Citrus Sinensis ID: 031203

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160----
Protein Sequence
MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD
Secondary Structure (PSIPRED)
ccccHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHcccccccHHHEEEEEEEccccccEEEEEcccccccccEEEEEccccHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHccccccccEEEEEEEcccccEEEccHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHEccccccccEEEEEEEEcccEEEEEEEcccccEEEEcEEEEcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHccccccccEEEEEEEcccccEEEccHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDeecgprlfkcdpaghffghkatsaglKEQEAINFLEKkmkndpaftfQETVQTAISTLQSVLQEdfkaseievgvvskenpefrvLSIEEIDEHLTAISERD
Flexible Loop (DISEMBL)
mtadartlVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASeievgvvskenpefrvlsieeidehltaiserd
Low Complexity Region (SEG)
MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD
Disordered region (IsUnstruct)
********VQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEI***********
Disordered Region (DISOPRED)
MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISE**
Disordered Region (DISEMBL)
MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD
Disordered Region (DISPRO)
MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAIS***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	164	2.2.26 [Sep-21-2011]
Q9XG77	246	Proteasome subunit alpha	N/A	no	1.0	0.666	0.902	2e-84
O48551	246	Proteasome subunit alpha	no	no	1.0	0.666	0.884	3e-84
O81146	246	Proteasome subunit alpha	yes	no	1.0	0.666	0.835	3e-80
O81147	246	Proteasome subunit alpha	no	no	1.0	0.666	0.835	6e-79
Q9LSU3	246	Proteasome subunit alpha	yes	no	1.0	0.666	0.823	5e-76
Q9QUM9	246	Proteasome subunit alpha	yes	no	1.0	0.666	0.609	8e-56
P60901	246	Proteasome subunit alpha	yes	no	1.0	0.666	0.609	9e-56
P60900	246	Proteasome subunit alpha	yes	no	1.0	0.666	0.609	9e-56
Q2YDE4	246	Proteasome subunit alpha	yes	no	1.0	0.666	0.609	9e-56
Q9XZJ4	244	Proteasome subunit alpha	yes	no	0.975	0.655	0.574	7e-48

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

 Score =  310 bits (795), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 148/164 (90%), Positives = 156/164 (95%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           MTADARTLVQQAR EAAEFRFKYGYEMPVDVL+KWIADKSQVYTQHAYMRPLGVVAM+L 
Sbjct: 83  MTADARTLVQQARNEAAEFRFKYGYEMPVDVLSKWIADKSQVYTQHAYMRPLGVVAMILG 142

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           IDEE GP+LFKCDPAGHFFGHKATSAG KEQEAINFLEKKMKNDPAF+++ETVQTAIS L
Sbjct: 143 IDEEKGPQLFKCDPAGHFFGHKATSAGSKEQEAINFLEKKMKNDPAFSYEETVQTAISAL 202

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
           QSVLQEDFKASEIEVGVV KE+P FRVL+ EEIDEHLTAISERD
Sbjct: 203 QSVLQEDFKASEIEVGVVKKEDPIFRVLTTEEIDEHLTAISERD 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 =  310 bits (793), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 145/164 (88%), Positives = 157/164 (95%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           MTADARTLVQQAR EAAEFRF YGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVL 
Sbjct: 83  MTADARTLVQQARNEAAEFRFTYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLG 142

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ID+E GP+L+KCDPAGH+FGHKATSAGLK+QEAINFLEKKMKNDP+FT++ETVQTAIS L
Sbjct: 143 IDDEYGPQLYKCDPAGHYFGHKATSAGLKDQEAINFLEKKMKNDPSFTYEETVQTAISAL 202

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
           QSVLQEDFKA+EIEVGVV K+NPEFRVL+ +EIDEHLTAISERD
Sbjct: 203 QSVLQEDFKATEIEVGVVRKDNPEFRVLTTDEIDEHLTAISERD 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 =  296 bits (759), Expect = 3e-80,   Method: Compositional matrix adjust.
 Identities = 137/164 (83%), Positives = 152/164 (92%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADAR+LVQQAR +AAEFRF YGYEMPVD+LAKWIADKSQVYTQHAYMRPLGVVAMV+ 
Sbjct: 83  ITADARSLVQQARNQAAEFRFTYGYEMPVDILAKWIADKSQVYTQHAYMRPLGVVAMVMG 142

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           +DEE GP L+KCDPAGHF+GHKATSAG+KEQEA+NFLEKKMK +P+FTF ETVQTAIS L
Sbjct: 143 VDEENGPLLYKCDPAGHFYGHKATSAGMKEQEAVNFLEKKMKENPSFTFDETVQTAISAL 202

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
           QSVLQEDFKA+EIEVGVV  ENPEFR L+ EEI+EHLTAISERD
Sbjct: 203 QSVLQEDFKATEIEVGVVRAENPEFRALTTEEIEEHLTAISERD 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 =  292 bits (748), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 137/164 (83%), Positives = 150/164 (91%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           MTAD+R+LVQQAR EAAEFRF+YGYEMP D+LAKWIADKSQVYTQHAYMRPLGVVAMVL 
Sbjct: 83  MTADSRSLVQQARNEAAEFRFQYGYEMPADILAKWIADKSQVYTQHAYMRPLGVVAMVLG 142

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           IDEE GP L+KCDPAGHF+GHKATSAG+KEQEA+NFLEKKMK +PAFT+ ETVQTAIS L
Sbjct: 143 IDEERGPLLYKCDPAGHFYGHKATSAGMKEQEAVNFLEKKMKENPAFTYDETVQTAISAL 202

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
           QSVLQEDFKA+EIEVGVV  ++P FR L  EEIDEHLTAISERD
Sbjct: 203 QSVLQEDFKATEIEVGVVRADDPLFRSLRTEEIDEHLTAISERD 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 =  283 bits (723), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 135/164 (82%), Positives = 149/164 (90%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADAR+LV QAR EAAEFRFK+GYEMPVDVLAKWIADK+QVYTQHAYMRPLGVVAMVL 
Sbjct: 83  LTADARSLVYQARNEAAEFRFKWGYEMPVDVLAKWIADKAQVYTQHAYMRPLGVVAMVLG 142

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            DEE   +LFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMK+DP F+++ETVQ AIS L
Sbjct: 143 YDEEKNAQLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKDDPQFSYEETVQIAISAL 202

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
           QSVLQEDFKA+EIEVGVV K++  FR L+ EEID+HLTAISERD
Sbjct: 203 QSVLQEDFKATEIEVGVVRKDDRVFRALTTEEIDQHLTAISERD 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 =  215 bits (548), Expect = 8e-56,   Method: Compositional matrix adjust.
 Identities = 100/164 (60%), Positives = 135/164 (82%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           MTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD SQVYTQ+A MRPLG   +++ 
Sbjct: 83  MTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIG 142

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +FLEKK+K    +TF++TV+TAI+ L
Sbjct: 143 IDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCL 202

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
            +VL  DFK SEIEVGVV+ ENP+FR+L+  EID HL A++ERD
Sbjct: 203 STVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVALAERD 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 =  215 bits (548), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 100/164 (60%), Positives = 135/164 (82%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           MTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD SQVYTQ+A MRPLG   +++ 
Sbjct: 83  MTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIG 142

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +FLEKK+K    +TF++TV+TAI+ L
Sbjct: 143 IDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCL 202

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
            +VL  DFK SEIEVGVV+ ENP+FR+L+  EID HL A++ERD
Sbjct: 203 STVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVALAERD 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 =  215 bits (548), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 100/164 (60%), Positives = 135/164 (82%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           MTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD SQVYTQ+A MRPLG   +++ 
Sbjct: 83  MTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIG 142

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +FLEKK+K    +TF++TV+TAI+ L
Sbjct: 143 IDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCL 202

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
            +VL  DFK SEIEVGVV+ ENP+FR+L+  EID HL A++ERD
Sbjct: 203 STVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVALAERD 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 =  215 bits (548), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 100/164 (60%), Positives = 135/164 (82%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           MTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD SQVYTQ+A MRPLG   +++ 
Sbjct: 83  MTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIG 142

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +FLEKK+K    +TF++TV+TAI+ L
Sbjct: 143 IDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCL 202

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
            +VL  DFK SEIEVGVV+ ENP+FR+L+  EID HL A++ERD
Sbjct: 203 STVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVALAERD 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 =  189 bits (480), Expect = 7e-48,   Method: Compositional matrix adjust.
 Identities = 93/162 (57%), Positives = 120/162 (74%), Gaps = 2/162 (1%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSID 62
           AD+R+ VQ+ARYEAA FR+KYGYEMPVDVL + IAD +QVYTQ+A MRPLG   ++++ D
Sbjct: 85  ADSRSQVQKARYEAANFRYKYGYEMPVDVLCRRIADINQVYTQNAEMRPLGCSMVLIAYD 144

Query: 63  EECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQS 122
            E GP ++K DPAG+F G KA S G K  EA ++LEKK K  P  + ++ +Q AIS L S
Sbjct: 145 NEIGPSVYKTDPAGYFSGFKACSVGAKTLEANSYLEKKYK--PNLSEEKAIQLAISCLSS 202

Query: 123 VLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
           VL  DFK + IE+GVVSK +P FR+L   EI+EHLT I+E+D
Sbjct: 203 VLAIDFKPNGIEIGVVSKSDPTFRILDEREIEEHLTKIAEKD 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	164
255583952	246	proteasome subunit alpha type, putative	1.0	0.666	0.914	4e-84
356545355	368	PREDICTED: proteasome subunit alpha type	1.0	0.445	0.896	3e-83
12229948	246	RecName: Full=Proteasome subunit alpha t	1.0	0.666	0.902	1e-82
351721962	246	proteasome subunit alpha type-6 [Glycine	1.0	0.666	0.884	2e-82
449447912	246	PREDICTED: proteasome subunit alpha type	1.0	0.666	0.890	2e-82
211906468	246	20S proteasome subunit alpha-1 [Gossypiu	1.0	0.666	0.890	5e-82
225442079	246	PREDICTED: proteasome subunit alpha type	1.0	0.666	0.884	8e-82
217075112	246	unknown [Medicago truncatula] gi|3885172	1.0	0.666	0.865	8e-82
255648341	246	unknown [Glycine max]	1.0	0.666	0.884	1e-81
388519097	246	unknown [Lotus japonicus]	1.0	0.666	0.878	4e-81

>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 =  315 bits (807), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 150/164 (91%), Positives = 156/164 (95%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           MTADARTLVQQAR EAAEFRFKYGYEMPVDVLAKWIADKSQ+YTQHAYMRPLGVVAMVL 
Sbjct: 83  MTADARTLVQQARNEAAEFRFKYGYEMPVDVLAKWIADKSQIYTQHAYMRPLGVVAMVLG 142

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ID+E GPRL+KCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFT++ETVQTAIS L
Sbjct: 143 IDDEYGPRLYKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTYEETVQTAISAL 202

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
           QSVLQEDFKA+EIEVGVV  ENP FRVLS EEIDEHLTAISERD
Sbjct: 203 QSVLQEDFKATEIEVGVVRTENPVFRVLSTEEIDEHLTAISERD 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 =  312 bits (800), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 147/164 (89%), Positives = 157/164 (95%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           MTADARTLVQQAR EAAEFRF YGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVL 
Sbjct: 205 MTADARTLVQQARNEAAEFRFTYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLG 264

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ID+E GP+L+KCDPAGH+FGHKATSAGLK+QEAINFLEKKMKNDP+FT++ETVQTAIS L
Sbjct: 265 IDDEYGPQLYKCDPAGHYFGHKATSAGLKDQEAINFLEKKMKNDPSFTYEETVQTAISAL 324

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
           QSVLQEDFKA+EIEVGVV KENPEFRVL+ EEIDEHLTAISERD
Sbjct: 325 QSVLQEDFKATEIEVGVVRKENPEFRVLTTEEIDEHLTAISERD 368

Source: Glycine max

Species: Glycine max

Genus: Glycine

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 =  310 bits (795), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 148/164 (90%), Positives = 156/164 (95%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           MTADARTLVQQAR EAAEFRFKYGYEMPVDVL+KWIADKSQVYTQHAYMRPLGVVAM+L 
Sbjct: 83  MTADARTLVQQARNEAAEFRFKYGYEMPVDVLSKWIADKSQVYTQHAYMRPLGVVAMILG 142

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           IDEE GP+LFKCDPAGHFFGHKATSAG KEQEAINFLEKKMKNDPAF+++ETVQTAIS L
Sbjct: 143 IDEEKGPQLFKCDPAGHFFGHKATSAGSKEQEAINFLEKKMKNDPAFSYEETVQTAISAL 202

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
           QSVLQEDFKASEIEVGVV KE+P FRVL+ EEIDEHLTAISERD
Sbjct: 203 QSVLQEDFKASEIEVGVVKKEDPIFRVLTTEEIDEHLTAISERD 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 =  310 bits (793), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 145/164 (88%), Positives = 157/164 (95%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           MTADARTLVQQAR EAAEFRF YGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVL 
Sbjct: 83  MTADARTLVQQARNEAAEFRFTYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLG 142

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ID+E GP+L+KCDPAGH+FGHKATSAGLK+QEAINFLEKKMKNDP+FT++ETVQTAIS L
Sbjct: 143 IDDEYGPQLYKCDPAGHYFGHKATSAGLKDQEAINFLEKKMKNDPSFTYEETVQTAISAL 202

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
           QSVLQEDFKA+EIEVGVV K+NPEFRVL+ +EIDEHLTAISERD
Sbjct: 203 QSVLQEDFKATEIEVGVVRKDNPEFRVLTTDEIDEHLTAISERD 246

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  309 bits (792), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 146/164 (89%), Positives = 155/164 (94%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADAR+LVQQAR EAAEFRF+YGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVL 
Sbjct: 83  ITADARSLVQQARNEAAEFRFQYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLG 142

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ID+E GPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFT+ ETVQTAIS L
Sbjct: 143 IDDEYGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTYDETVQTAISAL 202

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
           QSVLQEDFKA+EIEVGVV  +NP FRVL+ EE+DEHLTAISERD
Sbjct: 203 QSVLQEDFKATEIEVGVVRSDNPIFRVLTTEEVDEHLTAISERD 246

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  308 bits (789), Expect = 5e-82,   Method: Compositional matrix adjust.
 Identities = 146/164 (89%), Positives = 155/164 (94%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           MTADARTLVQQAR EAAEFRF+YGYEMPVDVL+KWIADKSQVYTQHAYMRPLGVVAMVL 
Sbjct: 83  MTADARTLVQQARNEAAEFRFRYGYEMPVDVLSKWIADKSQVYTQHAYMRPLGVVAMVLG 142

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           IDEE GP+L+KCDPAGHF+GHKATSAG KEQEAINFLEKKMKNDPAFT++ETVQTAIS L
Sbjct: 143 IDEEKGPQLYKCDPAGHFYGHKATSAGSKEQEAINFLEKKMKNDPAFTYEETVQTAISAL 202

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
           QSVLQEDFKA+EIEVGVV  +NP FRVLS EEIDEHLTAISERD
Sbjct: 203 QSVLQEDFKATEIEVGVVKADNPAFRVLSTEEIDEHLTAISERD 246

Source: Gossypium hirsutum

Species: Gossypium hirsutum

Genus: Gossypium

Family: Malvaceae

Order: Malvales

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 =  307 bits (787), Expect = 8e-82,   Method: Compositional matrix adjust.
 Identities = 145/164 (88%), Positives = 154/164 (93%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           MTADARTLVQQAR EAAEFRF+YGYEMPVDVLA+WIADKSQVYTQHAYMRPLGVVAM+L 
Sbjct: 83  MTADARTLVQQARNEAAEFRFRYGYEMPVDVLARWIADKSQVYTQHAYMRPLGVVAMILG 142

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ID+E GPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAF++ ETVQTAIS L
Sbjct: 143 IDDENGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFSYDETVQTAISAL 202

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
           QSVLQEDFK +EIEVGVV  ++P FRVLS EEIDEHLTAISERD
Sbjct: 203 QSVLQEDFKPNEIEVGVVRTDSPAFRVLSTEEIDEHLTAISERD 246

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  307 bits (787), Expect = 8e-82,   Method: Compositional matrix adjust.
 Identities = 142/164 (86%), Positives = 157/164 (95%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADARTLVQQAR EAAE+RF+YGYEMPVDVL+KW+ADKSQVYTQHAYMRPLGVVAMVL 
Sbjct: 83  ITADARTLVQQARNEAAEYRFRYGYEMPVDVLSKWVADKSQVYTQHAYMRPLGVVAMVLG 142

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ID+E GP+L+KCDPAGH+FGHKATSAGLK+QEAINFLEKKMKNDP+FT+ ETVQTAIS L
Sbjct: 143 IDDELGPQLYKCDPAGHYFGHKATSAGLKDQEAINFLEKKMKNDPSFTYAETVQTAISAL 202

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
           QSVLQEDFKA+EIEVGVV K+NPEFRVLS +EIDEHLTAISERD
Sbjct: 203 QSVLQEDFKATEIEVGVVQKDNPEFRVLSTDEIDEHLTAISERD 246

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  306 bits (785), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 145/164 (88%), Positives = 156/164 (95%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           MTADARTLVQQAR EAAEFRF YGYE+PVDVLAKWIADKSQVYTQHAYMRPLGVVAMVL 
Sbjct: 83  MTADARTLVQQARNEAAEFRFTYGYEIPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLG 142

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ID+E G +L+KCDPAGH+FGHKATSAGLK+QEAINFLEKKMKNDP+FT++ETVQTAIS L
Sbjct: 143 IDDEYGLQLYKCDPAGHYFGHKATSAGLKDQEAINFLEKKMKNDPSFTYEETVQTAISAL 202

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
           QSVLQEDFKA+EIEVGVV KENPEFRVL+ EEIDEHLTAISERD
Sbjct: 203 QSVLQEDFKATEIEVGVVRKENPEFRVLTTEEIDEHLTAISERD 246

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  305 bits (782), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 144/164 (87%), Positives = 155/164 (94%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           MTADARTLVQQAR EAAEFR  YGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVL 
Sbjct: 83  MTADARTLVQQARNEAAEFRHTYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLG 142

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ID+E G +L+KCDPAGH+FGHKATSAGLK+QEAINFLEKKMKNDP+FT++ETVQTAIS L
Sbjct: 143 IDDENGAQLYKCDPAGHYFGHKATSAGLKDQEAINFLEKKMKNDPSFTYEETVQTAISAL 202

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
           QSVLQEDFKA+EIEVGVV K+NPEFRVLS +EIDEHLTAISERD
Sbjct: 203 QSVLQEDFKATEIEVGVVRKDNPEFRVLSTDEIDEHLTAISERD 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	164
TAIR|locus:2157106	246	PAA1 "proteasome alpha subunit	1.0	0.666	0.835	1.8e-71
TAIR|locus:2064727	246	PAA2 "20S proteasome subunit P	1.0	0.666	0.835	2.6e-70
UNIPROTKB|E2RMN2	246	PSMA6 "Proteasome subunit alph	1.0	0.666	0.615	1.3e-50
ZFIN|ZDB-GENE-020326-1	246	psma6a "proteasome (prosome, m	1.0	0.666	0.609	1.7e-50
UNIPROTKB|Q2YDE4	246	PSMA6 "Proteasome subunit alph	1.0	0.666	0.609	2.8e-50
UNIPROTKB|B4DQR4	167	PSMA6 "Proteasome subunit alph	1.0	0.982	0.609	2.8e-50
UNIPROTKB|B4DXJ9	227	PSMA6 "cDNA FLJ51729, highly s	1.0	0.722	0.609	2.8e-50
UNIPROTKB|P60900	246	PSMA6 "Proteasome subunit alph	1.0	0.666	0.609	2.8e-50
UNIPROTKB|F2Z5N0	246	PSMA6 "Proteasome subunit alph	1.0	0.666	0.609	2.8e-50
MGI|MGI:1347006	246	Psma6 "proteasome (prosome, ma	1.0	0.666	0.609	2.8e-50

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

 Score = 723 (259.6 bits), Expect = 1.8e-71, P = 1.8e-71
 Identities = 137/164 (83%), Positives = 152/164 (92%)

Query:     1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
             +TADAR+LVQQAR +AAEFRF YGYEMPVD+LAKWIADKSQVYTQHAYMRPLGVVAMV+ 
Sbjct:    83 ITADARSLVQQARNQAAEFRFTYGYEMPVDILAKWIADKSQVYTQHAYMRPLGVVAMVMG 142

Query:    61 IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
             +DEE GP L+KCDPAGHF+GHKATSAG+KEQEA+NFLEKKMK +P+FTF ETVQTAIS L
Sbjct:   143 VDEENGPLLYKCDPAGHFYGHKATSAGMKEQEAVNFLEKKMKENPSFTFDETVQTAISAL 202

Query:   121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
             QSVLQEDFKA+EIEVGVV  ENPEFR L+ EEI+EHLTAISERD
Sbjct:   203 QSVLQEDFKATEIEVGVVRAENPEFRALTTEEIEEHLTAISERD 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 = 712 (255.7 bits), Expect = 2.6e-70, P = 2.6e-70
 Identities = 137/164 (83%), Positives = 150/164 (91%)

Query:     1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
             MTAD+R+LVQQAR EAAEFRF+YGYEMP D+LAKWIADKSQVYTQHAYMRPLGVVAMVL 
Sbjct:    83 MTADSRSLVQQARNEAAEFRFQYGYEMPADILAKWIADKSQVYTQHAYMRPLGVVAMVLG 142

Query:    61 IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
             IDEE GP L+KCDPAGHF+GHKATSAG+KEQEA+NFLEKKMK +PAFT+ ETVQTAIS L
Sbjct:   143 IDEERGPLLYKCDPAGHFYGHKATSAGMKEQEAVNFLEKKMKENPAFTYDETVQTAISAL 202

Query:   121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
             QSVLQEDFKA+EIEVGVV  ++P FR L  EEIDEHLTAISERD
Sbjct:   203 QSVLQEDFKATEIEVGVVRADDPLFRSLRTEEIDEHLTAISERD 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 = 526 (190.2 bits), Expect = 1.3e-50, P = 1.3e-50
 Identities = 101/164 (61%), Positives = 135/164 (82%)

Query:     1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
             MTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD SQVYTQ+A MRPLG   +++ 
Sbjct:    83 MTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIG 142

Query:    61 IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
             IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +FLEKK+K    +TF++TV+TAI+ L
Sbjct:   143 IDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCL 202

Query:   121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
              +VL  DFK SEIEVGVV+ ENP+FR+LS  EID HL A++ERD
Sbjct:   203 STVLSIDFKPSEIEVGVVTVENPKFRILSEAEIDAHLVALAERD 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

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

 Score = 525 (189.9 bits), Expect = 1.7e-50, P = 1.7e-50
 Identities = 100/164 (60%), Positives = 133/164 (81%)

Query:     1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
             MTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD SQVYTQ+A MRPLG   +V+ 
Sbjct:    83 MTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMIVVG 142

Query:    61 IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
             +DEE GP+++KCDPAG++ G KAT+AG+K+ EA +FLEKK+K    +TF +TV+TAIS L
Sbjct:   143 VDEELGPQVYKCDPAGYYCGFKATAAGVKQTEATSFLEKKIKKKLDWTFDQTVETAISCL 202

Query:   121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
              +VL  DFK SE+E+GVV+ E P+FR+LS  EID HL A++ERD
Sbjct:   203 STVLAIDFKPSELEIGVVTTEEPKFRILSESEIDTHLMALTERD 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

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

 Score = 523 (189.2 bits), Expect = 2.8e-50, P = 2.8e-50
 Identities = 100/164 (60%), Positives = 135/164 (82%)

Query:     1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
             MTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD SQVYTQ+A MRPLG   +++ 
Sbjct:    83 MTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIG 142

Query:    61 IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
             IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +FLEKK+K    +TF++TV+TAI+ L
Sbjct:   143 IDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCL 202

Query:   121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
              +VL  DFK SEIEVGVV+ ENP+FR+L+  EID HL A++ERD
Sbjct:   203 STVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVALAERD 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|B4DQR4 PSMA6 "Proteasome subunit alpha type-6" [Homo sapiens (taxid:9606)]

 Score = 523 (189.2 bits), Expect = 2.8e-50, P = 2.8e-50
 Identities = 100/164 (60%), Positives = 135/164 (82%)

Query:     1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
             MTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD SQVYTQ+A MRPLG   +++ 
Sbjct:     4 MTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIG 63

Query:    61 IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
             IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +FLEKK+K    +TF++TV+TAI+ L
Sbjct:    64 IDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCL 123

Query:   121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
              +VL  DFK SEIEVGVV+ ENP+FR+L+  EID HL A++ERD
Sbjct:   124 STVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVALAERD 167

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

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005839 "proteasome core complex" evidence=IEA

GO:0016363 "nuclear matrix" evidence=IEA

GO:0030017 "sarcomere" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

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

 Score = 523 (189.2 bits), Expect = 2.8e-50, P = 2.8e-50
 Identities = 100/164 (60%), Positives = 135/164 (82%)

Query:     1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
             MTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD SQVYTQ+A MRPLG   +++ 
Sbjct:    64 MTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIG 123

Query:    61 IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
             IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +FLEKK+K    +TF++TV+TAI+ L
Sbjct:   124 IDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCL 183

Query:   121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
              +VL  DFK SEIEVGVV+ ENP+FR+L+  EID HL A++ERD
Sbjct:   184 STVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVALAERD 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 = 523 (189.2 bits), Expect = 2.8e-50, P = 2.8e-50
 Identities = 100/164 (60%), Positives = 135/164 (82%)

Query:     1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
             MTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD SQVYTQ+A MRPLG   +++ 
Sbjct:    83 MTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIG 142

Query:    61 IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
             IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +FLEKK+K    +TF++TV+TAI+ L
Sbjct:   143 IDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCL 202

Query:   121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
              +VL  DFK SEIEVGVV+ ENP+FR+L+  EID HL A++ERD
Sbjct:   203 STVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVALAERD 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 = 523 (189.2 bits), Expect = 2.8e-50, P = 2.8e-50
 Identities = 100/164 (60%), Positives = 135/164 (82%)

Query:     1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
             MTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD SQVYTQ+A MRPLG   +++ 
Sbjct:    83 MTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIG 142

Query:    61 IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
             IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +FLEKK+K    +TF++TV+TAI+ L
Sbjct:   143 IDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCL 202

Query:   121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
              +VL  DFK SEIEVGVV+ ENP+FR+L+  EID HL A++ERD
Sbjct:   203 STVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVALAERD 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 = 523 (189.2 bits), Expect = 2.8e-50, P = 2.8e-50
 Identities = 100/164 (60%), Positives = 135/164 (82%)

Query:     1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
             MTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD SQVYTQ+A MRPLG   +++ 
Sbjct:    83 MTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIG 142

Query:    61 IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
             IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +FLEKK+K    +TF++TV+TAI+ L
Sbjct:   143 IDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCL 202

Query:   121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
              +VL  DFK SEIEVGVV+ ENP+FR+L+  EID HL A++ERD
Sbjct:   203 STVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVALAERD 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

---

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	0.6097	1.0	0.6666	yes	no
Q9XZJ4	PSA6_DROME	3, ., 4, ., 2, 5, ., 1	0.5740	0.9756	0.6557	yes	no
O94517	PSA1_SCHPO	3, ., 4, ., 2, 5, ., 1	0.5487	0.9756	0.6557	yes	no
Q9LSU3	PSA6_ORYSJ	3, ., 4, ., 2, 5, ., 1	0.8231	1.0	0.6666	yes	no
O81146	PSA6A_ARATH	3, ., 4, ., 2, 5, ., 1	0.8353	1.0	0.6666	yes	no
Q2YDE4	PSA6_BOVIN	3, ., 4, ., 2, 5, ., 1	0.6097	1.0	0.6666	yes	no
Q9XG77	PSA6_TOBAC	3, ., 4, ., 2, 5, ., 1	0.9024	1.0	0.6666	N/A	no
P60901	PSA6_RAT	3, ., 4, ., 2, 5, ., 1	0.6097	1.0	0.6666	yes	no
P60900	PSA6_HUMAN	3, ., 4, ., 2, 5, ., 1	0.6097	1.0	0.6666	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	164
cd03754	215	cd03754, proteasome_alpha_type_6, proteasome_alpha	9e-88
cd01911	209	cd01911, proteasome_alpha, proteasome alpha subuni	3e-71
cd01906	182	cd01906, proteasome_protease_HslV, proteasome_prot	6e-42
PRK03996	241	PRK03996, PRK03996, proteasome subunit alpha; Prov	4e-41
pfam00227	188	pfam00227, Proteasome, Proteasome subunit	2e-39
TIGR03633	224	TIGR03633, arc_protsome_A, proteasome endopeptidas	7e-38
COG0638	236	COG0638, PRE1, 20S proteasome, alpha and beta subu	6e-34
cd03750	227	cd03750, proteasome_alpha_type_2, proteasome_alpha	9e-34
cd03756	211	cd03756, proteasome_alpha_archeal, proteasome_alph	1e-32
cd03749	211	cd03749, proteasome_alpha_type_1, proteasome_alpha	6e-27
PTZ00246	253	PTZ00246, PTZ00246, proteasome subunit alpha; Prov	2e-26
cd03752	213	cd03752, proteasome_alpha_type_4, proteasome_alpha	1e-24
cd03755	207	cd03755, proteasome_alpha_type_7, proteasome_alpha	1e-22
cd01901	164	cd01901, Ntn_hydrolase, The Ntn hydrolases (N-term	3e-22
cd03751	212	cd03751, proteasome_alpha_type_3, proteasome_alpha	6e-21
cd03753	213	cd03753, proteasome_alpha_type_5, proteasome_alpha	5e-19
cd03764	188	cd03764, proteasome_beta_archeal, Archeal proteaso	6e-08
TIGR03634	185	TIGR03634, arc_protsome_B, proteasome endopeptidas	2e-06
cd01912	189	cd01912, proteasome_beta, proteasome beta subunit	4e-05

>gnl|CDD|239723 cd03754, proteasome_alpha_type_6, proteasome_alpha_type_6

 Score =  255 bits (653), Expect = 9e-88
 Identities = 98/140 (70%), Positives = 120/140 (85%), Gaps = 2/140 (1%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           M AD+R+ VQ+ARYEAAEF++KYGYEMPVDVLAK IAD +QVYTQHAYMRPLGV  +++ 
Sbjct: 76  MIADSRSQVQRARYEAAEFKYKYGYEMPVDVLAKRIADINQVYTQHAYMRPLGVSMILIG 135

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAF--TFQETVQTAIS 118
           IDEE GP+L+KCDPAG+F G+KAT+AG+KEQEA NFLEKK+K  P    +++ETV+ AIS
Sbjct: 136 IDEELGPQLYKCDPAGYFAGYKATAAGVKEQEATNFLEKKLKKKPDLIESYEETVELAIS 195

Query: 119 TLQSVLQEDFKASEIEVGVV 138
            LQ+VL  DFKA+EIEVGVV
Sbjct: 196 CLQTVLSTDFKATEIEVGVV 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 =  213 bits (544), Expect = 3e-71
 Identities = 69/138 (50%), Positives = 95/138 (68%), Gaps = 2/138 (1%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADAR LV +AR EA  +R+ YG  +PV+VL K IAD +QVYTQ+  +RP GV  ++  
Sbjct: 74  LTADARVLVNRARVEAQNYRYTYGEPIPVEVLVKRIADLAQVYTQYGGVRPFGVSLLIAG 133

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            DEE GP+L++ DP+G +FG+KAT+ G   QEA  FLEK+ K D   T +E ++ A+  L
Sbjct: 134 YDEEGGPQLYQTDPSGTYFGYKATAIGKGSQEAKTFLEKRYKKDL--TLEEAIKLALKAL 191

Query: 121 QSVLQEDFKASEIEVGVV 138
           + VL+ED KA  IE+ VV
Sbjct: 192 KEVLEEDKKAKNIEIAVV 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 =  138 bits (349), Expect = 6e-42
 Identities = 58/139 (41%), Positives = 85/139 (61%), Gaps = 5/139 (3%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADA+TLV++ R EA  +R +YG  +PV+ LAK +A+    YTQ   +RPLGV  +V  
Sbjct: 48  LAADAQTLVERLRKEAQLYRLRYGEPIPVEALAKLLANLLYEYTQS--LRPLGVSLLVAG 105

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           +DEE GP+L+  DP+G +  +KAT+ G   Q A+  LEK  K D   T +E ++ A+  L
Sbjct: 106 VDEEGGPQLYSVDPSGSYIEYKATAIGSGSQYALGILEKLYKPDM--TLEEAIELALKAL 163

Query: 121 QSVLQEDF-KASEIEVGVV 138
           +S L+ D      IEV V+
Sbjct: 164 KSALERDLYSGGNIEVAVI 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|235192 PRK03996, PRK03996, proteasome subunit alpha; Provisional

 Score =  137 bits (348), Expect = 4e-41
 Identities = 58/162 (35%), Positives = 90/162 (55%), Gaps = 3/162 (1%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADAR L+ +AR EA   R  YG  + V+ L K I D  Q YTQH  +RP GV  ++  
Sbjct: 83  LVADARVLIDRARVEAQINRLTYGEPIGVETLTKKICDHKQQYTQHGGVRPFGVALLIAG 142

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           +D+  GPRLF+ DP+G +  +KAT+ G      + FLEK  K D   + +E ++ A+  L
Sbjct: 143 VDDG-GPRLFETDPSGAYLEYKATAIGAGRDTVMEFLEKNYKED--LSLEEAIELALKAL 199

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISE 162
               +       +E+  +  E  +FR LS+EEI+++L  + +
Sbjct: 200 AKANEGKLDPENVEIAYIDVETKKFRKLSVEEIEKYLEKLLK 241

Length = 241

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

 Score =  131 bits (333), Expect = 2e-39
 Identities = 59/139 (42%), Positives = 81/139 (58%), Gaps = 4/139 (2%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADA+TLV  AR EA  +R +YG  + V+ LAK IADK Q YTQ++  RP GV  ++  
Sbjct: 53  LAADAQTLVDYARAEAQLYRLRYGRPISVE-LAKRIADKLQAYTQYSGRRPYGVSLLIAG 111

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            DE+ GP L+  DP+G    +KAT+ G   Q A  FLEK  K D   T +E V+ A+  L
Sbjct: 112 YDEDGGPHLYSIDPSGSVIEYKATAIGSGSQYAYGFLEKLYKPD--MTLEEAVELAVKAL 169

Query: 121 QSVLQED-FKASEIEVGVV 138
           +  ++ D      IEV V+
Sbjct: 170 KEAIERDALSGGNIEVAVI 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|163366 TIGR03633, arc_protsome_A, proteasome endopeptidase complex, archaeal, alpha subunit

 Score =  128 bits (325), Expect = 7e-38
 Identities = 59/152 (38%), Positives = 88/152 (57%), Gaps = 3/152 (1%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADAR L+ +AR EA   R  YG  + V+ LAK I D  Q YTQH  +RP GV  ++  
Sbjct: 76  LVADARVLIDRARIEAQINRLTYGEPIDVETLAKKICDLKQQYTQHGGVRPFGVALLIAG 135

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           +D+  GPRLF+ DP+G    +KAT+ G   Q    FLEK+ + D   +  E ++ A+  L
Sbjct: 136 VDDG-GPRLFETDPSGALLEYKATAIGAGRQAVTEFLEKEYRED--LSLDEAIELALKAL 192

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEE 152
            S +++      +EV  ++ E+ +FR LS+EE
Sbjct: 193 YSAVEDKLTPENVEVAYITVEDKKFRKLSVEE 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 =  118 bits (299), Expect = 6e-34
 Identities = 62/164 (37%), Positives = 97/164 (59%), Gaps = 7/164 (4%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADA+ LV+ AR EA  +R +YG  + V+ LAK +++  Q YTQ    RP GV  +V  
Sbjct: 78  LAADAQVLVRYARAEAQLYRLRYGEPISVEALAKLLSNILQEYTQ--SGRPYGVSLLVAG 135

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           +D+  GPRL+  DP+G +  +KAT+ G   Q A  FLEK+ + D   + +E ++ A+  L
Sbjct: 136 VDDG-GPRLYSTDPSGSYNEYKATAIGSGSQFAYGFLEKEYRED--LSLEEAIELAVKAL 192

Query: 121 QSVLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 163
           ++ ++ D      IEV V++K+   FR L  EEI + L  +SE+
Sbjct: 193 RAAIERDAASGGGIEVAVITKDEG-FRKLDGEEIKKLLDDLSEK 235

Length = 236

>gnl|CDD|239719 cd03750, proteasome_alpha_type_2, proteasome_alpha_type_2

 Score =  118 bits (297), Expect = 9e-34
 Identities = 56/157 (35%), Positives = 83/157 (52%), Gaps = 4/157 (2%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           M  D R LV++AR  A ++   YG  +PV  L + IA   Q YTQ   +RP GV  ++  
Sbjct: 74  MGPDFRVLVKKARKIAQQYYLVYGEPIPVSQLVREIASVMQEYTQSGGVRPFGVSLLIAG 133

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            DE  GP L++ DP+G +F  KAT+ G     A  FLEK+   D     ++ + TAI TL
Sbjct: 134 WDEG-GPYLYQVDPSGSYFTWKATAIGKNYSNAKTFLEKRYNED--LELEDAIHTAILTL 190

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 157
           +   +       IE+G+  +    FR+L+  EI ++L
Sbjct: 191 KEGFEGQMTEKNIEIGICGETKG-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 =  114 bits (288), Expect = 1e-32
 Identities = 54/139 (38%), Positives = 81/139 (58%), Gaps = 3/139 (2%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADAR L+ +AR EA   R  YG  + V+VL K I D  Q YTQH  +RP GV  ++  
Sbjct: 75  LVADARVLIDRARVEAQIHRLTYGEPIDVEVLVKKICDLKQQYTQHGGVRPFGVALLIAG 134

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           +D+  GPRLF+ DP+G +  +KAT+ G   Q    FLEK+ K D   + +E ++ A+  L
Sbjct: 135 VDDG-GPRLFETDPSGAYNEYKATAIGSGRQAVTEFLEKEYKED--MSLEEAIELALKAL 191

Query: 121 QSVLQEDFKASEIEVGVVS 139
            + L+E+     +E+  V+
Sbjct: 192 YAALEENETPENVEIAYVT 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 =  100 bits (250), Expect = 6e-27
 Identities = 46/140 (32%), Positives = 76/140 (54%), Gaps = 3/140 (2%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADAR L +  R E   +RF Y   +PV  L   +A+K+Q+ TQ    RP GV  ++  
Sbjct: 72  LTADARVLSRYMRQECLNYRFVYDSPIPVSRLVSKVAEKAQINTQRYGRRPYGVGLLIAG 131

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            DE  GP LF+  P+G++F +KATS G + Q A  +LE+  +     + +E ++ A+  L
Sbjct: 132 YDES-GPHLFQTCPSGNYFEYKATSIGARSQSARTYLERHFEEFEDCSLEELIKHALRAL 190

Query: 121 QSVLQ--EDFKASEIEVGVV 138
           +  L   ++     + + +V
Sbjct: 191 RETLPGEQELTIKNVSIAIV 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 =   99 bits (249), Expect = 2e-26
 Identities = 58/169 (34%), Positives = 90/169 (53%), Gaps = 7/169 (4%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADA  L+ Q R  A  +R+ YG   PV+ L   I D  Q YTQ   +RP GV  +   
Sbjct: 79  LTADANILINQCRLYAQRYRYTYGEPQPVEQLVVQICDLKQSYTQFGGLRPFGVSFLFAG 138

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            DE  G +L+  DP+G++ G KAT+ G   Q A + L+++ K D   T ++ +  A   L
Sbjct: 139 YDENLGYQLYHTDPSGNYSGWKATAIGQNNQTAQSILKQEWKED--LTLEQGLLLAAKVL 196

Query: 121 -QSVLQEDFKASEIEVGVVSKENPEF----RVLSIEEIDEHLTAISERD 164
            +S+     KA +IEVG++S    +     ++LS +EI E L  +++  
Sbjct: 197 TKSMDSTSPKADKIEVGILSHGETDGEPIQKMLSEKEIAELLKKVTQEY 245

Length = 253

>gnl|CDD|239721 cd03752, proteasome_alpha_type_4, proteasome_alpha_type_4

 Score = 94.3 bits (235), Expect = 1e-24
 Identities = 41/139 (29%), Positives = 75/139 (53%), Gaps = 3/139 (2%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +T+DA  L+  AR  A  + + Y   +PV+ L + + D  Q YTQ+  +RP GV  +   
Sbjct: 77  ITSDANILINYARLIAQRYLYSYQEPIPVEQLVQRLCDIKQGYTQYGGLRPFGVSFLYAG 136

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D+  G +L++ DP+G++ G KAT+ G   Q A + L++  K+D   T +E +  A+  L
Sbjct: 137 WDKHYGFQLYQSDPSGNYSGWKATAIGNNNQAAQSLLKQDYKDDM--TLEEALALAVKVL 194

Query: 121 -QSVLQEDFKASEIEVGVV 138
            +++      + ++E   +
Sbjct: 195 SKTMDSTKLTSEKLEFATL 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 = 89.0 bits (221), Expect = 1e-22
 Identities = 45/135 (33%), Positives = 71/135 (52%), Gaps = 2/135 (1%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADAR L+ +AR E    R      + V+ + ++IA   Q YTQ   +RP G+  +++ 
Sbjct: 74  LTADARVLINRARLECQSHRLTVEDPVTVEYITRYIAGLQQRYTQSGGVRPFGISTLIVG 133

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D +  PRL++ DP+G +   KA + G   +    FLEK  K +   T  +T++ AI  L
Sbjct: 134 FDPDGTPRLYQTDPSGTYSAWKANAIGRNSKTVREFLEKNYKEE--MTRDDTIKLAIKAL 191

Query: 121 QSVLQEDFKASEIEV 135
             V+Q   K  E+ V
Sbjct: 192 LEVVQSGSKNIELAV 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|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 = 86.7 bits (215), Expect = 3e-22
 Identities = 47/123 (38%), Positives = 67/123 (54%), Gaps = 7/123 (5%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADA+TLV++ R     +R +YG  + V  LAK +A   QVYTQ    RP GV  +V  
Sbjct: 48  LAADAQTLVRRLREALQLYRLRYGEPISVVALAKELAKLLQVYTQ---GRPFGVNLIVAG 104

Query: 61  IDEECGPRLFKCDPAGHFFGH-KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAIST 119
           +DE  G  L+  DP+G    +  A + G + Q A + LEK  K D   T +E V+ A+  
Sbjct: 105 VDEG-GGNLYYIDPSGPVIENPGAVATGSRSQRAKSLLEKLYKPDM--TLEEAVELALKA 161

Query: 120 LQS 122
           L+S
Sbjct: 162 LKS 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|239720 cd03751, proteasome_alpha_type_3, proteasome_alpha_type_3

 Score = 84.6 bits (210), Expect = 6e-21
 Identities = 48/138 (34%), Positives = 73/138 (52%), Gaps = 6/138 (4%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSID 62
           AD R LV +AR EA  +R  YG  +PV VLA  +A     YT ++ +RP G   ++   D
Sbjct: 79  ADGRHLVSRAREEAENYRDNYGTPIPVKVLADRVAMYMHAYTLYSSVRPFGCSVLLGGYD 138

Query: 63  EECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQS 122
            + GP+L+  +P+G  +G+   + G  +Q A   LEK   ++   T +E V+ A   +  
Sbjct: 139 SD-GPQLYMIEPSGVSYGYFGCAIGKGKQAAKTELEKLKFSE--LTCREAVKEAAKIIYI 195

Query: 123 VLQE--DFKASEIEVGVV 138
           V  E  D KA E+E+  V
Sbjct: 196 VHDEIKD-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 = 79.7 bits (197), Expect = 5e-19
 Identities = 46/143 (32%), Positives = 76/143 (53%), Gaps = 8/143 (5%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVY-----TQHAYMRPLGVV 55
           + ADARTL+  AR EA   RF Y   M V+ + + ++D +  +      + A  RP GV 
Sbjct: 74  LIADARTLIDHARVEAQNHRFTYNEPMTVESVTQAVSDLALQFGEGDDGKKAMSRPFGVA 133

Query: 56  AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQT 115
            ++  +DE  GP+LF  DP+G F    A + G   + A + L++K   D   T +E  + 
Sbjct: 134 LLIAGVDEN-GPQLFHTDPSGTFTRCDAKAIGSGSEGAQSSLQEKYHKD--MTLEEAEKL 190

Query: 116 AISTLQSVLQEDFKASEIEVGVV 138
           A+S L+ V++E   ++ +E+  V
Sbjct: 191 ALSILKQVMEEKLNSTNVELATV 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 = 49.6 bits (119), Expect = 6e-08
 Identities = 42/148 (28%), Positives = 69/148 (46%), Gaps = 10/148 (6%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSID 62
            DA++LV+  + EA  +  + G  M +  LA  +   S +     Y  P  V  ++  +D
Sbjct: 50  GDAQSLVRILKAEARLYELRRGRPMSIKALATLL---SNILNSSKYF-PYIVQLLIGGVD 105

Query: 63  EECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQS 122
           EE GP L+  DP G     K T+ G     A   LE + K D   T +E  + AI  ++S
Sbjct: 106 EE-GPHLYSLDPLGSIIEDKYTATGSGSPYAYGVLEDEYKED--MTVEEAKKLAIRAIKS 162

Query: 123 VLQED-FKASEIEVGVVSKENPEFRVLS 149
            ++ D      I+V V++K+   ++ L 
Sbjct: 163 AIERDSASGDGIDVVVITKD--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 = 45.3 bits (108), Expect = 2e-06
 Identities = 39/141 (27%), Positives = 68/141 (48%), Gaps = 8/141 (5%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSID 62
            DA++LV+  + EA  +  + G  M V  LA  +   S +   + +  P  V  +V  +D
Sbjct: 51  GDAQSLVRILKAEAKLYELRRGRPMSVKALATLL---SNILNSNRFF-PFIVQLLVGGVD 106

Query: 63  EECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQS 122
           EE GP L+  DPAG       T+ G     A   LE + + D   + +E  + A+  ++S
Sbjct: 107 EE-GPHLYSLDPAGGIIEDDYTATGSGSPVAYGVLEDEYRED--MSVEEAKKLAVRAIKS 163

Query: 123 VLQED-FKASEIEVGVVSKEN 142
            ++ D    + I+V V++K+ 
Sbjct: 164 AIERDVASGNGIDVAVITKDG 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 = 41.7 bits (99), Expect = 4e-05
 Identities = 22/117 (18%), Positives = 42/117 (35%), Gaps = 21/117 (17%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSID 62
           AD + L +  +     +  + G E+ V   A  +   S +   +    P  V  +V  +D
Sbjct: 50  ADTQALTRLLKRNLRLYELRNGRELSVKAAANLL---SNILYSYRGF-PYYVSLIVGGVD 105

Query: 63  EECGPRLFKCDPAGHFFGHKATSAG-----------------LKEQEAINFLEKKMK 102
           +  GP L+  DP G        + G                 +  +EA+  ++K + 
Sbjct: 106 KGGGPFLYYVDPLGSLIEAPFVATGSGSKYAYGILDRGYKPDMTLEEAVELVKKAID 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	164
KOG0181	233	consensus 20S proteasome, regulatory subunit alpha	100.0
cd03750	227	proteasome_alpha_type_2 proteasome_alpha_type_2. T	100.0
KOG0183	249	consensus 20S proteasome, regulatory subunit alpha	100.0
PTZ00246	253	proteasome subunit alpha; Provisional	100.0
KOG0182	246	consensus 20S proteasome, regulatory subunit alpha	100.0
COG0638	236	PRE1 20S proteasome, alpha and beta subunits [Post	100.0
PRK03996	241	proteasome subunit alpha; Provisional	100.0
KOG0178	249	consensus 20S proteasome, regulatory subunit alpha	100.0
KOG0176	241	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
cd03754	215	proteasome_alpha_type_6 proteasome_alpha_type_6. T	100.0
cd03749	211	proteasome_alpha_type_1 proteasome_alpha_type_1. T	100.0
TIGR03633	224	arc_protsome_A proteasome endopeptidase complex, a	100.0
PTZ00488	247	Proteasome subunit beta type-5; Provisional	100.0
cd03760	197	proteasome_beta_type_4 proteasome beta type-4 subu	100.0
cd03752	213	proteasome_alpha_type_4 proteasome_alpha_type_4. T	100.0
cd03751	212	proteasome_alpha_type_3 proteasome_alpha_type_3. T	100.0
cd03755	207	proteasome_alpha_type_7 proteasome_alpha_type_7. T	100.0
KOG0863	264	consensus 20S proteasome, regulatory subunit alpha	100.0
TIGR03691	228	20S_bact_alpha proteasome, alpha subunit, bacteria	100.0
cd03761	188	proteasome_beta_type_5 proteasome beta type-5 subu	100.0
cd03759	195	proteasome_beta_type_3 proteasome beta type-3 subu	100.0
cd03765	236	proteasome_beta_bacterial Bacterial proteasome, be	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
cd03764	188	proteasome_beta_archeal Archeal proteasome, beta s	100.0
cd03753	213	proteasome_alpha_type_5 proteasome_alpha_type_5. T	100.0
cd01911	209	proteasome_alpha proteasome alpha subunit. The 20S	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
cd01912	189	proteasome_beta proteasome beta subunit. The 20S p	100.0
PF00227	190	Proteasome: Proteasome subunit; InterPro: IPR00135	100.0
KOG0184	254	consensus 20S proteasome, regulatory subunit alpha	99.97
cd01906	182	proteasome_protease_HslV proteasome_protease_HslV.	99.97
KOG0175	285	consensus 20S proteasome, regulatory subunit beta	99.96
KOG0177	200	consensus 20S proteasome, regulatory subunit beta	99.94
KOG0179	235	consensus 20S proteasome, regulatory subunit beta	99.93
KOG0174	224	consensus 20S proteasome, regulatory subunit beta	99.92
KOG0173	271	consensus 20S proteasome, regulatory subunit beta	99.9
KOG0180	204	consensus 20S proteasome, regulatory subunit beta	99.89
cd01901	164	Ntn_hydrolase The Ntn hydrolases (N-terminal nucle	99.88
KOG0185	256	consensus 20S proteasome, regulatory subunit beta	99.8
cd01913	171	protease_HslV Protease HslV and the ATPase/chapero	99.79
PRK05456	172	ATP-dependent protease subunit HslV; Provisional	99.78
TIGR03692	171	ATP_dep_HslV ATP-dependent protease HslVU, peptida	99.75
COG3484	255	Predicted proteasome-type protease [Posttranslatio	97.25
COG5405	178	HslV ATP-dependent protease HslVU (ClpYQ), peptida	96.1
KOG3361	157	consensus Iron binding protein involved in Fe-S cl	87.61
PF03646	107	FlaG: FlaG protein; InterPro: IPR005186 Although t	81.06

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

Probab=100.00  E-value=3.4e-40  Score=241.99  Aligned_cols=155  Identities=35%  Similarity=0.582  Sum_probs=149.2

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      |.||+|.|++..|..++.|...|+++||+..|+..++..+|+|||++|.|||||+++|||||. ++|.||++||||++..
T Consensus        79 mgpD~RvlV~~~rkiAe~Yy~vY~e~~pt~qlv~~~asvmQEyTqsgGvrPFGvslliaG~~~-~~p~LyQvdPSGsyf~  157 (233)
T KOG0181|consen   79 MGPDYRVLVHKSRKIAEQYYRVYGEPIPTTQLVQEVASVMQEYTQSGGVRPFGVSLLIAGWDE-GGPLLYQVDPSGSYFA  157 (233)
T ss_pred             CCCceeehhhHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEeecCC-CceeEEEECCccceee
Confidence            579999999999999999999999999999999999999999999999999999999999998 7999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHHHHHHh
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAI  160 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~~l~~~  160 (164)
                      |+++|+|.+...++++||++|  +++|.+++++..|+.+|++..+..+++++|||+++..+  .|++++++||+++|+.+
T Consensus       158 wkatA~Gkn~v~aktFlEkR~--~edleldd~ihtailtlkE~fege~~~~nieigv~~~~--~F~~lt~~eI~d~l~~l  233 (233)
T KOG0181|consen  158 WKATAMGKNYVNAKTFLEKRY--NEDLELDDAIHTAILTLKESFEGEMTAKNIEIGVCGEN--GFRRLTPAEIEDYLASL  233 (233)
T ss_pred             hhhhhhccCcchHHHHHHHHh--ccccccchHHHHHHHHHHHHhccccccCceEEEEecCC--ceeecCHHHHHHHHhcC
Confidence            999999999999999999998  78999999999999999999999999999999999854  49999999999999764

>cd03750 proteasome_alpha_type_2 proteasome_alpha_type_2

Probab=100.00  E-value=6.8e-39  Score=247.96  Aligned_cols=154  Identities=36%  Similarity=0.595  Sum_probs=146.5

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.|++++|.+++.|++.+|++++++.++++|++++|.||++++.|||+|++||+|||+ .||+||++||+|++.+
T Consensus        74 ~~~D~~~l~~~~r~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rP~~v~~li~G~D~-~g~~Ly~~d~~G~~~~  152 (227)
T cd03750          74 MGPDFRVLVKKARKIAQQYYLVYGEPIPVSQLVREIASVMQEYTQSGGVRPFGVSLLIAGWDE-GGPYLYQVDPSGSYFT  152 (227)
T ss_pred             cHHhHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCCCCCChheEEEEEEEeC-CCCEEEEECCCCCEEe
Confidence            468999999999999999999999999999999999999999999999999999999999997 6999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLT  158 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~~l~  158 (164)
                      ++++|+|+|++.++++||++|  +++||++||++++++||..+.+|++...+++|++|++++ ++++++++||++++.
T Consensus       153 ~~~~a~G~g~~~~~~~Le~~~--~~~ms~eeai~l~~~~l~~~~~~~l~~~~iev~iv~~~~-~~~~~~~~ei~~~~~  227 (227)
T cd03750         153 WKATAIGKNYSNAKTFLEKRY--NEDLELEDAIHTAILTLKEGFEGQMTEKNIEIGICGETK-GFRLLTPAEIKDYLA  227 (227)
T ss_pred             eeEEEECCCCHHHHHHHHhhc--cCCCCHHHHHHHHHHHHHHHhcccCCCCcEEEEEEECCC-CEEECCHHHHHHHhC
Confidence            999999999999999999999  589999999999999999999988877799999999875 499999999999873

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=9.1e-40  Score=242.77  Aligned_cols=158  Identities=34%  Similarity=0.529  Sum_probs=150.0

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      |+||++.|++++|.+|++|++..+.|+++++++++|+.+.|.|||++|.||||+|.+|+|||+++.|.||.+||+|.+.+
T Consensus        77 l~aDArilinrArvecqShrlt~edpvtveyitRyiA~~kQrYTqs~grRPFGvs~Li~GfD~~g~p~lyqtePsG~f~e  156 (249)
T KOG0183|consen   77 LTADARILINRARVECQSHRLTLEDPVTVEYITRYIAGLKQRYTQSNGRRPFGVSTLIGGFDPDGTPRLYQTEPSGIFSE  156 (249)
T ss_pred             CCccceeehhhHhHhhhhhhcccCCCcHHHHHHHHHHHhhhhhhccCCcccccceEEEEeeCCCCCeeeEeeCCCcchhh
Confidence            68999999999999999999999999999999999999999999999999999999999999987899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHHHHHHh
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAI  160 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~~l~~~  160 (164)
                      |++.|||.+++.++.+|||+|...+-.|..++++|++++|..+.+.  ..++||+++++..+. ++.+++++|+.++..+
T Consensus       157 wka~aiGr~sk~VrEflEK~y~e~~~~~~~~~ikL~ir~LleVvqs--~~~nie~aVm~~~~~-~~~l~~~~I~~~v~~i  233 (249)
T KOG0183|consen  157 WKANAIGRSSKTVREFLEKNYKEEAIATEGETIKLAIRALLEVVQS--GGKNIEVAVMKRRKD-LKMLESEEIDDIVKEI  233 (249)
T ss_pred             hhccccccccHHHHHHHHHhcccccccccccHHHHHHHHHHHHhhc--CCCeeEEEEEecCCc-eeecCHHHHHHHHHHH
Confidence            9999999999999999999997666789999999999999999853  556999999999876 9999999999999988


Q ss_pred             h
Q 031203          161 S  161 (164)
Q Consensus       161 ~  161 (164)
                      +
T Consensus       234 e  234 (249)
T KOG0183|consen  234 E  234 (249)
T ss_pred             H
Confidence            7

>PTZ00246 proteasome subunit alpha; Provisional

Probab=100.00  E-value=1.8e-38  Score=249.19  Aligned_cols=160  Identities=34%  Similarity=0.541  Sum_probs=150.9

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.+++++|.+++.|++.++++++++.+++.+++.+|.|+|+++.|||+|++||||||+++||+||.+||+|++.+
T Consensus        79 ~~~D~~~l~~~~r~~~~~~~~~~~~~~~v~~l~~~l~~~~q~~~~~~~~rP~~v~~li~G~D~~~gp~Ly~~D~~Gs~~~  158 (253)
T PTZ00246         79 LTADANILINQCRLYAQRYRYTYGEPQPVEQLVVQICDLKQSYTQFGGLRPFGVSFLFAGYDENLGYQLYHTDPSGNYSG  158 (253)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccccCcccCCEEEEEEEEeCCCCcEEEEECCCCCEec
Confidence            46899999999999999999999999999999999999999999999999999999999999657999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCC----CcEEEcCHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKEN----PEFRVLSIEEIDE  155 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~----~~~k~l~~~ei~~  155 (164)
                      ++++|+|+|+..++++|+++|  +++||+|||++++++||..+.+++..++ +++|++|++++    +.|++++++||++
T Consensus       159 ~~~~a~G~gs~~~~~~Le~~~--~~~ms~eeai~l~~~al~~~~~~d~~s~~~vev~ii~~~~~~~~~~~~~l~~~ei~~  236 (253)
T PTZ00246        159 WKATAIGQNNQTAQSILKQEW--KEDLTLEQGLLLAAKVLTKSMDSTSPKADKIEVGILSHGETDGEPIQKMLSEKEIAE  236 (253)
T ss_pred             ceEEEECCCcHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHHhccCCCCCcEEEEEEecCCcCCCCCeEECCHHHHHH
Confidence            999999999999999999998  6899999999999999999999887765 99999999874    3499999999999


Q ss_pred             HHHHhhc
Q 031203          156 HLTAISE  162 (164)
Q Consensus       156 ~l~~~~~  162 (164)
                      +|.++.+
T Consensus       237 ~l~~~~~  243 (253)
T PTZ00246        237 LLKKVTQ  243 (253)
T ss_pred             HHHHHhh
Confidence            9999874

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

Probab=100.00  E-value=1.3e-38  Score=236.24  Aligned_cols=164  Identities=68%  Similarity=1.024  Sum_probs=160.1

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++..++++|.++.++++.||.+||++.||++++++.|.|||..-+||+||.+++.|+|++.||.+|.+||.|-+..
T Consensus        83 ~~aDar~~v~rar~eAa~~~yk~Gyemp~DiL~k~~Ad~~QvytQ~a~mRplg~~~~~i~~D~E~gP~vYk~DpAGyy~g  162 (246)
T KOG0182|consen   83 MIADARSQVQRARYEAAEFRYKYGYEMPCDILAKRMADKSQVYTQNAAMRPLGVAATLIGVDEERGPSVYKTDPAGYYYG  162 (246)
T ss_pred             CCcchHHHHHHHHHHHHhhhhhcCCCCCHHHHHHHHhhHHHHHhhhhhhcccceeEEEEEeccccCcceEeecCcccccc
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHHHHHHh
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAI  160 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~~l~~~  160 (164)
                      ++++|.|-..+.+.++|||+|+.+.++|.+|++++|+.||..++.-|..+..+||+++++++++|++|+.+||+++|..|
T Consensus       163 ~kAtaaG~Kq~e~tsfLEKk~Kk~~~~t~~e~ve~ai~al~~sl~~Dfk~se~EVgvv~~~~p~f~~Ls~~eie~hL~~I  242 (246)
T KOG0182|consen  163 FKATAAGVKQQEATSFLEKKYKKDIDLTFEETVETAISALQSSLGIDFKSSELEVGVVTVDNPEFRILSAEEIEEHLQAI  242 (246)
T ss_pred             ceeeecccchhhHHHHHHHhhccCccchHHHHHHHHHHHHHHHHhcccCCcceEEEEEEcCCcceeeccHHHHHHHHHHh
Confidence            99999999999999999999987778999999999999999999989999999999999999999999999999999999


Q ss_pred             hccC
Q 031203          161 SERD  164 (164)
Q Consensus       161 ~~~~  164 (164)
                      .|||
T Consensus       243 AEkd  246 (246)
T KOG0182|consen  243 AEKD  246 (246)
T ss_pred             hhcC
Confidence            9997

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

Probab=100.00  E-value=4.7e-38  Score=244.40  Aligned_cols=157  Identities=39%  Similarity=0.623  Sum_probs=149.1

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.||++.|++++|.+|+.|++.+|++|+|+.+++++|+++|.|+++  .|||||++||||+|+ ++|+||++||+|++.+
T Consensus        78 ~~aDa~~lv~~~r~~a~~~~~~~~~~i~v~~la~~ls~~l~~~~~~--~rP~gv~~iiaG~d~-~~p~Ly~~Dp~G~~~~  154 (236)
T COG0638          78 LAADAQVLVRYARAEAQLYRLRYGEPISVEALAKLLSNILQEYTQS--GRPYGVSLLVAGVDD-GGPRLYSTDPSGSYNE  154 (236)
T ss_pred             CcHhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhccC--cccceEEEEEEEEcC-CCCeEEEECCCCceee
Confidence            5799999999999999999999999999999999999999999987  899999999999999 8999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEIDEHLTA  159 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~~~l~~  159 (164)
                      ++++|+|+|++.++++||++|  +++|++|||++++++||..+.+||..++ +++|+++++++ +++.+++++++.++..
T Consensus       155 ~~~~a~Gsgs~~a~~~Le~~y--~~~m~~eeai~la~~al~~a~~rd~~s~~~~~v~vi~~~~-~~~~~~~~~~~~~~~~  231 (236)
T COG0638         155 YKATAIGSGSQFAYGFLEKEY--REDLSLEEAIELAVKALRAAIERDAASGGGIEVAVITKDE-GFRKLDGEEIKKLLDD  231 (236)
T ss_pred             cCEEEEcCCcHHHHHHHHhhc--cCCCCHHHHHHHHHHHHHHHHhccccCCCCeEEEEEEcCC-CeEEcCHHHHHHHHHH
Confidence            999999999999999999998  6889999999999999999999998655 88999999974 4999999999999998


Q ss_pred             hhcc
Q 031203          160 ISER  163 (164)
Q Consensus       160 ~~~~  163 (164)
                      +.++
T Consensus       232 ~~~~  235 (236)
T COG0638         232 LSEK  235 (236)
T ss_pred             Hhhc
Confidence            8765

>PRK03996 proteasome subunit alpha; Provisional

Probab=100.00  E-value=9e-38  Score=243.63  Aligned_cols=157  Identities=36%  Similarity=0.632  Sum_probs=149.0

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.+++++|.+++.|++.++++++|+.+++++++.+|.|+|+++.|||+|++||||||+ +||+||.+||+|++.+
T Consensus        83 ~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~~~~~~~rP~~~~~ilaG~d~-~gp~Ly~id~~G~~~~  161 (241)
T PRK03996         83 LVADARVLIDRARVEAQINRLTYGEPIGVETLTKKICDHKQQYTQHGGVRPFGVALLIAGVDD-GGPRLFETDPSGAYLE  161 (241)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhcCCCCccchheEEEEEEEeC-CcCEEEEECCCCCeec
Confidence            468999999999999999999999999999999999999999999999999999999999997 7899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHHHHHHh
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAI  160 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~~l~~~  160 (164)
                      ++++|+|+++..++++|+++|  +++|+++||++++++||..+.+++.....++|+++++++++|+.++++||++++.++
T Consensus       162 ~~~~a~G~g~~~~~~~Le~~~--~~~~s~eeai~l~~~al~~~~~~~~~~~~i~i~ii~~~~~~~~~~~~~ei~~~~~~~  239 (241)
T PRK03996        162 YKATAIGAGRDTVMEFLEKNY--KEDLSLEEAIELALKALAKANEGKLDPENVEIAYIDVETKKFRKLSVEEIEKYLEKL  239 (241)
T ss_pred             ceEEEECCCcHHHHHHHHHhc--ccCCCHHHHHHHHHHHHHHHhccCCCCCcEEEEEEECCCCcEEECCHHHHHHHHHHh
Confidence            999999999999999999998  688999999999999999998876655599999999998789999999999999875

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

Probab=100.00  E-value=1.1e-37  Score=231.18  Aligned_cols=162  Identities=30%  Similarity=0.501  Sum_probs=151.2

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|+..|++.+|..+|.|.+.||++||++.|++.+++++|.|||++|.||||||||.+|||...|.+||+.||||++..
T Consensus        79 lt~DAnvL~n~aRi~AQ~yl~~y~e~iP~eqLv~~lcdiKQayTQygG~RPFGVSfLYaGwd~~~gyqLy~SdPSGny~g  158 (249)
T KOG0178|consen   79 LTSDANVLKNYARIIAQRYLFRYGEEIPCEQLVTFLCDIKQAYTQYGGKRPFGVSFLYAGWDDRYGYQLYQSDPSGNYGG  158 (249)
T ss_pred             ccccHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHHhhccCcCCCceeeeeeceecCcceEEEecCCCCCccc
Confidence            57999999999999999999999999999999999999999999999999999999999999988999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhcc-CCCCeEEEEEEEcCCC--cEEEcCHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENP--EFRVLSIEEIDEHL  157 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d-~~~~~iei~ii~~~~~--~~k~l~~~ei~~~l  157 (164)
                      |++.|+|.++..+...|.+.|+ ...++++||+.+|++.|...++.. +.+..+||+.++++..  .+++++++||.++|
T Consensus       159 Wka~ciG~N~~Aa~s~Lkqdyk-dd~~~~~eA~~laikvL~kt~d~~~lt~eklEia~~~k~~~k~v~~i~~~~ev~kll  237 (249)
T KOG0178|consen  159 WKATCIGANSGAAQSMLKQDYK-DDENDLEEAKALAIKVLSKTLDSGSLTAEKLEIATITKDCNKTVLKILKKDEVLKLL  237 (249)
T ss_pred             cceeeeccchHHHHHHHHhhhc-cccccHHHHHHHHHHHHHhhcccCCCChhheEEEEEEecCCceEEEecCHHHHHHHH
Confidence            9999999999999999999985 345679999999999999999875 5667999999998764  48899999999999


Q ss_pred             HHhhcc
Q 031203          158 TAISER  163 (164)
Q Consensus       158 ~~~~~~  163 (164)
                      .+++++
T Consensus       238 ~k~~~~  243 (249)
T KOG0178|consen  238 EKYHET  243 (249)
T ss_pred             HHhhhh
Confidence            998853

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

Probab=100.00  E-value=2.3e-37  Score=227.52  Aligned_cols=155  Identities=30%  Similarity=0.550  Sum_probs=146.1

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhcc-----CccccceeeEEEEEcCCCCCeEEEeCCC
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHA-----YMRPLGVVAMVLSIDEECGPRLFKCDPA   75 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~-----~~rP~gv~~iiaG~d~~~gp~Ly~~dp~   75 (164)
                      |.+|++.|++++|.+|++|.+.||++|+++.+++.+|++...|-...     ..|||||++|+||+|+ +||+||..|||
T Consensus        81 l~aDarTlve~arv~~qnh~f~Y~e~i~VEs~tq~v~~LaLrFGe~~~~~~~msRPFGValliAG~D~-~gpqL~h~dPS  159 (241)
T KOG0176|consen   81 LIADARTLVERARVETQNHWFTYGEPISVESLTQAVSDLALRFGEGDDEEAIMSRPFGVALLIAGHDE-TGPQLYHLDPS  159 (241)
T ss_pred             cccchHHHHHHHHHHhhhceeecCCcccHHHHHHHHHHHHhHhCCCcchhhhhcCCcceEEEEeeccC-CCceEEEeCCC
Confidence            67999999999999999999999999999999999999998886542     3699999999999997 89999999999


Q ss_pred             cceeeeeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHH
Q 031203           76 GHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE  155 (164)
Q Consensus        76 G~~~~~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~  155 (164)
                      |++..+++-|||+|+..+.+.|++.|  .++|+++||+.+++..|+.+++..+++.|+++.+|++++. |++++++|++.
T Consensus       160 Gtf~~~~AKAIGSgsEga~~~L~~e~--~~~ltL~ea~~~~L~iLkqVMeeKl~~~Nvev~~vt~e~~-f~~~t~EE~~~  236 (241)
T KOG0176|consen  160 GTFIRYKAKAIGSGSEGAESSLQEEY--HKDLTLKEAEKIVLKILKQVMEEKLNSNNVEVAVVTPEGE-FHIYTPEEVEQ  236 (241)
T ss_pred             CceEEecceeccccchHHHHHHHHHH--hhcccHHHHHHHHHHHHHHHHHHhcCccceEEEEEcccCc-eEecCHHHHHH
Confidence            99999999999999999999999999  5889999999999999999999999999999999999864 99999999999


Q ss_pred             HHHH
Q 031203          156 HLTA  159 (164)
Q Consensus       156 ~l~~  159 (164)
                      ++..
T Consensus       237 ~i~~  240 (241)
T KOG0176|consen  237 VIKR  240 (241)
T ss_pred             HHhc
Confidence            9865

>TIGR03690 20S_bact_beta proteasome, beta subunit, bacterial type

Probab=100.00  E-value=1.8e-36  Score=233.29  Aligned_cols=157  Identities=22%  Similarity=0.234  Sum_probs=143.2

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCC-CCCeEEEeCCCc-ce
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEE-CGPRLFKCDPAG-HF   78 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~-~gp~Ly~~dp~G-~~   78 (164)
                      +.+|++.|++++|.+++.|+++++++|+|+.++++|++++|.++ .+++|||+|++||||||++ ++|+||++||+| ++
T Consensus        50 ~~aD~~~l~~~~r~~~~~~~~~~~~~i~~~~la~~ls~~~~~~~-~~~~rp~~v~~iiaG~D~~~~~~~Ly~~Dp~G~~~  128 (219)
T TIGR03690        50 TAGLAIELVRLFQVELEHYEKIEGVPLTLDGKANRLAAMVRGNL-PAAMQGLAVVPLLAGYDLDAGAGRIFSYDVTGGRY  128 (219)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhhh-hhccCCceEEEEEEEECCCCCCcEEEEEeCCCCee
Confidence            46899999999999999999999999999999999999999887 4568999999999999964 579999999999 57


Q ss_pred             eeeeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCe--------EEEEEEEcCCCcEEEcCH
Q 031203           79 FGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASE--------IEVGVVSKENPEFRVLSI  150 (164)
Q Consensus        79 ~~~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~--------iei~ii~~~~~~~k~l~~  150 (164)
                      ..++++|+|+|++.++++||++|  +++||.+||++++++||..+.++|..+++        ++|++|++++  |+++++
T Consensus       129 ~~~~~~a~G~g~~~a~~~Le~~~--~~~ms~eeai~l~~~al~~~~~~d~~s~~~~~~~~~~~ei~ii~~~g--~~~l~~  204 (219)
T TIGR03690       129 EERGYHAVGSGSVFAKGALKKLY--SPDLDEDDALRVAVEALYDAADDDSATGGPDLVRGIYPTVVVITADG--ARRVPE  204 (219)
T ss_pred             ecCCeEEEeccHHHHHHHHHhcC--CCCcCHHHHHHHHHHHHHHHHhcccccCCcccccccccEEEEEccCc--eEEcCH
Confidence            77799999999999999999998  68999999999999999999999975552        3999997654  999999


Q ss_pred             HHHHHHHHHhhc
Q 031203          151 EEIDEHLTAISE  162 (164)
Q Consensus       151 ~ei~~~l~~~~~  162 (164)
                      +||++++.++.+
T Consensus       205 ~ei~~~~~~~~~  216 (219)
T TIGR03690       205 SELEELARAIVE  216 (219)
T ss_pred             HHHHHHHHHHHh
Confidence            999999999875

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=4.1e-36  Score=227.25  Aligned_cols=138  Identities=16%  Similarity=0.261  Sum_probs=130.5

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.||++.|++++|.+++.|++.++++++|+.+++++++++|.|++++  |||++++||||||+++||+||.+||+|++.+
T Consensus        49 ~~aD~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~l~~~~~~~~~~~--rP~~~~~li~G~d~~~~p~Ly~~d~~G~~~~  126 (193)
T cd03758          49 EAGDRLQFAEYIQKNIQLYKMRNGYELSPKAAANFTRRELAESLRSR--TPYQVNLLLAGYDKVEGPSLYYIDYLGTLVK  126 (193)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcC--CCeEEEEEEEEEcCCCCcEEEEECCCcceEE
Confidence            46999999999999999999999999999999999999999887643  8999999999999767899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCC
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKEN  142 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~  142 (164)
                      ++++|+|+|++.++++||++|  +++||.|||++++.+|+..+.+||..++ +++|++|++++
T Consensus       127 ~~~~a~G~gs~~~~~~Le~~~--~~~ms~eeai~l~~~a~~~~~~rd~~~~~~i~i~ii~~~g  187 (193)
T cd03758         127 VPYAAHGYGAYFCLSILDRYY--KPDMTVEEALELMKKCIKELKKRFIINLPNFTVKVVDKDG  187 (193)
T ss_pred             CCeeEEeecHHHHHHHHHhcc--CCCCCHHHHHHHHHHHHHHHHHhccccCCceEEEEEcCCC
Confidence            999999999999999999998  5899999999999999999999998776 99999999886

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=4.3e-36  Score=230.62  Aligned_cols=138  Identities=71%  Similarity=1.098  Sum_probs=130.7

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.|++++|.+++.|+++++++|+|+.+|+++++++|.||++++.|||+|++||||||+++||+||++||+|++.+
T Consensus        76 ~~~D~~~l~~~~r~~~~~~~~~~~~~i~v~~la~~ls~~~q~yt~~~~~RP~~v~~ii~G~D~~~gp~Ly~~Dp~Gs~~~  155 (215)
T cd03754          76 MIADSRSQVQRARYEAAEFKYKYGYEMPVDVLAKRIADINQVYTQHAYMRPLGVSMILIGIDEELGPQLYKCDPAGYFAG  155 (215)
T ss_pred             chhhHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhCCCCCcCCeeEEEEEEEeCCCCeEEEEEcCCccEEe
Confidence            47999999999999999999999999999999999999999999999999999999999999767999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCC--CHHHHHHHHHHHHHhhhhccCCCCeEEEEEE
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAF--TFQETVQTAISTLQSVLQEDFKASEIEVGVV  138 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~l--s~eea~~l~~~al~~~~~~d~~~~~iei~ii  138 (164)
                      ++++|+|+|++.++++||++|+.+.+|  |.|||++++++||..+.+||+...++||+|+
T Consensus       156 ~~~~a~G~gs~~~~~~Le~~~~~~~~~~~s~eeai~l~~~al~~~~~rd~~~~~~ei~~~  215 (215)
T cd03754         156 YKATAAGVKEQEATNFLEKKLKKKPDLIESYEETVELAISCLQTVLSTDFKATEIEVGVV  215 (215)
T ss_pred             EEEEEECCCcHHHHHHHHHHhccccccCCCHHHHHHHHHHHHHHHhcccCCCCcEEEEEC
Confidence            999999999999999999999644468  9999999999999999999988669999985

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=6e-36  Score=229.20  Aligned_cols=138  Identities=33%  Similarity=0.571  Sum_probs=130.6

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.|++++|.+++.|+++++++++|+.+|+.+++.+|.||++++.|||+|++||+|||+ .||+||++||+|++.+
T Consensus        72 ~~~D~~~l~~~~r~~~~~~~~~~~~~~~v~~la~~is~~~~~~t~~~~~rP~~v~~ii~G~D~-~gp~Ly~~Dp~G~~~~  150 (211)
T cd03749          72 LTADARVLSRYMRQECLNYRFVYDSPIPVSRLVSKVAEKAQINTQRYGRRPYGVGLLIAGYDE-SGPHLFQTCPSGNYFE  150 (211)
T ss_pred             ChHhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCCCCceEEEEEEEEcC-CCCeEEEECCCcCEee
Confidence            479999999999999999999999999999999999999999999999999999999999997 6899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhcc--CCCCeEEEEEEE
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQED--FKASEIEVGVVS  139 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d--~~~~~iei~ii~  139 (164)
                      ++++|+|+|++.++++||++|+.+++||++||+++++++|..++++|  ....+|||++|+
T Consensus       151 ~~~~a~G~g~~~a~~~Le~~~~~~~~ms~ee~i~~~~~~l~~~~~~~~~~~~~~iei~ii~  211 (211)
T cd03749         151 YKATSIGARSQSARTYLERHFEEFEDCSLEELIKHALRALRETLPGEQELTIKNVSIAIVG  211 (211)
T ss_pred             eeEEEECCCcHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhccCCCCCCCcEEEEEEC
Confidence            99999999999999999999965579999999999999999999876  555699999984

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=1.1e-35  Score=229.56  Aligned_cols=148  Identities=40%  Similarity=0.646  Sum_probs=139.6

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.+.++++.++..|+++++++++|+.+++++++.+|.|+++++.|||+|++||||||+ +||+||.+||+|++.+
T Consensus        76 ~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~ls~~l~~~~~~~~~rP~~v~~ll~G~d~-~~~~Ly~~D~~G~~~~  154 (224)
T TIGR03633        76 LVADARVLIDRARIEAQINRLTYGEPIDVETLAKKICDLKQQYTQHGGVRPFGVALLIAGVDD-GGPRLFETDPSGALLE  154 (224)
T ss_pred             cHHhHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCCCccccceEEEEEEEeC-CcCEEEEECCCCCeec
Confidence            468999999999999999999999999999999999999999999999999999999999996 7999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEE  152 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~e  152 (164)
                      ++++|+|+++..++++|+++|  +++||.+||++++++||..+.+ |..++ +++|++|+++++.|+.++++|
T Consensus       155 ~~~~a~G~g~~~~~~~L~~~~--~~~~~~eeai~l~~~al~~~~~-d~~~~~~i~i~ii~~~g~~~~~~~~~~  224 (224)
T TIGR03633       155 YKATAIGAGRQAVTEFLEKEY--REDLSLDEAIELALKALYSAVE-DKLTPENVEVAYITVEDKKFRKLSVEE  224 (224)
T ss_pred             ceEEEECCCCHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHhc-ccCCCCcEEEEEEEcCCCcEEECCCCC
Confidence            999999999999999999998  6899999999999999999987 65554 999999999887799998875

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=3.9e-35  Score=229.27  Aligned_cols=151  Identities=17%  Similarity=0.208  Sum_probs=139.6

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCcccccee--eEEEEEcCCCCCeEEEeCCCcce
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVV--AMVLSIDEECGPRLFKCDPAGHF   78 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~--~iiaG~d~~~gp~Ly~~dp~G~~   78 (164)
                      +.+|++.|++++|.+++.|++++|++|+|+.++++|++++|.|      |||+++  +||||||+ .||+||++||+|++
T Consensus        87 ~~aD~~~l~~~lr~~~~~y~~~~g~~isv~~la~~ls~~l~~~------R~~~~~v~~iiaG~D~-~gp~Ly~vDp~Gs~  159 (247)
T PTZ00488         87 GAADCSFWERELAMQCRLYELRNGELISVAAASKILANIVWNY------KGMGLSMGTMICGWDK-KGPGLFYVDNDGTR  159 (247)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhc------CCCCeeEEEEEEEEeC-CCCEEEEEcCCcce
Confidence            4689999999999999999999999999999999999999654      566555  89999997 78999999999999


Q ss_pred             eeeeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHHHHH
Q 031203           79 FGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEIDEHL  157 (164)
Q Consensus        79 ~~~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~~~l  157 (164)
                      .+++++|+|+|+..++++||+.|  +++||.+||++++++||..+.+||..++ +++|++|++++  ++.++++||++++
T Consensus       160 ~~~~~~a~G~gs~~~~~~Le~~~--k~dms~eEai~l~~kal~~~~~Rd~~sg~~~ei~iI~k~g--~~~l~~~ei~~~l  235 (247)
T PTZ00488        160 LHGNMFSCGSGSTYAYGVLDAGF--KWDLNDEEAQDLGRRAIYHATFRDAYSGGAINLYHMQKDG--WKKISADDCFDLH  235 (247)
T ss_pred             eecCCEEEccCHHHHHHHHHhcC--cCCCCHHHHHHHHHHHHHHHHHhccccCCCeEEEEEcCCc--cEECCHHHHHHHH
Confidence            99999999999999999999998  5789999999999999999999997766 99999999775  8999999999999


Q ss_pred             HHhhc
Q 031203          158 TAISE  162 (164)
Q Consensus       158 ~~~~~  162 (164)
                      .++++
T Consensus       236 ~~~~~  240 (247)
T PTZ00488        236 QKYAA  240 (247)
T ss_pred             HHHhh
Confidence            99873

>cd03760 proteasome_beta_type_4 proteasome beta type-4 subunit

Probab=100.00  E-value=2.8e-35  Score=223.28  Aligned_cols=140  Identities=19%  Similarity=0.224  Sum_probs=129.6

Q ss_pred             CCchHHHHHHHHHHHHH-HHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCccee
Q 031203            1 MTADARTLVQQARYEAA-EFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFF   79 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~-~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~   79 (164)
                      +.+|++.|++++|.+++ .+++.++++++|+.++++|++++  |+|++++|||+|++||||||+++||+||++||+|++.
T Consensus        50 ~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~~la~~i~~~~--y~~~~~~rP~~v~~iiaG~D~~~gp~Ly~~D~~G~~~  127 (197)
T cd03760          50 DYADFQYLKRLLDQLVIDDECLDDGHSLSPKEIHSYLTRVL--YNRRSKMNPLWNTLVVGGVDNEGEPFLGYVDLLGTAY  127 (197)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH--HHHhhcCCCceEEEEEEEEcCCCCEEEEEEcCCccEE
Confidence            46899999999999987 57788999999999999999986  9998899999999999999976789999999999999


Q ss_pred             eeeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCC
Q 031203           80 GHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKEN  142 (164)
Q Consensus        80 ~~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~  142 (164)
                      +++++|+|+|+..++++||++|+++++||.+||++++++||..+.+||..++ +++|++|++++
T Consensus       128 ~~~~~a~G~g~~~~~~~Le~~~~~~~~ms~eea~~l~~~~l~~~~~rd~~~~~~~~i~ii~~~g  191 (197)
T cd03760         128 EDPHVATGFGAYLALPLLREAWEKKPDLTEEEARALIEECMKVLYYRDARSINKYQIAVVTKEG  191 (197)
T ss_pred             ECCEeEEccHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHHHHHHhccccCCceEEEEECCCC
Confidence            9999999999999999999999533389999999999999999999997666 99999999875

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.

>cd03752 proteasome_alpha_type_4 proteasome_alpha_type_4

Probab=100.00  E-value=3.4e-35  Score=225.29  Aligned_cols=136  Identities=29%  Similarity=0.491  Sum_probs=129.2

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.+++++|.+++.|++++|++|+|+.+++.|+..+|.|||+++.|||+|++||+|||++.||+||.+||+|++.+
T Consensus        77 ~~~D~~~l~~~~r~~~~~~~~~~~~~i~v~~la~~ls~~~~~~t~~~~~RP~~v~~li~G~D~~~g~~ly~~d~~G~~~~  156 (213)
T cd03752          77 ITSDANILINYARLIAQRYLYSYQEPIPVEQLVQRLCDIKQGYTQYGGLRPFGVSFLYAGWDKHYGFQLYQSDPSGNYSG  156 (213)
T ss_pred             ChHhHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcCCCcccceeEEEEEEEeCCCCCEEEEECCCCCeee
Confidence            46999999999999999999999999999999999999999999999999999999999999767999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCC-CeEEEEEE
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKA-SEIEVGVV  138 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~-~~iei~ii  138 (164)
                      ++++|+|+++..++++||++|  +++||++||++++++||..+.+|+... .++||+++
T Consensus       157 ~~~~a~G~gs~~~~~~Le~~y--~~~ms~eea~~l~~~al~~~~~r~~~~~~~~ei~~~  213 (213)
T cd03752         157 WKATAIGNNNQAAQSLLKQDY--KDDMTLEEALALAVKVLSKTMDSTKLTSEKLEFATL  213 (213)
T ss_pred             eeEEEECCCcHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHHhccCCCCCcEEEEEC
Confidence            999999999999999999998  689999999999999999999988555 48999875

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=3.2e-35  Score=225.29  Aligned_cols=135  Identities=35%  Similarity=0.459  Sum_probs=128.2

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|++++|.+++.|++++|++++|+.++++|++++|.||++++.|||+|++||+|||+ +||+||.+||+|++.+
T Consensus        77 ~~~D~~~l~~~~r~~~~~y~~~~~~~~~v~~la~~ls~~~~~~t~~~~~rP~~vs~li~G~D~-~gp~Ly~~D~~Gs~~~  155 (212)
T cd03751          77 LLADGRHLVSRAREEAENYRDNYGTPIPVKVLADRVAMYMHAYTLYSSVRPFGCSVLLGGYDS-DGPQLYMIEPSGVSYG  155 (212)
T ss_pred             ChHhHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccCCCcCCceEEEEEEEEeC-CcCEEEEECCCCCEEe
Confidence            479999999999999999999999999999999999999999999999999999999999997 7899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhc-cCCCCeEEEEEE
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQE-DFKASEIEVGVV  138 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~-d~~~~~iei~ii  138 (164)
                      ++++|+|+|+..++++||++|  +++||++||+++++++|+.+++. +....+|||+++
T Consensus       156 ~~~~a~G~g~~~a~~~Lek~~--~~dms~eeai~l~~~~L~~~~~~~~~~~~~iei~~~  212 (212)
T cd03751         156 YFGCAIGKGKQAAKTELEKLK--FSELTCREAVKEAAKIIYIVHDEIKDKAFELELSWV  212 (212)
T ss_pred             eEEEEECCCCHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHhhccCCCCccEEEEEC
Confidence            999999999999999999999  68999999999999999999984 466679999875

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=4.2e-35  Score=223.91  Aligned_cols=134  Identities=33%  Similarity=0.564  Sum_probs=127.3

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|.+++|.+++.|+++++++|+|+.++++|++++|.|+++++.|||+|++||+|||+++||+||.+||+|++.+
T Consensus        74 ~~~D~~~l~~~~r~~~~~~~~~~~~~i~~~~la~~ls~~~~~y~~~~~~rP~~vs~ii~G~D~~~~p~Ly~iD~~G~~~~  153 (207)
T cd03755          74 LTADARVLINRARLECQSHRLTVEDPVTVEYITRYIAGLQQRYTQSGGVRPFGISTLIVGFDPDGTPRLYQTDPSGTYSA  153 (207)
T ss_pred             chhhHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcccCcccceeEEEEEEEeCCCCeEEEEECCCcCEEc
Confidence            46999999999999999999999999999999999999999999999999999999999999867999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEE
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVV  138 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii  138 (164)
                      ++++|+|+|++.++++||++|  +++||.+||++++++||..+.+  .+..++||+++
T Consensus       154 ~~~~a~G~gs~~~~~~Le~~~--~~~ms~eeai~l~~~~l~~~~~--~~~~~~e~~~~  207 (207)
T cd03755         154 WKANAIGRNSKTVREFLEKNY--KEEMTRDDTIKLAIKALLEVVQ--SGSKNIELAVM  207 (207)
T ss_pred             ceEEEECCCCHHHHHHHHhhc--cCCCCHHHHHHHHHHHHHHHhC--CCCCeEEEEEC
Confidence            999999999999999999999  6899999999999999999985  45559999985

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=7e-35  Score=218.74  Aligned_cols=160  Identities=32%  Similarity=0.515  Sum_probs=152.3

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      |++|++.|.+++|.+|..+++.|++++|+..++..|++.+|..||+.+.|||||+++|+|+|+ .||+||.++|+|++.+
T Consensus        77 Lt~Darvl~~Ylr~ec~~~~~~~~r~~pv~rl~~~l~~k~q~~Tq~ygrRpYGVGllv~gYDe-~G~hl~e~~Psg~v~e  155 (264)
T KOG0863|consen   77 LTADARVLSRYLRQECLNSRFIYGRPLPVLRLVEDLGDKAQENTQRYGRRPYGVGLLVAGYDE-SGPHLYEFCPSGNVFE  155 (264)
T ss_pred             cCcchHHHHHHHHHHHhhhhhccCCcccHHHHHHHHHHHHhhhhhhhCCccccceEEEEeecC-CCceeEEEcCCccEEE
Confidence            689999999999999999999999999999999999999999999999999999999999998 8999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhc--cCCCCeEEEEEEEcCCCcEEEcCHHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQE--DFKASEIEVGVVSKENPEFRVLSIEEIDEHLT  158 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~--d~~~~~iei~ii~~~~~~~k~l~~~ei~~~l~  158 (164)
                      +++.+||+.||.+.++||++...+++++.||.+..+++||...+..  +++..+++|+|+.++.+ |.+++.+++.+++.
T Consensus       156 ~~g~sIGsRSQsARTyLEr~~e~f~~~~~eELI~~gi~Alr~tlp~de~lt~~nvsI~Ivgkd~p-f~~~d~~~~~k~~~  234 (264)
T KOG0863|consen  156 CKGMSIGSRSQSARTYLERNLEEFEDSSPEELIKHGIMALRETLPEDEDLTGENVSIAIVGKDEP-FTILDQKDVAKYVD  234 (264)
T ss_pred             EeeeecccchhhHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhcCcccccccceeEEEEEeCCCc-eEeecHHHHHHHHH
Confidence            9999999999999999999988889999999999999999999874  46677999999999987 99999999999987


Q ss_pred             Hhhc
Q 031203          159 AISE  162 (164)
Q Consensus       159 ~~~~  162 (164)
                      ....
T Consensus       235 ~~~~  238 (264)
T KOG0863|consen  235 LFKK  238 (264)
T ss_pred             Hhhc
Confidence            7653

>TIGR03691 20S_bact_alpha proteasome, alpha subunit, bacterial type

Probab=100.00  E-value=8e-35  Score=225.09  Aligned_cols=154  Identities=16%  Similarity=0.198  Sum_probs=137.1

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcC-CCCCeEEEeCCCcce
Q 031203            1 MTADARTLVQQARYEAAEFRFKYG-YEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDE-ECGPRLFKCDPAGHF   78 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~-~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~-~~gp~Ly~~dp~G~~   78 (164)
                      +.+|++.++++++.+++.|++.++ .+++++.+++++++.+..++ +++.|||||++||+|||+ +.||+||++||+|++
T Consensus        67 ~~~D~~~lv~~~r~~a~~~~~~~~~~~~~v~~la~~~tq~~~~~~-~~~~RP~gvs~Li~G~d~~~~gp~Ly~vDpsG~~  145 (228)
T TIGR03691        67 KYNEFENLRRAGIRYADMRGYSYDRRDVTGRGLANAYAQTLGTIF-TEQQKPYEVEICVAEVGETPDQDQLYRITFDGSI  145 (228)
T ss_pred             CHHHHHHHHHHHHHHHHHHhhhcCCCCccHHHHHHHHHhhccccc-ccccCcceEEEEEEEEcCCCCCCEEEEECCCCCc
Confidence            468999999999999999999998 78999999988888776666 567899999999999985 478999999999999


Q ss_pred             eeee-EEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhh--cc-CCCCeEEEEEEEcCC--CcEEEcCHHH
Q 031203           79 FGHK-ATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQ--ED-FKASEIEVGVVSKEN--PEFRVLSIEE  152 (164)
Q Consensus        79 ~~~~-~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~--~d-~~~~~iei~ii~~~~--~~~k~l~~~e  152 (164)
                      .+++ ++|+|+|++.++++||++|  +++||+|||++++++||..+++  ++ ++..++||+++++++  +.|++|+++|
T Consensus       146 ~~~~~~~aiG~gs~~a~~~Lek~y--~~~ms~eeai~la~~aL~~~~~~~r~~~~~~~iEv~ii~k~~~~~~f~~l~~~e  223 (228)
T TIGR03691       146 VDERGFVVMGGTTEPIATALKESY--RDGLSLADALGLAVQALRAGGNGEKRELDAASLEVAVLDRSRPRRAFRRITGEA  223 (228)
T ss_pred             eeccceEEECCChHHHHHHHHHhc--CCCCCHHHHHHHHHHHHHHHhccccccCCccceEEEEEeCCCCccceEECCHHH
Confidence            9976 8999999999999999998  5899999999999999999964  32 566699999999753  4699999999


Q ss_pred             HHHHH
Q 031203          153 IDEHL  157 (164)
Q Consensus       153 i~~~l  157 (164)
                      |+++|
T Consensus       224 i~~~l  228 (228)
T TIGR03691       224 LERLL  228 (228)
T ss_pred             HHhhC
Confidence            99874

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.

>cd03761 proteasome_beta_type_5 proteasome beta type-5 subunit

Probab=100.00  E-value=1.3e-34  Score=218.20  Aligned_cols=139  Identities=17%  Similarity=0.216  Sum_probs=129.7

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.|++++|.+++.|++++|++|+|+.+++++++++|.|++    .||+|++||||||+ +||+||++||+|++.+
T Consensus        48 ~~~D~~~l~~~~r~~~~~y~~~~~~~i~~~~la~~ls~~l~~~~~----~~~~v~~li~G~D~-~g~~L~~~dp~G~~~~  122 (188)
T cd03761          48 GAADCQYWERVLGRECRLYELRNKERISVAAASKLLSNMLYQYKG----MGLSMGTMICGWDK-TGPGLYYVDSDGTRLK  122 (188)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhcCC----CCeEEEEEEEEEeC-CCCEEEEEcCCceEEE
Confidence            468999999999999999999999999999999999999988754    48999999999997 7999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEc
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVL  148 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l  148 (164)
                      ++++|+|+|++.++++||++|  +++||.|||++++++||..+.+||..++ +++|++|++++  ++++
T Consensus       123 ~~~~a~G~g~~~~~~~Le~~~--~~~~s~eea~~l~~~~l~~~~~rd~~sg~~~~v~ii~~~g--~~~~  187 (188)
T cd03761         123 GDLFSVGSGSTYAYGVLDSGY--RYDLSVEEAYDLARRAIYHATHRDAYSGGNVNLYHVREDG--WRKI  187 (188)
T ss_pred             cCeEEEcccHHHHHHHHHhcC--CCCCCHHHHHHHHHHHHHHHHHhcccCCCCeEEEEEcCCc--eEEc
Confidence            999999999999999999998  6899999999999999999999998776 99999999886  4544

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.

>cd03759 proteasome_beta_type_3 proteasome beta type-3 subunit

Probab=100.00  E-value=1.1e-34  Score=219.66  Aligned_cols=141  Identities=19%  Similarity=0.254  Sum_probs=129.4

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.|++++|.+++.|+++++++|+|+.++++|++++  |+++  .|||+|++||||||+++||+||++||+|++..
T Consensus        51 ~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~l--y~~r--~~P~~v~~ii~G~D~~~~p~Ly~~D~~G~~~~  126 (195)
T cd03759          51 LATDVQTLAQKLRFRVNLYRLREEREIKPKTFSSLISSLL--YEKR--FGPYFVEPVVAGLDPDGKPFICTMDLIGCPSI  126 (195)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHH--HHhc--CCCceEEEEEEEEcCCCCEEEEEEcCCCcccc
Confidence            3689999999999999999999999999999999999998  7653  68999999999999767899999999999988


Q ss_pred             ee-EEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEE
Q 031203           81 HK-ATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRV  147 (164)
Q Consensus        81 ~~-~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~  147 (164)
                      ++ ++|+|+|++.++++||++|  +++||.+||++++++||..+.+||..++ +++|++|++++...+.
T Consensus       127 ~~~~~a~G~g~~~~~~~Le~~~--~~~~s~~ea~~l~~~~l~~~~~rd~~~~~~~~i~ii~~~g~~~~~  193 (195)
T cd03759         127 PSDFVVSGTASEQLYGMCESLW--RPDMEPDELFETISQALLSAVDRDALSGWGAVVYIITKDKVTTRT  193 (195)
T ss_pred             cCCEEEEcccHHHHHHHHHhcc--CCCCCHHHHHHHHHHHHHHHHhhCcccCCceEEEEEcCCcEEEEe
Confidence            87 9999999999999999998  6899999999999999999999997766 9999999988753443

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.

>cd03765 proteasome_beta_bacterial Bacterial proteasome, beta subunit

Probab=100.00  E-value=9.5e-35  Score=225.29  Aligned_cols=140  Identities=12%  Similarity=0.184  Sum_probs=127.8

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHH-HhhhhccC-----ccccceeeEEEEEcCCCCCeEEEeC
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGY-EMPVDVLAKWIADKS-QVYTQHAY-----MRPLGVVAMVLSIDEECGPRLFKCD   73 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~-~i~~~~l~~~ls~~~-q~yt~~~~-----~rP~gv~~iiaG~d~~~gp~Ly~~d   73 (164)
                      ++||++.|++++|.+++.|++++|+ +++++.+|+++++++ |.++|+.+     .|||||++||||||++.||+||++|
T Consensus        51 ~~aD~~~l~~~~r~~~~~~~~~~g~~~~~v~~la~~i~~~l~~~~~q~~~~~~~~~rp~gvslIigG~D~~~Gp~LY~id  130 (236)
T cd03765          51 NLATTQAVISLLQRDLEDPEETNLLNAPTMFDAARYVGETLREVQEQDREALKKAGIDFSASFILGGQIKGEEPRLFLIY  130 (236)
T ss_pred             cHHHHHHHHHHHHHHHHhhHHhhCCCCCCHHHHHHHHHHHHHHHHhhcccccccCCcceEEEEEEEeEECCCCCEEEEEC
Confidence            4689999999999999999999999 899999999999985 55666664     4899999999999966899999999


Q ss_pred             CCcceeeee----EEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCC
Q 031203           74 PAGHFFGHK----ATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENP  143 (164)
Q Consensus        74 p~G~~~~~~----~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~  143 (164)
                      |+|++.+++    ++|+|+ ++.++++||++|  +++||+|||+++|++||..+++||..++ +++|++|+++|.
T Consensus       131 psG~~~e~~a~~~~~AiG~-~~~a~~~Lek~y--k~~ms~eeai~la~~al~~a~~rd~~sg~~iev~vI~k~G~  202 (236)
T cd03765         131 PQGNFIEATPDTPFLQIGE-TKYGKPILDRVI--TPDTSLEDAAKCALVSMDSTMRSNLSVGPPLDLLVYERDSL  202 (236)
T ss_pred             CCCCEEeecCCCceeeeCC-chhhHHHHHHhc--CCCCCHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEEECCCe
Confidence            999999994    589996 799999999999  5799999999999999999999998777 899999999864

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.

>cd03756 proteasome_alpha_archeal proteasome_alpha_archeal

Probab=100.00  E-value=7.6e-34  Score=217.48  Aligned_cols=136  Identities=38%  Similarity=0.639  Sum_probs=130.2

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.+.++++.+++.|+++++++++++.+++++++.+|.|+++++.|||+|++||||||+ .||+||.+||+|++.+
T Consensus        75 ~~~D~~~l~~~l~~~~~~~~~~~~~~~~~~~la~~ls~~~~~~~~~~~~rP~~v~~ll~G~D~-~~~~ly~vd~~G~~~~  153 (211)
T cd03756          75 LVADARVLIDRARVEAQIHRLTYGEPIDVEVLVKKICDLKQQYTQHGGVRPFGVALLIAGVDD-GGPRLFETDPSGAYNE  153 (211)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCCCeechhEEEEEEEEeC-CCCEEEEECCCCCeee
Confidence            468999999999999999999999999999999999999999999999999999999999997 7999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEE
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVS  139 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~  139 (164)
                      ++++|+|++++.++++|+++|  +++||++||++++++||..+.+++....+++|++|+
T Consensus       154 ~~~~a~G~g~~~~~~~Le~~~--~~~m~~~ea~~l~~~~l~~~~~~~~~~~~~~v~ii~  210 (211)
T cd03756         154 YKATAIGSGRQAVTEFLEKEY--KEDMSLEEAIELALKALYAALEENETPENVEIAYVT  210 (211)
T ss_pred             eEEEEECCCCHHHHHHHHhhc--cCCCCHHHHHHHHHHHHHHHhcccCCCCcEEEEEEe
Confidence            999999999999999999999  689999999999999999999888855599999996

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=2e-33  Score=215.41  Aligned_cols=139  Identities=17%  Similarity=0.338  Sum_probs=128.5

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.||++.+++++|.+++.|++++|++|+|+.+++++++++  |++  +.|||+|++||||||++++|+||.+||+|++.+
T Consensus        56 ~~aD~~~l~~~~r~~~~~~~~~~g~~i~~~~la~~ls~~l--y~~--R~~P~~~~~iiaG~D~~~~p~Ly~~D~~G~~~~  131 (212)
T cd03757          56 FQADILALTKRLKARIKMYKYSHNKEMSTEAIAQLLSTIL--YSR--RFFPYYVFNILAGIDEEGKGVVYSYDPVGSYER  131 (212)
T ss_pred             hHHHHHHHHHHHHHHHHHHhHHhCCCCCHHHHHHHHHHHH--Hhh--cCCCeEEEEEEEEEcCCCCEEEEEEcCccCeee
Confidence            3689999999999999999999999999999999999998  554  357999999999999767799999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhc-------CCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCC
Q 031203           81 HKATSAGLKEQEAINFLEKKMK-------NDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENP  143 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~-------~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~  143 (164)
                      ++++|+|+|+..++++||+.|+       ++++||++||++++.+||..+.+||..++ +++|++|++++.
T Consensus       132 ~~~~a~G~g~~~~~~~Le~~~~~~~~~~~~~~~ms~eea~~l~~~~l~~~~~rd~~sg~~i~i~iit~~g~  202 (212)
T cd03757         132 ETYSAGGSASSLIQPLLDNQVGRKNQNNVERTPLSLEEAVSLVKDAFTSAAERDIYTGDSLEIVIITKDGI  202 (212)
T ss_pred             cCEEEEeecHHHHHHHHHHHHHhhccCcCCCCCCCHHHHHHHHHHHHHHHHHhCcccCCCEEEEEEcCCCE
Confidence            9999999999999999999984       24899999999999999999999997776 999999999874

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=3.1e-33  Score=209.93  Aligned_cols=134  Identities=27%  Similarity=0.432  Sum_probs=127.2

Q ss_pred             CchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceeee
Q 031203            2 TADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGH   81 (164)
Q Consensus         2 ~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~~   81 (164)
                      .+|++.|.++++.+++.|++.++++++|+.++++|++++|.+    ++|||+|++||||||+ +||+||.+||+|++.++
T Consensus        50 ~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~~~~~----~~rP~~v~~ivaG~d~-~g~~Ly~~d~~G~~~~~  124 (185)
T TIGR03634        50 VGDAQSLVRILKAEAKLYELRRGRPMSVKALATLLSNILNSN----RFFPFIVQLLVGGVDE-EGPHLYSLDPAGGIIED  124 (185)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhc----CCCCeEEEEEEEEEeC-CCCEEEEECCCCCeEEC
Confidence            589999999999999999999999999999999999999764    6899999999999997 78999999999999999


Q ss_pred             eEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCC
Q 031203           82 KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKEN  142 (164)
Q Consensus        82 ~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~  142 (164)
                      +++++|+++..++++||++|  +++||++||++++++||..+.+|+..++ +++|++|+++|
T Consensus       125 ~~~a~G~g~~~~~~~Le~~~--~~~~s~~ea~~l~~~~l~~~~~r~~~~~~~~~v~ii~~~g  184 (185)
T TIGR03634       125 DYTATGSGSPVAYGVLEDEY--REDMSVEEAKKLAVRAIKSAIERDVASGNGIDVAVITKDG  184 (185)
T ss_pred             CEEEEcCcHHHHHHHHHhcC--CCCCCHHHHHHHHHHHHHHHHHhcccCCCCEEEEEEcCCC
Confidence            99999999999999999999  5899999999999999999999997776 89999999875

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.

>cd03764 proteasome_beta_archeal Archeal proteasome, beta subunit

Probab=100.00  E-value=5.8e-33  Score=209.02  Aligned_cols=139  Identities=27%  Similarity=0.413  Sum_probs=130.3

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.|.++++.+++.|++.++++++++.+++++++.+|.+    ++|||+|++||||||+ ++|+||.+||+|++.+
T Consensus        48 ~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~~~~----~~~P~~~~~lvaG~d~-~~~~ly~~D~~G~~~~  122 (188)
T cd03764          48 SVGDAQSLVRILKAEARLYELRRGRPMSIKALATLLSNILNSS----KYFPYIVQLLIGGVDE-EGPHLYSLDPLGSIIE  122 (188)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhc----CCCCcEEEEEEEEEeC-CCCEEEEECCCCCEEE
Confidence            4689999999999999999999999999999999999999664    5799999999999997 7899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEc
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVL  148 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l  148 (164)
                      ++++|+|+|++.++++|++.|  +++||.+||++++++||..+.+||..++ +++|+++++++  ++++
T Consensus       123 ~~~~a~G~g~~~~~~~L~~~~--~~~~~~~ea~~l~~~~l~~~~~rd~~~~~~i~i~iv~~~g--~~~~  187 (188)
T cd03764         123 DKYTATGSGSPYAYGVLEDEY--KEDMTVEEAKKLAIRAIKSAIERDSASGDGIDVVVITKDG--YKEL  187 (188)
T ss_pred             cCEEEEcCcHHHHHHHHHhcC--CCCCCHHHHHHHHHHHHHHHHhhcCCCCCcEEEEEECCCC--eEeC
Confidence            999999999999999999998  6899999999999999999999997766 89999999875  7765

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.

>cd03753 proteasome_alpha_type_5 proteasome_alpha_type_5

Probab=100.00  E-value=7.4e-33  Score=212.29  Aligned_cols=135  Identities=33%  Similarity=0.577  Sum_probs=126.8

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhc-----cCccccceeeEEEEEcCCCCCeEEEeCCC
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH-----AYMRPLGVVAMVLSIDEECGPRLFKCDPA   75 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~-----~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~   75 (164)
                      +.+|++.+.+++|.+++.|++++|++|+|+.++++|++++|.|++.     ++.|||+|++||||||+ +||+||.+||+
T Consensus        74 ~~~D~~~l~~~~r~~~~~~~~~~~~~i~~~~~~~~ls~~~~~~~~~~~~~~~~~rP~~v~~ii~G~D~-~gp~Ly~vd~~  152 (213)
T cd03753          74 LIADARTLIDHARVEAQNHRFTYNEPMTVESVTQAVSDLALQFGEGDDGKKAMSRPFGVALLIAGVDE-NGPQLFHTDPS  152 (213)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhCcccccccccccceEEEEEEEEcC-CCCEEEEECCC
Confidence            4689999999999999999999999999999999999999999874     34799999999999997 79999999999


Q ss_pred             cceeeeeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEE
Q 031203           76 GHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVV  138 (164)
Q Consensus        76 G~~~~~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii  138 (164)
                      |++.+++++|+|++++.++++|+++|  +++||.+||++++++||+.+.++++...++||+++
T Consensus       153 G~~~~~~~~a~G~~~~~~~~~L~~~~--~~~ls~eeai~l~~~~l~~~~~~~~~~~~~ei~~~  213 (213)
T cd03753         153 GTFTRCDAKAIGSGSEGAQSSLQEKY--HKDMTLEEAEKLALSILKQVMEEKLNSTNVELATV  213 (213)
T ss_pred             CCeecccEEEECCCcHHHHHHHHhhc--cCCCCHHHHHHHHHHHHHHHhcccCCCCcEEEEEC
Confidence            99999999999999999999999998  68899999999999999999888877779999975

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=1.1e-32  Score=210.71  Aligned_cols=136  Identities=49%  Similarity=0.789  Sum_probs=129.2

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.+.++++.++..|++++|++++++.+++++++++|.|+++++.|||+|++||+|||+++||+||.+||+|++.+
T Consensus        74 ~~~D~~~l~~~l~~~~~~~~~~~g~~~~~~~la~~ls~~~~~~~~~~~~rP~~v~~iv~G~d~~~~~~Ly~iD~~G~~~~  153 (209)
T cd01911          74 LTADARVLVNRARVEAQNYRYTYGEPIPVEVLVKRIADLAQVYTQYGGVRPFGVSLLIAGYDEEGGPQLYQTDPSGTYFG  153 (209)
T ss_pred             CcHhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCccChhheEEEEEEcCCCCcEEEEECCCCCeee
Confidence            46899999999999999999999999999999999999999999999999999999999999866999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEE
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVV  138 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii  138 (164)
                      ++++++|+|+..++++|++.|  +++||.+||++++++||..+.+||+....++|+++
T Consensus       154 ~~~~a~G~g~~~~~~~L~~~~--~~~ms~~ea~~l~~~~l~~~~~~d~~~~~~~i~i~  209 (209)
T cd01911         154 YKATAIGKGSQEAKTFLEKRY--KKDLTLEEAIKLALKALKEVLEEDKKAKNIEIAVV  209 (209)
T ss_pred             eeEEEeCCCcHHHHHHHHHhc--ccCCCHHHHHHHHHHHHHHHHhccCCCCcEEEEEC
Confidence            999999999999999999999  68999999999999999999999993348999875

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.

>cd03763 proteasome_beta_type_7 proteasome beta type-7 subunit

Probab=100.00  E-value=1.7e-32  Score=206.79  Aligned_cols=139  Identities=17%  Similarity=0.269  Sum_probs=128.3

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.|++++|.+++.|+++++++++++.++++|++.+|.|.     .||+|++||||||+ +||+||.+||+|++.+
T Consensus        48 ~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~l~~~~-----~p~~v~~ivaG~d~-~g~~ly~~d~~G~~~~  121 (189)
T cd03763          48 TAADTEAVTNMISSNLELHRLNTGRKPRVVTALTMLKQHLFRYQ-----GHIGAALVLGGVDY-TGPHLYSIYPHGSTDK  121 (189)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHcC-----CccceeEEEEeEcC-CCCEEEEECCCCCEEe
Confidence            36899999999999999999999999999999999999997652     29999999999997 6899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcC
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLS  149 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~  149 (164)
                      ++++|+|+++..++++|+++|  +++||.+||++++++||..+.+||+.++ +++|++|++++  +.+..
T Consensus       122 ~~~~a~G~~~~~~~~~L~~~~--~~~ls~~ea~~l~~~~l~~~~~rd~~~~~~~~v~ii~~~g--~~~~~  187 (189)
T cd03763         122 LPFVTMGSGSLAAMSVLEDRY--KPDMTEEEAKKLVCEAIEAGIFNDLGSGSNVDLCVITKDG--VEYLR  187 (189)
T ss_pred             cCEEEEcCCHHHHHHHHHhhc--CCCCCHHHHHHHHHHHHHHHHHhcCcCCCceEEEEEcCCc--EEEec
Confidence            999999999999999999999  5899999999999999999999998766 89999999886  45443

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=2.9e-32  Score=205.21  Aligned_cols=135  Identities=16%  Similarity=0.257  Sum_probs=127.1

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.|.++++.+++.|++.++++++++.+++++++++|.|     .|||+|++||||||++.||+||.+||+|++.+
T Consensus        48 ~~~D~~~l~~~l~~~~~~~~~~~~~~~~~~~~a~~l~~~~~~~-----~~~~~~~~ii~G~d~~~gp~ly~~d~~G~~~~  122 (188)
T cd03762          48 SAADTQAIADYVRYYLDMHSIELGEPPLVKTAASLFKNLCYNY-----KEMLSAGIIVAGWDEQNGGQVYSIPLGGMLIR  122 (188)
T ss_pred             cHHHHHHHHHHHHHHHHHhHHhhCCCCCHHHHHHHHHHHHHhc-----cccceeeEEEEEEcCCCCcEEEEECCCCCEEe
Confidence            4689999999999999999999999999999999999998655     37999999999999767899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCC
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKEN  142 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~  142 (164)
                      ++++++|+|+..++++|++.|  +++||.+||++++++||..+.+||..++ +++|++|++++
T Consensus       123 ~~~~~~G~g~~~~~~~Le~~~--~~~~s~~ea~~l~~~al~~~~~rd~~~~~~~~i~~i~~~g  183 (188)
T cd03762         123 QPFAIGGSGSTYIYGYVDANY--KPGMTLEECIKFVKNALSLAMSRDGSSGGVIRLVIITKDG  183 (188)
T ss_pred             cCEEEEcccHHHHHHHHHhcC--CCCCCHHHHHHHHHHHHHHHHHhccccCCCEEEEEECCCC
Confidence            999999999999999999998  6899999999999999999999998776 99999999886

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.

>cd01912 proteasome_beta proteasome beta subunit

Probab=100.00  E-value=1.1e-31  Score=202.02  Aligned_cols=136  Identities=22%  Similarity=0.403  Sum_probs=127.9

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.|+++++.++..|++.++++++++.+++++++.+|.+++    |||++++||||||++++|+||.+||+|++.+
T Consensus        48 ~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~----~P~~~~~iv~G~d~~~~~~l~~id~~G~~~~  123 (189)
T cd01912          48 SAADTQALTRLLKRNLRLYELRNGRELSVKAAANLLSNILYSYRG----FPYYVSLIVGGVDKGGGPFLYYVDPLGSLIE  123 (189)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhcCC----CCeEEEEEEEEEcCCCCeEEEEECCCCCeEe
Confidence            468999999999999999999999999999999999999976643    8999999999999767899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCC
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKEN  142 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~  142 (164)
                      ++++|+|++++.++++|++.|  +++||++||++++.+||..+.++|..++ .++|++|++++
T Consensus       124 ~~~~a~G~~~~~~~~~Le~~~--~~~~s~~ea~~~~~~~l~~~~~~d~~~~~~~~v~vi~~~g  184 (189)
T cd01912         124 APFVATGSGSKYAYGILDRGY--KPDMTLEEAVELVKKAIDSAIERDLSSGGGVDVAVITKDG  184 (189)
T ss_pred             cCEEEEcccHHHHHHHHHhcc--CCCCCHHHHHHHHHHHHHHHHHhcCccCCcEEEEEECCCC
Confidence            999999999999999999999  6889999999999999999999987766 89999999886

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=1.9e-31  Score=200.41  Aligned_cols=136  Identities=35%  Similarity=0.572  Sum_probs=129.5

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.+.++++.++..|++.++.+++++.+++.+++.+|.+++++++|||++++|+||||++++|+||.+||+|++.+
T Consensus        53 ~~~D~~~l~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~p~~~~~li~G~d~~~~~~l~~vd~~G~~~~  132 (190)
T PF00227_consen   53 LTADFQYLIRRLREEAQEYRFSYGRPISPEYLAKAIASLIQNYTYRSGRRPYGVSLLIAGYDEDGGPQLYSVDPSGSYIE  132 (190)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHSSGTCHHHHHHHHHHHHHHHHHHTTTSTTSEEEEEEEEETTTEEEEEEEETTSEEEE
T ss_pred             cccchHHHHhhhcccchhhhhccCccccchhhhhhhHHHHhhhcccccccCccccceeeeeccccccceeeecccccccc
Confidence            36899999999999999999999999999999999999999999999999999999999999866699999999999999


Q ss_pred             e-eEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEE
Q 031203           81 H-KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVV  138 (164)
Q Consensus        81 ~-~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii  138 (164)
                      + +++|+|+|++.++++|++.|  .++||++||++++++||..+.++|..++ +++|+||
T Consensus       133 ~~~~~aiG~g~~~~~~~l~~~~--~~~~~~~ea~~~~~~~l~~~~~~d~~~~~~~~v~vi  190 (190)
T PF00227_consen  133 CKRFAAIGSGSQFAQPILEKLY--KPDLSLEEAIELALKALKEAIDRDILSGDNIEVAVI  190 (190)
T ss_dssp             BSSEEEESTTHHHHHHHHHHHH--TTTSSHHHHHHHHHHHHHHHHHHBTTSTSEEEEEEE
T ss_pred             ccccccchhcchhhhHHHHhhc--cCCCCHHHHHHHHHHHHHHHHhhCCccCCeEEEEEC
Confidence            9 69999999999999999999  6899999999999999999999987666 9999986

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 ....

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

Probab=99.97  E-value=4.5e-31  Score=197.32  Aligned_cols=155  Identities=33%  Similarity=0.438  Sum_probs=137.6

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      |.||.+.+++++|.++.+|+-.|+.|+|...++.+++++.|.||.++..||||++.|+++||. +||+||.+||||....
T Consensus        81 l~~Dg~~l~~~ar~ea~~~~~~y~~piP~~~la~rva~yvh~~Tly~~vRpfG~~~~~~~yd~-~g~~LymiepSG~~~~  159 (254)
T KOG0184|consen   81 LIPDGRHLVNRARDEAASWRKNYGDPIPGKHLADRVADYVHAFTLYSSVRPFGASTILGSYDD-EGPQLYMIEPSGSSYG  159 (254)
T ss_pred             cccchHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHhhhheeehhhccccccceEEEEEEeC-CCceEEEEcCCCCccc
Confidence            579999999999999999999999999999999999999999999999999999999999996 8999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccC-CCCeEEEEEEEcCCCcEEEcCHHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDF-KASEIEVGVVSKENPEFRVLSIEEIDEHLT  158 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~-~~~~iei~ii~~~~~~~k~l~~~ei~~~l~  158 (164)
                      |+++|+|.|.|.+++.|||.-  ..+|+.+|+++.+.+.|+.+.+..- ....+||+|+..++++....-|+|+-+...
T Consensus       160 Y~~aaiGKgrq~aKtElEKL~--~~~mt~~e~VkeaakIiY~~HDe~KdK~feiEm~wvg~eTnG~h~~vp~el~~ea~  236 (254)
T KOG0184|consen  160 YKGAAIGKGRQAAKTELEKLK--IDEMTCKELVKEAAKIIYKVHDENKDKEFEIEMGWVGEETNGLHEKVPSELLEEAE  236 (254)
T ss_pred             eeeeeccchhHHHHHHHHhcc--cccccHHHHHHHHHheeEeecccccCcceEEEEEEEEeecCCccccCcHHHHHHHH
Confidence            999999999999999999984  5689999999999999998875432 233799999998765555555556654443

>cd01906 proteasome_protease_HslV proteasome_protease_HslV

Probab=99.97  E-value=1.2e-30  Score=194.78  Aligned_cols=134  Identities=43%  Similarity=0.705  Sum_probs=126.4

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.|.+.++.++..|++.++++++++.+++++++.+|.++++  .|||++++|+||||+..+|+||.+||+|++.+
T Consensus        48 ~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~--~~p~~~~~lv~G~d~~~~~~Ly~id~~G~~~~  125 (182)
T cd01906          48 LAADAQTLVERLRKEAQLYRLRYGEPIPVEALAKLLANLLYEYTQS--LRPLGVSLLVAGVDEEGGPQLYSVDPSGSYIE  125 (182)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhCCC--ccChheEEEEEEEeCCCCcEEEEECCCCCEee
Confidence            3689999999999999999999999999999999999999999875  89999999999999767999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEE
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVV  138 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii  138 (164)
                      ++++|+|+++..+.++|++.|  +++||.+||++++++||..+.+++..++ .++|+++
T Consensus       126 ~~~~a~G~g~~~~~~~L~~~~--~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~~~i~ii  182 (182)
T cd01906         126 YKATAIGSGSQYALGILEKLY--KPDMTLEEAIELALKALKSALERDLYSGGNIEVAVI  182 (182)
T ss_pred             ccEEEECCCcHHHHHHHHHHc--cCCCCHHHHHHHHHHHHHHHHcccCCCCCCEEEEEC
Confidence            999999999999999999998  5789999999999999999999988665 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=99.96  E-value=2.9e-28  Score=185.63  Aligned_cols=151  Identities=17%  Similarity=0.172  Sum_probs=139.7

Q ss_pred             CchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceeee
Q 031203            2 TADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGH   81 (164)
Q Consensus         2 ~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~~   81 (164)
                      +||++.+.+.+..+|++|++++++.|+|...++.||+++.+|   .|+ .+.++.+|+|||+ .||.||.+|..|+-.+.
T Consensus       120 AADCqfWer~L~kecRL~eLRnkeriSVsaASKllsN~~y~Y---kGm-GLsmGtMi~G~Dk-~GP~lyYVDseG~Rl~G  194 (285)
T KOG0175|consen  120 AADCQFWERVLAKECRLHELRNKERISVSAASKLLSNMVYQY---KGM-GLSMGTMIAGWDK-KGPGLYYVDSEGTRLSG  194 (285)
T ss_pred             chhhHHHHHHHHHHHHHHHHhcCcceehHHHHHHHHHHHhhc---cCc-chhheeeEeeccC-CCCceEEEcCCCCEecC
Confidence            589999999999999999999999999999999999999544   455 6788999999998 89999999999999999


Q ss_pred             eEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHHHHHHHh
Q 031203           82 KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEIDEHLTAI  160 (164)
Q Consensus        82 ~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~~~l~~~  160 (164)
                      +-.++|+|+..|+++|+..|  ++|||.|||.+|+++||..+..||..|+ .+.++.|+.++  +..+++.++.+++.++
T Consensus       195 ~~FSVGSGs~yAYGVLDsgY--r~dls~eEA~~L~rrAI~hAThRDaySGG~vnlyHv~edG--W~~v~~~Dv~~L~~~~  270 (285)
T KOG0175|consen  195 DLFSVGSGSTYAYGVLDSGY--RYDLSDEEAYDLARRAIYHATHRDAYSGGVVNLYHVKEDG--WVKVSNTDVSELHYHY  270 (285)
T ss_pred             ceEeecCCCceeEEeeccCC--CCCCCHHHHHHHHHHHHHHHHhcccccCceEEEEEECCcc--ceecCCccHHHHHHHH
Confidence            99999999999999999998  6889999999999999999999999998 79999999986  8899999999985554


Q ss_pred             h
Q 031203          161 S  161 (164)
Q Consensus       161 ~  161 (164)
                      .
T Consensus       271 ~  271 (285)
T KOG0175|consen  271 Y  271 (285)
T ss_pred             H
Confidence            3

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

Probab=99.94  E-value=5.5e-26  Score=166.31  Aligned_cols=138  Identities=16%  Similarity=0.245  Sum_probs=128.7

Q ss_pred             CchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceeee
Q 031203            2 TADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGH   81 (164)
Q Consensus         2 ~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~~   81 (164)
                      .+|+-.+.+++...++.|++++|.+++|+.+++++++.+..+-  ++.+||.|++|+||+|++.||.||++|..|+..+.
T Consensus        50 ~GDt~qF~eyi~~Ni~LYkirnGyeLSp~~aahFtR~~La~~L--Rsr~~yqV~~LvaGYd~~~gp~L~~iDyla~~~~v  127 (200)
T KOG0177|consen   50 AGDTVQFTEYIQKNIQLYKIRNGYELSPSAAAHFTRRELAESL--RSRTPYQVNILVAGYDPEEGPELYYIDYLATLVSV  127 (200)
T ss_pred             CCceehHHHHHHhhhhHHhhhcCCcCCHHHHHHHHHHHHHHHH--hcCCCceEEEEEeccCCCCCCceeeehhhhhcccC
Confidence            4789999999999999999999999999999999999997774  45789999999999999889999999999999999


Q ss_pred             eEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhcc-CCCCeEEEEEEEcCCC
Q 031203           82 KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQED-FKASEIEVGVVSKENP  143 (164)
Q Consensus        82 ~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d-~~~~~iei~ii~~~~~  143 (164)
                      ++++.|.++.++.++|+.+|  +|+||.+||+.+..+|+.++.+|- ++-.++.|.||+++|.
T Consensus       128 py~~hGy~~~f~~sIlDr~Y--~pdmt~eea~~lmkKCv~El~kRlvin~~~f~v~IVdkdGi  188 (200)
T KOG0177|consen  128 PYAAHGYGSYFCLSILDRYY--KPDMTIEEALDLMKKCVLELKKRLVINLPGFIVKIVDKDGI  188 (200)
T ss_pred             CcccccchhhhhHHHHHhhh--CCCCCHHHHHHHHHHHHHHHHHhcccCCCCcEEEEEcCCCc
Confidence            99999999999999999998  699999999999999999999884 4556999999999973

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

Probab=99.93  E-value=5.2e-25  Score=163.54  Aligned_cols=144  Identities=17%  Similarity=0.336  Sum_probs=131.4

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|+..|++.++...+.|+..++..|++..+|+.|+.++  |.  .++.||.|..|+||+|+++++.+|+.||.|++.+
T Consensus        77 F~aD~l~L~k~i~~r~~~Y~~~h~k~ms~~s~A~lls~~L--Y~--kRFFPYYv~~ilaGiDeeGKG~VySyDPvGsyer  152 (235)
T KOG0179|consen   77 FYADTLALVKVIKSRIKQYEHDHNKKMSIHSAAQLLSTIL--YS--KRFFPYYVFNILAGIDEEGKGAVYSYDPVGSYER  152 (235)
T ss_pred             chhhHHHHHHHHHHHHHHHhhcccccccHHHHHHHHHHHH--hh--cccccceeeeeeecccccCceeEEeecCCcceee
Confidence            4689999999999999999999999999999999999999  63  4688999999999999999999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhc---------CCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEc
Q 031203           81 HKATSAGLKEQEAINFLEKKMK---------NDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVL  148 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~---------~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l  148 (164)
                      ..+.|-|+++.+++++|++...         ++..||+|+|+.++..++..+.+||+..+ .++|+|+++++...+.+
T Consensus       153 ~~~~AgGsa~~mI~PfLDnQi~~kn~~~e~~~~~~Ls~e~ai~lv~d~F~SAaERdI~tGD~l~i~I~tk~gV~~e~~  230 (235)
T KOG0179|consen  153 VTCRAGGSAASMIQPFLDNQIGHKNQNLENAERTPLSLERAIRLVKDAFTSAAERDIYTGDKLEICIITKDGVEVETL  230 (235)
T ss_pred             eeeecCCcchhhhhhhhhhhccCcCcccccCcccccCHHHHHHHHHHHhhhhhhcccccCCcEEEEEEecCCEEEEee
Confidence            9999999999999999998642         13578999999999999999999999998 89999999987544433

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

Probab=99.92  E-value=9.7e-25  Score=160.45  Aligned_cols=150  Identities=16%  Similarity=0.224  Sum_probs=138.0

Q ss_pred             CchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceeee
Q 031203            2 TADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGH   81 (164)
Q Consensus         2 ~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~~   81 (164)
                      ++|.|.+.+.++.....|..+++.++++...++.+++++.+|     ..-+.+++||||||++.|.++|.+--.|++.+-
T Consensus        68 AADtQaiaD~~~Y~L~~~~~q~~~~p~v~~aA~l~r~~~Y~~-----re~L~AgliVAGwD~~~gGqVY~iplGG~l~rq  142 (224)
T KOG0174|consen   68 AADTQAIADIVRYHLELYTIQENKPPLVHTAASLFREICYNY-----REMLSAGLIVAGWDEKEGGQVYSIPLGGSLTRQ  142 (224)
T ss_pred             hhhHHHHHHHHHHHHHHhhhhcCCCchHHHHHHHHHHHHHhC-----HHhhhcceEEeecccccCceEEEeecCceEeec
Confidence            689999999999999999999999999999999999999443     224789999999999899999999888888889


Q ss_pred             eEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHHHHHH
Q 031203           82 KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEIDEHLT  158 (164)
Q Consensus        82 ~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~~~l~  158 (164)
                      +++.-|+||.+++++++.+|  +|+||+||++.++.+|+..++.||-.|+ .|.+.+|+++|..++++.+|++.++..
T Consensus       143 ~~aIgGSGStfIYGf~D~~~--r~nMt~EE~~~fvk~Av~lAi~rDGsSGGviR~~~I~~~Gver~~~~~d~~~~~~v  218 (224)
T KOG0174|consen  143 PFAIGGSGSTFIYGFCDANW--RPNMTLEECVRFVKNAVSLAIERDGSSGGVIRLVIINKAGVERRFFPGDKLGQFAV  218 (224)
T ss_pred             ceeeccCCceeeeeeehhhc--CCCCCHHHHHHHHHHHHHHHHhccCCCCCEEEEEEEccCCceEEEecCCccccccc
Confidence            99999999999999999999  6899999999999999999999999988 799999999998899999998876543

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

Probab=99.90  E-value=7.7e-23  Score=155.65  Aligned_cols=134  Identities=18%  Similarity=0.288  Sum_probs=123.9

Q ss_pred             CchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceeee
Q 031203            2 TADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGH   81 (164)
Q Consensus         2 ~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~~   81 (164)
                      ++|...+.+.+-.+...|++..++.++|-...+++.+.+..|   .|  -.|+.+||+|+|+ .|||||.+-|.|+....
T Consensus        86 AADte~vt~m~ss~l~Lh~l~t~R~~rVv~A~~mlkQ~LFrY---qG--~IgA~LiiGGvD~-TGpHLy~i~phGStd~~  159 (271)
T KOG0173|consen   86 AADTEMVTRMISSNLELHRLNTGRKPRVVTALRMLKQHLFRY---QG--HIGAALILGGVDP-TGPHLYSIHPHGSTDKL  159 (271)
T ss_pred             hhhHHHHHHHHHHHHHHHHhccCCCCceeeHHHHHHHHHHHh---cC--cccceeEEccccC-CCCceEEEcCCCCcCcc
Confidence            578999999999999999999999999999999998888444   34  4799999999999 89999999999999999


Q ss_pred             eEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCC
Q 031203           82 KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENP  143 (164)
Q Consensus        82 ~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~  143 (164)
                      +++++|||+..+++.||.+|  +||||.|||.+|+..|+...+..|+.|+ ++.++||++.+.
T Consensus       160 Pf~alGSGslaAmsvlEsr~--k~dlt~eea~~Lv~eAi~AGi~nDLgSGsnvdlcVI~~~~~  220 (271)
T KOG0173|consen  160 PFTALGSGSLAAMSVLESRW--KPDLTKEEAIKLVCEAIAAGIFNDLGSGSNVDLCVITKKGV  220 (271)
T ss_pred             ceeeeccchHHHHHHHHHhc--CcccCHHHHHHHHHHHHHhhhccccCCCCceeEEEEeCCCc
Confidence            99999999999999999999  6999999999999999999999999999 999999997553

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

Probab=99.89  E-value=4.1e-22  Score=144.21  Aligned_cols=137  Identities=15%  Similarity=0.264  Sum_probs=129.7

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      |++|+|.|.++++..-..|++++++.|.|+.+++++|+++  |.+  ++-||.+..+|||.|++++|.|..+|..|+...
T Consensus        56 latDvqtl~~~~~fr~nLy~lre~R~i~P~~~s~mvS~~l--Yek--RfgpYf~~PvVAGl~~~~kPfIc~mD~IGc~~~  131 (204)
T KOG0180|consen   56 LATDVQTLLERLRFRKNLYELREEREIKPETFSSMVSSLL--YEK--RFGPYFTEPVVAGLDDDNKPFICGMDLIGCIDA  131 (204)
T ss_pred             cchhHHHHHHHHHHHHhHHHhhhhcccCcHHHHHHHHHHH--HHh--hcCCcccceeEeccCCCCCeeEeecccccCcCc
Confidence            5789999999999999999999999999999999999999  654  577999999999999989999999999999987


Q ss_pred             e-eEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCC
Q 031203           81 H-KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENP  143 (164)
Q Consensus        81 ~-~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~  143 (164)
                      - .+++.|.++...++++|..|  +|+|..|++++.+.+||.++.+||+-|+ +..+.+|++++.
T Consensus       132 ~~DFVvsGTa~e~L~GmCE~ly--~pnmepd~LFetisQa~Lna~DRDalSGwGa~vyiI~kdkv  194 (204)
T KOG0180|consen  132 PKDFVVSGTASEQLYGMCEALY--EPNMEPDELFETISQALLNAVDRDALSGWGAVVYIITKDKV  194 (204)
T ss_pred             cCCeEEecchHHHHHHHHHHhc--CCCCCHHHHHHHHHHHHHhHhhhhhhccCCeEEEEEccchh
Confidence            5 79999999999999999999  6999999999999999999999999999 999999999864

>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=99.88  E-value=2.1e-21  Score=140.66  Aligned_cols=115  Identities=39%  Similarity=0.588  Sum_probs=109.8

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.+.++++.+++.|++.++.++++..+++.+++.++.+++   .||+++++||||+|+ ++|+||.+||+|++..
T Consensus        48 ~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~p~~~~~iiag~~~-~~~~l~~id~~g~~~~  123 (164)
T cd01901          48 LAADAQTLVRRLREALQLYRLRYGEPISVVALAKELAKLLQVYTQ---GRPFGVNLIVAGVDE-GGGNLYYIDPSGPVIE  123 (164)
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcC---CCCcceEEEEEEEcC-CCCEEEEECCCcCEee
Confidence            358999999999999999999999999999999999999998876   799999999999998 8999999999999999


Q ss_pred             e-eEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHH
Q 031203           81 H-KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQ  121 (164)
Q Consensus        81 ~-~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~  121 (164)
                      + .++++|+++..+.++|++.|  +++++.+++++++.+||.
T Consensus       124 ~~~~~~~G~~~~~~~~~l~~~~--~~~~~~~~~~~~~~~~l~  163 (164)
T cd01901         124 NPGAVATGSRSQRAKSLLEKLY--KPDMTLEEAVELALKALK  163 (164)
T ss_pred             cCcEEEECCCCHHHHHHHHHHh--cCCCCHHHHHHHHHHHHh
Confidence            9 99999999999999999998  578999999999999985

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

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

Probab=99.80  E-value=2.2e-19  Score=135.59  Aligned_cols=148  Identities=16%  Similarity=0.212  Sum_probs=131.8

Q ss_pred             CchHHHHHHHHHHHHHHHH-HHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            2 TADARTLVQQARYEAAEFR-FKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         2 ~~D~~~l~~~~~~~~~~~~-~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      .+|+|.+.+.+.....+.. +.-|+.+.|+.+..+|+..+  |.+++.+.|+...++|||+|..+.|.|-.+|--|...+
T Consensus        90 isD~Q~i~r~L~~l~iedn~~~Dg~~l~Pk~ih~yltrvl--Y~rRsKmnPlwntlvVgGv~~~g~~~lg~V~~~G~~Y~  167 (256)
T KOG0185|consen   90 ISDFQYIQRVLEQLVIEDNRLDDGQSLGPKAIHSYLTRVL--YARRSKMNPLWNTLVVGGVDNTGEPFLGYVDLLGVAYE  167 (256)
T ss_pred             HHHHHHHHHHHHHHHhcccccccccccChHHHHHHHHHHH--HHhhhccCchhhheeEeeecCCCCeeEEEEeecccccc
Confidence            4799999999988777644 44469999999999999999  98999999999999999999877799999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhc-CCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMK-NDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEI  153 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~-~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei  153 (164)
                      .+..|+|.|...+.++|++.|+ ..++++.+||..++.+|+...+.||+.+. .++|++|+++|  +.+-.|..|
T Consensus       168 ~~~vATGfg~hLa~P~lR~~~~~k~~~~s~eeA~~li~~cMrVL~YRD~ra~n~fqva~v~~eG--v~i~~p~qv  240 (256)
T KOG0185|consen  168 SPVVATGFGAHLALPLLRDEWEKKGEDLSREEAEALIEKCMRVLYYRDARASNEFQVATVDEEG--VTISKPYQV  240 (256)
T ss_pred             CchhhhhhHHHhhhHHHHHhhhccchhhHHHHHHHHHHHHHHHHhccccccccceEEEEEcccc--eEecCceee
Confidence            9999999999999999999996 45799999999999999999999999877 89999999975  455555444

>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=99.79  E-value=3.1e-18  Score=126.64  Aligned_cols=115  Identities=14%  Similarity=0.066  Sum_probs=93.4

Q ss_pred             CchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccc-eeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            2 TADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLG-VVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         2 ~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~g-v~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      .+|++.|.++++.+++.|+++.++     .+++.++.+.     ..+.+|+. +.+|+++||     +||.+||.|++.+
T Consensus        50 ~aD~~~l~~~~~~~~~~y~~~~~~-----~aa~l~~~l~-----~~~~~~~l~a~~iv~~~~-----~ly~id~~G~~ie  114 (171)
T cd01913          50 TADAFTLFERFEAKLEQYPGNLLR-----AAVELAKDWR-----TDRYLRRLEAMLIVADKE-----HTLLISGNGDVIE  114 (171)
T ss_pred             HHHHHHHHHHHHHHHHHhhchHHH-----HHHHHHHHHH-----hccCcCceEEEEEEeCCC-----cEEEECCCCCEec
Confidence            589999999999999999999884     4444444332     11345665 666665443     8999999999999


Q ss_pred             ee--EEeecCChHHHHHHHHHhhcCCC-CCCHHHHHHHHHHHHHhhhhccCCCC-eEEEE
Q 031203           81 HK--ATSAGLKEQEAINFLEKKMKNDP-AFTFQETVQTAISTLQSVLQEDFKAS-EIEVG  136 (164)
Q Consensus        81 ~~--~~aiG~~s~~~~~~Le~~~~~~~-~ls~eea~~l~~~al~~~~~~d~~~~-~iei~  136 (164)
                      .+  ++++||||.+++++||.+|  ++ +||   +.++|++|+..+++||..++ +|.|-
T Consensus       115 ~~~~~~a~GSGS~ya~g~ld~~y--k~~~ms---~~~la~~Av~~A~~rd~~tg~~i~~~  169 (171)
T cd01913         115 PDDGIAAIGSGGNYALAAARALL--DHTDLS---AEEIARKALKIAADICIYTNHNITVE  169 (171)
T ss_pred             cCCCeEEEeCCHHHHHHHHHHhh--ccCCCC---HHHHHHHHHHHHHhhCcccCCCEEEE
Confidence            84  9999999999999999998  57 499   55999999999999999888 77764

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.

>PRK05456 ATP-dependent protease subunit HslV; Provisional

Probab=99.78  E-value=5e-18  Score=126.07  Aligned_cols=117  Identities=16%  Similarity=0.156  Sum_probs=95.7

Q ss_pred             CchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceeee
Q 031203            2 TADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGH   81 (164)
Q Consensus         2 ~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~~   81 (164)
                      .+|+|.|.+.++.+++.|+.  +.   ++.+++.++.+.    .+...+|+.+++|++  |+   |+||.+||.|++.+.
T Consensus        51 ~aD~q~l~~~l~~~~~~y~~--~~---~~~~a~l~~~l~----~~~~~~~l~~~~lv~--d~---~~ly~id~~G~~~~~  116 (172)
T PRK05456         51 TADAFTLFERFEAKLEEHQG--NL---LRAAVELAKDWR----TDRYLRRLEAMLIVA--DK---EHSLIISGNGDVIEP  116 (172)
T ss_pred             HHHHHHHHHHHHHHHHHccC--cc---HHHHHHHHHHHH----hccCCCccEEEEEEE--cC---CcEEEECCCCcEecc
Confidence            58999999999999999882  22   466665554332    122246888999994  44   699999999999776


Q ss_pred             --eEEeecCChHHHHHHHHHhhcCC-CCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEE
Q 031203           82 --KATSAGLKEQEAINFLEKKMKND-PAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGV  137 (164)
Q Consensus        82 --~~~aiG~~s~~~~~~Le~~~~~~-~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~i  137 (164)
                        +++++|+|+.++.++||++|  + |+|   ||++++++|+..+.+||..++ ++.|-.
T Consensus       117 ~~~~~a~GSGs~~a~g~ld~~y--~~~~m---eA~~la~kai~~A~~Rd~~sg~~i~v~~  171 (172)
T PRK05456        117 EDGIIAIGSGGNYALAAARALL--ENTDL---SAEEIAEKALKIAADICIYTNHNITIEE  171 (172)
T ss_pred             CCCeEEEecCHHHHHHHHHHhh--hcCCC---CHHHHHHHHHHHHHHhCeeCCCcEEEEE
Confidence              79999999999999999998  5 889   999999999999999999887 777643

>TIGR03692 ATP_dep_HslV ATP-dependent protease HslVU, peptidase subunit

Probab=99.75  E-value=2.2e-17  Score=122.16  Aligned_cols=116  Identities=13%  Similarity=0.096  Sum_probs=92.4

Q ss_pred             CchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCcccc-ceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            2 TADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPL-GVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         2 ~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~-gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      .+|++.|.++++.+++.|++..     .+.+++.++++.    .+ ..+|+ .+.+|++||     ++||.+||.|++.+
T Consensus        50 ~aD~q~l~~~~~~~~~~y~~~~-----~~~~a~l~~~~~----~~-~~~~~l~a~~iv~~~-----~~ly~i~~~G~~ie  114 (171)
T TIGR03692        50 TADAFTLFERFEAKLEEYQGNL-----TRAAVELAKDWR----TD-RYLRRLEAMLIVADK-----ETSLLISGTGDVIE  114 (171)
T ss_pred             HHHHHHHHHHHHHHHHHccCch-----HHHHHHHHHHHh----hc-ccccccEEEEEEEcC-----CCEEEEcCCCcEec
Confidence            5899999999999999988743     366666655531    11 23344 366666644     38999999999999


Q ss_pred             e--eEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEE
Q 031203           81 H--KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVG  136 (164)
Q Consensus        81 ~--~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~  136 (164)
                      .  +++++||||.+++++||.+|+ .++|+   |+++|++|+..+++||..++ +|.|-
T Consensus       115 ~~~~~~a~GSGS~~a~g~ld~~y~-~~~~s---a~~la~~Av~~A~~rd~~sg~~i~v~  169 (171)
T TIGR03692       115 PEDGIAAIGSGGNYALAAARALLR-NTDLS---AEEIAREALKIAADICIYTNHNITIE  169 (171)
T ss_pred             cCCCeEEEeCCHHHHHHHHHHhhh-cCCCC---HHHHHHHHHHHHHhhCccCCCCEEEE
Confidence            6  599999999999999999994 36677   99999999999999999888 77764

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

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

Probab=97.25  E-value=0.00065  Score=51.36  Aligned_cols=113  Identities=12%  Similarity=0.167  Sum_probs=84.2

Q ss_pred             CCHHHHHHHHHHHHHhhhhccC------ccccceeeEEEEEcCCCCCeEEEeCCCcceeee----eEEeecCChHHHHHH
Q 031203           27 MPVDVLAKWIADKSQVYTQHAY------MRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGH----KATSAGLKEQEAINF   96 (164)
Q Consensus        27 i~~~~l~~~ls~~~q~yt~~~~------~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~~----~~~aiG~~s~~~~~~   96 (164)
                      .++-..+..++....+--.+.+      .--|.||+|++|.=...-|.||.+-|.|++.+.    .+--||. +..-+++
T Consensus        79 ~sm~eattlvgetvrEv~~rds~~leka~~dfn~sfllGGQI~G~pp~Ly~IYpqGNFIqaT~etpf~QiGE-tKYGKPi  157 (255)
T COG3484          79 PSMYEATTLVGETVREVQARDSPALEKAGIDFNCSFLLGGQIKGEPPRLYLIYPQGNFIQATPETPFLQIGE-TKYGKPI  157 (255)
T ss_pred             hhHHHHHHHHHHHHHHHHhccCchhhccCcceeEEEEEcceecCCCceeEEEccCCCeeecCCCCceeEccc-cccCchh
Confidence            3555666666665533211110      125789999999855344899999999999873    5777875 4567899


Q ss_pred             HHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCC
Q 031203           97 LEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKEN  142 (164)
Q Consensus        97 Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~  142 (164)
                      |++.+  .-++++||+.+.|+-.+...++.+++-+ -+.+.++.++.
T Consensus       158 ldR~i--~~~~pLeea~kcaLvS~DSTlkSNiSVGlPldLl~~e~ds  202 (255)
T COG3484         158 LDRTI--TYDTPLEEAAKCALVSFDSTLKSNISVGLPLDLLVYEADS  202 (255)
T ss_pred             hhhhh--hccCCHHHHhhheEEecchhhhccccccCCceeEEEeccc
Confidence            99987  5679999999999999988888888877 78888888875

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

Probab=96.10  E-value=0.09  Score=38.55  Aligned_cols=105  Identities=21%  Similarity=0.236  Sum_probs=71.3

Q ss_pred             CchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceeee
Q 031203            2 TADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGH   81 (164)
Q Consensus         2 ~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~~   81 (164)
                      ++|+..|-+++..+++.|.   |   .+...+..+++-.  ++. .-.|-+-.-++|+  |+   -.+|-+.-.|-..+.
T Consensus        54 tADaftLfe~fe~kle~~~---g---~L~raavelaKdw--r~D-k~lr~LEAmllVa--d~---~~il~isG~gdV~ep  119 (178)
T COG5405          54 TADAFTLFERFEAKLEQYQ---G---DLFRAAVELAKDW--RTD-KYLRKLEAMLLVA--DK---THILIITGNGDVIEP  119 (178)
T ss_pred             chhHHHHHHHHHHHHHHcc---C---cHHHHHHHHHHhh--hhh-hHHHHHhhheeEe--CC---CcEEEEecCcceecC
Confidence            6899999999999998864   2   1222344444333  222 1245566777776  54   358888888888774


Q ss_pred             --eEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhh
Q 031203           82 --KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVL  124 (164)
Q Consensus        82 --~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~  124 (164)
                        ...+||||-.++.+.-...++ ++++|.+|   ++.++|..+-
T Consensus       120 e~~~~aIGSGgnyAl~AarAl~~-~~~lsA~e---Ia~~sl~iA~  160 (178)
T COG5405         120 EDDIIAIGSGGNYALSAARALME-NTELSARE---IAEKSLKIAG  160 (178)
T ss_pred             CCCeEEEcCCchHHHHHHHHHHh-ccCCCHHH---HHHHHHhhhh
Confidence              489999999999999888874 45666554   5666666554

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

Probab=87.61  E-value=1.2  Score=31.62  Aligned_cols=44  Identities=20%  Similarity=0.160  Sum_probs=39.5

Q ss_pred             EEeCCCcceeeeeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHH
Q 031203           70 FKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQT  115 (164)
Q Consensus        70 y~~dp~G~~~~~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l  115 (164)
                      ..+|-+|.+...++-..|.||..+-+-+-..|  -..+|+||+.++
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            46788999999999999999999999999988  578999999875

>PF03646 FlaG: FlaG protein; InterPro: IPR005186 Although these proteins are known to be important for flagellar their exact function is unknown

Probab=81.06  E-value=6.2  Score=26.58  Aligned_cols=33  Identities=24%  Similarity=0.328  Sum_probs=25.5

Q ss_pred             CCeEEEEEEEcCCC-cEEEcCHHHHHHHHHHhhc
Q 031203          130 ASEIEVGVVSKENP-EFRVLSIEEIDEHLTAISE  162 (164)
Q Consensus       130 ~~~iei~ii~~~~~-~~k~l~~~ei~~~l~~~~~  162 (164)
                      ++.+-|.|++++++ .+|.++|+++-++..+|.+
T Consensus        65 ~~~~vVkViD~~T~eVIRqIP~Ee~l~l~~~l~e   98 (107)
T PF03646_consen   65 SGRVVVKVIDKETGEVIRQIPPEELLDLAKRLRE   98 (107)
T ss_dssp             TTEEEEEEEETTT-SEEEEE-HHHHHHHHHHHHH
T ss_pred             CCcEEEEEEECCCCcEEEeCCcHHHHHHHHHHHH
Confidence            45788999999876 5689999999998887753

; PDB: 2HC5_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	164
3unb_G	246	Mouse Constitutive 20s Proteasome In Complex With P		8e-57
1iru_A	246	Crystal Structure Of The Mammalian 20s Proteasome A		8e-57
1ryp_A	243	Crystal Structure Of The 20s Proteasome From Yeast		1e-35
1g0u_G	252	A Gated Channel Into The Proteasome Core Particle L		1e-35
3h4p_A	264	Proteasome 20s Core Particle From Methanocaldococcu		2e-23
2ku1_A	237	Dynamic Regulation Of Archaeal Proteasome Gate Open		5e-20
3jrm_A	227	Crystal Structure Of Archaeal 20s Proteasome In Com		5e-20
1yau_A	233	Structure Of Archeabacterial 20s Proteasome- Pa26 C		5e-20
2ku2_A	237	Dynamic Regulation Of Archaeal Proteasome Gate Open		5e-20
1pma_A	233	Proteasome From Thermoplasma Acidophilum Length = 2		5e-20
1yar_A	233	Structure Of Archeabacterial 20s Proteasome Mutant		6e-20
1j2q_A	237	20s Proteasome In Complex With Calpain-inhibitor I		2e-19
1j2p_A	246	Alpha-Ring From The Proteasome From Archaeoglobus F		4e-19
3une_C	248	Mouse Constitutive 20s Proteasome Length = 248		8e-19
3unb_C	248	Mouse Constitutive 20s Proteasome In Complex With P		9e-19
1iru_B	233	Crystal Structure Of The Mammalian 20s Proteasome A		1e-17
3unb_A	234	Mouse Constitutive 20s Proteasome In Complex With P		2e-17
1iru_D	248	Crystal Structure Of The Mammalian 20s Proteasome A		3e-17
1iru_F	263	Crystal Structure Of The Mammalian 20s Proteasome A		4e-17
3unb_E	263	Mouse Constitutive 20s Proteasome In Complex With P		4e-17
1vsy_D	227	Proteasome Activator Complex Length = 227		2e-16
1ryp_D	241	Crystal Structure Of The 20s Proteasome From Yeast		2e-16
1g0u_C	243	A Gated Channel Into The Proteasome Core Particle L		2e-16
1vsy_B	231	Proteasome Activator Complex Length = 231		2e-16
1ryp_B	250	Crystal Structure Of The 20s Proteasome From Yeast		2e-16
1fnt_D	254	Crystal Structure Of The 20s Proteasome From Yeast		2e-16
1vsy_C	232	Proteasome Activator Complex Length = 232		2e-15
1g0u_B	245	A Gated Channel Into The Proteasome Core Particle L		2e-15
1ryp_C	244	Crystal Structure Of The 20s Proteasome From Yeast		2e-15
3oeu_B	235	Structure Of Yeast 20s Open-Gate Proteasome With Co		2e-15
1z7q_C	258	Crystal Structure Of The 20s Proteasome From Yeast		2e-15
1iru_C	261	Crystal Structure Of The Mammalian 20s Proteasome A		7e-15
3unb_B	261	Mouse Constitutive 20s Proteasome In Complex With P		6e-14
3unb_D	241	Mouse Constitutive 20s Proteasome In Complex With P		2e-12
1iru_E	241	Crystal Structure Of The Mammalian 20s Proteasome A		2e-12
3unb_F	255	Mouse Constitutive 20s Proteasome In Complex With P		1e-11
1iru_G	254	Crystal Structure Of The Mammalian 20s Proteasome A		2e-11
1z7q_G	288	Crystal Structure Of The 20s Proteasome From Yeast		6e-11
1g0u_F	248	A Gated Channel Into The Proteasome Core Particle L		7e-11
1fnt_G	287	Crystal Structure Of The 20s Proteasome From Yeast		7e-11
3oeu_F	242	Structure Of Yeast 20s Open-Gate Proteasome With Co		7e-11
1ryp_G	244	Crystal Structure Of The 20s Proteasome From Yeast		7e-11
1g0u_D	241	A Gated Channel Into The Proteasome Core Particle L		3e-09
1vsy_E	250	Proteasome Activator Complex Length = 250		6e-09
1ryp_E	242	Crystal Structure Of The 20s Proteasome From Yeast		7e-09
2z5c_C	262	Crystal Structure Of A Novel Chaperone Complex For		7e-09
4g4s_E	261	Structure Of Proteasome-Pba1-Pba2 Complex Length =		7e-09
1fnt_E	260	Crystal Structure Of The 20s Proteasome From Yeast		7e-09
3sdi_E	233	Structure Of Yeast 20s Open-Gate Proteasome With Co		6e-08
1g0u_E	234	A Gated Channel Into The Proteasome Core Particle L		7e-08
1fnt_F	234	Crystal Structure Of The 20s Proteasome From Yeast		3e-07
4g4s_F	235	Structure Of Proteasome-Pba1-Pba2 Complex Length =		3e-07
1ryp_F	233	Crystal Structure Of The 20s Proteasome From Yeast		4e-07

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

Iteration: 1
 Score =  215 bits (548), Expect = 8e-57,   Method: Compositional matrix adjust.
 Identities = 100/164 (60%), Positives = 135/164 (82%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           MTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD SQVYTQ+A MRPLG   +++ 
Sbjct: 83  MTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIG 142
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +FLEKK+K    +TF++TV+TAI+ L
Sbjct: 143 IDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCL 202
Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
            +VL  DFK SEIEVGVV+ ENP+FR+L+  EID HL A++ERD
Sbjct: 203 STVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVALAERD 246

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

Iteration: 1
 Score =  215 bits (548), Expect = 8e-57,   Method: Compositional matrix adjust.
 Identities = 100/164 (60%), Positives = 135/164 (82%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           MTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD SQVYTQ+A MRPLG   +++ 
Sbjct: 83  MTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIG 142
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +FLEKK+K    +TF++TV+TAI+ L
Sbjct: 143 IDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCL 202
Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
            +VL  DFK SEIEVGVV+ ENP+FR+L+  EID HL A++ERD
Sbjct: 203 STVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVALAERD 246

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

Iteration: 1
 Score =  145 bits (365), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 81/166 (48%), Positives = 115/166 (69%), Gaps = 7/166 (4%)
Query: 4   DARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDE 63
           DAR    +A+ EAAEFR+KYGY+MP DVLAK +A+ SQ+YTQ AYMRPLGV+   +S+DE
Sbjct: 80  DARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQRAYMRPLGVILTFVSVDE 139
Query: 64  ECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLE---KKMKNDPAF--TFQETVQTAIS 118
           E GP ++K DPAG++ G+KAT+ G K+QE    LE   KK K D     ++++ V+ AI+
Sbjct: 140 ELGPSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKKSKIDHINEESWEKVVEFAIT 199
Query: 119 TLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
            +   L  +F  +++EVGV +K+  +F  LS E I+E L AI+E+D
Sbjct: 200 HMIDALGTEFSKNDLEVGVATKD--KFFTLSAENIEERLVAIAEQD 243

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

Iteration: 1
 Score =  145 bits (365), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 81/166 (48%), Positives = 115/166 (69%), Gaps = 7/166 (4%)
Query: 4   DARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDE 63
           DAR    +A+ EAAEFR+KYGY+MP DVLAK +A+ SQ+YTQ AYMRPLGV+   +S+DE
Sbjct: 89  DARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQRAYMRPLGVILTFVSVDE 148
Query: 64  ECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLE---KKMKNDPAF--TFQETVQTAIS 118
           E GP ++K DPAG++ G+KAT+ G K+QE    LE   KK K D     ++++ V+ AI+
Sbjct: 149 ELGPSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKKSKIDHINEESWEKVVEFAIT 208
Query: 119 TLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
            +   L  +F  +++EVGV +K+  +F  LS E I+E L AI+E+D
Sbjct: 209 HMIDALGTEFSKNDLEVGVATKD--KFFTLSAENIEERLVAIAEQD 252

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

Iteration: 1
 Score =  105 bits (261), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 55/152 (36%), Positives = 89/152 (58%), Gaps = 4/152 (2%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADAR L+ +AR EA  +R  YG E+ +++LAK I D  Q YTQH  +RP GV  ++  
Sbjct: 85  LVADARVLIDRARLEAQIYRLTYGEEISIEMLAKKICDIKQAYTQHGGVRPFGVSLLIAG 144
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ID+    RLF+ DP+G    +KAT+ G      +  LEK+ ++D   T  E ++ AI+ L
Sbjct: 145 IDKN-EARLFETDPSGALIEYKATAIGSGRPVVMELLEKEYRDD--ITLDEGLELAITAL 201
Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEE 152
                ED K   ++V +++ ++ +F+ + +EE
Sbjct: 202 TKA-NEDIKPENVDVCIITVKDAQFKKIPVEE 232

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

Iteration: 1
 Score = 93.6 bits (231), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 56/157 (35%), Positives = 88/157 (56%), Gaps = 4/157 (2%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADAR LV  AR  A + +  YG  + ++ L K +AD+ Q YTQ+  +RP GV  +   
Sbjct: 85  LVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGVSLIFAG 144
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ID + GPRLF CDPAG    +KAT+ G  +   ++FLE++ K +     +E V   I  L
Sbjct: 145 ID-QIGPRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKEN--LPEKEAVTLGIKAL 201
Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 157
           +S L+E  +    E+  ++  N ++R+   EE+ + L
Sbjct: 202 KSSLEEGEELKAPEIASITVGN-KYRIYDQEEVKKFL 237

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

Iteration: 1
 Score = 93.6 bits (231), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 59/159 (37%), Positives = 88/159 (55%), Gaps = 8/159 (5%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADAR LV  AR  A + +  YG  + ++ L K +AD+ Q YTQ+  +RP GV  +   
Sbjct: 75  LVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGVSLIFAG 134
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ID + GPRLF CDPAG    +KAT+ G  +   ++FLE++ K +     +E V   I  L
Sbjct: 135 ID-QIGPRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKEN--LPEKEAVTLGIKAL 191
Query: 121 QSVLQ--EDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 157
           +S L+  E+ KA EI    V     ++R+   EE+ + L
Sbjct: 192 KSSLEEGEELKAPEIASITVGN---KYRIYDQEEVKKFL 227

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

Iteration: 1
 Score = 93.6 bits (231), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 56/157 (35%), Positives = 88/157 (56%), Gaps = 4/157 (2%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADAR LV  AR  A + +  YG  + ++ L K +AD+ Q YTQ+  +RP GV  +   
Sbjct: 81  LVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGVSLIFAG 140
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ID + GPRLF CDPAG    +KAT+ G  +   ++FLE++ K +     +E V   I  L
Sbjct: 141 ID-QIGPRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKEN--LPEKEAVTLGIKAL 197
Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 157
           +S L+E  +    E+  ++  N ++R+   EE+ + L
Sbjct: 198 KSSLEEGEELKAPEIASITVGN-KYRIYDQEEVKKFL 233

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

Iteration: 1
 Score = 93.6 bits (231), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 59/159 (37%), Positives = 88/159 (55%), Gaps = 8/159 (5%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADAR LV  AR  A + +  YG  + ++ L K +AD+ Q YTQ+  +RP GV  +   
Sbjct: 85  LVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGVSLIFAG 144
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ID + GPRLF CDPAG    +KAT+ G  +   ++FLE++ K +     +E V   I  L
Sbjct: 145 ID-QIGPRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKEN--LPEKEAVTLGIKAL 201
Query: 121 QSVLQ--EDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 157
           +S L+  E+ KA EI    V     ++R+   EE+ + L
Sbjct: 202 KSSLEEGEELKAPEIASITVGN---KYRIYDQEEVKKFL 237

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

Iteration: 1
 Score = 93.6 bits (231), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 56/157 (35%), Positives = 88/157 (56%), Gaps = 4/157 (2%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADAR LV  AR  A + +  YG  + ++ L K +AD+ Q YTQ+  +RP GV  +   
Sbjct: 81  LVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGVSLIFAG 140
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ID + GPRLF CDPAG    +KAT+ G  +   ++FLE++ K +     +E V   I  L
Sbjct: 141 ID-QIGPRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKEN--LPEKEAVTLGIKAL 197
Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 157
           +S L+E  +    E+  ++  N ++R+   EE+ + L
Sbjct: 198 KSSLEEGEELKAPEIASITVGN-KYRIYDQEEVKKFL 233

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

Iteration: 1
 Score = 93.2 bits (230), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 56/157 (35%), Positives = 88/157 (56%), Gaps = 4/157 (2%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADAR LV  AR  A + +  YG  + ++ L K +AD+ Q YTQ+  +RP GV  +   
Sbjct: 81  LVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGVSLIFAG 140
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ID + GPRLF CDPAG    +KAT+ G  +   ++FLE++ K +     +E V   I  L
Sbjct: 141 ID-QIGPRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKEN--LPEKEAVTLGIKAL 197
Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 157
           +S L+E  +    E+  ++  N ++R+   EE+ + L
Sbjct: 198 KSSLEEGEELKAPEIASITVGN-KYRIYDQEEVKKFL 233

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

Iteration: 1
 Score = 91.7 bits (226), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 52/163 (31%), Positives = 87/163 (53%), Gaps = 4/163 (2%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADAR L+ +AR EA   R  Y   + V  LAK I D  Q YTQ+  +RP GV  ++  
Sbjct: 72  LVADARVLIDRARIEAQINRLTYDEPITVKELAKKICDFKQQYTQYGGVRPFGVSLLIAG 131
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           +DE   P+L++ DP+G    +KAT+ G+       F EK+ ++D   +F + +   +  +
Sbjct: 132 VDEV--PKLYETDPSGALLEYKATAIGMGRNAVTEFFEKEYRDD--LSFDDAMVLGLVAM 187
Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 163
              ++ +     IEVG V  ++  F+ +S EE+  ++   +ER
Sbjct: 188 GLSIESELVPENIEVGYVKVDDRTFKEVSPEELKPYVERANER 230

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

Iteration: 1
 Score = 90.1 bits (222), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 51/163 (31%), Positives = 87/163 (53%), Gaps = 4/163 (2%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADAR L+ +AR EA   R  Y   + V  LAK I D  Q YTQ+  +RP GV  ++  
Sbjct: 81  LVADARVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQYGGVRPFGVSLLIAG 140
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ++E   P+L++ DP+G    +KAT+ G+       F EK+ ++D   +F + +   +  +
Sbjct: 141 VNEV--PKLYETDPSGALLEYKATAIGMGRMAVTEFFEKEYRDD--LSFDDAMVLGLVAM 196
Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 163
              ++ +     IEVG V  ++  F+ +S EE+  ++   +ER
Sbjct: 197 GLSIESELVPENIEVGYVKVDDRTFKEVSPEELKPYVERANER 239

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

Iteration: 1
 Score = 89.4 bits (220), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 50/157 (31%), Positives = 85/157 (54%), Gaps = 3/157 (1%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADAR ++ +AR E    R      + V+ + ++IA   Q YTQ    RP G+ A+++ 
Sbjct: 76  LTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGISALIVG 135
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D +  PRL++ DP+G +   KA + G   +    FLEK   +D   T   T++  I  L
Sbjct: 136 FDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDDAIETDDLTIKLVIKAL 195
Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 157
             V+Q   K   IE+ V+ ++ P  ++L+ EEI++++
Sbjct: 196 LEVVQSGGK--NIELAVMRRDQP-LKILNPEEIEKYV 229

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

Iteration: 1
 Score = 89.4 bits (220), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 50/157 (31%), Positives = 85/157 (54%), Gaps = 3/157 (1%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADAR ++ +AR E    R      + V+ + ++IA   Q YTQ    RP G+ A+++ 
Sbjct: 76  LTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGISALIVG 135
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D +  PRL++ DP+G +   KA + G   +    FLEK   +D   T   T++  I  L
Sbjct: 136 FDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDDAIETDDLTIKLVIKAL 195
Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 157
             V+Q   K   IE+ V+ ++ P  ++L+ EEI++++
Sbjct: 196 LEVVQSGGK--NIELAVMRRDQP-LKILNPEEIEKYV 229

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

Iteration: 1
 Score = 85.5 bits (210), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 53/161 (32%), Positives = 81/161 (50%), Gaps = 5/161 (3%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           M  D R LV +AR  A ++   Y   +P   L + +A   Q YTQ   +RP GV  ++  
Sbjct: 78  MGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGVSLLICG 137
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            + E  P LF+ DP+G +F  KAT+ G        FLEK+   D     ++ + TAI TL
Sbjct: 138 WN-EGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNED--LELEDAIHTAILTL 194
Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAIS 161
           +   +       IEVG+ ++    FR L+  E+ ++L AI+
Sbjct: 195 KESFEGQMTEDNIEVGICNEAG--FRRLTPTEVKDYLAAIA 233

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

Iteration: 1
 Score = 85.1 bits (209), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 53/161 (32%), Positives = 81/161 (50%), Gaps = 5/161 (3%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           M  D R LV +AR  A ++   Y   +P   L + +A   Q YTQ   +RP GV  ++  
Sbjct: 79  MGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGVSLLICG 138
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            + E  P LF+ DP+G +F  KAT+ G        FLEK+   D     ++ + TAI TL
Sbjct: 139 WN-EGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNED--LELEDAIHTAILTL 195
Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAIS 161
           +   +       IEVG+ ++    FR L+  E+ ++L AI+
Sbjct: 196 KESFEGQMTEDNIEVGICNEAG--FRRLTPTEVRDYLAAIA 234

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

Iteration: 1
 Score = 84.3 bits (207), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 47/157 (29%), Positives = 82/157 (52%), Gaps = 3/157 (1%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADAR ++ +AR E    R      + V+ + ++IA   Q YTQ    RP G+ A+++ 
Sbjct: 76  LTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGISALIVG 135
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D +  PRL++ DP+G +   KA + G   +    FLEK   ++   T   T++  I  L
Sbjct: 136 FDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEAIETDDLTIKLVIKAL 195
Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 157
             V+Q   K  E+    V + +   ++L+ EEI++++
Sbjct: 196 LEVVQSGGKNIEL---AVMRRDQSLKILNPEEIEKYV 229

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

Iteration: 1
 Score = 84.0 bits (206), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 49/165 (29%), Positives = 81/165 (49%), Gaps = 4/165 (2%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADAR L    R E  + RF +   +PV  L   I  K+Q+ TQ    RP GV  ++  
Sbjct: 77  LTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAG 136
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D + GP +F+  P+ ++F  +A S G + Q A  +LE+ M         E V+  +  L
Sbjct: 137 YD-DMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFMECNLNELVKHGLRAL 195
Query: 121 QSVL--QEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 163
           +  L  ++D     + +G+V K+  EF +   +++   L  + ER
Sbjct: 196 RETLPAEQDLTTKNVSIGIVGKDL-EFTIYDDDDVSPFLEGLEER 239

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

Iteration: 1
 Score = 84.0 bits (206), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 49/165 (29%), Positives = 81/165 (49%), Gaps = 4/165 (2%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADAR L    R E  + RF +   +PV  L   I  K+Q+ TQ    RP GV  ++  
Sbjct: 77  LTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAG 136
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D + GP +F+  P+ ++F  +A S G + Q A  +LE+ M         E V+  +  L
Sbjct: 137 YD-DMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFMECNLDELVKHGLRAL 195
Query: 121 QSVL--QEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 163
           +  L  ++D     + +G+V K+  EF +   +++   L  + ER
Sbjct: 196 RETLPAEQDLTTKNVSIGIVGKDL-EFTIYDDDDVSPFLDGLEER 239

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

Iteration: 1
 Score = 81.6 bits (200), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 51/164 (31%), Positives = 88/164 (53%), Gaps = 5/164 (3%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + AD+R L+++AR EA   R      + V+ L +++A   Q YTQ   +RP GV  ++  
Sbjct: 62  LNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLIAG 121
Query: 61  ID-EECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKM-KNDPAFTFQETVQTAIS 118
            D  +  P+L++ +P+G +    A + G   +    FLEK   + +P  T +E V+  + 
Sbjct: 122 FDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKEPPATVEECVKLTVR 181
Query: 119 TLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISE 162
           +L  V+Q    A  IE+ VV K + +   LS EEI++++T I +
Sbjct: 182 SLLEVVQTG--AKNIEITVV-KPDSDIVALSSEEINQYVTQIEQ 222

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

Iteration: 1
 Score = 81.6 bits (200), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 51/164 (31%), Positives = 88/164 (53%), Gaps = 5/164 (3%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + AD+R L+++AR EA   R      + V+ L +++A   Q YTQ   +RP GV  ++  
Sbjct: 76  LNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLIAG 135
Query: 61  ID-EECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKM-KNDPAFTFQETVQTAIS 118
            D  +  P+L++ +P+G +    A + G   +    FLEK   + +P  T +E V+  + 
Sbjct: 136 FDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKEPPATVEECVKLTVR 195
Query: 119 TLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISE 162
           +L  V+Q    A  IE+ VV K + +   LS EEI++++T I +
Sbjct: 196 SLLEVVQTG--AKNIEITVV-KPDSDIVALSSEEINQYVTQIEQ 236

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

Iteration: 1
 Score = 81.6 bits (200), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 51/164 (31%), Positives = 88/164 (53%), Gaps = 5/164 (3%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + AD+R L+++AR EA   R      + V+ L +++A   Q YTQ   +RP GV  ++  
Sbjct: 78  LNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLIAG 137
Query: 61  ID-EECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKM-KNDPAFTFQETVQTAIS 118
            D  +  P+L++ +P+G +    A + G   +    FLEK   + +P  T +E V+  + 
Sbjct: 138 FDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKEPPATVEECVKLTVR 197
Query: 119 TLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISE 162
           +L  V+Q    A  IE+ VV K + +   LS EEI++++T I +
Sbjct: 198 SLLEVVQTG--AKNIEITVV-KPDSDIVALSSEEINQYVTQIEQ 238

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

Iteration: 1
 Score = 81.6 bits (200), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 52/175 (29%), Positives = 86/175 (49%), Gaps = 17/175 (9%)
Query: 1   MTADARTLVQQARYEA-AEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVL 59
           M  D R LV ++R  A   ++  YG   P  +L   +A   Q  TQ   +RP GV  ++ 
Sbjct: 59  MGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIA 118
Query: 60  SIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAIST 119
             DE  G  L++ DP+G +F  KAT+ G     A  FLEK+  ++     ++ +  A+ T
Sbjct: 119 GHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWNDE--LELEDAIHIALLT 176
Query: 120 LQSVLQEDFKASEIEVGVVSKENPE--------------FRVLSIEEIDEHLTAI 160
           L+  ++ +F    IE+ ++  ENP+              FR L+ +EI++ L A+
Sbjct: 177 LKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTSQEINDRLEAL 231

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

Iteration: 1
 Score = 81.6 bits (200), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 52/175 (29%), Positives = 86/175 (49%), Gaps = 17/175 (9%)
Query: 1   MTADARTLVQQARYEA-AEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVL 59
           M  D R LV ++R  A   ++  YG   P  +L   +A   Q  TQ   +RP GV  ++ 
Sbjct: 78  MGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIA 137
Query: 60  SIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAIST 119
             DE  G  L++ DP+G +F  KAT+ G     A  FLEK+  ++     ++ +  A+ T
Sbjct: 138 GHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWNDE--LELEDAIHIALLT 195
Query: 120 LQSVLQEDFKASEIEVGVVSKENPE--------------FRVLSIEEIDEHLTAI 160
           L+  ++ +F    IE+ ++  ENP+              FR L+ +EI++ L A+
Sbjct: 196 LKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTSQEINDRLEAL 250

>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 = 81.3 bits (199), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 51/162 (31%), Positives = 87/162 (53%), Gaps = 5/162 (3%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + AD+R L+++AR EA   R      + V+ L +++A   Q YTQ   +RP GV  ++  
Sbjct: 78  LNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLIAG 137
Query: 61  ID-EECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKM-KNDPAFTFQETVQTAIS 118
            D  +  P+L++ +P+G +    A + G   +    FLEK   + +P  T +E V+  + 
Sbjct: 138 FDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKEPPATVEECVKLTVR 197
Query: 119 TLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAI 160
           +L  V+Q    A  IE+ VV K + +   LS EEI++++T I
Sbjct: 198 SLLEVVQTG--AKNIEITVV-KPDSDIVALSSEEINQYVTQI 236

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

Iteration: 1
 Score = 78.6 bits (192), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 39/120 (32%), Positives = 64/120 (53%), Gaps = 2/120 (1%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADA  L+  AR  A  +   Y  ++PV++L + ++D  Q YTQH  +RP GV  +   
Sbjct: 67  LTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAG 126
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D+  G +L+  +P+G++ G KA S G     A   L+   K+D      + ++ A+ TL
Sbjct: 127 YDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKDD--MKVDDAIELALKTL 184

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

Iteration: 1
 Score = 78.2 bits (191), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 39/120 (32%), Positives = 64/120 (53%), Gaps = 2/120 (1%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADA  L+  AR  A  +   Y  ++PV++L + ++D  Q YTQH  +RP GV  +   
Sbjct: 80  LTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAG 139
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D+  G +L+  +P+G++ G KA S G     A   L+   K+D      + ++ A+ TL
Sbjct: 140 YDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKDD--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 = 78.2 bits (191), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 39/120 (32%), Positives = 64/120 (53%), Gaps = 2/120 (1%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADA  L+  AR  A  +   Y  ++PV++L + ++D  Q YTQH  +RP GV  +   
Sbjct: 79  LTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAG 138
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D+  G +L+  +P+G++ G KA S G     A   L+   K+D      + ++ A+ TL
Sbjct: 139 YDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKDD--MKVDDAIELALKTL 196

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

Iteration: 1
 Score = 78.2 bits (191), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 39/120 (32%), Positives = 64/120 (53%), Gaps = 2/120 (1%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADA  L+  AR  A  +   Y  ++PV++L + ++D  Q YTQH  +RP GV  +   
Sbjct: 70  LTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAG 129
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D+  G +L+  +P+G++ G KA S G     A   L+   K+D      + ++ A+ TL
Sbjct: 130 YDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKDD--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 = 78.2 bits (191), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 39/120 (32%), Positives = 64/120 (53%), Gaps = 2/120 (1%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADA  L+  AR  A  +   Y  ++PV++L + ++D  Q YTQH  +RP GV  +   
Sbjct: 80  LTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAG 139
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D+  G +L+  +P+G++ G KA S G     A   L+   K+D      + ++ A+ TL
Sbjct: 140 YDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKDD--MKVDDAIELALKTL 197

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

Iteration: 1
 Score = 76.3 bits (186), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 44/158 (27%), Positives = 80/158 (50%), Gaps = 4/158 (2%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +T+DA  L  + R  A  +  +Y   +P + L   + D  Q YTQ    RP GV  + + 
Sbjct: 79  ITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIG 138
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D+  G +L++ DP+G++ G KAT  G     A++ L++  K +   T +  +  AI  L
Sbjct: 139 WDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK-EGEMTLKSALALAIKVL 197
Query: 121 QSVLQ-EDFKASEIEVGVVSKENPE--FRVLSIEEIDE 155
              +      A ++E+  +++EN +   RVL  +E+++
Sbjct: 198 NKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQ 235

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

Iteration: 1
 Score = 73.6 bits (179), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 42/158 (26%), Positives = 80/158 (50%), Gaps = 4/158 (2%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +T+DA  L  + R  A  +  +Y   +P + L   + D  Q YTQ    RP GV  + + 
Sbjct: 79  ITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIG 138
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D+  G +L++ DP+G++ G KAT  G     A++ L++  K +   T +  +  A+  L
Sbjct: 139 WDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK-EGEMTLKSALALAVKVL 197
Query: 121 QSVLQ-EDFKASEIEVGVVSKENPE--FRVLSIEEIDE 155
              +      A ++E+  +++E+ +   RVL  +E+++
Sbjct: 198 NKTMDVSKLSAEKVEIATLTRESGKTVIRVLKQKEVEQ 235

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 44/160 (27%), Positives = 84/160 (52%), Gaps = 9/160 (5%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH-----AYMRPLGVV 55
           + ADA+TL+ +AR E     F Y   M V+ + + +++ +  + +      A  RP GV 
Sbjct: 81  LIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMSRPFGVA 140
Query: 56  AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQT 115
            +   +DE+ GP+LF  DP+G F    A + G   + A + L++      + T +E +++
Sbjct: 141 LLFGGVDEK-GPQLFHMDPSGTFVQCDARAIGSASEGAQSSLQEVYHK--SMTLKEAIKS 197
Query: 116 AISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 155
           ++  L+ V++E   A+ IE+  V +    F + + EE++E
Sbjct: 198 SLIILKQVMEEKLNATNIELATV-QPGQNFHMFTKEELEE 236

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

Iteration: 1
 Score = 67.8 bits (164), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 44/160 (27%), Positives = 84/160 (52%), Gaps = 9/160 (5%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH-----AYMRPLGVV 55
           + ADA+TL+ +AR E     F Y   M V+ + + +++ +  + +      A  RP GV 
Sbjct: 81  LIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMSRPFGVA 140
Query: 56  AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQT 115
            +   +DE+ GP+LF  DP+G F    A + G   + A + L++      + T +E +++
Sbjct: 141 LLFGGVDEK-GPQLFHMDPSGTFVQCDARAIGSASEGAQSSLQELYHK--SMTLKEAIKS 197
Query: 116 AISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE 155
           ++  L+ V++E   A+ IE+  V +    F + + EE++E
Sbjct: 198 SLIILKQVMEEKLNATNIELATV-QPGQNFHMFTKEELEE 236

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

Iteration: 1
 Score = 65.5 bits (158), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 35/99 (35%), Positives = 53/99 (53%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADAR+L   AR EA+ FR  +GY +P+  LA  +A     YT ++ +RP G   M+ S
Sbjct: 81  LLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGCSFMLGS 140
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEK 99
                G +L+  DP+G  +G+   + G   Q A   +EK
Sbjct: 141 YSANDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEK 179

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

Iteration: 1
 Score = 65.1 bits (157), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 35/99 (35%), Positives = 53/99 (53%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADAR+L   AR EA+ FR  +GY +P+  LA  +A     YT ++ +RP G   M+ S
Sbjct: 80  LLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGCSFMLGS 139
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEK 99
                G +L+  DP+G  +G+   + G   Q A   +EK
Sbjct: 140 YSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEK 178

>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 = 63.2 bits (152), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 39/136 (28%), Positives = 67/136 (49%), Gaps = 3/136 (2%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +  D R LV + R EAA F+  Y   +P+   A  +    Q +T +  +RP GV  +   
Sbjct: 81  LIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGG 140
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDP-AFTFQETVQTAIST 119
           +D+  G  L+  +P+G ++G+K  + G   Q A   LEK + + P   + +E V+ A   
Sbjct: 141 VDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKI 199
Query: 120 LQSVLQEDFKASEIEV 135
           +  +  ED K  + E+
Sbjct: 200 IY-LAHEDNKEKDFEL 214

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

Iteration: 1
 Score = 63.2 bits (152), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 39/136 (28%), Positives = 67/136 (49%), Gaps = 3/136 (2%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +  D R LV + R EAA F+  Y   +P+   A  +    Q +T +  +RP GV  +   
Sbjct: 81  LIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGG 140
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDP-AFTFQETVQTAIST 119
           +D+  G  L+  +P+G ++G+K  + G   Q A   LEK + + P   + +E V+ A   
Sbjct: 141 VDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKI 199
Query: 120 LQSVLQEDFKASEIEV 135
           +  +  ED K  + E+
Sbjct: 200 IY-LAHEDNKEKDFEL 214

>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 = 63.2 bits (152), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 39/136 (28%), Positives = 67/136 (49%), Gaps = 3/136 (2%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +  D R LV + R EAA F+  Y   +P+   A  +    Q +T +  +RP GV  +   
Sbjct: 80  LIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGG 139
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDP-AFTFQETVQTAIST 119
           +D+  G  L+  +P+G ++G+K  + G   Q A   LEK + + P   + +E V+ A   
Sbjct: 140 VDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKI 198
Query: 120 LQSVLQEDFKASEIEV 135
           +  +  ED K  + E+
Sbjct: 199 IY-LAHEDNKEKDFEL 213

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

Iteration: 1
 Score = 63.2 bits (152), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 39/136 (28%), Positives = 67/136 (49%), Gaps = 3/136 (2%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +  D R LV + R EAA F+  Y   +P+   A  +    Q +T +  +RP GV  +   
Sbjct: 75  LIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGG 134
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDP-AFTFQETVQTAIST 119
           +D+  G  L+  +P+G ++G+K  + G   Q A   LEK + + P   + +E V+ A   
Sbjct: 135 VDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKI 193
Query: 120 LQSVLQEDFKASEIEV 135
           +  +  ED K  + E+
Sbjct: 194 IY-LAHEDNKEKDFEL 208

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

Iteration: 1
 Score = 63.2 bits (152), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 39/136 (28%), Positives = 67/136 (49%), Gaps = 3/136 (2%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +  D R LV + R EAA F+  Y   +P+   A  +    Q +T +  +RP GV  +   
Sbjct: 77  LIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGG 136
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDP-AFTFQETVQTAIST 119
           +D+  G  L+  +P+G ++G+K  + G   Q A   LEK + + P   + +E V+ A   
Sbjct: 137 VDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKI 195
Query: 120 LQSVLQEDFKASEIEV 135
           +  +  ED K  + E+
Sbjct: 196 IY-LAHEDNKEKDFEL 210

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

Iteration: 1
 Score = 57.8 bits (138), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 38/166 (22%), Positives = 83/166 (50%), Gaps = 10/166 (6%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADAR++++ AR  A      Y  ++ V+ L + + D   +    A  RP GV  ++  
Sbjct: 81  LTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCD---LAAAAAMSRPFGVALLIAG 137
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKND--PAFTFQETVQTAIS 118
            D + G +LF  +P+G F+ + A + G   + A    + ++ N+   + T +E     + 
Sbjct: 138 HDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGA----QAELLNEWHSSLTLKEAELLVLK 193
Query: 119 TLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
            L+ V++E    +  ++  ++K++  F++   E+  E +  + E++
Sbjct: 194 ILKQVMEEKLDENNAQLSCITKQDG-FKIYDNEKTAELIKELKEKE 238

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 38/172 (22%), Positives = 85/172 (49%), Gaps = 13/172 (7%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHA------YMRPLGV 54
           +TADAR++++ AR  A      Y  ++ V+ L + + D +  + + A        RP GV
Sbjct: 81  LTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLMSRPFGV 140
Query: 55  VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKND--PAFTFQET 112
             ++   D + G +LF  +P+G F+ + A + G   + A    + ++ N+   + T +E 
Sbjct: 141 ALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGA----QAELLNEWHSSLTLKEA 196
Query: 113 VQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
               +  L+ V++E    +  ++  ++K++  F++   E+  E +  + E++
Sbjct: 197 ELLVLKILKQVMEEKLDENNAQLSCITKQDG-FKIYDNEKTAELIKELKEKE 247

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 38/172 (22%), Positives = 85/172 (49%), Gaps = 13/172 (7%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHA------YMRPLGV 54
           +TADAR++++ AR  A      Y  ++ V+ L + + D +  + + A        RP GV
Sbjct: 73  LTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLMSRPFGV 132
Query: 55  VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKND--PAFTFQET 112
             ++   D + G +LF  +P+G F+ + A + G   + A    + ++ N+   + T +E 
Sbjct: 133 ALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGA----QAELLNEWHSSLTLKEA 188
Query: 113 VQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
               +  L+ V++E    +  ++  ++K++  F++   E+  E +  + E++
Sbjct: 189 ELLVLKILKQVMEEKLDENNAQLSCITKQDG-FKIYDNEKTAELIKELKEKE 239

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 38/172 (22%), Positives = 85/172 (49%), Gaps = 13/172 (7%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHA------YMRPLGV 54
           +TADAR++++ AR  A      Y  ++ V+ L + + D +  + + A        RP GV
Sbjct: 83  LTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLMSRPFGV 142
Query: 55  VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKND--PAFTFQET 112
             ++   D + G +LF  +P+G F+ + A + G   + A    + ++ N+   + T +E 
Sbjct: 143 ALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGA----QAELLNEWHSSLTLKEA 198
Query: 113 VQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
               +  L+ V++E    +  ++  ++K++  F++   E+  E +  + E++
Sbjct: 199 ELLVLKILKQVMEEKLDENNAQLSCITKQDG-FKIYDNEKTAELIKELKEKE 249

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 38/172 (22%), Positives = 85/172 (49%), Gaps = 13/172 (7%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHA------YMRPLGV 54
           +TADAR++++ AR  A      Y  ++ V+ L + + D +  + + A        RP GV
Sbjct: 82  LTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLMSRPFGV 141
Query: 55  VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKND--PAFTFQET 112
             ++   D + G +LF  +P+G F+ + A + G   + A    + ++ N+   + T +E 
Sbjct: 142 ALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGA----QAELLNEWHSSLTLKEA 197
Query: 113 VQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
               +  L+ V++E    +  ++  ++K++  F++   E+  E +  + E++
Sbjct: 198 ELLVLKILKQVMEEKLDENNAQLSCITKQDG-FKIYDNEKTAELIKELKEKE 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 = 56.6 bits (135), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 38/172 (22%), Positives = 85/172 (49%), Gaps = 13/172 (7%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHA------YMRPLGV 54
           +TADAR++++ AR  A      Y  ++ V+ L + + D +  + + A        RP GV
Sbjct: 81  LTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLMSRPFGV 140
Query: 55  VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKND--PAFTFQET 112
             ++   D + G +LF  +P+G F+ + A + G   + A    + ++ N+   + T +E 
Sbjct: 141 ALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGA----QAELLNEWHSSLTLKEA 196
Query: 113 VQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
               +  L+ V++E    +  ++  ++K++  F++   E+  E +  + E++
Sbjct: 197 ELLVLKILKQVMEEKLDENNAQLSCITKQDG-FKIYDNEKTAELIKELKEKE 247

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 41/163 (25%), Positives = 74/163 (45%), Gaps = 11/163 (6%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +  DAR L    R +       +  ++ V+     + DK+Q  TQ A  RP GV  +++ 
Sbjct: 76  LAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSAGGRPYGVGLLIIG 135
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEK------KMKNDPAFTFQETVQ 114
            D+  G  L +  P+G+      T+ G + Q A  +LE+      K+  +P    +  V+
Sbjct: 136 YDKS-GAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVE 194
Query: 115 TAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 157
            AIS  QS+  E      + + +V K+ P F +   E + +++
Sbjct: 195 -AIS--QSLRDESLTVDNLSIAIVGKDTP-FTIYDGEAVAKYI 233

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 41/163 (25%), Positives = 74/163 (45%), Gaps = 11/163 (6%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +  DAR L    R +       +  ++ V+     + DK+Q  TQ A  RP GV  +++ 
Sbjct: 77  LAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSAGGRPYGVGLLIIG 136
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEK------KMKNDPAFTFQETVQ 114
            D+  G  L +  P+G+      T+ G + Q A  +LE+      K+  +P    +  V+
Sbjct: 137 YDKS-GAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVE 195
Query: 115 TAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 157
            AIS  QS+  E      + + +V K+ P F +   E + +++
Sbjct: 196 -AIS--QSLRDESLTVDNLSIAIVGKDTP-FTIYDGEAVAKYI 234

>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 = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 40/163 (24%), Positives = 73/163 (44%), Gaps = 11/163 (6%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +  DAR L    R +       +  ++ V+     + DK+Q  TQ    RP GV  +++ 
Sbjct: 77  LAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRPYGVGLLIIG 136
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEK------KMKNDPAFTFQETVQ 114
            D+  G  L +  P+G+      T+ G + Q A  +LE+      K+  +P    +  V+
Sbjct: 137 YDKS-GAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVE 195
Query: 115 TAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 157
            AIS  QS+  E      + + +V K+ P F +   E + +++
Sbjct: 196 -AIS--QSLRDESLTVDNLSIAIVGKDTP-FTIYDGEAVAKYI 234

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 40/163 (24%), Positives = 73/163 (44%), Gaps = 11/163 (6%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +  DAR L    R +       +  ++ V+     + DK+Q  TQ    RP GV  +++ 
Sbjct: 78  LAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRPYGVGLLIIG 137
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEK------KMKNDPAFTFQETVQ 114
            D+  G  L +  P+G+      T+ G + Q A  +LE+      K+  +P    +  V+
Sbjct: 138 YDKS-GAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVE 196
Query: 115 TAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 157
            AIS  QS+  E      + + +V K+ P F +   E + +++
Sbjct: 197 -AIS--QSLRDESLTVDNLSIAIVGKDTP-FTIYDGEAVAKYI 235

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 40/163 (24%), Positives = 73/163 (44%), Gaps = 11/163 (6%)
Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +  DAR L    R +       +  ++ V+     + DK+Q  TQ    RP GV  +++ 
Sbjct: 76  LAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRPYGVGLLIIG 135
Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEK------KMKNDPAFTFQETVQ 114
            D+  G  L +  P+G+      T+ G + Q A  +LE+      K+  +P    +  V+
Sbjct: 136 YDKS-GAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVE 194
Query: 115 TAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 157
            AIS  QS+  E      + + +V K+ P F +   E + +++
Sbjct: 195 -AIS--QSLRDESLTVDNLSIAIVGKDTP-FTIYDGEAVAKYI 233

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	164
1iru_A	246	20S proteasome; cell cycle, immune response, prote	7e-81
1ryp_A	243	20S proteasome; multicatalytic proteinase, protein	2e-76
1j2p_A	246	Alpha-ring, proteasome alpha subunit; hydrolase; 2	5e-73
1iru_D	248	20S proteasome; cell cycle, immune response, prote	1e-72
1yar_A	233	Proteasome alpha subunit; proteasome 20S, PA26 pro	6e-72
1ryp_E	242	20S proteasome; multicatalytic proteinase, protein	2e-71
1ryp_B	250	20S proteasome; multicatalytic proteinase, protein	3e-71
1iru_B	233	20S proteasome; cell cycle, immune response, prote	3e-71
1ryp_C	244	20S proteasome; multicatalytic proteinase, protein	9e-71
1ryp_F	233	20S proteasome; multicatalytic proteinase, protein	2e-70
3h4p_A	264	Proteasome subunit alpha; core particle, cytoplasm	3e-70
1iru_F	263	20S proteasome; cell cycle, immune response, prote	3e-70
1iru_C	261	20S proteasome; cell cycle, immune response, prote	3e-70
1ryp_D	241	20S proteasome; multicatalytic proteinase, protein	3e-70
1iru_E	241	20S proteasome; cell cycle, immune response, prote	2e-69
1iru_G	254	20S proteasome; cell cycle, immune response, prote	1e-66
3nzj_F	288	Proteasome component C1; ubiquitin, protein degrad	6e-61
1ryp_G	244	20S proteasome; multicatalytic proteinase, protein	1e-60
1q5q_A	259	Proteasome alpha-type subunit 1; proteasome assemb	2e-24
3mi0_A	248	Proteasome subunit alpha; enzyme inhibitors, lacto	2e-21
3unf_H	234	Proteasome subunit beta type-10; antigen presentat	8e-18
1yar_H	217	Proteasome beta subunit; proteasome 20S, PA26 prot	2e-17
3nzj_H	261	Proteasome component PUP1; ubiquitin, protein degr	4e-16
1ryp_I	222	20S proteasome; multicatalytic proteinase, protein	8e-16
1iru_I	234	20S proteasome; cell cycle, immune response, prote	4e-14
1ryp_L	212	20S proteasome; multicatalytic proteinase, protein	3e-12
3nzj_K	287	Proteasome component PRE2; ubiquitin, protein degr	5e-12
1q5q_H	235	Proteasome beta-type subunit 1; proteasome assembl	2e-11
1iru_L	204	20S proteasome; cell cycle, immune response, prote	5e-10
1iru_L	204	20S proteasome; cell cycle, immune response, prote	7e-10
1j2q_H	202	Proteasome beta subunit; ubiquitin, CP, hydrolase;	2e-09
1iru_H	205	20S proteasome; cell cycle, immune response, prote	2e-09
1iru_K	201	20S proteasome; cell cycle, immune response, prote	3e-08
3unf_N	199	Proteasome subunit beta type-9; antigen presentati	3e-08
1ryp_K	198	20S proteasome; multicatalytic proteinase, protein	7e-08
1ryp_M	222	20S proteasome; multicatalytic proteinase, protein	1e-06
1iru_M	213	20S proteasome; cell cycle, immune response, prote	2e-06
1iru_N	219	20S proteasome; cell cycle, immune response, prote	3e-06
1iru_J	205	20S proteasome; cell cycle, immune response, prote	1e-05
1ryp_H	205	20S proteasome; multicatalytic proteinase, protein	2e-05
1ryp_J	204	20S proteasome; multicatalytic proteinase, protein	3e-05

>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 =  238 bits (610), Expect = 7e-81
 Identities = 100/164 (60%), Positives = 135/164 (82%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           MTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD SQVYTQ+A MRPLG   +++ 
Sbjct: 83  MTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIG 142

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +FLEKK+K    +TF++TV+TAI+ L
Sbjct: 143 IDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCL 202

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
            +VL  DFK SEIEVGVV+ ENP+FR+L+  EID HL A++ERD
Sbjct: 203 STVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVALAERD 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 =  227 bits (580), Expect = 2e-76
 Identities = 78/169 (46%), Positives = 112/169 (66%), Gaps = 7/169 (4%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
              DAR    +A+ EAAEFR+KYGY+MP DVLAK +A+ SQ+YTQ AYMRPLGV+   +S
Sbjct: 77  PIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQRAYMRPLGVILTFVS 136

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAF-----TFQETVQT 115
           +DEE GP ++K DPAG++ G+KAT+ G K+QE    LE   K          ++++ V+ 
Sbjct: 137 VDEELGPSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKKSKIDHINEESWEKVVEF 196

Query: 116 AISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
           AI+ +   L  +F  +++EVGV +K+  +F  LS E I+E L AI+E+D
Sbjct: 197 AITHMIDALGTEFSKNDLEVGVATKD--KFFTLSAENIEERLVAIAEQD 243

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

 Score =  218 bits (557), Expect = 5e-73
 Identities = 51/163 (31%), Positives = 87/163 (53%), Gaps = 4/163 (2%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADAR L+ +AR EA   R  Y   + V  LAK I D  Q YTQ+  +RP GV  ++  
Sbjct: 81  LVADARVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQYGGVRPFGVSLLIAG 140

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ++E   P+L++ DP+G    +KAT+ G+       F EK+ ++D   +F + +   +  +
Sbjct: 141 VNE--VPKLYETDPSGALLEYKATAIGMGRMAVTEFFEKEYRDD--LSFDDAMVLGLVAM 196

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 163
              ++ +     IEVG V  ++  F+ +S EE+  ++   +ER
Sbjct: 197 GLSIESELVPENIEVGYVKVDDRTFKEVSPEELKPYVERANER 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 =  217 bits (555), Expect = 1e-72
 Identities = 49/164 (29%), Positives = 86/164 (52%), Gaps = 3/164 (1%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADAR ++ +AR E    R      + V+ + ++IA   Q YTQ    RP G+ A+++ 
Sbjct: 76  LTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGISALIVG 135

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D +  PRL++ DP+G +   KA + G   +    FLEK   ++   T   T++  I  L
Sbjct: 136 FDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEAIETDDLTIKLVIKAL 195

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
             V+Q   K   IE+ V+ ++    ++L+ EEI++++  I +  
Sbjct: 196 LEVVQSGGK--NIELAVMRRDQS-LKILNPEEIEKYVAEIEKEK 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 =  215 bits (549), Expect = 6e-72
 Identities = 56/157 (35%), Positives = 87/157 (55%), Gaps = 4/157 (2%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADAR LV  AR  A + +  YG  + ++ L K +AD+ Q YTQ+  +RP GV  +   
Sbjct: 81  LVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGVSLIFAG 140

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ID+  GPRLF CDPAG    +KAT+ G  +   ++FLE++ K +     +E V   I  L
Sbjct: 141 IDQI-GPRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKEN--LPEKEAVTLGIKAL 197

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 157
           +S L+E  +    E+  ++  N  +R+   EE+ + L
Sbjct: 198 KSSLEEGEELKAPEIASITVGNK-YRIYDQEEVKKFL 233

>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 =  214 bits (546), Expect = 2e-71
 Identities = 38/170 (22%), Positives = 82/170 (48%), Gaps = 9/170 (5%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHA------YMRPLGV 54
           +TADAR++++ AR  A      Y  ++ V+ L + + D +  + + A        RP GV
Sbjct: 73  LTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLMSRPFGV 132

Query: 55  VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQ 114
             ++   D + G +LF  +P+G F+ + A + G   + A   L  +  +    T +E   
Sbjct: 133 ALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNEWHSS--LTLKEAEL 190

Query: 115 TAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
             +  L+ V++E    +  ++  ++K++  F++   E+  E +  + E++
Sbjct: 191 LVLKILKQVMEEKLDENNAQLSCITKQDG-FKIYDNEKTAELIKELKEKE 239

>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 =  214 bits (546), Expect = 3e-71
 Identities = 52/175 (29%), Positives = 85/175 (48%), Gaps = 17/175 (9%)

Query: 1   MTADARTLVQQARYEA-AEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVL 59
           M  D R LV ++R  A   ++  YG   P  +L   +A   Q  TQ   +RP GV  ++ 
Sbjct: 78  MGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIA 137

Query: 60  SIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAIST 119
             DE  G  L++ DP+G +F  KAT+ G     A  FLEK+  ++     ++ +  A+ T
Sbjct: 138 GHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWNDE--LELEDAIHIALLT 195

Query: 120 LQSVLQEDFKASEIEVGVVSKENP--------------EFRVLSIEEIDEHLTAI 160
           L+  ++ +F    IE+ ++  ENP               FR L+ +EI++ L A+
Sbjct: 196 LKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTSQEINDRLEAL 250

>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 =  213 bits (544), Expect = 3e-71
 Identities = 53/161 (32%), Positives = 81/161 (50%), Gaps = 5/161 (3%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           M  D R LV +AR  A ++   Y   +P   L + +A   Q YTQ   +RP GV  ++  
Sbjct: 78  MGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGVSLLICG 137

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            +E   P LF+ DP+G +F  KAT+ G        FLEK+   D     ++ + TAI TL
Sbjct: 138 WNEG-RPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNED--LELEDAIHTAILTL 194

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAIS 161
           +   +       IEVG+ ++    FR L+  E+ ++L AI+
Sbjct: 195 KESFEGQMTEDNIEVGICNEAG--FRRLTPTEVKDYLAAIA 233

>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 =  212 bits (542), Expect = 9e-71
 Identities = 44/163 (26%), Positives = 75/163 (46%), Gaps = 7/163 (4%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADA  L+  AR  A  +   Y  ++PV++L + ++D  Q YTQH  +RP GV  +   
Sbjct: 79  LTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAG 138

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D+  G +L+  +P+G++ G KA S G     A   L+   K+D      + ++ A+ TL
Sbjct: 139 YDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKDD--MKVDDAIELALKTL 196

Query: 121 QSVLQE-DFKASEIEVGVVSKE----NPEFRVLSIEEIDEHLT 158
                        +E   + K         ++   +EI + L 
Sbjct: 197 SKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILV 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 =  211 bits (539), Expect = 2e-70
 Identities = 33/160 (20%), Positives = 68/160 (42%), Gaps = 5/160 (3%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +  DAR L    R +       +  ++ V+     + DK+Q  TQ    RP GV  +++ 
Sbjct: 76  LAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRPYGVGLLIIG 135

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPA--FTFQETVQTAIS 118
            D+  G  L +  P+G+      T+ G + Q A  +LE+ +           E ++  + 
Sbjct: 136 YDKS-GAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVE 194

Query: 119 TLQSVLQE-DFKASEIEVGVVSKENPEFRVLSIEEIDEHL 157
            +   L++       + + +V K+ P F +   E + +++
Sbjct: 195 AISQSLRDESLTVDNLSIAIVGKDTP-FTIYDGEAVAKYI 233

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

 Score =  212 bits (541), Expect = 3e-70
 Identities = 56/163 (34%), Positives = 95/163 (58%), Gaps = 4/163 (2%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADAR L+ +AR EA  +R  YG E+ +++LAK I D  Q YTQH  +RP GV  ++  
Sbjct: 85  LVADARVLIDRARLEAQIYRLTYGEEISIEMLAKKICDIKQAYTQHGGVRPFGVSLLIAG 144

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ID+    RLF+ DP+G    +KAT+ G      +  LEK+ ++D   T  E ++ AI+ L
Sbjct: 145 IDKN-EARLFETDPSGALIEYKATAIGSGRPVVMELLEKEYRDD--ITLDEGLELAITAL 201

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 163
                ED K   ++V +++ ++ +F+ + +EEI + +  + ++
Sbjct: 202 TKAN-EDIKPENVDVCIITVKDAQFKKIPVEEIKKLIEKVKKK 243

>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 =  212 bits (541), Expect = 3e-70
 Identities = 48/165 (29%), Positives = 79/165 (47%), Gaps = 4/165 (2%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADAR L    R E  + RF +   +PV  L   I  K+Q+ TQ    RP GV  ++  
Sbjct: 77  LTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAG 136

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D+  GP +F+  P+ ++F  +A S G + Q A  +LE+ M         E V+  +  L
Sbjct: 137 YDDM-GPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFMECNLNELVKHGLRAL 195

Query: 121 QSVLQ--EDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 163
           +  L   +D     + +G+V K+   F +   +++   L  + ER
Sbjct: 196 RETLPAEQDLTTKNVSIGIVGKDLE-FTIYDDDDVSPFLEGLEER 239

>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 =  211 bits (540), Expect = 3e-70
 Identities = 45/167 (26%), Positives = 83/167 (49%), Gaps = 4/167 (2%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +T+DA  L  + R  A  +  +Y   +P + L   + D  Q YTQ    RP GV  + + 
Sbjct: 79  ITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIG 138

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D+  G +L++ DP+G++ G KAT  G     A++ L++  K +   T +  +  AI  L
Sbjct: 139 WDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK-EGEMTLKSALALAIKVL 197

Query: 121 QSVLQED-FKASEIEVGVVSKENPE--FRVLSIEEIDEHLTAISERD 164
              +      A ++E+  +++EN +   RVL  +E+++ +    E +
Sbjct: 198 NKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKHEEEE 244

>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 =  210 bits (538), Expect = 3e-70
 Identities = 50/166 (30%), Positives = 86/166 (51%), Gaps = 5/166 (3%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + AD+R L+++AR EA   R      + V+ L +++A   Q YTQ   +RP GV  ++  
Sbjct: 76  LNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLIAG 135

Query: 61  ID-EECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMK-NDPAFTFQETVQTAIS 118
            D  +  P+L++ +P+G +    A + G   +    FLEK     +P  T +E V+  + 
Sbjct: 136 FDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKEPPATVEECVKLTVR 195

Query: 119 TLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
           +L  V+Q   K   IE+ VV  ++     LS EEI++++T I +  
Sbjct: 196 SLLEVVQTGAK--NIEITVVKPDSD-IVALSSEEINQYVTQIEQEK 238

>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 =  209 bits (534), Expect = 2e-69
 Identities = 45/165 (27%), Positives = 84/165 (50%), Gaps = 9/165 (5%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH-----AYMRPLGVV 55
           + ADA+TL+ +AR E     F Y   M V+ + + +++ +  + +      A  RP GV 
Sbjct: 81  LIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMSRPFGVA 140

Query: 56  AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQT 115
            +   +DE+ GP+LF  DP+G F    A + G   + A + L++        T +E +++
Sbjct: 141 LLFGGVDEK-GPQLFHMDPSGTFVQCDARAIGSASEGAQSSLQELYHKS--MTLKEAIKS 197

Query: 116 AISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAI 160
           ++  L+ V++E   A+ IE+  V      F + + EE++E +  I
Sbjct: 198 SLIILKQVMEEKLNATNIELATVQPGQN-FHMFTKEELEEVIKDI 241

>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 =  202 bits (516), Expect = 1e-66
 Identities = 46/164 (28%), Positives = 77/164 (46%), Gaps = 3/164 (1%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADAR+L   AR EA+ FR  +GY +P+  LA  +A     YT ++ +RP G   M+ S
Sbjct: 80  LLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGCSFMLGS 139

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
                G +L+  DP+G  +G+   + G   Q A   +EK    +   T ++ V+     +
Sbjct: 140 YSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQMKE--MTCRDIVKEVAKII 197

Query: 121 QSVLQE-DFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 163
             V  E   KA E+E+  V +       +  ++I E     ++ 
Sbjct: 198 YIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEKYAKE 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 =  189 bits (481), Expect = 6e-61
 Identities = 41/166 (24%), Positives = 77/166 (46%), Gaps = 5/166 (3%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +  D R LV + R EAA F+  Y   +P+   A  +    Q +T +  +RP GV  +   
Sbjct: 81  LIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGG 140

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDP-AFTFQETVQTAIST 119
           +D+  G  L+  +P+G ++G+K  + G   Q A   LEK + + P   + +E V+ A   
Sbjct: 141 VDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKI 199

Query: 120 LQSVLQE-DFKASEIEVGVVS--KENPEFRVLSIEEIDEHLTAISE 162
           +    ++   K  E+E+   S  + N   + +  + + E +    +
Sbjct: 200 IYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAIDFAQK 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 =  186 bits (475), Expect = 1e-60
 Identities = 41/166 (24%), Positives = 78/166 (46%), Gaps = 5/166 (3%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +  D R LV + R EAA F+  Y   +P+   A  +    Q +T +  +RP GV  +   
Sbjct: 77  LIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGG 136

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPA-FTFQETVQTAIST 119
           +D+  G  L+  +P+G ++G+K  + G   Q A   LEK + + P   + +E V+ A   
Sbjct: 137 VDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKI 195

Query: 120 LQSVLQED-FKASEIEVGVVS--KENPEFRVLSIEEIDEHLTAISE 162
           +    +++  K  E+E+   S  + N   + +  + + E +    +
Sbjct: 196 IYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAIDFAQK 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 = 94.3 bits (234), Expect = 2e-24
 Identities = 28/175 (16%), Positives = 59/175 (33%), Gaps = 17/175 (9%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYE-MPVDVLAKWIADK-SQVYTQHAYMRPLGV---V 55
              +   L +     A    + Y    +    LA   A     ++T+    +P  V   V
Sbjct: 67  KYNEFENLRRAGIVHADMRGYSYDRRDVTGRSLANAYAQTLGTIFTEQ--PKPYEVEICV 124

Query: 56  AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAIN-FLEKKMKNDPAFTFQETVQ 114
           A V  +     P+L++    G     +         E I   + +  + D     +  V 
Sbjct: 125 AEVGRVGSPKAPQLYRITYDGSIVDEQHFVVMGGTTEPIATAMRESYRADL--DLEAAVG 182

Query: 115 TAISTLQSVLQED-----FKASEIEVGVVSKENPE--FRVLSIEEIDEHLTAISE 162
            A++ L+     +        + +EV V+ +  P   FR ++   +++ + A   
Sbjct: 183 IAVNALRQGGAGEGEKRNVDVASLEVAVLDQSRPRRAFRRIAGTALEQLVPAEPA 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 = 86.5 bits (214), Expect = 2e-21
 Identities = 27/178 (15%), Positives = 53/178 (29%), Gaps = 17/178 (9%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYE-MPVDVLAKWIADKSQVYTQHAYMRPLGV---VA 56
              +   L +     A    + Y    +    LA   A            +P  V   VA
Sbjct: 67  KFNEFDNLRRGGIQFADTRGYAYDRRDVTGRQLANVYAQTLGT-IFTEQAKPYEVELCVA 125

Query: 57  MVLSIDEECGPRLFKCDPAGHFF-GHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQT 115
            V    E   P L++    G           G   +   N L++    +   +  + ++ 
Sbjct: 126 EVAHYGETKRPELYRITYDGSIADEPHFVVMGGTTEPIANALKESYAENA--SLTDALRI 183

Query: 116 AISTLQSVLQED-------FKASEIEVGVVSKENPE--FRVLSIEEIDEHLTAISERD 164
           A++ L++   +           + +EV V+    P   FR ++   +   L       
Sbjct: 184 AVAALRAGSADTSGGDQPTLGVASLEVAVLDANRPRRAFRRITGSALQALLVDQESPQ 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 = 76.1 bits (188), Expect = 8e-18
 Identities = 24/155 (15%), Positives = 56/155 (36%), Gaps = 9/155 (5%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + AD     + A  +        G E  V  + + +      Y  H     +G   +V  
Sbjct: 48  VAADTEMTTRMAASKMELHALSTGREPRVATVTRILRQTLFRYQGH-----VGASLVVGG 102

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           +D   GP+L++  P G +     T+ G  +  A+  LE + + +   T +   +  +  +
Sbjct: 103 VDLN-GPQLYEVHPHGSYSRLPFTALGSGQGAAVALLEDRFQPN--MTLEAAQELLVEAI 159

Query: 121 QSVLQED-FKASEIEVGVVSKENPEFRVLSIEEID 154
            + +  D      ++  V++    + +       +
Sbjct: 160 TAGILSDLGSGGNVDACVITAGGAKLQRALSTPTE 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 = 75.0 bits (185), Expect = 2e-17
 Identities = 34/161 (21%), Positives = 62/161 (38%), Gaps = 10/161 (6%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSID 62
            DA+ LV+  + E   +R +    MP++ +A  +++            P  V  +V  ID
Sbjct: 58  GDAQVLVRYMKAELELYRLQRRVNMPIEAVATLLSNMLNQVK----YMPYMVQLLVGGID 113

Query: 63  EECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQS 122
               P +F  D AG        S G         LE +       T  E V   I  + +
Sbjct: 114 T--APHVFSIDAAGGSVEDIYASTGSGSPFVYGVLESQYSEK--MTVDEGVDLVIRAISA 169

Query: 123 VLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISE 162
             Q D      I+V V+++++  +  L  ++I+  +  +  
Sbjct: 170 AKQRDSASGGMIDVAVITRKD-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 = 72.4 bits (178), Expect = 4e-16
 Identities = 28/155 (18%), Positives = 47/155 (30%), Gaps = 9/155 (5%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSID 62
           AD   + Q               E  V    + +           Y   +G   +V  +D
Sbjct: 79  ADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQ-----HLFKYQGHIGAYLIVAGVD 133

Query: 63  EECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQS 122
              G  LF     G        S G     A+  LE   K D   T +E ++ A   +Q+
Sbjct: 134 PT-GSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQD--LTKEEAIKLASDAIQA 190

Query: 123 VLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEH 156
            +  D    S ++V V+        + +    +  
Sbjct: 191 GIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVR 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 = 70.8 bits (174), Expect = 8e-16
 Identities = 28/140 (20%), Positives = 44/140 (31%), Gaps = 9/140 (6%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSID 62
           AD   + Q               E  V    + +           Y   +G   +V  +D
Sbjct: 50  ADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQ-----HLFKYQGHIGAYLIVAGVD 104

Query: 63  EECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQS 122
              G  LF     G        S G     A+  LE   K D   T +E ++ A   +Q+
Sbjct: 105 PT-GSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQD--LTKEEAIKLASDAIQA 161

Query: 123 VLQED-FKASEIEVGVVSKE 141
            +  D    S ++V V+   
Sbjct: 162 GIWNDLGSGSNVDVCVMEIG 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 = 66.2 bits (162), Expect = 4e-14
 Identities = 26/144 (18%), Positives = 44/144 (30%), Gaps = 9/144 (6%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSID 62
           AD     Q             G    V    + +           Y   +G   ++  +D
Sbjct: 50  ADTDMTTQLISSNLELHSLSTGRLPRVVTANRMLKQ-----MLFRYRGYIGAALVLGGVD 104

Query: 63  EECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQS 122
              GP L+   P G        + G     A+   E K + D     +E        + +
Sbjct: 105 VT-GPHLYSIYPHGSTDKLPYVTMGSGSLAAMAVFEDKFRPD--MEEEEAKNLVSEAIAA 161

Query: 123 VLQED-FKASEIEVGVVSKENPEF 145
            +  D    S I++ V+SK   +F
Sbjct: 162 GIFNDLGSGSNIDLCVISKNKLDF 185

>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 = 61.1 bits (149), Expect = 3e-12
 Identities = 20/162 (12%), Positives = 52/162 (32%), Gaps = 9/162 (5%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSID 62
           AD +        +      +    + V   +K +++    Y        L +  M+    
Sbjct: 50  ADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGA----GLSMGTMICGYT 105

Query: 63  EECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQS 122
            + GP ++  D  G          G  +  A   L+   K D   + ++ +     ++ +
Sbjct: 106 RKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWD--LSVEDALYLGKRSILA 163

Query: 123 VLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 163
               D +    + +  V+++   +      ++ E    + E 
Sbjct: 164 AAHRDAYSGGSVNLYHVTEDG--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 = 61.3 bits (149), Expect = 5e-12
 Identities = 20/162 (12%), Positives = 52/162 (32%), Gaps = 9/162 (5%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSID 62
           AD +        +      +    + V   +K +++    Y        L +  M+    
Sbjct: 125 ADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGA----GLSMGTMICGYT 180

Query: 63  EECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQS 122
            + GP ++  D  G          G  +  A   L+   K D   + ++ +     ++ +
Sbjct: 181 RKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWD--LSVEDALYLGKRSILA 238

Query: 123 VLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 163
               D +    + +  V+++   +      ++ E    + E 
Sbjct: 239 AAHRDAYSGGSVNLYHVTEDG--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 = 59.1 bits (143), Expect = 2e-11
 Identities = 32/176 (18%), Positives = 57/176 (32%), Gaps = 20/176 (11%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSID 62
             A  LV+    E   +    G  +  D  A  +A   +     A M+ L VV +++  D
Sbjct: 50  GIAIELVRLFAVELEHYEKIEGVPLTFDGKANRLASMVRGN-LGAAMQGLAVVPLLVGYD 108

Query: 63  -----EECGPRLFKCDPAGHFFGHKA--TSAGLKEQEAINFLEKKMKNDPAFTFQETVQT 115
                E    R+   D  G  +  +A   + G     A + L+K    D     +  ++ 
Sbjct: 109 LDADDESRAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALKKIYSPD--SDEETALRA 166

Query: 116 AISTLQSVLQED--------FKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 163
           AI +L     +D         +        +++       +S E   E    I   
Sbjct: 167 AIESLYDAADDDSATGGPDLTRGIYPTAVTITQAG--AVHVSEETTSELARRIVAE 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 = 54.9 bits (133), Expect = 5e-10
 Identities = 22/155 (14%), Positives = 51/155 (32%), Gaps = 10/155 (6%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSID 62
           AD     +    +   +  +    + V   +K +A+    Y        L +  M+   D
Sbjct: 50  ADCSFWERLLARQCRIYELRNKERISVAAASKLLANMVYQYKGM----GLSMGTMICGWD 105

Query: 63  EECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQS 122
           +  GP L+  D  G+       S G     A   +++    D     ++    A   +  
Sbjct: 106 KR-GPGLYYVDSEGNRISGATFSVGSGSVYAYGVMDRGYSYD--LEVEQAYDLARRAIYQ 162

Query: 123 VLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEH 156
               D +    + +  V ++   +  +S + + + 
Sbjct: 163 ATYRDAYSGGAVNLYHVREDG--WIRVSSDNVADL 195

>1j2q_H Proteasome beta subunit; ubiquitin, CP, hydrolase; HET: CIB; 2.83A {Archaeoglobus fulgidus} SCOP: d.153.1.4 Length = 202

 Score = 53.3 bits (129), Expect = 2e-09
 Identities = 34/162 (20%), Positives = 64/162 (39%), Gaps = 11/162 (6%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSID 62
            DA+ L +  + EA  +  +   +  V  +A   ++    Y       P  V  ++  ID
Sbjct: 50  GDAQFLARIIKIEANLYEIRRERKPTVRAIATLTSNLLNSYRYF----PYLVQLLIGGID 105

Query: 63  EECGPRLFKCDPAG-HFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQ 121
            E G  ++  DP G         + G     A   LE +   +      E V+ A+  + 
Sbjct: 106 SE-GKSIYSIDPIGGAIEEKDIVATGSGSLTAYGVLEDRFTPE--IGVDEAVELAVRAIY 162

Query: 122 SVLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISE 162
           S ++ D      I+V  ++++  EF   S EE+++ L    +
Sbjct: 163 SAMKRDSASGDGIDVVKITED--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 = 53.0 bits (128), Expect = 2e-09
 Identities = 21/152 (13%), Positives = 49/152 (32%), Gaps = 8/152 (5%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSID 62
           AD + +     Y+      +      V   A    +       + Y   L    ++   D
Sbjct: 50  ADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKE-----MCYRYREDLMAGIIIAGWD 104

Query: 63  EECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQS 122
            + G +++     G          G        +++   +     T +E +Q   + L  
Sbjct: 105 PQEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREG--MTKEECLQFTANALAL 162

Query: 123 VLQED-FKASEIEVGVVSKENPEFRVLSIEEI 153
            ++ D      I +  +++   E +VL  ++I
Sbjct: 163 AMERDGSSGGVIRLAAIAESGVERQVLLGDQI 194

>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 = 49.9 bits (120), Expect = 3e-08
 Identities = 19/140 (13%), Positives = 44/140 (31%), Gaps = 5/140 (3%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSID 62
            D     +  +     ++ + GYE+     A +   +  +        P  V  ++   D
Sbjct: 51  GDTVQFAEYIQKNVQLYKMRNGYELSPTAAANFT--RRNLADCLRSRTPYHVNLLLAGYD 108

Query: 63  EECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQS 122
           E  GP L+  D           + G      ++ L++        + +  V+     L+ 
Sbjct: 109 EHEGPALYYMDYLAALAKAPFAAHGYGAFLTLSILDRYYTPT--ISRERAVELLRKCLEE 166

Query: 123 VLQED-FKASEIEVGVVSKE 141
           + +          V ++ K 
Sbjct: 167 LQKRFILNLPTFSVRIIDKN 186

>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 = 49.9 bits (120), Expect = 3e-08
 Identities = 22/152 (14%), Positives = 46/152 (30%), Gaps = 9/152 (5%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSID 62
           ADA+ +   A Y+      +      V   A  + +       + Y   L    +V   D
Sbjct: 50  ADAQAIADMAAYQLELHGLELEEPPLVLAAANVVKN-----ISYKYREDLLAHLIVAGWD 104

Query: 63  EECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQS 122
           +            G       T  G        +++   K     T +E  +   + +  
Sbjct: 105 QR-EGGQVYGTMGGMLIRQPFTIGGSGSSYIYGYVDAAYKPG--MTPEECRRFTTNAITL 161

Query: 123 VLQED-FKASEIEVGVVSKENPEFRVLSIEEI 153
            +  D      I +  ++    + RV+  +E+
Sbjct: 162 AMNRDGSSGGVIYLVTITAAGVDHRVILGDEL 193

>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 = 48.7 bits (117), Expect = 7e-08
 Identities = 20/141 (14%), Positives = 50/141 (35%), Gaps = 6/141 (4%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSID 62
            D     +  +     +  +  YE+    ++ ++  + ++       RP  V  ++   D
Sbjct: 51  GDTVQFAEYIQANIQLYSIREDYELSPQAVSSFV--RQELAKSIRSRRPYQVNVLIGGYD 108

Query: 63  EEC-GPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQ 121
           ++   P L++ D  G        + G       + L+   + D   T +E +      +Q
Sbjct: 109 KKKNKPELYQIDYLGTKVELPYGAHGYSGFYTFSLLDHHYRPD--MTTEEGLDLLKLCVQ 166

Query: 122 SVLQED-FKASEIEVGVVSKE 141
            + +        + V +V K+
Sbjct: 167 ELEKRMPMDFKGVIVKIVDKD 187

>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 = 45.4 bits (108), Expect = 1e-06
 Identities = 24/163 (14%), Positives = 55/163 (33%), Gaps = 21/163 (12%)

Query: 3   ADARTLVQQARYEAAEFRFKY-GYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSI 61
           AD   LV++ +     + F +   ++ ++  A+ I              P  V  ++  +
Sbjct: 59  ADGDALVKRFKNSVKWYHFDHNDKKLSINSAARNIQHLLYGKRF----FPYYVHTIIAGL 114

Query: 62  DEECGPRLFKCDPAGHFFGHKATSAG---------------LKEQEAINFLEKKMKNDPA 106
           DE+    ++  DP G +   +  + G                K Q       K  K    
Sbjct: 115 DEDGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYEPGTNGKVKKPLKY 174

Query: 107 FTFQETVQTAISTLQSVLQEDFKA-SEIEVGVVSKENPEFRVL 148
            + +E ++    +  S  +   +    +E+ +V+K+       
Sbjct: 175 LSVEEVIKLVRDSFTSATERHIQVGDGLEILIVTKDGVRKEFY 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 = 44.5 bits (106), Expect = 2e-06
 Identities = 22/157 (14%), Positives = 48/157 (30%), Gaps = 18/157 (11%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMR---PLGVVAMVL 59
            D  TL +        ++      M    +A  ++          Y R   P  V  ++ 
Sbjct: 59  GDCLTLTKIIEARLKMYKHSNNKAMTTGAIAAMLS-------TILYSRRFFPYYVYNIIG 111

Query: 60  SIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKND-------PAFTFQET 112
            +DEE    ++  DP G +      + G         L+ ++             +    
Sbjct: 112 GLDEEGKGAVYSFDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVEHVPLSLDRA 171

Query: 113 VQTAISTLQSVLQED-FKASEIEVGVVSKENPEFRVL 148
           ++       S  + D +    + + +V+KE      +
Sbjct: 172 MRLVKDVFISAAERDVYTGDALRICIVTKEGIREETV 208

>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 = 44.5 bits (106), Expect = 3e-06
 Identities = 21/145 (14%), Positives = 50/145 (34%), Gaps = 5/145 (3%)

Query: 3   ADARTLVQQARYEAAEFRFKY-GYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSI 61
           AD + L Q       +      G+      +  W+     +Y++ + M PL    ++   
Sbjct: 58  ADFQYLKQVLGQMVIDEELLGDGHSYSPRAIHSWL--TRAMYSRRSKMNPLWNTMVIGGY 115

Query: 62  DEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQ 121
            +     L   D  G  +   + + G     A   L + ++  P  +  E        ++
Sbjct: 116 ADG-ESFLGYVDMLGVAYEAPSLATGYGAYLAQPLLREVLEKQPVLSQTEARDLVERCMR 174

Query: 122 SVLQEDFKA-SEIEVGVVSKENPEF 145
            +   D ++ +  +   V+++  E 
Sbjct: 175 VLYYRDARSYNRFQTATVTEKGVEI 199

>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 = 42.5 bits (101), Expect = 1e-05
 Identities = 21/152 (13%), Positives = 49/152 (32%), Gaps = 15/152 (9%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMR---PLGVVAMVL 59
            D +T+ Q+ ++    +  K G ++    L   +A          Y +   P     ++ 
Sbjct: 58  TDVQTVAQRLKFRLNLYELKEGRQIKPYTLMSMVA-------NLLYEKRFGPYYTEPVIA 110

Query: 60  SIDEE-CGPRLFKCDPAG-HFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAI 117
            +D +   P +   D  G          +G   ++     E   + +         +T  
Sbjct: 111 GLDPKTFKPFICSLDLIGCPMVTDDFVVSGTCAEQMYGMCESLWEPN--MDPDHLFETIS 168

Query: 118 STLQSVLQED-FKASEIEVGVVSKENPEFRVL 148
             + + +  D      + V ++ K+    R L
Sbjct: 169 QAMLNAVDRDAVSGMGVIVHIIEKDKITTRTL 200

>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 = 42.2 bits (100), Expect = 2e-05
 Identities = 23/155 (14%), Positives = 52/155 (33%), Gaps = 11/155 (7%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSID 62
           AD + +    +Y    +  +YG        A    +       +     L    +V   D
Sbjct: 59  ADTQAIADIVQYHLELYTSQYGTPSTETA-ASVFKE-----LCYENKDNLTAGIIVAGYD 112

Query: 63  EECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQS 122
           ++    ++     G         AG        + +K  + +   + +ETV     +L  
Sbjct: 113 DKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFREN--MSKEETVDFIKHSLSQ 170

Query: 123 VLQEDFKAS--EIEVGVVSKENPEFRVLSIEEIDE 155
            ++ D  +S   I + V++    E  +   +E ++
Sbjct: 171 AIKWD-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 = 41.4 bits (98), Expect = 3e-05
 Identities = 25/152 (16%), Positives = 49/152 (32%), Gaps = 15/152 (9%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMR---PLGVVAMVL 59
            D  TL +  RY+   ++ K    +  +   + ++          Y R   P  V  +V 
Sbjct: 57  TDVTTLNEMFRYKTNLYKLKEERAIEPETFTQLVS-------SSLYERRFGPYFVGPVVA 109

Query: 60  SIDEECG-PRLFKCDPAGHF-FGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAI 117
            I+ + G P +   D  G          +G    +     E   + +     ++  +T  
Sbjct: 110 GINSKSGKPFIAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPN--LEPEDLFETIS 167

Query: 118 STLQSVLQED-FKASEIEVGVVSKENPEFRVL 148
             L +    D        V ++ K+    R L
Sbjct: 168 QALLNAADRDALSGWGAVVYIIKKDEVVKRYL 199

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	164
1ryp_A	243	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_A	246	20S proteasome; cell cycle, immune response, prote	100.0
1iru_C	261	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_C	244	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_B	233	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_E	242	20S proteasome; multicatalytic proteinase, protein	100.0
1ryp_D	241	20S proteasome; multicatalytic proteinase, protein	100.0
3h4p_A	264	Proteasome subunit alpha; core particle, cytoplasm	100.0
3h4p_a	219	Proteasome subunit beta; core particle, cytoplasm,	100.0
1iru_F	263	20S proteasome; cell cycle, immune response, prote	100.0
1yar_A	233	Proteasome alpha subunit; proteasome 20S, PA26 pro	100.0
1iru_D	248	20S proteasome; cell cycle, immune response, prote	100.0
1j2p_A	246	Alpha-ring, proteasome alpha subunit; hydrolase; 2	100.0
1iru_G	254	20S proteasome; cell cycle, immune response, prote	100.0
3mi0_A	248	Proteasome subunit alpha; enzyme inhibitors, lacto	100.0
1ryp_F	233	20S proteasome; multicatalytic proteinase, protein	100.0
1j2q_H	202	Proteasome beta subunit; ubiquitin, CP, hydrolase;	100.0
1iru_E	241	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_B	250	20S proteasome; multicatalytic proteinase, protein	100.0
1yar_H	217	Proteasome beta subunit; proteasome 20S, PA26 prot	100.0
1q5q_H	235	Proteasome beta-type subunit 1; proteasome assembl	100.0
3nzj_F	288	Proteasome component C1; ubiquitin, protein degrad	100.0
1ryp_L	212	20S proteasome; multicatalytic proteinase, protein	100.0
1ryp_G	244	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_H	205	20S proteasome; cell cycle, immune response, prote	100.0
1iru_L	204	20S proteasome; cell cycle, immune response, prote	100.0
1q5q_A	259	Proteasome alpha-type subunit 1; proteasome assemb	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
1ryp_K	198	20S proteasome; multicatalytic proteinase, protein	100.0
2jay_A	291	Proteasome; hydrolase; 1.99A {Mycobacterium tuberc	100.0
1iru_N	219	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_N	233	20S proteasome; multicatalytic proteinase, protein	100.0
3unf_H	234	Proteasome subunit beta type-10; antigen presentat	100.0
1iru_M	213	20S proteasome; cell cycle, immune response, prote	100.0
3unf_N	199	Proteasome subunit beta type-9; antigen presentati	100.0
1ryp_J	204	20S proteasome; multicatalytic proteinase, protein	100.0
1g0u_M	266	Proteasome component PRE4; ubiquitin, degradation,	100.0
1ryp_M	222	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_K	201	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_I	222	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_J	205	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_H	205	20S proteasome; multicatalytic proteinase, protein	100.0
3nzj_H	261	Proteasome component PUP1; ubiquitin, protein degr	100.0
1iru_I	234	20S proteasome; cell cycle, immune response, prote	100.0
1m4y_A	171	ATP-dependent protease HSLV; N-terminal catalytic	99.91
2z3b_A	180	ATP-dependent protease HSLV; N-terminal nucleophIl	99.91
1g3k_A	174	ATP-dependent protease HSLV; hydrolase; 1.90A {Hae	99.91
2hc5_A	117	ORF 99, hypothetical protein YVYC; NESG, GFT-PSI,	83.13

>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=5.5e-41  Score=260.76  Aligned_cols=162  Identities=48%  Similarity=0.777  Sum_probs=152.4

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.|++++|.+++.|+++++++|+|+.++++|++++|.|++++++|||+|++||||||+++||+||++||+|++.+
T Consensus        77 ~~aD~~~l~~~~r~~~~~~~~~~~~~~~v~~la~~l~~~l~~y~~~~~~rP~~v~~lvaG~D~~~gp~Ly~~dp~G~~~~  156 (243)
T 1ryp_A           77 PIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVG  156 (243)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTSCCCSCEEEEEEEETTTEEEEEEECTTSCEEE
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhccCCccccceEEEEEEEcCCCCcEEEEEcCCCCEEE
Confidence            46899999999999999999999999999999999999999999998999999999999999767999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCC-----CCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDP-----AFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE  155 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~-----~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~  155 (164)
                      ++++|+|+|++.++++||++|++.+     +||++||++++++||..++++|.+..+++|++|++++  |++++++||++
T Consensus       157 ~~~~a~G~gs~~a~~~Le~~~~~~~~~~~~~ms~eea~~l~~~al~~~~~rd~s~~~iev~vi~~~g--~~~l~~~ei~~  234 (243)
T 1ryp_A          157 YKATATGPKQQEITTNLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDK--FFTLSAENIEE  234 (243)
T ss_dssp             BSEEEESTTHHHHHHHHHHHHHHHCSSSCCCSSHHHHHHHHHHHHHHHHTCCCCTTSEEEEEEETTE--EEECCHHHHHH
T ss_pred             EEEEEECCCcHHHHHHHHHHhhhcccccccCCCHHHHHHHHHHHHHHHhcccCCCCcEEEEEEECCC--eEECCHHHHHH
Confidence            9999999999999999999995311     8999999999999999999999554599999999985  99999999999


Q ss_pred             HHHHhhccC
Q 031203          156 HLTAISERD  164 (164)
Q Consensus       156 ~l~~~~~~~  164 (164)
                      ++.+++++|
T Consensus       235 ~~~~~~~~~  243 (243)
T 1ryp_A          235 RLVAIAEQD  243 (243)
T ss_dssp             HHHHHTTTC
T ss_pred             HHHHhhccC
Confidence            999999886

>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=3.3e-40  Score=256.79  Aligned_cols=164  Identities=61%  Similarity=0.978  Sum_probs=152.9

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      ++||++.|+++++.+++.|+++++++++|+.+++++++++|.|+++++.|||+|++||||||+++||+||.+||+|++.+
T Consensus        83 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~y~~~~~~rp~~v~~lvaG~D~~~gp~Ly~idp~G~~~~  162 (246)
T 1iru_A           83 MTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCG  162 (246)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSBCCCSEEEEEEEEETTTEEEEEEECTTSCEEE
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcCCCCCCcceEEEEEEEeCCCCeEEEEEcCCeeEEE
Confidence            46899999999999999999999999999999999999999999998999999999999999767899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHHHHHHh
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAI  160 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~~l~~~  160 (164)
                      ++++|+|+|++.++++||++|+++++||++||++++++||..+.++|.+..+++|++|++++..|++++++||++++.++
T Consensus       163 ~~~~aiG~gs~~a~~~Le~~~~~~~~ms~eea~~la~~al~~~~~rd~sg~~i~v~vi~~~g~~~~~l~~~ei~~~~~~~  242 (246)
T 1iru_A          163 FKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVAL  242 (246)
T ss_dssp             BSEEEEETTHHHHHHHHHHHTTSCCCCCHHHHHHHHHHHHHHHTTCCCCTTSEEEEEEETTEEEEEECCHHHHHHHHHHH
T ss_pred             eeEEEECCCcHHHHHHHHHhhcccCCCCHHHHHHHHHHHHHHHhcccCCCCcEEEEEEECCCCeEEECCHHHHHHHHHHh
Confidence            99999999999999999999953339999999999999999999999444499999999987669999999999999999


Q ss_pred             hccC
Q 031203          161 SERD  164 (164)
Q Consensus       161 ~~~~  164 (164)
                      +++|
T Consensus       243 ~~~~  246 (246)
T 1iru_A          243 AERD  246 (246)
T ss_dssp             HTC-
T ss_pred             hccC
Confidence            8876

>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=4.8e-39  Score=252.31  Aligned_cols=161  Identities=27%  Similarity=0.474  Sum_probs=152.0

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|+++++.+++.|++.++++++|+.+++++++++|.|+++++.|||+|++||||||+.+||+||.+||+|++.+
T Consensus        79 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rP~~v~~lvaG~D~~~gp~Ly~idp~G~~~~  158 (261)
T 1iru_C           79 ITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGG  158 (261)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBSSCCCCCEEEEEEEEETTTEEEEEEEETTTEEEE
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccccCcCcceEEEEEEEEeCCCCcEEEEECCCceEEe
Confidence            46899999999999999999999999999999999999999999999999999999999999657899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCC-CCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCC--cEEEcCHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDP-AFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENP--EFRVLSIEEIDEH  156 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~-~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~--~~k~l~~~ei~~~  156 (164)
                      ++++|+|+|++.++++|+++|  ++ +||++||++++++||..+.++|..++ +++|++|+++++  .|++++++||+++
T Consensus       159 ~~~~aiGsgs~~a~~~Le~~~--~~~~ms~eeA~~la~~al~~~~~~d~~sg~~i~v~vi~~~~~~~~~~~l~~~ei~~~  236 (261)
T 1iru_C          159 WKATCIGNNSAAAVSMLKQDY--KEGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQL  236 (261)
T ss_dssp             CSEEEESTTTTHHHHHHHHHC--CTTCCCHHHHHHHHHHHHHHSSSCTTCCSTTCEEEEEECCSSSCEEEECCHHHHHHH
T ss_pred             eeeEEeCcccHHHHHHHHHhh--ccCCCCHHHHHHHHHHHHHHHHhccCCCCCcEEEEEEEcCCCeeeEEECCHHHHHHH
Confidence            999999999999999999999  57 89999999999999999999987766 899999999875  3899999999999


Q ss_pred             HHHhhcc
Q 031203          157 LTAISER  163 (164)
Q Consensus       157 l~~~~~~  163 (164)
                      +.++.++
T Consensus       237 l~~~~~~  243 (261)
T 1iru_C          237 IKKHEEE  243 (261)
T ss_dssp             HHHHHTT
T ss_pred             HHHHHhc
Confidence            9999754

>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=1.1e-38  Score=247.89  Aligned_cols=160  Identities=26%  Similarity=0.480  Sum_probs=150.1

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|+++++.+++.|++.++++++|+.+++++++++|.|++++++|||+|++||||||+++||+||.+||+|++.+
T Consensus        79 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rp~~v~~lvaG~D~~~gp~Ly~idp~G~~~~  158 (244)
T 1ryp_C           79 LTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTG  158 (244)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSCCCCCEEEEEEEEETTTEEEEEEECTTCCEEE
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhccCCccceEEEEEEEEEcCCCCCEEEEECCCccEEe
Confidence            46899999999999999999999999999999999999999999999999999999999999448999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhc-cCCCCeEEEEEEE--cCCCc--EEEcCHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQE-DFKASEIEVGVVS--KENPE--FRVLSIEEIDE  155 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~-d~~~~~iei~ii~--~~~~~--~k~l~~~ei~~  155 (164)
                      ++++|+|+|++.++++||++|  +++||+|||++++++||..+.++ +.+..+++|++|+  ++++.  |++++++||++
T Consensus       159 ~~~~aiGsgs~~a~~~Le~~~--~~~ms~eea~~la~~al~~~~~rd~~sg~~i~v~vi~~~~~~~~~~~~~l~~~ei~~  236 (244)
T 1ryp_C          159 WKAISVGANTSAAQTLLQMDY--KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKD  236 (244)
T ss_dssp             BSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHCSSSSCCGGGEEEEEEECCSSSSSCEEEECCHHHHHH
T ss_pred             eeEEEECCCcHHHHHHHHHhh--hcCCCHHHHHHHHHHHHHHHhccccCCCCcEEEEEEEeecCCCceeEEECCHHHHHH
Confidence            999999999999999999998  58999999999999999999998 5553499999999  88765  99999999999


Q ss_pred             HHHHhhc
Q 031203          156 HLTAISE  162 (164)
Q Consensus       156 ~l~~~~~  162 (164)
                      ++.+++.
T Consensus       237 ~~~~~~~  243 (244)
T 1ryp_C          237 ILVKTGI  243 (244)
T ss_dssp             HHHHHTC
T ss_pred             HHHHhhc
Confidence            9998863

>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=9.2e-39  Score=246.78  Aligned_cols=156  Identities=33%  Similarity=0.554  Sum_probs=147.9

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|+++++.+++.|+++++++++|+.+++++++++|.|++++++|||+|++||||||+ +||+||.+||+|++.+
T Consensus        78 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~y~~~~~~rP~~v~~lvaG~D~-~gp~Ly~id~~G~~~~  156 (233)
T 1iru_B           78 MGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGVSLLICGWNE-GRPYLFQSDPSGAYFA  156 (233)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCSEEEEEEEECS-SSEEEEEECTTSCEEE
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCcCCCCCcEEEEEEEEEeC-CCCeEEEECCCCCEEE
Confidence            468999999999999999999999999999999999999999999989999999999999996 7999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHHHHHHh
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAI  160 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~~l~~~  160 (164)
                      ++++|+|+|++.++++||++|  +++||+|||++++++||..+.++|.+..+++|++|++++  |++++++||++++.++
T Consensus       157 ~~~~aiG~gs~~a~~~Le~~~--~~~ms~eea~~la~~al~~~~~~d~sg~~i~v~vi~~~g--~~~l~~~ei~~~~~~~  232 (233)
T 1iru_B          157 WKATAMGKNYVNGKTFLEKRY--NEDLELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAG--FRRLTPTEVKDYLAAI  232 (233)
T ss_dssp             BSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHTTCCSCCCSSSEEEEEEETTE--EEECCHHHHHHHHTTC
T ss_pred             eeEEEECCCCHHHHHHHHHHh--ccCCCHHHHHHHHHHHHHHHhhccCCCCCEEEEEEECCC--EEECCHHHHHHHHHhc
Confidence            999999999999999999998  578999999999999999999999655599999999985  9999999999999876


Q ss_pred             h
Q 031203          161 S  161 (164)
Q Consensus       161 ~  161 (164)
                      +
T Consensus       233 ~  233 (233)
T 1iru_B          233 A  233 (233)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=6.9e-39  Score=248.76  Aligned_cols=160  Identities=24%  Similarity=0.455  Sum_probs=150.4

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccC------ccccceeeEEEEEcCCCCCeEEEeCC
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAY------MRPLGVVAMVLSIDEECGPRLFKCDP   74 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~------~rP~gv~~iiaG~d~~~gp~Ly~~dp   74 (164)
                      +++|++.|+++++.+++.|++.++++++|+.+++++++++|.||++++      .|||+|++||||||+++||+||.+||
T Consensus        73 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~~~~l~~RP~~v~~lvaG~D~~~gp~Ly~idp  152 (242)
T 1ryp_E           73 LTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEP  152 (242)
T ss_dssp             SGGGHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCCBSSCTTSCCCBSSCCSEEEEEEEEETTTEEEEEEECT
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccccCcccccccCcceEEEEEEEEeCCCCCEEEEECC
Confidence            479999999999999999999999999999999999999999999988      99999999999999558999999999


Q ss_pred             CcceeeeeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHH
Q 031203           75 AGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEID  154 (164)
Q Consensus        75 ~G~~~~~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~  154 (164)
                      +|++.+++++|+|+|++.++++||++|  +++||++||++++++||..+.+++.+..+++|++|+++++ |++++++||+
T Consensus       153 ~G~~~~~~~~aiGsgs~~a~~~Le~~~--~~~ms~eea~~la~~al~~~~~~~~sg~~i~v~vi~~~~~-~~~~~~~ei~  229 (242)
T 1ryp_E          153 SGTFYRYNAKAIGSGSEGAQAELLNEW--HSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDG-FKIYDNEKTA  229 (242)
T ss_dssp             TSCEEEBSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHCSSCCCTTSEEEEEEETTTE-EEECCHHHHH
T ss_pred             CCCEeccCEEEECCCCHHHHHHHHHhh--ccCCCHHHHHHHHHHHHHHHhhccCCCCcEEEEEEECCCC-eEECCHHHHH
Confidence            999999999999999999999999998  5889999999999999999999855444999999999876 9999999999


Q ss_pred             HHHHHhhcc
Q 031203          155 EHLTAISER  163 (164)
Q Consensus       155 ~~l~~~~~~  163 (164)
                      +++.++.++
T Consensus       230 ~~~~~~~~~  238 (242)
T 1ryp_E          230 ELIKELKEK  238 (242)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHhhh
Confidence            999998754

>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=2e-38  Score=246.05  Aligned_cols=160  Identities=31%  Similarity=0.531  Sum_probs=148.8

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCC-CCCeEEEeCCCccee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEE-CGPRLFKCDPAGHFF   79 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~-~gp~Ly~~dp~G~~~   79 (164)
                      +++|++.|+++++.+++.|++.++++++|+.+++++++++|.|||++++|||+|++||||||++ +||+||.+||+|++.
T Consensus        76 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rP~~v~~lvaG~D~~~~gp~Ly~idp~G~~~  155 (241)
T 1ryp_D           76 LNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYS  155 (241)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSSTTBCCCSEEEEEEECCTTCCSCEEEEECTTSCEE
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHccCCCCCCcceeeEEEEEcCCCCCeeEEEECCCCCEE
Confidence            4689999999999999999999999999999999999999999999899999999999999975 789999999999999


Q ss_pred             eeeEEeecCChHHHHHHHHHhhcC-CCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHHHHH
Q 031203           80 GHKATSAGLKEQEAINFLEKKMKN-DPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLT  158 (164)
Q Consensus        80 ~~~~~aiG~~s~~~~~~Le~~~~~-~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~~l~  158 (164)
                      +++++|+|+|++.++++||++|+. +++||++||++++++||..+.+  .+..+++|++|++++ .|++++++||++++.
T Consensus       156 ~~~~~aiG~gs~~a~~~Le~~~~~~~~~ms~eea~~l~~~al~~~~~--~sg~~i~v~vi~~~~-~~~~l~~~ei~~~~~  232 (241)
T 1ryp_D          156 SWSAQTIGRNSKTVREFLEKNYDRKEPPATVEECVKLTVRSLLEVVQ--TGAKNIEITVVKPDS-DIVALSSEEINQYVT  232 (241)
T ss_dssp             EBSEEEESTTHHHHHHHHHTTCCTTSCCCSHHHHHHHHHHHHHHHHC--SCSTTEEEEEEETTT-EEEECCHHHHHHHHH
T ss_pred             EeeeEEECCCcHHHHHHHHHhhhcccCCCCHHHHHHHHHHHHHHHhc--CCCCcEEEEEEECCC-cEEECCHHHHHHHHH
Confidence            999999999999999999999843 5789999999999999999985  444499999999987 499999999999999


Q ss_pred             Hhhcc
Q 031203          159 AISER  163 (164)
Q Consensus       159 ~~~~~  163 (164)
                      ++.++
T Consensus       233 ~~~~~  237 (241)
T 1ryp_D          233 QIEQE  237 (241)
T ss_dssp             HHTHH
T ss_pred             HHhhh
Confidence            98743

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

Probab=100.00  E-value=2.3e-39  Score=254.53  Aligned_cols=158  Identities=34%  Similarity=0.602  Sum_probs=149.9

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      ++||++.|+++++.+++.|++.++++++|+.++++|++++|.||+++++|||+|++||||||+ +||+||++||+|++.+
T Consensus        85 ~~aD~~~l~~~~r~~~~~y~~~~~~~i~v~~la~~l~~~~~~yt~~~~~rP~~v~~lvaG~D~-~gp~Ly~iDp~G~~~~  163 (264)
T 3h4p_A           85 LVADARVLIDRARLEAQIYRLTYGEEISIEMLAKKICDIKQAYTQHGGVRPFGVSLLIAGIDK-NEARLFETDPSGALIE  163 (264)
T ss_dssp             CSHHHHHHHTTHHHHHHHHHHTTCSCCCHHHHHHHHHHHHHHTTSBSSCCCCSEEEEEEEEET-TEEEEEEECTTCCCEE
T ss_pred             chHHHHHHHHHHHHHHHhhHHhcCCCCCHHHHHHHHHHHHHHHhhccCCCCeeEEEEEEEEeC-CcCEEEEECCCceEEe
Confidence            479999999999999999999999999999999999999999999999999999999999997 7999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHHHHHHh
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAI  160 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~~l~~~  160 (164)
                      ++++|+|+|++.++++|++.|  +++||++||++++++||..++++ ....+++|++|++++.+|++++++||++++.++
T Consensus       164 ~~~~aiGsgs~~a~~~Le~~~--~~~ms~eea~~la~~al~~a~~~-~sg~~iev~vi~~~~~~~~~l~~~ei~~~~~~~  240 (264)
T 3h4p_A          164 YKATAIGSGRPVVMELLEKEY--RDDITLDEGLELAITALTKANED-IKPENVDVCIITVKDAQFKKIPVEEIKKLIEKV  240 (264)
T ss_dssp             ESEEEESTTHHHHTTTHHHHC--CTTCCSHHHHHHHHHHHHHHSSS-CCTTSEEEEEEETTTTEEEECCTTTTGGGTTTT
T ss_pred             cCeEEECCCHHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHHhc-cCCCeEEEEEEEeCCCcEEECCHHHHHHHHHHH
Confidence            999999999999999999998  68999999999999999999987 555599999999887779999999999999988


Q ss_pred             hc
Q 031203          161 SE  162 (164)
Q Consensus       161 ~~  162 (164)
                      .+
T Consensus       241 ~~  242 (264)
T 3h4p_A          241 KK  242 (264)
T ss_dssp             TT
T ss_pred             HH
Confidence            74

>3h4p_a Proteasome subunit beta; core particle, cytoplasm, hydrolase, protease, threonine protease; 4.10A {Methanocaldococcus jannaschii}

Probab=100.00  E-value=1.8e-38  Score=243.23  Aligned_cols=155  Identities=23%  Similarity=0.347  Sum_probs=145.1

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|+++++.+++.|+++++++++|+.+++++++++|.|    +.|||+|++||||||+.+||+||.+||+|++.+
T Consensus        49 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~----~~~P~~v~~lvaG~D~~~gp~Ly~idp~G~~~~  124 (219)
T 3h4p_a           49 SVGDAQAIVRLLIAEAKLYKMRTGRNIPPLACATLLSNILHSS----RMFPFLTQIIIGGYDLLEGAKLFSLDPLGGMNE  124 (219)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHT----TTTTCCCCCEEEEEETTTEEEEEEECSSCCEEE
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHh----cCCCceEEEEEEEEeCCCCcEEEEECCCCceEe
Confidence            4689999999999999999999999999999999999999776    368999999999999867899999999999999


Q ss_pred             ee-EEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHHHHHH
Q 031203           81 HK-ATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEIDEHLT  158 (164)
Q Consensus        81 ~~-~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~~~l~  158 (164)
                      ++ ++|+|+|++.++++||++|  +++||++||++++++||..++++|..++ +++|++|++++  |++++++||+++|.
T Consensus       125 ~~~~~aiG~gs~~a~~~Le~~~--~~~ms~eea~~la~~al~~~~~rd~~sg~~i~v~vi~~~g--~~~l~~~ei~~~l~  200 (219)
T 3h4p_a          125 EKTFTATGSGSPIAYGVLEAGY--DRDMSVEEGIKLALNALKSAMERDTFSGNGISLAVITKDG--VKIFEDEEIEKILD  200 (219)
T ss_dssp             CSSEEEESTTHHHHHHHHHTSC--CTTCCHHHHHHHHHHHHHHHHTSCSSCCSCCCEEEEETTE--EEECCHHHHHHHHH
T ss_pred             cCCEEEEcCCHHHHHHHHHHhc--CCCCCHHHHHHHHHHHHHHHHhhcCCCCCcEEEEEEeCCC--eEEcCHHHHHHHHH
Confidence            99 9999999999999999998  5899999999999999999999998876 89999999973  99999999999999


Q ss_pred             Hhhcc
Q 031203          159 AISER  163 (164)
Q Consensus       159 ~~~~~  163 (164)
                      +++++
T Consensus       201 ~~~~~  205 (219)
T 3h4p_a          201 SMKAK  205 (219)
T ss_dssp             HCC--
T ss_pred             Hhhcc
Confidence            99853

>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=1.2e-38  Score=250.28  Aligned_cols=159  Identities=28%  Similarity=0.494  Sum_probs=149.1

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|+++++.+++.|++.++++++|+.+++++++++|.|||+++.|||+|++||||||+ +||+||.+||+|++.+
T Consensus        77 ~~aD~~~l~~~~~~~~~~~~~~~~~~i~v~~la~~l~~~l~~~t~~~~~RP~~v~~lvaG~D~-~gp~Ly~idp~G~~~~  155 (263)
T 1iru_F           77 LTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAGYDD-MGPHIFQTCPSANYFD  155 (263)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEET-TEEEEEEECSSSCEEE
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHhhcccccccceEEEEEEEEcC-CCCEEEEECCCCCEEE
Confidence            468999999999999999999999999999999999999999999999999999999999998 7999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhcc-CCCC-eEEEEEEEcCCCcEEEcCHHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQED-FKAS-EIEVGVVSKENPEFRVLSIEEIDEHLT  158 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d-~~~~-~iei~ii~~~~~~~k~l~~~ei~~~l~  158 (164)
                      ++++|+|+|++.++++||++|++.++||++||++++++||..++++| ..++ +++|++|+++++ |++++++||++++.
T Consensus       156 ~~~~aiGsgs~~a~~~Le~~~~~~~~ms~eea~~la~~al~~~~~rd~~~sg~~iev~vi~~~~~-~~~l~~~ei~~~~~  234 (263)
T 1iru_F          156 CRAMSIGARSQSARTYLERHMSEFMECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLE-FTIYDDDDVSPFLE  234 (263)
T ss_dssp             ESEEEESTTHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCTTCCCCTTTEEEEEEETTEE-EEEECSGGGHHHHT
T ss_pred             eeEEEcCcccHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHhccccCCCCcEEEEEEECCCC-eEECCHHHHHHHHH
Confidence            99999999999999999999953348999999999999999999998 3444 999999999864 99999999999999


Q ss_pred             Hhh
Q 031203          159 AIS  161 (164)
Q Consensus       159 ~~~  161 (164)
                      ++.
T Consensus       235 ~~~  237 (263)
T 1iru_F          235 GLE  237 (263)
T ss_dssp             TCC
T ss_pred             HHh
Confidence            876

>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=3.4e-38  Score=243.60  Aligned_cols=153  Identities=36%  Similarity=0.561  Sum_probs=145.4

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|+++++.+++.|+++++++++|+.+++++++++|.|+++++.|||+|++||||||+ +||+||.+||+|++.+
T Consensus        81 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a~~l~~~~~~~~~~~~~rp~~v~~lvaG~D~-~gp~Ly~id~~G~~~~  159 (233)
T 1yar_A           81 LVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGVSLIFAGIDQ-IGPRLFDCDPAGTINE  159 (233)
T ss_dssp             BHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBTTBCCCCEEEEEEEECS-SCEEEEEECTTCCEEE
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCcCCcCcceEEEEEEEEeC-CCCEEEEECCCCCEEe
Confidence            368999999999999999999999999999999999999999999999999999999999998 7999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL  157 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~~l  157 (164)
                      ++++|+|+|++.++++||++|  +++||++||++++++||..+.++|++..+++|++|+++++ |++++++||+++|
T Consensus       160 ~~~~aiG~gs~~a~~~Le~~~--~~~~s~eea~~la~~al~~~~~~d~s~~~i~v~vi~~~~~-~~~~~~~ei~~~l  233 (233)
T 1yar_A          160 YKATAIGSGKDAVVSFLEREY--KENLPEKEAVTLGIKALKSSLEEGEELKAPEIASITVGNK-YRIYDQEEVKKFL  233 (233)
T ss_dssp             BSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHTSCSSCCCCCCEEEEEETTSC-CEECCHHHHHTTC
T ss_pred             eeEEEEcCCcHHHHHHHHHHh--ccCCCHHHHHHHHHHHHHHHhhccCCCCcEEEEEEECCCC-EEECCHHHHHhhC
Confidence            999999999999999999998  5789999999999999999999998544999999999875 9999999998764

>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=3.2e-38  Score=245.97  Aligned_cols=158  Identities=30%  Similarity=0.510  Sum_probs=148.0

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|+++++.+++.|+++++++++|+.+++++++++|.|||+++.|||+|++||||||+++||+||.+||+|++.+
T Consensus        76 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rp~~v~~lvaG~D~~~gp~Ly~idp~G~~~~  155 (248)
T 1iru_D           76 LTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHA  155 (248)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCEEEEEEEECSSSCEEEEEECTTSCEEE
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhccCCcccccEEEEEEEEeCCCCcEEEEEcCCCcEEE
Confidence            46899999999999999999999999999999999999999999998999999999999999558999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCC--CHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAF--TFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLT  158 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~l--s~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~~l~  158 (164)
                      ++++|+|+|++.++++||++|  +++|  |++||++++++||..+.+  .+..+++|++|+++++ |++++++||++++.
T Consensus       156 ~~~~aiG~gs~~a~~~Le~~~--~~~m~~s~eea~~la~~al~~~~~--~sg~~i~v~vi~~~g~-~~~l~~~ei~~~~~  230 (248)
T 1iru_D          156 WKANAIGRGAKSVREFLEKNY--TDEAIETDDLTIKLVIKALLEVVQ--SGGKNIELAVMRRDQS-LKILNPEEIEKYVA  230 (248)
T ss_dssp             BSEEEESTTHHHHHHHHTTTC--CSSTTCSHHHHHHHHHHHHHTTSC--TTSTTCCEEEEESSSC-EECCCHHHHHHHTT
T ss_pred             eeEEEECCCcHHHHHHHHHhh--cccccCCHHHHHHHHHHHHHHHHc--CCCCcEEEEEEECCCc-EEECCHHHHHHHHH
Confidence            999999999999999999998  5789  999999999999999986  3444899999999875 99999999999999


Q ss_pred             Hhhcc
Q 031203          159 AISER  163 (164)
Q Consensus       159 ~~~~~  163 (164)
                      ++.++
T Consensus       231 ~~~~~  235 (248)
T 1iru_D          231 EIEKE  235 (248)
T ss_dssp             TTTTT
T ss_pred             HHHhc
Confidence            88754

>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=1.5e-37  Score=241.92  Aligned_cols=156  Identities=31%  Similarity=0.497  Sum_probs=146.8

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|+++++.+++.|++.++++++|+.+++++++++|.|+++++.|||+|++||||||  +||+||.+||+|++.+
T Consensus        81 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~y~~~~~~rp~~v~~lvaG~D--~gp~Ly~idp~G~~~~  158 (246)
T 1j2p_A           81 LVADARVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQYGGVRPFGVSLLIAGVN--EVPKLYETDPSGALLE  158 (246)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCEEEEEEEES--SSEEEEEECTTCCEEE
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCcccccEEEEEEEEC--CCCEEEEECCCceEEe
Confidence            46899999999999999999999999999999999999999999999999999999999999  6899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEE-cCCCcEEEcCHHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVS-KENPEFRVLSIEEIDEHLT  158 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~-~~~~~~k~l~~~ei~~~l~  158 (164)
                      ++++|+|+|++.++++||+.|  +++||++||++++++||..+.++ ..++ +++|++|+ +++ +|++++++||++++.
T Consensus       159 ~~~~aiGsgs~~a~~~Le~~~--~~~ms~eea~~la~~al~~~~~~-~~sg~~i~v~vi~~~~~-~~~~l~~~ei~~~~~  234 (246)
T 1j2p_A          159 YKATAIGMGRMAVTEFFEKEY--RDDLSFDDAMVLGLVAMGLSIES-ELVPENIEVGYVKVDDR-TFKEVSPEELKPYVE  234 (246)
T ss_dssp             BSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHTS-CCCGGGEEEEEEETTTC-CCEECCHHHHHHHHH
T ss_pred             eeEEEECCCcHHHHHHHHHHh--ccCCCHHHHHHHHHHHHHHHhhc-cCCCCcEEEEEEEcCCC-ceEECCHHHHHHHHH
Confidence            999999999999999999998  57899999999999999999988 5555 99999999 654 499999999999999


Q ss_pred             Hhhc
Q 031203          159 AISE  162 (164)
Q Consensus       159 ~~~~  162 (164)
                      ++.+
T Consensus       235 ~~~~  238 (246)
T 1j2p_A          235 RANE  238 (246)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8863

>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=6.1e-38  Score=245.13  Aligned_cols=159  Identities=27%  Similarity=0.359  Sum_probs=148.1

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|+++++.+++.|+++++++++|+.+++++++++|.|++++++|||+|++||||||+++||+||.+||+|++.+
T Consensus        80 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rP~~v~~lvaG~D~~~gp~Ly~idp~G~~~~  159 (254)
T 1iru_G           80 LLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYG  159 (254)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSBSSBCCCSEEEEEEEEETTTEEEEEEECTTCCEEE
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhccccccccceEEEEEEEEeCCCCcEEEEEcCCCCEEe
Confidence            46899999999999999999999999999999999999999999999999999999999999558999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCC-cEEEcCHHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENP-EFRVLSIEEIDEHLT  158 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~-~~k~l~~~ei~~~l~  158 (164)
                      ++++|+|+|++.++++||+.|  .++||++||++++++||..+.+++..++ +++|++|+++.+ .|+++++++|++++.
T Consensus       160 ~~~~aiGsgs~~a~~~Le~~~--~~~ms~eea~~la~~al~~~~~~~~~~~~~iev~vi~~~~~g~~~~l~~~~i~~~~~  237 (254)
T 1iru_G          160 YWGCAIGKARQAAKTEIEKLQ--MKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEK  237 (254)
T ss_dssp             BSEEEESTTHHHHHHHHTTSC--GGGCCHHHHHHHHHHHHHHHSCSSSSCCEEEEEEECBTTTTTCCEECCHHHHHHHHH
T ss_pred             eeeEEecCccHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHHhhccCCCCcEEEEEEEcCCCCCeEECCHHHHHHHHH
Confidence            999999999999999999998  5789999999999999999988776555 899999998733 499999999999998


Q ss_pred             Hhh
Q 031203          159 AIS  161 (164)
Q Consensus       159 ~~~  161 (164)
                      .+.
T Consensus       238 ~~~  240 (254)
T 1iru_G          238 YAK  240 (254)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            764

>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=1e-37  Score=242.96  Aligned_cols=157  Identities=16%  Similarity=0.212  Sum_probs=139.8

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHHH-HHHHhhhhccCccccceeeEEEEEcC---CCCCeEEEeCCC
Q 031203            1 MTADARTLVQQARYEAAEFRFKYG-YEMPVDVLAKWIA-DKSQVYTQHAYMRPLGVVAMVLSIDE---ECGPRLFKCDPA   75 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~-~~i~~~~l~~~ls-~~~q~yt~~~~~rP~gv~~iiaG~d~---~~gp~Ly~~dp~   75 (164)
                      +++|++.|.+.++..++.|++.++ ++++++.|+++++ .+.|.|||  ++|||||++||||||+   .+||+||++||+
T Consensus        67 ~~aD~~~l~~~~~~~~~l~~~~~~~~~i~v~~la~~l~~~l~q~yt~--~~rP~gv~~liaG~D~~~~~~gp~Ly~~Dp~  144 (248)
T 3mi0_A           67 KFNEFDNLRRGGIQFADTRGYAYDRRDVTGRQLANVYAQTLGTIFTE--QAKPYEVELCVAEVAHYGETKRPELYRITYD  144 (248)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHHHHHHHHHHH--SSSCCCEEEEEEECCCTTCCCCCEEEEECTT
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHhcc--CCCCceEEEEEEEEcCCCCCCCCEEEEECCC
Confidence            468999999999999999999999 9999999999999 78899997  7899999999999997   479999999999


Q ss_pred             cceee-eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhh-------hccCCCCeEEEEEEEcCC--CcE
Q 031203           76 GHFFG-HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVL-------QEDFKASEIEVGVVSKEN--PEF  145 (164)
Q Consensus        76 G~~~~-~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~-------~~d~~~~~iei~ii~~~~--~~~  145 (164)
                      |++.. ++++|+|+|++.++++||++|  +++||++||++++++||..++       ++++...+++|++|++++  +.|
T Consensus       145 G~~~~e~~~~a~Gsgs~~a~~~Le~~y--~~~mt~eeai~la~~aL~~~~~~~~~~~~~~~~~~~iev~vv~~~g~~~~f  222 (248)
T 3mi0_A          145 GSIADEPHFVVMGGTTEPIANALKESY--AENASLTDALRIAVAALRAGSADTSGGDQPTLGVASLEVAVLDANRPRRAF  222 (248)
T ss_dssp             SCEEEESSEEEESSCHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHC------------CCTTEEEEEEETTSSSCCE
T ss_pred             eEEeecccEEEECccHHHHHHHHHhhc--CCCCCHHHHHHHHHHHHHHHHhhcccCcccccCCCcEEEEEEECCCCcccE
Confidence            99995 999999999999999999998  688999999999999999999       567777899999999985  469


Q ss_pred             EEcCHHHHHHHHHHhh
Q 031203          146 RVLSIEEIDEHLTAIS  161 (164)
Q Consensus       146 k~l~~~ei~~~l~~~~  161 (164)
                      ++++++||+++|.+++
T Consensus       223 ~~l~~~ei~~~l~~~~  238 (248)
T 3mi0_A          223 RRITGSALQALLVDQE  238 (248)
T ss_dssp             EECCHHHHHHTC----
T ss_pred             EECCHHHHHHHHHHcC
Confidence            9999999999998775

>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=1.9e-38  Score=245.04  Aligned_cols=154  Identities=22%  Similarity=0.382  Sum_probs=143.1

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      ++||++.|+++++.+++.|+++++++++|+.+++++++++|.|||+++.|||+|++||||||+ .||+||.+||+|++.+
T Consensus        76 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rp~~v~~lvaG~D~-~gp~Ly~idp~G~~~~  154 (233)
T 1ryp_F           76 LAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRPYGVGLLIIGYDK-SGAHLLEFQPSGNVTE  154 (233)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEET-TEEEEEEECTTSCEEE
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcccCCcCcceEEEEEEEeC-CcCEEEEECCCCCeee
Confidence            468999999999999999999999999999999999999999999999999999999999998 7999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCC--CHHHHHHHHHHHHHhhhhcc-CCCC-eEEEEEEEcCCCcEEEcCHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAF--TFQETVQTAISTLQSVLQED-FKAS-EIEVGVVSKENPEFRVLSIEEIDEH  156 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~l--s~eea~~l~~~al~~~~~~d-~~~~-~iei~ii~~~~~~~k~l~~~ei~~~  156 (164)
                      ++++|+|+|++.++++||++|++.++|  |+|||++++++||..++ +| ..++ +++|++|+++++ |++++++||+++
T Consensus       155 ~~~~aiG~gs~~a~~~Le~~~~~~~~m~~s~eea~~~a~~al~~~~-~d~~~s~~~i~v~vi~~~~~-~~~l~~~ei~~~  232 (233)
T 1ryp_F          155 LYGTAIGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVEAISQSL-RDESLTVDNLSIAIVGKDTP-FTIYDGEAVAKY  232 (233)
T ss_dssp             ESEEEESTTHHHHHHHHHHHHHHHTTCCSCHHHHHHHHHHHHTTSC-CSSCCCTTTEEEEEEETTEE-EEEEEGGGGGGG
T ss_pred             eeEEEECCCcHHHHHHHHHHhccccccCCCHHHHHHHHHHHHHHHh-hcccCCCCcEEEEEEECCCC-EEECCHHHHHhh
Confidence            999999999999999999999532389  99999999999999999 66 4444 999999999865 999999999876


Q ss_pred             H
Q 031203          157 L  157 (164)
Q Consensus       157 l  157 (164)
                      |
T Consensus       233 l  233 (233)
T 1ryp_F          233 I  233 (233)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1j2q_H Proteasome beta subunit; ubiquitin, CP, hydrolase; HET: CIB; 2.83A {Archaeoglobus fulgidus} SCOP: d.153.1.4

Probab=100.00  E-value=3.5e-37  Score=233.14  Aligned_cols=152  Identities=22%  Similarity=0.338  Sum_probs=142.7

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|+++++.+++.|+++++++++++.+++++++.+|.+    +.|||+|++||||||+ +||+||.+||+|++.+
T Consensus        48 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~~~~~----r~rp~~~~~lvaG~D~-~gp~Ly~id~~G~~~~  122 (202)
T 1j2q_H           48 SVGDAQFLARIIKIEANLYEIRRERKPTVRAIATLTSNLLNSY----RYFPYLVQLLIGGIDS-EGKSIYSIDPIGGAIE  122 (202)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHT----TTSCCCEEEEEEEEET-TEEEEEEECTTCCEEE
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhh----CCCCceEEEEEEEEeC-CCCEEEEECCCCCeee
Confidence            4689999999999999999999999999999999999999664    3789999999999998 7899999999999999


Q ss_pred             ee-EEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHHHHHH
Q 031203           81 HK-ATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEIDEHLT  158 (164)
Q Consensus        81 ~~-~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~~~l~  158 (164)
                      ++ ++|+|+|++.++++||++|  +++||++||++++++||..+.++|..++ +++|++|++++  |++++++||++++.
T Consensus       123 ~~~~~aiG~g~~~a~~~Le~~~--~~~~s~eea~~la~~al~~~~~~d~~s~~~i~v~vi~~~g--~~~l~~~ei~~~~~  198 (202)
T 1j2q_H          123 EKDIVATGSGSLTAYGVLEDRF--TPEIGVDEAVELAVRAIYSAMKRDSASGDGIDVVKITEDE--FYQYSPEEVEQILA  198 (202)
T ss_dssp             ESSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHTTCTTSCSCEEEEEECSSC--EEECHHHHHHHHGG
T ss_pred             cCCEEEEcCCHHHHHHHHHhhc--CCCcCHHHHHHHHHHHHHHHHhcCCCCCCcEEEEEEeCCC--eEEeCHHHHHHHHH
Confidence            99 9999999999999999998  5889999999999999999999998765 89999999983  99999999999998


Q ss_pred             Hhh
Q 031203          159 AIS  161 (164)
Q Consensus       159 ~~~  161 (164)
                      +++
T Consensus       199 ~~~  201 (202)
T 1j2q_H          199 KFR  201 (202)
T ss_dssp             GTT
T ss_pred             Hhh
Confidence            873

>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=1.4e-37  Score=241.37  Aligned_cols=156  Identities=28%  Similarity=0.523  Sum_probs=146.7

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccC-----ccccceeeEEEEEcCCCCCeEEEeCCC
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAY-----MRPLGVVAMVLSIDEECGPRLFKCDPA   75 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~-----~rP~gv~~iiaG~d~~~gp~Ly~~dp~   75 (164)
                      ++||++.|+++++.+++.|+++++++++|+.+++++++++|.|+++++     .|||+|++||||||. +||+||.+||+
T Consensus        81 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a~~l~~~~~~y~~~~~~~~l~~rp~~v~~lvaG~D~-~gp~Ly~idp~  159 (241)
T 1iru_E           81 LIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMSRPFGVALLFGGVDE-KGPQLFHMDPS  159 (241)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCBCSTTCCSSCBSSCCCEEEEEEEEET-TEEEEEEECTT
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhccccccccccccceEEEEEEEEeC-CCCEEEEECCC
Confidence            468999999999999999999999999999999999999999999887     899999999999995 89999999999


Q ss_pred             cceeeeeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHH
Q 031203           76 GHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE  155 (164)
Q Consensus        76 G~~~~~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~  155 (164)
                      |++.+++++|+|+|++.++++||+.|  +++||+|||++++++||..+.++..+..+++|++|+++++ |++++++||++
T Consensus       160 G~~~~~~~~aiGsgs~~a~~~Le~~~--~~~ms~eea~~la~~al~~~~~~~~sg~~i~v~vi~~~~~-~~~l~~~ei~~  236 (241)
T 1iru_E          160 GTFVQCDARAIGSASEGAQSSLQELY--HKSMTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQN-FHMFTKEELEE  236 (241)
T ss_dssp             SCEEEBSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHCSSCCCTTSEEEEEECSSSC-CEECCHHHHHH
T ss_pred             CcEEecceEEECCCcHHHHHHHHHHh--ccCCCHHHHHHHHHHHHHHHhhccCCCCCEEEEEEECCCC-eEECCHHHHHH
Confidence            99999999999999999999999998  5889999999999999999998844444999999999987 99999999999


Q ss_pred             HHHHh
Q 031203          156 HLTAI  160 (164)
Q Consensus       156 ~l~~~  160 (164)
                      ++.++
T Consensus       237 ~~~~~  241 (241)
T 1iru_E          237 VIKDI  241 (241)
T ss_dssp             HHTTC
T ss_pred             HHHhC
Confidence            99754

>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=4.7e-37  Score=239.56  Aligned_cols=158  Identities=33%  Similarity=0.542  Sum_probs=147.4

Q ss_pred             CCchHHHHHHHHHHHHHH-HHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCccee
Q 031203            1 MTADARTLVQQARYEAAE-FRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFF   79 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~-~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~   79 (164)
                      +++|++.|+++++.+++. |+..++.+++++.+++.+++++|.|++++++|||+|++||||||+++||+||.+||+|++.
T Consensus        78 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~~a~~~~~~~~~~~~rp~~v~~lvaG~D~~~gp~Ly~idp~G~~~  157 (250)
T 1ryp_B           78 MGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYF  157 (250)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCCEEEEEEEEETTTEEEEEEECTTSCEE
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHhcCCcccceEEEEEEEEcCCCCcEEEEECCCCCEE
Confidence            468999999999999999 9999999999999999999999999999899999999999999976789999999999999


Q ss_pred             eeeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCC--------------CcE
Q 031203           80 GHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKEN--------------PEF  145 (164)
Q Consensus        80 ~~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~--------------~~~  145 (164)
                      +++++|+|+|++.++++||++|  +++||+|||++++++||..+++++.+..+++|++|++++              +.|
T Consensus       158 ~~~~~aiGsgs~~a~~~Le~~~--~~~ms~eea~~la~~al~~~~~~~~sg~~i~v~vi~~~~~~~~~~~~~~~~~~~~~  235 (250)
T 1ryp_B          158 PWKATAIGKGSVAAKTFLEKRW--NDELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRF  235 (250)
T ss_dssp             EBSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHCCSCCSTTTEEEEEECSCCGGGTSEESCSSCCCCSE
T ss_pred             eeceeEecCccHHHHHHHHHHh--ccCCCHHHHHHHHHHHHHHHhccccCCCCEEEEEEEccccccccccccccCCCCCe
Confidence            9999999999999999999998  589999999999999999999887754599999999862              359


Q ss_pred             EEcCHHHHHHHHHHh
Q 031203          146 RVLSIEEIDEHLTAI  160 (164)
Q Consensus       146 k~l~~~ei~~~l~~~  160 (164)
                      ++++++||++++.++
T Consensus       236 ~~l~~~ei~~~l~~~  250 (250)
T 1ryp_B          236 RKLTSQEINDRLEAL  250 (250)
T ss_dssp             EECCHHHHHHHHTTC
T ss_pred             EECCHHHHHHHHHhC
Confidence            999999999998753

>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=1.6e-36  Score=232.02  Aligned_cols=152  Identities=22%  Similarity=0.357  Sum_probs=142.0

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|+++++.+++.|+++++++++|+.+++++++.+|.+    +.|||+|++||||||  +||+||.+||+|++.+
T Consensus        56 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~----r~rp~~v~~lvaG~D--~gp~Ly~idp~G~~~~  129 (217)
T 1yar_H           56 LVGDAQVLVRYMKAELELYRLQRRVNMPIEAVATLLSNMLNQV----KYMPYMVQLLVGGID--TAPHVFSIDAAGGSVE  129 (217)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHT----TTSCCCEEEEEEEES--SSEEEEEECTTCCEEE
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhc----CCCCceEEEEEEEEC--CCCEEEEECCCCCeEe
Confidence            4689999999999999999999999999999999999999654    378999999999999  6899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEIDEHLTA  159 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~~~l~~  159 (164)
                      ++++|+|+|++.++++||+.|  +++||+|||++++++||..+.++|..++ +++|++|+++++ |++++++||++++.+
T Consensus       130 ~~~~aiGsgs~~a~~~Le~~~--~~~~s~eea~~la~~al~~~~~rd~~s~~~i~v~vi~~~~g-~~~~~~~ei~~~~~~  206 (217)
T 1yar_H          130 DIYASTGSGSPFVYGVLESQY--SEKMTVDEGVDLVIRAISAAKQRDSASGGMIDVAVITRKDG-YVQLPTDQIESRIRK  206 (217)
T ss_dssp             ESEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHCTTCCSCCEEEEEETTTE-EEECCHHHHHHHHHH
T ss_pred             cCEEEEcCCHHHHHHHHHhhc--ccCCCHHHHHHHHHHHHHHHHhccCCCCCcEEEEEEECCCC-EEEcCHHHHHHHHHH
Confidence            999999999999999999998  5899999999999999999999998765 899999999443 999999999999988


Q ss_pred             hh
Q 031203          160 IS  161 (164)
Q Consensus       160 ~~  161 (164)
                      +.
T Consensus       207 ~~  208 (217)
T 1yar_H          207 LG  208 (217)
T ss_dssp             HT
T ss_pred             HH
Confidence            75

>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=1.2e-36  Score=235.43  Aligned_cols=157  Identities=19%  Similarity=0.167  Sum_probs=146.5

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCC-----CeEEEeCCC
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECG-----PRLFKCDPA   75 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~g-----p~Ly~~dp~   75 (164)
                      +++|++.|+++++.+++.|++.++++++++.+++.|++++|.|+++. +|||+|++||||||+++|     |+||.+||+
T Consensus        48 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~-~rp~~v~~lvaG~D~~~g~~~~~p~Ly~idp~  126 (235)
T 1q5q_H           48 TAGIAIELVRLFAVELEHYEKIEGVPLTFDGKANRLASMVRGNLGAA-MQGLAVVPLLVGYDLDADDESRAGRIVSYDVV  126 (235)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHTTHHHH-TTTCCEEEEEEEECTTCSSTTSCEEEEEECTT
T ss_pred             cHHHHHHHHHHHHHHHHHhHHHhCCCCCHHHHHHHHHHHHHHHHHhh-hcccceEEEEEEEECCCCccCCCCEEEEECCC
Confidence            46899999999999999999999999999999999999999998765 899999999999998557     999999999


Q ss_pred             cceeee--eEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCe---E-----EEEEEEcCCCcE
Q 031203           76 GHFFGH--KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASE---I-----EVGVVSKENPEF  145 (164)
Q Consensus        76 G~~~~~--~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~---i-----ei~ii~~~~~~~  145 (164)
                      |++.++  +++|+|+|++.++++||+.|  +++||++||++++++||..+.++|..+++   +     +|++|++++  |
T Consensus       127 G~~~~~~~~~~aiGsgs~~a~~~Le~~~--~~~ms~eeA~~la~~al~~a~~~d~~sg~~~~i~~~~~ev~vi~~~g--~  202 (235)
T 1q5q_H          127 GGRYEERAGYHAVGSGSLFAKSALKKIY--SPDSDEETALRAAIESLYDAADDDSATGGPDLTRGIYPTAVTITQAG--A  202 (235)
T ss_dssp             SCEEECCSSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHCTTTCCCBTTTTBCCEEEEEETTE--E
T ss_pred             CceEEeCCCeEEECCCHHHHHHHHHhhc--CCCCCHHHHHHHHHHHHHHHHhhCcccCCcccccccccEEEEEeCCC--e
Confidence            999999  99999999999999999998  58999999999999999999999988764   2     999999874  9


Q ss_pred             EEcCHHHHHHHHHHhhc
Q 031203          146 RVLSIEEIDEHLTAISE  162 (164)
Q Consensus       146 k~l~~~ei~~~l~~~~~  162 (164)
                      ++++++||++++.++.+
T Consensus       203 ~~l~~~ei~~~~~~~~~  219 (235)
T 1q5q_H          203 VHVSEETTSELARRIVA  219 (235)
T ss_dssp             EECCHHHHHHHHHHHHH
T ss_pred             EEeCHHHHHHHHHHHHH
Confidence            99999999999998874

>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=1.8e-36  Score=240.39  Aligned_cols=155  Identities=25%  Similarity=0.395  Sum_probs=141.6

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|++++|.+++.|+++++++|+++.++++|++++|.||+++++|||+|++||||||+ +||+||++||+|++.+
T Consensus        81 ~~aD~~~l~~~lr~e~~~y~~~~~~~i~v~~lA~~l~~~l~~yt~~~~~rP~gv~~lvaG~D~-~Gp~Ly~iDp~G~~~~  159 (288)
T 3nzj_F           81 LIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGGVDK-NGAHLYMLEPSGSYWG  159 (288)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSCTTBCCCCEEEEEEEEET-TEEEEEEECTTSCEEE
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHcCCcCCHHHHHHHHHHHHHHHHHhccCCCceEEEEEEEEeC-CCCEEEEECCCCCEEE
Confidence            468999999999999999999999999999999999999999999999999999999999998 7899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhc-CCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEc--CCCcEEEcCHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMK-NDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSK--ENPEFRVLSIEEIDEH  156 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~-~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~--~~~~~k~l~~~ei~~~  156 (164)
                      ++++|+|+|++.++++||++++ ++++||++||++++++||..+++++..++ .+||+||++  +++.++.++.+++++.
T Consensus       160 ~~~~aiGsgs~~a~~~Lek~~~~~~~~ms~eEAv~la~~al~~a~~~~~~~~~~iev~vIt~~~~~~~~~~vp~~~~~~~  239 (288)
T 3nzj_F          160 YKGAATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEA  239 (288)
T ss_dssp             BSEEEESTTHHHHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHGGGGTTSEEEEEEEEEETTTSTTCCEECCHHHHHHH
T ss_pred             cCEEEEcCcHHHHHHHHHHhccccCCCCCHHHHHHHHHHHHHHHHhcccCCCCeEEEEEEEecCCCceEEECCHHHHHHH
Confidence            9999999999999999999922 27899999999999999999999887666 899999999  3445667777766654

>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=8.1e-37  Score=232.77  Aligned_cols=154  Identities=12%  Similarity=0.158  Sum_probs=144.5

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|+++++.+++.|+++++++++|+.+++++++++|.|+++    ||+|++||||||+++||+||.+||+|++.+
T Consensus        48 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~----p~~v~~lvaG~D~~~gp~Ly~idp~G~~~~  123 (212)
T 1ryp_L           48 GAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGA----GLSMGTMICGYTRKEGPTIYYVDSDGTRLK  123 (212)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTS----CCCBEEEEEEEETTTEEEEEEEETTCCEEE
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhhCCC----CceEEEEEEEEeCCCCCEEEEEcCCceeEe
Confidence            4689999999999999999999999999999999999999998763    999999999999657999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEIDEHLTA  159 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~~~l~~  159 (164)
                      ++++|+|+|++.++++||++|  +++||++||++++++||..+.++|..++ +++|++|++++  +++++++||++++.+
T Consensus       124 ~~~~aiGsgs~~a~~~Le~~~--~~~~s~eea~~la~~al~~~~~rd~~s~~~i~v~vi~~~g--~~~~~~~ei~~~~~~  199 (212)
T 1ryp_L          124 GDIFCVGSGQTFAYGVLDSNY--KWDLSVEDALYLGKRSILAAAHRDAYSGGSVNLYHVTEDG--WIYHGNHDVGELFWK  199 (212)
T ss_dssp             CSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTE--EEEEEEEEHHHHHHH
T ss_pred             cCCEEEcCCHHHHHHHHHhhC--CCCCCHHHHHHHHHHHHHHHHHhccccCCceEEEEEcCCc--eEEECHHHHHHHHHH
Confidence            999999999999999999998  5889999999999999999999997766 99999999874  999999999999988


Q ss_pred             hhc
Q 031203          160 ISE  162 (164)
Q Consensus       160 ~~~  162 (164)
                      +.+
T Consensus       200 ~~~  202 (212)
T 1ryp_L          200 VKE  202 (212)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            764

>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=4.5e-36  Score=233.31  Aligned_cols=157  Identities=24%  Similarity=0.376  Sum_probs=143.3

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|+++++.+++.|+++++++++++.+++++++++|.||+++++|||+|++||||||+ +||+||.+||+|++.+
T Consensus        77 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rp~~v~~lvaG~D~-~gp~Ly~idp~G~~~~  155 (244)
T 1ryp_G           77 LIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGGVDK-NGAHLYMLEPSGSYWG  155 (244)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSCTTBCCCCEEEEEEEEET-TEEEEEEECTTSCEEE
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCccCceEEEEEEEEeC-CcCEEEEECCCCCEEE
Confidence            468999999999999999999999999999999999999999999988999999999999997 7999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHh---hcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEc-CCCcEEEcCHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKK---MKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSK-ENPEFRVLSIEEIDE  155 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~---~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~-~~~~~k~l~~~ei~~  155 (164)
                      ++++|+|+|++.++++||+.   |  +++||++||++++++||..+.++|..++ +++|++|++ +..+++.+.|+++.+
T Consensus       156 ~~~~aiG~gs~~a~~~Le~~~~~~--~~~ms~eea~~la~~al~~~~~~d~~s~~~iev~vi~~~~~~g~~~~~~~~~~~  233 (244)
T 1ryp_G          156 YKGAATGKGRQSAKAELEKLVDHH--PEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQ  233 (244)
T ss_dssp             BSEEEESTTHHHHHHHHHHHHHHC--TTCCCHHHHHHHHHHHHHHHGGGGTTSCEEEEEEEEETTTTTTSEEECCTHHHH
T ss_pred             eeEEEECCChHHHHHHHHHhHhhc--CCCCCHHHHHHHHHHHHHHHHhccCCCCCeEEEEEEEecCCCCeeeeChHHHHH
Confidence            99999999999999999997   7  5789999999999999999999998776 899999997 222367777777766


Q ss_pred             HHHHh
Q 031203          156 HLTAI  160 (164)
Q Consensus       156 ~l~~~  160 (164)
                      ...+.
T Consensus       234 ~~~~~  238 (244)
T 1ryp_G          234 EAIDF  238 (244)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55544

>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=4.2e-37  Score=233.19  Aligned_cols=152  Identities=14%  Similarity=0.193  Sum_probs=142.4

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|+++++.+++.|+++++++++|+.+++++++.+|.|++     ||++++||||||+++||+||.+||+|++.+
T Consensus        48 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~-----p~~~~~lvaG~D~~~gp~ly~~d~~G~~~~  122 (205)
T 1iru_H           48 SAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEMCYRYRE-----DLMAGIIIAGWDPQEGGQVYSVPMGGMMVR  122 (205)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHTTT-----TCCEEEEEEEEETTTEEEEEEECTTSCCEE
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhcCc-----CccEEEEEEEEeCCCCCEEEEECCCCcEEe
Confidence            468999999999999999999999999999999999999988864     999999999999867899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEIDEHLTA  159 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~~~l~~  159 (164)
                      ++++++|+|++.++++||++|  +++||++||++++++||..+.++|..++ +++|++|++++..+++++++||++++.+
T Consensus       123 ~~~~a~Gsgs~~a~~~Le~~~--~~~~s~eea~~l~~~al~~~~~~d~~s~~~i~v~vi~~~g~~~~~l~~~ei~~~~~~  200 (205)
T 1iru_H          123 QSFAIGGSGSSYIYGYVDATY--REGMTKEECLQFTANALALAMERDGSSGGVIRLAAIAESGVERQVLLGDQIPKFAVA  200 (205)
T ss_dssp             CSEEEESGGGGGGHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHBTTCCSCEEEEEEETTEEEEEEECGGGSCCCCCC
T ss_pred             cCEEEECCCHHHHHHHHHHhc--CCCCCHHHHHHHHHHHHHHHHHhccccCCcEEEEEEeCCCeEEEEeChHHhhHHHhh
Confidence            999999999999999999998  5789999999999999999999997766 9999999998766899999999887654

>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=3.1e-36  Score=228.23  Aligned_cols=153  Identities=14%  Similarity=0.179  Sum_probs=143.4

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|+++++.+++.|++.++++++++.+++++++.+|.|++    +||+|++||||||+ +||+||.+||+|++.+
T Consensus        48 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~r~----~~~~v~~lvaG~D~-~gp~Ly~idp~G~~~~  122 (204)
T 1iru_L           48 GAADCSFWERLLARQCRIYELRNKERISVAAASKLLANMVYQYKG----MGLSMGTMICGWDK-RGPGLYYVDSEGNRIS  122 (204)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHTTTT----SCCCBEEEEEEECS-SSEEEEEEESSSCEEE
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhCC----CCeeEEEEEEEEeC-CCCEEEEECCCCcEEE
Confidence            468999999999999999999999999999999999999988753    49999999999998 7999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEIDEHLTA  159 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~~~l~~  159 (164)
                      ++++|+|+|++.++++||++|  +++||++||++++++||..+.++|..++ +++|++|++++  |++++++||++++.+
T Consensus       123 ~~~~aiG~gs~~a~~~Le~~~--~~~~s~eea~~l~~~al~~~~~rd~~s~~~i~v~vi~~~g--~~~l~~~ei~~~~~~  198 (204)
T 1iru_L          123 GATFSVGSGSVYAYGVMDRGY--SYDLEVEQAYDLARRAIYQATYRDAYSGGAVNLYHVREDG--WIRVSSDNVADLHEK  198 (204)
T ss_dssp             CSEEEESTTHHHHHHHHHTTC--CTTCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEECSSC--EEEEEEEEHHHHHHH
T ss_pred             eCCEEEEcCHHHHHHHHhccC--CCCCCHHHHHHHHHHHHHHHHHhCccCCCceEEEEEeCCc--eEEeCHHHHHHHHHH
Confidence            999999999999999999998  5789999999999999999999997655 99999999874  999999999999998


Q ss_pred             hhc
Q 031203          160 ISE  162 (164)
Q Consensus       160 ~~~  162 (164)
                      +..
T Consensus       199 ~~~  201 (204)
T 1iru_L          199 YSG  201 (204)
T ss_dssp             HTC
T ss_pred             hcc
Confidence            863

>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=4.8e-36  Score=235.02  Aligned_cols=159  Identities=14%  Similarity=0.221  Sum_probs=140.8

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHHHH-HHHhhhhccCccccceeeEEEEEc--C-CCCCeEEEeCCC
Q 031203            1 MTADARTLVQQARYEAAEFRFKYG-YEMPVDVLAKWIAD-KSQVYTQHAYMRPLGVVAMVLSID--E-ECGPRLFKCDPA   75 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~-~~i~~~~l~~~ls~-~~q~yt~~~~~rP~gv~~iiaG~d--~-~~gp~Ly~~dp~   75 (164)
                      +++|++.|+++++.+++.|++.++ ++++++.+++++++ +.|.|+  ++.|||+|++||||||  + .+||+||++||+
T Consensus        67 ~~aD~~~l~~~~~~~~~~~~~~~~~~~i~v~~la~~l~~~l~q~yt--~~~rP~~v~~lvaG~D~~~~~~gp~Ly~idp~  144 (259)
T 1q5q_A           67 KYNEFENLRRAGIVHADMRGYSYDRRDVTGRSLANAYAQTLGTIFT--EQPKPYEVEICVAEVGRVGSPKAPQLYRITYD  144 (259)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHHHHHHHHHH--HSSSCCCEEEEEEECCCSSCCCCCEEEEEETT
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHhc--cCCCCceEEEEEEEEcccCCCCCCEEEEECCC
Confidence            468999999999999999999998 49999999999999 788898  3689999999999999  2 489999999999


Q ss_pred             ccee-eeeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhh-----hccCCCCeEEEEEEEcCC--CcEEE
Q 031203           76 GHFF-GHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVL-----QEDFKASEIEVGVVSKEN--PEFRV  147 (164)
Q Consensus        76 G~~~-~~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~-----~~d~~~~~iei~ii~~~~--~~~k~  147 (164)
                      |++. .++++|+|++++.++++||++|  +++||++||++++++||..++     ++|+...+++|++|++++  .+|++
T Consensus       145 G~~~~~~~~~aiG~gs~~a~~~Le~~~--~~~ms~eea~~la~~al~~~~~~~~~~rd~sg~~iev~vi~~~~~~~~~~~  222 (259)
T 1q5q_A          145 GSIVDEQHFVVMGGTTEPIATAMRESY--RADLDLEAAVGIAVNALRQGGAGEGEKRNVDVASLEVAVLDQSRPRRAFRR  222 (259)
T ss_dssp             SCEEEESSEEEESSSHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHTTCC--------CCSSCSEEEEEETTSSSCCEEE
T ss_pred             CceeeCCCEEEECCChHHHHHHHHhhc--cCCCCHHHHHHHHHHHHHHHhhcccccccCCCCcEEEEEEECCCCcCCeEE
Confidence            9999 7899999999999999999998  588999999999999999999     888844499999999985  24999


Q ss_pred             cCHHHHHHHHHHhhcc
Q 031203          148 LSIEEIDEHLTAISER  163 (164)
Q Consensus       148 l~~~ei~~~l~~~~~~  163 (164)
                      ++++||++++.++.++
T Consensus       223 l~~~ei~~~~~~~~~~  238 (259)
T 1q5q_A          223 IAGTALEQLVPAEPAA  238 (259)
T ss_dssp             CCHHHHHTTSCCC---
T ss_pred             CCHHHHHHHHHHhhhc
Confidence            9999999999887643

>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=6.5e-36  Score=237.15  Aligned_cols=155  Identities=12%  Similarity=0.158  Sum_probs=146.0

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|+++++.+|+.|+++++++++|+.+++++++++|.|++    +||++++||||||+++||+||.+||+|++.+
T Consensus       123 ~~AD~~~l~~~lr~~~~~y~~~~~~~isv~~la~~ls~~l~~~r~----~p~~v~~lvaG~D~~~gp~Ly~iDp~G~~~~  198 (287)
T 3nzj_K          123 GAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKG----AGLSMGTMICGYTRKEGPTIYYVDSDGTRLK  198 (287)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTT----SCCCEEEEEEEEETTTEEEEEEEETTCCEEE
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhcC----CCceEEEEEEEEcCCCCCEEEEECCCceEEE
Confidence            468999999999999999999999999999999999999988765    3999999999999658999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEIDEHLTA  159 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~~~l~~  159 (164)
                      ++++|+|+|++.++++||+.|  +++||++||++++++||..+.+||..++ +++|++|++++  |++++++||++++.+
T Consensus       199 ~~~~AiGsgs~~a~~~Le~~y--~~dms~eEAi~la~~aL~~a~~rD~~sg~~i~V~vItkdg--~~~l~~~ev~~~l~~  274 (287)
T 3nzj_K          199 GDIFCVGSGQTFAYGVLDSNY--KWDLSVEDALYLGKRSILAAAHRDAYSGGSVNLYHVTEDG--WIYHGNHDVGELFWK  274 (287)
T ss_dssp             CSEEEESTTHHHHHHHHHTSC--CTTCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTE--EEEEEEEEHHHHHHH
T ss_pred             cCeEEEecchHHHHHHHHHhh--cCCCCHHHHHHHHHHHHHHHHhhCcCCCCceEEEEEeCCC--EEEeCHHHHHHHHHH
Confidence            999999999999999999998  5899999999999999999999999887 99999999984  999999999999998


Q ss_pred             hhcc
Q 031203          160 ISER  163 (164)
Q Consensus       160 ~~~~  163 (164)
                      +.|+
T Consensus       275 ~~e~  278 (287)
T 3nzj_K          275 VKEE  278 (287)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            8853

>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=4e-35  Score=233.29  Aligned_cols=157  Identities=19%  Similarity=0.167  Sum_probs=146.4

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCC-----CeEEEeCCC
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECG-----PRLFKCDPA   75 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~g-----p~Ly~~dp~   75 (164)
                      +++|++.|+++++.+++.|++.++++++++.++++|++++|.|+++. .|||+|++||||||+++|     |+||++||+
T Consensus       113 ~~aD~~~l~~~~r~~~~~y~~~~g~~isv~~la~~la~~l~~~~~~~-~rp~~v~lLvaG~D~~~g~~~~~p~Ly~iDp~  191 (294)
T 1q5r_H          113 TAGIAIELVRLFAVELEHYEKIEGVPLTFDGKANRLASMVRGNLGAA-MQGLAVVPLLVGYDLDADDESRAGRIVSYDVV  191 (294)
T ss_dssp             BHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHHH-TTTTCEEEEEEEECTTCSCTTSCEEEEEECSS
T ss_pred             cHHHHHHHHHHHHHHHHHhhHhhCCCCCHHHHHHHHHHHHHHHHhhh-cCCcceEEEEEEEeCCCCcCCCCCEEEEECCC
Confidence            36899999999999999999999999999999999999999998765 899999999999998546     999999999


Q ss_pred             cceeee--eEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCe---E-----EEEEEEcCCCcE
Q 031203           76 GHFFGH--KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASE---I-----EVGVVSKENPEF  145 (164)
Q Consensus        76 G~~~~~--~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~---i-----ei~ii~~~~~~~  145 (164)
                      |++.++  +++|+|+|++.++++||++|  +++||++||++++++||..+.++|+.++.   +     +|++|++++  |
T Consensus       192 G~~~e~~~~~~AiGsgs~~a~~~Le~~y--~~~ms~eEAi~la~~aL~~a~~rD~~sG~~~~ir~i~~ev~vI~~~g--~  267 (294)
T 1q5r_H          192 GGRYEERAGYHAVGSGSLFAKSALKKIY--SPDSDEETALRAAIESLYDAADDDSATGGPDLTRGIYPTAVTITQAG--A  267 (294)
T ss_dssp             SCEEECCSSEEEESTTHHHHHHHHHHHC--CSSCCHHHHHHHHHHHHHHHHHHCTTTCCCBTTTTBCCEEEEEETTE--E
T ss_pred             CeEEecCCCeEEEecCcHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHHhhccccCCchhhcccCCEEEEEECCC--E
Confidence            999999  89999999999999999998  58999999999999999999999988753   5     999999874  9


Q ss_pred             EEcCHHHHHHHHHHhhc
Q 031203          146 RVLSIEEIDEHLTAISE  162 (164)
Q Consensus       146 k~l~~~ei~~~l~~~~~  162 (164)
                      ++++++||++++.++.+
T Consensus       268 ~~l~~~ei~~~l~~i~~  284 (294)
T 1q5r_H          268 VHVSEETTSELARRIVA  284 (294)
T ss_dssp             EECCHHHHHHHHHHHCC
T ss_pred             EEcCHHHHHHHHHHHHH
Confidence            99999999999999874

>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=9.4e-35  Score=219.08  Aligned_cols=144  Identities=15%  Similarity=0.211  Sum_probs=133.0

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcC-CCCCeEEEeCCCccee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDE-ECGPRLFKCDPAGHFF   79 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~-~~gp~Ly~~dp~G~~~   79 (164)
                      +++|++.|+++++.+++.|+++++++++|+.+++++++.+|.|++.  ++||+|++||||||+ ++||+||.+||+|++.
T Consensus        49 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~l~~~~~~--r~p~~v~~lvaG~D~~~~~p~Ly~idp~G~~~  126 (198)
T 1ryp_K           49 EAGDTVQFAEYIQANIQLYSIREDYELSPQAVSSFVRQELAKSIRS--RRPYQVNVLIGGYDKKKNKPELYQIDYLGTKV  126 (198)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHTTS--SSCCCEEEEEEEEETTTTEEEEEEECTTCCEE
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhccc--CCCceEEEEEEEEeCCCCCcEEEEECCCCCEE
Confidence            4689999999999999999999999999999999999999887642  359999999999996 4799999999999999


Q ss_pred             eeeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCH
Q 031203           80 GHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSI  150 (164)
Q Consensus        80 ~~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~  150 (164)
                      +++++|+|+|++.++++||+.|  +++||+|||++++++||..+.++|..++ +++|++|++++  ++++++
T Consensus       127 ~~~~~aiG~g~~~a~~~Le~~~--~~~~s~eea~~l~~~al~~~~~~d~~s~~~i~v~vi~~~g--~~~~~~  194 (198)
T 1ryp_K          127 ELPYGAHGYSGFYTFSLLDHHY--RPDMTTEEGLDLLKLCVQELEKRMPMDFKGVIVKIVDKDG--IRQVDD  194 (198)
T ss_dssp             ECSEEECTTHHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHCSBCCCCEEEEEEETTE--EEEECC
T ss_pred             ECCEEEEcccHHHHHHHHHhhc--CCCCCHHHHHHHHHHHHHHHHHhCccCCCceEEEEEcCCC--EEEecc
Confidence            9999999999999999999998  5789999999999999999999997766 99999999974  887765

>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=9.8e-35  Score=230.84  Aligned_cols=157  Identities=15%  Similarity=0.090  Sum_probs=136.3

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCC-----CeEEEeCCC
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECG-----PRLFKCDPA   75 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~g-----p~Ly~~dp~   75 (164)
                      +++|++.|+++++.+++.|++.++++++++.+++.+++++|.|++ .++|||+|++||||||+.++     |+||++||+
T Consensus       105 ~~aD~~~l~~~lr~~~~~y~~~~~~~i~v~~la~~la~~l~~~~~-~~~rpf~v~~lvaG~D~~g~~~~~~p~Ly~iDp~  183 (291)
T 2jay_A          105 TAAVAVEFARLYAVELEHYEKLEGVPLTFAGKINRLAIMVRGNLA-AAMQGLLALPLLAGYDIHASDPQSAGRIVSFDAA  183 (291)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHTCHH-HHHHTCCCEEEEEEECTTCSCSTTCEEEEEECTT
T ss_pred             cHHHHHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHHhhh-hhccccceeEEEEEEeCCCCcCCCCCEEEEECCC
Confidence            468999999999999999999999999999999999999999876 46899999999999998555     899999999


Q ss_pred             ccee--eeeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeE--------EEEEEEcCCCcE
Q 031203           76 GHFF--GHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEI--------EVGVVSKENPEF  145 (164)
Q Consensus        76 G~~~--~~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~i--------ei~ii~~~~~~~  145 (164)
                      |++.  +++++|+|+|++.++++||+.|  +++||++||++++++||..++++|+.++++        +|++|++++  |
T Consensus       184 G~~~e~~~~~~aiGsgs~~a~~~Le~~~--~~~ms~eEAi~la~~aL~~a~~~D~~sg~~e~vr~~~~~v~vi~~dg--~  259 (291)
T 2jay_A          184 GGWNIEEEGYQAVGSGSLFAKSSMKKLY--SQVTDGDSGLRVAVEALYDAADDDSATGGPDLVRGIFPTAVIIDADG--A  259 (291)
T ss_dssp             SCEEECSSSEEEESTTHHHHHHHHHHHG--GGCCSHHHHHHHHHHHHHHC----------------CCEEEEEETTE--E
T ss_pred             CcEEecCCCEEEEecCHHHHHHHHHHhc--CCCCCHHHHHHHHHHHHHHHHhhCCCCCCcccccccCCEEEEEECCC--e
Confidence            9999  7899999999999999999999  578999999999999999999999988876        599999984  9


Q ss_pred             EEcCHHHHHHHHHHhhc
Q 031203          146 RVLSIEEIDEHLTAISE  162 (164)
Q Consensus       146 k~l~~~ei~~~l~~~~~  162 (164)
                      ++++++||++++.++.+
T Consensus       260 ~~l~~~ei~~~~~~~~~  276 (291)
T 2jay_A          260 VDVPESRIAELARAIIE  276 (291)
T ss_dssp             EECCHHHHHHHHHHC--
T ss_pred             EEcCHHHHHHHHHHHHH
Confidence            99999999999998874

>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=1.8e-35  Score=226.36  Aligned_cols=150  Identities=13%  Similarity=0.171  Sum_probs=139.0

Q ss_pred             CchHHHHHHHHHHHHHHHHH-HhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            2 TADARTLVQQARYEAAEFRF-KYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         2 ~~D~~~l~~~~~~~~~~~~~-~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      ++|++.|+++++.+++.|++ +++++++++.+++++++.+  |++++++|||+|++||||||+ +||+||.+||+|++.+
T Consensus        57 ~aD~~~l~~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~l--y~~r~~~~P~~v~~lvaG~D~-~gp~Ly~id~~G~~~~  133 (219)
T 1iru_N           57 YADFQYLKQVLGQMVIDEELLGDGHSYSPRAIHSWLTRAM--YSRRSKMNPLWNTMVIGGYAD-GESFLGYVDMLGVAYE  133 (219)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCSSCCCCHHHHHHHHHHHH--HHHHHTTCCCCEEEEEEEEET-TEEEEEEECSSCCEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH--HHhcccCCCceEEEEEEEEEC-CCCEEEEECCCCCeEE
Confidence            68999999999999999998 9999999999999999998  667777999999999999998 6999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEIDEH  156 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~~~  156 (164)
                      ++++|+|+|++.++++||+.|++.++||++||++++++||..+.++|..++ +++|++|++++  ++++++++|+..
T Consensus       134 ~~~~aiGsgs~~a~~~Le~~~~~~~~mt~eea~~l~~~al~~~~~~d~~sg~~i~v~vi~~~g--~~~~~~~~i~~~  208 (219)
T 1iru_N          134 APSLATGYGAYLAQPLLREVLEKQPVLSQTEARDLVERCMRVLYYRDARSYNRFQTATVTEKG--VEIEGPLSTETN  208 (219)
T ss_dssp             CSEEECTTHHHHTHHHHHHHHTSCSCCCHHHHHHHHHHHHHHHHHHBTTCCSCEEEEEEETTE--EEEEEEECCCCC
T ss_pred             CCeEEECccHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHHHHHHhcCcCCCcEEEEEEcCCC--EEEcCCeeccch
Confidence            999999999999999999999532399999999999999999999998766 99999999975  899999887654

>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=1.1e-35  Score=229.62  Aligned_cols=153  Identities=12%  Similarity=0.194  Sum_probs=140.5

Q ss_pred             CCchHHHHHHHHHHHHHHHHH-----HhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCC
Q 031203            1 MTADARTLVQQARYEAAEFRF-----KYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPA   75 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~-----~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~   75 (164)
                      +++|++.|+++++.+++.|++     +++++++++.+++++++.+  |++++++|||+|++||||||+++||+||.+||+
T Consensus        56 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~l--y~~r~~~~P~~v~~lvaG~D~~~gp~Ly~id~~  133 (233)
T 1ryp_N           56 DISDMQHIERLLKDLVTENAYDNPLADAEEALEPSYIFEYLATVM--YQRRSKMNPLWNAIIVAGVQSNGDQFLRYVNLL  133 (233)
T ss_dssp             EHHHHHHHHHHHHHHHHHHHTTCTTTTTTTSCCHHHHHHHHHHHH--HHHHHTTCCCCEEEEEEEECTTSCEEEEEEETT
T ss_pred             cHHHHHHHHHHHHHHHHHHhhccchhhcCCCCCHHHHHHHHHHHH--HHhcCCCCCceEEEEEEEEcCCCCEEEEEECCC
Confidence            368999999999999999999     9999999999999999998  777777899999999999998569999999999


Q ss_pred             cceeeeeEEeecCChHHHHHHHHHhhcCCC---CCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHH
Q 031203           76 GHFFGHKATSAGLKEQEAINFLEKKMKNDP---AFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIE  151 (164)
Q Consensus        76 G~~~~~~~~aiG~~s~~~~~~Le~~~~~~~---~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~  151 (164)
                      |++.+++++|+|+|++.++++||+.|++.+   +||+|||++++++||..+.++|+.++ +++|++|+++++ +++++++
T Consensus       134 G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~~~~~ms~eea~~la~~al~~~~~rd~~sg~~i~v~vi~~~~g-~~~~~~~  212 (233)
T 1ryp_N          134 GVTYSSPTLATGFGAHMANPLLRKVVDRESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKNTG-LTFKKNL  212 (233)
T ss_dssp             CCEECCSEEECTHHHHHHHHHHTTTCSSGGGGGGCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTTE-EEEEEEE
T ss_pred             cCeEEcCEEEECcCHHHHHHHHHHhhccccccCCCCHHHHHHHHHHHHHHHHHhcccCCCcEEEEEEECCCC-eEEcChH
Confidence            999999999999999999999999984211   89999999999999999999998776 999999999843 9999998


Q ss_pred             HHHHH
Q 031203          152 EIDEH  156 (164)
Q Consensus       152 ei~~~  156 (164)
                      ||+++
T Consensus       213 ~i~~~  217 (233)
T 1ryp_N          213 QVENM  217 (233)
T ss_dssp             ECCSC
T ss_pred             hcccc
Confidence            88766

>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=1.5e-34  Score=223.46  Aligned_cols=144  Identities=17%  Similarity=0.294  Sum_probs=134.3

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      ++||++.|+++++.+++.|+++++++++++.+++++++.++.|     .+||++++||||||+ +||+||++||+|++.+
T Consensus        48 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~l~~~-----~~p~~v~llvaG~D~-~gp~Ly~idp~G~~~~  121 (234)
T 3unf_H           48 VAADTEMTTRMAASKMELHALSTGREPRVATVTRILRQTLFRY-----QGHVGASLVVGGVDL-NGPQLYEVHPHGSYSR  121 (234)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHCSCCCHHHHHHHHHHHHHHT-----TTCSCEEEEEEEEET-TEEEEEEECTTSCEEE
T ss_pred             cHHHHHHHHHHHHHHHHhhHHhcCCCCCHHHHHHHHHHHHHhc-----CCCccEEEEEEEEeC-CCCEEEEECCCCCEEe
Confidence            4689999999999999999999999999999999999998654     469999999999998 7999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEID  154 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~  154 (164)
                      ++++|+|+|++.++++||++|  +++||+|||++++++||..+..+|+.++ +++|++|++++  ++++.+.+|+
T Consensus       122 ~~~~aiGsgs~~a~~~Le~~~--~~~ms~eeA~~la~~al~~~~~~D~~sg~~iev~vi~~dg--~~~l~~~~i~  192 (234)
T 3unf_H          122 LPFTALGSGQGAAVALLEDRF--QPNMTLEAAQELLVEAITAGILSDLGSGGNVDACVITAGG--AKLQRALSTP  192 (234)
T ss_dssp             CSEEEEETTHHHHHHHHHHHC--CSSCCHHHHHHHHHHHHHHHHHHBTTCCSCEEEEEEESSC--EEEEEEEECC
T ss_pred             ccEEEEcCCchhhHHHHHhcc--CCCCCHHHHHHHHHHHHHHHHhhcCCCCCcEEEEEEECCC--EEEeCceecc
Confidence            999999999999999999998  5899999999999999999999998776 99999999984  8988887764

>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=9.3e-34  Score=215.92  Aligned_cols=139  Identities=15%  Similarity=0.270  Sum_probs=129.0

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      ++||++.|+++++.+++.|+++++++++|+.+++++++.+  |+++  .|||+|++||||||++++|+||.+||+|++.+
T Consensus        57 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~--y~~r--~~P~~v~~lvaG~D~~g~p~Ly~id~~G~~~~  132 (213)
T 1iru_M           57 FHGDCLTLTKIIEARLKMYKHSNNKAMTTGAIAAMLSTIL--YSRR--FFPYYVYNIIGGLDEEGKGAVYSFDPVGSYQR  132 (213)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHH--HHTT--TSCCCEEEEEEEECTTSCEEEEEECTTSCEEE
T ss_pred             cHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHH--HhhC--CCCceEEEEEEEEcCCCCEEEEEECCCCCEEE
Confidence            4689999999999999999999999999999999999999  7764  79999999999999756699999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhc-------CCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCC
Q 031203           81 HKATSAGLKEQEAINFLEKKMK-------NDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENP  143 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~-------~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~  143 (164)
                      ++++|+|+|++.++++||+.|+       ++++||+|||++++++||..+.++|..++ +++|++|++++.
T Consensus       133 ~~~~aiGsg~~~a~~~Le~~~~~~~~~~~~~~~~s~eea~~l~~~al~~~~~~d~~s~~~i~v~vi~~~g~  203 (213)
T 1iru_M          133 DSFKAGGSASAMLQPLLDNQVGFKNMQNVEHVPLSLDRAMRLVKDVFISAAERDVYTGDALRICIVTKEGI  203 (213)
T ss_dssp             ESEEEEETTHHHHHHHHHHHTTCCSCSSCCCCCCCHHHHHHHHHHHHHHHHHHBTTSCSEEEEEEEETTEE
T ss_pred             CCEEEEeeCHHHHHHHHhhccccccccccCCCCCCHHHHHHHHHHHHHHHHHhCCccCCcEEEEEEcCCCe
Confidence            9999999999999999999943       25899999999999999999999998766 999999999864

>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=8.3e-35  Score=219.53  Aligned_cols=149  Identities=16%  Similarity=0.192  Sum_probs=136.6

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|+++++.+++.|+++++++++++.+++++++.+|.|     .|||+|++||||||+++||+||.  |+|++..
T Consensus        48 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a~~l~~~l~~~-----~~p~~v~~lvaG~D~~~~p~ly~--p~G~~~~  120 (199)
T 3unf_N           48 SAADAQAIADMAAYQLELHGLELEEPPLVLAAANVVKNISYKY-----REDLLAHLIVAGWDQREGGQVYG--TMGGMLI  120 (199)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHT-----TTTCCCCEEEEEEETTTEEEEEE--CGGGCCE
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhc-----CCCceEEEEEEEEeCCCCcEEEE--ECCCcee
Confidence            4689999999999999999999999999999999999999654     46999999999999867899999  9999877


Q ss_pred             ee-EEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHHHHHH
Q 031203           81 HK-ATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEIDEHLT  158 (164)
Q Consensus        81 ~~-~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~~~l~  158 (164)
                      +. ++++|+|++.++++||++|  +++||+|||++++++||..+.++|..++ +++|++|++++..|++++++||++++.
T Consensus       121 ~~~~~~~Gsgs~~a~~~Le~~~--~~~ms~eea~~la~~al~~~~~~d~~sg~~i~v~vi~~~g~~~~~l~~~ei~~~~~  198 (199)
T 3unf_N          121 RQPFTIGGSGSSYIYGYVDAAY--KPGMTPEECRRFTTNAITLAMNRDGSSGGVIYLVTITAAGVDHRVILGDELPKFYD  198 (199)
T ss_dssp             ECSEEEEEGGGGGGHHHHHHHC--CSSCCHHHHHHHHHHHHHHHHHHCTTCCSCEEEEEECSSCEEEEEECGGGSCCCCC
T ss_pred             cCCEEEEccCHHHHHHHHHhhc--CCCCCHHHHHHHHHHHHHHHHHhccccCCCeEEEEEcCCCEEEEEcCcccCccccc
Confidence            75 6667999999999999998  5899999999999999999999999876 999999999987799999999987653

>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=3.9e-33  Score=211.22  Aligned_cols=142  Identities=17%  Similarity=0.222  Sum_probs=129.4

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcC-CCCCeEEEeCCCccee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDE-ECGPRLFKCDPAGHFF   79 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~-~~gp~Ly~~dp~G~~~   79 (164)
                      +++|++.|+++++.+++.|+++++++++|+.+++++++.+  |+++.+  ||+|++||||||+ ++||+||.+||+|++.
T Consensus        55 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~--y~~~~~--P~~v~~lvaG~D~~~~gp~Ly~idp~G~~~  130 (204)
T 1ryp_J           55 LATDVTTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSL--YERRFG--PYFVGPVVAGINSKSGKPFIAGFDLIGCID  130 (204)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHH--HTTTTS--CCCEEEEEEEECTTTCCEEEEEECTTCCEE
T ss_pred             cHHHHHHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHH--HHhcCC--CceEEEEEEEEeCCCCceEEEEECCCCCcc
Confidence            4689999999999999999999999999999999999999  887643  9999999999996 4789999999999997


Q ss_pred             ee-eEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEc
Q 031203           80 GH-KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVL  148 (164)
Q Consensus        80 ~~-~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l  148 (164)
                      .+ .++|+|+|++.++++||+.|  +++||+|||++++++||..+.++|..++ +++|++|++++..++.+
T Consensus       131 ~~~~~~aiG~gs~~a~~~Le~~~--~~~~s~eea~~l~~~al~~~~~~d~~s~~~i~v~vi~~~g~~~~~~  199 (204)
T 1ryp_J          131 EAKDFIVSGTASDQLFGMCESLY--EPNLEPEDLFETISQALLNAADRDALSGWGAVVYIIKKDEVVKRYL  199 (204)
T ss_dssp             CCSSEEEEETTHHHHHHHHHHHC--CSSCCHHHHHHHHHHHHHHHHTTBTTSCSCEEEEEEESSCEEEEEE
T ss_pred             ccCceeEeccCHHHHHHHHhhhc--CCCcCHHHHHHHHHHHHHHHHHhCcccCCcEEEEEEcCCCEEEEEe
Confidence            76 56999999999999999998  5899999999999999999999998766 99999999987545544

>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=9.2e-35  Score=228.55  Aligned_cols=153  Identities=12%  Similarity=0.194  Sum_probs=140.3

Q ss_pred             CCchHHHHHHHHHHHHHHHHH-----HhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCC
Q 031203            1 MTADARTLVQQARYEAAEFRF-----KYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPA   75 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~-----~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~   75 (164)
                      +++|++.|++++|.+++.|++     .++++++++.+++++++++  |++++++|||+|++||||||+++||+||.+||+
T Consensus        89 ~~aD~~~l~~~lr~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~l--y~~r~~~~P~~v~~lvaG~D~~~gp~Ly~idp~  166 (266)
T 1g0u_M           89 DISDMQHIERLLKDLVTENAYDNPLADAEEALEPSYIFEYLATVM--YQRRSKMNPLWNAIIVAGVQSNGDQFLRYVNLL  166 (266)
T ss_dssp             EHHHHHHHHHHHHHHHHHHHTTCTTTTTTTSCCHHHHHHHHHHHH--HHHHHTTCCCCEEEEEEEECTTSCEEEEEEETT
T ss_pred             CHHHHHHHHHHHHHHHHHhhhccchhhcCCCCCHHHHHHHHHHHH--HHhccCCCCceEEEEEEEEcCCCCEEEEEECCC
Confidence            368999999999999999998     9999999999999999998  777777899999999999998569999999999


Q ss_pred             cceeeeeEEeecCChHHHHHHHHHhhcCCC---CCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHH
Q 031203           76 GHFFGHKATSAGLKEQEAINFLEKKMKNDP---AFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIE  151 (164)
Q Consensus        76 G~~~~~~~~aiG~~s~~~~~~Le~~~~~~~---~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~  151 (164)
                      |++.+++++|+|+|++.++++||+.|+..+   +||+|||++++++||..+.++|+.++ +++|++|+++++ +++++++
T Consensus       167 G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~~~~~ms~eeA~~la~~al~~a~~rd~~sg~~i~v~vI~k~~g-~~~~~~~  245 (266)
T 1g0u_M          167 GVTYSSPTLATGFGAHMANPLLRKVVDRESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKNTG-LTFKKNL  245 (266)
T ss_dssp             CCEECCSEEECTHHHHTHHHHHTTTCSSGGGGGGCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTTE-EEEEEEE
T ss_pred             CCEEeCCEEEEccCHHHHHHHHHHhhcccccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCcEEEEEEECCCC-eEEcCHH
Confidence            999999999999999999999999984211   89999999999999999999998776 999999999843 9999998


Q ss_pred             HHHHH
Q 031203          152 EIDEH  156 (164)
Q Consensus       152 ei~~~  156 (164)
                      ||+++
T Consensus       246 ei~~~  250 (266)
T 1g0u_M          246 QVENM  250 (266)
T ss_dssp             ECCCC
T ss_pred             Hhhhh
Confidence            88765

>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=4.4e-33  Score=213.62  Aligned_cols=139  Identities=17%  Similarity=0.330  Sum_probs=128.5

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCccee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYG-YEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFF   79 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~-~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~   79 (164)
                      +++|++.|+++++.+++.|++.++ ++++++.+++++++.+  |++  +.|||+|++||||||++++|+||.+||+|++.
T Consensus        57 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~l--y~~--r~~P~~v~~ivaG~D~~g~p~Ly~~dp~G~~~  132 (222)
T 1ryp_M           57 FAADGDALVKRFKNSVKWYHFDHNDKKLSINSAARNIQHLL--YGK--RFFPYYVHTIIAGLDEDGKGAVYSFDPVGSYE  132 (222)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHH--HTT--TTSCCCEEEEEEEECTTSCEEEEEECTTSCEE
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHH--Hhc--CCCCceEEEEEEEEcCCCCeEEEEECCCcCEE
Confidence            468999999999999999999999 9999999999999998  654  37899999999999975669999999999999


Q ss_pred             eeeEEeecCChHHHHHHHHHhhc---------------CCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCC
Q 031203           80 GHKATSAGLKEQEAINFLEKKMK---------------NDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENP  143 (164)
Q Consensus        80 ~~~~~aiG~~s~~~~~~Le~~~~---------------~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~  143 (164)
                      +++++|+|+|++.++++||+.++               ++++||+|||++++++||..+.++|+.++ +++|++|++++.
T Consensus       133 ~~~~~a~Gsg~~~a~~~Le~~~~~~~~~~~~~~~~~~~~~~~~s~eeA~~la~~al~~a~~rd~~sg~~i~v~vi~~~g~  212 (222)
T 1ryp_M          133 REQCRAGGAAASLIMPFLDNQVNFKNQYEPGTNGKVKKPLKYLSVEEVIKLVRDSFTSATERHIQVGDGLEILIVTKDGV  212 (222)
T ss_dssp             EESEEEEETTHHHHHHHHHHHTSCTTCBCTTSTTCSBCCCCCCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTEE
T ss_pred             ecCEEEEcCcHHHHHHHHhcccccccccccccccccccCCCCCCHHHHHHHHHHHHHHHHHhcccCCCcEEEEEEcCCCe
Confidence            99999999999999999999853               36899999999999999999999998766 999999999864

>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=3e-33  Score=211.38  Aligned_cols=143  Identities=15%  Similarity=0.224  Sum_probs=129.1

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|+++++.+++.|+++++++++|+.+++++++.+. |. ..+.|||+|++||||||+++||+||.+||+|++.+
T Consensus        49 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a~~~~~~l~-~~-~~~~~p~~~~~lvaG~D~~~gp~Ly~id~~G~~~~  126 (201)
T 1iru_K           49 EAGDTVQFAEYIQKNVQLYKMRNGYELSPTAAANFTRRNLA-DC-LRSRTPYHVNLLLAGYDEHEGPALYYMDYLAALAK  126 (201)
T ss_dssp             STTHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHH-HH-HTSSSCCCEEEEEEEEETTTEEEEEEECTTCCEEE
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH-HH-HhcCCCccEEEEEEEEeCCCCeEEEEECCCcCeEE
Confidence            47999999999999999999999999999999999987652 22 12347999999999999767899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcC
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLS  149 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~  149 (164)
                      ++++|+|+|++.++++||++|  +++||++||++++++||..+.++|..++ +++|++|++++  +++++
T Consensus       127 ~~~~aiGsgs~~a~~~Le~~~--~~~~s~eea~~l~~~al~~a~~rd~~sg~~i~v~vi~~~g--~~~~~  192 (201)
T 1iru_K          127 APFAAHGYGAFLTLSILDRYY--TPTISRERAVELLRKCLEELQKRFILNLPTFSVRIIDKNG--IHDLD  192 (201)
T ss_dssp             CSEEEESHHHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHTBCBCCCCEEEEEEETTE--EECCC
T ss_pred             CCEEEECCcHHHHHHHHHhcc--cCCCCHHHHHHHHHHHHHHHHhhccccCCceEEEEEcCCC--eEEee
Confidence            999999999999999999998  5889999999999999999999999877 89999999985  66655

>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=4e-33  Score=213.91  Aligned_cols=140  Identities=19%  Similarity=0.186  Sum_probs=130.0

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      ++||++.|+++++.+++.|+++++++++++.+++++++.++.|     .|||++++||||||+ +||+||.+||+|++.+
T Consensus        48 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a~~l~~~l~~~-----~~p~~v~~lvaG~D~-~gp~Ly~idp~G~~~~  121 (222)
T 1ryp_I           48 TAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKY-----QGHIGAYLIVAGVDP-TGSHLFSIHAHGSTDV  121 (222)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHT-----TTCSCEEEEEEEEET-TEEEEEEECTTSCEEE
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhhc-----CCCCCeeEEEEEEeC-CCCEEEEECCCCCEEe
Confidence            4689999999999999999999999999999999999998654     479999999999998 7899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcC
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLS  149 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~  149 (164)
                      ++++|+|+|++.++++||++|  +++||+|||++++++||..++++|..++ +++|++|+++++ ++++.
T Consensus       122 ~~~~aiGsgs~~a~~~Le~~~--~~~ms~eeA~~la~~al~~~~~~d~~sg~~i~v~vi~~~g~-~~~~~  188 (222)
T 1ryp_I          122 GYYLSLGSGSLAAMAVLESHW--KQDLTKEEAIKLASDAIQAGIWNDLGSGSNVDVCVMEIGKD-AEYLR  188 (222)
T ss_dssp             CSEEEESTTHHHHHHHHHHHC--CSSCCHHHHHHHHHHHHHHHHHHCTTCCSCEEEEEEETTSC-EEEEE
T ss_pred             cCEEEECCCHHHHHHHHHhhC--CCCcCHHHHHHHHHHHHHHHHhccccCCCcEEEEEEECCCC-EEEEe
Confidence            999999999999999999998  5889999999999999999999998766 899999999863 66554

>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=5e-33  Score=210.73  Aligned_cols=143  Identities=15%  Similarity=0.251  Sum_probs=130.0

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcC-CCCCeEEEeCCCccee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDE-ECGPRLFKCDPAGHFF   79 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~-~~gp~Ly~~dp~G~~~   79 (164)
                      +++|++.|+++++.+++.|+++++++++++.+++++++.+  |+++  ..||+|++||||||+ ++||+||.+||+|++.
T Consensus        56 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~--y~~r--~~P~~v~~lvaG~D~~~~~p~Ly~idp~G~~~  131 (205)
T 1iru_J           56 LATDVQTVAQRLKFRLNLYELKEGRQIKPYTLMSMVANLL--YEKR--FGPYYTEPVIAGLDPKTFKPFICSLDLIGCPM  131 (205)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHH--HTTT--TSCCSCCCEEEEECTTSCCEEEEEECTTCCEE
T ss_pred             cHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHH--HHhc--CCCceEEEEEEEEeCCCCCeEEEEECCCCCcc
Confidence            4689999999999999999999999999999999999999  8875  349999999999995 4789999999999997


Q ss_pred             ee-eEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcC
Q 031203           80 GH-KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLS  149 (164)
Q Consensus        80 ~~-~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~  149 (164)
                      .+ .++|+|+|++.++++||+.|  +++||+|||++++++||..+.++|..++ +++|++|++++..++.++
T Consensus       132 ~~~~~~aiG~gs~~a~~~Le~~~--~~~~s~eea~~l~~~al~~~~~~d~~s~~~i~v~vi~~~g~~~~~~~  201 (205)
T 1iru_J          132 VTDDFVVSGTCAEQMYGMCESLW--EPNMDPDHLFETISQAMLNAVDRDAVSGMGVIVHIIEKDKITTRTLK  201 (205)
T ss_dssp             ECSSEEEEETTHHHHHHHHHHHC--CSSCCHHHHHHHHHHHHHHHGGGBTTSCSCEEEEEEESSBEEEEEBC
T ss_pred             ccCCeeEeeeCHHHHHHHHhccc--CCCCCHHHHHHHHHHHHHHHHHhCcccCCceEEEEEcCCCEEEEEee
Confidence            76 56999999999999999998  5799999999999999999999998866 999999999875455443

>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=8e-33  Score=209.70  Aligned_cols=140  Identities=15%  Similarity=0.182  Sum_probs=129.2

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|+++++.+++.|++++++ ++|+.+++++++.+|.|+++     |++++||||||+++||+||.+||+|++.+
T Consensus        57 ~~aD~~~l~~~~~~~~~~~~~~~~~-~~v~~la~~l~~~~~~~~~~-----~~~~~lvaG~D~~~gp~Ly~id~~G~~~~  130 (205)
T 1ryp_H           57 SAADTQAIADIVQYHLELYTSQYGT-PSTETAASVFKELCYENKDN-----LTAGIIVAGYDDKNKGEVYTIPLGGSVHK  130 (205)
T ss_dssp             BHHHHHHHHHHHHHHHHHHHHHHSS-CCHHHHHHHHHHHHHHTTTT-----CCEEEEEEEEETTTEEEEEEECTTSCCEE
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhhhcC-----ceEEEEEEEEecCCCcEEEEECCCccEEe
Confidence            3689999999999999999999999 99999999999999988652     99999999999767899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEc
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVL  148 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l  148 (164)
                      ++++|+|+|++.++++||++|  +++||++||++++++||..+.++|..++ +++|++|++++...+.+
T Consensus       131 ~~~~aiGsgs~~a~~~Le~~~--~~~~s~eea~~l~~~al~~a~~~d~~sg~~i~v~vi~~~g~~~~~~  197 (205)
T 1ryp_H          131 LPYAIAGSGSTFIYGYCDKNF--RENMSKEETVDFIKHSLSQAIKWDGSSGGVIRMVVLTAAGVERLIF  197 (205)
T ss_dssp             ESEEEESGGGGGGHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHBTTCCSCEEEEEEETTEEEEEEE
T ss_pred             cCEEEEEecHHHHHHHHHhcc--CCCCCHHHHHHHHHHHHHHHHHhCCccCCeEEEEEEcCCCEEEEEe
Confidence            999999999999999999998  5889999999999999999999998766 99999999987533334

>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=1.7e-32  Score=214.98  Aligned_cols=140  Identities=19%  Similarity=0.186  Sum_probs=129.4

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      ++||++.|+++++.+++.|++.++++++++.+++++++.++.|     .|||++++||||||+ .||+||++||+|++.+
T Consensus        77 ~~aD~~~l~~~lr~~~~~~~~~~~~~~~v~~~a~~l~~~l~~~-----~~~~gv~llvaG~D~-~Gp~Ly~iDp~G~~~~  150 (261)
T 3nzj_H           77 TAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKY-----QGHIGAYLIVAGVDP-TGSHLFSIHAHGSTDV  150 (261)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHT-----TTCSCEEEEEEEEET-TEEEEEEECTTSCEEE
T ss_pred             CHHHHHHHHHHHHHHHHHhHHhhCCCCCHHHHHHHHHHHHHHh-----cCcccEEEEEEEEeC-CCCEEEEECCCccEEe
Confidence            4689999999999999999999999999999999999988443     469999999999998 7899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcC
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLS  149 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~  149 (164)
                      ++++|+|+|++.++++||++|  +++||+|||++++++||..+..+|..++ +++|++|+++++ ++++.
T Consensus       151 ~~~~aiGsgs~~a~~~Le~~~--~~~ms~eEA~~la~~al~~a~~rD~~sg~~iev~vI~kdg~-~~~~~  217 (261)
T 3nzj_H          151 GYYLSLGSGSLAAMAVLESHW--KQDLTKEEAIKLASDAIQAGIWNDLGSGSNVDVCVMEIGKD-AEYLR  217 (261)
T ss_dssp             CSEEEESTTHHHHHHHHHHHC--CSSCCHHHHHHHHHHHHHHHHHHCTTCCSCEEEEEEETTSC-EEEEE
T ss_pred             cCeEEeccchHHHHHHHHHHh--ccCCCHHHHHHHHHHHHHHHHhhCCCCCCcEEEEEEECCCc-EEEec
Confidence            999999999999999999998  6899999999999999999999998776 999999999975 55543

>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=5e-32  Score=209.33  Aligned_cols=140  Identities=18%  Similarity=0.215  Sum_probs=129.8

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      ++||++.|+++++.+++.|+++++++++++.+++++++.++.|     .+||++++||||||+ +||+||.+||+|++.+
T Consensus        48 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~l~~~-----~~~~~v~llvaG~D~-~gp~Ly~idp~G~~~~  121 (234)
T 1iru_I           48 TAADTDMTTQLISSNLELHSLSTGRLPRVVTANRMLKQMLFRY-----RGYIGAALVLGGVDV-TGPHLYSIYPHGSTDK  121 (234)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHCSCCCHHHHHHHHHHHHHHT-----TTCSCEEEEEEEECS-SCEEEEEECTTSCEEE
T ss_pred             cHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHhc-----CCCCceeEEEEEEcC-CCCEEEEECCCCCEEe
Confidence            4689999999999999999999999999999999999998654     359999999999998 7899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSI  150 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~  150 (164)
                      ++++|+|+|++.++++||+.|  +++||++||++++++||..+..+|..++ +++|++|++++  ++++.+
T Consensus       122 ~~~~aiGsgs~~a~~~Le~~~--~~~ms~eeA~~la~~al~~a~~~d~~sg~~i~v~vi~k~g--~~~~~~  188 (234)
T 1iru_I          122 LPYVTMGSGSLAAMAVFEDKF--RPDMEEEEAKNLVSEAIAAGIFNDLGSGSNIDLCVISKNK--LDFLRP  188 (234)
T ss_dssp             CSEEEESTTHHHHHHHHHHSC--CTTCCHHHHHTHHHHHHHHHHHHCTTCCSCEEEEEEETTE--EECCSE
T ss_pred             cCEEEECCchHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHHHhcccCCCCEEEEEEECCc--EEEEcc
Confidence            999999999999999999998  5889999999999999999999998876 99999999974  676654

>1m4y_A ATP-dependent protease HSLV; N-terminal catalytic threonine residue, hydrolase; 2.10A {Thermotoga maritima} SCOP: d.153.1.4

Probab=99.91  E-value=4.4e-24  Score=157.36  Aligned_cols=120  Identities=17%  Similarity=0.168  Sum_probs=101.5

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|+++++.+++.|+++         +++.++++.|.++++++.|||++++|++  |   ||+||.+||+|++.+
T Consensus        49 ~~aD~~~l~~~~~~~~~~~~~~---------~~~~~~~l~~~~~~~~~~~~~~~~~lv~--D---~p~Ly~~d~~G~~~~  114 (171)
T 1m4y_A           49 SVADAMTLFDRFEAKLREWGGN---------LTKAAVELAKDWRTDRVLRRLEALLLVA--D---KENIFIISGNGEVIQ  114 (171)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTTC---------HHHHHHHHHHHHHHCTTGGGCCCEEEEE--C---SSCEEEECTTSCEEC
T ss_pred             cHHHHHHHHHHHHHHHHHhccc---------HHHHHHHHHHHHHHhCCCCceEEEEEEE--c---CCEEEEECCCCCEEe
Confidence            4689999999999999988744         2444455555566677788999999988  5   799999999999999


Q ss_pred             ee--EEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEE
Q 031203           81 HK--ATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVV  138 (164)
Q Consensus        81 ~~--~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii  138 (164)
                      ++  ++|+|+|++.++++||+.|+. ++||.   .+++++||..+.+||..++ +++|.++
T Consensus       115 ~~~~~~a~Gsgs~~a~~~le~~~~~-~~ms~---~~l~~~al~~a~~rd~~sg~~i~v~~~  171 (171)
T 1m4y_A          115 PDDDAAAIGSGGPYALAAAKALLRN-TDLSA---REIVEKAMTIAGEICIYTNQNIVIEEV  171 (171)
T ss_dssp             CSSSEEEESTTHHHHHHHHHHHHHH-CCCCH---HHHHHHHHHHHHHHCTTCCSCCEEEEC
T ss_pred             cCCCEEEECCcHHHHHHHHHHhccc-CCCCH---HHHHHHHHHHHHHhCcccCCeEEEEEC
Confidence            88  999999999999999999941 78997   6789999999999998877 8888763

>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=99.91  E-value=7e-24  Score=157.64  Aligned_cols=121  Identities=17%  Similarity=0.176  Sum_probs=104.1

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|.++++.+++.|+   |      .+++.++++.|.++++...|||++++|||  |   ||+||.+||+|++.+
T Consensus        55 ~~aD~~~l~~~~~~~~~~y~---g------~~~~~~~~l~~~~~~~~~~rp~~~~~lva--d---~p~ly~~d~~G~~~~  120 (180)
T 2z3b_A           55 SVADAFTLFEKFEAKLEEYN---G------NLKRAAVELAKEWRSDKVLRKLEAMLIVM--N---QDTLLLVSGTGEVIE  120 (180)
T ss_dssp             CHHHHHHHHHHHHHHHHHTT---T------CHHHHHHHHHHHHHHCTTGGGCCCCEEEE--C---SSCEEEECTTCCEEC
T ss_pred             hHHHHHHHHHHHHHHHHHhc---C------ChHHHHHHHHHHHHhhhCcCcceEEEEEE--c---CCeEEEECCCCcEEE
Confidence            46899999999999999987   3      34445556667788888899999999999  3   699999999999998


Q ss_pred             e--eEEeecCChHHHHHHHHHhhcCCC-CCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEE
Q 031203           81 H--KATSAGLKEQEAINFLEKKMKNDP-AFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVV  138 (164)
Q Consensus        81 ~--~~~aiG~~s~~~~~~Le~~~~~~~-~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii  138 (164)
                      +  +++|+|+|++.++++||+.|++.+ +||.||   ++.+||..+.++|..++ +++|.+|
T Consensus       121 ~~~~~~a~Gsgs~~a~~~le~~~~~~~~~mt~ee---l~~~al~~a~~rd~~sg~~i~v~~i  179 (180)
T 2z3b_A          121 PDDGILAIGSGGNYALAAGRALKKHAGESMSASE---IARAALETAGEICVYTNDQIILEEL  179 (180)
T ss_dssp             CSSSEEEESTTHHHHHHHHHHHHHHHGGGCCHHH---HHHHHHHHHHHHCTTCCSCCEEEEE
T ss_pred             eCCCEEEECCCHHHHHHHHHHhhhccCCCCCHHH---HHHHHHHHHHHhcCccCCeEEEEEE
Confidence            4  999999999999999999994211 899999   46799999999999888 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=99.91  E-value=7.9e-24  Score=156.47  Aligned_cols=121  Identities=14%  Similarity=0.090  Sum_probs=103.6

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|.++++.+++.|++      +   ++..++.+.|.++++++.||+  +.+++|+|   ||+||.+||+|++.+
T Consensus        49 ~~aD~~~l~~~~~~~~~~~~~------~---~~~~~~~l~~~~~~~~~~r~~--~~~l~g~d---~p~Ly~~d~~G~~~~  114 (174)
T 1g3k_A           49 GTADAFTLFELFERKLEMHQG------H---LLKSAVELAKDWRTDRALRKL--EAMLIVAD---EKESLIITGIGDVVQ  114 (174)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTT------C---HHHHHHHHHHHHHHSTTGGGC--CCEEEEEC---SSCEEEEETTTEEEC
T ss_pred             cHHHHHHHHHHHHHHHHHhcC------c---HHHHHHHHHHHHHhccCcCcc--eEEEEEEC---CCEEEEEcCCCcEEe
Confidence            468999999999999999875      3   355556666777877778886  57778887   699999999999999


Q ss_pred             ee---EEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEE
Q 031203           81 HK---ATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVS  139 (164)
Q Consensus        81 ~~---~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~  139 (164)
                      ++   ++|+|+|++.++++||+.|+ .++||.+   +++.+||..+.++|..++ +++|.+|+
T Consensus       115 ~~~~~~~a~Gsgs~~a~~~le~~~~-~~~mt~~---~l~~~al~~a~~rd~~sg~~i~v~~i~  173 (174)
T 1g3k_A          115 PEEDQILAIGSGGNYALSAARALVE-NTELSAH---EIVEKSLRIAGDICVFTNTNFTIEELP  173 (174)
T ss_dssp             CCTTCEEEESTTHHHHHHHHHHHHH-HCCCCHH---HHHHHHHHHHHHHCTTCCSCCEEEEEC
T ss_pred             cCCCcEEEEcccHHHHHHHHHHhcc-cCCCCHH---HHHHHHHHHHHHhccccCCceEEEEec
Confidence            88   99999999999999999994 1789965   799999999999998877 89999985

>2hc5_A ORF 99, hypothetical protein YVYC; NESG, GFT-PSI, protein structure initiative, northeast structural genomics consortium, alpha-beta, FLAG; NMR {Bacillus subtilis} SCOP: d.352.1.1

Probab=83.13  E-value=3.3  Score=27.80  Aligned_cols=33  Identities=18%  Similarity=0.211  Sum_probs=27.3

Q ss_pred             CCeEEEEEEEcCCC-cEEEcCHHHHHHHHHHhhc
Q 031203          130 ASEIEVGVVSKENP-EFRVLSIEEIDEHLTAISE  162 (164)
Q Consensus       130 ~~~iei~ii~~~~~-~~k~l~~~ei~~~l~~~~~  162 (164)
                      ++.+-|.|++++++ .+|.++|+++-++..++.+
T Consensus        66 ~~~~vVkVvD~~TgEVIRqIPpEe~L~l~~~l~e   99 (117)
T 2hc5_A           66 LNEYYVKVIEDSTNEVIREIPPKRWLDFYAAMTE   99 (117)
T ss_dssp             TTEEEEEEEETTTTEEEEEECHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEECCCCcEEEeCChHHHHHHHHHHHH
Confidence            45788999999876 4689999999998887753

---

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	164
d1irua_	244	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	2e-53
d1rypa_	243	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	1e-42
d1iruf_	238	d.153.1.4 (F:) Proteasome alpha subunit (non-catal	4e-40
d1irud_	243	d.153.1.4 (D:) Proteasome alpha subunit (non-catal	4e-39
d1irue_	234	d.153.1.4 (E:) Proteasome alpha subunit (non-catal	3e-38
d1rypb_	250	d.153.1.4 (B:) Proteasome alpha subunit (non-catal	4e-38
d1yara1	221	d.153.1.4 (A:13-233) Proteasome alpha subunit (non	1e-36
d1iruc_	250	d.153.1.4 (C:) Proteasome alpha subunit (non-catal	4e-36
d1rypd_	241	d.153.1.4 (D:) Proteasome alpha subunit (non-catal	5e-36
d1irug_	245	d.153.1.4 (G:) Proteasome alpha subunit (non-catal	6e-36
d1rypf_	233	d.153.1.4 (F:) Proteasome alpha subunit (non-catal	1e-35
d1rypc_	244	d.153.1.4 (C:) Proteasome alpha subunit (non-catal	5e-35
d1j2pa_	243	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	9e-35
d1rype_	242	d.153.1.4 (E:) Proteasome alpha subunit (non-catal	2e-34
d1rypg_	244	d.153.1.4 (G:) Proteasome alpha subunit (non-catal	5e-34
d1irub_	233	d.153.1.4 (B:) Proteasome alpha subunit (non-catal	7e-32
d1q5qa_	227	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	2e-28
d1iruh_	202	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	3e-20
d1yarh1	203	d.153.1.4 (H:1-203) Proteasome beta subunit (catal	1e-18
d1ryp1_	222	d.153.1.4 (1:) Proteasome beta subunit (catalytic)	5e-18
d1ryph_	205	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	1e-15
d1j2qh_	202	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	2e-15
d1rypj_	204	d.153.1.4 (J:) Proteasome beta subunit (catalytic)	2e-14
d1rypk_	198	d.153.1.4 (K:) Proteasome beta subunit (catalytic)	3e-14

>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 =  167 bits (425), Expect = 2e-53
 Identities = 99/163 (60%), Positives = 134/163 (82%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           MTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD SQVYTQ+A MRPLG   +++ 
Sbjct: 82  MTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIG 141

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           IDEE GP+++KCDPAG++ G KAT+AG+K+ E+ +FLEKK+K    +TF++TV+TAI+ L
Sbjct: 142 IDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCL 201

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 163
            +VL  DFK SEIEVGVV+ ENP+FR+L+  EID HL A++ER
Sbjct: 202 STVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVALAER 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 =  139 bits (352), Expect = 1e-42
 Identities = 78/169 (46%), Positives = 112/169 (66%), Gaps = 7/169 (4%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
              DAR    +A+ EAAEFR+KYGY+MP DVLAK +A+ SQ+YTQ AYMRPLGV+   +S
Sbjct: 77  PIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQRAYMRPLGVILTFVS 136

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKND-----PAFTFQETVQT 115
           +DEE GP ++K DPAG++ G+KAT+ G K+QE    LE   K          ++++ V+ 
Sbjct: 137 VDEELGPSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKKSKIDHINEESWEKVVEF 196

Query: 116 AISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
           AI+ +   L  +F  +++EVGV +K+  +F  LS E I+E L AI+E+D
Sbjct: 197 AITHMIDALGTEFSKNDLEVGVATKD--KFFTLSAENIEERLVAIAEQD 243

>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 =  133 bits (335), Expect = 4e-40
 Identities = 48/165 (29%), Positives = 79/165 (47%), Gaps = 4/165 (2%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADAR L    R E  + RF +   +PV  L   I  K+Q+ TQ    RP GV  ++  
Sbjct: 74  LTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAG 133

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D+  GP +F+  P+ ++F  +A S G + Q A  +LE+ M         E V+  +  L
Sbjct: 134 YDDM-GPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFMECNLNELVKHGLRAL 192

Query: 121 QSVLQ--EDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 163
           +  L   +D     + +G+V K+   F +   +++   L  + ER
Sbjct: 193 RETLPAEQDLTTKNVSIGIVGKDLE-FTIYDDDDVSPFLEGLEER 236

>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 =  130 bits (329), Expect = 4e-39
 Identities = 49/163 (30%), Positives = 86/163 (52%), Gaps = 3/163 (1%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADAR ++ +AR E    R      + V+ + ++IA   Q YTQ    RP G+ A+++ 
Sbjct: 75  LTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGISALIVG 134

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D +  PRL++ DP+G +   KA + G   +    FLEK   ++   T   T++  I  L
Sbjct: 135 FDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEAIETDDLTIKLVIKAL 194

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 163
             V+Q   K   IE+ V+ ++    ++L+ EEI++++  I + 
Sbjct: 195 LEVVQSGGK--NIELAVMRRDQS-LKILNPEEIEKYVAEIEKE 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 =  128 bits (323), Expect = 3e-38
 Identities = 45/165 (27%), Positives = 84/165 (50%), Gaps = 9/165 (5%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH-----AYMRPLGVV 55
           + ADA+TL+ +AR E     F Y   M V+ + + +++ +  + +      A  RP GV 
Sbjct: 74  LIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMSRPFGVA 133

Query: 56  AMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQT 115
            +   +DE+ GP+LF  DP+G F    A + G   + A + L++        T +E +++
Sbjct: 134 LLFGGVDEK-GPQLFHMDPSGTFVQCDARAIGSASEGAQSSLQELYHKS--MTLKEAIKS 190

Query: 116 AISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAI 160
           ++  L+ V++E   A+ IE+  V      F + + EE++E +  I
Sbjct: 191 SLIILKQVMEEKLNATNIELATVQPGQN-FHMFTKEELEEVIKDI 234

>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 =  128 bits (323), Expect = 4e-38
 Identities = 52/175 (29%), Positives = 86/175 (49%), Gaps = 17/175 (9%)

Query: 1   MTADARTLVQQARYEAA-EFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVL 59
           M  D R LV ++R  A   ++  YG   P  +L   +A   Q  TQ   +RP GV  ++ 
Sbjct: 78  MGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIA 137

Query: 60  SIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAIST 119
             DE  G  L++ DP+G +F  KAT+ G     A  FLEK+  ++     ++ +  A+ T
Sbjct: 138 GHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWNDE--LELEDAIHIALLT 195

Query: 120 LQSVLQEDFKASEIEVGVVSKENPE--------------FRVLSIEEIDEHLTAI 160
           L+  ++ +F    IE+ ++  ENP+              FR L+ +EI++ L A+
Sbjct: 196 LKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTSQEINDRLEAL 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 =  124 bits (311), Expect = 1e-36
 Identities = 56/157 (35%), Positives = 87/157 (55%), Gaps = 4/157 (2%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADAR LV  AR  A + +  YG  + ++ L K +AD+ Q YTQ+  +RP GV  +   
Sbjct: 69  LVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGVSLIFAG 128

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ID+  GPRLF CDPAG    +KAT+ G  +   ++FLE++ K +     +E V   I  L
Sbjct: 129 IDQI-GPRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKEN--LPEKEAVTLGIKAL 185

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL 157
           +S L+E  +    E+  ++  N  +R+   EE+ + L
Sbjct: 186 KSSLEEGEELKAPEIASITVGNK-YRIYDQEEVKKFL 221

>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 =  123 bits (309), Expect = 4e-36
 Identities = 44/167 (26%), Positives = 82/167 (49%), Gaps = 4/167 (2%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +T+DA  L  + R  A  +  +Y   +P + L   + D  Q YTQ    RP GV  + + 
Sbjct: 78  ITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIG 137

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D+  G +L++ DP+G++ G KAT  G     A++ L++    +   T +  +  AI  L
Sbjct: 138 WDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQD-YKEGEMTLKSALALAIKVL 196

Query: 121 QSVLQED-FKASEIEVGVVSKENPE--FRVLSIEEIDEHLTAISERD 164
              +      A ++E+  +++EN +   RVL  +E+++ +    E +
Sbjct: 197 NKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKHEEEE 243

>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 =  122 bits (308), Expect = 5e-36
 Identities = 50/165 (30%), Positives = 85/165 (51%), Gaps = 5/165 (3%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + AD+R L+++AR EA   R      + V+ L +++A   Q YTQ   +RP GV  ++  
Sbjct: 76  LNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLIAG 135

Query: 61  IDEE-CGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMK-NDPAFTFQETVQTAIS 118
            D     P+L++ +P+G +    A + G   +    FLEK     +P  T +E V+  + 
Sbjct: 136 FDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKEPPATVEECVKLTVR 195

Query: 119 TLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 163
           +L  V+Q   K   IE+ VV  ++     LS EEI++++T I + 
Sbjct: 196 SLLEVVQTGAK--NIEITVVKPDSD-IVALSSEEINQYVTQIEQE 237

>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 =  122 bits (308), Expect = 6e-36
 Identities = 46/164 (28%), Positives = 77/164 (46%), Gaps = 3/164 (1%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADAR+L   AR EA+ FR  +GY +P+  LA  +A     YT ++ +RP G   M+ S
Sbjct: 80  LLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGCSFMLGS 139

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
                G +L+  DP+G  +G+   + G   Q A   +EK    +   T ++ V+     +
Sbjct: 140 YSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQMKE--MTCRDIVKEVAKII 197

Query: 121 QSVLQE-DFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 163
             V  E   KA E+E+  V +       +  ++I E     ++ 
Sbjct: 198 YIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEKYAKE 241

>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 =  121 bits (305), Expect = 1e-35
 Identities = 33/160 (20%), Positives = 69/160 (43%), Gaps = 5/160 (3%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +  DAR L    R +       +  ++ V+     + DK+Q  TQ    RP GV  +++ 
Sbjct: 76  LAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRPYGVGLLIIG 135

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKND--PAFTFQETVQTAIS 118
            D + G  L +  P+G+      T+ G + Q A  +LE+ +           E ++  + 
Sbjct: 136 YD-KSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVE 194

Query: 119 TLQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEHL 157
            +   L+++      + + +V K+ P F +   E + +++
Sbjct: 195 AISQSLRDESLTVDNLSIAIVGKDTP-FTIYDGEAVAKYI 233

>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 =  120 bits (302), Expect = 5e-35
 Identities = 44/162 (27%), Positives = 76/162 (46%), Gaps = 7/162 (4%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +TADA  L+  AR  A  +   Y  ++PV++L + ++D  Q YTQH  +RP GV  +   
Sbjct: 79  LTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAG 138

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D+  G +L+  +P+G++ G KA S G     A   L+   K+D      + ++ A+ TL
Sbjct: 139 YDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKDD--MKVDDAIELALKTL 196

Query: 121 QSVLQED-FKASEIEVGVVSKENPE----FRVLSIEEIDEHL 157
                        +E   + K   +     ++   +EI + L
Sbjct: 197 SKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDIL 238

>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 =  119 bits (300), Expect = 9e-35
 Identities = 51/163 (31%), Positives = 87/163 (53%), Gaps = 4/163 (2%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           + ADAR L+ +AR EA   R  Y   + V  LAK I D  Q YTQ+  +RP GV  ++  
Sbjct: 78  LVADARVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQYGGVRPFGVSLLIAG 137

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ++E   P+L++ DP+G    +KAT+ G+       F EK+ ++D   +F + +   +  +
Sbjct: 138 VNEV--PKLYETDPSGALLEYKATAIGMGRMAVTEFFEKEYRDD--LSFDDAMVLGLVAM 193

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISER 163
              ++ +     IEVG V  ++  F+ +S EE+  ++   +ER
Sbjct: 194 GLSIESELVPENIEVGYVKVDDRTFKEVSPEELKPYVERANER 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 =  118 bits (297), Expect = 2e-34
 Identities = 37/170 (21%), Positives = 81/170 (47%), Gaps = 9/170 (5%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH------AYMRPLGV 54
           +TADAR++++ AR  A      Y  ++ V+ L + + D +  + +          RP GV
Sbjct: 73  LTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLMSRPFGV 132

Query: 55  VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQ 114
             ++   D + G +LF  +P+G F+ + A + G   + A   L  +  +    T +E   
Sbjct: 133 ALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNEWHSS--LTLKEAEL 190

Query: 115 TAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISERD 164
             +  L+ V++E    +  ++  ++K++  F++   E+  E +  + E++
Sbjct: 191 LVLKILKQVMEEKLDENNAQLSCITKQDG-FKIYDNEKTAELIKELKEKE 239

>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 =  117 bits (295), Expect = 5e-34
 Identities = 38/167 (22%), Positives = 75/167 (44%), Gaps = 4/167 (2%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +  D R LV + R EAA F+  Y   +P+   A  +    Q +T +  +RP GV  +   
Sbjct: 77  LIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGG 136

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKN-DPAFTFQETVQTAIST 119
           +D+  G  L+  +P+G ++G+K  + G   Q A   LEK + +     + +E V+ A   
Sbjct: 137 VDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKI 195

Query: 120 LQSVLQED-FKASEIEVGVVSKENPE-FRVLSIEEIDEHLTAISERD 164
           +    +++  K  E+E+   S             ++ +     ++++
Sbjct: 196 IYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAIDFAQKE 242

>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 =  112 bits (280), Expect = 7e-32
 Identities = 53/161 (32%), Positives = 81/161 (50%), Gaps = 5/161 (3%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           M  D R LV +AR  A ++   Y   +P   L + +A   Q YTQ   +RP GV  ++  
Sbjct: 78  MGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGVSLLICG 137

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            +E   P LF+ DP+G +F  KAT+ G        FLEK+   D     ++ + TAI TL
Sbjct: 138 WNEGR-PYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNED--LELEDAIHTAILTL 194

Query: 121 QSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAIS 161
           +   +       IEVG+ ++    FR L+  E+ ++L AI+
Sbjct: 195 KESFEGQMTEDNIEVGICNEAG--FRRLTPTEVKDYLAAIA 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 =  102 bits (256), Expect = 2e-28
 Identities = 24/170 (14%), Positives = 52/170 (30%), Gaps = 13/170 (7%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGY-EMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVL 59
              +   L +     A    + Y   ++    LA   A            +P  V   V 
Sbjct: 59  KYNEFENLRRAGIVHADMRGYSYDRRDVTGRSLANAYAQT-LGTIFTEQPKPYEVEICVA 117

Query: 60  SIDE---ECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTA 116
            +        P+L++    G     +         E I    ++         +  V  A
Sbjct: 118 EVGRVGSPKAPQLYRITYDGSIVDEQHFVVMGGTTEPIATAMRES-YRADLDLEAAVGIA 176

Query: 117 ISTLQSVLQED-----FKASEIEVGVVSKENPE--FRVLSIEEIDEHLTA 159
           ++ L+     +        + +EV V+ +  P   FR ++   +++ + A
Sbjct: 177 VNALRQGGAGEGEKRNVDVASLEVAVLDQSRPRRAFRRIAGTALEQLVPA 226

>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 = 80.9 bits (199), Expect = 3e-20
 Identities = 22/159 (13%), Positives = 50/159 (31%), Gaps = 8/159 (5%)

Query: 3   ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSID 62
           AD + +     Y+      +      V   A    +         Y   L    ++   D
Sbjct: 50  ADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEMCY-----RYREDLMAGIIIAGWD 104

Query: 63  EECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQS 122
            + G +++     G          G        +++   +     T +E +Q   + L  
Sbjct: 105 PQEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREG--MTKEECLQFTANALAL 162

Query: 123 VLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEHLTAI 160
            ++ D      I +  +++   E +VL  ++I +   A 
Sbjct: 163 AMERDGSSGGVIRLAAIAESGVERQVLLGDQIPKFAVAT 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 = 76.8 bits (188), Expect = 1e-18
 Identities = 34/161 (21%), Positives = 63/161 (39%), Gaps = 10/161 (6%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +  DA+ LV+  + E   +R +    MP++ +A  +++         YM  L    +V  
Sbjct: 48  LVGDAQVLVRYMKAELELYRLQRRVNMPIEAVATLLSNMLNQVKYMPYMVQL----LVGG 103

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
           ID      +F  D AG        S G         LE +       T  E V   I  +
Sbjct: 104 IDTAP--HVFSIDAAGGSVEDIYASTGSGSPFVYGVLESQYSEK--MTVDEGVDLVIRAI 159

Query: 121 QSVLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEHLTAI 160
            +  Q D      I+V V+++++  +  L  ++I+  +  +
Sbjct: 160 SAAKQRDSASGGMIDVAVITRKDG-YVQLPTDQIESRIRKL 199

>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 = 75.6 bits (185), Expect = 5e-18
 Identities = 22/157 (14%), Positives = 55/157 (35%), Gaps = 19/157 (12%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
             AD   LV++ +     + F +  +          A   Q         P  V  ++  
Sbjct: 57  FAADGDALVKRFKNSVKWYHFDHNDKKLSI---NSAARNIQHLLYGKRFFPYYVHTIIAG 113

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAF------------- 107
           +DE+    ++  DP G +   +  + G      + FL+ ++     +             
Sbjct: 114 LDEDGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYEPGTNGKVKKPLK 173

Query: 108 --TFQETVQTAISTLQSVLQEDFKASE-IEVGVVSKE 141
             + +E ++    +  S  +   +  + +E+ +V+K+
Sbjct: 174 YLSVEEVIKLVRDSFTSATERHIQVGDGLEILIVTKD 210

>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 = 69.0 bits (168), Expect = 1e-15
 Identities = 22/156 (14%), Positives = 49/156 (31%), Gaps = 9/156 (5%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
             AD + +    +Y    +  +YG            A        +     L    +V  
Sbjct: 57  SAADTQAIADIVQYHLELYTSQYGTPST------ETAASVFKELCYENKDNLTAGIIVAG 110

Query: 61  IDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL 120
            D++    ++     G         AG        + +K  + +   + +ETV     +L
Sbjct: 111 YDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFREN--MSKEETVDFIKHSL 168

Query: 121 QSVLQED-FKASEIEVGVVSKENPEFRVLSIEEIDE 155
              ++ D      I + V++    E  +   +E ++
Sbjct: 169 SQAIKWDGSSGGVIRMVVLTAAGVERLIFYPDEYEQ 204

>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 = 68.7 bits (167), Expect = 2e-15
 Identities = 32/164 (19%), Positives = 65/164 (39%), Gaps = 11/164 (6%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
              DA+ L +  + EA  +  +   +  V  +A   ++    Y    Y+     V +++ 
Sbjct: 48  SVGDAQFLARIIKIEANLYEIRRERKPTVRAIATLTSNLLNSYRYFPYL-----VQLLIG 102

Query: 61  IDEECGPRLFKCDPAGHFFGHK-ATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAIST 119
             +  G  ++  DP G     K   + G     A   LE +   +      E V+ A+  
Sbjct: 103 GIDSEGKSIYSIDPIGGAIEEKDIVATGSGSLTAYGVLEDRFTPE--IGVDEAVELAVRA 160

Query: 120 LQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEIDEHLTAISE 162
           + S ++ D      I+V  ++++  EF   S EE+++ L    +
Sbjct: 161 IYSAMKRDSASGDGIDVVKITED--EFYQYSPEEVEQILAKFRK 202

>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 = 65.6 bits (159), Expect = 2e-14
 Identities = 23/150 (15%), Positives = 50/150 (33%), Gaps = 7/150 (4%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
           +  D  TL +  RY+   ++ K    +  +   + ++          Y     V  +V  
Sbjct: 55  LATDVTTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYF----VGPVVAG 110

Query: 61  IDEECG-PRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAIST 119
           I+ + G P +   D  G     K         + +  + + +   P    ++  +T    
Sbjct: 111 INSKSGKPFIAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYE-PNLEPEDLFETISQA 169

Query: 120 LQSVLQEDFKASE-IEVGVVSKENPEFRVL 148
           L +    D  +     V ++ K+    R L
Sbjct: 170 LLNAADRDALSGWGAVVYIIKKDEVVKRYL 199

>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 = 64.8 bits (157), Expect = 3e-14
 Identities = 21/155 (13%), Positives = 52/155 (33%), Gaps = 8/155 (5%)

Query: 1   MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLS 60
              D     +  +     +  +  YE+    ++ ++  +     +    RP  V  ++  
Sbjct: 49  EAGDTVQFAEYIQANIQLYSIREDYELSPQAVSSFVRQELAKSIR--SRRPYQVNVLIGG 106

Query: 61  IDEEC-GPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAIST 119
            D++   P L++ D  G        + G       + L+   +  P  T +E +      
Sbjct: 107 YDKKKNKPELYQIDYLGTKVELPYGAHGYSGFYTFSLLDHHYR--PDMTTEEGLDLLKLC 164

Query: 120 LQSVLQED-FKASEIEVGVVSKENPEFRVLSIEEI 153
           +Q + +        + V +V K+    R +   + 
Sbjct: 165 VQELEKRMPMDFKGVIVKIVDKD--GIRQVDDFQA 197

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	164
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
d1iruf_	238	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rypf_	233	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1irue_	234	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rype_	242	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1yara1	221	Proteasome alpha subunit (non-catalytic) {Archaeon	100.0
d1irug_	245	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rypb_	250	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1rypd_	241	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1irud_	243	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rypc_	244	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1rypg_	244	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1irub_	233	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1yarh1	203	Proteasome beta subunit (catalytic) {Archaeon Ther	100.0
d1irul_	201	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d1rypk_	198	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1j2qh_	202	Proteasome beta subunit (catalytic) {Archaeon Arch	100.0
d1ryph_	205	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1rypl_	212	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1q5qa_	227	Proteasome alpha subunit (non-catalytic) {Rhodococ	100.0
d1iruh_	202	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d1ryp2_	233	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1irui_	220	Proteasome beta subunit (catalytic) {Cow (Bos taur	99.98
d1q5qh_	224	Proteasome beta subunit (catalytic) {Rhodococcus e	99.97
d1rypi_	222	Proteasome beta subunit (catalytic) {Baker's yeast	99.97
d1iru2_	217	Proteasome beta subunit (catalytic) {Cow (Bos taur	99.97
d1rypj_	204	Proteasome beta subunit (catalytic) {Baker's yeast	99.97
d1ryp1_	222	Proteasome beta subunit (catalytic) {Baker's yeast	99.97
d1iruj_	204	Proteasome beta subunit (catalytic) {Cow (Bos taur	99.97
d1iruk_	199	Proteasome beta subunit (catalytic) {Cow (Bos taur	99.96
d1iru1_	213	Proteasome beta subunit (catalytic) {Cow (Bos taur	99.95
d2z3ba1	180	HslV (ClpQ) protease {Bacillus subtilis [TaxId: 14	99.41
d1m4ya_	171	HslV (ClpQ) protease {Thermotoga maritima [TaxId:	99.23
d1g3ka_	173	HslV (ClpQ) protease {Haemophilus influenzae [TaxI	99.15
d1cuka1	48	DNA helicase RuvA subunit, C-terminal domain {Esch	85.32

>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=1.1e-42  Score=268.69  Aligned_cols=163  Identities=61%  Similarity=0.975  Sum_probs=156.9

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.|++++|.+|+.|++.++++++++.+++.+++++|.||++++.|||+|++||||||+++||+||.+||+|++.+
T Consensus        82 ~~~D~~~l~~~~r~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rP~~v~~ll~G~D~~~g~~Ly~~Dp~G~~~~  161 (244)
T d1irua_          82 MTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCG  161 (244)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSBCCCSEEEEEEEEETTTEEEEEEECTTSCEEE
T ss_pred             chHHHHHHHHHHHHHHHHHHHHcCCCCCchHHHHHHHHHHHHHhcccccCccceeeEEEEEcCCCCcEEEEEcCCccEEe
Confidence            46899999999999999999999999999999999999999999999999999999999999877899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHHHHHHh
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAI  160 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~~l~~~  160 (164)
                      ++++|+|+|+..++++||++|...++||++||++++++||..+.++|..+++++|+|+++++++|++++++||+++|.++
T Consensus       162 ~~~~a~G~gs~~~~~~Le~~~~~~~d~t~eeai~l~~~~l~~~~~~d~~~~~iev~ii~~~~~~~~~l~~~ei~~~l~~~  241 (244)
T d1irua_         162 FKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVAL  241 (244)
T ss_dssp             BSEEEEETTHHHHHHHHHHHTTSCCCCCHHHHHHHHHHHHHHHTTCCCCTTSEEEEEEETTEEEEEECCHHHHHHHHHHH
T ss_pred             cceEeccCchhHHHHHHHhccccccCCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEEEeCCCcEEECCHHHHHHHHHHH
Confidence            99999999999999999999976789999999999999999999999888899999999998779999999999999999


Q ss_pred             hcc
Q 031203          161 SER  163 (164)
Q Consensus       161 ~~~  163 (164)
                      .||
T Consensus       242 ~~r  244 (244)
T d1irua_         242 AER  244 (244)
T ss_dssp             HTC
T ss_pred             hcC
Confidence            986

>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=3.2e-40  Score=254.62  Aligned_cols=162  Identities=48%  Similarity=0.767  Sum_probs=153.9

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.+++++|.+++.|++.++++++++.+++++++++|.|+++++.|||+|++||||||+++||+||++||+|++.+
T Consensus        77 ~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~ls~~~~~~~~~~~~rP~~v~~ll~G~D~~~g~~Ly~~Dp~G~~~~  156 (243)
T d1rypa_          77 PIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVG  156 (243)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTSCCCSCEEEEEEEETTTEEEEEEECTTSCEEE
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcccccCccceEEEEEEccCCCCeEEEEcCCEEEEe
Confidence            46899999999999999999999999999999999999999999999999999999999999867899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcC-----CCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKN-----DPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE  155 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~-----~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~  155 (164)
                      ++++|+|+|+..++++|+++|+.     .+++|.+||++++++||..+.++|.+..+++|+++++++  |++++++||++
T Consensus       157 ~~~~a~G~gs~~~~~~Le~~~~~~~~~~~~~~s~eeav~la~~~l~~~~~~d~~~~~iei~iitk~g--~~~l~~eeI~~  234 (243)
T d1rypa_         157 YKATATGPKQQEITTNLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDK--FFTLSAENIEE  234 (243)
T ss_dssp             BSEEEESTTHHHHHHHHHHHHHHHCSSSCCCSSHHHHHHHHHHHHHHHHTCCCCTTSEEEEEEETTE--EEECCHHHHHH
T ss_pred             cceEEeCccHHHHHHHHHHHhhcccccccccccHHHHHHHHHHHHHHHhhccCCCCcEEEEEEeCCc--eEEeCHHHHHH
Confidence            99999999999999999999852     356899999999999999999999877799999999984  99999999999


Q ss_pred             HHHHhhccC
Q 031203          156 HLTAISERD  164 (164)
Q Consensus       156 ~l~~~~~~~  164 (164)
                      ++.++.|||
T Consensus       235 ~l~~i~e~~  243 (243)
T d1rypa_         235 RLVAIAEQD  243 (243)
T ss_dssp             HHHHHTTTC
T ss_pred             HHHHHhccC
Confidence            999999997

>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=3.3e-40  Score=255.51  Aligned_cols=163  Identities=27%  Similarity=0.482  Sum_probs=153.1

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.+++++|.+|..|++.+|++++++.+++.+++++|.||+++++|||+|++||+|||+++||+||.+||+|++.+
T Consensus        78 ~~~D~~~l~~~~r~~~~~~~~~~~~~i~~~~la~~l~~~~~~~~~~~~~rP~~~~~li~G~D~~~gp~Ly~~Dp~G~~~~  157 (250)
T d1iruc_          78 ITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGG  157 (250)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBSSCCCCCEEEEEEEEETTTEEEEEEEETTTEEEE
T ss_pred             ccchHHHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHHHhhhccCCcceEEEEEEEEcCCCCCEEEEEcccccEee
Confidence            46899999999999999999999999999999999999999999999999999999999999867899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCC--cEEEcCHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENP--EFRVLSIEEIDEHL  157 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~--~~k~l~~~ei~~~l  157 (164)
                      ++++|+|+|++.++++|+++|+ .++||++||++++++||..++++|..++ +++|++|+++++  .|++++++||++++
T Consensus       158 ~~~~a~G~gs~~a~~~Le~~y~-~~~ms~eeai~la~~al~~~~~~d~~~~~~iei~ii~~~~~~~~~~~l~~~Ei~~~l  236 (250)
T d1iruc_         158 WKATCIGNNSAAAVSMLKQDYK-EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLI  236 (250)
T ss_dssp             CSEEEESTTTTHHHHHHHHHCC-TTCCCHHHHHHHHHHHHHHSSSCTTCCSTTCEEEEEECCSSSCEEEECCHHHHHHHH
T ss_pred             eeEEEeCcChHHHHHHHHhhcc-cCCCCHHHHHHHHHHHHHHHhcccCCCCCeEEEEEEEcCCCceeEEECCHHHHHHHH
Confidence            9999999999999999999984 3589999999999999999998886655 999999999875  38999999999999


Q ss_pred             HHhhccC
Q 031203          158 TAISERD  164 (164)
Q Consensus       158 ~~~~~~~  164 (164)
                      .++.|++
T Consensus       237 ~~~~e~~  243 (250)
T d1iruc_         237 KKHEEEE  243 (250)
T ss_dssp             HHHHTTT
T ss_pred             HHHHHHh
Confidence            9998764

>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=2.1e-39  Score=250.08  Aligned_cols=159  Identities=31%  Similarity=0.527  Sum_probs=152.3

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.++++++.++..|+++++++++++.+++.+++.+|.||+++++|||+|++|+||||+  +|+||.+||+|++.+
T Consensus        78 ~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~rP~~~~~il~G~D~--~p~Ly~~Dp~G~~~~  155 (243)
T d1j2pa_          78 LVADARVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQYGGVRPFGVSLLIAGVNE--VPKLYETDPSGALLE  155 (243)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCEEEEEEEESS--SEEEEEECTTCCEEE
T ss_pred             cccHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHHHHhhhccCCccceeEEEEEecC--CceEEEEeccCceee
Confidence            468999999999999999999999999999999999999999999999999999999999986  599999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHHHHHHh
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAI  160 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~~l~~~  160 (164)
                      ++++|+|+|++.++++|++.|  +++||++||++++++||..+.++|+.++++||+++++++..|++++++||++++.++
T Consensus       156 ~~~~a~G~g~~~a~~~Le~~y--~~~ms~eeai~la~~~l~~~~~~d~~~~~iei~iv~~~~~~~~~l~~~ei~~~~~~~  233 (243)
T d1j2pa_         156 YKATAIGMGRMAVTEFFEKEY--RDDLSFDDAMVLGLVAMGLSIESELVPENIEVGYVKVDDRTFKEVSPEELKPYVERA  233 (243)
T ss_dssp             BSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHTSCCCGGGEEEEEEETTTCCCEECCHHHHHHHHHHH
T ss_pred             eeEEEeCCCcHHHHHHHHhhc--ccCCCHHHHHHHHHHHHHHHHhcccCCCceEEEEEEeCCCcEEECCHHHHHHHHHHH
Confidence            999999999999999999998  689999999999999999999999988899999999887679999999999999999


Q ss_pred             hcc
Q 031203          161 SER  163 (164)
Q Consensus       161 ~~~  163 (164)
                      +||
T Consensus       234 ~e~  236 (243)
T d1j2pa_         234 NER  236 (243)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            875

>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=4.5e-40  Score=253.14  Aligned_cols=161  Identities=29%  Similarity=0.520  Sum_probs=150.8

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.++++++.++..|++++|++++++.+++.|++++|.|+++++.|||+|++||||||+ +||+||++||+|++.+
T Consensus        74 ~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~l~~~~~~y~~~~~~rP~~v~~il~G~D~-~gp~Ly~~D~~G~~~~  152 (238)
T d1iruf_          74 LTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAGYDD-MGPHIFQTCPSANYFD  152 (238)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEET-TEEEEEEECSSSCEEE
T ss_pred             cchHHHHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHHHhhccCCCcccceEEEEEEcC-CCceEEEEcCCCCEEe
Confidence            468999999999999999999999999999999999999999999999999999999999998 7999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhcc--CCCCeEEEEEEEcCCCcEEEcCHHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQED--FKASEIEVGVVSKENPEFRVLSIEEIDEHLT  158 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d--~~~~~iei~ii~~~~~~~k~l~~~ei~~~l~  158 (164)
                      ++++|+|+|++.++++|+++|++..++|++||+++|++||..++.++  ....+|||++|+++++ |++++++||+++|.
T Consensus       153 ~~~~a~G~g~~~~~~~Lek~~~~~~~~~~~eav~lai~al~~~~~~~~~~~~~~iev~ii~k~~~-~~~l~~~ei~~~l~  231 (238)
T d1iruf_         153 CRAMSIGARSQSARTYLERHMSEFMECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLE-FTIYDDDDVSPFLE  231 (238)
T ss_dssp             ESEEEESTTHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCTTCCCCTTTEEEEEEETTEE-EEEECSGGGHHHHT
T ss_pred             eeeEEECCCchhhHHHHHhhcccccCCCHHHHHHHHHHHHHHHHhhcccCCCCcEEEEEEeCCCC-EEECCHHHHHHHHH
Confidence            99999999999999999999965446799999999999999998764  3455899999999865 99999999999999


Q ss_pred             Hhhcc
Q 031203          159 AISER  163 (164)
Q Consensus       159 ~~~~~  163 (164)
                      .++||
T Consensus       232 ~i~ek  236 (238)
T d1iruf_         232 GLEER  236 (238)
T ss_dssp             TCCCC
T ss_pred             HHHhC
Confidence            99876

>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=6.1e-40  Score=251.69  Aligned_cols=155  Identities=21%  Similarity=0.374  Sum_probs=145.5

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.+++++|.+|+.|++.++++|+++.+++.+++++|.||++++.|||||++||||||+ +||+||.+||+|++.+
T Consensus        76 ~~~D~~~l~~~~r~~~~~~~~~~~~~i~~~~la~~l~~~~~~~t~~~~~RP~gv~~il~G~d~-~g~~Ly~idp~G~~~~  154 (233)
T d1rypf_          76 LAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRPYGVGLLIIGYDK-SGAHLLEFQPSGNVTE  154 (233)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEET-TEEEEEEECTTSCEEE
T ss_pred             ccccHHHHHHHHHHHHHhhhhhcCCCCcHHHHHHHHHHHHHHHhcccccCCccceEEEEEEcC-CCCEEEEEccccceec
Confidence            468999999999999999999999999999999999999999999999999999999999998 6899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhc--CCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMK--NDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEIDEHL  157 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~--~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~~~l  157 (164)
                      ++++|+|+|++.++++|+++|+  ++++|+++||++++++||..+.++|..++ ++||++|+++++ |++++++||+++|
T Consensus       155 ~~~~aiG~gs~~a~~~Le~~~~~~~~~dms~eeai~l~~~~l~~~~~~d~~~~~~iev~ii~k~~~-~~~l~~~ei~~~i  233 (233)
T d1rypf_         155 LYGTAIGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTP-FTIYDGEAVAKYI  233 (233)
T ss_dssp             ESEEEESTTHHHHHHHHHHHHHHHTTCCSCHHHHHHHHHHHHTTSCCSSCCCTTTEEEEEEETTEE-EEEEEGGGGGGGC
T ss_pred             ccEEEecCchHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHHhccCCCCCeEEEEEEECCCC-eEECCHHHHHhhC
Confidence            9999999999999999998763  36799999999999999999998876554 999999999986 9999999998764

>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=1.4e-39  Score=249.73  Aligned_cols=156  Identities=28%  Similarity=0.523  Sum_probs=147.9

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccC-----ccccceeeEEEEEcCCCCCeEEEeCCC
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAY-----MRPLGVVAMVLSIDEECGPRLFKCDPA   75 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~-----~rP~gv~~iiaG~d~~~gp~Ly~~dp~   75 (164)
                      +.+|++.++++++.++..|++.+|++++++.+++.|++++|.|||+.+     .|||+|++|+||||+ +||+||.+||+
T Consensus        74 ~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~i~~~~~~~t~~~~~~~~~~rP~~~~~il~G~D~-~gp~Ly~idp~  152 (234)
T d1irue_          74 LIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMSRPFGVALLFGGVDE-KGPQLFHMDPS  152 (234)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCBCSTTCCSSCBSSCCCEEEEEEEEET-TEEEEEEECTT
T ss_pred             ccchHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHhhcccccccccccceEEEEEEEEcC-CCCEEEEEecC
Confidence            468999999999999999999999999999999999999999999865     799999999999998 79999999999


Q ss_pred             cceeeeeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHH
Q 031203           76 GHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDE  155 (164)
Q Consensus        76 G~~~~~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~  155 (164)
                      |++.+++++|+|+|++.++++||++|  +++|+++||++++++||+.+.+++..++++||++|+++++ |++++++||++
T Consensus       153 G~~~~~~~~a~G~gs~~~~~~Le~~~--~~~~~~eeai~~a~~al~~~~~~~~~~~~iei~ii~~~~~-~k~l~~~ei~~  229 (234)
T d1irue_         153 GTFVQCDARAIGSASEGAQSSLQELY--HKSMTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQN-FHMFTKEELEE  229 (234)
T ss_dssp             SCEEEBSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHCSSCCCTTSEEEEEECSSSC-CEECCHHHHHH
T ss_pred             cccceeeeEEeCCchHHHHHHHHHhh--ccCCCHHHHHHHHHHHHHHHHhccCCCCCEEEEEEECCCC-EEECCHHHHHH
Confidence            99999999999999999999999998  6899999999999999999998888778999999998875 99999999999


Q ss_pred             HHHHh
Q 031203          156 HLTAI  160 (164)
Q Consensus       156 ~l~~~  160 (164)
                      ++.+|
T Consensus       230 ~l~~i  234 (234)
T d1irue_         230 VIKDI  234 (234)
T ss_dssp             HHTTC
T ss_pred             HHHhC
Confidence            99864

>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=2.4e-39  Score=249.53  Aligned_cols=161  Identities=24%  Similarity=0.461  Sum_probs=152.3

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhcc------CccccceeeEEEEEcCCCCCeEEEeCC
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHA------YMRPLGVVAMVLSIDEECGPRLFKCDP   74 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~------~~rP~gv~~iiaG~d~~~gp~Ly~~dp   74 (164)
                      +.+|++.++++++.+++.|++.++++++++.++++|++++|.|||+.      ++|||+|++||+|||++++|+||.+||
T Consensus        73 ~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~rP~~~~~ii~G~D~~~~p~L~~idp  152 (242)
T d1rype_          73 LTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEP  152 (242)
T ss_dssp             SGGGHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCCBSSCTTSCCCBSSCCSEEEEEEEEETTTEEEEEEECT
T ss_pred             cchhHHHHHHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHhccccccchhccccceEEEEEEEeccccceEEEEEcC
Confidence            47999999999999999999999999999999999999999998865      379999999999999867899999999


Q ss_pred             CcceeeeeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHH
Q 031203           75 AGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEID  154 (164)
Q Consensus        75 ~G~~~~~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~  154 (164)
                      +|++.+++++|+|+|++.++++|+++|  +++||++||++++++||+.+.++++.+++++|++|+++++ |+++++++|+
T Consensus       153 ~G~~~~~~~~a~G~gs~~~~~~Le~~~--~~~ms~~ea~~la~~~l~~~~~~~~~~~~~~v~~i~~~~g-~~~l~~~~i~  229 (242)
T d1rype_         153 SGTFYRYNAKAIGSGSEGAQAELLNEW--HSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDG-FKIYDNEKTA  229 (242)
T ss_dssp             TSCEEEBSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHCSSCCCTTSEEEEEEETTTE-EEECCHHHHH
T ss_pred             CCceeccceeecccchHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHHhccCCCCceEEEEEECCCC-eEECCHHHHH
Confidence            999999999999999999999999998  6899999999999999999999999888999999998765 9999999999


Q ss_pred             HHHHHhhccC
Q 031203          155 EHLTAISERD  164 (164)
Q Consensus       155 ~~l~~~~~~~  164 (164)
                      +++.++.|||
T Consensus       230 ~~~~~i~e~~  239 (242)
T d1rype_         230 ELIKELKEKE  239 (242)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHhh
Confidence            9999999875

>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=3.4e-39  Score=245.57  Aligned_cols=153  Identities=36%  Similarity=0.561  Sum_probs=146.4

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.++++++.+++.|++.++++++++.+++.+++++|.|++++++|||++++||||||+ +||+||.+||+|++.+
T Consensus        69 ~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~a~~~~~~~~~~~~rP~~~~~li~G~d~-~gp~Ly~id~~G~~~~  147 (221)
T d1yara1          69 LVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGVSLIFAGIDQ-IGPRLFDCDPAGTINE  147 (221)
T ss_dssp             BHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBTTBCCCCEEEEEEEECS-SCEEEEEECTTCCEEE
T ss_pred             ccchHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhhhccCCCcceEEEEEEEec-CCCeEEEEcCCccEEE
Confidence            368999999999999999999999999999999999999999999999999999999999997 7999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHL  157 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~~l  157 (164)
                      ++++|+|+|+..++++|+++|  +++||++||++++++||..+++++...++++|++++++++ |++++++||+++|
T Consensus       148 ~~~~a~G~g~~~~~~~Le~~~--~~~ms~~ea~~la~~~l~~~~~~~~~~~~~ei~~i~~~~~-~r~l~~~ei~~~l  221 (221)
T d1yara1         148 YKATAIGSGKDAVVSFLEREY--KENLPEKEAVTLGIKALKSSLEEGEELKAPEIASITVGNK-YRIYDQEEVKKFL  221 (221)
T ss_dssp             BSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHTSCSSCCCCCCEEEEEETTSC-CEECCHHHHHTTC
T ss_pred             eeEEEECCchHHHHHHHHHHh--hccccHHHHHHHHHHHHHHHHhccCCCCCcEEEEEEcCCC-EEECCHHHHHHhC
Confidence            999999999999999999998  6899999999999999999998888778999999998875 9999999999864

>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=4.5e-39  Score=248.54  Aligned_cols=159  Identities=28%  Similarity=0.364  Sum_probs=145.9

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.|++++|.+|+.|++++|++++++.++++|++++|.|||++++|||+|++||||||+++||+||.+||+|++.+
T Consensus        80 ~~~D~~~l~~~~~~~~~~~~~~~g~~i~~~~la~~la~~~~~~t~~~~~rP~~vs~li~G~D~~~gp~Ly~iDp~G~~~~  159 (245)
T d1irug_          80 LLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYG  159 (245)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSBSSBCCCSEEEEEEEEETTTEEEEEEECTTCCEEE
T ss_pred             CchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhccccccccceEEEEEEEcCCCCceEEEEcCCceEEe
Confidence            46899999999999999999999999999999999999999999999999999999999999767999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEIDEHLTA  159 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~~~l~~  159 (164)
                      ++++|+|+|++.++++||+.|  +++||.+||++++++||+.+.+++.... ++||++|+++++.++++.|.|+.+.+.+
T Consensus       160 ~~~~a~G~gs~~a~~~Le~~~--~~dmt~eea~~l~~~~l~~~~~~~~~~~~~iei~~v~~~~~~~~~~~~~e~~~~~~~  237 (245)
T d1irug_         160 YWGCAIGKARQAAKTEIEKLQ--MKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEK  237 (245)
T ss_dssp             BSEEEESTTHHHHHHHHTTSC--GGGCCHHHHHHHHHHHHHHHSCSSSSCCEEEEEEECBTTTTTCCEECCHHHHHHHHH
T ss_pred             eeEEEECCccHHHHHHHHhhc--CCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEEEEecCCCeEEEChHHHHHHHHH
Confidence            999999999999999999998  5889999999999999999987765555 8999999987655677777787777666


Q ss_pred             hh
Q 031203          160 IS  161 (164)
Q Consensus       160 ~~  161 (164)
                      ..
T Consensus       238 ~~  239 (245)
T d1irug_         238 YA  239 (245)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

>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=2.1e-38  Score=245.30  Aligned_cols=158  Identities=33%  Similarity=0.543  Sum_probs=148.2

Q ss_pred             CCchHHHHHHHHHHHHH-HHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCccee
Q 031203            1 MTADARTLVQQARYEAA-EFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFF   79 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~-~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~   79 (164)
                      +++|++.++++++.+++ +|+..++++++++.+++.+++++|.|+++++.|||+|++||||||+.+||+||++||+|++.
T Consensus        78 ~~~D~~~l~~~~~~~~~~~y~~~~~~~~~~~~la~~~~~~~~~~~~~~~~rp~~v~~li~G~D~~~gp~Ly~id~~G~~~  157 (250)
T d1rypb_          78 MGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYF  157 (250)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCCEEEEEEEEETTTEEEEEEECTTSCEE
T ss_pred             cccHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhcCCcCeeEEEEEEEecCCCCCEEEEEcCcEEEE
Confidence            46899999999999997 48999999999999999999999999999999999999999999987789999999999999


Q ss_pred             eeeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCC--------------CcE
Q 031203           80 GHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKEN--------------PEF  145 (164)
Q Consensus        80 ~~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~--------------~~~  145 (164)
                      +++++|+|+|+..++++||++|  +++||++||++++++||..+.++|.+..+++|++|++++              +.|
T Consensus       158 ~~~~~a~G~gs~~a~~~Le~~~--~~~ms~eea~~la~~al~~~~~~d~s~~~iev~vi~~~~~~~~~~~~v~~~~~~~f  235 (250)
T d1rypb_         158 PWKATAIGKGSVAAKTFLEKRW--NDELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRF  235 (250)
T ss_dssp             EBSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHCCSCCSTTTEEEEEECSCCGGGTSEESCSSCCCCSE
T ss_pred             EeeEEecCcchHHHHHHHHHhc--ccCCCHHHHHHHHHHHHHHHhhccCCCCCEEEEEEeCCCcccccccccccccCCce
Confidence            9999999999999999999998  689999999999999999999999876699999998753              359


Q ss_pred             EEcCHHHHHHHHHHh
Q 031203          146 RVLSIEEIDEHLTAI  160 (164)
Q Consensus       146 k~l~~~ei~~~l~~~  160 (164)
                      ++++++||+++|++|
T Consensus       236 r~ls~eei~~~l~~l  250 (250)
T d1rypb_         236 RKLTSQEINDRLEAL  250 (250)
T ss_dssp             EECCHHHHHHHHTTC
T ss_pred             EECCHHHHHHHHHhC
Confidence            999999999999864

>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=3.6e-38  Score=242.81  Aligned_cols=160  Identities=31%  Similarity=0.529  Sum_probs=149.1

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCC-CCCeEEEeCCCccee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEE-CGPRLFKCDPAGHFF   79 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~-~gp~Ly~~dp~G~~~   79 (164)
                      +.+|++.|+++++.+++.|++.+|++++++.+++++++++|.||+++++|||+|++||||||++ +||+||.+||+|++.
T Consensus        76 ~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~i~~~~~~~t~~~~~rP~~v~~li~G~d~~~~~p~Ly~idp~G~~~  155 (241)
T d1rypd_          76 LNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYS  155 (241)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSSTTBCCCSEEEEEEECCTTCCSCEEEEECTTSCEE
T ss_pred             ccchHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHhhccccCcccceEEEEEEccccCcceEEEecCCEEEE
Confidence            4689999999999999999999999999999999999999999999999999999999999964 589999999999999


Q ss_pred             eeeEEeecCChHHHHHHHHHhhcC-CCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHHHHH
Q 031203           80 GHKATSAGLKEQEAINFLEKKMKN-DPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLT  158 (164)
Q Consensus        80 ~~~~~aiG~~s~~~~~~Le~~~~~-~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~~l~  158 (164)
                      +++++|+|+|++.++++|++.|+. .++||.+|++++|++||..+.+.  +..+++|+|++++++ |++++++||+++|.
T Consensus       156 ~~~~~a~G~gs~~~~~~Le~~~~~~~~~~t~~e~i~lal~al~~~~~~--~~~~iei~ii~~d~~-~~~l~~~ei~~~l~  232 (241)
T d1rypd_         156 SWSAQTIGRNSKTVREFLEKNYDRKEPPATVEECVKLTVRSLLEVVQT--GAKNIEITVVKPDSD-IVALSSEEINQYVT  232 (241)
T ss_dssp             EBSEEEESTTHHHHHHHHHTTCCTTSCCCSHHHHHHHHHHHHHHHHCS--CSTTEEEEEEETTTE-EEECCHHHHHHHHH
T ss_pred             eeCeEEECcCHHHHHHHHHHhhhcccCCCCHHHHHHHHHHHHHHHhcC--CCCcEEEEEEECCCC-EEECCHHHHHHHHH
Confidence            999999999999999999999954 46899999999999999998754  455999999999874 99999999999999


Q ss_pred             Hhhcc
Q 031203          159 AISER  163 (164)
Q Consensus       159 ~~~~~  163 (164)
                      +++++
T Consensus       233 ~i~~~  237 (241)
T d1rypd_         233 QIEQE  237 (241)
T ss_dssp             HHTHH
T ss_pred             HHHHH
Confidence            99864

>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-38  Score=245.56  Aligned_cols=160  Identities=30%  Similarity=0.517  Sum_probs=146.3

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.++++++.+|+.|++.+|.+|+++.+++++++++|.||+++++|||+|++||+|||+++||+||++||+|++.+
T Consensus        75 ~~~D~~~l~~~~~~~~~~~~~~~~~~i~v~~la~~ls~~~~~~t~~~~~rp~~v~~li~G~D~~~~p~Ly~idp~G~~~~  154 (243)
T d1irud_          75 LTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHA  154 (243)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCEEEEEEEECSSSCEEEEEECTTSCEEE
T ss_pred             chhhHHHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHhcccCCccceEEEEEEEcCCCCCEEEEecCcEEEEe
Confidence            46899999999999999999999999999999999999999999999999999999999999767899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHHHHHHh
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAI  160 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~~l~~~  160 (164)
                      ++++|+|+|++.++++|+++|+.+..++.++++++++++|......  +.++++|++++++++ |++++++||++++.++
T Consensus       155 ~~~~a~G~gs~~a~~~Lek~~~~~~~~~~~~~i~~ai~~l~~~~~~--~~~~vei~ii~k~~~-~~~l~~~eI~~~l~~i  231 (243)
T d1irud_         155 WKANAIGRGAKSVREFLEKNYTDEAIETDDLTIKLVIKALLEVVQS--GGKNIELAVMRRDQS-LKILNPEEIEKYVAEI  231 (243)
T ss_dssp             BSEEEESTTHHHHHHHHTTTCCSSTTCSHHHHHHHHHHHHHTTSCT--TSTTCCEEEEESSSC-EECCCHHHHHHHTTTT
T ss_pred             ccEEEECCChHHHHHHHHHhcccCCCccHHHHHHHHHHHHHHHhcC--CCCcEEEEEEECCCC-EEECCHHHHHHHHHHH
Confidence            9999999999999999999995443448888999999999877643  344899999999865 9999999999999998


Q ss_pred             hcc
Q 031203          161 SER  163 (164)
Q Consensus       161 ~~~  163 (164)
                      +++
T Consensus       232 ~~~  234 (243)
T d1irud_         232 EKE  234 (243)
T ss_dssp             TTT
T ss_pred             Hhh
Confidence            843

>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=3.2e-37  Score=237.85  Aligned_cols=158  Identities=27%  Similarity=0.466  Sum_probs=149.7

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.++++++.+++.|++.++++++++.+++.+++++|.|++++++|||+|++||||||+++||+||.+||+|++.+
T Consensus        79 ~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~rP~~~~~ll~G~d~~~gp~Ly~id~~Gs~~~  158 (244)
T d1rypc_          79 LTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTG  158 (244)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSCCCCCEEEEEEEEETTTEEEEEEECTTCCEEE
T ss_pred             ccCcHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhhhhccccCccceeEEEEEEecCCCceEEEecCCCcEee
Confidence            46899999999999999999999999999999999999999999999999999999999999867899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCC----cEEEcCHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENP----EFRVLSIEEIDE  155 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~----~~k~l~~~ei~~  155 (164)
                      ++++|+|+|+..+.++|++.|  +++||++||++++++||..+.++|..++ ++||++|++++.    .+++++++||++
T Consensus       159 ~~~~a~G~g~~~a~~~Le~~~--~~~ms~eeai~l~~~al~~a~~~d~~~~~~iei~ii~~~~~~~~~~~~~~~~~Ei~~  236 (244)
T d1rypc_         159 WKAISVGANTSAAQTLLQMDY--KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKD  236 (244)
T ss_dssp             BSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHCSSSSCCGGGEEEEEEECCSSSSSCEEEECCHHHHHH
T ss_pred             eeeeeccchhHHHHHHHHhcc--cCCCCHHHHHHHHHHHHHHHHhccCCCCCcEEEEEEECCCcccceeEEECCHHHHHH
Confidence            999999999999999999998  6899999999999999999999998877 899999998863    388999999999


Q ss_pred             HHHHh
Q 031203          156 HLTAI  160 (164)
Q Consensus       156 ~l~~~  160 (164)
                      +|.+-
T Consensus       237 ~l~k~  241 (244)
T d1rypc_         237 ILVKT  241 (244)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            99864

>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=3.6e-36  Score=232.01  Aligned_cols=161  Identities=24%  Similarity=0.383  Sum_probs=143.8

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.|+++++.+++.|++.++++++++.+++.+++++|.||++++.|||+|++||||||+ +||+||.+||+|++.+
T Consensus        77 ~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~t~~~~~RP~~~~~iiaG~D~-~gp~Ly~idp~Gs~~~  155 (244)
T d1rypg_          77 LIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGGVDK-NGAHLYMLEPSGSYWG  155 (244)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSCTTBCCCCEEEEEEEEET-TEEEEEEECTTSCEEE
T ss_pred             chhhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhcccccCCceEEEEEEEEeC-CCCEEEEEcCCccEEe
Confidence            468999999999999999999999999999999999999999999999999999999999998 7999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhh-cCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcC--CCcEEEcCHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKM-KNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKE--NPEFRVLSIEEIDEH  156 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~-~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~--~~~~k~l~~~ei~~~  156 (164)
                      ++++|+|+|+..++++||+.. +++++||.+||++++++||..+.+++.... +++|++++.+  ++.++.++.++++++
T Consensus       156 ~~~~a~G~gs~~~~~~Lek~~~~~~~~mt~eeai~la~~~L~~~~~~~~~~~~~iev~ii~~~~~~~~~~~~~~e~~~~~  235 (244)
T d1rypg_         156 YKGAATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEA  235 (244)
T ss_dssp             BSEEEESTTHHHHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHGGGGTTSCEEEEEEEEETTTTTTSEEECCTHHHHHH
T ss_pred             cCeEecCCccHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHhcccCCCCeEEEEEEEEEcCCCeEEECCHHHHHHH
Confidence            999999999999999999731 126899999999999999999998776655 8999999853  334677777777777


Q ss_pred             HHHhhc
Q 031203          157 LTAISE  162 (164)
Q Consensus       157 l~~~~~  162 (164)
                      +...++
T Consensus       236 ~~~~~~  241 (244)
T d1rypg_         236 IDFAQK  241 (244)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            766543

>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=2.8e-36  Score=230.68  Aligned_cols=155  Identities=34%  Similarity=0.555  Sum_probs=148.7

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.|+++++.+++.|+++++++++++.+++.+++++|.|+++++.|||+++++++|+|+ +||+||.+||+|++.+
T Consensus        78 ~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~p~~~~~li~g~d~-~~~~ly~id~~G~~~~  156 (233)
T d1irub_          78 MGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGVSLLICGWNE-GRPYLFQSDPSGAYFA  156 (233)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCSEEEEEEEECS-SSEEEEEECTTSCEEE
T ss_pred             cchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhccccccceEEEeeeeccc-CCceEEEEcCCcceEe
Confidence            368999999999999999999999999999999999999999999999999999999999998 8999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEEcCCCcEEEcCHHHHHHHHHHh
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASEIEVGVVSKENPEFRVLSIEEIDEHLTAI  160 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~iei~ii~~~~~~~k~l~~~ei~~~l~~~  160 (164)
                      ++++|+|+|+..++++|++.|  +++||++||++++++||..+.++|+.+++++|+++++++  +++++|+||+++|.++
T Consensus       157 ~~~~a~G~gs~~~~~~Le~~~--~~~ms~eea~~l~~~~L~~~~~~d~~~~~vev~ii~~~g--~~~l~~~eI~~~l~~i  232 (233)
T d1irub_         157 WKATAMGKNYVNGKTFLEKRY--NEDLELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAG--FRRLTPTEVKDYLAAI  232 (233)
T ss_dssp             BSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHTTCCSCCCSSSEEEEEEETTE--EEECCHHHHHHHHTTC
T ss_pred             ccceecCCcHHHHHHHHHhhc--ccCccHHHHHHHHHHHHHHHHhccCCCCcEEEEEEeCCC--eEECCHHHHHHHHHHh
Confidence            999999999999999999998  689999999999999999999999987899999999874  9999999999999876

>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=1.6e-35  Score=222.21  Aligned_cols=152  Identities=22%  Similarity=0.358  Sum_probs=141.6

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +++|++.++++++.+++.|++.++++++++.+++++++++|.+    +.|||++++|+||+|+  +|+||.+||+|++.+
T Consensus        48 ~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~~~~~----~~~p~~~~~lvaG~d~--~p~l~~~d~~G~~~~  121 (203)
T d1yarh1          48 LVGDAQVLVRYMKAELELYRLQRRVNMPIEAVATLLSNMLNQV----KYMPYMVQLLVGGIDT--APHVFSIDAAGGSVE  121 (203)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHT----TTSCCCEEEEEEEESS--SEEEEEECTTCCEEE
T ss_pred             CcchHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHhh----ccCCccceeEEEEEcC--CCeeEecCCccceec
Confidence            3689999999999999999999999999999999999988654    4689999999999986  599999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEIDEHLTA  159 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~~~l~~  159 (164)
                      ++++|+|+|++.+.++|+++|  +++||.+||++++.+||..+.++|..++ +++|++|+++++ |+.++++||++++.+
T Consensus       122 ~~~~a~G~g~~~~~~~L~~~~--~~~~s~eea~~l~~~~l~~~~~~d~~~~~~v~v~ii~~~~g-~~~l~~~ei~~~~~~  198 (203)
T d1yarh1         122 DIYASTGSGSPFVYGVLESQY--SEKMTVDEGVDLVIRAISAAKQRDSASGGMIDVAVITRKDG-YVQLPTDQIESRIRK  198 (203)
T ss_dssp             ESEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHCTTCCSCCEEEEEETTTE-EEECCHHHHHHHHHH
T ss_pred             ccccccCCCcHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHHHhcCCCCCeEEEEEEECCCC-EEECCHHHHHHHHHH
Confidence            999999999999999999998  6899999999999999999999998776 799999998764 999999999999988


Q ss_pred             hh
Q 031203          160 IS  161 (164)
Q Consensus       160 ~~  161 (164)
                      +.
T Consensus       199 ~~  200 (203)
T d1yarh1         199 LG  200 (203)
T ss_dssp             HT
T ss_pred             hC
Confidence            64

>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=5.3e-35  Score=219.20  Aligned_cols=152  Identities=14%  Similarity=0.176  Sum_probs=142.5

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      ..+|++.++++++.+++.|++.++++++++.+++++++++|.|+    .+||+++++++|+|+ +||+||.+||+|++.+
T Consensus        48 ~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~~~~~~----~~p~~~~~lvaG~d~-~~~~l~~~d~~G~~~~  122 (201)
T d1irul_          48 GAADCSFWERLLARQCRIYELRNKERISVAAASKLLANMVYQYK----GMGLSMGTMICGWDK-RGPGLYYVDSEGNRIS  122 (201)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHTTT----TSCCCBEEEEEEECS-SSEEEEEEESSSCEEE
T ss_pred             ccchHHHHHHHHHHHHHHHHHhcCCCCchhHHHHHHHHHhhhcc----CCCceEEEEEEEEec-CCceEEEEccCceEEE
Confidence            36899999999999999999999999999999999999997654    479999999999998 7999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEIDEHLTA  159 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~~~l~~  159 (164)
                      ++++|+|+|++.++++|++.|  +++||.+||++++++||..+.++|..++ .++|++|+++|  +++++++||.+++.+
T Consensus       123 ~~~~a~G~g~~~~~~~Le~~~--~~~ms~eea~~l~~~~l~~~~~~d~~sg~~~~v~~i~~~G--~~~i~~~ev~~~~~~  198 (201)
T d1irul_         123 GATFSVGSGSVYAYGVMDRGY--SYDLEVEQAYDLARRAIYQATYRDAYSGGAVNLYHVREDG--WIRVSSDNVADLHEK  198 (201)
T ss_dssp             CSEEEESTTHHHHHHHHHTTC--CTTCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEECSSC--EEEEEEEEHHHHHHH
T ss_pred             eeeEEecCchHHHHHHHHhhc--cCCCCHHHHHHHHHHHHHHHHHhCCCCCCceEEEEEeCCc--eEEECHHHHHHHHHh
Confidence            999999999999999999998  6899999999999999999999998777 99999999985  888999999999887


Q ss_pred             hh
Q 031203          160 IS  161 (164)
Q Consensus       160 ~~  161 (164)
                      ++
T Consensus       199 ~~  200 (201)
T d1irul_         199 YS  200 (201)
T ss_dssp             HT
T ss_pred             hc
Confidence            64

>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=4.2e-35  Score=219.30  Aligned_cols=147  Identities=14%  Similarity=0.196  Sum_probs=135.9

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCC-CCCeEEEeCCCccee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEE-CGPRLFKCDPAGHFF   79 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~-~gp~Ly~~dp~G~~~   79 (164)
                      +.+|++.|.+.++.+++.|+++++++++|+.+++++++.++.+++  +.|||++++||||||+. +||+||.+||+|++.
T Consensus        49 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~--~~~P~~~~~liaG~D~~~~~p~L~~id~~G~~~  126 (198)
T d1rypk_          49 EAGDTVQFAEYIQANIQLYSIREDYELSPQAVSSFVRQELAKSIR--SRRPYQVNVLIGGYDKKKNKPELYQIDYLGTKV  126 (198)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHTT--SSSCCCEEEEEEEEETTTTEEEEEEECTTCCEE
T ss_pred             CcccHHHHHHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHHh--cccccceEEEEEEEecCCCceEEEEecccccEE
Confidence            358999999999999999999999999999999999999866543  57999999999999974 589999999999999


Q ss_pred             eeeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHH
Q 031203           80 GHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEI  153 (164)
Q Consensus        80 ~~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei  153 (164)
                      +++++|+|+|+..++++|+++|  +++||.+||++++.+||..+..+|..++ +++|++|+++|  ++.+++.++
T Consensus       127 ~~~~~a~G~gs~~~~~~Le~~~--~~~~~~eea~~l~~~~l~~~~~~d~~s~~~~~v~vi~~dG--~~~~~~~~~  197 (198)
T d1rypk_         127 ELPYGAHGYSGFYTFSLLDHHY--RPDMTTEEGLDLLKLCVQELEKRMPMDFKGVIVKIVDKDG--IRQVDDFQA  197 (198)
T ss_dssp             ECSEEECTTHHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHCSBCCCCEEEEEEETTE--EEEECCCSC
T ss_pred             ecceEEEeccchhhHHHHHhcc--cccCCHHHHHHHHHHHHHHHHHhcCcCCCcEEEEEEcCCC--eEEcchhcc
Confidence            9999999999999999999998  6899999999999999999999998777 89999999985  899888765

>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=2.3e-34  Score=215.33  Aligned_cols=152  Identities=22%  Similarity=0.336  Sum_probs=142.0

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.|+++++.+++.|++.++.+++++.+++++++++|.|+    .|||++++|+||||+ .||+||.+||+|+..+
T Consensus        48 ~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~----~~p~~~~~lvaG~d~-~~~~l~~~d~~G~~~~  122 (202)
T d1j2qh_          48 SVGDAQFLARIIKIEANLYEIRRERKPTVRAIATLTSNLLNSYR----YFPYLVQLLIGGIDS-EGKSIYSIDPIGGAIE  122 (202)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTT----TSCCCEEEEEEEEET-TEEEEEEECTTCCEEE
T ss_pred             cchhHHHHHHHHHHHhhhhhhccCCCccHHHHHHHHHHHHhhhc----ccceeeEEEEEEEcC-CCceEEEEeCCCCeEe
Confidence            36899999999999999999999999999999999999998765    469999999999998 7899999999999877


Q ss_pred             e-eEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHHHHHH
Q 031203           81 H-KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEIDEHLT  158 (164)
Q Consensus        81 ~-~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~~~l~  158 (164)
                      + .++|+|+|++.++++|+++|  +++||.+||++++++||..+.++|..++ +++|++|++++  +++++++||++++.
T Consensus       123 ~~~~~a~G~g~~~~~~~Le~~~--~~~ms~~ea~~l~~~al~~~~~~d~~~g~~v~v~~i~~~g--~~~~~~~ei~~~l~  198 (202)
T d1j2qh_         123 EKDIVATGSGSLTAYGVLEDRF--TPEIGVDEAVELAVRAIYSAMKRDSASGDGIDVVKITEDE--FYQYSPEEVEQILA  198 (202)
T ss_dssp             ESSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHTTCTTSCSCEEEEEECSSC--EEECHHHHHHHHGG
T ss_pred             ecceEEccCChHHHHHHHHhhc--CCCCCHHHHHHHHHHHHHHHHHhcCCCCCeEEEEEEECCC--EEEeCHHHHHHHHH
Confidence            6 58999999999999999998  6899999999999999999999998877 89999999985  89999999999999


Q ss_pred             Hhh
Q 031203          159 AIS  161 (164)
Q Consensus       159 ~~~  161 (164)
                      ++.
T Consensus       199 ~~~  201 (202)
T d1j2qh_         199 KFR  201 (202)
T ss_dssp             GTT
T ss_pred             Hhh
Confidence            875

>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=7.8e-35  Score=219.07  Aligned_cols=146  Identities=15%  Similarity=0.184  Sum_probs=134.4

Q ss_pred             CchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceeee
Q 031203            2 TADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGH   81 (164)
Q Consensus         2 ~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~~   81 (164)
                      .+|++.|+++++.+++.|+++++++ ++..+++.++++++.     +.+||++++||||||++++|+||.+||+|++.++
T Consensus        58 ~aD~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~-----~~~p~~~~~lvaG~d~~~~p~Ly~~d~~G~~~~~  131 (205)
T d1ryph_          58 AADTQAIADIVQYHLELYTSQYGTP-STETAASVFKELCYE-----NKDNLTAGIIVAGYDDKNKGEVYTIPLGGSVHKL  131 (205)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSSC-CHHHHHHHHHHHHHH-----TTTTCCEEEEEEEEETTTEEEEEEECTTSCCEEE
T ss_pred             hhHHHHHHHHHHHHHHHHHHHcCCc-cHHHHHHHHHHHHHh-----CccCceEEEEEEeecCCCCcEEEEECCCCcEEec
Confidence            6899999999999999999999976 578899999988732     3579999999999998788999999999999999


Q ss_pred             eEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHHH
Q 031203           82 KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEIDE  155 (164)
Q Consensus        82 ~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~~  155 (164)
                      +++|+|+|+..++++|++.|  +++||.+||++++++||..+.++|+.++ +++|++|+++|..++.+.|+|+++
T Consensus       132 ~~~a~G~g~~~~~~~Le~~~--~~~ms~~ea~~l~~~al~~a~~rD~~sg~~v~v~iitk~G~~~~~~~~~e~~~  204 (205)
T d1ryph_         132 PYAIAGSGSTFIYGYCDKNF--RENMSKEETVDFIKHSLSQAIKWDGSSGGVIRMVVLTAAGVERLIFYPDEYEQ  204 (205)
T ss_dssp             SEEEESGGGGGGHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHBTTCCSCEEEEEEETTEEEEEEECHHHHTC
T ss_pred             CeEEeecCcHHHHHHHHhhh--hcccCHHHHHHHHHHHHHHHHHhcCcCCCCEEEEEEcCCceEEEecCcccccc
Confidence            99999999999999999998  6899999999999999999999999877 899999999986677899999875

>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=2.6e-34  Score=217.10  Aligned_cols=155  Identities=12%  Similarity=0.153  Sum_probs=144.3

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.|+++++.+++.|++.++++++|+.+++++++++|.|.    .+|++++.+++|+|+++||+||.+||+|++.+
T Consensus        48 ~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~ls~~~~~~~----~~p~~~~~~l~G~~~~~g~~Ly~id~~G~~~~  123 (212)
T d1rypl_          48 GAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYK----GAGLSMGTMICGYTRKEGPTIYYVDSDGTRLK  123 (212)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTT----TSCCCBEEEEEEEETTTEEEEEEEETTCCEEE
T ss_pred             chHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhc----cCCcceEeeeeEeecCCCCEEEEECCCceEEe
Confidence            36899999999999999999999999999999999999997653    45899999999998878999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEIDEHLTA  159 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~~~l~~  159 (164)
                      ++++|+|+|++.++++|+++|  +++||.+||++++++||..+.+||..++ +++|++|++++  +++++++||.+++.+
T Consensus       124 ~~~~a~G~gs~~~~~~Le~~~--~~~mt~~ea~~l~~~al~~~~~rd~~sg~~v~v~vi~~~g--~~~~~~~ev~~~~~~  199 (212)
T d1rypl_         124 GDIFCVGSGQTFAYGVLDSNY--KWDLSVEDALYLGKRSILAAAHRDAYSGGSVNLYHVTEDG--WIYHGNHDVGELFWK  199 (212)
T ss_dssp             CSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTE--EEEEEEEEHHHHHHH
T ss_pred             cceEEEccCcccchhHHHHhc--cCCCCHHHHHHHHHHHHHHHHHhcCCCCCceEEEEEcCCc--eEEeCHHHHHHHHHH
Confidence            999999999999999999998  6899999999999999999999999887 89999999985  999999999999988


Q ss_pred             hhcc
Q 031203          160 ISER  163 (164)
Q Consensus       160 ~~~~  163 (164)
                      +.++
T Consensus       200 ~~~~  203 (212)
T d1rypl_         200 VKEE  203 (212)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            8754

>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=3.3e-34  Score=218.88  Aligned_cols=155  Identities=14%  Similarity=0.198  Sum_probs=133.5

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCC---CCCeEEEeCCCc
Q 031203            1 MTADARTLVQQARYEAAEFRFKYG-YEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEE---CGPRLFKCDPAG   76 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~-~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~---~gp~Ly~~dp~G   76 (164)
                      +.+|++.|+++++.+|+.|++.++ .+++++.+++.++++++. ++..++|||||++||||||..   +||+||.+||+|
T Consensus        59 ~~aD~~~l~~~~r~~~~~~~~~~~~~~~~~~~la~~~~~~~~~-~~~~~~rP~gvs~lvaG~D~~g~~~~p~Ly~vDpsG  137 (227)
T d1q5qa_          59 KYNEFENLRRAGIVHADMRGYSYDRRDVTGRSLANAYAQTLGT-IFTEQPKPYEVEICVAEVGRVGSPKAPQLYRITYDG  137 (227)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHHHHHHH-HHHHSSSCCCEEEEEEECCCSSCCCCCEEEEEETTS
T ss_pred             chHHHHHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHH-HHHhcCCCceEEEEEEEEecCCCCCCCEEEEEcccc
Confidence            468999999999999999999998 568999999999988664 344567999999999999863   579999999999


Q ss_pred             ceeeee-EEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccC-----CCCeEEEEEEEcCCC--cEEEc
Q 031203           77 HFFGHK-ATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDF-----KASEIEVGVVSKENP--EFRVL  148 (164)
Q Consensus        77 ~~~~~~-~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~-----~~~~iei~ii~~~~~--~~k~l  148 (164)
                      ++.+++ +++.|++++.++++|+++|  +++||++||+++|++||+.++.+|.     ...++||+|++++++  .|+++
T Consensus       138 ~~~~~~~~~~~g~~s~~~~~~Le~~y--~~~ms~eea~~la~~aL~~a~~~d~~~~~~~~~~ievavi~k~~~~~~fr~l  215 (227)
T d1q5qa_         138 SIVDEQHFVVMGGTTEPIATAMRESY--RADLDLEAAVGIAVNALRQGGAGEGEKRNVDVASLEVAVLDQSRPRRAFRRI  215 (227)
T ss_dssp             CEEEESSEEEESSSHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHTTCC--------CCSSCSEEEEEETTSSSCCEEEC
T ss_pred             ceeeecccccCCCchHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHhhcccccCCcCcceEEEEEEECCCCccceEEc
Confidence            998876 5677788999999999998  6899999999999999999998764     345799999999874  69999


Q ss_pred             CHHHHHHHHH
Q 031203          149 SIEEIDEHLT  158 (164)
Q Consensus       149 ~~~ei~~~l~  158 (164)
                      +++||+++|.
T Consensus       216 ~~~ei~~~l~  225 (227)
T d1q5qa_         216 AGTALEQLVP  225 (227)
T ss_dssp             CHHHHHTTSC
T ss_pred             CHHHHHHHhc
Confidence            9999998875

>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=4.7e-34  Score=214.12  Aligned_cols=150  Identities=14%  Similarity=0.184  Sum_probs=140.0

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.++++++.+++.|+++++++++|+.+++++++.++.|     .+||++++|++|||+.++|+||.+||.|++.+
T Consensus        48 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~l~~~-----~~p~~~~~lvaG~d~~~~~~l~~~d~~g~~~~  122 (202)
T d1iruh_          48 SAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEMCYRY-----REDLMAGIIIAGWDPQEGGQVYSVPMGGMMVR  122 (202)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHT-----TTTCCEEEEEEEEETTTEEEEEEECTTSCCEE
T ss_pred             chHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHhh-----ccceeEEEEEEEeecCCCcEEEEECCCCceee
Confidence            4689999999999999999999999999999999999999654     36999999999999878899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHHHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEIDEHL  157 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei~~~l  157 (164)
                      ++++|+|+|+..++++|++.|  +++||.+||++++++||..+.++|..++ +++|++|+++|.+++.+++|||+++.
T Consensus       123 ~~~~a~G~g~~~a~~~L~~~~--~~~~~~~ea~~l~~~al~~a~~rD~~sg~~i~v~vi~~~G~~~~~~~~d~~~~~~  198 (202)
T d1iruh_         123 QSFAIGGSGSSYIYGYVDATY--REGMTKEECLQFTANALALAMERDGSSGGVIRLAAIAESGVERQVLLGDQIPKFA  198 (202)
T ss_dssp             CSEEEESGGGGGGHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHBTTCCSCEEEEEEETTEEEEEEECGGGSCCCC
T ss_pred             cceeEEeCCHHHHHHHHHHhh--ccCCcHHHHHHHHHHHHHHHHhhCCCCCCCEEEEEEeCCCeEEEEcCHHHhhhhh
Confidence            999999999999999999998  6899999999999999999999999887 89999999998777889999887653

>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=1.4e-33  Score=215.84  Aligned_cols=152  Identities=13%  Similarity=0.206  Sum_probs=139.8

Q ss_pred             CchHHHHHHHHHHHHHHHHHHh-----CCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCc
Q 031203            2 TADARTLVQQARYEAAEFRFKY-----GYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAG   76 (164)
Q Consensus         2 ~~D~~~l~~~~~~~~~~~~~~~-----~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G   76 (164)
                      .+|++.|.++++.++..|++++     +.+++++.+++++++.+  |+++.++|||+|++||+|||+.++|+||.+||+|
T Consensus        57 ~~D~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~~--y~~~~~~~P~~~~~liaG~d~~g~~~ly~~d~~G  134 (233)
T d1ryp2_          57 ISDMQHIERLLKDLVTENAYDNPLADAEEALEPSYIFEYLATVM--YQRRSKMNPLWNAIIVAGVQSNGDQFLRYVNLLG  134 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCTTTTTTTSCCHHHHHHHHHHHH--HHHHHTTCCCCEEEEEEEECTTSCEEEEEEETTC
T ss_pred             chHHHHHHHHHHHHHHHHHHhhCCCCCCcccCHHHHHHHHHHHH--HhhccccCCceeEEEEEEEcCCCCeEEEEEcCCC
Confidence            5899999999999999999987     56789999999999987  8888889999999999999986778999999999


Q ss_pred             ceeeeeEEeecCChHHHHHHHHHhhcC---CCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHH
Q 031203           77 HFFGHKATSAGLKEQEAINFLEKKMKN---DPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEE  152 (164)
Q Consensus        77 ~~~~~~~~aiG~~s~~~~~~Le~~~~~---~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~e  152 (164)
                      ++.+++++|+|+|++.++++|++.|+.   .|+||.|||++++++||..+++||+.++ +++|++|+++++ ++++.+++
T Consensus       135 ~~~~~~~~a~G~g~~~a~~~Le~~~~~~~~~~~ms~eeA~~l~~~al~~~~~rD~~sg~~i~i~~itkd~g-~~~~~~~~  213 (233)
T d1ryp2_         135 VTYSSPTLATGFGAHMANPLLRKVVDRESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKNTG-LTFKKNLQ  213 (233)
T ss_dssp             CEECCSEEECTHHHHHHHHHHTTTCCSGGGGGGCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTTE-EEEEEEEE
T ss_pred             cEEeeeeEEecCccHHHHHHHHHHHhhcccccccCHHHHHHHHHHHHHHHHHhcccCCCCEEEEEEECCCC-EEECChhc
Confidence            999999999999999999999999853   2789999999999999999999999888 899999999875 99999988


Q ss_pred             HHHH
Q 031203          153 IDEH  156 (164)
Q Consensus       153 i~~~  156 (164)
                      |+..
T Consensus       214 ie~~  217 (233)
T d1ryp2_         214 VENM  217 (233)
T ss_dssp             CCSC
T ss_pred             chhh
Confidence            8654

>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=99.98  E-value=5.4e-32  Score=205.34  Aligned_cols=142  Identities=18%  Similarity=0.214  Sum_probs=131.5

Q ss_pred             CchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceeee
Q 031203            2 TADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGH   81 (164)
Q Consensus         2 ~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~~   81 (164)
                      .+|++.++++++.+++.|++++|++++++.++++++++++.     ..+||++++|+||||+ +||+||.+||+|++.++
T Consensus        49 ~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~~y~-----~~~p~~~~~ivaG~D~-~g~~L~~id~~G~~~~~  122 (220)
T d1irui_          49 AADTDMTTQLISSNLELHSLSTGRLPRVVTANRMLKQMLFR-----YRGYIGAALVLGGVDV-TGPHLYSIYPHGSTDKL  122 (220)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHCSCCCHHHHHHHHHHHHHH-----TTTCSCEEEEEEEECS-SCEEEEEECTTSCEEEC
T ss_pred             cHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhhhhh-----cccccceeEEEEEEeC-CCcEEEEEeCCCcEEEe
Confidence            58999999999999999999999999999999999998832     3579999999999998 78999999999999999


Q ss_pred             eEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHH
Q 031203           82 KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEI  153 (164)
Q Consensus        82 ~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei  153 (164)
                      +++|+|+|+..++++|++.|  +++||++||++++++||..+.++|..++ +++|++|++++  ++++.|.++
T Consensus       123 ~~~a~Gsgs~~a~~~L~~~~--~~~~s~~ea~~l~~~al~~~~~~D~~sg~~i~i~vitkdg--~~~~~~~~~  191 (220)
T d1irui_         123 PYVTMGSGSLAAMAVFEDKF--RPDMEEEEAKNLVSEAIAAGIFNDLGSGSNIDLCVISKNK--LDFLRPYTV  191 (220)
T ss_dssp             SEEEESTTHHHHHHHHHHSC--CTTCCHHHHHTHHHHHHHHHHHHCTTCCSCEEEEEEETTE--EECCSEEEC
T ss_pred             eEEEEccccHHHHHHHHHhc--ccCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEECCC--eEEeCcccc
Confidence            99999999999999999998  6899999999999999999999998877 89999999985  677776654

>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=99.97  E-value=6.8e-31  Score=199.18  Aligned_cols=157  Identities=20%  Similarity=0.163  Sum_probs=143.1

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEc-----CCCCCeEEEeCCC
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSID-----EECGPRLFKCDPA   75 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d-----~~~gp~Ly~~dp~   75 (164)
                      +.+|++.+.++++.+++.|++.++.+++++.+++++++.+|.|++ ...||+++.++++|++     ..++|+||.+||+
T Consensus        48 ~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~g~~~~g~d~~~~~~l~~~d~~  126 (224)
T d1q5qh_          48 TAGIAIELVRLFAVELEHYEKIEGVPLTFDGKANRLASMVRGNLG-AAMQGLAVVPLLVGYDLDADDESRAGRIVSYDVV  126 (224)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHTTHH-HHTTTCCEEEEEEEECTTCSSTTSCEEEEEECTT
T ss_pred             cchHHHHHHHHHHHHhHHHHHhhCCCccHHHHHHHHHHHHHHhhc-ccccCccceeeEEEeecccccccCCceEEEEEcc
Confidence            368999999999999999999999999999999999999999876 4578999999988876     3468999999999


Q ss_pred             cceeee--eEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCCe--------EEEEEEEcCCCcE
Q 031203           76 GHFFGH--KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKASE--------IEVGVVSKENPEF  145 (164)
Q Consensus        76 G~~~~~--~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~~--------iei~ii~~~~~~~  145 (164)
                      |+..++  +++|+|+|+..++++||++|  +++||.+||++++++||..+.++|..|++        +++.++++++  |
T Consensus       127 G~~~~~~~~~~a~GsG~~~a~~~Le~~~--~~~mt~~ea~~l~~~al~~a~~rD~~SGg~~~~~~~~~~~~~i~~~g--~  202 (224)
T d1q5qh_         127 GGRYEERAGYHAVGSGSLFAKSALKKIY--SPDSDEETALRAAIESLYDAADDDSATGGPDLTRGIYPTAVTITQAG--A  202 (224)
T ss_dssp             SCEEECCSSEEEESTTHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHHCTTTCCCBTTTTBCCEEEEEETTE--E
T ss_pred             CcEEEeccceeeecCccHHHHHHHHHhh--cccCCHHHHHHHHHHHHHHHHhhccccCCcccccccceEEEEEeCCc--E
Confidence            998776  57999999999999999998  68999999999999999999999998873        7899999885  9


Q ss_pred             EEcCHHHHHHHHHHhhc
Q 031203          146 RVLSIEEIDEHLTAISE  162 (164)
Q Consensus       146 k~l~~~ei~~~l~~~~~  162 (164)
                      ++++++||++++.++.+
T Consensus       203 ~~l~~~ei~~~~~~~~~  219 (224)
T d1q5qh_         203 VHVSEETTSELARRIVA  219 (224)
T ss_dssp             EECCHHHHHHHHHHHHH
T ss_pred             EEcCHHHHHHHHHHHHH
Confidence            99999999999999874

>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=99.97  E-value=3.3e-31  Score=201.35  Aligned_cols=140  Identities=19%  Similarity=0.189  Sum_probs=128.5

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.|.++++.++..|++.++.++++..+++++++.+.     ...|||++++|+||+|+ +||+||.+||+|++.+
T Consensus        48 ~~aD~~~l~~~l~~~~~~~~~~~~~~~~v~~~a~~l~~~~~-----~~~~p~~~~~l~aG~d~-~g~~Ly~id~~G~~~~  121 (222)
T d1rypi_          48 TAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLF-----KYQGHIGAYLIVAGVDP-TGSHLFSIHAHGSTDV  121 (222)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHH-----HTTTCSCEEEEEEEEET-TEEEEEEECTTSCEEE
T ss_pred             cchHHHHHHHHHHHHHHHhhhhhCCCCcHHHHHHHHHHHHH-----hhhhccceeEEEEEEcC-CCcEEEEEecCcceEE
Confidence            36899999999999999999999999999999999998872     23579999999999998 8999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcC
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLS  149 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~  149 (164)
                      ++++|+|+|++.++++|+++|  +++||++||++++++||..+.++|..++ +++|+++++++. .+.+.
T Consensus       122 ~~~~a~Gsg~~~a~~~Le~~~--k~~ms~eea~~l~~~al~~a~~~D~~sg~~i~i~vi~~~~~-~~~~~  188 (222)
T d1rypi_         122 GYYLSLGSGSLAAMAVLESHW--KQDLTKEEAIKLASDAIQAGIWNDLGSGSNVDVCVMEIGKD-AEYLR  188 (222)
T ss_dssp             CSEEEESTTHHHHHHHHHHHC--CSSCCHHHHHHHHHHHHHHHHHHCTTCCSCEEEEEEETTSC-EEEEE
T ss_pred             eeEEEECCCcHHHHHHHHhhc--cCCCCHHHHHHHHHHHHHHHhcccCCCCCcEEEEEEEcCCC-eEEec
Confidence            999999999999999999998  6899999999999999999999999887 899999998764 44443

>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=99.97  E-value=1.2e-31  Score=202.97  Aligned_cols=147  Identities=14%  Similarity=0.163  Sum_probs=134.8

Q ss_pred             CchHHHHHHHHHHHHHHHHHH-hCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            2 TADARTLVQQARYEAAEFRFK-YGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         2 ~~D~~~l~~~~~~~~~~~~~~-~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      .+|++.|++.++.++..+++. ++.+++|+.+++++++.+  |+++.+.|||++++|++|+|+ ++|+||.+||+|++.+
T Consensus        57 ~aD~~~l~~~~~~~~~~~~~~~~~~~~~v~~~a~~l~~~~--y~~~~~~~p~~~~~li~G~d~-~~~~l~~~D~~G~~~~  133 (217)
T d1iru2_          57 YADFQYLKQVLGQMVIDEELLGDGHSYSPRAIHSWLTRAM--YSRRSKMNPLWNTMVIGGYAD-GESFLGYVDMLGVAYE  133 (217)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCSSCCCCHHHHHHHHHHHH--HHHHHTTCCCCEEEEEEEEET-TEEEEEEECSSCCEEE
T ss_pred             cHHHHHHHHHHHHHHHHhhhhcCCCCCCHHHHHHHHHHHH--HHhccccCcccceEEEEEEcC-CCcEEEEEecCceeEe
Confidence            589999999999999988765 469999999999999977  888888999999999999997 7999999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHHHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIEEI  153 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~ei  153 (164)
                      ++++|+|+|+..++++|++.|++.++||.+||++++++||..+.++|..++ +++|++|+++|  +++..|.++
T Consensus       134 ~~~~a~G~g~~~a~~~Le~~~~~~~~lt~~ea~~l~~~al~~a~~rd~~sg~~i~i~vi~~~G--~~~~~~~~~  205 (217)
T d1iru2_         134 APSLATGYGAYLAQPLLREVLEKQPVLSQTEARDLVERCMRVLYYRDARSYNRFQTATVTEKG--VEIEGPLST  205 (217)
T ss_dssp             CSEEECTTHHHHTHHHHHHHHTSCSCCCHHHHHHHHHHHHHHHHHHBTTCCSCEEEEEEETTE--EEEEEEECC
T ss_pred             eeEEeccCcHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHhcCcCCCcEEEEEEeCCC--EEEcCCeec
Confidence            999999999999999999998777999999999999999999999998887 89999999986  566666544

>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=99.97  E-value=4.6e-30  Score=192.13  Aligned_cols=137  Identities=17%  Similarity=0.232  Sum_probs=126.0

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCC-CeEEEeCCCccee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECG-PRLFKCDPAGHFF   79 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~g-p~Ly~~dp~G~~~   79 (164)
                      +++|++.|.++++.+++.|+++++.+++++.+++++++.+|.+    ..+||+|+++++|||+++| |+||.+||+|++.
T Consensus        55 ~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~l~~~----~~~p~~v~~li~G~d~~~g~~~L~~~D~~G~~~  130 (204)
T d1rypj_          55 LATDVTTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYER----RFGPYFVGPVVAGINSKSGKPFIAGFDLIGCID  130 (204)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHTT----TTSCCCEEEEEEEECTTTCCEEEEEECTTCCEE
T ss_pred             cchHHHHHHHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHHhh----cccceeeeEEEEEEecCCCcceEEEeCCCCccc
Confidence            3689999999999999999999999999999999999998543    3579999999999997554 8999999999998


Q ss_pred             eee-EEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCC
Q 031203           80 GHK-ATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENP  143 (164)
Q Consensus        80 ~~~-~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~  143 (164)
                      +++ ++++|+|+..++++|++.|  +++||.+||++++++||..+.++|+.++ +++|++|++++.
T Consensus       131 ~~~~~~~~G~g~~~a~~~l~~~~--~~~ms~~ea~~l~~~al~~a~~~d~~sg~~~~v~ii~kdg~  194 (204)
T d1rypj_         131 EAKDFIVSGTASDQLFGMCESLY--EPNLEPEDLFETISQALLNAADRDALSGWGAVVYIIKKDEV  194 (204)
T ss_dssp             CCSSEEEEETTHHHHHHHHHHHC--CSSCCHHHHHHHHHHHHHHHHTTBTTSCSCEEEEEEESSCE
T ss_pred             cccCcEEeecchHHHHHHHHhcc--ccCCCHHHHHHHHHHHHHHHHHhcCccCCeEEEEEEECCce
Confidence            875 8899999999999999998  6899999999999999999999998877 899999999974

>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=99.97  E-value=1.2e-29  Score=192.25  Aligned_cols=139  Identities=16%  Similarity=0.308  Sum_probs=124.9

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCccee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYG-YEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFF   79 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~-~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~   79 (164)
                      +.+|++.|+++++.+++.|++.++ .++++..++++++..+    ++.+.|||+|+++|+|||++++|+||.+||+|++.
T Consensus        57 ~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~p~~~~~li~G~d~~~~~~Ly~~D~~G~~~  132 (222)
T d1ryp1_          57 FAADGDALVKRFKNSVKWYHFDHNDKKLSINSAARNIQHLL----YGKRFFPYYVHTIIAGLDEDGKGAVYSFDPVGSYE  132 (222)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHH----HTTTTSCCCEEEEEEEECTTSCEEEEEECTTSCEE
T ss_pred             ChHHHHHHHHHHHHHhhhhhhhcCCCCCcHHHHHHHHHHHH----HhhhhhhheeeeeEEEEeCCCCeEEEEECCCcEEE
Confidence            468999999999999999999986 5678888887776655    45578999999999999987779999999999999


Q ss_pred             eeeEEeecCChHHHHHHHHHhhcCC---------------CCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCC
Q 031203           80 GHKATSAGLKEQEAINFLEKKMKND---------------PAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENP  143 (164)
Q Consensus        80 ~~~~~aiG~~s~~~~~~Le~~~~~~---------------~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~  143 (164)
                      +++++|+|+|++.++++||++|+..               ++||.+||++++++||..+.++|+.++ +++|++|+++|.
T Consensus       133 ~~~~~a~G~g~~~a~~~Le~~~~~~~~~~~~~~~~~~~~~~~lt~~ea~~l~~~al~~a~~rd~~sg~~v~v~iitkdGv  212 (222)
T d1ryp1_         133 REQCRAGGAAASLIMPFLDNQVNFKNQYEPGTNGKVKKPLKYLSVEEVIKLVRDSFTSATERHIQVGDGLEILIVTKDGV  212 (222)
T ss_dssp             EESEEEEETTHHHHHHHHHHHTSCTTCBCTTSTTCSBCCCCCCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTEE
T ss_pred             EeceEEEcccHHHHHHHHHHhhccccccCcccchhhhcccccccHHHHHHHHHHHHHHHHHhcccCCCcEEEEEEeCCCE
Confidence            9999999999999999999998522               689999999999999999999999988 799999999864

>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=99.97  E-value=2.6e-29  Score=188.36  Aligned_cols=142  Identities=15%  Similarity=0.216  Sum_probs=127.8

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCC-CCeEEEeCCCccee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEEC-GPRLFKCDPAGHFF   79 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~-gp~Ly~~dp~G~~~   79 (164)
                      +.+|++.|++.++.+++.|++.++.+++|+.+++++++.+|.+    +++||+|++||||||+++ +|.+|.+||+|...
T Consensus        55 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~~~~~----~~~p~~~~~lvaG~D~~~~~~~~~~~d~~g~~~  130 (204)
T d1iruj_          55 LATDVQTVAQRLKFRLNLYELKEGRQIKPYTLMSMVANLLYEK----RFGPYYTEPVIAGLDPKTFKPFICSLDLIGCPM  130 (204)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHTT----TTSCCSCCCEEEEECTTSCCEEEEEECTTCCEE
T ss_pred             CchHHHHHHHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHh----hhccceeEEEEEEEcCCCCceEEEEecCCCcee
Confidence            3689999999999999999999999999999999999998543    467999999999999753 57899999999987


Q ss_pred             ee-eEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEc
Q 031203           80 GH-KATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVL  148 (164)
Q Consensus        80 ~~-~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l  148 (164)
                      .+ .++++|+|++.++++|++.|  +++||.+||++++++||..+.++|..++ +++|++|++++...+.+
T Consensus       131 ~~~~~~~~G~g~~~~~~~l~~~~--~~~ms~~ea~~l~~~al~~a~~rd~~sg~~~~v~ii~k~gi~~~~~  199 (204)
T d1iruj_         131 VTDDFVVSGTCAEQMYGMCESLW--EPNMDPDHLFETISQAMLNAVDRDAVSGMGVIVHIIEKDKITTRTL  199 (204)
T ss_dssp             ECSSEEEEETTHHHHHHHHHHHC--CSSCCHHHHHHHHHHHHHHHGGGBTTSCSCEEEEEEESSBEEEEEB
T ss_pred             eecceEEechhHHHHHHHHHhcc--ccCCCHHHHHHHHHHHHHHHHhhcccCCCcEEEEEEeCCCEEEEEE
Confidence            76 57999999999999999998  6889999999999999999999999888 89999999997544433

>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=99.96  E-value=8.3e-29  Score=183.06  Aligned_cols=145  Identities=14%  Similarity=0.208  Sum_probs=133.8

Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceee
Q 031203            1 MTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFG   80 (164)
Q Consensus         1 l~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~   80 (164)
                      +.+|++.+.++++.+++.|+..++.+++++.+++.+++..+.+  ....+|++++++++|||...+|+||.+||+|.+..
T Consensus        49 ~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~~~~~~aG~d~~~~~~l~~~~~~g~~~~  126 (199)
T d1iruk_          49 EAGDTVQFAEYIQKNVQLYKMRNGYELSPTAAANFTRRNLADC--LRSRTPYHVNLLLAGYDEHEGPALYYMDYLAALAK  126 (199)
T ss_dssp             STTHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHH--HTSSSCCCEEEEEEEEETTTEEEEEEECTTCCEEE
T ss_pred             cchHHHHHHHHHHHHhhhhhhhcCCcCcHHHHHHHHHHHHHHH--hhccCCcceeeeecceeccCCceEEeecccceEEe
Confidence            3689999999999999999999999999999999999988544  45678999999999999877899999999999999


Q ss_pred             eeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCCcEEEcCHH
Q 031203           81 HKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENPEFRVLSIE  151 (164)
Q Consensus        81 ~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~~~k~l~~~  151 (164)
                      ++++++|+|++.++++|++.|  +++||++||++++++||..+.++|..++ +++|++|+++|  ++.+++.
T Consensus       127 ~~~~a~G~gs~~a~~~l~~~~--~~~~~~~ea~~l~~~al~~~~~~d~~sg~~~~v~vv~~~g--~~~~~~~  194 (199)
T d1iruk_         127 APFAAHGYGAFLTLSILDRYY--TPTISRERAVELLRKCLEELQKRFILNLPTFSVRIIDKNG--IHDLDNI  194 (199)
T ss_dssp             CSEEEESHHHHHHHHHHHHHC--CTTCCHHHHHHHHHHHHHHHHHTBCBCCCCEEEEEEETTE--EECCCCB
T ss_pred             eeeeeecccchhhhHHHHHhc--cCCCCHHHHHHHHHHHHHHHHHhcCCcCCceEEEEEcCCC--eEEcCCc
Confidence            999999999999999999998  6899999999999999999999998887 89999999986  7776653

>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=99.95  E-value=4.7e-27  Score=175.94  Aligned_cols=138  Identities=14%  Similarity=0.215  Sum_probs=128.7

Q ss_pred             CchHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceeee
Q 031203            2 TADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGH   81 (164)
Q Consensus         2 ~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~~   81 (164)
                      .+|++.+.++++.+++.|++.++.+++++.++++++..+|.+    ..+|++++++++|||..++|.+|.+||.|++..+
T Consensus        58 ~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~g~d~~~~~~l~~~d~~g~~~~~  133 (213)
T d1iru1_          58 HGDCLTLTKIIEARLKMYKHSNNKAMTTGAIAAMLSTILYSR----RFFPYYVYNIIGGLDEEGKGAVYSFDPVGSYQRD  133 (213)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHTT----TTSCCCEEEEEEEECTTSCEEEEEECTTSCEEEE
T ss_pred             cchHHHHHHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHH----HhhhcccccceEEEecCCCcEEEecCCcceeeec
Confidence            589999999999999999999999999999999999998765    3569999999999999788999999999999999


Q ss_pred             eEEeecCChHHHHHHHHHhhcC-------CCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEEEcCCC
Q 031203           82 KATSAGLKEQEAINFLEKKMKN-------DPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVVSKENP  143 (164)
Q Consensus        82 ~~~aiG~~s~~~~~~Le~~~~~-------~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii~~~~~  143 (164)
                      +++++|+|+..+++.|++.|++       .++||++||++++++||..+.++|+.++ +++|++|+++|.
T Consensus       134 ~~~a~G~g~~~a~~~l~~~~~~~~~~~~~~~~~s~~ea~~~~~~~l~~~~~~d~~sg~~~~v~~i~k~G~  203 (213)
T d1iru1_         134 SFKAGGSASAMLQPLLDNQVGFKNMQNVEHVPLSLDRAMRLVKDVFISAAERDVYTGDALRICIVTKEGI  203 (213)
T ss_dssp             SEEEEETTHHHHHHHHHHHTTCCSCSSCCCCCCCHHHHHHHHHHHHHHHHHHBTTSCSEEEEEEEETTEE
T ss_pred             CeeeecCccHHHHHHHHHhhcccchhcccccCCCHHHHHHHHHHHHHHHHHhcCCCCCceEEEEEeCCCE
Confidence            9999999999999999998753       3789999999999999999999999888 799999999874

>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=99.41  E-value=2.3e-14  Score=103.88  Aligned_cols=122  Identities=13%  Similarity=-0.036  Sum_probs=81.6

Q ss_pred             chHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhccCccccceeeEEEEEcCCCCCeEEEeCCCcceeeee
Q 031203            3 ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVVAMVLSIDEECGPRLFKCDPAGHFFGHK   82 (164)
Q Consensus         3 ~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~ls~~~q~yt~~~~~rP~gv~~iiaG~d~~~gp~Ly~~dp~G~~~~~~   82 (164)
                      +|.+.+.+..+.+...+     ..-....+.............+....++.+....+|++. .++.++..+++|      
T Consensus        57 ~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~------  124 (180)
T d2z3ba1          57 ADAFTLFEKFEAKLEEY-----NGNLKRAAVELAKEWRSDKVLRKLEAMLIVMNQDTLLLV-SGTGEVIEPDDG------  124 (180)
T ss_dssp             HHHHHHHHHHHHHHHHT-----TTCHHHHHHHHHHHHHHCTTGGGCCCCEEEECSSCEEEE-CTTCCEECCSSS------
T ss_pred             HHHHHHHHHHHHHHHhh-----ccccchhHHHHHHHHhHHHHHHHhhcceeeeeccccccc-cCCceeeccccc------
Confidence            45666666555544332     222222222222222222222333344555555566665 566777666665      


Q ss_pred             EEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eEEEEEE
Q 031203           83 ATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EIEVGVV  138 (164)
Q Consensus        83 ~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~iei~ii  138 (164)
                      +.|+|+|+..|++.|++.|  +++||.+||++++.+||+.|.++|+.++ +++|-+|
T Consensus       125 ~~a~GSGs~~A~g~l~~~~--~~~~s~~eA~~l~~~Al~~A~e~dvyT~~~~~~~~i  179 (180)
T d2z3ba1         125 ILAIGSGGNYALAAGRALK--KHAGESMSASEIARAALETAGEICVYTNDQIILEEL  179 (180)
T ss_dssp             EEEESTTHHHHHHHHHHHH--HHHGGGCCHHHHHHHHHHHHHHHCTTCCSCCEEEEE
T ss_pred             EEEEcCchHHHHHHHHHHh--hcCCCccCHHHHHHHHHHHHHhhcEEcCCcEEEEEe
Confidence            7899999999999999999  5789999999999999999999999987 7887765

>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=99.23  E-value=5.8e-12  Score=89.99  Aligned_cols=80  Identities=9%  Similarity=0.025  Sum_probs=66.5

Q ss_pred             ceeeEEEEEcCCCCCeEEEeCCCcceeeeeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-
Q 031203           53 GVVAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-  131 (164)
Q Consensus        53 gv~~iiaG~d~~~gp~Ly~~dp~G~~~~~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-  131 (164)
                      ....++.+++. .+|.++..|+.|......+.|+|+|+..|++.|+.+++ +++++   |.+++++||..|.++|+.++ 
T Consensus        90 ~~~~~~~~~~~-~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~l~~~~~-~~~~~---a~el~~~Ai~~A~e~dvyTg~  164 (171)
T d1m4ya_          90 RLEALLLVADK-ENIFIISGNGEVIQPDDDAAAIGSGGPYALAAAKALLR-NTDLS---AREIVEKAMTIAGEICIYTNQ  164 (171)
T ss_dssp             GCCCEEEEECS-SCEEEECTTSCEECCSSSEEEESTTHHHHHHHHHHHHH-HCCCC---HHHHHHHHHHHHHHHCTTCCS
T ss_pred             ccccccceecC-CcceEEecCCceeeecCCEEEEcchHHHHHHHHHhhcc-CCCCC---HHHHHHHHHHHHHhhceEcCC
Confidence            33445555666 78999999999999999999999999999999999774 35665   66789999999999999988 


Q ss_pred             eEEEEE
Q 031203          132 EIEVGV  137 (164)
Q Consensus       132 ~iei~i  137 (164)
                      +++|-.
T Consensus       165 ~~~i~~  170 (171)
T d1m4ya_         165 NIVIEE  170 (171)
T ss_dssp             CCEEEE
T ss_pred             cEEEEE
Confidence            787754

>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=99.15  E-value=6.4e-11  Score=84.61  Aligned_cols=80  Identities=10%  Similarity=-0.036  Sum_probs=67.5

Q ss_pred             eeEEEEEcCCCCCeEEEeCCCcceeeeeEEeecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHhhhhccCCCC-eE
Q 031203           55 VAMVLSIDEECGPRLFKCDPAGHFFGHKATSAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTLQSVLQEDFKAS-EI  133 (164)
Q Consensus        55 ~~iiaG~d~~~gp~Ly~~dp~G~~~~~~~~aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al~~~~~~d~~~~-~i  133 (164)
                      ...+.|+|..++|.++..|+.|.+.+..+.|+|+|+..|.+.|+.+++    ++.++|.++|++||..|.++|+.++ ++
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~GSGs~~A~~~l~~~~~----~~~~~A~ela~~Ai~~Aae~dvyTgd~~  167 (173)
T d1g3ka_          92 EAMLIVADEKESLIITGIGDVVQPEEDQILAIGSGGNYALSAARALVE----NTELSAHEIVEKSLRIAGDICVFTNTNF  167 (173)
T ss_dssp             CCEEEEECSSCEEEEETTTEEECCCTTCEEEESTTHHHHHHHHHHHHH----HCCCCHHHHHHHHHHHHHHHCTTCCSCC
T ss_pred             ccccccccCCCcceecccCceEEecCCCEEEecchHHHHHHHHHHhhh----cCCCCHHHHHHHHHHHHHhhcEEcCCcE
Confidence            344445566588999999999999999999999999999999999873    4556788899999999999999988 78


Q ss_pred             EEEEE
Q 031203          134 EVGVV  138 (164)
Q Consensus       134 ei~ii  138 (164)
                      +|-.|
T Consensus       168 ~i~~~  172 (173)
T d1g3ka_         168 TIEEL  172 (173)
T ss_dssp             EEEEE
T ss_pred             EEEEC
Confidence            77654

>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=85.32  E-value=0.34  Score=26.04  Aligned_cols=34  Identities=24%  Similarity=0.325  Sum_probs=28.8

Q ss_pred             eecCChHHHHHHHHHhhcCCCCCCHHHHHHHHHHHH
Q 031203           85 SAGLKEQEAINFLEKKMKNDPAFTFQETVQTAISTL  120 (164)
Q Consensus        85 aiG~~s~~~~~~Le~~~~~~~~ls~eea~~l~~~al  120 (164)
                      +.|+....+...+.+..  .+++|.|+.|+.|++++
T Consensus        14 ~LGY~~~ea~~av~~i~--~~~~s~E~lIk~ALk~m   47 (48)
T d1cuka1          14 ALGYKPQEASRMVSKIA--RPDASSETLIREALRAA   47 (48)
T ss_dssp             HHTCCHHHHHHHHHHSC--CSSCCHHHHHHHHHHTT
T ss_pred             HcCCCHHHHHHHHHHhc--CCCCCHHHHHHHHHHHh
Confidence            56899999999999875  68899999999888754