Citrus Sinensis ID: 029560

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-
Protein Sequence
MQDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD
Secondary Structure (PSIPRED)
ccccccccccccEEEEEcccEEEEEEccHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHcccccccHHHEEEEEEEccccccEEEEEcccccccccEEEEEcccHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHccccccccEEEEEEEcccccEEEccHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccEcHHHcccEEEcccccEEEEEccHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHEccccccccEEEEEEEEcccEEEEEEEcccccEEEEcEEEEcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHcccccccEEEEEEEcccccEEEccHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
mqdklldhtsvthlfPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDeecgprlfkcdpaghffghkatsaglKEQEAINFLEKkmkndpaftfQETVQTAISTLQSVLQEdfkaseievgvvskenpefrvLSIEEIDEHLTAISERD
Flexible Loop (DISEMBL)
mqdklldhtsvthlfPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASeievgvvskenpefrvlsieeidehltaiserd
Low Complexity Region (SEG)
MQDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD
Disordered region (IsUnstruct)
******DHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEI***********
Disordered Region (DISOPRED)
MQDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISE**
Disordered Region (DISEMBL)
MQDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD
Disordered Region (DISPRO)
**DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAIS***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MQDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD
Positional Conservation
no confident homologs detected

---

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	191	2.2.26 [Sep-21-2011]
Q9XG77	246	Proteasome subunit alpha	N/A	no	0.989	0.768	0.904	1e-98
O48551	246	Proteasome subunit alpha	no	no	0.989	0.768	0.894	1e-98
O81146	246	Proteasome subunit alpha	yes	no	0.989	0.768	0.835	1e-93
O81147	246	Proteasome subunit alpha	no	no	0.989	0.768	0.835	2e-92
Q9LSU3	246	Proteasome subunit alpha	yes	no	0.989	0.768	0.841	2e-91
Q9QUM9	246	Proteasome subunit alpha	yes	no	0.989	0.768	0.608	2e-65
P60901	246	Proteasome subunit alpha	yes	no	0.989	0.768	0.608	2e-65
P60900	246	Proteasome subunit alpha	yes	no	0.989	0.768	0.608	2e-65
Q2YDE4	246	Proteasome subunit alpha	yes	no	0.989	0.768	0.608	2e-65
Q9XZJ4	244	Proteasome subunit alpha	yes	no	0.942	0.737	0.571	5e-54

>sp|Q9XG77|PSA6_TOBAC Proteasome subunit alpha type-6 OS=Nicotiana tabacum GN=PAA1 PE=2 SV=1

 Score =  358 bits (919), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 171/189 (90%), Positives = 180/189 (95%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD TSV+HLFPITKYLGLLATGMTADARTLVQQAR EAAEFRFKYGYEMPVDVL+KW
Sbjct: 58  DKLLDQTSVSHLFPITKYLGLLATGMTADARTLVQQARNEAAEFRFKYGYEMPVDVLSKW 117

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IADKSQVYTQHAYMRPLGVVAM+L IDEE GP+LFKCDPAGHFFGHKATSAG KEQEAIN
Sbjct: 118 IADKSQVYTQHAYMRPLGVVAMILGIDEEKGPQLFKCDPAGHFFGHKATSAGSKEQEAIN 177

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKKMKNDPAF+++ETVQTAIS LQSVLQEDFKASEIEVGVV KE+P FRVL+ EEIDE
Sbjct: 178 FLEKKMKNDPAFSYEETVQTAISALQSVLQEDFKASEIEVGVVKKEDPIFRVLTTEEIDE 237

Query: 183 HLTAISERD 191
           HLTAISERD
Sbjct: 238 HLTAISERD 246

The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.
Nicotiana tabacum (taxid: 4097)
EC: 3EC: .EC: 4EC: .EC: 2EC: 5EC: .EC: 1

>sp|O48551|PSA6_SOYBN Proteasome subunit alpha type-6 OS=Glycine max GN=PAA1 PE=2 SV=2

 Score =  358 bits (919), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 169/189 (89%), Positives = 182/189 (96%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD+TSVTHLFPITKYLGLLATGMTADARTLVQQAR EAAEFRF YGYEMPVDVLAKW
Sbjct: 58  DKLLDNTSVTHLFPITKYLGLLATGMTADARTLVQQARNEAAEFRFTYGYEMPVDVLAKW 117

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IADKSQVYTQHAYMRPLGVVAMVL ID+E GP+L+KCDPAGH+FGHKATSAGLK+QEAIN
Sbjct: 118 IADKSQVYTQHAYMRPLGVVAMVLGIDDEYGPQLYKCDPAGHYFGHKATSAGLKDQEAIN 177

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKKMKNDP+FT++ETVQTAIS LQSVLQEDFKA+EIEVGVV K+NPEFRVL+ +EIDE
Sbjct: 178 FLEKKMKNDPSFTYEETVQTAISALQSVLQEDFKATEIEVGVVRKDNPEFRVLTTDEIDE 237

Query: 183 HLTAISERD 191
           HLTAISERD
Sbjct: 238 HLTAISERD 246

The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.

Glycine max (taxid: 3847)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|O81146|PSA6A_ARATH Proteasome subunit alpha type-6-A OS=Arabidopsis thaliana GN=PAA1 PE=1 SV=2

 Score =  342 bits (877), Expect = 1e-93,   Method: Compositional matrix adjust.
 Identities = 158/189 (83%), Positives = 176/189 (93%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD +SVTHLFPITKY+GL+ATG+TADAR+LVQQAR +AAEFRF YGYEMPVD+LAKW
Sbjct: 58  DKLLDQSSVTHLFPITKYIGLVATGITADARSLVQQARNQAAEFRFTYGYEMPVDILAKW 117

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IADKSQVYTQHAYMRPLGVVAMV+ +DEE GP L+KCDPAGHF+GHKATSAG+KEQEA+N
Sbjct: 118 IADKSQVYTQHAYMRPLGVVAMVMGVDEENGPLLYKCDPAGHFYGHKATSAGMKEQEAVN 177

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKKMK +P+FTF ETVQTAIS LQSVLQEDFKA+EIEVGVV  ENPEFR L+ EEI+E
Sbjct: 178 FLEKKMKENPSFTFDETVQTAISALQSVLQEDFKATEIEVGVVRAENPEFRALTTEEIEE 237

Query: 183 HLTAISERD 191
           HLTAISERD
Sbjct: 238 HLTAISERD 246

The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|O81147|PSA6B_ARATH Proteasome subunit alpha type-6-B OS=Arabidopsis thaliana GN=PAA2 PE=1 SV=1

 Score =  338 bits (866), Expect = 2e-92,   Method: Compositional matrix adjust.
 Identities = 158/189 (83%), Positives = 174/189 (92%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD +SV+HLFP+TKYLGLLATGMTAD+R+LVQQAR EAAEFRF+YGYEMP D+LAKW
Sbjct: 58  DKLLDQSSVSHLFPVTKYLGLLATGMTADSRSLVQQARNEAAEFRFQYGYEMPADILAKW 117

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IADKSQVYTQHAYMRPLGVVAMVL IDEE GP L+KCDPAGHF+GHKATSAG+KEQEA+N
Sbjct: 118 IADKSQVYTQHAYMRPLGVVAMVLGIDEERGPLLYKCDPAGHFYGHKATSAGMKEQEAVN 177

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKKMK +PAFT+ ETVQTAIS LQSVLQEDFKA+EIEVGVV  ++P FR L  EEIDE
Sbjct: 178 FLEKKMKENPAFTYDETVQTAISALQSVLQEDFKATEIEVGVVRADDPLFRSLRTEEIDE 237

Query: 183 HLTAISERD 191
           HLTAISERD
Sbjct: 238 HLTAISERD 246

The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|Q9LSU3|PSA6_ORYSJ Proteasome subunit alpha type-6 OS=Oryza sativa subsp. japonica GN=PAA1 PE=2 SV=1

 Score =  334 bits (856), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 159/189 (84%), Positives = 174/189 (92%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLDHTSVTHLFPITKY+GLLATG+TADAR+LV QAR EAAEFRFK+GYEMPVDVLAKW
Sbjct: 58  DKLLDHTSVTHLFPITKYIGLLATGLTADARSLVYQARNEAAEFRFKWGYEMPVDVLAKW 117

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IADK+QVYTQHAYMRPLGVVAMVL  DEE   +LFKCDPAGHFFGHKATSAGLKEQEAIN
Sbjct: 118 IADKAQVYTQHAYMRPLGVVAMVLGYDEEKNAQLFKCDPAGHFFGHKATSAGLKEQEAIN 177

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKKMK+DP F+++ETVQ AIS LQSVLQEDFKA+EIEVGVV K++  FR L+ EEID+
Sbjct: 178 FLEKKMKDDPQFSYEETVQIAISALQSVLQEDFKATEIEVGVVRKDDRVFRALTTEEIDQ 237

Query: 183 HLTAISERD 191
           HLTAISERD
Sbjct: 238 HLTAISERD 246

The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|Q9QUM9|PSA6_MOUSE Proteasome subunit alpha type-6 OS=Mus musculus GN=Psma6 PE=1 SV=1

 Score =  248 bits (633), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 115/189 (60%), Positives = 155/189 (82%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K 
Sbjct: 58  DKLLDSSTVTHLFKITESIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKR 117

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IAD SQVYTQ+A MRPLG   +++ IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +
Sbjct: 118 IADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTS 177

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKK+K    +TF++TV+TAI+ L +VL  DFK SEIEVGVV+ ENP+FR+L+  EID 
Sbjct: 178 FLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDA 237

Query: 183 HLTAISERD 191
           HL A++ERD
Sbjct: 238 HLVALAERD 246

The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|P60901|PSA6_RAT Proteasome subunit alpha type-6 OS=Rattus norvegicus GN=Psma6 PE=1 SV=1

 Score =  248 bits (633), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 115/189 (60%), Positives = 155/189 (82%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K 
Sbjct: 58  DKLLDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKR 117

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IAD SQVYTQ+A MRPLG   +++ IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +
Sbjct: 118 IADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTS 177

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKK+K    +TF++TV+TAI+ L +VL  DFK SEIEVGVV+ ENP+FR+L+  EID 
Sbjct: 178 FLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDA 237

Query: 183 HLTAISERD 191
           HL A++ERD
Sbjct: 238 HLVALAERD 246

The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|P60900|PSA6_HUMAN Proteasome subunit alpha type-6 OS=Homo sapiens GN=PSMA6 PE=1 SV=1

 Score =  248 bits (633), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 115/189 (60%), Positives = 155/189 (82%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K 
Sbjct: 58  DKLLDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKR 117

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IAD SQVYTQ+A MRPLG   +++ IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +
Sbjct: 118 IADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTS 177

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKK+K    +TF++TV+TAI+ L +VL  DFK SEIEVGVV+ ENP+FR+L+  EID 
Sbjct: 178 FLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDA 237

Query: 183 HLTAISERD 191
           HL A++ERD
Sbjct: 238 HLVALAERD 246

The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|Q2YDE4|PSA6_BOVIN Proteasome subunit alpha type-6 OS=Bos taurus GN=PSMA6 PE=1 SV=1

 Score =  248 bits (633), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 115/189 (60%), Positives = 155/189 (82%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K 
Sbjct: 58  DKLLDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKR 117

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IAD SQVYTQ+A MRPLG   +++ IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +
Sbjct: 118 IADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTS 177

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKK+K    +TF++TV+TAI+ L +VL  DFK SEIEVGVV+ ENP+FR+L+  EID 
Sbjct: 178 FLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDA 237

Query: 183 HLTAISERD 191
           HL A++ERD
Sbjct: 238 HLVALAERD 246

The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.

Bos taurus (taxid: 9913)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|Q9XZJ4|PSA6_DROME Proteasome subunit alpha type-6 OS=Drosophila melanogaster GN=Prosalpha1 PE=2 SV=2

 Score =  210 bits (534), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 104/182 (57%), Positives = 133/182 (73%), Gaps = 2/182 (1%)

Query: 10  SVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQV 69
           +VTHLF ITK +G   TG  AD+R+ VQ+ARYEAA FR+KYGYEMPVDVL + IAD +QV
Sbjct: 65  TVTHLFRITKDIGCAMTGRIADSRSQVQKARYEAANFRYKYGYEMPVDVLCRRIADINQV 124

Query: 70  YTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMK 129
           YTQ+A MRPLG   ++++ D E GP ++K DPAG+F G KA S G K  EA ++LEKK K
Sbjct: 125 YTQNAEMRPLGCSMVLIAYDNEIGPSVYKTDPAGYFSGFKACSVGAKTLEANSYLEKKYK 184

Query: 130 NDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISE 189
             P  + ++ +Q AIS L SVL  DFK + IE+GVVSK +P FR+L   EI+EHLT I+E
Sbjct: 185 --PNLSEEKAIQLAISCLSSVLAIDFKPNGIEIGVVSKSDPTFRILDEREIEEHLTKIAE 242

Query: 190 RD 191
           +D
Sbjct: 243 KD 244

The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.

Drosophila melanogaster (taxid: 7227)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

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	191
255583952	246	proteasome subunit alpha type, putative	0.989	0.768	0.925	2e-99
356545355	368	PREDICTED: proteasome subunit alpha type	0.989	0.513	0.904	5e-98
217075112	246	unknown [Medicago truncatula] gi|3885172	0.989	0.768	0.883	5e-97
12229948	246	RecName: Full=Proteasome subunit alpha t	0.989	0.768	0.904	6e-97
351721962	246	proteasome subunit alpha type-6 [Glycine	0.989	0.768	0.894	6e-97
211906468	246	20S proteasome subunit alpha-1 [Gossypiu	0.989	0.768	0.894	3e-96
255648341	246	unknown [Glycine max]	0.989	0.768	0.894	4e-96
225442079	246	PREDICTED: proteasome subunit alpha type	0.989	0.768	0.888	7e-96
449447912	246	PREDICTED: proteasome subunit alpha type	0.989	0.768	0.894	7e-96
388519097	246	unknown [Lotus japonicus]	0.989	0.768	0.883	4e-95

>gi|255583952|ref|XP_002532723.1| proteasome subunit alpha type, putative [Ricinus communis] gi|223527531|gb|EEF29654.1| proteasome subunit alpha type, putative [Ricinus communis]

 Score =  366 bits (940), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 175/189 (92%), Positives = 181/189 (95%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQAR EAAEFRFKYGYEMPVDVLAKW
Sbjct: 58  DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARNEAAEFRFKYGYEMPVDVLAKW 117

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IADKSQ+YTQHAYMRPLGVVAMVL ID+E GPRL+KCDPAGHFFGHKATSAGLKEQEAIN
Sbjct: 118 IADKSQIYTQHAYMRPLGVVAMVLGIDDEYGPRLYKCDPAGHFFGHKATSAGLKEQEAIN 177

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKKMKNDPAFT++ETVQTAIS LQSVLQEDFKA+EIEVGVV  ENP FRVLS EEIDE
Sbjct: 178 FLEKKMKNDPAFTYEETVQTAISALQSVLQEDFKATEIEVGVVRTENPVFRVLSTEEIDE 237

Query: 183 HLTAISERD 191
           HLTAISERD
Sbjct: 238 HLTAISERD 246

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356545355|ref|XP_003541109.1| PREDICTED: proteasome subunit alpha type-6-like [Glycine max]

 Score =  362 bits (928), Expect = 5e-98,   Method: Compositional matrix adjust.
 Identities = 171/189 (90%), Positives = 182/189 (96%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD+TSVTHLFPITKYLGLLATGMTADARTLVQQAR EAAEFRF YGYEMPVDVLAKW
Sbjct: 180 DKLLDNTSVTHLFPITKYLGLLATGMTADARTLVQQARNEAAEFRFTYGYEMPVDVLAKW 239

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IADKSQVYTQHAYMRPLGVVAMVL ID+E GP+L+KCDPAGH+FGHKATSAGLK+QEAIN
Sbjct: 240 IADKSQVYTQHAYMRPLGVVAMVLGIDDEYGPQLYKCDPAGHYFGHKATSAGLKDQEAIN 299

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKKMKNDP+FT++ETVQTAIS LQSVLQEDFKA+EIEVGVV KENPEFRVL+ EEIDE
Sbjct: 300 FLEKKMKNDPSFTYEETVQTAISALQSVLQEDFKATEIEVGVVRKENPEFRVLTTEEIDE 359

Query: 183 HLTAISERD 191
           HLTAISERD
Sbjct: 360 HLTAISERD 368

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217075112|gb|ACJ85916.1| unknown [Medicago truncatula] gi|388517215|gb|AFK46669.1| unknown [Medicago truncatula]

 Score =  358 bits (920), Expect = 5e-97,   Method: Compositional matrix adjust.
 Identities = 167/189 (88%), Positives = 182/189 (96%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLDHTSVTHLFPITKYLGLLATG+TADARTLVQQAR EAAE+RF+YGYEMPVDVL+KW
Sbjct: 58  DKLLDHTSVTHLFPITKYLGLLATGITADARTLVQQARNEAAEYRFRYGYEMPVDVLSKW 117

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           +ADKSQVYTQHAYMRPLGVVAMVL ID+E GP+L+KCDPAGH+FGHKATSAGLK+QEAIN
Sbjct: 118 VADKSQVYTQHAYMRPLGVVAMVLGIDDELGPQLYKCDPAGHYFGHKATSAGLKDQEAIN 177

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKKMKNDP+FT+ ETVQTAIS LQSVLQEDFKA+EIEVGVV K+NPEFRVLS +EIDE
Sbjct: 178 FLEKKMKNDPSFTYAETVQTAISALQSVLQEDFKATEIEVGVVQKDNPEFRVLSTDEIDE 237

Query: 183 HLTAISERD 191
           HLTAISERD
Sbjct: 238 HLTAISERD 246

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|12229948|sp|Q9XG77.1|PSA6_TOBAC RecName: Full=Proteasome subunit alpha type-6; AltName: Full=20S proteasome alpha subunit A; AltName: Full=20S proteasome subunit alpha-1 gi|4539545|emb|CAB39975.1| PRCI [Nicotiana tabacum]

 Score =  358 bits (919), Expect = 6e-97,   Method: Compositional matrix adjust.
 Identities = 171/189 (90%), Positives = 180/189 (95%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD TSV+HLFPITKYLGLLATGMTADARTLVQQAR EAAEFRFKYGYEMPVDVL+KW
Sbjct: 58  DKLLDQTSVSHLFPITKYLGLLATGMTADARTLVQQARNEAAEFRFKYGYEMPVDVLSKW 117

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IADKSQVYTQHAYMRPLGVVAM+L IDEE GP+LFKCDPAGHFFGHKATSAG KEQEAIN
Sbjct: 118 IADKSQVYTQHAYMRPLGVVAMILGIDEEKGPQLFKCDPAGHFFGHKATSAGSKEQEAIN 177

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKKMKNDPAF+++ETVQTAIS LQSVLQEDFKASEIEVGVV KE+P FRVL+ EEIDE
Sbjct: 178 FLEKKMKNDPAFSYEETVQTAISALQSVLQEDFKASEIEVGVVKKEDPIFRVLTTEEIDE 237

Query: 183 HLTAISERD 191
           HLTAISERD
Sbjct: 238 HLTAISERD 246

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351721962|ref|NP_001238251.1| proteasome subunit alpha type-6 [Glycine max] gi|12229897|sp|O48551.2|PSA6_SOYBN RecName: Full=Proteasome subunit alpha type-6; AltName: Full=20S proteasome alpha subunit A; AltName: Full=20S proteasome subunit alpha-1; AltName: Full=Proteasome iota subunit gi|3377794|gb|AAC28135.1| proteasome IOTA subunit [Glycine max]

 Score =  358 bits (919), Expect = 6e-97,   Method: Compositional matrix adjust.
 Identities = 169/189 (89%), Positives = 182/189 (96%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD+TSVTHLFPITKYLGLLATGMTADARTLVQQAR EAAEFRF YGYEMPVDVLAKW
Sbjct: 58  DKLLDNTSVTHLFPITKYLGLLATGMTADARTLVQQARNEAAEFRFTYGYEMPVDVLAKW 117

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IADKSQVYTQHAYMRPLGVVAMVL ID+E GP+L+KCDPAGH+FGHKATSAGLK+QEAIN
Sbjct: 118 IADKSQVYTQHAYMRPLGVVAMVLGIDDEYGPQLYKCDPAGHYFGHKATSAGLKDQEAIN 177

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKKMKNDP+FT++ETVQTAIS LQSVLQEDFKA+EIEVGVV K+NPEFRVL+ +EIDE
Sbjct: 178 FLEKKMKNDPSFTYEETVQTAISALQSVLQEDFKATEIEVGVVRKDNPEFRVLTTDEIDE 237

Query: 183 HLTAISERD 191
           HLTAISERD
Sbjct: 238 HLTAISERD 246

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|211906468|gb|ACJ11727.1| 20S proteasome subunit alpha-1 [Gossypium hirsutum]

 Score =  356 bits (913), Expect = 3e-96,   Method: Compositional matrix adjust.
 Identities = 169/189 (89%), Positives = 179/189 (94%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD TSVTHLFPITK+LGLLATGMTADARTLVQQAR EAAEFRF+YGYEMPVDVL+KW
Sbjct: 58  DKLLDQTSVTHLFPITKFLGLLATGMTADARTLVQQARNEAAEFRFRYGYEMPVDVLSKW 117

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IADKSQVYTQHAYMRPLGVVAMVL IDEE GP+L+KCDPAGHF+GHKATSAG KEQEAIN
Sbjct: 118 IADKSQVYTQHAYMRPLGVVAMVLGIDEEKGPQLYKCDPAGHFYGHKATSAGSKEQEAIN 177

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKKMKNDPAFT++ETVQTAIS LQSVLQEDFKA+EIEVGVV  +NP FRVLS EEIDE
Sbjct: 178 FLEKKMKNDPAFTYEETVQTAISALQSVLQEDFKATEIEVGVVKADNPAFRVLSTEEIDE 237

Query: 183 HLTAISERD 191
           HLTAISERD
Sbjct: 238 HLTAISERD 246

Source: Gossypium hirsutum

Species: Gossypium hirsutum

Genus: Gossypium

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255648341|gb|ACU24622.1| unknown [Glycine max]

 Score =  355 bits (912), Expect = 4e-96,   Method: Compositional matrix adjust.
 Identities = 169/189 (89%), Positives = 181/189 (95%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD+TSVTHLFPITKYLGLLATGMTADARTLVQQAR EAAEFRF YGYE+PVDVLAKW
Sbjct: 58  DKLLDNTSVTHLFPITKYLGLLATGMTADARTLVQQARNEAAEFRFTYGYEIPVDVLAKW 117

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IADKSQVYTQHAYMRPLGVVAMVL ID+E G +L+KCDPAGH+FGHKATSAGLK+QEAIN
Sbjct: 118 IADKSQVYTQHAYMRPLGVVAMVLGIDDEYGLQLYKCDPAGHYFGHKATSAGLKDQEAIN 177

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKKMKNDP+FT++ETVQTAIS LQSVLQEDFKA+EIEVGVV KENPEFRVL+ EEIDE
Sbjct: 178 FLEKKMKNDPSFTYEETVQTAISALQSVLQEDFKATEIEVGVVRKENPEFRVLTTEEIDE 237

Query: 183 HLTAISERD 191
           HLTAISERD
Sbjct: 238 HLTAISERD 246

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225442079|ref|XP_002271929.1| PREDICTED: proteasome subunit alpha type-6 isoform 1 [Vitis vinifera] gi|147797489|emb|CAN73517.1| hypothetical protein VITISV_005460 [Vitis vinifera] gi|297742984|emb|CBI35851.3| unnamed protein product [Vitis vinifera]

 Score =  355 bits (910), Expect = 7e-96,   Method: Compositional matrix adjust.
 Identities = 168/189 (88%), Positives = 178/189 (94%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD TSVTHLFPITK+LGLLATGMTADARTLVQQAR EAAEFRF+YGYEMPVDVLA+W
Sbjct: 58  DKLLDQTSVTHLFPITKFLGLLATGMTADARTLVQQARNEAAEFRFRYGYEMPVDVLARW 117

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IADKSQVYTQHAYMRPLGVVAM+L ID+E GPRLFKCDPAGHFFGHKATSAGLKEQEAIN
Sbjct: 118 IADKSQVYTQHAYMRPLGVVAMILGIDDENGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 177

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKKMKNDPAF++ ETVQTAIS LQSVLQEDFK +EIEVGVV  ++P FRVLS EEIDE
Sbjct: 178 FLEKKMKNDPAFSYDETVQTAISALQSVLQEDFKPNEIEVGVVRTDSPAFRVLSTEEIDE 237

Query: 183 HLTAISERD 191
           HLTAISERD
Sbjct: 238 HLTAISERD 246

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449447912|ref|XP_004141710.1| PREDICTED: proteasome subunit alpha type-6-like [Cucumis sativus] gi|449480500|ref|XP_004155912.1| PREDICTED: proteasome subunit alpha type-6-like [Cucumis sativus]

 Score =  355 bits (910), Expect = 7e-96,   Method: Compositional matrix adjust.
 Identities = 169/189 (89%), Positives = 178/189 (94%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD TSVTHLF ITKYLGLLATG+TADAR+LVQQAR EAAEFRF+YGYEMPVDVLAKW
Sbjct: 58  DKLLDQTSVTHLFSITKYLGLLATGITADARSLVQQARNEAAEFRFQYGYEMPVDVLAKW 117

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IADKSQVYTQHAYMRPLGVVAMVL ID+E GPRLFKCDPAGHFFGHKATSAGLKEQEAIN
Sbjct: 118 IADKSQVYTQHAYMRPLGVVAMVLGIDDEYGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 177

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKKMKNDPAFT+ ETVQTAIS LQSVLQEDFKA+EIEVGVV  +NP FRVL+ EE+DE
Sbjct: 178 FLEKKMKNDPAFTYDETVQTAISALQSVLQEDFKATEIEVGVVRSDNPIFRVLTTEEVDE 237

Query: 183 HLTAISERD 191
           HLTAISERD
Sbjct: 238 HLTAISERD 246

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388519097|gb|AFK47610.1| unknown [Lotus japonicus]

 Score =  352 bits (903), Expect = 4e-95,   Method: Compositional matrix adjust.
 Identities = 167/189 (88%), Positives = 179/189 (94%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD TSV+HLFPITKYLGLLATGMTADARTLVQQAR EAAEFR  YGYEMPVDVLAKW
Sbjct: 58  DKLLDQTSVSHLFPITKYLGLLATGMTADARTLVQQARNEAAEFRHTYGYEMPVDVLAKW 117

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IADKSQVYTQHAYMRPLGVVAMVL ID+E G +L+KCDPAGH+FGHKATSAGLK+QEAIN
Sbjct: 118 IADKSQVYTQHAYMRPLGVVAMVLGIDDENGAQLYKCDPAGHYFGHKATSAGLKDQEAIN 177

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKKMKNDP+FT++ETVQTAIS LQSVLQEDFKA+EIEVGVV K+NPEFRVLS +EIDE
Sbjct: 178 FLEKKMKNDPSFTYEETVQTAISALQSVLQEDFKATEIEVGVVRKDNPEFRVLSTDEIDE 237

Query: 183 HLTAISERD 191
           HLTAISERD
Sbjct: 238 HLTAISERD 246

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	191
TAIR|locus:2157106	246	PAA1 "proteasome alpha subunit	0.989	0.768	0.835	1.9e-83
TAIR|locus:2064727	246	PAA2 "20S proteasome subunit P	0.989	0.768	0.835	2.8e-82
UNIPROTKB|E2RMN2	246	PSMA6 "Proteasome subunit alph	0.989	0.768	0.613	7.3e-59
UNIPROTKB|Q2YDE4	246	PSMA6 "Proteasome subunit alph	0.989	0.768	0.608	1.5e-58
UNIPROTKB|B4DXJ9	227	PSMA6 "cDNA FLJ51729, highly s	0.989	0.832	0.608	1.5e-58
UNIPROTKB|P60900	246	PSMA6 "Proteasome subunit alph	0.989	0.768	0.608	1.5e-58
UNIPROTKB|F2Z5N0	246	PSMA6 "Proteasome subunit alph	0.989	0.768	0.608	1.5e-58
MGI|MGI:1347006	246	Psma6 "proteasome (prosome, ma	0.989	0.768	0.608	1.5e-58
RGD|61849	246	Psma6 "proteasome (prosome, ma	0.989	0.768	0.608	1.5e-58
ZFIN|ZDB-GENE-020326-1	246	psma6a "proteasome (prosome, m	0.989	0.768	0.603	3.2e-58

TAIR|locus:2157106 PAA1 "proteasome alpha subunit A1" [Arabidopsis thaliana (taxid:3702)]

 Score = 836 (299.3 bits), Expect = 1.9e-83, P = 1.9e-83
 Identities = 158/189 (83%), Positives = 176/189 (93%)

Query:     3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
             DKLLD +SVTHLFPITKY+GL+ATG+TADAR+LVQQAR +AAEFRF YGYEMPVD+LAKW
Sbjct:    58 DKLLDQSSVTHLFPITKYIGLVATGITADARSLVQQARNQAAEFRFTYGYEMPVDILAKW 117

Query:    63 IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
             IADKSQVYTQHAYMRPLGVVAMV+ +DEE GP L+KCDPAGHF+GHKATSAG+KEQEA+N
Sbjct:   118 IADKSQVYTQHAYMRPLGVVAMVMGVDEENGPLLYKCDPAGHFYGHKATSAGMKEQEAVN 177

Query:   123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
             FLEKKMK +P+FTF ETVQTAIS LQSVLQEDFKA+EIEVGVV  ENPEFR L+ EEI+E
Sbjct:   178 FLEKKMKENPSFTFDETVQTAISALQSVLQEDFKATEIEVGVVRAENPEFRALTTEEIEE 237

Query:   183 HLTAISERD 191
             HLTAISERD
Sbjct:   238 HLTAISERD 246

GO:0004175 "endopeptidase activity" evidence=IEA

GO:0004298 "threonine-type endopeptidase activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005839 "proteasome core complex" evidence=IEA;TAS

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

GO:0008233 "peptidase activity" evidence=ISS

GO:0019773 "proteasome core complex, alpha-subunit complex" evidence=IEA

GO:0051603 "proteolysis involved in cellular protein catabolic process" evidence=IEA

GO:0005774 "vacuolar membrane" evidence=IDA

GO:0010043 "response to zinc ion" evidence=IEP

GO:0000502 "proteasome complex" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

TAIR|locus:2064727 PAA2 "20S proteasome subunit PAA2" [Arabidopsis thaliana (taxid:3702)]

 Score = 825 (295.5 bits), Expect = 2.8e-82, P = 2.8e-82
 Identities = 158/189 (83%), Positives = 174/189 (92%)

Query:     3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
             DKLLD +SV+HLFP+TKYLGLLATGMTAD+R+LVQQAR EAAEFRF+YGYEMP D+LAKW
Sbjct:    58 DKLLDQSSVSHLFPVTKYLGLLATGMTADSRSLVQQARNEAAEFRFQYGYEMPADILAKW 117

Query:    63 IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
             IADKSQVYTQHAYMRPLGVVAMVL IDEE GP L+KCDPAGHF+GHKATSAG+KEQEA+N
Sbjct:   118 IADKSQVYTQHAYMRPLGVVAMVLGIDEERGPLLYKCDPAGHFYGHKATSAGMKEQEAVN 177

Query:   123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
             FLEKKMK +PAFT+ ETVQTAIS LQSVLQEDFKA+EIEVGVV  ++P FR L  EEIDE
Sbjct:   178 FLEKKMKENPAFTYDETVQTAISALQSVLQEDFKATEIEVGVVRADDPLFRSLRTEEIDE 237

Query:   183 HLTAISERD 191
             HLTAISERD
Sbjct:   238 HLTAISERD 246

GO:0004175 "endopeptidase activity" evidence=IEA

GO:0004298 "threonine-type endopeptidase activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005839 "proteasome core complex" evidence=IEA;TAS

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

GO:0008233 "peptidase activity" evidence=ISS

GO:0019773 "proteasome core complex, alpha-subunit complex" evidence=IEA

GO:0051603 "proteolysis involved in cellular protein catabolic process" evidence=IEA

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0000502 "proteasome complex" evidence=IDA

UNIPROTKB|E2RMN2 PSMA6 "Proteasome subunit alpha type" [Canis lupus familiaris (taxid:9615)]

 Score = 604 (217.7 bits), Expect = 7.3e-59, P = 7.3e-59
 Identities = 116/189 (61%), Positives = 155/189 (82%)

Query:     3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
             DKLLD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K 
Sbjct:    58 DKLLDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKR 117

Query:    63 IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
             IAD SQVYTQ+A MRPLG   +++ IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +
Sbjct:   118 IADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTS 177

Query:   123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
             FLEKK+K    +TF++TV+TAI+ L +VL  DFK SEIEVGVV+ ENP+FR+LS  EID 
Sbjct:   178 FLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILSEAEIDA 237

Query:   183 HLTAISERD 191
             HL A++ERD
Sbjct:   238 HLVALAERD 246

GO:0051092 "positive regulation of NF-kappaB transcription factor activity" evidence=IEA

GO:0051059 "NF-kappaB binding" evidence=IEA

GO:0016363 "nuclear matrix" evidence=IEA

GO:0005844 "polysome" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004298 "threonine-type endopeptidase activity" evidence=IEA

GO:0019773 "proteasome core complex, alpha-subunit complex" evidence=IEA

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

UNIPROTKB|Q2YDE4 PSMA6 "Proteasome subunit alpha type-6" [Bos taurus (taxid:9913)]

 Score = 601 (216.6 bits), Expect = 1.5e-58, P = 1.5e-58
 Identities = 115/189 (60%), Positives = 155/189 (82%)

Query:     3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
             DKLLD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K 
Sbjct:    58 DKLLDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKR 117

Query:    63 IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
             IAD SQVYTQ+A MRPLG   +++ IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +
Sbjct:   118 IADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTS 177

Query:   123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
             FLEKK+K    +TF++TV+TAI+ L +VL  DFK SEIEVGVV+ ENP+FR+L+  EID 
Sbjct:   178 FLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDA 237

Query:   183 HLTAISERD 191
             HL A++ERD
Sbjct:   238 HLVALAERD 246

GO:0000932 "cytoplasmic mRNA processing body" evidence=ISS

GO:0005839 "proteasome core complex" evidence=ISS

GO:0051092 "positive regulation of NF-kappaB transcription factor activity" evidence=IEA

GO:0051059 "NF-kappaB binding" evidence=IEA

GO:0016363 "nuclear matrix" evidence=IEA

GO:0005844 "polysome" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004298 "threonine-type endopeptidase activity" evidence=IEA

GO:0019773 "proteasome core complex, alpha-subunit complex" evidence=IEA

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

UNIPROTKB|B4DXJ9 PSMA6 "cDNA FLJ51729, highly similar to Proteasome subunit alpha type 6 (EC 3.4.25.1)" [Homo sapiens (taxid:9606)]

 Score = 601 (216.6 bits), Expect = 1.5e-58, P = 1.5e-58
 Identities = 115/189 (60%), Positives = 155/189 (82%)

Query:     3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
             DKLLD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K 
Sbjct:    39 DKLLDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKR 98

Query:    63 IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
             IAD SQVYTQ+A MRPLG   +++ IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +
Sbjct:    99 IADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTS 158

Query:   123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
             FLEKK+K    +TF++TV+TAI+ L +VL  DFK SEIEVGVV+ ENP+FR+L+  EID 
Sbjct:   159 FLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDA 218

Query:   183 HLTAISERD 191
             HL A++ERD
Sbjct:   219 HLVALAERD 227

GO:0004298 "threonine-type endopeptidase activity" evidence=IEA

GO:0005839 "proteasome core complex" evidence=IEA

GO:0051603 "proteolysis involved in cellular protein catabolic process" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

UNIPROTKB|P60900 PSMA6 "Proteasome subunit alpha type-6" [Homo sapiens (taxid:9606)]

 Score = 601 (216.6 bits), Expect = 1.5e-58, P = 1.5e-58
 Identities = 115/189 (60%), Positives = 155/189 (82%)

Query:     3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
             DKLLD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K 
Sbjct:    58 DKLLDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKR 117

Query:    63 IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
             IAD SQVYTQ+A MRPLG   +++ IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +
Sbjct:   118 IADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTS 177

Query:   123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
             FLEKK+K    +TF++TV+TAI+ L +VL  DFK SEIEVGVV+ ENP+FR+L+  EID 
Sbjct:   178 FLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDA 237

Query:   183 HLTAISERD 191
             HL A++ERD
Sbjct:   238 HLVALAERD 246

GO:0004298 "threonine-type endopeptidase activity" evidence=IEA

GO:0005839 "proteasome core complex" evidence=ISS;NAS

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

GO:0004175 "endopeptidase activity" evidence=NAS

GO:0003723 "RNA binding" evidence=IDA;NAS

GO:0000932 "cytoplasmic mRNA processing body" evidence=ISS

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:0051059 "NF-kappaB binding" evidence=IPI

GO:0030017 "sarcomere" evidence=ISS

GO:0030016 "myofibril" evidence=ISS

GO:0016363 "nuclear matrix" evidence=ISS

GO:0019773 "proteasome core complex, alpha-subunit complex" evidence=IDA;TAS

GO:0051092 "positive regulation of NF-kappaB transcription factor activity" evidence=IMP

GO:0050727 "regulation of inflammatory response" evidence=IC

GO:0051603 "proteolysis involved in cellular protein catabolic process" evidence=IMP

GO:0035639 "purine ribonucleoside triphosphate binding" evidence=NAS

GO:0005844 "polysome" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

UNIPROTKB|F2Z5N0 PSMA6 "Proteasome subunit alpha type" [Sus scrofa (taxid:9823)]

 Score = 601 (216.6 bits), Expect = 1.5e-58, P = 1.5e-58
 Identities = 115/189 (60%), Positives = 155/189 (82%)

Query:     3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
             DKLLD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K 
Sbjct:    58 DKLLDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKR 117

Query:    63 IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
             IAD SQVYTQ+A MRPLG   +++ IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +
Sbjct:   118 IADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTS 177

Query:   123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
             FLEKK+K    +TF++TV+TAI+ L +VL  DFK SEIEVGVV+ ENP+FR+L+  EID 
Sbjct:   178 FLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDA 237

Query:   183 HLTAISERD 191
             HL A++ERD
Sbjct:   238 HLVALAERD 246

GO:0051092 "positive regulation of NF-kappaB transcription factor activity" evidence=IEA

GO:0051059 "NF-kappaB binding" evidence=IEA

GO:0016363 "nuclear matrix" evidence=IEA

GO:0005844 "polysome" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004298 "threonine-type endopeptidase activity" evidence=IEA

GO:0019773 "proteasome core complex, alpha-subunit complex" evidence=IEA

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

MGI|MGI:1347006 Psma6 "proteasome (prosome, macropain) subunit, alpha type 6" [Mus musculus (taxid:10090)]

 Score = 601 (216.6 bits), Expect = 1.5e-58, P = 1.5e-58
 Identities = 115/189 (60%), Positives = 155/189 (82%)

Query:     3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
             DKLLD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K 
Sbjct:    58 DKLLDSSTVTHLFKITESIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKR 117

Query:    63 IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
             IAD SQVYTQ+A MRPLG   +++ IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +
Sbjct:   118 IADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTS 177

Query:   123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
             FLEKK+K    +TF++TV+TAI+ L +VL  DFK SEIEVGVV+ ENP+FR+L+  EID 
Sbjct:   178 FLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDA 237

Query:   183 HLTAISERD 191
             HL A++ERD
Sbjct:   238 HLVALAERD 246

GO:0000502 "proteasome complex" evidence=IEA

GO:0003723 "RNA binding" evidence=ISO;IDA

GO:0004175 "endopeptidase activity" evidence=IEA

GO:0004298 "threonine-type endopeptidase activity" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=IDA

GO:0005839 "proteasome core complex" evidence=IDA

GO:0005844 "polysome" evidence=ISO

GO:0006508 "proteolysis" evidence=IEA

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

GO:0007519 "skeletal muscle tissue development" evidence=NAS

GO:0008233 "peptidase activity" evidence=IEA

GO:0016363 "nuclear matrix" evidence=IDA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0019773 "proteasome core complex, alpha-subunit complex" evidence=ISO

GO:0030016 "myofibril" evidence=ISO

GO:0030017 "sarcomere" evidence=ISO

GO:0051059 "NF-kappaB binding" evidence=ISO

GO:0051092 "positive regulation of NF-kappaB transcription factor activity" evidence=ISO

GO:0051603 "proteolysis involved in cellular protein catabolic process" evidence=ISO

RGD|61849 Psma6 "proteasome (prosome, macropain) subunit, alpha type 6" [Rattus norvegicus (taxid:10116)]

 Score = 601 (216.6 bits), Expect = 1.5e-58, P = 1.5e-58
 Identities = 115/189 (60%), Positives = 155/189 (82%)

Query:     3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
             DKLLD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K 
Sbjct:    58 DKLLDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKR 117

Query:    63 IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
             IAD SQVYTQ+A MRPLG   +++ IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +
Sbjct:   118 IADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTS 177

Query:   123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
             FLEKK+K    +TF++TV+TAI+ L +VL  DFK SEIEVGVV+ ENP+FR+L+  EID 
Sbjct:   178 FLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDA 237

Query:   183 HLTAISERD 191
             HL A++ERD
Sbjct:   238 HLVALAERD 246

GO:0000932 "cytoplasmic mRNA processing body" evidence=ISS

GO:0003723 "RNA binding" evidence=ISO;ISS

GO:0004298 "threonine-type endopeptidase activity" evidence=IEA

GO:0005634 "nucleus" evidence=ISO;ISS

GO:0005737 "cytoplasm" evidence=ISO

GO:0005739 "mitochondrion" evidence=IEA;ISO

GO:0005839 "proteasome core complex" evidence=ISO;ISS

GO:0005844 "polysome" evidence=ISO;ISS

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

GO:0016363 "nuclear matrix" evidence=ISO;ISS

GO:0019773 "proteasome core complex, alpha-subunit complex" evidence=ISO;ISS

GO:0030016 "myofibril" evidence=IDA

GO:0030017 "sarcomere" evidence=IDA

GO:0051059 "NF-kappaB binding" evidence=IEA;ISO

GO:0051092 "positive regulation of NF-kappaB transcription factor activity" evidence=ISO;ISS

GO:0051603 "proteolysis involved in cellular protein catabolic process" evidence=ISO;ISS

ZFIN|ZDB-GENE-020326-1 psma6a "proteasome (prosome, macropain) subunit, alpha type, 6a" [Danio rerio (taxid:7955)]

 Score = 598 (215.6 bits), Expect = 3.2e-58, P = 3.2e-58
 Identities = 114/189 (60%), Positives = 153/189 (80%)

Query:     3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
             DKLLD ++VTHLF IT+ +G + +GMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K 
Sbjct:    58 DKLLDSSTVTHLFRITENIGCVMSGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKR 117

Query:    63 IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
             IAD SQVYTQ+A MRPLG   +V+ +DEE GP+++KCDPAG++ G KAT+AG+K+ EA +
Sbjct:   118 IADISQVYTQNAEMRPLGCCMIVVGVDEELGPQVYKCDPAGYYCGFKATAAGVKQTEATS 177

Query:   123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
             FLEKK+K    +TF +TV+TAIS L +VL  DFK SE+E+GVV+ E P+FR+LS  EID 
Sbjct:   178 FLEKKIKKKLDWTFDQTVETAISCLSTVLAIDFKPSELEIGVVTTEEPKFRILSESEIDT 237

Query:   183 HLTAISERD 191
             HL A++ERD
Sbjct:   238 HLMALTERD 246

GO:0051603 "proteolysis involved in cellular protein catabolic process" evidence=IEA

GO:0004298 "threonine-type endopeptidase activity" evidence=IEA

GO:0004175 "endopeptidase activity" evidence=IEA

GO:0005839 "proteasome core complex" evidence=IEA

GO:0019773 "proteasome core complex, alpha-subunit complex" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0008233 "peptidase activity" evidence=IEA

GO:0000502 "proteasome complex" evidence=IEA

GO:0006508 "proteolysis" 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)
Q9QUM9	PSA6_MOUSE	3, ., 4, ., 2, 5, ., 1	0.6084	0.9895	0.7682	yes	no
Q9XZJ4	PSA6_DROME	3, ., 4, ., 2, 5, ., 1	0.5714	0.9424	0.7377	yes	no
O94517	PSA1_SCHPO	3, ., 4, ., 2, 5, ., 1	0.5445	0.9790	0.7663	yes	no
Q9LSU3	PSA6_ORYSJ	3, ., 4, ., 2, 5, ., 1	0.8412	0.9895	0.7682	yes	no
O81146	PSA6A_ARATH	3, ., 4, ., 2, 5, ., 1	0.8359	0.9895	0.7682	yes	no
Q2YDE4	PSA6_BOVIN	3, ., 4, ., 2, 5, ., 1	0.6084	0.9895	0.7682	yes	no
Q9XG77	PSA6_TOBAC	3, ., 4, ., 2, 5, ., 1	0.9047	0.9895	0.7682	N/A	no
P60901	PSA6_RAT	3, ., 4, ., 2, 5, ., 1	0.6084	0.9895	0.7682	yes	no
P60900	PSA6_HUMAN	3, ., 4, ., 2, 5, ., 1	0.6084	0.9895	0.7682	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.4.25.1	0.991
3rd Layer	3.4.25	0.976

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00034058001	RecName- Full=Proteasome subunit alpha type; EC=3.4.25.1;; The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity (By similarity) (246 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00015420001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (191 aa)			•	•	•	•	•		0.945
	GSVIVG00024499001	RecName- Full=Proteasome subunit beta type; EC=3.4.25.1;; The proteasome is a multicatalytic pr [...] (245 aa)			•	•	•	•	•		0.945
	GSVIVG00014791001	SubName- Full=Putative uncharacterized protein (Chromosome chr18 scaffold_1, whole genome shotg [...] (309 aa)				•	•	•	•		0.932
	GSVIVG00023752001	SubName- Full=Putative uncharacterized protein (Chromosome chr7 scaffold_31, whole genome shotg [...] (205 aa)			•	•	•	•	•		0.926
	GSVIVG00010470001	SubName- Full=Chromosome chr17 scaffold_263, whole genome shotgun sequence; (386 aa)				•	•	•			0.911
	GSVIVG00026350001	RecName- Full=Proteasome subunit beta type; EC=3.4.25.1;; The proteasome is a multicatalytic pr [...] (223 aa)			•	•	•	•	•		0.901
	GSVIVG00030725001	RecName- Full=Proteasome subunit beta type; EC=3.4.25.1;; The proteasome is a multicatalytic pr [...] (250 aa)			•	•	•	•	•		0.899
	GSVIVG00035048001	RecName- Full=Proteasome subunit beta type; EC=3.4.25.1;; The proteasome is a multicatalytic pr [...] (272 aa)				•	•	•	•		0.879
	GSVIVG00036762001	SubName- Full=Chromosome chr4 scaffold_83, whole genome shotgun sequence; (440 aa)				•	•	•	•		0.845
	GSVIVG00006696001	SubName- Full=Chromosome chr2 scaffold_176, whole genome shotgun sequence; (267 aa)				•	•	•	•		0.798

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	191
cd03754	215	cd03754, proteasome_alpha_type_6, proteasome_alpha	1e-103
cd01911	209	cd01911, proteasome_alpha, proteasome alpha subuni	4e-82
cd01906	182	cd01906, proteasome_protease_HslV, proteasome_prot	2e-48
pfam00227	188	pfam00227, Proteasome, Proteasome subunit	6e-47
PRK03996	241	PRK03996, PRK03996, proteasome subunit alpha; Prov	2e-45
TIGR03633	224	TIGR03633, arc_protsome_A, proteasome endopeptidas	2e-42
COG0638	236	COG0638, PRE1, 20S proteasome, alpha and beta subu	1e-39
cd03750	227	cd03750, proteasome_alpha_type_2, proteasome_alpha	3e-39
cd03756	211	cd03756, proteasome_alpha_archeal, proteasome_alph	7e-37
cd03749	211	cd03749, proteasome_alpha_type_1, proteasome_alpha	1e-30
PTZ00246	253	PTZ00246, PTZ00246, proteasome subunit alpha; Prov	6e-28
cd01901	164	cd01901, Ntn_hydrolase, The Ntn hydrolases (N-term	2e-27
cd03752	213	cd03752, proteasome_alpha_type_4, proteasome_alpha	6e-27
cd03755	207	cd03755, proteasome_alpha_type_7, proteasome_alpha	8e-25
cd03751	212	cd03751, proteasome_alpha_type_3, proteasome_alpha	1e-24
cd03753	213	cd03753, proteasome_alpha_type_5, proteasome_alpha	6e-24
cd03764	188	cd03764, proteasome_beta_archeal, Archeal proteaso	3e-11
TIGR03634	185	TIGR03634, arc_protsome_B, proteasome endopeptidas	3e-10
cd01912	189	cd01912, proteasome_beta, proteasome beta subunit	3e-09
cd03757	212	cd03757, proteasome_beta_type_1, proteasome beta t	0.001

>gnl|CDD|239723 cd03754, proteasome_alpha_type_6, proteasome_alpha_type_6

 Score =  296 bits (759), Expect = e-103
 Identities = 112/167 (67%), Positives = 140/167 (83%), Gaps = 2/167 (1%)

Query: 1   MQDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA 60
           + DKL+D ++VTHLF IT  +G + TGM AD+R+ VQ+ARYEAAEF++KYGYEMPVDVLA
Sbjct: 49  VPDKLIDPSTVTHLFRITDEIGCVMTGMIADSRSQVQRARYEAAEFKYKYGYEMPVDVLA 108

Query: 61  KWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEA 120
           K IAD +QVYTQHAYMRPLGV  +++ IDEE GP+L+KCDPAG+F G+KAT+AG+KEQEA
Sbjct: 109 KRIADINQVYTQHAYMRPLGVSMILIGIDEELGPQLYKCDPAGYFAGYKATAAGVKEQEA 168

Query: 121 INFLEKKMKNDPAF--TFQETVQTAISTLQSVLQEDFKASEIEVGVV 165
            NFLEKK+K  P    +++ETV+ AIS LQ+VL  DFKA+EIEVGVV
Sbjct: 169 TNFLEKKLKKKPDLIESYEETVELAISCLQTVLSTDFKATEIEVGVV 215

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 215

>gnl|CDD|238892 cd01911, proteasome_alpha, proteasome alpha subunit

 Score =  241 bits (619), Expect = 4e-82
 Identities = 79/164 (48%), Positives = 109/164 (66%), Gaps = 2/164 (1%)

Query: 2   QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAK 61
             KLLD +SV  +F I  ++G    G+TADAR LV +AR EA  +R+ YG  +PV+VL K
Sbjct: 48  TSKLLDPSSVEKIFKIDDHIGCAVAGLTADARVLVNRARVEAQNYRYTYGEPIPVEVLVK 107

Query: 62  WIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAI 121
            IAD +QVYTQ+  +RP GV  ++   DEE GP+L++ DP+G +FG+KAT+ G   QEA 
Sbjct: 108 RIADLAQVYTQYGGVRPFGVSLLIAGYDEEGGPQLYQTDPSGTYFGYKATAIGKGSQEAK 167

Query: 122 NFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVV 165
            FLEK+ K D   T +E ++ A+  L+ VL+ED KA  IE+ VV
Sbjct: 168 TFLEKRYKKDL--TLEEAIKLALKALKEVLEEDKKAKNIEIAVV 209

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 different alpha and 10 different beta proteasome subunit genes while archaea have one of each. Length = 209

>gnl|CDD|238887 cd01906, proteasome_protease_HslV, proteasome_protease_HslV

 Score =  155 bits (394), Expect = 2e-48
 Identities = 65/165 (39%), Positives = 97/165 (58%), Gaps = 6/165 (3%)

Query: 3   DKLLDH-TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAK 61
             LL   ++V  +F I  ++G    G+ ADA+TLV++ R EA  +R +YG  +PV+ LAK
Sbjct: 22  SGLLVASSTVEKIFKIDDHIGCAFAGLAADAQTLVERLRKEAQLYRLRYGEPIPVEALAK 81

Query: 62  WIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAI 121
            +A+    YTQ   +RPLGV  +V  +DEE GP+L+  DP+G +  +KAT+ G   Q A+
Sbjct: 82  LLANLLYEYTQS--LRPLGVSLLVAGVDEEGGPQLYSVDPSGSYIEYKATAIGSGSQYAL 139

Query: 122 NFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDF-KASEIEVGVV 165
             LEK  K D   T +E ++ A+  L+S L+ D      IEV V+
Sbjct: 140 GILEKLYKPDM--TLEEAIELALKALKSALERDLYSGGNIEVAVI 182

This group contains the eukaryotic proteosome alpha and beta subunits and the prokaryotic protease hslV subunit. Proteasomes are large multimeric self-compartmentalizing proteases, involved in the clearance of misfolded proteins, the breakdown of regulatory proteins, and the processing of proteins such as the preparation of peptides for immune presentation. Two main proteasomal types are distinguished by their different tertiary structures: the eukaryotic/archeal 20S proteasome and the prokaryotic proteasome-like heat shock protein encoded by heat shock locus V, hslV. The proteasome core particle is a highly conserved cylindrical structure made up of non-identical subunits that have their active sites on the inner walls of a large central cavity. The proteasome subunits of bacteria, archaea, and eukaryotes all share a conserved Ntn (N terminal nucleophile) hydrolase fold and a catalytic mechanism involving an N-terminal nucleophilic threonine that is exposed by post-translational processing of an inactive propeptide. Length = 182

>gnl|CDD|215805 pfam00227, Proteasome, Proteasome subunit

 Score =  151 bits (385), Expect = 6e-47
 Identities = 67/166 (40%), Positives = 94/166 (56%), Gaps = 4/166 (2%)

Query: 1   MQDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA 60
              KLL   +V  +F I  ++G+   G+ ADA+TLV  AR EA  +R +YG  + V+ LA
Sbjct: 26  RGSKLLSKDTVEKIFKIDDHIGMAFAGLAADAQTLVDYARAEAQLYRLRYGRPISVE-LA 84

Query: 61  KWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEA 120
           K IADK Q YTQ++  RP GV  ++   DE+ GP L+  DP+G    +KAT+ G   Q A
Sbjct: 85  KRIADKLQAYTQYSGRRPYGVSLLIAGYDEDGGPHLYSIDPSGSVIEYKATAIGSGSQYA 144

Query: 121 INFLEKKMKNDPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVV 165
             FLEK  K D   T +E V+ A+  L+  ++ D      IEV V+
Sbjct: 145 YGFLEKLYKPD--MTLEEAVELAVKALKEAIERDALSGGNIEVAVI 188

The proteasome is a multisubunit structure that degrades proteins. Protein degradation is an essential component of regulation because proteins can become misfolded, damaged, or unnecessary. Proteasomes and their homologues vary greatly in complexity: from HslV (heat shock locus v), which is encoded by 1 gene in bacteria, to the eukaryotic 20S proteasome, which is encoded by more than 14 genes. Recently evidence of two novel groups of bacterial proteasomes was proposed. The first is Anbu, which is sparsely distributed among cyanobacteria and proteobacteria. The second is call beta-proteobacteria proteasome homologue (BPH). Length = 188

>gnl|CDD|235192 PRK03996, PRK03996, proteasome subunit alpha; Provisional

 Score =  149 bits (379), Expect = 2e-45
 Identities = 64/186 (34%), Positives = 104/186 (55%), Gaps = 3/186 (1%)

Query: 4   KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWI 63
            L++ +S+  +F I  ++G  + G+ ADAR L+ +AR EA   R  YG  + V+ L K I
Sbjct: 59  PLIEPSSIEKIFKIDDHIGAASAGLVADARVLIDRARVEAQINRLTYGEPIGVETLTKKI 118

Query: 64  ADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINF 123
            D  Q YTQH  +RP GV  ++  +D+  GPRLF+ DP+G +  +KAT+ G      + F
Sbjct: 119 CDHKQQYTQHGGVRPFGVALLIAGVDDG-GPRLFETDPSGAYLEYKATAIGAGRDTVMEF 177

Query: 124 LEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEH 183
           LEK  K D   + +E ++ A+  L    +       +E+  +  E  +FR LS+EEI+++
Sbjct: 178 LEKNYKED--LSLEEAIELALKALAKANEGKLDPENVEIAYIDVETKKFRKLSVEEIEKY 235

Query: 184 LTAISE 189
           L  + +
Sbjct: 236 LEKLLK 241

Length = 241

>gnl|CDD|163366 TIGR03633, arc_protsome_A, proteasome endopeptidase complex, archaeal, alpha subunit

 Score =  141 bits (357), Expect = 2e-42
 Identities = 66/176 (37%), Positives = 103/176 (58%), Gaps = 3/176 (1%)

Query: 4   KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWI 63
           KL++ +S+  +F I  ++G   +G+ ADAR L+ +AR EA   R  YG  + V+ LAK I
Sbjct: 52  KLVEPSSIEKIFKIDDHIGAATSGLVADARVLIDRARIEAQINRLTYGEPIDVETLAKKI 111

Query: 64  ADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINF 123
            D  Q YTQH  +RP GV  ++  +D+  GPRLF+ DP+G    +KAT+ G   Q    F
Sbjct: 112 CDLKQQYTQHGGVRPFGVALLIAGVDDG-GPRLFETDPSGALLEYKATAIGAGRQAVTEF 170

Query: 124 LEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEE 179
           LEK+ + D   +  E ++ A+  L S +++      +EV  ++ E+ +FR LS+EE
Sbjct: 171 LEKEYRED--LSLDEAIELALKALYSAVEDKLTPENVEVAYITVEDKKFRKLSVEE 224

This protein family describes the archaeal proteasome alpha subunit, homologous to both the beta subunit and to the alpha and beta subunits of eukaryotic proteasome subunits. This family is universal in the first 29 complete archaeal genomes but occasionally is duplicated [Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 224

>gnl|CDD|223711 COG0638, PRE1, 20S proteasome, alpha and beta subunits [Posttranslational modification, protein turnover, chaperones]

 Score =  134 bits (340), Expect = 1e-39
 Identities = 67/184 (36%), Positives = 108/184 (58%), Gaps = 7/184 (3%)

Query: 8   HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKS 67
            ++V  +F I  ++G+   G+ ADA+ LV+ AR EA  +R +YG  + V+ LAK +++  
Sbjct: 58  SSNVEKIFKIDDHIGMAIAGLAADAQVLVRYARAEAQLYRLRYGEPISVEALAKLLSNIL 117

Query: 68  QVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKK 127
           Q YTQ    RP GV  +V  +D+  GPRL+  DP+G +  +KAT+ G   Q A  FLEK+
Sbjct: 118 QEYTQ--SGRPYGVSLLVAGVDDG-GPRLYSTDPSGSYNEYKATAIGSGSQFAYGFLEKE 174

Query: 128 MKNDPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEHLTA 186
            + D   + +E ++ A+  L++ ++ D      IEV V++K+   FR L  EEI + L  
Sbjct: 175 YRED--LSLEEAIELAVKALRAAIERDAASGGGIEVAVITKDEG-FRKLDGEEIKKLLDD 231

Query: 187 ISER 190
           +SE+
Sbjct: 232 LSEK 235

Length = 236

>gnl|CDD|239719 cd03750, proteasome_alpha_type_2, proteasome_alpha_type_2

 Score =  133 bits (337), Expect = 3e-39
 Identities = 64/180 (35%), Positives = 99/180 (55%), Gaps = 4/180 (2%)

Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
           L+D +SV  +  IT ++G++ +GM  D R LV++AR  A ++   YG  +PV  L + IA
Sbjct: 51  LIDESSVHKVEQITPHIGMVYSGMGPDFRVLVKKARKIAQQYYLVYGEPIPVSQLVREIA 110

Query: 65  DKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFL 124
              Q YTQ   +RP GV  ++   DE  GP L++ DP+G +F  KAT+ G     A  FL
Sbjct: 111 SVMQEYTQSGGVRPFGVSLLIAGWDEG-GPYLYQVDPSGSYFTWKATAIGKNYSNAKTFL 169

Query: 125 EKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 184
           EK+   D     ++ + TAI TL+   +       IE+G+  +    FR+L+  EI ++L
Sbjct: 170 EKRYNED--LELEDAIHTAILTLKEGFEGQMTEKNIEIGICGETKG-FRLLTPAEIKDYL 226

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 227

>gnl|CDD|239725 cd03756, proteasome_alpha_archeal, proteasome_alpha_archeal

 Score =  126 bits (319), Expect = 7e-37
 Identities = 60/163 (36%), Positives = 95/163 (58%), Gaps = 3/163 (1%)

Query: 4   KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWI 63
           KL++  S+  ++ I  ++G   +G+ ADAR L+ +AR EA   R  YG  + V+VL K I
Sbjct: 51  KLVEPESIEKIYKIDDHVGAATSGLVADARVLIDRARVEAQIHRLTYGEPIDVEVLVKKI 110

Query: 64  ADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINF 123
            D  Q YTQH  +RP GV  ++  +D+  GPRLF+ DP+G +  +KAT+ G   Q    F
Sbjct: 111 CDLKQQYTQHGGVRPFGVALLIAGVDDG-GPRLFETDPSGAYNEYKATAIGSGRQAVTEF 169

Query: 124 LEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVS 166
           LEK+ K D   + +E ++ A+  L + L+E+     +E+  V+
Sbjct: 170 LEKEYKED--MSLEEAIELALKALYAALEENETPENVEIAYVT 210

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 211

>gnl|CDD|239718 cd03749, proteasome_alpha_type_1, proteasome_alpha_type_1

 Score =  110 bits (278), Expect = 1e-30
 Identities = 49/154 (31%), Positives = 84/154 (54%), Gaps = 3/154 (1%)

Query: 14  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 73
           +F +  ++G+   G+TADAR L +  R E   +RF Y   +PV  L   +A+K+Q+ TQ 
Sbjct: 58  IFKVDDHIGIAIAGLTADARVLSRYMRQECLNYRFVYDSPIPVSRLVSKVAEKAQINTQR 117

Query: 74  AYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPA 133
              RP GV  ++   DE  GP LF+  P+G++F +KATS G + Q A  +LE+  +    
Sbjct: 118 YGRRPYGVGLLIAGYDES-GPHLFQTCPSGNYFEYKATSIGARSQSARTYLERHFEEFED 176

Query: 134 FTFQETVQTAISTLQSVLQ--EDFKASEIEVGVV 165
            + +E ++ A+  L+  L   ++     + + +V
Sbjct: 177 CSLEELIKHALRALRETLPGEQELTIKNVSIAIV 210

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 211

>gnl|CDD|173491 PTZ00246, PTZ00246, proteasome subunit alpha; Provisional

 Score =  104 bits (262), Expect = 6e-28
 Identities = 64/194 (32%), Positives = 100/194 (51%), Gaps = 8/194 (4%)

Query: 4   KLLDH-TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           KLLD       ++ I  ++     G+TADA  L+ Q R  A  +R+ YG   PV+ L   
Sbjct: 54  KLLDPGKINEKIYKIDSHIFCAVAGLTADANILINQCRLYAQRYRYTYGEPQPVEQLVVQ 113

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           I D  Q YTQ   +RP GV  +    DE  G +L+  DP+G++ G KAT+ G   Q A +
Sbjct: 114 ICDLKQSYTQFGGLRPFGVSFLFAGYDENLGYQLYHTDPSGNYSGWKATAIGQNNQTAQS 173

Query: 123 FLEKKMKNDPAFTFQETVQTAISTL-QSVLQEDFKASEIEVGVVSKENPEF----RVLSI 177
            L+++ K D   T ++ +  A   L +S+     KA +IEVG++S    +     ++LS 
Sbjct: 174 ILKQEWKED--LTLEQGLLLAAKVLTKSMDSTSPKADKIEVGILSHGETDGEPIQKMLSE 231

Query: 178 EEIDEHLTAISERD 191
           +EI E L  +++  
Sbjct: 232 KEIAELLKKVTQEY 245

Length = 253

>gnl|CDD|238884 cd01901, Ntn_hydrolase, The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid

 Score =  101 bits (253), Expect = 2e-27
 Identities = 49/142 (34%), Positives = 72/142 (50%), Gaps = 7/142 (4%)

Query: 9   TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQ 68
           + V  +      +     G+ ADA+TLV++ R     +R +YG  + V  LAK +A   Q
Sbjct: 29  SPVIKIGKNEDGIAWGLAGLAADAQTLVRRLREALQLYRLRYGEPISVVALAKELAKLLQ 88

Query: 69  VYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGH-KATSAGLKEQEAINFLEKK 127
           VYTQ    RP GV  +V  +DE  G  L+  DP+G    +  A + G + Q A + LEK 
Sbjct: 89  VYTQ---GRPFGVNLIVAGVDEG-GGNLYYIDPSGPVIENPGAVATGSRSQRAKSLLEKL 144

Query: 128 MKNDPAFTFQETVQTAISTLQS 149
            K D   T +E V+ A+  L+S
Sbjct: 145 YKPDM--TLEEAVELALKALKS 164

N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences. Length = 164

>gnl|CDD|239721 cd03752, proteasome_alpha_type_4, proteasome_alpha_type_4

 Score =  101 bits (253), Expect = 6e-27
 Identities = 48/164 (29%), Positives = 86/164 (52%), Gaps = 4/164 (2%)

Query: 4   KLLDH-TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           KLLD   S   ++ I  ++     G+T+DA  L+  AR  A  + + Y   +PV+ L + 
Sbjct: 52  KLLDQSFSSEKIYKIDDHIACAVAGITSDANILINYARLIAQRYLYSYQEPIPVEQLVQR 111

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           + D  Q YTQ+  +RP GV  +    D+  G +L++ DP+G++ G KAT+ G   Q A +
Sbjct: 112 LCDIKQGYTQYGGLRPFGVSFLYAGWDKHYGFQLYQSDPSGNYSGWKATAIGNNNQAAQS 171

Query: 123 FLEKKMKNDPAFTFQETVQTAISTL-QSVLQEDFKASEIEVGVV 165
            L++  K+D   T +E +  A+  L +++      + ++E   +
Sbjct: 172 LLKQDYKDDM--TLEEALALAVKVLSKTMDSTKLTSEKLEFATL 213

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 213

>gnl|CDD|239724 cd03755, proteasome_alpha_type_7, proteasome_alpha_type_7

 Score = 95.5 bits (238), Expect = 8e-25
 Identities = 51/159 (32%), Positives = 82/159 (51%), Gaps = 2/159 (1%)

Query: 4   KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWI 63
           KL D  +V  +  +  ++ L   G+TADAR L+ +AR E    R      + V+ + ++I
Sbjct: 50  KLQDPRTVRKICMLDDHVCLAFAGLTADARVLINRARLECQSHRLTVEDPVTVEYITRYI 109

Query: 64  ADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINF 123
           A   Q YTQ   +RP G+  +++  D +  PRL++ DP+G +   KA + G   +    F
Sbjct: 110 AGLQQRYTQSGGVRPFGISTLIVGFDPDGTPRLYQTDPSGTYSAWKANAIGRNSKTVREF 169

Query: 124 LEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEV 162
           LEK  K +   T  +T++ AI  L  V+Q   K  E+ V
Sbjct: 170 LEKNYKEE--MTRDDTIKLAIKALLEVVQSGSKNIELAV 206

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 207

>gnl|CDD|239720 cd03751, proteasome_alpha_type_3, proteasome_alpha_type_3

 Score = 95.4 bits (238), Expect = 1e-24
 Identities = 54/166 (32%), Positives = 87/166 (52%), Gaps = 6/166 (3%)

Query: 2   QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAK 61
             KL +  S   +F + +++G+   G+ AD R LV +AR EA  +R  YG  +PV VLA 
Sbjct: 51  TSKLYEPGSNKRIFNVDRHIGIAVAGLLADGRHLVSRAREEAENYRDNYGTPIPVKVLAD 110

Query: 62  WIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAI 121
            +A     YT ++ +RP G   ++   D + GP+L+  +P+G  +G+   + G  +Q A 
Sbjct: 111 RVAMYMHAYTLYSSVRPFGCSVLLGGYDSD-GPQLYMIEPSGVSYGYFGCAIGKGKQAAK 169

Query: 122 NFLEKKMKNDPAFTFQETVQTAISTLQSVLQE--DFKASEIEVGVV 165
             LEK   ++   T +E V+ A   +  V  E  D KA E+E+  V
Sbjct: 170 TELEKLKFSE--LTCREAVKEAAKIIYIVHDEIKD-KAFELELSWV 212

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 212

>gnl|CDD|239722 cd03753, proteasome_alpha_type_5, proteasome_alpha_type_5

 Score = 93.6 bits (233), Expect = 6e-24
 Identities = 52/167 (31%), Positives = 89/167 (53%), Gaps = 8/167 (4%)

Query: 4   KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWI 63
            L++ +SV  +  I  ++G   +G+ ADARTL+  AR EA   RF Y   M V+ + + +
Sbjct: 50  PLMEPSSVEKIMEIDDHIGCAMSGLIADARTLIDHARVEAQNHRFTYNEPMTVESVTQAV 109

Query: 64  ADKSQVY-----TQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQ 118
           +D +  +      + A  RP GV  ++  +DE  GP+LF  DP+G F    A + G   +
Sbjct: 110 SDLALQFGEGDDGKKAMSRPFGVALLIAGVDEN-GPQLFHTDPSGTFTRCDAKAIGSGSE 168

Query: 119 EAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVV 165
            A + L++K   D   T +E  + A+S L+ V++E   ++ +E+  V
Sbjct: 169 GAQSSLQEKYHKD--MTLEEAEKLALSILKQVMEEKLNSTNVELATV 213

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 213

>gnl|CDD|239733 cd03764, proteasome_beta_archeal, Archeal proteasome, beta subunit

 Score = 59.2 bits (144), Expect = 3e-11
 Identities = 46/170 (27%), Positives = 77/170 (45%), Gaps = 10/170 (5%)

Query: 8   HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKS 67
             +V  +F I   + +   G   DA++LV+  + EA  +  + G  M +  LA  +   S
Sbjct: 28  SKNVKKIFQIDDKIAMTIAGSVGDAQSLVRILKAEARLYELRRGRPMSIKALATLL---S 84

Query: 68  QVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKK 127
            +     Y  P  V  ++  +DEE GP L+  DP G     K T+ G     A   LE +
Sbjct: 85  NILNSSKYF-PYIVQLLIGGVDEE-GPHLYSLDPLGSIIEDKYTATGSGSPYAYGVLEDE 142

Query: 128 MKNDPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVLS 176
            K D   T +E  + AI  ++S ++ D      I+V V++K+   ++ L 
Sbjct: 143 YKED--MTVEEAKKLAIRAIKSAIERDSASGDGIDVVVITKD--GYKELE 188

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme for non-lysosomal protein degradation in both the cytosol and the nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are both members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 188

>gnl|CDD|234287 TIGR03634, arc_protsome_B, proteasome endopeptidase complex, archaeal, beta subunit

 Score = 56.4 bits (137), Expect = 3e-10
 Identities = 43/163 (26%), Positives = 76/163 (46%), Gaps = 8/163 (4%)

Query: 8   HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKS 67
             +   +F I  Y+ +   G   DA++LV+  + EA  +  + G  M V  LA  +   S
Sbjct: 29  SKNAKKVFQIDDYIAMTIAGSVGDAQSLVRILKAEAKLYELRRGRPMSVKALATLL---S 85

Query: 68  QVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKK 127
            +   + +  P  V  +V  +DEE GP L+  DPAG       T+ G     A   LE +
Sbjct: 86  NILNSNRFF-PFIVQLLVGGVDEE-GPHLYSLDPAGGIIEDDYTATGSGSPVAYGVLEDE 143

Query: 128 MKNDPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKEN 169
            + D   + +E  + A+  ++S ++ D    + I+V V++K+ 
Sbjct: 144 YRED--MSVEEAKKLAVRAIKSAIERDVASGNGIDVAVITKDG 184

This protein family describes the archaeal proteasome beta subunit, homologous to both the alpha subunit and to the alpha and beta subunits of eukaryotic proteasome subunits. This family is universal in the first 29 complete archaeal genomes but occasionally is duplicated [Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 185

>gnl|CDD|238893 cd01912, proteasome_beta, proteasome beta subunit

 Score = 53.6 bits (130), Expect = 3e-09
 Identities = 26/133 (19%), Positives = 49/133 (36%), Gaps = 21/133 (15%)

Query: 14  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 73
           +F I+  + L   G  AD + L +  +     +  + G E+ V   A  +   S +   +
Sbjct: 34  IFKISDNILLGTAGSAADTQALTRLLKRNLRLYELRNGRELSVKAAANLL---SNILYSY 90

Query: 74  AYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAG-----------------LK 116
               P  V  +V  +D+  GP L+  DP G        + G                 + 
Sbjct: 91  RGF-PYYVSLIVGGVDKGGGPFLYYVDPLGSLIEAPFVATGSGSKYAYGILDRGYKPDMT 149

Query: 117 EQEAINFLEKKMK 129
            +EA+  ++K + 
Sbjct: 150 LEEAVELVKKAID 162

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 189

>gnl|CDD|239726 cd03757, proteasome_beta_type_1, proteasome beta type-1 subunit

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 26/127 (20%), Positives = 49/127 (38%), Gaps = 15/127 (11%)

Query: 14  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 73
           +F +T    L ++G  AD   L ++ +     +++ +  EM  + +A       Q+ +  
Sbjct: 42  IFKLTDKCVLGSSGFQADILALTKRLKARIKMYKYSHNKEMSTEAIA-------QLLSTI 94

Query: 74  AYMR---PLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLE----- 125
            Y R   P  V  ++  IDEE    ++  DP G +     ++ G         L+     
Sbjct: 95  LYSRRFFPYYVFNILAGIDEEGKGVVYSYDPVGSYERETYSAGGSASSLIQPLLDNQVGR 154

Query: 126 KKMKNDP 132
           K   N  
Sbjct: 155 KNQNNVE 161

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 212

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	191
cd03750	227	proteasome_alpha_type_2 proteasome_alpha_type_2. T	100.0
KOG0176	241	consensus 20S proteasome, regulatory subunit alpha	100.0
KOG0182	246	consensus 20S proteasome, regulatory subunit alpha	100.0
PRK03996	241	proteasome subunit alpha; Provisional	100.0
PTZ00246	253	proteasome subunit alpha; Provisional	100.0
COG0638	236	PRE1 20S proteasome, alpha and beta subunits [Post	100.0
KOG0181	233	consensus 20S proteasome, regulatory subunit alpha	100.0
TIGR03690	219	20S_bact_beta proteasome, beta subunit, bacterial	100.0
cd03758	193	proteasome_beta_type_2 proteasome beta type-2 subu	100.0
KOG0183	249	consensus 20S proteasome, regulatory subunit alpha	100.0
cd03760	197	proteasome_beta_type_4 proteasome beta type-4 subu	100.0
cd03754	215	proteasome_alpha_type_6 proteasome_alpha_type_6. T	100.0
TIGR03633	224	arc_protsome_A proteasome endopeptidase complex, a	100.0
PTZ00488	247	Proteasome subunit beta type-5; Provisional	100.0
cd03759	195	proteasome_beta_type_3 proteasome beta type-3 subu	100.0
cd03761	188	proteasome_beta_type_5 proteasome beta type-5 subu	100.0
cd03755	207	proteasome_alpha_type_7 proteasome_alpha_type_7. T	100.0
cd03749	211	proteasome_alpha_type_1 proteasome_alpha_type_1. T	100.0
cd03751	212	proteasome_alpha_type_3 proteasome_alpha_type_3. T	100.0
KOG0178	249	consensus 20S proteasome, regulatory subunit alpha	100.0
cd03752	213	proteasome_alpha_type_4 proteasome_alpha_type_4. T	100.0
KOG0863	264	consensus 20S proteasome, regulatory subunit alpha	100.0
TIGR03691	228	20S_bact_alpha proteasome, alpha subunit, bacteria	100.0
cd03756	211	proteasome_alpha_archeal proteasome_alpha_archeal.	100.0
cd03757	212	proteasome_beta_type_1 proteasome beta type-1 subu	100.0
TIGR03634	185	arc_protsome_B proteasome endopeptidase complex, a	100.0
cd03765	236	proteasome_beta_bacterial Bacterial proteasome, be	100.0
cd03764	188	proteasome_beta_archeal Archeal proteasome, beta s	100.0
cd03763	189	proteasome_beta_type_7 proteasome beta type-7 subu	100.0
cd03762	188	proteasome_beta_type_6 proteasome beta type-6 subu	100.0
cd01911	209	proteasome_alpha proteasome alpha subunit. The 20S	100.0
cd03753	213	proteasome_alpha_type_5 proteasome_alpha_type_5. T	100.0
PF00227	190	Proteasome: Proteasome subunit; InterPro: IPR00135	100.0
cd01912	189	proteasome_beta proteasome beta subunit. The 20S p	100.0
KOG0184	254	consensus 20S proteasome, regulatory subunit alpha	100.0
cd01906	182	proteasome_protease_HslV proteasome_protease_HslV.	100.0
KOG0175	285	consensus 20S proteasome, regulatory subunit beta	100.0
KOG0177	200	consensus 20S proteasome, regulatory subunit beta	100.0
KOG0179	235	consensus 20S proteasome, regulatory subunit beta	99.98
KOG0185	256	consensus 20S proteasome, regulatory subunit beta	99.96
KOG0174	224	consensus 20S proteasome, regulatory subunit beta	99.96
KOG0173	271	consensus 20S proteasome, regulatory subunit beta	99.95
KOG0180	204	consensus 20S proteasome, regulatory subunit beta	99.94
cd01901	164	Ntn_hydrolase The Ntn hydrolases (N-terminal nucle	99.94
PRK05456	172	ATP-dependent protease subunit HslV; Provisional	99.93
cd01913	171	protease_HslV Protease HslV and the ATPase/chapero	99.93
TIGR03692	171	ATP_dep_HslV ATP-dependent protease HslVU, peptida	99.92
COG5405	178	HslV ATP-dependent protease HslVU (ClpYQ), peptida	99.01
COG3484	255	Predicted proteasome-type protease [Posttranslatio	97.42
KOG3361	157	consensus Iron binding protein involved in Fe-S cl	87.39

>cd03750 proteasome_alpha_type_2 proteasome_alpha_type_2

Probab=100.00  E-value=2e-44  Score=286.16  Aligned_cols=179  Identities=35%  Similarity=0.583  Sum_probs=170.9

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      .++|+.+++.+||++|++|++|++||+.+|++.+.+++|.+++.|++++|++++++.++++|++.+|+|+++++.|||+|
T Consensus        48 ~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rP~~v  127 (227)
T cd03750          48 PSPLIDESSVHKVEQITPHIGMVYSGMGPDFRVLVKKARKIAQQYYLVYGEPIPVSQLVREIASVMQEYTQSGGVRPFGV  127 (227)
T ss_pred             CccccCCCCcceEEEEcCCEEEEEeEcHHhHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCCCCCChhe
Confidence            36788889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCCeEE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIE  161 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~~ie  161 (191)
                      ++||+|||+ .||+||.+||+|++.+++++|+|+|++.++++||++|+  ++||++||++++++||+.+.+|++...+++
T Consensus       128 ~~li~G~D~-~g~~Ly~~d~~G~~~~~~~~a~G~g~~~~~~~Le~~~~--~~ms~eeai~l~~~~l~~~~~~~l~~~~ie  204 (227)
T cd03750         128 SLLIAGWDE-GGPYLYQVDPSGSYFTWKATAIGKNYSNAKTFLEKRYN--EDLELEDAIHTAILTLKEGFEGQMTEKNIE  204 (227)
T ss_pred             EEEEEEEeC-CCCEEEEECCCCCEEeeeEEEECCCCHHHHHHHHhhcc--CCCCHHHHHHHHHHHHHHHhcccCCCCcEE
Confidence            999999997 68999999999999999999999999999999999984  789999999999999999999888777999


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHHH
Q 029560          162 VGVVSKENPEFRVLSIEEIDEHL  184 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~~  184 (191)
                      |+++++++ ++++++++||++++
T Consensus       205 v~iv~~~~-~~~~~~~~ei~~~~  226 (227)
T cd03750         205 IGICGETK-GFRLLTPAEIKDYL  226 (227)
T ss_pred             EEEEECCC-CEEECCHHHHHHHh
Confidence            99999874 49999999999986

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>KOG0176 consensus 20S proteasome, regulatory subunit alpha type PSMA5/PUP2 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=7.6e-45  Score=271.94  Aligned_cols=182  Identities=30%  Similarity=0.544  Sum_probs=172.1

Q ss_pred             CCCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhh-----cC
Q 029560            1 MQDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH-----AY   75 (191)
Q Consensus         1 ~~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~-----~~   75 (191)
                      +.|+|++++.++||++|++||+|++||+.+|++.+++++|.+|++|++.||++|+++.+++.++++..+|-..     ..
T Consensus        54 itSpLm~p~sveKi~eid~HIgca~SGl~aDarTlve~arv~~qnh~f~Y~e~i~VEs~tq~v~~LaLrFGe~~~~~~~m  133 (241)
T KOG0176|consen   54 ITSPLMEPSSVEKIVEIDDHIGCAMSGLIADARTLVERARVETQNHWFTYGEPISVESLTQAVSDLALRFGEGDDEEAIM  133 (241)
T ss_pred             ccCcccCchhhhhheehhhceeeeccccccchHHHHHHHHHHhhhceeecCCcccHHHHHHHHHHHHhHhCCCcchhhhh
Confidence            4799999999999999999999999999999999999999999999999999999999999999999877543     23


Q ss_pred             cccccceeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccC
Q 029560           76 MRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDF  155 (191)
Q Consensus        76 ~rP~~v~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~  155 (191)
                      .|||||++|+||+|+ .||+||..||+|++++|++.|||+|+..|...|++.|  .++|+++||+.+++..|+.+++..+
T Consensus       134 sRPFGValliAG~D~-~gpqL~h~dPSGtf~~~~AKAIGSgsEga~~~L~~e~--~~~ltL~ea~~~~L~iLkqVMeeKl  210 (241)
T KOG0176|consen  134 SRPFGVALLIAGHDE-TGPQLYHLDPSGTFIRYKAKAIGSGSEGAESSLQEEY--HKDLTLKEAEKIVLKILKQVMEEKL  210 (241)
T ss_pred             cCCcceEEEEeeccC-CCceEEEeCCCCceEEecceeccccchHHHHHHHHHH--hhcccHHHHHHHHHHHHHHHHHHhc
Confidence            599999999999997 8999999999999999999999999999999999998  4889999999999999999999999


Q ss_pred             CCCeEEEEEEEeCCCcEEEcCHHHHHHHHHH
Q 029560          156 KASEIEVGVVSKENPEFRVLSIEEIDEHLTA  186 (191)
Q Consensus       156 ~~~~iei~iv~~~~~~~~~~~~~~i~~~~~~  186 (191)
                      ++.|+++++|++++ +|+.++++|++.++.+
T Consensus       211 ~~~Nvev~~vt~e~-~f~~~t~EE~~~~i~~  240 (241)
T KOG0176|consen  211 NSNNVEVAVVTPEG-EFHIYTPEEVEQVIKR  240 (241)
T ss_pred             CccceEEEEEcccC-ceEecCHHHHHHHHhc
Confidence            99999999999987 4999999999998865

>KOG0182 consensus 20S proteasome, regulatory subunit alpha type PSMA6/SCL1 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.3e-43  Score=266.46  Aligned_cols=190  Identities=67%  Similarity=1.008  Sum_probs=186.1

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      |.||++++++..+|+|..+|+|+++|+.+|++..+.++|.++.++++.||.+||++.|+++++++.|.|||+..+||+||
T Consensus        57 pDKLld~~tvt~~f~itk~ig~v~tG~~aDar~~v~rar~eAa~~~yk~Gyemp~DiL~k~~Ad~~QvytQ~a~mRplg~  136 (246)
T KOG0182|consen   57 PDKLLDSSTVTHLFRITKKIGCVITGMIADARSQVQRARYEAAEFRYKYGYEMPCDILAKRMADKSQVYTQNAAMRPLGV  136 (246)
T ss_pred             cccccccccceeEEEeeccceEEEecCCcchHHHHHHHHHHHHhhhhhcCCCCCHHHHHHHHhhHHHHHhhhhhhcccce
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCCeEE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIE  161 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~~ie  161 (191)
                      .+++.|+|++.||.+|.+||.|-+..++++|.|...+.+..+||++++++.++|.+|++++++.||..++..|..+..+|
T Consensus       137 ~~~~i~~D~E~gP~vYk~DpAGyy~g~kAtaaG~Kq~e~tsfLEKk~Kk~~~~t~~e~ve~ai~al~~sl~~Dfk~se~E  216 (246)
T KOG0182|consen  137 AATLIGVDEERGPSVYKTDPAGYYYGFKATAAGVKQQEATSFLEKKYKKDIDLTFEETVETAISALQSSLGIDFKSSELE  216 (246)
T ss_pred             eEEEEEeccccCcceEeecCccccccceeeecccchhhHHHHHHHhhccCccchHHHHHHHHHHHHHHHHhcccCCcceE
Confidence            99999999999999999999999999999999999999999999999877779999999999999999999999999999


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHHHHHhhccC
Q 029560          162 VGVVSKENPEFRVLSIEEIDEHLTAISERD  191 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~~~~~~~~~  191 (191)
                      |+++++++++|++|+.+||+++|..|+|||
T Consensus       217 Vgvv~~~~p~f~~Ls~~eie~hL~~IAEkd  246 (246)
T KOG0182|consen  217 VGVVTVDNPEFRILSAEEIEEHLQAIAEKD  246 (246)
T ss_pred             EEEEEcCCcceeeccHHHHHHHHHHhhhcC
Confidence            999999999999999999999999999998

>PRK03996 proteasome subunit alpha; Provisional

Probab=100.00  E-value=9.9e-43  Score=278.78  Aligned_cols=182  Identities=34%  Similarity=0.623  Sum_probs=172.6

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      +.++.+++.+||++|++|++|++||+.+|++.+.++++.++..|++.++++++++.+++++++.+|.|+++++.|||+|+
T Consensus        58 ~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~~~~~~~rP~~~~  137 (241)
T PRK03996         58 SPLIEPSSIEKIFKIDDHIGAASAGLVADARVLIDRARVEAQINRLTYGEPIGVETLTKKICDHKQQYTQHGGVRPFGVA  137 (241)
T ss_pred             CcccCCCccceEEEEcCCEEEEEcccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhcCCCCccchheE
Confidence            56777889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCCeEEE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEV  162 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~~iei  162 (191)
                      +||||||. .||+||.+||+|++.+++++|+|+|+..++++||+.|  +++|+++||++++++||..+.+++....+++|
T Consensus       138 ~ilaG~d~-~gp~Ly~id~~G~~~~~~~~a~G~g~~~~~~~Le~~~--~~~~s~eeai~l~~~al~~~~~~~~~~~~i~i  214 (241)
T PRK03996        138 LLIAGVDD-GGPRLFETDPSGAYLEYKATAIGAGRDTVMEFLEKNY--KEDLSLEEAIELALKALAKANEGKLDPENVEI  214 (241)
T ss_pred             EEEEEEeC-CcCEEEEECCCCCeecceEEEECCCcHHHHHHHHHhc--ccCCCHHHHHHHHHHHHHHHhccCCCCCcEEE
Confidence            99999997 6899999999999999999999999999999999998  48899999999999999999887655558999


Q ss_pred             EEEEeCCCcEEEcCHHHHHHHHHHh
Q 029560          163 GVVSKENPEFRVLSIEEIDEHLTAI  187 (191)
Q Consensus       163 ~iv~~~~~~~~~~~~~~i~~~~~~~  187 (191)
                      +++++++++|+.++++||++++.++
T Consensus       215 ~ii~~~~~~~~~~~~~ei~~~~~~~  239 (241)
T PRK03996        215 AYIDVETKKFRKLSVEEIEKYLEKL  239 (241)
T ss_pred             EEEECCCCcEEECCHHHHHHHHHHh
Confidence            9999998789999999999999875

>PTZ00246 proteasome subunit alpha; Provisional

Probab=100.00  E-value=1.2e-42  Score=280.06  Aligned_cols=184  Identities=33%  Similarity=0.510  Sum_probs=172.0

Q ss_pred             CccccC-CCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            3 DKLLDH-TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         3 s~l~~~-~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      ++++.+ ++++|||+|++|++|+++|+.+|++.+.+.+|.++..|++.++++++++.+++.++..+|.|+|++++|||+|
T Consensus        53 ~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~v~~l~~~l~~~~q~~~~~~~~rP~~v  132 (253)
T PTZ00246         53 SKLLDPGKINEKIYKIDSHIFCAVAGLTADANILINQCRLYAQRYRYTYGEPQPVEQLVVQICDLKQSYTQFGGLRPFGV  132 (253)
T ss_pred             CcCccCCCCcccEEEecCCEEEEEEEcHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccccCcccCCE
Confidence            445554 4689999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EI  160 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~i  160 (191)
                      ++||+|||+++||+||.+||+|++.+++++|+|+|++.++++||++|  +++||++||++++++||+.+.++|..++ ++
T Consensus       133 ~~li~G~D~~~gp~Ly~~D~~Gs~~~~~~~a~G~gs~~~~~~Le~~~--~~~ms~eeai~l~~~al~~~~~~d~~s~~~v  210 (253)
T PTZ00246        133 SFLFAGYDENLGYQLYHTDPSGNYSGWKATAIGQNNQTAQSILKQEW--KEDLTLEQGLLLAAKVLTKSMDSTSPKADKI  210 (253)
T ss_pred             EEEEEEEeCCCCcEEEEECCCCCEecceEEEECCCcHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHHhccCCCCCcE
Confidence            99999999757899999999999999999999999999999999998  4799999999999999999999987765 89


Q ss_pred             EEEEEEeCC----CcEEEcCHHHHHHHHHHhh
Q 029560          161 EVGVVSKEN----PEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       161 ei~iv~~~~----~~~~~~~~~~i~~~~~~~~  188 (191)
                      +|+++++++    +.|+.++++||++++.++.
T Consensus       211 ev~ii~~~~~~~~~~~~~l~~~ei~~~l~~~~  242 (253)
T PTZ00246        211 EVGILSHGETDGEPIQKMLSEKEIAELLKKVT  242 (253)
T ss_pred             EEEEEecCCcCCCCCeEECCHHHHHHHHHHHh
Confidence            999999874    3599999999999999886

>COG0638 PRE1 20S proteasome, alpha and beta subunits [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=8.6e-43  Score=277.78  Aligned_cols=180  Identities=37%  Similarity=0.620  Sum_probs=169.5

Q ss_pred             cccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeE
Q 029560            5 LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAM   84 (191)
Q Consensus         5 l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~i   84 (191)
                      ++.+++++|||+|+|||+|++||+.+|++.+++++|.+++.|++.++++|+++.+++.+++++|.|+++  .|||+|++|
T Consensus        55 ~~~~~~~~Ki~~I~d~i~~~~sG~~aDa~~lv~~~r~~a~~~~~~~~~~i~v~~la~~ls~~l~~~~~~--~rP~gv~~i  132 (236)
T COG0638          55 LIASSNVEKIFKIDDHIGMAIAGLAADAQVLVRYARAEAQLYRLRYGEPISVEALAKLLSNILQEYTQS--GRPYGVSLL  132 (236)
T ss_pred             eecccccceEEEecCCEEEEeccCcHhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhccC--cccceEEEE
Confidence            455567999999999999999999999999999999999999999999999999999999999999987  899999999


Q ss_pred             EEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEEE
Q 029560           85 VLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVG  163 (191)
Q Consensus        85 v~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei~  163 (191)
                      |||+|+ ++|+||++||+|++.+++++|+|+|++.++++||+.|  +++|++|||++++++||+.+.+||..++ +++|+
T Consensus       133 iaG~d~-~~p~Ly~~Dp~G~~~~~~~~a~Gsgs~~a~~~Le~~y--~~~m~~eeai~la~~al~~a~~rd~~s~~~~~v~  209 (236)
T COG0638         133 VAGVDD-GGPRLYSTDPSGSYNEYKATAIGSGSQFAYGFLEKEY--REDLSLEEAIELAVKALRAAIERDAASGGGIEVA  209 (236)
T ss_pred             EEEEcC-CCCeEEEECCCCceeecCEEEEcCCcHHHHHHHHhhc--cCCCCHHHHHHHHHHHHHHHHhccccCCCCeEEE
Confidence            999998 8999999999999999999999999999999999998  5889999999999999999999999665 88999


Q ss_pred             EEEeCCCcEEEcCHHHHHHHHHHhhcc
Q 029560          164 VVSKENPEFRVLSIEEIDEHLTAISER  190 (191)
Q Consensus       164 iv~~~~~~~~~~~~~~i~~~~~~~~~~  190 (191)
                      ++++++ +++.++++++..++..+..+
T Consensus       210 vi~~~~-~~~~~~~~~~~~~~~~~~~~  235 (236)
T COG0638         210 VITKDE-GFRKLDGEEIKKLLDDLSEK  235 (236)
T ss_pred             EEEcCC-CeEEcCHHHHHHHHHHHhhc
Confidence            999974 49999999999999887654

>KOG0181 consensus 20S proteasome, regulatory subunit alpha type PSMA2/PRE8 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.4e-43  Score=263.30  Aligned_cols=181  Identities=34%  Similarity=0.557  Sum_probs=173.6

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      .|.|++...++|++.|.+||+|.+||+.+|++.+++..|+.++.|...|++++|+..|++.++..+|+|||+++.|||||
T Consensus        53 ~s~L~~~~sv~KV~~i~~~IG~vYSGmgpD~RvlV~~~rkiAe~Yy~vY~e~~pt~qlv~~~asvmQEyTqsgGvrPFGv  132 (233)
T KOG0181|consen   53 VSPLVDEESVRKVEKITPHIGCVYSGMGPDYRVLVHKSRKIAEQYYRVYGEPIPTTQLVQEVASVMQEYTQSGGVRPFGV  132 (233)
T ss_pred             CCccchhhhhhhHhhccCCcceEEecCCCceeehhhHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHhhcCCccccce
Confidence            47788899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCCeEE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIE  161 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~~ie  161 (191)
                      +++|||||+ ++|.||++||+|+++.|+++|+|.+...++++||++|  .++|.+++++..|+.+|++..+..+++.++|
T Consensus       133 slliaG~~~-~~p~LyQvdPSGsyf~wkatA~Gkn~v~aktFlEkR~--~edleldd~ihtailtlkE~fege~~~~nie  209 (233)
T KOG0181|consen  133 SLLIAGWDE-GGPLLYQVDPSGSYFAWKATAMGKNYVNAKTFLEKRY--NEDLELDDAIHTAILTLKESFEGEMTAKNIE  209 (233)
T ss_pred             EEEEeecCC-CceeEEEECCccceeehhhhhhccCcchHHHHHHHHh--ccccccchHHHHHHHHHHHHhccccccCceE
Confidence            999999998 7999999999999999999999999999999999998  5889999999999999999999999999999


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHHHHHh
Q 029560          162 VGVVSKENPEFRVLSIEEIDEHLTAI  187 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~~~~~  187 (191)
                      |+++...  +|+.+++.||+.++..+
T Consensus       210 igv~~~~--~F~~lt~~eI~d~l~~l  233 (233)
T KOG0181|consen  210 IGVCGEN--GFRRLTPAEIEDYLASL  233 (233)
T ss_pred             EEEecCC--ceeecCHHHHHHHHhcC
Confidence            9999955  49999999999998753

>TIGR03690 20S_bact_beta proteasome, beta subunit, bacterial type

Probab=100.00  E-value=5.1e-42  Score=270.98  Aligned_cols=182  Identities=21%  Similarity=0.263  Sum_probs=167.1

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      ++++.+++++|||+|++|++|+++|+.+|++.+.+++|.+++.|+++++++++++.++++|++++|.++ ...+|||+|+
T Consensus        25 g~~~~~~~~~KI~~i~~~i~~~~sG~~aD~~~l~~~~r~~~~~~~~~~~~~i~~~~la~~ls~~~~~~~-~~~~rp~~v~  103 (219)
T TIGR03690        25 GNMIASRDVEKVYPTDEYSAVGIAGTAGLAIELVRLFQVELEHYEKIEGVPLTLDGKANRLAAMVRGNL-PAAMQGLAVV  103 (219)
T ss_pred             CcEEEcCCcceEEEcCCcEEEEecccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhhh-hhccCCceEE
Confidence            378888999999999999999999999999999999999999999999999999999999999998877 4558999999


Q ss_pred             eEEEEEcCC-CCCeEEEECCCcc-eeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCCe-
Q 029560           83 AMVLSIDEE-CGPRLFKCDPAGH-FFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASE-  159 (191)
Q Consensus        83 ~iv~G~d~~-~~p~Ly~~d~~G~-~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~~-  159 (191)
                      +||||||++ ++|+||.+||+|+ +..++++|+|+|++.++++||++|  +++||.+||++++++||..+.+||..+++ 
T Consensus       104 ~iiaG~D~~~~~~~Ly~~Dp~G~~~~~~~~~a~G~g~~~a~~~Le~~~--~~~ms~eeai~l~~~al~~~~~~d~~s~~~  181 (219)
T TIGR03690       104 PLLAGYDLDAGAGRIFSYDVTGGRYEERGYHAVGSGSVFAKGALKKLY--SPDLDEDDALRVAVEALYDAADDDSATGGP  181 (219)
T ss_pred             EEEEEECCCCCCcEEEEEeCCCCeeecCCeEEEeccHHHHHHHHHhcC--CCCcCHHHHHHHHHHHHHHHHhcccccCCc
Confidence            999999964 6799999999995 767789999999999999999998  48999999999999999999999986542 


Q ss_pred             -------EEEEEEEeCCCcEEEcCHHHHHHHHHHhhc
Q 029560          160 -------IEVGVVSKENPEFRVLSIEEIDEHLTAISE  189 (191)
Q Consensus       160 -------iei~iv~~~~~~~~~~~~~~i~~~~~~~~~  189 (191)
                             ++|+++++++  |+.++++||++++.++.+
T Consensus       182 ~~~~~~~~ei~ii~~~g--~~~l~~~ei~~~~~~~~~  216 (219)
T TIGR03690       182 DLVRGIYPTVVVITADG--ARRVPESELEELARAIVE  216 (219)
T ss_pred             ccccccccEEEEEccCc--eEEcCHHHHHHHHHHHHh
Confidence                   3999998664  999999999999998874

Members of this family are the beta subunit of the 20S proteasome as found in Actinobacteria such as Mycobacterium, Rhodococcus, and Streptomyces. In Streptomyces, maturation during proteasome assembly was shown to remove a 53-amino acid propeptide. Most of the length of the propeptide is not included in this model.

>cd03758 proteasome_beta_type_2 proteasome beta type-2 subunit

Probab=100.00  E-value=4.3e-42  Score=266.61  Aligned_cols=166  Identities=16%  Similarity=0.255  Sum_probs=155.7

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      +.++.+++++|||+|++|++|++||+.+|++.|.+++|.+++.|++.++++++++.+++++++.+|.|++.+  |||+++
T Consensus        24 ~~~~~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~l~~~~~~~~~~~--rP~~~~  101 (193)
T cd03758          24 SILVLKDDEDKIYKLSDHKLMACSGEAGDRLQFAEYIQKNIQLYKMRNGYELSPKAAANFTRRELAESLRSR--TPYQVN  101 (193)
T ss_pred             CcEEEecCcccEEEeCCCeEEEEccchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcC--CCeEEE
Confidence            456888999999999999999999999999999999999999999999999999999999999999886543  899999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIE  161 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~ie  161 (191)
                      +||+|||++++|+||.+||+|++.+++++|+|+|++.++++||+.|+  ++||.|||++++++||+.+.+||..++ +++
T Consensus       102 ~li~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~--~~ms~eeai~l~~~a~~~~~~rd~~~~~~i~  179 (193)
T cd03758         102 LLLAGYDKVEGPSLYYIDYLGTLVKVPYAAHGYGAYFCLSILDRYYK--PDMTVEEALELMKKCIKELKKRFIINLPNFT  179 (193)
T ss_pred             EEEEEEcCCCCcEEEEECCCcceEECCeeEEeecHHHHHHHHHhccC--CCCCHHHHHHHHHHHHHHHHHhccccCCceE
Confidence            99999997678999999999999999999999999999999999984  899999999999999999999998776 899


Q ss_pred             EEEEEeCCCcEEE
Q 029560          162 VGVVSKENPEFRV  174 (191)
Q Consensus       162 i~iv~~~~~~~~~  174 (191)
                      |++|+++|  ++.
T Consensus       180 i~ii~~~g--~~~  190 (193)
T cd03758         180 VKVVDKDG--IRD  190 (193)
T ss_pred             EEEEcCCC--eEe
Confidence            99999886  554

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis.Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>KOG0183 consensus 20S proteasome, regulatory subunit alpha type PSMA7/PRE6 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=5.8e-43  Score=264.72  Aligned_cols=184  Identities=32%  Similarity=0.481  Sum_probs=173.9

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      -.+|++.+++.||..+++|++|+++|+.+|++.+++++|.+|+.|+++.+.|+++++++++|+.+.|.|||..+.||||+
T Consensus        51 v~~Lq~~r~~rkI~~ld~hV~mafaGl~aDArilinrArvecqShrlt~edpvtveyitRyiA~~kQrYTqs~grRPFGv  130 (249)
T KOG0183|consen   51 VPKLQDERTVRKISMLDDHVVMAFAGLTADARILINRARVECQSHRLTLEDPVTVEYITRYIAGLKQRYTQSNGRRPFGV  130 (249)
T ss_pred             hhhhhhhhhhhhheeecceeeEEecCCCccceeehhhHhHhhhhhhcccCCCcHHHHHHHHHHHhhhhhhccCCcccccc
Confidence            35899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCCeEE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIE  161 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~~ie  161 (191)
                      +.||+|||+.+.|+||++||+|.+.+|++.|+|.+++.++.+||+.|.+.+-.|..++++|++++|.++..  ....++|
T Consensus       131 s~Li~GfD~~g~p~lyqtePsG~f~ewka~aiGr~sk~VrEflEK~y~e~~~~~~~~~ikL~ir~LleVvq--s~~~nie  208 (249)
T KOG0183|consen  131 STLIGGFDPDGTPRLYQTEPSGIFSEWKANAIGRSSKTVREFLEKNYKEEAIATEGETIKLAIRALLEVVQ--SGGKNIE  208 (249)
T ss_pred             eEEEEeeCCCCCeeeEeeCCCcchhhhhccccccccHHHHHHHHHhcccccccccccHHHHHHHHHHHHhh--cCCCeeE
Confidence            99999999988899999999999999999999999999999999999766678999999999999999974  3455999


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHHHHHhh
Q 029560          162 VGVVSKENPEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~~~~~~  188 (191)
                      ++++...++ ++.++.++|+.++..++
T Consensus       209 ~aVm~~~~~-~~~l~~~~I~~~v~~ie  234 (249)
T KOG0183|consen  209 VAVMKRRKD-LKMLESEEIDDIVKEIE  234 (249)
T ss_pred             EEEEecCCc-eeecCHHHHHHHHHHHH
Confidence            999999875 99999999999998775

>cd03760 proteasome_beta_type_4 proteasome beta type-4 subunit

Probab=100.00  E-value=1.9e-41  Score=263.82  Aligned_cols=169  Identities=19%  Similarity=0.231  Sum_probs=156.0

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHH-HHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAA-EFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~-~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      ++++.+++++|||+|++|++|+++|+.+|++.+.+++|.+++ .|++.++.+++++.++++|++++  |++++++|||+|
T Consensus        25 ~~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~~la~~i~~~~--y~~~~~~rP~~v  102 (197)
T cd03760          25 GSLARFKNVERIFKVGDNTLLGASGDYADFQYLKRLLDQLVIDDECLDDGHSLSPKEIHSYLTRVL--YNRRSKMNPLWN  102 (197)
T ss_pred             cceeecCCCCcEEEecCcEEEEeCcchHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH--HHHhhcCCCceE
Confidence            578888999999999999999999999999999999999987 57788999999999999999986  899989999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EI  160 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~i  160 (191)
                      ++||||||++++|+||.+||+|++.+++++|+|+|+..++++||+.|++.++||.+||++++++||+.+.+||..++ ++
T Consensus       103 ~~iiaG~D~~~gp~Ly~~D~~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~~~ms~eea~~l~~~~l~~~~~rd~~~~~~~  182 (197)
T cd03760         103 TLVVGGVDNEGEPFLGYVDLLGTAYEDPHVATGFGAYLALPLLREAWEKKPDLTEEEARALIEECMKVLYYRDARSINKY  182 (197)
T ss_pred             EEEEEEEcCCCCEEEEEEcCCccEEECCEeEEccHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHHHHHHhccccCCce
Confidence            99999999767899999999999999999999999999999999999533389999999999999999999997665 89


Q ss_pred             EEEEEEeCCCcEEEc
Q 029560          161 EVGVVSKENPEFRVL  175 (191)
Q Consensus       161 ei~iv~~~~~~~~~~  175 (191)
                      +|++|+++|  +++-
T Consensus       183 ~i~ii~~~g--~~~~  195 (197)
T cd03760         183 QIAVVTKEG--VEIE  195 (197)
T ss_pred             EEEEECCCC--EEeC
Confidence            999999986  5543

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis.Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>cd03754 proteasome_alpha_type_6 proteasome_alpha_type_6

Probab=100.00  E-value=4.4e-41  Score=264.93  Aligned_cols=164  Identities=68%  Similarity=1.057  Sum_probs=154.4

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      +++++.+++.+|||+|++|++|++||+.+|++.+.+++|.++..|+++++++|+++.+++.+++++|.|+++++.|||+|
T Consensus        50 ~~~~i~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~i~v~~la~~ls~~~q~yt~~~~~RP~~v  129 (215)
T cd03754          50 PDKLIDPSTVTHLFRITDEIGCVMTGMIADSRSQVQRARYEAAEFKYKYGYEMPVDVLAKRIADINQVYTQHAYMRPLGV  129 (215)
T ss_pred             cccccCCcccCceEEEcCCEEEEEEechhhHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhCCCCCcCCee
Confidence            35677777899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCC--CHHHHHHHHHHHHHhhhcccCCCCe
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAF--TFQETVQTAISTLQSVLQEDFKASE  159 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~--s~eea~~l~~~~l~~~~~~d~~~~~  159 (191)
                      ++||||||+++||+||.+||+|++.+++++|+|+|++.++++||++|+...+|  |.|||++++++||..+.+||....+
T Consensus       130 ~~ii~G~D~~~gp~Ly~~Dp~Gs~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~~~s~eeai~l~~~al~~~~~rd~~~~~  209 (215)
T cd03754         130 SMILIGIDEELGPQLYKCDPAGYFAGYKATAAGVKEQEATNFLEKKLKKKPDLIESYEETVELAISCLQTVLSTDFKATE  209 (215)
T ss_pred             EEEEEEEeCCCCeEEEEEcCCccEEeEEEEEECCCcHHHHHHHHHHhccccccCCCHHHHHHHHHHHHHHHhcccCCCCc
Confidence            99999999767999999999999999999999999999999999999644468  9999999999999999999988669


Q ss_pred             EEEEEE
Q 029560          160 IEVGVV  165 (191)
Q Consensus       160 iei~iv  165 (191)
                      +||+||
T Consensus       210 ~ei~~~  215 (215)
T cd03754         210 IEVGVV  215 (215)
T ss_pred             EEEEEC
Confidence            999985

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>TIGR03633 arc_protsome_A proteasome endopeptidase complex, archaeal, alpha subunit

Probab=100.00  E-value=7.1e-41  Score=265.36  Aligned_cols=173  Identities=38%  Similarity=0.640  Sum_probs=163.3

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      +.++.+++.+||++|+++++|++||+.+|++.+.+.++.++..|++.++++++++.++++|++.+|.|+++++.|||+|+
T Consensus        51 ~~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~ls~~l~~~~~~~~~rP~~v~  130 (224)
T TIGR03633        51 SKLVEPSSIEKIFKIDDHIGAATSGLVADARVLIDRARIEAQINRLTYGEPIDVETLAKKICDLKQQYTQHGGVRPFGVA  130 (224)
T ss_pred             ccccCCCccceEEEECCCEEEEEeecHHhHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCCCccccceE
Confidence            56777789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIE  161 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~ie  161 (191)
                      +||+|||+ ++|+||.+||.|++.+++++|+|+|+..++++|++.|  +++|+.+||++++++||..+.+ |..++ +++
T Consensus       131 ~ll~G~d~-~~~~Ly~~D~~G~~~~~~~~a~G~g~~~~~~~L~~~~--~~~~~~eeai~l~~~al~~~~~-d~~~~~~i~  206 (224)
T TIGR03633       131 LLIAGVDD-GGPRLFETDPSGALLEYKATAIGAGRQAVTEFLEKEY--REDLSLDEAIELALKALYSAVE-DKLTPENVE  206 (224)
T ss_pred             EEEEEEeC-CcCEEEEECCCCCeecceEEEECCCCHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHhc-ccCCCCcEE
Confidence            99999996 7899999999999999999999999999999999998  4889999999999999999997 65554 899


Q ss_pred             EEEEEeCCCcEEEcCHHH
Q 029560          162 VGVVSKENPEFRVLSIEE  179 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~  179 (191)
                      |++|+++|+.|+.++++|
T Consensus       207 i~ii~~~g~~~~~~~~~~  224 (224)
T TIGR03633       207 VAYITVEDKKFRKLSVEE  224 (224)
T ss_pred             EEEEEcCCCcEEECCCCC
Confidence            999999987799998875

This protein family describes the archaeal proteasome alpha subunit, homologous to both the beta subunit and to the alpha and beta subunits of eukaryotic proteasome subunits. This family is universal in the first 29 complete archaeal genomes but occasionally is duplicated.

>PTZ00488 Proteasome subunit beta type-5; Provisional

Probab=100.00  E-value=1.6e-40  Score=266.19  Aligned_cols=175  Identities=18%  Similarity=0.205  Sum_probs=163.3

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc-
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV-   81 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v-   81 (191)
                      +.++.+++++|||+|++|++|++||+.+|++.+.+++|.+++.|+++++++|+++.++++|+++++.+      |||++ 
T Consensus        62 g~li~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~lr~~~~~y~~~~g~~isv~~la~~ls~~l~~~------R~~~~~  135 (247)
T PTZ00488         62 GPYIASQSVKKVIEINPTLLGTMAGGAADCSFWERELAMQCRLYELRNGELISVAAASKILANIVWNY------KGMGLS  135 (247)
T ss_pred             CCEEEcCCcCceEEcCCCEEEEeCcCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhc------CCCCee
Confidence            47888899999999999999999999999999999999999999999999999999999999998644      55554 


Q ss_pred             -eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-e
Q 029560           82 -VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-E  159 (191)
Q Consensus        82 -~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~  159 (191)
                       ++||||||+ .||+||++||+|++.+++++|+|+|+..++++||+.|+  ++||.+||++++++||+.+.+||..++ +
T Consensus       136 v~~iiaG~D~-~gp~Ly~vDp~Gs~~~~~~~a~G~gs~~~~~~Le~~~k--~dms~eEai~l~~kal~~~~~Rd~~sg~~  212 (247)
T PTZ00488        136 MGTMICGWDK-KGPGLFYVDNDGTRLHGNMFSCGSGSTYAYGVLDAGFK--WDLNDEEAQDLGRRAIYHATFRDAYSGGA  212 (247)
T ss_pred             EEEEEEEEeC-CCCEEEEEcCCcceeecCCEEEccCHHHHHHHHHhcCc--CCCCHHHHHHHHHHHHHHHHHhccccCCC
Confidence             589999996 68999999999999999999999999999999999984  789999999999999999999998775 8


Q ss_pred             EEEEEEEeCCCcEEEcCHHHHHHHHHHhh
Q 029560          160 IEVGVVSKENPEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       160 iei~iv~~~~~~~~~~~~~~i~~~~~~~~  188 (191)
                      ++|++|+++|  ++.++++||++++.++.
T Consensus       213 ~ei~iI~k~g--~~~l~~~ei~~~l~~~~  239 (247)
T PTZ00488        213 INLYHMQKDG--WKKISADDCFDLHQKYA  239 (247)
T ss_pred             eEEEEEcCCc--cEECCHHHHHHHHHHHh
Confidence            9999999875  99999999999999886

>cd03759 proteasome_beta_type_3 proteasome beta type-3 subunit

Probab=100.00  E-value=1.3e-40  Score=258.73  Aligned_cols=166  Identities=19%  Similarity=0.241  Sum_probs=151.5

Q ss_pred             Ccccc-CCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            3 DKLLD-HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         3 s~l~~-~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      ++++. +++++|||+|++|++|++||..+|++.+.+++|.+++.|+++++++++++.++++|++++  |+++  .+||+|
T Consensus        25 ~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~l--y~~r--~~P~~v  100 (195)
T cd03759          25 VQQQTVSTDFQKVFRIGDRLYIGLAGLATDVQTLAQKLRFRVNLYRLREEREIKPKTFSSLISSLL--YEKR--FGPYFV  100 (195)
T ss_pred             cCCEeEecCCCeEEEeCCCEEEEccchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHH--HHhc--CCCceE
Confidence            45555 457899999999999999999999999999999999999999999999999999999998  6653  589999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceecee-eeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-e
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHK-ATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-E  159 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~-~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~  159 (191)
                      ++||||||++++|+||.+||+|++..++ ++|+|+|++.++++||+.|  +++||.+||++++++||+.+.+||..++ +
T Consensus       101 ~~ii~G~D~~~~p~Ly~~D~~G~~~~~~~~~a~G~g~~~~~~~Le~~~--~~~~s~~ea~~l~~~~l~~~~~rd~~~~~~  178 (195)
T cd03759         101 EPVVAGLDPDGKPFICTMDLIGCPSIPSDFVVSGTASEQLYGMCESLW--RPDMEPDELFETISQALLSAVDRDALSGWG  178 (195)
T ss_pred             EEEEEEEcCCCCEEEEEEcCCCcccccCCEEEEcccHHHHHHHHHhcc--CCCCCHHHHHHHHHHHHHHHHhhCcccCCc
Confidence            9999999976789999999999998887 9999999999999999998  4789999999999999999999998775 8


Q ss_pred             EEEEEEEeCCCcEEE
Q 029560          160 IEVGVVSKENPEFRV  174 (191)
Q Consensus       160 iei~iv~~~~~~~~~  174 (191)
                      ++|++|+++|...+.
T Consensus       179 ~~i~ii~~~g~~~~~  193 (195)
T cd03759         179 AVVYIITKDKVTTRT  193 (195)
T ss_pred             eEEEEEcCCcEEEEe
Confidence            999999998754443

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>cd03761 proteasome_beta_type_5 proteasome beta type-5 subunit

Probab=100.00  E-value=1.6e-40  Score=256.77  Aligned_cols=163  Identities=17%  Similarity=0.231  Sum_probs=153.1

Q ss_pred             ccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccccee
Q 029560            4 KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVA   83 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~   83 (191)
                      .++.+++.+|||+|++|++|+++|+.+|++.|.+++|.+++.|++.++++++++.+++++++++|.|++    .||+|++
T Consensus        24 ~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i~~~~la~~ls~~l~~~~~----~~~~v~~   99 (188)
T cd03761          24 SYIASQTVKKVIEINPYLLGTMAGGAADCQYWERVLGRECRLYELRNKERISVAAASKLLSNMLYQYKG----MGLSMGT   99 (188)
T ss_pred             cEEEcCCcceEEEccCcEEEEeCccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhcCC----CCeEEEE
Confidence            577788999999999999999999999999999999999999999999999999999999999987743    5899999


Q ss_pred             EEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEE
Q 029560           84 MVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEV  162 (191)
Q Consensus        84 iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei  162 (191)
                      ||||||+ .||+||++||+|++.+++++|+|+|++.++++||++|  +++||.+||++++++||+.+.+||..++ +++|
T Consensus       100 li~G~D~-~g~~L~~~dp~G~~~~~~~~a~G~g~~~~~~~Le~~~--~~~~s~eea~~l~~~~l~~~~~rd~~sg~~~~v  176 (188)
T cd03761         100 MICGWDK-TGPGLYYVDSDGTRLKGDLFSVGSGSTYAYGVLDSGY--RYDLSVEEAYDLARRAIYHATHRDAYSGGNVNL  176 (188)
T ss_pred             EEEEEeC-CCCEEEEEcCCceEEEcCeEEEcccHHHHHHHHHhcC--CCCCCHHHHHHHHHHHHHHHHHhcccCCCCeEE
Confidence            9999996 7899999999999999999999999999999999998  4899999999999999999999998776 8999


Q ss_pred             EEEEeCCCcEEEc
Q 029560          163 GVVSKENPEFRVL  175 (191)
Q Consensus       163 ~iv~~~~~~~~~~  175 (191)
                      ++|+++|  ++++
T Consensus       177 ~ii~~~g--~~~~  187 (188)
T cd03761         177 YHVREDG--WRKI  187 (188)
T ss_pred             EEEcCCc--eEEc
Confidence            9999886  5654

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>cd03755 proteasome_alpha_type_7 proteasome_alpha_type_7

Probab=100.00  E-value=2.4e-40  Score=259.40  Aligned_cols=159  Identities=31%  Similarity=0.522  Sum_probs=150.6

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      ++++.+++.+||++|++|++|++||+.+|++.+.+++|.+++.|++.++++|+++.++++|++++|+|+++++.|||+|+
T Consensus        49 ~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~i~~~~la~~ls~~~~~y~~~~~~rP~~vs  128 (207)
T cd03755          49 AKLQDPRTVRKICMLDDHVCLAFAGLTADARVLINRARLECQSHRLTVEDPVTVEYITRYIAGLQQRYTQSGGVRPFGIS  128 (207)
T ss_pred             CcccCCCccCcEEEECCCEEEEEecchhhHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcccCcccceeE
Confidence            56777888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCCeEEE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEV  162 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~~iei  162 (191)
                      +||+|||++++|+||.+||+|++.+++++|+|+|++.++++||++|  +++||.+||++++++||..+.+  ....++||
T Consensus       129 ~ii~G~D~~~~p~Ly~iD~~G~~~~~~~~a~G~gs~~~~~~Le~~~--~~~ms~eeai~l~~~~l~~~~~--~~~~~~e~  204 (207)
T cd03755         129 TLIVGFDPDGTPRLYQTDPSGTYSAWKANAIGRNSKTVREFLEKNY--KEEMTRDDTIKLAIKALLEVVQ--SGSKNIEL  204 (207)
T ss_pred             EEEEEEeCCCCeEEEEECCCcCEEcceEEEECCCCHHHHHHHHhhc--cCCCCHHHHHHHHHHHHHHHhC--CCCCeEEE
Confidence            9999999767999999999999999999999999999999999998  4889999999999999999986  44458999


Q ss_pred             EEE
Q 029560          163 GVV  165 (191)
Q Consensus       163 ~iv  165 (191)
                      +++
T Consensus       205 ~~~  207 (207)
T cd03755         205 AVM  207 (207)
T ss_pred             EEC
Confidence            875

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>cd03749 proteasome_alpha_type_1 proteasome_alpha_type_1

Probab=100.00  E-value=5.2e-40  Score=258.21  Aligned_cols=157  Identities=31%  Similarity=0.559  Sum_probs=149.0

Q ss_pred             CCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeEEEEE
Q 029560            9 TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSI   88 (191)
Q Consensus         9 ~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~iv~G~   88 (191)
                      ++.+|||+|++|++|++||+.+|++.+.+++|.+++.|+++++++++++.+++.+++.+|.||++.+.|||+|++||+||
T Consensus        53 ~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~v~~la~~is~~~~~~t~~~~~rP~~v~~ii~G~  132 (211)
T cd03749          53 SYQKKIFKVDDHIGIAIAGLTADARVLSRYMRQECLNYRFVYDSPIPVSRLVSKVAEKAQINTQRYGRRPYGVGLLIAGY  132 (211)
T ss_pred             CccccEEEeCCCEEEEEEeChHhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCCCCceEEEEEEEE
Confidence            46699999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhccc--CCCCeEEEEEEE
Q 029560           89 DEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQED--FKASEIEVGVVS  166 (191)
Q Consensus        89 d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d--~~~~~iei~iv~  166 (191)
                      |+ .||+||.+||+|++.+++++|+|+|++.++++||++|+++++||++||+++++++|+.+.++|  ....+|||++++
T Consensus       133 D~-~gp~Ly~~Dp~G~~~~~~~~a~G~g~~~a~~~Le~~~~~~~~ms~ee~i~~~~~~l~~~~~~~~~~~~~~iei~ii~  211 (211)
T cd03749         133 DE-SGPHLFQTCPSGNYFEYKATSIGARSQSARTYLERHFEEFEDCSLEELIKHALRALRETLPGEQELTIKNVSIAIVG  211 (211)
T ss_pred             cC-CCCeEEEECCCcCEeeeeEEEECCCcHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhccCCCCCCCcEEEEEEC
Confidence            97 689999999999999999999999999999999999975579999999999999999999887  445699999984

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>cd03751 proteasome_alpha_type_3 proteasome_alpha_type_3

Probab=100.00  E-value=5.4e-40  Score=258.16  Aligned_cols=161  Identities=33%  Similarity=0.468  Sum_probs=151.6

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      .++++.+++++|||+|++|++|++||+.+|++.+.+++|.+++.|++.++++++++.++++|++.+|.|++++++|||+|
T Consensus        51 ~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~~~v~~la~~ls~~~~~~t~~~~~rP~~v  130 (212)
T cd03751          51 TSKLYEPGSNKRIFNVDRHIGIAVAGLLADGRHLVSRAREEAENYRDNYGTPIPVKVLADRVAMYMHAYTLYSSVRPFGC  130 (212)
T ss_pred             cccccCcchhcceeEecCcEEEEEEEChHhHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccCCCcCCceE
Confidence            35777788999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcc-cCCCCeE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQE-DFKASEI  160 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~-d~~~~~i  160 (191)
                      ++||+|||+ +||+||.+||+|++.+++++|+|+|+..++++||++|  +++||++||+++++++|+.+++. +....++
T Consensus       131 s~li~G~D~-~gp~Ly~~D~~Gs~~~~~~~a~G~g~~~a~~~Lek~~--~~dms~eeai~l~~~~L~~~~~~~~~~~~~i  207 (212)
T cd03751         131 SVLLGGYDS-DGPQLYMIEPSGVSYGYFGCAIGKGKQAAKTELEKLK--FSELTCREAVKEAAKIIYIVHDEIKDKAFEL  207 (212)
T ss_pred             EEEEEEEeC-CcCEEEEECCCCCEEeeEEEEECCCCHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHhhccCCCCccE
Confidence            999999996 6899999999999999999999999999999999998  48899999999999999999974 3566699


Q ss_pred             EEEEE
Q 029560          161 EVGVV  165 (191)
Q Consensus       161 ei~iv  165 (191)
                      ||+++
T Consensus       208 ei~~~  212 (212)
T cd03751         208 ELSWV  212 (212)
T ss_pred             EEEEC
Confidence            99874

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>KOG0178 consensus 20S proteasome, regulatory subunit alpha type PSMA4/PRE9 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=3.5e-40  Score=249.03  Aligned_cols=187  Identities=29%  Similarity=0.498  Sum_probs=172.9

Q ss_pred             CCccccC-CCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccc
Q 029560            2 QDKLLDH-TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLG   80 (191)
Q Consensus         2 ~s~l~~~-~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~   80 (191)
                      +|||+++ ...+||++|+||++|+++|+++|+..|++.+|..+++|.++||++||++.|++.++++.|.|||+.+.||||
T Consensus        52 t~kll~t~~~~EKiY~l~d~iaC~vaGlt~DAnvL~n~aRi~AQ~yl~~y~e~iP~eqLv~~lcdiKQayTQygG~RPFG  131 (249)
T KOG0178|consen   52 TSKLLDTSIPMEKIYKLNDNIACAVAGLTSDANVLKNYARIIAQRYLFRYGEEIPCEQLVTFLCDIKQAYTQYGGKRPFG  131 (249)
T ss_pred             chhhhhccccHHHhhhcCCceEEEEecccccHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHHhhccCcCCCc
Confidence            5778776 678999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhccc-CCCCe
Q 029560           81 VVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQED-FKASE  159 (191)
Q Consensus        81 v~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d-~~~~~  159 (191)
                      ||+|.+|||...|.+||+.||+|++..|++.++|.+++.+...|..-|+ ...++++||.++|++.|...++.. +.+..
T Consensus       132 VSfLYaGwd~~~gyqLy~SdPSGny~gWka~ciG~N~~Aa~s~Lkqdyk-dd~~~~~eA~~laikvL~kt~d~~~lt~ek  210 (249)
T KOG0178|consen  132 VSFLYAGWDDRYGYQLYQSDPSGNYGGWKATCIGANSGAAQSMLKQDYK-DDENDLEEAKALAIKVLSKTLDSGSLTAEK  210 (249)
T ss_pred             eeeeeeceecCcceEEEecCCCCCccccceeeeccchHHHHHHHHhhhc-cccccHHHHHHHHHHHHHhhcccCCCChhh
Confidence            9999999999789999999999999999999999999999999999885 345679999999999999999875 55679


Q ss_pred             EEEEEEEeCCC--cEEEcCHHHHHHHHHHhhc
Q 029560          160 IEVGVVSKENP--EFRVLSIEEIDEHLTAISE  189 (191)
Q Consensus       160 iei~iv~~~~~--~~~~~~~~~i~~~~~~~~~  189 (191)
                      +|++.++++..  .+++++++||.++|+++.+
T Consensus       211 lEia~~~k~~~k~v~~i~~~~ev~kll~k~~~  242 (249)
T KOG0178|consen  211 LEIATITKDCNKTVLKILKKDEVLKLLEKYHE  242 (249)
T ss_pred             eEEEEEEecCCceEEEecCHHHHHHHHHHhhh
Confidence            99999998753  3789999999999998863

>cd03752 proteasome_alpha_type_4 proteasome_alpha_type_4

Probab=100.00  E-value=8.5e-40  Score=257.36  Aligned_cols=161  Identities=29%  Similarity=0.486  Sum_probs=151.1

Q ss_pred             CccccC-CCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            3 DKLLDH-TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         3 s~l~~~-~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      ++++.+ ++.+||++|++|++|++||+.+|++.+.+++|.+++.|+++++++|+++.+++.|+..+|.|||+++.|||+|
T Consensus        51 ~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~i~v~~la~~ls~~~~~~t~~~~~RP~~v  130 (213)
T cd03752          51 SKLLDQSFSSEKIYKIDDHIACAVAGITSDANILINYARLIAQRYLYSYQEPIPVEQLVQRLCDIKQGYTQYGGLRPFGV  130 (213)
T ss_pred             CcccCCCcCcceEEEecCCEEEEEecChHhHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcCCCccccee
Confidence            445554 4999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCC-CeE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKA-SEI  160 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~-~~i  160 (191)
                      ++||+|||++.||+||.+||+|++.+++++|+|+|+..++++||+.|  +++||++||++++++||..+.+||... .++
T Consensus       131 ~~li~G~D~~~g~~ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~y--~~~ms~eea~~l~~~al~~~~~r~~~~~~~~  208 (213)
T cd03752         131 SFLYAGWDKHYGFQLYQSDPSGNYSGWKATAIGNNNQAAQSLLKQDY--KDDMTLEEALALAVKVLSKTMDSTKLTSEKL  208 (213)
T ss_pred             EEEEEEEeCCCCCEEEEECCCCCeeeeeEEEECCCcHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHHhccCCCCCcE
Confidence            99999999757899999999999999999999999999999999998  489999999999999999999988655 489


Q ss_pred             EEEEE
Q 029560          161 EVGVV  165 (191)
Q Consensus       161 ei~iv  165 (191)
                      +|+++
T Consensus       209 ei~~~  213 (213)
T cd03752         209 EFATL  213 (213)
T ss_pred             EEEEC
Confidence            99875

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>KOG0863 consensus 20S proteasome, regulatory subunit alpha type PSMA1/PRE5 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.4e-39  Score=248.70  Aligned_cols=177  Identities=31%  Similarity=0.516  Sum_probs=168.1

Q ss_pred             CCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeEEEEE
Q 029560            9 TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSI   88 (191)
Q Consensus         9 ~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~iv~G~   88 (191)
                      ..++|||+||+|++++++|+++|++.|.+++|.+|..+++.|++++|+..|...|.+.+|..||+.+.|||||.++++||
T Consensus        58 s~QkKi~~iD~h~g~siAGLt~Darvl~~Ylr~ec~~~~~~~~r~~pv~rl~~~l~~k~q~~Tq~ygrRpYGVGllv~gY  137 (264)
T KOG0863|consen   58 SHQKKIFKIDDHIGISIAGLTADARVLSRYLRQECLNSRFIYGRPLPVLRLVEDLGDKAQENTQRYGRRPYGVGLLVAGY  137 (264)
T ss_pred             HhhheeEecccccceEEeccCcchHHHHHHHHHHHhhhhhccCCcccHHHHHHHHHHHHhhhhhhhCCccccceEEEEee
Confidence            36799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcc--cCCCCeEEEEEEE
Q 029560           89 DEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQE--DFKASEIEVGVVS  166 (191)
Q Consensus        89 d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~--d~~~~~iei~iv~  166 (191)
                      |+ .||+||+++|+|++.++++.+||+.||.++++||++...+++++.||.+..+++||+.+...  ++...+++|+|+.
T Consensus       138 De-~G~hl~e~~Psg~v~e~~g~sIGsRSQsARTyLEr~~e~f~~~~~eELI~~gi~Alr~tlp~de~lt~~nvsI~Ivg  216 (264)
T KOG0863|consen  138 DE-SGPHLYEFCPSGNVFECKGMSIGSRSQSARTYLERNLEEFEDSSPEELIKHGIMALRETLPEDEDLTGENVSIAIVG  216 (264)
T ss_pred             cC-CCceeEEEcCCccEEEEeeeecccchhhHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhcCcccccccceeEEEEEe
Confidence            98 79999999999999999999999999999999999988789999999999999999999874  4556699999999


Q ss_pred             eCCCcEEEcCHHHHHHHHHHh
Q 029560          167 KENPEFRVLSIEEIDEHLTAI  187 (191)
Q Consensus       167 ~~~~~~~~~~~~~i~~~~~~~  187 (191)
                      ++.+ |..++.+++.+++...
T Consensus       217 kd~p-f~~~d~~~~~k~~~~~  236 (264)
T KOG0863|consen  217 KDEP-FTILDQKDVAKYVDLF  236 (264)
T ss_pred             CCCc-eEeecHHHHHHHHHHh
Confidence            9987 9999999999887544

>TIGR03691 20S_bact_alpha proteasome, alpha subunit, bacterial type

Probab=100.00  E-value=3.5e-39  Score=255.59  Aligned_cols=173  Identities=16%  Similarity=0.220  Sum_probs=155.1

Q ss_pred             CCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHHHHHHHHhhhhcCcccccceeEEEE
Q 029560            9 TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYG-YEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS   87 (191)
Q Consensus         9 ~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~-~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~iv~G   87 (191)
                      ++++|||+|+||++|+++|+.+|++.++++++.+++.|++.++ .+++++.+++++++.+..++ +++.|||+|++||+|
T Consensus        48 ~~~~KI~~I~d~ig~~~sG~~~D~~~lv~~~r~~a~~~~~~~~~~~~~v~~la~~~tq~~~~~~-~~~~RP~gvs~Li~G  126 (228)
T TIGR03691        48 RSLHKISELYDRIGFAAVGKYNEFENLRRAGIRYADMRGYSYDRRDVTGRGLANAYAQTLGTIF-TEQQKPYEVEICVAE  126 (228)
T ss_pred             CCcCcEEEecCCEEEEEcCCHHHHHHHHHHHHHHHHHHhhhcCCCCccHHHHHHHHHhhccccc-ccccCcceEEEEEEE
Confidence            5789999999999999999999999999999999999999998 68999999988777776555 567899999999999


Q ss_pred             EcC-CCCCeEEEECCCcceecee-eeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhc--cc-CCCCeEEE
Q 029560           88 IDE-ECGPRLFKCDPAGHFFGHK-ATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQ--ED-FKASEIEV  162 (191)
Q Consensus        88 ~d~-~~~p~Ly~~d~~G~~~~~~-~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~--~d-~~~~~iei  162 (191)
                      ||+ +.||+||.+||+|++.+++ ++|+|+|++.+.++||++|  +++||++||++++++||+.+.+  |+ +...++||
T Consensus       127 ~d~~~~gp~Ly~vDpsG~~~~~~~~~aiG~gs~~a~~~Lek~y--~~~ms~eeai~la~~aL~~~~~~~r~~~~~~~iEv  204 (228)
T TIGR03691       127 VGETPDQDQLYRITFDGSIVDERGFVVMGGTTEPIATALKESY--RDGLSLADALGLAVQALRAGGNGEKRELDAASLEV  204 (228)
T ss_pred             EcCCCCCCEEEEECCCCCceeccceEEECCChHHHHHHHHHhc--CCCCCHHHHHHHHHHHHHHHhccccccCCccceEE
Confidence            985 4789999999999999976 8999999999999999998  4799999999999999999964  43 55569999


Q ss_pred             EEEEeCC--CcEEEcCHHHHHHHH
Q 029560          163 GVVSKEN--PEFRVLSIEEIDEHL  184 (191)
Q Consensus       163 ~iv~~~~--~~~~~~~~~~i~~~~  184 (191)
                      +++++++  +.|+.++++||+++|
T Consensus       205 ~ii~k~~~~~~f~~l~~~ei~~~l  228 (228)
T TIGR03691       205 AVLDRSRPRRAFRRITGEALERLL  228 (228)
T ss_pred             EEEeCCCCccceEECCHHHHHhhC
Confidence            9999753  459999999999874

Members of this family are the alpha subunit of the 20S proteasome as found in Actinobacteria such as Mycobacterium, Rhodococcus, and Streptomyces. In most Actinobacteria (an exception is Propionibacterium acnes), the proteasome is accompanied by a system of tagging proteins for degradation with Pup.

>cd03756 proteasome_alpha_archeal proteasome_alpha_archeal

Probab=100.00  E-value=5.1e-39  Score=252.58  Aligned_cols=161  Identities=36%  Similarity=0.625  Sum_probs=153.5

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      +.++.+++.+||++|++|++|++||+.+|++.+.+.++.+++.|+++++++++++.+++.|++.+|.|+++++.|||+|+
T Consensus        50 ~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~l~~~~~~~~~~~~~~~~~~~la~~ls~~~~~~~~~~~~rP~~v~  129 (211)
T cd03756          50 SKLVEPESIEKIYKIDDHVGAATSGLVADARVLIDRARVEAQIHRLTYGEPIDVEVLVKKICDLKQQYTQHGGVRPFGVA  129 (211)
T ss_pred             CcccCCCccceEEEEcCCEEEEEecCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCCCeechhEE
Confidence            46777889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCCeEEE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEV  162 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~~iei  162 (191)
                      +||+|||+ .+|+||.+||+|++.+++++|+|+|++.++++||+.|  +++||++||++++++||..+.+++....+++|
T Consensus       130 ~ll~G~D~-~~~~ly~vd~~G~~~~~~~~a~G~g~~~~~~~Le~~~--~~~m~~~ea~~l~~~~l~~~~~~~~~~~~~~v  206 (211)
T cd03756         130 LLIAGVDD-GGPRLFETDPSGAYNEYKATAIGSGRQAVTEFLEKEY--KEDMSLEEAIELALKALYAALEENETPENVEI  206 (211)
T ss_pred             EEEEEEeC-CCCEEEEECCCCCeeeeEEEEECCCCHHHHHHHHhhc--cCCCCHHHHHHHHHHHHHHHhcccCCCCcEEE
Confidence            99999997 7899999999999999999999999999999999998  48999999999999999999988885559999


Q ss_pred             EEEE
Q 029560          163 GVVS  166 (191)
Q Consensus       163 ~iv~  166 (191)
                      ++|+
T Consensus       207 ~ii~  210 (211)
T cd03756         207 AYVT  210 (211)
T ss_pred             EEEe
Confidence            9987

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>cd03757 proteasome_beta_type_1 proteasome beta type-1 subunit

Probab=100.00  E-value=3.4e-39  Score=253.73  Aligned_cols=165  Identities=18%  Similarity=0.327  Sum_probs=151.3

Q ss_pred             Ccc-ccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            3 DKL-LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         3 s~l-~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      +++ +.+++++|||+|++|++|++||..+|++.+.+++|.+++.|+++++++++++.++++|++++  |++  +.|||+|
T Consensus        30 ~~~~~~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~~r~~~~~~~~~~g~~i~~~~la~~ls~~l--y~~--R~~P~~~  105 (212)
T cd03757          30 EGYSILSRDSPKIFKLTDKCVLGSSGFQADILALTKRLKARIKMYKYSHNKEMSTEAIAQLLSTIL--YSR--RFFPYYV  105 (212)
T ss_pred             cCCEeEeCCCCeEEEcCCCEEEEccchHHHHHHHHHHHHHHHHHHhHHhCCCCCHHHHHHHHHHHH--Hhh--cCCCeEE
Confidence            344 44689999999999999999999999999999999999999999999999999999999998  543  3579999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhc-------CCCCCCHHHHHHHHHHHHHhhhccc
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMK-------NDPAFTFQETVQTAISTLQSVLQED  154 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~-------~~~~~s~eea~~l~~~~l~~~~~~d  154 (191)
                      ++||||||++++|+||.+||+|++.+++++|+|+|+..++++||+.|+       +.++||++||++++++||+.+.+||
T Consensus       106 ~~iiaG~D~~~~p~Ly~~D~~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~~~~~~~~~~ms~eea~~l~~~~l~~~~~rd  185 (212)
T cd03757         106 FNILAGIDEEGKGVVYSYDPVGSYERETYSAGGSASSLIQPLLDNQVGRKNQNNVERTPLSLEEAVSLVKDAFTSAAERD  185 (212)
T ss_pred             EEEEEEEcCCCCEEEEEEcCccCeeecCEEEEeecHHHHHHHHHHHHHhhccCcCCCCCCCHHHHHHHHHHHHHHHHHhC
Confidence            999999997678999999999999999999999999999999999984       2489999999999999999999999


Q ss_pred             CCCC-eEEEEEEEeCCCc
Q 029560          155 FKAS-EIEVGVVSKENPE  171 (191)
Q Consensus       155 ~~~~-~iei~iv~~~~~~  171 (191)
                      +.++ +++|++|+++|..
T Consensus       186 ~~sg~~i~i~iit~~g~~  203 (212)
T cd03757         186 IYTGDSLEIVIITKDGIE  203 (212)
T ss_pred             cccCCCEEEEEEcCCCEE
Confidence            8776 8999999999753

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>TIGR03634 arc_protsome_B proteasome endopeptidase complex, archaeal, beta subunit

Probab=100.00  E-value=5.3e-39  Score=247.63  Aligned_cols=160  Identities=25%  Similarity=0.445  Sum_probs=151.5

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      ++++.+++++|||+|++|++|++||..+|++.+.++++.+++.|+..++++++++.++++|++.+|.+    ++|||+|+
T Consensus        24 ~~~i~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~~~~~----~~rP~~v~   99 (185)
T TIGR03634        24 GNFVASKNAKKVFQIDDYIAMTIAGSVGDAQSLVRILKAEAKLYELRRGRPMSVKALATLLSNILNSN----RFFPFIVQ   99 (185)
T ss_pred             CCEEecCCcccEEEcCCCEEEEcCchHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhc----CCCCeEEE
Confidence            46778889999999999999999999999999999999999999999999999999999999999754    68999999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIE  161 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~ie  161 (191)
                      +||||||+ .||+||.+||+|++.+++++|+|+|+..++++||++|+  ++||++||++++++||+.+.+||..++ +++
T Consensus       100 ~ivaG~d~-~g~~Ly~~d~~G~~~~~~~~a~G~g~~~~~~~Le~~~~--~~~s~~ea~~l~~~~l~~~~~r~~~~~~~~~  176 (185)
T TIGR03634       100 LLVGGVDE-EGPHLYSLDPAGGIIEDDYTATGSGSPVAYGVLEDEYR--EDMSVEEAKKLAVRAIKSAIERDVASGNGID  176 (185)
T ss_pred             EEEEEEeC-CCCEEEEECCCCCeEECCEEEEcCcHHHHHHHHHhcCC--CCCCHHHHHHHHHHHHHHHHHhcccCCCCEE
Confidence            99999997 68999999999999999999999999999999999984  899999999999999999999998775 899


Q ss_pred             EEEEEeCC
Q 029560          162 VGVVSKEN  169 (191)
Q Consensus       162 i~iv~~~~  169 (191)
                      |++++++|
T Consensus       177 v~ii~~~g  184 (185)
T TIGR03634       177 VAVITKDG  184 (185)
T ss_pred             EEEEcCCC
Confidence            99999886

This protein family describes the archaeal proteasome beta subunit, homologous to both the alpha subunit and to the alpha and beta subunits of eukaryotic proteasome subunits. This family is universal in the first 29 complete archaeal genomes but occasionally is duplicated.

>cd03765 proteasome_beta_bacterial Bacterial proteasome, beta subunit

Probab=100.00  E-value=5e-39  Score=255.23  Aligned_cols=166  Identities=13%  Similarity=0.209  Sum_probs=150.6

Q ss_pred             CCccccCCCCcceEEec----CcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHHH-HhhhhcC
Q 029560            2 QDKLLDHTSVTHLFPIT----KYLGLLATGMTADARTLVQQARYEAAEFRFKYGY-EMPVDVLAKWIADKSQ-VYTQHAY   75 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~----~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~-~~~~~~l~~~l~~~~~-~~t~~~~   75 (191)
                      +++|+..++.+||++|+    +|++|++||+.+|++.+++++|.+++.|++++|+ +++++.++++++++++ .++|+.+
T Consensus        21 ~~~l~~~~~~~KI~~I~~~~d~~I~~~~sG~~aD~~~l~~~~r~~~~~~~~~~g~~~~~v~~la~~i~~~l~~~~~q~~~  100 (236)
T cd03765          21 NAGVDNISTYRKMFVFSVPGERVIVLLTAGNLATTQAVISLLQRDLEDPEETNLLNAPTMFDAARYVGETLREVQEQDRE  100 (236)
T ss_pred             cCCCccccccceEEEecCCCCCEEEEEcCCcHHHHHHHHHHHHHHHHhhHHhhCCCCCCHHHHHHHHHHHHHHHHhhccc
Confidence            45677777899999998    9999999999999999999999999999999999 8999999999999854 4556554


Q ss_pred             -----cccccceeEEEEEcCCCCCeEEEECCCcceecee----eeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHH
Q 029560           76 -----MRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHK----ATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAIST  146 (191)
Q Consensus        76 -----~rP~~v~~iv~G~d~~~~p~Ly~~d~~G~~~~~~----~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~  146 (191)
                           .|||+|++||||||++.||+||.+||+|++.+++    ++|+|+ ++.++++||++|+  ++||+|||++++++|
T Consensus       101 ~~~~~~rp~gvslIigG~D~~~Gp~LY~idpsG~~~e~~a~~~~~AiG~-~~~a~~~Lek~yk--~~ms~eeai~la~~a  177 (236)
T cd03765         101 ALKKAGIDFSASFILGGQIKGEEPRLFLIYPQGNFIEATPDTPFLQIGE-TKYGKPILDRVIT--PDTSLEDAAKCALVS  177 (236)
T ss_pred             ccccCCcceEEEEEEEeEECCCCCEEEEECCCCCEEeecCCCceeeeCC-chhhHHHHHHhcC--CCCCHHHHHHHHHHH
Confidence                 4899999999999965789999999999999995    479996 7999999999984  799999999999999


Q ss_pred             HHhhhcccCCCC-eEEEEEEEeCCC
Q 029560          147 LQSVLQEDFKAS-EIEVGVVSKENP  170 (191)
Q Consensus       147 l~~~~~~d~~~~-~iei~iv~~~~~  170 (191)
                      |..+++||..++ +|+|++|+++|.
T Consensus       178 l~~a~~rd~~sg~~iev~vI~k~G~  202 (236)
T cd03765         178 MDSTMRSNLSVGPPLDLLVYERDSL  202 (236)
T ss_pred             HHHHHHhcCCCCCCEEEEEEECCCe
Confidence            999999998776 899999999974

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>cd03764 proteasome_beta_archeal Archeal proteasome, beta subunit

Probab=100.00  E-value=1.1e-38  Score=246.43  Aligned_cols=163  Identities=25%  Similarity=0.421  Sum_probs=153.7

Q ss_pred             ccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccccee
Q 029560            4 KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVA   83 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~   83 (191)
                      .++.+++.+||++|++|++++++|+.+|++.+.++++.+++.|++.++++++++.+++++++.+|.+    ++|||+|++
T Consensus        24 ~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~~~~----~~~P~~~~~   99 (188)
T cd03764          24 NFIASKNVKKIFQIDDKIAMTIAGSVGDAQSLVRILKAEARLYELRRGRPMSIKALATLLSNILNSS----KYFPYIVQL   99 (188)
T ss_pred             CEEecCCcccEEEccCCEEEEcCccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhc----CCCCcEEEE
Confidence            6777899999999999999999999999999999999999999999999999999999999999654    579999999


Q ss_pred             EEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEE
Q 029560           84 MVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEV  162 (191)
Q Consensus        84 iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei  162 (191)
                      ||||||+ ++|+||.+||+|++.+++++|+|+|++.+.++|++.|  +++||++||++++++||+.+.+||..++ +++|
T Consensus       100 lvaG~d~-~~~~ly~~D~~G~~~~~~~~a~G~g~~~~~~~L~~~~--~~~~~~~ea~~l~~~~l~~~~~rd~~~~~~i~i  176 (188)
T cd03764         100 LIGGVDE-EGPHLYSLDPLGSIIEDKYTATGSGSPYAYGVLEDEY--KEDMTVEEAKKLAIRAIKSAIERDSASGDGIDV  176 (188)
T ss_pred             EEEEEeC-CCCEEEEECCCCCEEEcCEEEEcCcHHHHHHHHHhcC--CCCCCHHHHHHHHHHHHHHHHhhcCCCCCcEEE
Confidence            9999997 7899999999999999999999999999999999998  4889999999999999999999998775 8999


Q ss_pred             EEEEeCCCcEEEc
Q 029560          163 GVVSKENPEFRVL  175 (191)
Q Consensus       163 ~iv~~~~~~~~~~  175 (191)
                      ++++++|  ++++
T Consensus       177 ~iv~~~g--~~~~  187 (188)
T cd03764         177 VVITKDG--YKEL  187 (188)
T ss_pred             EEECCCC--eEeC
Confidence            9999886  7776

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme for non-lysosomal protein degradation in both the cytosol and the nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are both members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>cd03763 proteasome_beta_type_7 proteasome beta type-7 subunit

Probab=100.00  E-value=2.4e-38  Score=244.82  Aligned_cols=163  Identities=16%  Similarity=0.253  Sum_probs=151.3

Q ss_pred             ccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccccee
Q 029560            4 KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVA   83 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~   83 (191)
                      .++.+++++|||+|++|++|+++|..+|++.+.++++.+++.|+++++++++++.++++|++.++.|.     .||+|++
T Consensus        24 ~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~l~~~~-----~p~~v~~   98 (189)
T cd03763          24 PIVADKNCEKIHYIAPNIYCCGAGTAADTEAVTNMISSNLELHRLNTGRKPRVVTALTMLKQHLFRYQ-----GHIGAAL   98 (189)
T ss_pred             ceEEcCCccceEEecCCEEEEcCccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHcC-----CccceeE
Confidence            46667899999999999999999999999999999999999999999999999999999999997652     3999999


Q ss_pred             EEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEE
Q 029560           84 MVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEV  162 (191)
Q Consensus        84 iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei  162 (191)
                      ||||||+ .||+||.+||+|++.+++++|+|+|+..++++|+++|  +++||++||++++++||+.+.+||+.++ +++|
T Consensus        99 ivaG~d~-~g~~ly~~d~~G~~~~~~~~a~G~~~~~~~~~L~~~~--~~~ls~~ea~~l~~~~l~~~~~rd~~~~~~~~v  175 (189)
T cd03763          99 VLGGVDY-TGPHLYSIYPHGSTDKLPFVTMGSGSLAAMSVLEDRY--KPDMTEEEAKKLVCEAIEAGIFNDLGSGSNVDL  175 (189)
T ss_pred             EEEeEcC-CCCEEEEECCCCCEEecCEEEEcCCHHHHHHHHHhhc--CCCCCHHHHHHHHHHHHHHHHHhcCcCCCceEE
Confidence            9999997 6899999999999999999999999999999999998  4899999999999999999999998765 8999


Q ss_pred             EEEEeCCCcEEEcC
Q 029560          163 GVVSKENPEFRVLS  176 (191)
Q Consensus       163 ~iv~~~~~~~~~~~  176 (191)
                      ++|+++|  +++..
T Consensus       176 ~ii~~~g--~~~~~  187 (189)
T cd03763         176 CVITKDG--VEYLR  187 (189)
T ss_pred             EEEcCCc--EEEec
Confidence            9999987  56544

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>cd03762 proteasome_beta_type_6 proteasome beta type-6 subunit

Probab=100.00  E-value=3.9e-38  Score=243.43  Aligned_cols=159  Identities=15%  Similarity=0.236  Sum_probs=150.0

Q ss_pred             ccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccccee
Q 029560            4 KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVA   83 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~   83 (191)
                      .++.+++++|||+|++|++|++||+.+|++.+.++++.+++.|+++++++++++.++++++++++.+     .|||+|++
T Consensus        24 ~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~l~~~~~~~~~~~~~~~~~~~~a~~l~~~~~~~-----~~~~~~~~   98 (188)
T cd03762          24 SYVANRVTDKLTQLHDRIYCCRSGSAADTQAIADYVRYYLDMHSIELGEPPLVKTAASLFKNLCYNY-----KEMLSAGI   98 (188)
T ss_pred             ceEEcCCcccEEEccCCEEEEecccHHHHHHHHHHHHHHHHHhHHhhCCCCCHHHHHHHHHHHHHhc-----cccceeeE
Confidence            5677889999999999999999999999999999999999999999999999999999999998655     37999999


Q ss_pred             EEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEE
Q 029560           84 MVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEV  162 (191)
Q Consensus        84 iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei  162 (191)
                      ||||||++.||+||.+||.|++.+++++++|+|+..++++||+.|  +++||++||++++++||+.+.+||+.++ +++|
T Consensus        99 ii~G~d~~~gp~ly~~d~~G~~~~~~~~~~G~g~~~~~~~Le~~~--~~~~s~~ea~~l~~~al~~~~~rd~~~~~~~~i  176 (188)
T cd03762          99 IVAGWDEQNGGQVYSIPLGGMLIRQPFAIGGSGSTYIYGYVDANY--KPGMTLEECIKFVKNALSLAMSRDGSSGGVIRL  176 (188)
T ss_pred             EEEEEcCCCCcEEEEECCCCCEEecCEEEEcccHHHHHHHHHhcC--CCCCCHHHHHHHHHHHHHHHHHhccccCCCEEE
Confidence            999999757899999999999999999999999999999999998  4889999999999999999999998776 8999


Q ss_pred             EEEEeCC
Q 029560          163 GVVSKEN  169 (191)
Q Consensus       163 ~iv~~~~  169 (191)
                      ++|+++|
T Consensus       177 ~~i~~~g  183 (188)
T cd03762         177 VIITKDG  183 (188)
T ss_pred             EEECCCC
Confidence            9999887

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>cd01911 proteasome_alpha proteasome alpha subunit

Probab=100.00  E-value=4.9e-38  Score=246.65  Aligned_cols=161  Identities=48%  Similarity=0.766  Sum_probs=151.8

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      +.++.+++.+||++|+++++|++||..+|++.+.+.++.++..|+++++++++++.+++++++.+|.|+++++.|||+|+
T Consensus        49 ~~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~l~~~~~~~~~~~g~~~~~~~la~~ls~~~~~~~~~~~~rP~~v~  128 (209)
T cd01911          49 SKLLDPSSVEKIFKIDDHIGCAVAGLTADARVLVNRARVEAQNYRYTYGEPIPVEVLVKRIADLAQVYTQYGGVRPFGVS  128 (209)
T ss_pred             ccccCCcccceEEEecCCeEEEeccCcHhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCccChhhe
Confidence            34566789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCCeEEE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEV  162 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~~iei  162 (191)
                      +||+|||++++|+||.+||.|++.+++++|+|+|+..++++|++.|  .++||.+||++++++||..+.+||+...+++|
T Consensus       129 ~iv~G~d~~~~~~Ly~iD~~G~~~~~~~~a~G~g~~~~~~~L~~~~--~~~ms~~ea~~l~~~~l~~~~~~d~~~~~~~i  206 (209)
T cd01911         129 LLIAGYDEEGGPQLYQTDPSGTYFGYKATAIGKGSQEAKTFLEKRY--KKDLTLEEAIKLALKALKEVLEEDKKAKNIEI  206 (209)
T ss_pred             EEEEEEcCCCCcEEEEECCCCCeeeeeEEEeCCCcHHHHHHHHHhc--ccCCCHHHHHHHHHHHHHHHHhccCCCCcEEE
Confidence            9999999866999999999999999999999999999999999999  48899999999999999999999993348999


Q ss_pred             EEE
Q 029560          163 GVV  165 (191)
Q Consensus       163 ~iv  165 (191)
                      +++
T Consensus       207 ~i~  209 (209)
T cd01911         207 AVV  209 (209)
T ss_pred             EEC
Confidence            874

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 different alpha and 10 different beta proteasome subunit genes while archaea have one of each.

>cd03753 proteasome_alpha_type_5 proteasome_alpha_type_5

Probab=100.00  E-value=5.5e-38  Score=247.08  Aligned_cols=160  Identities=32%  Similarity=0.563  Sum_probs=149.8

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhh-----cCcc
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH-----AYMR   77 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~-----~~~r   77 (191)
                      ++++..++++||++|++|++|++||+.+|++.+.+.+|.+++.|+++++++++++.++++|++.+|.|++.     .+.|
T Consensus        49 ~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~i~~~~~~~~ls~~~~~~~~~~~~~~~~~r  128 (213)
T cd03753          49 SPLMEPSSVEKIMEIDDHIGCAMSGLIADARTLIDHARVEAQNHRFTYNEPMTVESVTQAVSDLALQFGEGDDGKKAMSR  128 (213)
T ss_pred             CcCcCCCccceEEEEcCCEEEEEecCHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhCcccccccccc
Confidence            46777788999999999999999999999999999999999999999999999999999999999999874     3469


Q ss_pred             cccceeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCC
Q 029560           78 PLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKA  157 (191)
Q Consensus        78 P~~v~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~  157 (191)
                      ||+|++||+|||+ +||+||.+||+|++.+++++|+|++++.++++|+++|+  ++||++||++++++||+.+.+++...
T Consensus       129 P~~v~~ii~G~D~-~gp~Ly~vd~~G~~~~~~~~a~G~~~~~~~~~L~~~~~--~~ls~eeai~l~~~~l~~~~~~~~~~  205 (213)
T cd03753         129 PFGVALLIAGVDE-NGPQLFHTDPSGTFTRCDAKAIGSGSEGAQSSLQEKYH--KDMTLEEAEKLALSILKQVMEEKLNS  205 (213)
T ss_pred             cceEEEEEEEEcC-CCCEEEEECCCCCeecccEEEECCCcHHHHHHHHhhcc--CCCCHHHHHHHHHHHHHHHhcccCCC
Confidence            9999999999997 78999999999999999999999999999999999984  78999999999999999998887777


Q ss_pred             CeEEEEEE
Q 029560          158 SEIEVGVV  165 (191)
Q Consensus       158 ~~iei~iv  165 (191)
                      .+++|+++
T Consensus       206 ~~~ei~~~  213 (213)
T cd03753         206 TNVELATV  213 (213)
T ss_pred             CcEEEEEC
Confidence            79999875

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>PF00227 Proteasome: Proteasome subunit; InterPro: IPR001353 ATP-dependent protease complexes are present in all three kingdoms of life, where they rid the cell of misfolded or damaged proteins and control the level of certain regulatory proteins

Probab=100.00  E-value=3.7e-37  Score=237.76  Aligned_cols=161  Identities=33%  Similarity=0.538  Sum_probs=152.0

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      +.++.+++++|||+|++|+++++||..+|++.+.++++.++..|++.++.+++++.+++.+++.++.+++++++|||+++
T Consensus        28 ~~~~~~~~~~ki~~i~~~i~~~~sG~~~D~~~l~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~p~~~~  107 (190)
T PF00227_consen   28 SKLRSPNTVDKIFKINDNIIIGFSGLTADFQYLIRRLREEAQEYRFSYGRPISPEYLAKAIASLIQNYTYRSGRRPYGVS  107 (190)
T ss_dssp             TEEEESSTSSSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHHHHHHHHHHHHHHHHHHTTTSTTSEE
T ss_pred             cccccccccceeeeccCcceeeccccccchHHHHhhhcccchhhhhccCccccchhhhhhhHHHHhhhcccccccCcccc
Confidence            44556666899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceece-eeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGH-KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EI  160 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~-~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~i  160 (191)
                      +|+||||++++|+||.+||+|++.++ +++|+|+|++.++++|++.|  .++||++||++++++||+.+.++|..++ ++
T Consensus       108 ~li~G~d~~~~~~l~~vd~~G~~~~~~~~~aiG~g~~~~~~~l~~~~--~~~~~~~ea~~~~~~~l~~~~~~d~~~~~~~  185 (190)
T PF00227_consen  108 LLIAGYDEDGGPQLYSVDPSGSYIECKRFAAIGSGSQFAQPILEKLY--KPDLSLEEAIELALKALKEAIDRDILSGDNI  185 (190)
T ss_dssp             EEEEEEETTTEEEEEEEETTSEEEEBSSEEEESTTHHHHHHHHHHHH--TTTSSHHHHHHHHHHHHHHHHHHBTTSTSEE
T ss_pred             ceeeeeccccccceeeeccccccccccccccchhcchhhhHHHHhhc--cCCCCHHHHHHHHHHHHHHHHhhCCccCCeE
Confidence            99999998667999999999999999 69999999999999999999  5899999999999999999999997665 89


Q ss_pred             EEEEE
Q 029560          161 EVGVV  165 (191)
Q Consensus       161 ei~iv  165 (191)
                      +|+||
T Consensus       186 ~v~vi  190 (190)
T PF00227_consen  186 EVAVI  190 (190)
T ss_dssp             EEEEE
T ss_pred             EEEEC
Confidence            99986

They include the proteasome in Eukaryotes, Archaea, and Actinomycetales and the HslVU (ClpQY, clpXP) complex in other eubacteria. Genes homologous to eubacterial HslV (ClpQ) and HslU (ClpY, clpX) have also been demonstrated in to be present in the genome of trypanosomatid protozoa []. The proteasome (or macropain) (3.4.25.1 from EC) [, , , , ] is a eukaryotic and archaeal multicatalytic proteinase complex that seems to be involved in an ATP/ubiquitin-dependent nonlysosomal proteolytic pathway. In eukaryotes the proteasome is composed of about 28 distinct subunits which form a highly ordered ring-shaped structure (20S ring) of about 700 kDa. Most proteasome subunits can be classified, on the basis on sequence similarities into two groups, alpha (A) and beta (B). The prokaryotic ATP-dependent proteasome is coded for by the heat-shock locus VU (HslVU). It consists of HslV, the protease (MEROPS peptidase subfamily T1B), and HslU, IPR004491 from INTERPRO, the ATPase and chaperone belonging to the AAA/Clp/Hsp100 family. The crystal structure of Thermotoga maritima HslV has been determined to 2.1-A resolution. The structure of the dodecameric enzyme is well conserved compared to those from Escherichia coli and Haemophilus influenzae [, ]. This entry contains threonine peptidases and non-peptidase homologs belong to MEROPS peptidase family T1 (proteasome family, clan PB(T)). The family consists of the protease components of the archaeal and bacterial proteasomes and the alpha and beta subunits of the eukaryotic proteasome. ; GO: 0004298 threonine-type endopeptidase activity, 0051603 proteolysis involved in cellular protein catabolic process, 0005839 proteasome core complex; PDB: 3KRD_1 3H6F_M 2FHH_F 3HF9_F 2FHG_D 3HFA_B 3H6I_K 3MI0_A 3MFE_1 3MKA_F ....

>cd01912 proteasome_beta proteasome beta subunit

Probab=100.00  E-value=4.7e-37  Score=237.36  Aligned_cols=160  Identities=22%  Similarity=0.382  Sum_probs=149.7

Q ss_pred             cccc-CCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            4 KLLD-HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         4 ~l~~-~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      .++. +++++|||+|+++++|++||+.+|++.+.++++.++..|++.++++++++.+++++++.++.+++    |||+++
T Consensus        23 ~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~----~P~~~~   98 (189)
T cd01912          23 GSLVASRNFDKIFKISDNILLGTAGSAADTQALTRLLKRNLRLYELRNGRELSVKAAANLLSNILYSYRG----FPYYVS   98 (189)
T ss_pred             CcEEEcCCcCcEEEccCCEEEEccccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhcCC----CCeEEE
Confidence            3444 78999999999999999999999999999999999999999999999999999999999976543    899999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIE  161 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~ie  161 (191)
                      +||||||++++|+||.+||+|++.+++++|+|++++.+.++||+.|  +++||++||++++.+||..+.+||..++ +++
T Consensus        99 ~iv~G~d~~~~~~l~~id~~G~~~~~~~~a~G~~~~~~~~~Le~~~--~~~~s~~ea~~~~~~~l~~~~~~d~~~~~~~~  176 (189)
T cd01912          99 LIVGGVDKGGGPFLYYVDPLGSLIEAPFVATGSGSKYAYGILDRGY--KPDMTLEEAVELVKKAIDSAIERDLSSGGGVD  176 (189)
T ss_pred             EEEEEEcCCCCeEEEEECCCCCeEecCEEEEcccHHHHHHHHHhcc--CCCCCHHHHHHHHHHHHHHHHHhcCccCCcEE
Confidence            9999999767899999999999999999999999999999999998  4889999999999999999999997765 899


Q ss_pred             EEEEEeCC
Q 029560          162 VGVVSKEN  169 (191)
Q Consensus       162 i~iv~~~~  169 (191)
                      |++++++|
T Consensus       177 v~vi~~~g  184 (189)
T cd01912         177 VAVITKDG  184 (189)
T ss_pred             EEEECCCC
Confidence            99999886

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>KOG0184 consensus 20S proteasome, regulatory subunit alpha type PSMA3/PRE10 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=3.6e-37  Score=234.36  Aligned_cols=185  Identities=30%  Similarity=0.440  Sum_probs=167.2

Q ss_pred             CCCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccc
Q 029560            1 MQDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLG   80 (191)
Q Consensus         1 ~~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~   80 (191)
                      +.|||..++..+|||.|++||+|+++|+.+|.+.+.+.+|.++..|+.+|+.|+|...++..+++++|.||.++..||||
T Consensus        54 i~SkLy~p~sn~ri~~V~r~iG~avaGl~~Dg~~l~~~ar~ea~~~~~~y~~piP~~~la~rva~yvh~~Tly~~vRpfG  133 (254)
T KOG0184|consen   54 ITSKLYEPGSNERIFSVDRHIGMAVAGLIPDGRHLVNRARDEAASWRKNYGDPIPGKHLADRVADYVHAFTLYSSVRPFG  133 (254)
T ss_pred             ecccccccCCCCceEeecccccEEEeccccchHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHhhhheeehhhcccccc
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCC-CCe
Q 029560           81 VVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFK-ASE  159 (191)
Q Consensus        81 v~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~-~~~  159 (191)
                      ++.|+++||. +||+||.++|+|..+.|+++|+|.|.|.|++.|||+-  ...|+.+|+++.+.+.|..+.+..-. ...
T Consensus       134 ~~~~~~~yd~-~g~~LymiepSG~~~~Y~~aaiGKgrq~aKtElEKL~--~~~mt~~e~VkeaakIiY~~HDe~KdK~fe  210 (254)
T KOG0184|consen  134 ASTILGSYDD-EGPQLYMIEPSGSSYGYKGAAIGKGRQAAKTELEKLK--IDEMTCKELVKEAAKIIYKVHDENKDKEFE  210 (254)
T ss_pred             ceEEEEEEeC-CCceEEEEcCCCCccceeeeeccchhHHHHHHHHhcc--cccccHHHHHHHHHheeEeecccccCcceE
Confidence            9999999996 8999999999999999999999999999999999983  56899999999999999999865333 347


Q ss_pred             EEEEEEEeCCCcEEEcCHHHHHHHHHHhh
Q 029560          160 IEVGVVSKENPEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       160 iei~iv~~~~~~~~~~~~~~i~~~~~~~~  188 (191)
                      +||.|+..++++.+..-|+||-+...++.
T Consensus       211 iEm~wvg~eTnG~h~~vp~el~~ea~~~a  239 (254)
T KOG0184|consen  211 IEMGWVGEETNGLHEKVPSELLEEAEKYA  239 (254)
T ss_pred             EEEEEEEeecCCccccCcHHHHHHHHHHH
Confidence            99999997765555555557766655543

>cd01906 proteasome_protease_HslV proteasome_protease_HslV

Probab=100.00  E-value=7.5e-36  Score=229.03  Aligned_cols=154  Identities=41%  Similarity=0.684  Sum_probs=146.3

Q ss_pred             CCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeEEEE
Q 029560            8 HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS   87 (191)
Q Consensus         8 ~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~iv~G   87 (191)
                      +++++|||+|+++++|+++|..+|++.+.+.++.++..|++.++++++++.++++|++.+|.++++  .|||++++||+|
T Consensus        28 ~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~--~~p~~~~~lv~G  105 (182)
T cd01906          28 SSTVEKIFKIDDHIGCAFAGLAADAQTLVERLRKEAQLYRLRYGEPIPVEALAKLLANLLYEYTQS--LRPLGVSLLVAG  105 (182)
T ss_pred             CCCcceEEEECCCEEEEEeeCHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhCCC--ccChheEEEEEE
Confidence            678999999999999999999999999999999999999999999999999999999999988875  899999999999


Q ss_pred             EcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEEEEE
Q 029560           88 IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVV  165 (191)
Q Consensus        88 ~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei~iv  165 (191)
                      ||++++|+||.+||+|++.+++++|+|+|++.++++||+.|+  ++||.+||++++++||..+.++|..++ +++|+++
T Consensus       106 ~d~~~~~~Ly~id~~G~~~~~~~~a~G~g~~~~~~~L~~~~~--~~~s~~ea~~l~~~~l~~~~~~~~~~~~~~~i~ii  182 (182)
T cd01906         106 VDEEGGPQLYSVDPSGSYIEYKATAIGSGSQYALGILEKLYK--PDMTLEEAIELALKALKSALERDLYSGGNIEVAVI  182 (182)
T ss_pred             EeCCCCcEEEEECCCCCEeeccEEEECCCcHHHHHHHHHHcc--CCCCHHHHHHHHHHHHHHHHcccCCCCCCEEEEEC
Confidence            997678999999999999999999999999999999999984  789999999999999999999998665 8999875

This group contains the eukaryotic proteosome alpha and beta subunits and the prokaryotic protease hslV subunit. Proteasomes are large multimeric self-compartmentalizing proteases, involved in the clearance of misfolded proteins, the breakdown of regulatory proteins, and the processing of proteins such as the preparation of peptides for immune presentation. Two main proteasomal types are distinguished by their different tertiary structures: the eukaryotic/archeal 20S proteasome and the prokaryotic proteasome-like heat shock protein encoded by heat shock locus V, hslV. The proteasome core particle is a highly conserved cylindrical structure made up of non-identical subunits that have their active sites on the inner walls of a large central cavity. The proteasome subunits of bacteria, archaea, and eukaryotes all share a conserved Ntn (N terminal nucleophile) hydrolase fold and a catalytic mechanism involving an N-terminal nucleo

>KOG0175 consensus 20S proteasome, regulatory subunit beta type PSMB5/PSMB8/PRE2 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=3.9e-33  Score=216.31  Aligned_cols=177  Identities=17%  Similarity=0.183  Sum_probs=165.7

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      -.+|.+++++||++||++++-+++|-+||++.+.+.+.++|+.|++++++.|++...++.|++++.+|   +++ .+.+.
T Consensus        94 G~YIasqtv~KVIeIn~ylLGTmAGgAADCqfWer~L~kecRL~eLRnkeriSVsaASKllsN~~y~Y---kGm-GLsmG  169 (285)
T KOG0175|consen   94 GSYIASQTVKKVIEINPYLLGTMAGGAADCQFWERVLAKECRLHELRNKERISVSAASKLLSNMVYQY---KGM-GLSMG  169 (285)
T ss_pred             cceeechhhceeeeechhhhhcccCcchhhHHHHHHHHHHHHHHHHhcCcceehHHHHHHHHHHHhhc---cCc-chhhe
Confidence            35889999999999999999999999999999999999999999999999999999999999999655   444 67899


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIE  161 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~ie  161 (191)
                      .+|||||+ .||.||.||..|+..+-+-.++|+||.+|+++|+..|  ++|||.|||.+|+++++..|..||..|+ -+.
T Consensus       170 tMi~G~Dk-~GP~lyYVDseG~Rl~G~~FSVGSGs~yAYGVLDsgY--r~dls~eEA~~L~rrAI~hAThRDaySGG~vn  246 (285)
T KOG0175|consen  170 TMIAGWDK-KGPGLYYVDSEGTRLSGDLFSVGSGSTYAYGVLDSGY--RYDLSDEEAYDLARRAIYHATHRDAYSGGVVN  246 (285)
T ss_pred             eeEeeccC-CCCceEEEcCCCCEecCceEeecCCCceeEEeeccCC--CCCCCHHHHHHHHHHHHHHHHhcccccCceEE
Confidence            99999998 8999999999999999999999999999999999997  5889999999999999999999999998 589


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHHHHHhh
Q 029560          162 VGVVSKENPEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~~~~~~  188 (191)
                      ++.|+++|  |..+++.++.+++.++.
T Consensus       247 lyHv~edG--W~~v~~~Dv~~L~~~~~  271 (285)
T KOG0175|consen  247 LYHVKEDG--WVKVSNTDVSELHYHYY  271 (285)
T ss_pred             EEEECCcc--ceecCCccHHHHHHHHH
Confidence            99999996  99999999999976654

>KOG0177 consensus 20S proteasome, regulatory subunit beta type PSMB2/PRE1 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.2e-32  Score=203.67  Aligned_cols=168  Identities=15%  Similarity=0.240  Sum_probs=155.5

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      |-++-.++.+|++.|++|+.|+++|..+|+..+.+++.+.++.|+.++|.+++|+..++++++.+.++.  ++.+||.|+
T Consensus        24 si~~~k~~~dK~~~ls~~~lm~~~Ge~GDt~qF~eyi~~Ni~LYkirnGyeLSp~~aahFtR~~La~~L--Rsr~~yqV~  101 (200)
T KOG0177|consen   24 SILVLKDDHDKIHRLSDHILMATVGEAGDTVQFTEYIQKNIQLYKIRNGYELSPSAAAHFTRRELAESL--RSRTPYQVN  101 (200)
T ss_pred             ceEEecccccceEEeccceeeeeecCCCceehHHHHHHhhhhHHhhhcCCcCCHHHHHHHHHHHHHHHH--hcCCCceEE
Confidence            456667899999999999999999999999999999999999999999999999999999999998874  446899999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccC-CCCeEE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDF-KASEIE  161 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~-~~~~ie  161 (191)
                      +|+||+|++.||.||++|..|+..+.++++.|.++.++.++|++.|  +|+||.+||+++..+|+.++..|-. +-.+|.
T Consensus       102 ~LvaGYd~~~gp~L~~iDyla~~~~vpy~~hGy~~~f~~sIlDr~Y--~pdmt~eea~~lmkKCv~El~kRlvin~~~f~  179 (200)
T KOG0177|consen  102 ILVAGYDPEEGPELYYIDYLATLVSVPYAAHGYGSYFCLSILDRYY--KPDMTIEEALDLMKKCVLELKKRLVINLPGFI  179 (200)
T ss_pred             EEEeccCCCCCCceeeehhhhhcccCCcccccchhhhhHHHHHhhh--CCCCCHHHHHHHHHHHHHHHHHhcccCCCCcE
Confidence            9999999988999999999999999999999999999999999998  5999999999999999999998854 446999


Q ss_pred             EEEEEeCCCcEEEcC
Q 029560          162 VGVVSKENPEFRVLS  176 (191)
Q Consensus       162 i~iv~~~~~~~~~~~  176 (191)
                      |.||+|+|  .+.++
T Consensus       180 v~IVdkdG--ir~~~  192 (200)
T KOG0177|consen  180 VKIVDKDG--IRKLD  192 (200)
T ss_pred             EEEEcCCC--ceecc
Confidence            99999997  55554

>KOG0179 consensus 20S proteasome, regulatory subunit beta type PSMB1/PRE7 [Posttranslational modification, protein turnover, chaperones]

Probab=99.98  E-value=1.8e-31  Score=201.62  Aligned_cols=166  Identities=17%  Similarity=0.337  Sum_probs=154.1

Q ss_pred             ccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeEE
Q 029560            6 LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMV   85 (191)
Q Consensus         6 ~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~iv   85 (191)
                      +.++..+|||+++|+++++.||.++|+..|...++.+.+.|++.++..|++..+|+.|+.++  |  ..++.||.+..++
T Consensus        55 I~sR~~~Ki~~l~D~~vl~~sGF~aD~l~L~k~i~~r~~~Y~~~h~k~ms~~s~A~lls~~L--Y--~kRFFPYYv~~il  130 (235)
T KOG0179|consen   55 INSRDQSKIFKLGDNIVLGSSGFYADTLALVKVIKSRIKQYEHDHNKKMSIHSAAQLLSTIL--Y--SKRFFPYYVFNIL  130 (235)
T ss_pred             eeccccchheeccCceEEecccchhhHHHHHHHHHHHHHHHhhcccccccHHHHHHHHHHHH--h--hcccccceeeeee
Confidence            56799999999999999999999999999999999999999999999999999999999999  5  5678999999999


Q ss_pred             EEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhc---------CCCCCCHHHHHHHHHHHHHhhhcccCC
Q 029560           86 LSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMK---------NDPAFTFQETVQTAISTLQSVLQEDFK  156 (191)
Q Consensus        86 ~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~---------~~~~~s~eea~~l~~~~l~~~~~~d~~  156 (191)
                      +|+|+++++.+|.+||.|++.+..+.|-|+++..++|+|+.++.         +...+|+|+|+.++.+++..|.+||..
T Consensus       131 aGiDeeGKG~VySyDPvGsyer~~~~AgGsa~~mI~PfLDnQi~~kn~~~e~~~~~~Ls~e~ai~lv~d~F~SAaERdI~  210 (235)
T KOG0179|consen  131 AGIDEEGKGAVYSYDPVGSYERVTCRAGGSAASMIQPFLDNQIGHKNQNLENAERTPLSLERAIRLVKDAFTSAAERDIY  210 (235)
T ss_pred             ecccccCceeEEeecCCcceeeeeeecCCcchhhhhhhhhhhccCcCcccccCcccccCHHHHHHHHHHHhhhhhhcccc
Confidence            99999999999999999999999999999999999999998853         134689999999999999999999999


Q ss_pred             CC-eEEEEEEEeCCCcEEEc
Q 029560          157 AS-EIEVGVVSKENPEFRVL  175 (191)
Q Consensus       157 ~~-~iei~iv~~~~~~~~~~  175 (191)
                      .+ +++|+|++++|...+.+
T Consensus       211 tGD~l~i~I~tk~gV~~e~~  230 (235)
T KOG0179|consen  211 TGDKLEICIITKDGVEVETL  230 (235)
T ss_pred             cCCcEEEEEEecCCEEEEee
Confidence            87 89999999998654444

>KOG0185 consensus 20S proteasome, regulatory subunit beta type PSMB4/PRE4 [Posttranslational modification, protein turnover, chaperones]

Probab=99.96  E-value=3.9e-29  Score=191.90  Aligned_cols=173  Identities=17%  Similarity=0.215  Sum_probs=157.4

Q ss_pred             cccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHH-HHhCCCCCHHHHHHHHHHHHHHhhhhcCccccccee
Q 029560            5 LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFR-FKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVA   83 (191)
Q Consensus         5 l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~-~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~   83 (191)
                      |..-++++|||+++||+++|+||..+|+|.+.+.+.....+.. +..|..+.|+.++.+|++.+  |..++.+.|++..+
T Consensus        66 laR~~nVeRi~kVgdntllG~sGdisD~Q~i~r~L~~l~iedn~~~Dg~~l~Pk~ih~yltrvl--Y~rRsKmnPlwntl  143 (256)
T KOG0185|consen   66 LARYKNVERIFKVGDNTLLGASGDISDFQYIQRVLEQLVIEDNRLDDGQSLGPKAIHSYLTRVL--YARRSKMNPLWNTL  143 (256)
T ss_pred             hhhhcCceeeEEecCceEEecCccHHHHHHHHHHHHHHHhcccccccccccChHHHHHHHHHHH--HHhhhccCchhhhe
Confidence            4456799999999999999999999999999999998887744 55678999999999999999  88899999999999


Q ss_pred             EEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhc-CCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEE
Q 029560           84 MVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMK-NDPAFTFQETVQTAISTLQSVLQEDFKAS-EIE  161 (191)
Q Consensus        84 iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~-~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~ie  161 (191)
                      +|||+|.++.|+|..+|..|..++.+..|+|.|+..|.++|++.|. +.++++.+||.+++.+||+...+||+.+. +|+
T Consensus       144 vVgGv~~~g~~~lg~V~~~G~~Y~~~~vATGfg~hLa~P~lR~~~~~k~~~~s~eeA~~li~~cMrVL~YRD~ra~n~fq  223 (256)
T KOG0185|consen  144 VVGGVDNTGEPFLGYVDLLGVAYESPVVATGFGAHLALPLLRDEWEKKGEDLSREEAEALIEKCMRVLYYRDARASNEFQ  223 (256)
T ss_pred             eEeeecCCCCeeEEEEeeccccccCchhhhhhHHHhhhHHHHHhhhccchhhHHHHHHHHHHHHHHHHhccccccccceE
Confidence            9999998788999999999999999999999999999999999996 45799999999999999999999999886 799


Q ss_pred             EEEEEeCCCcEEEcCHHHHH
Q 029560          162 VGVVSKENPEFRVLSIEEID  181 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~  181 (191)
                      |++||++|  +.+-.|..|+
T Consensus       224 va~v~~eG--v~i~~p~qv~  241 (256)
T KOG0185|consen  224 VATVDEEG--VTISKPYQVK  241 (256)
T ss_pred             EEEEcccc--eEecCceeee
Confidence            99999986  5665555544

>KOG0174 consensus 20S proteasome, regulatory subunit beta type PSMB6/PSMB9/PRE3 [Posttranslational modification, protein turnover, chaperones]

Probab=99.96  E-value=2.4e-28  Score=182.76  Aligned_cols=175  Identities=17%  Similarity=0.227  Sum_probs=159.4

Q ss_pred             ccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccccee
Q 029560            4 KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVA   83 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~   83 (191)
                      .++.++..+|+-+|.|+|+||-||.++|.|.+.+.++.....|..+.+.++++...++.++.+..+|     ..-+..++
T Consensus        43 ayvanRvtDKlT~itD~i~cCRSGSAADtQaiaD~~~Y~L~~~~~q~~~~p~v~~aA~l~r~~~Y~~-----re~L~Agl  117 (224)
T KOG0174|consen   43 AYVANRVTDKLTPITDNIYCCRSGSAADTQAIADIVRYHLELYTIQENKPPLVHTAASLFREICYNY-----REMLSAGL  117 (224)
T ss_pred             HHHHhhhcccceeccccEEEecCCchhhHHHHHHHHHHHHHHhhhhcCCCchHHHHHHHHHHHHHhC-----HHhhhcce
Confidence            4677889999999999999999999999999999999999999999999999999999999988544     23478999


Q ss_pred             EEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEE
Q 029560           84 MVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEV  162 (191)
Q Consensus        84 iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei  162 (191)
                      ||||||++.|.++|.+-.-|+..+-.++.-|+||.+++++++.+|  +|+||+||++++..+|+..++.||-.|+ -|.+
T Consensus       118 iVAGwD~~~gGqVY~iplGG~l~rq~~aIgGSGStfIYGf~D~~~--r~nMt~EE~~~fvk~Av~lAi~rDGsSGGviR~  195 (224)
T KOG0174|consen  118 IVAGWDEKEGGQVYSIPLGGSLTRQPFAIGGSGSTFIYGFCDANW--RPNMTLEECVRFVKNAVSLAIERDGSSGGVIRL  195 (224)
T ss_pred             EEeecccccCceEEEeecCceEeecceeeccCCceeeeeeehhhc--CCCCCHHHHHHHHHHHHHHHHhccCCCCCEEEE
Confidence            999999988999999977777877788888999999999999999  5999999999999999999999999987 6899


Q ss_pred             EEEEeCCCcEEEcCHHHHHHHHH
Q 029560          163 GVVSKENPEFRVLSIEEIDEHLT  185 (191)
Q Consensus       163 ~iv~~~~~~~~~~~~~~i~~~~~  185 (191)
                      .+++++|...+.+.++++.++..
T Consensus       196 ~~I~~~Gver~~~~~d~~~~~~v  218 (224)
T KOG0174|consen  196 VIINKAGVERRFFPGDKLGQFAV  218 (224)
T ss_pred             EEEccCCceEEEecCCccccccc
Confidence            99999999889999998876643

>KOG0173 consensus 20S proteasome, regulatory subunit beta type PSMB7/PSMB10/PUP1 [Posttranslational modification, protein turnover, chaperones]

Probab=99.95  E-value=2.8e-27  Score=183.38  Aligned_cols=162  Identities=17%  Similarity=0.282  Sum_probs=149.5

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      ...++.++.+||+.|.++|+||.+|-++|...+.+.+..+...++++.++.+++-...+.|.+.+..|     ..-.|+.
T Consensus        60 G~IvaDKnC~KIH~ia~~IyccGAGtAADte~vt~m~ss~l~Lh~l~t~R~~rVv~A~~mlkQ~LFrY-----qG~IgA~  134 (271)
T KOG0173|consen   60 GPIVADKNCEKIHFIAPNIYCCGAGTAADTEMVTRMISSNLELHRLNTGRKPRVVTALRMLKQHLFRY-----QGHIGAA  134 (271)
T ss_pred             CCeeecchhHHHhhcccceEEccCCchhhHHHHHHHHHHHHHHHHhccCCCCceeeHHHHHHHHHHHh-----cCcccce
Confidence            35678899999999999999999999999999999999999999999999999988889999888655     2358999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIE  161 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~ie  161 (191)
                      +|++|+|. .||+||.+-|.|+....++.++|||+..|+.+||.+|  .|+|+.|||++|+.+|+...+..|+.|+ |++
T Consensus       135 LiiGGvD~-TGpHLy~i~phGStd~~Pf~alGSGslaAmsvlEsr~--k~dlt~eea~~Lv~eAi~AGi~nDLgSGsnvd  211 (271)
T KOG0173|consen  135 LILGGVDP-TGPHLYSIHPHGSTDKLPFTALGSGSLAAMSVLESRW--KPDLTKEEAIKLVCEAIAAGIFNDLGSGSNVD  211 (271)
T ss_pred             eEEccccC-CCCceEEEcCCCCcCccceeeeccchHHHHHHHHHhc--CcccCHHHHHHHHHHHHHhhhccccCCCCcee
Confidence            99999998 8999999999999999999999999999999999999  5999999999999999999999999997 999


Q ss_pred             EEEEEeCCCcE
Q 029560          162 VGVVSKENPEF  172 (191)
Q Consensus       162 i~iv~~~~~~~  172 (191)
                      ++||++.+..|
T Consensus       212 lcVI~~~~~~~  222 (271)
T KOG0173|consen  212 LCVITKKGVEY  222 (271)
T ss_pred             EEEEeCCCccc
Confidence            99999765433

>KOG0180 consensus 20S proteasome, regulatory subunit beta type PSMB3/PUP3 [Posttranslational modification, protein turnover, chaperones]

Probab=99.94  E-value=8.5e-26  Score=166.22  Aligned_cols=158  Identities=18%  Similarity=0.265  Sum_probs=149.2

Q ss_pred             cCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeEEE
Q 029560            7 DHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVL   86 (191)
Q Consensus         7 ~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~iv~   86 (191)
                      .+.+.+|||+|.|++++|.+|+..|++.+.++++..-+.|+++.++.|.|+.+++.+|.++  |  ..++.||.+..+||
T Consensus        35 istdf~ki~~igdr~y~GL~glatDvqtl~~~~~fr~nLy~lre~R~i~P~~~s~mvS~~l--Y--ekRfgpYf~~PvVA  110 (204)
T KOG0180|consen   35 ISTDFQKIFKIGDRLYLGLTGLATDVQTLLERLRFRKNLYELREEREIKPETFSSMVSSLL--Y--EKRFGPYFTEPVVA  110 (204)
T ss_pred             eeccchhheecCCeeEEeccccchhHHHHHHHHHHHHhHHHhhhhcccCcHHHHHHHHHHH--H--HhhcCCcccceeEe
Confidence            3678999999999999999999999999999999999999999999999999999999999  5  34678999999999


Q ss_pred             EEcCCCCCeEEEECCCcceece-eeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEEEE
Q 029560           87 SIDEECGPRLFKCDPAGHFFGH-KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGV  164 (191)
Q Consensus        87 G~d~~~~p~Ly~~d~~G~~~~~-~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei~i  164 (191)
                      |.|+.++|+|..+|..|+.... ++.+.|.++...++.-|..|  +|+|..|++++.+.++|..+.+||+-|| +..|.+
T Consensus       111 Gl~~~~kPfIc~mD~IGc~~~~~DFVvsGTa~e~L~GmCE~ly--~pnmepd~LFetisQa~Lna~DRDalSGwGa~vyi  188 (204)
T KOG0180|consen  111 GLDDDNKPFICGMDLIGCIDAPKDFVVSGTASEQLYGMCEALY--EPNMEPDELFETISQALLNAVDRDALSGWGAVVYI  188 (204)
T ss_pred             ccCCCCCeeEeecccccCcCccCCeEEecchHHHHHHHHHHhc--CCCCCHHHHHHHHHHHHHhHhhhhhhccCCeEEEE
Confidence            9999889999999999998776 89999999999999999999  5999999999999999999999999998 999999


Q ss_pred             EEeCCC
Q 029560          165 VSKENP  170 (191)
Q Consensus       165 v~~~~~  170 (191)
                      |+|+..
T Consensus       189 I~kdkv  194 (204)
T KOG0180|consen  189 ITKDKV  194 (204)
T ss_pred             Eccchh
Confidence            999864

>cd01901 Ntn_hydrolase The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid

Probab=99.94  E-value=7.8e-25  Score=163.39  Aligned_cols=135  Identities=36%  Similarity=0.505  Sum_probs=129.4

Q ss_pred             CCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeEEEE
Q 029560            8 HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS   87 (191)
Q Consensus         8 ~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~iv~G   87 (191)
                      .....|++.++++++++++|..+|++.+.++++.+++.|++.++.++++..+++.+++.++.+++   .||+++++||+|
T Consensus        28 ~~~~~ki~~~~~~~~~~~sG~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~p~~~~~iiag  104 (164)
T cd01901          28 GSPVIKIGKNEDGIAWGLAGLAADAQTLVRRLREALQLYRLRYGEPISVVALAKELAKLLQVYTQ---GRPFGVNLIVAG  104 (164)
T ss_pred             CCCcceEEEecCCeEEEEecChHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcC---CCCcceEEEEEE
Confidence            56889999999999999999999999999999999999999999999999999999999998876   799999999999


Q ss_pred             EcCCCCCeEEEECCCcceece-eeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHH
Q 029560           88 IDEECGPRLFKCDPAGHFFGH-KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQ  148 (191)
Q Consensus        88 ~d~~~~p~Ly~~d~~G~~~~~-~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~  148 (191)
                      +|+ ++|+||.+||.|++.++ .++++|.++..+.++|++.|+  ++|+.+|+++++.+||.
T Consensus       105 ~~~-~~~~l~~id~~g~~~~~~~~~~~G~~~~~~~~~l~~~~~--~~~~~~~~~~~~~~~l~  163 (164)
T cd01901         105 VDE-GGGNLYYIDPSGPVIENPGAVATGSRSQRAKSLLEKLYK--PDMTLEEAVELALKALK  163 (164)
T ss_pred             EcC-CCCEEEEECCCcCEeecCcEEEECCCCHHHHHHHHHHhc--CCCCHHHHHHHHHHHHh
Confidence            998 88999999999999999 999999999999999999984  77999999999999986

N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either t

>PRK05456 ATP-dependent protease subunit HslV; Provisional

Probab=99.93  E-value=6.4e-25  Score=166.76  Aligned_cols=144  Identities=14%  Similarity=0.112  Sum_probs=119.5

Q ss_pred             CccccCCCCcceEEe-cCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            3 DKLLDHTSVTHLFPI-TKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i-~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      +.++.+++.+||++| ++|++|++||..+|++.|.+.++.+++.|+.  +.   ++..++.+..+.    .....+|+.+
T Consensus        24 g~~v~~~~~~KI~~i~~d~i~~~~aG~~aD~q~l~~~l~~~~~~y~~--~~---~~~~a~l~~~l~----~~~~~~~l~~   94 (172)
T PRK05456         24 GNTVMKGNARKVRRLYNGKVLAGFAGSTADAFTLFERFEAKLEEHQG--NL---LRAAVELAKDWR----TDRYLRRLEA   94 (172)
T ss_pred             CcEEEcCCCceEEEeCCCCEEEEEeccHHHHHHHHHHHHHHHHHccC--cc---HHHHHHHHHHHH----hccCCCccEE
Confidence            457788999999999 9999999999999999999999999999882  22   455554433221    1233468889


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceece--eeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGH--KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-  158 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~--~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-  158 (191)
                      ++|++  |+   |+||.+||.|+..+.  ++.|+|+|+.+++++|+++|+ .++|   ||++++++|++.+.+||..++ 
T Consensus        95 ~~lv~--d~---~~ly~id~~G~~~~~~~~~~a~GSGs~~a~g~ld~~y~-~~~m---eA~~la~kai~~A~~Rd~~sg~  165 (172)
T PRK05456         95 MLIVA--DK---EHSLIISGNGDVIEPEDGIIAIGSGGNYALAAARALLE-NTDL---SAEEIAEKALKIAADICIYTNH  165 (172)
T ss_pred             EEEEE--cC---CcEEEECCCCcEeccCCCeEEEecCHHHHHHHHHHhhh-cCCC---CHHHHHHHHHHHHHHhCeeCCC
Confidence            99994  54   689999999999777  799999999999999999983 2889   999999999999999999886 


Q ss_pred             eEEEEE
Q 029560          159 EIEVGV  164 (191)
Q Consensus       159 ~iei~i  164 (191)
                      +|+|-.
T Consensus       166 ~i~v~~  171 (172)
T PRK05456        166 NITIEE  171 (172)
T ss_pred             cEEEEE
Confidence            777654

>cd01913 protease_HslV Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome

Probab=99.93  E-value=2e-24  Score=163.13  Aligned_cols=142  Identities=11%  Similarity=0.023  Sum_probs=116.7

Q ss_pred             CccccCCCCcceEEecC-cEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccc-
Q 029560            3 DKLLDHTSVTHLFPITK-YLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLG-   80 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~-~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~-   80 (191)
                      +.++.+++.+||++|+| |++|+++|..+|++.|.++++.+++.|+.+.++     .+++.+..+.    .+ +.+|+. 
T Consensus        23 G~~v~~~~~~Ki~~i~d~~i~~~~aG~~aD~~~l~~~~~~~~~~y~~~~~~-----~aa~l~~~l~----~~-~~~~~l~   92 (171)
T cd01913          23 GNTVMKGNARKVRRLYNGKVIAGFAGSTADAFTLFERFEAKLEQYPGNLLR-----AAVELAKDWR----TD-RYLRRLE   92 (171)
T ss_pred             ccEEEcCCcceEEEeCCCCEEEEecccHHHHHHHHHHHHHHHHHhhchHHH-----HHHHHHHHHH----hc-cCcCceE
Confidence            45788999999999999 999999999999999999999999999988774     3334333322    11 335555 


Q ss_pred             ceeEEEEEcCCCCCeEEEECCCcceecee--eeecCCChHHHHHHHHHhhcCCC-CCCHHHHHHHHHHHHHhhhcccCCC
Q 029560           81 VVAMVLSIDEECGPRLFKCDPAGHFFGHK--ATSAGLKEQEAINFLEKKMKNDP-AFTFQETVQTAISTLQSVLQEDFKA  157 (191)
Q Consensus        81 v~~iv~G~d~~~~p~Ly~~d~~G~~~~~~--~~a~G~gs~~~~~~Le~~~~~~~-~~s~eea~~l~~~~l~~~~~~d~~~  157 (191)
                      +.+++++||     +||.+||.|+..+.+  +.|+||||.+|+++||.+|+  + +||   +.++|++|++.|.+||..+
T Consensus        93 a~~iv~~~~-----~ly~id~~G~~ie~~~~~~a~GSGS~ya~g~ld~~yk--~~~ms---~~~la~~Av~~A~~rd~~t  162 (171)
T cd01913          93 AMLIVADKE-----HTLLISGNGDVIEPDDGIAAIGSGGNYALAAARALLD--HTDLS---AEEIARKALKIAADICIYT  162 (171)
T ss_pred             EEEEEeCCC-----cEEEECCCCCEeccCCCeEEEeCCHHHHHHHHHHhhc--cCCCC---HHHHHHHHHHHHHhhCccc
Confidence            666665443     799999999999984  99999999999999999984  6 498   6699999999999999988


Q ss_pred             C-eEEEEE
Q 029560          158 S-EIEVGV  164 (191)
Q Consensus       158 ~-~iei~i  164 (191)
                      + +|.|-.
T Consensus       163 g~~i~~~~  170 (171)
T cd01913         163 NHNITVEE  170 (171)
T ss_pred             CCCEEEEe
Confidence            7 777654

HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the interior walls of the cavity. HslV shares significant sequence and structural similarity with the proteasomal beta-subunit and both are members of the Ntn-family of hydrolases. HslV has a nucleophilic threonine residue at its N-terminus that is exposed after processing of the propeptide and is directly involved in active site catalysis.

>TIGR03692 ATP_dep_HslV ATP-dependent protease HslVU, peptidase subunit

Probab=99.92  E-value=3e-24  Score=162.14  Aligned_cols=144  Identities=13%  Similarity=0.131  Sum_probs=115.5

Q ss_pred             CccccCCCCcceEEe-cCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            3 DKLLDHTSVTHLFPI-TKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i-~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      +.++.+++.+||++| ++|++|+++|..+|++.|.++++.+++.|+...     .+.+++.+++    +..+...+.+.+
T Consensus        23 g~~v~~~~~~Ki~~i~~d~i~~~~aG~~aD~q~l~~~~~~~~~~y~~~~-----~~~~a~l~~~----~~~~~~~~~l~a   93 (171)
T TIGR03692        23 GNTVMKGNARKVRRLYNGKVLAGFAGSTADAFTLFERFEAKLEEYQGNL-----TRAAVELAKD----WRTDRYLRRLEA   93 (171)
T ss_pred             ceEEEcCCCCeEEEeCCCCEEEEecchHHHHHHHHHHHHHHHHHccCch-----HHHHHHHHHH----HhhcccccccEE
Confidence            457789999999999 599999999999999999999999999987743     2444444443    211222223336


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceece--eeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGH--KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-  158 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~--~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-  158 (191)
                      .+|++||     |+||.+||.|.+.++  ++.++||||.+++++||..|+ .++|+   |+++|+++++.|.+||..++ 
T Consensus        94 ~~iv~~~-----~~ly~i~~~G~~ie~~~~~~a~GSGS~~a~g~ld~~y~-~~~~s---a~~la~~Av~~A~~rd~~sg~  164 (171)
T TIGR03692        94 MLIVADK-----ETSLLISGTGDVIEPEDGIAAIGSGGNYALAAARALLR-NTDLS---AEEIAREALKIAADICIYTNH  164 (171)
T ss_pred             EEEEEcC-----CCEEEEcCCCcEeccCCCeEEEeCCHHHHHHHHHHhhh-cCCCC---HHHHHHHHHHHHHhhCccCCC
Confidence            6666544     379999999999997  599999999999999999984 36676   99999999999999999887 


Q ss_pred             eEEEEE
Q 029560          159 EIEVGV  164 (191)
Q Consensus       159 ~iei~i  164 (191)
                      +|.|-.
T Consensus       165 ~i~v~~  170 (171)
T TIGR03692       165 NITIEE  170 (171)
T ss_pred             CEEEEe
Confidence            777653

The ATP-dependent protease HslVU, a complex of hexameric HslU active as a protein-unfolding ATPase and dodecameric HslV, the catalytic threonine protease.

>COG5405 HslV ATP-dependent protease HslVU (ClpYQ), peptidase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=99.01  E-value=3.7e-09  Score=77.88  Aligned_cols=140  Identities=15%  Similarity=0.152  Sum_probs=102.3

Q ss_pred             CCCcceEEec-CcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeEEEE
Q 029560            9 TSVTHLFPIT-KYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS   87 (191)
Q Consensus         9 ~~~~Ki~~i~-~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~iv~G   87 (191)
                      .+..|+.+|. .+++.|++|.++|+..|.+.+..+++.|.         ..|.+..-++.+.+......|.+-.-++|+ 
T Consensus        33 ~narKvRkl~~gkvlaGFAGstADaftLfe~fe~kle~~~---------g~L~raavelaKdwr~Dk~lr~LEAmllVa-  102 (178)
T COG5405          33 GNARKVRRLYNGKVLAGFAGSTADAFTLFERFEAKLEQYQ---------GDLFRAAVELAKDWRTDKYLRKLEAMLLVA-  102 (178)
T ss_pred             ccHHHHHHHcCCcEEEEecccchhHHHHHHHHHHHHHHcc---------CcHHHHHHHHHHhhhhhhHHHHHhhheeEe-
Confidence            4455555554 49999999999999999999999998873         334444445555554445567777778887 


Q ss_pred             EcCCCCCeEEEECCCcceece--eeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEEEE
Q 029560           88 IDEECGPRLFKCDPAGHFFGH--KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGV  164 (191)
Q Consensus        88 ~d~~~~p~Ly~~d~~G~~~~~--~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei~i  164 (191)
                       |+   -.+|-+...|.+.+.  ...|||||..+|.......++ .+++   +|.+++.++|..+-+-+.++. ++.|-.
T Consensus       103 -d~---~~il~isG~gdV~epe~~~~aIGSGgnyAl~AarAl~~-~~~l---sA~eIa~~sl~iA~eiciyTN~ni~ve~  174 (178)
T COG5405         103 -DK---THILIITGNGDVIEPEDDIIAIGSGGNYALSAARALME-NTEL---SAREIAEKSLKIAGDICIYTNHNIVVEE  174 (178)
T ss_pred             -CC---CcEEEEecCcceecCCCCeEEEcCCchHHHHHHHHHHh-ccCC---CHHHHHHHHHhhhheEEEecCCcEEEEE
Confidence             44   348889999998876  589999999999999998874 4566   566778888888775555543 666655


Q ss_pred             EE
Q 029560          165 VS  166 (191)
Q Consensus       165 v~  166 (191)
                      +.
T Consensus       175 l~  176 (178)
T COG5405         175 LR  176 (178)
T ss_pred             ee
Confidence            43

>COG3484 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]

Probab=97.42  E-value=0.0037  Score=48.24  Aligned_cols=146  Identities=12%  Similarity=0.106  Sum_probs=102.5

Q ss_pred             EEEEEecchHHHHHHHHHHHHHHHHHHHH-hCCCCCHHHHHHHHHHHHHHhhhhc------CcccccceeEEEEEcCCCC
Q 029560           21 LGLLATGMTADARTLVQQARYEAAEFRFK-YGYEMPVDVLAKWIADKSQVYTQHA------YMRPLGVVAMVLSIDEECG   93 (191)
Q Consensus        21 i~~~~sG~~~D~~~l~~~~~~~~~~~~~~-~~~~~~~~~l~~~l~~~~~~~t~~~------~~rP~~v~~iv~G~d~~~~   93 (191)
                      ++++-+|-.+-.|.+.+.+....+.-.-. --.-.+.-..+..+...+.+-.-+.      .---|.|++|++|-=...-
T Consensus        45 lvl~taGNLA~tQaV~~ll~e~~~~d~~~~L~n~~sm~eattlvgetvrEv~~rds~~leka~~dfn~sfllGGQI~G~p  124 (255)
T COG3484          45 LVLCTAGNLAITQAVLHLLDERIQRDDGDSLLNIPSMYEATTLVGETVREVQARDSPALEKAGIDFNCSFLLGGQIKGEP  124 (255)
T ss_pred             EEEEecCccHHHHHHHHHHHHHhhccchhhhhcchhHHHHHHHHHHHHHHHHhccCchhhccCcceeEEEEEcceecCCC
Confidence            56677999999999999888776522211 1122345555666666654332111      1235889999999876445


Q ss_pred             CeEEEECCCcceece----eeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEEEEEEeC
Q 029560           94 PRLFKCDPAGHFFGH----KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKE  168 (191)
Q Consensus        94 p~Ly~~d~~G~~~~~----~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei~iv~~~  168 (191)
                      |.||.+-|.|++.+.    .+.-+|.. .+-+++|++.+.  .+++++||.+.++-.+-..+..++.-| -+++-++.++
T Consensus       125 p~Ly~IYpqGNFIqaT~etpf~QiGEt-KYGKPildR~i~--~~~pLeea~kcaLvS~DSTlkSNiSVGlPldLl~~e~d  201 (255)
T COG3484         125 PRLYLIYPQGNFIQATPETPFLQIGET-KYGKPILDRTIT--YDTPLEEAAKCALVSFDSTLKSNISVGLPLDLLVYEAD  201 (255)
T ss_pred             ceeEEEccCCCeeecCCCCceeEcccc-ccCchhhhhhhh--ccCCHHHHhhheEEecchhhhccccccCCceeEEEecc
Confidence            899999999999874    57777754 567899999874  679999999999888877776565555 5777777766


Q ss_pred             C
Q 029560          169 N  169 (191)
Q Consensus       169 ~  169 (191)
                      -
T Consensus       202 s  202 (255)
T COG3484         202 S  202 (255)
T ss_pred             c
Confidence            3

>KOG3361 consensus Iron binding protein involved in Fe-S cluster formation [Energy production and conversion]

Probab=87.39  E-value=1.3  Score=32.06  Aligned_cols=44  Identities=20%  Similarity=0.160  Sum_probs=39.2

Q ss_pred             EEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHH
Q 029560           97 FKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQT  142 (191)
Q Consensus        97 y~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l  142 (191)
                      ..+|-+|.+...++-..|.||..|-.-+-..|  -..+|+|||.++
T Consensus        71 Ikvd~~g~I~dakFKTFGCGSAIASSS~aTew--vkgkt~dea~kI  114 (157)
T KOG3361|consen   71 IKVDDSGVIEDAKFKTFGCGSAIASSSLATEW--VKGKTLDEALKI  114 (157)
T ss_pred             EEECCCCcEEEeeeeecccchHhhhhHHHHHH--HccccHHHHHhc
Confidence            57888999999999999999999999999888  477999999865

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	191
3unb_G	246	Mouse Constitutive 20s Proteasome In Complex With P		2e-66
1iru_A	246	Crystal Structure Of The Mammalian 20s Proteasome A		2e-66
1g0u_G	252	A Gated Channel Into The Proteasome Core Particle L		7e-43
1ryp_A	243	Crystal Structure Of The 20s Proteasome From Yeast		7e-43
3h4p_A	264	Proteasome 20s Core Particle From Methanocaldococcu		2e-26
1iru_B	233	Crystal Structure Of The Mammalian 20s Proteasome A		1e-23
3jrm_A	227	Crystal Structure Of Archaeal 20s Proteasome In Com		1e-23
3unb_A	234	Mouse Constitutive 20s Proteasome In Complex With P		1e-23
1yau_A	233	Structure Of Archeabacterial 20s Proteasome- Pa26 C		1e-23
2ku1_A	237	Dynamic Regulation Of Archaeal Proteasome Gate Open		1e-23
1yar_A	233	Structure Of Archeabacterial 20s Proteasome Mutant		1e-23
2ku2_A	237	Dynamic Regulation Of Archaeal Proteasome Gate Open		1e-23
1pma_A	233	Proteasome From Thermoplasma Acidophilum Length = 2		1e-23
1j2q_A	237	20s Proteasome In Complex With Calpain-inhibitor I		1e-22
1j2p_A	246	Alpha-Ring From The Proteasome From Archaeoglobus F		3e-22
3unb_C	248	Mouse Constitutive 20s Proteasome In Complex With P		2e-20
3une_C	248	Mouse Constitutive 20s Proteasome Length = 248		2e-20
1iru_D	248	Crystal Structure Of The Mammalian 20s Proteasome A		6e-19
1iru_F	263	Crystal Structure Of The Mammalian 20s Proteasome A		7e-19
3unb_E	263	Mouse Constitutive 20s Proteasome In Complex With P		8e-19
1ryp_B	250	Crystal Structure Of The 20s Proteasome From Yeast		4e-18
1vsy_B	231	Proteasome Activator Complex Length = 231		4e-18
1vsy_D	227	Proteasome Activator Complex Length = 227		1e-17
1ryp_D	241	Crystal Structure Of The 20s Proteasome From Yeast		1e-17
1g0u_C	243	A Gated Channel Into The Proteasome Core Particle L		1e-17
1fnt_D	254	Crystal Structure Of The 20s Proteasome From Yeast		1e-17
1vsy_C	232	Proteasome Activator Complex Length = 232		2e-17
1g0u_B	245	A Gated Channel Into The Proteasome Core Particle L		2e-17
1ryp_C	244	Crystal Structure Of The 20s Proteasome From Yeast		3e-17
3oeu_B	235	Structure Of Yeast 20s Open-Gate Proteasome With Co		3e-17
1z7q_C	258	Crystal Structure Of The 20s Proteasome From Yeast		3e-17
1iru_C	261	Crystal Structure Of The Mammalian 20s Proteasome A		5e-16
3unb_F	255	Mouse Constitutive 20s Proteasome In Complex With P		6e-16
1iru_G	254	Crystal Structure Of The Mammalian 20s Proteasome A		8e-16
1iru_E	241	Crystal Structure Of The Mammalian 20s Proteasome A		2e-15
3unb_D	241	Mouse Constitutive 20s Proteasome In Complex With P		2e-15
3unb_B	261	Mouse Constitutive 20s Proteasome In Complex With P		4e-15
1fnt_G	287	Crystal Structure Of The 20s Proteasome From Yeast		4e-13
1z7q_G	288	Crystal Structure Of The 20s Proteasome From Yeast		5e-13
3oeu_F	242	Structure Of Yeast 20s Open-Gate Proteasome With Co		5e-13
1g0u_D	241	A Gated Channel Into The Proteasome Core Particle L		5e-13
1g0u_F	248	A Gated Channel Into The Proteasome Core Particle L		5e-13
1ryp_G	244	Crystal Structure Of The 20s Proteasome From Yeast		5e-13
1vsy_E	250	Proteasome Activator Complex Length = 250		1e-12
4g4s_E	261	Structure Of Proteasome-Pba1-Pba2 Complex Length =		2e-12
1fnt_E	260	Crystal Structure Of The 20s Proteasome From Yeast		2e-12
2z5c_C	262	Crystal Structure Of A Novel Chaperone Complex For		2e-12
1ryp_E	242	Crystal Structure Of The 20s Proteasome From Yeast		2e-12
3sdi_E	233	Structure Of Yeast 20s Open-Gate Proteasome With Co		1e-09
1g0u_E	234	A Gated Channel Into The Proteasome Core Particle L		1e-09
1ryp_F	233	Crystal Structure Of The 20s Proteasome From Yeast		7e-09
1fnt_F	234	Crystal Structure Of The 20s Proteasome From Yeast		8e-09
4g4s_F	235	Structure Of Proteasome-Pba1-Pba2 Complex Length =		8e-09
3c91_H	203	Thermoplasma Acidophilum 20s Proteasome With An Ope		2e-06
1ya7_H	217	Implications For Interactions Of Proteasome With Pa		2e-06
1pma_B	211	Proteasome From Thermoplasma Acidophilum Length = 2		2e-06

>pdb|3UNB|G Chain G, Mouse Constitutive 20s Proteasome In Complex With Pr-957 Length = 246

Iteration: 1
 Score =  248 bits (633), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 115/189 (60%), Positives = 155/189 (82%)
Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K 
Sbjct: 58  DKLLDSSTVTHLFKITESIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKR 117
Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IAD SQVYTQ+A MRPLG   +++ IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +
Sbjct: 118 IADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTS 177
Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKK+K    +TF++TV+TAI+ L +VL  DFK SEIEVGVV+ ENP+FR+L+  EID 
Sbjct: 178 FLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDA 237
Query: 183 HLTAISERD 191
           HL A++ERD
Sbjct: 238 HLVALAERD 246

>pdb|1IRU|A Chain A, Crystal Structure Of The Mammalian 20s Proteasome At 2.75 A Resolution Length = 246

Iteration: 1
 Score =  248 bits (633), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 115/189 (60%), Positives = 155/189 (82%)
Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K 
Sbjct: 58  DKLLDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKR 117
Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IAD SQVYTQ+A MRPLG   +++ IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +
Sbjct: 118 IADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTS 177
Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKK+K    +TF++TV+TAI+ L +VL  DFK SEIEVGVV+ ENP+FR+L+  EID 
Sbjct: 178 FLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDA 237
Query: 183 HLTAISERD 191
           HL A++ERD
Sbjct: 238 HLVALAERD 246

>pdb|1G0U|G Chain G, A Gated Channel Into The Proteasome Core Particle Length = 252

Iteration: 1
 Score =  169 bits (429), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 92/194 (47%), Positives = 135/194 (69%), Gaps = 7/194 (3%)
Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD T+V+++F I++ +G++  G   DAR    +A+ EAAEFR+KYGY+MP DVLAK 
Sbjct: 61  DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR 120
Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           +A+ SQ+YTQ AYMRPLGV+   +S+DEE GP ++K DPAG++ G+KAT+ G K+QE   
Sbjct: 121 MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT 180
Query: 123 FLE---KKMKNDPAF--TFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSI 177
            LE   KK K D     ++++ V+ AI+ +   L  +F  +++EVGV +K+  +F  LS 
Sbjct: 181 NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKD--KFFTLSA 238
Query: 178 EEIDEHLTAISERD 191
           E I+E L AI+E+D
Sbjct: 239 ENIEERLVAIAEQD 252

>pdb|1RYP|A Chain A, Crystal Structure Of The 20s Proteasome From Yeast At 2.4 Angstroms Resolution Length = 243

Iteration: 1
 Score =  169 bits (429), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 92/194 (47%), Positives = 135/194 (69%), Gaps = 7/194 (3%)
Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD T+V+++F I++ +G++  G   DAR    +A+ EAAEFR+KYGY+MP DVLAK 
Sbjct: 52  DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR 111
Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           +A+ SQ+YTQ AYMRPLGV+   +S+DEE GP ++K DPAG++ G+KAT+ G K+QE   
Sbjct: 112 MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT 171
Query: 123 FLE---KKMKNDPAF--TFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSI 177
            LE   KK K D     ++++ V+ AI+ +   L  +F  +++EVGV +K+  +F  LS 
Sbjct: 172 NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKD--KFFTLSA 229
Query: 178 EEIDEHLTAISERD 191
           E I+E L AI+E+D
Sbjct: 230 ENIEERLVAIAEQD 243

>pdb|3H4P|A Chain A, Proteasome 20s Core Particle From Methanocaldococcus Jannaschii Length = 264

Iteration: 1
 Score =  115 bits (288), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 61/179 (34%), Positives = 102/179 (56%), Gaps = 4/179 (2%)
Query: 1   MQDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA 60
           +  KL+   S+  +F I  ++    +G+ ADAR L+ +AR EA  +R  YG E+ +++LA
Sbjct: 58  ITSKLVKIRSIEKIFQIDDHVAAATSGLVADARVLIDRARLEAQIYRLTYGEEISIEMLA 117
Query: 61  KWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEA 120
           K I D  Q YTQH  +RP GV  ++  ID+    RLF+ DP+G    +KAT+ G      
Sbjct: 118 KKICDIKQAYTQHGGVRPFGVSLLIAGIDKN-EARLFETDPSGALIEYKATAIGSGRPVV 176
Query: 121 INFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEE 179
           +  LEK+ ++D   T  E ++ AI+ L     ED K   ++V +++ ++ +F+ + +EE
Sbjct: 177 MELLEKEYRDD--ITLDEGLELAITALTKA-NEDIKPENVDVCIITVKDAQFKKIPVEE 232

>pdb|1IRU|B Chain B, Crystal Structure Of The Mammalian 20s Proteasome At 2.75 A Resolution Length = 233

Iteration: 1
 Score =  106 bits (264), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 64/184 (34%), Positives = 97/184 (52%), Gaps = 5/184 (2%)
Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
           L D  SV  + PITK++GL+ +GM  D R LV +AR  A ++   Y   +P   L + +A
Sbjct: 55  LYDERSVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVA 114
Query: 65  DKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFL 124
              Q YTQ   +RP GV  ++   + E  P LF+ DP+G +F  KAT+ G        FL
Sbjct: 115 SVMQEYTQSGGVRPFGVSLLICGWN-EGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFL 173
Query: 125 EKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 184
           EK+   D     ++ + TAI TL+   +       IEVG+ ++    FR L+  E+ ++L
Sbjct: 174 EKRYNED--LELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAG--FRRLTPTEVKDYL 229
Query: 185 TAIS 188
            AI+
Sbjct: 230 AAIA 233

>pdb|3JRM|A Chain A, Crystal Structure Of Archaeal 20s Proteasome In Complex With Mutated P26 Activator Length = 227

Iteration: 1
 Score =  105 bits (263), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 64/186 (34%), Positives = 103/186 (55%), Gaps = 8/186 (4%)
Query: 1   MQDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA 60
           ++ +L++  S+  +  I  Y+  + +G+ ADAR LV  AR  A + +  YG  + ++ L 
Sbjct: 48  VRSRLIEQNSIEKIQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLV 107
Query: 61  KWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEA 120
           K +AD+ Q YTQ+  +RP GV  +   ID + GPRLF CDPAG    +KAT+ G  +   
Sbjct: 108 KRVADQMQQYTQYGGVRPYGVSLIFAGID-QIGPRLFDCDPAGTINEYKATAIGSGKDAV 166
Query: 121 INFLEKKMKNDPAFTFQETVQTAISTLQSVLQ--EDFKASEIEVGVVSKENPEFRVLSIE 178
           ++FLE++ K +     +E V   I  L+S L+  E+ KA EI    V     ++R+   E
Sbjct: 167 VSFLEREYKEN--LPEKEAVTLGIKALKSSLEEGEELKAPEIASITVGN---KYRIYDQE 221
Query: 179 EIDEHL 184
           E+ + L
Sbjct: 222 EVKKFL 227

>pdb|3UNB|A Chain A, Mouse Constitutive 20s Proteasome In Complex With Pr-957 Length = 234

Iteration: 1
 Score =  105 bits (263), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 64/184 (34%), Positives = 97/184 (52%), Gaps = 5/184 (2%)
Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
           L D  SV  + PITK++GL+ +GM  D R LV +AR  A ++   Y   +P   L + +A
Sbjct: 56  LYDERSVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVA 115
Query: 65  DKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFL 124
              Q YTQ   +RP GV  ++   + E  P LF+ DP+G +F  KAT+ G        FL
Sbjct: 116 SVMQEYTQSGGVRPFGVSLLICGWN-EGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFL 174
Query: 125 EKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 184
           EK+   D     ++ + TAI TL+   +       IEVG+ ++    FR L+  E+ ++L
Sbjct: 175 EKRYNED--LELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAG--FRRLTPTEVRDYL 230
Query: 185 TAIS 188
            AI+
Sbjct: 231 AAIA 234

>pdb|1YAU|A Chain A, Structure Of Archeabacterial 20s Proteasome- Pa26 Complex Length = 233

Iteration: 1
 Score =  105 bits (263), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 61/184 (33%), Positives = 103/184 (55%), Gaps = 4/184 (2%)
Query: 1   MQDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA 60
           ++ +L++  S+  +  I  Y+  + +G+ ADAR LV  AR  A + +  YG  + ++ L 
Sbjct: 54  VRSRLIEQNSIEKIQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLV 113
Query: 61  KWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEA 120
           K +AD+ Q YTQ+  +RP GV  +   ID + GPRLF CDPAG    +KAT+ G  +   
Sbjct: 114 KRVADQMQQYTQYGGVRPYGVSLIFAGID-QIGPRLFDCDPAGTINEYKATAIGSGKDAV 172
Query: 121 INFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEI 180
           ++FLE++ K +     +E V   I  L+S L+E  +    E+  ++  N ++R+   EE+
Sbjct: 173 VSFLEREYKEN--LPEKEAVTLGIKALKSSLEEGEELKAPEIASITVGN-KYRIYDQEEV 229
Query: 181 DEHL 184
            + L
Sbjct: 230 KKFL 233

>pdb|2KU1|A Chain A, Dynamic Regulation Of Archaeal Proteasome Gate Opening As Studied By Trosy-Nmr Length = 237

Iteration: 1
 Score =  105 bits (263), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 61/184 (33%), Positives = 103/184 (55%), Gaps = 4/184 (2%)
Query: 1   MQDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA 60
           ++ +L++  S+  +  I  Y+  + +G+ ADAR LV  AR  A + +  YG  + ++ L 
Sbjct: 58  VRSRLIEQNSIEKIQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLV 117
Query: 61  KWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEA 120
           K +AD+ Q YTQ+  +RP GV  +   ID + GPRLF CDPAG    +KAT+ G  +   
Sbjct: 118 KRVADQMQQYTQYGGVRPYGVSLIFAGID-QIGPRLFDCDPAGTINEYKATAIGSGKDAV 176
Query: 121 INFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEI 180
           ++FLE++ K +     +E V   I  L+S L+E  +    E+  ++  N ++R+   EE+
Sbjct: 177 VSFLEREYKEN--LPEKEAVTLGIKALKSSLEEGEELKAPEIASITVGN-KYRIYDQEEV 233
Query: 181 DEHL 184
            + L
Sbjct: 234 KKFL 237

>pdb|1YAR|A Chain A, Structure Of Archeabacterial 20s Proteasome Mutant D9s- Pa26 Complex Length = 233

Iteration: 1
 Score =  105 bits (263), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 64/186 (34%), Positives = 103/186 (55%), Gaps = 8/186 (4%)
Query: 1   MQDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA 60
           ++ +L++  S+  +  I  Y+  + +G+ ADAR LV  AR  A + +  YG  + ++ L 
Sbjct: 54  VRSRLIEQNSIEKIQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLV 113
Query: 61  KWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEA 120
           K +AD+ Q YTQ+  +RP GV  +   ID + GPRLF CDPAG    +KAT+ G  +   
Sbjct: 114 KRVADQMQQYTQYGGVRPYGVSLIFAGID-QIGPRLFDCDPAGTINEYKATAIGSGKDAV 172
Query: 121 INFLEKKMKNDPAFTFQETVQTAISTLQSVLQ--EDFKASEIEVGVVSKENPEFRVLSIE 178
           ++FLE++ K +     +E V   I  L+S L+  E+ KA EI    V     ++R+   E
Sbjct: 173 VSFLEREYKEN--LPEKEAVTLGIKALKSSLEEGEELKAPEIASITVGN---KYRIYDQE 227
Query: 179 EIDEHL 184
           E+ + L
Sbjct: 228 EVKKFL 233

>pdb|2KU2|A Chain A, Dynamic Regulation Of Archaeal Proteasome Gate Opening As Studied By Trosy-Nmr Length = 237

Iteration: 1
 Score =  105 bits (263), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 61/184 (33%), Positives = 103/184 (55%), Gaps = 4/184 (2%)
Query: 1   MQDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA 60
           ++ +L++  S+  +  I  Y+  + +G+ ADAR LV  AR  A + +  YG  + ++ L 
Sbjct: 58  VRSRLIEQNSIEKIQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLV 117
Query: 61  KWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEA 120
           K +AD+ Q YTQ+  +RP GV  +   ID + GPRLF CDPAG    +KAT+ G  +   
Sbjct: 118 KRVADQMQQYTQYGGVRPYGVSLIFAGID-QIGPRLFDCDPAGTINEYKATAIGSGKDAV 176
Query: 121 INFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEI 180
           ++FLE++ K +     +E V   I  L+S L+E  +    E+  ++  N ++R+   EE+
Sbjct: 177 VSFLEREYKEN--LPEKEAVTLGIKALKSSLEEGEELKAPEIASITVGN-KYRIYDQEEV 233
Query: 181 DEHL 184
            + L
Sbjct: 234 KKFL 237

>pdb|1PMA|A Chain A, Proteasome From Thermoplasma Acidophilum Length = 233

Iteration: 1
 Score =  105 bits (262), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 64/186 (34%), Positives = 103/186 (55%), Gaps = 8/186 (4%)
Query: 1   MQDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA 60
           ++ +L++  S+  +  I  Y+  + +G+ ADAR LV  AR  A + +  YG  + ++ L 
Sbjct: 54  VRSRLIEQNSIEKIQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLV 113
Query: 61  KWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEA 120
           K +AD+ Q YTQ+  +RP GV  +   ID + GPRLF CDPAG    +KAT+ G  +   
Sbjct: 114 KRVADQMQQYTQYGGVRPYGVSLIFAGID-QIGPRLFDCDPAGTINEYKATAIGSGKDAV 172
Query: 121 INFLEKKMKNDPAFTFQETVQTAISTLQSVLQ--EDFKASEIEVGVVSKENPEFRVLSIE 178
           ++FLE++ K +     +E V   I  L+S L+  E+ KA EI    V     ++R+   E
Sbjct: 173 VSFLEREYKEN--LPEKEAVTLGIKALKSSLEEGEELKAPEIASITVGN---KYRIYDQE 227
Query: 179 EIDEHL 184
           E+ + L
Sbjct: 228 EVKKFL 233

>pdb|1J2Q|A Chain A, 20s Proteasome In Complex With Calpain-inhibitor I From Archaeoglobus Fulgidus Length = 237

Iteration: 1
 Score =  102 bits (255), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 57/187 (30%), Positives = 101/187 (54%), Gaps = 4/187 (2%)
Query: 4   KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWI 63
           KLL+  ++  ++ I +++    +G+ ADAR L+ +AR EA   R  Y   + V  LAK I
Sbjct: 48  KLLEADTIEKIYKIDEHICAATSGLVADARVLIDRARIEAQINRLTYDEPITVKELAKKI 107
Query: 64  ADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINF 123
            D  Q YTQ+  +RP GV  ++  +DE   P+L++ DP+G    +KAT+ G+       F
Sbjct: 108 CDFKQQYTQYGGVRPFGVSLLIAGVDEV--PKLYETDPSGALLEYKATAIGMGRNAVTEF 165
Query: 124 LEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEH 183
            EK+ ++D   +F + +   +  +   ++ +     IEVG V  ++  F+ +S EE+  +
Sbjct: 166 FEKEYRDD--LSFDDAMVLGLVAMGLSIESELVPENIEVGYVKVDDRTFKEVSPEELKPY 223
Query: 184 LTAISER 190
           +   +ER
Sbjct: 224 VERANER 230

>pdb|1J2P|A Chain A, Alpha-Ring From The Proteasome From Archaeoglobus Fulgidus Length = 246

Iteration: 1
 Score =  101 bits (251), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 56/187 (29%), Positives = 101/187 (54%), Gaps = 4/187 (2%)
Query: 4   KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWI 63
           KLL+  ++  ++ I +++    +G+ ADAR L+ +AR EA   R  Y   + V  LAK I
Sbjct: 57  KLLEKDTIEKIYKIDEHICAATSGLVADARVLIDRARIEAQINRLTYDIPITVKELAKKI 116
Query: 64  ADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINF 123
            D  Q YTQ+  +RP GV  ++  ++E   P+L++ DP+G    +KAT+ G+       F
Sbjct: 117 CDFKQQYTQYGGVRPFGVSLLIAGVNEV--PKLYETDPSGALLEYKATAIGMGRMAVTEF 174
Query: 124 LEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEH 183
            EK+ ++D   +F + +   +  +   ++ +     IEVG V  ++  F+ +S EE+  +
Sbjct: 175 FEKEYRDD--LSFDDAMVLGLVAMGLSIESELVPENIEVGYVKVDDRTFKEVSPEELKPY 232
Query: 184 LTAISER 190
           +   +ER
Sbjct: 233 VERANER 239

>pdb|3UNB|C Chain C, Mouse Constitutive 20s Proteasome In Complex With Pr-957 Length = 248

Iteration: 1
 Score = 95.5 bits (236), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 55/181 (30%), Positives = 95/181 (52%), Gaps = 3/181 (1%)
Query: 4   KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWI 63
           KL D  +V  +  +   + +   G+TADAR ++ +AR E    R      + V+ + ++I
Sbjct: 52  KLQDERTVRKICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYI 111
Query: 64  ADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINF 123
           A   Q YTQ    RP G+ A+++  D +  PRL++ DP+G +   KA + G   +    F
Sbjct: 112 ASLKQRYTQSNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREF 171
Query: 124 LEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEH 183
           LEK   +D   T   T++  I  L  V+Q   K   IE+ V+ ++ P  ++L+ EEI+++
Sbjct: 172 LEKNYTDDAIETDDLTIKLVIKALLEVVQSGGK--NIELAVMRRDQP-LKILNPEEIEKY 228
Query: 184 L 184
           +
Sbjct: 229 V 229

>pdb|3UNE|C Chain C, Mouse Constitutive 20s Proteasome Length = 248

Iteration: 1
 Score = 95.5 bits (236), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 55/181 (30%), Positives = 95/181 (52%), Gaps = 3/181 (1%)
Query: 4   KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWI 63
           KL D  +V  +  +   + +   G+TADAR ++ +AR E    R      + V+ + ++I
Sbjct: 52  KLQDERTVRKICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYI 111
Query: 64  ADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINF 123
           A   Q YTQ    RP G+ A+++  D +  PRL++ DP+G +   KA + G   +    F
Sbjct: 112 ASLKQRYTQSNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREF 171
Query: 124 LEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEH 183
           LEK   +D   T   T++  I  L  V+Q   K   IE+ V+ ++ P  ++L+ EEI+++
Sbjct: 172 LEKNYTDDAIETDDLTIKLVIKALLEVVQSGGK--NIELAVMRRDQP-LKILNPEEIEKY 228
Query: 184 L 184
           +
Sbjct: 229 V 229

>pdb|1IRU|D Chain D, Crystal Structure Of The Mammalian 20s Proteasome At 2.75 A Resolution Length = 248

Iteration: 1
 Score = 90.1 bits (222), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 52/181 (28%), Positives = 92/181 (50%), Gaps = 3/181 (1%)
Query: 4   KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWI 63
           KL D  +V  +  +   + +   G+TADAR ++ +AR E    R      + V+ + ++I
Sbjct: 52  KLQDERTVRKICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYI 111
Query: 64  ADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINF 123
           A   Q YTQ    RP G+ A+++  D +  PRL++ DP+G +   KA + G   +    F
Sbjct: 112 ASLKQRYTQSNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREF 171
Query: 124 LEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEH 183
           LEK   ++   T   T++  I  L  V+Q   K  E+    V + +   ++L+ EEI+++
Sbjct: 172 LEKNYTDEAIETDDLTIKLVIKALLEVVQSGGKNIEL---AVMRRDQSLKILNPEEIEKY 228
Query: 184 L 184
           +
Sbjct: 229 V 229

>pdb|1IRU|F Chain F, Crystal Structure Of The Mammalian 20s Proteasome At 2.75 A Resolution Length = 263

Iteration: 1
 Score = 90.1 bits (222), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 51/176 (28%), Positives = 87/176 (49%), Gaps = 4/176 (2%)
Query: 17  ITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYM 76
           +  ++G+   G+TADAR L    R E  + RF +   +PV  L   I  K+Q+ TQ    
Sbjct: 66  VDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGR 125
Query: 77  RPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTF 136
           RP GV  ++   D + GP +F+  P+ ++F  +A S G + Q A  +LE+ M        
Sbjct: 126 RPYGVGLLIAGYD-DMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFMECNL 184
Query: 137 QETVQTAISTLQSVL--QEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 190
            E V+  +  L+  L  ++D     + +G+V K+  EF +   +++   L  + ER
Sbjct: 185 NELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDL-EFTIYDDDDVSPFLEGLEER 239

>pdb|3UNB|E Chain E, Mouse Constitutive 20s Proteasome In Complex With Pr-957 Length = 263

Iteration: 1
 Score = 89.7 bits (221), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 51/176 (28%), Positives = 87/176 (49%), Gaps = 4/176 (2%)
Query: 17  ITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYM 76
           +  ++G+   G+TADAR L    R E  + RF +   +PV  L   I  K+Q+ TQ    
Sbjct: 66  VDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGR 125
Query: 77  RPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTF 136
           RP GV  ++   D + GP +F+  P+ ++F  +A S G + Q A  +LE+ M        
Sbjct: 126 RPYGVGLLIAGYD-DMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFMECNL 184
Query: 137 QETVQTAISTLQSVL--QEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 190
            E V+  +  L+  L  ++D     + +G+V K + EF +   +++   L  + ER
Sbjct: 185 DELVKHGLRALRETLPAEQDLTTKNVSIGIVGK-DLEFTIYDDDDVSPFLDGLEER 239

>pdb|1RYP|B Chain B, Crystal Structure Of The 20s Proteasome From Yeast At 2.4 Angstroms Resolution Length = 250

Iteration: 1
 Score = 87.4 bits (215), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 55/186 (29%), Positives = 93/186 (50%), Gaps = 17/186 (9%)
Query: 17  ITKYLGLLATGMTADARTLVQQARYEA-AEFRFKYGYEMPVDVLAKWIADKSQVYTQHAY 75
           +T  +G + +GM  D R LV ++R  A   ++  YG   P  +L   +A   Q  TQ   
Sbjct: 67  LTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGG 126
Query: 76  MRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFT 135
           +RP GV  ++   DE  G  L++ DP+G +F  KAT+ G     A  FLEK+  ++    
Sbjct: 127 VRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWNDE--LE 184
Query: 136 FQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPE--------------FRVLSIEEID 181
            ++ +  A+ TL+  ++ +F    IE+ ++  ENP+              FR L+ +EI+
Sbjct: 185 LEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTSQEIN 244
Query: 182 EHLTAI 187
           + L A+
Sbjct: 245 DRLEAL 250

>pdb|1VSY|B Chain B, Proteasome Activator Complex Length = 231

Iteration: 1
 Score = 87.4 bits (215), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 55/186 (29%), Positives = 93/186 (50%), Gaps = 17/186 (9%)
Query: 17  ITKYLGLLATGMTADARTLVQQARYEA-AEFRFKYGYEMPVDVLAKWIADKSQVYTQHAY 75
           +T  +G + +GM  D R LV ++R  A   ++  YG   P  +L   +A   Q  TQ   
Sbjct: 48  LTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGG 107
Query: 76  MRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFT 135
           +RP GV  ++   DE  G  L++ DP+G +F  KAT+ G     A  FLEK+  ++    
Sbjct: 108 VRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWNDE--LE 165
Query: 136 FQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPE--------------FRVLSIEEID 181
            ++ +  A+ TL+  ++ +F    IE+ ++  ENP+              FR L+ +EI+
Sbjct: 166 LEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTSQEIN 225
Query: 182 EHLTAI 187
           + L A+
Sbjct: 226 DRLEAL 231

>pdb|1VSY|D Chain D, Proteasome Activator Complex Length = 227

Iteration: 1
 Score = 86.3 bits (212), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 57/191 (29%), Positives = 101/191 (52%), Gaps = 8/191 (4%)
Query: 1   MQDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA 60
           +QD  +  + V+    I  ++ L  +G+ AD+R L+++AR EA   R      + V+ L 
Sbjct: 38  LQDTRITPSKVSK---IDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLT 94
Query: 61  KWIADKSQVYTQHAYMRPLGVVAMVLSID-EECGPRLFKCDPAGHFFGHKATSAGLKEQE 119
           +++A   Q YTQ   +RP GV  ++   D  +  P+L++ +P+G +    A + G   + 
Sbjct: 95  RYVAGVQQRYTQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKT 154
Query: 120 AINFLEKKM-KNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIE 178
              FLEK   + +P  T +E V+  + +L  V+Q    A  IE+ VV K + +   LS E
Sbjct: 155 VREFLEKNYDRKEPPATVEECVKLTVRSLLEVVQTG--AKNIEITVV-KPDSDIVALSSE 211
Query: 179 EIDEHLTAISE 189
           EI++++T I +
Sbjct: 212 EINQYVTQIEQ 222

>pdb|1RYP|D Chain D, Crystal Structure Of The 20s Proteasome From Yeast At 2.4 Angstroms Resolution Length = 241

Iteration: 1
 Score = 85.9 bits (211), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 57/191 (29%), Positives = 101/191 (52%), Gaps = 8/191 (4%)
Query: 1   MQDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA 60
           +QD  +  + V+    I  ++ L  +G+ AD+R L+++AR EA   R      + V+ L 
Sbjct: 52  LQDTRITPSKVSK---IDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLT 108
Query: 61  KWIADKSQVYTQHAYMRPLGVVAMVLSID-EECGPRLFKCDPAGHFFGHKATSAGLKEQE 119
           +++A   Q YTQ   +RP GV  ++   D  +  P+L++ +P+G +    A + G   + 
Sbjct: 109 RYVAGVQQRYTQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKT 168
Query: 120 AINFLEKKM-KNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIE 178
              FLEK   + +P  T +E V+  + +L  V+Q    A  IE+ VV K + +   LS E
Sbjct: 169 VREFLEKNYDRKEPPATVEECVKLTVRSLLEVVQTG--AKNIEITVV-KPDSDIVALSSE 225
Query: 179 EIDEHLTAISE 189
           EI++++T I +
Sbjct: 226 EINQYVTQIEQ 236

>pdb|1G0U|C Chain C, A Gated Channel Into The Proteasome Core Particle Length = 243

Iteration: 1
 Score = 85.9 bits (211), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 57/191 (29%), Positives = 101/191 (52%), Gaps = 8/191 (4%)
Query: 1   MQDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA 60
           +QD  +  + V+    I  ++ L  +G+ AD+R L+++AR EA   R      + V+ L 
Sbjct: 54  LQDTRITPSKVSK---IDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLT 110
Query: 61  KWIADKSQVYTQHAYMRPLGVVAMVLSID-EECGPRLFKCDPAGHFFGHKATSAGLKEQE 119
           +++A   Q YTQ   +RP GV  ++   D  +  P+L++ +P+G +    A + G   + 
Sbjct: 111 RYVAGVQQRYTQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKT 170
Query: 120 AINFLEKKM-KNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIE 178
              FLEK   + +P  T +E V+  + +L  V+Q    A  IE+ VV K + +   LS E
Sbjct: 171 VREFLEKNYDRKEPPATVEECVKLTVRSLLEVVQTG--AKNIEITVV-KPDSDIVALSSE 227
Query: 179 EIDEHLTAISE 189
           EI++++T I +
Sbjct: 228 EINQYVTQIEQ 238

>pdb|1FNT|D Chain D, Crystal Structure Of The 20s Proteasome From Yeast In Complex With The Proteasome Activator Pa26 From Trypanosome Brucei At 3.2 Angstroms Resolution Length = 254

Iteration: 1
 Score = 85.9 bits (211), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 57/189 (30%), Positives = 100/189 (52%), Gaps = 8/189 (4%)
Query: 1   MQDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA 60
           +QD  +  + V+    I  ++ L  +G+ AD+R L+++AR EA   R      + V+ L 
Sbjct: 54  LQDTRITPSKVSK---IDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLT 110
Query: 61  KWIADKSQVYTQHAYMRPLGVVAMVLSID-EECGPRLFKCDPAGHFFGHKATSAGLKEQE 119
           +++A   Q YTQ   +RP GV  ++   D  +  P+L++ +P+G +    A + G   + 
Sbjct: 111 RYVAGVQQRYTQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKT 170
Query: 120 AINFLEKKM-KNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIE 178
              FLEK   + +P  T +E V+  + +L  V+Q    A  IE+ VV K + +   LS E
Sbjct: 171 VREFLEKNYDRKEPPATVEECVKLTVRSLLEVVQTG--AKNIEITVV-KPDSDIVALSSE 227
Query: 179 EIDEHLTAI 187
           EI++++T I
Sbjct: 228 EINQYVTQI 236

>pdb|1VSY|C Chain C, Proteasome Activator Complex Length = 232

Iteration: 1
 Score = 85.1 bits (209), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 43/139 (30%), Positives = 72/139 (51%), Gaps = 2/139 (1%)
Query: 9   TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQ 68
           TS   L+ +   + +   G+TADA  L+  AR  A  +   Y  ++PV++L + ++D  Q
Sbjct: 48  TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ 107
Query: 69  VYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKM 128
            YTQH  +RP GV  +    D+  G +L+  +P+G++ G KA S G     A   L+   
Sbjct: 108 GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY 167
Query: 129 KNDPAFTFQETVQTAISTL 147
           K+D      + ++ A+ TL
Sbjct: 168 KDD--MKVDDAIELALKTL 184

>pdb|1G0U|B Chain B, A Gated Channel Into The Proteasome Core Particle Length = 245

Iteration: 1
 Score = 84.7 bits (208), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 43/139 (30%), Positives = 72/139 (51%), Gaps = 2/139 (1%)
Query: 9   TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQ 68
           TS   L+ +   + +   G+TADA  L+  AR  A  +   Y  ++PV++L + ++D  Q
Sbjct: 61  TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ 120
Query: 69  VYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKM 128
            YTQH  +RP GV  +    D+  G +L+  +P+G++ G KA S G     A   L+   
Sbjct: 121 GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY 180
Query: 129 KNDPAFTFQETVQTAISTL 147
           K+D      + ++ A+ TL
Sbjct: 181 KDD--MKVDDAIELALKTL 197

>pdb|1RYP|C Chain C, Crystal Structure Of The 20s Proteasome From Yeast At 2.4 Angstroms Resolution Length = 244

Iteration: 1
 Score = 84.7 bits (208), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 43/139 (30%), Positives = 72/139 (51%), Gaps = 2/139 (1%)
Query: 9   TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQ 68
           TS   L+ +   + +   G+TADA  L+  AR  A  +   Y  ++PV++L + ++D  Q
Sbjct: 60  TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ 119
Query: 69  VYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKM 128
            YTQH  +RP GV  +    D+  G +L+  +P+G++ G KA S G     A   L+   
Sbjct: 120 GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY 179
Query: 129 KNDPAFTFQETVQTAISTL 147
           K+D      + ++ A+ TL
Sbjct: 180 KDD--MKVDDAIELALKTL 196

>pdb|3OEU|B Chain B, Structure Of Yeast 20s Open-Gate Proteasome With Compound 24 Length = 235

Iteration: 1
 Score = 84.7 bits (208), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 43/139 (30%), Positives = 72/139 (51%), Gaps = 2/139 (1%)
Query: 9   TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQ 68
           TS   L+ +   + +   G+TADA  L+  AR  A  +   Y  ++PV++L + ++D  Q
Sbjct: 51  TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ 110
Query: 69  VYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKM 128
            YTQH  +RP GV  +    D+  G +L+  +P+G++ G KA S G     A   L+   
Sbjct: 111 GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY 170
Query: 129 KNDPAFTFQETVQTAISTL 147
           K+D      + ++ A+ TL
Sbjct: 171 KDD--MKVDDAIELALKTL 187

>pdb|1Z7Q|C Chain C, Crystal Structure Of The 20s Proteasome From Yeast In Complex With The Proteasome Activator Pa26 From Trypanosome Brucei At 3.2 Angstroms Resolution Length = 258

Iteration: 1
 Score = 84.7 bits (208), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 43/139 (30%), Positives = 72/139 (51%), Gaps = 2/139 (1%)
Query: 9   TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQ 68
           TS   L+ +   + +   G+TADA  L+  AR  A  +   Y  ++PV++L + ++D  Q
Sbjct: 61  TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ 120
Query: 69  VYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKM 128
            YTQH  +RP GV  +    D+  G +L+  +P+G++ G KA S G     A   L+   
Sbjct: 121 GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY 180
Query: 129 KNDPAFTFQETVQTAISTL 147
           K+D      + ++ A+ TL
Sbjct: 181 KDD--MKVDDAIELALKTL 197

>pdb|1IRU|C Chain C, Crystal Structure Of The Mammalian 20s Proteasome At 2.75 A Resolution Length = 261

Iteration: 1
 Score = 80.9 bits (198), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 49/183 (26%), Positives = 91/183 (49%), Gaps = 5/183 (2%)
Query: 4   KLLDHTSVTH-LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           KLLD    +  ++ + + +     G+T+DA  L  + R  A  +  +Y   +P + L   
Sbjct: 54  KLLDEVFFSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTA 113
Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           + D  Q YTQ    RP GV  + +  D+  G +L++ DP+G++ G KAT  G     A++
Sbjct: 114 LCDIKQAYTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVS 173
Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQ-EDFKASEIEVGVVSKENPE--FRVLSIEE 179
            L++  K +   T +  +  AI  L   +      A ++E+  +++EN +   RVL  +E
Sbjct: 174 MLKQDYK-EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKE 232
Query: 180 IDE 182
           +++
Sbjct: 233 VEQ 235

>pdb|3UNB|F Chain F, Mouse Constitutive 20s Proteasome In Complex With Pr-957 Length = 255

Iteration: 1
 Score = 80.5 bits (197), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 42/123 (34%), Positives = 66/123 (53%)
Query: 4   KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWI 63
           KL +  S   LF + +++G+   G+ ADAR+L   AR EA+ FR  +GY +P+  LA  +
Sbjct: 57  KLYEEGSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRV 116
Query: 64  ADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINF 123
           A     YT ++ +RP G   M+ S     G +L+  DP+G  +G+   + G   Q A   
Sbjct: 117 AMYVHAYTLYSAVRPFGCSFMLGSYSANDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTE 176
Query: 124 LEK 126
           +EK
Sbjct: 177 IEK 179

>pdb|1IRU|G Chain G, Crystal Structure Of The Mammalian 20s Proteasome At 2.75 A Resolution Length = 254

Iteration: 1
 Score = 80.1 bits (196), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 42/123 (34%), Positives = 66/123 (53%)
Query: 4   KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWI 63
           KL +  S   LF + +++G+   G+ ADAR+L   AR EA+ FR  +GY +P+  LA  +
Sbjct: 56  KLYEEGSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRV 115
Query: 64  ADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINF 123
           A     YT ++ +RP G   M+ S     G +L+  DP+G  +G+   + G   Q A   
Sbjct: 116 AMYVHAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTE 175
Query: 124 LEK 126
           +EK
Sbjct: 176 IEK 178

>pdb|1IRU|E Chain E, Crystal Structure Of The Mammalian 20s Proteasome At 2.75 A Resolution Length = 241

Iteration: 1
 Score = 79.0 bits (193), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 50/188 (26%), Positives = 99/188 (52%), Gaps = 9/188 (4%)
Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
           L++ +S+  +  I  ++G   +G+ ADA+TL+ +AR E     F Y   M V+ + + ++
Sbjct: 58  LMEPSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVS 117
Query: 65  DKSQVYTQH-----AYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQE 119
           + +  + +      A  RP GV  +   +DE+ GP+LF  DP+G F    A + G   + 
Sbjct: 118 NLALQFGEEDADPGAMSRPFGVALLFGGVDEK-GPQLFHMDPSGTFVQCDARAIGSASEG 176
Query: 120 AINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEE 179
           A + L++      + T +E +++++  L+ V++E   A+ IE+  V +    F + + EE
Sbjct: 177 AQSSLQELYHK--SMTLKEAIKSSLIILKQVMEEKLNATNIELATV-QPGQNFHMFTKEE 233
Query: 180 IDEHLTAI 187
           ++E +  I
Sbjct: 234 LEEVIKDI 241

>pdb|3UNB|D Chain D, Mouse Constitutive 20s Proteasome In Complex With Pr-957 Length = 241

Iteration: 1
 Score = 79.0 bits (193), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 50/188 (26%), Positives = 99/188 (52%), Gaps = 9/188 (4%)
Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
           L++ +S+  +  I  ++G   +G+ ADA+TL+ +AR E     F Y   M V+ + + ++
Sbjct: 58  LMEPSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVS 117
Query: 65  DKSQVYTQH-----AYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQE 119
           + +  + +      A  RP GV  +   +DE+ GP+LF  DP+G F    A + G   + 
Sbjct: 118 NLALQFGEEDADPGAMSRPFGVALLFGGVDEK-GPQLFHMDPSGTFVQCDARAIGSASEG 176
Query: 120 AINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEE 179
           A + L++      + T +E +++++  L+ V++E   A+ IE+  V +    F + + EE
Sbjct: 177 AQSSLQEVYHK--SMTLKEAIKSSLIILKQVMEEKLNATNIELATV-QPGQNFHMFTKEE 233
Query: 180 IDEHLTAI 187
           ++E +  I
Sbjct: 234 LEEVIKDI 241

>pdb|3UNB|B Chain B, Mouse Constitutive 20s Proteasome In Complex With Pr-957 Length = 261

Iteration: 1
 Score = 77.8 bits (190), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 47/183 (25%), Positives = 91/183 (49%), Gaps = 5/183 (2%)
Query: 4   KLLDHTSVTH-LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           KLLD    +  ++ + + +     G+T+DA  L  + R  A  +  +Y   +P + L   
Sbjct: 54  KLLDEVFFSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTA 113
Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           + D  Q YTQ    RP GV  + +  D+  G +L++ DP+G++ G KAT  G     A++
Sbjct: 114 LCDIKQAYTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVS 173
Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQ-EDFKASEIEVGVVSKENPE--FRVLSIEE 179
            L++  K +   T +  +  A+  L   +      A ++E+  +++E+ +   RVL  +E
Sbjct: 174 MLKQDYK-EGEMTLKSALALAVKVLNKTMDVSKLSAEKVEIATLTRESGKTVIRVLKQKE 232
Query: 180 IDE 182
           +++
Sbjct: 233 VEQ 235

>pdb|1FNT|G Chain G, Crystal Structure Of The 20s Proteasome From Yeast In Complex With The Proteasome Activator Pa26 From Trypanosome Brucei At 3.2 Angstroms Resolution Length = 287

Iteration: 1
 Score = 70.9 bits (172), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 41/147 (27%), Positives = 75/147 (51%), Gaps = 3/147 (2%)
Query: 17  ITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYM 76
           + +++G + +G+  D R LV + R EAA F+  Y   +P+   A  +    Q +T +  +
Sbjct: 69  VDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSV 128
Query: 77  RPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDP-AFT 135
           RP GV  +   +D+  G  L+  +P+G ++G+K  + G   Q A   LEK + + P   +
Sbjct: 129 RPFGVSTIFGGVDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGLS 187
Query: 136 FQETVQTAISTLQSVLQEDFKASEIEV 162
            +E V+ A   +  +  ED K  + E+
Sbjct: 188 AREAVKQAAKIIY-LAHEDNKEKDFEL 213

>pdb|1Z7Q|G Chain G, Crystal Structure Of The 20s Proteasome From Yeast In Complex With The Proteasome Activator Pa26 From Trypanosome Brucei At 3.2 Angstroms Resolution Length = 288

Iteration: 1
 Score = 70.9 bits (172), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 41/147 (27%), Positives = 75/147 (51%), Gaps = 3/147 (2%)
Query: 17  ITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYM 76
           + +++G + +G+  D R LV + R EAA F+  Y   +P+   A  +    Q +T +  +
Sbjct: 70  VDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSV 129
Query: 77  RPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDP-AFT 135
           RP GV  +   +D+  G  L+  +P+G ++G+K  + G   Q A   LEK + + P   +
Sbjct: 130 RPFGVSTIFGGVDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGLS 188
Query: 136 FQETVQTAISTLQSVLQEDFKASEIEV 162
            +E V+ A   +  +  ED K  + E+
Sbjct: 189 AREAVKQAAKIIY-LAHEDNKEKDFEL 214

>pdb|3OEU|F Chain F, Structure Of Yeast 20s Open-Gate Proteasome With Compound 24 Length = 242

Iteration: 1
 Score = 70.9 bits (172), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 41/147 (27%), Positives = 75/147 (51%), Gaps = 3/147 (2%)
Query: 17  ITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYM 76
           + +++G + +G+  D R LV + R EAA F+  Y   +P+   A  +    Q +T +  +
Sbjct: 64  VDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSV 123
Query: 77  RPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDP-AFT 135
           RP GV  +   +D+  G  L+  +P+G ++G+K  + G   Q A   LEK + + P   +
Sbjct: 124 RPFGVSTIFGGVDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGLS 182
Query: 136 FQETVQTAISTLQSVLQEDFKASEIEV 162
            +E V+ A   +  +  ED K  + E+
Sbjct: 183 AREAVKQAAKIIY-LAHEDNKEKDFEL 208

>pdb|1G0U|D Chain D, A Gated Channel Into The Proteasome Core Particle Length = 241

Iteration: 1
 Score = 70.5 bits (171), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 44/189 (23%), Positives = 96/189 (50%), Gaps = 10/189 (5%)
Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
           LL+  S+  +  I +++G   +G+TADAR++++ AR  A      Y  ++ V+ L + + 
Sbjct: 58  LLESDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVC 117
Query: 65  DKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFL 124
           D   +    A  RP GV  ++   D + G +LF  +P+G F+ + A + G   + A    
Sbjct: 118 D---LAAAAAMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGA---- 170
Query: 125 EKKMKND--PAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           + ++ N+   + T +E     +  L+ V++E    +  ++  ++K++  F++   E+  E
Sbjct: 171 QAELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDG-FKIYDNEKTAE 229
Query: 183 HLTAISERD 191
            +  + E++
Sbjct: 230 LIKELKEKE 238

>pdb|1G0U|F Chain F, A Gated Channel Into The Proteasome Core Particle Length = 248

Iteration: 1
 Score = 70.5 bits (171), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 41/147 (27%), Positives = 75/147 (51%), Gaps = 3/147 (2%)
Query: 17  ITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYM 76
           + +++G + +G+  D R LV + R EAA F+  Y   +P+   A  +    Q +T +  +
Sbjct: 70  VDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSV 129
Query: 77  RPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDP-AFT 135
           RP GV  +   +D+  G  L+  +P+G ++G+K  + G   Q A   LEK + + P   +
Sbjct: 130 RPFGVSTIFGGVDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGLS 188
Query: 136 FQETVQTAISTLQSVLQEDFKASEIEV 162
            +E V+ A   +  +  ED K  + E+
Sbjct: 189 AREAVKQAAKIIY-LAHEDNKEKDFEL 214

>pdb|1RYP|G Chain G, Crystal Structure Of The 20s Proteasome From Yeast At 2.4 Angstroms Resolution Length = 244

Iteration: 1
 Score = 70.5 bits (171), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 41/147 (27%), Positives = 75/147 (51%), Gaps = 3/147 (2%)
Query: 17  ITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYM 76
           + +++G + +G+  D R LV + R EAA F+  Y   +P+   A  +    Q +T +  +
Sbjct: 66  VDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSV 125
Query: 77  RPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDP-AFT 135
           RP GV  +   +D+  G  L+  +P+G ++G+K  + G   Q A   LEK + + P   +
Sbjct: 126 RPFGVSTIFGGVDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGLS 184
Query: 136 FQETVQTAISTLQSVLQEDFKASEIEV 162
            +E V+ A   +  +  ED K  + E+
Sbjct: 185 AREAVKQAAKIIY-LAHEDNKEKDFEL 210

>pdb|1VSY|E Chain E, Proteasome Activator Complex Length = 250

Iteration: 1
 Score = 69.3 bits (168), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 44/195 (22%), Positives = 98/195 (50%), Gaps = 13/195 (6%)
Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
           LL+  S+  +  I +++G   +G+TADAR++++ AR  A      Y  ++ V+ L + + 
Sbjct: 58  LLESDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVC 117
Query: 65  DKSQVYTQHA------YMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQ 118
           D +  + + A        RP GV  ++   D + G +LF  +P+G F+ + A + G   +
Sbjct: 118 DLALRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSE 177
Query: 119 EAINFLEKKMKND--PAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLS 176
            A    + ++ N+   + T +E     +  L+ V++E    +  ++  ++K++  F++  
Sbjct: 178 GA----QAELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDG-FKIYD 232
Query: 177 IEEIDEHLTAISERD 191
            E+  E +  + E++
Sbjct: 233 NEKTAELIKELKEKE 247

>pdb|4G4S|E Chain E, Structure Of Proteasome-Pba1-Pba2 Complex Length = 261

Iteration: 1
 Score = 68.9 bits (167), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 44/195 (22%), Positives = 98/195 (50%), Gaps = 13/195 (6%)
Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
           LL+  S+  +  I +++G   +G+TADAR++++ AR  A      Y  ++ V+ L + + 
Sbjct: 59  LLESDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVC 118
Query: 65  DKSQVYTQHA------YMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQ 118
           D +  + + A        RP GV  ++   D + G +LF  +P+G F+ + A + G   +
Sbjct: 119 DLALRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSE 178
Query: 119 EAINFLEKKMKND--PAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLS 176
            A    + ++ N+   + T +E     +  L+ V++E    +  ++  ++K++  F++  
Sbjct: 179 GA----QAELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDG-FKIYD 233
Query: 177 IEEIDEHLTAISERD 191
            E+  E +  + E++
Sbjct: 234 NEKTAELIKELKEKE 248

>pdb|1FNT|E Chain E, Crystal Structure Of The 20s Proteasome From Yeast In Complex With The Proteasome Activator Pa26 From Trypanosome Brucei At 3.2 Angstroms Resolution Length = 260

Iteration: 1
 Score = 68.9 bits (167), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 44/195 (22%), Positives = 98/195 (50%), Gaps = 13/195 (6%)
Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
           LL+  S+  +  I +++G   +G+TADAR++++ AR  A      Y  ++ V+ L + + 
Sbjct: 58  LLESDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVC 117
Query: 65  DKSQVYTQHA------YMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQ 118
           D +  + + A        RP GV  ++   D + G +LF  +P+G F+ + A + G   +
Sbjct: 118 DLALRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSE 177
Query: 119 EAINFLEKKMKND--PAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLS 176
            A    + ++ N+   + T +E     +  L+ V++E    +  ++  ++K++  F++  
Sbjct: 178 GA----QAELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDG-FKIYD 232
Query: 177 IEEIDEHLTAISERD 191
            E+  E +  + E++
Sbjct: 233 NEKTAELIKELKEKE 247

>pdb|2Z5C|C Chain C, Crystal Structure Of A Novel Chaperone Complex For Yeast 20s Proteasome Assembly Length = 262

Iteration: 1
 Score = 68.9 bits (167), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 44/195 (22%), Positives = 98/195 (50%), Gaps = 13/195 (6%)
Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
           LL+  S+  +  I +++G   +G+TADAR++++ AR  A      Y  ++ V+ L + + 
Sbjct: 60  LLESDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVC 119
Query: 65  DKSQVYTQHA------YMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQ 118
           D +  + + A        RP GV  ++   D + G +LF  +P+G F+ + A + G   +
Sbjct: 120 DLALRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSE 179
Query: 119 EAINFLEKKMKND--PAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLS 176
            A    + ++ N+   + T +E     +  L+ V++E    +  ++  ++K++  F++  
Sbjct: 180 GA----QAELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDG-FKIYD 234
Query: 177 IEEIDEHLTAISERD 191
            E+  E +  + E++
Sbjct: 235 NEKTAELIKELKEKE 249

>pdb|1RYP|E Chain E, Crystal Structure Of The 20s Proteasome From Yeast At 2.4 Angstroms Resolution Length = 242

Iteration: 1
 Score = 68.9 bits (167), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 44/195 (22%), Positives = 98/195 (50%), Gaps = 13/195 (6%)
Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
           LL+  S+  +  I +++G   +G+TADAR++++ AR  A      Y  ++ V+ L + + 
Sbjct: 50  LLESDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVC 109
Query: 65  DKSQVYTQHA------YMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQ 118
           D +  + + A        RP GV  ++   D + G +LF  +P+G F+ + A + G   +
Sbjct: 110 DLALRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSE 169
Query: 119 EAINFLEKKMKND--PAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLS 176
            A    + ++ N+   + T +E     +  L+ V++E    +  ++  ++K++  F++  
Sbjct: 170 GA----QAELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDG-FKIYD 224
Query: 177 IEEIDEHLTAISERD 191
            E+  E +  + E++
Sbjct: 225 NEKTAELIKELKEKE 239

>pdb|3SDI|E Chain E, Structure Of Yeast 20s Open-Gate Proteasome With Compound 20 Length = 233

Iteration: 1
 Score = 59.3 bits (142), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 44/172 (25%), Positives = 80/172 (46%), Gaps = 11/172 (6%)
Query: 19  KYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRP 78
           +++GL   G+  DAR L    R +       +  ++ V+     + DK+Q  TQ A  RP
Sbjct: 67  EHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSAGGRP 126
Query: 79  LGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEK------KMKNDP 132
            GV  +++  D+  G  L +  P+G+      T+ G + Q A  +LE+      K+  +P
Sbjct: 127 YGVGLLIIGYDKS-GAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIKIDGNP 185
Query: 133 AFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 184
               +  V+ AIS  QS+  E      + + +V K+ P F +   E + +++
Sbjct: 186 DELIKAGVE-AIS--QSLRDESLTVDNLSIAIVGKDTP-FTIYDGEAVAKYI 233

>pdb|1G0U|E Chain E, A Gated Channel Into The Proteasome Core Particle Length = 234

Iteration: 1
 Score = 59.3 bits (142), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 44/172 (25%), Positives = 80/172 (46%), Gaps = 11/172 (6%)
Query: 19  KYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRP 78
           +++GL   G+  DAR L    R +       +  ++ V+     + DK+Q  TQ A  RP
Sbjct: 68  EHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSAGGRP 127
Query: 79  LGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEK------KMKNDP 132
            GV  +++  D+  G  L +  P+G+      T+ G + Q A  +LE+      K+  +P
Sbjct: 128 YGVGLLIIGYDKS-GAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIKIDGNP 186
Query: 133 AFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 184
               +  V+ AIS  QS+  E      + + +V K+ P F +   E + +++
Sbjct: 187 DELIKAGVE-AIS--QSLRDESLTVDNLSIAIVGKDTP-FTIYDGEAVAKYI 234

>pdb|1RYP|F Chain F, Crystal Structure Of The 20s Proteasome From Yeast At 2.4 Angstroms Resolution Length = 233

Iteration: 1
 Score = 56.6 bits (135), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 43/172 (25%), Positives = 79/172 (45%), Gaps = 11/172 (6%)
Query: 19  KYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRP 78
           +++GL   G+  DAR L    R +       +  ++ V+     + DK+Q  TQ    RP
Sbjct: 67  EHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRP 126
Query: 79  LGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEK------KMKNDP 132
            GV  +++  D+  G  L +  P+G+      T+ G + Q A  +LE+      K+  +P
Sbjct: 127 YGVGLLIIGYDKS-GAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIKIDGNP 185
Query: 133 AFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 184
               +  V+ AIS  QS+  E      + + +V K+ P F +   E + +++
Sbjct: 186 DELIKAGVE-AIS--QSLRDESLTVDNLSIAIVGKDTP-FTIYDGEAVAKYI 233

>pdb|1FNT|F Chain F, Crystal Structure Of The 20s Proteasome From Yeast In Complex With The Proteasome Activator Pa26 From Trypanosome Brucei At 3.2 Angstroms Resolution Length = 234

Iteration: 1
 Score = 56.6 bits (135), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 43/172 (25%), Positives = 79/172 (45%), Gaps = 11/172 (6%)
Query: 19  KYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRP 78
           +++GL   G+  DAR L    R +       +  ++ V+     + DK+Q  TQ    RP
Sbjct: 68  EHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRP 127
Query: 79  LGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEK------KMKNDP 132
            GV  +++  D+  G  L +  P+G+      T+ G + Q A  +LE+      K+  +P
Sbjct: 128 YGVGLLIIGYDKS-GAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIKIDGNP 186
Query: 133 AFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 184
               +  V+ AIS  QS+  E      + + +V K+ P F +   E + +++
Sbjct: 187 DELIKAGVE-AIS--QSLRDESLTVDNLSIAIVGKDTP-FTIYDGEAVAKYI 234

>pdb|4G4S|F Chain F, Structure Of Proteasome-Pba1-Pba2 Complex Length = 235

Iteration: 1
 Score = 56.6 bits (135), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 43/172 (25%), Positives = 79/172 (45%), Gaps = 11/172 (6%)
Query: 19  KYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRP 78
           +++GL   G+  DAR L    R +       +  ++ V+     + DK+Q  TQ    RP
Sbjct: 69  EHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRP 128
Query: 79  LGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEK------KMKNDP 132
            GV  +++  D+  G  L +  P+G+      T+ G + Q A  +LE+      K+  +P
Sbjct: 129 YGVGLLIIGYDKS-GAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIKIDGNP 187
Query: 133 AFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 184
               +  V+ AIS  QS+  E      + + +V K+ P F +   E + +++
Sbjct: 188 DELIKAGVE-AIS--QSLRDESLTVDNLSIAIVGKDTP-FTIYDGEAVAKYI 235

>pdb|3C91|H Chain H, Thermoplasma Acidophilum 20s Proteasome With An Open Gate Length = 203

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 43/163 (26%), Positives = 68/163 (41%), Gaps = 9/163 (5%)
Query: 8   HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKS 67
           H +   LF I  Y G+   G+  DA+ LV+  + E   +R +    MP++ +A  +   S
Sbjct: 28  HKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKAELELYRLQRRVNMPIEAVATLL---S 84
Query: 68  QVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKK 127
            +  Q  YM P  V  +V  ID    P +F  D AG        S G         LE +
Sbjct: 85  NMLNQVKYM-PYMVQLLVGGID--TAPHVFSIDAAGGSVEDIYASTGSGSPFVYGVLESQ 141
Query: 128 MKNDPAFTFQETVQTAISTLQSVLQEDFKASE-IEVGVVSKEN 169
                  T  E V   I  + +  Q D  +   I+V V+++++
Sbjct: 142 YSEK--MTVDEGVDLVIRAISAAKQRDSASGGMIDVAVITRKD 182

>pdb|1YA7|H Chain H, Implications For Interactions Of Proteasome With Pan And Pa700 From The 1.9 A Structure Of A Proteasome-11s Activator Complex Length = 217

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 43/163 (26%), Positives = 68/163 (41%), Gaps = 9/163 (5%)
Query: 8   HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKS 67
           H +   LF I  Y G+   G+  DA+ LV+  + E   +R +    MP++ +A  +   S
Sbjct: 36  HKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKAELELYRLQRRVNMPIEAVATLL---S 92
Query: 68  QVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKK 127
            +  Q  YM P  V  +V  ID    P +F  D AG        S G         LE +
Sbjct: 93  NMLNQVKYM-PYMVQLLVGGID--TAPHVFSIDAAGGSVEDIYASTGSGSPFVYGVLESQ 149
Query: 128 MKNDPAFTFQETVQTAISTLQSVLQEDFKASE-IEVGVVSKEN 169
                  T  E V   I  + +  Q D  +   I+V V+++++
Sbjct: 150 YSEK--MTVDEGVDLVIRAISAAKQRDSASGGMIDVAVITRKD 190

>pdb|1PMA|B Chain B, Proteasome From Thermoplasma Acidophilum Length = 211

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 43/163 (26%), Positives = 68/163 (41%), Gaps = 9/163 (5%)
Query: 8   HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKS 67
           H +   LF I  Y G+   G+  DA+ LV+  + E   +R +    MP++ +A  +   S
Sbjct: 36  HKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKAELELYRLQRRVNMPIEAVATLL---S 92
Query: 68  QVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKK 127
            +  Q  YM P  V  +V  ID    P +F  D AG        S G         LE +
Sbjct: 93  NMLNQVKYM-PYMVQLLVGGID--TAPHVFSIDAAGGSVEDIYASTGSGSPFVYGVLESQ 149
Query: 128 MKNDPAFTFQETVQTAISTLQSVLQEDFKASE-IEVGVVSKEN 169
                  T  E V   I  + +  Q D  +   I+V V+++++
Sbjct: 150 YSEK--MTVDEGVDLVIRAISAAKQRDSASGGMIDVAVITRKD 190

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	191
1iru_A	246	20S proteasome; cell cycle, immune response, prote	5e-92
1ryp_A	243	20S proteasome; multicatalytic proteinase, protein	1e-87
1j2p_A	246	Alpha-ring, proteasome alpha subunit; hydrolase; 2	1e-84
1iru_D	248	20S proteasome; cell cycle, immune response, prote	3e-84
1yar_A	233	Proteasome alpha subunit; proteasome 20S, PA26 pro	3e-83
1iru_B	233	20S proteasome; cell cycle, immune response, prote	8e-83
1ryp_B	250	20S proteasome; multicatalytic proteinase, protein	1e-82
1ryp_E	242	20S proteasome; multicatalytic proteinase, protein	3e-82
3h4p_A	264	Proteasome subunit alpha; core particle, cytoplasm	6e-82
1iru_E	241	20S proteasome; cell cycle, immune response, prote	6e-80
1ryp_D	241	20S proteasome; multicatalytic proteinase, protein	7e-80
1iru_C	261	20S proteasome; cell cycle, immune response, prote	1e-79
1ryp_C	244	20S proteasome; multicatalytic proteinase, protein	2e-79
1ryp_F	233	20S proteasome; multicatalytic proteinase, protein	4e-79
1iru_F	263	20S proteasome; cell cycle, immune response, prote	4e-79
1iru_G	254	20S proteasome; cell cycle, immune response, prote	2e-77
3nzj_F	288	Proteasome component C1; ubiquitin, protein degrad	4e-72
1ryp_G	244	20S proteasome; multicatalytic proteinase, protein	1e-71
1q5q_A	259	Proteasome alpha-type subunit 1; proteasome assemb	8e-30
3mi0_A	248	Proteasome subunit alpha; enzyme inhibitors, lacto	2e-26
3unf_H	234	Proteasome subunit beta type-10; antigen presentat	4e-21
1yar_H	217	Proteasome beta subunit; proteasome 20S, PA26 prot	5e-20
3nzj_H	261	Proteasome component PUP1; ubiquitin, protein degr	3e-19
1ryp_I	222	20S proteasome; multicatalytic proteinase, protein	8e-19
1iru_I	234	20S proteasome; cell cycle, immune response, prote	2e-17
1q5r_H	294	Proteasome beta-type subunit 1; proteasome assembl	2e-15
1ryp_L	212	20S proteasome; multicatalytic proteinase, protein	4e-15
3nzj_K	287	Proteasome component PRE2; ubiquitin, protein degr	7e-15
1q5q_H	235	Proteasome beta-type subunit 1; proteasome assembl	5e-14
1iru_L	204	20S proteasome; cell cycle, immune response, prote	7e-13
1iru_L	204	20S proteasome; cell cycle, immune response, prote	1e-12
1j2q_H	202	Proteasome beta subunit; ubiquitin, CP, hydrolase;	3e-12
1iru_H	205	20S proteasome; cell cycle, immune response, prote	3e-12
2jay_A	291	Proteasome; hydrolase; 1.99A {Mycobacterium tuberc	4e-12
1iru_K	201	20S proteasome; cell cycle, immune response, prote	1e-11
1g0u_M	266	Proteasome component PRE4; ubiquitin, degradation,	2e-11
1ryp_N	233	20S proteasome; multicatalytic proteinase, protein	7e-11
1ryp_K	198	20S proteasome; multicatalytic proteinase, protein	7e-11
3unf_N	199	Proteasome subunit beta type-9; antigen presentati	7e-11
1ryp_M	222	20S proteasome; multicatalytic proteinase, protein	4e-10
1iru_M	213	20S proteasome; cell cycle, immune response, prote	7e-10
1iru_J	205	20S proteasome; cell cycle, immune response, prote	3e-09
1iru_N	219	20S proteasome; cell cycle, immune response, prote	4e-09
1ryp_H	205	20S proteasome; multicatalytic proteinase, protein	1e-08
1ryp_J	204	20S proteasome; multicatalytic proteinase, protein	1e-07

>1iru_A 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_G* 3une_G 3unf_G* 3unh_G Length = 246

 Score =  267 bits (686), Expect = 5e-92
 Identities = 115/190 (60%), Positives = 155/190 (81%)

Query: 2   QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAK 61
            DKLLD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K
Sbjct: 57  PDKLLDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCK 116

Query: 62  WIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAI 121
            IAD SQVYTQ+A MRPLG   +++ IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ 
Sbjct: 117 RIADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTEST 176

Query: 122 NFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEID 181
           +FLEKK+K    +TF++TV+TAI+ L +VL  DFK SEIEVGVV+ ENP+FR+L+  EID
Sbjct: 177 SFLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEID 236

Query: 182 EHLTAISERD 191
            HL A++ERD
Sbjct: 237 AHLVALAERD 246

>1ryp_A 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_G* 1g65_G 1vsy_A 2f16_G* 2fak_G* 2fny_G* 2gpl_G* 3d29_G* 3dy3_G* 3dy4_G* 3e47_G* 3gpj_G* 3gpt_G* 3gpw_G* 3hye_G* 3l5q_A 3mg0_G* 3mg4_G* 3oeu_G* 3oev_G* ... Length = 243

 Score =  256 bits (657), Expect = 1e-87
 Identities = 89/195 (45%), Positives = 132/195 (67%), Gaps = 7/195 (3%)

Query: 2   QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAK 61
            DKLLD T+V+++F I++ +G++  G   DAR    +A+ EAAEFR+KYGY+MP DVLAK
Sbjct: 51  PDKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAK 110

Query: 62  WIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAI 121
            +A+ SQ+YTQ AYMRPLGV+   +S+DEE GP ++K DPAG++ G+KAT+ G K+QE  
Sbjct: 111 RMANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEIT 170

Query: 122 NFLEKKMKNDPAF-----TFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLS 176
             LE   K          ++++ V+ AI+ +   L  +F  +++EVGV +K+  +F  LS
Sbjct: 171 TNLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKD--KFFTLS 228

Query: 177 IEEIDEHLTAISERD 191
            E I+E L AI+E+D
Sbjct: 229 AENIEERLVAIAEQD 243

>1j2p_A Alpha-ring, proteasome alpha subunit; hydrolase; 2.60A {Archaeoglobus fulgidus} SCOP: d.153.1.4 PDB: 1j2q_A* Length = 246

 Score =  249 bits (637), Expect = 1e-84
 Identities = 56/189 (29%), Positives = 101/189 (53%), Gaps = 4/189 (2%)

Query: 2   QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAK 61
             KLL+  ++  ++ I +++    +G+ ADAR L+ +AR EA   R  Y   + V  LAK
Sbjct: 55  GSKLLEKDTIEKIYKIDEHICAATSGLVADARVLIDRARIEAQINRLTYDIPITVKELAK 114

Query: 62  WIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAI 121
            I D  Q YTQ+  +RP GV  ++  ++E   P+L++ DP+G    +KAT+ G+      
Sbjct: 115 KICDFKQQYTQYGGVRPFGVSLLIAGVNE--VPKLYETDPSGALLEYKATAIGMGRMAVT 172

Query: 122 NFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEID 181
            F EK+ ++D   +F + +   +  +   ++ +     IEVG V  ++  F+ +S EE+ 
Sbjct: 173 EFFEKEYRDD--LSFDDAMVLGLVAMGLSIESELVPENIEVGYVKVDDRTFKEVSPEELK 230

Query: 182 EHLTAISER 190
            ++   +ER
Sbjct: 231 PYVERANER 239

>1iru_D 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unf_C* 3une_C* 3unh_C 3unb_C* Length = 248

 Score =  248 bits (635), Expect = 3e-84
 Identities = 54/190 (28%), Positives = 96/190 (50%), Gaps = 3/190 (1%)

Query: 2   QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAK 61
             KL D  +V  +  +   + +   G+TADAR ++ +AR E    R      + V+ + +
Sbjct: 50  VAKLQDERTVRKICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITR 109

Query: 62  WIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAI 121
           +IA   Q YTQ    RP G+ A+++  D +  PRL++ DP+G +   KA + G   +   
Sbjct: 110 YIASLKQRYTQSNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVR 169

Query: 122 NFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEID 181
            FLEK   ++   T   T++  I  L  V+Q   K   IE+ V+ ++    ++L+ EEI+
Sbjct: 170 EFLEKNYTDEAIETDDLTIKLVIKALLEVVQSGGK--NIELAVMRRDQS-LKILNPEEIE 226

Query: 182 EHLTAISERD 191
           +++  I +  
Sbjct: 227 KYVAEIEKEK 236

>1yar_A Proteasome alpha subunit; proteasome 20S, PA26 proteasome activator 11S, hydrolase-HYD activator complex; 1.90A {Thermoplasma acidophilum} SCOP: d.153.1.4 PDB: 1ya7_A 1pma_A 3c91_A 3c92_A 3ipm_A 2ku1_A 2ku2_A 1yau_A 3jrm_A 3jse_A 3jtl_A Length = 233

 Score =  245 bits (627), Expect = 3e-83
 Identities = 61/183 (33%), Positives = 101/183 (55%), Gaps = 4/183 (2%)

Query: 2   QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAK 61
           + +L++  S+  +  I  Y+  + +G+ ADAR LV  AR  A + +  YG  + ++ L K
Sbjct: 55  RSRLIEQNSIEKIQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVK 114

Query: 62  WIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAI 121
            +AD+ Q YTQ+  +RP GV  +   ID+  GPRLF CDPAG    +KAT+ G  +   +
Sbjct: 115 RVADQMQQYTQYGGVRPYGVSLIFAGIDQI-GPRLFDCDPAGTINEYKATAIGSGKDAVV 173

Query: 122 NFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEID 181
           +FLE++ K +     +E V   I  L+S L+E  +    E+  ++  N  +R+   EE+ 
Sbjct: 174 SFLEREYKEN--LPEKEAVTLGIKALKSSLEEGEELKAPEIASITVGNK-YRIYDQEEVK 230

Query: 182 EHL 184
           + L
Sbjct: 231 KFL 233

>1iru_B 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_A* 3une_A 3unf_A* 3unh_A Length = 233

 Score =  244 bits (624), Expect = 8e-83
 Identities = 64/187 (34%), Positives = 98/187 (52%), Gaps = 5/187 (2%)

Query: 2   QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAK 61
           +  L D  SV  + PITK++GL+ +GM  D R LV +AR  A ++   Y   +P   L +
Sbjct: 52  KSILYDERSVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQ 111

Query: 62  WIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAI 121
            +A   Q YTQ   +RP GV  ++   +E   P LF+ DP+G +F  KAT+ G       
Sbjct: 112 RVASVMQEYTQSGGVRPFGVSLLICGWNEG-RPYLFQSDPSGAYFAWKATAMGKNYVNGK 170

Query: 122 NFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEID 181
            FLEK+   D     ++ + TAI TL+   +       IEVG+ ++    FR L+  E+ 
Sbjct: 171 TFLEKRYNED--LELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAG--FRRLTPTEVK 226

Query: 182 EHLTAIS 188
           ++L AI+
Sbjct: 227 DYLAAIA 233

>1ryp_B 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_B 1g0u_A* 1jd2_A* 1g65_A 1z7q_B 2f16_A* 2fak_A* 2fny_A* 2gpl_A* 2zcy_A* 3bdm_A* 3d29_A* 3dy3_A* 3dy4_A* 3e47_A* 3gpj_A* 3gpt_A* 3gpw_A* 3hye_A* 3mg0_A* ... Length = 250

 Score =  244 bits (624), Expect = 1e-82
 Identities = 56/201 (27%), Positives = 97/201 (48%), Gaps = 17/201 (8%)

Query: 2   QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEA-AEFRFKYGYEMPVDVLA 60
              L    +++ +  +T  +G + +GM  D R LV ++R  A   ++  YG   P  +L 
Sbjct: 52  SSPLAMSETLSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLV 111

Query: 61  KWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEA 120
             +A   Q  TQ   +RP GV  ++   DE  G  L++ DP+G +F  KAT+ G     A
Sbjct: 112 SEVAKIMQEATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAA 171

Query: 121 INFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENP---------- 170
             FLEK+  ++     ++ +  A+ TL+  ++ +F    IE+ ++  ENP          
Sbjct: 172 KTFLEKRWNDE--LELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPT 229

Query: 171 ----EFRVLSIEEIDEHLTAI 187
                FR L+ +EI++ L A+
Sbjct: 230 DKGPRFRKLTSQEINDRLEAL 250

>1ryp_E 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_D* 1g65_D 2f16_D* 2fak_D* 2fny_D* 2gpl_D* 3d29_D* 3dy3_D* 3dy4_D* 3e47_D* 3gpj_D* 3gpt_D* 3gpw_D* 3hye_D* 3mg0_D* 3mg4_D* 3okj_D* 3shj_D* 3tdd_D* 2z5c_C ... Length = 242

 Score =  242 bits (621), Expect = 3e-82
 Identities = 44/196 (22%), Positives = 95/196 (48%), Gaps = 9/196 (4%)

Query: 2   QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAK 61
              LL+  S+  +  I +++G   +G+TADAR++++ AR  A      Y  ++ V+ L +
Sbjct: 47  TSPLLESDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQ 106

Query: 62  WIADKSQVYTQHA------YMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGL 115
            + D +  + + A        RP GV  ++   D + G +LF  +P+G F+ + A + G 
Sbjct: 107 SVCDLALRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGS 166

Query: 116 KEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVL 175
             + A   L  +  +    T +E     +  L+ V++E    +  ++  ++K++  F++ 
Sbjct: 167 GSEGAQAELLNEWHSS--LTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDG-FKIY 223

Query: 176 SIEEIDEHLTAISERD 191
             E+  E +  + E++
Sbjct: 224 DNEKTAELIKELKEKE 239

>3h4p_A Proteasome subunit alpha; core particle, cytoplasm, hydrolase, protease, threonine protease; 4.10A {Methanocaldococcus jannaschii} Length = 264

 Score =  243 bits (621), Expect = 6e-82
 Identities = 62/189 (32%), Positives = 107/189 (56%), Gaps = 4/189 (2%)

Query: 2   QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAK 61
             KL+   S+  +F I  ++    +G+ ADAR L+ +AR EA  +R  YG E+ +++LAK
Sbjct: 59  TSKLVKIRSIEKIFQIDDHVAAATSGLVADARVLIDRARLEAQIYRLTYGEEISIEMLAK 118

Query: 62  WIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAI 121
            I D  Q YTQH  +RP GV  ++  ID+    RLF+ DP+G    +KAT+ G      +
Sbjct: 119 KICDIKQAYTQHGGVRPFGVSLLIAGIDKN-EARLFETDPSGALIEYKATAIGSGRPVVM 177

Query: 122 NFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEID 181
             LEK+ ++D   T  E ++ AI+ L     ED K   ++V +++ ++ +F+ + +EEI 
Sbjct: 178 ELLEKEYRDD--ITLDEGLELAITALTKAN-EDIKPENVDVCIITVKDAQFKKIPVEEIK 234

Query: 182 EHLTAISER 190
           + +  + ++
Sbjct: 235 KLIEKVKKK 243

>1iru_E 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_D* 3une_D 3unf_D* 3unh_D Length = 241

 Score =  237 bits (606), Expect = 6e-80
 Identities = 50/191 (26%), Positives = 97/191 (50%), Gaps = 9/191 (4%)

Query: 2   QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAK 61
              L++ +S+  +  I  ++G   +G+ ADA+TL+ +AR E     F Y   M V+ + +
Sbjct: 55  TSPLMEPSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQ 114

Query: 62  WIADKSQVYTQH-----AYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLK 116
            +++ +  + +      A  RP GV  +   +DE+ GP+LF  DP+G F    A + G  
Sbjct: 115 AVSNLALQFGEEDADPGAMSRPFGVALLFGGVDEK-GPQLFHMDPSGTFVQCDARAIGSA 173

Query: 117 EQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLS 176
            + A + L++        T +E +++++  L+ V++E   A+ IE+  V      F + +
Sbjct: 174 SEGAQSSLQELYHKS--MTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQN-FHMFT 230

Query: 177 IEEIDEHLTAI 187
            EE++E +  I
Sbjct: 231 KEELEEVIKDI 241

>1ryp_D 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_C* 1g65_C 2f16_C* 2fak_C* 2fny_C* 2gpl_C* 3d29_C* 3dy3_C* 3dy4_C* 3e47_C* 3gpj_C* 3gpt_C* 3gpw_C* 3hye_C* 3mg0_C* 3mg4_C* 3oeu_C* 3oev_C* 3okj_C* 3shj_C* ... Length = 241

 Score =  236 bits (605), Expect = 7e-80
 Identities = 56/193 (29%), Positives = 98/193 (50%), Gaps = 6/193 (3%)

Query: 2   QDKLLDH-TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA 60
             KL D   + + +  I  ++ L  +G+ AD+R L+++AR EA   R      + V+ L 
Sbjct: 49  TLKLQDTRITPSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLT 108

Query: 61  KWIADKSQVYTQHAYMRPLGVVAMVLSID-EECGPRLFKCDPAGHFFGHKATSAGLKEQE 119
           +++A   Q YTQ   +RP GV  ++   D  +  P+L++ +P+G +    A + G   + 
Sbjct: 109 RYVAGVQQRYTQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKT 168

Query: 120 AINFLEKKMK-NDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIE 178
              FLEK     +P  T +E V+  + +L  V+Q   K   IE+ VV  ++     LS E
Sbjct: 169 VREFLEKNYDRKEPPATVEECVKLTVRSLLEVVQTGAK--NIEITVVKPDSD-IVALSSE 225

Query: 179 EIDEHLTAISERD 191
           EI++++T I +  
Sbjct: 226 EINQYVTQIEQEK 238

>1iru_C 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_B* 3une_B 3unf_B* 3unh_B Length = 261

 Score =  237 bits (606), Expect = 1e-79
 Identities = 50/194 (25%), Positives = 94/194 (48%), Gaps = 5/194 (2%)

Query: 2   QDKLLDHTSVTH-LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA 60
             KLLD    +  ++ + + +     G+T+DA  L  + R  A  +  +Y   +P + L 
Sbjct: 52  IHKLLDEVFFSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLV 111

Query: 61  KWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEA 120
             + D  Q YTQ    RP GV  + +  D+  G +L++ DP+G++ G KAT  G     A
Sbjct: 112 TALCDIKQAYTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAA 171

Query: 121 INFLEKKMKNDPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPE--FRVLSI 177
           ++ L++  K +   T +  +  AI  L   +      A ++E+  +++EN +   RVL  
Sbjct: 172 VSMLKQDYK-EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQ 230

Query: 178 EEIDEHLTAISERD 191
           +E+++ +    E +
Sbjct: 231 KEVEQLIKKHEEEE 244

>1ryp_C 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_B* 1g65_B 2f16_B* 2fak_B* 2fny_B* 2gpl_B* 3d29_B* 3dy3_B* 3dy4_B* 3e47_B* 3gpj_B* 3gpt_B* 3gpw_B* 3hye_B* 3mg0_B* 3mg4_B* 3okj_B* 3shj_B* 3tdd_B* 3nzj_B* ... Length = 244

 Score =  236 bits (603), Expect = 2e-79
 Identities = 50/190 (26%), Positives = 86/190 (45%), Gaps = 8/190 (4%)

Query: 2   QDKLLD-HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA 60
              LL+  TS   L+ +   + +   G+TADA  L+  AR  A  +   Y  ++PV++L 
Sbjct: 52  TSTLLEQDTSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILV 111

Query: 61  KWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEA 120
           + ++D  Q YTQH  +RP GV  +    D+  G +L+  +P+G++ G KA S G     A
Sbjct: 112 RRLSDIKQGYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAA 171

Query: 121 INFLEKKMKNDPAFTFQETVQTAISTLQSVLQE-DFKASEIEVGVVSKE----NPEFRVL 175
              L+   K+D      + ++ A+ TL             +E   + K         ++ 
Sbjct: 172 QTLLQMDYKDD--MKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIF 229

Query: 176 SIEEIDEHLT 185
             +EI + L 
Sbjct: 230 KPQEIKDILV 239

>1ryp_F 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_E* 1g65_E 2f16_E* 2fak_E* 2fny_E* 2gpl_E* 3d29_E* 3dy3_E* 3dy4_E* 3e47_E* 3gpj_E* 3gpt_E* 3gpw_E* 3hye_E* 3mg0_E* 3mg4_E* 3oeu_E* 3oev_E* 3okj_E* 3shj_E* ... Length = 233

 Score =  234 bits (600), Expect = 4e-79
 Identities = 38/186 (20%), Positives = 78/186 (41%), Gaps = 7/186 (3%)

Query: 2   QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAK 61
            D+L        +    +++GL   G+  DAR L    R +       +  ++ V+    
Sbjct: 52  ADELSS--YQKKIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGH 109

Query: 62  WIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAI 121
            + DK+Q  TQ    RP GV  +++  D+  G  L +  P+G+      T+ G + Q A 
Sbjct: 110 LLCDKAQKNTQSYGGRPYGVGLLIIGYDKS-GAHLLEFQPSGNVTELYGTAIGARSQGAK 168

Query: 122 NFLEKKMKNDPA--FTFQETVQTAISTLQSVLQE-DFKASEIEVGVVSKENPEFRVLSIE 178
            +LE+ +           E ++  +  +   L++       + + +V K+ P F +   E
Sbjct: 169 TYLERTLDTFIKIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTP-FTIYDGE 227

Query: 179 EIDEHL 184
            + +++
Sbjct: 228 AVAKYI 233

>1iru_F 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_E* 3une_E 3unf_E* 3unh_E Length = 263

 Score =  235 bits (602), Expect = 4e-79
 Identities = 52/191 (27%), Positives = 89/191 (46%), Gaps = 6/191 (3%)

Query: 2   QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAK 61
           Q +L        +  +  ++G+   G+TADAR L    R E  + RF +   +PV  L  
Sbjct: 53  QSELAA--HQKKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVS 110

Query: 62  WIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAI 121
            I  K+Q+ TQ    RP GV  ++   D+  GP +F+  P+ ++F  +A S G + Q A 
Sbjct: 111 LIGSKTQIPTQRYGRRPYGVGLLIAGYDDM-GPHIFQTCPSANYFDCRAMSIGARSQSAR 169

Query: 122 NFLEKKMKNDPAFTFQETVQTAISTLQSVLQ--EDFKASEIEVGVVSKENPEFRVLSIEE 179
            +LE+ M         E V+  +  L+  L   +D     + +G+V K+   F +   ++
Sbjct: 170 TYLERHMSEFMECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLE-FTIYDDDD 228

Query: 180 IDEHLTAISER 190
           +   L  + ER
Sbjct: 229 VSPFLEGLEER 239

>1iru_G 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_F* 3une_F 3unf_F* 3unh_F Length = 254

 Score =  231 bits (590), Expect = 2e-77
 Identities = 53/190 (27%), Positives = 90/190 (47%), Gaps = 3/190 (1%)

Query: 2   QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAK 61
             KL +  S   LF + +++G+   G+ ADAR+L   AR EA+ FR  +GY +P+  LA 
Sbjct: 54  LSKLYEEGSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLAD 113

Query: 62  WIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAI 121
            +A     YT ++ +RP G   M+ S     G +L+  DP+G  +G+   + G   Q A 
Sbjct: 114 RVAMYVHAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAK 173

Query: 122 NFLEKKMKNDPAFTFQETVQTAISTLQSVLQE-DFKASEIEVGVVSKENPEFRVLSIEEI 180
             +EK    +   T ++ V+     +  V  E   KA E+E+  V +       +  ++I
Sbjct: 174 TEIEKLQMKE--MTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDI 231

Query: 181 DEHLTAISER 190
            E     ++ 
Sbjct: 232 REEAEKYAKE 241

>3nzj_F Proteasome component C1; ubiquitin, protein degradation, N-terminal nucleophilic HYDR 19S regulatory particle; HET: TY5 TRO MES; 2.40A {Saccharomyces cerevisiae} PDB: 1z7q_G* 3nzw_F* 3nzx_F* 3un4_F* 3un8_F* 3bdm_F* 1fnt_G* 2zcy_F* Length = 288

 Score =  218 bits (558), Expect = 4e-72
 Identities = 46/192 (23%), Positives = 89/192 (46%), Gaps = 5/192 (2%)

Query: 2   QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAK 61
             KLL       +  + +++G + +G+  D R LV + R EAA F+  Y   +P+   A 
Sbjct: 55  TSKLLVPQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFAD 114

Query: 62  WIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAI 121
            +    Q +T +  +RP GV  +   +D+  G  L+  +P+G ++G+K  + G   Q A 
Sbjct: 115 RLGQYVQAHTLYNSVRPFGVSTIFGGVDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAK 173

Query: 122 NFLEKKMKNDP-AFTFQETVQTAISTLQSVLQE-DFKASEIEVGVVS--KENPEFRVLSI 177
             LEK + + P   + +E V+ A   +    ++   K  E+E+   S  + N   + +  
Sbjct: 174 AELEKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKG 233

Query: 178 EEIDEHLTAISE 189
           + + E +    +
Sbjct: 234 DLLQEAIDFAQK 245

>1ryp_G 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_F* 1g65_F 1vsy_G 2f16_F* 2fak_F* 2fny_F* 2gpl_F* 3d29_F* 3dy3_F* 3dy4_F* 3e47_F* 3gpj_F* 3gpt_F* 3gpw_F* 3hye_F* 3l5q_L 3mg0_F* 3mg4_F* 3okj_F* 3shj_F* ... Length = 244

 Score =  215 bits (551), Expect = 1e-71
 Identities = 46/192 (23%), Positives = 90/192 (46%), Gaps = 5/192 (2%)

Query: 2   QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAK 61
             KLL       +  + +++G + +G+  D R LV + R EAA F+  Y   +P+   A 
Sbjct: 51  TSKLLVPQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFAD 110

Query: 62  WIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAI 121
            +    Q +T +  +RP GV  +   +D+  G  L+  +P+G ++G+K  + G   Q A 
Sbjct: 111 RLGQYVQAHTLYNSVRPFGVSTIFGGVDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAK 169

Query: 122 NFLEKKMKNDPA-FTFQETVQTAISTLQSVLQED-FKASEIEVGVVS--KENPEFRVLSI 177
             LEK + + P   + +E V+ A   +    +++  K  E+E+   S  + N   + +  
Sbjct: 170 AELEKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKG 229

Query: 178 EEIDEHLTAISE 189
           + + E +    +
Sbjct: 230 DLLQEAIDFAQK 241

>1q5q_A Proteasome alpha-type subunit 1; proteasome assembly, Pro-peptide, inter-subunit contacts, RH erythropolis, hydrolase; 2.60A {Rhodococcus erythropolis} SCOP: d.153.1.4 PDB: 2h6j_A 1q5r_A Length = 259

 Score =  109 bits (273), Expect = 8e-30
 Identities = 33/194 (17%), Positives = 68/194 (35%), Gaps = 17/194 (8%)

Query: 9   TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYE-MPVDVLAKWIADK- 66
           T++  +  +   LG  A G   +   L +     A    + Y    +    LA   A   
Sbjct: 48  TALHKVSELYDRLGFAAVGKYNEFENLRRAGIVHADMRGYSYDRRDVTGRSLANAYAQTL 107

Query: 67  SQVYTQHAYMRPLGV---VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN- 122
             ++T+    +P  V   VA V  +     P+L++    G     +         E I  
Sbjct: 108 GTIFTEQ--PKPYEVEICVAEVGRVGSPKAPQLYRITYDGSIVDEQHFVVMGGTTEPIAT 165

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQED-----FKASEIEVGVVSKENPE--FRVL 175
            + +  + D     +  V  A++ L+     +        + +EV V+ +  P   FR +
Sbjct: 166 AMRESYRADL--DLEAAVGIAVNALRQGGAGEGEKRNVDVASLEVAVLDQSRPRRAFRRI 223

Query: 176 SIEEIDEHLTAISE 189
           +   +++ + A   
Sbjct: 224 AGTALEQLVPAEPA 237

>3mi0_A Proteasome subunit alpha; enzyme inhibitors, lactones, proteasome endopeptidase comple mycobacterium tuberculosis, hydrolase; HET: SA6; 2.20A {Mycobacterium tuberculosis} PDB: 3h6f_A 3krd_A* 3h6i_A* 3mka_A 2fhh_A* 2fhg_A 3hfa_D 3hf9_A 3mfe_D Length = 248

 Score =  100 bits (250), Expect = 2e-26
 Identities = 31/197 (15%), Positives = 61/197 (30%), Gaps = 17/197 (8%)

Query: 9   TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYE-MPVDVLAKWIADKS 67
            S+  +  +   +G  A G   +   L +     A    + Y    +    LA   A   
Sbjct: 48  RSLQKISELYDRVGFAAAGKFNEFDNLRRGGIQFADTRGYAYDRRDVTGRQLANVYAQTL 107

Query: 68  QVYTQHAYMRPLGV---VAMVLSIDEECGPRLFKCDPAGHFF-GHKATSAGLKEQEAINF 123
                    +P  V   VA V    E   P L++    G           G   +   N 
Sbjct: 108 GT-IFTEQAKPYEVELCVAEVAHYGETKRPELYRITYDGSIADEPHFVVMGGTTEPIANA 166

Query: 124 LEKKMKNDPAFTFQETVQTAISTLQSVLQED-------FKASEIEVGVVSKENPE--FRV 174
           L++    +   +  + ++ A++ L++   +           + +EV V+    P   FR 
Sbjct: 167 LKESYAENA--SLTDALRIAVAALRAGSADTSGGDQPTLGVASLEVAVLDANRPRRAFRR 224

Query: 175 LSIEEIDEHLTAISERD 191
           ++   +   L       
Sbjct: 225 ITGSALQALLVDQESPQ 241

>3unf_H Proteasome subunit beta type-10; antigen presentation, drug development, protein degradation, hydrolase-hydrolase inhibitor complex; HET: 04C; 2.90A {Mus musculus} PDB: 3unh_H Length = 234

 Score = 85.8 bits (213), Expect = 4e-21
 Identities = 27/178 (15%), Positives = 63/178 (35%), Gaps = 9/178 (5%)

Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
           ++   S   +  I   +     G+ AD     + A  +        G E  V  + + + 
Sbjct: 25  VVADKSCEKIHFIAPKIYCCGAGVAADTEMTTRMAASKMELHALSTGREPRVATVTRILR 84

Query: 65  DKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFL 124
                Y  H     +G   +V  +D   GP+L++  P G +     T+ G  +  A+  L
Sbjct: 85  QTLFRYQGH-----VGASLVVGGVDLN-GPQLYEVHPHGSYSRLPFTALGSGQGAAVALL 138

Query: 125 EKKMKNDPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEID 181
           E + + +   T +   +  +  + + +  D      ++  V++    + +       +
Sbjct: 139 EDRFQPN--MTLEAAQELLVEAITAGILSDLGSGGNVDACVITAGGAKLQRALSTPTE 194

>1yar_H Proteasome beta subunit; proteasome 20S, PA26 proteasome activator 11S, hydrolase-HYD activator complex; 1.90A {Thermoplasma acidophilum} SCOP: d.153.1.4 PDB: 1ya7_H 1yau_H 3ipm_H 1pma_B 3jrm_H 3c92_H 3c91_H 3jse_H 3jtl_H Length = 217

 Score = 82.7 bits (205), Expect = 5e-20
 Identities = 40/177 (22%), Positives = 70/177 (39%), Gaps = 10/177 (5%)

Query: 14  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 73
           LF I  Y G+   G+  DA+ LV+  + E   +R +    MP++ +A  +++        
Sbjct: 42  LFQIDTYTGMTIAGLVGDAQVLVRYMKAELELYRLQRRVNMPIEAVATLLSNMLNQVK-- 99

Query: 74  AYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPA 133
               P  V  +V  ID    P +F  D AG        S G         LE +      
Sbjct: 100 --YMPYMVQLLVGGIDT--APHVFSIDAAGGSVEDIYASTGSGSPFVYGVLESQYSEK-- 153

Query: 134 FTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISE 189
            T  E V   I  + +  Q D      I+V V+++++  +  L  ++I+  +  +  
Sbjct: 154 MTVDEGVDLVIRAISAAKQRDSASGGMIDVAVITRKD-GYVQLPTDQIESRIRKLGL 209

>3nzj_H Proteasome component PUP1; ubiquitin, protein degradation, N-terminal nucleophilic HYDR 19S regulatory particle; HET: TY5 TRO MES; 2.40A {Saccharomyces cerevisiae} PDB: 3nzw_H* 3nzx_H* Length = 261

 Score = 81.6 bits (202), Expect = 3e-19
 Identities = 31/171 (18%), Positives = 52/171 (30%), Gaps = 9/171 (5%)

Query: 14  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 73
           L  I+  +     G  AD   + Q               E  V    + +          
Sbjct: 63  LHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQ-----HLF 117

Query: 74  AYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPA 133
            Y   +G   +V  +D   G  LF     G        S G     A+  LE   K D  
Sbjct: 118 KYQGHIGAYLIVAGVDPT-GSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQD-- 174

Query: 134 FTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEH 183
            T +E ++ A   +Q+ +  D    S ++V V+        + +    +  
Sbjct: 175 LTKEEAIKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVR 225

>1ryp_I 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1g0u_H* 1jd2_H* 1g65_H 1vsy_I 1z7q_I 2f16_H* 2fak_H* 2fny_H* 2gpl_H* 3d29_H* 3dy3_H* 3dy4_H* 3e47_H* 3gpj_H* 3gpt_H* 3gpw_H* 3hye_H* 3l5q_M 3mg0_H* 3mg4_H* ... Length = 222

 Score = 79.6 bits (197), Expect = 8e-19
 Identities = 31/156 (19%), Positives = 49/156 (31%), Gaps = 9/156 (5%)

Query: 14  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 73
           L  I+  +     G  AD   + Q               E  V    + +          
Sbjct: 34  LHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQ-----HLF 88

Query: 74  AYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPA 133
            Y   +G   +V  +D   G  LF     G        S G     A+  LE   K D  
Sbjct: 89  KYQGHIGAYLIVAGVDPT-GSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQD-- 145

Query: 134 FTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKE 168
            T +E ++ A   +Q+ +  D    S ++V V+   
Sbjct: 146 LTKEEAIKLASDAIQAGIWNDLGSGSNVDVCVMEIG 181

>1iru_I 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_H* 3une_H Length = 234

 Score = 76.2 bits (188), Expect = 2e-17
 Identities = 28/160 (17%), Positives = 49/160 (30%), Gaps = 9/160 (5%)

Query: 14  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 73
           +  I+  +     G  AD     Q             G    V    + +          
Sbjct: 34  IHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGRLPRVVTANRMLKQ-----MLF 88

Query: 74  AYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPA 133
            Y   +G   ++  +D   GP L+   P G        + G     A+   E K + D  
Sbjct: 89  RYRGYIGAALVLGGVDVT-GPHLYSIYPHGSTDKLPYVTMGSGSLAAMAVFEDKFRPD-- 145

Query: 134 FTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEF 172
              +E        + + +  D    S I++ V+SK   +F
Sbjct: 146 MEEEEAKNLVSEAIAAGIFNDLGSGSNIDLCVISKNKLDF 185

>1q5r_H Proteasome beta-type subunit 1; proteasome assembly, Pro-peptide, inter-subunit contacts, hydrolase; 3.10A {Rhodococcus erythropolis} SCOP: d.153.1.4 PDB: 2h6j_H Length = 294

 Score = 71.2 bits (174), Expect = 2e-15
 Identities = 34/192 (17%), Positives = 62/192 (32%), Gaps = 20/192 (10%)

Query: 14  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 73
           ++   +Y      G    A  LV+    E   +    G  +  D  A  +A   +     
Sbjct: 99  VYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEGVPLTFDGKANRLASMVRGN-LG 157

Query: 74  AYMRPLGVVAMVLSID-----EECGPRLFKCDPAGHFFGHKA--TSAGLKEQEAINFLEK 126
           A M+ L VV +++  D     E    R+   D  G  +  +A   + G     A + L+K
Sbjct: 158 AAMQGLAVVPLLVGYDLDADDESRAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALKK 217

Query: 127 KMKNDPAFTFQETVQTAISTLQSVLQED--------FKASEIEVGVVSKENPEFRVLSIE 178
               D     +  ++ AI +L     +D         +        +++       +S E
Sbjct: 218 IYSPD--SDEETALRAAIESLYDAADDDSATGGPDLTRGIYPTAVTITQAG--AVHVSEE 273

Query: 179 EIDEHLTAISER 190
              E    I   
Sbjct: 274 TTSELARRIVAE 285

>1ryp_L 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_L 1vsy_L 1z7q_L 3l5q_P 1g65_K* 1g0u_K* 1jd2_K* 2f16_K* 2fak_K* 2fny_K* 2gpl_K* 2zcy_K* 3bdm_K* 3d29_K* 3dy3_K* 3dy4_K* 3e47_K* 3gpj_K* 3gpt_K* 3gpw_K* ... Length = 212

 Score = 69.6 bits (171), Expect = 4e-15
 Identities = 23/178 (12%), Positives = 57/178 (32%), Gaps = 9/178 (5%)

Query: 14  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 73
           +  I  +L     G  AD +        +      +    + V   +K +++    Y   
Sbjct: 34  VIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGA 93

Query: 74  AYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPA 133
                L +  M+     + GP ++  D  G          G  +  A   L+   K D  
Sbjct: 94  ----GLSMGTMICGYTRKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWD-- 147

Query: 134 FTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 190
            + ++ +     ++ +    D +    + +  V+++   +      ++ E    + E 
Sbjct: 148 LSVEDALYLGKRSILAAAHRDAYSGGSVNLYHVTEDG--WIYHGNHDVGELFWKVKEE 203

>3nzj_K Proteasome component PRE2; ubiquitin, protein degradation, N-terminal nucleophilic HYDR 19S regulatory particle; HET: TY5 TRO MES; 2.40A {Saccharomyces cerevisiae} PDB: 3nzw_K* 3nzx_K* Length = 287

 Score = 70.2 bits (172), Expect = 7e-15
 Identities = 23/178 (12%), Positives = 57/178 (32%), Gaps = 9/178 (5%)

Query: 14  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 73
           +  I  +L     G  AD +        +      +    + V   +K +++    Y   
Sbjct: 109 VIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGA 168

Query: 74  AYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPA 133
                L +  M+     + GP ++  D  G          G  +  A   L+   K D  
Sbjct: 169 ----GLSMGTMICGYTRKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWD-- 222

Query: 134 FTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 190
            + ++ +     ++ +    D +    + +  V+++   +      ++ E    + E 
Sbjct: 223 LSVEDALYLGKRSILAAAHRDAYSGGSVNLYHVTEDG--WIYHGNHDVGELFWKVKEE 278

>1q5q_H Proteasome beta-type subunit 1; proteasome assembly, Pro-peptide, inter-subunit contacts, RH erythropolis, hydrolase; 2.60A {Rhodococcus erythropolis} SCOP: d.153.1.4 Length = 235

 Score = 66.8 bits (163), Expect = 5e-14
 Identities = 34/192 (17%), Positives = 62/192 (32%), Gaps = 20/192 (10%)

Query: 14  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 73
           ++   +Y      G    A  LV+    E   +    G  +  D  A  +A   +     
Sbjct: 34  VYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEGVPLTFDGKANRLASMVRGN-LG 92

Query: 74  AYMRPLGVVAMVLSID-----EECGPRLFKCDPAGHFFGHKA--TSAGLKEQEAINFLEK 126
           A M+ L VV +++  D     E    R+   D  G  +  +A   + G     A + L+K
Sbjct: 93  AAMQGLAVVPLLVGYDLDADDESRAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALKK 152

Query: 127 KMKNDPAFTFQETVQTAISTLQSVLQED--------FKASEIEVGVVSKENPEFRVLSIE 178
               D     +  ++ AI +L     +D         +        +++       +S E
Sbjct: 153 IYSPD--SDEETALRAAIESLYDAADDDSATGGPDLTRGIYPTAVTITQAG--AVHVSEE 208

Query: 179 EIDEHLTAISER 190
              E    I   
Sbjct: 209 TTSELARRIVAE 220

>1iru_L 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_K* 3une_K 3unf_K* 3unh_K Length = 204

 Score = 63.4 bits (155), Expect = 7e-13
 Identities = 26/171 (15%), Positives = 56/171 (32%), Gaps = 10/171 (5%)

Query: 14  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 73
           +  I  YL     G  AD     +    +   +  +    + V   +K +A+    Y   
Sbjct: 34  VIEINPYLLGTMAGGAADCSFWERLLARQCRIYELRNKERISVAAASKLLANMVYQYKGM 93

Query: 74  AYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPA 133
                L +  M+   D+  GP L+  D  G+       S G     A   +++    D  
Sbjct: 94  ----GLSMGTMICGWDKR-GPGLYYVDSEGNRISGATFSVGSGSVYAYGVMDRGYSYD-- 146

Query: 134 FTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEH 183
              ++    A   +      D +    + +  V ++   +  +S + + + 
Sbjct: 147 LEVEQAYDLARRAIYQATYRDAYSGGAVNLYHVREDG--WIRVSSDNVADL 195

>1j2q_H Proteasome beta subunit; ubiquitin, CP, hydrolase; HET: CIB; 2.83A {Archaeoglobus fulgidus} SCOP: d.153.1.4 Length = 202

 Score = 61.8 bits (151), Expect = 3e-12
 Identities = 36/178 (20%), Positives = 70/178 (39%), Gaps = 11/178 (6%)

Query: 14  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 73
           ++ I   + +   G   DA+ L +  + EA  +  +   +  V  +A   ++    Y   
Sbjct: 34  IYQIADRMAMTTAGSVGDAQFLARIIKIEANLYEIRRERKPTVRAIATLTSNLLNSYRYF 93

Query: 74  AYMRPLGVVAMVLSIDEECGPRLFKCDPAG-HFFGHKATSAGLKEQEAINFLEKKMKNDP 132
               P  V  ++  ID E G  ++  DP G         + G     A   LE +   + 
Sbjct: 94  ----PYLVQLLIGGIDSE-GKSIYSIDPIGGAIEEKDIVATGSGSLTAYGVLEDRFTPE- 147

Query: 133 AFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISE 189
                E V+ A+  + S ++ D      I+V  ++++  EF   S EE+++ L    +
Sbjct: 148 -IGVDEAVELAVRAIYSAMKRDSASGDGIDVVKITED--EFYQYSPEEVEQILAKFRK 202

>1iru_H 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_N* 3une_N Length = 205

 Score = 61.5 bits (150), Expect = 3e-12
 Identities = 25/168 (14%), Positives = 55/168 (32%), Gaps = 8/168 (4%)

Query: 14  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 73
           L PI   +    +G  AD + +     Y+      +      V   A    +       +
Sbjct: 34  LTPIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKE-----MCY 88

Query: 74  AYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPA 133
            Y   L    ++   D + G +++     G          G        +++   +    
Sbjct: 89  RYREDLMAGIIIAGWDPQEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREG-- 146

Query: 134 FTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEI 180
            T +E +Q   + L   ++ D      I +  +++   E +VL  ++I
Sbjct: 147 MTKEECLQFTANALALAMERDGSSGGVIRLAAIAESGVERQVLLGDQI 194

>2jay_A Proteasome; hydrolase; 1.99A {Mycobacterium tuberculosis} PDB: 3mka_C 3mi0_C* 2fhg_H* 2fhh_H 3krd_C* 3mfe_G 3hfa_H* 3h6i_C 3h6f_C 3hf9_H 3mfe_H Length = 291

 Score = 62.2 bits (151), Expect = 4e-12
 Identities = 30/203 (14%), Positives = 55/203 (27%), Gaps = 16/203 (7%)

Query: 1   MQDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA 60
            Q  ++    V  ++    Y      G  A A    +    E   +    G  +      
Sbjct: 78  TQGNMISGRDVRKVYITDDYTATGIAGTAAVAVEFARLYAVELEHYEKLEGVPLTFAGKI 137

Query: 61  KWIADKSQVYTQHAYMRPLGVVAMVLSIDEEC-----GPRLFKCDPAGHFF--GHKATSA 113
             +A   +     A M+ L  + ++   D          R+   D AG +        + 
Sbjct: 138 NRLAIMVRGNL-AAAMQGLLALPLLAGYDIHASDPQSAGRIVSFDAAGGWNIEEEGYQAV 196

Query: 114 GLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQED------FKASEIEVGVVSK 167
           G     A + ++K             ++ A+  L     +D           I    V  
Sbjct: 197 GSGSLFAKSSMKKLYSQV--TDGDSGLRVAVEALYDAADDDSATGGPDLVRGIFPTAVII 254

Query: 168 ENPEFRVLSIEEIDEHLTAISER 190
           +      +    I E   AI E 
Sbjct: 255 DADGAVDVPESRIAELARAIIES 277

>1iru_K 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_J* 3une_J 3unf_J* 3unh_J Length = 201

 Score = 59.9 bits (146), Expect = 1e-11
 Identities = 23/156 (14%), Positives = 53/156 (33%), Gaps = 5/156 (3%)

Query: 14  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 73
           +F +++ + LL  G   D     +  +     ++ + GYE+     A +   +  +    
Sbjct: 35  MFKMSEKILLLCVGEAGDTVQFAEYIQKNVQLYKMRNGYELSPTAAANFT--RRNLADCL 92

Query: 74  AYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPA 133
               P  V  ++   DE  GP L+  D           + G      ++ L++       
Sbjct: 93  RSRTPYHVNLLLAGYDEHEGPALYYMDYLAALAKAPFAAHGYGAFLTLSILDRYYTPT-- 150

Query: 134 FTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKE 168
            + +  V+     L+ + +          V ++ K 
Sbjct: 151 ISRERAVELLRKCLEELQKRFILNLPTFSVRIIDKN 186

>1g0u_M Proteasome component PRE4; ubiquitin, degradation, protease, NTN-hydrolase; 2.40A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 2zcy_M* 3bdm_M* 3mg6_M* 3mg7_M* 3mg8_M* 3nzj_M* 3nzw_M* 3nzx_M* Length = 266

 Score = 59.7 bits (145), Expect = 2e-11
 Identities = 22/170 (12%), Positives = 58/170 (34%), Gaps = 11/170 (6%)

Query: 8   HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKY-----GYEMPVDVLAKW 62
              V  L P+     +  +G  +D + + +  +    E  +          +    + ++
Sbjct: 69  FNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLADAEEALEPSYIFEY 128

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           +   + +Y + + M PL    +V  +       L   +  G  +     + G     A  
Sbjct: 129 L--ATVMYQRRSKMNPLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFGAHMANP 186

Query: 123 FLEKKMKND---PAFTFQETVQTAISTLQSVLQEDFKA-SEIEVGVVSKE 168
            L K +  +   P  T Q   +  ++ ++ +   D ++     + ++ K 
Sbjct: 187 LLRKVVDRESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKN 236

>1ryp_N 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_N* 1jd2_M* 1g65_M 1vsy_N 1z7q_N 2f16_M* 2fak_M* 2fny_M* 2gpl_M* 3d29_M* 3dy3_M* 3dy4_M* 3e47_M* 3gpj_M* 3gpt_M* 3gpw_M* 3hye_M* 3l5q_R 3mg0_M* 3mg4_M* ... Length = 233

 Score = 58.5 bits (142), Expect = 7e-11
 Identities = 22/170 (12%), Positives = 58/170 (34%), Gaps = 11/170 (6%)

Query: 8   HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKY-----GYEMPVDVLAKW 62
              V  L P+     +  +G  +D + + +  +    E  +          +    + ++
Sbjct: 36  FNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLADAEEALEPSYIFEY 95

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           +   + +Y + + M PL    +V  +       L   +  G  +     + G     A  
Sbjct: 96  L--ATVMYQRRSKMNPLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFGAHMANP 153

Query: 123 FLEKKMKND---PAFTFQETVQTAISTLQSVLQEDFKA-SEIEVGVVSKE 168
            L K +  +   P  T Q   +  ++ ++ +   D ++     + ++ K 
Sbjct: 154 LLRKVVDRESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKN 203

>1ryp_K 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_K 1g0u_J* 1jd2_J* 1g65_J 1vsy_K 1z7q_K 2f16_J* 2fak_J* 2fny_J* 2gpl_J* 2zcy_J* 3bdm_J* 3d29_J* 3dy3_J* 3dy4_J* 3e47_J* 3gpj_J* 3gpt_J* 3gpw_J* 3hye_J* ... Length = 198

 Score = 57.6 bits (140), Expect = 7e-11
 Identities = 21/157 (13%), Positives = 55/157 (35%), Gaps = 6/157 (3%)

Query: 14  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 73
              ++ +  +   G   D     +  +     +  +  YE+    ++ ++  + ++    
Sbjct: 35  TRQLSPHTLMSFAGEAGDTVQFAEYIQANIQLYSIREDYELSPQAVSSFV--RQELAKSI 92

Query: 74  AYMRPLGVVAMVLSIDEEC-GPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDP 132
              RP  V  ++   D++   P L++ D  G        + G       + L+   + D 
Sbjct: 93  RSRRPYQVNVLIGGYDKKKNKPELYQIDYLGTKVELPYGAHGYSGFYTFSLLDHHYRPD- 151

Query: 133 AFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKE 168
             T +E +      +Q + +        + V +V K+
Sbjct: 152 -MTTEEGLDLLKLCVQELEKRMPMDFKGVIVKIVDKD 187

>3unf_N Proteasome subunit beta type-9; antigen presentation, drug development, protein degradation, hydrolase-hydrolase inhibitor complex; HET: 04C; 2.90A {Mus musculus} PDB: 3unh_N Length = 199

 Score = 57.6 bits (140), Expect = 7e-11
 Identities = 25/168 (14%), Positives = 53/168 (31%), Gaps = 9/168 (5%)

Query: 14  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 73
           L P+ + +    +G  ADA+ +   A Y+      +      V   A  + +       +
Sbjct: 34  LSPLHQRIFCALSGSAADAQAIADMAAYQLELHGLELEEPPLVLAAANVVKN-----ISY 88

Query: 74  AYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPA 133
            Y   L    +V   D+            G       T  G        +++   K    
Sbjct: 89  KYREDLLAHLIVAGWDQR-EGGQVYGTMGGMLIRQPFTIGGSGSSYIYGYVDAAYKPG-- 145

Query: 134 FTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEI 180
            T +E  +   + +   +  D      I +  ++    + RV+  +E+
Sbjct: 146 MTPEECRRFTTNAITLAMNRDGSSGGVIYLVTITAAGVDHRVILGDEL 193

>1ryp_M 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_M* 1jd2_L* 1g65_L 1vsy_M 1z7q_M 2f16_L* 2fak_L* 2fny_L* 2gpl_L* 3d29_L* 3dy3_L* 3dy4_L* 3e47_L* 3gpj_L* 3gpt_L* 3gpw_L* 3hye_L* 3l5q_Q 3mg0_L* 3mg4_L* ... Length = 222

 Score = 56.2 bits (136), Expect = 4e-10
 Identities = 27/185 (14%), Positives = 61/185 (32%), Gaps = 21/185 (11%)

Query: 8   HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKY-GYEMPVDVLAKWIADK 66
                 +F     + + A G  AD   LV++ +     + F +   ++ ++  A+ I   
Sbjct: 37  SRYEPKVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKLSINSAARNIQHL 96

Query: 67  SQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAG------------ 114
                      P  V  ++  +DE+    ++  DP G +   +  + G            
Sbjct: 97  LYGKRF----FPYYVHTIIAGLDEDGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFLDN 152

Query: 115 ---LKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKA-SEIEVGVVSKENP 170
               K Q       K  K     + +E ++    +  S  +   +    +E+ +V+K+  
Sbjct: 153 QVNFKNQYEPGTNGKVKKPLKYLSVEEVIKLVRDSFTSATERHIQVGDGLEILIVTKDGV 212

Query: 171 EFRVL 175
                
Sbjct: 213 RKEFY 217

>1iru_M 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_L* 3une_L 3unf_L* 3unh_L Length = 213

 Score = 55.3 bits (134), Expect = 7e-10
 Identities = 24/179 (13%), Positives = 54/179 (30%), Gaps = 18/179 (10%)

Query: 8   HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKS 67
                  + +T    +  +G   D  TL +        ++      M    +A  ++   
Sbjct: 37  TRDSPKCYKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMTTGAIAAMLS--- 93

Query: 68  QVYTQHAYMR---PLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFL 124
                  Y R   P  V  ++  +DEE    ++  DP G +      + G         L
Sbjct: 94  ----TILYSRRFFPYYVYNIIGGLDEEGKGAVYSFDPVGSYQRDSFKAGGSASAMLQPLL 149

Query: 125 EKKMKND-------PAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVL 175
           + ++             +    ++       S  + D +    + + +V+KE      +
Sbjct: 150 DNQVGFKNMQNVEHVPLSLDRAMRLVKDVFISAAERDVYTGDALRICIVTKEGIREETV 208

>1iru_J 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_I* 3une_I 3unf_I* 3unh_I Length = 205

 Score = 53.3 bits (129), Expect = 3e-09
 Identities = 25/168 (14%), Positives = 57/168 (33%), Gaps = 15/168 (8%)

Query: 14  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 73
           +FP+   L +   G+  D +T+ Q+ ++    +  K G ++    L   +A         
Sbjct: 42  IFPMGDRLYIGLAGLATDVQTVAQRLKFRLNLYELKEGRQIKPYTLMSMVA-------NL 94

Query: 74  AYMR---PLGVVAMVLSIDEE-CGPRLFKCDPAG-HFFGHKATSAGLKEQEAINFLEKKM 128
            Y +   P     ++  +D +   P +   D  G          +G   ++     E   
Sbjct: 95  LYEKRFGPYYTEPVIAGLDPKTFKPFICSLDLIGCPMVTDDFVVSGTCAEQMYGMCESLW 154

Query: 129 KNDPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVL 175
           + +         +T    + + +  D      + V ++ K+    R L
Sbjct: 155 EPN--MDPDHLFETISQAMLNAVDRDAVSGMGVIVHIIEKDKITTRTL 200

>1iru_N 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_M* 3une_M 3unf_M* 3unh_M Length = 219

 Score = 53.0 bits (128), Expect = 4e-09
 Identities = 24/161 (14%), Positives = 56/161 (34%), Gaps = 5/161 (3%)

Query: 14  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKY-GYEMPVDVLAKWIADKSQVYTQ 72
           +  +     L A+G  AD + L Q       +      G+      +  W+     +Y++
Sbjct: 42  IMRVNNSTMLGASGDYADFQYLKQVLGQMVIDEELLGDGHSYSPRAIHSWL--TRAMYSR 99

Query: 73  HAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDP 132
            + M PL    ++    +     L   D  G  +   + + G     A   L + ++  P
Sbjct: 100 RSKMNPLWNTMVIGGYADG-ESFLGYVDMLGVAYEAPSLATGYGAYLAQPLLREVLEKQP 158

Query: 133 AFTFQETVQTAISTLQSVLQEDFKA-SEIEVGVVSKENPEF 172
             +  E        ++ +   D ++ +  +   V+++  E 
Sbjct: 159 VLSQTEARDLVERCMRVLYYRDARSYNRFQTATVTEKGVEI 199

>1ryp_H 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 3nzj_N* 3nzw_N* 3nzx_N* 1vsy_H 3l5q_B 1g65_N* 1fnt_H 1g0u_N* 1jd2_N* 1z7q_H 2f16_N* 2fak_N* 2fny_N* 2gpl_N* 2zcy_N* 3bdm_N* 3d29_N* 3dy3_N* 3dy4_N* 3e47_N* ... Length = 205

 Score = 51.4 bits (124), Expect = 1e-08
 Identities = 25/171 (14%), Positives = 57/171 (33%), Gaps = 11/171 (6%)

Query: 14  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 73
           L  +   +    +G  AD + +    +Y    +  +YG        A    +       +
Sbjct: 43  LTRVHDKIWCCRSGSAADTQAIADIVQYHLELYTSQYGTPSTETA-ASVFKE-----LCY 96

Query: 74  AYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPA 133
                L    +V   D++    ++     G         AG        + +K  + +  
Sbjct: 97  ENKDNLTAGIIVAGYDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFREN-- 154

Query: 134 FTFQETVQTAISTLQSVLQEDFKAS--EIEVGVVSKENPEFRVLSIEEIDE 182
            + +ETV     +L   ++ D  +S   I + V++    E  +   +E ++
Sbjct: 155 MSKEETVDFIKHSLSQAIKWD-GSSGGVIRMVVLTAAGVERLIFYPDEYEQ 204

>1ryp_J 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_I* 1g65_I 1vsy_J 2f16_I* 2fak_I* 2fny_I* 2gpl_I* 3d29_I* 3dy3_I* 3dy4_I* 3e47_I* 3gpj_I* 3gpt_I* 3gpw_I* 3hye_I* 3l5q_N 3mg0_I* 3mg4_I* 3oeu_I* 3oev_I* ... Length = 204

 Score = 49.1 bits (118), Expect = 1e-07
 Identities = 27/174 (15%), Positives = 54/174 (31%), Gaps = 16/174 (9%)

Query: 8   HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKS 67
                 +F        +  G+  D  TL +  RY+   ++ K    +  +   + ++   
Sbjct: 36  SNKFEKIFHYGHVFLGIT-GLATDVTTLNEMFRYKTNLYKLKEERAIEPETFTQLVS--- 91

Query: 68  QVYTQHAYMR---PLGVVAMVLSIDEECG-PRLFKCDPAGHF-FGHKATSAGLKEQEAIN 122
                  Y R   P  V  +V  I+ + G P +   D  G          +G    +   
Sbjct: 92  ----SSLYERRFGPYFVGPVVAGINSKSGKPFIAGFDLIGCIDEAKDFIVSGTASDQLFG 147

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVL 175
             E   + +     ++  +T    L +    D        V ++ K+    R L
Sbjct: 148 MCESLYEPN--LEPEDLFETISQALLNAADRDALSGWGAVVYIIKKDEVVKRYL 199

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	191
1ryp_A	243	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_A	246	20S proteasome; cell cycle, immune response, prote	100.0
1iru_B	233	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_C	244	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_C	261	20S proteasome; cell cycle, immune response, prote	100.0
1yar_A	233	Proteasome alpha subunit; proteasome 20S, PA26 pro	100.0
3h4p_A	264	Proteasome subunit alpha; core particle, cytoplasm	100.0
1ryp_D	241	20S proteasome; multicatalytic proteinase, protein	100.0
1ryp_E	242	20S proteasome; multicatalytic proteinase, protein	100.0
3h4p_a	219	Proteasome subunit beta; core particle, cytoplasm,	100.0
1iru_D	248	20S proteasome; cell cycle, immune response, prote	100.0
1iru_G	254	20S proteasome; cell cycle, immune response, prote	100.0
1j2q_H	202	Proteasome beta subunit; ubiquitin, CP, hydrolase;	100.0
1j2p_A	246	Alpha-ring, proteasome alpha subunit; hydrolase; 2	100.0
1iru_F	263	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_B	250	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_E	241	20S proteasome; cell cycle, immune response, prote	100.0
3mi0_A	248	Proteasome subunit alpha; enzyme inhibitors, lacto	100.0
1q5q_H	235	Proteasome beta-type subunit 1; proteasome assembl	100.0
1yar_H	217	Proteasome beta subunit; proteasome 20S, PA26 prot	100.0
1ryp_F	233	20S proteasome; multicatalytic proteinase, protein	100.0
1ryp_L	212	20S proteasome; multicatalytic proteinase, protein	100.0
3nzj_F	288	Proteasome component C1; ubiquitin, protein degrad	100.0
1iru_L	204	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_G	244	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_H	205	20S proteasome; cell cycle, immune response, prote	100.0
3nzj_K	287	Proteasome component PRE2; ubiquitin, protein degr	100.0
1q5r_H	294	Proteasome beta-type subunit 1; proteasome assembl	100.0
1iru_N	219	20S proteasome; cell cycle, immune response, prote	100.0
1q5q_A	259	Proteasome alpha-type subunit 1; proteasome assemb	100.0
1ryp_K	198	20S proteasome; multicatalytic proteinase, protein	100.0
1ryp_N	233	20S proteasome; multicatalytic proteinase, protein	100.0
2jay_A	291	Proteasome; hydrolase; 1.99A {Mycobacterium tuberc	100.0
3unf_H	234	Proteasome subunit beta type-10; antigen presentat	100.0
3unf_N	199	Proteasome subunit beta type-9; antigen presentati	100.0
1iru_M	213	20S proteasome; cell cycle, immune response, prote	100.0
1iru_K	201	20S proteasome; cell cycle, immune response, prote	100.0
1g0u_M	266	Proteasome component PRE4; ubiquitin, degradation,	100.0
1ryp_M	222	20S proteasome; multicatalytic proteinase, protein	100.0
1ryp_I	222	20S proteasome; multicatalytic proteinase, protein	100.0
1ryp_H	205	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_J	205	20S proteasome; cell cycle, immune response, prote	100.0
3nzj_H	261	Proteasome component PUP1; ubiquitin, protein degr	100.0
1ryp_J	204	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_I	234	20S proteasome; cell cycle, immune response, prote	100.0
1m4y_A	171	ATP-dependent protease HSLV; N-terminal catalytic	99.97
2z3b_A	180	ATP-dependent protease HSLV; N-terminal nucleophIl	99.97
1g3k_A	174	ATP-dependent protease HSLV; hydrolase; 1.90A {Hae	99.97

>1ryp_A 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_G* 1g65_G 1vsy_A 2f16_G* 2fak_G* 2fny_G* 2gpl_G* 3d29_G* 3dy3_G* 3dy4_G* 3e47_G* 3gpj_G* 3gpt_G* 3gpw_G* 3hye_G* 3l5q_A 3mg0_G* 3mg4_G* 3oeu_G* 3oev_G* ...

Probab=100.00  E-value=2.7e-46  Score=298.60  Aligned_cols=188  Identities=47%  Similarity=0.776  Sum_probs=177.9

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      +++|+.+++++||++|++|++|+++|+.+|++.+.++++.+++.|+++++++++++.+++++++++|.|++++++|||+|
T Consensus        51 ~~~l~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~r~~~~~~~~~~~~~~~v~~la~~l~~~l~~y~~~~~~rP~~v  130 (243)
T 1ryp_A           51 PDKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQRAYMRPLGV  130 (243)
T ss_dssp             CCTTBCGGGCCSEEECSSSCEEEEESCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTSCCCSC
T ss_pred             CccccCCCcCCceEEECCCEEEEEEecHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhccCCccccce
Confidence            46888899999999999999999999999999999999999999999999999999999999999999999989999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCC-----CCCHHHHHHHHHHHHHhhhcccCC
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDP-----AFTFQETVQTAISTLQSVLQEDFK  156 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~-----~~s~eea~~l~~~~l~~~~~~d~~  156 (191)
                      ++||||||+++||+||.+||+|++.+++++|+|+|++.++++||+.|++.+     +||++||++++++||..+.+||..
T Consensus       131 ~~lvaG~D~~~gp~Ly~~dp~G~~~~~~~~a~G~gs~~a~~~Le~~~~~~~~~~~~~ms~eea~~l~~~al~~~~~rd~s  210 (243)
T 1ryp_A          131 ILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFS  210 (243)
T ss_dssp             EEEEEEEETTTEEEEEEECTTSCEEEBSEEEESTTHHHHHHHHHHHHHHHCSSSCCCSSHHHHHHHHHHHHHHHHTCCCC
T ss_pred             EEEEEEEcCCCCcEEEEEcCCCCEEEEEEEEECCCcHHHHHHHHHHhhhcccccccCCCHHHHHHHHHHHHHHHhcccCC
Confidence            999999997678999999999999999999999999999999999996311     899999999999999999999954


Q ss_pred             CCeEEEEEEEeCCCcEEEcCHHHHHHHHHHhhccC
Q 029560          157 ASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD  191 (191)
Q Consensus       157 ~~~iei~iv~~~~~~~~~~~~~~i~~~~~~~~~~~  191 (191)
                      ..+++|++|++++  |++++++||++++.++.++|
T Consensus       211 ~~~iev~vi~~~g--~~~l~~~ei~~~~~~~~~~~  243 (243)
T 1ryp_A          211 KNDLEVGVATKDK--FFTLSAENIEERLVAIAEQD  243 (243)
T ss_dssp             TTSEEEEEEETTE--EEECCHHHHHHHHHHHTTTC
T ss_pred             CCcEEEEEEECCC--eEECCHHHHHHHHHHhhccC
Confidence            4599999999986  99999999999999999887

>1iru_A 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_G* 3une_G 3unf_G* 3unh_G

Probab=100.00  E-value=1e-45  Score=295.73  Aligned_cols=190  Identities=61%  Similarity=0.967  Sum_probs=178.0

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      +++++.+++++||++|++|++|+++|..+|++.|.++++.+++.|+++++++++++.+++++++++|.|+++.++|||+|
T Consensus        57 ~~~l~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~y~~~~~~rp~~v  136 (246)
T 1iru_A           57 PDKLLDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGC  136 (246)
T ss_dssp             CCSSBCGGGCCSEEESSSSCEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSBCCCSE
T ss_pred             CCcccCCCccCceEEECCCEEEEEeccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcCCCCCCcce
Confidence            35788889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCCeEE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIE  161 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~~ie  161 (191)
                      ++||||||+++||+||.+||+|++.+++++|+|+|++.++++||++|++.++||++||++++++||..+.+||....+++
T Consensus       137 ~~lvaG~D~~~gp~Ly~idp~G~~~~~~~~aiG~gs~~a~~~Le~~~~~~~~ms~eea~~la~~al~~~~~rd~sg~~i~  216 (246)
T 1iru_A          137 CMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIE  216 (246)
T ss_dssp             EEEEEEEETTTEEEEEEECTTSCEEEBSEEEEETTHHHHHHHHHHHTTSCCCCCHHHHHHHHHHHHHHHTTCCCCTTSEE
T ss_pred             EEEEEEEeCCCCeEEEEEcCCeeEEEeeEEEECCCcHHHHHHHHHhhcccCCCCHHHHHHHHHHHHHHHhcccCCCCcEE
Confidence            99999999767899999999999999999999999999999999999533399999999999999999999994434899


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHHHHHhhccC
Q 029560          162 VGVVSKENPEFRVLSIEEIDEHLTAISERD  191 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~~~~~~~~~  191 (191)
                      |++|+++++.|++++++||++++.++.++|
T Consensus       217 v~vi~~~g~~~~~l~~~ei~~~~~~~~~~~  246 (246)
T 1iru_A          217 VGVVTVENPKFRILTEAEIDAHLVALAERD  246 (246)
T ss_dssp             EEEEETTEEEEEECCHHHHHHHHHHHHTC-
T ss_pred             EEEEECCCCeEEECCHHHHHHHHHHhhccC
Confidence            999999876699999999999999999887

>1iru_B 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_A* 3une_A 3unf_A* 3unh_A

Probab=100.00  E-value=3.7e-44  Score=284.53  Aligned_cols=182  Identities=35%  Similarity=0.562  Sum_probs=172.9

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      +++++.+++++||++|++|++|++||..+|++.+.++++.+++.|+++++++++++.+++++++++|.|++++++|||+|
T Consensus        52 ~~~l~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~y~~~~~~rP~~v  131 (233)
T 1iru_B           52 KSILYDERSVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGV  131 (233)
T ss_dssp             CCSSBCSTTCCSSEESSSSEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCSE
T ss_pred             CccccccccCCeEEEECCCEEEEEEEccHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCcCCCCCcEE
Confidence            46788899999999999999999999999999999999999999999999999999999999999999999989999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCCeEE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIE  161 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~~ie  161 (191)
                      ++||||||+ +||+||.+||+|++.++++.|+|+|++.++++||++|+  ++||++||++++++||..+.++|....+++
T Consensus       132 ~~lvaG~D~-~gp~Ly~id~~G~~~~~~~~aiG~gs~~a~~~Le~~~~--~~ms~eea~~la~~al~~~~~~d~sg~~i~  208 (233)
T 1iru_B          132 SLLICGWNE-GRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYN--EDLELEDAIHTAILTLKESFEGQMTEDNIE  208 (233)
T ss_dssp             EEEEEEECS-SSEEEEEECTTSCEEEBSEEEESTTHHHHHHHHHHHCC--TTCCHHHHHHHHHHHHHTTCCSCCCSSSEE
T ss_pred             EEEEEEEeC-CCCeEEEECCCCCEEEeeEEEECCCCHHHHHHHHHHhc--cCCCHHHHHHHHHHHHHHHhhccCCCCCEE
Confidence            999999995 78999999999999999999999999999999999984  789999999999999999999996545999


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHHHHHhh
Q 029560          162 VGVVSKENPEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~~~~~~  188 (191)
                      |++|++++  |++++++||++++.+++
T Consensus       209 v~vi~~~g--~~~l~~~ei~~~~~~~~  233 (233)
T 1iru_B          209 VGICNEAG--FRRLTPTEVKDYLAAIA  233 (233)
T ss_dssp             EEEEETTE--EEECCHHHHHHHHTTCC
T ss_pred             EEEEECCC--EEECCHHHHHHHHHhcC
Confidence            99999986  99999999999998763

>1ryp_C 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_B* 1g65_B 2f16_B* 2fak_B* 2fny_B* 2gpl_B* 3d29_B* 3dy3_B* 3dy4_B* 3e47_B* 3gpj_B* 3gpt_B* 3gpw_B* 3hye_B* 3mg0_B* 3mg4_B* 3okj_B* 3shj_B* 3tdd_B* 3nzj_B* ...

Probab=100.00  E-value=1.2e-43  Score=283.29  Aligned_cols=185  Identities=26%  Similarity=0.494  Sum_probs=173.6

Q ss_pred             CCcccc-CCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccc
Q 029560            2 QDKLLD-HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLG   80 (191)
Q Consensus         2 ~s~l~~-~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~   80 (191)
                      .++++. +++++||++|++|++|++||..+|++.|.++++.+++.|+++++++++++.+++++++++|.|++++++|||+
T Consensus        52 ~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rp~~  131 (244)
T 1ryp_C           52 TSTLLEQDTSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFG  131 (244)
T ss_dssp             CCSSBCSTTCCSSEEESSSSEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSCCCCC
T ss_pred             CCcCccCCCCCCcEEEECCCEEEEEEEcHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhccCCccceE
Confidence            356666 8899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcc-cCCCCe
Q 029560           81 VVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQE-DFKASE  159 (191)
Q Consensus        81 v~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~-d~~~~~  159 (191)
                      |++||||||+++||+||.+||+|++.+++++|+|+|++.++++||++|+  ++||++||++++++||..+.+| +....+
T Consensus       132 v~~lvaG~D~~~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~--~~ms~eea~~la~~al~~~~~rd~~sg~~  209 (244)
T 1ryp_C          132 VSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYK--DDMKVDDAIELALKTLSKTTDSSALTYDR  209 (244)
T ss_dssp             EEEEEEEEETTTEEEEEEECTTCCEEEBSEEEESTTHHHHHHHHHHHCC--TTCCHHHHHHHHHHHHHHHCSSSSCCGGG
T ss_pred             EEEEEEEEcCCCCCEEEEECCCccEEeeeEEEECCCcHHHHHHHHHhhh--cCCCHHHHHHHHHHHHHHHhccccCCCCc
Confidence            9999999994478999999999999999999999999999999999984  7899999999999999999999 554348


Q ss_pred             EEEEEEE--eCCCc--EEEcCHHHHHHHHHHhh
Q 029560          160 IEVGVVS--KENPE--FRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       160 iei~iv~--~~~~~--~~~~~~~~i~~~~~~~~  188 (191)
                      ++|++|+  +++++  |+.++++||++++.++.
T Consensus       210 i~v~vi~~~~~~~~~~~~~l~~~ei~~~~~~~~  242 (244)
T 1ryp_C          210 LEFATIRKGANDGEVYQKIFKPQEIKDILVKTG  242 (244)
T ss_dssp             EEEEEEECCSSSSSCEEEECCHHHHHHHHHHHT
T ss_pred             EEEEEEEeecCCCceeEEECCHHHHHHHHHHhh
Confidence            9999999  98865  99999999999999875

>1iru_C 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_B* 3une_B 3unf_B* 3unh_B

Probab=100.00  E-value=1.4e-43  Score=285.53  Aligned_cols=186  Identities=26%  Similarity=0.473  Sum_probs=173.2

Q ss_pred             CccccCC-CCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            3 DKLLDHT-SVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         3 s~l~~~~-~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      ++++... +++||++|++|++|++||+.+|++.|.++++.+++.|+++++++++++.+++++++++|.|+++.++|||+|
T Consensus        53 ~g~~~~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rP~~v  132 (261)
T 1iru_C           53 HKLLDEVFFSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGV  132 (261)
T ss_dssp             CTTBCCCSSCSSEEECSSSEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBSSCCCCCE
T ss_pred             CcccccCCCCccEEEecCCEEEEEeEcHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccccCcCcceE
Confidence            3444444 599999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCC-CCCHHHHHHHHHHHHHhhhcccCCCC-e
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDP-AFTFQETVQTAISTLQSVLQEDFKAS-E  159 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~-~~s~eea~~l~~~~l~~~~~~d~~~~-~  159 (191)
                      ++||||||+++||+||.+||+|++.+++++|+|+|++.++++||++|+  + +||++||++++++||..+.++|..++ +
T Consensus       133 ~~lvaG~D~~~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~--~~~ms~eeA~~la~~al~~~~~~d~~sg~~  210 (261)
T 1iru_C          133 SLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK--EGEMTLKSALALAIKVLNKTMDVSKLSAEK  210 (261)
T ss_dssp             EEEEEEEETTTEEEEEEEETTTEEEECSEEEESTTTTHHHHHHHHHCC--TTCCCHHHHHHHHHHHHHHSSSCTTCCSTT
T ss_pred             EEEEEEEeCCCCcEEEEECCCceEEeeeeEEeCcccHHHHHHHHHhhc--cCCCCHHHHHHHHHHHHHHHHhccCCCCCc
Confidence            999999996578999999999999999999999999999999999984  6 89999999999999999999987765 8


Q ss_pred             EEEEEEEeCCCc--EEEcCHHHHHHHHHHhhcc
Q 029560          160 IEVGVVSKENPE--FRVLSIEEIDEHLTAISER  190 (191)
Q Consensus       160 iei~iv~~~~~~--~~~~~~~~i~~~~~~~~~~  190 (191)
                      ++|++|+++++.  |++++++||++++.++.++
T Consensus       211 i~v~vi~~~~~~~~~~~l~~~ei~~~l~~~~~~  243 (261)
T 1iru_C          211 VEIATLTRENGKTVIRVLKQKEVEQLIKKHEEE  243 (261)
T ss_dssp             CEEEEEECCSSSCEEEECCHHHHHHHHHHHHTT
T ss_pred             EEEEEEEcCCCeeeEEECCHHHHHHHHHHHHhc
Confidence            999999998753  8999999999999998654

>1yar_A Proteasome alpha subunit; proteasome 20S, PA26 proteasome activator 11S, hydrolase-HYD activator complex; 1.90A {Thermoplasma acidophilum} SCOP: d.153.1.4 PDB: 1ya7_A 1pma_A 3c91_A 3c92_A 3ipm_A 2ku1_A 2ku2_A 1yau_A 3jrm_A 3jse_A 3jtl_A

Probab=100.00  E-value=1.5e-43  Score=280.98  Aligned_cols=179  Identities=34%  Similarity=0.565  Sum_probs=170.1

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      +++++.+++.+||++|++|++|++||..+|++.+.++++.+++.|+++++++++++.+++++++++|.|+++++.|||+|
T Consensus        55 ~~~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a~~l~~~~~~~~~~~~~rp~~v  134 (233)
T 1yar_A           55 RSRLIEQNSIEKIQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGV  134 (233)
T ss_dssp             CCTTBCSTTCCSEEEEETTEEEEEEEBHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBTTBCCCCE
T ss_pred             CcccccccccCeEEEecCCEEEEEeeCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCcCCcCcceE
Confidence            45788889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCCeEE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIE  161 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~~ie  161 (191)
                      ++||||||+ +||+||.+||+|++.+++++|+|+|++.++++||+.|+  ++||++||++++++||..+.++|+...+++
T Consensus       135 ~~lvaG~D~-~gp~Ly~id~~G~~~~~~~~aiG~gs~~a~~~Le~~~~--~~~s~eea~~la~~al~~~~~~d~s~~~i~  211 (233)
T 1yar_A          135 SLIFAGIDQ-IGPRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYK--ENLPEKEAVTLGIKALKSSLEEGEELKAPE  211 (233)
T ss_dssp             EEEEEEECS-SCEEEEEECTTCCEEEBSEEEESTTHHHHHHHHHHHCC--TTCCHHHHHHHHHHHHHHTSCSSCCCCCCE
T ss_pred             EEEEEEEeC-CCCEEEEECCCCCEEeeeEEEEcCCcHHHHHHHHHHhc--cCCCHHHHHHHHHHHHHHHhhccCCCCcEE
Confidence            999999997 78999999999999999999999999999999999984  789999999999999999999998545899


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHHH
Q 029560          162 VGVVSKENPEFRVLSIEEIDEHL  184 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~~  184 (191)
                      |++|+++++ |++++++||+++|
T Consensus       212 v~vi~~~~~-~~~~~~~ei~~~l  233 (233)
T 1yar_A          212 IASITVGNK-YRIYDQEEVKKFL  233 (233)
T ss_dssp             EEEEETTSC-CEECCHHHHHTTC
T ss_pred             EEEEECCCC-EEECCHHHHHhhC
Confidence            999999975 9999999998753

>3h4p_A Proteasome subunit alpha; core particle, cytoplasm, hydrolase, protease, threonine protease; 4.10A {Methanocaldococcus jannaschii}

Probab=100.00  E-value=2.1e-44  Score=290.62  Aligned_cols=183  Identities=32%  Similarity=0.580  Sum_probs=174.0

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      +++|+.+++++||++|++|++|+++|+.+|++.|+++++.+++.|+++++++++++.+++.|++++|.|++++++|||+|
T Consensus        59 ~~~li~~~~~~KI~~i~d~i~~~~aG~~aD~~~l~~~~r~~~~~y~~~~~~~i~v~~la~~l~~~~~~yt~~~~~rP~~v  138 (264)
T 3h4p_A           59 TSKLVKIRSIEKIFQIDDHVAAATSGLVADARVLIDRARLEAQIYRLTYGEEISIEMLAKKICDIKQAYTQHGGVRPFGV  138 (264)
T ss_dssp             CSTTBCTTTCCCEEEEETTEEEEEEECSHHHHHHHTTHHHHHHHHHHTTCSCCCHHHHHHHHHHHHHHTTSBSSCCCCSE
T ss_pred             cCCccccCccccEEEecCcEEEEeccchHHHHHHHHHHHHHHHhhHHhcCCCCCHHHHHHHHHHHHHHHhhccCCCCeeE
Confidence            45788899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCCeEE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIE  161 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~~ie  161 (191)
                      ++||||||+ +||+||.+||+|++.+++++|+|+|++.++++||+.|  +++||++||++++++||..+.++ ....+++
T Consensus       139 ~~lvaG~D~-~gp~Ly~iDp~G~~~~~~~~aiGsgs~~a~~~Le~~~--~~~ms~eea~~la~~al~~a~~~-~sg~~ie  214 (264)
T 3h4p_A          139 SLLIAGIDK-NEARLFETDPSGALIEYKATAIGSGRPVVMELLEKEY--RDDITLDEGLELAITALTKANED-IKPENVD  214 (264)
T ss_dssp             EEEEEEEET-TEEEEEEECTTCCCEEESEEEESTTHHHHTTTHHHHC--CTTCCSHHHHHHHHHHHHHHSSS-CCTTSEE
T ss_pred             EEEEEEEeC-CcCEEEEECCCceEEecCeEEECCCHHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHHhc-cCCCeEE
Confidence            999999997 7899999999999999999999999999999999998  48999999999999999999987 5445999


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHHHHHhh
Q 029560          162 VGVVSKENPEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~~~~~~  188 (191)
                      |++|++++.+|++++++||++++.++.
T Consensus       215 v~vi~~~~~~~~~l~~~ei~~~~~~~~  241 (264)
T 3h4p_A          215 VCIITVKDAQFKKIPVEEIKKLIEKVK  241 (264)
T ss_dssp             EEEEETTTTEEEECCTTTTGGGTTTTT
T ss_pred             EEEEEeCCCcEEECCHHHHHHHHHHHH
Confidence            999998877799999999999998885

>1ryp_D 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_C* 1g65_C 2f16_C* 2fak_C* 2fny_C* 2gpl_C* 3d29_C* 3dy3_C* 3dy4_C* 3e47_C* 3gpj_C* 3gpt_C* 3gpw_C* 3hye_C* 3mg0_C* 3mg4_C* 3oeu_C* 3oev_C* 3okj_C* 3shj_C* ...

Probab=100.00  E-value=3.2e-43  Score=280.43  Aligned_cols=184  Identities=30%  Similarity=0.487  Sum_probs=170.6

Q ss_pred             CccccCC-CCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            3 DKLLDHT-SVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         3 s~l~~~~-~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      ++++..+ +++||++|++|++|+++|+.+|++.|.++++.+++.|+++++++++++.+++++++++|.||+++++|||+|
T Consensus        50 ~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rP~~v  129 (241)
T 1ryp_D           50 LKLQDTRITPSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGV  129 (241)
T ss_dssp             SCCBCTTTSCCSEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSSTTBCCCSE
T ss_pred             ccCccccCCcCcEEEecCCEEEEEeecHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHccCCCCCCcce
Confidence            4555554 999999999999999999999999999999999999999999999999999999999999999989999999


Q ss_pred             eeEEEEEcCC-CCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcC-CCCCCHHHHHHHHHHHHHhhhcccCCCCe
Q 029560           82 VAMVLSIDEE-CGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKN-DPAFTFQETVQTAISTLQSVLQEDFKASE  159 (191)
Q Consensus        82 ~~iv~G~d~~-~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~-~~~~s~eea~~l~~~~l~~~~~~d~~~~~  159 (191)
                      ++||||||++ ++|+||.+||+|++.++++.|+|+|++.++++||++|.. +++||++||++++++||..+.+  ....+
T Consensus       130 ~~lvaG~D~~~~gp~Ly~idp~G~~~~~~~~aiG~gs~~a~~~Le~~~~~~~~~ms~eea~~l~~~al~~~~~--~sg~~  207 (241)
T 1ryp_D          130 STLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKEPPATVEECVKLTVRSLLEVVQ--TGAKN  207 (241)
T ss_dssp             EEEEEECCTTCCSCEEEEECTTSCEEEBSEEEESTTHHHHHHHHHTTCCTTSCCCSHHHHHHHHHHHHHHHHC--SCSTT
T ss_pred             eeEEEEEcCCCCCeeEEEECCCCCEEEeeeEEECCCcHHHHHHHHHhhhcccCCCCHHHHHHHHHHHHHHHhc--CCCCc
Confidence            9999999975 789999999999999999999999999999999999833 4789999999999999999995  44458


Q ss_pred             EEEEEEEeCCCcEEEcCHHHHHHHHHHhhc
Q 029560          160 IEVGVVSKENPEFRVLSIEEIDEHLTAISE  189 (191)
Q Consensus       160 iei~iv~~~~~~~~~~~~~~i~~~~~~~~~  189 (191)
                      ++|++|++++ +|++++++||++++.++.+
T Consensus       208 i~v~vi~~~~-~~~~l~~~ei~~~~~~~~~  236 (241)
T 1ryp_D          208 IEITVVKPDS-DIVALSSEEINQYVTQIEQ  236 (241)
T ss_dssp             EEEEEEETTT-EEEECCHHHHHHHHHHHTH
T ss_pred             EEEEEEECCC-cEEECCHHHHHHHHHHHhh
Confidence            9999999987 4999999999999998864

>1ryp_E 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_D* 1g65_D 2f16_D* 2fak_D* 2fny_D* 2gpl_D* 3d29_D* 3dy3_D* 3dy4_D* 3e47_D* 3gpj_D* 3gpt_D* 3gpw_D* 3hye_D* 3mg0_D* 3mg4_D* 3okj_D* 3shj_D* 3tdd_D* 2z5c_C ...

Probab=100.00  E-value=7e-44  Score=284.42  Aligned_cols=186  Identities=24%  Similarity=0.458  Sum_probs=173.8

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcC------
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAY------   75 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~------   75 (191)
                      .++++.+++++||++|++|++|++||..+|++.+.++++.+++.|+++++++++++.+++.+++++|.||++++      
T Consensus        47 ~~g~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~~~~l~  126 (242)
T 1ryp_E           47 TSPLLESDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLM  126 (242)
T ss_dssp             SSTTBCGGGCCCEEEEETTEEEEEEESGGGHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCCBSSCTTSCCCB
T ss_pred             CCcCccCccCCceEEEcCCEEEEEeecHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccccCcccccc
Confidence            45666688999999999999999999999999999999999999999999999999999999999999999887      


Q ss_pred             cccccceeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccC
Q 029560           76 MRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDF  155 (191)
Q Consensus        76 ~rP~~v~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~  155 (191)
                      .|||+|++||||||+++||+||.+||+|++.++++.|+|+|++.++++||++|  .++||++||++++++||..+.+|+.
T Consensus       127 ~RP~~v~~lvaG~D~~~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~--~~~ms~eea~~la~~al~~~~~~~~  204 (242)
T 1ryp_E          127 SRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNEW--HSSLTLKEAELLVLKILKQVMEEKL  204 (242)
T ss_dssp             SSCCSEEEEEEEEETTTEEEEEEECTTSCEEEBSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHCSSCC
T ss_pred             cCcceEEEEEEEEeCCCCCEEEEECCCCCEeccCEEEECCCCHHHHHHHHHhh--ccCCCHHHHHHHHHHHHHHHhhccC
Confidence            99999999999999557899999999999999999999999999999999998  4789999999999999999999855


Q ss_pred             CCCeEEEEEEEeCCCcEEEcCHHHHHHHHHHhhcc
Q 029560          156 KASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER  190 (191)
Q Consensus       156 ~~~~iei~iv~~~~~~~~~~~~~~i~~~~~~~~~~  190 (191)
                      ...+++|++|+++++ |++++++||++++.++.++
T Consensus       205 sg~~i~v~vi~~~~~-~~~~~~~ei~~~~~~~~~~  238 (242)
T 1ryp_E          205 DENNAQLSCITKQDG-FKIYDNEKTAELIKELKEK  238 (242)
T ss_dssp             CTTSEEEEEEETTTE-EEECCHHHHHHHHHHHHHH
T ss_pred             CCCcEEEEEEECCCC-eEECCHHHHHHHHHHHhhh
Confidence            445899999999986 9999999999999988754

>3h4p_a Proteasome subunit beta; core particle, cytoplasm, hydrolase, protease, threonine protease; 4.10A {Methanocaldococcus jannaschii}

Probab=100.00  E-value=1.5e-43  Score=278.61  Aligned_cols=178  Identities=23%  Similarity=0.372  Sum_probs=167.7

Q ss_pred             ccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccccee
Q 029560            4 KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVA   83 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~   83 (191)
                      .++.+++++||++|++|++|+++|+.+|++.+.++++.+++.|+++++++++++.++++++++++.|    ++|||+|++
T Consensus        25 ~~i~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~----~~~P~~v~~  100 (219)
T 3h4p_a           25 NLVADKEAKKLYKIDDYIAMTIAGSVGDAQAIVRLLIAEAKLYKMRTGRNIPPLACATLLSNILHSS----RMFPFLTQI  100 (219)
T ss_dssp             TEEEETTCCCEEEEETTEEEECCSCHHHHHHHHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHT----TTTTCCCCC
T ss_pred             CEeeccccceeEEecCCEEEEeeEcHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHh----cCCCceEEE
Confidence            4677899999999999999999999999999999999999999999999999999999999999765    368999999


Q ss_pred             EEEEEcCCCCCeEEEECCCcceecee-eeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEE
Q 029560           84 MVLSIDEECGPRLFKCDPAGHFFGHK-ATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIE  161 (191)
Q Consensus        84 iv~G~d~~~~p~Ly~~d~~G~~~~~~-~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~ie  161 (191)
                      ||||||+++||+||.+||+|++.+++ +.|+|+|++.++++||++|  .++||++||++++++||..+.+||..++ +++
T Consensus       101 lvaG~D~~~gp~Ly~idp~G~~~~~~~~~aiG~gs~~a~~~Le~~~--~~~ms~eea~~la~~al~~~~~rd~~sg~~i~  178 (219)
T 3h4p_a          101 IIGGYDLLEGAKLFSLDPLGGMNEEKTFTATGSGSPIAYGVLEAGY--DRDMSVEEGIKLALNALKSAMERDTFSGNGIS  178 (219)
T ss_dssp             EEEEEETTTEEEEEEECSSCCEEECSSEEEESTTHHHHHHHHHTSC--CTTCCHHHHHHHHHHHHHHHHTSCSSCCSCCC
T ss_pred             EEEEEeCCCCcEEEEECCCCceEecCCEEEEcCCHHHHHHHHHHhc--CCCCCHHHHHHHHHHHHHHHHhhcCCCCCcEE
Confidence            99999986789999999999999998 9999999999999999998  4799999999999999999999998775 899


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHHHHHhhc
Q 029560          162 VGVVSKENPEFRVLSIEEIDEHLTAISE  189 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~~~~~~~  189 (191)
                      |++|++++  |++++++||+++|.++++
T Consensus       179 v~vi~~~g--~~~l~~~ei~~~l~~~~~  204 (219)
T 3h4p_a          179 LAVITKDG--VKIFEDEEIEKILDSMKA  204 (219)
T ss_dssp             EEEEETTE--EEECCHHHHHHHHHHCC-
T ss_pred             EEEEeCCC--eEEcCHHHHHHHHHHhhc
Confidence            99999984  999999999999999874

>1iru_D 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unf_C* 3une_C* 3unh_C 3unb_C*

Probab=100.00  E-value=2e-43  Score=282.79  Aligned_cols=184  Identities=29%  Similarity=0.482  Sum_probs=172.4

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      +++++.+++++||++|++|++|+++|+.+|++.+.++++.+++.|+++++++++++.+++++++++|.|+++++.|||+|
T Consensus        50 ~~~l~~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rp~~v  129 (248)
T 1iru_D           50 VAKLQDERTVRKICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGI  129 (248)
T ss_dssp             CCSSSCGGGGCSEEESSSSCEEEEEECHHHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCE
T ss_pred             cccCccCCCCCcEEEEcCCEEEEEeecHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhccCCcccccE
Confidence            45688888999999999999999999999999999999999999999999999999999999999999999989999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCC--CHHHHHHHHHHHHHhhhcccCCCCe
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAF--TFQETVQTAISTLQSVLQEDFKASE  159 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~--s~eea~~l~~~~l~~~~~~d~~~~~  159 (191)
                      ++||||||++++|+||.+||+|++.+++++|+|+|++.++++||++|+  ++|  |++||++++++||..+.+  ....+
T Consensus       130 ~~lvaG~D~~~gp~Ly~idp~G~~~~~~~~aiG~gs~~a~~~Le~~~~--~~m~~s~eea~~la~~al~~~~~--~sg~~  205 (248)
T 1iru_D          130 SALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYT--DEAIETDDLTIKLVIKALLEVVQ--SGGKN  205 (248)
T ss_dssp             EEEEEEECSSSCEEEEEECTTSCEEEBSEEEESTTHHHHHHHHTTTCC--SSTTCSHHHHHHHHHHHHHTTSC--TTSTT
T ss_pred             EEEEEEEeCCCCcEEEEEcCCCcEEEeeEEEECCCcHHHHHHHHHhhc--ccccCCHHHHHHHHHHHHHHHHc--CCCCc
Confidence            999999995579999999999999999999999999999999999984  789  999999999999999986  33458


Q ss_pred             EEEEEEEeCCCcEEEcCHHHHHHHHHHhhcc
Q 029560          160 IEVGVVSKENPEFRVLSIEEIDEHLTAISER  190 (191)
Q Consensus       160 iei~iv~~~~~~~~~~~~~~i~~~~~~~~~~  190 (191)
                      ++|++|+++++ |++++++||++++.++.++
T Consensus       206 i~v~vi~~~g~-~~~l~~~ei~~~~~~~~~~  235 (248)
T 1iru_D          206 IELAVMRRDQS-LKILNPEEIEKYVAEIEKE  235 (248)
T ss_dssp             CCEEEEESSSC-EECCCHHHHHHHTTTTTTT
T ss_pred             EEEEEEECCCc-EEECCHHHHHHHHHHHHhc
Confidence            99999999874 9999999999999988654

>1iru_G 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_F* 3une_F 3unf_F* 3unh_F

Probab=100.00  E-value=5.4e-43  Score=281.12  Aligned_cols=185  Identities=27%  Similarity=0.383  Sum_probs=171.9

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      +++++..++++||++|++|++|+++|..+|++.|.++++.+++.|+++++++++++.+++++++++|.|++++++|||+|
T Consensus        54 ~~g~~~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rP~~v  133 (254)
T 1iru_G           54 LSKLYEEGSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGC  133 (254)
T ss_dssp             SCTTBCTTTTCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSBSSBCCCSE
T ss_pred             CCCCcCcCcCCcEEEECCCEEEEEecChHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhccccccccceE
Confidence            45667778999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EI  160 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~i  160 (191)
                      ++||||||+++||+||.+||+|++.+++++|+|+|++.++++||+.|.  ++||++||++++++||..+.+++..++ ++
T Consensus       134 ~~lvaG~D~~~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~--~~ms~eea~~la~~al~~~~~~~~~~~~~i  211 (254)
T 1iru_G          134 SFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQM--KEMTCRDIVKEVAKIIYIVHDEVKDKAFEL  211 (254)
T ss_dssp             EEEEEEEETTTEEEEEEECTTCCEEEBSEEEESTTHHHHHHHHTTSCG--GGCCHHHHHHHHHHHHHHHSCSSSSCCEEE
T ss_pred             EEEEEEEeCCCCcEEEEEcCCCCEEeeeeEEecCccHHHHHHHHHhcc--CCCCHHHHHHHHHHHHHHHHhhccCCCCcE
Confidence            999999995478999999999999999999999999999999999974  789999999999999999998876454 89


Q ss_pred             EEEEEEeCCC-cEEEcCHHHHHHHHHHhh
Q 029560          161 EVGVVSKENP-EFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       161 ei~iv~~~~~-~~~~~~~~~i~~~~~~~~  188 (191)
                      +|++|+++.+ +|++++++++++++..+.
T Consensus       212 ev~vi~~~~~g~~~~l~~~~i~~~~~~~~  240 (254)
T 1iru_G          212 ELSWVGELTNGRHEIVPKDIREEAEKYAK  240 (254)
T ss_dssp             EEEECBTTTTTCCEECCHHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCCeEECCHHHHHHHHHHHH
Confidence            9999998732 499999999999998764

>1j2q_H Proteasome beta subunit; ubiquitin, CP, hydrolase; HET: CIB; 2.83A {Archaeoglobus fulgidus} SCOP: d.153.1.4

Probab=100.00  E-value=9.8e-43  Score=270.75  Aligned_cols=176  Identities=20%  Similarity=0.351  Sum_probs=166.1

Q ss_pred             ccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccccee
Q 029560            4 KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVA   83 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~   83 (191)
                      +++.+++++||++|++|++|+++|..+|++.+.++++.+++.|+++++++++++.+++++++.++.+    +.|||++++
T Consensus        24 ~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~~~~~----r~rp~~~~~   99 (202)
T 1j2q_H           24 NFIASKAAKKIYQIADRMAMTTAGSVGDAQFLARIIKIEANLYEIRRERKPTVRAIATLTSNLLNSY----RYFPYLVQL   99 (202)
T ss_dssp             TEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHT----TTSCCCEEE
T ss_pred             CEEeeccccCEEEcCCCEEEEecccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhh----CCCCceEEE
Confidence            6788899999999999999999999999999999999999999999999999999999999999653    378999999


Q ss_pred             EEEEEcCCCCCeEEEECCCcceecee-eeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEE
Q 029560           84 MVLSIDEECGPRLFKCDPAGHFFGHK-ATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIE  161 (191)
Q Consensus        84 iv~G~d~~~~p~Ly~~d~~G~~~~~~-~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~ie  161 (191)
                      ||||||+ +||+||.+||+|++.+++ ++|+|+|++.++++||+.|+  ++||++||++++++||..+.+||..++ +++
T Consensus       100 lvaG~D~-~gp~Ly~id~~G~~~~~~~~~aiG~g~~~a~~~Le~~~~--~~~s~eea~~la~~al~~~~~~d~~s~~~i~  176 (202)
T 1j2q_H          100 LIGGIDS-EGKSIYSIDPIGGAIEEKDIVATGSGSLTAYGVLEDRFT--PEIGVDEAVELAVRAIYSAMKRDSASGDGID  176 (202)
T ss_dssp             EEEEEET-TEEEEEEECTTCCEEEESSEEEESTTHHHHHHHHHHHCC--TTCCHHHHHHHHHHHHHHHHTTCTTSCSCEE
T ss_pred             EEEEEeC-CCCEEEEECCCCCeeecCCEEEEcCCHHHHHHHHHhhcC--CCcCHHHHHHHHHHHHHHHHhcCCCCCCcEE
Confidence            9999997 789999999999999999 99999999999999999984  789999999999999999999998665 899


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHHHHHhh
Q 029560          162 VGVVSKENPEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~~~~~~  188 (191)
                      |++|++++  |+.++++||++++.+++
T Consensus       177 v~vi~~~g--~~~l~~~ei~~~~~~~~  201 (202)
T 1j2q_H          177 VVKITEDE--FYQYSPEEVEQILAKFR  201 (202)
T ss_dssp             EEEECSSC--EEECHHHHHHHHGGGTT
T ss_pred             EEEEeCCC--eEEeCHHHHHHHHHHhh
Confidence            99999984  99999999999998774

>1j2p_A Alpha-ring, proteasome alpha subunit; hydrolase; 2.60A {Archaeoglobus fulgidus} SCOP: d.153.1.4 PDB: 1j2q_A*

Probab=100.00  E-value=1.7e-42  Score=276.99  Aligned_cols=181  Identities=29%  Similarity=0.494  Sum_probs=170.5

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      +++++.+++++||++|++|++|+++|..+|++.+.++++.+++.|+++++++++++.+++.+++++|.|+++.+.|||+|
T Consensus        55 ~~~l~~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~y~~~~~~rp~~v  134 (246)
T 1j2p_A           55 GSKLLEKDTIEKIYKIDEHICAATSGLVADARVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQYGGVRPFGV  134 (246)
T ss_dssp             SCTTBCGGGCCSEEECSSSEEEEEEECHHHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCE
T ss_pred             CccccccCccCcEEEECCCEEEEEeEccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCcccccE
Confidence            45677788999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EI  160 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~i  160 (191)
                      ++||||||  +||+||.+||+|++.++++.|+|+|++.++++||+.|+  ++||++||++++++||..+.++ ..++ ++
T Consensus       135 ~~lvaG~D--~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~--~~ms~eea~~la~~al~~~~~~-~~sg~~i  209 (246)
T 1j2p_A          135 SLLIAGVN--EVPKLYETDPSGALLEYKATAIGMGRMAVTEFFEKEYR--DDLSFDDAMVLGLVAMGLSIES-ELVPENI  209 (246)
T ss_dssp             EEEEEEES--SSEEEEEECTTCCEEEBSEEEESTTHHHHHHHHHHHCC--TTCCHHHHHHHHHHHHHHHHTS-CCCGGGE
T ss_pred             EEEEEEEC--CCCEEEEECCCceEEeeeEEEECCCcHHHHHHHHHHhc--cCCCHHHHHHHHHHHHHHHhhc-cCCCCcE
Confidence            99999999  68999999999999999999999999999999999984  7899999999999999999988 4444 89


Q ss_pred             EEEEEE-eCCCcEEEcCHHHHHHHHHHhh
Q 029560          161 EVGVVS-KENPEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       161 ei~iv~-~~~~~~~~~~~~~i~~~~~~~~  188 (191)
                      +|++|+ +++ +|++++++||++++.++.
T Consensus       210 ~v~vi~~~~~-~~~~l~~~ei~~~~~~~~  237 (246)
T 1j2p_A          210 EVGYVKVDDR-TFKEVSPEELKPYVERAN  237 (246)
T ss_dssp             EEEEEETTTC-CCEECCHHHHHHHHHHHH
T ss_pred             EEEEEEcCCC-ceEECCHHHHHHHHHHHH
Confidence            999999 655 499999999999998875

>1iru_F 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_E* 3une_E 3unf_E* 3unh_E

Probab=100.00  E-value=8e-43  Score=281.37  Aligned_cols=178  Identities=26%  Similarity=0.479  Sum_probs=168.1

Q ss_pred             CCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeEEEEE
Q 029560            9 TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSI   88 (191)
Q Consensus         9 ~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~iv~G~   88 (191)
                      ++.+||++|++|++|++||+.+|++.|.++++.+++.|+++++++++++.+++++++++|.|||+++.|||+|++|||||
T Consensus        58 ~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~i~v~~la~~l~~~l~~~t~~~~~RP~~v~~lvaG~  137 (263)
T 1iru_F           58 AHQKKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAGY  137 (263)
T ss_dssp             CCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEE
T ss_pred             cchhcEEEEcCCEEEEEeCCHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHhhcccccccceEEEEEEEE
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhccc-CCC-CeEEEEEEE
Q 029560           89 DEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQED-FKA-SEIEVGVVS  166 (191)
Q Consensus        89 d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d-~~~-~~iei~iv~  166 (191)
                      |+ +||+||.+||+|++.+++++|+|+|++.++++||+.|++.++||++||++++++||..+.+|| ..+ .+++|++|+
T Consensus       138 D~-~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~~ms~eea~~la~~al~~~~~rd~~~sg~~iev~vi~  216 (263)
T 1iru_F          138 DD-MGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFMECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVG  216 (263)
T ss_dssp             ET-TEEEEEEECSSSCEEEESEEEESTTHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCTTCCCCTTTEEEEEEE
T ss_pred             cC-CCCEEEEECCCCCEEEeeEEEcCcccHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHhccccCCCCcEEEEEEE
Confidence            97 789999999999999999999999999999999999963348999999999999999999998 344 489999999


Q ss_pred             eCCCcEEEcCHHHHHHHHHHhh
Q 029560          167 KENPEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       167 ~~~~~~~~~~~~~i~~~~~~~~  188 (191)
                      ++++ |+++++++|++++.++.
T Consensus       217 ~~~~-~~~l~~~ei~~~~~~~~  237 (263)
T 1iru_F          217 KDLE-FTIYDDDDVSPFLEGLE  237 (263)
T ss_dssp             TTEE-EEEECSGGGHHHHTTCC
T ss_pred             CCCC-eEECCHHHHHHHHHHHh
Confidence            9863 99999999999998875

>1ryp_B 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_B 1g0u_A* 1jd2_A* 1g65_A 1z7q_B 2f16_A* 2fak_A* 2fny_A* 2gpl_A* 2zcy_A* 3bdm_A* 3d29_A* 3dy3_A* 3dy4_A* 3e47_A* 3gpj_A* 3gpt_A* 3gpw_A* 3hye_A* 3mg0_A* ...

Probab=100.00  E-value=2.4e-42  Score=276.73  Aligned_cols=184  Identities=30%  Similarity=0.492  Sum_probs=172.2

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHH-HHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAE-FRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLG   80 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~-~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~   80 (191)
                      .++++.+++++||++|++|++|++||..+|++.+.++++.+++. |+..++.+++++.+++.+++++|.|++++++|||+
T Consensus        52 ~~~l~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~~a~~~~~~~~~~~~rp~~  131 (250)
T 1ryp_B           52 SSPLAMSETLSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFG  131 (250)
T ss_dssp             SCSSBCGGGCCSSEEEETTEEEEEEECHHHHHHHHHHHHHHHHHTTHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCC
T ss_pred             CCccccCcccCceEEECCCEEEEeeeCHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHhcCCcccce
Confidence            36788889999999999999999999999999999999999999 99999999999999999999999999999999999


Q ss_pred             ceeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCCeE
Q 029560           81 VVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEI  160 (191)
Q Consensus        81 v~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~~i  160 (191)
                      |++||||||+++||+||.+||+|++.+++++|+|+|++.++++||+.|+  ++||++||++++++||..+.+++....++
T Consensus       132 v~~lvaG~D~~~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~--~~ms~eea~~la~~al~~~~~~~~sg~~i  209 (250)
T 1ryp_B          132 VSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN--DELELEDAIHIALLTLKESVEGEFNGDTI  209 (250)
T ss_dssp             EEEEEEEEETTTEEEEEEECTTSCEEEBSEEEESTTHHHHHHHHHHHCC--TTCCHHHHHHHHHHHHHHHCCSCCSTTTE
T ss_pred             EEEEEEEEcCCCCcEEEEECCCCCEEeeceeEecCccHHHHHHHHHHhc--cCCCHHHHHHHHHHHHHHHhccccCCCCE
Confidence            9999999997678999999999999999999999999999999999984  78999999999999999999887754599


Q ss_pred             EEEEEEeC--------------CCcEEEcCHHHHHHHHHHh
Q 029560          161 EVGVVSKE--------------NPEFRVLSIEEIDEHLTAI  187 (191)
Q Consensus       161 ei~iv~~~--------------~~~~~~~~~~~i~~~~~~~  187 (191)
                      +|++|+++              ++.|++++++||++++.++
T Consensus       210 ~v~vi~~~~~~~~~~~~~~~~~~~~~~~l~~~ei~~~l~~~  250 (250)
T 1ryp_B          210 ELAIIGDENPDLLGYTGIPTDKGPRFRKLTSQEINDRLEAL  250 (250)
T ss_dssp             EEEEECSCCGGGTSEESCSSCCCCSEEECCHHHHHHHHTTC
T ss_pred             EEEEEEccccccccccccccCCCCCeEECCHHHHHHHHHhC
Confidence            99999986              2359999999999998753

>1iru_E 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_D* 3une_D 3unf_D* 3unh_D

Probab=100.00  E-value=1.5e-42  Score=276.63  Aligned_cols=182  Identities=27%  Similarity=0.510  Sum_probs=170.4

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcC-----c
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAY-----M   76 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~-----~   76 (191)
                      .++++.+++++||++|++|++|++||..+|++.+.++++.+++.|+++++++++++.+++.+++++|.|+++.+     .
T Consensus        55 ~~g~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a~~l~~~~~~y~~~~~~~~l~~  134 (241)
T 1iru_E           55 TSPLMEPSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMS  134 (241)
T ss_dssp             CCTTBCTTSCCSEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCBCSTTCCSSCBS
T ss_pred             CCcCcCccccceEEEEcCCEEEEEeeChHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccccccccc
Confidence            35666688999999999999999999999999999999999999999999999999999999999999999887     8


Q ss_pred             ccccceeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCC
Q 029560           77 RPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFK  156 (191)
Q Consensus        77 rP~~v~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~  156 (191)
                      |||+|++||||||. +||+||.+||+|++.++++.|+|+|++.++++||+.|+  ++||++||++++++||..+.+++..
T Consensus       135 rp~~v~~lvaG~D~-~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~--~~ms~eea~~la~~al~~~~~~~~s  211 (241)
T 1iru_E          135 RPFGVALLFGGVDE-KGPQLFHMDPSGTFVQCDARAIGSASEGAQSSLQELYH--KSMTLKEAIKSSLIILKQVMEEKLN  211 (241)
T ss_dssp             SCCCEEEEEEEEET-TEEEEEEECTTSCEEEBSEEEESTTHHHHHHHHHHHCC--TTCCHHHHHHHHHHHHHHHCSSCCC
T ss_pred             ccceEEEEEEEEeC-CCCEEEEECCCCcEEecceEEECCCcHHHHHHHHHHhc--cCCCHHHHHHHHHHHHHHHhhccCC
Confidence            99999999999995 88999999999999999999999999999999999984  7899999999999999999998444


Q ss_pred             CCeEEEEEEEeCCCcEEEcCHHHHHHHHHHh
Q 029560          157 ASEIEVGVVSKENPEFRVLSIEEIDEHLTAI  187 (191)
Q Consensus       157 ~~~iei~iv~~~~~~~~~~~~~~i~~~~~~~  187 (191)
                      ..+++|++++++++ |++++++||++++.++
T Consensus       212 g~~i~v~vi~~~~~-~~~l~~~ei~~~~~~~  241 (241)
T 1iru_E          212 ATNIELATVQPGQN-FHMFTKEELEEVIKDI  241 (241)
T ss_dssp             TTSEEEEEECSSSC-CEECCHHHHHHHHTTC
T ss_pred             CCCEEEEEEECCCC-eEECCHHHHHHHHHhC
Confidence            45899999999987 9999999999998753

>3mi0_A Proteasome subunit alpha; enzyme inhibitors, lactones, proteasome endopeptidase comple mycobacterium tuberculosis, hydrolase; HET: SA6; 2.20A {Mycobacterium tuberculosis} SCOP: d.153.1.4 PDB: 3h6f_A 3krd_A* 3h6i_A* 3mka_A 2fhh_A* 2fhg_A 3hfa_D 3hf9_A 3mfe_D

Probab=100.00  E-value=3.7e-42  Score=274.91  Aligned_cols=177  Identities=16%  Similarity=0.229  Sum_probs=158.6

Q ss_pred             CCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHHH-HHHHHhhhhcCcccccceeEE
Q 029560            8 HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYG-YEMPVDVLAKWIA-DKSQVYTQHAYMRPLGVVAMV   85 (191)
Q Consensus         8 ~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~-~~~~~~~l~~~l~-~~~~~~t~~~~~rP~~v~~iv   85 (191)
                      +++++|||+|++|++|+++|+.+|++.|.+.++.+++.|+++++ ++++++.|+++++ .+.|.|||  ++|||+|++||
T Consensus        47 ~~~~~KI~~I~d~i~~~~aG~~aD~~~l~~~~~~~~~l~~~~~~~~~i~v~~la~~l~~~l~q~yt~--~~rP~gv~~li  124 (248)
T 3mi0_A           47 SRSLQKISELYDRVGFAAAGKFNEFDNLRRGGIQFADTRGYAYDRRDVTGRQLANVYAQTLGTIFTE--QAKPYEVELCV  124 (248)
T ss_dssp             CSSSCSEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHHHHHHHHHHH--SSSCCCEEEEE
T ss_pred             CCCCCCeEEECCCEEEEEccCHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHhcc--CCCCceEEEEE
Confidence            56899999999999999999999999999999999999999999 8999999999999 77888987  78999999999


Q ss_pred             EEEcC---CCCCeEEEECCCcceec-eeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhh-------ccc
Q 029560           86 LSIDE---ECGPRLFKCDPAGHFFG-HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVL-------QED  154 (191)
Q Consensus        86 ~G~d~---~~~p~Ly~~d~~G~~~~-~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~-------~~d  154 (191)
                      ||||+   .+||+||++||+|++.. ++++|+|+|++.++++||++|  +++||++||++++++||..+.       +++
T Consensus       125 aG~D~~~~~~gp~Ly~~Dp~G~~~~e~~~~a~Gsgs~~a~~~Le~~y--~~~mt~eeai~la~~aL~~~~~~~~~~~~~~  202 (248)
T 3mi0_A          125 AEVAHYGETKRPELYRITYDGSIADEPHFVVMGGTTEPIANALKESY--AENASLTDALRIAVAALRAGSADTSGGDQPT  202 (248)
T ss_dssp             EECCCTTCCCCCEEEEECTTSCEEEESSEEEESSCHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHC-----------
T ss_pred             EEEcCCCCCCCCEEEEECCCeEEeecccEEEECccHHHHHHHHHhhc--CCCCCHHHHHHHHHHHHHHHHhhcccCcccc
Confidence            99997   47899999999999995 999999999999999999998  478999999999999999999       677


Q ss_pred             CCCCeEEEEEEEeCC--CcEEEcCHHHHHHHHHHhh
Q 029560          155 FKASEIEVGVVSKEN--PEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       155 ~~~~~iei~iv~~~~--~~~~~~~~~~i~~~~~~~~  188 (191)
                      +...+++|++|++++  +.|++++++||++++.++.
T Consensus       203 ~~~~~iev~vv~~~g~~~~f~~l~~~ei~~~l~~~~  238 (248)
T 3mi0_A          203 LGVASLEVAVLDANRPRRAFRRITGSALQALLVDQE  238 (248)
T ss_dssp             -CCTTEEEEEEETTSSSCCEEECCHHHHHHTC----
T ss_pred             cCCCcEEEEEEECCCCcccEEECCHHHHHHHHHHcC
Confidence            777799999999985  4699999999999988764

>1q5q_H Proteasome beta-type subunit 1; proteasome assembly, Pro-peptide, inter-subunit contacts, RH erythropolis, hydrolase; 2.60A {Rhodococcus erythropolis} SCOP: d.153.1.4

Probab=100.00  E-value=4.6e-42  Score=272.81  Aligned_cols=182  Identities=19%  Similarity=0.188  Sum_probs=170.2

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      ++++.+++++||++|++|++|++||..+|++.|.++++.+++.|+++++++++++.+++.|+++++.++++. +|||+|+
T Consensus        23 g~l~~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~-~rp~~v~  101 (235)
T 1q5q_H           23 GNLIASRDVEKVYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEGVPLTFDGKANRLASMVRGNLGAA-MQGLAVV  101 (235)
T ss_dssp             TTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHTTHHHH-TTTCCEE
T ss_pred             CCEEecCCcCcEEEeCCcEEEEcCCcHHHHHHHHHHHHHHHHHhHHHhCCCCCHHHHHHHHHHHHHHHHHhh-hcccceE
Confidence            368888999999999999999999999999999999999999999999999999999999999999988765 8999999


Q ss_pred             eEEEEEcCCCC-----CeEEEECCCcceece--eeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccC
Q 029560           83 AMVLSIDEECG-----PRLFKCDPAGHFFGH--KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDF  155 (191)
Q Consensus        83 ~iv~G~d~~~~-----p~Ly~~d~~G~~~~~--~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~  155 (191)
                      +||||||++++     |+||.+||+|++.++  ++.|+|+|+++++++||+.|  .++||++||++++++||..+.++|.
T Consensus       102 ~lvaG~D~~~g~~~~~p~Ly~idp~G~~~~~~~~~~aiGsgs~~a~~~Le~~~--~~~ms~eeA~~la~~al~~a~~~d~  179 (235)
T 1q5q_H          102 PLLVGYDLDADDESRAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALKKIY--SPDSDEETALRAAIESLYDAADDDS  179 (235)
T ss_dssp             EEEEEECTTCSSTTSCEEEEEECTTSCEEECCSSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHCT
T ss_pred             EEEEEEECCCCccCCCCEEEEECCCCceEEeCCCeEEECCCHHHHHHHHHhhc--CCCCCHHHHHHHHHHHHHHHHhhCc
Confidence            99999998557     999999999999999  99999999999999999998  4889999999999999999999998


Q ss_pred             CCCe---E-----EEEEEEeCCCcEEEcCHHHHHHHHHHhhc
Q 029560          156 KASE---I-----EVGVVSKENPEFRVLSIEEIDEHLTAISE  189 (191)
Q Consensus       156 ~~~~---i-----ei~iv~~~~~~~~~~~~~~i~~~~~~~~~  189 (191)
                      .+++   +     +|++|++++  |++++++++++++.++.+
T Consensus       180 ~sg~~~~i~~~~~ev~vi~~~g--~~~l~~~ei~~~~~~~~~  219 (235)
T 1q5q_H          180 ATGGPDLTRGIYPTAVTITQAG--AVHVSEETTSELARRIVA  219 (235)
T ss_dssp             TTCCCBTTTTBCCEEEEEETTE--EEECCHHHHHHHHHHHHH
T ss_pred             ccCCcccccccccEEEEEeCCC--eEEeCHHHHHHHHHHHHH
Confidence            8763   2     999999874  999999999999998863

>1yar_H Proteasome beta subunit; proteasome 20S, PA26 proteasome activator 11S, hydrolase-HYD activator complex; 1.90A {Thermoplasma acidophilum} SCOP: d.153.1.4 PDB: 1ya7_H 1yau_H 3ipm_H 1pma_B 3jrm_H 3c92_H 3c91_H 3jse_H 3jtl_H

Probab=100.00  E-value=7.4e-42  Score=268.63  Aligned_cols=176  Identities=23%  Similarity=0.391  Sum_probs=165.3

Q ss_pred             ccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccccee
Q 029560            4 KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVA   83 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~   83 (191)
                      +++.+++++||++|++|++|++||..+|++.+.++++.+++.|+++++++++++.+++.+++.++.+    +.|||+|++
T Consensus        32 ~l~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~----r~rp~~v~~  107 (217)
T 1yar_H           32 NFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKAELELYRLQRRVNMPIEAVATLLSNMLNQV----KYMPYMVQL  107 (217)
T ss_dssp             TEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHT----TTSCCCEEE
T ss_pred             CEEecCccCCeEEeCCCEEEEeCcCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhc----CCCCceEEE
Confidence            6788899999999999999999999999999999999999999999999999999999999999653    378999999


Q ss_pred             EEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEE
Q 029560           84 MVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEV  162 (191)
Q Consensus        84 iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei  162 (191)
                      ||||||  +||+||.+||+|++.+++++|+|+|++.++++||+.|+  ++||+|||++++++||..+.+||..++ +++|
T Consensus       108 lvaG~D--~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~--~~~s~eea~~la~~al~~~~~rd~~s~~~i~v  183 (217)
T 1yar_H          108 LVGGID--TAPHVFSIDAAGGSVEDIYASTGSGSPFVYGVLESQYS--EKMTVDEGVDLVIRAISAAKQRDSASGGMIDV  183 (217)
T ss_dssp             EEEEES--SSEEEEEECTTCCEEEESEEEESTTHHHHHHHHHHHCC--TTCCHHHHHHHHHHHHHHHHHHCTTCCSCCEE
T ss_pred             EEEEEC--CCCEEEEECCCCCeEecCEEEEcCCHHHHHHHHHhhcc--cCCCHHHHHHHHHHHHHHHHhccCCCCCcEEE
Confidence            999999  57999999999999999999999999999999999984  789999999999999999999998665 8999


Q ss_pred             EEEEeCCCcEEEcCHHHHHHHHHHhh
Q 029560          163 GVVSKENPEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       163 ~iv~~~~~~~~~~~~~~i~~~~~~~~  188 (191)
                      ++++++. +|++++++||++++.++.
T Consensus       184 ~vi~~~~-g~~~~~~~ei~~~~~~~~  208 (217)
T 1yar_H          184 AVITRKD-GYVQLPTDQIESRIRKLG  208 (217)
T ss_dssp             EEEETTT-EEEECCHHHHHHHHHHHT
T ss_pred             EEEECCC-CEEEcCHHHHHHHHHHHH
Confidence            9999843 399999999999998875

>1ryp_F 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_E* 1g65_E 2f16_E* 2fak_E* 2fny_E* 2gpl_E* 3d29_E* 3dy3_E* 3dy4_E* 3e47_E* 3gpj_E* 3gpt_E* 3gpw_E* 3hye_E* 3mg0_E* 3mg4_E* 3oeu_E* 3oev_E* 3okj_E* 3shj_E* ...

Probab=100.00  E-value=1.4e-42  Score=275.41  Aligned_cols=173  Identities=21%  Similarity=0.376  Sum_probs=162.0

Q ss_pred             CCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeEEEEE
Q 029560            9 TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSI   88 (191)
Q Consensus         9 ~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~iv~G~   88 (191)
                      ++.+||++|++|++|++||..+|++.+.++++.+++.|+++++++++++.+++.+++++|.|||+.+.|||+|++|||||
T Consensus        57 ~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rp~~v~~lvaG~  136 (233)
T 1ryp_F           57 SYQKKIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRPYGVGLLIIGY  136 (233)
T ss_dssp             CCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEE
T ss_pred             cccCcEEEEcCCEEEEEEechHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcccCCcCcceEEEEEEE
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCC--CHHHHHHHHHHHHHhhhccc-CCC-CeEEEEE
Q 029560           89 DEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAF--TFQETVQTAISTLQSVLQED-FKA-SEIEVGV  164 (191)
Q Consensus        89 d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~--s~eea~~l~~~~l~~~~~~d-~~~-~~iei~i  164 (191)
                      |+ .||+||.+||+|++.+++++|+|+|++.++++||++|++.++|  |++||++++++||..+. +| ..+ .+++|++
T Consensus       137 D~-~gp~Ly~idp~G~~~~~~~~aiG~gs~~a~~~Le~~~~~~~~m~~s~eea~~~a~~al~~~~-~d~~~s~~~i~v~v  214 (233)
T 1ryp_F          137 DK-SGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVEAISQSL-RDESLTVDNLSIAI  214 (233)
T ss_dssp             ET-TEEEEEEECTTSCEEEESEEEESTTHHHHHHHHHHHHHHHTTCCSCHHHHHHHHHHHHTTSC-CSSCCCTTTEEEEE
T ss_pred             eC-CcCEEEEECCCCCeeeeeEEEECCCcHHHHHHHHHHhccccccCCCHHHHHHHHHHHHHHHh-hcccCCCCcEEEEE
Confidence            98 7899999999999999999999999999999999999632389  99999999999999999 76 444 4899999


Q ss_pred             EEeCCCcEEEcCHHHHHHHH
Q 029560          165 VSKENPEFRVLSIEEIDEHL  184 (191)
Q Consensus       165 v~~~~~~~~~~~~~~i~~~~  184 (191)
                      |+++++ |++++++||+++|
T Consensus       215 i~~~~~-~~~l~~~ei~~~l  233 (233)
T 1ryp_F          215 VGKDTP-FTIYDGEAVAKYI  233 (233)
T ss_dssp             EETTEE-EEEEEGGGGGGGC
T ss_pred             EECCCC-EEECCHHHHHhhC
Confidence            999864 9999999998753

>1ryp_L 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_L 1vsy_L 1z7q_L 3l5q_P 1g65_K* 1g0u_K* 1jd2_K* 2f16_K* 2fak_K* 2fny_K* 2gpl_K* 2zcy_K* 3bdm_K* 3d29_K* 3dy3_K* 3dy4_K* 3e47_K* 3gpj_K* 3gpt_K* 3gpw_K* ...

Probab=100.00  E-value=2.7e-42  Score=270.15  Aligned_cols=178  Identities=12%  Similarity=0.172  Sum_probs=167.4

Q ss_pred             ccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccccee
Q 029560            4 KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVA   83 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~   83 (191)
                      +++.+++++||++|++|++|++||..+|++.+.++++.+++.|+++++++++++.+++++++.+|.|++    .||++++
T Consensus        24 ~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~----~p~~v~~   99 (212)
T 1ryp_L           24 NWVASQTVKRVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKG----AGLSMGT   99 (212)
T ss_dssp             TEEEESCCCCEEEEETTEEEECCBCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTT----SCCCBEE
T ss_pred             CeEecCcccceeeeCCcEEEEccccHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhhCC----CCceEEE
Confidence            678889999999999999999999999999999999999999999999999999999999999998875    3999999


Q ss_pred             EEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEE
Q 029560           84 MVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEV  162 (191)
Q Consensus        84 iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei  162 (191)
                      ||||||++++|+||.+||+|++.++++.|+|+|+++++++||++|  +++||++||++++++||..+.+||..++ +++|
T Consensus       100 lvaG~D~~~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~--~~~~s~eea~~la~~al~~~~~rd~~s~~~i~v  177 (212)
T 1ryp_L          100 MICGYTRKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNY--KWDLSVEDALYLGKRSILAAAHRDAYSGGSVNL  177 (212)
T ss_dssp             EEEEEETTTEEEEEEEETTCCEEECSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHBTTCCSEEEE
T ss_pred             EEEEEeCCCCCEEEEEcCCceeEecCCEEEcCCHHHHHHHHHhhC--CCCCCHHHHHHHHHHHHHHHHHhccccCCceEE
Confidence            999999657899999999999999999999999999999999998  4789999999999999999999997765 8999


Q ss_pred             EEEEeCCCcEEEcCHHHHHHHHHHhhc
Q 029560          163 GVVSKENPEFRVLSIEEIDEHLTAISE  189 (191)
Q Consensus       163 ~iv~~~~~~~~~~~~~~i~~~~~~~~~  189 (191)
                      +++++++  |++++++||++++.++.+
T Consensus       178 ~vi~~~g--~~~~~~~ei~~~~~~~~~  202 (212)
T 1ryp_L          178 YHVTEDG--WIYHGNHDVGELFWKVKE  202 (212)
T ss_dssp             EEEETTE--EEEEEEEEHHHHHHHHHH
T ss_pred             EEEcCCc--eEEECHHHHHHHHHHHHH
Confidence            9999874  999999999999887753

>3nzj_F Proteasome component C1; ubiquitin, protein degradation, N-terminal nucleophilic HYDR 19S regulatory particle; HET: TY5 TRO MES; 2.40A {Saccharomyces cerevisiae} PDB: 1z7q_G* 3nzw_F* 3nzx_F* 3un4_F* 3un8_F* 4b4t_G 4g4s_G* 3bdm_F* 1fnt_G* 2zcy_F*

Probab=100.00  E-value=2.5e-41  Score=275.23  Aligned_cols=181  Identities=25%  Similarity=0.389  Sum_probs=165.0

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      +++++..++++||++|++||+|+++|+.+|++.|+++++.+++.|+++++++++++.++++|++++|.||+++++|||+|
T Consensus        55 t~gl~~~~~~~KI~~I~d~i~~~~aG~~aD~~~l~~~lr~e~~~y~~~~~~~i~v~~lA~~l~~~l~~yt~~~~~rP~gv  134 (288)
T 3nzj_F           55 TSKLLVPQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGV  134 (288)
T ss_dssp             CCTTBCTTCSCCCEEETTTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSCTTBCCCCE
T ss_pred             ccCCccccccceEEEEcCCEEEEecCcHHHHHHHHHHHHHHHHHHHHHcCCcCCHHHHHHHHHHHHHHHHHhccCCCceE
Confidence            45677777899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhc-CCCCCCHHHHHHHHHHHHHhhhcccCCCC-e
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMK-NDPAFTFQETVQTAISTLQSVLQEDFKAS-E  159 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~-~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~  159 (191)
                      ++||||||+ +||+||.+||+|++.+++++|+|+|++.++++||++++ +.++||++||++++++||..+.+++..++ +
T Consensus       135 ~~lvaG~D~-~Gp~Ly~iDp~G~~~~~~~~aiGsgs~~a~~~Lek~~~~~~~~ms~eEAv~la~~al~~a~~~~~~~~~~  213 (288)
T 3nzj_F          135 STIFGGVDK-NGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFE  213 (288)
T ss_dssp             EEEEEEEET-TEEEEEEECTTSCEEEBSEEEESTTHHHHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHGGGGTTSEEE
T ss_pred             EEEEEEEeC-CCCEEEEECCCCCEEEcCEEEEcCcHHHHHHHHHHhccccCCCCCHHHHHHHHHHHHHHHHhcccCCCCe
Confidence            999999998 78999999999999999999999999999999999932 36899999999999999999999987665 8


Q ss_pred             EEEEEEEe-C-CCcEEEcCHHHHHHH
Q 029560          160 IEVGVVSK-E-NPEFRVLSIEEIDEH  183 (191)
Q Consensus       160 iei~iv~~-~-~~~~~~~~~~~i~~~  183 (191)
                      ++|+||++ + ++.++.++.+++++.
T Consensus       214 iev~vIt~~~~~~~~~~vp~~~~~~~  239 (288)
T 3nzj_F          214 LEISWCSLSETNGLHKFVKGDLLQEA  239 (288)
T ss_dssp             EEEEEEETTTSTTCCEECCHHHHHHH
T ss_pred             EEEEEEEecCCCceEEECCHHHHHHH
Confidence            99999998 4 444666777666543

>1iru_L 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_K* 3une_K 3unf_K* 3unh_K

Probab=100.00  E-value=8.1e-42  Score=265.94  Aligned_cols=176  Identities=15%  Similarity=0.198  Sum_probs=166.0

Q ss_pred             ccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccccee
Q 029560            4 KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVA   83 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~   83 (191)
                      +++.+++++||++|++|++|++||+.+|++.+.++++.+++.|+++++++++++.+++++++.+|.|++    +||+|++
T Consensus        24 ~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~r~----~~~~v~~   99 (204)
T 1iru_L           24 AYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQCRIYELRNKERISVAAASKLLANMVYQYKG----MGLSMGT   99 (204)
T ss_dssp             TEEEESCCCCEEEEETTEEEECCBCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHTTTT----SCCCBEE
T ss_pred             CEEEcCcccceEEcCCCEEEEccCcHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhCC----CCeeEEE
Confidence            677889999999999999999999999999999999999999999999999999999999999987643    5999999


Q ss_pred             EEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEE
Q 029560           84 MVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEV  162 (191)
Q Consensus        84 iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei  162 (191)
                      ||||||+ +||+||.+||+|++.++++.|+|+|++.++++||++|+  ++||.+||++++++||..+.+||..++ +++|
T Consensus       100 lvaG~D~-~gp~Ly~idp~G~~~~~~~~aiG~gs~~a~~~Le~~~~--~~~s~eea~~l~~~al~~~~~rd~~s~~~i~v  176 (204)
T 1iru_L          100 MICGWDK-RGPGLYYVDSEGNRISGATFSVGSGSVYAYGVMDRGYS--YDLEVEQAYDLARRAIYQATYRDAYSGGAVNL  176 (204)
T ss_dssp             EEEEECS-SSEEEEEEESSSCEEECSEEEESTTHHHHHHHHHTTCC--TTCCHHHHHHHHHHHHHHHHHHBTTCCSEEEE
T ss_pred             EEEEEeC-CCCEEEEECCCCcEEEeCCEEEEcCHHHHHHHHhccCC--CCCCHHHHHHHHHHHHHHHHHhCccCCCceEE
Confidence            9999997 78999999999999999999999999999999999984  789999999999999999999997654 8999


Q ss_pred             EEEEeCCCcEEEcCHHHHHHHHHHhh
Q 029560          163 GVVSKENPEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       163 ~iv~~~~~~~~~~~~~~i~~~~~~~~  188 (191)
                      ++|++++  |+.++++||++++.++.
T Consensus       177 ~vi~~~g--~~~l~~~ei~~~~~~~~  200 (204)
T 1iru_L          177 YHVREDG--WIRVSSDNVADLHEKYS  200 (204)
T ss_dssp             EEECSSC--EEEEEEEEHHHHHHHHT
T ss_pred             EEEeCCc--eEEeCHHHHHHHHHHhc
Confidence            9999875  99999999999999886

>1ryp_G 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_F* 1g65_F 1vsy_G 2f16_F* 2fak_F* 2fny_F* 2gpl_F* 3d29_F* 3dy3_F* 3dy4_F* 3e47_F* 3gpj_F* 3gpt_F* 3gpw_F* 3hye_F* 3l5q_L 3mg0_F* 3mg4_F* 3okj_F* 3shj_F* ...

Probab=100.00  E-value=2.9e-41  Score=269.63  Aligned_cols=184  Identities=23%  Similarity=0.366  Sum_probs=167.6

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      +++++..+..+||++|++|++|++||+.+|++.+.++++.+++.|+++++++++++.+++++++++|.||+++++|||+|
T Consensus        51 ~~g~~~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rp~~v  130 (244)
T 1ryp_G           51 TSKLLVPQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGV  130 (244)
T ss_dssp             CCTTBCTTTSCCCEEETTTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSCTTBCCCCE
T ss_pred             CCCCccccccCceEEecCCEEEEEcccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCccCceE
Confidence            45566666779999999999999999999999999999999999999999999999999999999999999988999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHh---hcCCCCCCHHHHHHHHHHHHHhhhcccCCCC
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKK---MKNDPAFTFQETVQTAISTLQSVLQEDFKAS  158 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~---~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~  158 (191)
                      ++||||||+ +||+||.+||+|++.+++++|+|+|++.++++||+.   |  +++||++||++++++||..+.++|..++
T Consensus       131 ~~lvaG~D~-~gp~Ly~idp~G~~~~~~~~aiG~gs~~a~~~Le~~~~~~--~~~ms~eea~~la~~al~~~~~~d~~s~  207 (244)
T 1ryp_G          131 STIFGGVDK-NGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHH--PEGLSAREAVKQAAKIIYLAHEDNKEKD  207 (244)
T ss_dssp             EEEEEEEET-TEEEEEEECTTSCEEEBSEEEESTTHHHHHHHHHHHHHHC--TTCCCHHHHHHHHHHHHHHHGGGGTTSC
T ss_pred             EEEEEEEeC-CcCEEEEECCCCCEEEeeEEEECCChHHHHHHHHHhHhhc--CCCCCHHHHHHHHHHHHHHHHhccCCCC
Confidence            999999997 789999999999999999999999999999999997   6  4789999999999999999999998765


Q ss_pred             -eEEEEEEEe-CCCcEEEcCHHHHHHHHHHhh
Q 029560          159 -EIEVGVVSK-ENPEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       159 -~iei~iv~~-~~~~~~~~~~~~i~~~~~~~~  188 (191)
                       +++|++|++ +..+++.+.|+++-+..++.+
T Consensus       208 ~~iev~vi~~~~~~g~~~~~~~~~~~~~~~~~  239 (244)
T 1ryp_G          208 FELEISWCSLSETNGLHKFVKGDLLQEAIDFA  239 (244)
T ss_dssp             EEEEEEEEETTTTTTSEEECCTHHHHHHHHHH
T ss_pred             CeEEEEEEEecCCCCeeeeChHHHHHHHHHHH
Confidence             899999997 222377777777776666554

>1iru_H 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_N* 3une_N

Probab=100.00  E-value=1.5e-42  Score=270.31  Aligned_cols=175  Identities=15%  Similarity=0.200  Sum_probs=164.9

Q ss_pred             cccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeE
Q 029560            5 LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAM   84 (191)
Q Consensus         5 l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~i   84 (191)
                      ++.+++++||++|++|++|++||+.+|++.+.++++.+++.|+++++++++++.+++++++.+|.|++     ||++++|
T Consensus        25 ~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~-----p~~~~~l   99 (205)
T 1iru_H           25 YIANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEMCYRYRE-----DLMAGII   99 (205)
T ss_dssp             EEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHTTT-----TCCEEEE
T ss_pred             EEecCCcCceEEcCCCEEEEcCccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhcCc-----CccEEEE
Confidence            77788999999999999999999999999999999999999999999999999999999999988764     9999999


Q ss_pred             EEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEEE
Q 029560           85 VLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVG  163 (191)
Q Consensus        85 v~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei~  163 (191)
                      |||||+++||+||.+||+|++.+++++|+|+|++.++++||++|  +++||++||++++++||..+.+||..++ +++|+
T Consensus       100 vaG~D~~~gp~ly~~d~~G~~~~~~~~a~Gsgs~~a~~~Le~~~--~~~~s~eea~~l~~~al~~~~~~d~~s~~~i~v~  177 (205)
T 1iru_H          100 IAGWDPQEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATY--REGMTKEECLQFTANALALAMERDGSSGGVIRLA  177 (205)
T ss_dssp             EEEEETTTEEEEEEECTTSCCEECSEEEESGGGGGGHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHBTTCCSCEEEE
T ss_pred             EEEEeCCCCCEEEEECCCCcEEecCEEEECCCHHHHHHHHHHhc--CCCCCHHHHHHHHHHHHHHHHHhccccCCcEEEE
Confidence            99999767899999999999999999999999999999999998  4789999999999999999999997765 89999


Q ss_pred             EEEeCCCcEEEcCHHHHHHHHHH
Q 029560          164 VVSKENPEFRVLSIEEIDEHLTA  186 (191)
Q Consensus       164 iv~~~~~~~~~~~~~~i~~~~~~  186 (191)
                      +|++++..++.++++||++++.+
T Consensus       178 vi~~~g~~~~~l~~~ei~~~~~~  200 (205)
T 1iru_H          178 AIAESGVERQVLLGDQIPKFAVA  200 (205)
T ss_dssp             EEETTEEEEEEECGGGSCCCCCC
T ss_pred             EEeCCCeEEEEeChHHhhHHHhh
Confidence            99999866889999999887754

>3nzj_K Proteasome component PRE2; ubiquitin, protein degradation, N-terminal nucleophilic HYDR 19S regulatory particle; HET: TY5 TRO MES; 2.40A {Saccharomyces cerevisiae} PDB: 3nzw_K* 3nzx_K* 4b4t_5

Probab=100.00  E-value=3.4e-41  Score=274.39  Aligned_cols=179  Identities=12%  Similarity=0.171  Sum_probs=168.8

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      ++++.+++++||++|++|++|+++|..+|++.|.++++.+++.|+++++++++++.++++++++++.|++    +||+++
T Consensus        98 G~li~~~~~~KI~~I~d~i~~~~aG~~AD~~~l~~~lr~~~~~y~~~~~~~isv~~la~~ls~~l~~~r~----~p~~v~  173 (287)
T 3nzj_K           98 GNWVASQTVKKVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKG----AGLSMG  173 (287)
T ss_dssp             TTEEEESCCCCEEEEETTEEEECEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTT----SCCCEE
T ss_pred             CceeecCCcceEEEEcCcEEEEecCCHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhcC----CCceEE
Confidence            3677889999999999999999999999999999999999999999999999999999999999987754    499999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIE  161 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~ie  161 (191)
                      +||||||+++||+||.+||+|++.++++.|+|+|++.++++||+.|  +++||++||++++++||..+.+||..++ +++
T Consensus       174 ~lvaG~D~~~gp~Ly~iDp~G~~~~~~~~AiGsgs~~a~~~Le~~y--~~dms~eEAi~la~~aL~~a~~rD~~sg~~i~  251 (287)
T 3nzj_K          174 TMICGYTRKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNY--KWDLSVEDALYLGKRSILAAAHRDAYSGGSVN  251 (287)
T ss_dssp             EEEEEEETTTEEEEEEEETTCCEEECSEEEESTTHHHHHHHHHTSC--CTTCCHHHHHHHHHHHHHHHHHHBTTCCSEEE
T ss_pred             EEEEEEcCCCCCEEEEECCCceEEEcCeEEEecchHHHHHHHHHhh--cCCCCHHHHHHHHHHHHHHHHhhCcCCCCceE
Confidence            9999999658899999999999999999999999999999999998  4789999999999999999999999886 899


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHHHHHhhc
Q 029560          162 VGVVSKENPEFRVLSIEEIDEHLTAISE  189 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~~~~~~~  189 (191)
                      |++|+++|  |++++++||++++.++++
T Consensus       252 V~vItkdg--~~~l~~~ev~~~l~~~~e  277 (287)
T 3nzj_K          252 LYHVTEDG--WIYHGNHDVGELFWKVKE  277 (287)
T ss_dssp             EEEEETTE--EEEEEEEEHHHHHHHHHH
T ss_pred             EEEEeCCC--EEEeCHHHHHHHHHHHHH
Confidence            99999985  999999999999988874

>1q5r_H Proteasome beta-type subunit 1; proteasome assembly, Pro-peptide, inter-subunit contacts, hydrolase; 3.10A {Rhodococcus erythropolis} SCOP: d.153.1.4 PDB: 2h6j_H

Probab=100.00  E-value=1.9e-40  Score=270.77  Aligned_cols=182  Identities=19%  Similarity=0.185  Sum_probs=170.3

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      ++++.+++++|||+|++|++|+++|..+|++.|.++++.+++.|+++++++++++.+++.|++++|.|+++. +|||+|+
T Consensus        88 G~li~~~~~~KI~~I~~~i~~~~aG~~aD~~~l~~~~r~~~~~y~~~~g~~isv~~la~~la~~l~~~~~~~-~rp~~v~  166 (294)
T 1q5r_H           88 GNLIASRDVEAVYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEGVPLTFDGKANRLASMVRGNLGAA-MQGLAVV  166 (294)
T ss_dssp             TTEEEESCCCCEEEEETTEEEEEEEBHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHHH-TTTTCEE
T ss_pred             CceeecCCcceEEEECCcEEEEEeecHHHHHHHHHHHHHHHHHhhHhhCCCCCHHHHHHHHHHHHHHHHhhh-cCCcceE
Confidence            368888999999999999999999999999999999999999999999999999999999999999988765 8999999


Q ss_pred             eEEEEEcCCCC-----CeEEEECCCcceece--eeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccC
Q 029560           83 AMVLSIDEECG-----PRLFKCDPAGHFFGH--KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDF  155 (191)
Q Consensus        83 ~iv~G~d~~~~-----p~Ly~~d~~G~~~~~--~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~  155 (191)
                      +||+|||++++     |+||.+||+|++.++  ++.|+|+|+++++++||++|  +++||++||++++++||..+.++|.
T Consensus       167 lLvaG~D~~~g~~~~~p~Ly~iDp~G~~~e~~~~~~AiGsgs~~a~~~Le~~y--~~~ms~eEAi~la~~aL~~a~~rD~  244 (294)
T 1q5r_H          167 PLLVGYDLDADDESRAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALKKIY--SPDSDEETALRAAIESLYDAADDDS  244 (294)
T ss_dssp             EEEEEECTTCSCTTSCEEEEEECSSSCEEECCSSEEEESTTHHHHHHHHHHHC--CSSCCHHHHHHHHHHHHHHHHHHCT
T ss_pred             EEEEEEeCCCCcCCCCCEEEEECCCCeEEecCCCeEEEecCcHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHHhhcc
Confidence            99999998546     999999999999999  89999999999999999998  4789999999999999999999998


Q ss_pred             CCCe---E-----EEEEEEeCCCcEEEcCHHHHHHHHHHhhc
Q 029560          156 KASE---I-----EVGVVSKENPEFRVLSIEEIDEHLTAISE  189 (191)
Q Consensus       156 ~~~~---i-----ei~iv~~~~~~~~~~~~~~i~~~~~~~~~  189 (191)
                      .+++   +     +|++|++++  |++++++||++++.++.+
T Consensus       245 ~sG~~~~ir~i~~ev~vI~~~g--~~~l~~~ei~~~l~~i~~  284 (294)
T 1q5r_H          245 ATGGPDLTRGIYPTAVTITQAG--AVHVSEETTSELARRIVA  284 (294)
T ss_dssp             TTCCCBTTTTBCCEEEEEETTE--EEECCHHHHHHHHHHHCC
T ss_pred             ccCCchhhcccCCEEEEEECCC--EEEcCHHHHHHHHHHHHH
Confidence            8753   5     999999874  999999999999998863

>1iru_N 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_M* 3une_M 3unf_M* 3unh_M

Probab=100.00  E-value=2.9e-41  Score=265.54  Aligned_cols=177  Identities=14%  Similarity=0.175  Sum_probs=164.1

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHH-HhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRF-KYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~-~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      .+++.+++++||++|++|++|+++|..+|++.|.++++.+++.|++ +++++++++.+++++++.+  |+++.++|||+|
T Consensus        31 g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~l--y~~r~~~~P~~v  108 (219)
T 1iru_N           31 GSLARFRNISRIMRVNNSTMLGASGDYADFQYLKQVLGQMVIDEELLGDGHSYSPRAIHSWLTRAM--YSRRSKMNPLWN  108 (219)
T ss_dssp             TTEEEECSCCCEEEETTTEEEEEEEEHHHHHHHHHHHHHHHHHHHHHCSSCCCCHHHHHHHHHHHH--HHHHHTTCCCCE
T ss_pred             CcEEecCCCCceEEeCCCEEEEeccCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH--HHhcccCCCceE
Confidence            3677789999999999999999999999999999999999999998 9999999999999999998  666778999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EI  160 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~i  160 (191)
                      ++||||||+ ++|+||.+||+|++.++++.|+|+|++.++++||+.|++.++||++||++++++||..+.+||..++ ++
T Consensus       109 ~~lvaG~D~-~gp~Ly~id~~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~~mt~eea~~l~~~al~~~~~~d~~sg~~i  187 (219)
T 1iru_N          109 TMVIGGYAD-GESFLGYVDMLGVAYEAPSLATGYGAYLAQPLLREVLEKQPVLSQTEARDLVERCMRVLYYRDARSYNRF  187 (219)
T ss_dssp             EEEEEEEET-TEEEEEEECSSCCEEECSEEECTTHHHHTHHHHHHHHTSCSCCCHHHHHHHHHHHHHHHHHHBTTCCSCE
T ss_pred             EEEEEEEEC-CCCEEEEECCCCCeEECCeEEECccHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHHHHHHhcCcCCCcE
Confidence            999999997 6999999999999999999999999999999999999532399999999999999999999998765 89


Q ss_pred             EEEEEEeCCCcEEEcCHHHHHHHH
Q 029560          161 EVGVVSKENPEFRVLSIEEIDEHL  184 (191)
Q Consensus       161 ei~iv~~~~~~~~~~~~~~i~~~~  184 (191)
                      +|++|++++  ++.+++++|+..+
T Consensus       188 ~v~vi~~~g--~~~~~~~~i~~~~  209 (219)
T 1iru_N          188 QTATVTEKG--VEIEGPLSTETNW  209 (219)
T ss_dssp             EEEEEETTE--EEEEEEECCCCCC
T ss_pred             EEEEEcCCC--EEEcCCeeccchh
Confidence            999999985  9999998887654

>1q5q_A Proteasome alpha-type subunit 1; proteasome assembly, Pro-peptide, inter-subunit contacts, RH erythropolis, hydrolase; 2.60A {Rhodococcus erythropolis} SCOP: d.153.1.4 PDB: 2h6j_A 1q5r_A

Probab=100.00  E-value=2e-40  Score=266.80  Aligned_cols=178  Identities=16%  Similarity=0.244  Sum_probs=159.6

Q ss_pred             CCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCC-CCCHHHHHHHHHH-HHHHhhhhcCcccccceeEE
Q 029560            8 HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGY-EMPVDVLAKWIAD-KSQVYTQHAYMRPLGVVAMV   85 (191)
Q Consensus         8 ~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~-~~~~~~l~~~l~~-~~~~~t~~~~~rP~~v~~iv   85 (191)
                      +++++|||+|++|++|+++|+.+|++.|.++++.+++.|++.++. +++++.+++++++ +.|.|+  .++|||+|++||
T Consensus        47 s~~~~KI~~I~d~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~i~v~~la~~l~~~l~q~yt--~~~rP~~v~~lv  124 (259)
T 1q5q_A           47 STALHKVSELYDRLGFAAVGKYNEFENLRRAGIVHADMRGYSYDRRDVTGRSLANAYAQTLGTIFT--EQPKPYEVEICV  124 (259)
T ss_dssp             CSSSCSEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHHHHHHHHHH--HSSSCCCEEEEE
T ss_pred             CCCcCcEEEeCCCEEEEEccCHHHHHHHHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHhc--cCCCCceEEEEE
Confidence            468899999999999999999999999999999999999999984 9999999999999 677787  468999999999


Q ss_pred             EEEc--C-CCCCeEEEECCCccee-ceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhh-----cccCC
Q 029560           86 LSID--E-ECGPRLFKCDPAGHFF-GHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVL-----QEDFK  156 (191)
Q Consensus        86 ~G~d--~-~~~p~Ly~~d~~G~~~-~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~-----~~d~~  156 (191)
                      ||||  + ++||+||.+||+|++. .++++|+|+|++.++++||++|  .++||++||++++++||..+.     +||+.
T Consensus       125 aG~D~~~~~~gp~Ly~idp~G~~~~~~~~~aiG~gs~~a~~~Le~~~--~~~ms~eea~~la~~al~~~~~~~~~~rd~s  202 (259)
T 1q5q_A          125 AEVGRVGSPKAPQLYRITYDGSIVDEQHFVVMGGTTEPIATAMRESY--RADLDLEAAVGIAVNALRQGGAGEGEKRNVD  202 (259)
T ss_dssp             EECCCSSCCCCCEEEEEETTSCEEEESSEEEESSSHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHTTCC--------CC
T ss_pred             EEEcccCCCCCCEEEEECCCCceeeCCCEEEECCChHHHHHHHHhhc--cCCCCHHHHHHHHHHHHHHHhhcccccccCC
Confidence            9999  2 4799999999999999 7899999999999999999998  478999999999999999999     89994


Q ss_pred             CCeEEEEEEEeCC--CcEEEcCHHHHHHHHHHhhc
Q 029560          157 ASEIEVGVVSKEN--PEFRVLSIEEIDEHLTAISE  189 (191)
Q Consensus       157 ~~~iei~iv~~~~--~~~~~~~~~~i~~~~~~~~~  189 (191)
                      ..+++|++|++++  .+|+++++++|+.++.++.+
T Consensus       203 g~~iev~vi~~~~~~~~~~~l~~~ei~~~~~~~~~  237 (259)
T 1q5q_A          203 VASLEVAVLDQSRPRRAFRRIAGTALEQLVPAEPA  237 (259)
T ss_dssp             SSCSEEEEEETTSSSCCEEECCHHHHHTTSCCC--
T ss_pred             CCcEEEEEEECCCCcCCeEECCHHHHHHHHHHhhh
Confidence            4589999999985  24999999999999887754

>1ryp_K 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_K 1g0u_J* 1jd2_J* 1g65_J 1vsy_K 1z7q_K 2f16_J* 2fak_J* 2fny_J* 2gpl_J* 2zcy_J* 3bdm_J* 3d29_J* 3dy3_J* 3dy4_J* 3e47_J* 3gpj_J* 3gpt_J* 3gpw_J* 3hye_J* ...

Probab=100.00  E-value=5e-40  Score=254.70  Aligned_cols=167  Identities=14%  Similarity=0.174  Sum_probs=154.1

Q ss_pred             cccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeE
Q 029560            5 LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAM   84 (191)
Q Consensus         5 l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~i   84 (191)
                      ++.+++++||++|++|++|+++|+.+|++.+.++++.+++.|+++++++++++.+++.+++.++.|++.  ++||++++|
T Consensus        26 ~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~l~~~~~~--r~p~~v~~l  103 (198)
T 1ryp_K           26 SVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYIQANIQLYSIREDYELSPQAVSSFVRQELAKSIRS--RRPYQVNVL  103 (198)
T ss_dssp             EEEESCCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHTTS--SSCCCEEEE
T ss_pred             EEEecCCCceEEeCCCEEEEeccCHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhccc--CCCceEEEE
Confidence            344679999999999999999999999999999999999999999999999999999999999877632  359999999


Q ss_pred             EEEEcC-CCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEE
Q 029560           85 VLSIDE-ECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEV  162 (191)
Q Consensus        85 v~G~d~-~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei  162 (191)
                      |||||+ +++|+||.+||+|++.++++.|+|+|++.++++||+.|+  ++||++||++++++||..+.+||..++ +++|
T Consensus       104 vaG~D~~~~~p~Ly~idp~G~~~~~~~~aiG~g~~~a~~~Le~~~~--~~~s~eea~~l~~~al~~~~~~d~~s~~~i~v  181 (198)
T 1ryp_K          104 IGGYDKKKNKPELYQIDYLGTKVELPYGAHGYSGFYTFSLLDHHYR--PDMTTEEGLDLLKLCVQELEKRMPMDFKGVIV  181 (198)
T ss_dssp             EEEEETTTTEEEEEEECTTCCEEECSEEECTTHHHHHHHHHHHHCC--TTCCHHHHHHHHHHHHHHHHHHCSBCCCCEEE
T ss_pred             EEEEeCCCCCcEEEEECCCCCEEECCEEEEcccHHHHHHHHHhhcC--CCCCHHHHHHHHHHHHHHHHHhCccCCCceEE
Confidence            999996 478999999999999999999999999999999999984  789999999999999999999997765 8999


Q ss_pred             EEEEeCCCcEEEcCH
Q 029560          163 GVVSKENPEFRVLSI  177 (191)
Q Consensus       163 ~iv~~~~~~~~~~~~  177 (191)
                      ++|++++  ++.+++
T Consensus       182 ~vi~~~g--~~~~~~  194 (198)
T 1ryp_K          182 KIVDKDG--IRQVDD  194 (198)
T ss_dssp             EEEETTE--EEEECC
T ss_pred             EEEcCCC--EEEecc
Confidence            9999985  888775

>1ryp_N 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_N* 1jd2_M* 1g65_M 1vsy_N 1z7q_N 2f16_M* 2fak_M* 2fny_M* 2gpl_M* 3d29_M* 3dy3_M* 3dy4_M* 3e47_M* 3gpj_M* 3gpt_M* 3gpw_M* 3hye_M* 3l5q_R 3mg0_M* 3mg4_M* ...

Probab=100.00  E-value=3.8e-41  Score=267.19  Aligned_cols=178  Identities=14%  Similarity=0.218  Sum_probs=164.5

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHH-----HhCCCCCHHHHHHHHHHHHHHhhhhcCcc
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRF-----KYGYEMPVDVLAKWIADKSQVYTQHAYMR   77 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~-----~~~~~~~~~~l~~~l~~~~~~~t~~~~~r   77 (191)
                      +.++.+++++||++|++|++|+++|..+|++.|.++++.+++.|++     +++++++++.+++++++.+  |+++.++|
T Consensus        31 g~~~~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~l--y~~r~~~~  108 (233)
T 1ryp_N           31 GSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLADAEEALEPSYIFEYLATVM--YQRRSKMN  108 (233)
T ss_dssp             TTEEEESCCCCEEEETTTEEEEEEEEHHHHHHHHHHHHHHHHHHHTTCTTTTTTTSCCHHHHHHHHHHHH--HHHHHTTC
T ss_pred             CCeeecCCcCceEEeCCCEEEEccccHHHHHHHHHHHHHHHHHHhhccchhhcCCCCCHHHHHHHHHHHH--HHhcCCCC
Confidence            3577889999999999999999999999999999999999999999     9999999999999999998  67777889


Q ss_pred             cccceeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCC---CCCHHHHHHHHHHHHHhhhccc
Q 029560           78 PLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDP---AFTFQETVQTAISTLQSVLQED  154 (191)
Q Consensus        78 P~~v~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~---~~s~eea~~l~~~~l~~~~~~d  154 (191)
                      ||+|++||||||++++|+||.+||+|++.++++.|+|+|++.++++||+.|++.+   +||++||++++++||..+.+||
T Consensus       109 P~~v~~lvaG~D~~~gp~Ly~id~~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~~~~~ms~eea~~la~~al~~~~~rd  188 (233)
T 1ryp_N          109 PLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFGAHMANPLLRKVVDRESDIPKTTVQVAEEAIVNAMRVLYYRD  188 (233)
T ss_dssp             CCCEEEEEEEECTTSCEEEEEEETTCCEECCSEEECTHHHHHHHHHHTTTCSSGGGGGGCCHHHHHHHHHHHHHHHHHHB
T ss_pred             CceEEEEEEEEcCCCCEEEEEECCCcCeEEcCEEEECcCHHHHHHHHHHhhccccccCCCCHHHHHHHHHHHHHHHHHhc
Confidence            9999999999998568999999999999999999999999999999999985211   8999999999999999999999


Q ss_pred             CCCC-eEEEEEEEeCCCcEEEcCHHHHHHH
Q 029560          155 FKAS-EIEVGVVSKENPEFRVLSIEEIDEH  183 (191)
Q Consensus       155 ~~~~-~iei~iv~~~~~~~~~~~~~~i~~~  183 (191)
                      ..++ +++|++|++++ +++.+++++|+.+
T Consensus       189 ~~sg~~i~v~vi~~~~-g~~~~~~~~i~~~  217 (233)
T 1ryp_N          189 ARSSRNFSLAIIDKNT-GLTFKKNLQVENM  217 (233)
T ss_dssp             TTCCSEEEEEEEETTT-EEEEEEEEECCSC
T ss_pred             ccCCCcEEEEEEECCC-CeEEcChHhcccc
Confidence            8765 89999999983 2999999988776

>2jay_A Proteasome; hydrolase; 1.99A {Mycobacterium tuberculosis} PDB: 3mka_C 3mi0_C* 2fhg_H* 2fhh_H 3krd_C* 3mfe_G 3hfa_H* 3h6i_C 3h6f_C 3hf9_H 3mfe_H

Probab=100.00  E-value=7e-40  Score=267.21  Aligned_cols=181  Identities=15%  Similarity=0.117  Sum_probs=156.5

Q ss_pred             ccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccccee
Q 029560            4 KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVA   83 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~   83 (191)
                      .++.+++++||++|++|++|+++|..+|++.|.++++.+++.|++.++++++++.+++.++++++.|++ ..+|||+|++
T Consensus        81 ~li~~~~~~KI~~i~d~i~~~~aG~~aD~~~l~~~lr~~~~~y~~~~~~~i~v~~la~~la~~l~~~~~-~~~rpf~v~~  159 (291)
T 2jay_A           81 NMISGRDVRKVYITDDYTATGIAGTAAVAVEFARLYAVELEHYEKLEGVPLTFAGKINRLAIMVRGNLA-AAMQGLLALP  159 (291)
T ss_dssp             ----CCCCCCEEEEETTEEEEEESCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHTCHH-HHHHTCCCEE
T ss_pred             CeeecCCcccEEEeCCcEEEEEcccHHHHHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHHhhh-hhccccceeE
Confidence            367789999999999999999999999999999999999999999999999999999999999998865 4578999999


Q ss_pred             EEEEEcCCCC-----CeEEEECCCccee--ceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCC
Q 029560           84 MVLSIDEECG-----PRLFKCDPAGHFF--GHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFK  156 (191)
Q Consensus        84 iv~G~d~~~~-----p~Ly~~d~~G~~~--~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~  156 (191)
                      ||||||++++     |+||.+||+|++.  ++++.|+|+|+++++++||+.|+  ++||++||++++++||..+.++|+.
T Consensus       160 lvaG~D~~g~~~~~~p~Ly~iDp~G~~~e~~~~~~aiGsgs~~a~~~Le~~~~--~~ms~eEAi~la~~aL~~a~~~D~~  237 (291)
T 2jay_A          160 LLAGYDIHASDPQSAGRIVSFDAAGGWNIEEEGYQAVGSGSLFAKSSMKKLYS--QVTDGDSGLRVAVEALYDAADDDSA  237 (291)
T ss_dssp             EEEEECTTCSCSTTCEEEEEECTTSCEEECSSSEEEESTTHHHHHHHHHHHGG--GCCSHHHHHHHHHHHHHHC------
T ss_pred             EEEEEeCCCCcCCCCCEEEEECCCCcEEecCCCEEEEecCHHHHHHHHHHhcC--CCCCHHHHHHHHHHHHHHHHhhCCC
Confidence            9999998555     8999999999998  88999999999999999999985  7899999999999999999999998


Q ss_pred             CCeE--------EEEEEEeCCCcEEEcCHHHHHHHHHHhhc
Q 029560          157 ASEI--------EVGVVSKENPEFRVLSIEEIDEHLTAISE  189 (191)
Q Consensus       157 ~~~i--------ei~iv~~~~~~~~~~~~~~i~~~~~~~~~  189 (191)
                      ++++        +|++|++++  |++++++||++++.++.+
T Consensus       238 sg~~e~vr~~~~~v~vi~~dg--~~~l~~~ei~~~~~~~~~  276 (291)
T 2jay_A          238 TGGPDLVRGIFPTAVIIDADG--AVDVPESRIAELARAIIE  276 (291)
T ss_dssp             ----------CCEEEEEETTE--EEECCHHHHHHHHHHC--
T ss_pred             CCCcccccccCCEEEEEECCC--eEEcCHHHHHHHHHHHHH
Confidence            8876        599999984  999999999999998863

>3unf_H Proteasome subunit beta type-10; antigen presentation, drug development, protein degradation, hydrolase-hydrolase inhibitor complex; HET: 04C; 2.90A {Mus musculus} PDB: 3unh_H

Probab=100.00  E-value=8.4e-40  Score=259.47  Aligned_cols=168  Identities=16%  Similarity=0.274  Sum_probs=156.4

Q ss_pred             cccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeE
Q 029560            5 LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAM   84 (191)
Q Consensus         5 l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~i   84 (191)
                      ++.+++++||++|++|++|++||..+|++.+.++++.+++.|+++++++++++.+++.+++.++.|     .+||++++|
T Consensus        25 ~v~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~l~~~-----~~p~~v~ll   99 (234)
T 3unf_H           25 VVADKSCEKIHFIAPKIYCCGAGVAADTEMTTRMAASKMELHALSTGREPRVATVTRILRQTLFRY-----QGHVGASLV   99 (234)
T ss_dssp             EEEESSCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHCSCCCHHHHHHHHHHHHHHT-----TTCSCEEEE
T ss_pred             EeccCccccEEEecCCEEEEecccHHHHHHHHHHHHHHHHhhHHhcCCCCCHHHHHHHHHHHHHhc-----CCCccEEEE
Confidence            355689999999999999999999999999999999999999999999999999999999998654     469999999


Q ss_pred             EEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEEE
Q 029560           85 VLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVG  163 (191)
Q Consensus        85 v~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei~  163 (191)
                      |||||+ +||+||.+||+|++.++++.|+|+|++.++++||+.|  +++||++||++++++||..+.++|..++ +++|+
T Consensus       100 vaG~D~-~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~--~~~ms~eeA~~la~~al~~~~~~D~~sg~~iev~  176 (234)
T 3unf_H          100 VGGVDL-NGPQLYEVHPHGSYSRLPFTALGSGQGAAVALLEDRF--QPNMTLEAAQELLVEAITAGILSDLGSGGNVDAC  176 (234)
T ss_dssp             EEEEET-TEEEEEEECTTSCEEECSEEEEETTHHHHHHHHHHHC--CSSCCHHHHHHHHHHHHHHHHHHBTTCCSCEEEE
T ss_pred             EEEEeC-CCCEEEEECCCCCEEeccEEEEcCCchhhHHHHHhcc--CCCCCHHHHHHHHHHHHHHHHhhcCCCCCcEEEE
Confidence            999998 7899999999999999999999999999999999998  4799999999999999999999998765 89999


Q ss_pred             EEEeCCCcEEEcCHHHHHH
Q 029560          164 VVSKENPEFRVLSIEEIDE  182 (191)
Q Consensus       164 iv~~~~~~~~~~~~~~i~~  182 (191)
                      +++++|  ++.+++.+++.
T Consensus       177 vi~~dg--~~~l~~~~i~~  193 (234)
T 3unf_H          177 VITAGG--AKLQRALSTPT  193 (234)
T ss_dssp             EEESSC--EEEEEEEECCC
T ss_pred             EEECCC--EEEeCceeccc
Confidence            999995  89988877653

>3unf_N Proteasome subunit beta type-9; antigen presentation, drug development, protein degradation, hydrolase-hydrolase inhibitor complex; HET: 04C; 2.90A {Mus musculus} PDB: 3unh_N

Probab=100.00  E-value=3.1e-40  Score=256.06  Aligned_cols=172  Identities=16%  Similarity=0.194  Sum_probs=158.8

Q ss_pred             ccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccccee
Q 029560            4 KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVA   83 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~   83 (191)
                      .++.+++++||++|++|++|+++|..+|++.+.++++.+++.|+++++++++++.++++++++++.+     .|||++++
T Consensus        24 ~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a~~l~~~l~~~-----~~p~~v~~   98 (199)
T 3unf_N           24 TAVVNRVFDKLSPLHQRIFCALSGSAADAQAIADMAAYQLELHGLELEEPPLVLAAANVVKNISYKY-----REDLLAHL   98 (199)
T ss_dssp             TEEEESSCCCEEEEETTEEEEECSCHHHHHHHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHT-----TTTCCCCE
T ss_pred             ceeEccccCceEEcCCCEEEEecccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhc-----CCCceEEE
Confidence            3778899999999999999999999999999999999999999999999999999999999999654     46999999


Q ss_pred             EEEEEcCCCCCeEEEECCCcceecee-eeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEE
Q 029560           84 MVLSIDEECGPRLFKCDPAGHFFGHK-ATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIE  161 (191)
Q Consensus        84 iv~G~d~~~~p~Ly~~d~~G~~~~~~-~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~ie  161 (191)
                      ||||||++++|+||.  |+|++..+. ++++|+|++.++++||++|+  ++||++||++++++||..+.+||..++ +++
T Consensus        99 lvaG~D~~~~p~ly~--p~G~~~~~~~~~~~Gsgs~~a~~~Le~~~~--~~ms~eea~~la~~al~~~~~~d~~sg~~i~  174 (199)
T 3unf_N           99 IVAGWDQREGGQVYG--TMGGMLIRQPFTIGGSGSSYIYGYVDAAYK--PGMTPEECRRFTTNAITLAMNRDGSSGGVIY  174 (199)
T ss_dssp             EEEEEETTTEEEEEE--CGGGCCEECSEEEEEGGGGGGHHHHHHHCC--SSCCHHHHHHHHHHHHHHHHHHCTTCCSCEE
T ss_pred             EEEEEeCCCCcEEEE--ECCCceecCCEEEEccCHHHHHHHHHhhcC--CCCCHHHHHHHHHHHHHHHHHhccccCCCeE
Confidence            999999867899999  999987775 55569999999999999984  899999999999999999999999775 899


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHHH
Q 029560          162 VGVVSKENPEFRVLSIEEIDEHL  184 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~~  184 (191)
                      |++|++++..++.++++||++++
T Consensus       175 v~vi~~~g~~~~~l~~~ei~~~~  197 (199)
T 3unf_N          175 LVTITAAGVDHRVILGDELPKFY  197 (199)
T ss_dssp             EEEECSSCEEEEEECGGGSCCCC
T ss_pred             EEEEcCCCEEEEEcCcccCcccc
Confidence            99999998779999999998765

>1iru_M 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_L* 3une_L 3unf_L* 3unh_L

Probab=100.00  E-value=4.5e-39  Score=251.96  Aligned_cols=161  Identities=14%  Similarity=0.258  Sum_probs=149.7

Q ss_pred             ccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeEE
Q 029560            6 LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMV   85 (191)
Q Consensus         6 ~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~iv   85 (191)
                      +.+++++||++|++|++|++||..+|++.|.++++.+++.|+++++++++++.++++|++.+  |+++  .|||++++||
T Consensus        35 ~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~--y~~r--~~P~~v~~lv  110 (213)
T 1iru_M           35 IHTRDSPKCYKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMTTGAIAAMLSTIL--YSRR--FFPYYVYNII  110 (213)
T ss_dssp             EEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHH--HHTT--TSCCCEEEEE
T ss_pred             EecCCCCcEEEcCCCEEEEccccHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHH--HhhC--CCCceEEEEE
Confidence            44579999999999999999999999999999999999999999999999999999999998  6655  7999999999


Q ss_pred             EEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhc-------CCCCCCHHHHHHHHHHHHHhhhcccCCCC
Q 029560           86 LSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMK-------NDPAFTFQETVQTAISTLQSVLQEDFKAS  158 (191)
Q Consensus        86 ~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~-------~~~~~s~eea~~l~~~~l~~~~~~d~~~~  158 (191)
                      ||||++++|+||.+||+|++.++++.|+|+|++.++++||+.|+       +.++||++||++++++||..+.++|..++
T Consensus       111 aG~D~~g~p~Ly~id~~G~~~~~~~~aiGsg~~~a~~~Le~~~~~~~~~~~~~~~~s~eea~~l~~~al~~~~~~d~~s~  190 (213)
T 1iru_M          111 GGLDEEGKGAVYSFDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVEHVPLSLDRAMRLVKDVFISAAERDVYTG  190 (213)
T ss_dssp             EEECTTSCEEEEEECTTSCEEEESEEEEETTHHHHHHHHHHHTTCCSCSSCCCCCCCHHHHHHHHHHHHHHHHHHBTTSC
T ss_pred             EEEcCCCCEEEEEECCCCCEEECCEEEEeeCHHHHHHHHhhccccccccccCCCCCCHHHHHHHHHHHHHHHHHhCCccC
Confidence            99997567999999999999999999999999999999999953       24799999999999999999999998765


Q ss_pred             -eEEEEEEEeCCC
Q 029560          159 -EIEVGVVSKENP  170 (191)
Q Consensus       159 -~iei~iv~~~~~  170 (191)
                       +++|++|++++.
T Consensus       191 ~~i~v~vi~~~g~  203 (213)
T 1iru_M          191 DALRICIVTKEGI  203 (213)
T ss_dssp             SEEEEEEEETTEE
T ss_pred             CcEEEEEEcCCCe
Confidence             899999999874

>1iru_K 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_J* 3une_J 3unf_J* 3unh_J

Probab=100.00  E-value=4.1e-39  Score=250.14  Aligned_cols=168  Identities=15%  Similarity=0.227  Sum_probs=153.1

Q ss_pred             ccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccccee
Q 029560            4 KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVA   83 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~   83 (191)
                      +++.+++++||++|++|++|+++|..+|++.+.++++.+++.|+++++++++++.+++++++.+. |.. ...|||++++
T Consensus        25 ~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a~~~~~~l~-~~~-~~~~p~~~~~  102 (201)
T 1iru_K           25 IVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYIQKNVQLYKMRNGYELSPTAAANFTRRNLA-DCL-RSRTPYHVNL  102 (201)
T ss_dssp             TEEEESSCCCEEECSSSEEEEEEESTTHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHH-HHH-TSSSCCCEEE
T ss_pred             cEEEccCcceEEEecCCEEEEeCcCHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH-HHH-hcCCCccEEE
Confidence            57888999999999999999999999999999999999999999999999999999999987652 222 2347999999


Q ss_pred             EEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEE
Q 029560           84 MVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEV  162 (191)
Q Consensus        84 iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei  162 (191)
                      ||||||++++|+||.+||+|++.++++.|+|+|++.++++||+.|  +++||++||++++++||..+.+||..++ +++|
T Consensus       103 lvaG~D~~~gp~Ly~id~~G~~~~~~~~aiGsgs~~a~~~Le~~~--~~~~s~eea~~l~~~al~~a~~rd~~sg~~i~v  180 (201)
T 1iru_K          103 LLAGYDEHEGPALYYMDYLAALAKAPFAAHGYGAFLTLSILDRYY--TPTISRERAVELLRKCLEELQKRFILNLPTFSV  180 (201)
T ss_dssp             EEEEEETTTEEEEEEECTTCCEEECSEEEESHHHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHTBCBCCCCEEE
T ss_pred             EEEEEeCCCCeEEEEECCCcCeEECCEEEECCcHHHHHHHHHhcc--cCCCCHHHHHHHHHHHHHHHHhhccccCCceEE
Confidence            999999767899999999999999999999999999999999998  4789999999999999999999999775 8999


Q ss_pred             EEEEeCCCcEEEcCH
Q 029560          163 GVVSKENPEFRVLSI  177 (191)
Q Consensus       163 ~iv~~~~~~~~~~~~  177 (191)
                      ++|+++|  ++.+++
T Consensus       181 ~vi~~~g--~~~~~~  193 (201)
T 1iru_K          181 RIIDKNG--IHDLDN  193 (201)
T ss_dssp             EEEETTE--EECCCC
T ss_pred             EEEcCCC--eEEeec
Confidence            9999986  776653

>1g0u_M Proteasome component PRE4; ubiquitin, degradation, protease, NTN-hydrolase; 2.40A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 2zcy_M* 3bdm_M* 3mg6_M* 3mg7_M* 3mg8_M* 3nzj_M* 3nzw_M* 3nzx_M*

Probab=100.00  E-value=8.8e-40  Score=263.99  Aligned_cols=178  Identities=14%  Similarity=0.218  Sum_probs=164.2

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHH-----HhCCCCCHHHHHHHHHHHHHHhhhhcCcc
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRF-----KYGYEMPVDVLAKWIADKSQVYTQHAYMR   77 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~-----~~~~~~~~~~l~~~l~~~~~~~t~~~~~r   77 (191)
                      +.++.+++++||++|++|++|+++|..+|++.|.++++.+++.|++     +++++++++.+++++++++  |+++.++|
T Consensus        64 g~~i~~~~~~KI~~i~d~i~~~~aG~~aD~~~l~~~lr~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~l--y~~r~~~~  141 (266)
T 1g0u_M           64 GSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLADAEEALEPSYIFEYLATVM--YQRRSKMN  141 (266)
T ss_dssp             TTEEEECCCCCEEECTTSEEEEEEEEHHHHHHHHHHHHHHHHHHHTTCTTTTTTTSCCHHHHHHHHHHHH--HHHHHTTC
T ss_pred             CceeecCCcCcEEEcCCCEEEEeccCHHHHHHHHHHHHHHHHHhhhccchhhcCCCCCHHHHHHHHHHHH--HHhccCCC
Confidence            3577888999999999999999999999999999999999999998     9999999999999999998  67777889


Q ss_pred             cccceeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCC---CCCHHHHHHHHHHHHHhhhccc
Q 029560           78 PLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDP---AFTFQETVQTAISTLQSVLQED  154 (191)
Q Consensus        78 P~~v~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~---~~s~eea~~l~~~~l~~~~~~d  154 (191)
                      ||+|++||||||++++|+||.+||+|++.++++.|+|+|++.++++||+.|++.+   +||++||++++++||..+.+||
T Consensus       142 P~~v~~lvaG~D~~~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~~~~~ms~eeA~~la~~al~~a~~rd  221 (266)
T 1g0u_M          142 PLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFGAHMANPLLRKVVDRESDIPKTTVQVAEEAIVNAMRVLYYRD  221 (266)
T ss_dssp             CCCEEEEEEEECTTSCEEEEEEETTCCEECCSEEECTHHHHTHHHHHTTTCSSGGGGGGCCHHHHHHHHHHHHHHHHHHB
T ss_pred             CceEEEEEEEEcCCCCEEEEEECCCCCEEeCCEEEEccCHHHHHHHHHHhhcccccCCCCCHHHHHHHHHHHHHHHHHhc
Confidence            9999999999998568999999999999999999999999999999999985211   8999999999999999999999


Q ss_pred             CCCC-eEEEEEEEeCCCcEEEcCHHHHHHH
Q 029560          155 FKAS-EIEVGVVSKENPEFRVLSIEEIDEH  183 (191)
Q Consensus       155 ~~~~-~iei~iv~~~~~~~~~~~~~~i~~~  183 (191)
                      ..++ +++|++|++++ +++++++++|+.+
T Consensus       222 ~~sg~~i~v~vI~k~~-g~~~~~~~ei~~~  250 (266)
T 1g0u_M          222 ARSSRNFSLAIIDKNT-GLTFKKNLQVENM  250 (266)
T ss_dssp             TTCCSEEEEEEEETTT-EEEEEEEEECCCC
T ss_pred             CCCCCcEEEEEEECCC-CeEEcCHHHhhhh
Confidence            8765 89999999983 2999999888776

>1ryp_M 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_M* 1jd2_L* 1g65_L 1vsy_M 1z7q_M 2f16_L* 2fak_L* 2fny_L* 2gpl_L* 3d29_L* 3dy3_L* 3dy4_L* 3e47_L* 3gpj_L* 3gpt_L* 3gpw_L* 3hye_L* 3l5q_Q 3mg0_L* 3mg4_L* ...

Probab=100.00  E-value=1.5e-38  Score=250.55  Aligned_cols=161  Identities=16%  Similarity=0.324  Sum_probs=149.7

Q ss_pred             ccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHHHHHHHHhhhhcCcccccceeE
Q 029560            6 LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYG-YEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAM   84 (191)
Q Consensus         6 ~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~-~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~i   84 (191)
                      +.+++++||++|++|++|+++|..+|++.|.++++.+++.|+++++ ++++++.+++.+++.+  |+++  ++||++++|
T Consensus        35 i~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~l--y~~r--~~P~~v~~i  110 (222)
T 1ryp_M           35 INSRYEPKVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKLSINSAARNIQHLL--YGKR--FFPYYVHTI  110 (222)
T ss_dssp             EEESCCCCCEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHH--HTTT--TSCCCEEEE
T ss_pred             ecCCCcCcEEEeCCCEEEEccccHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHH--HhcC--CCCceEEEE
Confidence            4678999999999999999999999999999999999999999999 9999999999999998  5443  789999999


Q ss_pred             EEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhc---------------CCCCCCHHHHHHHHHHHHHh
Q 029560           85 VLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMK---------------NDPAFTFQETVQTAISTLQS  149 (191)
Q Consensus        85 v~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~---------------~~~~~s~eea~~l~~~~l~~  149 (191)
                      |||||++++|+||.+||+|++.++++.|+|+|++.++++||+.++               +.++||+|||++++++||..
T Consensus       111 vaG~D~~g~p~Ly~~dp~G~~~~~~~~a~Gsg~~~a~~~Le~~~~~~~~~~~~~~~~~~~~~~~~s~eeA~~la~~al~~  190 (222)
T 1ryp_M          111 IAGLDEDGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYEPGTNGKVKKPLKYLSVEEVIKLVRDSFTS  190 (222)
T ss_dssp             EEEECTTSCEEEEEECTTSCEEEESEEEEETTHHHHHHHHHHHTSCTTCBCTTSTTCSBCCCCCCCHHHHHHHHHHHHHH
T ss_pred             EEEEcCCCCeEEEEECCCcCEEecCEEEEcCcHHHHHHHHhcccccccccccccccccccCCCCCCHHHHHHHHHHHHHH
Confidence            999997567999999999999999999999999999999999853               35899999999999999999


Q ss_pred             hhcccCCCC-eEEEEEEEeCCC
Q 029560          150 VLQEDFKAS-EIEVGVVSKENP  170 (191)
Q Consensus       150 ~~~~d~~~~-~iei~iv~~~~~  170 (191)
                      +.+||..++ +++|++|++++.
T Consensus       191 a~~rd~~sg~~i~v~vi~~~g~  212 (222)
T 1ryp_M          191 ATERHIQVGDGLEILIVTKDGV  212 (222)
T ss_dssp             HHHHBTTCCSEEEEEEEETTEE
T ss_pred             HHHhcccCCCcEEEEEEcCCCe
Confidence            999998765 899999999874

>1ryp_I 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1g0u_H* 1jd2_H* 1g65_H 1vsy_I 1z7q_I 2f16_H* 2fak_H* 2fny_H* 2gpl_H* 3d29_H* 3dy3_H* 3dy4_H* 3e47_H* 3gpj_H* 3gpt_H* 3gpw_H* 3hye_H* 3l5q_M 3mg0_H* 3mg4_H* ...

Probab=100.00  E-value=2.3e-38  Score=249.54  Aligned_cols=164  Identities=18%  Similarity=0.187  Sum_probs=151.7

Q ss_pred             cccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeE
Q 029560            5 LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAM   84 (191)
Q Consensus         5 l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~i   84 (191)
                      ++.+++++||++|++|++|++||..+|++.+.++++.+++.|+++++++++++.+++.+++.++.|     .|||++++|
T Consensus        25 ~~~~~~~~KI~~i~d~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a~~l~~~l~~~-----~~p~~v~~l   99 (222)
T 1ryp_I           25 IVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKY-----QGHIGAYLI   99 (222)
T ss_dssp             EEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHT-----TTCSCEEEE
T ss_pred             eeecCCcccEEEecCCEEEEecccHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhhc-----CCCCCeeEE
Confidence            355678999999999999999999999999999999999999999999999999999999998654     479999999


Q ss_pred             EEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEEE
Q 029560           85 VLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVG  163 (191)
Q Consensus        85 v~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei~  163 (191)
                      |||||+ +||+||.+||+|++.++++.|+|+|++.++++||+.|  +++||++||++++++||..+.+||..++ +++|+
T Consensus       100 vaG~D~-~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~--~~~ms~eeA~~la~~al~~~~~~d~~sg~~i~v~  176 (222)
T 1ryp_I          100 VAGVDP-TGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHW--KQDLTKEEAIKLASDAIQAGIWNDLGSGSNVDVC  176 (222)
T ss_dssp             EEEEET-TEEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHHC--CSSCCHHHHHHHHHHHHHHHHHHCTTCCSCEEEE
T ss_pred             EEEEeC-CCCEEEEECCCCCEEecCEEEECCCHHHHHHHHHhhC--CCCcCHHHHHHHHHHHHHHHHhccccCCCcEEEE
Confidence            999998 7899999999999999999999999999999999998  4789999999999999999999998765 89999


Q ss_pred             EEEeCCCcEEEcCH
Q 029560          164 VVSKENPEFRVLSI  177 (191)
Q Consensus       164 iv~~~~~~~~~~~~  177 (191)
                      +++++++ ++.+.+
T Consensus       177 vi~~~g~-~~~~~~  189 (222)
T 1ryp_I          177 VMEIGKD-AEYLRN  189 (222)
T ss_dssp             EEETTSC-EEEEEE
T ss_pred             EEECCCC-EEEEec
Confidence            9999863 666543

>1ryp_H 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 3nzj_N* 3nzw_N* 3nzx_N* 1vsy_H 3l5q_B 1g65_N* 1fnt_H 1g0u_N* 1jd2_N* 1z7q_H 2f16_N* 2fak_N* 2fny_N* 2gpl_N* 2zcy_N* 3bdm_N* 3d29_N* 3dy3_N* 3dy4_N* 3e47_N* ...

Probab=100.00  E-value=2.8e-38  Score=246.19  Aligned_cols=163  Identities=14%  Similarity=0.174  Sum_probs=151.4

Q ss_pred             cccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeE
Q 029560            5 LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAM   84 (191)
Q Consensus         5 l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~i   84 (191)
                      ++.+++.+||++|++|++|++||..+|++.+.++++.+++.|++++++ ++++.+++.+++.+|.|+++     |++++|
T Consensus        34 ~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~-~~v~~la~~l~~~~~~~~~~-----~~~~~l  107 (205)
T 1ryp_H           34 YIANRVTDKLTRVHDKIWCCRSGSAADTQAIADIVQYHLELYTSQYGT-PSTETAASVFKELCYENKDN-----LTAGII  107 (205)
T ss_dssp             EEEESSCCCEEEEETTEEEEEEEBHHHHHHHHHHHHHHHHHHHHHHSS-CCHHHHHHHHHHHHHHTTTT-----CCEEEE
T ss_pred             EEEcCCcCceEEcCCCEEEEccCCHHHHHHHHHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhhhcC-----ceEEEE
Confidence            677889999999999999999999999999999999999999999999 99999999999999988652     999999


Q ss_pred             EEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEEE
Q 029560           85 VLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVG  163 (191)
Q Consensus        85 v~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei~  163 (191)
                      |||||+++||+||.+||+|++.++++.|+|+|++.++++||++|  +++||++||++++++||..+.+||..++ +++|+
T Consensus       108 vaG~D~~~gp~Ly~id~~G~~~~~~~~aiGsgs~~a~~~Le~~~--~~~~s~eea~~l~~~al~~a~~~d~~sg~~i~v~  185 (205)
T 1ryp_H          108 VAGYDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNF--RENMSKEETVDFIKHSLSQAIKWDGSSGGVIRMV  185 (205)
T ss_dssp             EEEEETTTEEEEEEECTTSCCEEESEEEESGGGGGGHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHBTTCCSCEEEE
T ss_pred             EEEEecCCCcEEEEECCCccEEecCEEEEEecHHHHHHHHHhcc--CCCCCHHHHHHHHHHHHHHHHHhCCccCCeEEEE
Confidence            99999767899999999999999999999999999999999998  4789999999999999999999998765 89999


Q ss_pred             EEEeCCCcEEEc
Q 029560          164 VVSKENPEFRVL  175 (191)
Q Consensus       164 iv~~~~~~~~~~  175 (191)
                      +|++++...+.+
T Consensus       186 vi~~~g~~~~~~  197 (205)
T 1ryp_H          186 VLTAAGVERLIF  197 (205)
T ss_dssp             EEETTEEEEEEE
T ss_pred             EEcCCCEEEEEe
Confidence            999987533334

>1iru_J 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_I* 3une_I 3unf_I* 3unh_I

Probab=100.00  E-value=4.2e-38  Score=245.14  Aligned_cols=163  Identities=17%  Similarity=0.272  Sum_probs=149.1

Q ss_pred             CCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeEEEE
Q 029560            8 HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS   87 (191)
Q Consensus         8 ~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~iv~G   87 (191)
                      +++++||++|++|++|++||..+|++.+.++++.+++.|+++++++++++.+++.+++.+  |+++  ..||++++||||
T Consensus        36 ~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~--y~~r--~~P~~v~~lvaG  111 (205)
T 1iru_J           36 TTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFRLNLYELKEGRQIKPYTLMSMVANLL--YEKR--FGPYYTEPVIAG  111 (205)
T ss_dssp             ESCCCCEEECSTTEEEECCSCHHHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHH--HTTT--TSCCSCCCEEEE
T ss_pred             ecCCccEEEeCCCEEEEccccHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHH--HHhc--CCCceEEEEEEE
Confidence            458999999999999999999999999999999999999999999999999999999999  7765  349999999999


Q ss_pred             EcC-CCCCeEEEECCCcceece-eeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEEEE
Q 029560           88 IDE-ECGPRLFKCDPAGHFFGH-KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGV  164 (191)
Q Consensus        88 ~d~-~~~p~Ly~~d~~G~~~~~-~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei~i  164 (191)
                      ||+ +++|+||.+||+|++.++ .++|+|+|++.++++||+.|  +++||++||++++++||..+.++|..++ +++|++
T Consensus       112 ~D~~~~~p~Ly~idp~G~~~~~~~~~aiG~gs~~a~~~Le~~~--~~~~s~eea~~l~~~al~~~~~~d~~s~~~i~v~v  189 (205)
T 1iru_J          112 LDPKTFKPFICSLDLIGCPMVTDDFVVSGTCAEQMYGMCESLW--EPNMDPDHLFETISQAMLNAVDRDAVSGMGVIVHI  189 (205)
T ss_dssp             ECTTSCCEEEEEECTTCCEEECSSEEEEETTHHHHHHHHHHHC--CSSCCHHHHHHHHHHHHHHHGGGBTTSCSCEEEEE
T ss_pred             EeCCCCCeEEEEECCCCCccccCCeeEeeeCHHHHHHHHhccc--CCCCCHHHHHHHHHHHHHHHHHhCcccCCceEEEE
Confidence            995 478999999999999766 56999999999999999998  4789999999999999999999998765 899999


Q ss_pred             EEeCCCcEEEcC
Q 029560          165 VSKENPEFRVLS  176 (191)
Q Consensus       165 v~~~~~~~~~~~  176 (191)
                      |++++..++.++
T Consensus       190 i~~~g~~~~~~~  201 (205)
T 1iru_J          190 IEKDKITTRTLK  201 (205)
T ss_dssp             EESSBEEEEEBC
T ss_pred             EcCCCEEEEEee
Confidence            999975455443

>3nzj_H Proteasome component PUP1; ubiquitin, protein degradation, N-terminal nucleophilic HYDR 19S regulatory particle; HET: TY5 TRO MES; 2.40A {Saccharomyces cerevisiae} PDB: 3nzw_H* 3nzx_H* 4b4t_2

Probab=100.00  E-value=6.5e-38  Score=252.07  Aligned_cols=165  Identities=18%  Similarity=0.185  Sum_probs=152.9

Q ss_pred             ccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccccee
Q 029560            4 KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVA   83 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~   83 (191)
                      .++.+++++||++|++|++|++||..+|++.+.++++.+++.|+++++++++++.+++.+++.++.|     .+||++++
T Consensus        53 ~li~~~~~~KI~~I~d~i~~~~aG~~aD~~~l~~~lr~~~~~~~~~~~~~~~v~~~a~~l~~~l~~~-----~~~~gv~l  127 (261)
T 3nzj_H           53 PIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKY-----QGHIGAYL  127 (261)
T ss_dssp             TEEEETTCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHT-----TTCSCEEE
T ss_pred             CeeccCCcceEEEEcCCEEEEeccCHHHHHHHHHHHHHHHHHhHHhhCCCCCHHHHHHHHHHHHHHh-----cCcccEEE
Confidence            5677899999999999999999999999999999999999999999999999999999999988543     47999999


Q ss_pred             EEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEE
Q 029560           84 MVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEV  162 (191)
Q Consensus        84 iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei  162 (191)
                      ||||||+ .||+||.+||+|++.++++.|+|+|++.++++||++|  .++||+|||++++++||..+.++|..++ +++|
T Consensus       128 lvaG~D~-~Gp~Ly~iDp~G~~~~~~~~aiGsgs~~a~~~Le~~~--~~~ms~eEA~~la~~al~~a~~rD~~sg~~iev  204 (261)
T 3nzj_H          128 IVAGVDP-TGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHW--KQDLTKEEAIKLASDAIQAGIWNDLGSGSNVDV  204 (261)
T ss_dssp             EEEEEET-TEEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHHC--CSSCCHHHHHHHHHHHHHHHHHHCTTCCSCEEE
T ss_pred             EEEEEeC-CCCEEEEECCCccEEecCeEEeccchHHHHHHHHHHh--ccCCCHHHHHHHHHHHHHHHHhhCCCCCCcEEE
Confidence            9999998 7899999999999999999999999999999999998  4899999999999999999999998775 8999


Q ss_pred             EEEEeCCCcEEEcCH
Q 029560          163 GVVSKENPEFRVLSI  177 (191)
Q Consensus       163 ~iv~~~~~~~~~~~~  177 (191)
                      ++|+++++ ++.+.+
T Consensus       205 ~vI~kdg~-~~~~~~  218 (261)
T 3nzj_H          205 CVMEIGKD-AEYLRN  218 (261)
T ss_dssp             EEEETTSC-EEEEEE
T ss_pred             EEEECCCc-EEEecc
Confidence            99999985 555443

>1ryp_J 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_I* 1g65_I 1vsy_J 2f16_I* 2fak_I* 2fny_I* 2gpl_I* 3d29_I* 3dy3_I* 3dy4_I* 3e47_I* 3gpj_I* 3gpt_I* 3gpw_I* 3hye_I* 3l5q_N 3mg0_I* 3mg4_I* 3oeu_I* 3oev_I* ...

Probab=100.00  E-value=1.4e-37  Score=242.02  Aligned_cols=161  Identities=17%  Similarity=0.223  Sum_probs=147.6

Q ss_pred             CCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeEEEE
Q 029560            8 HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS   87 (191)
Q Consensus         8 ~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~iv~G   87 (191)
                      +++++||++|+ |++|+++|..+|++.+.++++.+++.|+++++++++++.+++.+++.+  |+++.  .||++++||||
T Consensus        36 ~~~~~Ki~~i~-~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~--y~~~~--~P~~v~~lvaG  110 (204)
T 1ryp_J           36 SNKFEKIFHYG-HVFLGITGLATDVTTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSL--YERRF--GPYFVGPVVAG  110 (204)
T ss_dssp             ESCCCCEEEET-TEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHH--HTTTT--SCCCEEEEEEE
T ss_pred             eCCcceEEEeC-CEEEEeeEcHHHHHHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHH--HHhcC--CCceEEEEEEE
Confidence            45899999999 999999999999999999999999999999999999999999999999  77753  39999999999


Q ss_pred             EcC-CCCCeEEEECCCcceece-eeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEEEE
Q 029560           88 IDE-ECGPRLFKCDPAGHFFGH-KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGV  164 (191)
Q Consensus        88 ~d~-~~~p~Ly~~d~~G~~~~~-~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei~i  164 (191)
                      ||+ +++|+||.+||+|++.++ .++|+|+|++.++++||+.|  +++||++||++++++||..+.++|..++ +++|++
T Consensus       111 ~D~~~~gp~Ly~idp~G~~~~~~~~~aiG~gs~~a~~~Le~~~--~~~~s~eea~~l~~~al~~~~~~d~~s~~~i~v~v  188 (204)
T 1ryp_J          111 INSKSGKPFIAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLY--EPNLEPEDLFETISQALLNAADRDALSGWGAVVYI  188 (204)
T ss_dssp             ECTTTCCEEEEEECTTCCEECCSSEEEEETTHHHHHHHHHHHC--CSSCCHHHHHHHHHHHHHHHHTTBTTSCSCEEEEE
T ss_pred             EeCCCCceEEEEECCCCCccccCceeEeccCHHHHHHHHhhhc--CCCcCHHHHHHHHHHHHHHHHHhCcccCCcEEEEE
Confidence            996 478999999999999776 56999999999999999998  4789999999999999999999998765 899999


Q ss_pred             EEeCCCcEEEc
Q 029560          165 VSKENPEFRVL  175 (191)
Q Consensus       165 v~~~~~~~~~~  175 (191)
                      |++++..++.+
T Consensus       189 i~~~g~~~~~~  199 (204)
T 1ryp_J          189 IKKDEVVKRYL  199 (204)
T ss_dssp             EESSCEEEEEE
T ss_pred             EcCCCEEEEEe
Confidence            99998545444

>1iru_I 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_H* 3une_H

Probab=100.00  E-value=4.2e-37  Score=244.11  Aligned_cols=163  Identities=17%  Similarity=0.201  Sum_probs=151.0

Q ss_pred             ccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeEE
Q 029560            6 LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMV   85 (191)
Q Consensus         6 ~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~iv   85 (191)
                      +.+++++||++|++|++|++||..+|++.+.++++.+++.|+++++++++++.+++.+++.++.|     .+||++++||
T Consensus        26 ~~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~l~~~-----~~~~~v~llv  100 (234)
T 1iru_I           26 VADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGRLPRVVTANRMLKQMLFRY-----RGYIGAALVL  100 (234)
T ss_dssp             EEESSCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHCSCCCHHHHHHHHHHHHHHT-----TTCSCEEEEE
T ss_pred             eccCcccceEEecCCEEEEecCcHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHhc-----CCCCceeEEE
Confidence            44578999999999999999999999999999999999999999999999999999999988654     3599999999


Q ss_pred             EEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEEEE
Q 029560           86 LSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGV  164 (191)
Q Consensus        86 ~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei~i  164 (191)
                      ||||+ .||+||.+||+|++.++++.|+|+|++.++++||++|  +++||++||++++++||..+.++|..++ +++|++
T Consensus       101 aG~D~-~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~--~~~ms~eeA~~la~~al~~a~~~d~~sg~~i~v~v  177 (234)
T 1iru_I          101 GGVDV-TGPHLYSIYPHGSTDKLPYVTMGSGSLAAMAVFEDKF--RPDMEEEEAKNLVSEAIAAGIFNDLGSGSNIDLCV  177 (234)
T ss_dssp             EEECS-SCEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHSC--CTTCCHHHHHTHHHHHHHHHHHHCTTCCSCEEEEE
T ss_pred             EEEcC-CCCEEEEECCCCCEEecCEEEECCchHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHHHhcccCCCCEEEEE
Confidence            99998 7899999999999999999999999999999999998  4789999999999999999999998765 899999


Q ss_pred             EEeCCCcEEEcCHH
Q 029560          165 VSKENPEFRVLSIE  178 (191)
Q Consensus       165 v~~~~~~~~~~~~~  178 (191)
                      +++++  ++.+.+.
T Consensus       178 i~k~g--~~~~~~~  189 (234)
T 1iru_I          178 ISKNK--LDFLRPY  189 (234)
T ss_dssp             EETTE--EECCSEE
T ss_pred             EECCc--EEEEcce
Confidence            99985  7766643

>1m4y_A ATP-dependent protease HSLV; N-terminal catalytic threonine residue, hydrolase; 2.10A {Thermotoga maritima} SCOP: d.153.1.4

Probab=99.97  E-value=2.1e-30  Score=196.27  Aligned_cols=144  Identities=15%  Similarity=0.121  Sum_probs=125.8

Q ss_pred             ccccCCCCcceEEe-cCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            4 KLLDHTSVTHLFPI-TKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i-~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      +++.+++++||++| ++|++|+++|..+|++.+.++++.+++.|+.+         +.+.++++.+.+++++..|||+++
T Consensus        24 ~~i~~~~~~Ki~~i~~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~---------~~~~~~~l~~~~~~~~~~~~~~~~   94 (171)
T 1m4y_A           24 STVLKGNARKVRKLGEGKVLAGFAGSVADAMTLFDRFEAKLREWGGN---------LTKAAVELAKDWRTDRVLRRLEAL   94 (171)
T ss_dssp             TEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHHHHHHHHHHTTTC---------HHHHHHHHHHHHHHCTTGGGCCCE
T ss_pred             CEEEeCCcceEEEeCCCCEEEEeCccHHHHHHHHHHHHHHHHHhccc---------HHHHHHHHHHHHHHhCCCCceEEE
Confidence            67888999999999 99999999999999999999999999988743         245555555567777778899999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceecee--eeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-e
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHK--ATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-E  159 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~--~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~  159 (191)
                      +|++  |   +|+||.+||+|++.+++  +.|+|+|+++++++||+.|++ ++||.   ++++++||+.+.+||..++ +
T Consensus        95 ~lv~--D---~p~Ly~~d~~G~~~~~~~~~~a~Gsgs~~a~~~le~~~~~-~~ms~---~~l~~~al~~a~~rd~~sg~~  165 (171)
T 1m4y_A           95 LLVA--D---KENIFIISGNGEVIQPDDDAAAIGSGGPYALAAAKALLRN-TDLSA---REIVEKAMTIAGEICIYTNQN  165 (171)
T ss_dssp             EEEE--C---SSCEEEECTTSCEECCSSSEEEESTTHHHHHHHHHHHHHH-CCCCH---HHHHHHHHHHHHHHCTTCCSC
T ss_pred             EEEE--c---CCEEEEECCCCCEEecCCCEEEECCcHHHHHHHHHHhccc-CCCCH---HHHHHHHHHHHHHhCcccCCe
Confidence            9998  5   69999999999999988  999999999999999999842 78986   6789999999999999876 8


Q ss_pred             EEEEEE
Q 029560          160 IEVGVV  165 (191)
Q Consensus       160 iei~iv  165 (191)
                      ++|.++
T Consensus       166 i~v~~~  171 (171)
T 1m4y_A          166 IVIEEV  171 (171)
T ss_dssp             CEEEEC
T ss_pred             EEEEEC
Confidence            888763

>2z3b_A ATP-dependent protease HSLV; N-terminal nucleophIle hydrolase; 2.50A {Bacillus subtilis} SCOP: d.153.1.4 PDB: 2z3a_A 1yyf_D* 3ty6_A

Probab=99.97  E-value=4.1e-30  Score=196.32  Aligned_cols=145  Identities=14%  Similarity=0.142  Sum_probs=127.8

Q ss_pred             cc-ccCCCCcceEEe-cCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            4 KL-LDHTSVTHLFPI-TKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         4 ~l-~~~~~~~Ki~~i-~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      .+ +.+++++||++| ++|++|+++|..+|++.|.++++.+++.|+   +      .+.+.++++.+.++++..+|||++
T Consensus        29 ~~~i~~~~~~KI~~i~~~~i~~~~aG~~aD~~~l~~~~~~~~~~y~---g------~~~~~~~~l~~~~~~~~~~rp~~~   99 (180)
T 2z3b_A           29 QAVVMKHTARKVRKLFNGKVLAGFAGSVADAFTLFEKFEAKLEEYN---G------NLKRAAVELAKEWRSDKVLRKLEA   99 (180)
T ss_dssp             TTEEEESCCCCEEEETTTTEEEEECSCHHHHHHHHHHHHHHHHHTT---T------CHHHHHHHHHHHHHHCTTGGGCCC
T ss_pred             CceEecCCCCcEEEECCCCEEEEeCchHHHHHHHHHHHHHHHHHhc---C------ChHHHHHHHHHHHHhhhCcCcceE
Confidence            45 889999999999 999999999999999999999999999987   3      345555666777888888999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceec--eeeeecCCChHHHHHHHHHhhcCCC-CCCHHHHHHHHHHHHHhhhcccCCCC
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFG--HKATSAGLKEQEAINFLEKKMKNDP-AFTFQETVQTAISTLQSVLQEDFKAS  158 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~--~~~~a~G~gs~~~~~~Le~~~~~~~-~~s~eea~~l~~~~l~~~~~~d~~~~  158 (191)
                      ++||+  |   +|+||.+||+|++.+  +++.|+|+|+++++++||+.|++.+ +||.||   ++.+||+.+.+||..++
T Consensus       100 ~~lva--d---~p~ly~~d~~G~~~~~~~~~~a~Gsgs~~a~~~le~~~~~~~~~mt~ee---l~~~al~~a~~rd~~sg  171 (180)
T 2z3b_A          100 MLIVM--N---QDTLLLVSGTGEVIEPDDGILAIGSGGNYALAAGRALKKHAGESMSASE---IARAALETAGEICVYTN  171 (180)
T ss_dssp             CEEEE--C---SSCEEEECTTCCEECCSSSEEEESTTHHHHHHHHHHHHHHHGGGCCHHH---HHHHHHHHHHHHCTTCC
T ss_pred             EEEEE--c---CCeEEEECCCCcEEEeCCCEEEECCCHHHHHHHHHHhhhccCCCCCHHH---HHHHHHHHHHHhcCccC
Confidence            99999  4   599999999999998  4999999999999999999995211 799999   46799999999999886


Q ss_pred             -eEEEEEE
Q 029560          159 -EIEVGVV  165 (191)
Q Consensus       159 -~iei~iv  165 (191)
                       +++|.+|
T Consensus       172 ~~i~v~~i  179 (180)
T 2z3b_A          172 DQIILEEL  179 (180)
T ss_dssp             SCCEEEEE
T ss_pred             CeEEEEEE
Confidence             8999887

>1g3k_A ATP-dependent protease HSLV; hydrolase; 1.90A {Haemophilus influenzae} SCOP: d.153.1.4 PDB: 1g3i_G 1jjw_A 1kyi_G* 1ofh_G* 1ofi_G* 1e94_A* 1g4a_B* 1g4b_M 1hqy_A* 1ht1_C* 1ht2_A* 1ned_A

Probab=99.97  E-value=4.1e-30  Score=195.28  Aligned_cols=145  Identities=13%  Similarity=0.065  Sum_probs=127.0

Q ss_pred             ccccCCCCcceEEe-cCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            4 KLLDHTSVTHLFPI-TKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i-~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      .++.+++++||++| ++|++|+++|+.+|++.|.++++.+++.|+.      +   +.+.++.+.+.+++++..||+  +
T Consensus        24 ~~i~~~~~~Ki~~i~~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~------~---~~~~~~~l~~~~~~~~~~r~~--~   92 (174)
T 1g3k_A           24 NTVMKGNARKVRRLYNGKVLAGFAGGTADAFTLFELFERKLEMHQG------H---LLKSAVELAKDWRTDRALRKL--E   92 (174)
T ss_dssp             TEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHHHHHHHHHHTTT------C---HHHHHHHHHHHHHHSTTGGGC--C
T ss_pred             CeeEeCCCCcEEEECCCCEEEEeCccHHHHHHHHHHHHHHHHHhcC------c---HHHHHHHHHHHHHhccCcCcc--e
Confidence            47788999999999 9999999999999999999999999999875      2   355566666777787778886  5


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceecee---eeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHK---ATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-  158 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~---~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-  158 (191)
                      .+++|+|   +|+||.+||+|++.+++   +.|+|+|+++++++||++|+. ++||.+   +++++||+.+.+||..++ 
T Consensus        93 ~~l~g~d---~p~Ly~~d~~G~~~~~~~~~~~a~Gsgs~~a~~~le~~~~~-~~mt~~---~l~~~al~~a~~rd~~sg~  165 (174)
T 1g3k_A           93 AMLIVAD---EKESLIITGIGDVVQPEEDQILAIGSGGNYALSAARALVEN-TELSAH---EIVEKSLRIAGDICVFTNT  165 (174)
T ss_dssp             CEEEEEC---SSCEEEEETTTEEECCCTTCEEEESTTHHHHHHHHHHHHHH-CCCCHH---HHHHHHHHHHHHHCTTCCS
T ss_pred             EEEEEEC---CCEEEEEcCCCcEEecCCCcEEEEcccHHHHHHHHHHhccc-CCCCHH---HHHHHHHHHHHHhccccCC
Confidence            6888887   69999999999999988   999999999999999999942 789854   799999999999999875 


Q ss_pred             eEEEEEEE
Q 029560          159 EIEVGVVS  166 (191)
Q Consensus       159 ~iei~iv~  166 (191)
                      +++|.+|+
T Consensus       166 ~i~v~~i~  173 (174)
T 1g3k_A          166 NFTIEELP  173 (174)
T ss_dssp             CCEEEEEC
T ss_pred             ceEEEEec
Confidence            89999986

---

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	191
d1irua_	244	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	4e-60
d1rypa_	243	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	2e-48
d1irud_	243	d.153.1.4 (D:) Proteasome alpha subunit (non-catal	2e-46
d1irue_	234	d.153.1.4 (E:) Proteasome alpha subunit (non-catal	1e-44
d1iruf_	238	d.153.1.4 (F:) Proteasome alpha subunit (non-catal	6e-44
d1rypb_	250	d.153.1.4 (B:) Proteasome alpha subunit (non-catal	2e-43
d1yara1	221	d.153.1.4 (A:13-233) Proteasome alpha subunit (non	2e-42
d1irug_	245	d.153.1.4 (G:) Proteasome alpha subunit (non-catal	2e-42
d1rypd_	241	d.153.1.4 (D:) Proteasome alpha subunit (non-catal	4e-41
d1j2pa_	243	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	5e-41
d1rype_	242	d.153.1.4 (E:) Proteasome alpha subunit (non-catal	7e-41
d1iruc_	250	d.153.1.4 (C:) Proteasome alpha subunit (non-catal	1e-40
d1rypf_	233	d.153.1.4 (F:) Proteasome alpha subunit (non-catal	4e-40
d1rypg_	244	d.153.1.4 (G:) Proteasome alpha subunit (non-catal	8e-40
d1rypc_	244	d.153.1.4 (C:) Proteasome alpha subunit (non-catal	1e-37
d1irub_	233	d.153.1.4 (B:) Proteasome alpha subunit (non-catal	3e-37
d1q5qa_	227	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	1e-34
d1ryp2_	233	d.153.1.4 (2:) Proteasome beta subunit (catalytic)	2e-29
d1iruh_	202	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	6e-25
d1yarh1	203	d.153.1.4 (H:1-203) Proteasome beta subunit (catal	3e-24
d1rypl_	212	d.153.1.4 (L:) Proteasome beta subunit (catalytic)	4e-24
d1ryp1_	222	d.153.1.4 (1:) Proteasome beta subunit (catalytic)	9e-24
d1irul_	201	d.153.1.4 (L:) Proteasome beta subunit (catalytic)	2e-22
d1q5qh_	224	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	2e-22
d1j2qh_	202	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	1e-21
d1iruj_	204	d.153.1.4 (J:) Proteasome beta subunit (catalytic)	9e-21
d1ryph_	205	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	9e-20
d1irui_	220	d.153.1.4 (I:) Proteasome beta subunit (catalytic)	7e-19
d1rypk_	198	d.153.1.4 (K:) Proteasome beta subunit (catalytic)	9e-19
d1iruk_	199	d.153.1.4 (K:) Proteasome beta subunit (catalytic)	1e-16
d1rypj_	204	d.153.1.4 (J:) Proteasome beta subunit (catalytic)	1e-16

>d1irua_ d.153.1.4 (A:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 244

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  185 bits (471), Expect = 4e-60
 Identities = 114/188 (60%), Positives = 154/188 (81%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K 
Sbjct: 57  DKLLDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKR 116

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IAD SQVYTQ+A MRPLG   +++ IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +
Sbjct: 117 IADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTS 176

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEKK+K    +TF++TV+TAI+ L +VL  DFK SEIEVGVV+ ENP+FR+L+  EID 
Sbjct: 177 FLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDA 236

Query: 183 HLTAISER 190
           HL A++ER
Sbjct: 237 HLVALAER 244

>d1rypa_ d.153.1.4 (A:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 243

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  156 bits (394), Expect = 2e-48
 Identities = 89/194 (45%), Positives = 132/194 (68%), Gaps = 7/194 (3%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           DKLLD T+V+++F I++ +G++  G   DAR    +A+ EAAEFR+KYGY+MP DVLAK 
Sbjct: 52  DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR 111

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           +A+ SQ+YTQ AYMRPLGV+   +S+DEE GP ++K DPAG++ G+KAT+ G K+QE   
Sbjct: 112 MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT 171

Query: 123 FLEKKMKND-----PAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSI 177
            LE   K          ++++ V+ AI+ +   L  +F  +++EVGV +K+  +F  LS 
Sbjct: 172 NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKD--KFFTLSA 229

Query: 178 EEIDEHLTAISERD 191
           E I+E L AI+E+D
Sbjct: 230 ENIEERLVAIAEQD 243

>d1irud_ d.153.1.4 (D:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 243

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  150 bits (380), Expect = 2e-46
 Identities = 54/188 (28%), Positives = 96/188 (51%), Gaps = 3/188 (1%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
            KL D  +V  +  +   + +   G+TADAR ++ +AR E    R      + V+ + ++
Sbjct: 50  AKLQDERTVRKICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRY 109

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           IA   Q YTQ    RP G+ A+++  D +  PRL++ DP+G +   KA + G   +    
Sbjct: 110 IASLKQRYTQSNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVRE 169

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEK   ++   T   T++  I  L  V+Q   K   IE+ V+ ++    ++L+ EEI++
Sbjct: 170 FLEKNYTDEAIETDDLTIKLVIKALLEVVQSGGK--NIELAVMRRDQS-LKILNPEEIEK 226

Query: 183 HLTAISER 190
           ++  I + 
Sbjct: 227 YVAEIEKE 234

>d1irue_ d.153.1.4 (E:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 234

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  145 bits (367), Expect = 1e-44
 Identities = 50/190 (26%), Positives = 97/190 (51%), Gaps = 9/190 (4%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
             L++ +S+  +  I  ++G   +G+ ADA+TL+ +AR E     F Y   M V+ + + 
Sbjct: 49  SPLMEPSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQA 108

Query: 63  IADKSQVYTQH-----AYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKE 117
           +++ +  + +      A  RP GV  +   +DE+ GP+LF  DP+G F    A + G   
Sbjct: 109 VSNLALQFGEEDADPGAMSRPFGVALLFGGVDEK-GPQLFHMDPSGTFVQCDARAIGSAS 167

Query: 118 QEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSI 177
           + A + L++        T +E +++++  L+ V++E   A+ IE+  V      F + + 
Sbjct: 168 EGAQSSLQELYHKS--MTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQN-FHMFTK 224

Query: 178 EEIDEHLTAI 187
           EE++E +  I
Sbjct: 225 EELEEVIKDI 234

>d1iruf_ d.153.1.4 (F:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 238

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  144 bits (364), Expect = 6e-44
 Identities = 50/184 (27%), Positives = 86/184 (46%), Gaps = 4/184 (2%)

Query: 9   TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQ 68
                +  +  ++G+   G+TADAR L    R E  + RF +   +PV  L   I  K+Q
Sbjct: 55  AHQKKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQ 114

Query: 69  VYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKM 128
           + TQ    RP GV  ++   D+  GP +F+  P+ ++F  +A S G + Q A  +LE+ M
Sbjct: 115 IPTQRYGRRPYGVGLLIAGYDDM-GPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHM 173

Query: 129 KNDPAFTFQETVQTAISTLQSVLQ--EDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTA 186
                    E V+  +  L+  L   +D     + +G+V K+   F +   +++   L  
Sbjct: 174 SEFMECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLE-FTIYDDDDVSPFLEG 232

Query: 187 ISER 190
           + ER
Sbjct: 233 LEER 236

>d1rypb_ d.153.1.4 (B:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 250

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  143 bits (361), Expect = 2e-43
 Identities = 56/200 (28%), Positives = 98/200 (49%), Gaps = 17/200 (8%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAA-EFRFKYGYEMPVDVLAK 61
             L    +++ +  +T  +G + +GM  D R LV ++R  A   ++  YG   P  +L  
Sbjct: 53  SPLAMSETLSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVS 112

Query: 62  WIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAI 121
            +A   Q  TQ   +RP GV  ++   DE  G  L++ DP+G +F  KAT+ G     A 
Sbjct: 113 EVAKIMQEATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAK 172

Query: 122 NFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPE---------- 171
            FLEK+  ++     ++ +  A+ TL+  ++ +F    IE+ ++  ENP+          
Sbjct: 173 TFLEKRWNDE--LELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTD 230

Query: 172 ----FRVLSIEEIDEHLTAI 187
               FR L+ +EI++ L A+
Sbjct: 231 KGPRFRKLTSQEINDRLEAL 250

>d1yara1 d.153.1.4 (A:13-233) Proteasome alpha subunit (non-catalytic) {Archaeon Thermoplasma acidophilum [TaxId: 2303]} Length = 221

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

 Score =  139 bits (352), Expect = 2e-42
 Identities = 61/182 (33%), Positives = 100/182 (54%), Gaps = 4/182 (2%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
            +L++  S+  +  I  Y+  + +G+ ADAR LV  AR  A + +  YG  + ++ L K 
Sbjct: 44  SRLIEQNSIEKIQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKR 103

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           +AD+ Q YTQ+  +RP GV  +   ID+  GPRLF CDPAG    +KAT+ G  +   ++
Sbjct: 104 VADQMQQYTQYGGVRPYGVSLIFAGIDQI-GPRLFDCDPAGTINEYKATAIGSGKDAVVS 162

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLE++ K +     +E V   I  L+S L+E  +    E+  ++  N  +R+   EE+ +
Sbjct: 163 FLEREYKEN--LPEKEAVTLGIKALKSSLEEGEELKAPEIASITVGNK-YRIYDQEEVKK 219

Query: 183 HL 184
            L
Sbjct: 220 FL 221

>d1irug_ d.153.1.4 (G:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 245

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  140 bits (353), Expect = 2e-42
 Identities = 52/187 (27%), Positives = 89/187 (47%), Gaps = 3/187 (1%)

Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
           L +  S   LF + +++G+   G+ ADAR+L   AR EA+ FR  +GY +P+  LA  +A
Sbjct: 57  LYEEGSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVA 116

Query: 65  DKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFL 124
                YT ++ +RP G   M+ S     G +L+  DP+G  +G+   + G   Q A   +
Sbjct: 117 MYVHAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEI 176

Query: 125 EKKMKNDPAFTFQETVQTAISTLQSVLQE-DFKASEIEVGVVSKENPEFRVLSIEEIDEH 183
           EK    +   T ++ V+     +  V  E   KA E+E+  V +       +  ++I E 
Sbjct: 177 EKLQMKE--MTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREE 234

Query: 184 LTAISER 190
               ++ 
Sbjct: 235 AEKYAKE 241

>d1rypd_ d.153.1.4 (D:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 241

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  137 bits (345), Expect = 4e-41
 Identities = 56/191 (29%), Positives = 97/191 (50%), Gaps = 6/191 (3%)

Query: 3   DKLLD-HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAK 61
            KL D   + + +  I  ++ L  +G+ AD+R L+++AR EA   R      + V+ L +
Sbjct: 50  LKLQDTRITPSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTR 109

Query: 62  WIADKSQVYTQHAYMRPLGVVAMVLSIDEE-CGPRLFKCDPAGHFFGHKATSAGLKEQEA 120
           ++A   Q YTQ   +RP GV  ++   D     P+L++ +P+G +    A + G   +  
Sbjct: 110 YVAGVQQRYTQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTV 169

Query: 121 INFLEKKMK-NDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEE 179
             FLEK     +P  T +E V+  + +L  V+Q   K   IE+ VV  ++     LS EE
Sbjct: 170 REFLEKNYDRKEPPATVEECVKLTVRSLLEVVQTGAK--NIEITVVKPDSD-IVALSSEE 226

Query: 180 IDEHLTAISER 190
           I++++T I + 
Sbjct: 227 INQYVTQIEQE 237

>d1j2pa_ d.153.1.4 (A:) Proteasome alpha subunit (non-catalytic) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 243

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score =  137 bits (345), Expect = 5e-41
 Identities = 56/188 (29%), Positives = 101/188 (53%), Gaps = 4/188 (2%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
            KLL+  ++  ++ I +++    +G+ ADAR L+ +AR EA   R  Y   + V  LAK 
Sbjct: 53  SKLLEKDTIEKIYKIDEHICAATSGLVADARVLIDRARIEAQINRLTYDIPITVKELAKK 112

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           I D  Q YTQ+  +RP GV  ++  ++E   P+L++ DP+G    +KAT+ G+       
Sbjct: 113 ICDFKQQYTQYGGVRPFGVSLLIAGVNEV--PKLYETDPSGALLEYKATAIGMGRMAVTE 170

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           F EK+ ++D   +F + +   +  +   ++ +     IEVG V  ++  F+ +S EE+  
Sbjct: 171 FFEKEYRDD--LSFDDAMVLGLVAMGLSIESELVPENIEVGYVKVDDRTFKEVSPEELKP 228

Query: 183 HLTAISER 190
           ++   +ER
Sbjct: 229 YVERANER 236

>d1rype_ d.153.1.4 (E:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 242

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  136 bits (343), Expect = 7e-41
 Identities = 43/195 (22%), Positives = 94/195 (48%), Gaps = 9/195 (4%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
             LL+  S+  +  I +++G   +G+TADAR++++ AR  A      Y  ++ V+ L + 
Sbjct: 48  SPLLESDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQS 107

Query: 63  IADKSQVYTQH------AYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLK 116
           + D +  + +          RP GV  ++   D + G +LF  +P+G F+ + A + G  
Sbjct: 108 VCDLALRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSG 167

Query: 117 EQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLS 176
            + A   L  +  +    T +E     +  L+ V++E    +  ++  ++K++  F++  
Sbjct: 168 SEGAQAELLNEWHSS--LTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDG-FKIYD 224

Query: 177 IEEIDEHLTAISERD 191
            E+  E +  + E++
Sbjct: 225 NEKTAELIKELKEKE 239

>d1iruc_ d.153.1.4 (C:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 250

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  135 bits (342), Expect = 1e-40
 Identities = 49/193 (25%), Positives = 93/193 (48%), Gaps = 5/193 (2%)

Query: 3   DKLLDHTSVTH-LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAK 61
            KLLD    +  ++ + + +     G+T+DA  L  + R  A  +  +Y   +P + L  
Sbjct: 52  HKLLDEVFFSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVT 111

Query: 62  WIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAI 121
            + D  Q YTQ    RP GV  + +  D+  G +L++ DP+G++ G KAT  G     A+
Sbjct: 112 ALCDIKQAYTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAV 171

Query: 122 NFLEKKMKNDPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPE--FRVLSIE 178
           + L++    +   T +  +  AI  L   +      A ++E+  +++EN +   RVL  +
Sbjct: 172 SMLKQD-YKEGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQK 230

Query: 179 EIDEHLTAISERD 191
           E+++ +    E +
Sbjct: 231 EVEQLIKKHEEEE 243

>d1rypf_ d.153.1.4 (F:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 233

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  134 bits (338), Expect = 4e-40
 Identities = 36/179 (20%), Positives = 77/179 (43%), Gaps = 5/179 (2%)

Query: 9   TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQ 68
           +    +    +++GL   G+  DAR L    R +       +  ++ V+     + DK+Q
Sbjct: 57  SYQKKIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQ 116

Query: 69  VYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKM 128
             TQ    RP GV  +++  D + G  L +  P+G+      T+ G + Q A  +LE+ +
Sbjct: 117 KNTQSYGGRPYGVGLLIIGYD-KSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTL 175

Query: 129 KND--PAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEHL 184
                      E ++  +  +   L+++      + + +V K+ P F +   E + +++
Sbjct: 176 DTFIKIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTP-FTIYDGEAVAKYI 233

>d1rypg_ d.153.1.4 (G:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 244

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  133 bits (337), Expect = 8e-40
 Identities = 43/192 (22%), Positives = 87/192 (45%), Gaps = 4/192 (2%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
            KLL       +  + +++G + +G+  D R LV + R EAA F+  Y   +P+   A  
Sbjct: 52  SKLLVPQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADR 111

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           +    Q +T +  +RP GV  +   +D+  G  L+  +P+G ++G+K  + G   Q A  
Sbjct: 112 LGQYVQAHTLYNSVRPFGVSTIFGGVDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKA 170

Query: 123 FLEKKMKN-DPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPE-FRVLSIEE 179
            LEK + +     + +E V+ A   +    +++  K  E+E+   S             +
Sbjct: 171 ELEKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGD 230

Query: 180 IDEHLTAISERD 191
           + +     ++++
Sbjct: 231 LLQEAIDFAQKE 242

>d1rypc_ d.153.1.4 (C:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 244

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  127 bits (321), Expect = 1e-37
 Identities = 49/185 (26%), Positives = 85/185 (45%), Gaps = 7/185 (3%)

Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
           L   TS   L+ +   + +   G+TADA  L+  AR  A  +   Y  ++PV++L + ++
Sbjct: 56  LEQDTSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLS 115

Query: 65  DKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFL 124
           D  Q YTQH  +RP GV  +    D+  G +L+  +P+G++ G KA S G     A   L
Sbjct: 116 DIKQGYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLL 175

Query: 125 EKKMKNDPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPE----FRVLSIEE 179
           +   K+D      + ++ A+ TL             +E   + K   +     ++   +E
Sbjct: 176 QMDYKDD--MKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQE 233

Query: 180 IDEHL 184
           I + L
Sbjct: 234 IKDIL 238

>d1irub_ d.153.1.4 (B:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 233

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  127 bits (319), Expect = 3e-37
 Identities = 64/186 (34%), Positives = 97/186 (52%), Gaps = 5/186 (2%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
             L D  SV  + PITK++GL+ +GM  D R LV +AR  A ++   Y   +P   L + 
Sbjct: 53  SILYDERSVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQR 112

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           +A   Q YTQ   +RP GV  ++   +E   P LF+ DP+G +F  KAT+ G        
Sbjct: 113 VASVMQEYTQSGGVRPFGVSLLICGWNEGR-PYLFQSDPSGAYFAWKATAMGKNYVNGKT 171

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 182
           FLEK+   D     ++ + TAI TL+   +       IEVG+ ++    FR L+  E+ +
Sbjct: 172 FLEKRYNED--LELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAG--FRRLTPTEVKD 227

Query: 183 HLTAIS 188
           +L AI+
Sbjct: 228 YLAAIA 233

>d1q5qa_ d.153.1.4 (A:) Proteasome alpha subunit (non-catalytic) {Rhodococcus erythropolis [TaxId: 1833]} Length = 227

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Rhodococcus erythropolis [TaxId: 1833]

 Score =  119 bits (300), Expect = 1e-34
 Identities = 30/190 (15%), Positives = 63/190 (33%), Gaps = 15/190 (7%)

Query: 9   TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGY-EMPVDVLAKWIADKS 67
           T++  +  +   LG  A G   +   L +     A    + Y   ++    LA   A   
Sbjct: 40  TALHKVSELYDRLGFAAVGKYNEFENLRRAGIVHADMRGYSYDRRDVTGRSLANAYAQT- 98

Query: 68  QVYTQHAYMRPLGVVAMVLSIDE---ECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN-F 123
                    +P  V   V  +        P+L++    G     +         E I   
Sbjct: 99  LGTIFTEQPKPYEVEICVAEVGRVGSPKAPQLYRITYDGSIVDEQHFVVMGGTTEPIATA 158

Query: 124 LEKKMKNDPAFTFQETVQTAISTLQSVLQED-----FKASEIEVGVVSKENPE--FRVLS 176
           + +  + D     +  V  A++ L+     +        + +EV V+ +  P   FR ++
Sbjct: 159 MRESYRAD--LDLEAAVGIAVNALRQGGAGEGEKRNVDVASLEVAVLDQSRPRRAFRRIA 216

Query: 177 IEEIDEHLTA 186
              +++ + A
Sbjct: 217 GTALEQLVPA 226

>d1ryp2_ d.153.1.4 (2:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 233

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  106 bits (266), Expect = 2e-29
 Identities = 25/198 (12%), Positives = 65/198 (32%), Gaps = 12/198 (6%)

Query: 2   QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKY-----GYEMPV 56
              LL    V  L P+     +  +G  +D + + +  +    E  +          +  
Sbjct: 30  YGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLADAEEALEP 89

Query: 57  DVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLK 116
             + +++A    +Y + + M PL    +V  +       L   +  G  +     + G  
Sbjct: 90  SYIFEYLAT--VMYQRRSKMNPLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFG 147

Query: 117 EQEAINFLEKKMKNDPAF---TFQETVQTAISTLQSVLQEDFKASE-IEVGVVSKENPEF 172
              A   L K +  +      T Q   +  ++ ++ +   D ++S    + ++ K     
Sbjct: 148 AHMANPLLRKVVDRESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKNTG-L 206

Query: 173 RVLSIEEIDEHLTAISER 190
                 +++      ++ 
Sbjct: 207 TFKKNLQVENMKWDFAKD 224

>d1iruh_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 202

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score = 94.4 bits (234), Expect = 6e-25
 Identities = 26/184 (14%), Positives = 59/184 (32%), Gaps = 8/184 (4%)

Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
            + +     L PI   +    +G  AD + +     Y+      +      V   A    
Sbjct: 25  YIANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFK 84

Query: 65  DKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFL 124
           +       + Y   L    ++   D + G +++     G          G        ++
Sbjct: 85  EM-----CYRYREDLMAGIIIAGWDPQEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYV 139

Query: 125 EKKMKNDPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEH 183
           +   +     T +E +Q   + L   ++ D      I +  +++   E +VL  ++I + 
Sbjct: 140 DATYREG--MTKEECLQFTANALALAMERDGSSGGVIRLAAIAESGVERQVLLGDQIPKF 197

Query: 184 LTAI 187
             A 
Sbjct: 198 AVAT 201

>d1yarh1 d.153.1.4 (H:1-203) Proteasome beta subunit (catalytic) {Archaeon Thermoplasma acidophilum [TaxId: 2303]} Length = 203

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

 Score = 92.2 bits (228), Expect = 3e-24
 Identities = 41/186 (22%), Positives = 74/186 (39%), Gaps = 10/186 (5%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
           +  + H +   LF I  Y G+   G+  DA+ LV+  + E   +R +    MP++ +A  
Sbjct: 23  ENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKAELELYRLQRRVNMPIEAVATL 82

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
           +++         YM  L    +V  ID      +F  D AG        S G        
Sbjct: 83  LSNMLNQVKYMPYMVQL----LVGGIDTAP--HVFSIDAAGGSVEDIYASTGSGSPFVYG 136

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEID 181
            LE +       T  E V   I  + +  Q D      I+V V+++++  +  L  ++I+
Sbjct: 137 VLESQYSEK--MTVDEGVDLVIRAISAAKQRDSASGGMIDVAVITRKDG-YVQLPTDQIE 193

Query: 182 EHLTAI 187
             +  +
Sbjct: 194 SRIRKL 199

>d1rypl_ d.153.1.4 (L:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 212

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 92.1 bits (228), Expect = 4e-24
 Identities = 24/187 (12%), Positives = 60/187 (32%), Gaps = 9/187 (4%)

Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
            +   +V  +  I  +L     G  AD +        +      +    + V   +K ++
Sbjct: 25  WVASQTVKRVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREKERISVAAASKILS 84

Query: 65  DKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFL 124
           +    Y        L +  M+     + GP ++  D  G          G  +  A   L
Sbjct: 85  NLVYQYKGA----GLSMGTMICGYTRKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVL 140

Query: 125 EKKMKNDPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEH 183
           +   K D   + ++ +     ++ +    D +    + +  V+++   +      ++ E 
Sbjct: 141 DSNYKWD--LSVEDALYLGKRSILAAAHRDAYSGGSVNLYHVTEDG--WIYHGNHDVGEL 196

Query: 184 LTAISER 190
              + E 
Sbjct: 197 FWKVKEE 203

>d1ryp1_ d.153.1.4 (1:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 222

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 91.4 bits (226), Expect = 9e-24
 Identities = 26/183 (14%), Positives = 64/183 (34%), Gaps = 19/183 (10%)

Query: 2   QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAK 61
            D  ++      +F     + + A G  AD   LV++ +     + F +  +        
Sbjct: 31  TDYSINSRYEPKVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKLSI---N 87

Query: 62  WIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAI 121
             A   Q         P  V  ++  +DE+    ++  DP G +   +  + G      +
Sbjct: 88  SAARNIQHLLYGKRFFPYYVHTIIAGLDEDGKGAVYSFDPVGSYEREQCRAGGAAASLIM 147

Query: 122 NFLEKKMKNDPAF---------------TFQETVQTAISTLQSVLQEDFKASE-IEVGVV 165
            FL+ ++     +               + +E ++    +  S  +   +  + +E+ +V
Sbjct: 148 PFLDNQVNFKNQYEPGTNGKVKKPLKYLSVEEVIKLVRDSFTSATERHIQVGDGLEILIV 207

Query: 166 SKE 168
           +K+
Sbjct: 208 TKD 210

>d1irul_ d.153.1.4 (L:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 201

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score = 87.5 bits (216), Expect = 2e-22
 Identities = 24/181 (13%), Positives = 58/181 (32%), Gaps = 10/181 (5%)

Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
            +   +V  +  I  YL     G  AD     +    +   +  +    + V   +K +A
Sbjct: 25  YIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQCRIYELRNKERISVAAASKLLA 84

Query: 65  DKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFL 124
           +    Y           +  ++   ++ GP L+  D  G+       S G     A   +
Sbjct: 85  NMVYQYKGMGLS-----MGTMICGWDKRGPGLYYVDSEGNRISGATFSVGSGSVYAYGVM 139

Query: 125 EKKMKNDPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEH 183
           ++    D     ++    A   +      D +    + +  V ++   +  +S + + + 
Sbjct: 140 DRGYSYD--LEVEQAYDLARRAIYQATYRDAYSGGAVNLYHVRED--GWIRVSSDNVADL 195

Query: 184 L 184
            
Sbjct: 196 H 196

>d1q5qh_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Rhodococcus erythropolis [TaxId: 1833]} Length = 224

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Rhodococcus erythropolis [TaxId: 1833]

 Score = 88.0 bits (217), Expect = 2e-22
 Identities = 37/198 (18%), Positives = 62/198 (31%), Gaps = 14/198 (7%)

Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
           L+    V  ++   +Y      G    A  LV+    E   +    G  +  D  A  +A
Sbjct: 25  LIASRDVEKVYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEGVPLTFDGKANRLA 84

Query: 65  DKSQVYTQHAY----MRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKA--TSAGLKEQ 118
              +     A     + PL V   + + DE    R+   D  G  +  +A   + G    
Sbjct: 85  SMVRGNLGAAMQGLAVVPLLVGYDLDADDESRAGRIVSYDVVGGRYEERAGYHAVGSGSL 144

Query: 119 EAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQED------FKASEIEVGVVSKENPEF 172
            A + L+K    D     +  ++ AI +L     +D           I    V+      
Sbjct: 145 FAKSALKKIYSPD--SDEETALRAAIESLYDAADDDSATGGPDLTRGIYPTAVTITQAGA 202

Query: 173 RVLSIEEIDEHLTAISER 190
             +S E   E    I   
Sbjct: 203 VHVSEETTSELARRIVAE 220

>d1j2qh_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 202

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 85.6 bits (211), Expect = 1e-21
 Identities = 34/189 (17%), Positives = 73/189 (38%), Gaps = 11/189 (5%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
              +   +   ++ I   + +   G   DA+ L +  + EA  +  +   +  V  +A  
Sbjct: 23  GNFIASKAAKKIYQIADRMAMTTAGSVGDAQFLARIIKIEANLYEIRRERKPTVRAIATL 82

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHK-ATSAGLKEQEAI 121
            ++    Y    Y+     V +++   +  G  ++  DP G     K   + G     A 
Sbjct: 83  TSNLLNSYRYFPYL-----VQLLIGGIDSEGKSIYSIDPIGGAIEEKDIVATGSGSLTAY 137

Query: 122 NFLEKKMKNDPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEI 180
             LE +   +      E V+ A+  + S ++ D      I+V  ++++  EF   S EE+
Sbjct: 138 GVLEDRFTPE--IGVDEAVELAVRAIYSAMKRDSASGDGIDVVKITED--EFYQYSPEEV 193

Query: 181 DEHLTAISE 189
           ++ L    +
Sbjct: 194 EQILAKFRK 202

>d1iruj_ d.153.1.4 (J:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 204

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score = 83.4 bits (205), Expect = 9e-21
 Identities = 25/175 (14%), Positives = 58/175 (33%), Gaps = 7/175 (4%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
              L  T    +FP+   L +   G+  D +T+ Q+ ++    +  K G ++    L   
Sbjct: 30  QAQLVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFRLNLYELKEGRQIKPYTLMSM 89

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGP-RLFKCDPAGHFFGHKATSAGLKEQEAI 121
           +A+            P     ++  +D +     +   D  G               E +
Sbjct: 90  VAN----LLYEKRFGPYYTEPVIAGLDPKTFKPFICSLDLIGCPMVTDDFVVSGTCAEQM 145

Query: 122 NFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASE-IEVGVVSKENPEFRVL 175
             + + +  +P        +T    + + +  D  +   + V ++ K+    R L
Sbjct: 146 YGMCESL-WEPNMDPDHLFETISQAMLNAVDRDAVSGMGVIVHIIEKDKITTRTL 199

>d1ryph_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 205

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 80.6 bits (198), Expect = 9e-20
 Identities = 24/181 (13%), Positives = 56/181 (30%), Gaps = 9/181 (4%)

Query: 3   DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKW 62
              + +     L  +   +    +G  AD + +    +Y    +  +YG           
Sbjct: 32  GAYIANRVTDKLTRVHDKIWCCRSGSAADTQAIADIVQYHLELYTSQYGTPST------E 85

Query: 63  IADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN 122
            A        +     L    +V   D++    ++     G         AG        
Sbjct: 86  TAASVFKELCYENKDNLTAGIIVAGYDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYG 145

Query: 123 FLEKKMKNDPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEID 181
           + +K  + +   + +ETV     +L   ++ D      I + V++    E  +   +E +
Sbjct: 146 YCDKNFREN--MSKEETVDFIKHSLSQAIKWDGSSGGVIRMVVLTAAGVERLIFYPDEYE 203

Query: 182 E 182
           +
Sbjct: 204 Q 204

>d1irui_ d.153.1.4 (I:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 220

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score = 78.7 bits (193), Expect = 7e-19
 Identities = 28/169 (16%), Positives = 53/169 (31%), Gaps = 9/169 (5%)

Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
           ++   + + +  I+  +     G  AD     Q             G    V    + + 
Sbjct: 25  VVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGRLPRVVTANRMLK 84

Query: 65  DKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFL 124
                     Y   +G   ++  +D   GP L+   P G        + G     A+   
Sbjct: 85  QM-----LFRYRGYIGAALVLGGVDVT-GPHLYSIYPHGSTDKLPYVTMGSGSLAAMAVF 138

Query: 125 EKKMKNDPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEF 172
           E K + D     +E        + + +  D    S I++ V+SK   +F
Sbjct: 139 EDKFRPD--MEEEEAKNLVSEAIAAGIFNDLGSGSNIDLCVISKNKLDF 185

>d1rypk_ d.153.1.4 (K:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 198

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 77.9 bits (191), Expect = 9e-19
 Identities = 23/178 (12%), Positives = 59/178 (33%), Gaps = 8/178 (4%)

Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
            +   S      ++ +  +   G   D     +  +     +  +  YE+    ++ ++ 
Sbjct: 26  SVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYIQANIQLYSIREDYELSPQAVSSFVR 85

Query: 65  DKSQVYTQHAYMRPLGVVAMVLSIDEEC-GPRLFKCDPAGHFFGHKATSAGLKEQEAINF 123
            +     +    RP  V  ++   D++   P L++ D  G        + G       + 
Sbjct: 86  QELAKSIR--SRRPYQVNVLIGGYDKKKNKPELYQIDYLGTKVELPYGAHGYSGFYTFSL 143

Query: 124 LEKKMKNDPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEI 180
           L+   +  P  T +E +      +Q + +        + V +V K+    R +   + 
Sbjct: 144 LDHHYR--PDMTTEEGLDLLKLCVQELEKRMPMDFKGVIVKIVDKD--GIRQVDDFQA 197

>d1iruk_ d.153.1.4 (K:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 199

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score = 72.6 bits (177), Expect = 1e-16
 Identities = 25/179 (13%), Positives = 57/179 (31%), Gaps = 12/179 (6%)

Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
           +        +F +++ + LL  G   D     +  +     ++ + GYE+     A +  
Sbjct: 26  VQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYIQKNVQLYKMRNGYELSPTAAANFTR 85

Query: 65  DKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFL 124
                  +     P  V  ++   DE  GP L+  D           + G      ++ L
Sbjct: 86  RNLADCLR--SRTPYHVNLLLAGYDEHEGPALYYMDYLAALAKAPFAAHGYGAFLTLSIL 143

Query: 125 EKKMKNDPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEIDE 182
           ++        + +  V+     L+ + +          V ++ K         I ++D 
Sbjct: 144 DRYYTPT--ISRERAVELLRKCLEELQKRFILNLPTFSVRIIDKNG-------IHDLDN 193

>d1rypj_ d.153.1.4 (J:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 204

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 72.5 bits (177), Expect = 1e-16
 Identities = 28/173 (16%), Positives = 57/173 (32%), Gaps = 8/173 (4%)

Query: 5   LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 64
           L        +F     + L  TG+  D  TL +  RY+   ++ K    +  +   + ++
Sbjct: 33  LGVSNKFEKIFHYGH-VFLGITGLATDVTTLNEMFRYKTNLYKLKEERAIEPETFTQLVS 91

Query: 65  DKSQVYTQHAYMRPLGVVAMVLSIDEECG-PRLFKCDPAGHFFGHKATSAGLKEQEAINF 123
                     Y     V  +V  I+ + G P +   D  G     K         + +  
Sbjct: 92  SSLYERRFGPYF----VGPVVAGINSKSGKPFIAGFDLIGCIDEAKDFIVSGTASDQLFG 147

Query: 124 LEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASE-IEVGVVSKENPEFRVL 175
           + + +   P    ++  +T    L +    D  +     V ++ K+    R L
Sbjct: 148 MCESLYE-PNLEPEDLFETISQALLNAADRDALSGWGAVVYIIKKDEVVKRYL 199

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	191
d1irua_	244	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rypa_	243	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1iruc_	250	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1j2pa_	243	Proteasome alpha subunit (non-catalytic) {Archaeon	100.0
d1yara1	221	Proteasome alpha subunit (non-catalytic) {Archaeon	100.0
d1irue_	234	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rype_	242	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1irug_	245	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1iruf_	238	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rypb_	250	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1rypf_	233	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1irud_	243	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rypd_	241	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1rypc_	244	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1yarh1	203	Proteasome beta subunit (catalytic) {Archaeon Ther	100.0
d1irub_	233	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rypg_	244	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1irul_	201	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d1j2qh_	202	Proteasome beta subunit (catalytic) {Archaeon Arch	100.0
d1rypk_	198	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1rypl_	212	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1ryph_	205	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1iruh_	202	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d1q5qa_	227	Proteasome alpha subunit (non-catalytic) {Rhodococ	100.0
d1ryp2_	233	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1irui_	220	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d1iru2_	217	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d1rypi_	222	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1q5qh_	224	Proteasome beta subunit (catalytic) {Rhodococcus e	100.0
d1ryp1_	222	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1iruj_	204	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d1rypj_	204	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1iruk_	199	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d1iru1_	213	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d1m4ya_	171	HslV (ClpQ) protease {Thermotoga maritima [TaxId:	99.72
d2z3ba1	180	HslV (ClpQ) protease {Bacillus subtilis [TaxId: 14	99.67
d1g3ka_	173	HslV (ClpQ) protease {Haemophilus influenzae [TaxI	99.66
d1cuka1	48	DNA helicase RuvA subunit, C-terminal domain {Esch	83.17

>d1irua_ d.153.1.4 (A:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=5.6e-48  Score=306.56  Aligned_cols=189  Identities=60%  Similarity=0.964  Sum_probs=181.5

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      +++++.+++++|||+|++|++|++||+.+|++.+.+.+|.+++.|++.++++++++.+++.+++++|.||+++++|||+|
T Consensus        56 ~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rP~~v  135 (244)
T d1irua_          56 PDKLLDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGC  135 (244)
T ss_dssp             CCSSBCGGGCCSEEESSSSCEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSBCCCSE
T ss_pred             ccccccCCccceEEEecCCcEEEEecchHHHHHHHHHHHHHHHHHHHHcCCCCCchHHHHHHHHHHHHHhcccccCccce
Confidence            46777788999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCCeEE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIE  161 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~~ie  161 (191)
                      ++||+|||+++||+||.+||+|++.+++++|+|+|++.++++||++|.+.++||++||++++++||+.+.++|..+++++
T Consensus       136 ~~ll~G~D~~~g~~Ly~~Dp~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~d~t~eeai~l~~~~l~~~~~~d~~~~~ie  215 (244)
T d1irua_         136 CMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIE  215 (244)
T ss_dssp             EEEEEEEETTTEEEEEEECTTSCEEEBSEEEEETTHHHHHHHHHHHTTSCCCCCHHHHHHHHHHHHHHHTTCCCCTTSEE
T ss_pred             eeEEEEEcCCCCcEEEEEcCCccEEecceEeccCchhHHHHHHHhccccccCCCHHHHHHHHHHHHHHHHhcCCCCCcEE
Confidence            99999999867899999999999999999999999999999999999767899999999999999999999998888999


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHHHHHhhcc
Q 029560          162 VGVVSKENPEFRVLSIEEIDEHLTAISER  190 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~~~~~~~~  190 (191)
                      |+|+++++++|++++++||+++|.++++|
T Consensus       216 v~ii~~~~~~~~~l~~~ei~~~l~~~~~r  244 (244)
T d1irua_         216 VGVVTVENPKFRILTEAEIDAHLVALAER  244 (244)
T ss_dssp             EEEEETTEEEEEECCHHHHHHHHHHHHTC
T ss_pred             EEEEEeCCCcEEECCHHHHHHHHHHHhcC
Confidence            99999998789999999999999999886

>d1rypa_ d.153.1.4 (A:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=2.5e-45  Score=291.02  Aligned_cols=188  Identities=47%  Similarity=0.768  Sum_probs=179.2

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      +++++.+++++||++|++|++|++||+.+|++.+.++++.+++.|++.++++++++.+++.+++.+|.|+++.+.|||+|
T Consensus        51 ~~~l~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~ls~~~~~~~~~~~~rP~~v  130 (243)
T d1rypa_          51 PDKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQRAYMRPLGV  130 (243)
T ss_dssp             CCTTBCGGGCCSEEECSSSCEEEEESCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTSCCCSC
T ss_pred             cccccccCcccceEecCCCEEEEEecCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcccccCccc
Confidence            46788889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcC-----CCCCCHHHHHHHHHHHHHhhhcccCC
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKN-----DPAFTFQETVQTAISTLQSVLQEDFK  156 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~-----~~~~s~eea~~l~~~~l~~~~~~d~~  156 (191)
                      ++||+|||+++||+||.+||+|++.+++++|+|+|+..++++||++|++     .+++|.+||++++++||+.+.++|..
T Consensus       131 ~~ll~G~D~~~g~~Ly~~Dp~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~~~~~~s~eeav~la~~~l~~~~~~d~~  210 (243)
T d1rypa_         131 ILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFS  210 (243)
T ss_dssp             EEEEEEEETTTEEEEEEECTTSCEEEBSEEEESTTHHHHHHHHHHHHHHHCSSSCCCSSHHHHHHHHHHHHHHHHTCCCC
T ss_pred             eEEEEEEccCCCCeEEEEcCCEEEEecceEEeCccHHHHHHHHHHHhhcccccccccccHHHHHHHHHHHHHHHhhccCC
Confidence            9999999987789999999999999999999999999999999999952     35789999999999999999999987


Q ss_pred             CCeEEEEEEEeCCCcEEEcCHHHHHHHHHHhhccC
Q 029560          157 ASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD  191 (191)
Q Consensus       157 ~~~iei~iv~~~~~~~~~~~~~~i~~~~~~~~~~~  191 (191)
                      ..+++|+++++++  |++++++||++++..+++||
T Consensus       211 ~~~iei~iitk~g--~~~l~~eeI~~~l~~i~e~~  243 (243)
T d1rypa_         211 KNDLEVGVATKDK--FFTLSAENIEERLVAIAEQD  243 (243)
T ss_dssp             TTSEEEEEEETTE--EEECCHHHHHHHHHHHTTTC
T ss_pred             CCcEEEEEEeCCc--eEEeCHHHHHHHHHHHhccC
Confidence            7799999999985  99999999999999999998

>d1iruc_ d.153.1.4 (C:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=8.6e-45  Score=289.07  Aligned_cols=186  Identities=25%  Similarity=0.449  Sum_probs=174.1

Q ss_pred             cccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeE
Q 029560            5 LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAM   84 (191)
Q Consensus         5 l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~i   84 (191)
                      ++.+++.+|||+|++|++|++||+.+|++.+++.++.++..|++.++++++++.+++.+++++|.|+++.++|||+|++|
T Consensus        55 ~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~i~~~~la~~l~~~~~~~~~~~~~rP~~~~~l  134 (250)
T d1iruc_          55 LDEVFFSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLL  134 (250)
T ss_dssp             BCCCSSCSSEEECSSSEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBSSCCCCCEEEE
T ss_pred             cccCcccceEEECCCcEEEEeecccchHHHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHHHhhhccCCcceEEEE
Confidence            34567889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEEE
Q 029560           85 VLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVG  163 (191)
Q Consensus        85 v~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei~  163 (191)
                      |+|||+++||+||.+||+|++.+++++|+|+|++.++++||++|+ .++||++||++++++||+.+.++|..++ +++|+
T Consensus       135 i~G~D~~~gp~Ly~~Dp~G~~~~~~~~a~G~gs~~a~~~Le~~y~-~~~ms~eeai~la~~al~~~~~~d~~~~~~iei~  213 (250)
T d1iruc_         135 YIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK-EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIA  213 (250)
T ss_dssp             EEEEETTTEEEEEEEETTTEEEECSEEEESTTTTHHHHHHHHHCC-TTCCCHHHHHHHHHHHHHHSSSCTTCCSTTCEEE
T ss_pred             EEEEcCCCCCEEEEEcccccEeeeeEEEeCcChHHHHHHHHhhcc-cCCCCHHHHHHHHHHHHHHHhcccCCCCCeEEEE
Confidence            999998678999999999999999999999999999999999984 3589999999999999999999886665 89999


Q ss_pred             EEEeCCCc--EEEcCHHHHHHHHHHhhccC
Q 029560          164 VVSKENPE--FRVLSIEEIDEHLTAISERD  191 (191)
Q Consensus       164 iv~~~~~~--~~~~~~~~i~~~~~~~~~~~  191 (191)
                      ++++++++  |+.++++||++++.++.+++
T Consensus       214 ii~~~~~~~~~~~l~~~Ei~~~l~~~~e~~  243 (250)
T d1iruc_         214 TLTRENGKTVIRVLKQKEVEQLIKKHEEEE  243 (250)
T ss_dssp             EEECCSSSCEEEECCHHHHHHHHHHHHTTT
T ss_pred             EEEcCCCceeEEECCHHHHHHHHHHHHHHh
Confidence            99998753  89999999999999988653

>d1j2pa_ d.153.1.4 (A:) Proteasome alpha subunit (non-catalytic) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=100.00  E-value=1e-44  Score=287.47  Aligned_cols=185  Identities=30%  Similarity=0.519  Sum_probs=175.6

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      ++.++.+++++|||+|++|++|++||..+|++.+.++++.++..|+++++++++++.+++.++..+|.|++++++|||+|
T Consensus        52 ~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~rP~~~  131 (243)
T d1j2pa_          52 GSKLLEKDTIEKIYKIDEHICAATSGLVADARVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQYGGVRPFGV  131 (243)
T ss_dssp             SCTTBCGGGCCSEEECSSSEEEEEEECHHHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCE
T ss_pred             cccCccccccccEeecCCcEEEEeeecccHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHHHHhhhccCCccce
Confidence            35566778899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCCeEE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIE  161 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~~ie  161 (191)
                      ++|++|+|+  +|+||.+||+|++.+++++|+|+|++.++++||+.|  .++||++||++++++||+.+.++|+.+++||
T Consensus       132 ~~il~G~D~--~p~Ly~~Dp~G~~~~~~~~a~G~g~~~a~~~Le~~y--~~~ms~eeai~la~~~l~~~~~~d~~~~~ie  207 (243)
T d1j2pa_         132 SLLIAGVNE--VPKLYETDPSGALLEYKATAIGMGRMAVTEFFEKEY--RDDLSFDDAMVLGLVAMGLSIESELVPENIE  207 (243)
T ss_dssp             EEEEEEESS--SEEEEEECTTCCEEEBSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHTSCCCGGGEE
T ss_pred             eEEEEEecC--CceEEEEeccCceeeeeEEEeCCCcHHHHHHHHhhc--ccCCCHHHHHHHHHHHHHHHHhcccCCCceE
Confidence            999999986  599999999999999999999999999999999998  4899999999999999999999998888999


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHHHHHhhcc
Q 029560          162 VGVVSKENPEFRVLSIEEIDEHLTAISER  190 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~~~~~~~~  190 (191)
                      |+++++++.+|++++++||+++++++++|
T Consensus       208 i~iv~~~~~~~~~l~~~ei~~~~~~~~e~  236 (243)
T d1j2pa_         208 VGYVKVDDRTFKEVSPEELKPYVERANER  236 (243)
T ss_dssp             EEEEETTTCCCEECCHHHHHHHHHHHHHH
T ss_pred             EEEEEeCCCcEEECCHHHHHHHHHHHHHH
Confidence            99999876679999999999999988764

>d1yara1 d.153.1.4 (A:13-233) Proteasome alpha subunit (non-catalytic) {Archaeon Thermoplasma acidophilum [TaxId: 2303]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

Probab=100.00  E-value=2.6e-44  Score=281.47  Aligned_cols=179  Identities=34%  Similarity=0.560  Sum_probs=170.7

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      .++++.+++.+|||+|++|++|+++|..+|++.+.+.++.++..|+++++++++++.+++.++.++|.|++++++|||++
T Consensus        43 ~~~~~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~a~~~~~~~~~~~~rP~~~  122 (221)
T d1yara1          43 RSRLIEQNSIEKIQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGV  122 (221)
T ss_dssp             CCTTBCSTTCCSEEEEETTEEEEEEEBHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBTTBCCCCE
T ss_pred             CCcccccCccceEEEecCCceEEeeeccchHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhhhccCCCcce
Confidence            36778889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCCeEE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIE  161 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~~ie  161 (191)
                      ++||+|||+ +||+||.+||+|++.+++++|+|+|++.++++|+++|  +++||++||++++++||+.+.+++...++++
T Consensus       123 ~~li~G~d~-~gp~Ly~id~~G~~~~~~~~a~G~g~~~~~~~Le~~~--~~~ms~~ea~~la~~~l~~~~~~~~~~~~~e  199 (221)
T d1yara1         123 SLIFAGIDQ-IGPRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREY--KENLPEKEAVTLGIKALKSSLEEGEELKAPE  199 (221)
T ss_dssp             EEEEEEECS-SCEEEEEECTTCCEEEBSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHTSCSSCCCCCCE
T ss_pred             EEEEEEEec-CCCeEEEEcCCccEEEeeEEEECCchHHHHHHHHHHh--hccccHHHHHHHHHHHHHHHHhccCCCCCcE
Confidence            999999997 7899999999999999999999999999999999998  4899999999999999999998888777999


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHHH
Q 029560          162 VGVVSKENPEFRVLSIEEIDEHL  184 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~~  184 (191)
                      |++++++++ |++++++||+++|
T Consensus       200 i~~i~~~~~-~r~l~~~ei~~~l  221 (221)
T d1yara1         200 IASITVGNK-YRIYDQEEVKKFL  221 (221)
T ss_dssp             EEEEETTSC-CEECCHHHHHTTC
T ss_pred             EEEEEcCCC-EEECCHHHHHHhC
Confidence            999998875 9999999999764

>d1irue_ d.153.1.4 (E:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=2.1e-44  Score=284.19  Aligned_cols=182  Identities=27%  Similarity=0.510  Sum_probs=171.8

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcC-----c
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAY-----M   76 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~-----~   76 (191)
                      .++++..++.+||++|++|++|++||+.+|++.+.+.++.++..|++.++++++++.+++.|++++|.|||+.+     .
T Consensus        48 ~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~i~~~~~~~t~~~~~~~~~~  127 (234)
T d1irue_          48 TSPLMEPSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMS  127 (234)
T ss_dssp             CCTTBCTTSCCSEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCBCSTTCCSSCBS
T ss_pred             cCCCcccCcccCEEEccCcEEEEEeeccchHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHhhccccccccc
Confidence            45677889999999999999999999999999999999999999999999999999999999999999998865     7


Q ss_pred             ccccceeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCC
Q 029560           77 RPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFK  156 (191)
Q Consensus        77 rP~~v~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~  156 (191)
                      |||+|++|+||||+ +||+||.+||+|++.+++++|+|+|++.++++||+.|  +++|+++||++++++||+.+.+++..
T Consensus       128 rP~~~~~il~G~D~-~gp~Ly~idp~G~~~~~~~~a~G~gs~~~~~~Le~~~--~~~~~~eeai~~a~~al~~~~~~~~~  204 (234)
T d1irue_         128 RPFGVALLFGGVDE-KGPQLFHMDPSGTFVQCDARAIGSASEGAQSSLQELY--HKSMTLKEAIKSSLIILKQVMEEKLN  204 (234)
T ss_dssp             SCCCEEEEEEEEET-TEEEEEEECTTSCEEEBSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHCSSCCC
T ss_pred             ccceEEEEEEEEcC-CCCEEEEEecCcccceeeeEEeCCchHHHHHHHHHhh--ccCCCHHHHHHHHHHHHHHHHhccCC
Confidence            99999999999998 7899999999999999999999999999999999998  48899999999999999999988887


Q ss_pred             CCeEEEEEEEeCCCcEEEcCHHHHHHHHHHh
Q 029560          157 ASEIEVGVVSKENPEFRVLSIEEIDEHLTAI  187 (191)
Q Consensus       157 ~~~iei~iv~~~~~~~~~~~~~~i~~~~~~~  187 (191)
                      +++++|++++++++ |++++++||++++.+|
T Consensus       205 ~~~iei~ii~~~~~-~k~l~~~ei~~~l~~i  234 (234)
T d1irue_         205 ATNIELATVQPGQN-FHMFTKEELEEVIKDI  234 (234)
T ss_dssp             TTSEEEEEECSSSC-CEECCHHHHHHHHTTC
T ss_pred             CCCEEEEEEECCCC-EEECCHHHHHHHHHhC
Confidence            77999999998764 9999999999999764

>d1rype_ d.153.1.4 (E:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1.8e-44  Score=285.85  Aligned_cols=187  Identities=24%  Similarity=0.465  Sum_probs=175.8

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhc------C
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHA------Y   75 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~------~   75 (191)
                      .++++..++++|||+|+++++|++||+.+|++.+.++++.++..|++.++++++++.++++|++++|.|+|+.      +
T Consensus        47 ~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~  126 (242)
T d1rype_          47 TSPLLESDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLM  126 (242)
T ss_dssp             SSTTBCGGGCCCEEEEETTEEEEEEESGGGHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCCBSSCTTSCCCB
T ss_pred             cCcCcccCccceEEEcCCCEEEEEeecchhHHHHHHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHhccccccchhc
Confidence            3567778889999999999999999999999999999999999999999999999999999999999988764      4


Q ss_pred             cccccceeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccC
Q 029560           76 MRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDF  155 (191)
Q Consensus        76 ~rP~~v~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~  155 (191)
                      +|||+|++||+|||++++|+||.+||+|++.+++++|+|+|++.++++||++|  .++||++||++++++||+.+.+++.
T Consensus       127 ~rP~~~~~ii~G~D~~~~p~L~~idp~G~~~~~~~~a~G~gs~~~~~~Le~~~--~~~ms~~ea~~la~~~l~~~~~~~~  204 (242)
T d1rype_         127 SRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNEW--HSSLTLKEAELLVLKILKQVMEEKL  204 (242)
T ss_dssp             SSCCSEEEEEEEEETTTEEEEEEECTTSCEEEBSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHCSSCC
T ss_pred             cccceEEEEEEEeccccceEEEEEcCCCceeccceeecccchHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHHhccC
Confidence            79999999999999877899999999999999999999999999999999998  5899999999999999999999998


Q ss_pred             CCCeEEEEEEEeCCCcEEEcCHHHHHHHHHHhhccC
Q 029560          156 KASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD  191 (191)
Q Consensus       156 ~~~~iei~iv~~~~~~~~~~~~~~i~~~~~~~~~~~  191 (191)
                      .+++++|++|++++ +|+++++++|++++.++.+||
T Consensus       205 ~~~~~~v~~i~~~~-g~~~l~~~~i~~~~~~i~e~~  239 (242)
T d1rype_         205 DENNAQLSCITKQD-GFKIYDNEKTAELIKELKEKE  239 (242)
T ss_dssp             CTTSEEEEEEETTT-EEEECCHHHHHHHHHHHHHHH
T ss_pred             CCCceEEEEEECCC-CeEECCHHHHHHHHHHHHHhh
Confidence            88899999999876 499999999999999998875

>d1irug_ d.153.1.4 (G:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=3.9e-44  Score=284.41  Aligned_cols=185  Identities=28%  Similarity=0.388  Sum_probs=171.0

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      .++++.+++.+||++|++|++|++||+.+|++.++++++.++..|++++|++++++.++++|++++|.|||++++|||+|
T Consensus        54 ~~~~~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~g~~i~~~~la~~la~~~~~~t~~~~~rP~~v  133 (245)
T d1irug_          54 LSKLYEEGSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGC  133 (245)
T ss_dssp             SCTTBCTTTTCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSBSSBCCCSE
T ss_pred             cccccccCccceEEEcCCCEEEEeccCchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhccccccccce
Confidence            45677889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EI  160 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~i  160 (191)
                      ++||+|||+++||+||.+||+|++.+++++|+|+|++.++++||+.|+  ++||.+||++++++||+.+.+++...+ ++
T Consensus       134 s~li~G~D~~~gp~Ly~iDp~G~~~~~~~~a~G~gs~~a~~~Le~~~~--~dmt~eea~~l~~~~l~~~~~~~~~~~~~i  211 (245)
T d1irug_         134 SFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQM--KEMTCRDIVKEVAKIIYIVHDEVKDKAFEL  211 (245)
T ss_dssp             EEEEEEEETTTEEEEEEECTTCCEEEBSEEEESTTHHHHHHHHTTSCG--GGCCHHHHHHHHHHHHHHHSCSSSSCCEEE
T ss_pred             EEEEEEEcCCCCceEEEEcCCceEEeeeEEEECCccHHHHHHHHhhcC--CCCCHHHHHHHHHHHHHHHHhhccCCCceE
Confidence            999999998689999999999999999999999999999999999984  889999999999999999997765544 89


Q ss_pred             EEEEEEeCCCcEEEcCHHHHHHHHHHhh
Q 029560          161 EVGVVSKENPEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       161 ei~iv~~~~~~~~~~~~~~i~~~~~~~~  188 (191)
                      +|++|++++++++++.|.|+.+.+.++.
T Consensus       212 ei~~v~~~~~~~~~~~~~e~~~~~~~~~  239 (245)
T d1irug_         212 ELSWVGELTNGRHEIVPKDIREEAEKYA  239 (245)
T ss_dssp             EEEECBTTTTTCCEECCHHHHHHHHHHH
T ss_pred             EEEEEEecCCCeEEEChHHHHHHHHHHH
Confidence            9999998766677777778877777665

>d1iruf_ d.153.1.4 (F:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=7e-44  Score=281.90  Aligned_cols=185  Identities=28%  Similarity=0.494  Sum_probs=171.1

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      ++.+..  +.+||++|+++++|++||+.+|++.+++.++.++..|++++|++++++.+++.+++..|.|+++.++|||++
T Consensus        50 ~~~~~~--~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~l~~~~~~y~~~~~~rP~~v  127 (238)
T d1iruf_          50 QSELAA--HQKKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGV  127 (238)
T ss_dssp             SSTTBC--CCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTCCCCCE
T ss_pred             ccCCCC--ccceEEEeCCceEEEEeccchHHHHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHHHhhccCCCcccc
Confidence            345554  558999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccC--CCCe
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDF--KASE  159 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~--~~~~  159 (191)
                      ++||||||+ +||+||.+||+|++.+++++|+|+|++.++++||++|++..++|++||++++++||+.++.++.  ...+
T Consensus       128 ~~il~G~D~-~gp~Ly~~D~~G~~~~~~~~a~G~g~~~~~~~Lek~~~~~~~~~~~eav~lai~al~~~~~~~~~~~~~~  206 (238)
T d1iruf_         128 GLLIAGYDD-MGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFMECNLNELVKHGLRALRETLPAEQDLTTKN  206 (238)
T ss_dssp             EEEEEEEET-TEEEEEEECSSSCEEEESEEEESTTHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCTTCCCCTTT
T ss_pred             eEEEEEEcC-CCceEEEEcCCCCEEeeeeEEECCCchhhHHHHHhhcccccCCCHHHHHHHHHHHHHHHHhhcccCCCCc
Confidence            999999998 7899999999999999999999999999999999999744467999999999999999987653  4458


Q ss_pred             EEEEEEEeCCCcEEEcCHHHHHHHHHHhhcc
Q 029560          160 IEVGVVSKENPEFRVLSIEEIDEHLTAISER  190 (191)
Q Consensus       160 iei~iv~~~~~~~~~~~~~~i~~~~~~~~~~  190 (191)
                      |+|++++++++ |++++++||++++.++++|
T Consensus       207 iev~ii~k~~~-~~~l~~~ei~~~l~~i~ek  236 (238)
T d1iruf_         207 VSIGIVGKDLE-FTIYDDDDVSPFLEGLEER  236 (238)
T ss_dssp             EEEEEEETTEE-EEEECSGGGHHHHTTCCCC
T ss_pred             EEEEEEeCCCC-EEECCHHHHHHHHHHHHhC
Confidence            99999999874 9999999999999999876

>d1rypb_ d.153.1.4 (B:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=2.4e-43  Score=280.69  Aligned_cols=184  Identities=30%  Similarity=0.501  Sum_probs=172.6

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHH-HHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAE-FRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLG   80 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~-~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~   80 (191)
                      .++++.+++.+||++|++|++|++||+.+|++.++++++.++.. |+..++++++++.+++.+++++|.|+++++.|||+
T Consensus        52 ~~~~~~~~~~~ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~y~~~~~~~~~~~~la~~~~~~~~~~~~~~~~rp~~  131 (250)
T d1rypb_          52 SSPLAMSETLSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFG  131 (250)
T ss_dssp             SCSSBCGGGCCSSEEEETTEEEEEEECHHHHHHHHHHHHHHHHHTTHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCC
T ss_pred             CCccccccccceeEeccCCEEEEeeecccHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhcCCcCee
Confidence            45677788999999999999999999999999999999999875 89999999999999999999999999999999999


Q ss_pred             ceeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCCeE
Q 029560           81 VVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEI  160 (191)
Q Consensus        81 v~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~~i  160 (191)
                      |++||+|||+++||+||.+||.|++.+++++|+|+|+..++++||++|  +++||++||++++++||+.+.++|....++
T Consensus       132 v~~li~G~D~~~gp~Ly~id~~G~~~~~~~~a~G~gs~~a~~~Le~~~--~~~ms~eea~~la~~al~~~~~~d~s~~~i  209 (250)
T d1rypb_         132 VSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRW--NDELELEDAIHIALLTLKESVEGEFNGDTI  209 (250)
T ss_dssp             EEEEEEEEETTTEEEEEEECTTSCEEEBSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHCCSCCSTTTE
T ss_pred             EEEEEEEecCCCCCEEEEEcCcEEEEEeeEEecCcchHHHHHHHHHhc--ccCCCHHHHHHHHHHHHHHHhhccCCCCCE
Confidence            999999999877899999999999999999999999999999999998  589999999999999999999999876699


Q ss_pred             EEEEEEeCC--------------CcEEEcCHHHHHHHHHHh
Q 029560          161 EVGVVSKEN--------------PEFRVLSIEEIDEHLTAI  187 (191)
Q Consensus       161 ei~iv~~~~--------------~~~~~~~~~~i~~~~~~~  187 (191)
                      +|++|++++              +.|++++++||+++++.|
T Consensus       210 ev~vi~~~~~~~~~~~~v~~~~~~~fr~ls~eei~~~l~~l  250 (250)
T d1rypb_         210 ELAIIGDENPDLLGYTGIPTDKGPRFRKLTSQEINDRLEAL  250 (250)
T ss_dssp             EEEEECSCCGGGTSEESCSSCCCCSEEECCHHHHHHHHTTC
T ss_pred             EEEEEeCCCcccccccccccccCCceEECCHHHHHHHHHhC
Confidence            999998764              359999999999999864

>d1rypf_ d.153.1.4 (F:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=6.9e-44  Score=281.13  Aligned_cols=175  Identities=21%  Similarity=0.367  Sum_probs=164.7

Q ss_pred             CCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeEEEE
Q 029560            8 HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS   87 (191)
Q Consensus         8 ~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~iv~G   87 (191)
                      .+..+||++|++|++|++||+.+|++.++++++.+++.|++.++++++++.+++.|++++|.||++.+.|||||++||+|
T Consensus        56 ~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~i~~~~la~~l~~~~~~~t~~~~~RP~gv~~il~G  135 (233)
T d1rypf_          56 SSYQKKIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRPYGVGLLIIG  135 (233)
T ss_dssp             BCCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEE
T ss_pred             CcchheEEEcCCCEEEEEeeccccHHHHHHHHHHHHHhhhhhcCCCCcHHHHHHHHHHHHHHHhcccccCCccceEEEEE
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhc--CCCCCCHHHHHHHHHHHHHhhhcccCCC-CeEEEEE
Q 029560           88 IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMK--NDPAFTFQETVQTAISTLQSVLQEDFKA-SEIEVGV  164 (191)
Q Consensus        88 ~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~--~~~~~s~eea~~l~~~~l~~~~~~d~~~-~~iei~i  164 (191)
                      ||+ +||+||.+||+|++.+++++|+|+|++.++++||++|.  +.++|+++||++++++||+.+.++|..+ .++||++
T Consensus       136 ~d~-~g~~Ly~idp~G~~~~~~~~aiG~gs~~a~~~Le~~~~~~~~~dms~eeai~l~~~~l~~~~~~d~~~~~~iev~i  214 (233)
T d1rypf_         136 YDK-SGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAI  214 (233)
T ss_dssp             EET-TEEEEEEECTTSCEEEESEEEESTTHHHHHHHHHHHHHHHTTCCSCHHHHHHHHHHHHTTSCCSSCCCTTTEEEEE
T ss_pred             EcC-CCCEEEEEccccceecccEEEecCchHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHHhccCCCCCeEEEEE
Confidence            998 68999999999999999999999999999999999874  3579999999999999999999888655 4999999


Q ss_pred             EEeCCCcEEEcCHHHHHHHH
Q 029560          165 VSKENPEFRVLSIEEIDEHL  184 (191)
Q Consensus       165 v~~~~~~~~~~~~~~i~~~~  184 (191)
                      ++++++ |++++++||++++
T Consensus       215 i~k~~~-~~~l~~~ei~~~i  233 (233)
T d1rypf_         215 VGKDTP-FTIYDGEAVAKYI  233 (233)
T ss_dssp             EETTEE-EEEEEGGGGGGGC
T ss_pred             EECCCC-eEECCHHHHHhhC
Confidence            999985 9999999998763

>d1irud_ d.153.1.4 (D:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=1.3e-43  Score=281.07  Aligned_cols=185  Identities=29%  Similarity=0.491  Sum_probs=170.6

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      .++++.+++.+|||+|++|++|++||+.+|++.+++.++.++..|+++++.+++++.++++|++++|.||+++++|||+|
T Consensus        49 ~~~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~v~~la~~ls~~~~~~t~~~~~rp~~v  128 (243)
T d1irud_          49 VAKLQDERTVRKICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGI  128 (243)
T ss_dssp             CCSSSCGGGGCSEEESSSSCEEEEEECHHHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCE
T ss_pred             cCcccCCCccccEEECCCCEEEEEEEchhhHHHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHhcccCCccce
Confidence            46888899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCCeEE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIE  161 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~~ie  161 (191)
                      ++||+|||++++|+||.+||+|++.+++++|+|+|++.++++||+.|++...++.++++++++++|......  ...+++
T Consensus       129 ~~li~G~D~~~~p~Ly~idp~G~~~~~~~~a~G~gs~~a~~~Lek~~~~~~~~~~~~~i~~ai~~l~~~~~~--~~~~ve  206 (243)
T d1irud_         129 SALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEAIETDDLTIKLVIKALLEVVQS--GGKNIE  206 (243)
T ss_dssp             EEEEEEECSSSCEEEEEECTTSCEEEBSEEEESTTHHHHHHHHTTTCCSSTTCSHHHHHHHHHHHHHTTSCT--TSTTCC
T ss_pred             EEEEEEEcCCCCCEEEEecCcEEEEeccEEEECCChHHHHHHHHHhcccCCCccHHHHHHHHHHHHHHHhcC--CCCcEE
Confidence            999999997678999999999999999999999999999999999986443448888999999999887643  334899


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHHHHHhhc
Q 029560          162 VGVVSKENPEFRVLSIEEIDEHLTAISE  189 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~~~~~~~  189 (191)
                      |++++++++ |++++++||++++.++++
T Consensus       207 i~ii~k~~~-~~~l~~~eI~~~l~~i~~  233 (243)
T d1irud_         207 LAVMRRDQS-LKILNPEEIEKYVAEIEK  233 (243)
T ss_dssp             EEEEESSSC-EECCCHHHHHHHTTTTTT
T ss_pred             EEEEECCCC-EEECCHHHHHHHHHHHHh
Confidence            999999864 999999999999999873

>d1rypd_ d.153.1.4 (D:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=7.2e-43  Score=276.54  Aligned_cols=185  Identities=30%  Similarity=0.492  Sum_probs=170.6

Q ss_pred             Ccccc-CCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            3 DKLLD-HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         3 s~l~~-~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      ++++. .++.+||++|++|++|++||+.+|++.+.+.++.++..|+++++++++++.++++++.++|.||++.++|||+|
T Consensus        50 ~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~i~~~~~~~t~~~~~rP~~v  129 (241)
T d1rypd_          50 LKLQDTRITPSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGV  129 (241)
T ss_dssp             SCCBCTTTSCCSEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSSTTBCCCSE
T ss_pred             ccCcccccccccEEEeCCCEEEEeeeccchHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHhhccccCcccc
Confidence            44444 46889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCC-CCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcC-CCCCCHHHHHHHHHHHHHhhhcccCCCCe
Q 029560           82 VAMVLSIDEE-CGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKN-DPAFTFQETVQTAISTLQSVLQEDFKASE  159 (191)
Q Consensus        82 ~~iv~G~d~~-~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~-~~~~s~eea~~l~~~~l~~~~~~d~~~~~  159 (191)
                      ++||||||++ ++|+||.+||+|++.+++++|+|+|++.++++||+.|+. .++||.+||+++|++||+.+.+++  ..+
T Consensus       130 ~~li~G~d~~~~~p~Ly~idp~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~~t~~e~i~lal~al~~~~~~~--~~~  207 (241)
T d1rypd_         130 STLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKEPPATVEECVKLTVRSLLEVVQTG--AKN  207 (241)
T ss_dssp             EEEEEECCTTCCSCEEEEECTTSCEEEBSEEEESTTHHHHHHHHHTTCCTTSCCCSHHHHHHHHHHHHHHHHCSC--STT
T ss_pred             eEEEEEEccccCcceEEEecCCEEEEeeCeEEECcCHHHHHHHHHHhhhcccCCCCHHHHHHHHHHHHHHHhcCC--CCc
Confidence            9999999964 589999999999999999999999999999999999954 468999999999999999988543  458


Q ss_pred             EEEEEEEeCCCcEEEcCHHHHHHHHHHhhcc
Q 029560          160 IEVGVVSKENPEFRVLSIEEIDEHLTAISER  190 (191)
Q Consensus       160 iei~iv~~~~~~~~~~~~~~i~~~~~~~~~~  190 (191)
                      ++|+++++++ +|++++++||++++.+++++
T Consensus       208 iei~ii~~d~-~~~~l~~~ei~~~l~~i~~~  237 (241)
T d1rypd_         208 IEITVVKPDS-DIVALSSEEINQYVTQIEQE  237 (241)
T ss_dssp             EEEEEEETTT-EEEECCHHHHHHHHHHHTHH
T ss_pred             EEEEEEECCC-CEEECCHHHHHHHHHHHHHH
Confidence            9999999987 49999999999999999854

>d1rypc_ d.153.1.4 (C:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=3.9e-42  Score=272.74  Aligned_cols=181  Identities=26%  Similarity=0.461  Sum_probs=171.0

Q ss_pred             cccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeE
Q 029560            5 LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAM   84 (191)
Q Consensus         5 l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~i   84 (191)
                      ++.+++.+||++|++|++|+++|..+|++.+.+.++.+++.|++.++++++++.+++.++++++.|+++.++|||+|++|
T Consensus        56 ~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~rP~~~~~l  135 (244)
T d1rypc_          56 LEQDTSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFI  135 (244)
T ss_dssp             BCSTTCCSSEEESSSSEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSCCCCCEEEE
T ss_pred             cccCCccceEEEcCCCeEEEEecccCcHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhhhhccccCccceeEE
Confidence            45567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEEE
Q 029560           85 VLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVG  163 (191)
Q Consensus        85 v~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei~  163 (191)
                      |+|||+++||+||.+||.|++.+++++|+|+|+..++++|++.|  +++||++||++++++||+.+.+||..++ +++|+
T Consensus       136 l~G~d~~~gp~Ly~id~~Gs~~~~~~~a~G~g~~~a~~~Le~~~--~~~ms~eeai~l~~~al~~a~~~d~~~~~~iei~  213 (244)
T d1rypc_         136 YAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY--KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFA  213 (244)
T ss_dssp             EEEEETTTEEEEEEECTTCCEEEBSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHCSSSSCCGGGEEEE
T ss_pred             EEEEecCCCceEEEecCCCcEeeeeeeeccchhHHHHHHHHhcc--cCCCCHHHHHHHHHHHHHHHHhccCCCCCcEEEE
Confidence            99999867899999999999999999999999999999999998  5899999999999999999999998876 79999


Q ss_pred             EEEeCCC----cEEEcCHHHHHHHHHHh
Q 029560          164 VVSKENP----EFRVLSIEEIDEHLTAI  187 (191)
Q Consensus       164 iv~~~~~----~~~~~~~~~i~~~~~~~  187 (191)
                      +|++++.    .++.++++||++++.+-
T Consensus       214 ii~~~~~~~~~~~~~~~~~Ei~~~l~k~  241 (244)
T d1rypc_         214 TIRKGANDGEVYQKIFKPQEIKDILVKT  241 (244)
T ss_dssp             EEECCSSSSSCEEEECCHHHHHHHHHHH
T ss_pred             EEECCCcccceeEEECCHHHHHHHHHHh
Confidence            9998863    27899999999999763

>d1yarh1 d.153.1.4 (H:1-203) Proteasome beta subunit (catalytic) {Archaeon Thermoplasma acidophilum [TaxId: 2303]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

Probab=100.00  E-value=1.1e-41  Score=263.12  Aligned_cols=177  Identities=23%  Similarity=0.395  Sum_probs=165.2

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      ++++.+++++|||+|++|++||+||..+|++.+.++++.+++.|++.++.+++++.++++++++.+.+    +.|||+++
T Consensus        23 ~~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~~~~~----~~~p~~~~   98 (203)
T d1yarh1          23 ENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKAELELYRLQRRVNMPIEAVATLLSNMLNQV----KYMPYMVQ   98 (203)
T ss_dssp             TTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHT----TTSCCCEE
T ss_pred             CCEeecCCcccEEEecCCeeeecCCCcchHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHhh----ccCCccce
Confidence            45778899999999999999999999999999999999999999999999999999999999987644    46899999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIE  161 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~ie  161 (191)
                      +|+||+|+  +|+||.+||+|++.+++++|+|+|++.++++|+++|  .++||.+||++++++||+.+.+||..++ +++
T Consensus        99 ~lvaG~d~--~p~l~~~d~~G~~~~~~~~a~G~g~~~~~~~L~~~~--~~~~s~eea~~l~~~~l~~~~~~d~~~~~~v~  174 (203)
T d1yarh1          99 LLVGGIDT--APHVFSIDAAGGSVEDIYASTGSGSPFVYGVLESQY--SEKMTVDEGVDLVIRAISAAKQRDSASGGMID  174 (203)
T ss_dssp             EEEEEESS--SEEEEEECTTCCEEEESEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHCTTCCSCCE
T ss_pred             eEEEEEcC--CCeeEecCCccceecccccccCCCcHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHHHhcCCCCCeEE
Confidence            99999986  599999999999999999999999999999999998  4899999999999999999999998776 799


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHHHHHhh
Q 029560          162 VGVVSKENPEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~~~~~~  188 (191)
                      |+++++++ +|++++++||++++.++.
T Consensus       175 v~ii~~~~-g~~~l~~~ei~~~~~~~~  200 (203)
T d1yarh1         175 VAVITRKD-GYVQLPTDQIESRIRKLG  200 (203)
T ss_dssp             EEEEETTT-EEEECCHHHHHHHHHHHT
T ss_pred             EEEEECCC-CEEECCHHHHHHHHHHhC
Confidence            99999876 499999999999998864

>d1irub_ d.153.1.4 (B:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=9.6e-42  Score=268.54  Aligned_cols=182  Identities=35%  Similarity=0.564  Sum_probs=173.1

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      .++++..++.+|||+|++|++|+++|..+|++.+.++++.+++.|+++++++++++.+++.++++++.+++...+|||++
T Consensus        52 ~~~~~~~~~~~ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~p~~~  131 (233)
T d1irub_          52 KSILYDERSVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGV  131 (233)
T ss_dssp             CCSSBCSTTCCSSEESSSSEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCSE
T ss_pred             ccCCccccccceEEEecCceEEEEeccchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhccccccceE
Confidence            34566789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCCeEE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIE  161 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~~ie  161 (191)
                      +++++|+|+ ++|+||.+||.|++.+++++|+|+|+..++++|++.|  +++||++||++++++||+.+.++|+.+.+|+
T Consensus       132 ~~li~g~d~-~~~~ly~id~~G~~~~~~~~a~G~gs~~~~~~Le~~~--~~~ms~eea~~l~~~~L~~~~~~d~~~~~ve  208 (233)
T d1irub_         132 SLLICGWNE-GRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRY--NEDLELEDAIHTAILTLKESFEGQMTEDNIE  208 (233)
T ss_dssp             EEEEEEECS-SSEEEEEECTTSCEEEBSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHTTCCSCCCSSSEE
T ss_pred             EEeeeeccc-CCceEEEEcCCcceEeccceecCCcHHHHHHHHHhhc--ccCccHHHHHHHHHHHHHHHHhccCCCCcEE
Confidence            999999997 8899999999999999999999999999999999998  5899999999999999999999999878999


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHHHHHhh
Q 029560          162 VGVVSKENPEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~~~~~~  188 (191)
                      |++++++|  +++++|+||++++.+++
T Consensus       209 v~ii~~~g--~~~l~~~eI~~~l~~i~  233 (233)
T d1irub_         209 VGICNEAG--FRRLTPTEVKDYLAAIA  233 (233)
T ss_dssp             EEEEETTE--EEECCHHHHHHHHTTCC
T ss_pred             EEEEeCCC--eEECCHHHHHHHHHHhC
Confidence            99999885  99999999999998763

>d1rypg_ d.153.1.4 (G:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1.3e-40  Score=263.88  Aligned_cols=186  Identities=24%  Similarity=0.372  Sum_probs=166.1

Q ss_pred             CCccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            2 QDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         2 ~s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      .++++..++.+||++|++|++|+++|+.+|++.++++++.+++.|++.++++++++.+++.+++.+|.||++++.|||+|
T Consensus        51 ~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~t~~~~~RP~~~  130 (244)
T d1rypg_          51 TSKLLVPQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGV  130 (244)
T ss_dssp             CCTTBCTTTSCCCEEETTTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSCTTBCCCCE
T ss_pred             CCCCccccccceEEEccCceEEEEccchhhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhcccccCCceE
Confidence            35677777889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhh-cCCCCCCHHHHHHHHHHHHHhhhcccCCCC-e
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKM-KNDPAFTFQETVQTAISTLQSVLQEDFKAS-E  159 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~-~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~  159 (191)
                      ++||+|||+ +||+||.+||+|++.+++++|+|+|+..++++||+.. .+.++||++||++++++||+.+.+++.... +
T Consensus       131 ~~iiaG~D~-~gp~Ly~idp~Gs~~~~~~~a~G~gs~~~~~~Lek~~~~~~~~mt~eeai~la~~~L~~~~~~~~~~~~~  209 (244)
T d1rypg_         131 STIFGGVDK-NGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFE  209 (244)
T ss_dssp             EEEEEEEET-TEEEEEEECTTSCEEEBSEEEESTTHHHHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHGGGGTTSCEE
T ss_pred             EEEEEEEeC-CCCEEEEEcCCccEEecCeEecCCccHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHhcccCCCCe
Confidence            999999998 7999999999999999999999999999999999742 225899999999999999999998776655 8


Q ss_pred             EEEEEEEeC--CCcEEEcCHHHHHHHHHHhh
Q 029560          160 IEVGVVSKE--NPEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       160 iei~iv~~~--~~~~~~~~~~~i~~~~~~~~  188 (191)
                      ++|++++.+  ++.++.++.+++++++....
T Consensus       210 iev~ii~~~~~~~~~~~~~~e~~~~~~~~~~  240 (244)
T d1rypg_         210 LEISWCSLSETNGLHKFVKGDLLQEAIDFAQ  240 (244)
T ss_dssp             EEEEEEETTTTTTSEEECCTHHHHHHHHHHH
T ss_pred             EEEEEEEEEcCCCeEEECCHHHHHHHHHHHH
Confidence            999999843  33466777777777665543

>d1irul_ d.153.1.4 (L:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=2.8e-41  Score=260.51  Aligned_cols=177  Identities=15%  Similarity=0.193  Sum_probs=166.3

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      ..++.+++++|||+|+++++|+++|..+|++.+.++++.+++.|++.++++++++.++++++++++.++    .+||+++
T Consensus        23 g~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~~~~~~----~~p~~~~   98 (201)
T d1irul_          23 GAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQCRIYELRNKERISVAAASKLLANMVYQYK----GMGLSMG   98 (201)
T ss_dssp             TTEEEESCCCCEEEEETTEEEECCBCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHTTT----TSCCCBE
T ss_pred             CCEeecCCcccEEEeCCcEEEEEcCccchHHHHHHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhhhcc----CCCceEE
Confidence            356778899999999999999999999999999999999999999999999999999999999997553    5799999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIE  161 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~ie  161 (191)
                      ++++|+|+ .+|+||.+||+|++.+++++|+|+|+++++++||+.|  +++||.+||++++++||+.+.+||..++ +++
T Consensus        99 ~lvaG~d~-~~~~l~~~d~~G~~~~~~~~a~G~g~~~~~~~Le~~~--~~~ms~eea~~l~~~~l~~~~~~d~~sg~~~~  175 (201)
T d1irul_          99 TMICGWDK-RGPGLYYVDSEGNRISGATFSVGSGSVYAYGVMDRGY--SYDLEVEQAYDLARRAIYQATYRDAYSGGAVN  175 (201)
T ss_dssp             EEEEEECS-SSEEEEEEESSSCEEECSEEEESTTHHHHHHHHHTTC--CTTCCHHHHHHHHHHHHHHHHHHBTTCCSEEE
T ss_pred             EEEEEEec-CCceEEEEccCceEEEeeeEEecCchHHHHHHHHhhc--cCCCCHHHHHHHHHHHHHHHHHhCCCCCCceE
Confidence            99999998 7899999999999999999999999999999999998  4889999999999999999999998776 899


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHHHHHhh
Q 029560          162 VGVVSKENPEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~~~~~~  188 (191)
                      |++++++|  +++++++||.++..+++
T Consensus       176 v~~i~~~G--~~~i~~~ev~~~~~~~~  200 (201)
T d1irul_         176 LYHVREDG--WIRVSSDNVADLHEKYS  200 (201)
T ss_dssp             EEEECSSC--EEEEEEEEHHHHHHHHT
T ss_pred             EEEEeCCc--eEEECHHHHHHHHHhhc
Confidence            99999986  89999999999998875

>d1j2qh_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=100.00  E-value=2.1e-40  Score=255.32  Aligned_cols=177  Identities=20%  Similarity=0.347  Sum_probs=165.6

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      ++++.+++.+|||+|++|++|++||..+|++.+.++++.+++.|++.++.+++++.+++++++++|.|+    .|||+++
T Consensus        23 ~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~----~~p~~~~   98 (202)
T d1j2qh_          23 GNFIASKAAKKIYQIADRMAMTTAGSVGDAQFLARIIKIEANLYEIRRERKPTVRAIATLTSNLLNSYR----YFPYLVQ   98 (202)
T ss_dssp             TTEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTT----TSCCCEE
T ss_pred             CCeeccCccceEEEecCcEEEEecCcchhHHHHHHHHHHHhhhhhhccCCCccHHHHHHHHHHHHhhhc----ccceeeE
Confidence            467788899999999999999999999999999999999999999999999999999999999997664    4799999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceece-eeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGH-KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EI  160 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~-~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~i  160 (191)
                      +|++|+|+ .+|+||.+||+|++..+ .++|+|+|++.++++|+++|  .++||++||++++++||+.+.++|..++ ++
T Consensus        99 ~lvaG~d~-~~~~l~~~d~~G~~~~~~~~~a~G~g~~~~~~~Le~~~--~~~ms~~ea~~l~~~al~~~~~~d~~~g~~v  175 (202)
T d1j2qh_          99 LLIGGIDS-EGKSIYSIDPIGGAIEEKDIVATGSGSLTAYGVLEDRF--TPEIGVDEAVELAVRAIYSAMKRDSASGDGI  175 (202)
T ss_dssp             EEEEEEET-TEEEEEEECTTCCEEEESSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHTTCTTSCSCE
T ss_pred             EEEEEEcC-CCceEEEEeCCCCeEeecceEEccCChHHHHHHHHhhc--CCCCCHHHHHHHHHHHHHHHHHhcCCCCCeE
Confidence            99999998 78999999999998776 58999999999999999998  5899999999999999999999998876 79


Q ss_pred             EEEEEEeCCCcEEEcCHHHHHHHHHHhh
Q 029560          161 EVGVVSKENPEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       161 ei~iv~~~~~~~~~~~~~~i~~~~~~~~  188 (191)
                      +|++++++|  +++++++||++++.++.
T Consensus       176 ~v~~i~~~g--~~~~~~~ei~~~l~~~~  201 (202)
T d1j2qh_         176 DVVKITEDE--FYQYSPEEVEQILAKFR  201 (202)
T ss_dssp             EEEEECSSC--EEECHHHHHHHHGGGTT
T ss_pred             EEEEEECCC--EEEeCHHHHHHHHHHhh
Confidence            999999985  99999999999998875

>d1rypk_ d.153.1.4 (K:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=5e-41  Score=258.54  Aligned_cols=171  Identities=13%  Similarity=0.147  Sum_probs=158.6

Q ss_pred             ccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccccee
Q 029560            4 KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVA   83 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~   83 (191)
                      .++.+++.+||++|++|++|+++|..+|++.+.+.++.+++.|+++++.+++++.+++++++.++.++  +..|||++++
T Consensus        25 ~~~~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~--~~~~P~~~~~  102 (198)
T d1rypk_          25 ISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYIQANIQLYSIREDYELSPQAVSSFVRQELAKSI--RSRRPYQVNV  102 (198)
T ss_dssp             TEEEESCCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHT--TSSSCCCEEE
T ss_pred             CEeecCccceEEEecCCEEEEecCCcccHHHHHHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHH--hcccccceEE
Confidence            45667899999999999999999999999999999999999999999999999999999999986554  4579999999


Q ss_pred             EEEEEcCC-CCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEE
Q 029560           84 MVLSIDEE-CGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIE  161 (191)
Q Consensus        84 iv~G~d~~-~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~ie  161 (191)
                      ||||||+. +||+||.+||+|++.+++++|+|+|+..++++||++|  +++||.+||++++++||+.+.+||..++ +++
T Consensus       103 liaG~D~~~~~p~L~~id~~G~~~~~~~~a~G~gs~~~~~~Le~~~--~~~~~~eea~~l~~~~l~~~~~~d~~s~~~~~  180 (198)
T d1rypk_         103 LIGGYDKKKNKPELYQIDYLGTKVELPYGAHGYSGFYTFSLLDHHY--RPDMTTEEGLDLLKLCVQELEKRMPMDFKGVI  180 (198)
T ss_dssp             EEEEEETTTTEEEEEEECTTCCEEECSEEECTTHHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHCSBCCCCEE
T ss_pred             EEEEEecCCCceEEEEecccccEEecceEEEeccchhhHHHHHhcc--cccCCHHHHHHHHHHHHHHHHHhcCcCCCcEE
Confidence            99999974 5899999999999999999999999999999999998  4899999999999999999999998776 899


Q ss_pred             EEEEEeCCCcEEEcCHHHH
Q 029560          162 VGVVSKENPEFRVLSIEEI  180 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i  180 (191)
                      |++|+++|  +++++++++
T Consensus       181 v~vi~~dG--~~~~~~~~~  197 (198)
T d1rypk_         181 VKIVDKDG--IRQVDDFQA  197 (198)
T ss_dssp             EEEEETTE--EEEECCCSC
T ss_pred             EEEEcCCC--eEEcchhcc
Confidence            99999985  899988765

>d1rypl_ d.153.1.4 (L:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=2.7e-40  Score=256.93  Aligned_cols=179  Identities=12%  Similarity=0.163  Sum_probs=167.2

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      ..++.+++++|||+|++|++|+++|..+|++.+.++++.++..|++.++++++++.++++++++++.|    ..+|+++.
T Consensus        23 g~~i~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~ls~~~~~~----~~~p~~~~   98 (212)
T d1rypl_          23 GNWVASQTVKRVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQY----KGAGLSMG   98 (212)
T ss_dssp             TTEEEESCCCCEEEEETTEEEECCBCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHT----TTSCCCBE
T ss_pred             CceeecCCcceEEEECCcEEEEeccchHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHh----ccCCcceE
Confidence            35677899999999999999999999999999999999999999999999999999999999999755    34699999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIE  161 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~ie  161 (191)
                      .+++|+|.++||+||.+||+|++.+++++|+|+|++.++++||++|  +++||++||++++++||+.+.+||..++ +++
T Consensus        99 ~~l~G~~~~~g~~Ly~id~~G~~~~~~~~a~G~gs~~~~~~Le~~~--~~~mt~~ea~~l~~~al~~~~~rd~~sg~~v~  176 (212)
T d1rypl_          99 TMICGYTRKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNY--KWDLSVEDALYLGKRSILAAAHRDAYSGGSVN  176 (212)
T ss_dssp             EEEEEEETTTEEEEEEEETTCCEEECSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHBTTCCSEEE
T ss_pred             eeeeEeecCCCCEEEEECCCceEEecceEEEccCcccchhHHHHhc--cCCCCHHHHHHHHHHHHHHHHHhcCCCCCceE
Confidence            9999998878999999999999999999999999999999999998  4889999999999999999999999886 899


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHHHHHhhc
Q 029560          162 VGVVSKENPEFRVLSIEEIDEHLTAISE  189 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~~~~~~~  189 (191)
                      |++|+++|  +++++++||.+++.++.+
T Consensus       177 v~vi~~~g--~~~~~~~ev~~~~~~~~~  202 (212)
T d1rypl_         177 LYHVTEDG--WIYHGNHDVGELFWKVKE  202 (212)
T ss_dssp             EEEEETTE--EEEEEEEEHHHHHHHHHH
T ss_pred             EEEEcCCc--eEEeCHHHHHHHHHHHHH
Confidence            99999986  999999999999888763

>d1ryph_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=2.2e-40  Score=256.25  Aligned_cols=172  Identities=14%  Similarity=0.170  Sum_probs=158.0

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      +.++.+++++||++|++|++|+++|..+|++.+.++++.+++.|+++++++ ++..+++.++++++.     +.+||+++
T Consensus        32 g~~i~~~~~~ki~~i~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~-----~~~p~~~~  105 (205)
T d1ryph_          32 GAYIANRVTDKLTRVHDKIWCCRSGSAADTQAIADIVQYHLELYTSQYGTP-STETAASVFKELCYE-----NKDNLTAG  105 (205)
T ss_dssp             TTEEEESSCCCEEEEETTEEEEEEEBHHHHHHHHHHHHHHHHHHHHHHSSC-CHHHHHHHHHHHHHH-----TTTTCCEE
T ss_pred             CceeeccccceEEEccCceEEeeccchhHHHHHHHHHHHHHHHHHHHcCCc-cHHHHHHHHHHHHHh-----CccCceEE
Confidence            457778899999999999999999999999999999999999999999965 578889999888742     34799999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIE  161 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~ie  161 (191)
                      +||||||++++|+||.+||.|++.+++++|+|+|+..++++||+.|  +++||.+||++++++||+.+.+||+.++ +++
T Consensus       106 ~lvaG~d~~~~p~Ly~~d~~G~~~~~~~~a~G~g~~~~~~~Le~~~--~~~ms~~ea~~l~~~al~~a~~rD~~sg~~v~  183 (205)
T d1ryph_         106 IIVAGYDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNF--RENMSKEETVDFIKHSLSQAIKWDGSSGGVIR  183 (205)
T ss_dssp             EEEEEEETTTEEEEEEECTTSCCEEESEEEESGGGGGGHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHBTTCCSCEE
T ss_pred             EEEEeecCCCCcEEEEECCCCcEEecCeEEeecCcHHHHHHHHhhh--hcccCHHHHHHHHHHHHHHHHHhcCcCCCCEE
Confidence            9999999878899999999999999999999999999999999998  5899999999999999999999999876 899


Q ss_pred             EEEEEeCCCcEEEcCHHHHHH
Q 029560          162 VGVVSKENPEFRVLSIEEIDE  182 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~  182 (191)
                      |++||++|..+..+.|+|+++
T Consensus       184 v~iitk~G~~~~~~~~~e~~~  204 (205)
T d1ryph_         184 MVVLTAAGVERLIFYPDEYEQ  204 (205)
T ss_dssp             EEEEETTEEEEEEECHHHHTC
T ss_pred             EEEEcCCceEEEecCcccccc
Confidence            999999987677899999864

>d1iruh_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=1.1e-39  Score=251.70  Aligned_cols=174  Identities=14%  Similarity=0.194  Sum_probs=162.6

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      ..++.+++++||++|++|++|+++|..+|++.+.+.++.+++.|++.++++++++.+++++++.++.+     .+||+++
T Consensus        23 g~~i~~~~~~KI~~i~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~l~~~-----~~p~~~~   97 (202)
T d1iruh_          23 GSYIANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEMCYRY-----REDLMAG   97 (202)
T ss_dssp             TTEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHT-----TTTCCEE
T ss_pred             CCeeecCCcceEEEcCCcEEEEeccchHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHhh-----ccceeEE
Confidence            35677899999999999999999999999999999999999999999999999999999999998654     3699999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIE  161 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~ie  161 (191)
                      +|++|||+.++|+||.+||.|++.+.+++|+|+|+..++++|++.|  .++||.+||++++++||..+.+||+.++ +++
T Consensus        98 ~lvaG~d~~~~~~l~~~d~~g~~~~~~~~a~G~g~~~a~~~L~~~~--~~~~~~~ea~~l~~~al~~a~~rD~~sg~~i~  175 (202)
T d1iruh_          98 IIIAGWDPQEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATY--REGMTKEECLQFTANALALAMERDGSSGGVIR  175 (202)
T ss_dssp             EEEEEEETTTEEEEEEECTTSCCEECSEEEESGGGGGGHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHBTTCCSCEE
T ss_pred             EEEEEeecCCCcEEEEECCCCceeecceeEEeCCHHHHHHHHHHhh--ccCCcHHHHHHHHHHHHHHHHhhCCCCCCCEE
Confidence            9999999878899999999999999999999999999999999998  5889999999999999999999999886 899


Q ss_pred             EEEEEeCCCcEEEcCHHHHHHH
Q 029560          162 VGVVSKENPEFRVLSIEEIDEH  183 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~~~  183 (191)
                      |++|+++|..++.++++||+++
T Consensus       176 v~vi~~~G~~~~~~~~d~~~~~  197 (202)
T d1iruh_         176 LAAIAESGVERQVLLGDQIPKF  197 (202)
T ss_dssp             EEEEETTEEEEEEECGGGSCCC
T ss_pred             EEEEeCCCeEEEEcCHHHhhhh
Confidence            9999999877778999988655

>d1q5qa_ d.153.1.4 (A:) Proteasome alpha subunit (non-catalytic) {Rhodococcus erythropolis [TaxId: 1833]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Rhodococcus erythropolis [TaxId: 1833]

Probab=100.00  E-value=6.1e-39  Score=251.68  Aligned_cols=175  Identities=15%  Similarity=0.223  Sum_probs=151.8

Q ss_pred             CCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHHHHhhhhcCcccccceeEEE
Q 029560            8 HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGY-EMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVL   86 (191)
Q Consensus         8 ~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~-~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~iv~   86 (191)
                      +++.+||++|+|||+|+++|+.+|++.|+++++.++..|+++++. +++++.+++.++++++. ++..++|||+|++|||
T Consensus        39 ~~s~~KI~~i~~~i~~~~sG~~aD~~~l~~~~r~~~~~~~~~~~~~~~~~~~la~~~~~~~~~-~~~~~~rP~gvs~lva  117 (227)
T d1q5qa_          39 STALHKVSELYDRLGFAAVGKYNEFENLRRAGIVHADMRGYSYDRRDVTGRSLANAYAQTLGT-IFTEQPKPYEVEICVA  117 (227)
T ss_dssp             CSSSCSEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHHHHHHH-HHHHSSSCCCEEEEEE
T ss_pred             CCCcceEEEecCceEEEecCchHHHHHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHH-HHHhcCCCceEEEEEE
Confidence            357899999999999999999999999999999999999999985 68999999999998763 4455679999999999


Q ss_pred             EEcCC---CCCeEEEECCCcceecee-eeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCC-----C
Q 029560           87 SIDEE---CGPRLFKCDPAGHFFGHK-ATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFK-----A  157 (191)
Q Consensus        87 G~d~~---~~p~Ly~~d~~G~~~~~~-~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~-----~  157 (191)
                      |||..   ++|+||.+||+|++.+++ +++.|++++.++++|+++|  +++||++||+++|++||+.+.++|..     .
T Consensus       118 G~D~~g~~~~p~Ly~vDpsG~~~~~~~~~~~g~~s~~~~~~Le~~y--~~~ms~eea~~la~~aL~~a~~~d~~~~~~~~  195 (227)
T d1q5qa_         118 EVGRVGSPKAPQLYRITYDGSIVDEQHFVVMGGTTEPIATAMRESY--RADLDLEAAVGIAVNALRQGGAGEGEKRNVDV  195 (227)
T ss_dssp             ECCCSSCCCCCEEEEEETTSCEEEESSEEEESSSHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHTTCC--------CCS
T ss_pred             EEecCCCCCCCEEEEEccccceeeecccccCCCchHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHhhcccccCCcCc
Confidence            99963   579999999999998876 4666788999999999998  48999999999999999999988743     3


Q ss_pred             CeEEEEEEEeCCC--cEEEcCHHHHHHHHH
Q 029560          158 SEIEVGVVSKENP--EFRVLSIEEIDEHLT  185 (191)
Q Consensus       158 ~~iei~iv~~~~~--~~~~~~~~~i~~~~~  185 (191)
                      .++||++++++++  .|++++++||+++|+
T Consensus       196 ~~ievavi~k~~~~~~fr~l~~~ei~~~l~  225 (227)
T d1q5qa_         196 ASLEVAVLDQSRPRRAFRRIAGTALEQLVP  225 (227)
T ss_dssp             SCSEEEEEETTSSSCCEEECCHHHHHTTSC
T ss_pred             ceEEEEEEECCCCccceEEcCHHHHHHHhc
Confidence            4799999998864  599999999998875

>d1ryp2_ d.153.1.4 (2:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=3.6e-40  Score=259.58  Aligned_cols=183  Identities=14%  Similarity=0.207  Sum_probs=167.0

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHh-----CCCCCHHHHHHHHHHHHHHhhhhcCcc
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKY-----GYEMPVDVLAKWIADKSQVYTQHAYMR   77 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~-----~~~~~~~~l~~~l~~~~~~~t~~~~~r   77 (191)
                      +.++.+++++|||+|++|++|+++|..+|++.+.+.++.++..|++.+     +.+++++.+++++++.+  |+++.++|
T Consensus        31 g~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~~--y~~~~~~~  108 (233)
T d1ryp2_          31 GSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLADAEEALEPSYIFEYLATVM--YQRRSKMN  108 (233)
T ss_dssp             TTEEEESCCCCEEEETTTEEEEEEEEHHHHHHHHHHHHHHHHHHHTTCTTTTTTTSCCHHHHHHHHHHHH--HHHHHTTC
T ss_pred             CCeeecCCcceEEEeCCCEEEEeccCchHHHHHHHHHHHHHHHHHHhhCCCCCCcccCHHHHHHHHHHHH--HhhccccC
Confidence            567888999999999999999999999999999999999999999877     56789999999999987  78888899


Q ss_pred             cccceeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcC---CCCCCHHHHHHHHHHHHHhhhccc
Q 029560           78 PLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKN---DPAFTFQETVQTAISTLQSVLQED  154 (191)
Q Consensus        78 P~~v~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~---~~~~s~eea~~l~~~~l~~~~~~d  154 (191)
                      ||+|++||+|||++++|+||.+||.|++.+++++|+|+|+++++++|++.|+.   .|+||.|||++++++||+.+.+||
T Consensus       109 P~~~~~liaG~d~~g~~~ly~~d~~G~~~~~~~~a~G~g~~~a~~~Le~~~~~~~~~~~ms~eeA~~l~~~al~~~~~rD  188 (233)
T d1ryp2_         109 PLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFGAHMANPLLRKVVDRESDIPKTTVQVAEEAIVNAMRVLYYRD  188 (233)
T ss_dssp             CCCEEEEEEEECTTSCEEEEEEETTCCEECCSEEECTHHHHHHHHHHTTTCCSGGGGGGCCHHHHHHHHHHHHHHHHHHB
T ss_pred             CceeEEEEEEEcCCCCeEEEEEcCCCcEEeeeeEEecCccHHHHHHHHHHHhhcccccccCHHHHHHHHHHHHHHHHHhc
Confidence            99999999999987789999999999999999999999999999999999853   278999999999999999999999


Q ss_pred             CCCC-eEEEEEEEeCCCcEEEcCHHHHHHHHHHhh
Q 029560          155 FKAS-EIEVGVVSKENPEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       155 ~~~~-~iei~iv~~~~~~~~~~~~~~i~~~~~~~~  188 (191)
                      +.++ +|+|++|+++++ ++++++++|+.....++
T Consensus       189 ~~sg~~i~i~~itkd~g-~~~~~~~~ie~~~~~~a  222 (233)
T d1ryp2_         189 ARSSRNFSLAIIDKNTG-LTFKKNLQVENMKWDFA  222 (233)
T ss_dssp             TTCCSEEEEEEEETTTE-EEEEEEEECCSCCCGGG
T ss_pred             ccCCCCEEEEEEECCCC-EEECChhcchhhhhhHh
Confidence            9887 899999999874 99999998877544443

>d1irui_ d.153.1.4 (I:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=4.9e-38  Score=245.37  Aligned_cols=169  Identities=16%  Similarity=0.200  Sum_probs=155.9

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      +.++.+++.+||++|++|++|+++|..+|++.+.+.++.+++.|++.++++++++.++++++++++.     ..+||+++
T Consensus        23 g~~i~~~~~~KI~~i~~~i~~~~aG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~~y~-----~~~p~~~~   97 (220)
T d1irui_          23 GMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGRLPRVVTANRMLKQMLFR-----YRGYIGAA   97 (220)
T ss_dssp             SSBEEESSCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHCSCCCHHHHHHHHHHHHHH-----TTTCSCEE
T ss_pred             CCEeecCCcccEEEecCcEEEEEccccHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhhhhh-----ccccccee
Confidence            3466778999999999999999999999999999999999999999999999999999999998842     34799999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIE  161 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~ie  161 (191)
                      +|++|+|+ +||+||.+||.|++.+++++|+|+|+.+++++|++.|  +++||.+||++++++||+.+.+||+.++ +|+
T Consensus        98 ~ivaG~D~-~g~~L~~id~~G~~~~~~~~a~Gsgs~~a~~~L~~~~--~~~~s~~ea~~l~~~al~~~~~~D~~sg~~i~  174 (220)
T d1irui_          98 LVLGGVDV-TGPHLYSIYPHGSTDKLPYVTMGSGSLAAMAVFEDKF--RPDMEEEEAKNLVSEAIAAGIFNDLGSGSNID  174 (220)
T ss_dssp             EEEEEECS-SCEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHSC--CTTCCHHHHHTHHHHHHHHHHHHCTTCCSCEE
T ss_pred             EEEEEEeC-CCcEEEEEeCCCcEEEeeEEEEccccHHHHHHHHHhc--ccCCCHHHHHHHHHHHHHHhhccCCCCCCcEE
Confidence            99999998 7899999999999999999999999999999999998  5889999999999999999999998876 899


Q ss_pred             EEEEEeCCCcEEEcCHHHHH
Q 029560          162 VGVVSKENPEFRVLSIEEID  181 (191)
Q Consensus       162 i~iv~~~~~~~~~~~~~~i~  181 (191)
                      |++||++|  ++.+.+.+++
T Consensus       175 i~vitkdg--~~~~~~~~~~  192 (220)
T d1irui_         175 LCVISKNK--LDFLRPYTVP  192 (220)
T ss_dssp             EEEEETTE--EECCSEEECC
T ss_pred             EEEEECCC--eEEeCccccc
Confidence            99999986  7887776553

>d1iru2_ d.153.1.4 (2:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=1.4e-37  Score=242.24  Aligned_cols=174  Identities=14%  Similarity=0.176  Sum_probs=159.5

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHH-hCCCCCHHHHHHHHHHHHHHhhhhcCcccccc
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFK-YGYEMPVDVLAKWIADKSQVYTQHAYMRPLGV   81 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~-~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v   81 (191)
                      +.++.+++.+||++|++|++||++|..+|++.+.+.++.++..|++. ++.+++++.+++++++.+  |+++...|||++
T Consensus        31 g~~~~~~~~~KI~~i~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~v~~~a~~l~~~~--y~~~~~~~p~~~  108 (217)
T d1iru2_          31 GSLARFRNISRIMRVNNSTMLGASGDYADFQYLKQVLGQMVIDEELLGDGHSYSPRAIHSWLTRAM--YSRRSKMNPLWN  108 (217)
T ss_dssp             TTEEEECSCCCEEEETTTEEEEEEEEHHHHHHHHHHHHHHHHHHHHHCSSCCCCHHHHHHHHHHHH--HHHHHTTCCCCE
T ss_pred             CCeeecCCcceEEEeCCCeEEEeccccHHHHHHHHHHHHHHHHhhhhcCCCCCCHHHHHHHHHHHH--HHhccccCcccc
Confidence            45777899999999999999999999999999999999999887754 578999999999999977  788888999999


Q ss_pred             eeEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eE
Q 029560           82 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EI  160 (191)
Q Consensus        82 ~~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~i  160 (191)
                      ++|++|+|. ++|+||.+||+|++.+++++|+|+|+++++++|++.|++.++||.+||++++++||+.+.+||..++ ++
T Consensus       109 ~~li~G~d~-~~~~l~~~D~~G~~~~~~~~a~G~g~~~a~~~Le~~~~~~~~lt~~ea~~l~~~al~~a~~rd~~sg~~i  187 (217)
T d1iru2_         109 TMVIGGYAD-GESFLGYVDMLGVAYEAPSLATGYGAYLAQPLLREVLEKQPVLSQTEARDLVERCMRVLYYRDARSYNRF  187 (217)
T ss_dssp             EEEEEEEET-TEEEEEEECSSCCEEECSEEECTTHHHHTHHHHHHHHTSCSCCCHHHHHHHHHHHHHHHHHHBTTCCSCE
T ss_pred             eEEEEEEcC-CCcEEEEEecCceeEeeeEEeccCcHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHhcCcCCCcE
Confidence            999999997 7899999999999999999999999999999999998777999999999999999999999998886 79


Q ss_pred             EEEEEEeCCCcEEEcCHHHHH
Q 029560          161 EVGVVSKENPEFRVLSIEEID  181 (191)
Q Consensus       161 ei~iv~~~~~~~~~~~~~~i~  181 (191)
                      +|++|+++|  ++...|.+++
T Consensus       188 ~i~vi~~~G--~~~~~~~~~~  206 (217)
T d1iru2_         188 QTATVTEKG--VEIEGPLSTE  206 (217)
T ss_dssp             EEEEEETTE--EEEEEEECCC
T ss_pred             EEEEEeCCC--EEEcCCeecc
Confidence            999999986  6666665543

>d1rypi_ d.153.1.4 (I:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=8e-37  Score=238.84  Aligned_cols=165  Identities=18%  Similarity=0.193  Sum_probs=151.7

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      +.++.+++.+|||+|++|++||++|..+|++.+.+.++.++..|++.++.++++..+++.+++.++     ...+||+++
T Consensus        23 g~~~~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~l~~~~~~~~~~~~~~~~v~~~a~~l~~~~~-----~~~~p~~~~   97 (222)
T d1rypi_          23 GPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLF-----KYQGHIGAY   97 (222)
T ss_dssp             TTEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHH-----HTTTCSCEE
T ss_pred             CceeecCCcccEEEEcCCEEEEecccchHHHHHHHHHHHHHHHhhhhhCCCCcHHHHHHHHHHHHH-----hhhhcccee
Confidence            457778899999999999999999999999999999999999999999999999999999988773     235799999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIE  161 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~ie  161 (191)
                      +|++|+|+ +||+||.+||+|++.+++++|+|+|++.++++|+++|  +++||++||++++++||+.+.+||..++ +++
T Consensus        98 ~l~aG~d~-~g~~Ly~id~~G~~~~~~~~a~Gsg~~~a~~~Le~~~--k~~ms~eea~~l~~~al~~a~~~D~~sg~~i~  174 (222)
T d1rypi_          98 LIVAGVDP-TGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHW--KQDLTKEEAIKLASDAIQAGIWNDLGSGSNVD  174 (222)
T ss_dssp             EEEEEEET-TEEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHHC--CSSCCHHHHHHHHHHHHHHHHHHCTTCCSCEE
T ss_pred             EEEEEEcC-CCcEEEEEecCcceEEeeEEEECCCcHHHHHHHHhhc--cCCCCHHHHHHHHHHHHHHHhcccCCCCCcEE
Confidence            99999998 7999999999999999999999999999999999998  4899999999999999999999999886 899


Q ss_pred             EEEEEeCCCcEEEcC
Q 029560          162 VGVVSKENPEFRVLS  176 (191)
Q Consensus       162 i~iv~~~~~~~~~~~  176 (191)
                      |+++++++. .+.+.
T Consensus       175 i~vi~~~~~-~~~~~  188 (222)
T d1rypi_         175 VCVMEIGKD-AEYLR  188 (222)
T ss_dssp             EEEEETTSC-EEEEE
T ss_pred             EEEEEcCCC-eEEec
Confidence            999998754 45443

>d1q5qh_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Rhodococcus erythropolis [TaxId: 1833]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Rhodococcus erythropolis [TaxId: 1833]

Probab=100.00  E-value=1.7e-36  Score=236.77  Aligned_cols=181  Identities=19%  Similarity=0.186  Sum_probs=165.8

Q ss_pred             CccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            3 DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         3 s~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      +.++.+++++||++|++|++|+++|..+|++.+.++++.+++.|++.++.+++++.+++++++.++.|++ ...+|+++.
T Consensus        23 g~~i~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~  101 (224)
T d1q5qh_          23 GNLIASRDVEKVYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEGVPLTFDGKANRLASMVRGNLG-AAMQGLAVV  101 (224)
T ss_dssp             TTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHTTHH-HHTTTCCEE
T ss_pred             CCEeecCCcceEEEeCCcEEEEecccchHHHHHHHHHHHHhHHHHHhhCCCccHHHHHHHHHHHHHHhhc-ccccCccce
Confidence            3567788999999999999999999999999999999999999999999999999999999999998865 557899999


Q ss_pred             eEEEEEc-----CCCCCeEEEECCCcceece--eeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccC
Q 029560           83 AMVLSID-----EECGPRLFKCDPAGHFFGH--KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDF  155 (191)
Q Consensus        83 ~iv~G~d-----~~~~p~Ly~~d~~G~~~~~--~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~  155 (191)
                      ++++|++     .+++|+||.+||+|+..++  ++.|+|+|+.+|+++||++|  +++||.+||++++++||+.+.+||.
T Consensus       102 ~~~~g~~~~g~d~~~~~~l~~~d~~G~~~~~~~~~~a~GsG~~~a~~~Le~~~--~~~mt~~ea~~l~~~al~~a~~rD~  179 (224)
T d1q5qh_         102 PLLVGYDLDADDESRAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALKKIY--SPDSDEETALRAAIESLYDAADDDS  179 (224)
T ss_dssp             EEEEEECTTCSSTTSCEEEEEECTTSCEEECCSSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHCT
T ss_pred             eeEEEeecccccccCCceEEEEEccCcEEEeccceeeecCccHHHHHHHHHhh--cccCCHHHHHHHHHHHHHHHHhhcc
Confidence            9999886     3468999999999998765  67999999999999999998  4889999999999999999999999


Q ss_pred             CCCe--------EEEEEEEeCCCcEEEcCHHHHHHHHHHhh
Q 029560          156 KASE--------IEVGVVSKENPEFRVLSIEEIDEHLTAIS  188 (191)
Q Consensus       156 ~~~~--------iei~iv~~~~~~~~~~~~~~i~~~~~~~~  188 (191)
                      .+++        +++++++++|  |++++++||++++.++.
T Consensus       180 ~SGg~~~~~~~~~~~~~i~~~g--~~~l~~~ei~~~~~~~~  218 (224)
T d1q5qh_         180 ATGGPDLTRGIYPTAVTITQAG--AVHVSEETTSELARRIV  218 (224)
T ss_dssp             TTCCCBTTTTBCCEEEEEETTE--EEECCHHHHHHHHHHHH
T ss_pred             ccCCcccccccceEEEEEeCCc--EEEcCHHHHHHHHHHHH
Confidence            8863        7899999986  99999999999999886

>d1ryp1_ d.153.1.4 (1:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1.5e-35  Score=231.19  Aligned_cols=163  Identities=15%  Similarity=0.287  Sum_probs=146.3

Q ss_pred             ccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            4 KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYG-YEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~-~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      .++.+++++||++|++|++|++||..+|++.+.++++.+++.|++.++ .++++..+++.++...    ++.+.|||+|+
T Consensus        33 ~~i~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~p~~~~  108 (222)
T d1ryp1_          33 YSINSRYEPKVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKLSINSAARNIQHLL----YGKRFFPYYVH  108 (222)
T ss_dssp             TEEEESCCCCCEECSTTCEEEEEESHHHHHHHHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHH----HTTTTSCCCEE
T ss_pred             CEeccCCcceEEEecCCEEEEeccChHHHHHHHHHHHHHhhhhhhhcCCCCCcHHHHHHHHHHHH----Hhhhhhhheee
Confidence            345678999999999999999999999999999999999999999876 4678877777666544    46678999999


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCC---------------CCCCHHHHHHHHHHHH
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKND---------------PAFTFQETVQTAISTL  147 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~---------------~~~s~eea~~l~~~~l  147 (191)
                      +||+|||++++|+||.+||+|++.+++++|+|+|++.++++||++|+..               ++||.+||++++++||
T Consensus       109 ~li~G~d~~~~~~Ly~~D~~G~~~~~~~~a~G~g~~~a~~~Le~~~~~~~~~~~~~~~~~~~~~~~lt~~ea~~l~~~al  188 (222)
T d1ryp1_         109 TIIAGLDEDGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYEPGTNGKVKKPLKYLSVEEVIKLVRDSF  188 (222)
T ss_dssp             EEEEEECTTSCEEEEEECTTSCEEEESEEEEETTHHHHHHHHHHHTSCTTCBCTTSTTCSBCCCCCCCHHHHHHHHHHHH
T ss_pred             eeEEEEeCCCCeEEEEECCCcEEEEeceEEEcccHHHHHHHHHHhhccccccCcccchhhhcccccccHHHHHHHHHHHH
Confidence            9999999877899999999999999999999999999999999998521               6899999999999999


Q ss_pred             HhhhcccCCCC-eEEEEEEEeCCC
Q 029560          148 QSVLQEDFKAS-EIEVGVVSKENP  170 (191)
Q Consensus       148 ~~~~~~d~~~~-~iei~iv~~~~~  170 (191)
                      ..+.+||+.++ +++|++||++|.
T Consensus       189 ~~a~~rd~~sg~~v~v~iitkdGv  212 (222)
T d1ryp1_         189 TSATERHIQVGDGLEILIVTKDGV  212 (222)
T ss_dssp             HHHHHHBTTCCSEEEEEEEETTEE
T ss_pred             HHHHHhcccCCCcEEEEEEeCCCE
Confidence            99999999887 799999999973

>d1iruj_ d.153.1.4 (J:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=2e-35  Score=227.99  Aligned_cols=166  Identities=16%  Similarity=0.237  Sum_probs=150.1

Q ss_pred             ccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccccee
Q 029560            4 KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVA   83 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~   83 (191)
                      .++.+++.+|||+|++|++||++|..+|++.+.+.++.+++.|++.++.+++++.++++++++++.    .+++||+|++
T Consensus        31 ~~~~~~~~~Ki~~I~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~~~~----~~~~p~~~~~  106 (204)
T d1iruj_          31 AQLVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFRLNLYELKEGRQIKPYTLMSMVANLLYE----KRFGPYYTEP  106 (204)
T ss_dssp             TEEEESCCCCEEECSTTEEEECCSCHHHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHT----TTTSCCSCCC
T ss_pred             CeeEcCcccEEEEeCCCeEEEeccCchHHHHHHHHHHHhhhhhhhhcccccchHHHHHHHHHHHHH----hhhccceeEE
Confidence            356678999999999999999999999999999999999999999999999999999999998854    3468999999


Q ss_pred             EEEEEcCCC-CCeEEEECCCcceece-eeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eE
Q 029560           84 MVLSIDEEC-GPRLFKCDPAGHFFGH-KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EI  160 (191)
Q Consensus        84 iv~G~d~~~-~p~Ly~~d~~G~~~~~-~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~i  160 (191)
                      ||||||+++ +|.+|.+||.|....+ .++++|+|++.++++|++.|  +++||.+||++++++||+.+.+||..++ ++
T Consensus       107 lvaG~D~~~~~~~~~~~d~~g~~~~~~~~~~~G~g~~~~~~~l~~~~--~~~ms~~ea~~l~~~al~~a~~rd~~sg~~~  184 (204)
T d1iruj_         107 VIAGLDPKTFKPFICSLDLIGCPMVTDDFVVSGTCAEQMYGMCESLW--EPNMDPDHLFETISQAMLNAVDRDAVSGMGV  184 (204)
T ss_dssp             EEEEECTTSCCEEEEEECTTCCEEECSSEEEEETTHHHHHHHHHHHC--CSSCCHHHHHHHHHHHHHHHGGGBTTSCSCE
T ss_pred             EEEEEcCCCCceEEEEecCCCceeeecceEEechhHHHHHHHHHhcc--ccCCCHHHHHHHHHHHHHHHHhhcccCCCcE
Confidence            999999743 6889999999997766 57899999999999999998  4889999999999999999999999886 89


Q ss_pred             EEEEEEeCCCcEEEc
Q 029560          161 EVGVVSKENPEFRVL  175 (191)
Q Consensus       161 ei~iv~~~~~~~~~~  175 (191)
                      +|++|+++|...+.+
T Consensus       185 ~v~ii~k~gi~~~~~  199 (204)
T d1iruj_         185 IVHIIEKDKITTRTL  199 (204)
T ss_dssp             EEEEEESSBEEEEEB
T ss_pred             EEEEEeCCCEEEEEE
Confidence            999999998544443

>d1rypj_ d.153.1.4 (J:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1.7e-34  Score=222.48  Aligned_cols=159  Identities=16%  Similarity=0.196  Sum_probs=145.6

Q ss_pred             cccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeE
Q 029560            5 LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAM   84 (191)
Q Consensus         5 l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~i   84 (191)
                      ++.+++.+|||++ +|++|+++|..+|++.+.++++.+++.|+++++.+++++.++++|++.++.    ...+||+++++
T Consensus        33 ~~~~~~~~Ki~~i-~~i~~~~~G~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~l~~----~~~~p~~v~~l  107 (204)
T d1rypj_          33 LGVSNKFEKIFHY-GHVFLGITGLATDVTTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYE----RRFGPYFVGPV  107 (204)
T ss_dssp             EEEESCCCCEEEE-TTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHT----TTTSCCCEEEE
T ss_pred             EeecCcccEEEEc-CCEEEEecCcchHHHHHHHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHHh----hcccceeeeEE
Confidence            4556889999999 599999999999999999999999999999999999999999999998853    34589999999


Q ss_pred             EEEEcCCC-CCeEEEECCCcceece-eeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEE
Q 029560           85 VLSIDEEC-GPRLFKCDPAGHFFGH-KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIE  161 (191)
Q Consensus        85 v~G~d~~~-~p~Ly~~d~~G~~~~~-~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~ie  161 (191)
                      ++|||+.+ .|+||++||+|++.++ .++++|+|++.++++|++.|  .++||.+||++++++||..+.++|..++ +++
T Consensus       108 i~G~d~~~g~~~L~~~D~~G~~~~~~~~~~~G~g~~~a~~~l~~~~--~~~ms~~ea~~l~~~al~~a~~~d~~sg~~~~  185 (204)
T d1rypj_         108 VAGINSKSGKPFIAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLY--EPNLEPEDLFETISQALLNAADRDALSGWGAV  185 (204)
T ss_dssp             EEEECTTTCCEEEEEECTTCCEECCSSEEEEETTHHHHHHHHHHHC--CSSCCHHHHHHHHHHHHHHHHTTBTTSCSCEE
T ss_pred             EEEEecCCCcceEEEeCCCCccccccCcEEeecchHHHHHHHHhcc--ccCCCHHHHHHHHHHHHHHHHHhcCccCCeEE
Confidence            99999644 4999999999999877 47888999999999999998  5899999999999999999999998876 899


Q ss_pred             EEEEEeCCC
Q 029560          162 VGVVSKENP  170 (191)
Q Consensus       162 i~iv~~~~~  170 (191)
                      |++++++|.
T Consensus       186 v~ii~kdg~  194 (204)
T d1rypj_         186 VYIIKKDEV  194 (204)
T ss_dssp             EEEEESSCE
T ss_pred             EEEEECCce
Confidence            999999974

>d1iruk_ d.153.1.4 (K:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=4e-35  Score=223.73  Aligned_cols=169  Identities=15%  Similarity=0.220  Sum_probs=156.4

Q ss_pred             cccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeE
Q 029560            5 LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAM   84 (191)
Q Consensus         5 l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~i   84 (191)
                      ++.+++.+|||+|+++++++++|..+|++.+.++++.+++.|+..++.+++++.+++.++...+.  +....+|++++++
T Consensus        26 ~~~~~~~~Ki~~i~~~i~~~~~G~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~~~~~~~~~~~~  103 (199)
T d1iruk_          26 VQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYIQKNVQLYKMRNGYELSPTAAANFTRRNLAD--CLRSRTPYHVNLL  103 (199)
T ss_dssp             EEEESSCCCEEECSSSEEEEEEESTTHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHH--HHTSSSCCCEEEE
T ss_pred             eeecCCcceEEEecCcEEEEecccchHHHHHHHHHHHHhhhhhhhcCCcCcHHHHHHHHHHHHHH--HhhccCCcceeee
Confidence            45568899999999999999999999999999999999999999999999999999999998854  4566789999999


Q ss_pred             EEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEEE
Q 029560           85 VLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVG  163 (191)
Q Consensus        85 v~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei~  163 (191)
                      ++|||+.++|+||.+||.|.+..++++|+|+|++.++++|++.|  .++||++||++++++||+.+.++|+.++ +++|+
T Consensus       104 ~aG~d~~~~~~l~~~~~~g~~~~~~~~a~G~gs~~a~~~l~~~~--~~~~~~~ea~~l~~~al~~~~~~d~~sg~~~~v~  181 (199)
T d1iruk_         104 LAGYDEHEGPALYYMDYLAALAKAPFAAHGYGAFLTLSILDRYY--TPTISRERAVELLRKCLEELQKRFILNLPTFSVR  181 (199)
T ss_dssp             EEEEETTTEEEEEEECTTCCEEECSEEEESHHHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHTBCBCCCCEEEE
T ss_pred             ecceeccCCceEEeecccceEEeeeeeeecccchhhhHHHHHhc--cCCCCHHHHHHHHHHHHHHHHHhcCCcCCceEEE
Confidence            99999877899999999999999999999999999999999998  5889999999999999999999998886 89999


Q ss_pred             EEEeCCCcEEEcCHHH
Q 029560          164 VVSKENPEFRVLSIEE  179 (191)
Q Consensus       164 iv~~~~~~~~~~~~~~  179 (191)
                      +|+++|  ++.+++..
T Consensus       182 vv~~~g--~~~~~~~~  195 (199)
T d1iruk_         182 IIDKNG--IHDLDNIS  195 (199)
T ss_dssp             EEETTE--EECCCCBC
T ss_pred             EEcCCC--eEEcCCcc
Confidence            999986  88877643

>d1iru1_ d.153.1.4 (1:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=7.9e-33  Score=213.73  Aligned_cols=163  Identities=13%  Similarity=0.199  Sum_probs=151.4

Q ss_pred             ccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccccee
Q 029560            4 KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVA   83 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~   83 (191)
                      .++.+++++||++|++|++++++|..+|++.+.++++.+++.|++.++.++++..+++.+++.++.+    ..+|+++++
T Consensus        33 ~~~~~~~~~KI~~i~~~i~~~~aG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~  108 (213)
T d1iru1_          33 FSIHTRDSPKCYKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMTTGAIAAMLSTILYSR----RFFPYYVYN  108 (213)
T ss_dssp             TEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHTT----TTSCCCEEE
T ss_pred             ceeeccccCEEEEcCCCEEEEecCccchHHHHHHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHH----Hhhhccccc
Confidence            3556788999999999999999999999999999999999999999999999999999999988654    457999999


Q ss_pred             EEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcC-------CCCCCHHHHHHHHHHHHHhhhcccCC
Q 029560           84 MVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKN-------DPAFTFQETVQTAISTLQSVLQEDFK  156 (191)
Q Consensus        84 iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~-------~~~~s~eea~~l~~~~l~~~~~~d~~  156 (191)
                      +++|||.+++|.+|.+||.|++.++++.|+|+|+.++++.||+.|.+       .++||++||++++++||..+.++|+.
T Consensus       109 ~~~g~d~~~~~~l~~~d~~g~~~~~~~~a~G~g~~~a~~~l~~~~~~~~~~~~~~~~~s~~ea~~~~~~~l~~~~~~d~~  188 (213)
T d1iru1_         109 IIGGLDEEGKGAVYSFDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVEHVPLSLDRAMRLVKDVFISAAERDVY  188 (213)
T ss_dssp             EEEEECTTSCEEEEEECTTSCEEEESEEEEETTHHHHHHHHHHHTTCCSCSSCCCCCCCHHHHHHHHHHHHHHHHHHBTT
T ss_pred             ceEEEecCCCcEEEecCCcceeeecCeeeecCccHHHHHHHHHhhcccchhcccccCCCHHHHHHHHHHHHHHHHHhcCC
Confidence            99999998889999999999999999999999999999999998752       37899999999999999999999998


Q ss_pred             CC-eEEEEEEEeCCC
Q 029560          157 AS-EIEVGVVSKENP  170 (191)
Q Consensus       157 ~~-~iei~iv~~~~~  170 (191)
                      ++ +++|++||++|.
T Consensus       189 sg~~~~v~~i~k~G~  203 (213)
T d1iru1_         189 TGDALRICIVTKEGI  203 (213)
T ss_dssp             SCSEEEEEEEETTEE
T ss_pred             CCCceEEEEEeCCCE
Confidence            87 799999999973

>d1m4ya_ d.153.1.4 (A:) HslV (ClpQ) protease {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: HslV (ClpQ) protease
species: Thermotoga maritima [TaxId: 2336]

Probab=99.72  E-value=6.2e-18  Score=125.29  Aligned_cols=146  Identities=7%  Similarity=-0.097  Sum_probs=109.2

Q ss_pred             ccccCCCCcceEEecCcEEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCccccccee
Q 029560            4 KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVA   83 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~   83 (191)
                      .++.+++.+||++|+++++++.+|..+|.+.+......+...+..     ..........+..+.     ....++....
T Consensus        24 ~~i~~r~~~Ki~~i~~~~~~~~~g~~ad~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~-----~~~~~~~~~~   93 (171)
T d1m4ya_          24 STVLKGNARKVRKLGEGKVLAGFAGSVADAMTLFDRFEAKLREWG-----GNLTKAAVELAKDWR-----TDRVLRRLEA   93 (171)
T ss_dssp             TEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHHHHHHHHHHTT-----TCHHHHHHHHHHHHH-----HCTTGGGCCC
T ss_pred             CEEEeCCcceEEEecCCcEEEEEeechhhHHHHHHHHHHHHHHhh-----ccchhhHHHHHHHHH-----Hhhhhccccc
Confidence            467789999999999999999999999999887766655443322     122222222222221     1122344445


Q ss_pred             EEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEE
Q 029560           84 MVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEV  162 (191)
Q Consensus        84 iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei  162 (191)
                      ++.+.+. ++|+++..|+.|......+.|+|+|+.+|++.|+.+++ .++|   +|.+++++||+.|.++|..++ +++|
T Consensus        94 ~~~~~~~-~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~l~~~~~-~~~~---~a~el~~~Ai~~A~e~dvyTg~~~~i  168 (171)
T d1m4ya_          94 LLLVADK-ENIFIISGNGEVIQPDDDAAAIGSGGPYALAAAKALLR-NTDL---SAREIVEKAMTIAGEICIYTNQNIVI  168 (171)
T ss_dssp             EEEEECS-SCEEEECTTSCEECCSSSEEEESTTHHHHHHHHHHHHH-HCCC---CHHHHHHHHHHHHHHHCTTCCSCCEE
T ss_pred             ccceecC-CcceEEecCCceeeecCCEEEEcchHHHHHHHHHhhcc-CCCC---CHHHHHHHHHHHHHhhceEcCCcEEE
Confidence            5556665 78999999999999999999999999999999999874 3566   577899999999999999987 7877


Q ss_pred             EE
Q 029560          163 GV  164 (191)
Q Consensus       163 ~i  164 (191)
                      ..
T Consensus       169 ~~  170 (171)
T d1m4ya_         169 EE  170 (171)
T ss_dssp             EE
T ss_pred             EE
Confidence            64

>d2z3ba1 d.153.1.4 (A:1-180) HslV (ClpQ) protease {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: HslV (ClpQ) protease
species: Bacillus subtilis [TaxId: 1423]

Probab=99.67  E-value=1.6e-16  Score=118.71  Aligned_cols=146  Identities=12%  Similarity=-0.049  Sum_probs=100.6

Q ss_pred             ccCCCCcceEEecCc-EEEEEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccceeE
Q 029560            6 LDHTSVTHLFPITKY-LGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAM   84 (191)
Q Consensus         6 ~~~~~~~Ki~~i~~~-i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~~i   84 (191)
                      +.+...+|++.++++ ++++.+|..+|.+.+.+..+.+...++.     -....+.............+....++.+...
T Consensus        32 ~~~~~~~ki~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  106 (180)
T d2z3ba1          32 VMKHTARKVRKLFNGKVLAGFAGSVADAFTLFEKFEAKLEEYNG-----NLKRAAVELAKEWRSDKVLRKLEAMLIVMNQ  106 (180)
T ss_dssp             EEESCCCCEEEETTTTEEEEECSCHHHHHHHHHHHHHHHHHTTT-----CHHHHHHHHHHHHHHCTTGGGCCCCEEEECS
T ss_pred             EecccceEEEEecccceecccchHHHHHHHHHHHHHHHHHhhcc-----ccchhHHHHHHHHhHHHHHHHhhcceeeeec
Confidence            334568999999875 8888899999999999887766654422     1122222222222221222333334444444


Q ss_pred             EEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEEEE
Q 029560           85 VLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVG  163 (191)
Q Consensus        85 v~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~iei~  163 (191)
                      .+|++. .++.++..++.|      +.|+|+|+.+|++.|+..|+  ++||.+||++++++||+.|.++|..++ +++|.
T Consensus       107 ~~~~~~-~~~~~~~~~~~~------~~a~GSGs~~A~g~l~~~~~--~~~s~~eA~~l~~~Al~~A~e~dvyT~~~~~~~  177 (180)
T d2z3ba1         107 DTLLLV-SGTGEVIEPDDG------ILAIGSGGNYALAAGRALKK--HAGESMSASEIARAALETAGEICVYTNDQIILE  177 (180)
T ss_dssp             SCEEEE-CTTCCEECCSSS------EEEESTTHHHHHHHHHHHHH--HHGGGCCHHHHHHHHHHHHHHHCTTCCSCCEEE
T ss_pred             cccccc-cCCceeeccccc------EEEEcCchHHHHHHHHHHhh--cCCCccCHHHHHHHHHHHHHhhcEEcCCcEEEE
Confidence            445554 445555555444      78999999999999999995  789999999999999999999999886 78777


Q ss_pred             EE
Q 029560          164 VV  165 (191)
Q Consensus       164 iv  165 (191)
                      +|
T Consensus       178 ~i  179 (180)
T d2z3ba1         178 EL  179 (180)
T ss_dssp             EE
T ss_pred             Ee
Confidence            65

>d1g3ka_ d.153.1.4 (A:) HslV (ClpQ) protease {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: HslV (ClpQ) protease
species: Haemophilus influenzae [TaxId: 727]

Probab=99.66  E-value=4.2e-16  Score=115.49  Aligned_cols=147  Identities=11%  Similarity=-0.081  Sum_probs=101.3

Q ss_pred             ccccCCCCcceEEecCcEEE-EEecchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhhcCcccccce
Q 029560            4 KLLDHTSVTHLFPITKYLGL-LATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV   82 (191)
Q Consensus         4 ~l~~~~~~~Ki~~i~~~i~~-~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~t~~~~~rP~~v~   82 (191)
                      .++.+++.+||++|++++++ +.+|...+.+.+.+..+....     .. ..+....+..++..+.    .....+....
T Consensus        24 ~~i~~r~~~Ki~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~-~~~~~~~~~~~~~~~~----~~~~~~~~~~   93 (173)
T d1g3ka_          24 NTVMKGNARKVRRLYNGKVLAGFAGGTADAFTLFELFERKLE-----MH-QGHLLKSAVELAKDWR----TDRALRKLEA   93 (173)
T ss_dssp             TEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHHHHHHHHH-----HT-TTCHHHHHHHHHHHHH----HSTTGGGCCC
T ss_pred             CEeEcCCcceEEEecCCcEEEEeeehhHhHHHHHHHHHHHHH-----hh-cCcchhHHHHHHHHHH----Hhhhhccccc
Confidence            46778999999999888555 455555554444433322221     12 2233333344443332    2223344344


Q ss_pred             eEEEEEcCCCCCeEEEECCCcceeceeeeecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhcccCCCC-eEE
Q 029560           83 AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIE  161 (191)
Q Consensus        83 ~iv~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l~~~~~~d~~~~-~ie  161 (191)
                      . +.+++.+++|.++..|+.|...+..+.|+|+|+.+|++.|+.+++    ++.+||.+++++||+.|.++|..++ +++
T Consensus        94 ~-~~~~~~~~~~~~~~~~~~~~~~~~~~~a~GSGs~~A~~~l~~~~~----~~~~~A~ela~~Ai~~Aae~dvyTgd~~~  168 (173)
T d1g3ka_          94 M-LIVADEKESLIITGIGDVVQPEEDQILAIGSGGNYALSAARALVE----NTELSAHEIVEKSLRIAGDICVFTNTNFT  168 (173)
T ss_dssp             E-EEEECSSCEEEEETTTEEECCCTTCEEEESTTHHHHHHHHHHHHH----HCCCCHHHHHHHHHHHHHHHCTTCCSCCE
T ss_pred             c-cccccCCCcceecccCceEEecCCCEEEecchHHHHHHHHHHhhh----cCCCCHHHHHHHHHHHHHhhcEEcCCcEE
Confidence            4 445555588999999999999999999999999999999999874    4556899999999999999999886 787


Q ss_pred             EEEE
Q 029560          162 VGVV  165 (191)
Q Consensus       162 i~iv  165 (191)
                      |.+|
T Consensus       169 i~~~  172 (173)
T d1g3ka_         169 IEEL  172 (173)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            7654

>d1cuka1 a.5.1.1 (A:156-203) DNA helicase RuvA subunit, C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: DNA helicase RuvA subunit, C-terminal domain
family: DNA helicase RuvA subunit, C-terminal domain
domain: DNA helicase RuvA subunit, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=83.17  E-value=0.54  Score=25.69  Aligned_cols=35  Identities=23%  Similarity=0.316  Sum_probs=28.9

Q ss_pred             eecCCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHH
Q 029560          111 TSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL  147 (191)
Q Consensus       111 ~a~G~gs~~~~~~Le~~~~~~~~~s~eea~~l~~~~l  147 (191)
                      .+.|+....+...+.+..  .+++|.|+.++.+++++
T Consensus        13 ~~LGY~~~ea~~av~~i~--~~~~s~E~lIk~ALk~m   47 (48)
T d1cuka1          13 VALGYKPQEASRMVSKIA--RPDASSETLIREALRAA   47 (48)
T ss_dssp             HHHTCCHHHHHHHHHHSC--CSSCCHHHHHHHHHHTT
T ss_pred             HHcCCCHHHHHHHHHHhc--CCCCCHHHHHHHHHHHh
Confidence            367999999999999874  57899999998887754