Citrus Sinensis ID: 031996

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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-------15
Protein Sequence
MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPSEL
Secondary Structure (PSIPRED)
cccccccccccccccccccccHHHHHHHHHHHHcccccEEEEEcccEEEEEEEccccccccccccccEEEEEEccEEEEEEccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHcccccHHHHEEEEEEEcccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccHHHHHHHHHcccccccEEEEEccccEEEEEEcccccccEcHHHcccEEEcccccEEEEEccHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHEccccccccEEEEEEEcccccc
Coil and Loop (DISEMBL)
msrgsgggydrhitifspegrlfQVEYAFKAVKAAGvtsigvrgkdsVCVVtqkkvpdklldhtsvthlfPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPSEL
Flexible Loop (DISEMBL)
msrgsgggydrhitifspegRLFQVEYAFKAVKAAGvtsigvrgkdsvCVVTQKkvpdklldhtsvthLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPSEL
Low Complexity Region (SEG)
MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPSEL
Disordered region (IsUnstruct)
********YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAI****
Disordered Region (DISOPRED)
******G****HITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS**
Disordered Region (DISEMBL)
********YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPSEL
Disordered Region (DISPRO)
*********DRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPSEL
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	149	2.2.26 [Sep-21-2011]
Q9XG77	246	Proteasome subunit alpha	N/A	no	0.959	0.581	0.923	2e-74
O48551	246	Proteasome subunit alpha	no	no	0.912	0.552	0.948	5e-73
O81147	246	Proteasome subunit alpha	yes	no	0.912	0.552	0.911	1e-71
Q9LSU3	246	Proteasome subunit alpha	yes	no	0.912	0.552	0.919	2e-71
O81146	246	Proteasome subunit alpha	no	no	0.912	0.552	0.904	6e-71
P60901	246	Proteasome subunit alpha	yes	no	0.959	0.581	0.685	5e-55
P60900	246	Proteasome subunit alpha	yes	no	0.959	0.581	0.685	5e-55
Q2YDE4	246	Proteasome subunit alpha	yes	no	0.959	0.581	0.685	5e-55
Q9QUM9	246	Proteasome subunit alpha	yes	no	0.959	0.581	0.685	5e-55
Q9XZJ4	244	Proteasome subunit alpha	yes	no	0.946	0.577	0.617	4e-47

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

 Score =  277 bits (708), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 132/143 (92%), Positives = 137/143 (95%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAG+TSIGVRGKDSVCVVTQKKVPDKL
Sbjct: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGITSIGVRGKDSVCVVTQKKVPDKL 60

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LD TSV+HLFPITKYLGLLATGMTADARTLVQQAR EAAEFRFKYGYEMPVDVL+KWIAD
Sbjct: 61  LDQTSVSHLFPITKYLGLLATGMTADARTLVQQARNEAAEFRFKYGYEMPVDVLSKWIAD 120

Query: 121 KSQVYTQHAYMRPLGVGLFLIEI 143
           KSQVYTQHAYMRPLGV   ++ I
Sbjct: 121 KSQVYTQHAYMRPLGVVAMILGI 143

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 =  272 bits (696), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 129/136 (94%), Positives = 133/136 (97%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGSGGGY+RHITIFSPEGRLFQVEYAFKAVKAAG+TSIGVRGKDS+CVVT KKVPDKL
Sbjct: 1   MSRGSGGGYNRHITIFSPEGRLFQVEYAFKAVKAAGITSIGVRGKDSICVVTHKKVPDKL 60

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LD+TSVTHLFPITKYLGLLATGMTADARTLVQQAR EAAEFRF YGYEMPVDVLAKWIAD
Sbjct: 61  LDNTSVTHLFPITKYLGLLATGMTADARTLVQQARNEAAEFRFTYGYEMPVDVLAKWIAD 120

Query: 121 KSQVYTQHAYMRPLGV 136
           KSQVYTQHAYMRPLGV
Sbjct: 121 KSQVYTQHAYMRPLGV 136

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

 Score =  268 bits (684), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 124/136 (91%), Positives = 132/136 (97%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGSG GYDRHITIFSPEGRLFQVEYAFKAVKAAG+TSIGVRGKDSVCVVTQKKVPDKL
Sbjct: 1   MSRGSGAGYDRHITIFSPEGRLFQVEYAFKAVKAAGITSIGVRGKDSVCVVTQKKVPDKL 60

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LD +SV+HLFP+TKYLGLLATGMTAD+R+LVQQAR EAAEFRF+YGYEMP D+LAKWIAD
Sbjct: 61  LDQSSVSHLFPVTKYLGLLATGMTADSRSLVQQARNEAAEFRFQYGYEMPADILAKWIAD 120

Query: 121 KSQVYTQHAYMRPLGV 136
           KSQVYTQHAYMRPLGV
Sbjct: 121 KSQVYTQHAYMRPLGV 136

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 =  266 bits (681), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 125/136 (91%), Positives = 133/136 (97%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRG+G GYDRHITIFSPEGRL+QVEYAFKAVK+AGVTSIGVRGKDSVCVVTQKKVPDKL
Sbjct: 1   MSRGTGAGYDRHITIFSPEGRLYQVEYAFKAVKSAGVTSIGVRGKDSVCVVTQKKVPDKL 60

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LDHTSVTHLFPITKY+GLLATG+TADAR+LV QAR EAAEFRFK+GYEMPVDVLAKWIAD
Sbjct: 61  LDHTSVTHLFPITKYIGLLATGLTADARSLVYQARNEAAEFRFKWGYEMPVDVLAKWIAD 120

Query: 121 KSQVYTQHAYMRPLGV 136
           K+QVYTQHAYMRPLGV
Sbjct: 121 KAQVYTQHAYMRPLGV 136

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

 Score =  265 bits (678), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 123/136 (90%), Positives = 131/136 (96%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGSG GYDRHITIFSPEGRLFQVEYAFKAVK AG+TSIGVRGKDSVCVVTQKKVPDKL
Sbjct: 1   MSRGSGAGYDRHITIFSPEGRLFQVEYAFKAVKTAGITSIGVRGKDSVCVVTQKKVPDKL 60

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LD +SVTHLFPITKY+GL+ATG+TADAR+LVQQAR +AAEFRF YGYEMPVD+LAKWIAD
Sbjct: 61  LDQSSVTHLFPITKYIGLVATGITADARSLVQQARNQAAEFRFTYGYEMPVDILAKWIAD 120

Query: 121 KSQVYTQHAYMRPLGV 136
           KSQVYTQHAYMRPLGV
Sbjct: 121 KSQVYTQHAYMRPLGV 136

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

 Score =  212 bits (540), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 98/143 (68%), Positives = 119/143 (83%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGS  G+DRHITIFSPEGRL+QVEYAFKA+   G+TS+ VRGKD   +VTQKKVPDKL
Sbjct: 1   MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL 60

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD
Sbjct: 61  LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD 120

Query: 121 KSQVYTQHAYMRPLGVGLFLIEI 143
            SQVYTQ+A MRPLG  + LI I
Sbjct: 121 ISQVYTQNAEMRPLGCCMILIGI 143

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 =  212 bits (540), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 98/143 (68%), Positives = 119/143 (83%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGS  G+DRHITIFSPEGRL+QVEYAFKA+   G+TS+ VRGKD   +VTQKKVPDKL
Sbjct: 1   MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL 60

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD
Sbjct: 61  LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD 120

Query: 121 KSQVYTQHAYMRPLGVGLFLIEI 143
            SQVYTQ+A MRPLG  + LI I
Sbjct: 121 ISQVYTQNAEMRPLGCCMILIGI 143

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 =  212 bits (540), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 98/143 (68%), Positives = 119/143 (83%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGS  G+DRHITIFSPEGRL+QVEYAFKA+   G+TS+ VRGKD   +VTQKKVPDKL
Sbjct: 1   MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL 60

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD
Sbjct: 61  LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD 120

Query: 121 KSQVYTQHAYMRPLGVGLFLIEI 143
            SQVYTQ+A MRPLG  + LI I
Sbjct: 121 ISQVYTQNAEMRPLGCCMILIGI 143

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

 Score =  212 bits (540), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 98/143 (68%), Positives = 119/143 (83%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGS  G+DRHITIFSPEGRL+QVEYAFKA+   G+TS+ VRGKD   +VTQKKVPDKL
Sbjct: 1   MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL 60

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD
Sbjct: 61  LDSSTVTHLFKITESIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD 120

Query: 121 KSQVYTQHAYMRPLGVGLFLIEI 143
            SQVYTQ+A MRPLG  + LI I
Sbjct: 121 ISQVYTQNAEMRPLGCCMILIGI 143

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

 Score =  186 bits (472), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 87/141 (61%), Positives = 107/141 (75%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGS  G+DRHITIFSPEGRL+QVEYAFKA+    +T++ ++  D   V TQKKV +K 
Sbjct: 1   MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAIAQENITTVALKSGDCAVVATQKKVTEKN 60

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           +   +VTHLF ITK +G   TG  AD+R+ VQ+ARYEAA FR+KYGYEMPVDVL + IAD
Sbjct: 61  IVPETVTHLFRITKDIGCAMTGRIADSRSQVQKARYEAANFRYKYGYEMPVDVLCRRIAD 120

Query: 121 KSQVYTQHAYMRPLGVGLFLI 141
            +QVYTQ+A MRPLG  + LI
Sbjct: 121 INQVYTQNAEMRPLGCSMVLI 141

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	149
356545355	368	PREDICTED: proteasome subunit alpha type	0.912	0.369	0.963	1e-72
12229948	246	RecName: Full=Proteasome subunit alpha t	0.959	0.581	0.923	1e-72
255583952	246	proteasome subunit alpha type, putative	0.912	0.552	0.970	1e-72
255648341	246	unknown [Glycine max]	0.912	0.552	0.955	5e-72
217075112	246	unknown [Medicago truncatula] gi|3885172	0.912	0.552	0.941	9e-72
225442079	246	PREDICTED: proteasome subunit alpha type	0.959	0.581	0.909	9e-72
211906468	246	20S proteasome subunit alpha-1 [Gossypiu	0.912	0.552	0.948	1e-71
357451023	246	Proteasome subunit alpha type [Medicago	0.912	0.552	0.955	2e-71
388517479	246	unknown [Medicago truncatula]	0.912	0.552	0.955	3e-71
388519097	246	unknown [Lotus japonicus]	0.912	0.552	0.948	3e-71

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

 Score =  277 bits (709), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 131/136 (96%), Positives = 134/136 (98%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAG+TSIGVRGKDS+CVVTQKKVPDKL
Sbjct: 123 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGITSIGVRGKDSICVVTQKKVPDKL 182

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LD+TSVTHLFPITKYLGLLATGMTADARTLVQQAR EAAEFRF YGYEMPVDVLAKWIAD
Sbjct: 183 LDNTSVTHLFPITKYLGLLATGMTADARTLVQQARNEAAEFRFTYGYEMPVDVLAKWIAD 242

Query: 121 KSQVYTQHAYMRPLGV 136
           KSQVYTQHAYMRPLGV
Sbjct: 243 KSQVYTQHAYMRPLGV 258

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 =  277 bits (708), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 132/143 (92%), Positives = 137/143 (95%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAG+TSIGVRGKDSVCVVTQKKVPDKL
Sbjct: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGITSIGVRGKDSVCVVTQKKVPDKL 60

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LD TSV+HLFPITKYLGLLATGMTADARTLVQQAR EAAEFRFKYGYEMPVDVL+KWIAD
Sbjct: 61  LDQTSVSHLFPITKYLGLLATGMTADARTLVQQARNEAAEFRFKYGYEMPVDVLSKWIAD 120

Query: 121 KSQVYTQHAYMRPLGVGLFLIEI 143
           KSQVYTQHAYMRPLGV   ++ I
Sbjct: 121 KSQVYTQHAYMRPLGVVAMILGI 143

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>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 =  276 bits (707), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 132/136 (97%), Positives = 134/136 (98%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKA+GVTSIGV GKDSVCVVTQKKVPDKL
Sbjct: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKASGVTSIGVCGKDSVCVVTQKKVPDKL 60

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LDHTSVTHLFPITKYLGLLATGMTADARTLVQQAR EAAEFRFKYGYEMPVDVLAKWIAD
Sbjct: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARNEAAEFRFKYGYEMPVDVLAKWIAD 120

Query: 121 KSQVYTQHAYMRPLGV 136
           KSQ+YTQHAYMRPLGV
Sbjct: 121 KSQIYTQHAYMRPLGV 136

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  275 bits (702), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 130/136 (95%), Positives = 134/136 (98%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAG+TSIGVRGKDS+CVVTQKKVPDKL
Sbjct: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGITSIGVRGKDSICVVTQKKVPDKL 60

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LD+TSVTHLFPITKYLGLLATGMTADARTLVQQAR EAAEFRF YGYE+PVDVLAKWIAD
Sbjct: 61  LDNTSVTHLFPITKYLGLLATGMTADARTLVQQARNEAAEFRFTYGYEIPVDVLAKWIAD 120

Query: 121 KSQVYTQHAYMRPLGV 136
           KSQVYTQHAYMRPLGV
Sbjct: 121 KSQVYTQHAYMRPLGV 136

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  274 bits (701), Expect = 9e-72,   Method: Compositional matrix adjust.
 Identities = 128/136 (94%), Positives = 135/136 (99%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVK+AG+TSIGVRGKDSVCVVTQKKVPDKL
Sbjct: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKSAGITSIGVRGKDSVCVVTQKKVPDKL 60

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LDHTSVTHLFPITKYLGLLATG+TADARTLVQQAR EAAE+RF+YGYEMPVDVL+KW+AD
Sbjct: 61  LDHTSVTHLFPITKYLGLLATGITADARTLVQQARNEAAEYRFRYGYEMPVDVLSKWVAD 120

Query: 121 KSQVYTQHAYMRPLGV 136
           KSQVYTQHAYMRPLGV
Sbjct: 121 KSQVYTQHAYMRPLGV 136

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  274 bits (700), Expect = 9e-72,   Method: Compositional matrix adjust.
 Identities = 130/143 (90%), Positives = 137/143 (95%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKA+G+TSIGVRGKDSVCVVTQKKVPDKL
Sbjct: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKASGITSIGVRGKDSVCVVTQKKVPDKL 60

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LD TSVTHLFPITK+LGLLATGMTADARTLVQQAR EAAEFRF+YGYEMPVDVLA+WIAD
Sbjct: 61  LDQTSVTHLFPITKFLGLLATGMTADARTLVQQARNEAAEFRFRYGYEMPVDVLARWIAD 120

Query: 121 KSQVYTQHAYMRPLGVGLFLIEI 143
           KSQVYTQHAYMRPLGV   ++ I
Sbjct: 121 KSQVYTQHAYMRPLGVVAMILGI 143

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  273 bits (699), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 129/136 (94%), Positives = 133/136 (97%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAG+TSIGVRGKDSVC VTQKKVPDKL
Sbjct: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGITSIGVRGKDSVCFVTQKKVPDKL 60

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LD TSVTHLFPITK+LGLLATGMTADARTLVQQAR EAAEFRF+YGYEMPVDVL+KWIAD
Sbjct: 61  LDQTSVTHLFPITKFLGLLATGMTADARTLVQQARNEAAEFRFRYGYEMPVDVLSKWIAD 120

Query: 121 KSQVYTQHAYMRPLGV 136
           KSQVYTQHAYMRPLGV
Sbjct: 121 KSQVYTQHAYMRPLGV 136

Source: Gossypium hirsutum

Species: Gossypium hirsutum

Genus: Gossypium

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357451023|ref|XP_003595788.1| Proteasome subunit alpha type [Medicago truncatula] gi|355484836|gb|AES66039.1| Proteasome subunit alpha type [Medicago truncatula] gi|388521863|gb|AFK48993.1| unknown [Medicago truncatula]

 Score =  273 bits (697), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 130/136 (95%), Positives = 132/136 (97%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAG+TSIGVRG DSVCVVTQKKVPDKL
Sbjct: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGITSIGVRGNDSVCVVTQKKVPDKL 60

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LD TSVTHLFPITKYLGLLATGMTADARTLVQQAR EAAEFR K+GYEMPVDVLAKWIAD
Sbjct: 61  LDQTSVTHLFPITKYLGLLATGMTADARTLVQQARNEAAEFRHKFGYEMPVDVLAKWIAD 120

Query: 121 KSQVYTQHAYMRPLGV 136
           KSQVYTQHAYMRPLGV
Sbjct: 121 KSQVYTQHAYMRPLGV 136

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388517479|gb|AFK46801.1| unknown [Medicago truncatula]

 Score =  272 bits (696), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 130/136 (95%), Positives = 132/136 (97%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAG+TSIGVRG DSVCVVTQKKVPDKL
Sbjct: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGITSIGVRGNDSVCVVTQKKVPDKL 60

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LD TSVTHLFPITKYLGLLATGMTADARTLVQQAR EAAEFR K+GYEMPVDVLAKWIAD
Sbjct: 61  LDQTSVTHLFPITKYLGLLATGMTADARTLVQQARNEAAEFRHKFGYEMPVDVLAKWIAD 120

Query: 121 KSQVYTQHAYMRPLGV 136
           KSQVYTQHAYMRPLGV
Sbjct: 121 KSQVYTQHAYMRPLGV 136

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  272 bits (696), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 129/136 (94%), Positives = 132/136 (97%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAG+TSIGVRGKDS+CVVTQKKVPDKL
Sbjct: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGITSIGVRGKDSICVVTQKKVPDKL 60

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LD TSV+HLFPITKYLGLLATGMTADARTLVQQAR EAAEFR  YGYEMPVDVLAKWIAD
Sbjct: 61  LDQTSVSHLFPITKYLGLLATGMTADARTLVQQARNEAAEFRHTYGYEMPVDVLAKWIAD 120

Query: 121 KSQVYTQHAYMRPLGV 136
           KSQVYTQHAYMRPLGV
Sbjct: 121 KSQVYTQHAYMRPLGV 136

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	149
TAIR|locus:2064727	246	PAA2 "20S proteasome subunit P	0.959	0.581	0.874	2.3e-64
TAIR|locus:2157106	246	PAA1 "proteasome alpha subunit	0.912	0.552	0.904	1.2e-63
UNIPROTKB|F1NEQ6	249	PSMA6 "Proteasome subunit alph	0.959	0.574	0.685	5.2e-49
UNIPROTKB|G5E5C3	245	PSMA6 "Proteasome subunit alph	0.959	0.583	0.685	6.7e-49
UNIPROTKB|Q2YDE4	246	PSMA6 "Proteasome subunit alph	0.959	0.581	0.685	6.7e-49
UNIPROTKB|E2RMN2	246	PSMA6 "Proteasome subunit alph	0.959	0.581	0.685	6.7e-49
UNIPROTKB|G3V295	203	PSMA6 "Proteasome subunit alph	0.959	0.704	0.685	6.7e-49
UNIPROTKB|P60900	246	PSMA6 "Proteasome subunit alph	0.959	0.581	0.685	6.7e-49
UNIPROTKB|F2Z5N0	246	PSMA6 "Proteasome subunit alph	0.959	0.581	0.685	6.7e-49
MGI|MGI:1347006	246	Psma6 "proteasome (prosome, ma	0.959	0.581	0.685	6.7e-49

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

 Score = 656 (236.0 bits), Expect = 2.3e-64, P = 2.3e-64
 Identities = 125/143 (87%), Positives = 135/143 (94%)

Query:     1 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
             MSRGSG GYDRHITIFSPEGRLFQVEYAFKAVKAAG+TSIGVRGKDSVCVVTQKKVPDKL
Sbjct:     1 MSRGSGAGYDRHITIFSPEGRLFQVEYAFKAVKAAGITSIGVRGKDSVCVVTQKKVPDKL 60

Query:    61 LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
             LD +SV+HLFP+TKYLGLLATGMTAD+R+LVQQAR EAAEFRF+YGYEMP D+LAKWIAD
Sbjct:    61 LDQSSVSHLFPVTKYLGLLATGMTADSRSLVQQARNEAAEFRFQYGYEMPADILAKWIAD 120

Query:   121 KSQVYTQHAYMRPLGVGLFLIEI 143
             KSQVYTQHAYMRPLGV   ++ I
Sbjct:   121 KSQVYTQHAYMRPLGVVAMVLGI 143

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

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

 Score = 649 (233.5 bits), Expect = 1.2e-63, P = 1.2e-63
 Identities = 123/136 (90%), Positives = 131/136 (96%)

Query:     1 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
             MSRGSG GYDRHITIFSPEGRLFQVEYAFKAVK AG+TSIGVRGKDSVCVVTQKKVPDKL
Sbjct:     1 MSRGSGAGYDRHITIFSPEGRLFQVEYAFKAVKTAGITSIGVRGKDSVCVVTQKKVPDKL 60

Query:    61 LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
             LD +SVTHLFPITKY+GL+ATG+TADAR+LVQQAR +AAEFRF YGYEMPVD+LAKWIAD
Sbjct:    61 LDQSSVTHLFPITKYIGLVATGITADARSLVQQARNQAAEFRFTYGYEMPVDILAKWIAD 120

Query:   121 KSQVYTQHAYMRPLGV 136
             KSQVYTQHAYMRPLGV
Sbjct:   121 KSQVYTQHAYMRPLGV 136

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

UNIPROTKB|F1NEQ6 PSMA6 "Proteasome subunit alpha type" [Gallus gallus (taxid:9031)]

 Score = 511 (184.9 bits), Expect = 5.2e-49, P = 5.2e-49
 Identities = 98/143 (68%), Positives = 119/143 (83%)

Query:     1 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
             MSRGS  G+DRHITIFSPEGRL+QVEYAFKA+   G+TS+ VRGKDS  +VTQKKVPDKL
Sbjct:     4 MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDSAVIVTQKKVPDKL 63

Query:    61 LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
             LD  +VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGY++PVD+L K IAD
Sbjct:    64 LDSNTVTHLFSITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYDIPVDMLCKRIAD 123

Query:   121 KSQVYTQHAYMRPLGVGLFLIEI 143
              SQVYTQ+A MRPLG  + LI I
Sbjct:   124 ISQVYTQNAEMRPLGCCMILIGI 146

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

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

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005844 "polysome" evidence=IEA

GO:0016363 "nuclear matrix" evidence=IEA

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

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

UNIPROTKB|G5E5C3 PSMA6 "Proteasome subunit alpha type" [Bos taurus (taxid:9913)]

 Score = 510 (184.6 bits), Expect = 6.7e-49, P = 6.7e-49
 Identities = 98/143 (68%), Positives = 119/143 (83%)

Query:     1 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
             MSRGS  G+DRHITIFSPEGRL+QVEYAFKA+   G+TS+ VRGKD   +VTQKKVPDKL
Sbjct:     1 MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL 60

Query:    61 LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
             LD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD
Sbjct:    61 LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD 120

Query:   121 KSQVYTQHAYMRPLGVGLFLIEI 143
              SQVYTQ+A MRPLG  + LI I
Sbjct:   121 ISQVYTQNAEMRPLGCCMILIGI 143

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

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

GO:0016363 "nuclear matrix" evidence=IEA

GO:0005844 "polysome" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

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

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

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

 Score = 510 (184.6 bits), Expect = 6.7e-49, P = 6.7e-49
 Identities = 98/143 (68%), Positives = 119/143 (83%)

Query:     1 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
             MSRGS  G+DRHITIFSPEGRL+QVEYAFKA+   G+TS+ VRGKD   +VTQKKVPDKL
Sbjct:     1 MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL 60

Query:    61 LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
             LD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD
Sbjct:    61 LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD 120

Query:   121 KSQVYTQHAYMRPLGVGLFLIEI 143
              SQVYTQ+A MRPLG  + LI I
Sbjct:   121 ISQVYTQNAEMRPLGCCMILIGI 143

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

 Score = 510 (184.6 bits), Expect = 6.7e-49, P = 6.7e-49
 Identities = 98/143 (68%), Positives = 119/143 (83%)

Query:     1 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
             MSRGS  G+DRHITIFSPEGRL+QVEYAFKA+   G+TS+ VRGKD   +VTQKKVPDKL
Sbjct:     1 MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL 60

Query:    61 LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
             LD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD
Sbjct:    61 LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD 120

Query:   121 KSQVYTQHAYMRPLGVGLFLIEI 143
              SQVYTQ+A MRPLG  + LI I
Sbjct:   121 ISQVYTQNAEMRPLGCCMILIGI 143

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|G3V295 PSMA6 "Proteasome subunit alpha type" [Homo sapiens (taxid:9606)]

 Score = 510 (184.6 bits), Expect = 6.7e-49, P = 6.7e-49
 Identities = 98/143 (68%), Positives = 119/143 (83%)

Query:     1 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
             MSRGS  G+DRHITIFSPEGRL+QVEYAFKA+   G+TS+ VRGKD   +VTQKKVPDKL
Sbjct:     1 MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL 60

Query:    61 LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
             LD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD
Sbjct:    61 LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD 120

Query:   121 KSQVYTQHAYMRPLGVGLFLIEI 143
              SQVYTQ+A MRPLG  + LI I
Sbjct:   121 ISQVYTQNAEMRPLGCCMILIGI 143

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

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

 Score = 510 (184.6 bits), Expect = 6.7e-49, P = 6.7e-49
 Identities = 98/143 (68%), Positives = 119/143 (83%)

Query:     1 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
             MSRGS  G+DRHITIFSPEGRL+QVEYAFKA+   G+TS+ VRGKD   +VTQKKVPDKL
Sbjct:     1 MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL 60

Query:    61 LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
             LD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD
Sbjct:    61 LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD 120

Query:   121 KSQVYTQHAYMRPLGVGLFLIEI 143
              SQVYTQ+A MRPLG  + LI I
Sbjct:   121 ISQVYTQNAEMRPLGCCMILIGI 143

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 = 510 (184.6 bits), Expect = 6.7e-49, P = 6.7e-49
 Identities = 98/143 (68%), Positives = 119/143 (83%)

Query:     1 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
             MSRGS  G+DRHITIFSPEGRL+QVEYAFKA+   G+TS+ VRGKD   +VTQKKVPDKL
Sbjct:     1 MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL 60

Query:    61 LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
             LD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD
Sbjct:    61 LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD 120

Query:   121 KSQVYTQHAYMRPLGVGLFLIEI 143
              SQVYTQ+A MRPLG  + LI I
Sbjct:   121 ISQVYTQNAEMRPLGCCMILIGI 143

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 = 510 (184.6 bits), Expect = 6.7e-49, P = 6.7e-49
 Identities = 98/143 (68%), Positives = 119/143 (83%)

Query:     1 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
             MSRGS  G+DRHITIFSPEGRL+QVEYAFKA+   G+TS+ VRGKD   +VTQKKVPDKL
Sbjct:     1 MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL 60

Query:    61 LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
             LD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD
Sbjct:    61 LDSSTVTHLFKITESIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD 120

Query:   121 KSQVYTQHAYMRPLGVGLFLIEI 143
              SQVYTQ+A MRPLG  + LI I
Sbjct:   121 ISQVYTQNAEMRPLGCCMILIGI 143

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)
Q9LSU3	PSA6_ORYSJ	3, ., 4, ., 2, 5, ., 1	0.9191	0.9127	0.5528	yes	no
O81147	PSA6B_ARATH	3, ., 4, ., 2, 5, ., 1	0.9117	0.9127	0.5528	yes	no
Q9XG77	PSA6_TOBAC	3, ., 4, ., 2, 5, ., 1	0.9230	0.9597	0.5813	N/A	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	0.946
3rd Layer	3.4.25	0.963

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	149
cd03754	215	cd03754, proteasome_alpha_type_6, proteasome_alpha	4e-93
cd01911	209	cd01911, proteasome_alpha, proteasome alpha subuni	7e-78
PRK03996	241	PRK03996, PRK03996, proteasome subunit alpha; Prov	2e-46
COG0638	236	COG0638, PRE1, 20S proteasome, alpha and beta subu	3e-45
TIGR03633	224	TIGR03633, arc_protsome_A, proteasome endopeptidas	2e-44
cd03756	211	cd03756, proteasome_alpha_archeal, proteasome_alph	2e-44
cd03751	212	cd03751, proteasome_alpha_type_3, proteasome_alpha	8e-38
cd03752	213	cd03752, proteasome_alpha_type_4, proteasome_alpha	9e-37
cd03753	213	cd03753, proteasome_alpha_type_5, proteasome_alpha	1e-36
cd03749	211	cd03749, proteasome_alpha_type_1, proteasome_alpha	5e-36
cd03750	227	cd03750, proteasome_alpha_type_2, proteasome_alpha	4e-34
cd03755	207	cd03755, proteasome_alpha_type_7, proteasome_alpha	8e-34
cd01906	182	cd01906, proteasome_protease_HslV, proteasome_prot	8e-33
pfam00227	188	pfam00227, Proteasome, Proteasome subunit	3e-31
PTZ00246	253	PTZ00246, PTZ00246, proteasome subunit alpha; Prov	1e-28
cd01901	164	cd01901, Ntn_hydrolase, The Ntn hydrolases (N-term	2e-22
pfam10584	23	pfam10584, Proteasome_A_N, Proteasome subunit A N-	2e-12
smart00948	23	smart00948, Proteasome_A_N, Proteasome subunit A N	1e-11
cd01912	189	cd01912, proteasome_beta, proteasome beta subunit	1e-05
TIGR03634	185	TIGR03634, arc_protsome_B, proteasome endopeptidas	7e-05
cd03764	188	cd03764, proteasome_beta_archeal, Archeal proteaso	8e-05

>gnl|CDD|239723 cd03754, proteasome_alpha_type_6, proteasome_alpha_type_6

 Score =  268 bits (687), Expect = 4e-93
 Identities = 102/136 (75%), Positives = 118/136 (86%)

Query: 8   GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVT 67
           G+DRHITIFSPEGRL+QVEYAFKAVK AG+TS+ VRGKD   VVTQKKVPDKL+D ++VT
Sbjct: 1   GFDRHITIFSPEGRLYQVEYAFKAVKNAGLTSVAVRGKDCAVVVTQKKVPDKLIDPSTVT 60

Query: 68  HLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQ 127
           HLF IT  +G + TGM AD+R+ VQ+ARYEAAEF++KYGYEMPVDVLAK IAD +QVYTQ
Sbjct: 61  HLFRITDEIGCVMTGMIADSRSQVQRARYEAAEFKYKYGYEMPVDVLAKRIADINQVYTQ 120

Query: 128 HAYMRPLGVGLFLIEI 143
           HAYMRPLGV + LI I
Sbjct: 121 HAYMRPLGVSMILIGI 136

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 =  229 bits (586), Expect = 7e-78
 Identities = 72/133 (54%), Positives = 93/133 (69%), Gaps = 1/133 (0%)

Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YDR IT FSPEGRLFQVEYA +AVK    T++G++GKD V +  +KKV  KLLD +SV  
Sbjct: 1   YDRSITTFSPEGRLFQVEYALEAVKNGS-TAVGIKGKDGVVLAVEKKVTSKLLDPSSVEK 59

Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +F I  ++G    G+TADAR LV +AR EA  +R+ YG  +PV+VL K IAD +QVYTQ+
Sbjct: 60  IFKIDDHIGCAVAGLTADARVLVNRARVEAQNYRYTYGEPIPVEVLVKRIADLAQVYTQY 119

Query: 129 AYMRPLGVGLFLI 141
             +RP GV L + 
Sbjct: 120 GGVRPFGVSLLIA 132

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|235192 PRK03996, PRK03996, proteasome subunit alpha; Provisional

 Score =  150 bits (381), Expect = 2e-46
 Identities = 62/131 (47%), Positives = 85/131 (64%), Gaps = 1/131 (0%)

Query: 8   GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVT 67
           GYDR ITIFSP+GRL+QVEYA +AVK  G T++GV+ KD V +   K++   L++ +S+ 
Sbjct: 9   GYDRAITIFSPDGRLYQVEYAREAVKR-GTTAVGVKTKDGVVLAVDKRITSPLIEPSSIE 67

Query: 68  HLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQ 127
            +F I  ++G  + G+ ADAR L+ +AR EA   R  YG  + V+ L K I D  Q YTQ
Sbjct: 68  KIFKIDDHIGAASAGLVADARVLIDRARVEAQINRLTYGEPIGVETLTKKICDHKQQYTQ 127

Query: 128 HAYMRPLGVGL 138
           H  +RP GV L
Sbjct: 128 HGGVRPFGVAL 138

Length = 241

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

 Score =  147 bits (373), Expect = 3e-45
 Identities = 63/132 (47%), Positives = 86/132 (65%), Gaps = 3/132 (2%)

Query: 8   GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLD-HTSV 66
           GYDR ITIFSPEGRLFQVEYA +AVK  G T++G++GKD V +   K+    LL   ++V
Sbjct: 2   GYDRAITIFSPEGRLFQVEYALEAVKRGGTTTVGIKGKDGVVLAADKRATSGLLIASSNV 61

Query: 67  THLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYT 126
             +F I  ++G+   G+ ADA+ LV+ AR EA  +R +YG  + V+ LAK +++  Q YT
Sbjct: 62  EKIFKIDDHIGMAIAGLAADAQVLVRYARAEAQLYRLRYGEPISVEALAKLLSNILQEYT 121

Query: 127 QHAYMRPLGVGL 138
           Q    RP GV L
Sbjct: 122 Q--SGRPYGVSL 131

Length = 236

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

 Score =  145 bits (367), Expect = 2e-44
 Identities = 62/131 (47%), Positives = 87/131 (66%), Gaps = 1/131 (0%)

Query: 8   GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVT 67
           GYDR IT+FSP+GRL+QVEYA +AVK  G T++G++ KD V +   K++  KL++ +S+ 
Sbjct: 2   GYDRAITVFSPDGRLYQVEYAREAVKR-GTTAVGIKTKDGVVLAVDKRITSKLVEPSSIE 60

Query: 68  HLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQ 127
            +F I  ++G   +G+ ADAR L+ +AR EA   R  YG  + V+ LAK I D  Q YTQ
Sbjct: 61  KIFKIDDHIGAATSGLVADARVLIDRARIEAQINRLTYGEPIDVETLAKKICDLKQQYTQ 120

Query: 128 HAYMRPLGVGL 138
           H  +RP GV L
Sbjct: 121 HGGVRPFGVAL 131

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|239725 cd03756, proteasome_alpha_archeal, proteasome_alpha_archeal

 Score =  144 bits (365), Expect = 2e-44
 Identities = 60/131 (45%), Positives = 86/131 (65%), Gaps = 1/131 (0%)

Query: 8   GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVT 67
           GYDR IT+FSP+GRL+QVEYA +AVK  G T++G++ K+ V +   K++  KL++  S+ 
Sbjct: 1   GYDRAITVFSPDGRLYQVEYAREAVKR-GTTALGIKCKEGVVLAVDKRITSKLVEPESIE 59

Query: 68  HLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQ 127
            ++ I  ++G   +G+ ADAR L+ +AR EA   R  YG  + V+VL K I D  Q YTQ
Sbjct: 60  KIYKIDDHVGAATSGLVADARVLIDRARVEAQIHRLTYGEPIDVEVLVKKICDLKQQYTQ 119

Query: 128 HAYMRPLGVGL 138
           H  +RP GV L
Sbjct: 120 HGGVRPFGVAL 130

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|239720 cd03751, proteasome_alpha_type_3, proteasome_alpha_type_3

 Score =  127 bits (322), Expect = 8e-38
 Identities = 58/135 (42%), Positives = 83/135 (61%), Gaps = 1/135 (0%)

Query: 6   GGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTS 65
           G GYD   + FSP+GR+FQVEYA KAV+ +G T+IG+R KD V +  +K V  KL +  S
Sbjct: 1   GTGYDLSASTFSPDGRVFQVEYANKAVENSG-TAIGIRCKDGVVLAVEKLVTSKLYEPGS 59

Query: 66  VTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVY 125
              +F + +++G+   G+ AD R LV +AR EA  +R  YG  +PV VLA  +A     Y
Sbjct: 60  NKRIFNVDRHIGIAVAGLLADGRHLVSRAREEAENYRDNYGTPIPVKVLADRVAMYMHAY 119

Query: 126 TQHAYMRPLGVGLFL 140
           T ++ +RP G  + L
Sbjct: 120 TLYSSVRPFGCSVLL 134

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|239721 cd03752, proteasome_alpha_type_4, proteasome_alpha_type_4

 Score =  124 bits (314), Expect = 9e-37
 Identities = 54/134 (40%), Positives = 77/134 (57%), Gaps = 3/134 (2%)

Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDH-TSVT 67
           YD   TIFSPEGRL+QVEYA +A+  AG   +G+  KD + +  +KKV  KLLD   S  
Sbjct: 3   YDSRTTIFSPEGRLYQVEYAMEAISHAGTC-LGILAKDGIVLAAEKKVTSKLLDQSFSSE 61

Query: 68  HLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQ 127
            ++ I  ++     G+T+DA  L+  AR  A  + + Y   +PV+ L + + D  Q YTQ
Sbjct: 62  KIYKIDDHIACAVAGITSDANILINYARLIAQRYLYSYQEPIPVEQLVQRLCDIKQGYTQ 121

Query: 128 HAYMRPLGVGLFLI 141
           +  +RP GV  FL 
Sbjct: 122 YGGLRPFGVS-FLY 134

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|239722 cd03753, proteasome_alpha_type_5, proteasome_alpha_type_5

 Score =  124 bits (314), Expect = 1e-36
 Identities = 53/135 (39%), Positives = 81/135 (60%), Gaps = 6/135 (4%)

Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YDR +  FSPEGRLFQVEYA +A+K  G T+IG++ K+ V +  +K++   L++ +SV  
Sbjct: 1   YDRGVNTFSPEGRLFQVEYAIEAIKL-GSTAIGIKTKEGVVLAVEKRITSPLMEPSSVEK 59

Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVY--- 125
           +  I  ++G   +G+ ADARTL+  AR EA   RF Y   M V+ + + ++D +  +   
Sbjct: 60  IMEIDDHIGCAMSGLIADARTLIDHARVEAQNHRFTYNEPMTVESVTQAVSDLALQFGEG 119

Query: 126 --TQHAYMRPLGVGL 138
              + A  RP GV L
Sbjct: 120 DDGKKAMSRPFGVAL 134

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|239718 cd03749, proteasome_alpha_type_1, proteasome_alpha_type_1

 Score =  123 bits (310), Expect = 5e-36
 Identities = 51/133 (38%), Positives = 77/133 (57%), Gaps = 3/133 (2%)

Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YD  +T +SP+GRLFQVEYA +AVK  G  ++G++ K    +V  K+   +L  +     
Sbjct: 1   YDTDVTTWSPQGRLFQVEYAMEAVKQ-GSATVGLKSKTHAVLVALKRATSELSSYQK--K 57

Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +F +  ++G+   G+TADAR L +  R E   +RF Y   +PV  L   +A+K+Q+ TQ 
Sbjct: 58  IFKVDDHIGIAIAGLTADARVLSRYMRQECLNYRFVYDSPIPVSRLVSKVAEKAQINTQR 117

Query: 129 AYMRPLGVGLFLI 141
              RP GVGL + 
Sbjct: 118 YGRRPYGVGLLIA 130

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|239719 cd03750, proteasome_alpha_type_2, proteasome_alpha_type_2

 Score =  118 bits (298), Expect = 4e-34
 Identities = 54/132 (40%), Positives = 81/132 (61%), Gaps = 1/132 (0%)

Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           Y   +T FSP G+L Q+EYA  AV ++G  S+G++  + V + T+KKVP  L+D +SV  
Sbjct: 1   YSFSLTTFSPSGKLVQIEYALAAV-SSGAPSVGIKAANGVVLATEKKVPSPLIDESSVHK 59

Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +  IT ++G++ +GM  D R LV++AR  A ++   YG  +PV  L + IA   Q YTQ 
Sbjct: 60  VEQITPHIGMVYSGMGPDFRVLVKKARKIAQQYYLVYGEPIPVSQLVREIASVMQEYTQS 119

Query: 129 AYMRPLGVGLFL 140
             +RP GV L +
Sbjct: 120 GGVRPFGVSLLI 131

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|239724 cd03755, proteasome_alpha_type_7, proteasome_alpha_type_7

 Score =  117 bits (294), Expect = 8e-34
 Identities = 55/128 (42%), Positives = 78/128 (60%), Gaps = 1/128 (0%)

Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YDR IT+FSP+G LFQVEYA +AV+  G T++GVRGKD V +  +KK   KL D  +V  
Sbjct: 1   YDRAITVFSPDGHLFQVEYAQEAVRK-GTTAVGVRGKDCVVLGVEKKSVAKLQDPRTVRK 59

Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +  +  ++ L   G+TADAR L+ +AR E    R      + V+ + ++IA   Q YTQ 
Sbjct: 60  ICMLDDHVCLAFAGLTADARVLINRARLECQSHRLTVEDPVTVEYITRYIAGLQQRYTQS 119

Query: 129 AYMRPLGV 136
             +RP G+
Sbjct: 120 GGVRPFGI 127

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|238887 cd01906, proteasome_protease_HslV, proteasome_protease_HslV

 Score =  113 bits (286), Expect = 8e-33
 Identities = 42/105 (40%), Positives = 64/105 (60%), Gaps = 3/105 (2%)

Query: 38  TSIGVRGKDSVCVVTQKKVPDKLLDH-TSVTHLFPITKYLGLLATGMTADARTLVQQARY 96
           T +G++GKD V +   K+V   LL   ++V  +F I  ++G    G+ ADA+TLV++ R 
Sbjct: 2   TIVGIKGKDGVVLAADKRVTSGLLVASSTVEKIFKIDDHIGCAFAGLAADAQTLVERLRK 61

Query: 97  EAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLI 141
           EA  +R +YG  +PV+ LAK +A+    YTQ   +RPLGV L + 
Sbjct: 62  EAQLYRLRYGEPIPVEALAKLLANLLYEYTQS--LRPLGVSLLVA 104

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

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

 Score =  109 bits (276), Expect = 3e-31
 Identities = 46/108 (42%), Positives = 65/108 (60%), Gaps = 3/108 (2%)

Query: 36  GVTSIGVRGKDSVCVVTQKKVP--DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQ 93
           G T +G++GKD V +   K+     KLL   +V  +F I  ++G+   G+ ADA+TLV  
Sbjct: 4   GTTIVGIKGKDGVVLAADKRATRGSKLLSKDTVEKIFKIDDHIGMAFAGLAADAQTLVDY 63

Query: 94  ARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLI 141
           AR EA  +R +YG  + V+ LAK IADK Q YTQ++  RP GV L + 
Sbjct: 64  ARAEAQLYRLRYGRPISVE-LAKRIADKLQAYTQYSGRRPYGVSLLIA 110

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|173491 PTZ00246, PTZ00246, proteasome subunit alpha; Provisional

 Score =  105 bits (263), Expect = 1e-28
 Identities = 57/142 (40%), Positives = 76/142 (53%), Gaps = 7/142 (4%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSR     YD   T FSPEGRL+QVEYA +A+  A +T +G+  K+ V +   K +  KL
Sbjct: 1   MSRR----YDSRTTTFSPEGRLYQVEYALEAINNASLT-VGILCKEGVILGADKPISSKL 55

Query: 61  LDH-TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 119
           LD       ++ I  ++     G+TADA  L+ Q R  A  +R+ YG   PV+ L   I 
Sbjct: 56  LDPGKINEKIYKIDSHIFCAVAGLTADANILINQCRLYAQRYRYTYGEPQPVEQLVVQIC 115

Query: 120 DKSQVYTQHAYMRPLGVGLFLI 141
           D  Q YTQ   +RP GV  FL 
Sbjct: 116 DLKQSYTQFGGLRPFGVS-FLF 136

Length = 253

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

 Score = 86.7 bits (215), Expect = 2e-22
 Identities = 34/102 (33%), Positives = 51/102 (50%), Gaps = 4/102 (3%)

Query: 38  TSIGVRGKDSVCVVTQKKVPDKLLDH-TSVTHLFPITKYLGLLATGMTADARTLVQQARY 96
           TS+ ++GK  V +   K++   L    + V  +      +     G+ ADA+TLV++ R 
Sbjct: 2   TSVAIKGKGGVVLAADKRLSSGLPVAGSPVIKIGKNEDGIAWGLAGLAADAQTLVRRLRE 61

Query: 97  EAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGL 138
               +R +YG  + V  LAK +A   QVYTQ    RP GV L
Sbjct: 62  ALQLYRLRYGEPISVVALAKELAKLLQVYTQ---GRPFGVNL 100

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|204518 pfam10584, Proteasome_A_N, Proteasome subunit A N-terminal signature

 Score = 57.4 bits (140), Expect = 2e-12
 Identities = 18/23 (78%), Positives = 20/23 (86%)

Query: 9  YDRHITIFSPEGRLFQVEYAFKA 31
          YDR +T FSP+GRLFQVEYA KA
Sbjct: 1  YDRSLTTFSPDGRLFQVEYAMKA 23

This domain is conserved in the A subunits of the proteasome complex proteins. Length = 23

>gnl|CDD|198016 smart00948, Proteasome_A_N, Proteasome subunit A N-terminal signature Add an annotation

 Score = 55.2 bits (134), Expect = 1e-11
 Identities = 17/23 (73%), Positives = 20/23 (86%)

Query: 9  YDRHITIFSPEGRLFQVEYAFKA 31
          YDR +T FSP+GRLFQVEYA +A
Sbjct: 1  YDRSLTTFSPDGRLFQVEYAMEA 23

This domain is conserved in the A subunits of the proteasome complex proteins. Length = 23

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

 Score = 42.4 bits (101), Expect = 1e-05
 Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 1/83 (1%)

Query: 38  TSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH-LFPITKYLGLLATGMTADARTLVQQARY 96
           T +G++GKD V +    +     L  +     +F I+  + L   G  AD + L +  + 
Sbjct: 2   TIVGIKGKDGVVLAADTRASAGSLVASRNFDKIFKISDNILLGTAGSAADTQALTRLLKR 61

Query: 97  EAAEFRFKYGYEMPVDVLAKWIA 119
               +  + G E+ V   A  ++
Sbjct: 62  NLRLYELRNGRELSVKAAANLLS 84

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

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

 Score = 40.7 bits (96), Expect = 7e-05
 Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 1/82 (1%)

Query: 36  GVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQA 94
           G T++G++ KD V +   K+      +   +   +F I  Y+ +   G   DA++LV+  
Sbjct: 1   GTTTVGIKCKDGVVLAADKRASMGNFVASKNAKKVFQIDDYIAMTIAGSVGDAQSLVRIL 60

Query: 95  RYEAAEFRFKYGYEMPVDVLAK 116
           + EA  +  + G  M V  LA 
Sbjct: 61  KAEAKLYELRRGRPMSVKALAT 82

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|239733 cd03764, proteasome_beta_archeal, Archeal proteasome, beta subunit

 Score = 40.3 bits (95), Expect = 8e-05
 Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 1/83 (1%)

Query: 38  TSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARY 96
           T++G+  KD V +   K+      +   +V  +F I   + +   G   DA++LV+  + 
Sbjct: 2   TTVGIVCKDGVVLAADKRASMGNFIASKNVKKIFQIDDKIAMTIAGSVGDAQSLVRILKA 61

Query: 97  EAAEFRFKYGYEMPVDVLAKWIA 119
           EA  +  + G  M +  LA  ++
Sbjct: 62  EARLYELRRGRPMSIKALATLLS 84

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	149
KOG0184	254	consensus 20S proteasome, regulatory subunit alpha	100.0
cd03754	215	proteasome_alpha_type_6 proteasome_alpha_type_6. T	100.0
cd03751	212	proteasome_alpha_type_3 proteasome_alpha_type_3. T	100.0
cd03750	227	proteasome_alpha_type_2 proteasome_alpha_type_2. T	100.0
cd03755	207	proteasome_alpha_type_7 proteasome_alpha_type_7. T	100.0
cd03752	213	proteasome_alpha_type_4 proteasome_alpha_type_4. T	100.0
PRK03996	241	proteasome subunit alpha; Provisional	100.0
cd03749	211	proteasome_alpha_type_1 proteasome_alpha_type_1. T	100.0
PTZ00246	253	proteasome subunit alpha; Provisional	100.0
cd03756	211	proteasome_alpha_archeal proteasome_alpha_archeal.	100.0
KOG0178	249	consensus 20S proteasome, regulatory subunit alpha	100.0
KOG0183	249	consensus 20S proteasome, regulatory subunit alpha	100.0
TIGR03633	224	arc_protsome_A proteasome endopeptidase complex, a	100.0
cd01911	209	proteasome_alpha proteasome alpha subunit. The 20S	100.0
cd03753	213	proteasome_alpha_type_5 proteasome_alpha_type_5. T	100.0
KOG0176	241	consensus 20S proteasome, regulatory subunit alpha	100.0
KOG0182	246	consensus 20S proteasome, regulatory subunit alpha	100.0
COG0638	236	PRE1 20S proteasome, alpha and beta subunits [Post	100.0
KOG0181	233	consensus 20S proteasome, regulatory subunit alpha	100.0
KOG0863	264	consensus 20S proteasome, regulatory subunit alpha	100.0
cd03760	197	proteasome_beta_type_4 proteasome beta type-4 subu	99.97
cd03758	193	proteasome_beta_type_2 proteasome beta type-2 subu	99.97
cd03759	195	proteasome_beta_type_3 proteasome beta type-3 subu	99.97
TIGR03690	219	20S_bact_beta proteasome, beta subunit, bacterial	99.96
TIGR03691	228	20S_bact_alpha proteasome, alpha subunit, bacteria	99.96
cd03761	188	proteasome_beta_type_5 proteasome beta type-5 subu	99.96
TIGR03634	185	arc_protsome_B proteasome endopeptidase complex, a	99.96
cd03757	212	proteasome_beta_type_1 proteasome beta type-1 subu	99.96
PF00227	190	Proteasome: Proteasome subunit; InterPro: IPR00135	99.96
cd03762	188	proteasome_beta_type_6 proteasome beta type-6 subu	99.95
PTZ00488	247	Proteasome subunit beta type-5; Provisional	99.95
cd03764	188	proteasome_beta_archeal Archeal proteasome, beta s	99.95
cd03765	236	proteasome_beta_bacterial Bacterial proteasome, be	99.95
cd01906	182	proteasome_protease_HslV proteasome_protease_HslV.	99.95
cd01912	189	proteasome_beta proteasome beta subunit. The 20S p	99.94
cd03763	189	proteasome_beta_type_7 proteasome beta type-7 subu	99.94
KOG0177	200	consensus 20S proteasome, regulatory subunit beta	99.9
KOG0179	235	consensus 20S proteasome, regulatory subunit beta	99.89
KOG0174	224	consensus 20S proteasome, regulatory subunit beta	99.87
cd01901	164	Ntn_hydrolase The Ntn hydrolases (N-terminal nucle	99.86
KOG0185	256	consensus 20S proteasome, regulatory subunit beta	99.86
KOG0180	204	consensus 20S proteasome, regulatory subunit beta	99.85
cd01913	171	protease_HslV Protease HslV and the ATPase/chapero	99.82
PRK05456	172	ATP-dependent protease subunit HslV; Provisional	99.81
KOG0175	285	consensus 20S proteasome, regulatory subunit beta	99.8
TIGR03692	171	ATP_dep_HslV ATP-dependent protease HslVU, peptida	99.79
KOG0173	271	consensus 20S proteasome, regulatory subunit beta	99.73
PF10584	23	Proteasome_A_N: Proteasome subunit A N-terminal si	99.56
COG5405	178	HslV ATP-dependent protease HslVU (ClpYQ), peptida	98.66
COG3484	255	Predicted proteasome-type protease [Posttranslatio	93.51
PF09894	194	DUF2121: Uncharacterized protein conserved in arch	84.38

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

Probab=100.00  E-value=3.9e-47  Score=284.30  Aligned_cols=145  Identities=38%  Similarity=0.596  Sum_probs=141.4

Q ss_pred             CCCCCCCCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEE
Q 031996            1 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLA   80 (149)
Q Consensus         1 m~~~~~~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~   80 (149)
                      ||+ +|++||++.++||||||+||+|||+|||++ ++|+|||||||||||++||..+|+|..++.+.||+.|++||+|++
T Consensus         1 MSs-IGtGyDls~s~fSpdGrvfQveYA~KAven-~~T~IGIk~kdGVVl~vEKli~SkLy~p~sn~ri~~V~r~iG~av   78 (254)
T KOG0184|consen    1 MSS-IGTGYDLSASTFSPDGRVFQVEYAQKAVEN-SGTCIGIKCKDGVVLAVEKLITSKLYEPGSNERIFSVDRHIGMAV   78 (254)
T ss_pred             CCc-ccccccccceeeCCCCceehHHHHHHHHhc-CCcEEEEecCCeEEEEEeeeecccccccCCCCceEeecccccEEE
Confidence            886 999999999999999999999999999998 789999999999999999999999999999999999999999999


Q ss_pred             eccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996           81 TGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        81 sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      +|+.+|++.+++++|.++..|+.+|+.|+|.+.++..++.++|.||.++..||||++.|+++||.++
T Consensus        79 aGl~~Dg~~l~~~ar~ea~~~~~~y~~piP~~~la~rva~yvh~~Tly~~vRpfG~~~~~~~yd~~g  145 (254)
T KOG0184|consen   79 AGLIPDGRHLVNRARDEAASWRKNYGDPIPGKHLADRVADYVHAFTLYSSVRPFGASTILGSYDDEG  145 (254)
T ss_pred             eccccchHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHhhhheeehhhccccccceEEEEEEeCCC
Confidence            9999999999999999999999999999999999999999999999999999999999999999654

>cd03754 proteasome_alpha_type_6 proteasome_alpha_type_6

Probab=100.00  E-value=3.7e-46  Score=285.16  Aligned_cols=139  Identities=73%  Similarity=1.121  Sum_probs=133.3

Q ss_pred             CCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHH
Q 031996            8 GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADA   87 (149)
Q Consensus         8 ~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~   87 (149)
                      +||+++|+||||||++|+|||+||+++.|+|+|||+++||||||+|++.++.++..++.+||++|++|++|++||+.+|+
T Consensus         1 ~yd~~~~~fsp~Grl~Qveya~~a~~~~g~t~igi~~~d~Vvlaad~r~~~~~i~~~~~~Ki~~I~~~i~~~~sG~~~D~   80 (215)
T cd03754           1 GFDRHITIFSPEGRLYQVEYAFKAVKNAGLTSVAVRGKDCAVVVTQKKVPDKLIDPSTVTHLFRITDEIGCVMTGMIADS   80 (215)
T ss_pred             CCCCCCeeECCCCeEeHHHhHHHHHhcCCccEEEEEeCCEEEEEEeccccccccCCcccCceEEEcCCEEEEEEechhhH
Confidence            59999999999999999999999998778899999999999999999998777766788999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           88 RTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        88 ~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +.+.+++|.++.+|+++++++|+++.||+++++++|.|+++++.|||+|++||||||++
T Consensus        81 ~~l~~~~r~~~~~~~~~~~~~i~v~~la~~ls~~~q~yt~~~~~RP~~v~~ii~G~D~~  139 (215)
T cd03754          81 RSQVQRARYEAAEFKYKYGYEMPVDVLAKRIADINQVYTQHAYMRPLGVSMILIGIDEE  139 (215)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhCCCCCcCCeeEEEEEEEeCC
Confidence            99999999999999999999999999999999999999999999999999999999964

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=4.3e-46  Score=284.33  Aligned_cols=139  Identities=40%  Similarity=0.627  Sum_probs=134.1

Q ss_pred             CCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHH
Q 031996            7 GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTAD   86 (149)
Q Consensus         7 ~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D   86 (149)
                      .+||+++|+||||||++|+|||++|+++ |+|+|||+++||||||+|++.++.++..++.+||++|++|++|++||+.+|
T Consensus         2 ~~yd~~~t~fsp~Grl~Qveya~~a~~~-G~tvIgik~kdgVvla~d~r~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D   80 (212)
T cd03751           2 TGYDLSASTFSPDGRVFQVEYANKAVEN-SGTAIGIRCKDGVVLAVEKLVTSKLYEPGSNKRIFNVDRHIGIAVAGLLAD   80 (212)
T ss_pred             CCccCCCceECCCCcchHHHHHHHHHhc-CCCEEEEEeCCEEEEEEEccccccccCcchhcceeEecCcEEEEEEEChHh
Confidence            5899999999999999999999999987 999999999999999999999888777778899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           87 ARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        87 ~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      ++.+.+++|.+++.|+++++++|+|+.+++++++++|.|+++++.|||+|++||+|||++
T Consensus        81 ~~~l~~~~r~~~~~y~~~~~~~~~v~~la~~ls~~~~~~t~~~~~rP~~vs~li~G~D~~  140 (212)
T cd03751          81 GRHLVSRAREEAENYRDNYGTPIPVKVLADRVAMYMHAYTLYSSVRPFGCSVLLGGYDSD  140 (212)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccCCCcCCceEEEEEEEEeCC
Confidence            999999999999999999999999999999999999999999999999999999999964

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.

>cd03750 proteasome_alpha_type_2 proteasome_alpha_type_2

Probab=100.00  E-value=1e-45  Score=284.70  Aligned_cols=137  Identities=39%  Similarity=0.635  Sum_probs=133.2

Q ss_pred             CCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHHH
Q 031996            9 YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADAR   88 (149)
Q Consensus         9 yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~   88 (149)
                      ||+++|+||||||++|||||++|+++ |+|+|||+++||||||+|++.+++++.+++.+||++|++|++|++||+.+|++
T Consensus         1 yd~~~t~fsp~Grl~QveyA~~av~~-G~t~igik~~dgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~   79 (227)
T cd03750           1 YSFSLTTFSPSGKLVQIEYALAAVSS-GAPSVGIKAANGVVLATEKKVPSPLIDESSVHKVEQITPHIGMVYSGMGPDFR   79 (227)
T ss_pred             CCCCCceECCCCeEhHHHHHHHHHHc-CCCEEEEEeCCEEEEEEeecCCccccCCCCcceEEEEcCCEEEEEeEcHHhHH
Confidence            89999999999999999999999987 99999999999999999999998888888999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           89 TLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        89 ~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      .+++++|.++++|++++|++|+++.+++++++++|.|+++++.|||+|++||+|||++
T Consensus        80 ~l~~~~r~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rP~~v~~li~G~D~~  137 (227)
T cd03750          80 VLVKKARKIAQQYYLVYGEPIPVSQLVREIASVMQEYTQSGGVRPFGVSLLIAGWDEG  137 (227)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCCCCCChheEEEEEEEeCC
Confidence            9999999999999999999999999999999999999999899999999999999964

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=1.5e-45  Score=280.17  Aligned_cols=138  Identities=40%  Similarity=0.640  Sum_probs=132.8

Q ss_pred             CCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHHH
Q 031996            9 YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADAR   88 (149)
Q Consensus         9 yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~   88 (149)
                      ||+++|+||||||++|+|||++|+++ |+|+|||+++||||||+|++..+.++.+++.+||++|++|++|++||+.+|++
T Consensus         1 ~d~~~~~fsp~Gr~~Qveya~~av~~-G~t~Igik~~dgVvlaad~~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~   79 (207)
T cd03755           1 YDRAITVFSPDGHLFQVEYAQEAVRK-GTTAVGVRGKDCVVLGVEKKSVAKLQDPRTVRKICMLDDHVCLAFAGLTADAR   79 (207)
T ss_pred             CCCCCceECCCCeEeHHHHHHHHHHc-CCCEEEEEeCCEEEEEEecCCCCcccCCCccCcEEEECCCEEEEEecchhhHH
Confidence            89999999999999999999999987 99999999999999999999887787777899999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996           89 TLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        89 ~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      .+.+++|.++++|+++++++|+++.+++++++++|+|+++++.|||+|++||+|||+++
T Consensus        80 ~l~~~~r~~~~~~~~~~~~~i~~~~la~~ls~~~~~y~~~~~~rP~~vs~ii~G~D~~~  138 (207)
T cd03755          80 VLINRARLECQSHRLTVEDPVTVEYITRYIAGLQQRYTQSGGVRPFGISTLIVGFDPDG  138 (207)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcccCcccceeEEEEEEEeCCC
Confidence            99999999999999999999999999999999999999999999999999999999753

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=2.6e-45  Score=279.99  Aligned_cols=138  Identities=37%  Similarity=0.606  Sum_probs=132.2

Q ss_pred             CCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCcccccc-ccccceeeecCcEEEEEeccHHH
Q 031996            8 GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDH-TSVTHLFPITKYLGLLATGMTAD   86 (149)
Q Consensus         8 ~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~-~~~~KI~~I~~~i~~~~sG~~~D   86 (149)
                      +||+++|+||||||++|+|||+||+++ |+|+|||+++||||||+|++.+++++.. ++.+||++|++|++|++||+.+|
T Consensus         2 ~yd~~~~~fsp~Grl~Qveya~~a~~~-G~t~igi~~~dgVvla~d~r~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D   80 (213)
T cd03752           2 RYDSRTTIFSPEGRLYQVEYAMEAISH-AGTCLGILAKDGIVLAAEKKVTSKLLDQSFSSEKIYKIDDHIACAVAGITSD   80 (213)
T ss_pred             CcCCCCceECCCCEEhHHHhHHHHHhc-CCCEEEEEeCCEEEEEEEeccCCcccCCCcCcceEEEecCCEEEEEecChHh
Confidence            699999999999999999999999997 9999999999999999999999766654 48899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           87 ARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        87 ~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      ++.+++++|.++++|+++++++|+++.+++.++..+|.||++++.|||+|++||+|||++
T Consensus        81 ~~~l~~~~r~~~~~~~~~~~~~i~v~~la~~ls~~~~~~t~~~~~RP~~v~~li~G~D~~  140 (213)
T cd03752          81 ANILINYARLIAQRYLYSYQEPIPVEQLVQRLCDIKQGYTQYGGLRPFGVSFLYAGWDKH  140 (213)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcCCCcccceeEEEEEEEeCC
Confidence            999999999999999999999999999999999999999999999999999999999963

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.

>PRK03996 proteasome subunit alpha; Provisional

Probab=100.00  E-value=1.1e-44  Score=281.18  Aligned_cols=144  Identities=44%  Similarity=0.714  Sum_probs=138.7

Q ss_pred             CCCCCCCCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEE
Q 031996            1 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLA   80 (149)
Q Consensus         1 m~~~~~~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~   80 (149)
                      |+ +++++||.++|+||||||++|+|||.+|+++ |+|+|||+++||||||+|++.++.++.+++.+||++|++|++|++
T Consensus         3 ~~-~~~~~y~~~~~~fsp~Gr~~Q~eya~~av~~-G~t~igik~~dgVvlaad~r~~~~~~~~~~~~KI~~I~~~i~~~~   80 (241)
T PRK03996          3 MQ-PQQMGYDRAITIFSPDGRLYQVEYAREAVKR-GTTAVGVKTKDGVVLAVDKRITSPLIEPSSIEKIFKIDDHIGAAS   80 (241)
T ss_pred             CC-ccccccCCCCceECCCCeEhHHHHHHHHHHh-CCCEEEEEeCCEEEEEEeccCCCcccCCCccceEEEEcCCEEEEE
Confidence            56 6999999999999999999999999999987 999999999999999999999988887788999999999999999


Q ss_pred             eccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           81 TGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        81 sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      ||+.+|++.+++++|.++..|+++++++++++.+++++++.+|.|+++++.|||+|++||||||++
T Consensus        81 sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~~~~~~~rP~~~~~ilaG~d~~  146 (241)
T PRK03996         81 AGLVADARVLIDRARVEAQINRLTYGEPIGVETLTKKICDHKQQYTQHGGVRPFGVALLIAGVDDG  146 (241)
T ss_pred             cccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhcCCCCccchheEEEEEEEeCC
Confidence            999999999999999999999999999999999999999999999999899999999999999964

>cd03749 proteasome_alpha_type_1 proteasome_alpha_type_1

Probab=100.00  E-value=2.6e-44  Score=274.19  Aligned_cols=135  Identities=38%  Similarity=0.647  Sum_probs=128.8

Q ss_pred             CCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHHH
Q 031996            9 YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADAR   88 (149)
Q Consensus         9 yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~   88 (149)
                      ||+++|+||||||++|+|||++|+++ |+|+|||+++||||||+|++.++.+.  ++.+||++|++|++|++||+.+|++
T Consensus         1 yd~~~t~fsp~Grl~Qveya~~av~~-G~t~IgIk~~dgVvlaad~r~~~~l~--~~~~KI~~I~~~i~~~~sG~~~D~~   77 (211)
T cd03749           1 YDTDVTTWSPQGRLFQVEYAMEAVKQ-GSATVGLKSKTHAVLVALKRATSELS--SYQKKIFKVDDHIGIAIAGLTADAR   77 (211)
T ss_pred             CCCCCceECCCCeEeHHHHHHHHHhc-CCCEEEEEeCCEEEEEEeccCccccC--CccccEEEeCCCEEEEEEeChHhHH
Confidence            89999999999999999999999987 99999999999999999999877653  3668999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           89 TLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        89 ~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      .+.+++|.++++|+++++++|+++.+++++++++|.||++.+.|||+|++||+|||++
T Consensus        78 ~l~~~~r~~~~~~~~~~~~~~~v~~la~~is~~~~~~t~~~~~rP~~v~~ii~G~D~~  135 (211)
T cd03749          78 VLSRYMRQECLNYRFVYDSPIPVSRLVSKVAEKAQINTQRYGRRPYGVGLLIAGYDES  135 (211)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCCCCceEEEEEEEEcCC
Confidence            9999999999999999999999999999999999999998899999999999999964

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.

>PTZ00246 proteasome subunit alpha; Provisional

Probab=100.00  E-value=3e-44  Score=280.50  Aligned_cols=141  Identities=38%  Similarity=0.600  Sum_probs=133.8

Q ss_pred             CCCCCCCCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCcccccc-ccccceeeecCcEEEE
Q 031996            1 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDH-TSVTHLFPITKYLGLL   79 (149)
Q Consensus         1 m~~~~~~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~-~~~~KI~~I~~~i~~~   79 (149)
                      |++    +||+++|+|||||||+|||||+||+++ |+|+|||+++||||||+|++.++.++.. ++.+||++|++|++|+
T Consensus         1 ~~~----~yd~~~~~fsp~Grl~QvEYA~~av~~-g~t~Igik~~dgVvlaad~r~s~~~~~~~~~~~KI~~I~~~i~~~   75 (253)
T PTZ00246          1 MSR----RYDSRTTTFSPEGRLYQVEYALEAINN-ASLTVGILCKEGVILGADKPISSKLLDPGKINEKIYKIDSHIFCA   75 (253)
T ss_pred             CCC----ccCCCCceECCCCEEhHHHHHHHHHHh-CCCEEEEEECCEEEEEEecCCCCcCccCCCCcccEEEecCCEEEE
Confidence            665    899999999999999999999999997 9999999999999999999999766655 4689999999999999


Q ss_pred             EeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           80 ATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        80 ~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      ++|+.+|++.+.+.+|.++..|++.++++++++.+++.++..+|.|+++++.|||+|++||+|||++
T Consensus        76 ~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~v~~l~~~l~~~~q~~~~~~~~rP~~v~~li~G~D~~  142 (253)
T PTZ00246         76 VAGLTADANILINQCRLYAQRYRYTYGEPQPVEQLVVQICDLKQSYTQFGGLRPFGVSFLFAGYDEN  142 (253)
T ss_pred             EEEcHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccccCcccCCEEEEEEEEeCC
Confidence            9999999999999999999999999999999999999999999999999999999999999999953

>cd03756 proteasome_alpha_archeal proteasome_alpha_archeal

Probab=100.00  E-value=9e-44  Score=271.05  Aligned_cols=138  Identities=43%  Similarity=0.745  Sum_probs=133.2

Q ss_pred             CCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHH
Q 031996            8 GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADA   87 (149)
Q Consensus         8 ~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~   87 (149)
                      +||.++|+||||||++|+|||.||+++ |+|+|||+++||||||+|++.++.++..++.+||++|+++++|++||+.+|+
T Consensus         1 ~y~~~~~~fsp~G~l~Q~eya~~av~~-G~t~igik~~dgvvla~d~~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~   79 (211)
T cd03756           1 GYDRAITVFSPDGRLYQVEYAREAVKR-GTTALGIKCKEGVVLAVDKRITSKLVEPESIEKIYKIDDHVGAATSGLVADA   79 (211)
T ss_pred             CCCCCCceECCCCeEhHHHHHHHHHHc-CCCEEEEEECCEEEEEEeccCCCcccCCCccceEEEEcCCEEEEEecCHHHH
Confidence            599999999999999999999999987 9999999999999999999998877777889999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           88 RTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        88 ~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +.+.++++.+++.|+++++++++++.+++++++.+|.|+++++.|||+|++||+|||+.
T Consensus        80 ~~l~~~l~~~~~~~~~~~~~~~~~~~la~~ls~~~~~~~~~~~~rP~~v~~ll~G~D~~  138 (211)
T cd03756          80 RVLIDRARVEAQIHRLTYGEPIDVEVLVKKICDLKQQYTQHGGVRPFGVALLIAGVDDG  138 (211)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCCCeechhEEEEEEEEeCC
Confidence            99999999999999999999999999999999999999998899999999999999964

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

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

Probab=100.00  E-value=5.4e-44  Score=265.77  Aligned_cols=141  Identities=40%  Similarity=0.659  Sum_probs=135.8

Q ss_pred             CCCCCCCCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCcccccc-ccccceeeecCcEEEE
Q 031996            1 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDH-TSVTHLFPITKYLGLL   79 (149)
Q Consensus         1 m~~~~~~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~-~~~~KI~~I~~~i~~~   79 (149)
                      |||    +||...|+||||||++|||||++++.++| |+|||-++||||||++++.+++|.+. ...+||++|+||++|+
T Consensus         1 msr----~ydsrttiFspEGRLyQVEyAmeais~aG-t~iGila~DGvvLa~e~k~t~kll~t~~~~EKiY~l~d~iaC~   75 (249)
T KOG0178|consen    1 MSR----RYDSRTTIFSPEGRLYQVEYAMEAISHAG-TCIGILASDGVVLAGENKVTSKLLDTSIPMEKIYKLNDNIACA   75 (249)
T ss_pred             CCc----CcCCcccccCCCcchHHHHHHHHHHhhhc-ceeEEEecCceEEEeecccchhhhhccccHHHhhhcCCceEEE
Confidence            888    89999999999999999999999999865 99999999999999999999999864 5789999999999999


Q ss_pred             EeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           80 ATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        80 ~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      ++|+++|+..+++++|..++.|.++||++||++.|+..++++-|.|||+++.||||||+|.+|||..
T Consensus        76 vaGlt~DAnvL~n~aRi~AQ~yl~~y~e~iP~eqLv~~lcdiKQayTQygG~RPFGVSfLYaGwd~~  142 (249)
T KOG0178|consen   76 VAGLTSDANVLKNYARIIAQRYLFRYGEEIPCEQLVTFLCDIKQAYTQYGGKRPFGVSFLYAGWDDR  142 (249)
T ss_pred             EecccccHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHHhhccCcCCCceeeeeeceecC
Confidence            9999999999999999999999999999999999999999999999999999999999999999974

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

Probab=100.00  E-value=2.1e-44  Score=268.49  Aligned_cols=139  Identities=37%  Similarity=0.579  Sum_probs=136.2

Q ss_pred             CCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHH
Q 031996            8 GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADA   87 (149)
Q Consensus         8 ~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~   87 (149)
                      +||+.+|+|||||||+|+|||++|+++ |+|+||++++|+|||+.+++...+|++.+...||-.+++|++|+|||+.+|+
T Consensus         3 rydraltvFSPDGhL~QVEYAqEAvrk-GstaVgvrg~~~vvlgvEkkSv~~Lq~~r~~rkI~~ld~hV~mafaGl~aDA   81 (249)
T KOG0183|consen    3 RYDRALTVFSPDGHLFQVEYAQEAVRK-GSTAVGVRGNNCVVLGVEKKSVPKLQDERTVRKISMLDDHVVMAFAGLTADA   81 (249)
T ss_pred             ccccceEEECCCCCEEeeHhHHHHHhc-CceEEEeccCceEEEEEeecchhhhhhhhhhhhheeecceeeEEecCCCccc
Confidence            499999999999999999999999998 9999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996           88 RTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        88 ~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      +.+++++|-+|++|+++.+.|++++.++++|+.+-|.||++.+.||||+++||+|||+++
T Consensus        82 rilinrArvecqShrlt~edpvtveyitRyiA~~kQrYTqs~grRPFGvs~Li~GfD~~g  141 (249)
T KOG0183|consen   82 RILINRARVECQSHRLTLEDPVTVEYITRYIAGLKQRYTQSNGRRPFGVSTLIGGFDPDG  141 (249)
T ss_pred             eeehhhHhHhhhhhhcccCCCcHHHHHHHHHHHhhhhhhccCCcccccceEEEEeeCCCC
Confidence            999999999999999999999999999999999999999999999999999999999875

>TIGR03633 arc_protsome_A proteasome endopeptidase complex, archaeal, alpha subunit

Probab=100.00  E-value=3.4e-43  Score=270.04  Aligned_cols=138  Identities=45%  Similarity=0.755  Sum_probs=133.0

Q ss_pred             CCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHH
Q 031996            8 GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADA   87 (149)
Q Consensus         8 ~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~   87 (149)
                      +||.++|+||||||++|+|||++|+++ |+|+|||+++||||||+|++.++.++..++.+||++|+++++|++||+.+|+
T Consensus         2 ~~~~~~~~f~p~Grl~Qieya~~av~~-G~tvigi~~~dgvvlaad~r~~~~~~~~~~~~KI~~i~~~i~~~~sG~~~D~   80 (224)
T TIGR03633         2 GYDRAITVFSPDGRLYQVEYAREAVKR-GTTAVGIKTKDGVVLAVDKRITSKLVEPSSIEKIFKIDDHIGAATSGLVADA   80 (224)
T ss_pred             CCCCCCceECCCCeEeHHHHHHHHHHc-CCCEEEEEECCEEEEEEeccCCccccCCCccceEEEECCCEEEEEeecHHhH
Confidence            499999999999999999999999987 9999999999999999999999888777889999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           88 RTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        88 ~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +.+.++++.++..|+++++++++++.+++++++++|.|+++++.|||+|++||+|||+.
T Consensus        81 ~~l~~~~~~~~~~~~~~~~~~~~~~~la~~ls~~l~~~~~~~~~rP~~v~~ll~G~d~~  139 (224)
T TIGR03633        81 RVLIDRARIEAQINRLTYGEPIDVETLAKKICDLKQQYTQHGGVRPFGVALLIAGVDDG  139 (224)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCCCccccceEEEEEEEeCC
Confidence            99999999999999999999999999999999999999998889999999999999953

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.

>cd01911 proteasome_alpha proteasome alpha subunit

Probab=100.00  E-value=4.5e-43  Score=266.76  Aligned_cols=137  Identities=53%  Similarity=0.847  Sum_probs=132.1

Q ss_pred             CCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHHH
Q 031996            9 YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADAR   88 (149)
Q Consensus         9 yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~   88 (149)
                      ||.++|+||||||++|+|||++++.+ |+|+|||+++||||||+|++.+..++..++.+||++|+++++|++||+.+|++
T Consensus         1 ~~~~~~~f~~~G~~~q~eya~~~~~~-G~tvigi~~~dgVvlaaD~~~~~~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~   79 (209)
T cd01911           1 YDRSITTFSPEGRLFQVEYALEAVKN-GSTAVGIKGKDGVVLAVEKKVTSKLLDPSSVEKIFKIDDHIGCAVAGLTADAR   79 (209)
T ss_pred             CCCCCccCCCCCEEeHHHHHHHHHHc-CCCEEEEEECCEEEEEEEecCCccccCCcccceEEEecCCeEEEeccCcHhHH
Confidence            89999999999999999999999986 99999999999999999999997677668899999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           89 TLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        89 ~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      .+.++++.++.+|+++++++|+++.+|+++++++|.|+++++.|||+|++||+|||++
T Consensus        80 ~l~~~l~~~~~~~~~~~g~~~~~~~la~~ls~~~~~~~~~~~~rP~~v~~iv~G~d~~  137 (209)
T cd01911          80 VLVNRARVEAQNYRYTYGEPIPVEVLVKRIADLAQVYTQYGGVRPFGVSLLIAGYDEE  137 (209)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCccChhheEEEEEEcCC
Confidence            9999999999999999999999999999999999999999999999999999999975

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

>cd03753 proteasome_alpha_type_5 proteasome_alpha_type_5

Probab=100.00  E-value=1.1e-42  Score=265.30  Aligned_cols=137  Identities=38%  Similarity=0.681  Sum_probs=129.8

Q ss_pred             CCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHHH
Q 031996            9 YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADAR   88 (149)
Q Consensus         9 yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~   88 (149)
                      ||.++|+||||||++|+|||++++++ |+|+|||+++||||||+|++.++.+...++.+||++|++|++|++||+.+|++
T Consensus         1 ~~~~~~~f~p~G~~~Q~eya~~a~~~-G~t~igik~~dgVvlaad~r~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~   79 (213)
T cd03753           1 YDRGVNTFSPEGRLFQVEYAIEAIKL-GSTAIGIKTKEGVVLAVEKRITSPLMEPSSVEKIMEIDDHIGCAMSGLIADAR   79 (213)
T ss_pred             CCCCCccCCCCCeEhHHHHHHHHHhc-CCCEEEEEeCCEEEEEEecccCCcCcCCCccceEEEEcCCEEEEEecCHHHHH
Confidence            89999999999999999999999987 99999999999999999999987777777899999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcC-----CccccceEEEEEEEeCC
Q 031996           89 TLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHA-----YMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        89 ~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~-----~~rP~~v~~liaG~D~~  146 (149)
                      .+.+++|.+++.|+++++++|+++.+++++++++|+|++..     +.|||+|++||+|||++
T Consensus        80 ~l~~~~r~~~~~~~~~~~~~i~~~~~~~~ls~~~~~~~~~~~~~~~~~rP~~v~~ii~G~D~~  142 (213)
T cd03753          80 TLIDHARVEAQNHRFTYNEPMTVESVTQAVSDLALQFGEGDDGKKAMSRPFGVALLIAGVDEN  142 (213)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhCcccccccccccceEEEEEEEEcCC
Confidence            99999999999999999999999999999999999998643     46999999999999964

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

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

Probab=100.00  E-value=2.1e-43  Score=260.50  Aligned_cols=139  Identities=38%  Similarity=0.650  Sum_probs=131.1

Q ss_pred             CCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHH
Q 031996            8 GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADA   87 (149)
Q Consensus         8 ~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~   87 (149)
                      .||+.+++||||||+||||||.+|++ .|+|.|||++++|||||++||.+++|..++..+||++|++||+|++||+.+|+
T Consensus         7 eydrgVNTfSpEGRlfQVEYaieAik-LGsTaIGv~TkEgVvL~vEKritSpLm~p~sveKi~eid~HIgca~SGl~aDa   85 (241)
T KOG0176|consen    7 EYDRGVNTFSPEGRLFQVEYAIEAIK-LGSTAIGVKTKEGVVLAVEKRITSPLMEPSSVEKIVEIDDHIGCAMSGLIADA   85 (241)
T ss_pred             HhcccccccCCCceeeehhhHHHHHh-cCCceeeeeccceEEEEEeccccCcccCchhhhhheehhhceeeeccccccch
Confidence            59999999999999999999999997 59999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCC-----ccccceEEEEEEEeCCC
Q 031996           88 RTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAY-----MRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        88 ~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~-----~rP~~v~~liaG~D~~~  147 (149)
                      +++++++|.++++|.+.|+++|+++.+.+.++++-..|.....     .|||||++|+||+|+++
T Consensus        86 rTlve~arv~~qnh~f~Y~e~i~VEs~tq~v~~LaLrFGe~~~~~~~msRPFGValliAG~D~~g  150 (241)
T KOG0176|consen   86 RTLVERARVETQNHWFTYGEPISVESLTQAVSDLALRFGEGDDEEAIMSRPFGVALLIAGHDETG  150 (241)
T ss_pred             HHHHHHHHHHhhhceeecCCcccHHHHHHHHHHHHhHhCCCcchhhhhcCCcceEEEEeeccCCC
Confidence            9999999999999999999999999999999999887754322     48999999999999654

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

Probab=100.00  E-value=1e-41  Score=253.72  Aligned_cols=147  Identities=71%  Similarity=1.072  Sum_probs=144.1

Q ss_pred             CCCCCCCCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEE
Q 031996            1 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLA   80 (149)
Q Consensus         1 m~~~~~~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~   80 (149)
                      ||||+.++||+++|+||||||++|||||.||+++.|-|+||+|+||++|+++.|+.+.+|++++....+|+|+++|+|++
T Consensus         1 ~s~gs~agfDrhitIFspeGrLyQVEYafkAin~~gltsVavrgkDcavvvsqKkvpDKLld~~tvt~~f~itk~ig~v~   80 (246)
T KOG0182|consen    1 MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQAGLTSVAVRGKDCAVVVTQKKVPDKLLDSSTVTHLFRITKKIGCVI   80 (246)
T ss_pred             CCCCCcCCccceEEEECCCceEEeeehHHHHhhcCCCceEEEcCCceEEEEecccCcccccccccceeEEEeeccceEEE
Confidence            89999999999999999999999999999999998999999999999999999999999999988999999999999999


Q ss_pred             eccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996           81 TGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        81 sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      +|+.+|++..++++|.++.+++++||.+||++.||++++++.|.|||+..+||+||.+++.|+|++.
T Consensus        81 tG~~aDar~~v~rar~eAa~~~yk~Gyemp~DiL~k~~Ad~~QvytQ~a~mRplg~~~~~i~~D~E~  147 (246)
T KOG0182|consen   81 TGMIADARSQVQRARYEAAEFRYKYGYEMPCDILAKRMADKSQVYTQNAAMRPLGVAATLIGVDEER  147 (246)
T ss_pred             ecCCcchHHHHHHHHHHHHhhhhhcCCCCCHHHHHHHHhhHHHHHhhhhhhcccceeEEEEEecccc
Confidence            9999999999999999999999999999999999999999999999999999999999999999864

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

Probab=100.00  E-value=3.4e-40  Score=255.46  Aligned_cols=136  Identities=46%  Similarity=0.778  Sum_probs=129.5

Q ss_pred             CCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCcccc-ccccccceeeecCcEEEEEeccHHH
Q 031996            8 GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLL-DHTSVTHLFPITKYLGLLATGMTAD   86 (149)
Q Consensus         8 ~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~-~~~~~~KI~~I~~~i~~~~sG~~~D   86 (149)
                      +||+.+++|||||+++|+|||.+++++.|+|+|||+++||||||+|+|.++.++ ..++.+||++|+||++|++||+.+|
T Consensus         2 ~~~~~~~~fsp~g~l~q~e~a~~a~~~~gtT~vgik~~dgVVlaadkr~t~~~~~~~~~~~Ki~~I~d~i~~~~sG~~aD   81 (236)
T COG0638           2 GYDRAITIFSPEGRLFQVEYALEAVKRGGTTTVGIKGKDGVVLAADKRATSGLLIASSNVEKIFKIDDHIGMAIAGLAAD   81 (236)
T ss_pred             CCcCcceeECCCCchHHHHHHHHHHHcCCceEEEEEecCEEEEEEeccCCCCceecccccceEEEecCCEEEEeccCcHh
Confidence            699999999999999999999999998779999999999999999999996654 4566999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeC
Q 031996           87 ARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAI  145 (149)
Q Consensus        87 ~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~  145 (149)
                      ++.+++++|.+++.|++.++++|+|+.+++.+++++|.|+++  .|||+|++||||+|+
T Consensus        82 a~~lv~~~r~~a~~~~~~~~~~i~v~~la~~ls~~l~~~~~~--~rP~gv~~iiaG~d~  138 (236)
T COG0638          82 AQVLVRYARAEAQLYRLRYGEPISVEALAKLLSNILQEYTQS--GRPYGVSLLVAGVDD  138 (236)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhccC--cccceEEEEEEEEcC
Confidence            999999999999999999999999999999999999999885  899999999999998

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

Probab=100.00  E-value=3.3e-40  Score=243.03  Aligned_cols=139  Identities=37%  Similarity=0.553  Sum_probs=135.6

Q ss_pred             CCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHH
Q 031996            8 GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADA   87 (149)
Q Consensus         8 ~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~   87 (149)
                      +|..++|+|||+|++-|+|||+.|+.+ |.+.|||+..||||||++|+..+.|.+.....|+++|.+||+|.+||+.+|.
T Consensus         5 ~y~fslTtFSpsGKL~QieyAL~Av~~-G~~SvGi~A~nGvVlatekk~~s~L~~~~sv~KV~~i~~~IG~vYSGmgpD~   83 (233)
T KOG0181|consen    5 GYSFSLTTFSPSGKLVQIEYALTAVVN-GQTSVGIKAANGVVLATEKKDVSPLVDEESVRKVEKITPHIGCVYSGMGPDY   83 (233)
T ss_pred             ccceeeEEEcCCCceehHHHHHHHHhC-CCCceeeeecCceEEEeccCCCCccchhhhhhhHhhccCCcceEEecCCCce
Confidence            799999999999999999999999987 9999999999999999999999999998899999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996           88 RTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        88 ~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      +.+++..|+.++.|...|+++||+..|...++..+|+|||+++.|||||+++|||||+.+
T Consensus        84 RvlV~~~rkiAe~Yy~vY~e~~pt~qlv~~~asvmQEyTqsgGvrPFGvslliaG~~~~~  143 (233)
T KOG0181|consen   84 RVLVHKSRKIAEQYYRVYGEPIPTTQLVQEVASVMQEYTQSGGVRPFGVSLLIAGWDEGG  143 (233)
T ss_pred             eehhhHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEeecCCCc
Confidence            999999999999999999999999999999999999999999999999999999999864

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

Probab=100.00  E-value=3.6e-39  Score=242.64  Aligned_cols=138  Identities=37%  Similarity=0.585  Sum_probs=132.2

Q ss_pred             CCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHH
Q 031996            7 GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTAD   86 (149)
Q Consensus         7 ~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D   86 (149)
                      +.||.++|+|||+||++|||||++|+++ |++.||+|.++..||++-++..+.|..  ..+|||+||+|++++++|+++|
T Consensus         4 nqyd~d~t~wsPqGrl~QvEya~Eavkq-GsatVGLks~thaVLvAl~r~~seLss--~QkKi~~iD~h~g~siAGLt~D   80 (264)
T KOG0863|consen    4 NQYDNDVTTWSPQGRLHQVEYAMEAVKQ-GSATVGLKSRTHAVLVALKRAQSELSS--HQKKIFKIDDHIGISIAGLTAD   80 (264)
T ss_pred             ccccCceeEECCcceehHHHHHHHHHhc-ccceEeecccceEEEeeeccchhHHHH--hhheeEecccccceEEeccCcc
Confidence            5799999999999999999999999998 999999999999999999998877654  5679999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996           87 ARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        87 ~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      ++.+++++|.+|..++..|++++|+..|...+.+.+|..|++.+.|||||.++++|||+.+
T Consensus        81 arvl~~Ylr~ec~~~~~~~~r~~pv~rl~~~l~~k~q~~Tq~ygrRpYGVGllv~gYDe~G  141 (264)
T KOG0863|consen   81 ARVLSRYLRQECLNSRFIYGRPLPVLRLVEDLGDKAQENTQRYGRRPYGVGLLVAGYDESG  141 (264)
T ss_pred             hHHHHHHHHHHHhhhhhccCCcccHHHHHHHHHHHHhhhhhhhCCccccceEEEEeecCCC
Confidence            9999999999999999999999999999999999999999999999999999999999865

>cd03760 proteasome_beta_type_4 proteasome beta type-4 subunit

Probab=99.97  E-value=7.6e-30  Score=192.52  Aligned_cols=110  Identities=18%  Similarity=0.203  Sum_probs=102.8

Q ss_pred             cCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHH-HHHHHhCCCCCHH
Q 031996           35 AGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAA-EFRFKYGYEMPVD  112 (149)
Q Consensus        35 ~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~-~~~~~~~~~~~~~  112 (149)
                      +|+|+|||+++||||||+|++.+ +.++.+++.+|||+|++|++|+++|+.+|++.+++++|.+++ .|+++++++|+++
T Consensus         1 ~G~T~igi~~kdgVvlaad~r~~~~~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~   80 (197)
T cd03760           1 TGTSVIAIKYKDGVIIAADTLGSYGSLARFKNVERIFKVGDNTLLGASGDYADFQYLKRLLDQLVIDDECLDDGHSLSPK   80 (197)
T ss_pred             CCceEEEEEeCCcEEEEEcCcccccceeecCCCCcEEEecCcEEEEeCcchHHHHHHHHHHHHHHHHHHHHhCCCCCCHH
Confidence            48899999999999999999999 788888899999999999999999999999999999999987 5778899999999


Q ss_pred             HHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          113 VLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       113 ~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      .+++++++++  |+++++.|||+|++||||||++
T Consensus        81 ~la~~i~~~~--y~~~~~~rP~~v~~iiaG~D~~  112 (197)
T cd03760          81 EIHSYLTRVL--YNRRSKMNPLWNTLVVGGVDNE  112 (197)
T ss_pred             HHHHHHHHHH--HHHhhcCCCceEEEEEEEEcCC
Confidence            9999999986  5777789999999999999964

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.

>cd03758 proteasome_beta_type_2 proteasome beta type-2 subunit

Probab=99.97  E-value=1.7e-29  Score=190.21  Aligned_cols=108  Identities=17%  Similarity=0.270  Sum_probs=101.9

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      +|+|||+++||||||+|++.+ +.++.+++.+|||+|+++++|++||+.+|++.+++++|.+++.|+++++++++++.++
T Consensus         2 ~t~igi~~~dgVvlaad~r~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~i~~~~la   81 (193)
T cd03758           2 ETLIGIKGKDFVILAADTSAARSILVLKDDEDKIYKLSDHKLMACSGEAGDRLQFAEYIQKNIQLYKMRNGYELSPKAAA   81 (193)
T ss_pred             ceEEEEEeCCEEEEEEcCccccCcEEEecCcccEEEeCCCeEEEEccchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            699999999999999999997 6778888999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++++++|.|+++ + |||++++||+|||++
T Consensus        82 ~~l~~~~~~~~~~-~-rP~~~~~li~G~d~~  110 (193)
T cd03758          82 NFTRRELAESLRS-R-TPYQVNLLLAGYDKV  110 (193)
T ss_pred             HHHHHHHHHHhhc-C-CCeEEEEEEEEEcCC
Confidence            9999999988764 3 899999999999964

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=99.97  E-value=2.4e-29  Score=189.62  Aligned_cols=108  Identities=19%  Similarity=0.282  Sum_probs=100.0

Q ss_pred             CceEEEEEcCCeEEEEEeccCCccccc-cccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Q 031996           36 GVTSIGVRGKDSVCVVTQKKVPDKLLD-HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVL  114 (149)
Q Consensus        36 G~t~igik~kdgVvlaad~~~~~~l~~-~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~l  114 (149)
                      |+|+|||+++||||||+|++.++.++. .++.+|||+|++|++|++||+.+|++.+++++|.+++.|+++++++|+++.+
T Consensus         3 G~t~igik~~dgVvlaad~~~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~l   82 (195)
T cd03759           3 GGAVVAMAGKDCVAIASDLRLGVQQQTVSTDFQKVFRIGDRLYIGLAGLATDVQTLAQKLRFRVNLYRLREEREIKPKTF   82 (195)
T ss_pred             CceEEEEEcCCEEEEEEccccccCCEeEecCCCeEEEeCCCEEEEccchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Confidence            899999999999999999999877765 4578999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996          115 AKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus       115 a~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      +++++++++  ++  +.|||+|++||||||+++
T Consensus        83 a~~l~~~ly--~~--r~~P~~v~~ii~G~D~~~  111 (195)
T cd03759          83 SSLISSLLY--EK--RFGPYFVEPVVAGLDPDG  111 (195)
T ss_pred             HHHHHHHHH--Hh--cCCCceEEEEEEEEcCCC
Confidence            999999985  44  468999999999999654

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.

>TIGR03690 20S_bact_beta proteasome, beta subunit, bacterial type

Probab=99.96  E-value=3.6e-29  Score=191.85  Aligned_cols=110  Identities=18%  Similarity=0.230  Sum_probs=104.3

Q ss_pred             CceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Q 031996           36 GVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVL  114 (149)
Q Consensus        36 G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~l  114 (149)
                      |+|+|||+++||||||+|++.+ +.++.+++.+||++|++|++|++||+.+|++.+++++|.+++.|+++++++|+++.+
T Consensus         2 G~T~igi~~kdgVvlaad~r~~~g~~~~~~~~~KI~~i~~~i~~~~sG~~aD~~~l~~~~r~~~~~~~~~~~~~i~~~~l   81 (219)
T TIGR03690         2 GTTIVALTYPGGVLMAGDRRATQGNMIASRDVEKVYPTDEYSAVGIAGTAGLAIELVRLFQVELEHYEKIEGVPLTLDGK   81 (219)
T ss_pred             CcEEEEEEECCEEEEEECCccccCcEEEcCCcceEEEcCCcEEEEecccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHH
Confidence            8899999999999999999999 588888899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          115 AKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       115 a~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++|++++|.++. ...|||+|++||||||++
T Consensus        82 a~~ls~~~~~~~~-~~~rp~~v~~iiaG~D~~  112 (219)
T TIGR03690        82 ANRLAAMVRGNLP-AAMQGLAVVPLLAGYDLD  112 (219)
T ss_pred             HHHHHHHHHhhhh-hccCCceEEEEEEEECCC
Confidence            9999999998774 468999999999999953

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.

>TIGR03691 20S_bact_alpha proteasome, alpha subunit, bacterial type

Probab=99.96  E-value=8e-29  Score=191.06  Aligned_cols=112  Identities=17%  Similarity=0.184  Sum_probs=103.3

Q ss_pred             hhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHH
Q 031996           25 VEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFK  104 (149)
Q Consensus        25 ~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~  104 (149)
                      -|||++|+++ |+|+|||+++||||||+|++.       ++.+|||+|+||++|+++|+.+|++.++++++.+++.|+++
T Consensus        17 ~EYA~kav~~-g~T~VGIk~kdgVVLaaek~~-------~~~~KI~~I~d~ig~~~sG~~~D~~~lv~~~r~~a~~~~~~   88 (228)
T TIGR03691        17 AELARKGIAR-GRSVVVLTYADGILFVAENPS-------RSLHKISELYDRIGFAAVGKYNEFENLRRAGIRYADMRGYS   88 (228)
T ss_pred             HHHHHHHHHc-CCcEEEEEeCCeEEEEEecCC-------CCcCcEEEecCCEEEEEcCCHHHHHHHHHHHHHHHHHHhhh
Confidence            5999999987 999999999999999999972       35789999999999999999999999999999999999999


Q ss_pred             hC-CCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeC
Q 031996          105 YG-YEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAI  145 (149)
Q Consensus       105 ~~-~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~  145 (149)
                      ++ .+++++.+|+++++.++.++ +++.|||+|++||+|||+
T Consensus        89 ~~~~~~~v~~la~~~tq~~~~~~-~~~~RP~gvs~Li~G~d~  129 (228)
T TIGR03691        89 YDRRDVTGRGLANAYAQTLGTIF-TEQQKPYEVEICVAEVGE  129 (228)
T ss_pred             cCCCCccHHHHHHHHHhhccccc-ccccCcceEEEEEEEEcC
Confidence            98 78999999998888887666 567899999999999985

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=99.96  E-value=1.6e-28  Score=184.23  Aligned_cols=106  Identities=15%  Similarity=0.186  Sum_probs=99.6

Q ss_pred             ceEEEEEcCCeEEEEEeccCCc-cccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVPD-KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~~-~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      +|+|||+++||||||+|++.++ .++.+++.+|||+|++|++|++||+.+|++.+++++|.+++.|+++++++|+++.++
T Consensus         1 tT~igi~~kdgVvla~d~r~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i~~~~la   80 (188)
T cd03761           1 TTTLAFIFQGGVIVAVDSRATAGSYIASQTVKKVIEINPYLLGTMAGGAADCQYWERVLGRECRLYELRNKERISVAAAS   80 (188)
T ss_pred             CcEEEEEECCEEEEEEcCCccCCcEEEcCCcceEEEccCcEEEEeCccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            5899999999999999999995 677778999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++++++|.+++    .||+|++||||||++
T Consensus        81 ~~ls~~l~~~~~----~~~~v~~li~G~D~~  107 (188)
T cd03761          81 KLLSNMLYQYKG----MGLSMGTMICGWDKT  107 (188)
T ss_pred             HHHHHHHHhcCC----CCeEEEEEEEEEeCC
Confidence            999999997753    489999999999964

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=99.96  E-value=2.3e-28  Score=182.50  Aligned_cols=107  Identities=23%  Similarity=0.424  Sum_probs=101.8

Q ss_pred             CceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Q 031996           36 GVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVL  114 (149)
Q Consensus        36 G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~l  114 (149)
                      |+|+|||+++||||||+|++.+ +.++.+++.+|||+|+++++++++|..+|++.+.++++.+++.|++.++++++++.+
T Consensus         1 G~t~igi~~~dgVvla~d~~~~~~~~i~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~   80 (185)
T TIGR03634         1 GTTTVGIKCKDGVVLAADKRASMGNFVASKNAKKVFQIDDYIAMTIAGSVGDAQSLVRILKAEAKLYELRRGRPMSVKAL   80 (185)
T ss_pred             CCcEEEEEeCCEEEEEEcCcccCCCEEecCCcccEEEcCCCEEEEcCchHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHH
Confidence            7899999999999999999998 788888899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          115 AKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       115 a~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      ++++++++|.+    +.|||+|++||||||++
T Consensus        81 a~~l~~~~~~~----~~rP~~v~~ivaG~d~~  108 (185)
T TIGR03634        81 ATLLSNILNSN----RFFPFIVQLLVGGVDEE  108 (185)
T ss_pred             HHHHHHHHHhc----CCCCeEEEEEEEEEeCC
Confidence            99999999865    68999999999999965

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.

>cd03757 proteasome_beta_type_1 proteasome beta type-1 subunit

Probab=99.96  E-value=1.9e-28  Score=186.93  Aligned_cols=111  Identities=16%  Similarity=0.240  Sum_probs=101.2

Q ss_pred             hhccCceEEEEEcCCeEEEEEeccCCccc-cccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCC
Q 031996           32 VKAAGVTSIGVRGKDSVCVVTQKKVPDKL-LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMP  110 (149)
Q Consensus        32 v~~~G~t~igik~kdgVvlaad~~~~~~l-~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~  110 (149)
                      +++ |+|+|||+++||||||+|++.+..+ +.+++.+||++|++|++|++||+.+|++.+.+++|.++++|+++++++|+
T Consensus         5 ~~~-G~Tvigik~~dgVvlaaD~r~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~~r~~~~~~~~~~g~~i~   83 (212)
T cd03757           5 TDN-GGTVLAIAGNDFAVIAGDTRLSEGYSILSRDSPKIFKLTDKCVLGSSGFQADILALTKRLKARIKMYKYSHNKEMS   83 (212)
T ss_pred             cCC-CccEEEEEcCCEEEEEECCccccCCEeEeCCCCeEEEcCCCEEEEccchHHHHHHHHHHHHHHHHHHhHHhCCCCC
Confidence            444 9999999999999999999999655 44678999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996          111 VDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus       111 ~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      ++.++++++++++.  +  +.|||+|++||||||+++
T Consensus        84 ~~~la~~ls~~ly~--~--R~~P~~~~~iiaG~D~~~  116 (212)
T cd03757          84 TEAIAQLLSTILYS--R--RFFPYYVFNILAGIDEEG  116 (212)
T ss_pred             HHHHHHHHHHHHHh--h--cCCCeEEEEEEEEEcCCC
Confidence            99999999999963  3  357999999999999654

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=99.96  E-value=4.2e-28  Score=180.88  Aligned_cols=115  Identities=35%  Similarity=0.541  Sum_probs=106.8

Q ss_pred             hhccCceEEEEEcCCeEEEEEeccCC--ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCC
Q 031996           32 VKAAGVTSIGVRGKDSVCVVTQKKVP--DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEM  109 (149)
Q Consensus        32 v~~~G~t~igik~kdgVvlaad~~~~--~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~  109 (149)
                      |++ |+|+|||+++||||||+|++.+  +.+..++..+||++|++|+++++||+.+|++.+.++++.++..|++.+++++
T Consensus         1 v~~-G~t~vgi~~~dgvvla~d~~~~~g~~~~~~~~~~ki~~i~~~i~~~~sG~~~D~~~l~~~l~~~~~~~~~~~~~~~   79 (190)
T PF00227_consen    1 VNN-GTTVVGIKGKDGVVLAADKRISYGSKLRSPNTVDKIFKINDNIIIGFSGLTADFQYLIRRLREEAQEYRFSYGRPI   79 (190)
T ss_dssp             HHT-SBEEEEEEESSEEEEEEEEEEEETTEEEESSTSSSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGT
T ss_pred             CCC-CeEEEEEEECCEEEEEEccccccccccccccccceeeeccCcceeeccccccchHHHHhhhcccchhhhhccCccc
Confidence            455 9999999999999999999998  4544555579999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996          110 PVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus       110 ~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      +++.+++.++.+++.++++++.|||++++|++|||+++
T Consensus        80 ~~~~l~~~~~~~~~~~~~~~~~~p~~~~~li~G~d~~~  117 (190)
T PF00227_consen   80 SPEYLAKAIASLIQNYTYRSGRRPYGVSLLIAGYDEDG  117 (190)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTTTSTTSEEEEEEEEETTT
T ss_pred             cchhhhhhhHHHHhhhcccccccCccccceeeeecccc
Confidence            99999999999999999998999999999999999765

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 ....

>cd03762 proteasome_beta_type_6 proteasome beta type-6 subunit

Probab=99.95  E-value=2.7e-27  Score=177.23  Aligned_cols=105  Identities=15%  Similarity=0.181  Sum_probs=98.3

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      +|+|||+++||||||+|++.+ +.++.+++.+||++|++|++|++||+.+|++.+.++++.+++.|+++++++++++.++
T Consensus         1 ~t~igi~~~dgVvla~D~r~~~g~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~l~~~~~~~~~~~~~~~~~~~~a   80 (188)
T cd03762           1 TTIIAVEYDGGVVLGADSRTSTGSYVANRVTDKLTQLHDRIYCCRSGSAADTQAIADYVRYYLDMHSIELGEPPLVKTAA   80 (188)
T ss_pred             CeEEEEEECCeEEEEEcccccCCceEEcCCcccEEEccCCEEEEecccHHHHHHHHHHHHHHHHHhHHhhCCCCCHHHHH
Confidence            589999999999999999998 4677778899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++++++|.++     |||+|++||||||++
T Consensus        81 ~~l~~~~~~~~-----~~~~~~~ii~G~d~~  106 (188)
T cd03762          81 SLFKNLCYNYK-----EMLSAGIIVAGWDEQ  106 (188)
T ss_pred             HHHHHHHHhcc-----ccceeeEEEEEEcCC
Confidence            99999998653     689999999999963

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.

>PTZ00488 Proteasome subunit beta type-5; Provisional

Probab=99.95  E-value=2.7e-27  Score=184.46  Aligned_cols=110  Identities=15%  Similarity=0.223  Sum_probs=99.9

Q ss_pred             HhhccCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCC
Q 031996           31 AVKAAGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEM  109 (149)
Q Consensus        31 av~~~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~  109 (149)
                      .+.+ |+|+|||+++||||||+|++.+ +.++.+++.+||++|++|+++++||+.+|++.+++++|.+++.|+++++++|
T Consensus        35 ~~~~-G~T~IgIk~kdgVvlAaD~r~~~g~li~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~lr~~~~~y~~~~g~~i  113 (247)
T PTZ00488         35 EFAH-GTTTLAFKYGGGIIIAVDSKATAGPYIASQSVKKVIEINPTLLGTMAGGAADCSFWERELAMQCRLYELRNGELI  113 (247)
T ss_pred             ccCC-CceEEEEEeCCEEEEEEecCcccCCEEEcCCcCceEEcCCCEEEEeCcCHHHHHHHHHHHHHHHHHHHHHHCCCC
Confidence            3455 9999999999999999999998 6888888999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHhhcCCccccc--eEEEEEEEeCCC
Q 031996          110 PVDVLAKWIADKSQVYTQHAYMRPLG--VGLFLIEIAIPS  147 (149)
Q Consensus       110 ~~~~la~~l~~~~~~~t~~~~~rP~~--v~~liaG~D~~~  147 (149)
                      +++.+|++|++++|.+      |||+  +++||||||+++
T Consensus       114 sv~~la~~ls~~l~~~------R~~~~~v~~iiaG~D~~g  147 (247)
T PTZ00488        114 SVAAASKILANIVWNY------KGMGLSMGTMICGWDKKG  147 (247)
T ss_pred             CHHHHHHHHHHHHHhc------CCCCeeEEEEEEEEeCCC
Confidence            9999999999999854      4555  558999999653

>cd03764 proteasome_beta_archeal Archeal proteasome, beta subunit

Probab=99.95  E-value=5e-27  Score=175.76  Aligned_cols=106  Identities=22%  Similarity=0.365  Sum_probs=100.2

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      +|+|||+++||||||+|++.+ +.++.+++.+||++|++|++++++|+.+|++.+.+++|.+++.|++.++++++++.++
T Consensus         1 tt~iai~~~dgvvia~d~r~~~g~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~   80 (188)
T cd03764           1 TTTVGIVCKDGVVLAADKRASMGNFIASKNVKKIFQIDDKIAMTIAGSVGDAQSLVRILKAEARLYELRRGRPMSIKALA   80 (188)
T ss_pred             CcEEEEEeCCEEEEEEccccccCCEEecCCcccEEEccCCEEEEcCccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            589999999999999999998 5777788999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++++++|.+    +.|||+|++||||||++
T Consensus        81 ~~i~~~~~~~----~~~P~~~~~lvaG~d~~  107 (188)
T cd03764          81 TLLSNILNSS----KYFPYIVQLLIGGVDEE  107 (188)
T ss_pred             HHHHHHHHhc----CCCCcEEEEEEEEEeCC
Confidence            9999999864    57999999999999963

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.

>cd03765 proteasome_beta_bacterial Bacterial proteasome, beta subunit

Probab=99.95  E-value=7.5e-27  Score=180.74  Aligned_cols=109  Identities=8%  Similarity=0.095  Sum_probs=98.9

Q ss_pred             eEEEEEcCCeEEEEEeccCCccccccccccceeeec----CcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCC-CCCHH
Q 031996           38 TSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPIT----KYLGLLATGMTADARTLVQQARYEAAEFRFKYGY-EMPVD  112 (149)
Q Consensus        38 t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~----~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~-~~~~~  112 (149)
                      =+|||+++||||||+|++.++.++..++.+||++|+    +|++|+.||+.+|++.+++++|.++++|++++|+ +||++
T Consensus         2 ~~vGIk~kdGVVLaadkr~~~~l~~~~~~~KI~~I~~~~d~~I~~~~sG~~aD~~~l~~~~r~~~~~~~~~~g~~~~~v~   81 (236)
T cd03765           2 YCLGIKLDAGLVFASDSRTNAGVDNISTYRKMFVFSVPGERVIVLLTAGNLATTQAVISLLQRDLEDPEETNLLNAPTMF   81 (236)
T ss_pred             eEEEEEeCCeEEEEEccCccCCCccccccceEEEecCCCCCEEEEEcCCcHHHHHHHHHHHHHHHHhhHHhhCCCCCCHH
Confidence            489999999999999999988877666889999998    9999999999999999999999999999999999 89999


Q ss_pred             HHHHHHHHHHHH-HhhcCC-----ccccceEEEEEEEeCC
Q 031996          113 VLAKWIADKSQV-YTQHAY-----MRPLGVGLFLIEIAIP  146 (149)
Q Consensus       113 ~la~~l~~~~~~-~t~~~~-----~rP~~v~~liaG~D~~  146 (149)
                      .+|++++++++. +++..+     .|||+|++||+|||++
T Consensus        82 ~la~~i~~~l~~~~~q~~~~~~~~~rp~gvslIigG~D~~  121 (236)
T cd03765          82 DAARYVGETLREVQEQDREALKKAGIDFSASFILGGQIKG  121 (236)
T ss_pred             HHHHHHHHHHHHHHhhcccccccCCcceEEEEEEEeEECC
Confidence            999999998664 455543     4899999999999953

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.

>cd01906 proteasome_protease_HslV proteasome_protease_HslV

Probab=99.95  E-value=1.5e-26  Score=171.38  Aligned_cols=108  Identities=39%  Similarity=0.655  Sum_probs=101.2

Q ss_pred             ceEEEEEcCCeEEEEEeccCCccccc-cccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVPDKLLD-HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~~~l~~-~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      +|+|||+++||||||+|++.++.+.. .++.+|||+|+++++++++|+.+|++.+.+++++++..|+++++++++++.++
T Consensus         1 tt~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~   80 (182)
T cd01906           1 TTIVGIKGKDGVVLAADKRVTSGLLVASSTVEKIFKIDDHIGCAFAGLAADAQTLVERLRKEAQLYRLRYGEPIPVEALA   80 (182)
T ss_pred             CcEEEEEeCCEEEEEEecccCCcCeecCCCcceEEEECCCEEEEEeeCHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            58999999999999999999855544 77899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++++++|++++.  .|||++++|++|||++
T Consensus        81 ~~l~~~~~~~~~~--~~p~~~~~lv~G~d~~  109 (182)
T cd01906          81 KLLANLLYEYTQS--LRPLGVSLLVAGVDEE  109 (182)
T ss_pred             HHHHHHHHHhCCC--ccChheEEEEEEEeCC
Confidence            9999999998874  8999999999999963

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

>cd01912 proteasome_beta proteasome beta subunit

Probab=99.94  E-value=1.5e-26  Score=172.96  Aligned_cols=106  Identities=21%  Similarity=0.331  Sum_probs=99.0

Q ss_pred             ceEEEEEcCCeEEEEEeccCCccccc-cccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVPDKLLD-HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~~~l~~-~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      +|+|||+++||||||+|++.+..+.. .++.+|||+|++++++++||+.+|++.+.++++.++..|++.++++++++.++
T Consensus         1 tt~i~i~~~dgVvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~   80 (189)
T cd01912           1 TTIVGIKGKDGVVLAADTRASAGSLVASRNFDKIFKISDNILLGTAGSAADTQALTRLLKRNLRLYELRNGRELSVKAAA   80 (189)
T ss_pred             CcEEEEEeCCEEEEEEcCCcccCcEEEcCCcCcEEEccCCEEEEccccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            58999999999999999999965554 78899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++++++|.+++    |||++++||||||++
T Consensus        81 ~~l~~~~~~~~~----~P~~~~~iv~G~d~~  107 (189)
T cd01912          81 NLLSNILYSYRG----FPYYVSLIVGGVDKG  107 (189)
T ss_pred             HHHHHHHHhcCC----CCeEEEEEEEEEcCC
Confidence            999999986653    899999999999974

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.

>cd03763 proteasome_beta_type_7 proteasome beta type-7 subunit

Probab=99.94  E-value=1.4e-26  Score=173.64  Aligned_cols=105  Identities=16%  Similarity=0.201  Sum_probs=97.9

Q ss_pred             ceEEEEEcCCeEEEEEeccCCc-cccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVPD-KLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~~-~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      +|+|||+++||||||+|++.++ .++..++.+|||+|+++++|+++|+.+|++.+.+++|.+++.|+++++++++++.++
T Consensus         1 tt~igi~~~dgvvlaad~r~~~g~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a   80 (189)
T cd03763           1 TTIVGVVFKDGVVLGADTRATEGPIVADKNCEKIHYIAPNIYCCGAGTAADTEAVTNMISSNLELHRLNTGRKPRVVTAL   80 (189)
T ss_pred             CeEEEEEECCeEEEEEcCCcccCceEEcCCccceEEecCCEEEEcCccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            5899999999999999999985 566677899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++++.+|.|.     .||+|++||||||++
T Consensus        81 ~~l~~~l~~~~-----~p~~v~~ivaG~d~~  106 (189)
T cd03763          81 TMLKQHLFRYQ-----GHIGAALVLGGVDYT  106 (189)
T ss_pred             HHHHHHHHHcC-----CccceeEEEEeEcCC
Confidence            99999998653     399999999999965

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.

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

Probab=99.90  E-value=2.6e-23  Score=152.84  Aligned_cols=109  Identities=13%  Similarity=0.238  Sum_probs=102.3

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      .+++||++.|+|++|+|+... +-++.+++.+|+++|++++.|+++|..+|+.++.+++.+++++|+.++|.+++|..+|
T Consensus         2 e~llGIkg~dfvilAsDt~~~~si~~~k~~~dK~~~ls~~~lm~~~Ge~GDt~qF~eyi~~Ni~LYkirnGyeLSp~~aa   81 (200)
T KOG0177|consen    2 ETLLGIKGPDFVILASDTSAARSILVLKDDHDKIHRLSDHILMATVGEAGDTVQFTEYIQKNIQLYKIRNGYELSPSAAA   81 (200)
T ss_pred             ceEEEeecCCEEEEeecchhhcceEEecccccceEEeccceeeeeecCCCceehHHHHHHhhhhHHhhhcCCcCCHHHHH
Confidence            489999999999999999987 6666788999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      +++++.++++.+  ..+||.|++|+||+|++.
T Consensus        82 hFtR~~La~~LR--sr~~yqV~~LvaGYd~~~  111 (200)
T KOG0177|consen   82 HFTRRELAESLR--SRTPYQVNILVAGYDPEE  111 (200)
T ss_pred             HHHHHHHHHHHh--cCCCceEEEEEeccCCCC
Confidence            999999999875  578999999999999764

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

Probab=99.89  E-value=9.5e-23  Score=152.03  Aligned_cols=112  Identities=16%  Similarity=0.227  Sum_probs=103.6

Q ss_pred             hccCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCH
Q 031996           33 KAAGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPV  111 (149)
Q Consensus        33 ~~~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~  111 (149)
                      ..+|+|++||.+.|+.|+|+|+|.+ +.-+..++.+|||+++|+++++.+|.++|+..+.+.++...+.|++.++..|++
T Consensus        26 ~~NGGT~vaIaG~dFavvA~DTR~s~gy~I~sR~~~Ki~~l~D~~vl~~sGF~aD~l~L~k~i~~r~~~Y~~~h~k~ms~  105 (235)
T KOG0179|consen   26 EDNGGTTVAIAGEDFAVVAGDTRMSSGYNINSRDQSKIFKLGDNIVLGSSGFYADTLALVKVIKSRIKQYEHDHNKKMSI  105 (235)
T ss_pred             ccCCceEEEEcCCceEEEecccccccceeeeccccchheeccCceEEecccchhhHHHHHHHHHHHHHHHhhcccccccH
Confidence            3448899999999999999999998 455667899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCCC
Q 031996          112 DVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPSE  148 (149)
Q Consensus       112 ~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~~  148 (149)
                      ..+|+.|+..+|    ..++.||++..+|+|+|++++
T Consensus       106 ~s~A~lls~~LY----~kRFFPYYv~~ilaGiDeeGK  138 (235)
T KOG0179|consen  106 HSAAQLLSTILY----SKRFFPYYVFNILAGIDEEGK  138 (235)
T ss_pred             HHHHHHHHHHHh----hcccccceeeeeeecccccCc
Confidence            999999999996    347899999999999999774

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

Probab=99.87  E-value=4.7e-22  Score=146.88  Aligned_cols=108  Identities=18%  Similarity=0.235  Sum_probs=101.5

Q ss_pred             cCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHH
Q 031996           35 AGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDV  113 (149)
Q Consensus        35 ~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~  113 (149)
                      +|||++|+++++||||++|.|.+ +.++.++-.+|+.+|.|+|+||.||.++|.|.+++.++..+..|..+++.++.+..
T Consensus        18 tGTTImAv~y~gGVvlGaDSRTs~GayvanRvtDKlT~itD~i~cCRSGSAADtQaiaD~~~Y~L~~~~~q~~~~p~v~~   97 (224)
T KOG0174|consen   18 TGTTIMAVEYDGGVVLGADSRTSTGAYVANRVTDKLTPITDNIYCCRSGSAADTQAIADIVRYHLELYTIQENKPPLVHT   97 (224)
T ss_pred             cCceEEEEEEcCcEEEeccCCccchHHHHhhhcccceeccccEEEecCCchhhHHHHHHHHHHHHHHhhhhcCCCchHHH
Confidence            69999999999999999999998 78888899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996          114 LAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus       114 la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      .|+.++++.|+|..     -+...+|+||||++.
T Consensus        98 aA~l~r~~~Y~~re-----~L~AgliVAGwD~~~  126 (224)
T KOG0174|consen   98 AASLFREICYNYRE-----MLSAGLIVAGWDEKE  126 (224)
T ss_pred             HHHHHHHHHHhCHH-----hhhcceEEeeccccc
Confidence            99999999987643     488999999999864

>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=99.86  E-value=1.4e-20  Score=135.09  Aligned_cols=106  Identities=32%  Similarity=0.444  Sum_probs=99.4

Q ss_pred             ceEEEEEcCCeEEEEEeccCCccccc-cccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVPDKLLD-HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~~~l~~-~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      +|+||++++||||||+|++.+..+.. .....||+.++++++++++|..+|++.+.++++.++..|+++++.++++..++
T Consensus         1 ~t~i~i~~~~gvila~d~~~~~~~~~~~~~~~ki~~~~~~~~~~~sG~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (164)
T cd01901           1 STSVAIKGKGGVVLAADKRLSSGLPVAGSPVIKIGKNEDGIAWGLAGLAADAQTLVRRLREALQLYRLRYGEPISVVALA   80 (164)
T ss_pred             CcEEEEEeCCEEEEEEecccCccCeecCCCcceEEEecCCeEEEEecChHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            48999999999999999999855544 67889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAI  145 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~  145 (149)
                      +.+++.++.+++   .||+++++||+|+|+
T Consensus        81 ~~~~~~~~~~~~---~~p~~~~~iiag~~~  107 (164)
T cd01901          81 KELAKLLQVYTQ---GRPFGVNLIVAGVDE  107 (164)
T ss_pred             HHHHHHHHHhcC---CCCcceEEEEEEEcC
Confidence            999999998876   799999999999995

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=99.86  E-value=1.9e-21  Score=147.15  Aligned_cols=131  Identities=18%  Similarity=0.233  Sum_probs=112.3

Q ss_pred             cceeCCCCcchhhhhH--------HHHhhccCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEecc
Q 031996           13 ITIFSPEGRLFQVEYA--------FKAVKAAGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGM   83 (149)
Q Consensus        13 ~t~fsp~G~~~Q~eya--------~~av~~~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~   83 (149)
                      .++|.|.|..  ++-|        +.+.- +||++||+|++||||||+|+..+ +++...++.+||++++||+++++||.
T Consensus        13 ~~~f~~~~~~--m~~a~~~~~qrt~~p~v-TGTSVla~ky~~GVviaaD~lgSYGslaR~~nVeRi~kVgdntllG~sGd   89 (256)
T KOG0185|consen   13 PGTFYPSGSL--MENAGDYPIQRTLNPIV-TGTSVLALKYKDGVVIAADTLGSYGSLARYKNVERIFKVGDNTLLGASGD   89 (256)
T ss_pred             CCcCcCccch--hhhccCCCcccccCcee-ccceEEEEEecCceEEEecccccchhhhhhcCceeeEEecCceEEecCcc
Confidence            5677787544  3333        23333 59999999999999999999999 88888899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHH-HHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCCC
Q 031996           84 TADARTLVQQARYEAAEFR-FKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPSE  148 (149)
Q Consensus        84 ~~D~~~l~~~~r~~~~~~~-~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~~  148 (149)
                      .+|.|.|.+.+.....+.. +..|..+.|+.++++|...+|  .+++.+.|++.+++|+|+|+++|
T Consensus        90 isD~Q~i~r~L~~l~iedn~~~Dg~~l~Pk~ih~yltrvlY--~rRsKmnPlwntlvVgGv~~~g~  153 (256)
T KOG0185|consen   90 ISDFQYIQRVLEQLVIEDNRLDDGQSLGPKAIHSYLTRVLY--ARRSKMNPLWNTLVVGGVDNTGE  153 (256)
T ss_pred             HHHHHHHHHHHHHHHhcccccccccccChHHHHHHHHHHHH--HhhhccCchhhheeEeeecCCCC
Confidence            9999999999988777744 556799999999999999996  56778999999999999998765

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

Probab=99.85  E-value=5.8e-21  Score=138.83  Aligned_cols=109  Identities=16%  Similarity=0.245  Sum_probs=101.1

Q ss_pred             CceEEEEEcCCeEEEEEeccCCcccc-ccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Q 031996           36 GVTSIGVRGKDSVCVVTQKKVPDKLL-DHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVL  114 (149)
Q Consensus        36 G~t~igik~kdgVvlaad~~~~~~l~-~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~l  114 (149)
                      |++++|+++||+|.||+|.|.....+ ..++++|||+|.|+++++.+|+..|.+++.++++...++|+++.++.|.|+.+
T Consensus         8 Gg~vvAM~gk~cvaIa~D~RlG~q~~tistdf~ki~~igdr~y~GL~glatDvqtl~~~~~fr~nLy~lre~R~i~P~~~   87 (204)
T KOG0180|consen    8 GGSVVAMAGKNCVAIASDLRLGVQSQTISTDFQKIFKIGDRLYLGLTGLATDVQTLLERLRFRKNLYELREEREIKPETF   87 (204)
T ss_pred             CceEEEEeCCceEEEEeccccceeeeeeeccchhheecCCeeEEeccccchhHHHHHHHHHHHHhHHHhhhhcccCcHHH
Confidence            88999999999999999999984443 46789999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhcCCccccceEEEEEEEeCCCC
Q 031996          115 AKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPSE  148 (149)
Q Consensus       115 a~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~~  148 (149)
                      ++.++.++|+    .++.||-+.++|||+|++++
T Consensus        88 s~mvS~~lYe----kRfgpYf~~PvVAGl~~~~k  117 (204)
T KOG0180|consen   88 SSMVSSLLYE----KRFGPYFTEPVVAGLDDDNK  117 (204)
T ss_pred             HHHHHHHHHH----hhcCCcccceeEeccCCCCC
Confidence            9999999974    27889999999999998765

>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=99.82  E-value=1.6e-19  Score=133.51  Aligned_cols=98  Identities=14%  Similarity=0.051  Sum_probs=81.8

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecC-cEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITK-YLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVL  114 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~-~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~l  114 (149)
                      +|+|||+++||||||+|+|.+ +.++.+++.+||++|++ |++|++||..+|+++|.++++.++++|+.+.++     .+
T Consensus         1 tTivgi~~~dgVvlaaD~r~t~G~~v~~~~~~Ki~~i~d~~i~~~~aG~~aD~~~l~~~~~~~~~~y~~~~~~-----~a   75 (171)
T cd01913           1 TTILAVRKNGKVVIAGDGQVTLGNTVMKGNARKVRRLYNGKVIAGFAGSTADAFTLFERFEAKLEQYPGNLLR-----AA   75 (171)
T ss_pred             CeEEEEEECCEEEEEECCceEeccEEEcCCcceEEEeCCCCEEEEecccHHHHHHHHHHHHHHHHHhhchHHH-----HH
Confidence            699999999999999999998 77888899999999999 999999999999999999999999999998774     44


Q ss_pred             HHHHHHHHHHHhhcCCccccc-eEEEEEEEe
Q 031996          115 AKWIADKSQVYTQHAYMRPLG-VGLFLIEIA  144 (149)
Q Consensus       115 a~~l~~~~~~~t~~~~~rP~~-v~~liaG~D  144 (149)
                      ++.+..++.     .+.+|+. +.+|+++||
T Consensus        76 a~l~~~l~~-----~~~~~~l~a~~iv~~~~  101 (171)
T cd01913          76 VELAKDWRT-----DRYLRRLEAMLIVADKE  101 (171)
T ss_pred             HHHHHHHHh-----ccCcCceEEEEEEeCCC
Confidence            554443321     1445565 777887665

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=99.81  E-value=3.6e-19  Score=131.97  Aligned_cols=99  Identities=19%  Similarity=0.197  Sum_probs=82.1

Q ss_pred             CceEEEEEcCCeEEEEEeccCC-ccccccccccceeee-cCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHH
Q 031996           36 GVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPI-TKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDV  113 (149)
Q Consensus        36 G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I-~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~  113 (149)
                      |+|++||+++||||||+|+|.+ +.++.+++.+||++| +++++|++||..+|++.|.++++.++++|+.  +.   ++.
T Consensus         1 gtTivgi~~~dgVvlaaD~r~s~g~~v~~~~~~KI~~i~~d~i~~~~aG~~aD~q~l~~~l~~~~~~y~~--~~---~~~   75 (172)
T PRK05456          1 GTTILAVRRNGKVAIAGDGQVTLGNTVMKGNARKVRRLYNGKVLAGFAGSTADAFTLFERFEAKLEEHQG--NL---LRA   75 (172)
T ss_pred             CcEEEEEEECCEEEEEECCceEeCcEEEcCCCceEEEeCCCCEEEEEeccHHHHHHHHHHHHHHHHHccC--cc---HHH
Confidence            6899999999999999999998 778888899999999 9999999999999999999999999999982  22   466


Q ss_pred             HHHHHHHHHHHHhhcCCccccceEEEEEEE
Q 031996          114 LAKWIADKSQVYTQHAYMRPLGVGLFLIEI  143 (149)
Q Consensus       114 la~~l~~~~~~~t~~~~~rP~~v~~liaG~  143 (149)
                      +++....+.    .....+|+.+++|++++
T Consensus        76 ~a~l~~~l~----~~~~~~~l~~~~lv~d~  101 (172)
T PRK05456         76 AVELAKDWR----TDRYLRRLEAMLIVADK  101 (172)
T ss_pred             HHHHHHHHH----hccCCCccEEEEEEEcC
Confidence            665543332    12234688899999644

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

Probab=99.80  E-value=2.5e-19  Score=137.26  Aligned_cols=109  Identities=17%  Similarity=0.220  Sum_probs=101.5

Q ss_pred             cCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHH
Q 031996           35 AGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDV  113 (149)
Q Consensus        35 ~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~  113 (149)
                      +|||++|+|++.|||+|+|.|++ +.++.....+||..|+++++-+.+|-++|++.+-+.+.++|.+|++++++.|+|..
T Consensus        70 hGTTTLAF~f~~GvivAvDSRAs~G~YIasqtv~KVIeIn~ylLGTmAGgAADCqfWer~L~kecRL~eLRnkeriSVsa  149 (285)
T KOG0175|consen   70 HGTTTLAFKFKGGVIVAVDSRASAGSYIASQTVKKVIEINPYLLGTMAGGAADCQFWERVLAKECRLHELRNKERISVSA  149 (285)
T ss_pred             CCceEEEEEecCcEEEEEeccccccceeechhhceeeeechhhhhcccCcchhhHHHHHHHHHHHHHHHHhcCcceehHH
Confidence            49999999999999999999999 78888889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996          114 LAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus       114 la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      .++.++++++.|.   ++ -+.+..+|+|||+.+
T Consensus       150 ASKllsN~~y~Yk---Gm-GLsmGtMi~G~Dk~G  179 (285)
T KOG0175|consen  150 ASKLLSNMVYQYK---GM-GLSMGTMIAGWDKKG  179 (285)
T ss_pred             HHHHHHHHHhhcc---Cc-chhheeeEeeccCCC
Confidence            9999999998764   33 477889999999865

>TIGR03692 ATP_dep_HslV ATP-dependent protease HslVU, peptidase subunit

Probab=99.79  E-value=6.6e-19  Score=130.18  Aligned_cols=98  Identities=16%  Similarity=0.124  Sum_probs=79.9

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeee-cCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPI-TKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVL  114 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I-~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~l  114 (149)
                      +|++||+++||||||+|+|.+ +.++.+++.+||++| ++|++|++||..+|+++|.++++.++++|+...     .+.+
T Consensus         1 tTivgi~~~dgVvlaaD~r~s~g~~v~~~~~~Ki~~i~~d~i~~~~aG~~aD~q~l~~~~~~~~~~y~~~~-----~~~~   75 (171)
T TIGR03692         1 TTILAVRRNGKVVIAGDGQVTLGNTVMKGNARKVRRLYNGKVLAGFAGSTADAFTLFERFEAKLEEYQGNL-----TRAA   75 (171)
T ss_pred             CeEEEEEECCEEEEEECCceEeceEEEcCCCCeEEEeCCCCEEEEecchHHHHHHHHHHHHHHHHHccCch-----HHHH
Confidence            699999999999999999998 788888999999999 599999999999999999999999999988743     3555


Q ss_pred             HHHHHHHHHHHhhcCCcc-ccceEEEEEEEe
Q 031996          115 AKWIADKSQVYTQHAYMR-PLGVGLFLIEIA  144 (149)
Q Consensus       115 a~~l~~~~~~~t~~~~~r-P~~v~~liaG~D  144 (149)
                      ++.++++    ..+ .++ .+.+.+|++|||
T Consensus        76 a~l~~~~----~~~-~~~~~l~a~~iv~~~~  101 (171)
T TIGR03692        76 VELAKDW----RTD-RYLRRLEAMLIVADKE  101 (171)
T ss_pred             HHHHHHH----hhc-ccccccEEEEEEEcCC
Confidence            6655542    111 333 344888887765

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

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

Probab=99.73  E-value=1.4e-17  Score=127.35  Aligned_cols=112  Identities=19%  Similarity=0.227  Sum_probs=102.9

Q ss_pred             HHhhccCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCC
Q 031996           30 KAVKAAGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYE  108 (149)
Q Consensus        30 ~av~~~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~  108 (149)
                      ++.+ +|||++|+.+||||||++|+|++ +.++..++.+||+.|.++|+|+.+|-++|...+.+-+..+..+|+++.++.
T Consensus        32 ~~tk-TGTtIvgv~~k~gvIlgADtRaT~G~IvaDKnC~KIH~ia~~IyccGAGtAADte~vt~m~ss~l~Lh~l~t~R~  110 (271)
T KOG0173|consen   32 KATK-TGTTIVGVIFKDGVILGADTRATEGPIVADKNCEKIHFIAPNIYCCGAGTAADTEMVTRMISSNLELHRLNTGRK  110 (271)
T ss_pred             cccc-cCcEEEEEEeCCeEEEeecccccCCCeeecchhHHHhhcccceEEccCCchhhHHHHHHHHHHHHHHHHhccCCC
Confidence            4454 69999999999999999999999 788888899999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996          109 MPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus       109 ~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      ++|-...+.+.+.++.|.-     -.++.+||+|+|..+
T Consensus       111 ~rVv~A~~mlkQ~LFrYqG-----~IgA~LiiGGvD~TG  144 (271)
T KOG0173|consen  111 PRVVTALRMLKQHLFRYQG-----HIGAALILGGVDPTG  144 (271)
T ss_pred             CceeeHHHHHHHHHHHhcC-----cccceeEEccccCCC
Confidence            9999999999999987643     489999999999875

>PF10584 Proteasome_A_N: Proteasome subunit A N-terminal signature; InterPro: IPR000426 The proteasome (or macropain) (3

Probab=99.56  E-value=1.9e-15  Score=75.28  Aligned_cols=23  Identities=83%  Similarity=1.328  Sum_probs=22.2

Q ss_pred             CCcccceeCCCCcchhhhhHHHH
Q 031996            9 YDRHITIFSPEGRLFQVEYAFKA   31 (149)
Q Consensus         9 yd~~~t~fsp~G~~~Q~eya~~a   31 (149)
                      ||.++|+||||||++|||||+||
T Consensus         1 YD~~~t~FSp~Grl~QVEYA~~A   23 (23)
T PF10584_consen    1 YDRSITTFSPDGRLFQVEYAMKA   23 (23)
T ss_dssp             TSSSTTSBBTTSSBHHHHHHHHH
T ss_pred             CCCCceeECCCCeEEeeEeeecC
Confidence            89999999999999999999987

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). This family contains the alpha subunit sequences which range from 210 to 290 amino acids. These sequences are classified as non-peptidase homologues in MEROPS peptidase family T1 (clan PB(T)). ; GO: 0004175 endopeptidase activity, 0006511 ubiquitin-dependent protein catabolic process, 0019773 proteasome core complex, alpha-subunit complex; PDB: 3H4P_M 1IRU_O 3UN4_U 1FNT_A 3OEV_G 3OEU_U 3SDK_U 3DY3_G 3MG7_G 3L5Q_C ....

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

Probab=98.66  E-value=6.3e-08  Score=70.37  Aligned_cols=98  Identities=18%  Similarity=0.154  Sum_probs=72.4

Q ss_pred             cCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecC-cEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHH
Q 031996           35 AGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITK-YLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVD  112 (149)
Q Consensus        35 ~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~-~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~  112 (149)
                      .+||++++|-++-|++|+|.+.+ +..+.+.+..|+.+|.+ +++.+|+|.++|+.++.+.+..+++.|.-.      +.
T Consensus         3 h~TTiv~vr~~gkv~iagDGQVtlG~tvmK~narKvRkl~~gkvlaGFAGstADaftLfe~fe~kle~~~g~------L~   76 (178)
T COG5405           3 HMTTIVAVRKNGKVVIAGDGQVTLGNTVMKGNARKVRRLYNGKVLAGFAGSTADAFTLFERFEAKLEQYQGD------LF   76 (178)
T ss_pred             eeEEEEEEeeCCeEEEecCceEeecceeeeccHHHHHHHcCCcEEEEecccchhHHHHHHHHHHHHHHccCc------HH
Confidence            37999999999999999999998 77776777666666655 899999999999999999999999887422      11


Q ss_pred             HHHHHHHHHHHHHhhcCCccccceEEEEE
Q 031996          113 VLAKWIADKSQVYTQHAYMRPLGVGLFLI  141 (149)
Q Consensus       113 ~la~~l~~~~~~~t~~~~~rP~~v~~lia  141 (149)
                      ..+..+++-.+   .-..+|-+..-+|++
T Consensus        77 raavelaKdwr---~Dk~lr~LEAmllVa  102 (178)
T COG5405          77 RAAVELAKDWR---TDKYLRKLEAMLLVA  102 (178)
T ss_pred             HHHHHHHHhhh---hhhHHHHHhhheeEe
Confidence            23333333332   223456677777776

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

Probab=93.51  E-value=0.84  Score=34.92  Aligned_cols=106  Identities=8%  Similarity=-0.025  Sum_probs=66.4

Q ss_pred             ceEEEEEcCCeEEEEEeccCCccccccccccceeee---cCc-EEEEEeccHHHHHHHHHHHHHHHHH--HHHHhCCCCC
Q 031996           37 VTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPI---TKY-LGLLATGMTADARTLVQQARYEAAE--FRFKYGYEMP  110 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I---~~~-i~~~~sG~~~D~~~l~~~~r~~~~~--~~~~~~~~~~  110 (149)
                      +=|+|++-..|.|+++|.|.+...=.....+|.|.-   .+. ++++.+|.-+=.|.+.+.+.+..+.  .+.-. .-++
T Consensus         2 TYCv~l~l~~GlVf~sDsRTNAGvD~istfkKl~~~~~pGdRvlvl~taGNLA~tQaV~~ll~e~~~~d~~~~L~-n~~s   80 (255)
T COG3484           2 TYCVGLILDFGLVFGSDSRTNAGVDYISTFKKLFVFELPGDRVLVLCTAGNLAITQAVLHLLDERIQRDDGDSLL-NIPS   80 (255)
T ss_pred             ceEEEEEeccceEEecccccccCchHHHHHHHHhhccCCCceEEEEEecCccHHHHHHHHHHHHHhhccchhhhh-cchh
Confidence            458999999999999999987322111234444422   233 4566799999999888888666541  22212 2345


Q ss_pred             HHHHHHHHHHHHHHHhhcCC------ccccceEEEEEEE
Q 031996          111 VDVLAKWIADKSQVYTQHAY------MRPLGVGLFLIEI  143 (149)
Q Consensus       111 ~~~la~~l~~~~~~~t~~~~------~rP~~v~~liaG~  143 (149)
                      +-..+..++....+-.-+..      ---|.|++|++|-
T Consensus        81 m~eattlvgetvrEv~~rds~~leka~~dfn~sfllGGQ  119 (255)
T COG3484          81 MYEATTLVGETVREVQARDSPALEKAGIDFNCSFLLGGQ  119 (255)
T ss_pred             HHHHHHHHHHHHHHHHhccCchhhccCcceeEEEEEcce
Confidence            66666777766655422211      1258899999984

>PF09894 DUF2121: Uncharacterized protein conserved in archaea (DUF2121); InterPro: IPR016754 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function

Probab=84.38  E-value=1.7  Score=32.78  Aligned_cols=19  Identities=21%  Similarity=0.333  Sum_probs=17.4

Q ss_pred             ceEEEEEcCCeEEEEEecc
Q 031996           37 VTSIGVRGKDSVCVVTQKK   55 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~   55 (149)
                      +-+||.-+++|.|+|.|+|
T Consensus         2 SLII~y~GknGaViaGDkR   20 (194)
T PF09894_consen    2 SLIIAYYGKNGAVIAGDKR   20 (194)
T ss_pred             eEEEEEecCCCcEEeccce
Confidence            4689999999999999997

They do show distant similarity to NTPases and to nucleic acid binding enzymes.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	149
1iru_A	246	Crystal Structure Of The Mammalian 20s Proteasome A		5e-56
3unb_G	246	Mouse Constitutive 20s Proteasome In Complex With P		5e-56
1ryp_A	243	Crystal Structure Of The 20s Proteasome From Yeast		7e-44
1g0u_G	252	A Gated Channel Into The Proteasome Core Particle L		4e-43
3h4p_A	264	Proteasome 20s Core Particle From Methanocaldococcu		1e-29
1j2p_A	246	Alpha-Ring From The Proteasome From Archaeoglobus F		2e-27
2ku1_A	237	Dynamic Regulation Of Archaeal Proteasome Gate Open		2e-25
1pma_A	233	Proteasome From Thermoplasma Acidophilum Length = 2		2e-25
3jrm_A	227	Crystal Structure Of Archaeal 20s Proteasome In Com		2e-25
1j2q_A	237	20s Proteasome In Complex With Calpain-inhibitor I		3e-25
1iru_G	254	Crystal Structure Of The Mammalian 20s Proteasome A		4e-25
3unb_F	255	Mouse Constitutive 20s Proteasome In Complex With P		4e-25
1yar_A	233	Structure Of Archeabacterial 20s Proteasome Mutant		1e-24
1ryp_C	244	Crystal Structure Of The 20s Proteasome From Yeast		3e-24
1z7q_C	258	Crystal Structure Of The 20s Proteasome From Yeast		3e-24
1g0u_B	245	A Gated Channel Into The Proteasome Core Particle L		3e-24
1yau_A	233	Structure Of Archeabacterial 20s Proteasome- Pa26 C		6e-24
2ku2_A	237	Dynamic Regulation Of Archaeal Proteasome Gate Open		6e-24
3oeu_B	235	Structure Of Yeast 20s Open-Gate Proteasome With Co		7e-23
3une_C	248	Mouse Constitutive 20s Proteasome Length = 248		2e-22
1iru_D	248	Crystal Structure Of The Mammalian 20s Proteasome A		3e-22
3unb_C	248	Mouse Constitutive 20s Proteasome In Complex With P		5e-22
3unb_D	241	Mouse Constitutive 20s Proteasome In Complex With P		7e-22
3unb_A	234	Mouse Constitutive 20s Proteasome In Complex With P		1e-21
1iru_B	233	Crystal Structure Of The Mammalian 20s Proteasome A		1e-21
1iru_E	241	Crystal Structure Of The Mammalian 20s Proteasome A		3e-21
1vsy_C	232	Proteasome Activator Complex Length = 232		5e-21
1g0u_D	241	A Gated Channel Into The Proteasome Core Particle L		7e-21
2z5c_C	262	Crystal Structure Of A Novel Chaperone Complex For		3e-20
4g4s_E	261	Structure Of Proteasome-Pba1-Pba2 Complex Length =		3e-20
1fnt_E	260	Crystal Structure Of The 20s Proteasome From Yeast		3e-20
1fnt_D	254	Crystal Structure Of The 20s Proteasome From Yeast		3e-20
1vsy_E	250	Proteasome Activator Complex Length = 250		3e-20
1g0u_C	243	A Gated Channel Into The Proteasome Core Particle L		3e-20
1ryp_D	241	Crystal Structure Of The 20s Proteasome From Yeast		3e-20
1ryp_E	242	Crystal Structure Of The 20s Proteasome From Yeast		2e-19
1z7q_G	288	Crystal Structure Of The 20s Proteasome From Yeast		2e-19
1g0u_F	248	A Gated Channel Into The Proteasome Core Particle L		2e-19
1fnt_G	287	Crystal Structure Of The 20s Proteasome From Yeast		2e-19
1ryp_G	244	Crystal Structure Of The 20s Proteasome From Yeast		2e-19
1iru_C	261	Crystal Structure Of The Mammalian 20s Proteasome A		5e-19
3unb_B	261	Mouse Constitutive 20s Proteasome In Complex With P		5e-19
3oeu_F	242	Structure Of Yeast 20s Open-Gate Proteasome With Co		5e-19
1iru_F	263	Crystal Structure Of The Mammalian 20s Proteasome A		9e-19
3unb_E	263	Mouse Constitutive 20s Proteasome In Complex With P		1e-18
3sdi_E	233	Structure Of Yeast 20s Open-Gate Proteasome With Co		7e-16
1g0u_E	234	A Gated Channel Into The Proteasome Core Particle L		7e-16
1fnt_F	234	Crystal Structure Of The 20s Proteasome From Yeast		4e-15
4g4s_F	235	Structure Of Proteasome-Pba1-Pba2 Complex Length =		4e-15
1ryp_F	233	Crystal Structure Of The 20s Proteasome From Yeast		5e-15
1ryp_B	250	Crystal Structure Of The 20s Proteasome From Yeast		6e-15
1vsy_D	227	Proteasome Activator Complex Length = 227		1e-13
1vsy_B	231	Proteasome Activator Complex Length = 231		8e-11
1ya7_H	217	Implications For Interactions Of Proteasome With Pa		8e-08
1pma_B	211	Proteasome From Thermoplasma Acidophilum Length = 2		8e-08
3c91_H	203	Thermoplasma Acidophilum 20s Proteasome With An Ope		3e-07

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

Iteration: 1
 Score =  212 bits (540), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 98/143 (68%), Positives = 119/143 (83%)
Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGS  G+DRHITIFSPEGRL+QVEYAFKA+   G+TS+ VRGKD   +VTQKKVPDKL
Sbjct: 1   MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL 60
Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD
Sbjct: 61  LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD 120
Query: 121 KSQVYTQHAYMRPLGVGLFLIEI 143
            SQVYTQ+A MRPLG  + LI I
Sbjct: 121 ISQVYTQNAEMRPLGCCMILIGI 143

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

Iteration: 1
 Score =  212 bits (540), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 98/143 (68%), Positives = 119/143 (83%)
Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGS  G+DRHITIFSPEGRL+QVEYAFKA+   G+TS+ VRGKD   +VTQKKVPDKL
Sbjct: 1   MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL 60
Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD
Sbjct: 61  LDSSTVTHLFKITESIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD 120
Query: 121 KSQVYTQHAYMRPLGVGLFLIEI 143
            SQVYTQ+A MRPLG  + LI I
Sbjct: 121 ISQVYTQNAEMRPLGCCMILIGI 143

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

Iteration: 1
 Score =  172 bits (436), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 82/137 (59%), Positives = 105/137 (76%)
Query: 7   GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSV 66
            GYDRHITIFSPEGRL+QVEYAFKA     + S+ VRGKD   V++QKKVPDKLLD T+V
Sbjct: 1   AGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPTTV 60
Query: 67  THLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYT 126
           +++F I++ +G++  G   DAR    +A+ EAAEFR+KYGY+MP DVLAK +A+ SQ+YT
Sbjct: 61  SYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYT 120
Query: 127 QHAYMRPLGVGLFLIEI 143
           Q AYMRPLGV L  + +
Sbjct: 121 QRAYMRPLGVILTFVSV 137

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

Iteration: 1
 Score =  169 bits (429), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 81/135 (60%), Positives = 104/135 (77%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YDRHITIFSPEGRL+QVEYAFKA     + S+ VRGKD   V++QKKVPDKLLD T+V++
Sbjct: 12  YDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPTTVSY 71
Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +F I++ +G++  G   DAR    +A+ EAAEFR+KYGY+MP DVLAK +A+ SQ+YTQ 
Sbjct: 72  IFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQR 131
Query: 129 AYMRPLGVGLFLIEI 143
           AYMRPLGV L  + +
Sbjct: 132 AYMRPLGVILTFVSV 146

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

Iteration: 1
 Score =  125 bits (314), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 60/134 (44%), Positives = 86/134 (64%), Gaps = 1/134 (0%)
Query: 7   GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSV 66
             YDR IT+FSPEGRL+QVEYA +AV+  G T+IG+  KD V +   +++  KL+   S+
Sbjct: 10  SAYDRAITVFSPEGRLYQVEYAREAVRR-GTTAIGIACKDGVVLAVDRRITSKLVKIRSI 68
Query: 67  THLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYT 126
             +F I  ++    +G+ ADAR L+ +AR EA  +R  YG E+ +++LAK I D  Q YT
Sbjct: 69  EKIFQIDDHVAAATSGLVADARVLIDRARLEAQIYRLTYGEEISIEMLAKKICDIKQAYT 128
Query: 127 QHAYMRPLGVGLFL 140
           QH  +RP GV L +
Sbjct: 129 QHGGVRPFGVSLLI 142

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

Iteration: 1
 Score =  117 bits (294), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 60/133 (45%), Positives = 86/133 (64%), Gaps = 1/133 (0%)
Query: 8   GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVT 67
           GYDR IT+FSP+GRLFQVEYA +AVK  G T+IG++ K+ V ++  K+V  KLL+  ++ 
Sbjct: 7   GYDRAITVFSPDGRLFQVEYAREAVKR-GATAIGIKCKEGVILIADKRVGSKLLEKDTIE 65
Query: 68  HLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQ 127
            ++ I +++    +G+ ADAR L+ +AR EA   R  Y   + V  LAK I D  Q YTQ
Sbjct: 66  KIYKIDEHICAATSGLVADARVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQ 125
Query: 128 HAYMRPLGVGLFL 140
           +  +RP GV L +
Sbjct: 126 YGGVRPFGVSLLI 138

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

Iteration: 1
 Score =  110 bits (276), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 56/132 (42%), Positives = 85/132 (64%), Gaps = 1/132 (0%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YDR IT+FSP+GRLFQVEYA +AVK  G T++G++  + V +++ KKV  +L++  S+  
Sbjct: 12  YDRAITVFSPDGRLFQVEYAREAVKK-GSTALGMKFANGVLLISDKKVRSRLIEQNSIEK 70
Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +  I  Y+  + +G+ ADAR LV  AR  A + +  YG  + ++ L K +AD+ Q YTQ+
Sbjct: 71  IQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQY 130
Query: 129 AYMRPLGVGLFL 140
             +RP GV L  
Sbjct: 131 GGVRPYGVSLIF 142

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

Iteration: 1
 Score =  110 bits (276), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 56/132 (42%), Positives = 85/132 (64%), Gaps = 1/132 (0%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YDR IT+FSP+GRLFQVEYA +AVK  G T++G++  + V +++ KKV  +L++  S+  
Sbjct: 8   YDRAITVFSPDGRLFQVEYAREAVKK-GSTALGMKFANGVLLISDKKVRSRLIEQNSIEK 66
Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +  I  Y+  + +G+ ADAR LV  AR  A + +  YG  + ++ L K +AD+ Q YTQ+
Sbjct: 67  IQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQY 126
Query: 129 AYMRPLGVGLFL 140
             +RP GV L  
Sbjct: 127 GGVRPYGVSLIF 138

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

Iteration: 1
 Score =  110 bits (276), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 56/133 (42%), Positives = 85/133 (63%), Gaps = 1/133 (0%)
Query: 8   GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVT 67
            YDR IT+FSP+GRLFQVEYA +AVK  G T++G++  + V +++ KKV  +L++  S+ 
Sbjct: 1   AYDRAITVFSPDGRLFQVEYAREAVKK-GSTALGMKFANGVLLISDKKVRSRLIEQNSIE 59
Query: 68  HLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQ 127
            +  I  Y+  + +G+ ADAR LV  AR  A + +  YG  + ++ L K +AD+ Q YTQ
Sbjct: 60  KIQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQ 119
Query: 128 HAYMRPLGVGLFL 140
           +  +RP GV L  
Sbjct: 120 YGGVRPYGVSLIF 132

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

Iteration: 1
 Score =  110 bits (275), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 57/130 (43%), Positives = 83/130 (63%), Gaps = 1/130 (0%)
Query: 11  RHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLF 70
           R IT+FSP+GRLFQVEYA +AVK  G T+IG++ K+ V ++  K+V  KLL+  ++  ++
Sbjct: 1   RAITVFSPDGRLFQVEYAREAVKR-GATAIGIKCKEGVILIADKRVGSKLLEADTIEKIY 59
Query: 71  PITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAY 130
            I +++    +G+ ADAR L+ +AR EA   R  Y   + V  LAK I D  Q YTQ+  
Sbjct: 60  KIDEHICAATSGLVADARVLIDRARIEAQINRLTYDEPITVKELAKKICDFKQQYTQYGG 119
Query: 131 MRPLGVGLFL 140
           +RP GV L +
Sbjct: 120 VRPFGVSLLI 129

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

Iteration: 1
 Score =  110 bits (274), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 57/135 (42%), Positives = 81/135 (60%), Gaps = 1/135 (0%)
Query: 6   GGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTS 65
           G GYD   + FSP+GR+FQVEYA KAV+ +  T+IG+R KD V    +K V  KL +  S
Sbjct: 4   GTGYDLSASTFSPDGRVFQVEYAMKAVENSS-TAIGIRCKDGVVFGVEKLVLSKLYEEGS 62
Query: 66  VTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVY 125
              LF + +++G+   G+ ADAR+L   AR EA+ FR  +GY +P+  LA  +A     Y
Sbjct: 63  NKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAY 122
Query: 126 TQHAYMRPLGVGLFL 140
           T ++ +RP G    L
Sbjct: 123 TLYSAVRPFGCSFML 137

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

Iteration: 1
 Score =  110 bits (274), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 57/135 (42%), Positives = 81/135 (60%), Gaps = 1/135 (0%)
Query: 6   GGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTS 65
           G GYD   + FSP+GR+FQVEYA KAV+ +  T+IG+R KD V    +K V  KL +  S
Sbjct: 5   GTGYDLSASTFSPDGRVFQVEYAMKAVENSS-TAIGIRCKDGVVFGVEKLVLSKLYEEGS 63
Query: 66  VTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVY 125
              LF + +++G+   G+ ADAR+L   AR EA+ FR  +GY +P+  LA  +A     Y
Sbjct: 64  NKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAY 123
Query: 126 TQHAYMRPLGVGLFL 140
           T ++ +RP G    L
Sbjct: 124 TLYSAVRPFGCSFML 138

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

Iteration: 1
 Score =  108 bits (269), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 55/132 (41%), Positives = 84/132 (63%), Gaps = 1/132 (0%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           Y R IT+FSP+GRLFQVEYA +AVK  G T++G++  + V +++ KKV  +L++  S+  
Sbjct: 8   YSRAITVFSPDGRLFQVEYAREAVKK-GSTALGMKFANGVLLISDKKVRSRLIEQNSIEK 66
Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +  I  Y+  + +G+ ADAR LV  AR  A + +  YG  + ++ L K +AD+ Q YTQ+
Sbjct: 67  IQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQY 126
Query: 129 AYMRPLGVGLFL 140
             +RP GV L  
Sbjct: 127 GGVRPYGVSLIF 138

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

Iteration: 1
 Score =  107 bits (266), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 52/132 (39%), Positives = 78/132 (59%), Gaps = 2/132 (1%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDH-TSVT 67
           YD   TIFSPEGRL+QVEYA +++  AG T+IG+   D + +  ++KV   LL+  TS  
Sbjct: 5   YDSRTTIFSPEGRLYQVEYALESISHAG-TAIGIMASDGIVLAAERKVTSTLLEQDTSTE 63
Query: 68  HLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQ 127
            L+ +   + +   G+TADA  L+  AR  A  +   Y  ++PV++L + ++D  Q YTQ
Sbjct: 64  KLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQ 123
Query: 128 HAYMRPLGVGLF 139
           H  +RP GV   
Sbjct: 124 HGGLRPFGVSFI 135

>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 =  107 bits (266), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 52/132 (39%), Positives = 78/132 (59%), Gaps = 2/132 (1%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDH-TSVT 67
           YD   TIFSPEGRL+QVEYA +++  AG T+IG+   D + +  ++KV   LL+  TS  
Sbjct: 6   YDSRTTIFSPEGRLYQVEYALESISHAG-TAIGIMASDGIVLAAERKVTSTLLEQDTSTE 64
Query: 68  HLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQ 127
            L+ +   + +   G+TADA  L+  AR  A  +   Y  ++PV++L + ++D  Q YTQ
Sbjct: 65  KLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQ 124
Query: 128 HAYMRPLGVGLF 139
           H  +RP GV   
Sbjct: 125 HGGLRPFGVSFI 136

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

Iteration: 1
 Score =  107 bits (266), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 52/132 (39%), Positives = 78/132 (59%), Gaps = 2/132 (1%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDH-TSVT 67
           YD   TIFSPEGRL+QVEYA +++  AG T+IG+   D + +  ++KV   LL+  TS  
Sbjct: 6   YDSRTTIFSPEGRLYQVEYALESISHAG-TAIGIMASDGIVLAAERKVTSTLLEQDTSTE 64
Query: 68  HLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQ 127
            L+ +   + +   G+TADA  L+  AR  A  +   Y  ++PV++L + ++D  Q YTQ
Sbjct: 65  KLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQ 124
Query: 128 HAYMRPLGVGLF 139
           H  +RP GV   
Sbjct: 125 HGGLRPFGVSFI 136

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

Iteration: 1
 Score =  106 bits (264), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 57/140 (40%), Positives = 87/140 (62%), Gaps = 2/140 (1%)
Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           M +G   G  R IT+FSP+GRLFQVEYA +AVK  G T++G++  + V +++ KKV  +L
Sbjct: 1   MQQGQMAG-GRAITVFSPDGRLFQVEYAREAVKK-GSTALGMKFANGVLLISDKKVRSRL 58
Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           ++  S+  +  I  Y+  + +G+ ADAR LV  AR  A + +  YG  + ++ L K +AD
Sbjct: 59  IEQNSIEKIQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVAD 118
Query: 121 KSQVYTQHAYMRPLGVGLFL 140
           + Q YTQ+  +RP GV L  
Sbjct: 119 QMQQYTQYGGVRPYGVSLIF 138

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

Iteration: 1
 Score =  106 bits (264), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 57/140 (40%), Positives = 87/140 (62%), Gaps = 2/140 (1%)
Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           M +G   G  R IT+FSP+GRLFQVEYA +AVK  G T++G++  + V +++ KKV  +L
Sbjct: 5   MQQGQMAG-GRAITVFSPDGRLFQVEYAREAVKK-GSTALGMKFANGVLLISDKKVRSRL 62
Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           ++  S+  +  I  Y+  + +G+ ADAR LV  AR  A + +  YG  + ++ L K +AD
Sbjct: 63  IEQNSIEKIQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVAD 122
Query: 121 KSQVYTQHAYMRPLGVGLFL 140
           + Q YTQ+  +RP GV L  
Sbjct: 123 QMQQYTQYGGVRPYGVSLIF 142

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

Iteration: 1
 Score =  102 bits (255), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 50/127 (39%), Positives = 76/127 (59%), Gaps = 2/127 (1%)
Query: 14  TIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDH-TSVTHLFPI 72
           TIFSPEGRL+QVEYA +++  AG T+IG+   D + +  ++KV   LL+  TS   L+ +
Sbjct: 1   TIFSPEGRLYQVEYALESISHAG-TAIGIMASDGIVLAAERKVTSTLLEQDTSTEKLYKL 59
Query: 73  TKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMR 132
              + +   G+TADA  L+  AR  A  +   Y  ++PV++L + ++D  Q YTQH  +R
Sbjct: 60  NDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLR 119
Query: 133 PLGVGLF 139
           P GV   
Sbjct: 120 PFGVSFI 126

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

Iteration: 1
 Score =  100 bits (250), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 54/133 (40%), Positives = 78/133 (58%), Gaps = 1/133 (0%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YDR IT+FSP+G LFQVEYA +AVK  G T++GVRGKD V +  +KK   KL D  +V  
Sbjct: 3   YDRAITVFSPDGHLFQVEYAQEAVKK-GSTAVGVRGKDIVVLGVEKKSVAKLQDERTVRK 61
Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +  +   + +   G+TADAR ++ +AR E    R      + V+ + ++IA   Q YTQ 
Sbjct: 62  ICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQS 121
Query: 129 AYMRPLGVGLFLI 141
              RP G+   ++
Sbjct: 122 NGRRPFGISALIV 134

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

Iteration: 1
 Score =  100 bits (249), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 53/133 (39%), Positives = 78/133 (58%), Gaps = 1/133 (0%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YDR IT+FSP+G LFQVEYA +AVK  G T++GVRG+D V +  +KK   KL D  +V  
Sbjct: 3   YDRAITVFSPDGHLFQVEYAQEAVKK-GSTAVGVRGRDIVVLGVEKKSVAKLQDERTVRK 61
Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +  +   + +   G+TADAR ++ +AR E    R      + V+ + ++IA   Q YTQ 
Sbjct: 62  ICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQS 121
Query: 129 AYMRPLGVGLFLI 141
              RP G+   ++
Sbjct: 122 NGRRPFGISALIV 134

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

Iteration: 1
 Score = 99.8 bits (247), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 54/133 (40%), Positives = 77/133 (57%), Gaps = 1/133 (0%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YDR IT+FSP+G LFQVEYA +AVK  G T++GVRGKD V +   KK   KL D  +V  
Sbjct: 3   YDRAITVFSPDGHLFQVEYAQEAVKK-GSTAVGVRGKDIVVLGVAKKSVAKLQDERTVRK 61
Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +  +   + +   G+TADAR ++ +AR E    R      + V+ + ++IA   Q YTQ 
Sbjct: 62  ICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQS 121
Query: 129 AYMRPLGVGLFLI 141
              RP G+   ++
Sbjct: 122 NGRRPFGISALIV 134

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

Iteration: 1
 Score = 99.4 bits (246), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 48/137 (35%), Positives = 80/137 (58%), Gaps = 6/137 (4%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YDR +  FSPEGRLFQVEYA +A+K  G T+IG++  + VC+  +K++   L++ +S+  
Sbjct: 8   YDRGVNTFSPEGRLFQVEYAIEAIKL-GSTAIGIQTSEGVCLAVEKRITSPLMEPSSIEK 66
Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +  I  ++G   +G+ ADA+TL+ +AR E     F Y   M V+ + + +++ +  + + 
Sbjct: 67  IVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEE 126
Query: 129 -----AYMRPLGVGLFL 140
                A  RP GV L  
Sbjct: 127 DADPGAMSRPFGVALLF 143

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

Iteration: 1
 Score = 98.6 bits (244), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 54/133 (40%), Positives = 76/133 (57%), Gaps = 1/133 (0%)
Query: 8   GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVT 67
           GY   +T FSP G+L Q+EYA  AV A G  S+G++  + V + T+KK    L D  SV 
Sbjct: 5   GYSFSLTTFSPSGKLVQIEYALAAV-AGGAPSVGIKAANGVVLATEKKQKSILYDERSVH 63
Query: 68  HLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQ 127
            + PITK++GL+ +GM  D R LV +AR  A ++   Y   +P   L + +A   Q YTQ
Sbjct: 64  KVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQ 123
Query: 128 HAYMRPLGVGLFL 140
              +RP GV L +
Sbjct: 124 SGGVRPFGVSLLI 136

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

Iteration: 1
 Score = 98.6 bits (244), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 54/133 (40%), Positives = 76/133 (57%), Gaps = 1/133 (0%)
Query: 8   GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVT 67
           GY   +T FSP G+L Q+EYA  AV A G  S+G++  + V + T+KK    L D  SV 
Sbjct: 4   GYSFSLTTFSPSGKLVQIEYALAAV-AGGAPSVGIKAANGVVLATEKKQKSILYDERSVH 62
Query: 68  HLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQ 127
            + PITK++GL+ +GM  D R LV +AR  A ++   Y   +P   L + +A   Q YTQ
Sbjct: 63  KVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQ 122
Query: 128 HAYMRPLGVGLFL 140
              +RP GV L +
Sbjct: 123 SGGVRPFGVSLLI 135

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

Iteration: 1
 Score = 97.1 bits (240), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 47/137 (34%), Positives = 79/137 (57%), Gaps = 6/137 (4%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YDR +  FSPEGRLFQVEY  +A+K  G T+IG++  + VC+  +K++   L++ +S+  
Sbjct: 8   YDRGVNTFSPEGRLFQVEYDIEAIKL-GSTAIGIQTSEGVCLAVEKRITSPLMEPSSIEK 66
Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +  I  ++G   +G+ ADA+TL+ +AR E     F Y   M V+ + + +++ +  + + 
Sbjct: 67  IVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEE 126
Query: 129 -----AYMRPLGVGLFL 140
                A  RP GV L  
Sbjct: 127 DADPGAMSRPFGVALLF 143

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

Iteration: 1
 Score = 96.7 bits (239), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 47/124 (37%), Positives = 73/124 (58%), Gaps = 2/124 (1%)
Query: 17  SPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDH-TSVTHLFPITKY 75
           SPEGRL+QVEYA +++  AG T+IG+   D + +  ++KV   LL+  TS   L+ +   
Sbjct: 1   SPEGRLYQVEYALESISHAG-TAIGIMASDGIVLAAERKVTSTLLEQDTSTEKLYKLNDK 59
Query: 76  LGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLG 135
           + +   G+TADA  L+  AR  A  +   Y  ++PV++L + ++D  Q YTQH  +RP G
Sbjct: 60  IAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFG 119
Query: 136 VGLF 139
           V   
Sbjct: 120 VSFI 123

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

Iteration: 1
 Score = 95.9 bits (237), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 48/132 (36%), Positives = 78/132 (59%), Gaps = 4/132 (3%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YDR ++ FSPEGRLFQVEY+ +A+K  G T+IG+  K+ V +  +K+    LL+  S+  
Sbjct: 8   YDRGVSTFSPEGRLFQVEYSLEAIKL-GSTAIGIATKEGVVLGVEKRATSPLLESDSIEK 66
Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +  I +++G   +G+TADAR++++ AR  A      Y  ++ V+ L + + D   +    
Sbjct: 67  IVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCD---LAAAA 123
Query: 129 AYMRPLGVGLFL 140
           A  RP GV L +
Sbjct: 124 AMSRPFGVALLI 135

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

Iteration: 1
 Score = 94.0 bits (232), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 48/138 (34%), Positives = 80/138 (57%), Gaps = 7/138 (5%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YDR ++ FSPEGRLFQVEY+ +A+K  G T+IG+  K+ V +  +K+    LL+  S+  
Sbjct: 10  YDRGVSTFSPEGRLFQVEYSLEAIKL-GSTAIGIATKEGVVLGVEKRATSPLLESDSIEK 68
Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +  I +++G   +G+TADAR++++ AR  A      Y  ++ V+ L + + D +  + + 
Sbjct: 69  IVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEG 128
Query: 129 A------YMRPLGVGLFL 140
           A        RP GV L +
Sbjct: 129 ASGEERLMSRPFGVALLI 146

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

Iteration: 1
 Score = 94.0 bits (232), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 48/138 (34%), Positives = 80/138 (57%), Gaps = 7/138 (5%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YDR ++ FSPEGRLFQVEY+ +A+K  G T+IG+  K+ V +  +K+    LL+  S+  
Sbjct: 9   YDRGVSTFSPEGRLFQVEYSLEAIKL-GSTAIGIATKEGVVLGVEKRATSPLLESDSIEK 67
Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +  I +++G   +G+TADAR++++ AR  A      Y  ++ V+ L + + D +  + + 
Sbjct: 68  IVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEG 127
Query: 129 A------YMRPLGVGLFL 140
           A        RP GV L +
Sbjct: 128 ASGEERLMSRPFGVALLI 145

>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 = 94.0 bits (232), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 48/138 (34%), Positives = 80/138 (57%), Gaps = 7/138 (5%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YDR ++ FSPEGRLFQVEY+ +A+K  G T+IG+  K+ V +  +K+    LL+  S+  
Sbjct: 8   YDRGVSTFSPEGRLFQVEYSLEAIKL-GSTAIGIATKEGVVLGVEKRATSPLLESDSIEK 66
Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +  I +++G   +G+TADAR++++ AR  A      Y  ++ V+ L + + D +  + + 
Sbjct: 67  IVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEG 126
Query: 129 A------YMRPLGVGLFL 140
           A        RP GV L +
Sbjct: 127 ASGEERLMSRPFGVALLI 144

>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 = 94.0 bits (232), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 50/135 (37%), Positives = 81/135 (60%), Gaps = 2/135 (1%)
Query: 7   GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLD-HTS 65
            GYDR ++IFSP+G +FQVEYA +AVK  G  ++GV+GK+ V +  +++   KL D   +
Sbjct: 2   SGYDRALSIFSPDGHIFQVEYALEAVKR-GTCAVGVKGKNCVVLGCERRSTLKLQDTRIT 60
Query: 66  VTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVY 125
            + +  I  ++ L  +G+ AD+R L+++AR EA   R      + V+ L +++A   Q Y
Sbjct: 61  PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY 120
Query: 126 TQHAYMRPLGVGLFL 140
           TQ   +RP GV   +
Sbjct: 121 TQSGGVRPFGVSTLI 135

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

Iteration: 1
 Score = 94.0 bits (232), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 48/138 (34%), Positives = 80/138 (57%), Gaps = 7/138 (5%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YDR ++ FSPEGRLFQVEY+ +A+K  G T+IG+  K+ V +  +K+    LL+  S+  
Sbjct: 8   YDRGVSTFSPEGRLFQVEYSLEAIKL-GSTAIGIATKEGVVLGVEKRATSPLLESDSIEK 66
Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +  I +++G   +G+TADAR++++ AR  A      Y  ++ V+ L + + D +  + + 
Sbjct: 67  IVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEG 126
Query: 129 A------YMRPLGVGLFL 140
           A        RP GV L +
Sbjct: 127 ASGEERLMSRPFGVALLI 144

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

Iteration: 1
 Score = 93.6 bits (231), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 50/135 (37%), Positives = 81/135 (60%), Gaps = 2/135 (1%)
Query: 7   GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLD-HTS 65
            GYDR ++IFSP+G +FQVEYA +AVK  G  ++GV+GK+ V +  +++   KL D   +
Sbjct: 2   SGYDRALSIFSPDGHIFQVEYALEAVKR-GTCAVGVKGKNCVVLGCERRSTLKLQDTRIT 60
Query: 66  VTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVY 125
            + +  I  ++ L  +G+ AD+R L+++AR EA   R      + V+ L +++A   Q Y
Sbjct: 61  PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY 120
Query: 126 TQHAYMRPLGVGLFL 140
           TQ   +RP GV   +
Sbjct: 121 TQSGGVRPFGVSTLI 135

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

Iteration: 1
 Score = 93.6 bits (231), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 50/134 (37%), Positives = 81/134 (60%), Gaps = 2/134 (1%)
Query: 8   GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLD-HTSV 66
           GYDR ++IFSP+G +FQVEYA +AVK  G  ++GV+GK+ V +  +++   KL D   + 
Sbjct: 1   GYDRALSIFSPDGHIFQVEYALEAVKR-GTCAVGVKGKNCVVLGCERRSTLKLQDTRITP 59
Query: 67  THLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYT 126
           + +  I  ++ L  +G+ AD+R L+++AR EA   R      + V+ L +++A   Q YT
Sbjct: 60  SKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYT 119
Query: 127 QHAYMRPLGVGLFL 140
           Q   +RP GV   +
Sbjct: 120 QSGGVRPFGVSTLI 133

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

Iteration: 1
 Score = 91.3 bits (225), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 47/137 (34%), Positives = 79/137 (57%), Gaps = 7/137 (5%)
Query: 10  DRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHL 69
           DR ++ FSPEGRLFQVEY+ +A+K  G T+IG+  K+ V +  +K+    LL+  S+  +
Sbjct: 1   DRGVSTFSPEGRLFQVEYSLEAIKL-GSTAIGIATKEGVVLGVEKRATSPLLESDSIEKI 59
Query: 70  FPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHA 129
             I +++G   +G+TADAR++++ AR  A      Y  ++ V+ L + + D +  + + A
Sbjct: 60  VEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGA 119
Query: 130 ------YMRPLGVGLFL 140
                   RP GV L +
Sbjct: 120 SGEERLMSRPFGVALLI 136

>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 = 90.9 bits (224), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 49/131 (37%), Positives = 73/131 (55%), Gaps = 1/131 (0%)
Query: 6   GGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTS 65
           G GYD   ++FSP+GR FQVEYA KAV+  G TSIG++  D V    +K +  KLL    
Sbjct: 5   GTGYDLSNSVFSPDGRNFQVEYAVKAVEN-GTTSIGIKCNDGVVFAVEKLITSKLLVPQK 63
Query: 66  VTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVY 125
              +  + +++G + +G+  D R LV + R EAA F+  Y   +P+   A  +    Q +
Sbjct: 64  NVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAH 123
Query: 126 TQHAYMRPLGV 136
           T +  +RP GV
Sbjct: 124 TLYNSVRPFGV 134

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

Iteration: 1
 Score = 90.9 bits (224), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 49/131 (37%), Positives = 73/131 (55%), Gaps = 1/131 (0%)
Query: 6   GGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTS 65
           G GYD   ++FSP+GR FQVEYA KAV+  G TSIG++  D V    +K +  KLL    
Sbjct: 5   GTGYDLSNSVFSPDGRNFQVEYAVKAVEN-GTTSIGIKCNDGVVFAVEKLITSKLLVPQK 63
Query: 66  VTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVY 125
              +  + +++G + +G+  D R LV + R EAA F+  Y   +P+   A  +    Q +
Sbjct: 64  NVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAH 123
Query: 126 TQHAYMRPLGV 136
           T +  +RP GV
Sbjct: 124 TLYNSVRPFGV 134

>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 = 90.9 bits (224), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 49/131 (37%), Positives = 73/131 (55%), Gaps = 1/131 (0%)
Query: 6   GGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTS 65
           G GYD   ++FSP+GR FQVEYA KAV+  G TSIG++  D V    +K +  KLL    
Sbjct: 4   GTGYDLSNSVFSPDGRNFQVEYAVKAVEN-GTTSIGIKCNDGVVFAVEKLITSKLLVPQK 62
Query: 66  VTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVY 125
              +  + +++G + +G+  D R LV + R EAA F+  Y   +P+   A  +    Q +
Sbjct: 63  NVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAH 122
Query: 126 TQHAYMRPLGV 136
           T +  +RP GV
Sbjct: 123 TLYNSVRPFGV 133

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

Iteration: 1
 Score = 90.9 bits (224), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 49/131 (37%), Positives = 73/131 (55%), Gaps = 1/131 (0%)
Query: 6   GGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTS 65
           G GYD   ++FSP+GR FQVEYA KAV+  G TSIG++  D V    +K +  KLL    
Sbjct: 1   GTGYDLSNSVFSPDGRNFQVEYAVKAVEN-GTTSIGIKCNDGVVFAVEKLITSKLLVPQK 59
Query: 66  VTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVY 125
              +  + +++G + +G+  D R LV + R EAA F+  Y   +P+   A  +    Q +
Sbjct: 60  NVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAH 119
Query: 126 TQHAYMRPLGV 136
           T +  +RP GV
Sbjct: 120 TLYNSVRPFGV 130

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

Iteration: 1
 Score = 89.7 bits (221), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 48/134 (35%), Positives = 71/134 (52%), Gaps = 2/134 (1%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YD   TIFSPEGRL+QVEYA +A+  AG T +G+   D V +  +++   KLLD    + 
Sbjct: 5   YDSRTTIFSPEGRLYQVEYAMEAIGHAG-TCLGILANDGVLLAAERRNIHKLLDEVFFSE 63
Query: 69  -LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQ 127
            ++ + + +     G+T+DA  L  + R  A  +  +Y   +P + L   + D  Q YTQ
Sbjct: 64  KIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQ 123
Query: 128 HAYMRPLGVGLFLI 141
               RP GV L  I
Sbjct: 124 FGGKRPFGVSLLYI 137

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

Iteration: 1
 Score = 89.7 bits (221), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 48/134 (35%), Positives = 71/134 (52%), Gaps = 2/134 (1%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YD   TIFSPEGRL+QVEYA +A+  AG T +G+   D V +  +++   KLLD    + 
Sbjct: 5   YDSRTTIFSPEGRLYQVEYAMEAIGHAG-TCLGILANDGVLLAAERRNIHKLLDEVFFSE 63
Query: 69  -LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQ 127
            ++ + + +     G+T+DA  L  + R  A  +  +Y   +P + L   + D  Q YTQ
Sbjct: 64  KIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQ 123
Query: 128 HAYMRPLGVGLFLI 141
               RP GV L  I
Sbjct: 124 FGGKRPFGVSLLYI 137

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

Iteration: 1
 Score = 89.7 bits (221), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 48/129 (37%), Positives = 72/129 (55%), Gaps = 1/129 (0%)
Query: 8   GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVT 67
           GYD   ++FSP+GR FQVEYA KAV+  G TSIG++  D V    +K +  KLL      
Sbjct: 1   GYDLSNSVFSPDGRNFQVEYAVKAVEN-GTTSIGIKCNDGVVFAVEKLITSKLLVPQKNV 59
Query: 68  HLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQ 127
            +  + +++G + +G+  D R LV + R EAA F+  Y   +P+   A  +    Q +T 
Sbjct: 60  KIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTL 119
Query: 128 HAYMRPLGV 136
           +  +RP GV
Sbjct: 120 YNSVRPFGV 128

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

Iteration: 1
 Score = 89.0 bits (219), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 47/132 (35%), Positives = 73/132 (55%), Gaps = 3/132 (2%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YD  +T++SP+GR+ Q+EYA +AVK  G  ++G++ K    +V  K+   +L  H     
Sbjct: 6   YDNDVTVWSPQGRIHQIEYAMEAVKQ-GSATVGLKSKTHAVLVALKRAQSELAAHQK--K 62
Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +  +  ++G+   G+TADAR L    R E  + RF +   +PV  L   I  K+Q+ TQ 
Sbjct: 63  ILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQR 122
Query: 129 AYMRPLGVGLFL 140
              RP GVGL +
Sbjct: 123 YGRRPYGVGLLI 134

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

Iteration: 1
 Score = 89.0 bits (219), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 47/132 (35%), Positives = 73/132 (55%), Gaps = 3/132 (2%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YD  +T++SP+GR+ Q+EYA +AVK  G  ++G++ K    +V  K+   +L  H     
Sbjct: 6   YDNDVTVWSPQGRIHQIEYAMEAVKQ-GSATVGLKSKTHAVLVALKRAQSELAAHQK--K 62
Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +  +  ++G+   G+TADAR L    R E  + RF +   +PV  L   I  K+Q+ TQ 
Sbjct: 63  ILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQR 122
Query: 129 AYMRPLGVGLFL 140
              RP GVGL +
Sbjct: 123 YGRRPYGVGLLI 134

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

Iteration: 1
 Score = 79.3 bits (194), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 46/135 (34%), Positives = 67/135 (49%), Gaps = 3/135 (2%)
Query: 7   GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSV 66
             YD     FSP GRLFQVEYA +A+K   VT +G+R      +V  K+  D+L  +   
Sbjct: 3   NNYDGDTVTFSPTGRLFQVEYALEAIKQGSVT-VGLRSNTHAVLVALKRNADELSSYQK- 60
Query: 67  THLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYT 126
             +    +++GL   G+  DAR L    R +       +  ++ V+     + DK+Q  T
Sbjct: 61  -KIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNT 119
Query: 127 QHAYMRPLGVGLFLI 141
           Q A  RP GVGL +I
Sbjct: 120 QSAGGRPYGVGLLII 134

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

Iteration: 1
 Score = 79.3 bits (194), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 46/135 (34%), Positives = 67/135 (49%), Gaps = 3/135 (2%)
Query: 7   GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSV 66
             YD     FSP GRLFQVEYA +A+K   VT +G+R      +V  K+  D+L  +   
Sbjct: 4   NNYDGDTVTFSPTGRLFQVEYALEAIKQGSVT-VGLRSNTHAVLVALKRNADELSSYQK- 61
Query: 67  THLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYT 126
             +    +++GL   G+  DAR L    R +       +  ++ V+     + DK+Q  T
Sbjct: 62  -KIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNT 120
Query: 127 QHAYMRPLGVGLFLI 141
           Q A  RP GVGL +I
Sbjct: 121 QSAGGRPYGVGLLII 135

>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 = 76.6 bits (187), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 45/135 (33%), Positives = 66/135 (48%), Gaps = 3/135 (2%)
Query: 7   GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSV 66
             YD     FSP GRLFQVEYA +A+K   VT +G+R      +V  K+  D+L  +   
Sbjct: 4   NNYDGDTVTFSPTGRLFQVEYALEAIKQGSVT-VGLRSNTHAVLVALKRNADELSSYQK- 61
Query: 67  THLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYT 126
             +    +++GL   G+  DAR L    R +       +  ++ V+     + DK+Q  T
Sbjct: 62  -KIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNT 120
Query: 127 QHAYMRPLGVGLFLI 141
           Q    RP GVGL +I
Sbjct: 121 QSYGGRPYGVGLLII 135

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

Iteration: 1
 Score = 76.6 bits (187), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 45/135 (33%), Positives = 66/135 (48%), Gaps = 3/135 (2%)
Query: 7   GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSV 66
             YD     FSP GRLFQVEYA +A+K   VT +G+R      +V  K+  D+L  +   
Sbjct: 5   NNYDGDTVTFSPTGRLFQVEYALEAIKQGSVT-VGLRSNTHAVLVALKRNADELSSYQK- 62
Query: 67  THLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYT 126
             +    +++GL   G+  DAR L    R +       +  ++ V+     + DK+Q  T
Sbjct: 63  -KIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNT 121
Query: 127 QHAYMRPLGVGLFLI 141
           Q    RP GVGL +I
Sbjct: 122 QSYGGRPYGVGLLII 136

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

Iteration: 1
 Score = 76.6 bits (187), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 45/135 (33%), Positives = 66/135 (48%), Gaps = 3/135 (2%)
Query: 7   GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSV 66
             YD     FSP GRLFQVEYA +A+K   VT +G+R      +V  K+  D+L  +   
Sbjct: 3   NNYDGDTVTFSPTGRLFQVEYALEAIKQGSVT-VGLRSNTHAVLVALKRNADELSSYQK- 60
Query: 67  THLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYT 126
             +    +++GL   G+  DAR L    R +       +  ++ V+     + DK+Q  T
Sbjct: 61  -KIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNT 119
Query: 127 QHAYMRPLGVGLFLI 141
           Q    RP GVGL +I
Sbjct: 120 QSYGGRPYGVGLLII 134

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

Iteration: 1
 Score = 76.3 bits (186), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 46/133 (34%), Positives = 72/133 (54%), Gaps = 2/133 (1%)
Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           Y   +T FSP G+L Q++YA  AVK  GVTS+G++  + V + T+KK    L    +++ 
Sbjct: 5   YSFSLTTFSPSGKLGQIDYALTAVKQ-GVTSLGIKATNGVVIATEKKSSSPLAMSETLSK 63
Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEA-AEFRFKYGYEMPVDVLAKWIADKSQVYTQ 127
           +  +T  +G + +GM  D R LV ++R  A   ++  YG   P  +L   +A   Q  TQ
Sbjct: 64  VSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQ 123
Query: 128 HAYMRPLGVGLFL 140
              +RP GV L +
Sbjct: 124 SGGVRPFGVSLLI 136

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

Iteration: 1
 Score = 72.0 bits (175), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 41/120 (34%), Positives = 69/120 (57%), Gaps = 2/120 (1%)
Query: 22  LFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLD-HTSVTHLFPITKYLGLLA 80
           +FQVEYA +AVK  G  ++GV+GK+ V +  +++   KL D   + + +  I  ++ L  
Sbjct: 1   IFQVEYALEAVKR-GTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSKVSKIDSHVVLSF 59
Query: 81  TGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFL 140
           +G+ AD+R L+++AR EA   R      + V+ L +++A   Q YTQ   +RP GV   +
Sbjct: 60  SGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLI 119

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

Iteration: 1
 Score = 62.4 bits (150), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 39/118 (33%), Positives = 63/118 (53%), Gaps = 2/118 (1%)
Query: 24  QVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGM 83
           Q++YA  AVK  GVTS+G++  + V + T+KK    L    +++ +  +T  +G + +GM
Sbjct: 1   QIDYALTAVKQ-GVTSLGIKATNGVVIATEKKSSSPLAMSETLSKVSLLTPDIGAVYSGM 59
Query: 84  TADARTLVQQARYEA-AEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFL 140
             D R LV ++R  A   ++  YG   P  +L   +A   Q  TQ   +RP GV L +
Sbjct: 60  GPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLI 117

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 29/103 (28%), Positives = 53/103 (51%), Gaps = 1/103 (0%)
Query: 36  GVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQA 94
           G T++G+  KD+V + T+++V  +  + H +   LF I  Y G+   G+  DA+ LV+  
Sbjct: 8   GTTTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYM 67
Query: 95  RYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVG 137
           + E   +R +    MP++ +A  +++         YM  L VG
Sbjct: 68  KAELELYRLQRRVNMPIEAVATLLSNMLNQVKYMPYMVQLLVG 110

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 29/103 (28%), Positives = 53/103 (51%), Gaps = 1/103 (0%)
Query: 36  GVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQA 94
           G T++G+  KD+V + T+++V  +  + H +   LF I  Y G+   G+  DA+ LV+  
Sbjct: 8   GTTTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYM 67
Query: 95  RYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVG 137
           + E   +R +    MP++ +A  +++         YM  L VG
Sbjct: 68  KAELELYRLQRRVNMPIEAVATLLSNMLNQVKYMPYMVQLLVG 110

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 28/101 (27%), Positives = 52/101 (51%), Gaps = 1/101 (0%)
Query: 38  TSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARY 96
           T++G+  KD+V + T+++V  +  + H +   LF I  Y G+   G+  DA+ LV+  + 
Sbjct: 2   TTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKA 61
Query: 97  EAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVG 137
           E   +R +    MP++ +A  +++         YM  L VG
Sbjct: 62  ELELYRLQRRVNMPIEAVATLLSNMLNQVKYMPYMVQLLVG 102

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	149
1iru_A	246	20S proteasome; cell cycle, immune response, prote	1e-82
1ryp_A	243	20S proteasome; multicatalytic proteinase, protein	4e-79
3nzj_F	288	Proteasome component C1; ubiquitin, protein degrad	5e-77
1iru_B	233	20S proteasome; cell cycle, immune response, prote	7e-77
1iru_D	248	20S proteasome; cell cycle, immune response, prote	1e-76
1ryp_G	244	20S proteasome; multicatalytic proteinase, protein	3e-76
1ryp_B	250	20S proteasome; multicatalytic proteinase, protein	9e-75
1iru_E	241	20S proteasome; cell cycle, immune response, prote	7e-73
1iru_F	263	20S proteasome; cell cycle, immune response, prote	7e-73
3h4p_A	264	Proteasome subunit alpha; core particle, cytoplasm	4e-72
1yar_A	233	Proteasome alpha subunit; proteasome 20S, PA26 pro	2e-71
1iru_G	254	20S proteasome; cell cycle, immune response, prote	2e-70
1j2p_A	246	Alpha-ring, proteasome alpha subunit; hydrolase; 2	3e-70
1ryp_D	241	20S proteasome; multicatalytic proteinase, protein	2e-69
1ryp_F	233	20S proteasome; multicatalytic proteinase, protein	2e-68
1iru_C	261	20S proteasome; cell cycle, immune response, prote	5e-68
1ryp_C	244	20S proteasome; multicatalytic proteinase, protein	3e-66
1ryp_E	242	20S proteasome; multicatalytic proteinase, protein	4e-66
1q5q_A	259	Proteasome alpha-type subunit 1; proteasome assemb	6e-17
3mi0_A	248	Proteasome subunit alpha; enzyme inhibitors, lacto	3e-16
3unf_H	234	Proteasome subunit beta type-10; antigen presentat	1e-12
3nzj_H	261	Proteasome component PUP1; ubiquitin, protein degr	4e-12
1q5r_H	294	Proteasome beta-type subunit 1; proteasome assembl	7e-11
1ryp_I	222	20S proteasome; multicatalytic proteinase, protein	2e-10
1iru_I	234	20S proteasome; cell cycle, immune response, prote	1e-09
1yar_H	217	Proteasome beta subunit; proteasome 20S, PA26 prot	4e-09
1q5q_H	235	Proteasome beta-type subunit 1; proteasome assembl	5e-09
2jay_A	291	Proteasome; hydrolase; 1.99A {Mycobacterium tuberc	1e-08
1ryp_K	198	20S proteasome; multicatalytic proteinase, protein	1e-08
1iru_K	201	20S proteasome; cell cycle, immune response, prote	1e-07
3nzj_K	287	Proteasome component PRE2; ubiquitin, protein degr	5e-07
1j2q_H	202	Proteasome beta subunit; ubiquitin, CP, hydrolase;	8e-06
1iru_M	213	20S proteasome; cell cycle, immune response, prote	1e-05
1g0u_M	266	Proteasome component PRE4; ubiquitin, degradation,	1e-05
1ryp_L	212	20S proteasome; multicatalytic proteinase, protein	2e-05
3unf_N	199	Proteasome subunit beta type-9; antigen presentati	2e-05
1iru_J	205	20S proteasome; cell cycle, immune response, prote	5e-05
1iru_L	204	20S proteasome; cell cycle, immune response, prote	5e-05
1iru_H	205	20S proteasome; cell cycle, immune response, prote	8e-05
1ryp_N	233	20S proteasome; multicatalytic proteinase, protein	9e-05
1ryp_M	222	20S proteasome; multicatalytic proteinase, protein	1e-04
1ryp_M	222	20S proteasome; multicatalytic proteinase, protein	1e-04
1ryp_J	204	20S proteasome; multicatalytic proteinase, protein	2e-04

>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 =  242 bits (620), Expect = 1e-82
 Identities = 97/141 (68%), Positives = 118/141 (83%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSRGS  G+DRHITIFSPEGRL+QVEYAFKA+   G+TS+ VRGKD   +VTQKKVPDKL
Sbjct: 1   MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL 60

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           LD ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD
Sbjct: 61  LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD 120

Query: 121 KSQVYTQHAYMRPLGVGLFLI 141
            SQVYTQ+A MRPLG  + LI
Sbjct: 121 ISQVYTQNAEMRPLGCCMILI 141

>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 =  233 bits (596), Expect = 4e-79
 Identities = 82/135 (60%), Positives = 104/135 (77%)

Query: 7   GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSV 66
            GYDRHITIFSPEGRL+QVEYAFKA     + S+ VRGKD   V++QKKVPDKLLD T+V
Sbjct: 1   AGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPTTV 60

Query: 67  THLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYT 126
           +++F I++ +G++  G   DAR    +A+ EAAEFR+KYGY+MP DVLAK +A+ SQ+YT
Sbjct: 61  SYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYT 120

Query: 127 QHAYMRPLGVGLFLI 141
           Q AYMRPLGV L  +
Sbjct: 121 QRAYMRPLGVILTFV 135

>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 =  229 bits (586), Expect = 5e-77
 Identities = 49/141 (34%), Positives = 74/141 (52%), Gaps = 2/141 (1%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           M+   G GYD   ++FSP+GR FQVEYA KAV+    TSIG++  D V    +K +  KL
Sbjct: 1   MT-SIGTGYDLSNSVFSPDGRNFQVEYAVKAVENGT-TSIGIKCNDGVVFAVEKLITSKL 58

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           L       +  + +++G + +G+  D R LV + R EAA F+  Y   +P+   A  +  
Sbjct: 59  LVPQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQ 118

Query: 121 KSQVYTQHAYMRPLGVGLFLI 141
             Q +T +  +RP GV     
Sbjct: 119 YVQAHTLYNSVRPFGVSTIFG 139

>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 =  227 bits (580), Expect = 7e-77
 Identities = 52/137 (37%), Positives = 75/137 (54%), Gaps = 1/137 (0%)

Query: 5   SGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHT 64
           +  GY   +T FSP G+L Q+EYA  AV      S+G++  + V + T+KK    L D  
Sbjct: 1   AERGYSFSLTTFSPSGKLVQIEYALAAVAGGA-PSVGIKAANGVVLATEKKQKSILYDER 59

Query: 65  SVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQV 124
           SV  + PITK++GL+ +GM  D R LV +AR  A ++   Y   +P   L + +A   Q 
Sbjct: 60  SVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQE 119

Query: 125 YTQHAYMRPLGVGLFLI 141
           YTQ   +RP GV L + 
Sbjct: 120 YTQSGGVRPFGVSLLIC 136

>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 =  226 bits (579), Expect = 1e-76
 Identities = 52/134 (38%), Positives = 77/134 (57%), Gaps = 1/134 (0%)

Query: 8   GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVT 67
            YDR IT+FSP+G LFQVEYA +AVK    T++GVRG+D V +  +KK   KL D  +V 
Sbjct: 2   SYDRAITVFSPDGHLFQVEYAQEAVKKGS-TAVGVRGRDIVVLGVEKKSVAKLQDERTVR 60

Query: 68  HLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQ 127
            +  +   + +   G+TADAR ++ +AR E    R      + V+ + ++IA   Q YTQ
Sbjct: 61  KICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQ 120

Query: 128 HAYMRPLGVGLFLI 141
               RP G+   ++
Sbjct: 121 SNGRRPFGISALIV 134

>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 =  225 bits (577), Expect = 3e-76
 Identities = 48/136 (35%), Positives = 72/136 (52%), Gaps = 1/136 (0%)

Query: 6   GGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTS 65
           G GYD   ++FSP+GR FQVEYA KAV+    TSIG++  D V    +K +  KLL    
Sbjct: 1   GTGYDLSNSVFSPDGRNFQVEYAVKAVENGT-TSIGIKCNDGVVFAVEKLITSKLLVPQK 59

Query: 66  VTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVY 125
              +  + +++G + +G+  D R LV + R EAA F+  Y   +P+   A  +    Q +
Sbjct: 60  NVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAH 119

Query: 126 TQHAYMRPLGVGLFLI 141
           T +  +RP GV     
Sbjct: 120 TLYNSVRPFGVSTIFG 135

>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 =  222 bits (568), Expect = 9e-75
 Identities = 45/142 (31%), Positives = 72/142 (50%), Gaps = 6/142 (4%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           M+      Y   +T FSP G+L Q++YA  AVK    TS+G++  + V + T+KK    L
Sbjct: 1   MTDR----YSFSLTTFSPSGKLGQIDYALTAVKQGV-TSLGIKATNGVVIATEKKSSSPL 55

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEA-AEFRFKYGYEMPVDVLAKWIA 119
               +++ +  +T  +G + +GM  D R LV ++R  A   ++  YG   P  +L   +A
Sbjct: 56  AMSETLSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVA 115

Query: 120 DKSQVYTQHAYMRPLGVGLFLI 141
              Q  TQ   +RP GV L + 
Sbjct: 116 KIMQEATQSGGVRPFGVSLLIA 137

>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 =  217 bits (555), Expect = 7e-73
 Identities = 46/142 (32%), Positives = 79/142 (55%), Gaps = 6/142 (4%)

Query: 5   SGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHT 64
           +   YDR +  FSPEGRLFQVEY  +A+K    T+IG++  + VC+  +K++   L++ +
Sbjct: 4   TRSEYDRGVNTFSPEGRLFQVEYDIEAIKLGS-TAIGIQTSEGVCLAVEKRITSPLMEPS 62

Query: 65  SVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQV 124
           S+  +  I  ++G   +G+ ADA+TL+ +AR E     F Y   M V+ + + +++ +  
Sbjct: 63  SIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQ 122

Query: 125 YTQH-----AYMRPLGVGLFLI 141
           + +      A  RP GV L   
Sbjct: 123 FGEEDADPGAMSRPFGVALLFG 144

>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 =  217 bits (556), Expect = 7e-73
 Identities = 47/141 (33%), Positives = 73/141 (51%), Gaps = 6/141 (4%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           M R     YD  +T++SP+GR+ Q+EYA +AVK     ++G++ K    +V  K+   +L
Sbjct: 1   MFRN---QYDNDVTVWSPQGRIHQIEYAMEAVKQGS-ATVGLKSKTHAVLVALKRAQSEL 56

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
                   +  +  ++G+   G+TADAR L    R E  + RF +   +PV  L   I  
Sbjct: 57  AA--HQKKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGS 114

Query: 121 KSQVYTQHAYMRPLGVGLFLI 141
           K+Q+ TQ    RP GVGL + 
Sbjct: 115 KTQIPTQRYGRRPYGVGLLIA 135

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

 Score =  216 bits (552), Expect = 4e-72
 Identities = 60/141 (42%), Positives = 86/141 (60%), Gaps = 1/141 (0%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           M       YDR IT+FSPEGRL+QVEYA +AV+    T+IG+  KD V +   +++  KL
Sbjct: 4   MQMVPPSAYDRAITVFSPEGRLYQVEYAREAVRRGT-TAIGIACKDGVVLAVDRRITSKL 62

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           +   S+  +F I  ++    +G+ ADAR L+ +AR EA  +R  YG E+ +++LAK I D
Sbjct: 63  VKIRSIEKIFQIDDHVAAATSGLVADARVLIDRARLEAQIYRLTYGEEISIEMLAKKICD 122

Query: 121 KSQVYTQHAYMRPLGVGLFLI 141
             Q YTQH  +RP GV L + 
Sbjct: 123 IKQAYTQHGGVRPFGVSLLIA 143

>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 =  213 bits (544), Expect = 2e-71
 Identities = 56/141 (39%), Positives = 86/141 (60%), Gaps = 2/141 (1%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           M +G    Y R IT+FSP+GRLFQVEYA +AVK    T++G++  + V +++ KKV  +L
Sbjct: 1   MQQGQMA-YSRAITVFSPDGRLFQVEYAREAVKKGS-TALGMKFANGVLLISDKKVRSRL 58

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           ++  S+  +  I  Y+  + +G+ ADAR LV  AR  A + +  YG  + ++ L K +AD
Sbjct: 59  IEQNSIEKIQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVAD 118

Query: 121 KSQVYTQHAYMRPLGVGLFLI 141
           + Q YTQ+  +RP GV L   
Sbjct: 119 QMQQYTQYGGVRPYGVSLIFA 139

>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 =  211 bits (540), Expect = 2e-70
 Identities = 57/138 (41%), Positives = 81/138 (58%), Gaps = 1/138 (0%)

Query: 4   GSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDH 63
             G GYD   + FSP+GR+FQVEYA KAV+ +  T+IG+R KD V    +K V  KL + 
Sbjct: 2   SIGTGYDLSASTFSPDGRVFQVEYAMKAVENSS-TAIGIRCKDGVVFGVEKLVLSKLYEE 60

Query: 64  TSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQ 123
            S   LF + +++G+   G+ ADAR+L   AR EA+ FR  +GY +P+  LA  +A    
Sbjct: 61  GSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVH 120

Query: 124 VYTQHAYMRPLGVGLFLI 141
            YT ++ +RP G    L 
Sbjct: 121 AYTLYSAVRPFGCSFMLG 138

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

 Score =  211 bits (538), Expect = 3e-70
 Identities = 60/141 (42%), Positives = 86/141 (60%), Gaps = 2/141 (1%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           M      GYDR IT+FSP+GRLFQVEYA +AVK    T+IG++ K+ V ++  K+V  KL
Sbjct: 1   MHL-PQMGYDRAITVFSPDGRLFQVEYAREAVKRGA-TAIGIKCKEGVILIADKRVGSKL 58

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIAD 120
           L+  ++  ++ I +++    +G+ ADAR L+ +AR EA   R  Y   + V  LAK I D
Sbjct: 59  LEKDTIEKIYKIDEHICAATSGLVADARVLIDRARIEAQINRLTYDIPITVKELAKKICD 118

Query: 121 KSQVYTQHAYMRPLGVGLFLI 141
             Q YTQ+  +RP GV L + 
Sbjct: 119 FKQQYTQYGGVRPFGVSLLIA 139

>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 =  208 bits (531), Expect = 2e-69
 Identities = 49/135 (36%), Positives = 80/135 (59%), Gaps = 2/135 (1%)

Query: 8   GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDH-TSV 66
           GYDR ++IFSP+G +FQVEYA +AVK     ++GV+GK+ V +  +++   KL D   + 
Sbjct: 1   GYDRALSIFSPDGHIFQVEYALEAVKRGT-CAVGVKGKNCVVLGCERRSTLKLQDTRITP 59

Query: 67  THLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYT 126
           + +  I  ++ L  +G+ AD+R L+++AR EA   R      + V+ L +++A   Q YT
Sbjct: 60  SKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYT 119

Query: 127 QHAYMRPLGVGLFLI 141
           Q   +RP GV   + 
Sbjct: 120 QSGGVRPFGVSTLIA 134

>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 =  205 bits (525), Expect = 2e-68
 Identities = 43/134 (32%), Positives = 64/134 (47%), Gaps = 3/134 (2%)

Query: 8   GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVT 67
            YD     FSP GRLFQVEYA +A+K     ++G+R      +V  K+  D+L       
Sbjct: 4   NYDGDTVTFSPTGRLFQVEYALEAIKQGS-VTVGLRSNTHAVLVALKRNADELSS--YQK 60

Query: 68  HLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQ 127
            +    +++GL   G+  DAR L    R +       +  ++ V+     + DK+Q  TQ
Sbjct: 61  KIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQ 120

Query: 128 HAYMRPLGVGLFLI 141
               RP GVGL +I
Sbjct: 121 SYGGRPYGVGLLII 134

>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 =  205 bits (524), Expect = 5e-68
 Identities = 51/142 (35%), Positives = 74/142 (52%), Gaps = 6/142 (4%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           MSR     YD   TIFSPEGRL+QVEYA +A+  AG T +G+   D V +  +++   KL
Sbjct: 1   MSRR----YDSRTTIFSPEGRLYQVEYAMEAIGHAG-TCLGILANDGVLLAAERRNIHKL 55

Query: 61  LDHTSVTH-LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA 119
           LD    +  ++ + + +     G+T+DA  L  + R  A  +  +Y   +P + L   + 
Sbjct: 56  LDEVFFSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALC 115

Query: 120 DKSQVYTQHAYMRPLGVGLFLI 141
           D  Q YTQ    RP GV L  I
Sbjct: 116 DIKQAYTQFGGKRPFGVSLLYI 137

>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 =  200 bits (511), Expect = 3e-66
 Identities = 52/135 (38%), Positives = 78/135 (57%), Gaps = 2/135 (1%)

Query: 8   GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLD-HTSV 66
            YD   TIFSPEGRL+QVEYA +++  AG T+IG+   D + +  ++KV   LL+  TS 
Sbjct: 4   RYDSRTTIFSPEGRLYQVEYALESISHAG-TAIGIMASDGIVLAAERKVTSTLLEQDTST 62

Query: 67  THLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYT 126
             L+ +   + +   G+TADA  L+  AR  A  +   Y  ++PV++L + ++D  Q YT
Sbjct: 63  EKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYT 122

Query: 127 QHAYMRPLGVGLFLI 141
           QH  +RP GV     
Sbjct: 123 QHGGLRPFGVSFIYA 137

>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 =  200 bits (510), Expect = 4e-66
 Identities = 46/138 (33%), Positives = 78/138 (56%), Gaps = 7/138 (5%)

Query: 10  DRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHL 69
           DR ++ FSPEGRLFQVEY+ +A+K    T+IG+  K+ V +  +K+    LL+  S+  +
Sbjct: 1   DRGVSTFSPEGRLFQVEYSLEAIKLGS-TAIGIATKEGVVLGVEKRATSPLLESDSIEKI 59

Query: 70  FPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHA 129
             I +++G   +G+TADAR++++ AR  A      Y  ++ V+ L + + D +  + + A
Sbjct: 60  VEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGA 119

Query: 130 ------YMRPLGVGLFLI 141
                   RP GV L + 
Sbjct: 120 SGEERLMSRPFGVALLIA 137

>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 = 73.9 bits (181), Expect = 6e-17
 Identities = 24/131 (18%), Positives = 46/131 (35%), Gaps = 13/131 (9%)

Query: 17  SPEGRLFQ-VEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKY 75
           S E  +    E A K +   G + + +  +D V  V +          T++  +  +   
Sbjct: 8   SAEQIMRDRSELARKGIAR-GRSVVVLTFRDGVLFVAENPS-------TALHKVSELYDR 59

Query: 76  LGLLATGMTADARTLVQQARYEAAEFRFKYGYE-MPVDVLAKWIADK-SQVYTQHAYMRP 133
           LG  A G   +   L +     A    + Y    +    LA   A     ++T+    +P
Sbjct: 60  LGFAAVGKYNEFENLRRAGIVHADMRGYSYDRRDVTGRSLANAYAQTLGTIFTEQ--PKP 117

Query: 134 LGVGLFLIEIA 144
             V + + E+ 
Sbjct: 118 YEVEICVAEVG 128

>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 = 71.9 bits (176), Expect = 3e-16
 Identities = 24/134 (17%), Positives = 42/134 (31%), Gaps = 11/134 (8%)

Query: 17  SPEGRLFQ-VEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKY 75
           SPE  + +  E A K +     + + +     V  V +           S+  +  +   
Sbjct: 8   SPEQAMRERSELARKGIAR-AKSVVALAYAGGVLFVAENP-------SRSLQKISELYDR 59

Query: 76  LGLLATGMTADARTLVQQARYEAAEFRFKYGYE-MPVDVLAKWIADKSQVYTQHAYMRPL 134
           +G  A G   +   L +     A    + Y    +    LA   A            +P 
Sbjct: 60  VGFAAAGKFNEFDNLRRGGIQFADTRGYAYDRRDVTGRQLANVYAQTLGT-IFTEQAKPY 118

Query: 135 GVGLFLIEIAIPSE 148
            V L + E+A   E
Sbjct: 119 EVELCVAEVAHYGE 132

>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 = 61.9 bits (151), Expect = 1e-12
 Identities = 17/102 (16%), Positives = 32/102 (31%), Gaps = 6/102 (5%)

Query: 38  TSIGVRGKDSVCVVTQKKVPDKLL-DHTSVTHLFPITKYLGLLATGMTADARTLVQQARY 96
           T  G+  +D V +    +  +  +    S   +  I   +     G+ AD     + A  
Sbjct: 2   TIAGLVFRDGVILGADTRATNDSVVADKSCEKIHFIAPKIYCCGAGVAADTEMTTRMAAS 61

Query: 97  EAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGL 138
           +        G E  V  + + +      Y  H     +G  L
Sbjct: 62  KMELHALSTGREPRVATVTRILRQTLFRYQGH-----VGASL 98

>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 = 60.8 bits (148), Expect = 4e-12
 Identities = 17/126 (13%), Positives = 36/126 (28%), Gaps = 6/126 (4%)

Query: 16  FSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITK 74
           +     L +  +      + G T +GV+  + V +    +     ++   +   L  I+ 
Sbjct: 9   YQRNNFLAENSHTQPKATSTGTTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISP 68

Query: 75  YLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPL 134
            +     G  AD   + Q               E  V    + +           Y   +
Sbjct: 69  KIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQ-----HLFKYQGHI 123

Query: 135 GVGLFL 140
           G  L +
Sbjct: 124 GAYLIV 129

>1q5r_H Proteasome beta-type subunit 1; proteasome assembly, Pro-peptide, inter-subunit contacts, hydrolase; 3.10A {Rhodococcus erythropolis} SCOP: d.153.1.4 PDB: 2h6j_H Length = 294

 Score = 57.7 bits (139), Expect = 7e-11
 Identities = 24/134 (17%), Positives = 41/134 (30%), Gaps = 3/134 (2%)

Query: 8   GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSV 66
             +  I   S   R      +       G T + +  K  V +   ++     L+    V
Sbjct: 38  LPENRIGHRSHSTRGGDGMESGDLAPH-GTTIVALTYKGGVLLAGDRRATQGNLIASRDV 96

Query: 67  THLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYT 126
             ++   +Y      G    A  LV+    E   +    G  +  D  A  +A   +   
Sbjct: 97  EAVYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEGVPLTFDGKANRLASMVRGN- 155

Query: 127 QHAYMRPLGVGLFL 140
             A M+ L V   L
Sbjct: 156 LGAAMQGLAVVPLL 169

>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 = 55.4 bits (134), Expect = 2e-10
 Identities = 15/104 (14%), Positives = 30/104 (28%), Gaps = 6/104 (5%)

Query: 38  TSIGVRGKDSVCVVTQKKV-PDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARY 96
           T +GV+  + V +    +     ++   +   L  I+  +     G  AD   + Q    
Sbjct: 2   TIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGS 61

Query: 97  EAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFL 140
                      E  V    + +           Y   +G  L +
Sbjct: 62  NIELHSLYTSREPRVVSALQMLKQ-----HLFKYQGHIGAYLIV 100

>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 = 53.8 bits (130), Expect = 1e-09
 Identities = 16/104 (15%), Positives = 28/104 (26%), Gaps = 6/104 (5%)

Query: 38  TSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH-LFPITKYLGLLATGMTADARTLVQQARY 96
           T  GV  KD + +    +  + ++        +  I+  +     G  AD     Q    
Sbjct: 2   TIAGVVYKDGIVLGADTRATEGMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISS 61

Query: 97  EAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFL 140
                    G    V    + +           Y   +G  L L
Sbjct: 62  NLELHSLSTGRLPRVVTANRMLKQ-----MLFRYRGYIGAALVL 100

>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 = 52.2 bits (126), Expect = 4e-09
 Identities = 27/110 (24%), Positives = 54/110 (49%), Gaps = 6/110 (5%)

Query: 30  KAVKAAGVTSIGVRGKDSVCVVTQKKV-PDKLLDHTSVTHLFPITKYLGLLATGMTADAR 88
           + ++  G T++G+  KD+V + T+++V  +  + H +   LF I  Y G+   G+  DA+
Sbjct: 3   QTLET-GTTTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQ 61

Query: 89  TLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGL 138
            LV+  + E   +R +    MP++ +A  +++            P  V L
Sbjct: 62  VLVRYMKAELELYRLQRRVNMPIEAVATLLSNMLNQVK----YMPYMVQL 107

>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 = 52.1 bits (125), Expect = 5e-09
 Identities = 20/104 (19%), Positives = 35/104 (33%), Gaps = 2/104 (1%)

Query: 38  TSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARY 96
           T + +  K  V +   ++     L+    V  ++   +Y      G    A  LV+    
Sbjct: 2   TIVALTYKGGVLLAGDRRATQGNLIASRDVEKVYVTDEYSAAGIAGTAGIAIELVRLFAV 61

Query: 97  EAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFL 140
           E   +    G  +  D  A  +A   +     A M+ L V   L
Sbjct: 62  ELEHYEKIEGVPLTFDGKANRLASMVRGN-LGAAMQGLAVVPLL 104

>2jay_A Proteasome; hydrolase; 1.99A {Mycobacterium tuberculosis} PDB: 3mka_C 3mi0_C* 2fhg_H* 2fhh_H 3krd_C* 3mfe_G 3hfa_H* 3h6i_C 3h6f_C 3hf9_H 3mfe_H Length = 291

 Score = 51.5 bits (123), Expect = 1e-08
 Identities = 14/104 (13%), Positives = 30/104 (28%), Gaps = 2/104 (1%)

Query: 36  GVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQA 94
           G T + ++    V +   ++     ++    V  ++    Y      G  A A    +  
Sbjct: 57  GTTIVALKYPGGVVMAGDRRSTQGNMISGRDVRKVYITDDYTATGIAGTAAVAVEFARLY 116

Query: 95  RYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGL 138
             E   +    G  +        +A   +     A M+ L    
Sbjct: 117 AVELEHYEKLEGVPLTFAGKINRLAIMVRGNL-AAAMQGLLALP 159

>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 = 50.3 bits (121), Expect = 1e-08
 Identities = 15/113 (13%), Positives = 37/113 (32%), Gaps = 21/113 (18%)

Query: 38  TSIGVRGKDSVCV----------VTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADA 87
             +G+R +DSV +             K   DK            ++ +  +   G   D 
Sbjct: 3   IILGIRVQDSVILASSKAVTRGISVLKDSDDKT---------RQLSPHTLMSFAGEAGDT 53

Query: 88  RTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFL 140
               +  +     +  +  YE+    ++ ++  + ++       RP  V + +
Sbjct: 54  VQFAEYIQANIQLYSIREDYELSPQAVSSFV--RQELAKSIRSRRPYQVNVLI 104

>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 = 48.0 bits (115), Expect = 1e-07
 Identities = 23/113 (20%), Positives = 39/113 (34%), Gaps = 21/113 (18%)

Query: 38  TSIGVRGKDSVCV----------VTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADA 87
             IG++G D V V          V  K   DK+         F +++ + LL  G   D 
Sbjct: 3   YLIGIQGPDYVLVASDRVAASNIVQMKDDHDKM---------FKMSEKILLLCVGEAGDT 53

Query: 88  RTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFL 140
               +  +     ++ + GYE+     A +   +  +        P  V L L
Sbjct: 54  VQFAEYIQKNVQLYKMRNGYELSPTAAANFT--RRNLADCLRSRTPYHVNLLL 104

>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 = 46.7 bits (111), Expect = 5e-07
 Identities = 14/127 (11%), Positives = 36/127 (28%), Gaps = 5/127 (3%)

Query: 6   GGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKV-PDKLLDHT 64
                + +   + + R    +         G T++  R +  + V    +      +   
Sbjct: 49  IASPQQFLRAHTDDSRNPDCKIKIAH----GTTTLAFRFQGGIIVAVDSRATAGNWVASQ 104

Query: 65  SVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQV 124
           +V  +  I  +L     G  AD +        +      +    + V   +K +++    
Sbjct: 105 TVKKVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQ 164

Query: 125 YTQHAYM 131
           Y      
Sbjct: 165 YKGAGLS 171

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

 Score = 42.6 bits (101), Expect = 8e-06
 Identities = 20/109 (18%), Positives = 38/109 (34%), Gaps = 19/109 (17%)

Query: 38  TSIGVRGKDSVCVV--------TQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADART 89
           T++G+  KD   VV            +  K     +   ++ I   + +   G   DA+ 
Sbjct: 2   TTVGLVCKD--GVVMATEKRATMGNFIASK-----AAKKIYQIADRMAMTTAGSVGDAQF 54

Query: 90  LVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGL 138
           L +  + EA  +  +   +  V  +A   ++    Y       P  V L
Sbjct: 55  LARIIKIEANLYEIRRERKPTVRAIATLTSNLLNSYRYF----PYLVQL 99

>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 = 42.2 bits (100), Expect = 1e-05
 Identities = 15/116 (12%), Positives = 32/116 (27%), Gaps = 25/116 (21%)

Query: 36  GVTSIGVRGKDSVCVV--------TQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADA 87
           G T + + G+D    +            +  +          + +T    +  +G   D 
Sbjct: 9   GGTILAIAGED--FAIVASDTRLSEGFSIHTR-----DSPKCYKLTDKTVIGCSGFHGDC 61

Query: 88  RTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMR---PLGVGLFL 140
            TL +        ++      M    +A  ++          Y R   P  V   +
Sbjct: 62  LTLTKIIEARLKMYKHSNNKAMTTGAIAAMLS-------TILYSRRFFPYYVYNII 110

>1g0u_M Proteasome component PRE4; ubiquitin, degradation, protease, NTN-hydrolase; 2.40A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 2zcy_M* 3bdm_M* 3mg6_M* 3mg7_M* 3mg8_M* 3nzj_M* 3nzw_M* 3nzx_M* Length = 266

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 15/114 (13%), Positives = 39/114 (34%), Gaps = 18/114 (15%)

Query: 36  GVTSIGVRGKDSVCVVTQKKVPDKLL------DHTSVTHLFPITKYLGLLATGMTADART 89
           G + I ++  + V +       D L           V  L P+     +  +G  +D + 
Sbjct: 41  GTSVISMKYDNGVIIAA-----DNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQH 95

Query: 90  LVQQARYEAAEFRFKY-----GYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGL 138
           + +  +    E  +          +    + +++   + +Y + + M PL   +
Sbjct: 96  IERLLKDLVTENAYDNPLADAEEALEPSYIFEYL--ATVMYQRRSKMNPLWNAI 147

>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 = 41.5 bits (98), Expect = 2e-05
 Identities = 12/95 (12%), Positives = 29/95 (30%), Gaps = 1/95 (1%)

Query: 38  TSIGVRGKDSVCVVTQKKV-PDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARY 96
           T++  R +  + V    +      +   +V  +  I  +L     G  AD +        
Sbjct: 2   TTLAFRFQGGIIVAVDSRATAGNWVASQTVKRVIEINPFLLGTMAGGAADCQFWETWLGS 61

Query: 97  EAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYM 131
           +      +    + V   +K +++    Y      
Sbjct: 62  QCRLHELREKERISVAAASKILSNLVYQYKGAGLS 96

>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 = 41.4 bits (98), Expect = 2e-05
 Identities = 18/109 (16%), Positives = 32/109 (29%), Gaps = 20/109 (18%)

Query: 38  TSIGVRGKDSVCVV--------TQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADART 89
           T + V       VV            V ++         L P+ + +    +G  ADA+ 
Sbjct: 2   TIMAVEFDG--GVVVGSDSRVSAGTAVVNR-----VFDKLSPLHQRIFCALSGSAADAQA 54

Query: 90  LVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGL 138
           +   A Y+      +      V   A  + +       + Y   L   L
Sbjct: 55  IADMAAYQLELHGLELEEPPLVLAAANVVKN-----ISYKYREDLLAHL 98

>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 = 40.6 bits (96), Expect = 5e-05
 Identities = 19/114 (16%), Positives = 39/114 (34%), Gaps = 25/114 (21%)

Query: 36  GVTSIGVRGKDSVCVV--------TQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADA 87
           G   + ++GK+  CV          Q ++            +FP+   L +   G+  D 
Sbjct: 8   GGAVMAMKGKN--CVAIAADRRFGIQAQLVTT-----DFQKIFPMGDRLYIGLAGLATDV 60

Query: 88  RTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMR---PLGVGL 138
           +T+ Q+ ++    +  K G ++    L   +A          Y +   P     
Sbjct: 61  QTVAQRLKFRLNLYELKEGRQIKPYTLMSMVA-------NLLYEKRFGPYYTEP 107

>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 = 40.3 bits (95), Expect = 5e-05
 Identities = 12/72 (16%), Positives = 23/72 (31%), Gaps = 4/72 (5%)

Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +  I  YL     G  AD     +    +   +  +    + V   +K +A+    Y   
Sbjct: 34  VIEINPYLLGTMAGGAADCSFWERLLARQCRIYELRNKERISVAAASKLLANMVYQYKGM 93

Query: 129 AYMRPLGVGLFL 140
                L +G  +
Sbjct: 94  ----GLSMGTMI 101

>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 = 39.9 bits (94), Expect = 8e-05
 Identities = 12/72 (16%), Positives = 22/72 (30%), Gaps = 5/72 (6%)

Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           L PI   +    +G  AD + +     Y+      +      V   A    +       +
Sbjct: 34  LTPIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKE-----MCY 88

Query: 129 AYMRPLGVGLFL 140
            Y   L  G+ +
Sbjct: 89  RYREDLMAGIII 100

>1ryp_N 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_N* 1jd2_M* 1g65_M 1vsy_N 1z7q_N 2f16_M* 2fak_M* 2fny_M* 2gpl_M* 3d29_M* 3dy3_M* 3dy4_M* 3e47_M* 3gpj_M* 3gpt_M* 3gpw_M* 3hye_M* 3l5q_R 3mg0_M* 3mg4_M* ... Length = 233

 Score = 40.0 bits (94), Expect = 9e-05
 Identities = 15/114 (13%), Positives = 39/114 (34%), Gaps = 18/114 (15%)

Query: 36  GVTSIGVRGKDSVCVVTQKKVPDKLL------DHTSVTHLFPITKYLGLLATGMTADART 89
           G + I ++  + V +       D L           V  L P+     +  +G  +D + 
Sbjct: 8   GTSVISMKYDNGVIIAA-----DNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQH 62

Query: 90  LVQQARYEAAEFRFKY-----GYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGL 138
           + +  +    E  +          +    + +++   + +Y + + M PL   +
Sbjct: 63  IERLLKDLVTENAYDNPLADAEEALEPSYIFEYL--ATVMYQRRSKMNPLWNAI 114

>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 = 39.6 bits (93), Expect = 1e-04
 Identities = 17/107 (15%), Positives = 35/107 (32%), Gaps = 20/107 (18%)

Query: 36  GVTSIGVRGKDSVCV----------VTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTA 85
           G T +G+ G+D   +              +   K+         F     + + A G  A
Sbjct: 9   GGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKV---------FDCGDNIVMSANGFAA 59

Query: 86  DARTLVQQARYEAAEFRFKY-GYEMPVDVLAKWIADKSQVYTQHAYM 131
           D   LV++ +     + F +   ++ ++  A+ I           Y 
Sbjct: 60  DGDALVKRFKNSVKWYHFDHNDKKLSINSAARNIQHLLYGKRFFPYY 106

>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 = 39.1 bits (92), Expect = 2e-04
 Identities = 20/112 (17%), Positives = 35/112 (31%), Gaps = 22/112 (19%)

Query: 36  GVTSIGVRGKDSVCVVTQKKVPDK------LLDHTSVTHLFPITKYLGLLATGMTADART 89
           G   + + GKD V +       D       L        +F        +  G+  D  T
Sbjct: 8   GGIVVAMTGKDCVAIAC-----DLRLGSQSLGVSNKFEKIFHYGHVFLGIT-GLATDVTT 61

Query: 90  LVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMR---PLGVGL 138
           L +  RY+   ++ K    +  +   + ++          Y R   P  VG 
Sbjct: 62  LNEMFRYKTNLYKLKEERAIEPETFTQLVS-------SSLYERRFGPYFVGP 106

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	149
3nzj_F	288	Proteasome component C1; ubiquitin, protein degrad	100.0
3h4p_A	264	Proteasome subunit alpha; core particle, cytoplasm	100.0
1ryp_A	243	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_A	246	20S proteasome; cell cycle, immune response, prote	100.0
1iru_G	254	20S proteasome; cell cycle, immune response, prote	100.0
1iru_B	233	20S proteasome; cell cycle, immune response, prote	100.0
1yar_A	233	Proteasome alpha subunit; proteasome 20S, PA26 pro	100.0
1ryp_G	244	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_D	248	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_C	244	20S proteasome; multicatalytic proteinase, protein	100.0
1ryp_D	241	20S proteasome; multicatalytic proteinase, protein	100.0
1ryp_F	233	20S proteasome; multicatalytic proteinase, protein	100.0
1j2p_A	246	Alpha-ring, proteasome alpha subunit; hydrolase; 2	100.0
1iru_C	261	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_B	250	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_F	263	20S proteasome; cell cycle, immune response, prote	100.0
1iru_E	241	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_E	242	20S proteasome; multicatalytic proteinase, protein	100.0
1q5q_A	259	Proteasome alpha-type subunit 1; proteasome assemb	100.0
3mi0_A	248	Proteasome subunit alpha; enzyme inhibitors, lacto	99.97
2jay_A	291	Proteasome; hydrolase; 1.99A {Mycobacterium tuberc	99.97
1q5r_H	294	Proteasome beta-type subunit 1; proteasome assembl	99.96
1ryp_N	233	20S proteasome; multicatalytic proteinase, protein	99.96
1yar_H	217	Proteasome beta subunit; proteasome 20S, PA26 prot	99.96
1iru_M	213	20S proteasome; cell cycle, immune response, prote	99.96
1iru_N	219	20S proteasome; cell cycle, immune response, prote	99.96
3nzj_K	287	Proteasome component PRE2; ubiquitin, protein degr	99.96
1g0u_M	266	Proteasome component PRE4; ubiquitin, degradation,	99.96
3h4p_a	219	Proteasome subunit beta; core particle, cytoplasm,	99.96
1q5q_H	235	Proteasome beta-type subunit 1; proteasome assembl	99.96
1j2q_H	202	Proteasome beta subunit; ubiquitin, CP, hydrolase;	99.96
1ryp_H	205	20S proteasome; multicatalytic proteinase, protein	99.96
1ryp_M	222	20S proteasome; multicatalytic proteinase, protein	99.96
1ryp_K	198	20S proteasome; multicatalytic proteinase, protein	99.95
1iru_H	205	20S proteasome; cell cycle, immune response, prote	99.95
3nzj_H	261	Proteasome component PUP1; ubiquitin, protein degr	99.95
1ryp_J	204	20S proteasome; multicatalytic proteinase, protein	99.95
1ryp_L	212	20S proteasome; multicatalytic proteinase, protein	99.95
1iru_J	205	20S proteasome; cell cycle, immune response, prote	99.95
3unf_N	199	Proteasome subunit beta type-9; antigen presentati	99.95
1iru_L	204	20S proteasome; cell cycle, immune response, prote	99.95
1iru_K	201	20S proteasome; cell cycle, immune response, prote	99.95
3unf_H	234	Proteasome subunit beta type-10; antigen presentat	99.94
1ryp_I	222	20S proteasome; multicatalytic proteinase, protein	99.94
1iru_I	234	20S proteasome; cell cycle, immune response, prote	99.94
2z3b_A	180	ATP-dependent protease HSLV; N-terminal nucleophIl	99.88
1m4y_A	171	ATP-dependent protease HSLV; N-terminal catalytic	99.87
1g3k_A	174	ATP-dependent protease HSLV; hydrolase; 1.90A {Hae	99.86

>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=6.7e-47  Score=299.25  Aligned_cols=144  Identities=35%  Similarity=0.547  Sum_probs=135.4

Q ss_pred             CCCCCCCCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEE
Q 031996            1 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLA   80 (149)
Q Consensus         1 m~~~~~~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~   80 (149)
                      || .+|++||+++|+||||||+||||||+||+++ |+|+|||+++||||||+|++.++.++..+..+||++|++|++|++
T Consensus         1 m~-~~~~~yd~~~t~fSP~Grl~QvEYA~kAv~~-GtT~Vgik~kdGVVlAaD~r~t~gl~~~~~~~KI~~I~d~i~~~~   78 (288)
T 3nzj_F            1 MT-SIGTGYDLSNSVFSPDGRNFQVEYAVKAVEN-GTTSIGIKCNDGVVFAVEKLITSKLLVPQKNVKIQVVDRHIGCVY   78 (288)
T ss_dssp             -----CCCTTSSTTCCCTTSCCHHHHHHHHHHHT-SCCEEEEEETTEEEEEEEEEECCTTBCTTCSCCCEEETTTEEEEE
T ss_pred             CC-CCcCCccCCcccCCCCCchHHHHHHHHHHhc-CCcEEEEEECCEEEEEEcCCcccCCccccccceEEEEcCCEEEEe
Confidence            88 4999999999999999999999999999997 999999999999999999999977776667899999999999999


Q ss_pred             eccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           81 TGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        81 sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      ||+.+|++.+++++|.+++.|+++++++|+++.+|+++++++|.||+++++|||+|++||||||++
T Consensus        79 aG~~aD~~~l~~~lr~e~~~y~~~~~~~i~v~~lA~~l~~~l~~yt~~~~~rP~gv~~lvaG~D~~  144 (288)
T 3nzj_F           79 SGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGGVDKN  144 (288)
T ss_dssp             EECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSCTTBCCCCEEEEEEEEETT
T ss_pred             cCcHHHHHHHHHHHHHHHHHHHHHcCCcCCHHHHHHHHHHHHHHHHHhccCCCceEEEEEEEEeCC
Confidence            999999999999999999999999999999999999999999999999899999999999999974

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

Probab=100.00  E-value=3.2e-47  Score=297.91  Aligned_cols=145  Identities=43%  Similarity=0.713  Sum_probs=129.3

Q ss_pred             CCCCCCCCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEE
Q 031996            1 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLA   80 (149)
Q Consensus         1 m~~~~~~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~   80 (149)
                      |...++++||+++|+|||||||||||||++|+++ |+|+|||+++||||||+|++.+++++.+++.+||++|++|++|++
T Consensus         4 ~~~~~~~~yd~~~t~fSp~Grl~QvEYA~~av~~-Gtt~vgi~~~dgVVlaaD~r~~~~li~~~~~~KI~~i~d~i~~~~   82 (264)
T 3h4p_A            4 MQMVPPSAYDRAITVFSPEGRLYQVEYAREAVRR-GTTAIGIACKDGVVLAVDRRITSKLVKIRSIEKIFQIDDHVAAAT   82 (264)
T ss_dssp             ------------CCCCCSSSSCHHHHHHHHHHHH-SCCEEEECCSSEEEEEEECCCCSTTBCTTTCCCEEEEETTEEEEE
T ss_pred             CcCCCccccCCCcceECCCCeeHHHHhHHHHHhc-CCcEEEEEECCEEEEEEecCccCCccccCccccEEEecCcEEEEe
Confidence            5556788999999999999999999999999986 999999999999999999999988888889999999999999999


Q ss_pred             eccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           81 TGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        81 sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      ||+.+|++.+++++|.+++.|+++++++|+++.+++++++++|.|+++++.|||+|++||||||++
T Consensus        83 aG~~aD~~~l~~~~r~~~~~y~~~~~~~i~v~~la~~l~~~~~~yt~~~~~rP~~v~~lvaG~D~~  148 (264)
T 3h4p_A           83 SGLVADARVLIDRARLEAQIYRLTYGEEISIEMLAKKICDIKQAYTQHGGVRPFGVSLLIAGIDKN  148 (264)
T ss_dssp             EECSHHHHHHHTTHHHHHHHHHHTTCSCCCHHHHHHHHHHHHHHTTSBSSCCCCSEEEEEEEEETT
T ss_pred             ccchHHHHHHHHHHHHHHHhhHHhcCCCCCHHHHHHHHHHHHHHHhhccCCCCeeEEEEEEEEeCC
Confidence            999999999999999999999999999999999999999999999998899999999999999964

>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=2e-46  Score=289.76  Aligned_cols=139  Identities=59%  Similarity=0.962  Sum_probs=134.3

Q ss_pred             CCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHH
Q 031996            8 GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADA   87 (149)
Q Consensus         8 ~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~   87 (149)
                      +||+++|+|||||||+|+|||+||+++.|+|+|||+++||||||+|++.+++++.+++.+||++|++|++|++||+.+|+
T Consensus         2 ~yd~~~t~fsp~Grl~QvEYA~~av~~~Gtt~vgi~~~dgVvlaad~r~~~~l~~~~~~~Ki~~i~~~i~~~~aG~~aD~   81 (243)
T 1ryp_A            2 GYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPTTVSYIFCISRTIGMVVNGPIPDA   81 (243)
T ss_dssp             GGGGTSSSCCTTSCCHHHHHHHHHTTTTCCCEEEEECSSEEEEEEECCCCCTTBCGGGCCSEEECSSSCEEEEESCHHHH
T ss_pred             CCCCCCceECCCCeeHHHHHHHHHHhcCCCcEEEEEeCCEEEEEEEecCCccccCCCcCCceEEECCCEEEEEEecHHHH
Confidence            69999999999999999999999998548999999999999999999999999888899999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           88 RTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        88 ~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +.+++++|.++++|+++++++|+++.+++++++++|.|+++++.|||+|++||||||++
T Consensus        82 ~~l~~~~r~~~~~~~~~~~~~~~v~~la~~l~~~l~~y~~~~~~rP~~v~~lvaG~D~~  140 (243)
T 1ryp_A           82 RNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQRAYMRPLGVILTFVSVDEE  140 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTSCCCSCEEEEEEEETT
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhccCCccccceEEEEEEEcCC
Confidence            99999999999999999999999999999999999999998889999999999999963

>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=6.9e-46  Score=287.18  Aligned_cols=144  Identities=65%  Similarity=1.015  Sum_probs=137.8

Q ss_pred             CCCCCCCCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEE
Q 031996            1 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLA   80 (149)
Q Consensus         1 m~~~~~~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~   80 (149)
                      ||+  +++||+++|+||||||++|||||++|++++|+|+|||+++||||||+|++.+++++.+++.+||++|++|++|++
T Consensus         3 m~~--~~~yd~~~t~fsp~Grl~QvEya~~av~~~Gtt~vgi~~~dgVvlaaD~r~~~~l~~~~~~~Ki~~i~~~i~~~~   80 (246)
T 1iru_A            3 RGS--SAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTVTHLFKITENIGCVM   80 (246)
T ss_dssp             CSC--CCTTTTTSSCCCTTSCCHHHHHHHHHHHTTCCEEEEEECSSEEEEEEECCCCCSSBCGGGCCSEEESSSSCEEEE
T ss_pred             CCc--cCCcCCCCccCCCCCeehHHHHHHHHHhcCCCCEEEEEeCCEEEEEEeecCCCcccCCCccCceEEECCCEEEEE
Confidence            564  579999999999999999999999999865999999999999999999999988888889999999999999999


Q ss_pred             eccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           81 TGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        81 sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      ||+.+|++.+.++++.++++|+++++++|+++.+++++++++|.|+++.+.|||+|++||||||++
T Consensus        81 aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~y~~~~~~rp~~v~~lvaG~D~~  146 (246)
T 1iru_A           81 TGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIGIDEE  146 (246)
T ss_dssp             EECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSBCCCSEEEEEEEEETT
T ss_pred             eccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcCCCCCCcceEEEEEEEeCC
Confidence            999999999999999999999999999999999999999999999998889999999999999963

>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=7.9e-46  Score=288.33  Aligned_cols=141  Identities=40%  Similarity=0.661  Sum_probs=135.2

Q ss_pred             CCCCCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEecc
Q 031996            4 GSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGM   83 (149)
Q Consensus         4 ~~~~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~   83 (149)
                      +.+++||+++|+|||||||+|+|||++|+++ |+|+|||+++||||||+|++.+..+...++.+||++|++|++|++||+
T Consensus         2 ~~~~~yd~~~t~fsp~Grl~QvEyA~~av~~-Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~KI~~i~~~i~~~~aG~   80 (254)
T 1iru_G            2 SIGTGYDLSASTFSPDGRVFQVEYAMKAVEN-SSTAIGIRCKDGVVFGVEKLVLSKLYEEGSNKRLFNVDRHVGMAVAGL   80 (254)
T ss_dssp             CCCSSTTSCTTCCCTTSCCHHHHHHHHHHHT-SCCEEEEECSSBEEEEEEEECSCTTBCTTTTCCEEEEETTEEEEEEEC
T ss_pred             CcccccCCCCccCCcCCccHHHHhHHHHHhc-CCCEEEEEECCEEEEEEecccCCCCcCcCcCCcEEEECCCEEEEEecC
Confidence            4677999999999999999999999999997 999999999999999999999977766788899999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeC
Q 031996           84 TADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAI  145 (149)
Q Consensus        84 ~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~  145 (149)
                      .+|++.++++++.+++.|+++++++|+++.+++++++++|.|++++++|||+|++||||||+
T Consensus        81 ~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rP~~v~~lvaG~D~  142 (254)
T 1iru_G           81 LADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGCSFMLGSYSV  142 (254)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSBSSBCCCSEEEEEEEEET
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhccccccccceEEEEEEEEeC
Confidence            99999999999999999999999999999999999999999999888999999999999994

>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=1.3e-45  Score=283.57  Aligned_cols=139  Identities=38%  Similarity=0.593  Sum_probs=134.6

Q ss_pred             CCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHH
Q 031996            7 GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTAD   86 (149)
Q Consensus         7 ~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D   86 (149)
                      ++||+++|+|||||||+|+|||++++++ |+|+|||+++||||||+|++.+++++.+++.+||++|++|++|++||+.+|
T Consensus         3 ~~yd~~~t~fsp~Grl~QvEya~~av~~-Gtt~vgi~~~dgVvlaaD~r~~~~l~~~~~~~Ki~~i~~~i~~~~aG~~aD   81 (233)
T 1iru_B            3 RGYSFSLTTFSPSGKLVQIEYALAAVAG-GAPSVGIKAANGVVLATEKKQKSILYDERSVHKVEPITKHIGLVYSGMGPD   81 (233)
T ss_dssp             CCCCSBSCCCCTTSCCHHHHHHHHHHHT-SCCEEEEECSSCEEEEEECCCCCSSBCSTTCCSSEESSSSEEEEEEECHHH
T ss_pred             CCccCCceeECCCCeEehhHhHHHHHHc-CCcEEEEEeCCEEEEEEEecCCccccccccCCeEEEECCCEEEEEEEccHH
Confidence            5799999999999999999999999997 999999999999999999999988888889999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           87 ARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        87 ~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      ++.+.++++.+++.|+++++++++++.+++++++++|.|++++++|||+|++||||||++
T Consensus        82 ~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~y~~~~~~rP~~v~~lvaG~D~~  141 (233)
T 1iru_B           82 YRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGVSLLICGWNEG  141 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCSEEEEEEEECSS
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCcCCCCCcEEEEEEEEEeCC
Confidence            999999999999999999999999999999999999999998889999999999999954

>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=1e-45  Score=284.10  Aligned_cols=139  Identities=40%  Similarity=0.640  Sum_probs=128.1

Q ss_pred             CCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHH
Q 031996            7 GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTAD   86 (149)
Q Consensus         7 ~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D   86 (149)
                      ++||+++|+||||||++|+|||++|+++ |+|+|||+++||||||+|++.+++++.+++.+||++|++|++|++||+.+|
T Consensus         6 ~~yd~~~t~fsp~Grl~QvEya~~av~~-Gtt~vgi~~~dgVvlaaD~r~~~~~~~~~~~~Ki~~i~~~i~~~~aG~~aD   84 (233)
T 1yar_A            6 MAYSRAITVFSPDGRLFQVEYAREAVKK-GSTALGMKFANGVLLISDKKVRSRLIEQNSIEKIQLIDDYVAAVTSGLVAD   84 (233)
T ss_dssp             -------CCCCTTSCCHHHHHHHHHHTT-SCCEEEEEETTEEEEEECCCCCCTTBCSTTCCSEEEEETTEEEEEEEBHHH
T ss_pred             ccCCCCCceECcCCeeHHHHhHHHHHhc-CCcEEEEEECCEEEEEEeccCCcccccccccCeEEEecCCEEEEEeeCHHH
Confidence            5899999999999999999999999987 999999999999999999999987888888999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           87 ARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        87 ~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      ++.+.++++.++++|+++++++++++.+++++++++|.|+++++.|||++++||||||++
T Consensus        85 ~~~l~~~~~~~~~~~~~~~~~~~~v~~~a~~l~~~~~~~~~~~~~rp~~v~~lvaG~D~~  144 (233)
T 1yar_A           85 ARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGVSLIFAGIDQI  144 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBTTBCCCCEEEEEEEECSS
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCcCCcCcceEEEEEEEEeCC
Confidence            999999999999999999999999999999999999999998889999999999999963

>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=1.4e-45  Score=285.49  Aligned_cols=140  Identities=35%  Similarity=0.552  Sum_probs=133.3

Q ss_pred             CCCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHH
Q 031996            6 GGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTA   85 (149)
Q Consensus         6 ~~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~   85 (149)
                      |++||+++|+||||||++|+|||++|+++ |+|+|||+++||||||+|++.++.+...+..+||++|++|++|++||+.+
T Consensus         1 ~~~yd~~~t~fsp~Grl~QvEya~~av~~-Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~KI~~i~~~i~~~~aG~~a   79 (244)
T 1ryp_G            1 GTGYDLSNSVFSPDGRNFQVEYAVKAVEN-GTTSIGIKCNDGVVFAVEKLITSKLLVPQKNVKIQVVDRHIGCVYSGLIP   79 (244)
T ss_dssp             CCCTTSSTTCCCTTSCCHHHHHHHHHHHT-SCCEEEEEETTEEEEEEEEECCCTTBCTTTSCCCEEETTTEEEEEEECHH
T ss_pred             CCCccCCcccCCcCCchHHHHhHHHHHHC-CCCEEEEEECCEEEEEEecccCCCCccccccCceEEecCCEEEEEcccHH
Confidence            46899999999999999999999999997 99999999999999999999997776666669999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           86 DARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        86 D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      |++.+.++++.++++|+++++++++++.+++++++++|.||++++.|||++++||+|||++
T Consensus        80 D~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rp~~v~~lvaG~D~~  140 (244)
T 1ryp_G           80 DGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGGVDKN  140 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSCTTBCCCCEEEEEEEEETT
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCccCceEEEEEEEEeCC
Confidence            9999999999999999999999999999999999999999998889999999999999964

>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=2.8e-45  Score=284.31  Aligned_cols=137  Identities=39%  Similarity=0.636  Sum_probs=132.7

Q ss_pred             CCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHHH
Q 031996            9 YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADAR   88 (149)
Q Consensus         9 yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~   88 (149)
                      ||+++|+|||||||+|+|||++|+++ |+|+|||+++||||||+|++.++.++.+++.+||++|++|++|++||+.+|++
T Consensus         3 yd~~~t~fsp~Grl~QvEYA~~av~~-Gtt~vgi~~~dgVvlaaD~r~~~~l~~~~~~~KI~~i~~~i~~~~aG~~aD~~   81 (248)
T 1iru_D            3 YDRAITVFSPDGHLFQVEYAQEAVKK-GSTAVGVRGRDIVVLGVEKKSVAKLQDERTVRKICALDDNVCMAFAGLTADAR   81 (248)
T ss_dssp             CCCCCSCCCTTSCCHHHHHHHHHHHT-SCCEEEECCSSEEEEEECCCCCCSSSCGGGGCSEEESSSSCEEEEEECHHHHH
T ss_pred             ccCCCceECCCCcchHHHHHHHHHHc-CCCEEEEEeCCEEEEEEeecccccCccCCCCCcEEEEcCCEEEEEeecHHHHH
Confidence            99999999999999999999999997 99999999999999999999997788788899999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           89 TLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        89 ~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      .+.++++.++++|+++++++|+++.+++++++++|.|+++++.|||+|++||||||++
T Consensus        82 ~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rp~~v~~lvaG~D~~  139 (248)
T 1iru_D           82 IVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGISALIVGFDFD  139 (248)
T ss_dssp             HHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCEEEEEEEECSS
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhccCCcccccEEEEEEEEeCC
Confidence            9999999999999999999999999999999999999998889999999999999943

>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=6.3e-45  Score=281.40  Aligned_cols=137  Identities=36%  Similarity=0.655  Sum_probs=132.6

Q ss_pred             CCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccc-cccccceeeecCcEEEEEeccHHH
Q 031996            8 GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLD-HTSVTHLFPITKYLGLLATGMTAD   86 (149)
Q Consensus         8 ~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~-~~~~~KI~~I~~~i~~~~sG~~~D   86 (149)
                      +||+++|+||||||++|+|||++|+++ |+|+|||+++||||||+|++.++.+.. +++.+||++|++|++|++||+.+|
T Consensus         4 ~yd~~~t~fsp~Grl~QvEyA~~av~~-Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD   82 (244)
T 1ryp_C            4 RYDSRTTIFSPEGRLYQVEYALESISH-AGTAIGIMASDGIVLAAERKVTSTLLEQDTSTEKLYKLNDKIAVAVAGLTAD   82 (244)
T ss_dssp             GGCCCTTCBCTTSCBHHHHHHHHHHTT-SCCEEEEEETTEEEEEEECSSCCSSBCSTTCCSSEEESSSSEEEEEEECHHH
T ss_pred             ccCCCCceECcCCeeHHHHhHHHHHhc-CCcEEEEEeCCEEEEEEeeccCCcCccCCCCCCcEEEECCCEEEEEEEcHHH
Confidence            799999999999999999999999987 999999999999999999999977766 788999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeC
Q 031996           87 ARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAI  145 (149)
Q Consensus        87 ~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~  145 (149)
                      ++.+.++++.++++|+++++++|+++.+++++++++|.|+++++.|||+|++||||||+
T Consensus        83 ~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rp~~v~~lvaG~D~  141 (244)
T 1ryp_C           83 AEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAGYDD  141 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSCCCCCEEEEEEEEET
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhccCCccceEEEEEEEEEcC
Confidence            99999999999999999999999999999999999999999989999999999999993

>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=5.6e-45  Score=281.34  Aligned_cols=138  Identities=36%  Similarity=0.614  Sum_probs=131.8

Q ss_pred             CCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccc-cccceeeecCcEEEEEeccHHH
Q 031996            8 GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHT-SVTHLFPITKYLGLLATGMTAD   86 (149)
Q Consensus         8 ~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~-~~~KI~~I~~~i~~~~sG~~~D   86 (149)
                      +||+++|+||||||++|+|||+||+++ |+|+|||+++||||||+|++.+..+...+ +.+||++|++|++|++||+.+|
T Consensus         1 ~yd~~~t~fsp~Grl~QvEya~~av~~-Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD   79 (241)
T 1ryp_D            1 GYDRALSIFSPDGHIFQVEYALEAVKR-GTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSKVSKIDSHVVLSFSGLNAD   79 (241)
T ss_dssp             CCCCCCSCCBTTTBCHHHHHHHHHHTT-SCCEEEEECSSCEEEEEECCCSSCCBCTTTSCCSEEEEETTEEEEEEECHHH
T ss_pred             CCCCCceeECCCCcchHHHHHHHHHHc-CCCEEEEEeCCEEEEEEeeccCccCccccCCcCcEEEecCCEEEEEeecHHH
Confidence            599999999999999999999999987 99999999999999999999997666554 8999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           87 ARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        87 ~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      ++.+.++++.+++.|+++++++|+++.+++++++++|.|+++++.|||+|++||||||++
T Consensus        80 ~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rP~~v~~lvaG~D~~  139 (241)
T 1ryp_D           80 SRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLIAGFDPR  139 (241)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSSTTBCCCSEEEEEEECCTT
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHccCCCCCCcceeeEEEEEcCC
Confidence            999999999999999999999999999999999999999998889999999999999973

>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=4.1e-45  Score=280.85  Aligned_cols=136  Identities=32%  Similarity=0.520  Sum_probs=130.7

Q ss_pred             CCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHH
Q 031996            8 GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADA   87 (149)
Q Consensus         8 ~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~   87 (149)
                      +||+++|+||||||++|+|||++|+++ |+|+|||+++||||||+|++.+..+.  ++.+||++|++|++|++||+.+|+
T Consensus         4 ~yd~~~t~fsp~Grl~QvEyA~~av~~-Gtt~vgi~~~dgVvlaaD~r~~~~l~--~~~~Ki~~i~~~i~~~~aG~~aD~   80 (233)
T 1ryp_F            4 NYDGDTVTFSPTGRLFQVEYALEAIKQ-GSVTVGLRSNTHAVLVALKRNADELS--SYQKKIIKCDEHMGLSLAGLAPDA   80 (233)
T ss_dssp             HHSSCTTCCCTTSCCHHHHHHHHHHHT-SCCEEEEECSSEEEEEEECCCSSTTB--CCCCCEEEEETTEEEEEEECHHHH
T ss_pred             cccCCCccCCCCCeehHHHHHHHHHHc-CCCEEEEEcCCEEEEEEEeccccccc--cccCcEEEEcCCEEEEEEechHHH
Confidence            699999999999999999999999997 99999999999999999999997765  477999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           88 RTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        88 ~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +.++++++.+++.|+++++++||++.+++++++++|.||++.+.|||+|++||||||++
T Consensus        81 ~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rp~~v~~lvaG~D~~  139 (233)
T 1ryp_F           81 RVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRPYGVGLLIIGYDKS  139 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEETT
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcccCCcCcceEEEEEEEeCC
Confidence            99999999999999999999999999999999999999999899999999999999964

>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=9.6e-45  Score=280.89  Aligned_cols=137  Identities=44%  Similarity=0.706  Sum_probs=133.1

Q ss_pred             CCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHH
Q 031996            7 GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTAD   86 (149)
Q Consensus         7 ~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D   86 (149)
                      ++||+++|+|||||||+|+|||++++++ |+|+|||+++||||||+|++.+++++.+++.+||++|++|++|++||+.+|
T Consensus         6 ~~yd~~~t~fsp~Grl~QvEya~~av~~-Gtt~vgi~~~dgVvlaaD~r~~~~l~~~~~~~KI~~i~~~i~~~~aG~~aD   84 (246)
T 1j2p_A            6 MGYDRAITVFSPDGRLFQVEYAREAVKR-GATAIGIKCKEGVILIADKRVGSKLLEKDTIEKIYKIDEHICAATSGLVAD   84 (246)
T ss_dssp             TTSSSCTTCCCTTSCCHHHHHHHHHHHT-SCCEEEEEETTEEEEEEECCCSCTTBCGGGCCSEEECSSSEEEEEEECHHH
T ss_pred             cCcCCCCceECCCCeehHHHhHHHHHHc-CCcEEEEEECCEEEEEEeccCCccccccCccCcEEEECCCEEEEEeEccHH
Confidence            3899999999999999999999999997 999999999999999999999988877888999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEe
Q 031996           87 ARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIA  144 (149)
Q Consensus        87 ~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D  144 (149)
                      ++.+.++++.+++.|+++++++++++.+++++++++|.|+++++.|||++++||||||
T Consensus        85 ~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~y~~~~~~rp~~v~~lvaG~D  142 (246)
T 1j2p_A           85 ARVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQYGGVRPFGVSLLIAGVN  142 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCEEEEEEEES
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCcccccEEEEEEEEC
Confidence            9999999999999999999999999999999999999999988899999999999999

>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=8.6e-45  Score=283.47  Aligned_cols=141  Identities=35%  Similarity=0.561  Sum_probs=132.7

Q ss_pred             CCCCCCCCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCcccccc-ccccceeeecCcEEEE
Q 031996            1 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDH-TSVTHLFPITKYLGLL   79 (149)
Q Consensus         1 m~~~~~~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~-~~~~KI~~I~~~i~~~   79 (149)
                      |++    +||+++|+|||||||+|+|||++|+++ |+|+|||+++||||||+|++.+..+... ++.+||++|++|++|+
T Consensus         1 m~~----~yd~~~t~fsp~Grl~QvEYA~~av~~-Gtt~vgi~~~dgVVlaaD~r~~~g~~~~~~~~~KI~~i~~~i~~~   75 (261)
T 1iru_C            1 MSR----RYDSRTTIFSPEGRLYQVEYAMEAIGH-AGTCLGILANDGVLLAAERRNIHKLLDEVFFSEKIYKLNEDMACS   75 (261)
T ss_dssp             -CT----TTCCCTTCCCTTSCCHHHHHHHHHHTT-SCCEEEEBCSSEEEEEECCCCCCTTBCCCSSCSSEEECSSSEEEE
T ss_pred             CCC----ccCCCCccCCCCCeehHHHhHHHHHhc-CCcEEEEEeCCEEEEEEecccCCcccccCCCCccEEEecCCEEEE
Confidence            665    899999999999999999999999987 9999999999999999999999666554 4589999999999999


Q ss_pred             EeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           80 ATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        80 ~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +||+.+|++.++++++.+++.|+++++++++++.+++++++++|.|+++++.|||+|++||||||++
T Consensus        76 ~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rP~~v~~lvaG~D~~  142 (261)
T 1iru_C           76 VAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIGWDKH  142 (261)
T ss_dssp             EEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBSSCCCCCEEEEEEEEETT
T ss_pred             EeEcHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccccCcCcceEEEEEEEEeCC
Confidence            9999999999999999999999999999999999999999999999998889999999999999963

>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=1.7e-44  Score=280.01  Aligned_cols=141  Identities=33%  Similarity=0.492  Sum_probs=135.8

Q ss_pred             CCCCCCCCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEE
Q 031996            1 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLA   80 (149)
Q Consensus         1 m~~~~~~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~   80 (149)
                      |++    +||+++|+||||||++|+|||++|+++ |+|+|||+++||||||+|++.++.++.+++.+||++|++|++|++
T Consensus         1 ~~~----~yd~~~t~fsp~Grl~QvEyA~~av~~-Gtt~vgi~~~dgVvlaaD~r~~~~l~~~~~~~Ki~~i~~~i~~~~   75 (250)
T 1ryp_B            1 MTD----RYSFSLTTFSPSGKLGQIDYALTAVKQ-GVTSLGIKATNGVVIATEKKSSSPLAMSETLSKVSLLTPDIGAVY   75 (250)
T ss_dssp             CCC----CCCSBSSCBCTTSCBHHHHHHHHHHHT-SCCEEEEEETTEEEEEEECCCSCSSBCGGGCCSSEEEETTEEEEE
T ss_pred             CCC----cccCCceeECCCCccHHHHhHHHHHHc-CCcEEEEEECCEEEEEEeccCCCccccCcccCceEEECCCEEEEe
Confidence            665    899999999999999999999999997 999999999999999999999988888889999999999999999


Q ss_pred             eccHHHHHHHHHHHHHHHHH-HHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           81 TGMTADARTLVQQARYEAAE-FRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        81 sG~~~D~~~l~~~~r~~~~~-~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      ||+.+|++.+.++++.+++. |++.++.+++++.+++.++++++.++++.++|||+|++||||||++
T Consensus        76 aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~~a~~~~~~~~~~~~rp~~v~~lvaG~D~~  142 (250)
T 1ryp_B           76 SGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIAGHDEF  142 (250)
T ss_dssp             EECHHHHHHHHHHHHHHHHHTTHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCCEEEEEEEEETT
T ss_pred             eeCHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHhcCCcccceEEEEEEEEcCC
Confidence            99999999999999999999 9999999999999999999999999998888999999999999974

>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=3.5e-44  Score=280.44  Aligned_cols=137  Identities=34%  Similarity=0.576  Sum_probs=131.4

Q ss_pred             CCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHH
Q 031996            7 GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTAD   86 (149)
Q Consensus         7 ~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D   86 (149)
                      ++||+++|+|||||||+|+|||+||+++ |+|+|||+++||||||+|++.+..+.  ++.+||++|++|++|++||+.+|
T Consensus         4 ~~yd~~~t~fsP~Grl~QvEYA~~av~~-Gtt~vgi~~~dgVVlaaD~r~~~gl~--~~~~KI~~i~~~i~~~~aG~~aD   80 (263)
T 1iru_F            4 NQYDNDVTVWSPQGRIHQIEYAMEAVKQ-GSATVGLKSKTHAVLVALKRAQSELA--AHQKKILHVDNHIGISIAGLTAD   80 (263)
T ss_dssp             CTTTSCTTCCCTTSCCHHHHHHHHHHHH-SCCEEEEECSSEEEEEEECCCSSTTB--CCCCCEEEEETTEEEEEEECHHH
T ss_pred             CCCCCCCccCCCCCeehHHHHHHHHHHc-CCcEEEEEeCCEEEEEEecccccccc--cchhcEEEEcCCEEEEEeCCHHH
Confidence            5799999999999999999999999997 99999999999999999999997764  47799999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           87 ARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        87 ~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      ++.++++++.+++.|+++++++|+++.+++++++++|.|+++++.|||+|++||||||++
T Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~i~v~~la~~l~~~l~~~t~~~~~RP~~v~~lvaG~D~~  140 (263)
T 1iru_F           81 ARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAGYDDM  140 (263)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEETT
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHhhcccccccceEEEEEEEEcCC
Confidence            999999999999999999999999999999999999999998889999999999999964

>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=8.9e-45  Score=280.22  Aligned_cols=138  Identities=33%  Similarity=0.642  Sum_probs=130.9

Q ss_pred             CCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHH
Q 031996            7 GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTAD   86 (149)
Q Consensus         7 ~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D   86 (149)
                      ++||+++|+||||||++|+|||++|+++ |+|+|||+++||||||+|++.+..+..+++.+||++|++|++|++||+.+|
T Consensus         6 ~~yd~~~t~fsp~Grl~QvEya~~av~~-Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~Ki~~i~~~i~~~~aG~~aD   84 (241)
T 1iru_E            6 SEYDRGVNTFSPEGRLFQVEYDIEAIKL-GSTAIGIQTSEGVCLAVEKRITSPLMEPSSIEKIVEIDAHIGCAMSGLIAD   84 (241)
T ss_dssp             --CCCCTTCBCTTSCBHHHHHHHHHHTT-SCCEEEEEETTEEEEEEECCCCCTTBCTTSCCSEEEEETTEEEEEEECHHH
T ss_pred             CCCCCCCceECCCCccHHHHHHHHHHHc-CCcEEEEEcCCEEEEEEecccCCcCcCccccceEEEEcCCEEEEEeeChHH
Confidence            5899999999999999999999999987 999999999999999999999976666788999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCC-----ccccceEEEEEEEeC
Q 031996           87 ARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAY-----MRPLGVGLFLIEIAI  145 (149)
Q Consensus        87 ~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~-----~rP~~v~~liaG~D~  145 (149)
                      ++.+.++++.+++.|+++++++++++.+++++++++|.|+++.+     .|||+|++||||||+
T Consensus        85 ~~~l~~~~~~~~~~~~~~~~~~~~v~~~a~~l~~~~~~y~~~~~~~~l~~rp~~v~~lvaG~D~  148 (241)
T 1iru_E           85 AKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMSRPFGVALLFGGVDE  148 (241)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCBCSTTCCSSCBSSCCCEEEEEEEEET
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhccccccccccccceEEEEEEEEeC
Confidence            99999999999999999999999999999999999999998777     899999999999994

>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=1.1e-43  Score=274.07  Aligned_cols=136  Identities=35%  Similarity=0.609  Sum_probs=129.9

Q ss_pred             CcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHHHH
Q 031996           10 DRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADART   89 (149)
Q Consensus        10 d~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~   89 (149)
                      |+++|+|||||||+|||||++|+++ |+|+|||+++||||||+|++.++.+..+++.+||++|++|++|++||+.+|++.
T Consensus         1 d~~~t~fsp~Grl~QvEyA~~av~~-Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~   79 (242)
T 1ryp_E            1 DRGVSTFSPEGRLFQVEYSLEAIKL-GSTAIGIATKEGVVLGVEKRATSPLLESDSIEKIVEIDRHIGCAMSGLTADARS   79 (242)
T ss_dssp             CCCTTCBCTTSCBHHHHHHHHHHTT-SCCEEEEECSSCEEEEEECCCSSTTBCGGGCCCEEEEETTEEEEEEESGGGHHH
T ss_pred             CCCCceECCCCcChHHHhHHHHHHc-CCCEEEEEECCEEEEEEeecCCCcCccCccCCceEEEcCCEEEEEeecHHHHHH
Confidence            6789999999999999999999987 999999999999999999999977766788999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCC------ccccceEEEEEEEeCC
Q 031996           90 LVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAY------MRPLGVGLFLIEIAIP  146 (149)
Q Consensus        90 l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~------~rP~~v~~liaG~D~~  146 (149)
                      ++++++.+++.|+++++++++++.+++++++++|.|+++++      .|||+|++||||||++
T Consensus        80 l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~~~~l~~RP~~v~~lvaG~D~~  142 (242)
T 1ryp_E           80 MIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLMSRPFGVALLIAGHDAD  142 (242)
T ss_dssp             HHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCCBSSCTTSCCCBSSCCSEEEEEEEEETT
T ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccccCcccccccCcceEEEEEEEEeCC
Confidence            99999999999999999999999999999999999998877      8999999999999943

>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=1e-33  Score=220.73  Aligned_cols=121  Identities=20%  Similarity=0.244  Sum_probs=110.3

Q ss_pred             ceeCCCCcch-hhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHHHHHHH
Q 031996           14 TIFSPEGRLF-QVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQ   92 (149)
Q Consensus        14 t~fsp~G~~~-Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~   92 (149)
                      --|||||++. |+|||++++++ |+|+|||+++||||||+|++       .++.+||++|++|++|++||+.+|++.+++
T Consensus         5 ~~~sPe~~~~~qvEYA~~av~~-Gtt~vgi~~~dgVVlaaD~r-------s~~~~KI~~I~d~i~~~~aG~~aD~~~l~~   76 (259)
T 1q5q_A            5 YYASAEQIMRDRSELARKGIAR-GRSVVVLTFRDGVLFVAENP-------STALHKVSELYDRLGFAAVGKYNEFENLRR   76 (259)
T ss_dssp             ----CHHHHHHHHHHHHHHHHT-SCCEEEEECSSEEEEEECCS-------CSSSCSEEEEETTEEEEEEECHHHHHHHHH
T ss_pred             cccCHHHHHHHHHHHHHHHHhc-CCcEEEEEeCCEEEEEEecC-------CCCcCcEEEeCCCEEEEEccCHHHHHHHHH
Confidence            3589999995 99999999997 99999999999999999998       357889999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhC-CCCCHHHHHHHHHH-HHHHHhhcCCccccceEEEEEEEe
Q 031996           93 QARYEAAEFRFKYG-YEMPVDVLAKWIAD-KSQVYTQHAYMRPLGVGLFLIEIA  144 (149)
Q Consensus        93 ~~r~~~~~~~~~~~-~~~~~~~la~~l~~-~~~~~t~~~~~rP~~v~~liaG~D  144 (149)
                      +++.+++.|++.++ ++|+++.+++++++ +.|.|+.  +.|||+|++||||||
T Consensus        77 ~~~~~~~~~~~~~~~~~i~v~~la~~l~~~l~q~yt~--~~rP~~v~~lvaG~D  128 (259)
T 1q5q_A           77 AGIVHADMRGYSYDRRDVTGRSLANAYAQTLGTIFTE--QPKPYEVEICVAEVG  128 (259)
T ss_dssp             HHHHHHHHHHHHSCGGGCCHHHHHHHHHHHHHHHHHH--SSSCCCEEEEEEECC
T ss_pred             HHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHhcc--CCCCceEEEEEEEEc
Confidence            99999999999998 49999999999999 6677873  789999999999999

>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=99.97  E-value=4.4e-31  Score=204.78  Aligned_cols=112  Identities=19%  Similarity=0.230  Sum_probs=106.4

Q ss_pred             hhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHH
Q 031996           24 QVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRF  103 (149)
Q Consensus        24 Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~  103 (149)
                      ++|||+||+++ |+|+|||+++||||||+|++       .++.+||++|++|++|+++|+.+|++.|.+.++.+++.|++
T Consensus        16 r~EYA~~av~~-GtT~vgi~~kdgVVlaadkr-------~~~~~KI~~I~d~i~~~~aG~~aD~~~l~~~~~~~~~l~~~   87 (248)
T 3mi0_A           16 RSELARKGIAR-AKSVVALAYAGGVLFVAENP-------SRSLQKISELYDRVGFAAAGKFNEFDNLRRGGIQFADTRGY   87 (248)
T ss_dssp             HHHHHHHHHHT-SCCEEEEEETTEEEEEEECC-------CSSSCSEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHhC-CCcEEEEEeCCEEEEEEeCC-------CCCCCCeEEECCCEEEEEccCHHHHHHHHHHHHHHHHHHHH
Confidence            57999999987 99999999999999999999       34788999999999999999999999999999999999999


Q ss_pred             HhC-CCCCHHHHHHHHH-HHHHHHhhcCCccccceEEEEEEEeC
Q 031996          104 KYG-YEMPVDVLAKWIA-DKSQVYTQHAYMRPLGVGLFLIEIAI  145 (149)
Q Consensus       104 ~~~-~~~~~~~la~~l~-~~~~~~t~~~~~rP~~v~~liaG~D~  145 (149)
                      +++ ++++++.|+++++ .+.|.|++  ++|||+|++||||||+
T Consensus        88 ~~~~~~i~v~~la~~l~~~l~q~yt~--~~rP~gv~~liaG~D~  129 (248)
T 3mi0_A           88 AYDRRDVTGRQLANVYAQTLGTIFTE--QAKPYEVELCVAEVAH  129 (248)
T ss_dssp             HSCGGGCCHHHHHHHHHHHHHHHHHH--SSSCCCEEEEEEECCC
T ss_pred             hcCCCCCCHHHHHHHHHHHHHHHhcc--CCCCceEEEEEEEEcC
Confidence            999 9999999999999 77888987  7999999999999997

>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=99.97  E-value=4.2e-30  Score=203.33  Aligned_cols=138  Identities=13%  Similarity=0.089  Sum_probs=98.2

Q ss_pred             CCCCcccceeCCCCcc-----hh--hhhHHHHhhccCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEE
Q 031996            7 GGYDRHITIFSPEGRL-----FQ--VEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGL   78 (149)
Q Consensus         7 ~~yd~~~t~fsp~G~~-----~Q--~eya~~av~~~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~   78 (149)
                      ..|+.-.....||.-.     ++  .|||++ +++ |+|+|||+++||||||+|++.+ +.++.+++.+||++|++|++|
T Consensus        23 ~~f~~~~~~~~~~~l~~~~~~~~~~~~ya~~-v~~-GtTiVgi~~kdGVVlAaD~r~t~g~li~~~~~~KI~~i~d~i~~  100 (291)
T 2jay_A           23 SSFTDFLRRQAPELLPASISGGAPLAGGDAQ-LPH-GTTIVALKYPGGVVMAGDRRSTQGNMISGRDVRKVYITDDYTAT  100 (291)
T ss_dssp             -------------------------------------CCEEEEEETTEEEEEECCC--------CCCCCCEEEEETTEEE
T ss_pred             ccHHHHhhhcChhhccccccccCcCcccccc-ccC-CcEEEEEEECCEEEEEECCCccCCCeeecCCcccEEEeCCcEEE
Confidence            3565556666666332     22  689999 876 9999999999999999999998 457778889999999999999


Q ss_pred             EEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996           79 LATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        79 ~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      ++||+.+|++.++++++.+++.|+++++++++++.+++.+++++|.++. ...|||+|++||||||+++
T Consensus       101 ~~aG~~aD~~~l~~~lr~~~~~y~~~~~~~i~v~~la~~la~~l~~~~~-~~~rpf~v~~lvaG~D~~g  168 (291)
T 2jay_A          101 GIAGTAAVAVEFARLYAVELEHYEKLEGVPLTFAGKINRLAIMVRGNLA-AAMQGLLALPLLAGYDIHA  168 (291)
T ss_dssp             EEESCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHTCHH-HHHHTCCCEEEEEEECTTC
T ss_pred             EEcccHHHHHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHHhhh-hhccccceeEEEEEEeCCC
Confidence            9999999999999999999999999999999999999999999998865 3578999999999999753

>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=99.96  E-value=1e-29  Score=201.40  Aligned_cols=117  Identities=17%  Similarity=0.166  Sum_probs=109.8

Q ss_pred             HHHHhhccCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhC
Q 031996           28 AFKAVKAAGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYG  106 (149)
Q Consensus        28 a~~av~~~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~  106 (149)
                      |+||+++ |+|+|||+++||||||+|++.+ ++++..++.+||++|++|++|++||+.+|++.++++++.++++|+++++
T Consensus        58 a~~Av~~-GtTiVgIk~kdGVVlAaD~r~t~G~li~~~~~~KI~~I~~~i~~~~aG~~aD~~~l~~~~r~~~~~y~~~~g  136 (294)
T 1q5r_H           58 SGDLAPH-GTTIVALTYKGGVLLAGDRRATQGNLIASRDVEAVYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEG  136 (294)
T ss_dssp             --CCSCB-CCCEEEEECSSCEEEEECCCEEETTEEEESCCCCEEEEETTEEEEEEEBHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHhc-CceEEEEEECCEEEEEEcCccccCceeecCCcceEEEECCcEEEEEeecHHHHHHHHHHHHHHHHHhhHhhC
Confidence            8899987 9999999999999999999999 5888888999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          107 YEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       107 ~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      ++++++.++++|++++|.++++ ..|||+|++||+|||++
T Consensus       137 ~~isv~~la~~la~~l~~~~~~-~~rp~~v~lLvaG~D~~  175 (294)
T 1q5r_H          137 VPLTFDGKANRLASMVRGNLGA-AMQGLAVVPLLVGYDLD  175 (294)
T ss_dssp             SCCCHHHHHHHHHHHHHHHHHH-HTTTTCEEEEEEEECTT
T ss_pred             CCCCHHHHHHHHHHHHHHHHhh-hcCCcceEEEEEEEeCC
Confidence            9999999999999999998875 38999999999999976

>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=99.96  E-value=1.2e-29  Score=194.66  Aligned_cols=114  Identities=13%  Similarity=0.206  Sum_probs=106.1

Q ss_pred             HHhhccCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHH-----
Q 031996           30 KAVKAAGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRF-----  103 (149)
Q Consensus        30 ~av~~~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~-----  103 (149)
                      +++++ |+|+|||+++||||||+|++.+ +.++.+++.+||++|++|++|++||+.+|++.+.+++|.+++.|++     
T Consensus         3 ~av~~-Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~   81 (233)
T 1ryp_N            3 QPIVT-GTSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLA   81 (233)
T ss_dssp             CCCEE-ECCEEEEEETTEEEEEEECCEEETTEEEESCCCCEEEETTTEEEEEEEEHHHHHHHHHHHHHHHHHHHTTCTTT
T ss_pred             ccccC-CceEEEEEECCEEEEEEcCccccCCeeecCCcCceEEeCCCEEEEccccHHHHHHHHHHHHHHHHHHhhccchh
Confidence            56776 9999999999999999999998 5788888999999999999999999999999999999999999999     


Q ss_pred             HhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          104 KYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       104 ~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++++|+++.++++++++++  +++.+.|||++++||||||++
T Consensus        82 ~~~~~~~v~~la~~l~~~ly--~~r~~~~P~~v~~lvaG~D~~  122 (233)
T 1ryp_N           82 DAEEALEPSYIFEYLATVMY--QRRSKMNPLWNAIIVAGVQSN  122 (233)
T ss_dssp             TTTTSCCHHHHHHHHHHHHH--HHHHTTCCCCEEEEEEEECTT
T ss_pred             hcCCCCCHHHHHHHHHHHHH--HhcCCCCCceEEEEEEEEcCC
Confidence            99999999999999999996  455578999999999999975

>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=99.96  E-value=5.5e-29  Score=189.19  Aligned_cols=110  Identities=25%  Similarity=0.473  Sum_probs=99.8

Q ss_pred             HHhhccCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCC
Q 031996           30 KAVKAAGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYE  108 (149)
Q Consensus        30 ~av~~~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~  108 (149)
                      +++.+ |+|+|||+++||||||+|++.+ ++++.+++.+||++|+++++|++||+.+|++.+.++++.+++.|+++++++
T Consensus         3 ~~~~~-Gtt~vgi~~~dgVvlaaD~r~~~g~l~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~   81 (217)
T 1yar_H            3 QTLET-GTTTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKAELELYRLQRRVN   81 (217)
T ss_dssp             -------CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCC-CccEEEEEeCCEEEEEEcCCCCCCCEEecCccCCeEEeCCCEEEEeCcCHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence            35665 9999999999999999999998 578888899999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEe
Q 031996          109 MPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIA  144 (149)
Q Consensus       109 ~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D  144 (149)
                      ++++.+++++++.+|.+    +.|||++++||||||
T Consensus        82 ~~v~~la~~l~~~~~~~----r~rp~~v~~lvaG~D  113 (217)
T 1yar_H           82 MPIEAVATLLSNMLNQV----KYMPYMVQLLVGGID  113 (217)
T ss_dssp             CCHHHHHHHHHHHHHHT----TTSCCCEEEEEEEES
T ss_pred             CCHHHHHHHHHHHHHhc----CCCCceEEEEEEEEC
Confidence            99999999999999864    478999999999999

>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=99.96  E-value=8e-29  Score=187.46  Aligned_cols=111  Identities=14%  Similarity=0.186  Sum_probs=101.6

Q ss_pred             hhccCceEEEEEcCCeEEEEEeccCCccc-cccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCC
Q 031996           32 VKAAGVTSIGVRGKDSVCVVTQKKVPDKL-LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMP  110 (149)
Q Consensus        32 v~~~G~t~igik~kdgVvlaad~~~~~~l-~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~  110 (149)
                      +++ |+|+|||+++||||||+|++.++.+ +..++.+||++|++|++|++||+.+|++.+.++++.+++.|+++++++++
T Consensus         6 v~~-Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~   84 (213)
T 1iru_M            6 VFN-GGTILAIAGEDFAIVASDTRLSEGFSIHTRDSPKCYKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMT   84 (213)
T ss_dssp             CCC-CCEEEEEEETTEEEEEEECCEEETTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCC
T ss_pred             cCC-CCcEEEEEeCCEEEEEECCCcccCCEEecCCCCcEEEcCCCEEEEccccHHHHHHHHHHHHHHHHHHHHhcCCCCC
Confidence            444 9999999999999999999999554 44578999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996          111 VDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus       111 ~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      ++.++++++++++  +++  .|||++++||||||+++
T Consensus        85 v~~la~~l~~~~y--~~r--~~P~~v~~lvaG~D~~g  117 (213)
T 1iru_M           85 TGAIAAMLSTILY--SRR--FFPYYVYNIIGGLDEEG  117 (213)
T ss_dssp             HHHHHHHHHHHHH--HTT--TSCCCEEEEEEEECTTS
T ss_pred             HHHHHHHHHHHHH--hhC--CCCceEEEEEEEEcCCC
Confidence            9999999999984  553  79999999999999754

>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=99.96  E-value=1.3e-29  Score=192.65  Aligned_cols=114  Identities=16%  Similarity=0.178  Sum_probs=106.0

Q ss_pred             HHhhccCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHH-HhCC
Q 031996           30 KAVKAAGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRF-KYGY  107 (149)
Q Consensus        30 ~av~~~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~-~~~~  107 (149)
                      +++++ |+|+|||+++||||||+|++.+ +.++.+++.+||++|++|++|++||+.+|++.+.+++|.+++.|++ ++++
T Consensus         3 ~av~~-Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~   81 (219)
T 1iru_N            3 NPMVT-GTSVLGVKFEGGVVIAADMLGSYGSLARFRNISRIMRVNNSTMLGASGDYADFQYLKQVLGQMVIDEELLGDGH   81 (219)
T ss_dssp             SCCSE-ECCCEEEEETTEEEEEEECCEEETTEEEECSCCCEEEETTTEEEEEEEEHHHHHHHHHHHHHHHHHHHHHCSSC
T ss_pred             CCccC-CceEEEEEeCCEEEEEECCccccCcEEecCCCCceEEeCCCEEEEeccCHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence            56776 9999999999999999999998 5888888999999999999999999999999999999999999998 9999


Q ss_pred             CCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          108 EMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       108 ~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++++.++++++++++.  ++++.|||++++||||||+.
T Consensus        82 ~~~v~~la~~l~~~ly~--~r~~~~P~~v~~lvaG~D~~  118 (219)
T 1iru_N           82 SYSPRAIHSWLTRAMYS--RRSKMNPLWNTMVIGGYADG  118 (219)
T ss_dssp             CCCHHHHHHHHHHHHHH--HHHTTCCCCEEEEEEEEETT
T ss_pred             CCCHHHHHHHHHHHHHH--hcccCCCceEEEEEEEEECC
Confidence            99999999999999964  45578999999999999964

>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=99.96  E-value=8.1e-29  Score=195.63  Aligned_cols=116  Identities=13%  Similarity=0.151  Sum_probs=100.8

Q ss_pred             hhHHHHhhccCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHH
Q 031996           26 EYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFK  104 (149)
Q Consensus        26 eya~~av~~~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~  104 (149)
                      .++..++.+ |+|+|||+++||||||+|++.+ +.++..++.+||++|++|++|++||+.+|++.+.++++.+++.|+++
T Consensus        66 ~~~~~~v~~-GtT~vgik~~dGVVlAaD~r~t~G~li~~~~~~KI~~I~d~i~~~~aG~~AD~~~l~~~lr~~~~~y~~~  144 (287)
T 3nzj_K           66 PDCKIKIAH-GTTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELR  144 (287)
T ss_dssp             -----------CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEECEECHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchhhhecc-CceEEEEEECCEEEEEEccccccCceeecCCcceEEEEcCcEEEEecCCHHHHHHHHHHHHHHHHHHHHH
Confidence            367889986 9999999999999999999998 68888889999999999999999999999999999999999999999


Q ss_pred             hCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          105 YGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       105 ~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      ++++++++.+++++++++|.|++    +||++++||||||++
T Consensus       145 ~~~~isv~~la~~ls~~l~~~r~----~p~~v~~lvaG~D~~  182 (287)
T 3nzj_K          145 EKERISVAAASKILSNLVYQYKG----AGLSMGTMICGYTRK  182 (287)
T ss_dssp             HSSCCCHHHHHHHHHHHHHHTTT----SCCCEEEEEEEEETT
T ss_pred             hCCCCCHHHHHHHHHHHHHhhcC----CCceEEEEEEEEcCC
Confidence            99999999999999999997764    399999999999954

>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=99.96  E-value=2.5e-29  Score=196.55  Aligned_cols=119  Identities=13%  Similarity=0.187  Sum_probs=108.5

Q ss_pred             hhhHHHHhhccCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHH
Q 031996           25 VEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRF  103 (149)
Q Consensus        25 ~eya~~av~~~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~  103 (149)
                      .+.+++++++ |+|+|||+++||||||+|++.+ +.++.+++.+||++|++|++|++||+.+|++.+++++|.+++.|++
T Consensus        31 ~~~~~~av~~-GtT~vgi~~~dgVVlAaD~r~t~g~~i~~~~~~KI~~i~d~i~~~~aG~~aD~~~l~~~lr~~~~~~~~  109 (266)
T 1g0u_M           31 MVNTQQPIVT-GTSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAY  109 (266)
T ss_dssp             ---CCCCCEE-ECCEEEEEETTEEEEEEECCEEETTEEEECCCCCEEECTTSEEEEEEEEHHHHHHHHHHHHHHHHHHHT
T ss_pred             hhhhccCccc-CceEEEEEECCEEEEEEcCCcccCceeecCCcCcEEEcCCCEEEEeccCHHHHHHHHHHHHHHHHHhhh
Confidence            4667889986 9999999999999999999998 5778888999999999999999999999999999999999999998


Q ss_pred             -----HhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          104 -----KYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       104 -----~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                           +++++++++.++++++++++  +++.+.|||+|++||||||++
T Consensus       110 ~~~~~~~~~~~~v~~la~~l~~~ly--~~r~~~~P~~v~~lvaG~D~~  155 (266)
T 1g0u_M          110 DNPLADAEEALEPSYIFEYLATVMY--QRRSKMNPLWNAIIVAGVQSN  155 (266)
T ss_dssp             TCTTTTTTTSCCHHHHHHHHHHHHH--HHHHTTCCCCEEEEEEEECTT
T ss_pred             ccchhhcCCCCCHHHHHHHHHHHHH--HhccCCCCceEEEEEEEEcCC
Confidence                 99999999999999999985  455578999999999999975

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

Probab=99.96  E-value=1e-28  Score=188.07  Aligned_cols=107  Identities=20%  Similarity=0.326  Sum_probs=100.4

Q ss_pred             CceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Q 031996           36 GVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVL  114 (149)
Q Consensus        36 G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~l  114 (149)
                      |+|+|||+++||||||+|++.+ +.++..++.+||++|++|++|++||+.+|++.+.++++.+++.|+++++++++++.+
T Consensus         1 Gtt~vgi~~~dgVvlaaD~r~~~g~~i~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~l   80 (219)
T 3h4p_a            1 MTTTVGLICDDAVILATDKRASLGNLVADKEAKKLYKIDDYIAMTIAGSVGDAQAIVRLLIAEAKLYKMRTGRNIPPLAC   80 (219)
T ss_dssp             -CCEEEEEETTEEEEECCCCEEETTEEEETTCCCEEEEETTEEEECCSCHHHHHHHHHHHHHHHHHHHHHTSSCCCHHHH
T ss_pred             CccEEEEEECCEEEEEEcCCcccCCEeeccccceeEEecCCEEEEeeEcHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHH
Confidence            7899999999999999999998 457778899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          115 AKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       115 a~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      ++++++++|.+    +.|||+|++||||||++
T Consensus        81 a~~l~~~~~~~----~~~P~~v~~lvaG~D~~  108 (219)
T 3h4p_a           81 ATLLSNILHSS----RMFPFLTQIIIGGYDLL  108 (219)
T ss_dssp             HHHHHHHHHHT----TTTTCCCCCEEEEEETT
T ss_pred             HHHHHHHHHHh----cCCCceEEEEEEEEeCC
Confidence            99999999865    46899999999999973

>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=99.96  E-value=2.2e-28  Score=187.90  Aligned_cols=109  Identities=17%  Similarity=0.181  Sum_probs=103.9

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      +|+|||+++||||||+|++.+ ++++.+++.+||++|+++++|++||+.+|++.++++++.+++.|+++++++|+++.++
T Consensus         1 tT~vgi~~~dgVVlaaD~r~~~g~l~~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la   80 (235)
T 1q5q_H            1 TTIVALTYKGGVLLAGDRRATQGNLIASRDVEKVYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEGVPLTFDGKA   80 (235)
T ss_dssp             CCEEEEECSSCEEEEECCCEEETTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             CeEEEEEECCEEEEEECCCCCcCCEEecCCcCcEEEeCCcEEEEcCCcHHHHHHHHHHHHHHHHHhHHHhCCCCCHHHHH
Confidence            589999999999999999999 5888888999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +.+++++|.++++ ..|||+|++||||||++
T Consensus        81 ~~l~~~~~~~~~~-~~rp~~v~~lvaG~D~~  110 (235)
T 1q5q_H           81 NRLASMVRGNLGA-AMQGLAVVPLLVGYDLD  110 (235)
T ss_dssp             HHHHHHHHTTHHH-HTTTCCEEEEEEEECTT
T ss_pred             HHHHHHHHHHHHh-hhcccceEEEEEEEECC
Confidence            9999999998875 38999999999999976

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

Probab=99.96  E-value=3.6e-28  Score=182.48  Aligned_cols=106  Identities=20%  Similarity=0.322  Sum_probs=100.3

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      +|+|||+++||||||+|++.+ +.++.+++.+||++|++|++|++||+.+|++.+.++++.+++.|+++++++|+++.++
T Consensus         1 tt~vgi~~~dgVvlaad~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~a   80 (202)
T 1j2q_H            1 TTTVGLVCKDGVVMATEKRATMGNFIASKAAKKIYQIADRMAMTTAGSVGDAQFLARIIKIEANLYEIRRERKPTVRAIA   80 (202)
T ss_dssp             CCEEEEEETTEEEEEEECCEEETTEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             CcEEEEEeCCEEEEEECCCcCcCCEEeeccccCEEEcCCCEEEEecccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            589999999999999999998 5788888999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++++++|.+    +.|||++++||||||++
T Consensus        81 ~~l~~~~~~~----r~rp~~~~~lvaG~D~~  107 (202)
T 1j2q_H           81 TLTSNLLNSY----RYFPYLVQLLIGGIDSE  107 (202)
T ss_dssp             HHHHHHHHHT----TTSCCCEEEEEEEEETT
T ss_pred             HHHHHHHHhh----CCCCceEEEEEEEEeCC
Confidence            9999999863    47899999999999964

>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=99.96  E-value=1.6e-28  Score=184.96  Aligned_cols=111  Identities=14%  Similarity=0.197  Sum_probs=103.4

Q ss_pred             HHHhhccCceEEEEEcCCeEEEEEeccCCcc-ccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCC
Q 031996           29 FKAVKAAGVTSIGVRGKDSVCVVTQKKVPDK-LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGY  107 (149)
Q Consensus        29 ~~av~~~G~t~igik~kdgVvlaad~~~~~~-l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~  107 (149)
                      .+++++ |+|+|||+++||||||+|++.+.. ++.+++.+||++|++|++|++||+.+|++.+.++++.++++|++++++
T Consensus         3 ~~av~~-Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~   81 (205)
T 1ryp_H            3 KGEVSL-GASIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKIWCCRSGSAADTQAIADIVQYHLELYTSQYGT   81 (205)
T ss_dssp             TTCCBC-CCCEEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEEBHHHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             CCCCcC-CceEEEEEeCCEEEEEEcCCcccCcEEEcCCcCceEEcCCCEEEEccCCHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            467876 999999999999999999999854 777888999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          108 EMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       108 ~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                       ++++.+++++++++|.|+++     |++++||||||++
T Consensus        82 -~~v~~la~~l~~~~~~~~~~-----~~~~~lvaG~D~~  114 (205)
T 1ryp_H           82 -PSTETAASVFKELCYENKDN-----LTAGIIVAGYDDK  114 (205)
T ss_dssp             -CCHHHHHHHHHHHHHHTTTT-----CCEEEEEEEEETT
T ss_pred             -CCHHHHHHHHHHHHHhhhcC-----ceEEEEEEEEecC
Confidence             99999999999999988652     9999999999973

>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=99.96  E-value=6e-28  Score=184.03  Aligned_cols=111  Identities=15%  Similarity=0.223  Sum_probs=101.7

Q ss_pred             hhccCceEEEEEcCCeEEEEEeccCCccc-cccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhC-CCC
Q 031996           32 VKAAGVTSIGVRGKDSVCVVTQKKVPDKL-LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYG-YEM  109 (149)
Q Consensus        32 v~~~G~t~igik~kdgVvlaad~~~~~~l-~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~-~~~  109 (149)
                      +++ |+|+|||+++||||||+|++.+..+ +..++.+||++|++|++|++||+.+|++.+.++++.+++.|+++++ +++
T Consensus         6 v~~-Gtt~vgi~~~dgVvlaaD~r~~~g~~i~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~   84 (222)
T 1ryp_M            6 GDN-GGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKL   84 (222)
T ss_dssp             CCC-CCEEEEEECSSCEEEEEECCEEETTEEEESCCCCCEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHTTTCCC
T ss_pred             ccC-CccEEEEEeCCEEEEEEecccccCCEecCCCcCcEEEeCCCEEEEccccHHHHHHHHHHHHHHHHHHHHHcCCCCC
Confidence            454 9999999999999999999999544 4677899999999999999999999999999999999999999999 999


Q ss_pred             CHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996          110 PVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus       110 ~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      +++.+|+++++.++  ++  +.|||++++||||||+++
T Consensus        85 ~v~~la~~l~~~ly--~~--r~~P~~v~~ivaG~D~~g  118 (222)
T 1ryp_M           85 SINSAARNIQHLLY--GK--RFFPYYVHTIIAGLDEDG  118 (222)
T ss_dssp             CHHHHHHHHHHHHH--TT--TTSCCCEEEEEEEECTTS
T ss_pred             CHHHHHHHHHHHHH--hc--CCCCceEEEEEEEEcCCC
Confidence            99999999999985  43  478999999999999754

>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=99.95  E-value=7.3e-28  Score=180.23  Aligned_cols=107  Identities=14%  Similarity=0.178  Sum_probs=98.9

Q ss_pred             ceEEEEEcCCeEEEEEeccCCcc-ccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVPDK-LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~~~-l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      +|+|||+++||||||+|++.+.. ++.+++.+||++|++|+++++||+.+|++.+.++++.+++.|+++++++++++.++
T Consensus         2 tt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la   81 (198)
T 1ryp_K            2 DIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYIQANIQLYSIREDYELSPQAVS   81 (198)
T ss_dssp             CCEEEEECSSCEEEEEECCEEETTEEEESCCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHH
T ss_pred             ceEEEEEECCEEEEEECCCcccCCEEEecCCCceEEeCCCEEEEeccCHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHH
Confidence            69999999999999999999844 44467899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAI  145 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~  145 (149)
                      +++++.+|.+++  ..+||++++||||||+
T Consensus        82 ~~l~~~l~~~~~--~r~p~~v~~lvaG~D~  109 (198)
T 1ryp_K           82 SFVRQELAKSIR--SRRPYQVNVLIGGYDK  109 (198)
T ss_dssp             HHHHHHHHHHTT--SSSCCCEEEEEEEEET
T ss_pred             HHHHHHHHHhcc--cCCCceEEEEEEEEeC
Confidence            999999998874  2359999999999996

>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=99.95  E-value=6.1e-28  Score=181.62  Aligned_cols=105  Identities=14%  Similarity=0.180  Sum_probs=99.6

Q ss_pred             ceEEEEEcCCeEEEEEeccCCcc-ccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVPDK-LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~~~-l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      +|+|||+++||||||+|++.++. ++.+++.+||++|++|++|++||+.+|++.+.+++|.+++.|+++++++++++.++
T Consensus         1 tt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la   80 (205)
T 1iru_H            1 TTIMAVQFDGGVVLGADSRTTTGSYIANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAA   80 (205)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHH
T ss_pred             CcEEEEEeCCEEEEEEcCCcccCcEEecCCcCceEEcCCCEEEEcCccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            58999999999999999999955 77788899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++++++|.|++     ||++++||||||++
T Consensus        81 ~~l~~~~~~~~~-----p~~~~~lvaG~D~~  106 (205)
T 1iru_H           81 SLFKEMCYRYRE-----DLMAGIIIAGWDPQ  106 (205)
T ss_dssp             HHHHHHHHHTTT-----TCCEEEEEEEEETT
T ss_pred             HHHHHHHHhcCc-----CccEEEEEEEEeCC
Confidence            999999998764     99999999999974

>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=99.95  E-value=8.1e-28  Score=187.68  Aligned_cols=112  Identities=16%  Similarity=0.188  Sum_probs=98.9

Q ss_pred             HHHhhccCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCC
Q 031996           29 FKAVKAAGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGY  107 (149)
Q Consensus        29 ~~av~~~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~  107 (149)
                      .||+++ |+|+|||+++||||||+|++.+ +.++..++.+||++|++|++|++||+.+|++.+.++++.+++.|++++++
T Consensus        23 ~kav~~-GtTivgi~~kdGVVlAaD~r~t~g~li~~~~~~KI~~I~d~i~~~~aG~~aD~~~l~~~lr~~~~~~~~~~~~  101 (261)
T 3nzj_H           23 PKATST-GTTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSR  101 (261)
T ss_dssp             --------CCEEEEEETTEEEEEEECCEEETTEEEETTCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHTS
T ss_pred             Cccccc-CceEEEEEECCEEEEEEcCCcccCCeeccCCcceEEEEcCCEEEEeccCHHHHHHHHHHHHHHHHHhHHhhCC
Confidence            688986 9999999999999999999998 56777889999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          108 EMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       108 ~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++++.+++++++.++.|     .|||++++||||||++
T Consensus       102 ~~~v~~~a~~l~~~l~~~-----~~~~gv~llvaG~D~~  135 (261)
T 3nzj_H          102 EPRVVSALQMLKQHLFKY-----QGHIGAYLIVAGVDPT  135 (261)
T ss_dssp             CCCHHHHHHHHHHHHHHT-----TTCSCEEEEEEEEETT
T ss_pred             CCCHHHHHHHHHHHHHHh-----cCcccEEEEEEEEeCC
Confidence            999999999999998743     4699999999999974

>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=99.95  E-value=2.4e-27  Score=178.26  Aligned_cols=106  Identities=20%  Similarity=0.333  Sum_probs=97.9

Q ss_pred             cCceEEEEEcCCeEEEEEeccCCccccc-cccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHH
Q 031996           35 AGVTSIGVRGKDSVCVVTQKKVPDKLLD-HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDV  113 (149)
Q Consensus        35 ~G~t~igik~kdgVvlaad~~~~~~l~~-~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~  113 (149)
                      +|+|+|||+++||||||+|++.+..+.. .++.+||++|+ |++|++||+.+|++.+.++++.+++.|+++++++++++.
T Consensus         7 ~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~-~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~   85 (204)
T 1ryp_J            7 NGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYG-HVFLGITGLATDVTTLNEMFRYKTNLYKLKEERAIEPET   85 (204)
T ss_dssp             SCCEEEEEECSSEEEEEEECCEEETTEEEESCCCCEEEET-TEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHH
T ss_pred             CCCeEEEEEeCCEEEEEEcCCcccCCEEeeCCcceEEEeC-CEEEEeeEcHHHHHHHHHHHHHHHHHHhhccCCCCCHHH
Confidence            4999999999999999999999965554 45899999999 999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhcCCccccceEEEEEEEeC
Q 031996          114 LAKWIADKSQVYTQHAYMRPLGVGLFLIEIAI  145 (149)
Q Consensus       114 la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~  145 (149)
                      +++++++++  |+++  ..||++++||||||+
T Consensus        86 la~~l~~~~--y~~~--~~P~~v~~lvaG~D~  113 (204)
T 1ryp_J           86 FTQLVSSSL--YERR--FGPYFVGPVVAGINS  113 (204)
T ss_dssp             HHHHHHHHH--HTTT--TSCCCEEEEEEEECT
T ss_pred             HHHHHHHHH--HHhc--CCCceEEEEEEEEeC
Confidence            999999999  5664  349999999999996

>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=99.95  E-value=1.3e-27  Score=180.76  Aligned_cols=106  Identities=13%  Similarity=0.165  Sum_probs=100.5

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      +|+|||+++||||||+|++.+ ++++.+++.+||++|++|++|++||+.+|++.+.++++.+++.|+++++++++++.++
T Consensus         1 tt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la   80 (212)
T 1ryp_L            1 TTTLAFRFQGGIIVAVDSRATAGNWVASQTVKRVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREKERISVAAAS   80 (212)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEECCBCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             CcEEEEEeCCEEEEEEcCCcccCCeEecCcccceeeeCCcEEEEccccHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            589999999999999999998 4788888999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++++++|.|++.    ||++++||||||++
T Consensus        81 ~~l~~~~~~~~~~----p~~v~~lvaG~D~~  107 (212)
T 1ryp_L           81 KILSNLVYQYKGA----GLSMGTMICGYTRK  107 (212)
T ss_dssp             HHHHHHHHHTTTS----CCCBEEEEEEEETT
T ss_pred             HHHHHHHHhhCCC----CceEEEEEEEEeCC
Confidence            9999999988753    99999999999953

>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=99.95  E-value=1.2e-27  Score=180.05  Aligned_cols=107  Identities=17%  Similarity=0.320  Sum_probs=98.8

Q ss_pred             cCceEEEEEcCCeEEEEEeccCCccccc-cccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHH
Q 031996           35 AGVTSIGVRGKDSVCVVTQKKVPDKLLD-HTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDV  113 (149)
Q Consensus        35 ~G~t~igik~kdgVvlaad~~~~~~l~~-~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~  113 (149)
                      +|+|+|||+++||||||+|++.+..+.. .++.+||++|++|++|++||+.+|++.+.++++.+++.|+++++++++++.
T Consensus         7 ~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~   86 (205)
T 1iru_J            7 NGGAVMAMKGKNCVAIAADRRFGIQAQLVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFRLNLYELKEGRQIKPYT   86 (205)
T ss_dssp             SCCEEEEEECSSEEEEEEECCEEETTEEEESCCCCEEECSTTEEEECCSCHHHHHHHHHHHHHHHHHHHHHSSSCCCHHH
T ss_pred             CCCeEEEEEeCCEEEEEECCccccCCeEeecCCccEEEeCCCEEEEccccHHHHHHHHHHHHHHHHHHHhhcCCCCCHHH
Confidence            4999999999999999999999965554 458899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhcCCccccceEEEEEEEeC
Q 031996          114 LAKWIADKSQVYTQHAYMRPLGVGLFLIEIAI  145 (149)
Q Consensus       114 la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~  145 (149)
                      +++++++++  |+++  ..||++++||||||+
T Consensus        87 la~~l~~~~--y~~r--~~P~~v~~lvaG~D~  114 (205)
T 1iru_J           87 LMSMVANLL--YEKR--FGPYYTEPVIAGLDP  114 (205)
T ss_dssp             HHHHHHHHH--HTTT--TSCCSCCCEEEEECT
T ss_pred             HHHHHHHHH--HHhc--CCCceEEEEEEEEeC
Confidence            999999999  5653  459999999999995

>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=99.95  E-value=1.4e-27  Score=178.77  Aligned_cols=105  Identities=18%  Similarity=0.149  Sum_probs=98.9

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      ||+|||+++||||||+|++.+ +.++..++.+||++|++|++|++||+.+|++.+.+++|.+++.|+++++++++++.++
T Consensus         1 TT~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a   80 (199)
T 3unf_N            1 TTIMAVEFDGGVVVGSDSRVSAGTAVVNRVFDKLSPLHQRIFCALSGSAADAQAIADMAAYQLELHGLELEEPPLVLAAA   80 (199)
T ss_dssp             CEEEEEECSSCEEEEECCCEEETTEEEESSCCCEEEEETTEEEEECSCHHHHHHHHHHHHHHHHHHHHHTTSCCCHHHHH
T ss_pred             CeEEEEEeCCeEEEEECCcccCCceeEccccCceEEcCCCEEEEecccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            699999999999999999998 4577788999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++++++|.+     .|||++++||||||++
T Consensus        81 ~~l~~~l~~~-----~~p~~v~~lvaG~D~~  106 (199)
T 3unf_N           81 NVVKNISYKY-----REDLLAHLIVAGWDQR  106 (199)
T ss_dssp             HHHHHHHHHT-----TTTCCCCEEEEEEETT
T ss_pred             HHHHHHHHhc-----CCCceEEEEEEEEeCC
Confidence            9999999854     4599999999999974

>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=99.95  E-value=3.1e-27  Score=177.67  Aligned_cols=106  Identities=15%  Similarity=0.194  Sum_probs=99.7

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      +|+|||+++||||||+|++.+ +.++.+++.+||++|++|++|++||+.+|++.+.++++.+++.|+++++++++++.++
T Consensus         1 tt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la   80 (204)
T 1iru_L            1 TTTLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQCRIYELRNKERISVAAAS   80 (204)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEECCBCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             CeEEEEEeCCEEEEEEcCCcccCCEEEcCcccceEEcCCCEEEEccCcHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            589999999999999999998 4788888999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++++++|.++    .+||+|++||||||++
T Consensus        81 ~~l~~~~~~~r----~~~~~v~~lvaG~D~~  107 (204)
T 1iru_L           81 KLLANMVYQYK----GMGLSMGTMICGWDKR  107 (204)
T ss_dssp             HHHHHHHHTTT----TSCCCBEEEEEEECSS
T ss_pred             HHHHHHHHHhC----CCCeeEEEEEEEEeCC
Confidence            99999999764    3599999999999964

>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=99.95  E-value=7.2e-27  Score=175.27  Aligned_cols=108  Identities=18%  Similarity=0.278  Sum_probs=98.2

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      +|+|||+++||||||+|++.+ +.++.+++.+||++|++|+++++||+.+|++.+.++++.+++.|+++++++++++.++
T Consensus         2 tt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a   81 (201)
T 1iru_K            2 EYLIGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYIQKNVQLYKMRNGYELSPTAAA   81 (201)
T ss_dssp             CCEEEEECSSEEEEEEECCEEETTEEEESSCCCEEECSSSEEEEEEESTTHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             ceEEEEEeCCEEEEEEcCccccCcEEEccCcceEEEecCCEEEEeCcCHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            699999999999999999998 4788888999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++++.+..+ .+ ..|||++++||||||++
T Consensus        82 ~~~~~~l~~~-~~-~~~p~~~~~lvaG~D~~  110 (201)
T 1iru_K           82 NFTRRNLADC-LR-SRTPYHVNLLLAGYDEH  110 (201)
T ss_dssp             HHHHHHHHHH-HT-SSSCCCEEEEEEEEETT
T ss_pred             HHHHHHHHHH-Hh-cCCCccEEEEEEEEeCC
Confidence            9998876322 22 33799999999999974

>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=99.94  E-value=1.3e-26  Score=178.31  Aligned_cols=105  Identities=15%  Similarity=0.182  Sum_probs=97.6

Q ss_pred             ceEEEEEcCCeEEEEEeccCCccc-cccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVPDKL-LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~~~l-~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      ||+|||+++||||||+|+|.++.+ +..++.+||++|++|++|++||+.+|++.+.++++.++++|+++++++++++.++
T Consensus         1 TT~vgi~~kdgVVlaaD~r~t~g~~v~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la   80 (234)
T 3unf_H            1 TTIAGLVFRDGVILGADTRATNDSVVADKSCEKIHFIAPKIYCCGAGVAADTEMTTRMAASKMELHALSTGREPRVATVT   80 (234)
T ss_dssp             CEEEEEECSSEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHCSCCCHHHHH
T ss_pred             CeEEEEEeCCEEEEEECCCcccCCEeccCccccEEEecCCEEEEecccHHHHHHHHHHHHHHHHhhHHhcCCCCCHHHHH
Confidence            699999999999999999999554 4567899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      ++++++++.|     .+||++++||||||++
T Consensus        81 ~~l~~~l~~~-----~~p~~v~llvaG~D~~  106 (234)
T 3unf_H           81 RILRQTLFRY-----QGHVGASLVVGGVDLN  106 (234)
T ss_dssp             HHHHHHHHHT-----TTCSCEEEEEEEEETT
T ss_pred             HHHHHHHHhc-----CCCccEEEEEEEEeCC
Confidence            9999999854     3599999999999974

>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=99.94  E-value=1.8e-26  Score=175.88  Aligned_cols=105  Identities=14%  Similarity=0.172  Sum_probs=97.4

Q ss_pred             ceEEEEEcCCeEEEEEeccCCcc-ccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVPDK-LLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~~~-l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      +|+|||+++||||||+|++.++. ++..++.+||++|++|++|++||+.+|++.+.++++.+++.|+++++++++++.++
T Consensus         1 TT~vgi~~~dgVvlaaD~r~t~g~~~~~~~~~KI~~i~d~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a   80 (222)
T 1ryp_I            1 TTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSAL   80 (222)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHH
T ss_pred             CeEEEEEECCEEEEEEcCCcccCCeeecCCcccEEEecCCEEEEecccHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            58999999999999999999854 45567889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++++.++.|     .|||++++||||||++
T Consensus        81 ~~l~~~l~~~-----~~p~~v~~lvaG~D~~  106 (222)
T 1ryp_I           81 QMLKQHLFKY-----QGHIGAYLIVAGVDPT  106 (222)
T ss_dssp             HHHHHHHHHT-----TTCSCEEEEEEEEETT
T ss_pred             HHHHHHHhhc-----CCCCCeeEEEEEEeCC
Confidence            9999998754     4799999999999974

>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=99.94  E-value=7.4e-26  Score=173.87  Aligned_cols=105  Identities=15%  Similarity=0.159  Sum_probs=96.9

Q ss_pred             ceEEEEEcCCeEEEEEeccCCccc-cccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVPDKL-LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~~~l-~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      +|+|||+++||||||+|++.+..+ +..++.+||++|++|++|++||+.+|++.+.++++.++++|+++++++++++.++
T Consensus         1 TTivgi~~~dgVVlaaD~r~t~g~~~~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la   80 (234)
T 1iru_I            1 TTIAGVVYKDGIVLGADTRATEGMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGRLPRVVTAN   80 (234)
T ss_dssp             CCEEEEEETTEEEEEECCCEESSSBEEESSCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHCSCCCHHHHH
T ss_pred             CeEEEEEeCCEEEEEEcCCcccCceeccCcccceEEecCCEEEEecCcHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHH
Confidence            589999999999999999998554 4457889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++++.+|.|     .+||++++||||||++
T Consensus        81 ~~l~~~l~~~-----~~~~~v~llvaG~D~~  106 (234)
T 1iru_I           81 RMLKQMLFRY-----RGYIGAALVLGGVDVT  106 (234)
T ss_dssp             HHHHHHHHHT-----TTCSCEEEEEEEECSS
T ss_pred             HHHHHHHHhc-----CCCCceeEEEEEEcCC
Confidence            9999998765     3599999999999974

>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=99.88  E-value=1.1e-22  Score=150.48  Aligned_cols=98  Identities=16%  Similarity=0.189  Sum_probs=85.2

Q ss_pred             cCceEEEEEcCCeEEEEEeccCC-ccc-cccccccceeee-cCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCH
Q 031996           35 AGVTSIGVRGKDSVCVVTQKKVP-DKL-LDHTSVTHLFPI-TKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPV  111 (149)
Q Consensus        35 ~G~t~igik~kdgVvlaad~~~~-~~l-~~~~~~~KI~~I-~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~  111 (149)
                      +|+|+|||+++||||||+|++.+ +.+ +.+++.+||++| ++|+++++||+.+|++.+.++++.++++|+   +  +  
T Consensus         4 ~GtTivgi~~~dgVvlaaD~r~t~g~~~i~~~~~~KI~~i~~~~i~~~~aG~~aD~~~l~~~~~~~~~~y~---g--~--   76 (180)
T 2z3b_A            4 HATTIFAVQHKGRSAMSGDGQVTFGQAVVMKHTARKVRKLFNGKVLAGFAGSVADAFTLFEKFEAKLEEYN---G--N--   76 (180)
T ss_dssp             CCCCEEEEEETTEEEEEECCCEEETTTEEEESCCCCEEEETTTTEEEEECSCHHHHHHHHHHHHHHHHHTT---T--C--
T ss_pred             CCeEEEEEEECCEEEEEECCCccCCCceEecCCCCcEEEECCCCEEEEeCchHHHHHHHHHHHHHHHHHhc---C--C--
Confidence            49999999999999999999998 467 888999999999 999999999999999999999999999987   3  2  


Q ss_pred             HHHHHHHHHHHHHHhhcCCccccceEEEEE
Q 031996          112 DVLAKWIADKSQVYTQHAYMRPLGVGLFLI  141 (149)
Q Consensus       112 ~~la~~l~~~~~~~t~~~~~rP~~v~~lia  141 (149)
                        +.+.++.+.+.+++....|||++++||+
T Consensus        77 --~~~~~~~l~~~~~~~~~~rp~~~~~lva  104 (180)
T 2z3b_A           77 --LKRAAVELAKEWRSDKVLRKLEAMLIVM  104 (180)
T ss_dssp             --HHHHHHHHHHHHHHCTTGGGCCCCEEEE
T ss_pred             --hHHHHHHHHHHHHhhhCcCcceEEEEEE
Confidence              3333444555566677889999999999

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

Probab=99.87  E-value=3.3e-22  Score=146.57  Aligned_cols=96  Identities=15%  Similarity=0.097  Sum_probs=81.7

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeee-cCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPI-TKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVL  114 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I-~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~l  114 (149)
                      +|+|||+++||||||+|++.+ +.++.+++.+||++| ++|+++++||+.+|++.+.+++|.++++|+.+     .++.+
T Consensus         1 tt~vgi~~~dgVvlaaD~r~~~g~~i~~~~~~Ki~~i~~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~-----~~~~~   75 (171)
T 1m4y_A            1 TTILVVRRNGQTVMGGDGQVTFGSTVLKGNARKVRKLGEGKVLAGFAGSVADAMTLFDRFEAKLREWGGN-----LTKAA   75 (171)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHHHHHHHHHHTTTC-----HHHHH
T ss_pred             CeEEEEEECCEEEEEECCCcccCCEEEeCCcceEEEeCCCCEEEEeCccHHHHHHHHHHHHHHHHHhccc-----HHHHH
Confidence            589999999999999999998 578888899999999 99999999999999999999999999998744     24444


Q ss_pred             HHHHHHHHHHHhhcCCccccceEEEEE
Q 031996          115 AKWIADKSQVYTQHAYMRPLGVGLFLI  141 (149)
Q Consensus       115 a~~l~~~~~~~t~~~~~rP~~v~~lia  141 (149)
                      ++.    .+.+++++..|||++++|++
T Consensus        76 ~~l----~~~~~~~~~~~~~~~~~lv~   98 (171)
T 1m4y_A           76 VEL----AKDWRTDRVLRRLEALLLVA   98 (171)
T ss_dssp             HHH----HHHHHHCTTGGGCCCEEEEE
T ss_pred             HHH----HHHHHHhCCCCceEEEEEEE
Confidence            443    33445555678999999998

>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=99.86  E-value=1.6e-21  Score=143.27  Aligned_cols=97  Identities=19%  Similarity=0.113  Sum_probs=81.1

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeee-cCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPI-TKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVL  114 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I-~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~l  114 (149)
                      +|+|||+++||||||+|++.+ +.++.+++.+||++| ++|+++++||+.+|++.+.+++|.++++|+.      ++   
T Consensus         1 tT~vgi~~~dgVvlaaD~r~t~g~~i~~~~~~Ki~~i~~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~------~~---   71 (174)
T 1g3k_A            1 TTIVSVRRNGQVVVGGDGQVSLGNTVMKGNARKVRRLYNGKVLAGFAGGTADAFTLFELFERKLEMHQG------HL---   71 (174)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHHHHHHHHHHTTT------CH---
T ss_pred             CeEEEEEECCEEEEEECCCCccCCeeEeCCCCcEEEECCCCEEEEeCccHHHHHHHHHHHHHHHHHhcC------cH---
Confidence            589999999999999999998 457788899999999 9999999999999999999999999999875      33   


Q ss_pred             HHHHHHHHHHHhhcCCccccceEEEEEEEe
Q 031996          115 AKWIADKSQVYTQHAYMRPLGVGLFLIEIA  144 (149)
Q Consensus       115 a~~l~~~~~~~t~~~~~rP~~v~~liaG~D  144 (149)
                      ...++.+.+.+++++..||++  ++++|+|
T Consensus        72 ~~~~~~l~~~~~~~~~~r~~~--~~l~g~d   99 (174)
T 1g3k_A           72 LKSAVELAKDWRTDRALRKLE--AMLIVAD   99 (174)
T ss_dssp             HHHHHHHHHHHHHSTTGGGCC--CEEEEEC
T ss_pred             HHHHHHHHHHHHhccCcCcce--EEEEEEC
Confidence            344444455556666677865  6777777

---

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	149
d1irua_	244	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	1e-54
d1irug_	245	d.153.1.4 (G:) Proteasome alpha subunit (non-catal	3e-48
d1rypg_	244	d.153.1.4 (G:) Proteasome alpha subunit (non-catal	3e-47
d1rypa_	243	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	4e-46
d1irue_	234	d.153.1.4 (E:) Proteasome alpha subunit (non-catal	2e-44
d1j2pa_	243	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	2e-44
d1irud_	243	d.153.1.4 (D:) Proteasome alpha subunit (non-catal	7e-44
d1rypd_	241	d.153.1.4 (D:) Proteasome alpha subunit (non-catal	2e-43
d1rypf_	233	d.153.1.4 (F:) Proteasome alpha subunit (non-catal	2e-43
d1iruc_	250	d.153.1.4 (C:) Proteasome alpha subunit (non-catal	5e-43
d1rype_	242	d.153.1.4 (E:) Proteasome alpha subunit (non-catal	1e-42
d1rypc_	244	d.153.1.4 (C:) Proteasome alpha subunit (non-catal	2e-42
d1irub_	233	d.153.1.4 (B:) Proteasome alpha subunit (non-catal	3e-42
d1iruf_	238	d.153.1.4 (F:) Proteasome alpha subunit (non-catal	8e-42
d1rypb_	250	d.153.1.4 (B:) Proteasome alpha subunit (non-catal	1e-41
d1yara1	221	d.153.1.4 (A:13-233) Proteasome alpha subunit (non	4e-40
d1q5qa_	227	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	3e-24
d1ryp2_	233	d.153.1.4 (2:) Proteasome beta subunit (catalytic)	7e-17
d1ryp1_	222	d.153.1.4 (1:) Proteasome beta subunit (catalytic)	2e-16
d1iru2_	217	d.153.1.4 (2:) Proteasome beta subunit (catalytic)	6e-15
d1rypj_	204	d.153.1.4 (J:) Proteasome beta subunit (catalytic)	1e-14
d1yarh1	203	d.153.1.4 (H:1-203) Proteasome beta subunit (catal	2e-14
d1iru1_	213	d.153.1.4 (1:) Proteasome beta subunit (catalytic)	3e-14
d1rypk_	198	d.153.1.4 (K:) Proteasome beta subunit (catalytic)	3e-13
d1iruj_	204	d.153.1.4 (J:) Proteasome beta subunit (catalytic)	5e-13
d1iruk_	199	d.153.1.4 (K:) Proteasome beta subunit (catalytic)	6e-13
d1rypi_	222	d.153.1.4 (I:) Proteasome beta subunit (catalytic)	1e-12
d1irui_	220	d.153.1.4 (I:) Proteasome beta subunit (catalytic)	1e-12
d1irul_	201	d.153.1.4 (L:) Proteasome beta subunit (catalytic)	2e-12
d1q5qh_	224	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	2e-12
d1rypl_	212	d.153.1.4 (L:) Proteasome beta subunit (catalytic)	5e-12
d1j2qh_	202	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	6e-12
d1iruh_	202	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	1e-10
d1ryph_	205	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	2e-09

>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 =  169 bits (430), Expect = 1e-54
 Identities = 97/142 (68%), Positives = 118/142 (83%)

Query: 2   SRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLL 61
           SRGS  G+DRHITIFSPEGRL+QVEYAFKA+   G+TS+ VRGKD   +VTQKKVPDKLL
Sbjct: 1   SRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLL 60

Query: 62  DHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADK 121
           D ++VTHLF IT+ +G + TGMTAD+R+ VQ+ARYEAA +++KYGYE+PVD+L K IAD 
Sbjct: 61  DSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADI 120

Query: 122 SQVYTQHAYMRPLGVGLFLIEI 143
           SQVYTQ+A MRPLG  + LI I
Sbjct: 121 SQVYTQNAEMRPLGCCMILIGI 142

>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 =  154 bits (389), Expect = 3e-48
 Identities = 57/138 (41%), Positives = 80/138 (57%), Gaps = 1/138 (0%)

Query: 6   GGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTS 65
           G GYD   + FSP+GR+FQVEYA KAV+    T+IG+R KD V    +K V  KL +  S
Sbjct: 4   GTGYDLSASTFSPDGRVFQVEYAMKAVEN-SSTAIGIRCKDGVVFGVEKLVLSKLYEEGS 62

Query: 66  VTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVY 125
              LF + +++G+   G+ ADAR+L   AR EA+ FR  +GY +P+  LA  +A     Y
Sbjct: 63  NKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAY 122

Query: 126 TQHAYMRPLGVGLFLIEI 143
           T ++ +RP G    L   
Sbjct: 123 TLYSAVRPFGCSFMLGSY 140

>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 =  151 bits (382), Expect = 3e-47
 Identities = 49/136 (36%), Positives = 73/136 (53%), Gaps = 1/136 (0%)

Query: 6   GGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTS 65
           G GYD   ++FSP+GR FQVEYA KAV+  G TSIG++  D V    +K +  KLL    
Sbjct: 1   GTGYDLSNSVFSPDGRNFQVEYAVKAVEN-GTTSIGIKCNDGVVFAVEKLITSKLLVPQK 59

Query: 66  VTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVY 125
              +  + +++G + +G+  D R LV + R EAA F+  Y   +P+   A  +    Q +
Sbjct: 60  NVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAH 119

Query: 126 TQHAYMRPLGVGLFLI 141
           T +  +RP GV     
Sbjct: 120 TLYNSVRPFGVSTIFG 135

>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 =  148 bits (374), Expect = 4e-46
 Identities = 82/134 (61%), Positives = 104/134 (77%)

Query: 8   GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVT 67
           GYDRHITIFSPEGRL+QVEYAFKA     + S+ VRGKD   V++QKKVPDKLLD T+V+
Sbjct: 2   GYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPTTVS 61

Query: 68  HLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQ 127
           ++F I++ +G++  G   DAR    +A+ EAAEFR+KYGY+MP DVLAK +A+ SQ+YTQ
Sbjct: 62  YIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQ 121

Query: 128 HAYMRPLGVGLFLI 141
            AYMRPLGV L  +
Sbjct: 122 RAYMRPLGVILTFV 135

>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 =  144 bits (363), Expect = 2e-44
 Identities = 47/138 (34%), Positives = 79/138 (57%), Gaps = 6/138 (4%)

Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YDR +  FSPEGRLFQVEY  +A+K  G T+IG++  + VC+  +K++   L++ +S+  
Sbjct: 1   YDRGVNTFSPEGRLFQVEYDIEAIKL-GSTAIGIQTSEGVCLAVEKRITSPLMEPSSIEK 59

Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +  I  ++G   +G+ ADA+TL+ +AR E     F Y   M V+ + + +++ +  + + 
Sbjct: 60  IVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEE 119

Query: 129 -----AYMRPLGVGLFLI 141
                A  RP GV L   
Sbjct: 120 DADPGAMSRPFGVALLFG 137

>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 =  144 bits (363), Expect = 2e-44
 Identities = 61/142 (42%), Positives = 89/142 (62%), Gaps = 1/142 (0%)

Query: 8   GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVT 67
           GYDR IT+FSP+GRLFQVEYA +AVK  G T+IG++ K+ V ++  K+V  KLL+  ++ 
Sbjct: 4   GYDRAITVFSPDGRLFQVEYAREAVKR-GATAIGIKCKEGVILIADKRVGSKLLEKDTIE 62

Query: 68  HLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQ 127
            ++ I +++    +G+ ADAR L+ +AR EA   R  Y   + V  LAK I D  Q YTQ
Sbjct: 63  KIYKIDEHICAATSGLVADARVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQ 122

Query: 128 HAYMRPLGVGLFLIEIAIPSEL 149
           +  +RP GV L +  +    +L
Sbjct: 123 YGGVRPFGVSLLIAGVNEVPKL 144

>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 =  142 bits (359), Expect = 7e-44
 Identities = 53/133 (39%), Positives = 78/133 (58%), Gaps = 1/133 (0%)

Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YDR IT+FSP+G LFQVEYA +AVK  G T++GVRG+D V +  +KK   KL D  +V  
Sbjct: 2   YDRAITVFSPDGHLFQVEYAQEAVKK-GSTAVGVRGRDIVVLGVEKKSVAKLQDERTVRK 60

Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +  +   + +   G+TADAR ++ +AR E    R      + V+ + ++IA   Q YTQ 
Sbjct: 61  ICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQS 120

Query: 129 AYMRPLGVGLFLI 141
              RP G+   ++
Sbjct: 121 NGRRPFGISALIV 133

>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 =  141 bits (356), Expect = 2e-43
 Identities = 50/135 (37%), Positives = 81/135 (60%), Gaps = 2/135 (1%)

Query: 8   GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLD-HTSV 66
           GYDR ++IFSP+G +FQVEYA +AVK  G  ++GV+GK+ V +  +++   KL D   + 
Sbjct: 1   GYDRALSIFSPDGHIFQVEYALEAVK-RGTCAVGVKGKNCVVLGCERRSTLKLQDTRITP 59

Query: 67  THLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYT 126
           + +  I  ++ L  +G+ AD+R L+++AR EA   R      + V+ L +++A   Q YT
Sbjct: 60  SKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYT 119

Query: 127 QHAYMRPLGVGLFLI 141
           Q   +RP GV   + 
Sbjct: 120 QSGGVRPFGVSTLIA 134

>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 =  140 bits (355), Expect = 2e-43
 Identities = 44/133 (33%), Positives = 65/133 (48%), Gaps = 3/133 (2%)

Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YD     FSP GRLFQVEYA +A+K  G  ++G+R      +V  K+  D+L        
Sbjct: 5   YDGDTVTFSPTGRLFQVEYALEAIK-QGSVTVGLRSNTHAVLVALKRNADELSS--YQKK 61

Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +    +++GL   G+  DAR L    R +       +  ++ V+     + DK+Q  TQ 
Sbjct: 62  IIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQS 121

Query: 129 AYMRPLGVGLFLI 141
              RP GVGL +I
Sbjct: 122 YGGRPYGVGLLII 134

>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 =  140 bits (354), Expect = 5e-43
 Identities = 46/135 (34%), Positives = 69/135 (51%), Gaps = 2/135 (1%)

Query: 8   GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVT 67
            YD   TIFSPEGRL+QVEYA +A+     T +G+   D V +  +++   KLLD    +
Sbjct: 3   RYDSRTTIFSPEGRLYQVEYAMEAIG-HAGTCLGILANDGVLLAAERRNIHKLLDEVFFS 61

Query: 68  H-LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYT 126
             ++ + + +     G+T+DA  L  + R  A  +  +Y   +P + L   + D  Q YT
Sbjct: 62  EKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYT 121

Query: 127 QHAYMRPLGVGLFLI 141
           Q    RP GV L  I
Sbjct: 122 QFGGKRPFGVSLLYI 136

>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 =  139 bits (350), Expect = 1e-42
 Identities = 46/140 (32%), Positives = 78/140 (55%), Gaps = 7/140 (5%)

Query: 10  DRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHL 69
           DR ++ FSPEGRLFQVEY+ +A+K  G T+IG+  K+ V +  +K+    LL+  S+  +
Sbjct: 1   DRGVSTFSPEGRLFQVEYSLEAIKL-GSTAIGIATKEGVVLGVEKRATSPLLESDSIEKI 59

Query: 70  FPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH- 128
             I +++G   +G+TADAR++++ AR  A      Y  ++ V+ L + + D +  + +  
Sbjct: 60  VEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGA 119

Query: 129 -----AYMRPLGVGLFLIEI 143
                   RP GV L +   
Sbjct: 120 SGEERLMSRPFGVALLIAGH 139

>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 =  138 bits (349), Expect = 2e-42
 Identities = 50/135 (37%), Positives = 76/135 (56%), Gaps = 2/135 (1%)

Query: 8   GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLD-HTSV 66
            YD   TIFSPEGRL+QVEYA +++     T+IG+   D + +  ++KV   LL+  TS 
Sbjct: 4   RYDSRTTIFSPEGRLYQVEYALESIS-HAGTAIGIMASDGIVLAAERKVTSTLLEQDTST 62

Query: 67  THLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYT 126
             L+ +   + +   G+TADA  L+  AR  A  +   Y  ++PV++L + ++D  Q YT
Sbjct: 63  EKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYT 122

Query: 127 QHAYMRPLGVGLFLI 141
           QH  +RP GV     
Sbjct: 123 QHGGLRPFGVSFIYA 137

>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 =  138 bits (348), Expect = 3e-42
 Identities = 53/136 (38%), Positives = 76/136 (55%), Gaps = 1/136 (0%)

Query: 5   SGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHT 64
           +  GY   +T FSP G+L Q+EYA  AV   G  S+G++  + V + T+KK    L D  
Sbjct: 1   AERGYSFSLTTFSPSGKLVQIEYALAAVAG-GAPSVGIKAANGVVLATEKKQKSILYDER 59

Query: 65  SVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQV 124
           SV  + PITK++GL+ +GM  D R LV +AR  A ++   Y   +P   L + +A   Q 
Sbjct: 60  SVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQE 119

Query: 125 YTQHAYMRPLGVGLFL 140
           YTQ   +RP GV L +
Sbjct: 120 YTQSGGVRPFGVSLLI 135

>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 =  137 bits (345), Expect = 8e-42
 Identities = 46/133 (34%), Positives = 72/133 (54%), Gaps = 3/133 (2%)

Query: 9   YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH 68
           YD  +T++SP+GR+ Q+EYA +AVK  G  ++G++ K    +V  K+   +L        
Sbjct: 3   YDNDVTVWSPQGRIHQIEYAMEAVK-QGSATVGLKSKTHAVLVALKRAQSELAA--HQKK 59

Query: 69  LFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQH 128
           +  +  ++G+   G+TADAR L    R E  + RF +   +PV  L   I  K+Q+ TQ 
Sbjct: 60  ILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQR 119

Query: 129 AYMRPLGVGLFLI 141
              RP GVGL + 
Sbjct: 120 YGRRPYGVGLLIA 132

>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 =  137 bits (345), Expect = 1e-41
 Identities = 47/142 (33%), Positives = 74/142 (52%), Gaps = 6/142 (4%)

Query: 1   MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL 60
           M+      Y   +T FSP G+L Q++YA  AVK  GVTS+G++  + V + T+KK    L
Sbjct: 1   MTDR----YSFSLTTFSPSGKLGQIDYALTAVK-QGVTSLGIKATNGVVIATEKKSSSPL 55

Query: 61  LDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAA-EFRFKYGYEMPVDVLAKWIA 119
               +++ +  +T  +G + +GM  D R LV ++R  A   ++  YG   P  +L   +A
Sbjct: 56  AMSETLSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVA 115

Query: 120 DKSQVYTQHAYMRPLGVGLFLI 141
              Q  TQ   +RP GV L + 
Sbjct: 116 KIMQEATQSGGVRPFGVSLLIA 137

>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 =  132 bits (332), Expect = 4e-40
 Identities = 52/128 (40%), Positives = 81/128 (63%), Gaps = 1/128 (0%)

Query: 14  TIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPIT 73
           T+FSP+GRLFQVEYA +AVK  G T++G++  + V +++ KKV  +L++  S+  +  I 
Sbjct: 1   TVFSPDGRLFQVEYAREAVKK-GSTALGMKFANGVLLISDKKVRSRLIEQNSIEKIQLID 59

Query: 74  KYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRP 133
            Y+  + +G+ ADAR LV  AR  A + +  YG  + ++ L K +AD+ Q YTQ+  +RP
Sbjct: 60  DYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRP 119

Query: 134 LGVGLFLI 141
            GV L   
Sbjct: 120 YGVSLIFA 127

>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 = 91.2 bits (226), Expect = 3e-24
 Identities = 21/121 (17%), Positives = 41/121 (33%), Gaps = 10/121 (8%)

Query: 24  QVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGM 83
           + E A K +   G + + +  +D V  V +          T++  +  +   LG  A G 
Sbjct: 8   RSELARKGIAR-GRSVVVLTFRDGVLFVAENPS-------TALHKVSELYDRLGFAAVGK 59

Query: 84  TADARTLVQQARYEAAEFRFKYGY-EMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIE 142
             +   L +     A    + Y   ++    LA   A            +P  V + + E
Sbjct: 60  YNEFENLRRAGIVHADMRGYSYDRRDVTGRSLANAYAQT-LGTIFTEQPKPYEVEICVAE 118

Query: 143 I 143
           +
Sbjct: 119 V 119

>d1ryp2_ d.153.1.4 (2:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 233

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 72.1 bits (176), Expect = 7e-17
 Identities = 16/112 (14%), Positives = 40/112 (35%), Gaps = 8/112 (7%)

Query: 36  GVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQA 94
           G + I ++  + V +          LL    V  L P+     +  +G  +D + + +  
Sbjct: 8   GTSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLL 67

Query: 95  RYEAAEFRFKY-----GYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLI 141
           +    E  +          +    + +++A    +Y + + M PL   + + 
Sbjct: 68  KDLVTENAYDNPLADAEEALEPSYIFEYLAT--VMYQRRSKMNPLWNAIIVA 117

>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 = 70.6 bits (172), Expect = 2e-16
 Identities = 17/107 (15%), Positives = 33/107 (30%), Gaps = 4/107 (3%)

Query: 36  GVTSIGVRGKDSVCVVTQKKVPDKLL-DHTSVTHLFPITKYLGLLATGMTADARTLVQQA 94
           G T +G+ G+D   +    +       +      +F     + + A G  AD   LV++ 
Sbjct: 9   GGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNIVMSANGFAADGDALVKRF 68

Query: 95  RYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLI 141
           +     + F +  +          A   Q         P  V   + 
Sbjct: 69  KNSVKWYHFDHNDKKLSI---NSAARNIQHLLYGKRFFPYYVHTIIA 112

>d1iru2_ d.153.1.4 (2:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 217

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 = 66.7 bits (162), Expect = 6e-15
 Identities = 18/108 (16%), Positives = 40/108 (37%), Gaps = 4/108 (3%)

Query: 36  GVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQA 94
           G + +GV+ +  V +          L    +++ +  +     L A+G  AD + L Q  
Sbjct: 8   GTSVLGVKFEGGVVIAADMLGSYGSLARFRNISRIMRVNNSTMLGASGDYADFQYLKQVL 67

Query: 95  RYEAAEFRFKY-GYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLI 141
                +      G+      +  W+     +Y++ + M PL   + + 
Sbjct: 68  GQMVIDEELLGDGHSYSPRAIHSWLTR--AMYSRRSKMNPLWNTMVIG 113

>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 = 66.0 bits (160), Expect = 1e-14
 Identities = 18/112 (16%), Positives = 39/112 (34%)

Query: 36  GVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQAR 95
           G   + + GKD V +    ++  + L  ++         ++ L  TG+  D  TL +  R
Sbjct: 8   GGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDVTTLNEMFR 67

Query: 96  YEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS 147
           Y+   ++ K    +  +   + ++          Y     V     +   P 
Sbjct: 68  YKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPF 119

>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 = 65.2 bits (158), Expect = 2e-14
 Identities = 28/101 (27%), Positives = 52/101 (51%), Gaps = 1/101 (0%)

Query: 38  TSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARY 96
           T++G+  KD+V + T+++V  +  + H +   LF I  Y G+   G+  DA+ LV+  + 
Sbjct: 2   TTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKA 61

Query: 97  EAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVG 137
           E   +R +    MP++ +A  +++         YM  L VG
Sbjct: 62  ELELYRLQRRVNMPIEAVATLLSNMLNQVKYMPYMVQLLVG 102

>d1iru1_ d.153.1.4 (1:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 213

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 = 64.5 bits (156), Expect = 3e-14
 Identities = 16/108 (14%), Positives = 34/108 (31%), Gaps = 1/108 (0%)

Query: 36  GVTSIGVRGKDSVCVVTQKKVPDKLLDH-TSVTHLFPITKYLGLLATGMTADARTLVQQA 94
           G T + + G+D   V +  ++ +    H       + +T    +  +G   D  TL +  
Sbjct: 9   GGTILAIAGEDFAIVASDTRLSEGFSIHTRDSPKCYKLTDKTVIGCSGFHGDCLTLTKII 68

Query: 95  RYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIE 142
                 ++      M    +A  ++          Y     +G    E
Sbjct: 69  EARLKMYKHSNNKAMTTGAIAAMLSTILYSRRFFPYYVYNIIGGLDEE 116

>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 = 61.7 bits (149), Expect = 3e-13
 Identities = 14/107 (13%), Positives = 37/107 (34%), Gaps = 3/107 (2%)

Query: 38  TSIGVRGKDSVCVVTQKKVPDKLLDHTSVTH-LFPITKYLGLLATGMTADARTLVQQARY 96
             +G+R +DSV + + K V   +            ++ +  +   G   D     +  + 
Sbjct: 3   IILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYIQA 62

Query: 97  EAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEI 143
               +  +  YE+    ++ ++  +     +    RP  V + +   
Sbjct: 63  NIQLYSIREDYELSPQAVSSFVRQELAKSIR--SRRPYQVNVLIGGY 107

>d1iruj_ d.153.1.4 (J:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 204

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score = 61.4 bits (148), Expect = 5e-13
 Identities = 17/103 (16%), Positives = 40/103 (38%), Gaps = 1/103 (0%)

Query: 36  GVTSIGVRGKDSVCVVTQKKVPDKLLDHT-SVTHLFPITKYLGLLATGMTADARTLVQQA 94
           G   + ++GK+ V +   ++   +    T     +FP+   L +   G+  D +T+ Q+ 
Sbjct: 7   GGAVMAMKGKNCVAIAADRRFGIQAQLVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRL 66

Query: 95  RYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVG 137
           ++    +  K G ++    L   +A+         Y     + 
Sbjct: 67  KFRLNLYELKEGRQIKPYTLMSMVANLLYEKRFGPYYTEPVIA 109

>d1iruk_ d.153.1.4 (K:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 199

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score = 61.0 bits (147), Expect = 6e-13
 Identities = 19/105 (18%), Positives = 38/105 (36%), Gaps = 3/105 (2%)

Query: 38  TSIGVRGKDSVCVVTQKKVPDKLLDH-TSVTHLFPITKYLGLLATGMTADARTLVQQARY 96
             IG++G D V V + +     ++        +F +++ + LL  G   D     +  + 
Sbjct: 3   YLIGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYIQK 62

Query: 97  EAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLI 141
               ++ + GYE+     A +         +     P  V L L 
Sbjct: 63  NVQLYKMRNGYELSPTAAANFTRRNLADCLR--SRTPYHVNLLLA 105

>d1rypi_ d.153.1.4 (I:) 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 = 60.6 bits (146), Expect = 1e-12
 Identities = 15/101 (14%), Positives = 29/101 (28%), Gaps = 1/101 (0%)

Query: 38  TSIGVRGKDSVCVVTQKKV-PDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARY 96
           T +GV+  + V +    +     ++   +   L  I+  +     G  AD   + Q    
Sbjct: 2   TIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGS 61

Query: 97  EAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVG 137
                      E  V    + +      Y  H     +  G
Sbjct: 62  NIELHSLYTSREPRVVSALQMLKQHLFKYQGHIGAYLIVAG 102

>d1irui_ d.153.1.4 (I:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 220

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score = 60.6 bits (146), Expect = 1e-12
 Identities = 14/102 (13%), Positives = 30/102 (29%), Gaps = 1/102 (0%)

Query: 38  TSIGVRGKDSVCVVTQKKVPDKLLDHT-SVTHLFPITKYLGLLATGMTADARTLVQQARY 96
           T  GV  KD + +    +  + ++    + + +  I+  +     G  AD     Q    
Sbjct: 2   TIAGVVYKDGIVLGADTRATEGMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISS 61

Query: 97  EAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGL 138
                    G    V    + +      Y  +     +  G+
Sbjct: 62  NLELHSLSTGRLPRVVTANRMLKQMLFRYRGYIGAALVLGGV 103

>d1irul_ d.153.1.4 (L:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 201

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score = 59.8 bits (144), Expect = 2e-12
 Identities = 14/95 (14%), Positives = 29/95 (30%), Gaps = 1/95 (1%)

Query: 38  TSIGVRGKDSVCVVTQKKVPDKLL-DHTSVTHLFPITKYLGLLATGMTADARTLVQQARY 96
           T++  + +  V V    +          +V  +  I  YL     G  AD     +    
Sbjct: 2   TTLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLAR 61

Query: 97  EAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYM 131
           +   +  +    + V   +K +A+    Y      
Sbjct: 62  QCRIYELRNKERISVAAASKLLANMVYQYKGMGLS 96

>d1q5qh_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Rhodococcus erythropolis [TaxId: 1833]} Length = 224

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Rhodococcus erythropolis [TaxId: 1833]

 Score = 59.9 bits (144), Expect = 2e-12
 Identities = 19/105 (18%), Positives = 34/105 (32%), Gaps = 2/105 (1%)

Query: 38  TSIGVRGKDSVCVVTQKKVPDKLL-DHTSVTHLFPITKYLGLLATGMTADARTLVQQARY 96
           T + +  K  V +   ++     L     V  ++   +Y      G    A  LV+    
Sbjct: 2   TIVALTYKGGVLLAGDRRATQGNLIASRDVEKVYVTDEYSAAGIAGTAGIAIELVRLFAV 61

Query: 97  EAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLI 141
           E   +    G  +  D  A  +A   +       M+ L V   L+
Sbjct: 62  ELEHYEKIEGVPLTFDGKANRLASMVRGNLGA-AMQGLAVVPLLV 105

>d1rypl_ d.153.1.4 (L:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 212

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 58.6 bits (141), Expect = 5e-12
 Identities = 12/95 (12%), Positives = 29/95 (30%), Gaps = 1/95 (1%)

Query: 38  TSIGVRGKDSVCVVTQKKV-PDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARY 96
           T++  R +  + V    +      +   +V  +  I  +L     G  AD +        
Sbjct: 2   TTLAFRFQGGIIVAVDSRATAGNWVASQTVKRVIEINPFLLGTMAGGAADCQFWETWLGS 61

Query: 97  EAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYM 131
           +      +    + V   +K +++    Y      
Sbjct: 62  QCRLHELREKERISVAAASKILSNLVYQYKGAGLS 96

>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 = 58.3 bits (140), Expect = 6e-12
 Identities = 20/101 (19%), Positives = 43/101 (42%), Gaps = 1/101 (0%)

Query: 38  TSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARY 96
           T++G+  KD V + T+K+      +   +   ++ I   + +   G   DA+ L +  + 
Sbjct: 2   TTVGLVCKDGVVMATEKRATMGNFIASKAAKKIYQIADRMAMTTAGSVGDAQFLARIIKI 61

Query: 97  EAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVG 137
           EA  +  +   +  V  +A   ++    Y    Y+  L +G
Sbjct: 62  EANLYEIRRERKPTVRAIATLTSNLLNSYRYFPYLVQLLIG 102

>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 = 54.7 bits (131), Expect = 1e-10
 Identities = 14/102 (13%), Positives = 28/102 (27%), Gaps = 1/102 (0%)

Query: 38  TSIGVRGKDSVCVVTQKKVPDKLL-DHTSVTHLFPITKYLGLLATGMTADARTLVQQARY 96
           T + V+    V +    +        +     L PI   +    +G  AD + +     Y
Sbjct: 2   TIMAVQFDGGVVLGADSRTTTGSYIANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTY 61

Query: 97  EAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGL 138
           +      +      V   A    +    Y +      +  G 
Sbjct: 62  QLGFHSIELNEPPLVHTAASLFKEMCYRYREDLMAGIIIAGW 103

>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 = 51.7 bits (123), Expect = 2e-09
 Identities = 15/107 (14%), Positives = 32/107 (29%), Gaps = 7/107 (6%)

Query: 36  GVTSIGVRGKDSVCVVTQKKV-PDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQA 94
           G + + V  KD V +    +      + +     L  +   +    +G  AD + +    
Sbjct: 9   GASIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKIWCCRSGSAADTQAIADIV 68

Query: 95  RYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLI 141
           +Y    +  +YG            A        +     L  G+ + 
Sbjct: 69  QYHLELYTSQYGTPST------ETAASVFKELCYENKDNLTAGIIVA 109

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	149
d1irua_	244	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1irug_	245	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rypg_	244	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1iruc_	250	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rypf_	233	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1rypa_	243	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1irud_	243	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rypb_	250	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1iruf_	238	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1j2pa_	243	Proteasome alpha subunit (non-catalytic) {Archaeon	100.0
d1rypd_	241	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1irue_	234	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rypc_	244	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1yara1	221	Proteasome alpha subunit (non-catalytic) {Archaeon	100.0
d1irub_	233	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rype_	242	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1q5qa_	227	Proteasome alpha subunit (non-catalytic) {Rhodococ	99.97
d1rypk_	198	Proteasome beta subunit (catalytic) {Baker's yeast	99.96
d1yarh1	203	Proteasome beta subunit (catalytic) {Archaeon Ther	99.96
d1iruj_	204	Proteasome beta subunit (catalytic) {Cow (Bos taur	99.95
d1irul_	201	Proteasome beta subunit (catalytic) {Cow (Bos taur	99.95
d1ryp2_	233	Proteasome beta subunit (catalytic) {Baker's yeast	99.95
d1j2qh_	202	Proteasome beta subunit (catalytic) {Archaeon Arch	99.95
d1iruh_	202	Proteasome beta subunit (catalytic) {Cow (Bos taur	99.95
d1ryph_	205	Proteasome beta subunit (catalytic) {Baker's yeast	99.94
d1ryp1_	222	Proteasome beta subunit (catalytic) {Baker's yeast	99.94
d1rypj_	204	Proteasome beta subunit (catalytic) {Baker's yeast	99.94
d1iru1_	213	Proteasome beta subunit (catalytic) {Cow (Bos taur	99.94
d1rypl_	212	Proteasome beta subunit (catalytic) {Baker's yeast	99.93
d1irui_	220	Proteasome beta subunit (catalytic) {Cow (Bos taur	99.93
d1iru2_	217	Proteasome beta subunit (catalytic) {Cow (Bos taur	99.93
d1iruk_	199	Proteasome beta subunit (catalytic) {Cow (Bos taur	99.92
d1rypi_	222	Proteasome beta subunit (catalytic) {Baker's yeast	99.92
d1q5qh_	224	Proteasome beta subunit (catalytic) {Rhodococcus e	99.92
d1m4ya_	171	HslV (ClpQ) protease {Thermotoga maritima [TaxId:	99.42
d2z3ba1	180	HslV (ClpQ) protease {Bacillus subtilis [TaxId: 14	99.41
d1g3ka_	173	HslV (ClpQ) protease {Haemophilus influenzae [TaxI	99.37
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	80.7

>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=3.4e-48  Score=298.22  Aligned_cols=146  Identities=66%  Similarity=1.041  Sum_probs=140.1

Q ss_pred             CCCCCCCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEe
Q 031996            2 SRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLAT   81 (149)
Q Consensus         2 ~~~~~~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~s   81 (149)
                      |||++++||+++|+||||||++|||||+||+++.|+|+|||+++||||||+|++.++.++.+++.+||++|++|++|++|
T Consensus         1 ~~~~~~gyd~~~t~Fsp~Grl~QvEYA~kav~~gg~t~igIk~~dgVVlaad~r~~~~~~~~~~~~KI~~I~~~i~~~~s   80 (244)
T d1irua_           1 SRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTVTHLFKITENIGCVMT   80 (244)
T ss_dssp             CCSCCCTTTTTSSCCCTTSCCHHHHHHHHHHHTTCCEEEEEECSSEEEEEEECCCCCSSBCGGGCCSEEESSSSCEEEEE
T ss_pred             CCCCCCCcCCCCceECCCCeEhHHHHHHHHHHhCCccEEEEEcCCEEEEEEecccccccccCCccceEEEecCCcEEEEe
Confidence            68999999999999999999999999999999855689999999999999999998888778889999999999999999


Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996           82 GMTADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        82 G~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      |+.+|++.+++++|.+++.|+++++++++++.+++++++++|.++++++.|||+|++||+|||+++
T Consensus        81 G~~~D~~~l~~~~r~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rP~~v~~ll~G~D~~~  146 (244)
T d1irua_          81 GMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIGIDEEQ  146 (244)
T ss_dssp             ECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSBCCCSEEEEEEEEETTT
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHcCCCCCchHHHHHHHHHHHHHhcccccCccceeeEEEEEcCCC
Confidence            999999999999999999999999999999999999999999999999999999999999999753

>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=1.8e-47  Score=294.54  Aligned_cols=142  Identities=40%  Similarity=0.654  Sum_probs=136.6

Q ss_pred             CCCCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccH
Q 031996            5 SGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMT   84 (149)
Q Consensus         5 ~~~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~   84 (149)
                      .+++||+++|+|||||||+|||||+||+++ |+|+|||+++||||||+|++.++.++..++.+||++|++|++|++||+.
T Consensus         3 ~~~~yd~~~t~Fsp~Grl~QvEYa~~av~~-G~t~VGik~~dgVvlaad~~~~~~~~~~~~~~Ki~~I~~~i~~~~sG~~   81 (245)
T d1irug_           3 IGTGYDLSASTFSPDGRVFQVEYAMKAVEN-SSTAIGIRCKDGVVFGVEKLVLSKLYEEGSNKRLFNVDRHVGMAVAGLL   81 (245)
T ss_dssp             CCSSTTSCTTCCCTTSCCHHHHHHHHHHHT-SCCEEEEECSSBEEEEEEEECSCTTBCTTTTCCEEEEETTEEEEEEECH
T ss_pred             CccccCCCCceECCCCeehHHHHHHHHHHc-CCcEEEEEeCCEEEEEEeccccccccccCccceEEEcCCCEEEEeccCc
Confidence            677999999999999999999999999987 9999999999999999999988777777888999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996           85 ADARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        85 ~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      +|++.+++++|.++.+|+++++++|+++.|++++++++|.||++++.|||+|++||+|||+++
T Consensus        82 ~D~~~l~~~~~~~~~~~~~~~g~~i~~~~la~~la~~~~~~t~~~~~rP~~vs~li~G~D~~~  144 (245)
T d1irug_          82 ADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGCSFMLGSYSVND  144 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSBSSBCCCSEEEEEEEEETTT
T ss_pred             hhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhccccccccceEEEEEEEcCCC
Confidence            999999999999999999999999999999999999999999999999999999999999754

>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=2.3e-46  Score=287.99  Aligned_cols=141  Identities=35%  Similarity=0.549  Sum_probs=135.0

Q ss_pred             CCCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHH
Q 031996            6 GGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTA   85 (149)
Q Consensus         6 ~~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~   85 (149)
                      |++||+++|+||||||++|||||+||+++ |+|+|||+++||||||+|++.++.+...+..+||++|++|++|+++|+.+
T Consensus         1 ~~gyd~~~t~fsp~Grl~QvEya~kav~~-G~t~igik~~dgVvlaad~~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~   79 (244)
T d1rypg_           1 GTGYDLSNSVFSPDGRNFQVEYAVKAVEN-GTTSIGIKCNDGVVFAVEKLITSKLLVPQKNVKIQVVDRHIGCVYSGLIP   79 (244)
T ss_dssp             CCCTTSSTTCCCTTSCCHHHHHHHHHHHT-SCCEEEEEETTEEEEEEEEECCCTTBCTTTSCCCEEETTTEEEEEEECHH
T ss_pred             CCCcCCCCceECCCCeehHHHHHHHHHHc-CCCEEEEEeCCEEEEEEecccCCCCccccccceEEEccCceEEEEccchh
Confidence            57899999999999999999999999997 99999999999999999999997776666778999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996           86 DARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        86 D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      |++.++++++.+++.|+++++++++++.+++.++.++|.||++++.|||+|++||+|||+++
T Consensus        80 D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~t~~~~~RP~~~~~iiaG~D~~g  141 (244)
T d1rypg_          80 DGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGGVDKNG  141 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSCTTBCCCCEEEEEEEEETTE
T ss_pred             hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhcccccCCceEEEEEEEEeCCC
Confidence            99999999999999999999999999999999999999999999999999999999999753

>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=7.4e-46  Score=285.90  Aligned_cols=140  Identities=31%  Similarity=0.502  Sum_probs=133.1

Q ss_pred             CCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccc-cccccccceeeecCcEEEEEeccHH
Q 031996            7 GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKL-LDHTSVTHLFPITKYLGLLATGMTA   85 (149)
Q Consensus         7 ~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l-~~~~~~~KI~~I~~~i~~~~sG~~~   85 (149)
                      ++||+++|+|||||||+|||||+||+++ |+|+|||+++||||||+|++.++.+ +..++.+||++|++|++|++||+.+
T Consensus         2 ~~yd~~~t~fsp~Grl~QvEyA~kav~~-G~tvvgik~~dgVvlaad~~~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~   80 (250)
T d1iruc_           2 RRYDSRTTIFSPEGRLYQVEYAMEAIGH-AGTCLGILANDGVLLAAERRNIHKLLDEVFFSEKIYKLNEDMACSVAGITS   80 (250)
T ss_dssp             TTTCCCTTCCCTTSCCHHHHHHHHHHTT-SCCEEEEBCSSEEEEEECCCCCCTTBCCCSSCSSEEECSSSEEEEEEECHH
T ss_pred             CccCCCCeeECCCCcchHHHHHHHHHhc-CCcEEEEEeCCEEEEEEeCccccCCcccCcccceEEECCCcEEEEeecccc
Confidence            4899999999999999999999999987 9999999999999999999998554 4566789999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996           86 DARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        86 D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      |++.+++++|.++..|+++++++++++.+++.+++++|.++++++.|||+|++||+|||+++
T Consensus        81 D~~~l~~~~r~~~~~~~~~~~~~i~~~~la~~l~~~~~~~~~~~~~rP~~~~~li~G~D~~~  142 (250)
T d1iruc_          81 DANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIGWDKHY  142 (250)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBSSCCCCCEEEEEEEEETTT
T ss_pred             hHHHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHHHhhhccCCcceEEEEEEEEcCCC
Confidence            99999999999999999999999999999999999999999999999999999999999764

>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=5e-46  Score=284.32  Aligned_cols=138  Identities=32%  Similarity=0.514  Sum_probs=131.7

Q ss_pred             CCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHH
Q 031996            7 GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTAD   86 (149)
Q Consensus         7 ~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D   86 (149)
                      ++||+++|+||||||++|||||+||+++ |+|+|||+++||||||+|++.++.+.  ++.+||++|++|++|++||+.+|
T Consensus         3 ~~yd~~~t~FspdGrl~QvEyA~kav~~-g~t~igi~~~dgvvlaad~~~~~~l~--~~~~KI~~I~~~i~~~~sG~~~D   79 (233)
T d1rypf_           3 NNYDGDTVTFSPTGRLFQVEYALEAIKQ-GSVTVGLRSNTHAVLVALKRNADELS--SYQKKIIKCDEHMGLSLAGLAPD   79 (233)
T ss_dssp             HHHSSCTTCCCTTSCCHHHHHHHHHHHT-SCCEEEEECSSEEEEEEECCCSSTTB--CCCCCEEEEETTEEEEEEECHHH
T ss_pred             ccccCCCceECCCCcChHHHHHHHHHHc-CCCEEEEEECCeEEEEEeccccccCC--cchheEEEcCCCEEEEEeecccc
Confidence            4699999999999999999999999987 99999999999999999999987764  46789999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996           87 ARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        87 ~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      ++.+++++|.+++.|+++++++|+++.+|+.+++++|+||++.+.|||||++||+|||+++
T Consensus        80 ~~~l~~~~r~~~~~~~~~~~~~i~~~~la~~l~~~~~~~t~~~~~RP~gv~~il~G~d~~g  140 (233)
T d1rypf_          80 ARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRPYGVGLLIIGYDKSG  140 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEETTE
T ss_pred             HHHHHHHHHHHHHhhhhhcCCCCcHHHHHHHHHHHHHHHhcccccCCccceEEEEEEcCCC
Confidence            9999999999999999999999999999999999999999999999999999999999763

>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=5.8e-46  Score=285.33  Aligned_cols=141  Identities=58%  Similarity=0.944  Sum_probs=135.7

Q ss_pred             CCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHH
Q 031996            7 GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTAD   86 (149)
Q Consensus         7 ~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D   86 (149)
                      ++||+++|+|||||||+|||||+||+++.|+|+|||+++||||||+|++.+++++..++.+||++|++|++|++||+.+|
T Consensus         1 ~gyd~~~t~fsp~Grl~QvEYA~~av~~~g~T~igik~~dgVvlaad~r~~~~l~~~~~~~KI~~i~~~i~~~~sG~~~D   80 (243)
T d1rypa_           1 AGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPTTVSYIFCISRTIGMVVNGPIPD   80 (243)
T ss_dssp             CGGGGTSSSCCTTSCCHHHHHHHHHTTTTCCCEEEEECSSEEEEEEECCCCCTTBCGGGCCSEEECSSSCEEEEESCHHH
T ss_pred             CCCCCCCCeECCCCeehHHHHHHHHHHccCceEEEEEcCCEEEEEEeccccccccccCcccceEecCCCEEEEEecCcHH
Confidence            47999999999999999999999999986779999999999999999999888888888999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996           87 ARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        87 ~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      ++.+++++|.++++|+++++++++++.+++++++++|.|+++.+.|||+|++||+|||+++
T Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~ls~~~~~~~~~~~~rP~~v~~ll~G~D~~~  141 (243)
T d1rypa_          81 ARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQRAYMRPLGVILTFVSVDEEL  141 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTSCCCSCEEEEEEEETTT
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcccccCccceEEEEEEccCC
Confidence            9999999999999999999999999999999999999999999999999999999999764

>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=6.5e-46  Score=285.14  Aligned_cols=139  Identities=38%  Similarity=0.629  Sum_probs=134.7

Q ss_pred             CCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHH
Q 031996            8 GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADA   87 (149)
Q Consensus         8 ~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~   87 (149)
                      .||+++|+|||||||+|||||+||+++ |+|+|||+++||||||+|++.++.++.+++.+||++|++|++|++||+.+|+
T Consensus         1 ~yd~~~t~Fsp~Grl~QvEya~kav~~-G~Tvvgik~~dgVvla~d~r~~~~~~~~~~~~KI~~i~~~i~~~~sG~~~D~   79 (243)
T d1irud_           1 SYDRAITVFSPDGHLFQVEYAQEAVKK-GSTAVGVRGRDIVVLGVEKKSVAKLQDERTVRKICALDDNVCMAFAGLTADA   79 (243)
T ss_dssp             CCCCCCSCCCTTSCCHHHHHHHHHHHT-SCCEEEECCSSEEEEEECCCCCCSSSCGGGGCSEEESSSSCEEEEEECHHHH
T ss_pred             CCCCCCeeECCCCcchHHHHHHHHHhc-CCCEEEEEeCCEEEEEEeccccCcccCCCccccEEECCCCEEEEEEEchhhH
Confidence            399999999999999999999999986 9999999999999999999988888888899999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996           88 RTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        88 ~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      +.+++.++.++..|+++++.+|+++.+++++++++|.||++++.|||+|++||+|||+++
T Consensus        80 ~~l~~~~~~~~~~~~~~~~~~i~v~~la~~ls~~~~~~t~~~~~rp~~v~~li~G~D~~~  139 (243)
T d1irud_          80 RIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGISALIVGFDFDG  139 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCEEEEEEEECSSS
T ss_pred             HHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHhcccCCccceEEEEEEEcCCC
Confidence            999999999999999999999999999999999999999999999999999999999764

>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=1.8e-45  Score=283.58  Aligned_cols=142  Identities=33%  Similarity=0.490  Sum_probs=135.1

Q ss_pred             CCCCCCCCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEE
Q 031996            1 MSRGSGGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLA   80 (149)
Q Consensus         1 m~~~~~~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~   80 (149)
                      |+.    +||+++|+|||||||+|+|||+||+++ |+|+|||+++||||||+|++.++.++..++.+||++|++|++|++
T Consensus         1 m~~----~yd~~~t~fsp~G~l~QvEyA~kav~~-G~tvvgi~~~dgVvlaad~r~~~~~~~~~~~~ki~~I~~~i~~~~   75 (250)
T d1rypb_           1 MTD----RYSFSLTTFSPSGKLGQIDYALTAVKQ-GVTSLGIKATNGVVIATEKKSSSPLAMSETLSKVSLLTPDIGAVY   75 (250)
T ss_dssp             CCC----CCCSBSSCBCTTSCBHHHHHHHHHHHT-SCCEEEEEETTEEEEEEECCCSCSSBCGGGCCSSEEEETTEEEEE
T ss_pred             CCc----cccCCCceECCCCeehHHHHHHHHHHc-CCCEEEEEeCCEEEEEEecccCCccccccccceeEeccCCEEEEe
Confidence            665    899999999999999999999999987 999999999999999999998877777788999999999999999


Q ss_pred             eccHHHHHHHHHHHHHHHHH-HHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996           81 TGMTADARTLVQQARYEAAE-FRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        81 sG~~~D~~~l~~~~r~~~~~-~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      ||+.+|++.++++++.+++. |++.++++++++.+++++++++|.|+++++.|||+|++||+|||++.
T Consensus        76 sG~~~D~~~l~~~~~~~~~~~y~~~~~~~~~~~~la~~~~~~~~~~~~~~~~rp~~v~~li~G~D~~~  143 (250)
T d1rypb_          76 SGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIAGHDEFN  143 (250)
T ss_dssp             EECHHHHHHHHHHHHHHHHHTTHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCCEEEEEEEEETTT
T ss_pred             eecccHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhcCCcCeeEEEEEEEecCCC
Confidence            99999999999999999975 89999999999999999999999999999999999999999999753

>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=3.2e-45  Score=280.57  Aligned_cols=137  Identities=34%  Similarity=0.573  Sum_probs=131.3

Q ss_pred             CCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHH
Q 031996            7 GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTAD   86 (149)
Q Consensus         7 ~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D   86 (149)
                      ++||+++|+||||||++|||||+||+++ |+|+|||+++||||||+|++.++.+..  +.+||++|+++++|++||+.+|
T Consensus         1 ~~yd~~~tiFsp~Grl~QvEYA~kav~~-G~t~vgik~~dgVvlaad~~~~~~~~~--~~~KI~~I~~~i~~~~sG~~~D   77 (238)
T d1iruf_           1 NQYDNDVTVWSPQGRIHQIEYAMEAVKQ-GSATVGLKSKTHAVLVALKRAQSELAA--HQKKILHVDNHIGISIAGLTAD   77 (238)
T ss_dssp             CTTTSCTTCCCTTSCCHHHHHHHHHHHH-SCCEEEEECSSEEEEEEECCCSSTTBC--CCCCEEEEETTEEEEEEECHHH
T ss_pred             CCCCCCCeeECCCCcchHHHHHHHHHhc-CCCEEEEEeCCEEEEEEecccccCCCC--ccceEEEeCCceEEEEeccchH
Confidence            5799999999999999999999999987 999999999999999999999877654  4579999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           87 ARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        87 ~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      ++.++++++.++..|++++|++++++.+++++++++|.|+++.+.|||++++||||||++
T Consensus        78 ~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~l~~~~~~y~~~~~~rP~~v~~il~G~D~~  137 (238)
T d1iruf_          78 ARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAGYDDM  137 (238)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEETT
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHHHhhccCCCcccceEEEEEEcCC
Confidence            999999999999999999999999999999999999999999999999999999999975

>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=5.4e-45  Score=280.09  Aligned_cols=141  Identities=43%  Similarity=0.674  Sum_probs=134.6

Q ss_pred             CCCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHH
Q 031996            6 GGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTA   85 (149)
Q Consensus         6 ~~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~   85 (149)
                      +=+||+++|+||||||++|||||+||+++ |+|+|||+++||||||+|++.+..+...++.+||++|++|++|++||+.+
T Consensus         2 ~~gyd~~~t~fsp~Grl~QvEya~kav~~-G~t~Igik~~dgVvlaad~r~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~   80 (243)
T d1j2pa_           2 QMGYDRAITVFSPDGRLFQVEYAREAVKR-GATAIGIKCKEGVILIADKRVGSKLLEKDTIEKIYKIDEHICAATSGLVA   80 (243)
T ss_dssp             CTTSSSCTTCCCTTSCCHHHHHHHHHHHT-SCCEEEEEETTEEEEEEECCCSCTTBCGGGCCSEEECSSSEEEEEEECHH
T ss_pred             CCCcCCCCccCCCCCcchHHHHHHHHHHc-CCCEEEEEECCEEEEEEecCccccCccccccccEeecCCcEEEEeeeccc
Confidence            34799999999999999999999999987 99999999999999999999997777677889999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996           86 DARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        86 D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      |++.++++++.++.+|+++++++++++.+++++++.+|.++++++.|||+|++|++|||+..
T Consensus        81 D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~rP~~~~~il~G~D~~p  142 (243)
T d1j2pa_          81 DARVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQYGGVRPFGVSLLIAGVNEVP  142 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCEEEEEEEESSSE
T ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHHHHhhhccCCccceeEEEEEecCCc
Confidence            99999999999999999999999999999999999999999999999999999999999754

>d1rypd_ d.153.1.4 (D:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=7.1e-45  Score=279.03  Aligned_cols=138  Identities=36%  Similarity=0.616  Sum_probs=131.8

Q ss_pred             CCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccc-cccccceeeecCcEEEEEeccHHH
Q 031996            8 GYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLD-HTSVTHLFPITKYLGLLATGMTAD   86 (149)
Q Consensus         8 ~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~-~~~~~KI~~I~~~i~~~~sG~~~D   86 (149)
                      +||+++|+||||||++|||||+||+++ |+|+|||+++||||||+|++.+..+.. ..+.+||++|++|++|++||+.+|
T Consensus         1 gyd~~~t~fsp~Grl~QvEya~kav~~-G~tvIgik~~dgVvlaad~~~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D   79 (241)
T d1rypd_           1 GYDRALSIFSPDGHIFQVEYALEAVKR-GTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSKVSKIDSHVVLSFSGLNAD   79 (241)
T ss_dssp             CCCCCCSCCBTTTBCHHHHHHHHHHTT-SCCEEEEECSSCEEEEEECCCSSCCBCTTTSCCSEEEEETTEEEEEEECHHH
T ss_pred             CCCCCCceECCCCcEeHHHHHHHHHHc-CCCEEEEEeCCEEEEEEEccccccCcccccccccEEEeCCCEEEEeeeccch
Confidence            599999999999999999999999987 999999999999999999999966654 457899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996           87 ARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus        87 ~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      ++.+++++|.+++.|+++++++++++.++++++.++|.||++.+.|||+|++||+|||+.
T Consensus        80 ~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~i~~~~~~~t~~~~~rP~~v~~li~G~d~~  139 (241)
T d1rypd_          80 SRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLIAGFDPR  139 (241)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSSTTBCCCSEEEEEEECCTT
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHhhccccCcccceEEEEEEccc
Confidence            999999999999999999999999999999999999999999999999999999999964

>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=1.2e-44  Score=276.65  Aligned_cols=138  Identities=33%  Similarity=0.642  Sum_probs=131.6

Q ss_pred             CCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHHH
Q 031996            9 YDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADAR   88 (149)
Q Consensus         9 yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~   88 (149)
                      ||+++|+||||||++|||||+||+++ |+|+|||+++||||||+|++.+..++..++.+||++|++|++|++||+.+|++
T Consensus         1 yd~~~t~fsp~G~l~QvEYa~kav~~-G~t~vgik~~dgVvlaad~~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~   79 (234)
T d1irue_           1 YDRGVNTFSPEGRLFQVEYDIEAIKL-GSTAIGIQTSEGVCLAVEKRITSPLMEPSSIEKIVEIDAHIGCAMSGLIADAK   79 (234)
T ss_dssp             CCCCTTCBCTTSCBHHHHHHHHHHTT-SCCEEEEEETTEEEEEEECCCCCTTBCTTSCCSEEEEETTEEEEEEECHHHHH
T ss_pred             CCCCCceECCCCcchHHHHHHHHHHc-CCCEEEEEeCCEEEEEEecCccCCCcccCcccCEEEccCcEEEEEeeccchHH
Confidence            89999999999999999999999987 99999999999999999999887777778889999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCC-----ccccceEEEEEEEeCCC
Q 031996           89 TLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAY-----MRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        89 ~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~-----~rP~~v~~liaG~D~~~  147 (149)
                      .+++.+|.++..|+++++++++++.+++++++++|.||++.+     .|||+|++|+||||+++
T Consensus        80 ~l~~~~~~~~~~~~~~~~~~i~~~~la~~i~~~~~~~t~~~~~~~~~~rP~~~~~il~G~D~~g  143 (234)
T d1irue_          80 TLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMSRPFGVALLFGGVDEKG  143 (234)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCBCSTTCCSSCBSSCCCEEEEEEEEETTE
T ss_pred             HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHhhcccccccccccceEEEEEEEEcCCC
Confidence            999999999999999999999999999999999999988755     69999999999999763

>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=5.3e-44  Score=274.47  Aligned_cols=140  Identities=35%  Similarity=0.611  Sum_probs=133.0

Q ss_pred             CCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCcc-ccccccccceeeecCcEEEEEeccHH
Q 031996            7 GGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDK-LLDHTSVTHLFPITKYLGLLATGMTA   85 (149)
Q Consensus         7 ~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~-l~~~~~~~KI~~I~~~i~~~~sG~~~   85 (149)
                      .+||+++|+||||||++|||||+||+++ |+|+|||+++||||||+|++.++. ++..++.+||++|++|++++++|+.+
T Consensus         3 ~~yd~~~t~fsp~G~~~Qveya~~ai~~-G~T~vgi~~~dgVvlaad~r~s~~~~~~~~~~~KI~~i~~~i~~~~sG~~~   81 (244)
T d1rypc_           3 RRYDSRTTIFSPEGRLYQVEYALESISH-AGTAIGIMASDGIVLAAERKVTSTLLEQDTSTEKLYKLNDKIAVAVAGLTA   81 (244)
T ss_dssp             GGGCCCTTCBCTTSCBHHHHHHHHHHTT-SCCEEEEEETTEEEEEEECSSCCSSBCSTTCCSSEEESSSSEEEEEEECHH
T ss_pred             CccCCCceeECCCCcChHHHHHHHHHhc-CCCEEEEEeCCEEEEEEeCCccCCCcccCCccceEEEcCCCeEEEEecccC
Confidence            4799999999999999999999999987 999999999999999999999854 44567789999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996           86 DARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        86 D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      |++.++++++.+++.|+++++++++++.++++++++++.|++++++|||++++||+|||+++
T Consensus        82 D~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~rP~~~~~ll~G~d~~~  143 (244)
T d1rypc_          82 DAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAGYDDRY  143 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSCCCCCEEEEEEEEETTT
T ss_pred             cHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhhhhccccCccceeEEEEEEecCC
Confidence            99999999999999999999999999999999999999999999999999999999999764

>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=3.1e-43  Score=266.54  Aligned_cols=133  Identities=40%  Similarity=0.637  Sum_probs=128.5

Q ss_pred             ceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHHHHHHHH
Q 031996           14 TIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQ   93 (149)
Q Consensus        14 t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~   93 (149)
                      |+||||||++|+|||+||+++ |+|+|||+++||||||+|++.+++++.+++.+||++|++|++++++|+.+|++.++++
T Consensus         1 t~fsp~G~l~QvEYa~~av~~-G~t~vgi~~~dgVvlaad~r~~~~~~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~   79 (221)
T d1yara1           1 TVFSPDGRLFQVEYAREAVKK-GSTALGMKFANGVLLISDKKVRSRLIEQNSIEKIQLIDDYVAAVTSGLVADARVLVDF   79 (221)
T ss_dssp             CCCCTTSCCHHHHHHHHHHTT-SCCEEEEEETTEEEEEECCCCCCTTBCSTTCCSEEEEETTEEEEEEEBHHHHHHHHHH
T ss_pred             CeECCCCcchHHHHHHHHHhc-CCcEEEEEeCCEEEEEEecccCCcccccCccceEEEecCCceEEeeeccchHHHHHHH
Confidence            789999999999999999986 9999999999999999999998888888889999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996           94 ARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        94 ~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      +|.++..|+++++++++++.++++++.++|.++++++.|||++++||+|||+++
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~l~~~~a~~~~~~~~~~~~rP~~~~~li~G~d~~g  133 (221)
T d1yara1          80 ARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGVSLIFAGIDQIG  133 (221)
T ss_dssp             HHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBTTBCCCCEEEEEEEECSSC
T ss_pred             HHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhhhccCCCcceEEEEEEEecCC
Confidence            999999999999999999999999999999999999999999999999999753

>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=4.6e-43  Score=266.94  Aligned_cols=141  Identities=38%  Similarity=0.583  Sum_probs=134.6

Q ss_pred             CCCCCcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHH
Q 031996            6 GGGYDRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTA   85 (149)
Q Consensus         6 ~~~yd~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~   85 (149)
                      +.+||+++|+||||||++|||||+||+++ |+|+|||+++||||||+|++.+..++..++.+|||+|++|++|+++|+.+
T Consensus         2 ~~gyd~~~t~fsp~Gr~~Qveya~kav~~-G~tvigik~~dgVvlaaD~r~~~~~~~~~~~~ki~~i~~~i~~~~sG~~~   80 (233)
T d1irub_           2 ERGYSFSLTTFSPSGKLVQIEYALAAVAG-GAPSVGIKAANGVVLATEKKQKSILYDERSVHKVEPITKHIGLVYSGMGP   80 (233)
T ss_dssp             CCCCCSBSCCCCTTSCCHHHHHHHHHHHT-SCCEEEEECSSCEEEEEECCCCCSSBCSTTCCSSEESSSSEEEEEEECHH
T ss_pred             CCCcCCCCCeECCCCcChHHHHHHHHHHc-CCCEEEEEeCCEEEEEEeCCcccCCccccccceEEEecCceEEEEeccch
Confidence            45899999999999999999999999987 99999999999999999999987666778899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996           86 DARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        86 D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      |++.++++++.++++|+++++++++++.+++.+++++|.+++....|||+++++++|+|+++
T Consensus        81 D~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~p~~~~~li~g~d~~~  142 (233)
T d1irub_          81 DYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGVSLLICGWNEGR  142 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCSEEEEEEEECSSS
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhccccccceEEEeeeecccCC
Confidence            99999999999999999999999999999999999999999999999999999999998754

>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=2.1e-43  Score=270.68  Aligned_cols=137  Identities=34%  Similarity=0.610  Sum_probs=129.6

Q ss_pred             CcccceeCCCCcchhhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHHHH
Q 031996           10 DRHITIFSPEGRLFQVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADART   89 (149)
Q Consensus        10 d~~~t~fsp~G~~~Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~   89 (149)
                      |+++|+||||||++|||||+||+++ |+|+|||+++||||||+|++.+.++...++.+|||+|+++++|++||+.+|++.
T Consensus         1 d~~~t~fsp~G~l~Qveya~~a~~~-G~t~Vgi~~~dgVvla~d~r~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~   79 (242)
T d1rype_           1 DRGVSTFSPEGRLFQVEYSLEAIKL-GSTAIGIATKEGVVLGVEKRATSPLLESDSIEKIVEIDRHIGCAMSGLTADARS   79 (242)
T ss_dssp             CCCTTCBCTTSCBHHHHHHHHHHTT-SCCEEEEECSSCEEEEEECCCSSTTBCGGGCCCEEEEETTEEEEEEESGGGHHH
T ss_pred             CCCcceECCCCcchHHHHHHHHHHc-CCCEEEEEeCCEEEEEEeCCccCcCcccCccceEEEcCCCEEEEEeecchhHHH
Confidence            6889999999999999999999987 999999999999999999999877877788899999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcC------CccccceEEEEEEEeCCC
Q 031996           90 LVQQARYEAAEFRFKYGYEMPVDVLAKWIADKSQVYTQHA------YMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus        90 l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~~~~~t~~~------~~rP~~v~~liaG~D~~~  147 (149)
                      ++++++.+++.|+++++++++++.+++++++++|.|+++.      +.|||+|++||+|||+++
T Consensus        80 l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~rP~~~~~ii~G~D~~~  143 (242)
T d1rype_          80 MIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLMSRPFGVALLIAGHDADD  143 (242)
T ss_dssp             HHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCCBSSCTTSCCCBSSCCSEEEEEEEEETTT
T ss_pred             HHHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHhccccccchhccccceEEEEEEEecccc
Confidence            9999999999999999999999999999999999887754      369999999999999765

>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=99.97  E-value=6.3e-31  Score=199.58  Aligned_cols=115  Identities=17%  Similarity=0.194  Sum_probs=104.1

Q ss_pred             hhhhHHHHhhccCceEEEEEcCCeEEEEEeccCCccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHH
Q 031996           24 QVEYAFKAVKAAGVTSIGVRGKDSVCVVTQKKVPDKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRF  103 (149)
Q Consensus        24 Q~eya~~av~~~G~t~igik~kdgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~  103 (149)
                      |+|||+||+++ |+|+|||+++||||||+|+|.+       ..+||++|++||+|+++|+.+|++.+++++|.++..|++
T Consensus         8 q~eyA~~av~~-GtT~vgi~~~~GVvlaad~r~~-------s~~KI~~i~~~i~~~~sG~~aD~~~l~~~~r~~~~~~~~   79 (227)
T d1q5qa_           8 RSELARKGIAR-GRSVVVLTFRDGVLFVAENPST-------ALHKVSELYDRLGFAAVGKYNEFENLRRAGIVHADMRGY   79 (227)
T ss_dssp             HHHHHHHHHHT-SCCEEEEECSSEEEEEECCSCS-------SSCSEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhc-CCCEEEEEECCEEEEEEccCCC-------CcceEEEecCceEEEecCchHHHHHHHHHHHHHHHHHHH
Confidence            99999999986 9999999999999999999864       357999999999999999999999999999999999999


Q ss_pred             HhCC-CCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996          104 KYGY-EMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus       104 ~~~~-~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      +++. +++++.+++.++++++.. ...+.|||+|++||||||..+
T Consensus        80 ~~~~~~~~~~~la~~~~~~~~~~-~~~~~rP~gvs~lvaG~D~~g  123 (227)
T d1q5qa_          80 SYDRRDVTGRSLANAYAQTLGTI-FTEQPKPYEVEICVAEVGRVG  123 (227)
T ss_dssp             HSCGGGCCHHHHHHHHHHHHHHH-HHHSSSCCCEEEEEEECCCSS
T ss_pred             HhCCCCCcHHHHHHHHHHHHHHH-HHhcCCCceEEEEEEEEecCC
Confidence            9984 689999999999987633 334779999999999999643

>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=99.96  E-value=2e-28  Score=181.64  Aligned_cols=108  Identities=14%  Similarity=0.173  Sum_probs=101.4

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      +|+|||+++||||||+|++.+ +.++..++.+||++|++|++|++||..+|++.+.++++.+++.|+++++++++++.++
T Consensus         2 ~tiigi~~~dgVvlaaD~r~s~g~~~~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   81 (198)
T d1rypk_           2 DIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYIQANIQLYSIREDYELSPQAVS   81 (198)
T ss_dssp             CCEEEEECSSCEEEEEECCEEETTEEEESCCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHH
T ss_pred             eEEEEEEECCEEEEEEcCCcccCCEeecCccceEEEecCCEEEEecCCcccHHHHHHHHHHHHHHHHHHhCCCcchHHHH
Confidence            699999999999999999998 5666678899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      ++++++++.+++  +.|||++++||||||++
T Consensus        82 ~~i~~~~~~~~~--~~~P~~~~~liaG~D~~  110 (198)
T d1rypk_          82 SFVRQELAKSIR--SRRPYQVNVLIGGYDKK  110 (198)
T ss_dssp             HHHHHHHHHHTT--SSSCCCEEEEEEEEETT
T ss_pred             HHHHHHHHHHHh--cccccceEEEEEEEecC
Confidence            999999987765  57999999999999964

>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=99.96  E-value=1.5e-28  Score=182.85  Aligned_cols=107  Identities=25%  Similarity=0.448  Sum_probs=100.5

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      ||+|||+++||||||+|++.+ +.++.+++.+||++|++|++|++||..+|++.++++++.+++.|++.++++++++.++
T Consensus         1 TT~igi~~kdgVvia~D~r~s~~~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a   80 (203)
T d1yarh1           1 TTTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKAELELYRLQRRVNMPIEAVA   80 (203)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             CcEEEEEECCEEEEEECCCcccCCEeecCCcccEEEecCCeeeecCCCcchHHHHHHHHHHHHHHHHHhcCCCCcHHHHH
Confidence            699999999999999999987 7787888999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      ++++++++.+    +.|||++++|+||+|+++
T Consensus        81 ~~l~~~~~~~----~~~p~~~~~lvaG~d~~p  108 (203)
T d1yarh1          81 TLLSNMLNQV----KYMPYMVQLLVGGIDTAP  108 (203)
T ss_dssp             HHHHHHHHHT----TTSCCCEEEEEEEESSSE
T ss_pred             HHHHHHHHhh----ccCCccceeEEEEEcCCC
Confidence            9999988744    568999999999999754

>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=99.95  E-value=2.7e-28  Score=181.65  Aligned_cols=109  Identities=17%  Similarity=0.291  Sum_probs=101.3

Q ss_pred             cCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHH
Q 031996           35 AGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDV  113 (149)
Q Consensus        35 ~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~  113 (149)
                      +|+|+|||+++||||||+|++.+ +.++..++.+||++|++|++|+++|..+|++.+.++++.+++.|++.++.+++++.
T Consensus         6 nG~Tvigi~~~dgVvlaaD~r~s~g~~~~~~~~~Ki~~I~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~   85 (204)
T d1iruj_           6 NGGAVMAMKGKNCVAIAADRRFGIQAQLVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFRLNLYELKEGRQIKPYT   85 (204)
T ss_dssp             SCCEEEEEECSSEEEEEEECCEEETTEEEESCCCCEEECSTTEEEECCSCHHHHHHHHHHHHHHHHHHHHHSSSCCCHHH
T ss_pred             CCceEEEEEECCEEEEEECCCcccCCeeEcCcccEEEEeCCCeEEEeccCchHHHHHHHHHHHhhhhhhhhcccccchHH
Confidence            39999999999999999999998 56667788999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996          114 LAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus       114 la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      +++++++.+|.+    +.+||+|++||||||+++
T Consensus        86 ~a~~l~~~~~~~----~~~p~~~~~lvaG~D~~~  115 (204)
T d1iruj_          86 LMSMVANLLYEK----RFGPYYTEPVIAGLDPKT  115 (204)
T ss_dssp             HHHHHHHHHHTT----TTSCCSCCCEEEEECTTS
T ss_pred             HHHHHHHHHHHh----hhccceeEEEEEEEcCCC
Confidence            999999998743    467999999999999753

>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=99.95  E-value=1.4e-27  Score=177.44  Aligned_cols=107  Identities=15%  Similarity=0.187  Sum_probs=100.2

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      ||+|||+++||||||+|++.+ +.++..++.+|||+|+++++|+++|..+|++.+.+.++.+++.|++.++++++++.++
T Consensus         1 TT~igi~~~dgVvlaaD~~~t~g~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a   80 (201)
T d1irul_           1 TTTLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQCRIYELRNKERISVAAAS   80 (201)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEECCBCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             CeEEEEEECCEEEEEEcCccccCCEeecCCcccEEEeCCcEEEEEcCccchHHHHHHHHHHHHHHHHHhcCCCCchhHHH
Confidence            699999999999999999988 6777788899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      +++++++|.+    +.+||+++++++|+|+++
T Consensus        81 ~~l~~~~~~~----~~~p~~~~~lvaG~d~~~  108 (201)
T d1irul_          81 KLLANMVYQY----KGMGLSMGTMICGWDKRG  108 (201)
T ss_dssp             HHHHHHHHTT----TTSCCCBEEEEEEECSSS
T ss_pred             HHHHHHhhhc----cCCCceEEEEEEEEecCC
Confidence            9999999855    357999999999999753

>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=99.95  E-value=5e-28  Score=183.51  Aligned_cols=116  Identities=13%  Similarity=0.213  Sum_probs=105.1

Q ss_pred             HHhhccCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHh---
Q 031996           30 KAVKAAGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKY---  105 (149)
Q Consensus        30 ~av~~~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~---  105 (149)
                      +++. +|+|+|||+++||||||+|++.+ +.++..++.+||++|++|++|+++|..+|++.+.+.++.++..|++++   
T Consensus         3 ~~i~-tGtTivgi~~~dgVvlaaD~r~s~g~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~l~~~~~~~~~~~~~~   81 (233)
T d1ryp2_           3 QPIV-TGTSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLA   81 (233)
T ss_dssp             CCCE-EECCEEEEEETTEEEEEEECCEEETTEEEESCCCCEEEETTTEEEEEEEEHHHHHHHHHHHHHHHHHHHTTCTTT
T ss_pred             CCcc-ccceEEEEEECCEEEEEECCCcccCCeeecCCcceEEEeCCCEEEEeccCchHHHHHHHHHHHHHHHHHHhhCCC
Confidence            3455 49999999999999999999987 788888889999999999999999999999999999999999999886   


Q ss_pred             --CCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCCC
Q 031996          106 --GYEMPVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPSE  148 (149)
Q Consensus       106 --~~~~~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~~  148 (149)
                        +.+++++.+++++++.++  +++.+.|||++++||+|||++++
T Consensus        82 ~~~~~~~~~~~a~~l~~~~y--~~~~~~~P~~~~~liaG~d~~g~  124 (233)
T d1ryp2_          82 DAEEALEPSYIFEYLATVMY--QRRSKMNPLWNAIIVAGVQSNGD  124 (233)
T ss_dssp             TTTTSCCHHHHHHHHHHHHH--HHHHTTCCCCEEEEEEEECTTSC
T ss_pred             CCCcccCHHHHHHHHHHHHH--hhccccCCceeEEEEEEEcCCCC
Confidence              678899999999999875  55568899999999999998764

>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=99.95  E-value=3.9e-27  Score=174.47  Aligned_cols=107  Identities=20%  Similarity=0.326  Sum_probs=100.7

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      ||+|||+++||||||+|++.+ +.++.+++.+|||+|+++++|++||..+|++.+.++++.+++.|++.++++++++.++
T Consensus         1 TT~vgi~~~dgVvlaaD~r~s~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a   80 (202)
T d1j2qh_           1 TTTVGLVCKDGVVMATEKRATMGNFIASKAAKKIYQIADRMAMTTAGSVGDAQFLARIIKIEANLYEIRRERKPTVRAIA   80 (202)
T ss_dssp             CCEEEEEETTEEEEEEECCEEETTEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             CcEEEEEECCEEEEEECCCcccCCeeccCccceEEEecCcEEEEecCcchhHHHHHHHHHHHhhhhhhccCCCccHHHHH
Confidence            699999999999999999988 7788888899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      +++++++|.++    .|||++++|+||+|+++
T Consensus        81 ~~~~~~~~~~~----~~p~~~~~lvaG~d~~~  108 (202)
T d1j2qh_          81 TLTSNLLNSYR----YFPYLVQLLIGGIDSEG  108 (202)
T ss_dssp             HHHHHHHHHTT----TSCCCEEEEEEEEETTE
T ss_pred             HHHHHHHhhhc----ccceeeEEEEEEEcCCC
Confidence            99999998764    46999999999999753

>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=99.95  E-value=4.5e-27  Score=174.72  Aligned_cols=106  Identities=14%  Similarity=0.174  Sum_probs=99.6

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      ||+|||+++||||||+|++.+ +.++..++.+||++|++|++++++|..+|++.+.+.++.+++.|+++++++++++.++
T Consensus         1 TTivai~~~dgVvlaaD~r~t~g~~i~~~~~~KI~~i~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~a   80 (202)
T d1iruh_           1 TTIMAVQFDGGVVLGADSRTTTGSYIANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAA   80 (202)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHH
T ss_pred             CeEEEEEECCEEEEEECCccccCCeeecCCcceEEEcCCcEEEEeccchHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHH
Confidence            699999999999999999998 6777788899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      +++++.+|.+     .+||++++|++|||+++
T Consensus        81 ~~l~~~l~~~-----~~p~~~~~lvaG~d~~~  107 (202)
T d1iruh_          81 SLFKEMCYRY-----REDLMAGIIIAGWDPQE  107 (202)
T ss_dssp             HHHHHHHHHT-----TTTCCEEEEEEEEETTT
T ss_pred             HHHHHHHHhh-----ccceeEEEEEEEeecCC
Confidence            9999999854     35999999999999764

>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=99.94  E-value=8.7e-27  Score=173.78  Aligned_cols=109  Identities=15%  Similarity=0.211  Sum_probs=98.8

Q ss_pred             hhccCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCC
Q 031996           32 VKAAGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMP  110 (149)
Q Consensus        32 v~~~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~  110 (149)
                      ++ +|+|+|||+++||||||+|++.+ +.++.+++.+||++|++|++|+++|..+|++.+.++++.+++.|+++++++ +
T Consensus         6 v~-~GtTivgi~~~dgVvlaaD~r~s~g~~i~~~~~~ki~~i~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~-~   83 (205)
T d1ryph_           6 VS-LGASIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKIWCCRSGSAADTQAIADIVQYHLELYTSQYGTP-S   83 (205)
T ss_dssp             CB-CCCCEEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEEBHHHHHHHHHHHHHHHHHHHHHHSSC-C
T ss_pred             cc-CcceEEEEEECCEEEEEECCccccCceeeccccceEEEccCceEEeeccchhHHHHHHHHHHHHHHHHHHHcCCc-c
Confidence            55 49999999999999999999998 677777889999999999999999999999999999999999999999975 5


Q ss_pred             HHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996          111 VDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus       111 ~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      +..+++.++++++.     +.+||++++||||||+++
T Consensus        84 ~~~~~~~~~~~~~~-----~~~p~~~~~lvaG~d~~~  115 (205)
T d1ryph_          84 TETAASVFKELCYE-----NKDNLTAGIIVAGYDDKN  115 (205)
T ss_dssp             HHHHHHHHHHHHHH-----TTTTCCEEEEEEEEETTT
T ss_pred             HHHHHHHHHHHHHh-----CccCceEEEEEEeecCCC
Confidence            78899999998863     347999999999999764

>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=99.94  E-value=1.6e-26  Score=173.70  Aligned_cols=110  Identities=16%  Similarity=0.231  Sum_probs=97.8

Q ss_pred             cCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhC-CCCCHH
Q 031996           35 AGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYG-YEMPVD  112 (149)
Q Consensus        35 ~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~-~~~~~~  112 (149)
                      +|+|+|||+++||||||+|++.+ +.++..++.+||++|++|+++++||+.+|++.+.++++.+++.|++.++ .++++.
T Consensus         8 nG~Tivgi~~~dgVviaaD~r~s~~~~i~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~   87 (222)
T d1ryp1_           8 NGGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKLSIN   87 (222)
T ss_dssp             CCCEEEEEECSSCEEEEEECCEEETTEEEESCCCCCEECSTTCEEEEEESHHHHHHHHHHHHHHHHHHHHHTTTCCCCHH
T ss_pred             CCcEEEEEEECCEEEEEECCCcccCCEeccCCcceEEEecCCEEEEeccChHHHHHHHHHHHHHhhhhhhhcCCCCCcHH
Confidence            49999999999999999999998 5556677899999999999999999999999999999999999999876 568888


Q ss_pred             HHHHHHHHHHHHHhhcCCccccceEEEEEEEeCCCC
Q 031996          113 VLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPSE  148 (149)
Q Consensus       113 ~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~~  148 (149)
                      .++++++..++    ..+.|||+++++|+|||++++
T Consensus        88 ~~~~~~~~~~~----~~~~~p~~~~~li~G~d~~~~  119 (222)
T d1ryp1_          88 SAARNIQHLLY----GKRFFPYYVHTIIAGLDEDGK  119 (222)
T ss_dssp             HHHHHHHHHHH----TTTTSCCCEEEEEEEECTTSC
T ss_pred             HHHHHHHHHHH----hhhhhhheeeeeEEEEeCCCC
Confidence            88887776654    457899999999999998764

>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=99.94  E-value=6.7e-26  Score=168.08  Aligned_cols=107  Identities=19%  Similarity=0.256  Sum_probs=98.3

Q ss_pred             cCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHH
Q 031996           35 AGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDV  113 (149)
Q Consensus        35 ~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~  113 (149)
                      +|+|+|||+++||||||+|++.+ +.++..++.+|||++ +|++++++|..+|++.+.++++.+++.|+++++++++++.
T Consensus         7 nG~Tivgi~~~d~VvlaaD~r~~~~~~~~~~~~~Ki~~i-~~i~~~~~G~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~   85 (204)
T d1rypj_           7 NGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHY-GHVFLGITGLATDVTTLNEMFRYKTNLYKLKEERAIEPET   85 (204)
T ss_dssp             SCCEEEEEECSSEEEEEEECCEEETTEEEESCCCCEEEE-TTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHH
T ss_pred             CCeEEEEEEECCEEEEEEcCCcccCCEeecCcccEEEEc-CCEEEEecCcchHHHHHHHHHHHHHHHHHHhcCCCCcchH
Confidence            39999999999999999999998 556666788999999 5999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          114 LAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       114 la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++++++.+|.+    ..+||+++++++|||+.
T Consensus        86 la~~l~~~l~~~----~~~p~~v~~li~G~d~~  114 (204)
T d1rypj_          86 FTQLVSSSLYER----RFGPYFVGPVVAGINSK  114 (204)
T ss_dssp             HHHHHHHHHHTT----TTSCCCEEEEEEEECTT
T ss_pred             HHHHHHHHHHhh----cccceeeeEEEEEEecC
Confidence            999999998743    45799999999999964

>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=99.94  E-value=4.7e-26  Score=169.09  Aligned_cols=110  Identities=13%  Similarity=0.139  Sum_probs=101.6

Q ss_pred             cCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHH
Q 031996           35 AGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDV  113 (149)
Q Consensus        35 ~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~  113 (149)
                      +|+|+|||+++||||||+|++.+ +.++..++.+||++|++|++++++|..+|++.+.+++|.+++.|+++++.+++++.
T Consensus         8 nG~Tivai~~~dgVviaaD~r~t~g~~~~~~~~~KI~~i~~~i~~~~aG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~   87 (213)
T d1iru1_           8 NGGTILAIAGEDFAIVASDTRLSEGFSIHTRDSPKCYKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMTTGA   87 (213)
T ss_dssp             CCCEEEEEEETTEEEEEEECCEEETTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHH
T ss_pred             CCcEEEEEEECCEEEEEECCccccCceeeccccCEEEEcCCCEEEEecCccchHHHHHHHHHHHHHHHHHhhCCchhHHH
Confidence            39999999999999999999988 55666778899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhcCCccccceEEEEEEEeCCCC
Q 031996          114 LAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIPSE  148 (149)
Q Consensus       114 la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~~  148 (149)
                      ++++++..+|.+    ..+|++++.+++|||.+++
T Consensus        88 ~~~~~~~~~~~~----~~~~~~~~~~~~g~d~~~~  118 (213)
T d1iru1_          88 IAAMLSTILYSR----RFFPYYVYNIIGGLDEEGK  118 (213)
T ss_dssp             HHHHHHHHHHTT----TTSCCCEEEEEEEECTTSC
T ss_pred             HHHHHHHHHHHH----HhhhcccccceEEEecCCC
Confidence            999999999854    4569999999999998653

>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=99.93  E-value=4.1e-26  Score=170.71  Aligned_cols=107  Identities=13%  Similarity=0.150  Sum_probs=99.9

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      ||+|||++|||||||+|++.+ +.++..++.+|||+|++|++|+++|..+|++.+++.++.+++.|++.++++++++.++
T Consensus         1 TT~iai~~kdgVvlaaD~r~t~g~~i~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a   80 (212)
T d1rypl_           1 TTTLAFRFQGGIIVAVDSRATAGNWVASQTVKRVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREKERISVAAAS   80 (212)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEECCBCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             CeEEEEEECCEEEEEEcCccccCceeecCCcceEEEECCcEEEEeccchHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHH
Confidence            699999999999999999987 6777788999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      +++++++|.|    ..+|++++.+++|+|++.
T Consensus        81 ~~ls~~~~~~----~~~p~~~~~~l~G~~~~~  108 (212)
T d1rypl_          81 KILSNLVYQY----KGAGLSMGTMICGYTRKE  108 (212)
T ss_dssp             HHHHHHHHHT----TTSCCCBEEEEEEEETTT
T ss_pred             HHHHHHHHHh----ccCCcceEeeeeEeecCC
Confidence            9999999865    345999999999998764

>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=99.93  E-value=8.3e-26  Score=169.89  Aligned_cols=106  Identities=15%  Similarity=0.147  Sum_probs=98.4

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      ||+|||+|+||||||+|++.+ +.++..++.+||++|++|++|+++|..+|++.+.+.++.+++.|+++++++++++.++
T Consensus         1 TTivgi~~~dgVvlaaD~r~s~g~~i~~~~~~KI~~i~~~i~~~~aG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a   80 (220)
T d1irui_           1 TTIAGVVYKDGIVLGADTRATEGMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGRLPRVVTAN   80 (220)
T ss_dssp             CCEEEEEETTEEEEEECCCEESSSBEEESSCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHCSCCCHHHHH
T ss_pred             CeEEEEEECCEEEEEEcCCcccCCEeecCCcccEEEecCcEEEEEccccHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHH
Confidence            699999999999999999998 5666677889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      ++++++++.     ..+||++++|++|||+++
T Consensus        81 ~~l~~~~y~-----~~~p~~~~~ivaG~D~~g  107 (220)
T d1irui_          81 RMLKQMLFR-----YRGYIGAALVLGGVDVTG  107 (220)
T ss_dssp             HHHHHHHHH-----TTTCSCEEEEEEEECSSC
T ss_pred             HHHHhhhhh-----cccccceeEEEEEEeCCC
Confidence            999999863     347999999999999764

>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=99.93  E-value=7.5e-26  Score=169.74  Aligned_cols=112  Identities=16%  Similarity=0.183  Sum_probs=101.6

Q ss_pred             hhccCceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHH-hCCCC
Q 031996           32 VKAAGVTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFK-YGYEM  109 (149)
Q Consensus        32 v~~~G~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~-~~~~~  109 (149)
                      +. +|+|+|||+++||||||+|++.+ +.++..++.+||++|++|++|+++|..+|++.+.+.++.++..|+.. ++.++
T Consensus         5 ~~-~GtTivgi~~~dgVviaaD~r~t~g~~~~~~~~~KI~~i~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~~   83 (217)
T d1iru2_           5 MV-TGTSVLGVKFEGGVVIAADMLGSYGSLARFRNISRIMRVNNSTMLGASGDYADFQYLKQVLGQMVIDEELLGDGHSY   83 (217)
T ss_dssp             CS-EECCCEEEEETTEEEEEEECCEEETTEEEECSCCCEEEETTTEEEEEEEEHHHHHHHHHHHHHHHHHHHHHCSSCCC
T ss_pred             cC-cccEEEEEEECCEEEEEEcCCcccCCeeecCCcceEEEeCCCeEEEeccccHHHHHHHHHHHHHHHHhhhhcCCCCC
Confidence            44 49999999999999999999987 67787889999999999999999999999999999999999988765 57999


Q ss_pred             CHHHHHHHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          110 PVDVLAKWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       110 ~~~~la~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++.++++++++++  +++...|||++++|++|+|+.
T Consensus        84 ~v~~~a~~l~~~~y--~~~~~~~p~~~~~li~G~d~~  118 (217)
T d1iru2_          84 SPRAIHSWLTRAMY--SRRSKMNPLWNTMVIGGYADG  118 (217)
T ss_dssp             CHHHHHHHHHHHHH--HHHHTTCCCCEEEEEEEEETT
T ss_pred             CHHHHHHHHHHHHH--HhccccCcccceEEEEEEcCC
Confidence            99999999999875  555688999999999999964

>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=99.92  E-value=7.5e-25  Score=160.10  Aligned_cols=109  Identities=17%  Similarity=0.273  Sum_probs=100.7

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      +|+|||+++||||||+|++.+ +.++.+++.+||++|+++++++++|..+|++.+.++++.++..|+..++.+++++.++
T Consensus         2 t~ivgi~~kdgVviaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~~G~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   81 (199)
T d1iruk_           2 EYLIGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYIQKNVQLYKMRNGYELSPTAAA   81 (199)
T ss_dssp             CCEEEEECSSEEEEEEECCEEETTEEEESSCCCEEECSSSEEEEEEESTTHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             eEEEEEEECCEEEEEECCCccCCCeeecCCcceEEEecCcEEEEecccchHHHHHHHHHHHHhhhhhhhcCCcCcHHHHH
Confidence            689999999999999999998 5555667889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIPS  147 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~~  147 (149)
                      +.+++.++.+.  ...+|++++++++|||++.
T Consensus        82 ~~l~~~~~~~~--~~~~~~~~~~~~aG~d~~~  111 (199)
T d1iruk_          82 NFTRRNLADCL--RSRTPYHVNLLLAGYDEHE  111 (199)
T ss_dssp             HHHHHHHHHHH--TSSSCCCEEEEEEEEETTT
T ss_pred             HHHHHHHHHHh--hccCCcceeeeecceeccC
Confidence            99999887654  3678999999999999865

>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=99.92  E-value=7.9e-25  Score=164.92  Aligned_cols=105  Identities=14%  Similarity=0.171  Sum_probs=98.1

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      ||+|||+++||||||+|++.+ +.++..++.+||++|++|++|+++|..+|++.+.+.++.++..|++.++.++++..++
T Consensus         1 TTiVgik~~dGVviaaD~r~s~g~~~~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~l~~~~~~~~~~~~~~~~v~~~a   80 (222)
T d1rypi_           1 TTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSAL   80 (222)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHH
T ss_pred             CeEEEEEECCEEEEEECCCcccCceeecCCcccEEEEcCCEEEEecccchHHHHHHHHHHHHHHHhhhhhCCCCcHHHHH
Confidence            699999999999999999998 6777788899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeCC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAIP  146 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~~  146 (149)
                      +++++.++.     ..+||+++++++|+|++
T Consensus        81 ~~l~~~~~~-----~~~p~~~~~l~aG~d~~  106 (222)
T d1rypi_          81 QMLKQHLFK-----YQGHIGAYLIVAGVDPT  106 (222)
T ss_dssp             HHHHHHHHH-----TTTCSCEEEEEEEEETT
T ss_pred             HHHHHHHHh-----hhhccceeEEEEEEcCC
Confidence            999998753     35799999999999975

>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=99.92  E-value=7.8e-25  Score=164.28  Aligned_cols=108  Identities=19%  Similarity=0.195  Sum_probs=101.7

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEFRFKYGYEMPVDVLA  115 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la  115 (149)
                      ||+|||+++||||||+|++.+ +.++..++.+||++|++|++++++|..+|++.+.++++.+++.|+++++.+++++.++
T Consensus         1 TTivgi~~kdgVvlaaD~r~s~g~~i~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   80 (224)
T d1q5qh_           1 TTIVALTYKGGVLLAGDRRATQGNLIASRDVEKVYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEGVPLTFDGKA   80 (224)
T ss_dssp             CCEEEEECSSCEEEEECCCEEETTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             CeEEEEEECCEEEEEECCCcccCCEeecCCcceEEEeCCcEEEEecccchHHHHHHHHHHHHhHHHHHhhCCCccHHHHH
Confidence            699999999999999999988 6777778899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCccccceEEEEEEEeC
Q 031996          116 KWIADKSQVYTQHAYMRPLGVGLFLIEIAI  145 (149)
Q Consensus       116 ~~l~~~~~~~t~~~~~rP~~v~~liaG~D~  145 (149)
                      +++++++|.+++ ...+|+++.++++|+|.
T Consensus        81 ~~~~~~~~~~~~-~~~~~~~~~~~~~g~~~  109 (224)
T d1q5qh_          81 NRLASMVRGNLG-AAMQGLAVVPLLVGYDL  109 (224)
T ss_dssp             HHHHHHHHTTHH-HHTTTCCEEEEEEEECT
T ss_pred             HHHHHHHHHhhc-ccccCccceeeEEEeec
Confidence            999999998875 46889999999999874

>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=99.42  E-value=5.5e-13  Score=94.80  Aligned_cols=65  Identities=8%  Similarity=-0.076  Sum_probs=58.3

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEEEeccHHHHHHHHHHHHHHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLLATGMTADARTLVQQARYEAAEF  101 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~  101 (149)
                      ||+|||+++||||||+|+|.+ +.++..++.+||++|+++++++.+|..+|.+.+......+...+
T Consensus         1 TTivav~~~~gVviAaDtR~S~G~~i~~r~~~Ki~~i~~~~~~~~~g~~ad~~~~~~~~~~~~~~~   66 (171)
T d1m4ya_           1 TTILVVRRNGQTVMGGDGQVTFGSTVLKGNARKVRKLGEGKVLAGFAGSVADAMTLFDRFEAKLRE   66 (171)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEECCEEEEEECCCcccCCEEEeCCcceEEEecCCcEEEEEeechhhHHHHHHHHHHHHHH
Confidence            699999999999999999998 78888899999999999999999999999998887766555443

>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=1.9e-13  Score=98.23  Aligned_cols=67  Identities=16%  Similarity=0.119  Sum_probs=56.0

Q ss_pred             cCceEEEEEcCCeEEEEEeccCC-cccccc-ccccceeeecCc-EEEEEeccHHHHHHHHHHHHHHHHHH
Q 031996           35 AGVTSIGVRGKDSVCVVTQKKVP-DKLLDH-TSVTHLFPITKY-LGLLATGMTADARTLVQQARYEAAEF  101 (149)
Q Consensus        35 ~G~t~igik~kdgVvlaad~~~~-~~l~~~-~~~~KI~~I~~~-i~~~~sG~~~D~~~l~~~~r~~~~~~  101 (149)
                      +|||+|||+++||||||+|+|.+ ++++.. ...+|+++++++ ++++.+|...|.+.+.+..+.+...+
T Consensus         4 ~GTTivai~~~dGVvlAaDtR~S~G~~i~~~~~~~ki~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~   73 (180)
T d2z3ba1           4 HATTIFAVQHKGRSAMSGDGQVTFGQAVVMKHTARKVRKLFNGKVLAGFAGSVADAFTLFEKFEAKLEEY   73 (180)
T ss_dssp             CCCCEEEEEETTEEEEEECCCEEETTTEEEESCCCCEEEETTTTEEEEECSCHHHHHHHHHHHHHHHHHT
T ss_pred             CCeEEEEEEECCEEEEEECCcccCCceeEecccceEEEEecccceecccchHHHHHHHHHHHHHHHHHhh
Confidence            49999999999999999999998 555544 457899999875 78888999999999998887666543

>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=99.37  E-value=2.4e-12  Score=91.66  Aligned_cols=56  Identities=25%  Similarity=0.183  Sum_probs=45.1

Q ss_pred             ceEEEEEcCCeEEEEEeccCC-ccccccccccceeeecCcEEEE-EeccHHHHHHHHH
Q 031996           37 VTSIGVRGKDSVCVVTQKKVP-DKLLDHTSVTHLFPITKYLGLL-ATGMTADARTLVQ   92 (149)
Q Consensus        37 ~t~igik~kdgVvlaad~~~~-~~l~~~~~~~KI~~I~~~i~~~-~sG~~~D~~~l~~   92 (149)
                      ||+|||+++||||||+|+|++ +.++..++.+||++|+++++++ .+|...+.+.+.+
T Consensus         1 TTivai~~~dGVVlAaDtRaS~G~~i~~r~~~Ki~~i~~~~~~~~~~~~~~~~~~~~~   58 (173)
T d1g3ka_           1 TTIVSVRRNGQVVVGGDGQVSLGNTVMKGNARKVRRLYNGKVLAGFAGGTADAFTLFE   58 (173)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHH
T ss_pred             CeEEEEEECCEEEEEECCCcccCCEeEcCCcceEEEecCCcEEEEeeehhHhHHHHHH
Confidence            699999999999999999999 7888889999999998885554 4555444444443

>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaF
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=80.70  E-value=1.9  Score=23.56  Aligned_cols=33  Identities=15%  Similarity=0.172  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 031996           87 ARTLVQQARYEAAEFRFKYGYEMPVDVLAKWIA  119 (149)
Q Consensus        87 ~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~  119 (149)
                      .+....++++....+...+|++|+++.+|..+.
T Consensus        10 ~~e~~~ki~~~~~~l~q~lgRePT~~EiA~~l~   42 (57)
T d1l0oc_          10 LKEMGNKIRKAKDELSKTRGRAPTVTEIADHLG   42 (57)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHC
Confidence            456777888888889999999999999998764