIFFDELDSlAP~RG~sGDSGG-VMDRVVSQLLAELDgls~~~s~~VFViGATNRPDLLDpALLRPGRF  834 (953)
T KOG0736|consen  756 VFERARSAAPCVIFFDELDSLAPNRGRSGDSGG-VMDRVVSQLLAELDGLSDSSSQDVFVIGATNRPDLLDPALLRPGRF  834 (953)
T ss_pred             HHHHhhccCCeEEEeccccccCccCCCCCCccc-cHHHHHHHHHHHhhcccCCCCCceEEEecCCCccccChhhcCCCcc
Confidence            699999999999999999999999976655443 467899999999999985  46899999999999999999999999


Q ss_pred             ceEEEeCCC-CHHHHHHHHHHHhcCCCCCCcccHHHHHHHc-CCCCHHHHHHhhC
Q psy522           79 DRKIEFPLP-DEKTKRRIFNIHTSRMTLAEDVNLQELIMAK-DDLSGADIKAICT  131 (131)
Q Consensus        79 ~~~i~~~~P-~~~~R~~il~~~l~~~~~~~~~~~~~la~~t-~g~s~~di~~l~~  131 (131)
                      |+.++++++ +.+.+..+++...+++.+++++|+.++|+.+ ..|||||+.+||.
T Consensus       835 DKLvyvG~~~d~esk~~vL~AlTrkFkLdedVdL~eiAk~cp~~~TGADlYsLCS  889 (953)
T KOG0736|consen  835 DKLVYVGPNEDAESKLRVLEALTRKFKLDEDVDLVEIAKKCPPNMTGADLYSLCS  889 (953)
T ss_pred             ceeEEecCCccHHHHHHHHHHHHHHccCCCCcCHHHHHhhCCcCCchhHHHHHHH
Confidence            999999998 8999999999999999999999999999997 6899999999983

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

Probab=99.97  E-value=9.8e-30  Score=188.33  Aligned_cols=131  Identities=60%  Similarity=1.046  Sum_probs=119.5

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|..|+.++|+||||||+|.++.++..............+.+++..++++....+++||+|||+++.+|++++||||||+
T Consensus       230 lf~~A~~~~P~ILfIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~~ld~~~~~~~v~VI~aTN~~d~LDpAllR~GRfd~  309 (398)
T PTZ00454        230 VFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDR  309 (398)
T ss_pred             HHHHHHhcCCeEEEEECHhhhccccccccCCccHHHHHHHHHHHHHhhccCCCCCEEEEEecCCchhCCHHHcCCCcccE
Confidence            48899999999999999999998875554444555677889999999998777889999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .|++++|+.++|..||+.++.+.++..++++..++..|+||||+||+++|+
T Consensus       310 ~I~~~~P~~~~R~~Il~~~~~~~~l~~dvd~~~la~~t~g~sgaDI~~l~~  360 (398)
T PTZ00454        310 KIEFPLPDRRQKRLIFQTITSKMNLSEEVDLEDFVSRPEKISAADIAAICQ  360 (398)
T ss_pred             EEEeCCcCHHHHHHHHHHHHhcCCCCcccCHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999999999999988888999999999999999999999984

>KOG0735|consensus

Probab=99.96  E-value=1.5e-29  Score=193.32  Aligned_cols=127  Identities=35%  Similarity=0.644  Sum_probs=118.2

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|++|+..+|||+|+||+|++.++|+..+.+..   .++++++|++|||...-++|+++|+|.+|+.||||++||||+|+
T Consensus       752 lF~rA~~a~PCiLFFDEfdSiAPkRGhDsTGVT---DRVVNQlLTelDG~Egl~GV~i~aaTsRpdliDpALLRpGRlD~  828 (952)
T KOG0735|consen  752 LFERAQSAKPCILFFDEFDSIAPKRGHDSTGVT---DRVVNQLLTELDGAEGLDGVYILAATSRPDLIDPALLRPGRLDK  828 (952)
T ss_pred             HHHHhhccCCeEEEeccccccCcccCCCCCCch---HHHHHHHHHhhccccccceEEEEEecCCccccCHhhcCCCccce
Confidence            599999999999999999999999966555443   46899999999998887999999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhh
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAIC  130 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~  130 (131)
                      .++.+.|++.+|.+|++.+........+.|+..+|..|+||||+||..|+
T Consensus       829 ~v~C~~P~~~eRl~il~~ls~s~~~~~~vdl~~~a~~T~g~tgADlq~ll  878 (952)
T KOG0735|consen  829 LVYCPLPDEPERLEILQVLSNSLLKDTDVDLECLAQKTDGFTGADLQSLL  878 (952)
T ss_pred             eeeCCCCCcHHHHHHHHHHhhccCCccccchHHHhhhcCCCchhhHHHHH
Confidence            99999999999999999999988888999999999999999999999876

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

Probab=99.96  E-value=1.9e-29  Score=192.06  Aligned_cols=131  Identities=46%  Similarity=0.744  Sum_probs=121.3

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|++|++++||||||||+|++...|+..........-++++++|.+||++..+.+|+++++||+|+-+|++++||||||+
T Consensus       234 LF~qAkk~aP~IIFIDEiDAvGr~Rg~g~GggnderEQTLNQlLvEmDGF~~~~gviviaaTNRpdVlD~ALlRpgRFDR  313 (596)
T COG0465         234 LFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGGNEGVIVIAATNRPDVLDPALLRPGRFDR  313 (596)
T ss_pred             HHHHhhccCCCeEEEehhhhcccccCCCCCCCchHHHHHHHHHHhhhccCCCCCceEEEecCCCcccchHhhcCCCCcce
Confidence            59999999999999999999999986554444445568999999999999888899999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      +|.++.|+...|.+|++-+.++.++.+++|+..+|..|.||+++|++.+++
T Consensus       314 qI~V~~PDi~gRe~IlkvH~~~~~l~~~Vdl~~iAr~tpGfsGAdL~nl~N  364 (596)
T COG0465         314 QILVELPDIKGREQILKVHAKNKPLAEDVDLKKIARGTPGFSGADLANLLN  364 (596)
T ss_pred             eeecCCcchhhHHHHHHHHhhcCCCCCcCCHHHHhhhCCCcccchHhhhHH
Confidence            999999999999999999999999999999999999999999999999874

>KOG0728|consensus

Probab=99.96  E-value=3.4e-29  Score=173.17  Aligned_cols=131  Identities=58%  Similarity=1.004  Sum_probs=125.3

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|-.|++++|||||.||+|++...|.+.+.+..++..+++.++++++|++....++-||.+||+.+-+|++++||||+|+
T Consensus       232 lfvmarehapsiifmdeidsigs~r~e~~~ggdsevqrtmlellnqldgfeatknikvimatnridild~allrpgridr  311 (404)
T KOG0728|consen  232 LFVMAREHAPSIIFMDEIDSIGSSRVESGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDILDPALLRPGRIDR  311 (404)
T ss_pred             HHHHHHhcCCceEeeecccccccccccCCCCccHHHHHHHHHHHHhccccccccceEEEEeccccccccHhhcCCCcccc
Confidence            48899999999999999999999998877777888899999999999999999999999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .|+||+|+.+.|.+|++.+.+..++...+++..+|+...|.||++++.+|+
T Consensus       312 kiefp~p~e~ar~~ilkihsrkmnl~rgi~l~kiaekm~gasgaevk~vct  362 (404)
T KOG0728|consen  312 KIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAEKMPGASGAEVKGVCT  362 (404)
T ss_pred             cccCCCCCHHHHHHHHHHhhhhhchhcccCHHHHHHhCCCCccchhhhhhh
Confidence            999999999999999999999999999999999999999999999999884

>KOG0731|consensus

Probab=99.96  E-value=8.8e-29  Score=191.63  Aligned_cols=131  Identities=47%  Similarity=0.802  Sum_probs=119.0

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCC-CCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccc
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYD-SNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRID   79 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~   79 (131)
                      +|..||.++|||||+||+|++...|+. .....+.+-.+.++++|.+||+...+..|+|+++||+++-+|++++||||||
T Consensus       395 lf~~ar~~aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~~~~~vi~~a~tnr~d~ld~allrpGRfd  474 (774)
T KOG0731|consen  395 LFPLARKNAPSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGFETSKGVIVLAATNRPDILDPALLRPGRFD  474 (774)
T ss_pred             HHHHhhccCCeEEEecccccccccccccccCCCChHHHHHHHHHHHHhcCCcCCCcEEEEeccCCccccCHHhcCCCccc
Confidence            599999999999999999999999842 2223334455899999999999988888999999999999999999999999


Q ss_pred             eEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           80 RKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        80 ~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      ++|+++.|+..+|..|++.+++..+.. +++++..+|..|.||+|+||..+|+
T Consensus       475 r~i~i~~p~~~~r~~i~~~h~~~~~~~~e~~dl~~~a~~t~gf~gadl~n~~n  527 (774)
T KOG0731|consen  475 RQIQIDLPDVKGRASILKVHLRKKKLDDEDVDLSKLASLTPGFSGADLANLCN  527 (774)
T ss_pred             cceeccCCchhhhHHHHHHHhhccCCCcchhhHHHHHhcCCCCcHHHHHhhhh
Confidence            999999999999999999999999886 7788999999999999999999986

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.96  E-value=1.8e-28  Score=193.62  Aligned_cols=129  Identities=47%  Similarity=0.772  Sum_probs=116.9

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|+..+||||||||+|.+++.++.....  .....++++++..++++...++++||+|||+|+.||++++||||||+
T Consensus       538 ~f~~A~~~~p~iifiDEid~l~~~r~~~~~~--~~~~~~~~~lL~~ldg~~~~~~v~vI~aTn~~~~ld~allRpgRfd~  615 (733)
T TIGR01243       538 IFRKARQAAPAIIFFDEIDAIAPARGARFDT--SVTDRIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDR  615 (733)
T ss_pred             HHHHHHhcCCEEEEEEChhhhhccCCCCCCc--cHHHHHHHHHHHHhhcccCCCCEEEEEeCCChhhCCHhhcCCCccce
Confidence            5899999999999999999999888543222  23457888999999999888899999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .+++++|+.++|.+||+.++++.+...++++..+|..|+||||+||+.+|+
T Consensus       616 ~i~v~~Pd~~~R~~i~~~~~~~~~~~~~~~l~~la~~t~g~sgadi~~~~~  666 (733)
T TIGR01243       616 LILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCR  666 (733)
T ss_pred             EEEeCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999999999999988888899999999999999999999874

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.

>KOG0739|consensus

Probab=99.96  E-value=9.7e-30  Score=179.08  Aligned_cols=125  Identities=34%  Similarity=0.569  Sum_probs=110.8

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCC-CCeEEEeeCCCCCcccccccCCCccc
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSR-GDVKVIMATNRIETLDPALIRPGRID   79 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~v~vi~ttn~~~~id~~l~~~grf~   79 (131)
                      +|+.||+++||||||||+|.++..++++.+.   ...++..+||.+|.++-.. ++|+|+|+||-||.+|.+++|  ||+
T Consensus       217 LFemARe~kPSIIFiDEiDslcg~r~enEse---asRRIKTEfLVQMqGVG~d~~gvLVLgATNiPw~LDsAIRR--RFe  291 (439)
T KOG0739|consen  217 LFEMARENKPSIIFIDEIDSLCGSRSENESE---ASRRIKTEFLVQMQGVGNDNDGVLVLGATNIPWVLDSAIRR--RFE  291 (439)
T ss_pred             HHHHHHhcCCcEEEeehhhhhccCCCCCchH---HHHHHHHHHHHhhhccccCCCceEEEecCCCchhHHHHHHH--Hhh
Confidence            5999999999999999999999988554333   3467889999999998665 689999999999999999999  999


Q ss_pred             eEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHhh
Q psy522           80 RKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAIC  130 (131)
Q Consensus        80 ~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l~  130 (131)
                      ++|++|+|+...|..||+.++...+.. .+.|+.+|+..|+||||+||.-++
T Consensus       292 kRIYIPLPe~~AR~~MF~lhlG~tp~~LT~~d~~eL~~kTeGySGsDisivV  343 (439)
T KOG0739|consen  292 KRIYIPLPEAHARARMFKLHLGDTPHVLTEQDFKELARKTEGYSGSDISIVV  343 (439)
T ss_pred             cceeccCCcHHHhhhhheeccCCCccccchhhHHHHHhhcCCCCcCceEEEe
Confidence            999999999999999999998876654 567899999999999999987554

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=99.96  E-value=3.8e-28  Score=179.97  Aligned_cols=131  Identities=60%  Similarity=1.018  Sum_probs=118.6

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|+.++|+||||||+|.++.++..............+..++..++++...+++.||+|||.++.+|++++|||||+.
T Consensus       216 ~f~~a~~~~p~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~~~~~~~v~VI~aTn~~~~ld~allRpgRfd~  295 (389)
T PRK03992        216 LFELAREKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDR  295 (389)
T ss_pred             HHHHHHhcCCeEEEEechhhhhcccccCCCCccHHHHHHHHHHHHhccccCCCCCEEEEEecCChhhCCHHHcCCccCce
Confidence            48889999999999999999998876554444455667888899999988777899999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .|++++|+.++|.+||+.++++..+..+.++..++..|+||+|+||+.+|+
T Consensus       296 ~I~v~~P~~~~R~~Il~~~~~~~~~~~~~~~~~la~~t~g~sgadl~~l~~  346 (389)
T PRK03992        296 IIEVPLPDEEGRLEILKIHTRKMNLADDVDLEELAELTEGASGADLKAICT  346 (389)
T ss_pred             EEEECCCCHHHHHHHHHHHhccCCCCCcCCHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999999999999988888899999999999999999999984

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.96  E-value=2.7e-28  Score=185.59  Aligned_cols=131  Identities=44%  Similarity=0.723  Sum_probs=117.4

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|+.++|+||||||+|.++.+++.............++.++..++++...++++||+|||.++.+|++++||||||+
T Consensus       139 ~f~~a~~~~p~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~~~~v~vI~aTn~~~~ld~al~r~gRfd~  218 (495)
T TIGR01241       139 LFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAATNRPDVLDPALLRPGRFDR  218 (495)
T ss_pred             HHHHHHhcCCCEEEEechhhhhhccccCcCCccHHHHHHHHHHHhhhccccCCCCeEEEEecCChhhcCHHHhcCCcceE
Confidence            48899999999999999999998875433333344557888999999999888899999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .|+++.|+.++|.+|++.+++......+.++..++..|.|||++||+.+|+
T Consensus       219 ~i~i~~Pd~~~R~~il~~~l~~~~~~~~~~l~~la~~t~G~sgadl~~l~~  269 (495)
T TIGR01241       219 QVVVDLPDIKGREEILKVHAKNKKLAPDVDLKAVARRTPGFSGADLANLLN  269 (495)
T ss_pred             EEEcCCCCHHHHHHHHHHHHhcCCCCcchhHHHHHHhCCCCCHHHHHHHHH
Confidence            999999999999999999999887777889999999999999999999874

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.

>KOG0652|consensus

Probab=99.96  E-value=2e-28  Score=170.16  Aligned_cols=129  Identities=60%  Similarity=1.045  Sum_probs=123.1

Q ss_pred             HHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceE
Q psy522            2 FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRK   81 (131)
Q Consensus         2 F~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~   81 (131)
                      |..|+..+|+||||||+|++..+|-...........+.+.++++++|++++...|-||++||+.+-+||+++|.||+|+.
T Consensus       257 FaLAKEkaP~IIFIDElDAIGtKRfDSek~GDREVQRTMLELLNQLDGFss~~~vKviAATNRvDiLDPALlRSGRLDRK  336 (424)
T KOG0652|consen  257 FALAKEKAPTIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSSDDRVKVIAATNRVDILDPALLRSGRLDRK  336 (424)
T ss_pred             HHHhhccCCeEEEEechhhhccccccccccccHHHHHHHHHHHHhhcCCCCccceEEEeecccccccCHHHhhccccccc
Confidence            88999999999999999999999976666777788899999999999999999999999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhh
Q psy522           82 IEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAIC  130 (131)
Q Consensus        82 i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~  130 (131)
                      |+||.|+.+.|..|++.+.++....+++++.++|..|++|.|++.+++|
T Consensus       337 IEfP~Pne~aRarIlQIHsRKMnv~~DvNfeELaRsTddFNGAQcKAVc  385 (424)
T KOG0652|consen  337 IEFPHPNEEARARILQIHSRKMNVSDDVNFEELARSTDDFNGAQCKAVC  385 (424)
T ss_pred             ccCCCCChHHHHHHHHHhhhhcCCCCCCCHHHHhhcccccCchhheeee
Confidence            9999999999999999999999999999999999999999999998876

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.96  E-value=3.7e-28  Score=189.30  Aligned_cols=131  Identities=40%  Similarity=0.715  Sum_probs=118.8

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|+..+||||||||+|.++..++...........+.++.++..++++....+++||+|||+|+.+|++++||||||+
T Consensus       236 ~f~~a~~~~P~IifIDEiD~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~~~~~vivIaaTN~p~~lD~Al~RpgRfdr  315 (644)
T PRK10733        236 MFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDR  315 (644)
T ss_pred             HHHHHHhcCCcEEEehhHhhhhhccCCCCCCCchHHHHHHHHHHHhhhcccCCCCeeEEEecCChhhcCHHHhCCcccce
Confidence            47889999999999999999998876543334444567889999999999888899999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .++++.|+.++|.+||+.+++..++..+.++..++..|.|||++||..+|+
T Consensus       316 ~i~v~~Pd~~~R~~Il~~~~~~~~l~~~~d~~~la~~t~G~sgadl~~l~~  366 (644)
T PRK10733        316 QVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVN  366 (644)
T ss_pred             EEEcCCCCHHHHHHHHHHHhhcCCCCCcCCHHHHHhhCCCCCHHHHHHHHH
Confidence            999999999999999999999998888899999999999999999999984

>CHL00195 ycf46 Ycf46; Provisional

Probab=99.95  E-value=5.1e-28  Score=182.78  Aligned_cols=127  Identities=25%  Similarity=0.452  Sum_probs=108.1

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|+.++||||||||+|.++..+...++  .....+++..++..++.  .+.+++||+|||+++.+|++++|+||||+
T Consensus       310 ~f~~A~~~~P~IL~IDEID~~~~~~~~~~d--~~~~~rvl~~lL~~l~~--~~~~V~vIaTTN~~~~Ld~allR~GRFD~  385 (489)
T CHL00195        310 MIRIAEALSPCILWIDEIDKAFSNSESKGD--SGTTNRVLATFITWLSE--KKSPVFVVATANNIDLLPLEILRKGRFDE  385 (489)
T ss_pred             HHHHHHhcCCcEEEehhhhhhhccccCCCC--chHHHHHHHHHHHHHhc--CCCceEEEEecCChhhCCHHHhCCCcCCe
Confidence            488899999999999999999876533222  22345677788877774  45689999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCC--CcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLA--EDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~--~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .++++.|+.++|.+||+.++.+....  .+.++..+|..|+||||+||+++|+
T Consensus       386 ~i~v~lP~~~eR~~Il~~~l~~~~~~~~~~~dl~~La~~T~GfSGAdI~~lv~  438 (489)
T CHL00195        386 IFFLDLPSLEEREKIFKIHLQKFRPKSWKKYDIKKLSKLSNKFSGAEIEQSII  438 (489)
T ss_pred             EEEeCCcCHHHHHHHHHHHHhhcCCCcccccCHHHHHhhcCCCCHHHHHHHHH
Confidence            99999999999999999999886543  4788999999999999999999873

>KOG0726|consensus

Probab=99.95  E-value=6.9e-29  Score=174.42  Aligned_cols=131  Identities=95%  Similarity=1.380  Sum_probs=125.8

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|..++|||+||||+|++..+|-..++..+.+..+.+.++|+++|++.+.+.|-||.+||..+++||++.||||+|+
T Consensus       270 lF~vA~e~apSIvFiDEIdAiGtKRyds~SggerEiQrtmLELLNQldGFdsrgDvKvimATnrie~LDPaLiRPGrIDr  349 (440)
T KOG0726|consen  270 LFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR  349 (440)
T ss_pred             HHHHHHhcCCceEEeehhhhhccccccCCCccHHHHHHHHHHHHHhccCccccCCeEEEEecccccccCHhhcCCCcccc
Confidence            59999999999999999999999998888888888999999999999999999999999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .|.|+.|+...++.||..+..+..+..++++.++...-+-+||+||+++|.
T Consensus       350 KIef~~pDe~TkkkIf~IHTs~Mtl~~dVnle~li~~kddlSGAdIkAict  400 (440)
T KOG0726|consen  350 KIEFPLPDEKTKKKIFQIHTSRMTLAEDVNLEELIMTKDDLSGADIKAICT  400 (440)
T ss_pred             ccccCCCchhhhceeEEEeecccchhccccHHHHhhcccccccccHHHHHH
Confidence            999999999999999999999999999999999999999999999999984

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

Probab=99.95  E-value=6.5e-28  Score=183.52  Aligned_cols=128  Identities=48%  Similarity=0.727  Sum_probs=115.7

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|++.+||||||||+|++++.++.......   ..++.+++..++++....+|+||++||.|+.+|++++||||||.
T Consensus       327 ~F~~A~~~~p~iiFiDEiDs~~~~r~~~~~~~~---~r~~~~lL~~~d~~e~~~~v~vi~aTN~p~~ld~a~lR~gRfd~  403 (494)
T COG0464         327 LFEKARKLAPSIIFIDEIDSLASGRGPSEDGSG---RRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDR  403 (494)
T ss_pred             HHHHHHcCCCcEEEEEchhhhhccCCCCCchHH---HHHHHHHHHHhcCCCccCceEEEecCCCccccCHhhcccCccce
Confidence            599999999999999999999999854433332   57899999999999999999999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCC--CCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTL--AEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~--~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .+++++|+.++|.+||+.++.+...  ..++++..++..|+||+++||+.+|+
T Consensus       404 ~i~v~~pd~~~r~~i~~~~~~~~~~~~~~~~~~~~l~~~t~~~sgadi~~i~~  456 (494)
T COG0464         404 LIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALVR  456 (494)
T ss_pred             EeecCCCCHHHHHHHHHHHhcccCCcchhhhhHHHHHHHhcCCCHHHHHHHHH
Confidence            9999999999999999999996554  47899999999999999999999874

>KOG0727|consensus

Probab=99.95  E-value=4.3e-28  Score=167.90  Aligned_cols=131  Identities=62%  Similarity=1.077  Sum_probs=125.4

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|..|++++|+||||||+|++..+|=..+.+...+..+++.+++++||++...-+|-||.+||+.+.+||+++||||+|+
T Consensus       240 vfrlakenapsiifideidaiatkrfdaqtgadrevqril~ellnqmdgfdq~~nvkvimatnradtldpallrpgrldr  319 (408)
T KOG0727|consen  240 VFRLAKENAPSIIFIDEIDAIATKRFDAQTGADREVQRILIELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDR  319 (408)
T ss_pred             HHHHHhccCCcEEEeehhhhHhhhhccccccccHHHHHHHHHHHHhccCcCcccceEEEEecCcccccCHhhcCCccccc
Confidence            59999999999999999999999997777777888899999999999999988999999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .|+||.|++.+++-+|.....++.+.+++|+.++..+.+..|++||.++|+
T Consensus       320 kiefplpdrrqkrlvf~titskm~ls~~vdle~~v~rpdkis~adi~aicq  370 (408)
T KOG0727|consen  320 KIEFPLPDRRQKRLVFSTITSKMNLSDEVDLEDLVARPDKISGADINAICQ  370 (408)
T ss_pred             cccCCCCchhhhhhhHHhhhhcccCCcccCHHHHhcCccccchhhHHHHHH
Confidence            999999999999999999999999999999999999999999999999985

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

Probab=99.95  E-value=1.3e-27  Score=178.33  Aligned_cols=131  Identities=90%  Similarity=1.328  Sum_probs=118.9

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|..|+.++|+||||||+|.++.++..............+.+++..++++....++.||+|||+++.+|++++||||||.
T Consensus       268 lF~~A~~~~P~ILfIDEID~l~~kR~~~~sgg~~e~qr~ll~LL~~Ldg~~~~~~V~VI~ATNr~d~LDpaLlRpGRfd~  347 (438)
T PTZ00361        268 LFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDR  347 (438)
T ss_pred             HHHHHHhCCCcEEeHHHHHHHhccCCCCCCcccHHHHHHHHHHHHHHhhhcccCCeEEEEecCChHHhhHHhccCCeeEE
Confidence            48889999999999999999998876554555555667888999999998777889999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .|+|+.|+.++|.+||+.++.+..+..++++..++..++|||++||+.+|+
T Consensus       348 ~I~~~~Pd~~~R~~Il~~~~~k~~l~~dvdl~~la~~t~g~sgAdI~~i~~  398 (438)
T PTZ00361        348 KIEFPNPDEKTKRRIFEIHTSKMTLAEDVDLEEFIMAKDELSGADIKAICT  398 (438)
T ss_pred             EEEeCCCCHHHHHHHHHHHHhcCCCCcCcCHHHHHHhcCCCCHHHHHHHHH
Confidence            999999999999999999999988888899999999999999999999984

>KOG0737|consensus

Probab=99.95  E-value=8.5e-28  Score=172.61  Aligned_cols=126  Identities=35%  Similarity=0.591  Sum_probs=116.5

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCC--eEEEeeCCCCCcccccccCCCcc
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGD--VKVIMATNRIETLDPALIRPGRI   78 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--v~vi~ttn~~~~id~~l~~~grf   78 (131)
                      +|..|.+.+||||||||+|.++..|   +...+.....+.++|...+||+.++++  |+|+|+||+|..+|.+++|  |+
T Consensus       178 vFslAsKl~P~iIFIDEvds~L~~R---~s~dHEa~a~mK~eFM~~WDGl~s~~~~rVlVlgATNRP~DlDeAiiR--R~  252 (386)
T KOG0737|consen  178 VFSLASKLQPSIIFIDEVDSFLGQR---RSTDHEATAMMKNEFMALWDGLSSKDSERVLVLGATNRPFDLDEAIIR--RL  252 (386)
T ss_pred             HHhhhhhcCcceeehhhHHHHHhhc---ccchHHHHHHHHHHHHHHhccccCCCCceEEEEeCCCCCccHHHHHHH--hC
Confidence            5889999999999999999999888   244455666788899999999988865  9999999999999999999  99


Q ss_pred             ceEEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           79 DRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        79 ~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .+.++++.|+.++|.+|++-+++..++.+++|++++|..|+||||+||+.+|+
T Consensus       253 p~rf~V~lP~~~qR~kILkviLk~e~~e~~vD~~~iA~~t~GySGSDLkelC~  305 (386)
T KOG0737|consen  253 PRRFHVGLPDAEQRRKILKVILKKEKLEDDVDLDEIAQMTEGYSGSDLKELCR  305 (386)
T ss_pred             cceeeeCCCchhhHHHHHHHHhcccccCcccCHHHHHHhcCCCcHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999984

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

Probab=99.95  E-value=8.3e-28  Score=166.61  Aligned_cols=124  Identities=36%  Similarity=0.582  Sum_probs=113.4

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|++|++.+|||+||||+|++.-.|.-.+-  ......+++.+|+.||++.++.+|+.|++||.|+.+|+++++  ||+.
T Consensus       202 ly~rA~~~aPcivFiDE~DAiaLdRryQel--RGDVsEiVNALLTelDgi~eneGVvtIaaTN~p~~LD~aiRs--RFEe  277 (368)
T COG1223         202 LYERARKAAPCIVFIDELDAIALDRRYQEL--RGDVSEIVNALLTELDGIKENEGVVTIAATNRPELLDPAIRS--RFEE  277 (368)
T ss_pred             HHHHHHhcCCeEEEehhhhhhhhhhhHHHh--cccHHHHHHHHHHhccCcccCCceEEEeecCChhhcCHHHHh--hhhh
Confidence            488999999999999999999988743222  234668999999999999988999999999999999999999  9999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHH
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKA  128 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~  128 (131)
                      .|+|.+|+.++|.+|+++|.+.+++.-+.++..++..|.|+|++||+.
T Consensus       278 EIEF~LP~~eEr~~ile~y~k~~Plpv~~~~~~~~~~t~g~SgRdike  325 (368)
T COG1223         278 EIEFKLPNDEERLEILEYYAKKFPLPVDADLRYLAAKTKGMSGRDIKE  325 (368)
T ss_pred             eeeeeCCChHHHHHHHHHHHHhCCCccccCHHHHHHHhCCCCchhHHH
Confidence            999999999999999999999999998889999999999999999975

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.95  E-value=2.7e-27  Score=194.96  Aligned_cols=122  Identities=20%  Similarity=0.271  Sum_probs=102.4

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCC---CCCCeEEEeeCCCCCcccccccCCCc
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFD---SRGDVKVIMATNRIETLDPALIRPGR   77 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~~v~vi~ttn~~~~id~~l~~~gr   77 (131)
                      +|+.|++++||||||||+|++..+..     .    ...+..+++.|++..   ...+|+||||||+|+.||||++||||
T Consensus      1724 lFelARk~SPCIIFIDEIDaL~~~ds-----~----~ltL~qLLneLDg~~~~~s~~~VIVIAATNRPD~LDPALLRPGR 1794 (2281)
T CHL00206       1724 QFELAKAMSPCIIWIPNIHDLNVNES-----N----YLSLGLLVNSLSRDCERCSTRNILVIASTHIPQKVDPALIAPNK 1794 (2281)
T ss_pred             HHHHHHHCCCeEEEEEchhhcCCCcc-----c----eehHHHHHHHhccccccCCCCCEEEEEeCCCcccCCHhHcCCCC
Confidence            49999999999999999999986521     0    124677788888753   34689999999999999999999999


Q ss_pred             cceEEEeCCCCHHHHHHHHHHHh--cCCCCCCc-ccHHHHHHHcCCCCHHHHHHhhC
Q psy522           78 IDRKIEFPLPDEKTKRRIFNIHT--SRMTLAED-VNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        78 f~~~i~~~~P~~~~R~~il~~~l--~~~~~~~~-~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      ||+.|+++.|+..+|++++..++  ++.....+ .++..+|..|.|||||||+.||+
T Consensus      1795 FDR~I~Ir~Pd~p~R~kiL~ILl~tkg~~L~~~~vdl~~LA~~T~GfSGADLanLvN 1851 (2281)
T CHL00206       1795 LNTCIKIRRLLIPQQRKHFFTLSYTRGFHLEKKMFHTNGFGSITMGSNARDLVALTN 1851 (2281)
T ss_pred             CCeEEEeCCCCchhHHHHHHHHHhhcCCCCCcccccHHHHHHhCCCCCHHHHHHHHH
Confidence            99999999999999999988654  44444433 57999999999999999999985

>CHL00176 ftsH cell division protein; Validated

Probab=99.94  E-value=4.7e-27  Score=182.17  Aligned_cols=131  Identities=44%  Similarity=0.725  Sum_probs=118.0

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|+.++||||||||+|.+...++.............+..++..++++....+++||++||+++.+|++++||||||+
T Consensus       267 lF~~A~~~~P~ILfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~~~~~ViVIaaTN~~~~LD~ALlRpGRFd~  346 (638)
T CHL00176        267 LFKKAKENSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDR  346 (638)
T ss_pred             HHHHHhcCCCcEEEEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhccccCCCCeeEEEecCchHhhhhhhhccccCce
Confidence            48899999999999999999998775544444455567889999999998888899999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .+.+++|+.++|.+||+.+++......+.++..+|..|.||+++||+.+|+
T Consensus       347 ~I~v~lPd~~~R~~IL~~~l~~~~~~~d~~l~~lA~~t~G~sgaDL~~lvn  397 (638)
T CHL00176        347 QITVSLPDREGRLDILKVHARNKKLSPDVSLELIARRTPGFSGADLANLLN  397 (638)
T ss_pred             EEEECCCCHHHHHHHHHHHHhhcccchhHHHHHHHhcCCCCCHHHHHHHHH
Confidence            999999999999999999999877778889999999999999999999874

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=99.94  E-value=1.2e-25  Score=165.63  Aligned_cols=131  Identities=60%  Similarity=0.980  Sum_probs=116.6

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|+.++|+||||||+|.++..+..............+..++..++++...+++.||+|||.++.+|+++++||||+.
T Consensus       207 ~f~~a~~~~p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~~~~~~v~vI~ttn~~~~ld~al~r~grfd~  286 (364)
T TIGR01242       207 IFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPDILDPALLRPGRFDR  286 (364)
T ss_pred             HHHHHHhcCCcEEEhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhCCCCCCCEEEEEecCChhhCChhhcCcccCce
Confidence            37788999999999999999998775544444455667788899999988777889999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .|+++.|+.++|.+||+.++.......+.++..++..|+||+|+||..+|+
T Consensus       287 ~i~v~~P~~~~r~~Il~~~~~~~~l~~~~~~~~la~~t~g~sg~dl~~l~~  337 (364)
T TIGR01242       287 IIEVPLPDFEGRLEILKIHTRKMKLAEDVDLEAIAKMTEGASGADLKAICT  337 (364)
T ss_pred             EEEeCCcCHHHHHHHHHHHHhcCCCCccCCHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999999999998888777789999999999999999999874

Many proteins may score above the trusted cutoff because an internal

>KOG0740|consensus

Probab=99.92  E-value=1.8e-25  Score=164.77  Aligned_cols=126  Identities=37%  Similarity=0.539  Sum_probs=109.3

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCC--CCeEEEeeCCCCCcccccccCCCcc
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSR--GDVKVIMATNRIETLDPALIRPGRI   78 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~--~~v~vi~ttn~~~~id~~l~~~grf   78 (131)
                      +|..|+..+|+|||+||+|.++.+|+....+.   ..+...+++.++++....  ++|+||||||.||.+|.+++|  ||
T Consensus       237 lf~vAr~~qPsvifidEidslls~Rs~~e~e~---srr~ktefLiq~~~~~s~~~drvlvigaTN~P~e~Dea~~R--rf  311 (428)
T KOG0740|consen  237 LFKVARSLQPSVIFIDEIDSLLSKRSDNEHES---SRRLKTEFLLQFDGKNSAPDDRVLVIGATNRPWELDEAARR--RF  311 (428)
T ss_pred             HHHHHHhcCCeEEEechhHHHHhhcCCccccc---chhhhhHHHhhhccccCCCCCeEEEEecCCCchHHHHHHHH--Hh
Confidence            59999999999999999999999994332222   346777888888876544  589999999999999999999  99


Q ss_pred             ceEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           79 DRKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        79 ~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .+.+++|.|+.+.|..+|..+++..+.. .+.++..+++.|+||+++||.++|.
T Consensus       312 ~kr~yiplPd~etr~~~~~~ll~~~~~~l~~~d~~~l~~~Tegysgsdi~~l~k  365 (428)
T KOG0740|consen  312 VKRLYIPLPDYETRSLLWKQLLKEQPNGLSDLDISLLAKVTEGYSGSDITALCK  365 (428)
T ss_pred             hceeeecCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCcccccHHHHHH
Confidence            9999999999999999999999887443 5678999999999999999999984

>KOG0730|consensus

Probab=99.92  E-value=8.8e-25  Score=166.17  Aligned_cols=126  Identities=39%  Similarity=0.658  Sum_probs=115.3

Q ss_pred             CHHHHHhcC-CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccc
Q psy522            1 LFRVAEEHA-PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRID   79 (131)
Q Consensus         1 vF~~A~~~~-p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~   79 (131)
                      +|++|..++ |++|||||+|.+++++.....    ...++..+++..+++.....+++|+++||+|++||++++| ||||
T Consensus       269 ~f~~a~k~~~psii~IdEld~l~p~r~~~~~----~e~Rv~sqlltL~dg~~~~~~vivl~atnrp~sld~alRR-gRfd  343 (693)
T KOG0730|consen  269 AFAEALKFQVPSIIFIDELDALCPKREGADD----VESRVVSQLLTLLDGLKPDAKVIVLAATNRPDSLDPALRR-GRFD  343 (693)
T ss_pred             HHHHHhccCCCeeEeHHhHhhhCCcccccch----HHHHHHHHHHHHHhhCcCcCcEEEEEecCCccccChhhhc-CCCc
Confidence            489999999 999999999999999854433    3457888888889998878899999999999999999999 9999


Q ss_pred             eEEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           80 RKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        80 ~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      +.+.++.|+..+|.+|++.+.+.++...+.++..+|..|.||+|+|+..+|+
T Consensus       344 ~ev~IgiP~~~~RldIl~~l~k~~~~~~~~~l~~iA~~thGyvGaDL~~l~~  395 (693)
T KOG0730|consen  344 REVEIGIPGSDGRLDILRVLTKKMNLLSDVDLEDIAVSTHGYVGADLAALCR  395 (693)
T ss_pred             ceeeecCCCchhHHHHHHHHHHhcCCcchhhHHHHHHHccchhHHHHHHHHH
Confidence            9999999999999999999999999888899999999999999999999874

>KOG0729|consensus

Probab=99.91  E-value=9.7e-25  Score=152.30  Aligned_cols=131  Identities=53%  Similarity=0.953  Sum_probs=123.3

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|+..+-||||+||+|++...|=..+....++..+.+.++++++|++...+++-|+.+||+|+.+||+++||||+|+
T Consensus       262 lf~martkkaciiffdeidaiggarfddg~ggdnevqrtmleli~qldgfdprgnikvlmatnrpdtldpallrpgrldr  341 (435)
T KOG0729|consen  262 LFEMARTKKACIIFFDEIDAIGGARFDDGAGGDNEVQRTMLELINQLDGFDPRGNIKVLMATNRPDTLDPALLRPGRLDR  341 (435)
T ss_pred             HHHHhcccceEEEEeeccccccCccccCCCCCcHHHHHHHHHHHHhccCCCCCCCeEEEeecCCCCCcCHhhcCCccccc
Confidence            59999999999999999999999986666667788889999999999999999999999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .++|.+|+-+.|..||+.+.+...+..++-|.-+|..+..-||+||.++|.
T Consensus       342 kvef~lpdlegrt~i~kihaksmsverdir~ellarlcpnstgaeirsvct  392 (435)
T KOG0729|consen  342 KVEFGLPDLEGRTHIFKIHAKSMSVERDIRFELLARLCPNSTGAEIRSVCT  392 (435)
T ss_pred             ceeccCCcccccceeEEEeccccccccchhHHHHHhhCCCCcchHHHHHHH
Confidence            999999999999999999999998888888999999999999999999884

>KOG0732|consensus

Probab=99.91  E-value=4.6e-24  Score=169.51  Aligned_cols=128  Identities=43%  Similarity=0.672  Sum_probs=112.3

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|++++|+|||+||+|.+.+.|+..+...+   ..+..++|..|+++...+.|+|||+||+|+.+|++++||||||+
T Consensus       355 lFeeA~k~qPSIIffdeIdGlapvrSskqEqih---~SIvSTLLaLmdGldsRgqVvvigATnRpda~dpaLRRPgrfdr  431 (1080)
T KOG0732|consen  355 LFEEAQKTQPSIIFFDEIDGLAPVRSSKQEQIH---ASIVSTLLALMDGLDSRGQVVVIGATNRPDAIDPALRRPGRFDR  431 (1080)
T ss_pred             HHHHHhccCceEEeccccccccccccchHHHhh---hhHHHHHHHhccCCCCCCceEEEcccCCccccchhhcCCcccce
Confidence            599999999999999999999999855444333   36788999999999999999999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .+++++|+.+.|.+|+.....+-... ...-+..+|+.|.||-|+||+.+|+
T Consensus       432 ef~f~lp~~~ar~~Il~Ihtrkw~~~i~~~l~~~la~~t~gy~gaDlkaLCT  483 (1080)
T KOG0732|consen  432 EFYFPLPDVDARAKILDIHTRKWEPPISRELLLWLAEETSGYGGADLKALCT  483 (1080)
T ss_pred             eEeeeCCchHHHHHHHHHhccCCCCCCCHHHHHHHHHhccccchHHHHHHHH
Confidence            99999999999999999987765422 2334777999999999999999984

>TIGR03689 pup_AAA proteasome ATPase

Probab=99.91  E-value=8.9e-24  Score=160.03  Aligned_cols=124  Identities=34%  Similarity=0.479  Sum_probs=100.8

Q ss_pred             CHHHHHhc----CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCC
Q psy522            1 LFRVAEEH----APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPG   76 (131)
Q Consensus         1 vF~~A~~~----~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~g   76 (131)
                      +|+.|+..    .|+||||||+|.++.+++......  ....++.+++..++++...++++||+|||+++.||++++|||
T Consensus       277 iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~~~s~d--~e~~il~~LL~~LDgl~~~~~ViVI~ATN~~d~LDpALlRpG  354 (512)
T TIGR03689       277 IFQRAREKASDGRPVIVFFDEMDSIFRTRGSGVSSD--VETTVVPQLLSELDGVESLDNVIVIGASNREDMIDPAILRPG  354 (512)
T ss_pred             HHHHHHHHhhcCCCceEEEehhhhhhcccCCCccch--HHHHHHHHHHHHhcccccCCceEEEeccCChhhCCHhhcCcc
Confidence            46677664    799999999999998874332222  234677899999999988789999999999999999999999


Q ss_pred             ccceEEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           77 RIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        77 rf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      |||..|++++|+.++|.+||+.++....     .+...+..+.|++++++..+|+
T Consensus       355 RfD~~I~~~~Pd~e~r~~Il~~~l~~~l-----~l~~~l~~~~g~~~a~~~al~~  404 (512)
T TIGR03689       355 RLDVKIRIERPDAEAAADIFSKYLTDSL-----PLDADLAEFDGDREATAAALIQ  404 (512)
T ss_pred             ccceEEEeCCCCHHHHHHHHHHHhhccC-----CchHHHHHhcCCCHHHHHHHHH
Confidence            9999999999999999999999987521     1122334579999999998874

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.

>KOG0651|consensus

Probab=99.90  E-value=7.8e-24  Score=149.65  Aligned_cols=130  Identities=49%  Similarity=0.907  Sum_probs=121.2

Q ss_pred             HHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceE
Q psy522            2 FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRK   81 (131)
Q Consensus         2 F~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~   81 (131)
                      |..|+.+.|||||+||+|++...+.+..........+++.+++++|++...-++|-+|.|||+|+.+|++++||||.|+.
T Consensus       218 f~yA~~~~pciifmdeiDAigGRr~se~Ts~dreiqrTLMeLlnqmdgfd~l~rVk~ImatNrpdtLdpaLlRpGRldrk  297 (388)
T KOG0651|consen  218 FRYAREVIPCIIFMDEIDAIGGRRFSEGTSSDREIQRTLMELLNQMDGFDTLHRVKTIMATNRPDTLDPALLRPGRLDRK  297 (388)
T ss_pred             HHHHhhhCceEEeehhhhhhccEEeccccchhHHHHHHHHHHHHhhccchhcccccEEEecCCccccchhhcCCccccce
Confidence            78999999999999999999998876667777788899999999999998889999999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           82 IEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        82 i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      +.+|.|+...|..+++.+-+......+++..++.+.++||.++|+...|+
T Consensus       298 ~~iPlpne~~r~~I~Kih~~~i~~~Geid~eaivK~~d~f~gad~rn~~t  347 (388)
T KOG0651|consen  298 VEIPLPNEQARLGILKIHVQPIDFHGEIDDEAILKLVDGFNGADLRNVCT  347 (388)
T ss_pred             eccCCcchhhceeeEeeccccccccccccHHHHHHHHhccChHHHhhhcc
Confidence            99999999999999998888777778899999999999999999988774

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

Probab=99.89  E-value=1.8e-22  Score=146.59  Aligned_cols=115  Identities=20%  Similarity=0.198  Sum_probs=91.5

Q ss_pred             CHHHHHhc-----CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCC------------CCCCCeEEEeeCC
Q psy522            1 LFRVAEEH-----APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGF------------DSRGDVKVIMATN   63 (131)
Q Consensus         1 vF~~A~~~-----~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~------------~~~~~v~vi~ttn   63 (131)
                      +|+.|++.     +||||||||+|++++.+++.+  .......+..++++.+|++            ...++|+||+|||
T Consensus       199 ~F~~A~~~a~~~~aPcVLFIDEIDA~~g~r~~~~--~tv~~qiV~~tLLnl~D~p~~v~l~G~w~~~~~~~~V~VIaTTN  276 (413)
T PLN00020        199 RYREAADIIKKKGKMSCLFINDLDAGAGRFGTTQ--YTVNNQMVNGTLMNIADNPTNVSLGGDWREKEEIPRVPIIVTGN  276 (413)
T ss_pred             HHHHHHHHhhccCCCeEEEEehhhhcCCCCCCCC--cchHHHHHHHHHHHHhcCCccccccccccccccCCCceEEEeCC
Confidence            47888764     699999999999999885322  2211223336888888763            2346799999999


Q ss_pred             CCCcccccccCCCccceEEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCC
Q psy522           64 RIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD  120 (131)
Q Consensus        64 ~~~~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g  120 (131)
                      +|+.||++++||||||+.+  ..|+.++|.+|++.+++..++. ..++..++..+.|
T Consensus       277 rpd~LDpALlRpGRfDk~i--~lPd~e~R~eIL~~~~r~~~l~-~~dv~~Lv~~f~g  330 (413)
T PLN00020        277 DFSTLYAPLIRDGRMEKFY--WAPTREDRIGVVHGIFRDDGVS-REDVVKLVDTFPG  330 (413)
T ss_pred             CcccCCHhHcCCCCCCcee--CCCCHHHHHHHHHHHhccCCCC-HHHHHHHHHcCCC
Confidence            9999999999999999865  6899999999999999987765 4688888888877

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.88  E-value=4.2e-22  Score=157.69  Aligned_cols=128  Identities=47%  Similarity=0.767  Sum_probs=113.1

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|..+.|+||||||+|.++.++.......   ...+...++..++++...++++||++||.++.+|++++++|||+.
T Consensus       263 lf~~a~~~~p~il~iDEid~l~~~r~~~~~~~---~~~~~~~Ll~~ld~l~~~~~vivI~atn~~~~ld~al~r~gRfd~  339 (733)
T TIGR01243       263 IFKEAEENAPSIIFIDEIDAIAPKREEVTGEV---EKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDR  339 (733)
T ss_pred             HHHHHHhcCCcEEEeehhhhhcccccCCcchH---HHHHHHHHHHHhhccccCCCEEEEeecCChhhcCHHHhCchhccE
Confidence            48889999999999999999998874433322   235677888888988777899999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .+.++.|+.++|.+||+.+.+......+.++..+++.|.||+++||..+|+
T Consensus       340 ~i~i~~P~~~~R~~Il~~~~~~~~l~~d~~l~~la~~t~G~~gadl~~l~~  390 (733)
T TIGR01243       340 EIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEVTHGFVGADLAALAK  390 (733)
T ss_pred             EEEeCCcCHHHHHHHHHHHhcCCCCccccCHHHHHHhCCCCCHHHHHHHHH
Confidence            999999999999999999999888877889999999999999999998863

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>KOG0741|consensus

Probab=99.86  E-value=7.2e-23  Score=153.13  Aligned_cols=121  Identities=36%  Similarity=0.615  Sum_probs=105.8

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      =.||++||+|+++..|++..+... .-..+++++|..||++..-++++|||-||+.+.||+|++|||||+.++++.+||+
T Consensus       325 LHIIIFDEiDAICKqRGS~~g~TG-VhD~VVNQLLsKmDGVeqLNNILVIGMTNR~DlIDEALLRPGRlEVqmEIsLPDE  403 (744)
T KOG0741|consen  325 LHIIIFDEIDAICKQRGSMAGSTG-VHDTVVNQLLSKMDGVEQLNNILVIGMTNRKDLIDEALLRPGRLEVQMEISLPDE  403 (744)
T ss_pred             ceEEEehhhHHHHHhcCCCCCCCC-ccHHHHHHHHHhcccHHhhhcEEEEeccCchhhHHHHhcCCCceEEEEEEeCCCc
Confidence            468999999999999876443222 1236899999999999888999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhcCC----CCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           90 KTKRRIFNIHTSRM----TLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        90 ~~R~~il~~~l~~~----~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      +.|.+|++.+.+++    .+..++|+.++|..|..|||++|+.+++
T Consensus       404 ~gRlQIl~IHT~rMre~~~l~~dVdl~elA~lTKNfSGAEleglVk  449 (744)
T KOG0741|consen  404 KGRLQILKIHTKRMRENNKLSADVDLKELAALTKNFSGAELEGLVK  449 (744)
T ss_pred             cCceEEEEhhhhhhhhcCCCCCCcCHHHHHHHhcCCchhHHHHHHH
Confidence            99999999887654    3457899999999999999999999873

>KOG0735|consensus

Probab=99.71  E-value=4e-17  Score=125.89  Aligned_cols=129  Identities=21%  Similarity=0.341  Sum_probs=101.5

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcC-C-CCCCCeEEEeeCCCCCcccccccCCCcc
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDG-F-DSRGDVKVIMATNRIETLDPALIRPGRI   78 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~-~~~~~v~vi~ttn~~~~id~~l~~~grf   78 (131)
                      +|..|-+++||||++|++|.++...++.++ +.......+..+++++-. + ..+..+.||||.+..+.+++-+.+|++|
T Consensus       486 vfse~~~~~PSiIvLDdld~l~~~s~~e~~-q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~qtl~~~L~s~~~F  564 (952)
T KOG0735|consen  486 VFSEALWYAPSIIVLDDLDCLASASSNENG-QDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQELQTLNPLLVSPLLF  564 (952)
T ss_pred             HHHHHHhhCCcEEEEcchhhhhccCcccCC-cchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhhhhcChhhcCccce
Confidence            588999999999999999999984433333 333344455555543332 2 2234589999999999999999999999


Q ss_pred             ceEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHhh
Q psy522           79 DRKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAIC  130 (131)
Q Consensus        79 ~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l~  130 (131)
                      +.++.+++|+..+|.+|+++.+++.... ...|+..++..|+||.+.|++.++
T Consensus       565 q~~~~L~ap~~~~R~~IL~~~~s~~~~~~~~~dLd~ls~~TEGy~~~DL~ifV  617 (952)
T KOG0735|consen  565 QIVIALPAPAVTRRKEILTTIFSKNLSDITMDDLDFLSVKTEGYLATDLVIFV  617 (952)
T ss_pred             EEEEecCCcchhHHHHHHHHHHHhhhhhhhhHHHHHHHHhcCCccchhHHHHH
Confidence            9999999999999999999999876533 334566699999999999999876

>KOG0742|consensus

Probab=99.70  E-value=9.9e-17  Score=117.76  Aligned_cols=124  Identities=29%  Similarity=0.444  Sum_probs=98.5

Q ss_pred             CHHHHHhcCCeE-EEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccc
Q psy522            1 LFRVAEEHAPSI-VFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRID   79 (131)
Q Consensus         1 vF~~A~~~~p~i-i~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~   79 (131)
                      +|++|+.....+ |||||+|+++.+|.+  ...+......++.+|-...  ..+.+++++.+||.|..+|.++..  |||
T Consensus       434 lFDWakkS~rGLllFIDEADAFLceRnk--tymSEaqRsaLNAlLfRTG--dqSrdivLvlAtNrpgdlDsAV~D--Rid  507 (630)
T KOG0742|consen  434 LFDWAKKSRRGLLLFIDEADAFLCERNK--TYMSEAQRSALNALLFRTG--DQSRDIVLVLATNRPGDLDSAVND--RID  507 (630)
T ss_pred             HHHHHhhcccceEEEehhhHHHHHHhch--hhhcHHHHHHHHHHHHHhc--ccccceEEEeccCCccchhHHHHh--hhh
Confidence            699998877654 788999999988843  3444455677777774443  234579999999999999999999  999


Q ss_pred             eEEEeCCCCHHHHHHHHHHHhcCCCCC---------------------------CcccHHHHHHHcCCCCHHHHHHhh
Q psy522           80 RKIEFPLPDEKTKRRIFNIHTSRMTLA---------------------------EDVNLQELIMAKDDLSGADIKAIC  130 (131)
Q Consensus        80 ~~i~~~~P~~~~R~~il~~~l~~~~~~---------------------------~~~~~~~la~~t~g~s~~di~~l~  130 (131)
                      ..|+||+|..++|..++..|+..+-..                           .+..+++.|..|+||||++|.+|+
T Consensus       508 e~veFpLPGeEERfkll~lYlnkyi~~~~~~~~~~~~~~lfkk~sQ~i~l~~~~t~~~~~EaAkkTeGfSGREiakLv  585 (630)
T KOG0742|consen  508 EVVEFPLPGEEERFKLLNLYLNKYILKPATSGKPGKWSHLFKKESQRIKLAGFDTGRKCSEAAKKTEGFSGREIAKLV  585 (630)
T ss_pred             heeecCCCChHHHHHHHHHHHHHHhcCcCCCCCCchhhHHHhhhhheeeeccchHHHHHHHHHHhccCCcHHHHHHHH
Confidence            999999999999999999987543211                           011278899999999999999986

>KOG0736|consensus

Probab=99.69  E-value=2.1e-16  Score=122.70  Aligned_cols=125  Identities=25%  Similarity=0.377  Sum_probs=106.8

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|.+|+.++|+|||+-++|.+..++.+   +...+..+.+...+..-+.....++++||+||++.+.+++.+++  .|-+
T Consensus       482 ~f~~a~~~~pavifl~~~dvl~id~dg---ged~rl~~~i~~~ls~e~~~~~~~~~ivv~t~~s~~~lp~~i~~--~f~~  556 (953)
T KOG0736|consen  482 IFSRARRCSPAVLFLRNLDVLGIDQDG---GEDARLLKVIRHLLSNEDFKFSCPPVIVVATTSSIEDLPADIQS--LFLH  556 (953)
T ss_pred             HHHHHhhcCceEEEEeccceeeecCCC---chhHHHHHHHHHHHhcccccCCCCceEEEEeccccccCCHHHHH--hhhh
Confidence            489999999999999999999855522   34445556666666522233356789999999999999999999  8888


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhh
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAIC  130 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~  130 (131)
                      .|.++.|++++|.+|+++|+.+..+..++.+..++.+|.||+.+|+++++
T Consensus       557 ei~~~~lse~qRl~iLq~y~~~~~~n~~v~~k~~a~~t~gfs~~~L~~l~  606 (953)
T KOG0736|consen  557 EIEVPALSEEQRLEILQWYLNHLPLNQDVNLKQLARKTSGFSFGDLEALV  606 (953)
T ss_pred             hccCCCCCHHHHHHHHHHHHhccccchHHHHHHHHHhcCCCCHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999875

>KOG0743|consensus

Probab=99.64  E-value=1.6e-15  Score=112.18  Aligned_cols=120  Identities=26%  Similarity=0.304  Sum_probs=90.9

Q ss_pred             cCCeEEEecccccccCcCCCCCCC--c-h-hHHHHHHHHHHHHhcCCCCCC--CeEEEeeCCCCCcccccccCCCccceE
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSG--G-E-REIQRTMLELLNQLDGFDSRG--DVKVIMATNRIETLDPALIRPGRIDRK   81 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~--~-~-~~~~~~~~~~l~~~~~~~~~~--~v~vi~ttn~~~~id~~l~~~grf~~~   81 (131)
                      ...|||+|++||+-+.-+......  . + ....-+++.+|+.+||+.+.-  -.|+|+|||+++.+|||++||||.|.+
T Consensus       285 ~~kSIivIEDIDcs~~l~~~~~~~~~~~~~~~~~VTlSGLLNfiDGlwSscg~ERIivFTTNh~EkLDPALlRpGRmDmh  364 (457)
T KOG0743|consen  285 PNKSILLIEDIDCSFDLRERRKKKKENFEGDLSRVTLSGLLNFLDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDMH  364 (457)
T ss_pred             CCCcEEEEeecccccccccccccccccccCCcceeehHHhhhhhccccccCCCceEEEEecCChhhcCHhhcCCCcceeE
Confidence            446999999999987544322211  1 1 122357788999999997774  699999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCC--CCHHHHHHh
Q psy522           82 IEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD--LSGADIKAI  129 (131)
Q Consensus        82 i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g--~s~~di~~l  129 (131)
                      |+++..+.++-+.++..|+....  +-.-+.++...-+|  .||||+...
T Consensus       365 I~mgyCtf~~fK~La~nYL~~~~--~h~L~~eie~l~~~~~~tPA~V~e~  412 (457)
T KOG0743|consen  365 IYMGYCTFEAFKTLASNYLGIEE--DHRLFDEIERLIEETEVTPAQVAEE  412 (457)
T ss_pred             EEcCCCCHHHHHHHHHHhcCCCC--CcchhHHHHHHhhcCccCHHHHHHH
Confidence            99999999999999999997643  12234445444444  699998753

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=99.54  E-value=3.3e-14  Score=90.21  Aligned_cols=82  Identities=44%  Similarity=0.676  Sum_probs=66.3

Q ss_pred             CHHHHHhcC-CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCC-CCeEEEeeCCCCCcccccccCCCcc
Q psy522            1 LFRVAEEHA-PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSR-GDVKVIMATNRIETLDPALIRPGRI   78 (131)
Q Consensus         1 vF~~A~~~~-p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~v~vi~ttn~~~~id~~l~~~grf   78 (131)
                      +|..|+... |+||+|||+|.++.+.   +..........+..++..++..... +++++|+|||.++.+++.++| +||
T Consensus        49 ~~~~~~~~~~~~vl~iDe~d~l~~~~---~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~~~~i~~~l~~-~rf  124 (132)
T PF00004_consen   49 FFKKAKKSAKPCVLFIDEIDKLFPKS---QPSSSSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNSPDKIDPALLR-SRF  124 (132)
T ss_dssp             HHHHHHHTSTSEEEEEETGGGTSHHC---STSSSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESSGGGSCHHHHS-TTS
T ss_pred             ccccccccccceeeeeccchhccccc---ccccccccccccceeeecccccccccccceeEEeeCChhhCCHhHHh-CCC
Confidence            377888887 9999999999999877   2223333456777888888887666 579999999999999999998 899


Q ss_pred             ceEEEeCC
Q psy522           79 DRKIEFPL   86 (131)
Q Consensus        79 ~~~i~~~~   86 (131)
                      +..++++.
T Consensus       125 ~~~i~~~~  132 (132)
T PF00004_consen  125 DRRIEFPL  132 (132)
T ss_dssp             EEEEEE-S
T ss_pred             cEEEEcCC
Confidence            99999874

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 ....

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

Probab=99.47  E-value=9.5e-13  Score=100.68  Aligned_cols=126  Identities=45%  Similarity=0.599  Sum_probs=110.9

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|+..+|+++++|++|.+.+.+..   ........+..+++..++++.... +++++.||.+..+++++++||||+.
T Consensus        68 ~~~~a~~~~~~ii~~d~~~~~~~~~~~---~~~~~~~~v~~~l~~~~d~~~~~~-v~~~~~~~~~~~~~~a~~~~~~~~~  143 (494)
T COG0464          68 LFEEAEKLAPSIIFIDEIDALAPKRSS---DQGEVERRVVAQLLALMDGLKRGQ-VIVIGATNRPDGLDPAKRRPGRFDR  143 (494)
T ss_pred             HHHHHHHhCCCeEeechhhhcccCccc---cccchhhHHHHHHHHhcccccCCc-eEEEeecCCccccChhHhCccccce
Confidence            478999999999999999999998865   222234467788888888887445 9999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhh
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAIC  130 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~  130 (131)
                      .+.+..|+...|.+++....+......+.++..++..+.||+++|+..+|
T Consensus       144 ~~~~~~~~~~~~~ei~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~l~  193 (494)
T COG0464         144 EIEVNLPDEAGRLEILQIHTRLMFLGPPGTGKTLAARTVGKSGADLGALA  193 (494)
T ss_pred             eeecCCCCHHHHHHHHHHHHhcCCCcccccHHHHHHhcCCccHHHHHHHH
Confidence            99999999999999999998888777788999999999999999999887

>KOG0744|consensus

Probab=99.20  E-value=1.6e-11  Score=88.17  Aligned_cols=116  Identities=21%  Similarity=0.328  Sum_probs=91.2

Q ss_pred             EEEecccccccCcCCCCC-CCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCHH
Q psy522           12 IVFIDEIDAVGTKRYDSN-SGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEK   90 (131)
Q Consensus        12 ii~iDe~d~l~~~~~~~~-~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~   90 (131)
                      .++|||+|++...|.+.. ........++++.+|+++|.++..++|++++|+|..++||.|+..  |-|-..++++|+.+
T Consensus       253 fvLIDEVESLa~aR~s~~S~~EpsDaIRvVNalLTQlDrlK~~~NvliL~TSNl~~siD~AfVD--RADi~~yVG~Pt~~  330 (423)
T KOG0744|consen  253 FVLIDEVESLAAARTSASSRNEPSDAIRVVNALLTQLDRLKRYPNVLILATSNLTDSIDVAFVD--RADIVFYVGPPTAE  330 (423)
T ss_pred             EEEeHHHHHHHHHHHhhhcCCCCchHHHHHHHHHHHHHHhccCCCEEEEeccchHHHHHHHhhh--HhhheeecCCccHH
Confidence            478899999998885443 333456678999999999999999999999999999999999999  99999999999999


Q ss_pred             HHHHHHHHHhcCC---CC------C---------CcccHHHHHHH-cCCCCHHHHHHh
Q psy522           91 TKRRIFNIHTSRM---TL------A---------EDVNLQELIMA-KDDLSGADIKAI  129 (131)
Q Consensus        91 ~R~~il~~~l~~~---~~------~---------~~~~~~~la~~-t~g~s~~di~~l  129 (131)
                      .|.+|++.++...   ++      +         .+...+.++.. +.|+||+-|.+|
T Consensus       331 ai~~IlkscieEL~~~gIi~~~~~s~~~~~~i~~~~~~~~~~~~~~~~gLSGRtlrkL  388 (423)
T KOG0744|consen  331 AIYEILKSCIEELISSGIILFHQRSTGVKEFIKYQKALRNILIELSTVGLSGRTLRKL  388 (423)
T ss_pred             HHHHHHHHHHHHHHhcCeeeeeccchhhhHHhHhhHhHHHHHHHHhhcCCccchHhhh
Confidence            9999998875321   00      0         11123334443 589999888765

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

Probab=99.04  E-value=5.4e-10  Score=89.15  Aligned_cols=90  Identities=31%  Similarity=0.415  Sum_probs=67.3

Q ss_pred             HHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCC-----cccccccCCC
Q psy522            2 FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE-----TLDPALIRPG   76 (131)
Q Consensus         2 F~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~-----~id~~l~~~g   76 (131)
                      |..+++..|+||||||+|.++..+...+  .......++..++       ..+.+.+||+|+.++     ..|+++.|  
T Consensus       271 ~~~l~~~~~~ILfIDEIh~L~g~g~~~~--g~~d~~nlLkp~L-------~~g~i~vIgATt~~E~~~~~~~D~AL~r--  339 (758)
T PRK11034        271 LKQLEQDTNSILFIDEIHTIIGAGAASG--GQVDAANLIKPLL-------SSGKIRVIGSTTYQEFSNIFEKDRALAR--  339 (758)
T ss_pred             HHHHHhcCCCEEEeccHHHHhccCCCCC--cHHHHHHHHHHHH-------hCCCeEEEecCChHHHHHHhhccHHHHh--
Confidence            5567778899999999999987763222  1222223333333       457899999999765     57999999  


Q ss_pred             ccceEEEeCCCCHHHHHHHHHHHhcCC
Q psy522           77 RIDRKIEFPLPDEKTKRRIFNIHTSRM  103 (131)
Q Consensus        77 rf~~~i~~~~P~~~~R~~il~~~l~~~  103 (131)
                      ||+ .|.++.|+.+++..|++.+...+
T Consensus       340 RFq-~I~v~ePs~~~~~~IL~~~~~~y  365 (758)
T PRK11034        340 RFQ-KIDITEPSIEETVQIINGLKPKY  365 (758)
T ss_pred             hCc-EEEeCCCCHHHHHHHHHHHHHHh
Confidence            996 79999999999999999875544

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

Probab=99.01  E-value=1.6e-09  Score=86.62  Aligned_cols=111  Identities=22%  Similarity=0.253  Sum_probs=76.3

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCC-----CcccccccCC
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRI-----ETLDPALIRP   75 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~-----~~id~~l~~~   75 (131)
                      +|+.|+++.|+||||||+|.++......++..  .....+...   +    ..+.+.+||+|+..     ...|+++.| 
T Consensus       266 i~~~~~~~~~~ILfiDEih~l~~~g~~~~~~~--~~~~~L~~~---l----~~g~i~~IgaTt~~e~~~~~~~d~al~r-  335 (731)
T TIGR02639       266 VVSEIEKEPNAILFIDEIHTIVGAGATSGGSM--DASNLLKPA---L----SSGKLRCIGSTTYEEYKNHFEKDRALSR-  335 (731)
T ss_pred             HHHHHhccCCeEEEEecHHHHhccCCCCCccH--HHHHHHHHH---H----hCCCeEEEEecCHHHHHHHhhhhHHHHH-
Confidence            46777788899999999999987653222211  122222222   2    35679999999963     357999999 


Q ss_pred             CccceEEEeCCCCHHHHHHHHHHHhcCC----CCC-CcccHHHHHHHcCCCCH
Q psy522           76 GRIDRKIEFPLPDEKTKRRIFNIHTSRM----TLA-EDVNLQELIMAKDDLSG  123 (131)
Q Consensus        76 grf~~~i~~~~P~~~~R~~il~~~l~~~----~~~-~~~~~~~la~~t~g~s~  123 (131)
                       ||. .|.++.|+.+++.+|++.+...+    .+. .+..+..++..+.+|-+
T Consensus       336 -Rf~-~i~v~~p~~~~~~~il~~~~~~~e~~~~v~i~~~al~~~~~ls~ryi~  386 (731)
T TIGR02639       336 -RFQ-KIDVGEPSIEETVKILKGLKEKYEEFHHVKYSDEALEAAVELSARYIN  386 (731)
T ss_pred             -hCc-eEEeCCCCHHHHHHHHHHHHHHHHhccCcccCHHHHHHHHHhhhcccc
Confidence             997 79999999999999999765432    221 33346666666666543

>CHL00181 cbbX CbbX; Provisional

Probab=98.95  E-value=9.3e-09  Score=73.91  Aligned_cols=89  Identities=21%  Similarity=0.268  Sum_probs=63.8

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCC--C---cccccccCCCccceEE
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRI--E---TLDPALIRPGRIDRKI   82 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~--~---~id~~l~~~grf~~~i   82 (131)
                      ..+.||||||+|.+...++.  ...   .......++..|+.  ..+.++||++++..  +   .++|++++  ||+..|
T Consensus       121 a~ggVLfIDE~~~l~~~~~~--~~~---~~e~~~~L~~~me~--~~~~~~vI~ag~~~~~~~~~~~np~L~s--R~~~~i  191 (287)
T CHL00181        121 AMGGVLFIDEAYYLYKPDNE--RDY---GSEAIEILLQVMEN--QRDDLVVIFAGYKDRMDKFYESNPGLSS--RIANHV  191 (287)
T ss_pred             ccCCEEEEEccchhccCCCc--cch---HHHHHHHHHHHHhc--CCCCEEEEEeCCcHHHHHHHhcCHHHHH--hCCceE
Confidence            45689999999998754311  111   23455666666664  23567777777532  1   23689999  999999


Q ss_pred             EeCCCCHHHHHHHHHHHhcCCCC
Q psy522           83 EFPLPDEKTKRRIFNIHTSRMTL  105 (131)
Q Consensus        83 ~~~~P~~~~R~~il~~~l~~~~~  105 (131)
                      +|++++.+++.+|++.++.....
T Consensus       192 ~F~~~t~~el~~I~~~~l~~~~~  214 (287)
T CHL00181        192 DFPDYTPEELLQIAKIMLEEQQY  214 (287)
T ss_pred             EcCCcCHHHHHHHHHHHHHHhcC
Confidence            99999999999999999976543

>TIGR00763 lon ATP-dependent protease La

Probab=98.93  E-value=6e-09  Score=83.78  Aligned_cols=88  Identities=26%  Similarity=0.395  Sum_probs=60.9

Q ss_pred             HHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHH------hcCC----CCCCCeEEEeeCCCCCccccc
Q psy522            2 FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQ------LDGF----DSRGDVKVIMATNRIETLDPA   71 (131)
Q Consensus         2 F~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~------~~~~----~~~~~v~vi~ttn~~~~id~~   71 (131)
                      |..|..+.| ||+|||+|.+.+...  ++ .    ...+.+++..      .+.+    ...+++++|+|||.++.+|++
T Consensus       408 l~~~~~~~~-villDEidk~~~~~~--~~-~----~~aLl~~ld~~~~~~f~d~~~~~~~d~s~v~~I~TtN~~~~i~~~  479 (775)
T TIGR00763       408 LKKAKTKNP-LFLLDEIDKIGSSFR--GD-P----ASALLEVLDPEQNNAFSDHYLDVPFDLSKVIFIATANSIDTIPRP  479 (775)
T ss_pred             HHHhCcCCC-EEEEechhhcCCccC--CC-H----HHHHHHhcCHHhcCccccccCCceeccCCEEEEEecCCchhCCHH
Confidence            345555565 889999999985431  11 1    1122222211      1111    112578999999999999999


Q ss_pred             ccCCCccceEEEeCCCCHHHHHHHHHHHh
Q psy522           72 LIRPGRIDRKIEFPLPDEKTKRRIFNIHT  100 (131)
Q Consensus        72 l~~~grf~~~i~~~~P~~~~R~~il~~~l  100 (131)
                      +++  ||+ .|.++.|+.+++.+|++.++
T Consensus       480 L~~--R~~-vi~~~~~~~~e~~~I~~~~l  505 (775)
T TIGR00763       480 LLD--RME-VIELSGYTEEEKLEIAKKYL  505 (775)
T ss_pred             HhC--Cee-EEecCCCCHHHHHHHHHHHH
Confidence            999  996 78999999999999998876

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=98.81  E-value=1.6e-08  Score=81.86  Aligned_cols=109  Identities=23%  Similarity=0.306  Sum_probs=75.3

Q ss_pred             HHHHHh-cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCC-----cccccccCC
Q psy522            2 FRVAEE-HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE-----TLDPALIRP   75 (131)
Q Consensus         2 F~~A~~-~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~-----~id~~l~~~   75 (131)
                      |+.++. ..++||||||++.+...++..+. .  ....++...       ...+.+.+||||+..+     .+|+++.| 
T Consensus       272 i~e~~~~~~~~ILfIDEih~l~~~g~~~~~-~--d~~n~Lkp~-------l~~G~l~~IgaTT~~e~~~~~~~d~AL~r-  340 (852)
T TIGR03345       272 IDEVKASPQPIILFIDEAHTLIGAGGQAGQ-G--DAANLLKPA-------LARGELRTIAATTWAEYKKYFEKDPALTR-  340 (852)
T ss_pred             HHHHHhcCCCeEEEEeChHHhccCCCcccc-c--cHHHHhhHH-------hhCCCeEEEEecCHHHHhhhhhccHHHHH-
Confidence            555654 46899999999999877632211 1  111222222       2457899999998643     48999999 


Q ss_pred             CccceEEEeCCCCHHHHHHHHHHHhcCCC----CC-CcccHHHHHHHcCCCCH
Q psy522           76 GRIDRKIEFPLPDEKTKRRIFNIHTSRMT----LA-EDVNLQELIMAKDDLSG  123 (131)
Q Consensus        76 grf~~~i~~~~P~~~~R~~il~~~l~~~~----~~-~~~~~~~la~~t~g~s~  123 (131)
                       ||. .|.++.|+.+++..|++.+...+.    +. .+..+..++..+.+|-+
T Consensus       341 -Rf~-~i~v~eps~~~~~~iL~~~~~~~e~~~~v~i~d~al~~~~~ls~ryi~  391 (852)
T TIGR03345       341 -RFQ-VVKVEEPDEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVELSHRYIP  391 (852)
T ss_pred             -hCe-EEEeCCCCHHHHHHHHHHHHHhhhhcCCCeeCHHHHHHHHHHcccccc
Confidence             995 899999999999999876654332    22 34457777888877754

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.

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=98.79  E-value=5.3e-08  Score=69.92  Aligned_cols=89  Identities=20%  Similarity=0.285  Sum_probs=64.3

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCC--CCc---ccccccCCCccceEE
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNR--IET---LDPALIRPGRIDRKI   82 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~--~~~---id~~l~~~grf~~~i   82 (131)
                      ..+++|||||++.+...+.  ....   .......++..|+.  ...++++|++++.  ++.   ++|++.+  ||...|
T Consensus       120 a~~gvL~iDEi~~L~~~~~--~~~~---~~~~~~~Ll~~le~--~~~~~~vI~a~~~~~~~~~~~~np~L~s--R~~~~i  190 (284)
T TIGR02880       120 AMGGVLFIDEAYYLYRPDN--ERDY---GQEAIEILLQVMEN--QRDDLVVILAGYKDRMDSFFESNPGFSS--RVAHHV  190 (284)
T ss_pred             ccCcEEEEechhhhccCCC--ccch---HHHHHHHHHHHHhc--CCCCEEEEEeCCcHHHHHHHhhCHHHHh--hCCcEE
Confidence            3468999999999865431  1111   22455566666764  3356777777663  233   3799999  999999


Q ss_pred             EeCCCCHHHHHHHHHHHhcCCCC
Q psy522           83 EFPLPDEKTKRRIFNIHTSRMTL  105 (131)
Q Consensus        83 ~~~~P~~~~R~~il~~~l~~~~~  105 (131)
                      +||+++.+++.+|++++++....
T Consensus       191 ~fp~l~~edl~~I~~~~l~~~~~  213 (284)
T TIGR02880       191 DFPDYSEAELLVIAGLMLKEQQY  213 (284)
T ss_pred             EeCCcCHHHHHHHHHHHHHHhcc
Confidence            99999999999999999987543

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.

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=98.74  E-value=8.8e-08  Score=67.92  Aligned_cols=88  Identities=18%  Similarity=0.210  Sum_probs=62.3

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCC-----CcccccccCCCccceEEE
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRI-----ETLDPALIRPGRIDRKIE   83 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~-----~~id~~l~~~grf~~~i~   83 (131)
                      .++||||||+|.+....      ........+..++..++..  .+.+++|+++...     ..++|++++  ||+..++
T Consensus       105 ~~~VL~IDE~~~L~~~~------~~~~~~~~i~~Ll~~~e~~--~~~~~vila~~~~~~~~~~~~~p~L~s--Rf~~~i~  174 (261)
T TIGR02881       105 LGGVLFIDEAYSLARGG------EKDFGKEAIDTLVKGMEDN--RNEFVLILAGYSDEMDYFLSLNPGLRS--RFPISID  174 (261)
T ss_pred             cCCEEEEechhhhccCC------ccchHHHHHHHHHHHHhcc--CCCEEEEecCCcchhHHHHhcChHHHh--ccceEEE
Confidence            46899999999986321      1111234566777777653  3455565554322     236889999  9999999


Q ss_pred             eCCCCHHHHHHHHHHHhcCCCCC
Q psy522           84 FPLPDEKTKRRIFNIHTSRMTLA  106 (131)
Q Consensus        84 ~~~P~~~~R~~il~~~l~~~~~~  106 (131)
                      ++.++.+++.+|++.++......
T Consensus       175 f~~~~~~el~~Il~~~~~~~~~~  197 (261)
T TIGR02881       175 FPDYTVEELMEIAERMVKEREYK  197 (261)
T ss_pred             ECCCCHHHHHHHHHHHHHHcCCc
Confidence            99999999999999999865543

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.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=98.68  E-value=6.2e-08  Score=78.67  Aligned_cols=108  Identities=19%  Similarity=0.196  Sum_probs=72.8

Q ss_pred             HHHH-HhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCC-----cccccccCC
Q psy522            2 FRVA-EEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE-----TLDPALIRP   75 (131)
Q Consensus         2 F~~A-~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~-----~id~~l~~~   75 (131)
                      |+.+ +...|+||||||++.+.++++..+. ..  ...++.       ..-..+.+.+||+|+..+     .+|+++.| 
T Consensus       263 ~~~~~~~~~~~ILfIDEih~l~~~~~~~~~-~d--~~~~lk-------p~l~~g~l~~IgaTt~~e~r~~~~~d~al~r-  331 (857)
T PRK10865        263 LNDLAKQEGNVILFIDELHTMVGAGKADGA-MD--AGNMLK-------PALARGELHCVGATTLDEYRQYIEKDAALER-  331 (857)
T ss_pred             HHHHHHcCCCeEEEEecHHHhccCCCCccc-hh--HHHHhc-------chhhcCCCeEEEcCCCHHHHHHhhhcHHHHh-
Confidence            4443 3457899999999999876632221 11  122222       222457899999999876     48999999 


Q ss_pred             CccceEEEeCCCCHHHHHHHHHHHhcCCCCC-----CcccHHHHHHHcCCCC
Q psy522           76 GRIDRKIEFPLPDEKTKRRIFNIHTSRMTLA-----EDVNLQELIMAKDDLS  122 (131)
Q Consensus        76 grf~~~i~~~~P~~~~R~~il~~~l~~~~~~-----~~~~~~~la~~t~g~s  122 (131)
                       ||+ .|.++.|+.+++..|++.+...+...     .+..+...+..+.+|-
T Consensus       332 -Rf~-~i~v~eP~~~~~~~iL~~l~~~~e~~~~v~~~d~a~~~a~~ls~ry~  381 (857)
T PRK10865        332 -RFQ-KVFVAEPSVEDTIAILRGLKERYELHHHVQITDPAIVAAATLSHRYI  381 (857)
T ss_pred             -hCC-EEEeCCCCHHHHHHHHHHHhhhhccCCCCCcCHHHHHHHHHHhhccc
Confidence             997 68999999999999999876544322     2233444555555554

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.68  E-value=1.3e-07  Score=68.25  Aligned_cols=67  Identities=13%  Similarity=0.109  Sum_probs=55.7

Q ss_pred             CCeEEEeeCCCCCcccccccCCCccceEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCC
Q psy522           54 GDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLS  122 (131)
Q Consensus        54 ~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s  122 (131)
                      +++.+|++|+.+..+++++++  ||...+.+++|+.++..++++......... ++..+..++..+.|+.
T Consensus       128 ~~~~li~~t~~~~~l~~~l~s--R~~~~~~l~~l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~p  195 (305)
T TIGR00635       128 PPFTLVGATTRAGMLTSPLRD--RFGIILRLEFYTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTP  195 (305)
T ss_pred             CCeEEEEecCCccccCHHHHh--hcceEEEeCCCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCc
Confidence            458899999999999999999  999899999999999999999887755444 2334777888888864

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.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=98.66  E-value=8.1e-08  Score=78.03  Aligned_cols=109  Identities=19%  Similarity=0.190  Sum_probs=73.6

Q ss_pred             HHHHHh-cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCC-----cccccccCC
Q psy522            2 FRVAEE-HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE-----TLDPALIRP   75 (131)
Q Consensus         2 F~~A~~-~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~-----~id~~l~~~   75 (131)
                      |..+.. ..|+||||||++.+++..+..+.   .....+       +......+.+.+||+|+..+     ..|+++.| 
T Consensus       258 l~~~~~~~~~~ILfIDEih~l~~~g~~~~~---~d~~~~-------Lk~~l~~g~i~~IgaTt~~e~r~~~~~d~al~r-  326 (852)
T TIGR03346       258 LNEVTKSEGQIILFIDELHTLVGAGKAEGA---MDAGNM-------LKPALARGELHCIGATTLDEYRKYIEKDAALER-  326 (852)
T ss_pred             HHHHHhcCCCeEEEeccHHHhhcCCCCcch---hHHHHH-------hchhhhcCceEEEEeCcHHHHHHHhhcCHHHHh-
Confidence            445544 36899999999999875432211   111112       12223457899999999764     47999999 


Q ss_pred             CccceEEEeCCCCHHHHHHHHHHHhcCCCCC-----CcccHHHHHHHcCCCCH
Q psy522           76 GRIDRKIEFPLPDEKTKRRIFNIHTSRMTLA-----EDVNLQELIMAKDDLSG  123 (131)
Q Consensus        76 grf~~~i~~~~P~~~~R~~il~~~l~~~~~~-----~~~~~~~la~~t~g~s~  123 (131)
                       ||. .|.++.|+.+++..|++.+...+...     .+..+..++..+.+|-+
T Consensus       327 -Rf~-~i~v~~p~~~~~~~iL~~~~~~~e~~~~v~~~d~~i~~~~~ls~~yi~  377 (852)
T TIGR03346       327 -RFQ-PVFVDEPTVEDTISILRGLKERYEVHHGVRITDPAIVAAATLSHRYIT  377 (852)
T ss_pred             -cCC-EEEeCCCCHHHHHHHHHHHHHHhccccCCCCCHHHHHHHHHhcccccc
Confidence             996 68999999999999999876554332     23346666666766643

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.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=98.65  E-value=1.4e-07  Score=68.97  Aligned_cols=67  Identities=13%  Similarity=0.109  Sum_probs=56.3

Q ss_pred             CCeEEEeeCCCCCcccccccCCCccceEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCC
Q psy522           54 GDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLS  122 (131)
Q Consensus        54 ~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s  122 (131)
                      +++.+|++|+.+..+++.+++  ||+..+.+++|+.+++.++++......+.. ++.-+..++..+.|..
T Consensus       149 ~~~~li~at~~~~~l~~~L~s--Rf~~~~~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~p  216 (328)
T PRK00080        149 PPFTLIGATTRAGLLTSPLRD--RFGIVQRLEFYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTP  216 (328)
T ss_pred             CCceEEeecCCcccCCHHHHH--hcCeeeecCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCc
Confidence            457899999999999999999  999999999999999999999887766554 2334778898888864

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=98.60  E-value=1.9e-07  Score=70.09  Aligned_cols=106  Identities=17%  Similarity=0.275  Sum_probs=70.0

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcc---cccccCCCccc--eEEE
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETL---DPALIRPGRID--RKIE   83 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~i---d~~l~~~grf~--~~i~   83 (131)
                      .+.+|+|||+|.+..++      .      ....++..++.....+..++|+++..|..+   ++.+++  ||.  ..+.
T Consensus       199 ~~dlLiiDDi~~l~~~~------~------~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~S--Rl~~g~~v~  264 (405)
T TIGR00362       199 SVDLLLIDDIQFLAGKE------R------TQEEFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRS--RFEWGLVVD  264 (405)
T ss_pred             hCCEEEEehhhhhcCCH------H------HHHHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhh--hccCCeEEE
Confidence            36799999999986443      1      111233333332234455677666667664   578888  986  5799


Q ss_pred             eCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHh
Q psy522           84 FPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAI  129 (131)
Q Consensus        84 ~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l  129 (131)
                      +++|+.++|..|++..+...+.. ++..+..+|+...| +.++|+.+
T Consensus       265 i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~-~~r~l~~~  310 (405)
T TIGR00362       265 IEPPDLETRLAILQKKAEEEGLELPDEVLEFIAKNIRS-NVRELEGA  310 (405)
T ss_pred             eCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-CHHHHHHH
Confidence            99999999999999998766554 33346667776654 45555543

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).

>PRK06893 DNA replication initiation factor; Validated

Probab=98.53  E-value=1.9e-07  Score=65.10  Aligned_cols=100  Identities=14%  Similarity=0.168  Sum_probs=63.6

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCC-eEEEeeCCCCCccc---ccccCCCccceEEEe
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGD-VKVIMATNRIETLD---PALIRPGRIDRKIEF   84 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~-v~vi~ttn~~~~id---~~l~~~grf~~~i~~   84 (131)
                      +..+|+|||++.+..+.      ..   ...   +++.++.....++ +++++++..|..++   +.+.+..+++..+.+
T Consensus        91 ~~dlLilDDi~~~~~~~------~~---~~~---l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l  158 (229)
T PRK06893         91 QQDLVCLDDLQAVIGNE------EW---ELA---IFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQL  158 (229)
T ss_pred             cCCEEEEeChhhhcCCh------HH---HHH---HHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHHHHhcCCeeeC
Confidence            46799999999986433      11   112   3333333333343 45666666788776   789984445688999


Q ss_pred             CCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           85 PLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        85 ~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      ++|+.++|.++++......++. ++.-+..++.+..|
T Consensus       159 ~~pd~e~~~~iL~~~a~~~~l~l~~~v~~~L~~~~~~  195 (229)
T PRK06893        159 NDLTDEQKIIVLQRNAYQRGIELSDEVANFLLKRLDR  195 (229)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccC
Confidence            9999999999999887654443 22224455555443

>CHL00095 clpC Clp protease ATP binding subunit

Probab=98.53  E-value=3.6e-07  Score=74.07  Aligned_cols=110  Identities=24%  Similarity=0.263  Sum_probs=76.0

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCC-----cccccccCC
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE-----TLDPALIRP   75 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~-----~id~~l~~~   75 (131)
                      +|+.++...|+||||||++.++...+..+. .  .....+...+       ..+.+.+||+|+..+     ..|+++.+ 
T Consensus       263 i~~~~~~~~~~ILfiDEih~l~~~g~~~g~-~--~~a~lLkp~l-------~rg~l~~IgaTt~~ey~~~ie~D~aL~r-  331 (821)
T CHL00095        263 IFDEIQENNNIILVIDEVHTLIGAGAAEGA-I--DAANILKPAL-------ARGELQCIGATTLDEYRKHIEKDPALER-  331 (821)
T ss_pred             HHHHHHhcCCeEEEEecHHHHhcCCCCCCc-c--cHHHHhHHHH-------hCCCcEEEEeCCHHHHHHHHhcCHHHHh-
Confidence            467778888999999999999977643222 1  1222333222       356789999999754     47899999 


Q ss_pred             CccceEEEeCCCCHHHHHHHHHHHhc----CCCCC-CcccHHHHHHHcCCCCH
Q psy522           76 GRIDRKIEFPLPDEKTKRRIFNIHTS----RMTLA-EDVNLQELIMAKDDLSG  123 (131)
Q Consensus        76 grf~~~i~~~~P~~~~R~~il~~~l~----~~~~~-~~~~~~~la~~t~g~s~  123 (131)
                       ||. .|.++.|+.++...|++....    ..+.. ++..+..++..+.||.+
T Consensus       332 -Rf~-~I~v~ep~~~e~~aILr~l~~~~e~~~~v~i~deal~~i~~ls~~yi~  382 (821)
T CHL00095        332 -RFQ-PVYVGEPSVEETIEILFGLRSRYEKHHNLSISDKALEAAAKLSDQYIA  382 (821)
T ss_pred             -cce-EEecCCCCHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhccCc
Confidence             996 589999999999999976532    22222 33346677777777765

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=98.52  E-value=3.8e-07  Score=69.38  Aligned_cols=104  Identities=16%  Similarity=0.279  Sum_probs=68.6

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCc---ccccccCCCccc--eEEE
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIET---LDPALIRPGRID--RKIE   83 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~---id~~l~~~grf~--~~i~   83 (131)
                      .+.+|+|||++.+..++.            ....++..++.....++.++|+++..|..   +++.+++  ||.  ..+.
T Consensus       211 ~~dlLiiDDi~~l~~~~~------------~~~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~l~S--Rl~~gl~v~  276 (450)
T PRK00149        211 SVDVLLIDDIQFLAGKER------------TQEEFFHTFNALHEAGKQIVLTSDRPPKELPGLEERLRS--RFEWGLTVD  276 (450)
T ss_pred             cCCEEEEehhhhhcCCHH------------HHHHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHh--HhcCCeeEE
Confidence            578999999999854430            11223333333333445567777667666   6788999  995  5899


Q ss_pred             eCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHH
Q psy522           84 FPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIK  127 (131)
Q Consensus        84 ~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~  127 (131)
                      +++|+.++|.+|++..+...+.. ++.-+..+|....| +.++|+
T Consensus       277 i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~-~~R~l~  320 (450)
T PRK00149        277 IEPPDLETRIAILKKKAEEEGIDLPDEVLEFIAKNITS-NVRELE  320 (450)
T ss_pred             ecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHcCcCC-CHHHHH
Confidence            99999999999999998765443 23336666666554 344443

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=98.45  E-value=8.7e-07  Score=67.28  Aligned_cols=105  Identities=18%  Similarity=0.237  Sum_probs=67.8

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcc---cccccCCCcc--ceEEE
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETL---DPALIRPGRI--DRKIE   83 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~i---d~~l~~~grf--~~~i~   83 (131)
                      +|.+|+|||++.+..+..            ....++..++.+...++.+++++.+.|..+   .+.+++  ||  +..+.
T Consensus       194 ~~dvLlIDDi~~l~~~~~------------~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~rL~S--R~~~gl~v~  259 (440)
T PRK14088        194 KVDVLLIDDVQFLIGKTG------------VQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVS--RFQMGLVAK  259 (440)
T ss_pred             cCCEEEEechhhhcCcHH------------HHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHHHHhh--HHhcCceEe
Confidence            688999999998865420            111222233333334456677666777764   567888  87  46788


Q ss_pred             eCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHH
Q psy522           84 FPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKA  128 (131)
Q Consensus        84 ~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~  128 (131)
                      +++|+.+.|.+|++..+...+.. ++.-+..++....| +.++|+.
T Consensus       260 i~~pd~e~r~~IL~~~~~~~~~~l~~ev~~~Ia~~~~~-~~R~L~g  304 (440)
T PRK14088        260 LEPPDEETRKKIARKMLEIEHGELPEEVLNFVAENVDD-NLRRLRG  304 (440)
T ss_pred             eCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHhcccc-CHHHHHH
Confidence            99999999999999998754443 22336667776554 3444443

>PRK08727 hypothetical protein; Validated

Probab=98.40  E-value=9.3e-07  Score=61.78  Aligned_cols=99  Identities=18%  Similarity=0.340  Sum_probs=62.4

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcc---cccccCCCcc--ceEE
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETL---DPALIRPGRI--DRKI   82 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~i---d~~l~~~grf--~~~i   82 (131)
                      .+..+|+|||+|.+..+.      ..   ...+..+++..   ...+.-+++.+...|..+   ++.+++  ||  ...+
T Consensus        92 ~~~dlLiIDDi~~l~~~~------~~---~~~lf~l~n~~---~~~~~~vI~ts~~~p~~l~~~~~dL~S--Rl~~~~~~  157 (233)
T PRK08727         92 EGRSLVALDGLESIAGQR------ED---EVALFDFHNRA---RAAGITLLYTARQMPDGLALVLPDLRS--RLAQCIRI  157 (233)
T ss_pred             hcCCEEEEeCcccccCCh------HH---HHHHHHHHHHH---HHcCCeEEEECCCChhhhhhhhHHHHH--HHhcCceE
Confidence            345799999999886543      11   11222333333   223333444444467766   689999  97  5678


Q ss_pred             EeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           83 EFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        83 ~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      .+++|+.++|.++++......++. ++..+..++..+.|
T Consensus       158 ~l~~~~~e~~~~iL~~~a~~~~l~l~~e~~~~La~~~~r  196 (233)
T PRK08727        158 GLPVLDDVARAAVLRERAQRRGLALDEAAIDWLLTHGER  196 (233)
T ss_pred             EecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCC
Confidence            999999999999999866543443 22335667776554

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=98.36  E-value=2.4e-06  Score=66.90  Aligned_cols=106  Identities=15%  Similarity=0.210  Sum_probs=66.9

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCC---cccccccCCCcc--ceEE
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE---TLDPALIRPGRI--DRKI   82 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~---~id~~l~~~grf--~~~i   82 (131)
                      ..+.+|+|||++.+..+.      .      ....+++.++.+...++-+||.+...|.   .+++.|++  ||  ...+
T Consensus       376 ~~~DLLlIDDIq~l~gke------~------tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~S--Rf~~GLvv  441 (617)
T PRK14086        376 REMDILLVDDIQFLEDKE------S------TQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRN--RFEWGLIT  441 (617)
T ss_pred             hcCCEEEEehhccccCCH------H------HHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHh--hhhcCceE
Confidence            457899999999986543      1      1122333333333444445554444454   46789999  88  6677


Q ss_pred             EeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHH
Q psy522           83 EFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKA  128 (131)
Q Consensus        83 ~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~  128 (131)
                      .+..|+.+.|.+||+.......+. ++.-+..|+.+..+ +.++|+.
T Consensus       442 ~I~~PD~EtR~aIL~kka~~r~l~l~~eVi~yLa~r~~r-nvR~Leg  487 (617)
T PRK14086        442 DVQPPELETRIAILRKKAVQEQLNAPPEVLEFIASRISR-NIRELEG  487 (617)
T ss_pred             EcCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhccC-CHHHHHH
Confidence            999999999999999998876655 22235556665443 3444443

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=98.35  E-value=4.7e-06  Score=64.74  Aligned_cols=70  Identities=19%  Similarity=0.194  Sum_probs=52.1

Q ss_pred             eEEEeeCCCCCcccccccCCCccceEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHhh
Q psy522           56 VKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAIC  130 (131)
Q Consensus        56 v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l~  130 (131)
                      .++.+||+.|+.+++++++  |+. .+.+++++.++..+++++.++..+.. ++..+..++..+.  +++++..++
T Consensus       235 rlI~ATt~~p~~L~paLrs--R~~-~I~f~pL~~eei~~Il~~~a~k~~i~is~~al~~I~~y~~--n~Rel~nll  305 (531)
T TIGR02902       235 RLIGATTRNPEEIPPALRS--RCV-EIFFRPLLDEEIKEIAKNAAEKIGINLEKHALELIVKYAS--NGREAVNIV  305 (531)
T ss_pred             EEEEEecCCcccCChHHhh--hhh-eeeCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhh--hHHHHHHHH
Confidence            5566777889999999999  985 78899999999999999998876654 2223454555443  567776654

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.

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

Probab=98.34  E-value=1.5e-06  Score=60.23  Aligned_cols=108  Identities=19%  Similarity=0.305  Sum_probs=66.4

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcc---cccccCCCccc--eEE
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETL---DPALIRPGRID--RKI   82 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~i---d~~l~~~grf~--~~i   82 (131)
                      ....+|+||+++.+..+.            .+...++..++.+...++.+++++...|..+   ++.+++  ||.  ..+
T Consensus        96 ~~~DlL~iDDi~~l~~~~------------~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~~~~L~S--Rl~~Gl~~  161 (219)
T PF00308_consen   96 RSADLLIIDDIQFLAGKQ------------RTQEELFHLFNRLIESGKQLILTSDRPPSELSGLLPDLRS--RLSWGLVV  161 (219)
T ss_dssp             CTSSEEEEETGGGGTTHH------------HHHHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS-HHHHH--HHHCSEEE
T ss_pred             hcCCEEEEecchhhcCch------------HHHHHHHHHHHHHHhhCCeEEEEeCCCCccccccChhhhh--hHhhcchh
Confidence            345799999999986432            1223333444443455667777776777765   678888  874  589


Q ss_pred             EeCCCCHHHHHHHHHHHhcCCCCCCccc-HHHHHHHcCCCCHHHHHHhh
Q psy522           83 EFPLPDEKTKRRIFNIHTSRMTLAEDVN-LQELIMAKDDLSGADIKAIC  130 (131)
Q Consensus        83 ~~~~P~~~~R~~il~~~l~~~~~~~~~~-~~~la~~t~g~s~~di~~l~  130 (131)
                      .+.+|+.+.|.++++......+..-+.+ +.-++....+ +.++|+.++
T Consensus       162 ~l~~pd~~~r~~il~~~a~~~~~~l~~~v~~~l~~~~~~-~~r~L~~~l  209 (219)
T PF00308_consen  162 ELQPPDDEDRRRILQKKAKERGIELPEEVIEYLARRFRR-DVRELEGAL  209 (219)
T ss_dssp             EE----HHHHHHHHHHHHHHTT--S-HHHHHHHHHHTTS-SHHHHHHHH
T ss_pred             hcCCCCHHHHHHHHHHHHHHhCCCCcHHHHHHHHHhhcC-CHHHHHHHH
Confidence            9999999999999999988776663333 4556665443 667766553

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.

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.29  E-value=5.9e-06  Score=61.31  Aligned_cols=97  Identities=16%  Similarity=0.289  Sum_probs=69.1

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      ..|++|||+|.+-.              ...+.++..++.  ..+.+.+|.+|+.++.+.+.+++  |+ ..+.+++|+.
T Consensus       120 ~kviIIDEa~~l~~--------------~a~naLLk~lEe--~~~~~~fIl~t~~~~~l~~tI~S--Rc-~~~~~~~l~~  180 (363)
T PRK14961        120 FKVYLIDEVHMLSR--------------HSFNALLKTLEE--PPQHIKFILATTDVEKIPKTILS--RC-LQFKLKIISE  180 (363)
T ss_pred             ceEEEEEChhhcCH--------------HHHHHHHHHHhc--CCCCeEEEEEcCChHhhhHHHHh--hc-eEEeCCCCCH
Confidence            35999999998731              233445655654  23466777778888999999998  88 5799999999


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHH
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADI  126 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di  126 (131)
                      ++..++++..++..+.. ++..+..++..+.| +++++
T Consensus       181 ~el~~~L~~~~~~~g~~i~~~al~~ia~~s~G-~~R~a  217 (363)
T PRK14961        181 EKIFNFLKYILIKESIDTDEYALKLIAYHAHG-SMRDA  217 (363)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHH
Confidence            99999999887765543 33346667777766 44443

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.24  E-value=4.6e-06  Score=57.55  Aligned_cols=106  Identities=18%  Similarity=0.278  Sum_probs=64.0

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCccc---ccccCCCcc--ceEEEe
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLD---PALIRPGRI--DRKIEF   84 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id---~~l~~~grf--~~~i~~   84 (131)
                      +.+|+|||+|.+....      .   ....+..++..+.   ..+..++++++..+..++   +.+.+  ||  ...+.+
T Consensus        91 ~~lLvIDdi~~l~~~~------~---~~~~L~~~l~~~~---~~~~~iIits~~~~~~~~~~~~~L~~--r~~~~~~i~l  156 (226)
T TIGR03420        91 ADLVCLDDVEAIAGQP------E---WQEALFHLYNRVR---EAGGRLLIAGRAAPAQLPLRLPDLRT--RLAWGLVFQL  156 (226)
T ss_pred             CCEEEEeChhhhcCCh------H---HHHHHHHHHHHHH---HcCCeEEEECCCChHHCCcccHHHHH--HHhcCeeEec
Confidence            4689999999874321      0   0123333433332   223345555444554443   67777  76  478999


Q ss_pred             CCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHhh
Q psy522           85 PLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAIC  130 (131)
Q Consensus        85 ~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l~  130 (131)
                      ++|+.+++..+++.+....+.. .+.-+..++.. -+-+++++..++
T Consensus       157 ~~l~~~e~~~~l~~~~~~~~~~~~~~~l~~L~~~-~~gn~r~L~~~l  202 (226)
T TIGR03420       157 PPLSDEEKIAALQSRAARRGLQLPDEVADYLLRH-GSRDMGSLMALL  202 (226)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHh-ccCCHHHHHHHH
Confidence            9999999999999887655443 22235666664 444566666553

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.

>PRK08084 DNA replication initiation factor; Provisional

Probab=98.23  E-value=2.6e-06  Score=59.62  Aligned_cols=96  Identities=18%  Similarity=0.205  Sum_probs=59.7

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCC-eEEEeeCCCCCc---ccccccCCCccc--eEEEe
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGD-VKVIMATNRIET---LDPALIRPGRID--RKIEF   84 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~-v~vi~ttn~~~~---id~~l~~~grf~--~~i~~   84 (131)
                      .+|+|||++.+..+.     ..+    ..+-.+++.   ....++ .+++.+++.|..   +.+.+++  |+.  ..+.+
T Consensus        99 dlliiDdi~~~~~~~-----~~~----~~lf~l~n~---~~e~g~~~li~ts~~~p~~l~~~~~~L~S--Rl~~g~~~~l  164 (235)
T PRK08084         99 SLVCIDNIECIAGDE-----LWE----MAIFDLYNR---ILESGRTRLLITGDRPPRQLNLGLPDLAS--RLDWGQIYKL  164 (235)
T ss_pred             CEEEEeChhhhcCCH-----HHH----HHHHHHHHH---HHHcCCCeEEEeCCCChHHcCcccHHHHH--HHhCCceeee
Confidence            589999999875432     111    122222222   223343 455555556666   5799999  985  88999


Q ss_pred             CCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           85 PLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        85 ~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      ++|+.++|.++++......++. ++.-+..++.+..|
T Consensus       165 ~~~~~~~~~~~l~~~a~~~~~~l~~~v~~~L~~~~~~  201 (235)
T PRK08084        165 QPLSDEEKLQALQLRARLRGFELPEDVGRFLLKRLDR  201 (235)
T ss_pred             cCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhhcC
Confidence            9999999999998855544443 22235556666544

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=98.23  E-value=4.4e-06  Score=63.68  Aligned_cols=108  Identities=18%  Similarity=0.204  Sum_probs=68.2

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcc---cccccCCCcc--ceEE
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETL---DPALIRPGRI--DRKI   82 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~i---d~~l~~~grf--~~~i   82 (131)
                      ..+.+|+|||++.+..+.            .....+...++.....++.+|+++...|+.+   ++.+++  ||  +..+
T Consensus       205 ~~~dvLiIDDiq~l~~k~------------~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l~~l~~rL~S--R~~~Gl~~  270 (450)
T PRK14087        205 CQNDVLIIDDVQFLSYKE------------KTNEIFFTIFNNFIENDKQLFFSSDKSPELLNGFDNRLIT--RFNMGLSI  270 (450)
T ss_pred             ccCCEEEEeccccccCCH------------HHHHHHHHHHHHHHHcCCcEEEECCCCHHHHhhccHHHHH--HHhCCcee
Confidence            456799999999885432            1222233333333344444555555556555   688999  88  5788


Q ss_pred             EeCCCCHHHHHHHHHHHhcCCCC--C-CcccHHHHHHHcCCCCHHHHHHhh
Q psy522           83 EFPLPDEKTKRRIFNIHTSRMTL--A-EDVNLQELIMAKDDLSGADIKAIC  130 (131)
Q Consensus        83 ~~~~P~~~~R~~il~~~l~~~~~--~-~~~~~~~la~~t~g~s~~di~~l~  130 (131)
                      .+.+|+.++|.+++++.+...+.  . ++.-+..++....| +++.+..++
T Consensus       271 ~L~~pd~e~r~~iL~~~~~~~gl~~~l~~evl~~Ia~~~~g-d~R~L~gaL  320 (450)
T PRK14087        271 AIQKLDNKTATAIIKKEIKNQNIKQEVTEEAINFISNYYSD-DVRKIKGSV  320 (450)
T ss_pred             ccCCcCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHccCC-CHHHHHHHH
Confidence            89999999999999999876543  1 22235566776665 455555443

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.23  E-value=7.3e-06  Score=62.60  Aligned_cols=94  Identities=14%  Similarity=0.174  Sum_probs=70.6

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      ...|++|||+|.+-.              ...+.+|..++.  ....+++|.+|+.++.|++.+++  |+. .+.|..++
T Consensus       121 ~~KV~IIDEah~Ls~--------------~A~NALLKtLEE--Pp~~viFILaTte~~kI~~TI~S--RCq-~~~f~~ls  181 (484)
T PRK14956        121 KYKVYIIDEVHMLTD--------------QSFNALLKTLEE--PPAHIVFILATTEFHKIPETILS--RCQ-DFIFKKVP  181 (484)
T ss_pred             CCEEEEEechhhcCH--------------HHHHHHHHHhhc--CCCceEEEeecCChhhccHHHHh--hhh-eeeecCCC
Confidence            456999999999832              245556666653  33578899999999999999999  984 78899999


Q ss_pred             HHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCC
Q psy522           89 EKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDL  121 (131)
Q Consensus        89 ~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~  121 (131)
                      .++-.+.+++.+...+.. .+..+..++..+.|-
T Consensus       182 ~~~i~~~L~~i~~~Egi~~e~eAL~~Ia~~S~Gd  215 (484)
T PRK14956        182 LSVLQDYSEKLCKIENVQYDQEGLFWIAKKGDGS  215 (484)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCh
Confidence            988888888888766554 333467777777763

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=98.23  E-value=1e-05  Score=60.74  Aligned_cols=94  Identities=14%  Similarity=0.157  Sum_probs=64.3

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      ..|++|||+|.+...              ..+.++..++..  .+++++|.+|++++.+.+.+++  |+ ..++|++|+.
T Consensus       118 ~kViiIDead~m~~~--------------aanaLLk~LEep--~~~~~fIL~a~~~~~llpTIrS--Rc-~~i~f~~~~~  178 (394)
T PRK07940        118 WRIVVIEDADRLTER--------------AANALLKAVEEP--PPRTVWLLCAPSPEDVLPTIRS--RC-RHVALRTPSV  178 (394)
T ss_pred             cEEEEEechhhcCHH--------------HHHHHHHHhhcC--CCCCeEEEEECChHHChHHHHh--hC-eEEECCCCCH
Confidence            359999999998422              234566666642  3345555555559999999999  98 5899999999


Q ss_pred             HHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHH
Q psy522           90 KTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADI  126 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di  126 (131)
                      ++..+++...   .+.. ......++..+.|..+.-+
T Consensus       179 ~~i~~~L~~~---~~~~-~~~a~~la~~s~G~~~~A~  211 (394)
T PRK07940        179 EAVAEVLVRR---DGVD-PETARRAARASQGHIGRAR  211 (394)
T ss_pred             HHHHHHHHHh---cCCC-HHHHHHHHHHcCCCHHHHH
Confidence            9977777632   2232 2345667888888766544

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=98.22  E-value=6.6e-06  Score=65.78  Aligned_cols=93  Identities=17%  Similarity=0.187  Sum_probs=69.9

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      ..|++|||+|.|-.              ...+.+|+.|+.  ..+.+.+|.+||+++.|.+.|++  |+ ..+.|..++.
T Consensus       120 ~KVIIIDEah~LT~--------------~A~NALLKtLEE--PP~~v~FILaTtd~~KIp~TIrS--RC-q~f~Fk~Ls~  180 (830)
T PRK07003        120 FKVYMIDEVHMLTN--------------HAFNAMLKTLEE--PPPHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPA  180 (830)
T ss_pred             ceEEEEeChhhCCH--------------HHHHHHHHHHHh--cCCCeEEEEEECChhhccchhhh--he-EEEecCCcCH
Confidence            46899999998832              234455555553  23578899999999999999999  99 5899999999


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCC
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDL  121 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~  121 (131)
                      ++-.+.++..+...++. .+..+..|+....|-
T Consensus       181 eeIv~~L~~Il~~EgI~id~eAL~lIA~~A~Gs  213 (830)
T PRK07003        181 GHIVSHLERILGEERIAFEPQALRLLARAAQGS  213 (830)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCC
Confidence            99999999888765544 333466677776663

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=98.21  E-value=6.3e-06  Score=62.72  Aligned_cols=98  Identities=19%  Similarity=0.314  Sum_probs=61.9

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCc---ccccccCCCccc--eEE
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIET---LDPALIRPGRID--RKI   82 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~---id~~l~~~grf~--~~i   82 (131)
                      ..+.+|+|||++.+..+.     ....    .+..+++.+   ...++.++++++..|..   +++.+++  ||.  ..+
T Consensus       201 ~~~dvLiIDDiq~l~~k~-----~~qe----elf~l~N~l---~~~~k~IIlts~~~p~~l~~l~~rL~S--R~~~Gl~~  266 (445)
T PRK12422        201 RNVDALFIEDIEVFSGKG-----ATQE----EFFHTFNSL---HTEGKLIVISSTCAPQDLKAMEERLIS--RFEWGIAI  266 (445)
T ss_pred             ccCCEEEEcchhhhcCCh-----hhHH----HHHHHHHHH---HHCCCcEEEecCCCHHHHhhhHHHHHh--hhcCCeEE
Confidence            356799999999875432     1111    222222222   22344566666555654   5789999  995  889


Q ss_pred             EeCCCCHHHHHHHHHHHhcCCCCCC-cccHHHHHHHcC
Q psy522           83 EFPLPDEKTKRRIFNIHTSRMTLAE-DVNLQELIMAKD  119 (131)
Q Consensus        83 ~~~~P~~~~R~~il~~~l~~~~~~~-~~~~~~la~~t~  119 (131)
                      .+++|+.+.|.+|++......+..- +.-+..++....
T Consensus       267 ~l~~pd~e~r~~iL~~k~~~~~~~l~~evl~~la~~~~  304 (445)
T PRK12422        267 PLHPLTKEGLRSFLERKAEALSIRIEETALDFLIEALS  304 (445)
T ss_pred             ecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcC
Confidence            9999999999999999887665442 222444555443

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=98.18  E-value=1.1e-05  Score=59.39  Aligned_cols=91  Identities=19%  Similarity=0.272  Sum_probs=65.5

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCHH
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEK   90 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~   90 (131)
                      -||+|||+|.+..              ...+.++..++.  ..+.+++|.+|++++.+.+.+++  |+. .+.+++|+.+
T Consensus       119 ~vviidea~~l~~--------------~~~~~Ll~~le~--~~~~~~lIl~~~~~~~l~~~l~s--r~~-~~~~~~~~~~  179 (355)
T TIGR02397       119 KVYIIDEVHMLSK--------------SAFNALLKTLEE--PPEHVVFILATTEPHKIPATILS--RCQ-RFDFKRIPLE  179 (355)
T ss_pred             eEEEEeChhhcCH--------------HHHHHHHHHHhC--CccceeEEEEeCCHHHHHHHHHh--hee-EEEcCCCCHH
Confidence            5899999988731              234456666654  23467777888889999999999  884 7899999999


Q ss_pred             HHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           91 TKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        91 ~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      +...+++..++..+.. ++..+..+++.+.|
T Consensus       180 ~l~~~l~~~~~~~g~~i~~~a~~~l~~~~~g  210 (355)
T TIGR02397       180 DIVERLKKILDKEGIKIEDEALELIARAADG  210 (355)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            9999999988766543 22335556666554

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.

>PRK05642 DNA replication initiation factor; Validated

Probab=98.17  E-value=1.1e-05  Score=56.46  Aligned_cols=96  Identities=18%  Similarity=0.238  Sum_probs=61.5

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcc---cccccCCCcc--ceEEEeC
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETL---DPALIRPGRI--DRKIEFP   85 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~i---d~~l~~~grf--~~~i~~~   85 (131)
                      .+|+|||++.+..+.      .      ....+++.++.....++.++++++..|..+   .+.+++  ||  ...+.+.
T Consensus        99 d~LiiDDi~~~~~~~------~------~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~S--Rl~~gl~~~l~  164 (234)
T PRK05642         99 ELVCLDDLDVIAGKA------D------WEEALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKS--RLTLALVFQMR  164 (234)
T ss_pred             CEEEEechhhhcCCh------H------HHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHH--HHhcCeeeecC
Confidence            578999999875443      1      112233444444455677888887766554   588999  98  4677889


Q ss_pred             CCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           86 LPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        86 ~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      +|+.++|.++++......++. ++.-+..+++...|
T Consensus       165 ~~~~e~~~~il~~ka~~~~~~l~~ev~~~L~~~~~~  200 (234)
T PRK05642        165 GLSDEDKLRALQLRASRRGLHLTDEVGHFILTRGTR  200 (234)
T ss_pred             CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC
Confidence            999999999999555443333 22224445555443

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.17  E-value=2.6e-05  Score=57.60  Aligned_cols=81  Identities=23%  Similarity=0.305  Sum_probs=57.0

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcC-CCCCCCeEEEeeCCCCC---cccccccCCCccc-eEE
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDG-FDSRGDVKVIMATNRIE---TLDPALIRPGRID-RKI   82 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~~v~vi~ttn~~~---~id~~l~~~grf~-~~i   82 (131)
                      ..|.||+|||+|.+....       .    ..+..++...+. -....++.+|+++|.++   .+++.+.+  ||. ..+
T Consensus       128 ~~~~vlvIDE~d~L~~~~-------~----~~L~~l~~~~~~~~~~~~~v~lI~i~n~~~~~~~l~~~~~s--~~~~~~i  194 (365)
T TIGR02928       128 GDSLIIVLDEIDYLVGDD-------D----DLLYQLSRARSNGDLDNAKVGVIGISNDLKFRENLDPRVKS--SLCEEEI  194 (365)
T ss_pred             CCeEEEEECchhhhccCC-------c----HHHHhHhccccccCCCCCeEEEEEEECCcchHhhcCHHHhc--cCCccee
Confidence            457899999999997221       1    123333322111 11235788999999875   57888887  775 679


Q ss_pred             EeCCCCHHHHHHHHHHHhc
Q psy522           83 EFPLPDEKTKRRIFNIHTS  101 (131)
Q Consensus        83 ~~~~P~~~~R~~il~~~l~  101 (131)
                      .+++++.++..+|++..+.
T Consensus       195 ~f~p~~~~e~~~il~~r~~  213 (365)
T TIGR02928       195 IFPPYDAEELRDILENRAE  213 (365)
T ss_pred             eeCCCCHHHHHHHHHHHHH
Confidence            9999999999999998875

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.

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.13  E-value=1.7e-05  Score=60.75  Aligned_cols=92  Identities=18%  Similarity=0.272  Sum_probs=66.1

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      ..||+|||+|.+..              .....++..++.  ..+.+++|++|+.+..+++++++  |+. .+.+.+|+.
T Consensus       118 ~kVvIIDE~h~Lt~--------------~a~~~LLk~LE~--p~~~vv~Ilattn~~kl~~~L~S--R~~-vv~f~~l~~  178 (472)
T PRK14962        118 YKVYIIDEVHMLTK--------------EAFNALLKTLEE--PPSHVVFVLATTNLEKVPPTIIS--RCQ-VIEFRNISD  178 (472)
T ss_pred             eEEEEEEChHHhHH--------------HHHHHHHHHHHh--CCCcEEEEEEeCChHhhhHHHhc--CcE-EEEECCccH
Confidence            46999999998832              234455666654  23467777777788899999999  884 899999999


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      ++...+++..+...+.. .+..+..++..+.|
T Consensus       179 ~el~~~L~~i~~~egi~i~~eal~~Ia~~s~G  210 (472)
T PRK14962        179 ELIIKRLQEVAEAEGIEIDREALSFIAKRASG  210 (472)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCC
Confidence            99999999887654433 22335666665544

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=98.12  E-value=2.1e-05  Score=60.76  Aligned_cols=98  Identities=18%  Similarity=0.287  Sum_probs=70.9

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-|++|||+|.+..              ...+.++..++.  ..+.+++|++|+.++.+++.+++  |+ ..+.+..++.
T Consensus       129 ~KVvIIDEa~~Ls~--------------~a~naLLk~LEe--pp~~~vfI~aTte~~kI~~tI~S--Rc-~~~ef~~ls~  189 (507)
T PRK06645        129 HKIFIIDEVHMLSK--------------GAFNALLKTLEE--PPPHIIFIFATTEVQKIPATIIS--RC-QRYDLRRLSF  189 (507)
T ss_pred             cEEEEEEChhhcCH--------------HHHHHHHHHHhh--cCCCEEEEEEeCChHHhhHHHHh--cc-eEEEccCCCH
Confidence            45899999988731              234455666653  34567888888888999999999  88 4789999999


Q ss_pred             HHHHHHHHHHhcCCCCCCc-ccHHHHHHHcCCCCHHHHH
Q psy522           90 KTKRRIFNIHTSRMTLAED-VNLQELIMAKDDLSGADIK  127 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~~~-~~~~~la~~t~g~s~~di~  127 (131)
                      ++...+++..++..+..-+ ..+..++..+.| +.+++.
T Consensus       190 ~el~~~L~~i~~~egi~ie~eAL~~Ia~~s~G-slR~al  227 (507)
T PRK06645        190 EEIFKLLEYITKQENLKTDIEALRIIAYKSEG-SARDAV  227 (507)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHH
Confidence            9999999999886665422 336667777666 444443

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.10  E-value=1.2e-05  Score=65.30  Aligned_cols=80  Identities=23%  Similarity=0.280  Sum_probs=57.5

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCC---CCcccccccCCCccce-EEEe
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNR---IETLDPALIRPGRIDR-KIEF   84 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~---~~~id~~l~~~grf~~-~i~~   84 (131)
                      ...||+|||+|.|..+.       +    .++-.++....  ....+++|||.+|.   ++.+++.+++  ||.. .+.|
T Consensus       869 ~v~IIILDEID~L~kK~-------Q----DVLYnLFR~~~--~s~SKLiLIGISNdlDLperLdPRLRS--RLg~eeIvF  933 (1164)
T PTZ00112        869 NVSILIIDEIDYLITKT-------Q----KVLFTLFDWPT--KINSKLVLIAISNTMDLPERLIPRCRS--RLAFGRLVF  933 (1164)
T ss_pred             cceEEEeehHhhhCccH-------H----HHHHHHHHHhh--ccCCeEEEEEecCchhcchhhhhhhhh--ccccccccC
Confidence            35799999999997532       1    23333333222  23457999999985   6677888888  7653 4888


Q ss_pred             CCCCHHHHHHHHHHHhcCC
Q psy522           85 PLPDEKTKRRIFNIHTSRM  103 (131)
Q Consensus        85 ~~P~~~~R~~il~~~l~~~  103 (131)
                      ++++.++..+|++.-+...
T Consensus       934 ~PYTaEQL~dILk~RAe~A  952 (1164)
T PTZ00112        934 SPYKGDEIEKIIKERLENC  952 (1164)
T ss_pred             CCCCHHHHHHHHHHHHHhC
Confidence            9999999999999987753

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

Probab=98.09  E-value=1.3e-05  Score=64.78  Aligned_cols=80  Identities=23%  Similarity=0.363  Sum_probs=55.6

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHH------hcCC----CCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQ------LDGF----DSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~------~~~~----~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      .||+|||+|.+.....  ++     ....+.+++..      .|.+    ..-+++++|+|+|+. .|++++++  ||+ 
T Consensus       418 ~villDEidk~~~~~~--g~-----~~~aLlevld~~~~~~~~d~~~~~~~dls~v~~i~TaN~~-~i~~aLl~--R~~-  486 (784)
T PRK10787        418 PLFLLDEIDKMSSDMR--GD-----PASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNSM-NIPAPLLD--RME-  486 (784)
T ss_pred             CEEEEEChhhcccccC--CC-----HHHHHHHHhccccEEEEecccccccccCCceEEEEcCCCC-CCCHHHhc--cee-
Confidence            3899999999865431  11     11233333321      0111    112679999999987 59999999  996 


Q ss_pred             EEEeCCCCHHHHHHHHHHHhc
Q psy522           81 KIEFPLPDEKTKRRIFNIHTS  101 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~  101 (131)
                      .|.+..++.++..+|.+.++.
T Consensus       487 ii~~~~~t~eek~~Ia~~~L~  507 (784)
T PRK10787        487 VIRLSGYTEDEKLNIAKRHLL  507 (784)
T ss_pred             eeecCCCCHHHHHHHHHHhhh
Confidence            789999999999999998874

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=98.08  E-value=2.7e-05  Score=60.92  Aligned_cols=97  Identities=19%  Similarity=0.260  Sum_probs=69.2

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-|++|||+|.+..              ...+.++..++.  ..+.+++|.+|+.++.+++.+++  |+. .+.|.+|+.
T Consensus       120 ~kViIIDE~~~Lt~--------------~a~naLLKtLEe--pp~~~ifIlatt~~~ki~~tI~S--Rc~-~~~f~~~~~  180 (559)
T PRK05563        120 YKVYIIDEVHMLST--------------GAFNALLKTLEE--PPAHVIFILATTEPHKIPATILS--RCQ-RFDFKRISV  180 (559)
T ss_pred             eEEEEEECcccCCH--------------HHHHHHHHHhcC--CCCCeEEEEEeCChhhCcHHHHh--Hhe-EEecCCCCH
Confidence            45899999998731              234556666664  23467777777889999999999  885 688999999


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHH
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADI  126 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di  126 (131)
                      ++-...++..++..+.. .+..+..++..+.| +.++.
T Consensus       181 ~ei~~~L~~i~~~egi~i~~~al~~ia~~s~G-~~R~a  217 (559)
T PRK05563        181 EDIVERLKYILDKEGIEYEDEALRLIARAAEG-GMRDA  217 (559)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHH
Confidence            99999999888766554 22346666776665 44443

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=98.08  E-value=2.9e-05  Score=52.34  Aligned_cols=88  Identities=17%  Similarity=0.235  Sum_probs=63.1

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      .+-||+|||+|.+-..              ..+.++..++..  .+..++|.+|+.+..+.+++++  |+. .+.+++|+
T Consensus        96 ~~kviiide~~~l~~~--------------~~~~Ll~~le~~--~~~~~~il~~~~~~~l~~~i~s--r~~-~~~~~~~~  156 (188)
T TIGR00678        96 GRRVVIIEDAERMNEA--------------AANALLKTLEEP--PPNTLFILITPSPEKLLPTIRS--RCQ-VLPFPPLS  156 (188)
T ss_pred             CeEEEEEechhhhCHH--------------HHHHHHHHhcCC--CCCeEEEEEECChHhChHHHHh--hcE-EeeCCCCC
Confidence            3568999999888421              334566666652  3456677777788999999999  874 89999999


Q ss_pred             HHHHHHHHHHHhcCCCCCCcccHHHHHHHcCC
Q psy522           89 EKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD  120 (131)
Q Consensus        89 ~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g  120 (131)
                      .++...+++..    +++ +..+..++..+.|
T Consensus       157 ~~~~~~~l~~~----gi~-~~~~~~i~~~~~g  183 (188)
T TIGR00678       157 EEALLQWLIRQ----GIS-EEAAELLLALAGG  183 (188)
T ss_pred             HHHHHHHHHHc----CCC-HHHHHHHHHHcCC
Confidence            99988888776    233 2346667776665

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.

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.08  E-value=1.3e-05  Score=63.24  Aligned_cols=92  Identities=16%  Similarity=0.205  Sum_probs=69.0

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      ..|++|||+|.+..              ...+.+|+.++.  ..+++++|.+|+.++.|.+.+++  |+ ..+.|+.++.
T Consensus       125 ~KViIIDEah~Ls~--------------~AaNALLKTLEE--PP~~v~FILaTtep~kLlpTIrS--RC-q~f~f~~ls~  185 (700)
T PRK12323        125 FKVYMIDEVHMLTN--------------HAFNAMLKTLEE--PPEHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPP  185 (700)
T ss_pred             ceEEEEEChHhcCH--------------HHHHHHHHhhcc--CCCCceEEEEeCChHhhhhHHHH--HH-HhcccCCCCh
Confidence            46999999999832              244566666663  34578899999999999999999  98 5899999999


Q ss_pred             HHHHHHHHHHhcCCCCCCc-ccHHHHHHHcCC
Q psy522           90 KTKRRIFNIHTSRMTLAED-VNLQELIMAKDD  120 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~~~-~~~~~la~~t~g  120 (131)
                      ++-.+.+++.+...++..+ ..+..++..+.|
T Consensus       186 eei~~~L~~Il~~Egi~~d~eAL~~IA~~A~G  217 (700)
T PRK12323        186 GHIVSHLDAILGEEGIAHEVNALRLLAQAAQG  217 (700)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            9999998888765554422 235556666655

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=98.06  E-value=2.2e-05  Score=62.07  Aligned_cols=92  Identities=22%  Similarity=0.274  Sum_probs=69.0

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-|++|||+|.+-.              ...+.+|..++.  ..+.+.+|.+|+.++.|.+.+++  |+ ..+.|.+++.
T Consensus       120 ~KV~IIDEah~Ls~--------------~a~NALLKtLEE--Pp~~v~FIL~Tt~~~kLl~TI~S--RC-~~~~f~~Ls~  180 (647)
T PRK07994        120 FKVYLIDEVHMLSR--------------HSFNALLKTLEE--PPEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDV  180 (647)
T ss_pred             CEEEEEechHhCCH--------------HHHHHHHHHHHc--CCCCeEEEEecCCccccchHHHh--hh-eEeeCCCCCH
Confidence            45999999998832              245566666663  34567888888899999999999  97 6899999999


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      ++-...+++.+...++. .+..+..++..+.|
T Consensus       181 ~ei~~~L~~il~~e~i~~e~~aL~~Ia~~s~G  212 (647)
T PRK07994        181 EQIRQQLEHILQAEQIPFEPRALQLLARAADG  212 (647)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            99999999887655443 22346667776666

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=98.03  E-value=3.7e-05  Score=55.78  Aligned_cols=73  Identities=19%  Similarity=0.401  Sum_probs=53.2

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      .+.+|+|||+|.+..+.          ....+..++   +..  .+++.+|.|||.+..+++.+++  ||. .+.++.|+
T Consensus       100 ~~~vliiDe~d~l~~~~----------~~~~L~~~l---e~~--~~~~~~Ilt~n~~~~l~~~l~s--R~~-~i~~~~p~  161 (316)
T PHA02544        100 GGKVIIIDEFDRLGLAD----------AQRHLRSFM---EAY--SKNCSFIITANNKNGIIEPLRS--RCR-VIDFGVPT  161 (316)
T ss_pred             CCeEEEEECcccccCHH----------HHHHHHHHH---Hhc--CCCceEEEEcCChhhchHHHHh--hce-EEEeCCCC
Confidence            47899999999872211          123333333   322  2456788899999999999999  995 78999999


Q ss_pred             HHHHHHHHHHH
Q psy522           89 EKTKRRIFNIH   99 (131)
Q Consensus        89 ~~~R~~il~~~   99 (131)
                      .+++.++++.+
T Consensus       162 ~~~~~~il~~~  172 (316)
T PHA02544        162 KEEQIEMMKQM  172 (316)
T ss_pred             HHHHHHHHHHH
Confidence            99998887654

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=97.99  E-value=2.5e-05  Score=58.31  Aligned_cols=100  Identities=19%  Similarity=0.228  Sum_probs=63.2

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCC---CcccccccCCCccc-eEEE
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRI---ETLDPALIRPGRID-RKIE   83 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~---~~id~~l~~~grf~-~~i~   83 (131)
                      ..+.||+|||+|.+....      ..    ..+..++..++... ..++.+|+++|..   +.+++.+.+  ||. ..++
T Consensus       137 ~~~~viviDE~d~l~~~~------~~----~~l~~l~~~~~~~~-~~~v~vI~i~~~~~~~~~l~~~~~s--~~~~~~i~  203 (394)
T PRK00411        137 DRVLIVALDDINYLFEKE------GN----DVLYSLLRAHEEYP-GARIGVIGISSDLTFLYILDPRVKS--VFRPEEIY  203 (394)
T ss_pred             CCEEEEEECCHhHhhccC------Cc----hHHHHHHHhhhccC-CCeEEEEEEECCcchhhhcCHHHHh--cCCcceee
Confidence            356899999999997221      01    23444444444332 2367788888765   346777776  664 5789


Q ss_pred             eCCCCHHHHHHHHHHHhcCCC---CCCcccHHHHHHHcCC
Q psy522           84 FPLPDEKTKRRIFNIHTSRMT---LAEDVNLQELIMAKDD  120 (131)
Q Consensus        84 ~~~P~~~~R~~il~~~l~~~~---~~~~~~~~~la~~t~g  120 (131)
                      +++++.++..++++..+....   .-.+..+..+++.+.+
T Consensus       204 f~py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~  243 (394)
T PRK00411        204 FPPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAR  243 (394)
T ss_pred             cCCCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHH
Confidence            999999999999998875321   1122235556666533

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.98  E-value=4.4e-05  Score=62.06  Aligned_cols=93  Identities=19%  Similarity=0.165  Sum_probs=65.5

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      ..-|+||||+|.|-.              ...+.+|+.|+..  .+.+++|++|+.++.|.+.|++  |+ ..+.|..++
T Consensus       120 ~~KV~IIDEad~lt~--------------~a~NaLLK~LEEp--P~~~~fIl~tt~~~kLl~TIrS--Rc-~~v~F~~l~  180 (824)
T PRK07764        120 RYKIFIIDEAHMVTP--------------QGFNALLKIVEEP--PEHLKFIFATTEPDKVIGTIRS--RT-HHYPFRLVP  180 (824)
T ss_pred             CceEEEEechhhcCH--------------HHHHHHHHHHhCC--CCCeEEEEEeCChhhhhHHHHh--he-eEEEeeCCC
Confidence            345999999999842              2455666666642  3567788888888899999999  87 578999999


Q ss_pred             HHHHHHHHHHHhcCCCCCC-cccHHHHHHHcCC
Q psy522           89 EKTKRRIFNIHTSRMTLAE-DVNLQELIMAKDD  120 (131)
Q Consensus        89 ~~~R~~il~~~l~~~~~~~-~~~~~~la~~t~g  120 (131)
                      .++-..+++..+...++.- +..+..++..+.|
T Consensus       181 ~~~l~~~L~~il~~EGv~id~eal~lLa~~sgG  213 (824)
T PRK07764        181 PEVMRGYLERICAQEGVPVEPGVLPLVIRAGGG  213 (824)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            9998888888876555432 2223444444444

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.98  E-value=5.7e-05  Score=59.61  Aligned_cols=97  Identities=15%  Similarity=0.173  Sum_probs=69.4

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCHH
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEK   90 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~   90 (131)
                      -|++|||+|.+...              ..+.++..++.  ..+.+.+|.+|+.++.+.+.+++  |+ ..+.|..++.+
T Consensus       126 KV~IIDEvh~Ls~~--------------a~NaLLKtLEE--PP~~~~fIL~Ttd~~kil~TIlS--Rc-~~~~f~~Ls~e  186 (618)
T PRK14951        126 KVFMIDEVHMLTNT--------------AFNAMLKTLEE--PPEYLKFVLATTDPQKVPVTVLS--RC-LQFNLRPMAPE  186 (618)
T ss_pred             eEEEEEChhhCCHH--------------HHHHHHHhccc--CCCCeEEEEEECCchhhhHHHHH--hc-eeeecCCCCHH
Confidence            49999999997422              34456666653  23567778888889999999999  88 68999999999


Q ss_pred             HHHHHHHHHhcCCCCCC-cccHHHHHHHcCCCCHHHHH
Q psy522           91 TKRRIFNIHTSRMTLAE-DVNLQELIMAKDDLSGADIK  127 (131)
Q Consensus        91 ~R~~il~~~l~~~~~~~-~~~~~~la~~t~g~s~~di~  127 (131)
                      +-...++..+...++.- +..+..++..+.| +.+++.
T Consensus       187 ei~~~L~~i~~~egi~ie~~AL~~La~~s~G-slR~al  223 (618)
T PRK14951        187 TVLEHLTQVLAAENVPAEPQALRLLARAARG-SMRDAL  223 (618)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHH
Confidence            99999988877665542 2336667776665 344443

>PRK04132 replication factor C small subunit; Provisional

Probab=97.97  E-value=4.9e-05  Score=61.77  Aligned_cols=91  Identities=16%  Similarity=0.253  Sum_probs=66.7

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCHH
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEK   90 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~   90 (131)
                      -|++|||+|.+-.              ...+.++..|+.  ..+.+.+|.+||.++.+.+.+++  |+ ..+.|++|+.+
T Consensus       632 KVvIIDEaD~Lt~--------------~AQnALLk~lEe--p~~~~~FILi~N~~~kIi~tIrS--RC-~~i~F~~ls~~  692 (846)
T PRK04132        632 KIIFLDEADALTQ--------------DAQQALRRTMEM--FSSNVRFILSCNYSSKIIEPIQS--RC-AIFRFRPLRDE  692 (846)
T ss_pred             EEEEEECcccCCH--------------HHHHHHHHHhhC--CCCCeEEEEEeCChhhCchHHhh--hc-eEEeCCCCCHH
Confidence            5999999999842              233445555553  23578899999999999999999  98 58999999999


Q ss_pred             HHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           91 TKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        91 ~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      +-...++..+...++. ++..+..++..+.|
T Consensus       693 ~i~~~L~~I~~~Egi~i~~e~L~~Ia~~s~G  723 (846)
T PRK04132        693 DIAKRLRYIAENEGLELTEEGLQAILYIAEG  723 (846)
T ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHHHcCC
Confidence            8888888877654443 23345566665555

>PRK04195 replication factor C large subunit; Provisional

Probab=97.96  E-value=7.9e-05  Score=57.33  Aligned_cols=95  Identities=14%  Similarity=0.220  Sum_probs=63.2

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccc-cccCCCccceEEEeCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDP-ALIRPGRIDRKIEFPLP   87 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~-~l~~~grf~~~i~~~~P   87 (131)
                      .+.||+|||+|.+..+.      ..    .....++..+.    ..+..+|.+||.+..++. .+++  |+ ..|.|++|
T Consensus        98 ~~kvIiIDEaD~L~~~~------d~----~~~~aL~~~l~----~~~~~iIli~n~~~~~~~k~Lrs--r~-~~I~f~~~  160 (482)
T PRK04195         98 RRKLILLDEVDGIHGNE------DR----GGARAILELIK----KAKQPIILTANDPYDPSLRELRN--AC-LMIEFKRL  160 (482)
T ss_pred             CCeEEEEecCccccccc------ch----hHHHHHHHHHH----cCCCCEEEeccCccccchhhHhc--cc-eEEEecCC
Confidence            57899999999986522      11    12223333333    223346667888888877 5665  54 57999999


Q ss_pred             CHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           88 DEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        88 ~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      +.++...+++..+...+.. .+..+..++..+.|
T Consensus       161 ~~~~i~~~L~~i~~~egi~i~~eaL~~Ia~~s~G  194 (482)
T PRK04195        161 STRSIVPVLKRICRKEGIECDDEALKEIAERSGG  194 (482)
T ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            9999999999988766554 23346667766554

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.92  E-value=4.3e-05  Score=59.15  Aligned_cols=98  Identities=19%  Similarity=0.203  Sum_probs=69.1

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCHH
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEK   90 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~   90 (131)
                      -|++|||+|.+..              ...+.++..++..  .+.+.+|.+|+.++.+++.+++  |+ ..+++.+++.+
T Consensus       121 kV~iIDE~~~ls~--------------~a~naLLk~LEep--p~~~~fIlattd~~kl~~tI~S--Rc-~~~~f~~l~~~  181 (509)
T PRK14958        121 KVYLIDEVHMLSG--------------HSFNALLKTLEEP--PSHVKFILATTDHHKLPVTVLS--RC-LQFHLAQLPPL  181 (509)
T ss_pred             EEEEEEChHhcCH--------------HHHHHHHHHHhcc--CCCeEEEEEECChHhchHHHHH--Hh-hhhhcCCCCHH
Confidence            5999999998842              2345566666642  3467788888889999999999  88 57889999999


Q ss_pred             HHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHH
Q psy522           91 TKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKA  128 (131)
Q Consensus        91 ~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~  128 (131)
                      +-...+++.+...+.. .+..+..++..+.| +.+++..
T Consensus       182 ~i~~~l~~il~~egi~~~~~al~~ia~~s~G-slR~al~  219 (509)
T PRK14958        182 QIAAHCQHLLKEENVEFENAALDLLARAANG-SVRDALS  219 (509)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-cHHHHHH
Confidence            8888888888766554 22336666666655 4555444

>PRK09087 hypothetical protein; Validated

Probab=97.92  E-value=2.5e-05  Score=54.40  Aligned_cols=92  Identities=18%  Similarity=0.233  Sum_probs=61.5

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcc---cccccCCCccc--eEEEeC
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETL---DPALIRPGRID--RKIEFP   85 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~i---d~~l~~~grf~--~~i~~~   85 (131)
                      .+|+|||+|.+..        .+.    .   +++.++.+...++.++|+++..|..+   .+.+++  ||.  ..+.+.
T Consensus        89 ~~l~iDDi~~~~~--------~~~----~---lf~l~n~~~~~g~~ilits~~~p~~~~~~~~dL~S--Rl~~gl~~~l~  151 (226)
T PRK09087         89 GPVLIEDIDAGGF--------DET----G---LFHLINSVRQAGTSLLMTSRLWPSSWNVKLPDLKS--RLKAATVVEIG  151 (226)
T ss_pred             CeEEEECCCCCCC--------CHH----H---HHHHHHHHHhCCCeEEEECCCChHHhccccccHHH--HHhCCceeecC
Confidence            4788999997621        111    1   23333333344566777777655543   578999  884  789999


Q ss_pred             CCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcC
Q psy522           86 LPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKD  119 (131)
Q Consensus        86 ~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~  119 (131)
                      +|+.+.|.++++..+...+.. ++.-+..++.+..
T Consensus       152 ~pd~e~~~~iL~~~~~~~~~~l~~ev~~~La~~~~  186 (226)
T PRK09087        152 EPDDALLSQVIFKLFADRQLYVDPHVVYYLVSRME  186 (226)
T ss_pred             CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhh
Confidence            999999999999998776554 3333556666655

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.90  E-value=7.7e-05  Score=59.12  Aligned_cols=99  Identities=17%  Similarity=0.204  Sum_probs=70.9

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      +..|++|||+|.+-.              ...+.++..++.  ..+.+.+|.+|+.+..+++.+++  |+ ..+.|.+++
T Consensus       118 k~KV~IIDEVh~LS~--------------~A~NALLKtLEE--PP~~v~FILaTtd~~kIp~TIlS--RC-q~feFkpLs  178 (702)
T PRK14960        118 RFKVYLIDEVHMLST--------------HSFNALLKTLEE--PPEHVKFLFATTDPQKLPITVIS--RC-LQFTLRPLA  178 (702)
T ss_pred             CcEEEEEechHhcCH--------------HHHHHHHHHHhc--CCCCcEEEEEECChHhhhHHHHH--hh-heeeccCCC
Confidence            346999999998732              134455656654  23567788888889999999998  88 589999999


Q ss_pred             HHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHH
Q psy522           89 EKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIK  127 (131)
Q Consensus        89 ~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~  127 (131)
                      .++-...++..+...+.. .+..+..++..+.| +.+++.
T Consensus       179 ~eEI~k~L~~Il~kEgI~id~eAL~~IA~~S~G-dLRdAL  217 (702)
T PRK14960        179 VDEITKHLGAILEKEQIAADQDAIWQIAESAQG-SLRDAL  217 (702)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHH
Confidence            999999999888766554 23346667776665 444443

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.90  E-value=6.1e-05  Score=57.95  Aligned_cols=99  Identities=15%  Similarity=0.218  Sum_probs=72.0

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-|++|||+|.+..              ...+.++..++.  ..+.+.+|.+|+.++.+++.+++  |+ ..+.+.+++.
T Consensus       117 ~KVvIIDEah~Ls~--------------~A~NaLLK~LEe--Pp~~v~fIlatte~~Kl~~tI~S--Rc-~~~~f~~l~~  177 (491)
T PRK14964        117 FKVYIIDEVHMLSN--------------SAFNALLKTLEE--PAPHVKFILATTEVKKIPVTIIS--RC-QRFDLQKIPT  177 (491)
T ss_pred             ceEEEEeChHhCCH--------------HHHHHHHHHHhC--CCCCeEEEEEeCChHHHHHHHHH--hh-eeeecccccH
Confidence            45899999988732              245566777764  33567788888888999999999  88 4799999999


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHH
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKA  128 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~  128 (131)
                      ++....++..+...+.. .+..+..+++.+.| +.+++..
T Consensus       178 ~el~~~L~~ia~~Egi~i~~eAL~lIa~~s~G-slR~als  216 (491)
T PRK14964        178 DKLVEHLVDIAKKENIEHDEESLKLIAENSSG-SMRNALF  216 (491)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHH
Confidence            99999999888766554 33346667777765 4554433

>PLN03025 replication factor C subunit; Provisional

Probab=97.89  E-value=5.9e-05  Score=55.04  Aligned_cols=93  Identities=14%  Similarity=0.188  Sum_probs=62.9

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      .+.|++|||+|.+....              ...++..++.+  .+...+|.+||.++.+.+.+++  |+ ..+.+++|+
T Consensus        99 ~~kviiiDE~d~lt~~a--------------q~aL~~~lE~~--~~~t~~il~~n~~~~i~~~L~S--Rc-~~i~f~~l~  159 (319)
T PLN03025         99 RHKIVILDEADSMTSGA--------------QQALRRTMEIY--SNTTRFALACNTSSKIIEPIQS--RC-AIVRFSRLS  159 (319)
T ss_pred             CeEEEEEechhhcCHHH--------------HHHHHHHHhcc--cCCceEEEEeCCccccchhHHH--hh-hcccCCCCC
Confidence            35799999999984321              12233333322  2335577788888899999999  87 479999999


Q ss_pred             HHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           89 EKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        89 ~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      .++....++..++..+.. .+..+..++..+.|
T Consensus       160 ~~~l~~~L~~i~~~egi~i~~~~l~~i~~~~~g  192 (319)
T PLN03025        160 DQEILGRLMKVVEAEKVPYVPEGLEAIIFTADG  192 (319)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            999999999887765543 22335555555443

>CHL00195 ycf46 Ycf46; Provisional

Probab=97.89  E-value=0.00011  Score=56.58  Aligned_cols=104  Identities=19%  Similarity=0.324  Sum_probs=73.4

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      |+|+++.|++.++...         ...+.+..+.....   ..++.+|+.+.+  ..+|+.+.+   +-..+.+|+|+.
T Consensus        82 ~~~~vl~d~h~~~~~~---------~~~r~l~~l~~~~~---~~~~~~i~~~~~--~~~p~el~~---~~~~~~~~lP~~  144 (489)
T CHL00195         82 PALFLLKDFNRFLNDI---------SISRKLRNLSRILK---TQPKTIIIIASE--LNIPKELKD---LITVLEFPLPTE  144 (489)
T ss_pred             CcEEEEecchhhhcch---------HHHHHHHHHHHHHH---hCCCEEEEEcCC--CCCCHHHHh---ceeEEeecCcCH
Confidence            7899999999998321         13344444444333   345555555543  567777775   335789999999


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHhh
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAIC  130 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l~  130 (131)
                      ++..++++.+....+.. .+.+++.++..+.|+|..+++.++
T Consensus       145 ~ei~~~l~~~~~~~~~~~~~~~~~~l~~~~~gls~~~~~~~~  186 (489)
T CHL00195        145 SEIKKELTRLIKSLNIKIDSELLENLTRACQGLSLERIRRVL  186 (489)
T ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCHHHHHHHH
Confidence            99999998887654433 445688999999999999998764

>PRK06620 hypothetical protein; Validated

Probab=97.89  E-value=2.3e-05  Score=54.18  Aligned_cols=90  Identities=18%  Similarity=0.312  Sum_probs=59.6

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCc--ccccccCCCccc--eEEEeC
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIET--LDPALIRPGRID--RKIEFP   85 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~--id~~l~~~grf~--~~i~~~   85 (131)
                      ..+++|||+|.+   .       +    ..+-.+++.+   ...++.++|+++..|..  + +++++  |+.  ..+.++
T Consensus        86 ~d~lliDdi~~~---~-------~----~~lf~l~N~~---~e~g~~ilits~~~p~~l~l-~~L~S--Rl~~gl~~~l~  145 (214)
T PRK06620         86 YNAFIIEDIENW---Q-------E----PALLHIFNII---NEKQKYLLLTSSDKSRNFTL-PDLSS--RIKSVLSILLN  145 (214)
T ss_pred             CCEEEEeccccc---h-------H----HHHHHHHHHH---HhcCCEEEEEcCCCccccch-HHHHH--HHhCCceEeeC
Confidence            368999999943   1       1    1222333333   35567788888876665  5 78999  884  479999


Q ss_pred             CCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcC
Q psy522           86 LPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKD  119 (131)
Q Consensus        86 ~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~  119 (131)
                      +|+.+.+.++++......++. ++.-++.++....
T Consensus       146 ~pd~~~~~~~l~k~~~~~~l~l~~ev~~~L~~~~~  180 (214)
T PRK06620        146 SPDDELIKILIFKHFSISSVTISRQIIDFLLVNLP  180 (214)
T ss_pred             CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcc
Confidence            999999999999887755443 2223455555544

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=97.88  E-value=0.00013  Score=56.72  Aligned_cols=97  Identities=21%  Similarity=0.227  Sum_probs=68.4

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCHH
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEK   90 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~   90 (131)
                      -|++|||+|.+-.              ...+.++..+...  .+.+.+|.+|+.+..+.+.+++  |+ ..+++.+++.+
T Consensus       119 KVvIIDEad~Lt~--------------~A~NALLK~LEEp--p~~t~FIL~ttd~~kL~~tI~S--Rc-~~~~F~~Ls~~  179 (535)
T PRK08451        119 KIFIIDEVHMLTK--------------EAFNALLKTLEEP--PSYVKFILATTDPLKLPATILS--RT-QHFRFKQIPQN  179 (535)
T ss_pred             EEEEEECcccCCH--------------HHHHHHHHHHhhc--CCceEEEEEECChhhCchHHHh--hc-eeEEcCCCCHH
Confidence            4899999988732              2344566666643  3456777777888999999999  86 58999999999


Q ss_pred             HHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHH
Q psy522           91 TKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIK  127 (131)
Q Consensus        91 ~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~  127 (131)
                      +-...+++.+...+.. .+..+..++..+.| +.+++.
T Consensus       180 ei~~~L~~Il~~EGi~i~~~Al~~Ia~~s~G-dlR~al  216 (535)
T PRK08451        180 SIISHLKTILEKEGVSYEPEALEILARSGNG-SLRDTL  216 (535)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-cHHHHH
Confidence            9888888888765544 22346666666555 444443

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.87  E-value=0.00013  Score=56.48  Aligned_cols=93  Identities=19%  Similarity=0.231  Sum_probs=68.0

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      .+.||+|||+|.+..              ..++.++..++.  ..+.+++|.+|+.++.+.+.+.+  |+. .+.|.+|+
T Consensus       116 ~~kVVIIDEad~ls~--------------~a~naLLk~LEe--p~~~t~~Il~t~~~~kl~~~I~S--Rc~-~~~f~~ls  176 (504)
T PRK14963        116 GRKVYILDEAHMMSK--------------SAFNALLKTLEE--PPEHVIFILATTEPEKMPPTILS--RTQ-HFRFRRLT  176 (504)
T ss_pred             CCeEEEEECccccCH--------------HHHHHHHHHHHh--CCCCEEEEEEcCChhhCChHHhc--ceE-EEEecCCC
Confidence            456999999986621              234556666654  23467788888999999999999  875 79999999


Q ss_pred             HHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           89 EKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        89 ~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      .++-...+++.++..+.. .+..+..++..+.|
T Consensus       177 ~~el~~~L~~i~~~egi~i~~~Al~~ia~~s~G  209 (504)
T PRK14963        177 EEEIAGKLRRLLEAEGREAEPEALQLVARLADG  209 (504)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            999999999988766554 22335666666655

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

Probab=97.84  E-value=7.9e-05  Score=55.96  Aligned_cols=94  Identities=21%  Similarity=0.317  Sum_probs=66.0

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCccc---ccccCCCcc--ceEEEe
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLD---PALIRPGRI--DRKIEF   84 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id---~~l~~~grf--~~~i~~   84 (131)
                      =.+++|||++.+..+.            ++..++.+.+..+...++-+++.+-..|..++   +.+++  ||  ...+.+
T Consensus       176 ~dlllIDDiq~l~gk~------------~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~S--R~~~Gl~~~I  241 (408)
T COG0593         176 LDLLLIDDIQFLAGKE------------RTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLRS--RLEWGLVVEI  241 (408)
T ss_pred             cCeeeechHhHhcCCh------------hHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHHH--HHhceeEEee
Confidence            3589999999997664            22333444444445566677777777888875   88999  97  567888


Q ss_pred             CCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHH
Q psy522           85 PLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMA  117 (131)
Q Consensus        85 ~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~  117 (131)
                      .+|+.+.|.+|++......++. ++.-...++.+
T Consensus       242 ~~Pd~e~r~aiL~kka~~~~~~i~~ev~~~la~~  275 (408)
T COG0593         242 EPPDDETRLAILRKKAEDRGIEIPDEVLEFLAKR  275 (408)
T ss_pred             CCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence            8999999999999977665555 22224445554

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.83  E-value=0.00019  Score=53.22  Aligned_cols=92  Identities=18%  Similarity=0.253  Sum_probs=63.9

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      +.||++||+|.+..              .....++..++.  ..+..++|.+|+.+..+.+++.+  |+. .+.+++|+.
T Consensus       109 ~kiviIDE~~~l~~--------------~~~~~ll~~le~--~~~~~~~Il~~~~~~kl~~~l~s--r~~-~v~~~~~~~  169 (367)
T PRK14970        109 YKIYIIDEVHMLSS--------------AAFNAFLKTLEE--PPAHAIFILATTEKHKIIPTILS--RCQ-IFDFKRITI  169 (367)
T ss_pred             cEEEEEeChhhcCH--------------HHHHHHHHHHhC--CCCceEEEEEeCCcccCCHHHHh--cce-eEecCCccH
Confidence            46999999987732              134455555554  23345666677778899999998  774 689999999


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      ++...++...+...+.. ++..+..++..+.|
T Consensus       170 ~~l~~~l~~~~~~~g~~i~~~al~~l~~~~~g  201 (367)
T PRK14970        170 KDIKEHLAGIAVKEGIKFEDDALHIIAQKADG  201 (367)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCC
Confidence            99999998877765543 23345666666544

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.82  E-value=0.00012  Score=50.82  Aligned_cols=104  Identities=14%  Similarity=0.189  Sum_probs=60.7

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCC-CC--cccccccCCCcc--ceEEE
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNR-IE--TLDPALIRPGRI--DRKIE   83 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~-~~--~id~~l~~~grf--~~~i~   83 (131)
                      ...+|+|||+|.+-..       .    ...+..+++..   ...+..++|.+++. +.  .+.+.+.+  ||  ...+.
T Consensus        90 ~~~~liiDdi~~l~~~-------~----~~~L~~~~~~~---~~~~~~~vl~~~~~~~~~~~l~~~L~s--r~~~~~~i~  153 (227)
T PRK08903         90 EAELYAVDDVERLDDA-------Q----QIALFNLFNRV---RAHGQGALLVAGPAAPLALPLREDLRT--RLGWGLVYE  153 (227)
T ss_pred             cCCEEEEeChhhcCch-------H----HHHHHHHHHHH---HHcCCcEEEEeCCCCHHhCCCCHHHHH--HHhcCeEEE
Confidence            3578999999986321       1    12233333333   23344334444443 32  24567777  77  47999


Q ss_pred             eCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHh
Q psy522           84 FPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAI  129 (131)
Q Consensus        84 ~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l  129 (131)
                      +++|+.+++..+++.+..+.++. ++.-+..++....| +..++..+
T Consensus       154 l~pl~~~~~~~~l~~~~~~~~v~l~~~al~~L~~~~~g-n~~~l~~~  199 (227)
T PRK08903        154 LKPLSDADKIAALKAAAAERGLQLADEVPDYLLTHFRR-DMPSLMAL  199 (227)
T ss_pred             ecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccC-CHHHHHHH
Confidence            99999999999999887665554 22235556664333 34444443

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=97.81  E-value=0.00021  Score=52.93  Aligned_cols=93  Identities=16%  Similarity=0.165  Sum_probs=63.4

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      ..-|++|||+|.+-.              ...+.++..++..  ..+.++|..|+.++.+.+.+++  |+ ..+.+++|+
T Consensus       141 ~~rVviIDeAd~l~~--------------~aanaLLk~LEEp--p~~~~fiLit~~~~~llptIrS--Rc-~~i~l~pl~  201 (351)
T PRK09112        141 NWRIVIIDPADDMNR--------------NAANAILKTLEEP--PARALFILISHSSGRLLPTIRS--RC-QPISLKPLD  201 (351)
T ss_pred             CceEEEEEchhhcCH--------------HHHHHHHHHHhcC--CCCceEEEEECChhhccHHHHh--hc-cEEEecCCC
Confidence            456999999999832              2334466666642  3355666667889999999999  98 599999999


Q ss_pred             HHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCC
Q psy522           89 EKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDL  121 (131)
Q Consensus        89 ~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~  121 (131)
                      .++-..++.+......+. +..+..++..+.|-
T Consensus       202 ~~~~~~~L~~~~~~~~~~-~~~~~~i~~~s~G~  233 (351)
T PRK09112        202 DDELKKALSHLGSSQGSD-GEITEALLQRSKGS  233 (351)
T ss_pred             HHHHHHHHHHhhcccCCC-HHHHHHHHHHcCCC
Confidence            999999998743222211 22255566666664

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=97.80  E-value=8e-05  Score=54.94  Aligned_cols=57  Identities=18%  Similarity=0.353  Sum_probs=46.8

Q ss_pred             HHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCHHHHHHHHHHH
Q psy522           38 RTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIH   99 (131)
Q Consensus        38 ~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~   99 (131)
                      ...+.+|+.++.  ..+++++|.+|++++.+.|.+++  |+ ..+.+++|+.++..+.+...
T Consensus       147 ~AaNaLLKtLEE--Pp~~t~fiL~t~~~~~LLpTI~S--Rc-q~i~~~~~~~~~~~~~L~~~  203 (342)
T PRK06964        147 AAANALLKTLEE--PPPGTVFLLVSARIDRLLPTILS--RC-RQFPMTVPAPEAAAAWLAAQ  203 (342)
T ss_pred             HHHHHHHHHhcC--CCcCcEEEEEECChhhCcHHHHh--cC-EEEEecCCCHHHHHHHHHHc
Confidence            345667777774  45678999999999999999999  99 58999999999988888653

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=97.80  E-value=0.0002  Score=57.37  Aligned_cols=92  Identities=16%  Similarity=0.265  Sum_probs=67.9

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      ..|++|||+|.+-.              ...+.++..++.  ..+.+++|.+|+.++.|++.+++  |+. .+.+.+|+.
T Consensus       119 ~KV~IIDEa~~LT~--------------~A~NALLKtLEE--PP~~tifILaTte~~KLl~TI~S--Rcq-~ieF~~L~~  179 (725)
T PRK07133        119 YKIYIIDEVHMLSK--------------SAFNALLKTLEE--PPKHVIFILATTEVHKIPLTILS--RVQ-RFNFRRISE  179 (725)
T ss_pred             CEEEEEEChhhCCH--------------HHHHHHHHHhhc--CCCceEEEEEcCChhhhhHHHHh--hce-eEEccCCCH
Confidence            46999999998732              245556666664  34567888888889999999999  885 899999999


Q ss_pred             HHHHHHHHHHhcCCCCCCc-ccHHHHHHHcCC
Q psy522           90 KTKRRIFNIHTSRMTLAED-VNLQELIMAKDD  120 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~~~-~~~~~la~~t~g  120 (131)
                      ++-...++..+...+..-+ ..+..++..+.|
T Consensus       180 eeI~~~L~~il~kegI~id~eAl~~LA~lS~G  211 (725)
T PRK07133        180 DEIVSRLEFILEKENISYEKNALKLIAKLSSG  211 (725)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            9999999887766554422 235566666655

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.79  E-value=0.00011  Score=58.00  Aligned_cols=92  Identities=14%  Similarity=0.200  Sum_probs=67.4

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      ..||+|||+|.+-.              ...+.++..++.  ..+.+++|++|+.++.+.+.+++  |+. .+.|+.++.
T Consensus       120 ~kVIIIDEad~Lt~--------------~a~naLLk~LEE--P~~~~ifILaTt~~~kll~TI~S--Rcq-~i~F~pLs~  180 (624)
T PRK14959        120 YKVFIIDEAHMLTR--------------EAFNALLKTLEE--PPARVTFVLATTEPHKFPVTIVS--RCQ-HFTFTRLSE  180 (624)
T ss_pred             ceEEEEEChHhCCH--------------HHHHHHHHHhhc--cCCCEEEEEecCChhhhhHHHHh--hhh-ccccCCCCH
Confidence            46999999998832              234556666664  23568888889999999999998  884 789999999


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      ++-..+++..+...+.. .+..+..+++.+.|
T Consensus       181 ~eL~~~L~~il~~egi~id~eal~lIA~~s~G  212 (624)
T PRK14959        181 AGLEAHLTKVLGREGVDYDPAAVRLIARRAAG  212 (624)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            99999998877765543 22335666766665

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=97.78  E-value=0.00016  Score=56.70  Aligned_cols=97  Identities=18%  Similarity=0.229  Sum_probs=69.0

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-|++|||+|.+-.              ...+.++..++.  ..+.+++|++|+.++.+.+.+++  |+. .+.+.+++.
T Consensus       120 ~KVvIIDEa~~Ls~--------------~a~naLLK~LEe--pp~~~vfI~~tte~~kL~~tI~S--Rc~-~~~f~~l~~  180 (563)
T PRK06647        120 YRVYIIDEVHMLSN--------------SAFNALLKTIEE--PPPYIVFIFATTEVHKLPATIKS--RCQ-HFNFRLLSL  180 (563)
T ss_pred             CEEEEEEChhhcCH--------------HHHHHHHHhhcc--CCCCEEEEEecCChHHhHHHHHH--hce-EEEecCCCH
Confidence            45899999988731              244556666664  34568888888888999999999  886 689999999


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHH
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADI  126 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di  126 (131)
                      ++...+++..+...+.. .+..+..++..+.| +.+++
T Consensus       181 ~el~~~L~~i~~~egi~id~eAl~lLa~~s~G-dlR~a  217 (563)
T PRK06647        181 EKIYNMLKKVCLEDQIKYEDEALKWIAYKSTG-SVRDA  217 (563)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHH
Confidence            99999998887655544 22345666766665 34443

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=97.78  E-value=0.00011  Score=57.77  Aligned_cols=91  Identities=19%  Similarity=0.304  Sum_probs=66.3

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCHH
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEK   90 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~   90 (131)
                      -|++|||+|.+-.              ...+.++..++.  ..+.+++|.+|+.+..+.+.+++  |+. .+.+++|+.+
T Consensus       121 KVIIIDEad~Lt~--------------~A~NaLLKtLEE--Pp~~tvfIL~Tt~~~KLl~TI~S--Rcq-~ieF~~Ls~~  181 (605)
T PRK05896        121 KVYIIDEAHMLST--------------SAWNALLKTLEE--PPKHVVFIFATTEFQKIPLTIIS--RCQ-RYNFKKLNNS  181 (605)
T ss_pred             EEEEEechHhCCH--------------HHHHHHHHHHHh--CCCcEEEEEECCChHhhhHHHHh--hhh-hcccCCCCHH
Confidence            4899999998731              133456666664  33467888888889999999999  885 7999999999


Q ss_pred             HHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           91 TKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        91 ~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      +-...++..+...+.. ++..+..++..+.|
T Consensus       182 eL~~~L~~il~kegi~Is~eal~~La~lS~G  212 (605)
T PRK05896        182 ELQELLKSIAKKEKIKIEDNAIDKIADLADG  212 (605)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            9999999887665533 22335666666665

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.78  E-value=0.00019  Score=55.27  Aligned_cols=92  Identities=16%  Similarity=0.273  Sum_probs=65.6

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      +-|++|||+|.+..              ...+.++..+...  .+.+++|.+|+.++.+++.+.+  |+. .+.+++|+.
T Consensus       120 ~KVvIIDEad~Lt~--------------~a~naLLk~LEep--p~~~v~Il~tt~~~kl~~tI~S--Rc~-~i~f~~ls~  180 (486)
T PRK14953        120 YKVYIIDEAHMLTK--------------EAFNALLKTLEEP--PPRTIFILCTTEYDKIPPTILS--RCQ-RFIFSKPTK  180 (486)
T ss_pred             eeEEEEEChhhcCH--------------HHHHHHHHHHhcC--CCCeEEEEEECCHHHHHHHHHH--hce-EEEcCCCCH
Confidence            46999999997732              2334556666542  3345666666778889999998  875 799999999


Q ss_pred             HHHHHHHHHHhcCCCCCC-cccHHHHHHHcCC
Q psy522           90 KTKRRIFNIHTSRMTLAE-DVNLQELIMAKDD  120 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~~-~~~~~~la~~t~g  120 (131)
                      ++...+++..++..+... +..+..++..+.|
T Consensus       181 ~el~~~L~~i~k~egi~id~~al~~La~~s~G  212 (486)
T PRK14953        181 EQIKEYLKRICNEEKIEYEEKALDLLAQASEG  212 (486)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            999999999888766542 2336667776665

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=97.77  E-value=0.00022  Score=51.96  Aligned_cols=90  Identities=16%  Similarity=0.258  Sum_probs=58.3

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      +.+|+|||+|.+-..           ....   +...++...  +...+|.+|+.+..+.+.+.+  |+ ..+.+.+|+.
T Consensus       126 ~~vlilDe~~~l~~~-----------~~~~---L~~~le~~~--~~~~~Il~~~~~~~~~~~L~s--r~-~~v~~~~~~~  186 (337)
T PRK12402        126 YKTILLDNAEALRED-----------AQQA---LRRIMEQYS--RTCRFIIATRQPSKLIPPIRS--RC-LPLFFRAPTD  186 (337)
T ss_pred             CcEEEEeCcccCCHH-----------HHHH---HHHHHHhcc--CCCeEEEEeCChhhCchhhcC--Cc-eEEEecCCCH
Confidence            469999999987321           1122   333333322  234455566667778788888  76 4789999999


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHc
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAK  118 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t  118 (131)
                      ++...+++..+...+.. .+..+..++..+
T Consensus       187 ~~~~~~l~~~~~~~~~~~~~~al~~l~~~~  216 (337)
T PRK12402        187 DELVDVLESIAEAEGVDYDDDGLELIAYYA  216 (337)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHc
Confidence            99999999988766544 223355555554

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=97.76  E-value=0.0002  Score=54.79  Aligned_cols=94  Identities=19%  Similarity=0.238  Sum_probs=67.1

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCC
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLP   87 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P   87 (131)
                      ....||+|||+|.+..              ...+.++..++..  .+.+++|++|+.++.+.+.+++  |+. .+.++++
T Consensus       120 ~~~kvvIIdead~lt~--------------~~~n~LLk~lEep--~~~~~~Il~t~~~~kl~~tI~s--Rc~-~v~f~~l  180 (451)
T PRK06305        120 SRYKIYIIDEVHMLTK--------------EAFNSLLKTLEEP--PQHVKFFLATTEIHKIPGTILS--RCQ-KMHLKRI  180 (451)
T ss_pred             CCCEEEEEecHHhhCH--------------HHHHHHHHHhhcC--CCCceEEEEeCChHhcchHHHH--hce-EEeCCCC
Confidence            3467999999988742              1345566666652  3467777888888999999999  884 7899999


Q ss_pred             CHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           88 DEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        88 ~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      +.++-...++..++..+.. .+..+..++..+.|
T Consensus       181 ~~~el~~~L~~~~~~eg~~i~~~al~~L~~~s~g  214 (451)
T PRK06305        181 PEETIIDKLALIAKQEGIETSREALLPIARAAQG  214 (451)
T ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            9999888888877655443 22335556666554

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.75  E-value=0.00028  Score=57.65  Aligned_cols=93  Identities=19%  Similarity=0.233  Sum_probs=69.5

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-|++|||+|.+-.              ...+.++..|+.  ..+.+.+|++|+.+..|.+.+++  |+ ..+.|++++.
T Consensus       120 ~KViIIDEAh~LT~--------------eAqNALLKtLEE--PP~~vrFILaTTe~~kLl~TIlS--RC-q~f~fkpLs~  180 (944)
T PRK14949        120 FKVYLIDEVHMLSR--------------SSFNALLKTLEE--PPEHVKFLLATTDPQKLPVTVLS--RC-LQFNLKSLTQ  180 (944)
T ss_pred             cEEEEEechHhcCH--------------HHHHHHHHHHhc--cCCCeEEEEECCCchhchHHHHH--hh-eEEeCCCCCH
Confidence            46999999999832              355666766664  34567788888889999999999  88 5899999999


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCC
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDL  121 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~  121 (131)
                      ++-.+.+++.+...++. .+..+..++..+.|-
T Consensus       181 eEI~~~L~~il~~EgI~~edeAL~lIA~~S~Gd  213 (944)
T PRK14949        181 DEIGTQLNHILTQEQLPFEAEALTLLAKAANGS  213 (944)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCC
Confidence            99999999888654443 222366677777763

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=97.72  E-value=0.00024  Score=52.22  Aligned_cols=72  Identities=19%  Similarity=0.380  Sum_probs=56.3

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      ..-|++||++|.+-.              ...+.+++.++.  ..+++++|.+|++++.+.+.+++  |+. .+.|++|+
T Consensus       106 ~~kv~iI~~a~~m~~--------------~aaNaLLK~LEE--Pp~~~~fiL~t~~~~~ll~TI~S--Rc~-~~~~~~~~  166 (328)
T PRK05707        106 GRKVVLIEPAEAMNR--------------NAANALLKSLEE--PSGDTVLLLISHQPSRLLPTIKS--RCQ-QQACPLPS  166 (328)
T ss_pred             CCeEEEECChhhCCH--------------HHHHHHHHHHhC--CCCCeEEEEEECChhhCcHHHHh--hce-eeeCCCcC
Confidence            345788899998842              345566666664  33578899999999999999999  996 59999999


Q ss_pred             HHHHHHHHHHH
Q psy522           89 EKTKRRIFNIH   99 (131)
Q Consensus        89 ~~~R~~il~~~   99 (131)
                      .++-.+.+...
T Consensus       167 ~~~~~~~L~~~  177 (328)
T PRK05707        167 NEESLQWLQQA  177 (328)
T ss_pred             HHHHHHHHHHh
Confidence            99888777654

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.72  E-value=0.00019  Score=56.03  Aligned_cols=92  Identities=15%  Similarity=0.275  Sum_probs=65.9

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-|++|||+|.+-.              ...+.++..++.  ..+.+++|++|+.+..+.+.+++  |+ ..+++.+++.
T Consensus       120 ~kViIIDEa~~ls~--------------~a~naLLK~LEe--pp~~v~fIL~Ttd~~kil~tI~S--Rc-~~~~f~~Ls~  180 (546)
T PRK14957        120 YKVYLIDEVHMLSK--------------QSFNALLKTLEE--PPEYVKFILATTDYHKIPVTILS--RC-IQLHLKHISQ  180 (546)
T ss_pred             cEEEEEechhhccH--------------HHHHHHHHHHhc--CCCCceEEEEECChhhhhhhHHH--he-eeEEeCCCCH
Confidence            46999999988732              244556666664  23456777777778999988998  88 6899999999


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      ++-...++..+...+.. .+..+..++..+.|
T Consensus       181 ~eI~~~L~~il~~egi~~e~~Al~~Ia~~s~G  212 (546)
T PRK14957        181 ADIKDQLKIILAKENINSDEQSLEYIAYHAKG  212 (546)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            99888888877765544 22335666666654

>PRK13342 recombination factor protein RarA; Reviewed

Probab=97.71  E-value=0.00032  Score=53.02  Aligned_cols=91  Identities=24%  Similarity=0.346  Sum_probs=61.2

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCC-C-CCcccccccCCCccceEEEeCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATN-R-IETLDPALIRPGRIDRKIEFPL   86 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn-~-~~~id~~l~~~grf~~~i~~~~   86 (131)
                      ...||||||+|.+...              ....++..++    .+.+++|++|. . ...+++++++  |+ ..+.+++
T Consensus        92 ~~~vL~IDEi~~l~~~--------------~q~~LL~~le----~~~iilI~att~n~~~~l~~aL~S--R~-~~~~~~~  150 (413)
T PRK13342         92 RRTILFIDEIHRFNKA--------------QQDALLPHVE----DGTITLIGATTENPSFEVNPALLS--RA-QVFELKP  150 (413)
T ss_pred             CceEEEEechhhhCHH--------------HHHHHHHHhh----cCcEEEEEeCCCChhhhccHHHhc--cc-eeeEeCC
Confidence            5689999999987422              1223333333    35677777653 3 4578999999  98 6899999


Q ss_pred             CCHHHHHHHHHHHhcCC--CC-C-CcccHHHHHHHcCC
Q psy522           87 PDEKTKRRIFNIHTSRM--TL-A-EDVNLQELIMAKDD  120 (131)
Q Consensus        87 P~~~~R~~il~~~l~~~--~~-~-~~~~~~~la~~t~g  120 (131)
                      |+.++...+++..+...  +. . .+..+..++..+.|
T Consensus       151 ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s~G  188 (413)
T PRK13342        151 LSEEDIEQLLKRALEDKERGLVELDDEALDALARLANG  188 (413)
T ss_pred             CCHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhCCC
Confidence            99999999999887542  11 1 22235566666654

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.70  E-value=0.00031  Score=55.28  Aligned_cols=92  Identities=22%  Similarity=0.246  Sum_probs=66.0

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-|++|||+|.+-.              ...+.++..++.  ..+.+++|.+|+.++.+.+.+++  |+ ..+.|..++.
T Consensus       119 ~KVvIIDEah~Lt~--------------~A~NALLK~LEE--pp~~~~fIL~tte~~kll~TI~S--Rc-~~~~F~~l~~  179 (584)
T PRK14952        119 YRIFIVDEAHMVTT--------------AGFNALLKIVEE--PPEHLIFIFATTEPEKVLPTIRS--RT-HHYPFRLLPP  179 (584)
T ss_pred             ceEEEEECCCcCCH--------------HHHHHHHHHHhc--CCCCeEEEEEeCChHhhHHHHHH--hc-eEEEeeCCCH
Confidence            35899999988732              245556666664  33568888888888999999999  86 5899999999


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      ++-.++++..+...+.. .+..+..++..+.|
T Consensus       180 ~~i~~~L~~i~~~egi~i~~~al~~Ia~~s~G  211 (584)
T PRK14952        180 RTMRALIARICEQEGVVVDDAVYPLVIRAGGG  211 (584)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            99888998888766543 22234555555444

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=97.67  E-value=0.00051  Score=50.33  Aligned_cols=81  Identities=14%  Similarity=0.151  Sum_probs=57.7

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHH-----hc----CCCCCCCeEEEeeCCCCC------------c
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQ-----LD----GFDSRGDVKVIMATNRIE------------T   67 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~-----~~----~~~~~~~v~vi~ttn~~~------------~   67 (131)
                      .+.++++||+|..-++           ....++.+|+.     +.    .+...+.+.||||.|..+            .
T Consensus       134 ~g~illlDEin~a~p~-----------~~~~L~~lLE~~~~l~i~~~~~~i~~hp~FrviAT~Np~g~Gd~~G~y~Gt~~  202 (327)
T TIGR01650       134 HNVALCFDEYDAGRPD-----------VMFVIQRVLEAGGKLTLLDQNRVIRAHPAFRLFATANTIGLGDTTGLYHGTQQ  202 (327)
T ss_pred             CCeEEEechhhccCHH-----------HHHHHHHHhccCCeEEECCCceEecCCCCeEEEEeeCCCCcCCCCcceeeeec
Confidence            4589999999986322           33455555542     11    122335688999999755            3


Q ss_pred             ccccccCCCccceEEEeCCCCHHHHHHHHHHHhcC
Q psy522           68 LDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSR  102 (131)
Q Consensus        68 id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~  102 (131)
                      ++.+++.  ||-..+.+++|+.++-.+|+......
T Consensus       203 l~~A~lD--RF~i~~~~~Yp~~e~E~~Il~~~~~~  235 (327)
T TIGR01650       203 INQAQMD--RWSIVTTLNYLEHDNEAAIVLAKAKG  235 (327)
T ss_pred             CCHHHHh--heeeEeeCCCCCHHHHHHHHHhhccC
Confidence            5889999  99888899999999999999876543

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.

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.66  E-value=0.00012  Score=57.59  Aligned_cols=91  Identities=20%  Similarity=0.268  Sum_probs=66.2

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCHH
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEK   90 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~   90 (131)
                      -|++|||+|.+..              ...+.++..++.  ..+.+++|.+|+.++.|.+.+++  |+. .+.|..++.+
T Consensus       121 KVvIIdev~~Lt~--------------~a~naLLk~LEe--pp~~~~fIl~t~~~~kl~~tI~S--Rc~-~~~f~~l~~~  181 (576)
T PRK14965        121 KIFIIDEVHMLST--------------NAFNALLKTLEE--PPPHVKFIFATTEPHKVPITILS--RCQ-RFDFRRIPLQ  181 (576)
T ss_pred             eEEEEEChhhCCH--------------HHHHHHHHHHHc--CCCCeEEEEEeCChhhhhHHHHH--hhh-hhhcCCCCHH
Confidence            4899999988732              234556666664  34568888888999999999999  874 7889999999


Q ss_pred             HHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           91 TKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        91 ~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      +-...+...++..+.. .+..+..++..+.|
T Consensus       182 ~i~~~L~~i~~~egi~i~~~al~~la~~a~G  212 (576)
T PRK14965        182 KIVDRLRYIADQEGISISDAALALVARKGDG  212 (576)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC
Confidence            8888888877766544 22345556666655

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

Probab=97.60  E-value=0.00079  Score=50.94  Aligned_cols=27  Identities=26%  Similarity=0.305  Sum_probs=22.6

Q ss_pred             cccccCCCccceEEEeCCCCHHHHHHHHH
Q psy522           69 DPALIRPGRIDRKIEFPLPDEKTKRRIFN   97 (131)
Q Consensus        69 d~~l~~~grf~~~i~~~~P~~~~R~~il~   97 (131)
                      .|+|+.  |++..+.+.+.+.++...|+.
T Consensus       296 ~PEflg--Rld~iv~f~~L~~~~L~~Il~  322 (412)
T PRK05342        296 IPEFIG--RLPVVATLEELDEEALVRILT  322 (412)
T ss_pred             hHHHhC--CCCeeeecCCCCHHHHHHHHH
Confidence            344444  999999999999999999997

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=97.60  E-value=0.00057  Score=50.92  Aligned_cols=74  Identities=14%  Similarity=0.166  Sum_probs=56.8

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCC
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLP   87 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P   87 (131)
                      ..|-|++|||+|.+-.              ...+.++..+..  ..+.+++|.+|+.++.+.+.+++  |+. .+.+++|
T Consensus       140 ~~~kVviIDead~m~~--------------~aanaLLK~LEe--pp~~~~~IL~t~~~~~llpti~S--Rc~-~i~l~~l  200 (365)
T PRK07471        140 GGWRVVIVDTADEMNA--------------NAANALLKVLEE--PPARSLFLLVSHAPARLLPTIRS--RCR-KLRLRPL  200 (365)
T ss_pred             CCCEEEEEechHhcCH--------------HHHHHHHHHHhc--CCCCeEEEEEECCchhchHHhhc--cce-EEECCCC
Confidence            4678999999998732              244456666653  23456788889999999999998  884 8999999


Q ss_pred             CHHHHHHHHHHHh
Q psy522           88 DEKTKRRIFNIHT  100 (131)
Q Consensus        88 ~~~~R~~il~~~l  100 (131)
                      +.++-.+++....
T Consensus       201 ~~~~i~~~L~~~~  213 (365)
T PRK07471        201 APEDVIDALAAAG  213 (365)
T ss_pred             CHHHHHHHHHHhc
Confidence            9999888887753

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.59  E-value=0.00037  Score=54.29  Aligned_cols=92  Identities=16%  Similarity=0.172  Sum_probs=66.5

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      ..|++|||+|.+..              ...+.++..++.  ..+.+++|.+|++++.+.+.+++  |+ ..+.|+.|+.
T Consensus       120 ~kVvIIDEad~ls~--------------~a~naLLK~LEe--pp~~~~fIL~t~d~~kil~tI~S--Rc-~~~~f~~l~~  180 (527)
T PRK14969        120 FKVYIIDEVHMLSK--------------SAFNAMLKTLEE--PPEHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPP  180 (527)
T ss_pred             ceEEEEcCcccCCH--------------HHHHHHHHHHhC--CCCCEEEEEEeCChhhCchhHHH--HH-HHHhcCCCCH
Confidence            35999999998732              234556666664  33567788888889999988998  87 5899999999


Q ss_pred             HHHHHHHHHHhcCCCCCC-cccHHHHHHHcCC
Q psy522           90 KTKRRIFNIHTSRMTLAE-DVNLQELIMAKDD  120 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~~-~~~~~~la~~t~g  120 (131)
                      ++-...+...+...+... +..+..++..+.|
T Consensus       181 ~~i~~~L~~il~~egi~~~~~al~~la~~s~G  212 (527)
T PRK14969        181 PLIVSHLQHILEQENIPFDATALQLLARAAAG  212 (527)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            998888888876555442 2335666666655

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.59  E-value=0.00036  Score=55.66  Aligned_cols=98  Identities=19%  Similarity=0.166  Sum_probs=69.5

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      ..|++|||+|.+-.              ...+.++..++.  ..+.+.+|.+|+.++.+.+.+++  |+ ..+.|+.++.
T Consensus       120 ~KVIIIDEad~Ls~--------------~A~NALLKtLEE--Pp~~v~fILaTtd~~kL~~TIrS--RC-~~f~f~~Ls~  180 (709)
T PRK08691        120 YKVYIIDEVHMLSK--------------SAFNAMLKTLEE--PPEHVKFILATTDPHKVPVTVLS--RC-LQFVLRNMTA  180 (709)
T ss_pred             cEEEEEECccccCH--------------HHHHHHHHHHHh--CCCCcEEEEEeCCccccchHHHH--HH-hhhhcCCCCH
Confidence            46999999987631              234456666664  23567888888999999999998  88 4788889999


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHH
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIK  127 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~  127 (131)
                      ++-...+++.+...++. .+..+..|+..+.| +.+++.
T Consensus       181 eeI~~~L~~Il~kEgi~id~eAL~~Ia~~A~G-slRdAl  218 (709)
T PRK08691        181 QQVADHLAHVLDSEKIAYEPPALQLLGRAAAG-SMRDAL  218 (709)
T ss_pred             HHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCC-CHHHHH
Confidence            99999999988876654 22336666666554 344443

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

Probab=97.59  E-value=0.00041  Score=48.26  Aligned_cols=97  Identities=19%  Similarity=0.241  Sum_probs=62.8

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCC-----CC-----------CCeEEEeeCCCCCcccccc
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFD-----SR-----------GDVKVIMATNRIETLDPAL   72 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----~~-----------~~v~vi~ttn~~~~id~~l   72 (131)
                      ...||||||++.+-..              +...++..|++..     ..           ++..+||+|.....+.+.+
T Consensus       101 ~~~ILFIDEIHRlnk~--------------~qe~LlpamEd~~idiiiG~g~~ar~~~~~l~~FTligATTr~g~ls~pL  166 (233)
T PF05496_consen  101 EGDILFIDEIHRLNKA--------------QQEILLPAMEDGKIDIIIGKGPNARSIRINLPPFTLIGATTRAGLLSSPL  166 (233)
T ss_dssp             TT-EEEECTCCC--HH--------------HHHHHHHHHHCSEEEEEBSSSSS-BEEEEE----EEEEEESSGCCTSHCC
T ss_pred             CCcEEEEechhhccHH--------------HHHHHHHHhccCeEEEEeccccccceeeccCCCceEeeeeccccccchhH
Confidence            4689999999998432              2222333333210     11           4689999999999999999


Q ss_pred             cCCCccceEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCC
Q psy522           73 IRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDL  121 (131)
Q Consensus        73 ~~~grf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~  121 (131)
                      +.  ||.....+..=+.++-.+|++......++. .+.-..++|.++.|-
T Consensus       167 rd--RFgi~~~l~~Y~~~el~~Iv~r~a~~l~i~i~~~~~~~Ia~rsrGt  214 (233)
T PF05496_consen  167 RD--RFGIVLRLEFYSEEELAKIVKRSARILNIEIDEDAAEEIARRSRGT  214 (233)
T ss_dssp             CT--TSSEEEE----THHHHHHHHHHCCHCTT-EE-HHHHHHHHHCTTTS
T ss_pred             Hh--hcceecchhcCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHhcCCC
Confidence            99  999888999999999999998877666655 333477788888774

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.

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.58  E-value=0.0008  Score=48.65  Aligned_cols=92  Identities=13%  Similarity=0.233  Sum_probs=63.2

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      +.+|+|||+|.+...              ....++..++...  +...+|.++|.+..+.+.+.+  |+. .+++++|+.
T Consensus       103 ~~vviiDe~~~l~~~--------------~~~~L~~~le~~~--~~~~lIl~~~~~~~l~~~l~s--r~~-~~~~~~l~~  163 (319)
T PRK00440        103 FKIIFLDEADNLTSD--------------AQQALRRTMEMYS--QNTRFILSCNYSSKIIDPIQS--RCA-VFRFSPLKK  163 (319)
T ss_pred             ceEEEEeCcccCCHH--------------HHHHHHHHHhcCC--CCCeEEEEeCCccccchhHHH--Hhh-eeeeCCCCH
Confidence            568999999988321              1123344444332  335566677888888888888  875 589999999


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      ++...+++.+++..+.. .+..+..++..+.|
T Consensus       164 ~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~g  195 (319)
T PRK00440        164 EAVAERLRYIAENEGIEITDDALEAIYYVSEG  195 (319)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            99999999988766553 33346667776655

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

Probab=97.57  E-value=0.00029  Score=55.98  Aligned_cols=91  Identities=21%  Similarity=0.293  Sum_probs=61.1

Q ss_pred             HHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHH--HHHHHhcCCCCC----CCeEEEeeCCCCCcccccccCCC
Q psy522            3 RVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTML--ELLNQLDGFDSR----GDVKVIMATNRIETLDPALIRPG   76 (131)
Q Consensus         3 ~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~--~~l~~~~~~~~~----~~v~vi~ttn~~~~id~~l~~~g   76 (131)
                      .+|....| +++|||+|.+...-  .+++. +.+..++.  +--+..|.+-.-    +.|++|+|+|+.+.||..++.  
T Consensus       412 kka~~~NP-v~LLDEIDKm~ss~--rGDPa-SALLEVLDPEQN~~F~DhYLev~yDLS~VmFiaTANsl~tIP~PLlD--  485 (782)
T COG0466         412 KKAGVKNP-VFLLDEIDKMGSSF--RGDPA-SALLEVLDPEQNNTFSDHYLEVPYDLSKVMFIATANSLDTIPAPLLD--  485 (782)
T ss_pred             HHhCCcCC-eEEeechhhccCCC--CCChH-HHHHhhcCHhhcCchhhccccCccchhheEEEeecCccccCChHHhc--
Confidence            34555666 77889999997543  12222 12222221  001112222221    479999999999999999999  


Q ss_pred             ccceEEEeCCCCHHHHHHHHHHHh
Q psy522           77 RIDRKIEFPLPDEKTKRRIFNIHT  100 (131)
Q Consensus        77 rf~~~i~~~~P~~~~R~~il~~~l  100 (131)
                      |.+ .|.+.-=+.++..+|-+.||
T Consensus       486 RME-iI~lsgYt~~EKl~IAk~~L  508 (782)
T COG0466         486 RME-VIRLSGYTEDEKLEIAKRHL  508 (782)
T ss_pred             cee-eeeecCCChHHHHHHHHHhc
Confidence            996 78888889999999999886

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

Probab=97.56  E-value=0.0025  Score=44.93  Aligned_cols=110  Identities=18%  Similarity=0.271  Sum_probs=70.7

Q ss_pred             hcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcC-CCC-CCCeEEEeeCCCCCcccccccC----------
Q psy522            7 EHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDG-FDS-RGDVKVIMATNRIETLDPALIR----------   74 (131)
Q Consensus         7 ~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~-~~~v~vi~ttn~~~~id~~l~~----------   74 (131)
                      ...+-|||+|++-  |...       +.    .-..+...+++ +.. .++|++.+|+|+-+.+++.+..          
T Consensus       104 ~~~kFIlf~DDLs--Fe~~-------d~----~yk~LKs~LeGgle~~P~NvliyATSNRRHLv~E~~~d~~~~~~~eih  170 (249)
T PF05673_consen  104 RPYKFILFCDDLS--FEEG-------DT----EYKALKSVLEGGLEARPDNVLIYATSNRRHLVPESFSDREDIQDDEIH  170 (249)
T ss_pred             CCCCEEEEecCCC--CCCC-------cH----HHHHHHHHhcCccccCCCcEEEEEecchhhccchhhhhccCCCccccC
Confidence            3457899999863  3322       11    11223333454 322 3579999999988777664432          


Q ss_pred             -----------CCccceEEEeCCCCHHHHHHHHHHHhcCCCCCCc-ccHHH----HHHHcCCCCHHHHHHh
Q psy522           75 -----------PGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAED-VNLQE----LIMAKDDLSGADIKAI  129 (131)
Q Consensus        75 -----------~grf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~-~~~~~----la~~t~g~s~~di~~l  129 (131)
                                 ..||...|.|.+|+.++-.+|+++++...++.-+ ..+..    .|..-.|.||+-=.+.
T Consensus       171 ~~d~~eEklSLsDRFGL~l~F~~~~q~~YL~IV~~~~~~~g~~~~~e~l~~~Al~wa~~rg~RSGRtA~QF  241 (249)
T PF05673_consen  171 PSDTIEEKLSLSDRFGLWLSFYPPDQEEYLAIVRHYAERYGLELDEEELRQEALQWALRRGGRSGRTARQF  241 (249)
T ss_pred             cchHHHHHHhHHHhCCcEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHcCCCCHHHHHHH
Confidence                       2389999999999999999999999987766532 22222    2333456777654443

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

Probab=97.54  E-value=0.00039  Score=50.97  Aligned_cols=78  Identities=27%  Similarity=0.366  Sum_probs=53.5

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHH----hcC---CCCCCCeEEEeeCC-----CCCcccccccCCCcc
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQ----LDG---FDSRGDVKVIMATN-----RIETLDPALIRPGRI   78 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~----~~~---~~~~~~v~vi~ttn-----~~~~id~~l~~~grf   78 (131)
                      +|+++||++..-++           ....+.+.++.    ..+   +.-..+.+||+|.|     ....+++++++  ||
T Consensus       114 ~ill~DEInra~p~-----------~q~aLl~~l~e~~vtv~~~~~~~~~~~f~viaT~Np~e~~g~~~l~eA~ld--Rf  180 (329)
T COG0714         114 VILLLDEINRAPPE-----------VQNALLEALEERQVTVPGLTTIRLPPPFIVIATQNPGEYEGTYPLPEALLD--RF  180 (329)
T ss_pred             eEEEEeccccCCHH-----------HHHHHHHHHhCcEEEECCcCCcCCCCCCEEEEccCccccCCCcCCCHHHHh--hE
Confidence            59999999775322           23344444433    111   22336789999999     67778999999  99


Q ss_pred             ceEEEeCCC-CHHHHHHHHHHHhc
Q psy522           79 DRKIEFPLP-DEKTKRRIFNIHTS  101 (131)
Q Consensus        79 ~~~i~~~~P-~~~~R~~il~~~l~  101 (131)
                      -..++++.| ..++...+......
T Consensus       181 ~~~~~v~yp~~~~e~~~i~~~~~~  204 (329)
T COG0714         181 LLRIYVDYPDSEEEERIILARVGG  204 (329)
T ss_pred             EEEEecCCCCchHHHHHHHHhCcc
Confidence            999999999 66666666665543

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

Probab=97.53  E-value=0.00049  Score=51.43  Aligned_cols=79  Identities=24%  Similarity=0.380  Sum_probs=56.5

Q ss_pred             CHHHHHhcC----CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCC-C-CCcccccccC
Q psy522            1 LFRVAEEHA----PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATN-R-IETLDPALIR   74 (131)
Q Consensus         1 vF~~A~~~~----p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn-~-~~~id~~l~~   74 (131)
                      +|+.|++..    ..|||+||+..+-..+              ...||-.+    +.+.+++||+|. + .-++.+++++
T Consensus        92 i~e~a~~~~~~gr~tiLflDEIHRfnK~Q--------------QD~lLp~v----E~G~iilIGATTENPsF~ln~ALlS  153 (436)
T COG2256          92 IIEEARKNRLLGRRTILFLDEIHRFNKAQ--------------QDALLPHV----ENGTIILIGATTENPSFELNPALLS  153 (436)
T ss_pred             HHHHHHHHHhcCCceEEEEehhhhcChhh--------------hhhhhhhh----cCCeEEEEeccCCCCCeeecHHHhh
Confidence            366775443    5899999999985433              12233333    467888998665 4 4568999999


Q ss_pred             CCccceEEEeCCCCHHHHHHHHHHHh
Q psy522           75 PGRIDRKIEFPLPDEKTKRRIFNIHT  100 (131)
Q Consensus        75 ~grf~~~i~~~~P~~~~R~~il~~~l  100 (131)
                        |. ..+.+.+.+.++-.++++..+
T Consensus       154 --R~-~vf~lk~L~~~di~~~l~ra~  176 (436)
T COG2256         154 --RA-RVFELKPLSSEDIKKLLKRAL  176 (436)
T ss_pred             --hh-heeeeecCCHHHHHHHHHHHH
Confidence              87 367888889999999998843

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

Probab=97.51  E-value=0.00056  Score=52.93  Aligned_cols=92  Identities=17%  Similarity=0.285  Sum_probs=71.7

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-|++|||++-+.              ...++.+|..+..  ....|++|.+|..++.+|..+++  |+. ++.+...+.
T Consensus       120 yKVyiIDEvHMLS--------------~~afNALLKTLEE--PP~hV~FIlATTe~~Kip~TIlS--Rcq-~f~fkri~~  180 (515)
T COG2812         120 YKVYIIDEVHMLS--------------KQAFNALLKTLEE--PPSHVKFILATTEPQKIPNTILS--RCQ-RFDFKRLDL  180 (515)
T ss_pred             ceEEEEecHHhhh--------------HHHHHHHhccccc--CccCeEEEEecCCcCcCchhhhh--ccc-cccccCCCH
Confidence            4588899987662              2466777766653  34579999999999999999999  984 788899999


Q ss_pred             HHHHHHHHHHhcCCCCCCcc-cHHHHHHHcCC
Q psy522           90 KTKRRIFNIHTSRMTLAEDV-NLQELIMAKDD  120 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~~~~-~~~~la~~t~g  120 (131)
                      ++-...+.+.+...++.-+. -+.-++...+|
T Consensus       181 ~~I~~~L~~i~~~E~I~~e~~aL~~ia~~a~G  212 (515)
T COG2812         181 EEIAKHLAAILDKEGINIEEDALSLIARAAEG  212 (515)
T ss_pred             HHHHHHHHHHHHhcCCccCHHHHHHHHHHcCC
Confidence            99999999999888777443 36667777776

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

Probab=97.51  E-value=0.00052  Score=55.57  Aligned_cols=82  Identities=20%  Similarity=0.313  Sum_probs=57.3

Q ss_pred             HHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcC--CCC-------CCCeEEEeeCCCC---------
Q psy522            4 VAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDG--FDS-------RGDVKVIMATNRI---------   65 (131)
Q Consensus         4 ~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~--~~~-------~~~v~vi~ttn~~---------   65 (131)
                      ..+++..+||||||+|.+-+              .+.+.++..++.  +..       -.++++|+|||.-         
T Consensus       552 ~v~~~p~sVlllDEieka~~--------------~v~~~LLq~ld~G~ltd~~g~~vd~rn~iiI~TsN~g~~~~~~~~~  617 (758)
T PRK11034        552 AVIKHPHAVLLLDEIEKAHP--------------DVFNLLLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSI  617 (758)
T ss_pred             HHHhCCCcEEEeccHhhhhH--------------HHHHHHHHHHhcCeeecCCCceecCCCcEEEEeCCcCHHHHhhccc
Confidence            34556679999999999832              234444444442  111       1368899999932         


Q ss_pred             ----------------CcccccccCCCccceEEEeCCCCHHHHHHHHHHHhc
Q psy522           66 ----------------ETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTS  101 (131)
Q Consensus        66 ----------------~~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~  101 (131)
                                      ..+.|.++.  |+|..|.|++.+.++..+|+..++.
T Consensus       618 g~~~~~~~~~~~~~~~~~f~pefl~--Rid~ii~f~~L~~~~l~~I~~~~l~  667 (758)
T PRK11034        618 GLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTDVIHQVVDKFIV  667 (758)
T ss_pred             CcccchhhHHHHHHHHHhcCHHHHc--cCCEEEEcCCCCHHHHHHHHHHHHH
Confidence                            124577777  9999999999999999999987754

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

Probab=97.50  E-value=0.001  Score=50.29  Aligned_cols=59  Identities=15%  Similarity=0.237  Sum_probs=36.9

Q ss_pred             ccccCCCccceEEEeCCCCHHHHHHHHHHH----hcC-------CCCC---CcccHHHHHHH--cCCCCHHHHHHhh
Q psy522           70 PALIRPGRIDRKIEFPLPDEKTKRRIFNIH----TSR-------MTLA---EDVNLQELIMA--KDDLSGADIKAIC  130 (131)
Q Consensus        70 ~~l~~~grf~~~i~~~~P~~~~R~~il~~~----l~~-------~~~~---~~~~~~~la~~--t~g~s~~di~~l~  130 (131)
                      |+|+.  |++..+.+.+.+.++...|+..-    +++       .++.   .+.-+..+++.  ..+|-.+-|..++
T Consensus       303 PEflg--Rld~Iv~f~pL~~~~L~~Il~~~~n~l~kq~~~~l~~~gi~L~~t~~a~~~Ia~~~~~~~~GAR~Lr~ii  377 (413)
T TIGR00382       303 PEFIG--RLPVIATLEKLDEEALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKKALERKTGARGLRSIV  377 (413)
T ss_pred             HHHhC--CCCeEeecCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCeEEEECHHHHHHHHHhCCCCCCCchHHHHHH
Confidence            55555  99999999999999999998652    221       1222   12226667765  2445556665543

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

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=97.50  E-value=0.00059  Score=46.69  Aligned_cols=105  Identities=17%  Similarity=0.303  Sum_probs=54.3

Q ss_pred             CeEEEeccccccc-CcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCccc------ccccCCCccceEE
Q psy522           10 PSIVFIDEIDAVG-TKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLD------PALIRPGRIDRKI   82 (131)
Q Consensus        10 p~ii~iDe~d~l~-~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id------~~l~~~grf~~~i   82 (131)
                      ..||+|||++.+. ...      ....   .+..+.+.++......++.+|.+........      ..+.  ||+.. +
T Consensus       119 ~~iiviDe~~~~~~~~~------~~~~---~~~~l~~~~~~~~~~~~~~~v~~~S~~~~~~~~~~~~~~~~--~~~~~-~  186 (234)
T PF01637_consen  119 KVIIVIDEFQYLAIASE------EDKD---FLKSLRSLLDSLLSQQNVSIVITGSSDSLMEEFLDDKSPLF--GRFSH-I  186 (234)
T ss_dssp             CEEEEEETGGGGGBCTT------TTHH---HHHHHHHHHHH----TTEEEEEEESSHHHHHHTT-TTSTTT--T---E-E
T ss_pred             cEEEEEecHHHHhhccc------chHH---HHHHHHHHHhhccccCCceEEEECCchHHHHHhhcccCccc--cccce-E
Confidence            4899999999998 221      1122   3333333334333344444444333321111      1222  47776 9


Q ss_pred             EeCCCCHHHHHHHHHHHhcCCC-C-CCcccHHHHHHHcCCCCHHHHH
Q psy522           83 EFPLPDEKTKRRIFNIHTSRMT-L-AEDVNLQELIMAKDDLSGADIK  127 (131)
Q Consensus        83 ~~~~P~~~~R~~il~~~l~~~~-~-~~~~~~~~la~~t~g~s~~di~  127 (131)
                      .+++.+.++..+++...+.... + ..+.++..+...|.|+ |.-|.
T Consensus       187 ~l~~l~~~e~~~~~~~~~~~~~~~~~~~~~~~~i~~~~gG~-P~~l~  232 (234)
T PF01637_consen  187 ELKPLSKEEAREFLKELFKELIKLPFSDEDIEEIYSLTGGN-PRYLQ  232 (234)
T ss_dssp             EE----HHHHHHHHHHHHHCC------HHHHHHHHHHHTT--HHHHH
T ss_pred             EEeeCCHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHhCCC-HHHHh
Confidence            9999999999999999876651 1 2556788899999997 44443

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

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.49  E-value=0.00073  Score=53.31  Aligned_cols=98  Identities=17%  Similarity=0.223  Sum_probs=67.0

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-||+|||+|.+-.              ...+.++..++..  .+.+++|.+|+.++.+.+.+++  |+. .+.|..++.
T Consensus       121 ~kVvIIDEa~~L~~--------------~a~naLLk~LEep--p~~tv~Il~t~~~~kll~tI~S--R~~-~i~f~~l~~  181 (585)
T PRK14950        121 YKVYIIDEVHMLST--------------AAFNALLKTLEEP--PPHAIFILATTEVHKVPATILS--RCQ-RFDFHRHSV  181 (585)
T ss_pred             eEEEEEeChHhCCH--------------HHHHHHHHHHhcC--CCCeEEEEEeCChhhhhHHHHh--ccc-eeeCCCCCH
Confidence            45899999987732              2344566666643  2456777777778888888988  874 688999999


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHH
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIK  127 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~  127 (131)
                      ++-..+++..+...+.. .+..+..++..+.| +..++.
T Consensus       182 ~el~~~L~~~a~~egl~i~~eal~~La~~s~G-dlr~al  219 (585)
T PRK14950        182 ADMAAHLRKIAAAEGINLEPGALEAIARAATG-SMRDAE  219 (585)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHH
Confidence            99888888887665543 22235666666665 444443

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

Probab=97.49  E-value=0.00025  Score=57.11  Aligned_cols=86  Identities=26%  Similarity=0.293  Sum_probs=62.2

Q ss_pred             HHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCc-----ccccccCCCc
Q psy522            3 RVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIET-----LDPALIRPGR   77 (131)
Q Consensus         3 ~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~-----id~~l~~~gr   77 (131)
                      +..+...+.|+||||++.+.+...+.++  .-....++.-.|       ..+.+-+||+|..-+.     =|+|+-|  |
T Consensus       256 ~ev~~~~~vILFIDEiHtiVGAG~~~G~--a~DAaNiLKPaL-------ARGeL~~IGATT~~EYRk~iEKD~AL~R--R  324 (786)
T COG0542         256 KEVEKSKNVILFIDEIHTIVGAGATEGG--AMDAANLLKPAL-------ARGELRCIGATTLDEYRKYIEKDAALER--R  324 (786)
T ss_pred             HHHhcCCCeEEEEechhhhcCCCccccc--ccchhhhhHHHH-------hcCCeEEEEeccHHHHHHHhhhchHHHh--c
Confidence            4556667999999999999988754332  122233444333       3466778888875333     3899999  9


Q ss_pred             cceEEEeCCCCHHHHHHHHHHHh
Q psy522           78 IDRKIEFPLPDEKTKRRIFNIHT  100 (131)
Q Consensus        78 f~~~i~~~~P~~~~R~~il~~~l  100 (131)
                      |. .|.+.-|+.++-..|++-+-
T Consensus       325 FQ-~V~V~EPs~e~ti~ILrGlk  346 (786)
T COG0542         325 FQ-KVLVDEPSVEDTIAILRGLK  346 (786)
T ss_pred             Cc-eeeCCCCCHHHHHHHHHHHH
Confidence            96 89999999999999997653

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.47  E-value=0.00062  Score=54.02  Aligned_cols=92  Identities=17%  Similarity=0.224  Sum_probs=64.5

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-|++|||+|.+-.              ...+.++..++.  ..+.+++|++|++++.+-+.+++  |+ ..+.|..++.
T Consensus       122 ~KViIIDEad~Lt~--------------~a~naLLK~LEe--Pp~~tvfIL~t~~~~~llpTIrS--Rc-~~~~f~~l~~  182 (620)
T PRK14948        122 WKVYVIDECHMLST--------------AAFNALLKTLEE--PPPRVVFVLATTDPQRVLPTIIS--RC-QRFDFRRIPL  182 (620)
T ss_pred             ceEEEEECccccCH--------------HHHHHHHHHHhc--CCcCeEEEEEeCChhhhhHHHHh--he-eEEEecCCCH
Confidence            35999999998832              244566766664  33567888888889999999999  88 4788888888


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      ++-...+.+.....+.. ....+..+++.+.|
T Consensus       183 ~ei~~~L~~ia~kegi~is~~al~~La~~s~G  214 (620)
T PRK14948        183 EAMVQHLSEIAEKESIEIEPEALTLVAQRSQG  214 (620)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC
Confidence            88777777766654433 22236666666665

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

Probab=97.47  E-value=0.00056  Score=43.04  Aligned_cols=68  Identities=43%  Similarity=0.618  Sum_probs=42.7

Q ss_pred             HHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcC-CCCCCCeEEEeeCCCCC--cccccccCCCccceE
Q psy522            5 AEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDG-FDSRGDVKVIMATNRIE--TLDPALIRPGRIDRK   81 (131)
Q Consensus         5 A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~~v~vi~ttn~~~--~id~~l~~~grf~~~   81 (131)
                      +....+.+|++||++.+...           ....+..++..... .....++.+|+++|...  .+++.+.+  ||+..
T Consensus        80 ~~~~~~~~lilDe~~~~~~~-----------~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~~~~~~~~~~~--r~~~~  146 (151)
T cd00009          80 AEKAKPGVLFIDEIDSLSRG-----------AQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYD--RLDIR  146 (151)
T ss_pred             hccCCCeEEEEeChhhhhHH-----------HHHHHHHHHHhcCceeccCCCeEEEEecCccccCCcChhHHh--hhccE
Confidence            44567899999999987211           11122222222211 01135788889998776  77888888  99877


Q ss_pred             EEeC
Q psy522           82 IEFP   85 (131)
Q Consensus        82 i~~~   85 (131)
                      +.++
T Consensus       147 i~~~  150 (151)
T cd00009         147 IVIP  150 (151)
T ss_pred             eecC
Confidence            7775

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.

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=97.45  E-value=0.00096  Score=52.71  Aligned_cols=97  Identities=20%  Similarity=0.244  Sum_probs=67.8

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-|++|||+|.+..              ...+.++..++.  ..+.+++|.+|+.++.+.+.+++  |+ ..+.+..|+.
T Consensus       133 ~KVvIIDEad~Ls~--------------~a~naLLKtLEe--Pp~~~~fIl~tte~~kll~tI~S--Rc-q~~~f~~l~~  193 (598)
T PRK09111        133 YKVYIIDEVHMLST--------------AAFNALLKTLEE--PPPHVKFIFATTEIRKVPVTVLS--RC-QRFDLRRIEA  193 (598)
T ss_pred             cEEEEEEChHhCCH--------------HHHHHHHHHHHh--CCCCeEEEEEeCChhhhhHHHHh--he-eEEEecCCCH
Confidence            46899999988732              234556666654  23457777777888889889998  88 4799999999


Q ss_pred             HHHHHHHHHHhcCCCCCC-cccHHHHHHHcCCCCHHHH
Q psy522           90 KTKRRIFNIHTSRMTLAE-DVNLQELIMAKDDLSGADI  126 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~~-~~~~~~la~~t~g~s~~di  126 (131)
                      ++-..+++..++..+..- +..+..++..+.| +.+++
T Consensus       194 ~el~~~L~~i~~kegi~i~~eAl~lIa~~a~G-dlr~a  230 (598)
T PRK09111        194 DVLAAHLSRIAAKEGVEVEDEALALIARAAEG-SVRDG  230 (598)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHH
Confidence            999999988877665442 2335556666655 34433

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

Probab=97.44  E-value=0.00056  Score=55.25  Aligned_cols=82  Identities=22%  Similarity=0.310  Sum_probs=58.2

Q ss_pred             HHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCC--C-------CCCCeEEEeeCCCCC--------
Q psy522            4 VAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGF--D-------SRGDVKVIMATNRIE--------   66 (131)
Q Consensus         4 ~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~-------~~~~v~vi~ttn~~~--------   66 (131)
                      ..+.+..+||+|||+|.+-+              ...+.+++.+++-  .       .-.++++|+|||...        
T Consensus       548 ~~~~~p~~VvllDEieka~~--------------~~~~~Ll~~ld~g~~~d~~g~~vd~~~~iii~Tsn~g~~~~~~~~~  613 (731)
T TIGR02639       548 AVRKHPHCVLLLDEIEKAHP--------------DIYNILLQVMDYATLTDNNGRKADFRNVILIMTSNAGASEMSKPPI  613 (731)
T ss_pred             HHHhCCCeEEEEechhhcCH--------------HHHHHHHHhhccCeeecCCCcccCCCCCEEEECCCcchhhhhhccC
Confidence            34567789999999997632              2334444444431  0       113578999998632        


Q ss_pred             -----------------cccccccCCCccceEEEeCCCCHHHHHHHHHHHhc
Q psy522           67 -----------------TLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTS  101 (131)
Q Consensus        67 -----------------~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~  101 (131)
                                       .+.|.++.  |+|..+.|.+.+.++..+|++..+.
T Consensus       614 ~f~~~~~~~~~~~~~~~~f~pef~~--Rid~Vi~F~pLs~e~l~~Iv~~~L~  663 (731)
T TIGR02639       614 GFGSENVESKSDKAIKKLFSPEFRN--RLDAIIHFNPLSEEVLEKIVQKFVD  663 (731)
T ss_pred             CcchhhhHHHHHHHHHhhcChHHHh--cCCeEEEcCCCCHHHHHHHHHHHHH
Confidence                             14567776  9999999999999999999998875

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=97.44  E-value=0.00083  Score=47.76  Aligned_cols=77  Identities=22%  Similarity=0.336  Sum_probs=52.3

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHh----cCC-------CCCCCeEEEeeCCCC-----Cccccccc
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQL----DGF-------DSRGDVKVIMATNRI-----ETLDPALI   73 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~----~~~-------~~~~~v~vi~ttn~~-----~~id~~l~   73 (131)
                      +.+|++||+|.+-+.           ....+..+++.-    .+.       ...++..+|+|+|..     ..++++++
T Consensus       106 g~~lllDEi~r~~~~-----------~q~~Ll~~Le~~~~~i~~~~~~~~~i~~~~~frvIaTsN~~~~~g~~~l~~aL~  174 (262)
T TIGR02640       106 GFTLVYDEFTRSKPE-----------TNNVLLSVFEEGVLELPGKRGTSRYVDVHPEFRVIFTSNPVEYAGVHETQDALL  174 (262)
T ss_pred             CCEEEEcchhhCCHH-----------HHHHHHHHhcCCeEEccCCCCCCceEecCCCCEEEEeeCCccccceecccHHHH
Confidence            479999999985321           223334444320    000       112357799999965     35689999


Q ss_pred             CCCccceEEEeCCCCHHHHHHHHHHHh
Q psy522           74 RPGRIDRKIEFPLPDEKTKRRIFNIHT  100 (131)
Q Consensus        74 ~~grf~~~i~~~~P~~~~R~~il~~~l  100 (131)
                      +  || ..++++.|+.++-.+|++...
T Consensus       175 ~--R~-~~i~i~~P~~~~e~~Il~~~~  198 (262)
T TIGR02640       175 D--RL-ITIFMDYPDIDTETAILRAKT  198 (262)
T ss_pred             h--hc-EEEECCCCCHHHHHHHHHHhh
Confidence            9  99 589999999999999998754

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).

>KOG0989|consensus

Probab=97.43  E-value=0.00075  Score=48.90  Aligned_cols=91  Identities=16%  Similarity=0.238  Sum_probs=65.0

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCHH
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEK   90 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~   90 (131)
                      -|++|||+|.+..+              ....+...|+.  ....+.+|..||+++.|+.-+.+  |+. .+.|++...+
T Consensus       131 KiiIlDEcdsmtsd--------------aq~aLrr~mE~--~s~~trFiLIcnylsrii~pi~S--RC~-KfrFk~L~d~  191 (346)
T KOG0989|consen  131 KIIILDECDSMTSD--------------AQAALRRTMED--FSRTTRFILICNYLSRIIRPLVS--RCQ-KFRFKKLKDE  191 (346)
T ss_pred             eEEEEechhhhhHH--------------HHHHHHHHHhc--cccceEEEEEcCChhhCChHHHh--hHH-HhcCCCcchH
Confidence            68999999998533              33344445554  23468899999999999999999  986 5667777666


Q ss_pred             HHHHHHHHHhcCCCCCCc-ccHHHHHHHcCC
Q psy522           91 TKRRIFNIHTSRMTLAED-VNLQELIMAKDD  120 (131)
Q Consensus        91 ~R~~il~~~l~~~~~~~~-~~~~~la~~t~g  120 (131)
                      ....-|+......++.-+ .-++.+++.++|
T Consensus       192 ~iv~rL~~Ia~~E~v~~d~~al~~I~~~S~G  222 (346)
T KOG0989|consen  192 DIVDRLEKIASKEGVDIDDDALKLIAKISDG  222 (346)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC
Confidence            666677777666655532 337777877766

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=97.40  E-value=0.0015  Score=47.91  Aligned_cols=69  Identities=19%  Similarity=0.296  Sum_probs=53.2

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCHH
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEK   90 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~   90 (131)
                      -|++||++|.+-.              ...+.+|+.++.  ..+++++|.+|+.++.+.|.+++  |+. .+.+++|+.+
T Consensus       115 kV~iI~~ae~m~~--------------~AaNaLLKtLEE--Pp~~~~fiL~~~~~~~lLpTIrS--RCq-~i~~~~~~~~  175 (319)
T PRK08769        115 QVVIVDPADAINR--------------AACNALLKTLEE--PSPGRYLWLISAQPARLPATIRS--RCQ-RLEFKLPPAH  175 (319)
T ss_pred             EEEEeccHhhhCH--------------HHHHHHHHHhhC--CCCCCeEEEEECChhhCchHHHh--hhe-EeeCCCcCHH
Confidence            5899999999832              344556666664  34568888889999999999999  995 7899999998


Q ss_pred             HHHHHHHH
Q psy522           91 TKRRIFNI   98 (131)
Q Consensus        91 ~R~~il~~   98 (131)
                      +-.+.+..
T Consensus       176 ~~~~~L~~  183 (319)
T PRK08769        176 EALAWLLA  183 (319)
T ss_pred             HHHHHHHH
Confidence            87766653

>KOG2004|consensus

Probab=97.40  E-value=0.00057  Score=54.51  Aligned_cols=87  Identities=22%  Similarity=0.362  Sum_probs=57.3

Q ss_pred             hcCCeEEEecccccccCcCCCCCCCchhHHHHHH-----HHHHHHhcCCC-CCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            7 EHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTM-----LELLNQLDGFD-SRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         7 ~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~-----~~~l~~~~~~~-~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      .+.| +++|||+|.+...  ..+++.+ .+..++     ..|+...=++. .-.+|++|+|+|..+.||+.++.  |.+ 
T Consensus       504 t~NP-liLiDEvDKlG~g--~qGDPas-ALLElLDPEQNanFlDHYLdVp~DLSkVLFicTAN~idtIP~pLlD--RME-  576 (906)
T KOG2004|consen  504 TENP-LILIDEVDKLGSG--HQGDPAS-ALLELLDPEQNANFLDHYLDVPVDLSKVLFICTANVIDTIPPPLLD--RME-  576 (906)
T ss_pred             CCCc-eEEeehhhhhCCC--CCCChHH-HHHHhcChhhccchhhhccccccchhheEEEEeccccccCChhhhh--hhh-
Confidence            3444 7888999999732  2222222 111222     12221111111 12579999999999999999999  996 


Q ss_pred             EEEeCCCCHHHHHHHHHHHh
Q psy522           81 KIEFPLPDEKTKRRIFNIHT  100 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l  100 (131)
                      .|.++-=..++..+|-+.||
T Consensus       577 vIelsGYv~eEKv~IA~~yL  596 (906)
T KOG2004|consen  577 VIELSGYVAEEKVKIAERYL  596 (906)
T ss_pred             eeeccCccHHHHHHHHHHhh
Confidence            78888778899999998886

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

Probab=97.36  E-value=0.00074  Score=51.49  Aligned_cols=34  Identities=29%  Similarity=0.317  Sum_probs=27.3

Q ss_pred             CCCCCCeEEEeeCCCCC----cccccccCCCccceEEEeCC
Q psy522           50 FDSRGDVKVIMATNRIE----TLDPALIRPGRIDRKIEFPL   86 (131)
Q Consensus        50 ~~~~~~v~vi~ttn~~~----~id~~l~~~grf~~~i~~~~   86 (131)
                      +....++.+|||+|..+    .+|.|++|  ||. .|.+.+
T Consensus       320 f~iP~Nl~IIgTMNt~Drs~~~lD~AlrR--RF~-fi~i~p  357 (459)
T PRK11331        320 FYVPENVYIIGLMNTADRSLAVVDYALRR--RFS-FIDIEP  357 (459)
T ss_pred             ccCCCCeEEEEecCccccchhhccHHHHh--hhh-eEEecC
Confidence            33446799999999877    79999999  995 566665

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=97.36  E-value=0.00083  Score=49.48  Aligned_cols=77  Identities=19%  Similarity=0.383  Sum_probs=52.7

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHh------cCC--CCCCCeEEEeeCCCCC-cccccccCCCccceE
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQL------DGF--DSRGDVKVIMATNRIE-TLDPALIRPGRIDRK   81 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~------~~~--~~~~~v~vi~ttn~~~-~id~~l~~~grf~~~   81 (131)
                      .+||+||++.+-.+           ....+.+.+..-      ++.  ....++++++|+|-.+ .++++++.  ||...
T Consensus       130 GiL~lDEInrl~~~-----------~q~~Lle~mee~~v~v~r~G~~~~~p~rfiviAt~NP~e~~l~~aLld--RF~~~  196 (334)
T PRK13407        130 GYLYIDEVNLLEDH-----------IVDLLLDVAQSGENVVEREGLSIRHPARFVLVGSGNPEEGELRPQLLD--RFGLS  196 (334)
T ss_pred             CeEEecChHhCCHH-----------HHHHHHHHHHcCCeEEEECCeEEecCCCEEEEecCCcccCCCCHHHHh--hcceE
Confidence            58999999987321           223333333211      111  1124689999988534 58999999  99999


Q ss_pred             EEeCCCCH-HHHHHHHHHHh
Q psy522           82 IEFPLPDE-KTKRRIFNIHT  100 (131)
Q Consensus        82 i~~~~P~~-~~R~~il~~~l  100 (131)
                      +.+++|.. ++|.+|++...
T Consensus       197 v~v~~~~~~~e~~~il~~~~  216 (334)
T PRK13407        197 VEVRSPRDVETRVEVIRRRD  216 (334)
T ss_pred             EEcCCCCcHHHHHHHHHHhh
Confidence            99999866 99999998754

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=97.34  E-value=0.00088  Score=49.04  Aligned_cols=70  Identities=16%  Similarity=0.238  Sum_probs=54.7

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      --|++||++|.+-.              ...+.+|+.++.  ..+++++|.+|+.++.+-|.+++  |+. .+.+++|+.
T Consensus       109 ~kV~iI~~ae~m~~--------------~AaNaLLKtLEE--Pp~~t~fiL~t~~~~~lLpTI~S--RCq-~~~~~~~~~  169 (319)
T PRK06090        109 YRLFVIEPADAMNE--------------SASNALLKTLEE--PAPNCLFLLVTHNQKRLLPTIVS--RCQ-QWVVTPPST  169 (319)
T ss_pred             ceEEEecchhhhCH--------------HHHHHHHHHhcC--CCCCeEEEEEECChhhChHHHHh--cce-eEeCCCCCH
Confidence            35888888888732              345667776764  44578999999999999999999  995 889999999


Q ss_pred             HHHHHHHHH
Q psy522           90 KTKRRIFNI   98 (131)
Q Consensus        90 ~~R~~il~~   98 (131)
                      ++-.+.+..
T Consensus       170 ~~~~~~L~~  178 (319)
T PRK06090        170 AQAMQWLKG  178 (319)
T ss_pred             HHHHHHHHH
Confidence            988777654

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=97.32  E-value=0.00088  Score=49.17  Aligned_cols=70  Identities=16%  Similarity=0.281  Sum_probs=54.3

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCHH
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEK   90 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~   90 (131)
                      -|++||++|.+-.              ...+.+|+.++.  +.+.+++|.+|+.++.+.+.+++  |+. .+.+++|+.+
T Consensus       109 KV~iI~~a~~m~~--------------~AaNaLLKtLEE--Pp~~~~fiL~t~~~~~llpTI~S--RC~-~~~~~~~~~~  169 (325)
T PRK06871        109 KVVYIQGAERLTE--------------AAANALLKTLEE--PRPNTYFLLQADLSAALLPTIYS--RCQ-TWLIHPPEEQ  169 (325)
T ss_pred             eEEEEechhhhCH--------------HHHHHHHHHhcC--CCCCeEEEEEECChHhCchHHHh--hce-EEeCCCCCHH
Confidence            4788888888732              345566766664  44678899999999999999999  984 7899999999


Q ss_pred             HHHHHHHHH
Q psy522           91 TKRRIFNIH   99 (131)
Q Consensus        91 ~R~~il~~~   99 (131)
                      +-.+.+...
T Consensus       170 ~~~~~L~~~  178 (325)
T PRK06871        170 QALDWLQAQ  178 (325)
T ss_pred             HHHHHHHHH
Confidence            887777653

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=97.27  E-value=0.0049  Score=48.99  Aligned_cols=48  Identities=21%  Similarity=0.231  Sum_probs=38.7

Q ss_pred             CeEEEe-eCCCCCcccccccCCCccceEEEeCCCCHHHHHHHHHHHhcCCCC
Q psy522           55 DVKVIM-ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTL  105 (131)
Q Consensus        55 ~v~vi~-ttn~~~~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~~~~  105 (131)
                      .+++|+ ||+.++.+++++++  ||. .+.+++.+.++...|++..+.....
T Consensus       323 ~~VLI~aTt~~~~~l~~aLrS--R~~-~i~~~pls~edi~~Il~~~a~~~~v  371 (615)
T TIGR02903       323 DFVLIGATTRDPEEINPALRS--RCA-EVFFEPLTPEDIALIVLNAAEKINV  371 (615)
T ss_pred             eEEEEEeccccccccCHHHHh--cee-EEEeCCCCHHHHHHHHHHHHHHcCC
Confidence            355555 55678999999999  997 6788999999999999999876543

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.

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=97.26  E-value=0.0008  Score=49.58  Aligned_cols=70  Identities=14%  Similarity=0.147  Sum_probs=55.2

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      --|++||++|.+-.              ...+.+|+.++.  +.+++++|.+|++++.+.+.++|  |+. .+.+++|+.
T Consensus       109 ~kV~iI~~ae~m~~--------------~AaNaLLKtLEE--Pp~~t~fiL~t~~~~~lLpTIrS--RCq-~~~~~~~~~  169 (334)
T PRK07993        109 AKVVWLPDAALLTD--------------AAANALLKTLEE--PPENTWFFLACREPARLLATLRS--RCR-LHYLAPPPE  169 (334)
T ss_pred             ceEEEEcchHhhCH--------------HHHHHHHHHhcC--CCCCeEEEEEECChhhChHHHHh--ccc-cccCCCCCH
Confidence            45888888888732              355667777774  45678999999999999999999  986 689999999


Q ss_pred             HHHHHHHHH
Q psy522           90 KTKRRIFNI   98 (131)
Q Consensus        90 ~~R~~il~~   98 (131)
                      ++-.+.+..
T Consensus       170 ~~~~~~L~~  178 (334)
T PRK07993        170 QYALTWLSR  178 (334)
T ss_pred             HHHHHHHHH
Confidence            887777653

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

Probab=97.23  E-value=0.0016  Score=52.52  Aligned_cols=72  Identities=21%  Similarity=0.323  Sum_probs=51.2

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCC-C-CCcccccccCCCccceEEEeCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATN-R-IETLDPALIRPGRIDRKIEFPL   86 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn-~-~~~id~~l~~~grf~~~i~~~~   86 (131)
                      ...+|||||+|.+....              ...++..++    .+.+++|++|. . ...+++++++  |+ ..+.+++
T Consensus       109 ~~~IL~IDEIh~Ln~~q--------------QdaLL~~lE----~g~IiLI~aTTenp~~~l~~aL~S--R~-~v~~l~p  167 (725)
T PRK13341        109 KRTILFIDEVHRFNKAQ--------------QDALLPWVE----NGTITLIGATTENPYFEVNKALVS--RS-RLFRLKS  167 (725)
T ss_pred             CceEEEEeChhhCCHHH--------------HHHHHHHhc----CceEEEEEecCCChHhhhhhHhhc--cc-cceecCC
Confidence            45799999999874221              122333332    35677777654 3 3568899998  75 4689999


Q ss_pred             CCHHHHHHHHHHHhc
Q psy522           87 PDEKTKRRIFNIHTS  101 (131)
Q Consensus        87 P~~~~R~~il~~~l~  101 (131)
                      ++.++...+++..+.
T Consensus       168 Ls~edi~~IL~~~l~  182 (725)
T PRK13341        168 LSDEDLHQLLKRALQ  182 (725)
T ss_pred             CCHHHHHHHHHHHHH
Confidence            999999999999886

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

Probab=97.23  E-value=0.0015  Score=46.19  Aligned_cols=56  Identities=14%  Similarity=0.165  Sum_probs=41.6

Q ss_pred             ccCCCccceEEEeCCCCHHHHHHHHHHHhcCCCCC-----CcccHHHHHHHcCCCCHHHHHHhh
Q psy522           72 LIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLA-----EDVNLQELIMAKDDLSGADIKAIC  130 (131)
Q Consensus        72 l~~~grf~~~i~~~~P~~~~R~~il~~~l~~~~~~-----~~~~~~~la~~t~g~s~~di~~l~  130 (131)
                      +.+  |+...+++++.+.++-.+++.+.+...+..     .+..+..+...+.|.. ..|..+|
T Consensus       179 l~~--r~~~~~~l~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p-~~i~~l~  239 (269)
T TIGR03015       179 LRQ--RIIASCHLGPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIP-RLINILC  239 (269)
T ss_pred             HHh--heeeeeeCCCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcc-cHHHHHH
Confidence            555  788889999999999999999888654321     2235777889999984 4476665

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.

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=97.19  E-value=0.0015  Score=48.17  Aligned_cols=77  Identities=18%  Similarity=0.333  Sum_probs=52.4

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHh------cCCC--CCCCeEEEeeCCCCC-cccccccCCCccce
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQL------DGFD--SRGDVKVIMATNRIE-TLDPALIRPGRIDR   80 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~------~~~~--~~~~v~vi~ttn~~~-~id~~l~~~grf~~   80 (131)
                      ..+||+||++.+-.+           ....+.+.+..=      ++..  ...++++|+|.|-.+ .+++++..  ||..
T Consensus       132 ~GvL~lDEi~~L~~~-----------~Q~~Ll~~l~~g~~~v~r~G~~~~~~~r~iviat~np~eg~l~~~Lld--Rf~l  198 (337)
T TIGR02030       132 RGILYIDEVNLLEDH-----------LVDVLLDVAASGWNVVEREGISIRHPARFVLVGSGNPEEGELRPQLLD--RFGL  198 (337)
T ss_pred             CCEEEecChHhCCHH-----------HHHHHHHHHHhCCeEEEECCEEEEcCCCEEEEeccccccCCCCHHHHh--hcce
Confidence            478999999987321           222333333210      1111  123688888888544 68999999  9999


Q ss_pred             EEEeCCCCH-HHHHHHHHHH
Q psy522           81 KIEFPLPDE-KTKRRIFNIH   99 (131)
Q Consensus        81 ~i~~~~P~~-~~R~~il~~~   99 (131)
                      .+.++.|.. ++|.+|++..
T Consensus       199 ~i~l~~p~~~eer~eIL~~~  218 (337)
T TIGR02030       199 HAEIRTVRDVELRVEIVERR  218 (337)
T ss_pred             EEECCCCCCHHHHHHHHHhh
Confidence            999999965 8999999874

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.11  E-value=0.0037  Score=51.42  Aligned_cols=111  Identities=14%  Similarity=0.275  Sum_probs=68.4

Q ss_pred             HHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCC--CC-------CCCeEEEeeCCCCCc------
Q psy522            3 RVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGF--DS-------RGDVKVIMATNRIET------   67 (131)
Q Consensus         3 ~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~-------~~~v~vi~ttn~~~~------   67 (131)
                      +..++++.+||+|||+|..-+              ...+.++..++.=  ..       -.+.++|.|||....      
T Consensus       662 ~~v~~~p~svvllDEieka~~--------------~v~~~Llq~ld~g~l~d~~Gr~vd~~n~iiI~TSNlg~~~~~~~~  727 (852)
T TIGR03345       662 EAVRRKPYSVVLLDEVEKAHP--------------DVLELFYQVFDKGVMEDGEGREIDFKNTVILLTSNAGSDLIMALC  727 (852)
T ss_pred             HHHHhCCCcEEEEechhhcCH--------------HHHHHHHHHhhcceeecCCCcEEeccccEEEEeCCCchHHHHHhc
Confidence            345678889999999986421              1333344444421  01       145889999885211      


Q ss_pred             -----------------------ccccccCCCccceEEEeCCCCHHHHHHHHHHHhcCC--------CCC---CcccHHH
Q psy522           68 -----------------------LDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRM--------TLA---EDVNLQE  113 (131)
Q Consensus        68 -----------------------id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~~--------~~~---~~~~~~~  113 (131)
                                             +.|+|++  |++ .|.|.+.+.++-.+|+...+...        +..   .+.-+..
T Consensus       728 ~~~~~~~~~~~~~~~~~~~~~~~f~PEfln--Ri~-iI~F~pLs~e~l~~Iv~~~L~~l~~rl~~~~gi~l~i~d~a~~~  804 (852)
T TIGR03345       728 ADPETAPDPEALLEALRPELLKVFKPAFLG--RMT-VIPYLPLDDDVLAAIVRLKLDRIARRLKENHGAELVYSEALVEH  804 (852)
T ss_pred             cCcccCcchHHHHHHHHHHHHHhccHHHhc--cee-EEEeCCCCHHHHHHHHHHHHHHHHHHHHHhcCceEEECHHHHHH
Confidence                                   4566777  897 88999999999999998876431        222   1222555


Q ss_pred             HHHHcCC--CCHHHHHHhh
Q psy522          114 LIMAKDD--LSGADIKAIC  130 (131)
Q Consensus       114 la~~t~g--~s~~di~~l~  130 (131)
                      |+....+  |-.+.|..++
T Consensus       805 La~~g~~~~~GAR~L~r~I  823 (852)
T TIGR03345       805 IVARCTEVESGARNIDAIL  823 (852)
T ss_pred             HHHHcCCCCCChHHHHHHH
Confidence            6666432  4456665544

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.

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=97.10  E-value=0.0016  Score=47.79  Aligned_cols=70  Identities=17%  Similarity=0.275  Sum_probs=52.4

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-|++|||+|.+-.              ...+.++..++.  ..+.+++|.+|+.++.+.+.+++  |+. .+++++|+.
T Consensus       111 ~kvviI~~a~~~~~--------------~a~NaLLK~LEE--Pp~~~~~Il~t~~~~~ll~TIrS--Rc~-~i~~~~~~~  171 (329)
T PRK08058        111 KKVYIIEHADKMTA--------------SAANSLLKFLEE--PSGGTTAILLTENKHQILPTILS--RCQ-VVEFRPLPP  171 (329)
T ss_pred             ceEEEeehHhhhCH--------------HHHHHHHHHhcC--CCCCceEEEEeCChHhCcHHHHh--hce-eeeCCCCCH
Confidence            35888899887732              244567777764  34567788888899999999999  884 799999999


Q ss_pred             HHHHHHHHH
Q psy522           90 KTKRRIFNI   98 (131)
Q Consensus        90 ~~R~~il~~   98 (131)
                      ++-...++.
T Consensus       172 ~~~~~~L~~  180 (329)
T PRK08058        172 ESLIQRLQE  180 (329)
T ss_pred             HHHHHHHHH
Confidence            887666653

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.09  E-value=0.0015  Score=40.60  Aligned_cols=76  Identities=28%  Similarity=0.371  Sum_probs=45.5

Q ss_pred             HHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCC-CCcccccccCCCccce
Q psy522            2 FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNR-IETLDPALIRPGRIDR   80 (131)
Q Consensus         2 F~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~-~~~id~~l~~~grf~~   80 (131)
                      ++.|+...|.+|++||++.+......       .. ....................+|+++|. ....+..+..  |++.
T Consensus        71 ~~~~~~~~~~viiiDei~~~~~~~~~-------~~-~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~--~~~~  140 (148)
T smart00382       71 LALARKLKPDVLILDEITSLLDAEQE-------AL-LLLLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR--RFDR  140 (148)
T ss_pred             HHHHHhcCCCEEEEECCcccCCHHHH-------HH-HHhhhhhHHHHHHHhcCCCEEEEEeCCCccCchhhhhh--ccce
Confidence            56777778899999999998755410       00 000000000111123356788888886 5556666666  8888


Q ss_pred             EEEeCCC
Q psy522           81 KIEFPLP   87 (131)
Q Consensus        81 ~i~~~~P   87 (131)
                      .+.+..+
T Consensus       141 ~~~~~~~  147 (148)
T smart00382      141 RIVLLLI  147 (148)
T ss_pred             EEEecCC
Confidence            8887665

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.08  E-value=0.005  Score=48.95  Aligned_cols=91  Identities=16%  Similarity=0.226  Sum_probs=65.4

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCHH
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEK   90 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~   90 (131)
                      -|++|||+|.+..              ...+.++..++..  .+.+++|.+|+.+..|-+.+++  |+. .+.+.+++.+
T Consensus       123 KVvIIdea~~Ls~--------------~a~naLLK~LEep--p~~tifIL~tt~~~kIl~tI~S--Rc~-iv~f~~ls~~  183 (614)
T PRK14971        123 KIYIIDEVHMLSQ--------------AAFNAFLKTLEEP--PSYAIFILATTEKHKILPTILS--RCQ-IFDFNRIQVA  183 (614)
T ss_pred             EEEEEECcccCCH--------------HHHHHHHHHHhCC--CCCeEEEEEeCCchhchHHHHh--hhh-eeecCCCCHH
Confidence            3899999888732              2445666666643  3456677777778899999999  874 6999999999


Q ss_pred             HHHHHHHHHhcCCCCCCc-ccHHHHHHHcCC
Q psy522           91 TKRRIFNIHTSRMTLAED-VNLQELIMAKDD  120 (131)
Q Consensus        91 ~R~~il~~~l~~~~~~~~-~~~~~la~~t~g  120 (131)
                      +-...++..+...+..-+ ..+..++..+.|
T Consensus       184 ei~~~L~~ia~~egi~i~~~al~~La~~s~g  214 (614)
T PRK14971        184 DIVNHLQYVASKEGITAEPEALNVIAQKADG  214 (614)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            988888888776665532 236667776654

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=97.08  E-value=0.0065  Score=44.23  Aligned_cols=89  Identities=9%  Similarity=0.181  Sum_probs=59.8

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-|++||++|.+-.              ...+.++..++.  ..+.+++|.+|++++.+.+.+++  |+. .+.+++|+.
T Consensus        94 ~kv~iI~~ad~m~~--------------~a~naLLK~LEe--pp~~t~~il~~~~~~~ll~TI~S--Rc~-~~~~~~~~~  154 (313)
T PRK05564         94 KKVIIIYNSEKMTE--------------QAQNAFLKTIEE--PPKGVFIILLCENLEQILDTIKS--RCQ-IYKLNRLSK  154 (313)
T ss_pred             ceEEEEechhhcCH--------------HHHHHHHHHhcC--CCCCeEEEEEeCChHhCcHHHHh--hce-eeeCCCcCH
Confidence            45888899887731              244566666764  33456666677889999999999  884 899999999


Q ss_pred             HHHHHHHHHHhcCCCCCCcccHHHHHHHcCC
Q psy522           90 KTKRRIFNIHTSRMTLAEDVNLQELIMAKDD  120 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~~~~~~~~la~~t~g  120 (131)
                      ++-..+++....+  . .+.....++..+.|
T Consensus       155 ~~~~~~l~~~~~~--~-~~~~~~~l~~~~~g  182 (313)
T PRK05564        155 EEIEKFISYKYND--I-KEEEKKSAIAFSDG  182 (313)
T ss_pred             HHHHHHHHHHhcC--C-CHHHHHHHHHHcCC
Confidence            9887777655432  1 12234445555555

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.08  E-value=0.0017  Score=48.85  Aligned_cols=91  Identities=13%  Similarity=0.184  Sum_probs=61.4

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCHH
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEK   90 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~   90 (131)
                      -|++|||+|.+..              ...+.++..++.  ..+..++|.+|+.+..+.+.+++  |+. .+.+.+++.+
T Consensus       129 kvvIIdea~~l~~--------------~~~~~LLk~LEe--p~~~t~~Il~t~~~~kl~~tl~s--R~~-~v~f~~l~~~  189 (397)
T PRK14955        129 RVYIIDEVHMLSI--------------AAFNAFLKTLEE--PPPHAIFIFATTELHKIPATIAS--RCQ-RFNFKRIPLE  189 (397)
T ss_pred             EEEEEeChhhCCH--------------HHHHHHHHHHhc--CCCCeEEEEEeCChHHhHHHHHH--HHH-HhhcCCCCHH
Confidence            5889999988732              123345555553  23456666677778889889988  775 7889999998


Q ss_pred             HHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           91 TKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        91 ~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      +-...++..++..+.. .+..+..++..+.|
T Consensus       190 ei~~~l~~~~~~~g~~i~~~al~~l~~~s~g  220 (397)
T PRK14955        190 EIQQQLQGICEAEGISVDADALQLIGRKAQG  220 (397)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            8888888877654433 22235556666655

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

Probab=97.06  E-value=0.014  Score=41.19  Aligned_cols=86  Identities=19%  Similarity=0.279  Sum_probs=60.1

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcC-CCCC-CCeEEEeeCCCCCccccccc-------------
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDG-FDSR-GDVKVIMATNRIETLDPALI-------------   73 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~-~~v~vi~ttn~~~~id~~l~-------------   73 (131)
                      .+-|||+|++-  |..       .. ...+.+...|   ++ +... .+|++-+|+|+.+.|++.+.             
T Consensus       139 ~kFIlFcDDLS--Fe~-------gd-~~yK~LKs~L---eG~ve~rP~NVl~YATSNRRHLl~e~~~dn~~~~~eih~~e  205 (287)
T COG2607         139 EKFILFCDDLS--FEE-------GD-DAYKALKSAL---EGGVEGRPANVLFYATSNRRHLLPEDMKDNEGSTGEIHPSE  205 (287)
T ss_pred             ceEEEEecCCC--CCC-------Cc-hHHHHHHHHh---cCCcccCCCeEEEEEecCCcccccHhhhhCCCcccccChhH
Confidence            46889999872  211       11 1223344333   44 3333 57999999999888874332             


Q ss_pred             -------CCCccceEEEeCCCCHHHHHHHHHHHhcCCCCCC
Q psy522           74 -------RPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAE  107 (131)
Q Consensus        74 -------~~grf~~~i~~~~P~~~~R~~il~~~l~~~~~~~  107 (131)
                             -..||+..+.|.+|+.++-..|+.+|.++++++-
T Consensus       206 aveEKlSlSDRFGLwL~F~~~~Q~~YL~~V~~~a~~~~l~~  246 (287)
T COG2607         206 AVEEKLSLSDRFGLWLSFYPCDQDEYLKIVDHYAKHFGLDI  246 (287)
T ss_pred             HHHHhhchhhhcceeecccCCCHHHHHHHHHHHHHHcCCCC
Confidence                   2348999999999999999999999999888774

>PHA02244 ATPase-like protein

Probab=97.03  E-value=0.0077  Score=45.03  Aligned_cols=70  Identities=27%  Similarity=0.349  Sum_probs=46.1

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHH-----HhcCC-CCCCCeEEEeeCCCC-----------Cccccc
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLN-----QLDGF-DSRGDVKVIMATNRI-----------ETLDPA   71 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~-----~~~~~-~~~~~v~vi~ttn~~-----------~~id~~   71 (131)
                      ...+++|||++.+-+.           ....++.++.     ..++. ...+++.+|+|+|.+           ..++++
T Consensus       180 ~GgvLiLDEId~a~p~-----------vq~~L~~lLd~r~l~l~g~~i~~h~~FRlIATsN~~~~G~~~~y~G~k~L~~A  248 (383)
T PHA02244        180 KGGLFFIDEIDASIPE-----------ALIIINSAIANKFFDFADERVTAHEDFRVISAGNTLGKGADHIYVARNKIDGA  248 (383)
T ss_pred             cCCEEEEeCcCcCCHH-----------HHHHHHHHhccCeEEecCcEEecCCCEEEEEeeCCCccCcccccCCCcccCHH
Confidence            4589999999987432           2233333332     11111 223578999999963           578999


Q ss_pred             ccCCCccceEEEeCCCCHHHH
Q psy522           72 LIRPGRIDRKIEFPLPDEKTK   92 (131)
Q Consensus        72 l~~~grf~~~i~~~~P~~~~R   92 (131)
                      ++.  ||- .|++..|+.-+.
T Consensus       249 llD--RFv-~I~~dyp~~~E~  266 (383)
T PHA02244        249 TLD--RFA-PIEFDYDEKIEH  266 (383)
T ss_pred             HHh--hcE-EeeCCCCcHHHH
Confidence            999  995 799999984443

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=97.01  E-value=0.0065  Score=44.44  Aligned_cols=90  Identities=17%  Similarity=0.274  Sum_probs=61.3

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-|++||++|.+-.              ...+.++..++...   +.++|..|+.++.+-+.+++  |+ ..+.+++|+.
T Consensus       125 ~kVvII~~ae~m~~--------------~aaNaLLK~LEEPp---~~~fILi~~~~~~Ll~TI~S--Rc-q~i~f~~l~~  184 (314)
T PRK07399        125 RKVVVIEDAETMNE--------------AAANALLKTLEEPG---NGTLILIAPSPESLLPTIVS--RC-QIIPFYRLSD  184 (314)
T ss_pred             ceEEEEEchhhcCH--------------HHHHHHHHHHhCCC---CCeEEEEECChHhCcHHHHh--hc-eEEecCCCCH
Confidence            46788888877632              24455666666543   44677777899999999999  98 5899999999


Q ss_pred             HHHHHHHHHHhcCCCCCCcccHHHHHHHcCCC
Q psy522           90 KTKRRIFNIHTSRMTLAEDVNLQELIMAKDDL  121 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~  121 (131)
                      ++-.+++........  .+.+...++....|=
T Consensus       185 ~~~~~~L~~~~~~~~--~~~~~~~l~~~a~Gs  214 (314)
T PRK07399        185 EQLEQVLKRLGDEEI--LNINFPELLALAQGS  214 (314)
T ss_pred             HHHHHHHHHhhcccc--chhHHHHHHHHcCCC
Confidence            998888887533211  112245566655553

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=97.01  E-value=0.0096  Score=43.11  Aligned_cols=67  Identities=16%  Similarity=0.345  Sum_probs=47.9

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-|++||++|.+-.              ...+.+|+.++.  +.+++++|.+|++++.+-|.+++  |+. .++|+. +.
T Consensus       105 ~kV~II~~ad~m~~--------------~AaNaLLKtLEE--Pp~~t~~iL~t~~~~~lLpTI~S--Rcq-~i~f~~-~~  164 (290)
T PRK07276        105 QQVFIIKDADKMHV--------------NAANSLLKVIEE--PQSEIYIFLLTNDENKVLPTIKS--RTQ-IFHFPK-NE  164 (290)
T ss_pred             cEEEEeehhhhcCH--------------HHHHHHHHHhcC--CCCCeEEEEEECChhhCchHHHH--cce-eeeCCC-cH
Confidence            36888999988842              345566666664  34568899999999999999999  984 777765 44


Q ss_pred             HHHHHHH
Q psy522           90 KTKRRIF   96 (131)
Q Consensus        90 ~~R~~il   96 (131)
                      ++-.+++
T Consensus       165 ~~~~~~L  171 (290)
T PRK07276        165 AYLIQLL  171 (290)
T ss_pred             HHHHHHH
Confidence            4433444

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.99  E-value=0.0038  Score=49.58  Aligned_cols=92  Identities=14%  Similarity=0.193  Sum_probs=63.7

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-|++|||+|.+..              ...+.++..++..  .+.+++|.+|+.++.+.+.+++  |+ ..+.+.+++.
T Consensus       128 ~KVvIIdEad~Lt~--------------~a~naLLK~LEeP--p~~tv~IL~t~~~~kLl~TI~S--Rc-~~vef~~l~~  188 (620)
T PRK14954        128 YRVYIIDEVHMLST--------------AAFNAFLKTLEEP--PPHAIFIFATTELHKIPATIAS--RC-QRFNFKRIPL  188 (620)
T ss_pred             CEEEEEeChhhcCH--------------HHHHHHHHHHhCC--CCCeEEEEEeCChhhhhHHHHh--hc-eEEecCCCCH
Confidence            35889999888732              2345566666643  2346666667778999999998  77 4899999999


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      ++-...++..++..+.. .+..+..++..+.|
T Consensus       189 ~ei~~~L~~i~~~egi~I~~eal~~La~~s~G  220 (620)
T PRK14954        189 DEIQSQLQMICRAEGIQIDADALQLIARKAQG  220 (620)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCC
Confidence            99888888777654433 22345666666665

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=96.96  E-value=0.0027  Score=47.09  Aligned_cols=78  Identities=18%  Similarity=0.351  Sum_probs=53.2

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHH----h--cCCC--CCCCeEEEeeCCCCC-cccccccCCCccce
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQ----L--DGFD--SRGDVKVIMATNRIE-TLDPALIRPGRIDR   80 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~----~--~~~~--~~~~v~vi~ttn~~~-~id~~l~~~grf~~   80 (131)
                      ..+||+||++.+-..           ....+...+..    +  ++..  ...++++|+|.|-.+ .+++++..  ||..
T Consensus       145 ~GiL~lDEInrL~~~-----------~Q~~LLeam~e~~~~ier~G~s~~~p~rfiviaT~np~eg~l~~~Lld--Rf~l  211 (350)
T CHL00081        145 RGILYVDEVNLLDDH-----------LVDILLDSAASGWNTVEREGISIRHPARFVLVGSGNPEEGELRPQLLD--RFGM  211 (350)
T ss_pred             CCEEEecChHhCCHH-----------HHHHHHHHHHhCCeEEeeCCeeeecCCCEEEEeccCcccCCCCHHHHH--HhCc
Confidence            378999999987432           12223333321    1  1111  123688888888544 58999999  9999


Q ss_pred             EEEeCCCC-HHHHHHHHHHHh
Q psy522           81 KIEFPLPD-EKTKRRIFNIHT  100 (131)
Q Consensus        81 ~i~~~~P~-~~~R~~il~~~l  100 (131)
                      .+.+..|+ .+.|.+|++...
T Consensus       212 ~i~l~~~~~~~~e~~il~~~~  232 (350)
T CHL00081        212 HAEIRTVKDPELRVKIVEQRT  232 (350)
T ss_pred             eeecCCCCChHHHHHHHHhhh
Confidence            99999997 699999998754

>PRK06581 DNA polymerase III subunit delta'; Validated

Probab=96.96  E-value=0.0039  Score=43.97  Aligned_cols=76  Identities=11%  Similarity=0.131  Sum_probs=57.0

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-|++|+++|.+-.              ...+.+|..++.  +.+.+++|..|..++.+.+.+++  |+- .+.++.|+.
T Consensus        90 ~KViII~~ae~mt~--------------~AANALLKtLEE--PP~~t~fILit~~~~~LLpTIrS--RCq-~i~~~~p~~  150 (263)
T PRK06581         90 YKVAIIYSAELMNL--------------NAANSCLKILED--APKNSYIFLITSRAASIISTIRS--RCF-KINVRSSIL  150 (263)
T ss_pred             cEEEEEechHHhCH--------------HHHHHHHHhhcC--CCCCeEEEEEeCChhhCchhHhh--ceE-EEeCCCCCH
Confidence            35777788777732              345566766664  44568888888889999999999  984 789999999


Q ss_pred             HHHHHHHHHHhcCCC
Q psy522           90 KTKRRIFNIHTSRMT  104 (131)
Q Consensus        90 ~~R~~il~~~l~~~~  104 (131)
                      ..-.+.+...+....
T Consensus       151 ~~~~e~~~~~~~p~~  165 (263)
T PRK06581        151 HAYNELYSQFIQPIA  165 (263)
T ss_pred             HHHHHHHHHhccccc
Confidence            888888877766543

>CHL00095 clpC Clp protease ATP binding subunit

Probab=96.94  E-value=0.0049  Score=50.56  Aligned_cols=84  Identities=21%  Similarity=0.277  Sum_probs=57.3

Q ss_pred             HHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCC---------CCCCeEEEeeCCCCCc------
Q psy522            3 RVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFD---------SRGDVKVIMATNRIET------   67 (131)
Q Consensus         3 ~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---------~~~~v~vi~ttn~~~~------   67 (131)
                      +..+.+..+||+|||+|..-+              ...+.++..++.-.         .-.+.++|.|||....      
T Consensus       605 ~~~~~~p~~VvllDeieka~~--------------~v~~~Llq~le~g~~~d~~g~~v~~~~~i~I~Tsn~g~~~i~~~~  670 (821)
T CHL00095        605 EAVRKKPYTVVLFDEIEKAHP--------------DIFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTSNLGSKVIETNS  670 (821)
T ss_pred             HHHHhCCCeEEEECChhhCCH--------------HHHHHHHHHhccCceecCCCcEEecCceEEEEeCCcchHHHHhhc
Confidence            344556669999999998622              23444444444310         1246899999995321      


Q ss_pred             -------------------------------ccccccCCCccceEEEeCCCCHHHHHHHHHHHhcC
Q psy522           68 -------------------------------LDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSR  102 (131)
Q Consensus        68 -------------------------------id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~  102 (131)
                                                     ..|.|+.  |+|..+.|.+.+.++-.+|+...+..
T Consensus       671 ~~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~f~pefln--Rid~ii~F~pL~~~~l~~Iv~~~l~~  734 (821)
T CHL00095        671 GGLGFELSENQLSEKQYKRLSNLVNEELKQFFRPEFLN--RLDEIIVFRQLTKNDVWEIAEIMLKN  734 (821)
T ss_pred             cccCCcccccccccccHHHHHHHHHHHHHHhcCHHHhc--cCCeEEEeCCCCHHHHHHHHHHHHHH
Confidence                                           1245666  99999999999999999999877653

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

Probab=96.86  E-value=0.0039  Score=41.22  Aligned_cols=61  Identities=23%  Similarity=0.305  Sum_probs=42.0

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCC
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLP   87 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P   87 (131)
                      ...-|++||++|.+-.              ...+.++..|+.  ....+++|.+|++++.|-+.+++  |+- .+.+++.
T Consensus       101 ~~~KviiI~~ad~l~~--------------~a~NaLLK~LEe--pp~~~~fiL~t~~~~~il~TI~S--Rc~-~i~~~~l  161 (162)
T PF13177_consen  101 GKYKVIIIDEADKLTE--------------EAQNALLKTLEE--PPENTYFILITNNPSKILPTIRS--RCQ-VIRFRPL  161 (162)
T ss_dssp             SSSEEEEEETGGGS-H--------------HHHHHHHHHHHS--TTTTEEEEEEES-GGGS-HHHHT--TSE-EEEE---
T ss_pred             CCceEEEeehHhhhhH--------------HHHHHHHHHhcC--CCCCEEEEEEECChHHChHHHHh--hce-EEecCCC
Confidence            3467999999999842              355566666664  34679999999999999999999  873 5666543

...

>KOG0741|consensus

Probab=96.82  E-value=0.0037  Score=48.69  Aligned_cols=92  Identities=18%  Similarity=0.226  Sum_probs=62.3

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCC-CeEEEeeCCCCCccc-ccccCCCcc
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRG-DVKVIMATNRIETLD-PALIRPGRI   78 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~v~vi~ttn~~~~id-~~l~~~grf   78 (131)
                      +|+-|.+..-+||++|++|.|..-- +-+.   .....++..++-.+.....++ +.++++||+..+-+- -.+..  +|
T Consensus       590 ~F~DAYkS~lsiivvDdiErLiD~v-pIGP---RfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~i~~--~F  663 (744)
T KOG0741|consen  590 IFEDAYKSPLSIIVVDDIERLLDYV-PIGP---RFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMGILD--CF  663 (744)
T ss_pred             HHHHhhcCcceEEEEcchhhhhccc-ccCc---hhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcCHHH--hh
Confidence            5889999999999999999987433 1111   122345555666666655554 578888888766663 34556  99


Q ss_pred             ceEEEeCCCCH-HHHHHHHHH
Q psy522           79 DRKIEFPLPDE-KTKRRIFNI   98 (131)
Q Consensus        79 ~~~i~~~~P~~-~~R~~il~~   98 (131)
                      +..+++|..+. ++-.+++..
T Consensus       664 ~~~i~Vpnl~~~~~~~~vl~~  684 (744)
T KOG0741|consen  664 SSTIHVPNLTTGEQLLEVLEE  684 (744)
T ss_pred             hheeecCccCchHHHHHHHHH
Confidence            99999998755 565555543

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

Probab=96.79  E-value=0.009  Score=43.13  Aligned_cols=66  Identities=14%  Similarity=0.095  Sum_probs=55.8

Q ss_pred             CCeEEEeeCCCCCcccccccCCCccceEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCC
Q psy522           54 GDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDL  121 (131)
Q Consensus        54 ~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~  121 (131)
                      ++..+||+|.....+..-++.  ||.....+..=+.++-.+|+...-+..... .+....++|.++.|.
T Consensus       150 ppFTLIGATTr~G~lt~PLrd--RFGi~~rlefY~~~eL~~Iv~r~a~~l~i~i~~~~a~eIA~rSRGT  216 (332)
T COG2255         150 PPFTLIGATTRAGMLTNPLRD--RFGIIQRLEFYTVEELEEIVKRSAKILGIEIDEEAALEIARRSRGT  216 (332)
T ss_pred             CCeeEeeeccccccccchhHH--hcCCeeeeecCCHHHHHHHHHHHHHHhCCCCChHHHHHHHHhccCC
Confidence            578999999999999999999  999999999999999999999887766655 333467788888774

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=96.79  E-value=0.0058  Score=50.34  Aligned_cols=81  Identities=23%  Similarity=0.357  Sum_probs=54.7

Q ss_pred             HHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcC--CC-------CCCCeEEEeeCCCCCc--------
Q psy522            5 AEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDG--FD-------SRGDVKVIMATNRIET--------   67 (131)
Q Consensus         5 A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~--~~-------~~~~v~vi~ttn~~~~--------   67 (131)
                      .+.+.-+||+|||+|.+-+              .+.+.++..++.  +.       .-.+.++|+|||....        
T Consensus       663 v~~~p~~vlllDeieka~~--------------~v~~~Ll~~l~~g~l~d~~g~~vd~rn~iiI~TSn~g~~~~~~~~~~  728 (852)
T TIGR03346       663 VRRKPYSVVLFDEVEKAHP--------------DVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNLGSQFIQELAGG  728 (852)
T ss_pred             HHcCCCcEEEEeccccCCH--------------HHHHHHHHHHhcCceecCCCeEEecCCcEEEEeCCcchHhHhhhccc
Confidence            3555667999999997621              233334444432  11       1145789999997221        


Q ss_pred             -----------------ccccccCCCccceEEEeCCCCHHHHHHHHHHHhc
Q psy522           68 -----------------LDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTS  101 (131)
Q Consensus        68 -----------------id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~  101 (131)
                                       ..|.|..  |+|..+.+.+++.+....|+...+.
T Consensus       729 ~~~~~~~~~~~~~~~~~F~pel~~--Rid~IivF~PL~~e~l~~I~~l~L~  777 (852)
T TIGR03346       729 DDYEEMREAVMEVLRAHFRPEFLN--RIDEIVVFHPLGREQIARIVEIQLG  777 (852)
T ss_pred             ccHHHHHHHHHHHHHhhcCHHHhc--CcCeEEecCCcCHHHHHHHHHHHHH
Confidence                             2356666  9999999999999999999987764

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.

>KOG2035|consensus

Probab=96.78  E-value=0.0075  Score=43.46  Aligned_cols=92  Identities=16%  Similarity=0.272  Sum_probs=67.9

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCHH
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEK   90 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~   90 (131)
                      -+++|-|+|.+..+.       +..+.+++...         .+.+-+|..+|+...+=+.+++  |+ ..|.+|+|+.+
T Consensus       129 Kvvvi~ead~LT~dA-------Q~aLRRTMEkY---------s~~~RlIl~cns~SriIepIrS--RC-l~iRvpaps~e  189 (351)
T KOG2035|consen  129 KVVVINEADELTRDA-------QHALRRTMEKY---------SSNCRLILVCNSTSRIIEPIRS--RC-LFIRVPAPSDE  189 (351)
T ss_pred             EEEEEechHhhhHHH-------HHHHHHHHHHH---------hcCceEEEEecCcccchhHHhh--he-eEEeCCCCCHH
Confidence            478889999885432       22233333322         1356788899999999999998  76 46999999999


Q ss_pred             HHHHHHHHHhcCCCCC-CcccHHHHHHHcCCC
Q psy522           91 TKRRIFNIHTSRMTLA-EDVNLQELIMAKDDL  121 (131)
Q Consensus        91 ~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~  121 (131)
                      +-..++...+++.++. +..-+.++++.+.|=
T Consensus       190 eI~~vl~~v~~kE~l~lp~~~l~rIa~kS~~n  221 (351)
T KOG2035|consen  190 EITSVLSKVLKKEGLQLPKELLKRIAEKSNRN  221 (351)
T ss_pred             HHHHHHHHHHHHhcccCcHHHHHHHHHHhccc
Confidence            9999999999887776 444578888887763

>PF05729 NACHT: NACHT domain

Probab=96.74  E-value=0.013  Score=37.83  Aligned_cols=88  Identities=16%  Similarity=0.236  Sum_probs=50.8

Q ss_pred             HHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCC--CCCcccccccCCCccceE
Q psy522            4 VAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATN--RIETLDPALIRPGRIDRK   81 (131)
Q Consensus         4 ~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn--~~~~id~~l~~~grf~~~   81 (131)
                      .+....+.+|+||.+|.+......   .........+..++..    ...+++-++.|++  ....+...+...    ..
T Consensus        76 ~~~~~~~~llilDglDE~~~~~~~---~~~~~~~~~l~~l~~~----~~~~~~~liit~r~~~~~~~~~~~~~~----~~  144 (166)
T PF05729_consen   76 LLEKNKRVLLILDGLDELEEQDQS---QERQRLLDLLSQLLPQ----ALPPGVKLIITSRPRAFPDLRRRLKQA----QI  144 (166)
T ss_pred             HHHcCCceEEEEechHhcccchhh---hHHHHHHHHHHHHhhh----ccCCCCeEEEEEcCChHHHHHHhcCCC----cE
Confidence            345667889999999999764321   1122233344444432    1122333344433  222233333331    57


Q ss_pred             EEeCCCCHHHHHHHHHHHhcC
Q psy522           82 IEFPLPDEKTKRRIFNIHTSR  102 (131)
Q Consensus        82 i~~~~P~~~~R~~il~~~l~~  102 (131)
                      +.++..+.+++.++++.++++
T Consensus       145 ~~l~~~~~~~~~~~~~~~f~~  165 (166)
T PF05729_consen  145 LELEPFSEEDIKQYLRKYFSN  165 (166)
T ss_pred             EEECCCCHHHHHHHHHHHhhc
Confidence            899999999999999999875

>smart00350 MCM minichromosome maintenance proteins

Probab=96.73  E-value=0.0069  Score=47.11  Aligned_cols=79  Identities=22%  Similarity=0.294  Sum_probs=52.8

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHh------cCCC--CCCCeEEEeeCCCCC-------------cc
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQL------DGFD--SRGDVKVIMATNRIE-------------TL   68 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~------~~~~--~~~~v~vi~ttn~~~-------------~i   68 (131)
                      ..+++|||+|.+-.+           ....+.+.+++-      .++.  -..+..||||+|-.+             .+
T Consensus       301 ~Gil~iDEi~~l~~~-----------~q~~L~e~me~~~i~i~k~G~~~~l~~~~~viAa~NP~~g~y~~~~~~~~n~~l  369 (509)
T smart00350      301 NGVCCIDEFDKMDDS-----------DRTAIHEAMEQQTISIAKAGITTTLNARCSVLAAANPIGGRYDPKLTPEENIDL  369 (509)
T ss_pred             CCEEEEechhhCCHH-----------HHHHHHHHHhcCEEEEEeCCEEEEecCCcEEEEEeCCCCcccCCCcChhhccCC
Confidence            468999999987422           223333333220      1111  114688999999532             69


Q ss_pred             cccccCCCccceEEEe-CCCCHHHHHHHHHHHhc
Q psy522           69 DPALIRPGRIDRKIEF-PLPDEKTKRRIFNIHTS  101 (131)
Q Consensus        69 d~~l~~~grf~~~i~~-~~P~~~~R~~il~~~l~  101 (131)
                      ++++++  |||..+.+ ..|+.+...+|.++.+.
T Consensus       370 ~~~lLs--RFdLi~~~~d~~~~~~d~~i~~~i~~  401 (509)
T smart00350      370 PAPILS--RFDLLFVVLDEVDEERDRELAKHVVD  401 (509)
T ss_pred             ChHHhC--ceeeEEEecCCCChHHHHHHHHHHHH
Confidence            999999  99976554 78999999999998654

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=96.72  E-value=0.011  Score=44.51  Aligned_cols=84  Identities=19%  Similarity=0.400  Sum_probs=58.7

Q ss_pred             HHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHH------hcCCCCC--CCeEEEeeCC-CCCcccccccC
Q psy522            4 VAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQ------LDGFDSR--GDVKVIMATN-RIETLDPALIR   74 (131)
Q Consensus         4 ~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~------~~~~~~~--~~v~vi~ttn-~~~~id~~l~~   74 (131)
                      .|++|. .|+++||+-.|- .          .+.-++...+..      .+|++-.  -++++|||+| ....|-+-|+.
T Consensus       140 La~AnR-GIlYvDEvnlL~-d----------~lvd~LLd~aaeG~n~vereGisi~hpa~fvligTmNPEeGeLrpqLlD  207 (423)
T COG1239         140 LARANR-GILYVDEVNLLD-D----------HLVDALLDVAAEGVNDVEREGISIRHPARFLLIGTMNPEEGELRPQLLD  207 (423)
T ss_pred             hhhccC-CEEEEecccccc-H----------HHHHHHHHHHHhCCceeeeCceeeccCccEEEEeecCccccccchhhHh
Confidence            356676 899999997662 1          122333333322      2233333  3699999999 46678888888


Q ss_pred             CCccceEEEeCCC-CHHHHHHHHHHHhc
Q psy522           75 PGRIDRKIEFPLP-DEKTKRRIFNIHTS  101 (131)
Q Consensus        75 ~grf~~~i~~~~P-~~~~R~~il~~~l~  101 (131)
                        ||...+.+..| +.++|.+|.+.-+.
T Consensus       208 --Rfg~~v~~~~~~~~~~rv~Ii~r~~~  233 (423)
T COG1239         208 --RFGLEVDTHYPLDLEERVEIIRRRLA  233 (423)
T ss_pred             --hhcceeeccCCCCHHHHHHHHHHHHH
Confidence              99999999988 88999999987654

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

Probab=96.65  E-value=0.0053  Score=45.37  Aligned_cols=82  Identities=23%  Similarity=0.321  Sum_probs=54.6

Q ss_pred             CeEEEecccccccCcCCCCC-CCchhHHHHHHHHHHHHhcCC--------CCCCCeEEEeeCC----CCCcccccccCCC
Q psy522           10 PSIVFIDEIDAVGTKRYDSN-SGGEREIQRTMLELLNQLDGF--------DSRGDVKVIMATN----RIETLDPALIRPG   76 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~-~~~~~~~~~~~~~~l~~~~~~--------~~~~~v~vi~ttn----~~~~id~~l~~~g   76 (131)
                      -.||||||+|.++.+.+..+ +.+..   .+..-+|-.+.+.        -.++.+++||+-.    .|..+=|.+--  
T Consensus       251 ~GIvFIDEIDKIa~~~~~g~~dvSRE---GVQRDlLPlvEGstV~TKyG~VkTdHILFIasGAFh~sKPSDLiPELQG--  325 (444)
T COG1220         251 NGIVFIDEIDKIAKRGGSGGPDVSRE---GVQRDLLPLVEGSTVSTKYGPVKTDHILFIASGAFHVAKPSDLIPELQG--  325 (444)
T ss_pred             cCeEEEehhhHHHhcCCCCCCCcchh---hhcccccccccCceeeccccccccceEEEEecCceecCChhhcChhhcC--
Confidence            46999999999987764222 21221   1222333333331        2335699998643    46677677765  


Q ss_pred             ccceEEEeCCCCHHHHHHHH
Q psy522           77 RIDRKIEFPLPDEKTKRRIF   96 (131)
Q Consensus        77 rf~~~i~~~~P~~~~R~~il   96 (131)
                      ||.-++++...+.+....||
T Consensus       326 RfPIRVEL~~Lt~~Df~rIL  345 (444)
T COG1220         326 RFPIRVELDALTKEDFERIL  345 (444)
T ss_pred             CCceEEEcccCCHHHHHHHH
Confidence            99999999999999988887

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

Probab=96.63  E-value=0.0035  Score=47.55  Aligned_cols=83  Identities=25%  Similarity=0.331  Sum_probs=55.5

Q ss_pred             CCeEEEecccccccCcCCCCC-CCchhHHHHHHHHHHHHhcCC--------CCCCCeEEEeeCC----CCCcccccccCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSN-SGGEREIQRTMLELLNQLDGF--------DSRGDVKVIMATN----RIETLDPALIRP   75 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~-~~~~~~~~~~~~~~l~~~~~~--------~~~~~v~vi~ttn----~~~~id~~l~~~   75 (131)
                      +-.||||||+|+++.+.++.+ +.+.   ..+...+|..+.+-        -.++.+++|++=.    .|..+=|.|.. 
T Consensus       249 ~~GIVfiDEiDKIa~~~~~~~~DvS~---eGVQ~~LLki~EG~~v~~k~~~i~T~~ILFI~~GAF~~~kp~DlIPEl~G-  324 (443)
T PRK05201        249 QNGIVFIDEIDKIAARGGSSGPDVSR---EGVQRDLLPLVEGSTVSTKYGMVKTDHILFIASGAFHVSKPSDLIPELQG-  324 (443)
T ss_pred             cCCEEEEEcchhhcccCCCCCCCCCc---cchhcccccccccceeeecceeEECCceeEEecCCcCCCChhhccHHHhC-
Confidence            457999999999997753211 1111   12344455555541        2235688887533    35566677776 


Q ss_pred             CccceEEEeCCCCHHHHHHHH
Q psy522           76 GRIDRKIEFPLPDEKTKRRIF   96 (131)
Q Consensus        76 grf~~~i~~~~P~~~~R~~il   96 (131)
                       ||...+.+.+++.+.-..||
T Consensus       325 -R~Pi~v~L~~L~~~dL~~IL  344 (443)
T PRK05201        325 -RFPIRVELDALTEEDFVRIL  344 (443)
T ss_pred             -ccceEEECCCCCHHHHHHHh
Confidence             99999999999999988887

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

Probab=96.56  E-value=0.013  Score=42.38  Aligned_cols=70  Identities=23%  Similarity=0.351  Sum_probs=50.7

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      ..-||+|||+|.+...              ..+.++..+..  ......+|.+||.++.+-+-+++  |+. .+.|++|+
T Consensus       109 ~~kviiidead~mt~~--------------A~nallk~lEe--p~~~~~~il~~n~~~~il~tI~S--Rc~-~i~f~~~~  169 (325)
T COG0470         109 GYKVVIIDEADKLTED--------------AANALLKTLEE--PPKNTRFILITNDPSKILPTIRS--RCQ-RIRFKPPS  169 (325)
T ss_pred             CceEEEeCcHHHHhHH--------------HHHHHHHHhcc--CCCCeEEEEEcCChhhccchhhh--cce-eeecCCch
Confidence            3578999999998542              33334444442  34578899999999999999999  884 78888877


Q ss_pred             HHHHHHHHH
Q psy522           89 EKTKRRIFN   97 (131)
Q Consensus        89 ~~~R~~il~   97 (131)
                      ...+....+
T Consensus       170 ~~~~i~~~e  178 (325)
T COG0470         170 RLEAIAWLE  178 (325)
T ss_pred             HHHHHHHhh
Confidence            776666555

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=96.53  E-value=0.0057  Score=46.44  Aligned_cols=83  Identities=25%  Similarity=0.333  Sum_probs=54.5

Q ss_pred             CCeEEEecccccccCcCCCCC-CCchhHHHHHHHHHHHHhcCC--------CCCCCeEEEeeCC----CCCcccccccCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSN-SGGEREIQRTMLELLNQLDGF--------DSRGDVKVIMATN----RIETLDPALIRP   75 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~-~~~~~~~~~~~~~~l~~~~~~--------~~~~~v~vi~ttn----~~~~id~~l~~~   75 (131)
                      +-.||||||+|+++.+..+.+ +.+..   .+...+|..+.+-        -.++++++|++-.    .|..+=|.|.- 
T Consensus       247 ~~GIVfiDEiDKIa~~~~~~~~DvS~e---GVQ~~LLkilEGt~v~~k~~~v~T~~ILFI~~GAF~~~kp~DlIPEl~G-  322 (441)
T TIGR00390       247 QSGIIFIDEIDKIAKKGESSGADVSRE---GVQRDLLPIVEGSTVNTKYGMVKTDHILFIAAGAFQLAKPSDLIPELQG-  322 (441)
T ss_pred             cCCEEEEEchhhhcccCCCCCCCCCcc---chhccccccccCceeeecceeEECCceeEEecCCcCCCChhhccHHHhC-
Confidence            567999999999997652211 11111   2334455555541        2235688887644    35555566665 


Q ss_pred             CccceEEEeCCCCHHHHHHHH
Q psy522           76 GRIDRKIEFPLPDEKTKRRIF   96 (131)
Q Consensus        76 grf~~~i~~~~P~~~~R~~il   96 (131)
                       ||...+.+.+++.+.-..||
T Consensus       323 -R~Pi~v~L~~L~~edL~rIL  342 (441)
T TIGR00390       323 -RFPIRVELQALTTDDFERIL  342 (441)
T ss_pred             -ccceEEECCCCCHHHHHHHh
Confidence             99999999999999988887

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

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

Probab=96.42  E-value=0.019  Score=41.66  Aligned_cols=81  Identities=19%  Similarity=0.286  Sum_probs=49.6

Q ss_pred             hcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCC---------C-
Q psy522            7 EHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRP---------G-   76 (131)
Q Consensus         7 ~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~---------g-   76 (131)
                      ...|-||+|||+|.+-++.          ...++.    .+..+-..+++++|.+.+. +.+-.++...         | 
T Consensus       170 ~~~~iViiIDdLDR~~~~~----------i~~~l~----~ik~~~~~~~i~~Il~~D~-~~l~~ai~~~~~~~~~~~~~~  234 (325)
T PF07693_consen  170 SKKRIVIIIDDLDRCSPEE----------IVELLE----AIKLLLDFPNIIFILAFDP-EILEKAIEKNYGEGFDEIDGR  234 (325)
T ss_pred             CCceEEEEEcchhcCCcHH----------HHHHHH----HHHHhcCCCCeEEEEEecH-HHHHHHHHhhcCcccccccHH
Confidence            3567899999999984432          222333    2222223467777777763 3332222221         0 


Q ss_pred             -----ccceEEEeCCCCHHHHHHHHHHHhcC
Q psy522           77 -----RIDRKIEFPLPDEKTKRRIFNIHTSR  102 (131)
Q Consensus        77 -----rf~~~i~~~~P~~~~R~~il~~~l~~  102 (131)
                           -|+..+.+|.|+..+...++...+..
T Consensus       235 ~yLeKiiq~~~~lP~~~~~~~~~~~~~~~~~  265 (325)
T PF07693_consen  235 EYLEKIIQVPFSLPPPSPSDLERYLNELLES  265 (325)
T ss_pred             HHHHhhcCeEEEeCCCCHHHHHHHHHHHHHH
Confidence                 36788999999999888888777543

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

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

Probab=96.34  E-value=0.013  Score=47.52  Aligned_cols=83  Identities=23%  Similarity=0.404  Sum_probs=59.5

Q ss_pred             HHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcC--CCC-C------CCeEEEeeCCCCCc------
Q psy522            3 RVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDG--FDS-R------GDVKVIMATNRIET------   67 (131)
Q Consensus         3 ~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~--~~~-~------~~v~vi~ttn~~~~------   67 (131)
                      +..|++..|||+|||+|+-           ++   .+++.|++-+|.  +.. +      .+.++|+|||.-..      
T Consensus       587 EaVRr~PySViLlDEIEKA-----------Hp---dV~nilLQVlDdGrLTD~~Gr~VdFrNtiIImTSN~Gs~~i~~~~  652 (786)
T COG0542         587 EAVRRKPYSVILLDEIEKA-----------HP---DVFNLLLQVLDDGRLTDGQGRTVDFRNTIIIMTSNAGSEEILRDA  652 (786)
T ss_pred             HhhhcCCCeEEEechhhhc-----------CH---HHHHHHHHHhcCCeeecCCCCEEecceeEEEEecccchHHHHhhc
Confidence            3456777899999999874           22   366666666663  111 1      24899999995321      


Q ss_pred             ----------------------ccccccCCCccceEEEeCCCCHHHHHHHHHHHhc
Q psy522           68 ----------------------LDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTS  101 (131)
Q Consensus        68 ----------------------id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~  101 (131)
                                            ..|+|+.  |+|..|.|.+.+++.-.+|+...+.
T Consensus       653 ~~~~~~~~~~~~~~v~~~l~~~F~PEFLN--Rid~II~F~~L~~~~l~~Iv~~~L~  706 (786)
T COG0542         653 DGDDFADKEALKEAVMEELKKHFRPEFLN--RIDEIIPFNPLSKEVLERIVDLQLN  706 (786)
T ss_pred             cccccchhhhHHHHHHHHHHhhCCHHHHh--hcccEEeccCCCHHHHHHHHHHHHH
Confidence                                  2355666  9999999999999999999988764

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=96.33  E-value=0.016  Score=45.95  Aligned_cols=78  Identities=13%  Similarity=0.289  Sum_probs=52.6

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHh----c--CCCC--CCCeEEEeeCCCCC---cccccccCCCccc
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQL----D--GFDS--RGDVKVIMATNRIE---TLDPALIRPGRID   79 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~----~--~~~~--~~~v~vi~ttn~~~---~id~~l~~~grf~   79 (131)
                      .+||+||++.+-..           ....+.+.+..=    .  +...  ..++.+|+|+|..+   .+++++..  ||.
T Consensus        86 GvL~lDEi~rl~~~-----------~q~~Ll~al~~g~v~i~r~G~~~~~p~~f~lIAt~np~e~~g~L~~~Lld--Rf~  152 (589)
T TIGR02031        86 GVLYVDMANLLDDG-----------LSNRLLQALDEGVVIVEREGISVVHPAKFALIATYDPAEGGGGLPDHLLD--RLA  152 (589)
T ss_pred             CcEeccchhhCCHH-----------HHHHHHHHHHcCCeEEEECCCceeecCceEEEEecCCccccCCCCHHHHH--hcc
Confidence            58999999887432           223333333211    0  1111  13588999998654   78999999  999


Q ss_pred             eEEEeCC-CCHHHHHHHHHHHhc
Q psy522           80 RKIEFPL-PDEKTKRRIFNIHTS  101 (131)
Q Consensus        80 ~~i~~~~-P~~~~R~~il~~~l~  101 (131)
                      .++.+.. |+.++|.+|++..+.
T Consensus       153 l~v~~~~~~~~~er~eil~~~~~  175 (589)
T TIGR02031       153 LHVSLEDVASQDLRVEIVRRERC  175 (589)
T ss_pred             CeeecCCCCCHHHHHHHHHHHHH
Confidence            9888875 588889999988763

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.

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=96.31  E-value=0.0046  Score=39.41  Aligned_cols=22  Identities=32%  Similarity=0.625  Sum_probs=18.7

Q ss_pred             CeEEEeeCCCCC----cccccccCCCcc
Q psy522           55 DVKVIMATNRIE----TLDPALIRPGRI   78 (131)
Q Consensus        55 ~v~vi~ttn~~~----~id~~l~~~grf   78 (131)
                      +..+|+|+|...    .+++++++  ||
T Consensus       114 ~~~ii~t~N~~~~~~~~l~~al~~--Rf  139 (139)
T PF07728_consen  114 NFRIIATMNPRDKGRKELSPALLD--RF  139 (139)
T ss_dssp             -EEEEEEESSST--TTTTCHHHHT--T-
T ss_pred             ceEEEEEEcCCCCCcCcCCHHHHh--hC
Confidence            389999999888    89999999  87

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

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

Probab=96.27  E-value=0.022  Score=42.54  Aligned_cols=80  Identities=24%  Similarity=0.308  Sum_probs=58.2

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCC---CcccccccCCCccc-eEEE
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRI---ETLDPALIRPGRID-RKIE   83 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~---~~id~~l~~~grf~-~~i~   83 (131)
                      ..+.||++||+|.|..+.+           ..+-+++..-...  ..++.+|+.+|..   +.+|+.+.+  +|. ..|.
T Consensus       122 ~~~~IvvLDEid~L~~~~~-----------~~LY~L~r~~~~~--~~~v~vi~i~n~~~~~~~ld~rv~s--~l~~~~I~  186 (366)
T COG1474         122 GKTVIVILDEVDALVDKDG-----------EVLYSLLRAPGEN--KVKVSIIAVSNDDKFLDYLDPRVKS--SLGPSEIV  186 (366)
T ss_pred             CCeEEEEEcchhhhccccc-----------hHHHHHHhhcccc--ceeEEEEEEeccHHHHHHhhhhhhh--ccCcceee
Confidence            4578899999999987652           2444444333332  4578999999975   467899998  652 4478


Q ss_pred             eCCCCHHHHHHHHHHHhcC
Q psy522           84 FPLPDEKTKRRIFNIHTSR  102 (131)
Q Consensus        84 ~~~P~~~~R~~il~~~l~~  102 (131)
                      |++=+.+|-..|++.-...
T Consensus       187 F~pY~a~el~~Il~~R~~~  205 (366)
T COG1474         187 FPPYTAEELYDILRERVEE  205 (366)
T ss_pred             eCCCCHHHHHHHHHHHHHh
Confidence            8888999999999887653

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=96.20  E-value=0.01  Score=43.60  Aligned_cols=70  Identities=16%  Similarity=0.305  Sum_probs=50.1

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-|+++|++|.+-.              ...+.++..++...  ..+.+|.+|++++.+.+.+++  |+ ..+.|++|+.
T Consensus       114 ~kV~iiEp~~~Ld~--------------~a~naLLk~LEep~--~~~~~Ilvth~~~~ll~ti~S--Rc-~~~~~~~~~~  174 (325)
T PRK08699        114 LRVILIHPAESMNL--------------QAANSLLKVLEEPP--PQVVFLLVSHAADKVLPTIKS--RC-RKMVLPAPSH  174 (325)
T ss_pred             ceEEEEechhhCCH--------------HHHHHHHHHHHhCc--CCCEEEEEeCChHhChHHHHH--Hh-hhhcCCCCCH
Confidence            45888899888732              23334444555432  346677799999999999999  88 4788999999


Q ss_pred             HHHHHHHHH
Q psy522           90 KTKRRIFNI   98 (131)
Q Consensus        90 ~~R~~il~~   98 (131)
                      ++-.+.+..
T Consensus       175 ~~~~~~L~~  183 (325)
T PRK08699        175 EEALAYLRE  183 (325)
T ss_pred             HHHHHHHHh
Confidence            987777654

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=96.19  E-value=0.017  Score=46.11  Aligned_cols=74  Identities=20%  Similarity=0.321  Sum_probs=51.5

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcC---------C--CCCCCeEEEeeCCC-CCcccccccCCCcc
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDG---------F--DSRGDVKVIMATNR-IETLDPALIRPGRI   78 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~---------~--~~~~~v~vi~ttn~-~~~id~~l~~~grf   78 (131)
                      .||||||++.+-..              +...++..|+.         .  ....++.+|+|+|- ...+.++++.  ||
T Consensus       128 GiL~lDEi~~l~~~--------------~q~~Ll~~le~g~~~v~r~g~~~~~~~~~~lIat~np~eg~l~~~L~d--R~  191 (633)
T TIGR02442       128 GILYIDEVNLLDDH--------------LVDVLLDAAAMGVNRVEREGLSVSHPARFVLIGTMNPEEGDLRPQLLD--RF  191 (633)
T ss_pred             CeEEeChhhhCCHH--------------HHHHHHHHHhcCCEEEEECCceeeecCCeEEEEecCCCCCCCCHHHHh--hc
Confidence            58999999987422              23333333331         1  11135899999884 3468899999  99


Q ss_pred             ceEEEeCCC-CHHHHHHHHHHHh
Q psy522           79 DRKIEFPLP-DEKTKRRIFNIHT  100 (131)
Q Consensus        79 ~~~i~~~~P-~~~~R~~il~~~l  100 (131)
                      +.++.++.| +.++|.+++++.+
T Consensus       192 ~l~i~v~~~~~~~~~~~il~~~~  214 (633)
T TIGR02442       192 GLCVDVAAPRDPEERVEIIRRRL  214 (633)
T ss_pred             ceEEEccCCCchHHHHHHHHHHH
Confidence            999999987 5788888887654

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.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=96.19  E-value=0.019  Score=47.40  Aligned_cols=80  Identities=26%  Similarity=0.373  Sum_probs=53.7

Q ss_pred             hcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcC--CC-------CCCCeEEEeeCCCCC-----------
Q psy522            7 EHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDG--FD-------SRGDVKVIMATNRIE-----------   66 (131)
Q Consensus         7 ~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~--~~-------~~~~v~vi~ttn~~~-----------   66 (131)
                      ....+||+|||+|.+-+              ...+.++..++.  +.       .-.+.++|.|||...           
T Consensus       668 ~~p~~vLllDEieka~~--------------~v~~~Ll~ile~g~l~d~~gr~vd~rn~iiI~TSN~g~~~~~~~~~~~~  733 (857)
T PRK10865        668 RRPYSVILLDEVEKAHP--------------DVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNLGSDLIQERFGELD  733 (857)
T ss_pred             hCCCCeEEEeehhhCCH--------------HHHHHHHHHHhhCceecCCceEEeecccEEEEeCCcchHHHHHhccccc
Confidence            33448999999987521              133334444432  11       113467899999731           


Q ss_pred             --------------cccccccCCCccceEEEeCCCCHHHHHHHHHHHhcC
Q psy522           67 --------------TLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSR  102 (131)
Q Consensus        67 --------------~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~  102 (131)
                                    .+.|+|+.  |+|..+.+.+++.+.-.+|++.++..
T Consensus       734 ~~~~~~~~~~~~~~~f~PELln--Rld~iivF~PL~~edl~~Iv~~~L~~  781 (857)
T PRK10865        734 YAHMKELVLGVVSHNFRPEFIN--RIDEVVVFHPLGEQHIASIAQIQLQR  781 (857)
T ss_pred             hHHHHHHHHHHHcccccHHHHH--hCCeeEecCCCCHHHHHHHHHHHHHH
Confidence                          23467887  99999999999999999999887754

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=95.92  E-value=0.0079  Score=40.79  Aligned_cols=68  Identities=16%  Similarity=0.121  Sum_probs=41.1

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLP   87 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P   87 (131)
                      ..++|+|||+..+++.+.......    ...+ .++...    ...+.-++.+|.++..||+.++.  +.+.++++..+
T Consensus        79 ~~~liviDEa~~~~~~r~~~~~~~----~~~~-~~l~~h----Rh~g~diiliTQ~~~~id~~ir~--lve~~~~~~k~  146 (193)
T PF05707_consen   79 KGSLIVIDEAQNFFPSRSWKGKKV----PEII-EFLAQH----RHYGWDIILITQSPSQIDKFIRD--LVEYHYHCRKL  146 (193)
T ss_dssp             TT-EEEETTGGGTSB---T-T--------HHH-HGGGGC----CCTT-EEEEEES-GGGB-HHHHC--CEEEEEEEEE-
T ss_pred             CCcEEEEECChhhcCCCccccccc----hHHH-HHHHHh----CcCCcEEEEEeCCHHHHhHHHHH--HHheEEEEEee
Confidence            479999999999998884321111    1222 333222    23467899999999999999998  99988888655

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=95.87  E-value=0.045  Score=39.83  Aligned_cols=71  Identities=17%  Similarity=0.309  Sum_probs=49.2

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      ..-|++||++|.+.              ....+.++..++.  ..+.+++|.+|+.++.+-+.+++  |+. .+.+.+|+
T Consensus        90 ~~KvvII~~~e~m~--------------~~a~NaLLK~LEE--Pp~~t~~il~~~~~~kll~TI~S--Rc~-~~~f~~l~  150 (299)
T PRK07132         90 QKKILIIKNIEKTS--------------NSLLNALLKTIEE--PPKDTYFLLTTKNINKVLPTIVS--RCQ-VFNVKEPD  150 (299)
T ss_pred             CceEEEEecccccC--------------HHHHHHHHHHhhC--CCCCeEEEEEeCChHhChHHHHh--CeE-EEECCCCC
Confidence            34567777766652              1244566777765  34567777777788999999998  874 79999998


Q ss_pred             HHHHHHHHHH
Q psy522           89 EKTKRRIFNI   98 (131)
Q Consensus        89 ~~~R~~il~~   98 (131)
                      .++-.+.+..
T Consensus       151 ~~~l~~~l~~  160 (299)
T PRK07132        151 QQKILAKLLS  160 (299)
T ss_pred             HHHHHHHHHH
Confidence            8886665543

>KOG2228|consensus

Probab=95.80  E-value=0.03  Score=41.43  Aligned_cols=76  Identities=20%  Similarity=0.275  Sum_probs=51.7

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCC-CCCCeEEEeeCCCCC---cccccccCCCccceE-EEe
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFD-SRGDVKVIMATNRIE---TLDPALIRPGRIDRK-IEF   84 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~v~vi~ttn~~~---~id~~l~~~grf~~~-i~~   84 (131)
                      |.|.++||+|.+++-.           ++++  +.+.+|-.. .+.++.+||.|.+.+   .+...+.+  ||.++ |++
T Consensus       138 ~ViFIldEfDlf~~h~-----------rQtl--lYnlfDisqs~r~Piciig~Ttrld~lE~LEKRVKS--RFshr~I~m  202 (408)
T KOG2228|consen  138 KVIFILDEFDLFAPHS-----------RQTL--LYNLFDISQSARAPICIIGVTTRLDILELLEKRVKS--RFSHRVIFM  202 (408)
T ss_pred             eEEEEeehhhccccch-----------hhHH--HHHHHHHHhhcCCCeEEEEeeccccHHHHHHHHHHh--hcccceeec
Confidence            5667779999987543           1222  233344322 246899999887654   45678888  99877 777


Q ss_pred             CCC-CHHHHHHHHHHHh
Q psy522           85 PLP-DEKTKRRIFNIHT  100 (131)
Q Consensus        85 ~~P-~~~~R~~il~~~l  100 (131)
                      .+| .-++-..+++..+
T Consensus       203 ~~~~~l~~yv~l~r~ll  219 (408)
T KOG2228|consen  203 LPSLPLGDYVDLYRKLL  219 (408)
T ss_pred             cCCCChHHHHHHHHHHh
Confidence            765 7888888888887

>PF14516 AAA_35: AAA-like domain

Probab=95.72  E-value=0.18  Score=37.11  Aligned_cols=104  Identities=15%  Similarity=0.134  Sum_probs=59.6

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCC--eEEEeeCCCCCcccccc-cCCCccceEEEe
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGD--VKVIMATNRIETLDPAL-IRPGRIDRKIEF   84 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--v~vi~ttn~~~~id~~l-~~~grf~~~i~~   84 (131)
                      .+|-||+|||+|.++...     .........+..+.+.-.....-.+  .+++++|..  .+.... .+|=.+...+.+
T Consensus       126 ~~~lVL~iDEiD~l~~~~-----~~~~dF~~~LR~~~~~~~~~~~~~~L~li~~~~t~~--~~~~~~~~SPFNIg~~i~L  198 (331)
T PF14516_consen  126 DKPLVLFIDEIDRLFEYP-----QIADDFFGLLRSWYEQRKNNPIWQKLRLILAGSTED--YIILDINQSPFNIGQPIEL  198 (331)
T ss_pred             CCCEEEEEechhhhccCc-----chHHHHHHHHHHHHHhcccCcccceEEEEEecCccc--ccccCCCCCCcccccceeC
Confidence            579999999999998643     1122344455555442221111122  333333322  222222 344445678899


Q ss_pred             CCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCC
Q psy522           85 PLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDL  121 (131)
Q Consensus        85 ~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~  121 (131)
                      +..+.++-..+++.+-..  .... .+..+-..|.|.
T Consensus       199 ~~Ft~~ev~~L~~~~~~~--~~~~-~~~~l~~~tgGh  232 (331)
T PF14516_consen  199 PDFTPEEVQELAQRYGLE--FSQE-QLEQLMDWTGGH  232 (331)
T ss_pred             CCCCHHHHHHHHHhhhcc--CCHH-HHHHHHHHHCCC
Confidence            988999999998877433  2222 377788888885

>KOG2028|consensus

Probab=95.59  E-value=0.075  Score=40.02  Aligned_cols=79  Identities=24%  Similarity=0.291  Sum_probs=53.5

Q ss_pred             CHHHHHh-----cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCC-CC-Cccccccc
Q psy522            1 LFRVAEE-----HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATN-RI-ETLDPALI   73 (131)
Q Consensus         1 vF~~A~~-----~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn-~~-~~id~~l~   73 (131)
                      +|+.|+.     ...+||||||+..+...+              ...||-.    -+.+.|++||+|. +| -.+..+++
T Consensus       209 ife~aq~~~~l~krkTilFiDEiHRFNksQ--------------QD~fLP~----VE~G~I~lIGATTENPSFqln~aLl  270 (554)
T KOG2028|consen  209 IFEQAQNEKSLTKRKTILFIDEIHRFNKSQ--------------QDTFLPH----VENGDITLIGATTENPSFQLNAALL  270 (554)
T ss_pred             HHHHHHHHHhhhcceeEEEeHHhhhhhhhh--------------hhcccce----eccCceEEEecccCCCccchhHHHH
Confidence            3556654     347999999999875433              1122211    2457789998765 33 45789999


Q ss_pred             CCCccceEEEeCCCCHHHHHHHHHHHh
Q psy522           74 RPGRIDRKIEFPLPDEKTKRRIFNIHT  100 (131)
Q Consensus        74 ~~grf~~~i~~~~P~~~~R~~il~~~l  100 (131)
                      +  |+- .+.+...+.+.-..|+.+..
T Consensus       271 S--RC~-VfvLekL~~n~v~~iL~rai  294 (554)
T KOG2028|consen  271 S--RCR-VFVLEKLPVNAVVTILMRAI  294 (554)
T ss_pred             h--ccc-eeEeccCCHHHHHHHHHHHH
Confidence            9  874 67778888888888887743

>PRK13531 regulatory ATPase RavA; Provisional

Probab=95.53  E-value=0.043  Score=42.51  Aligned_cols=73  Identities=22%  Similarity=0.236  Sum_probs=42.9

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcC-C-------CCCCCeEEEeeCCC-CC--cccccccCCCccc
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDG-F-------DSRGDVKVIMATNR-IE--TLDPALIRPGRID   79 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~-------~~~~~v~vi~ttn~-~~--~id~~l~~~grf~   79 (131)
                      .++|+||+...-+              ++.+.++..|.. .       ..-+..++++|||. |+  ...+++..  ||-
T Consensus       109 ~lLfLDEI~rasp--------------~~QsaLLeam~Er~~t~g~~~~~lp~rfiv~ATN~LPE~g~~leAL~D--RFl  172 (498)
T PRK13531        109 EIVFLDEIWKAGP--------------AILNTLLTAINERRFRNGAHEEKIPMRLLVTASNELPEADSSLEALYD--RML  172 (498)
T ss_pred             cEEeecccccCCH--------------HHHHHHHHHHHhCeEecCCeEEeCCCcEEEEECCCCcccCCchHHhHh--hEE
Confidence            4899999964321              244444444421 0       11123455555563 22  12248888  998


Q ss_pred             eEEEeCCCC-HHHHHHHHHHH
Q psy522           80 RKIEFPLPD-EKTKRRIFNIH   99 (131)
Q Consensus        80 ~~i~~~~P~-~~~R~~il~~~   99 (131)
                      ..+.+++|+ .++..+|+...
T Consensus       173 iri~vp~l~~~~~e~~lL~~~  193 (498)
T PRK13531        173 IRLWLDKVQDKANFRSMLTSQ  193 (498)
T ss_pred             EEEECCCCCchHHHHHHHHcc
Confidence            899999996 56667777653

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

Probab=95.38  E-value=0.035  Score=40.38  Aligned_cols=110  Identities=20%  Similarity=0.301  Sum_probs=64.0

Q ss_pred             HHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcc--cccccCCCccce
Q psy522            3 RVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETL--DPALIRPGRIDR   80 (131)
Q Consensus         3 ~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~i--d~~l~~~grf~~   80 (131)
                      ...+..++-+|+|||+..++....    .    -.+.+..++..+.+- -+=+++.+||-.....+  |+.+.+  ||+ 
T Consensus       139 ~llr~~~vrmLIIDE~H~lLaGs~----~----~qr~~Ln~LK~L~Ne-L~ipiV~vGt~~A~~al~~D~QLa~--RF~-  206 (302)
T PF05621_consen  139 RLLRRLGVRMLIIDEFHNLLAGSY----R----KQREFLNALKFLGNE-LQIPIVGVGTREAYRALRTDPQLAS--RFE-  206 (302)
T ss_pred             HHHHHcCCcEEEeechHHHhcccH----H----HHHHHHHHHHHHhhc-cCCCeEEeccHHHHHHhccCHHHHh--ccC-
Confidence            456788899999999999875431    1    122333333333221 11257778876655554  677878  997 


Q ss_pred             EEEeCC-CCHHHHHHHHHHHhcCCCCC--Ccc---c-HHHHHHHcCCCCHH
Q psy522           81 KIEFPL-PDEKTKRRIFNIHTSRMTLA--EDV---N-LQELIMAKDDLSGA  124 (131)
Q Consensus        81 ~i~~~~-P~~~~R~~il~~~l~~~~~~--~~~---~-~~~la~~t~g~s~~  124 (131)
                      .+.+|. ...++...++..+-+..++.  ..+   + ...+-..|+|.+|.
T Consensus       207 ~~~Lp~W~~d~ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~~s~G~iG~  257 (302)
T PF05621_consen  207 PFELPRWELDEEFRRLLASFERALPLRKPSNLASPELARRIHERSEGLIGE  257 (302)
T ss_pred             CccCCCCCCCcHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHcCCchHH
Confidence            455553 23344455677765555443  112   2 34566778898764

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

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=95.37  E-value=0.07  Score=38.06  Aligned_cols=59  Identities=14%  Similarity=0.147  Sum_probs=43.7

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCC
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLP   87 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P   87 (131)
                      --|++|+++|.+-.              ...+.+|..++.  +.+++++|.+|+.++.+.+.+++  |+. .+.++.+
T Consensus        89 ~KV~II~~ae~m~~--------------~AaNaLLK~LEE--Pp~~t~fiLit~~~~~lLpTI~S--RCq-~~~~~~~  147 (261)
T PRK05818         89 KKIYIIYGIEKLNK--------------QSANSLLKLIEE--PPKNTYGIFTTRNENNILNTILS--RCV-QYVVLSK  147 (261)
T ss_pred             CEEEEeccHhhhCH--------------HHHHHHHHhhcC--CCCCeEEEEEECChHhCchHhhh--hee-eeecCCh
Confidence            35777788777632              355667777764  45678999999999999999999  974 4566665

>KOG1514|consensus

Probab=95.35  E-value=0.1  Score=41.99  Aligned_cols=82  Identities=17%  Similarity=0.270  Sum_probs=52.9

Q ss_pred             hcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcc----cccccCCCccc-eE
Q psy522            7 EHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETL----DPALIRPGRID-RK   81 (131)
Q Consensus         7 ~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~i----d~~l~~~grf~-~~   81 (131)
                      ...|+||+|||+|.|+...           ..++-.+++-.  ...+.+++||+..|..+..    ...+.+  |.+ .+
T Consensus       506 ~~~~~VvLiDElD~Lvtr~-----------QdVlYn~fdWp--t~~~sKLvvi~IaNTmdlPEr~l~nrvsS--Rlg~tR  570 (767)
T KOG1514|consen  506 KRSTTVVLIDELDILVTRS-----------QDVLYNIFDWP--TLKNSKLVVIAIANTMDLPERLLMNRVSS--RLGLTR  570 (767)
T ss_pred             CCCCEEEEeccHHHHhccc-----------HHHHHHHhcCC--cCCCCceEEEEecccccCHHHHhccchhh--hcccee
Confidence            3468999999999998754           12333333211  1234567777777753332    223333  432 46


Q ss_pred             EEeCCCCHHHHHHHHHHHhcCC
Q psy522           82 IEFPLPDEKTKRRIFNIHTSRM  103 (131)
Q Consensus        82 i~~~~P~~~~R~~il~~~l~~~  103 (131)
                      |.|.+=+.+|-++|+..-|++.
T Consensus       571 i~F~pYth~qLq~Ii~~RL~~~  592 (767)
T KOG1514|consen  571 ICFQPYTHEQLQEIISARLKGL  592 (767)
T ss_pred             eecCCCCHHHHHHHHHHhhcch
Confidence            7777779999999999998876

>PF05872 DUF853: Bacterial protein of unknown function (DUF853); InterPro: IPR008571 Members of this family have a P-loop containing nucleotide triphosphate hydrolases fold

Probab=95.24  E-value=0.051  Score=41.69  Aligned_cols=89  Identities=10%  Similarity=0.192  Sum_probs=56.9

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEE--EeCCCC
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKI--EFPLPD   88 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i--~~~~P~   88 (131)
                      -|+||||++.+|...       ...+...+.++...+    .+.+|-|+..|.+|..||..++.  -+..+|  -+..-+
T Consensus       257 lVfFfDEAHLLF~da-------~kall~~ieqvvrLI----RSKGVGv~fvTQ~P~DiP~~VL~--QLGnrIQHaLRAfT  323 (502)
T PF05872_consen  257 LVFFFDEAHLLFNDA-------PKALLDKIEQVVRLI----RSKGVGVYFVTQNPTDIPDDVLG--QLGNRIQHALRAFT  323 (502)
T ss_pred             EEEEEechhhhhcCC-------CHHHHHHHHHHHHHh----hccCceEEEEeCCCCCCCHHHHH--hhhhHHHHHHhcCC
Confidence            457799999999654       333444455555444    35578899999999999999998  555555  455556


Q ss_pred             HHHHHHHHHHHhcCCCCCCcccHHH
Q psy522           89 EKTKRRIFNIHTSRMTLAEDVNLQE  113 (131)
Q Consensus        89 ~~~R~~il~~~l~~~~~~~~~~~~~  113 (131)
                      ..+++.+-. ....+...+..|+.+
T Consensus       324 P~DqKavk~-aa~tfr~np~~d~~~  347 (502)
T PF05872_consen  324 PKDQKAVKA-AAETFRPNPAFDTEE  347 (502)
T ss_pred             HhHHHHHHH-HHHhCCCCccccHHH
Confidence            666655533 334444444455443

This family is restricted to bacterial proteins, none of which have currently been characterised.

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

Probab=95.20  E-value=0.069  Score=40.05  Aligned_cols=77  Identities=19%  Similarity=0.306  Sum_probs=42.9

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCC------------CCCcccccccCCCc
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATN------------RIETLDPALIRPGR   77 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn------------~~~~id~~l~~~gr   77 (131)
                      |.|+||||++-|=              ...++.+-..++.  +-.++++++ ||            +|+-+|..|+.  |
T Consensus       279 pGVLFIDEvHmLD--------------iEcFsfLnralEs--~~sPiiIlA-TNRg~~~irGt~~~sphGiP~DlLD--R  339 (398)
T PF06068_consen  279 PGVLFIDEVHMLD--------------IECFSFLNRALES--ELSPIIILA-TNRGITKIRGTDIISPHGIPLDLLD--R  339 (398)
T ss_dssp             E-EEEEESGGGSB--------------HHHHHHHHHHHTS--TT--EEEEE-ES-SEEE-BTTS-EEETT--HHHHT--T
T ss_pred             cceEEecchhhcc--------------HHHHHHHHHHhcC--CCCcEEEEe-cCceeeeccCccCcCCCCCCcchHh--h
Confidence            8999999997761              1233322233331  223455444 45            56678888888  7


Q ss_pred             cceEEEeCCCCHHHHHHHHHHHhcCCCCC
Q psy522           78 IDRKIEFPLPDEKTKRRIFNIHTSRMTLA  106 (131)
Q Consensus        78 f~~~i~~~~P~~~~R~~il~~~l~~~~~~  106 (131)
                      + ..|...+-+.++-.+|++.-++...+.
T Consensus       340 l-lII~t~py~~~ei~~Il~iR~~~E~v~  367 (398)
T PF06068_consen  340 L-LIIRTKPYSEEEIKQILKIRAKEEDVE  367 (398)
T ss_dssp             E-EEEEE----HHHHHHHHHHHHHHCT--
T ss_pred             c-EEEECCCCCHHHHHHHHHhhhhhhcCc
Confidence            7 467777789999999999888765544

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

>PRK08485 DNA polymerase III subunit delta'; Validated

Probab=94.98  E-value=0.1  Score=35.88  Aligned_cols=58  Identities=16%  Similarity=0.172  Sum_probs=44.8

Q ss_pred             HHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce------------EEEeCCCCHHHHHHHHHHH
Q psy522           38 RTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR------------KIEFPLPDEKTKRRIFNIH   99 (131)
Q Consensus        38 ~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~------------~i~~~~P~~~~R~~il~~~   99 (131)
                      ...+.+|..+..  +..++++|..|..+..+.+.+++  |+..            .+.+...+.++-.+.++..
T Consensus        69 ~A~NaLLK~LEE--Pp~~~~fiL~t~~~~~llpTI~S--Rc~~~~~~~~~~~~~l~l~l~~l~~~~i~~~L~~~  138 (206)
T PRK08485         69 EAQNALLKILEE--PPKNICFIIVAKSKNLLLPTIRS--RLIIEKRKQKKPVKPLDLDLKKLDLKDIYEFLKEL  138 (206)
T ss_pred             HHHHHHHHHhcC--CCCCeEEEEEeCChHhCchHHHh--hheeccccccccccccccccCCCCHHHHHHHHHHH
Confidence            355667766664  44568888888889999999999  8753            5778888999988888883

>PRK09862 putative ATP-dependent protease; Provisional

Probab=94.85  E-value=0.13  Score=40.10  Aligned_cols=35  Identities=26%  Similarity=0.463  Sum_probs=28.2

Q ss_pred             CCeEEEeeCCCCC---------------------cccccccCCCccceEEEeCCCCHH
Q psy522           54 GDVKVIMATNRIE---------------------TLDPALIRPGRIDRKIEFPLPDEK   90 (131)
Q Consensus        54 ~~v~vi~ttn~~~---------------------~id~~l~~~grf~~~i~~~~P~~~   90 (131)
                      .++.+|+|+|-..                     .++..++.  |||.++.++.|+.+
T Consensus       336 a~f~lIAa~NP~pcG~~~~~~c~c~~~~~~~Y~~~ls~plLD--RfdL~v~v~~~~~~  391 (506)
T PRK09862        336 ARFQLVAAMNPSPTGHYQGNHNRCTPEQTLRYLNRLSGPFLD--RFDLSLEIPLPPPG  391 (506)
T ss_pred             CCEEEEEeecCccceecCCCCCCcCHHHHHHHHhhCCHhHHh--hccEEEEeCCCCHH
Confidence            3589999999632                     46778888  99999999998755

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=94.80  E-value=0.062  Score=35.88  Aligned_cols=55  Identities=24%  Similarity=0.317  Sum_probs=33.0

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCC--C-------CCCCeEEEeeCCCCCcc
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGF--D-------SRGDVKVIMATNRIETL   68 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~-------~~~~v~vi~ttn~~~~i   68 (131)
                      .||||||+|+..+..   +.........+...++..+++-  .       ...++++|+|+|.-...
T Consensus        70 gVVllDEidKa~~~~---~~~~~v~~~~V~~~LL~~le~g~~~d~~g~~vd~~n~ifI~Tsn~~~~~  133 (171)
T PF07724_consen   70 GVVLLDEIDKAHPSN---SGGADVSGEGVQNSLLQLLEGGTLTDSYGRTVDTSNIIFIMTSNFGAEE  133 (171)
T ss_dssp             TEEEEETGGGCSHTT---TTCSHHHHHHHHHHHHHHHHHSEEEETTCCEEEGTTEEEEEEESSSTHH
T ss_pred             hhhhhHHHhhccccc---cccchhhHHHHHHHHHHHhcccceecccceEEEeCCceEEEecccccch
Confidence            499999999987652   1222222234555666655431  1       11569999999965444

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=94.78  E-value=0.068  Score=38.77  Aligned_cols=58  Identities=21%  Similarity=0.349  Sum_probs=42.1

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCC
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLP   87 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P   87 (131)
                      -|++|+++|.+-.              ...+.+|+.++.  ..+++++|..|+.++.+.|.+++  |+. .+.|+++
T Consensus        97 kv~ii~~ad~mt~--------------~AaNaLLK~LEE--Pp~~~~fiL~~~~~~~ll~TI~S--Rcq-~~~~~~~  154 (290)
T PRK05917         97 KIYIIHEADRMTL--------------DAISAFLKVLED--PPQHGVIILTSAKPQRLPPTIRS--RSL-SIHIPME  154 (290)
T ss_pred             eEEEEechhhcCH--------------HHHHHHHHHhhc--CCCCeEEEEEeCChhhCcHHHHh--cce-EEEccch
Confidence            4777788877732              344556666664  44678889999999999999999  884 5667654

>PF12846 AAA_10: AAA-like domain

Probab=94.73  E-value=0.03  Score=39.83  Aligned_cols=72  Identities=26%  Similarity=0.311  Sum_probs=53.2

Q ss_pred             hcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCccc-----ccccCCCccceE
Q psy522            7 EHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLD-----PALIRPGRIDRK   81 (131)
Q Consensus         7 ~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id-----~~l~~~grf~~~   81 (131)
                      ...|.++++||+..+....         .....+..++....    +.++.++.+|+.+..++     ++++.  -+...
T Consensus       218 ~~~~~~i~iDEa~~~~~~~---------~~~~~~~~~~~~~R----k~g~~~~l~tQ~~~~l~~~~~~~~i~~--n~~~~  282 (304)
T PF12846_consen  218 RGRPKIIVIDEAHNFLSNP---------SGAEFLDELLREGR----KYGVGLILATQSPSDLPKSPIEDAILA--NCNTK  282 (304)
T ss_pred             CCceEEEEeCCcccccccc---------chhhhhhHHHHHHH----hcCCEEEEeeCCHHHHhccchHHHHHH--hCCcE
Confidence            3678999999998887653         12234445554443    45678999999999999     78888  88888


Q ss_pred             EEeCCCCHHHHH
Q psy522           82 IEFPLPDEKTKR   93 (131)
Q Consensus        82 i~~~~P~~~~R~   93 (131)
                      +.+...+.+.+.
T Consensus       283 i~~~~~~~~~~~  294 (304)
T PF12846_consen  283 IIFRLEDSDDAE  294 (304)
T ss_pred             EEecCChHHHHH
Confidence            888888877766

>KOG1942|consensus

Probab=94.49  E-value=0.67  Score=34.14  Aligned_cols=89  Identities=24%  Similarity=0.367  Sum_probs=46.8

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCC-------------CCCcccccccC
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATN-------------RIETLDPALIR   74 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn-------------~~~~id~~l~~   74 (131)
                      .-|.|+||||+.-+=              ...+..+-..+.+  .-.++++++ ||             .|+-+|+.++.
T Consensus       295 lvPGVLFIDEVhMLD--------------iEcFTyL~kalES--~iaPivifA-sNrG~~~irGt~d~~sPhGip~dllD  357 (456)
T KOG1942|consen  295 LVPGVLFIDEVHMLD--------------IECFTYLHKALES--PIAPIVIFA-SNRGMCTIRGTEDILSPHGIPPDLLD  357 (456)
T ss_pred             hcCcceEeeehhhhh--------------hHHHHHHHHHhcC--CCCceEEEe-cCCcceeecCCcCCCCCCCCCHHHhh
Confidence            348999999997651              1334444444432  113444443 33             35566777776


Q ss_pred             CCccceEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHH
Q psy522           75 PGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIM  116 (131)
Q Consensus        75 ~grf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~  116 (131)
                        |+--.=.++. +.++-++|++.-.+..++. .+..+..++.
T Consensus       358 --Rl~Iirt~~y-~~~e~r~Ii~~Ra~~E~l~~~e~a~~~l~~  397 (456)
T KOG1942|consen  358 --RLLIIRTLPY-DEEEIRQIIKIRAQVEGLQVEEEALDLLAE  397 (456)
T ss_pred             --heeEEeeccC-CHHHHHHHHHHHHhhhcceecHHHHHHHHh
Confidence              6532222333 5566667777666555554 2223444544

>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite

Probab=94.26  E-value=0.14  Score=37.79  Aligned_cols=81  Identities=23%  Similarity=0.284  Sum_probs=45.1

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHH-hcCCCCC-------CCeEEEeeCCCCC-------------cc
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQ-LDGFDSR-------GDVKVIMATNRIE-------------TL   68 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~-~~~~~~~-------~~v~vi~ttn~~~-------------~i   68 (131)
                      ..|++|||+|.+-..           ....+.+.+++ .-.+...       -+.-|+|++|-..             .+
T Consensus       122 ~GiccIDe~dk~~~~-----------~~~~l~eaMEqq~isi~kagi~~~l~ar~svlaa~NP~~g~~~~~~~~~~ni~l  190 (331)
T PF00493_consen  122 GGICCIDEFDKMKED-----------DRDALHEAMEQQTISIAKAGIVTTLNARCSVLAAANPKFGRYDPNKSLSENINL  190 (331)
T ss_dssp             TSEEEECTTTT--CH-----------HHHHHHHHHHCSCEEECTSSSEEEEE---EEEEEE--TT--S-TTS-CGCCT-S
T ss_pred             Cceeeecccccccch-----------HHHHHHHHHHcCeeccchhhhcccccchhhhHHHHhhhhhhcchhhhhHHhccc
Confidence            379999999997432           12333333332 1112221       2478999998655             48


Q ss_pred             cccccCCCccceEEEe-CCCCHHHHHHHHHHHhcCC
Q psy522           69 DPALIRPGRIDRKIEF-PLPDEKTKRRIFNIHTSRM  103 (131)
Q Consensus        69 d~~l~~~grf~~~i~~-~~P~~~~R~~il~~~l~~~  103 (131)
                      ++.+++  |||..+.+ ..|+.+.=..+.++.+...
T Consensus       191 ~~~LLS--RFDLif~l~D~~d~~~D~~la~~il~~~  224 (331)
T PF00493_consen  191 PPPLLS--RFDLIFLLRDKPDEEEDERLAEHILDSH  224 (331)
T ss_dssp             -CCCHC--C-SEEECC--TTT-HHHHHHHHHHHTTT
T ss_pred             chhhHh--hcCEEEEeccccccccccccceEEEecc
Confidence            899999  99977665 5778877777888777654

; InterPro: IPR001208 MCM proteins are DNA-dependent ATPases required for the initiation of eukaryotic DNA replication [, , ]. In eukaryotes there is a family of six proteins, MCM2 to MCM7. They were first identified in yeast where most of them have a direct role in the initiation of chromosomal DNA replication by interacting directly with autonomously replicating sequences (ARS). They were thus called minichromosome maintenance proteins, MCM proteins []. This family is also present in the archebacteria in 1 to 4 copies. Methanocaldococcus jannaschii (Methanococcus jannaschii) has four members, MJ0363, MJ0961, MJ1489 and MJECL13. The "MCM motif" contains Walker-A and Walker-B type nucleotide binding motifs. The diagnostic sequence defining the MCMs is IDEFDKM. Only Mcm2 (aka Cdc19 or Nda1) has been subjected to mutational analysis in this region, and most mutations abolish its activity []. The presence of a putative ATP-binding domain implies that these proteins may be involved in an ATP-consuming step in the initiation of DNA replication in eukaryotes. The MCM proteins bind together in a large complex []. Within this complex, individual subunits associate with different affinities, and there is a tightly associated core of Mcm4 (Cdc21), Mcm6 (Mis5) and Mcm7 []. This core complex in human MCMs has been associated with helicase activity in vitro [], leading to the suggestion that the MCM proteins are the eukaryotic replicative helicase. Schizosaccharomyces pombe (Fission yeast) MCMs, like those in metazoans, are found in the nucleus throughout the cell cycle. This is in contrast to the Saccharomyces cerevisiae (Baker's yeast) in which MCM proteins move in and out of the nucleus during each cell cycle. The assembly of the MCM complex in S. pombe is required for MCM localisation, ensuring that only intact MCM complexes remain in the nucleus [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 3F8T_A 3F9V_A.

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

Probab=94.25  E-value=0.11  Score=38.44  Aligned_cols=25  Identities=32%  Similarity=0.587  Sum_probs=18.8

Q ss_pred             HHHhcCCeEEEecccccccCcCCCCC
Q psy522            4 VAEEHAPSIVFIDEIDAVGTKRYDSN   29 (131)
Q Consensus         4 ~A~~~~p~ii~iDe~d~l~~~~~~~~   29 (131)
                      .+++.. .||+|||+|.+.++..+++
T Consensus       158 V~rAer-GIIyIDEIDKIarkSeN~S  182 (408)
T COG1219         158 VERAER-GIIYIDEIDKIARKSENPS  182 (408)
T ss_pred             HHHHhC-CeEEEechhhhhccCCCCC
Confidence            344444 8999999999998876553

>KOG0990|consensus

Probab=93.99  E-value=0.17  Score=37.20  Aligned_cols=75  Identities=16%  Similarity=0.272  Sum_probs=49.9

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      .+-.+++||+|++..+.       ++.+++++       ..+  +.++.+..-+|++..+.|++.+  ||. .+.+.+.+
T Consensus       131 ~fKlvILDEADaMT~~A-------QnALRRvi-------ek~--t~n~rF~ii~n~~~ki~pa~qs--Rct-rfrf~pl~  191 (360)
T KOG0990|consen  131 AFKLVILDEADAMTRDA-------QNALRRVI-------EKY--TANTRFATISNPPQKIHPAQQS--RCT-RFRFAPLT  191 (360)
T ss_pred             ceeEEEecchhHhhHHH-------HHHHHHHH-------HHh--ccceEEEEeccChhhcCchhhc--ccc-cCCCCCCC
Confidence            57789999999986543       22222222       211  2344555778999999999999  986 55666667


Q ss_pred             HHHHHHHHHHHhcC
Q psy522           89 EKTKRRIFNIHTSR  102 (131)
Q Consensus        89 ~~~R~~il~~~l~~  102 (131)
                      .++-...+.+.+..
T Consensus       192 ~~~~~~r~shi~e~  205 (360)
T KOG0990|consen  192 MAQQTERQSHIRES  205 (360)
T ss_pred             hhhhhhHHHHHHhc
Confidence            66666666666543

>KOG1968|consensus

Probab=93.90  E-value=0.34  Score=40.27  Aligned_cols=97  Identities=18%  Similarity=0.255  Sum_probs=62.9

Q ss_pred             EEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCHHH
Q psy522           12 IVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKT   91 (131)
Q Consensus        12 ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~~   91 (131)
                      ||++||+|.++. .       .......+..+..       ...+-+|.+||....-...-..  +-...++|+.|+.+.
T Consensus       431 vil~devD~~~~-~-------dRg~v~~l~~l~~-------ks~~Piv~~cndr~~p~sr~~~--~~~~~l~f~kP~~~~  493 (871)
T KOG1968|consen  431 LILMDEVDGMFG-E-------DRGGVSKLSSLCK-------KSSRPLVCTCNDRNLPKSRALS--RACSDLRFSKPSSEL  493 (871)
T ss_pred             EEEEeccccccc-h-------hhhhHHHHHHHHH-------hccCCeEEEecCCCCccccchh--hhcceeeecCCcHHH
Confidence            899999999986 2       1112223333332       2234588888887766654444  433569999999999


Q ss_pred             HHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHh
Q psy522           92 KRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAI  129 (131)
Q Consensus        92 R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l  129 (131)
                      ...-+..++....+. ..-.+.++.+.+    ++||.+.
T Consensus       494 i~~ri~si~~se~~ki~~~~l~~~s~~~----~~DiR~~  528 (871)
T KOG1968|consen  494 IRSRIMSICKSEGIKISDDVLEEISKLS----GGDIRQI  528 (871)
T ss_pred             HHhhhhhhhcccceecCcHHHHHHHHhc----ccCHHHH
Confidence            988888887765544 334577777775    5666554

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

Probab=93.61  E-value=1.2  Score=31.79  Aligned_cols=111  Identities=17%  Similarity=0.146  Sum_probs=68.2

Q ss_pred             HhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCC-ccc---ccccCCCccceE
Q psy522            6 EEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE-TLD---PALIRPGRIDRK   81 (131)
Q Consensus         6 ~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~-~id---~~l~~~grf~~~   81 (131)
                      +...|-++++||++.+....           ...+.-+.+.-.+...--+++.+|-...-. ---   ..+..  |++-.
T Consensus       128 ~g~r~v~l~vdEah~L~~~~-----------le~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~lr~~~l~e~~~--R~~ir  194 (269)
T COG3267         128 KGKRPVVLMVDEAHDLNDSA-----------LEALRLLTNLEEDSSKLLSIVLIGQPKLRPRLRLPVLRELEQ--RIDIR  194 (269)
T ss_pred             hCCCCeEEeehhHhhhChhH-----------HHHHHHHHhhcccccCceeeeecCCcccchhhchHHHHhhhh--eEEEE
Confidence            34557899999999885432           223333333333222223477777643211 111   23334  78877


Q ss_pred             EEeCCCCHHHHHHHHHHHhcCCCCC----CcccHHHHHHHcCCCCHHHHHHhh
Q psy522           82 IEFPLPDEKTKRRIFNIHTSRMTLA----EDVNLQELIMAKDDLSGADIKAIC  130 (131)
Q Consensus        82 i~~~~P~~~~R~~il~~~l~~~~~~----~~~~~~~la~~t~g~s~~di~~l~  130 (131)
                      +.+++-+.++-..++++.++..+..    .+..+..+...+.|| |.-|..+|
T Consensus       195 ~~l~P~~~~~t~~yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg~-P~lin~~~  246 (269)
T COG3267         195 IELPPLTEAETGLYLRHRLEGAGLPEPLFSDDALLLIHEASQGI-PRLINNLA  246 (269)
T ss_pred             EecCCcChHHHHHHHHHHHhccCCCcccCChhHHHHHHHHhccc-hHHHHHHH
Confidence            8889999999999999998766443    334477788888885 66565554

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

Probab=92.94  E-value=1.8  Score=32.69  Aligned_cols=89  Identities=18%  Similarity=0.251  Sum_probs=50.0

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCC-----------CCCcccccccCCCcc
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATN-----------RIETLDPALIRPGRI   78 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn-----------~~~~id~~l~~~grf   78 (131)
                      |.||||||+.-|=              ...+..+-..+.+  .-.+++++||..           +|+-||..++.  |.
T Consensus       292 pGVLFIDEvHmLD--------------IE~FsFlnrAlEs--e~aPIii~AtNRG~~kiRGTd~~sPhGIP~DlLD--Rl  353 (450)
T COG1224         292 PGVLFIDEVHMLD--------------IECFSFLNRALES--ELAPIIILATNRGMTKIRGTDIESPHGIPLDLLD--RL  353 (450)
T ss_pred             cceEEEechhhhh--------------HHHHHHHHHHhhc--ccCcEEEEEcCCceeeecccCCcCCCCCCHhhhh--he
Confidence            8999999997651              1222222222221  113455554432           35667777776  65


Q ss_pred             ceEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHH
Q psy522           79 DRKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMA  117 (131)
Q Consensus        79 ~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~  117 (131)
                       ..|...+=++++-++|++.-.+...+. .+..+..|+..
T Consensus       354 -lII~t~py~~~EireIi~iRa~ee~i~l~~~Ale~L~~i  392 (450)
T COG1224         354 -LIISTRPYSREEIREIIRIRAKEEDIELSDDALEYLTDI  392 (450)
T ss_pred             -eEEecCCCCHHHHHHHHHHhhhhhccccCHHHHHHHHhh
Confidence             244444558999999998877655544 22234445443

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=92.88  E-value=0.41  Score=38.29  Aligned_cols=44  Identities=20%  Similarity=0.385  Sum_probs=31.7

Q ss_pred             CeEEEeeCCC--CCcccccccCCCccc---eEEEeCC--C-CHHHHHHHHHHHh
Q psy522           55 DVKVIMATNR--IETLDPALIRPGRID---RKIEFPL--P-DEKTKRRIFNIHT  100 (131)
Q Consensus        55 ~v~vi~ttn~--~~~id~~l~~~grf~---~~i~~~~--P-~~~~R~~il~~~l  100 (131)
                      .+.+|+++|.  ...+++.+++  ||+   ..+.++.  | +.+.|..+.+...
T Consensus       268 dvrvIa~~~~~~l~~l~~~l~~--rf~~y~v~v~~~~~~~~~~e~~~~~~~~i~  319 (608)
T TIGR00764       268 DFILVASGNLDDLEGMHPALRS--RIRGYGYEVYMKDTMPDTPENRDKLVQFVA  319 (608)
T ss_pred             ceEEEEECCHHHHhhcCHHHHH--HhcCCeEEEEeeccCCCCHHHHHHHHHHHH
Confidence            5788898885  3678999999  999   6666653  3 6777766655543

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

>PRK14700 recombination factor protein RarA; Provisional

Probab=92.86  E-value=0.46  Score=34.61  Aligned_cols=48  Identities=19%  Similarity=0.232  Sum_probs=40.1

Q ss_pred             CCCCeEEEeeCC-C-CCcccccccCCCccceEEEeCCCCHHHHHHHHHHHhcC
Q psy522           52 SRGDVKVIMATN-R-IETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSR  102 (131)
Q Consensus        52 ~~~~v~vi~ttn-~-~~~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~  102 (131)
                      +.+.+++||+|. + --.+.+++++  |+ +.+.+.+++.++-..+++..+..
T Consensus         5 E~G~i~LIGATTENP~f~vn~ALlS--R~-~v~~l~~L~~~di~~il~ral~~   54 (300)
T PRK14700          5 ESGKIILIGATTENPTYYLNDALVS--RL-FILRLKRLSLVATQKLIEKALSQ   54 (300)
T ss_pred             cCCcEEEEeecCCCccceecHhhhh--hh-heeeecCCCHHHHHHHHHHHHHh
Confidence            457788998775 4 4568999999  98 58999999999999999998864

>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []

Probab=92.69  E-value=0.86  Score=32.33  Aligned_cols=98  Identities=16%  Similarity=0.193  Sum_probs=52.3

Q ss_pred             hcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCC
Q psy522            7 EHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPL   86 (131)
Q Consensus         7 ~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~   86 (131)
                      ...+++|+||+++...                .+..+...+..  ...+.-+|.||.... +-.....   -...+.++.
T Consensus        99 ~~~~~LlVlDdv~~~~----------------~~~~l~~~~~~--~~~~~kilvTTR~~~-v~~~~~~---~~~~~~l~~  156 (287)
T PF00931_consen   99 KDKRCLLVLDDVWDEE----------------DLEELREPLPS--FSSGSKILVTTRDRS-VAGSLGG---TDKVIELEP  156 (287)
T ss_dssp             CCTSEEEEEEEE-SHH----------------HH-------HC--HHSS-EEEEEESCGG-GGTTHHS---CEEEEECSS
T ss_pred             ccccceeeeeeecccc----------------ccccccccccc--ccccccccccccccc-ccccccc---ccccccccc
Confidence            3448999999986542                11112111111  122455677777642 2222221   157899999


Q ss_pred             CCHHHHHHHHHHHhcCCC----CCCcccHHHHHHHcCCCCHHHHH
Q psy522           87 PDEKTKRRIFNIHTSRMT----LAEDVNLQELIMAKDDLSGADIK  127 (131)
Q Consensus        87 P~~~~R~~il~~~l~~~~----~~~~~~~~~la~~t~g~s~~di~  127 (131)
                      .+.++..+++........    ...+.....+++.+.|+ |--|.
T Consensus       157 L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~gl-PLal~  200 (287)
T PF00931_consen  157 LSEEEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGL-PLALK  200 (287)
T ss_dssp             --HHHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT--HHHHH
T ss_pred             ccccccccccccccccccccccccccccccccccccccc-ccccc
Confidence            999999999999865443    11222367788888876 43333

This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A.

>KOG2227|consensus

Probab=92.58  E-value=0.33  Score=37.56  Aligned_cols=102  Identities=17%  Similarity=0.128  Sum_probs=68.1

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccC----CCccceEEEe
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIR----PGRIDRKIEF   84 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~----~grf~~~i~~   84 (131)
                      .|-++++||.|.|.....           .++.++ -++.. ....++++||-+|..+.=|..+-|    -+.-...+.|
T Consensus       256 ~~~llVlDEmD~L~tr~~-----------~vLy~l-Fewp~-lp~sr~iLiGiANslDlTdR~LprL~~~~~~~P~~l~F  322 (529)
T KOG2227|consen  256 FMLLLVLDEMDHLITRSQ-----------TVLYTL-FEWPK-LPNSRIILIGIANSLDLTDRFLPRLNLDLTIKPKLLVF  322 (529)
T ss_pred             ceEEEEechhhHHhhccc-----------ceeeee-hhccc-CCcceeeeeeehhhhhHHHHHhhhhhhccCCCCceeee
Confidence            377899999999984331           122222 12222 234679999999988776654432    1233567888


Q ss_pred             CCCCHHHHHHHHHHHhcCCCCCCccc--HHHHHHHcCCCCH
Q psy522           85 PLPDEKTKRRIFNIHTSRMTLAEDVN--LQELIMAKDDLSG  123 (131)
Q Consensus        85 ~~P~~~~R~~il~~~l~~~~~~~~~~--~~~la~~t~g~s~  123 (131)
                      ++=+.++-.+|+..-+.........+  +.-.|....|.||
T Consensus       323 ~PYTk~qI~~Il~~rl~~~~t~~~~~~Aie~~ArKvaa~SG  363 (529)
T KOG2227|consen  323 PPYTKDQIVEILQQRLSEESTSIFLNAAIELCARKVAAPSG  363 (529)
T ss_pred             cCCCHHHHHHHHHHHHhcccccccchHHHHHHHHHhccCch
Confidence            88899999999999988776554333  5556777777765

>TIGR00368 Mg chelatase-related protein

Probab=92.38  E-value=0.53  Score=36.80  Aligned_cols=68  Identities=19%  Similarity=0.319  Sum_probs=42.5

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhc----C----CCCCCCeEEEeeCCCC-----C----------
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLD----G----FDSRGDVKVIMATNRI-----E----------   66 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~----~----~~~~~~v~vi~ttn~~-----~----------   66 (131)
                      ..+|||||++.+-.           .....+.+.++.-.    .    ..-..++.+|+++|--     .          
T Consensus       296 ~GvLfLDEi~e~~~-----------~~~~~L~~~LE~~~v~i~r~g~~~~~pa~frlIaa~Npcpcg~~~~~~~~c~c~~  364 (499)
T TIGR00368       296 NGVLFLDELPEFKR-----------SVLDALREPIEDGSISISRASAKIFYPARFQLVAAMNPCPCGHYGGKNTHCRCSP  364 (499)
T ss_pred             CCeEecCChhhCCH-----------HHHHHHHHHHHcCcEEEEecCcceeccCCeEEEEecCCcccCcCCCCcccccCCH
Confidence            37999999987632           12334444432210    0    0011368899999842     1          


Q ss_pred             --------cccccccCCCccceEEEeCCCCHH
Q psy522           67 --------TLDPALIRPGRIDRKIEFPLPDEK   90 (131)
Q Consensus        67 --------~id~~l~~~grf~~~i~~~~P~~~   90 (131)
                              .+...++.  |||..+.++.++.+
T Consensus       365 ~~~~~y~~~is~pllD--R~dl~~~~~~~~~~  394 (499)
T TIGR00368       365 QQISRYWNKLSGPFLD--RIDLSVEVPLLPPE  394 (499)
T ss_pred             HHHHHHhhhccHhHHh--hCCEEEEEcCCCHH
Confidence                    47788888  99999999977544

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=92.28  E-value=0.79  Score=38.32  Aligned_cols=78  Identities=21%  Similarity=0.348  Sum_probs=48.2

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhc------CCCC--CCCeEEEeeCCCCC-------------ccc
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLD------GFDS--RGDVKVIMATNRIE-------------TLD   69 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~------~~~~--~~~v~vi~ttn~~~-------------~id   69 (131)
                      .+++|||+|.+-..           ....+.+.+++-.      ++..  ..++.||||+|-.+             .++
T Consensus       559 GtL~IDEidkms~~-----------~Q~aLlEaMEqqtIsI~KaGi~~tL~ar~rVIAAaNP~~gryd~~~s~~eni~Lp  627 (915)
T PTZ00111        559 GVCCIDELDKCHNE-----------SRLSLYEVMEQQTVTIAKAGIVATLKAETAILASCNPINSRYNKNKAVIENINIS  627 (915)
T ss_pred             CeEEecchhhCCHH-----------HHHHHHHHHhCCEEEEecCCcceecCCCeEEEEEcCCcccccCcccCcccccCCC
Confidence            58899999987322           2233444442211      1111  14689999999632             367


Q ss_pred             ccccCCCccceEE-EeCCCCHHHHHHHHHHHhc
Q psy522           70 PALIRPGRIDRKI-EFPLPDEKTKRRIFNIHTS  101 (131)
Q Consensus        70 ~~l~~~grf~~~i-~~~~P~~~~R~~il~~~l~  101 (131)
                      +.+++  |||... .+..|+.+.=..|-.+.++
T Consensus       628 ~~LLS--RFDLIf~l~D~~d~~~D~~lA~hI~~  658 (915)
T PTZ00111        628 PSLFT--RFDLIYLVLDHIDQDTDQLISLSIAK  658 (915)
T ss_pred             hHHhh--hhcEEEEecCCCChHHHHHHHHHHHH
Confidence            99999  998664 4567787776666666553

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

Probab=91.62  E-value=0.53  Score=33.79  Aligned_cols=86  Identities=17%  Similarity=0.371  Sum_probs=48.9

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCC-------CCCeEEEeeCCCC---CcccccccCCCc
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDS-------RGDVKVIMATNRI---ETLDPALIRPGR   77 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-------~~~v~vi~ttn~~---~~id~~l~~~gr   77 (131)
                      .+..|+|+||+..-..+.     .......+.+.++++.=.-+..       -.++-++|+++-+   ..+++.+.|  .
T Consensus        99 ~k~lv~fiDDlN~p~~d~-----ygtq~~iElLRQ~i~~~g~yd~~~~~~~~i~~i~~vaa~~p~~Gr~~is~R~~r--~  171 (272)
T PF12775_consen   99 GKKLVLFIDDLNMPQPDK-----YGTQPPIELLRQLIDYGGFYDRKKLEWKSIEDIQFVAAMNPTGGRNPISPRFLR--H  171 (272)
T ss_dssp             SSEEEEEEETTT-S---T-----TS--HHHHHHHHHHHCSEEECTTTTEEEEECSEEEEEEESSTTT--SHHHHHHT--T
T ss_pred             CcEEEEEecccCCCCCCC-----CCCcCHHHHHHHHHHhcCcccCCCcEEEEEeeeEEEEecCCCCCCCCCChHHhh--h
Confidence            456899999986654332     2222234566666543211111       1358888988742   247888888  7


Q ss_pred             cceEEEeCCCCHHHHHHHHHHHhc
Q psy522           78 IDRKIEFPLPDEKTKRRIFNIHTS  101 (131)
Q Consensus        78 f~~~i~~~~P~~~~R~~il~~~l~  101 (131)
                      | ..+.++.|+.+.-..|+..++.
T Consensus       172 f-~i~~~~~p~~~sl~~If~~il~  194 (272)
T PF12775_consen  172 F-NILNIPYPSDESLNTIFSSILQ  194 (272)
T ss_dssp             E-EEEE----TCCHHHHHHHHHHH
T ss_pred             e-EEEEecCCChHHHHHHHHHHHh
Confidence            7 4899999999988888877664

>TIGR00602 rad24 checkpoint protein rad24

Probab=91.14  E-value=2.7  Score=34.01  Aligned_cols=79  Identities=14%  Similarity=0.296  Sum_probs=44.6

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHH-HhcCCCCCCCeEEEeeCC-CCC--------c------ccccc
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLN-QLDGFDSRGDVKVIMATN-RIE--------T------LDPAL   72 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~-~~~~~~~~~~v~vi~ttn-~~~--------~------id~~l   72 (131)
                      ...||||||+|.++...       .    ..+..++. ...   ..+.+.+|++++ .+.        .      +.+++
T Consensus       195 ~~~IILIDEiPn~~~r~-------~----~~lq~lLr~~~~---e~~~~pLI~I~TE~~~~~~~~~~~~f~~~~lL~~eL  260 (637)
T TIGR00602       195 DKKIILVEDLPNQFYRD-------T----RALHEILRWKYV---SIGRCPLVFIITESLEGDNNQRRLLFPAETIMNKEI  260 (637)
T ss_pred             ceeEEEeecchhhchhh-------H----HHHHHHHHHHhh---cCCCceEEEEecCCccccccccccccchhcccCHhH
Confidence            56799999999887432       1    12222322 111   233334444333 222        0      22566


Q ss_pred             cCCCccceEEEeCCCCHHHHHHHHHHHhcC
Q psy522           73 IRPGRIDRKIEFPLPDEKTKRRIFNIHTSR  102 (131)
Q Consensus        73 ~~~grf~~~i~~~~P~~~~R~~il~~~l~~  102 (131)
                      ++.-|. ..|.|++.+...-.+.|+..+..
T Consensus       261 ls~~rv-~~I~FnPia~t~l~K~L~rIl~~  289 (637)
T TIGR00602       261 LEEPRV-SNISFNPIAPTIMKKFLNRIVTI  289 (637)
T ss_pred             hcccce-eEEEeCCCCHHHHHHHHHHHHHh
Confidence            642233 37899999999988878777764

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

>KOG2170|consensus

Probab=91.01  E-value=1.7  Score=31.95  Aligned_cols=51  Identities=20%  Similarity=0.214  Sum_probs=35.2

Q ss_pred             cccCCCccceEEEeCCCCHHHHHHHHHHHhcCCCCCCccc-HHHHHHHcCCC
Q psy522           71 ALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVN-LQELIMAKDDL  121 (131)
Q Consensus        71 ~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~-~~~la~~t~g~  121 (131)
                      .+...++.|+.|.+.+.++..-...++..+.+.+...+.+ +.++++...-|
T Consensus       271 ~li~~~lid~fIPFLPLek~hV~~C~r~el~~rg~~~d~~~~erva~~l~ff  322 (344)
T KOG2170|consen  271 RLISNNLIDHFIPFLPLEKRHVRSCIRAELRKRGLAPDQDFVERVANSLSFF  322 (344)
T ss_pred             ccchhhHHhhccCcCcccHHHHHHHHHHHHHhcccccchHHHHHHHHhhccc
Confidence            3344445677788888888888888888888777665555 55666655433

>PF13304 AAA_21: AAA domain; PDB: 3QKS_B 1US8_B 1F2U_B 1F2T_B 3QKT_A 1II8_B 3QKR_B 3QKU_A

Probab=90.88  E-value=0.24  Score=33.70  Aligned_cols=45  Identities=36%  Similarity=0.489  Sum_probs=26.8

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCccc
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLD   69 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id   69 (131)
                      ++++|||.|.-+...          ....+..++....   . .++=||.||.+|.-||
T Consensus       259 ~illiDEpE~~LHp~----------~q~~l~~~l~~~~---~-~~~QviitTHSp~ild  303 (303)
T PF13304_consen  259 SILLIDEPENHLHPS----------WQRKLIELLKELS---K-KNIQVIITTHSPFILD  303 (303)
T ss_dssp             SEEEEESSSTTSSHH----------HHHHHHHHHHHTG---G-GSSEEEEEES-GGG--
T ss_pred             eEEEecCCcCCCCHH----------HHHHHHHHHHhhC---c-cCCEEEEeCccchhcC
Confidence            899999999876432          3333334443333   2 3455899999887654

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=90.78  E-value=0.55  Score=37.42  Aligned_cols=65  Identities=12%  Similarity=0.154  Sum_probs=43.5

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcC---------CCC--CCCeEEEeeCCCC---CcccccccCCC
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDG---------FDS--RGDVKVIMATNRI---ETLDPALIRPG   76 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~---------~~~--~~~v~vi~ttn~~---~~id~~l~~~g   76 (131)
                      .|||+||+..+-.              .++..+++-|+.         ...  ..++++|+|-|-.   ..+++.++.  
T Consensus        95 GvL~lDe~n~~~~--------------~~~~aLleame~G~vtIeR~G~s~~~Pa~F~LIat~~~~~~~~~L~~~lLD--  158 (584)
T PRK13406         95 GVLVLAMAERLEP--------------GTAARLAAALDTGEVRLERDGLALRLPARFGLVALDEGAEEDERAPAALAD--  158 (584)
T ss_pred             CEEEecCcccCCH--------------HHHHHHHHHHhCCcEEEEECCcEEecCCCcEEEecCCChhcccCCCHHhHh--
Confidence            7999999977632              244455554442         111  1358888874322   348899999  


Q ss_pred             ccceEEEeCCCCHHH
Q psy522           77 RIDRKIEFPLPDEKT   91 (131)
Q Consensus        77 rf~~~i~~~~P~~~~   91 (131)
                      ||+.++.++.|+..+
T Consensus       159 Rf~l~v~v~~~~~~~  173 (584)
T PRK13406        159 RLAFHLDLDGLALRD  173 (584)
T ss_pred             heEEEEEcCCCChHH
Confidence            999999999987654

>KOG0745|consensus

Probab=90.42  E-value=0.67  Score=35.78  Aligned_cols=20  Identities=35%  Similarity=0.670  Sum_probs=15.2

Q ss_pred             HHhcCCeEEEecccccccCcC
Q psy522            5 AEEHAPSIVFIDEIDAVGTKR   25 (131)
Q Consensus         5 A~~~~p~ii~iDe~d~l~~~~   25 (131)
                      +++.+ .||||||+|.+..+.
T Consensus       288 ekAQq-GIVflDEvDKi~~~~  307 (564)
T KOG0745|consen  288 EKAQQ-GIVFLDEVDKITKKA  307 (564)
T ss_pred             HHHhc-CeEEEehhhhhcccC
Confidence            34444 899999999998544

>KOG2383|consensus

Probab=90.35  E-value=0.089  Score=39.83  Aligned_cols=49  Identities=18%  Similarity=0.255  Sum_probs=30.7

Q ss_pred             CCCeEEEeeCCC-CCcccccccCCCccceEEEeCCCCHHHHHHHHHHHhcCCCCCCcccHH
Q psy522           53 RGDVKVIMATNR-IETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQ  112 (131)
Q Consensus        53 ~~~v~vi~ttn~-~~~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~  112 (131)
                      +++|+++||+|+ |+.+-..=+.     +...+|      ...+|++.+.-..+...+|+.
T Consensus       222 ~~GvVlvATSNR~P~dLYknGlQ-----R~~F~P------fI~~L~~rc~vi~ldS~vDYR  271 (467)
T KOG2383|consen  222 KNGVVLVATSNRAPEDLYKNGLQ-----RENFIP------FIALLEERCKVIQLDSGVDYR  271 (467)
T ss_pred             hCCeEEEEeCCCChHHHhhcchh-----hhhhhh------HHHHHHHhheEEecCCccchh
Confidence            348999999995 7777544333     233333      235667766666666667776

>PF05272 VirE: Virulence-associated protein E; InterPro: IPR007936 This family contains several bacterial virulence-associated protein E like proteins

Probab=90.26  E-value=0.79  Score=31.36  Aligned_cols=42  Identities=26%  Similarity=0.306  Sum_probs=26.2

Q ss_pred             CeEEEeeCCCCCcc-cccccCCCccceEEEeCC------CC----HHHHHHHHHHH
Q psy522           55 DVKVIMATNRIETL-DPALIRPGRIDRKIEFPL------PD----EKTKRRIFNIH   99 (131)
Q Consensus        55 ~v~vi~ttn~~~~i-d~~l~~~grf~~~i~~~~------P~----~~~R~~il~~~   99 (131)
                      ..++|||||..+-+ |+.=-|  || ..|.+..      |.    .+.|.++|...
T Consensus       140 ~~~figTtN~~~~L~D~TGnR--Rf-~~v~v~~~i~~~~~~~~~~~~~~~qlwAeA  192 (198)
T PF05272_consen  140 RAVFIGTTNDDDFLKDPTGNR--RF-WPVEVSKRIDIKSIDIDLLEEDRDQLWAEA  192 (198)
T ss_pred             eEEEEeccCCcceeeCCCCCe--EE-EEEEEcCcccccccchhhhHHHHHHHHHHH
Confidence            47899999998866 555666  77 3444443      22    23466666544

>PHA00012 I assembly protein

Probab=90.23  E-value=0.68  Score=34.39  Aligned_cols=57  Identities=11%  Similarity=0.145  Sum_probs=39.9

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIR   74 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~   74 (131)
                      .-+++++||+-..++.|+..+....     ...+++...    ...+.-+|..|.++..+|+.++.
T Consensus        81 ~gsLlVlDEaq~~fp~R~~~sk~p~-----~vie~l~~h----Rh~G~DvilITQ~ps~VDs~IR~  137 (361)
T PHA00012         81 KNGLLVLDECGTWFNSRSWNDKERQ-----PVIDWFLHA----RKLGWDIIFIIQDISIMDKQARE  137 (361)
T ss_pred             CCcEEEEECcccccCCCCcCcCCcH-----HHHHHHHHh----ccCCceEEEEcCCHHHHhHHHHH
Confidence            4579999999999998854432221     223333332    34567799999999999999974

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

Probab=88.48  E-value=0.11  Score=33.28  Aligned_cols=23  Identities=30%  Similarity=0.364  Sum_probs=13.6

Q ss_pred             CCeEEEeeCCCCC-----cccccccCCCcc
Q psy522           54 GDVKVIMATNRIE-----TLDPALIRPGRI   78 (131)
Q Consensus        54 ~~v~vi~ttn~~~-----~id~~l~~~grf   78 (131)
                      ++.+||||-|..+     .++++++.  ||
T Consensus       102 ~pf~ViATqNp~e~~Gty~Lpea~~D--RF  129 (131)
T PF07726_consen  102 DPFFVIATQNPVEQEGTYPLPEAQLD--RF  129 (131)
T ss_dssp             SS-EEEEEE-TT--S------HHHHT--TS
T ss_pred             CcEEEEEecCccccCceecCCHHHhc--cc
Confidence            4689999999766     57888887  77

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

>PLN03210 Resistant to P

Probab=87.62  E-value=8.8  Score=33.24  Aligned_cols=92  Identities=22%  Similarity=0.315  Sum_probs=52.0

Q ss_pred             hcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCC
Q psy522            7 EHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPL   86 (131)
Q Consensus         7 ~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~   86 (131)
                      ..++.+|++|++|..                .++..+....+..  .++..||.||.+.+.+     +....++.+.++.
T Consensus       294 ~~krvLLVLDdv~~~----------------~~l~~L~~~~~~~--~~GsrIIiTTrd~~vl-----~~~~~~~~~~v~~  350 (1153)
T PLN03210        294 KHRKVLIFIDDLDDQ----------------DVLDALAGQTQWF--GSGSRIIVITKDKHFL-----RAHGIDHIYEVCL  350 (1153)
T ss_pred             hCCeEEEEEeCCCCH----------------HHHHHHHhhCccC--CCCcEEEEEeCcHHHH-----HhcCCCeEEEecC
Confidence            356789999998642                1222222222211  2233455566654333     2235678899999


Q ss_pred             CCHHHHHHHHHHHhcCCCCCCccc----HHHHHHHcCCCC
Q psy522           87 PDEKTKRRIFNIHTSRMTLAEDVN----LQELIMAKDDLS  122 (131)
Q Consensus        87 P~~~~R~~il~~~l~~~~~~~~~~----~~~la~~t~g~s  122 (131)
                      |+.++..+++..+.-+....+ .+    -.++++.+.|+.
T Consensus       351 l~~~ea~~LF~~~Af~~~~~~-~~~~~l~~~iv~~c~GLP  389 (1153)
T PLN03210        351 PSNELALEMFCRSAFKKNSPP-DGFMELASEVALRAGNLP  389 (1153)
T ss_pred             CCHHHHHHHHHHHhcCCCCCc-HHHHHHHHHHHHHhCCCc
Confidence            999999999987653322221 12    334566677754

syringae 6; Provisional

>PRK05574 holA DNA polymerase III subunit delta; Reviewed

Probab=87.59  E-value=9  Score=27.92  Aligned_cols=83  Identities=13%  Similarity=0.105  Sum_probs=47.6

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCc---c---cccccCCCccceEEE
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIET---L---DPALIRPGRIDRKIE   83 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~---i---d~~l~~~grf~~~i~   83 (131)
                      .-+|++++++.+-.+.          ....+..+...+ +....+.++++..++..+.   +   -..+..  + ...+.
T Consensus        77 ~klvii~~~~~l~~~~----------~~~~l~~l~~~l-~~~~~~~~~li~~~~~~~~~~k~~k~~k~~~~--~-~~~~~  142 (340)
T PRK05574         77 RKLVELRLPEFLTGAK----------GEKALKRLEAYL-NPLPHPDLLLIVRLPKLDKAKKKSAWFKALKK--K-AVVVE  142 (340)
T ss_pred             CeEEEEECCCCCCchh----------HHHHHHHHHHhc-cCCCCCcEEEEEECCcCCHHHHhhHHHHHHHh--C-ceEEE
Confidence            4567777777653221          223444555545 3333334555555553222   1   123322  2 35778


Q ss_pred             eCCCCHHHHHHHHHHHhcCCCCC
Q psy522           84 FPLPDEKTKRRIFNIHTSRMTLA  106 (131)
Q Consensus        84 ~~~P~~~~R~~il~~~l~~~~~~  106 (131)
                      ++.|+..+...+++..++..+..
T Consensus       143 ~~~~~~~~~~~~i~~~~~~~g~~  165 (340)
T PRK05574        143 AQPPKEAELPQWIQQRLKQQGLQ  165 (340)
T ss_pred             cCCCCHHHHHHHHHHHHHHcCCC
Confidence            88999999999999998877654

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

Probab=87.46  E-value=0.84  Score=28.24  Aligned_cols=19  Identities=21%  Similarity=0.281  Sum_probs=14.3

Q ss_pred             HHHhcCCeEEEeccccccc
Q psy522            4 VAEEHAPSIVFIDEIDAVG   22 (131)
Q Consensus         4 ~A~~~~p~ii~iDe~d~l~   22 (131)
                      ..+.+...+|+|||+|.+.
T Consensus        82 ~l~~~~~~~lviDe~~~l~  100 (131)
T PF13401_consen   82 ALDRRRVVLLVIDEADHLF  100 (131)
T ss_dssp             HHHHCTEEEEEEETTHHHH
T ss_pred             HHHhcCCeEEEEeChHhcC
Confidence            3455555699999999975

>KOG1051|consensus

Probab=87.40  E-value=1.6  Score=36.54  Aligned_cols=49  Identities=22%  Similarity=0.278  Sum_probs=31.5

Q ss_pred             HHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCC--CC-C------CCeEEEeeCCC
Q psy522            2 FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGF--DS-R------GDVKVIMATNR   64 (131)
Q Consensus         2 F~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~-~------~~v~vi~ttn~   64 (131)
                      .+..+++.-+||||||+|.-           +.   ..++.++..+|.-  .. +      .+++||+|+|.
T Consensus       653 teavrrrP~sVVLfdeIEkA-----------h~---~v~n~llq~lD~GrltDs~Gr~Vd~kN~I~IMTsn~  710 (898)
T KOG1051|consen  653 TEAVKRRPYSVVLFEEIEKA-----------HP---DVLNILLQLLDRGRLTDSHGREVDFKNAIFIMTSNV  710 (898)
T ss_pred             HHHHhcCCceEEEEechhhc-----------CH---HHHHHHHHHHhcCccccCCCcEeeccceEEEEeccc
Confidence            45667888899999999873           12   2444444444431  11 1      35999999886

>PRK08116 hypothetical protein; Validated

Probab=87.28  E-value=1.3  Score=31.68  Aligned_cols=71  Identities=17%  Similarity=0.266  Sum_probs=34.8

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCC-CCcc----cccccCCCcc---ce
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNR-IETL----DPALIRPGRI---DR   80 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~-~~~i----d~~l~~~grf---~~   80 (131)
                      ...+|+|||+...-.         .......+..+   ++..... +..+|.|||. ++.+    +..+.+  |+   ..
T Consensus       178 ~~dlLviDDlg~e~~---------t~~~~~~l~~i---in~r~~~-~~~~IiTsN~~~~eL~~~~~~ri~s--Rl~e~~~  242 (268)
T PRK08116        178 NADLLILDDLGAERD---------TEWAREKVYNI---IDSRYRK-GLPTIVTTNLSLEELKNQYGKRIYD--RILEMCT  242 (268)
T ss_pred             CCCEEEEecccCCCC---------CHHHHHHHHHH---HHHHHHC-CCCEEEECCCCHHHHHHHHhHHHHH--HHHHcCE
Confidence            456999999854211         11112223333   3332222 2346667774 5554    556666  64   33


Q ss_pred             EEEeCCCCHHHHHHHH
Q psy522           81 KIEFPLPDEKTKRRIF   96 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il   96 (131)
                      .|.++-|+.  |..+.
T Consensus       243 ~v~~~g~d~--R~~~~  256 (268)
T PRK08116        243 PVENEGKSY--RKEIA  256 (268)
T ss_pred             EEEeeCcCh--hHHHH
Confidence            466666653  44443

>KOG1051|consensus

Probab=87.27  E-value=1.5  Score=36.73  Aligned_cols=83  Identities=25%  Similarity=0.282  Sum_probs=53.8

Q ss_pred             hcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCc-----ccccccCCCccceE
Q psy522            7 EHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIET-----LDPALIRPGRIDRK   81 (131)
Q Consensus         7 ~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~-----id~~l~~~grf~~~   81 (131)
                      .....|||+||+..+.....+   .........+...+       ..+.+.+||||..-+.     =||++-+  ||+ .
T Consensus       278 ~~~gvILfigelh~lvg~g~~---~~~~d~~nlLkp~L-------~rg~l~~IGatT~e~Y~k~iekdPalEr--rw~-l  344 (898)
T KOG1051|consen  278 GGGGVILFLGELHWLVGSGSN---YGAIDAANLLKPLL-------ARGGLWCIGATTLETYRKCIEKDPALER--RWQ-L  344 (898)
T ss_pred             CCCcEEEEecceeeeecCCCc---chHHHHHHhhHHHH-------hcCCeEEEecccHHHHHHHHhhCcchhh--Ccc-e
Confidence            345688999999999877643   11111122222222       3345999998874333     3899999  997 6


Q ss_pred             EEeCCCCHHHHHHHHHHHhcC
Q psy522           82 IEFPLPDEKTKRRIFNIHTSR  102 (131)
Q Consensus        82 i~~~~P~~~~R~~il~~~l~~  102 (131)
                      +.++.|+.+.-..+++..-..
T Consensus       345 ~~v~~pS~~~~~~iL~~l~~~  365 (898)
T KOG1051|consen  345 VLVPIPSVENLSLILPGLSER  365 (898)
T ss_pred             eEeccCcccchhhhhhhhhhh
Confidence            788999988766666655433

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=87.21  E-value=1.4  Score=32.60  Aligned_cols=79  Identities=18%  Similarity=0.258  Sum_probs=39.8

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhc--CC---C-CCCCeEEEeeCCCC-------CcccccccCCC
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLD--GF---D-SRGDVKVIMATNRI-------ETLDPALIRPG   76 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~---~-~~~~v~vi~ttn~~-------~~id~~l~~~g   76 (131)
                      ...|||||+|.+-..           ....+..+++.-.  .+   . ....+.+|++|+..       ..+.+.+..  
T Consensus        94 gGtL~Ldei~~L~~~-----------~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~at~~~l~~~~~~g~fr~dL~~--  160 (329)
T TIGR02974        94 GGTLFLDELATASLL-----------VQEKLLRVIEYGEFERVGGSQTLQVDVRLVCATNADLPALAAEGRFRADLLD--  160 (329)
T ss_pred             CCEEEeCChHhCCHH-----------HHHHHHHHHHcCcEEecCCCceeccceEEEEechhhHHHHhhcCchHHHHHH--
Confidence            578999999998432           2233333332211  00   0 11347888888742       123344444  


Q ss_pred             cc-ceEEEeCCCC--HHHHHHHHHHHhc
Q psy522           77 RI-DRKIEFPLPD--EKTKRRIFNIHTS  101 (131)
Q Consensus        77 rf-~~~i~~~~P~--~~~R~~il~~~l~  101 (131)
                      |+ ...|.+|+..  .+....++++++.
T Consensus       161 rl~~~~i~lPpLReR~eDI~~L~~~fl~  188 (329)
T TIGR02974       161 RLAFDVITLPPLRERQEDIMLLAEHFAI  188 (329)
T ss_pred             HhcchhcCCCchhhhhhhHHHHHHHHHH
Confidence            55 2345555543  3444555566553

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>PRK13539 cytochrome c biogenesis protein CcmA; Provisional

Probab=86.46  E-value=1.3  Score=30.14  Aligned_cols=65  Identities=18%  Similarity=0.056  Sum_probs=38.1

Q ss_pred             HHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEE
Q psy522            3 RVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKI   82 (131)
Q Consensus         3 ~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i   82 (131)
                      .+|-...|.++++||--.=+          .......+..++..+.   .+ +..+|.+|.+.+.++.        ++.+
T Consensus       139 a~al~~~p~llllDEPt~~L----------D~~~~~~l~~~l~~~~---~~-~~tiii~sH~~~~~~~--------~~~~  196 (207)
T PRK13539        139 ARLLVSNRPIWILDEPTAAL----------DAAAVALFAELIRAHL---AQ-GGIVIAATHIPLGLPG--------AREL  196 (207)
T ss_pred             HHHHhcCCCEEEEeCCcccC----------CHHHHHHHHHHHHHHH---HC-CCEEEEEeCCchhhcc--------CcEE
Confidence            45666789999999964322          2223344445554442   22 3457777787777764        3456


Q ss_pred             EeCCCCH
Q psy522           83 EFPLPDE   89 (131)
Q Consensus        83 ~~~~P~~   89 (131)
                      .+..|+.
T Consensus       197 ~~~~~~~  203 (207)
T PRK13539        197 DLGPFAA  203 (207)
T ss_pred             eecCccC
Confidence            6665543

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=86.11  E-value=2.3  Score=26.90  Aligned_cols=60  Identities=22%  Similarity=0.355  Sum_probs=32.0

Q ss_pred             HHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCC
Q psy522            3 RVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE   66 (131)
Q Consensus         3 ~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~   66 (131)
                      ..+....|.+++|||+..+..................+..+.....    +.++.+|.+++...
T Consensus        79 ~~~~~~~~~~lviDe~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~----~~~~~vv~~~~~~~  138 (165)
T cd01120          79 RLRERGGDDLIILDELTRLVRALREIREGYPGELDEELRELLERAR----KGGVTVIFTLQVPS  138 (165)
T ss_pred             HHHhCCCCEEEEEEcHHHHHHHHHHHHhcCChHHHHHHHHHHHHHh----cCCceEEEEEecCC
Confidence            4566778999999999988754311001112223344444444443    23455555555443

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=85.98  E-value=3.2  Score=29.10  Aligned_cols=63  Identities=29%  Similarity=0.389  Sum_probs=33.3

Q ss_pred             HHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEE
Q psy522            3 RVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKI   82 (131)
Q Consensus         3 ~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i   82 (131)
                      .+|-.+.|.+|+.||=          ...-+......+..++..+.   ...+..+|..|.+++.     -.  ++|+.|
T Consensus       154 ARAL~~~P~iilADEP----------TgnLD~~t~~~V~~ll~~~~---~~~g~tii~VTHd~~l-----A~--~~dr~i  213 (226)
T COG1136         154 ARALINNPKIILADEP----------TGNLDSKTAKEVLELLRELN---KERGKTIIMVTHDPEL-----AK--YADRVI  213 (226)
T ss_pred             HHHHhcCCCeEEeeCc----------cccCChHHHHHHHHHHHHHH---HhcCCEEEEEcCCHHH-----HH--hCCEEE
Confidence            5677789999999982          11122222233334444332   3334455566665433     33  566666


Q ss_pred             EeC
Q psy522           83 EFP   85 (131)
Q Consensus        83 ~~~   85 (131)
                      ++.
T Consensus       214 ~l~  216 (226)
T COG1136         214 ELK  216 (226)
T ss_pred             EEe
Confidence            653

>PF09820 AAA-ATPase_like: Predicted AAA-ATPase; InterPro: IPR018631 This entry is predicted to be an AAA-ATPase domain []

Probab=85.86  E-value=2.7  Score=30.33  Aligned_cols=111  Identities=13%  Similarity=0.025  Sum_probs=59.1

Q ss_pred             hcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCC-CCeEEEeeCCC-CCcccc--------cccCCC
Q psy522            7 EHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSR-GDVKVIMATNR-IETLDP--------ALIRPG   76 (131)
Q Consensus         7 ~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~v~vi~ttn~-~~~id~--------~l~~~g   76 (131)
                      ..+|.||+|||-|..+.+.-..+ .........+..++..+..-... ..+++-|.+.- ..++-+        ++..  
T Consensus       141 ~~~kvvlLIDEYD~p~~~~~~~~-e~~~~~~~~lr~ff~~~k~~~~~l~~~~iTGi~~i~k~si~S~lNn~~~~s~~~--  217 (284)
T PF09820_consen  141 YGKKVVLLIDEYDKPINDALSNG-EYYEEMREFLRNFFSVLKKDNPYLRFAFITGILPISKESIFSGLNNLEDISLDP--  217 (284)
T ss_pred             hCCceEEEecCccHHHHHHhhhh-HHHHHHHHHHHHHHHHhcccchhhhhhheeccchhhhccCccccCCceecccch--
Confidence            35689999999999886652222 12223334444444443321111 12333332221 111111        1222  


Q ss_pred             ccceEEEeCCCCHHHHHHHHHHHhcCCCC--CCcccHHHHHHHcCCCCH
Q psy522           77 RIDRKIEFPLPDEKTKRRIFNIHTSRMTL--AEDVNLQELIMAKDDLSG  123 (131)
Q Consensus        77 rf~~~i~~~~P~~~~R~~il~~~l~~~~~--~~~~~~~~la~~t~g~s~  123 (131)
                      +|+..+   --+++|-.++++.++.....  +.+..+..+-....||.-
T Consensus       218 ~f~~~~---GFT~~Ev~~ll~~~~~~~~~~~~~~~~~~~lk~wYdGY~F  263 (284)
T PF09820_consen  218 RFSEYF---GFTEEEVETLLKYYIENLAEEQDREELLEELKEWYDGYHF  263 (284)
T ss_pred             hHhhhc---CcCHHHHHHHHHHHHHHhhhccchHHHHHHHHHHcCCccc
Confidence            444222   23888999999999766544  345567778788888864

It is usually found together with IPR012547 from INTERPRO.

>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]

Probab=85.68  E-value=1.5  Score=35.62  Aligned_cols=79  Identities=22%  Similarity=0.261  Sum_probs=45.6

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHH-HHhcCCCCC-------CCeEEEeeCCCCC-------------cc
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELL-NQLDGFDSR-------GDVKVIMATNRIE-------------TL   68 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l-~~~~~~~~~-------~~v~vi~ttn~~~-------------~i   68 (131)
                      +.|..|||+|.+-..-           ...+++.+ ++.-++.+.       .+.-|+|++|-..             .+
T Consensus       384 ~Gv~cIDEfdKm~~~d-----------r~aihEaMEQQtIsIaKAGI~atLnARcsvLAAaNP~~Gryd~~~~~~enI~l  452 (682)
T COG1241         384 GGVCCIDEFDKMNEED-----------RVAIHEAMEQQTISIAKAGITATLNARCSVLAAANPKFGRYDPKKTVAENINL  452 (682)
T ss_pred             CCEEEEEeccCCChHH-----------HHHHHHHHHhcEeeecccceeeecchhhhhhhhhCCCCCcCCCCCCHHHhcCC
Confidence            6789999999873211           12222222 111122221       2466788888555             37


Q ss_pred             cccccCCCccceEEEeC-CCCHHHHHHHHHHHhc
Q psy522           69 DPALIRPGRIDRKIEFP-LPDEKTKRRIFNIHTS  101 (131)
Q Consensus        69 d~~l~~~grf~~~i~~~-~P~~~~R~~il~~~l~  101 (131)
                      ++.+++  |||..+.+. -|+.+.=..+..+.+.
T Consensus       453 ~~~lLS--RFDLifvl~D~~d~~~D~~ia~hil~  484 (682)
T COG1241         453 PAPLLS--RFDLIFVLKDDPDEEKDEEIAEHILD  484 (682)
T ss_pred             ChhHHh--hCCeeEEecCCCCccchHHHHHHHHH
Confidence            889999  999766654 4666655555555443

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=85.64  E-value=0.78  Score=31.14  Aligned_cols=62  Identities=13%  Similarity=0.232  Sum_probs=33.7

Q ss_pred             HHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCccc
Q psy522            5 AEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLD   69 (131)
Q Consensus         5 A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id   69 (131)
                      +.++.|.+|+||-+..++......  ... ...+.+..++..+..+..+.++.++.|+......+
T Consensus        93 ~~~~~~~lvVIDSis~l~~~~~~~--~~~-~~~~~l~~~~~~L~~~~~~~~v~vl~t~~~~~~~~  154 (209)
T TIGR02237        93 IDRDSASLVVVDSFTALYRLELSD--DRI-SRNRELARQLTLLLSLARKKNLAVVITNQVYTDVN  154 (209)
T ss_pred             HhhcCccEEEEeCcHHHhHHHhCC--ccH-HHHHHHHHHHHHHHHHHHHcCCEEEEEcccEEecC
Confidence            455689999999999987532111  111 11122333333344444456777887766444443

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

>COG1131 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]

Probab=85.34  E-value=2.8  Score=30.39  Aligned_cols=56  Identities=30%  Similarity=0.533  Sum_probs=35.9

Q ss_pred             HHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccc
Q psy522            2 FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDP   70 (131)
Q Consensus         2 F~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~   70 (131)
                      +..|-.+.|.++++||=          ..+-++.....+..++..+.   ..++..|+.||..++.+..
T Consensus       147 ia~aL~~~P~lliLDEP----------t~GLDp~~~~~~~~~l~~l~---~~g~~tvlissH~l~e~~~  202 (293)
T COG1131         147 IALALLHDPELLILDEP----------TSGLDPESRREIWELLRELA---KEGGVTILLSTHILEEAEE  202 (293)
T ss_pred             HHHHHhcCCCEEEECCC----------CcCCCHHHHHHHHHHHHHHH---hCCCcEEEEeCCcHHHHHH
Confidence            34567788999999993          23334444455555554443   4555788888888777643

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=84.76  E-value=3.9  Score=32.86  Aligned_cols=13  Identities=8%  Similarity=0.501  Sum_probs=10.5

Q ss_pred             CeEEEeccccccc
Q psy522           10 PSIVFIDEIDAVG   22 (131)
Q Consensus        10 p~ii~iDe~d~l~   22 (131)
                      ...|||||+|.+-
T Consensus       417 ~GtL~ldei~~l~  429 (638)
T PRK11388        417 GGTLFLEKVEYLS  429 (638)
T ss_pred             CCEEEEcChhhCC
Confidence            4679999999874

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=84.58  E-value=4.3  Score=30.77  Aligned_cols=15  Identities=27%  Similarity=0.561  Sum_probs=12.0

Q ss_pred             CCeEEEecccccccC
Q psy522            9 APSIVFIDEIDAVGT   23 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~   23 (131)
                      ....|||||+|.+-.
T Consensus       233 ~~gtl~ldei~~l~~  247 (441)
T PRK10365        233 DGGTLFLDEIGDISP  247 (441)
T ss_pred             CCCEEEEeccccCCH
Confidence            357899999999853

>KOG1969|consensus

Probab=84.49  E-value=13  Score=30.84  Aligned_cols=62  Identities=21%  Similarity=0.184  Sum_probs=41.0

Q ss_pred             eEEEeeCCCCCcccccccCCCccceEEEeCCCCHHHHHHHHHHHhcCCCCCCc-ccHHHHHHHcC
Q psy522           56 VKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAED-VNLQELIMAKD  119 (131)
Q Consensus        56 v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~-~~~~~la~~t~  119 (131)
                      .-+|+.||+  .--|+++.=--|-..++|.+|....-.+=|+..+...+...+ ..+..|++.|+
T Consensus       439 RPIICICNd--LYaPaLR~Lr~~A~ii~f~~p~~s~Lv~RL~~IC~rE~mr~d~~aL~~L~el~~  501 (877)
T KOG1969|consen  439 RPIICICND--LYAPALRPLRPFAEIIAFVPPSQSRLVERLNEICHRENMRADSKALNALCELTQ  501 (877)
T ss_pred             CCEEEEecC--ccchhhhhcccceEEEEecCCChhHHHHHHHHHHhhhcCCCCHHHHHHHHHHhc
Confidence            457888885  445777632358889999999888777777777766655432 23555555544

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=83.87  E-value=5.1  Score=29.50  Aligned_cols=77  Identities=16%  Similarity=0.283  Sum_probs=39.8

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCC-------CCCeEEEeeCCCC-------CcccccccCC
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDS-------RGDVKVIMATNRI-------ETLDPALIRP   75 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-------~~~v~vi~ttn~~-------~~id~~l~~~   75 (131)
                      ...|||||+|.+-..           ....+..+++.-. +..       ...+.+|+||+..       ..+.+.+.. 
T Consensus       101 gGtL~l~~i~~L~~~-----------~Q~~L~~~l~~~~-~~~~g~~~~~~~~~RiI~~s~~~l~~l~~~g~f~~dL~~-  167 (326)
T PRK11608        101 GGTLFLDELATAPML-----------VQEKLLRVIEYGE-LERVGGSQPLQVNVRLVCATNADLPAMVAEGKFRADLLD-  167 (326)
T ss_pred             CCeEEeCChhhCCHH-----------HHHHHHHHHhcCc-EEeCCCCceeeccEEEEEeCchhHHHHHHcCCchHHHHH-
Confidence            467999999998432           2223333332211 111       1247788887742       234455555 


Q ss_pred             Ccc-ceEEEeCCCC--HHHHHHHHHHHh
Q psy522           76 GRI-DRKIEFPLPD--EKTKRRIFNIHT  100 (131)
Q Consensus        76 grf-~~~i~~~~P~--~~~R~~il~~~l  100 (131)
                       || ...|.+|+..  .+....++++++
T Consensus       168 -~l~~~~i~lPpLReR~eDI~~L~~~fl  194 (326)
T PRK11608        168 -RLAFDVVQLPPLRERQSDIMLMAEHFA  194 (326)
T ss_pred             -hcCCCEEECCChhhhhhhHHHHHHHHH
Confidence             66 3456665541  234455666665

>PF13173 AAA_14: AAA domain

Probab=83.81  E-value=2.6  Score=26.33  Aligned_cols=64  Identities=23%  Similarity=0.318  Sum_probs=32.9

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcc--cccccCCCccceEEEeCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETL--DPALIRPGRIDRKIEFPL   86 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~i--d~~l~~~grf~~~i~~~~   86 (131)
                      .+.+|||||+..+-            .....+..+..   .   .+.+-+|.|++....+  +-+-.-+||.. .+++.+
T Consensus        61 ~~~~i~iDEiq~~~------------~~~~~lk~l~d---~---~~~~~ii~tgS~~~~l~~~~~~~l~gr~~-~~~l~P  121 (128)
T PF13173_consen   61 GKKYIFIDEIQYLP------------DWEDALKFLVD---N---GPNIKIILTGSSSSLLSKDIAESLAGRVI-EIELYP  121 (128)
T ss_pred             CCcEEEEehhhhhc------------cHHHHHHHHHH---h---ccCceEEEEccchHHHhhcccccCCCeEE-EEEECC
Confidence            57899999997761            12233333332   1   1223333333332222  11222345875 788888


Q ss_pred             CCHHH
Q psy522           87 PDEKT   91 (131)
Q Consensus        87 P~~~~   91 (131)
                      .+..|
T Consensus       122 lsf~E  126 (128)
T PF13173_consen  122 LSFRE  126 (128)
T ss_pred             CCHHH
Confidence            87765

>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]

Probab=83.45  E-value=13  Score=26.01  Aligned_cols=75  Identities=27%  Similarity=0.288  Sum_probs=46.6

Q ss_pred             HhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeC
Q psy522            6 EEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFP   85 (131)
Q Consensus         6 ~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~   85 (131)
                      +..+|.+|++|.-   .++.    ++     ..    ++..+.+-.-...|++|.+++..+.|-.+++- |-||+.|  .
T Consensus        43 ~~~~pDLILLDiY---mPd~----~G-----i~----lL~~ir~~~~~~DVI~iTAA~d~~tI~~alr~-Gv~DYLi--K  103 (224)
T COG4565          43 EEFKPDLILLDIY---MPDG----NG-----IE----LLPELRSQHYPVDVIVITAASDMETIKEALRY-GVVDYLI--K  103 (224)
T ss_pred             HhhCCCEEEEeec---cCCC----cc-----HH----HHHHHHhcCCCCCEEEEeccchHHHHHHHHhc-Cchhhee--c
Confidence            5578999998763   5443    11     12    33333332233579999999999999888775 8899655  3


Q ss_pred             CCCHHHHHHHHHHH
Q psy522           86 LPDEKTKRRIFNIH   99 (131)
Q Consensus        86 ~P~~~~R~~il~~~   99 (131)
                      |-..+.-.+-|..|
T Consensus       104 Pf~~eRl~~aL~~y  117 (224)
T COG4565         104 PFTFERLQQALTRY  117 (224)
T ss_pred             ceeHHHHHHHHHHH
Confidence            44554444444444

>COG4555 NatA ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]

Probab=83.37  E-value=4.2  Score=28.43  Aligned_cols=52  Identities=27%  Similarity=0.418  Sum_probs=32.8

Q ss_pred             HHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcc
Q psy522            3 RVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETL   68 (131)
Q Consensus         3 ~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~i   68 (131)
                      .+|--+.|+|+++||-          .++-+-...+.+..++.++.    ..+..+|.+|...+++
T Consensus       145 ARAlvh~P~i~vlDEP----------~sGLDi~~~r~~~dfi~q~k----~egr~viFSSH~m~Ev  196 (245)
T COG4555         145 ARALVHDPSILVLDEP----------TSGLDIRTRRKFHDFIKQLK----NEGRAVIFSSHIMQEV  196 (245)
T ss_pred             HHHHhcCCCeEEEcCC----------CCCccHHHHHHHHHHHHHhh----cCCcEEEEecccHHHH
Confidence            4667789999999994          12233334456666665553    3355677777766555

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=83.26  E-value=4.7  Score=25.48  Aligned_cols=15  Identities=13%  Similarity=0.410  Sum_probs=12.0

Q ss_pred             cCCeEEEeccccccc
Q psy522            8 HAPSIVFIDEIDAVG   22 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~   22 (131)
                      ..+..|+|+|+|.+-
T Consensus        68 a~~gtL~l~~i~~L~   82 (138)
T PF14532_consen   68 AKGGTLYLKNIDRLS   82 (138)
T ss_dssp             CTTSEEEEECGCCS-
T ss_pred             cCCCEEEECChHHCC
Confidence            367889999999984

>PRK13538 cytochrome c biogenesis protein CcmA; Provisional

Probab=82.45  E-value=7.3  Score=26.34  Aligned_cols=53  Identities=15%  Similarity=0.046  Sum_probs=31.7

Q ss_pred             HHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCccc
Q psy522            3 RVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLD   69 (131)
Q Consensus         3 ~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id   69 (131)
                      .+|-...|.++++||--.=+          +......+..++..+.   .. +..+|.+|++++.++
T Consensus       141 a~al~~~p~llllDEPt~~L----------D~~~~~~l~~~l~~~~---~~-~~tiii~sh~~~~i~  193 (204)
T PRK13538        141 ARLWLTRAPLWILDEPFTAI----------DKQGVARLEALLAQHA---EQ-GGMVILTTHQDLPVA  193 (204)
T ss_pred             HHHHhcCCCEEEEeCCCccC----------CHHHHHHHHHHHHHHH---HC-CCEEEEEecChhhhc
Confidence            45667889999999964322          2223345555555442   22 235666777777776

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=81.87  E-value=8.3  Score=27.47  Aligned_cols=17  Identities=24%  Similarity=0.391  Sum_probs=13.9

Q ss_pred             HHHHHhcCCeEEEeccc
Q psy522            2 FRVAEEHAPSIVFIDEI   18 (131)
Q Consensus         2 F~~A~~~~p~ii~iDe~   18 (131)
                      +.+|-...|-|+++||=
T Consensus       141 iARAL~~~P~lLLlDEP  157 (248)
T COG1116         141 IARALATRPKLLLLDEP  157 (248)
T ss_pred             HHHHHhcCCCEEEEcCC
Confidence            45677788999999994

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

Probab=81.82  E-value=18  Score=26.51  Aligned_cols=119  Identities=18%  Similarity=0.161  Sum_probs=68.5

Q ss_pred             CCeEEEecccccccCcCCC---CCCCchhHHHHHHHHHHHHhcCCCC-CCCeEE--EeeCCC---CC--cccccccCCCc
Q psy522            9 APSIVFIDEIDAVGTKRYD---SNSGGEREIQRTMLELLNQLDGFDS-RGDVKV--IMATNR---IE--TLDPALIRPGR   77 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~---~~~~~~~~~~~~~~~~l~~~~~~~~-~~~v~v--i~ttn~---~~--~id~~l~~~gr   77 (131)
                      .|.++-+|++..++....-   ....-...-..+...++..+.+-.. .++.++  +++|..   +.  .++.++.....
T Consensus       156 ~PVL~avD~~n~l~~~S~Y~~~~~~~I~~~~L~l~~~f~~~~s~~~~~~nG~~v~~l~~t~~~~~~~~~~l~~~L~~~~~  235 (309)
T PF10236_consen  156 PPVLVAVDGFNALFGPSAYRDPDFKPIHPHDLTLVRLFLDLLSGKRDFKNGAVVTALAATSVSNAPKSPTLPVALGGKEG  235 (309)
T ss_pred             CceEEEehhhHHhhCCccccCCCCccccHHHhhHHHHHHHHhcCccccCCCeEEEEEeccccccccCCccchhhhccccC
Confidence            4889999999999977421   1122233444555666665443212 234443  555543   33  45555554221


Q ss_pred             ------cc-------------eEEEeCCCCHHHHHHHHHHHhcCCCCCCccc----HHHHHHHcCCCCHHHHHH
Q psy522           78 ------ID-------------RKIEFPLPDEKTKRRIFNIHTSRMTLAEDVN----LQELIMAKDDLSGADIKA  128 (131)
Q Consensus        78 ------f~-------------~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~----~~~la~~t~g~s~~di~~  128 (131)
                            |.             ..+.++.-+++|-..++++|.....+....+    ...+. .+.|-.|+++..
T Consensus       236 ~~~~dPy~~~d~~~~~~l~~~~~i~v~~~s~~E~~~ll~yy~~~~~l~~~~~~~~~~e~~~-~~s~GNp~el~k  308 (309)
T PF10236_consen  236 FPHLDPYVKRDPRVAESLKGVKPIEVPRLSKEEARSLLEYYADSGWLRSRVDEELVLEKLF-LSSNGNPRELEK  308 (309)
T ss_pred             CCCCCCcccccHHHHHHhcCCceEEeCCCCHHHHHHHHHHHHHCCccccCCCCHHHHHHHH-HhcCCCHHHhcc
Confidence                  11             2688998899999999999987765553111    22222 234566777764

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

>TIGR01128 holA DNA polymerase III, delta subunit

Probab=81.58  E-value=8.6  Score=27.46  Aligned_cols=94  Identities=13%  Similarity=0.119  Sum_probs=51.3

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcc---cccccCCCccceEEEeCC
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETL---DPALIRPGRIDRKIEFPL   86 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~i---d~~l~~~grf~~~i~~~~   86 (131)
                      .-++++++++.+..+.             ....++..+...  .+..++|..++.++.-   ...+..-+ -...+.+..
T Consensus        47 ~kliii~~~~~~~~~~-------------~~~~L~~~l~~~--~~~~~~i~~~~~~~~~~~~~k~~~~~~-~~~~i~~~~  110 (302)
T TIGR01128        47 RRLVELRNPEGKPGAK-------------GLKALEEYLANP--PPDTLLLIEAPKLDKRKKLTKWLKALK-NAQIVECKT  110 (302)
T ss_pred             CeEEEEECCCCCCCHH-------------HHHHHHHHHhcC--CCCEEEEEecCCCCHhHHHHHHHHHhc-CeeEEEecC
Confidence            4578888887653221             234455555543  2344555555432221   11121100 224678889


Q ss_pred             CCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcC
Q psy522           87 PDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKD  119 (131)
Q Consensus        87 P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~  119 (131)
                      |+..+...+++..++..+.. .......++..+.
T Consensus       111 ~~~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~  144 (302)
T TIGR01128       111 PKEQELPRWIQARLKKLGLRIDPDAVQLLAELVE  144 (302)
T ss_pred             CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhC
Confidence            99999999999998877654 2223444554443

subunit around DNA forming a DNA sliding clamp.

>KOG2680|consensus

Probab=81.53  E-value=4.9  Score=29.89  Aligned_cols=39  Identities=15%  Similarity=0.176  Sum_probs=27.1

Q ss_pred             CCCcccccccCCCccceEEEeCCCCHHHHHHHHHHHhcCCCC
Q psy522           64 RIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTL  105 (131)
Q Consensus        64 ~~~~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~~~~  105 (131)
                      +|+-||-.++.  |. ..|...+-+.++-++||+.-+....+
T Consensus       338 SphGiP~D~lD--R~-lII~t~py~~~d~~~IL~iRc~EEdv  376 (454)
T KOG2680|consen  338 SPHGIPIDLLD--RM-LIISTQPYTEEDIKKILRIRCQEEDV  376 (454)
T ss_pred             CCCCCcHHHhh--hh-heeecccCcHHHHHHHHHhhhhhhcc
Confidence            46677777776  65 24554555899999999988775544

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=80.36  E-value=5.8  Score=28.36  Aligned_cols=53  Identities=23%  Similarity=0.374  Sum_probs=33.4

Q ss_pred             HHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcc
Q psy522            2 FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETL   68 (131)
Q Consensus         2 F~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~i   68 (131)
                      +++|-...|-++++||=   +       ..-+......+..++..+.   .. +..|+..|.+.+.+
T Consensus       150 lARAL~~~p~lllLDEP---~-------~gvD~~~~~~i~~lL~~l~---~e-g~tIl~vtHDL~~v  202 (254)
T COG1121         150 LARALAQNPDLLLLDEP---F-------TGVDVAGQKEIYDLLKELR---QE-GKTVLMVTHDLGLV  202 (254)
T ss_pred             HHHHhccCCCEEEecCC---c-------ccCCHHHHHHHHHHHHHHH---HC-CCEEEEEeCCcHHh
Confidence            57788899999999994   1       1222333445555655554   44 56677777766555

>KOG0481|consensus

Probab=80.21  E-value=2.2  Score=33.75  Aligned_cols=82  Identities=16%  Similarity=0.332  Sum_probs=42.7

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCC--CCCeEEEeeCCCC-----------Cccc--ccccC
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDS--RGDVKVIMATNRI-----------ETLD--PALIR   74 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~v~vi~ttn~~-----------~~id--~~l~~   74 (131)
                      -.|+.|||+|++-..   ..-.-+..+-++...+-.  .++.+  +.+.-|+|++|.+           +.||  +.+++
T Consensus       429 gGVvCIDEFDKMre~---DRVAIHEAMEQQTISIAK--AGITT~LNSRtSVLAAANpvfGRyDd~Kt~~dNIDf~~TILS  503 (729)
T KOG0481|consen  429 GGVVCIDEFDKMRED---DRVAIHEAMEQQTISIAK--AGITTTLNSRTSVLAAANPVFGRYDDTKTGEDNIDFMPTILS  503 (729)
T ss_pred             CCEEEeehhhccCch---hhhHHHHHHHhhhHHHhh--hcceeeecchhhhhhhcCCccccccccCCcccccchhhhHhh
Confidence            368999999998322   111112221111111111  12212  1356677887753           2343  77889


Q ss_pred             CCccceEEEeCCCCHHHHHHHHHH
Q psy522           75 PGRIDRKIEFPLPDEKTKRRIFNI   98 (131)
Q Consensus        75 ~grf~~~i~~~~P~~~~R~~il~~   98 (131)
                        |||..+-+.---.++|-..+..
T Consensus       504 --RFDmIFIVKD~h~~~~D~~lAk  525 (729)
T KOG0481|consen  504 --RFDMIFIVKDEHDEERDITLAK  525 (729)
T ss_pred             --hccEEEEEeccCcchhhhHHHH
Confidence              9998877776544445444433

>smart00763 AAA_PrkA PrkA AAA domain

Probab=80.20  E-value=3.2  Score=31.17  Aligned_cols=45  Identities=20%  Similarity=0.253  Sum_probs=37.7

Q ss_pred             eEEEeeCCCC-------CcccccccCCCccceEEEeCCC-CHHHHHHHHHHHhcCC
Q psy522           56 VKVIMATNRI-------ETLDPALIRPGRIDRKIEFPLP-DEKTKRRIFNIHTSRM  103 (131)
Q Consensus        56 v~vi~ttn~~-------~~id~~l~~~grf~~~i~~~~P-~~~~R~~il~~~l~~~  103 (131)
                      .++|+|||..       ....++|++  |+. .+.++.| +.++-.+|.++.+...
T Consensus       278 ~liia~sNe~e~~~~~~~k~~eaf~d--R~~-~i~vpY~l~~~~E~~Iy~k~~~~s  330 (361)
T smart00763      278 GLIIAHSNESEWQRFKSNKKNEALLD--RII-KVKVPYCLRVSEEAQIYEKLLRNS  330 (361)
T ss_pred             eEEEEeCCHHHHhhhhccccchhhhh--ceE-EEeCCCcCCHHHHHHHHHHHhccC
Confidence            6899999977       366899999  998 8999988 7888889999888743

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	131
4b4t_I	437	Near-Atomic Resolution Structural Model Of The Yeas		3e-58
4b4t_M	434	Near-Atomic Resolution Structural Model Of The Yeas		5e-43
3h4m_A	285	Aaa Atpase Domain Of The Proteasome- Activating Nuc		7e-43
4b4t_J	405	Near-Atomic Resolution Structural Model Of The Yeas		1e-41
4b4t_K	428	Near-Atomic Resolution Structural Model Of The Yeas		6e-40
4b4t_L	437	Near-Atomic Resolution Structural Model Of The Yeas		9e-37
4b4t_H	467	Near-Atomic Resolution Structural Model Of The Yeas		6e-36
3kds_E	465	Apo-ftsh Crystal Structure Length = 465		3e-27
2ce7_A	476	Edta Treated Length = 476		3e-27
1iy2_A	278	Crystal Structure Of The Ftsh Atpase Domain From Th		3e-26
1ixz_A	254	Crystal Structure Of The Ftsh Atpase Domain From Th		3e-26
4eiw_A	508	Whole Cytosolic Region Of Atp-Dependent Metalloprot		3e-26
2dhr_A	499	Whole Cytosolic Region Of Atp-Dependent Metalloprot		4e-26
1lv7_A	257	Crystal Structure Of The Aaa Domain Of Ftsh Length		1e-24
2r62_A	268	Crystal Structure Of Helicobacter Pylori Atp Depend		2e-24
3hu2_A	489	Structure Of P97 N-D1 R86a Mutant In Complex With A		4e-23
3hu3_A	489	Structure Of P97 N-D1 R155h Mutant In Complex With		4e-23
3hu1_A	489	Structure Of P97 N-D1 R95g Mutant In Complex With A		4e-23
1e32_A	458	Structure Of The N-Terminal Domain And The D1 Aaa D		4e-23
3cf1_A	806	Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Len		4e-23
1r7r_A	816	The Crystal Structure Of Murine P97VCP AT 3.6A Leng		5e-23
3cf0_A	301	Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH		3e-21
2qz4_A	262	Human Paraplegin, Aaa Domain In Complex With Adp Le		3e-21
2x8a_A	274	Human Nuclear Valosin Containing Protein Like (Nvl)		2e-16
2zam_A	444	Crystal Structure Of Mouse Skd1VPS4B APO-Form Lengt		4e-13
1xwi_A	322	Crystal Structure Of Vps4b Length = 322		6e-13
3d8b_A	357	Crystal Structure Of Human Fidgetin-Like Protein 1		1e-12
2rko_A	331	Crystal Structure Of The Vps4p-Dimer Length = 331		2e-11
2qp9_X	355	Crystal Structure Of S.Cerevisiae Vps4 Length = 355		3e-11
3eie_A	322	Crystal Structure Of S.Cerevisiae Vps4 In The So4-B		6e-11
3eih_A	340	Crystal Structure Of S.Cerevisiae Vps4 In The Prese		6e-11
3vfd_A	389	Human Spastin Aaa Domain Length = 389		2e-10
3b9p_A	297	Spastin Length = 297		4e-09
2dvw_B	83	Structure Of The Oncoprotein Gankyrin In Complex Wi		1e-05

>pdb|4B4T|I Chain I, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score =  219 bits (558), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 105/131 (80%), Positives = 118/131 (90%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           +F+VA E+APSIVFIDEIDA+GTKRYDSNSGGEREIQRTMLELLNQLDGFD RGDVKVIM
Sbjct: 267 IFKVAGENAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDDRGDVKVIM 326
Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATN+IETLDPALIRPGRIDRKI F  PD  TK++I  IHTS+M L+EDVNL+ L+  KDD
Sbjct: 327 ATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLSEDVNLETLVTTKDD 386
Query: 121 LSGADIKAICT 131
           LSGADI+A+CT
Sbjct: 387 LSGADIQAMCT 397

>pdb|4B4T|M Chain M, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 434

Iteration: 1
 Score =  169 bits (427), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 76/129 (58%), Positives = 102/129 (79%)
Query: 2   FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMA 61
           F +A+E AP+I+FIDE+DA+GTKR+DS   G+RE+QRTMLELLNQLDGF S   VKV+ A
Sbjct: 267 FALAKEKAPTIIFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQLDGFSSDDRVKVLAA 326
Query: 62  TNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDL 121
           TNR++ LDPAL+R GR+DRKIEFPLP E ++ +I  IH+ +MT  +D+N QEL  + D+ 
Sbjct: 327 TNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTDDDINWQELARSTDEF 386
Query: 122 SGADIKAIC 130
           +GA +KA+ 
Sbjct: 387 NGAQLKAVT 395

>pdb|3H4M|A Chain A, Aaa Atpase Domain Of The Proteasome- Activating Nucleotidase Length = 285

Iteration: 1
 Score =  168 bits (426), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 77/131 (58%), Positives = 104/131 (79%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           +F++A+E APSI+FIDEIDA+  KR D+ +GG+RE+QRT+++LL ++DGFD+RGDVK+I 
Sbjct: 102 IFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIG 161
Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + LDPA++RPGR DR IE P PDEK +  I  IHT +M LAEDVNL+E+    + 
Sbjct: 162 ATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEG 221
Query: 121 LSGADIKAICT 131
             GA++KAICT
Sbjct: 222 CVGAELKAICT 232

>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 405

Iteration: 1
 Score =  164 bits (415), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 72/131 (54%), Positives = 100/131 (76%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LF +A EHAPSI+F+DEID++G+ R + + GG+ E+QRTMLELLNQLDGF++  ++K+IM
Sbjct: 233 LFVMAREHAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFETSKNIKIIM 292
Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR++ LDPAL+RPGRIDRKIEFP P    +  I  IH+ +M L   +NL+++    + 
Sbjct: 293 ATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGINLRKVAEKMNG 352
Query: 121 LSGADIKAICT 131
            SGAD+K +CT
Sbjct: 353 CSGADVKGVCT 363

>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 428

Iteration: 1
 Score =  159 bits (401), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 76/131 (58%), Positives = 102/131 (77%), Gaps = 1/131 (0%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           +FR+A E+APSI+FIDE+D++ TKR+D+ +G +RE+QR ++ELL Q+DGFD   +VKVIM
Sbjct: 257 VFRLARENAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQSTNVKVIM 316
Query: 61  ATNRIETLDPALIRPGRIDRKIEFP-LPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKD 119
           ATNR +TLDPAL+RPGR+DRKIEFP L D + +R IF    S+M+LA + +L  LI+  D
Sbjct: 317 ATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLAPEADLDSLIIRND 376
Query: 120 DLSGADIKAIC 130
            LSGA I AI 
Sbjct: 377 SLSGAVIAAIM 387

>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score =  148 bits (373), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 64/131 (48%), Positives = 94/131 (71%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           +F  A+EH P I+F+DE+DA+G +R+   +  +REIQRT++ELL Q+DGFD+ G  K+IM
Sbjct: 266 MFAYAKEHEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFDNLGQTKIIM 325
Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR +TLDPAL+RPGR+DRK+E PLP+E  +  IF IHT+++    + + +  +   D 
Sbjct: 326 ATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEFDFEAAVKMSDG 385
Query: 121 LSGADIKAICT 131
            +GADI+   T
Sbjct: 386 FNGADIRNCAT 396

>pdb|4B4T|H Chain H, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 467

Iteration: 1
 Score =  145 bits (366), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 66/131 (50%), Positives = 93/131 (70%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LF +A      I+F DEIDAVG  R+D  +GG+ E+QRTMLEL+ QLDGFD RG++KV+ 
Sbjct: 294 LFEMARTKKACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDPRGNIKVMF 353
Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR  TLDPAL+RPGRIDRK+EF LPD + +  IF IH+  M++   +  + +     +
Sbjct: 354 ATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGIRWELISRLCPN 413
Query: 121 LSGADIKAICT 131
            +GA+++++CT
Sbjct: 414 STGAELRSVCT 424

>pdb|3KDS|E Chain E, Apo-ftsh Crystal Structure Length = 465

Iteration: 1
 Score =  116 bits (291), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 62/131 (47%), Positives = 83/131 (63%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LF  A+ HAP IVFIDEIDAVG  R     GG  E ++T+ +LL ++DGFDS+  + V+ 
Sbjct: 100 LFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMA 159
Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + LDPAL+RPGR D+KI    PD   +++I  IHT    LAEDVNL+ +      
Sbjct: 160 ATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAKRTPG 219
Query: 121 LSGADIKAICT 131
             GAD++ +  
Sbjct: 220 FVGADLENLVN 230

>pdb|2CE7|A Chain A, Edta Treated Length = 476

Iteration: 1
 Score =  116 bits (291), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 62/131 (47%), Positives = 83/131 (63%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LF  A+ HAP IVFIDEIDAVG  R     GG  E ++T+ +LL ++DGFDS+  + V+ 
Sbjct: 100 LFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMA 159
Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + LDPAL+RPGR D+KI    PD   +++I  IHT    LAEDVNL+ +      
Sbjct: 160 ATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAKRTPG 219
Query: 121 LSGADIKAICT 131
             GAD++ +  
Sbjct: 220 FVGADLENLVN 230

>pdb|1IY2|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 278

Iteration: 1
 Score =  113 bits (283), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 61/125 (48%), Positives = 77/125 (61%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LF  A+ HAP IVFIDEIDAVG KR     GG  E ++T+ +LL ++DGF+    + V+ 
Sbjct: 124 LFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMA 183
Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + LDPAL+RPGR DR+I    PD K + +I  IH     LAEDV+L  L      
Sbjct: 184 ATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPG 243
Query: 121 LSGAD 125
             GAD
Sbjct: 244 FVGAD 248

>pdb|1IXZ|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 254

Iteration: 1
 Score =  113 bits (282), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 61/125 (48%), Positives = 77/125 (61%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LF  A+ HAP IVFIDEIDAVG KR     GG  E ++T+ +LL ++DGF+    + V+ 
Sbjct: 100 LFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMA 159
Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + LDPAL+RPGR DR+I    PD K + +I  IH     LAEDV+L  L      
Sbjct: 160 ATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPG 219
Query: 121 LSGAD 125
             GAD
Sbjct: 220 FVGAD 224

>pdb|4EIW|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 508

Iteration: 1
 Score =  113 bits (282), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 61/125 (48%), Positives = 77/125 (61%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LF  A+ HAP IVFIDEIDAVG KR     GG  E ++T+ +LL ++DGF+    + V+ 
Sbjct: 124 LFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMA 183
Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + LDPAL+RPGR DR+I    PD K + +I  IH     LAEDV+L  L      
Sbjct: 184 ATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPG 243
Query: 121 LSGAD 125
             GAD
Sbjct: 244 FVGAD 248

>pdb|2DHR|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 499

Iteration: 1
 Score =  113 bits (282), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 61/125 (48%), Positives = 77/125 (61%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LF  A+ HAP IVFIDEIDAVG KR     GG  E ++T+ +LL ++DGF+    + V+ 
Sbjct: 115 LFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMA 174
Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + LDPAL+RPGR DR+I    PD K + +I  IH     LAEDV+L  L      
Sbjct: 175 ATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPG 234
Query: 121 LSGAD 125
             GAD
Sbjct: 235 FVGAD 239

>pdb|1LV7|A Chain A, Crystal Structure Of The Aaa Domain Of Ftsh Length = 257

Iteration: 1
 Score =  108 bits (269), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 53/126 (42%), Positives = 80/126 (63%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           +F  A++ AP I+FIDEIDAVG +R     GG  E ++T+ ++L ++DGF+    + VI 
Sbjct: 96  MFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIA 155
Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + LDPAL+RPGR DR++   LPD + + +I  +H  R+ LA D++   +      
Sbjct: 156 ATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPG 215
Query: 121 LSGADI 126
            SGAD+
Sbjct: 216 FSGADL 221

>pdb|2R62|A Chain A, Crystal Structure Of Helicobacter Pylori Atp Dependent Protease, Ftsh Length = 268

Iteration: 1
 Score =  107 bits (266), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 60/133 (45%), Positives = 80/133 (60%), Gaps = 2/133 (1%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNS-GGEREIQRTMLELLNQLDGFDS-RGDVKV 58
           LF  A++ APSI+FIDEIDA+G  R       G  E ++T+ +LL ++DGF S    V V
Sbjct: 95  LFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSENAPVIV 154
Query: 59  IMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAK 118
           + ATNR E LDPAL+RPGR DR++    PD   +  I  +H   + LA DVNLQE+    
Sbjct: 155 LAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAKLT 214
Query: 119 DDLSGADIKAICT 131
             L+GAD+  I  
Sbjct: 215 AGLAGADLANIIN 227

>pdb|3HU2|A Chain A, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  103 bits (256), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 54/130 (41%), Positives = 81/130 (62%), Gaps = 3/130 (2%)
Query: 2   FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMA 61
           F  AE++AP+I+FIDE+DA+  KR  ++   ER   R + +LL  +DG   R  V V+ A
Sbjct: 290 FEEAEKNAPAIIFIDELDAIAPKREKTHGEVER---RIVSQLLTLMDGLKQRAHVIVMAA 346
Query: 62  TNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDL 121
           TNR  ++DPAL R GR DR+++  +PD   +  I  IHT  M LA+DV+L+++       
Sbjct: 347 TNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGH 406
Query: 122 SGADIKAICT 131
            GAD+ A+C+
Sbjct: 407 VGADLAALCS 416

>pdb|3HU3|A Chain A, Structure Of P97 N-D1 R155h Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  103 bits (256), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 54/130 (41%), Positives = 81/130 (62%), Gaps = 3/130 (2%)
Query: 2   FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMA 61
           F  AE++AP+I+FIDE+DA+  KR  ++   ER   R + +LL  +DG   R  V V+ A
Sbjct: 290 FEEAEKNAPAIIFIDELDAIAPKREKTHGEVER---RIVSQLLTLMDGLKQRAHVIVMAA 346
Query: 62  TNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDL 121
           TNR  ++DPAL R GR DR+++  +PD   +  I  IHT  M LA+DV+L+++       
Sbjct: 347 TNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGH 406
Query: 122 SGADIKAICT 131
            GAD+ A+C+
Sbjct: 407 VGADLAALCS 416

>pdb|3HU1|A Chain A, Structure Of P97 N-D1 R95g Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  103 bits (256), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 54/130 (41%), Positives = 81/130 (62%), Gaps = 3/130 (2%)
Query: 2   FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMA 61
           F  AE++AP+I+FIDE+DA+  KR  ++   ER   R + +LL  +DG   R  V V+ A
Sbjct: 290 FEEAEKNAPAIIFIDELDAIAPKREKTHGEVER---RIVSQLLTLMDGLKQRAHVIVMAA 346
Query: 62  TNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDL 121
           TNR  ++DPAL R GR DR+++  +PD   +  I  IHT  M LA+DV+L+++       
Sbjct: 347 TNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGH 406
Query: 122 SGADIKAICT 131
            GAD+ A+C+
Sbjct: 407 VGADLAALCS 416

>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 =  102 bits (255), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 54/130 (41%), Positives = 81/130 (62%), Gaps = 3/130 (2%)
Query: 2   FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMA 61
           F  AE++AP+I+FIDE+DA+  KR  ++   ER   R + +LL  +DG   R  V V+ A
Sbjct: 290 FEEAEKNAPAIIFIDELDAIAPKREKTHGEVER---RIVSQLLTLMDGLKQRAHVIVMAA 346
Query: 62  TNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDL 121
           TNR  ++DPAL R GR DR+++  +PD   +  I  IHT  M LA+DV+L+++       
Sbjct: 347 TNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGH 406
Query: 122 SGADIKAICT 131
            GAD+ A+C+
Sbjct: 407 VGADLAALCS 416

>pdb|3CF1|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Length = 806

Iteration: 1
 Score =  102 bits (255), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 54/130 (41%), Positives = 81/130 (62%), Gaps = 3/130 (2%)
Query: 2   FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMA 61
           F  AE++AP+I+FIDE+DA+  KR  ++   ER   R + +LL  +DG   R  V V+ A
Sbjct: 290 FEEAEKNAPAIIFIDELDAIAPKREKTHGEVER---RIVSQLLTLMDGLKQRAHVIVMAA 346
Query: 62  TNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDL 121
           TNR  ++DPAL R GR DR+++  +PD   +  I  IHT  M LA+DV+L+++       
Sbjct: 347 TNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGH 406
Query: 122 SGADIKAICT 131
            GAD+ A+C+
Sbjct: 407 VGADLAALCS 416

>pdb|1R7R|A Chain A, The Crystal Structure Of Murine P97VCP AT 3.6A Length = 816

Iteration: 1
 Score =  102 bits (255), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 54/130 (41%), Positives = 81/130 (62%), Gaps = 3/130 (2%)
Query: 2   FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMA 61
           F  AE++AP+I+FIDE+DA+  KR  ++   ER   R + +LL  +DG   R  V V+ A
Sbjct: 290 FEEAEKNAPAIIFIDELDAIAPKREKTHGEVER---RIVSQLLTLMDGLKQRAHVIVMAA 346
Query: 62  TNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDL 121
           TNR  ++DPAL R GR DR+++  +PD   +  I  IHT  M LA+DV+L+++       
Sbjct: 347 TNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGH 406
Query: 122 SGADIKAICT 131
            GAD+ A+C+
Sbjct: 407 VGADLAALCS 416

>pdb|3CF0|A Chain A, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP Length = 301

Iteration: 1
 Score = 96.7 bits (239), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 47/130 (36%), Positives = 80/130 (61%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           +F  A + AP ++F DE+D++   R  +   G     R + ++L ++DG  ++ +V +I 
Sbjct: 100 IFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIG 159
Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + +DPA++RPGR+D+ I  PLPDEK++  I   +  +  +A+DV+L+ L    + 
Sbjct: 160 ATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNG 219
Query: 121 LSGADIKAIC 130
            SGAD+  IC
Sbjct: 220 FSGADLTEIC 229

>pdb|2QZ4|A Chain A, Human Paraplegin, Aaa Domain In Complex With Adp Length = 262

Iteration: 1
 Score = 96.7 bits (239), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 56/133 (42%), Positives = 76/133 (57%), Gaps = 3/133 (2%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSG-GEREIQRTMLELLNQLDGFDSRGDVKVI 59
           LF+ A   AP IV+IDEIDAVG KR  + SG    E ++T+ +LL ++DG  +   V V+
Sbjct: 90  LFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTDHVIVL 149
Query: 60  MATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNL--QELIMA 117
            +TNR + LD AL+RPGR+DR +   LP  + +R IF  H   + L +      Q L   
Sbjct: 150 ASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAEL 209
Query: 118 KDDLSGADIKAIC 130
               SGADI  IC
Sbjct: 210 TPGFSGADIANIC 222

>pdb|2X8A|A Chain A, Human Nuclear Valosin Containing Protein Like (Nvl), C- Terminal Aaa-Atpase Domain Length = 274

Iteration: 1
 Score = 80.5 bits (197), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 46/134 (34%), Positives = 77/134 (57%), Gaps = 8/134 (5%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           +F+ A+  AP ++F DE+DA+  +R D  +G      R + +LL ++DG ++R  V ++ 
Sbjct: 95  VFQRAKNSAPCVIFFDEVDALCPRRSDRETGAS---VRVVNQLLTEMDGLEARQQVFIMA 151
Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMT---LAEDVNLQELI-- 115
           ATNR + +DPA++RPGR+D+ +   LP    +  I    T   T   L  DVNL+ +   
Sbjct: 152 ATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTITKNGTKPPLDADVNLEAIAGD 211
Query: 116 MAKDDLSGADIKAI 129
           +  D  +GAD+ A+
Sbjct: 212 LRCDCYTGADLSAL 225

>pdb|2ZAM|A Chain A, Crystal Structure Of Mouse Skd1VPS4B APO-Form Length = 444

Iteration: 1
 Score = 69.7 bits (169), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 49/132 (37%), Positives = 74/132 (56%), Gaps = 9/132 (6%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGD-VKVI 59
           LF++A E+ PSI+FIDEID++   R ++ S   R I+    E L Q+ G     D + V+
Sbjct: 219 LFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIK---TEFLVQMQGVGVDNDGILVL 275
Query: 60  MATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIH--TSRMTLAEDVNLQELIMA 117
            ATN    LD A+ R  R +++I  PLP+   +  +F +H  +++ +L E  + QEL   
Sbjct: 276 GATNIPWVLDSAIRR--RFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTE-ADFQELGRK 332
Query: 118 KDDLSGADIKAI 129
            D  SGADI  I
Sbjct: 333 TDGYSGADISII 344

>pdb|1XWI|A Chain A, Crystal Structure Of Vps4b Length = 322

Iteration: 1
 Score = 69.3 bits (168), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 49/133 (36%), Positives = 74/133 (55%), Gaps = 9/133 (6%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGD-VKVI 59
           LF++A E+ PSI+FIDEID++   R ++ S   R I+    E L Q+ G     D + V+
Sbjct: 97  LFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKT---EFLVQMQGVGVDNDGILVL 153
Query: 60  MATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIH--TSRMTLAEDVNLQELIMA 117
            ATN    LD A+ R  R +++I  PLP+   +  +F +H  T++ +L E  + +EL   
Sbjct: 154 GATNIPWVLDSAIRR--RFEKRIYIPLPEPHARAAMFKLHLGTTQNSLTE-ADFRELGRK 210
Query: 118 KDDLSGADIKAIC 130
            D  SGADI  I 
Sbjct: 211 TDGYSGADISIIV 223

>pdb|3D8B|A Chain A, Crystal Structure Of Human Fidgetin-Like Protein 1 In Complex With Adp Length = 357

Iteration: 1
 Score = 68.6 bits (166), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 43/134 (32%), Positives = 75/134 (55%), Gaps = 10/134 (7%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTM-LELLNQLDGFDSRGD--VK 57
           LF VA    P+++FIDEID++ ++R D    GE E  R +  E L QLDG  +  +  + 
Sbjct: 168 LFAVARCQQPAVIFIDEIDSLLSQRGD----GEHESSRRIKTEFLVQLDGATTSSEDRIL 223
Query: 58  VIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRI-FNIHTSRMTLAEDVNLQELIM 116
           V+ ATNR + +D A  R  R+ +++  PLP+   +++I  N+ +       +  +++++ 
Sbjct: 224 VVGATNRPQEIDEAARR--RLVKRLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQIVQ 281
Query: 117 AKDDLSGADIKAIC 130
             D  SGAD+  +C
Sbjct: 282 QSDAFSGADMTQLC 295

>pdb|2RKO|A Chain A, Crystal Structure Of The Vps4p-Dimer Length = 331

Iteration: 1
 Score = 63.9 bits (154), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 49/133 (36%), Positives = 72/133 (54%), Gaps = 9/133 (6%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LF +A E+ PSI+FIDE+DA+   R +  S   R I+  +L  +N + G DS+G V V+ 
Sbjct: 111 LFAMARENKPSIIFIDEVDALTGTRGEGESEASRRIKTELLVQMNGV-GNDSQG-VLVLG 168
Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIH---TSRMTLAEDVNLQELIMA 117
           ATN    LD A+ R  R +R+I  PLPD   +  +F I+   T  +   ED   + L   
Sbjct: 169 ATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPCVLTKED--YRTLGAM 224
Query: 118 KDDLSGADIKAIC 130
            +  SG+DI  + 
Sbjct: 225 TEGYSGSDIAVVV 237

>pdb|2QP9|X Chain X, Crystal Structure Of S.Cerevisiae Vps4 Length = 355

Iteration: 1
 Score = 63.5 bits (153), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 48/133 (36%), Positives = 72/133 (54%), Gaps = 9/133 (6%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LF +A E+ PSI+FID++DA+   R +  S   R I+  +L  +N + G DS+G V V+ 
Sbjct: 135 LFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGV-GNDSQG-VLVLG 192
Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIH---TSRMTLAEDVNLQELIMA 117
           ATN    LD A+ R  R +R+I  PLPD   +  +F I+   T  +   ED   + L   
Sbjct: 193 ATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPSVLTKED--YRTLGAM 248
Query: 118 KDDLSGADIKAIC 130
            +  SG+DI  + 
Sbjct: 249 TEGYSGSDIAVVV 261

>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 = 6e-11,   Method: Compositional matrix adjust.
 Identities = 48/133 (36%), Positives = 72/133 (54%), Gaps = 9/133 (6%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LF +A E+ PSI+FID++DA+   R +  S   R I+  +L  +N + G DS+G V V+ 
Sbjct: 102 LFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGV-GNDSQG-VLVLG 159
Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIH---TSRMTLAEDVNLQELIMA 117
           ATN    LD A+ R  R +R+I  PLPD   +  +F I+   T  +   ED   + L   
Sbjct: 160 ATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPCVLTKED--YRTLGAM 215
Query: 118 KDDLSGADIKAIC 130
            +  SG+DI  + 
Sbjct: 216 TEGYSGSDIAVVV 228

>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 = 6e-11,   Method: Compositional matrix adjust.
 Identities = 48/133 (36%), Positives = 72/133 (54%), Gaps = 9/133 (6%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LF +A E+ PSI+FID++DA+   R +  S   R I+  +L  +N + G DS+G V V+ 
Sbjct: 120 LFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGV-GNDSQG-VLVLG 177
Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIH---TSRMTLAEDVNLQELIMA 117
           ATN    LD A+ R  R +R+I  PLPD   +  +F I+   T  +   ED   + L   
Sbjct: 178 ATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPCVLTKED--YRTLGAM 233
Query: 118 KDDLSGADIKAIC 130
            +  SG+DI  + 
Sbjct: 234 TEGYSGSDIAVVV 246

>pdb|3VFD|A Chain A, Human Spastin Aaa Domain Length = 389

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 48/137 (35%), Positives = 74/137 (54%), Gaps = 16/137 (11%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTM-LELLNQLDGFDSRGD--VK 57
           LF VA E  PSI+FID++D++  +R +    GE +  R +  E L + DG  S GD  V 
Sbjct: 199 LFAVARELQPSIIFIDQVDSLLCERRE----GEHDASRRLKTEFLIEFDGVQSAGDDRVL 254
Query: 58  VIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNI----HTSRMTLAEDVNLQE 113
           V+ ATNR + LD A++R  R  +++   LP+E+T+  +         S +T  E   L +
Sbjct: 255 VMGATNRPQELDEAVLR--RFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKE---LAQ 309
Query: 114 LIMAKDDLSGADIKAIC 130
           L    D  SG+D+ A+ 
Sbjct: 310 LARMTDGYSGSDLTALA 326

>pdb|3B9P|A Chain A, Spastin Length = 297

Iteration: 1
 Score = 56.6 bits (135), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 45/134 (33%), Positives = 67/134 (50%), Gaps = 9/134 (6%)
Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGD---VK 57
           LF VA    PSI+FIDE+D++ ++R  S     R   R   E L + DG     D   + 
Sbjct: 105 LFAVARHMQPSIIFIDEVDSLLSERSSSEHEASR---RLKTEFLVEFDGLPGNPDGDRIV 161
Query: 58  VIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVN-LQELIM 116
           V+ ATNR + LD A +R  R  +++   LPDE+T+  + N    +     D   L+ L  
Sbjct: 162 VLAATNRPQELDEAALR--RFTKRVYVSLPDEQTRELLLNRLLQKQGSPLDTEALRRLAK 219
Query: 117 AKDDLSGADIKAIC 130
             D  SG+D+ A+ 
Sbjct: 220 ITDGYSGSDLTALA 233

>pdb|2DVW|B Chain B, Structure Of The Oncoprotein Gankyrin In Complex With S6 Atpase Of The 26s Proteasome Length = 83

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 20/43 (46%), Positives = 31/43 (72%)
Query: 88  DEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAIC 130
           D + KR IF+  TS+M L+E+V+L++ +   D +SGADI +IC
Sbjct: 2   DRRQKRLIFSTITSKMNLSEEVDLEDYVARPDKISGADINSIC 44

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	131
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	3e-84
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	1e-49
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	4e-47
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	5e-45
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	1e-33
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	4e-43
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	5e-40
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	1e-37
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	1e-37
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	1e-37
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	2e-37
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	6e-37
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	7e-35
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	1e-34
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	1e-34
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	2e-34
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	8e-34
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	5e-33
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	1e-32
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	2e-32
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	7e-32
2krk_A	86	26S protease regulatory subunit 8; structural geno	2e-21
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	3e-21
3kw6_A	78	26S protease regulatory subunit 8; structural geno	2e-19
3aji_B	83	S6C, proteasome (prosome, macropain) 26S subunit,	1e-16
2dzn_B	82	26S protease regulatory subunit 6B homolog; ankyri	1e-14
3vlf_B	88	26S protease regulatory subunit 7 homolog; heat re	6e-06

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii} Length = 285

 Score =  247 bits (632), Expect = 3e-84
 Identities = 77/131 (58%), Positives = 104/131 (79%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           +F++A+E APSI+FIDEIDA+  KR D+ +GG+RE+QRT+++LL ++DGFD+RGDVK+I 
Sbjct: 102 IFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIG 161

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + LDPA++RPGR DR IE P PDEK +  I  IHT +M LAEDVNL+E+    + 
Sbjct: 162 ATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEG 221

Query: 121 LSGADIKAICT 131
             GA++KAICT
Sbjct: 222 CVGAELKAICT 232

>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 =  163 bits (415), Expect = 1e-49
 Identities = 54/131 (41%), Positives = 81/131 (61%), Gaps = 3/131 (2%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
            F  AE++AP+I+FIDE+DA+  KR  ++   ER   R + +LL  +DG   R  V V+ 
Sbjct: 289 AFEEAEKNAPAIIFIDELDAIAPKREKTHGEVER---RIVSQLLTLMDGLKQRAHVIVMA 345

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR  ++DPAL R GR DR+++  +PD   +  I  IHT  M LA+DV+L+++      
Sbjct: 346 ATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHG 405

Query: 121 LSGADIKAICT 131
             GAD+ A+C+
Sbjct: 406 HVGADLAALCS 416

>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 =  152 bits (387), Expect = 4e-47
 Identities = 47/130 (36%), Positives = 80/130 (61%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           +F  A + AP ++F DE+D++   R  +   G     R + ++L ++DG  ++ +V +I 
Sbjct: 100 IFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIG 159

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + +DPA++RPGR+D+ I  PLPDEK++  I   +  +  +A+DV+L+ L    + 
Sbjct: 160 ATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNG 219

Query: 121 LSGADIKAIC 130
            SGAD+  IC
Sbjct: 220 FSGADLTEIC 229

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens} Length = 274

 Score =  141 bits (358), Expect = 4e-43
 Identities = 45/135 (33%), Positives = 78/135 (57%), Gaps = 8/135 (5%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           +F+ A+  AP ++F DE+DA+  +R D  +G      R + +LL ++DG ++R  V ++ 
Sbjct: 95  VFQRAKNSAPCVIFFDEVDALCPRRSDRETGAS---VRVVNQLLTEMDGLEARQQVFIMA 151

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHT---SRMTLAEDVNLQEL--I 115
           ATNR + +DPA++RPGR+D+ +   LP    +  I    T   ++  L  DVNL+ +   
Sbjct: 152 ATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTITKNGTKPPLDADVNLEAIAGD 211

Query: 116 MAKDDLSGADIKAIC 130
           +  D  +GAD+ A+ 
Sbjct: 212 LRCDCYTGADLSALV 226

>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 =  133 bits (337), Expect = 5e-40
 Identities = 56/135 (41%), Positives = 77/135 (57%), Gaps = 7/135 (5%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGG---EREIQRTMLELLNQLDGFDSRGDVK 57
           LF+ A   AP IV+IDEIDAVG KR  + SG    E E  +T+ +LL ++DG  +   V 
Sbjct: 90  LFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEE--QTLNQLLVEMDGMGTTDHVI 147

Query: 58  VIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMA 117
           V+ +TNR + LD AL+RPGR+DR +   LP  + +R IF  H   + L +        +A
Sbjct: 148 VLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLA 207

Query: 118 KDD--LSGADIKAIC 130
           +     SGADI  IC
Sbjct: 208 ELTPGFSGADIANIC 222

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A Length = 293

 Score =  128 bits (323), Expect = 1e-37
 Identities = 26/144 (18%), Positives = 56/144 (38%), Gaps = 20/144 (13%)

Query: 1   LFRVAEE----HAPSIVFIDEIDAVGTKRYDSNSGG--EREIQRTMLELLN-----QLDG 49
            +R A E         +FI+++DA   +   +       + +  T++ + +     QL G
Sbjct: 87  RYREAAEIIRKGNMCCLFINDLDAGAGRMGGTTQYTVNNQMVNATLMNIADNPTNVQLPG 146

Query: 50  FD---SRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLA 106
                    V +I+  N   TL   LIR GR+++    P  +++          + +   
Sbjct: 147 MYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEKFYWAPTREDRIG------VCTGIFRT 200

Query: 107 EDVNLQELIMAKDDLSGADIKAIC 130
           ++V  ++++   D+  G  I    
Sbjct: 201 DNVPAEDVVKIVDNFPGQSIDFFG 224

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20 Length = 278

 Score =  127 bits (321), Expect = 1e-37
 Identities = 61/126 (48%), Positives = 78/126 (61%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LF  A+ HAP IVFIDEIDAVG KR     GG  E ++T+ +LL ++DGF+    + V+ 
Sbjct: 124 LFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMA 183

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + LDPAL+RPGR DR+I    PD K + +I  IH     LAEDV+L  L      
Sbjct: 184 ATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPG 243

Query: 121 LSGADI 126
             GAD+
Sbjct: 244 FVGADL 249

>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 =  127 bits (320), Expect = 1e-37
 Identities = 61/126 (48%), Positives = 78/126 (61%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LF  A+ HAP IVFIDEIDAVG KR     GG  E ++T+ +LL ++DGF+    + V+ 
Sbjct: 100 LFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMA 159

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + LDPAL+RPGR DR+I    PD K + +I  IH     LAEDV+L  L      
Sbjct: 160 ATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPG 219

Query: 121 LSGADI 126
             GAD+
Sbjct: 220 FVGADL 225

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20 Length = 257

 Score =  127 bits (320), Expect = 2e-37
 Identities = 53/126 (42%), Positives = 80/126 (63%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           +F  A++ AP I+FIDEIDAVG +R     GG  E ++T+ ++L ++DGF+    + VI 
Sbjct: 96  MFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIA 155

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + LDPAL+RPGR DR++   LPD + + +I  +H  R+ LA D++   +      
Sbjct: 156 ATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPG 215

Query: 121 LSGADI 126
            SGAD+
Sbjct: 216 FSGADL 221

>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 =  125 bits (317), Expect = 6e-37
 Identities = 60/130 (46%), Positives = 79/130 (60%), Gaps = 6/130 (4%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGG---EREIQRTMLELLNQLDGFDSRGD-V 56
           LF  A++ APSI+FIDEIDA+G  R          ERE  +T+ +LL ++DGF S    V
Sbjct: 95  LFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDERE--QTLNQLLAEMDGFGSENAPV 152

Query: 57  KVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIM 116
            V+ ATNR E LDPAL+RPGR DR++    PD   +  I  +H   + LA DVNLQE+  
Sbjct: 153 IVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAK 212

Query: 117 AKDDLSGADI 126
               L+GAD+
Sbjct: 213 LTAGLAGADL 222

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens} Length = 322

 Score =  121 bits (306), Expect = 7e-35
 Identities = 46/132 (34%), Positives = 69/132 (52%), Gaps = 7/132 (5%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGD-VKVI 59
           LF++A E+ PSI+FIDEID++   R ++ S   R   R   E L Q+ G     D + V+
Sbjct: 97  LFQLARENKPSIIFIDEIDSLCGSRSENESEAAR---RIKTEFLVQMQGVGVDNDGILVL 153

Query: 60  MATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAK 118
            ATN    LD A+ R  R +++I  PLP+   +  +F +H      +  + + +EL    
Sbjct: 154 GATNIPWVLDSAIRR--RFEKRIYIPLPEPHARAAMFKLHLGTTQNSLTEADFRELGRKT 211

Query: 119 DDLSGADIKAIC 130
           D  SGADI  I 
Sbjct: 212 DGYSGADISIIV 223

>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 =  123 bits (311), Expect = 1e-34
 Identities = 65/132 (49%), Positives = 79/132 (59%), Gaps = 12/132 (9%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGG--EREIQRTMLELLNQL----DGFDSRG 54
           LF  A+ HAP IVFIDEIDAVG  R     GG  ERE      + LNQL    DGFDS+ 
Sbjct: 100 LFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDERE------QTLNQLLVEMDGFDSKE 153

Query: 55  DVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQEL 114
            + V+ ATNR + LDPAL+RPGR D+KI    PD   +++I  IHT    LAEDVNL+ +
Sbjct: 154 GIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDVNLEII 213

Query: 115 IMAKDDLSGADI 126
                   GAD+
Sbjct: 214 AKRTPGFVGADL 225

>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 =  120 bits (304), Expect = 1e-34
 Identities = 44/132 (33%), Positives = 67/132 (50%), Gaps = 7/132 (5%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGD-VKVI 59
           LF +A E+ PSI+FID++DA+   R +  S   R   R   ELL Q++G  +    V V+
Sbjct: 102 LFAMARENKPSIIFIDQVDALTGTRGEGESEASR---RIKTELLVQMNGVGNDSQGVLVL 158

Query: 60  MATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRM-TLAEDVNLQELIMAK 118
            ATN    LD A+ R  R +R+I  PLPD   +  +F I+      +    + + L    
Sbjct: 159 GATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMT 216

Query: 119 DDLSGADIKAIC 130
           +  SG+DI  + 
Sbjct: 217 EGYSGSDIAVVV 228

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus} Length = 499

 Score =  123 bits (311), Expect = 2e-34
 Identities = 63/128 (49%), Positives = 79/128 (61%), Gaps = 4/128 (3%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGG--EREIQRTMLELLNQLDGFDSRGDVKV 58
           LF  A+ HAP IVFIDEIDAVG KR     GG  ERE  +T+ +LL ++DGF+    + V
Sbjct: 115 LFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDERE--QTLNQLLVEMDGFEKDTAIVV 172

Query: 59  IMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAK 118
           + ATNR + LDPAL+RPGR DR+I    PD K + +I  IH     LAEDV+L  L    
Sbjct: 173 MAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRT 232

Query: 119 DDLSGADI 126
               GAD+
Sbjct: 233 PGFVGADL 240

>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 =  119 bits (300), Expect = 8e-34
 Identities = 44/132 (33%), Positives = 68/132 (51%), Gaps = 7/132 (5%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGD-VKVI 59
           LF +A E+ PSI+FID++DA+   R +  S   R   R   ELL Q++G  +    V V+
Sbjct: 135 LFAMARENKPSIIFIDQVDALTGTRGEGESEASR---RIKTELLVQMNGVGNDSQGVLVL 191

Query: 60  MATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRM-TLAEDVNLQELIMAK 118
            ATN    LD A+ R  R +R+I  PLPD   +  +F I+     ++    + + L    
Sbjct: 192 GATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPSVLTKEDYRTLGAMT 249

Query: 119 DDLSGADIKAIC 130
           +  SG+DI  + 
Sbjct: 250 EGYSGSDIAVVV 261

>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 =  118 bits (298), Expect = 5e-33
 Identities = 47/132 (35%), Positives = 69/132 (52%), Gaps = 7/132 (5%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGD-VKVI 59
           LF++A E+ PSI+FIDEID++   R ++ S   R   R   E L Q+ G     D + V+
Sbjct: 219 LFQLARENKPSIIFIDEIDSLCGSRSENESEAAR---RIKTEFLVQMQGVGVDNDGILVL 275

Query: 60  MATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAK 118
            ATN    LD A+ R  R +++I  PLP+   +  +F +H      +  + + QEL    
Sbjct: 276 GATNIPWVLDSAIRR--RFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRKT 333

Query: 119 DDLSGADIKAIC 130
           D  SGADI  I 
Sbjct: 334 DGYSGADISIIV 345

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster} Length = 297

 Score =  115 bits (290), Expect = 1e-32
 Identities = 44/134 (32%), Positives = 67/134 (50%), Gaps = 9/134 (6%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGD---VK 57
           LF VA    PSI+FIDE+D++ ++R  S     R   R   E L + DG     D   + 
Sbjct: 105 LFAVARHMQPSIIFIDEVDSLLSERSSSEHEASR---RLKTEFLVEFDGLPGNPDGDRIV 161

Query: 58  VIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIM 116
           V+ ATNR + LD A +R  R  +++   LPDE+T+  + N    +     +   L+ L  
Sbjct: 162 VLAATNRPQELDEAALR--RFTKRVYVSLPDEQTRELLLNRLLQKQGSPLDTEALRRLAK 219

Query: 117 AKDDLSGADIKAIC 130
             D  SG+D+ A+ 
Sbjct: 220 ITDGYSGSDLTALA 233

>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 =  116 bits (291), Expect = 2e-32
 Identities = 42/134 (31%), Positives = 73/134 (54%), Gaps = 10/134 (7%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTML-ELLNQLDGFDSRGD--VK 57
           LF VA    P+++FIDEID++ ++R      GE E  R +  E L QLDG  +  +  + 
Sbjct: 168 LFAVARCQQPAVIFIDEIDSLLSQR----GDGEHESSRRIKTEFLVQLDGATTSSEDRIL 223

Query: 58  VIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSR-MTLAEDVNLQELIM 116
           V+ ATNR + +D A  R  R+ +++  PLP+   +++I     S+      +  +++++ 
Sbjct: 224 VVGATNRPQEIDEAARR--RLVKRLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQIVQ 281

Query: 117 AKDDLSGADIKAIC 130
             D  SGAD+  +C
Sbjct: 282 QSDAFSGADMTQLC 295

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens} Length = 389

 Score =  114 bits (288), Expect = 7e-32
 Identities = 44/133 (33%), Positives = 69/133 (51%), Gaps = 8/133 (6%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGD--VKV 58
           LF VA E  PSI+FID++D++  +R +      R   R   E L + DG  S GD  V V
Sbjct: 199 LFAVARELQPSIIFIDQVDSLLCERREGEHDASR---RLKTEFLIEFDGVQSAGDDRVLV 255

Query: 59  IMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRM-TLAEDVNLQELIMA 117
           + ATNR + LD A++R  R  +++   LP+E+T+  +      +  +      L +L   
Sbjct: 256 MGATNRPQELDEAVLR--RFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQLARM 313

Query: 118 KDDLSGADIKAIC 130
            D  SG+D+ A+ 
Sbjct: 314 TDGYSGSDLTALA 326

>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast structural genomics consortium (NESG), target HR3102A, PSI-2; NMR {Homo sapiens} Length = 86

 Score = 80.6 bits (200), Expect = 2e-21
 Identities = 15/50 (30%), Positives = 27/50 (54%)

Query: 82  IEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT 131
                P+E+ +  I  IH+ +M L   +NL+++       SGA++K +CT
Sbjct: 6   HHHSHPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCT 55

>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 = 85.2 bits (211), Expect = 3e-21
 Identities = 23/133 (17%), Positives = 43/133 (32%), Gaps = 10/133 (7%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGD-VKVI 59
           +F  A +   S V +D+I+ +          G R     +  LL  L     +G  + +I
Sbjct: 116 IFDDAYKSQLSCVVVDDIERLLDYV----PIGPRFSNLVLQALLVLLKKAPPQGRKLLII 171

Query: 60  MATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELI-MAK 118
             T+R + L   +         I   +P+  T  ++           +D     +    K
Sbjct: 172 GTTSRKDVLQ-EMEMLNAFSTTIH--VPNIATGEQLLEALELLGNF-KDKERTTIAQQVK 227

Query: 119 DDLSGADIKAICT 131
                  IK +  
Sbjct: 228 GKKVWIGIKKLLM 240

>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 = 75.6 bits (187), Expect = 2e-19
 Identities = 16/47 (34%), Positives = 28/47 (59%)

Query: 85  PLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT 131
           P P+E+ +  I  IH+ +M L   +NL+++       SGA++K +CT
Sbjct: 1   PPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCT 47

>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 = 68.5 bits (168), Expect = 1e-16
 Identities = 20/44 (45%), Positives = 31/44 (70%)

Query: 88  DEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT 131
           D + KR IF+  TS+M L+E+V+L++ +   D +SGADI +IC 
Sbjct: 2   DRRQKRLIFSTITSKMNLSEEVDLEDYVARPDKISGADINSICQ 45

>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 = 63.1 bits (154), Expect = 1e-14
 Identities = 18/40 (45%), Positives = 24/40 (60%)

Query: 92  KRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT 131
           +R IF    S+M+LA + +L  LI+  D LSGA I AI  
Sbjct: 3   RRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQ 42

>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 = 40.6 bits (96), Expect = 6e-06
 Identities = 10/44 (22%), Positives = 25/44 (56%)

Query: 88  DEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT 131
           D + +  IF IH+  M++   +  + +     + +GA+++++CT
Sbjct: 2   DLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCT 45

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	131
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	100.0
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	100.0
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	100.0
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	100.0
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	100.0
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	100.0
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	100.0
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.97
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.93
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.93
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	99.93
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.92
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	99.91
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.91
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.9
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.9
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.89
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.89
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.89
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.89
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.89
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.88
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.88
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.85
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.82
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.82
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.8
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.79
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.76
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.51
3kw6_A	78	26S protease regulatory subunit 8; structural geno	99.34
2krk_A	86	26S protease regulatory subunit 8; structural geno	99.28
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	99.21
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.16
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	99.08
3vlf_B	88	26S protease regulatory subunit 7 homolog; heat re	99.06
3aji_B	83	S6C, proteasome (prosome, macropain) 26S subunit,	99.03
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	98.97
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	98.96
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.94
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.93
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	98.92
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	98.92
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	98.8
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.8
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	98.8
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	98.74
3bos_A	242	Putative DNA replication factor; P-loop containing	98.74
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	98.74
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.73
2dzn_B	82	26S protease regulatory subunit 6B homolog; ankyri	98.71
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	98.7
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	98.63
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	98.63
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	98.59
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	98.55
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	98.53
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	98.5
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	98.5
2chq_A	319	Replication factor C small subunit; DNA-binding pr	98.48
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	98.44
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.42
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	98.41
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.4
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	98.38
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	98.38
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.38
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	98.36
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.36
2r44_A	331	Uncharacterized protein; putative ATPase, structur	98.35
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	98.34
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	98.33
3pvs_A	447	Replication-associated recombination protein A; ma	98.3
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	98.29
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	98.26
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	98.16
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	98.15
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	98.15
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	98.09
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	98.02
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	97.96
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	97.95
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	97.91
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	97.74
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	97.7
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	97.65
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	97.16
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	97.16
2fna_A	357	Conserved hypothetical protein; structural genomic	97.12
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	96.93
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	96.91
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	96.63
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	96.63
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	95.83
3co5_A	143	Putative two-component system transcriptional RES	95.31
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	94.85
3f8t_A	506	Predicted ATPase involved in replication control,	94.52
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	94.04
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	93.73
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	93.66
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	92.88
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	92.7
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	92.19
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	92.06
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	91.76
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	89.01
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	88.82
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	88.53
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	88.1
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	87.92
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	87.21
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	82.83

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.4e-36  Score=223.43  Aligned_cols=131  Identities=55%  Similarity=0.985  Sum_probs=123.2

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|+.++||||||||+|++++++...+.........+++++|+.||++...++|+||||||+|+.||+|++||||||+
T Consensus       233 lF~~Ar~~aP~IIFiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~V~vIaATNrpd~LDpAllRpGRfD~  312 (405)
T 4b4t_J          233 LFVMAREHAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFETSKNIKIIMATNRLDILDPALLRPGRIDR  312 (405)
T ss_dssp             HHHHHHHTCSEEEEEESSSCCTTSCSCSSSGGGGHHHHHHHHHHHHHHTTTCCCCEEEEEEESCSSSSCHHHHSTTSSCC
T ss_pred             HHHHHHHhCCceEeeecchhhccCCCCCCCCCcHHHHHHHHHHHHhhhccCCCCCeEEEeccCChhhCCHhHcCCCcCce
Confidence            59999999999999999999999987666666667778999999999999888999999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .|++++|+.++|.+||+.++++.++..++|+..+|..|+||||+||+.+|+
T Consensus       313 ~I~i~lPd~~~R~~Il~~~~~~~~l~~dvdl~~lA~~t~G~SGADi~~l~~  363 (405)
T 4b4t_J          313 KIEFPPPSVAARAEILRIHSRKMNLTRGINLRKVAEKMNGCSGADVKGVCT  363 (405)
T ss_dssp             EEECCCCCHHHHHHHHHHHHTTSBCCSSCCHHHHHHHCCSCCHHHHHHHHH
T ss_pred             EEEcCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHHHCCCCCHHHHHHHHH
Confidence            999999999999999999999999888999999999999999999999984

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=8.1e-36  Score=220.27  Aligned_cols=131  Identities=80%  Similarity=1.202  Sum_probs=122.8

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|..|++++||||||||+|+++.+|...+...+.....++.++|+.++++...++|+||+|||+|+.||+|++||||||+
T Consensus       267 lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~LL~~lDg~~~~~~ViVIaATNrpd~LDpALlRpGRfD~  346 (437)
T 4b4t_I          267 IFKVAGENAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDDRGDVKVIMATNKIETLDPALIRPGRIDR  346 (437)
T ss_dssp             HHHHHHHTCSEEEEEEEESSSSCCCSCSSCSSCCHHHHHHHHHHHHHHHCCCSSSEEEEEEESCSTTCCTTSSCTTTEEE
T ss_pred             HHHHHHhcCCcEEEEehhhhhcccCCCCCCCccHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCChhhcCHHHhcCCceeE
Confidence            58999999999999999999999997666666666778999999999999888999999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .|++++|+.++|.+||+.++++..+..++|+..+|..|+||||+||+.+|+
T Consensus       347 ~I~v~lPd~~~R~~Il~~~l~~~~l~~dvdl~~LA~~T~GfSGADI~~l~~  397 (437)
T 4b4t_I          347 KILFENPDLSTKKKILGIHTSKMNLSEDVNLETLVTTKDDLSGADIQAMCT  397 (437)
T ss_dssp             EECCCCCCHHHHHHHHHHHHTTSCBCSCCCHHHHHHHCCSCCHHHHHHHHH
T ss_pred             EEEcCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHHhCCCCCHHHHHHHHH
Confidence            999999999999999999999999888999999999999999999999984

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=4.1e-35  Score=218.01  Aligned_cols=131  Identities=49%  Similarity=0.913  Sum_probs=122.6

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|..|+.++||||||||+|+++.+|...+.........+++++|..|+++...++|+||+|||+|+.||+|++||||||+
T Consensus       266 ~F~~A~~~~P~IifiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~vivI~ATNrp~~LDpAllRpGRfD~  345 (437)
T 4b4t_L          266 MFAYAKEHEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFDNLGQTKIIMATNRPDTLDPALLRPGRLDR  345 (437)
T ss_dssp             HHHHHHHSCSEEEEEECCCSSSCCCSSSCCSSTTHHHHHHHHHHHHHHSSSCTTSSEEEEEESSTTSSCTTTTSTTSEEE
T ss_pred             HHHHHHhcCCceeeeecccccccccccCCCCcchHHHHHHHHHHHHhhcccCCCCeEEEEecCCchhhCHHHhCCCccce
Confidence            48999999999999999999999987666666666778899999999999888999999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .|++++|+.++|.+||+.++++.....++|+..+|..|+||||+||+.+|+
T Consensus       346 ~I~i~lPd~~~R~~Il~~~~~~~~~~~d~dl~~lA~~t~G~sGADi~~l~~  396 (437)
T 4b4t_L          346 KVEIPLPNEAGRLEIFKIHTAKVKKTGEFDFEAAVKMSDGFNGADIRNCAT  396 (437)
T ss_dssp             EECCCCCCHHHHHHHHHHHHHTSCBCSCCCHHHHHHTCCSCCHHHHHHHHH
T ss_pred             eeecCCcCHHHHHHHHHHHhcCCCCCcccCHHHHHHhCCCCCHHHHHHHHH
Confidence            999999999999999999999998888999999999999999999999984

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=2.4e-35  Score=219.13  Aligned_cols=131  Identities=58%  Similarity=0.990  Sum_probs=122.1

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|..|++++||||||||+|+++.+|...+.........++..+|+.|+++...++|+||||||+|+.||+|++||||||+
T Consensus       266 lF~~A~~~aP~IifiDEiDal~~~R~~~~~~~~~~~~~~~~~lL~~ldg~~~~~~ViVIaaTNrp~~LD~AllRpGRfD~  345 (434)
T 4b4t_M          266 AFALAKEKAPTIIFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQLDGFSSDDRVKVLAATNRVDVLDPALLRSGRLDR  345 (434)
T ss_dssp             HHHHHHHHCSEEEEEECTHHHHCCCSSGGGGTTHHHHHHHHHHHHHHTTSCSSCSSEEEEECSSCCCCCTTTCSTTSEEE
T ss_pred             HHHHHHhcCCeEEeecchhhhhhccCCCCCCCchHHHHHHHHHHHHhhccCCCCCEEEEEeCCCchhcCHhHhcCCceeE
Confidence            58999999999999999999999986655555556778899999999999888999999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .|++++|+.++|.+||+.++++.....++|+..+|..|+||||+||+.+|+
T Consensus       346 ~I~i~lPd~~~R~~Il~~~~~~~~~~~dvdl~~lA~~t~G~sGADi~~l~~  396 (434)
T 4b4t_M          346 KIEFPLPSEDSRAQILQIHSRKMTTDDDINWQELARSTDEFNGAQLKAVTV  396 (434)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHHSCBCSCCCHHHHHHHCSSCCHHHHHHHHH
T ss_pred             EEEeCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHHhCCCCCHHHHHHHHH
Confidence            999999999999999999999998888999999999999999999999984

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=9e-35  Score=216.40  Aligned_cols=131  Identities=50%  Similarity=0.913  Sum_probs=123.3

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|..|+.++||||||||+|+++.+|...+.........++.++|..|+++...++|+||+|||+|+.||++++||||||+
T Consensus       294 lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~ViVIaATNrpd~LDpALlRpGRFD~  373 (467)
T 4b4t_H          294 LFEMARTKKACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDPRGNIKVMFATNRPNTLDPALLRPGRIDR  373 (467)
T ss_dssp             HHHHHHHTCSEEEEEECCTTTSBCCSSSSCGGGGHHHHHHHHHHHHHHSSCCTTTEEEEEECSCTTSBCHHHHSTTTCCE
T ss_pred             HHHHHHhcCCceEeecccccccccccCcCCCccHHHHHHHHHHHHHhhccCCCCcEEEEeCCCCcccCChhhhccccccE
Confidence            58999999999999999999999997766666667778999999999999888999999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .|++++|+.++|.+||+.++++..+..++++..+|+.|+||||+||+.+|+
T Consensus       374 ~I~i~lPd~~~R~~Ilk~~l~~~~l~~dvdl~~LA~~T~GfSGADI~~l~~  424 (467)
T 4b4t_H          374 KVEFSLPDLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCT  424 (467)
T ss_dssp             EECCCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHHHCCSCCHHHHHHHHH
T ss_pred             EEEeCCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHCCCCCHHHHHHHHH
Confidence            999999999999999999999999888999999999999999999999984

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=2e-34  Score=213.99  Aligned_cols=131  Identities=58%  Similarity=0.978  Sum_probs=121.6

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|..|+.++||||||||+|+++.++.............+++++|+.|+++....+|+||||||+|+.||++++||||||+
T Consensus       257 lF~~A~~~aP~IifiDEiD~i~~~R~~~~~~~~~~~~r~l~~lL~~ldg~~~~~~v~vI~aTN~~~~LD~AllRpGRfd~  336 (428)
T 4b4t_K          257 VFRLARENAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQSTNVKVIMATNRADTLDPALLRPGRLDR  336 (428)
T ss_dssp             HHHHHHHTCSEEEEEECTHHHHCSCSSSCSCCCCHHHHHHHHHHHHHHHSCSSCSEEEEEEESCSSSCCHHHHSSSSEEE
T ss_pred             HHHHHHHcCCCeeechhhhhhhccccCCCCCCChHHHHHHHHHHHHhhCCCCCCCEEEEEecCChhhcChhhhcCCcceE
Confidence            58999999999999999999999987665555556678999999999999888999999999999999999999999999


Q ss_pred             EEEeC-CCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFP-LPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~-~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .|++| +|+.++|..||+.++++.+...++|+..+|..|+||||+||+.+|+
T Consensus       337 ~I~~p~lPd~~~R~~Il~~~~~~~~l~~~~dl~~lA~~t~G~sgadi~~l~~  388 (428)
T 4b4t_K          337 KIEFPSLRDRRERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQ  388 (428)
T ss_dssp             EEECCSSCCHHHHHHHHHHHHHSSCBCTTCCHHHHHHHTTTCCHHHHHHHHH
T ss_pred             EEEcCCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHHHCCCCCHHHHHHHHH
Confidence            99996 8999999999999999999888999999999999999999999984

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=100.00  E-value=5e-34  Score=224.51  Aligned_cols=131  Identities=36%  Similarity=0.674  Sum_probs=89.0

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|++++||||||||+|+++.+|+...........++++++|.+|+++....+|+||||||+|+.||++++||||||+
T Consensus       562 lF~~Ar~~~P~IifiDEiDsl~~~R~~~~~~~~~~~~rv~~~lL~~mdg~~~~~~V~vi~aTN~p~~lD~AllRpgRfd~  641 (806)
T 3cf2_A          562 IFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQ  641 (806)
T ss_dssp             HHHHHHTTCSEEEECSCGGGCC--------------CHHHHHHHHHHHSSCSSSSEEEECC-CCSSSSCHHHHSTTTSCC
T ss_pred             HHHHHHHcCCceeechhhhHHhhccCCCCCCCchHHHHHHHHHHHHHhCCCCCCCEEEEEeCCCchhCCHhHcCCCcceE
Confidence            59999999999999999999999986543333334457899999999999888899999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      +|++++|+.++|.+||+.++++.++..++|+..+|+.|+||||+||+.+|+
T Consensus       642 ~i~v~lPd~~~R~~il~~~l~~~~~~~~~dl~~la~~t~g~SGadi~~l~~  692 (806)
T 3cf2_A          642 LIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQ  692 (806)
T ss_dssp             EEEC-----CHHHHTTTTTSSCC--CCC----------------CHHHHHH
T ss_pred             EEEECCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHHhCCCCCHHHHHHHHH
Confidence            999999999999999999999998888999999999999999999999984

>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=3.3e-30  Score=202.95  Aligned_cols=128  Identities=41%  Similarity=0.694  Sum_probs=117.1

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|++++||||||||+|.+++++++.+...   ...++++++..|+++...++|+||+|||+++.||++++|||||++
T Consensus       289 lF~~A~~~~PsIIfIDEiDal~~~r~~~~~~~---~~riv~~LL~~mdg~~~~~~V~VIaaTN~~d~LD~ALrR~GRFd~  365 (806)
T 3cf2_A          289 AFEEAEKNAPAIIFIDELDAIAPKREKTHGEV---ERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDR  365 (806)
T ss_dssp             HHHHHTTSCSEEEEEESGGGTCCTTTTCCCTT---HHHHHHHHHTHHHHCCGGGCEEEEEECSSTTTSCTTTTSTTSSCE
T ss_pred             HHHHHHHcCCeEEEEehhcccccccCCCCChH---HHHHHHHHHHHHhcccccCCEEEEEecCChhhcCHHHhCCcccce
Confidence            48999999999999999999999886544433   346788899999998888899999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .|+++.|+.++|.+||+.++++.....++|+..+|..|+||+++||+.||+
T Consensus       366 ~I~i~~Pd~~~R~~IL~~~l~~~~~~~dvdl~~lA~~T~GfsgaDL~~Lv~  416 (806)
T 3cf2_A          366 EVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCS  416 (806)
T ss_dssp             EEECCCCCHHHHHHHHHHTCSSSEECTTCCHHHHHHHCCSCCHHHHHHHHH
T ss_pred             EEecCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHHhcCCCCHHHHHHHHH
Confidence            999999999999999999999998889999999999999999999999873

>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=99.93  E-value=3.9e-26  Score=163.13  Aligned_cols=131  Identities=36%  Similarity=0.674  Sum_probs=112.2

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|+..+|+||||||+|.+...++.............+..++..++++....+++||+|||.++.+|++++|||||+.
T Consensus       100 ~f~~a~~~~p~il~iDEid~l~~~~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~v~vi~atn~~~~ld~al~r~gRf~~  179 (301)
T 3cf0_A          100 IFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQ  179 (301)
T ss_dssp             HHHHHHHTCSEEEEECSTTHHHHHHTTTTCCSSCSCCHHHHHHHHHHHSSCTTSSEEEEEEESCGGGSCGGGGSTTSSCE
T ss_pred             HHHHHHhcCCeEEEEEChHHHhhccCCCcCCcchHHHHHHHHHHHHhhcccCCCCEEEEEecCCccccChHHhcCCccce
Confidence            47889999999999999999987764332211111234667788888888777789999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .+++++|+.++|.+|++++++..+...++++..++..+.||+|+||+.+|+
T Consensus       180 ~i~i~~p~~~~r~~il~~~l~~~~~~~~~~~~~la~~~~g~sg~dl~~l~~  230 (301)
T 3cf0_A          180 LIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQ  230 (301)
T ss_dssp             EEECCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHHTCSSCCHHHHHHHHH
T ss_pred             EEecCCcCHHHHHHHHHHHHccCCCCccchHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999999999999888777889999999999999999999874

>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=99.93  E-value=1e-25  Score=169.50  Aligned_cols=131  Identities=47%  Similarity=0.745  Sum_probs=111.4

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|+.++|+||||||+|.+..+++.............++.++..++++....+++||+|||.++.+|++++|||||+.
T Consensus       100 lf~~A~~~~p~ILfIDEid~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~~~~~~~viVIaaTn~~~~Ld~allR~gRFd~  179 (476)
T 2ce7_A          100 LFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPGRFDK  179 (476)
T ss_dssp             HHHHHHHTCSEEEEEETGGGTCCC---------CHHHHHHHHHHHHHHHSCGGGTEEEEEEESCGGGSCGGGGSTTSSCE
T ss_pred             HHHHHHhcCCCEEEEechhhhhhhcccccCcCcHHHHHHHHHHHHHHhccCCCCCEEEEEecCChhhhchhhcccCccee
Confidence            48899999999999999999998775432233334456788899999887667789999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .+.+++|+.++|.+|++.+++..++..+.++..++..|.||+++||+.+|+
T Consensus       180 ~i~i~~Pd~~~R~~Il~~~~~~~~l~~~v~l~~la~~t~G~sgadL~~lv~  230 (476)
T 2ce7_A          180 KIVVDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAKRTPGFVGADLENLVN  230 (476)
T ss_dssp             EEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             EeecCCCCHHHHHHHHHHHHHhCCCcchhhHHHHHHhcCCCcHHHHHHHHH
Confidence            999999999999999999999888888889999999999999999999874

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=99.93  E-value=2e-25  Score=157.74  Aligned_cols=128  Identities=34%  Similarity=0.604  Sum_probs=105.2

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|+...|+++++||+|.++..++....   .......+.++..+++...+..++++++||.|+.+|++++||||||+
T Consensus        95 vf~~a~~~~p~i~~~Deid~~~~~r~~~~~---~~~~~~~~~~l~~Lsgg~~~~~~i~ia~tn~p~~LD~al~r~gRfd~  171 (274)
T 2x8a_A           95 VFQRAKNSAPCVIFFDEVDALCPRRSDRET---GASVRVVNQLLTEMDGLEARQQVFIMAATNRPDIIDPAILRPGRLDK  171 (274)
T ss_dssp             HHHHHHHTCSEEEEEETCTTTCC------------CTTHHHHHHHHHHTCCSTTCEEEEEEESCGGGSCHHHHSTTSSCE
T ss_pred             HHHHHHhcCCCeEeeehhhhhhcccCCCcc---hHHHHHHHHHHHhhhcccccCCEEEEeecCChhhCCHhhcCcccCCe
Confidence            478888899999999999998876532211   11234677888999998888889999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcC---CCCCCcccHHHHHHHc--CCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSR---MTLAEDVNLQELIMAK--DDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~---~~~~~~~~~~~la~~t--~g~s~~di~~l~~  131 (131)
                      .|++++|+.++|.+||+.++++   .....++++..+|..|  +||||+||+.+|+
T Consensus       172 ~i~~~~P~~~~r~~il~~~~~~~~~~~~~~~~~~~~la~~~~~~g~sgadl~~l~~  227 (274)
T 2x8a_A          172 TLFVGLPPPADRLAILKTITKNGTKPPLDADVNLEAIAGDLRCDCYTGADLSALVR  227 (274)
T ss_dssp             EEECCSCCHHHHHHHHHHHTTTTBTTBBCTTCCHHHHHTCSGGGSCCHHHHHHHHH
T ss_pred             EEEeCCcCHHHHHHHHHHHHhcccCCCCccccCHHHHHHhhccCCcCHHHHHHHHH
Confidence            9999999999999999999864   2345688999999975  5999999999874

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=99.92  E-value=5.4e-24  Score=148.57  Aligned_cols=131  Identities=40%  Similarity=0.715  Sum_probs=113.7

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|+...|+++|+||+|.+...+..............+..++..++++....+++||+|||.++.+|++++|+|||+.
T Consensus        96 ~~~~a~~~~~~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~vI~~tn~~~~l~~~l~r~~rf~~  175 (257)
T 1lv7_A           96 MFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDR  175 (257)
T ss_dssp             HHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEEESCTTTSCGGGGSTTSSCE
T ss_pred             HHHHHHHcCCeeehhhhhhhhccCCCCCcCCCchHHHHHHHHHHHHhhCcccCCCEEEEEeeCCchhCCHHHcCCCcCCe
Confidence            37888888999999999999988764432222333446778888999988777889999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .+++++|+.++|.+|++.+++..++..+.++..++..+.||+++||+.+|+
T Consensus       176 ~i~i~~P~~~~r~~il~~~~~~~~l~~~~~~~~la~~~~G~~~~dl~~l~~  226 (257)
T 1lv7_A          176 QVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVN  226 (257)
T ss_dssp             EEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             EEEeCCCCHHHHHHHHHHHHhcCCCCccccHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999999999999888888888999999999999999998863

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=99.91  E-value=4.1e-24  Score=154.04  Aligned_cols=126  Identities=34%  Similarity=0.554  Sum_probs=110.1

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCC-CCCeEEEeeCCCCCcccccccCCCccc
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDS-RGDVKVIMATNRIETLDPALIRPGRID   79 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~v~vi~ttn~~~~id~~l~~~grf~   79 (131)
                      +|..|+..+|+||||||+|.+..+++...   ......++.+++..++++.. ..+++||+|||.++.+|++++|  ||+
T Consensus        97 lf~~a~~~~~~vl~iDEid~l~~~~~~~~---~~~~~~~~~~ll~~ld~~~~~~~~v~vI~atn~~~~ld~al~r--Rf~  171 (322)
T 1xwi_A           97 LFQLARENKPSIIFIDEIDSLCGSRSENE---SEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFE  171 (322)
T ss_dssp             HHHHHHHTSSEEEEEETTTGGGCCSSSCC---TTHHHHHHHHHHHHHHCSSSCCTTEEEEEEESCTTTSCHHHHH--TCC
T ss_pred             HHHHHHhcCCcEEEeecHHHhcccccccc---chHHHHHHHHHHHHHhcccccCCCEEEEEecCCcccCCHHHHh--hcC
Confidence            47889999999999999999998875432   22345678889999998864 4789999999999999999999  999


Q ss_pred             eEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           80 RKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        80 ~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      ..+++++|+.++|.+|++.++...+.. .+.++..++..|.||+|+||+.+|+
T Consensus       172 ~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~~  224 (322)
T 1xwi_A          172 KRIYIPLPEPHARAAMFKLHLGTTQNSLTEADFRELGRKTDGYSGADISIIVR  224 (322)
T ss_dssp             EEEECCCCCHHHHHHHHHHHHTTCCBCCCHHHHHHHHHTCTTCCHHHHHHHHH
T ss_pred             eEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999999999999887654 5678999999999999999999984

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=99.91  E-value=1.2e-23  Score=148.57  Aligned_cols=131  Identities=59%  Similarity=0.996  Sum_probs=117.8

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|..++...|+||||||+|.+..++..............+..++..++++...+++++|+|||.++.++++++++|||+.
T Consensus       102 ~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~~vI~ttn~~~~l~~~l~~~~Rf~~  181 (285)
T 3h4m_A          102 IFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFDR  181 (285)
T ss_dssp             HHHHHHHTCSEEEEEETTHHHHBCCSSSCCGGGGHHHHHHHHHHHHHHTTCSSSSEEEEEECSCGGGBCHHHHSTTSEEE
T ss_pred             HHHHHHHcCCeEEEEECHHHhcccCccccCCccHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCchhcCHHHcCCCcCCe
Confidence            37788999999999999999998876555555556677888899999888777899999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .+.++.|+.++|.+|++.++.......+.++..++..+.||+++||..+|+
T Consensus       182 ~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~l~~~~~g~~~~~i~~l~~  232 (285)
T 3h4m_A          182 IIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAELKAICT  232 (285)
T ss_dssp             EEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHHCTTCCHHHHHHHHH
T ss_pred             EEEECCCCHHHHHHHHHHHHhcCCCCCcCCHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999999999999888878889999999999999999999873

>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=99.90  E-value=2.5e-23  Score=145.01  Aligned_cols=131  Identities=47%  Similarity=0.741  Sum_probs=108.9

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.+....|+++++||+|.+...+..............+..++..+++...+..++++++||.|+.+|++++|+|||+.
T Consensus       100 ~~~~~~~~~~~i~~~Deid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~g~~~~~~~i~~a~t~~p~~ld~~l~r~~rf~~  179 (254)
T 1ixz_A          100 LFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDR  179 (254)
T ss_dssp             HHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGGGSCGGGGSTTSSCE
T ss_pred             HHHHHHhcCCeEEEehhhhhhhcccCccccccchHHHHHHHHHHHHHhCCCCCCCEEEEEccCCchhCCHHHcCCCcCCe
Confidence            36777778899999999999987664321122234456778888899988777789999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .++++.|+.++|.+||+.++++..+..+.++..++..+.||+++||+.+|+
T Consensus       180 ~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~G~~~~dl~~~~~  230 (254)
T 1ixz_A          180 QIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLN  230 (254)
T ss_dssp             EEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             EEeeCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999999999998887778888999999999999999999873

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=99.90  E-value=1.3e-23  Score=158.78  Aligned_cols=130  Identities=46%  Similarity=0.737  Sum_probs=112.9

Q ss_pred             HHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceE
Q psy522            2 FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRK   81 (131)
Q Consensus         2 F~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~   81 (131)
                      |+.|+...|+|+||||+|.+...++.............++.++..+++...+..++++++||.|+.+|++++|||||+..
T Consensus       116 fq~a~~~~p~il~IDEId~l~~~r~~~~~~~~~e~~~~l~~LL~~Ldg~~~~~~viviAatn~p~~LD~aLlr~gRfdr~  195 (499)
T 2dhr_A          116 FETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQ  195 (499)
T ss_dssp             TTTSSSSSSCEEEEECGGGTCCCSSSSTTTSSHHHHHHHHHHHHHGGGCCSSCCCEEEECCSCGGGSCTTTSSTTSSCCE
T ss_pred             HHHHHhcCCCEEEEehHHHHHHhhccCcCCCcHHHHHHHHHHHHHhcccccCccEEEEEecCChhhcCcccccccccceE
Confidence            66677788999999999999877643222223344577889999999887778899999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           82 IEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        82 i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      +.++.|+.++|.+||+.++++..+..+.++..++..|.||+++||+.+|+
T Consensus       196 i~i~~Pd~~~R~~IL~~~~~~~~l~~dv~l~~lA~~t~G~~gadL~~lv~  245 (499)
T 2dhr_A          196 IAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLN  245 (499)
T ss_dssp             EECCCCCHHHHHHHHHHTTSSSCCCCSSTTHHHHTTSCSCCHHHHHHHHH
T ss_pred             EecCCCCHHHHHHHHHHHHhcCCCChHHHHHHHHHhcCCCCHHHHHHHHH
Confidence            99999999999999999998888888888999999999999999999874

>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=99.89  E-value=4.5e-23  Score=148.42  Aligned_cols=126  Identities=34%  Similarity=0.515  Sum_probs=105.6

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCC-CCCCeEEEeeCCCCCcccccccCCCccc
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFD-SRGDVKVIMATNRIETLDPALIRPGRID   79 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~v~vi~ttn~~~~id~~l~~~grf~   79 (131)
                      +|..|+..+|+||||||+|.+..++.......   ...+...++..++++. ...+++||+|||.++.+|++++|  ||+
T Consensus       102 ~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~---~~~~~~~ll~~l~~~~~~~~~v~vi~atn~~~~ld~al~~--Rf~  176 (322)
T 3eie_A          102 LFAMARENKPSIIFIDQVDALTGTRGEGESEA---SRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFE  176 (322)
T ss_dssp             HHHHHHHTSSEEEEEECGGGGSCC------CC---THHHHHHHHHHHGGGGTSCCCEEEEEEESCGGGSCHHHHH--HCC
T ss_pred             HHHHHHhcCCeEEEechhhhhhccCCCCcchH---HHHHHHHHHHHhccccccCCceEEEEecCChhhCCHHHHc--ccC
Confidence            47889999999999999999998774433222   3456778888888774 44689999999999999999999  999


Q ss_pred             eEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           80 RKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        80 ~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      ..+++++|+.++|.+|++.++...... .+.++..++..|+||+++||..+|+
T Consensus       177 ~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~l~~la~~t~g~sg~di~~l~~  229 (322)
T 3eie_A          177 RRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVK  229 (322)
T ss_dssp             EEEECCCCCHHHHHHHHHHHHTTCCCCCCHHHHHHHHHTTTTCCHHHHHHHHH
T ss_pred             eEEEeCCCCHHHHHHHHHHHhccCCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999999999999887654 5678999999999999999999873

>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=99.89  E-value=9.8e-23  Score=153.93  Aligned_cols=128  Identities=41%  Similarity=0.700  Sum_probs=112.9

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|...+|++|||||+|.+..+++....   .....+...++..+++.....+++||+|||.++.+|++++++|||+.
T Consensus       289 ~f~~A~~~~p~iLfLDEId~l~~~~~~~~~---~~~~~~~~~LL~~ld~~~~~~~v~vIaaTn~~~~Ld~al~r~gRf~~  365 (489)
T 3hu3_A          289 AFEEAEKNAPAIIFIDELDAIAPKREKTHG---EVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDR  365 (489)
T ss_dssp             HHHHHHHTCSEEEEEESHHHHCBCTTSCCC---HHHHHHHHHHHHHHHHSCTTSCEEEEEEESCGGGBCGGGGSTTSSCE
T ss_pred             HHHHHHhcCCcEEEecchhhhccccccccc---hHHHHHHHHHHHHhhccccCCceEEEEecCCccccCHHHhCCCcCce
Confidence            388899999999999999999987743322   22345677788888877777889999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .++++.|+.++|.+||+.+++......+.++..++..+.||+++||..||+
T Consensus       366 ~i~i~~P~~~eR~~IL~~~~~~~~l~~~~~l~~la~~t~g~s~~dL~~L~~  416 (489)
T 3hu3_A          366 EVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCS  416 (489)
T ss_dssp             EEECCCCCHHHHHHHHHHHTTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             EEEeCCCCHHHHHHHHHHHHhcCCCcchhhHHHHHHHccCCcHHHHHHHHH
Confidence            999999999999999999999988888889999999999999999999873

>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=99.89  E-value=7.9e-23  Score=149.06  Aligned_cols=126  Identities=34%  Similarity=0.517  Sum_probs=104.0

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCC-CCCeEEEeeCCCCCcccccccCCCccc
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDS-RGDVKVIMATNRIETLDPALIRPGRID   79 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~v~vi~ttn~~~~id~~l~~~grf~   79 (131)
                      +|..|+..+|+||||||+|.+...+...+.   .....+...++..++++.. ..+++||+|||.++.+|++++|  ||+
T Consensus       135 ~f~~a~~~~~~vl~iDEid~l~~~r~~~~~---~~~~~~~~~ll~~l~~~~~~~~~v~vI~atn~~~~ld~al~r--Rf~  209 (355)
T 2qp9_X          135 LFAMARENKPSIIFIDQVDALTGTRGEGES---EASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFE  209 (355)
T ss_dssp             HHHHHHHTSSEEEEEECGGGGTC------C---THHHHHHHHHHHHHHHCC---CCEEEEEEESCGGGSCHHHHH--TCC
T ss_pred             HHHHHHHcCCeEEEEechHhhcccCCCCcc---hHHHHHHHHHHHHhhcccccCCCeEEEeecCCcccCCHHHHc--ccC
Confidence            478889999999999999999887643322   2344567788888887754 4679999999999999999999  999


Q ss_pred             eEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           80 RKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        80 ~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      ..+++++|+.++|.+||+.++...+.. .+.++..|+..|+||+|+||..+|+
T Consensus       210 ~~i~i~~P~~~~r~~il~~~l~~~~~~~~~~~l~~la~~t~G~sg~dl~~l~~  262 (355)
T 2qp9_X          210 RRIYIPLPDLAARTTMFEINVGDTPSVLTKEDYRTLGAMTEGYSGSDIAVVVK  262 (355)
T ss_dssp             EEEECCCCCHHHHHHHHHHHHTTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             EEEEeCCcCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999999999999887654 5678999999999999999999874

>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=99.89  E-value=1.2e-22  Score=151.94  Aligned_cols=126  Identities=36%  Similarity=0.562  Sum_probs=109.0

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCC-CCCeEEEeeCCCCCcccccccCCCccc
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDS-RGDVKVIMATNRIETLDPALIRPGRID   79 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~v~vi~ttn~~~~id~~l~~~grf~   79 (131)
                      +|..|+..+|+||||||+|.++..+.....   .....+...++..++++.. ..+++||+|||.++.+|++++|  ||+
T Consensus       219 ~f~~a~~~~~~vl~iDEid~l~~~~~~~~~---~~~~~~~~~lL~~l~~~~~~~~~v~vI~atn~~~~ld~al~r--Rf~  293 (444)
T 2zan_A          219 LFQLARENKPSIIFIDEIDSLCGSRSENES---EAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFE  293 (444)
T ss_dssp             HHHHHHHSCSEEEEESCTTTTCCCSSCCCC---GGGHHHHHHHHTTTTCSSCCCSSCEEEEEESCGGGSCHHHHT--TCC
T ss_pred             HHHHHHHcCCeEEEEechHhhccCCCCccc---cHHHHHHHHHHHHHhCcccCCCCEEEEecCCCccccCHHHHh--hcc
Confidence            478899999999999999999987754322   2234677889999998754 4689999999999999999999  999


Q ss_pred             eEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           80 RKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        80 ~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      ..+++++|+.++|..||+.++...+.. .+.++..++..|+||+|+||..+|+
T Consensus       294 ~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~~  346 (444)
T 2zan_A          294 KRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRKTDGYSGADISIIVR  346 (444)
T ss_dssp             EEEECCCCCHHHHHHHHHHHHTTSCEECCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             eEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999999999999877654 5678999999999999999999874

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=99.88  E-value=2.8e-22  Score=141.52  Aligned_cols=131  Identities=47%  Similarity=0.741  Sum_probs=109.2

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.+....|+++++||+|.+...+..............+..++..+++...+..++++++||.|+.+|++++|++||+.
T Consensus       124 ~~~~~~~~~~~i~~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~lsgg~~~~~~i~~a~t~~p~~ld~~l~r~~rf~~  203 (278)
T 1iy2_A          124 LFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDR  203 (278)
T ss_dssp             HHHHHHTSCSEEEEEETHHHHHCC--------CHHHHHHHHHHHHHHTTCCTTCCEEEEEEESCTTSSCHHHHSTTSSCC
T ss_pred             HHHHHHhcCCcEEehhhhHhhhcccccccCCcchHHHHHHHHHHHHHhCCCCCCCEEEEEecCCchhCCHhHcCCCcCCe
Confidence            37778878899999999999876653211112233456778888899987777789999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .+++++|+.++|.+||+.+++...+..+.++..++..+.||+++||+.+|+
T Consensus       204 ~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~G~~~~dl~~l~~  254 (278)
T 1iy2_A          204 QIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLN  254 (278)
T ss_dssp             EEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             EEEeCCcCHHHHHHHHHHHHccCCCCcccCHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999999999998887778888999999999999999998863

>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=99.88  E-value=2e-22  Score=140.40  Aligned_cols=131  Identities=43%  Similarity=0.691  Sum_probs=99.2

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCC-chhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccc
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSG-GEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRID   79 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~   79 (131)
                      +|+.|+...|+||||||+|.+..++...... ........+..++..+++.....++++|+|||.++.+|++++++|||+
T Consensus        90 ~~~~a~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~~vi~~tn~~~~ld~~l~~~~R~~  169 (262)
T 2qz4_A           90 LFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTDHVIVLASTNRADILDGALMRPGRLD  169 (262)
T ss_dssp             HHHHHHHTCSEEEEEECC-------------------CHHHHHHHHHHHTCCTTCCEEEEEEESCGGGGGSGGGSTTSCC
T ss_pred             HHHHHHhcCCeEEEEeCcchhhccccccccCccchhHHHHHHHHHHHhhCcCCCCCEEEEecCCChhhcCHHHhcCCcCC
Confidence            3778888899999999999998776432211 122233567788888888777788999999999999999999999999


Q ss_pred             eEEEeCCCCHHHHHHHHHHHhcCCCCCCccc--HHHHHHHcCCCCHHHHHHhhC
Q psy522           80 RKIEFPLPDEKTKRRIFNIHTSRMTLAEDVN--LQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        80 ~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~--~~~la~~t~g~s~~di~~l~~  131 (131)
                      ..+++++|+.++|.+|+++++...+.....+  +..++..+.||+++||..+|+
T Consensus       170 ~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~~~l~~~~~g~~~~~l~~l~~  223 (262)
T 2qz4_A          170 RHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANICN  223 (262)
T ss_dssp             EEEECCSCCHHHHHHHHHHHHHHTTCCBTHHHHHHHHHHTCTTCCHHHHHHHHH
T ss_pred             eEEEeCCcCHHHHHHHHHHHHHhCCCCcchhhHHHHHHHHCCCCCHHHHHHHHH
Confidence            9999999999999999999998776654333  578999999999999998873

>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=99.85  E-value=1.1e-22  Score=142.61  Aligned_cols=131  Identities=46%  Similarity=0.724  Sum_probs=103.2

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCC-CchhHHHHHHHHHHHHhcCCCCC-CCeEEEeeCCCCCcccccccCCCcc
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNS-GGEREIQRTMLELLNQLDGFDSR-GDVKVIMATNRIETLDPALIRPGRI   78 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~-~~v~vi~ttn~~~~id~~l~~~grf   78 (131)
                      +|+.|+..+|+||||||+|.+..++...+. .........+..++..+++.... .++++|+|||.++.+|++++++|||
T Consensus        95 ~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~ttn~~~~ld~~l~r~~Rf  174 (268)
T 2r62_A           95 LFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRF  174 (268)
T ss_dssp             THHHHHHSCSCEEEESCGGGTTC----------CCCSCSSTTTTTTTTTCSSCSCSCCEEEECBSCCTTSCGGGGSSSSS
T ss_pred             HHHHHHhcCCeEEEEeChhhhcccccccccCCCchhHHHHHHHHHHHhhCcccCCCCEEEEEecCCchhcCHhHcCCCCC
Confidence            588899999999999999999876532110 00001112445566777765443 4599999999999999999999999


Q ss_pred             ceEEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           79 DRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        79 ~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      +..+++++|+.++|.++|+.+++......+.++..++..+.||+++||..+|+
T Consensus       175 ~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~g~~g~dl~~l~~  227 (268)
T 2r62_A          175 DRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAKLTAGLAGADLANIIN  227 (268)
T ss_dssp             CCCCBCCCCCTTTHHHHHHHHTSSSCCCSSCCTTTTTSSSCSSCHHHHHHHHH
T ss_pred             CeEEEecCcCHHHHHHHHHHHHhcCCCCCccCHHHHHHHcCCCCHHHHHHHHH
Confidence            99999999999999999999999887777778888999999999999998863

>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=99.82  E-value=5.4e-20  Score=134.11  Aligned_cols=126  Identities=32%  Similarity=0.555  Sum_probs=101.6

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCC--CCCeEEEeeCCCCCcccccccCCCcc
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDS--RGDVKVIMATNRIETLDPALIRPGRI   78 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~v~vi~ttn~~~~id~~l~~~grf   78 (131)
                      +|..|+..+|+||||||+|.+...++...   .......+..++..+++...  ..+++||+|||.++.+++++++  ||
T Consensus       168 ~~~~a~~~~~~vl~iDEid~l~~~~~~~~---~~~~~~~~~~lL~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~--Rf  242 (357)
T 3d8b_A          168 LFAVARCQQPAVIFIDEIDSLLSQRGDGE---HESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAARR--RL  242 (357)
T ss_dssp             HHHHHHHTCSEEEEEETHHHHTBC---------CHHHHHHHHHHHHHHC----CCCCEEEEEEESCGGGBCHHHHT--TC
T ss_pred             HHHHHHhcCCeEEEEeCchhhhccCCCCc---chHHHHHHHHHHHHHhcccccCCCCEEEEEecCChhhCCHHHHh--hC
Confidence            37788889999999999999987763322   22344677788888887643  3579999999999999999999  99


Q ss_pred             ceEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           79 DRKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        79 ~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      +..++++.|+.++|.++++.++...... .+.++..++..+.||+++||..+|+
T Consensus       243 ~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~l~~la~~t~G~s~~dl~~l~~  296 (357)
T 3d8b_A          243 VKRLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQIVQQSDAFSGADMTQLCR  296 (357)
T ss_dssp             CEEEECCCCCHHHHHHHHHHHHHTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             ceEEEeCCcCHHHHHHHHHHHHhhcCCCccHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            9999999999999999999999776544 4557899999999999999999874

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=99.82  E-value=1.1e-19  Score=128.96  Aligned_cols=126  Identities=33%  Similarity=0.540  Sum_probs=98.9

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCC---CCeEEEeeCCCCCcccccccCCCc
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSR---GDVKVIMATNRIETLDPALIRPGR   77 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~v~vi~ttn~~~~id~~l~~~gr   77 (131)
                      +|..|+..+|+||||||+|.+...++.......   ......++..+++....   .++++|++||.++.+++++++  |
T Consensus       105 ~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~---~~~~~~ll~~l~~~~~~~~~~~v~vi~~tn~~~~l~~~l~~--R  179 (297)
T 3b9p_A          105 LFAVARHMQPSIIFIDEVDSLLSERSSSEHEAS---RRLKTEFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALR--R  179 (297)
T ss_dssp             HHHHHHHTCSEEEEEETGGGTSBCC-----CCS---HHHHHHHHHHHHHCC------CEEEEEEESCGGGBCHHHHH--H
T ss_pred             HHHHHHHcCCcEEEeccHHHhccccccCcchHH---HHHHHHHHHHHhcccccCCCCcEEEEeecCChhhCCHHHHh--h
Confidence            367888899999999999999887743322222   23455666666665433   579999999999999999999  9


Q ss_pred             cceEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           78 IDRKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        78 f~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      |+..+++++|+.++|..+++.++...+.. .+.++..++..+.||+++||..+|+
T Consensus       180 ~~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~~la~~~~g~~~~~l~~l~~  234 (297)
T 3b9p_A          180 FTKRVYVSLPDEQTRELLLNRLLQKQGSPLDTEALRRLAKITDGYSGSDLTALAK  234 (297)
T ss_dssp             CCEEEECCCCCHHHHHHHHHHHHGGGSCCSCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             CCeEEEeCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            99999999999999999999998765543 4456888999999999999998873

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=99.80  E-value=5.3e-19  Score=130.08  Aligned_cols=126  Identities=33%  Similarity=0.497  Sum_probs=98.7

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCC--CCCeEEEeeCCCCCcccccccCCCcc
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDS--RGDVKVIMATNRIETLDPALIRPGRI   78 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~v~vi~ttn~~~~id~~l~~~grf   78 (131)
                      +|..|+..+|+||||||+|.++..+......   ....+...++..+++...  ..+++||+|||.++.+++++++  ||
T Consensus       199 ~~~~a~~~~~~il~iDEid~l~~~~~~~~~~---~~~~~~~~ll~~l~~~~~~~~~~v~vI~atn~~~~l~~~l~~--R~  273 (389)
T 3vfd_A          199 LFAVARELQPSIIFIDQVDSLLCERREGEHD---ASRRLKTEFLIEFDGVQSAGDDRVLVMGATNRPQELDEAVLR--RF  273 (389)
T ss_dssp             HHHHHHHSSSEEEEEETGGGGC--------C---THHHHHHHHHHHHHHHC-----CEEEEEEESCGGGCCHHHHT--TC
T ss_pred             HHHHHHhcCCeEEEEECchhhcccCCCccch---HHHHHHHHHHHHhhcccccCCCCEEEEEecCCchhcCHHHHc--Cc
Confidence            4788999999999999999998876432222   234566667777776544  3579999999999999999999  99


Q ss_pred             ceEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           79 DRKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        79 ~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      +..++++.|+.++|.+||+.++...... .+.++..++..+.||++++|..||+
T Consensus       274 ~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~~~~la~~~~g~~~~~l~~L~~  327 (389)
T 3vfd_A          274 IKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQLARMTDGYSGSDLTALAK  327 (389)
T ss_dssp             CEEEECCCCCHHHHHHHHHHHHTTSCCCSCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             ceEEEcCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            9999999999999999999999876544 4457889999999999999998873

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=99.79  E-value=5.3e-20  Score=130.99  Aligned_cols=120  Identities=21%  Similarity=0.270  Sum_probs=83.7

Q ss_pred             HHHH----HhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCC-----------CCCCeEEEeeCCCCC
Q psy522            2 FRVA----EEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFD-----------SRGDVKVIMATNRIE   66 (131)
Q Consensus         2 F~~A----~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----------~~~~v~vi~ttn~~~   66 (131)
                      |..|    ++.+|+||||||+|.+.+.+... .........+...+++.+++..           ..++++||+|||.++
T Consensus        88 f~~a~~~~~~~~~~vl~iDEiD~~~~~~~~~-~~~~~~~~~v~~~Ll~~ld~~~~~~~~~~~~~~~~~~v~vI~ttN~~~  166 (293)
T 3t15_A           88 YREAAEIIRKGNMCCLFINDLDAGAGRMGGT-TQYTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFS  166 (293)
T ss_dssp             HHHHHHHHTTSSCCCEEEECCC---------------CHHHHHHHHHHHHHCCC-----------CCCCCCEEEECSSCC
T ss_pred             HHHHHHHHhcCCCeEEEEechhhhcCCCCCC-ccccchHHHHHHHHHHHhccccccccccccccccCCCcEEEEecCCcc
Confidence            5555    67899999999999998855321 1111122344556666665332           446799999999999


Q ss_pred             cccccccCCCccceEEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHH
Q psy522           67 TLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKA  128 (131)
Q Consensus        67 ~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~  128 (131)
                      .+|++++|||||+..++  .|+.++|.+|++.++...    ++++..++..++||++++|..
T Consensus       167 ~ld~al~R~~R~d~~i~--~P~~~~r~~Il~~~~~~~----~~~~~~l~~~~~~~~~~~l~~  222 (293)
T 3t15_A          167 TLYAPLIRDGRMEKFYW--APTREDRIGVCTGIFRTD----NVPAEDVVKIVDNFPGQSIDF  222 (293)
T ss_dssp             C--CHHHHHHHEEEEEE--CCCHHHHHHHHHHHHGGG----CCCHHHHHHHHHHSCSCCHHH
T ss_pred             cCCHHHhCCCCCceeEe--CcCHHHHHHHHHHhccCC----CCCHHHHHHHhCCCCcccHHH
Confidence            99999999999998887  579999999999888743    567888999999999998863

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=99.51  E-value=9.9e-18  Score=125.65  Aligned_cols=120  Identities=18%  Similarity=0.218  Sum_probs=70.9

Q ss_pred             HHHH---HhcCCeEEEecccccccCcCCCCCCCchh-HHH---------------HHHHHHHHHhc--CCCCCCCeEEEe
Q psy522            2 FRVA---EEHAPSIVFIDEIDAVGTKRYDSNSGGER-EIQ---------------RTMLELLNQLD--GFDSRGDVKVIM   60 (131)
Q Consensus         2 F~~A---~~~~p~ii~iDe~d~l~~~~~~~~~~~~~-~~~---------------~~~~~~l~~~~--~~~~~~~v~vi~   60 (131)
                      |+.|   +..+|+||||||+|.++.+++........ ...               .+...++..++  ++...+.+++++
T Consensus       116 f~~a~~~~~~~~~il~iDEid~l~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ll~~l~~~~~~~~~~v~i~a  195 (456)
T 2c9o_A          116 FRRAIGLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFESLQKERVEAGDVIYIEA  195 (456)
T ss_dssp             HHHTEEEEEEEEEEEEEEEEEEEEEC--------------CEEEEEEETTEEEEEEECHHHHHHHHHTTCCTTEEEEEET
T ss_pred             HHHHHhhhhcCCcEEEEechhhcccccCCCCCCCcchHHHHHHHHHhccccchhHhhhHHHHHHHhhccCCCCCEEEEEc
Confidence            6667   77889999999999999888543211110 000               11123444443  333444577779


Q ss_pred             eCCCCCcccccccCCCccce--EEEeCCC--CHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhh
Q psy522           61 ATNRIETLDPALIRPGRIDR--KIEFPLP--DEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAIC  130 (131)
Q Consensus        61 ttn~~~~id~~l~~~grf~~--~i~~~~P--~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~  130 (131)
                      |||.++.+|+++.||||||.  .++++.|  +.++|.+|++.+..       .+++.++..|+|  |+||..+|
T Consensus       196 ttn~~~~ld~a~~r~~rfd~~~~~~v~~p~~~~~~R~~il~~~~~-------~dl~~~a~~t~g--gadl~~l~  260 (456)
T 2c9o_A          196 NSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQDVTL-------HDLDVANARPQG--GQDILSMM  260 (456)
T ss_dssp             TTCCEEEEEEETTSCCTTSCSSSSEECCCCSCSEEEEEEEEEEEH-------HHHHHTC---------------
T ss_pred             CCCCcccCChhhcCCcccCcceeEecCCCchhHHHHHHHHHHHHH-------HHHHHHHHhCCC--hhHHHHHH
Confidence            99999999999999999998  6677777  45788888876553       268889999999  99999887

>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Homo sapiens}

Probab=99.34  E-value=1.1e-12  Score=75.91  Aligned_cols=47  Identities=34%  Similarity=0.698  Sum_probs=44.4

Q ss_pred             CCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           85 PLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        85 ~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      |+|+.++|.+||+.++++.+...++|+..+|..|+||||+||+.+|+
T Consensus         1 plPd~~~R~~Il~~~l~~~~~~~~~dl~~la~~t~G~SGADi~~l~~   47 (78)
T 3kw6_A            1 PPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCT   47 (78)
T ss_dssp             CCCCHHHHHHHHHHHHTTSEECTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCCccCHHHHHHHcCCCCHHHHHHHHH
Confidence            68999999999999999998888899999999999999999999984

>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast structural genomics consortium (NESG), target HR3102A, PSI-2; NMR {Homo sapiens}

Probab=99.28  E-value=2.7e-12  Score=75.62  Aligned_cols=48  Identities=31%  Similarity=0.636  Sum_probs=45.0

Q ss_pred             eCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           84 FPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        84 ~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      -.+|+.++|.+||+.++++.++..++|+..||+.|+||||+||+.+|+
T Consensus         8 ~~~Pd~~~R~~IL~~~l~~~~l~~dvdl~~LA~~T~G~SGADL~~l~~   55 (86)
T 2krk_A            8 HSHPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCT   55 (86)
T ss_dssp             CCCCCHHHHHHHHHHHTTTSEECTTCCCHHHHHTCSSCCHHHHHHHHH
T ss_pred             CCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHHHHHHHH
Confidence            468999999999999999998888899999999999999999999984

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=99.21  E-value=2.7e-11  Score=84.76  Aligned_cols=119  Identities=13%  Similarity=0.101  Sum_probs=80.1

Q ss_pred             HHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCC-CCeEEEeeCCCCCcccc-cccCCCccc
Q psy522            2 FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSR-GDVKVIMATNRIETLDP-ALIRPGRID   79 (131)
Q Consensus         2 F~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~v~vi~ttn~~~~id~-~l~~~grf~   79 (131)
                      |+.+....|++|+|||+|.++..+.... ....   ..+..+...+++.... .++++|+|||.++.+++ .+.+  ||+
T Consensus       117 ~~~~~~~~~~vl~iDEid~l~~~~~~~~-~~~~---~~l~~L~~~~~~~~~~~~~~~ii~ttn~~~~l~~~~l~~--rf~  190 (272)
T 1d2n_A          117 FDDAYKSQLSCVVVDDIERLLDYVPIGP-RFSN---LVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEMLN--AFS  190 (272)
T ss_dssp             HHHHHTSSEEEEEECCHHHHTTCBTTTT-BCCH---HHHHHHHHHTTCCCSTTCEEEEEEEESCHHHHHHTTCTT--TSS
T ss_pred             HHHHHhcCCcEEEEEChhhhhccCCCCh-hHHH---HHHHHHHHHhcCccCCCCCEEEEEecCChhhcchhhhhc--ccc
Confidence            5667777899999999999987653221 1222   3445555556655433 46889999999999988 6666  999


Q ss_pred             eEEEeCCCCH-HHHHHHHHHHhcCCCCCCcccHHHHHHHcCCC----CHHHHHHhh
Q psy522           80 RKIEFPLPDE-KTKRRIFNIHTSRMTLAEDVNLQELIMAKDDL----SGADIKAIC  130 (131)
Q Consensus        80 ~~i~~~~P~~-~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~----s~~di~~l~  130 (131)
                      ..+.+|+++. ++...++..   ...+ .+.++..++..+.||    ...++..++
T Consensus       191 ~~i~~p~l~~r~~i~~i~~~---~~~~-~~~~~~~l~~~~~g~~~~g~ir~l~~~l  242 (272)
T 1d2n_A          191 TTIHVPNIATGEQLLEALEL---LGNF-KDKERTTIAQQVKGKKVWIGIKKLLMLI  242 (272)
T ss_dssp             EEEECCCEEEHHHHHHHHHH---HTCS-CHHHHHHHHHHHTTSEEEECHHHHHHHH
T ss_pred             eEEcCCCccHHHHHHHHHHh---cCCC-CHHHHHHHHHHhcCCCccccHHHHHHHH
Confidence            9998877654 444444443   2222 345688899999998    556655543

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=99.16  E-value=4.6e-11  Score=84.74  Aligned_cols=114  Identities=18%  Similarity=0.190  Sum_probs=76.7

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCC-----cccccccCCCccceEE
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE-----TLDPALIRPGRIDRKI   82 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~-----~id~~l~~~grf~~~i   82 (131)
                      ..++||||||+|.++..++.  .....   ..+..++..++.  ...++++|++||.++     .+++++++  ||+..+
T Consensus       129 ~~~~vl~iDEid~l~~~~~~--~~~~~---~~~~~Ll~~l~~--~~~~~~~i~~~~~~~~~~~~~~~~~l~~--R~~~~i  199 (309)
T 3syl_A          129 AMGGVLFIDEAYYLYRPDNE--RDYGQ---EAIEILLQVMEN--NRDDLVVILAGYADRMENFFQSNPGFRS--RIAHHI  199 (309)
T ss_dssp             HTTSEEEEETGGGSCCCC-----CCTH---HHHHHHHHHHHH--CTTTCEEEEEECHHHHHHHHHHSTTHHH--HEEEEE
T ss_pred             cCCCEEEEEChhhhccCCCc--ccccH---HHHHHHHHHHhc--CCCCEEEEEeCChHHHHHHHhhCHHHHH--hCCeEE
Confidence            35789999999999866532  11222   344555555553  345788889988643     35799999  999999


Q ss_pred             EeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHc------CCC-CHHHHHHhh
Q psy522           83 EFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAK------DDL-SGADIKAIC  130 (131)
Q Consensus        83 ~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t------~g~-s~~di~~l~  130 (131)
                      ++++|+.+++.+|+++++...+.. .+..+..++...      ..+ .++++..++
T Consensus       200 ~~~~~~~~~~~~il~~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~gn~r~l~~~l  255 (309)
T 3syl_A          200 EFPDYSDEELFEIAGHMLDDQNYQMTPEAETALRAYIGLRRNQPHFANARSIRNAL  255 (309)
T ss_dssp             EECCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHTTSSSCCHHHHHHHHH
T ss_pred             EcCCcCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhccCCCCCcHHHHHHHH
Confidence            999999999999999999866544 222344455542      222 356666554

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=99.08  E-value=2.9e-11  Score=92.45  Aligned_cols=85  Identities=24%  Similarity=0.289  Sum_probs=60.5

Q ss_pred             HHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCC-------------CCCeEEEeeCCCCCcc
Q psy522            2 FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDS-------------RGDVKVIMATNRIETL   68 (131)
Q Consensus         2 F~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-------------~~~v~vi~ttn~~~~i   68 (131)
                      |..|....| |+||||+|.+......          .....++..++....             ...+++|+|||.++.+
T Consensus       169 ~~~a~~~~~-vl~lDEid~l~~~~~~----------~~~~~LL~~ld~~~~~~~~~~~~~~~~~~~~v~iI~ttN~~~~l  237 (543)
T 3m6a_A          169 MKKAGKLNP-VFLLDEIDKMSSDFRG----------DPSSAMLEVLDPEQNSSFSDHYIEETFDLSKVLFIATANNLATI  237 (543)
T ss_dssp             HHTTCSSSE-EEEEEESSSCC-------------------CCGGGTCTTTTTBCCCSSSCCCCBCSSCEEEEECSSTTTS
T ss_pred             HHHhhccCC-EEEEhhhhhhhhhhcc----------CHHHHHHHHHhhhhcceeecccCCeeecccceEEEeccCccccC
Confidence            444555665 9999999999765421          122334444443211             1568999999999999


Q ss_pred             cccccCCCccceEEEeCCCCHHHHHHHHHHHh
Q psy522           69 DPALIRPGRIDRKIEFPLPDEKTKRRIFNIHT  100 (131)
Q Consensus        69 d~~l~~~grf~~~i~~~~P~~~~R~~il~~~l  100 (131)
                      ++++++  ||+ .|.++.|+.+++.+|++.++
T Consensus       238 ~~aL~~--R~~-vi~~~~~~~~e~~~Il~~~l  266 (543)
T 3m6a_A          238 PGPLRD--RME-IINIAGYTEIEKLEIVKDHL  266 (543)
T ss_dssp             CHHHHH--HEE-EEECCCCCHHHHHHHHHHTH
T ss_pred             CHHHHh--hcc-eeeeCCCCHHHHHHHHHHHH
Confidence            999999  996 79999999999999999886

>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=99.06  E-value=1.1e-10  Score=68.93  Aligned_cols=44  Identities=23%  Similarity=0.519  Sum_probs=41.2

Q ss_pred             CHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           88 DEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        88 ~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      |.++|.+||+.++++.+...++|+..||+.|+||||+||+.+|+
T Consensus         2 d~~~R~~Il~~~~~~~~~~~dvdl~~lA~~t~G~SGADl~~l~~   45 (88)
T 3vlf_B            2 DLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCT   45 (88)
T ss_dssp             CSSHHHHHHHHHHTTSCBCSCCCHHHHHHTCSSCCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHCCCCCCCccCHHHHHHHcCCCcHHHHHHHHH
Confidence            56899999999999999888999999999999999999999984

>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=99.03  E-value=1.9e-10  Score=67.09  Aligned_cols=44  Identities=45%  Similarity=0.808  Sum_probs=41.4

Q ss_pred             CHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           88 DEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        88 ~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      +.++|.+||+.++++.+...++|+..+|..|+||||+||+.+|+
T Consensus         2 d~~~R~~Il~~~l~~~~~~~~vdl~~la~~t~G~SGADi~~l~~   45 (83)
T 3aji_B            2 DRRQKRLIFSTITSKMNLSEEVDLEDYVARPDKISGADINSICQ   45 (83)
T ss_dssp             CHHHHHHHHHHHHTTSCBCTTCCTHHHHTSSCCCCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhCCCCCCcccCHHHHHHHcCCCCHHHHHHHHH
Confidence            78999999999999998888899999999999999999999984

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=98.97  E-value=2.4e-09  Score=76.80  Aligned_cols=108  Identities=16%  Similarity=0.200  Sum_probs=75.0

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhc------------CCC-CCCCeEEEeeCCCCCcccccccC
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLD------------GFD-SRGDVKVIMATNRIETLDPALIR   74 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~------------~~~-~~~~v~vi~ttn~~~~id~~l~~   74 (131)
                      ..+++|||||+|.+...           ....+...+..-.            .+. ..+++++|++||....+++++++
T Consensus       105 ~~~~vl~lDEi~~l~~~-----------~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~i~atn~~~~l~~~L~~  173 (338)
T 3pfi_A          105 SEGDILFIDEIHRLSPA-----------IEEVLYPAMEDYRLDIIIGSGPAAQTIKIDLPKFTLIGATTRAGMLSNPLRD  173 (338)
T ss_dssp             CTTCEEEEETGGGCCHH-----------HHHHHHHHHHTSCC---------CCCCCCCCCCCEEEEEESCGGGSCHHHHT
T ss_pred             cCCCEEEEechhhcCHH-----------HHHHHHHHHHhccchhhcccCccccceecCCCCeEEEEeCCCccccCHHHHh
Confidence            46899999999998421           1222333332211            000 11258999999999999999999


Q ss_pred             CCccceEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHh
Q psy522           75 PGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAI  129 (131)
Q Consensus        75 ~grf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l  129 (131)
                        ||+..+.+++|+.+++..+++.++...+.. .+..+..++..+.|. ++++..+
T Consensus       174 --R~~~~i~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~l~~~~~G~-~r~l~~~  226 (338)
T 3pfi_A          174 --RFGMQFRLEFYKDSELALILQKAALKLNKTCEEKAALEIAKRSRST-PRIALRL  226 (338)
T ss_dssp             --TCSEEEECCCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHHTTTTC-HHHHHHH
T ss_pred             --hcCEEeeCCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcC-HHHHHHH
Confidence              999999999999999999999998765543 233466677766664 4555443

>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=98.96  E-value=4.3e-09  Score=74.90  Aligned_cols=109  Identities=14%  Similarity=0.118  Sum_probs=77.6

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhc-----CCC--------CCCCeEEEeeCCCCCcccccccC
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLD-----GFD--------SRGDVKVIMATNRIETLDPALIR   74 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~-----~~~--------~~~~v~vi~ttn~~~~id~~l~~   74 (131)
                      ..+.+|||||+|.+...           ....+..++....     +..        ...++.+|++||.+..+++++.+
T Consensus        89 ~~~~~l~lDEi~~l~~~-----------~~~~L~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~~i~~t~~~~~~~~~l~~  157 (324)
T 1hqc_A           89 EEGDILFIDEIHRLSRQ-----------AEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLS  157 (324)
T ss_dssp             CTTCEEEETTTTSCCHH-----------HHHHHHHHHHHSEEEECCSSSSSCCCEEEECCCCEEEEEESCCSSCSCSTTT
T ss_pred             cCCCEEEEECCcccccc-----------hHHHHHHHHHhhhhHHhccccccccccccCCCCEEEEEeCCCcccCCHHHHh
Confidence            46789999999987422           1223333333321     000        11358899999999999999999


Q ss_pred             CCccceEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHhh
Q psy522           75 PGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAIC  130 (131)
Q Consensus        75 ~grf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l~  130 (131)
                        ||+..+.+++|+.+++..+++.++...+.. .+..+..++..+.|. ++++..++
T Consensus       158 --R~~~~i~l~~~~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~-~r~l~~~l  211 (324)
T 1hqc_A          158 --RFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGT-MRVAKRLF  211 (324)
T ss_dssp             --TCSCEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHSCSC-HHHHHHHH
T ss_pred             --cccEEEecCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHccCC-HHHHHHHH
Confidence              999899999999999999999998765544 233477788888775 56666553

>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=98.94  E-value=6.3e-09  Score=70.25  Aligned_cols=103  Identities=21%  Similarity=0.248  Sum_probs=77.0

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCC
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLP   87 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P   87 (131)
                      ..|.+|+|||+|.+..              .....++..++.  ...++.+|++|+.+..+++.+.+  |+ ..+.+++|
T Consensus       125 ~~~~vlviDe~~~l~~--------------~~~~~l~~~l~~--~~~~~~~i~~t~~~~~~~~~l~~--r~-~~i~l~~l  185 (250)
T 1njg_A          125 GRFKVYLIDEVHMLSR--------------HSFNALLKTLEE--PPEHVKFLLATTDPQKLPVTILS--RC-LQFHLKAL  185 (250)
T ss_dssp             SSSEEEEEETGGGSCH--------------HHHHHHHHHHHS--CCTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCC
T ss_pred             CCceEEEEECcccccH--------------HHHHHHHHHHhc--CCCceEEEEEeCChHhCCHHHHH--Hh-hhccCCCC
Confidence            3579999999999731              133344555543  24578899999999999999998  76 68999999


Q ss_pred             CHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHhh
Q psy522           88 DEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAIC  130 (131)
Q Consensus        88 ~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l~  130 (131)
                      +.++..++++.++...+.. .+..+..+++.+.| .++.+..++
T Consensus       186 ~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G-~~~~~~~~~  228 (250)
T 1njg_A          186 DVEQIRHQLEHILNEEHIAHEPRALQLLARAAEG-SLRDALSLT  228 (250)
T ss_dssp             CHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHTT-CHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCC-CHHHHHHHH
Confidence            9999999999988654433 33347788888888 677777654

>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=98.93  E-value=1.4e-09  Score=81.15  Aligned_cols=107  Identities=18%  Similarity=0.240  Sum_probs=73.2

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCc---ccccccCCCccc--eEEE
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIET---LDPALIRPGRID--RKIE   83 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~---id~~l~~~grf~--~~i~   83 (131)
                      .|.||+|||+|.+..++         .....   ++..++.....+..++|+|.+.+..   +++.+++  ||.  ..+.
T Consensus       194 ~~~vL~IDEi~~l~~~~---------~~q~~---l~~~l~~l~~~~~~iIitt~~~~~~l~~l~~~L~s--R~~~g~~i~  259 (440)
T 2z4s_A          194 KVDILLIDDVQFLIGKT---------GVQTE---LFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVS--RFQMGLVAK  259 (440)
T ss_dssp             TCSEEEEECGGGGSSCH---------HHHHH---HHHHHHHHHTTTCEEEEEESSCGGGCSSCCHHHHH--HHHSSBCCB
T ss_pred             CCCEEEEeCcccccCCh---------HHHHH---HHHHHHHHHHCCCeEEEEECCCHHHHHHHHHHHHh--hccCCeEEE
Confidence            78999999999986532         01122   2222222224456677777766666   7899999  986  7899


Q ss_pred             eCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHhh
Q psy522           84 FPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAIC  130 (131)
Q Consensus        84 ~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l~  130 (131)
                      +++|+.++|.++++..+...+.. ++..+..++..+.| +++++..++
T Consensus       260 l~~p~~e~r~~iL~~~~~~~~~~i~~e~l~~la~~~~g-n~R~l~~~L  306 (440)
T 2z4s_A          260 LEPPDEETRKSIARKMLEIEHGELPEEVLNFVAENVDD-NLRRLRGAI  306 (440)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHCCS-CHHHHHHHH
T ss_pred             eCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-CHHHHHHHH
Confidence            99999999999999987643332 22236778887766 577776554

>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=98.92  E-value=4e-09  Score=74.46  Aligned_cols=86  Identities=27%  Similarity=0.346  Sum_probs=63.0

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCC--------CCCCeEEEee----CCCCCcccccccCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFD--------SRGDVKVIMA----TNRIETLDPALIRPG   76 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--------~~~~v~vi~t----tn~~~~id~~l~~~g   76 (131)
                      .++||||||+|.+.......  ........+...++..+++..        ...++++|++    ++.+..+++++++  
T Consensus       116 ~~~vl~iDEi~~l~~~~~~~--~~~~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~l~~~l~~--  191 (310)
T 1ofh_A          116 QNGIVFIDEIDKICKKGEYS--GADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG--  191 (310)
T ss_dssp             HHCEEEEECGGGGSCCSSCC--SSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSSCGGGSCHHHHH--
T ss_pred             CCCEEEEEChhhcCcccccc--ccchhHHHHHHHHHHHhcCCeEecccccccCCcEEEEEcCCcccCCcccCCHHHHh--
Confidence            47899999999998765321  122222233455666666431        2346888888    5688999999999  


Q ss_pred             ccceEEEeCCCCHHHHHHHHHH
Q psy522           77 RIDRKIEFPLPDEKTKRRIFNI   98 (131)
Q Consensus        77 rf~~~i~~~~P~~~~R~~il~~   98 (131)
                      ||+..+++++|+.+++.+|++.
T Consensus       192 R~~~~i~~~~~~~~~~~~il~~  213 (310)
T 1ofh_A          192 RLPIRVELTALSAADFERILTE  213 (310)
T ss_dssp             TCCEEEECCCCCHHHHHHHHHS
T ss_pred             hCCceEEcCCcCHHHHHHHHHh
Confidence            9998999999999999999983

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=98.92  E-value=2.5e-09  Score=77.44  Aligned_cols=102  Identities=16%  Similarity=0.175  Sum_probs=73.8

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeC-----------CCCCcccccccCCCcc
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMAT-----------NRIETLDPALIRPGRI   78 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~tt-----------n~~~~id~~l~~~grf   78 (131)
                      |+||||||+|.+..              .....++..++..  ..+++++++.           |.+..+++++++  ||
T Consensus       190 ~~vl~IDEi~~l~~--------------~~~~~L~~~le~~--~~~~~ii~t~~~~~~i~~t~~~~~~~l~~~l~s--R~  251 (368)
T 3uk6_A          190 PGVLFIDEVHMLDI--------------ESFSFLNRALESD--MAPVLIMATNRGITRIRGTSYQSPHGIPIDLLD--RL  251 (368)
T ss_dssp             BCEEEEESGGGSBH--------------HHHHHHHHHTTCT--TCCEEEEEESCSEEECBTSSCEEETTCCHHHHT--TE
T ss_pred             CceEEEhhccccCh--------------HHHHHHHHHhhCc--CCCeeeeecccceeeeeccCCCCcccCCHHHHh--hc
Confidence            78999999998842              2334455555432  2346655554           357889999999  99


Q ss_pred             ceEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHhh
Q psy522           79 DRKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAIC  130 (131)
Q Consensus        79 ~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l~  130 (131)
                      .. +.+++|+.+++.++++..+...+.. .+..+..++..+.|.+++++..++
T Consensus       252 ~~-i~~~~~~~~e~~~il~~~~~~~~~~~~~~~l~~l~~~~~~G~~r~~~~ll  303 (368)
T 3uk6_A          252 LI-VSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLI  303 (368)
T ss_dssp             EE-EEECCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             cE-EEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhcCCCHHHHHHHH
Confidence            76 8999999999999999988754443 333477788888756788877765

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=98.80  E-value=1.1e-08  Score=73.03  Aligned_cols=104  Identities=15%  Similarity=0.276  Sum_probs=71.1

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCC---cccccccCCCccc--eEEE
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE---TLDPALIRPGRID--RKIE   83 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~---~id~~l~~~grf~--~~i~   83 (131)
                      .|.+|||||++.+..++         .....+..+++.+   ...+..+++++++.+.   .+++++.+  ||.  ..+.
T Consensus        98 ~~~vL~iDEi~~l~~~~---------~~~~~l~~~l~~~---~~~~~~iii~~~~~~~~l~~l~~~L~s--R~~~~~~i~  163 (324)
T 1l8q_A           98 SVDLLLLDDVQFLSGKE---------RTQIEFFHIFNTL---YLLEKQIILASDRHPQKLDGVSDRLVS--RFEGGILVE  163 (324)
T ss_dssp             TCSEEEEECGGGGTTCH---------HHHHHHHHHHHHH---HHTTCEEEEEESSCGGGCTTSCHHHHH--HHHTSEEEE
T ss_pred             CCCEEEEcCcccccCCh---------HHHHHHHHHHHHH---HHCCCeEEEEecCChHHHHHhhhHhhh--cccCceEEE
Confidence            48999999999986532         0112222232222   2345678888888777   68999999  996  7899


Q ss_pred             eCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHh
Q psy522           84 FPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAI  129 (131)
Q Consensus        84 ~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l  129 (131)
                      +++ +.++|.++++..+...+.. ++..+..++..+ | ..+++..+
T Consensus       164 l~~-~~~e~~~il~~~~~~~~~~l~~~~l~~l~~~~-g-~~r~l~~~  207 (324)
T 1l8q_A          164 IEL-DNKTRFKIIKEKLKEFNLELRKEVIDYLLENT-K-NVREIEGK  207 (324)
T ss_dssp             CCC-CHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHC-S-SHHHHHHH
T ss_pred             eCC-CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhC-C-CHHHHHHH
Confidence            999 9999999999998754443 233477788877 4 45655544

>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=98.80  E-value=2.3e-08  Score=66.79  Aligned_cols=99  Identities=14%  Similarity=0.176  Sum_probs=70.5

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCC
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLP   87 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P   87 (131)
                      ..|.+|+|||+|.+...           ....+..+   ++.  ...++.+|++||.++.+++++.+  ||. .+.+++|
T Consensus       101 ~~~~vliiDe~~~l~~~-----------~~~~l~~~---l~~--~~~~~~~i~~~~~~~~~~~~l~~--r~~-~i~~~~~  161 (226)
T 2chg_A          101 APFKIIFLDEADALTAD-----------AQAALRRT---MEM--YSKSCRFILSCNYVSRIIEPIQS--RCA-VFRFKPV  161 (226)
T ss_dssp             CSCEEEEEETGGGSCHH-----------HHHHHHHH---HHH--TTTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCC
T ss_pred             cCceEEEEeChhhcCHH-----------HHHHHHHH---HHh--cCCCCeEEEEeCChhhcCHHHHH--hCc-eeecCCC
Confidence            56899999999998432           11223333   332  23567889999999999999999  997 8999999


Q ss_pred             CHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHH
Q psy522           88 DEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADI  126 (131)
Q Consensus        88 ~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di  126 (131)
                      +.++..++++..+...+.. .+..+..++..+.|- +..+
T Consensus       162 ~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g~-~r~l  200 (226)
T 2chg_A          162 PKEAMKKRLLEICEKEGVKITEDGLEALIYISGGD-FRKA  200 (226)
T ss_dssp             CHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTTC-HHHH
T ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCC-HHHH
Confidence            9999999999987643333 223466677777663 4433

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=98.80  E-value=3.6e-09  Score=83.50  Aligned_cols=89  Identities=30%  Similarity=0.397  Sum_probs=64.9

Q ss_pred             HHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCC-----cccccccCCC
Q psy522            2 FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE-----TLDPALIRPG   76 (131)
Q Consensus         2 F~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~-----~id~~l~~~g   76 (131)
                      |+.++...++||||||+|.++++.....  ....       ..+.+..+...+.+.+|++|+.++     .+|+++.+  
T Consensus       271 ~~~~~~~~~~iL~IDEi~~l~~~~~~~~--~~~~-------~~~~L~~~l~~~~~~~I~at~~~~~~~~~~~d~aL~~--  339 (758)
T 1r6b_X          271 LKQLEQDTNSILFIDEIHTIIGAGAASG--GQVD-------AANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRALAR--  339 (758)
T ss_dssp             HHHHSSSSCEEEEETTTTTTTTSCCSSS--CHHH-------HHHHHSSCSSSCCCEEEEEECHHHHHCCCCCTTSSGG--
T ss_pred             HHHHHhcCCeEEEEechHHHhhcCCCCc--chHH-------HHHHHHHHHhCCCeEEEEEeCchHHhhhhhcCHHHHh--
Confidence            4556666789999999999987653221  1111       122333444567788999998653     57899999  


Q ss_pred             ccceEEEeCCCCHHHHHHHHHHHhcC
Q psy522           77 RIDRKIEFPLPDEKTKRRIFNIHTSR  102 (131)
Q Consensus        77 rf~~~i~~~~P~~~~R~~il~~~l~~  102 (131)
                      ||+ .+.++.|+.++|.++++.+...
T Consensus       340 Rf~-~i~v~~p~~~e~~~il~~l~~~  364 (758)
T 1r6b_X          340 RFQ-KIDITEPSIEETVQIINGLKPK  364 (758)
T ss_dssp             GEE-EEECCCCCHHHHHHHHHHHHHH
T ss_pred             Cce-EEEcCCCCHHHHHHHHHHHHHH
Confidence            998 7999999999999999987643

>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=98.74  E-value=4.1e-10  Score=84.07  Aligned_cols=74  Identities=14%  Similarity=0.065  Sum_probs=5.0

Q ss_pred             ecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEee-CCCCCcccccccCCCccceEEEeCCCCHH-HH
Q psy522           15 IDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMA-TNRIETLDPALIRPGRIDRKIEFPLPDEK-TK   92 (131)
Q Consensus        15 iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~t-tn~~~~id~~l~~~grf~~~i~~~~P~~~-~R   92 (131)
                      +||+|.+....   ..   .....++..++..|+++.....+  +++ ||+++.+|++++||||||+.|+++.|+.. .|
T Consensus       113 ~De~d~~~~~~---~~---~~e~rvl~~LL~~~dg~~~~~~v--~a~~TN~~~~ld~aL~rggr~D~~i~i~lP~~~~~~  184 (444)
T 1g41_A          113 QQEIAKNRARA---ED---VAEERILDALLPPAKNQWGEVEN--HDSHSSTRQAFRKKLREGQLDDKEIEIDVSAGVSMG  184 (444)
T ss_dssp             HHHHHSCC------------------------------------------------------------------------
T ss_pred             hhhhhhhhccc---hh---hHHHHHHHHHHHHhhcccccccc--ccccccCHHHHHHHHHcCCCcceEEEEcCCCCccch
Confidence            67766654222   11   12246788888899988665554  455 99999999999999999999999999988 77


Q ss_pred             HHHH
Q psy522           93 RRIF   96 (131)
Q Consensus        93 ~~il   96 (131)
                      .+|+
T Consensus       185 ~ei~  188 (444)
T 1g41_A          185 VEIM  188 (444)
T ss_dssp             ----
T ss_pred             hhhh
Confidence            7775

>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=98.74  E-value=7.9e-09  Score=70.16  Aligned_cols=107  Identities=13%  Similarity=0.145  Sum_probs=68.2

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCe-EEEeeCCCCC---cccccccCCCccc--eE
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDV-KVIMATNRIE---TLDPALIRPGRID--RK   81 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v-~vi~ttn~~~---~id~~l~~~grf~--~~   81 (131)
                      ..|.+|+|||+|.+....         .....+..++...   ...+.+ ++++++..+.   .+++.+.+  ||.  ..
T Consensus       103 ~~~~vliiDe~~~~~~~~---------~~~~~l~~~l~~~---~~~~~~~ii~~~~~~~~~~~~~~~~l~~--r~~~~~~  168 (242)
T 3bos_A          103 EQFDLICIDDVDAVAGHP---------LWEEAIFDLYNRV---AEQKRGSLIVSASASPMEAGFVLPDLVS--RMHWGLT  168 (242)
T ss_dssp             GGSSEEEEETGGGGTTCH---------HHHHHHHHHHHHH---HHHCSCEEEEEESSCTTTTTCCCHHHHH--HHHHSEE
T ss_pred             cCCCEEEEeccccccCCH---------HHHHHHHHHHHHH---HHcCCCeEEEEcCCCHHHHHHhhhhhhh--HhhcCce
Confidence            347899999999985432         0112233333222   223344 5555555554   45688888  886  89


Q ss_pred             EEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHh
Q psy522           82 IEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAI  129 (131)
Q Consensus        82 i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l  129 (131)
                      +.+++|+.+++.++++.++...+.. .+..+..++..+.| +.+++..+
T Consensus       169 i~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g-~~r~l~~~  216 (242)
T 3bos_A          169 YQLQPMMDDEKLAALQRRAAMRGLQLPEDVGRFLLNRMAR-DLRTLFDV  216 (242)
T ss_dssp             EECCCCCGGGHHHHHHHHHHHTTCCCCHHHHHHHHHHTTT-CHHHHHHH
T ss_pred             EEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHccC-CHHHHHHH
Confidence            9999999999999999998754433 22346667777765 56665554

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=98.74  E-value=2.4e-08  Score=72.26  Aligned_cols=99  Identities=18%  Similarity=0.205  Sum_probs=69.0

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCC---CcccccccCCCccce-EEEe
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRI---ETLDPALIRPGRIDR-KIEF   84 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~---~~id~~l~~~grf~~-~i~~   84 (131)
                      .|.+|+|||+|.+...+         .....+..++..+.......++.+|++||.+   +.+++.+.+  ||.. .+.+
T Consensus       130 ~~~vlilDEi~~l~~~~---------~~~~~l~~l~~~~~~~~~~~~~~~I~~t~~~~~~~~l~~~l~~--r~~~~~i~l  198 (387)
T 2v1u_A          130 GIYIIVLDEIDFLPKRP---------GGQDLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKS--SLGEVELVF  198 (387)
T ss_dssp             SEEEEEEETTTHHHHST---------THHHHHHHHHHGGGCC-----CEEEEECSCSTTSSSSCHHHHT--TTTSEECCB
T ss_pred             CeEEEEEccHhhhcccC---------CCChHHHhHhhchhhcCCCceEEEEEEECCCchHhhhCHHHHh--cCCCeEEee
Confidence            48899999999986432         0124555566655543225578999999987   788999999  9975 8999


Q ss_pred             CCCCHHHHHHHHHHHhcC----CCCCCcccHHHHHHHcC
Q psy522           85 PLPDEKTKRRIFNIHTSR----MTLAEDVNLQELIMAKD  119 (131)
Q Consensus        85 ~~P~~~~R~~il~~~l~~----~~~~~~~~~~~la~~t~  119 (131)
                      ++|+.++..++++..+..    ..+. +..+..++..+.
T Consensus       199 ~~l~~~~~~~il~~~~~~~~~~~~~~-~~~~~~l~~~~~  236 (387)
T 2v1u_A          199 PPYTAPQLRDILETRAEEAFNPGVLD-PDVVPLCAALAA  236 (387)
T ss_dssp             CCCCHHHHHHHHHHHHHHHBCTTTBC-SSHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHhhccCCCCC-HHHHHHHHHHHH
Confidence            999999999999988753    2222 223666777666

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.73  E-value=5.7e-09  Score=68.25  Aligned_cols=78  Identities=24%  Similarity=0.310  Sum_probs=53.7

Q ss_pred             HhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCC-----cccccccCCCccce
Q psy522            6 EEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE-----TLDPALIRPGRIDR   80 (131)
Q Consensus         6 ~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~-----~id~~l~~~grf~~   80 (131)
                      +...|+||+|||+|.+...+.......   ....+..++       ..+++.+|++||.+.     .+++++++  ||+ 
T Consensus       112 ~~~~~~vl~iDe~~~l~~~~~~~~~~~---~~~~l~~~~-------~~~~~~~i~~~~~~~~~~~~~~~~~l~~--r~~-  178 (195)
T 1jbk_A          112 KQEGNVILFIDELHTMVGAGKADGAMD---AGNMLKPAL-------ARGELHCVGATTLDEYRQYIEKDAALER--RFQ-  178 (195)
T ss_dssp             HSTTTEEEEEETGGGGTT------CCC---CHHHHHHHH-------HTTSCCEEEEECHHHHHHHTTTCHHHHT--TEE-
T ss_pred             hcCCCeEEEEeCHHHHhccCcccchHH---HHHHHHHhh-------ccCCeEEEEeCCHHHHHHHHhcCHHHHH--Hhc-
Confidence            345689999999999976542211111   122333333       234677888888776     78999999  998 


Q ss_pred             EEEeCCCCHHHHHHHH
Q psy522           81 KIEFPLPDEKTKRRIF   96 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il   96 (131)
                      .+++++|+.++|.+|+
T Consensus       179 ~i~~~~p~~~~~~~il  194 (195)
T 1jbk_A          179 KVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             EEECCCCCHHHHHTTC
T ss_pred             eeecCCCCHHHHHHHh
Confidence            6999999999998875

>2dzn_B 26S protease regulatory subunit 6B homolog; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} PDB: 2dzo_B

Probab=98.71  E-value=7.3e-10  Score=64.47  Aligned_cols=42  Identities=43%  Similarity=0.611  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           90 KTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      ++|.+||+.++++.++..++|+..+|..|+||||+||+.+|+
T Consensus         1 ~~R~~Il~~~l~~~~~~~~vdl~~lA~~t~G~SGADi~~l~~   42 (82)
T 2dzn_B            1 MERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQ   42 (82)
T ss_dssp             -------------CEECTTCCSTTTTTSSCCCCHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCCCCCcCCHHHHHHHcCCCCHHHHHHHHH
Confidence            479999999999988878899999999999999999999984

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=98.70  E-value=1.4e-08  Score=71.92  Aligned_cols=112  Identities=16%  Similarity=0.288  Sum_probs=73.3

Q ss_pred             HhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCC------CCCCeEEEeeCCC---------------
Q psy522            6 EEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFD------SRGDVKVIMATNR---------------   64 (131)
Q Consensus         6 ~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~------~~~~v~vi~ttn~---------------   64 (131)
                      +....+||||||+|.+-.           .....+..++..-.-..      .-.++++|+|||.               
T Consensus       116 ~~~~~~vl~lDEi~~l~~-----------~~~~~Ll~~le~~~~~~~~~~~~~~~~~iiI~ttn~~~~~i~~~~~~~~~~  184 (311)
T 4fcw_A          116 RRRPYSVILFDAIEKAHP-----------DVFNILLQMLDDGRLTDSHGRTVDFRNTVIIMTSNLGSPLILEGLQKGWPY  184 (311)
T ss_dssp             HHCSSEEEEEETGGGSCH-----------HHHHHHHHHHHHSEEECTTSCEEECTTEEEEEEESTTHHHHHTTTTSCCCS
T ss_pred             HhCCCeEEEEeChhhcCH-----------HHHHHHHHHHhcCEEEcCCCCEEECCCcEEEEecccCHHHHHhhhcccccH
Confidence            344559999999998732           12233333333211000      1136789999998               


Q ss_pred             -----------CCcccccccCCCccceEEEeCCCCHHHHHHHHHHHhcCC-------CCC---CcccHHHHHHHcC--CC
Q psy522           65 -----------IETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRM-------TLA---EDVNLQELIMAKD--DL  121 (131)
Q Consensus        65 -----------~~~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~~-------~~~---~~~~~~~la~~t~--g~  121 (131)
                                 ...+++++.+  ||+..+.+++|+.+++..|+++++...       ...   .+..+..++...-  ..
T Consensus       185 ~~l~~~~~~~~~~~~~~~l~~--R~~~~~~~~p~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~g  262 (311)
T 4fcw_A          185 ERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRPLTKEQIRQIVEIQMSYLRARLAEKRISLELTEAAKDFLAERGYDPVF  262 (311)
T ss_dssp             STHHHHTHHHHHHHSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHTHHHHHHHHTTTCEEEECHHHHHHHHHHSCBTTT
T ss_pred             HHHHHHHHHHHHHhCCHHHHh--cCCeEEEeCCCCHHHHHHHHHHHHHHHHHHHHhCCcEEEeCHHHHHHHHHhCCCccC
Confidence                       5578899998  999999999999999999999987542       111   2223555666544  56


Q ss_pred             CHHHHHHhh
Q psy522          122 SGADIKAIC  130 (131)
Q Consensus       122 s~~di~~l~  130 (131)
                      ..++|+.++
T Consensus       263 n~R~L~~~i  271 (311)
T 4fcw_A          263 GARPLRRVI  271 (311)
T ss_dssp             BTTTHHHHH
T ss_pred             CchhHHHHH
Confidence            677776654

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=98.63  E-value=1.4e-08  Score=81.33  Aligned_cols=87  Identities=24%  Similarity=0.294  Sum_probs=54.1

Q ss_pred             HHHHHhc-CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCC----cccccccCCC
Q psy522            2 FRVAEEH-APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE----TLDPALIRPG   76 (131)
Q Consensus         2 F~~A~~~-~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~----~id~~l~~~g   76 (131)
                      |..++.. .|+||||||+|.+.+.....+   .......+..++       ..+.+.+|++||.++    .+++++.+  
T Consensus       255 ~~~~~~~~~~~iL~IDEi~~l~~~~~~~g---~~~~~~~L~~~l-------~~~~i~~I~at~~~~~~~~~~d~aL~r--  322 (854)
T 1qvr_A          255 IQEVVQSQGEVILFIDELHTVVGAGKAEG---AVDAGNMLKPAL-------ARGELRLIGATTLDEYREIEKDPALER--  322 (854)
T ss_dssp             HHHHHTTCSSEEEEECCC----------------------HHHH-------HTTCCCEEEEECHHHHHHHTTCTTTCS--
T ss_pred             HHHHHhcCCCeEEEEecHHHHhccCCccc---hHHHHHHHHHHH-------hCCCeEEEEecCchHHhhhccCHHHHh--
Confidence            4555554 789999999999986653211   111222333333       235677999998765    47999999  


Q ss_pred             ccceEEEeCCCCHHHHHHHHHHHhc
Q psy522           77 RIDRKIEFPLPDEKTKRRIFNIHTS  101 (131)
Q Consensus        77 rf~~~i~~~~P~~~~R~~il~~~l~  101 (131)
                      ||+. +.++.|+.+++.+|++.++.
T Consensus       323 Rf~~-i~l~~p~~~e~~~iL~~~~~  346 (854)
T 1qvr_A          323 RFQP-VYVDEPTVEETISILRGLKE  346 (854)
T ss_dssp             CCCC-EEECCCCHHHHHHHHHHHHH
T ss_pred             CCce-EEeCCCCHHHHHHHHHhhhh
Confidence            9985 99999999999999987765

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=98.63  E-value=9.6e-08  Score=69.37  Aligned_cols=91  Identities=20%  Similarity=0.245  Sum_probs=58.9

Q ss_pred             HhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCC-------------------CCCCeEEEeeCCCC-
Q psy522            6 EEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFD-------------------SRGDVKVIMATNRI-   65 (131)
Q Consensus         6 ~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-------------------~~~~v~vi~ttn~~-   65 (131)
                      ....|+||||||+|.+...+.+.+.........+...++..|++..                   ...++++|+++|.. 
T Consensus       113 ~~~~~~vl~lDEid~l~~~~~~~~~~~~~~~~~~~~~Ll~~leg~~~~~~~~~~~~~~~~~~~~i~tsn~~~i~~g~~~~  192 (363)
T 3hws_A          113 QKAQRGIVYIDQIDKISRKSDNPSITRDVSGEGVQQALLKLIEGTVAAVPPQGGRKHPQQEFLQVDTSKILFICGGAFAG  192 (363)
T ss_dssp             HHHHHCEEEEECHHHHCCCSSCC---CHHHHHHHHHHHHHHHHCC----------------CCCCCTTSSEEEEEECCTT
T ss_pred             HhcCCcEEEEeChhhhcccccccccccccchHHHHHHHHHHhcCceeeccCccccccCCCceEEEECCCceEEecCCcHH
Confidence            3446899999999999887754443333333346666666666321                   11233444444421 


Q ss_pred             ---------C------------------------------c-----ccccccCCCccceEEEeCCCCHHHHHHHHHH
Q psy522           66 ---------E------------------------------T-----LDPALIRPGRIDRKIEFPLPDEKTKRRIFNI   98 (131)
Q Consensus        66 ---------~------------------------------~-----id~~l~~~grf~~~i~~~~P~~~~R~~il~~   98 (131)
                               .                              .     +.+++..  ||+..+.+++|+.+++..|+..
T Consensus       193 l~~~i~~~~~~~~~~gf~~~~~~~~~~~~~~~l~~~v~~~~l~~~~~~~~l~~--R~~~~~~~~pl~~~~~~~I~~~  267 (363)
T 3hws_A          193 LDKVISHRVETGSGIGFGATVKAKSDKASEGELLAQVEPEDLIKFGLIPEFIG--RLPVVATLNELSEEALIQILKE  267 (363)
T ss_dssp             HHHHHHHHHCCCC------------CCSCHHHHHHTCCHHHHHHHTCCHHHHT--TCCEEEECCCCCHHHHHHHHHS
T ss_pred             HHHHHHHhhhccccCCccccccccccchhhHHHHHhCCHHHHHHcCCCHHHhc--ccCeeeecCCCCHHHHHHHHHH
Confidence                     1                              1     6778887  9999999999999999999986

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=98.59  E-value=8.2e-08  Score=72.18  Aligned_cols=97  Identities=24%  Similarity=0.276  Sum_probs=66.6

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCC-----cccccccCC
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE-----TLDPALIRP   75 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~-----~id~~l~~~   75 (131)
                      +|..++...|.|||||      ...            ...    +.+......+.+.+|++||.++     .+|+++++ 
T Consensus       259 ~~~~~~~~~~~iLfiD------~~~------------~a~----~~L~~~L~~g~v~vI~at~~~e~~~~~~~~~al~~-  315 (468)
T 3pxg_A          259 VMDEIRQAGNIILFID------AAI------------DAS----NILKPSLARGELQCIGATTLDEYRKYIEKDAALER-  315 (468)
T ss_dssp             HHHHHHTCCCCEEEEC------C------------------------CCCTTSSSCEEEEECCTTTTHHHHTTCSHHHH-
T ss_pred             HHHHHHhcCCeEEEEe------Cch------------hHH----HHHHHhhcCCCEEEEecCCHHHHHHHhhcCHHHHH-
Confidence            3667778889999999      100            011    1122223456799999999887     68999999 


Q ss_pred             CccceEEEeCCCCHHHHHHHHHHHhcCC----CCC-CcccHHHHHHHcCCCC
Q psy522           76 GRIDRKIEFPLPDEKTKRRIFNIHTSRM----TLA-EDVNLQELIMAKDDLS  122 (131)
Q Consensus        76 grf~~~i~~~~P~~~~R~~il~~~l~~~----~~~-~~~~~~~la~~t~g~s  122 (131)
                       ||. .+.++.|+.+++.+|++.++..+    +.. .+..+..++..+.+|.
T Consensus       316 -Rf~-~i~v~~p~~e~~~~iL~~~~~~~~~~~~~~i~~~al~~l~~~s~~~~  365 (468)
T 3pxg_A          316 -RFQ-PIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYI  365 (468)
T ss_dssp             -SEE-EEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHHHHHHHHHHHHHSS
T ss_pred             -hCc-cceeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHh
Confidence             997 59999999999999999987663    222 2233566666655544

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=98.55  E-value=1.1e-07  Score=75.12  Aligned_cols=78  Identities=26%  Similarity=0.268  Sum_probs=58.4

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCC-----cccccccCC
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE-----TLDPALIRP   75 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~-----~id~~l~~~   75 (131)
                      +|..++...|+|||||      ...            ...+    .+......+.+.+|++||..+     .+|++++| 
T Consensus       259 ~~~~~~~~~~~iLfiD------~~~------------~~~~----~L~~~l~~~~v~~I~at~~~~~~~~~~~d~al~r-  315 (758)
T 3pxi_A          259 VMDEIRQAGNIILFID------AAI------------DASN----ILKPSLARGELQCIGATTLDEYRKYIEKDAALER-  315 (758)
T ss_dssp             HHHHHHTCCCCEEEEC------C------------------------CCCTTSSSCEEEEECCTTTTHHHHTTCSHHHH-
T ss_pred             HHHHHHhcCCEEEEEc------Cch------------hHHH----HHHHHHhcCCEEEEeCCChHHHHHHhhccHHHHh-
Confidence            3677888899999999      000            0111    122223456799999999888     79999999 


Q ss_pred             CccceEEEeCCCCHHHHHHHHHHHhcCC
Q psy522           76 GRIDRKIEFPLPDEKTKRRIFNIHTSRM  103 (131)
Q Consensus        76 grf~~~i~~~~P~~~~R~~il~~~l~~~  103 (131)
                       ||. .|.++.|+.+++.+|++.+...+
T Consensus       316 -Rf~-~i~v~~p~~~~~~~il~~~~~~~  341 (758)
T 3pxi_A          316 -RFQ-PIQVDQPSVDESIQILQGLRDRY  341 (758)
T ss_dssp             -SEE-EEECCCCCHHHHHHHHHHTTTTS
T ss_pred             -hCc-EEEeCCCCHHHHHHHHHHHHHHH
Confidence             994 69999999999999999887663

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=98.53  E-value=5.9e-07  Score=64.86  Aligned_cols=101  Identities=22%  Similarity=0.259  Sum_probs=73.3

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      .+.||+|||+|.+..              .....++..++.  ..+++++|++|+.+..+.+.+++  |+ ..+.+++|+
T Consensus       119 ~~~vliiDe~~~l~~--------------~~~~~Ll~~le~--~~~~~~~Il~~~~~~~l~~~l~s--r~-~~i~~~~l~  179 (373)
T 1jr3_A          119 RFKVYLIDEVHMLSR--------------HSFNALLKTLEE--PPEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALD  179 (373)
T ss_dssp             SSEEEEEECGGGSCH--------------HHHHHHHHHHHS--CCSSEEEEEEESCGGGSCHHHHT--TS-EEEECCCCC
T ss_pred             CeEEEEEECcchhcH--------------HHHHHHHHHHhc--CCCceEEEEEeCChHhCcHHHHh--he-eEeeCCCCC
Confidence            478999999998732              133444555553  34578888889999999999998  87 689999999


Q ss_pred             HHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHh
Q psy522           89 EKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAI  129 (131)
Q Consensus        89 ~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l  129 (131)
                      .++...+++..+...+.. .+..+..++..+.| .+.++..+
T Consensus       180 ~~~~~~~l~~~~~~~~~~~~~~a~~~l~~~~~G-~~r~~~~~  220 (373)
T 1jr3_A          180 VEQIRHQLEHILNEEHIAHEPRALQLLARAAEG-SLRDALSL  220 (373)
T ss_dssp             HHHHHHHHHHHHHHHTCCBCHHHHHHHHHHSSS-CHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHCCC-CHHHHHHH
Confidence            999999999988654443 22336678888877 45555443

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.50  E-value=6.2e-07  Score=64.49  Aligned_cols=100  Identities=15%  Similarity=0.221  Sum_probs=70.3

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCC
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLP   87 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P   87 (131)
                      ..|.||+|||++.+- .             .....++..+...  ..++.+|.+|+.++.+.+.+++  |+ ..+.+++|
T Consensus       133 ~~~~vlilDE~~~L~-~-------------~~~~~L~~~le~~--~~~~~~Il~t~~~~~l~~~l~s--R~-~~~~~~~~  193 (354)
T 1sxj_E          133 HRYKCVIINEANSLT-K-------------DAQAALRRTMEKY--SKNIRLIMVCDSMSPIIAPIKS--QC-LLIRCPAP  193 (354)
T ss_dssp             -CCEEEEEECTTSSC-H-------------HHHHHHHHHHHHS--TTTEEEEEEESCSCSSCHHHHT--TS-EEEECCCC
T ss_pred             CCCeEEEEeCccccC-H-------------HHHHHHHHHHHhh--cCCCEEEEEeCCHHHHHHHHHh--hc-eEEecCCc
Confidence            367899999999852 1             1222333333332  2357888888999999999999  98 78999999


Q ss_pred             CHHHHHHHHHHHhcCCCCC-C-cccHHHHHHHcCCCCHHHHH
Q psy522           88 DEKTKRRIFNIHTSRMTLA-E-DVNLQELIMAKDDLSGADIK  127 (131)
Q Consensus        88 ~~~~R~~il~~~l~~~~~~-~-~~~~~~la~~t~g~s~~di~  127 (131)
                      +.++..++++..+...+.. + +..+..++..+.|- .+++.
T Consensus       194 ~~~~~~~~l~~~~~~~~~~~~~~~~l~~i~~~~~G~-~r~a~  234 (354)
T 1sxj_E          194 SDSEISTILSDVVTNERIQLETKDILKRIAQASNGN-LRVSL  234 (354)
T ss_dssp             CHHHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTTC-HHHHH
T ss_pred             CHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCCC-HHHHH
Confidence            9999999999988654443 2 34577788877663 44433

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=98.50  E-value=1.3e-07  Score=68.55  Aligned_cols=90  Identities=21%  Similarity=0.362  Sum_probs=64.3

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHH-HHHHHHHhcCCCCCCCeEEEeeCCCC---CcccccccCCCccceEEEeCC
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRT-MLELLNQLDGFDSRGDVKVIMATNRI---ETLDPALIRPGRIDRKIEFPL   86 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~v~vi~ttn~~---~~id~~l~~~grf~~~i~~~~   86 (131)
                      .||+|||+|.+...+.      .    .. +..++...      .++.+|+|||.+   +.+++.+.+  ||...+.+++
T Consensus       135 ~vlilDEi~~l~~~~~------~----~~~l~~l~~~~------~~~~iI~~t~~~~~~~~l~~~l~s--r~~~~i~l~~  196 (384)
T 2qby_B          135 AIIYLDEVDTLVKRRG------G----DIVLYQLLRSD------ANISVIMISNDINVRDYMEPRVLS--SLGPSVIFKP  196 (384)
T ss_dssp             EEEEEETTHHHHHSTT------S----HHHHHHHHTSS------SCEEEEEECSSTTTTTTSCHHHHH--TCCCEEEECC
T ss_pred             CEEEEECHHHhccCCC------C----ceeHHHHhcCC------cceEEEEEECCCchHhhhCHHHHh--cCCCeEEECC
Confidence            4999999999864320      1    12 33333211      678999999987   788999999  9878999999


Q ss_pred             CCHHHHHHHHHHHhcC----CCCCCcccHHHHHHHcC
Q psy522           87 PDEKTKRRIFNIHTSR----MTLAEDVNLQELIMAKD  119 (131)
Q Consensus        87 P~~~~R~~il~~~l~~----~~~~~~~~~~~la~~t~  119 (131)
                      |+.++..++++..+..    ..+ .+..+..++..+.
T Consensus       197 l~~~~~~~il~~~~~~~~~~~~~-~~~~~~~i~~~~~  232 (384)
T 2qby_B          197 YDAEQLKFILSKYAEYGLIKGTY-DDEILSYIAAISA  232 (384)
T ss_dssp             CCHHHHHHHHHHHHHHTSCTTSC-CSHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhhcccCCc-CHHHHHHHHHHHH
Confidence            9999999999998752    222 2234666777665

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=98.48  E-value=6.8e-07  Score=63.08  Aligned_cols=94  Identities=15%  Similarity=0.217  Sum_probs=69.6

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCC
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLP   87 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P   87 (131)
                      ..+.||+|||+|.+...              ....++..++.  ..+.+.+|++||.+..+++.+.+  |+. .+.+++|
T Consensus       101 ~~~~vliiDe~~~l~~~--------------~~~~L~~~le~--~~~~~~~i~~~~~~~~l~~~l~s--r~~-~i~~~~~  161 (319)
T 2chq_A          101 APFKIIFLDEADALTAD--------------AQAALRRTMEM--YSKSCRFILSCNYVSRIIEPIQS--RCA-VFRFKPV  161 (319)
T ss_dssp             CCCEEEEEETGGGSCHH--------------HHHTTGGGTSS--SSSSEEEEEEESCGGGSCHHHHT--TCE-EEECCCC
T ss_pred             CCceEEEEeCCCcCCHH--------------HHHHHHHHHHh--cCCCCeEEEEeCChhhcchHHHh--hCe-EEEecCC
Confidence            34799999999998421              22334444443  23568899999999999999999  886 8999999


Q ss_pred             CHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           88 DEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        88 ~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      +.++...++...+...+.. .+..+..++..+.|
T Consensus       162 ~~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~~~G  195 (319)
T 2chq_A          162 PKEAMKKRLLEICEKEGVKITEDGLEALIYISGG  195 (319)
T ss_dssp             CHHHHHHHHHHHHHTTCCCBCHHHHHHHHHTTTT
T ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            9999999999988766554 22346667766655

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=98.44  E-value=4.4e-07  Score=71.76  Aligned_cols=88  Identities=20%  Similarity=0.287  Sum_probs=59.9

Q ss_pred             HHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcC------CCCCCCeEEEeeCCCCCc--------
Q psy522            2 FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDG------FDSRGDVKVIMATNRIET--------   67 (131)
Q Consensus         2 F~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~------~~~~~~v~vi~ttn~~~~--------   67 (131)
                      +...+...++||||||+|.+-           ......+..+++.-.-      .....++++|+|||.+..        
T Consensus       572 ~~~~~~~~~~vl~lDEi~~~~-----------~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn~~~~~~~~~~~~  640 (758)
T 3pxi_A          572 TEKVRRKPYSVVLLDAIEKAH-----------PDVFNILLQVLEDGRLTDSKGRTVDFRNTILIMTSNVGASEKDKVMGE  640 (758)
T ss_dssp             HHHHHHCSSSEEEEECGGGSC-----------HHHHHHHHHHHHHSBCC-----CCBCTTCEEEEEESSSTTCCHHHHHH
T ss_pred             hHHHHhCCCeEEEEeCccccC-----------HHHHHHHHHHhccCeEEcCCCCEeccCCeEEEEeCCCChhhHHHHHHH
Confidence            345666778999999999862           1223334444433110      011235799999996544        


Q ss_pred             ----ccccccCCCccceEEEeCCCCHHHHHHHHHHHhcC
Q psy522           68 ----LDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSR  102 (131)
Q Consensus        68 ----id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~  102 (131)
                          +.+++++  ||+..+.+++|+.+++..|++.++..
T Consensus       641 ~~~~f~p~l~~--Rl~~~i~~~~l~~~~~~~i~~~~l~~  677 (758)
T 3pxi_A          641 LKRAFRPEFIN--RIDEIIVFHSLEKKHLTEIVSLMSDQ  677 (758)
T ss_dssp             HHHHSCHHHHT--TSSEEEECC--CHHHHHHHHHHHHHH
T ss_pred             HHhhCCHHHHh--hCCeEEecCCCCHHHHHHHHHHHHHH
Confidence                7888888  99999999999999999999988754

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=98.42  E-value=2.9e-07  Score=66.45  Aligned_cols=96  Identities=20%  Similarity=0.274  Sum_probs=64.4

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCC---CcccccccCCCccc-eEEEeC
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRI---ETLDPALIRPGRID-RKIEFP   85 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~---~~id~~l~~~grf~-~~i~~~   85 (131)
                      |.||+|||+|.+.....      .    ..+..++..++.. ...++.+|++|+.+   +.+++.+.+  ||. ..+.++
T Consensus       129 ~~vlilDE~~~l~~~~~------~----~~l~~l~~~~~~~-~~~~~~~I~~~~~~~~~~~~~~~~~~--r~~~~~i~l~  195 (386)
T 2qby_A          129 QVVIVLDEIDAFVKKYN------D----DILYKLSRINSEV-NKSKISFIGITNDVKFVDLLDPRVKS--SLSEEEIIFP  195 (386)
T ss_dssp             CEEEEEETHHHHHHSSC------S----THHHHHHHHHHSC-CC--EEEEEEESCGGGGGGCTTHHHH--TTTTEEEEEC
T ss_pred             eEEEEEcChhhhhccCc------C----HHHHHHhhchhhc-CCCeEEEEEEECCCChHhhhCHHHhc--cCCCeeEEeC
Confidence            89999999999864321      0    2344444445443 34578889999876   567888888  775 489999


Q ss_pred             CCCHHHHHHHHHHHhcC----CCCCCcccHHHHHHHcC
Q psy522           86 LPDEKTKRRIFNIHTSR----MTLAEDVNLQELIMAKD  119 (131)
Q Consensus        86 ~P~~~~R~~il~~~l~~----~~~~~~~~~~~la~~t~  119 (131)
                      +++.++..++++..+..    ..+. +..+..++..+.
T Consensus       196 ~l~~~~~~~il~~~~~~~~~~~~~~-~~~~~~l~~~~~  232 (386)
T 2qby_A          196 PYNAEELEDILTKRAQMAFKPGVLP-DNVIKLCAALAA  232 (386)
T ss_dssp             CCCHHHHHHHHHHHHHHHBCSSCSC-HHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhhccCCCCC-HHHHHHHHHHHH
Confidence            99999999999987642    2222 223455666555

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=98.41  E-value=3.6e-06  Score=60.54  Aligned_cols=95  Identities=15%  Similarity=0.138  Sum_probs=69.1

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      .+.|++|||+|.+..              ...+.++..++.  ..+++++|.+|+.++.+.+.+++  |+. .+.+++|+
T Consensus       108 ~~kvviIdead~l~~--------------~a~naLLk~lEe--p~~~~~~Il~t~~~~~l~~ti~S--Rc~-~~~~~~~~  168 (334)
T 1a5t_A          108 GAKVVWVTDAALLTD--------------AAANALLKTLEE--PPAETWFFLATREPERLLATLRS--RCR-LHYLAPPP  168 (334)
T ss_dssp             SCEEEEESCGGGBCH--------------HHHHHHHHHHTS--CCTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCC
T ss_pred             CcEEEEECchhhcCH--------------HHHHHHHHHhcC--CCCCeEEEEEeCChHhCcHHHhh--cce-eeeCCCCC
Confidence            468999999999842              133456666664  34568888899999999999999  885 79999999


Q ss_pred             HHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHH
Q psy522           89 EKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIK  127 (131)
Q Consensus        89 ~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~  127 (131)
                      .++..++++...   .. .+..+..++..+.|- ++...
T Consensus       169 ~~~~~~~L~~~~---~~-~~~~~~~l~~~s~G~-~r~a~  202 (334)
T 1a5t_A          169 EQYAVTWLSREV---TM-SQDALLAALRLSAGS-PGAAL  202 (334)
T ss_dssp             HHHHHHHHHHHC---CC-CHHHHHHHHHHTTTC-HHHHH
T ss_pred             HHHHHHHHHHhc---CC-CHHHHHHHHHHcCCC-HHHHH
Confidence            999999998775   22 223456677776663 44433

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.40  E-value=7.5e-07  Score=62.97  Aligned_cols=95  Identities=12%  Similarity=0.142  Sum_probs=67.9

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      .+.||+|||+|.+...              ....++..++.  ..+.+.+|.+||.+..+++.+.+  |+. .+.+++|+
T Consensus       107 ~~~viiiDe~~~l~~~--------------~~~~L~~~le~--~~~~~~~il~~~~~~~l~~~l~s--r~~-~i~~~~~~  167 (323)
T 1sxj_B          107 KHKIVILDEADSMTAG--------------AQQALRRTMEL--YSNSTRFAFACNQSNKIIEPLQS--QCA-ILRYSKLS  167 (323)
T ss_dssp             CCEEEEEESGGGSCHH--------------HHHTTHHHHHH--TTTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCC
T ss_pred             CceEEEEECcccCCHH--------------HHHHHHHHHhc--cCCCceEEEEeCChhhchhHHHh--hce-EEeecCCC
Confidence            4789999999998432              12223333332  23567888888999999999999  876 89999999


Q ss_pred             HHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCC
Q psy522           89 EKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLS  122 (131)
Q Consensus        89 ~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s  122 (131)
                      .++..++++..+...+.. .+..+..++..+.|-.
T Consensus       168 ~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~~  202 (323)
T 1sxj_B          168 DEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEGDM  202 (323)
T ss_dssp             HHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCH
Confidence            999999999887643333 2334667777776643

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=98.38  E-value=6.4e-08  Score=63.07  Aligned_cols=68  Identities=29%  Similarity=0.394  Sum_probs=46.6

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCC-----cccccccCCCccceEEE
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE-----TLDPALIRPGRIDRKIE   83 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~-----~id~~l~~~grf~~~i~   83 (131)
                      .|.+|+|||+|.+...+...+..  ......+..++       ...++.+|++||.+.     .+++++++  ||+ .+.
T Consensus       115 ~~~vl~iDe~~~l~~~~~~~~~~--~~~~~~l~~~~-------~~~~~~ii~~~~~~~~~~~~~~~~~l~~--R~~-~i~  182 (187)
T 2p65_A          115 GQVVMFIDEIHTVVGAGAVAEGA--LDAGNILKPML-------ARGELRCIGATTVSEYRQFIEKDKALER--RFQ-QIL  182 (187)
T ss_dssp             TSEEEEETTGGGGSSSSSSCTTS--CCTHHHHHHHH-------HTTCSCEEEEECHHHHHHHTTTCHHHHH--HEE-EEE
T ss_pred             CceEEEEeCHHHhcccccccccc--hHHHHHHHHHH-------hcCCeeEEEecCHHHHHHHHhccHHHHH--hcC-ccc
Confidence            68999999999998655311111  11222333333       235678899998765     68999999  998 499


Q ss_pred             eCCCC
Q psy522           84 FPLPD   88 (131)
Q Consensus        84 ~~~P~   88 (131)
                      +++|+
T Consensus       183 i~~p~  187 (187)
T 2p65_A          183 VEQPS  187 (187)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            99986

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=98.38  E-value=5.7e-07  Score=71.04  Aligned_cols=112  Identities=16%  Similarity=0.208  Sum_probs=73.7

Q ss_pred             HHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCC--C-------CCCeEEEeeCCCCC-------
Q psy522            3 RVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFD--S-------RGDVKVIMATNRIE-------   66 (131)
Q Consensus         3 ~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~-------~~~v~vi~ttn~~~-------   66 (131)
                      ...+...++||||||+|.+-           .   .+.+.++..++.-.  .       -.++++|+|||...       
T Consensus       551 ~~~~~~~~~vl~lDEi~~~~-----------~---~~~~~Ll~~le~~~~~~~~g~~~~~~~~~iI~tsN~~~~~~~~~~  616 (758)
T 1r6b_X          551 DAVIKHPHAVLLLDEIEKAH-----------P---DVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKS  616 (758)
T ss_dssp             HHHHHCSSEEEEEETGGGSC-----------H---HHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEECSSCC------
T ss_pred             HHHHhCCCcEEEEeCccccC-----------H---HHHHHHHHHhcCcEEEcCCCCEEecCCeEEEEecCcchhhhhhcc
Confidence            34456668999999999862           1   23444444444210  0       14588999999754       


Q ss_pred             ------------------cccccccCCCccceEEEeCCCCHHHHHHHHHHHhcCC-------C--CC-CcccHHHHHHHc
Q psy522           67 ------------------TLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRM-------T--LA-EDVNLQELIMAK  118 (131)
Q Consensus        67 ------------------~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~~-------~--~~-~~~~~~~la~~t  118 (131)
                                        .+++++++  ||+..|.+++|+.+++..|++.++...       .  +. .+.-+..+++..
T Consensus       617 ~g~~~~~~~~~~~~~~~~~~~~~l~~--R~~~~i~~~~l~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~a~~~l~~~~  694 (758)
T 1r6b_X          617 IGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTDVIHQVVDKFIVELQVQLDQKGVSLEVSQEARNWLAEKG  694 (758)
T ss_dssp             -----------CHHHHHHHSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHHHHHHHHTTEEEEECHHHHHHHHHHH
T ss_pred             cCccccchHHHHHHHHHHhcCHHHHh--hCCcceeeCCCCHHHHHHHHHHHHHHHHHHHHHCCcEEEeCHHHHHHHHHhC
Confidence                              67888998  999999999999999999999987632       1  11 122255566543


Q ss_pred             --CCCCHHHHHHhh
Q psy522          119 --DDLSGADIKAIC  130 (131)
Q Consensus       119 --~g~s~~di~~l~  130 (131)
                        .++..+++..++
T Consensus       695 ~~~~~g~R~l~~~i  708 (758)
T 1r6b_X          695 YDRAMGARPMARVI  708 (758)
T ss_dssp             CBTTTBTTTHHHHH
T ss_pred             CCcCCCchHHHHHH
Confidence              345566666553

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=98.38  E-value=1.9e-06  Score=61.01  Aligned_cols=94  Identities=16%  Similarity=0.236  Sum_probs=68.6

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCC
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLP   87 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P   87 (131)
                      ..+.+|+|||+|.+...              ....++..++.  ....+.+|++||.+..+++.+.+  |+. .+.+++|
T Consensus       109 ~~~~vliiDe~~~l~~~--------------~~~~L~~~le~--~~~~~~~i~~~~~~~~l~~~l~s--r~~-~~~~~~l  169 (327)
T 1iqp_A          109 ASFKIIFLDEADALTQD--------------AQQALRRTMEM--FSSNVRFILSCNYSSKIIEPIQS--RCA-IFRFRPL  169 (327)
T ss_dssp             CSCEEEEEETGGGSCHH--------------HHHHHHHHHHH--TTTTEEEEEEESCGGGSCHHHHH--TEE-EEECCCC
T ss_pred             CCCeEEEEeCCCcCCHH--------------HHHHHHHHHHh--cCCCCeEEEEeCCccccCHHHHh--hCc-EEEecCC
Confidence            35789999999998421              12233333332  23467888899999999999999  886 8999999


Q ss_pred             CHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           88 DEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        88 ~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      +.++...+++..+...+.. .+..+..++..+.|
T Consensus       170 ~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g  203 (327)
T 1iqp_A          170 RDEDIAKRLRYIAENEGLELTEEGLQAILYIAEG  203 (327)
T ss_dssp             CHHHHHHHHHHHHHTTTCEECHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHCCC
Confidence            9999999999988765543 23346667777766

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.36  E-value=2.3e-06  Score=61.25  Aligned_cols=94  Identities=14%  Similarity=0.227  Sum_probs=67.4

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      .+.||+|||+|.+...              ....++..++..  .....+|.+||.+..+++.+++  |+. .+.+++|+
T Consensus       133 ~~~vliiDE~~~l~~~--------------~~~~Ll~~le~~--~~~~~~il~~~~~~~l~~~l~s--R~~-~i~~~~~~  193 (353)
T 1sxj_D          133 PYKIIILDEADSMTAD--------------AQSALRRTMETY--SGVTRFCLICNYVTRIIDPLAS--QCS-KFRFKALD  193 (353)
T ss_dssp             SCEEEEETTGGGSCHH--------------HHHHHHHHHHHT--TTTEEEEEEESCGGGSCHHHHH--HSE-EEECCCCC
T ss_pred             CceEEEEECCCccCHH--------------HHHHHHHHHHhc--CCCceEEEEeCchhhCcchhhc--cCc-eEEeCCCC
Confidence            4569999999998432              122333334432  2346677788999999999999  986 89999999


Q ss_pred             HHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCC
Q psy522           89 EKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDL  121 (131)
Q Consensus        89 ~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~  121 (131)
                      .++...+++..+...+.. .+..+..++..+.|.
T Consensus       194 ~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~~~G~  227 (353)
T 1sxj_D          194 ASNAIDRLRFISEQENVKCDDGVLERILDISAGD  227 (353)
T ss_dssp             HHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCC
Confidence            999999999987655433 233467777777764

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.36  E-value=1.2e-06  Score=62.89  Aligned_cols=79  Identities=6%  Similarity=0.130  Sum_probs=58.9

Q ss_pred             hcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCc----ccccccCCCccc-eE
Q psy522            7 EHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIET----LDPALIRPGRID-RK   81 (131)
Q Consensus         7 ~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~----id~~l~~~grf~-~~   81 (131)
                      ...|.||+|||+|.+. .+            ..+..++....  ....++++|+++|..+.    +++++++  ||+ ..
T Consensus       130 ~~~~~ii~lDE~d~l~-~q------------~~L~~l~~~~~--~~~s~~~vI~i~n~~d~~~~~L~~~v~S--R~~~~~  192 (318)
T 3te6_A          130 KKRKTLILIQNPENLL-SE------------KILQYFEKWIS--SKNSKLSIICVGGHNVTIREQINIMPSL--KAHFTE  192 (318)
T ss_dssp             GSCEEEEEEECCSSSC-CT------------HHHHHHHHHHH--CSSCCEEEEEECCSSCCCHHHHHTCHHH--HTTEEE
T ss_pred             cCCceEEEEecHHHhh-cc------------hHHHHHHhccc--ccCCcEEEEEEecCcccchhhcchhhhc--cCCceE
Confidence            4568999999999997 11            23444443222  24467999999998754    5667778  887 68


Q ss_pred             EEeCCCCHHHHHHHHHHHhcC
Q psy522           82 IEFPLPDEKTKRRIFNIHTSR  102 (131)
Q Consensus        82 i~~~~P~~~~R~~il~~~l~~  102 (131)
                      |.|++.+.++-.+|++..+..
T Consensus       193 i~F~pYt~~el~~Il~~Rl~~  213 (318)
T 3te6_A          193 IKLNKVDKNELQQMIITRLKS  213 (318)
T ss_dssp             EECCCCCHHHHHHHHHHHHHH
T ss_pred             EEeCCCCHHHHHHHHHHHHHh
Confidence            999999999999999988765

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=98.35  E-value=1.1e-06  Score=62.76  Aligned_cols=79  Identities=19%  Similarity=0.332  Sum_probs=55.5

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHh----cC--CCCCCCeEEEeeCCCCC-----cccccccCCCccc
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQL----DG--FDSRGDVKVIMATNRIE-----TLDPALIRPGRID   79 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~----~~--~~~~~~v~vi~ttn~~~-----~id~~l~~~grf~   79 (131)
                      +|+||||+|.+-..           ....+...++.-    .+  .....++++|+|+|..+     .+++++++  ||+
T Consensus       111 ~vl~iDEi~~~~~~-----------~~~~Ll~~l~~~~~~~~g~~~~~~~~~~viat~np~~~~~~~~l~~~l~~--Rf~  177 (331)
T 2r44_A          111 NFILADEVNRSPAK-----------VQSALLECMQEKQVTIGDTTYPLDNPFLVLATQNPVEQEGTYPLPEAQVD--RFM  177 (331)
T ss_dssp             SEEEEETGGGSCHH-----------HHHHHHHHHHHSEEEETTEEEECCSSCEEEEEECTTCCSCCCCCCHHHHT--TSS
T ss_pred             cEEEEEccccCCHH-----------HHHHHHHHHhcCceeeCCEEEECCCCEEEEEecCCCcccCcccCCHHHHh--hee
Confidence            79999999986321           122333333321    01  11234678888888433     38999999  999


Q ss_pred             eEEEeCCCCHHHHHHHHHHHhcC
Q psy522           80 RKIEFPLPDEKTKRRIFNIHTSR  102 (131)
Q Consensus        80 ~~i~~~~P~~~~R~~il~~~l~~  102 (131)
                      ..+.++.|+.++|.+|++..+..
T Consensus       178 ~~i~i~~p~~~~~~~il~~~~~~  200 (331)
T 2r44_A          178 MKIHLTYLDKESELEVMRRVSNM  200 (331)
T ss_dssp             EEEECCCCCHHHHHHHHHHHHCT
T ss_pred             EEEEcCCCCHHHHHHHHHhcccc
Confidence            89999999999999999998765

>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=98.34  E-value=3.1e-06  Score=60.60  Aligned_cols=76  Identities=18%  Similarity=0.299  Sum_probs=53.5

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHH----hcCCCC----CCCeEEEeeCCCC-CcccccccCCCccce
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQ----LDGFDS----RGDVKVIMATNRI-ETLDPALIRPGRIDR   80 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~----~~~~~~----~~~v~vi~ttn~~-~~id~~l~~~grf~~   80 (131)
                      +.+|||||+|.+...           ....+..+++.    +.....    ..++++|+|||.. ..+++++++  ||+.
T Consensus       145 ~~vl~iDEi~~l~~~-----------~~~~Ll~~le~~~~~~~~~g~~~~~~~~~~li~~~n~~~~~l~~~L~~--R~~~  211 (350)
T 1g8p_A          145 RGYLYIDECNLLEDH-----------IVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLD--RFGL  211 (350)
T ss_dssp             TEEEEETTGGGSCHH-----------HHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHT--TCSE
T ss_pred             CCEEEEeChhhCCHH-----------HHHHHHHHHhcCceEEEecceEEeeCCceEEEEEeCCCCCCCCHHHHh--hcce
Confidence            689999999987422           12233333332    111000    1368999999964 489999999  9999


Q ss_pred             EEEeCCC-CHHHHHHHHHH
Q psy522           81 KIEFPLP-DEKTKRRIFNI   98 (131)
Q Consensus        81 ~i~~~~P-~~~~R~~il~~   98 (131)
                      .+.+++| +.++|.+|+++
T Consensus       212 ~~~l~~~~~~~~~~~il~~  230 (350)
T 1g8p_A          212 SVEVLSPRDVETRVEVIRR  230 (350)
T ss_dssp             EEECCCCCSHHHHHHHHHH
T ss_pred             EEEcCCCCcHHHHHHHHHH
Confidence            9999999 78888888876

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=98.33  E-value=1.6e-06  Score=61.74  Aligned_cols=95  Identities=21%  Similarity=0.319  Sum_probs=64.7

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      .+.||+|||+|.+...          .....+..+++..     .+++.+|+|||.+..+++++++  ||. .+.+++|+
T Consensus       105 ~~~vliiDEi~~l~~~----------~~~~~L~~~le~~-----~~~~~iI~~~n~~~~l~~~l~s--R~~-~i~~~~~~  166 (324)
T 3u61_B          105 RQKVIVIDEFDRSGLA----------ESQRHLRSFMEAY-----SSNCSIIITANNIDGIIKPLQS--RCR-VITFGQPT  166 (324)
T ss_dssp             CEEEEEEESCCCGGGH----------HHHHHHHHHHHHH-----GGGCEEEEEESSGGGSCTTHHH--HSE-EEECCCCC
T ss_pred             CCeEEEEECCcccCcH----------HHHHHHHHHHHhC-----CCCcEEEEEeCCccccCHHHHh--hCc-EEEeCCCC
Confidence            5789999999998511          1122333333322     2457889999999999999999  995 79999999


Q ss_pred             HHHHHHHHHHHhc-------CCCCC-Cc-ccHHHHHHHcCCC
Q psy522           89 EKTKRRIFNIHTS-------RMTLA-ED-VNLQELIMAKDDL  121 (131)
Q Consensus        89 ~~~R~~il~~~l~-------~~~~~-~~-~~~~~la~~t~g~  121 (131)
                      .++|.++++.++.       ..+.. .+ ..+..++..+.|-
T Consensus       167 ~~e~~~il~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~gd  208 (324)
T 3u61_B          167 DEDKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVKKNFPD  208 (324)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCBSCHHHHHHHHHHTCSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHhCCCC
Confidence            9998777655432       12222 22 3466777776664

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=98.30  E-value=1.3e-06  Score=65.33  Aligned_cols=92  Identities=17%  Similarity=0.246  Sum_probs=60.9

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeC--CCCCcccccccCCCccceEEEeC
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMAT--NRIETLDPALIRPGRIDRKIEFP   85 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~tt--n~~~~id~~l~~~grf~~~i~~~   85 (131)
                      ..+.||||||+|.+....              ...++..++.    +.+++|++|  |....+++++++  |+. .+.++
T Consensus       105 ~~~~iLfIDEI~~l~~~~--------------q~~LL~~le~----~~v~lI~att~n~~~~l~~aL~s--R~~-v~~l~  163 (447)
T 3pvs_A          105 GRRTILFVDEVHRFNKSQ--------------QDAFLPHIED----GTITFIGATTENPSFELNSALLS--RAR-VYLLK  163 (447)
T ss_dssp             TCCEEEEEETTTCC--------------------CCHHHHHT----TSCEEEEEESSCGGGSSCHHHHT--TEE-EEECC
T ss_pred             CCCcEEEEeChhhhCHHH--------------HHHHHHHHhc----CceEEEecCCCCcccccCHHHhC--cee-EEeeC
Confidence            468999999999984332              1223444432    456666655  345689999999  986 78899


Q ss_pred             CCCHHHHHHHHHHHhcCCC-------CC-CcccHHHHHHHcCC
Q psy522           86 LPDEKTKRRIFNIHTSRMT-------LA-EDVNLQELIMAKDD  120 (131)
Q Consensus        86 ~P~~~~R~~il~~~l~~~~-------~~-~~~~~~~la~~t~g  120 (131)
                      +|+.++...+++..+....       .. .+..+..++..+.|
T Consensus       164 ~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~al~~L~~~~~G  206 (447)
T 3pvs_A          164 SLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNG  206 (447)
T ss_dssp             CCCHHHHHHHHHHHHHCTTTSSTTSSEECCHHHHHHHHHHHCS
T ss_pred             CcCHHHHHHHHHHHHHHHhhhhccccCcCCHHHHHHHHHHCCC
Confidence            9999999999999987621       11 22235666666555

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=98.29  E-value=1.6e-06  Score=62.82  Aligned_cols=95  Identities=11%  Similarity=0.056  Sum_probs=66.7

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCC--CCCeEEEeeCCCC---CcccccccCCCccce-E
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDS--RGDVKVIMATNRI---ETLDPALIRPGRIDR-K   81 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~v~vi~ttn~~---~~id~~l~~~grf~~-~   81 (131)
                      ..|.||+|||+|.+  .         .   ..+..++..+.....  ..++.+|++||.+   +.+++.+.+  ||.. .
T Consensus       124 ~~~~vlilDE~~~l--~---------~---~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~~~~~l~~~~~~--r~~~~~  187 (389)
T 1fnn_A          124 DLYMFLVLDDAFNL--A---------P---DILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRG--IMGKYV  187 (389)
T ss_dssp             TCCEEEEEETGGGS--C---------H---HHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSCHHHHH--HHTTCE
T ss_pred             CCeEEEEEECcccc--c---------h---HHHHHHHHHHHhCCCCCcCCEEEEEEECCchHHHHhCHHhhh--cCCCce
Confidence            45899999999998  1         1   234444444443322  1478889999887   667888888  8875 8


Q ss_pred             EEeCCCCHHHHHHHHHHHhcC---CCCCCcccHHHHHHHc
Q psy522           82 IEFPLPDEKTKRRIFNIHTSR---MTLAEDVNLQELIMAK  118 (131)
Q Consensus        82 i~~~~P~~~~R~~il~~~l~~---~~~~~~~~~~~la~~t  118 (131)
                      +.+++++.++..++++..+..   ...-.+..+..++..+
T Consensus       188 i~~~pl~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~  227 (389)
T 1fnn_A          188 IRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADIT  227 (389)
T ss_dssp             EECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHH
T ss_pred             EEeCCCCHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHH
Confidence            999999999999999888753   1111333467788888

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.26  E-value=3.3e-06  Score=64.15  Aligned_cols=96  Identities=14%  Similarity=0.230  Sum_probs=60.9

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCC
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLP   87 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P   87 (131)
                      ..+.||+|||+|.+.....        .....+..++..     ...++++++++.....+++ +.   |+...+.+++|
T Consensus       147 ~~~~vliIDEid~l~~~~~--------~~l~~L~~~l~~-----~~~~iIli~~~~~~~~l~~-l~---~r~~~i~f~~~  209 (516)
T 1sxj_A          147 GKHFVIIMDEVDGMSGGDR--------GGVGQLAQFCRK-----TSTPLILICNERNLPKMRP-FD---RVCLDIQFRRP  209 (516)
T ss_dssp             TTSEEEEECSGGGCCTTST--------THHHHHHHHHHH-----CSSCEEEEESCTTSSTTGG-GT---TTSEEEECCCC
T ss_pred             CCCeEEEEECCCccchhhH--------HHHHHHHHHHHh-----cCCCEEEEEcCCCCccchh-hH---hceEEEEeCCC
Confidence            5689999999999975431        112233333322     2334666665555455543 44   44568999999


Q ss_pred             CHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           88 DEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        88 ~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      +.+++.++++..+...+.. .+..+..+++.+.|
T Consensus       210 ~~~~~~~~L~~i~~~~~~~i~~~~l~~la~~s~G  243 (516)
T 1sxj_A          210 DANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRG  243 (516)
T ss_dssp             CHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHTTT
T ss_pred             CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            9999999998876543322 22347788888766

>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=98.16  E-value=4.1e-06  Score=62.69  Aligned_cols=90  Identities=17%  Similarity=0.246  Sum_probs=62.3

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEee---------CC---CCCcccccccCCCc
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMA---------TN---RIETLDPALIRPGR   77 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~t---------tn---~~~~id~~l~~~gr   77 (131)
                      |.|++|||+|.+-              ....+.++..+...  ..++++++|         ++   .++.+++.+++  |
T Consensus       296 ~~VliIDEa~~l~--------------~~a~~aLlk~lEe~--~~~~~il~tn~~~~~i~~~~~~~~~~~l~~~i~s--R  357 (456)
T 2c9o_A          296 PGVLFVDEVHMLD--------------IECFTYLHRALESS--IAPIVIFASNRGNCVIRGTEDITSPHGIPLDLLD--R  357 (456)
T ss_dssp             ECEEEEESGGGCB--------------HHHHHHHHHHTTST--TCCEEEEEECCSEEECBTTSSCEEETTCCHHHHT--T
T ss_pred             ceEEEEechhhcC--------------HHHHHHHHHHhhcc--CCCEEEEecCCccccccccccccccccCChhHHh--h
Confidence            4699999999983              13556667777653  233655566         43   37889999999  9


Q ss_pred             cceEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHc
Q psy522           78 IDRKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAK  118 (131)
Q Consensus        78 f~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t  118 (131)
                      |.. +.+++++.++..++++..+...+.. .+..+..++..+
T Consensus       358 ~~~-~~~~~~~~~e~~~iL~~~~~~~~~~~~~~~~~~i~~~a  398 (456)
T 2c9o_A          358 VMI-IRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIG  398 (456)
T ss_dssp             EEE-EECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHH
T ss_pred             cce-eeCCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHc
Confidence            976 6999999999999998876533222 222345555554

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=98.15  E-value=1.2e-05  Score=57.72  Aligned_cols=72  Identities=18%  Similarity=0.148  Sum_probs=56.8

Q ss_pred             CeEEEeeCCCCCcccccccCCCccceEEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHh
Q psy522           55 DVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAI  129 (131)
Q Consensus        55 ~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l  129 (131)
                      .+.++++|+.+..+++.+++  ||...+.+++|+.++..++++...+..+.. .+..+..++..+.|. ++++..+
T Consensus       150 ~~~li~at~~~~~Ls~~l~s--R~~l~~~Ld~~~~~~l~~iL~~~~~~~~~~~~~~~~~~ia~~~~G~-~R~a~~l  222 (334)
T 1in4_A          150 PFTLVGATTRSGLLSSPLRS--RFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGT-PRIAIRL  222 (334)
T ss_dssp             CCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTTC-HHHHHHH
T ss_pred             CeEEEEecCCcccCCHHHHH--hcCceeeCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhcCCC-hHHHHHH
Confidence            46788899999999999999  999889999999999999999887654443 233477788888774 4555443

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=98.15  E-value=2.5e-06  Score=68.35  Aligned_cols=110  Identities=18%  Similarity=0.268  Sum_probs=72.6

Q ss_pred             HHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCC---------CCCCeEEEeeCCCC----------
Q psy522            5 AEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFD---------SRGDVKVIMATNRI----------   65 (131)
Q Consensus         5 A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---------~~~~v~vi~ttn~~----------   65 (131)
                      .+...++||||||+|.+-.              .+.+.++..++.-.         .-.++++|+|||..          
T Consensus       656 ~~~~~~~vl~lDEi~~l~~--------------~~~~~Ll~~l~~~~~~~~~g~~vd~~~~iiI~tsn~~~~~~~~~~~~  721 (854)
T 1qvr_A          656 VRRRPYSVILFDEIEKAHP--------------DVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPLILEGLQK  721 (854)
T ss_dssp             HHHCSSEEEEESSGGGSCH--------------HHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCTTHHHHHHHHHT
T ss_pred             HHhCCCeEEEEecccccCH--------------HHHHHHHHHhccCceECCCCCEeccCCeEEEEecCcChHHHhhhccc
Confidence            4455679999999997621              34555555555321         01368899999962          


Q ss_pred             ----------------CcccccccCCCccceEEEeCCCCHHHHHHHHHHHhcCC---------CCC-CcccHHHHHHHcC
Q psy522           66 ----------------ETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRM---------TLA-EDVNLQELIMAKD  119 (131)
Q Consensus        66 ----------------~~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~~---------~~~-~~~~~~~la~~t~  119 (131)
                                      ..+.++|+.  ||+..+.+.+|+.++...|+++++...         ... .+.-+..++...-
T Consensus       722 ~~~~~~l~~~v~~~~~~~f~~~l~~--Rl~~~i~~~pl~~edi~~i~~~~l~~~~~~~~~~~~~~~~~~~a~~~L~~~~~  799 (854)
T 1qvr_A          722 GWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRPLTKEQIRQIVEIQLSYLRARLAEKRISLELTEAAKDFLAERGY  799 (854)
T ss_dssp             TCCHHHHHHHHHHHHHTTSCHHHHH--TCSBCCBCCCCCHHHHHHHHHHHHHHHHHHHHTTTCEEEECHHHHHHHHHHHC
T ss_pred             ccchHHHHHHHHHHHHhhCCHHHHH--hcCeEEeCCCCCHHHHHHHHHHHHHHHHHHHHhCCceEEECHHHHHHHHHcCC
Confidence                            234567777  999999999999999999999887521         111 1223555666544


Q ss_pred             --CCCHHHHHHhh
Q psy522          120 --DLSGADIKAIC  130 (131)
Q Consensus       120 --g~s~~di~~l~  130 (131)
                        .+..++|+.++
T Consensus       800 ~~~gn~R~L~~~i  812 (854)
T 1qvr_A          800 DPVFGARPLRRVI  812 (854)
T ss_dssp             BTTTBTSTHHHHH
T ss_pred             CCCCChHHHHHHH
Confidence              56667776654

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=98.09  E-value=6.4e-06  Score=63.67  Aligned_cols=80  Identities=28%  Similarity=0.310  Sum_probs=54.8

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhc------CC--CCCCCeEEEeeCCCCC-------------cc
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLD------GF--DSRGDVKVIMATNRIE-------------TL   68 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~------~~--~~~~~v~vi~ttn~~~-------------~i   68 (131)
                      .+|+||||+|.+-..           ....+.++++.-.      +.  ....++.+|+|||.++             .+
T Consensus       392 ~gil~IDEid~l~~~-----------~q~~Ll~~le~~~i~i~~~g~~~~~~~~~~vIaatNp~~G~~~~~~~~~~ni~l  460 (595)
T 3f9v_A          392 GGIAVIDEIDKMRDE-----------DRVAIHEAMEQQTVSIAKAGIVAKLNARAAVIAAGNPKFGRYISERPVSDNINL  460 (595)
T ss_dssp             SSEECCTTTTCCCSH-----------HHHHHHHHHHSSSEEEESSSSEEEECCCCEEEEEECCTTCCSCTTSCSCTTTCS
T ss_pred             CCcEEeehhhhCCHh-----------HhhhhHHHHhCCEEEEecCCcEEEecCceEEEEEcCCcCCccCcccCchhccCC
Confidence            489999999997432           1233333433210      11  1124688999999876             89


Q ss_pred             cccccCCCccc-eEEEeCCCCHHHHHHHHHHHhcCC
Q psy522           69 DPALIRPGRID-RKIEFPLPDEKTKRRIFNIHTSRM  103 (131)
Q Consensus        69 d~~l~~~grf~-~~i~~~~P~~~~R~~il~~~l~~~  103 (131)
                      ++++++  ||| ..+..+.|+.+ ...|.++.+...
T Consensus       461 ~~aLl~--RFDl~~~~~~~~~~e-~~~i~~~il~~~  493 (595)
T 3f9v_A          461 PPTILS--RFDLIFILKDQPGEQ-DRELANYILDVH  493 (595)
T ss_dssp             CSSSGG--GCSCCEEECCTTHHH-HHHHHHHHHTTT
T ss_pred             CHHHHh--hCeEEEEeCCCCCHH-HHHHHHHHHHHh
Confidence            999999  998 45666778888 888888887643

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=98.02  E-value=1.3e-05  Score=58.34  Aligned_cols=28  Identities=21%  Similarity=0.177  Sum_probs=24.0

Q ss_pred             ccccccCCCccceEEEeCCCCHHHHHHHHH
Q psy522           68 LDPALIRPGRIDRKIEFPLPDEKTKRRIFN   97 (131)
Q Consensus        68 id~~l~~~grf~~~i~~~~P~~~~R~~il~   97 (131)
                      +.+.+.+  ||+..+.+++++.++...++.
T Consensus       256 ~~p~l~~--R~~~~i~~~~l~~~~l~~i~~  283 (376)
T 1um8_A          256 LIPELIG--RLPVLSTLDSISLEAMVDILQ  283 (376)
T ss_dssp             CCHHHHT--TCCEEEECCCCCHHHHHHHHH
T ss_pred             CChHHhc--CCCceeeccCCCHHHHHHHHh
Confidence            4567777  898899999999999999886

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=97.96  E-value=1.9e-05  Score=69.56  Aligned_cols=85  Identities=19%  Similarity=0.349  Sum_probs=61.6

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCC--------CCeEEEeeCCCCC-----cccccccCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSR--------GDVKVIMATNRIE-----TLDPALIRP   75 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~--------~~v~vi~ttn~~~-----~id~~l~~~   75 (131)
                      +++||||||+|....++.     ........+.++++. +++...        .++.+|||||.|.     .|+++++| 
T Consensus      1336 k~~VlFiDEinmp~~d~y-----g~q~~lelLRq~le~-gg~yd~~~~~~~~~~~i~lIaA~Npp~~gGR~~l~~rllR- 1408 (2695)
T 4akg_A         1336 KNLVLFCDEINLPKLDKY-----GSQNVVLFLRQLMEK-QGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFTR- 1408 (2695)
T ss_dssp             SCEEEEEETTTCSCCCSS-----SCCHHHHHHHHHHHT-SSEECTTTCCEEEEESEEEEEEECCTTSTTCCCCCHHHHT-
T ss_pred             ceEEEEeccccccccccc-----CchhHHHHHHHHHhc-CCEEEcCCCcEEEecCEEEEEecCCCccCCCccCChhhhh-
Confidence            458999999987433321     122344566666632 222111        3589999999985     89999999 


Q ss_pred             CccceEEEeCCCCHHHHHHHHHHHhcC
Q psy522           76 GRIDRKIEFPLPDEKTKRRIFNIHTSR  102 (131)
Q Consensus        76 grf~~~i~~~~P~~~~R~~il~~~l~~  102 (131)
                       || ..+.++.|+.+++..|+..++..
T Consensus      1409 -rf-~vi~i~~P~~~~l~~I~~~il~~ 1433 (2695)
T 4akg_A         1409 -HA-AILYLGYPSGKSLSQIYEIYYKA 1433 (2695)
T ss_dssp             -TE-EEEECCCCTTTHHHHHHHHHHHH
T ss_pred             -ee-eEEEeCCCCHHHHHHHHHHHHHH
Confidence             99 78999999999999999888753

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=97.95  E-value=1.5e-05  Score=60.45  Aligned_cols=76  Identities=21%  Similarity=0.248  Sum_probs=48.1

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcC-------C-CCCCCeEEEeeCCC-CC--cccccccCCCc
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDG-------F-DSRGDVKVIMATNR-IE--TLDPALIRPGR   77 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~-------~-~~~~~v~vi~ttn~-~~--~id~~l~~~gr   77 (131)
                      .++||||||++.+-+              .....++..|+.       . ...+..++|+|||. |+  ...+++++  |
T Consensus       109 ~~~IL~IDEI~r~~~--------------~~q~~LL~~lee~~v~i~G~~~~~~~~~iI~ATN~lpe~~~~~~aLld--R  172 (500)
T 3nbx_X          109 EAEIVFLDEIWKAGP--------------AILNTLLTAINERQFRNGAHVEKIPMRLLVAASNELPEADSSLEALYD--R  172 (500)
T ss_dssp             GCSEEEEESGGGCCH--------------HHHHHHHHHHHSSEEECSSSEEECCCCEEEEEESSCCCTTCTTHHHHT--T
T ss_pred             cceeeeHHhHhhhcH--------------HHHHHHHHHHHHHhccCCCCcCCcchhhhhhccccCCCccccHHHHHH--H
Confidence            467999999976421              233334444431       1 11123355667774 22  13358999  9


Q ss_pred             cceEEEeCCCCH-HHHHHHHHHHh
Q psy522           78 IDRKIEFPLPDE-KTKRRIFNIHT  100 (131)
Q Consensus        78 f~~~i~~~~P~~-~~R~~il~~~l  100 (131)
                      |...+.+++|+. +++.+|++...
T Consensus       173 F~~~i~v~~p~~~ee~~~IL~~~~  196 (500)
T 3nbx_X          173 MLIRLWLDKVQDKANFRSMLTSQQ  196 (500)
T ss_dssp             CCEEEECCSCCCHHHHHHHHTCCC
T ss_pred             HHHHHHHHHhhhhhhHHHHHhccc
Confidence            999999999976 78889987654

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.91  E-value=6.2e-05  Score=53.97  Aligned_cols=92  Identities=16%  Similarity=0.229  Sum_probs=63.6

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      +.|+++||+|.+...              ....++..++..  ...+.+|.+||.+..+.+.+++  |+. .+.+++++.
T Consensus       111 ~~viiiDe~~~l~~~--------------~~~~L~~~le~~--~~~~~~il~~n~~~~i~~~i~s--R~~-~~~~~~l~~  171 (340)
T 1sxj_C          111 FKLIILDEADAMTNA--------------AQNALRRVIERY--TKNTRFCVLANYAHKLTPALLS--QCT-RFRFQPLPQ  171 (340)
T ss_dssp             CEEEEETTGGGSCHH--------------HHHHHHHHHHHT--TTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCH
T ss_pred             ceEEEEeCCCCCCHH--------------HHHHHHHHHhcC--CCCeEEEEEecCccccchhHHh--hce-eEeccCCCH
Confidence            689999999987421              122233334432  2456777888999999999999  986 789999999


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      ++..+.+...+...+.. .+..+..++..+.|
T Consensus       172 ~~~~~~l~~~~~~~~~~i~~~~~~~i~~~s~G  203 (340)
T 1sxj_C          172 EAIERRIANVLVHEKLKLSPNAEKALIELSNG  203 (340)
T ss_dssp             HHHHHHHHHHHHTTTCCBCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            99999998888544332 22235556665554

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=97.74  E-value=8.3e-05  Score=54.13  Aligned_cols=102  Identities=12%  Similarity=0.161  Sum_probs=63.5

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCC-CC--CCeEEEeeCCCCC---ccc---ccccCCCcc
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFD-SR--GDVKVIMATNRIE---TLD---PALIRPGRI   78 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~--~~v~vi~ttn~~~---~id---~~l~~~grf   78 (131)
                      ..|.||+|||+|.+...+.     ...   ..+..++..+.... ..  .++.+|++|+.++   .++   +.+.+  +|
T Consensus       137 ~~~~llvlDe~~~l~~~~~-----~~~---~~l~~l~~~~~~~~~~~~~~~v~lI~~~~~~~~~~~l~~~~~~~~~--~~  206 (412)
T 1w5s_A          137 NHYLLVILDEFQSMLSSPR-----IAA---EDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVES--QI  206 (412)
T ss_dssp             TCEEEEEEESTHHHHSCTT-----SCH---HHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHT--TC
T ss_pred             CCeEEEEEeCHHHHhhccC-----cch---HHHHHHHHHHHhcccCCCCceEEEEEEeccccHHHHHhhhcchhhh--hc
Confidence            4689999999999864310     011   12222222222221 12  5788888887655   344   56667  66


Q ss_pred             ceEEEeCCCCHHHHHHHHHHHhcCCC---CCCcccHHHHHHHcC
Q psy522           79 DRKIEFPLPDEKTKRRIFNIHTSRMT---LAEDVNLQELIMAKD  119 (131)
Q Consensus        79 ~~~i~~~~P~~~~R~~il~~~l~~~~---~~~~~~~~~la~~t~  119 (131)
                      ...+.+++++.++..+++...+....   ...+..+..++..+.
T Consensus       207 ~~~i~l~~l~~~e~~~ll~~~~~~~~~~~~~~~~~~~~i~~~~~  250 (412)
T 1w5s_A          207 GFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYG  250 (412)
T ss_dssp             SEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHC
T ss_pred             CCeeeeCCCCHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHH
Confidence            66699999999999999987654211   112334667788888

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=97.70  E-value=6.1e-05  Score=53.65  Aligned_cols=70  Identities=14%  Similarity=0.206  Sum_probs=55.4

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-|++|||+|.+-.              ...+.++..++.  ..+.+++|.+|+.++.+.+.+++  |   .+.+++|+.
T Consensus        83 ~kvviIdead~lt~--------------~a~naLLk~LEe--p~~~t~fIl~t~~~~kl~~tI~S--R---~~~f~~l~~  141 (305)
T 2gno_A           83 RKYVIVHDCERMTQ--------------QAANAFLKALEE--PPEYAVIVLNTRRWHYLLPTIKS--R---VFRVVVNVP  141 (305)
T ss_dssp             SEEEEETTGGGBCH--------------HHHHHTHHHHHS--CCTTEEEEEEESCGGGSCHHHHT--T---SEEEECCCC
T ss_pred             ceEEEeccHHHhCH--------------HHHHHHHHHHhC--CCCCeEEEEEECChHhChHHHHc--e---eEeCCCCCH
Confidence            46999999999842              234456666664  34567888888899999999999  8   799999999


Q ss_pred             HHHHHHHHHHh
Q psy522           90 KTKRRIFNIHT  100 (131)
Q Consensus        90 ~~R~~il~~~l  100 (131)
                      ++-.++++..+
T Consensus       142 ~~i~~~L~~~~  152 (305)
T 2gno_A          142 KEFRDLVKEKI  152 (305)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHh
Confidence            99999888775

>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=97.65  E-value=0.00051  Score=51.38  Aligned_cols=84  Identities=27%  Similarity=0.361  Sum_probs=58.2

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCC--------CCCCeEEEeeC----CCCCcccccccCCCc
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFD--------SRGDVKVIMAT----NRIETLDPALIRPGR   77 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--------~~~~v~vi~tt----n~~~~id~~l~~~gr   77 (131)
                      ..|+++||+|++....++  .........+...+|..+++-.        ..+++++|+|.    +.|..+-|.++.  |
T Consensus       251 ~~il~~DEidki~~~~~~--~~~D~s~egvq~aLL~~le~~~~~~~~~~~d~~~ilfI~~gaf~~~~~~dlipel~~--R  326 (444)
T 1g41_A          251 NGIVFIDEIDKICKKGEY--SGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG--R  326 (444)
T ss_dssp             HCEEEEETGGGGSCCSSC--SSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSCCGGGSCHHHHT--T
T ss_pred             CCeeeHHHHHHHhhccCC--CCCCchHHHHHHHHHHHhcccccccccceecCCcEEEEeccccccCChhhcchHHhc--c
Confidence            358999999999866432  1222222234556677677521        34578899886    244545577888  9


Q ss_pred             cceEEEeCCCCHHHHHHHHH
Q psy522           78 IDRKIEFPLPDEKTKRRIFN   97 (131)
Q Consensus        78 f~~~i~~~~P~~~~R~~il~   97 (131)
                      |...+.++..+.++...|+.
T Consensus       327 ~~i~i~l~~lt~~e~~~Il~  346 (444)
T 1g41_A          327 LPIRVELTALSAADFERILT  346 (444)
T ss_dssp             CCEEEECCCCCHHHHHHHHH
T ss_pred             cceeeeCCCCCHHHHHHHHH
Confidence            99999999999999999983

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=97.16  E-value=0.0013  Score=44.00  Aligned_cols=72  Identities=18%  Similarity=0.198  Sum_probs=49.5

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      .++||+|||++.+++.+.....  ..       .++..+..- .....-+|.+|+.+..++.+++.  |++.+++++.|.
T Consensus        87 ~~~vliIDEAq~l~~~~~~~~e--~~-------rll~~l~~~-r~~~~~iil~tq~~~~l~~~lr~--ri~~~~~l~~~~  154 (199)
T 2r2a_A           87 IGSIVIVDEAQDVWPARSAGSK--IP-------ENVQWLNTH-RHQGIDIFVLTQGPKLLDQNLRT--LVRKHYHIASNK  154 (199)
T ss_dssp             TTCEEEETTGGGTSBCCCTTCC--CC-------HHHHGGGGT-TTTTCEEEEEESCGGGBCHHHHT--TEEEEEEEEECS
T ss_pred             CceEEEEEChhhhccCccccch--hH-------HHHHHHHhc-CcCCeEEEEECCCHHHHhHHHHH--HhheEEEEcCcc
Confidence            4789999999999866522111  11       133344332 23455667777889999999998  999999999876


Q ss_pred             HHHH
Q psy522           89 EKTK   92 (131)
Q Consensus        89 ~~~R   92 (131)
                      ...|
T Consensus       155 ~~~~  158 (199)
T 2r2a_A          155 MGMR  158 (199)
T ss_dssp             SCCE
T ss_pred             cCcc
Confidence            5544

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=97.16  E-value=0.013  Score=41.35  Aligned_cols=105  Identities=17%  Similarity=0.189  Sum_probs=61.1

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccc-----ccc--CCCccce
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDP-----ALI--RPGRIDR   80 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~-----~l~--~~grf~~   80 (131)
                      ..|.+|+|||++.+....    ..........+..+...      .+++.+|.|++....+..     ...  -.||+..
T Consensus       127 ~~~~vlvlDe~~~~~~~~----~~~~~~~~~~L~~~~~~------~~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~~  196 (350)
T 2qen_A          127 LGEFIVAFDEAQYLRFYG----SRGGKELLALFAYAYDS------LPNLKIILTGSEVGLLHDFLKITDYESPLYGRIAG  196 (350)
T ss_dssp             HSCEEEEEETGGGGGGBT----TTTTHHHHHHHHHHHHH------CTTEEEEEEESSHHHHHHHHCTTCTTSTTTTCCCE
T ss_pred             cCCEEEEEeCHHHHhccC----ccchhhHHHHHHHHHHh------cCCeEEEEECCcHHHHHHHHhhcCCCCccccCccc
Confidence            349999999999986411    00112223333333322      135556655543211111     101  1247767


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLS  122 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s  122 (131)
                      .+.+++.+.++-.+++...+...+.. ....+..+...|.|+.
T Consensus       197 ~i~l~pl~~~e~~~~l~~~~~~~~~~~~~~~~~~i~~~tgG~P  239 (350)
T 2qen_A          197 EVLVKPFDKDTSVEFLKRGFREVNLDVPENEIEEAVELLDGIP  239 (350)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHTTCH
T ss_pred             eeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCH
Confidence            89999999999999998877544333 2335677888888874

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=97.12  E-value=0.0048  Score=43.67  Aligned_cols=100  Identities=11%  Similarity=0.085  Sum_probs=59.0

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCccccc-----c--cCCCccceE
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPA-----L--IRPGRIDRK   81 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~-----l--~~~grf~~~   81 (131)
                      .|.+|+|||++.+....   .. .   ....+..+...      ..++.+|.|++....+...     .  .-.||+...
T Consensus       137 ~~~vlvlDe~~~~~~~~---~~-~---~~~~l~~~~~~------~~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~  203 (357)
T 2fna_A          137 DNVIIVLDEAQELVKLR---GV-N---LLPALAYAYDN------LKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFST  203 (357)
T ss_dssp             SCEEEEEETGGGGGGCT---TC-C---CHHHHHHHHHH------CTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEE
T ss_pred             CCeEEEEECHHHhhccC---ch-h---HHHHHHHHHHc------CCCeEEEEEcCchHHHHHHHhccCCCCccccCccce
Confidence            48999999999986421   01 1   12233333322      1355666666543222211     0  012466678


Q ss_pred             EEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCC
Q psy522           82 IEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLS  122 (131)
Q Consensus        82 i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s  122 (131)
                      +.+++.+.++-.+++...+...+...+ +...+...|.|+.
T Consensus       204 i~l~~l~~~e~~~~l~~~~~~~~~~~~-~~~~i~~~t~G~P  243 (357)
T 2fna_A          204 VELKPFSREEAIEFLRRGFQEADIDFK-DYEVVYEKIGGIP  243 (357)
T ss_dssp             EEECCCCHHHHHHHHHHHHHHHTCCCC-CHHHHHHHHCSCH
T ss_pred             eecCCCCHHHHHHHHHHHHHHcCCCCC-cHHHHHHHhCCCH
Confidence            999999999999999887653232222 2377888888873

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=96.93  E-value=0.0012  Score=46.70  Aligned_cols=79  Identities=22%  Similarity=0.296  Sum_probs=42.3

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcC--C----CCCCCeEEEeeCCCC-C------cccccccCCC
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDG--F----DSRGDVKVIMATNRI-E------TLDPALIRPG   76 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~--~----~~~~~v~vi~ttn~~-~------~id~~l~~~g   76 (131)
                      +.+|||||+|.+-..           ....+..+++.-.-  +    .....+.+|+|||.. .      .+++.+..  
T Consensus        97 ~g~L~LDEi~~l~~~-----------~q~~Ll~~l~~~~~~~~g~~~~~~~~~riI~atn~~l~~~v~~g~fr~~L~~--  163 (304)
T 1ojl_A           97 GGTLFLDEIGDISPL-----------MQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYY--  163 (304)
T ss_dssp             TSEEEEESCTTCCHH-----------HHHHHHHHHHSSBCCBTTBCCCCBCCCEEEEEESSCHHHHHHHTSSCHHHHH--
T ss_pred             CCEEEEeccccCCHH-----------HHHHHHHHHhcCEeeecCCcccccCCeEEEEecCccHHHHHHhCCcHHHHHh--
Confidence            579999999998421           22233333332110  0    011357889999864 1      23455555  


Q ss_pred             ccc-eEEEeCCCC--HHHHHHHHHHHhc
Q psy522           77 RID-RKIEFPLPD--EKTKRRIFNIHTS  101 (131)
Q Consensus        77 rf~-~~i~~~~P~--~~~R~~il~~~l~  101 (131)
                      ||. ..+.+|+..  .++...++++++.
T Consensus       164 Rl~~~~i~lPpL~eR~edi~~l~~~~l~  191 (304)
T 1ojl_A          164 RLNVVAIEMPSLRQRREDIPLLADHFLR  191 (304)
T ss_dssp             HHSSEEEECCCSGGGGGGHHHHHHHHHH
T ss_pred             hcCeeEEeccCHHHhHhhHHHHHHHHHH
Confidence            663 335555544  3455556766654

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=96.91  E-value=0.00043  Score=59.13  Aligned_cols=69  Identities=14%  Similarity=0.161  Sum_probs=49.3

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCC---CCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCccc
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRY---DSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLD   69 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~---~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id   69 (131)
                      +|.+|+...|++|++|++|++++.+.   ..++.+..-..+.+++++..++++....+|+||+|....+.+.
T Consensus      1152 ~~~~ar~~~~~~i~~d~~~al~~~~~~~g~~~~~~~~~~~r~~~q~l~~~~~~~~~~~v~v~~~n~~~~~~~ 1223 (1706)
T 3cmw_A         1152 CDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNLKQSNTLLIFINQIRMKIG 1223 (1706)
T ss_dssp             HHHHHHHTCCSEEEESCGGGCCCHHHHHSCTTCCCTTHHHHHHHHHHHHHHHHHHHTTCEEEEEECEEECTT
T ss_pred             HHHHHHhcCCeEEEeCchHhcCcccccccccccccccHHHHHHHHHHHHHHhhhccCCeEEEEeccccccch
Confidence            46789999999999999999999843   2222222233456889999999877777888885554445554

>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=96.63  E-value=0.0019  Score=44.45  Aligned_cols=80  Identities=16%  Similarity=0.254  Sum_probs=45.5

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhc--CC----CCCCCeEEEeeCCCC-C------cccccccCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLD--GF----DSRGDVKVIMATNRI-E------TLDPALIRP   75 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~----~~~~~v~vi~ttn~~-~------~id~~l~~~   75 (131)
                      .+.+|||||+|.+-..           ....+..+++.-.  ..    ....++.+|+|||.+ .      .+++.+.+ 
T Consensus       100 ~~~~l~lDEi~~l~~~-----------~q~~Ll~~l~~~~~~~~g~~~~~~~~~~iI~atn~~~~~~~~~~~~~~~L~~-  167 (265)
T 2bjv_A          100 DGGTLFLDELATAPMM-----------VQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVNEGTFRADLLD-  167 (265)
T ss_dssp             TTSEEEEESGGGSCHH-----------HHHHHHHHHHHCEECCCCC--CEECCCEEEEEESSCHHHHHHHTSSCHHHHH-
T ss_pred             CCcEEEEechHhcCHH-----------HHHHHHHHHHhCCeecCCCcccccCCeEEEEecCcCHHHHHHcCCccHHHHH-
Confidence            4689999999988421           2233334443210  00    011357888888863 2      36778888 


Q ss_pred             Cccc-eEEEeCCCCH--HHHHHHHHHHhc
Q psy522           76 GRID-RKIEFPLPDE--KTKRRIFNIHTS  101 (131)
Q Consensus        76 grf~-~~i~~~~P~~--~~R~~il~~~l~  101 (131)
                       ||. ..+.+|+...  ++...+++++++
T Consensus       168 -Rl~~~~i~lp~L~~R~~di~~l~~~~l~  195 (265)
T 2bjv_A          168 -ALAFDVVQLPPLRERESDIMLMAEYFAI  195 (265)
T ss_dssp             -HHCSEEEECCCGGGCHHHHHHHHHHHHH
T ss_pred             -hhcCcEEeCCChhhhhHHHHHHHHHHHH
Confidence             885 3555555543  455556555543

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=96.63  E-value=0.0042  Score=48.02  Aligned_cols=74  Identities=18%  Similarity=0.285  Sum_probs=44.7

Q ss_pred             CeEEEeeCCCC--CcccccccCCCccc---eEEEeCC--C-CHHHHHHHHHHHhcCCC-----CC-CcccHHHHHHHc--
Q psy522           55 DVKVIMATNRI--ETLDPALIRPGRID---RKIEFPL--P-DEKTKRRIFNIHTSRMT-----LA-EDVNLQELIMAK--  118 (131)
Q Consensus        55 ~v~vi~ttn~~--~~id~~l~~~grf~---~~i~~~~--P-~~~~R~~il~~~l~~~~-----~~-~~~~~~~la~~t--  118 (131)
                      ++.+|+|||..  +.+++++++  ||.   ..+.++.  + +.+....+++.+.+...     .. .+..+..+....  
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            57899999975  689999999  996   5666653  2 45556666655433211     11 222344454432  


Q ss_pred             -CCC------CHHHHHHhh
Q psy522          119 -DDL------SGADIKAIC  130 (131)
Q Consensus       119 -~g~------s~~di~~l~  130 (131)
                       .|-      +.+++..++
T Consensus       330 ~~g~r~~l~~~~R~l~~ll  348 (604)
T 3k1j_A          330 RAGRKGHLTLRLRDLGGIV  348 (604)
T ss_dssp             TTCSTTEEECCHHHHHHHH
T ss_pred             hhccccccccCHHHHHHHH
Confidence             552      677777665

>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=95.83  E-value=0.037  Score=39.42  Aligned_cols=93  Identities=12%  Similarity=0.099  Sum_probs=57.2

Q ss_pred             CeEEEeccccc-ccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCC-----CCcccccccCCCccceEEE
Q psy522           10 PSIVFIDEIDA-VGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNR-----IETLDPALIRPGRIDRKIE   83 (131)
Q Consensus        10 p~ii~iDe~d~-l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~-----~~~id~~l~~~grf~~~i~   83 (131)
                      .-||+|||+|. +..+              ..+.++..+... ..+.++++.+++.     ...+.+.+.+  |. ..+.
T Consensus        77 ~kvvii~~~~~kl~~~--------------~~~aLl~~le~p-~~~~~~il~~~~~~~~~~~~k~~~~i~s--r~-~~~~  138 (343)
T 1jr3_D           77 RQTLLLLLPENGPNAA--------------INEQLLTLTGLL-HDDLLLIVRGNKLSKAQENAAWFTALAN--RS-VQVT  138 (343)
T ss_dssp             CEEEEEECCSSCCCTT--------------HHHHHHHHHTTC-BTTEEEEEEESCCCTTTTTSHHHHHHTT--TC-EEEE
T ss_pred             CeEEEEECCCCCCChH--------------HHHHHHHHHhcC-CCCeEEEEEcCCCChhhHhhHHHHHHHh--Cc-eEEE
Confidence            56899999887 5211              233355555542 2233444455442     3467888888  66 4789


Q ss_pred             eCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           84 FPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        84 ~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      +.+|+.++....++..++..+.. ....+..++..+.|
T Consensus       139 ~~~l~~~~l~~~l~~~~~~~g~~i~~~a~~~l~~~~~g  176 (343)
T 1jr3_D          139 CQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEG  176 (343)
T ss_dssp             ECCCCTTHHHHHHHHHHHHTTCEECHHHHHHHHHSSTT
T ss_pred             eeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhch
Confidence            99999999998998888766544 22234445554443

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=95.31  E-value=0.04  Score=34.31  Aligned_cols=61  Identities=15%  Similarity=0.297  Sum_probs=33.7

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCC-CCc----ccccccCCCcc-ceEE
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNR-IET----LDPALIRPGRI-DRKI   82 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~-~~~----id~~l~~~grf-~~~i   82 (131)
                      .+.+|||||+|.+-..           ....+..+++..    ...++.+|+|||. ++.    +++.+..  || ...|
T Consensus        75 ~~~~l~lDei~~l~~~-----------~q~~Ll~~l~~~----~~~~~~iI~~tn~~~~~~~~~~~~~L~~--rl~~~~i  137 (143)
T 3co5_A           75 EGGVLYVGDIAQYSRN-----------IQTGITFIIGKA----ERCRVRVIASCSYAAGSDGISCEEKLAG--LFSESVV  137 (143)
T ss_dssp             TTSEEEEEECTTCCHH-----------HHHHHHHHHHHH----TTTTCEEEEEEEECTTTC--CHHHHHHH--HSSSEEE
T ss_pred             CCCeEEEeChHHCCHH-----------HHHHHHHHHHhC----CCCCEEEEEecCCCHHHHHhCccHHHHH--HhcCcEE
Confidence            3589999999998432           122333344332    1345778888884 333    3334444  43 3456


Q ss_pred             EeCC
Q psy522           83 EFPL   86 (131)
Q Consensus        83 ~~~~   86 (131)
                      .+|+
T Consensus       138 ~lPp  141 (143)
T 3co5_A          138 RIPP  141 (143)
T ss_dssp             EECC
T ss_pred             eCCC
Confidence            6665

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=94.85  E-value=0.095  Score=47.72  Aligned_cols=84  Identities=15%  Similarity=0.235  Sum_probs=58.0

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCC-------CCCeEEEeeCCCC-----CcccccccCCCc
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDS-------RGDVKVIMATNRI-----ETLDPALIRPGR   77 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-------~~~v~vi~ttn~~-----~~id~~l~~~gr   77 (131)
                      ..|+|+||++---.+     ....+.....+.+++..-.-+..       -.++.+|||+|.|     ..++++++|  |
T Consensus      1375 ~~VlFiDDiNmp~~D-----~yGtQ~~ielLrqlld~~g~yd~~~~~~~~i~d~~~vaamnPp~~gGr~~l~~Rf~r--~ 1447 (3245)
T 3vkg_A         1375 WLVVFCDEINLPSTD-----KYGTQRVITFIRQMVEKGGFWRTSDHTWIKLDKIQFVGACNPPTDAGRVQLTHRFLR--H 1447 (3245)
T ss_dssp             EEEEEETTTTCCCCC-----TTSCCHHHHHHHHHHHHSEEEETTTTEEEEESSEEEEEEECCTTSTTCCCCCHHHHT--T
T ss_pred             eEEEEecccCCCCcc-----ccccccHHHHHHHHHHcCCeEECCCCeEEEecCeEEEEEcCCCCCCCCccCCHHHHh--h
Confidence            479999999753222     12223345666777654211111       1468899999977     469999999  9


Q ss_pred             cceEEEeCCCCHHHHHHHHHHHhc
Q psy522           78 IDRKIEFPLPDEKTKRRIFNIHTS  101 (131)
Q Consensus        78 f~~~i~~~~P~~~~R~~il~~~l~  101 (131)
                      |. .++++.|+.++-..|+..++.
T Consensus      1448 F~-vi~i~~ps~esL~~If~til~ 1470 (3245)
T 3vkg_A         1448 AP-ILLVDFPSTSSLTQIYGTFNR 1470 (3245)
T ss_dssp             CC-EEECCCCCHHHHHHHHHHHHH
T ss_pred             ce-EEEeCCCCHHHHHHHHHHHHH
Confidence            96 699999999999999876654

>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=94.52  E-value=0.036  Score=41.96  Aligned_cols=68  Identities=19%  Similarity=0.269  Sum_probs=39.7

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHH----hcCCCCCCCeEEEeeCCCCC-----------cccccccCC
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQ----LDGFDSRGDVKVIMATNRIE-----------TLDPALIRP   75 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~----~~~~~~~~~v~vi~ttn~~~-----------~id~~l~~~   75 (131)
                      .++|+||++.+-.+           ....+.+.+++    +.+..-..++.||||+|-.+           .+++++++ 
T Consensus       302 Gvl~lDEIn~~~~~-----------~qsaLlEaMEe~~VtI~G~~lparf~VIAA~NP~~~yd~~~s~~~~~Lp~alLD-  369 (506)
T 3f8t_A          302 GILAVDHLEGAPEP-----------HRWALMEAMDKGTVTVDGIALNARCAVLAAINPGEQWPSDPPIARIDLDQDFLS-  369 (506)
T ss_dssp             SEEEEECCTTCCHH-----------HHHHHHHHHHHSEEEETTEEEECCCEEEEEECCCC--CCSCGGGGCCSCHHHHT-
T ss_pred             CeeehHhhhhCCHH-----------HHHHHHHHHhCCcEEECCEEcCCCeEEEEEeCcccccCCCCCccccCCChHHhh-
Confidence            78999999886321           22333333332    12221124689999999754           78899999 


Q ss_pred             CccceEEE-eCCCCHHH
Q psy522           76 GRIDRKIE-FPLPDEKT   91 (131)
Q Consensus        76 grf~~~i~-~~~P~~~~   91 (131)
                       |||..+. ++.|+.+.
T Consensus       370 -RFDLi~i~~d~pd~e~  385 (506)
T 3f8t_A          370 -HFDLIAFLGVDPRPGE  385 (506)
T ss_dssp             -TCSEEEETTC------
T ss_pred             -heeeEEEecCCCChhH
Confidence             9986443 45565443

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=94.04  E-value=0.013  Score=42.22  Aligned_cols=58  Identities=21%  Similarity=0.331  Sum_probs=28.7

Q ss_pred             EEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccc
Q psy522           12 IVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPAL   72 (131)
Q Consensus        12 ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l   72 (131)
                      +|+||+++.+............  ..+.+.+++..+.++....++.+|+++| +...++++
T Consensus       185 LLVIDsI~aL~~~~~~~s~~G~--v~~~lrqlL~~L~~~~k~~gvtVIlttn-p~s~deal  242 (331)
T 2vhj_A          185 VIVIDSLKNVIGAAGGNTTSGG--ISRGAFDLLSDIGAMAASRGCVVIASLN-PTSNDDKI  242 (331)
T ss_dssp             EEEEECCTTTC-------------CCHHHHHHHHHHHHHHHHHTCEEEEECC-CSSCSSSH
T ss_pred             EEEEecccccccccccccccch--HHHHHHHHHHHHHHHHhhCCCEEEEEeC-CcccchhH
Confidence            9999999998654422111000  0122333444443333344567888888 56666554

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=93.73  E-value=0.33  Score=35.19  Aligned_cols=76  Identities=11%  Similarity=0.128  Sum_probs=50.1

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccc--------cccCCCccc
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDP--------ALIRPGRID   79 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~--------~l~~~grf~   79 (131)
                      ..|.++++||+..++...       .......+..++....    +.++.++.+|+++..+..        +++.  ..+
T Consensus       261 ~~~~~i~iDEa~~~~~~~-------~~~~~~~l~~~~~~~R----k~g~~~~~~tQ~~~d~~~~~~~~~~~~il~--n~~  327 (392)
T 4ag6_A          261 RERTVLVVDEAWMLVDPQ-------TPQAIAFLRDTSKRIR----KYNGSLIVISQNVIDFLAPEVQRYGQALLD--NPT  327 (392)
T ss_dssp             CTTCEEEETTGGGGCCTT-------CTHHHHHHHHHHHHGG----GGTCEEEEEESCGGGGGSTTTHHHHHHHHH--SCS
T ss_pred             CccEEEEEecHHHHhCcC-------chHHHHHHHHHHHHhh----hhCeEEEEEcCCHHHhhChhhHHHHHHHHH--hhh
Confidence            458999999999998632       1123345556665553    345678888898888864        4555  677


Q ss_pred             eEEEeCCCCHHHHHHHHH
Q psy522           80 RKIEFPLPDEKTKRRIFN   97 (131)
Q Consensus        80 ~~i~~~~P~~~~R~~il~   97 (131)
                      ..|.++.+. .++..+.+
T Consensus       328 ~~i~l~~~~-~~~~~~~~  344 (392)
T 4ag6_A          328 YKLLLAQGE-KDLEAITT  344 (392)
T ss_dssp             EEEECSCCH-HHHHHHHH
T ss_pred             hhheeCCCh-hhHHHHHH
Confidence            888888764 44444433

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=93.66  E-value=0.028  Score=35.49  Aligned_cols=61  Identities=13%  Similarity=0.296  Sum_probs=33.3

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCe-EEEeeCCCCCccc--ccccCCCccceEEEeC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDV-KVIMATNRIETLD--PALIRPGRIDRKIEFP   85 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v-~vi~ttn~~~~id--~~l~~~grf~~~i~~~   85 (131)
                      +|.+|+|||++.+....           ...+..+++.+.   ..+.. ++|+|...|..+.  +.+.+  |+..-..+.
T Consensus        83 ~~~lLilDE~~~~~~~~-----------~~~l~~li~~~~---~~g~~~iiits~~~p~~l~~~~~L~S--Rl~~g~~~~  146 (149)
T 2kjq_A           83 EAEYLAVDQVEKLGNEE-----------QALLFSIFNRFR---NSGKGFLLLGSEYTPQQLVIREDLRT--RMAYCLVYE  146 (149)
T ss_dssp             GCSEEEEESTTCCCSHH-----------HHHHHHHHHHHH---HHTCCEEEEEESSCTTTSSCCHHHHH--HGGGSEECC
T ss_pred             CCCEEEEeCccccChHH-----------HHHHHHHHHHHH---HcCCcEEEEECCCCHHHccccHHHHH--HHhcCeeEE
Confidence            57899999998753221           123333333322   23333 5554444565554  77888  876554443

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=92.88  E-value=0.14  Score=39.57  Aligned_cols=75  Identities=16%  Similarity=0.294  Sum_probs=54.2

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCC--cccccccCCCccceEEEeCCC
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE--TLDPALIRPGRIDRKIEFPLP   87 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~--~id~~l~~~grf~~~i~~~~P   87 (131)
                      +-+|+|||+..++....       ......+..+..    ....-++.+|.+|++|.  .++..++.  -|..+|.+...
T Consensus       344 ~ivvVIDE~~~L~~~~~-------~~~~~~L~~Iar----~GRa~GIhLIlaTQRPs~d~I~~~Ira--n~~~RI~lrv~  410 (574)
T 2iut_A          344 TIVVVVDEFADMMMIVG-------KKVEELIARIAQ----KARAAGIHLILATQRPSVDVITGLIKA--NIPTRIAFQVS  410 (574)
T ss_dssp             EEEEEESCCTTHHHHTC-------HHHHHHHHHHHH----HCTTTTEEEEEEESCCCTTTSCHHHHH--TCCEEEEECCS
T ss_pred             cEEEEEeCHHHHhhhhh-------HHHHHHHHHHHH----HHhhCCeEEEEEecCcccccccHHHHh--hhccEEEEEcC
Confidence            36899999998875321       122233333332    22445799999999988  89988888  89999999999


Q ss_pred             CHHHHHHHHH
Q psy522           88 DEKTKRRIFN   97 (131)
Q Consensus        88 ~~~~R~~il~   97 (131)
                      +..+...++.
T Consensus       411 s~~Dsr~ILd  420 (574)
T 2iut_A          411 SKIDSRTILD  420 (574)
T ss_dssp             CHHHHHHHHS
T ss_pred             CHHHHHHhcC
Confidence            9988888873

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=92.70  E-value=0.052  Score=39.71  Aligned_cols=69  Identities=22%  Similarity=0.303  Sum_probs=43.9

Q ss_pred             cCCeEEEecccccccC-cCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCC
Q psy522            8 HAPSIVFIDEIDAVGT-KRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPL   86 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~   86 (131)
                      .+..++++||++.+.. .+.-. ....  . .....+.+.+++     .+.|+.+||+++.+ +++.+||+++..++...
T Consensus       215 ~q~~~~l~dd~~~~~~~~r~l~-~~~~--~-~~~~~l~~~ldG-----~v~v~~~tn~~~~l-~alf~pg~ld~~~~~l~  284 (377)
T 1svm_A          215 IDQFLVVFEDVKGTGGESRDLP-SGQG--I-NNLDNLRDYLDG-----SVKVNLEKKHLNKR-TQIFPPGIVTMNEYSVP  284 (377)
T ss_dssp             TTCSCEEETTCCCSTTTTTTCC-CCSH--H-HHHHTTHHHHHC-----SSCEEECCSSSCCE-EECCCCEEEEECSCCCC
T ss_pred             cchhHHHHHHHHHHHHHHhhcc-ccCc--c-hHHHHHHHHhcC-----CCeEeeccCchhhH-HHhhcCcccChhHHhhc
Confidence            3456789999999875 22111 1111  1 122334444554     34578889999999 79999999987776644

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=92.19  E-value=0.18  Score=31.25  Aligned_cols=40  Identities=8%  Similarity=0.089  Sum_probs=23.6

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNR   64 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~   64 (131)
                      ...+|||||+|.+-..           ....   ++..+..  ...++.+|+|||.
T Consensus        76 ~~g~l~ldei~~l~~~-----------~q~~---Ll~~l~~--~~~~~~~I~~t~~  115 (145)
T 3n70_A           76 QGGTLVLSHPEHLTRE-----------QQYH---LVQLQSQ--EHRPFRLIGIGDT  115 (145)
T ss_dssp             TTSCEEEECGGGSCHH-----------HHHH---HHHHHHS--SSCSSCEEEEESS
T ss_pred             CCcEEEEcChHHCCHH-----------HHHH---HHHHHhh--cCCCEEEEEECCc
Confidence            4579999999988422           1222   3333332  2335667888885

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=92.06  E-value=0.11  Score=45.64  Aligned_cols=65  Identities=15%  Similarity=0.156  Sum_probs=40.7

Q ss_pred             HHHHHhcCCeEEEecccccccCcC---CCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCC
Q psy522            2 FRVAEEHAPSIVFIDEIDAVGTKR---YDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE   66 (131)
Q Consensus         2 F~~A~~~~p~ii~iDe~d~l~~~~---~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~   66 (131)
                      +..++..+|++|+||+++.+.+..   +..++.......+.+.+++..+.+.....++++|+|.....
T Consensus      1498 ~~lvr~~~~~lVVIDsi~al~p~~~~~g~~~~~~~~~~~R~lsqlL~~L~~~~~~~~v~VI~tNq~~~ 1565 (2050)
T 3cmu_A         1498 DALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNLKQSNTLLIFINQIRM 1565 (2050)
T ss_dssp             HHHHHHTCCSEEEESCGGGCCCHHHHHSCTTCCCTTHHHHHHHHHHHHHHHHHHTTTCEEEEEECEEE
T ss_pred             HHHHhcCCCCEEEEcChhHhcccccccccccccccchHHHHHHHHHHHHHHHHHhCCcEEEEEccccc
Confidence            456788999999999999998753   11122122112345566666666655666777777755433

>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=91.76  E-value=0.43  Score=43.12  Aligned_cols=86  Identities=14%  Similarity=0.131  Sum_probs=54.9

Q ss_pred             HHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcC-----------CCCCCCeEEEeeCC----CCC
Q psy522            2 FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDG-----------FDSRGDVKVIMATN----RIE   66 (131)
Q Consensus         2 F~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~-----------~~~~~~v~vi~ttn----~~~   66 (131)
                      |.-|.... +.+++||++.+-..       .-+.+...+..+...+..           +.-.++..+++|.|    ...
T Consensus       691 ~~g~~~~G-aw~~~DE~nr~~~e-------vLs~l~~~l~~i~~al~~~~~~i~~~g~~i~l~~~~~vfiT~NPgy~g~~  762 (2695)
T 4akg_A          691 LVGITQIG-AWGCFDEFNRLDEK-------VLSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPGYNGRS  762 (2695)
T ss_dssp             HHHHHHHT-CEEEEETTTSSCHH-------HHHHHHHHHHHHHHHHHHTCSEEECSSSEEECCTTCEEEEEECCCSSSSC
T ss_pred             HHHHHhcC-CEeeehhhhhcChH-------HHHHHHHHHHHHHHHHHcCCcEEeeCCcEEecCCCceEEEEeCCCccCcc
Confidence            33344444 89999999886321       112222333333333311           12234577888888    567


Q ss_pred             cccccccCCCccceEEEeCCCCHHHHHHHHHH
Q psy522           67 TLDPALIRPGRIDRKIEFPLPDEKTKRRIFNI   98 (131)
Q Consensus        67 ~id~~l~~~grf~~~i~~~~P~~~~R~~il~~   98 (131)
                      .+|+++++  || +.+.+..|+.+...+++..
T Consensus       763 eLP~~Lk~--~F-r~v~m~~Pd~~~i~ei~l~  791 (2695)
T 4akg_A          763 ELPENLKK--SF-REFSMKSPQSGTIAEMILQ  791 (2695)
T ss_dssp             CCCHHHHT--TE-EEEECCCCCHHHHHHHHHH
T ss_pred             cccHHHHh--he-EEEEeeCCCHHHHHHHHHH
Confidence            89999999  99 5899999999998888643

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=89.01  E-value=0.97  Score=32.87  Aligned_cols=78  Identities=23%  Similarity=0.370  Sum_probs=40.4

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHh--cCCCCC----CCeEEEeeCCCCCcccccccCCCcc-----
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQL--DGFDSR----GDVKVIMATNRIETLDPALIRPGRI-----   78 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~----~~v~vi~ttn~~~~id~~l~~~grf-----   78 (131)
                      ..+|||||++.+-..           ....+..+++.-  ..+...    -.+.+|+|||..  +. .+...|+|     
T Consensus       232 ~gtlfldei~~l~~~-----------~q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~at~~~--l~-~~~~~g~fr~dl~  297 (387)
T 1ny5_A          232 GGTLFLDEIGELSLE-----------AQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRN--IK-ELVKEGKFREDLY  297 (387)
T ss_dssp             TSEEEEESGGGCCHH-----------HHHHHHHHHHHSEECCBTCCSBEECCCEEEEEESSC--HH-HHHHTTSSCHHHH
T ss_pred             CcEEEEcChhhCCHH-----------HHHHHHHHHhcCcEEeCCCCceeeccEEEEEeCCCC--HH-HHHHcCCccHHHH
Confidence            368999999998322           234444454431  111111    257788888852  11 22223444     


Q ss_pred             ----ceEEEeCCCC--HHHHHHHHHHHhc
Q psy522           79 ----DRKIEFPLPD--EKTKRRIFNIHTS  101 (131)
Q Consensus        79 ----~~~i~~~~P~--~~~R~~il~~~l~  101 (131)
                          ...|++|+..  .+....+.++++.
T Consensus       298 ~rl~~~~i~lPpLreR~~Di~~l~~~~l~  326 (387)
T 1ny5_A          298 YRLGVIEIEIPPLRERKEDIIPLANHFLK  326 (387)
T ss_dssp             HHHTTEEEECCCGGGCHHHHHHHHHHHHH
T ss_pred             HhhcCCeecCCcchhccccHHHHHHHHHH
Confidence                2345555542  3555566666654

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=88.82  E-value=0.19  Score=32.13  Aligned_cols=14  Identities=7%  Similarity=0.380  Sum_probs=11.5

Q ss_pred             cCCeEEEecccccc
Q psy522            8 HAPSIVFIDEIDAV   21 (131)
Q Consensus         8 ~~p~ii~iDe~d~l   21 (131)
                      ..|.+|+|||++..
T Consensus        99 ~~~~llilDE~~~~  112 (180)
T 3ec2_A           99 LNSPVLVLDDLGSE  112 (180)
T ss_dssp             HTCSEEEEETCSSS
T ss_pred             cCCCEEEEeCCCCC
Confidence            46899999999754

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=88.53  E-value=3.3  Score=26.59  Aligned_cols=15  Identities=27%  Similarity=0.547  Sum_probs=12.3

Q ss_pred             HhcCCeEEEeccccc
Q psy522            6 EEHAPSIVFIDEIDA   20 (131)
Q Consensus         6 ~~~~p~ii~iDe~d~   20 (131)
                      -...|.++++||++-
T Consensus        96 l~~~p~llilDEigp  110 (178)
T 1ye8_A           96 KKDRRKVIIIDEIGK  110 (178)
T ss_dssp             HHCTTCEEEECCCST
T ss_pred             cccCCCEEEEeCCCC
Confidence            567899999999753

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A

Probab=88.10  E-value=1.2  Score=32.19  Aligned_cols=77  Identities=25%  Similarity=0.395  Sum_probs=42.0

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHh--cCCCCC----CCeEEEeeCCCCCcccccccCCCccc-----
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQL--DGFDSR----GDVKVIMATNRIETLDPALIRPGRID-----   79 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~----~~v~vi~ttn~~~~id~~l~~~grf~-----   79 (131)
                      ..|||||++.+-..           ....+..+++.=  ..+...    -.+-+|++||.  .+. .....|+|.     
T Consensus       224 gtlfldei~~l~~~-----------~Q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~at~~--~l~-~~v~~g~fr~dL~~  289 (368)
T 3dzd_A          224 GTLFLDEVGELDQR-----------VQAKLLRVLETGSFTRLGGNQKIEVDIRVISATNK--NLE-EEIKKGNFREDLYY  289 (368)
T ss_dssp             SEEEEETGGGSCHH-----------HHHHHHHHHHHSEECCBTCCCBEECCCEEEEEESS--CHH-HHHHTTSSCHHHHH
T ss_pred             CeEEecChhhCCHH-----------HHHHHHHHHHhCCcccCCCCcceeeeeEEEEecCC--CHH-HHHHcCCccHHHHH
Confidence            67999999998322           233444444321  111111    14668888873  222 222334553     


Q ss_pred             ----eEEEeCCCCH--HHHHHHHHHHhc
Q psy522           80 ----RKIEFPLPDE--KTKRRIFNIHTS  101 (131)
Q Consensus        80 ----~~i~~~~P~~--~~R~~il~~~l~  101 (131)
                          ..|++|+...  +....++++++.
T Consensus       290 rl~~~~i~lPpLreR~~Di~~l~~~~l~  317 (368)
T 3dzd_A          290 RLSVFQIYLPPLRERGKDVILLAEYFLK  317 (368)
T ss_dssp             HHTSEEEECCCGGGSTTHHHHHHHHHHH
T ss_pred             HhCCeEEeCCChhhchhhHHHHHHHHHH
Confidence                2577777644  666777777764

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=87.92  E-value=3.5  Score=31.26  Aligned_cols=86  Identities=12%  Similarity=0.190  Sum_probs=49.4

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEe-CC
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEF-PL   86 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~-~~   86 (131)
                      .+|.+|+|||++..                ..    +.   .+  .++..||.||+....... . . |.. ..+.. +.
T Consensus       235 ~~~~LLVLDdv~~~----------------~~----l~---~l--~~~~~ilvTsR~~~~~~~-~-~-~~~-~~v~~l~~  285 (591)
T 1z6t_A          235 HPRSLLILDDVWDS----------------WV----LK---AF--DSQCQILLTTRDKSVTDS-V-M-GPK-YVVPVESS  285 (591)
T ss_dssp             CTTCEEEEEEECCH----------------HH----HH---TT--CSSCEEEEEESCGGGGTT-C-C-SCE-EEEECCSS
T ss_pred             CCCeEEEEeCCCCH----------------HH----HH---Hh--cCCCeEEEECCCcHHHHh-c-C-CCc-eEeecCCC
Confidence            36899999999641                01    11   11  234567777776442221 1 1 121 22322 46


Q ss_pred             CCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCC
Q psy522           87 PDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLS  122 (131)
Q Consensus        87 P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s  122 (131)
                      .+.++-.+++.................+++.+.|..
T Consensus       286 L~~~ea~~L~~~~~~~~~~~~~~~~~~i~~~~~G~P  321 (591)
T 1z6t_A          286 LGKEKGLEILSLFVNMKKADLPEQAHSIIKECKGSP  321 (591)
T ss_dssp             CCHHHHHHHHHHHHTSCGGGSCTHHHHHHHHHTTCH
T ss_pred             CCHHHHHHHHHHHhCCCcccccHHHHHHHHHhCCCc
Confidence            789999999988875422112334778889898873

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=87.21  E-value=0.43  Score=36.31  Aligned_cols=77  Identities=19%  Similarity=0.358  Sum_probs=52.3

Q ss_pred             CCe-EEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCC--cccccccCCCccceEEEeC
Q psy522            9 APS-IVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIE--TLDPALIRPGRIDRKIEFP   85 (131)
Q Consensus         9 ~p~-ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~--~id~~l~~~grf~~~i~~~   85 (131)
                      -|- +|++||+..++...       ..    .+..++..+......-++.+|.+|++|.  .++..++.  -|..+|.+.
T Consensus       296 lP~ivlvIDE~~~ll~~~-------~~----~~~~~l~~Lar~gRa~GI~LIlaTQrp~~dvl~~~i~~--n~~~RI~lr  362 (512)
T 2ius_A          296 EPYIVVLVDEFADLMMTV-------GK----KVEELIARLAQKARAAGIHLVLATQRPSVDVITGLIKA--NIPTRIAFT  362 (512)
T ss_dssp             CCEEEEEEETHHHHHHHH-------HH----HHHHHHHHHHHHCGGGTEEEEEEESCCCTTTSCHHHHH--HCCEEEEEC
T ss_pred             CCcEEEEEeCHHHHHhhh-------hH----HHHHHHHHHHHHhhhCCcEEEEEecCCccccccHHHHh--hcCCeEEEE
Confidence            464 89999997776421       11    1222333222222334688889999887  68888888  898999999


Q ss_pred             CCCHHHHHHHHHH
Q psy522           86 LPDEKTKRRIFNI   98 (131)
Q Consensus        86 ~P~~~~R~~il~~   98 (131)
                      ..+..+...++..
T Consensus       363 v~s~~dsr~ilg~  375 (512)
T 2ius_A          363 VSSKIDSRTILDQ  375 (512)
T ss_dssp             CSSHHHHHHHHSS
T ss_pred             cCCHHHHHHhcCC
Confidence            9999998888753

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=82.83  E-value=3.3  Score=30.23  Aligned_cols=71  Identities=17%  Similarity=0.239  Sum_probs=50.4

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCccc--------ccccCCCccc
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLD--------PALIRPGRID   79 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id--------~~l~~~grf~   79 (131)
                      ..|.++++||+-.+..-.             .+..++...    .+.++.++..|.++..+.        .+++.  -+.
T Consensus       278 ~~~~~~~lDE~~~l~~~~-------------~l~~~~~~~----R~~g~~~~~~~Qs~~ql~~~yG~~~a~~i~~--n~~  338 (437)
T 1e9r_A          278 KRRLWLFIDELASLEKLA-------------SLADALTKG----RKAGLRVVAGLQSTSQLDDVYGVKEAQTLRA--SFR  338 (437)
T ss_dssp             TCCEEEEESCGGGSCBCS-------------SHHHHHHHC----TTTTEEEEEEESCHHHHHHHHCHHHHHHHHT--TCC
T ss_pred             CccEEEEEEcccccccch-------------hHHHHHHHH----hccCCEEEEEecCHHHHHHHHCHHHHHHHHh--ccC
Confidence            458999999999886422             233344433    345788999999988886        45776  788


Q ss_pred             eEEEeCCC--CHHHHHHHHH
Q psy522           80 RKIEFPLP--DEKTKRRIFN   97 (131)
Q Consensus        80 ~~i~~~~P--~~~~R~~il~   97 (131)
                      ..+.++..  +.+....+-+
T Consensus       339 ~~i~~~~~~~d~~ta~~~s~  358 (437)
T 1e9r_A          339 SLVVLGGSRTDPKTNEDMSL  358 (437)
T ss_dssp             EEEEEECCTTCHHHHHHHHH
T ss_pred             cEEEEeCCCCCHHHHHHHHH
Confidence            89999988  7777665543

---

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	131
d1lv7a_	256	c.37.1.20 (A:) AAA domain of cell division protein	1e-51
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	9e-51
d1r7ra3	265	c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p	3e-34
d1w44a_	321	c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [Ta	1e-23
d1e32a2	258	c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p	4e-19
d1svma_	362	c.37.1.20 (A:) Papillomavirus large T antigen heli	2e-11
d1d2na_	246	c.37.1.20 (A:) Hexamerization domain of N-ethylmal	7e-10
d1gvnb_	273	c.37.1.21 (B:) Plasmid maintenance system epsilon/	6e-09
d1ofha_	309	c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId	2e-05

>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 =  161 bits (410), Expect = 1e-51
 Identities = 53/131 (40%), Positives = 81/131 (61%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           +F  A++ AP I+FIDEIDAVG +R     GG  E ++T+ ++L ++DGF+    + VI 
Sbjct: 96  MFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIA 155

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + LDPAL+RPGR DR++   LPD + + +I  +H  R+ LA D++   +      
Sbjct: 156 ATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPG 215

Query: 121 LSGADIKAICT 131
            SGAD+  +  
Sbjct: 216 FSGADLANLVN 226

>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 =  159 bits (403), Expect = 9e-51
 Identities = 61/131 (46%), Positives = 80/131 (61%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           LF  A+ HAP IVFIDEIDAVG KR     GG  E ++T+ +LL ++DGF+    + V+ 
Sbjct: 93  LFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMA 152

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + LDPAL+RPGR DR+I    PD K + +I  IH     LAEDV+L  L      
Sbjct: 153 ATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPG 212

Query: 121 LSGADIKAICT 131
             GAD++ +  
Sbjct: 213 FVGADLENLLN 223

>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 =  117 bits (294), Expect = 3e-34
 Identities = 47/131 (35%), Positives = 80/131 (61%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           +F  A + AP ++F DE+D++   R  +   G     R + ++L ++DG  ++ +V +I 
Sbjct: 92  IFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIG 151

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDD 120
           ATNR + +DPA++RPGR+D+ I  PLPDEK++  I   +  +  +A+DV+L+ L    + 
Sbjct: 152 ATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNG 211

Query: 121 LSGADIKAICT 131
            SGAD+  IC 
Sbjct: 212 FSGADLTEICQ 222

>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 = 90.9 bits (225), Expect = 1e-23
 Identities = 16/128 (12%), Positives = 37/128 (28%), Gaps = 12/128 (9%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIM 60
           + R   +H   ++ ID +  V      + + G     R   +LL+ +    +     VI 
Sbjct: 176 IARAMLQHR--VIVIDSLKNVIGAAGGNTTSGGIS--RGAFDLLSDIGAMAASRGCVVIA 231

Query: 61  ATNRIE---TLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRM-----TLAEDVNLQ 112
           + N       +   +    R +        D   + ++       +     TL       
Sbjct: 232 SLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTSYGEH 291

Query: 113 ELIMAKDD 120
            ++     
Sbjct: 292 SVLTIHTS 299

>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 = 77.8 bits (190), Expect = 4e-19
 Identities = 52/130 (40%), Positives = 80/130 (61%), Gaps = 3/130 (2%)

Query: 2   FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMA 61
           F  AE++AP+I+FIDE+DA+  KR  ++       +R + +LL  +DG   R  V V+ A
Sbjct: 90  FEEAEKNAPAIIFIDELDAIAPKREKTHGE---VERRIVSQLLTLMDGLKQRAHVIVMAA 146

Query: 62  TNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDL 121
           TNR  ++DPAL R GR DR+++  +PD   +  I  IHT  M LA+DV+L+++       
Sbjct: 147 TNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGH 206

Query: 122 SGADIKAICT 131
            GAD+ A+C+
Sbjct: 207 VGADLAALCS 216

>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 = 57.4 bits (138), Expect = 2e-11
 Identities = 14/128 (10%), Positives = 28/128 (21%), Gaps = 16/128 (12%)

Query: 5   AEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNR 64
                PS   I+ +D +      S      +        +              I+  N 
Sbjct: 216 ESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPP----------GIVTMNE 265

Query: 65  IETLDPALIRPGRIDRKIEFPLPDEKTK-RRIFNIHTSRMTLAEDVNLQELIMAKDDLSG 123
                       R  ++I+F   D              +  +     +  L+M       
Sbjct: 266 ---YSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRII--QSGIALLLMLIWYRPV 320

Query: 124 ADIKAICT 131
           A+      
Sbjct: 321 AEFAQSIQ 328

>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 = 52.6 bits (125), Expect = 7e-10
 Identities = 22/130 (16%), Positives = 39/130 (30%), Gaps = 10/130 (7%)

Query: 2   FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKV-IM 60
           F  A +   S V +D+I+ +            R     +  LL  L     +G   + I 
Sbjct: 93  FDDAYKSQLSCVVVDDIERLLDYVPIG----PRFSNLVLQALLVLLKKAPPQGRKLLIIG 148

Query: 61  ATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELI-MAKD 119
            T+R + L    +        I    P+  T  ++           +D     +    K 
Sbjct: 149 TTSRKDVLQEMEML-NAFSTTIHV--PNIATGEQLLEALELLGNF-KDKERTTIAQQVKG 204

Query: 120 DLSGADIKAI 129
                 IK +
Sbjct: 205 KKVWIGIKKL 214

>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 = 50.3 bits (119), Expect = 6e-09
 Identities = 11/139 (7%), Positives = 32/139 (23%), Gaps = 11/139 (7%)

Query: 1   LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLEL--------LNQLDGFDS 52
           + +    ++  +                  G  R     +             ++     
Sbjct: 86  VVKHVTPYSNRMTEAIISRLSDQGYNLVIEGTGRTTDVPIQTATMLQAKGYETKMYVMAV 145

Query: 53  RGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQ 112
                 +    R ET+        R   K    +  +     +  +H + +     +  +
Sbjct: 146 PKINSYLGTIERYETMYADDPMTARATPKQAHDIVVKNLPTNLETLHKTGLFSDIRLYNR 205

Query: 113 ELIMAKDDLSGADIKAICT 131
           E +      S  +  +I  
Sbjct: 206 EGVKL---YSSLETPSISP 221

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]} Length = 309

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

 Score = 40.2 bits (93), Expect = 2e-05
 Identities = 23/107 (21%), Positives = 39/107 (36%), Gaps = 12/107 (11%)

Query: 8   HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATN---- 63
               IVFIDEID +  K   S +   RE      +LL  ++G        ++   +    
Sbjct: 114 EQNGIVFIDEIDKICKKGEYSGADVSRE--GVQRDLLPLVEGSTVSTKHGMVKTDHILFI 171

Query: 64  ---RIETLDPALIRP---GRIDRKIEFPLPDEKTKRRIFNIHTSRMT 104
                +   P+ + P   GR+  ++E          RI     + +T
Sbjct: 172 ASGAFQVARPSDLIPELQGRLPIRVELTALSAADFERILTEPHASLT 218

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	131
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	100.0
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	100.0
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	100.0
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.98
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.66
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.65
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.12
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	98.65
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.58
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	98.51
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	98.47
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	98.45
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.36
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.32
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.29
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	98.28
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	98.28
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	98.25
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.18
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	98.06
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	97.88
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	97.62
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.46
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.46
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.43
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.06
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	96.99
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	95.94
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	95.86
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	95.19
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	92.91
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	92.77
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	87.05
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	86.43
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	85.76
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	83.94
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	83.48
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	83.19
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	82.24
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	82.15
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	82.12

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=2.5e-34  Score=199.89  Aligned_cols=131  Identities=40%  Similarity=0.715  Sum_probs=120.6

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|++++||||||||+|.++.+++...........+++++++..++++..+++++||||||+|+.||++++||||||+
T Consensus        96 ~f~~A~~~~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~v~vIatTn~~~~ld~al~R~gRfd~  175 (256)
T d1lv7a_          96 MFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDR  175 (256)
T ss_dssp             HHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEEESCTTTSCGGGGSTTSSCE
T ss_pred             HHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCcccCCHhHcCCCCCCE
Confidence            48999999999999999999999886655555555667889999999999888899999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .|++++|+.++|.+||+.++++.+...+.++..+++.|+|||++||+.+|+
T Consensus       176 ~i~i~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~G~s~adi~~l~~  226 (256)
T d1lv7a_         176 QVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVN  226 (256)
T ss_dssp             EEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             EEECCCcCHHHHHHHHHHhccCCCcCcccCHHHHHHhCCCCCHHHHHHHHH
Confidence            999999999999999999999998888899999999999999999999873

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=3.4e-34  Score=198.38  Aligned_cols=131  Identities=47%  Similarity=0.741  Sum_probs=115.0

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|+.++||||||||+|.++.+++............+++.++..|+++...++|+||+|||+|+.+|++++|||||++
T Consensus        93 ~f~~a~~~~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~vivi~tTn~~~~ld~al~R~~Rf~~  172 (247)
T d1ixza_          93 LFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDR  172 (247)
T ss_dssp             HHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGGGSCGGGGSTTSSCE
T ss_pred             HHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCccccCHhHcCCCCCcE
Confidence            48899999999999999999999886665555566778899999999999888899999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .|++++|+.++|.+||+.++...+...+.++..+++.|+|||++||+.+|+
T Consensus       173 ~i~~~~P~~~eR~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~lv~  223 (247)
T d1ixza_         173 QIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLN  223 (247)
T ss_dssp             EEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             EEEECCcCHHHHHHHHHHHhcccCCccccCHHHHHHHCCCCCHHHHHHHHH
Confidence            999999999999999999999988888899999999999999999999874

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=100.00  E-value=7.3e-33  Score=192.75  Aligned_cols=128  Identities=41%  Similarity=0.710  Sum_probs=114.8

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|+.|++++||||||||+|.++.++++......   ..++..++..++.....++++||+|||+|+.+|++++||||||+
T Consensus        89 ~f~~A~~~~p~il~iDeid~l~~~r~~~~~~~~---~~~~~~~~~~~~~~~~~~~vlvi~tTn~~~~ld~al~r~gRfd~  165 (258)
T d1e32a2          89 AFEEAEKNAPAIIFIDELDAIAPKREKTHGEVE---RRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDR  165 (258)
T ss_dssp             HHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTH---HHHHHHHHHHHHTCCCSSCEEEEEEESCGGGSCGGGTSTTSSCE
T ss_pred             HHHHHHhcCCeEEEehhhhhhccCCCCCCCchH---HHHHHHhccccccccccCCccEEEeCCCccccchhhhhcccccc
Confidence            489999999999999999999998865443333   35667777778888788899999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .|++++|+.++|.+||+.++++.....+.++..+|+.|+|||++||+.+|+
T Consensus       166 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~G~s~adl~~lv~  216 (258)
T d1e32a2         166 EVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCS  216 (258)
T ss_dssp             EEECCCCCHHHHHHHHHHTTTTSCBCTTCCHHHHHHHCTTCCHHHHHHHHH
T ss_pred             eeECCCCCHHHHHHHhhhhccCcccccccchhhhhhcccCCCHHHHHHHHH
Confidence            999999999999999999999988888899999999999999999999874

>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=99.98  E-value=6.1e-33  Score=193.84  Aligned_cols=131  Identities=36%  Similarity=0.674  Sum_probs=112.0

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccce
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDR   80 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~   80 (131)
                      +|..|+.++||||||||+|.++.+++...........++++.++..++++..+++++||||||+++.||++++|||||++
T Consensus        92 ~f~~A~~~~p~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gRf~~  171 (265)
T d1r7ra3          92 IFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQ  171 (265)
T ss_dssp             HHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC------CCEEEECCBSCTTTSCGGGSSTTSEE
T ss_pred             HHHHHHhcCCcceeHHhhhhccccCCCcCCCCcHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCCchhCCHHHhCCCCccE
Confidence            48899999999999999999999886666666566667889999999998888889999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhhC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAICT  131 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~~  131 (131)
                      .|++++|+.++|.+||+.++++.....+.++..++..|+|||++||+.+|+
T Consensus       172 ~i~~~~p~~~~R~~il~~~l~~~~~~~~~~l~~la~~t~g~s~~di~~lv~  222 (265)
T d1r7ra3         172 LIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQ  222 (265)
T ss_dssp             EEECCCCCCHHHHHHHHHHTTCC----CCCCHHHHHHHCSSCCHHHHHHHH
T ss_pred             EEEecchHHHHHHHHHHHHhccCCchhhhhHHHHHhcCCCCCHHHHHHHHH
Confidence            999999999999999999999888888899999999999999999999874

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=99.66  E-value=1.8e-17  Score=113.78  Aligned_cols=114  Identities=15%  Similarity=0.092  Sum_probs=79.7

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCC-CCeEEEeeCCCCCcccccccCCCccc
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSR-GDVKVIMATNRIETLDPALIRPGRID   79 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~v~vi~ttn~~~~id~~l~~~grf~   79 (131)
                      +|+.|++++||||||||+|.++..+...... .   ..++..++..+++.... .+|+||||||+++.+|++.++ +||+
T Consensus        92 if~~A~~~~p~il~iDEid~l~~~~~~~~~~-~---~~~~~~ll~~l~~~~~~~~~v~vi~tTn~~~~ld~~~~~-~rF~  166 (246)
T d1d2na_          92 IFDDAYKSQLSCVVVDDIERLLDYVPIGPRF-S---NLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEML-NAFS  166 (246)
T ss_dssp             HHHHHHTSSEEEEEECCHHHHTTCBTTTTBC-C---HHHHHHHHHHTTCCCSTTCEEEEEEEESCHHHHHHTTCT-TTSS
T ss_pred             hhhhhhhcccceeehhhhhhHhhhcccccch-h---HHHHHHHHHHhcCCCccccceeeeeccCChhhccchhhc-Cccc
Confidence            4899999999999999999998776432221 2   24666778888876544 469999999999999876443 5999


Q ss_pred             eEEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCC
Q psy522           80 RKIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLS  122 (131)
Q Consensus        80 ~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s  122 (131)
                      ..|++|.+  .+|.++++.+..... -.+.++..++..+.|.+
T Consensus       167 ~~i~~P~~--~~r~~il~~l~~~~~-~~~~~~~~i~~~~~g~~  206 (246)
T d1d2na_         167 TTIHVPNI--ATGEQLLEALELLGN-FKDKERTTIAQQVKGKK  206 (246)
T ss_dssp             EEEECCCE--EEHHHHHHHHHHHTC-SCHHHHHHHHHHHTTSE
T ss_pred             eEEecCCc--hhHHHHHHHHHhccC-CChHHHHHHHHHcCCCc
Confidence            99998554  233344443322222 23456788888888854

>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=99.65  E-value=1.1e-19  Score=128.64  Aligned_cols=100  Identities=14%  Similarity=0.193  Sum_probs=75.8

Q ss_pred             CHHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCC---CCcccccccCCCc
Q psy522            1 LFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNR---IETLDPALIRPGR   77 (131)
Q Consensus         1 vF~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~---~~~id~~l~~~gr   77 (131)
                      +|+.|+.  ||||||||+|.+.++++.......  ..++++++|.+||++....+|+||||||.   ++.+++++.||||
T Consensus       176 ~f~~a~~--~~ilf~DEid~~~~~r~~~~~~~~--~~r~v~~lL~e~dg~~~~~~v~viaatN~~~~~~~i~~~~~r~~R  251 (321)
T d1w44a_         176 IARAMLQ--HRVIVIDSLKNVIGAAGGNTTSGG--ISRGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASR  251 (321)
T ss_dssp             HHHHHHH--CSEEEEECCTTTC-------------CCHHHHHHHHHHHHHHHHHTCEEEEECCCCCCCHHHHHHHHHHHH
T ss_pred             HHHHHhh--ccEEEeehhhhhccccccCCCCCc--chhhhhhhhhhccccccCCCeEEEEeCCCcccccchhhhhhccCc
Confidence            5888875  899999999999998854333222  22588999999999877788999999994   2445667789999


Q ss_pred             cceEEEeCCCCHHHHHHHHHHHhcCCC
Q psy522           78 IDRKIEFPLPDEKTKRRIFNIHTSRMT  104 (131)
Q Consensus        78 f~~~i~~~~P~~~~R~~il~~~l~~~~  104 (131)
                      |+..++++.|+.+.|.+|++.+..++.
T Consensus       252 f~~~v~v~~pd~~~r~~il~~~~~~~~  278 (321)
T d1w44a_         252 SNSTSLVISTDVDGEWQVLTRTGEGLQ  278 (321)
T ss_dssp             HSCSEEEEECSSTTEEEEEEECBTTCC
T ss_pred             ccceeecCCCChHHHHHHHHHhccCcc
Confidence            999999999999999999987766553

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=99.12  E-value=5.3e-11  Score=83.47  Aligned_cols=88  Identities=25%  Similarity=0.308  Sum_probs=65.4

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCC--------CCCeEEEee----CCCCCcccccccCC
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDS--------RGDVKVIMA----TNRIETLDPALIRP   75 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--------~~~v~vi~t----tn~~~~id~~l~~~   75 (131)
                      .+||||||||+|++.+.+....  .+.....+++.+|..+++...        ..++++|++    ++.++.++|+++. 
T Consensus       114 ~~~~IIf~DEIdki~~~~~~~~--~~~~~~gv~~~LL~~~dg~~~~~~~~~i~~s~ilfi~~ga~~~~~~~~~~p~l~~-  190 (309)
T d1ofha_         114 EQNGIVFIDEIDKICKKGEYSG--ADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG-  190 (309)
T ss_dssp             HHHCEEEEECGGGGSCCSSCCS--SHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSSCGGGSCHHHHH-
T ss_pred             cCCceEEehhhhhhhhhccCcc--cchhhhHHHHHhhHHhcCCEEecCCeEEEccceeEEeccchhhcCcccchhhhhh-
Confidence            4689999999999987663322  222223466778888887321        234667766    6788888999986 


Q ss_pred             CccceEEEeCCCCHHHHHHHHHHH
Q psy522           76 GRIDRKIEFPLPDEKTKRRIFNIH   99 (131)
Q Consensus        76 grf~~~i~~~~P~~~~R~~il~~~   99 (131)
                       ||+..+.++.|+.+++.+|+..+
T Consensus       191 -R~~~~i~~~~~~~~~~~~Il~~~  213 (309)
T d1ofha_         191 -RLPIRVELTALSAADFERILTEP  213 (309)
T ss_dssp             -TCCEEEECCCCCHHHHHHHHHSS
T ss_pred             -hhheeeeccCCCHHHHHHHHHHH
Confidence             99999999999999999998654

>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=98.65  E-value=9.4e-08  Score=63.69  Aligned_cols=72  Identities=15%  Similarity=0.105  Sum_probs=59.1

Q ss_pred             CCeEEEeeCCCCCcccccccCCCccceEEEeCCCCHHHHHHHHHHHhcCCCCCCc-ccHHHHHHHcCCCCHHHHHH
Q psy522           54 GDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAED-VNLQELIMAKDDLSGADIKA  128 (131)
Q Consensus        54 ~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~~~~~~~-~~~~~la~~t~g~s~~di~~  128 (131)
                      .++++|++||.+..+++.+++  ||...+.++.|+.+++..+++......+...+ ..+..++..+.| +++.+..
T Consensus       133 ~~~~~I~at~~~~~~~~~~~~--r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~i~~~s~g-d~R~ai~  205 (238)
T d1in4a2         133 QPFTLVGATTRSGLLSSPLRS--RFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRG-TPRIAIR  205 (238)
T ss_dssp             CCCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTT-CHHHHHH
T ss_pred             CCeEEEEecCCCcccccccee--eeeEEEEecCCCHHHHHHHHHHhhhhccchhhHHHHHHHHHhCCC-CHHHHHH
Confidence            478999999999999999999  99999999999999999999999877665533 347777777666 4555544

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.58  E-value=8.9e-08  Score=64.11  Aligned_cols=93  Identities=13%  Similarity=0.219  Sum_probs=67.7

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      ...+++|||+|.+....              ...++..++.  ....+.+|++||+++.+++.+++  || ..|++++|+
T Consensus       131 ~~~iiiide~d~l~~~~--------------~~~l~~~~e~--~~~~~~~Il~tn~~~~i~~~l~s--R~-~~i~~~~~~  191 (252)
T d1sxje2         131 RYKCVIINEANSLTKDA--------------QAALRRTMEK--YSKNIRLIMVCDSMSPIIAPIKS--QC-LLIRCPAPS  191 (252)
T ss_dssp             CCEEEEEECTTSSCHHH--------------HHHHHHHHHH--STTTEEEEEEESCSCSSCHHHHT--TS-EEEECCCCC
T ss_pred             CceEEEecccccccccc--------------chhhhccccc--ccccccceeeeccccchhhhhhc--ch-heeeecccc
Confidence            35689999999873221              2222333332  24567889999999999999999  99 589999999


Q ss_pred             HHHHHHHHHHHhcCCCCC--CcccHHHHHHHcCC
Q psy522           89 EKTKRRIFNIHTSRMTLA--EDVNLQELIMAKDD  120 (131)
Q Consensus        89 ~~~R~~il~~~l~~~~~~--~~~~~~~la~~t~g  120 (131)
                      .++..+++...++..+..  .+.-+..++..+.|
T Consensus       192 ~~~~~~~l~~i~~~e~~~~~~~~~l~~i~~~s~G  225 (252)
T d1sxje2         192 DSEISTILSDVVTNERIQLETKDILKRIAQASNG  225 (252)
T ss_dssp             HHHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTT
T ss_pred             hhhHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCC
Confidence            999999999887654332  33346778887776

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=98.51  E-value=1e-07  Score=63.15  Aligned_cols=105  Identities=16%  Similarity=0.288  Sum_probs=73.0

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCccc---ccccCCCccc--eEEE
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLD---PALIRPGRID--RKIE   83 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id---~~l~~~grf~--~~i~   83 (131)
                      .-.+|+|||+|.+..+.            ..-..+...++.....++.+++++...|..++   +.+.+  |+.  ..+.
T Consensus        97 ~~dll~iDDi~~i~~~~------------~~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~~~dL~S--RL~~g~~~~  162 (213)
T d1l8qa2          97 SVDLLLLDDVQFLSGKE------------RTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVS--RFEGGILVE  162 (213)
T ss_dssp             TCSEEEEECGGGGTTCH------------HHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHH--HHHTSEEEE
T ss_pred             hccchhhhhhhhhcCch------------HHHHHHHHHHHHHhhccceEEEecCCcchhccccchHHHH--HhhCceEEE
Confidence            35789999999997554            12222333333334567778888888888775   77888  874  5666


Q ss_pred             eCCCCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHHHHhh
Q psy522           84 FPLPDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADIKAIC  130 (131)
Q Consensus        84 ~~~P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di~~l~  130 (131)
                      ++ |+.+.|.++++.+....++. ++.-+..+++++.  +.+||+.++
T Consensus       163 i~-p~d~~~~~iL~~~a~~rgl~l~~~v~~yl~~~~~--~~R~L~~~l  207 (213)
T d1l8qa2         163 IE-LDNKTRFKIIKEKLKEFNLELRKEVIDYLLENTK--NVREIEGKI  207 (213)
T ss_dssp             CC-CCHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHCS--SHHHHHHHH
T ss_pred             EC-CCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcC--cHHHHHHHH
Confidence            76 66789999999998877666 3344777888874  688887764

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=98.47  E-value=3.2e-07  Score=60.78  Aligned_cols=100  Identities=16%  Similarity=0.224  Sum_probs=74.5

Q ss_pred             hcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCC
Q psy522            7 EHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPL   86 (131)
Q Consensus         7 ~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~   86 (131)
                      ...+.|+++||+|.+....           ...   ++..+..  ...++.+|++||.+..+++++++  ||. .+.+++
T Consensus       107 ~~~~~iilide~d~~~~~~-----------~~~---ll~~l~~--~~~~~~~i~~~n~~~~i~~~l~s--R~~-~i~~~~  167 (231)
T d1iqpa2         107 GASFKIIFLDEADALTQDA-----------QQA---LRRTMEM--FSSNVRFILSCNYSSKIIEPIQS--RCA-IFRFRP  167 (231)
T ss_dssp             GCSCEEEEEETGGGSCHHH-----------HHH---HHHHHHH--TTTTEEEEEEESCGGGSCHHHHH--TEE-EEECCC
T ss_pred             CCCceEEeehhhhhcchhH-----------HHH---Hhhhccc--CCcceEEEeccCChhhchHhHhC--ccc-cccccc
Confidence            3457899999999875432           112   2333331  23568899999999999999999  985 799999


Q ss_pred             CCHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCCCCHHHH
Q psy522           87 PDEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDDLSGADI  126 (131)
Q Consensus        87 P~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g~s~~di  126 (131)
                      |+..+...+++..+...++. .+..+..+++.+.| +.++.
T Consensus       168 ~~~~~~~~~l~~~~~~e~i~i~~~~l~~I~~~~~g-diR~a  207 (231)
T d1iqpa2         168 LRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEG-DMRRA  207 (231)
T ss_dssp             CCHHHHHHHHHHHHHTTTCEECHHHHHHHHHHHTT-CHHHH
T ss_pred             cchhhHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC-CHHHH
Confidence            99999999999999877765 44457888887766 44443

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.45  E-value=3.4e-07  Score=61.26  Aligned_cols=92  Identities=22%  Similarity=0.276  Sum_probs=68.0

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-|++|||+|.+-..              ..+.++..++.  ..+.+.+|++||.++.+.+++++  |+ ..+.+++|+.
T Consensus       116 ~kviiIde~d~l~~~--------------~q~~Llk~lE~--~~~~~~~il~tn~~~~i~~~i~S--Rc-~~i~~~~~~~  176 (239)
T d1njfa_         116 FKVYLIDEVHMLSRH--------------SFNALLKTLEE--PPEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDV  176 (239)
T ss_dssp             SEEEEEETGGGSCHH--------------HHHHHHHHHHS--CCTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCH
T ss_pred             CEEEEEECcccCCHH--------------HHHHHHHHHhc--CCCCeEEEEEcCCccccChhHhh--hh-cccccccCcH
Confidence            458999999998321              22345555553  34678899999999999999999  98 5899999999


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      ++-..++...+...+.. ++..+..++..+.|
T Consensus       177 ~~i~~~l~~i~~~e~~~~~~~~l~~i~~~s~G  208 (239)
T d1njfa_         177 EQIRHQLEHILNEEHIAHEPRALQLLARAAEG  208 (239)
T ss_dssp             HHHHHHHHHHHHHHTCCBCHHHHHHHHHHTTT
T ss_pred             HHhhhHHHHHHhhhccCCCHHHHHHHHHHcCC
Confidence            99888888877644433 33347777777766

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.36  E-value=2.8e-06  Score=55.91  Aligned_cols=93  Identities=16%  Similarity=0.203  Sum_probs=69.9

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      ...++++||+|.+...              ....++..++.  ....++++.+||.+..+++.+++  |+ ..+.+++|+
T Consensus        99 ~~kiiiiDe~d~~~~~--------------~~~~Ll~~le~--~~~~~~~~~~~~~~~~i~~~i~s--r~-~~i~~~~~~  159 (227)
T d1sxjc2          99 GFKLIILDEADAMTNA--------------AQNALRRVIER--YTKNTRFCVLANYAHKLTPALLS--QC-TRFRFQPLP  159 (227)
T ss_dssp             SCEEEEETTGGGSCHH--------------HHHHHHHHHHH--TTTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCC
T ss_pred             CeEEEEEeccccchhh--------------HHHHHHHHhhh--cccceeeccccCcHHHhHHHHHH--HH-hhhcccccc
Confidence            3469999999987432              12223333332  23468889999999999999999  88 478999999


Q ss_pred             HHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           89 EKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        89 ~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      .++-..++...+...+.. ++..+..+++.+.|
T Consensus       160 ~~~i~~~l~~I~~~e~i~i~~~~l~~i~~~s~G  192 (227)
T d1sxjc2         160 QEAIERRIANVLVHEKLKLSPNAEKALIELSNG  192 (227)
T ss_dssp             HHHHHHHHHHHHHTTTCCBCHHHHHHHHHHHTT
T ss_pred             ccccccccccccccccccCCHHHHHHHHHHcCC
Confidence            999999999988776665 34457888888776

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.32  E-value=3e-06  Score=55.52  Aligned_cols=96  Identities=18%  Similarity=0.177  Sum_probs=69.4

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      +.-|++|||+|.+..              ...+.++..++.  ....+++|.+|+++..+.+.+++  |+ ..+.+++|+
T Consensus       108 ~~kviIide~d~l~~--------------~a~n~Llk~lEe--p~~~~~fIl~t~~~~~ll~tI~S--Rc-~~i~~~~~~  168 (207)
T d1a5ta2         108 GAKVVWVTDAALLTD--------------AAANALLKTLEE--PPAETWFFLATREPERLLATLRS--RC-RLHYLAPPP  168 (207)
T ss_dssp             SCEEEEESCGGGBCH--------------HHHHHHHHHHTS--CCTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCC
T ss_pred             ccceEEechhhhhhh--------------hhhHHHHHHHHh--hcccceeeeeecChhhhhhhhcc--ee-EEEecCCCC
Confidence            456999999999853              244556666664  34678999999999999999999  98 699999999


Q ss_pred             HHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHH
Q psy522           89 EKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKA  128 (131)
Q Consensus        89 ~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~  128 (131)
                      .++-..+++.-.   .. ++..+..++..+.| ++++.-.
T Consensus       169 ~~~~~~~L~~~~---~~-~~~~~~~i~~~s~G-s~r~al~  203 (207)
T d1a5ta2         169 EQYAVTWLSREV---TM-SQDALLAALRLSAG-SPGAALA  203 (207)
T ss_dssp             HHHHHHHHHHHC---CC-CHHHHHHHHHHTTT-CHHHHHH
T ss_pred             HHHHHHHHHHcC---CC-CHHHHHHHHHHcCC-CHHHHHH
Confidence            998888776432   22 23346667776655 4554433

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.29  E-value=1.9e-06  Score=58.74  Aligned_cols=86  Identities=30%  Similarity=0.368  Sum_probs=62.5

Q ss_pred             HHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCC-----CCcccccccCCC
Q psy522            2 FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNR-----IETLDPALIRPG   76 (131)
Q Consensus         2 F~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~-----~~~id~~l~~~g   76 (131)
                      ++.+......|+|+||++.++...++.++  +..       +-+.+..+-..+.+-+||+|..     ...-|++|.|  
T Consensus       103 ~~~~~~~~~iIlfiDeih~l~~~g~~~g~--~~d-------~a~~Lkp~L~rg~i~vIgatT~eey~~~~e~d~al~r--  171 (268)
T d1r6bx2         103 LKQLEQDTNSILFIDEIHTIIGAGAASGG--QVD-------AANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRALAR--  171 (268)
T ss_dssp             HHHHSSSSCEEEEETTTTTTTTSCCSSSC--HHH-------HHHHHSSCSSSCCCEEEEEECHHHHHCCCCCTTSSGG--
T ss_pred             HHHhhccCCceEEecchHHHhcCCCCCCc--ccc-------HHHHhhHHHhCCCCeEEEeCCHHHHHHHHhhcHHHHh--
Confidence            45666778899999999999976533221  211       2233344556778889998873     2234899999  


Q ss_pred             ccceEEEeCCCCHHHHHHHHHHH
Q psy522           77 RIDRKIEFPLPDEKTKRRIFNIH   99 (131)
Q Consensus        77 rf~~~i~~~~P~~~~R~~il~~~   99 (131)
                      ||. .|.+..|+.++-..|++.+
T Consensus       172 rF~-~I~V~Eps~e~t~~IL~~~  193 (268)
T d1r6bx2         172 RFQ-KIDITEPSIEETVQIINGL  193 (268)
T ss_dssp             GEE-EEECCCCCHHHHHHHHHHH
T ss_pred             hhc-ccccCCCCHHHHHHHHHHh
Confidence            996 8999999999999999764

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=98.28  E-value=2.9e-06  Score=56.27  Aligned_cols=65  Identities=11%  Similarity=0.004  Sum_probs=54.0

Q ss_pred             CCeEEEeeCCCCCcccccccCCCccceEEEeCCCCHHHHHHHHHHHhcCCCCCC-cccHHHHHHHcCC
Q psy522           54 GDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSRMTLAE-DVNLQELIMAKDD  120 (131)
Q Consensus        54 ~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~~~~~~~-~~~~~~la~~t~g  120 (131)
                      +++++|++|+++...++..++  |+...+.+..|+.+++..+++..+...+... ...+..++..+.|
T Consensus       134 ~~~~~i~~~~~~~~~~~~~l~--~~~~~~~~~~~~~~~~~~i~~~~~~~~~i~~~~~~l~~ia~~s~g  199 (239)
T d1ixsb2         134 PRFTLIGATTRPGLITAPLLS--RFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRG  199 (239)
T ss_dssp             CCCEEEEEESCCSSCSCGGGG--GCSEEEECCCCCHHHHHHHHHHHHGGGCCCBCHHHHHHHHHHTTS
T ss_pred             CCEEEEeeccCcccccchhhc--ccceeeEeeccChhhhhHHHHHHHHHhCCccchHHHHHHHHHcCC
Confidence            568888999998888888888  8888899999999999999999888766553 3347778888887

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.28  E-value=2.1e-06  Score=57.22  Aligned_cols=96  Identities=15%  Similarity=0.223  Sum_probs=63.1

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCC
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLP   87 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P   87 (131)
                      ..+.++++||+|.+....      ..     ....++.....  ...+++++++++....+++ ++   |+...++|++|
T Consensus       122 ~~~~vi~ide~~~~~~~~------~~-----~~~~~~~~~~~--~~~~ii~i~~~~~~~~~~~-l~---~~~~~i~f~~~  184 (253)
T d1sxja2         122 GKHFVIIMDEVDGMSGGD------RG-----GVGQLAQFCRK--TSTPLILICNERNLPKMRP-FD---RVCLDIQFRRP  184 (253)
T ss_dssp             TTSEEEEECSGGGCCTTS------TT-----HHHHHHHHHHH--CSSCEEEEESCTTSSTTGG-GT---TTSEEEECCCC
T ss_pred             ccceEEEeeeccccccch------hh-----hhHHHhhhhcc--ccccccccccccccccccc-cc---ceeeeeecccc
Confidence            347899999999986543      11     12222222221  2245677766666666663 44   55578999999


Q ss_pred             CHHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           88 DEKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        88 ~~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      +.+++..+++..+...++. .+..+..++..+.|
T Consensus       185 ~~~~i~~~l~~i~~~e~i~i~~~~l~~i~~~s~G  218 (253)
T d1sxja2         185 DANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRG  218 (253)
T ss_dssp             CHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHTTT
T ss_pred             chhHHHHHHHHHHHHhCCCCCHHHHHHHHHhCCC
Confidence            9999999999988643333 33458889988766

>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=98.25  E-value=1.8e-07  Score=66.49  Aligned_cols=69  Identities=13%  Similarity=0.047  Sum_probs=52.1

Q ss_pred             EEEeeCCCCCcccccccCCCccceEEEeCCCCHHHHH-HHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHhh
Q psy522           57 KVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKR-RIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAIC  130 (131)
Q Consensus        57 ~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~~~R~-~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l~  130 (131)
                      .+|+|||+   .+.++.+||||+..+++..|+...|. +++..++++....  .+...++..+.|++++|+.+++
T Consensus       258 p~i~ttN~---~~~~~~r~~Rf~~~i~~~~~~~~~~~~~~l~~i~~~~~l~--~~~~~L~~li~~~s~~D~~~~i  327 (362)
T d1svma_         258 PGIVTMNE---YSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRIIQ--SGIALLLMLIWYRPVAEFAQSI  327 (362)
T ss_dssp             CEEEEECS---CCCCHHHHTTEEEEEECCCCHHHHHHHHTCTHHHHTTCTT--CHHHHHHHHHHHSCGGGSCGGG
T ss_pred             Cceeeccc---ccccccccccCceEEeecCCCcHHHHHHHHHHHhcccCCC--CCHHHHHHHccCCCHHHHHHHH
Confidence            37889995   56677789999999999999877764 4555666665554  3456688888999999987765

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.18  E-value=3.3e-06  Score=55.64  Aligned_cols=92  Identities=14%  Similarity=0.226  Sum_probs=67.7

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      ..|++|||+|.+....           ...+..++   ..  ......+|.+++....+.+.+++  || ..+.|++|+.
T Consensus       109 ~~viiiDe~d~l~~~~-----------~~~l~~~~---~~--~~~~~~~i~~~~~~~~~~~~l~s--r~-~~i~f~~~~~  169 (237)
T d1sxjd2         109 YKIIILDEADSMTADA-----------QSALRRTM---ET--YSGVTRFCLICNYVTRIIDPLAS--QC-SKFRFKALDA  169 (237)
T ss_dssp             CEEEEETTGGGSCHHH-----------HHHHHHHH---HH--TTTTEEEEEEESCGGGSCHHHHH--HS-EEEECCCCCH
T ss_pred             ceEEEEecccccCHHH-----------HHHHhhcc---cc--ccccccccccccccccccccccc--hh-hhhccccccc
Confidence            3489999999985321           11222222   21  23456778888999999999999  98 5899999999


Q ss_pred             HHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           90 KTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        90 ~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      ++...+++..+...++. ++..+..+++.+.|
T Consensus       170 ~~~~~~L~~i~~~e~i~i~~~~l~~ia~~s~g  201 (237)
T d1sxjd2         170 SNAIDRLRFISEQENVKCDDGVLERILDISAG  201 (237)
T ss_dssp             HHHHHHHHHHHHTTTCCCCHHHHHHHHHHTSS
T ss_pred             cccchhhhhhhhhhcCcCCHHHHHHHHHHcCC
Confidence            99999999998876654 33447788888766

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.06  E-value=4.8e-06  Score=54.77  Aligned_cols=93  Identities=12%  Similarity=0.160  Sum_probs=67.2

Q ss_pred             CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCC
Q psy522            9 APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPD   88 (131)
Q Consensus         9 ~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~   88 (131)
                      ...++++||+|.+....              ...++..+..  ......++.+|+....+.+++++  ||. .+.+++|+
T Consensus       101 ~~kviiiDe~d~~~~~~--------------~~~ll~~~e~--~~~~~~~i~~~~~~~~i~~~l~s--r~~-~i~~~~~~  161 (224)
T d1sxjb2         101 KHKIVILDEADSMTAGA--------------QQALRRTMEL--YSNSTRFAFACNQSNKIIEPLQS--QCA-ILRYSKLS  161 (224)
T ss_dssp             CCEEEEEESGGGSCHHH--------------HHTTHHHHHH--TTTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCC
T ss_pred             ceEEEEEecccccchhH--------------HHHHhhhccc--cccceeeeeccCchhhhhhHHHH--HHH-Hhhhcccc
Confidence            35699999999985432              1122233331  34567888889999999999999  984 79999999


Q ss_pred             HHHHHHHHHHHhcCCCCC-CcccHHHHHHHcCC
Q psy522           89 EKTKRRIFNIHTSRMTLA-EDVNLQELIMAKDD  120 (131)
Q Consensus        89 ~~~R~~il~~~l~~~~~~-~~~~~~~la~~t~g  120 (131)
                      .++...++...+...+.. ++..+..++..+.|
T Consensus       162 ~~~i~~~l~~i~~~e~~~i~~~~l~~I~~~s~G  194 (224)
T d1sxjb2         162 DEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEG  194 (224)
T ss_dssp             HHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTT
T ss_pred             hhhhHHHHHHHHHhcccCCCHHHHHHHHHHcCC
Confidence            999999999888755444 23346777777655

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=97.88  E-value=1.3e-05  Score=53.61  Aligned_cols=107  Identities=15%  Similarity=0.176  Sum_probs=71.1

Q ss_pred             hcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcc------cccccCCCccce
Q psy522            7 EHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETL------DPALIRPGRIDR   80 (131)
Q Consensus         7 ~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~i------d~~l~~~grf~~   80 (131)
                      ...+.++++|++|.+.....     ........+..+.+.+..........+|+.++.++..      .+.+.+  ||..
T Consensus       130 ~~~~~~~iide~d~l~~~~~-----~~~~~~~~l~~l~~~l~~~~~~~~~~~i~i~~~~~~~~~~~~~~~~~~~--r~~~  202 (287)
T d1w5sa2         130 ENHYLLVILDEFQSMLSSPR-----IAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVES--QIGF  202 (287)
T ss_dssp             HTCEEEEEEESTHHHHSCTT-----SCHHHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHT--TCSE
T ss_pred             ccCccccceeEEEEeccccc-----cchhHHHHHHHHHHhcchhhcccceeEEeecccHHHHHHHHhhccchhc--ccce
Confidence            44567889999999976542     1222334455555656665566677777777655543      367777  9999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCC---CcccHHHHHHHcCC
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLA---EDVNLQELIMAKDD  120 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~---~~~~~~~la~~t~g  120 (131)
                      .+++++++.++..+|++..++.....   .+..+..+|+.+.+
T Consensus       203 ~i~f~~y~~~el~~Il~~r~~~~~~~~~~~~~al~~ia~~~~~  245 (287)
T d1w5sa2         203 KLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGE  245 (287)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCG
T ss_pred             eeeccCCcHHHHHHHHhhhHHHhhccCCCCHHHHHHHHHHHhc
Confidence            99999999999999999876432111   22236667776643

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.62  E-value=1.6e-05  Score=51.66  Aligned_cols=82  Identities=22%  Similarity=0.269  Sum_probs=52.0

Q ss_pred             HHHHHhc-CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCC-----CcccccccCC
Q psy522            2 FRVAEEH-APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRI-----ETLDPALIRP   75 (131)
Q Consensus         2 F~~A~~~-~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~-----~~id~~l~~~   75 (131)
                      ++.+..+ .+.|+||||+..++...+..+. .  ....++.-.+       ..+.+-+||+|...     -.-|+++.| 
T Consensus       107 l~e~~~~~~~iILfIDeih~l~~~g~~~g~-~--d~~~~Lkp~L-------~rg~l~~IgatT~eey~~~~e~d~aL~r-  175 (195)
T d1jbka_         107 LNDLAKQEGNVILFIDELHTMVGAGKADGA-M--DAGNMLKPAL-------ARGELHCVGATTLDEYRQYIEKDAALER-  175 (195)
T ss_dssp             HHHHHHSTTTEEEEEETGGGGTT------C-C--CCHHHHHHHH-------HTTSCCEEEEECHHHHHHHTTTCHHHHT-
T ss_pred             HHHHhcCCCcEEEEcchHHHHhcCCCCCCc-c--cHHHHHHHHH-------hCCCceEEecCCHHHHHHHHHcCHHHHh-
Confidence            3444444 4689999999999876533221 1  1224444444       24566777777632     233899999 


Q ss_pred             CccceEEEeCCCCHHHHHHHH
Q psy522           76 GRIDRKIEFPLPDEKTKRRIF   96 (131)
Q Consensus        76 grf~~~i~~~~P~~~~R~~il   96 (131)
                       ||. .|.+..|+.++-..|+
T Consensus       176 -rF~-~I~V~Ep~~e~t~~IL  194 (195)
T d1jbka_         176 -RFQ-KVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             -TEE-EEECCCCCHHHHHTTC
T ss_pred             -cCC-EeecCCCCHHHHHHHh
Confidence             996 8999999999877664

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=97.46  E-value=0.00016  Score=49.99  Aligned_cols=81  Identities=21%  Similarity=0.371  Sum_probs=58.0

Q ss_pred             HHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcC--C-------CCCCCeEEEeeCCC----------
Q psy522            4 VAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDG--F-------DSRGDVKVIMATNR----------   64 (131)
Q Consensus         4 ~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~--~-------~~~~~v~vi~ttn~----------   64 (131)
                      ..+++.-+||+|||+|+.-+           .   +...++..++.  +       -...+.++|+|||.          
T Consensus       120 ~~~~~p~~Vvl~DEieK~~~-----------~---v~~~ll~~l~~g~~~~~~gr~v~~~~~i~i~tsnlG~~~i~~~~~  185 (315)
T d1qvra3         120 AVRRRPYSVILFDEIEKAHP-----------D---VFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPLILEGLQ  185 (315)
T ss_dssp             HHHHCSSEEEEESSGGGSCH-----------H---HHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCTTHHHHHHHHH
T ss_pred             HHHhCCCcEEEEehHhhcCH-----------H---HHHHHHHHhccCceeCCCCcEecCcceEEEEecccChHHHhhhcc
Confidence            34566679999999999632           2   33334444432  1       11146999999995          


Q ss_pred             ----------------CCcccccccCCCccceEEEeCCCCHHHHHHHHHHHh
Q psy522           65 ----------------IETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHT  100 (131)
Q Consensus        65 ----------------~~~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l  100 (131)
                                      ...+.|.++.  |||..+.+.+.+.++-..|+...+
T Consensus       186 ~~~~~~~~~~~~~~~l~~~f~pEfln--Rid~Ii~F~~L~~~~~~~I~~~~l  235 (315)
T d1qvra3         186 KGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRPLTKEQIRQIVEIQL  235 (315)
T ss_dssp             TTCCHHHHHHHHHHHHHTTSCHHHHH--TCSBCCBCCCCCHHHHHHHHHHHH
T ss_pred             cccchhhhhHHHHHHHHhhcCHHHHh--cCCeeeeccchhhhhhHHHHHHHH
Confidence                            2447888888  999999999999999999987654

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.46  E-value=0.00011  Score=47.56  Aligned_cols=62  Identities=16%  Similarity=0.299  Sum_probs=47.4

Q ss_pred             CeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccccccCCCccceEEEeCCCCH
Q psy522           10 PSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDE   89 (131)
Q Consensus        10 p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~~l~~~grf~~~i~~~~P~~   89 (131)
                      .-|++|||+|.+-.              ...+.++..++.  ..+.+++|.+|++++.+.+.+++  |+ ..+.++.|..
T Consensus        80 ~KviIId~ad~l~~--------------~aqNaLLK~LEE--Pp~~t~fiLit~~~~~ll~TI~S--RC-~~i~~~~p~~  140 (198)
T d2gnoa2          80 RKYVIVHDCERMTQ--------------QAANAFLKALEE--PPEYAVIVLNTRRWHYLLPTIKS--RV-FRVVVNVPKE  140 (198)
T ss_dssp             SEEEEETTGGGBCH--------------HHHHHTHHHHHS--CCTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCHH
T ss_pred             CEEEEEeCccccch--------------hhhhHHHHHHhC--CCCCceeeeccCChhhCHHHHhc--ce-EEEeCCCchH
Confidence            45999999999842              244556666663  34578889999999999999999  98 5788888864


Q ss_pred             H
Q psy522           90 K   90 (131)
Q Consensus        90 ~   90 (131)
                      .
T Consensus       141 ~  141 (198)
T d2gnoa2         141 F  141 (198)
T ss_dssp             H
T ss_pred             H
Confidence            3

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=97.43  E-value=7.1e-05  Score=53.31  Aligned_cols=84  Identities=24%  Similarity=0.282  Sum_probs=47.7

Q ss_pred             HHHhc-CCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCC--C--cccccccCCCcc
Q psy522            4 VAEEH-APSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRI--E--TLDPALIRPGRI   78 (131)
Q Consensus         4 ~A~~~-~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~--~--~id~~l~~~grf   78 (131)
                      .+... .+.||||||+..++...+..+   ......++.-.|       ..+.+-+||+|..-  .  .=|++|.|  ||
T Consensus       109 ~~~~~~~~~ilfide~h~l~~~g~~~g---~~d~a~~Lkp~L-------~rg~~~~I~~tT~~ey~~~e~d~al~r--rF  176 (387)
T d1qvra2         109 EVVQSQGEVILFIDELHTVVGAGKAEG---AVDAGNMLKPAL-------ARGELRLIGATTLDEYREIEKDPALER--RF  176 (387)
T ss_dssp             HHHTTCSSEEEEECCC----------------------HHHH-------HTTCCCEEEEECHHHHHHHTTCTTTCS--CC
T ss_pred             HhccCCCceEEEeccHHHHhcCCCCCC---cccHHHHHHHHH-------hCCCcceeeecCHHHHHHhcccHHHHH--hc
Confidence            44444 478899999999987653221   112234444444       34566677777621  1  12899999  99


Q ss_pred             ceEEEeCCCCHHHHHHHHHHHh
Q psy522           79 DRKIEFPLPDEKTKRRIFNIHT  100 (131)
Q Consensus        79 ~~~i~~~~P~~~~R~~il~~~l  100 (131)
                      . .|.+..|+.++-..|++...
T Consensus       177 ~-~v~v~ep~~~~~~~il~~~~  197 (387)
T d1qvra2         177 Q-PVYVDEPTVEETISILRGLK  197 (387)
T ss_dssp             C-CEEECCCCHHHHHHHHHHHH
T ss_pred             c-cccCCCCcHHHHHHHHHHHH
Confidence            6 89999999999999998664

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.06  E-value=0.0015  Score=44.91  Aligned_cols=85  Identities=18%  Similarity=0.316  Sum_probs=57.4

Q ss_pred             HHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHH---hcCC---CCCCCeEEEeeCCCCC-----------
Q psy522            4 VAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQ---LDGF---DSRGDVKVIMATNRIE-----------   66 (131)
Q Consensus         4 ~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~---~~~~---~~~~~v~vi~ttn~~~-----------   66 (131)
                      ..+.+..+|+++||+|..-+           .....+.+++..   .++.   ..-...++|.|||...           
T Consensus       116 ~~~~~~~~vvl~DeieKa~~-----------~V~~~lLqild~G~ltd~~Gr~vdf~n~iiI~Tsnig~~~i~~~~~~~~  184 (315)
T d1r6bx3         116 AVIKHPHAVLLLDEIEKAHP-----------DVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLI  184 (315)
T ss_dssp             HHHHCSSEEEEEETGGGSCH-----------HHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEECSSCC----------
T ss_pred             HHHhCccchhhhcccccccc-----------hHhhhhHHhhccceecCCCCCccCccceEEEeccchhhHHHHhhhccch
Confidence            44667789999999998632           223333333332   1111   1124688999999421           


Q ss_pred             --------------cccccccCCCccceEEEeCCCCHHHHHHHHHHHhc
Q psy522           67 --------------TLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTS  101 (131)
Q Consensus        67 --------------~id~~l~~~grf~~~i~~~~P~~~~R~~il~~~l~  101 (131)
                                    .+.|.++.  |+|..+.+.+.+.++-..|+..++.
T Consensus       185 ~~~~~~~~~~~l~~~f~pEfln--Rid~ii~f~~l~~~~~~~I~~~~l~  231 (315)
T d1r6bx3         185 HQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTDVIHQVVDKFIV  231 (315)
T ss_dssp             -------CHHHHHHHSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHH
T ss_pred             hhhhhHhHHHHHHHhcCHHHHh--hhhhhhcccchhhhHHHHHHHHHHH
Confidence                          35777887  9999999999999999988877653

>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=96.99  E-value=0.0023  Score=43.95  Aligned_cols=72  Identities=19%  Similarity=0.302  Sum_probs=50.3

Q ss_pred             eEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcC---------CCC--CCCeEEEeeCC-CCCcccccccCCCcc
Q psy522           11 SIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDG---------FDS--RGDVKVIMATN-RIETLDPALIRPGRI   78 (131)
Q Consensus        11 ~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~---------~~~--~~~v~vi~ttn-~~~~id~~l~~~grf   78 (131)
                      .|+|+||++.+-+              ++.+.+++-|+.         ...  .-++++++|+| .+..++++++.  ||
T Consensus       129 gvl~iDEi~~~~~--------------~~~~aLl~~me~~~v~i~r~g~~~~~p~~f~liaa~Np~~~~l~~~llD--Rf  192 (333)
T d1g8pa_         129 GYLYIDECNLLED--------------HIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLD--RF  192 (333)
T ss_dssp             EEEEETTGGGSCH--------------HHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHT--TC
T ss_pred             cEeecccHHHHHH--------------HHHHHHhhhhcCCeEEecccCceecCCCCEEEEEecCccccccccchhh--hh
Confidence            7999999988632              244444444431         111  13588999999 47779999999  99


Q ss_pred             ceEEEeCCC-CHHHHHHHHHH
Q psy522           79 DRKIEFPLP-DEKTKRRIFNI   98 (131)
Q Consensus        79 ~~~i~~~~P-~~~~R~~il~~   98 (131)
                      +..+.++.| +.+.|.++...
T Consensus       193 ~~~i~v~~~~~~~~~~~~~~~  213 (333)
T d1g8pa_         193 GLSVEVLSPRDVETRVEVIRR  213 (333)
T ss_dssp             SEEEECCCCCSHHHHHHHHHH
T ss_pred             cceeeccCcchhhHHHHHHHh
Confidence            999999987 66666665543

>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=95.94  E-value=0.0038  Score=40.80  Aligned_cols=99  Identities=12%  Similarity=0.056  Sum_probs=59.1

Q ss_pred             hcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCC---CcccccccCCCcc-ceEE
Q psy522            7 EHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRI---ETLDPALIRPGRI-DRKI   82 (131)
Q Consensus         7 ~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~---~~id~~l~~~grf-~~~i   82 (131)
                      ...+.++++|++|.+....           ......++..+.. ....++.+|++++..   +.+++.+.+  |+ ...|
T Consensus       122 ~~~~~~~~~~~~d~~~~~~-----------~~~~~~~~~~~~~-~~~~~~~~i~~~~~~~~~~~~~~~~~~--r~~~~~i  187 (276)
T d1fnna2         122 RDLYMFLVLDDAFNLAPDI-----------LSTFIRLGQEADK-LGAFRIALVIVGHNDAVLNNLDPSTRG--IMGKYVI  187 (276)
T ss_dssp             TTCCEEEEEETGGGSCHHH-----------HHHHHHHTTCHHH-HSSCCEEEEEEESSTHHHHTSCHHHHH--HHTTCEE
T ss_pred             cccccccchhHHHHhhhhh-----------hhhHHHHHhcccc-ccccceEEeecCCchhhhhhcchhhhh--hhcchhc
Confidence            3457788889988874321           1111222211111 123467788888864   456777777  65 3568


Q ss_pred             EeCCCCHHHHHHHHHHHhcCCCC---CCcccHHHHHHHcC
Q psy522           83 EFPLPDEKTKRRIFNIHTSRMTL---AEDVNLQELIMAKD  119 (131)
Q Consensus        83 ~~~~P~~~~R~~il~~~l~~~~~---~~~~~~~~la~~t~  119 (131)
                      .+++|+.+++.+|+++.+.....   -.+..+..++..+.
T Consensus       188 ~~~~~~~~e~~~il~~r~~~~~~~~~~~~~~l~~ia~~~~  227 (276)
T d1fnna2         188 RFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITG  227 (276)
T ss_dssp             ECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHS
T ss_pred             cccchhHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhh
Confidence            99999999999999887653111   12333555666553

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=95.86  E-value=0.0086  Score=41.87  Aligned_cols=28  Identities=21%  Similarity=0.177  Sum_probs=24.0

Q ss_pred             ccccccCCCccceEEEeCCCCHHHHHHHHH
Q psy522           68 LDPALIRPGRIDRKIEFPLPDEKTKRRIFN   97 (131)
Q Consensus        68 id~~l~~~grf~~~i~~~~P~~~~R~~il~   97 (131)
                      +.|.|+.  ||+..+.|.+.+++.-.+|+.
T Consensus       252 f~PEf~g--Ri~~iv~f~~L~~~~l~~Il~  279 (364)
T d1um8a_         252 LIPELIG--RLPVLSTLDSISLEAMVDILQ  279 (364)
T ss_dssp             CCHHHHT--TCCEEEECCCCCHHHHHHHHH
T ss_pred             hHHHHHH--HhcchhhHhhhhHHHHHHHHH
Confidence            4556666  999999999999999999985

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=95.19  E-value=0.044  Score=35.38  Aligned_cols=107  Identities=9%  Similarity=0.039  Sum_probs=61.9

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCC---Ccccccc----cCCCccce
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRI---ETLDPAL----IRPGRIDR   80 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~---~~id~~l----~~~grf~~   80 (131)
                      .++.++++||++.+.....   ..    ....+..+..      ...++..+.+....   ..+....    .-.||+..
T Consensus       135 ~~~~~i~id~~~~~~~~~~---~~----~~~~l~~~~~------~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~  201 (283)
T d2fnaa2         135 KDNVIIVLDEAQELVKLRG---VN----LLPALAYAYD------NLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFS  201 (283)
T ss_dssp             SSCEEEEEETGGGGGGCTT---CC----CHHHHHHHHH------HCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCE
T ss_pred             ccccccccchhhhhcccch---HH----HHHHHHHHHH------hhhhhhhhhccccchHHHHHHHhhhhcchhccccee
Confidence            5688999999999865431   11    1122222221      12333334333221   1111111    11246678


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCCCCCCcccHHHHHHHcCCCCHHHHHHh
Q psy522           81 KIEFPLPDEKTKRRIFNIHTSRMTLAEDVNLQELIMAKDDLSGADIKAI  129 (131)
Q Consensus        81 ~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~l  129 (131)
                      .+++++.+.++..++++..+.......+ ++..+.+.+.|. |.-|..+
T Consensus       202 ~i~L~~l~~~e~~~~l~~~~~~~~~~~~-~~~~i~~~~~G~-P~~L~~~  248 (283)
T d2fnaa2         202 TVELKPFSREEAIEFLRRGFQEADIDFK-DYEVVYEKIGGI-PGWLTYF  248 (283)
T ss_dssp             EEEECCCCHHHHHHHHHHHHHHHTCCCC-CHHHHHHHHCSC-HHHHHHH
T ss_pred             EEeeCCCCHHHHHHHHHhhhhhcCCCHH-HHHHHHHHhCCC-HHHHHHH
Confidence            8999999999999999888776555443 467788888887 5555443

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=87.05  E-value=1.8  Score=25.47  Aligned_cols=20  Identities=30%  Similarity=0.609  Sum_probs=15.7

Q ss_pred             HHHHHhcCCeEEEecccccc
Q psy522            2 FRVAEEHAPSIVFIDEIDAV   21 (131)
Q Consensus         2 F~~A~~~~p~ii~iDe~d~l   21 (131)
                      +..+....|.++++||+...
T Consensus        92 l~~~~~~~~~vlllDE~~~~  111 (178)
T d1ye8a1          92 YREAKKDRRKVIIIDEIGKM  111 (178)
T ss_dssp             HHHHHHCTTCEEEECCCSTT
T ss_pred             HHHHHhcCCCceeecCCCcc
Confidence            35567889999999997544

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=86.43  E-value=1.7  Score=27.95  Aligned_cols=13  Identities=31%  Similarity=0.626  Sum_probs=10.6

Q ss_pred             CeEEEeccccccc
Q psy522           10 PSIVFIDEIDAVG   22 (131)
Q Consensus        10 p~ii~iDe~d~l~   22 (131)
                      ...|||||+|.+-
T Consensus        95 gGtL~l~~i~~L~  107 (247)
T d1ny5a2          95 GGTLFLDEIGELS  107 (247)
T ss_dssp             TSEEEEESGGGCC
T ss_pred             CCEEEEeChHhCC
Confidence            3579999999983

>d1w1wa_ c.37.1.12 (A:) Smc head domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.76  E-value=0.27  Score=33.67  Aligned_cols=49  Identities=12%  Similarity=0.207  Sum_probs=28.8

Q ss_pred             cCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcccc
Q psy522            8 HAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDP   70 (131)
Q Consensus         8 ~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id~   70 (131)
                      ..+.+++|||+|.-+...          ....+..++..+.+.    ..=+|.+|..|..++.
T Consensus       353 ~~~pililDE~d~~Ld~~----------~~~~~~~~l~~~~~~----~~Q~I~iTH~~~~~~~  401 (427)
T d1w1wa_         353 QPSPFFVLDEVDAALDIT----------NVQRIAAYIRRHRNP----DLQFIVISLKNTMFEK  401 (427)
T ss_dssp             SCCSEEEESSTTTTCCHH----------HHHHHHHHHHHHCBT----TBEEEEECSCHHHHTT
T ss_pred             CCCCEEEEeCCCCCCCHH----------HHHHHHHHHHHHhCC----CCEEEEEeCCHHHHHh
Confidence            445589999999865432          233444455444321    2237778888776653

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=83.94  E-value=2.4  Score=27.43  Aligned_cols=17  Identities=24%  Similarity=0.245  Sum_probs=13.6

Q ss_pred             HHHHhcCCeEEEecccc
Q psy522            3 RVAEEHAPSIVFIDEID   19 (131)
Q Consensus         3 ~~A~~~~p~ii~iDe~d   19 (131)
                      .+|-...|.|+++||.=
T Consensus       164 ARal~~~p~ililDEpt  180 (253)
T d3b60a1         164 ARALLRDSPILILDEAT  180 (253)
T ss_dssp             HHHHHHCCSEEEEETTT
T ss_pred             HHHHhcCCCEEEecccc
Confidence            45666789999999963

>d1e69a_ c.37.1.12 (A:) Smc head domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=83.48  E-value=1.1  Score=29.28  Aligned_cols=49  Identities=16%  Similarity=0.210  Sum_probs=30.2

Q ss_pred             HhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCccc
Q psy522            6 EEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLD   69 (131)
Q Consensus         6 ~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~id   69 (131)
                      ....|.+++|||.|.-+...          ....+..++..+..     ..=||.||.+|.-++
T Consensus       238 ~~~~~~~~~iDEpe~~Lhp~----------~~~~l~~~l~~~~~-----~~QviitTHsp~~~~  286 (308)
T d1e69a_         238 EIKPSPFYVLDEVDSPLDDY----------NAERFKRLLKENSK-----HTQFIVITHNKIVME  286 (308)
T ss_dssp             TTSCCSEEEEESCCSSCCHH----------HHHHHHHHHHHHTT-----TSEEEEECCCTTGGG
T ss_pred             hhccCchhhhhhccccCCHH----------HHHHHHHHHHHhcc-----CCEEEEEECCHHHHH
Confidence            44568899999998754322          23344444444431     223778899988776

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.19  E-value=0.65  Score=30.28  Aligned_cols=54  Identities=15%  Similarity=0.175  Sum_probs=29.5

Q ss_pred             HHHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCCCcc
Q psy522            2 FRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETL   68 (131)
Q Consensus         2 F~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~~~i   68 (131)
                      +.+|-.+.|.|+++||.=+-          -+......   +++.+..+....+..+|..|.+.+.+
T Consensus       162 iARal~~~p~ililDEpTs~----------LD~~~~~~---i~~~l~~l~~~~~~Tvi~itH~l~~~  215 (251)
T d1jj7a_         162 LARALIRKPCVLILDDATSA----------LDANSQLQ---VEQLLYESPERYSRSVLLITQHLSLV  215 (251)
T ss_dssp             HHHHHTTCCSEEEEESTTTT----------CCHHHHHH---HHHHHHTCGGGGGCEEEEECSCHHHH
T ss_pred             EeeccccCCcEEEecCcCcc----------cChhhHHH---HHHHHHHHhhhcCCEEEEEeCCHHHH
Confidence            35667788999999996222          12222223   33334444444445566677664433

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=82.24  E-value=1.9  Score=27.62  Aligned_cols=50  Identities=20%  Similarity=0.374  Sum_probs=29.1

Q ss_pred             HHHHhcCCeEEEecccccccCcCCCCCCCchhHHHHHHHHHHHHhcCCCCCCCeEEEeeCCCC
Q psy522            3 RVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRI   65 (131)
Q Consensus         3 ~~A~~~~p~ii~iDe~d~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~vi~ttn~~   65 (131)
                      .+|-.+.|.||++||-          ...-+......+..++..+.   ...++.+|.+|.++
T Consensus       157 AraL~~~P~lLllDEP----------Ts~LD~~~~~~i~~~l~~l~---~~~g~tii~vTHd~  206 (230)
T d1l2ta_         157 ARALANNPPIILADQP----------TGALDSKTGEKIMQLLKKLN---EEDGKTVVVVTHDI  206 (230)
T ss_dssp             HHHHTTCCSEEEEEST----------TTTSCHHHHHHHHHHHHHHH---HTTCCEEEEECSCH
T ss_pred             HhhhhcCCCEEEecCC----------ccccCHHHHHHHHHHHHHHH---HhhCCEEEEECCCH
Confidence            4567788999999994          22233334444444554442   34455666666643

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=82.15  E-value=3.8  Score=26.25  Aligned_cols=17  Identities=29%  Similarity=0.374  Sum_probs=13.7

Q ss_pred             HHHHhcCCeEEEecccc
Q psy522            3 RVAEEHAPSIVFIDEID   19 (131)
Q Consensus         3 ~~A~~~~p~ii~iDe~d   19 (131)
                      .+|-...|.|+++||.=
T Consensus       151 ARal~~~p~ililDEpt  167 (241)
T d2pmka1         151 ARALVNNPKILIFDEAT  167 (241)
T ss_dssp             HHHHTTCCSEEEECCCC
T ss_pred             hhhhhcccchhhhhCCc
Confidence            46667889999999963

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=82.12  E-value=1.1  Score=29.32  Aligned_cols=19  Identities=21%  Similarity=0.317  Sum_probs=14.5

Q ss_pred             HHHHHhcCCeEEEeccccc
Q psy522            2 FRVAEEHAPSIVFIDEIDA   20 (131)
Q Consensus         2 F~~A~~~~p~ii~iDe~d~   20 (131)
                      +.+|-...|.|+++||.-+
T Consensus       165 iARal~~~p~ililDEpts  183 (255)
T d2hyda1         165 IARIFLNNPPILILDEATS  183 (255)
T ss_dssp             HHHHHHHCCSEEEEESTTT
T ss_pred             HHHHHhcCCCEEEEeCccc
Confidence            3456668899999999744