Citrus Sinensis ID: 025716

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------25
Protein Sequence
MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKKAAAEAAKKGPPKET
Secondary Structure (PSIPRED)
cccccccccEEcccccHHHHHHHHHHHHccccEEEEEcccEEEEEEEcccccccccccccccEEEEcccEEEEEEcccccHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHcccccccHHHEEEEEEEccccccccEEEEcccccccccEEEEEccccHHHHHHHHHHcccccHHHHHHHHHHHHHHHHcccccEEEEEEEEccccEEEccHHHHHHHHHHHHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
ccHcccccccEcccccEHHHHHHHHHHHccccEEEEEccccEEEEEEcccccccEcHHHcccEEEEEccEEEEEEEcHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHccccccEccccEEEEEEEEEcccEcEEEEEEcccccEEEEcEEEEcccHHHHHHHHHcccccccccccHHHHHHHHHHHHccccccEEEEEEEcccEEEcccHHHHHHHHHHHHHHHHHHHHHHccccccc
Coil and Loop (DISEMBL)
marydraitvfspdghlFQVEYALEAVRKgnaavgvrgTDTIVLGVEKkstvklqdsrsvrkIVSLDNHIALACAGLKADARVLINRARIEcqshrltvedpvTVEYITRYIAGLQQKytqsggvrpfglstlivgfdpytgvpslyqtdpsgtfsawkanatgrnsnSMREFLEKNYKETSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKKAAAEAakkgppket
Flexible Loop (DISEMBL)
marydraitvfspdghlFQVEYALEAVRKgnaavgvrgtdtivlgvekkstvklqdsrsvrkiVSLDNHIALACAGLKADARVLINRARiecqshrltvedpvtVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKAnatgrnsnsMREFLEKNyketsgqeTIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKKAAaeaakkgppket
Low Complexity Region (SEG)
MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMVaeieakkaaaeaakkGPPKET
Disordered region (IsUnstruct)
*****RAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAW**************************ETIKLAIRALLEVVESGGKNIEVAVMTR*************************************
Disordered Region (DISOPRED)
*ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMVA********************
Disordered Region (DISEMBL)
MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAK***************
Disordered Region (DISPRO)
***YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKKAAA***********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQxxxxxxxxxxxxxxxxxxxxxAAKKGPPKET
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	249	2.2.26 [Sep-21-2011]
O24616	250	Proteasome subunit alpha	yes	no	1.0	0.996	0.928	1e-126
O24030	259	Proteasome subunit alpha	N/A	no	0.915	0.880	0.934	1e-125
Q9SXU1	249	Proteasome subunit alpha	N/A	no	0.915	0.915	0.929	1e-125
P30186	250	Proteasome subunit alpha	yes	no	0.915	0.912	0.917	1e-122
Q0J006	249	Proteasome subunit alpha	yes	no	0.915	0.915	0.916	1e-122
A2Z3I9	249	Proteasome subunit alpha	N/A	no	0.915	0.915	0.916	1e-122
Q6YT00	249	Proteasome subunit alpha	yes	no	0.915	0.915	0.912	1e-121
A2YXU2	249	Proteasome subunit alpha	N/A	no	0.915	0.915	0.912	1e-121
P34120	250	Proteasome subunit alpha	yes	no	0.935	0.932	0.705	4e-95
Q9CWH6	250	Proteasome subunit alpha	yes	no	0.963	0.96	0.680	2e-94

>sp|O24616|PSA7B_ARATH Proteasome subunit alpha type-7-B OS=Arabidopsis thaliana GN=PAD2 PE=1 SV=2

 Score =  451 bits (1159), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 232/250 (92%), Positives = 245/250 (98%), Gaps = 1/250 (0%)

Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDT+VL VEKKST KLQDSRS 
Sbjct: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTVVLAVEKKSTPKLQDSRSA 60

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
           RKIVSLDNHIALACAGLKADARVLIN+ARIECQSHRLT+EDPVTVEYITRYIAGLQQKYT
Sbjct: 61  RKIVSLDNHIALACAGLKADARVLINKARIECQSHRLTLEDPVTVEYITRYIAGLQQKYT 120

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           QSGGVRPFGLSTLIVGFDPY+ +PSLYQTDPSGTFSAWKANATGRNSNS+REFLEKNYKE
Sbjct: 121 QSGGVRPFGLSTLIVGFDPYSRLPSLYQTDPSGTFSAWKANATGRNSNSIREFLEKNYKE 180

Query: 181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREK-GLKQLDEAEIDAMVAEIEAKKAAAE 239
           +SGQETIKLAIRALLEVVESGGKNIEVAVMTRE+ GL+QL+EAEIDA+VA+IEA+KAAAE
Sbjct: 181 SSGQETIKLAIRALLEVVESGGKNIEVAVMTREETGLRQLEEAEIDAIVAKIEAEKAAAE 240

Query: 240 AAKKGPPKET 249
           AAKKGPPKET
Sbjct: 241 AAKKGPPKET 250

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: 3EC: .EC: 4EC: .EC: 2EC: 5EC: .EC: 1

>sp|O24030|PSA7_SOLLC Proteasome subunit alpha type-7 OS=Solanum lycopersicum GN=PAD1 PE=2 SV=1

 Score =  447 bits (1151), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 213/228 (93%), Positives = 225/228 (98%)

Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           MARYDRAITVFSPDGHLFQVEYA+EAVRKGNAAVGVRGTDT+VLGVEKKST KLQDSRSV
Sbjct: 1   MARYDRAITVFSPDGHLFQVEYAMEAVRKGNAAVGVRGTDTVVLGVEKKSTPKLQDSRSV 60

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
           RKIV+LD+HIALACAGLKADARVL+N+ARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT
Sbjct: 61  RKIVNLDDHIALACAGLKADARVLVNKARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           QSGGVRPFGLSTLI+GFDP+TGVPSLYQTDPSGTFSAWKANATGRNSNS REFLEKNYKE
Sbjct: 121 QSGGVRPFGLSTLIIGFDPHTGVPSLYQTDPSGTFSAWKANATGRNSNSTREFLEKNYKE 180

Query: 181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
           TSGQET+KLAIRALLEVVESGGKNIEVAVMT+E GLKQL+EAEIDA+V
Sbjct: 181 TSGQETVKLAIRALLEVVESGGKNIEVAVMTKEHGLKQLEEAEIDAIV 228

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.

Solanum lycopersicum (taxid: 4081)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|Q9SXU1|PSA7_CICAR Proteasome subunit alpha type-7 OS=Cicer arietinum GN=PAD1 PE=2 SV=1

 Score =  447 bits (1150), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 212/228 (92%), Positives = 224/228 (98%)

Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTD +VLGVEKKST KLQD+RSV
Sbjct: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDNVVLGVEKKSTAKLQDTRSV 60

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
           RKIV+LD+HIALACAGLKADARVLINRAR+ECQSHRLTVEDPVTVEYITRYIAGLQQKYT
Sbjct: 61  RKIVNLDDHIALACAGLKADARVLINRARVECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           QSGGVRPFGLSTLIVGFDPYTG PSLYQTDPSGTFSAWKANATGRNSNS+REFLEKN+KE
Sbjct: 121 QSGGVRPFGLSTLIVGFDPYTGSPSLYQTDPSGTFSAWKANATGRNSNSIREFLEKNFKE 180

Query: 181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
           TSGQET+KLAIRALLEVVESGGKNIEVAVMT+E GL+QL+EAEIDA+V
Sbjct: 181 TSGQETVKLAIRALLEVVESGGKNIEVAVMTKENGLRQLEEAEIDAIV 228

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.

Cicer arietinum (taxid: 3827)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|P30186|PSA7A_ARATH Proteasome subunit alpha type-7-A OS=Arabidopsis thaliana GN=PAD1 PE=1 SV=1

 Score =  437 bits (1123), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 210/229 (91%), Positives = 222/229 (96%), Gaps = 1/229 (0%)

Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDT+VL VEKKST KLQDSRS 
Sbjct: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTVVLAVEKKSTPKLQDSRSA 60

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
           RKIVSLDNHIALACAGLKADARVLIN+ARIECQSHRLT+EDPVTVEYITRYIAGLQQKYT
Sbjct: 61  RKIVSLDNHIALACAGLKADARVLINKARIECQSHRLTLEDPVTVEYITRYIAGLQQKYT 120

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           QSGGVRPFGLSTLIVGFDPYT +P+LYQTDPSGTFSAWKANATGRNSNS+REFLEKNYKE
Sbjct: 121 QSGGVRPFGLSTLIVGFDPYTRIPALYQTDPSGTFSAWKANATGRNSNSIREFLEKNYKE 180

Query: 181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKG-LKQLDEAEIDAMV 228
           ++GQET+KLAIRALLEVVESGGKNIEVAVMTRE+G LKQL+E EID +V
Sbjct: 181 SAGQETVKLAIRALLEVVESGGKNIEVAVMTREEGVLKQLEEEEIDIIV 229

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. Mediates the association of the SCF(TIR1) E3 ubiquitin ligase complex with the proteasome.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|Q0J006|PSA7B_ORYSJ Proteasome subunit alpha type-7-B OS=Oryza sativa subsp. japonica GN=PAD1 PE=2 SV=1

 Score =  436 bits (1120), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 209/228 (91%), Positives = 219/228 (96%)

Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRG+DT+VLGVEKKST KLQDSRSV
Sbjct: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGSDTVVLGVEKKSTPKLQDSRSV 60

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
           RKI SLD HIALACAGLKADARVLINRAR+ECQSHRLTVED VTVEYITRYIAGLQQKYT
Sbjct: 61  RKIASLDTHIALACAGLKADARVLINRARVECQSHRLTVEDAVTVEYITRYIAGLQQKYT 120

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           QSGGVRPFGLSTLIVGFDPYT  P+LYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE
Sbjct: 121 QSGGVRPFGLSTLIVGFDPYTDKPALYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180

Query: 181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
           TSG+ETIKLAIRALLEVVESGGKNIE+AVMT++ GL+QL+EAEID  V
Sbjct: 181 TSGKETIKLAIRALLEVVESGGKNIEIAVMTQKDGLRQLEEAEIDEYV 228

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|A2Z3I9|PSA7B_ORYSI Proteasome subunit alpha type-7-B OS=Oryza sativa subsp. indica GN=PAD1 PE=2 SV=1

 Score =  436 bits (1120), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 209/228 (91%), Positives = 219/228 (96%)

Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRG+DT+VLGVEKKST KLQDSRSV
Sbjct: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGSDTVVLGVEKKSTPKLQDSRSV 60

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
           RKI SLD HIALACAGLKADARVLINRAR+ECQSHRLTVED VTVEYITRYIAGLQQKYT
Sbjct: 61  RKIASLDTHIALACAGLKADARVLINRARVECQSHRLTVEDAVTVEYITRYIAGLQQKYT 120

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           QSGGVRPFGLSTLIVGFDPYT  P+LYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE
Sbjct: 121 QSGGVRPFGLSTLIVGFDPYTDKPALYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180

Query: 181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
           TSG+ETIKLAIRALLEVVESGGKNIE+AVMT++ GL+QL+EAEID  V
Sbjct: 181 TSGKETIKLAIRALLEVVESGGKNIEIAVMTQKDGLRQLEEAEIDEYV 228

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. indica (taxid: 39946)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|Q6YT00|PSA7A_ORYSJ Proteasome subunit alpha type-7-A OS=Oryza sativa subsp. japonica GN=Os08g0548900 PE=2 SV=1

 Score =  435 bits (1119), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 208/228 (91%), Positives = 219/228 (96%)

Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDT+VLGVEKKST KLQDSRS+
Sbjct: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTVVLGVEKKSTPKLQDSRSM 60

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
           RKI SLD HIALACAGLKADARVLINRAR+ECQSHRLTVEDPVTVEYITRYIAGLQQKYT
Sbjct: 61  RKIASLDTHIALACAGLKADARVLINRARVECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           QSGGVRPFGLSTLIVGFDPYT  P+LYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK+
Sbjct: 121 QSGGVRPFGLSTLIVGFDPYTEKPALYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKD 180

Query: 181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
           TSG+ETIKLAIRALLEVVESGGKNIE+AVMT + GL++L+EAEID  V
Sbjct: 181 TSGKETIKLAIRALLEVVESGGKNIEIAVMTHKDGLRELEEAEIDEYV 228

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|A2YXU2|PSA7A_ORYSI Proteasome subunit alpha type-7-A OS=Oryza sativa subsp. indica GN=OsI_029135 PE=2 SV=2

 Score =  435 bits (1119), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 208/228 (91%), Positives = 219/228 (96%)

Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDT+VLGVEKKST KLQDSRS+
Sbjct: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTVVLGVEKKSTPKLQDSRSM 60

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
           RKI SLD HIALACAGLKADARVLINRAR+ECQSHRLTVEDPVTVEYITRYIAGLQQKYT
Sbjct: 61  RKIASLDTHIALACAGLKADARVLINRARVECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           QSGGVRPFGLSTLIVGFDPYT  P+LYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK+
Sbjct: 121 QSGGVRPFGLSTLIVGFDPYTEKPALYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKD 180

Query: 181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
           TSG+ETIKLAIRALLEVVESGGKNIE+AVMT + GL++L+EAEID  V
Sbjct: 181 TSGKETIKLAIRALLEVVESGGKNIEIAVMTHKDGLRELEEAEIDEYV 228

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. indica (taxid: 39946)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|P34120|PSA7_DICDI Proteasome subunit alpha type-7 OS=Dictyostelium discoideum GN=psmA7 PE=3 SV=1

 Score =  347 bits (891), Expect = 4e-95,   Method: Compositional matrix adjust.
 Identities = 165/234 (70%), Positives = 201/234 (85%), Gaps = 1/234 (0%)

Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
           ARYDRAITVFSPDGHLFQVEYA+EAVRKG  AVGVRG D IVLGVEKK+T KLQD+RS+R
Sbjct: 4   ARYDRAITVFSPDGHLFQVEYAMEAVRKGTVAVGVRGKDVIVLGVEKKATAKLQDARSIR 63

Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           KIV LD+HI L  AGL AD+RVLI++A +ECQS+RLTVED  +VEYI+++IAG+QQ+YTQ
Sbjct: 64  KIVKLDDHICLTFAGLTADSRVLISKALMECQSYRLTVEDSPSVEYISKFIAGIQQRYTQ 123

Query: 122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET 181
           SGGVRPFG+STLIVGFD   G P+LYQTDPSG++S+WKA A GR+S S+ EFLEKNY + 
Sbjct: 124 SGGVRPFGISTLIVGFDT-DGTPNLYQTDPSGSYSSWKAAAIGRSSKSVGEFLEKNYTDV 182

Query: 182 SGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKK 235
           S +E+IKLA+RALLE+VESG KNIE+AV+  ++ +  LDE EID +VA +EA+K
Sbjct: 183 SEEESIKLAVRALLEIVESGNKNIEIAVIRNKQPIVLLDEQEIDKLVAVVEAEK 236

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.

Dictyostelium discoideum (taxid: 44689)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|Q9CWH6|PSA7L_MOUSE Proteasome subunit alpha type-7-like OS=Mus musculus GN=Psma8 PE=2 SV=1

 Score =  345 bits (885), Expect = 2e-94,   Method: Compositional matrix adjust.
 Identities = 166/244 (68%), Positives = 203/244 (83%), Gaps = 4/244 (1%)

Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
           +RYDRAITVFSPDGHLFQVEYA EAV+KG+ AVG+RGT+ +VLGVEKKS  KLQD R+VR
Sbjct: 3   SRYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGIRGTNIVVLGVEKKSVAKLQDERTVR 62

Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           KI +LD+H+ +A AGL ADARV+I+RAR+ECQSH+LTVEDPVTVEYITR+IA L+QKYTQ
Sbjct: 63  KICALDDHVCMAFAGLTADARVVISRARVECQSHKLTVEDPVTVEYITRFIATLKQKYTQ 122

Query: 122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE- 180
           S G RPFG+S LIVGFD   G+P LYQTDPSGT+ AWKANA GR++ ++REFLEKNY E 
Sbjct: 123 SNGRRPFGISALIVGFDD-DGIPRLYQTDPSGTYHAWKANAIGRSAKTVREFLEKNYTED 181

Query: 181 --TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKKAAA 238
             ++ +E IKLAI+ALLEVV+SGGKNIE+A++ R++ LK     EI+  V+EIE +K  A
Sbjct: 182 AISNDKEAIKLAIKALLEVVQSGGKNIELAIIRRDQPLKMFSAKEIELEVSEIEREKDEA 241

Query: 239 EAAK 242
           E  K
Sbjct: 242 EKTK 245

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

Mus musculus (taxid: 10090)

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	249
225431090	249	PREDICTED: proteasome subunit alpha type	1.0	1.0	0.955	1e-129
225428005	249	PREDICTED: proteasome subunit alpha type	1.0	1.0	0.947	1e-128
82621184	249	proteasome-like protein alpha subunit-li	1.0	1.0	0.935	1e-126
449434142	249	PREDICTED: proteasome subunit alpha type	0.915	0.915	0.942	1e-124
15239271	250	proteasome subunit alpha type-7-B [Arabi	1.0	0.996	0.928	1e-124
76160964	249	proteasome, alpha subunit-like protein [	0.915	0.915	0.938	1e-124
449456827	251	PREDICTED: proteasome subunit alpha type	0.915	0.908	0.938	1e-124
356502736	249	PREDICTED: proteasome subunit alpha type	0.915	0.915	0.938	1e-124
2511580	235	multicatalytic endopeptidase [Arabidopsi	0.939	0.995	0.923	1e-124
297794401	250	hypothetical protein ARALYDRAFT_920118 [	1.0	0.996	0.928	1e-124

>gi|225431090|ref|XP_002264052.1| PREDICTED: proteasome subunit alpha type-7 [Vitis vinifera] gi|297734987|emb|CBI17349.3| unnamed protein product [Vitis vinifera]

 Score =  466 bits (1199), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 238/249 (95%), Positives = 247/249 (99%)

Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKST KLQDSR+V
Sbjct: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTAKLQDSRTV 60

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
           RKIV+LD+HIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT
Sbjct: 61  RKIVNLDDHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE
Sbjct: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180

Query: 181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKKAAAEA 240
           TSGQET+KLAIRALLEVVESGGKNIE+AVMTRE GL+QLDEAEIDA+VAEIEA+KAAAEA
Sbjct: 181 TSGQETVKLAIRALLEVVESGGKNIEIAVMTREHGLRQLDEAEIDAIVAEIEAEKAAAEA 240

Query: 241 AKKGPPKET 249
           AKKGPPK+T
Sbjct: 241 AKKGPPKDT 249

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225428005|ref|XP_002278162.1| PREDICTED: proteasome subunit alpha type-7 [Vitis vinifera] gi|297744621|emb|CBI37883.3| unnamed protein product [Vitis vinifera]

 Score =  463 bits (1192), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 236/249 (94%), Positives = 247/249 (99%)

Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKST KLQDSR+V
Sbjct: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTAKLQDSRTV 60

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
           RKIV+LD+HIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT
Sbjct: 61  RKIVNLDDHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           QSGGVRPFGLSTLI+GFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE
Sbjct: 121 QSGGVRPFGLSTLIIGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180

Query: 181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKKAAAEA 240
           TSGQET+KLAIRALLEVVESGGKNIE+AVMT+E GL+QL+EAEIDA+VAEIEA+KAAAEA
Sbjct: 181 TSGQETVKLAIRALLEVVESGGKNIEIAVMTKEHGLRQLEEAEIDAIVAEIEAEKAAAEA 240

Query: 241 AKKGPPKET 249
           AKKGPPKET
Sbjct: 241 AKKGPPKET 249

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|82621184|gb|ABB86280.1| proteasome-like protein alpha subunit-like [Solanum tuberosum]

 Score =  457 bits (1177), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 233/249 (93%), Positives = 246/249 (98%)

Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           MARYDRAITVFSPDGHLFQVEYA+EAVRKGNAAVGVRGTDT+VLGVEKKST KLQDSRSV
Sbjct: 1   MARYDRAITVFSPDGHLFQVEYAMEAVRKGNAAVGVRGTDTVVLGVEKKSTPKLQDSRSV 60

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
           RKIV+LD+HIALACAGLKADARVL+N+ARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT
Sbjct: 61  RKIVNLDDHIALACAGLKADARVLVNKARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           QSGGVRPFGLSTLI+GFDP+TGVPSLYQTDPSGTFSAWKANATGRNSNS REFLEKNYKE
Sbjct: 121 QSGGVRPFGLSTLIIGFDPHTGVPSLYQTDPSGTFSAWKANATGRNSNSTREFLEKNYKE 180

Query: 181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKKAAAEA 240
           TSGQET+KLAIRALLEVVESGGKNIEVAVMT+E GLKQL+EAEIDA+VAEIEA+KAAAEA
Sbjct: 181 TSGQETVKLAIRALLEVVESGGKNIEVAVMTKEHGLKQLEEAEIDAIVAEIEAEKAAAEA 240

Query: 241 AKKGPPKET 249
           AKKGPPKET
Sbjct: 241 AKKGPPKET 249

Source: Solanum tuberosum

Species: Solanum tuberosum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449434142|ref|XP_004134855.1| PREDICTED: proteasome subunit alpha type-7-like [Cucumis sativus] gi|449491326|ref|XP_004158862.1| PREDICTED: proteasome subunit alpha type-7-like [Cucumis sativus]

 Score =  451 bits (1159), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 215/228 (94%), Positives = 225/228 (98%)

Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKK+T KLQDSRSV
Sbjct: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKATPKLQDSRSV 60

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
           RKIV+LD+HIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT
Sbjct: 61  RKIVNLDDHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           QSGGVRPFGLSTLI+GFDPYTG PSLYQTDPSGTFSAWKANATGRNSNS+REFLEKNYKE
Sbjct: 121 QSGGVRPFGLSTLIIGFDPYTGAPSLYQTDPSGTFSAWKANATGRNSNSIREFLEKNYKE 180

Query: 181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
           TSGQET+KLAIRALLEVVESGGKNIEVAVMT+E GL+QL+EAEIDA+V
Sbjct: 181 TSGQETVKLAIRALLEVVESGGKNIEVAVMTKEHGLRQLEEAEIDALV 228

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15239271|ref|NP_201415.1| proteasome subunit alpha type-7-B [Arabidopsis thaliana] gi|12229893|sp|O24616.2|PSA7B_ARATH RecName: Full=Proteasome subunit alpha type-7-B; AltName: Full=20S proteasome alpha subunit D-2; AltName: Full=Proteasome component 6B; AltName: Full=Proteasome component 6C; AltName: Full=Proteasome subunit alpha type-4 gi|3421082|gb|AAC32059.1| 20S proteasome subunit PAD2 [Arabidopsis thaliana] gi|10177129|dbj|BAB10419.1| 20S proteasome subunit PAD2 [Arabidopsis thaliana] gi|332010781|gb|AED98164.1| proteasome subunit alpha type-7-B [Arabidopsis thaliana]

 Score =  451 bits (1159), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 232/250 (92%), Positives = 245/250 (98%), Gaps = 1/250 (0%)

Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDT+VL VEKKST KLQDSRS 
Sbjct: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTVVLAVEKKSTPKLQDSRSA 60

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
           RKIVSLDNHIALACAGLKADARVLIN+ARIECQSHRLT+EDPVTVEYITRYIAGLQQKYT
Sbjct: 61  RKIVSLDNHIALACAGLKADARVLINKARIECQSHRLTLEDPVTVEYITRYIAGLQQKYT 120

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           QSGGVRPFGLSTLIVGFDPY+ +PSLYQTDPSGTFSAWKANATGRNSNS+REFLEKNYKE
Sbjct: 121 QSGGVRPFGLSTLIVGFDPYSRLPSLYQTDPSGTFSAWKANATGRNSNSIREFLEKNYKE 180

Query: 181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREK-GLKQLDEAEIDAMVAEIEAKKAAAE 239
           +SGQETIKLAIRALLEVVESGGKNIEVAVMTRE+ GL+QL+EAEIDA+VA+IEA+KAAAE
Sbjct: 181 SSGQETIKLAIRALLEVVESGGKNIEVAVMTREETGLRQLEEAEIDAIVAKIEAEKAAAE 240

Query: 240 AAKKGPPKET 249
           AAKKGPPKET
Sbjct: 241 AAKKGPPKET 250

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|76160964|gb|ABA40445.1| proteasome, alpha subunit-like protein [Solanum tuberosum]

 Score =  450 bits (1158), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 214/228 (93%), Positives = 225/228 (98%)

Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           MARYDRAITVFSPDGHLFQVEYA+EAVRKGNAAVGVRGTDT+VLGVEKKST KLQDSRSV
Sbjct: 1   MARYDRAITVFSPDGHLFQVEYAMEAVRKGNAAVGVRGTDTVVLGVEKKSTPKLQDSRSV 60

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
           RKIV+LDNHIALACAGLKADARVL+N+ARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT
Sbjct: 61  RKIVNLDNHIALACAGLKADARVLVNKARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           QSGGVRPFGLSTLI+GFDP+TGVPSLYQTDPSGTFSAWKANATGRNSNS REFLEKNYKE
Sbjct: 121 QSGGVRPFGLSTLIIGFDPHTGVPSLYQTDPSGTFSAWKANATGRNSNSTREFLEKNYKE 180

Query: 181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
           TSGQET+KLAIRALLEVVESGGKNIEVAVMT+E GLKQL+EAEIDA+V
Sbjct: 181 TSGQETVKLAIRALLEVVESGGKNIEVAVMTKEDGLKQLEEAEIDAIV 228

Source: Solanum tuberosum

Species: Solanum tuberosum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449456827|ref|XP_004146150.1| PREDICTED: proteasome subunit alpha type-7-like [Cucumis sativus]

 Score =  450 bits (1157), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 214/228 (93%), Positives = 225/228 (98%)

Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRG+DTIVLGVEKKST KLQDSRSV
Sbjct: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGSDTIVLGVEKKSTPKLQDSRSV 60

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
           RKIV+LD+HIALACAGLKADARVLINRAR+ECQSHRLTVEDPVTVEYITRYIAGLQQKYT
Sbjct: 61  RKIVNLDDHIALACAGLKADARVLINRARVECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           QSGGVRPFGLSTLI+GFDPYTG PSLYQTDPSGTFS+WKANATGRNSNS+REFLEKNYKE
Sbjct: 121 QSGGVRPFGLSTLIIGFDPYTGTPSLYQTDPSGTFSSWKANATGRNSNSIREFLEKNYKE 180

Query: 181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
           TSGQET+KLAIRALLEVVESGGKNIEVAVMT+E GLKQL+EAEIDA+V
Sbjct: 181 TSGQETVKLAIRALLEVVESGGKNIEVAVMTKEHGLKQLEEAEIDAIV 228

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356502736|ref|XP_003520172.1| PREDICTED: proteasome subunit alpha type-7-like isoform 1 [Glycine max] gi|356502738|ref|XP_003520173.1| PREDICTED: proteasome subunit alpha type-7-like isoform 2 [Glycine max]

 Score =  449 bits (1156), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 214/228 (93%), Positives = 223/228 (97%)

Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTD +VLGVEKKST KLQDSRSV
Sbjct: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDNVVLGVEKKSTAKLQDSRSV 60

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
           RKIV+LDNHIALACAGLKADARVLINRAR+ECQSHRLTVEDPVTVEYITRYIAGLQQKYT
Sbjct: 61  RKIVNLDNHIALACAGLKADARVLINRARVECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           QSGGVRPFGLSTLIVGFDPYTG PSLYQTDPSGTFSAWKANATGRNSNS+REFLEKNYK+
Sbjct: 121 QSGGVRPFGLSTLIVGFDPYTGSPSLYQTDPSGTFSAWKANATGRNSNSIREFLEKNYKD 180

Query: 181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
           TSGQET+KLAIRALLEVVESGGKNIEVAVMT+E GL QL+EAEIDA+V
Sbjct: 181 TSGQETVKLAIRALLEVVESGGKNIEVAVMTKEHGLHQLEEAEIDAIV 228

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|2511580|emb|CAA73622.1| multicatalytic endopeptidase [Arabidopsis thaliana] gi|2511582|emb|CAA73623.1| multicatalytic endopeptidase [Arabidopsis thaliana]

 Score =  449 bits (1155), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 217/235 (92%), Positives = 230/235 (97%), Gaps = 1/235 (0%)

Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDT+VL VEKKST KLQDSRS 
Sbjct: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTVVLAVEKKSTPKLQDSRSA 60

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
           RKIVSLDNHIALACAGLKADARVLIN+ARIECQSHRLT+EDPVTVEYITRYIAGLQQKYT
Sbjct: 61  RKIVSLDNHIALACAGLKADARVLINKARIECQSHRLTLEDPVTVEYITRYIAGLQQKYT 120

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           QSGGVRPFGLSTLIVGFDPY+ +PSLYQTDPSGTFSAWKANATGRNSNS+REFLEKNYKE
Sbjct: 121 QSGGVRPFGLSTLIVGFDPYSRLPSLYQTDPSGTFSAWKANATGRNSNSIREFLEKNYKE 180

Query: 181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREK-GLKQLDEAEIDAMVAEIEAK 234
           +SGQETIKLAIRALLEVVESGGKNIEVAVMTRE+ GL+QL+EAEIDA+VA+IEA+
Sbjct: 181 SSGQETIKLAIRALLEVVESGGKNIEVAVMTREETGLRQLEEAEIDAIVAKIEAE 235

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297794401|ref|XP_002865085.1| hypothetical protein ARALYDRAFT_920118 [Arabidopsis lyrata subsp. lyrata] gi|297310920|gb|EFH41344.1| hypothetical protein ARALYDRAFT_920118 [Arabidopsis lyrata subsp. lyrata]

 Score =  449 bits (1154), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 232/250 (92%), Positives = 244/250 (97%), Gaps = 1/250 (0%)

Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           MARYDRAITVFSPDGHLFQVEYALEAVRKGNA VGVRGTDT+VL VEKKST KLQDSRS 
Sbjct: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNATVGVRGTDTVVLAVEKKSTPKLQDSRSA 60

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
           RKIVSLDNHIALACAGLKADARVLIN+ARIECQSHRLT+EDPVTVEYITRYIAGLQQKYT
Sbjct: 61  RKIVSLDNHIALACAGLKADARVLINKARIECQSHRLTLEDPVTVEYITRYIAGLQQKYT 120

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           QSGGVRPFGLSTLIVGFDPY+ +PSLYQTDPSGTFSAWKANATGRNSNS+REFLEKNYKE
Sbjct: 121 QSGGVRPFGLSTLIVGFDPYSRLPSLYQTDPSGTFSAWKANATGRNSNSIREFLEKNYKE 180

Query: 181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREK-GLKQLDEAEIDAMVAEIEAKKAAAE 239
           +SGQETIKLAIRALLEVVESGGKNIEVAVMTRE+ GL+QL+EAEIDA+VAEIEA+KAAAE
Sbjct: 181 SSGQETIKLAIRALLEVVESGGKNIEVAVMTREETGLRQLEEAEIDAIVAEIEAEKAAAE 240

Query: 240 AAKKGPPKET 249
           AAKKGPPKET
Sbjct: 241 AAKKGPPKET 250

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	249
TAIR|locus:2156962	250	PAD2 "proteasome alpha subunit	1.0	0.996	0.876	1.6e-111
TAIR|locus:2080833	250	PAD1 "20S proteasome alpha sub	1.0	0.996	0.86	7.8e-110
DICTYBASE|DDB_G0272831	250	psmA7 "proteasome subunit alph	0.907	0.904	0.709	1.7e-82
ZFIN|ZDB-GENE-040426-2194	251	psma8 "proteasome (prosome, ma	0.907	0.900	0.704	1.7e-82
UNIPROTKB|E2RF52	250	PSMA8 "Proteasome subunit alph	0.907	0.904	0.704	2.8e-82
UNIPROTKB|Q9PTW9	251	psma7 "Proteasome subunit alph	0.907	0.900	0.7	4.5e-82
UNIPROTKB|F1SBA5	250	PSMA8 "Proteasome subunit alph	0.907	0.904	0.7	1.2e-81
MGI|MGI:1920927	250	Psma8 "proteasome (prosome, ma	0.907	0.904	0.691	4.1e-81
UNIPROTKB|O14818	248	PSMA7 "Proteasome subunit alph	0.899	0.903	0.706	6.6e-81
UNIPROTKB|Q3ZBG0	248	PSMA7 "Proteasome subunit alph	0.899	0.903	0.706	1.1e-80

TAIR|locus:2156962 PAD2 "proteasome alpha subunit D2" [Arabidopsis thaliana (taxid:3702)]

 Score = 1101 (392.6 bits), Expect = 1.6e-111, P = 1.6e-111
 Identities = 219/250 (87%), Positives = 230/250 (92%)

Query:     1 MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
             MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDT+VL VEKKST KLQDSRS 
Sbjct:     1 MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTVVLAVEKKSTPKLQDSRSA 60

Query:    61 RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
             RKIVSLDNHIALACAGLKADARVLIN+ARIECQSHRLT+EDPVTVEYITRYIAGLQQKYT
Sbjct:    61 RKIVSLDNHIALACAGLKADARVLINKARIECQSHRLTLEDPVTVEYITRYIAGLQQKYT 120

Query:   121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
             QSGGVRPFGLSTLIVGFDPY+ +PSLYQTDPSGTFSAWKANATGRNSNS+REFLEKNYKE
Sbjct:   121 QSGGVRPFGLSTLIVGFDPYSRLPSLYQTDPSGTFSAWKANATGRNSNSIREFLEKNYKE 180

Query:   181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREK-GLKQLDEAEIDAMVXXXXXXXXXXX 239
             +SGQETIKLAIRALLEVVESGGKNIEVAVMTRE+ GL+QL+EAEIDA+V           
Sbjct:   181 SSGQETIKLAIRALLEVVESGGKNIEVAVMTREETGLRQLEEAEIDAIVAKIEAEKAAAE 240

Query:   240 XXXXGPPKET 249
                 GPPKET
Sbjct:   241 AAKKGPPKET 250

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;ISS

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

GO:0009507 "chloroplast" evidence=IDA

GO:0005773 "vacuole" evidence=IDA

GO:0000502 "proteasome complex" evidence=IDA

TAIR|locus:2080833 PAD1 "20S proteasome alpha subunit PAD1" [Arabidopsis thaliana (taxid:3702)]

 Score = 1085 (387.0 bits), Expect = 7.8e-110, P = 7.8e-110
 Identities = 215/250 (86%), Positives = 227/250 (90%)

Query:     1 MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
             MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDT+VL VEKKST KLQDSRS 
Sbjct:     1 MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTVVLAVEKKSTPKLQDSRSA 60

Query:    61 RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
             RKIVSLDNHIALACAGLKADARVLIN+ARIECQSHRLT+EDPVTVEYITRYIAGLQQKYT
Sbjct:    61 RKIVSLDNHIALACAGLKADARVLINKARIECQSHRLTLEDPVTVEYITRYIAGLQQKYT 120

Query:   121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
             QSGGVRPFGLSTLIVGFDPYT +P+LYQTDPSGTFSAWKANATGRNSNS+REFLEKNYKE
Sbjct:   121 QSGGVRPFGLSTLIVGFDPYTRIPALYQTDPSGTFSAWKANATGRNSNSIREFLEKNYKE 180

Query:   181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKG-LKQLDEAEIDAMVXXXXXXXXXXX 239
             ++GQET+KLAIRALLEVVESGGKNIEVAVMTRE+G LKQL+E EID +V           
Sbjct:   181 SAGQETVKLAIRALLEVVESGGKNIEVAVMTREEGVLKQLEEEEIDIIVAEIEAEKAAAE 240

Query:   240 XXXXGPPKET 249
                 GP KET
Sbjct:   241 AAKKGPAKET 250

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;RCA;TAS

GO:0008233 "peptidase activity" evidence=ISS

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005819 "spindle" evidence=IDA

GO:0009524 "phragmoplast" evidence=IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0005773 "vacuole" evidence=IDA

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0005774 "vacuolar membrane" evidence=IDA

GO:0000502 "proteasome complex" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0006094 "gluconeogenesis" evidence=RCA

GO:0006096 "glycolysis" evidence=RCA

GO:0006833 "water transport" evidence=RCA

GO:0006972 "hyperosmotic response" evidence=RCA

GO:0007030 "Golgi organization" evidence=RCA

GO:0009266 "response to temperature stimulus" evidence=RCA

GO:0009651 "response to salt stress" evidence=RCA

GO:0009853 "photorespiration" evidence=RCA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=RCA

GO:0043248 "proteasome assembly" evidence=RCA

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

GO:0051788 "response to misfolded protein" evidence=RCA

GO:0080129 "proteasome core complex assembly" evidence=RCA

DICTYBASE|DDB_G0272831 psmA7 "proteasome subunit alpha type 7" [Dictyostelium discoideum (taxid:44689)]

 Score = 827 (296.2 bits), Expect = 1.7e-82, P = 1.7e-82
 Identities = 161/227 (70%), Positives = 195/227 (85%)

Query:     2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
             ARYDRAITVFSPDGHLFQVEYA+EAVRKG  AVGVRG D IVLGVEKK+T KLQD+RS+R
Sbjct:     4 ARYDRAITVFSPDGHLFQVEYAMEAVRKGTVAVGVRGKDVIVLGVEKKATAKLQDARSIR 63

Query:    62 KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
             KIV LD+HI L  AGL AD+RVLI++A +ECQS+RLTVED  +VEYI+++IAG+QQ+YTQ
Sbjct:    64 KIVKLDDHICLTFAGLTADSRVLISKALMECQSYRLTVEDSPSVEYISKFIAGIQQRYTQ 123

Query:   122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET 181
             SGGVRPFG+STLIVGFD   G P+LYQTDPSG++S+WKA A GR+S S+ EFLEKNY + 
Sbjct:   124 SGGVRPFGISTLIVGFDT-DGTPNLYQTDPSGSYSSWKAAAIGRSSKSVGEFLEKNYTDV 182

Query:   182 SGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
             S +E+IKLA+RALLE+VESG KNIE+AV+  ++ +  LDE EID +V
Sbjct:   183 SEEESIKLAVRALLEIVESGNKNIEIAVIRNKQPIVLLDEQEIDKLV 229

GO:0008233 "peptidase activity" evidence=IEA;IDA

GO:0006508 "proteolysis" evidence=IEA;IDA

GO:0005737 "cytoplasm" evidence=IEA;IDA

GO:0005634 "nucleus" evidence=IEA;IDA

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

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

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

GO:0005839 "proteasome core complex" evidence=IEA

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

GO:0004175 "endopeptidase activity" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0000502 "proteasome complex" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

ZFIN|ZDB-GENE-040426-2194 psma8 "proteasome (prosome, macropain) subunit, alpha type, 8" [Danio rerio (taxid:7955)]

 Score = 827 (296.2 bits), Expect = 1.7e-82, P = 1.7e-82
 Identities = 162/230 (70%), Positives = 192/230 (83%)

Query:     2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
             ARYDRAITVFSPDGHLFQVEYA EAV+KG+ AVG+RG D +VLGVEKKS  KLQ+ R+VR
Sbjct:     3 ARYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGIRGKDIVVLGVEKKSVAKLQEERTVR 62

Query:    62 KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
             KI +LD H+ +A AGL ADAR++INRAR+ECQSHRLTVEDPVTVEYITRYIA L+Q+YTQ
Sbjct:    63 KICALDEHVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIATLKQRYTQ 122

Query:   122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE- 180
             S G RPFG+S LIVGFD Y G P LYQTDPSGT+ AWKANA GR++ ++REFLEKNY + 
Sbjct:   123 SNGRRPFGISALIVGFD-YDGTPRLYQTDPSGTYHAWKANAIGRSAKTVREFLEKNYTDE 181

Query:   181 --TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
                S  + IKLAI+ALLEVV+SGGKNIE+AV+ R + LK L+  EI+ +V
Sbjct:   182 AIASDNDAIKLAIKALLEVVQSGGKNIELAVIRRNQPLKILESKEIETLV 231

GO:0004175 "endopeptidase activity" evidence=IEA

GO:0005839 "proteasome core complex" evidence=IEA

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

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

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

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

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000502 "proteasome complex" evidence=IEA

GO:0006508 "proteolysis" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0008233 "peptidase activity" evidence=IEA

UNIPROTKB|E2RF52 PSMA8 "Proteasome subunit alpha type" [Canis lupus familiaris (taxid:9615)]

 Score = 825 (295.5 bits), Expect = 2.8e-82, P = 2.8e-82
 Identities = 162/230 (70%), Positives = 191/230 (83%)

Query:     2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
             +RYDRAITVFSPDGHLFQVEYA EAV+KG+ AVG+RGTD +VLGVEKKS  KLQD R+VR
Sbjct:     3 SRYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGIRGTDIVVLGVEKKSVAKLQDERTVR 62

Query:    62 KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
             KI +LD+H+ +A AGL ADARV+INRAR+ECQSH+LTVEDPVTVEYITR+IA L+QKYTQ
Sbjct:    63 KICALDDHVCMAFAGLTADARVVINRARVECQSHKLTVEDPVTVEYITRFIATLKQKYTQ 122

Query:   122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE- 180
             S G RPFG+S LIVGFD   G+P LYQTDPSGT+ AWKANA GR++ ++REFLEKNY E 
Sbjct:   123 SNGRRPFGISALIVGFDD-DGIPRLYQTDPSGTYHAWKANAIGRSAKTVREFLEKNYTED 181

Query:   181 --TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
                +  E IKLAIRALLEVV+SGGKNIE+A++ R + LK     EI+  V
Sbjct:   182 AIANDNEAIKLAIRALLEVVQSGGKNIELAIIRRNQPLKMFSAKEIELQV 231

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" 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|Q9PTW9 psma7 "Proteasome subunit alpha type-7" [Carassius auratus (taxid:7957)]

 Score = 823 (294.8 bits), Expect = 4.5e-82, P = 4.5e-82
 Identities = 161/230 (70%), Positives = 192/230 (83%)

Query:     2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
             ARYDRAITVFSPDGHLFQVEYA EAV+KG+ AVG+RG D +VLGVEKKS  KLQ+ R+VR
Sbjct:     3 ARYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGIRGKDIVVLGVEKKSVAKLQEERTVR 62

Query:    62 KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
             KI +LD H+ +A AGL ADAR++INRAR+ECQSHRLTVEDPVTVEYITRYIA L+Q+YTQ
Sbjct:    63 KICALDEHVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIATLKQRYTQ 122

Query:   122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE- 180
             S G RPFG+S LIVGFD + G P LYQTDPSGT+ AWKANA GR++ ++REFLEKNY + 
Sbjct:   123 SNGRRPFGISALIVGFD-FDGTPRLYQTDPSGTYHAWKANAIGRSAKTVREFLEKNYTDE 181

Query:   181 --TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
                S  + IKLAI+ALLEVV+SGGKNIE+AV+ R + LK L+  EI+ +V
Sbjct:   182 AIASDNDAIKLAIKALLEVVQSGGKNIELAVIRRNQPLKILESKEIETLV 231

GO:0005839 "proteasome core complex" evidence=ISS

UNIPROTKB|F1SBA5 PSMA8 "Proteasome subunit alpha type" [Sus scrofa (taxid:9823)]

 Score = 819 (293.4 bits), Expect = 1.2e-81, P = 1.2e-81
 Identities = 161/230 (70%), Positives = 190/230 (82%)

Query:     2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
             +RYDRAITVFSPDGHLFQVEYA EAV+KG+ AV +RGTD +VLGVEKKS  KLQD R+VR
Sbjct:     3 SRYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVAIRGTDIVVLGVEKKSVAKLQDERTVR 62

Query:    62 KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
             KI +LD+H+ +A AGL ADARV+INRAR+ECQSH+LTVEDPVTVEYITR+IA L+QKYTQ
Sbjct:    63 KICALDDHVCMAFAGLTADARVVINRARVECQSHKLTVEDPVTVEYITRFIATLKQKYTQ 122

Query:   122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE- 180
             S G RPFG+S LIVGFD   G+P LYQTDPSGT+ AWKANA GR++ ++REFLEKNY E 
Sbjct:   123 SNGRRPFGISALIVGFDD-DGIPRLYQTDPSGTYHAWKANAIGRSAKTVREFLEKNYTED 181

Query:   181 --TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
                +  E IKLAIRALLEVV+SGGKNIE+A++ R + LK     EI+  V
Sbjct:   182 AIANDNEAIKLAIRALLEVVQSGGKNIELAIIRRNQPLKMFSAKEIELQV 231

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" 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:1920927 Psma8 "proteasome (prosome, macropain) subunit, alpha type, 8" [Mus musculus (taxid:10090)]

 Score = 814 (291.6 bits), Expect = 4.1e-81, P = 4.1e-81
 Identities = 159/230 (69%), Positives = 194/230 (84%)

Query:     2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
             +RYDRAITVFSPDGHLFQVEYA EAV+KG+ AVG+RGT+ +VLGVEKKS  KLQD R+VR
Sbjct:     3 SRYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGIRGTNIVVLGVEKKSVAKLQDERTVR 62

Query:    62 KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
             KI +LD+H+ +A AGL ADARV+I+RAR+ECQSH+LTVEDPVTVEYITR+IA L+QKYTQ
Sbjct:    63 KICALDDHVCMAFAGLTADARVVISRARVECQSHKLTVEDPVTVEYITRFIATLKQKYTQ 122

Query:   122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE- 180
             S G RPFG+S LIVGFD   G+P LYQTDPSGT+ AWKANA GR++ ++REFLEKNY E 
Sbjct:   123 SNGRRPFGISALIVGFDD-DGIPRLYQTDPSGTYHAWKANAIGRSAKTVREFLEKNYTED 181

Query:   181 --TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
               ++ +E IKLAI+ALLEVV+SGGKNIE+A++ R++ LK     EI+  V
Sbjct:   182 AISNDKEAIKLAIKALLEVVQSGGKNIELAIIRRDQPLKMFSAKEIELEV 231

GO:0000502 "proteasome complex" evidence=IEA

GO:0004175 "endopeptidase activity" evidence=IEA

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

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005839 "proteasome core complex" evidence=IEA

GO:0006508 "proteolysis" evidence=IEA

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

GO:0008233 "peptidase activity" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

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

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

UNIPROTKB|O14818 PSMA7 "Proteasome subunit alpha type-7" [Homo sapiens (taxid:9606)]

 Score = 812 (290.9 bits), Expect = 6.6e-81, P = 6.6e-81
 Identities = 161/228 (70%), Positives = 190/228 (83%)

Query:     4 YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
             YDRAITVFSPDGHLFQVEYA EAV+KG+ AVGVRG D +VLGVEKKS  KLQD R+VRKI
Sbjct:     3 YDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVRKI 62

Query:    64 VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
              +LD+++ +A AGL ADAR++INRAR+ECQSHRLTVEDPVTVEYITRYIA L+Q+YTQS 
Sbjct:    63 CALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSN 122

Query:   124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG 183
             G RPFG+S LIVGFD + G P LYQTDPSGT+ AWKANA GR + S+REFLEKNY + + 
Sbjct:   123 GRRPFGISALIVGFD-FDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEAI 181

Query:   184 QE---TIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
             +    TIKL I+ALLEVV+SGGKNIE+AVM R++ LK L+  EI+  V
Sbjct:   182 ETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYV 229

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

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

GO:0019048 "virus-host interaction" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005839 "proteasome core complex" evidence=ISS

GO:0000502 "proteasome complex" evidence=TAS

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:0042802 "identical protein binding" evidence=IPI

UNIPROTKB|Q3ZBG0 PSMA7 "Proteasome subunit alpha type-7" [Bos taurus (taxid:9913)]

 Score = 810 (290.2 bits), Expect = 1.1e-80, P = 1.1e-80
 Identities = 161/228 (70%), Positives = 190/228 (83%)

Query:     4 YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
             YDRAITVFSPDGHLFQVEYA EAV+KG+ AVGVRG D +VLGVEKKS  KLQD R+VRKI
Sbjct:     3 YDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGKDIVVLGVEKKSVAKLQDERTVRKI 62

Query:    64 VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
              +LD+++ +A AGL ADAR++INRAR+ECQSHRLTVEDPVTVEYITRYIA L+Q+YTQS 
Sbjct:    63 CALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSN 122

Query:   124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG 183
             G RPFG+S LIVGFD + G P LYQTDPSGT+ AWKANA GR + S+REFLEKNY + + 
Sbjct:   123 GRRPFGISALIVGFD-FDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEAI 181

Query:   184 QE---TIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
             +    TIKL I+ALLEVV+SGGKNIE+AVM R++ LK L+  EI+  V
Sbjct:   182 ETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQPLKILNPEEIEKYV 229

GO:0005839 "proteasome core complex" evidence=ISS

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0042802 "identical protein 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

---

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)
C3NHC6	PSA_SULIN	3, ., 4, ., 2, 5, ., 1	0.4311	0.8473	0.8755	yes	no
Q9UXC6	PSA_SULSO	3, ., 4, ., 2, 5, ., 1	0.4311	0.8473	0.8755	yes	no
O59219	PSA_PYRHO	3, ., 4, ., 2, 5, ., 1	0.4977	0.8875	0.85	yes	no
Q9SXU1	PSA7_CICAR	3, ., 4, ., 2, 5, ., 1	0.9298	0.9156	0.9156	N/A	no
P30186	PSA7A_ARATH	3, ., 4, ., 2, 5, ., 1	0.9170	0.9156	0.912	yes	no
O14818	PSA7_HUMAN	3, ., 4, ., 2, 5, ., 1	0.7074	0.9036	0.9072	yes	no
P34120	PSA7_DICDI	3, ., 4, ., 2, 5, ., 1	0.7051	0.9357	0.932	yes	no
O13268	PSA7_CHICK	3, ., 4, ., 2, 5, ., 1	0.6950	0.8795	0.8795	yes	no
Q4R7D9	PSA7L_MACFA	3, ., 4, ., 2, 5, ., 1	0.6956	0.9076	0.904	N/A	no
P40303	PSA4_YEAST	3, ., 4, ., 2, 5, ., 1	0.5805	0.9277	0.9094	yes	no
C4KHD9	PSA_SULIK	3, ., 4, ., 2, 5, ., 1	0.4311	0.8473	0.8755	yes	no
Q95005	PSA7_CAEEL	3, ., 4, ., 2, 5, ., 1	0.5769	0.9116	0.8972	yes	no
Q3ZBG0	PSA7_BOVIN	3, ., 4, ., 2, 5, ., 1	0.7074	0.9036	0.9072	no	no
Q0J006	PSA7B_ORYSJ	3, ., 4, ., 2, 5, ., 1	0.9166	0.9156	0.9156	yes	no
A2Z3I9	PSA7B_ORYSI	3, ., 4, ., 2, 5, ., 1	0.9166	0.9156	0.9156	N/A	no
Q9V122	PSA_PYRAB	3, ., 4, ., 2, 5, ., 1	0.4913	0.8995	0.8615	yes	no
O24616	PSA7B_ARATH	3, ., 4, ., 2, 5, ., 1	0.928	1.0	0.996	yes	no
C3NEC6	PSA_SULIY	3, ., 4, ., 2, 5, ., 1	0.4311	0.8473	0.8755	yes	no
O16811	PSA71_DROVI	3, ., 4, ., 2, 5, ., 1	0.6441	0.8674	0.8744	N/A	no
Q9PVY6	PSA7A_XENLA	3, ., 4, ., 2, 5, ., 1	0.6986	0.9036	0.9072	N/A	no
Q9PTW9	PSA7_CARAU	3, ., 4, ., 2, 5, ., 1	0.7012	0.9116	0.9043	N/A	no
Q8ZVM1	PSA_PYRAE	3, ., 4, ., 2, 5, ., 1	0.4625	0.8915	0.9135	yes	no
Q10329	PSA4_SCHPO	3, ., 4, ., 2, 5, ., 1	0.5573	0.9759	0.9382	yes	no
Q5JIU9	PSA_PYRKO	3, ., 4, ., 2, 5, ., 1	0.4763	0.9116	0.8730	yes	no
O24030	PSA7_SOLLC	3, ., 4, ., 2, 5, ., 1	0.9342	0.9156	0.8803	N/A	no
Q8TYB7	PSA_METKA	3, ., 4, ., 2, 5, ., 1	0.4713	0.8875	0.8983	yes	no
O29760	PSA_ARCFU	3, ., 4, ., 2, 5, ., 1	0.4585	0.8915	0.9024	yes	no
C3MQ43	PSA_SULIL	3, ., 4, ., 2, 5, ., 1	0.4311	0.8473	0.8755	yes	no
B6YSH9	PSA_THEON	3, ., 4, ., 2, 5, ., 1	0.4734	0.8835	0.8461	yes	no
C5A2C2	PSA_THEGJ	3, ., 4, ., 2, 5, ., 1	0.4823	0.8835	0.8461	yes	no
C3MVG1	PSA_SULIM	3, ., 4, ., 2, 5, ., 1	0.4311	0.8473	0.8755	yes	no
Q9PVQ1	PSA7B_XENLA	3, ., 4, ., 2, 5, ., 1	0.6986	0.9036	0.9109	N/A	no
P22769	PSA71_DROME	3, ., 4, ., 2, 5, ., 1	0.6441	0.8755	0.8755	yes	no
Q6YT00	PSA7A_ORYSJ	3, ., 4, ., 2, 5, ., 1	0.9122	0.9156	0.9156	yes	no
A2YXU2	PSA7A_ORYSI	3, ., 4, ., 2, 5, ., 1	0.9122	0.9156	0.9156	N/A	no
Q9NDA2	PSA7_TRYBB	3, ., 4, ., 2, 5, ., 1	0.5990	0.8433	0.8502	N/A	no
Q9CWH6	PSA7L_MOUSE	3, ., 4, ., 2, 5, ., 1	0.6803	0.9638	0.96	yes	no
Q8TPX5	PSA_METAC	3, ., 4, ., 2, 5, ., 1	0.4279	0.9518	0.9595	yes	no
A4YCU9	PSA_METS5	3, ., 4, ., 2, 5, ., 1	0.4298	0.8594	0.8916	yes	no
C6A459	PSA_THESM	3, ., 4, ., 2, 5, ., 1	0.4778	0.8835	0.8461	yes	no
Q8U0L6	PSA_PYRFU	3, ., 4, ., 2, 5, ., 1	0.4845	0.8875	0.85	yes	no
Q9Z2U0	PSA7_MOUSE	3, ., 4, ., 2, 5, ., 1	0.7074	0.9036	0.9072	no	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	0.993
3rd Layer	3.4.25	0.998

---

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	249
cd03755	207	cd03755, proteasome_alpha_type_7, proteasome_alpha	1e-145
cd01911	209	cd01911, proteasome_alpha, proteasome alpha subuni	1e-111
PRK03996	241	PRK03996, PRK03996, proteasome subunit alpha; Prov	4e-95
TIGR03633	224	TIGR03633, arc_protsome_A, proteasome endopeptidas	4e-85
cd03756	211	cd03756, proteasome_alpha_archeal, proteasome_alph	7e-81
COG0638	236	COG0638, PRE1, 20S proteasome, alpha and beta subu	1e-75
cd03750	227	cd03750, proteasome_alpha_type_2, proteasome_alpha	9e-72
cd03752	213	cd03752, proteasome_alpha_type_4, proteasome_alpha	3e-65
pfam00227	188	pfam00227, Proteasome, Proteasome subunit	9e-61
PTZ00246	253	PTZ00246, PTZ00246, proteasome subunit alpha; Prov	1e-60
cd03753	213	cd03753, proteasome_alpha_type_5, proteasome_alpha	3e-60
cd01906	182	cd01906, proteasome_protease_HslV, proteasome_prot	6e-58
cd03749	211	cd03749, proteasome_alpha_type_1, proteasome_alpha	3e-56
cd03751	212	cd03751, proteasome_alpha_type_3, proteasome_alpha	7e-51
cd03754	215	cd03754, proteasome_alpha_type_6, proteasome_alpha	7e-50
cd01901	164	cd01901, Ntn_hydrolase, The Ntn hydrolases (N-term	2e-36
cd01912	189	cd01912, proteasome_beta, proteasome beta subunit	5e-21
cd03764	188	cd03764, proteasome_beta_archeal, Archeal proteaso	8e-18
TIGR03634	185	TIGR03634, arc_protsome_B, proteasome endopeptidas	1e-16
pfam10584	23	pfam10584, Proteasome_A_N, Proteasome subunit A N-	9e-12
smart00948	23	smart00948, Proteasome_A_N, Proteasome subunit A N	2e-11
cd03763	189	cd03763, proteasome_beta_type_7, proteasome beta t	2e-07
COG0064	483	COG0064, GatB, Asp-tRNAAsn/Glu-tRNAGln amidotransf	4e-05
cd03758	193	cd03758, proteasome_beta_type_2, proteasome beta t	1e-04
cd03757	212	cd03757, proteasome_beta_type_1, proteasome beta t	4e-04
PRK05477	474	PRK05477, gatB, aspartyl/glutamyl-tRNA amidotransf	7e-04
smart00845	147	smart00845, GatB_Yqey, GatB domain	8e-04
PTZ00488	247	PTZ00488, PTZ00488, Proteasome subunit beta type-5	0.001
cd03761	188	cd03761, proteasome_beta_type_5, proteasome beta t	0.003

>gnl|CDD|239724 cd03755, proteasome_alpha_type_7, proteasome_alpha_type_7

 Score =  402 bits (1036), Expect = e-145
 Identities = 169/208 (81%), Positives = 184/208 (88%), Gaps = 2/208 (0%)

Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YDRAITVFSPDGHLFQVEYA EAVRKG  AVGVRG D +VLGVEKKS  KLQD R+VRKI
Sbjct: 1   YDRAITVFSPDGHLFQVEYAQEAVRKGTTAVGVRGKDCVVLGVEKKSVAKLQDPRTVRKI 60

Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
             LD+H+ LA AGL ADARVLINRAR+ECQSHRLTVEDPVTVEYITRYIAGLQQ+YTQSG
Sbjct: 61  CMLDDHVCLAFAGLTADARVLINRARLECQSHRLTVEDPVTVEYITRYIAGLQQRYTQSG 120

Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET-S 182
           GVRPFG+STLIVGFDP  G P LYQTDPSGT+SAWKANA GRNS ++REFLEKNYKE  +
Sbjct: 121 GVRPFGISTLIVGFDPD-GTPRLYQTDPSGTYSAWKANAIGRNSKTVREFLEKNYKEEMT 179

Query: 183 GQETIKLAIRALLEVVESGGKNIEVAVM 210
             +TIKLAI+ALLEVV+SG KNIE+AVM
Sbjct: 180 RDDTIKLAIKALLEVVQSGSKNIELAVM 207

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|238892 cd01911, proteasome_alpha, proteasome alpha subunit

 Score =  319 bits (820), Expect = e-111
 Identities = 121/210 (57%), Positives = 152/210 (72%), Gaps = 4/210 (1%)

Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YDR+IT FSP+G LFQVEYALEAV+ G+ AVG++G D +VL VEKK T KL D  SV KI
Sbjct: 1   YDRSITTFSPEGRLFQVEYALEAVKNGSTAVGIKGKDGVVLAVEKKVTSKLLDPSSVEKI 60

Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
             +D+HI  A AGL ADARVL+NRAR+E Q++R T  +P+ VE + + IA L Q YTQ G
Sbjct: 61  FKIDDHIGCAVAGLTADARVLVNRARVEAQNYRYTYGEPIPVEVLVKRIADLAQVYTQYG 120

Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET-S 182
           GVRPFG+S LI G+D   G P LYQTDPSGT+  +KA A G+ S   + FLEK YK+  +
Sbjct: 121 GVRPFGVSLLIAGYDEEGG-PQLYQTDPSGTYFGYKATAIGKGSQEAKTFLEKRYKKDLT 179

Query: 183 GQETIKLAIRALLEVVESG--GKNIEVAVM 210
            +E IKLA++AL EV+E     KNIE+AV+
Sbjct: 180 LEEAIKLALKALKEVLEEDKKAKNIEIAVV 209

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

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

 Score =  278 bits (714), Expect = 4e-95
 Identities = 113/236 (47%), Positives = 157/236 (66%), Gaps = 6/236 (2%)

Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
              YDRAIT+FSPDG L+QVEYA EAV++G  AVGV+  D +VL V+K+ T  L +  S+
Sbjct: 7   QMGYDRAITIFSPDGRLYQVEYAREAVKRGTTAVGVKTKDGVVLAVDKRITSPLIEPSSI 66

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
            KI  +D+HI  A AGL ADARVLI+RAR+E Q +RLT  +P+ VE +T+ I   +Q+YT
Sbjct: 67  EKIFKIDDHIGAASAGLVADARVLIDRARVEAQINRLTYGEPIGVETLTKKICDHKQQYT 126

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           Q GGVRPFG++ LI G D   G P L++TDPSG +  +KA A G   +++ EFLEKNYKE
Sbjct: 127 QHGGVRPFGVALLIAGVDD--GGPRLFETDPSGAYLEYKATAIGAGRDTVMEFLEKNYKE 184

Query: 181 T-SGQETIKLAIRALLEVVESGGK--NIEVAVMT-REKGLKQLDEAEIDAMVAEIE 232
             S +E I+LA++AL +  E      N+E+A +    K  ++L   EI+  + ++ 
Sbjct: 185 DLSLEEAIELALKALAKANEGKLDPENVEIAYIDVETKKFRKLSVEEIEKYLEKLL 240

Length = 241

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

 Score =  252 bits (646), Expect = 4e-85
 Identities = 114/224 (50%), Positives = 151/224 (67%), Gaps = 6/224 (2%)

Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YDRAITVFSPDG L+QVEYA EAV++G  AVG++  D +VL V+K+ T KL +  S+ KI
Sbjct: 3   YDRAITVFSPDGRLYQVEYAREAVKRGTTAVGIKTKDGVVLAVDKRITSKLVEPSSIEKI 62

Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
             +D+HI  A +GL ADARVLI+RARIE Q +RLT  +P+ VE + + I  L+Q+YTQ G
Sbjct: 63  FKIDDHIGAATSGLVADARVLIDRARIEAQINRLTYGEPIDVETLAKKICDLKQQYTQHG 122

Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET-S 182
           GVRPFG++ LI G D   G P L++TDPSG    +KA A G    ++ EFLEK Y+E  S
Sbjct: 123 GVRPFGVALLIAGVD--DGGPRLFETDPSGALLEYKATAIGAGRQAVTEFLEKEYREDLS 180

Query: 183 GQETIKLAIRALLEVVESG--GKNIEVAVMTREKGL-KQLDEAE 223
             E I+LA++AL   VE     +N+EVA +T E    ++L   E
Sbjct: 181 LDEAIELALKALYSAVEDKLTPENVEVAYITVEDKKFRKLSVEE 224

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

>gnl|CDD|239725 cd03756, proteasome_alpha_archeal, proteasome_alpha_archeal

 Score =  241 bits (616), Expect = 7e-81
 Identities = 107/211 (50%), Positives = 149/211 (70%), Gaps = 5/211 (2%)

Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YDRAITVFSPDG L+QVEYA EAV++G  A+G++  + +VL V+K+ T KL +  S+ KI
Sbjct: 2   YDRAITVFSPDGRLYQVEYAREAVKRGTTALGIKCKEGVVLAVDKRITSKLVEPESIEKI 61

Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
             +D+H+  A +GL ADARVLI+RAR+E Q HRLT  +P+ VE + + I  L+Q+YTQ G
Sbjct: 62  YKIDDHVGAATSGLVADARVLIDRARVEAQIHRLTYGEPIDVEVLVKKICDLKQQYTQHG 121

Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET-S 182
           GVRPFG++ LI G D   G P L++TDPSG ++ +KA A G    ++ EFLEK YKE  S
Sbjct: 122 GVRPFGVALLIAGVDD--GGPRLFETDPSGAYNEYKATAIGSGRQAVTEFLEKEYKEDMS 179

Query: 183 GQETIKLAIRALLEVVESG--GKNIEVAVMT 211
            +E I+LA++AL   +E     +N+E+A +T
Sbjct: 180 LEEAIELALKALYAALEENETPENVEIAYVT 210

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

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

 Score =  228 bits (584), Expect = 1e-75
 Identities = 110/240 (45%), Positives = 160/240 (66%), Gaps = 10/240 (4%)

Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNA-AVGVRGTDTIVLGVEKKSTVKLQD-SRS 59
           A YDRAIT+FSP+G LFQVEYALEAV++G    VG++G D +VL  +K++T  L   S +
Sbjct: 1   AGYDRAITIFSPEGRLFQVEYALEAVKRGGTTTVGIKGKDGVVLAADKRATSGLLIASSN 60

Query: 60  VRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKY 119
           V KI  +D+HI +A AGL ADA+VL+  AR E Q +RL   +P++VE + + ++ + Q+Y
Sbjct: 61  VEKIFKIDDHIGMAIAGLAADAQVLVRYARAEAQLYRLRYGEPISVEALAKLLSNILQEY 120

Query: 120 TQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK 179
           TQS   RP+G+S L+ G D   G P LY TDPSG+++ +KA A G  S     FLEK Y+
Sbjct: 121 TQS--GRPYGVSLLVAGVDD--GGPRLYSTDPSGSYNEYKATAIGSGSQFAYGFLEKEYR 176

Query: 180 ET-SGQETIKLAIRALLEVVESG---GKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKK 235
           E  S +E I+LA++AL   +E     G  IEVAV+T+++G ++LD  EI  ++ ++  K+
Sbjct: 177 EDLSLEEAIELAVKALRAAIERDAASGGGIEVAVITKDEGFRKLDGEEIKKLLDDLSEKE 236

Length = 236

>gnl|CDD|239719 cd03750, proteasome_alpha_type_2, proteasome_alpha_type_2

 Score =  218 bits (558), Expect = 9e-72
 Identities = 98/224 (43%), Positives = 130/224 (58%), Gaps = 5/224 (2%)

Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           Y  ++T FSP G L Q+EYAL AV  G  +VG++  + +VL  EKK    L D  SV K+
Sbjct: 1   YSFSLTTFSPSGKLVQIEYALAAVSSGAPSVGIKAANGVVLATEKKVPSPLIDESSVHKV 60

Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
             +  HI +  +G+  D RVL+ +AR   Q + L   +P+ V  + R IA + Q+YTQSG
Sbjct: 61  EQITPHIGMVYSGMGPDFRVLVKKARKIAQQYYLVYGEPIPVSQLVREIASVMQEYTQSG 120

Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG 183
           GVRPFG+S LI G+D   G P LYQ DPSG++  WKA A G+N ++ + FLEK Y E   
Sbjct: 121 GVRPFGVSLLIAGWD--EGGPYLYQVDPSGSYFTWKATAIGKNYSNAKTFLEKRYNEDLE 178

Query: 184 QE-TIKLAIRALLEVVESG--GKNIEVAVMTREKGLKQLDEAEI 224
            E  I  AI  L E  E     KNIE+ +    KG + L  AEI
Sbjct: 179 LEDAIHTAILTLKEGFEGQMTEKNIEIGICGETKGFRLLTPAEI 222

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|239721 cd03752, proteasome_alpha_type_4, proteasome_alpha_type_4

 Score =  201 bits (513), Expect = 3e-65
 Identities = 90/214 (42%), Positives = 133/214 (62%), Gaps = 10/214 (4%)

Query: 3   RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQD-SRSVR 61
           RYD   T+FSP+G L+QVEYA+EA+      +G+   D IVL  EKK T KL D S S  
Sbjct: 2   RYDSRTTIFSPEGRLYQVEYAMEAISHAGTCLGILAKDGIVLAAEKKVTSKLLDQSFSSE 61

Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           KI  +D+HIA A AG+ +DA +LIN AR+  Q +  + ++P+ VE + + +  ++Q YTQ
Sbjct: 62  KIYKIDDHIACAVAGITSDANILINYARLIAQRYLYSYQEPIPVEQLVQRLCDIKQGYTQ 121

Query: 122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET 181
            GG+RPFG+S L  G+D + G   LYQ+DPSG +S WKA A G N+ + +  L+++YK+ 
Sbjct: 122 YGGLRPFGVSFLYAGWDKHYGF-QLYQSDPSGNYSGWKATAIGNNNQAAQSLLKQDYKDD 180

Query: 182 SG-QETIKLAIRALLEVVESGGKNIEVAVMTREK 214
              +E + LA++ L        K ++   +T EK
Sbjct: 181 MTLEEALALAVKVL-------SKTMDSTKLTSEK 207

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|215805 pfam00227, Proteasome, Proteasome subunit

 Score =  189 bits (482), Expect = 9e-61
 Identities = 83/190 (43%), Positives = 115/190 (60%), Gaps = 8/190 (4%)

Query: 27  VRKGNAAVGVRGTDTIVLGVEKKSTV--KLQDSRSVRKIVSLDNHIALACAGLKADARVL 84
           V+ G   VG++G D +VL  +K++T   KL    +V KI  +D+HI +A AGL ADA+ L
Sbjct: 1   VKTGTTIVGIKGKDGVVLAADKRATRGSKLLSKDTVEKIFKIDDHIGMAFAGLAADAQTL 60

Query: 85  INRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVP 144
           ++ AR E Q +RL    P++VE + + IA   Q YTQ  G RP+G+S LI G+D   G P
Sbjct: 61  VDYARAEAQLYRLRYGRPISVE-LAKRIADKLQAYTQYSGRRPYGVSLLIAGYDE-DGGP 118

Query: 145 SLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET-SGQETIKLAIRALLEVVE---S 200
            LY  DPSG+   +KA A G  S     FLEK YK   + +E ++LA++AL E +E    
Sbjct: 119 HLYSIDPSGSVIEYKATAIGSGSQYAYGFLEKLYKPDMTLEEAVELAVKALKEAIERDAL 178

Query: 201 GGKNIEVAVM 210
            G NIEVAV+
Sbjct: 179 SGGNIEVAVI 188

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

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

 Score =  191 bits (486), Expect = 1e-60
 Identities = 96/252 (38%), Positives = 144/252 (57%), Gaps = 12/252 (4%)

Query: 3   RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQD-SRSVR 61
           RYD   T FSP+G L+QVEYALEA+   +  VG+   + ++LG +K  + KL D  +   
Sbjct: 4   RYDSRTTTFSPEGRLYQVEYALEAINNASLTVGILCKEGVILGADKPISSKLLDPGKINE 63

Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           KI  +D+HI  A AGL ADA +LIN+ R+  Q +R T  +P  VE +   I  L+Q YTQ
Sbjct: 64  KIYKIDSHIFCAVAGLTADANILINQCRLYAQRYRYTYGEPQPVEQLVVQICDLKQSYTQ 123

Query: 122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE- 180
            GG+RPFG+S L  G+D   G   LY TDPSG +S WKA A G+N+ + +  L++ +KE 
Sbjct: 124 FGGLRPFGVSFLFAGYDENLGY-QLYHTDPSGNYSGWKATAIGQNNQTAQSILKQEWKED 182

Query: 181 TSGQETIKLAIRALLEVVES---GGKNIEVAVMTR-----EKGLKQLDEAEIDAMVAEIE 232
            + ++ + LA + L + ++S       IEV +++      E   K L E EI  ++ ++ 
Sbjct: 183 LTLEQGLLLAAKVLTKSMDSTSPKADKIEVGILSHGETDGEPIQKMLSEKEIAELLKKV- 241

Query: 233 AKKAAAEAAKKG 244
            ++ A E     
Sbjct: 242 TQEYAKENTNNN 253

Length = 253

>gnl|CDD|239722 cd03753, proteasome_alpha_type_5, proteasome_alpha_type_5

 Score =  189 bits (481), Expect = 3e-60
 Identities = 89/215 (41%), Positives = 134/215 (62%), Gaps = 10/215 (4%)

Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YDR +  FSP+G LFQVEYA+EA++ G+ A+G++  + +VL VEK+ T  L +  SV KI
Sbjct: 1   YDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIKTKEGVVLAVEKRITSPLMEPSSVEKI 60

Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
           + +D+HI  A +GL ADAR LI+ AR+E Q+HR T  +P+TVE +T+ ++ L  ++ +  
Sbjct: 61  MEIDDHIGCAMSGLIADARTLIDHARVEAQNHRFTYNEPMTVESVTQAVSDLALQFGEGD 120

Query: 124 GV-----RPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNY 178
                  RPFG++ LI G D     P L+ TDPSGTF+   A A G  S   +  L++ Y
Sbjct: 121 DGKKAMSRPFGVALLIAGVDENG--PQLFHTDPSGTFTRCDAKAIGSGSEGAQSSLQEKY 178

Query: 179 -KETSGQETIKLAIRALLEVVES--GGKNIEVAVM 210
            K+ + +E  KLA+  L +V+E      N+E+A +
Sbjct: 179 HKDMTLEEAEKLALSILKQVMEEKLNSTNVELATV 213

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

>gnl|CDD|238887 cd01906, proteasome_protease_HslV, proteasome_protease_HslV

 Score =  181 bits (463), Expect = 6e-58
 Identities = 78/183 (42%), Positives = 108/183 (59%), Gaps = 8/183 (4%)

Query: 33  AVGVRGTDTIVLGVEKKSTVKLQD-SRSVRKIVSLDNHIALACAGLKADARVLINRARIE 91
            VG++G D +VL  +K+ T  L   S +V KI  +D+HI  A AGL ADA+ L+ R R E
Sbjct: 3   IVGIKGKDGVVLAADKRVTSGLLVASSTVEKIFKIDDHIGCAFAGLAADAQTLVERLRKE 62

Query: 92  CQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDP 151
            Q +RL   +P+ VE + + +A L  +YTQS  +RP G+S L+ G D   G P LY  DP
Sbjct: 63  AQLYRLRYGEPIPVEALAKLLANLLYEYTQS--LRPLGVSLLVAGVDEEGG-PQLYSVDP 119

Query: 152 SGTFSAWKANATGRNSNSMREFLEKNYKE-TSGQETIKLAIRALLEVVESG---GKNIEV 207
           SG++  +KA A G  S      LEK YK   + +E I+LA++AL   +E     G NIEV
Sbjct: 120 SGSYIEYKATAIGSGSQYALGILEKLYKPDMTLEEAIELALKALKSALERDLYSGGNIEV 179

Query: 208 AVM 210
           AV+
Sbjct: 180 AVI 182

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

>gnl|CDD|239718 cd03749, proteasome_alpha_type_1, proteasome_alpha_type_1

 Score =  178 bits (454), Expect = 3e-56
 Identities = 86/213 (40%), Positives = 126/213 (59%), Gaps = 11/213 (5%)

Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YD  +T +SP G LFQVEYA+EAV++G+A VG++     VL   K++T +L  S   +KI
Sbjct: 1   YDTDVTTWSPQGRLFQVEYAMEAVKQGSATVGLKSKTHAVLVALKRATSEL--SSYQKKI 58

Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
             +D+HI +A AGL ADARVL    R EC ++R   + P+ V  +   +A   Q  TQ  
Sbjct: 59  FKVDDHIGIAIAGLTADARVLSRYMRQECLNYRFVYDSPIPVSRLVSKVAEKAQINTQRY 118

Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKN---YKE 180
           G RP+G+  LI G+D     P L+QT PSG +  +KA + G  S S R +LE++   +++
Sbjct: 119 GRRPYGVGLLIAGYDESG--PHLFQTCPSGNYFEYKATSIGARSQSARTYLERHFEEFED 176

Query: 181 TSGQETIKLAIRALLEVVESGG----KNIEVAV 209
            S +E IK A+RAL E +        KN+ +A+
Sbjct: 177 CSLEELIKHALRALRETLPGEQELTIKNVSIAI 209

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 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 =  164 bits (418), Expect = 7e-51
 Identities = 75/195 (38%), Positives = 110/195 (56%), Gaps = 3/195 (1%)

Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YD + + FSPDG +FQVEYA +AV     A+G+R  D +VL VEK  T KL +  S ++I
Sbjct: 4   YDLSASTFSPDGRVFQVEYANKAVENSGTAIGIRCKDGVVLAVEKLVTSKLYEPGSNKRI 63

Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
            ++D HI +A AGL AD R L++RAR E +++R     P+ V+ +   +A     YT   
Sbjct: 64  FNVDRHIGIAVAGLLADGRHLVSRAREEAENYRDNYGTPIPVKVLADRVAMYMHAYTLYS 123

Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEK-NYKETS 182
            VRPFG S L+ G+D     P LY  +PSG    +   A G+   + +  LEK  + E +
Sbjct: 124 SVRPFGCSVLLGGYDSDG--PQLYMIEPSGVSYGYFGCAIGKGKQAAKTELEKLKFSELT 181

Query: 183 GQETIKLAIRALLEV 197
            +E +K A + +  V
Sbjct: 182 CREAVKEAAKIIYIV 196

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|239723 cd03754, proteasome_alpha_type_6, proteasome_alpha_type_6

 Score =  162 bits (412), Expect = 7e-50
 Identities = 79/214 (36%), Positives = 116/214 (54%), Gaps = 9/214 (4%)

Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGN-AAVGVRGTDTIVLGVEKKSTVKLQDSRSVRK 62
           +DR IT+FSP+G L+QVEYA +AV+     +V VRG D  V+  +KK   KL D  +V  
Sbjct: 2   FDRHITIFSPEGRLYQVEYAFKAVKNAGLTSVAVRGKDCAVVVTQKKVPDKLIDPSTVTH 61

Query: 63  IVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQS 122
           +  + + I     G+ AD+R  + RAR E    +      + V+ + + IA + Q YTQ 
Sbjct: 62  LFRITDEIGCVMTGMIADSRSQVQRARYEAAEFKYKYGYEMPVDVLAKRIADINQVYTQH 121

Query: 123 GGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE-- 180
             +RP G+S +++G D   G P LY+ DP+G F+ +KA A G        FLEK  K+  
Sbjct: 122 AYMRPLGVSMILIGIDEELG-PQLYKCDPAGYFAGYKATAAGVKEQEATNFLEKKLKKKP 180

Query: 181 ---TSGQETIKLAIRALLEVVESG--GKNIEVAV 209
               S +ET++LAI  L  V+ +      IEV V
Sbjct: 181 DLIESYEETVELAISCLQTVLSTDFKATEIEVGV 214

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|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 =  126 bits (318), Expect = 2e-36
 Identities = 59/167 (35%), Positives = 89/167 (53%), Gaps = 8/167 (4%)

Query: 33  AVGVRGTDTIVLGVEKKSTVKLQD-SRSVRKIVSLDNHIALACAGLKADARVLINRARIE 91
           +V ++G   +VL  +K+ +  L      V KI   ++ IA   AGL ADA+ L+ R R  
Sbjct: 3   SVAIKGKGGVVLAADKRLSSGLPVAGSPVIKIGKNEDGIAWGLAGLAADAQTLVRRLREA 62

Query: 92  CQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDP 151
            Q +RL   +P++V  + + +A L Q YTQ    RPFG++ ++ G D   G  +LY  DP
Sbjct: 63  LQLYRLRYGEPISVVALAKELAKLLQVYTQ---GRPFGVNLIVAGVDE--GGGNLYYIDP 117

Query: 152 SGTFSAW-KANATGRNSNSMREFLEKNYKE-TSGQETIKLAIRALLE 196
           SG       A ATG  S   +  LEK YK   + +E ++LA++AL  
Sbjct: 118 SGPVIENPGAVATGSRSQRAKSLLEKLYKPDMTLEEAVELALKALKS 164

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

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

 Score = 86.7 bits (216), Expect = 5e-21
 Identities = 51/189 (26%), Positives = 93/189 (49%), Gaps = 16/189 (8%)

Query: 34  VGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIEC 92
           VG++G D +VL  + +++   L  SR+  KI  + ++I L  AG  AD + L    +   
Sbjct: 4   VGIKGKDGVVLAADTRASAGSLVASRNFDKIFKISDNILLGTAGSAADTQALTRLLKRNL 63

Query: 93  QSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPS 152
           + + L     ++V+     ++ +   Y +     P+ +S ++ G D   G P LY  DP 
Sbjct: 64  RLYELRNGRELSVKAAANLLSNILYSY-RGF---PYYVSLIVGGVDKGGG-PFLYYVDPL 118

Query: 153 GTFSAWKAN--ATGRNSNSMREFLEKNYKE-TSGQETIKLAIRALLEVVE----SGGKNI 205
           G+    +A   ATG  S      L++ YK   + +E ++L  +A+   +E    SGG  +
Sbjct: 119 GSLI--EAPFVATGSGSKYAYGILDRGYKPDMTLEEAVELVKKAIDSAIERDLSSGG-GV 175

Query: 206 EVAVMTREK 214
           +VAV+T++ 
Sbjct: 176 DVAVITKDG 184

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|239733 cd03764, proteasome_beta_archeal, Archeal proteasome, beta subunit

 Score = 78.1 bits (193), Expect = 8e-18
 Identities = 59/193 (30%), Positives = 99/193 (51%), Gaps = 12/193 (6%)

Query: 33  AVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIE 91
            VG+   D +VL  +K++++     S++V+KI  +D+ IA+  AG   DA+ L+   + E
Sbjct: 3   TVGIVCKDGVVLAADKRASMGNFIASKNVKKIFQIDDKIAMTIAGSVGDAQSLVRILKAE 62

Query: 92  CQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDP 151
            + + L    P++++ +   ++ +      S    P+ +  LI G D     P LY  DP
Sbjct: 63  ARLYELRRGRPMSIKALATLLSNI----LNSSKYFPYIVQLLIGGVD--EEGPHLYSLDP 116

Query: 152 SGTFSAWKANATGRNSNSMREFLEKNYKE-TSGQETIKLAIRALLEVVE---SGGKNIEV 207
            G+    K  ATG  S      LE  YKE  + +E  KLAIRA+   +E   + G  I+V
Sbjct: 117 LGSIIEDKYTATGSGSPYAYGVLEDEYKEDMTVEEAKKLAIRAIKSAIERDSASGDGIDV 176

Query: 208 AVMTREKGLKQLD 220
            V+T++ G K+L+
Sbjct: 177 VVITKD-GYKELE 188

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

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

 Score = 74.9 bits (185), Expect = 1e-16
 Identities = 57/190 (30%), Positives = 97/190 (51%), Gaps = 13/190 (6%)

Query: 30  GNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRA 88
           G   VG++  D +VL  +K++++     S++ +K+  +D++IA+  AG   DA+ L+   
Sbjct: 1   GTTTVGIKCKDGVVLAADKRASMGNFVASKNAKKVFQIDDYIAMTIAGSVGDAQSLVRIL 60

Query: 89  RIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQ 148
           + E + + L    P++V+ +   ++ +      S    PF +  L+ G D   G P LY 
Sbjct: 61  KAEAKLYELRRGRPMSVKALATLLSNI----LNSNRFFPFIVQLLVGGVDE-EG-PHLYS 114

Query: 149 TDPSGTFSAWKANATGRNSNSMREFLEKNYKET-SGQETIKLAIRALLEVVE----SGGK 203
            DP+G        ATG  S      LE  Y+E  S +E  KLA+RA+   +E    SG  
Sbjct: 115 LDPAGGIIEDDYTATGSGSPVAYGVLEDEYREDMSVEEAKKLAVRAIKSAIERDVASGN- 173

Query: 204 NIEVAVMTRE 213
            I+VAV+T++
Sbjct: 174 GIDVAVITKD 183

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

 Score = 57.4 bits (140), Expect = 9e-12
 Identities = 17/23 (73%), Positives = 21/23 (91%)

Query: 4  YDRAITVFSPDGHLFQVEYALEA 26
          YDR++T FSPDG LFQVEYA++A
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 = 56.7 bits (138), Expect = 2e-11
 Identities = 18/23 (78%), Positives = 21/23 (91%)

Query: 4  YDRAITVFSPDGHLFQVEYALEA 26
          YDR++T FSPDG LFQVEYA+EA
Sbjct: 1  YDRSLTTFSPDGRLFQVEYAMEA 23

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

>gnl|CDD|239732 cd03763, proteasome_beta_type_7, proteasome beta type-7 subunit

 Score = 49.5 bits (119), Expect = 2e-07
 Identities = 49/190 (25%), Positives = 78/190 (41%), Gaps = 20/190 (10%)

Query: 34  VGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIEC 92
           VGV   D +VLG + ++T   +   ++  KI  +  +I    AG  AD   + N      
Sbjct: 4   VGVVFKDGVVLGADTRATEGPIVADKNCEKIHYIAPNIYCCGAGTAADTEAVTNMISSNL 63

Query: 93  QSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPS 152
           + HRL       V      +     +Y   G +   G + ++ G D YTG P LY   P 
Sbjct: 64  ELHRLNTGRKPRVVTALTMLKQHLFRY--QGHI---GAALVLGGVD-YTG-PHLYSIYPH 116

Query: 153 GTFSAWKANATGRNSNSMREFLEKNYKET-SGQETIKLAIRALLEVVESG-------GKN 204
           G+         G  S +    LE  YK   + +E  KL   A    +E+G       G N
Sbjct: 117 GSTDKLPFVTMGSGSLAAMSVLEDRYKPDMTEEEAKKLVCEA----IEAGIFNDLGSGSN 172

Query: 205 IEVAVMTREK 214
           +++ V+T++ 
Sbjct: 173 VDLCVITKDG 182

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|223142 COG0064, GatB, Asp-tRNAAsn/Glu-tRNAGln amidotransferase B subunit (PET112 homolog) [Translation, ribosomal structure and biogenesis]

 Score = 44.1 bits (105), Expect = 4e-05
 Identities = 22/64 (34%), Positives = 35/64 (54%), Gaps = 4/64 (6%)

Query: 186 TIKLAIRALLEVVESGGKNIEVAVMTREKGLKQL-DEAEIDAMVAE-IEAKKAAAEAAKK 243
           + K+A   + E++ +GGK+ E  +   EKGL Q+ DE E++ +V E +     A E  K 
Sbjct: 389 SGKIAKELVFEILANGGKDPEEII--EEKGLVQISDEGELEKIVDEVLAENPKAVEDYKS 446

Query: 244 GPPK 247
           G  K
Sbjct: 447 GKEK 450

Length = 483

>gnl|CDD|239727 cd03758, proteasome_beta_type_2, proteasome beta type-2 subunit

 Score = 41.8 bits (99), Expect = 1e-04
 Identities = 39/177 (22%), Positives = 74/177 (41%), Gaps = 27/177 (15%)

Query: 34  VGVRGTDTIVL---GVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKAD---------A 81
           +G++G D ++L       +S + L+D     KI  L +H  +AC+G   D          
Sbjct: 5   IGIKGKDFVILAADTSAARSILVLKDD--EDKIYKLSDHKLMACSGEAGDRLQFAEYIQK 62

Query: 82  RVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYT 141
            + + + R     +   +       +  R +A    +  +S    P+ ++ L+ G+D   
Sbjct: 63  NIQLYKMR-----NGYELSPKAAANFTRRELA----ESLRSRT--PYQVNLLLAGYDKVE 111

Query: 142 GVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET-SGQETIKLAIRALLEV 197
           G PSLY  D  GT       A G  +      L++ YK   + +E ++L  + + E+
Sbjct: 112 G-PSLYYIDYLGTLVKVPYAAHGYGAYFCLSILDRYYKPDMTVEEALELMKKCIKEL 167

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 = 193

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

 Score = 39.9 bits (94), Expect = 4e-04
 Identities = 38/170 (22%), Positives = 70/170 (41%), Gaps = 18/170 (10%)

Query: 57  SRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQ 116
           SR   KI  L +   L  +G +AD   L  R +   + ++ +    ++    T  IA L 
Sbjct: 36  SRDSPKIFKLTDKCVLGSSGFQADILALTKRLKARIKMYKYSHNKEMS----TEAIAQLL 91

Query: 117 QKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLE- 175
                S    P+ +  ++ G D   G   +Y  DP G++     +A G  S+ ++  L+ 
Sbjct: 92  STILYSRRFFPYYVFNILAGIDE-EGKGVVYSYDPVGSYERETYSAGGSASSLIQPLLDN 150

Query: 176 -------KNYKET--SGQETIKLAIRALLEVVESG---GKNIEVAVMTRE 213
                   N + T  S +E + L   A     E     G ++E+ ++T++
Sbjct: 151 QVGRKNQNNVERTPLSLEEAVSLVKDAFTSAAERDIYTGDSLEIVIITKD 200

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|235489 PRK05477, gatB, aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated

 Score = 40.1 bits (95), Expect = 7e-04
 Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 5/64 (7%)

Query: 186 TIKLAIRALLEVVESGGKNIEVAVMTREKGLKQL-DEAEIDAMVAE-IEAKKAAAEAAKK 243
           + K+A + + E +   G + +  V   EKGLKQ+ DE  ++A+V E + A   A E  K 
Sbjct: 384 SGKIA-KEVFEEMLETGGDPDEIV--EEKGLKQISDEGALEAIVDEVLAANPKAVEDYKA 440

Query: 244 GPPK 247
           G  K
Sbjct: 441 GKEK 444

Length = 474

>gnl|CDD|197913 smart00845, GatB_Yqey, GatB domain

 Score = 38.3 bits (90), Expect = 8e-04
 Identities = 26/65 (40%), Positives = 34/65 (52%), Gaps = 8/65 (12%)

Query: 185 ETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQL-DEAEIDAMVAE-IEAKKAAAEAAK 242
           +  K  +  LLE    GGK+ E  V   EKGLKQ+ DE E++A+V E I     A E  +
Sbjct: 59  KIAKEVLEELLE----GGKSPEEIV--EEKGLKQISDEGELEAIVDEVIAENPDAVEDYR 112

Query: 243 KGPPK 247
            G  K
Sbjct: 113 AGKKK 117

This domain is found in GatB and proteins related to bacterial Yqey. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB which transamidates Glu-tRNA to Gln-tRNA. The function of this domain is uncertain. It does however suggest that Yqey and its relatives have a role in tRNA metabolism. Length = 147

>gnl|CDD|185666 PTZ00488, PTZ00488, Proteasome subunit beta type-5; Provisional

 Score = 39.2 bits (91), Expect = 0.001
 Identities = 39/169 (23%), Positives = 74/169 (43%), Gaps = 12/169 (7%)

Query: 30  GNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRA 88
           G   +  +    I++ V+ K+T      S+SV+K++ ++  +    AG  AD        
Sbjct: 39  GTTTLAFKYGGGIIIAVDSKATAGPYIASQSVKKVIEINPTLLGTMAGGAADCSFWEREL 98

Query: 89  RIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLS--TLIVGFDPYTGVPSL 146
            ++C+ + L   + ++V   ++ +A +   Y      +  GLS  T+I G+D   G P L
Sbjct: 99  AMQCRLYELRNGELISVAAASKILANIVWNY------KGMGLSMGTMICGWDK-KG-PGL 150

Query: 147 YQTDPSGTFSAWKANATGRNSNSMREFLEKNYK-ETSGQETIKLAIRAL 194
           +  D  GT       + G  S      L+  +K + + +E   L  RA+
Sbjct: 151 FYVDNDGTRLHGNMFSCGSGSTYAYGVLDAGFKWDLNDEEAQDLGRRAI 199

Length = 247

>gnl|CDD|239730 cd03761, proteasome_beta_type_5, proteasome beta type-5 subunit

 Score = 37.2 bits (87), Expect = 0.003
 Identities = 42/160 (26%), Positives = 77/160 (48%), Gaps = 20/160 (12%)

Query: 42  IVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADA----RVLINRARIECQSHR 96
           +++ V+ ++T      S++V+K++ ++ ++    AG  AD     RVL      EC+ + 
Sbjct: 12  VIVAVDSRATAGSYIASQTVKKVIEINPYLLGTMAGGAADCQYWERVL----GRECRLYE 67

Query: 97  LTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLS--TLIVGFDPYTGVPSLYQTDPSGT 154
           L  ++ ++V   ++ ++ +  +Y      +  GLS  T+I G+D  TG P LY  D  GT
Sbjct: 68  LRNKERISVAAASKLLSNMLYQY------KGMGLSMGTMICGWDK-TG-PGLYYVDSDGT 119

Query: 155 FSAWKANATGRNSNSMREFLEKNYK-ETSGQETIKLAIRA 193
                  + G  S      L+  Y+ + S +E   LA RA
Sbjct: 120 RLKGDLFSVGSGSTYAYGVLDSGYRYDLSVEEAYDLARRA 159

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 = 188

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	249
KOG0183	249	consensus 20S proteasome, regulatory subunit alpha	100.0
cd03750	227	proteasome_alpha_type_2 proteasome_alpha_type_2. T	100.0
PTZ00246	253	proteasome subunit alpha; Provisional	100.0
KOG0176	241	consensus 20S proteasome, regulatory subunit alpha	100.0
PRK03996	241	proteasome subunit alpha; Provisional	100.0
cd03755	207	proteasome_alpha_type_7 proteasome_alpha_type_7. T	100.0
TIGR03633	224	arc_protsome_A proteasome endopeptidase complex, a	100.0
cd03751	212	proteasome_alpha_type_3 proteasome_alpha_type_3. T	100.0
cd03752	213	proteasome_alpha_type_4 proteasome_alpha_type_4. T	100.0
cd03754	215	proteasome_alpha_type_6 proteasome_alpha_type_6. T	100.0
KOG0181	233	consensus 20S proteasome, regulatory subunit alpha	100.0
cd03749	211	proteasome_alpha_type_1 proteasome_alpha_type_1. T	100.0
cd03756	211	proteasome_alpha_archeal proteasome_alpha_archeal.	100.0
COG0638	236	PRE1 20S proteasome, alpha and beta subunits [Post	100.0
cd01911	209	proteasome_alpha proteasome alpha subunit. The 20S	100.0
KOG0182	246	consensus 20S proteasome, regulatory subunit alpha	100.0
cd03753	213	proteasome_alpha_type_5 proteasome_alpha_type_5. T	100.0
KOG0184	254	consensus 20S proteasome, regulatory subunit alpha	100.0
KOG0178	249	consensus 20S proteasome, regulatory subunit alpha	100.0
KOG0863	264	consensus 20S proteasome, regulatory subunit alpha	100.0
TIGR03691	228	20S_bact_alpha proteasome, alpha subunit, bacteria	100.0
TIGR03690	219	20S_bact_beta proteasome, beta subunit, bacterial	100.0
PTZ00488	247	Proteasome subunit beta type-5; Provisional	100.0
cd03758	193	proteasome_beta_type_2 proteasome beta type-2 subu	100.0
cd03760	197	proteasome_beta_type_4 proteasome beta type-4 subu	100.0
cd03759	195	proteasome_beta_type_3 proteasome beta type-3 subu	100.0
cd03761	188	proteasome_beta_type_5 proteasome beta type-5 subu	100.0
TIGR03634	185	arc_protsome_B proteasome endopeptidase complex, a	100.0
cd03757	212	proteasome_beta_type_1 proteasome beta type-1 subu	100.0
cd03765	236	proteasome_beta_bacterial Bacterial proteasome, be	100.0
cd03764	188	proteasome_beta_archeal Archeal proteasome, beta s	100.0
cd03763	189	proteasome_beta_type_7 proteasome beta type-7 subu	100.0
cd03762	188	proteasome_beta_type_6 proteasome beta type-6 subu	100.0
PF00227	190	Proteasome: Proteasome subunit; InterPro: IPR00135	100.0
cd01912	189	proteasome_beta proteasome beta subunit. The 20S p	100.0
cd01906	182	proteasome_protease_HslV proteasome_protease_HslV.	100.0
KOG0177	200	consensus 20S proteasome, regulatory subunit beta	100.0
KOG0179	235	consensus 20S proteasome, regulatory subunit beta	100.0
KOG0175	285	consensus 20S proteasome, regulatory subunit beta	100.0
KOG0173	271	consensus 20S proteasome, regulatory subunit beta	99.97
KOG0174	224	consensus 20S proteasome, regulatory subunit beta	99.97
KOG0185	256	consensus 20S proteasome, regulatory subunit beta	99.97
PRK05456	172	ATP-dependent protease subunit HslV; Provisional	99.97
cd01901	164	Ntn_hydrolase The Ntn hydrolases (N-terminal nucle	99.97
KOG0180	204	consensus 20S proteasome, regulatory subunit beta	99.96
cd01913	171	protease_HslV Protease HslV and the ATPase/chapero	99.96
TIGR03692	171	ATP_dep_HslV ATP-dependent protease HslVU, peptida	99.95
PF10584	23	Proteasome_A_N: Proteasome subunit A N-terminal si	99.53
COG5405	178	HslV ATP-dependent protease HslVU (ClpYQ), peptida	99.44
COG3484	255	Predicted proteasome-type protease [Posttranslatio	99.4
PF09894	194	DUF2121: Uncharacterized protein conserved in arch	95.4
COG4079	293	Uncharacterized protein conserved in archaea [Func	81.02
KOG3361	157	consensus Iron binding protein involved in Fe-S cl	80.74

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

Probab=100.00  E-value=5.5e-63  Score=399.95  Aligned_cols=245  Identities=74%  Similarity=1.103  Sum_probs=233.4

Q ss_pred             CCCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhh
Q 025716            1 MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKAD   80 (249)
Q Consensus         1 ~~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D   80 (249)
                      |++||+.+|+|||||+|||||||++|+.+|+|+||++++|+|||+.++++..+|++.+...||..+++|++|+++|+.+|
T Consensus         1 msrydraltvFSPDGhL~QVEYAqEAvrkGstaVgvrg~~~vvlgvEkkSv~~Lq~~r~~rkI~~ld~hV~mafaGl~aD   80 (249)
T KOG0183|consen    1 MSRYDRALTVFSPDGHLFQVEYAQEAVRKGSTAVGVRGNNCVVLGVEKKSVPKLQDERTVRKISMLDDHVVMAFAGLTAD   80 (249)
T ss_pred             CCccccceEEECCCCCEEeeHhHHHHHhcCceEEEeccCceEEEEEeecchhhhhhhhhhhhheeecceeeEEecCCCcc
Confidence            78899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccce
Q 025716           81 ARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKA  160 (249)
Q Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~  160 (249)
                      ++.+++++|.+|+.|+++.+.+++++.++++++.+.|.|||.++.||||++++|+|+|+ ++.|.||++||+|.+.+|++
T Consensus        81 ArilinrArvecqShrlt~edpvtveyitRyiA~~kQrYTqs~grRPFGvs~Li~GfD~-~g~p~lyqtePsG~f~ewka  159 (249)
T KOG0183|consen   81 ARILINRARVECQSHRLTLEDPVTVEYITRYIAGLKQRYTQSNGRRPFGVSTLIGGFDP-DGTPRLYQTEPSGIFSEWKA  159 (249)
T ss_pred             ceeehhhHhHhhhhhhcccCCCcHHHHHHHHHHHhhhhhhccCCcccccceEEEEeeCC-CCCeeeEeeCCCcchhhhhc
Confidence            99999999999999999999999999999999999999999999999999999999998 78899999999999999999


Q ss_pred             EeecCCchHHHHHHHhhhccC--Cc-HHHHHHHHHHHHHHHhcCCCcEEEEEEEcCCCEEEcCHHHHHHHHHHHHHHHHH
Q 025716          161 NATGRNSNSMREFLEKNYKET--SG-QETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKKAA  237 (249)
Q Consensus       161 ~aiG~g~~~a~~~Le~~~~~~--~s-eeai~la~~~l~~~~~~~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i~~~~~~  237 (249)
                      .|+|.++..++.+|||+|.+.  .+ .+++++++++|.++.++++.++|++++++++.+++++.++|+.++..|+.+ .+
T Consensus       160 ~aiGr~sk~VrEflEK~y~e~~~~~~~~~ikL~ir~LleVvqs~~~nie~aVm~~~~~~~~l~~~~I~~~v~~ie~E-~e  238 (249)
T KOG0183|consen  160 NAIGRSSKTVREFLEKNYKEEAIATEGETIKLAIRALLEVVQSGGKNIEVAVMKRRKDLKMLESEEIDDIVKEIEQE-EE  238 (249)
T ss_pred             cccccccHHHHHHHHHhcccccccccccHHHHHHHHHHHHhhcCCCeeEEEEEecCCceeecCHHHHHHHHHHHHHH-HH
Confidence            999999999999999999876  56 899999999999999999999999999998779999999999999999988 55


Q ss_pred             HHHhhcCCCC
Q 025716          238 AEAAKKGPPK  247 (249)
Q Consensus       238 ~~~~~~~~~~  247 (249)
                      +++.++..++
T Consensus       239 ~e~~~~~~~~  248 (249)
T KOG0183|consen  239 AEAEKKKKKK  248 (249)
T ss_pred             HHHHhhcccC
Confidence            5555555443

>cd03750 proteasome_alpha_type_2 proteasome_alpha_type_2

Probab=100.00  E-value=3.8e-61  Score=410.20  Aligned_cols=223  Identities=43%  Similarity=0.708  Sum_probs=214.9

Q ss_pred             CCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHHH
Q 025716            4 YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARV   83 (249)
Q Consensus         4 yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~   83 (249)
                      ||+.+|+|||||||+|||||++|+++|+|+|||+++||||||+|++.+++++.+++.+||++|++|++|+++|+.+|++.
T Consensus         1 yd~~~t~fsp~Grl~QveyA~~av~~G~t~igik~~dgVvlaad~~~~~~l~~~~~~~KI~~I~~~i~~~~sG~~~D~~~   80 (227)
T cd03750           1 YSFSLTTFSPSGKLVQIEYALAAVSSGAPSVGIKAANGVVLATEKKVPSPLIDESSVHKVEQITPHIGMVYSGMGPDFRV   80 (227)
T ss_pred             CCCCCceECCCCeEhHHHHHHHHHHcCCCEEEEEeCCEEEEEEeecCCccccCCCCcceEEEEcCCEEEEEeEcHHhHHH
Confidence            89999999999999999999999999999999999999999999999888888889999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEee
Q 025716           84 LINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANAT  163 (249)
Q Consensus        84 l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~ai  163 (249)
                      +++++|.++..|++++|++++++.+++++++++|.|+++++.|||+|++||+|||+  .||+||.+||+|++.+++++|+
T Consensus        81 l~~~~r~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rP~~v~~li~G~D~--~g~~Ly~~d~~G~~~~~~~~a~  158 (227)
T cd03750          81 LVKKARKIAQQYYLVYGEPIPVSQLVREIASVMQEYTQSGGVRPFGVSLLIAGWDE--GGPYLYQVDPSGSYFTWKATAI  158 (227)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCCCCCChheEEEEEEEeC--CCCEEEEECCCCCEEeeeEEEE
Confidence            99999999999999999999999999999999999999999999999999999994  6999999999999999999999


Q ss_pred             cCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEEcCCCEEEcCHHHHHHHH
Q 025716          164 GRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEIDAMV  228 (249)
Q Consensus       164 G~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~--~~~~iei~~v~~~g~~~~~~~~ei~~~l  228 (249)
                      |+|+..++++||++|+++|+ +||++++++||..++.+  ++.++||++|++++.++.++++||++++
T Consensus       159 G~g~~~~~~~Le~~~~~~ms~eeai~l~~~~l~~~~~~~l~~~~iev~iv~~~~~~~~~~~~ei~~~~  226 (227)
T cd03750         159 GKNYSNAKTFLEKRYNEDLELEDAIHTAILTLKEGFEGQMTEKNIEIGICGETKGFRLLTPAEIKDYL  226 (227)
T ss_pred             CCCCHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHhcccCCCCcEEEEEEECCCCEEECCHHHHHHHh
Confidence            99999999999999999999 99999999999988864  6789999999997559999999999886

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=2.9e-60  Score=410.89  Aligned_cols=233  Identities=39%  Similarity=0.648  Sum_probs=220.5

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccC-CcccceEEecCCEEEEEecChhh
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDS-RSVRKIVSLDNHIALACAGLKAD   80 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~-~~~~Ki~~I~~~i~~~~sG~~~D   80 (249)
                      .+||+++|+|||||||+|||||+||+++|+|+|||+++||||||+|++.+++++.. ++.+||++|++|++++++|+.+|
T Consensus         3 ~~yd~~~~~fsp~Grl~QvEYA~~av~~g~t~Igik~~dgVvlaad~r~s~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D   82 (253)
T PTZ00246          3 RRYDSRTTTFSPEGRLYQVEYALEAINNASLTVGILCKEGVILGADKPISSKLLDPGKINEKIYKIDSHIFCAVAGLTAD   82 (253)
T ss_pred             CccCCCCceECCCCEEhHHHHHHHHHHhCCCEEEEEECCEEEEEEecCCCCcCccCCCCcccEEEecCCEEEEEEEcHHH
Confidence            46999999999999999999999999999999999999999999999998876554 46899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccce
Q 025716           81 ARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKA  160 (249)
Q Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~  160 (249)
                      ++.+.+.+|.++..|++.++.+++++.++++++..+|.|+|+++.|||+|++||+|||+ ++||+||.+||+|++.++++
T Consensus        83 ~~~l~~~~r~~~~~~~~~~~~~~~v~~l~~~l~~~~q~~~~~~~~rP~~v~~li~G~D~-~~gp~Ly~~D~~Gs~~~~~~  161 (253)
T PTZ00246         83 ANILINQCRLYAQRYRYTYGEPQPVEQLVVQICDLKQSYTQFGGLRPFGVSFLFAGYDE-NLGYQLYHTDPSGNYSGWKA  161 (253)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccccCcccCCEEEEEEEEeC-CCCcEEEEECCCCCEecceE
Confidence            99999999999999999999999999999999999999999999999999999999996 67999999999999999999


Q ss_pred             EeecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCC-----CEEEcCHHHHHHHHHHH
Q 025716          161 NATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES---GGKNIEVAVMTREK-----GLKQLDEAEIDAMVAEI  231 (249)
Q Consensus       161 ~aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g-----~~~~~~~~ei~~~l~~i  231 (249)
                      +|+|+++..++++|++.|+++|+ +||++++++||..+..+   ++++++|++|+++|     .|++++++||++++.++
T Consensus       162 ~a~G~gs~~~~~~Le~~~~~~ms~eeai~l~~~al~~~~~~d~~s~~~vev~ii~~~~~~~~~~~~~l~~~ei~~~l~~~  241 (253)
T PTZ00246        162 TAIGQNNQTAQSILKQEWKEDLTLEQGLLLAAKVLTKSMDSTSPKADKIEVGILSHGETDGEPIQKMLSEKEIAELLKKV  241 (253)
T ss_pred             EEECCCcHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHhccCCCCCcEEEEEEecCCcCCCCCeEECCHHHHHHHHHHH
Confidence            99999999999999999999999 99999999999999874   46899999999864     38999999999999999


Q ss_pred             HHHH
Q 025716          232 EAKK  235 (249)
Q Consensus       232 ~~~~  235 (249)
                      +++.
T Consensus       242 ~~~~  245 (253)
T PTZ00246        242 TQEY  245 (253)
T ss_pred             hhhh
Confidence            7655

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

Probab=100.00  E-value=3.2e-61  Score=385.39  Aligned_cols=228  Identities=40%  Similarity=0.693  Sum_probs=217.2

Q ss_pred             CCCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhh
Q 025716            1 MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKAD   80 (249)
Q Consensus         1 ~~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D   80 (249)
                      ++.||+.+++|||||||||||||.+|++.|+|.|||+.++||||+.++|++++|+.+...+||++|++||+|++||+.+|
T Consensus         5 rseydrgVNTfSpEGRlfQVEYaieAikLGsTaIGv~TkEgVvL~vEKritSpLm~p~sveKi~eid~HIgca~SGl~aD   84 (241)
T KOG0176|consen    5 RSEYDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGVKTKEGVVLAVEKRITSPLMEPSSVEKIVEIDDHIGCAMSGLIAD   84 (241)
T ss_pred             HHHhcccccccCCCceeeehhhHHHHHhcCCceeeeeccceEEEEEeccccCcccCchhhhhheehhhceeeeccccccc
Confidence            35699999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCC-----CccceeEEEEEeeeCCCCCceEEEECCCCce
Q 025716           81 ARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGG-----VRPFGLSTLIVGFDPYTGVPSLYQTDPSGTF  155 (249)
Q Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~-----~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~  155 (249)
                      ++.+++++|.+|++|++.||++++++.+.+.++++.-+|.....     .|||||++|+||+|  .+||+||..||+|++
T Consensus        85 arTlve~arv~~qnh~f~Y~e~i~VEs~tq~v~~LaLrFGe~~~~~~~msRPFGValliAG~D--~~gpqL~h~dPSGtf  162 (241)
T KOG0176|consen   85 ARTLVERARVETQNHWFTYGEPISVESLTQAVSDLALRFGEGDDEEAIMSRPFGVALLIAGHD--ETGPQLYHLDPSGTF  162 (241)
T ss_pred             hHHHHHHHHHHhhhceeecCCcccHHHHHHHHHHHHhHhCCCcchhhhhcCCcceEEEEeecc--CCCceEEEeCCCCce
Confidence            99999999999999999999999999999999999877764422     49999999999999  589999999999999


Q ss_pred             eccceEeecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEEcCCCEEEcCHHHHHHHHHH
Q 025716          156 SAWKANATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEIDAMVAE  230 (249)
Q Consensus       156 ~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~--~~~~iei~~v~~~g~~~~~~~~ei~~~l~~  230 (249)
                      ++|++.|||+|+..|.+.|++.|+++|+ +|++.+++..|+.+++.  +.+|+||..|++.|.|++++++|+++++..
T Consensus       163 ~~~~AKAIGSgsEga~~~L~~e~~~~ltL~ea~~~~L~iLkqVMeeKl~~~Nvev~~vt~e~~f~~~t~EE~~~~i~~  240 (241)
T KOG0176|consen  163 IRYKAKAIGSGSEGAESSLQEEYHKDLTLKEAEKIVLKILKQVMEEKLNSNNVEVAVVTPEGEFHIYTPEEVEQVIKR  240 (241)
T ss_pred             EEecceeccccchHHHHHHHHHHhhcccHHHHHHHHHHHHHHHHHHhcCccceEEEEEcccCceEecCHHHHHHHHhc
Confidence            9999999999999999999999999999 99999999999999975  788999999999988999999999998864

>PRK03996 proteasome subunit alpha; Provisional

Probab=100.00  E-value=3.9e-59  Score=401.16  Aligned_cols=228  Identities=49%  Similarity=0.801  Sum_probs=218.4

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhH
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADA   81 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~   81 (249)
                      ++||+++|+|||||||+|||||+||+++|+|+|||+++||||||+|++.++.+..+++.+||+.|++|++++++|+.+|+
T Consensus         8 ~~y~~~~~~fsp~Gr~~Q~eya~~av~~G~t~igik~~dgVvlaad~r~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~   87 (241)
T PRK03996          8 MGYDRAITIFSPDGRLYQVEYAREAVKRGTTAVGVKTKDGVVLAVDKRITSPLIEPSSIEKIFKIDDHIGAASAGLVADA   87 (241)
T ss_pred             cccCCCCceECCCCeEhHHHHHHHHHHhCCCEEEEEeCCEEEEEEeccCCCcccCCCccceEEEEcCCEEEEEcccHHHH
Confidence            47999999999999999999999999999999999999999999999998877777889999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceE
Q 025716           82 RVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKAN  161 (249)
Q Consensus        82 ~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~  161 (249)
                      +.++++++.++..|+++++++++++.+++++++.+|.|++.++.|||+|++||||||  ++||+||.+||+|++.+++++
T Consensus        88 ~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~~~~~~~rP~~~~~ilaG~d--~~gp~Ly~id~~G~~~~~~~~  165 (241)
T PRK03996         88 RVLIDRARVEAQINRLTYGEPIGVETLTKKICDHKQQYTQHGGVRPFGVALLIAGVD--DGGPRLFETDPSGAYLEYKAT  165 (241)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhcCCCCccchheEEEEEEEe--CCcCEEEEECCCCCeecceEE
Confidence            999999999999999999999999999999999999999999999999999999999  468999999999999999999


Q ss_pred             eecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEEcCC-CEEEcCHHHHHHHHHHH
Q 025716          162 ATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES--GGKNIEVAVMTREK-GLKQLDEAEIDAMVAEI  231 (249)
Q Consensus       162 aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~--~~~~iei~~v~~~g-~~~~~~~~ei~~~l~~i  231 (249)
                      |+|.++..++++||+.|+++|+ +||++++++||..+.+.  ++++++|++++++| .++.++++|++++++++
T Consensus       166 a~G~g~~~~~~~Le~~~~~~~s~eeai~l~~~al~~~~~~~~~~~~i~i~ii~~~~~~~~~~~~~ei~~~~~~~  239 (241)
T PRK03996        166 AIGAGRDTVMEFLEKNYKEDLSLEEAIELALKALAKANEGKLDPENVEIAYIDVETKKFRKLSVEEIEKYLEKL  239 (241)
T ss_pred             EECCCcHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHhccCCCCCcEEEEEEECCCCcEEECCHHHHHHHHHHh
Confidence            9999999999999999999999 99999999999999864  57789999999976 49999999999999876

>cd03755 proteasome_alpha_type_7 proteasome_alpha_type_7

Probab=100.00  E-value=1.6e-58  Score=388.90  Aligned_cols=206  Identities=82%  Similarity=1.231  Sum_probs=199.8

Q ss_pred             CCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHHH
Q 025716            4 YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARV   83 (249)
Q Consensus         4 yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~   83 (249)
                      ||+++|+|||||||+|||||++|+++|+|+|||+++||||||+|++.+..++.++..+||+.|++|++|++||+.+|++.
T Consensus         1 ~d~~~~~fsp~Gr~~Qveya~~av~~G~t~Igik~~dgVvlaad~~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~   80 (207)
T cd03755           1 YDRAITVFSPDGHLFQVEYAQEAVRKGTTAVGVRGKDCVVLGVEKKSVAKLQDPRTVRKICMLDDHVCLAFAGLTADARV   80 (207)
T ss_pred             CCCCCceECCCCeEeHHHHHHHHHHcCCCEEEEEeCCEEEEEEecCCCCcccCCCccCcEEEECCCEEEEEecchhhHHH
Confidence            89999999999999999999999999999999999999999999998877777778999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEee
Q 025716           84 LINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANAT  163 (249)
Q Consensus        84 l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~ai  163 (249)
                      +.+++|.++..|+++++++++++.++++++.++|.|+++++.|||+|++||+|||+ +++|+||.+||+|++.+++++|+
T Consensus        81 l~~~~r~~~~~~~~~~~~~i~~~~la~~ls~~~~~y~~~~~~rP~~vs~ii~G~D~-~~~p~Ly~iD~~G~~~~~~~~a~  159 (207)
T cd03755          81 LINRARLECQSHRLTVEDPVTVEYITRYIAGLQQRYTQSGGVRPFGISTLIVGFDP-DGTPRLYQTDPSGTYSAWKANAI  159 (207)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcccCcccceeEEEEEEEeC-CCCeEEEEECCCcCEEcceEEEE
Confidence            99999999999999999999999999999999999999999999999999999997 67999999999999999999999


Q ss_pred             cCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhcCCCcEEEEEE
Q 025716          164 GRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVESGGKNIEVAVM  210 (249)
Q Consensus       164 G~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~~~~~iei~~v  210 (249)
                      |+++..++++||++|+++|+ +||++++++||.++.+.++.++||+++
T Consensus       160 G~gs~~~~~~Le~~~~~~ms~eeai~l~~~~l~~~~~~~~~~~e~~~~  207 (207)
T cd03755         160 GRNSKTVREFLEKNYKEEMTRDDTIKLAIKALLEVVQSGSKNIELAVM  207 (207)
T ss_pred             CCCCHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHhCCCCCeEEEEEC
Confidence            99999999999999999999 999999999999999988889999975

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

>TIGR03633 arc_protsome_A proteasome endopeptidase complex, archaeal, alpha subunit

Probab=100.00  E-value=2.5e-58  Score=392.18  Aligned_cols=220  Identities=51%  Similarity=0.825  Sum_probs=209.9

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhH
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADA   81 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~   81 (249)
                      |+||.++|+|||||||+|||||++|+++|+|+|||+++||||||+|++.++.++.+++.+||+.|++|++|++||+.+|+
T Consensus         1 ~~~~~~~~~f~p~Grl~Qieya~~av~~G~tvigi~~~dgvvlaad~r~~~~~~~~~~~~KI~~i~~~i~~~~sG~~~D~   80 (224)
T TIGR03633         1 MGYDRAITVFSPDGRLYQVEYAREAVKRGTTAVGIKTKDGVVLAVDKRITSKLVEPSSIEKIFKIDDHIGAATSGLVADA   80 (224)
T ss_pred             CCCCCCCceECCCCeEeHHHHHHHHHHcCCCEEEEEECCEEEEEEeccCCccccCCCccceEEEECCCEEEEEeecHHhH
Confidence            79999999999999999999999999999999999999999999999998877777889999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceE
Q 025716           82 RVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKAN  161 (249)
Q Consensus        82 ~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~  161 (249)
                      +.+.+.++.++..|+++++++++++.+++++++.+|.|++.++.|||+|++||+|+|  +++|+||.+||.|++.+++++
T Consensus        81 ~~l~~~~~~~~~~~~~~~~~~~~~~~la~~ls~~l~~~~~~~~~rP~~v~~ll~G~d--~~~~~Ly~~D~~G~~~~~~~~  158 (224)
T TIGR03633        81 RVLIDRARIEAQINRLTYGEPIDVETLAKKICDLKQQYTQHGGVRPFGVALLIAGVD--DGGPRLFETDPSGALLEYKAT  158 (224)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCCCccccceEEEEEEEe--CCcCEEEEECCCCCeecceEE
Confidence            999999999999999999999999999999999999999999999999999999999  579999999999999999999


Q ss_pred             eecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEEcCCC-EEEcCHHH
Q 025716          162 ATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES--GGKNIEVAVMTREKG-LKQLDEAE  223 (249)
Q Consensus       162 aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~--~~~~iei~~v~~~g~-~~~~~~~e  223 (249)
                      ++|+++..++++|++.|+++|+ +||++++++||..+.+.  ++++++|++|+++|. |+.++++|
T Consensus       159 a~G~g~~~~~~~L~~~~~~~~~~eeai~l~~~al~~~~~d~~~~~~i~i~ii~~~g~~~~~~~~~~  224 (224)
T TIGR03633       159 AIGAGRQAVTEFLEKEYREDLSLDEAIELALKALYSAVEDKLTPENVEVAYITVEDKKFRKLSVEE  224 (224)
T ss_pred             EECCCCHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHhcccCCCCcEEEEEEEcCCCcEEECCCCC
Confidence            9999999999999999999999 99999999999998863  577899999999764 88887764

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.

>cd03751 proteasome_alpha_type_3 proteasome_alpha_type_3

Probab=100.00  E-value=1.9e-58  Score=389.54  Aligned_cols=207  Identities=36%  Similarity=0.546  Sum_probs=198.8

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhH
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADA   81 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~   81 (249)
                      .+||+.+|+|||||||+|||||++|+++|+|+|||+++||||||+|++.++.+..+++.+||+.|++|++++++|+.+|+
T Consensus         2 ~~yd~~~t~fsp~Grl~Qveya~~a~~~G~tvIgik~kdgVvla~d~r~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~   81 (212)
T cd03751           2 TGYDLSASTFSPDGRVFQVEYANKAVENSGTAIGIRCKDGVVLAVEKLVTSKLYEPGSNKRIFNVDRHIGIAVAGLLADG   81 (212)
T ss_pred             CCccCCCceECCCCcchHHHHHHHHHhcCCCEEEEEeCCEEEEEEEccccccccCcchhcceeEecCcEEEEEEEChHhH
Confidence            57999999999999999999999999999999999999999999999998877777789999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceE
Q 025716           82 RVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKAN  161 (249)
Q Consensus        82 ~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~  161 (249)
                      +.+.+++|.++..|+++++++++++.++++|++++|.|+++++.|||+|++||+|||  ++||+||.+||+|++.+++++
T Consensus        82 ~~l~~~~r~~~~~y~~~~~~~~~v~~la~~ls~~~~~~t~~~~~rP~~vs~li~G~D--~~gp~Ly~~D~~Gs~~~~~~~  159 (212)
T cd03751          82 RHLVSRAREEAENYRDNYGTPIPVKVLADRVAMYMHAYTLYSSVRPFGCSVLLGGYD--SDGPQLYMIEPSGVSYGYFGC  159 (212)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccCCCcCCceEEEEEEEEe--CCcCEEEEECCCCCEEeeEEE
Confidence            999999999999999999999999999999999999999999999999999999999  468999999999999999999


Q ss_pred             eecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHh---cCCCcEEEEEE
Q 025716          162 ATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVE---SGGKNIEVAVM  210 (249)
Q Consensus       162 aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~---~~~~~iei~~v  210 (249)
                      |+|+++..++++||++|+++|| +||+++++++|..+++   .+..++||+++
T Consensus       160 a~G~g~~~a~~~Lek~~~~dms~eeai~l~~~~L~~~~~~~~~~~~~iei~~~  212 (212)
T cd03751         160 AIGKGKQAAKTELEKLKFSELTCREAVKEAAKIIYIVHDEIKDKAFELELSWV  212 (212)
T ss_pred             EECCCCHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHhhccCCCCccEEEEEC
Confidence            9999999999999999999999 9999999999999998   35778999875

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=9.7e-58  Score=385.75  Aligned_cols=208  Identities=42%  Similarity=0.715  Sum_probs=198.7

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCccccc-CCcccceEEecCCEEEEEecChhh
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQD-SRSVRKIVSLDNHIALACAGLKAD   80 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~-~~~~~Ki~~I~~~i~~~~sG~~~D   80 (249)
                      .+||+.+|+|||||||+|||||+||+++|+|+|||+++||||||+|++.+++++. .++.+||++|++|++|++||+.+|
T Consensus         1 ~~yd~~~~~fsp~Grl~Qveya~~a~~~G~t~igi~~~dgVvla~d~r~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D   80 (213)
T cd03752           1 RRYDSRTTIFSPEGRLYQVEYAMEAISHAGTCLGILAKDGIVLAAEKKVTSKLLDQSFSSEKIYKIDDHIACAVAGITSD   80 (213)
T ss_pred             CCcCCCCceECCCCEEhHHHhHHHHHhcCCCEEEEEeCCEEEEEEEeccCCcccCCCcCcceEEEecCCEEEEEecChHh
Confidence            4799999999999999999999999999999999999999999999999887655 458999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccce
Q 025716           81 ARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKA  160 (249)
Q Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~  160 (249)
                      ++.+++++|.++..|+++++++++++.++++++..+|.|+++++.|||+|++||+|||+ +.||+||.+||+|++.++++
T Consensus        81 ~~~l~~~~r~~~~~~~~~~~~~i~v~~la~~ls~~~~~~t~~~~~RP~~v~~li~G~D~-~~g~~ly~~d~~G~~~~~~~  159 (213)
T cd03752          81 ANILINYARLIAQRYLYSYQEPIPVEQLVQRLCDIKQGYTQYGGLRPFGVSFLYAGWDK-HYGFQLYQSDPSGNYSGWKA  159 (213)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcCCCcccceeEEEEEEEeC-CCCCEEEEECCCCCeeeeeE
Confidence            99999999999999999999999999999999999999999999999999999999996 67999999999999999999


Q ss_pred             EeecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEE
Q 025716          161 NATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES---GGKNIEVAVM  210 (249)
Q Consensus       161 ~aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v  210 (249)
                      +|+|+++..++++||++|+++|+ +||++++++||..+.++   .+.++||++|
T Consensus       160 ~a~G~gs~~~~~~Le~~y~~~ms~eea~~l~~~al~~~~~r~~~~~~~~ei~~~  213 (213)
T cd03752         160 TAIGNNNQAAQSLLKQDYKDDMTLEEALALAVKVLSKTMDSTKLTSEKLEFATL  213 (213)
T ss_pred             EEECCCcHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHhccCCCCCcEEEEEC
Confidence            99999999999999999999999 99999999999999874   4678999875

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

>cd03754 proteasome_alpha_type_6 proteasome_alpha_type_6

Probab=100.00  E-value=7e-57  Score=380.92  Aligned_cols=207  Identities=38%  Similarity=0.631  Sum_probs=196.9

Q ss_pred             CCCCCCcccCCCCcchhhhhHHHHHcc-CCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhH
Q 025716            3 RYDRAITVFSPDGHLFQVEYALEAVRK-GNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADA   81 (249)
Q Consensus         3 ~yd~~~~~fsp~G~l~Qveya~kav~~-G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~   81 (249)
                      +||+++|+|||||||+|||||+||+++ |+|+|||+++||||||+|++.+..++..++.+||++|++|++|++||+.+|+
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            699999999999999999999999975 8899999999999999999998877666688999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceE
Q 025716           82 RVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKAN  161 (249)
Q Consensus        82 ~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~  161 (249)
                      +.+.+++|.++..|+++++++++++.+|+++++++|.|+++++.|||+|++||+|||+ ++||+||.+||+|++.+++++
T Consensus        81 ~~l~~~~r~~~~~~~~~~~~~i~v~~la~~ls~~~q~yt~~~~~RP~~v~~ii~G~D~-~~gp~Ly~~Dp~Gs~~~~~~~  159 (215)
T cd03754          81 RSQVQRARYEAAEFKYKYGYEMPVDVLAKRIADINQVYTQHAYMRPLGVSMILIGIDE-ELGPQLYKCDPAGYFAGYKAT  159 (215)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhCCCCCcCCeeEEEEEEEeC-CCCeEEEEEcCCccEEeEEEE
Confidence            9999999999999999999999999999999999999999999999999999999996 679999999999999999999


Q ss_pred             eecCCchHHHHHHHhhhccC--C--c-HHHHHHHHHHHHHHHhc--CCCcEEEEEE
Q 025716          162 ATGRNSNSMREFLEKNYKET--S--G-QETIKLAIRALLEVVES--GGKNIEVAVM  210 (249)
Q Consensus       162 aiG~g~~~a~~~Le~~~~~~--~--s-eeai~la~~~l~~~~~~--~~~~iei~~v  210 (249)
                      |+|+++..++++||++|+++  |  + +|+++++++||.++.++  .++++||+||
T Consensus       160 a~G~gs~~~~~~Le~~~~~~~~~~~s~eeai~l~~~al~~~~~rd~~~~~~ei~~~  215 (215)
T cd03754         160 AAGVKEQEATNFLEKKLKKKPDLIESYEETVELAISCLQTVLSTDFKATEIEVGVV  215 (215)
T ss_pred             EECCCcHHHHHHHHHHhccccccCCCHHHHHHHHHHHHHHHhcccCCCCcEEEEEC
Confidence            99999999999999999985  7  9 99999999999999875  5778999885

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.

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

Probab=100.00  E-value=1.2e-57  Score=364.15  Aligned_cols=226  Identities=41%  Similarity=0.682  Sum_probs=219.2

Q ss_pred             CCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHH
Q 025716            3 RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADAR   82 (249)
Q Consensus         3 ~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~   82 (249)
                      +|..++|+|||+|+|.|+|||+.|+.+|.+.|||+-.||||||++++..+.|++....+|++.|.+||+|.+||..+|++
T Consensus         5 ~y~fslTtFSpsGKL~QieyAL~Av~~G~~SvGi~A~nGvVlatekk~~s~L~~~~sv~KV~~i~~~IG~vYSGmgpD~R   84 (233)
T KOG0181|consen    5 GYSFSLTTFSPSGKLVQIEYALTAVVNGQTSVGIKAANGVVLATEKKDVSPLVDEESVRKVEKITPHIGCVYSGMGPDYR   84 (233)
T ss_pred             ccceeeEEEcCCCceehHHHHHHHHhCCCCceeeeecCceEEEeccCCCCccchhhhhhhHhhccCCcceEEecCCCcee
Confidence            68999999999999999999999999999999999999999999999999999888999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEe
Q 025716           83 VLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANA  162 (249)
Q Consensus        83 ~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~a  162 (249)
                      .+++..|..|++|...|++++++..|+..++..+|+|||+++.||||+++++||||  +++|.||++||+|++..|+++|
T Consensus        85 vlV~~~rkiAe~Yy~vY~e~~pt~qlv~~~asvmQEyTqsgGvrPFGvslliaG~~--~~~p~LyQvdPSGsyf~wkatA  162 (233)
T KOG0181|consen   85 VLVHKSRKIAEQYYRVYGEPIPTTQLVQEVASVMQEYTQSGGVRPFGVSLLIAGWD--EGGPLLYQVDPSGSYFAWKATA  162 (233)
T ss_pred             ehhhHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEeecC--CCceeEEEECCccceeehhhhh
Confidence            99999999999999999999999999999999999999999999999999999999  5799999999999999999999


Q ss_pred             ecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEEcCCCEEEcCHHHHHHHHHHH
Q 025716          163 TGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEIDAMVAEI  231 (249)
Q Consensus       163 iG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~--~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i  231 (249)
                      +|.+...++++|||+|+++|. ++++..|+..|++.++-  ..+++||+++..++ |+++++.||+++|+.|
T Consensus       163 ~Gkn~v~aktFlEkR~~edleldd~ihtailtlkE~fege~~~~nieigv~~~~~-F~~lt~~eI~d~l~~l  233 (233)
T KOG0181|consen  163 MGKNYVNAKTFLEKRYNEDLELDDAIHTAILTLKESFEGEMTAKNIEIGVCGENG-FRRLTPAEIEDYLASL  233 (233)
T ss_pred             hccCcchHHHHHHHHhccccccchHHHHHHHHHHHHhccccccCceEEEEecCCc-eeecCHHHHHHHHhcC
Confidence            999999999999999999999 99999999999999964  68899999999887 9999999999999764

>cd03749 proteasome_alpha_type_1 proteasome_alpha_type_1

Probab=100.00  E-value=1.9e-56  Score=377.27  Aligned_cols=204  Identities=42%  Similarity=0.666  Sum_probs=194.1

Q ss_pred             CCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHHH
Q 025716            4 YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARV   83 (249)
Q Consensus         4 yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~   83 (249)
                      ||+++|+|||||||+|||||++|+++|+|+|||+++||||||+|++.++.+.  ++.+||++|++|++|++||+.+|++.
T Consensus         1 yd~~~t~fsp~Grl~Qveya~~av~~G~t~IgIk~~dgVvlaad~r~~~~l~--~~~~KI~~I~~~i~~~~sG~~~D~~~   78 (211)
T cd03749           1 YDTDVTTWSPQGRLFQVEYAMEAVKQGSATVGLKSKTHAVLVALKRATSELS--SYQKKIFKVDDHIGIAIAGLTADARV   78 (211)
T ss_pred             CCCCCceECCCCeEeHHHHHHHHHhcCCCEEEEEeCCEEEEEEeccCccccC--CccccEEEeCCCEEEEEEeChHhHHH
Confidence            8999999999999999999999999999999999999999999999877753  35799999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEee
Q 025716           84 LINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANAT  163 (249)
Q Consensus        84 l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~ai  163 (249)
                      +.+++|.++..|+++++++++++.++++++..+|.|+++.+.|||+|++||+|||+  .||+||.+||+|++.+++++|+
T Consensus        79 l~~~~r~~~~~~~~~~~~~~~v~~la~~is~~~~~~t~~~~~rP~~v~~ii~G~D~--~gp~Ly~~Dp~G~~~~~~~~a~  156 (211)
T cd03749          79 LSRYMRQECLNYRFVYDSPIPVSRLVSKVAEKAQINTQRYGRRPYGVGLLIAGYDE--SGPHLFQTCPSGNYFEYKATSI  156 (211)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCCCCceEEEEEEEEcC--CCCeEEEECCCcCEeeeeEEEE
Confidence            99999999999999999999999999999999999999999999999999999994  6899999999999999999999


Q ss_pred             cCCchHHHHHHHhhhc--cCCc-HHHHHHHHHHHHHHHh----cCCCcEEEEEEE
Q 025716          164 GRNSNSMREFLEKNYK--ETSG-QETIKLAIRALLEVVE----SGGKNIEVAVMT  211 (249)
Q Consensus       164 G~g~~~a~~~Le~~~~--~~~s-eeai~la~~~l~~~~~----~~~~~iei~~v~  211 (249)
                      |+++..++++||++|+  ++|+ +|++++++++|+.++.    .++.+|||++|+
T Consensus       157 G~g~~~a~~~Le~~~~~~~~ms~ee~i~~~~~~l~~~~~~~~~~~~~~iei~ii~  211 (211)
T cd03749         157 GARSQSARTYLERHFEEFEDCSLEELIKHALRALRETLPGEQELTIKNVSIAIVG  211 (211)
T ss_pred             CCCcHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhccCCCCCCCcEEEEEEC
Confidence            9999999999999999  5999 9999999999999986    356899999973

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

>cd03756 proteasome_alpha_archeal proteasome_alpha_archeal

Probab=100.00  E-value=2.8e-56  Score=376.34  Aligned_cols=207  Identities=51%  Similarity=0.861  Sum_probs=199.6

Q ss_pred             CCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHH
Q 025716            3 RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADAR   82 (249)
Q Consensus         3 ~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~   82 (249)
                      +||.++|+|||||||+|+|||.||+++|+|+|||+++||||||+|++.++.++.+++.+||+.|++|++|++||+.+|++
T Consensus         1 ~y~~~~~~fsp~G~l~Q~eya~~av~~G~t~igik~~dgvvla~d~~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~   80 (211)
T cd03756           1 GYDRAITVFSPDGRLYQVEYAREAVKRGTTALGIKCKEGVVLAVDKRITSKLVEPESIEKIYKIDDHVGAATSGLVADAR   80 (211)
T ss_pred             CCCCCCceECCCCeEhHHHHHHHHHHcCCCEEEEEECCEEEEEEeccCCCcccCCCccceEEEEcCCEEEEEecCHHHHH
Confidence            69999999999999999999999999999999999999999999999987777778999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEe
Q 025716           83 VLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANA  162 (249)
Q Consensus        83 ~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~a  162 (249)
                      .+.+.++.+++.|+++++++++++.++++++..+|.|++.++.|||+|++||+|||  +++|+||.+||+|++.++++++
T Consensus        81 ~l~~~l~~~~~~~~~~~~~~~~~~~la~~ls~~~~~~~~~~~~rP~~v~~ll~G~D--~~~~~ly~vd~~G~~~~~~~~a  158 (211)
T cd03756          81 VLIDRARVEAQIHRLTYGEPIDVEVLVKKICDLKQQYTQHGGVRPFGVALLIAGVD--DGGPRLFETDPSGAYNEYKATA  158 (211)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCCCeechhEEEEEEEEe--CCCCEEEEECCCCCeeeeEEEE
Confidence            99999999999999999999999999999999999999999999999999999999  4799999999999999999999


Q ss_pred             ecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEE
Q 025716          163 TGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES--GGKNIEVAVMT  211 (249)
Q Consensus       163 iG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~--~~~~iei~~v~  211 (249)
                      +|+++..++++||++|+++|+ +||++++++||..+.+.  .+.+++|++|+
T Consensus       159 ~G~g~~~~~~~Le~~~~~~m~~~ea~~l~~~~l~~~~~~~~~~~~~~v~ii~  210 (211)
T cd03756         159 IGSGRQAVTEFLEKEYKEDMSLEEAIELALKALYAALEENETPENVEIAYVT  210 (211)
T ss_pred             ECCCCHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHhcccCCCCcEEEEEEe
Confidence            999999999999999999999 99999999999998864  57899999986

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.

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

Probab=100.00  E-value=2.2e-55  Score=376.07  Aligned_cols=229  Identities=48%  Similarity=0.805  Sum_probs=215.3

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccC-CcEEEEEeCCEEEEEEeccCCccc-ccCCcccceEEecCCEEEEEecChh
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKG-NAAVGVRGTDTIVLGVEKKSTVKL-QDSRSVRKIVSLDNHIALACAGLKA   79 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G-~t~igi~~~dgVvla~d~~~~~~l-~~~~~~~Ki~~I~~~i~~~~sG~~~   79 (249)
                      ++||+.+++|||+|+++|+|||.+++.+| +|+|||+++||||||+|+|.++++ +..++.+|||+|+|||+|++||+.+
T Consensus         1 ~~~~~~~~~fsp~g~l~q~e~a~~a~~~~gtT~vgik~~dgVVlaadkr~t~~~~~~~~~~~Ki~~I~d~i~~~~sG~~a   80 (236)
T COG0638           1 AGYDRAITIFSPEGRLFQVEYALEAVKRGGTTTVGIKGKDGVVLAADKRATSGLLIASSNVEKIFKIDDHIGMAIAGLAA   80 (236)
T ss_pred             CCCcCcceeECCCCchHHHHHHHHHHHcCCceEEEEEecCEEEEEEeccCCCCceecccccceEEEecCCEEEEeccCcH
Confidence            47999999999999999999999999875 999999999999999999999964 5556799999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccc
Q 025716           80 DARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWK  159 (249)
Q Consensus        80 D~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~  159 (249)
                      |++.|++++|.+|+.|++++|++++++.+++++++++|.|+++  .|||+|++||||+|+  ++|+||.+||+|++.+++
T Consensus        81 Da~~lv~~~r~~a~~~~~~~~~~i~v~~la~~ls~~l~~~~~~--~rP~gv~~iiaG~d~--~~p~Ly~~Dp~G~~~~~~  156 (236)
T COG0638          81 DAQVLVRYARAEAQLYRLRYGEPISVEALAKLLSNILQEYTQS--GRPYGVSLLVAGVDD--GGPRLYSTDPSGSYNEYK  156 (236)
T ss_pred             hHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhccC--cccceEEEEEEEEcC--CCCeEEEECCCCceeecC
Confidence            9999999999999999999999999999999999999999987  899999999999994  789999999999999999


Q ss_pred             eEeecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCHHHHHHHHHHHHHH
Q 025716          160 ANATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES---GGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAK  234 (249)
Q Consensus       160 ~~aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i~~~  234 (249)
                      ++|+|+|++.++++||+.|+++|+ |||++++++||.++.++   .+++++|++++++..++.++++++..++..+..+
T Consensus       157 ~~a~Gsgs~~a~~~Le~~y~~~m~~eeai~la~~al~~a~~rd~~s~~~~~v~vi~~~~~~~~~~~~~~~~~~~~~~~~  235 (236)
T COG0638         157 ATAIGSGSQFAYGFLEKEYREDLSLEEAIELAVKALRAAIERDAASGGGIEVAVITKDEGFRKLDGEEIKKLLDDLSEK  235 (236)
T ss_pred             EEEEcCCcHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHhccccCCCCeEEEEEEcCCCeEEcCHHHHHHHHHHHhhc
Confidence            999999999999999999999999 99999999999999985   3567899999995449999999999999887653

>cd01911 proteasome_alpha proteasome alpha subunit

Probab=100.00  E-value=2e-55  Score=370.57  Aligned_cols=206  Identities=59%  Similarity=0.909  Sum_probs=197.7

Q ss_pred             CCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHHH
Q 025716            4 YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARV   83 (249)
Q Consensus         4 yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~   83 (249)
                      ||+++|+|||||||+|+|||++++++|+|+|||+++||||+|+|++.+..++..++.+||++|++|++++++|+.+|++.
T Consensus         1 ~~~~~~~f~~~G~~~q~eya~~~~~~G~tvigi~~~dgVvlaaD~~~~~~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~   80 (209)
T cd01911           1 YDRSITTFSPEGRLFQVEYALEAVKNGSTAVGIKGKDGVVLAVEKKVTSKLLDPSSVEKIFKIDDHIGCAVAGLTADARV   80 (209)
T ss_pred             CCCCCccCCCCCEEeHHHHHHHHHHcCCCEEEEEECCEEEEEEEecCCccccCCcccceEEEecCCeEEEeccCcHhHHH
Confidence            89999999999999999999999999999999999999999999999887766688999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEee
Q 025716           84 LINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANAT  163 (249)
Q Consensus        84 l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~ai  163 (249)
                      +.+.++.++..|++++|++++++.+++++++++|.|+++++.|||+|++||+|||+ +++|+||.+||.|++.+++++++
T Consensus        81 l~~~l~~~~~~~~~~~g~~~~~~~la~~ls~~~~~~~~~~~~rP~~v~~iv~G~d~-~~~~~Ly~iD~~G~~~~~~~~a~  159 (209)
T cd01911          81 LVNRARVEAQNYRYTYGEPIPVEVLVKRIADLAQVYTQYGGVRPFGVSLLIAGYDE-EGGPQLYQTDPSGTYFGYKATAI  159 (209)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCccChhheEEEEEEcC-CCCcEEEEECCCCCeeeeeEEEe
Confidence            99999999999999999999999999999999999999999999999999999997 66999999999999999999999


Q ss_pred             cCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEE
Q 025716          164 GRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES--GGKNIEVAVM  210 (249)
Q Consensus       164 G~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~--~~~~iei~~v  210 (249)
                      |+++..++++|++.|+++|+ +||++++++||..+..+  .+++++|+++
T Consensus       160 G~g~~~~~~~L~~~~~~~ms~~ea~~l~~~~l~~~~~~d~~~~~~~i~i~  209 (209)
T cd01911         160 GKGSQEAKTFLEKRYKKDLTLEEAIKLALKALKEVLEEDKKAKNIEIAVV  209 (209)
T ss_pred             CCCcHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHhccCCCCcEEEEEC
Confidence            99999999999999999999 99999999999999875  5678898874

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.

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

Probab=100.00  E-value=3.4e-55  Score=354.13  Aligned_cols=233  Identities=36%  Similarity=0.581  Sum_probs=223.2

Q ss_pred             CCCCCCCCcccCCCCcchhhhhHHHHHcc-CCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChh
Q 025716            1 MARYDRAITVFSPDGHLFQVEYALEAVRK-GNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKA   79 (249)
Q Consensus         1 ~~~yd~~~~~fsp~G~l~Qveya~kav~~-G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~   79 (249)
                      +.+||+-+|+|||||||+|||||+||+++ |-|.||++++|++|+++.++..++|+++.....+|+|.++|+|+++|..+
T Consensus         6 ~agfDrhitIFspeGrLyQVEYafkAin~~gltsVavrgkDcavvvsqKkvpDKLld~~tvt~~f~itk~ig~v~tG~~a   85 (246)
T KOG0182|consen    6 SAGFDRHITIFSPEGRLYQVEYAFKAINQAGLTSVAVRGKDCAVVVTQKKVPDKLLDSSTVTHLFRITKKIGCVITGMIA   85 (246)
T ss_pred             cCCccceEEEECCCceEEeeehHHHHhhcCCCceEEEcCCceEEEEecccCcccccccccceeEEEeeccceEEEecCCc
Confidence            56899999999999999999999999988 78999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccc
Q 025716           80 DARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWK  159 (249)
Q Consensus        80 D~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~  159 (249)
                      |++..++++|.+|.++++.||++||++.||++++++.|.|||...+||+||.+++.|+|+ +.||.+|.+||.|-+..++
T Consensus        86 Dar~~v~rar~eAa~~~yk~Gyemp~DiL~k~~Ad~~QvytQ~a~mRplg~~~~~i~~D~-E~gP~vYk~DpAGyy~g~k  164 (246)
T KOG0182|consen   86 DARSQVQRARYEAAEFRYKYGYEMPCDILAKRMADKSQVYTQNAAMRPLGVAATLIGVDE-ERGPSVYKTDPAGYYYGFK  164 (246)
T ss_pred             chHHHHHHHHHHHHhhhhhcCCCCCHHHHHHHHhhHHHHHhhhhhhcccceeEEEEEecc-ccCcceEeecCccccccce
Confidence            999999999999999999999999999999999999999999999999999999999998 7899999999999999999


Q ss_pred             eEeecCCchHHHHHHHhhhccC--Cc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEEcC-CCEEEcCHHHHHHHHHHHHH
Q 025716          160 ANATGRNSNSMREFLEKNYKET--SG-QETIKLAIRALLEVVES--GGKNIEVAVMTRE-KGLKQLDEAEIDAMVAEIEA  233 (249)
Q Consensus       160 ~~aiG~g~~~a~~~Le~~~~~~--~s-eeai~la~~~l~~~~~~--~~~~iei~~v~~~-g~~~~~~~~ei~~~l~~i~~  233 (249)
                      +++.|.....+.++|||+|+++  ++ +|++++++.||..++..  ....+||++++++ +.|++|+.+||++.|..|++
T Consensus       165 AtaaG~Kq~e~tsfLEKk~Kk~~~~t~~e~ve~ai~al~~sl~~Dfk~se~EVgvv~~~~p~f~~Ls~~eie~hL~~IAE  244 (246)
T KOG0182|consen  165 ATAAGVKQQEATSFLEKKYKKDIDLTFEETVETAISALQSSLGIDFKSSELEVGVVTVDNPEFRILSAEEIEEHLQAIAE  244 (246)
T ss_pred             eeecccchhhHHHHHHHhhccCccchHHHHHHHHHHHHHHHHhcccCCcceEEEEEEcCCcceeeccHHHHHHHHHHhhh
Confidence            9999999999999999999987  67 99999999999999864  4678999999985 45999999999999999987


Q ss_pred             H
Q 025716          234 K  234 (249)
Q Consensus       234 ~  234 (249)
                      .
T Consensus       245 k  245 (246)
T KOG0182|consen  245 K  245 (246)
T ss_pred             c
Confidence            5

>cd03753 proteasome_alpha_type_5 proteasome_alpha_type_5

Probab=100.00  E-value=6.7e-55  Score=368.42  Aligned_cols=205  Identities=43%  Similarity=0.735  Sum_probs=194.4

Q ss_pred             CCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHHH
Q 025716            4 YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARV   83 (249)
Q Consensus         4 yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~   83 (249)
                      ||+++|+|||||||+|||||++|+++|+|+|||+++||||||+|++.++.+...++.+||+.|++|++|+++|+.+|++.
T Consensus         1 ~~~~~~~f~p~G~~~Q~eya~~a~~~G~t~igik~~dgVvlaad~r~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~   80 (213)
T cd03753           1 YDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIKTKEGVVLAVEKRITSPLMEPSSVEKIMEIDDHIGCAMSGLIADART   80 (213)
T ss_pred             CCCCCccCCCCCeEhHHHHHHHHHhcCCCEEEEEeCCEEEEEEecccCCcCcCCCccceEEEEcCCEEEEEecCHHHHHH
Confidence            89999999999999999999999999999999999999999999999887777778999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccC-----CCccceeEEEEEeeeCCCCCceEEEECCCCceecc
Q 025716           84 LINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG-----GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAW  158 (249)
Q Consensus        84 l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~-----~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~  158 (249)
                      +.+.+|.+++.|++++|++++++.++++++.++|.|++..     +.|||+|++||+|||  ++||+||.+||+|++.++
T Consensus        81 l~~~~r~~~~~~~~~~~~~i~~~~~~~~ls~~~~~~~~~~~~~~~~~rP~~v~~ii~G~D--~~gp~Ly~vd~~G~~~~~  158 (213)
T cd03753          81 LIDHARVEAQNHRFTYNEPMTVESVTQAVSDLALQFGEGDDGKKAMSRPFGVALLIAGVD--ENGPQLFHTDPSGTFTRC  158 (213)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhCcccccccccccceEEEEEEEEc--CCCCEEEEECCCCCeecc
Confidence            9999999999999999999999999999999999998743     469999999999999  478999999999999999


Q ss_pred             ceEeecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEE
Q 025716          159 KANATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES--GGKNIEVAVM  210 (249)
Q Consensus       159 ~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~--~~~~iei~~v  210 (249)
                      +++++|++++.++++|+++|+++|+ +||++++++||+.+.+.  ++.++||+++
T Consensus       159 ~~~a~G~~~~~~~~~L~~~~~~~ls~eeai~l~~~~l~~~~~~~~~~~~~ei~~~  213 (213)
T cd03753         159 DAKAIGSGSEGAQSSLQEKYHKDMTLEEAEKLALSILKQVMEEKLNSTNVELATV  213 (213)
T ss_pred             cEEEECCCcHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHhcccCCCCcEEEEEC
Confidence            9999999999999999999999999 99999999999998764  5778999875

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

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

Probab=100.00  E-value=1.6e-55  Score=358.33  Aligned_cols=222  Identities=34%  Similarity=0.508  Sum_probs=208.5

Q ss_pred             CCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHH
Q 025716            3 RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADAR   82 (249)
Q Consensus         3 ~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~   82 (249)
                      |||++.++||||||+||+|||+||+.+|+|+|||||+|||||++|+..+++|..+....||+.|++||+|+++|+.+|.+
T Consensus         7 GyDls~s~fSpdGrvfQveYA~KAven~~T~IGIk~kdGVVl~vEKli~SkLy~p~sn~ri~~V~r~iG~avaGl~~Dg~   86 (254)
T KOG0184|consen    7 GYDLSASTFSPDGRVFQVEYAQKAVENSGTCIGIKCKDGVVLAVEKLITSKLYEPGSNERIFSVDRHIGMAVAGLIPDGR   86 (254)
T ss_pred             cccccceeeCCCCceehHHHHHHHHhcCCcEEEEecCCeEEEEEeeeecccccccCCCCceEeecccccEEEeccccchH
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEe
Q 025716           83 VLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANA  162 (249)
Q Consensus        83 ~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~a  162 (249)
                      .++.++|.++.+|+.+|+.++|...++.++++++|.||.++..|||||+.|+++||  ++||+||.++|+|..+.|+++|
T Consensus        87 ~l~~~ar~ea~~~~~~y~~piP~~~la~rva~yvh~~Tly~~vRpfG~~~~~~~yd--~~g~~LymiepSG~~~~Y~~aa  164 (254)
T KOG0184|consen   87 HLVNRARDEAASWRKNYGDPIPGKHLADRVADYVHAFTLYSSVRPFGASTILGSYD--DEGPQLYMIEPSGSSYGYKGAA  164 (254)
T ss_pred             HHHHHHHHHHHHHHHhcCCCCchHHHHHHHHhhhheeehhhccccccceEEEEEEe--CCCceEEEEcCCCCccceeeee
Confidence            99999999999999999999999999999999999999999999999999999999  6899999999999999999999


Q ss_pred             ecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEc--CCCEEEcCHHHHHHH
Q 025716          163 TGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES---GGKNIEVAVMTR--EKGLKQLDEAEIDAM  227 (249)
Q Consensus       163 iG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~--~g~~~~~~~~ei~~~  227 (249)
                      +|.+.+.|++.|||.--.+|+ +|+++.+.+.|..+.+.   ....+|+.|+..  +|..+.++. ||-+.
T Consensus       165 iGKgrq~aKtElEKL~~~~mt~~e~VkeaakIiY~~HDe~KdK~feiEm~wvg~eTnG~h~~vp~-el~~e  234 (254)
T KOG0184|consen  165 IGKGRQAAKTELEKLKIDEMTCKELVKEAAKIIYKVHDENKDKEFEIEMGWVGEETNGLHEKVPS-ELLEE  234 (254)
T ss_pred             ccchhHHHHHHHHhcccccccHHHHHHHHHheeEeecccccCcceEEEEEEEEeecCCccccCcH-HHHHH
Confidence            999999999999999888999 99999999999999875   345789999986  564555555 55443

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

Probab=100.00  E-value=4.3e-55  Score=353.23  Aligned_cols=236  Identities=38%  Similarity=0.630  Sum_probs=221.3

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCccccc-CCcccceEEecCCEEEEEecChhh
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQD-SRSVRKIVSLDNHIALACAGLKAD   80 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~-~~~~~Ki~~I~~~i~~~~sG~~~D   80 (249)
                      .+||.--|+|||||||+|||||++++.+.+|+|||.++|||||+++++.+++|+. +...+||+.|+|||+|+++|+.+|
T Consensus         3 r~ydsrttiFspEGRLyQVEyAmeais~aGt~iGila~DGvvLa~e~k~t~kll~t~~~~EKiY~l~d~iaC~vaGlt~D   82 (249)
T KOG0178|consen    3 RRYDSRTTIFSPEGRLYQVEYAMEAISHAGTCIGILASDGVVLAGENKVTSKLLDTSIPMEKIYKLNDNIACAVAGLTSD   82 (249)
T ss_pred             cCcCCcccccCCCcchHHHHHHHHHHhhhcceeEEEecCceEEEeecccchhhhhccccHHHhhhcCCceEEEEeccccc
Confidence            3589999999999999999999999999999999999999999999999998755 468999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccce
Q 025716           81 ARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKA  160 (249)
Q Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~  160 (249)
                      +..|++++|..+++|.++||+++|++.|++.++++.|.|||++|.||||||+|.+|||. ..|.|||+.||+|++..|++
T Consensus        83 AnvL~n~aRi~AQ~yl~~y~e~iP~eqLv~~lcdiKQayTQygG~RPFGVSfLYaGwd~-~~gyqLy~SdPSGny~gWka  161 (249)
T KOG0178|consen   83 ANVLKNYARIIAQRYLFRYGEEIPCEQLVTFLCDIKQAYTQYGGKRPFGVSFLYAGWDD-RYGYQLYQSDPSGNYGGWKA  161 (249)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHHhhccCcCCCceeeeeeceec-CcceEEEecCCCCCccccce
Confidence            99999999999999999999999999999999999999999999999999999999997 78899999999999999999


Q ss_pred             EeecCCchHHHHHHHhhhccCCc--HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCC---CEEEcCHHHHHHHHHHHH
Q 025716          161 NATGRNSNSMREFLEKNYKETSG--QETIKLAIRALLEVVES---GGKNIEVAVMTREK---GLKQLDEAEIDAMVAEIE  232 (249)
Q Consensus       161 ~aiG~g~~~a~~~Le~~~~~~~s--eeai~la~~~l~~~~~~---~~~~iei~~v~~~g---~~~~~~~~ei~~~l~~i~  232 (249)
                      .++|.++..++..|.+.|+++..  +||..+|++.|...++.   +...+|++.++++.   .++.++++||.++++++.
T Consensus       162 ~ciG~N~~Aa~s~Lkqdykdd~~~~~eA~~laikvL~kt~d~~~lt~eklEia~~~k~~~k~v~~i~~~~ev~kll~k~~  241 (249)
T KOG0178|consen  162 TCIGANSGAAQSMLKQDYKDDENDLEEAKALAIKVLSKTLDSGSLTAEKLEIATITKDCNKTVLKILKKDEVLKLLEKYH  241 (249)
T ss_pred             eeeccchHHHHHHHHhhhccccccHHHHHHHHHHHHHhhcccCCCChhheEEEEEEecCCceEEEecCHHHHHHHHHHhh
Confidence            99999999999999999997654  99999999999999876   46789999999853   467899999999999998


Q ss_pred             HHHHHH
Q 025716          233 AKKAAA  238 (249)
Q Consensus       233 ~~~~~~  238 (249)
                      +.+.++
T Consensus       242 ~~~~~~  247 (249)
T KOG0178|consen  242 ETQRQA  247 (249)
T ss_pred             hhhhhc
Confidence            876544

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

Probab=100.00  E-value=5.5e-49  Score=321.67  Aligned_cols=226  Identities=36%  Similarity=0.593  Sum_probs=213.6

Q ss_pred             CCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHHH
Q 025716            4 YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARV   83 (249)
Q Consensus         4 yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~   83 (249)
                      ||..+|+|||+|||+|||||++|++.|++.||+|.++..||++-++..+.|-  ..++|||+|++|++++++|+++|++.
T Consensus         6 yd~d~t~wsPqGrl~QvEya~EavkqGsatVGLks~thaVLvAl~r~~seLs--s~QkKi~~iD~h~g~siAGLt~Darv   83 (264)
T KOG0863|consen    6 YDNDVTTWSPQGRLHQVEYAMEAVKQGSATVGLKSRTHAVLVALKRAQSELS--SHQKKIFKIDDHIGISIAGLTADARV   83 (264)
T ss_pred             ccCceeEECCcceehHHHHHHHHHhcccceEeecccceEEEeeeccchhHHH--HhhheeEecccccceEEeccCcchHH
Confidence            8999999999999999999999999999999999999999999988777653  36899999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEee
Q 025716           84 LINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANAT  163 (249)
Q Consensus        84 l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~ai  163 (249)
                      |.+++|.+|..++..|++++++..|...|.+.+|..||+.+.|||||.++++|||  +.||+||.+.|+|++.++++.+|
T Consensus        84 l~~Ylr~ec~~~~~~~~r~~pv~rl~~~l~~k~q~~Tq~ygrRpYGVGllv~gYD--e~G~hl~e~~Psg~v~e~~g~sI  161 (264)
T KOG0863|consen   84 LSRYLRQECLNSRFIYGRPLPVLRLVEDLGDKAQENTQRYGRRPYGVGLLVAGYD--ESGPHLYEFCPSGNVFECKGMSI  161 (264)
T ss_pred             HHHHHHHHHhhhhhccCCcccHHHHHHHHHHHHhhhhhhhCCccccceEEEEeec--CCCceeEEEcCCccEEEEeeeec
Confidence            9999999999999999999999999999999999999999999999999999999  58999999999999999999999


Q ss_pred             cCCchHHHHHHHhhhc--cCCc-HHHHHHHHHHHHHHHhc----CCCcEEEEEEEcCCCEEEcCHHHHHHHHHHHHH
Q 025716          164 GRNSNSMREFLEKNYK--ETSG-QETIKLAIRALLEVVES----GGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEA  233 (249)
Q Consensus       164 G~g~~~a~~~Le~~~~--~~~s-eeai~la~~~l~~~~~~----~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i~~  233 (249)
                      |+.++.++++||++..  ++++ ||+++.++.||++.+..    +..+++|+|+.+|..|..++.+++.+++.....
T Consensus       162 GsRSQsARTyLEr~~e~f~~~~~eELI~~gi~Alr~tlp~de~lt~~nvsI~Ivgkd~pf~~~d~~~~~k~~~~~~~  238 (264)
T KOG0863|consen  162 GSRSQSARTYLERNLEEFEDSSPEELIKHGIMALRETLPEDEDLTGENVSIAIVGKDEPFTILDQKDVAKYVDLFKK  238 (264)
T ss_pred             ccchhhHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhcCcccccccceeEEEEEeCCCceEeecHHHHHHHHHHhhc
Confidence            9999999999999876  4788 99999999999999863    467999999999988999999999998887764

>TIGR03691 20S_bact_alpha proteasome, alpha subunit, bacterial type

Probab=100.00  E-value=1.9e-46  Score=319.01  Aligned_cols=201  Identities=18%  Similarity=0.262  Sum_probs=184.2

Q ss_pred             hhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhc
Q 025716           20 VEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTV   99 (249)
Q Consensus        20 veya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~   99 (249)
                      -|||++|+++|+|+|||+++||||||+|++.       ++.+|||.|++|++|+++|+.+|++.++++++.++..|++++
T Consensus        17 ~EYA~kav~~g~T~VGIk~kdgVVLaaek~~-------~~~~KI~~I~d~ig~~~sG~~~D~~~lv~~~r~~a~~~~~~~   89 (228)
T TIGR03691        17 AELARKGIARGRSVVVLTYADGILFVAENPS-------RSLHKISELYDRIGFAAVGKYNEFENLRRAGIRYADMRGYSY   89 (228)
T ss_pred             HHHHHHHHHcCCcEEEEEeCCeEEEEEecCC-------CCcCcEEEecCCEEEEEcCCHHHHHHHHHHHHHHHHHHhhhc
Confidence            4999999999999999999999999999973       358899999999999999999999999999999999999999


Q ss_pred             C-CCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccc-eEeecCCchHHHHHHHhh
Q 025716          100 E-DPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWK-ANATGRNSNSMREFLEKN  177 (249)
Q Consensus       100 ~-~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~-~~aiG~g~~~a~~~Le~~  177 (249)
                      + .+++++.+++++++.++.++ +++.|||+|++|++|||+.+.||+||.+||+|++.+++ ++|+|++++.++++||++
T Consensus        90 ~~~~~~v~~la~~~tq~~~~~~-~~~~RP~gvs~Li~G~d~~~~gp~Ly~vDpsG~~~~~~~~~aiG~gs~~a~~~Lek~  168 (228)
T TIGR03691        90 DRRDVTGRGLANAYAQTLGTIF-TEQQKPYEVEICVAEVGETPDQDQLYRITFDGSIVDERGFVVMGGTTEPIATALKES  168 (228)
T ss_pred             CCCCccHHHHHHHHHhhccccc-ccccCcceEEEEEEEEcCCCCCCEEEEECCCCCceeccceEEECCChHHHHHHHHHh
Confidence            8 78999999998888887666 56789999999999998424689999999999999976 899999999999999999


Q ss_pred             hccCCc-HHHHHHHHHHHHHHHh-----cCCCcEEEEEEEcC---CCEEEcCHHHHHHHH
Q 025716          178 YKETSG-QETIKLAIRALLEVVE-----SGGKNIEVAVMTRE---KGLKQLDEAEIDAMV  228 (249)
Q Consensus       178 ~~~~~s-eeai~la~~~l~~~~~-----~~~~~iei~~v~~~---g~~~~~~~~ei~~~l  228 (249)
                      |+++|| +||++++++||..+.+     .++.+|||++++++   +.|+.++++||+++|
T Consensus       169 y~~~ms~eeai~la~~aL~~~~~~~r~~~~~~~iEv~ii~k~~~~~~f~~l~~~ei~~~l  228 (228)
T TIGR03691       169 YRDGLSLADALGLAVQALRAGGNGEKRELDAASLEVAVLDRSRPRRAFRRITGEALERLL  228 (228)
T ss_pred             cCCCCCHHHHHHHHHHHHHHHhccccccCCccceEEEEEeCCCCccceEECCHHHHHhhC
Confidence            999999 9999999999999964     46789999999964   359999999998864

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.

>TIGR03690 20S_bact_beta proteasome, beta subunit, bacterial type

Probab=100.00  E-value=2.9e-45  Score=310.80  Aligned_cols=204  Identities=19%  Similarity=0.314  Sum_probs=188.0

Q ss_pred             cCCcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHH
Q 025716           29 KGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEY  107 (249)
Q Consensus        29 ~G~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~  107 (249)
                      +|+|+|||+++||||||+|++.++ .++.+++.+|||.|++|++|+++|+.+|++.|.+++|.++..|+++++++++++.
T Consensus         1 ~G~T~igi~~kdgVvlaad~r~~~g~~~~~~~~~KI~~i~~~i~~~~sG~~aD~~~l~~~~r~~~~~~~~~~~~~i~~~~   80 (219)
T TIGR03690         1 HGTTIVALTYPGGVLMAGDRRATQGNMIASRDVEKVYPTDEYSAVGIAGTAGLAIELVRLFQVELEHYEKIEGVPLTLDG   80 (219)
T ss_pred             CCcEEEEEEECCEEEEEECCccccCcEEEcCCcceEEEcCCcEEEEecccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHH
Confidence            489999999999999999999987 7888889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCC-ceeccceEeecCCchHHHHHHHhhhccCCc-HH
Q 025716          108 ITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSG-TFSAWKANATGRNSNSMREFLEKNYKETSG-QE  185 (249)
Q Consensus       108 la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G-~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-ee  185 (249)
                      ++++|++++|.+++ ..+|||+|++||||||+.+++|+||.+||+| ++..++++|+|+|+..++++||+.|+++|| +|
T Consensus        81 la~~ls~~~~~~~~-~~~rp~~v~~iiaG~D~~~~~~~Ly~~Dp~G~~~~~~~~~a~G~g~~~a~~~Le~~~~~~ms~ee  159 (219)
T TIGR03690        81 KANRLAAMVRGNLP-AAMQGLAVVPLLAGYDLDAGAGRIFSYDVTGGRYEERGYHAVGSGSVFAKGALKKLYSPDLDEDD  159 (219)
T ss_pred             HHHHHHHHHHhhhh-hccCCceEEEEEEEECCCCCCcEEEEEeCCCCeeecCCeEEEeccHHHHHHHHHhcCCCCcCHHH
Confidence            99999999988874 4589999999999999523689999999999 577889999999999999999999999999 99


Q ss_pred             HHHHHHHHHHHHHhcC---CC--c-----EEEEEEEcCCCEEEcCHHHHHHHHHHHHHH
Q 025716          186 TIKLAIRALLEVVESG---GK--N-----IEVAVMTREKGLKQLDEAEIDAMVAEIEAK  234 (249)
Q Consensus       186 ai~la~~~l~~~~~~~---~~--~-----iei~~v~~~g~~~~~~~~ei~~~l~~i~~~  234 (249)
                      |++++++||..+.+++   ++  .     +||++++++| ++.++++||++++.++.+.
T Consensus       160 ai~l~~~al~~~~~~d~~s~~~~~~~~~~~ei~ii~~~g-~~~l~~~ei~~~~~~~~~~  217 (219)
T TIGR03690       160 ALRVAVEALYDAADDDSATGGPDLVRGIYPTVVVITADG-ARRVPESELEELARAIVES  217 (219)
T ss_pred             HHHHHHHHHHHHHhcccccCCcccccccccEEEEEccCc-eEEcCHHHHHHHHHHHHhc
Confidence            9999999999999853   33  3     3999999888 9999999999999988753

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.

>PTZ00488 Proteasome subunit beta type-5; Provisional

Probab=100.00  E-value=1.5e-44  Score=310.90  Aligned_cols=201  Identities=21%  Similarity=0.330  Sum_probs=187.1

Q ss_pred             HHccCCcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCC
Q 025716           26 AVRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVT  104 (249)
Q Consensus        26 av~~G~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~  104 (249)
                      .+.+|+|+|||+++||||||+|++.+. .++.+++.+||+.|++|++++++|+.+|++.|.+++|.++..|++++|++++
T Consensus        35 ~~~~G~T~IgIk~kdgVvlAaD~r~~~g~li~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~lr~~~~~y~~~~g~~is  114 (247)
T PTZ00488         35 EFAHGTTTLAFKYGGGIIIAVDSKATAGPYIASQSVKKVIEINPTLLGTMAGGAADCSFWERELAMQCRLYELRNGELIS  114 (247)
T ss_pred             ccCCCceEEEEEeCCEEEEEEecCcccCCEEEcCCcCceEEcCCCEEEEeCcCHHHHHHHHHHHHHHHHHHHHHHCCCCC
Confidence            356899999999999999999999886 7777889999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhccCCCcccee--EEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCC
Q 025716          105 VEYITRYIAGLQQKYTQSGGVRPFGL--STLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETS  182 (249)
Q Consensus       105 ~~~la~~ls~~~~~~t~~~~~rP~gv--~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~  182 (249)
                      ++.++++|+++++.+      ||+++  ++||||||  ++||+||++||+|++.+++++++|+|+..++++||+.|+++|
T Consensus       115 v~~la~~ls~~l~~~------R~~~~~v~~iiaG~D--~~gp~Ly~vDp~Gs~~~~~~~a~G~gs~~~~~~Le~~~k~dm  186 (247)
T PTZ00488        115 VAAASKILANIVWNY------KGMGLSMGTMICGWD--KKGPGLFYVDNDGTRLHGNMFSCGSGSTYAYGVLDAGFKWDL  186 (247)
T ss_pred             HHHHHHHHHHHHHhc------CCCCeeEEEEEEEEe--CCCCEEEEEcCCcceeecCCEEEccCHHHHHHHHHhcCcCCC
Confidence            999999999999754      55555  48999999  468999999999999999999999999999999999999999


Q ss_pred             c-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCHHHHHHHHHHHHHHH
Q 025716          183 G-QETIKLAIRALLEVVES---GGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKK  235 (249)
Q Consensus       183 s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i~~~~  235 (249)
                      + +||++++++||+++..+   ++++++|++|+++| ++.++++||++++.++++..
T Consensus       187 s~eEai~l~~kal~~~~~Rd~~sg~~~ei~iI~k~g-~~~l~~~ei~~~l~~~~~~~  242 (247)
T PTZ00488        187 NDEEAQDLGRRAIYHATFRDAYSGGAINLYHMQKDG-WKKISADDCFDLHQKYAAEK  242 (247)
T ss_pred             CHHHHHHHHHHHHHHHHHhccccCCCeEEEEEcCCc-cEECCHHHHHHHHHHHhhhc
Confidence            9 99999999999999874   57899999999998 99999999999999988543

>cd03758 proteasome_beta_type_2 proteasome beta type-2 subunit

Probab=100.00  E-value=2.9e-44  Score=299.13  Aligned_cols=185  Identities=21%  Similarity=0.328  Sum_probs=174.4

Q ss_pred             CcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      +|+|||+++||||||+|++.+. .++.+++.+|||+|++|++++++|..+|++.|.+++|.++..|+++++++++++.++
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            7899999999999999999976 567778999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIK  188 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~  188 (249)
                      +++++++|.|++..  |||+|++||+|||+ +++|+||.+||+|++.+++++|+|+|+.+++++||+.|+++|| +||++
T Consensus        82 ~~l~~~~~~~~~~~--rP~~~~~li~G~d~-~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~ms~eeai~  158 (193)
T cd03758          82 NFTRRELAESLRSR--TPYQVNLLLAGYDK-VEGPSLYYIDYLGTLVKVPYAAHGYGAYFCLSILDRYYKPDMTVEEALE  158 (193)
T ss_pred             HHHHHHHHHHhhcC--CCeEEEEEEEEEcC-CCCcEEEEECCCcceEECCeeEEeecHHHHHHHHHhccCCCCCHHHHHH
Confidence            99999999887653  89999999999996 6899999999999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEc
Q 025716          189 LAIRALLEVVES---GGKNIEVAVMTREKGLKQL  219 (249)
Q Consensus       189 la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~  219 (249)
                      ++++||+.+.++   ++++++|++|+++| ++.+
T Consensus       159 l~~~a~~~~~~rd~~~~~~i~i~ii~~~g-~~~~  191 (193)
T cd03758         159 LMKKCIKELKKRFIINLPNFTVKVVDKDG-IRDL  191 (193)
T ss_pred             HHHHHHHHHHHhccccCCceEEEEEcCCC-eEeC
Confidence            999999999874   57899999999998 6654

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.

>cd03760 proteasome_beta_type_4 proteasome beta type-4 subunit

Probab=100.00  E-value=2.3e-44  Score=300.66  Aligned_cols=187  Identities=18%  Similarity=0.219  Sum_probs=174.6

Q ss_pred             cCCcEEEEEeCCEEEEEEeccCC-cccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHH-HhhhhcCCCCCHH
Q 025716           29 KGNAAVGVRGTDTIVLGVEKKST-VKLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQ-SHRLTVEDPVTVE  106 (249)
Q Consensus        29 ~G~t~igi~~~dgVvla~d~~~~-~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~-~~~~~~~~~i~~~  106 (249)
                      .|+|+|||+++||||||+|++.+ ..++.+++.+|||+|++|++++++|+.+|++.+++++|.++. .|+++++++++++
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            48999999999999999999998 478888889999999999999999999999999999999987 4678899999999


Q ss_pred             HHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhcc--CCc-
Q 025716          107 YITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE--TSG-  183 (249)
Q Consensus       107 ~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~--~~s-  183 (249)
                      .+++++++++  |++++++|||+|++||||||+ +++|+||.+||+|++.+++++|+|+|+.+++++||+.|++  +|| 
T Consensus        81 ~la~~i~~~~--y~~~~~~rP~~v~~iiaG~D~-~~gp~Ly~~D~~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~~~ms~  157 (197)
T cd03760          81 EIHSYLTRVL--YNRRSKMNPLWNTLVVGGVDN-EGEPFLGYVDLLGTAYEDPHVATGFGAYLALPLLREAWEKKPDLTE  157 (197)
T ss_pred             HHHHHHHHHH--HHHhhcCCCceEEEEEEEEcC-CCCEEEEEEcCCccEEECCEeEEccHHHHHHHHHHhhcCCCCCCCH
Confidence            9999999986  788888999999999999995 5899999999999999999999999999999999999999  999 


Q ss_pred             HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEc
Q 025716          184 QETIKLAIRALLEVVES---GGKNIEVAVMTREKGLKQL  219 (249)
Q Consensus       184 eeai~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~  219 (249)
                      +|+++++++||+.+.++   ++++++|++|+++| ++.-
T Consensus       158 eea~~l~~~~l~~~~~rd~~~~~~~~i~ii~~~g-~~~~  195 (197)
T cd03760         158 EEARALIEECMKVLYYRDARSINKYQIAVVTKEG-VEIE  195 (197)
T ss_pred             HHHHHHHHHHHHHHHHhccccCCceEEEEECCCC-EEeC
Confidence            99999999999999874   57899999999998 6553

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

>cd03759 proteasome_beta_type_3 proteasome beta type-3 subunit

Probab=100.00  E-value=1.2e-43  Score=296.00  Aligned_cols=181  Identities=23%  Similarity=0.385  Sum_probs=169.5

Q ss_pred             cCCcEEEEEeCCEEEEEEeccCCccccc-CCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHH
Q 025716           29 KGNAAVGVRGTDTIVLGVEKKSTVKLQD-SRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEY  107 (249)
Q Consensus        29 ~G~t~igi~~~dgVvla~d~~~~~~l~~-~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~  107 (249)
                      +|+|+|||+++||||||+|++.+++++. .++.+|||+|++|++++++|..+|++.+++++|.++..|+++++++++++.
T Consensus         2 ~G~t~igik~~dgVvlaad~~~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~   81 (195)
T cd03759           2 NGGAVVAMAGKDCVAIASDLRLGVQQQTVSTDFQKVFRIGDRLYIGLAGLATDVQTLAQKLRFRVNLYRLREEREIKPKT   81 (195)
T ss_pred             CCceEEEEEcCCEEEEEEccccccCCEeEecCCCeEEEeCCCEEEEccchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHH
Confidence            6999999999999999999999887755 557899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccc-eEeecCCchHHHHHHHhhhccCCc-HH
Q 025716          108 ITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWK-ANATGRNSNSMREFLEKNYKETSG-QE  185 (249)
Q Consensus       108 la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~-~~aiG~g~~~a~~~Le~~~~~~~s-ee  185 (249)
                      +++++++++  |+++  .|||+|++||||||+ +++|+||.+||+|++..+. ++|+|+|++.++++||+.|+++|+ +|
T Consensus        82 la~~l~~~l--y~~r--~~P~~v~~ii~G~D~-~~~p~Ly~~D~~G~~~~~~~~~a~G~g~~~~~~~Le~~~~~~~s~~e  156 (195)
T cd03759          82 FSSLISSLL--YEKR--FGPYFVEPVVAGLDP-DGKPFICTMDLIGCPSIPSDFVVSGTASEQLYGMCESLWRPDMEPDE  156 (195)
T ss_pred             HHHHHHHHH--HHhc--CCCceEEEEEEEEcC-CCCEEEEEEcCCCcccccCCEEEEcccHHHHHHHHHhccCCCCCHHH
Confidence            999999998  5543  589999999999997 6789999999999998887 999999999999999999999999 99


Q ss_pred             HHHHHHHHHHHHHhc---CCCcEEEEEEEcCC
Q 025716          186 TIKLAIRALLEVVES---GGKNIEVAVMTREK  214 (249)
Q Consensus       186 ai~la~~~l~~~~~~---~~~~iei~~v~~~g  214 (249)
                      |++++++||..+..+   ++++++|++|+++|
T Consensus       157 a~~l~~~~l~~~~~rd~~~~~~~~i~ii~~~g  188 (195)
T cd03759         157 LFETISQALLSAVDRDALSGWGAVVYIITKDK  188 (195)
T ss_pred             HHHHHHHHHHHHHhhCcccCCceEEEEEcCCc
Confidence            999999999999874   57899999999998

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

>cd03761 proteasome_beta_type_5 proteasome beta type-5 subunit

Probab=100.00  E-value=2.3e-43  Score=292.56  Aligned_cols=182  Identities=19%  Similarity=0.326  Sum_probs=172.0

Q ss_pred             CcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      +|+|||+++||||||+|++.++ .++.+++.+|||+|++|++++++|+.+|++.|++++|.++..|+++++++++++.++
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            5899999999999999999988 567778899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIK  188 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~  188 (249)
                      +++++++|.+++    .||+|++||||||  ++||+||.+||+|++.+++++++|+|+.+++++||+.|+++|+ +||++
T Consensus        81 ~~ls~~l~~~~~----~~~~v~~li~G~D--~~g~~L~~~dp~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~~s~eea~~  154 (188)
T cd03761          81 KLLSNMLYQYKG----MGLSMGTMICGWD--KTGPGLYYVDSDGTRLKGDLFSVGSGSTYAYGVLDSGYRYDLSVEEAYD  154 (188)
T ss_pred             HHHHHHHHhcCC----CCeEEEEEEEEEe--CCCCEEEEEcCCceEEEcCeEEEcccHHHHHHHHHhcCCCCCCHHHHHH
Confidence            999999998864    4899999999999  5799999999999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEc
Q 025716          189 LAIRALLEVVES---GGKNIEVAVMTREKGLKQL  219 (249)
Q Consensus       189 la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~  219 (249)
                      ++++||..+.++   ++++++|++|+++| ++.+
T Consensus       155 l~~~~l~~~~~rd~~sg~~~~v~ii~~~g-~~~~  187 (188)
T cd03761         155 LARRAIYHATHRDAYSGGNVNLYHVREDG-WRKI  187 (188)
T ss_pred             HHHHHHHHHHHhcccCCCCeEEEEEcCCc-eEEc
Confidence            999999999874   57899999999998 7655

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

>TIGR03634 arc_protsome_B proteasome endopeptidase complex, archaeal, beta subunit

Probab=100.00  E-value=2.2e-42  Score=285.83  Aligned_cols=179  Identities=30%  Similarity=0.498  Sum_probs=170.0

Q ss_pred             CCcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHH
Q 025716           30 GNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYI  108 (249)
Q Consensus        30 G~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l  108 (249)
                      |+|+|||+++||||||+|++.+. .++.+++.+|||+|++|++++++|..+|++.+.++++.++..|+..++++++++.+
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            78999999999999999999885 67777889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHH
Q 025716          109 TRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETI  187 (249)
Q Consensus       109 a~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai  187 (249)
                      ++++++++|.+    +.|||+|++||||||+  +||+||.+||+|++.+++++++|+++.+++++||+.|+++|| +||+
T Consensus        81 a~~l~~~~~~~----~~rP~~v~~ivaG~d~--~g~~Ly~~d~~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~~s~~ea~  154 (185)
T TIGR03634        81 ATLLSNILNSN----RFFPFIVQLLVGGVDE--EGPHLYSLDPAGGIIEDDYTATGSGSPVAYGVLEDEYREDMSVEEAK  154 (185)
T ss_pred             HHHHHHHHHhc----CCCCeEEEEEEEEEeC--CCCEEEEECCCCCeEECCEEEEcCcHHHHHHHHHhcCCCCCCHHHHH
Confidence            99999999765    5799999999999994  689999999999999999999999999999999999999999 9999


Q ss_pred             HHHHHHHHHHHhc---CCCcEEEEEEEcCC
Q 025716          188 KLAIRALLEVVES---GGKNIEVAVMTREK  214 (249)
Q Consensus       188 ~la~~~l~~~~~~---~~~~iei~~v~~~g  214 (249)
                      +++++||+.+.++   ++.+++|++|+++|
T Consensus       155 ~l~~~~l~~~~~r~~~~~~~~~v~ii~~~g  184 (185)
T TIGR03634       155 KLAVRAIKSAIERDVASGNGIDVAVITKDG  184 (185)
T ss_pred             HHHHHHHHHHHHhcccCCCCEEEEEEcCCC
Confidence            9999999999874   57899999999987

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=100.00  E-value=2.8e-42  Score=291.20  Aligned_cols=185  Identities=19%  Similarity=0.370  Sum_probs=171.6

Q ss_pred             HccCCcEEEEEeCCEEEEEEeccCCccc-ccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCH
Q 025716           27 VRKGNAAVGVRGTDTIVLGVEKKSTVKL-QDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTV  105 (249)
Q Consensus        27 v~~G~t~igi~~~dgVvla~d~~~~~~l-~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~  105 (249)
                      +++|+|+|||+++||||||+|++.++++ +..++.+||++|++|++++++|..+|++.+.+++|.+++.|++++|+++++
T Consensus         5 ~~~G~Tvigik~~dgVvlaaD~r~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~~r~~~~~~~~~~g~~i~~   84 (212)
T cd03757           5 TDNGGTVLAIAGNDFAVIAGDTRLSEGYSILSRDSPKIFKLTDKCVLGSSGFQADILALTKRLKARIKMYKYSHNKEMST   84 (212)
T ss_pred             cCCCccEEEEEcCCEEEEEECCccccCCEeEeCCCCeEEEcCCCEEEEccchHHHHHHHHHHHHHHHHHHhHHhCCCCCH
Confidence            3689999999999999999999998866 446789999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhc------
Q 025716          106 EYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK------  179 (249)
Q Consensus       106 ~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~------  179 (249)
                      +.++++++.+++  .+  +.|||+|++||||||+ +++|+||.+||+|++.+++++|+|+|+.+++++||+.|+      
T Consensus        85 ~~la~~ls~~ly--~~--R~~P~~~~~iiaG~D~-~~~p~Ly~~D~~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~~~~~  159 (212)
T cd03757          85 EAIAQLLSTILY--SR--RFFPYYVFNILAGIDE-EGKGVVYSYDPVGSYERETYSAGGSASSLIQPLLDNQVGRKNQNN  159 (212)
T ss_pred             HHHHHHHHHHHH--hh--cCCCeEEEEEEEEEcC-CCCEEEEEEcCccCeeecCEEEEeecHHHHHHHHHHHHHhhccCc
Confidence            999999999984  33  2479999999999996 678999999999999999999999999999999999985      


Q ss_pred             ---cCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCCEE
Q 025716          180 ---ETSG-QETIKLAIRALLEVVES---GGKNIEVAVMTREKGLK  217 (249)
Q Consensus       180 ---~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g~~~  217 (249)
                         ++|| +||++++++||+.+..+   ++++++|++|+++| ++
T Consensus       160 ~~~~~ms~eea~~l~~~~l~~~~~rd~~sg~~i~i~iit~~g-~~  203 (212)
T cd03757         160 VERTPLSLEEAVSLVKDAFTSAAERDIYTGDSLEIVIITKDG-IE  203 (212)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHhCcccCCCEEEEEEcCCC-EE
Confidence               8999 99999999999999874   57899999999998 54

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

>cd03765 proteasome_beta_bacterial Bacterial proteasome, beta subunit

Probab=100.00  E-value=8.3e-42  Score=291.16  Aligned_cols=200  Identities=18%  Similarity=0.210  Sum_probs=174.9

Q ss_pred             CcEEEEEeCCEEEEEEeccCCcccccCCcccceEEec----CCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCC-CCCH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLD----NHIALACAGLKADARVLINRARIECQSHRLTVED-PVTV  105 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~----~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~-~i~~  105 (249)
                      +.+|||+++||||||+|+|.+++++..++.+||++|+    +|++|++||+.+|++.|++++|.+++.|++++|+ ++++
T Consensus         1 ~~~vGIk~kdGVVLaadkr~~~~l~~~~~~~KI~~I~~~~d~~I~~~~sG~~aD~~~l~~~~r~~~~~~~~~~g~~~~~v   80 (236)
T cd03765           1 TYCLGIKLDAGLVFASDSRTNAGVDNISTYRKMFVFSVPGERVIVLLTAGNLATTQAVISLLQRDLEDPEETNLLNAPTM   80 (236)
T ss_pred             CeEEEEEeCCeEEEEEccCccCCCccccccceEEEecCCCCCEEEEEcCCcHHHHHHHHHHHHHHHHhhHHhhCCCCCCH
Confidence            4689999999999999999988876666799999998    8999999999999999999999999999999999 8999


Q ss_pred             HHHHHHHHHHHH-hhhccCC-----CccceeEEEEEeeeCCCCCceEEEECCCCceecc----ceEeecCCchHHHHHHH
Q 025716          106 EYITRYIAGLQQ-KYTQSGG-----VRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAW----KANATGRNSNSMREFLE  175 (249)
Q Consensus       106 ~~la~~ls~~~~-~~t~~~~-----~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~----~~~aiG~g~~~a~~~Le  175 (249)
                      +.+|++++++++ .++++.+     .|||+|++||+|||+ +.||+||.+||+|++.++    +++|+|. +..++++||
T Consensus        81 ~~la~~i~~~l~~~~~q~~~~~~~~~rp~gvslIigG~D~-~~Gp~LY~idpsG~~~e~~a~~~~~AiG~-~~~a~~~Le  158 (236)
T cd03765          81 FDAARYVGETLREVQEQDREALKKAGIDFSASFILGGQIK-GEEPRLFLIYPQGNFIEATPDTPFLQIGE-TKYGKPILD  158 (236)
T ss_pred             HHHHHHHHHHHHHHHhhcccccccCCcceEEEEEEEeEEC-CCCCEEEEECCCCCEEeecCCCceeeeCC-chhhHHHHH
Confidence            999999999864 4566554     489999999999996 678999999999999998    5689996 699999999


Q ss_pred             hhhccCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEc---CHHHHHHHHHHHHH
Q 025716          176 KNYKETSG-QETIKLAIRALLEVVES---GGKNIEVAVMTREKGLKQL---DEAEIDAMVAEIEA  233 (249)
Q Consensus       176 ~~~~~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~---~~~ei~~~l~~i~~  233 (249)
                      ++|+++|| +||++++++||.++..+   ++.+|+|++|+++| ++..   --++=++++.++..
T Consensus       159 k~yk~~ms~eeai~la~~al~~a~~rd~~sg~~iev~vI~k~G-~~~~~~~~~~~~~~~~~~~~~  222 (236)
T cd03765         159 RVITPDTSLEDAAKCALVSMDSTMRSNLSVGPPLDLLVYERDS-LQVGHYRRIEEDDPYFAMIRK  222 (236)
T ss_pred             HhcCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEEECCC-eeeeeeEEecCCCHHHHHHHH
Confidence            99999999 99999999999999975   57899999999998 4331   12223456666654

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

>cd03764 proteasome_beta_archeal Archeal proteasome, beta subunit

Probab=100.00  E-value=8.6e-42  Score=283.08  Aligned_cols=183  Identities=31%  Similarity=0.493  Sum_probs=172.8

Q ss_pred             CcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      +|+|||+++||||||+|++.++ .++.+++.+||++|++|++++++|+.+|++.|.+.++.++..|++.++++++++.++
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            5899999999999999999987 677778999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIK  188 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~  188 (249)
                      +++++.+|.+    +.|||+|++||||||  +++|+||.+||+|++.+++++|+|+|+.+++++|++.|+++|+ +|+++
T Consensus        81 ~~i~~~~~~~----~~~P~~~~~lvaG~d--~~~~~ly~~D~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~~~~ea~~  154 (188)
T cd03764          81 TLLSNILNSS----KYFPYIVQLLIGGVD--EEGPHLYSLDPLGSIIEDKYTATGSGSPYAYGVLEDEYKEDMTVEEAKK  154 (188)
T ss_pred             HHHHHHHHhc----CCCCcEEEEEEEEEe--CCCCEEEEECCCCCEEEcCEEEEcCcHHHHHHHHHhcCCCCCCHHHHHH
Confidence            9999999765    579999999999999  4789999999999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcC
Q 025716          189 LAIRALLEVVES---GGKNIEVAVMTREKGLKQLD  220 (249)
Q Consensus       189 la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~  220 (249)
                      ++++||+.+.++   ++++++|++|+++| +++++
T Consensus       155 l~~~~l~~~~~rd~~~~~~i~i~iv~~~g-~~~~~  188 (188)
T cd03764         155 LAIRAIKSAIERDSASGDGIDVVVITKDG-YKELE  188 (188)
T ss_pred             HHHHHHHHHHhhcCCCCCcEEEEEECCCC-eEeCC
Confidence            999999999874   57899999999998 88764

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

>cd03763 proteasome_beta_type_7 proteasome beta type-7 subunit

Probab=100.00  E-value=2.6e-41  Score=280.45  Aligned_cols=183  Identities=24%  Similarity=0.322  Sum_probs=170.3

Q ss_pred             CcEEEEEeCCEEEEEEeccCCcc-cccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~~-l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      +|+|||+|+||||||+|+|.++. ++.+++.+|||.|++|++++++|..+|++.+.+++|.+++.|+++++++++++.++
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            58999999999999999999884 66677899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIK  188 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~  188 (249)
                      +++++.++.|.     .||+|++||||||  ++||+||.+||.|++.+++++++|+++..++++|+++|+++|| +||++
T Consensus        81 ~~l~~~l~~~~-----~p~~v~~ivaG~d--~~g~~ly~~d~~G~~~~~~~~a~G~~~~~~~~~L~~~~~~~ls~~ea~~  153 (189)
T cd03763          81 TMLKQHLFRYQ-----GHIGAALVLGGVD--YTGPHLYSIYPHGSTDKLPFVTMGSGSLAAMSVLEDRYKPDMTEEEAKK  153 (189)
T ss_pred             HHHHHHHHHcC-----CccceeEEEEeEc--CCCCEEEEECCCCCEEecCEEEEcCCHHHHHHHHHhhcCCCCCHHHHHH
Confidence            99999998653     3999999999999  4689999999999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCH
Q 025716          189 LAIRALLEVVES---GGKNIEVAVMTREKGLKQLDE  221 (249)
Q Consensus       189 la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~  221 (249)
                      ++++||+.+..+   ++++++|++|+++| ++...|
T Consensus       154 l~~~~l~~~~~rd~~~~~~~~v~ii~~~g-~~~~~~  188 (189)
T cd03763         154 LVCEAIEAGIFNDLGSGSNVDLCVITKDG-VEYLRN  188 (189)
T ss_pred             HHHHHHHHHHHhcCcCCCceEEEEEcCCc-EEEecC
Confidence            999999999875   57899999999998 765543

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

>cd03762 proteasome_beta_type_6 proteasome beta type-6 subunit

Probab=100.00  E-value=4e-41  Score=279.06  Aligned_cols=180  Identities=19%  Similarity=0.327  Sum_probs=169.7

Q ss_pred             CcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      +|+|||+++||||||+|++.++ .++.+++.+||++|++|++++++|+.+|++.|.++++.+++.|+.+++++++++.++
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            5899999999999999999988 566777899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIK  188 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~  188 (249)
                      +++++++|.++     |||+|++||||+|+ ++||+||.+||.|++.+++++++|+++..++++|++.|+++|+ +||++
T Consensus        81 ~~l~~~~~~~~-----~~~~~~~ii~G~d~-~~gp~ly~~d~~G~~~~~~~~~~G~g~~~~~~~Le~~~~~~~s~~ea~~  154 (188)
T cd03762          81 SLFKNLCYNYK-----EMLSAGIIVAGWDE-QNGGQVYSIPLGGMLIRQPFAIGGSGSTYIYGYVDANYKPGMTLEECIK  154 (188)
T ss_pred             HHHHHHHHhcc-----ccceeeEEEEEEcC-CCCcEEEEECCCCCEEecCEEEEcccHHHHHHHHHhcCCCCCCHHHHHH
Confidence            99999997654     78999999999996 6789999999999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHhc---CCCcEEEEEEEcCCCEE
Q 025716          189 LAIRALLEVVES---GGKNIEVAVMTREKGLK  217 (249)
Q Consensus       189 la~~~l~~~~~~---~~~~iei~~v~~~g~~~  217 (249)
                      ++++||..+..+   ++++++|++|+++| ++
T Consensus       155 l~~~al~~~~~rd~~~~~~~~i~~i~~~g-~~  185 (188)
T cd03762         155 FVKNALSLAMSRDGSSGGVIRLVIITKDG-VE  185 (188)
T ss_pred             HHHHHHHHHHHhccccCCCEEEEEECCCC-EE
Confidence            999999999985   57899999999998 44

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

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

Probab=100.00  E-value=4.1e-41  Score=278.67  Aligned_cols=183  Identities=40%  Similarity=0.689  Sum_probs=172.3

Q ss_pred             HccCCcEEEEEeCCEEEEEEeccCCc--ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCC
Q 025716           27 VRKGNAAVGVRGTDTIVLGVEKKSTV--KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVT  104 (249)
Q Consensus        27 v~~G~t~igi~~~dgVvla~d~~~~~--~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~  104 (249)
                      |++|+|+|||+++||||||+|++.+.  .+..+.+.+|||+|++|++++++|..+|++.+.++++.++..|++.++.+++
T Consensus         1 v~~G~t~vgi~~~dgvvla~d~~~~~g~~~~~~~~~~ki~~i~~~i~~~~sG~~~D~~~l~~~l~~~~~~~~~~~~~~~~   80 (190)
T PF00227_consen    1 VNNGTTVVGIKGKDGVVLAADKRISYGSKLRSPNTVDKIFKINDNIIIGFSGLTADFQYLIRRLREEAQEYRFSYGRPIS   80 (190)
T ss_dssp             HHTSBEEEEEEESSEEEEEEEEEEEETTEEEESSTSSSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTC
T ss_pred             CCCCeEEEEEEECCEEEEEEccccccccccccccccceeeeccCcceeeccccccchHHHHhhhcccchhhhhccCcccc
Confidence            57999999999999999999999884  4445555799999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceecc-ceEeecCCchHHHHHHHhhhccCCc
Q 025716          105 VEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAW-KANATGRNSNSMREFLEKNYKETSG  183 (249)
Q Consensus       105 ~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~-~~~aiG~g~~~a~~~Le~~~~~~~s  183 (249)
                      ++.+++.++..++.++++.++||++|++|++|||+ +++|+||.+||+|++.++ +++++|+|+..++++|++.|+++|+
T Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~p~~~~~li~G~d~-~~~~~l~~vd~~G~~~~~~~~~aiG~g~~~~~~~l~~~~~~~~~  159 (190)
T PF00227_consen   81 PEYLAKAIASLIQNYTYRSGRRPYGVSLLIAGYDE-DGGPQLYSVDPSGSYIECKRFAAIGSGSQFAQPILEKLYKPDLS  159 (190)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTTSTTSEEEEEEEEET-TTEEEEEEEETTSEEEEBSSEEEESTTHHHHHHHHHHHHTTTSS
T ss_pred             chhhhhhhHHHHhhhcccccccCccccceeeeecc-ccccceeeeccccccccccccccchhcchhhhHHHHhhccCCCC
Confidence            99999999999999999999999999999999997 677999999999999999 6999999999999999999999999


Q ss_pred             -HHHHHHHHHHHHHHHhc---CCCcEEEEEE
Q 025716          184 -QETIKLAIRALLEVVES---GGKNIEVAVM  210 (249)
Q Consensus       184 -eeai~la~~~l~~~~~~---~~~~iei~~v  210 (249)
                       +||++++++||+.+.++   ++++++|++|
T Consensus       160 ~~ea~~~~~~~l~~~~~~d~~~~~~~~v~vi  190 (190)
T PF00227_consen  160 LEEAIELALKALKEAIDRDILSGDNIEVAVI  190 (190)
T ss_dssp             HHHHHHHHHHHHHHHHHHBTTSTSEEEEEEE
T ss_pred             HHHHHHHHHHHHHHHHhhCCccCCeEEEEEC
Confidence             99999999999999874   5889999986

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

>cd01912 proteasome_beta proteasome beta subunit

Probab=100.00  E-value=1.5e-40  Score=275.51  Aligned_cols=182  Identities=26%  Similarity=0.425  Sum_probs=171.1

Q ss_pred             CcEEEEEeCCEEEEEEeccCCccccc-CCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTVKLQD-SRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~~l~~-~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      +|+|||+++||||||+|++.++++.. +++.+|||+|+++++++++|+.+|++.+.++++.++..|++.++++++++.++
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            58999999999999999999987654 78899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIK  188 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~  188 (249)
                      ++++++++.+++    |||+|++||||+|+ +++|+||.+||+|++.+++++++|.++..++++|++.|+++|+ +||++
T Consensus        81 ~~l~~~~~~~~~----~P~~~~~iv~G~d~-~~~~~l~~id~~G~~~~~~~~a~G~~~~~~~~~Le~~~~~~~s~~ea~~  155 (189)
T cd01912          81 NLLSNILYSYRG----FPYYVSLIVGGVDK-GGGPFLYYVDPLGSLIEAPFVATGSGSKYAYGILDRGYKPDMTLEEAVE  155 (189)
T ss_pred             HHHHHHHHhcCC----CCeEEEEEEEEEcC-CCCeEEEEECCCCCeEecCEEEEcccHHHHHHHHHhccCCCCCHHHHHH
Confidence            999999987764    89999999999996 5899999999999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHhc---CCCcEEEEEEEcCCCEEE
Q 025716          189 LAIRALLEVVES---GGKNIEVAVMTREKGLKQ  218 (249)
Q Consensus       189 la~~~l~~~~~~---~~~~iei~~v~~~g~~~~  218 (249)
                      ++++||+.+.++   ++.+++|++|+++| ++.
T Consensus       156 ~~~~~l~~~~~~d~~~~~~~~v~vi~~~g-~~~  187 (189)
T cd01912         156 LVKKAIDSAIERDLSSGGGVDVAVITKDG-VEE  187 (189)
T ss_pred             HHHHHHHHHHHhcCccCCcEEEEEECCCC-EEE
Confidence            999999998874   57899999999998 543

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=100.00  E-value=1.6e-39  Score=267.37  Aligned_cols=177  Identities=44%  Similarity=0.680  Sum_probs=167.0

Q ss_pred             CcEEEEEeCCEEEEEEeccCCccccc-CCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTVKLQD-SRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~~l~~-~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      +|+|||+++||||||+|++.++.+.. +++.+|||.|+++++++++|..+|++.+.+.++.++..|++.++++++++.++
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            58999999999999999999886544 77899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIK  188 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~  188 (249)
                      +++++++|.+++.  .|||++++|++|+|+ +++|+||.+||+|++.+++++++|+++..++++|++.|+++|+ +|+++
T Consensus        81 ~~l~~~~~~~~~~--~~p~~~~~lv~G~d~-~~~~~Ly~id~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~  157 (182)
T cd01906          81 KLLANLLYEYTQS--LRPLGVSLLVAGVDE-EGGPQLYSVDPSGSYIEYKATAIGSGSQYALGILEKLYKPDMTLEEAIE  157 (182)
T ss_pred             HHHHHHHHHhCCC--ccChheEEEEEEEeC-CCCcEEEEECCCCCEeeccEEEECCCcHHHHHHHHHHccCCCCHHHHHH
Confidence            9999999999876  799999999999996 5899999999999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHhc---CCCcEEEEEE
Q 025716          189 LAIRALLEVVES---GGKNIEVAVM  210 (249)
Q Consensus       189 la~~~l~~~~~~---~~~~iei~~v  210 (249)
                      ++++||..+.++   .+.+++|+++
T Consensus       158 l~~~~l~~~~~~~~~~~~~~~i~ii  182 (182)
T cd01906         158 LALKALKSALERDLYSGGNIEVAVI  182 (182)
T ss_pred             HHHHHHHHHHcccCCCCCCEEEEEC
Confidence            999999999875   4678999875

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

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

Probab=100.00  E-value=3e-37  Score=246.06  Aligned_cols=187  Identities=20%  Similarity=0.316  Sum_probs=175.1

Q ss_pred             CCcEEEEEeCCEEEEEEeccCCcc-cccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHH
Q 025716           30 GNAAVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYI  108 (249)
Q Consensus        30 G~t~igi~~~dgVvla~d~~~~~~-l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l  108 (249)
                      +.+++||++.|+|++|+|+..... ++.+++.+|++++++++.|+++|..+|+.++.+++.+.++.|+.++|.++||+..
T Consensus         1 Me~llGIkg~dfvilAsDt~~~~si~~~k~~~dK~~~ls~~~lm~~~Ge~GDt~qF~eyi~~Ni~LYkirnGyeLSp~~a   80 (200)
T KOG0177|consen    1 METLLGIKGPDFVILASDTSAARSILVLKDDHDKIHRLSDHILMATVGEAGDTVQFTEYIQKNIQLYKIRNGYELSPSAA   80 (200)
T ss_pred             CceEEEeecCCEEEEeecchhhcceEEecccccceEEeccceeeeeecCCCceehHHHHHHhhhhHHhhhcCCcCCHHHH
Confidence            467999999999999999987664 5678899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHH
Q 025716          109 TRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETI  187 (249)
Q Consensus       109 a~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai  187 (249)
                      |+++++.+..+.++  .+||-|++|+||+|+ +.||.||++|..|+..+.++++.|.++.++.++|++.|+|+|| +||+
T Consensus        81 ahFtR~~La~~LRs--r~~yqV~~LvaGYd~-~~gp~L~~iDyla~~~~vpy~~hGy~~~f~~sIlDr~Y~pdmt~eea~  157 (200)
T KOG0177|consen   81 AHFTRRELAESLRS--RTPYQVNILVAGYDP-EEGPELYYIDYLATLVSVPYAAHGYGSYFCLSILDRYYKPDMTIEEAL  157 (200)
T ss_pred             HHHHHHHHHHHHhc--CCCceEEEEEeccCC-CCCCceeeehhhhhcccCCcccccchhhhhHHHHHhhhCCCCCHHHHH
Confidence            99999999999863  489999999999999 7789999999999999999999999999999999999999999 9999


Q ss_pred             HHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcC
Q 025716          188 KLAIRALLEVVES---GGKNIEVAVMTREKGLKQLD  220 (249)
Q Consensus       188 ~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~  220 (249)
                      .+..+|+.++.++   +..+|.|.+|+||| .+.++
T Consensus       158 ~lmkKCv~El~kRlvin~~~f~v~IVdkdG-ir~~~  192 (200)
T KOG0177|consen  158 DLMKKCVLELKKRLVINLPGFIVKIVDKDG-IRKLD  192 (200)
T ss_pred             HHHHHHHHHHHHhcccCCCCcEEEEEcCCC-ceecc
Confidence            9999999998765   78899999999999 66554

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

Probab=100.00  E-value=9.9e-32  Score=217.48  Aligned_cols=182  Identities=19%  Similarity=0.385  Sum_probs=169.8

Q ss_pred             ccCCcEEEEEeCCEEEEEEeccCCccc-ccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHH
Q 025716           28 RKGNAAVGVRGTDTIVLGVEKKSTVKL-QDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVE  106 (249)
Q Consensus        28 ~~G~t~igi~~~dgVvla~d~~~~~~l-~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~  106 (249)
                      .||+|+|||.+.|+.|+|+|+|.++.+ +.+++.+|||+++|+++++.+|+.+|+..|...++...+.|+..++..|++.
T Consensus        27 ~NGGT~vaIaG~dFavvA~DTR~s~gy~I~sR~~~Ki~~l~D~~vl~~sGF~aD~l~L~k~i~~r~~~Y~~~h~k~ms~~  106 (235)
T KOG0179|consen   27 DNGGTTVAIAGEDFAVVAGDTRMSSGYNINSRDQSKIFKLGDNIVLGSSGFYADTLALVKVIKSRIKQYEHDHNKKMSIH  106 (235)
T ss_pred             cCCceEEEEcCCceEEEecccccccceeeeccccchheeccCceEEecccchhhHHHHHHHHHHHHHHHhhcccccccHH
Confidence            689999999999999999999998854 6789999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhc-------
Q 025716          107 YITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK-------  179 (249)
Q Consensus       107 ~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~-------  179 (249)
                      ..|++|+.+++  .  .++.||.+..||+|+|+ ++++.+|..||-|++.+..+.|.|+++..++++|+.+..       
T Consensus       107 s~A~lls~~LY--~--kRFFPYYv~~ilaGiDe-eGKG~VySyDPvGsyer~~~~AgGsa~~mI~PfLDnQi~~kn~~~e  181 (235)
T KOG0179|consen  107 SAAQLLSTILY--S--KRFFPYYVFNILAGIDE-EGKGAVYSYDPVGSYERVTCRAGGSAASMIQPFLDNQIGHKNQNLE  181 (235)
T ss_pred             HHHHHHHHHHh--h--cccccceeeeeeecccc-cCceeEEeecCCcceeeeeeecCCcchhhhhhhhhhhccCcCcccc
Confidence            99999999994  3  36789999999999997 789999999999999999999999999999999998643       


Q ss_pred             ----cCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCC
Q 025716          180 ----ETSG-QETIKLAIRALLEVVES---GGKNIEVAVMTREK  214 (249)
Q Consensus       180 ----~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g  214 (249)
                          ..|+ |+|++++..++..+.++   .+++++|+|++++|
T Consensus       182 ~~~~~~Ls~e~ai~lv~d~F~SAaERdI~tGD~l~i~I~tk~g  224 (235)
T KOG0179|consen  182 NAERTPLSLERAIRLVKDAFTSAAERDIYTGDKLEICIITKDG  224 (235)
T ss_pred             cCcccccCHHHHHHHHHHHhhhhhhcccccCCcEEEEEEecCC
Confidence                3578 99999999999999886   58899999999998

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

Probab=100.00  E-value=3.1e-32  Score=226.40  Aligned_cols=201  Identities=17%  Similarity=0.318  Sum_probs=186.4

Q ss_pred             HccCCcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCH
Q 025716           27 VRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTV  105 (249)
Q Consensus        27 v~~G~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~  105 (249)
                      ..+|||.+|++++.|||+|+|+|.+. .++.+...+||.+|+++..-+.+|-++|+++.-+.+.++|++|++++++-|+|
T Consensus        68 ~~hGTTTLAF~f~~GvivAvDSRAs~G~YIasqtv~KVIeIn~ylLGTmAGgAADCqfWer~L~kecRL~eLRnkeriSV  147 (285)
T KOG0175|consen   68 FAHGTTTLAFKFKGGVIVAVDSRASAGSYIASQTVKKVIEINPYLLGTMAGGAADCQFWERVLAKECRLHELRNKERISV  147 (285)
T ss_pred             ecCCceEEEEEecCcEEEEEeccccccceeechhhceeeeechhhhhcccCcchhhHHHHHHHHHHHHHHHHhcCcceeh
Confidence            36899999999999999999999998 57788899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-H
Q 025716          106 EYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-Q  184 (249)
Q Consensus       106 ~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-e  184 (249)
                      ...++.|+++++.|...    -+.+.++|||||  +.||.||++|..|+...-+-.++|+|+.+|.+.|+..|+++|+ +
T Consensus       148 saASKllsN~~y~YkGm----GLsmGtMi~G~D--k~GP~lyYVDseG~Rl~G~~FSVGSGs~yAYGVLDsgYr~dls~e  221 (285)
T KOG0175|consen  148 SAASKLLSNMVYQYKGM----GLSMGTMIAGWD--KKGPGLYYVDSEGTRLSGDLFSVGSGSTYAYGVLDSGYRYDLSDE  221 (285)
T ss_pred             HHHHHHHHHHHhhccCc----chhheeeEeecc--CCCCceEEEcCCCCEecCceEeecCCCceeEEeeccCCCCCCCHH
Confidence            99999999999887643    377888999999  6899999999999999999999999999999999999999999 9


Q ss_pred             HHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCHHHHHHHHHHHHHH
Q 025716          185 ETIKLAIRALLEVVES---GGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAK  234 (249)
Q Consensus       185 eai~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i~~~  234 (249)
                      ||.+|+++++..+..+   ++..+.++.|+++| +..++..++.++..++.+.
T Consensus       222 EA~~L~rrAI~hAThRDaySGG~vnlyHv~edG-W~~v~~~Dv~~L~~~~~e~  273 (285)
T KOG0175|consen  222 EAYDLARRAIYHATHRDAYSGGVVNLYHVKEDG-WVKVSNTDVSELHYHYYEV  273 (285)
T ss_pred             HHHHHHHHHHHHHHhcccccCceEEEEEECCcc-ceecCCccHHHHHHHHHHh
Confidence            9999999999988755   47789999999999 9999999999997777653

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

Probab=99.97  E-value=4e-31  Score=219.33  Aligned_cols=182  Identities=25%  Similarity=0.359  Sum_probs=167.5

Q ss_pred             HHccCCcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCC
Q 025716           26 AVRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVT  104 (249)
Q Consensus        26 av~~G~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~  104 (249)
                      +.+.|+|++|+.++||||+++|+|.+. .++..++.+||+.|.++|+||.+|..+|...+.+-+..+.++|.++.++.+.
T Consensus        33 ~tkTGTtIvgv~~k~gvIlgADtRaT~G~IvaDKnC~KIH~ia~~IyccGAGtAADte~vt~m~ss~l~Lh~l~t~R~~r  112 (271)
T KOG0173|consen   33 ATKTGTTIVGVIFKDGVILGADTRATEGPIVADKNCEKIHFIAPNIYCCGAGTAADTEMVTRMISSNLELHRLNTGRKPR  112 (271)
T ss_pred             ccccCcEEEEEEeCCeEEEeecccccCCCeeecchhHHHhhcccceEEccCCchhhHHHHHHHHHHHHHHHHhccCCCCc
Confidence            346799999999999999999999998 5667789999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-
Q 025716          105 VEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-  183 (249)
Q Consensus       105 ~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-  183 (249)
                      +-..-+++.+.+..|..     -.|+.+||+|+|  ..|||||.+-|.|+...-+|.++|+|+..++++||.+|+++|+ 
T Consensus       113 Vv~A~~mlkQ~LFrYqG-----~IgA~LiiGGvD--~TGpHLy~i~phGStd~~Pf~alGSGslaAmsvlEsr~k~dlt~  185 (271)
T KOG0173|consen  113 VVTALRMLKQHLFRYQG-----HIGAALILGGVD--PTGPHLYSIHPHGSTDKLPFTALGSGSLAAMSVLESRWKPDLTK  185 (271)
T ss_pred             eeeHHHHHHHHHHHhcC-----cccceeEEcccc--CCCCceEEEcCCCCcCccceeeeccchHHHHHHHHHhcCcccCH
Confidence            99888899998877653     478999999999  5899999999999999999999999999999999999999999 


Q ss_pred             HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCC
Q 025716          184 QETIKLAIRALLEVVES---GGKNIEVAVMTREK  214 (249)
Q Consensus       184 eeai~la~~~l~~~~~~---~~~~iei~~v~~~g  214 (249)
                      |||++|+.+|+..-+--   ++.|+++++|++.+
T Consensus       186 eea~~Lv~eAi~AGi~nDLgSGsnvdlcVI~~~~  219 (271)
T KOG0173|consen  186 EEAIKLVCEAIAAGIFNDLGSGSNVDLCVITKKG  219 (271)
T ss_pred             HHHHHHHHHHHHhhhccccCCCCceeEEEEeCCC
Confidence            99999999999987632   57899999999764

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

Probab=99.97  E-value=3.1e-31  Score=212.33  Aligned_cols=197  Identities=15%  Similarity=0.277  Sum_probs=178.4

Q ss_pred             HHccCCcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCC
Q 025716           26 AVRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVT  104 (249)
Q Consensus        26 av~~G~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~  104 (249)
                      .+..|+|++|+++++||||++|.|.+. .++.++-.+|+.+|.|||+||-||..+|.|.+.+.++..+..|..+++.+++
T Consensus        15 evstGTTImAv~y~gGVvlGaDSRTs~GayvanRvtDKlT~itD~i~cCRSGSAADtQaiaD~~~Y~L~~~~~q~~~~p~   94 (224)
T KOG0174|consen   15 EVSTGTTIMAVEYDGGVVLGADSRTSTGAYVANRVTDKLTPITDNIYCCRSGSAADTQAIADIVRYHLELYTIQENKPPL   94 (224)
T ss_pred             ccccCceEEEEEEcCcEEEeccCCccchHHHHhhhcccceeccccEEEecCCchhhHHHHHHHHHHHHHHhhhhcCCCch
Confidence            467999999999999999999999988 4677888999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-
Q 025716          105 VEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-  183 (249)
Q Consensus       105 ~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-  183 (249)
                      +...|+.++++.++|..     -+.+.+||||||+ +.|.++|.+.-.|+..+-++..-|+|+.+++++++.+|+++|+ 
T Consensus        95 v~~aA~l~r~~~Y~~re-----~L~AgliVAGwD~-~~gGqVY~iplGG~l~rq~~aIgGSGStfIYGf~D~~~r~nMt~  168 (224)
T KOG0174|consen   95 VHTAASLFREICYNYRE-----MLSAGLIVAGWDE-KEGGQVYSIPLGGSLTRQPFAIGGSGSTFIYGFCDANWRPNMTL  168 (224)
T ss_pred             HHHHHHHHHHHHHhCHH-----hhhcceEEeeccc-ccCceEEEeecCceEeecceeeccCCceeeeeeehhhcCCCCCH
Confidence            99999999999976642     3778999999998 8899999999999999999999999999999999999999999 


Q ss_pred             HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCCE-EEcCHHHHHHHH
Q 025716          184 QETIKLAIRALLEVVES---GGKNIEVAVMTREKGL-KQLDEAEIDAMV  228 (249)
Q Consensus       184 eeai~la~~~l~~~~~~---~~~~iei~~v~~~g~~-~~~~~~ei~~~l  228 (249)
                      ||++.+.++|+.-++.+   ++..|.+.+|+++|.- +.+.++++.++.
T Consensus       169 EE~~~fvk~Av~lAi~rDGsSGGviR~~~I~~~Gver~~~~~d~~~~~~  217 (224)
T KOG0174|consen  169 EECVRFVKNAVSLAIERDGSSGGVIRLVIINKAGVERRFFPGDKLGQFA  217 (224)
T ss_pred             HHHHHHHHHHHHHHHhccCCCCCEEEEEEEccCCceEEEecCCcccccc
Confidence            99999999999999876   4678999999999933 356677665543

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

Probab=99.97  E-value=6.4e-31  Score=216.10  Aligned_cols=212  Identities=18%  Similarity=0.255  Sum_probs=184.0

Q ss_pred             CcccCCCCcchhhhhHHH--------HHccCCcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecCh
Q 025716            8 ITVFSPDGHLFQVEYALE--------AVRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLK   78 (249)
Q Consensus         8 ~~~fsp~G~l~Qveya~k--------av~~G~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~   78 (249)
                      .++|.|.|..  ++-|..        ++-.|++|||+|++||||+|+|+..+. .+...++.+|+++++||+.+++||..
T Consensus        13 ~~~f~~~~~~--m~~a~~~~~qrt~~p~vTGTSVla~ky~~GVviaaD~lgSYGslaR~~nVeRi~kVgdntllG~sGdi   90 (256)
T KOG0185|consen   13 PGTFYPSGSL--MENAGDYPIQRTLNPIVTGTSVLALKYKDGVVIAADTLGSYGSLARYKNVERIFKVGDNTLLGASGDI   90 (256)
T ss_pred             CCcCcCccch--hhhccCCCcccccCceeccceEEEEEecCceEEEecccccchhhhhhcCceeeEEecCceEEecCccH
Confidence            5678888653  344433        344799999999999999999999988 67777899999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHhh-hhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceec
Q 025716           79 ADARVLINRARIECQSHR-LTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSA  157 (249)
Q Consensus        79 ~D~~~l~~~~~~~~~~~~-~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~  157 (249)
                      +|.|.|.+.+.....+.+ +--|+.+.|+.++.+|++.+  |.+++.+.|+...++|+|+|. ++.|.|-.+|-.|...+
T Consensus        91 sD~Q~i~r~L~~l~iedn~~~Dg~~l~Pk~ih~yltrvl--Y~rRsKmnPlwntlvVgGv~~-~g~~~lg~V~~~G~~Y~  167 (256)
T KOG0185|consen   91 SDFQYIQRVLEQLVIEDNRLDDGQSLGPKAIHSYLTRVL--YARRSKMNPLWNTLVVGGVDN-TGEPFLGYVDLLGVAYE  167 (256)
T ss_pred             HHHHHHHHHHHHHHhcccccccccccChHHHHHHHHHHH--HHhhhccCchhhheeEeeecC-CCCeeEEEEeecccccc
Confidence            999999999988776643 44569999999999999999  667889999999999999996 68899999999999999


Q ss_pred             cceEeecCCchHHHHHHHhhhc---cCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCHHHHH
Q 025716          158 WKANATGRNSNSMREFLEKNYK---ETSG-QETIKLAIRALLEVVES---GGKNIEVAVMTREKGLKQLDEAEID  225 (249)
Q Consensus       158 ~~~~aiG~g~~~a~~~Le~~~~---~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~~ei~  225 (249)
                      .+..|+|.|..+|.++|++.|.   ++++ +||..++.+|++.++.+   +.++|+|++|+++| +..-.|.+|+
T Consensus       168 ~~~vATGfg~hLa~P~lR~~~~~k~~~~s~eeA~~li~~cMrVL~YRD~ra~n~fqva~v~~eG-v~i~~p~qv~  241 (256)
T KOG0185|consen  168 SPVVATGFGAHLALPLLRDEWEKKGEDLSREEAEALIEKCMRVLYYRDARASNEFQVATVDEEG-VTISKPYQVK  241 (256)
T ss_pred             CchhhhhhHHHhhhHHHHHhhhccchhhHHHHHHHHHHHHHHHHhccccccccceEEEEEcccc-eEecCceeee
Confidence            9999999999999999999997   4678 99999999999999876   46689999999988 6665555443

>PRK05456 ATP-dependent protease subunit HslV; Provisional

Probab=99.97  E-value=2.8e-29  Score=204.55  Aligned_cols=163  Identities=16%  Similarity=0.153  Sum_probs=138.0

Q ss_pred             CCcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEe-cCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHH
Q 025716           30 GNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSL-DNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEY  107 (249)
Q Consensus        30 G~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I-~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~  107 (249)
                      |+|+|||+++||||||+|+|.+. .++.+++.+||++| ++|++|+++|..+|++.|.+.++.+++.|+.  +.   ++.
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            78999999999999999999987 56778899999999 9999999999999999999999999999983  22   355


Q ss_pred             HHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceecc--ceEeecCCchHHHHHHHhhhc-cCCcH
Q 025716          108 ITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAW--KANATGRNSNSMREFLEKNYK-ETSGQ  184 (249)
Q Consensus       108 la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~--~~~aiG~g~~~a~~~Le~~~~-~~~se  184 (249)
                      .++.+..+.    .....+|+.+.+|++  |    .|+||.+||.|++.+.  +++++|+|+.++.++|++.|+ ++|  
T Consensus        76 ~a~l~~~l~----~~~~~~~l~~~~lv~--d----~~~ly~id~~G~~~~~~~~~~a~GSGs~~a~g~ld~~y~~~~m--  143 (172)
T PRK05456         76 AVELAKDWR----TDRYLRRLEAMLIVA--D----KEHSLIISGNGDVIEPEDGIIAIGSGGNYALAAARALLENTDL--  143 (172)
T ss_pred             HHHHHHHHH----hccCCCccEEEEEEE--c----CCcEEEECCCCcEeccCCCeEEEecCHHHHHHHHHHhhhcCCC--
Confidence            554443321    122346888999984  5    2699999999999766  899999999999999999999 999  


Q ss_pred             HHHHHHHHHHHHHHhc---CCCcEEEEE
Q 025716          185 ETIKLAIRALLEVVES---GGKNIEVAV  209 (249)
Q Consensus       185 eai~la~~~l~~~~~~---~~~~iei~~  209 (249)
                      ||++++++|+.++..+   ++++|+|-.
T Consensus       144 eA~~la~kai~~A~~Rd~~sg~~i~v~~  171 (172)
T PRK05456        144 SAEEIAEKALKIAADICIYTNHNITIEE  171 (172)
T ss_pred             CHHHHHHHHHHHHHHhCeeCCCcEEEEE
Confidence            9999999999999876   466777653

>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=99.97  E-value=8e-29  Score=198.07  Aligned_cols=160  Identities=37%  Similarity=0.529  Sum_probs=152.1

Q ss_pred             CcEEEEEeCCEEEEEEeccCCccccc-CCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTVKLQD-SRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~~l~~-~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      +|+|||+++||||+|+|++.+..+.. .....|++.++++++++++|..+|++.+.++++.++..|++.++.++++..++
T Consensus         1 ~t~i~i~~~~gvila~d~~~~~~~~~~~~~~~ki~~~~~~~~~~~sG~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (164)
T cd01901           1 STSVAIKGKGGVVLAADKRLSSGLPVAGSPVIKIGKNEDGIAWGLAGLAADAQTLVRRLREALQLYRLRYGEPISVVALA   80 (164)
T ss_pred             CcEEEEEeCCEEEEEEecccCccCeecCCCcceEEEecCCeEEEEecChHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            57999999999999999999886544 66899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceecc-ceEeecCCchHHHHHHHhhhccCCc-HHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAW-KANATGRNSNSMREFLEKNYKETSG-QETI  187 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~-~~~aiG~g~~~a~~~Le~~~~~~~s-eeai  187 (249)
                      +.+++.++.+++   .||+++++|++|+|+  ++|+||.+||.|++..+ +++++|.++..+.++|++.|+++|+ +|++
T Consensus        81 ~~~~~~~~~~~~---~~p~~~~~iiag~~~--~~~~l~~id~~g~~~~~~~~~~~G~~~~~~~~~l~~~~~~~~~~~~~~  155 (164)
T cd01901          81 KELAKLLQVYTQ---GRPFGVNLIVAGVDE--GGGNLYYIDPSGPVIENPGAVATGSRSQRAKSLLEKLYKPDMTLEEAV  155 (164)
T ss_pred             HHHHHHHHHhcC---CCCcceEEEEEEEcC--CCCEEEEECCCcCEeecCcEEEECCCCHHHHHHHHHHhcCCCCHHHHH
Confidence            999999998887   699999999999994  78999999999999999 9999999999999999999999999 9999


Q ss_pred             HHHHHHHH
Q 025716          188 KLAIRALL  195 (249)
Q Consensus       188 ~la~~~l~  195 (249)
                      +++.+||.
T Consensus       156 ~~~~~~l~  163 (164)
T cd01901         156 ELALKALK  163 (164)
T ss_pred             HHHHHHHh
Confidence            99999985

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

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

Probab=99.96  E-value=4.2e-28  Score=191.00  Aligned_cols=182  Identities=21%  Similarity=0.325  Sum_probs=170.0

Q ss_pred             ccCCcEEEEEeCCEEEEEEeccCCcc-cccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHH
Q 025716           28 RKGNAAVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVE  106 (249)
Q Consensus        28 ~~G~t~igi~~~dgVvla~d~~~~~~-l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~  106 (249)
                      -+|+++||.+++|||.+|+|.|.... ...+++.+|||+|+|+++++.+|+..|++.+.++++..-+.|+++.++.|-|+
T Consensus         6 ynGg~vvAM~gk~cvaIa~D~RlG~q~~tistdf~ki~~igdr~y~GL~glatDvqtl~~~~~fr~nLy~lre~R~i~P~   85 (204)
T KOG0180|consen    6 YNGGSVVAMAGKNCVAIASDLRLGVQSQTISTDFQKIFKIGDRLYLGLTGLATDVQTLLERLRFRKNLYELREEREIKPE   85 (204)
T ss_pred             ecCceEEEEeCCceEEEEeccccceeeeeeeccchhheecCCeeEEeccccchhHHHHHHHHHHHHhHHHhhhhcccCcH
Confidence            48999999999999999999999874 34567899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceec-cceEeecCCchHHHHHHHhhhccCCc-H
Q 025716          107 YITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSA-WKANATGRNSNSMREFLEKNYKETSG-Q  184 (249)
Q Consensus       107 ~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~-~~~~aiG~g~~~a~~~Le~~~~~~~s-e  184 (249)
                      .++.++|.++++.    ++-||-+..+|||+|+ .++|+|..+|..|.... .++++.|.+++...+..|..|+|+|. +
T Consensus        86 ~~s~mvS~~lYek----RfgpYf~~PvVAGl~~-~~kPfIc~mD~IGc~~~~~DFVvsGTa~e~L~GmCE~ly~pnmepd  160 (204)
T KOG0180|consen   86 TFSSMVSSLLYEK----RFGPYFTEPVVAGLDD-DNKPFICGMDLIGCIDAPKDFVVSGTASEQLYGMCEALYEPNMEPD  160 (204)
T ss_pred             HHHHHHHHHHHHh----hcCCcccceeEeccCC-CCCeeEeecccccCcCccCCeEEecchHHHHHHHHHHhcCCCCCHH
Confidence            9999999999653    4569999999999998 89999999999999965 59999999999999999999999999 9


Q ss_pred             HHHHHHHHHHHHHHhc---CCCcEEEEEEEcCC
Q 025716          185 ETIKLAIRALLEVVES---GGKNIEVAVMTREK  214 (249)
Q Consensus       185 eai~la~~~l~~~~~~---~~~~iei~~v~~~g  214 (249)
                      ++.+.+.++|.+++++   +++...|.+|++|.
T Consensus       161 ~LFetisQa~Lna~DRDalSGwGa~vyiI~kdk  193 (204)
T KOG0180|consen  161 ELFETISQALLNAVDRDALSGWGAVVYIITKDK  193 (204)
T ss_pred             HHHHHHHHHHHhHhhhhhhccCCeEEEEEccch
Confidence            9999999999999987   58899999999987

>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=99.96  E-value=1.3e-27  Score=193.65  Aligned_cols=161  Identities=16%  Similarity=0.094  Sum_probs=132.7

Q ss_pred             CcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecC-CEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDN-HIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYI  108 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~-~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l  108 (249)
                      +|+|||+++||||||+|+|.+. .++.+++.+||++|++ |++|+++|..+|++.|.++++.+++.|+.+.++     ..
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            6899999999999999999987 5678889999999999 999999999999999999999999999988774     33


Q ss_pred             HHHHHHHHHhhhccCCCccce-eEEEEEeeeCCCCCceEEEECCCCceecc--ceEeecCCchHHHHHHHhhhccC-CcH
Q 025716          109 TRYIAGLQQKYTQSGGVRPFG-LSTLIVGFDPYTGVPSLYQTDPSGTFSAW--KANATGRNSNSMREFLEKNYKET-SGQ  184 (249)
Q Consensus       109 a~~ls~~~~~~t~~~~~rP~g-v~~ivaG~d~~~~gp~Ly~iDp~G~~~~~--~~~aiG~g~~~a~~~Le~~~~~~-~se  184 (249)
                      ++.+..++    . .+.+|+. +.+|++++      ++||.+||.|++.+.  ++.++|+|+.++.++||.+|+++ |+ 
T Consensus        76 a~l~~~l~----~-~~~~~~l~a~~iv~~~------~~ly~id~~G~~ie~~~~~~a~GSGS~ya~g~ld~~yk~~~ms-  143 (171)
T cd01913          76 VELAKDWR----T-DRYLRRLEAMLIVADK------EHTLLISGNGDVIEPDDGIAAIGSGGNYALAAARALLDHTDLS-  143 (171)
T ss_pred             HHHHHHHH----h-ccCcCceEEEEEEeCC------CcEEEECCCCCEeccCCCeEEEeCCHHHHHHHHHHhhccCCCC-
Confidence            33333322    1 1335655 65555543      389999999999998  49999999999999999999995 98 


Q ss_pred             HHHHHHHHHHHHHHhc---CCCcEEEEE
Q 025716          185 ETIKLAIRALLEVVES---GGKNIEVAV  209 (249)
Q Consensus       185 eai~la~~~l~~~~~~---~~~~iei~~  209 (249)
                       +.++|++|++.+.++   ++++|+|-.
T Consensus       144 -~~~la~~Av~~A~~rd~~tg~~i~~~~  170 (171)
T cd01913         144 -AEEIARKALKIAADICIYTNHNITVEE  170 (171)
T ss_pred             -HHHHHHHHHHHHHhhCcccCCCEEEEe
Confidence             338999999999876   466777643

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

>TIGR03692 ATP_dep_HslV ATP-dependent protease HslVU, peptidase subunit

Probab=99.95  E-value=4.5e-27  Score=190.46  Aligned_cols=162  Identities=15%  Similarity=0.131  Sum_probs=131.2

Q ss_pred             CcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEe-cCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSL-DNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYI  108 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I-~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l  108 (249)
                      +|+|||+++||||||+|+|.+. .++.+++.+||++| ++|++|+++|..+|++.|.++++.+++.|+.+.     .+.+
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            6899999999999999999887 56778899999999 599999999999999999999999999998743     2444


Q ss_pred             HHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceecc--ceEeecCCchHHHHHHHhhhc-cCCcHH
Q 025716          109 TRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAW--KANATGRNSNSMREFLEKNYK-ETSGQE  185 (249)
Q Consensus       109 a~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~--~~~aiG~g~~~a~~~Le~~~~-~~~see  185 (249)
                      ++.++.+    ..+...+.+.+.+|++|+      ++||.+||.|.+.++  +++++|+|+.++.++||.+|+ ++|  +
T Consensus        76 a~l~~~~----~~~~~~~~l~a~~iv~~~------~~ly~i~~~G~~ie~~~~~~a~GSGS~~a~g~ld~~y~~~~~--s  143 (171)
T TIGR03692        76 VELAKDW----RTDRYLRRLEAMLIVADK------ETSLLISGTGDVIEPEDGIAAIGSGGNYALAAARALLRNTDL--S  143 (171)
T ss_pred             HHHHHHH----hhcccccccEEEEEEEcC------CCEEEEcCCCcEeccCCCeEEEeCCHHHHHHHHHHhhhcCCC--C
Confidence            4444442    112122234466666543      389999999999996  699999999999999999995 555  4


Q ss_pred             HHHHHHHHHHHHHhc---CCCcEEEEE
Q 025716          186 TIKLAIRALLEVVES---GGKNIEVAV  209 (249)
Q Consensus       186 ai~la~~~l~~~~~~---~~~~iei~~  209 (249)
                      |+++++++++.+.++   ++++|.|-.
T Consensus       144 a~~la~~Av~~A~~rd~~sg~~i~v~~  170 (171)
T TIGR03692       144 AEEIAREALKIAADICIYTNHNITIEE  170 (171)
T ss_pred             HHHHHHHHHHHHHhhCccCCCCEEEEe
Confidence            999999999999876   466777653

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

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

Probab=99.53  E-value=5e-15  Score=79.05  Aligned_cols=23  Identities=78%  Similarity=1.314  Sum_probs=22.3

Q ss_pred             CCCCCcccCCCCcchhhhhHHHH
Q 025716            4 YDRAITVFSPDGHLFQVEYALEA   26 (249)
Q Consensus         4 yd~~~~~fsp~G~l~Qveya~ka   26 (249)
                      ||+++|+|||+|||+|||||+||
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            89999999999999999999997

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=99.44  E-value=1.6e-12  Score=102.20  Aligned_cols=168  Identities=17%  Similarity=0.151  Sum_probs=126.4

Q ss_pred             cCCcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecC-CEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHH
Q 025716           29 KGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDN-HIALACAGLKADARVLINRARIECQSHRLTVEDPVTVE  106 (249)
Q Consensus        29 ~G~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~-~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~  106 (249)
                      +++|+++++-++-|++++|.+++- ..+.+.+..|+-+|.. +++.+++|.++|+..|.+.+..+++.|.         .
T Consensus         3 h~TTiv~vr~~gkv~iagDGQVtlG~tvmK~narKvRkl~~gkvlaGFAGstADaftLfe~fe~kle~~~---------g   73 (178)
T COG5405           3 HMTTIVAVRKNGKVVIAGDGQVTLGNTVMKGNARKVRRLYNGKVLAGFAGSTADAFTLFERFEAKLEQYQ---------G   73 (178)
T ss_pred             eeEEEEEEeeCCeEEEecCceEeecceeeeccHHHHHHHcCCcEEEEecccchhHHHHHHHHHHHHHHcc---------C
Confidence            689999999999999999999876 4566667777766654 8999999999999999999999999887         3


Q ss_pred             HHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceecc--ceEeecCCchHHHHHHHhhhc-cCCc
Q 025716          107 YITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAW--KANATGRNSNSMREFLEKNYK-ETSG  183 (249)
Q Consensus       107 ~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~--~~~aiG~g~~~a~~~Le~~~~-~~~s  183 (249)
                      .|.+..-++.+.+.....+|.+.+-+||+--+      .+|.+...|.+.+.  +.++||+|..+|.+.....++ ++++
T Consensus        74 ~L~raavelaKdwr~Dk~lr~LEAmllVad~~------~il~isG~gdV~epe~~~~aIGSGgnyAl~AarAl~~~~~ls  147 (178)
T COG5405          74 DLFRAAVELAKDWRTDKYLRKLEAMLLVADKT------HILIITGNGDVIEPEDDIIAIGSGGNYALSAARALMENTELS  147 (178)
T ss_pred             cHHHHHHHHHHhhhhhhHHHHHhhheeEeCCC------cEEEEecCcceecCCCCeEEEcCCchHHHHHHHHHHhccCCC
Confidence            44555556666665555667788888887433      58899999998764  699999999999999888775 4776


Q ss_pred             -HHHHHHHHHHHHHHHhcCCCcEEEEEEE
Q 025716          184 -QETIKLAIRALLEVVESGGKNIEVAVMT  211 (249)
Q Consensus       184 -eeai~la~~~l~~~~~~~~~~iei~~v~  211 (249)
                       +|..+.++++--+.+..++.+|.|-.+.
T Consensus       148 A~eIa~~sl~iA~eiciyTN~ni~ve~l~  176 (178)
T COG5405         148 AREIAEKSLKIAGDICIYTNHNIVVEELR  176 (178)
T ss_pred             HHHHHHHHHhhhheEEEecCCcEEEEEee
Confidence             5544444433333333455666665543

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

Probab=99.40  E-value=9.3e-12  Score=101.32  Aligned_cols=215  Identities=18%  Similarity=0.196  Sum_probs=150.0

Q ss_pred             CCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEe---cCC-EEEEEecChhhHHHHHHHHHHHHHH--hhhhcCCCC
Q 025716           30 GNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSL---DNH-IALACAGLKADARVLINRARIECQS--HRLTVEDPV  103 (249)
Q Consensus        30 G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I---~~~-i~~~~sG~~~D~~~l~~~~~~~~~~--~~~~~~~~i  103 (249)
                      ++.|||++...|.|+++|+|....+-.....+|+|..   +++ ++++.+|..+-.|.+++.+.+..+.  ....+ .-+
T Consensus         1 MTYCv~l~l~~GlVf~sDsRTNAGvD~istfkKl~~~~~pGdRvlvl~taGNLA~tQaV~~ll~e~~~~d~~~~L~-n~~   79 (255)
T COG3484           1 MTYCVGLILDFGLVFGSDSRTNAGVDYISTFKKLFVFELPGDRVLVLCTAGNLAITQAVLHLLDERIQRDDGDSLL-NIP   79 (255)
T ss_pred             CceEEEEEeccceEEecccccccCchHHHHHHHHhhccCCCceEEEEEecCccHHHHHHHHHHHHHhhccchhhhh-cch
Confidence            4789999999999999999987654323356676554   233 5677899999999999988776652  11111 223


Q ss_pred             CHHHHHHHHHHHHHhhh-ccCC-----CccceeEEEEEeeeCCCCCceEEEECCCCceecc----ceEeecCCchHHHHH
Q 025716          104 TVEYITRYIAGLQQKYT-QSGG-----VRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAW----KANATGRNSNSMREF  173 (249)
Q Consensus       104 ~~~~la~~ls~~~~~~t-~~~~-----~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~----~~~aiG~g~~~a~~~  173 (249)
                      +.-..+..++....+-. +.+.     ---|.|++|++|.-. .+-|.||.|.|.|++.+.    ++.-+|.. .+-+++
T Consensus        80 sm~eattlvgetvrEv~~rds~~leka~~dfn~sfllGGQI~-G~pp~Ly~IYpqGNFIqaT~etpf~QiGEt-KYGKPi  157 (255)
T COG3484          80 SMYEATTLVGETVREVQARDSPALEKAGIDFNCSFLLGGQIK-GEPPRLYLIYPQGNFIQATPETPFLQIGET-KYGKPI  157 (255)
T ss_pred             hHHHHHHHHHHHHHHHHhccCchhhccCcceeEEEEEcceec-CCCceeEEEccCCCeeecCCCCceeEcccc-ccCchh
Confidence            44455555555443221 1111     123899999999875 455899999999999864    89999984 455999


Q ss_pred             HHhhhccCCc-HHHHHHHHHHHHHHHhcC---CCcEEEEEEEcCCCEE---EcCHHHHHHHHHHHHH-HHHH---HHHhh
Q 025716          174 LEKNYKETSG-QETIKLAIRALLEVVESG---GKNIEVAVMTREKGLK---QLDEAEIDAMVAEIEA-KKAA---AEAAK  242 (249)
Q Consensus       174 Le~~~~~~~s-eeai~la~~~l~~~~~~~---~~~iei~~v~~~g~~~---~~~~~ei~~~l~~i~~-~~~~---~~~~~  242 (249)
                      |++.+..++. +|+.++++-.+...+.++   +-.+++-++.+|- |+   .+--.|=++|+.+|.. |...   +=+++
T Consensus       158 ldR~i~~~~pLeea~kcaLvS~DSTlkSNiSVGlPldLl~~e~ds-~~v~~~~ri~edd~Y~a~ir~~W~~~lrq~f~~l  236 (255)
T COG3484         158 LDRTITYDTPLEEAAKCALVSFDSTLKSNISVGLPLDLLVYEADS-FSVRHTLRIREDDPYFAKIRSLWSSYLRQAFESL  236 (255)
T ss_pred             hhhhhhccCCHHHHhhheEEecchhhhccccccCCceeEEEeccc-eeeeeeeEeccCChHHHHHHHHHHHHHHHHHHhC
Confidence            9999999999 999999999999888764   5578999999884 32   2223334568888875 5533   22344


Q ss_pred             cCCCCC
Q 025716          243 KGPPKE  248 (249)
Q Consensus       243 ~~~~~~  248 (249)
                      ..||-+
T Consensus       237 pd~~~~  242 (255)
T COG3484         237 PDPPWE  242 (255)
T ss_pred             CCCccc
Confidence            455543

>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=95.40  E-value=1.1  Score=37.02  Aligned_cols=46  Identities=15%  Similarity=0.240  Sum_probs=37.9

Q ss_pred             hHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhcC---CCcEEEEEEEcC
Q 025716          168 NSMREFLEKNYKETSG-QETIKLAIRALLEVVESG---GKNIEVAVMTRE  213 (249)
Q Consensus       168 ~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~~---~~~iei~~v~~~  213 (249)
                      +.|...|.+.|++.|+ +++.++...+|.++...+   ...+++...++.
T Consensus       131 ~ia~~~lkk~~~~k~~l~~i~~i~~~i~~~~a~~tpsvS~~~d~~~~~~~  180 (194)
T PF09894_consen  131 EIANKELKKYWKPKMSLKDIENIFEKIMEEVASKTPSVSKEYDIYITTKK  180 (194)
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhcCCCccCcEEEEEeccc
Confidence            6788889999999999 999999999999985432   457888877763

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

>COG4079 Uncharacterized protein conserved in archaea [Function unknown]

Probab=81.02  E-value=35  Score=29.41  Aligned_cols=165  Identities=17%  Similarity=0.193  Sum_probs=89.1

Q ss_pred             CCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           30 GNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        30 G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      ++.+|+.-++||.|+|.|+|.                     +++-|.-.|-+.|-+.         +..|.--+-+.|+
T Consensus         1 MtLviay~gknGaviaGDrR~---------------------i~frgdee~re~lEek---------LYsGeIkteEEL~   50 (293)
T COG4079           1 MTLVIAYIGKNGAVIAGDRRE---------------------ITFRGDEEDREKLEEK---------LYSGEIKTEEELA   50 (293)
T ss_pred             CeEEEEEecCCCcEEeccceE---------------------EEEecChhHHHHHHHH---------hhcCccccHHHHH
Confidence            467899999999999999974                     2445555555544432         2335555666677


Q ss_pred             HHHHHHHHhhhc---cCCCccceeEEEEEeeeCC----CCCceEEEE-------CCCCceec-------cceEeecCC--
Q 025716          110 RYIAGLQQKYTQ---SGGVRPFGLSTLIVGFDPY----TGVPSLYQT-------DPSGTFSA-------WKANATGRN--  166 (249)
Q Consensus       110 ~~ls~~~~~~t~---~~~~rP~gv~~ivaG~d~~----~~gp~Ly~i-------Dp~G~~~~-------~~~~aiG~g--  166 (249)
                      +.+.++--.++-   ....|...-+++++-+...    -..-.+|.+       +-.|+-..       ....+.|..  
T Consensus        51 r~aeel~Vki~vtDdr~KVrk~~d~VvvGEV~s~~~~~vkRRRvYAT~Ga~aIvel~gs~vts~~~g~g~aiIv~Gnk~~  130 (293)
T COG4079          51 RKAEELGVKITVTDDRNKVRKRNDGVVVGEVSSVERGIVKRRRVYATAGAYAIVELRGSEVTSTSQGKGSAIIVFGNKFT  130 (293)
T ss_pred             HHHHHcCCEEEEEcchHhhhcccCcEEEEEeecccccceeeeEEeecCCceEEEEecCCeeEeeecCCCceEEEECcHHH
Confidence            666654311110   0111222223344433320    011233332       11222111       123333322  


Q ss_pred             chHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCC-CEEEcCHHHH
Q 025716          167 SNSMREFLEKNYKETSG-QETIKLAIRALLEVVES---GGKNIEVAVMTREK-GLKQLDEAEI  224 (249)
Q Consensus       167 ~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g-~~~~~~~~ei  224 (249)
                      -+.++.+|.++|.+.++ +++..+...+|..+..-   -...++++.++++- ++.++-..++
T Consensus       131 Ke~aneflk~~l~~k~~lqd~~dal~elfe~vss~tpsVskeydiy~vs~~~d~~~rl~kkDi  193 (293)
T COG4079         131 KEVANEFLKDNLTKKSKLQDAVDALMELFETVSSKTPSVSKEYDIYQVSSNVDPVLRLVKKDI  193 (293)
T ss_pred             HHHHHHHHHhhccCCCCHHHHHHHHHHHHHHhhcCCCcccceeEEEEecCCcCHHHHHHHHHH
Confidence            25677788888888888 88888877777766532   25678888888642 2444444444

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

Probab=80.74  E-value=2.9  Score=32.47  Aligned_cols=43  Identities=21%  Similarity=0.256  Sum_probs=39.2

Q ss_pred             EEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHHHH
Q 025716          147 YQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIKL  189 (249)
Q Consensus       147 y~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~l  189 (249)
                      ..+|-+|.+...+|-..|.|+..|.+-+-..|-..++ +|+.++
T Consensus        71 Ikvd~~g~I~dakFKTFGCGSAIASSS~aTewvkgkt~dea~kI  114 (157)
T KOG3361|consen   71 IKVDDSGVIEDAKFKTFGCGSAIASSSLATEWVKGKTLDEALKI  114 (157)
T ss_pred             EEECCCCcEEEeeeeecccchHhhhhHHHHHHHccccHHHHHhc
Confidence            3578899999999999999999999999999999999 998765

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	249
1iru_D	248	Crystal Structure Of The Mammalian 20s Proteasome A		2e-91
3une_C	248	Mouse Constitutive 20s Proteasome Length = 248		5e-91
3unb_C	248	Mouse Constitutive 20s Proteasome In Complex With P		2e-90
1g0u_C	243	A Gated Channel Into The Proteasome Core Particle L		4e-80
1fnt_D	254	Crystal Structure Of The 20s Proteasome From Yeast		5e-80
1ryp_D	241	Crystal Structure Of The 20s Proteasome From Yeast		2e-79
1vsy_D	227	Proteasome Activator Complex Length = 227		1e-71
3h4p_A	264	Proteasome 20s Core Particle From Methanocaldococcu		9e-49
1j2q_A	237	20s Proteasome In Complex With Calpain-inhibitor I		2e-48
1j2p_A	246	Alpha-Ring From The Proteasome From Archaeoglobus F		9e-48
3unb_A	234	Mouse Constitutive 20s Proteasome In Complex With P		3e-43
1iru_B	233	Crystal Structure Of The Mammalian 20s Proteasome A		3e-43
2ku1_A	237	Dynamic Regulation Of Archaeal Proteasome Gate Open		7e-43
3jrm_A	227	Crystal Structure Of Archaeal 20s Proteasome In Com		8e-43
1pma_A	233	Proteasome From Thermoplasma Acidophilum Length = 2		8e-43
1yar_A	233	Structure Of Archeabacterial 20s Proteasome Mutant		5e-42
1yau_A	233	Structure Of Archeabacterial 20s Proteasome- Pa26 C		3e-41
2ku2_A	237	Dynamic Regulation Of Archaeal Proteasome Gate Open		3e-41
1iru_C	261	Crystal Structure Of The Mammalian 20s Proteasome A		8e-41
3unb_B	261	Mouse Constitutive 20s Proteasome In Complex With P		1e-40
1z7q_C	258	Crystal Structure Of The 20s Proteasome From Yeast		2e-40
1ryp_C	244	Crystal Structure Of The 20s Proteasome From Yeast		2e-40
1g0u_B	245	A Gated Channel Into The Proteasome Core Particle L		2e-40
3oeu_B	235	Structure Of Yeast 20s Open-Gate Proteasome With Co		1e-38
3unb_D	241	Mouse Constitutive 20s Proteasome In Complex With P		9e-38
1iru_E	241	Crystal Structure Of The Mammalian 20s Proteasome A		5e-37
1vsy_C	232	Proteasome Activator Complex Length = 232		6e-37
1g0u_D	241	A Gated Channel Into The Proteasome Core Particle L		9e-37
4g4s_E	261	Structure Of Proteasome-Pba1-Pba2 Complex Length =		1e-36
1fnt_E	260	Crystal Structure Of The 20s Proteasome From Yeast		1e-36
2z5c_C	262	Crystal Structure Of A Novel Chaperone Complex For		1e-36
1vsy_E	250	Proteasome Activator Complex Length = 250		2e-36
1ryp_B	250	Crystal Structure Of The 20s Proteasome From Yeast		3e-36
1ryp_E	242	Crystal Structure Of The 20s Proteasome From Yeast		2e-35
1iru_A	246	Crystal Structure Of The Mammalian 20s Proteasome A		5e-34
3unb_G	246	Mouse Constitutive 20s Proteasome In Complex With P		8e-34
1iru_F	263	Crystal Structure Of The Mammalian 20s Proteasome A		5e-32
3unb_E	263	Mouse Constitutive 20s Proteasome In Complex With P		5e-32
1vsy_B	231	Proteasome Activator Complex Length = 231		4e-31
1g0u_F	248	A Gated Channel Into The Proteasome Core Particle L		6e-27
1z7q_G	288	Crystal Structure Of The 20s Proteasome From Yeast		6e-27
1fnt_G	287	Crystal Structure Of The 20s Proteasome From Yeast		6e-27
3oeu_F	242	Structure Of Yeast 20s Open-Gate Proteasome With Co		6e-27
1ryp_G	244	Crystal Structure Of The 20s Proteasome From Yeast		6e-27
3unb_F	255	Mouse Constitutive 20s Proteasome In Complex With P		9e-27
1iru_G	254	Crystal Structure Of The Mammalian 20s Proteasome A		2e-26
3sdi_E	233	Structure Of Yeast 20s Open-Gate Proteasome With Co		1e-25
1g0u_E	234	A Gated Channel Into The Proteasome Core Particle L		1e-25
1ryp_A	243	Crystal Structure Of The 20s Proteasome From Yeast		2e-25
1g0u_G	252	A Gated Channel Into The Proteasome Core Particle L		2e-25
1fnt_F	234	Crystal Structure Of The 20s Proteasome From Yeast		3e-25
4g4s_F	235	Structure Of Proteasome-Pba1-Pba2 Complex Length =		3e-25
1ryp_F	233	Crystal Structure Of The 20s Proteasome From Yeast		3e-25
1ya7_H	217	Implications For Interactions Of Proteasome With Pa		2e-10
1pma_B	211	Proteasome From Thermoplasma Acidophilum Length = 2		2e-10
3c91_H	203	Thermoplasma Acidophilum 20s Proteasome With An Ope		8e-10
1j2q_H	202	20s Proteasome In Complex With Calpain-inhibitor I		2e-07
3nzj_K	287	Crystal Structure Of Yeast 20s Proteasome In Comple		3e-05
1ryp_K	198	Crystal Structure Of The 20s Proteasome From Yeast		6e-05
4b4t_5	287	Near-Atomic Resolution Structural Model Of The Yeas		7e-05
3unf_H	234	Mouse 20s Immunoproteasome In Complex With Pr-957 L		1e-04
1g0u_K	212	A Gated Channel Into The Proteasome Core Particle L		1e-04
1ryp_M	222	Crystal Structure Of The 20s Proteasome From Yeast		1e-04
1g0u_L	241	A Gated Channel Into The Proteasome Core Particle L		2e-04
1ryp_L	212	Crystal Structure Of The 20s Proteasome From Yeast		3e-04

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

Iteration: 1
 Score =  331 bits (848), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 161/228 (70%), Positives = 190/228 (83%), Gaps = 4/228 (1%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YDRAITVFSPDGHLFQVEYA EAV+KG+ AVGVRG D +VLGVEKKS  KLQD R+VRKI
Sbjct: 3   YDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVRKI 62
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
            +LD+++ +A AGL ADAR++INRAR+ECQSHRLTVEDPVTVEYITRYIA L+Q+YTQS 
Sbjct: 63  CALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSN 122
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG 183
           G RPFG+S LIVGFD + G P LYQTDPSGT+ AWKANA GR + S+REFLEKNY + + 
Sbjct: 123 GRRPFGISALIVGFD-FDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEAI 181
Query: 184 QE---TIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
           +    TIKL I+ALLEVV+SGGKNIE+AVM R++ LK L+  EI+  V
Sbjct: 182 ETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYV 229

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

Iteration: 1
 Score =  330 bits (846), Expect = 5e-91,   Method: Compositional matrix adjust.
 Identities = 161/228 (70%), Positives = 190/228 (83%), Gaps = 4/228 (1%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YDRAITVFSPDGHLFQVEYA EAV+KG+ AVGVRG D +VLGVEKKS  KLQD R+VRKI
Sbjct: 3   YDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGKDIVVLGVEKKSVAKLQDERTVRKI 62
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
            +LD+++ +A AGL ADAR++INRAR+ECQSHRLTVEDPVTVEYITRYIA L+Q+YTQS 
Sbjct: 63  CALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSN 122
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG 183
           G RPFG+S LIVGFD + G P LYQTDPSGT+ AWKANA GR + S+REFLEKNY + + 
Sbjct: 123 GRRPFGISALIVGFD-FDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDDAI 181
Query: 184 QE---TIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
           +    TIKL I+ALLEVV+SGGKNIE+AVM R++ LK L+  EI+  V
Sbjct: 182 ETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQPLKILNPEEIEKYV 229

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

Iteration: 1
 Score =  328 bits (840), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 160/228 (70%), Positives = 189/228 (82%), Gaps = 4/228 (1%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YDRAITVFSPDGHLFQVEYA EAV+KG+ AVGVRG D +VLGV KKS  KLQD R+VRKI
Sbjct: 3   YDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGKDIVVLGVAKKSVAKLQDERTVRKI 62
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
            +LD+++ +A AGL ADAR++INRAR+ECQSHRLTVEDPVTVEYITRYIA L+Q+YTQS 
Sbjct: 63  CALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSN 122
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG 183
           G RPFG+S LIVGFD + G P LYQTDPSGT+ AWKANA GR + S+REFLEKNY + + 
Sbjct: 123 GRRPFGISALIVGFD-FDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDDAI 181
Query: 184 QE---TIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
           +    TIKL I+ALLEVV+SGGKNIE+AVM R++ LK L+  EI+  V
Sbjct: 182 ETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQPLKILNPEEIEKYV 229

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

Iteration: 1
 Score =  294 bits (752), Expect = 4e-80,   Method: Compositional matrix adjust.
 Identities = 136/233 (58%), Positives = 183/233 (78%), Gaps = 5/233 (2%)
Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSR-S 59
           M+ YDRA+++FSPDGH+FQVEYALEAV++G  AVGV+G + +VLG E++ST+KLQD+R +
Sbjct: 1   MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT 60
Query: 60  VRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKY 119
             K+  +D+H+ L+ +GL AD+R+LI +AR+E QSHRLT+EDPVTVEY+TRY+AG+QQ+Y
Sbjct: 61  PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY 120
Query: 120 TQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNY- 178
           TQSGGVRPFG+STLI GFDP    P LYQT+PSG +S+W A   GRNS ++REFLEKNY 
Sbjct: 121 TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD 180
Query: 179 -KETSG--QETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
            KE     +E +KL +R+LLEVV++G KNIE+ V+  +  +  L   EI+  V
Sbjct: 181 RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYV 233

>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 =  293 bits (751), Expect = 5e-80,   Method: Compositional matrix adjust.
 Identities = 136/233 (58%), Positives = 183/233 (78%), Gaps = 5/233 (2%)
Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSR-S 59
           M+ YDRA+++FSPDGH+FQVEYALEAV++G  AVGV+G + +VLG E++ST+KLQD+R +
Sbjct: 1   MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT 60
Query: 60  VRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKY 119
             K+  +D+H+ L+ +GL AD+R+LI +AR+E QSHRLT+EDPVTVEY+TRY+AG+QQ+Y
Sbjct: 61  PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY 120
Query: 120 TQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNY- 178
           TQSGGVRPFG+STLI GFDP    P LYQT+PSG +S+W A   GRNS ++REFLEKNY 
Sbjct: 121 TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD 180
Query: 179 -KETSG--QETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
            KE     +E +KL +R+LLEVV++G KNIE+ V+  +  +  L   EI+  V
Sbjct: 181 RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYV 233

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

Iteration: 1
 Score =  291 bits (746), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 135/230 (58%), Positives = 181/230 (78%), Gaps = 5/230 (2%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSR-SVRK 62
           YDRA+++FSPDGH+FQVEYALEAV++G  AVGV+G + +VLG E++ST+KLQD+R +  K
Sbjct: 2   YDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSK 61
Query: 63  IVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQS 122
           +  +D+H+ L+ +GL AD+R+LI +AR+E QSHRLT+EDPVTVEY+TRY+AG+QQ+YTQS
Sbjct: 62  VSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQS 121
Query: 123 GGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNY--KE 180
           GGVRPFG+STLI GFDP    P LYQT+PSG +S+W A   GRNS ++REFLEKNY  KE
Sbjct: 122 GGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKE 181
Query: 181 TSG--QETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
                +E +KL +R+LLEVV++G KNIE+ V+  +  +  L   EI+  V
Sbjct: 182 PPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYV 231

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

Iteration: 1
 Score =  265 bits (678), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 125/217 (57%), Positives = 168/217 (77%), Gaps = 5/217 (2%)
Query: 17  LFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSR-SVRKIVSLDNHIALACA 75
           +FQVEYALEAV++G  AVGV+G + +VLG E++ST+KLQD+R +  K+  +D+H+ L+ +
Sbjct: 1   IFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSKVSKIDSHVVLSFS 60
Query: 76  GLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIV 135
           GL AD+R+LI +AR+E QSHRLT+EDPVTVEY+TRY+AG+QQ+YTQSGGVRPFG+STLI 
Sbjct: 61  GLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLIA 120
Query: 136 GFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNY--KETSG--QETIKLAI 191
           GFDP    P LYQT+PSG +S+W A   GRNS ++REFLEKNY  KE     +E +KL +
Sbjct: 121 GFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKEPPATVEECVKLTV 180
Query: 192 RALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMV 228
           R+LLEVV++G KNIE+ V+  +  +  L   EI+  V
Sbjct: 181 RSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYV 217

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

Iteration: 1
 Score =  189 bits (481), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 99/210 (47%), Positives = 140/210 (66%), Gaps = 4/210 (1%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YDRAITVFSP+G L+QVEYA EAVR+G  A+G+   D +VL V+++ T KL   RS+ KI
Sbjct: 12  YDRAITVFSPEGRLYQVEYAREAVRRGTTAIGIACKDGVVLAVDRRITSKLVKIRSIEKI 71
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
             +D+H+A A +GL ADARVLI+RAR+E Q +RLT  + +++E + + I  ++Q YTQ G
Sbjct: 72  FQIDDHVAAATSGLVADARVLIDRARLEAQIYRLTYGEEISIEMLAKKICDIKQAYTQHG 131
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK-ETS 182
           GVRPFG+S LI G D       L++TDPSG    +KA A G     + E LEK Y+ + +
Sbjct: 132 GVRPFGVSLLIAGIDKNEA--RLFETDPSGALIEYKATAIGSGRPVVMELLEKEYRDDIT 189
Query: 183 GQETIKLAIRALLEVVES-GGKNIEVAVMT 211
             E ++LAI AL +  E    +N++V ++T
Sbjct: 190 LDEGLELAITALTKANEDIKPENVDVCIIT 219

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

Iteration: 1
 Score =  189 bits (479), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 103/227 (45%), Positives = 147/227 (64%), Gaps = 7/227 (3%)
Query: 6   RAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVS 65
           RAITVFSPDG LFQVEYA EAV++G  A+G++  + ++L  +K+   KL ++ ++ KI  
Sbjct: 1   RAITVFSPDGRLFQVEYAREAVKRGATAIGIKCKEGVILIADKRVGSKLLEADTIEKIYK 60
Query: 66  LDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGV 125
           +D HI  A +GL ADARVLI+RARIE Q +RLT ++P+TV+ + + I   +Q+YTQ GGV
Sbjct: 61  IDEHICAATSGLVADARVLIDRARIEAQINRLTYDEPITVKELAKKICDFKQQYTQYGGV 120
Query: 126 RPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET-SGQ 184
           RPFG+S LI G D    VP LY+TDPSG    +KA A G   N++ EF EK Y++  S  
Sbjct: 121 RPFGVSLLIAGVDE---VPKLYETDPSGALLEYKATAIGMGRNAVTEFFEKEYRDDLSFD 177
Query: 185 ETIKLAIRALLEVVESG--GKNIEVA-VMTREKGLKQLDEAEIDAMV 228
           + + L + A+   +ES    +NIEV  V   ++  K++   E+   V
Sbjct: 178 DAMVLGLVAMGLSIESELVPENIEVGYVKVDDRTFKEVSPEELKPYV 224

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

Iteration: 1
 Score =  186 bits (473), Expect = 9e-48,   Method: Compositional matrix adjust.
 Identities = 103/229 (44%), Positives = 146/229 (63%), Gaps = 7/229 (3%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YDRAITVFSPDG LFQVEYA EAV++G  A+G++  + ++L  +K+   KL +  ++ KI
Sbjct: 8   YDRAITVFSPDGRLFQVEYAREAVKRGATAIGIKCKEGVILIADKRVGSKLLEKDTIEKI 67
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
             +D HI  A +GL ADARVLI+RARIE Q +RLT + P+TV+ + + I   +Q+YTQ G
Sbjct: 68  YKIDEHICAATSGLVADARVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQYG 127
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK-ETS 182
           GVRPFG+S LI G +    VP LY+TDPSG    +KA A G    ++ EF EK Y+ + S
Sbjct: 128 GVRPFGVSLLIAGVNE---VPKLYETDPSGALLEYKATAIGMGRMAVTEFFEKEYRDDLS 184
Query: 183 GQETIKLAIRALLEVVESG--GKNIEVA-VMTREKGLKQLDEAEIDAMV 228
             + + L + A+   +ES    +NIEV  V   ++  K++   E+   V
Sbjct: 185 FDDAMVLGLVAMGLSIESELVPENIEVGYVKVDDRTFKEVSPEELKPYV 233

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

Iteration: 1
 Score =  171 bits (434), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 94/224 (41%), Positives = 132/224 (58%), Gaps = 6/224 (2%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           Y  ++T FSP G L Q+EYAL AV  G  +VG++  + +VL  EKK    L D RSV K+
Sbjct: 6   YSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDERSVHKV 65
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
             +  HI L  +G+  D RVL++RAR   Q + L  ++P+    + + +A + Q+YTQSG
Sbjct: 66  EPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSG 125
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE-TS 182
           GVRPFG+S LI G++   G P L+Q+DPSG + AWKA A G+N  + + FLEK Y E   
Sbjct: 126 GVRPFGVSLLICGWN--EGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNEDLE 183
Query: 183 GQETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEI 224
            ++ I  AI  L E  E      NIEV +   E G ++L   E+
Sbjct: 184 LEDAIHTAILTLKESFEGQMTEDNIEVGI-CNEAGFRRLTPTEV 226

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

Iteration: 1
 Score =  171 bits (433), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 94/224 (41%), Positives = 132/224 (58%), Gaps = 6/224 (2%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           Y  ++T FSP G L Q+EYAL AV  G  +VG++  + +VL  EKK    L D RSV K+
Sbjct: 5   YSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDERSVHKV 64
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
             +  HI L  +G+  D RVL++RAR   Q + L  ++P+    + + +A + Q+YTQSG
Sbjct: 65  EPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSG 124
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE-TS 182
           GVRPFG+S LI G++   G P L+Q+DPSG + AWKA A G+N  + + FLEK Y E   
Sbjct: 125 GVRPFGVSLLICGWN--EGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNEDLE 182
Query: 183 GQETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEI 224
            ++ I  AI  L E  E      NIEV +   E G ++L   E+
Sbjct: 183 LEDAIHTAILTLKESFEGQMTEDNIEVGI-CNEAGFRRLTPTEV 225

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

Iteration: 1
 Score =  170 bits (430), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 93/224 (41%), Positives = 139/224 (62%), Gaps = 5/224 (2%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YDRAITVFSPDG LFQVEYA EAV+KG+ A+G++  + ++L  +KK   +L +  S+ KI
Sbjct: 12  YDRAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQNSIEKI 71
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
             +D+++A   +GL ADARVL++ ARI  Q  ++T    V +E + + +A   Q+YTQ G
Sbjct: 72  QLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYG 131
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET-S 182
           GVRP+G+S +  G D     P L+  DP+GT + +KA A G   +++  FLE+ YKE   
Sbjct: 132 GVRPYGVSLIFAGIDQIG--PRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKENLP 189
Query: 183 GQETIKLAIRALLEVVESGG--KNIEVAVMTREKGLKQLDEAEI 224
            +E + L I+AL   +E G   K  E+A +T     +  D+ E+
Sbjct: 190 EKEAVTLGIKALKSSLEEGEELKAPEIASITVGNKYRIYDQEEV 233

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

Iteration: 1
 Score =  170 bits (430), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 93/224 (41%), Positives = 139/224 (62%), Gaps = 5/224 (2%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YDRAITVFSPDG LFQVEYA EAV+KG+ A+G++  + ++L  +KK   +L +  S+ KI
Sbjct: 2   YDRAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQNSIEKI 61
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
             +D+++A   +GL ADARVL++ ARI  Q  ++T    V +E + + +A   Q+YTQ G
Sbjct: 62  QLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYG 121
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET-S 182
           GVRP+G+S +  G D     P L+  DP+GT + +KA A G   +++  FLE+ YKE   
Sbjct: 122 GVRPYGVSLIFAGIDQIG--PRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKENLP 179
Query: 183 GQETIKLAIRALLEVVESGG--KNIEVAVMTREKGLKQLDEAEI 224
            +E + L I+AL   +E G   K  E+A +T     +  D+ E+
Sbjct: 180 EKEAVTLGIKALKSSLEEGEELKAPEIASITVGNKYRIYDQEEV 223

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

Iteration: 1
 Score =  170 bits (430), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 93/224 (41%), Positives = 139/224 (62%), Gaps = 5/224 (2%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YDRAITVFSPDG LFQVEYA EAV+KG+ A+G++  + ++L  +KK   +L +  S+ KI
Sbjct: 8   YDRAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQNSIEKI 67
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
             +D+++A   +GL ADARVL++ ARI  Q  ++T    V +E + + +A   Q+YTQ G
Sbjct: 68  QLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYG 127
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET-S 182
           GVRP+G+S +  G D     P L+  DP+GT + +KA A G   +++  FLE+ YKE   
Sbjct: 128 GVRPYGVSLIFAGIDQIG--PRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKENLP 185
Query: 183 GQETIKLAIRALLEVVESGG--KNIEVAVMTREKGLKQLDEAEI 224
            +E + L I+AL   +E G   K  E+A +T     +  D+ E+
Sbjct: 186 EKEAVTLGIKALKSSLEEGEELKAPEIASITVGNKYRIYDQEEV 229

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

Iteration: 1
 Score =  167 bits (423), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 92/224 (41%), Positives = 138/224 (61%), Gaps = 5/224 (2%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           Y RAITVFSPDG LFQVEYA EAV+KG+ A+G++  + ++L  +KK   +L +  S+ KI
Sbjct: 8   YSRAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQNSIEKI 67
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
             +D+++A   +GL ADARVL++ ARI  Q  ++T    V +E + + +A   Q+YTQ G
Sbjct: 68  QLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYG 127
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET-S 182
           GVRP+G+S +  G D     P L+  DP+GT + +KA A G   +++  FLE+ YKE   
Sbjct: 128 GVRPYGVSLIFAGIDQIG--PRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKENLP 185
Query: 183 GQETIKLAIRALLEVVESGG--KNIEVAVMTREKGLKQLDEAEI 224
            +E + L I+AL   +E G   K  E+A +T     +  D+ E+
Sbjct: 186 EKEAVTLGIKALKSSLEEGEELKAPEIASITVGNKYRIYDQEEV 229

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

Iteration: 1
 Score =  164 bits (416), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 91/222 (40%), Positives = 137/222 (61%), Gaps = 5/222 (2%)
Query: 6   RAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVS 65
           RAITVFSPDG LFQVEYA EAV+KG+ A+G++  + ++L  +KK   +L +  S+ KI  
Sbjct: 10  RAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQNSIEKIQL 69
Query: 66  LDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGV 125
           +D+++A   +GL ADARVL++ ARI  Q  ++T    V +E + + +A   Q+YTQ GGV
Sbjct: 70  IDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGV 129
Query: 126 RPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET-SGQ 184
           RP+G+S +  G D     P L+  DP+GT + +KA A G   +++  FLE+ YKE    +
Sbjct: 130 RPYGVSLIFAGIDQIG--PRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKENLPEK 187
Query: 185 ETIKLAIRALLEVVESGG--KNIEVAVMTREKGLKQLDEAEI 224
           E + L I+AL   +E G   K  E+A +T     +  D+ E+
Sbjct: 188 EAVTLGIKALKSSLEEGEELKAPEIASITVGNKYRIYDQEEV 229

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

Iteration: 1
 Score =  164 bits (416), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 91/222 (40%), Positives = 137/222 (61%), Gaps = 5/222 (2%)
Query: 6   RAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVS 65
           RAITVFSPDG LFQVEYA EAV+KG+ A+G++  + ++L  +KK   +L +  S+ KI  
Sbjct: 14  RAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQNSIEKIQL 73
Query: 66  LDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGV 125
           +D+++A   +GL ADARVL++ ARI  Q  ++T    V +E + + +A   Q+YTQ GGV
Sbjct: 74  IDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGV 133
Query: 126 RPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET-SGQ 184
           RP+G+S +  G D     P L+  DP+GT + +KA A G   +++  FLE+ YKE    +
Sbjct: 134 RPYGVSLIFAGIDQIG--PRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKENLPEK 191
Query: 185 ETIKLAIRALLEVVESGG--KNIEVAVMTREKGLKQLDEAEI 224
           E + L I+AL   +E G   K  E+A +T     +  D+ E+
Sbjct: 192 EAVTLGIKALKSSLEEGEELKAPEIASITVGNKYRIYDQEEV 233

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

Iteration: 1
 Score =  163 bits (413), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 87/237 (36%), Positives = 140/237 (59%), Gaps = 14/237 (5%)
Query: 3   RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV-R 61
           RYD   T+FSP+G L+QVEYA+EA+      +G+   D ++L  E+++  KL D      
Sbjct: 4   RYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVFFSE 63
Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           KI  L+  +A + AG+ +DA VL N  R+  Q + L  ++P+  E +   +  ++Q YTQ
Sbjct: 64  KIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQ 123
Query: 122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET 181
            GG RPFG+S L +G+D + G   LYQ+DPSG +  WKA   G NS +    L+++YKE 
Sbjct: 124 FGGKRPFGVSLLYIGWDKHYGF-QLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYKE- 181
Query: 182 SGQETIK----LAIRAL---LEVVESGGKNIEVAVMTREKG---LKQLDEAEIDAMV 228
            G+ T+K    LAI+ L   ++V +   + +E+A +TRE G   ++ L + E++ ++
Sbjct: 182 -GEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLI 237

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

Iteration: 1
 Score =  162 bits (410), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 86/237 (36%), Positives = 140/237 (59%), Gaps = 14/237 (5%)
Query: 3   RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV-R 61
           RYD   T+FSP+G L+QVEYA+EA+      +G+   D ++L  E+++  KL D      
Sbjct: 4   RYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVFFSE 63
Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           KI  L+  +A + AG+ +DA VL N  R+  Q + L  ++P+  E +   +  ++Q YTQ
Sbjct: 64  KIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQ 123
Query: 122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET 181
            GG RPFG+S L +G+D + G   LYQ+DPSG +  WKA   G NS +    L+++YKE 
Sbjct: 124 FGGKRPFGVSLLYIGWDKHYGF-QLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYKE- 181
Query: 182 SGQETIK----LAIRAL---LEVVESGGKNIEVAVMTREKG---LKQLDEAEIDAMV 228
            G+ T+K    LA++ L   ++V +   + +E+A +TRE G   ++ L + E++ ++
Sbjct: 182 -GEMTLKSALALAVKVLNKTMDVSKLSAEKVEIATLTRESGKTVIRVLKQKEVEQLI 237

>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 =  162 bits (410), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 83/201 (41%), Positives = 129/201 (64%), Gaps = 5/201 (2%)
Query: 3   RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKL--QDSRSV 60
           RYD   T+FSP+G L+QVEYALE++     A+G+  +D IVL  E+K T  L  QD+ S 
Sbjct: 5   RYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDT-ST 63
Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
            K+  L++ IA+A AGL ADA +LIN ARI  Q++  T  + + VE + R ++ ++Q YT
Sbjct: 64  EKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYT 123
Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           Q GG+RPFG+S +  G+D   G   LY ++PSG ++ WKA + G N+++ +  L+ +YK+
Sbjct: 124 QHGGLRPFGVSFIYAGYDDRYGY-QLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKD 182
Query: 181 TSG-QETIKLAIRALLEVVES 200
                + I+LA++ L +  +S
Sbjct: 183 DMKVDDAIELALKTLSKTTDS 203

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

Iteration: 1
 Score =  162 bits (409), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 83/201 (41%), Positives = 129/201 (64%), Gaps = 5/201 (2%)
Query: 3   RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKL--QDSRSV 60
           RYD   T+FSP+G L+QVEYALE++     A+G+  +D IVL  E+K T  L  QD+ S 
Sbjct: 4   RYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDT-ST 62
Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
            K+  L++ IA+A AGL ADA +LIN ARI  Q++  T  + + VE + R ++ ++Q YT
Sbjct: 63  EKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYT 122
Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           Q GG+RPFG+S +  G+D   G   LY ++PSG ++ WKA + G N+++ +  L+ +YK+
Sbjct: 123 QHGGLRPFGVSFIYAGYDDRYGY-QLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKD 181
Query: 181 TSG-QETIKLAIRALLEVVES 200
                + I+LA++ L +  +S
Sbjct: 182 DMKVDDAIELALKTLSKTTDS 202

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

Iteration: 1
 Score =  162 bits (409), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 83/201 (41%), Positives = 129/201 (64%), Gaps = 5/201 (2%)
Query: 3   RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKL--QDSRSV 60
           RYD   T+FSP+G L+QVEYALE++     A+G+  +D IVL  E+K T  L  QD+ S 
Sbjct: 5   RYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDT-ST 63
Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
            K+  L++ IA+A AGL ADA +LIN ARI  Q++  T  + + VE + R ++ ++Q YT
Sbjct: 64  EKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYT 123
Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           Q GG+RPFG+S +  G+D   G   LY ++PSG ++ WKA + G N+++ +  L+ +YK+
Sbjct: 124 QHGGLRPFGVSFIYAGYDDRYGY-QLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKD 182
Query: 181 TSG-QETIKLAIRALLEVVES 200
                + I+LA++ L +  +S
Sbjct: 183 DMKVDDAIELALKTLSKTTDS 203

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

Iteration: 1
 Score =  156 bits (394), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 80/195 (41%), Positives = 126/195 (64%), Gaps = 5/195 (2%)
Query: 9   TVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKL--QDSRSVRKIVSL 66
           T+FSP+G L+QVEYALE++     A+G+  +D IVL  E+K T  L  QD+ S  K+  L
Sbjct: 1   TIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDT-STEKLYKL 59
Query: 67  DNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVR 126
           ++ IA+A AGL ADA +LIN ARI  Q++  T  + + VE + R ++ ++Q YTQ GG+R
Sbjct: 60  NDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLR 119
Query: 127 PFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QE 185
           PFG+S +  G+D   G   LY ++PSG ++ WKA + G N+++ +  L+ +YK+     +
Sbjct: 120 PFGVSFIYAGYDDRYGY-QLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKDDMKVDD 178
Query: 186 TIKLAIRALLEVVES 200
            I+LA++ L +  +S
Sbjct: 179 AIELALKTLSKTTDS 193

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

Iteration: 1
 Score =  153 bits (386), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 84/235 (35%), Positives = 136/235 (57%), Gaps = 10/235 (4%)
Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
           + YDR +  FSP+G LFQVEYA+EA++ G+ A+G++ ++ + L VEK+ T  L +  S+ 
Sbjct: 6   SEYDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEPSSIE 65
Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           KIV +D HI  A +GL ADA+ LI++AR+E Q+H  T  + +TVE +T+ ++ L  ++ +
Sbjct: 66  KIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGE 125
Query: 122 SGG-----VRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEK 176
                    RPFG++ L  G D     P L+  DPSGTF    A A G  S   +  L++
Sbjct: 126 EDADPGAMSRPFGVALLFGGVDEKG--PQLFHMDPSGTFVQCDARAIGSASEGAQSSLQE 183
Query: 177 NY-KETSGQETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEIDAMV 228
            Y K  + +E IK ++  L +V+E      NIE+A +   +      + E++ ++
Sbjct: 184 VYHKSMTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVI 238

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

Iteration: 1
 Score =  150 bits (380), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 83/235 (35%), Positives = 135/235 (57%), Gaps = 10/235 (4%)
Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
           + YDR +  FSP+G LFQVEY +EA++ G+ A+G++ ++ + L VEK+ T  L +  S+ 
Sbjct: 6   SEYDRGVNTFSPEGRLFQVEYDIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEPSSIE 65
Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           KIV +D HI  A +GL ADA+ LI++AR+E Q+H  T  + +TVE +T+ ++ L  ++ +
Sbjct: 66  KIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGE 125
Query: 122 SGG-----VRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEK 176
                    RPFG++ L  G D     P L+  DPSGTF    A A G  S   +  L++
Sbjct: 126 EDADPGAMSRPFGVALLFGGVDEKG--PQLFHMDPSGTFVQCDARAIGSASEGAQSSLQE 183
Query: 177 NY-KETSGQETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEIDAMV 228
            Y K  + +E IK ++  L +V+E      NIE+A +   +      + E++ ++
Sbjct: 184 LYHKSMTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVI 238

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

Iteration: 1
 Score =  150 bits (379), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 78/192 (40%), Positives = 123/192 (64%), Gaps = 5/192 (2%)
Query: 12  SPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKL--QDSRSVRKIVSLDNH 69
           SP+G L+QVEYALE++     A+G+  +D IVL  E+K T  L  QD+ S  K+  L++ 
Sbjct: 1   SPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDT-STEKLYKLNDK 59
Query: 70  IALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFG 129
           IA+A AGL ADA +LIN ARI  Q++  T  + + VE + R ++ ++Q YTQ GG+RPFG
Sbjct: 60  IAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFG 119
Query: 130 LSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIK 188
           +S +  G+D   G   LY ++PSG ++ WKA + G N+++ +  L+ +YK+     + I+
Sbjct: 120 VSFIYAGYDDRYGY-QLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKDDMKVDDAIE 178
Query: 189 LAIRALLEVVES 200
           LA++ L +  +S
Sbjct: 179 LALKTLSKTTDS 190

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

Iteration: 1
 Score =  150 bits (378), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 83/222 (37%), Positives = 129/222 (58%), Gaps = 7/222 (3%)
Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
           + YDR ++ FSP+G LFQVEY+LEA++ G+ A+G+   + +VLGVEK++T  L +S S+ 
Sbjct: 6   SEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESDSIE 65
Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           KIV +D HI  A +GL ADAR +I  AR    +H L  ++ + VE +T+ +  L      
Sbjct: 66  KIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLAAAAAM 125
Query: 122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMR-EFLEKNYKE 180
           S   RPFG++ LI G D   G   L+  +PSGTF  + A A G  S   + E L + +  
Sbjct: 126 S---RPFGVALLIAGHDADDGY-QLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNEWHSS 181
Query: 181 TSGQETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLD 220
            + +E   L ++ L +V+E      N +++ +T++ G K  D
Sbjct: 182 LTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYD 223

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

Iteration: 1
 Score =  149 bits (376), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 82/228 (35%), Positives = 131/228 (57%), Gaps = 10/228 (4%)
Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
           + YDR ++ FSP+G LFQVEY+LEA++ G+ A+G+   + +VLGVEK++T  L +S S+ 
Sbjct: 7   SEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESDSIE 66
Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           KIV +D HI  A +GL ADAR +I  AR    +H L  ++ + VE +T+ +  L  ++ +
Sbjct: 67  KIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGE 126
Query: 122 SGG------VRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMR-EFL 174
                     RPFG++ LI G D   G   L+  +PSGTF  + A A G  S   + E L
Sbjct: 127 GASGEERLMSRPFGVALLIAGHDADDGY-QLFHAEPSGTFYRYNAKAIGSGSEGAQAELL 185
Query: 175 EKNYKETSGQETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLD 220
            + +   + +E   L ++ L +V+E      N +++ +T++ G K  D
Sbjct: 186 NEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYD 233

>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 =  149 bits (376), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 82/228 (35%), Positives = 131/228 (57%), Gaps = 10/228 (4%)
Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
           + YDR ++ FSP+G LFQVEY+LEA++ G+ A+G+   + +VLGVEK++T  L +S S+ 
Sbjct: 6   SEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESDSIE 65
Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           KIV +D HI  A +GL ADAR +I  AR    +H L  ++ + VE +T+ +  L  ++ +
Sbjct: 66  KIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGE 125
Query: 122 SGG------VRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMR-EFL 174
                     RPFG++ LI G D   G   L+  +PSGTF  + A A G  S   + E L
Sbjct: 126 GASGEERLMSRPFGVALLIAGHDADDGY-QLFHAEPSGTFYRYNAKAIGSGSEGAQAELL 184
Query: 175 EKNYKETSGQETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLD 220
            + +   + +E   L ++ L +V+E      N +++ +T++ G K  D
Sbjct: 185 NEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYD 232

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

Iteration: 1
 Score =  149 bits (376), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 82/228 (35%), Positives = 131/228 (57%), Gaps = 10/228 (4%)
Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
           + YDR ++ FSP+G LFQVEY+LEA++ G+ A+G+   + +VLGVEK++T  L +S S+ 
Sbjct: 8   SEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESDSIE 67
Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           KIV +D HI  A +GL ADAR +I  AR    +H L  ++ + VE +T+ +  L  ++ +
Sbjct: 68  KIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGE 127
Query: 122 SGG------VRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMR-EFL 174
                     RPFG++ LI G D   G   L+  +PSGTF  + A A G  S   + E L
Sbjct: 128 GASGEERLMSRPFGVALLIAGHDADDGY-QLFHAEPSGTFYRYNAKAIGSGSEGAQAELL 186
Query: 175 EKNYKETSGQETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLD 220
            + +   + +E   L ++ L +V+E      N +++ +T++ G K  D
Sbjct: 187 NEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYD 234

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

Iteration: 1
 Score =  149 bits (375), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 82/228 (35%), Positives = 131/228 (57%), Gaps = 10/228 (4%)
Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
           + YDR ++ FSP+G LFQVEY+LEA++ G+ A+G+   + +VLGVEK++T  L +S S+ 
Sbjct: 6   SEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESDSIE 65
Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           KIV +D HI  A +GL ADAR +I  AR    +H L  ++ + VE +T+ +  L  ++ +
Sbjct: 66  KIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGE 125
Query: 122 SGG------VRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMR-EFL 174
                     RPFG++ LI G D   G   L+  +PSGTF  + A A G  S   + E L
Sbjct: 126 GASGEERLMSRPFGVALLIAGHDADDGY-QLFHAEPSGTFYRYNAKAIGSGSEGAQAELL 184
Query: 175 EKNYKETSGQETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLD 220
            + +   + +E   L ++ L +V+E      N +++ +T++ G K  D
Sbjct: 185 NEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYD 232

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

Iteration: 1
 Score =  148 bits (373), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 85/216 (39%), Positives = 129/216 (59%), Gaps = 7/216 (3%)
Query: 3   RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRK 62
           RY  ++T FSP G L Q++YAL AV++G  ++G++ T+ +V+  EKKS+  L  S ++ K
Sbjct: 4   RYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSETLSK 63
Query: 63  IVSLDNHIALACAGLKADARVLINRAR--IECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
           +  L   I    +G+  D RVL++++R        R+  E P T + +   +A + Q+ T
Sbjct: 64  VSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPT-KLLVSEVAKIMQEAT 122
Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK- 179
           QSGGVRPFG+S LI G D + G  SLYQ DPSG++  WKA A G+ S + + FLEK +  
Sbjct: 123 QSGGVRPFGVSLLIAGHDEFNGF-SLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWND 181
Query: 180 ETSGQETIKLAIRALLEVVES--GGKNIEVAVMTRE 213
           E   ++ I +A+  L E VE    G  IE+A++  E
Sbjct: 182 ELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDE 217

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

Iteration: 1
 Score =  145 bits (367), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 81/225 (36%), Positives = 129/225 (57%), Gaps = 10/225 (4%)
Query: 5   DRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIV 64
           DR ++ FSP+G LFQVEY+LEA++ G+ A+G+   + +VLGVEK++T  L +S S+ KIV
Sbjct: 1   DRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESDSIEKIV 60
Query: 65  SLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGG 124
            +D HI  A +GL ADAR +I  AR    +H L  ++ + VE +T+ +  L  ++ +   
Sbjct: 61  EIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGAS 120
Query: 125 ------VRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMR-EFLEKN 177
                  RPFG++ LI G D   G   L+  +PSGTF  + A A G  S   + E L + 
Sbjct: 121 GEERLMSRPFGVALLIAGHDADDGY-QLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNEW 179
Query: 178 YKETSGQETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLD 220
           +   + +E   L ++ L +V+E      N +++ +T++ G K  D
Sbjct: 180 HSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYD 224

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

Iteration: 1
 Score =  140 bits (354), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 85/232 (36%), Positives = 128/232 (55%), Gaps = 8/232 (3%)
Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGN-AAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           A +DR IT+FSP+G L+QVEYA +A+ +G   +V VRG D  V+  +KK   KL DS +V
Sbjct: 7   AGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTV 66
Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
             +  +  +I     G+ AD+R  + RAR E  + +      + V+ + + IA + Q YT
Sbjct: 67  THLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYT 126
Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK- 179
           Q+  +RP G   +++G D   G P +Y+ DP+G +  +KA A G        FLEK  K 
Sbjct: 127 QNAEMRPLGCCMILIGIDEEQG-PQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKK 185
Query: 180 --ETSGQETIKLAIRALLEVVESGGK--NIEVAVMTREK-GLKQLDEAEIDA 226
             + + ++T++ AI  L  V+    K   IEV V+T E    + L EAEIDA
Sbjct: 186 KFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDA 237

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

Iteration: 1
 Score =  140 bits (352), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 85/232 (36%), Positives = 127/232 (54%), Gaps = 8/232 (3%)
Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGN-AAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           A +DR IT+FSP+G L+QVEYA +A+ +G   +V VRG D  V+  +KK   KL DS +V
Sbjct: 7   AGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTV 66
Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
             +  +   I     G+ AD+R  + RAR E  + +      + V+ + + IA + Q YT
Sbjct: 67  THLFKITESIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYT 126
Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK- 179
           Q+  +RP G   +++G D   G P +Y+ DP+G +  +KA A G        FLEK  K 
Sbjct: 127 QNAEMRPLGCCMILIGIDEEQG-PQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKK 185
Query: 180 --ETSGQETIKLAIRALLEVVESGGK--NIEVAVMTREK-GLKQLDEAEIDA 226
             + + ++T++ AI  L  V+    K   IEV V+T E    + L EAEIDA
Sbjct: 186 KFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDA 237

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

Iteration: 1
 Score =  134 bits (337), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 77/233 (33%), Positives = 128/233 (54%), Gaps = 11/233 (4%)
Query: 3   RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRK 62
           +YD  +TV+SP G + Q+EYA+EAV++G+A VG++     VL   K++  +L  +   +K
Sbjct: 5   QYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSEL--AAHQKK 62
Query: 63  IVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQS 122
           I+ +DNHI ++ AGL ADAR+L N  R EC   R   + P+ V  +   I    Q  TQ 
Sbjct: 63  ILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQR 122
Query: 123 GGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKN---YK 179
            G RP+G+  LI G+D     P ++QT PS  +   +A + G  S S R +LE++   + 
Sbjct: 123 YGRRPYGVGLLIAGYDDMG--PHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM 180
Query: 180 ETSGQETIKLAIRALLEVVES----GGKNIEVAVMTREKGLKQLDEAEIDAMV 228
           E +  E +K  +RAL E + +      KN+ + ++ ++      D+ ++   +
Sbjct: 181 ECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFL 233

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

Iteration: 1
 Score =  134 bits (337), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 77/233 (33%), Positives = 128/233 (54%), Gaps = 11/233 (4%)
Query: 3   RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRK 62
           +YD  +TV+SP G + Q+EYA+EAV++G+A VG++     VL   K++  +L  +   +K
Sbjct: 5   QYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSEL--AAHQKK 62
Query: 63  IVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQS 122
           I+ +DNHI ++ AGL ADAR+L N  R EC   R   + P+ V  +   I    Q  TQ 
Sbjct: 63  ILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQR 122
Query: 123 GGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKN---YK 179
            G RP+G+  LI G+D     P ++QT PS  +   +A + G  S S R +LE++   + 
Sbjct: 123 YGRRPYGVGLLIAGYDDMG--PHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM 180
Query: 180 ETSGQETIKLAIRALLEVVES----GGKNIEVAVMTREKGLKQLDEAEIDAMV 228
           E +  E +K  +RAL E + +      KN+ + ++ ++      D+ ++   +
Sbjct: 181 ECNLDELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFL 233

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

Iteration: 1
 Score =  131 bits (329), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 77/200 (38%), Positives = 119/200 (59%), Gaps = 7/200 (3%)
Query: 19  QVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLK 78
           Q++YAL AV++G  ++G++ T+ +V+  EKKS+  L  S ++ K+  L   I    +G+ 
Sbjct: 1   QIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSETLSKVSLLTPDIGAVYSGMG 60
Query: 79  ADARVLINRAR--IECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVG 136
            D RVL++++R        R+  E P T + +   +A + Q+ TQSGGVRPFG+S LI G
Sbjct: 61  PDYRVLVDKSRKVAHTSYKRIYGEYPPT-KLLVSEVAKIMQEATQSGGVRPFGVSLLIAG 119
Query: 137 FDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK-ETSGQETIKLAIRALL 195
            D + G  SLYQ DPSG++  WKA A G+ S + + FLEK +  E   ++ I +A+  L 
Sbjct: 120 HDEFNGF-SLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWNDELELEDAIHIALLTLK 178
Query: 196 EVVES--GGKNIEVAVMTRE 213
           E VE    G  IE+A++  E
Sbjct: 179 ESVEGEFNGDTIELAIIGDE 198

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

Iteration: 1
 Score =  117 bits (293), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 66/173 (38%), Positives = 93/173 (53%), Gaps = 2/173 (1%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YD + +VFSPDG  FQVEYA++AV  G  ++G++  D +V  VEK  T KL   +   KI
Sbjct: 8   YDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNVKI 67
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
             +D HI    +GL  D R L+NR R E  S +   + P+ +      +    Q +T   
Sbjct: 68  QVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYN 127
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEK 176
            VRPFG+ST+  G D       LY  +PSG++  +K  ATG+   S +  LEK
Sbjct: 128 SVRPFGVSTIFGGVDKNGA--HLYMLEPSGSYWGYKGAATGKGRQSAKAELEK 178

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

Iteration: 1
 Score =  117 bits (293), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 66/173 (38%), Positives = 93/173 (53%), Gaps = 2/173 (1%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YD + +VFSPDG  FQVEYA++AV  G  ++G++  D +V  VEK  T KL   +   KI
Sbjct: 8   YDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNVKI 67
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
             +D HI    +GL  D R L+NR R E  S +   + P+ +      +    Q +T   
Sbjct: 68  QVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYN 127
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEK 176
            VRPFG+ST+  G D       LY  +PSG++  +K  ATG+   S +  LEK
Sbjct: 128 SVRPFGVSTIFGGVDKNGA--HLYMLEPSGSYWGYKGAATGKGRQSAKAELEK 178

>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 =  117 bits (293), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 66/173 (38%), Positives = 93/173 (53%), Gaps = 2/173 (1%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YD + +VFSPDG  FQVEYA++AV  G  ++G++  D +V  VEK  T KL   +   KI
Sbjct: 7   YDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNVKI 66
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
             +D HI    +GL  D R L+NR R E  S +   + P+ +      +    Q +T   
Sbjct: 67  QVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYN 126
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEK 176
            VRPFG+ST+  G D       LY  +PSG++  +K  ATG+   S +  LEK
Sbjct: 127 SVRPFGVSTIFGGVDKNGA--HLYMLEPSGSYWGYKGAATGKGRQSAKAELEK 177

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

Iteration: 1
 Score =  117 bits (293), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 66/173 (38%), Positives = 93/173 (53%), Gaps = 2/173 (1%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YD + +VFSPDG  FQVEYA++AV  G  ++G++  D +V  VEK  T KL   +   KI
Sbjct: 2   YDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNVKI 61
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
             +D HI    +GL  D R L+NR R E  S +   + P+ +      +    Q +T   
Sbjct: 62  QVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYN 121
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEK 176
            VRPFG+ST+  G D       LY  +PSG++  +K  ATG+   S +  LEK
Sbjct: 122 SVRPFGVSTIFGGVDKNGA--HLYMLEPSGSYWGYKGAATGKGRQSAKAELEK 172

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

Iteration: 1
 Score =  117 bits (293), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 66/173 (38%), Positives = 93/173 (53%), Gaps = 2/173 (1%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YD + +VFSPDG  FQVEYA++AV  G  ++G++  D +V  VEK  T KL   +   KI
Sbjct: 4   YDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNVKI 63
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
             +D HI    +GL  D R L+NR R E  S +   + P+ +      +    Q +T   
Sbjct: 64  QVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYN 123
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEK 176
            VRPFG+ST+  G D       LY  +PSG++  +K  ATG+   S +  LEK
Sbjct: 124 SVRPFGVSTIFGGVDKNGA--HLYMLEPSGSYWGYKGAATGKGRQSAKAELEK 174

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

Iteration: 1
 Score =  116 bits (291), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 65/186 (34%), Positives = 102/186 (54%), Gaps = 2/186 (1%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YD + + FSPDG +FQVEYA++AV   + A+G+R  D +V GVEK    KL +  S +++
Sbjct: 8   YDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEGSNKRL 67
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
            ++D H+ +A AGL ADAR L + AR E  + R      + ++++   +A     YT   
Sbjct: 68  FNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYS 127
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEK-NYKETS 182
            VRPFG S ++  +    G   LY  DPSG    +   A G+   + +  +EK   KE +
Sbjct: 128 AVRPFGCSFMLGSYSANDG-AQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQMKEMT 186
Query: 183 GQETIK 188
            ++ +K
Sbjct: 187 CRDVVK 192

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

Iteration: 1
 Score =  115 bits (289), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 65/186 (34%), Positives = 102/186 (54%), Gaps = 2/186 (1%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YD + + FSPDG +FQVEYA++AV   + A+G+R  D +V GVEK    KL +  S +++
Sbjct: 7   YDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEGSNKRL 66
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
            ++D H+ +A AGL ADAR L + AR E  + R      + ++++   +A     YT   
Sbjct: 67  FNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYS 126
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEK-NYKETS 182
            VRPFG S ++  +    G   LY  DPSG    +   A G+   + +  +EK   KE +
Sbjct: 127 AVRPFGCSFMLGSYSVNDG-AQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQMKEMT 185
Query: 183 GQETIK 188
            ++ +K
Sbjct: 186 CRDIVK 191

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

Iteration: 1
 Score =  113 bits (282), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 67/173 (38%), Positives = 92/173 (53%), Gaps = 4/173 (2%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YD     FSP G LFQVEYALEA+++G+  VG+R     VL   K++  +L  S   +KI
Sbjct: 5   YDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADEL--SSYQKKI 62
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
           +  D H+ L+ AGL  DARVL N  R +C    L     + VE     +    QK TQS 
Sbjct: 63  IKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSA 122
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEK 176
           G RP+G+  LI+G+D  +G   L +  PSG  +     A G  S   + +LE+
Sbjct: 123 GGRPYGVGLLIIGYDK-SGA-HLLEFQPSGNVTELYGTAIGARSQGAKTYLER 173

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

Iteration: 1
 Score =  113 bits (282), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 67/173 (38%), Positives = 92/173 (53%), Gaps = 4/173 (2%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YD     FSP G LFQVEYALEA+++G+  VG+R     VL   K++  +L  S   +KI
Sbjct: 6   YDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADEL--SSYQKKI 63
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
           +  D H+ L+ AGL  DARVL N  R +C    L     + VE     +    QK TQS 
Sbjct: 64  IKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSA 123
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEK 176
           G RP+G+  LI+G+D  +G   L +  PSG  +     A G  S   + +LE+
Sbjct: 124 GGRPYGVGLLIIGYDK-SGA-HLLEFQPSGNVTELYGTAIGARSQGAKTYLER 174

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

Iteration: 1
 Score =  112 bits (280), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 76/224 (33%), Positives = 116/224 (51%), Gaps = 12/224 (5%)
Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNA-AVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           A YDR IT+FSP+G L+QVEYA +A  + N  ++ VRG D  V+  +KK   KL D  +V
Sbjct: 1   AGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPTTV 60
Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
             I  +   I +   G   DAR    RA+ E    R      +  + + + +A L Q YT
Sbjct: 61  SYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYT 120
Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK- 179
           Q   +RP G+    V  D   G PS+Y+TDP+G +  +KA ATG     +   LE ++K 
Sbjct: 121 QRAYMRPLGVILTFVSVDEELG-PSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKK 179
Query: 180 -------ETSGQETIKLAIRALLEVV--ESGGKNIEVAVMTREK 214
                  E S ++ ++ AI  +++ +  E    ++EV V T++K
Sbjct: 180 SKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDK 223

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

Iteration: 1
 Score =  112 bits (280), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 75/222 (33%), Positives = 115/222 (51%), Gaps = 12/222 (5%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNA-AVGVRGTDTIVLGVEKKSTVKLQDSRSVRK 62
           YDR IT+FSP+G L+QVEYA +A  + N  ++ VRG D  V+  +KK   KL D  +V  
Sbjct: 12  YDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPTTVSY 71
Query: 63  IVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQS 122
           I  +   I +   G   DAR    RA+ E    R      +  + + + +A L Q YTQ 
Sbjct: 72  IFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQR 131
Query: 123 GGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK--- 179
             +RP G+    V  D   G PS+Y+TDP+G +  +KA ATG     +   LE ++K   
Sbjct: 132 AYMRPLGVILTFVSVDEELG-PSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKKSK 190
Query: 180 -----ETSGQETIKLAIRALLEVV--ESGGKNIEVAVMTREK 214
                E S ++ ++ AI  +++ +  E    ++EV V T++K
Sbjct: 191 IDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDK 232

>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 =  112 bits (279), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 67/173 (38%), Positives = 92/173 (53%), Gaps = 4/173 (2%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YD     FSP G LFQVEYALEA+++G+  VG+R     VL   K++  +L  S   +KI
Sbjct: 6   YDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADEL--SSYQKKI 63
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
           +  D H+ L+ AGL  DARVL N  R +C    L     + VE     +    QK TQS 
Sbjct: 64  IKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSY 123
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEK 176
           G RP+G+  LI+G+D  +G   L +  PSG  +     A G  S   + +LE+
Sbjct: 124 GGRPYGVGLLIIGYDK-SGA-HLLEFQPSGNVTELYGTAIGARSQGAKTYLER 174

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

Iteration: 1
 Score =  112 bits (279), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 67/173 (38%), Positives = 92/173 (53%), Gaps = 4/173 (2%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YD     FSP G LFQVEYALEA+++G+  VG+R     VL   K++  +L  S   +KI
Sbjct: 7   YDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADEL--SSYQKKI 64
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
           +  D H+ L+ AGL  DARVL N  R +C    L     + VE     +    QK TQS 
Sbjct: 65  IKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSY 124
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEK 176
           G RP+G+  LI+G+D  +G   L +  PSG  +     A G  S   + +LE+
Sbjct: 125 GGRPYGVGLLIIGYDK-SGA-HLLEFQPSGNVTELYGTAIGARSQGAKTYLER 175

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

Iteration: 1
 Score =  112 bits (279), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 67/173 (38%), Positives = 92/173 (53%), Gaps = 4/173 (2%)
Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YD     FSP G LFQVEYALEA+++G+  VG+R     VL   K++  +L  S   +KI
Sbjct: 5   YDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADEL--SSYQKKI 62
Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
           +  D H+ L+ AGL  DARVL N  R +C    L     + VE     +    QK TQS 
Sbjct: 63  IKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSY 122
Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEK 176
           G RP+G+  LI+G+D  +G   L +  PSG  +     A G  S   + +LE+
Sbjct: 123 GGRPYGVGLLIIGYDK-SGA-HLLEFQPSGNVTELYGTAIGARSQGAKTYLER 173

>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 = 62.8 bits (151), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 52/209 (24%), Positives = 99/209 (47%), Gaps = 16/209 (7%)
Query: 25  EAVRKGNAAVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARV 83
           + +  G   VG+   D +++  E++ T++     ++ +K+  +D +  +  AGL  DA+V
Sbjct: 3   QTLETGTTTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQV 62
Query: 84  LINRARIECQSHRLTVEDPVTVEYITRYIAGL--QQKYTQSGGVRPFGLSTLIVGFDPYT 141
           L+   + E + +RL     + +E +   ++ +  Q KY       P+ +  L+ G D   
Sbjct: 63  LVRYMKAELELYRLQRRVNMPIEAVATLLSNMLNQVKYM------PYMVQLLVGGIDT-- 114
Query: 142 GVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE-TSGQETIKLAIRALLEVVE- 199
             P ++  D +G        +TG  S  +   LE  Y E  +  E + L IRA+    + 
Sbjct: 115 -APHVFSIDAAGGSVEDIYASTGSGSPFVYGVLESQYSEKMTVDEGVDLVIRAISAAKQR 173
Query: 200 --SGGKNIEVAVMTREKGLKQLDEAEIDA 226
             + G  I+VAV+TR+ G  QL   +I++
Sbjct: 174 DSASGGMIDVAVITRKDGYVQLPTDQIES 202

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

Iteration: 1
 Score = 62.8 bits (151), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 52/209 (24%), Positives = 99/209 (47%), Gaps = 16/209 (7%)
Query: 25  EAVRKGNAAVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARV 83
           + +  G   VG+   D +++  E++ T++     ++ +K+  +D +  +  AGL  DA+V
Sbjct: 3   QTLETGTTTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQV 62
Query: 84  LINRARIECQSHRLTVEDPVTVEYITRYIAGL--QQKYTQSGGVRPFGLSTLIVGFDPYT 141
           L+   + E + +RL     + +E +   ++ +  Q KY       P+ +  L+ G D   
Sbjct: 63  LVRYMKAELELYRLQRRVNMPIEAVATLLSNMLNQVKYM------PYMVQLLVGGIDT-- 114
Query: 142 GVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE-TSGQETIKLAIRALLEVVE- 199
             P ++  D +G        +TG  S  +   LE  Y E  +  E + L IRA+    + 
Sbjct: 115 -APHVFSIDAAGGSVEDIYASTGSGSPFVYGVLESQYSEKMTVDEGVDLVIRAISAAKQR 173
Query: 200 --SGGKNIEVAVMTREKGLKQLDEAEIDA 226
             + G  I+VAV+TR+ G  QL   +I++
Sbjct: 174 DSASGGMIDVAVITRKDGYVQLPTDQIES 202

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

Iteration: 1
 Score = 60.8 bits (146), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 51/200 (25%), Positives = 96/200 (48%), Gaps = 16/200 (8%)
Query: 34  VGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIEC 92
           VG+   D +++  E++ T++     ++ +K+  +D +  +  AGL  DA+VL+   + E 
Sbjct: 4   VGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKAEL 63
Query: 93  QSHRLTVEDPVTVEYITRYIAGL--QQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTD 150
           + +RL     + +E +   ++ +  Q KY       P+ +  L+ G D     P ++  D
Sbjct: 64  ELYRLQRRVNMPIEAVATLLSNMLNQVKYM------PYMVQLLVGGIDT---APHVFSID 114
Query: 151 PSGTFSAWKANATGRNSNSMREFLEKNYKE-TSGQETIKLAIRALLEVVE---SGGKNIE 206
            +G        +TG  S  +   LE  Y E  +  E + L IRA+    +   + G  I+
Sbjct: 115 AAGGSVEDIYASTGSGSPFVYGVLESQYSEKMTVDEGVDLVIRAISAAKQRDSASGGMID 174
Query: 207 VAVMTREKGLKQLDEAEIDA 226
           VAV+TR+ G  QL   +I++
Sbjct: 175 VAVITRKDGYVQLPTDQIES 194

>pdb|1J2Q|H Chain H, 20s Proteasome In Complex With Calpain-inhibitor I From Archaeoglobus Fulgidus Length = 202

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 52/187 (27%), Positives = 86/187 (45%), Gaps = 12/187 (6%)
Query: 34  VGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIEC 92
           VG+   D +V+  EK++T+     S++ +KI  + + +A+  AG   DA+ L    +IE 
Sbjct: 4   VGLVCKDGVVMATEKRATMGNFIASKAAKKIYQIADRMAMTTAGSVGDAQFLARIIKIEA 63
Query: 93  QSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDP- 151
             + +  E   TV    R IA L      S    P+ +  LI G D  +   S+Y  DP 
Sbjct: 64  NLYEIRRERKPTV----RAIATLTSNLLNSYRYFPYLVQLLIGGID--SEGKSIYSIDPI 117
Query: 152 SGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVE---SGGKNIEV 207
            G        ATG  S +    LE  +    G  E ++LA+RA+   ++   + G  I+V
Sbjct: 118 GGAIEEKDIVATGSGSLTAYGVLEDRFTPEIGVDEAVELAVRAIYSAMKRDSASGDGIDV 177
Query: 208 AVMTREK 214
             +T ++
Sbjct: 178 VKITEDE 184

>pdb|3NZJ|K Chain K, Crystal Structure Of Yeast 20s Proteasome In Complex With Ligand 2a Length = 287

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 37/171 (21%), Positives = 77/171 (45%), Gaps = 7/171 (4%)
Query: 27  VRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLI 85
           +  G   +  R    I++ V+ ++T      S++V+K++ ++  +    AG  AD +   
Sbjct: 72  IAHGTTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTMAGGAADCQFWE 131
Query: 86  NRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPS 145
                +C+ H L  ++ ++V   ++ ++ L  +Y  +G      + T+I G+    G P+
Sbjct: 132 TWLGSQCRLHELREKERISVAAASKILSNLVYQYKGAG----LSMGTMICGYTRKEG-PT 186
Query: 146 LYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK-ETSGQETIKLAIRALL 195
           +Y  D  GT         G         L+ NYK + S ++ + L  R++L
Sbjct: 187 IYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSIL 237

>pdb|1RYP|K Chain K, Crystal Structure Of The 20s Proteasome From Yeast At 2.4 Angstroms Resolution Length = 198

Iteration: 1
 Score = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 44/197 (22%), Positives = 88/197 (44%), Gaps = 12/197 (6%)
Query: 34  VGVRGTDTIVLGVEKKST---VKLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARI 90
           +G+R  D+++L   K  T     L+DS    K   L  H  ++ AG   D        + 
Sbjct: 5   LGIRVQDSVILASSKAVTRGISVLKDSDD--KTRQLSPHTLMSFAGEAGDTVQFAEYIQA 62
Query: 91  ECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTD 150
             Q + +  +  ++ + ++ ++     K  +S   RP+ ++ LI G+D     P LYQ D
Sbjct: 63  NIQLYSIREDYELSPQAVSSFVRQELAKSIRSR--RPYQVNVLIGGYDKKKNKPELYQID 120
Query: 151 PSGTFSAWKANATGRNSNSMREFLEKNYKET----SGQETIKLAIRALLEVVESGGKNIE 206
             GT       A G +       L+ +Y+       G + +KL ++ L + +    K + 
Sbjct: 121 YLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVI 180
Query: 207 VAVMTREKGLKQLDEAE 223
           V ++ ++ G++Q+D+ +
Sbjct: 181 VKIVDKD-GIRQVDDFQ 196

>pdb|4B4T|5 Chain 5, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 287

Iteration: 1
 Score = 44.3 bits (103), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 36/171 (21%), Positives = 77/171 (45%), Gaps = 7/171 (4%)
Query: 27  VRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLI 85
           +  G   +  R    I++ V+ ++T      S++V++++ ++  +    AG  AD +   
Sbjct: 72  IAHGTTTLAFRFQGGIIVAVDSRATAGNWVASQTVKRVIEINPFLLGTMAGGAADCQFWE 131
Query: 86  NRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPS 145
                +C+ H L  ++ ++V   ++ ++ L  +Y  +G      + T+I G+    G P+
Sbjct: 132 TWLGSQCRLHELREKERISVAAASKILSNLVYQYKGAG----LSMGTMICGYTRKEG-PT 186
Query: 146 LYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK-ETSGQETIKLAIRALL 195
           +Y  D  GT         G         L+ NYK + S ++ + L  R++L
Sbjct: 187 IYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSIL 237

>pdb|3UNF|H Chain H, Mouse 20s Immunoproteasome In Complex With Pr-957 Length = 234

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 48/181 (26%), Positives = 79/181 (43%), Gaps = 20/181 (11%)
Query: 40  DTIVLGVEKKSTVKLQDS----RSVRKIVSLDNHIALACAGLKADARVLINRARIECQSH 95
           D ++LG + ++T    DS    +S  KI  +   I    AG+ AD  +    A  + + H
Sbjct: 10  DGVILGADTRAT---NDSVVADKSCEKIHFIAPKIYCCGAGVAADTEMTTRMAASKMELH 66
Query: 96  RLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTF 155
            L+      V  +TR +     +Y    G      ++L+VG     G P LY+  P G++
Sbjct: 67  ALSTGREPRVATVTRILRQTLFRYQGHVG------ASLVVGGVDLNG-PQLYEVHPHGSY 119
Query: 156 SAWKANATGRNSNSMREFLEKNYKET----SGQETIKLAIRA-LLEVVESGGKNIEVAVM 210
           S     A G    +    LE  ++      + QE +  AI A +L  + SGG N++  V+
Sbjct: 120 SRLPFTALGSGQGAAVALLEDRFQPNMTLEAAQELLVEAITAGILSDLGSGG-NVDACVI 178
Query: 211 T 211
           T
Sbjct: 179 T 179

>pdb|1G0U|K Chain K, A Gated Channel Into The Proteasome Core Particle Length = 212

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 35/156 (22%), Positives = 73/156 (46%), Gaps = 7/156 (4%)
Query: 42  IVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVE 100
           I++ V+ ++T      S++V+K++ ++  +    AG  AD +        +C+ H L  +
Sbjct: 12  IIVAVDSRATAGNWVASQTVKKVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREK 71
Query: 101 DPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKA 160
           + ++V   ++ ++ L  +Y  +G      + T+I G+    G P++Y  D  GT      
Sbjct: 72  ERISVAAASKILSNLVYQYKGAG----LSMGTMICGYTRKEG-PTIYYVDSDGTRLKGDI 126
Query: 161 NATGRNSNSMREFLEKNYK-ETSGQETIKLAIRALL 195
              G         L+ NYK + S ++ + L  R++L
Sbjct: 127 FCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSIL 162

>pdb|1RYP|M Chain M, Crystal Structure Of The 20s Proteasome From Yeast At 2.4 Angstroms Resolution Length = 222

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 48/219 (21%), Positives = 90/219 (41%), Gaps = 28/219 (12%)
Query: 30  GNAAVGVRGTDTIVLGVEKKSTVKLQ-DSRSVRKIVSLDNHIALACAGLKADARVLINRA 88
           G   +G+ G D  VL  + ++      +SR   K+    ++I ++  G  AD   L+ R 
Sbjct: 9   GGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNIVMSANGFAADGDALVKRF 68
Query: 89  RIECQSHRLTVEDP-VTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLY 147
           +   + +     D  +++    R I    Q         P+ + T+I G D   G  ++Y
Sbjct: 69  KNSVKWYHFDHNDKKLSINSAARNI----QHLLYGKRFFPYYVHTIIAGLDE-DGKGAVY 123
Query: 148 QTDPSGTFSAWKANATGRNSNSMREFLEK--NYKE-----TSG-----------QETIKL 189
             DP G++   +  A G  ++ +  FL+   N+K      T+G           +E IKL
Sbjct: 124 SFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYEPGTNGKVKKPLKYLSVEEVIKL 183
Query: 190 AIRALLEVVESG---GKNIEVAVMTREKGLKQLDEAEID 225
              +     E     G  +E+ ++T++   K+  E + D
Sbjct: 184 VRDSFTSATERHIQVGDGLEILIVTKDGVRKEFYELKRD 222

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 48/219 (21%), Positives = 90/219 (41%), Gaps = 28/219 (12%)
Query: 30  GNAAVGVRGTDTIVLGVEKKSTVKLQ-DSRSVRKIVSLDNHIALACAGLKADARVLINRA 88
           G   +G+ G D  VL  + ++      +SR   K+    ++I ++  G  AD   L+ R 
Sbjct: 28  GGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNIVMSANGFAADGDALVKRF 87
Query: 89  RIECQSHRLTVEDP-VTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLY 147
           +   + +     D  +++    R I    Q         P+ + T+I G D   G  ++Y
Sbjct: 88  KNSVKWYHFDHNDKKLSINSAARNI----QHLLYGKRFFPYYVHTIIAGLDE-DGKGAVY 142
Query: 148 QTDPSGTFSAWKANATGRNSNSMREFLEK--NYKE-----TSG-----------QETIKL 189
             DP G++   +  A G  ++ +  FL+   N+K      T+G           +E IKL
Sbjct: 143 SFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYEPGTNGKVKKPLKYLSVEEVIKL 202
Query: 190 AIRALLEVVESG---GKNIEVAVMTREKGLKQLDEAEID 225
              +     E     G  +E+ ++T++   K+  E + D
Sbjct: 203 VRDSFTSATERHIQVGDGLEILIVTKDGVRKEFYELKRD 241

>pdb|1RYP|L Chain L, Crystal Structure Of The 20s Proteasome From Yeast At 2.4 Angstroms Resolution Length = 212

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 34/156 (21%), Positives = 73/156 (46%), Gaps = 7/156 (4%)
Query: 42  IVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVE 100
           I++ V+ ++T      S++V++++ ++  +    AG  AD +        +C+ H L  +
Sbjct: 12  IIVAVDSRATAGNWVASQTVKRVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREK 71
Query: 101 DPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKA 160
           + ++V   ++ ++ L  +Y  +G      + T+I G+    G P++Y  D  GT      
Sbjct: 72  ERISVAAASKILSNLVYQYKGAG----LSMGTMICGYTRKEG-PTIYYVDSDGTRLKGDI 126
Query: 161 NATGRNSNSMREFLEKNYK-ETSGQETIKLAIRALL 195
              G         L+ NYK + S ++ + L  R++L
Sbjct: 127 FCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSIL 162

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	249
1iru_D	248	20S proteasome; cell cycle, immune response, prote	1e-127
1ryp_D	241	20S proteasome; multicatalytic proteinase, protein	1e-121
1iru_F	263	20S proteasome; cell cycle, immune response, prote	1e-119
1iru_A	246	20S proteasome; cell cycle, immune response, prote	1e-115
1iru_E	241	20S proteasome; cell cycle, immune response, prote	1e-115
1ryp_A	243	20S proteasome; multicatalytic proteinase, protein	1e-113
1iru_B	233	20S proteasome; cell cycle, immune response, prote	1e-113
1ryp_B	250	20S proteasome; multicatalytic proteinase, protein	1e-111
1iru_C	261	20S proteasome; cell cycle, immune response, prote	1e-111
3h4p_A	264	Proteasome subunit alpha; core particle, cytoplasm	1e-109
1ryp_E	242	20S proteasome; multicatalytic proteinase, protein	1e-109
1yar_A	233	Proteasome alpha subunit; proteasome 20S, PA26 pro	1e-109
1ryp_F	233	20S proteasome; multicatalytic proteinase, protein	1e-108
1j2p_A	246	Alpha-ring, proteasome alpha subunit; hydrolase; 2	1e-108
1iru_G	254	20S proteasome; cell cycle, immune response, prote	1e-107
3nzj_F	288	Proteasome component C1; ubiquitin, protein degrad	1e-106
1ryp_C	244	20S proteasome; multicatalytic proteinase, protein	1e-106
1ryp_G	244	20S proteasome; multicatalytic proteinase, protein	1e-103
3mi0_A	248	Proteasome subunit alpha; enzyme inhibitors, lacto	5e-56
1q5q_A	259	Proteasome alpha-type subunit 1; proteasome assemb	9e-54
3unf_H	234	Proteasome subunit beta type-10; antigen presentat	2e-42
3nzj_H	261	Proteasome component PUP1; ubiquitin, protein degr	4e-42
1yar_H	217	Proteasome beta subunit; proteasome 20S, PA26 prot	2e-41
1ryp_I	222	20S proteasome; multicatalytic proteinase, protein	2e-38
1q5r_H	294	Proteasome beta-type subunit 1; proteasome assembl	4e-35
1iru_I	234	20S proteasome; cell cycle, immune response, prote	6e-35
3nzj_K	287	Proteasome component PRE2; ubiquitin, protein degr	1e-34
1ryp_K	198	20S proteasome; multicatalytic proteinase, protein	2e-33
1q5q_H	235	Proteasome beta-type subunit 1; proteasome assembl	5e-31
1ryp_L	212	20S proteasome; multicatalytic proteinase, protein	6e-31
1iru_L	204	20S proteasome; cell cycle, immune response, prote	3e-28
2jay_A	291	Proteasome; hydrolase; 1.99A {Mycobacterium tuberc	7e-28
2jay_A	291	Proteasome; hydrolase; 1.99A {Mycobacterium tuberc	9e-28
1j2q_H	202	Proteasome beta subunit; ubiquitin, CP, hydrolase;	6e-26
1ryp_M	222	20S proteasome; multicatalytic proteinase, protein	2e-24
1ryp_J	204	20S proteasome; multicatalytic proteinase, protein	2e-23
1iru_J	205	20S proteasome; cell cycle, immune response, prote	8e-22
1iru_H	205	20S proteasome; cell cycle, immune response, prote	1e-21
1iru_K	201	20S proteasome; cell cycle, immune response, prote	1e-21
3unf_N	199	Proteasome subunit beta type-9; antigen presentati	2e-21
1g0u_M	266	Proteasome component PRE4; ubiquitin, degradation,	9e-21
1ryp_N	233	20S proteasome; multicatalytic proteinase, protein	2e-20
1ryp_H	205	20S proteasome; multicatalytic proteinase, protein	3e-20
1iru_M	213	20S proteasome; cell cycle, immune response, prote	3e-19
1iru_N	219	20S proteasome; cell cycle, immune response, prote	2e-15
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-06

>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 =  360 bits (927), Expect = e-127
 Identities = 168/243 (69%), Positives = 197/243 (81%), Gaps = 4/243 (1%)

Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YDRAITVFSPDGHLFQVEYA EAV+KG+ AVGVRG D +VLGVEKKS  KLQD R+VRKI
Sbjct: 3   YDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVRKI 62

Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
            +LD+++ +A AGL ADAR++INRAR+ECQSHRLTVEDPVTVEYITRYIA L+Q+YTQS 
Sbjct: 63  CALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSN 122

Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE--- 180
           G RPFG+S LIVGFD   G P LYQTDPSGT+ AWKANA GR + S+REFLEKNY +   
Sbjct: 123 GRRPFGISALIVGFDF-DGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEAI 181

Query: 181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKKAAAEA 240
            +   TIKL I+ALLEVV+SGGKNIE+AVM R++ LK L+  EI+  VAEIE +K   E 
Sbjct: 182 ETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVAEIEKEKEENEK 241

Query: 241 AKK 243
            K+
Sbjct: 242 KKQ 244

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

 Score =  344 bits (884), Expect = e-121
 Identities = 136/238 (57%), Positives = 185/238 (77%), Gaps = 5/238 (2%)

Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSR-SVRK 62
           YDRA+++FSPDGH+FQVEYALEAV++G  AVGV+G + +VLG E++ST+KLQD+R +  K
Sbjct: 2   YDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSK 61

Query: 63  IVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQS 122
           +  +D+H+ L+ +GL AD+R+LI +AR+E QSHRLT+EDPVTVEY+TRY+AG+QQ+YTQS
Sbjct: 62  VSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQS 121

Query: 123 GGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET- 181
           GGVRPFG+STLI GFDP    P LYQT+PSG +S+W A   GRNS ++REFLEKNY    
Sbjct: 122 GGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKE 181

Query: 182 ---SGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKKA 236
              + +E +KL +R+LLEVV++G KNIE+ V+  +  +  L   EI+  V +IE +K 
Sbjct: 182 PPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEKQ 239

>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 =  339 bits (871), Expect = e-119
 Identities = 80/252 (31%), Positives = 131/252 (51%), Gaps = 13/252 (5%)

Query: 1   MAR--YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSR 58
           M R  YD  +TV+SP G + Q+EYA+EAV++G+A VG++     VL   K++  +L    
Sbjct: 1   MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAH- 59

Query: 59  SVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQK 118
             +KI+ +DNHI ++ AGL ADAR+L N  R EC   R   + P+ V  +   I    Q 
Sbjct: 60  -QKKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQI 118

Query: 119 YTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNY 178
            TQ  G RP+G+  LI G+D     P ++QT PS  +   +A + G  S S R +LE++ 
Sbjct: 119 PTQRYGRRPYGVGLLIAGYDDMG--PHIFQTCPSANYFDCRAMSIGARSQSARTYLERHM 176

Query: 179 KE---TSGQETIKLAIRALLEVVESGG----KNIEVAVMTREKGLKQLDEAEIDAMVAEI 231
            E    +  E +K  +RAL E + +      KN+ + ++ ++      D+ ++   +  +
Sbjct: 177 SEFMECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEGL 236

Query: 232 EAKKAAAEAAKK 243
           E +        +
Sbjct: 237 EERPQRKAQPAQ 248

>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 =  329 bits (846), Expect = e-115
 Identities = 85/240 (35%), Positives = 131/240 (54%), Gaps = 8/240 (3%)

Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNA-AVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           A +DR IT+FSP+G L+QVEYA +A+ +G   +V VRG D  V+  +KK   KL DS +V
Sbjct: 7   AGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTV 66

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
             +  +  +I     G+ AD+R  + RAR E  + +      + V+ + + IA + Q YT
Sbjct: 67  THLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYT 126

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           Q+  +RP G   +++G D   G P +Y+ DP+G +  +KA A G        FLEK  K+
Sbjct: 127 QNAEMRPLGCCMILIGIDEEQG-PQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKK 185

Query: 181 T---SGQETIKLAIRALLEVVESGGK--NIEVAVMTRE-KGLKQLDEAEIDAMVAEIEAK 234
               + ++T++ AI  L  V+    K   IEV V+T E    + L EAEIDA +  +  +
Sbjct: 186 KFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVALAER 245

>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 =  327 bits (842), Expect = e-115
 Identities = 83/239 (34%), Positives = 138/239 (57%), Gaps = 10/239 (4%)

Query: 1   MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
            + YDR +  FSP+G LFQVEY +EA++ G+ A+G++ ++ + L VEK+ T  L +  S+
Sbjct: 5   RSEYDRGVNTFSPEGRLFQVEYDIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEPSSI 64

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
            KIV +D HI  A +GL ADA+ LI++AR+E Q+H  T  + +TVE +T+ ++ L  ++ 
Sbjct: 65  EKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFG 124

Query: 121 QSGG-----VRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLE 175
           +         RPFG++ L  G D     P L+  DPSGTF    A A G  S   +  L+
Sbjct: 125 EEDADPGAMSRPFGVALLFGGVDEKG--PQLFHMDPSGTFVQCDARAIGSASEGAQSSLQ 182

Query: 176 KNYKET-SGQETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEIDAMVAEI 231
           + Y ++ + +E IK ++  L +V+E      NIE+A +   +      + E++ ++ +I
Sbjct: 183 ELYHKSMTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVIKDI 241

>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 =  324 bits (834), Expect = e-113
 Identities = 77/244 (31%), Positives = 123/244 (50%), Gaps = 13/244 (5%)

Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNA-AVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           A YDR IT+FSP+G L+QVEYA +A  + N  ++ VRG D  V+  +KK   KL D  +V
Sbjct: 1   AGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPTTV 60

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
             I  +   I +   G   DAR    RA+ E    R      +  + + + +A L Q YT
Sbjct: 61  SYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYT 120

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           Q   +RP G+    V  D   G PS+Y+TDP+G +  +KA ATG     +   LE ++K+
Sbjct: 121 QRAYMRPLGVILTFVSVDEELG-PSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKK 179

Query: 181 T--------SGQETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEIDAMVAE 230
           +        S ++ ++ AI  +++ + +     ++EV V T++K    L    I+  +  
Sbjct: 180 SKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDK-FFTLSAENIEERLVA 238

Query: 231 IEAK 234
           I  +
Sbjct: 239 IAEQ 242

>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 =  323 bits (830), Expect = e-113
 Identities = 95/233 (40%), Positives = 134/233 (57%), Gaps = 6/233 (2%)

Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
             Y  ++T FSP G L Q+EYAL AV  G  +VG++  + +VL  EKK    L D RSV 
Sbjct: 3   RGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDERSVH 62

Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           K+  +  HI L  +G+  D RVL++RAR   Q + L  ++P+    + + +A + Q+YTQ
Sbjct: 63  KVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQ 122

Query: 122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET 181
           SGGVRPFG+S LI G++     P L+Q+DPSG + AWKA A G+N  + + FLEK Y E 
Sbjct: 123 SGGVRPFGVSLLICGWNEGR--PYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNED 180

Query: 182 -SGQETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEIDAMVAEI 231
              ++ I  AI  L E  E      NIEV +   E G ++L   E+   +A I
Sbjct: 181 LELEDAIHTAILTLKESFEGQMTEDNIEVGICN-EAGFRRLTPTEVKDYLAAI 232

>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 =  319 bits (821), Expect = e-111
 Identities = 85/251 (33%), Positives = 137/251 (54%), Gaps = 21/251 (8%)

Query: 1   MA-RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRS 59
           M  RY  ++T FSP G L Q++YAL AV++G  ++G++ T+ +V+  EKKS+  L  S +
Sbjct: 1   MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET 60

Query: 60  VRKIVSLDNHIALACAGLKADARVLINRARIECQ-SHRLTVEDPVTVEYITRYIAGLQQK 118
           + K+  L   I    +G+  D RVL++++R     S++    +    + +   +A + Q+
Sbjct: 61  LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE 120

Query: 119 YTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNY 178
            TQSGGVRPFG+S LI G D + G  SLYQ DPSG++  WKA A G+ S + + FLEK +
Sbjct: 121 ATQSGGVRPFGVSLLIAGHDEFNG-FSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRW 179

Query: 179 KET-SGQETIKLAIRALLEVVES--GGKNIEVAVMTREKGL---------------KQLD 220
            +    ++ I +A+  L E VE    G  IE+A++  E                  ++L 
Sbjct: 180 NDELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLT 239

Query: 221 EAEIDAMVAEI 231
             EI+  +  +
Sbjct: 240 SQEINDRLEAL 250

>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 =  318 bits (818), Expect = e-111
 Identities = 91/253 (35%), Positives = 149/253 (58%), Gaps = 11/253 (4%)

Query: 1   MA-RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRS 59
           M+ RYD   T+FSP+G L+QVEYA+EA+      +G+   D ++L  E+++  KL D   
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF 60

Query: 60  V-RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQK 118
              KI  L+  +A + AG+ +DA VL N  R+  Q + L  ++P+  E +   +  ++Q 
Sbjct: 61  FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA 120

Query: 119 YTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNY 178
           YTQ GG RPFG+S L +G+D + G   LYQ+DPSG +  WKA   G NS +    L+++Y
Sbjct: 121 YTQFGGKRPFGVSLLYIGWDKHYG-FQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDY 179

Query: 179 KET--SGQETIKLAIRAL---LEVVESGGKNIEVAVMTREKG---LKQLDEAEIDAMVAE 230
           KE   + +  + LAI+ L   ++V +   + +E+A +TRE G   ++ L + E++ ++ +
Sbjct: 180 KEGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKK 239

Query: 231 IEAKKAAAEAAKK 243
            E ++A AE  KK
Sbjct: 240 HEEEEAKAEREKK 252

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

 Score =  315 bits (810), Expect = e-109
 Identities = 105/251 (41%), Positives = 158/251 (62%), Gaps = 5/251 (1%)

Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
           + YDRAITVFSP+G L+QVEYA EAVR+G  A+G+   D +VL V+++ T KL   RS+ 
Sbjct: 10  SAYDRAITVFSPEGRLYQVEYAREAVRRGTTAIGIACKDGVVLAVDRRITSKLVKIRSIE 69

Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           KI  +D+H+A A +GL ADARVLI+RAR+E Q +RLT  + +++E + + I  ++Q YTQ
Sbjct: 70  KIFQIDDHVAAATSGLVADARVLIDRARLEAQIYRLTYGEEISIEMLAKKICDIKQAYTQ 129

Query: 122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET 181
            GGVRPFG+S LI G D       L++TDPSG    +KA A G     + E LEK Y++ 
Sbjct: 130 HGGVRPFGVSLLIAGIDKNE--ARLFETDPSGALIEYKATAIGSGRPVVMELLEKEYRDD 187

Query: 182 -SGQETIKLAIRALLEVVES-GGKNIEVAVMTREKG-LKQLDEAEIDAMVAEIEAKKAAA 238
            +  E ++LAI AL +  E    +N++V ++T +    K++   EI  ++ +++ K    
Sbjct: 188 ITLDEGLELAITALTKANEDIKPENVDVCIITVKDAQFKKIPVEEIKKLIEKVKKKLNEE 247

Query: 239 EAAKKGPPKET 249
              ++   +ET
Sbjct: 248 NKKEEENREET 258

>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 =  314 bits (807), Expect = e-109
 Identities = 84/242 (34%), Positives = 138/242 (57%), Gaps = 10/242 (4%)

Query: 5   DRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIV 64
           DR ++ FSP+G LFQVEY+LEA++ G+ A+G+   + +VLGVEK++T  L +S S+ KIV
Sbjct: 1   DRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESDSIEKIV 60

Query: 65  SLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG- 123
            +D HI  A +GL ADAR +I  AR    +H L  ++ + VE +T+ +  L  ++ +   
Sbjct: 61  EIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGAS 120

Query: 124 -----GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNY 178
                  RPFG++ LI G D   G   L+  +PSGTF  + A A G  S   +  L   +
Sbjct: 121 GEERLMSRPFGVALLIAGHDADDG-YQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNEW 179

Query: 179 KET-SGQETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKK 235
             + + +E   L ++ L +V+E      N +++ +T++ G K  D  +   ++ E++ K+
Sbjct: 180 HSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELIKELKEKE 239

Query: 236 AA 237
           AA
Sbjct: 240 AA 241

>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 =  313 bits (805), Expect = e-109
 Identities = 92/230 (40%), Positives = 139/230 (60%), Gaps = 5/230 (2%)

Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
             Y RAITVFSPDG LFQVEYA EAV+KG+ A+G++  + ++L  +KK   +L +  S+ 
Sbjct: 6   MAYSRAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQNSIE 65

Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           KI  +D+++A   +GL ADARVL++ ARI  Q  ++T    V +E + + +A   Q+YTQ
Sbjct: 66  KIQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQ 125

Query: 122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET 181
            GGVRP+G+S +  G D     P L+  DP+GT + +KA A G   +++  FLE+ YKE 
Sbjct: 126 YGGVRPYGVSLIFAGIDQIG--PRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKEN 183

Query: 182 -SGQETIKLAIRALLEVVESG--GKNIEVAVMTREKGLKQLDEAEIDAMV 228
              +E + L I+AL   +E G   K  E+A +T     +  D+ E+   +
Sbjct: 184 LPEKEAVTLGIKALKSSLEEGEELKAPEIASITVGNKYRIYDQEEVKKFL 233

>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 =  310 bits (797), Expect = e-108
 Identities = 72/234 (30%), Positives = 109/234 (46%), Gaps = 12/234 (5%)

Query: 3   RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRK 62
            YD     FSP G LFQVEYALEA+++G+  VG+R     VL   K++  +L      +K
Sbjct: 4   NYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSY--QKK 61

Query: 63  IVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQS 122
           I+  D H+ L+ AGL  DARVL N  R +C    L     + VE     +    QK TQS
Sbjct: 62  IIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQS 121

Query: 123 GGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET- 181
            G RP+G+  LI+G+D       L +  PSG  +     A G  S   + +LE+      
Sbjct: 122 YGGRPYGVGLLIIGYDKSG--AHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFI 179

Query: 182 ----SGQETIKLAIRALLEVVESG---GKNIEVAVMTREKGLKQLDEAEIDAMV 228
               +  E IK  + A+ + +        N+ +A++ ++      D   +   +
Sbjct: 180 KIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI 233

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

 Score =  310 bits (796), Expect = e-108
 Identities = 105/246 (42%), Positives = 150/246 (60%), Gaps = 9/246 (3%)

Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
             YDRAITVFSPDG LFQVEYA EAV++G  A+G++  + ++L  +K+   KL +  ++ 
Sbjct: 6   MGYDRAITVFSPDGRLFQVEYAREAVKRGATAIGIKCKEGVILIADKRVGSKLLEKDTIE 65

Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           KI  +D HI  A +GL ADARVLI+RARIE Q +RLT + P+TV+ + + I   +Q+YTQ
Sbjct: 66  KIYKIDEHICAATSGLVADARVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQ 125

Query: 122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET 181
            GGVRPFG+S LI G +    VP LY+TDPSG    +KA A G    ++ EF EK Y++ 
Sbjct: 126 YGGVRPFGVSLLIAGVN---EVPKLYETDPSGALLEYKATAIGMGRMAVTEFFEKEYRDD 182

Query: 182 -SGQETIKLAIRALLEVVESG--GKNIEVAVMTRE-KGLKQLDEAEIDAMVAEIEAKKAA 237
            S  + + L + A+   +ES    +NIEV  +  + +  K++   E+   V     +   
Sbjct: 183 LSFDDAMVLGLVAMGLSIESELVPENIEVGYVKVDDRTFKEVSPEELKPYVERANERI-- 240

Query: 238 AEAAKK 243
            E  KK
Sbjct: 241 RELLKK 246

>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 =  308 bits (790), Expect = e-107
 Identities = 72/247 (29%), Positives = 123/247 (49%), Gaps = 7/247 (2%)

Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
             YD + + FSPDG +FQVEYA++AV   + A+G+R  D +V GVEK    KL +  S +
Sbjct: 5   TGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEGSNK 64

Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           ++ ++D H+ +A AGL ADAR L + AR E  + R      + ++++   +A     YT 
Sbjct: 65  RLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTL 124

Query: 122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET 181
              VRPFG S ++  +    G   LY  DPSG    +   A G+   + +  +EK   + 
Sbjct: 125 YSAVRPFGCSFMLGSYSVNDG-AQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQMKE 183

Query: 182 -SGQETIKLAIRALLEVVESG---GKNIEVAVMTRE-KGLKQLDEAEIDAMVAEIEAKKA 236
            + ++ +K   + +  V +        +E++ +     G  ++   +I    AE  AK++
Sbjct: 184 MTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREE-AEKYAKES 242

Query: 237 AAEAAKK 243
             E  + 
Sbjct: 243 LKEEDES 249

>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 =  307 bits (788), Expect = e-106
 Identities = 73/258 (28%), Positives = 115/258 (44%), Gaps = 12/258 (4%)

Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
             YD + +VFSPDG  FQVEYA++AV  G  ++G++  D +V  VEK  T KL   +   
Sbjct: 6   TGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNV 65

Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           KI  +D HI    +GL  D R L+NR R E  S +   + P+ +      +    Q +T 
Sbjct: 66  KIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTL 125

Query: 122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK-- 179
              VRPFG+ST+  G D       LY  +PSG++  +K  ATG+   S +  LEK     
Sbjct: 126 YNSVRPFGVSTIFGGVDKNG--AHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHH 183

Query: 180 --ETSGQETIKLAIRALLEVVESGG---KNIEVAVMTRE---KGLKQLDEAEIDAMVAEI 231
               S +E +K A + +    E        +E++  +        K +    +   +   
Sbjct: 184 PEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAIDFA 243

Query: 232 EAKKAAAEAAKKGPPKET 249
           + +    +   +      
Sbjct: 244 QKEINGDDDEDEDDSDNV 261

>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 =  305 bits (783), Expect = e-106
 Identities = 86/241 (35%), Positives = 138/241 (57%), Gaps = 11/241 (4%)

Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQD-SRSV 60
            RYD   T+FSP+G L+QVEYALE++     A+G+  +D IVL  E+K T  L +   S 
Sbjct: 3   RRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTST 62

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
            K+  L++ IA+A AGL ADA +LIN ARI  Q++  T  + + VE + R ++ ++Q YT
Sbjct: 63  EKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYT 122

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           Q GG+RPFG+S +  G+D   G   LY ++PSG ++ WKA + G N+++ +  L+ +YK+
Sbjct: 123 QHGGLRPFGVSFIYAGYDDRYG-YQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKD 181

Query: 181 T-SGQETIKLAIRALLEVVESG---GKNIEVAVMTREKG-----LKQLDEAEIDAMVAEI 231
                + I+LA++ L +  +S       +E A + +         K     EI  ++ + 
Sbjct: 182 DMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVKT 241

Query: 232 E 232
            
Sbjct: 242 G 242

>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 =  299 bits (768), Expect = e-103
 Identities = 73/243 (30%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
             YD + +VFSPDG  FQVEYA++AV  G  ++G++  D +V  VEK  T KL   +   
Sbjct: 2   TGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNV 61

Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           KI  +D HI    +GL  D R L+NR R E  S +   + P+ +      +    Q +T 
Sbjct: 62  KIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTL 121

Query: 122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK-- 179
              VRPFG+ST+  G D       LY  +PSG++  +K  ATG+   S +  LEK     
Sbjct: 122 YNSVRPFGVSTIFGGVDKNG--AHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHH 179

Query: 180 --ETSGQETIKLAIRALLEVVESGG---KNIEVAVMTREKG---LKQLDEAEIDAMVAEI 231
               S +E +K A + +    E        +E++  +  +     K +    +   +   
Sbjct: 180 PEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAIDFA 239

Query: 232 EAK 234
           + +
Sbjct: 240 QKE 242

>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 =  178 bits (453), Expect = 5e-56
 Identities = 41/248 (16%), Positives = 93/248 (37%), Gaps = 26/248 (10%)

Query: 12  SPDGHLFQ-VEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHI 70
           SP+  + +  E A + + +  + V +     ++   E  S       RS++KI  L + +
Sbjct: 8   SPEQAMRERSELARKGIARAKSVVALAYAGGVLFVAENPS-------RSLQKISELYDRV 60

Query: 71  ALACAGLKADARVLINRARIECQSHRLT-VEDPVTVEYITRYIAGLQQKYTQSGGVRPFG 129
             A AG   +   L         +         VT   +    A        +   +P+ 
Sbjct: 61  GFAAAGKFNEFDNLRRGGIQFADTRGYAYDRRDVTGRQLANVYAQTLGT-IFTEQAKPYE 119

Query: 130 LSTLI--VGFDPYTGVPSLYQTDPSGTFS-AWKANATGRNSNSMREFLEKNYKET-SGQE 185
           +   +  V     T  P LY+    G+ +        G  +  +   L+++Y E  S  +
Sbjct: 120 VELCVAEVAHYGETKRPELYRITYDGSIADEPHFVVMGGTTEPIANALKESYAENASLTD 179

Query: 186 TIKLAIRALLEVVESGG---------KNIEVAVMTREKG---LKQLDEAEIDAMVAEIEA 233
            +++A+ AL                  ++EVAV+   +     +++  + + A++ + E+
Sbjct: 180 ALRIAVAALRAGSADTSGGDQPTLGVASLEVAVLDANRPRRAFRRITGSALQALLVDQES 239

Query: 234 KKAAAEAA 241
            ++  E++
Sbjct: 240 PQSDGESS 247

>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 =  173 bits (439), Expect = 9e-54
 Identities = 38/247 (15%), Positives = 89/247 (36%), Gaps = 25/247 (10%)

Query: 19  QVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLK 78
           + E A + + +G + V +   D ++   E  ST       ++ K+  L + +  A  G  
Sbjct: 16  RSELARKGIARGRSVVVLTFRDGVLFVAENPST-------ALHKVSELYDRLGFAAVGKY 68

Query: 79  ADARVLINRARIECQSHRLT-VEDPVTVEYITRYIA-GLQQKYTQSGGVRPFGLSTLI-- 134
            +   L     +       +     VT   +    A  L   +T+    +P+ +   +  
Sbjct: 69  NEFENLRRAGIVHADMRGYSYDRRDVTGRSLANAYAQTLGTIFTE--QPKPYEVEICVAE 126

Query: 135 VGFDPYTGVPSLYQTDPSGTFSAWK-ANATGRNSNSMREFLEKNYKET-SGQETIKLAIR 192
           VG       P LY+    G+    +     G  +  +   + ++Y+     +  + +A+ 
Sbjct: 127 VGRVGSPKAPQLYRITYDGSIVDEQHFVVMGGTTEPIATAMRESYRADLDLEAAVGIAVN 186

Query: 193 ALLEVVESGG-------KNIEVAVMTRE---KGLKQLDEAEIDAMVAEIEAKKAAAEAAK 242
           AL +     G        ++EVAV+ +    +  +++    ++ +V    A  + +    
Sbjct: 187 ALRQGGAGEGEKRNVDVASLEVAVLDQSRPRRAFRRIAGTALEQLVPAEPAAASESAPEP 246

Query: 243 KGPPKET 249
           K   +  
Sbjct: 247 KPDTETK 253

>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 =  143 bits (363), Expect = 2e-42
 Identities = 43/189 (22%), Positives = 77/189 (40%), Gaps = 14/189 (7%)

Query: 33  AVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIE 91
             G+   D ++LG + ++T   +   +S  KI  +   I    AG+ AD  +    A  +
Sbjct: 3   IAGLVFRDGVILGADTRATNDSVVADKSCEKIHFIAPKIYCCGAGVAADTEMTTRMAASK 62

Query: 92  CQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDP 151
            + H L+      V  +TR +     +Y         G S ++ G D   G P LY+  P
Sbjct: 63  MELHALSTGREPRVATVTRILRQTLFRYQG-----HVGASLVVGGVDL-NG-PQLYEVHP 115

Query: 152 SGTFSAWKANATGRNSNSMREFLEKNYKET-SGQETIKLAIRALLEVVE----SGGKNIE 206
            G++S     A G    +    LE  ++   + +   +L + A+   +     SGG N++
Sbjct: 116 HGSYSRLPFTALGSGQGAAVALLEDRFQPNMTLEAAQELLVEAITAGILSDLGSGG-NVD 174

Query: 207 VAVMTREKG 215
             V+T    
Sbjct: 175 ACVITAGGA 183

>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 =  143 bits (362), Expect = 4e-42
 Identities = 49/231 (21%), Positives = 87/231 (37%), Gaps = 15/231 (6%)

Query: 11  FSPDGHLFQVEYAL-EAVRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDN 68
           +  +  L +  +   +A   G   VGV+  + +V+  + +ST   +   ++  K+  +  
Sbjct: 9   YQRNNFLAENSHTQPKATSTGTTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISP 68

Query: 69  HIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPF 128
            I  A AG  AD   +        + H L       V    + +     KY         
Sbjct: 69  KIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQG-----HI 123

Query: 129 GLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET-SGQETI 187
           G   ++ G DP TG   L+     G+       + G  S +    LE ++K+  + +E I
Sbjct: 124 GAYLIVAGVDP-TG-SHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEAI 181

Query: 188 KLAIRALLEVVE----SGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAK 234
           KLA  A+   +     SG  N++V VM   K  + L       +  E +  
Sbjct: 182 KLASDAIQAGIWNDLGSGS-NVDVCVMEIGKDAEYLRNYLTPNVREEKQKS 231

>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 =  140 bits (354), Expect = 2e-41
 Identities = 52/214 (24%), Positives = 101/214 (47%), Gaps = 14/214 (6%)

Query: 25  EAVRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARV 83
           + +  G   VG+   D +++  E++ T+      ++ +K+  +D +  +  AGL  DA+V
Sbjct: 3   QTLETGTTTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQV 62

Query: 84  LINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGV 143
           L+   + E + +RL     + +E +   ++ +  +        P+ +  L+ G D  T  
Sbjct: 63  LVRYMKAELELYRLQRRVNMPIEAVATLLSNMLNQVKY----MPYMVQLLVGGID--TA- 115

Query: 144 PSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET-SGQETIKLAIRALLEVVE--- 199
           P ++  D +G        +TG  S  +   LE  Y E  +  E + L IRA+    +   
Sbjct: 116 PHVFSIDAAGGSVEDIYASTGSGSPFVYGVLESQYSEKMTVDEGVDLVIRAISAAKQRDS 175

Query: 200 -SGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIE 232
            SGG  I+VAV+TR+ G  QL   +I++ + ++ 
Sbjct: 176 ASGG-MIDVAVITRKDGYVQLPTDQIESRIRKLG 208

>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 =  132 bits (335), Expect = 2e-38
 Identities = 46/208 (22%), Positives = 79/208 (37%), Gaps = 14/208 (6%)

Query: 33  AVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIE 91
            VGV+  + +V+  + +ST   +   ++  K+  +   I  A AG  AD   +       
Sbjct: 3   IVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSN 62

Query: 92  CQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDP 151
            + H L       V    + +     KY         G   ++ G DP TG   L+    
Sbjct: 63  IELHSLYTSREPRVVSALQMLKQHLFKYQG-----HIGAYLIVAGVDP-TG-SHLFSIHA 115

Query: 152 SGTFSAWKANATGRNSNSMREFLEKNYKET-SGQETIKLAIRALLEVVE----SGGKNIE 206
            G+       + G  S +    LE ++K+  + +E IKLA  A+   +     SG  N++
Sbjct: 116 HGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKLASDAIQAGIWNDLGSGS-NVD 174

Query: 207 VAVMTREKGLKQLDEAEIDAMVAEIEAK 234
           V VM   K  + L       +  E +  
Sbjct: 175 VCVMEIGKDAEYLRNYLTPNVREEKQKS 202

>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 =  125 bits (316), Expect = 4e-35
 Identities = 42/252 (16%), Positives = 86/252 (34%), Gaps = 20/252 (7%)

Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQ-DSRSVRK 62
            +  I   S          + +    G   V +     ++L  ++++T      SR V  
Sbjct: 39  PENRIGHRSHSTRGGDGMESGDLAPHGTTIVALTYKGGVLLAGDRRATQGNLIASRDVEA 98

Query: 63  IVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQS 122
           +   D + A   AG    A  L+    +E + +      P+T +     +A + +     
Sbjct: 99  VYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEGVPLTFDGKANRLASMVRGN-LG 157

Query: 123 GGVRPFGLSTLIVGFDPY----TGVPSLYQTDPSGTFSAWKAN--ATGRNSNSMREFLEK 176
             ++   +  L+VG+D      +    +   D  G     +A   A G  S   +  L+K
Sbjct: 158 AAMQGLAVVPLLVGYDLDADDESRAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALKK 217

Query: 177 NYKET-SGQETIKLAIRALLEVVE----SGGK------NIEVAVMTREKGLKQLDEAEID 225
            Y      +  ++ AI +L +  +    +GG             +T + G   + E    
Sbjct: 218 IYSPDSDEETALRAAIESLYDAADDDSATGGPDLTRGIYPTAVTIT-QAGAVHVSEETTS 276

Query: 226 AMVAEIEAKKAA 237
            +   I A++  
Sbjct: 277 ELARRIVAERTE 288

>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 =  123 bits (312), Expect = 6e-35
 Identities = 42/188 (22%), Positives = 71/188 (37%), Gaps = 14/188 (7%)

Query: 33  AVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIE 91
             GV   D IVLG + ++T   +   ++  KI  +  +I    AG  AD  +        
Sbjct: 3   IAGVVYKDGIVLGADTRATEGMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISSN 62

Query: 92  CQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDP 151
            + H L+      V    R +  +  +Y         G + ++ G D  TG P LY   P
Sbjct: 63  LELHSLSTGRLPRVVTANRMLKQMLFRYRG-----YIGAALVLGGVDV-TG-PHLYSIYP 115

Query: 152 SGTFSAWKANATGRNSNSMREFLEKNYKET-SGQETIKLAIRALLEVVE----SGGKNIE 206
            G+         G  S +     E  ++     +E   L   A+   +     SG  NI+
Sbjct: 116 HGSTDKLPYVTMGSGSLAAMAVFEDKFRPDMEEEEAKNLVSEAIAAGIFNDLGSGS-NID 174

Query: 207 VAVMTREK 214
           + V+++ K
Sbjct: 175 LCVISKNK 182

>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 =  124 bits (313), Expect = 1e-34
 Identities = 42/219 (19%), Positives = 93/219 (42%), Gaps = 13/219 (5%)

Query: 25  EAVRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARV 83
             +  G   +  R    I++ V+ ++T      S++V+K++ ++  +    AG  AD + 
Sbjct: 70  IKIAHGTTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTMAGGAADCQF 129

Query: 84  LINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGV 143
                  +C+ H L  ++ ++V   ++ ++ L  +Y          + T+I G+    G 
Sbjct: 130 WETWLGSQCRLHELREKERISVAAASKILSNLVYQYKG----AGLSMGTMICGYTRKEG- 184

Query: 144 PSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE-TSGQETIKLAIRALLEVVE--- 199
           P++Y  D  GT         G         L+ NYK   S ++ + L  R++L       
Sbjct: 185 PTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAAHRDA 244

Query: 200 -SGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKKAA 237
            SGG ++ +  +T E G       ++  +  +++ ++ +
Sbjct: 245 YSGG-SVNLYHVT-EDGWIYHGNHDVGELFWKVKEEEGS 281

>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 =  118 bits (299), Expect = 2e-33
 Identities = 40/196 (20%), Positives = 84/196 (42%), Gaps = 8/196 (4%)

Query: 34  VGVRGTDTIVLGVEKKSTVKLQD-SRSVRKIVSLDNHIALACAGLKADARVLINRARIEC 92
           +G+R  D+++L   K  T  +     S  K   L  H  ++ AG   D        +   
Sbjct: 5   LGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYIQANI 64

Query: 93  QSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPS 152
           Q + +  +  ++ + ++ ++     K  +S    P+ ++ LI G+D     P LYQ D  
Sbjct: 65  QLYSIREDYELSPQAVSSFVRQELAKSIRSRR--PYQVNVLIGGYDKKKNKPELYQIDYL 122

Query: 153 GTFSAWKANATGRNSNSMREFLEKNYKET-SGQETIKLAIRALLEVVE---SGGKNIEVA 208
           GT       A G +       L+ +Y+   + +E + L    + E+ +      K + V 
Sbjct: 123 GTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVIVK 182

Query: 209 VMTREKGLKQLDEAEI 224
           ++ ++ G++Q+D+ + 
Sbjct: 183 IVDKD-GIRQVDDFQA 197

>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 =  113 bits (285), Expect = 5e-31
 Identities = 40/223 (17%), Positives = 77/223 (34%), Gaps = 20/223 (8%)

Query: 33  AVGVRGTDTIVLGVEKKSTVKLQ-DSRSVRKIVSLDNHIALACAGLKADARVLINRARIE 91
            V +     ++L  ++++T      SR V K+   D + A   AG    A  L+    +E
Sbjct: 3   IVALTYKGGVLLAGDRRATQGNLIASRDVEKVYVTDEYSAAGIAGTAGIAIELVRLFAVE 62

Query: 92  CQSHRLTVEDPVTVEYITRYIAGLQQKY----TQSGGVRPFGLSTLIVGFDPYTGVPSLY 147
            + +      P+T +     +A + +       Q   V P  +   +   D       + 
Sbjct: 63  LEHYEKIEGVPLTFDGKANRLASMVRGNLGAAMQGLAVVPLLVGYDLDADDESRA-GRIV 121

Query: 148 QTDPSGTFSAWKAN--ATGRNSNSMREFLEKNYKET-SGQETIKLAIRALLEVVE----S 200
             D  G     +A   A G  S   +  L+K Y      +  ++ AI +L +  +    +
Sbjct: 122 SYDVVGGRYEERAGYHAVGSGSLFAKSALKKIYSPDSDEETALRAAIESLYDAADDDSAT 181

Query: 201 GGK------NIEVAVMTREKGLKQLDEAEIDAMVAEIEAKKAA 237
           GG             +T + G   + E     +   I A++  
Sbjct: 182 GGPDLTRGIYPTAVTIT-QAGAVHVSEETTSELARRIVAERTE 223

>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 =  113 bits (284), Expect = 6e-31
 Identities = 40/211 (18%), Positives = 91/211 (43%), Gaps = 13/211 (6%)

Query: 33  AVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIE 91
            +  R    I++ V+ ++T      S++V++++ ++  +    AG  AD +        +
Sbjct: 3   TLAFRFQGGIIVAVDSRATAGNWVASQTVKRVIEINPFLLGTMAGGAADCQFWETWLGSQ 62

Query: 92  CQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDP 151
           C+ H L  ++ ++V   ++ ++ L  +Y          + T+I G+    G P++Y  D 
Sbjct: 63  CRLHELREKERISVAAASKILSNLVYQYKG----AGLSMGTMICGYTRKEG-PTIYYVDS 117

Query: 152 SGTFSAWKANATGRNSNSMREFLEKNYKE-TSGQETIKLAIRALLEVVE----SGGKNIE 206
            GT         G         L+ NYK   S ++ + L  R++L        SGG ++ 
Sbjct: 118 DGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAAHRDAYSGG-SVN 176

Query: 207 VAVMTREKGLKQLDEAEIDAMVAEIEAKKAA 237
           +  +T E G       ++  +  +++ ++ +
Sbjct: 177 LYHVT-EDGWIYHGNHDVGELFWKVKEEEGS 206

>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 =  105 bits (265), Expect = 3e-28
 Identities = 35/206 (16%), Positives = 84/206 (40%), Gaps = 14/206 (6%)

Query: 34  VGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIEC 92
           +  +    +++  + ++T      S++V+K++ ++ ++    AG  AD          +C
Sbjct: 4   LAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQC 63

Query: 93  QSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPS 152
           + + L  ++ ++V   ++ +A +  +Y          + T+I G+D   G P LY  D  
Sbjct: 64  RIYELRNKERISVAAASKLLANMVYQYKG----MGLSMGTMICGWDK-RG-PGLYYVDSE 117

Query: 153 GTFSAWKANATGRNSNSMREFLEKNYKE-TSGQETIKLAIRALLEVVE----SGGKNIEV 207
           G   +    + G  S      +++ Y      ++   LA RA+ +       SGG  + +
Sbjct: 118 GNRISGATFSVGSGSVYAYGVMDRGYSYDLEVEQAYDLARRAIYQATYRDAYSGG-AVNL 176

Query: 208 AVMTREKGLKQLDEAEIDAMVAEIEA 233
             +  E G  ++    +  +  +   
Sbjct: 177 YHVR-EDGWIRVSSDNVADLHEKYSG 201

>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 =  106 bits (267), Expect = 7e-28
 Identities = 43/237 (18%), Positives = 90/237 (37%), Gaps = 18/237 (7%)

Query: 25  EAVRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARV 83
             +  G   V ++    +V+  +++ST   +   R VRK+   D++ A   AG  A A  
Sbjct: 52  AQLPHGTTIVALKYPGGVVMAGDRRSTQGNMISGRDVRKVYITDDYTATGIAGTAAVAVE 111

Query: 84  LINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPY--- 140
                 +E + +      P+T       +A + +    +   +      L+ G+D +   
Sbjct: 112 FARLYAVELEHYEKLEGVPLTFAGKINRLAIMVRGNLAAAM-QGLLALPLLAGYDIHASD 170

Query: 141 -TGVPSLYQTDPSGTFSAWKAN--ATGRNSNSMREFLEKNYKE-TSGQETIKLAIRALLE 196
                 +   D +G ++  +    A G  S   +  ++K Y + T G   +++A+ AL +
Sbjct: 171 PQSAGRIVSFDAAGGWNIEEEGYQAVGSGSLFAKSSMKKLYSQVTDGDSGLRVAVEALYD 230

Query: 197 VVE----SGG-----KNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKKAAAEAAKKG 244
             +    +GG          AV+    G   + E+ I  +   I   ++ A+     
Sbjct: 231 AADDDSATGGPDLVRGIFPTAVIIDADGAVDVPESRIAELARAIIESRSGADTFGSD 287

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

 Score = 99.6 bits (249), Expect = 6e-26
 Identities = 55/206 (26%), Positives = 91/206 (44%), Gaps = 15/206 (7%)

Query: 34  VGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIEC 92
           VG+   D +V+  EK++T+     S++ +KI  + + +A+  AG   DA+ L    +IE 
Sbjct: 4   VGLVCKDGVVMATEKRATMGNFIASKAAKKIYQIADRMAMTTAGSVGDAQFLARIIKIEA 63

Query: 93  QSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPS 152
             + +  E   TV  I    + L   Y       P+ +  LI G D   G  S+Y  DP 
Sbjct: 64  NLYEIRRERKPTVRAIATLTSNLLNSYRY----FPYLVQLLIGGIDS-EG-KSIYSIDPI 117

Query: 153 GT-FSAWKANATGRNSNSMREFLEKNYKET-SGQETIKLAIRALLEVVE----SGGKNIE 206
           G         ATG  S +    LE  +       E ++LA+RA+   ++    SG   I+
Sbjct: 118 GGAIEEKDIVATGSGSLTAYGVLEDRFTPEIGVDEAVELAVRAIYSAMKRDSASGD-GID 176

Query: 207 VAVMTREKGLKQLDEAEIDAMVAEIE 232
           V  +T E    Q    E++ ++A+  
Sbjct: 177 VVKIT-EDEFYQYSPEEVEQILAKFR 201

>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 = 96.3 bits (240), Expect = 2e-24
 Identities = 41/209 (19%), Positives = 80/209 (38%), Gaps = 30/209 (14%)

Query: 30  GNAAVGVRGTDTIVLGVEKKSTVKLQ-DSRSVRKIVSLDNHIALACAGLKADARVLINRA 88
           G   +G+ G D  VL  + ++      +SR   K+    ++I ++  G  AD   L+ R 
Sbjct: 9   GGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNIVMSANGFAADGDALVKRF 68

Query: 89  RIECQSHRLTVED-PVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLY 147
           +   + +     D  +++    R I  L           P+ + T+I G D   G  ++Y
Sbjct: 69  KNSVKWYHFDHNDKKLSINSAARNIQHLLYGKRF----FPYYVHTIIAGLDE-DGKGAVY 123

Query: 148 QTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG------------------QETIKL 189
             DP G++   +  A G  ++ +  FL+      +                   +E IKL
Sbjct: 124 SFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYEPGTNGKVKKPLKYLSVEEVIKL 183

Query: 190 AIRALLEVVE----SGGKNIEVAVMTREK 214
              +     E     G   +E+ ++T++ 
Sbjct: 184 VRDSFTSATERHIQVGD-GLEILIVTKDG 211

>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 = 92.7 bits (231), Expect = 2e-23
 Identities = 35/192 (18%), Positives = 71/192 (36%), Gaps = 13/192 (6%)

Query: 30  GNAAVGVRGTDTIVLGVEKKSTVKLQ-DSRSVRKIVSLDNHIALACAGLKADARVLINRA 88
           G   V + G D + +  + +   +    S    KI     H+ L   GL  D   L    
Sbjct: 8   GGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYG-HVFLGITGLATDVTTLNEMF 66

Query: 89  RIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQ 148
           R +   ++L  E  +  E  T+ ++    +        P+ +  ++ G +  +G P +  
Sbjct: 67  RYKTNLYKLKEERAIEPETFTQLVSSSLYERRFG----PYFVGPVVAGINSKSGKPFIAG 122

Query: 149 TDPSGTFSAWKA-NATGRNSNSMREFLEKNYKET-SGQETIKLAIRALLEVVE----SGG 202
            D  G     K    +G  S+ +    E  Y+     ++  +   +ALL   +    SG 
Sbjct: 123 FDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDALSGW 182

Query: 203 KNIEVAVMTREK 214
               V ++ +++
Sbjct: 183 -GAVVYIIKKDE 193

>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 = 88.8 bits (221), Expect = 8e-22
 Identities = 34/197 (17%), Positives = 75/197 (38%), Gaps = 22/197 (11%)

Query: 30  GNAAVGVRGTDTIVLGVEKKSTVKLQ-DSRSVRKIVSLDNHIALACAGLKADARVLINRA 88
           G A + ++G + + +  +++  ++ Q  +   +KI  + + + +  AGL  D + +  R 
Sbjct: 8   GGAVMAMKGKNCVAIAADRRFGIQAQLVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRL 67

Query: 89  RIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQ 148
           +     + L     +    +   +A L  +        P+    +I G DP T  P +  
Sbjct: 68  KFRLNLYELKEGRQIKPYTLMSMVANLLYEKRFG----PYYTEPVIAGLDPKTFKPFICS 123

Query: 149 TDPSGT------FSAWKANATGRNSNSMREFLEKNYKET-SGQETIKLAIRALLEVVE-- 199
            D  G       F       +G  +  M    E  ++         +   +A+L  V+  
Sbjct: 124 LDLIGCPMVTDDFV-----VSGTCAEQMYGMCESLWEPNMDPDHLFETISQAMLNAVDRD 178

Query: 200 --SGGKNIEVAVMTREK 214
             SG   + V ++ ++K
Sbjct: 179 AVSGM-GVIVHIIEKDK 194

>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 = 88.0 bits (219), Expect = 1e-21
 Identities = 35/187 (18%), Positives = 72/187 (38%), Gaps = 13/187 (6%)

Query: 34  VGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIEC 92
           + V+    +VLG + ++T      +R   K+  + + I    +G  AD + + +    + 
Sbjct: 4   MAVQFDGGVVLGADSRTTTGSYIANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTYQL 63

Query: 93  QSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPS 152
             H + + +P  V         +  +Y +           +I G+DP  G   +Y     
Sbjct: 64  GFHSIELNEPPLVHTAASLFKEMCYRYRE-----DLMAGIIIAGWDPQEG-GQVYSVPMG 117

Query: 153 GTFSAWKANATGRNSNSMREFLEKNYKE-TSGQETIKLAIRALLEVVE----SGGKNIEV 207
           G          G  S+ +  +++  Y+E  + +E ++    AL   +E    SGG  I +
Sbjct: 118 GMMVRQSFAIGGSGSSYIYGYVDATYREGMTKEECLQFTANALALAMERDGSSGG-VIRL 176

Query: 208 AVMTREK 214
           A +    
Sbjct: 177 AAIAESG 183

>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 = 88.0 bits (219), Expect = 1e-21
 Identities = 34/193 (17%), Positives = 76/193 (39%), Gaps = 11/193 (5%)

Query: 34  VGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIEC 92
           +G++G D +++  ++ +    +Q      K+  +   I L C G   D        +   
Sbjct: 5   IGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYIQKNV 64

Query: 93  QSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPS 152
           Q +++     ++      +         +S    P+ ++ L+ G+D + G P+LY  D  
Sbjct: 65  QLYKMRNGYELSPTAAANFTRRNLADCLRSRT--PYHVNLLLAGYDEHEG-PALYYMDYL 121

Query: 153 GTFSAWKANATGRNSNSMREFLEKNYKET-SGQETIKLAIRALLEVVE----SGGKNIEV 207
              +     A G  +      L++ Y  T S +  ++L  + L E+ +    +      V
Sbjct: 122 AALAKAPFAAHGYGAFLTLSILDRYYTPTISRERAVELLRKCLEELQKRFILNLP-TFSV 180

Query: 208 AVMTREKGLKQLD 220
            ++ +  G+  LD
Sbjct: 181 RIIDKN-GIHDLD 192

>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 = 87.6 bits (218), Expect = 2e-21
 Identities = 34/187 (18%), Positives = 68/187 (36%), Gaps = 14/187 (7%)

Query: 34  VGVRGTDTIVLGVEKKSTVKLQ-DSRSVRKIVSLDNHIALACAGLKADARVLINRARIEC 92
           + V     +V+G + + +      +R   K+  L   I  A +G  ADA+ + + A  + 
Sbjct: 4   MAVEFDGGVVVGSDSRVSAGTAVVNRVFDKLSPLHQRIFCALSGSAADAQAIADMAAYQL 63

Query: 93  QSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPS 152
           + H L +E+P  V      +  +  KY +           ++ G+D              
Sbjct: 64  ELHGLELEEPPLVLAAANVVKNISYKYRE-----DLLAHLIVAGWDQRE--GGQVYGTMG 116

Query: 153 GTFSAWKANATGRNSNSMREFLEKNYKE-TSGQETIKLAIRALLEVVE----SGGKNIEV 207
           G          G  S+ +  +++  YK   + +E  +    A+   +     SGG  I +
Sbjct: 117 GMLIRQPFTIGGSGSSYIYGYVDAAYKPGMTPEECRRFTTNAITLAMNRDGSSGG-VIYL 175

Query: 208 AVMTREK 214
             +T   
Sbjct: 176 VTITAAG 182

>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 = 87.5 bits (217), Expect = 9e-21
 Identities = 28/217 (12%), Positives = 74/217 (34%), Gaps = 16/217 (7%)

Query: 25  EAVRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARV 83
           + +  G + + ++  + +++  +   +   L     V +++ + ++  +  +G  +D + 
Sbjct: 36  QPIVTGTSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQH 95

Query: 84  LINRARIECQSHRLTVEDPVTVEYIT-RYIAGLQQK--YTQSGGVRPFGLSTLIVGFDPY 140
           +    +     +          E +   YI        Y +   + P   + ++ G    
Sbjct: 96  IERLLKDLVTENAYDNPLADAEEALEPSYIFEYLATVMYQRRSKMNPLWNAIIVAGVQS- 154

Query: 141 TGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG------QETIKLAIRAL 194
            G   L   +  G   +    ATG  ++     L K     S       Q   +  + A+
Sbjct: 155 NGDQFLRYVNLLGVTYSSPTLATGFGAHMANPLLRKVVDRESDIPKTTVQVAEEAIVNAM 214

Query: 195 LEVVE----SGGKNIEVAVMTREKGLKQLDEAEIDAM 227
             +      S   N  +A++ +  GL      +++ M
Sbjct: 215 RVLYYRDARSSR-NFSLAIIDKNTGLTFKKNLQVENM 250

>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 = 85.8 bits (213), Expect = 2e-20
 Identities = 28/218 (12%), Positives = 74/218 (33%), Gaps = 16/218 (7%)

Query: 24  LEAVRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADAR 82
            + +  G + + ++  + +++  +   +   L     V +++ + ++  +  +G  +D +
Sbjct: 2   QQPIVTGTSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQ 61

Query: 83  VLINRARIECQSHRLTVEDPVTVEYIT-RYIAGLQQK--YTQSGGVRPFGLSTLIVGFDP 139
            +    +     +          E +   YI        Y +   + P   + ++ G   
Sbjct: 62  HIERLLKDLVTENAYDNPLADAEEALEPSYIFEYLATVMYQRRSKMNPLWNAIIVAGVQS 121

Query: 140 YTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG------QETIKLAIRA 193
             G   L   +  G   +    ATG  ++     L K     S       Q   +  + A
Sbjct: 122 -NGDQFLRYVNLLGVTYSSPTLATGFGAHMANPLLRKVVDRESDIPKTTVQVAEEAIVNA 180

Query: 194 LLEVVE----SGGKNIEVAVMTREKGLKQLDEAEIDAM 227
           +  +      S   N  +A++ +  GL      +++ M
Sbjct: 181 MRVLYYRDARSSR-NFSLAIIDKNTGLTFKKNLQVENM 217

>1ryp_H 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 3nzj_N* 3nzw_N* 3nzx_N* 1vsy_H 3l5q_B 1g65_N* 1fnt_H 1g0u_N* 1jd2_N* 1z7q_H 2f16_N* 2fak_N* 2fny_N* 2gpl_N* 2zcy_N* 3bdm_N* 3d29_N* 3dy3_N* 3dy4_N* 3e47_N* ... Length = 205

 Score = 84.2 bits (209), Expect = 3e-20
 Identities = 34/194 (17%), Positives = 75/194 (38%), Gaps = 14/194 (7%)

Query: 27  VRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLI 85
           V  G + + V   D ++LG + ++T      +R   K+  + + I    +G  AD + + 
Sbjct: 6   VSLGASIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKIWCCRSGSAADTQAIA 65

Query: 86  NRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPS 145
           +  +   + +      P T    +      ++   ++          ++ G+D       
Sbjct: 66  DIVQYHLELYTSQYGTPSTETAASV----FKELCYENKD--NLTAGIIVAGYDD-KNKGE 118

Query: 146 LYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE-TSGQETIKLAIRALLEVVE----S 200
           +Y     G+         G  S  +  + +KN++E  S +ET+     +L + ++    S
Sbjct: 119 VYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSLSQAIKWDGSS 178

Query: 201 GGKNIEVAVMTREK 214
           GG  I + V+T   
Sbjct: 179 GG-VIRMVVLTAAG 191

>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 = 81.9 bits (203), Expect = 3e-19
 Identities = 32/202 (15%), Positives = 69/202 (34%), Gaps = 25/202 (12%)

Query: 30  GNAAVGVRGTDTIVLGVEKKSTVKLQ-DSRSVRKIVSLDNHIALACAGLKADARVLINRA 88
           G   + + G D  ++  + + +      +R   K   L +   + C+G   D   L    
Sbjct: 9   GGTILAIAGEDFAIVASDTRLSEGFSIHTRDSPKCYKLTDKTVIGCSGFHGDCLTLTKII 68

Query: 89  RIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLS--TLIVGFDPYTGVPSL 146
               + ++ +    +T   I   ++ +          R F      +I G D   G  ++
Sbjct: 69  EARLKMYKHSNNKAMTTGAIAAMLSTILYSR------RFFPYYVYNIIGGLDE-EGKGAV 121

Query: 147 YQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSGQ----------ETIKLAIRALLE 196
           Y  DP G++      A G  S  ++  L+      + Q            ++L     + 
Sbjct: 122 YSFDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVEHVPLSLDRAMRLVKDVFIS 181

Query: 197 VVE----SGGKNIEVAVMTREK 214
             E    +G   + + ++T+E 
Sbjct: 182 AAERDVYTGD-ALRICIVTKEG 202

>1iru_N 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_M* 3une_M 3unf_M* 3unh_M Length = 219

 Score = 71.9 bits (177), Expect = 2e-15
 Identities = 31/189 (16%), Positives = 62/189 (32%), Gaps = 14/189 (7%)

Query: 34  VGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIEC 92
           +GV+    +V+  +   +   L   R++ +I+ ++N   L  +G  AD + L        
Sbjct: 12  LGVKFEGGVVIAADMLGSYGSLARFRNISRIMRVNNSTMLGASGDYADFQYLKQVLGQMV 71

Query: 93  QSHRL-TVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDP 151
               L       +   I  ++              P   + +I G+    G   L   D 
Sbjct: 72  IDEELLGDGHSYSPRAIHSWLTRAMYSRRSKMN--PLWNTMVIGGYAD--GESFLGYVDM 127

Query: 152 SGTFSAWKANATGRNSNSMREFLEKNYKETSG---QETIKLAIRALLEVVE----SGGKN 204
            G      + ATG  +   +  L +  ++       E   L  R +  +      S    
Sbjct: 128 LGVAYEAPSLATGYGAYLAQPLLREVLEKQPVLSQTEARDLVERCMRVLYYRDARSYN-R 186

Query: 205 IEVAVMTRE 213
            + A +T +
Sbjct: 187 FQTATVTEK 195

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 46.0 bits (108), Expect = 6e-06
 Identities = 40/248 (16%), Positives = 80/248 (32%), Gaps = 62/248 (25%)

Query: 2   ARYDRAITVFSPDGHL-FQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
             +D  ++VF P  H+   +   L  +      V       +V  + K S V+ Q   S 
Sbjct: 373 KMFD-RLSVFPPSAHIPTIL---LSLIW---FDVIKSDVMVVVNKLHKYSLVEKQPKEST 425

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKY- 119
             I S+   + +      A  R +++   I        +  P   +Y   +I      + 
Sbjct: 426 ISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIG-----HH 480

Query: 120 ----TQSGGVRPFGLSTLIVGFDPYTGVPSLYQTD---------PSGTFSAWKANATGRN 166
                    +  F                 ++  D            T  AW  NA+G  
Sbjct: 481 LKNIEHPERMTLF---------------RMVFL-DFRFLEQKIRHDST--AW--NASGSI 520

Query: 167 SNSMREFLEKNYKE--TSGQETIKLAIRALLEVVESGGKN---------IEVAVMTREKG 215
            N++++   K YK          +  + A+L+ +    +N         + +A+M  ++ 
Sbjct: 521 LNTLQQL--KFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEA 578

Query: 216 LKQLDEAE 223
           +   +EA 
Sbjct: 579 I--FEEAH 584

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	249
1ryp_A	243	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_D	248	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_D	241	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_C	261	20S proteasome; cell cycle, immune response, prote	100.0
1iru_B	233	20S proteasome; cell cycle, immune response, prote	100.0
3h4p_A	264	Proteasome subunit alpha; core particle, cytoplasm	100.0
1iru_A	246	20S proteasome; cell cycle, immune response, prote	100.0
1j2p_A	246	Alpha-ring, proteasome alpha subunit; hydrolase; 2	100.0
1ryp_C	244	20S proteasome; multicatalytic proteinase, protein	100.0
1ryp_E	242	20S proteasome; multicatalytic proteinase, protein	100.0
1yar_A	233	Proteasome alpha subunit; proteasome 20S, PA26 pro	100.0
1iru_G	254	20S proteasome; cell cycle, immune response, prote	100.0
1iru_E	241	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_B	250	20S proteasome; multicatalytic proteinase, protein	100.0
1ryp_F	233	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_F	263	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_G	244	20S proteasome; multicatalytic proteinase, protein	100.0
3nzj_F	288	Proteasome component C1; ubiquitin, protein degrad	100.0
1q5q_A	259	Proteasome alpha-type subunit 1; proteasome assemb	100.0
3mi0_A	248	Proteasome subunit alpha; enzyme inhibitors, lacto	100.0
3h4p_a	219	Proteasome subunit beta; core particle, cytoplasm,	100.0
1yar_H	217	Proteasome beta subunit; proteasome 20S, PA26 prot	100.0
1j2q_H	202	Proteasome beta subunit; ubiquitin, CP, hydrolase;	100.0
3nzj_K	287	Proteasome component PRE2; ubiquitin, protein degr	100.0
1q5r_H	294	Proteasome beta-type subunit 1; proteasome assembl	100.0
2jay_A	291	Proteasome; hydrolase; 1.99A {Mycobacterium tuberc	100.0
1ryp_L	212	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_L	204	20S proteasome; cell cycle, immune response, prote	100.0
1q5q_H	235	Proteasome beta-type subunit 1; proteasome assembl	100.0
1iru_N	219	20S proteasome; cell cycle, immune response, prote	100.0
1iru_H	205	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_N	233	20S proteasome; multicatalytic proteinase, protein	100.0
1ryp_K	198	20S proteasome; multicatalytic proteinase, protein	100.0
1ryp_H	205	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_M	213	20S proteasome; cell cycle, immune response, prote	100.0
3nzj_H	261	Proteasome component PUP1; ubiquitin, protein degr	100.0
1g0u_M	266	Proteasome component PRE4; ubiquitin, degradation,	100.0
3unf_H	234	Proteasome subunit beta type-10; antigen presentat	100.0
1iru_K	201	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_M	222	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_J	205	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_J	204	20S proteasome; multicatalytic proteinase, protein	100.0
1ryp_I	222	20S proteasome; multicatalytic proteinase, protein	100.0
3unf_N	199	Proteasome subunit beta type-9; antigen presentati	100.0
1iru_I	234	20S proteasome; cell cycle, immune response, prote	100.0
2z3b_A	180	ATP-dependent protease HSLV; N-terminal nucleophIl	100.0
1g3k_A	174	ATP-dependent protease HSLV; hydrolase; 1.90A {Hae	100.0
1m4y_A	171	ATP-dependent protease HSLV; N-terminal catalytic	100.0

>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=5e-63  Score=424.62  Aligned_cols=230  Identities=32%  Similarity=0.529  Sum_probs=222.0

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHcc-CCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhh
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRK-GNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKAD   80 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~-G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D   80 (249)
                      ++||+.+|+|||||||+|||||+||+++ |+|+|||+++||||||+|+|.+.+++.+++.+||++|++|++|+++|+.+|
T Consensus         1 ~~yd~~~t~fsp~Grl~QvEYA~~av~~~Gtt~vgi~~~dgVvlaad~r~~~~l~~~~~~~Ki~~i~~~i~~~~aG~~aD   80 (243)
T 1ryp_A            1 AGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPTTVSYIFCISRTIGMVVNGPIPD   80 (243)
T ss_dssp             CGGGGTSSSCCTTSCCHHHHHHHHHTTTTCCCEEEEECSSEEEEEEECCCCCTTBCGGGCCSEEECSSSCEEEEESCHHH
T ss_pred             CCCCCCCceECCCCeeHHHHHHHHHHhcCCCcEEEEEeCCEEEEEEEecCCccccCCCcCCceEEECCCEEEEEEecHHH
Confidence            4799999999999999999999999999 999999999999999999999988888889999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccce
Q 025716           81 ARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKA  160 (249)
Q Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~  160 (249)
                      ++.|+++++.++..|+++++++++++.+++++++++|.|+++++.|||+|++||||||+ ++||+||.+||+|++.++++
T Consensus        81 ~~~l~~~~r~~~~~~~~~~~~~~~v~~la~~l~~~l~~y~~~~~~rP~~v~~lvaG~D~-~~gp~Ly~~dp~G~~~~~~~  159 (243)
T 1ryp_A           81 ARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQRAYMRPLGVILTFVSVDE-ELGPSIYKTDPAGYYVGYKA  159 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTSCCCSCEEEEEEEET-TTEEEEEEECTTSCEEEBSE
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhccCCccccceEEEEEEEcC-CCCcEEEEEcCCCCEEEEEE
Confidence            99999999999999999999999999999999999999999988999999999999996 58999999999999999999


Q ss_pred             EeecCCchHHHHHHHhhhcc-------CCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEEcCCCEEEcCHHHHHHHHHH
Q 025716          161 NATGRNSNSMREFLEKNYKE-------TSG-QETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEIDAMVAE  230 (249)
Q Consensus       161 ~aiG~g~~~a~~~Le~~~~~-------~~s-eeai~la~~~l~~~~~~--~~~~iei~~v~~~g~~~~~~~~ei~~~l~~  230 (249)
                      +++|+++..++++||+.|++       +|+ +||++++++||..+.++  ++++++|++|+++| +++++++||++++.+
T Consensus       160 ~a~G~gs~~a~~~Le~~~~~~~~~~~~~ms~eea~~l~~~al~~~~~rd~s~~~iev~vi~~~g-~~~l~~~ei~~~~~~  238 (243)
T 1ryp_A          160 TATGPKQQEITTNLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDK-FFTLSAENIEERLVA  238 (243)
T ss_dssp             EEESTTHHHHHHHHHHHHHHHCSSSCCCSSHHHHHHHHHHHHHHHHTCCCCTTSEEEEEEETTE-EEECCHHHHHHHHHH
T ss_pred             EEECCCcHHHHHHHHHHhhhcccccccCCCHHHHHHHHHHHHHHHhcccCCCCcEEEEEEECCC-eEECCHHHHHHHHHH
Confidence            99999999999999999999       999 99999999999999875  47799999999998 999999999999999


Q ss_pred             HHH
Q 025716          231 IEA  233 (249)
Q Consensus       231 i~~  233 (249)
                      |++
T Consensus       239 ~~~  241 (243)
T 1ryp_A          239 IAE  241 (243)
T ss_dssp             HTT
T ss_pred             hhc
Confidence            865

>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=8.7e-64  Score=430.57  Aligned_cols=232  Identities=72%  Similarity=1.095  Sum_probs=224.1

Q ss_pred             CCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHH
Q 025716            3 RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADAR   82 (249)
Q Consensus         3 ~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~   82 (249)
                      +||+.+|+|||||||+|||||++|+++|+|+|||+++||||||+|+|.+++++.+++.+||++|++|++++++|+.+|++
T Consensus         2 ~yd~~~t~fsp~Grl~QvEYA~~av~~Gtt~vgi~~~dgVvlaaD~r~~~~l~~~~~~~KI~~i~~~i~~~~aG~~aD~~   81 (248)
T 1iru_D            2 SYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVRKICALDDNVCMAFAGLTADAR   81 (248)
T ss_dssp             CCCCCCSCCCTTSCCHHHHHHHHHHHTSCCEEEECCSSEEEEEECCCCCCSSSCGGGGCSEEESSSSCEEEEEECHHHHH
T ss_pred             CccCCCceECCCCcchHHHHHHHHHHcCCCEEEEEeCCEEEEEEeecccccCccCCCCCcEEEEcCCEEEEEeecHHHHH
Confidence            49999999999999999999999999999999999999999999999999887778899999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEe
Q 025716           83 VLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANA  162 (249)
Q Consensus        83 ~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~a  162 (249)
                      .|+++++.+++.|+++++++++++.+++++++++|.|+++++.|||+|++||||||+ +++|+||.+||+|++.++++++
T Consensus        82 ~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rp~~v~~lvaG~D~-~~gp~Ly~idp~G~~~~~~~~a  160 (248)
T 1iru_D           82 IVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGISALIVGFDF-DGTPRLYQTDPSGTYHAWKANA  160 (248)
T ss_dssp             HHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCEEEEEEEECS-SSCEEEEEECTTSCEEEBSEEE
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhccCCcccccEEEEEEEEeC-CCCcEEEEEcCCCcEEEeeEEE
Confidence            999999999999999999999999999999999999999989999999999999996 6799999999999999999999


Q ss_pred             ecCCchHHHHHHHhhhccCC--c-HHHHHHHHHHHHHHHhcCCCcEEEEEEEcCCCEEEcCHHHHHHHHHHHHHHH
Q 025716          163 TGRNSNSMREFLEKNYKETS--G-QETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKK  235 (249)
Q Consensus       163 iG~g~~~a~~~Le~~~~~~~--s-eeai~la~~~l~~~~~~~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i~~~~  235 (249)
                      +|+++..++++||+.|+++|  + +||++++++||..+.+.++++++|++|+++|.+++++++||++++.++.+.+
T Consensus       161 iG~gs~~a~~~Le~~~~~~m~~s~eea~~la~~al~~~~~~sg~~i~v~vi~~~g~~~~l~~~ei~~~~~~~~~~~  236 (248)
T 1iru_D          161 IGRGAKSVREFLEKNYTDEAIETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVAEIEKEK  236 (248)
T ss_dssp             ESTTHHHHHHHHTTTCCSSTTCSHHHHHHHHHHHHHTTSCTTSTTCCEEEEESSSCEECCCHHHHHHHTTTTTTTT
T ss_pred             ECCCcHHHHHHHHHhhcccccCCHHHHHHHHHHHHHHHHcCCCCcEEEEEEECCCcEEECCHHHHHHHHHHHHhcc
Confidence            99999999999999999999  9 9999999999999988778899999999998899999999999999997654

>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=4e-62  Score=418.51  Aligned_cols=232  Identities=58%  Similarity=1.015  Sum_probs=221.9

Q ss_pred             CCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccC-CcccceEEecCCEEEEEecChhhH
Q 025716            3 RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDS-RSVRKIVSLDNHIALACAGLKADA   81 (249)
Q Consensus         3 ~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~-~~~~Ki~~I~~~i~~~~sG~~~D~   81 (249)
                      +||+.+|+|||||||+|||||++|+++|+|+|||+++||||||+|+|.+++++.. ++.+||++|++|++++++|+.+|+
T Consensus         1 ~yd~~~t~fsp~Grl~QvEya~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~   80 (241)
T 1ryp_D            1 GYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSKVSKIDSHVVLSFSGLNADS   80 (241)
T ss_dssp             CCCCCCSCCBTTTBCHHHHHHHHHHTTSCCEEEEECSSCEEEEEECCCSSCCBCTTTSCCSEEEEETTEEEEEEECHHHH
T ss_pred             CCCCCceeECCCCcchHHHHHHHHHHcCCCEEEEEeCCEEEEEEeeccCccCccccCCcCcEEEecCCEEEEEeecHHHH
Confidence            6999999999999999999999999999999999999999999999999976554 489999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCC-CCceEEEECCCCceeccce
Q 025716           82 RVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYT-GVPSLYQTDPSGTFSAWKA  160 (249)
Q Consensus        82 ~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~-~gp~Ly~iDp~G~~~~~~~  160 (249)
                      +.|.++++.+++.|+++++++++++.+++++++++|.|+++++.|||+|++||||||+ + ++|+||.+||+|++.++++
T Consensus        81 ~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rP~~v~~lvaG~D~-~~~gp~Ly~idp~G~~~~~~~  159 (241)
T 1ryp_D           81 RILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLIAGFDP-RDDEPKLYQTEPSGIYSSWSA  159 (241)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSSTTBCCCSEEEEEEECCT-TCCSCEEEEECTTSCEEEBSE
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHccCCCCCCcceeeEEEEEcC-CCCCeeEEEECCCCCEEEeee
Confidence            9999999999999999999999999999999999999999989999999999999995 4 8999999999999999999


Q ss_pred             EeecCCchHHHHHHHhhh---ccCCc-HHHHHHHHHHHHHHHhcCCCcEEEEEEEcCCCEEEcCHHHHHHHHHHHHHHH
Q 025716          161 NATGRNSNSMREFLEKNY---KETSG-QETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKK  235 (249)
Q Consensus       161 ~aiG~g~~~a~~~Le~~~---~~~~s-eeai~la~~~l~~~~~~~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i~~~~  235 (249)
                      +++|+|+..++++||+.|   +++|+ +||++++++||..+.+.++++++|++|+++|.+++++++||++++.++++++
T Consensus       160 ~aiG~gs~~a~~~Le~~~~~~~~~ms~eea~~l~~~al~~~~~~sg~~i~v~vi~~~~~~~~l~~~ei~~~~~~~~~~~  238 (241)
T 1ryp_D          160 QTIGRNSKTVREFLEKNYDRKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK  238 (241)
T ss_dssp             EEESTTHHHHHHHHHTTCCTTSCCCSHHHHHHHHHHHHHHHHCSCSTTEEEEEEETTTEEEECCHHHHHHHHHHHTHHH
T ss_pred             EEECCCcHHHHHHHHHhhhcccCCCCHHHHHHHHHHHHHHHhcCCCCcEEEEEEECCCcEEECCHHHHHHHHHHHhhhh
Confidence            999999999999999999   99999 9999999999999988778899999999987799999999999999996654

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

Probab=100.00  E-value=4.7e-62  Score=422.67  Aligned_cols=234  Identities=36%  Similarity=0.647  Sum_probs=221.3

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCccccc-CCcccceEEecCCEEEEEecChhh
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQD-SRSVRKIVSLDNHIALACAGLKAD   80 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~-~~~~~Ki~~I~~~i~~~~sG~~~D   80 (249)
                      ++||+.+|+|||||||+|||||++|+++|+|+|||+++||||||+|+|.++++.. +++.+||++|++|++++++|+.+|
T Consensus         3 ~~yd~~~t~fsp~Grl~QvEYA~~av~~Gtt~vgi~~~dgVVlaaD~r~~~g~~~~~~~~~KI~~i~~~i~~~~aG~~aD   82 (261)
T 1iru_C            3 RRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVFFSEKIYKLNEDMACSVAGITSD   82 (261)
T ss_dssp             TTTCCCTTCCCTTSCCHHHHHHHHHHTTSCCEEEEBCSSEEEEEECCCCCCTTBCCCSSCSSEEECSSSEEEEEEECHHH
T ss_pred             CccCCCCccCCCCCeehHHHhHHHHHhcCCcEEEEEeCCEEEEEEecccCCcccccCCCCccEEEecCCEEEEEeEcHHH
Confidence            4699999999999999999999999999999999999999999999999987654 445999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccce
Q 025716           81 ARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKA  160 (249)
Q Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~  160 (249)
                      ++.|+++++.++..|+++++++++++.+++++++++|.|+++++.|||+|++||||||+ ++||+||.+||+|++.++++
T Consensus        83 ~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rP~~v~~lvaG~D~-~~gp~Ly~idp~G~~~~~~~  161 (261)
T 1iru_C           83 ANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIGWDK-HYGFQLYQSDPSGNYGGWKA  161 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBSSCCCCCEEEEEEEEET-TTEEEEEEEETTTEEEECSE
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccccCcCcceEEEEEEEEeC-CCCcEEEEECCCceEEeeee
Confidence            99999999999999999999999999999999999999999999999999999999996 67999999999999999999


Q ss_pred             EeecCCchHHHHHHHhhhcc-CCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCC---EEEcCHHHHHHHHHHHH
Q 025716          161 NATGRNSNSMREFLEKNYKE-TSG-QETIKLAIRALLEVVES---GGKNIEVAVMTREKG---LKQLDEAEIDAMVAEIE  232 (249)
Q Consensus       161 ~aiG~g~~~a~~~Le~~~~~-~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g~---~~~~~~~ei~~~l~~i~  232 (249)
                      +++|+|+..++++|++.|++ +|+ +||++++++||..+.++   ++.+++|++|+++|.   |++++++||++++.++.
T Consensus       162 ~aiGsgs~~a~~~Le~~~~~~~ms~eeA~~la~~al~~~~~~d~~sg~~i~v~vi~~~~~~~~~~~l~~~ei~~~l~~~~  241 (261)
T 1iru_C          162 TCIGNNSAAAVSMLKQDYKEGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKHE  241 (261)
T ss_dssp             EEESTTTTHHHHHHHHHCCTTCCCHHHHHHHHHHHHHHSSSCTTCCSTTCEEEEEECCSSSCEEEECCHHHHHHHHHHHH
T ss_pred             EEeCcccHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHhccCCCCCcEEEEEEEcCCCeeeEEECCHHHHHHHHHHHH
Confidence            99999999999999999999 999 99999999999999875   477999999999874   89999999999999997


Q ss_pred             HHHH
Q 025716          233 AKKA  236 (249)
Q Consensus       233 ~~~~  236 (249)
                      +.+.
T Consensus       242 ~~~~  245 (261)
T 1iru_C          242 EEEA  245 (261)
T ss_dssp             TTTT
T ss_pred             hchh
Confidence            5443

>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=7.9e-62  Score=414.66  Aligned_cols=228  Identities=41%  Similarity=0.680  Sum_probs=219.5

Q ss_pred             CCCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhh
Q 025716            1 MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKAD   80 (249)
Q Consensus         1 ~~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D   80 (249)
                      .++||+.+|+|||||||+|||||++|+++|+|+|||+++||||||+|+|.+++++.+++.+||++|++|++++++|+.+|
T Consensus         2 ~~~yd~~~t~fsp~Grl~QvEya~~av~~Gtt~vgi~~~dgVvlaaD~r~~~~l~~~~~~~Ki~~i~~~i~~~~aG~~aD   81 (233)
T 1iru_B            2 ERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDERSVHKVEPITKHIGLVYSGMGPD   81 (233)
T ss_dssp             CCCCCSBSCCCCTTSCCHHHHHHHHHHHTSCCEEEEECSSCEEEEEECCCCCSSBCSTTCCSSEESSSSEEEEEEECHHH
T ss_pred             CCCccCCceeECCCCeEehhHhHHHHHHcCCcEEEEEeCCEEEEEEEecCCccccccccCCeEEEECCCEEEEEEEccHH
Confidence            36899999999999999999999999999999999999999999999999888888889999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccce
Q 025716           81 ARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKA  160 (249)
Q Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~  160 (249)
                      ++.|.++++.+++.|+++++++++++.+++++++++|.|+++++.|||+|++||||||  ++||+||.+||+|++.++++
T Consensus        82 ~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~y~~~~~~rP~~v~~lvaG~D--~~gp~Ly~id~~G~~~~~~~  159 (233)
T 1iru_B           82 YRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGVSLLICGWN--EGRPYLFQSDPSGAYFAWKA  159 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCSEEEEEEEEC--SSSEEEEEECTTSCEEEBSE
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCcCCCCCcEEEEEEEEEe--CCCCeEEEECCCCCEEEeeE
Confidence            9999999999999999999999999999999999999999998999999999999999  57899999999999999999


Q ss_pred             EeecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEEcCCCEEEcCHHHHHHHHHHH
Q 025716          161 NATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEIDAMVAEI  231 (249)
Q Consensus       161 ~aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~--~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i  231 (249)
                      +++|+|+..++++||+.|+++|+ +||++++++||..+.++  ++.+++|++|+++| +++++++||++++++|
T Consensus       160 ~aiG~gs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~d~sg~~i~v~vi~~~g-~~~l~~~ei~~~~~~~  232 (233)
T 1iru_B          160 TAMGKNYVNGKTFLEKRYNEDLELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAG-FRRLTPTEVKDYLAAI  232 (233)
T ss_dssp             EEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHTTCCSCCCSSSEEEEEEETTE-EEECCHHHHHHHHTTC
T ss_pred             EEECCCCHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhccCCCCCEEEEEEECCC-EEECCHHHHHHHHHhc
Confidence            99999999999999999999999 99999999999999875  46799999999998 9999999999998754

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

Probab=100.00  E-value=3.8e-63  Score=429.81  Aligned_cols=231  Identities=44%  Similarity=0.729  Sum_probs=216.0

Q ss_pred             CCCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhh
Q 025716            1 MARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKAD   80 (249)
Q Consensus         1 ~~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D   80 (249)
                      +++||+.+|+|||||||+|||||++|+++|+|+|||+++||||||+|+|.+++++.+++.+||++|++|++|+++|+.+|
T Consensus         9 ~~~yd~~~t~fSp~Grl~QvEYA~~av~~Gtt~vgi~~~dgVVlaaD~r~~~~li~~~~~~KI~~i~d~i~~~~aG~~aD   88 (264)
T 3h4p_A            9 PSAYDRAITVFSPEGRLYQVEYAREAVRRGTTAIGIACKDGVVLAVDRRITSKLVKIRSIEKIFQIDDHVAAATSGLVAD   88 (264)
T ss_dssp             -------CCCCCSSSSCHHHHHHHHHHHHSCCEEEECCSSEEEEEEECCCCSTTBCTTTCCCEEEEETTEEEEEEECSHH
T ss_pred             ccccCCCcceECCCCeeHHHHhHHHHHhcCCcEEEEEECCEEEEEEecCccCCccccCccccEEEecCcEEEEeccchHH
Confidence            36799999999999999999999999999999999999999999999999998888889999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccce
Q 025716           81 ARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKA  160 (249)
Q Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~  160 (249)
                      ++.|+++++.+++.|+++++++++++.+++++++++|.|+++++.|||+|++||||||  ++||+||.+||+|++.++++
T Consensus        89 ~~~l~~~~r~~~~~y~~~~~~~i~v~~la~~l~~~~~~yt~~~~~rP~~v~~lvaG~D--~~gp~Ly~iDp~G~~~~~~~  166 (264)
T 3h4p_A           89 ARVLIDRARLEAQIYRLTYGEEISIEMLAKKICDIKQAYTQHGGVRPFGVSLLIAGID--KNEARLFETDPSGALIEYKA  166 (264)
T ss_dssp             HHHHHTTHHHHHHHHHHTTCSCCCHHHHHHHHHHHHHHTTSBSSCCCCSEEEEEEEEE--TTEEEEEEECTTCCCEEESE
T ss_pred             HHHHHHHHHHHHHhhHHhcCCCCCHHHHHHHHHHHHHHHhhccCCCCeeEEEEEEEEe--CCcCEEEEECCCceEEecCe
Confidence            9999999999999999999999999999999999999999999999999999999999  47999999999999999999


Q ss_pred             EeecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHh-cCCCcEEEEEEEcC-CCEEEcCHHHHHHHHHHHHH
Q 025716          161 NATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVE-SGGKNIEVAVMTRE-KGLKQLDEAEIDAMVAEIEA  233 (249)
Q Consensus       161 ~aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~-~~~~~iei~~v~~~-g~~~~~~~~ei~~~l~~i~~  233 (249)
                      +|+|+|+..++++|++.|+++|+ +||++++++||..+.+ .++++++|++|+++ +.|++++++||++++.++.+
T Consensus       167 ~aiGsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~a~~~~sg~~iev~vi~~~~~~~~~l~~~ei~~~~~~~~~  242 (264)
T 3h4p_A          167 TAIGSGRPVVMELLEKEYRDDITLDEGLELAITALTKANEDIKPENVDVCIITVKDAQFKKIPVEEIKKLIEKVKK  242 (264)
T ss_dssp             EEESTTHHHHTTTHHHHCCTTCCSHHHHHHHHHHHHHHSSSCCTTSEEEEEEETTTTEEEECCTTTTGGGTTTTTT
T ss_pred             EEECCCHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEEEeCCCcEEECCHHHHHHHHHHHHH
Confidence            99999999999999999999999 9999999999999987 47789999999975 46999999999999998874

>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=2.9e-61  Score=414.37  Aligned_cols=231  Identities=36%  Similarity=0.593  Sum_probs=221.8

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHcc-CCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhh
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRK-GNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKAD   80 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~-G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D   80 (249)
                      ++||+.+|+|||||||+|||||++|+++ |+|+|||+++||||||+|+|.+.+++.+++.+||++|++|++++++|+.+|
T Consensus         7 ~~yd~~~t~fsp~Grl~QvEya~~av~~~Gtt~vgi~~~dgVvlaaD~r~~~~l~~~~~~~Ki~~i~~~i~~~~aG~~aD   86 (246)
T 1iru_A            7 AGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTVTHLFKITENIGCVMTGMTAD   86 (246)
T ss_dssp             CTTTTTSSCCCTTSCCHHHHHHHHHHHTTCCEEEEEECSSEEEEEEECCCCCSSBCGGGCCSEEESSSSCEEEEEECHHH
T ss_pred             CCcCCCCccCCCCCeehHHHHHHHHHhcCCCCEEEEEeCCEEEEEEeecCCCcccCCCccCceEEECCCEEEEEeccHHH
Confidence            4799999999999999999999999998 999999999999999999999888888889999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccce
Q 025716           81 ARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKA  160 (249)
Q Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~  160 (249)
                      ++.|.++++.++..|+++++++++++.+++++++++|.|+++++.|||+|++||||||+ ++||+||.+||+|++.++++
T Consensus        87 ~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~y~~~~~~rp~~v~~lvaG~D~-~~gp~Ly~idp~G~~~~~~~  165 (246)
T 1iru_A           87 SRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIGIDE-EQGPQVYKCDPAGYYCGFKA  165 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSBCCCSEEEEEEEEET-TTEEEEEEECTTSCEEEBSE
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcCCCCCCcceEEEEEEEeC-CCCeEEEEEcCCeeEEEeeE
Confidence            99999999999999999999999999999999999999999989999999999999996 58999999999999999999


Q ss_pred             EeecCCchHHHHHHHhhhcc--CCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEEcCCC-EEEcCHHHHHHHHHHHHH
Q 025716          161 NATGRNSNSMREFLEKNYKE--TSG-QETIKLAIRALLEVVES--GGKNIEVAVMTREKG-LKQLDEAEIDAMVAEIEA  233 (249)
Q Consensus       161 ~aiG~g~~~a~~~Le~~~~~--~~s-eeai~la~~~l~~~~~~--~~~~iei~~v~~~g~-~~~~~~~ei~~~l~~i~~  233 (249)
                      +++|+|+..++++||+.|++  +|+ +||++++++||..+.++  ++.+++|++|+++|. |++++++||++++.+|++
T Consensus       166 ~aiG~gs~~a~~~Le~~~~~~~~ms~eea~~la~~al~~~~~rd~sg~~i~v~vi~~~g~~~~~l~~~ei~~~~~~~~~  244 (246)
T 1iru_A          166 TAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVALAE  244 (246)
T ss_dssp             EEEETTHHHHHHHHHHHTTSCCCCCHHHHHHHHHHHHHHHTTCCCCTTSEEEEEEETTEEEEEECCHHHHHHHHHHHHT
T ss_pred             EEECCCcHHHHHHHHHhhcccCCCCHHHHHHHHHHHHHHHhcccCCCCcEEEEEEECCCCeEEECCHHHHHHHHHHhhc
Confidence            99999999999999999999  999 99999999999999875  477999999999985 899999999999999864

>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=7.4e-61  Score=411.84  Aligned_cols=233  Identities=43%  Similarity=0.711  Sum_probs=222.1

Q ss_pred             CCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHH
Q 025716            3 RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADAR   82 (249)
Q Consensus         3 ~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~   82 (249)
                      +||+.+|+|||||||+|||||++|+++|+|+|||+++||||||+|+|.+.+++.+++.+||++|++|++++++|+.+|++
T Consensus         7 ~yd~~~t~fsp~Grl~QvEya~~av~~Gtt~vgi~~~dgVvlaaD~r~~~~l~~~~~~~KI~~i~~~i~~~~aG~~aD~~   86 (246)
T 1j2p_A            7 GYDRAITVFSPDGRLFQVEYAREAVKRGATAIGIKCKEGVILIADKRVGSKLLEKDTIEKIYKIDEHICAATSGLVADAR   86 (246)
T ss_dssp             TSSSCTTCCCTTSCCHHHHHHHHHHHTSCCEEEEEETTEEEEEEECCCSCTTBCGGGCCSEEECSSSEEEEEEECHHHHH
T ss_pred             CcCCCCceECCCCeehHHHhHHHHHHcCCcEEEEEECCEEEEEEeccCCccccccCccCcEEEECCCEEEEEeEccHHHH
Confidence            69999999999999999999999999999999999999999999999998887788999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEe
Q 025716           83 VLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANA  162 (249)
Q Consensus        83 ~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~a  162 (249)
                      .|.++++.+++.|+++++++++++.+++++++++|.|+++++.|||+|++||||||   +||+||.+||+|++.+++++|
T Consensus        87 ~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~y~~~~~~rp~~v~~lvaG~D---~gp~Ly~idp~G~~~~~~~~a  163 (246)
T 1j2p_A           87 VLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQYGGVRPFGVSLLIAGVN---EVPKLYETDPSGALLEYKATA  163 (246)
T ss_dssp             HHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCEEEEEEEES---SSEEEEEECTTCCEEEBSEEE
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCcccccEEEEEEEEC---CCCEEEEECCCceEEeeeEEE
Confidence            99999999999999999999999999999999999999999999999999999998   689999999999999999999


Q ss_pred             ecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEE-cCCCEEEcCHHHHHHHHHHHHHHHHHH
Q 025716          163 TGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES--GGKNIEVAVMT-REKGLKQLDEAEIDAMVAEIEAKKAAA  238 (249)
Q Consensus       163 iG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~--~~~~iei~~v~-~~g~~~~~~~~ei~~~l~~i~~~~~~~  238 (249)
                      +|+|+..++++||+.|+++|+ +||++++++||..+.++  ++.+++|++|+ +++.+++++++||++++.++.+++.+.
T Consensus       164 iGsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~~~sg~~i~v~vi~~~~~~~~~l~~~ei~~~~~~~~~~~~~~  243 (246)
T 1j2p_A          164 IGMGRMAVTEFFEKEYRDDLSFDDAMVLGLVAMGLSIESELVPENIEVGYVKVDDRTFKEVSPEELKPYVERANERIREL  243 (246)
T ss_dssp             ESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHHTSCCCGGGEEEEEEETTTCCCEECCHHHHHHHHHHHHHHHHHH
T ss_pred             ECCCcHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhccCCCCcEEEEEEEcCCCceEECCHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999999 99999999999999874  57799999999 755699999999999999997655443

>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=6.1e-61  Score=411.85  Aligned_cols=231  Identities=37%  Similarity=0.652  Sum_probs=221.1

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCccccc-CCcccceEEecCCEEEEEecChhh
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQD-SRSVRKIVSLDNHIALACAGLKAD   80 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~-~~~~~Ki~~I~~~i~~~~sG~~~D   80 (249)
                      ++||+.+|+|||||||+|||||++|+++|+|+|||+++||||||+|+|.+++++. +++.+||++|++|++++++|+.+|
T Consensus         3 ~~yd~~~t~fsp~Grl~QvEyA~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD   82 (244)
T 1ryp_C            3 RRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTSTEKLYKLNDKIAVAVAGLTAD   82 (244)
T ss_dssp             GGGCCCTTCBCTTSCBHHHHHHHHHHTTSCCEEEEEETTEEEEEEECSSCCSSBCSTTCCSSEEESSSSEEEEEEECHHH
T ss_pred             CccCCCCceECcCCeeHHHHhHHHHHhcCCcEEEEEeCCEEEEEEeeccCCcCccCCCCCCcEEEECCCEEEEEEEcHHH
Confidence            3799999999999999999999999999999999999999999999999998766 788999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccce
Q 025716           81 ARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKA  160 (249)
Q Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~  160 (249)
                      ++.|.++++.+++.|+++++++++++.+++++++++|.|+++++.|||+|++||||||+ ++||+||.+||+|++.++++
T Consensus        83 ~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rp~~v~~lvaG~D~-~~gp~Ly~idp~G~~~~~~~  161 (244)
T 1ryp_C           83 AEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAGYDD-RYGYQLYTSNPSGNYTGWKA  161 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSCCCCCEEEEEEEEET-TTEEEEEEECTTCCEEEBSE
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhccCCccceEEEEEEEEEcC-CCCCEEEEECCCccEEeeeE
Confidence            99999999999999999999999999999999999999999999999999999999996 57999999999999999999


Q ss_pred             EeecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEE--cCCC---EEEcCHHHHHHHHHHH
Q 025716          161 NATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES---GGKNIEVAVMT--REKG---LKQLDEAEIDAMVAEI  231 (249)
Q Consensus       161 ~aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~--~~g~---~~~~~~~ei~~~l~~i  231 (249)
                      +++|+|+..++++||+.|+++|+ +||++++++||..+.++   ++.+++|++|+  ++|.   +++++++||++++.+|
T Consensus       162 ~aiGsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~rd~~sg~~i~v~vi~~~~~~~~~~~~~l~~~ei~~~~~~~  241 (244)
T 1ryp_C          162 ISVGANTSAAQTLLQMDYKDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVKT  241 (244)
T ss_dssp             EEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCSSSSCCGGGEEEEEEECCSSSSSCEEEECCHHHHHHHHHHH
T ss_pred             EEECCCcHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHhccccCCCCcEEEEEEEeecCCCceeEEECCHHHHHHHHHHh
Confidence            99999999999999999999999 99999999999999875   37799999999  9876   9999999999999988


Q ss_pred             HH
Q 025716          232 EA  233 (249)
Q Consensus       232 ~~  233 (249)
                      +.
T Consensus       242 ~~  243 (244)
T 1ryp_C          242 GI  243 (244)
T ss_dssp             TC
T ss_pred             hc
Confidence            63

>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=3.1e-61  Score=413.16  Aligned_cols=230  Identities=35%  Similarity=0.633  Sum_probs=220.3

Q ss_pred             CCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHHHH
Q 025716            5 DRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARVL   84 (249)
Q Consensus         5 d~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l   84 (249)
                      |+.+|+|||||||+|||||++|+++|+|+|||+++||||||+|+|.+++++.+++.+||++|++|++++++|+.+|++.|
T Consensus         1 d~~~t~fsp~Grl~QvEyA~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l   80 (242)
T 1ryp_E            1 DRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESDSIEKIVEIDRHIGCAMSGLTADARSM   80 (242)
T ss_dssp             CCCTTCBCTTSCBHHHHHHHHHHTTSCCEEEEECSSCEEEEEECCCSSTTBCGGGCCCEEEEETTEEEEEEESGGGHHHH
T ss_pred             CCCCceECCCCcChHHHhHHHHHHcCCCEEEEEECCEEEEEEeecCCCcCccCccCCceEEEcCCEEEEEeecHHHHHHH
Confidence            78899999999999999999999999999999999999999999999987667889999999999999999999999999


Q ss_pred             HHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCC------CccceeEEEEEeeeCCCCCceEEEECCCCceecc
Q 025716           85 INRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGG------VRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAW  158 (249)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~------~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~  158 (249)
                      +++++.+++.|+++++++++++.+++++++++|.|+++++      .|||+|++||||||+ ++||+||.+||+|++.++
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~~~~l~~RP~~v~~lvaG~D~-~~gp~Ly~idp~G~~~~~  159 (242)
T 1ryp_E           81 IEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLMSRPFGVALLIAGHDA-DDGYQLFHAEPSGTFYRY  159 (242)
T ss_dssp             HHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCCBSSCTTSCCCBSSCCSEEEEEEEEET-TTEEEEEEECTTSCEEEB
T ss_pred             HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccccCcccccccCcceEEEEEEEEeC-CCCCEEEEECCCCCEecc
Confidence            9999999999999999999999999999999999999888      899999999999996 679999999999999999


Q ss_pred             ceEeecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEEcCCCEEEcCHHHHHHHHHHHHHHH
Q 025716          159 KANATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKK  235 (249)
Q Consensus       159 ~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~--~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i~~~~  235 (249)
                      +++++|+|+..++++||+.|+++|+ +||++++++||..+.++  ++.+++|++|+++|.|++++++||++++.++.+++
T Consensus       160 ~~~aiGsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~~~sg~~i~v~vi~~~~~~~~~~~~ei~~~~~~~~~~~  239 (242)
T 1ryp_E          160 NAKAIGSGSEGAQAELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELIKELKEKE  239 (242)
T ss_dssp             SEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCSSCCCTTSEEEEEEETTTEEEECCHHHHHHHHHHHHHHH
T ss_pred             CEEEECCCCHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHhhccCCCCcEEEEEEECCCCeEECCHHHHHHHHHHHhhhh
Confidence            9999999999999999999999999 99999999999999874  57899999999998789999999999999996654

>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=4.1e-61  Score=410.24  Aligned_cols=224  Identities=41%  Similarity=0.648  Sum_probs=210.3

Q ss_pred             CCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHH
Q 025716            3 RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADAR   82 (249)
Q Consensus         3 ~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~   82 (249)
                      +||+.+|+|||||||+|||||++|+++|+|+|||+++||||||+|+|.+++++.+++.+||++|++|++++++|+.+|++
T Consensus         7 ~yd~~~t~fsp~Grl~QvEya~~av~~Gtt~vgi~~~dgVvlaaD~r~~~~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~   86 (233)
T 1yar_A            7 AYSRAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQNSIEKIQLIDDYVAAVTSGLVADAR   86 (233)
T ss_dssp             ------CCCCTTSCCHHHHHHHHHHTTSCCEEEEEETTEEEEEECCCCCCTTBCSTTCCSEEEEETTEEEEEEEBHHHHH
T ss_pred             cCCCCCceECcCCeeHHHHhHHHHHhcCCcEEEEEECCEEEEEEeccCCcccccccccCeEEEecCCEEEEEeeCHHHHH
Confidence            79999999999999999999999999999999999999999999999999888888999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEe
Q 025716           83 VLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANA  162 (249)
Q Consensus        83 ~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~a  162 (249)
                      .|.++++.+++.|+++++++++++.+++++++++|.|+++++.|||+|++||||||+  +||+||.+||+|++.++++++
T Consensus        87 ~l~~~~~~~~~~~~~~~~~~~~v~~~a~~l~~~~~~~~~~~~~rp~~v~~lvaG~D~--~gp~Ly~id~~G~~~~~~~~a  164 (233)
T 1yar_A           87 VLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGVSLIFAGIDQ--IGPRLFDCDPAGTINEYKATA  164 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBTTBCCCCEEEEEEEECS--SCEEEEEECTTCCEEEBSEEE
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCcCCcCcceEEEEEEEEeC--CCCEEEEECCCCCEEeeeEEE
Confidence            999999999999999999999999999999999999999999999999999999994  789999999999999999999


Q ss_pred             ecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEEcCCCEEEcCHHHHHHHH
Q 025716          163 TGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEIDAMV  228 (249)
Q Consensus       163 iG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~--~~~~iei~~v~~~g~~~~~~~~ei~~~l  228 (249)
                      +|+|+..++++||+.|+++|+ +||++++++||..+.++  ++++++|++|+++|.+++++++||+++|
T Consensus       165 iG~gs~~a~~~Le~~~~~~~s~eea~~la~~al~~~~~~d~s~~~i~v~vi~~~~~~~~~~~~ei~~~l  233 (233)
T 1yar_A          165 IGSGKDAVVSFLEREYKENLPEKEAVTLGIKALKSSLEEGEELKAPEIASITVGNKYRIYDQEEVKKFL  233 (233)
T ss_dssp             ESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHTSCSSCCCCCCEEEEEETTSCCEECCHHHHHTTC
T ss_pred             EcCCcHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhccCCCCcEEEEEEECCCCEEECCHHHHHhhC
Confidence            999999999999999999999 99999999999999875  4789999999999889999999998763

>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=4.3e-61  Score=415.13  Aligned_cols=231  Identities=28%  Similarity=0.414  Sum_probs=220.2

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhH
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADA   81 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~   81 (249)
                      ++||+.+|+|||||||+|||||++|+++|+|+|||+++||||||+|+|.++++...++.+||++|++|++|+++|+.+|+
T Consensus         5 ~~yd~~~t~fsp~Grl~QvEyA~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~KI~~i~~~i~~~~aG~~aD~   84 (254)
T 1iru_G            5 TGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEGSNKRLFNVDRHVGMAVAGLLADA   84 (254)
T ss_dssp             SSTTSCTTCCCTTSCCHHHHHHHHHHHTSCCEEEEECSSBEEEEEEEECSCTTBCTTTTCCEEEEETTEEEEEEECHHHH
T ss_pred             cccCCCCccCCcCCccHHHHhHHHHHhcCCCEEEEEECCEEEEEEecccCCCCcCcCcCCcEEEECCCEEEEEecChHHH
Confidence            57999999999999999999999999999999999999999999999999977666789999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceE
Q 025716           82 RVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKAN  161 (249)
Q Consensus        82 ~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~  161 (249)
                      +.|+++++.+++.|+++++++++++.+++++++++|.|++++++|||+|++||||||+ ++||+||.+||+|++.+++++
T Consensus        85 ~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rP~~v~~lvaG~D~-~~gp~Ly~idp~G~~~~~~~~  163 (254)
T 1iru_G           85 RSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGCSFMLGSYSV-NDGAQLYMIDPSGVSYGYWGC  163 (254)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSBSSBCCCSEEEEEEEEET-TTEEEEEEECTTCCEEEBSEE
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhccccccccceEEEEEEEEeC-CCCcEEEEEcCCCCEEeeeeE
Confidence            9999999999999999999999999999999999999999989999999999999996 689999999999999999999


Q ss_pred             eecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcC--CCEEEcCHHHHHHHHHHHHH
Q 025716          162 ATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES---GGKNIEVAVMTRE--KGLKQLDEAEIDAMVAEIEA  233 (249)
Q Consensus       162 aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~--g~~~~~~~~ei~~~l~~i~~  233 (249)
                      ++|+|+..++++||+.|+++|+ +||++++++||..+++.   ++.+++|++|+++  |.+++++++++++++..+..
T Consensus       164 aiGsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~~~~~~~~iev~vi~~~~~g~~~~l~~~~i~~~~~~~~~  241 (254)
T 1iru_G          164 AIGKARQAAKTEIEKLQMKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEKYAKE  241 (254)
T ss_dssp             EESTTHHHHHHHHTTSCGGGCCHHHHHHHHHHHHHHHSCSSSSCCEEEEEEECBTTTTTCCEECCHHHHHHHHHHHHH
T ss_pred             EecCccHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHhhccCCCCcEEEEEEEcCCCCCeEECCHHHHHHHHHHHHH
Confidence            9999999999999999999999 99999999999999875   4668999999987  56999999999999998754

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

Probab=100.00  E-value=1.2e-60  Score=409.36  Aligned_cols=226  Identities=36%  Similarity=0.645  Sum_probs=216.9

Q ss_pred             CCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHH
Q 025716            3 RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADAR   82 (249)
Q Consensus         3 ~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~   82 (249)
                      +||+.+|+|||||||+|||||++|+++|+|+|||+++||||||+|+|.+++++.+++.+||++|++|++++++|+.+|++
T Consensus         7 ~yd~~~t~fsp~Grl~QvEya~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~   86 (241)
T 1iru_E            7 EYDRGVNTFSPEGRLFQVEYDIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEPSSIEKIVEIDAHIGCAMSGLIADAK   86 (241)
T ss_dssp             -CCCCTTCBCTTSCBHHHHHHHHHHTTSCCEEEEEETTEEEEEEECCCCCTTBCTTSCCSEEEEETTEEEEEEECHHHHH
T ss_pred             CCCCCCceECCCCccHHHHHHHHHHHcCCcEEEEEcCCEEEEEEecccCCcCcCccccceEEEEcCCEEEEEeeChHHHH
Confidence            79999999999999999999999999999999999999999999999999876688899999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCC-----CccceeEEEEEeeeCCCCCceEEEECCCCceec
Q 025716           83 VLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGG-----VRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSA  157 (249)
Q Consensus        83 ~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~-----~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~  157 (249)
                      .|.++++.+++.|+++++++++++.+++++++++|.|+++.+     .|||+|++||||||  ++||+||.+||+|++.+
T Consensus        87 ~l~~~~~~~~~~~~~~~~~~~~v~~~a~~l~~~~~~y~~~~~~~~l~~rp~~v~~lvaG~D--~~gp~Ly~idp~G~~~~  164 (241)
T 1iru_E           87 TLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMSRPFGVALLFGGVD--EKGPQLFHMDPSGTFVQ  164 (241)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCBCSTTCCSSCBSSCCCEEEEEEEEE--TTEEEEEEECTTSCEEE
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhccccccccccccceEEEEEEEEe--CCCCEEEEECCCCcEEe
Confidence            999999999999999999999999999999999999999887     89999999999999  57999999999999999


Q ss_pred             cceEeecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEEcCCCEEEcCHHHHHHHHHH
Q 025716          158 WKANATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEIDAMVAE  230 (249)
Q Consensus       158 ~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~--~~~~iei~~v~~~g~~~~~~~~ei~~~l~~  230 (249)
                      ++++|+|+|+..++++||+.|+++|+ +||++++++||..+.++  ++.+++|++|+++|.+++++++||++++.+
T Consensus       165 ~~~~aiGsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~~~sg~~i~v~vi~~~~~~~~l~~~ei~~~~~~  240 (241)
T 1iru_E          165 CDARAIGSASEGAQSSLQELYHKSMTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVIKD  240 (241)
T ss_dssp             BSEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCSSCCCTTSEEEEEECSSSCCEECCHHHHHHHHTT
T ss_pred             cceEEECCCcHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhccCCCCCEEEEEEECCCCeEECCHHHHHHHHHh
Confidence            99999999999999999999999999 99999999999999874  578999999999988999999999999865

>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=3.6e-60  Score=408.49  Aligned_cols=228  Identities=36%  Similarity=0.600  Sum_probs=217.5

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhH
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADA   81 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~   81 (249)
                      ++||+.+|+|||||||+|||||++|+++|+|+|||+++||||||+|+|.+.+++.+++.+||++|++|++++++|..+|+
T Consensus         3 ~~yd~~~t~fsp~Grl~QvEyA~~av~~Gtt~vgi~~~dgVvlaaD~r~~~~l~~~~~~~Ki~~i~~~i~~~~aG~~aD~   82 (250)
T 1ryp_B            3 DRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSETLSKVSLLTPDIGAVYSGMGPDY   82 (250)
T ss_dssp             CCCCSBSSCBCTTSCBHHHHHHHHHHHTSCCEEEEEETTEEEEEEECCCSCSSBCGGGCCSSEEEETTEEEEEEECHHHH
T ss_pred             CcccCCceeECCCCccHHHHhHHHHHHcCCcEEEEEECCEEEEEEeccCCCccccCcccCceEEECCCEEEEeeeCHHHH
Confidence            47999999999999999999999999999999999999999999999998888888899999999999999999999999


Q ss_pred             HHHHHHHHHHHHH-hhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccce
Q 025716           82 RVLINRARIECQS-HRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKA  160 (249)
Q Consensus        82 ~~l~~~~~~~~~~-~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~  160 (249)
                      +.|.++++.+++. |++.++.+++++.+++.++++++.++++.++|||+|++||||||+ ++||+||.+||+|++.++++
T Consensus        83 ~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~~a~~~~~~~~~~~~rp~~v~~lvaG~D~-~~gp~Ly~idp~G~~~~~~~  161 (250)
T 1ryp_B           83 RVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIAGHDE-FNGFSLYQVDPSGSYFPWKA  161 (250)
T ss_dssp             HHHHHHHHHHHHHTTHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCCEEEEEEEEET-TTEEEEEEECTTSCEEEBSE
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHhcCCcccceEEEEEEEEcC-CCCcEEEEECCCCCEEeece
Confidence            9999999999999 999999999999999999999999999989999999999999996 57999999999999999999


Q ss_pred             EeecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEEcC---------------CCEEEcCHH
Q 025716          161 NATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES--GGKNIEVAVMTRE---------------KGLKQLDEA  222 (249)
Q Consensus       161 ~aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~--~~~~iei~~v~~~---------------g~~~~~~~~  222 (249)
                      +++|+|+..++++||+.|+++|+ +||++++++||..+..+  ++++++|++|+++               +.|++++++
T Consensus       162 ~aiGsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~~~sg~~i~v~vi~~~~~~~~~~~~~~~~~~~~~~~l~~~  241 (250)
T 1ryp_B          162 TAIGKGSVAAKTFLEKRWNDELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTSQ  241 (250)
T ss_dssp             EEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCCSCCSTTTEEEEEECSCCGGGTSEESCSSCCCCSEEECCHH
T ss_pred             eEecCccHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhccccCCCCEEEEEEEccccccccccccccCCCCCeEECCHH
Confidence            99999999999999999999999 99999999999999764  5789999999986               249999999


Q ss_pred             HHHHHHHH
Q 025716          223 EIDAMVAE  230 (249)
Q Consensus       223 ei~~~l~~  230 (249)
                      ||++++.+
T Consensus       242 ei~~~l~~  249 (250)
T 1ryp_B          242 EINDRLEA  249 (250)
T ss_dssp             HHHHHHTT
T ss_pred             HHHHHHHh
Confidence            99999864

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

Probab=100.00  E-value=1.7e-60  Score=406.42  Aligned_cols=222  Identities=32%  Similarity=0.532  Sum_probs=211.3

Q ss_pred             CCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHH
Q 025716            3 RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADAR   82 (249)
Q Consensus         3 ~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~   82 (249)
                      +||+.+|+|||||||+|||||++|+++|+|+|||+++||||||+|+|.+.++.  ++.+||++|++|++++++|+.+|++
T Consensus         4 ~yd~~~t~fsp~Grl~QvEyA~~av~~Gtt~vgi~~~dgVvlaaD~r~~~~l~--~~~~Ki~~i~~~i~~~~aG~~aD~~   81 (233)
T 1ryp_F            4 NYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELS--SYQKKIIKCDEHMGLSLAGLAPDAR   81 (233)
T ss_dssp             HHSSCTTCCCTTSCCHHHHHHHHHHHTSCCEEEEECSSEEEEEEECCCSSTTB--CCCCCEEEEETTEEEEEEECHHHHH
T ss_pred             cccCCCccCCCCCeehHHHHHHHHHHcCCCEEEEEcCCEEEEEEEeccccccc--cccCcEEEEcCCEEEEEEechHHHH
Confidence            69999999999999999999999999999999999999999999999988865  3789999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEe
Q 025716           83 VLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANA  162 (249)
Q Consensus        83 ~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~a  162 (249)
                      .|.++++.+++.|+++++++++++.+++++++++|.|+|+.+.|||+|++||||||+  +||+||.+||+|++.+++++|
T Consensus        82 ~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rp~~v~~lvaG~D~--~gp~Ly~idp~G~~~~~~~~a  159 (233)
T 1ryp_F           82 VLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRPYGVGLLIIGYDK--SGAHLLEFQPSGNVTELYGTA  159 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEET--TEEEEEEECTTSCEEEESEEE
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcccCCcCcceEEEEEEEeC--CcCEEEEECCCCCeeeeeEEE
Confidence            999999999999999999999999999999999999999999999999999999994  789999999999999999999


Q ss_pred             ecCCchHHHHHHHhhhcc--CC--c-HHHHHHHHHHHHHHHh---cCCCcEEEEEEEcCCCEEEcCHHHHHHHH
Q 025716          163 TGRNSNSMREFLEKNYKE--TS--G-QETIKLAIRALLEVVE---SGGKNIEVAVMTREKGLKQLDEAEIDAMV  228 (249)
Q Consensus       163 iG~g~~~a~~~Le~~~~~--~~--s-eeai~la~~~l~~~~~---~~~~~iei~~v~~~g~~~~~~~~ei~~~l  228 (249)
                      +|+|+..++++||+.|++  +|  + +||++++++||..+++   .++.+++|++|++++.|++++++||+++|
T Consensus       160 iG~gs~~a~~~Le~~~~~~~~m~~s~eea~~~a~~al~~~~~d~~~s~~~i~v~vi~~~~~~~~l~~~ei~~~l  233 (233)
T 1ryp_F          160 IGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI  233 (233)
T ss_dssp             ESTTHHHHHHHHHHHHHHHTTCCSCHHHHHHHHHHHHTTSCCSSCCCTTTEEEEEEETTEEEEEEEGGGGGGGC
T ss_pred             ECCCcHHHHHHHHHHhccccccCCCHHHHHHHHHHHHHHHhhcccCCCCcEEEEEEECCCCEEECCHHHHHhhC
Confidence            999999999999999999  99  9 9999999999999883   25789999999998559999999998763

>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=9.7e-60  Score=408.50  Aligned_cols=227  Identities=34%  Similarity=0.598  Sum_probs=217.0

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhH
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADA   81 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~   81 (249)
                      ++||+.+|+|||||||+|||||+||+++|+|+|||+++||||||+|+|.++++.  ++.+||++|++|++|+++|+.+|+
T Consensus         4 ~~yd~~~t~fsP~Grl~QvEYA~~av~~Gtt~vgi~~~dgVVlaaD~r~~~gl~--~~~~KI~~i~~~i~~~~aG~~aD~   81 (263)
T 1iru_F            4 NQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELA--AHQKKILHVDNHIGISIAGLTADA   81 (263)
T ss_dssp             CTTTSCTTCCCTTSCCHHHHHHHHHHHHSCCEEEEECSSEEEEEEECCCSSTTB--CCCCCEEEEETTEEEEEEECHHHH
T ss_pred             CCCCCCCccCCCCCeehHHHHHHHHHHcCCcEEEEEeCCEEEEEEecccccccc--cchhcEEEEcCCEEEEEeCCHHHH
Confidence            479999999999999999999999999999999999999999999999998864  378999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceE
Q 025716           82 RVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKAN  161 (249)
Q Consensus        82 ~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~  161 (249)
                      +.|+++++.++..|+++++++++++.+++++++++|.|+++++.|||+|++||||||  ++||+||.+||+|++.+++++
T Consensus        82 ~~l~~~~~~~~~~~~~~~~~~i~v~~la~~l~~~l~~~t~~~~~RP~~v~~lvaG~D--~~gp~Ly~idp~G~~~~~~~~  159 (263)
T 1iru_F           82 RLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAGYD--DMGPHIFQTCPSANYFDCRAM  159 (263)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEE--TTEEEEEEECSSSCEEEESEE
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHhhcccccccceEEEEEEEEc--CCCCEEEEECCCCCEEEeeEE
Confidence            999999999999999999999999999999999999999999999999999999999  478999999999999999999


Q ss_pred             eecCCchHHHHHHHhhhcc--CCc-HHHHHHHHHHHHHHHhc----CCCcEEEEEEEcCCCEEEcCHHHHHHHHHHHH
Q 025716          162 ATGRNSNSMREFLEKNYKE--TSG-QETIKLAIRALLEVVES----GGKNIEVAVMTREKGLKQLDEAEIDAMVAEIE  232 (249)
Q Consensus       162 aiG~g~~~a~~~Le~~~~~--~~s-eeai~la~~~l~~~~~~----~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i~  232 (249)
                      ++|+|+..++++||+.|++  +|+ +||++++++||..++++    ++.+++|++|++++.++++++++|++++.++.
T Consensus       160 aiGsgs~~a~~~Le~~~~~~~~ms~eea~~la~~al~~~~~rd~~~sg~~iev~vi~~~~~~~~l~~~ei~~~~~~~~  237 (263)
T 1iru_F          160 SIGARSQSARTYLERHMSEFMECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEGLE  237 (263)
T ss_dssp             EESTTHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCTTCCCCTTTEEEEEEETTEEEEEECSGGGHHHHTTCC
T ss_pred             EcCcccHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHhccccCCCCcEEEEEEECCCCeEECCHHHHHHHHHHHh
Confidence            9999999999999999998  999 99999999999999854    46789999999985599999999999999986

>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=6.8e-59  Score=399.13  Aligned_cols=224  Identities=33%  Similarity=0.482  Sum_probs=209.6

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhH
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADA   81 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~   81 (249)
                      ++||+++|+|||||||+|||||++|+++|+|+|||+++||||||+|++.++++......+||++|++|++++++|+.+|+
T Consensus         2 ~~yd~~~t~fsp~Grl~QvEya~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~KI~~i~~~i~~~~aG~~aD~   81 (244)
T 1ryp_G            2 TGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNVKIQVVDRHIGCVYSGLIPDG   81 (244)
T ss_dssp             CCTTSSTTCCCTTSCCHHHHHHHHHHHTSCCEEEEEETTEEEEEEEEECCCTTBCTTTSCCCEEETTTEEEEEEECHHHH
T ss_pred             CCccCCcccCCcCCchHHHHhHHHHHHCCCCEEEEEECCEEEEEEecccCCCCccccccCceEEecCCEEEEEcccHHHH
Confidence            68999999999999999999999999999999999999999999999999977665567999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceE
Q 025716           82 RVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKAN  161 (249)
Q Consensus        82 ~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~  161 (249)
                      +.|+++++.++..|+++++++++++.+++++++++|.|+++++.|||+|++||+|||  ++||+||.+||+|++.+++++
T Consensus        82 ~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rp~~v~~lvaG~D--~~gp~Ly~idp~G~~~~~~~~  159 (244)
T 1ryp_G           82 RHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGGVD--KNGAHLYMLEPSGSYWGYKGA  159 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSCTTBCCCCEEEEEEEEE--TTEEEEEEECTTSCEEEBSEE
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCccCceEEEEEEEEe--CCcCEEEEECCCCCEEEeeEE
Confidence            999999999999999999999999999999999999999998899999999999999  479999999999999999999


Q ss_pred             eecCCchHHHHHHHhh---hccCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEc---CCCEEEcCHHHHHHHH
Q 025716          162 ATGRNSNSMREFLEKN---YKETSG-QETIKLAIRALLEVVES---GGKNIEVAVMTR---EKGLKQLDEAEIDAMV  228 (249)
Q Consensus       162 aiG~g~~~a~~~Le~~---~~~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~---~g~~~~~~~~ei~~~l  228 (249)
                      ++|+|+..++++||+.   |+++|+ +||++++++||..+.++   ++.+++|++|++   +| ++.+.++++.+..
T Consensus       160 aiG~gs~~a~~~Le~~~~~~~~~ms~eea~~la~~al~~~~~~d~~s~~~iev~vi~~~~~~g-~~~~~~~~~~~~~  235 (244)
T 1ryp_G          160 ATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNG-LHKFVKGDLLQEA  235 (244)
T ss_dssp             EESTTHHHHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHGGGGTTSCEEEEEEEEETTTTTT-SEEECCTHHHHHH
T ss_pred             EECCChHHHHHHHHHhHhhcCCCCCHHHHHHHHHHHHHHHHhccCCCCCeEEEEEEEecCCCC-eeeeChHHHHHHH
Confidence            9999999999999997   999999 99999999999999875   466899999998   67 7777766654443

>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=6.2e-59  Score=407.26  Aligned_cols=225  Identities=32%  Similarity=0.468  Sum_probs=211.1

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhH
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADA   81 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~   81 (249)
                      ++||+++|+|||+|||+|||||+||+++|+|+|||+++||||||+|+|.+++++.....+||++|++||+|+++|+.+|+
T Consensus         6 ~~yd~~~t~fSP~Grl~QvEYA~kAv~~GtT~Vgik~kdGVVlAaD~r~t~gl~~~~~~~KI~~I~d~i~~~~aG~~aD~   85 (288)
T 3nzj_F            6 TGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNVKIQVVDRHIGCVYSGLIPDG   85 (288)
T ss_dssp             CCTTSSTTCCCTTSCCHHHHHHHHHHHTSCCEEEEEETTEEEEEEEEEECCTTBCTTCSCCCEEETTTEEEEEEECHHHH
T ss_pred             CCccCCcccCCCCCchHHHHHHHHHHhcCCcEEEEEECCEEEEEEcCCcccCCccccccceEEEEcCCEEEEecCcHHHH
Confidence            47999999999999999999999999999999999999999999999999987666678999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceE
Q 025716           82 RVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKAN  161 (249)
Q Consensus        82 ~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~  161 (249)
                      +.|+++++.+++.|+++++++++++.+++++++++|.|+++++.|||+|++||||||+  +||+||.+||+|++.+++++
T Consensus        86 ~~l~~~lr~e~~~y~~~~~~~i~v~~lA~~l~~~l~~yt~~~~~rP~gv~~lvaG~D~--~Gp~Ly~iDp~G~~~~~~~~  163 (288)
T 3nzj_F           86 RHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGGVDK--NGAHLYMLEPSGSYWGYKGA  163 (288)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSCTTBCCCCEEEEEEEEET--TEEEEEEECTTSCEEEBSEE
T ss_pred             HHHHHHHHHHHHHHHHHcCCcCCHHHHHHHHHHHHHHHHHhccCCCceEEEEEEEEeC--CCCEEEEECCCCCEEEcCEE
Confidence            9999999999999999999999999999999999999999999999999999999995  78999999999999999999


Q ss_pred             eecCCchHHHHHHHhh---hccCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEc---CCCEEEcCHHHHHHHH
Q 025716          162 ATGRNSNSMREFLEKN---YKETSG-QETIKLAIRALLEVVES---GGKNIEVAVMTR---EKGLKQLDEAEIDAMV  228 (249)
Q Consensus       162 aiG~g~~~a~~~Le~~---~~~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~---~g~~~~~~~~ei~~~l  228 (249)
                      ++|++++.++++||+.   |+++|+ +||++++++||..++++   .+.++||+||++   +|.+++++.+.+++..
T Consensus       164 aiGsgs~~a~~~Lek~~~~~~~~ms~eEAv~la~~al~~a~~~~~~~~~~iev~vIt~~~~~~~~~~vp~~~~~~~~  240 (288)
T 3nzj_F          164 ATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAI  240 (288)
T ss_dssp             EESTTHHHHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHGGGGTTSEEEEEEEEEETTTSTTCCEECCHHHHHHHH
T ss_pred             EEcCcHHHHHHHHHHhccccCCCCCHHHHHHHHHHHHHHHHhcccCCCCeEEEEEEEecCCCceEEECCHHHHHHHH
Confidence            9999999999999999   999999 99999999999999876   356799999998   3556677777766553

>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=2.5e-52  Score=361.14  Aligned_cols=232  Identities=15%  Similarity=0.253  Sum_probs=195.3

Q ss_pred             CcccCCCCcch-hhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHHHHHH
Q 025716            8 ITVFSPDGHLF-QVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARVLIN   86 (249)
Q Consensus         8 ~~~fsp~G~l~-Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~   86 (249)
                      +..|||||++. |||||++|+++|+|+|||+++||||||+|+|       +++.+||++|++||+|+++|+.+|++.|++
T Consensus         4 p~~~sPe~~~~~qvEYA~~av~~Gtt~vgi~~~dgVVlaaD~r-------s~~~~KI~~I~d~i~~~~aG~~aD~~~l~~   76 (259)
T 1q5q_A            4 PYYASAEQIMRDRSELARKGIARGRSVVVLTFRDGVLFVAENP-------STALHKVSELYDRLGFAAVGKYNEFENLRR   76 (259)
T ss_dssp             -----CHHHHHHHHHHHHHHHHTSCCEEEEECSSEEEEEECCS-------CSSSCSEEEEETTEEEEEEECHHHHHHHHH
T ss_pred             CcccCHHHHHHHHHHHHHHHHhcCCcEEEEEeCCEEEEEEecC-------CCCcCcEEEeCCCEEEEEccCHHHHHHHHH
Confidence            44689999996 9999999999999999999999999999998       256899999999999999999999999999


Q ss_pred             HHHHHHHHhhhhcC-CCCCHHHHHHHHHH-HHHhhhccCCCccceeEEEEEeee--CCCCCceEEEECCCCcee-ccceE
Q 025716           87 RARIECQSHRLTVE-DPVTVEYITRYIAG-LQQKYTQSGGVRPFGLSTLIVGFD--PYTGVPSLYQTDPSGTFS-AWKAN  161 (249)
Q Consensus        87 ~~~~~~~~~~~~~~-~~i~~~~la~~ls~-~~~~~t~~~~~rP~gv~~ivaG~d--~~~~gp~Ly~iDp~G~~~-~~~~~  161 (249)
                      +++.+++.|++.++ .+++++.+++++++ +.|.|+  .+.|||+|++||||||  +.++||+||.+||+|++. .++++
T Consensus        77 ~~~~~~~~~~~~~~~~~i~v~~la~~l~~~l~q~yt--~~~rP~~v~~lvaG~D~~~~~~gp~Ly~idp~G~~~~~~~~~  154 (259)
T 1q5q_A           77 AGIVHADMRGYSYDRRDVTGRSLANAYAQTLGTIFT--EQPKPYEVEICVAEVGRVGSPKAPQLYRITYDGSIVDEQHFV  154 (259)
T ss_dssp             HHHHHHHHHHHHSCGGGCCHHHHHHHHHHHHHHHHH--HSSSCCCEEEEEEECCCSSCCCCCEEEEEETTSCEEEESSEE
T ss_pred             HHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHhc--cCCCCceEEEEEEEEcccCCCCCCEEEEECCCCceeeCCCEE
Confidence            99999999999988 59999999999999 777788  3679999999999999  223789999999999999 88999


Q ss_pred             eecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHH-----hc--CCCcEEEEEEEcCC---CEEEcCHHHHHHHHHH
Q 025716          162 ATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVV-----ES--GGKNIEVAVMTREK---GLKQLDEAEIDAMVAE  230 (249)
Q Consensus       162 aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~-----~~--~~~~iei~~v~~~g---~~~~~~~~ei~~~l~~  230 (249)
                      ++|++++.++++||++|+++|+ +||++++++||..+.     ++  ++.+++|++|+++|   .|+++++++|++++.+
T Consensus       155 aiG~gs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~~~~~rd~sg~~iev~vi~~~~~~~~~~~l~~~ei~~~~~~  234 (259)
T 1q5q_A          155 VMGGTTEPIATAMRESYRADLDLEAAVGIAVNALRQGGAGEGEKRNVDVASLEVAVLDQSRPRRAFRRIAGTALEQLVPA  234 (259)
T ss_dssp             EESSSHHHHHHHHHHHCCTTCCHHHHHHHHHHHHTTCC--------CCSSCSEEEEEETTSSSCCEEECCHHHHHTTSCC
T ss_pred             EECCChHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHhhcccccccCCCCcEEEEEEECCCCcCCeEECCHHHHHHHHHH
Confidence            9999999999999999999999 999999999999887     43  57789999999985   6999999999999998


Q ss_pred             HHHHH----HHHHHhhcCCCCC
Q 025716          231 IEAKK----AAAEAAKKGPPKE  248 (249)
Q Consensus       231 i~~~~----~~~~~~~~~~~~~  248 (249)
                      +.+.+    ++..+..+++|..
T Consensus       235 ~~~~~~~~~~~~~~~~~~~~~~  256 (259)
T 1q5q_A          235 EPAAASESAPEPKPDTETKPAD  256 (259)
T ss_dssp             C---------------------
T ss_pred             hhhcccccccccCCCCCCCCcc
Confidence            87544    2333444555543

>3mi0_A Proteasome subunit alpha; enzyme inhibitors, lactones, proteasome endopeptidase comple mycobacterium tuberculosis, hydrolase; HET: SA6; 2.20A {Mycobacterium tuberculosis} SCOP: d.153.1.4 PDB: 3h6f_A 3krd_A* 3h6i_A* 3mka_A 2fhh_A* 2fhg_A 3hfa_D 3hf9_A 3mfe_D

Probab=100.00  E-value=1.8e-49  Score=340.71  Aligned_cols=209  Identities=19%  Similarity=0.311  Sum_probs=187.4

Q ss_pred             hhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhh
Q 025716           19 QVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLT   98 (249)
Q Consensus        19 Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~   98 (249)
                      ++|||+||+++|+|+|||+++||||||+|+|       +++.+|||+|++|++|+++|+.+|++.|.+.++.+++.|+++
T Consensus        16 r~EYA~~av~~GtT~vgi~~kdgVVlaadkr-------~~~~~KI~~I~d~i~~~~aG~~aD~~~l~~~~~~~~~l~~~~   88 (248)
T 3mi0_A           16 RSELARKGIARAKSVVALAYAGGVLFVAENP-------SRSLQKISELYDRVGFAAAGKFNEFDNLRRGGIQFADTRGYA   88 (248)
T ss_dssp             HHHHHHHHHHTSCCEEEEEETTEEEEEEECC-------CSSSCSEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHhCCCcEEEEEeCCEEEEEEeCC-------CCCCCCeEEECCCEEEEEccCHHHHHHHHHHHHHHHHHHHHh
Confidence            5899999999999999999999999999998       347899999999999999999999999999999999999999


Q ss_pred             cC-CCCCHHHHHHHHH-HHHHhhhccCCCccceeEEEEEeeeC--CCCCceEEEECCCCceec-cceEeecCCchHHHHH
Q 025716           99 VE-DPVTVEYITRYIA-GLQQKYTQSGGVRPFGLSTLIVGFDP--YTGVPSLYQTDPSGTFSA-WKANATGRNSNSMREF  173 (249)
Q Consensus        99 ~~-~~i~~~~la~~ls-~~~~~~t~~~~~rP~gv~~ivaG~d~--~~~gp~Ly~iDp~G~~~~-~~~~aiG~g~~~a~~~  173 (249)
                      ++ .+++++.|+++++ .+.|.|++  +.|||+|++||+|||+  ..+||+||++||+|++.. ++++|+|+|++.++++
T Consensus        89 ~~~~~i~v~~la~~l~~~l~q~yt~--~~rP~gv~~liaG~D~~~~~~gp~Ly~~Dp~G~~~~e~~~~a~Gsgs~~a~~~  166 (248)
T 3mi0_A           89 YDRRDVTGRQLANVYAQTLGTIFTE--QAKPYEVELCVAEVAHYGETKRPELYRITYDGSIADEPHFVVMGGTTEPIANA  166 (248)
T ss_dssp             SCGGGCCHHHHHHHHHHHHHHHHHH--SSSCCCEEEEEEECCCTTCCCCCEEEEECTTSCEEEESSEEEESSCHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHhcc--CCCCceEEEEEEEEcCCCCCCCCEEEEECCCeEEeecccEEEECccHHHHHHH
Confidence            99 9999999999999 77889997  6899999999999994  137999999999999995 9999999999999999


Q ss_pred             HHhhhccCCc-HHHHHHHHHHHHHHH-------h--cCCCcEEEEEEEcCC---CEEEcCHHHHHHHHHHHHHHHH
Q 025716          174 LEKNYKETSG-QETIKLAIRALLEVV-------E--SGGKNIEVAVMTREK---GLKQLDEAEIDAMVAEIEAKKA  236 (249)
Q Consensus       174 Le~~~~~~~s-eeai~la~~~l~~~~-------~--~~~~~iei~~v~~~g---~~~~~~~~ei~~~l~~i~~~~~  236 (249)
                      ||++|+++|+ +||++++++||.++.       +  .+++++||++|+++|   .|++++++||++++.+++..+.
T Consensus       167 Le~~y~~~mt~eeai~la~~aL~~~~~~~~~~~~~~~~~~~iev~vv~~~g~~~~f~~l~~~ei~~~l~~~~~~~~  242 (248)
T 3mi0_A          167 LKESYAENASLTDALRIAVAALRAGSADTSGGDQPTLGVASLEVAVLDANRPRRAFRRITGSALQALLVDQESPQS  242 (248)
T ss_dssp             HHHHCCTTCCHHHHHHHHHHHHHHC------------CCTTEEEEEEETTSSSCCEEECCHHHHHHTC--------
T ss_pred             HHhhcCCCCCHHHHHHHHHHHHHHHHhhcccCcccccCCCcEEEEEEECCCCcccEEECCHHHHHHHHHHcCCCcc
Confidence            9999999999 999999999999998       3  367899999999985   4999999999999999876553

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

Probab=100.00  E-value=1.2e-47  Score=324.29  Aligned_cols=206  Identities=24%  Similarity=0.389  Sum_probs=187.2

Q ss_pred             CCcEEEEEeCCEEEEEEeccCCcc-cccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHH
Q 025716           30 GNAAVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYI  108 (249)
Q Consensus        30 G~t~igi~~~dgVvla~d~~~~~~-l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l  108 (249)
                      |+|+|||+++||||||+|+|.++. ++.+++.+||++|++|++|+++|+.+|++.|+++++.+++.|+++++++++++.+
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            799999999999999999999874 6677899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccc-eEeecCCchHHHHHHHhhhccCCc-HHH
Q 025716          109 TRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWK-ANATGRNSNSMREFLEKNYKETSG-QET  186 (249)
Q Consensus       109 a~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~-~~aiG~g~~~a~~~Le~~~~~~~s-eea  186 (249)
                      ++++++++|.+    +.|||+|++||||||+ .+||+||.+||+|++.+++ ++++|+|++.++++||+.|+++|+ +||
T Consensus        81 a~~l~~~~~~~----~~~P~~v~~lvaG~D~-~~gp~Ly~idp~G~~~~~~~~~aiG~gs~~a~~~Le~~~~~~ms~eea  155 (219)
T 3h4p_a           81 ATLLSNILHSS----RMFPFLTQIIIGGYDL-LEGAKLFSLDPLGGMNEEKTFTATGSGSPIAYGVLEAGYDRDMSVEEG  155 (219)
T ss_dssp             HHHHHHHHHHT----TTTTCCCCCEEEEEET-TTEEEEEEECSSCCEEECSSEEEESTTHHHHHHHHHTSCCTTCCHHHH
T ss_pred             HHHHHHHHHHh----cCCCceEEEEEEEEeC-CCCcEEEEECCCCceEecCCEEEEcCCHHHHHHHHHHhcCCCCCHHHH
Confidence            99999999876    3589999999999996 5899999999999999999 999999999999999999999999 999


Q ss_pred             HHHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCHHHHHHHHHHHHHHHHHHHHh
Q 025716          187 IKLAIRALLEVVES---GGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKKAAAEAA  241 (249)
Q Consensus       187 i~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i~~~~~~~~~~  241 (249)
                      ++++++||..+.++   ++++++|++|+++| |++++++||+++|+++++++..++..
T Consensus       156 ~~la~~al~~~~~rd~~sg~~i~v~vi~~~g-~~~l~~~ei~~~l~~~~~~~~~~~~~  212 (219)
T 3h4p_a          156 IKLALNALKSAMERDTFSGNGISLAVITKDG-VKIFEDEEIEKILDSMKAKPKKKTTK  212 (219)
T ss_dssp             HHHHHHHHHHHHTSCSSCCSCCCEEEEETTE-EEECCHHHHHHHHHHCC---------
T ss_pred             HHHHHHHHHHHHhhcCCCCCcEEEEEEeCCC-eEEcCHHHHHHHHHHhhcccccccch
Confidence            99999999999976   46799999999998 99999999999999999877555544

>1yar_H Proteasome beta subunit; proteasome 20S, PA26 proteasome activator 11S, hydrolase-HYD activator complex; 1.90A {Thermoplasma acidophilum} SCOP: d.153.1.4 PDB: 1ya7_H 1yau_H 3ipm_H 1pma_B 3jrm_H 3c92_H 3c91_H 3jse_H 3jtl_H

Probab=100.00  E-value=9.5e-46  Score=312.17  Aligned_cols=200  Identities=24%  Similarity=0.406  Sum_probs=184.3

Q ss_pred             HHHccCCcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCC
Q 025716           25 EAVRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPV  103 (249)
Q Consensus        25 kav~~G~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i  103 (249)
                      .++.+|+|+|||+++||||||+|+|.++ .++.+++.+||++|++|++++++|+.+|++.|.++++.+++.|++++++++
T Consensus         3 ~~~~~Gtt~vgi~~~dgVvlaaD~r~~~g~l~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~   82 (217)
T 1yar_H            3 QTLETGTTTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKAELELYRLQRRVNM   82 (217)
T ss_dssp             ------CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCC
T ss_pred             CCCCCCccEEEEEeCCEEEEEEcCCCCCCCEEecCccCCeEEeCCCEEEEeCcCHHHHHHHHHHHHHHHHHHHHHHCCCC
Confidence            4678999999999999999999999987 677888999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc
Q 025716          104 TVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG  183 (249)
Q Consensus       104 ~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s  183 (249)
                      +++.+++++++.++.+    +.|||+|++||||||   +||+||.+||+|++.+++++|+|+|++.++++||+.|+++|+
T Consensus        83 ~v~~la~~l~~~~~~~----r~rp~~v~~lvaG~D---~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~s  155 (217)
T 1yar_H           83 PIEAVATLLSNMLNQV----KYMPYMVQLLVGGID---TAPHVFSIDAAGGSVEDIYASTGSGSPFVYGVLESQYSEKMT  155 (217)
T ss_dssp             CHHHHHHHHHHHHHHT----TTSCCCEEEEEEEES---SSEEEEEECTTCCEEEESEEEESTTHHHHHHHHHHHCCTTCC
T ss_pred             CHHHHHHHHHHHHHhc----CCCCceEEEEEEEEC---CCCEEEEECCCCCeEecCEEEEcCCHHHHHHHHHhhcccCCC
Confidence            9999999999999764    368999999999998   589999999999999999999999999999999999999999


Q ss_pred             -HHHHHHHHHHHHHHHhc---CCCcEEEEEEEc-CCCEEEcCHHHHHHHHHHHH
Q 025716          184 -QETIKLAIRALLEVVES---GGKNIEVAVMTR-EKGLKQLDEAEIDAMVAEIE  232 (249)
Q Consensus       184 -eeai~la~~~l~~~~~~---~~~~iei~~v~~-~g~~~~~~~~ei~~~l~~i~  232 (249)
                       +||++++++||..+.++   ++++++|++|++ +| +++++++||++++.+++
T Consensus       156 ~eea~~la~~al~~~~~rd~~s~~~i~v~vi~~~~g-~~~~~~~ei~~~~~~~~  208 (217)
T 1yar_H          156 VDEGVDLVIRAISAAKQRDSASGGMIDVAVITRKDG-YVQLPTDQIESRIRKLG  208 (217)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTCCSCCEEEEEETTTE-EEECCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHhccCCCCCcEEEEEEECCCC-EEEcCHHHHHHHHHHHH
Confidence             99999999999999875   477899999999 76 99999999999998875

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

Probab=100.00  E-value=1.7e-45  Score=307.19  Aligned_cols=195  Identities=28%  Similarity=0.433  Sum_probs=184.4

Q ss_pred             CcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      +|+|||+++||||||+|+|.++ .++.+++.+||++|++|++++++|+.+|++.|+++++.+++.|+++++++++++.++
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            6899999999999999999987 677788999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccc-eEeecCCchHHHHHHHhhhccCCc-HHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWK-ANATGRNSNSMREFLEKNYKETSG-QETI  187 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~-~~aiG~g~~~a~~~Le~~~~~~~s-eeai  187 (249)
                      +++++.++.+    +.|||+|++||||||+  +||+||.+||+|++.+++ ++++|+|++.++++||+.|+++|+ +||+
T Consensus        81 ~~l~~~~~~~----r~rp~~~~~lvaG~D~--~gp~Ly~id~~G~~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s~eea~  154 (202)
T 1j2q_H           81 TLTSNLLNSY----RYFPYLVQLLIGGIDS--EGKSIYSIDPIGGAIEEKDIVATGSGSLTAYGVLEDRFTPEIGVDEAV  154 (202)
T ss_dssp             HHHHHHHHHT----TTSCCCEEEEEEEEET--TEEEEEEECTTCCEEEESSEEEESTTHHHHHHHHHHHCCTTCCHHHHH
T ss_pred             HHHHHHHHhh----CCCCceEEEEEEEEeC--CCCEEEEECCCCCeeecCCEEEEcCCHHHHHHHHHhhcCCCcCHHHHH
Confidence            9999999764    3689999999999994  689999999999999999 999999999999999999999999 9999


Q ss_pred             HHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCHHHHHHHHHHHH
Q 025716          188 KLAIRALLEVVES---GGKNIEVAVMTREKGLKQLDEAEIDAMVAEIE  232 (249)
Q Consensus       188 ~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i~  232 (249)
                      +++++||..+.++   ++++++|++|+++| +++++++|+++++.+++
T Consensus       155 ~la~~al~~~~~~d~~s~~~i~v~vi~~~g-~~~l~~~ei~~~~~~~~  201 (202)
T 1j2q_H          155 ELAVRAIYSAMKRDSASGDGIDVVKITEDE-FYQYSPEEVEQILAKFR  201 (202)
T ss_dssp             HHHHHHHHHHHTTCTTSCSCEEEEEECSSC-EEECHHHHHHHHGGGTT
T ss_pred             HHHHHHHHHHHhcCCCCCCcEEEEEEeCCC-eEEeCHHHHHHHHHHhh
Confidence            9999999999875   47789999999997 99999999999998764

>3nzj_K Proteasome component PRE2; ubiquitin, protein degradation, N-terminal nucleophilic HYDR 19S regulatory particle; HET: TY5 TRO MES; 2.40A {Saccharomyces cerevisiae} PDB: 3nzw_K* 3nzx_K* 4b4t_5

Probab=100.00  E-value=9.8e-46  Score=323.54  Aligned_cols=208  Identities=17%  Similarity=0.317  Sum_probs=189.6

Q ss_pred             hHHHHHccCCcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcC
Q 025716           22 YALEAVRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVE  100 (249)
Q Consensus        22 ya~kav~~G~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~  100 (249)
                      ++.+++.+|+|+|||+++||||||+|+|.+. .++.+++.+||++|++|++++++|..+|++.|.++++.+++.|+++++
T Consensus        67 ~~~~~v~~GtT~vgik~~dGVVlAaD~r~t~G~li~~~~~~KI~~I~d~i~~~~aG~~AD~~~l~~~lr~~~~~y~~~~~  146 (287)
T 3nzj_K           67 DCKIKIAHGTTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREK  146 (287)
T ss_dssp             ---------CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEECEECHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             chhhheccCceEEEEEECCEEEEEEccccccCceeecCCcceEEEEcCcEEEEecCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence            7788999999999999999999999999987 677788999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhcc
Q 025716          101 DPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE  180 (249)
Q Consensus       101 ~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~  180 (249)
                      ++++++.+++++++++|.+++    +||++++||||||+ ++||+||.+||+|++.+++++++|+|+..++++||+.|++
T Consensus       147 ~~isv~~la~~ls~~l~~~r~----~p~~v~~lvaG~D~-~~gp~Ly~iDp~G~~~~~~~~AiGsgs~~a~~~Le~~y~~  221 (287)
T 3nzj_K          147 ERISVAAASKILSNLVYQYKG----AGLSMGTMICGYTR-KEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKW  221 (287)
T ss_dssp             SCCCHHHHHHHHHHHHHHTTT----SCCCEEEEEEEEET-TTEEEEEEEETTCCEEECSEEEESTTHHHHHHHHHTSCCT
T ss_pred             CCCCHHHHHHHHHHHHHhhcC----CCceEEEEEEEEcC-CCCCEEEEECCCceEEEcCeEEEecchHHHHHHHHHhhcC
Confidence            999999999999999988765    49999999999997 6899999999999999999999999999999999999999


Q ss_pred             CCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCHHHHHHHHHHHHHHH
Q 025716          181 TSG-QETIKLAIRALLEVVES---GGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKK  235 (249)
Q Consensus       181 ~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i~~~~  235 (249)
                      +|+ +||++++++||..+..+   ++++++|++|+++| ++++++++|++++.++++++
T Consensus       222 dms~eEAi~la~~aL~~a~~rD~~sg~~i~V~vItkdg-~~~l~~~ev~~~l~~~~e~~  279 (287)
T 3nzj_K          222 DLSVEDALYLGKRSILAAAHRDAYSGGSVNLYHVTEDG-WIYHGNHDVGELFWKVKEEE  279 (287)
T ss_dssp             TCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTE-EEEEEEEEHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHhhCcCCCCceEEEEEeCCC-EEEeCHHHHHHHHHHHHHhh
Confidence            999 99999999999999875   46899999999998 99999999999999998764

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

Probab=100.00  E-value=1.3e-45  Score=323.77  Aligned_cols=212  Identities=18%  Similarity=0.225  Sum_probs=193.9

Q ss_pred             HHHHHccCCcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCC
Q 025716           23 ALEAVRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVED  101 (249)
Q Consensus        23 a~kav~~G~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~  101 (249)
                      |++|+++|+|+|||+++||||||+|++.++ +++.+++.+||++|++|++|+++|+.+|++.|+++++.+++.|++++++
T Consensus        58 a~~Av~~GtTiVgIk~kdGVVlAaD~r~t~G~li~~~~~~KI~~I~~~i~~~~aG~~aD~~~l~~~~r~~~~~y~~~~g~  137 (294)
T 1q5r_H           58 SGDLAPHGTTIVALTYKGGVLLAGDRRATQGNLIASRDVEAVYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEGV  137 (294)
T ss_dssp             --CCSCBCCCEEEEECSSCEEEEECCCEEETTEEEESCCCCEEEEETTEEEEEEEBHHHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHhcCceEEEEEECCEEEEEEcCccccCceeecCCcceEEEECCcEEEEEeecHHHHHHHHHHHHHHHHHhhHhhCC
Confidence            889999999999999999999999999987 6888889999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCC-----ceEEEECCCCceecc--ceEeecCCchHHHHHH
Q 025716          102 PVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGV-----PSLYQTDPSGTFSAW--KANATGRNSNSMREFL  174 (249)
Q Consensus       102 ~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~g-----p~Ly~iDp~G~~~~~--~~~aiG~g~~~a~~~L  174 (249)
                      +++++.++++|++++|.++++. .|||+|++||+|||+ +++     |+||.+||+|++.++  +++++|+|+.+++++|
T Consensus       138 ~isv~~la~~la~~l~~~~~~~-~rp~~v~lLvaG~D~-~~g~~~~~p~Ly~iDp~G~~~e~~~~~~AiGsgs~~a~~~L  215 (294)
T 1q5r_H          138 PLTFDGKANRLASMVRGNLGAA-MQGLAVVPLLVGYDL-DADDESRAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSAL  215 (294)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHH-TTTTCEEEEEEEECT-TCSCTTSCEEEEEECSSSCEEECCSSEEEESTTHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHhhh-cCCcceEEEEEEEeC-CCCcCCCCCEEEEECCCCeEEecCCCeEEEecCcHHHHHHH
Confidence            9999999999999999988754 799999999999996 546     999999999999999  9999999999999999


Q ss_pred             HhhhccCCc-HHHHHHHHHHHHHHHhcC---C--CcE-----EEEEEEcCCCEEEcCHHHHHHHHHHHHHHHHH
Q 025716          175 EKNYKETSG-QETIKLAIRALLEVVESG---G--KNI-----EVAVMTREKGLKQLDEAEIDAMVAEIEAKKAA  237 (249)
Q Consensus       175 e~~~~~~~s-eeai~la~~~l~~~~~~~---~--~~i-----ei~~v~~~g~~~~~~~~ei~~~l~~i~~~~~~  237 (249)
                      |+.|+++|+ +||++++++||..+.+++   +  +++     +|++|+++| +++++++|+++++.++.+++.+
T Consensus       216 e~~y~~~ms~eEAi~la~~aL~~a~~rD~~sG~~~~ir~i~~ev~vI~~~g-~~~l~~~ei~~~l~~i~~~~~~  288 (294)
T 1q5r_H          216 KKIYSPDSDEETALRAAIESLYDAADDDSATGGPDLTRGIYPTAVTITQAG-AVHVSEETTSELARRIVAERTE  288 (294)
T ss_dssp             HHHCCSSCCHHHHHHHHHHHHHHHHHHCTTTCCCBTTTTBCCEEEEEETTE-EEECCHHHHHHHHHHHCC----
T ss_pred             HHhccCCCCHHHHHHHHHHHHHHHHhhccccCCchhhcccCCEEEEEECCC-EEEcCHHHHHHHHHHHHHHhhh
Confidence            999999999 999999999999998753   1  235     999999998 9999999999999999765443

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

Probab=100.00  E-value=1.8e-45  Score=322.55  Aligned_cols=229  Identities=16%  Similarity=0.193  Sum_probs=175.6

Q ss_pred             CCCCCCcccCCCCcc-----hh--hhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcc-cccCCcccceEEecCCEEEEE
Q 025716            3 RYDRAITVFSPDGHL-----FQ--VEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALAC   74 (249)
Q Consensus         3 ~yd~~~~~fsp~G~l-----~Q--veya~kav~~G~t~igi~~~dgVvla~d~~~~~~-l~~~~~~~Ki~~I~~~i~~~~   74 (249)
                      +|+..+....||.-.     +|  +|||++ +.+|+|+|||+++||||||+|+|.+++ ++.+++.+||++|++|++|++
T Consensus        24 ~f~~~~~~~~~~~l~~~~~~~~~~~~ya~~-v~~GtTiVgi~~kdGVVlAaD~r~t~g~li~~~~~~KI~~i~d~i~~~~  102 (291)
T 2jay_A           24 SFTDFLRRQAPELLPASISGGAPLAGGDAQ-LPHGTTIVALKYPGGVVMAGDRRSTQGNMISGRDVRKVYITDDYTATGI  102 (291)
T ss_dssp             -----------------------------------CCEEEEEETTEEEEEECCC--------CCCCCCEEEEETTEEEEE
T ss_pred             cHHHHhhhcChhhccccccccCcCcccccc-ccCCcEEEEEEECCEEEEEECCCccCCCeeecCCcccEEEeCCcEEEEE
Confidence            456666666666432     22  689999 999999999999999999999999885 677788999999999999999


Q ss_pred             ecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCC-----ceEEEE
Q 025716           75 AGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGV-----PSLYQT  149 (249)
Q Consensus        75 sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~g-----p~Ly~i  149 (249)
                      +|..+|++.|+++++.+++.|++.++++++++.++++++++++.+++ ...|||+|++||||||+ +++     |+||.+
T Consensus       103 aG~~aD~~~l~~~lr~~~~~y~~~~~~~i~v~~la~~la~~l~~~~~-~~~rpf~v~~lvaG~D~-~g~~~~~~p~Ly~i  180 (291)
T 2jay_A          103 AGTAAVAVEFARLYAVELEHYEKLEGVPLTFAGKINRLAIMVRGNLA-AAMQGLLALPLLAGYDI-HASDPQSAGRIVSF  180 (291)
T ss_dssp             ESCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHTCHH-HHHHTCCCEEEEEEECT-TCSCSTTCEEEEEE
T ss_pred             cccHHHHHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHHhhh-hhccccceeEEEEEEeC-CCCcCCCCCEEEEE
Confidence            99999999999999999999999999999999999999999998875 45789999999999996 555     999999


Q ss_pred             CCCCcee--ccceEeecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhcC--CCcE--------EEEEEEcCCCE
Q 025716          150 DPSGTFS--AWKANATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVESG--GKNI--------EVAVMTREKGL  216 (249)
Q Consensus       150 Dp~G~~~--~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~~--~~~i--------ei~~v~~~g~~  216 (249)
                      ||+|++.  +++++++|+|+.+++++||+.|+++|+ +||++++++||..+.+++  .+++        +|++|+++| +
T Consensus       181 Dp~G~~~e~~~~~~aiGsgs~~a~~~Le~~~~~~ms~eEAi~la~~aL~~a~~~D~~sg~~e~vr~~~~~v~vi~~dg-~  259 (291)
T 2jay_A          181 DAAGGWNIEEEGYQAVGSGSLFAKSSMKKLYSQVTDGDSGLRVAVEALYDAADDDSATGGPDLVRGIFPTAVIIDADG-A  259 (291)
T ss_dssp             CTTSCEEECSSSEEEESTTHHHHHHHHHHHGGGCCSHHHHHHHHHHHHHHC----------------CCEEEEEETTE-E
T ss_pred             CCCCcEEecCCCEEEEecCHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhhCCCCCCcccccccCCEEEEEECCC-e
Confidence            9999999  899999999999999999999999999 999999999999988753  2334        699999998 9


Q ss_pred             EEcCHHHHHHHHHHHHHHH
Q 025716          217 KQLDEAEIDAMVAEIEAKK  235 (249)
Q Consensus       217 ~~~~~~ei~~~l~~i~~~~  235 (249)
                      ++++++||++++.++.+.+
T Consensus       260 ~~l~~~ei~~~~~~~~~~~  278 (291)
T 2jay_A          260 VDVPESRIAELARAIIESR  278 (291)
T ss_dssp             EECCHHHHHHHHHHC----
T ss_pred             EEcCHHHHHHHHHHHHHhh
Confidence            9999999999999986643

>1ryp_L 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_L 1vsy_L 1z7q_L 3l5q_P 1g65_K* 1g0u_K* 1jd2_K* 2f16_K* 2fak_K* 2fny_K* 2gpl_K* 2zcy_K* 3bdm_K* 3d29_K* 3dy3_K* 3dy4_K* 3e47_K* 3gpj_K* 3gpt_K* 3gpw_K* ...

Probab=100.00  E-value=7e-45  Score=305.71  Aligned_cols=199  Identities=17%  Similarity=0.330  Sum_probs=188.3

Q ss_pred             CcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      +|+|||+++||||||+|+|.++ .++.+++.+||++|++|++++++|+.+|++.|.++++.+++.|+++++++++++.++
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            6899999999999999999988 688888999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIK  188 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~  188 (249)
                      +++++++|.|++.    ||+|++||||||+ +++|+||.+||+|++.+++++|+|+|+.+++++||+.|+++|| +||++
T Consensus        81 ~~l~~~~~~~~~~----p~~v~~lvaG~D~-~~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~s~eea~~  155 (212)
T 1ryp_L           81 KILSNLVYQYKGA----GLSMGTMICGYTR-KEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALY  155 (212)
T ss_dssp             HHHHHHHHHTTTS----CCCBEEEEEEEET-TTEEEEEEEETTCCEEECSEEEESTTHHHHHHHHHHHCCTTCCHHHHHH
T ss_pred             HHHHHHHHhhCCC----CceEEEEEEEEeC-CCCCEEEEEcCCceeEecCCEEEcCCHHHHHHHHHhhCCCCCCHHHHHH
Confidence            9999999988863    8999999999996 5799999999999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCHHHHHHHHHHHHHHH
Q 025716          189 LAIRALLEVVES---GGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKK  235 (249)
Q Consensus       189 la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i~~~~  235 (249)
                      ++++||..+.++   ++.+++|++|+++| +++++++|+++++.+++++.
T Consensus       156 la~~al~~~~~rd~~s~~~i~v~vi~~~g-~~~~~~~ei~~~~~~~~~~~  204 (212)
T 1ryp_L          156 LGKRSILAAAHRDAYSGGSVNLYHVTEDG-WIYHGNHDVGELFWKVKEEE  204 (212)
T ss_dssp             HHHHHHHHHHHHBTTCCSEEEEEEEETTE-EEEEEEEEHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccccCCceEEEEEcCCc-eEEECHHHHHHHHHHHHHhh
Confidence            999999999875   57899999999998 99999999999999886543

>1iru_L 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_K* 3une_K 3unf_K* 3unh_K

Probab=100.00  E-value=8.1e-45  Score=303.57  Aligned_cols=198  Identities=15%  Similarity=0.281  Sum_probs=186.0

Q ss_pred             CcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      +|+|||+++||||||+|+|.++ .++.+++.+||++|++|++++++|+.+|++.|.++++.+++.|+++++++++++.++
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            6899999999999999999988 677788999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIK  188 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~  188 (249)
                      +++++.+|.+++    +||+|++||||||  ++||+||.+||+|++.+++++|+|+|+..++++||+.|+++|+ +||++
T Consensus        81 ~~l~~~~~~~r~----~~~~v~~lvaG~D--~~gp~Ly~idp~G~~~~~~~~aiG~gs~~a~~~Le~~~~~~~s~eea~~  154 (204)
T 1iru_L           81 KLLANMVYQYKG----MGLSMGTMICGWD--KRGPGLYYVDSEGNRISGATFSVGSGSVYAYGVMDRGYSYDLEVEQAYD  154 (204)
T ss_dssp             HHHHHHHHTTTT----SCCCBEEEEEEEC--SSSEEEEEEESSSCEEECSEEEESTTHHHHHHHHHTTCCTTCCHHHHHH
T ss_pred             HHHHHHHHHhCC----CCeeEEEEEEEEe--CCCCEEEEECCCCcEEEeCCEEEEcCHHHHHHHHhccCCCCCCHHHHHH
Confidence            999999988753    5899999999999  4799999999999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCHHHHHHHHHHHHHHH
Q 025716          189 LAIRALLEVVES---GGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKK  235 (249)
Q Consensus       189 la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i~~~~  235 (249)
                      ++++||..+.++   ++++++|++|+++| +++++++|+++++++++.++
T Consensus       155 l~~~al~~~~~rd~~s~~~i~v~vi~~~g-~~~l~~~ei~~~~~~~~~~~  203 (204)
T 1iru_L          155 LARRAIYQATYRDAYSGGAVNLYHVREDG-WIRVSSDNVADLHEKYSGST  203 (204)
T ss_dssp             HHHHHHHHHHHHBTTCCSEEEEEEECSSC-EEEEEEEEHHHHHHHHTC--
T ss_pred             HHHHHHHHHHHhCccCCCceEEEEEeCCc-eEEeCHHHHHHHHHHhccCC
Confidence            999999999864   57899999999998 99999999999999986543

>1q5q_H Proteasome beta-type subunit 1; proteasome assembly, Pro-peptide, inter-subunit contacts, RH erythropolis, hydrolase; 2.60A {Rhodococcus erythropolis} SCOP: d.153.1.4

Probab=100.00  E-value=1.9e-44  Score=307.69  Aligned_cols=202  Identities=19%  Similarity=0.233  Sum_probs=188.1

Q ss_pred             CcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      +|+|||+++||||||+|+|.++ +++.+++.+||++|++|++|+++|+.+|++.|+++++.+++.|+++++++++++.++
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            6899999999999999999987 688888999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCC-----ceEEEECCCCceecc--ceEeecCCchHHHHHHHhhhccCC
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGV-----PSLYQTDPSGTFSAW--KANATGRNSNSMREFLEKNYKETS  182 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~g-----p~Ly~iDp~G~~~~~--~~~aiG~g~~~a~~~Le~~~~~~~  182 (249)
                      ++++++++.++++. .|||+|++||||||+ +++     |+||.+||+|++.++  +++++|+|+.+++++||+.|+++|
T Consensus        81 ~~l~~~~~~~~~~~-~rp~~v~~lvaG~D~-~~g~~~~~p~Ly~idp~G~~~~~~~~~~aiGsgs~~a~~~Le~~~~~~m  158 (235)
T 1q5q_H           81 NRLASMVRGNLGAA-MQGLAVVPLLVGYDL-DADDESRAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALKKIYSPDS  158 (235)
T ss_dssp             HHHHHHHHTTHHHH-TTTCCEEEEEEEECT-TCSSTTSCEEEEEECTTSCEEECCSSEEEESTTHHHHHHHHHHHCCTTC
T ss_pred             HHHHHHHHHHHHhh-hcccceEEEEEEEEC-CCCccCCCCEEEEECCCCceEEeCCCeEEECCCHHHHHHHHHhhcCCCC
Confidence            99999999988764 799999999999996 546     999999999999999  999999999999999999999999


Q ss_pred             c-HHHHHHHHHHHHHHHhcC---C--CcE-----EEEEEEcCCCEEEcCHHHHHHHHHHHHHHH
Q 025716          183 G-QETIKLAIRALLEVVESG---G--KNI-----EVAVMTREKGLKQLDEAEIDAMVAEIEAKK  235 (249)
Q Consensus       183 s-eeai~la~~~l~~~~~~~---~--~~i-----ei~~v~~~g~~~~~~~~ei~~~l~~i~~~~  235 (249)
                      + +||++++++||..+.+++   +  .++     +|++|+++| +++++++|+++++.++++++
T Consensus       159 s~eeA~~la~~al~~a~~~d~~sg~~~~i~~~~~ev~vi~~~g-~~~l~~~ei~~~~~~~~~~~  221 (235)
T 1q5q_H          159 DEETALRAAIESLYDAADDDSATGGPDLTRGIYPTAVTITQAG-AVHVSEETTSELARRIVAER  221 (235)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCTTTCCCBTTTTBCCEEEEEETTE-EEECCHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHhhCcccCCcccccccccEEEEEeCCC-eEEeCHHHHHHHHHHHHHHH
Confidence            9 999999999999998753   2  123     999999998 99999999999999996654

>1iru_N 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_M* 3une_M 3unf_M* 3unh_M

Probab=100.00  E-value=6e-45  Score=307.57  Aligned_cols=199  Identities=16%  Similarity=0.169  Sum_probs=185.0

Q ss_pred             HHHHccCCcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhh-hcCC
Q 025716           24 LEAVRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRL-TVED  101 (249)
Q Consensus        24 ~kav~~G~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~-~~~~  101 (249)
                      ++|+.+|+|+|||+++||||||+|+|.+. .++.+++.+||++|++|++++++|+.+|++.|.++++.+++.|++ ++++
T Consensus         2 ~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~   81 (219)
T 1iru_N            2 QNPMVTGTSVLGVKFEGGVVIAADMLGSYGSLARFRNISRIMRVNNSTMLGASGDYADFQYLKQVLGQMVIDEELLGDGH   81 (219)
T ss_dssp             CSCCSEECCCEEEEETTEEEEEEECCEEETTEEEECSCCCEEEETTTEEEEEEEEHHHHHHHHHHHHHHHHHHHHHCSSC
T ss_pred             CCCccCCceEEEEEeCCEEEEEECCccccCcEEecCCCCceEEeCCCEEEEeccCHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence            36788999999999999999999999987 677778999999999999999999999999999999999999998 9999


Q ss_pred             CCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhcc-
Q 025716          102 PVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE-  180 (249)
Q Consensus       102 ~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~-  180 (249)
                      +++++.+++++++.++  +++++.|||+|++||||||+  ++|+||.+||+|++.+++++++|+|++.++++||+.|++ 
T Consensus        82 ~~~v~~la~~l~~~ly--~~r~~~~P~~v~~lvaG~D~--~gp~Ly~id~~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~  157 (219)
T 1iru_N           82 SYSPRAIHSWLTRAMY--SRRSKMNPLWNTMVIGGYAD--GESFLGYVDMLGVAYEAPSLATGYGAYLAQPLLREVLEKQ  157 (219)
T ss_dssp             CCCHHHHHHHHHHHHH--HHHHTTCCCCEEEEEEEEET--TEEEEEEECSSCCEEECSEEECTTHHHHTHHHHHHHHTSC
T ss_pred             CCCHHHHHHHHHHHHH--HhcccCCCceEEEEEEEEEC--CCCEEEEECCCCCeEECCeEEECccHHHHHHHHHhhcCCC
Confidence            9999999999999985  45567899999999999994  699999999999999999999999999999999999999 


Q ss_pred             -CCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCHHHHHHH
Q 025716          181 -TSG-QETIKLAIRALLEVVES---GGKNIEVAVMTREKGLKQLDEAEIDAM  227 (249)
Q Consensus       181 -~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~~ei~~~  227 (249)
                       +|+ +||++++++||..+.++   ++.+++|++|+++| ++.+++++|+..
T Consensus       158 ~~mt~eea~~l~~~al~~~~~~d~~sg~~i~v~vi~~~g-~~~~~~~~i~~~  208 (219)
T 1iru_N          158 PVLSQTEARDLVERCMRVLYYRDARSYNRFQTATVTEKG-VEIEGPLSTETN  208 (219)
T ss_dssp             SCCCHHHHHHHHHHHHHHHHHHBTTCCSCEEEEEEETTE-EEEEEEECCCCC
T ss_pred             CCCCHHHHHHHHHHHHHHHHHhcCcCCCcEEEEEEcCCC-EEEcCCeeccch
Confidence             999 99999999999999875   47899999999998 999988777543

>1iru_H 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_N* 3une_N

Probab=100.00  E-value=2.8e-44  Score=300.55  Aligned_cols=194  Identities=18%  Similarity=0.295  Sum_probs=182.7

Q ss_pred             CcEEEEEeCCEEEEEEeccCCcc-cccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~~-l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      +|+|||+++||||||+|+|.+++ ++.+++.+||++|++|++++++|+.+|++.|.++++.+++.|+++++++++++.++
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            68999999999999999999986 77778899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIK  188 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~  188 (249)
                      +++++.+|.|++     ||++++||||||+ ++||+||.+||+|++.+++++++|+|+..++++||+.|+++|+ +||++
T Consensus        81 ~~l~~~~~~~~~-----p~~~~~lvaG~D~-~~gp~ly~~d~~G~~~~~~~~a~Gsgs~~a~~~Le~~~~~~~s~eea~~  154 (205)
T 1iru_H           81 SLFKEMCYRYRE-----DLMAGIIIAGWDP-QEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREGMTKEECLQ  154 (205)
T ss_dssp             HHHHHHHHHTTT-----TCCEEEEEEEEET-TTEEEEEEECTTSCCEECSEEEESGGGGGGHHHHHHHCCTTCCHHHHHH
T ss_pred             HHHHHHHHhcCc-----CccEEEEEEEEeC-CCCCEEEEECCCCcEEecCEEEECCCHHHHHHHHHHhcCCCCCHHHHHH
Confidence            999999998874     9999999999996 5799999999999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHhc---CCCcEEEEEEEcCCC-EEEcCHHHHHHHHHH
Q 025716          189 LAIRALLEVVES---GGKNIEVAVMTREKG-LKQLDEAEIDAMVAE  230 (249)
Q Consensus       189 la~~~l~~~~~~---~~~~iei~~v~~~g~-~~~~~~~ei~~~l~~  230 (249)
                      ++++||..+.++   ++++++|++|+++|. +++++++||++++++
T Consensus       155 l~~~al~~~~~~d~~s~~~i~v~vi~~~g~~~~~l~~~ei~~~~~~  200 (205)
T 1iru_H          155 FTANALALAMERDGSSGGVIRLAAIAESGVERQVLLGDQIPKFAVA  200 (205)
T ss_dssp             HHHHHHHHHHHHBTTCCSCEEEEEEETTEEEEEEECGGGSCCCCCC
T ss_pred             HHHHHHHHHHHhccccCCcEEEEEEeCCCeEEEEeChHHhhHHHhh
Confidence            999999999875   478999999999984 678999999887754

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

Probab=100.00  E-value=6.8e-45  Score=310.03  Aligned_cols=200  Identities=14%  Similarity=0.248  Sum_probs=186.2

Q ss_pred             HHHHccCCcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhh-----
Q 025716           24 LEAVRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRL-----   97 (249)
Q Consensus        24 ~kav~~G~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~-----   97 (249)
                      ++|+++|+|+|||+++||||||+|+|.+. .++.+++.+||++|++|++|+++|..+|++.|.++++.+++.|++     
T Consensus         2 ~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~   81 (233)
T 1ryp_N            2 QQPIVTGTSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLA   81 (233)
T ss_dssp             CCCCEEECCEEEEEETTEEEEEEECCEEETTEEEESCCCCEEEETTTEEEEEEEEHHHHHHHHHHHHHHHHHHHTTCTTT
T ss_pred             cccccCCceEEEEEECCEEEEEEcCccccCCeeecCCcCceEEeCCCEEEEccccHHHHHHHHHHHHHHHHHHhhccchh
Confidence            35788999999999999999999999987 577788999999999999999999999999999999999999999     


Q ss_pred             hcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhh
Q 025716           98 TVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKN  177 (249)
Q Consensus        98 ~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~  177 (249)
                      +++++++++.+++++++.+  |+++++.|||+|++||+|||+ +++|+||.+||+|++.+++++++|+|+..++++||+.
T Consensus        82 ~~~~~~~v~~la~~l~~~l--y~~r~~~~P~~v~~lvaG~D~-~~gp~Ly~id~~G~~~~~~~~aiGsgs~~a~~~Le~~  158 (233)
T 1ryp_N           82 DAEEALEPSYIFEYLATVM--YQRRSKMNPLWNAIIVAGVQS-NGDQFLRYVNLLGVTYSSPTLATGFGAHMANPLLRKV  158 (233)
T ss_dssp             TTTTSCCHHHHHHHHHHHH--HHHHHTTCCCCEEEEEEEECT-TSCEEEEEEETTCCEECCSEEECTHHHHHHHHHHTTT
T ss_pred             hcCCCCCHHHHHHHHHHHH--HHhcCCCCCceEEEEEEEEcC-CCCEEEEEECCCcCeEEcCEEEECcCHHHHHHHHHHh
Confidence            8999999999999999998  455567899999999999996 5699999999999999999999999999999999999


Q ss_pred             hcc-----CCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcC-CCEEEcCHHHHHHH
Q 025716          178 YKE-----TSG-QETIKLAIRALLEVVES---GGKNIEVAVMTRE-KGLKQLDEAEIDAM  227 (249)
Q Consensus       178 ~~~-----~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~-g~~~~~~~~ei~~~  227 (249)
                      |++     +|+ +||++++++||..+.++   ++.+++|++|+++ | ++.++++||+++
T Consensus       159 ~~~~~~~~~ms~eea~~la~~al~~~~~rd~~sg~~i~v~vi~~~~g-~~~~~~~~i~~~  217 (233)
T 1ryp_N          159 VDRESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKNTG-LTFKKNLQVENM  217 (233)
T ss_dssp             CSSGGGGGGCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTTE-EEEEEEEECCSC
T ss_pred             hccccccCCCCHHHHHHHHHHHHHHHHHhcccCCCcEEEEEEECCCC-eEEcChHhcccc
Confidence            999     999 99999999999999875   4789999999999 6 999988887665

>1ryp_K 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_K 1g0u_J* 1jd2_J* 1g65_J 1vsy_K 1z7q_K 2f16_J* 2fak_J* 2fny_J* 2gpl_J* 2zcy_J* 3bdm_J* 3d29_J* 3dy3_J* 3dy4_J* 3e47_J* 3gpj_J* 3gpt_J* 3gpw_J* 3hye_J* ...

Probab=100.00  E-value=3.8e-43  Score=292.09  Aligned_cols=189  Identities=21%  Similarity=0.297  Sum_probs=174.9

Q ss_pred             CCcEEEEEeCCEEEEEEeccCCccc-ccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHH
Q 025716           30 GNAAVGVRGTDTIVLGVEKKSTVKL-QDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYI  108 (249)
Q Consensus        30 G~t~igi~~~dgVvla~d~~~~~~l-~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l  108 (249)
                      ++|+|||+++||||||+|+|.++++ +.+++.+||++|++|++++++|+.+|++.|.++++.+++.|+++++++++++.+
T Consensus         1 Mtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~l   80 (198)
T 1ryp_K            1 MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYIQANIQLYSIREDYELSPQAV   80 (198)
T ss_dssp             CCCEEEEECSSCEEEEEECCEEETTEEEESCCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHH
T ss_pred             CceEEEEEECCEEEEEECCCcccCCEEEecCCCceEEeCCCEEEEeccCHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHH
Confidence            6899999999999999999998754 446789999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHH
Q 025716          109 TRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETI  187 (249)
Q Consensus       109 a~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai  187 (249)
                      ++++++.++.+++.  .+||+|++||||||+.+++|+||.+||+|++.+++++++|+|+..++++||+.|+++|+ +||+
T Consensus        81 a~~l~~~l~~~~~~--r~p~~v~~lvaG~D~~~~~p~Ly~idp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s~eea~  158 (198)
T 1ryp_K           81 SSFVRQELAKSIRS--RRPYQVNVLIGGYDKKKNKPELYQIDYLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGL  158 (198)
T ss_dssp             HHHHHHHHHHHTTS--SSCCCEEEEEEEEETTTTEEEEEEECTTCCEEECSEEECTTHHHHHHHHHHHHCCTTCCHHHHH
T ss_pred             HHHHHHHHHHhccc--CCCceEEEEEEEEeCCCCCcEEEEECCCCCEEECCEEEEcccHHHHHHHHHhhcCCCCCHHHHH
Confidence            99999999888742  25999999999999423789999999999999999999999999999999999999999 9999


Q ss_pred             HHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCH
Q 025716          188 KLAIRALLEVVES---GGKNIEVAVMTREKGLKQLDE  221 (249)
Q Consensus       188 ~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~  221 (249)
                      +++++||..+.++   ++++++|++|+++| ++++++
T Consensus       159 ~l~~~al~~~~~~d~~s~~~i~v~vi~~~g-~~~~~~  194 (198)
T 1ryp_K          159 DLLKLCVQELEKRMPMDFKGVIVKIVDKDG-IRQVDD  194 (198)
T ss_dssp             HHHHHHHHHHHHHCSBCCCCEEEEEEETTE-EEEECC
T ss_pred             HHHHHHHHHHHHhCccCCCceEEEEEcCCC-EEEecc
Confidence            9999999999875   57899999999998 888765

>1ryp_H 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 3nzj_N* 3nzw_N* 3nzx_N* 1vsy_H 3l5q_B 1g65_N* 1fnt_H 1g0u_N* 1jd2_N* 1z7q_H 2f16_N* 2fak_N* 2fny_N* 2gpl_N* 2zcy_N* 3bdm_N* 3d29_N* 3dy3_N* 3dy4_N* 3e47_N* ...

Probab=100.00  E-value=2.7e-43  Score=294.59  Aligned_cols=184  Identities=17%  Similarity=0.269  Sum_probs=174.7

Q ss_pred             HHHHccCCcEEEEEeCCEEEEEEeccCCcc-cccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCC
Q 025716           24 LEAVRKGNAAVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDP  102 (249)
Q Consensus        24 ~kav~~G~t~igi~~~dgVvla~d~~~~~~-l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~  102 (249)
                      ++|+++|+|+|||+++||||||+|+|.+++ ++.+++.+||++|++|++++++|..+|++.|.++++.+++.|++++++ 
T Consensus         3 ~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~-   81 (205)
T 1ryp_H            3 KGEVSLGASIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKIWCCRSGSAADTQAIADIVQYHLELYTSQYGT-   81 (205)
T ss_dssp             TTCCBCCCCEEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEEBHHHHHHHHHHHHHHHHHHHHHHSS-
T ss_pred             CCCCcCCceEEEEEeCCEEEEEEcCCcccCcEEEcCCcCceEEcCCCEEEEccCCHHHHHHHHHHHHHHHHHHHHHhCC-
Confidence            578999999999999999999999999886 777788999999999999999999999999999999999999999999 


Q ss_pred             CCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCC
Q 025716          103 VTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETS  182 (249)
Q Consensus       103 i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~  182 (249)
                      ++++.+++++++.+|.|++.     |++++||+|||+ ++||+||.+||+|++.+++++++|+|+..++++||+.|+++|
T Consensus        82 ~~v~~la~~l~~~~~~~~~~-----~~~~~lvaG~D~-~~gp~Ly~id~~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~  155 (205)
T 1ryp_H           82 PSTETAASVFKELCYENKDN-----LTAGIIVAGYDD-KNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENM  155 (205)
T ss_dssp             CCHHHHHHHHHHHHHHTTTT-----CCEEEEEEEEET-TTEEEEEEECTTSCCEEESEEEESGGGGGGHHHHHHHCCTTC
T ss_pred             CCHHHHHHHHHHHHHhhhcC-----ceEEEEEEEEec-CCCcEEEEECCCccEEecCEEEEEecHHHHHHHHHhccCCCC
Confidence            99999999999999988652     999999999996 578999999999999999999999999999999999999999


Q ss_pred             c-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCC
Q 025716          183 G-QETIKLAIRALLEVVES---GGKNIEVAVMTREK  214 (249)
Q Consensus       183 s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g  214 (249)
                      + +||++++++||..+.++   ++++++|++|+++|
T Consensus       156 s~eea~~l~~~al~~a~~~d~~sg~~i~v~vi~~~g  191 (205)
T 1ryp_H          156 SKEETVDFIKHSLSQAIKWDGSSGGVIRMVVLTAAG  191 (205)
T ss_dssp             CHHHHHHHHHHHHHHHHHHBTTCCSCEEEEEEETTE
T ss_pred             CHHHHHHHHHHHHHHHHHhCCccCCeEEEEEEcCCC
Confidence            9 99999999999999875   47899999999998

>1iru_M 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_L* 3une_L 3unf_L* 3unh_L

Probab=100.00  E-value=1.5e-42  Score=291.58  Aligned_cols=186  Identities=17%  Similarity=0.368  Sum_probs=172.9

Q ss_pred             HccCCcEEEEEeCCEEEEEEeccCCccc-ccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCH
Q 025716           27 VRKGNAAVGVRGTDTIVLGVEKKSTVKL-QDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTV  105 (249)
Q Consensus        27 v~~G~t~igi~~~dgVvla~d~~~~~~l-~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~  105 (249)
                      +++|+|+|||+++||||||+|+|.++++ +.+++.+||++|++|++++++|+.+|++.|+++++.+++.|++++++++++
T Consensus         6 v~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v   85 (213)
T 1iru_M            6 VFNGGTILAIAGEDFAIVASDTRLSEGFSIHTRDSPKCYKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMTT   85 (213)
T ss_dssp             CCCCCEEEEEEETTEEEEEEECCEEETTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCH
T ss_pred             cCCCCcEEEEEeCCEEEEEECCCcccCCEEecCCCCcEEEcCCCEEEEccccHHHHHHHHHHHHHHHHHHHHhcCCCCCH
Confidence            4689999999999999999999998865 445789999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhh--------
Q 025716          106 EYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKN--------  177 (249)
Q Consensus       106 ~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~--------  177 (249)
                      +.+++++++++  |+++  .|||+|++||||||+ +++|+||.+||+|++.+++++|+|+|+..++++||+.        
T Consensus        86 ~~la~~l~~~~--y~~r--~~P~~v~~lvaG~D~-~g~p~Ly~id~~G~~~~~~~~aiGsg~~~a~~~Le~~~~~~~~~~  160 (213)
T 1iru_M           86 GAIAAMLSTIL--YSRR--FFPYYVYNIIGGLDE-EGKGAVYSFDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQN  160 (213)
T ss_dssp             HHHHHHHHHHH--HHTT--TSCCCEEEEEEEECT-TSCEEEEEECTTSCEEEESEEEEETTHHHHHHHHHHHTTCCSCSS
T ss_pred             HHHHHHHHHHH--HhhC--CCCceEEEEEEEEcC-CCCEEEEEECCCCCEEECCEEEEeeCHHHHHHHHhhccccccccc
Confidence            99999999998  5654  699999999999996 5679999999999999999999999999999999999        


Q ss_pred             -hccCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEE
Q 025716          178 -YKETSG-QETIKLAIRALLEVVES---GGKNIEVAVMTREKGLKQ  218 (249)
Q Consensus       178 -~~~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~  218 (249)
                       |+++|+ +||++++++||..+.++   ++.+++|++|+++| ++.
T Consensus       161 ~~~~~~s~eea~~l~~~al~~~~~~d~~s~~~i~v~vi~~~g-~~~  205 (213)
T 1iru_M          161 VEHVPLSLDRAMRLVKDVFISAAERDVYTGDALRICIVTKEG-IRE  205 (213)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHHHBTTSCSEEEEEEEETTE-EEE
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHHhCCccCCcEEEEEEcCCC-eEE
Confidence             888999 99999999999999875   47899999999998 543

>3nzj_H Proteasome component PUP1; ubiquitin, protein degradation, N-terminal nucleophilic HYDR 19S regulatory particle; HET: TY5 TRO MES; 2.40A {Saccharomyces cerevisiae} PDB: 3nzw_H* 3nzx_H* 4b4t_2

Probab=100.00  E-value=1.8e-42  Score=299.32  Aligned_cols=190  Identities=23%  Similarity=0.287  Sum_probs=171.1

Q ss_pred             HHHHccCCcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCC
Q 025716           24 LEAVRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDP  102 (249)
Q Consensus        24 ~kav~~G~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~  102 (249)
                      .||+++|+|+|||+++||||||+|+|.++ .++.+++.+||++|++|++|+++|+.+|++.|.++++.+++.|+++++++
T Consensus        23 ~kav~~GtTivgi~~kdGVVlAaD~r~t~g~li~~~~~~KI~~I~d~i~~~~aG~~aD~~~l~~~lr~~~~~~~~~~~~~  102 (261)
T 3nzj_H           23 PKATSTGTTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSRE  102 (261)
T ss_dssp             -------CCEEEEEETTEEEEEEECCEEETTEEEETTCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHTSC
T ss_pred             CcccccCceEEEEEECCEEEEEEcCCcccCCeeccCCcceEEEEcCCEEEEeccCHHHHHHHHHHHHHHHHHhHHhhCCC
Confidence            68899999999999999999999999988 56777889999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCC
Q 025716          103 VTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETS  182 (249)
Q Consensus       103 i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~  182 (249)
                      ++++.+++++++.++.|     .|||++++||||||+  +||+||.+||+|++.+++++|+|+|+..++++||+.|+++|
T Consensus       103 ~~v~~~a~~l~~~l~~~-----~~~~gv~llvaG~D~--~Gp~Ly~iDp~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~m  175 (261)
T 3nzj_H          103 PRVVSALQMLKQHLFKY-----QGHIGAYLIVAGVDP--TGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDL  175 (261)
T ss_dssp             CCHHHHHHHHHHHHHHT-----TTCSCEEEEEEEEET--TEEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHHCCSSC
T ss_pred             CCHHHHHHHHHHHHHHh-----cCcccEEEEEEEEeC--CCCEEEEECCCccEEecCeEEeccchHHHHHHHHHHhccCC
Confidence            99999999999988654     369999999999995  68999999999999999999999999999999999999999


Q ss_pred             c-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcC
Q 025716          183 G-QETIKLAIRALLEVVES---GGKNIEVAVMTREKGLKQLD  220 (249)
Q Consensus       183 s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~  220 (249)
                      + +||++++++||..+..+   ++++++|++|+++|.++++.
T Consensus       176 s~eEA~~la~~al~~a~~rD~~sg~~iev~vI~kdg~~~~~~  217 (261)
T 3nzj_H          176 TKEEAIKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLR  217 (261)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCTTCCSCEEEEEEETTSCEEEEE
T ss_pred             CHHHHHHHHHHHHHHHHhhCCCCCCcEEEEEEECCCcEEEec
Confidence            9 99999999999999865   47899999999998666543

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

Probab=100.00  E-value=5e-44  Score=310.30  Aligned_cols=205  Identities=13%  Similarity=0.240  Sum_probs=187.6

Q ss_pred             hhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhh
Q 025716           19 QVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRL   97 (249)
Q Consensus        19 Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~   97 (249)
                      ..+.+++++.+|+|+|||+++||||||+|+|.+. .++.+++.+||++|++|++|+++|+.+|++.|++++|.+++.|++
T Consensus        30 ~~~~~~~av~~GtT~vgi~~~dgVVlAaD~r~t~g~~i~~~~~~KI~~i~d~i~~~~aG~~aD~~~l~~~lr~~~~~~~~  109 (266)
T 1g0u_M           30 PMVNTQQPIVTGTSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAY  109 (266)
T ss_dssp             ----CCCCCEEECCEEEEEETTEEEEEEECCEEETTEEEECCCCCEEECTTSEEEEEEEEHHHHHHHHHHHHHHHHHHHT
T ss_pred             chhhhccCcccCceEEEEEECCEEEEEEcCCcccCceeecCCcCcEEEcCCCEEEEeccCHHHHHHHHHHHHHHHHHhhh
Confidence            3566788899999999999999999999999987 577778899999999999999999999999999999999999998


Q ss_pred             -----hcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHH
Q 025716           98 -----TVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMRE  172 (249)
Q Consensus        98 -----~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~  172 (249)
                           +++++++++.+++++++++  |+++++.|||+|++||||||+ +++|+||.+||+|++.+++++++|+|+..+++
T Consensus       110 ~~~~~~~~~~~~v~~la~~l~~~l--y~~r~~~~P~~v~~lvaG~D~-~~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~  186 (266)
T 1g0u_M          110 DNPLADAEEALEPSYIFEYLATVM--YQRRSKMNPLWNAIIVAGVQS-NGDQFLRYVNLLGVTYSSPTLATGFGAHMANP  186 (266)
T ss_dssp             TCTTTTTTTSCCHHHHHHHHHHHH--HHHHHTTCCCCEEEEEEEECT-TSCEEEEEEETTCCEECCSEEECTHHHHTHHH
T ss_pred             ccchhhcCCCCCHHHHHHHHHHHH--HHhccCCCCceEEEEEEEEcC-CCCEEEEEECCCCCEEeCCEEEEccCHHHHHH
Confidence                 8999999999999999998  455567899999999999996 56999999999999999999999999999999


Q ss_pred             HHHhhhcc-----CCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcC-CCEEEcCHHHHHHH
Q 025716          173 FLEKNYKE-----TSG-QETIKLAIRALLEVVES---GGKNIEVAVMTRE-KGLKQLDEAEIDAM  227 (249)
Q Consensus       173 ~Le~~~~~-----~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~-g~~~~~~~~ei~~~  227 (249)
                      +||+.|++     +|+ +||++++++||..+.++   ++.+++|++|+++ | ++.++++||+++
T Consensus       187 ~Le~~~~~~~~~~~ms~eeA~~la~~al~~a~~rd~~sg~~i~v~vI~k~~g-~~~~~~~ei~~~  250 (266)
T 1g0u_M          187 LLRKVVDRESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKNTG-LTFKKNLQVENM  250 (266)
T ss_dssp             HHTTTCSSGGGGGGCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTTE-EEEEEEEECCCC
T ss_pred             HHHHhhcccccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCcEEEEEEECCCC-eEEcCHHHhhhh
Confidence            99999999     999 99999999999999875   4789999999999 7 999988877655

>3unf_H Proteasome subunit beta type-10; antigen presentation, drug development, protein degradation, hydrolase-hydrolase inhibitor complex; HET: 04C; 2.90A {Mus musculus} PDB: 3unh_H

Probab=100.00  E-value=2.4e-42  Score=294.39  Aligned_cols=187  Identities=22%  Similarity=0.319  Sum_probs=174.5

Q ss_pred             CcEEEEEeCCEEEEEEeccCCccc-ccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTVKL-QDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~~l-~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      ||+|||+++||||||+|+|.++++ +.+++.+||++|++|++|+++|..+|++.+.++++.++++|+++++++++++.++
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            689999999999999999998865 4567899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIK  188 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~  188 (249)
                      +++++.++.|     .+||+|++||||||+  +||+||.+||+|++.+++++|+|+|+..++++||+.|+++|+ +||++
T Consensus        81 ~~l~~~l~~~-----~~p~~v~llvaG~D~--~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~ms~eeA~~  153 (234)
T 3unf_H           81 RILRQTLFRY-----QGHVGASLVVGGVDL--NGPQLYEVHPHGSYSRLPFTALGSGQGAAVALLEDRFQPNMTLEAAQE  153 (234)
T ss_dssp             HHHHHHHHHT-----TTCSCEEEEEEEEET--TEEEEEEECTTSCEEECSEEEEETTHHHHHHHHHHHCCSSCCHHHHHH
T ss_pred             HHHHHHHHhc-----CCCccEEEEEEEEeC--CCCEEEEECCCCCEEeccEEEEcCCchhhHHHHHhccCCCCCHHHHHH
Confidence            9999999765     369999999999994  699999999999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCHHHHH
Q 025716          189 LAIRALLEVVES---GGKNIEVAVMTREKGLKQLDEAEID  225 (249)
Q Consensus       189 la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~~ei~  225 (249)
                      ++++||..+..+   ++++++|++|+++| ++.+++.+++
T Consensus       154 la~~al~~~~~~D~~sg~~iev~vi~~dg-~~~l~~~~i~  192 (234)
T 3unf_H          154 LLVEAITAGILSDLGSGGNVDACVITAGG-AKLQRALSTP  192 (234)
T ss_dssp             HHHHHHHHHHHHBTTCCSCEEEEEEESSC-EEEEEEEECC
T ss_pred             HHHHHHHHHHhhcCCCCCcEEEEEEECCC-EEEeCceecc
Confidence            999999999865   57899999999998 9988876653

>1iru_K 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_J* 3une_J 3unf_J* 3unh_J

Probab=100.00  E-value=8e-42  Score=284.79  Aligned_cols=187  Identities=16%  Similarity=0.276  Sum_probs=172.1

Q ss_pred             CCcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHH
Q 025716           30 GNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYI  108 (249)
Q Consensus        30 G~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l  108 (249)
                      ++|+|||+++||||||+|+|.++ .++.+++.+||++|++|++++++|+.+|++.+.++++.+++.|+++++++++++.+
T Consensus         1 Mtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~   80 (201)
T 1iru_K            1 MEYLIGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYIQKNVQLYKMRNGYELSPTAA   80 (201)
T ss_dssp             CCCEEEEECSSEEEEEEECCEEETTEEEESSCCCEEECSSSEEEEEEESTTHHHHHHHHHHHHHHHHHHHHSSCCCHHHH
T ss_pred             CceEEEEEeCCEEEEEEcCccccCcEEEccCcceEEEecCCEEEEeCcCHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHH
Confidence            68999999999999999999988 57778899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHH
Q 025716          109 TRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETI  187 (249)
Q Consensus       109 a~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai  187 (249)
                      ++++++.+....+  ..|||+|++||+|||+ +++|+||.+||+|++.+++++++|+|++.++++||+.|+++|+ +||+
T Consensus        81 a~~~~~~l~~~~~--~~~p~~~~~lvaG~D~-~~gp~Ly~id~~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~s~eea~  157 (201)
T 1iru_K           81 ANFTRRNLADCLR--SRTPYHVNLLLAGYDE-HEGPALYYMDYLAALAKAPFAAHGYGAFLTLSILDRYYTPTISRERAV  157 (201)
T ss_dssp             HHHHHHHHHHHHT--SSSCCCEEEEEEEEET-TTEEEEEEECTTCCEEECSEEEESHHHHHHHHHHHHHCCTTCCHHHHH
T ss_pred             HHHHHHHHHHHHh--cCCCccEEEEEEEEeC-CCCeEEEEECCCcCeEECCEEEECCcHHHHHHHHHhcccCCCCHHHHH
Confidence            9999876522222  2379999999999996 5799999999999999999999999999999999999999999 9999


Q ss_pred             HHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcC
Q 025716          188 KLAIRALLEVVES---GGKNIEVAVMTREKGLKQLD  220 (249)
Q Consensus       188 ~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~  220 (249)
                      +++++||..+.++   ++.+++|++|+++| +++++
T Consensus       158 ~l~~~al~~a~~rd~~sg~~i~v~vi~~~g-~~~~~  192 (201)
T 1iru_K          158 ELLRKCLEELQKRFILNLPTFSVRIIDKNG-IHDLD  192 (201)
T ss_dssp             HHHHHHHHHHHHTBCBCCCCEEEEEEETTE-EECCC
T ss_pred             HHHHHHHHHHHhhccccCCceEEEEEcCCC-eEEee
Confidence            9999999999875   47799999999998 87765

>1ryp_M 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_M* 1jd2_L* 1g65_L 1vsy_M 1z7q_M 2f16_L* 2fak_L* 2fny_L* 2gpl_L* 3d29_L* 3dy3_L* 3dy4_L* 3e47_L* 3gpj_L* 3gpt_L* 3gpw_L* 3hye_L* 3l5q_Q 3mg0_L* 3mg4_L* ...

Probab=100.00  E-value=1.2e-41  Score=288.05  Aligned_cols=186  Identities=22%  Similarity=0.406  Sum_probs=172.6

Q ss_pred             HccCCcEEEEEeCCEEEEEEeccCCccc-ccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcC-CCCC
Q 025716           27 VRKGNAAVGVRGTDTIVLGVEKKSTVKL-QDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVE-DPVT  104 (249)
Q Consensus        27 v~~G~t~igi~~~dgVvla~d~~~~~~l-~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~-~~i~  104 (249)
                      +++|+|+|||+++||||||+|+|.++++ +.+++.+||++|++|++++++|+.+|++.|.++++.+++.|+++++ ++++
T Consensus         6 v~~Gtt~vgi~~~dgVvlaaD~r~~~g~~i~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~   85 (222)
T 1ryp_M            6 GDNGGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKLS   85 (222)
T ss_dssp             CCCCCEEEEEECSSCEEEEEECCEEETTEEEESCCCCCEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHTTTCCCC
T ss_pred             ccCCccEEEEEeCCEEEEEEecccccCCEecCCCcCcEEEeCCCEEEEccccHHHHHHHHHHHHHHHHHHHHHcCCCCCC
Confidence            5789999999999999999999998865 4677899999999999999999999999999999999999999999 9999


Q ss_pred             HHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhh-------
Q 025716          105 VEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKN-------  177 (249)
Q Consensus       105 ~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~-------  177 (249)
                      ++.+++++++.+  |+++  .|||+|++||||||+ +++|+||.+||+|++.+++++|+|+|+.+++++||+.       
T Consensus        86 v~~la~~l~~~l--y~~r--~~P~~v~~ivaG~D~-~g~p~Ly~~dp~G~~~~~~~~a~Gsg~~~a~~~Le~~~~~~~~~  160 (222)
T 1ryp_M           86 INSAARNIQHLL--YGKR--FFPYYVHTIIAGLDE-DGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQY  160 (222)
T ss_dssp             HHHHHHHHHHHH--HTTT--TSCCCEEEEEEEECT-TSCEEEEEECTTSCEEEESEEEEETTHHHHHHHHHHHTSCTTCB
T ss_pred             HHHHHHHHHHHH--HhcC--CCCceEEEEEEEEcC-CCCeEEEEECCCcCEEecCEEEEcCcHHHHHHHHhccccccccc
Confidence            999999999998  4433  689999999999996 6679999999999999999999999999999999998       


Q ss_pred             ----------hccCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEE
Q 025716          178 ----------YKETSG-QETIKLAIRALLEVVES---GGKNIEVAVMTREKGLKQ  218 (249)
Q Consensus       178 ----------~~~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~  218 (249)
                                |+++|+ +||++++++||..+.++   ++++++|++|+++| ++.
T Consensus       161 ~~~~~~~~~~~~~~~s~eeA~~la~~al~~a~~rd~~sg~~i~v~vi~~~g-~~~  214 (222)
T 1ryp_M          161 EPGTNGKVKKPLKYLSVEEVIKLVRDSFTSATERHIQVGDGLEILIVTKDG-VRK  214 (222)
T ss_dssp             CTTSTTCSBCCCCCCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTE-EEE
T ss_pred             ccccccccccCCCCCCHHHHHHHHHHHHHHHHHhcccCCCcEEEEEEcCCC-eEE
Confidence                      889999 99999999999999875   47899999999998 543

>1iru_J 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_I* 3une_I 3unf_I* 3unh_I

Probab=100.00  E-value=1.2e-41  Score=284.58  Aligned_cols=185  Identities=18%  Similarity=0.317  Sum_probs=170.0

Q ss_pred             ccCCcEEEEEeCCEEEEEEeccCCccccc-CCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHH
Q 025716           28 RKGNAAVGVRGTDTIVLGVEKKSTVKLQD-SRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVE  106 (249)
Q Consensus        28 ~~G~t~igi~~~dgVvla~d~~~~~~l~~-~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~  106 (249)
                      .+|+|+|||+++||||||+|+|.++++.. +++.+||++|++|++++++|+.+|++.|.++++.+++.|+++++++++++
T Consensus         6 ~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~   85 (205)
T 1iru_J            6 YNGGAVMAMKGKNCVAIAADRRFGIQAQLVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFRLNLYELKEGRQIKPY   85 (205)
T ss_dssp             SSCCEEEEEECSSEEEEEEECCEEETTEEEESCCCCEEECSTTEEEECCSCHHHHHHHHHHHHHHHHHHHHHSSSCCCHH
T ss_pred             CCCCeEEEEEeCCEEEEEECCccccCCeEeecCCccEEEeCCCEEEEccccHHHHHHHHHHHHHHHHHHHhhcCCCCCHH
Confidence            68999999999999999999999886544 45899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceecc-ceEeecCCchHHHHHHHhhhccCCc-H
Q 025716          107 YITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAW-KANATGRNSNSMREFLEKNYKETSG-Q  184 (249)
Q Consensus       107 ~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~-~~~aiG~g~~~a~~~Le~~~~~~~s-e  184 (249)
                      .+++++++.+  |+++.  .||+|++||+|||+.+++|+||.+||+|++.++ +++++|+|+..++++||+.|+++|+ +
T Consensus        86 ~la~~l~~~~--y~~r~--~P~~v~~lvaG~D~~~~~p~Ly~idp~G~~~~~~~~~aiG~gs~~a~~~Le~~~~~~~s~e  161 (205)
T 1iru_J           86 TLMSMVANLL--YEKRF--GPYYTEPVIAGLDPKTFKPFICSLDLIGCPMVTDDFVVSGTCAEQMYGMCESLWEPNMDPD  161 (205)
T ss_dssp             HHHHHHHHHH--HTTTT--SCCSCCCEEEEECTTSCCEEEEEECTTCCEEECSSEEEEETTHHHHHHHHHHHCCSSCCHH
T ss_pred             HHHHHHHHHH--HHhcC--CCceEEEEEEEEeCCCCCeEEEEECCCCCccccCCeeEeeeCHHHHHHHHhcccCCCCCHH
Confidence            9999999999  66653  499999999999942478999999999999665 6799999999999999999999999 9


Q ss_pred             HHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCCEE
Q 025716          185 ETIKLAIRALLEVVES---GGKNIEVAVMTREKGLK  217 (249)
Q Consensus       185 eai~la~~~l~~~~~~---~~~~iei~~v~~~g~~~  217 (249)
                      ||++++++||..+.++   ++.+++|++|+++| ++
T Consensus       162 ea~~l~~~al~~~~~~d~~s~~~i~v~vi~~~g-~~  196 (205)
T 1iru_J          162 HLFETISQAMLNAVDRDAVSGMGVIVHIIEKDK-IT  196 (205)
T ss_dssp             HHHHHHHHHHHHHGGGBTTSCSCEEEEEEESSB-EE
T ss_pred             HHHHHHHHHHHHHHHhCcccCCceEEEEEcCCC-EE
Confidence            9999999999999876   47899999999998 43

>1ryp_J 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_I* 1g65_I 1vsy_J 2f16_I* 2fak_I* 2fny_I* 2gpl_I* 3d29_I* 3dy3_I* 3dy4_I* 3e47_I* 3gpj_I* 3gpt_I* 3gpw_I* 3hye_I* 3l5q_N 3mg0_I* 3mg4_I* 3oeu_I* 3oev_I* ...

Probab=100.00  E-value=2.9e-41  Score=282.00  Aligned_cols=185  Identities=18%  Similarity=0.291  Sum_probs=169.9

Q ss_pred             HccCCcEEEEEeCCEEEEEEeccCCccccc-CCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCH
Q 025716           27 VRKGNAAVGVRGTDTIVLGVEKKSTVKLQD-SRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTV  105 (249)
Q Consensus        27 v~~G~t~igi~~~dgVvla~d~~~~~~l~~-~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~  105 (249)
                      +.+|+|+|||+++||||||+|+|.+.++.. +++.+||++|+ |++++++|+.+|++.|.++++.+++.|++++++++++
T Consensus         5 ~~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~-~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v   83 (204)
T 1ryp_J            5 SINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYG-HVFLGITGLATDVTTLNEMFRYKTNLYKLKEERAIEP   83 (204)
T ss_dssp             GSSCCEEEEEECSSEEEEEEECCEEETTEEEESCCCCEEEET-TEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCH
T ss_pred             CCCCCeEEEEEeCCEEEEEEcCCcccCCEEeeCCcceEEEeC-CEEEEeeEcHHHHHHHHHHHHHHHHHHhhccCCCCCH
Confidence            468999999999999999999999886644 45899999999 9999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceecc-ceEeecCCchHHHHHHHhhhccCCc-
Q 025716          106 EYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAW-KANATGRNSNSMREFLEKNYKETSG-  183 (249)
Q Consensus       106 ~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~-~~~aiG~g~~~a~~~Le~~~~~~~s-  183 (249)
                      +.+++++++.+  |+++.  .||+|++||||||+.+++|+||.+||+|++..+ +++++|+|++.++++||+.|+++|+ 
T Consensus        84 ~~la~~l~~~~--y~~~~--~P~~v~~lvaG~D~~~~gp~Ly~idp~G~~~~~~~~~aiG~gs~~a~~~Le~~~~~~~s~  159 (204)
T 1ryp_J           84 ETFTQLVSSSL--YERRF--GPYFVGPVVAGINSKSGKPFIAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEP  159 (204)
T ss_dssp             HHHHHHHHHHH--HTTTT--SCCCEEEEEEEECTTTCCEEEEEECTTCCEECCSSEEEEETTHHHHHHHHHHHCCSSCCH
T ss_pred             HHHHHHHHHHH--HHhcC--CCceEEEEEEEEeCCCCceEEEEECCCCCccccCceeEeccCHHHHHHHHhhhcCCCcCH
Confidence            99999999999  77654  399999999999942478999999999999665 6799999999999999999999999 


Q ss_pred             HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCCEE
Q 025716          184 QETIKLAIRALLEVVES---GGKNIEVAVMTREKGLK  217 (249)
Q Consensus       184 eeai~la~~~l~~~~~~---~~~~iei~~v~~~g~~~  217 (249)
                      +||++++++||..+.++   ++.+++|++|+++| ++
T Consensus       160 eea~~l~~~al~~~~~~d~~s~~~i~v~vi~~~g-~~  195 (204)
T 1ryp_J          160 EDLFETISQALLNAADRDALSGWGAVVYIIKKDE-VV  195 (204)
T ss_dssp             HHHHHHHHHHHHHHHTTBTTSCSCEEEEEEESSC-EE
T ss_pred             HHHHHHHHHHHHHHHHhCcccCCcEEEEEEcCCC-EE
Confidence            99999999999999875   47899999999998 43

>1ryp_I 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1g0u_H* 1jd2_H* 1g65_H 1vsy_I 1z7q_I 2f16_H* 2fak_H* 2fny_H* 2gpl_H* 3d29_H* 3dy3_H* 3dy4_H* 3e47_H* 3gpj_H* 3gpt_H* 3gpw_H* 3hye_H* 3l5q_M 3mg0_H* 3mg4_H* ...

Probab=100.00  E-value=5e-41  Score=284.23  Aligned_cols=183  Identities=23%  Similarity=0.273  Sum_probs=170.4

Q ss_pred             CcEEEEEeCCEEEEEEeccCCccc-ccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTVKL-QDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~~l-~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      +|+|||+++||||||+|+|.++++ +.+++.+||++|++|++++++|..+|++.|.++++.+++.|+++++++++++.++
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            689999999999999999998854 5567899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIK  188 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~  188 (249)
                      +++++.++.|     .|||++++||||||+  +||+||.+||+|++.+++++|+|+|+..++++||+.|+++|+ +||++
T Consensus        81 ~~l~~~l~~~-----~~p~~v~~lvaG~D~--~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~ms~eeA~~  153 (222)
T 1ryp_I           81 QMLKQHLFKY-----QGHIGAYLIVAGVDP--TGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIK  153 (222)
T ss_dssp             HHHHHHHHHT-----TTCSCEEEEEEEEET--TEEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHHCCSSCCHHHHHH
T ss_pred             HHHHHHHhhc-----CCCCCeeEEEEEEeC--CCCEEEEECCCCCEEecCEEEECCCHHHHHHHHHhhCCCCcCHHHHHH
Confidence            9999998765     379999999999994  689999999999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcC
Q 025716          189 LAIRALLEVVES---GGKNIEVAVMTREKGLKQLD  220 (249)
Q Consensus       189 la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~  220 (249)
                      ++++||..++++   ++.+++|++|+++|+++.+.
T Consensus       154 la~~al~~~~~~d~~sg~~i~v~vi~~~g~~~~~~  188 (222)
T 1ryp_I          154 LASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLR  188 (222)
T ss_dssp             HHHHHHHHHHHHCTTCCSCEEEEEEETTSCEEEEE
T ss_pred             HHHHHHHHHHhccccCCCcEEEEEEECCCCEEEEe
Confidence            999999999875   47799999999987577654

>3unf_N Proteasome subunit beta type-9; antigen presentation, drug development, protein degradation, hydrolase-hydrolase inhibitor complex; HET: 04C; 2.90A {Mus musculus} PDB: 3unh_N

Probab=100.00  E-value=4.8e-42  Score=285.62  Aligned_cols=190  Identities=18%  Similarity=0.256  Sum_probs=175.1

Q ss_pred             CcEEEEEeCCEEEEEEeccCCcc-cccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~~-l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      ||+|||+++||||||+|+|.+++ ++.+++.+||++|++|++++++|+.+|++.|.++++.+++.|+++++++++++.++
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            68999999999999999999885 77788999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceecc-ceEeecCCchHHHHHHHhhhccCCc-HHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAW-KANATGRNSNSMREFLEKNYKETSG-QETI  187 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~-~~~aiG~g~~~a~~~Le~~~~~~~s-eeai  187 (249)
                      +++++.++.+     .|||+|++||||||+ +++|+||.  |+|++..+ +++++|+|+..++++||+.|+++|+ +||+
T Consensus        81 ~~l~~~l~~~-----~~p~~v~~lvaG~D~-~~~p~ly~--p~G~~~~~~~~~~~Gsgs~~a~~~Le~~~~~~ms~eea~  152 (199)
T 3unf_N           81 NVVKNISYKY-----REDLLAHLIVAGWDQ-REGGQVYG--TMGGMLIRQPFTIGGSGSSYIYGYVDAAYKPGMTPEECR  152 (199)
T ss_dssp             HHHHHHHHHT-----TTTCCCCEEEEEEET-TTEEEEEE--CGGGCCEECSEEEEEGGGGGGHHHHHHHCCSSCCHHHHH
T ss_pred             HHHHHHHHhc-----CCCceEEEEEEEEeC-CCCcEEEE--ECCCceecCCEEEEccCHHHHHHHHHhhcCCCCCHHHHH
Confidence            9999999764     369999999999996 57899999  99998665 5666799999999999999999999 9999


Q ss_pred             HHHHHHHHHHHhc---CCCcEEEEEEEcCC-CEEEcCHHHHHHHH
Q 025716          188 KLAIRALLEVVES---GGKNIEVAVMTREK-GLKQLDEAEIDAMV  228 (249)
Q Consensus       188 ~la~~~l~~~~~~---~~~~iei~~v~~~g-~~~~~~~~ei~~~l  228 (249)
                      +++++||..+.++   ++++++|++|+++| .++.++++||++++
T Consensus       153 ~la~~al~~~~~~d~~sg~~i~v~vi~~~g~~~~~l~~~ei~~~~  197 (199)
T 3unf_N          153 RFTTNAITLAMNRDGSSGGVIYLVTITAAGVDHRVILGDELPKFY  197 (199)
T ss_dssp             HHHHHHHHHHHHHCTTCCSCEEEEEECSSCEEEEEECGGGSCCCC
T ss_pred             HHHHHHHHHHHHhccccCCCeEEEEEcCCCEEEEEcCcccCcccc
Confidence            9999999999876   46899999999997 57889999987654

>1iru_I 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_H* 3une_H

Probab=100.00  E-value=3.1e-40  Score=281.48  Aligned_cols=183  Identities=22%  Similarity=0.307  Sum_probs=169.9

Q ss_pred             CcEEEEEeCCEEEEEEeccCCccc-ccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTVKL-QDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~~l-~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      +|+|||+++||||||+|+|.++++ +.+++.+||++|++|++++++|+.+|++.|.++++.+++.|+++++++++++.++
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            689999999999999999998865 4456899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIK  188 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~  188 (249)
                      +++++.++.|.     +||++++||||||+  +||+||.+||+|++.+++++++|+|++.++++||+.|+++|+ +||++
T Consensus        81 ~~l~~~l~~~~-----~~~~v~llvaG~D~--~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~ms~eeA~~  153 (234)
T 1iru_I           81 RMLKQMLFRYR-----GYIGAALVLGGVDV--TGPHLYSIYPHGSTDKLPYVTMGSGSLAAMAVFEDKFRPDMEEEEAKN  153 (234)
T ss_dssp             HHHHHHHHHTT-----TCSCEEEEEEEECS--SCEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHSCCTTCCHHHHHT
T ss_pred             HHHHHHHHhcC-----CCCceeEEEEEEcC--CCCEEEEECCCCCEEecCEEEECCchHHHHHHHHHhccCCCCHHHHHH
Confidence            99999987653     59999999999994  789999999999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCH
Q 025716          189 LAIRALLEVVES---GGKNIEVAVMTREKGLKQLDE  221 (249)
Q Consensus       189 la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~  221 (249)
                      ++++||..+..+   ++++++|++|+++| ++.+.+
T Consensus       154 la~~al~~a~~~d~~sg~~i~v~vi~k~g-~~~~~~  188 (234)
T 1iru_I          154 LVSEAIAAGIFNDLGSGSNIDLCVISKNK-LDFLRP  188 (234)
T ss_dssp             HHHHHHHHHHHHCTTCCSCEEEEEEETTE-EECCSE
T ss_pred             HHHHHHHHHHHhcccCCCCEEEEEEECCc-EEEEcc
Confidence            999999998875   37899999999997 776553

>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=100.00  E-value=3.4e-34  Score=234.90  Aligned_cols=165  Identities=16%  Similarity=0.133  Sum_probs=147.0

Q ss_pred             ccCCcEEEEEeCCEEEEEEeccCCc-cc-ccCCcccceEEe-cCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCC
Q 025716           28 RKGNAAVGVRGTDTIVLGVEKKSTV-KL-QDSRSVRKIVSL-DNHIALACAGLKADARVLINRARIECQSHRLTVEDPVT  104 (249)
Q Consensus        28 ~~G~t~igi~~~dgVvla~d~~~~~-~l-~~~~~~~Ki~~I-~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~  104 (249)
                      .+|+|+|||+++||||||+|+|.+. .+ +.+++.+||++| ++|++++++|..+|++.|.++++.+++.|+   +    
T Consensus         3 ~~GtTivgi~~~dgVvlaaD~r~t~g~~~i~~~~~~KI~~i~~~~i~~~~aG~~aD~~~l~~~~~~~~~~y~---g----   75 (180)
T 2z3b_A            3 FHATTIFAVQHKGRSAMSGDGQVTFGQAVVMKHTARKVRKLFNGKVLAGFAGSVADAFTLFEKFEAKLEEYN---G----   75 (180)
T ss_dssp             BCCCCEEEEEETTEEEEEECCCEEETTTEEEESCCCCEEEETTTTEEEEECSCHHHHHHHHHHHHHHHHHTT---T----
T ss_pred             CCCeEEEEEEECCEEEEEECCCccCCCceEecCCCCcEEEECCCCEEEEeCchHHHHHHHHHHHHHHHHHhc---C----
Confidence            5799999999999999999999988 56 888899999999 999999999999999999999999999988   3    


Q ss_pred             HHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceec--cceEeecCCchHHHHHHHhhhcc--
Q 025716          105 VEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSA--WKANATGRNSNSMREFLEKNYKE--  180 (249)
Q Consensus       105 ~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~--~~~~aiG~g~~~a~~~Le~~~~~--  180 (249)
                        .+.+.++++.+.++++...|||++++||+  |    +|+||.+||+|++.+  ++++|+|+|+.+++++||+.|++  
T Consensus        76 --~~~~~~~~l~~~~~~~~~~rp~~~~~lva--d----~p~ly~~d~~G~~~~~~~~~~a~Gsgs~~a~~~le~~~~~~~  147 (180)
T 2z3b_A           76 --NLKRAAVELAKEWRSDKVLRKLEAMLIVM--N----QDTLLLVSGTGEVIEPDDGILAIGSGGNYALAAGRALKKHAG  147 (180)
T ss_dssp             --CHHHHHHHHHHHHHHCTTGGGCCCCEEEE--C----SSCEEEECTTCCEECCSSSEEEESTTHHHHHHHHHHHHHHHG
T ss_pred             --ChHHHHHHHHHHHHhhhCcCcceEEEEEE--c----CCeEEEECCCCcEEEeCCCEEEECCCHHHHHHHHHHhhhccC
Confidence              34445556667777778889999999999  5    699999999999998  59999999999999999999998  


Q ss_pred             -CCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEE
Q 025716          181 -TSG-QETIKLAIRALLEVVES---GGKNIEVAVM  210 (249)
Q Consensus       181 -~~s-eeai~la~~~l~~~~~~---~~~~iei~~v  210 (249)
                       +|+ +|+   +++||..+.++   ++++++|.+|
T Consensus       148 ~~mt~eel---~~~al~~a~~rd~~sg~~i~v~~i  179 (180)
T 2z3b_A          148 ESMSASEI---ARAALETAGEICVYTNDQIILEEL  179 (180)
T ss_dssp             GGCCHHHH---HHHHHHHHHHHCTTCCSCCEEEEE
T ss_pred             CCCCHHHH---HHHHHHHHHHhcCccCCeEEEEEE
Confidence             999 884   66888888775   5788999887

>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=100.00  E-value=4.7e-33  Score=226.84  Aligned_cols=163  Identities=15%  Similarity=0.158  Sum_probs=143.3

Q ss_pred             CcEEEEEeCCEEEEEEeccCCcc-cccCCcccceEEe-cCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSL-DNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYI  108 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~~-l~~~~~~~Ki~~I-~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l  108 (249)
                      +|+|||+++||||||+|+|.+.+ ++.+++.+||++| ++|++++++|..+|++.|.++++.+++.|+.      +   +
T Consensus         1 tT~vgi~~~dgVvlaaD~r~t~g~~i~~~~~~Ki~~i~~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~------~---~   71 (174)
T 1g3k_A            1 TTIVSVRRNGQVVVGGDGQVSLGNTVMKGNARKVRRLYNGKVLAGFAGGTADAFTLFELFERKLEMHQG------H---L   71 (174)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHHHHHHHHHHTTT------C---H
T ss_pred             CeEEEEEECCEEEEEECCCCccCCeeEeCCCCcEEEECCCCEEEEeCccHHHHHHHHHHHHHHHHHhcC------c---H
Confidence            68999999999999999999874 7778899999999 9999999999999999999999999999985      2   3


Q ss_pred             HHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccc---eEeecCCchHHHHHHHhhhc-cCCc-
Q 025716          109 TRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWK---ANATGRNSNSMREFLEKNYK-ETSG-  183 (249)
Q Consensus       109 a~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~---~~aiG~g~~~a~~~Le~~~~-~~~s-  183 (249)
                      .+.++.+.+.++++...||++  ++++|+|    +|+||.+||+|++.+++   ++|+|+|+++++++||+.|+ ++|+ 
T Consensus        72 ~~~~~~l~~~~~~~~~~r~~~--~~l~g~d----~p~Ly~~d~~G~~~~~~~~~~~a~Gsgs~~a~~~le~~~~~~~mt~  145 (174)
T 1g3k_A           72 LKSAVELAKDWRTDRALRKLE--AMLIVAD----EKESLIITGIGDVVQPEEDQILAIGSGGNYALSAARALVENTELSA  145 (174)
T ss_dssp             HHHHHHHHHHHHHSTTGGGCC--CEEEEEC----SSCEEEEETTTEEECCCTTCEEEESTTHHHHHHHHHHHHHHCCCCH
T ss_pred             HHHHHHHHHHHHhccCcCcce--EEEEEEC----CCEEEEEcCCCcEEecCCCcEEEEcccHHHHHHHHHHhcccCCCCH
Confidence            555566666677777778865  5788886    69999999999999988   99999999999999999999 9999 


Q ss_pred             HHHHHHHHHHHHHHHhc---CCCcEEEEEEE
Q 025716          184 QETIKLAIRALLEVVES---GGKNIEVAVMT  211 (249)
Q Consensus       184 eeai~la~~~l~~~~~~---~~~~iei~~v~  211 (249)
                      +   +++++||..+.++   ++++++|.+|+
T Consensus       146 ~---~l~~~al~~a~~rd~~sg~~i~v~~i~  173 (174)
T 1g3k_A          146 H---EIVEKSLRIAGDICVFTNTNFTIEELP  173 (174)
T ss_dssp             H---HHHHHHHHHHHHHCTTCCSCCEEEEEC
T ss_pred             H---HHHHHHHHHHHHhccccCCceEEEEec
Confidence            6   5788888888765   57899999985

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

Probab=100.00  E-value=1.3e-32  Score=223.69  Aligned_cols=163  Identities=17%  Similarity=0.183  Sum_probs=140.5

Q ss_pred             CcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEe-cCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSL-DNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYI  108 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I-~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l  108 (249)
                      +|+|||+++||||||+|+|.+. .++.+++.+||++| ++|++++++|..+|++.|.++++.+++.|+.+         +
T Consensus         1 tt~vgi~~~dgVvlaaD~r~~~g~~i~~~~~~Ki~~i~~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~---------~   71 (171)
T 1m4y_A            1 TTILVVRRNGQTVMGGDGQVTFGSTVLKGNARKVRKLGEGKVLAGFAGSVADAMTLFDRFEAKLREWGGN---------L   71 (171)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHHHHHHHHHHTTTC---------H
T ss_pred             CeEEEEEECCEEEEEECCCcccCCEEEeCCcceEEEeCCCCEEEEeCccHHHHHHHHHHHHHHHHHhccc---------H
Confidence            6899999999999999999987 67788899999999 99999999999999999999999999998854         2


Q ss_pred             HHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccc--eEeecCCchHHHHHHHhhhc-cCCcHH
Q 025716          109 TRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWK--ANATGRNSNSMREFLEKNYK-ETSGQE  185 (249)
Q Consensus       109 a~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~--~~aiG~g~~~a~~~Le~~~~-~~~see  185 (249)
                      .+.++++.+.++++...|||++++|++  |    +|+||.+||+|++.+++  ++++|+|+++++++||+.|+ ++|+. 
T Consensus        72 ~~~~~~l~~~~~~~~~~~~~~~~~lv~--D----~p~Ly~~d~~G~~~~~~~~~~a~Gsgs~~a~~~le~~~~~~~ms~-  144 (171)
T 1m4y_A           72 TKAAVELAKDWRTDRVLRRLEALLLVA--D----KENIFIISGNGEVIQPDDDAAAIGSGGPYALAAAKALLRNTDLSA-  144 (171)
T ss_dssp             HHHHHHHHHHHHHCTTGGGCCCEEEEE--C----SSCEEEECTTSCEECCSSSEEEESTTHHHHHHHHHHHHHHCCCCH-
T ss_pred             HHHHHHHHHHHHHhCCCCceEEEEEEE--c----CCEEEEECCCCCEEecCCCEEEECCcHHHHHHHHHHhcccCCCCH-
Confidence            334444444556666678999998888  5    79999999999999988  99999999999999999999 99982 


Q ss_pred             HHHHHHHHHHHHHhc---CCCcEEEEEE
Q 025716          186 TIKLAIRALLEVVES---GGKNIEVAVM  210 (249)
Q Consensus       186 ai~la~~~l~~~~~~---~~~~iei~~v  210 (249)
                       ++++++||..+.++   ++++++|.++
T Consensus       145 -~~l~~~al~~a~~rd~~sg~~i~v~~~  171 (171)
T 1m4y_A          145 -REIVEKAMTIAGEICIYTNQNIVIEEV  171 (171)
T ss_dssp             -HHHHHHHHHHHHHHCTTCCSCCEEEEC
T ss_pred             -HHHHHHHHHHHHHhCcccCCeEEEEEC
Confidence             44688888888765   4778888753

---

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	249
d1irud_	243	d.153.1.4 (D:) Proteasome alpha subunit (non-catal	2e-84
d1rypd_	241	d.153.1.4 (D:) Proteasome alpha subunit (non-catal	8e-80
d1irua_	244	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	2e-79
d1iruf_	238	d.153.1.4 (F:) Proteasome alpha subunit (non-catal	9e-77
d1irue_	234	d.153.1.4 (E:) Proteasome alpha subunit (non-catal	4e-76
d1irug_	245	d.153.1.4 (G:) Proteasome alpha subunit (non-catal	2e-75
d1iruc_	250	d.153.1.4 (C:) Proteasome alpha subunit (non-catal	5e-75
d1rypf_	233	d.153.1.4 (F:) Proteasome alpha subunit (non-catal	4e-74
d1rypa_	243	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	4e-73
d1rype_	242	d.153.1.4 (E:) Proteasome alpha subunit (non-catal	7e-72
d1j2pa_	243	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	2e-71
d1rypb_	250	d.153.1.4 (B:) Proteasome alpha subunit (non-catal	5e-71
d1rypg_	244	d.153.1.4 (G:) Proteasome alpha subunit (non-catal	9e-71
d1rypc_	244	d.153.1.4 (C:) Proteasome alpha subunit (non-catal	4e-69
d1yara1	221	d.153.1.4 (A:13-233) Proteasome alpha subunit (non	1e-68
d1irub_	233	d.153.1.4 (B:) Proteasome alpha subunit (non-catal	1e-66
d1q5qa_	227	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	7e-46
d1ryp2_	233	d.153.1.4 (2:) Proteasome beta subunit (catalytic)	5e-39
d1rypk_	198	d.153.1.4 (K:) Proteasome beta subunit (catalytic)	1e-38
d1ryp1_	222	d.153.1.4 (1:) Proteasome beta subunit (catalytic)	3e-36
d1rypl_	212	d.153.1.4 (L:) Proteasome beta subunit (catalytic)	8e-36
d1yarh1	203	d.153.1.4 (H:1-203) Proteasome beta subunit (catal	2e-35
d1j2qh_	202	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	4e-32
d1irul_	201	d.153.1.4 (L:) Proteasome beta subunit (catalytic)	1e-31
d1rypj_	204	d.153.1.4 (J:) Proteasome beta subunit (catalytic)	2e-31
d1rypi_	222	d.153.1.4 (I:) Proteasome beta subunit (catalytic)	7e-31
d1q5qh_	224	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	7e-31
d1iru2_	217	d.153.1.4 (2:) Proteasome beta subunit (catalytic)	1e-29
d1iruh_	202	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	2e-29
d1irui_	220	d.153.1.4 (I:) Proteasome beta subunit (catalytic)	8e-29
d1iruj_	204	d.153.1.4 (J:) Proteasome beta subunit (catalytic)	1e-28
d1iruk_	199	d.153.1.4 (K:) Proteasome beta subunit (catalytic)	1e-26
d1ryph_	205	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	7e-25
d1iru1_	213	d.153.1.4 (1:) Proteasome beta subunit (catalytic)	9e-22
d2z3ba1	180	d.153.1.4 (A:1-180) HslV (ClpQ) protease {Bacillus	6e-04

>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 =  249 bits (638), Expect = 2e-84
 Identities = 167/243 (68%), Positives = 196/243 (80%), Gaps = 4/243 (1%)

Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YDRAITVFSPDGHLFQVEYA EAV+KG+ AVGVRG D +VLGVEKKS  KLQD R+VRKI
Sbjct: 2   YDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVRKI 61

Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
            +LD+++ +A AGL ADAR++INRAR+ECQSHRLTVEDPVTVEYITRYIA L+Q+YTQS 
Sbjct: 62  CALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSN 121

Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE--- 180
           G RPFG+S LIVGFD     P LYQTDPSGT+ AWKANA GR + S+REFLEKNY +   
Sbjct: 122 GRRPFGISALIVGFDFDGT-PRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEAI 180

Query: 181 TSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKKAAAEA 240
            +   TIKL I+ALLEVV+SGGKNIE+AVM R++ LK L+  EI+  VAEIE +K   E 
Sbjct: 181 ETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVAEIEKEKEENEK 240

Query: 241 AKK 243
            K+
Sbjct: 241 KKQ 243

>d1rypd_ d.153.1.4 (D:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 241

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  238 bits (607), Expect = 8e-80
 Identities = 135/237 (56%), Positives = 184/237 (77%), Gaps = 5/237 (2%)

Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDS-RSVRK 62
           YDRA+++FSPDGH+FQVEYALEAV++G  AVGV+G + +VLG E++ST+KLQD+  +  K
Sbjct: 2   YDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSK 61

Query: 63  IVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQS 122
           +  +D+H+ L+ +GL AD+R+LI +AR+E QSHRLT+EDPVTVEY+TRY+AG+QQ+YTQS
Sbjct: 62  VSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQS 121

Query: 123 GGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK--- 179
           GGVRPFG+STLI GFDP    P LYQT+PSG +S+W A   GRNS ++REFLEKNY    
Sbjct: 122 GGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKE 181

Query: 180 -ETSGQETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKK 235
              + +E +KL +R+LLEVV++G KNIE+ V+  +  +  L   EI+  V +IE +K
Sbjct: 182 PPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK 238

>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 =  237 bits (605), Expect = 2e-79
 Identities = 85/240 (35%), Positives = 131/240 (54%), Gaps = 8/240 (3%)

Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNA-AVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           A +DR IT+FSP+G L+QVEYA +A+ +G   +V VRG D  V+  +KK   KL DS +V
Sbjct: 6   AGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTV 65

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
             +  +  +I     G+ AD+R  + RAR E  + +      + V+ + + IA + Q YT
Sbjct: 66  THLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYT 125

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           Q+  +RP G   +++G D   G P +Y+ DP+G +  +KA A G        FLEK  K+
Sbjct: 126 QNAEMRPLGCCMILIGIDEEQG-PQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKK 184

Query: 181 ---TSGQETIKLAIRALLEVVESGGK--NIEVAVMTREK-GLKQLDEAEIDAMVAEIEAK 234
               + ++T++ AI  L  V+    K   IEV V+T E    + L EAEIDA +  +  +
Sbjct: 185 KFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVALAER 244

>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 =  230 bits (587), Expect = 9e-77
 Identities = 78/240 (32%), Positives = 129/240 (53%), Gaps = 11/240 (4%)

Query: 3   RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRK 62
           +YD  +TV+SP G + Q+EYA+EAV++G+A VG++     VL   K++  +L      +K
Sbjct: 2   QYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAA--HQKK 59

Query: 63  IVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQS 122
           I+ +DNHI ++ AGL ADAR+L N  R EC   R   + P+ V  +   I    Q  TQ 
Sbjct: 60  ILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQR 119

Query: 123 GGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK--- 179
            G RP+G+  LI G+D     P ++QT PS  +   +A + G  S S R +LE++     
Sbjct: 120 YGRRPYGVGLLIAGYDDMG--PHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM 177

Query: 180 ETSGQETIKLAIRALLEVVES----GGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKK 235
           E +  E +K  +RAL E + +      KN+ + ++ ++      D+ ++   +  +E + 
Sbjct: 178 ECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEGLEERP 237

>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 =  228 bits (582), Expect = 4e-76
 Identities = 83/236 (35%), Positives = 137/236 (58%), Gaps = 10/236 (4%)

Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YDR +  FSP+G LFQVEY +EA++ G+ A+G++ ++ + L VEK+ T  L +  S+ KI
Sbjct: 1   YDRGVNTFSPEGRLFQVEYDIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEPSSIEKI 60

Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
           V +D HI  A +GL ADA+ LI++AR+E Q+H  T  + +TVE +T+ ++ L  ++ +  
Sbjct: 61  VEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEED 120

Query: 124 G-----VRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNY 178
                  RPFG++ L  G D     P L+  DPSGTF    A A G  S   +  L++ Y
Sbjct: 121 ADPGAMSRPFGVALLFGGVDEKG--PQLFHMDPSGTFVQCDARAIGSASEGAQSSLQELY 178

Query: 179 KET-SGQETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEIDAMVAEI 231
            ++ + +E IK ++  L +V+E      NIE+A +   +      + E++ ++ +I
Sbjct: 179 HKSMTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVIKDI 234

>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 =  227 bits (579), Expect = 2e-75
 Identities = 72/247 (29%), Positives = 123/247 (49%), Gaps = 11/247 (4%)

Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
             YD + + FSPDG +FQVEYA++AV   + A+G+R  D +V GVEK    KL +  S +
Sbjct: 5   TGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEGSNK 64

Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           ++ ++D H+ +A AGL ADAR L + AR E  + R      + ++++   +A     YT 
Sbjct: 65  RLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTL 124

Query: 122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET 181
              VRPFG S ++  +        LY  DPSG    +   A G+   + +  +EK   + 
Sbjct: 125 YSAVRPFGCSFMLGSYS-VNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQMKE 183

Query: 182 -SGQETIKLAIRALLEVVES---GGKNIEVAVMTRE-KGLKQLDEAEIDAMVAEIEAKKA 236
            + ++ +K   + +  V +        +E++ +     G  ++   +I       EA+K 
Sbjct: 184 MTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIRE-----EAEKY 238

Query: 237 AAEAAKK 243
           A E+ K+
Sbjct: 239 AKESLKE 245

>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 =  226 bits (576), Expect = 5e-75
 Identities = 88/250 (35%), Positives = 145/250 (58%), Gaps = 10/250 (4%)

Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQD-SRSV 60
            RYD   T+FSP+G L+QVEYA+EA+      +G+   D ++L  E+++  KL D     
Sbjct: 2   RRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVFFS 61

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
            KI  L+  +A + AG+ +DA VL N  R+  Q + L  ++P+  E +   +  ++Q YT
Sbjct: 62  EKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYT 121

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNY-- 178
           Q GG RPFG+S L +G+D + G   LYQ+DPSG +  WKA   G NS +    L+++Y  
Sbjct: 122 QFGGKRPFGVSLLYIGWDKHYG-FQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYKE 180

Query: 179 KETSGQETIKLAIRAL---LEVVESGGKNIEVAVMTREKG---LKQLDEAEIDAMVAEIE 232
            E + +  + LAI+ L   ++V +   + +E+A +TRE G   ++ L + E++ ++ + E
Sbjct: 181 GEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKHE 240

Query: 233 AKKAAAEAAK 242
            ++A AE  K
Sbjct: 241 EEEAKAEREK 250

>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 =  223 bits (569), Expect = 4e-74
 Identities = 73/234 (31%), Positives = 110/234 (47%), Gaps = 12/234 (5%)

Query: 3   RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRK 62
            YD     FSP G LFQVEYALEA+++G+  VG+R     VL   K++  +L  S   +K
Sbjct: 4   NYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADEL--SSYQKK 61

Query: 63  IVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQS 122
           I+  D H+ L+ AGL  DARVL N  R +C    L     + VE     +    QK TQS
Sbjct: 62  IIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQS 121

Query: 123 GGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET- 181
            G RP+G+  LI+G+D       L +  PSG  +     A G  S   + +LE+      
Sbjct: 122 YGGRPYGVGLLIIGYDKSG--AHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFI 179

Query: 182 ----SGQETIKLAIRALLEVVESG---GKNIEVAVMTREKGLKQLDEAEIDAMV 228
               +  E IK  + A+ + +        N+ +A++ ++      D   +   +
Sbjct: 180 KIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI 233

>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 =  221 bits (563), Expect = 4e-73
 Identities = 76/244 (31%), Positives = 121/244 (49%), Gaps = 13/244 (5%)

Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGN-AAVGVRGTDTIVLGVEKKSTVKLQDSRSV 60
           A YDR IT+FSP+G L+QVEYA +A  + N  ++ VRG D  V+  +KK   KL D  +V
Sbjct: 1   AGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPTTV 60

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
             I  +   I +   G   DAR    RA+ E    R      +  + + + +A L Q YT
Sbjct: 61  SYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYT 120

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           Q   +RP G+    V  D   G PS+Y+TDP+G +  +KA ATG     +   LE ++K+
Sbjct: 121 QRAYMRPLGVILTFVSVDEELG-PSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKK 179

Query: 181 T--------SGQETIKLAIRALLEVVE--SGGKNIEVAVMTREKGLKQLDEAEIDAMVAE 230
           +        S ++ ++ AI  +++ +       ++EV V T++     L    I+  +  
Sbjct: 180 SKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKD-KFFTLSAENIEERLVA 238

Query: 231 IEAK 234
           I  +
Sbjct: 239 IAEQ 242

>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 =  218 bits (555), Expect = 7e-72
 Identities = 83/242 (34%), Positives = 137/242 (56%), Gaps = 10/242 (4%)

Query: 5   DRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIV 64
           DR ++ FSP+G LFQVEY+LEA++ G+ A+G+   + +VLGVEK++T  L +S S+ KIV
Sbjct: 1   DRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESDSIEKIV 60

Query: 65  SLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGG 124
            +D HI  A +GL ADAR +I  AR    +H L  ++ + VE +T+ +  L  ++ +   
Sbjct: 61  EIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGAS 120

Query: 125 ------VRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNY 178
                  RPFG++ LI G D       L+  +PSGTF  + A A G  S   +  L   +
Sbjct: 121 GEERLMSRPFGVALLIAGHDADD-GYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNEW 179

Query: 179 KET-SGQETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKK 235
             + + +E   L ++ L +V+E      N +++ +T++ G K  D  +   ++ E++ K+
Sbjct: 180 HSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELIKELKEKE 239

Query: 236 AA 237
           AA
Sbjct: 240 AA 241

>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 =  217 bits (553), Expect = 2e-71
 Identities = 103/244 (42%), Positives = 147/244 (60%), Gaps = 9/244 (3%)

Query: 4   YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKI 63
           YDRAITVFSPDG LFQVEYA EAV++G  A+G++  + ++L  +K+   KL +  ++ KI
Sbjct: 5   YDRAITVFSPDGRLFQVEYAREAVKRGATAIGIKCKEGVILIADKRVGSKLLEKDTIEKI 64

Query: 64  VSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSG 123
             +D HI  A +GL ADARVLI+RARIE Q +RLT + P+TV+ + + I   +Q+YTQ G
Sbjct: 65  YKIDEHICAATSGLVADARVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQYG 124

Query: 124 GVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNY-KETS 182
           GVRPFG+S LI G +     P LY+TDPSG    +KA A G    ++ EF EK Y  + S
Sbjct: 125 GVRPFGVSLLIAGVNEV---PKLYETDPSGALLEYKATAIGMGRMAVTEFFEKEYRDDLS 181

Query: 183 GQETIKLAIRALLEVVE--SGGKNIEVAVMTRE-KGLKQLDEAEIDAMVAEIEAKKAAAE 239
             + + L + A+   +E     +NIEV  +  + +  K++   E+   V     +    E
Sbjct: 182 FDDAMVLGLVAMGLSIESELVPENIEVGYVKVDDRTFKEVSPEELKPYVERANERI--RE 239

Query: 240 AAKK 243
             KK
Sbjct: 240 LLKK 243

>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 =  216 bits (550), Expect = 5e-71
 Identities = 86/251 (34%), Positives = 137/251 (54%), Gaps = 21/251 (8%)

Query: 1   MA-RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRS 59
           M  RY  ++T FSP G L Q++YAL AV++G  ++G++ T+ +V+  EKKS+  L  S +
Sbjct: 1   MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET 60

Query: 60  VRKIVSLDNHIALACAGLKADARVLINRARIECQ-SHRLTVEDPVTVEYITRYIAGLQQK 118
           + K+  L   I    +G+  D RVL++++R     S++    +    + +   +A + Q+
Sbjct: 61  LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE 120

Query: 119 YTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNY 178
            TQSGGVRPFG+S LI G D + G  SLYQ DPSG++  WKA A G+ S + + FLEK +
Sbjct: 121 ATQSGGVRPFGVSLLIAGHDEFNG-FSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRW 179

Query: 179 K-ETSGQETIKLAIRALLEVVES--GGKNIEVAVMTREKGL---------------KQLD 220
             E   ++ I +A+  L E VE    G  IE+A++  E                  ++L 
Sbjct: 180 NDELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLT 239

Query: 221 EAEIDAMVAEI 231
             EI+  +  +
Sbjct: 240 SQEINDRLEAL 250

>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 =  215 bits (548), Expect = 9e-71
 Identities = 78/248 (31%), Positives = 120/248 (48%), Gaps = 16/248 (6%)

Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVR 61
             YD + +VFSPDG  FQVEYA++AV  G  ++G++  D +V  VEK  T KL   +   
Sbjct: 2   TGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNV 61

Query: 62  KIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQ 121
           KI  +D HI    +GL  D R L+NR R E  S +   + P+ +      +    Q +T 
Sbjct: 62  KIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTL 121

Query: 122 SGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEK---NY 178
              VRPFG+ST+  G D       LY  +PSG++  +K  ATG+   S +  LEK   ++
Sbjct: 122 YNSVRPFGVSTIFGGVDK--NGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHH 179

Query: 179 KET-SGQETIKLAIRALLEVVESG---GKNIEVAVMTRE--KGLKQLDEAEIDAMVAEIE 232
            E  S +E +K A + +    E        +E++  +     GL +  + ++       E
Sbjct: 180 PEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQ-----E 234

Query: 233 AKKAAAEA 240
           A   A + 
Sbjct: 235 AIDFAQKE 242

>d1rypc_ d.153.1.4 (C:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 244

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  211 bits (537), Expect = 4e-69
 Identities = 86/239 (35%), Positives = 138/239 (57%), Gaps = 11/239 (4%)

Query: 2   ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQD-SRSV 60
            RYD   T+FSP+G L+QVEYALE++     A+G+  +D IVL  E+K T  L +   S 
Sbjct: 3   RRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTST 62

Query: 61  RKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYT 120
            K+  L++ IA+A AGL ADA +LIN ARI  Q++  T  + + VE + R ++ ++Q YT
Sbjct: 63  EKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYT 122

Query: 121 QSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE 180
           Q GG+RPFG+S +  G+D       LY ++PSG ++ WKA + G N+++ +  L+ +YK+
Sbjct: 123 QHGGLRPFGVSFIYAGYD-DRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKD 181

Query: 181 T-SGQETIKLAIRALLEVVESG---GKNIEVAVMTR-----EKGLKQLDEAEIDAMVAE 230
                + I+LA++ L +  +S       +E A + +     E   K     EI  ++ +
Sbjct: 182 DMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVK 240

>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 =  209 bits (532), Expect = 1e-68
 Identities = 88/223 (39%), Positives = 135/223 (60%), Gaps = 5/223 (2%)

Query: 9   TVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDN 68
           TVFSPDG LFQVEYA EAV+KG+ A+G++  + ++L  +KK   +L +  S+ KI  +D+
Sbjct: 1   TVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQNSIEKIQLIDD 60

Query: 69  HIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPF 128
           ++A   +GL ADARVL++ ARI  Q  ++T    V +E + + +A   Q+YTQ GGVRP+
Sbjct: 61  YVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPY 120

Query: 129 GLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETI 187
           G+S +  G D     P L+  DP+GT + +KA A G   +++  FLE+ YKE    +E +
Sbjct: 121 GVSLIFAGIDQIG--PRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKENLPEKEAV 178

Query: 188 KLAIRALLEVVESG--GKNIEVAVMTREKGLKQLDEAEIDAMV 228
            L I+AL   +E G   K  E+A +T     +  D+ E+   +
Sbjct: 179 TLGIKALKSSLEEGEELKAPEIASITVGNKYRIYDQEEVKKFL 221

>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 =  204 bits (519), Expect = 1e-66
 Identities = 96/232 (41%), Positives = 134/232 (57%), Gaps = 6/232 (2%)

Query: 3   RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRK 62
            Y  ++T FSP G L Q+EYAL AV  G  +VG++  + +VL  EKK    L D RSV K
Sbjct: 4   GYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDERSVHK 63

Query: 63  IVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQS 122
           +  +  HI L  +G+  D RVL++RAR   Q + L  ++P+    + + +A + Q+YTQS
Sbjct: 64  VEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQS 123

Query: 123 GGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETS 182
           GGVRPFG+S LI G+    G P L+Q+DPSG + AWKA A G+N  + + FLEK Y E  
Sbjct: 124 GGVRPFGVSLLICGW--NEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNEDL 181

Query: 183 G-QETIKLAIRALLEVVE--SGGKNIEVAVMTREKGLKQLDEAEIDAMVAEI 231
             ++ I  AI  L E  E      NIEV +   E G ++L   E+   +A I
Sbjct: 182 ELEDAIHTAILTLKESFEGQMTEDNIEVGICN-EAGFRRLTPTEVKDYLAAI 232

>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 =  150 bits (381), Expect = 7e-46
 Identities = 30/225 (13%), Positives = 78/225 (34%), Gaps = 23/225 (10%)

Query: 19  QVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLK 78
           + E A + + +G + V +   D ++   E  ST       ++ K+  L + +  A  G  
Sbjct: 8   RSELARKGIARGRSVVVLTFRDGVLFVAENPST-------ALHKVSELYDRLGFAAVGKY 60

Query: 79  ADARVLINRARIECQSHRLTVED-PVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGF 137
            +   L     +       + +   VT   +    A        +   +P+ +   +   
Sbjct: 61  NEFENLRRAGIVHADMRGYSYDRRDVTGRSLANAYAQTLG-TIFTEQPKPYEVEICVAEV 119

Query: 138 DP--YTGVPSLYQTDPSGTFSAWKANATGR-NSNSMREFLEKNYKE-TSGQETIKLAIRA 193
                   P LY+    G+    +        +  +   + ++Y+     +  + +A+ A
Sbjct: 120 GRVGSPKAPQLYRITYDGSIVDEQHFVVMGGTTEPIATAMRESYRADLDLEAAVGIAVNA 179

Query: 194 LLEVVES-------GGKNIEVAVMTRE---KGLKQLDEAEIDAMV 228
           L +              ++EVAV+ +    +  +++    ++ +V
Sbjct: 180 LRQGGAGEGEKRNVDVASLEVAVLDQSRPRRAFRRIAGTALEQLV 224

>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 =  133 bits (335), Expect = 5e-39
 Identities = 29/218 (13%), Positives = 79/218 (36%), Gaps = 18/218 (8%)

Query: 25  EAVRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARV 83
           + +  G + + ++  + +++  +   +   L     V +++ + ++  +  +G  +D + 
Sbjct: 3   QPIVTGTSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQH 62

Query: 84  LINRARIECQSHRL-----TVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFD 138
           +    +     +         E+ +   YI  Y+A     Y +   + P   + ++ G  
Sbjct: 63  IERLLKDLVTENAYDNPLADAEEALEPSYIFEYLA--TVMYQRRSKMNPLWNAIIVAGVQ 120

Query: 139 PYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKE------TSGQETIKLAIR 192
              G   L   +  G   +    ATG  ++     L K          T+ Q   +  + 
Sbjct: 121 SN-GDQFLRYVNLLGVTYSSPTLATGFGAHMANPLLRKVVDRESDIPKTTVQVAEEAIVN 179

Query: 193 ALLEVVE---SGGKNIEVAVMTREKGLKQLDEAEIDAM 227
           A+  +        +N  +A++ +  GL      +++ M
Sbjct: 180 AMRVLYYRDARSSRNFSLAIIDKNTGLTFKKNLQVENM 217

>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 =  131 bits (330), Expect = 1e-38
 Identities = 42/197 (21%), Positives = 86/197 (43%), Gaps = 8/197 (4%)

Query: 33  AVGVRGTDTIVLGVEKKSTVKLQD-SRSVRKIVSLDNHIALACAGLKADARVLINRARIE 91
            +G+R  D+++L   K  T  +     S  K   L  H  ++ AG   D        +  
Sbjct: 4   ILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYIQAN 63

Query: 92  CQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDP 151
            Q + +  +  ++ + ++ ++     K  +S   RP+ ++ LI G+D     P LYQ D 
Sbjct: 64  IQLYSIREDYELSPQAVSSFVRQELAKSIRSR--RPYQVNVLIGGYDKKKNKPELYQIDY 121

Query: 152 SGTFSAWKANATGRNSNSMREFLEKNYKET----SGQETIKLAIRALLEVVESGGKNIEV 207
            GT       A G +       L+ +Y+       G + +KL ++ L + +    K + V
Sbjct: 122 LGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVIV 181

Query: 208 AVMTREKGLKQLDEAEI 224
            ++ ++ G++Q+D+ + 
Sbjct: 182 KIVDKD-GIRQVDDFQA 197

>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 =  126 bits (316), Expect = 3e-36
 Identities = 42/219 (19%), Positives = 84/219 (38%), Gaps = 28/219 (12%)

Query: 30  GNAAVGVRGTDTIVLGVEKKSTVKLQ-DSRSVRKIVSLDNHIALACAGLKADARVLINRA 88
           G   +G+ G D  VL  + ++      +SR   K+    ++I ++  G  AD   L+ R 
Sbjct: 9   GGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNIVMSANGFAADGDALVKRF 68

Query: 89  RIECQSHRLT-VEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLY 147
           +   + +     +  +++    R      Q         P+ + T+I G D   G  ++Y
Sbjct: 69  KNSVKWYHFDHNDKKLSINSAARN----IQHLLYGKRFFPYYVHTIIAGLDE-DGKGAVY 123

Query: 148 QTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG------------------QETIKL 189
             DP G++   +  A G  ++ +  FL+      +                   +E IKL
Sbjct: 124 SFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYEPGTNGKVKKPLKYLSVEEVIKL 183

Query: 190 AIRALLEVVE---SGGKNIEVAVMTREKGLKQLDEAEID 225
              +     E     G  +E+ ++T++   K+  E + D
Sbjct: 184 VRDSFTSATERHIQVGDGLEILIVTKDGVRKEFYELKRD 222

>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 =  124 bits (312), Expect = 8e-36
 Identities = 38/212 (17%), Positives = 89/212 (41%), Gaps = 11/212 (5%)

Query: 33  AVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIE 91
            +  R    I++ V+ ++T      S++V++++ ++  +    AG  AD +        +
Sbjct: 3   TLAFRFQGGIIVAVDSRATAGNWVASQTVKRVIEINPFLLGTMAGGAADCQFWETWLGSQ 62

Query: 92  CQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDP 151
           C+ H L  ++ ++V   ++ ++ L  +Y          + T+I G+    G P++Y  D 
Sbjct: 63  CRLHELREKERISVAAASKILSNLVYQYKG----AGLSMGTMICGYTRKEG-PTIYYVDS 117

Query: 152 SGTFSAWKANATGRNSNSMREFLEKNYKE-TSGQETIKLAIRALLEVVE---SGGKNIEV 207
            GT         G         L+ NYK   S ++ + L  R++L         G ++ +
Sbjct: 118 DGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAAHRDAYSGGSVNL 177

Query: 208 AVMTREKGLKQLDEAEIDAMVAEIEAKKAAAE 239
             +T E G       ++  +  +++ ++ +  
Sbjct: 178 YHVT-EDGWIYHGNHDVGELFWKVKEEEGSFN 208

>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 =  122 bits (308), Expect = 2e-35
 Identities = 48/205 (23%), Positives = 93/205 (45%), Gaps = 12/205 (5%)

Query: 33  AVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIE 91
            VG+   D +++  E++ T++     ++ +K+  +D +  +  AGL  DA+VL+   + E
Sbjct: 3   TVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKAE 62

Query: 92  CQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDP 151
            + +RL     + +E +   +              P+ +  L+ G D    V   +  D 
Sbjct: 63  LELYRLQRRVNMPIEAVATLL----SNMLNQVKYMPYMVQLLVGGIDTAPHV---FSIDA 115

Query: 152 SGTFSAWKANATGRNSNSMREFLEKNYKE-TSGQETIKLAIRALLEVVE---SGGKNIEV 207
           +G        +TG  S  +   LE  Y E  +  E + L IRA+    +   + G  I+V
Sbjct: 116 AGGSVEDIYASTGSGSPFVYGVLESQYSEKMTVDEGVDLVIRAISAAKQRDSASGGMIDV 175

Query: 208 AVMTREKGLKQLDEAEIDAMVAEIE 232
           AV+TR+ G  QL   +I++ + ++ 
Sbjct: 176 AVITRKDGYVQLPTDQIESRIRKLG 200

>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 =  114 bits (286), Expect = 4e-32
 Identities = 51/206 (24%), Positives = 88/206 (42%), Gaps = 13/206 (6%)

Query: 33  AVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIE 91
            VG+   D +V+  EK++T+     S++ +KI  + + +A+  AG   DA+ L    +IE
Sbjct: 3   TVGLVCKDGVVMATEKRATMGNFIASKAAKKIYQIADRMAMTTAGSVGDAQFLARIIKIE 62

Query: 92  CQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDP 151
              + +  E   TV  I             S    P+ +  LI G D      S+Y  DP
Sbjct: 63  ANLYEIRRERKPTVRAIATLT----SNLLNSYRYFPYLVQLLIGGIDSEG--KSIYSIDP 116

Query: 152 SG-TFSAWKANATGRNSNSMREFLEKNYKET-SGQETIKLAIRALLEVVE---SGGKNIE 206
            G         ATG  S +    LE  +       E ++LA+RA+   ++   + G  I+
Sbjct: 117 IGGAIEEKDIVATGSGSLTAYGVLEDRFTPEIGVDEAVELAVRAIYSAMKRDSASGDGID 176

Query: 207 VAVMTREKGLKQLDEAEIDAMVAEIE 232
           V  +T +    Q    E++ ++A+  
Sbjct: 177 VVKITED-EFYQYSPEEVEQILAKFR 201

>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 =  113 bits (283), Expect = 1e-31
 Identities = 31/205 (15%), Positives = 81/205 (39%), Gaps = 12/205 (5%)

Query: 33  AVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIE 91
            +  +    +++  + ++T      S++V+K++ ++ ++    AG  AD          +
Sbjct: 3   TLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQ 62

Query: 92  CQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDP 151
           C+ + L  ++ ++V   ++ +A +  +Y          + T+I G+D     P LY  D 
Sbjct: 63  CRIYELRNKERISVAAASKLLANMVYQYKG----MGLSMGTMICGWDK--RGPGLYYVDS 116

Query: 152 SGTFSAWKANATGRNSNSMREFLEKNYKET-SGQETIKLAIRALLEVVE---SGGKNIEV 207
            G   +    + G  S      +++ Y      ++   LA RA+ +        G  + +
Sbjct: 117 EGNRISGATFSVGSGSVYAYGVMDRGYSYDLEVEQAYDLARRAIYQATYRDAYSGGAVNL 176

Query: 208 AVMTREKGLKQLDEAEIDAMVAEIE 232
             +  + G  ++    +  +  +  
Sbjct: 177 YHVRED-GWIRVSSDNVADLHEKYS 200

>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 =  112 bits (281), Expect = 2e-31
 Identities = 33/201 (16%), Positives = 75/201 (37%), Gaps = 9/201 (4%)

Query: 30  GNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARVLINRAR 89
           G   V + G D + +  + +   +     +  + +    H+ L   GL  D   L    R
Sbjct: 8   GGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDVTTLNEMFR 67

Query: 90  IECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQT 149
            +   ++L  E  +  E  T+ ++    +        P+ +  ++ G +  +G P +   
Sbjct: 68  YKTNLYKLKEERAIEPETFTQLVSSSLYERRF----GPYFVGPVVAGINSKSGKPFIAGF 123

Query: 150 DPSGTFSAWKAN-ATGRNSNSMREFLEKNYKET-SGQETIKLAIRALLEVVE---SGGKN 204
           D  G     K    +G  S+ +    E  Y+     ++  +   +ALL   +     G  
Sbjct: 124 DLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDALSGWG 183

Query: 205 IEVAVMTREKGLKQLDEAEID 225
             V ++ +++ +K+  +   D
Sbjct: 184 AVVYIIKKDEVVKRYLKMRQD 204

>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 =  111 bits (279), Expect = 7e-31
 Identities = 43/208 (20%), Positives = 76/208 (36%), Gaps = 12/208 (5%)

Query: 33  AVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIE 91
            VGV+  + +V+  + +ST   +   ++  K+  +   I  A AG  AD   +       
Sbjct: 3   IVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSN 62

Query: 92  CQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDP 151
            + H L       V    + +     KY         G   ++ G DP      L+    
Sbjct: 63  IELHSLYTSREPRVVSALQMLKQHLFKYQG-----HIGAYLIVAGVDP--TGSHLFSIHA 115

Query: 152 SGTFSAWKANATGRNSNSMREFLEKNYKE-TSGQETIKLAIRALLEVVE---SGGKNIEV 207
            G+       + G  S +    LE ++K+  + +E IKLA  A+   +      G N++V
Sbjct: 116 HGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKLASDAIQAGIWNDLGSGSNVDV 175

Query: 208 AVMTREKGLKQLDEAEIDAMVAEIEAKK 235
            VM   K  + L       +  E +   
Sbjct: 176 CVMEIGKDAEYLRNYLTPNVREEKQKSY 203

>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 =  111 bits (279), Expect = 7e-31
 Identities = 41/223 (18%), Positives = 82/223 (36%), Gaps = 20/223 (8%)

Query: 33  AVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIE 91
            V +     ++L  ++++T   L  SR V K+   D + A   AG    A  L+    +E
Sbjct: 3   IVALTYKGGVLLAGDRRATQGNLIASRDVEKVYVTDEYSAAGIAGTAGIAIELVRLFAVE 62

Query: 92  CQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYT----GVPSLY 147
            + +      P+T +     +A + +    +  ++   +  L+VG+D           + 
Sbjct: 63  LEHYEKIEGVPLTFDGKANRLASMVRGNLGA-AMQGLAVVPLLVGYDLDADDESRAGRIV 121

Query: 148 QTDPSGTFSAWKAN--ATGRNSNSMREFLEKNYKET-SGQETIKLAIRALLEVVE----S 200
             D  G     +A   A G  S   +  L+K Y      +  ++ AI +L +  +    +
Sbjct: 122 SYDVVGGRYEERAGYHAVGSGSLFAKSALKKIYSPDSDEETALRAAIESLYDAADDDSAT 181

Query: 201 GGK------NIEVAVMTREKGLKQLDEAEIDAMVAEIEAKKAA 237
           GG             +T + G   + E     +   I A++  
Sbjct: 182 GGPDLTRGIYPTAVTIT-QAGAVHVSEETTSELARRIVAERTE 223

>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 =  108 bits (270), Expect = 1e-29
 Identities = 34/209 (16%), Positives = 74/209 (35%), Gaps = 13/209 (6%)

Query: 25  EAVRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARV 83
             +  G + +GV+    +V+  +   +   L   R++ +I+ ++N   L  +G  AD + 
Sbjct: 3   NPMVTGTSVLGVKFEGGVVIAADMLGSYGSLARFRNISRIMRVNNSTMLGASGDYADFQY 62

Query: 84  LINRARIECQSH-RLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTG 142
           L             L      +   I  ++   +  Y++   + P   + +I G+    G
Sbjct: 63  LKQVLGQMVIDEELLGDGHSYSPRAIHSWLT--RAMYSRRSKMNPLWNTMVIGGYAD--G 118

Query: 143 VPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET---SGQETIKLAIRALLEVVE 199
              L   D  G      + ATG  +   +  L +  ++    S  E   L  R +  +  
Sbjct: 119 ESFLGYVDMLGVAYEAPSLATGYGAYLAQPLLREVLEKQPVLSQTEARDLVERCMRVLYY 178

Query: 200 ---SGGKNIEVAVMTREKGLKQLDEAEID 225
                    + A +T + G++       +
Sbjct: 179 RDARSYNRFQTATVTEK-GVEIEGPLSTE 206

>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 =  107 bits (269), Expect = 2e-29
 Identities = 35/192 (18%), Positives = 74/192 (38%), Gaps = 11/192 (5%)

Query: 33  AVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIE 91
            + V+    +VLG + ++T      +R   K+  + + I    +G  AD + + +    +
Sbjct: 3   IMAVQFDGGVVLGADSRTTTGSYIANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTYQ 62

Query: 92  CQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDP 151
              H + + +P  V         +  +Y +           +I G+DP  G   +Y    
Sbjct: 63  LGFHSIELNEPPLVHTAASLFKEMCYRYRE-----DLMAGIIIAGWDPQEG-GQVYSVPM 116

Query: 152 SGTFSAWKANATGRNSNSMREFLEKNYKE-TSGQETIKLAIRALLEVVE---SGGKNIEV 207
            G          G  S+ +  +++  Y+E  + +E ++    AL   +E   S G  I +
Sbjct: 117 GGMMVRQSFAIGGSGSSYIYGYVDATYREGMTKEECLQFTANALALAMERDGSSGGVIRL 176

Query: 208 AVMTREKGLKQL 219
           A +      +Q+
Sbjct: 177 AAIAESGVERQV 188

>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 =  106 bits (265), Expect = 8e-29
 Identities = 43/218 (19%), Positives = 76/218 (34%), Gaps = 17/218 (7%)

Query: 33  AVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIE 91
             GV   D IVLG + ++T   +   ++  KI  +  +I    AG  AD  +        
Sbjct: 3   IAGVVYKDGIVLGADTRATEGMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISSN 62

Query: 92  CQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDP 151
            + H L+      V    R +  +  +Y         G + ++ G D     P LY   P
Sbjct: 63  LELHSLSTGRLPRVVTANRMLKQMLFRYR-----GYIGAALVLGGVD--VTGPHLYSIYP 115

Query: 152 SGTFSAWKANATGRNSNSMREFLEKNYK-ETSGQETIKLAIRALLEVVE---SGGKNIEV 207
            G+         G  S +     E  ++ +   +E   L   A+   +      G NI++
Sbjct: 116 HGSTDKLPYVTMGSGSLAAMAVFEDKFRPDMEEEEAKNLVSEAIAAGIFNDLGSGSNIDL 175

Query: 208 AVMTREKGLKQLDEAEIDAMVAEIEAKKAAAEAAKKGP 245
            V+++   L  L        V   +  +      +KG 
Sbjct: 176 CVISKN-KLDFLRPYT----VPNKKGTRLGRYRCEKGT 208

>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 =  105 bits (262), Expect = 1e-28
 Identities = 31/191 (16%), Positives = 71/191 (37%), Gaps = 10/191 (5%)

Query: 30  GNAAVGVRGTDTIVLGVEKKSTVKLQ-DSRSVRKIVSLDNHIALACAGLKADARVLINRA 88
           G A + ++G + + +  +++  ++ Q  +   +KI  + + + +  AGL  D + +  R 
Sbjct: 7   GGAVMAMKGKNCVAIAADRRFGIQAQLVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRL 66

Query: 89  RIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQ 148
           +     + L     +    +   +A L  +        P+    +I G DP T  P +  
Sbjct: 67  KFRLNLYELKEGRQIKPYTLMSMVANLLYEKRF----GPYYTEPVIAGLDPKTFKPFICS 122

Query: 149 TDPSGTFSAWKANATGRN-SNSMREFLEKNYKET-SGQETIKLAIRALLEVVE---SGGK 203
            D  G              +  M    E  ++         +   +A+L  V+     G 
Sbjct: 123 LDLIGCPMVTDDFVVSGTCAEQMYGMCESLWEPNMDPDHLFETISQAMLNAVDRDAVSGM 182

Query: 204 NIEVAVMTREK 214
            + V ++ ++K
Sbjct: 183 GVIVHIIEKDK 193

>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 =  100 bits (249), Expect = 1e-26
 Identities = 32/193 (16%), Positives = 72/193 (37%), Gaps = 9/193 (4%)

Query: 34  VGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIEC 92
           +G++G D +++  ++ +    +Q      K+  +   I L C G   D        +   
Sbjct: 5   IGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYIQKNV 64

Query: 93  QSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPS 152
           Q +++     ++      +         +S    P+ ++ L+ G+D + G   LY  D  
Sbjct: 65  QLYKMRNGYELSPTAAANFTRRNLADCLRSRT--PYHVNLLLAGYDEHEGPA-LYYMDYL 121

Query: 153 GTFSAWKANATGRNSNSMREFLEKNYKE-TSGQETIKLAIRALLEVVE---SGGKNIEVA 208
              +     A G  +      L++ Y    S +  ++L  + L E+ +          V 
Sbjct: 122 AALAKAPFAAHGYGAFLTLSILDRYYTPTISRERAVELLRKCLEELQKRFILNLPTFSVR 181

Query: 209 VMTREKGLKQLDE 221
           ++ +  G+  LD 
Sbjct: 182 IIDKN-GIHDLDN 193

>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 = 96.0 bits (238), Expect = 7e-25
 Identities = 34/193 (17%), Positives = 71/193 (36%), Gaps = 12/193 (6%)

Query: 27  VRKGNAAVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLI 85
           V  G + + V   D ++LG + ++T      +R   K+  + + I    +G  AD + + 
Sbjct: 6   VSLGASIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKIWCCRSGSAADTQAIA 65

Query: 86  NRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPS 145
           +  +   + +      P T    +        K              ++ G+D       
Sbjct: 66  DIVQYHLELYTSQYGTPSTETAAS------VFKELCYENKDNLTAGIIVAGYDDKNK-GE 118

Query: 146 LYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET-SGQETIKLAIRALLEVVE---SG 201
           +Y     G+         G  S  +  + +KN++E  S +ET+     +L + ++   S 
Sbjct: 119 VYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSLSQAIKWDGSS 178

Query: 202 GKNIEVAVMTREK 214
           G  I + V+T   
Sbjct: 179 GGVIRMVVLTAAG 191

>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 = 87.6 bits (216), Expect = 9e-22
 Identities = 30/199 (15%), Positives = 65/199 (32%), Gaps = 19/199 (9%)

Query: 30  GNAAVGVRGTDTIVLGVEKKSTVKLQD-SRSVRKIVSLDNHIALACAGLKADARVLINRA 88
           G   + + G D  ++  + + +      +R   K   L +   + C+G   D   L    
Sbjct: 9   GGTILAIAGEDFAIVASDTRLSEGFSIHTRDSPKCYKLTDKTVIGCSGFHGDCLTLTKII 68

Query: 89  RIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQ 148
               + ++ +    +T   I   ++ +           P+ +  +I G D        Y 
Sbjct: 69  EARLKMYKHSNNKAMTTGAIAAMLSTILYSRRF----FPYYVYNIIGGLDEEGKGAV-YS 123

Query: 149 TDPSGTFSAWKANATGRNSNSMREFLEKNYK----------ETSGQETIKLAIRALLEVV 198
            DP G++      A G  S  ++  L+                S    ++L     +   
Sbjct: 124 FDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVEHVPLSLDRAMRLVKDVFISAA 183

Query: 199 E---SGGKNIEVAVMTREK 214
           E     G  + + ++T+E 
Sbjct: 184 ERDVYTGDALRICIVTKEG 202

>d2z3ba1 d.153.1.4 (A:1-180) HslV (ClpQ) protease {Bacillus subtilis [TaxId: 1423]} Length = 180

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]

 Score = 37.5 bits (86), Expect = 6e-04
 Identities = 25/170 (14%), Positives = 43/170 (25%), Gaps = 17/170 (10%)

Query: 29  KGNAAVGVRGTDTIVLGVEKKSTV--KLQDSRSVRKIVSLDNHIALACA-GLKADARVLI 85
                  V+      +  + + T    +    + RK+  L N   LA   G  ADA  L 
Sbjct: 4   HATTIFAVQHKGRSAMSGDGQVTFGQAVVMKHTARKVRKLFNGKVLAGFAGSVADAFTLF 63

Query: 86  NRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPS 145
            +   + + +   ++              + +K      V       L+ G         
Sbjct: 64  EKFEAKLEEYNGNLKRAAVELAKEWRSDKVLRKLEAMLIVMNQDTLLLVSGTGEVIEPDD 123

Query: 146 LYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKET-SGQETIKLAIRAL 194
                 SG   A  A                  K         ++A  AL
Sbjct: 124 GILAIGSGGNYALAA-------------GRALKKHAGESMSASEIARAAL 160

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	249
d1irud_	243	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rypd_	241	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1iruc_	250	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1j2pa_	243	Proteasome alpha subunit (non-catalytic) {Archaeon	100.0
d1irua_	244	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rypa_	243	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1irug_	245	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1irue_	234	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
d1rypc_	244	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1rypg_	244	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1rype_	242	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1irub_	233	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1yara1	221	Proteasome alpha subunit (non-catalytic) {Archaeon	100.0
d1rypf_	233	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1q5qa_	227	Proteasome alpha subunit (non-catalytic) {Rhodococ	100.0
d1yarh1	203	Proteasome beta subunit (catalytic) {Archaeon Ther	100.0
d1rypk_	198	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1irul_	201	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d1rypl_	212	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1j2qh_	202	Proteasome beta subunit (catalytic) {Archaeon Arch	100.0
d1ryph_	205	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1iruh_	202	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d1ryp2_	233	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1irui_	220	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d1q5qh_	224	Proteasome beta subunit (catalytic) {Rhodococcus e	100.0
d1rypi_	222	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1iru2_	217	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d1iruj_	204	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d1rypj_	204	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1ryp1_	222	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1iruk_	199	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d1iru1_	213	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d2z3ba1	180	HslV (ClpQ) protease {Bacillus subtilis [TaxId: 14	99.89
d1m4ya_	171	HslV (ClpQ) protease {Thermotoga maritima [TaxId:	99.87
d1g3ka_	173	HslV (ClpQ) protease {Haemophilus influenzae [TaxI	99.84

>d1irud_ d.153.1.4 (D:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=1.4e-64  Score=432.30  Aligned_cols=239  Identities=70%  Similarity=1.071  Sum_probs=227.5

Q ss_pred             CCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHH
Q 025716            3 RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADAR   82 (249)
Q Consensus         3 ~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~   82 (249)
                      +||+.+|+|||||||+|||||+||+++|+|+|||+++||||||+|++++.+++.+++.+||++|++|++|++||+.+|++
T Consensus         1 ~yd~~~t~Fsp~Grl~QvEya~kav~~G~Tvvgik~~dgVvla~d~r~~~~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~   80 (243)
T d1irud_           1 SYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVRKICALDDNVCMAFAGLTADAR   80 (243)
T ss_dssp             CCCCCCSCCCTTSCCHHHHHHHHHHHTSCCEEEECCSSEEEEEECCCCCCSSSCGGGGCSEEESSSSCEEEEEECHHHHH
T ss_pred             CCCCCCeeECCCCcchHHHHHHHHHhcCCCEEEEEeCCEEEEEEeccccCcccCCCccccEEECCCCEEEEEEEchhhHH
Confidence            59999999999999999999999999999999999999999999999887888888999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEe
Q 025716           83 VLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANA  162 (249)
Q Consensus        83 ~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~a  162 (249)
                      .++++++.++..|++++|.+++++.+++++++++|.|+++++.|||+|++||+|||+ +++|+||.+||+|++.+++++|
T Consensus        81 ~l~~~~~~~~~~~~~~~~~~i~v~~la~~ls~~~~~~t~~~~~rp~~v~~li~G~D~-~~~p~Ly~idp~G~~~~~~~~a  159 (243)
T d1irud_          81 IVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGISALIVGFDF-DGTPRLYQTDPSGTYHAWKANA  159 (243)
T ss_dssp             HHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCEEEEEEEECS-SSCEEEEEECTTSCEEEBSEEE
T ss_pred             HHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHhcccCCccceEEEEEEEcC-CCCCEEEEecCcEEEEeccEEE
Confidence            999999999999999999999999999999999999999999999999999999997 6799999999999999999999


Q ss_pred             ecCCchHHHHHHHhhhccCC--c-HHHHHHHHHHHHHHHhcCCCcEEEEEEEcCCCEEEcCHHHHHHHHHHHHHHHHHHH
Q 025716          163 TGRNSNSMREFLEKNYKETS--G-QETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKKAAAE  239 (249)
Q Consensus       163 iG~g~~~a~~~Le~~~~~~~--s-eeai~la~~~l~~~~~~~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i~~~~~~~~  239 (249)
                      +|+|+..++++||++|+++|  + ++++++++++|.+....+++++||+++++++.|++++++||++++.+|++++++++
T Consensus       160 ~G~gs~~a~~~Lek~~~~~~~~~~~~~i~~ai~~l~~~~~~~~~~vei~ii~k~~~~~~l~~~eI~~~l~~i~~~~~~~~  239 (243)
T d1irud_         160 IGRGAKSVREFLEKNYTDEAIETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVAEIEKEKEENE  239 (243)
T ss_dssp             ESTTHHHHHHHHTTTCCSSTTCSHHHHHHHHHHHHHTTSCTTSTTCCEEEEESSSCEECCCHHHHHHHTTTTTTTTTTTT
T ss_pred             ECCChHHHHHHHHHhcccCCCccHHHHHHHHHHHHHHHhcCCCCcEEEEEEECCCCEEECCHHHHHHHHHHHHhhhhhhh
Confidence            99999999999999999998  4 78999999999998888888999999999866999999999999999998776665


Q ss_pred             Hhh
Q 025716          240 AAK  242 (249)
Q Consensus       240 ~~~  242 (249)
                      .++
T Consensus       240 ~~~  242 (243)
T d1irud_         240 KKK  242 (243)
T ss_dssp             SSC
T ss_pred             hcc
Confidence            543

>d1rypd_ d.153.1.4 (D:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=3.7e-63  Score=422.92  Aligned_cols=234  Identities=58%  Similarity=1.002  Sum_probs=223.4

Q ss_pred             CCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCccccc-CCcccceEEecCCEEEEEecChhhH
Q 025716            3 RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQD-SRSVRKIVSLDNHIALACAGLKADA   81 (249)
Q Consensus         3 ~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~-~~~~~Ki~~I~~~i~~~~sG~~~D~   81 (249)
                      |||+++|+|||||||+|||||+||+++|+|+|||+++||||||+|++.++++.. ..+.+||++|++|++|++||+.+|+
T Consensus         1 gyd~~~t~fsp~Grl~QvEya~kav~~G~tvIgik~~dgVvlaad~~~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~   80 (241)
T d1rypd_           1 GYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSKVSKIDSHVVLSFSGLNADS   80 (241)
T ss_dssp             CCCCCCSCCBTTTBCHHHHHHHHHHTTSCCEEEEECSSCEEEEEECCCSSCCBCTTTSCCSEEEEETTEEEEEEECHHHH
T ss_pred             CCCCCCceECCCCcEeHHHHHHHHHHcCCCEEEEEeCCEEEEEEEccccccCcccccccccEEEeCCCEEEEeeeccchH
Confidence            799999999999999999999999999999999999999999999999987644 4678999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceE
Q 025716           82 RVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKAN  161 (249)
Q Consensus        82 ~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~  161 (249)
                      +.|+++++.++..|+++++.+++++.++++++.++|.|++++++|||+|++|++|||+.+++|+||.+||+|++.+++++
T Consensus        81 ~~l~~~~~~~~~~~~~~~~~~i~~~~la~~i~~~~~~~t~~~~~rP~~v~~li~G~d~~~~~p~Ly~idp~G~~~~~~~~  160 (241)
T d1rypd_          81 RILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQ  160 (241)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSSTTBCCCSEEEEEEECCTTCCSCEEEEECTTSCEEEBSEE
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHhhccccCcccceEEEEEEccccCcceEEEecCCEEEEeeCeE
Confidence            99999999999999999999999999999999999999999999999999999999974579999999999999999999


Q ss_pred             eecCCchHHHHHHHhhhcc---CCc-HHHHHHHHHHHHHHHhcCCCcEEEEEEEcCCCEEEcCHHHHHHHHHHHHHHHH
Q 025716          162 ATGRNSNSMREFLEKNYKE---TSG-QETIKLAIRALLEVVESGGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKKA  236 (249)
Q Consensus       162 aiG~g~~~a~~~Le~~~~~---~~s-eeai~la~~~l~~~~~~~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i~~~~~  236 (249)
                      |+|+|++.++++|++.|++   +|+ +|++++|++||+++.+.++.++||+++++++.+++++++||++++.+|++++.
T Consensus       161 a~G~gs~~~~~~Le~~~~~~~~~~t~~e~i~lal~al~~~~~~~~~~iei~ii~~d~~~~~l~~~ei~~~l~~i~~~~~  239 (241)
T d1rypd_         161 TIGRNSKTVREFLEKNYDRKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEKQ  239 (241)
T ss_dssp             EESTTHHHHHHHHHTTCCTTSCCCSHHHHHHHHHHHHHHHHCSCSTTEEEEEEETTTEEEECCHHHHHHHHHHHTHHHH
T ss_pred             EECcCHHHHHHHHHHhhhcccCCCCHHHHHHHHHHHHHHHhcCCCCcEEEEEEECCCCEEECCHHHHHHHHHHHHHHHh
Confidence            9999999999999999965   699 99999999999999988889999999999877999999999999999987664

>d1iruc_ d.153.1.4 (C:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=3.8e-63  Score=424.99  Aligned_cols=233  Identities=35%  Similarity=0.648  Sum_probs=220.8

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCccc-ccCCcccceEEecCCEEEEEecChhh
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKL-QDSRSVRKIVSLDNHIALACAGLKAD   80 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l-~~~~~~~Ki~~I~~~i~~~~sG~~~D   80 (249)
                      .+||+++|+|||||||+|||||+||+++|+|+|||+|+||||||+|++.++++ +.+++.+|||+|++|++|+++|+.+|
T Consensus         2 ~~yd~~~t~fsp~Grl~QvEyA~kav~~G~tvvgik~~dgVvlaad~~~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D   81 (250)
T d1iruc_           2 RRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVFFSEKIYKLNEDMACSVAGITSD   81 (250)
T ss_dssp             TTTCCCTTCCCTTSCCHHHHHHHHHHTTSCCEEEEBCSSEEEEEECCCCCCTTBCCCSSCSSEEECSSSEEEEEEECHHH
T ss_pred             CccCCCCeeECCCCcchHHHHHHHHHhcCCcEEEEEeCCEEEEEEeCccccCCcccCcccceEEECCCcEEEEeecccch
Confidence            58999999999999999999999999999999999999999999999998865 45667899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccce
Q 025716           81 ARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKA  160 (249)
Q Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~  160 (249)
                      ++.+++.+|.++..|++++|.+++++.+++.++.++|.+++.++.|||+|++||+|||+ ++||+||.+||+|++.++++
T Consensus        82 ~~~l~~~~r~~~~~~~~~~~~~i~~~~la~~l~~~~~~~~~~~~~rP~~~~~li~G~D~-~~gp~Ly~~Dp~G~~~~~~~  160 (250)
T d1iruc_          82 ANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIGWDK-HYGFQLYQSDPSGNYGGWKA  160 (250)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBSSCCCCCEEEEEEEEET-TTEEEEEEEETTTEEEECSE
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHHHhhhccCCcceEEEEEEEEcC-CCCCEEEEEcccccEeeeeE
Confidence            99999999999999999999999999999999999999999999999999999999997 78999999999999999999


Q ss_pred             EeecCCchHHHHHHHhhhcc-CCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCC---EEEcCHHHHHHHHHHHH
Q 025716          161 NATGRNSNSMREFLEKNYKE-TSG-QETIKLAIRALLEVVES---GGKNIEVAVMTREKG---LKQLDEAEIDAMVAEIE  232 (249)
Q Consensus       161 ~aiG~g~~~a~~~Le~~~~~-~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g~---~~~~~~~ei~~~l~~i~  232 (249)
                      +|+|+|++.++++|+++|++ +|+ +||++++++||+.++++   +++++||++|++++.   ++.++++||++++.+++
T Consensus       161 ~a~G~gs~~a~~~Le~~y~~~~ms~eeai~la~~al~~~~~~d~~~~~~iei~ii~~~~~~~~~~~l~~~Ei~~~l~~~~  240 (250)
T d1iruc_         161 TCIGNNSAAAVSMLKQDYKEGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKHE  240 (250)
T ss_dssp             EEESTTTTHHHHHHHHHCCTTCCCHHHHHHHHHHHHHHSSSCTTCCSTTCEEEEEECCSSSCEEEECCHHHHHHHHHHHH
T ss_pred             EEeCcChHHHHHHHHhhcccCCCCHHHHHHHHHHHHHHHhcccCCCCCeEEEEEEEcCCCceeEEECCHHHHHHHHHHHH
Confidence            99999999999999999985 899 99999999999999864   577999999998753   88999999999999998


Q ss_pred             HHH
Q 025716          233 AKK  235 (249)
Q Consensus       233 ~~~  235 (249)
                      +++
T Consensus       241 e~~  243 (250)
T d1iruc_         241 EEE  243 (250)
T ss_dssp             TTT
T ss_pred             HHh
Confidence            764

>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=6.4e-62  Score=415.71  Aligned_cols=233  Identities=43%  Similarity=0.710  Sum_probs=221.0

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhH
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADA   81 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~   81 (249)
                      ||||+++|+|||||||+|||||+||+++|+|+|||+++||||||+|++.++++....+.+|||+|++|++|++||+.+|+
T Consensus         3 ~gyd~~~t~fsp~Grl~QvEya~kav~~G~t~Igik~~dgVvlaad~r~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~   82 (243)
T d1j2pa_           3 MGYDRAITVFSPDGRLFQVEYAREAVKRGATAIGIKCKEGVILIADKRVGSKLLEKDTIEKIYKIDEHICAATSGLVADA   82 (243)
T ss_dssp             TTSSSCTTCCCTTSCCHHHHHHHHHHHTSCCEEEEEETTEEEEEEECCCSCTTBCGGGCCSEEECSSSEEEEEEECHHHH
T ss_pred             CCcCCCCccCCCCCcchHHHHHHHHHHcCCCEEEEEECCEEEEEEecCccccCccccccccEeecCCcEEEEeeecccHH
Confidence            89999999999999999999999999999999999999999999999998877777788999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceE
Q 025716           82 RVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKAN  161 (249)
Q Consensus        82 ~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~  161 (249)
                      +.++++++.++..|+++++.+++++.++++++..+|.++++++.|||+|++|++|+|+   +|+||.+||+|++.+++++
T Consensus        83 ~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~rP~~~~~il~G~D~---~p~Ly~~Dp~G~~~~~~~~  159 (243)
T d1j2pa_          83 RVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQYGGVRPFGVSLLIAGVNE---VPKLYETDPSGALLEYKAT  159 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCEEEEEEEESS---SEEEEEECTTCCEEEBSEE
T ss_pred             HHHHHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHHHHhhhccCCccceeEEEEEecC---CceEEEEeccCceeeeeEE
Confidence            9999999999999999999999999999999999999999999999999999999983   6999999999999999999


Q ss_pred             eecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEEcC-CCEEEcCHHHHHHHHHHHHHHHHH
Q 025716          162 ATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES--GGKNIEVAVMTRE-KGLKQLDEAEIDAMVAEIEAKKAA  237 (249)
Q Consensus       162 aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~--~~~~iei~~v~~~-g~~~~~~~~ei~~~l~~i~~~~~~  237 (249)
                      |+|+|+..++++|++.|+++|| +||++++++||+.+.++  ..++|||++++++ +.|+.++++||+++++++++.-.+
T Consensus       160 a~G~g~~~a~~~Le~~y~~~ms~eeai~la~~~l~~~~~~d~~~~~iei~iv~~~~~~~~~l~~~ei~~~~~~~~e~~~~  239 (243)
T d1j2pa_         160 AIGMGRMAVTEFFEKEYRDDLSFDDAMVLGLVAMGLSIESELVPENIEVGYVKVDDRTFKEVSPEELKPYVERANERIRE  239 (243)
T ss_dssp             EESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHHTSCCCGGGEEEEEEETTTCCCEECCHHHHHHHHHHHHHHHHH
T ss_pred             EeCCCcHHHHHHHHhhcccCCCHHHHHHHHHHHHHHHHhcccCCCceEEEEEEeCCCcEEECCHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999 99999999999999876  3568999999975 359999999999999998765543

>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=5e-62  Score=416.62  Aligned_cols=231  Identities=36%  Similarity=0.593  Sum_probs=218.9

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccCC-cEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhh
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKGN-AAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKAD   80 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G~-t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D   80 (249)
                      .|||+++|+|||||||+|||||+||+++|+ |+|||+++||||||+|++.++.++.+++.+||++|++|++|+++|+.+|
T Consensus         6 ~gyd~~~t~Fsp~Grl~QvEYA~kav~~gg~t~igIk~~dgVVlaad~r~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D   85 (244)
T d1irua_           6 AGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTVTHLFKITENIGCVMTGMTAD   85 (244)
T ss_dssp             CTTTTTSSCCCTTSCCHHHHHHHHHHHTTCCEEEEEECSSEEEEEEECCCCCSSBCGGGCCSEEESSSSCEEEEEECHHH
T ss_pred             CCcCCCCceECCCCeEhHHHHHHHHHHhCCccEEEEEcCCEEEEEEecccccccccCCccceEEEecCCcEEEEecchHH
Confidence            589999999999999999999999999875 8999999999999999999887777778999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccce
Q 025716           81 ARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKA  160 (249)
Q Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~  160 (249)
                      ++.|++++|.++.+|+++++++++++.++++++.++|.++++++.|||+|++||+|||+ ++||+||.+||+|++.++++
T Consensus        86 ~~~l~~~~r~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rP~~v~~ll~G~D~-~~g~~Ly~~Dp~G~~~~~~~  164 (244)
T d1irua_          86 SRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIGIDE-EQGPQVYKCDPAGYYCGFKA  164 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSBCCCSEEEEEEEEET-TTEEEEEEECTTSCEEEBSE
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCCCchHHHHHHHHHHHHHhcccccCccceeeEEEEEcC-CCCcEEEEEcCCccEEecce
Confidence            99999999999999999999999999999999999999999999999999999999997 67899999999999999999


Q ss_pred             EeecCCchHHHHHHHhhhc--cCCc-HHHHHHHHHHHHHHHhcC--CCcEEEEEEEcCC-CEEEcCHHHHHHHHHHHHH
Q 025716          161 NATGRNSNSMREFLEKNYK--ETSG-QETIKLAIRALLEVVESG--GKNIEVAVMTREK-GLKQLDEAEIDAMVAEIEA  233 (249)
Q Consensus       161 ~aiG~g~~~a~~~Le~~~~--~~~s-eeai~la~~~l~~~~~~~--~~~iei~~v~~~g-~~~~~~~~ei~~~l~~i~~  233 (249)
                      +|+|+++..++++||++|+  ++|+ +||++++++||..+++.+  .+++||+|+++++ .|++++++||+++|..+++
T Consensus       165 ~a~G~gs~~~~~~Le~~~~~~~d~t~eeai~l~~~~l~~~~~~d~~~~~iev~ii~~~~~~~~~l~~~ei~~~l~~~~~  243 (244)
T d1irua_         165 TAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVALAE  243 (244)
T ss_dssp             EEEETTHHHHHHHHHHHTTSCCCCCHHHHHHHHHHHHHHHTTCCCCTTSEEEEEEETTEEEEEECCHHHHHHHHHHHHT
T ss_pred             EeccCchhHHHHHHHhccccccCCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEEEeCCCcEEECCHHHHHHHHHHHhc
Confidence            9999999999999999995  4899 999999999999998763  5689999999875 5899999999999999875

>d1rypa_ d.153.1.4 (A:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=2.6e-62  Score=418.07  Aligned_cols=231  Identities=32%  Similarity=0.531  Sum_probs=220.1

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHcc-CCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhh
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRK-GNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKAD   80 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~-G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D   80 (249)
                      +|||+++|+|||||||+|||||+||+++ |+|+|||+++||||||+|+|.+++++..++.+||++|++|++|++||+.+|
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            5899999999999999999999999987 558999999999999999999888888888999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccce
Q 025716           81 ARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKA  160 (249)
Q Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~  160 (249)
                      ++.+.++++.++.+|+++++.+++++.+++++++++|.|++..+.|||+|++||+|||+ ++||+||.+||+|++.++++
T Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~ls~~~~~~~~~~~~rP~~v~~ll~G~D~-~~g~~Ly~~Dp~G~~~~~~~  159 (243)
T d1rypa_          81 ARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQRAYMRPLGVILTFVSVDE-ELGPSIYKTDPAGYYVGYKA  159 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTSCCCSCEEEEEEEET-TTEEEEEEECTTSCEEEBSE
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcccccCccceEEEEEEcc-CCCCeEEEEcCCEEEEecce
Confidence            99999999999999999999999999999999999999999999999999999999997 78999999999999999999


Q ss_pred             EeecCCchHHHHHHHhhhccC-------Cc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEEcCCCEEEcCHHHHHHHHHH
Q 025716          161 NATGRNSNSMREFLEKNYKET-------SG-QETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEIDAMVAE  230 (249)
Q Consensus       161 ~aiG~g~~~a~~~Le~~~~~~-------~s-eeai~la~~~l~~~~~~--~~~~iei~~v~~~g~~~~~~~~ei~~~l~~  230 (249)
                      +|+|+|+..++++|+++|+++       ++ +|+++++++||+.++.+  +++++||++++++| ++.++++||++++.+
T Consensus       160 ~a~G~gs~~~~~~Le~~~~~~~~~~~~~~s~eeav~la~~~l~~~~~~d~~~~~iei~iitk~g-~~~l~~eeI~~~l~~  238 (243)
T d1rypa_         160 TATGPKQQEITTNLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDK-FFTLSAENIEERLVA  238 (243)
T ss_dssp             EEESTTHHHHHHHHHHHHHHHCSSSCCCSSHHHHHHHHHHHHHHHHTCCCCTTSEEEEEEETTE-EEECCHHHHHHHHHH
T ss_pred             EEeCccHHHHHHHHHHHhhcccccccccccHHHHHHHHHHHHHHHhhccCCCCcEEEEEEeCCc-eEEeCHHHHHHHHHH
Confidence            999999999999999999854       58 99999999999999876  46789999999998 999999999999999


Q ss_pred             HHHH
Q 025716          231 IEAK  234 (249)
Q Consensus       231 i~~~  234 (249)
                      |+++
T Consensus       239 i~e~  242 (243)
T d1rypa_         239 IAEQ  242 (243)
T ss_dssp             HTTT
T ss_pred             Hhcc
Confidence            9875

>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=3e-62  Score=418.09  Aligned_cols=232  Identities=28%  Similarity=0.445  Sum_probs=216.6

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhH
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADA   81 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~   81 (249)
                      ++||+++|+|||||||+|||||+||+++|+|+|||+++||||||+|++.+++++..++.+||++|++|++|++||+.+|+
T Consensus         5 ~~yd~~~t~Fsp~Grl~QvEYa~~av~~G~t~VGik~~dgVvlaad~~~~~~~~~~~~~~Ki~~I~~~i~~~~sG~~~D~   84 (245)
T d1irug_           5 TGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEGSNKRLFNVDRHVGMAVAGLLADA   84 (245)
T ss_dssp             SSTTSCTTCCCTTSCCHHHHHHHHHHHTSCCEEEEECSSBEEEEEEEECSCTTBCTTTTCCEEEEETTEEEEEEECHHHH
T ss_pred             cccCCCCceECCCCeehHHHHHHHHHHcCCcEEEEEeCCEEEEEEeccccccccccCccceEEEcCCCEEEEeccCchhH
Confidence            58999999999999999999999999999999999999999999999988877777889999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceE
Q 025716           82 RVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKAN  161 (249)
Q Consensus        82 ~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~  161 (249)
                      +.++++++.++.+|++++|++++++.+++++++++|.|+++++.|||+|++||+|+|+ ++||+||.+||+|++.+++++
T Consensus        85 ~~l~~~~~~~~~~~~~~~g~~i~~~~la~~la~~~~~~t~~~~~rP~~vs~li~G~D~-~~gp~Ly~iDp~G~~~~~~~~  163 (245)
T d1irug_          85 RSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGCSFMLGSYSV-NDGAQLYMIDPSGVSYGYWGC  163 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSBSSBCCCSEEEEEEEEET-TTEEEEEEECTTCCEEEBSEE
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhccccccccceEEEEEEEcC-CCCceEEEEcCCceEEeeeEE
Confidence            9999999999999999999999999999999999999999999999999999999997 789999999999999999999


Q ss_pred             eecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcC-CCEEEcCHHHHHHHHHHHHHH
Q 025716          162 ATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES---GGKNIEVAVMTRE-KGLKQLDEAEIDAMVAEIEAK  234 (249)
Q Consensus       162 aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~-g~~~~~~~~ei~~~l~~i~~~  234 (249)
                      |+|++++.++++||+.|+++|| +||++++++||+.+++.   +..++||++|+++ +.++.+.+.|+.+...+..++
T Consensus       164 a~G~gs~~a~~~Le~~~~~dmt~eea~~l~~~~l~~~~~~~~~~~~~iei~~v~~~~~~~~~~~~~e~~~~~~~~~~~  241 (245)
T d1irug_         164 AIGKARQAAKTEIEKLQMKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEKYAKE  241 (245)
T ss_dssp             EESTTHHHHHHHHTTSCGGGCCHHHHHHHHHHHHHHHSCSSSSCCEEEEEEECBTTTTTCCEECCHHHHHHHHHHHHH
T ss_pred             EECCccHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEEEEecCCCeEEEChHHHHHHHHHHHHH
Confidence            9999999999999999999999 99999999999998864   3558999999874 346667777777777766654

>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=5.2e-62  Score=414.06  Aligned_cols=226  Identities=37%  Similarity=0.650  Sum_probs=215.6

Q ss_pred             CCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHHH
Q 025716            4 YDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARV   83 (249)
Q Consensus         4 yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~   83 (249)
                      ||+++|+|||||||+|||||+||+++|+|+|||+++||||||+|++.+.+++..++.+||++|++|++++++|+.+|++.
T Consensus         1 yd~~~t~fsp~G~l~QvEYa~kav~~G~t~vgik~~dgVvlaad~~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~   80 (234)
T d1irue_           1 YDRGVNTFSPEGRLFQVEYDIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEPSSIEKIVEIDAHIGCAMSGLIADAKT   80 (234)
T ss_dssp             CCCCTTCBCTTSCBHHHHHHHHHHTTSCCEEEEEETTEEEEEEECCCCCTTBCTTSCCSEEEEETTEEEEEEECHHHHHH
T ss_pred             CCCCCceECCCCcchHHHHHHHHHHcCCCEEEEEeCCEEEEEEecCccCCCcccCcccCEEEccCcEEEEEeeccchHHH
Confidence            89999999999999999999999999999999999999999999999888777788999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCC-----CccceeEEEEEeeeCCCCCceEEEECCCCceecc
Q 025716           84 LINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGG-----VRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAW  158 (249)
Q Consensus        84 l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~-----~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~  158 (249)
                      +++.++.++..|++++|++++++.+++++++++|.|+++.+     .|||+|++|+||||  ++||+||.+||+|++.++
T Consensus        81 l~~~~~~~~~~~~~~~~~~i~~~~la~~i~~~~~~~t~~~~~~~~~~rP~~~~~il~G~D--~~gp~Ly~idp~G~~~~~  158 (234)
T d1irue_          81 LIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMSRPFGVALLFGGVD--EKGPQLFHMDPSGTFVQC  158 (234)
T ss_dssp             HHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCBCSTTCCSSCBSSCCCEEEEEEEEE--TTEEEEEEECTTSCEEEB
T ss_pred             HHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHhhcccccccccccceEEEEEEEEc--CCCCEEEEEecCccccee
Confidence            99999999999999999999999999999999999998866     79999999999999  579999999999999999


Q ss_pred             ceEeecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEEcCCCEEEcCHHHHHHHHHHH
Q 025716          159 KANATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEIDAMVAEI  231 (249)
Q Consensus       159 ~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~--~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i  231 (249)
                      +++|+|+|++.++++||+.|+++|+ +||++++++||+.+.+.  ++.++||++|++++.|++++++||++++.+|
T Consensus       159 ~~~a~G~gs~~~~~~Le~~~~~~~~~eeai~~a~~al~~~~~~~~~~~~iei~ii~~~~~~k~l~~~ei~~~l~~i  234 (234)
T d1irue_         159 DARAIGSASEGAQSSLQELYHKSMTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVIKDI  234 (234)
T ss_dssp             SEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCSSCCCTTSEEEEEECSSSCCEECCHHHHHHHHTTC
T ss_pred             eeEEeCCchHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHhccCCCCCEEEEEEECCCCEEECCHHHHHHHHHhC
Confidence            9999999999999999999999999 99999999999998765  4678999999987669999999999998754

>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=1.2e-61  Score=415.50  Aligned_cols=229  Identities=36%  Similarity=0.603  Sum_probs=216.6

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhH
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADA   81 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~   81 (249)
                      .+||+++|+|||||||+|||||+||+++|+|+|||+++||||||+|++.+++++..++.+||+.|++|++|+++|+.+|+
T Consensus         3 ~~yd~~~t~fsp~G~l~QvEyA~kav~~G~tvvgi~~~dgVvlaad~r~~~~~~~~~~~~ki~~I~~~i~~~~sG~~~D~   82 (250)
T d1rypb_           3 DRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSETLSKVSLLTPDIGAVYSGMGPDY   82 (250)
T ss_dssp             CCCCSBSSCBCTTSCBHHHHHHHHHHHTSCCEEEEEETTEEEEEEECCCSCSSBCGGGCCSSEEEETTEEEEEEECHHHH
T ss_pred             ccccCCCceECCCCeehHHHHHHHHHHcCCCEEEEEeCCEEEEEEecccCCccccccccceeEeccCCEEEEeeecccHH
Confidence            35999999999999999999999999999999999999999999999988877777889999999999999999999999


Q ss_pred             HHHHHHHHHHHHH-hhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccce
Q 025716           82 RVLINRARIECQS-HRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKA  160 (249)
Q Consensus        82 ~~l~~~~~~~~~~-~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~  160 (249)
                      +.++++++.++.. |++.++.+++++.+++++++++|.|+++++.|||+|++||+|+|+ ++||+||.+||.|++.++++
T Consensus        83 ~~l~~~~~~~~~~~y~~~~~~~~~~~~la~~~~~~~~~~~~~~~~rp~~v~~li~G~D~-~~gp~Ly~id~~G~~~~~~~  161 (250)
T d1rypb_          83 RVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIAGHDE-FNGFSLYQVDPSGSYFPWKA  161 (250)
T ss_dssp             HHHHHHHHHHHHHTTHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCCEEEEEEEEET-TTEEEEEEECTTSCEEEBSE
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhcCCcCeeEEEEEEEecC-CCCCEEEEEcCcEEEEEeeE
Confidence            9999999999974 899999999999999999999999999999999999999999997 68899999999999999999


Q ss_pred             EeecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEEcCC---------------CEEEcCHH
Q 025716          161 NATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES--GGKNIEVAVMTREK---------------GLKQLDEA  222 (249)
Q Consensus       161 ~aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~--~~~~iei~~v~~~g---------------~~~~~~~~  222 (249)
                      +|+|+|+..++++||++|+++|+ +||++++++||+++.+.  ++.++||++|++++               .|++++++
T Consensus       162 ~a~G~gs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~d~s~~~iev~vi~~~~~~~~~~~~v~~~~~~~fr~ls~e  241 (250)
T d1rypb_         162 TAIGKGSVAAKTFLEKRWNDELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTSQ  241 (250)
T ss_dssp             EEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCCSCCSTTTEEEEEECSCCGGGTSEESCSSCCCCSEEECCHH
T ss_pred             EecCcchHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHhhccCCCCCEEEEEEeCCCcccccccccccccCCceEECCHH
Confidence            99999999999999999999999 99999999999998865  56789999998753               48999999


Q ss_pred             HHHHHHHHH
Q 025716          223 EIDAMVAEI  231 (249)
Q Consensus       223 ei~~~l~~i  231 (249)
                      ||++++++|
T Consensus       242 ei~~~l~~l  250 (250)
T d1rypb_         242 EINDRLEAL  250 (250)
T ss_dssp             HHHHHHTTC
T ss_pred             HHHHHHHhC
Confidence            999998754

>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=8.1e-62  Score=413.86  Aligned_cols=228  Identities=34%  Similarity=0.595  Sum_probs=216.1

Q ss_pred             CCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHH
Q 025716            3 RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADAR   82 (249)
Q Consensus         3 ~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~   82 (249)
                      +||+.+|+|||||||+|||||+||+++|+|+|||+++||||||+|++.++.+..  +.+||++|++|++|++||+.+|++
T Consensus         2 ~yd~~~tiFsp~Grl~QvEYA~kav~~G~t~vgik~~dgVvlaad~~~~~~~~~--~~~KI~~I~~~i~~~~sG~~~D~~   79 (238)
T d1iruf_           2 QYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAA--HQKKILHVDNHIGISIAGLTADAR   79 (238)
T ss_dssp             TTTSCTTCCCTTSCCHHHHHHHHHHHHSCCEEEEECSSEEEEEEECCCSSTTBC--CCCCEEEEETTEEEEEEECHHHHH
T ss_pred             CCCCCCeeECCCCcchHHHHHHHHHhcCCCEEEEEeCCEEEEEEecccccCCCC--ccceEEEeCCceEEEEeccchHHH
Confidence            699999999999999999999999999999999999999999999999887754  468999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEe
Q 025716           83 VLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANA  162 (249)
Q Consensus        83 ~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~a  162 (249)
                      .+++.++.++..|++++|++++++.++++++..+|.|+++++.|||+|++||||||  ++||+||.+||+|++.+++++|
T Consensus        80 ~l~~~~~~~~~~~~~~~~~~i~~~~l~~~l~~~~~~y~~~~~~rP~~v~~il~G~D--~~gp~Ly~~D~~G~~~~~~~~a  157 (238)
T d1iruf_          80 LLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAGYD--DMGPHIFQTCPSANYFDCRAMS  157 (238)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEE--TTEEEEEEECSSSCEEEESEEE
T ss_pred             HHHHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHHHhhccCCCcccceEEEEEEc--CCCceEEEEcCCCCEEeeeeEE
Confidence            99999999999999999999999999999999999999999999999999999999  4789999999999999999999


Q ss_pred             ecCCchHHHHHHHhhhccCC--c-HHHHHHHHHHHHHHHhc----CCCcEEEEEEEcCCCEEEcCHHHHHHHHHHHHHH
Q 025716          163 TGRNSNSMREFLEKNYKETS--G-QETIKLAIRALLEVVES----GGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAK  234 (249)
Q Consensus       163 iG~g~~~a~~~Le~~~~~~~--s-eeai~la~~~l~~~~~~----~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i~~~  234 (249)
                      +|+++..++++|+++|+++|  + +|+++++++||++++..    ++.+|||++|+++++|++++++||++++++|++.
T Consensus       158 ~G~g~~~~~~~Lek~~~~~~~~~~~eav~lai~al~~~~~~~~~~~~~~iev~ii~k~~~~~~l~~~ei~~~l~~i~ek  236 (238)
T d1iruf_         158 IGARSQSARTYLERHMSEFMECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEGLEER  236 (238)
T ss_dssp             ESTTHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCTTCCCCTTTEEEEEEETTEEEEEECSGGGHHHHTTCCCC
T ss_pred             ECCCchhhHHHHHhhcccccCCCHHHHHHHHHHHHHHHHhhcccCCCCcEEEEEEeCCCCEEECCHHHHHHHHHHHHhC
Confidence            99999999999999999865  7 99999999999988742    5678999999998779999999999999988763

>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=2.2e-60  Score=406.36  Aligned_cols=229  Identities=37%  Similarity=0.654  Sum_probs=217.5

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcc-cccCCcccceEEecCCEEEEEecChhh
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKAD   80 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~-l~~~~~~~Ki~~I~~~i~~~~sG~~~D   80 (249)
                      .+||+++|+|||||||+|||||+||+++|+|+|||+++||||||+|++.++. ++.+++.+||++|++|++++++|..+|
T Consensus         3 ~~yd~~~t~fsp~G~~~Qveya~~ai~~G~T~vgi~~~dgVvlaad~r~s~~~~~~~~~~~KI~~i~~~i~~~~sG~~~D   82 (244)
T d1rypc_           3 RRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTSTEKLYKLNDKIAVAVAGLTAD   82 (244)
T ss_dssp             GGGCCCTTCBCTTSCBHHHHHHHHHHTTSCCEEEEEETTEEEEEEECSSCCSSBCSTTCCSSEEESSSSEEEEEEECHHH
T ss_pred             CccCCCceeECCCCcChHHHHHHHHHhcCCCEEEEEeCCEEEEEEeCCccCCCcccCCccceEEEcCCCeEEEEecccCc
Confidence            5799999999999999999999999999999999999999999999999885 455677999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccce
Q 025716           81 ARVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKA  160 (249)
Q Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~  160 (249)
                      ++.+++.++.+++.|+++++.+++++.++++++.+++.|++++++|||+|++||+|+|+ ++||+||.+||.|++.++++
T Consensus        83 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~rP~~~~~ll~G~d~-~~gp~Ly~id~~Gs~~~~~~  161 (244)
T d1rypc_          83 AEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAGYDD-RYGYQLYTSNPSGNYTGWKA  161 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSCCCCCEEEEEEEEET-TTEEEEEEECTTCCEEEBSE
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhhhhccccCccceeEEEEEEec-CCCceEEEecCCCcEeeeee
Confidence            99999999999999999999999999999999999999999999999999999999997 78899999999999999999


Q ss_pred             EeecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCC-----EEEcCHHHHHHHHHHH
Q 025716          161 NATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES---GGKNIEVAVMTREKG-----LKQLDEAEIDAMVAEI  231 (249)
Q Consensus       161 ~aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g~-----~~~~~~~ei~~~l~~i  231 (249)
                      +|+|+|+..++++|++.|+++|+ +||++++++||+.+.++   +++++||++|++++.     ++.++++||++++.+-
T Consensus       162 ~a~G~g~~~a~~~Le~~~~~~ms~eeai~l~~~al~~a~~~d~~~~~~iei~ii~~~~~~~~~~~~~~~~~Ei~~~l~k~  241 (244)
T d1rypc_         162 ISVGANTSAAQTLLQMDYKDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVKT  241 (244)
T ss_dssp             EEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCSSSSCCGGGEEEEEEECCSSSSSCEEEECCHHHHHHHHHHH
T ss_pred             eeccchhHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHhccCCCCCcEEEEEEECCCcccceeEEECCHHHHHHHHHHh
Confidence            99999999999999999999999 99999999999999875   467899999998763     7889999999998763

>d1rypg_ d.153.1.4 (G:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=3.1e-60  Score=405.46  Aligned_cols=230  Identities=32%  Similarity=0.460  Sum_probs=214.6

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhH
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADA   81 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~   81 (249)
                      +|||+++|+|||||||+|||||+||+++|+|+|||+++||||||+|++.+++++...+.+||++|++|++++++|+.+|+
T Consensus         2 ~gyd~~~t~fsp~Grl~QvEya~kav~~G~t~igik~~dgVvlaad~~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~   81 (244)
T d1rypg_           2 TGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNVKIQVVDRHIGCVYSGLIPDG   81 (244)
T ss_dssp             CCTTSSTTCCCTTSCCHHHHHHHHHHHTSCCEEEEEETTEEEEEEEEECCCTTBCTTTSCCCEEETTTEEEEEEECHHHH
T ss_pred             CCcCCCCceECCCCeehHHHHHHHHHHcCCCEEEEEeCCEEEEEEecccCCCCccccccceEEEccCceEEEEccchhhH
Confidence            68999999999999999999999999999999999999999999999999877666678999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceE
Q 025716           82 RVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKAN  161 (249)
Q Consensus        82 ~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~  161 (249)
                      +.++++++.++..|+++++++++++.+++.++.++|.|+++++.|||+|++|++|||  ++||+||.+||+|++.+++++
T Consensus        82 ~~l~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~t~~~~~RP~~~~~iiaG~D--~~gp~Ly~idp~Gs~~~~~~~  159 (244)
T d1rypg_          82 RHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGGVD--KNGAHLYMLEPSGSYWGYKGA  159 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSCTTBCCCCEEEEEEEEE--TTEEEEEEECTTSCEEEBSEE
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhcccccCCceEEEEEEEEe--CCCCEEEEEcCCccEEecCeE
Confidence            999999999999999999999999999999999999999999999999999999999  579999999999999999999


Q ss_pred             eecCCchHHHHHHHh---hhccCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEc---CCCEEEcCHHHHHHHHHHH
Q 025716          162 ATGRNSNSMREFLEK---NYKETSG-QETIKLAIRALLEVVES---GGKNIEVAVMTR---EKGLKQLDEAEIDAMVAEI  231 (249)
Q Consensus       162 aiG~g~~~a~~~Le~---~~~~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~---~g~~~~~~~~ei~~~l~~i  231 (249)
                      |+|+|+..++++||+   .|+++|| +||++++++||..+++.   +..++||++++.   ++.++.++.++++++++..
T Consensus       160 a~G~gs~~~~~~Lek~~~~~~~~mt~eeai~la~~~L~~~~~~~~~~~~~iev~ii~~~~~~~~~~~~~~e~~~~~~~~~  239 (244)
T d1rypg_         160 ATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAIDFA  239 (244)
T ss_dssp             EESTTHHHHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHGGGGTTSCEEEEEEEEETTTTTTSEEECCTHHHHHHHHHH
T ss_pred             ecCCccHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHhcccCCCCeEEEEEEEEEcCCCeEEECCHHHHHHHHHHH
Confidence            999999999999996   6899999 99999999999999864   355899999974   4556777888888887776


Q ss_pred             HH
Q 025716          232 EA  233 (249)
Q Consensus       232 ~~  233 (249)
                      ++
T Consensus       240 ~~  241 (244)
T d1rypg_         240 QK  241 (244)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

>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=1e-60  Score=407.99  Aligned_cols=232  Identities=36%  Similarity=0.634  Sum_probs=219.0

Q ss_pred             CCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHHHH
Q 025716            5 DRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARVL   84 (249)
Q Consensus         5 d~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l   84 (249)
                      |+.+|+|||||||+|||||+||+++|+|+|||+++||||||+|++.+.++...++.+||+.|+++++|+++|+.+|++.+
T Consensus         1 d~~~t~fsp~G~l~Qveya~~a~~~G~t~Vgi~~~dgVvla~d~r~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l   80 (242)
T d1rype_           1 DRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESDSIEKIVEIDRHIGCAMSGLTADARSM   80 (242)
T ss_dssp             CCCTTCBCTTSCBHHHHHHHHHHTTSCCEEEEECSSCEEEEEECCCSSTTBCGGGCCCEEEEETTEEEEEEESGGGHHHH
T ss_pred             CCCcceECCCCcchHHHHHHHHHHcCCCEEEEEeCCEEEEEEeCCccCcCcccCccceEEEcCCCEEEEEeecchhHHHH
Confidence            78999999999999999999999999999999999999999999998888777789999999999999999999999999


Q ss_pred             HHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCC------CccceeEEEEEeeeCCCCCceEEEECCCCceecc
Q 025716           85 INRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGG------VRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAW  158 (249)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~------~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~  158 (249)
                      +++++.++..|+++++++++++.+++++++++|.|++..+      .|||+|++||+|+|+ +++|+||.+||+|++.++
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~rP~~~~~ii~G~D~-~~~p~L~~idp~G~~~~~  159 (242)
T d1rype_          81 IEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLMSRPFGVALLIAGHDA-DDGYQLFHAEPSGTFYRY  159 (242)
T ss_dssp             HHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCCBSSCTTSCCCBSSCCSEEEEEEEEET-TTEEEEEEECTTSCEEEB
T ss_pred             HHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHhccccccchhccccceEEEEEEEecc-ccceEEEEEcCCCceecc
Confidence            9999999999999999999999999999999999887653      699999999999997 788999999999999999


Q ss_pred             ceEeecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEEcCCCEEEcCHHHHHHHHHHHHHHH
Q 025716          159 KANATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKK  235 (249)
Q Consensus       159 ~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~--~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i~~~~  235 (249)
                      +++|+|+|+..++++|+++|+++|+ +||++++++||+.+.++  +.++++|++|+++..|+++++++|++++.+|.+++
T Consensus       160 ~~~a~G~gs~~~~~~Le~~~~~~ms~~ea~~la~~~l~~~~~~~~~~~~~~v~~i~~~~g~~~l~~~~i~~~~~~i~e~~  239 (242)
T d1rype_         160 NAKAIGSGSEGAQAELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELIKELKEKE  239 (242)
T ss_dssp             SEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCSSCCCTTSEEEEEEETTTEEEECCHHHHHHHHHHHHHHH
T ss_pred             ceeecccchHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHhccCCCCceEEEEEECCCCeEECCHHHHHHHHHHHHHhh
Confidence            9999999999999999999999999 99999999999999875  45689999999754499999999999999999876


Q ss_pred             HH
Q 025716          236 AA  237 (249)
Q Consensus       236 ~~  237 (249)
                      .+
T Consensus       240 ~~  241 (242)
T d1rype_         240 AA  241 (242)
T ss_dssp             TT
T ss_pred             hc
Confidence            54

>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=1.6e-60  Score=404.29  Aligned_cols=227  Identities=41%  Similarity=0.686  Sum_probs=218.5

Q ss_pred             CCCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhH
Q 025716            2 ARYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADA   81 (249)
Q Consensus         2 ~~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~   81 (249)
                      +|||+++|+|||||||+|||||+||+++|+|+|||+++||||||+|++.+++++..++.+|||+|++|++|+++|..+|+
T Consensus         3 ~gyd~~~t~fsp~Gr~~Qveya~kav~~G~tvigik~~dgVvlaaD~r~~~~~~~~~~~~ki~~i~~~i~~~~sG~~~D~   82 (233)
T d1irub_           3 RGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDERSVHKVEPITKHIGLVYSGMGPDY   82 (233)
T ss_dssp             CCCCSBSCCCCTTSCCHHHHHHHHHHHTSCCEEEEECSSCEEEEEECCCCCSSBCSTTCCSSEESSSSEEEEEEECHHHH
T ss_pred             CCcCCCCCeECCCCcChHHHHHHHHHHcCCCEEEEEeCCEEEEEEeCCcccCCccccccceEEEecCceEEEEeccchHH
Confidence            68999999999999999999999999999999999999999999999998877777889999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceE
Q 025716           82 RVLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKAN  161 (249)
Q Consensus        82 ~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~  161 (249)
                      +.++++++.++.+|+++++++++++.++++++.+++.+++....|||+++++++|+|  +++|+||.+||.|++.+++++
T Consensus        83 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~p~~~~~li~g~d--~~~~~ly~id~~G~~~~~~~~  160 (233)
T d1irub_          83 RVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGVSLLICGWN--EGRPYLFQSDPSGAYFAWKAT  160 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCSEEEEEEEEC--SSSEEEEEECTTSCEEEBSEE
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhccccccceEEEeeeecc--cCCceEEEEcCCcceEeccce
Confidence            999999999999999999999999999999999999999999999999999999998  689999999999999999999


Q ss_pred             eecCCchHHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEEcCCCEEEcCHHHHHHHHHHH
Q 025716          162 ATGRNSNSMREFLEKNYKETSG-QETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEIDAMVAEI  231 (249)
Q Consensus       162 aiG~g~~~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~--~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i  231 (249)
                      |+|+++.+++++|++.|+++|+ +||++++++||+.++++  +..+|||++++++| +++++++||++++.+|
T Consensus       161 a~G~gs~~~~~~Le~~~~~~ms~eea~~l~~~~L~~~~~~d~~~~~vev~ii~~~g-~~~l~~~eI~~~l~~i  232 (233)
T d1irub_         161 AMGKNYVNGKTFLEKRYNEDLELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAG-FRRLTPTEVKDYLAAI  232 (233)
T ss_dssp             EESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHTTCCSCCCSSSEEEEEEETTE-EEECCHHHHHHHHTTC
T ss_pred             ecCCcHHHHHHHHHhhcccCccHHHHHHHHHHHHHHHHhccCCCCcEEEEEEeCCC-eEECCHHHHHHHHHHh
Confidence            9999999999999999999999 99999999999998865  46789999999998 9999999999999765

>d1yara1 d.153.1.4 (A:13-233) Proteasome alpha subunit (non-catalytic) {Archaeon Thermoplasma acidophilum [TaxId: 2303]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

Probab=100.00  E-value=2.9e-60  Score=399.98  Aligned_cols=218  Identities=40%  Similarity=0.638  Sum_probs=209.2

Q ss_pred             cccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHHHHHHHH
Q 025716            9 TVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARVLINRA   88 (249)
Q Consensus         9 ~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~   88 (249)
                      |+|||||||+|||||+||+++|+|+|||+++||||||+|++.++++..+++.+||++|++|++++++|+.+|++.+.+++
T Consensus         1 t~fsp~G~l~QvEYa~~av~~G~t~vgi~~~dgVvlaad~r~~~~~~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~   80 (221)
T d1yara1           1 TVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQNSIEKIQLIDDYVAAVTSGLVADARVLVDFA   80 (221)
T ss_dssp             CCCCTTSCCHHHHHHHHHHTTSCCEEEEEETTEEEEEECCCCCCTTBCSTTCCSEEEEETTEEEEEEEBHHHHHHHHHHH
T ss_pred             CeECCCCcchHHHHHHHHHhcCCcEEEEEeCCEEEEEEecccCCcccccCccceEEEecCCceEEeeeccchHHHHHHHH
Confidence            79999999999999999999999999999999999999999888887888899999999999999999999999999999


Q ss_pred             HHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCch
Q 025716           89 RIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSN  168 (249)
Q Consensus        89 ~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~  168 (249)
                      |.++..|+++++++++++.++++++.+++.++++++.|||+|++||+|+|  ++||+||.+||+|++.+++++|+|+|+.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~l~~~~a~~~~~~~~~~~~rP~~~~~li~G~d--~~gp~Ly~id~~G~~~~~~~~a~G~g~~  158 (221)
T d1yara1          81 RISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGVSLIFAGID--QIGPRLFDCDPAGTINEYKATAIGSGKD  158 (221)
T ss_dssp             HHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBTTBCCCCEEEEEEEEC--SSCEEEEEECTTCCEEEBSEEEESTTHH
T ss_pred             HHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhhhccCCCcceEEEEEEEe--cCCCeEEEEcCCccEEEeeEEEECCchH
Confidence            99999999999999999999999999999999999999999999999999  5799999999999999999999999999


Q ss_pred             HHHHHHHhhhccCCc-HHHHHHHHHHHHHHHhc--CCCcEEEEEEEcCCCEEEcCHHHHHHHH
Q 025716          169 SMREFLEKNYKETSG-QETIKLAIRALLEVVES--GGKNIEVAVMTREKGLKQLDEAEIDAMV  228 (249)
Q Consensus       169 ~a~~~Le~~~~~~~s-eeai~la~~~l~~~~~~--~~~~iei~~v~~~g~~~~~~~~ei~~~l  228 (249)
                      .++++|++.|+++|+ +||++++++||+.+++.  +.++++|+++++++.+|+++++||+++|
T Consensus       159 ~~~~~Le~~~~~~ms~~ea~~la~~~l~~~~~~~~~~~~~ei~~i~~~~~~r~l~~~ei~~~l  221 (221)
T d1yara1         159 AVVSFLEREYKENLPEKEAVTLGIKALKSSLEEGEELKAPEIASITVGNKYRIYDQEEVKKFL  221 (221)
T ss_dssp             HHHHHHHHHCCTTCCHHHHHHHHHHHHHHTSCSSCCCCCCEEEEEETTSCCEECCHHHHHTTC
T ss_pred             HHHHHHHHHhhccccHHHHHHHHHHHHHHHHhccCCCCCcEEEEEEcCCCEEECCHHHHHHhC
Confidence            999999999999999 99999999999998865  4668999999987679999999998764

>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=7.3e-61  Score=406.76  Aligned_cols=222  Identities=33%  Similarity=0.541  Sum_probs=210.1

Q ss_pred             CCCCCCcccCCCCcchhhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHH
Q 025716            3 RYDRAITVFSPDGHLFQVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADAR   82 (249)
Q Consensus         3 ~yd~~~~~fsp~G~l~Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~   82 (249)
                      +||+.+|+|||||||+|||||+||+++|+|+|||+++||||||+|++.++.+.  .+.+||+.|++|++|++||+.+|++
T Consensus         4 ~yd~~~t~FspdGrl~QvEyA~kav~~g~t~igi~~~dgvvlaad~~~~~~l~--~~~~KI~~I~~~i~~~~sG~~~D~~   81 (233)
T d1rypf_           4 NYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELS--SYQKKIIKCDEHMGLSLAGLAPDAR   81 (233)
T ss_dssp             HHSSCTTCCCTTSCCHHHHHHHHHHHTSCCEEEEECSSEEEEEEECCCSSTTB--CCCCCEEEEETTEEEEEEECHHHHH
T ss_pred             cccCCCceECCCCcChHHHHHHHHHHcCCCEEEEEECCeEEEEEeccccccCC--cchheEEEcCCCEEEEEeeccccHH
Confidence            59999999999999999999999999999999999999999999999988764  4678999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEe
Q 025716           83 VLINRARIECQSHRLTVEDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANA  162 (249)
Q Consensus        83 ~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~a  162 (249)
                      .+++++|.+++.|+++++++++++.+++.+++++|.|++.++.|||+|++||+|+|  ++||+||.+||+|++.+++++|
T Consensus        82 ~l~~~~r~~~~~~~~~~~~~i~~~~la~~l~~~~~~~t~~~~~RP~gv~~il~G~d--~~g~~Ly~idp~G~~~~~~~~a  159 (233)
T d1rypf_          82 VLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRPYGVGLLIIGYD--KSGAHLLEFQPSGNVTELYGTA  159 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEE--TTEEEEEEECTTSCEEEESEEE
T ss_pred             HHHHHHHHHHHhhhhhcCCCCcHHHHHHHHHHHHHHHhcccccCCccceEEEEEEc--CCCCEEEEEccccceecccEEE
Confidence            99999999999999999999999999999999999999999999999999999999  4689999999999999999999


Q ss_pred             ecCCchHHHHHHHhhh----ccCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCHHHHHHHH
Q 025716          163 TGRNSNSMREFLEKNY----KETSG-QETIKLAIRALLEVVES---GGKNIEVAVMTREKGLKQLDEAEIDAMV  228 (249)
Q Consensus       163 iG~g~~~a~~~Le~~~----~~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~~ei~~~l  228 (249)
                      +|+|++.++++|++.|    +++|+ +|+++++++||..++.+   ++.++||++|+++++|++++++||++++
T Consensus       160 iG~gs~~a~~~Le~~~~~~~~~dms~eeai~l~~~~l~~~~~~d~~~~~~iev~ii~k~~~~~~l~~~ei~~~i  233 (233)
T d1rypf_         160 IGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI  233 (233)
T ss_dssp             ESTTHHHHHHHHHHHHHHHTTCCSCHHHHHHHHHHHHTTSCCSSCCCTTTEEEEEEETTEEEEEEEGGGGGGGC
T ss_pred             ecCchHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHHhccCCCCCeEEEEEEECCCCeEECCHHHHHhhC
Confidence            9999999999999866    56999 99999999999998754   4789999999998779999999998763

>d1q5qa_ d.153.1.4 (A:) Proteasome alpha subunit (non-catalytic) {Rhodococcus erythropolis [TaxId: 1833]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Rhodococcus erythropolis [TaxId: 1833]

Probab=100.00  E-value=3.2e-47  Score=321.23  Aligned_cols=203  Identities=15%  Similarity=0.261  Sum_probs=181.0

Q ss_pred             hhhhHHHHHccCCcEEEEEeCCEEEEEEeccCCcccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhh
Q 025716           19 QVEYALEAVRKGNAAVGVRGTDTIVLGVEKKSTVKLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLT   98 (249)
Q Consensus        19 Qveya~kav~~G~t~igi~~~dgVvla~d~~~~~~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~   98 (249)
                      |+|||+||+++|+|+|||+++||||||+|+|.+       +.+||++|++||+|+++|+.+|++.|+++++.+|+.|+++
T Consensus         8 q~eyA~~av~~GtT~vgi~~~~GVvlaad~r~~-------s~~KI~~i~~~i~~~~sG~~aD~~~l~~~~r~~~~~~~~~   80 (227)
T d1q5qa_           8 RSELARKGIARGRSVVVLTFRDGVLFVAENPST-------ALHKVSELYDRLGFAAVGKYNEFENLRRAGIVHADMRGYS   80 (227)
T ss_dssp             HHHHHHHHHHTSCCEEEEECSSEEEEEECCSCS-------SSCSEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCEEEEEECCEEEEEEccCCC-------CcceEEEecCceEEEecCchHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999863       3789999999999999999999999999999999999999


Q ss_pred             cC-CCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeC--CCCCceEEEECCCCceeccc-eEeecCCchHHHHHH
Q 025716           99 VE-DPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDP--YTGVPSLYQTDPSGTFSAWK-ANATGRNSNSMREFL  174 (249)
Q Consensus        99 ~~-~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~--~~~gp~Ly~iDp~G~~~~~~-~~aiG~g~~~a~~~L  174 (249)
                      |+ .+++++.+++.++++++.... .+.|||+|++||||||.  .+++|+||.+||+|++.+++ +++.|.+++.++++|
T Consensus        81 ~~~~~~~~~~la~~~~~~~~~~~~-~~~rP~gvs~lvaG~D~~g~~~~p~Ly~vDpsG~~~~~~~~~~~g~~s~~~~~~L  159 (227)
T d1q5qa_          81 YDRRDVTGRSLANAYAQTLGTIFT-EQPKPYEVEICVAEVGRVGSPKAPQLYRITYDGSIVDEQHFVVMGGTTEPIATAM  159 (227)
T ss_dssp             SCGGGCCHHHHHHHHHHHHHHHHH-HSSSCCCEEEEEEECCCSSCCCCCEEEEEETTSCEEEESSEEEESSSHHHHHHHH
T ss_pred             hCCCCCcHHHHHHHHHHHHHHHHH-hcCCCceEEEEEEEEecCCCCCCCEEEEEccccceeeecccccCCCchHHHHHHH
Confidence            98 568999999999988654433 35699999999999995  24689999999999998765 566778899999999


Q ss_pred             HhhhccCCc-HHHHHHHHHHHHHHHhc-------CCCcEEEEEEEcCC---CEEEcCHHHHHHHHH
Q 025716          175 EKNYKETSG-QETIKLAIRALLEVVES-------GGKNIEVAVMTREK---GLKQLDEAEIDAMVA  229 (249)
Q Consensus       175 e~~~~~~~s-eeai~la~~~l~~~~~~-------~~~~iei~~v~~~g---~~~~~~~~ei~~~l~  229 (249)
                      +++|+++|| +||++++++||+.++..       ++.++||++++++|   .|++++++||+++|+
T Consensus       160 e~~y~~~ms~eea~~la~~aL~~a~~~d~~~~~~~~~~ievavi~k~~~~~~fr~l~~~ei~~~l~  225 (227)
T d1q5qa_         160 RESYRADLDLEAAVGIAVNALRQGGAGEGEKRNVDVASLEVAVLDQSRPRRAFRRIAGTALEQLVP  225 (227)
T ss_dssp             HHHCCTTCCHHHHHHHHHHHHTTCC--------CCSSCSEEEEEETTSSSCCEEECCHHHHHTTSC
T ss_pred             HHhccCCCCHHHHHHHHHHHHHHHhhcccccCCcCcceEEEEEEECCCCccceEEcCHHHHHHHhc
Confidence            999999999 99999999999988753       35689999999875   599999999998864

>d1yarh1 d.153.1.4 (H:1-203) Proteasome beta subunit (catalytic) {Archaeon Thermoplasma acidophilum [TaxId: 2303]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

Probab=100.00  E-value=2e-44  Score=298.87  Aligned_cols=194  Identities=25%  Similarity=0.414  Sum_probs=181.5

Q ss_pred             CcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      ||+|||+++||||||+|+|.+. .++.+++.+|||+|++|++++++|..+|++.+.++++.+++.|++.++.+++++.++
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            6899999999999999999876 577788999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIK  188 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~  188 (249)
                      ++++++++.+    +.|||++++|+||+|.   +|+||.+||+|++.+++++|+|+|+..++++|+++|+++|| +||++
T Consensus        81 ~~l~~~~~~~----~~~p~~~~~lvaG~d~---~p~l~~~d~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~eea~~  153 (203)
T d1yarh1          81 TLLSNMLNQV----KYMPYMVQLLVGGIDT---APHVFSIDAAGGSVEDIYASTGSGSPFVYGVLESQYSEKMTVDEGVD  153 (203)
T ss_dssp             HHHHHHHHHT----TTSCCCEEEEEEEESS---SEEEEEECTTCCEEEESEEEESTTHHHHHHHHHHHCCTTCCHHHHHH
T ss_pred             HHHHHHHHhh----ccCCccceeEEEEEcC---CCeeEecCCccceecccccccCCCcHHHHHHHHHhccCCCCHHHHHH
Confidence            9999988755    4589999999999983   69999999999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCHHHHHHHHHHH
Q 025716          189 LAIRALLEVVES---GGKNIEVAVMTREKGLKQLDEAEIDAMVAEI  231 (249)
Q Consensus       189 la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i  231 (249)
                      ++++||+.+.++   ++++++|++++++..+++++++||++++.++
T Consensus       154 l~~~~l~~~~~~d~~~~~~v~v~ii~~~~g~~~l~~~ei~~~~~~~  199 (203)
T d1yarh1         154 LVIRAISAAKQRDSASGGMIDVAVITRKDGYVQLPTDQIESRIRKL  199 (203)
T ss_dssp             HHHHHHHHHHHHCTTCCSCCEEEEEETTTEEEECCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCCCeEEEEEEECCCCEEECCHHHHHHHHHHh
Confidence            999999998875   4678999999975459999999999999886

>d1rypk_ d.153.1.4 (K:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=4.3e-45  Score=301.93  Aligned_cols=192  Identities=20%  Similarity=0.279  Sum_probs=178.9

Q ss_pred             CCcEEEEEeCCEEEEEEeccCCcc-cccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHH
Q 025716           30 GNAAVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYI  108 (249)
Q Consensus        30 G~t~igi~~~dgVvla~d~~~~~~-l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l  108 (249)
                      ++|+|||+++||||||+|++.+.+ ++..++.+||++|++|++++++|..+|++.+.++++.++..|+++++.+++++.+
T Consensus         1 m~tiigi~~~dgVvlaaD~r~s~g~~~~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~   80 (198)
T d1rypk_           1 MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYIQANIQLYSIREDYELSPQAV   80 (198)
T ss_dssp             CCCEEEEECSSCEEEEEECCEEETTEEEESCCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHH
T ss_pred             CeEEEEEEECCEEEEEEcCCcccCCEeecCccceEEEecCCEEEEecCCcccHHHHHHHHHHHHHHHHHHhCCCcchHHH
Confidence            689999999999999999998874 4566789999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHH
Q 025716          109 TRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETI  187 (249)
Q Consensus       109 a~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai  187 (249)
                      +++++++++.+++  ..|||++++||||||+.++||+||.+||+|++.+++++++|+|+.+++++|+++|+++|+ +||+
T Consensus        81 ~~~i~~~~~~~~~--~~~P~~~~~liaG~D~~~~~p~L~~id~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~eea~  158 (198)
T d1rypk_          81 SSFVRQELAKSIR--SRRPYQVNVLIGGYDKKKNKPELYQIDYLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGL  158 (198)
T ss_dssp             HHHHHHHHHHHTT--SSSCCCEEEEEEEEETTTTEEEEEEECTTCCEEECSEEECTTHHHHHHHHHHHHCCTTCCHHHHH
T ss_pred             HHHHHHHHHHHHh--cccccceEEEEEEEecCCCceEEEEecccccEEecceEEEeccchhhHHHHHhcccccCCHHHHH
Confidence            9999999987765  469999999999999745799999999999999999999999999999999999999999 9999


Q ss_pred             HHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCHHHH
Q 025716          188 KLAIRALLEVVES---GGKNIEVAVMTREKGLKQLDEAEI  224 (249)
Q Consensus       188 ~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~~ei  224 (249)
                      +++++||+.+..+   ++++++|++|++|| +++++++++
T Consensus       159 ~l~~~~l~~~~~~d~~s~~~~~v~vi~~dG-~~~~~~~~~  197 (198)
T d1rypk_         159 DLLKLCVQELEKRMPMDFKGVIVKIVDKDG-IRQVDDFQA  197 (198)
T ss_dssp             HHHHHHHHHHHHHCSBCCCCEEEEEEETTE-EEEECCCSC
T ss_pred             HHHHHHHHHHHHhcCcCCCcEEEEEEcCCC-eEEcchhcc
Confidence            9999999998764   57789999999998 999988765

>d1irul_ d.153.1.4 (L:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=7e-45  Score=301.29  Aligned_cols=195  Identities=15%  Similarity=0.280  Sum_probs=183.9

Q ss_pred             CcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      ||+|||+++||||||+|++.+. .++.+++.+|||+|+++++|+++|..+|++.+.+.++.+++.|++.++.+++++.++
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            6999999999999999999887 566778899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIK  188 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~  188 (249)
                      +++++++|.++    .+||+++++++|+|  +++|+||.+||+|++.+++++|+|+|+.+++++|++.|+++|| +||++
T Consensus        81 ~~l~~~~~~~~----~~p~~~~~lvaG~d--~~~~~l~~~d~~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~ms~eea~~  154 (201)
T d1irul_          81 KLLANMVYQYK----GMGLSMGTMICGWD--KRGPGLYYVDSEGNRISGATFSVGSGSVYAYGVMDRGYSYDLEVEQAYD  154 (201)
T ss_dssp             HHHHHHHHTTT----TSCCCBEEEEEEEC--SSSEEEEEEESSSCEEECSEEEESTTHHHHHHHHHTTCCTTCCHHHHHH
T ss_pred             HHHHHHhhhcc----CCCceEEEEEEEEe--cCCceEEEEccCceEEEeeeEEecCchHHHHHHHHhhccCCCCHHHHHH
Confidence            99999998664    47999999999999  4799999999999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCHHHHHHHHHHHH
Q 025716          189 LAIRALLEVVES---GGKNIEVAVMTREKGLKQLDEAEIDAMVAEIE  232 (249)
Q Consensus       189 la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i~  232 (249)
                      ++++||+++.++   ++++++|++|+++| +++++++||.++.++++
T Consensus       155 l~~~~l~~~~~~d~~sg~~~~v~~i~~~G-~~~i~~~ev~~~~~~~~  200 (201)
T d1irul_         155 LARRAIYQATYRDAYSGGAVNLYHVREDG-WIRVSSDNVADLHEKYS  200 (201)
T ss_dssp             HHHHHHHHHHHHBTTCCSEEEEEEECSSC-EEEEEEEEHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCCCCCCceEEEEEeCCc-eEEECHHHHHHHHHhhc
Confidence            999999999875   57899999999999 99999999999988764

>d1rypl_ d.153.1.4 (L:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=4.1e-44  Score=299.03  Aligned_cols=199  Identities=17%  Similarity=0.323  Sum_probs=187.2

Q ss_pred             CcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      ||+|||+|+||||||+|++.++ .++.+++.+|||+|++|++|+++|..+|++.|+++++.++..|++.++.+++++.++
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            7999999999999999999887 567778899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIK  188 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~  188 (249)
                      ++++++++.|.    .+|+++..+++|+|+ +++|+||.+||+|++.+++++|+|+|+..++++|+++|+++|+ +||++
T Consensus        81 ~~ls~~~~~~~----~~p~~~~~~l~G~~~-~~g~~Ly~id~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~mt~~ea~~  155 (212)
T d1rypl_          81 KILSNLVYQYK----GAGLSMGTMICGYTR-KEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALY  155 (212)
T ss_dssp             HHHHHHHHHTT----TSCCCBEEEEEEEET-TTEEEEEEEETTCCEEECSEEEESTTHHHHHHHHHHHCCTTCCHHHHHH
T ss_pred             HHHHHHHHHhc----cCCcceEeeeeEeec-CCCCEEEEECCCceEEecceEEEccCcccchhHHHHhccCCCCHHHHHH
Confidence            99999998664    358999999999997 7899999999999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCHHHHHHHHHHHHHHH
Q 025716          189 LAIRALLEVVES---GGKNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKK  235 (249)
Q Consensus       189 la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i~~~~  235 (249)
                      ++++||+.+..+   ++++++|++|+++| +++++++||.+++.++++++
T Consensus       156 l~~~al~~~~~rd~~sg~~v~v~vi~~~g-~~~~~~~ev~~~~~~~~~~~  204 (212)
T d1rypl_         156 LGKRSILAAAHRDAYSGGSVNLYHVTEDG-WIYHGNHDVGELFWKVKEEE  204 (212)
T ss_dssp             HHHHHHHHHHHHBTTCCSEEEEEEEETTE-EEEEEEEEHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCCCceEEEEEcCCc-eEEeCHHHHHHHHHHHHHhh
Confidence            999999998865   57899999999998 99999999999999988765

>d1j2qh_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=100.00  E-value=8.1e-44  Score=294.57  Aligned_cols=195  Identities=27%  Similarity=0.432  Sum_probs=182.5

Q ss_pred             CcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      ||+|||+++||||||+|++.+. .++.+++.+|||+|++|++|+++|..+|++.|.++++.+++.|++.++.+++++.++
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            6899999999999999999876 577778899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceecc-ceEeecCCchHHHHHHHhhhccCCc-HHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAW-KANATGRNSNSMREFLEKNYKETSG-QETI  187 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~-~~~aiG~g~~~a~~~Le~~~~~~~s-eeai  187 (249)
                      +++++++|.++    .|||++++|++|+|  +++|+||.+||+|++.++ +++|+|+|+..++++|+++|+++|+ +||+
T Consensus        81 ~~~~~~~~~~~----~~p~~~~~lvaG~d--~~~~~l~~~d~~G~~~~~~~~~a~G~g~~~~~~~Le~~~~~~ms~~ea~  154 (202)
T d1j2qh_          81 TLTSNLLNSYR----YFPYLVQLLIGGID--SEGKSIYSIDPIGGAIEEKDIVATGSGSLTAYGVLEDRFTPEIGVDEAV  154 (202)
T ss_dssp             HHHHHHHHHTT----TSCCCEEEEEEEEE--TTEEEEEEECTTCCEEEESSEEEESTTHHHHHHHHHHHCCTTCCHHHHH
T ss_pred             HHHHHHHhhhc----ccceeeEEEEEEEc--CCCceEEEEeCCCCeEeecceEEccCChHHHHHHHHhhcCCCCCHHHHH
Confidence            99999998775    37999999999999  578999999999998765 6899999999999999999999999 9999


Q ss_pred             HHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCHHHHHHHHHHHH
Q 025716          188 KLAIRALLEVVES---GGKNIEVAVMTREKGLKQLDEAEIDAMVAEIE  232 (249)
Q Consensus       188 ~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~~ei~~~l~~i~  232 (249)
                      +++++||..+.++   ++++++|++|+++| +++++++||++++.+++
T Consensus       155 ~l~~~al~~~~~~d~~~g~~v~v~~i~~~g-~~~~~~~ei~~~l~~~~  201 (202)
T d1j2qh_         155 ELAVRAIYSAMKRDSASGDGIDVVKITEDE-FYQYSPEEVEQILAKFR  201 (202)
T ss_dssp             HHHHHHHHHHHTTCTTSCSCEEEEEECSSC-EEECHHHHHHHHGGGTT
T ss_pred             HHHHHHHHHHHHhcCCCCCeEEEEEEECCC-EEEeCHHHHHHHHHHhh
Confidence            9999999999875   46789999999998 99999999999998875

>d1ryph_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=5.6e-44  Score=296.83  Aligned_cols=193  Identities=17%  Similarity=0.265  Sum_probs=176.7

Q ss_pred             HccCCcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCH
Q 025716           27 VRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTV  105 (249)
Q Consensus        27 v~~G~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~  105 (249)
                      +++|+|+|||+|+||||||+|+|.+. .++.+++.+||++|++|++|+++|..+|++.|.++++.+++.|+++++++ ++
T Consensus         6 v~~GtTivgi~~~dgVvlaaD~r~s~g~~i~~~~~~ki~~i~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~-~~   84 (205)
T d1ryph_           6 VSLGASIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKIWCCRSGSAADTQAIADIVQYHLELYTSQYGTP-ST   84 (205)
T ss_dssp             CBCCCCEEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEEBHHHHHHHHHHHHHHHHHHHHHHSSC-CH
T ss_pred             ccCcceEEEEEECCEEEEEECCccccCceeeccccceEEEccCceEEeeccchhHHHHHHHHHHHHHHHHHHHcCCc-cH
Confidence            68999999999999999999999877 56677889999999999999999999999999999999999999999965 57


Q ss_pred             HHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-H
Q 025716          106 EYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-Q  184 (249)
Q Consensus       106 ~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-e  184 (249)
                      ..++++++.+++.+     .+||+|++||||||+ +++|+||.+||.|++.+++++|+|+|+.+++++|++.|+++|| +
T Consensus        85 ~~~~~~~~~~~~~~-----~~p~~~~~lvaG~d~-~~~p~Ly~~d~~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~ms~~  158 (205)
T d1ryph_          85 ETAASVFKELCYEN-----KDNLTAGIIVAGYDD-KNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKE  158 (205)
T ss_dssp             HHHHHHHHHHHHHT-----TTTCCEEEEEEEEET-TTEEEEEEECTTSCCEEESEEEESGGGGGGHHHHHHHCCTTCCHH
T ss_pred             HHHHHHHHHHHHhC-----ccCceEEEEEEeecC-CCCcEEEEECCCCcEEecCeEEeecCcHHHHHHHHhhhhcccCHH
Confidence            88999999988543     379999999999997 7899999999999999999999999999999999999999999 9


Q ss_pred             HHHHHHHHHHHHHHhc---CCCcEEEEEEEcCC-CEEEcCHHHHHH
Q 025716          185 ETIKLAIRALLEVVES---GGKNIEVAVMTREK-GLKQLDEAEIDA  226 (249)
Q Consensus       185 eai~la~~~l~~~~~~---~~~~iei~~v~~~g-~~~~~~~~ei~~  226 (249)
                      ||++++++||+.+.++   ++++++|++|+++| .++.+.++|+++
T Consensus       159 ea~~l~~~al~~a~~rD~~sg~~v~v~iitk~G~~~~~~~~~e~~~  204 (205)
T d1ryph_         159 ETVDFIKHSLSQAIKWDGSSGGVIRMVVLTAAGVERLIFYPDEYEQ  204 (205)
T ss_dssp             HHHHHHHHHHHHHHHHBTTCCSCEEEEEEETTEEEEEEECHHHHTC
T ss_pred             HHHHHHHHHHHHHHHhcCcCCCCEEEEEEcCCceEEEecCcccccc
Confidence            9999999999999875   57899999999998 233578999865

>d1iruh_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=2.1e-42  Score=286.50  Aligned_cols=191  Identities=18%  Similarity=0.303  Sum_probs=176.8

Q ss_pred             CcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      ||+|||+++||||||+|+|.+. .++.+++.+||++|++|++++++|..+|++.+.+.++.++++|+++++.+++++.++
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            6999999999999999999987 567778899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIK  188 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~  188 (249)
                      ++++++++.++     +||++++|++|+|+ +++|+||.+||.|++.+++++++|+|+.+++++|++.|+++|+ +||++
T Consensus        81 ~~l~~~l~~~~-----~p~~~~~lvaG~d~-~~~~~l~~~d~~g~~~~~~~~a~G~g~~~a~~~L~~~~~~~~~~~ea~~  154 (202)
T d1iruh_          81 SLFKEMCYRYR-----EDLMAGIIIAGWDP-QEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREGMTKEECLQ  154 (202)
T ss_dssp             HHHHHHHHHTT-----TTCCEEEEEEEEET-TTEEEEEEECTTSCCEECSEEEESGGGGGGHHHHHHHCCTTCCHHHHHH
T ss_pred             HHHHHHHHhhc-----cceeEEEEEEEeec-CCCcEEEEECCCCceeecceeEEeCCHHHHHHHHHHhhccCCcHHHHHH
Confidence            99999997653     69999999999998 7899999999999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHhc---CCCcEEEEEEEcCC-CEEEcCHHHHHHH
Q 025716          189 LAIRALLEVVES---GGKNIEVAVMTREK-GLKQLDEAEIDAM  227 (249)
Q Consensus       189 la~~~l~~~~~~---~~~~iei~~v~~~g-~~~~~~~~ei~~~  227 (249)
                      ++++||..+.++   ++++++|++|+++| .++.++++||..+
T Consensus       155 l~~~al~~a~~rD~~sg~~i~v~vi~~~G~~~~~~~~d~~~~~  197 (202)
T d1iruh_         155 FTANALALAMERDGSSGGVIRLAAIAESGVERQVLLGDQIPKF  197 (202)
T ss_dssp             HHHHHHHHHHHHBTTCCSCEEEEEEETTEEEEEEECGGGSCCC
T ss_pred             HHHHHHHHHHhhCCCCCCCEEEEEEeCCCeEEEEcCHHHhhhh
Confidence            999999999865   57799999999998 2245888887543

>d1ryp2_ d.153.1.4 (2:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=9.3e-43  Score=294.67  Aligned_cols=200  Identities=14%  Similarity=0.258  Sum_probs=182.6

Q ss_pred             HHHccCCcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhc----
Q 025716           25 EAVRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTV----   99 (249)
Q Consensus        25 kav~~G~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~----   99 (249)
                      +++.+|+|+|||+++||||||+|++.+. .++.+++.+||++|++|++++++|..+|++.+.+.++.++..|++++    
T Consensus         3 ~~i~tGtTivgi~~~dgVvlaaD~r~s~g~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~l~~~~~~~~~~~~~~~   82 (233)
T d1ryp2_           3 QPIVTGTSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLAD   82 (233)
T ss_dssp             CCCEEECCEEEEEETTEEEEEEECCEEETTEEEESCCCCEEEETTTEEEEEEEEHHHHHHHHHHHHHHHHHHHTTCTTTT
T ss_pred             CCccccceEEEEEECCEEEEEECCCcccCCeeecCCcceEEEeCCCEEEEeccCchHHHHHHHHHHHHHHHHHHhhCCCC
Confidence            5678999999999999999999999875 67777889999999999999999999999999999999999998876    


Q ss_pred             -CCCCCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhh
Q 025716          100 -EDPVTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNY  178 (249)
Q Consensus       100 -~~~i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~  178 (249)
                       +..++++.+++++++.+  |+++.+.|||+|++||+|+|+ +++|+||.+||.|++.+++++|+|+|+++++++|++.|
T Consensus        83 ~~~~~~~~~~a~~l~~~~--y~~~~~~~P~~~~~liaG~d~-~g~~~ly~~d~~G~~~~~~~~a~G~g~~~a~~~Le~~~  159 (233)
T d1ryp2_          83 AEEALEPSYIFEYLATVM--YQRRSKMNPLWNAIIVAGVQS-NGDQFLRYVNLLGVTYSSPTLATGFGAHMANPLLRKVV  159 (233)
T ss_dssp             TTTSCCHHHHHHHHHHHH--HHHHHTTCCCCEEEEEEEECT-TSCEEEEEEETTCCEECCSEEECTHHHHHHHHHHTTTC
T ss_pred             CCcccCHHHHHHHHHHHH--HhhccccCCceeEEEEEEEcC-CCCeEEEEEcCCCcEEeeeeEEecCccHHHHHHHHHHH
Confidence             57789999999999987  556667899999999999997 78899999999999999999999999999999999999


Q ss_pred             c-----cCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCHHHHHHH
Q 025716          179 K-----ETSG-QETIKLAIRALLEVVES---GGKNIEVAVMTREKGLKQLDEAEIDAM  227 (249)
Q Consensus       179 ~-----~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~~ei~~~  227 (249)
                      +     ++|+ +||++++++||+.+..+   ++++|+|++|++|+.++++++++|+..
T Consensus       160 ~~~~~~~~ms~eeA~~l~~~al~~~~~rD~~sg~~i~i~~itkd~g~~~~~~~~ie~~  217 (233)
T d1ryp2_         160 DRESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKNTGLTFKKNLQVENM  217 (233)
T ss_dssp             CSGGGGGGCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTTEEEEEEEEECCSC
T ss_pred             hhcccccccCHHHHHHHHHHHHHHHHHhcccCCCCEEEEEEECCCCEEECChhcchhh
Confidence            7     7899 99999999999999865   577999999999855999988887553

>d1irui_ d.153.1.4 (I:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=2.9e-41  Score=283.12  Aligned_cols=186  Identities=22%  Similarity=0.301  Sum_probs=173.3

Q ss_pred             CcEEEEEeCCEEEEEEeccCCcc-cccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~~-l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      ||+|||+|+||||||+|++.+++ ++.+++.+||++|++|++++++|..+|++.+.+.++.+++.|++++|..++++.++
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            68999999999999999999884 56677899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIK  188 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~  188 (249)
                      ++++++++.+     .+|+++++|++|+|  ++||+||.+||.|++.+++++|+|+|+.+++++|++.|+++|| +||++
T Consensus        81 ~~l~~~~y~~-----~~p~~~~~ivaG~D--~~g~~L~~id~~G~~~~~~~~a~Gsgs~~a~~~L~~~~~~~~s~~ea~~  153 (220)
T d1irui_          81 RMLKQMLFRY-----RGYIGAALVLGGVD--VTGPHLYSIYPHGSTDKLPYVTMGSGSLAAMAVFEDKFRPDMEEEEAKN  153 (220)
T ss_dssp             HHHHHHHHHT-----TTCSCEEEEEEEEC--SSCEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHSCCTTCCHHHHHT
T ss_pred             HHHHhhhhhc-----ccccceeEEEEEEe--CCCcEEEEEeCCCcEEEeeEEEEccccHHHHHHHHHhcccCCCHHHHHH
Confidence            9999998643     37999999999999  5789999999999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCHHHH
Q 025716          189 LAIRALLEVVES---GGKNIEVAVMTREKGLKQLDEAEI  224 (249)
Q Consensus       189 la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~~ei  224 (249)
                      ++++||..+..+   ++++|+|++|+++| ++++.+.++
T Consensus       154 l~~~al~~~~~~D~~sg~~i~i~vitkdg-~~~~~~~~~  191 (220)
T d1irui_         154 LVSEAIAAGIFNDLGSGSNIDLCVISKNK-LDFLRPYTV  191 (220)
T ss_dssp             HHHHHHHHHHHHCTTCCSCEEEEEEETTE-EECCSEEEC
T ss_pred             HHHHHHHHhhccCCCCCCcEEEEEEECCC-eEEeCcccc
Confidence            999999999875   47799999999998 888877654

>d1q5qh_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Rhodococcus erythropolis [TaxId: 1833]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Rhodococcus erythropolis [TaxId: 1833]

Probab=100.00  E-value=2.1e-40  Score=278.09  Aligned_cols=204  Identities=19%  Similarity=0.228  Sum_probs=185.5

Q ss_pred             CcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      ||+|||+++||||||+|++.++ .++.+++.+||++|++|++++++|..+|++.+.+.++.++..|++.++.++++..++
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            6899999999999999999887 566778899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeC----CCCCceEEEECCCCceecc--ceEeecCCchHHHHHHHhhhccCCc
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDP----YTGVPSLYQTDPSGTFSAW--KANATGRNSNSMREFLEKNYKETSG  183 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~----~~~gp~Ly~iDp~G~~~~~--~~~aiG~g~~~a~~~Le~~~~~~~s  183 (249)
                      +++++.++.+++. ..||+++.++++|++.    .+++|+||.+||+|++.++  +++|+|+|+.+++++||+.|+++||
T Consensus        81 ~~~~~~~~~~~~~-~~~~~~~~~~~~g~~~~g~d~~~~~~l~~~d~~G~~~~~~~~~~a~GsG~~~a~~~Le~~~~~~mt  159 (224)
T d1q5qh_          81 NRLASMVRGNLGA-AMQGLAVVPLLVGYDLDADDESRAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALKKIYSPDSD  159 (224)
T ss_dssp             HHHHHHHHTTHHH-HTTTCCEEEEEEEECTTCSSTTSCEEEEEECTTSCEEECCSSEEEESTTHHHHHHHHHHHCCTTCC
T ss_pred             HHHHHHHHHhhcc-cccCccceeeEEEeecccccccCCceEEEEEccCcEEEeccceeeecCccHHHHHHHHHhhcccCC
Confidence            9999999988764 5688888888887763    1568999999999998765  7899999999999999999999999


Q ss_pred             -HHHHHHHHHHHHHHHhcC---C-------CcEEEEEEEcCCCEEEcCHHHHHHHHHHHHHHHH
Q 025716          184 -QETIKLAIRALLEVVESG---G-------KNIEVAVMTREKGLKQLDEAEIDAMVAEIEAKKA  236 (249)
Q Consensus       184 -eeai~la~~~l~~~~~~~---~-------~~iei~~v~~~g~~~~~~~~ei~~~l~~i~~~~~  236 (249)
                       +||++++++||..+..++   +       .++++++++++| +++++++|+++++.++.+++-
T Consensus       160 ~~ea~~l~~~al~~a~~rD~~SGg~~~~~~~~~~~~~i~~~g-~~~l~~~ei~~~~~~~~~~~~  222 (224)
T d1q5qh_         160 EETALRAAIESLYDAADDDSATGGPDLTRGIYPTAVTITQAG-AVHVSEETTSELARRIVAERT  222 (224)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTTCCCBTTTTBCCEEEEEETTE-EEECCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhccccCCcccccccceEEEEEeCCc-EEEcCHHHHHHHHHHHHHHHh
Confidence             999999999999998752   2       258999999999 999999999999999988764

>d1rypi_ d.153.1.4 (I:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=6.5e-40  Score=275.36  Aligned_cols=183  Identities=22%  Similarity=0.248  Sum_probs=169.1

Q ss_pred             CcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      ||+|||+++||||||+|+|.+. .++.+++.+||++|++|++|+++|..+|++.+.+.++.++..|++.++.++++..++
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            6899999999999999999887 466777899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETIK  188 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai~  188 (249)
                      +++++.++.     ..+||++++|++|+|  ++||+||.+||+|++.+++++|+|+|+++++++|++.|+++|+ +||++
T Consensus        81 ~~l~~~~~~-----~~~p~~~~~l~aG~d--~~g~~Ly~id~~G~~~~~~~~a~Gsg~~~a~~~Le~~~k~~ms~eea~~  153 (222)
T d1rypi_          81 QMLKQHLFK-----YQGHIGAYLIVAGVD--PTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIK  153 (222)
T ss_dssp             HHHHHHHHH-----TTTCSCEEEEEEEEE--TTEEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHHCCSSCCHHHHHH
T ss_pred             HHHHHHHHh-----hhhccceeEEEEEEc--CCCcEEEEEecCcceEEeeEEEECCCcHHHHHHHHhhccCCCCHHHHHH
Confidence            999988753     247999999999999  5899999999999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcC
Q 025716          189 LAIRALLEVVES---GGKNIEVAVMTREKGLKQLD  220 (249)
Q Consensus       189 la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~  220 (249)
                      ++++||+.+.++   ++++++|+++++++..+++.
T Consensus       154 l~~~al~~a~~~D~~sg~~i~i~vi~~~~~~~~~~  188 (222)
T d1rypi_         154 LASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLR  188 (222)
T ss_dssp             HHHHHHHHHHHHCTTCCSCEEEEEEETTSCEEEEE
T ss_pred             HHHHHHHHHhcccCCCCCcEEEEEEEcCCCeEEec
Confidence            999999999876   47899999999876566554

>d1iru2_ d.153.1.4 (2:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=9.4e-41  Score=279.43  Aligned_cols=195  Identities=16%  Similarity=0.188  Sum_probs=176.0

Q ss_pred             HHHccCCcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhh-hcCCC
Q 025716           25 EAVRKGNAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRL-TVEDP  102 (249)
Q Consensus        25 kav~~G~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~-~~~~~  102 (249)
                      +++.+|+|+|||+++||||||+|+|.+. .++..++.+||++|++|++++++|..+|++.|.+.++.++..|++ .++.+
T Consensus         3 ~~~~~GtTivgi~~~dgVviaaD~r~t~g~~~~~~~~~KI~~i~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~   82 (217)
T d1iru2_           3 NPMVTGTSVLGVKFEGGVVIAADMLGSYGSLARFRNISRIMRVNNSTMLGASGDYADFQYLKQVLGQMVIDEELLGDGHS   82 (217)
T ss_dssp             SCCSEECCCEEEEETTEEEEEEECCEEETTEEEECSCCCEEEETTTEEEEEEEEHHHHHHHHHHHHHHHHHHHHHCSSCC
T ss_pred             CCcCcccEEEEEEECCEEEEEEcCCcccCCeeecCCcceEEEeCCCeEEEeccccHHHHHHHHHHHHHHHHhhhhcCCCC
Confidence            3567899999999999999999999876 567778899999999999999999999999999999999988765 45799


Q ss_pred             CCHHHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhc--c
Q 025716          103 VTVEYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK--E  180 (249)
Q Consensus       103 i~~~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~--~  180 (249)
                      ++++.+++++++++  |+++...|||++++|++|+|  +++|+||.+||+|++.+++++|+|+|+.+++++|++.|+  +
T Consensus        83 ~~v~~~a~~l~~~~--y~~~~~~~p~~~~~li~G~d--~~~~~l~~~D~~G~~~~~~~~a~G~g~~~a~~~Le~~~~~~~  158 (217)
T d1iru2_          83 YSPRAIHSWLTRAM--YSRRSKMNPLWNTMVIGGYA--DGESFLGYVDMLGVAYEAPSLATGYGAYLAQPLLREVLEKQP  158 (217)
T ss_dssp             CCHHHHHHHHHHHH--HHHHHTTCCCCEEEEEEEEE--TTEEEEEEECSSCCEEECSEEECTTHHHHTHHHHHHHHTSCS
T ss_pred             CCHHHHHHHHHHHH--HHhccccCcccceEEEEEEc--CCCcEEEEEecCceeEeeeEEeccCcHHHHHHHHHHHhcccC
Confidence            99999999999987  56666789999999999999  689999999999999999999999999999999999775  8


Q ss_pred             CCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCHHHH
Q 025716          181 TSG-QETIKLAIRALLEVVES---GGKNIEVAVMTREKGLKQLDEAEI  224 (249)
Q Consensus       181 ~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~~ei  224 (249)
                      +|+ +||++++++||+.+.++   ++++++|++|+++| +++..+.++
T Consensus       159 ~lt~~ea~~l~~~al~~a~~rd~~sg~~i~i~vi~~~G-~~~~~~~~~  205 (217)
T d1iru2_         159 VLSQTEARDLVERCMRVLYYRDARSYNRFQTATVTEKG-VEIEGPLST  205 (217)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHBTTCCSCEEEEEEETTE-EEEEEEECC
T ss_pred             CCCHHHHHHHHHHHHHHHHHhcCcCCCcEEEEEEeCCC-EEEcCCeec
Confidence            999 99999999999999875   57899999999998 776655444

>d1iruj_ d.153.1.4 (J:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=1.2e-39  Score=270.18  Aligned_cols=185  Identities=17%  Similarity=0.297  Sum_probs=170.0

Q ss_pred             ccCCcEEEEEeCCEEEEEEeccCCcc-cccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHH
Q 025716           28 RKGNAAVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVE  106 (249)
Q Consensus        28 ~~G~t~igi~~~dgVvla~d~~~~~~-l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~  106 (249)
                      -||+|+|||+++||||||+|++.+.+ ++.+++.+||++|++|++++++|..+|++.+.++++.+++.|++.++.+++++
T Consensus         5 ~nG~Tvigi~~~dgVvlaaD~r~s~g~~~~~~~~~Ki~~I~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~   84 (204)
T d1iruj_           5 YNGGAVMAMKGKNCVAIAADRRFGIQAQLVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFRLNLYELKEGRQIKPY   84 (204)
T ss_dssp             SSCCEEEEEECSSEEEEEEECCEEETTEEEESCCCCEEECSTTEEEECCSCHHHHHHHHHHHHHHHHHHHHHSSSCCCHH
T ss_pred             eCCceEEEEEECCEEEEEECCCcccCCeeEcCcccEEEEeCCCeEEEeccCchHHHHHHHHHHHhhhhhhhhcccccchH
Confidence            48999999999999999999999874 56678899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceecc-ceEeecCCchHHHHHHHhhhccCCc-H
Q 025716          107 YITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAW-KANATGRNSNSMREFLEKNYKETSG-Q  184 (249)
Q Consensus       107 ~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~-~~~aiG~g~~~a~~~Le~~~~~~~s-e  184 (249)
                      .++++++++++.+    ..+||+|++||||||+...+|.+|.+||.|....+ +++++|++++.++++|++.|+++|+ +
T Consensus        85 ~~a~~l~~~~~~~----~~~p~~~~~lvaG~D~~~~~~~~~~~d~~g~~~~~~~~~~~G~g~~~~~~~l~~~~~~~ms~~  160 (204)
T d1iruj_          85 TLMSMVANLLYEK----RFGPYYTEPVIAGLDPKTFKPFICSLDLIGCPMVTDDFVVSGTCAEQMYGMCESLWEPNMDPD  160 (204)
T ss_dssp             HHHHHHHHHHHTT----TTSCCSCCCEEEEECTTSCCEEEEEECTTCCEEECSSEEEEETTHHHHHHHHHHHCCSSCCHH
T ss_pred             HHHHHHHHHHHHh----hhccceeEEEEEEEcCCCCceEEEEecCCCceeeecceEEechhHHHHHHHHHhccccCCCHH
Confidence            9999999998764    35799999999999973457889999999987664 6899999999999999999999999 9


Q ss_pred             HHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCCEE
Q 025716          185 ETIKLAIRALLEVVES---GGKNIEVAVMTREKGLK  217 (249)
Q Consensus       185 eai~la~~~l~~~~~~---~~~~iei~~v~~~g~~~  217 (249)
                      ||++++++||+.+.++   ++++++|++|+++| ++
T Consensus       161 ea~~l~~~al~~a~~rd~~sg~~~~v~ii~k~g-i~  195 (204)
T d1iruj_         161 HLFETISQAMLNAVDRDAVSGMGVIVHIIEKDK-IT  195 (204)
T ss_dssp             HHHHHHHHHHHHHGGGBTTSCSCEEEEEEESSB-EE
T ss_pred             HHHHHHHHHHHHHHhhcccCCCcEEEEEEeCCC-EE
Confidence            9999999999999875   57899999999998 44

>d1rypj_ d.153.1.4 (J:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=3.6e-39  Score=266.92  Aligned_cols=182  Identities=19%  Similarity=0.293  Sum_probs=167.7

Q ss_pred             ccCCcEEEEEeCCEEEEEEeccCCcc-cccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHH
Q 025716           28 RKGNAAVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVE  106 (249)
Q Consensus        28 ~~G~t~igi~~~dgVvla~d~~~~~~-l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~  106 (249)
                      .||+|+|||+++||||||+|++.+.+ +...++.+|||++ +|++++++|..+|++.|.++++.+++.|+++++.+++++
T Consensus         6 ~nG~Tivgi~~~d~VvlaaD~r~~~~~~~~~~~~~Ki~~i-~~i~~~~~G~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~   84 (204)
T d1rypj_           6 INGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHY-GHVFLGITGLATDVTTLNEMFRYKTNLYKLKEERAIEPE   84 (204)
T ss_dssp             SSCCEEEEEECSSEEEEEEECCEEETTEEEESCCCCEEEE-TTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHH
T ss_pred             cCCeEEEEEEECCEEEEEEcCCcccCCEeecCcccEEEEc-CCEEEEecCcchHHHHHHHHHHHHHHHHHHhcCCCCcch
Confidence            47999999999999999999998874 5666789999999 599999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceecc-ceEeecCCchHHHHHHHhhhccCCc-H
Q 025716          107 YITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAW-KANATGRNSNSMREFLEKNYKETSG-Q  184 (249)
Q Consensus       107 ~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~-~~~aiG~g~~~a~~~Le~~~~~~~s-e  184 (249)
                      .+++++++.++.++    .+||+|++|++|||+.++.|+||.+||+|++.++ .++++|+|+..++++|++.|+++|+ +
T Consensus        85 ~la~~l~~~l~~~~----~~p~~v~~li~G~d~~~g~~~L~~~D~~G~~~~~~~~~~~G~g~~~a~~~l~~~~~~~ms~~  160 (204)
T d1rypj_          85 TFTQLVSSSLYERR----FGPYFVGPVVAGINSKSGKPFIAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPE  160 (204)
T ss_dssp             HHHHHHHHHHHTTT----TSCCCEEEEEEEECTTTCCEEEEEECTTCCEECCSSEEEEETTHHHHHHHHHHHCCSSCCHH
T ss_pred             HHHHHHHHHHHhhc----ccceeeeEEEEEEecCCCcceEEEeCCCCccccccCcEEeecchHHHHHHHHhccccCCCHH
Confidence            99999999986543    4799999999999974556999999999999876 5888999999999999999999999 9


Q ss_pred             HHHHHHHHHHHHHHhc---CCCcEEEEEEEcCC
Q 025716          185 ETIKLAIRALLEVVES---GGKNIEVAVMTREK  214 (249)
Q Consensus       185 eai~la~~~l~~~~~~---~~~~iei~~v~~~g  214 (249)
                      ||++++++||..+.++   ++++++|++|+++|
T Consensus       161 ea~~l~~~al~~a~~~d~~sg~~~~v~ii~kdg  193 (204)
T d1rypj_         161 DLFETISQALLNAADRDALSGWGAVVYIIKKDE  193 (204)
T ss_dssp             HHHHHHHHHHHHHHTTBTTSCSCEEEEEEESSC
T ss_pred             HHHHHHHHHHHHHHHhcCccCCeEEEEEEECCc
Confidence            9999999999999876   47899999999998

>d1ryp1_ d.153.1.4 (1:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=2.2e-39  Score=271.74  Aligned_cols=184  Identities=22%  Similarity=0.398  Sum_probs=167.3

Q ss_pred             ccCCcEEEEEeCCEEEEEEeccCCcc-cccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcC-CCCCH
Q 025716           28 RKGNAAVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVE-DPVTV  105 (249)
Q Consensus        28 ~~G~t~igi~~~dgVvla~d~~~~~~-l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~-~~i~~  105 (249)
                      +||+|+|||+++||||||+|++.+.. ++..++.+||++|++|++++++|..+|++.+.++++.++..|++.++ ..+++
T Consensus         7 ~nG~Tivgi~~~dgVviaaD~r~s~~~~i~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~   86 (222)
T d1ryp1_           7 DNGGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKLSI   86 (222)
T ss_dssp             CCCCEEEEEECSSCEEEEEECCEEETTEEEESCCCCCEECSTTCEEEEEESHHHHHHHHHHHHHHHHHHHHHTTTCCCCH
T ss_pred             CCCcEEEEEEECCEEEEEECCCcccCCEeccCCcceEEEecCCEEEEeccChHHHHHHHHHHHHHhhhhhhhcCCCCCcH
Confidence            68999999999999999999998874 45667899999999999999999999999999999999999998876 67888


Q ss_pred             HHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhc------
Q 025716          106 EYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK------  179 (249)
Q Consensus       106 ~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~------  179 (249)
                      ..++++++.+++    ..+.|||+|++||+|+|+ +++|+||.+||+|++.+++++|+|+|+++++++||+.|+      
T Consensus        87 ~~~~~~~~~~~~----~~~~~p~~~~~li~G~d~-~~~~~Ly~~D~~G~~~~~~~~a~G~g~~~a~~~Le~~~~~~~~~~  161 (222)
T d1ryp1_          87 NSAARNIQHLLY----GKRFFPYYVHTIIAGLDE-DGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYE  161 (222)
T ss_dssp             HHHHHHHHHHHH----TTTTSCCCEEEEEEEECT-TSCEEEEEECTTSCEEEESEEEEETTHHHHHHHHHHHTSCTTCBC
T ss_pred             HHHHHHHHHHHH----hhhhhhheeeeeEEEEeC-CCCeEEEEECCCcEEEEeceEEEcccHHHHHHHHHHhhccccccC
Confidence            888887776654    346799999999999997 778999999999999999999999999999999999997      


Q ss_pred             -----------cCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCCEE
Q 025716          180 -----------ETSG-QETIKLAIRALLEVVES---GGKNIEVAVMTREKGLK  217 (249)
Q Consensus       180 -----------~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g~~~  217 (249)
                                 ++|+ +||++++++||..+.++   ++++++|++|++|| ++
T Consensus       162 ~~~~~~~~~~~~~lt~~ea~~l~~~al~~a~~rd~~sg~~v~v~iitkdG-v~  213 (222)
T d1ryp1_         162 PGTNGKVKKPLKYLSVEEVIKLVRDSFTSATERHIQVGDGLEILIVTKDG-VR  213 (222)
T ss_dssp             TTSTTCSBCCCCCCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTE-EE
T ss_pred             cccchhhhcccccccHHHHHHHHHHHHHHHHHhcccCCCcEEEEEEeCCC-EE
Confidence                       6899 99999999999999875   46789999999998 54

>d1iruk_ d.153.1.4 (K:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=2.4e-38  Score=259.17  Aligned_cols=189  Identities=16%  Similarity=0.278  Sum_probs=175.6

Q ss_pred             CCcEEEEEeCCEEEEEEeccCCcc-cccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHH
Q 025716           30 GNAAVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYI  108 (249)
Q Consensus        30 G~t~igi~~~dgVvla~d~~~~~~-l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l  108 (249)
                      ++++|||+++||||||+|++.+.+ ++.+++.+||++|+++++++++|..+|++.+.++++.++..|..+++.+++++.+
T Consensus         1 Mt~ivgi~~kdgVviaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~~G~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~   80 (199)
T d1iruk_           1 MEYLIGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYIQKNVQLYKMRNGYELSPTAA   80 (199)
T ss_dssp             CCCEEEEECSSEEEEEEECCEEETTEEEESSCCCEEECSSSEEEEEEESTTHHHHHHHHHHHHHHHHHHHHSSCCCHHHH
T ss_pred             CeEEEEEEECCEEEEEECCCccCCCeeecCCcceEEEecCcEEEEecccchHHHHHHHHHHHHhhhhhhhcCCcCcHHHH
Confidence            689999999999999999998874 4556788999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHH
Q 025716          109 TRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETI  187 (249)
Q Consensus       109 a~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai  187 (249)
                      ++.++..++.+.+  ..+|++++++++|+|+ +++|+||.+||.|.+..++++++|+|+.+++++|++.|+++|+ +||+
T Consensus        81 ~~~l~~~~~~~~~--~~~~~~~~~~~aG~d~-~~~~~l~~~~~~g~~~~~~~~a~G~gs~~a~~~l~~~~~~~~~~~ea~  157 (199)
T d1iruk_          81 ANFTRRNLADCLR--SRTPYHVNLLLAGYDE-HEGPALYYMDYLAALAKAPFAAHGYGAFLTLSILDRYYTPTISRERAV  157 (199)
T ss_dssp             HHHHHHHHHHHHT--SSSCCCEEEEEEEEET-TTEEEEEEECTTCCEEECSEEEESHHHHHHHHHHHHHCCTTCCHHHHH
T ss_pred             HHHHHHHHHHHhh--ccCCcceeeeecceec-cCCceEEeecccceEEeeeeeeecccchhhhHHHHHhccCCCCHHHHH
Confidence            9999998876654  4589999999999997 7899999999999999999999999999999999999999999 9999


Q ss_pred             HHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEEcCHH
Q 025716          188 KLAIRALLEVVES---GGKNIEVAVMTREKGLKQLDEA  222 (249)
Q Consensus       188 ~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~~~~~  222 (249)
                      +++++||..+.++   ++++++|++|+++| ++++++.
T Consensus       158 ~l~~~al~~~~~~d~~sg~~~~v~vv~~~g-~~~~~~~  194 (199)
T d1iruk_         158 ELLRKCLEELQKRFILNLPTFSVRIIDKNG-IHDLDNI  194 (199)
T ss_dssp             HHHHHHHHHHHHTBCBCCCCEEEEEEETTE-EECCCCB
T ss_pred             HHHHHHHHHHHHhcCCcCCceEEEEEcCCC-eEEcCCc
Confidence            9999999999875   57899999999999 8887754

>d1iru1_ d.153.1.4 (1:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=3e-37  Score=256.10  Aligned_cols=185  Identities=16%  Similarity=0.331  Sum_probs=171.4

Q ss_pred             ccCCcEEEEEeCCEEEEEEeccCCcc-cccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHH
Q 025716           28 RKGNAAVGVRGTDTIVLGVEKKSTVK-LQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVE  106 (249)
Q Consensus        28 ~~G~t~igi~~~dgVvla~d~~~~~~-l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~  106 (249)
                      .||+|+|||+++||||||+|++.+.+ ++.+.+.+||++|++|++++++|..+|++.+.++++.+++.|+.+++.++++.
T Consensus         7 ~nG~Tivai~~~dgVviaaD~r~t~g~~~~~~~~~KI~~i~~~i~~~~aG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~   86 (213)
T d1iru1_           7 FNGGTILAIAGEDFAIVASDTRLSEGFSIHTRDSPKCYKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMTTG   86 (213)
T ss_dssp             CCCCEEEEEEETTEEEEEEECCEEETTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHH
T ss_pred             CCCcEEEEEEECCEEEEEECCccccCceeeccccCEEEEcCCCEEEEecCccchHHHHHHHHHHHHHHHHHhhCCchhHH
Confidence            58999999999999999999998874 56667899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhc-------
Q 025716          107 YITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK-------  179 (249)
Q Consensus       107 ~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~-------  179 (249)
                      .++++++..++.++    .+|++++++++|+|+ +++|++|.+||.|++..++++++|+|+.++.++|++.|+       
T Consensus        87 ~~~~~~~~~~~~~~----~~~~~~~~~~~g~d~-~~~~~l~~~d~~g~~~~~~~~a~G~g~~~a~~~l~~~~~~~~~~~~  161 (213)
T d1iru1_          87 AIAAMLSTILYSRR----FFPYYVYNIIGGLDE-EGKGAVYSFDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNV  161 (213)
T ss_dssp             HHHHHHHHHHHTTT----TSCCCEEEEEEEECT-TSCEEEEEECTTSCEEEESEEEEETTHHHHHHHHHHHTTCCSCSSC
T ss_pred             HHHHHHHHHHHHHH----hhhcccccceEEEec-CCCcEEEecCCcceeeecCeeeecCccHHHHHHHHHhhcccchhcc
Confidence            99999999997654    469999999999998 889999999999999999999999999999999998875       


Q ss_pred             --cCCc-HHHHHHHHHHHHHHHhc---CCCcEEEEEEEcCCCEEE
Q 025716          180 --ETSG-QETIKLAIRALLEVVES---GGKNIEVAVMTREKGLKQ  218 (249)
Q Consensus       180 --~~~s-eeai~la~~~l~~~~~~---~~~~iei~~v~~~g~~~~  218 (249)
                        ++|+ +||++++++||..+.++   ++.+++|++|+++| ++.
T Consensus       162 ~~~~~s~~ea~~~~~~~l~~~~~~d~~sg~~~~v~~i~k~G-~~~  205 (213)
T d1iru1_         162 EHVPLSLDRAMRLVKDVFISAAERDVYTGDALRICIVTKEG-IRE  205 (213)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHHHBTTSCSEEEEEEEETTE-EEE
T ss_pred             cccCCCHHHHHHHHHHHHHHHHHhcCCCCCceEEEEEeCCC-EEE
Confidence              6799 99999999999999875   57789999999998 543

>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=99.89  E-value=1.1e-22  Score=163.95  Aligned_cols=169  Identities=13%  Similarity=0.013  Sum_probs=122.6

Q ss_pred             cCCcEEEEEeCCEEEEEEeccCCc-ccc-cCCcccceEEecCC-EEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCH
Q 025716           29 KGNAAVGVRGTDTIVLGVEKKSTV-KLQ-DSRSVRKIVSLDNH-IALACAGLKADARVLINRARIECQSHRLTVEDPVTV  105 (249)
Q Consensus        29 ~G~t~igi~~~dgVvla~d~~~~~-~l~-~~~~~~Ki~~I~~~-i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~  105 (249)
                      +|||+|||+|+||||||+|+|.+. .++ .+...+|++.++++ ++++.+|...|.+.+.+.++.+...+.....     
T Consensus         4 ~GTTivai~~~dGVvlAaDtR~S~G~~i~~~~~~~ki~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~-----   78 (180)
T d2z3ba1           4 HATTIFAVQHKGRSAMSGDGQVTFGQAVVMKHTARKVRKLFNGKVLAGFAGSVADAFTLFEKFEAKLEEYNGNLK-----   78 (180)
T ss_dssp             CCCCEEEEEETTEEEEEECCCEEETTTEEEESCCCCEEEETTTTEEEEECSCHHHHHHHHHHHHHHHHHTTTCHH-----
T ss_pred             CCeEEEEEEECCEEEEEECCcccCCceeEecccceEEEEecccceecccchHHHHHHHHHHHHHHHHHhhccccc-----
Confidence            799999999999999999999986 343 34568899999875 7777899999999999888777655543221     


Q ss_pred             HHHHHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-H
Q 025716          106 EYITRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-Q  184 (249)
Q Consensus       106 ~~la~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-e  184 (249)
                      ..+.............+....++.+.....|++  ..++.++..+++|      +.++|+|+.+|.+.|+..|+++|+ +
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~------~~a~GSGs~~A~g~l~~~~~~~~s~~  150 (180)
T d2z3ba1          79 RAAVELAKEWRSDKVLRKLEAMLIVMNQDTLLL--VSGTGEVIEPDDG------ILAIGSGGNYALAAGRALKKHAGESM  150 (180)
T ss_dssp             HHHHHHHHHHHHCTTGGGCCCCEEEECSSCEEE--ECTTCCEECCSSS------EEEESTTHHHHHHHHHHHHHHHGGGC
T ss_pred             hhHHHHHHHHhHHHHHHHhhcceeeeecccccc--ccCCceeeccccc------EEEEcCchHHHHHHHHHHhhcCCCcc
Confidence            222222222222222222334444444455555  3456666665554      889999999999999999999999 9


Q ss_pred             HHHHHHHHHHHHHHhc---CCCcEEEEEE
Q 025716          185 ETIKLAIRALLEVVES---GGKNIEVAVM  210 (249)
Q Consensus       185 eai~la~~~l~~~~~~---~~~~iei~~v  210 (249)
                      ||++++++||+.+.++   ++++++|..|
T Consensus       151 eA~~l~~~Al~~A~e~dvyT~~~~~~~~i  179 (180)
T d2z3ba1         151 SASEIARAALETAGEICVYTNDQIILEEL  179 (180)
T ss_dssp             CHHHHHHHHHHHHHHHCTTCCSCCEEEEE
T ss_pred             CHHHHHHHHHHHHHhhcEEcCCcEEEEEe
Confidence            9999999999998875   4667777665

>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=99.87  E-value=1.6e-22  Score=161.36  Aligned_cols=165  Identities=13%  Similarity=-0.011  Sum_probs=123.1

Q ss_pred             CcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEEecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALACAGLKADARVLINRARIECQSHRLTVEDPVTVEYIT  109 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la  109 (249)
                      ||+|||+++||||||+|+|.+. .++.+++.+||++|+++++++.+|..+|.+.+......+...+...  .   .....
T Consensus         1 TTivav~~~~gVviAaDtR~S~G~~i~~r~~~Ki~~i~~~~~~~~~g~~ad~~~~~~~~~~~~~~~~~~--~---~~~~~   75 (171)
T d1m4ya_           1 TTILVVRRNGQTVMGGDGQVTFGSTVLKGNARKVRKLGEGKVLAGFAGSVADAMTLFDRFEAKLREWGG--N---LTKAA   75 (171)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHHHHHHHHHHTTT--C---HHHHH
T ss_pred             CeEEEEEECCEEEEEECCCcccCCEEEeCCcceEEEecCCcEEEEEeechhhHHHHHHHHHHHHHHhhc--c---chhhH
Confidence            6899999999999999999987 5777899999999999999999999999998877766655444322  1   12222


Q ss_pred             HHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhc-cCCcHHHHH
Q 025716          110 RYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYK-ETSGQETIK  188 (249)
Q Consensus       110 ~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~-~~~seeai~  188 (249)
                      ...+..+....     .++....++.+.+  +++|.++..|+.|.....+++|+|+|+.+|++.|+..++ ++|+  |.+
T Consensus        76 ~~~~~~~~~~~-----~~~~~~~~~~~~~--~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~l~~~~~~~~~~--a~e  146 (171)
T d1m4ya_          76 VELAKDWRTDR-----VLRRLEALLLVAD--KENIFIISGNGEVIQPDDDAAAIGSGGPYALAAAKALLRNTDLS--ARE  146 (171)
T ss_dssp             HHHHHHHHHCT-----TGGGCCCEEEEEC--SSCEEEECTTSCEECCSSSEEEESTTHHHHHHHHHHHHHHCCCC--HHH
T ss_pred             HHHHHHHHHhh-----hhcccccccceec--CCcceEEecCCceeeecCCEEEEcchHHHHHHHHHhhccCCCCC--HHH
Confidence            22222222111     1222233444455  689999999999999999999999999999999998765 4664  555


Q ss_pred             HHHHHHHHHHhc---CCCcEEEEE
Q 025716          189 LAIRALLEVVES---GGKNIEVAV  209 (249)
Q Consensus       189 la~~~l~~~~~~---~~~~iei~~  209 (249)
                      ++++||+.+.+.   ++++++|..
T Consensus       147 l~~~Ai~~A~e~dvyTg~~~~i~~  170 (171)
T d1m4ya_         147 IVEKAMTIAGEICIYTNQNIVIEE  170 (171)
T ss_dssp             HHHHHHHHHHHHCTTCCSCCEEEE
T ss_pred             HHHHHHHHHHhhceEcCCcEEEEE
Confidence            788888877765   567777754

>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=99.84  E-value=1.5e-20  Score=150.11  Aligned_cols=166  Identities=16%  Similarity=0.043  Sum_probs=117.4

Q ss_pred             CcEEEEEeCCEEEEEEeccCCc-ccccCCcccceEEecCCEEEEE-ecChhhHHHHHHHHHHHHHHhhhhcCCCCCHHHH
Q 025716           31 NAAVGVRGTDTIVLGVEKKSTV-KLQDSRSVRKIVSLDNHIALAC-AGLKADARVLINRARIECQSHRLTVEDPVTVEYI  108 (249)
Q Consensus        31 ~t~igi~~~dgVvla~d~~~~~-~l~~~~~~~Ki~~I~~~i~~~~-sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~l  108 (249)
                      ||+|||+++||||||+|+|.+. .++.+++.+||++|+++++++. +|...+.+.+.+..+.....+      .......
T Consensus         1 TTivai~~~dGVVlAaDtRaS~G~~i~~r~~~Ki~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~   74 (173)
T d1g3ka_           1 TTIVSVRRNGQVVVGGDGQVSLGNTVMKGNARKVRRLYNGKVLAGFAGGTADAFTLFELFERKLEMH------QGHLLKS   74 (173)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHHHHHHHHHHT------TTCHHHH
T ss_pred             CeEEEEEECCEEEEEECCCcccCCEeEcCCcceEEEecCCcEEEEeeehhHhHHHHHHHHHHHHHhh------cCcchhH
Confidence            6899999999999999999988 5677899999999988865554 555544444443333222222      1222333


Q ss_pred             HHHHHHHHHhhhccCCCccceeEEEEEeeeCCCCCceEEEECCCCceeccceEeecCCchHHHHHHHhhhccCCc-HHHH
Q 025716          109 TRYIAGLQQKYTQSGGVRPFGLSTLIVGFDPYTGVPSLYQTDPSGTFSAWKANATGRNSNSMREFLEKNYKETSG-QETI  187 (249)
Q Consensus       109 a~~ls~~~~~~t~~~~~rP~gv~~ivaG~d~~~~gp~Ly~iDp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s-eeai  187 (249)
                      +..++..+..    ....+.....++ +.+. ++++.++..|+.|.+.+.++.|+|+|+.+|.+.|+.+++  ++ ++|.
T Consensus        75 ~~~~~~~~~~----~~~~~~~~~~~~-~~~~-~~~~~~~~~~~~~~~~~~~~~a~GSGs~~A~~~l~~~~~--~~~~~A~  146 (173)
T d1g3ka_          75 AVELAKDWRT----DRALRKLEAMLI-VADE-KESLIITGIGDVVQPEEDQILAIGSGGNYALSAARALVE--NTELSAH  146 (173)
T ss_dssp             HHHHHHHHHH----STTGGGCCCEEE-EECS-SCEEEEETTTEEECCCTTCEEEESTTHHHHHHHHHHHHH--HCCCCHH
T ss_pred             HHHHHHHHHH----hhhhcccccccc-cccC-CCcceecccCceEEecCCCEEEecchHHHHHHHHHHhhh--cCCCCHH
Confidence            3333333321    122333344444 4454 789999999999999999999999999999999998875  45 6788


Q ss_pred             HHHHHHHHHHHhc---CCCcEEEEEE
Q 025716          188 KLAIRALLEVVES---GGKNIEVAVM  210 (249)
Q Consensus       188 ~la~~~l~~~~~~---~~~~iei~~v  210 (249)
                      +++++||+.+.++   ++++++|-.|
T Consensus       147 ela~~Ai~~Aae~dvyTgd~~~i~~~  172 (173)
T d1g3ka_         147 EIVEKSLRIAGDICVFTNTNFTIEEL  172 (173)
T ss_dssp             HHHHHHHHHHHHHCTTCCSCCEEEEE
T ss_pred             HHHHHHHHHHHhhcEEcCCcEEEEEC
Confidence            8999999988875   4677777654