Citrus Sinensis ID: 040809

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-
Protein Sequence
MSRRYDRQTTVFSPEGRLYQVDYMGCLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFGVAQPASEVS
Secondary Structure (PSIPRED)
ccccccccccccccccccHHHHHHEEHHHHccccccccccccccccEEEEcccEEEEEcccHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHccccEEEcccccccEEEEEEcccccEEEEccccHHHHHHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHcccccccccccccHHHHHHHHHcccccccEccEccccccccEEEccccEEEEEEEcHHHHHHHHHHHHHHHHHHHHHHcccccHccccccHHHHHHHHHHHHHHHcccccccHHHEEEEEEEEcccccEEEEEccHHHHHHHHHHccccccccccc
Coil and Loop (DISEMBL)
msrrydrqttvfspegrlyqvDYMGclvgennvtSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYqepiqdykdDMTRQEAVQLALKVLRKtmdstsltsekLELAEVFllpsgkvkyricspESLTMLLEnfgvaqpasevs
Flexible Loop (DISEMBL)
msrrydrqttvfspegrlyQVDYMGCLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPiqdykddmTRQEAVQLALKVLRKtmdstsltseklelaevfllpsgkvkYRICSPESLTMLLENfgvaqpasevs
Low Complexity Region (SEG)
MSRRYDRQTTVFSPEGRLYQVDYMGCLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTarvqarryayayqEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFGVAQPASEVS
Disordered region (IsUnstruct)
**********VFSPEGRLYQVDYMGCLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQDYKDDMTRQEAVQLALKVLRKTMD**SLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFGV********
Disordered Region (DISOPRED)
*SRRYDRQTTVFSPEGRLYQVDYMGCLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLEN***********
Disordered Region (DISEMBL)
*********TVFSPEGRLYQVDYMGCLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFGV********
Disordered Region (DISPRO)
*****DRQTTVFSPEGRLYQVDYMGCLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFGV********
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSRRYDRQTTVFSPEGRLYQVDYMGCLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFGVAQPASEVS
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	161	2.2.26 [Sep-21-2011]
O82530	249	Proteasome subunit alpha	N/A	no	0.540	0.349	0.695	5e-35
O81148	250	Proteasome subunit alpha	no	no	0.540	0.348	0.695	5e-35
P52427	250	Proteasome subunit alpha	N/A	no	0.540	0.348	0.685	1e-34
Q5VRG3	250	Proteasome subunit alpha	yes	no	0.540	0.348	0.666	1e-32
P0C8Y9	250	Proteasome subunit alpha	N/A	no	0.540	0.348	0.666	1e-32
P0C1G8	250	Proteasome subunit alpha	yes	no	0.540	0.348	0.666	1e-32
A2Y9X7	250	Proteasome subunit alpha	N/A	no	0.540	0.348	0.666	1e-32
P34119	250	Proteasome subunit alpha	yes	no	0.540	0.348	0.547	5e-25
P23638	258	Proteasome subunit alpha	yes	no	0.534	0.333	0.5	1e-20
Q9R1P0	261	Proteasome subunit alpha	yes	no	0.540	0.333	0.476	9e-19

>sp|O82530|PSA4_PETHY Proteasome subunit alpha type-4 OS=Petunia hybrida GN=PAC1 PE=2 SV=1

 Score =  146 bits (369), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 73/105 (69%), Positives = 82/105 (78%), Gaps = 18/105 (17%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTST 42
           MSRRYD +TT+FSPEGRLYQV+Y           +G        LVGE  VTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGISSKDGVVLVGEKKVTSKLLQTST 60

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           S+EKMYKIDDHVACAVAGIMSDANILINTARVQA+RY ++YQEP+
Sbjct: 61  SSEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTFSYQEPM 105

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.
Petunia hybrida (taxid: 4102)
EC: 3EC: .EC: 4EC: .EC: 2EC: 5EC: .EC: 1

>sp|O81148|PSA4_ARATH Proteasome subunit alpha type-4 OS=Arabidopsis thaliana GN=PAC1 PE=1 SV=1

 Score =  146 bits (369), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 73/105 (69%), Positives = 81/105 (77%), Gaps = 18/105 (17%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTST 42
           MSRRYD +TT+FSPEGRLYQV+Y           +G        L+GE  VTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLIGEKKVTSKLLQTST 60

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           SAEKMYKIDDHVACAVAGIMSDANILINTARVQA+RY + YQEP+
Sbjct: 61  SAEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTFMYQEPM 105

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

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|P52427|PSA4_SPIOL Proteasome subunit alpha type-4 OS=Spinacia oleracea GN=PAC1 PE=2 SV=1

 Score =  145 bits (365), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 72/105 (68%), Positives = 81/105 (77%), Gaps = 18/105 (17%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTST 42
           MSRRYD +TT+FSPEGRLYQV+Y           +G        L+GE  VTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILAKDGVVLIGEKKVTSKLLQTST 60

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           S EKMYKIDDHVACAVAGIMSDANILINTARVQA+RY ++YQEP+
Sbjct: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTFSYQEPM 105

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.

Spinacia oleracea (taxid: 3562)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|Q5VRG3|PSA4B_ORYSJ Proteasome subunit alpha type-4-2 OS=Oryza sativa subsp. japonica GN=Os06g0167600 PE=2 SV=1

 Score =  139 bits (349), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 70/105 (66%), Positives = 79/105 (75%), Gaps = 18/105 (17%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MGCL-------VGENNVTSKLLQTST 42
           MSRRYD +TT+FSPEGRLYQV+Y           +G L       VGE  VTSKLLQTS 
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSALGVLAADGVVLVGEKKVTSKLLQTSR 60

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           SAEKMYKID H+ACAVAGIMSDANIL+NTAR+ A+RYA +YQEPI
Sbjct: 61  SAEKMYKIDSHLACAVAGIMSDANILLNTARLHAQRYALSYQEPI 105

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|P0C8Y9|PSA4B_ORYSI Proteasome subunit alpha type-4-2 OS=Oryza sativa subsp. indica GN=OsI_021067 PE=1 SV=1

 Score =  139 bits (349), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 70/105 (66%), Positives = 79/105 (75%), Gaps = 18/105 (17%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MGCL-------VGENNVTSKLLQTST 42
           MSRRYD +TT+FSPEGRLYQV+Y           +G L       VGE  VTSKLLQTS 
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSALGVLAADGVVLVGEKKVTSKLLQTSR 60

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           SAEKMYKID H+ACAVAGIMSDANIL+NTAR+ A+RYA +YQEPI
Sbjct: 61  SAEKMYKIDSHLACAVAGIMSDANILLNTARLHAQRYALSYQEPI 105

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|P0C1G8|PSA4A_ORYSJ Proteasome subunit alpha type-4-1 OS=Oryza sativa subsp. japonica GN=PAC1 PE=2 SV=1

 Score =  139 bits (349), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 70/105 (66%), Positives = 79/105 (75%), Gaps = 18/105 (17%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MGCL-------VGENNVTSKLLQTST 42
           MSRRYD +TT+FSPEGRLYQV+Y           +G L       VGE  VTSKLLQTS 
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSALGVLAADGVVLVGEKKVTSKLLQTSR 60

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           SAEKMYKID H+ACAVAGIMSDANIL+NTAR+ A+RYA +YQEPI
Sbjct: 61  SAEKMYKIDSHLACAVAGIMSDANILLNTARLHAQRYALSYQEPI 105

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|A2Y9X7|PSA4A_ORYSI Proteasome subunit alpha type-4-1 OS=Oryza sativa subsp. indica GN=OsI_021120 PE=1 SV=2

 Score =  139 bits (349), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 70/105 (66%), Positives = 79/105 (75%), Gaps = 18/105 (17%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MGCL-------VGENNVTSKLLQTST 42
           MSRRYD +TT+FSPEGRLYQV+Y           +G L       VGE  VTSKLLQTS 
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSALGVLAADGVVLVGEKKVTSKLLQTSR 60

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           SAEKMYKID H+ACAVAGIMSDANIL+NTAR+ A+RYA +YQEPI
Sbjct: 61  SAEKMYKIDSHLACAVAGIMSDANILLNTARLHAQRYALSYQEPI 105

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|P34119|PSA4_DICDI Proteasome subunit alpha type-4 OS=Dictyostelium discoideum GN=psmA4 PE=2 SV=1

 Score =  113 bits (282), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 58/106 (54%), Positives = 74/106 (69%), Gaps = 19/106 (17%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDYM-------GCLVG-----------ENNVTSKLLQTST 42
           M+RRYD++TT+FSPEGR+YQV+Y        G  VG           E   T+KLL +ST
Sbjct: 1   MARRYDQRTTIFSPEGRVYQVEYAMTAIRHAGATVGILAKDGIVLAAEKKTTAKLLDSST 60

Query: 43  S-AEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           S +EKM+KID+HV CAVAGI SDANILIN AR+ ++R+ Y YQEP+
Sbjct: 61  SISEKMFKIDEHVVCAVAGITSDANILINYARLSSQRFFYQYQEPM 106

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|P23638|PSA3_YEAST Proteasome subunit alpha type-3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PRE9 PE=1 SV=1

 Score = 99.4 bits (246), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 52/104 (50%), Positives = 65/104 (62%), Gaps = 18/104 (17%)

Query: 2   SRRYDRQTTVFSPEGRLYQVDYM-------GCLVG-----------ENNVTSKLLQTSTS 43
           SRRYD +TT+FSPEGRLYQV+Y        G  +G           E  VTS LL+  TS
Sbjct: 3   SRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTS 62

Query: 44  AEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
            EK+YK++D +A AVAG+ +DA ILINTAR+ A+ Y   Y E I
Sbjct: 63  TEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDI 106

The proteasome degrades poly-ubiquitinated proteins in the cytoplasm and in the nucleus. It is essential for the regulated turnover of proteins and for the removal of misfolded proteins. The proteasome is a multicatalytic proteinase complex that 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. It has an ATP-dependent proteolytic activity.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|Q9R1P0|PSA4_MOUSE Proteasome subunit alpha type-4 OS=Mus musculus GN=Psma4 PE=1 SV=1

 Score = 92.8 bits (229), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 50/105 (47%), Positives = 64/105 (60%), Gaps = 18/105 (17%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MGCLV-------GENNVTSKLLQTST 42
           MSRRYD +TT+FSPEGRLYQV+Y           +G L         E     KLL    
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF 60

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
            +EK+YK+++ +AC+VAGI SDAN+L N  R+ A+RY   YQEPI
Sbjct: 61  FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPI 105

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

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

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	161
334186554	208	N-terminal nucleophile aminohydrolases (	1.0	0.774	0.581	4e-54
217075150	229	unknown [Medicago truncatula]	1.0	0.703	0.458	2e-42
356521060	250	PREDICTED: proteasome subunit alpha type	0.540	0.348	0.723	3e-34
255540109	250	proteasome subunit alpha type, putative	0.540	0.348	0.704	6e-34
225462543	250	PREDICTED: proteasome subunit alpha type	0.540	0.348	0.714	7e-34
255637334	250	unknown [Glycine max]	0.540	0.348	0.714	8e-34
356568146	250	PREDICTED: proteasome subunit alpha type	0.540	0.348	0.714	9e-34
356496249	250	PREDICTED: proteasome subunit alpha type	0.540	0.348	0.714	9e-34
77999303	248	proteasome-like protein alpha subunit [S	0.540	0.350	0.704	1e-33
76160982	256	proteasome alpha subunit-like protein [S	0.540	0.339	0.704	2e-33

>gi|334186554|ref|NP_001190735.1| N-terminal nucleophile aminohydrolases (Ntn hydrolases)-like protein [Arabidopsis thaliana] gi|332658164|gb|AEE83564.1| N-terminal nucleophile aminohydrolases (Ntn hydrolases)-like protein [Arabidopsis thaliana]

 Score =  215 bits (548), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 121/208 (58%), Positives = 139/208 (66%), Gaps = 47/208 (22%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTST 42
           MSRRYD +TT+FSPEGRLYQV+Y           +G        LVGE  VTSKLLQTS+
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILAKDGVVLVGEKKVTSKLLQTSS 60

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRY--AYAYQ----EPI--------- 87
           S EKMYKIDDHVACAVAGIMSDANILINTARVQA+R+   + +Q    +P          
Sbjct: 61  SMEKMYKIDDHVACAVAGIMSDANILINTARVQAQRWDRNHGFQLYMSDPSGNYGGWQAA 120

Query: 88  --------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGK 133
                         QDYKDD TR+E VQLA+KVL KTMDSTSLT+EKLELAE++L PS  
Sbjct: 121 AVGANNQAAQSILKQDYKDDATREEVVQLAIKVLSKTMDSTSLTAEKLELAELYLTPSKC 180

Query: 134 VKYRICSPESLTMLLENFGVAQPASEVS 161
           VKY + SP+SLT LL   GV QPA+E S
Sbjct: 181 VKYHVHSPDSLTKLLVKHGVTQPAAETS 208

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217075150|gb|ACJ85935.1| unknown [Medicago truncatula]

 Score =  176 bits (447), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 105/229 (45%), Positives = 126/229 (55%), Gaps = 68/229 (29%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTST 42
           MSRRYD +TT+FSPEGRLYQV+Y           +G        LVGE  VTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGTAIGILSKDGVVLVGEKKVTSKLLQTST 60

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQ---------DYKDD 93
           S EKMYKIDDHV CAVAGIMSDANILINTAR+QA+RY++AYQEP+          D K  
Sbjct: 61  STEKMYKIDDHVVCAVAGIMSDANILINTARIQAQRYSFAYQEPMPVEQLVQSLCDTKQG 120

Query: 94  MTRQEAV-----------------------------------------QLALKVLRKTMD 112
            T+   +                                         Q A  +L++   
Sbjct: 121 YTQFGGLRPFGVSFLFAGWDKNFGFQLYMSDPSGNYGGWKAGAIGANNQAAQSILKQDYK 180

Query: 113 STSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFGVAQPASEVS 161
                 E + LAEVFL PSGKVK+++CSPE+LT LL   GV QPA+E +
Sbjct: 181 DDITREEAVNLAEVFLAPSGKVKHQVCSPENLTKLLVKSGVTQPATETA 229

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356521060|ref|XP_003529176.1| PREDICTED: proteasome subunit alpha type-4-like isoform 1 [Glycine max] gi|356521062|ref|XP_003529177.1| PREDICTED: proteasome subunit alpha type-4-like isoform 2 [Glycine max]

 Score =  149 bits (377), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 76/105 (72%), Positives = 82/105 (78%), Gaps = 18/105 (17%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTST 42
           MSRRYD +TT+FSPEGRLYQV+Y           +G        LVGE  VTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGTAIGILSKDGVVLVGEKKVTSKLLQTST 60

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           S EKMYKIDDHVACAVAGIMSDANILINTARVQA+RYAYAYQEP+
Sbjct: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYAYAYQEPM 105

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255540109|ref|XP_002511119.1| proteasome subunit alpha type, putative [Ricinus communis] gi|223550234|gb|EEF51721.1| proteasome subunit alpha type, putative [Ricinus communis]

 Score =  148 bits (374), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 74/105 (70%), Positives = 79/105 (75%), Gaps = 18/105 (17%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDYM------------------GCLVGENNVTSKLLQTST 42
           MSRRYD +TT+FSPEGRLYQV+Y                     LVGE  VTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGTAIGILSKDGAVLVGEKKVTSKLLQTST 60

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           S EKMYKIDDHVACAVAGIMSDANILINTARVQA+RY YAYQEP+
Sbjct: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPM 105

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225462543|ref|XP_002266917.1| PREDICTED: proteasome subunit alpha type-4 isoform 2 [Vitis vinifera] gi|225462545|ref|XP_002266877.1| PREDICTED: proteasome subunit alpha type-4 isoform 1 [Vitis vinifera] gi|147799989|emb|CAN77245.1| hypothetical protein VITISV_018657 [Vitis vinifera]

 Score =  148 bits (374), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 75/105 (71%), Positives = 81/105 (77%), Gaps = 18/105 (17%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTST 42
           MSRRYD +TT+FSPEGRLYQV+Y           +G        LVGE  VTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGTAIGILSKDGVVLVGEKKVTSKLLQTST 60

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           S EKMYKIDDHVACAVAGIMSDANILINTARVQA+RY YAYQEP+
Sbjct: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPM 105

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255637334|gb|ACU18997.1| unknown [Glycine max]

 Score =  148 bits (373), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 75/105 (71%), Positives = 81/105 (77%), Gaps = 18/105 (17%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTST 42
           MSRRYD +TT+FSPEGRLYQV+Y           +G        LVGE  VTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGTAIGILSKDGVVLVGEKKVTSKLLQTST 60

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           S EKMYKIDDHVACAVAGIMSDANILINTARVQA+RY YAYQEP+
Sbjct: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPM 105

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356568146|ref|XP_003552274.1| PREDICTED: proteasome subunit alpha type-4-like isoform 1 [Glycine max]

 Score =  148 bits (373), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 75/105 (71%), Positives = 81/105 (77%), Gaps = 18/105 (17%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTST 42
           MSRRYD +TT+FSPEGRLYQV+Y           +G        LVGE  VTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGTAIGILSKDGVVLVGEKKVTSKLLQTST 60

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           S EKMYKIDDHVACAVAGIMSDANILINTARVQA+RY YAYQEP+
Sbjct: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPM 105

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356496249|ref|XP_003516981.1| PREDICTED: proteasome subunit alpha type-4-like isoform 1 [Glycine max] gi|356496251|ref|XP_003516982.1| PREDICTED: proteasome subunit alpha type-4-like isoform 2 [Glycine max]

 Score =  148 bits (373), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 75/105 (71%), Positives = 81/105 (77%), Gaps = 18/105 (17%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTST 42
           MSRRYD +TT+FSPEGRLYQV+Y           +G        LVGE  VTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGTAIGILSKDGVVLVGEKKVTSKLLQTST 60

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           S EKMYKIDDHVACAVAGIMSDANILINTARVQA+RY YAYQEP+
Sbjct: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPM 105

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|77999303|gb|ABB16998.1| proteasome-like protein alpha subunit [Solanum tuberosum]

 Score =  147 bits (371), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 74/105 (70%), Positives = 82/105 (78%), Gaps = 18/105 (17%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTST 42
           MSRRYD +TT+FSPEGRLYQV+Y           +G        LVGE  VTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           S+EKMYKIDDHVACAVAGIMSDANILINTARVQA+RY +AYQEP+
Sbjct: 61  SSEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTFAYQEPM 105

Source: Solanum tuberosum

Species: Solanum tuberosum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|76160982|gb|ABA40454.1| proteasome alpha subunit-like protein [Solanum tuberosum]

 Score =  147 bits (370), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 74/105 (70%), Positives = 82/105 (78%), Gaps = 18/105 (17%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTST 42
           MSRRYD +TT+FSPEGRLYQV+Y           +G        LVGE  VTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           S+EKMYKIDDHVACAVAGIMSDANILINTARVQA+RY +AYQEP+
Sbjct: 61  SSEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTFAYQEPM 105

Source: Solanum tuberosum

Species: Solanum tuberosum

Genus: Solanum

Family: Solanaceae

Order: Solanales

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	161
TAIR|locus:2090399	250	PAC1 "20S proteasome alpha sub	0.459	0.296	0.756	6.9e-54
ASPGD|ASPL0000051129	255	ssfA [Emericella nidulans (tax	0.447	0.282	0.430	2.9e-33
DICTYBASE|DDB_G0280969	250	psmA4 "proteasome subunit alph	0.378	0.244	0.532	8.9e-31
SGD|S000003367	258	PRE9 "Alpha 3 subunit of the 2	0.279	0.174	0.577	1e-28
POMBASE|SPAC13C5.01c	248	SPAC13C5.01c "20S proteasome c	0.273	0.177	0.613	7.8e-28
FB|FBgn0261394	264	Prosalpha3 "Proteasome alpha3	0.260	0.159	0.476	3.4e-23
WB|WBGene00003924	250	pas-3 [Caenorhabditis elegans	0.273	0.176	0.477	2.3e-22
CGD|CAL0004819	251	PRE9 [Candida albicans (taxid:	0.409	0.262	0.439	2.5e-21
UNIPROTKB|Q5AEB8	251	PRE9 "Putative uncharacterized	0.409	0.262	0.439	2.5e-21
UNIPROTKB|H0YN18	230	PSMA4 "Proteasome subunit alph	0.459	0.321	0.402	2.1e-19

TAIR|locus:2090399 PAC1 "20S proteasome alpha subunit C1" [Arabidopsis thaliana (taxid:3702)]

 Score = 267 (99.0 bits), Expect = 6.9e-54, Sum P(3) = 6.9e-54
 Identities = 56/74 (75%), Positives = 61/74 (82%)

Query:    88 QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTML 147
             QDYKDD TR+EAV+LALKVL KTMDSTSLTSEKLELAEV+L PS  VKY + SPESLT L
Sbjct:   177 QDYKDDATREEAVELALKVLTKTMDSTSLTSEKLELAEVYLTPSKTVKYHVHSPESLTKL 236

Query:   148 LENFGVAQPASEVS 161
             L   GV QPA+E S
Sbjct:   237 LVKHGVTQPAAETS 250

GO:0004175 "endopeptidase activity" evidence=IEA

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

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

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

GO:0008233 "peptidase activity" evidence=ISS

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

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

GO:0005773 "vacuole" evidence=IDA

GO:0022626 "cytosolic ribosome" evidence=IDA

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

GO:0000502 "proteasome complex" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0006094 "gluconeogenesis" evidence=RCA

GO:0006096 "glycolysis" evidence=RCA

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

ASPGD|ASPL0000051129 ssfA [Emericella nidulans (taxid:162425)]

 Score = 148 (57.2 bits), Expect = 2.9e-33, Sum P(3) = 2.9e-33
 Identities = 31/72 (43%), Positives = 46/72 (63%)

Query:    88 QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTML 147
             QDYK+D   +EA  +A+KVL KTMDST L+SEK+E A V     GK+ + + + + +  L
Sbjct:   177 QDYKEDCDLKEACAMAVKVLSKTMDSTKLSSEKIEFATVGKTKEGKIYHHLWNADEINAL 236

Query:   148 LENFGVAQPASE 159
             L+  G+A+   E
Sbjct:   237 LKEHGLAKVDDE 248

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

GO:0030010 "establishment of cell polarity" evidence=IGI

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

GO:0005634 "nucleus" evidence=IEA

GO:0034515 "proteasome storage granule" evidence=IEA

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

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

GO:0010499 "proteasomal ubiquitin-independent protein catabolic process" evidence=IEA

DICTYBASE|DDB_G0280969 psmA4 "proteasome subunit alpha type 4" [Dictyostelium discoideum (taxid:44689)]

 Score = 150 (57.9 bits), Expect = 8.9e-31, Sum P(3) = 8.9e-31
 Identities = 33/62 (53%), Positives = 39/62 (62%)

Query:    27 LVGENNVTSKLLQTSTS-AEKMYKIDDHVACAVAGIMSDANILINTXXXXXXXXXXXXXE 85
             L  E   T+KLL +STS +EKM+KID+HV CAVAGI SDANILIN              E
Sbjct:    45 LAAEKKTTAKLLDSSTSISEKMFKIDEHVVCAVAGITSDANILINYARLSSQRFFYQYQE 104

Query:    86 PI 87
             P+
Sbjct:   105 PM 106

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

GO:0006508 "proteolysis" evidence=IEA;IDA

GO:0005737 "cytoplasm" evidence=IEA;IPI

GO:0005634 "nucleus" evidence=IEA;IPI

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

SGD|S000003367 PRE9 "Alpha 3 subunit of the 20S proteasome" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 130 (50.8 bits), Expect = 1.0e-28, Sum P(3) = 1.0e-28
 Identities = 26/45 (57%), Positives = 33/45 (73%)

Query:    27 LVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINT 71
             L  E  VTS LL+  TS EK+YK++D +A AVAG+ +DA ILINT
Sbjct:    46 LAAERKVTSTLLEQDTSTEKLYKLNDKIAVAVAGLTADAEILINT 90

GO:0010499 "proteasomal ubiquitin-independent protein catabolic process" evidence=IDA

GO:0016787 "hydrolase activity" evidence=IEA

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

GO:0005839 "proteasome core complex" evidence=IEA

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

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

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

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

GO:0000502 "proteasome complex" evidence=IEA

GO:0034515 "proteasome storage granule" evidence=IDA

GO:0005634 "nucleus" evidence=IEA;IC

GO:0005737 "cytoplasm" evidence=IEA

GO:0042175 "nuclear outer membrane-endoplasmic reticulum membrane network" evidence=IC

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

GO:0003674 "molecular_function" evidence=ND

GO:0006508 "proteolysis" evidence=IEA

GO:0008233 "peptidase activity" evidence=IEA

GO:0004175 "endopeptidase activity" evidence=IEA

POMBASE|SPAC13C5.01c SPAC13C5.01c "20S proteasome complex subunit alpha 3 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 134 (52.2 bits), Expect = 7.8e-28, Sum P(3) = 7.8e-28
 Identities = 27/44 (61%), Positives = 33/44 (75%)

Query:    27 LVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILIN 70
             L  E  VTSKLL+   SAEK+Y I D++ CAVAG+ +DANILIN
Sbjct:    45 LAAEKKVTSKLLEQEESAEKLYHIGDNMLCAVAGLTADANILIN 88

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

GO:0005634 "nucleus" evidence=IC;IDA

GO:0005829 "cytosol" evidence=IDA

GO:0007346 "regulation of mitotic cell cycle" evidence=IC

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

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

GO:0004175 "endopeptidase activity" evidence=ISS

FB|FBgn0261394 Prosalpha3 "Proteasome alpha3 subunit" [Drosophila melanogaster (taxid:7227)]

 Score = 109 (43.4 bits), Expect = 3.4e-23, Sum P(3) = 3.4e-23
 Identities = 20/42 (47%), Positives = 32/42 (76%)

Query:    27 LVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANIL 68
             L  E   T+KLL ++  +EK+Y+++D++ C+VAGI SDAN+L
Sbjct:    45 LAAECRSTNKLLDSAIPSEKIYRLNDNMVCSVAGITSDANVL 86

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

GO:0004175 "endopeptidase activity" evidence=ISS;NAS;TAS

GO:0006508 "proteolysis" evidence=NAS

GO:0000502 "proteasome complex" evidence=NAS

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

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

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

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

GO:0000022 "mitotic spindle elongation" evidence=IMP

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0008283 "cell proliferation" evidence=IMP

GO:0005875 "microtubule associated complex" evidence=IDA

WB|WBGene00003924 pas-3 [Caenorhabditis elegans (taxid:6239)]

 Score = 111 (44.1 bits), Expect = 2.3e-22, Sum P(3) = 2.3e-22
 Identities = 21/44 (47%), Positives = 29/44 (65%)

Query:    27 LVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILIN 70
             +  E     KLL  S   EK+Y++ D+++C VAGI +DANILIN
Sbjct:    45 VAAERKNVHKLLDDSVMTEKVYRLSDNISCTVAGITADANILIN 88

GO:0004175 "endopeptidase activity" evidence=IEA

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

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

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

GO:0005839 "proteasome core complex" evidence=IEA

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

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0006898 "receptor-mediated endocytosis" evidence=IMP

GO:0002009 "morphogenesis of an epithelium" evidence=IMP

CGD|CAL0004819 PRE9 [Candida albicans (taxid:5476)]

 Score = 145 (56.1 bits), Expect = 2.5e-21, Sum P(2) = 2.5e-21
 Identities = 29/66 (43%), Positives = 48/66 (72%)

Query:    88 QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTML 147
             +DYKDD+T ++A +LA+KVL KTMD++++ SEKLE A + L    KV ++I + + + +L
Sbjct:   177 KDYKDDLTLKDACELAIKVLSKTMDASNINSEKLEFATLSLGKDNKVLHKIWNDKDIDIL 236

Query:   148 LENFGV 153
             ++  GV
Sbjct:   237 IKASGV 242

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

GO:0005839 "proteasome core complex" evidence=IDA

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

GO:0005634 "nucleus" evidence=IEA

GO:0034515 "proteasome storage granule" evidence=IEA

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

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

GO:0010499 "proteasomal ubiquitin-independent protein catabolic process" evidence=IEA

UNIPROTKB|Q5AEB8 PRE9 "Putative uncharacterized protein PRE9" [Candida albicans SC5314 (taxid:237561)]

 Score = 145 (56.1 bits), Expect = 2.5e-21, Sum P(2) = 2.5e-21
 Identities = 29/66 (43%), Positives = 48/66 (72%)

Query:    88 QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTML 147
             +DYKDD+T ++A +LA+KVL KTMD++++ SEKLE A + L    KV ++I + + + +L
Sbjct:   177 KDYKDDLTLKDACELAIKVLSKTMDASNINSEKLEFATLSLGKDNKVLHKIWNDKDIDIL 236

Query:   148 LENFGV 153
             ++  GV
Sbjct:   237 IKASGV 242

GO:0005839 "proteasome core complex" evidence=IDA

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

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

UNIPROTKB|H0YN18 PSMA4 "Proteasome subunit alpha type-4" [Homo sapiens (taxid:9606)]

 Score = 136 (52.9 bits), Expect = 2.1e-19, Sum P(2) = 2.1e-19
 Identities = 35/87 (40%), Positives = 46/87 (52%)

Query:     1 MSRRYDRQTTVFSPEGRLYQVDYMGCLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAG 60
             MSRRYD +TT+FSPE                N+  KLL     +EK+YK+++ +AC+VAG
Sbjct:     1 MSRRYDSRTTIFSPEAE------------RRNI-HKLLDEVFFSEKIYKLNEDMACSVAG 47

Query:    61 IMSDANILINTXXXXXXXXXXXXXEPI 87
             I SDAN+L N              EPI
Sbjct:    48 ITSDANVLTNELRLIAQRYLLQYQEPI 74

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

GO:0005839 "proteasome core complex" evidence=IEA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.4.25.1	0.946
3rd Layer	3.4.25	0.963

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00007080001	RecName- Full=Proteasome subunit alpha type; EC=3.4.25.1;; The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity (By similarity) (250 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00024499001	RecName- Full=Proteasome subunit beta type; EC=3.4.25.1;; The proteasome is a multicatalytic pr [...] (245 aa)			•	•	•	•	•		0.963
	GSVIVG00015420001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (191 aa)			•	•	•	•	•		0.961
	GSVIVG00014791001	SubName- Full=Putative uncharacterized protein (Chromosome chr18 scaffold_1, whole genome shotg [...] (309 aa)				•	•	•	•		0.939
	GSVIVG00023752001	SubName- Full=Putative uncharacterized protein (Chromosome chr7 scaffold_31, whole genome shotg [...] (205 aa)			•	•	•	•	•	•	0.920
	GSVIVG00010470001	SubName- Full=Chromosome chr17 scaffold_263, whole genome shotgun sequence; (386 aa)				•	•	•	•		0.914
	GSVIVG00026350001	RecName- Full=Proteasome subunit beta type; EC=3.4.25.1;; The proteasome is a multicatalytic pr [...] (223 aa)			•	•	•	•	•	•	0.894
	GSVIVG00030725001	RecName- Full=Proteasome subunit beta type; EC=3.4.25.1;; The proteasome is a multicatalytic pr [...] (250 aa)			•	•	•	•	•	•	0.891
	GSVIVG00035048001	RecName- Full=Proteasome subunit beta type; EC=3.4.25.1;; The proteasome is a multicatalytic pr [...] (272 aa)			•	•	•	•	•	•	0.889
	GSVIVG00036762001	SubName- Full=Chromosome chr4 scaffold_83, whole genome shotgun sequence; (440 aa)				•	•	•	•		0.858
	GSVIVG00006696001	SubName- Full=Chromosome chr2 scaffold_176, whole genome shotgun sequence; (267 aa)				•	•	•	•		0.807

---

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	161
cd03752	213	cd03752, proteasome_alpha_type_4, proteasome_alpha	2e-41
cd01911	209	cd01911, proteasome_alpha, proteasome alpha subuni	2e-32
PTZ00246	253	PTZ00246, PTZ00246, proteasome subunit alpha; Prov	5e-30
cd03756	211	cd03756, proteasome_alpha_archeal, proteasome_alph	8e-28
TIGR03633	224	TIGR03633, arc_protsome_A, proteasome endopeptidas	1e-27
PRK03996	241	PRK03996, PRK03996, proteasome subunit alpha; Prov	1e-27
cd03753	213	cd03753, proteasome_alpha_type_5, proteasome_alpha	4e-22
COG0638	236	COG0638, PRE1, 20S proteasome, alpha and beta subu	1e-21
cd03755	207	cd03755, proteasome_alpha_type_7, proteasome_alpha	3e-18
cd03751	212	cd03751, proteasome_alpha_type_3, proteasome_alpha	7e-17
cd03752	213	cd03752, proteasome_alpha_type_4, proteasome_alpha	2e-15
cd03749	211	cd03749, proteasome_alpha_type_1, proteasome_alpha	4e-15
cd01906	182	cd01906, proteasome_protease_HslV, proteasome_prot	1e-14
cd03754	215	cd03754, proteasome_alpha_type_6, proteasome_alpha	4e-14
pfam00227	188	pfam00227, Proteasome, Proteasome subunit	8e-11
cd03750	227	cd03750, proteasome_alpha_type_2, proteasome_alpha	1e-09
cd01901	164	cd01901, Ntn_hydrolase, The Ntn hydrolases (N-term	2e-09
PTZ00246	253	PTZ00246, PTZ00246, proteasome subunit alpha; Prov	3e-08
pfam10584	23	pfam10584, Proteasome_A_N, Proteasome subunit A N-	2e-07
smart00948	23	smart00948, Proteasome_A_N, Proteasome subunit A N	6e-07
cd01911	209	cd01911, proteasome_alpha, proteasome alpha subuni	1e-06
cd01906	182	cd01906, proteasome_protease_HslV, proteasome_prot	4e-06
cd03764	188	cd03764, proteasome_beta_archeal, Archeal proteaso	1e-05
PRK03996	241	PRK03996, PRK03996, proteasome subunit alpha; Prov	3e-05
pfam00227	188	pfam00227, Proteasome, Proteasome subunit	5e-05
TIGR03634	185	TIGR03634, arc_protsome_B, proteasome endopeptidas	6e-05
cd03753	213	cd03753, proteasome_alpha_type_5, proteasome_alpha	6e-04
COG0638	236	COG0638, PRE1, 20S proteasome, alpha and beta subu	8e-04
TIGR03633	224	TIGR03633, arc_protsome_A, proteasome endopeptidas	0.001
cd03756	211	cd03756, proteasome_alpha_archeal, proteasome_alph	0.002

>gnl|CDD|239721 cd03752, proteasome_alpha_type_4, proteasome_alpha_type_4

 Score =  137 bits (347), Expect = 2e-41
 Identities = 62/103 (60%), Positives = 72/103 (69%), Gaps = 18/103 (17%)

Query: 3   RRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSA 44
           RRYD +TT+FSPEGRLYQV+Y           +G        L  E  VTSKLL  S S+
Sbjct: 1   RRYDSRTTIFSPEGRLYQVEYAMEAISHAGTCLGILAKDGIVLAAEKKVTSKLLDQSFSS 60

Query: 45  EKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           EK+YKIDDH+ACAVAGI SDANILIN AR+ A+RY Y+YQEPI
Sbjct: 61  EKIYKIDDHIACAVAGITSDANILINYARLIAQRYLYSYQEPI 103

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|238892 cd01911, proteasome_alpha, proteasome alpha subunit

 Score =  114 bits (287), Expect = 2e-32
 Identities = 51/101 (50%), Positives = 63/101 (62%), Gaps = 19/101 (18%)

Query: 5   YDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAEK 46
           YDR  T FSPEGRL+QV+Y           +G        L  E  VTSKLL  S S EK
Sbjct: 1   YDRSITTFSPEGRLFQVEYALEAVKNGSTAVGIKGKDGVVLAVEKKVTSKLLDPS-SVEK 59

Query: 47  MYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           ++KIDDH+ CAVAG+ +DA +L+N ARV+A+ Y Y Y EPI
Sbjct: 60  IFKIDDHIGCAVAGLTADARVLVNRARVEAQNYRYTYGEPI 100

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|173491 PTZ00246, PTZ00246, proteasome subunit alpha; Provisional

 Score =  109 bits (273), Expect = 5e-30
 Identities = 52/104 (50%), Positives = 64/104 (61%), Gaps = 18/104 (17%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-------------MGC-----LVGENNVTSKLLQTST 42
           MSRRYD +TT FSPEGRLYQV+Y             + C     L  +  ++SKLL    
Sbjct: 1   MSRRYDSRTTTFSPEGRLYQVEYALEAINNASLTVGILCKEGVILGADKPISSKLLDPGK 60

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEP 86
             EK+YKID H+ CAVAG+ +DANILIN  R+ A+RY Y Y EP
Sbjct: 61  INEKIYKIDSHIFCAVAGLTADANILINQCRLYAQRYRYTYGEP 104

Length = 253

>gnl|CDD|239725 cd03756, proteasome_alpha_archeal, proteasome_alpha_archeal

 Score =  102 bits (256), Expect = 8e-28
 Identities = 45/101 (44%), Positives = 62/101 (61%), Gaps = 19/101 (18%)

Query: 5   YDRQTTVFSPEGRLYQVDY-------------MGC-----LVGENNVTSKLLQTSTSAEK 46
           YDR  TVFSP+GRLYQV+Y             + C     L  +  +TSKL++   S EK
Sbjct: 2   YDRAITVFSPDGRLYQVEYAREAVKRGTTALGIKCKEGVVLAVDKRITSKLVEPE-SIEK 60

Query: 47  MYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           +YKIDDHV  A +G+++DA +LI+ ARV+A+ +   Y EPI
Sbjct: 61  IYKIDDHVGAATSGLVADARVLIDRARVEAQIHRLTYGEPI 101

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|163366 TIGR03633, arc_protsome_A, proteasome endopeptidase complex, archaeal, alpha subunit

 Score =  102 bits (256), Expect = 1e-27
 Identities = 42/101 (41%), Positives = 61/101 (60%), Gaps = 19/101 (18%)

Query: 5   YDRQTTVFSPEGRLYQVDY-------------MGC-----LVGENNVTSKLLQTSTSAEK 46
           YDR  TVFSP+GRLYQV+Y             +       L  +  +TSKL++ S S EK
Sbjct: 3   YDRAITVFSPDGRLYQVEYAREAVKRGTTAVGIKTKDGVVLAVDKRITSKLVEPS-SIEK 61

Query: 47  MYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           ++KIDDH+  A +G+++DA +LI+ AR++A+     Y EPI
Sbjct: 62  IFKIDDHIGAATSGLVADARVLIDRARIEAQINRLTYGEPI 102

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|235192 PRK03996, PRK03996, proteasome subunit alpha; Provisional

 Score =  102 bits (257), Expect = 1e-27
 Identities = 42/101 (41%), Positives = 60/101 (59%), Gaps = 19/101 (18%)

Query: 5   YDRQTTVFSPEGRLYQVDY-------------MGC-----LVGENNVTSKLLQTSTSAEK 46
           YDR  T+FSP+GRLYQV+Y             +       L  +  +TS L++ S S EK
Sbjct: 10  YDRAITIFSPDGRLYQVEYAREAVKRGTTAVGVKTKDGVVLAVDKRITSPLIEPS-SIEK 68

Query: 47  MYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           ++KIDDH+  A AG+++DA +LI+ ARV+A+     Y EPI
Sbjct: 69  IFKIDDHIGAASAGLVADARVLIDRARVEAQINRLTYGEPI 109

Length = 241

>gnl|CDD|239722 cd03753, proteasome_alpha_type_5, proteasome_alpha_type_5

 Score = 87.8 bits (218), Expect = 4e-22
 Identities = 41/101 (40%), Positives = 61/101 (60%), Gaps = 19/101 (18%)

Query: 5   YDRQTTVFSPEGRLYQVDY------MG------------CLVGENNVTSKLLQTSTSAEK 46
           YDR    FSPEGRL+QV+Y      +G             L  E  +TS L++ S S EK
Sbjct: 1   YDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIKTKEGVVLAVEKRITSPLMEPS-SVEK 59

Query: 47  MYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           + +IDDH+ CA++G+++DA  LI+ ARV+A+ + + Y EP+
Sbjct: 60  IMEIDDHIGCAMSGLIADARTLIDHARVEAQNHRFTYNEPM 100

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

 Score = 87.0 bits (216), Expect = 1e-21
 Identities = 41/105 (39%), Positives = 57/105 (54%), Gaps = 19/105 (18%)

Query: 3   RRYDRQTTVFSPEGRLYQVDYMG-------------------CLVGENNVTSKLLQTSTS 43
             YDR  T+FSPEGRL+QV+Y                      L  +   TS LL  S++
Sbjct: 1   AGYDRAITIFSPEGRLFQVEYALEAVKRGGTTTVGIKGKDGVVLAADKRATSGLLIASSN 60

Query: 44  AEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQ 88
            EK++KIDDH+  A+AG+ +DA +L+  AR +A+ Y   Y EPI 
Sbjct: 61  VEKIFKIDDHIGMAIAGLAADAQVLVRYARAEAQLYRLRYGEPIS 105

Length = 236

>gnl|CDD|239724 cd03755, proteasome_alpha_type_7, proteasome_alpha_type_7

 Score = 77.4 bits (191), Expect = 3e-18
 Identities = 35/101 (34%), Positives = 52/101 (51%), Gaps = 19/101 (18%)

Query: 5   YDRQTTVFSPEGRLYQVDYM-------GCLVG-----------ENNVTSKLLQTSTSAEK 46
           YDR  TVFSP+G L+QV+Y           VG           E    +KL Q   +  K
Sbjct: 1   YDRAITVFSPDGHLFQVEYAQEAVRKGTTAVGVRGKDCVVLGVEKKSVAKL-QDPRTVRK 59

Query: 47  MYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           +  +DDHV  A AG+ +DA +LIN AR++ + +    ++P+
Sbjct: 60  ICMLDDHVCLAFAGLTADARVLINRARLECQSHRLTVEDPV 100

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

>gnl|CDD|239720 cd03751, proteasome_alpha_type_3, proteasome_alpha_type_3

 Score = 73.9 bits (182), Expect = 7e-17
 Identities = 34/101 (33%), Positives = 53/101 (52%), Gaps = 19/101 (18%)

Query: 5   YDRQTTVFSPEGRLYQVDYM-------GCLVG-----------ENNVTSKLLQTSTSAEK 46
           YD   + FSP+GR++QV+Y        G  +G           E  VTSKL +   S ++
Sbjct: 4   YDLSASTFSPDGRVFQVEYANKAVENSGTAIGIRCKDGVVLAVEKLVTSKLYEPG-SNKR 62

Query: 47  MYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           ++ +D H+  AVAG+++D   L++ AR +A  Y   Y  PI
Sbjct: 63  IFNVDRHIGIAVAGLLADGRHLVSRAREEAENYRDNYGTPI 103

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

>gnl|CDD|239721 cd03752, proteasome_alpha_type_4, proteasome_alpha_type_4

 Score = 70.1 bits (172), Expect = 2e-15
 Identities = 29/39 (74%), Positives = 33/39 (84%)

Query: 88  QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEV 126
           QDYKDDMT +EA+ LA+KVL KTMDST LTSEKLE A +
Sbjct: 175 QDYKDDMTLEEALALAVKVLSKTMDSTKLTSEKLEFATL 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|239718 cd03749, proteasome_alpha_type_1, proteasome_alpha_type_1

 Score = 69.2 bits (170), Expect = 4e-15
 Identities = 33/101 (32%), Positives = 50/101 (49%), Gaps = 21/101 (20%)

Query: 5  YDRQTTVFSPEGRLYQVDY------------------MGCLVGENNVTSKLLQTSTSAEK 46
          YD   T +SP+GRL+QV+Y                     LV     TS+L   S+  +K
Sbjct: 1  YDTDVTTWSPQGRLFQVEYAMEAVKQGSATVGLKSKTHAVLVALKRATSEL---SSYQKK 57

Query: 47 MYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
          ++K+DDH+  A+AG+ +DA +L    R +   Y + Y  PI
Sbjct: 58 IFKVDDHIGIAIAGLTADARVLSRYMRQECLNYRFVYDSPI 98

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|238887 cd01906, proteasome_protease_HslV, proteasome_protease_HslV

 Score = 67.1 bits (165), Expect = 1e-14
 Identities = 28/63 (44%), Positives = 39/63 (61%)

Query: 26 CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQE 85
           L  +  VTS LL  S++ EK++KIDDH+ CA AG+ +DA  L+   R +A+ Y   Y E
Sbjct: 13 VLAADKRVTSGLLVASSTVEKIFKIDDHIGCAFAGLAADAQTLVERLRKEAQLYRLRYGE 72

Query: 86 PIQ 88
          PI 
Sbjct: 73 PIP 75

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|239723 cd03754, proteasome_alpha_type_6, proteasome_alpha_type_6

 Score = 66.5 bits (163), Expect = 4e-14
 Identities = 32/103 (31%), Positives = 51/103 (49%), Gaps = 22/103 (21%)

Query: 5   YDRQTTVFSPEGRLYQVDYM-------------------GCLVGENNVTSKLLQTSTSAE 45
           +DR  T+FSPEGRLYQV+Y                      +V +  V  KL+  ST   
Sbjct: 2   FDRHITIFSPEGRLYQVEYAFKAVKNAGLTSVAVRGKDCAVVVTQKKVPDKLIDPST-VT 60

Query: 46  KMYKIDDHVACAVAGIMSDANILINTARVQAR--RYAYAYQEP 86
            +++I D + C + G+++D+   +  AR +A   +Y Y Y+ P
Sbjct: 61  HLFRITDEIGCVMTGMIADSRSQVQRARYEAAEFKYKYGYEMP 103

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|215805 pfam00227, Proteasome, Proteasome subunit

 Score = 57.2 bits (139), Expect = 8e-11
 Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 26 CLVGENNVTSK-LLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQ 84
           L  +   T    L +  + EK++KIDDH+  A AG+ +DA  L++ AR +A+ Y   Y 
Sbjct: 17 VLAADKRATRGSKLLSKDTVEKIFKIDDHIGMAFAGLAADAQTLVDYARAEAQLYRLRYG 76

Query: 85 EPI 87
           PI
Sbjct: 77 RPI 79

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|239719 cd03750, proteasome_alpha_type_2, proteasome_alpha_type_2

 Score = 54.2 bits (131), Expect = 1e-09
 Identities = 30/96 (31%), Positives = 44/96 (45%), Gaps = 19/96 (19%)

Query: 10  TVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAEKMYKID 51
           T FSP G+L Q++Y           +G        L  E  V S L+  S S  K+ +I 
Sbjct: 6   TTFSPSGKLVQIEYALAAVSSGAPSVGIKAANGVVLATEKKVPSPLIDES-SVHKVEQIT 64

Query: 52  DHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
            H+    +G+  D  +L+  AR  A++Y   Y EPI
Sbjct: 65  PHIGMVYSGMGPDFRVLVKKARKIAQQYYLVYGEPI 100

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|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 = 53.2 bits (128), Expect = 2e-09
 Identities = 20/82 (24%), Positives = 35/82 (42%), Gaps = 7/82 (8%)

Query: 27  LVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEP 86
           L  +  ++S L    +   K+ K +D +A  +AG+ +DA  L+   R   + Y   Y EP
Sbjct: 14  LAADKRLSSGLPVAGSPVIKIGKNEDGIAWGLAGLAADAQTLVRRLREALQLYRLRYGEP 73

Query: 87  IQDYKDDMTRQEAVQLALKVLR 108
           I             +   K+L+
Sbjct: 74  ISVV-------ALAKELAKLLQ 88

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|173491 PTZ00246, PTZ00246, proteasome subunit alpha; Provisional

 Score = 50.6 bits (121), Expect = 3e-08
 Identities = 17/37 (45%), Positives = 29/37 (78%)

Query: 88  QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELA 124
           Q++K+D+T ++ + LA KVL K+MDSTS  ++K+E+ 
Sbjct: 177 QEWKEDLTLEQGLLLAAKVLTKSMDSTSPKADKIEVG 213

Length = 253

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

 Score = 44.7 bits (107), Expect = 2e-07
 Identities = 13/19 (68%), Positives = 16/19 (84%)

Query: 5  YDRQTTVFSPEGRLYQVDY 23
          YDR  T FSP+GRL+QV+Y
Sbjct: 1  YDRSLTTFSPDGRLFQVEY 19

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 = 43.3 bits (103), Expect = 6e-07
 Identities = 13/19 (68%), Positives = 16/19 (84%)

Query: 5  YDRQTTVFSPEGRLYQVDY 23
          YDR  T FSP+GRL+QV+Y
Sbjct: 1  YDRSLTTFSPDGRLFQVEY 19

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

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

 Score = 45.5 bits (109), Expect = 1e-06
 Identities = 14/39 (35%), Positives = 27/39 (69%), Gaps = 1/39 (2%)

Query: 88  QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEV 126
           + YK D+T +EA++LALK L++ ++     ++ +E+A V
Sbjct: 172 KRYKKDLTLEEAIKLALKALKEVLEED-KKAKNIEIAVV 209

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

>gnl|CDD|238887 cd01906, proteasome_protease_HslV, proteasome_protease_HslV

 Score = 44.0 bits (105), Expect = 4e-06
 Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 2/48 (4%)

Query: 79  YAYAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEV 126
           YA    E  + YK DMT +EA++LALK L+  ++    +   +E+A +
Sbjct: 137 YALGILE--KLYKPDMTLEEAIELALKALKSALERDLYSGGNIEVAVI 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|239733 cd03764, proteasome_beta_archeal, Archeal proteasome, beta subunit

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 15/47 (31%), Positives = 27/47 (57%)

Query: 41 STSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
          S + +K+++IDD +A  +AG + DA  L+   + +AR Y      P+
Sbjct: 28 SKNVKKIFQIDDKIAMTIAGSVGDAQSLVRILKAEARLYELRRGRPM 74

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|235192 PRK03996, PRK03996, proteasome subunit alpha; Provisional

 Score = 42.1 bits (100), Expect = 3e-05
 Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 4/65 (6%)

Query: 88  QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTML 147
           ++YK+D++ +EA++LALK L K  +   L  E +E+A +        K+R  S E +   
Sbjct: 180 KNYKEDLSLEEAIELALKALAKANEG-KLDPENVEIAYI---DVETKKFRKLSVEEIEKY 235

Query: 148 LENFG 152
           LE   
Sbjct: 236 LEKLL 240

Length = 241

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

 Score = 41.4 bits (98), Expect = 5e-05
 Identities = 19/51 (37%), Positives = 34/51 (66%), Gaps = 2/51 (3%)

Query: 76  ARRYAYAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEV 126
             +YAY + E  + YK DMT +EAV+LA+K L++ ++  +L+   +E+A +
Sbjct: 140 GSQYAYGFLE--KLYKPDMTLEEAVELAVKALKEAIERDALSGGNIEVAVI 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|234287 TIGR03634, arc_protsome_B, proteasome endopeptidase complex, archaeal, beta subunit

 Score = 41.0 bits (97), Expect = 6e-05
 Identities = 14/39 (35%), Positives = 27/39 (69%)

Query: 41 STSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRY 79
          S +A+K+++IDD++A  +AG + DA  L+   + +A+ Y
Sbjct: 29 SKNAKKVFQIDDYIAMTIAGSVGDAQSLVRILKAEAKLY 67

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|239722 cd03753, proteasome_alpha_type_5, proteasome_alpha_type_5

 Score = 38.1 bits (89), Expect = 6e-04
 Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 1/45 (2%)

Query: 82  AYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEV 126
           A     + Y  DMT +EA +LAL +L++ M+   L S  +ELA V
Sbjct: 170 AQSSLQEKYHKDMTLEEAEKLALSILKQVMEEK-LNSTNVELATV 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|223711 COG0638, PRE1, 20S proteasome, alpha and beta subunits [Posttranslational modification, protein turnover, chaperones]

 Score = 38.0 bits (89), Expect = 8e-04
 Identities = 16/54 (29%), Positives = 35/54 (64%), Gaps = 2/54 (3%)

Query: 71  TARVQARRYAYAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELA 124
           TA     ++AY + E  ++Y++D++ +EA++LA+K LR  ++  + +   +E+A
Sbjct: 158 TAIGSGSQFAYGFLE--KEYREDLSLEEAIELAVKALRAAIERDAASGGGIEVA 209

Length = 236

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 19/54 (35%), Positives = 33/54 (61%), Gaps = 4/54 (7%)

Query: 89  DYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPE 142
           +Y++D++  EA++LALK L   ++   LT E +E+A + +    K K+R  S E
Sbjct: 174 EYREDLSLDEAIELALKALYSAVED-KLTPENVEVAYITV--EDK-KFRKLSVE 223

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 = 36.5 bits (85), Expect = 0.002
 Identities = 16/38 (42%), Positives = 26/38 (68%), Gaps = 1/38 (2%)

Query: 89  DYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEV 126
           +YK+DM+ +EA++LALK L   ++    T E +E+A V
Sbjct: 173 EYKEDMSLEEAIELALKALYAALEEN-ETPENVEIAYV 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	161
KOG0176	241	consensus 20S proteasome, regulatory subunit alpha	100.0
PTZ00246	253	proteasome subunit alpha; Provisional	100.0
KOG0178	249	consensus 20S proteasome, regulatory subunit alpha	100.0
cd03750	227	proteasome_alpha_type_2 proteasome_alpha_type_2. T	100.0
PRK03996	241	proteasome subunit alpha; Provisional	100.0
KOG0182	246	consensus 20S proteasome, regulatory subunit alpha	100.0
COG0638	236	PRE1 20S proteasome, alpha and beta subunits [Post	100.0
cd03752	213	proteasome_alpha_type_4 proteasome_alpha_type_4. T	100.0
KOG0181	233	consensus 20S proteasome, regulatory subunit alpha	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
KOG0183	249	consensus 20S proteasome, regulatory subunit alpha	100.0
cd03749	211	proteasome_alpha_type_1 proteasome_alpha_type_1. T	99.98
cd03755	207	proteasome_alpha_type_7 proteasome_alpha_type_7. T	99.98
KOG0184	254	consensus 20S proteasome, regulatory subunit alpha	99.97
cd03754	215	proteasome_alpha_type_6 proteasome_alpha_type_6. T	99.97
cd03756	211	proteasome_alpha_archeal proteasome_alpha_archeal.	99.97
KOG0863	264	consensus 20S proteasome, regulatory subunit alpha	99.97
cd03753	213	proteasome_alpha_type_5 proteasome_alpha_type_5. T	99.97
cd01911	209	proteasome_alpha proteasome alpha subunit. The 20S	99.97
PTZ00488	247	Proteasome subunit beta type-5; Provisional	99.94
TIGR03690	219	20S_bact_beta proteasome, beta subunit, bacterial	99.91
cd03761	188	proteasome_beta_type_5 proteasome beta type-5 subu	99.91
cd03759	195	proteasome_beta_type_3 proteasome beta type-3 subu	99.9
cd03758	193	proteasome_beta_type_2 proteasome beta type-2 subu	99.89
TIGR03691	228	20S_bact_alpha proteasome, alpha subunit, bacteria	99.88
cd03765	236	proteasome_beta_bacterial Bacterial proteasome, be	99.88
cd03757	212	proteasome_beta_type_1 proteasome beta type-1 subu	99.88
cd03762	188	proteasome_beta_type_6 proteasome beta type-6 subu	99.88
cd03763	189	proteasome_beta_type_7 proteasome beta type-7 subu	99.87
cd03764	188	proteasome_beta_archeal Archeal proteasome, beta s	99.87
cd03760	197	proteasome_beta_type_4 proteasome beta type-4 subu	99.87
TIGR03634	185	arc_protsome_B proteasome endopeptidase complex, a	99.86
KOG0174	224	consensus 20S proteasome, regulatory subunit beta	99.85
cd01912	189	proteasome_beta proteasome beta subunit. The 20S p	99.84
cd01906	182	proteasome_protease_HslV proteasome_protease_HslV.	99.8
PF00227	190	Proteasome: Proteasome subunit; InterPro: IPR00135	99.78
KOG0175	285	consensus 20S proteasome, regulatory subunit beta	99.76
KOG0179	235	consensus 20S proteasome, regulatory subunit beta	99.76
KOG0180	204	consensus 20S proteasome, regulatory subunit beta	99.71
cd01913	171	protease_HslV Protease HslV and the ATPase/chapero	99.7
PRK05456	172	ATP-dependent protease subunit HslV; Provisional	99.69
TIGR03692	171	ATP_dep_HslV ATP-dependent protease HslVU, peptida	99.65
KOG0173	271	consensus 20S proteasome, regulatory subunit beta	99.65
KOG0177	200	consensus 20S proteasome, regulatory subunit beta	99.64
PF10584	23	Proteasome_A_N: Proteasome subunit A N-terminal si	99.39
cd01901	164	Ntn_hydrolase The Ntn hydrolases (N-terminal nucle	99.17
KOG0185	256	consensus 20S proteasome, regulatory subunit beta	98.76
COG5405	178	HslV ATP-dependent protease HslVU (ClpYQ), peptida	94.98
COG3484	255	Predicted proteasome-type protease [Posttranslatio	80.11

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

Probab=100.00  E-value=1.1e-40  Score=249.20  Aligned_cols=143  Identities=40%  Similarity=0.743  Sum_probs=136.0

Q ss_pred             CCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHH
Q 040809            3 RRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSD   64 (161)
Q Consensus         3 ~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D   64 (161)
                      .-||+.+++|||+|||||||||                 | ||+++||.+++|+.++ +++||++|++||+|++||+.+|
T Consensus         6 seydrgVNTfSpEGRlfQVEYaieAikLGsTaIGv~TkEgVvL~vEKritSpLm~p~-sveKi~eid~HIgca~SGl~aD   84 (241)
T KOG0176|consen    6 SEYDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGVKTKEGVVLAVEKRITSPLMEPS-SVEKIVEIDDHIGCAMSGLIAD   84 (241)
T ss_pred             HHhcccccccCCCceeeehhhHHHHHhcCCceeeeeccceEEEEEeccccCcccCch-hhhhheehhhceeeeccccccc
Confidence            5799999999999999999999                 6 9999999999999998 8999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCc---------------------------------------------------------
Q 040809           65 ANILINTARVQARRYAYAYQEPI---------------------------------------------------------   87 (161)
Q Consensus        65 ~~~l~~~~r~~~~~y~~~~~~~i---------------------------------------------------------   87 (161)
                      ++++++++|.+|++|++.|+++|                                                         
T Consensus        85 arTlve~arv~~qnh~f~Y~e~i~VEs~tq~v~~LaLrFGe~~~~~~~msRPFGValliAG~D~~gpqL~h~dPSGtf~~  164 (241)
T KOG0176|consen   85 ARTLVERARVETQNHWFTYGEPISVESLTQAVSDLALRFGEGDDEEAIMSRPFGVALLIAGHDETGPQLYHLDPSGTFIR  164 (241)
T ss_pred             hHHHHHHHHHHhhhceeecCCcccHHHHHHHHHHHHhHhCCCcchhhhhcCCcceEEEEeeccCCCceEEEeCCCCceEE
Confidence            99999999999999999999999                                                         


Q ss_pred             ------------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHH
Q 040809           88 ------------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLE  149 (161)
Q Consensus        88 ------------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~  149 (161)
                                        +.|+++||++||+.+++..|+++++. +++.+|+++++|++++    .|++++++|+++++.
T Consensus       165 ~~AKAIGSgsEga~~~L~~e~~~~ltL~ea~~~~L~iLkqVMee-Kl~~~Nvev~~vt~e~----~f~~~t~EE~~~~i~  239 (241)
T KOG0176|consen  165 YKAKAIGSGSEGAESSLQEEYHKDLTLKEAEKIVLKILKQVMEE-KLNSNNVEVAVVTPEG----EFHIYTPEEVEQVIK  239 (241)
T ss_pred             ecceeccccchHHHHHHHHHHhhcccHHHHHHHHHHHHHHHHHH-hcCccceEEEEEcccC----ceEecCHHHHHHHHh
Confidence                              25899999999999999999999985 8999999999999986    699999999999987


Q ss_pred             Hh
Q 040809          150 NF  151 (161)
Q Consensus       150 ~~  151 (161)
                      ++
T Consensus       240 ~~  241 (241)
T KOG0176|consen  240 RL  241 (241)
T ss_pred             cC
Confidence            64

>PTZ00246 proteasome subunit alpha; Provisional

Probab=100.00  E-value=2.2e-39  Score=257.11  Aligned_cols=158  Identities=46%  Similarity=0.711  Sum_probs=144.3

Q ss_pred             CCCCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccH
Q 040809            1 MSRRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIM   62 (161)
Q Consensus         1 m~~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~   62 (161)
                      |+.+||+++|+|||||||+|||||                 | |||+|+|.+++++++++..+|||+|++||+|++||+.
T Consensus         1 ~~~~yd~~~~~fsp~Grl~QvEYA~~av~~g~t~Igik~~dgVvlaad~r~s~~~~~~~~~~~KI~~I~~~i~~~~sG~~   80 (253)
T PTZ00246          1 MSRRYDSRTTTFSPEGRLYQVEYALEAINNASLTVGILCKEGVILGADKPISSKLLDPGKINEKIYKIDSHIFCAVAGLT   80 (253)
T ss_pred             CCCccCCCCceECCCCEEhHHHHHHHHHHhCCCEEEEEECCEEEEEEecCCCCcCccCCCCcccEEEecCCEEEEEEEcH
Confidence            899999999999999999999999                 5 8999999999999988778999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCc-------------------------------------------------------
Q 040809           63 SDANILINTARVQARRYAYAYQEPI-------------------------------------------------------   87 (161)
Q Consensus        63 ~D~~~l~~~~r~~~~~y~~~~~~~i-------------------------------------------------------   87 (161)
                      +|++.+++.+|.+++.|++.+++++                                                       
T Consensus        81 ~D~~~l~~~~r~~~~~~~~~~~~~~~v~~l~~~l~~~~q~~~~~~~~rP~~v~~li~G~D~~~gp~Ly~~D~~Gs~~~~~  160 (253)
T PTZ00246         81 ADANILINQCRLYAQRYRYTYGEPQPVEQLVVQICDLKQSYTQFGGLRPFGVSFLFAGYDENLGYQLYHTDPSGNYSGWK  160 (253)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccccCcccCCEEEEEEEEeCCCCcEEEEECCCCCEecce
Confidence            9999999999999999999999876                                                       


Q ss_pred             ----------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCC-ceeEEECCHHHHHHHHHH
Q 040809           88 ----------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSG-KVKYRICSPESLTMLLEN  150 (161)
Q Consensus        88 ----------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g-~~~~~~l~~~ei~~~l~~  150 (161)
                                      ++|+++|+++||++++++||+.+.+++..++++++|++|+++++. ...|++|+++||+++|++
T Consensus       161 ~~a~G~gs~~~~~~Le~~~~~~ms~eeai~l~~~al~~~~~~d~~s~~~vev~ii~~~~~~~~~~~~~l~~~ei~~~l~~  240 (253)
T PTZ00246        161 ATAIGQNNQTAQSILKQEWKEDLTLEQGLLLAAKVLTKSMDSTSPKADKIEVGILSHGETDGEPIQKMLSEKEIAELLKK  240 (253)
T ss_pred             EEEECCCcHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHhccCCCCCcEEEEEEecCCcCCCCCeEECCHHHHHHHHHH
Confidence                            368999999999999999999999998899999999999987410 115999999999999999


Q ss_pred             hcccCCCC
Q 040809          151 FGVAQPAS  158 (161)
Q Consensus       151 ~~~~~~~~  158 (161)
                      ++++.+.+
T Consensus       241 ~~~~~~~~  248 (253)
T PTZ00246        241 VTQEYAKE  248 (253)
T ss_pred             Hhhhhhhh
Confidence            97766443

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

Probab=100.00  E-value=1.6e-37  Score=234.10  Aligned_cols=158  Identities=56%  Similarity=0.819  Sum_probs=147.3

Q ss_pred             CCCCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccH
Q 040809            1 MSRRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIM   62 (161)
Q Consensus         1 m~~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~   62 (161)
                      |+++||..+|+|||+|||+|||||                 | |||+++|.+++|++.+.+.+||++|+|||+|+++|+.
T Consensus         1 msr~ydsrttiFspEGRLyQVEyAmeais~aGt~iGila~DGvvLa~e~k~t~kll~t~~~~EKiY~l~d~iaC~vaGlt   80 (249)
T KOG0178|consen    1 MSRRYDSRTTIFSPEGRLYQVEYAMEAISHAGTCIGILASDGVVLAGENKVTSKLLDTSIPMEKIYKLNDNIACAVAGLT   80 (249)
T ss_pred             CCcCcCCcccccCCCcchHHHHHHHHHHhhhcceeEEEecCceEEEeecccchhhhhccccHHHhhhcCCceEEEEeccc
Confidence            999999999999999999999999                 7 9999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCc-------------------------------------------------------
Q 040809           63 SDANILINTARVQARRYAYAYQEPI-------------------------------------------------------   87 (161)
Q Consensus        63 ~D~~~l~~~~r~~~~~y~~~~~~~i-------------------------------------------------------   87 (161)
                      +|+..|++++|..+|+|.++||++|                                                       
T Consensus        81 ~DAnvL~n~aRi~AQ~yl~~y~e~iP~eqLv~~lcdiKQayTQygG~RPFGVSfLYaGwd~~~gyqLy~SdPSGny~gWk  160 (249)
T KOG0178|consen   81 SDANVLKNYARIIAQRYLFRYGEEIPCEQLVTFLCDIKQAYTQYGGKRPFGVSFLYAGWDDRYGYQLYQSDPSGNYGGWK  160 (249)
T ss_pred             ccHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHHhhccCcCCCceeeeeeceecCcceEEEecCCCCCccccc
Confidence            9999999999999999999999998                                                       


Q ss_pred             ----------------cCCCCC-CCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 040809           88 ----------------QDYKDD-MTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLEN  150 (161)
Q Consensus        88 ----------------~~y~~~-mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~  150 (161)
                                      +.|+++ ++++||+.+|++.|...++.++++.+.+|++.++++.+ ...++++.++||.++|.+
T Consensus       161 a~ciG~N~~Aa~s~Lkqdykdd~~~~~eA~~laikvL~kt~d~~~lt~eklEia~~~k~~~-k~v~~i~~~~ev~kll~k  239 (249)
T KOG0178|consen  161 ATCIGANSGAAQSMLKQDYKDDENDLEEAKALAIKVLSKTLDSGSLTAEKLEIATITKDCN-KTVLKILKKDEVLKLLEK  239 (249)
T ss_pred             eeeeccchHHHHHHHHhhhccccccHHHHHHHHHHHHHhhcccCCCChhheEEEEEEecCC-ceEEEecCHHHHHHHHHH
Confidence                            245655 45999999999999999999999999999999999875 336899999999999999


Q ss_pred             hcccCCCCC
Q 040809          151 FGVAQPASE  159 (161)
Q Consensus       151 ~~~~~~~~~  159 (161)
                      +...++++|
T Consensus       240 ~~~~~~~~~  248 (249)
T KOG0178|consen  240 YHETQRQAE  248 (249)
T ss_pred             hhhhhhhcc
Confidence            998888765

>cd03750 proteasome_alpha_type_2 proteasome_alpha_type_2

Probab=100.00  E-value=5.9e-36  Score=234.03  Aligned_cols=139  Identities=29%  Similarity=0.541  Sum_probs=128.6

Q ss_pred             CCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHH
Q 040809            5 YDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDAN   66 (161)
Q Consensus         5 y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~   66 (161)
                      ||+++|+|||||||+|||||                 | |||+|+|.++++..+ ++.+||++|++||+|++||+.+|++
T Consensus         1 yd~~~t~fsp~Grl~QveyA~~av~~G~t~igik~~dgVvlaad~~~~~~l~~~-~~~~KI~~I~~~i~~~~sG~~~D~~   79 (227)
T cd03750           1 YSFSLTTFSPSGKLVQIEYALAAVSSGAPSVGIKAANGVVLATEKKVPSPLIDE-SSVHKVEQITPHIGMVYSGMGPDFR   79 (227)
T ss_pred             CCCCCceECCCCeEhHHHHHHHHHHcCCCEEEEEeCCEEEEEEeecCCccccCC-CCcceEEEEcCCEEEEEeEcHHhHH
Confidence            89999999999999999999                 5 999999999777654 4889999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCc-----------------------------------------------------------
Q 040809           67 ILINTARVQARRYAYAYQEPI-----------------------------------------------------------   87 (161)
Q Consensus        67 ~l~~~~r~~~~~y~~~~~~~i-----------------------------------------------------------   87 (161)
                      .+++++|.+++.|++.+++++                                                           
T Consensus        80 ~l~~~~r~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rP~~v~~li~G~D~~g~~Ly~~d~~G~~~~~~~~a~G  159 (227)
T cd03750          80 VLVKKARKIAQQYYLVYGEPIPVSQLVREIASVMQEYTQSGGVRPFGVSLLIAGWDEGGPYLYQVDPSGSYFTWKATAIG  159 (227)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCCCCCChheEEEEEEEeCCCCEEEEECCCCCEEeeeEEEEC
Confidence            999999999999999999887                                                           


Q ss_pred             -----------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHH
Q 040809           88 -----------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLE  149 (161)
Q Consensus        88 -----------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~  149 (161)
                                 ++|+++||++||++++++||+.+..| .+++.+++|++|++++    .|+.++++||+++|.
T Consensus       160 ~g~~~~~~~Le~~~~~~ms~eeai~l~~~~l~~~~~~-~l~~~~iev~iv~~~~----~~~~~~~~ei~~~~~  227 (227)
T cd03750         160 KNYSNAKTFLEKRYNEDLELEDAIHTAILTLKEGFEG-QMTEKNIEIGICGETK----GFRLLTPAEIKDYLA  227 (227)
T ss_pred             CCCHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHhcc-cCCCCcEEEEEEECCC----CEEECCHHHHHHHhC
Confidence                       46899999999999999999999987 5799999999999863    599999999999873

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

>PRK03996 proteasome subunit alpha; Provisional

Probab=100.00  E-value=1.6e-34  Score=227.71  Aligned_cols=144  Identities=44%  Similarity=0.736  Sum_probs=133.4

Q ss_pred             CCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHH
Q 040809            3 RRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSD   64 (161)
Q Consensus         3 ~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D   64 (161)
                      .+||+++++|||||||+|||||                 | |||+|+|.++++... ++.+|||+|++|++|++||+.+|
T Consensus         8 ~~y~~~~~~fsp~Gr~~Q~eya~~av~~G~t~igik~~dgVvlaad~r~~~~~~~~-~~~~KI~~I~~~i~~~~sG~~~D   86 (241)
T PRK03996          8 MGYDRAITIFSPDGRLYQVEYAREAVKRGTTAVGVKTKDGVVLAVDKRITSPLIEP-SSIEKIFKIDDHIGAASAGLVAD   86 (241)
T ss_pred             cccCCCCceECCCCeEhHHHHHHHHHHhCCCEEEEEeCCEEEEEEeccCCCcccCC-CccceEEEEcCCEEEEEcccHHH
Confidence            7999999999999999999999                 5 999999999776654 48899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCc---------------------------------------------------------
Q 040809           65 ANILINTARVQARRYAYAYQEPI---------------------------------------------------------   87 (161)
Q Consensus        65 ~~~l~~~~r~~~~~y~~~~~~~i---------------------------------------------------------   87 (161)
                      ++.+++++|.+++.|++.+++++                                                         
T Consensus        87 ~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~~~~~~~rP~~~~~ilaG~d~~gp~Ly~id~~G~~~~~~~~a  166 (241)
T PRK03996         87 ARVLIDRARVEAQINRLTYGEPIGVETLTKKICDHKQQYTQHGGVRPFGVALLIAGVDDGGPRLFETDPSGAYLEYKATA  166 (241)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhcCCCCccchheEEEEEEEeCCcCEEEEECCCCCeecceEEE
Confidence            99999999999999999999887                                                         


Q ss_pred             -------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHh
Q 040809           88 -------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENF  151 (161)
Q Consensus        88 -------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~  151 (161)
                                   +.|+++|+++||++++++||..+.++ ..++++++|+||+++++   .|+.++++||+++++++
T Consensus       167 ~G~g~~~~~~~Le~~~~~~~s~eeai~l~~~al~~~~~~-~~~~~~i~i~ii~~~~~---~~~~~~~~ei~~~~~~~  239 (241)
T PRK03996        167 IGAGRDTVMEFLEKNYKEDLSLEEAIELALKALAKANEG-KLDPENVEIAYIDVETK---KFRKLSVEEIEKYLEKL  239 (241)
T ss_pred             ECCCcHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHhcc-CCCCCcEEEEEEECCCC---cEEECCHHHHHHHHHHh
Confidence                         36899999999999999999999986 78999999999999864   59999999999999875

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

Probab=100.00  E-value=1.9e-34  Score=217.64  Aligned_cols=147  Identities=33%  Similarity=0.628  Sum_probs=136.2

Q ss_pred             CCCCCCCcccCCCCceeeEecc---------------e----EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHH
Q 040809            3 RRYDRQTTVFSPEGRLYQVDYM---------------G----CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMS   63 (161)
Q Consensus         3 ~~y~~~~~~fsp~Grl~qveya---------------G----Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~   63 (161)
                      .+||+++|+|||+|||||||||               |    |++++|+.+.+|.+++ .+..+|+|+++|||+++|+.+
T Consensus         7 agfDrhitIFspeGrLyQVEYafkAin~~gltsVavrgkDcavvvsqKkvpDKLld~~-tvt~~f~itk~ig~v~tG~~a   85 (246)
T KOG0182|consen    7 AGFDRHITIFSPEGRLYQVEYAFKAINQAGLTSVAVRGKDCAVVVTQKKVPDKLLDSS-TVTHLFRITKKIGCVITGMIA   85 (246)
T ss_pred             CCccceEEEECCCceEEeeehHHHHhhcCCCceEEEcCCceEEEEecccCcccccccc-cceeEEEeeccceEEEecCCc
Confidence            6899999999999999999999               3    8999999999999987 799999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCc--------------------------------------------------------
Q 040809           64 DANILINTARVQARRYAYAYQEPI--------------------------------------------------------   87 (161)
Q Consensus        64 D~~~l~~~~r~~~~~y~~~~~~~i--------------------------------------------------------   87 (161)
                      |++..++++|.+|.+++|+||.+|                                                        
T Consensus        86 Dar~~v~rar~eAa~~~yk~Gyemp~DiL~k~~Ad~~QvytQ~a~mRplg~~~~~i~~D~E~gP~vYk~DpAGyy~g~kA  165 (246)
T KOG0182|consen   86 DARSQVQRARYEAAEFRYKYGYEMPCDILAKRMADKSQVYTQNAAMRPLGVAATLIGVDEERGPSVYKTDPAGYYYGFKA  165 (246)
T ss_pred             chHHHHHHHHHHHHhhhhhcCCCCCHHHHHHHHhhHHHHHhhhhhhcccceeEEEEEeccccCcceEeecCcccccccee
Confidence            999999999999999999999998                                                        


Q ss_pred             ---------------cCCCCC--CCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 040809           88 ---------------QDYKDD--MTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLEN  150 (161)
Q Consensus        88 ---------------~~y~~~--mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~  150 (161)
                                     ++||++  .|.+|++++|+.||..++.- +.+..++||++++++.+   .|+.|+.+||+++|+.
T Consensus       166 taaG~Kq~e~tsfLEKk~Kk~~~~t~~e~ve~ai~al~~sl~~-Dfk~se~EVgvv~~~~p---~f~~Ls~~eie~hL~~  241 (246)
T KOG0182|consen  166 TAAGVKQQEATSFLEKKYKKDIDLTFEETVETAISALQSSLGI-DFKSSELEVGVVTVDNP---EFRILSAEEIEEHLQA  241 (246)
T ss_pred             eecccchhhHHHHHHHhhccCccchHHHHHHHHHHHHHHHHhc-ccCCcceEEEEEEcCCc---ceeeccHHHHHHHHHH
Confidence                           346766  77999999999999999975 57888999999999864   6999999999999999


Q ss_pred             hccc
Q 040809          151 FGVA  154 (161)
Q Consensus       151 ~~~~  154 (161)
                      +++.
T Consensus       242 IAEk  245 (246)
T KOG0182|consen  242 IAEK  245 (246)
T ss_pred             hhhc
Confidence            9764

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

Probab=100.00  E-value=3.2e-34  Score=225.51  Aligned_cols=148  Identities=39%  Similarity=0.693  Sum_probs=139.3

Q ss_pred             CCCCCCCcccCCCCceeeEecc------------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHH
Q 040809            3 RRYDRQTTVFSPEGRLYQVDYM------------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMS   63 (161)
Q Consensus         3 ~~y~~~~~~fsp~Grl~qveya------------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~   63 (161)
                      .+||+.+++|||+||++|+|||                  | |||+|||.++++++.++..+|||+|+|||+|++||+.+
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            4799999999999999999999                  6 99999999999999998899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCc--------------------------------------------------------
Q 040809           64 DANILINTARVQARRYAYAYQEPI--------------------------------------------------------   87 (161)
Q Consensus        64 D~~~l~~~~r~~~~~y~~~~~~~i--------------------------------------------------------   87 (161)
                      |++.|++++|.+|+.|++.|+++|                                                        
T Consensus        81 Da~~lv~~~r~~a~~~~~~~~~~i~v~~la~~ls~~l~~~~~~~rP~gv~~iiaG~d~~~p~Ly~~Dp~G~~~~~~~~a~  160 (236)
T COG0638          81 DAQVLVRYARAEAQLYRLRYGEPISVEALAKLLSNILQEYTQSGRPYGVSLLVAGVDDGGPRLYSTDPSGSYNEYKATAI  160 (236)
T ss_pred             hHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhccCcccceEEEEEEEEcCCCCeEEEECCCCceeecCEEEE
Confidence            999999999999999999999998                                                        


Q ss_pred             ------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhccc
Q 040809           88 ------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFGVA  154 (161)
Q Consensus        88 ------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~~~  154 (161)
                                  ++|+++|++|||++++++||+++++||..++++++|++|+++.    .|+.++.+++..++..+...
T Consensus       161 Gsgs~~a~~~Le~~y~~~m~~eeai~la~~al~~a~~rd~~s~~~~~v~vi~~~~----~~~~~~~~~~~~~~~~~~~~  235 (236)
T COG0638         161 GSGSQFAYGFLEKEYREDLSLEEAIELAVKALRAAIERDAASGGGIEVAVITKDE----GFRKLDGEEIKKLLDDLSEK  235 (236)
T ss_pred             cCCcHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHhccccCCCCeEEEEEEcCC----CeEEcCHHHHHHHHHHHhhc
Confidence                        4689999999999999999999999999899999999999973    59999999999999887653

>cd03752 proteasome_alpha_type_4 proteasome_alpha_type_4

Probab=100.00  E-value=2.9e-34  Score=222.49  Aligned_cols=124  Identities=73%  Similarity=1.070  Sum_probs=118.4

Q ss_pred             CCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHH
Q 040809            3 RRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSD   64 (161)
Q Consensus         3 ~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D   64 (161)
                      ++||+++|+|||||||+|||||                 | |||+|+|.+++++++++..+|||+|++||+|++||+.+|
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            5899999999999999999999                 5 999999999999998878999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCc---------------------------------------------------------
Q 040809           65 ANILINTARVQARRYAYAYQEPI---------------------------------------------------------   87 (161)
Q Consensus        65 ~~~l~~~~r~~~~~y~~~~~~~i---------------------------------------------------------   87 (161)
                      ++.+++++|.+++.|+++|+++|                                                         
T Consensus        81 ~~~l~~~~r~~~~~~~~~~~~~i~v~~la~~ls~~~~~~t~~~~~RP~~v~~li~G~D~~~g~~ly~~d~~G~~~~~~~~  160 (213)
T cd03752          81 ANILINYARLIAQRYLYSYQEPIPVEQLVQRLCDIKQGYTQYGGLRPFGVSFLYAGWDKHYGFQLYQSDPSGNYSGWKAT  160 (213)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcCCCcccceeEEEEEEEeCCCCCEEEEECCCCCeeeeeEE
Confidence            99999999999999999999988                                                         


Q ss_pred             --------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEE
Q 040809           88 --------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEV  126 (161)
Q Consensus        88 --------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii  126 (161)
                                    +.|+++||++||++++++||+.+.+|+..+++++||++|
T Consensus       161 a~G~gs~~~~~~Le~~y~~~ms~eea~~l~~~al~~~~~r~~~~~~~~ei~~~  213 (213)
T cd03752         161 AIGNNNQAAQSLLKQDYKDDMTLEEALALAVKVLSKTMDSTKLTSEKLEFATL  213 (213)
T ss_pred             EECCCcHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHhccCCCCCcEEEEEC
Confidence                          368999999999999999999999998999999999985

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=6.9e-35  Score=217.60  Aligned_cols=144  Identities=28%  Similarity=0.509  Sum_probs=134.3

Q ss_pred             CCCCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccH
Q 040809            1 MSRRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIM   62 (161)
Q Consensus         1 m~~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~   62 (161)
                      |+.+|.+++|+|||.|+|.|+|||                 | |||++|+..++|.+.. ++.||++|.+||||++||+.
T Consensus         2 ~d~~y~fslTtFSpsGKL~QieyAL~Av~~G~~SvGi~A~nGvVlatekk~~s~L~~~~-sv~KV~~i~~~IG~vYSGmg   80 (233)
T KOG0181|consen    2 GDFGYSFSLTTFSPSGKLVQIEYALTAVVNGQTSVGIKAANGVVLATEKKDVSPLVDEE-SVRKVEKITPHIGCVYSGMG   80 (233)
T ss_pred             CCcccceeeEEEcCCCceehHHHHHHHHhCCCCceeeeecCceEEEeccCCCCccchhh-hhhhHhhccCCcceEEecCC
Confidence            346999999999999999999999                 7 9999999999999865 89999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCc-------------------------------------------------------
Q 040809           63 SDANILINTARVQARRYAYAYQEPI-------------------------------------------------------   87 (161)
Q Consensus        63 ~D~~~l~~~~r~~~~~y~~~~~~~i-------------------------------------------------------   87 (161)
                      ||+|.+++..|..|++|...|+++|                                                       
T Consensus        81 pD~RvlV~~~rkiAe~Yy~vY~e~~pt~qlv~~~asvmQEyTqsgGvrPFGvslliaG~~~~~p~LyQvdPSGsyf~wka  160 (233)
T KOG0181|consen   81 PDYRVLVHKSRKIAEQYYRVYGEPIPTTQLVQEVASVMQEYTQSGGVRPFGVSLLIAGWDEGGPLLYQVDPSGSYFAWKA  160 (233)
T ss_pred             CceeehhhHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEeecCCCceeEEEECCccceeehhh
Confidence            9999999999999999999999998                                                       


Q ss_pred             ---------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHh
Q 040809           88 ---------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENF  151 (161)
Q Consensus        88 ---------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~  151 (161)
                                     ++|.++|.++++|+.|+..|++..+. .++++||||+++..+     .|++|+++||+.+|+.+
T Consensus       161 tA~Gkn~v~aktFlEkR~~edleldd~ihtailtlkE~feg-e~~~~nieigv~~~~-----~F~~lt~~eI~d~l~~l  233 (233)
T KOG0181|consen  161 TAMGKNYVNAKTFLEKRYNEDLELDDAIHTAILTLKESFEG-EMTAKNIEIGVCGEN-----GFRRLTPAEIEDYLASL  233 (233)
T ss_pred             hhhccCcchHHHHHHHHhccccccchHHHHHHHHHHHHhcc-ccccCceEEEEecCC-----ceeecCHHHHHHHHhcC
Confidence                           36789999999999999999999974 899999999999843     59999999999999764

>TIGR03633 arc_protsome_A proteasome endopeptidase complex, archaeal, alpha subunit

Probab=100.00  E-value=1.9e-33  Score=219.36  Aligned_cols=135  Identities=44%  Similarity=0.770  Sum_probs=124.5

Q ss_pred             CCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHH
Q 040809            4 RYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDA   65 (161)
Q Consensus         4 ~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~   65 (161)
                      +||+++|+|||+|||+|||||                 | |||+|+|.++++... +..+||++|+++++|++||+.+|+
T Consensus         2 ~~~~~~~~f~p~Grl~Qieya~~av~~G~tvigi~~~dgvvlaad~r~~~~~~~~-~~~~KI~~i~~~i~~~~sG~~~D~   80 (224)
T TIGR03633         2 GYDRAITVFSPDGRLYQVEYAREAVKRGTTAVGIKTKDGVVLAVDKRITSKLVEP-SSIEKIFKIDDHIGAATSGLVADA   80 (224)
T ss_pred             CCCCCCceECCCCeEeHHHHHHHHHHcCCCEEEEEECCEEEEEEeccCCccccCC-CccceEEEECCCEEEEEeecHHhH
Confidence            799999999999999999999                 5 899999998776554 588999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCc----------------------------------------------------------
Q 040809           66 NILINTARVQARRYAYAYQEPI----------------------------------------------------------   87 (161)
Q Consensus        66 ~~l~~~~r~~~~~y~~~~~~~i----------------------------------------------------------   87 (161)
                      +.+.+++|.++..|++.+++++                                                          
T Consensus        81 ~~l~~~~~~~~~~~~~~~~~~~~~~~la~~ls~~l~~~~~~~~~rP~~v~~ll~G~d~~~~~Ly~~D~~G~~~~~~~~a~  160 (224)
T TIGR03633        81 RVLIDRARIEAQINRLTYGEPIDVETLAKKICDLKQQYTQHGGVRPFGVALLIAGVDDGGPRLFETDPSGALLEYKATAI  160 (224)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCCCccccceEEEEEEEeCCcCEEEEECCCCCeecceEEEE
Confidence            9999999999999999999877                                                          


Q ss_pred             ------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHH
Q 040809           88 ------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPES  143 (161)
Q Consensus        88 ------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~e  143 (161)
                                  +.|+++|+++||++++++||..+.+ +..++++++|++|+++++   .|++++++|
T Consensus       161 G~g~~~~~~~L~~~~~~~~~~eeai~l~~~al~~~~~-d~~~~~~i~i~ii~~~g~---~~~~~~~~~  224 (224)
T TIGR03633       161 GAGRQAVTEFLEKEYREDLSLDEAIELALKALYSAVE-DKLTPENVEVAYITVEDK---KFRKLSVEE  224 (224)
T ss_pred             CCCCHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHhc-ccCCCCcEEEEEEEcCCC---cEEECCCCC
Confidence                        3689999999999999999999998 789999999999999865   599998875

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=6.7e-33  Score=214.90  Aligned_cols=123  Identities=37%  Similarity=0.571  Sum_probs=115.2

Q ss_pred             CCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHH
Q 040809            3 RRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSD   64 (161)
Q Consensus         3 ~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D   64 (161)
                      ++||+++|+|||||||+|||||                 | |||+|+|.++.+...+ ..+|||+|++|++|++||+.+|
T Consensus         2 ~~yd~~~t~fsp~Grl~Qveya~~a~~~G~tvIgik~kdgVvla~d~r~~~~~~~~~-~~~KI~~I~~~i~~~~sG~~~D   80 (212)
T cd03751           2 TGYDLSASTFSPDGRVFQVEYANKAVENSGTAIGIRCKDGVVLAVEKLVTSKLYEPG-SNKRIFNVDRHIGIAVAGLLAD   80 (212)
T ss_pred             CCccCCCceECCCCcchHHHHHHHHHhcCCCEEEEEeCCEEEEEEEccccccccCcc-hhcceeEecCcEEEEEEEChHh
Confidence            6899999999999999999999                 5 8999999998877765 7899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCc---------------------------------------------------------
Q 040809           65 ANILINTARVQARRYAYAYQEPI---------------------------------------------------------   87 (161)
Q Consensus        65 ~~~l~~~~r~~~~~y~~~~~~~i---------------------------------------------------------   87 (161)
                      ++.+++++|.+++.|++.+++++                                                         
T Consensus        81 ~~~l~~~~r~~~~~y~~~~~~~~~v~~la~~ls~~~~~~t~~~~~rP~~vs~li~G~D~~gp~Ly~~D~~Gs~~~~~~~a  160 (212)
T cd03751          81 GRHLVSRAREEAENYRDNYGTPIPVKVLADRVAMYMHAYTLYSSVRPFGCSVLLGGYDSDGPQLYMIEPSGVSYGYFGCA  160 (212)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccCCCcCCceEEEEEEEEeCCcCEEEEECCCCCEEeeEEEE
Confidence            99999999999999999999887                                                         


Q ss_pred             -------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEE
Q 040809           88 -------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEV  126 (161)
Q Consensus        88 -------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii  126 (161)
                                   ++|+++||++||+++++++|+.+++..+..+++|||+++
T Consensus       161 ~G~g~~~a~~~Lek~~~~dms~eeai~l~~~~L~~~~~~~~~~~~~iei~~~  212 (212)
T cd03751         161 IGKGKQAAKTELEKLKFSELTCREAVKEAAKIIYIVHDEIKDKAFELELSWV  212 (212)
T ss_pred             ECCCCHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHhhccCCCCccEEEEEC
Confidence                         468999999999999999999999877799999999985

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

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

Probab=100.00  E-value=1.2e-33  Score=213.57  Aligned_cols=146  Identities=33%  Similarity=0.573  Sum_probs=132.3

Q ss_pred             CCCCCCCcccCCCCceeeEecc--------------e----EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHH
Q 040809            3 RRYDRQTTVFSPEGRLYQVDYM--------------G----CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSD   64 (161)
Q Consensus         3 ~~y~~~~~~fsp~Grl~qveya--------------G----Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D   64 (161)
                      ++||+.+|+|||||+|||||||              |    ||+.+|+...+|++.. ...||..+++|++|++||+.+|
T Consensus         2 srydraltvFSPDGhL~QVEYAqEAvrkGstaVgvrg~~~vvlgvEkkSv~~Lq~~r-~~rkI~~ld~hV~mafaGl~aD   80 (249)
T KOG0183|consen    2 SRYDRALTVFSPDGHLFQVEYAQEAVRKGSTAVGVRGNNCVVLGVEKKSVPKLQDER-TVRKISMLDDHVVMAFAGLTAD   80 (249)
T ss_pred             CccccceEEECCCCCEEeeHhHHHHHhcCceEEEeccCceEEEEEeecchhhhhhhh-hhhhheeecceeeEEecCCCcc
Confidence            5899999999999999999999              3    8999999999999865 7999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCc---------------------------------------------------------
Q 040809           65 ANILINTARVQARRYAYAYQEPI---------------------------------------------------------   87 (161)
Q Consensus        65 ~~~l~~~~r~~~~~y~~~~~~~i---------------------------------------------------------   87 (161)
                      +|.+++++|.+|+.|+++...|+                                                         
T Consensus        81 ArilinrArvecqShrlt~edpvtveyitRyiA~~kQrYTqs~grRPFGvs~Li~GfD~~g~p~lyqtePsG~f~ewka~  160 (249)
T KOG0183|consen   81 ARILINRARVECQSHRLTLEDPVTVEYITRYIAGLKQRYTQSNGRRPFGVSTLIGGFDPDGTPRLYQTEPSGIFSEWKAN  160 (249)
T ss_pred             ceeehhhHhHhhhhhhcccCCCcHHHHHHHHHHHhhhhhhccCCcccccceEEEEeeCCCCCeeeEeeCCCcchhhhhcc
Confidence            99999999999999999999998                                                         


Q ss_pred             --------------cCCCCC--CCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHh
Q 040809           88 --------------QDYKDD--MTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENF  151 (161)
Q Consensus        88 --------------~~y~~~--mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~  151 (161)
                                    +.|.+.  .+..++++|++++|.++.+.   ++.++|++|+++.+    .++.|+.++|..++..+
T Consensus       161 aiGr~sk~VrEflEK~y~e~~~~~~~~~ikL~ir~LleVvqs---~~~nie~aVm~~~~----~~~~l~~~~I~~~v~~i  233 (249)
T KOG0183|consen  161 AIGRSSKTVREFLEKNYKEEAIATEGETIKLAIRALLEVVQS---GGKNIEVAVMKRRK----DLKMLESEEIDDIVKEI  233 (249)
T ss_pred             ccccccHHHHHHHHHhcccccccccccHHHHHHHHHHHHhhc---CCCeeEEEEEecCC----ceeecCHHHHHHHHHHH
Confidence                          235554  67899999999999999964   68899999999875    59999999999999998


Q ss_pred             cccCC
Q 040809          152 GVAQP  156 (161)
Q Consensus       152 ~~~~~  156 (161)
                      .++.+
T Consensus       234 e~E~e  238 (249)
T KOG0183|consen  234 EQEEE  238 (249)
T ss_pred             HHHHH
Confidence            77743

>cd03749 proteasome_alpha_type_1 proteasome_alpha_type_1

Probab=99.98  E-value=8.4e-32  Score=208.52  Aligned_cols=120  Identities=36%  Similarity=0.651  Sum_probs=110.9

Q ss_pred             CCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHH
Q 040809            5 YDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDAN   66 (161)
Q Consensus         5 y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~   66 (161)
                      ||+++|+|||||||+|||||                 | |||+|+|.++++.   +..+|||+|++||+|++||+.+|++
T Consensus         1 yd~~~t~fsp~Grl~Qveya~~av~~G~t~IgIk~~dgVvlaad~r~~~~l~---~~~~KI~~I~~~i~~~~sG~~~D~~   77 (211)
T cd03749           1 YDTDVTTWSPQGRLFQVEYAMEAVKQGSATVGLKSKTHAVLVALKRATSELS---SYQKKIFKVDDHIGIAIAGLTADAR   77 (211)
T ss_pred             CCCCCceECCCCeEeHHHHHHHHHhcCCCEEEEEeCCEEEEEEeccCccccC---CccccEEEeCCCEEEEEEeChHhHH
Confidence            89999999999999999999                 5 8999999888753   3569999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCc-----------------------------------------------------------
Q 040809           67 ILINTARVQARRYAYAYQEPI-----------------------------------------------------------   87 (161)
Q Consensus        67 ~l~~~~r~~~~~y~~~~~~~i-----------------------------------------------------------   87 (161)
                      .+++++|.+++.|+++++++|                                                           
T Consensus        78 ~l~~~~r~~~~~~~~~~~~~~~v~~la~~is~~~~~~t~~~~~rP~~v~~ii~G~D~~gp~Ly~~Dp~G~~~~~~~~a~G  157 (211)
T cd03749          78 VLSRYMRQECLNYRFVYDSPIPVSRLVSKVAEKAQINTQRYGRRPYGVGLLIAGYDESGPHLFQTCPSGNYFEYKATSIG  157 (211)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCCCCceEEEEEEEEcCCCCeEEEECCCcCEeeeeEEEEC
Confidence            999999999999999999987                                                           


Q ss_pred             -----------cCCC--CCCCHHHHHHHHHHHHHHhhccCC-CCCCcEEEEEEE
Q 040809           88 -----------QDYK--DDMTRQEAVQLALKVLRKTMDSTS-LTSEKLELAEVF  127 (161)
Q Consensus        88 -----------~~y~--~~mt~eeai~la~~al~~~~~~~~-~~~~~iei~ii~  127 (161)
                                 ++|+  ++|+++|++++|+++|+.+++++. +++++|||++|+
T Consensus       158 ~g~~~a~~~Le~~~~~~~~ms~ee~i~~~~~~l~~~~~~~~~~~~~~iei~ii~  211 (211)
T cd03749         158 ARSQSARTYLERHFEEFEDCSLEELIKHALRALRETLPGEQELTIKNVSIAIVG  211 (211)
T ss_pred             CCcHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhccCCCCCCCcEEEEEEC
Confidence                       3577  599999999999999999999776 999999999984

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

>cd03755 proteasome_alpha_type_7 proteasome_alpha_type_7

Probab=99.98  E-value=8.9e-32  Score=207.73  Aligned_cols=118  Identities=39%  Similarity=0.680  Sum_probs=109.7

Q ss_pred             CCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHH
Q 040809            5 YDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDAN   66 (161)
Q Consensus         5 y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~   66 (161)
                      ||+++|+|||||||+|||||                 | |||+|+|.+..+... +..+|||+|++|++|++||+.+|++
T Consensus         1 ~d~~~~~fsp~Gr~~Qveya~~av~~G~t~Igik~~dgVvlaad~~~~~~~~~~-~~~~KI~~I~~~i~~~~sG~~~D~~   79 (207)
T cd03755           1 YDRAITVFSPDGHLFQVEYAQEAVRKGTTAVGVRGKDCVVLGVEKKSVAKLQDP-RTVRKICMLDDHVCLAFAGLTADAR   79 (207)
T ss_pred             CCCCCceECCCCeEeHHHHHHHHHHcCCCEEEEEeCCEEEEEEecCCCCcccCC-CccCcEEEECCCEEEEEecchhhHH
Confidence            89999999999999999999                 5 999999988876654 4789999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCc-----------------------------------------------------------
Q 040809           67 ILINTARVQARRYAYAYQEPI-----------------------------------------------------------   87 (161)
Q Consensus        67 ~l~~~~r~~~~~y~~~~~~~i-----------------------------------------------------------   87 (161)
                      .+++++|.+++.|+++++++|                                                           
T Consensus        80 ~l~~~~r~~~~~~~~~~~~~i~~~~la~~ls~~~~~y~~~~~~rP~~vs~ii~G~D~~~~p~Ly~iD~~G~~~~~~~~a~  159 (207)
T cd03755          80 VLINRARLECQSHRLTVEDPVTVEYITRYIAGLQQRYTQSGGVRPFGISTLIVGFDPDGTPRLYQTDPSGTYSAWKANAI  159 (207)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcccCcccceeEEEEEEEeCCCCeEEEEECCCcCEEcceEEEE
Confidence            999999999999999999988                                                           


Q ss_pred             ------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEE
Q 040809           88 ------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEV  126 (161)
Q Consensus        88 ------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii  126 (161)
                                  ++|+++||++||++++++||.++++   .+++++||++|
T Consensus       160 G~gs~~~~~~Le~~~~~~ms~eeai~l~~~~l~~~~~---~~~~~~e~~~~  207 (207)
T cd03755         160 GRNSKTVREFLEKNYKEEMTRDDTIKLAIKALLEVVQ---SGSKNIELAVM  207 (207)
T ss_pred             CCCCHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHhC---CCCCeEEEEEC
Confidence                        3689999999999999999999996   78999999985

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=99.97  E-value=4.6e-32  Score=205.91  Aligned_cols=149  Identities=36%  Similarity=0.543  Sum_probs=134.0

Q ss_pred             CC---CCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEe
Q 040809            1 MS---RRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVA   59 (161)
Q Consensus         1 m~---~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~s   59 (161)
                      |+   .|||++.++||||||+||||||                 | ||++||-.+++|+++. ..+|||.|+.||||+++
T Consensus         1 MSsIGtGyDls~s~fSpdGrvfQveYA~KAven~~T~IGIk~kdGVVl~vEKli~SkLy~p~-sn~ri~~V~r~iG~ava   79 (254)
T KOG0184|consen    1 MSSIGTGYDLSASTFSPDGRVFQVEYAQKAVENSGTCIGIKCKDGVVLAVEKLITSKLYEPG-SNERIFSVDRHIGMAVA   79 (254)
T ss_pred             CCcccccccccceeeCCCCceehHHHHHHHHhcCCcEEEEecCCeEEEEEeeeecccccccC-CCCceEeecccccEEEe
Confidence            77   8999999999999999999999                 6 9999999999999998 88999999999999999


Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhCCCc---------------------------------------c-----------C
Q 040809           60 GIMSDANILINTARVQARRYAYAYQEPI---------------------------------------Q-----------D   89 (161)
Q Consensus        60 G~~~D~~~l~~~~r~~~~~y~~~~~~~i---------------------------------------~-----------~   89 (161)
                      |+.||++.+++++|.++.+|+.+|+.|+                                       +           .
T Consensus        80 Gl~~Dg~~l~~~ar~ea~~~~~~y~~piP~~~la~rva~yvh~~Tly~~vRpfG~~~~~~~yd~~g~~LymiepSG~~~~  159 (254)
T KOG0184|consen   80 GLIPDGRHLVNRARDEAASWRKNYGDPIPGKHLADRVADYVHAFTLYSSVRPFGASTILGSYDDEGPQLYMIEPSGSSYG  159 (254)
T ss_pred             ccccchHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHhhhheeehhhccccccceEEEEEEeCCCceEEEEcCCCCccc
Confidence            9999999999999999999999999988                                       0           0


Q ss_pred             C--------------------CCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHH
Q 040809           90 Y--------------------KDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLE  149 (161)
Q Consensus        90 y--------------------~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~  149 (161)
                      |                    -++|+.+|+++-+.++|+.+++..+.....||++|++...+|   .+..-|+||.+...
T Consensus       160 Y~~aaiGKgrq~aKtElEKL~~~~mt~~e~VkeaakIiY~~HDe~KdK~feiEm~wvg~eTnG---~h~~vp~el~~ea~  236 (254)
T KOG0184|consen  160 YKGAAIGKGRQAAKTELEKLKIDEMTCKELVKEAAKIIYKVHDENKDKEFEIEMGWVGEETNG---LHEKVPSELLEEAE  236 (254)
T ss_pred             eeeeeccchhHHHHHHHHhcccccccHHHHHHHHHheeEeecccccCcceEEEEEEEEeecCC---ccccCcHHHHHHHH
Confidence            1                    258999999999999999999988889999999999998876   44555668888776


Q ss_pred             Hhcc
Q 040809          150 NFGV  153 (161)
Q Consensus       150 ~~~~  153 (161)
                      +++.
T Consensus       237 ~~a~  240 (254)
T KOG0184|consen  237 KYAK  240 (254)
T ss_pred             HHHH
Confidence            6643

>cd03754 proteasome_alpha_type_6 proteasome_alpha_type_6

Probab=99.97  E-value=2.1e-31  Score=206.90  Aligned_cols=121  Identities=31%  Similarity=0.667  Sum_probs=111.7

Q ss_pred             CCCCCCcccCCCCceeeEecc------------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHH
Q 040809            4 RYDRQTTVFSPEGRLYQVDYM------------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSD   64 (161)
Q Consensus         4 ~y~~~~~~fsp~Grl~qveya------------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D   64 (161)
                      +||+++|+|||||||+|||||                  | |||+|+|.+++++.++ ..+|||+|++||+|++||+.+|
T Consensus         1 ~yd~~~~~fsp~Grl~Qveya~~a~~~~g~t~igi~~~d~Vvlaad~r~~~~~i~~~-~~~Ki~~I~~~i~~~~sG~~~D   79 (215)
T cd03754           1 GFDRHITIFSPEGRLYQVEYAFKAVKNAGLTSVAVRGKDCAVVVTQKKVPDKLIDPS-TVTHLFRITDEIGCVMTGMIAD   79 (215)
T ss_pred             CCCCCCeeECCCCeEeHHHhHHHHHhcCCccEEEEEeCCEEEEEEeccccccccCCc-ccCceEEEcCCEEEEEEechhh
Confidence            699999999999999999999                  5 8999999998877765 7899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCc---------------------------------------------------------
Q 040809           65 ANILINTARVQARRYAYAYQEPI---------------------------------------------------------   87 (161)
Q Consensus        65 ~~~l~~~~r~~~~~y~~~~~~~i---------------------------------------------------------   87 (161)
                      ++.+++++|.+++.|+++|+++|                                                         
T Consensus        80 ~~~l~~~~r~~~~~~~~~~~~~i~v~~la~~ls~~~q~yt~~~~~RP~~v~~ii~G~D~~~gp~Ly~~Dp~Gs~~~~~~~  159 (215)
T cd03754          80 SRSQVQRARYEAAEFKYKYGYEMPVDVLAKRIADINQVYTQHAYMRPLGVSMILIGIDEELGPQLYKCDPAGYFAGYKAT  159 (215)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhCCCCCcCCeeEEEEEEEeCCCCeEEEEEcCCccEEeEEEE
Confidence            99999999999999999999988                                                         


Q ss_pred             --------------cCCCCC--C--CHHHHHHHHHHHHHHhhccCCCCCCcEEEEEE
Q 040809           88 --------------QDYKDD--M--TRQEAVQLALKVLRKTMDSTSLTSEKLELAEV  126 (161)
Q Consensus        88 --------------~~y~~~--m--t~eeai~la~~al~~~~~~~~~~~~~iei~ii  126 (161)
                                    ++|+++  |  |.+||++++++||.++++|+ ++++++||+||
T Consensus       160 a~G~gs~~~~~~Le~~~~~~~~~~~s~eeai~l~~~al~~~~~rd-~~~~~~ei~~~  215 (215)
T cd03754         160 AAGVKEQEATNFLEKKLKKKPDLIESYEETVELAISCLQTVLSTD-FKATEIEVGVV  215 (215)
T ss_pred             EECCCcHHHHHHHHHHhccccccCCCHHHHHHHHHHHHHHHhccc-CCCCcEEEEEC
Confidence                          246774  7  99999999999999999985 67999999986

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=99.97  E-value=4.3e-31  Score=204.39  Aligned_cols=122  Identities=50%  Similarity=0.818  Sum_probs=113.5

Q ss_pred             CCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHH
Q 040809            4 RYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDA   65 (161)
Q Consensus         4 ~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~   65 (161)
                      +||+++|+|||||||+|||||                 | |||+|+|.++++... ++.+|||+|+++++|++||+.+|+
T Consensus         1 ~y~~~~~~fsp~G~l~Q~eya~~av~~G~t~igik~~dgvvla~d~~~~~~~~~~-~~~~KI~~I~~~i~~~~sG~~~D~   79 (211)
T cd03756           1 GYDRAITVFSPDGRLYQVEYAREAVKRGTTALGIKCKEGVVLAVDKRITSKLVEP-ESIEKIYKIDDHVGAATSGLVADA   79 (211)
T ss_pred             CCCCCCceECCCCeEhHHHHHHHHHHcCCCEEEEEECCEEEEEEeccCCCcccCC-CccceEEEEcCCEEEEEecCHHHH
Confidence            699999999999999999999                 5 999999998777664 488999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCc----------------------------------------------------------
Q 040809           66 NILINTARVQARRYAYAYQEPI----------------------------------------------------------   87 (161)
Q Consensus        66 ~~l~~~~r~~~~~y~~~~~~~i----------------------------------------------------------   87 (161)
                      +.+++++|.+++.|++++++++                                                          
T Consensus        80 ~~l~~~l~~~~~~~~~~~~~~~~~~~la~~ls~~~~~~~~~~~~rP~~v~~ll~G~D~~~~~ly~vd~~G~~~~~~~~a~  159 (211)
T cd03756          80 RVLIDRARVEAQIHRLTYGEPIDVEVLVKKICDLKQQYTQHGGVRPFGVALLIAGVDDGGPRLFETDPSGAYNEYKATAI  159 (211)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCCCeechhEEEEEEEEeCCCCEEEEECCCCCeeeeEEEEE
Confidence            9999999999999999999887                                                          


Q ss_pred             ------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEE
Q 040809           88 ------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVF  127 (161)
Q Consensus        88 ------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~  127 (161)
                                  +.|+|+|+++||++++++||..+.++ ..++++++|++|+
T Consensus       160 G~g~~~~~~~Le~~~~~~m~~~ea~~l~~~~l~~~~~~-~~~~~~~~v~ii~  210 (211)
T cd03756         160 GSGRQAVTEFLEKEYKEDMSLEEAIELALKALYAALEE-NETPENVEIAYVT  210 (211)
T ss_pred             CCCCHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHhcc-cCCCCcEEEEEEe
Confidence                        36899999999999999999999986 4699999999996

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

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

Probab=99.97  E-value=2.5e-31  Score=202.92  Aligned_cols=149  Identities=30%  Similarity=0.513  Sum_probs=133.6

Q ss_pred             CC-CCCCCCCcccCCCCceeeEecc-----------e-------EEEEEcccCCCCcccCCCCCceEEecCceEEEEecc
Q 040809            1 MS-RRYDRQTTVFSPEGRLYQVDYM-----------G-------CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGI   61 (161)
Q Consensus         1 m~-~~y~~~~~~fsp~Grl~qveya-----------G-------Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~   61 (161)
                      |. +.||.++|+|||+|||+|||||           |       ||++-+|..+.|..   .+.|||+||+|++++++|+
T Consensus         1 Mfrnqyd~d~t~wsPqGrl~QvEya~EavkqGsatVGLks~thaVLvAl~r~~seLss---~QkKi~~iD~h~g~siAGL   77 (264)
T KOG0863|consen    1 MFRNQYDNDVTTWSPQGRLHQVEYAMEAVKQGSATVGLKSRTHAVLVALKRAQSELSS---HQKKIFKIDDHIGISIAGL   77 (264)
T ss_pred             CCcccccCceeEECCcceehHHHHHHHHHhcccceEeecccceEEEeeeccchhHHHH---hhheeEecccccceEEecc
Confidence            44 8899999999999999999999           2       99999999998853   6799999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCc-----------------c------------------------------------
Q 040809           62 MSDANILINTARVQARRYAYAYQEPI-----------------Q------------------------------------   88 (161)
Q Consensus        62 ~~D~~~l~~~~r~~~~~y~~~~~~~i-----------------~------------------------------------   88 (161)
                      .+|+|.|++++|.+|..|++.|++++                 +                                    
T Consensus        78 t~Darvl~~Ylr~ec~~~~~~~~r~~pv~rl~~~l~~k~q~~Tq~ygrRpYGVGllv~gYDe~G~hl~e~~Psg~v~e~~  157 (264)
T KOG0863|consen   78 TADARVLSRYLRQECLNSRFIYGRPLPVLRLVEDLGDKAQENTQRYGRRPYGVGLLVAGYDESGPHLYEFCPSGNVFECK  157 (264)
T ss_pred             CcchHHHHHHHHHHHhhhhhccCCcccHHHHHHHHHHHHhhhhhhhCCccccceEEEEeecCCCceeEEEcCCccEEEEe
Confidence            99999999999999999999999998                 0                                    


Q ss_pred             ------------CC-------CCCCCHHHHHHHHHHHHHHhhcc-CCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHH
Q 040809           89 ------------DY-------KDDMTRQEAVQLALKVLRKTMDS-TSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLL  148 (161)
Q Consensus        89 ------------~y-------~~~mt~eeai~la~~al~~~~~~-~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l  148 (161)
                                  -|       .++++.||+|+.++.||++++.. +.+++.|++|+||.++.    .|+.++.+++.+++
T Consensus       158 g~sIGsRSQsARTyLEr~~e~f~~~~~eELI~~gi~Alr~tlp~de~lt~~nvsI~Ivgkd~----pf~~~d~~~~~k~~  233 (264)
T KOG0863|consen  158 GMSIGSRSQSARTYLERNLEEFEDSSPEELIKHGIMALRETLPEDEDLTGENVSIAIVGKDE----PFTILDQKDVAKYV  233 (264)
T ss_pred             eeecccchhhHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhcCcccccccceeEEEEEeCCC----ceEeecHHHHHHHH
Confidence                        01       37999999999999999999984 48999999999999997    69999999999998


Q ss_pred             HHhcccCC
Q 040809          149 ENFGVAQP  156 (161)
Q Consensus       149 ~~~~~~~~  156 (161)
                      .......+
T Consensus       234 ~~~~~~~~  241 (264)
T KOG0863|consen  234 DLFKKVDE  241 (264)
T ss_pred             HHhhcCCC
Confidence            77654433

>cd03753 proteasome_alpha_type_5 proteasome_alpha_type_5

Probab=99.97  E-value=1.6e-30  Score=201.53  Aligned_cols=120  Identities=48%  Similarity=0.850  Sum_probs=110.4

Q ss_pred             CCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHH
Q 040809            5 YDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDAN   66 (161)
Q Consensus         5 y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~   66 (161)
                      ||+++|+|||||||+|||||                 | |||+|+|.++++...+ ..+||++|++||+|++||+.+|++
T Consensus         1 ~~~~~~~f~p~G~~~Q~eya~~a~~~G~t~igik~~dgVvlaad~r~~~~~~~~~-~~~KI~~I~~~i~~~~sG~~~D~~   79 (213)
T cd03753           1 YDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIKTKEGVVLAVEKRITSPLMEPS-SVEKIMEIDDHIGCAMSGLIADAR   79 (213)
T ss_pred             CCCCCccCCCCCeEhHHHHHHHHHhcCCCEEEEEeCCEEEEEEecccCCcCcCCC-ccceEEEEcCCEEEEEecCHHHHH
Confidence            89999999999999999999                 5 8999999988876654 789999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCc-----------------------------------------------------------
Q 040809           67 ILINTARVQARRYAYAYQEPI-----------------------------------------------------------   87 (161)
Q Consensus        67 ~l~~~~r~~~~~y~~~~~~~i-----------------------------------------------------------   87 (161)
                      .+++.+|.+++.|++.++++|                                                           
T Consensus        80 ~l~~~~r~~~~~~~~~~~~~i~~~~~~~~ls~~~~~~~~~~~~~~~~~rP~~v~~ii~G~D~~gp~Ly~vd~~G~~~~~~  159 (213)
T cd03753          80 TLIDHARVEAQNHRFTYNEPMTVESVTQAVSDLALQFGEGDDGKKAMSRPFGVALLIAGVDENGPQLFHTDPSGTFTRCD  159 (213)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhCcccccccccccceEEEEEEEEcCCCCEEEEECCCCCeeccc
Confidence            999999999999998888765                                                           


Q ss_pred             ----------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEE
Q 040809           88 ----------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEV  126 (161)
Q Consensus        88 ----------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii  126 (161)
                                      ++|+++|+++||++++++||+.+.++ .++++++||++|
T Consensus       160 ~~a~G~~~~~~~~~L~~~~~~~ls~eeai~l~~~~l~~~~~~-~~~~~~~ei~~~  213 (213)
T cd03753         160 AKAIGSGSEGAQSSLQEKYHKDMTLEEAEKLALSILKQVMEE-KLNSTNVELATV  213 (213)
T ss_pred             EEEECCCcHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHhcc-cCCCCcEEEEEC
Confidence                            36899999999999999999999875 699999999985

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

>cd01911 proteasome_alpha proteasome alpha subunit

Probab=99.97  E-value=6.6e-30  Score=197.44  Aligned_cols=120  Identities=53%  Similarity=0.930  Sum_probs=112.1

Q ss_pred             CCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHH
Q 040809            5 YDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDAN   66 (161)
Q Consensus         5 y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~   66 (161)
                      ||+++|+|||||||+|||||                 | |||+|+|.+.++.. .++.+|||+|+++++|+.||..+|++
T Consensus         1 ~~~~~~~f~~~G~~~q~eya~~~~~~G~tvigi~~~dgVvlaaD~~~~~~~~~-~~~~~KI~~i~~~i~~~~sG~~~D~~   79 (209)
T cd01911           1 YDRSITTFSPEGRLFQVEYALEAVKNGSTAVGIKGKDGVVLAVEKKVTSKLLD-PSSVEKIFKIDDHIGCAVAGLTADAR   79 (209)
T ss_pred             CCCCCccCCCCCEEeHHHHHHHHHHcCCCEEEEEECCEEEEEEEecCCccccC-CcccceEEEecCCeEEEeccCcHhHH
Confidence            89999999999999999999                 5 89999999987664 35889999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCc-----------------------------------------------------------
Q 040809           67 ILINTARVQARRYAYAYQEPI-----------------------------------------------------------   87 (161)
Q Consensus        67 ~l~~~~r~~~~~y~~~~~~~i-----------------------------------------------------------   87 (161)
                      .+.+.++..+..|++.++++|                                                           
T Consensus        80 ~l~~~l~~~~~~~~~~~g~~~~~~~la~~ls~~~~~~~~~~~~rP~~v~~iv~G~d~~~~~~Ly~iD~~G~~~~~~~~a~  159 (209)
T cd01911          80 VLVNRARVEAQNYRYTYGEPIPVEVLVKRIADLAQVYTQYGGVRPFGVSLLIAGYDEEGGPQLYQTDPSGTYFGYKATAI  159 (209)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCccChhheEEEEEEcCCCCcEEEEECCCCCeeeeeEEEe
Confidence            999999999999999999887                                                           


Q ss_pred             ------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEE
Q 040809           88 ------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEV  126 (161)
Q Consensus        88 ------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii  126 (161)
                                  +.|+++|+++||++++++||..+.+++. ++++++|+++
T Consensus       160 G~g~~~~~~~L~~~~~~~ms~~ea~~l~~~~l~~~~~~d~-~~~~~~i~i~  209 (209)
T cd01911         160 GKGSQEAKTFLEKRYKKDLTLEEAIKLALKALKEVLEEDK-KAKNIEIAVV  209 (209)
T ss_pred             CCCcHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHhccC-CCCcEEEEEC
Confidence                        3689999999999999999999999987 9999999985

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.

>PTZ00488 Proteasome subunit beta type-5; Provisional

Probab=99.94  E-value=9.9e-26  Score=178.40  Aligned_cols=141  Identities=17%  Similarity=0.213  Sum_probs=126.4

Q ss_pred             ccCCCCceeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc-
Q 040809           11 VFSPEGRLYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI-   87 (161)
Q Consensus        11 ~fsp~Grl~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i-   87 (161)
                      .++.-+.+.-|.|. | |||+|+|.+.+.++..++.+|||+|++|++|++||+.+|++.|++++|.+++.|++.++++| 
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            44445568888887 6 99999999975555556899999999999999999999999999999999999999999987 


Q ss_pred             -----------------------------------------------------------------cCCCCCCCHHHHHHH
Q 040809           88 -----------------------------------------------------------------QDYKDDMTRQEAVQL  102 (161)
Q Consensus        88 -----------------------------------------------------------------~~y~~~mt~eeai~l  102 (161)
                                                                                       +.|+++||.+||+++
T Consensus       115 v~~la~~ls~~l~~~R~~~~~v~~iiaG~D~~gp~Ly~vDp~Gs~~~~~~~a~G~gs~~~~~~Le~~~k~dms~eEai~l  194 (247)
T PTZ00488        115 VAAASKILANIVWNYKGMGLSMGTMICGWDKKGPGLFYVDNDGTRLHGNMFSCGSGSTYAYGVLDAGFKWDLNDEEAQDL  194 (247)
T ss_pred             HHHHHHHHHHHHHhcCCCCeeEEEEEEEEeCCCCEEEEEcCCcceeecCCEEEccCHHHHHHHHHhcCcCCCCHHHHHHH
Confidence                                                                             468999999999999


Q ss_pred             HHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhcccCC
Q 040809          103 ALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFGVAQP  156 (161)
Q Consensus       103 a~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~~~~~  156 (161)
                      +++||+.+.+|+..++++++|++|+++     +|+.|+++||+++++++.++++
T Consensus       195 ~~kal~~~~~Rd~~sg~~~ei~iI~k~-----g~~~l~~~ei~~~l~~~~~~~~  243 (247)
T PTZ00488        195 GRRAIYHATFRDAYSGGAINLYHMQKD-----GWKKISADDCFDLHQKYAAEKE  243 (247)
T ss_pred             HHHHHHHHHHhccccCCCeEEEEEcCC-----ccEECCHHHHHHHHHHHhhhcc
Confidence            999999999999999999999999976     4899999999999999876654

>TIGR03690 20S_bact_beta proteasome, beta subunit, bacterial type

Probab=99.91  E-value=1.7e-23  Score=163.00  Aligned_cols=132  Identities=21%  Similarity=0.274  Sum_probs=115.6

Q ss_pred             ceeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc-------
Q 040809           17 RLYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI-------   87 (161)
Q Consensus        17 rl~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i-------   87 (161)
                      .+.-+.+. | |||+|+|.+++.++.+++.+|||+|++|++|++||+.+|++.+++++|.+++.|++.++++|       
T Consensus         4 T~igi~~kdgVvlaad~r~~~g~~~~~~~~~KI~~i~~~i~~~~sG~~aD~~~l~~~~r~~~~~~~~~~~~~i~~~~la~   83 (219)
T TIGR03690         4 TIVALTYPGGVLMAGDRRATQGNMIASRDVEKVYPTDEYSAVGIAGTAGLAIELVRLFQVELEHYEKIEGVPLTLDGKAN   83 (219)
T ss_pred             EEEEEEECCEEEEEECCccccCcEEEcCCcceEEEcCCcEEEEecccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHH
Confidence            35666676 6 99999999985555555899999999999999999999999999999999999999999887       


Q ss_pred             -----------------------------------------------------------------cCCCCCCCHHHHHHH
Q 040809           88 -----------------------------------------------------------------QDYKDDMTRQEAVQL  102 (161)
Q Consensus        88 -----------------------------------------------------------------~~y~~~mt~eeai~l  102 (161)
                                                                                       ++|+++||.+||+++
T Consensus        84 ~ls~~~~~~~~~~~rp~~v~~iiaG~D~~~~~~~Ly~~Dp~G~~~~~~~~~a~G~g~~~a~~~Le~~~~~~ms~eeai~l  163 (219)
T TIGR03690        84 RLAAMVRGNLPAAMQGLAVVPLLAGYDLDAGAGRIFSYDVTGGRYEERGYHAVGSGSVFAKGALKKLYSPDLDEDDALRV  163 (219)
T ss_pred             HHHHHHHhhhhhccCCceEEEEEEEECCCCCCcEEEEEeCCCCeeecCCeEEEeccHHHHHHHHHhcCCCCcCHHHHHHH
Confidence                                                                             368999999999999


Q ss_pred             HHHHHHHhhccCCCCCCc-------EEEEEEEeCCCCceeEEECCHHHHHHHHHHhcc
Q 040809          103 ALKVLRKTMDSTSLTSEK-------LELAEVFLLPSGKVKYRICSPESLTMLLENFGV  153 (161)
Q Consensus       103 a~~al~~~~~~~~~~~~~-------iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~~  153 (161)
                      +++||..+.+++..+++.       +||++|+++     .|++|+++||+++++++.+
T Consensus       164 ~~~al~~~~~~d~~s~~~~~~~~~~~ei~ii~~~-----g~~~l~~~ei~~~~~~~~~  216 (219)
T TIGR03690       164 AVEALYDAADDDSATGGPDLVRGIYPTVVVITAD-----GARRVPESELEELARAIVE  216 (219)
T ss_pred             HHHHHHHHHhcccccCCcccccccccEEEEEccC-----ceEEcCHHHHHHHHHHHHh
Confidence            999999999987756653       399999755     4999999999999988754

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.

>cd03761 proteasome_beta_type_5 proteasome beta type-5 subunit

Probab=99.91  E-value=1.7e-23  Score=159.29  Aligned_cols=112  Identities=18%  Similarity=0.223  Sum_probs=103.2

Q ss_pred             eeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc---------
Q 040809           19 YQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI---------   87 (161)
Q Consensus        19 ~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i---------   87 (161)
                      .-+.|. | |||+|+|.+++.++.+++.+|||+|++|++|++||+.+|++.|++++|.+++.|++.|+++|         
T Consensus         4 igi~~kdgVvla~d~r~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i~~~~la~~l   83 (188)
T cd03761           4 LAFIFQGGVIVAVDSRATAGSYIASQTVKKVIEINPYLLGTMAGGAADCQYWERVLGRECRLYELRNKERISVAAASKLL   83 (188)
T ss_pred             EEEEECCEEEEEEcCCccCCcEEEcCCcceEEEccCcEEEEeCccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHH
Confidence            445555 6 99999999997777666899999999999999999999999999999999999999999988         


Q ss_pred             ---------------------------------------------------------cCCCCCCCHHHHHHHHHHHHHHh
Q 040809           88 ---------------------------------------------------------QDYKDDMTRQEAVQLALKVLRKT  110 (161)
Q Consensus        88 ---------------------------------------------------------~~y~~~mt~eeai~la~~al~~~  110 (161)
                                                                               ++|+++||++||++++++||+.+
T Consensus        84 s~~l~~~~~~~~~v~~li~G~D~~g~~L~~~dp~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~~s~eea~~l~~~~l~~~  163 (188)
T cd03761          84 SNMLYQYKGMGLSMGTMICGWDKTGPGLYYVDSDGTRLKGDLFSVGSGSTYAYGVLDSGYRYDLSVEEAYDLARRAIYHA  163 (188)
T ss_pred             HHHHHhcCCCCeEEEEEEEEEeCCCCEEEEEcCCceEEEcCeEEEcccHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHH
Confidence                                                                     46899999999999999999999


Q ss_pred             hccCCCCCCcEEEEEEEeCC
Q 040809          111 MDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus       111 ~~~~~~~~~~iei~ii~~~~  130 (161)
                      .+||..++++++|++|++++
T Consensus       164 ~~rd~~sg~~~~v~ii~~~g  183 (188)
T cd03761         164 THRDAYSGGNVNLYHVREDG  183 (188)
T ss_pred             HHhcccCCCCeEEEEEcCCc
Confidence            99999999999999999874

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

>cd03759 proteasome_beta_type_3 proteasome beta type-3 subunit

Probab=99.90  E-value=7.1e-23  Score=156.74  Aligned_cols=115  Identities=17%  Similarity=0.219  Sum_probs=106.9

Q ss_pred             CceeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc------
Q 040809           16 GRLYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI------   87 (161)
Q Consensus        16 Grl~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i------   87 (161)
                      |.+.-+-|. | |||+|+|.+++++++++..+|||+|++|++|++||+.+|++.+++++|.+++.|++.++++|      
T Consensus         4 ~t~igik~~dgVvlaad~~~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la   83 (195)
T cd03759           4 GAVVAMAGKDCVAIASDLRLGVQQQTVSTDFQKVFRIGDRLYIGLAGLATDVQTLAQKLRFRVNLYRLREEREIKPKTFS   83 (195)
T ss_pred             ceEEEEEcCCEEEEEEccccccCCEeEecCCCeEEEeCCCEEEEccchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            447777787 6 99999999999998776789999999999999999999999999999999999999999988      


Q ss_pred             --------------------------------------------------------------cCCCCCCCHHHHHHHHHH
Q 040809           88 --------------------------------------------------------------QDYKDDMTRQEAVQLALK  105 (161)
Q Consensus        88 --------------------------------------------------------------~~y~~~mt~eeai~la~~  105 (161)
                                                                                    +.|+++||.+||++++++
T Consensus        84 ~~l~~~ly~~r~~P~~v~~ii~G~D~~~~p~Ly~~D~~G~~~~~~~~~a~G~g~~~~~~~Le~~~~~~~s~~ea~~l~~~  163 (195)
T cd03759          84 SLISSLLYEKRFGPYFVEPVVAGLDPDGKPFICTMDLIGCPSIPSDFVVSGTASEQLYGMCESLWRPDMEPDELFETISQ  163 (195)
T ss_pred             HHHHHHHHHhcCCCceEEEEEEEEcCCCCEEEEEEcCCCcccccCCEEEEcccHHHHHHHHHhccCCCCCHHHHHHHHHH
Confidence                                                                          368999999999999999


Q ss_pred             HHHHhhccCCCCCCcEEEEEEEeCC
Q 040809          106 VLRKTMDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus       106 al~~~~~~~~~~~~~iei~ii~~~~  130 (161)
                      ||+.+.+|+..++++++|++|++++
T Consensus       164 ~l~~~~~rd~~~~~~~~i~ii~~~g  188 (195)
T cd03759         164 ALLSAVDRDALSGWGAVVYIITKDK  188 (195)
T ss_pred             HHHHHHhhCcccCCceEEEEEcCCc
Confidence            9999999999999999999999874

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

>cd03758 proteasome_beta_type_2 proteasome beta type-2 subunit

Probab=99.89  E-value=3.8e-22  Score=152.56  Aligned_cols=112  Identities=19%  Similarity=0.212  Sum_probs=102.0

Q ss_pred             eeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc---------
Q 040809           19 YQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI---------   87 (161)
Q Consensus        19 ~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i---------   87 (161)
                      ..+.|. | |||+|+|.+.+.++.+++.+|||+|++|++|++||+.+|++.|++++|.+++.|++.+++++         
T Consensus         5 igi~~~dgVvlaad~r~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~l   84 (193)
T cd03758           5 IGIKGKDFVILAADTSAARSILVLKDDEDKIYKLSDHKLMACSGEAGDRLQFAEYIQKNIQLYKMRNGYELSPKAAANFT   84 (193)
T ss_pred             EEEEeCCEEEEEEcCccccCcEEEecCcccEEEeCCCeEEEEccchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Confidence            445555 6 99999999887656566899999999999999999999999999999999999999999887         


Q ss_pred             ------------------------------------------------------------cCCCCCCCHHHHHHHHHHHH
Q 040809           88 ------------------------------------------------------------QDYKDDMTRQEAVQLALKVL  107 (161)
Q Consensus        88 ------------------------------------------------------------~~y~~~mt~eeai~la~~al  107 (161)
                                                                                  +.|+++||++||++++++|+
T Consensus        85 ~~~~~~~~~~~rP~~~~~li~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~ms~eeai~l~~~a~  164 (193)
T cd03758          85 RRELAESLRSRTPYQVNLLLAGYDKVEGPSLYYIDYLGTLVKVPYAAHGYGAYFCLSILDRYYKPDMTVEEALELMKKCI  164 (193)
T ss_pred             HHHHHHHhhcCCCeEEEEEEEEEcCCCCcEEEEECCCcceEECCeeEEeecHHHHHHHHHhccCCCCCHHHHHHHHHHHH
Confidence                                                                        46899999999999999999


Q ss_pred             HHhhccCCCCCCcEEEEEEEeCC
Q 040809          108 RKTMDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus       108 ~~~~~~~~~~~~~iei~ii~~~~  130 (161)
                      ..+.+||..++++++|++|++++
T Consensus       165 ~~~~~rd~~~~~~i~i~ii~~~g  187 (193)
T cd03758         165 KELKKRFIINLPNFTVKVVDKDG  187 (193)
T ss_pred             HHHHHhccccCCceEEEEEcCCC
Confidence            99999999999999999999874

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.

>TIGR03691 20S_bact_alpha proteasome, alpha subunit, bacterial type

Probab=99.88  E-value=4.9e-22  Score=155.67  Aligned_cols=115  Identities=25%  Similarity=0.360  Sum_probs=101.0

Q ss_pred             e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhC-CCc---------------
Q 040809           25 G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQ-EPI---------------   87 (161)
Q Consensus        25 G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~-~~i---------------   87 (161)
                      | |||+|++.        ++.+|||+|++||+|++||+.+|++.+++++|.+++.|++.|+ .++               
T Consensus        38 gVVLaaek~~--------~~~~KI~~I~d~ig~~~sG~~~D~~~lv~~~r~~a~~~~~~~~~~~~~v~~la~~~tq~~~~  109 (228)
T TIGR03691        38 GILFVAENPS--------RSLHKISELYDRIGFAAVGKYNEFENLRRAGIRYADMRGYSYDRRDVTGRGLANAYAQTLGT  109 (228)
T ss_pred             eEEEEEecCC--------CCcCcEEEecCCEEEEEcCCHHHHHHHHHHHHHHHHHHhhhcCCCCccHHHHHHHHHhhccc
Confidence            6 99999972        2579999999999999999999999999999999999999998 444               


Q ss_pred             ---------------------------------------------------------cCCCCCCCHHHHHHHHHHHHHHh
Q 040809           88 ---------------------------------------------------------QDYKDDMTRQEAVQLALKVLRKT  110 (161)
Q Consensus        88 ---------------------------------------------------------~~y~~~mt~eeai~la~~al~~~  110 (161)
                                                                               ++|+++||++||+++|++||+.+
T Consensus       110 ~~~~~~RP~gvs~Li~G~d~~~~gp~Ly~vDpsG~~~~~~~~~aiG~gs~~a~~~Lek~y~~~ms~eeai~la~~aL~~~  189 (228)
T TIGR03691       110 IFTEQQKPYEVEICVAEVGETPDQDQLYRITFDGSIVDERGFVVMGGTTEPIATALKESYRDGLSLADALGLAVQALRAG  189 (228)
T ss_pred             ccccccCcceEEEEEEEEcCCCCCCEEEEECCCCCceeccceEEECCChHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHH
Confidence                                                                     35899999999999999999999


Q ss_pred             hc--cCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHH
Q 040809          111 MD--STSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLL  148 (161)
Q Consensus       111 ~~--~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l  148 (161)
                      ++  ++.+++.++||++|+++.. ...|++|+++||+++|
T Consensus       190 ~~~~r~~~~~~~iEv~ii~k~~~-~~~f~~l~~~ei~~~l  228 (228)
T TIGR03691       190 GNGEKRELDAASLEVAVLDRSRP-RRAFRRITGEALERLL  228 (228)
T ss_pred             hccccccCCccceEEEEEeCCCC-ccceEECCHHHHHhhC
Confidence            64  5679999999999997531 2269999999999875

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.

>cd03765 proteasome_beta_bacterial Bacterial proteasome, beta subunit

Probab=99.88  E-value=4.6e-22  Score=156.37  Aligned_cols=122  Identities=15%  Similarity=0.124  Sum_probs=107.0

Q ss_pred             Eecc-e-EEEEEcccCCCCcccCCCCCceEEec----CceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCC-Cc------
Q 040809           21 VDYM-G-CLVGENNVTSKLLQTSTSAEKMYKID----DHVACAVAGIMSDANILINTARVQARRYAYAYQE-PI------   87 (161)
Q Consensus        21 veya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~----~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~-~i------   87 (161)
                      |.+. | |||+|+|.++++...+ +.+|||+|+    +||+||.||+.+|++.+++++|.+++.|++++|+ ++      
T Consensus         6 Ik~kdGVVLaadkr~~~~l~~~~-~~~KI~~I~~~~d~~I~~~~sG~~aD~~~l~~~~r~~~~~~~~~~g~~~~~v~~la   84 (236)
T cd03765           6 IKLDAGLVFASDSRTNAGVDNIS-TYRKMFVFSVPGERVIVLLTAGNLATTQAVISLLQRDLEDPEETNLLNAPTMFDAA   84 (236)
T ss_pred             EEeCCeEEEEEccCccCCCcccc-ccceEEEecCCCCCEEEEEcCCcHHHHHHHHHHHHHHHHhhHHhhCCCCCCHHHHH
Confidence            3444 6 9999999999988877 789999998    8999999999999999999999999999999999 56      


Q ss_pred             --------------------------------------------------------------------------cCCCCC
Q 040809           88 --------------------------------------------------------------------------QDYKDD   93 (161)
Q Consensus        88 --------------------------------------------------------------------------~~y~~~   93 (161)
                                                                                                ++|+++
T Consensus        85 ~~i~~~l~~~~~q~~~~~~~~~rp~gvslIigG~D~~~Gp~LY~idpsG~~~e~~a~~~~~AiG~~~~a~~~Lek~yk~~  164 (236)
T cd03765          85 RYVGETLREVQEQDREALKKAGIDFSASFILGGQIKGEEPRLFLIYPQGNFIEATPDTPFLQIGETKYGKPILDRVITPD  164 (236)
T ss_pred             HHHHHHHHHHHhhcccccccCCcceEEEEEEEeEECCCCCEEEEECCCCCEEeecCCCceeeeCCchhhHHHHHHhcCCC
Confidence                                                                                      246899


Q ss_pred             CCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHH
Q 040809           94 MTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPES  143 (161)
Q Consensus        94 mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~e  143 (161)
                      ||++||+++|++||.+++++|..++.+|+|++|++++.-....+++..++
T Consensus       165 ms~eeai~la~~al~~a~~rd~~sg~~iev~vI~k~G~~~~~~~~~~~~~  214 (236)
T cd03765         165 TSLEDAAKCALVSMDSTMRSNLSVGPPLDLLVYERDSLQVGHYRRIEEDD  214 (236)
T ss_pred             CCHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEEECCCeeeeeeEEecCCC
Confidence            99999999999999999999999999999999999854222566676655

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

>cd03757 proteasome_beta_type_1 proteasome beta type-1 subunit

Probab=99.88  E-value=5.4e-22  Score=153.76  Aligned_cols=115  Identities=16%  Similarity=0.276  Sum_probs=105.6

Q ss_pred             CceeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc------
Q 040809           16 GRLYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI------   87 (161)
Q Consensus        16 Grl~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i------   87 (161)
                      +.+.-+.|. | |||+|+|.++++++..+..+|||+|++|++|++||+.+|++.+++++|.+++.|++.++++|      
T Consensus         9 ~Tvigik~~dgVvlaaD~r~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~~r~~~~~~~~~~g~~i~~~~la   88 (212)
T cd03757           9 GTVLAIAGNDFAVIAGDTRLSEGYSILSRDSPKIFKLTDKCVLGSSGFQADILALTKRLKARIKMYKYSHNKEMSTEAIA   88 (212)
T ss_pred             ccEEEEEcCCEEEEEECCccccCCEeEeCCCCeEEEcCCCEEEEccchHHHHHHHHHHHHHHHHHHhHHhCCCCCHHHHH
Confidence            348889998 5 99999999999988666899999999999999999999999999999999999999999887      


Q ss_pred             -------------------------------------------------------------cCC---------CCCCCHH
Q 040809           88 -------------------------------------------------------------QDY---------KDDMTRQ   97 (161)
Q Consensus        88 -------------------------------------------------------------~~y---------~~~mt~e   97 (161)
                                                                                   +.|         +++||++
T Consensus        89 ~~ls~~ly~~R~~P~~~~~iiaG~D~~~~p~Ly~~D~~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~~~~~~~~~~ms~e  168 (212)
T cd03757          89 QLLSTILYSRRFFPYYVFNILAGIDEEGKGVVYSYDPVGSYERETYSAGGSASSLIQPLLDNQVGRKNQNNVERTPLSLE  168 (212)
T ss_pred             HHHHHHHHhhcCCCeEEEEEEEEEcCCCCEEEEEEcCccCeeecCEEEEeecHHHHHHHHHHHHHhhccCcCCCCCCCHH
Confidence                                                                         133         3899999


Q ss_pred             HHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCC
Q 040809           98 EAVQLALKVLRKTMDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus        98 eai~la~~al~~~~~~~~~~~~~iei~ii~~~~  130 (161)
                      ||++++++||+.+.+||..++++++|++|++++
T Consensus       169 ea~~l~~~~l~~~~~rd~~sg~~i~i~iit~~g  201 (212)
T cd03757         169 EAVSLVKDAFTSAAERDIYTGDSLEIVIITKDG  201 (212)
T ss_pred             HHHHHHHHHHHHHHHhCcccCCCEEEEEEcCCC
Confidence            999999999999999999999999999999875

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=99.88  E-value=1.3e-21  Score=148.67  Aligned_cols=112  Identities=18%  Similarity=0.292  Sum_probs=102.5

Q ss_pred             eeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc---------
Q 040809           19 YQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI---------   87 (161)
Q Consensus        19 ~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i---------   87 (161)
                      .-+-|. | |||+|+|.+.+.++.+++.+|||+|++|++|++||+.+|++.+.+.+|.+++.|++.+++++         
T Consensus         4 igi~~~dgVvla~D~r~~~g~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~l~~~~~~~~~~~~~~~~~~~~a~~l   83 (188)
T cd03762           4 IAVEYDGGVVLGADSRTSTGSYVANRVTDKLTQLHDRIYCCRSGSAADTQAIADYVRYYLDMHSIELGEPPLVKTAASLF   83 (188)
T ss_pred             EEEEECCeEEEEEcccccCCceEEcCCcccEEEccCCEEEEecccHHHHHHHHHHHHHHHHHhHHhhCCCCCHHHHHHHH
Confidence            345555 6 89999999997666666899999999999999999999999999999999999999999988         


Q ss_pred             ---------------------------------------------------------cCCCCCCCHHHHHHHHHHHHHHh
Q 040809           88 ---------------------------------------------------------QDYKDDMTRQEAVQLALKVLRKT  110 (161)
Q Consensus        88 ---------------------------------------------------------~~y~~~mt~eeai~la~~al~~~  110 (161)
                                                                               +.|+++||++||++++++||+.+
T Consensus        84 ~~~~~~~~~~~~~~~ii~G~d~~~gp~ly~~d~~G~~~~~~~~~~G~g~~~~~~~Le~~~~~~~s~~ea~~l~~~al~~~  163 (188)
T cd03762          84 KNLCYNYKEMLSAGIIVAGWDEQNGGQVYSIPLGGMLIRQPFAIGGSGSTYIYGYVDANYKPGMTLEECIKFVKNALSLA  163 (188)
T ss_pred             HHHHHhccccceeeEEEEEEcCCCCcEEEEECCCCCEEecCEEEEcccHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHH
Confidence                                                                     46899999999999999999999


Q ss_pred             hccCCCCCCcEEEEEEEeCC
Q 040809          111 MDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus       111 ~~~~~~~~~~iei~ii~~~~  130 (161)
                      .+||..++++++|++|++++
T Consensus       164 ~~rd~~~~~~~~i~~i~~~g  183 (188)
T cd03762         164 MSRDGSSGGVIRLVIITKDG  183 (188)
T ss_pred             HHhccccCCCEEEEEECCCC
Confidence            99999999999999999874

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

>cd03763 proteasome_beta_type_7 proteasome beta type-7 subunit

Probab=99.87  E-value=1.4e-21  Score=148.76  Aligned_cols=112  Identities=19%  Similarity=0.218  Sum_probs=102.5

Q ss_pred             eeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc---------
Q 040809           19 YQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI---------   87 (161)
Q Consensus        19 ~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i---------   87 (161)
                      ..+-|. | |||+|+|.+++.++..+..+|||+|+++++|++||+.+|++.+++++|.+++.|++.+++++         
T Consensus         4 igi~~~dgvvlaad~r~~~g~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~l   83 (189)
T cd03763           4 VGVVFKDGVVLGADTRATEGPIVADKNCEKIHYIAPNIYCCGAGTAADTEAVTNMISSNLELHRLNTGRKPRVVTALTML   83 (189)
T ss_pred             EEEEECCeEEEEEcCCcccCceEEcCCccceEEecCCEEEEcCccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Confidence            344555 6 99999999998777666889999999999999999999999999999999999999999887         


Q ss_pred             --------------------------------------------------------cCCCCCCCHHHHHHHHHHHHHHhh
Q 040809           88 --------------------------------------------------------QDYKDDMTRQEAVQLALKVLRKTM  111 (161)
Q Consensus        88 --------------------------------------------------------~~y~~~mt~eeai~la~~al~~~~  111 (161)
                                                                              ++|+|+||++||++++++||..+.
T Consensus        84 ~~~l~~~~~p~~v~~ivaG~d~~g~~ly~~d~~G~~~~~~~~a~G~~~~~~~~~L~~~~~~~ls~~ea~~l~~~~l~~~~  163 (189)
T cd03763          84 KQHLFRYQGHIGAALVLGGVDYTGPHLYSIYPHGSTDKLPFVTMGSGSLAAMSVLEDRYKPDMTEEEAKKLVCEAIEAGI  163 (189)
T ss_pred             HHHHHHcCCccceeEEEEeEcCCCCEEEEECCCCCEEecCEEEEcCCHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHH
Confidence                                                                    468999999999999999999999


Q ss_pred             ccCCCCCCcEEEEEEEeCC
Q 040809          112 DSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus       112 ~~~~~~~~~iei~ii~~~~  130 (161)
                      +|+..++++++|++|++++
T Consensus       164 ~rd~~~~~~~~v~ii~~~g  182 (189)
T cd03763         164 FNDLGSGSNVDLCVITKDG  182 (189)
T ss_pred             HhcCcCCCceEEEEEcCCc
Confidence            9999999999999999874

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=99.87  E-value=6.5e-21  Score=144.88  Aligned_cols=117  Identities=24%  Similarity=0.451  Sum_probs=105.4

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +..+.|. | |||+|+|.+++.++..+..+||++|++|++|+++|+.+|++.+.+.+|.+++.|++.+++++        
T Consensus         3 ~iai~~~dgvvia~d~r~~~g~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~   82 (188)
T cd03764           3 TVGIVCKDGVVLAADKRASMGNFIASKNVKKIFQIDDKIAMTIAGSVGDAQSLVRILKAEARLYELRRGRPMSIKALATL   82 (188)
T ss_pred             EEEEEeCCEEEEEEccccccCCEEecCCcccEEEccCCEEEEcCccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
Confidence            3456666 5 89999999987666666899999999999999999999999999999999999999999887        


Q ss_pred             ----------------------------------------------------------cCCCCCCCHHHHHHHHHHHHHH
Q 040809           88 ----------------------------------------------------------QDYKDDMTRQEAVQLALKVLRK  109 (161)
Q Consensus        88 ----------------------------------------------------------~~y~~~mt~eeai~la~~al~~  109 (161)
                                                                                +.|+++|+++||++++++||+.
T Consensus        83 i~~~~~~~~~~P~~~~~lvaG~d~~~~~ly~~D~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~~~~ea~~l~~~~l~~  162 (188)
T cd03764          83 LSNILNSSKYFPYIVQLLIGGVDEEGPHLYSLDPLGSIIEDKYTATGSGSPYAYGVLEDEYKEDMTVEEAKKLAIRAIKS  162 (188)
T ss_pred             HHHHHHhcCCCCcEEEEEEEEEeCCCCEEEEECCCCCEEEcCEEEEcCcHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHH
Confidence                                                                      3689999999999999999999


Q ss_pred             hhccCCCCCCcEEEEEEEeCCCCceeEEEC
Q 040809          110 TMDSTSLTSEKLELAEVFLLPSGKVKYRIC  139 (161)
Q Consensus       110 ~~~~~~~~~~~iei~ii~~~~~g~~~~~~l  139 (161)
                      +.+|+..++++++|++|++++     +++|
T Consensus       163 ~~~rd~~~~~~i~i~iv~~~g-----~~~~  187 (188)
T cd03764         163 AIERDSASGDGIDVVVITKDG-----YKEL  187 (188)
T ss_pred             HHhhcCCCCCcEEEEEECCCC-----eEeC
Confidence            999999999999999999773     7765

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

>cd03760 proteasome_beta_type_4 proteasome beta type-4 subunit

Probab=99.87  E-value=5.3e-21  Score=146.55  Aligned_cols=114  Identities=15%  Similarity=0.188  Sum_probs=100.2

Q ss_pred             ceeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHH-HHHHHhCCCc------
Q 040809           17 RLYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQAR-RYAYAYQEPI------   87 (161)
Q Consensus        17 rl~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~-~y~~~~~~~i------   87 (161)
                      .+.-+.+. | |||+|+|.+.+.++..+..+|||+|++|++|+++|+.+|++.+++++|.+++ .|++.++++|      
T Consensus         4 T~igi~~kdgVvlaad~r~~~~~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~~la   83 (197)
T cd03760           4 SVIAIKYKDGVIIAADTLGSYGSLARFKNVERIFKVGDNTLLGASGDYADFQYLKRLLDQLVIDDECLDDGHSLSPKEIH   83 (197)
T ss_pred             eEEEEEeCCcEEEEEcCcccccceeecCCCCcEEEecCcEEEEeCcchHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHH
Confidence            46677777 5 9999999985444444588999999999999999999999999999999997 5667888777      


Q ss_pred             ---------------------------------------------------------------cCCCC--CCCHHHHHHH
Q 040809           88 ---------------------------------------------------------------QDYKD--DMTRQEAVQL  102 (161)
Q Consensus        88 ---------------------------------------------------------------~~y~~--~mt~eeai~l  102 (161)
                                                                                     +.|++  +||++||+++
T Consensus        84 ~~i~~~~y~~~~~~rP~~v~~iiaG~D~~~gp~Ly~~D~~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~~~ms~eea~~l  163 (197)
T cd03760          84 SYLTRVLYNRRSKMNPLWNTLVVGGVDNEGEPFLGYVDLLGTAYEDPHVATGFGAYLALPLLREAWEKKPDLTEEEARAL  163 (197)
T ss_pred             HHHHHHHHHHhhcCCCceEEEEEEEEcCCCCEEEEEEcCCccEEECCEeEEccHHHHHHHHHHhhcCCCCCCCHHHHHHH
Confidence                                                                           36888  9999999999


Q ss_pred             HHHHHHHhhccCCCCCCcEEEEEEEeCC
Q 040809          103 ALKVLRKTMDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus       103 a~~al~~~~~~~~~~~~~iei~ii~~~~  130 (161)
                      +++||+.+.+|+..++++++|++|++++
T Consensus       164 ~~~~l~~~~~rd~~~~~~~~i~ii~~~g  191 (197)
T cd03760         164 IEECMKVLYYRDARSINKYQIAVVTKEG  191 (197)
T ss_pred             HHHHHHHHHHhccccCCceEEEEECCCC
Confidence            9999999999999999999999999874

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

>TIGR03634 arc_protsome_B proteasome endopeptidase complex, archaeal, beta subunit

Probab=99.86  E-value=6.6e-21  Score=144.43  Aligned_cols=113  Identities=22%  Similarity=0.434  Sum_probs=102.6

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +.-+.|. | |||+|+|.+.+.++..+..+|||+|++|++|++||..+|++.+.+++|.+++.|++.+++++        
T Consensus         4 ~igi~~~dgVvla~d~~~~~~~~i~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~   83 (185)
T TIGR03634         4 TVGIKCKDGVVLAADKRASMGNFVASKNAKKVFQIDDYIAMTIAGSVGDAQSLVRILKAEAKLYELRRGRPMSVKALATL   83 (185)
T ss_pred             EEEEEeCCEEEEEEcCcccCCCEEecCCcccEEEcCCCEEEEcCchHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
Confidence            4556666 6 89999999876666666899999999999999999999999999999999999999999887        


Q ss_pred             ----------------------------------------------------------cCCCCCCCHHHHHHHHHHHHHH
Q 040809           88 ----------------------------------------------------------QDYKDDMTRQEAVQLALKVLRK  109 (161)
Q Consensus        88 ----------------------------------------------------------~~y~~~mt~eeai~la~~al~~  109 (161)
                                                                                +.|+++||++||++++++||+.
T Consensus        84 l~~~~~~~~~rP~~v~~ivaG~d~~g~~Ly~~d~~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~~s~~ea~~l~~~~l~~  163 (185)
T TIGR03634        84 LSNILNSNRFFPFIVQLLVGGVDEEGPHLYSLDPAGGIIEDDYTATGSGSPVAYGVLEDEYREDMSVEEAKKLAVRAIKS  163 (185)
T ss_pred             HHHHHHhcCCCCeEEEEEEEEEeCCCCEEEEECCCCCeEECCEEEEcCcHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHH
Confidence                                                                      3689999999999999999999


Q ss_pred             hhccCCCCCCcEEEEEEEeCC
Q 040809          110 TMDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus       110 ~~~~~~~~~~~iei~ii~~~~  130 (161)
                      +.+++..++.+++|++|++++
T Consensus       164 ~~~r~~~~~~~~~v~ii~~~g  184 (185)
T TIGR03634       164 AIERDVASGNGIDVAVITKDG  184 (185)
T ss_pred             HHHhcccCCCCEEEEEEcCCC
Confidence            999999999999999999764

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.

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

Probab=99.85  E-value=4.4e-21  Score=143.52  Aligned_cols=129  Identities=16%  Similarity=0.300  Sum_probs=120.3

Q ss_pred             eeeEecce--EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYMG--CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveyaG--Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      |..|+|.|  ||++|.|.+.+-++.+|-.+|+.+|+|+|+||.||.++|.+++.+.++.....|...+++|+        
T Consensus        22 ImAv~y~gGVvlGaDSRTs~GayvanRvtDKlT~itD~i~cCRSGSAADtQaiaD~~~Y~L~~~~~q~~~~p~v~~aA~l  101 (224)
T KOG0174|consen   22 IMAVEYDGGVVLGADSRTSTGAYVANRVTDKLTPITDNIYCCRSGSAADTQAIADIVRYHLELYTIQENKPPLVHTAASL  101 (224)
T ss_pred             EEEEEEcCcEEEeccCCccchHHHHhhhcccceeccccEEEecCCchhhHHHHHHHHHHHHHHhhhhcCCCchHHHHHHH
Confidence            89999995  99999999999999999999999999999999999999999999999999999999999988        


Q ss_pred             ----------------------------------------------------------cCCCCCCCHHHHHHHHHHHHHH
Q 040809           88 ----------------------------------------------------------QDYKDDMTRQEAVQLALKVLRK  109 (161)
Q Consensus        88 ----------------------------------------------------------~~y~~~mt~eeai~la~~al~~  109 (161)
                                                                                +.|+|+||+||++.+..+|+..
T Consensus       102 ~r~~~Y~~re~L~AgliVAGwD~~~gGqVY~iplGG~l~rq~~aIgGSGStfIYGf~D~~~r~nMt~EE~~~fvk~Av~l  181 (224)
T KOG0174|consen  102 FREICYNYREMLSAGLIVAGWDEKEGGQVYSIPLGGSLTRQPFAIGGSGSTFIYGFCDANWRPNMTLEECVRFVKNAVSL  181 (224)
T ss_pred             HHHHHHhCHHhhhcceEEeecccccCceEEEeecCceEeecceeeccCCceeeeeeehhhcCCCCCHHHHHHHHHHHHHH
Confidence                                                                      3689999999999999999999


Q ss_pred             hhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHH
Q 040809          110 TMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLE  149 (161)
Q Consensus       110 ~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~  149 (161)
                      ++.||-.+|..|.+.+|++++-   .++.+.++++..+..
T Consensus       182 Ai~rDGsSGGviR~~~I~~~Gv---er~~~~~d~~~~~~v  218 (224)
T KOG0174|consen  182 AIERDGSSGGVIRLVIINKAGV---ERRFFPGDKLGQFAV  218 (224)
T ss_pred             HHhccCCCCCEEEEEEEccCCc---eEEEecCCccccccc
Confidence            9999999999999999999864   677888888766543

>cd01912 proteasome_beta proteasome beta subunit

Probab=99.84  E-value=5e-20  Score=139.81  Aligned_cols=113  Identities=22%  Similarity=0.333  Sum_probs=103.1

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +.-+.|. | |||+|+|.++++.+.....+|||+|+++++|++||+.+|++.+++++|.+++.|++.+++++        
T Consensus         3 ~i~i~~~dgVvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~   82 (189)
T cd01912           3 IVGIKGKDGVVLAADTRASAGSLVASRNFDKIFKISDNILLGTAGSAADTQALTRLLKRNLRLYELRNGRELSVKAAANL   82 (189)
T ss_pred             EEEEEeCCEEEEEEcCCcccCcEEEcCCcCcEEEccCCEEEEccccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHH
Confidence            3445565 6 99999999999988555899999999999999999999999999999999999999999877        


Q ss_pred             -----------------------------------------------------------cCCCCCCCHHHHHHHHHHHHH
Q 040809           88 -----------------------------------------------------------QDYKDDMTRQEAVQLALKVLR  108 (161)
Q Consensus        88 -----------------------------------------------------------~~y~~~mt~eeai~la~~al~  108 (161)
                                                                                 +.|+++|+++||++++++||.
T Consensus        83 l~~~~~~~~~~P~~~~~iv~G~d~~~~~~l~~id~~G~~~~~~~~a~G~~~~~~~~~Le~~~~~~~s~~ea~~~~~~~l~  162 (189)
T cd01912          83 LSNILYSYRGFPYYVSLIVGGVDKGGGPFLYYVDPLGSLIEAPFVATGSGSKYAYGILDRGYKPDMTLEEAVELVKKAID  162 (189)
T ss_pred             HHHHHHhcCCCCeEEEEEEEEEcCCCCeEEEEECCCCCeEecCEEEEcccHHHHHHHHHhccCCCCCHHHHHHHHHHHHH
Confidence                                                                       368999999999999999999


Q ss_pred             HhhccCCCCCCcEEEEEEEeCC
Q 040809          109 KTMDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus       109 ~~~~~~~~~~~~iei~ii~~~~  130 (161)
                      .+.+++..++.+++|++|++++
T Consensus       163 ~~~~~d~~~~~~~~v~vi~~~g  184 (189)
T cd01912         163 SAIERDLSSGGGVDVAVITKDG  184 (189)
T ss_pred             HHHHhcCccCCcEEEEEECCCC
Confidence            9999999999999999999874

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

>cd01906 proteasome_protease_HslV proteasome_protease_HslV

Probab=99.80  E-value=2.4e-18  Score=129.47  Aligned_cols=109  Identities=39%  Similarity=0.662  Sum_probs=98.7

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +.-|-|. | |||+|+|.++++.+..++.+|||+|+++++|+.+|+.+|++.+.+.++.++..|++.+++++        
T Consensus         3 ~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~   82 (182)
T cd01906           3 IVGIKGKDGVVLAADKRVTSGLLVASSTVEKIFKIDDHIGCAFAGLAADAQTLVERLRKEAQLYRLRYGEPIPVEALAKL   82 (182)
T ss_pred             EEEEEeCCEEEEEEecccCCcCeecCCCcceEEEECCCEEEEEeeCHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHH
Confidence            3455565 6 99999999999887556899999999999999999999999999999999999999998887        


Q ss_pred             -------------------------------------------------------------cCCCCCCCHHHHHHHHHHH
Q 040809           88 -------------------------------------------------------------QDYKDDMTRQEAVQLALKV  106 (161)
Q Consensus        88 -------------------------------------------------------------~~y~~~mt~eeai~la~~a  106 (161)
                                                                                   +.|+++||.+||++++++|
T Consensus        83 l~~~~~~~~~~~~p~~~~~lv~G~d~~~~~~Ly~id~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~  162 (182)
T cd01906          83 LANLLYEYTQSLRPLGVSLLVAGVDEEGGPQLYSVDPSGSYIEYKATAIGSGSQYALGILEKLYKPDMTLEEAIELALKA  162 (182)
T ss_pred             HHHHHHHhCCCccChheEEEEEEEeCCCCcEEEEECCCCCEeeccEEEECCCcHHHHHHHHHHccCCCCHHHHHHHHHHH
Confidence                                                                         3578999999999999999


Q ss_pred             HHHhhccCCCCCCcEEEEEE
Q 040809          107 LRKTMDSTSLTSEKLELAEV  126 (161)
Q Consensus       107 l~~~~~~~~~~~~~iei~ii  126 (161)
                      |..+.+++..++.+++|++|
T Consensus       163 l~~~~~~~~~~~~~~~i~ii  182 (182)
T cd01906         163 LKSALERDLYSGGNIEVAVI  182 (182)
T ss_pred             HHHHHcccCCCCCCEEEEEC
Confidence            99999998889999999985

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

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

Probab=99.78  E-value=2.5e-18  Score=130.19  Aligned_cols=110  Identities=28%  Similarity=0.544  Sum_probs=98.0

Q ss_pred             ceeeEecc-e-EEEEEcccCCCCcccCCC-CCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc------
Q 040809           17 RLYQVDYM-G-CLVGENNVTSKLLQTSTS-AEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI------   87 (161)
Q Consensus        17 rl~qveya-G-Vlaadkr~~~~l~~~~~~-~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i------   87 (161)
                      .+.-+-|. | |||+|+|.+.+..+..+. .+|||+|++|++|++||..+|++.+.++++.+++.|++.++.++      
T Consensus         6 t~vgi~~~dgvvla~d~~~~~g~~~~~~~~~~ki~~i~~~i~~~~sG~~~D~~~l~~~l~~~~~~~~~~~~~~~~~~~l~   85 (190)
T PF00227_consen    6 TVVGIKGKDGVVLAADKRISYGSKLRSPNTVDKIFKINDNIIIGFSGLTADFQYLIRRLREEAQEYRFSYGRPISPEYLA   85 (190)
T ss_dssp             EEEEEEESSEEEEEEEEEEEETTEEEESSTSSSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHHHHH
T ss_pred             EEEEEEECCEEEEEEccccccccccccccccceeeeccCcceeeccccccchHHHHhhhcccchhhhhccCccccchhhh
Confidence            36677777 5 999999999554442323 69999999999999999999999999999999999999999988      


Q ss_pred             ------------------------------------------------------------------cCCCCCCCHHHHHH
Q 040809           88 ------------------------------------------------------------------QDYKDDMTRQEAVQ  101 (161)
Q Consensus        88 ------------------------------------------------------------------~~y~~~mt~eeai~  101 (161)
                                                                                        +.|+++||++||++
T Consensus        86 ~~~~~~~~~~~~~~~~~p~~~~~li~G~d~~~~~~l~~vd~~G~~~~~~~~~aiG~g~~~~~~~l~~~~~~~~~~~ea~~  165 (190)
T PF00227_consen   86 KAIASLIQNYTYRSGRRPYGVSLLIAGYDEDGGPQLYSVDPSGSYIECKRFAAIGSGSQFAQPILEKLYKPDLSLEEAIE  165 (190)
T ss_dssp             HHHHHHHHHHHHHTTTSTTSEEEEEEEEETTTEEEEEEEETTSEEEEBSSEEEESTTHHHHHHHHHHHHTTTSSHHHHHH
T ss_pred             hhhHHHHhhhcccccccCccccceeeeeccccccceeeeccccccccccccccchhcchhhhHHHHhhccCCCCHHHHHH
Confidence                                                                              24689999999999


Q ss_pred             HHHHHHHHhhccCCCCCCcEEEEEE
Q 040809          102 LALKVLRKTMDSTSLTSEKLELAEV  126 (161)
Q Consensus       102 la~~al~~~~~~~~~~~~~iei~ii  126 (161)
                      ++++||+.+.+++..++++++|+||
T Consensus       166 ~~~~~l~~~~~~d~~~~~~~~v~vi  190 (190)
T PF00227_consen  166 LALKALKEAIDRDILSGDNIEVAVI  190 (190)
T ss_dssp             HHHHHHHHHHHHBTTSTSEEEEEEE
T ss_pred             HHHHHHHHHHhhCCccCCeEEEEEC
Confidence            9999999999999999999999987

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 ....

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

Probab=99.76  E-value=7.2e-18  Score=130.97  Aligned_cols=128  Identities=16%  Similarity=0.198  Sum_probs=118.1

Q ss_pred             e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc----------------
Q 040809           25 G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI----------------   87 (161)
Q Consensus        25 G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i----------------   87 (161)
                      | |+|+|.|++.+-+|.+..+.||..||+++.-+++|-++||+.+-+.+..+|+.|++++++.|                
T Consensus        82 GvivAvDSRAs~G~YIasqtv~KVIeIn~ylLGTmAGgAADCqfWer~L~kecRL~eLRnkeriSVsaASKllsN~~y~Y  161 (285)
T KOG0175|consen   82 GVIVAVDSRASAGSYIASQTVKKVIEINPYLLGTMAGGAADCQFWERVLAKECRLHELRNKERISVSAASKLLSNMVYQY  161 (285)
T ss_pred             cEEEEEeccccccceeechhhceeeeechhhhhcccCcchhhHHHHHHHHHHHHHHHHhcCcceehHHHHHHHHHHHhhc
Confidence            6 88999999999999999999999999999999999999999999999999999999999998                


Q ss_pred             --------------------------------------------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCC
Q 040809           88 --------------------------------------------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLT  117 (161)
Q Consensus        88 --------------------------------------------------~~y~~~mt~eeai~la~~al~~~~~~~~~~  117 (161)
                                                                        ..|+++|+.|||.+|+.+||.-+.-||..+
T Consensus       162 kGmGLsmGtMi~G~Dk~GP~lyYVDseG~Rl~G~~FSVGSGs~yAYGVLDsgYr~dls~eEA~~L~rrAI~hAThRDayS  241 (285)
T KOG0175|consen  162 KGMGLSMGTMIAGWDKKGPGLYYVDSEGTRLSGDLFSVGSGSTYAYGVLDSGYRYDLSDEEAYDLARRAIYHATHRDAYS  241 (285)
T ss_pred             cCcchhheeeEeeccCCCCceEEEcCCCCEecCceEeecCCCceeEEeeccCCCCCCCHHHHHHHHHHHHHHHHhccccc
Confidence                                                              368999999999999999999999999999


Q ss_pred             CCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhcccCCC
Q 040809          118 SEKLELAEVFLLPSGKVKYRICSPESLTMLLENFGVAQPA  157 (161)
Q Consensus       118 ~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~~~~~~  157 (161)
                      |.-+.+..|..++     +..++..++.++...+.+.+++
T Consensus       242 GG~vnlyHv~edG-----W~~v~~~Dv~~L~~~~~e~~~~  276 (285)
T KOG0175|consen  242 GGVVNLYHVKEDG-----WVKVSNTDVSELHYHYYEVAPP  276 (285)
T ss_pred             CceEEEEEECCcc-----ceecCCccHHHHHHHHHHhcCc
Confidence            9999999999873     8899999999996655444443

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

Probab=99.76  E-value=1e-17  Score=126.84  Aligned_cols=115  Identities=15%  Similarity=0.295  Sum_probs=103.0

Q ss_pred             CceeeEecce--EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc------
Q 040809           16 GRLYQVDYMG--CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI------   87 (161)
Q Consensus        16 Grl~qveyaG--Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i------   87 (161)
                      |.+..+.--+  |+|+|+|.++++.|.+|..+|||+++|++.++.||+++|+..|...++...+.|++.++..|      
T Consensus        30 GT~vaIaG~dFavvA~DTR~s~gy~I~sR~~~Ki~~l~D~~vl~~sGF~aD~l~L~k~i~~r~~~Y~~~h~k~ms~~s~A  109 (235)
T KOG0179|consen   30 GTTVAIAGEDFAVVAGDTRMSSGYNINSRDQSKIFKLGDNIVLGSSGFYADTLALVKVIKSRIKQYEHDHNKKMSIHSAA  109 (235)
T ss_pred             ceEEEEcCCceEEEecccccccceeeeccccchheeccCceEEecccchhhHHHHHHHHHHHHHHHhhcccccccHHHHH
Confidence            4454443323  99999999999999999999999999999999999999999999999999999999998888      


Q ss_pred             ------------------------------------------------------------------cCC------CCCCC
Q 040809           88 ------------------------------------------------------------------QDY------KDDMT   95 (161)
Q Consensus        88 ------------------------------------------------------------------~~y------~~~mt   95 (161)
                                                                                        +.+      ++.++
T Consensus       110 ~lls~~LY~kRFFPYYv~~ilaGiDeeGKG~VySyDPvGsyer~~~~AgGsa~~mI~PfLDnQi~~kn~~~e~~~~~~Ls  189 (235)
T KOG0179|consen  110 QLLSTILYSKRFFPYYVFNILAGIDEEGKGAVYSYDPVGSYERVTCRAGGSAASMIQPFLDNQIGHKNQNLENAERTPLS  189 (235)
T ss_pred             HHHHHHHhhcccccceeeeeeecccccCceeEEeecCCcceeeeeeecCCcchhhhhhhhhhhccCcCcccccCcccccC
Confidence                                                                              011      35789


Q ss_pred             HHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCC
Q 040809           96 RQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus        96 ~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~  130 (161)
                      +|+|++|+..+|..|.+|+..+|++++|+|+++++
T Consensus       190 ~e~ai~lv~d~F~SAaERdI~tGD~l~i~I~tk~g  224 (235)
T KOG0179|consen  190 LERAIRLVKDAFTSAAERDIYTGDKLEICIITKDG  224 (235)
T ss_pred             HHHHHHHHHHHhhhhhhcccccCCcEEEEEEecCC
Confidence            99999999999999999999999999999999985

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

Probab=99.71  E-value=6.6e-17  Score=119.21  Aligned_cols=105  Identities=17%  Similarity=0.244  Sum_probs=99.7

Q ss_pred             EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc------------------
Q 040809           26 CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI------------------   87 (161)
Q Consensus        26 Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i------------------   87 (161)
                      ++|+|+|.....+..++..+|||+|.|+++++.+|+++|.+++.+++|..-..|+++.++.|                  
T Consensus        21 aIa~D~RlG~q~~tistdf~ki~~igdr~y~GL~glatDvqtl~~~~~fr~nLy~lre~R~i~P~~~s~mvS~~lYekRf  100 (204)
T KOG0180|consen   21 AIASDLRLGVQSQTISTDFQKIFKIGDRLYLGLTGLATDVQTLLERLRFRKNLYELREEREIKPETFSSMVSSLLYEKRF  100 (204)
T ss_pred             EEEeccccceeeeeeeccchhheecCCeeEEeccccchhHHHHHHHHHHHHhHHHhhhhcccCcHHHHHHHHHHHHHhhc
Confidence            78999999988777778999999999999999999999999999999999999999999988                  


Q ss_pred             --------------------------------------------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCC
Q 040809           88 --------------------------------------------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLT  117 (161)
Q Consensus        88 --------------------------------------------------~~y~~~mt~eeai~la~~al~~~~~~~~~~  117 (161)
                                                                        ..|+|+|..|++++.+.+||.++.+||.++
T Consensus       101 gpYf~~PvVAGl~~~~kPfIc~mD~IGc~~~~~DFVvsGTa~e~L~GmCE~ly~pnmepd~LFetisQa~Lna~DRDalS  180 (204)
T KOG0180|consen  101 GPYFTEPVVAGLDDDNKPFICGMDLIGCIDAPKDFVVSGTASEQLYGMCEALYEPNMEPDELFETISQALLNAVDRDALS  180 (204)
T ss_pred             CCcccceeEeccCCCCCeeEeecccccCcCccCCeEEecchHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHhHhhhhhhc
Confidence                                                              258999999999999999999999999999


Q ss_pred             CCcEEEEEEEeCC
Q 040809          118 SEKLELAEVFLLP  130 (161)
Q Consensus       118 ~~~iei~ii~~~~  130 (161)
                      |++..+.||+|+.
T Consensus       181 GwGa~vyiI~kdk  193 (204)
T KOG0180|consen  181 GWGAVVYIITKDK  193 (204)
T ss_pred             cCCeEEEEEccch
Confidence            9999999999985

>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=99.70  E-value=9.5e-17  Score=120.37  Aligned_cols=105  Identities=19%  Similarity=0.228  Sum_probs=93.2

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecC-ceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc-------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDD-HVACAVAGIMSDANILINTARVQARRYAYAYQEPI-------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~-~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i-------   87 (161)
                      ++-|.|. | |||+|+|.+.+.++.++..+||++|++ |++|+.||..+|++.|.++++.+++.|+.+.++.+       
T Consensus         3 ivgi~~~dgVvlaaD~r~t~G~~v~~~~~~Ki~~i~d~~i~~~~aG~~aD~~~l~~~~~~~~~~y~~~~~~~aa~l~~~l   82 (171)
T cd01913           3 ILAVRKNGKVVIAGDGQVTLGNTVMKGNARKVRRLYNGKVIAGFAGSTADAFTLFERFEAKLEQYPGNLLRAAVELAKDW   82 (171)
T ss_pred             EEEEEECCEEEEEECCceEeccEEEcCCcceEEEeCCCCEEEEecccHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHH
Confidence            5667787 4 999999999999999999999999999 99999999999999999999999999997655443       


Q ss_pred             ----------------------------------------------------cCCCCC-CCHHHHHHHHHHHHHHhhccC
Q 040809           88 ----------------------------------------------------QDYKDD-MTRQEAVQLALKVLRKTMDST  114 (161)
Q Consensus        88 ----------------------------------------------------~~y~~~-mt~eeai~la~~al~~~~~~~  114 (161)
                                                                          ..|+++ |+   +.++|++|++.+++||
T Consensus        83 ~~~~~~~~l~a~~iv~~~~~ly~id~~G~~ie~~~~~~a~GSGS~ya~g~ld~~yk~~~ms---~~~la~~Av~~A~~rd  159 (171)
T cd01913          83 RTDRYLRRLEAMLIVADKEHTLLISGNGDVIEPDDGIAAIGSGGNYALAAARALLDHTDLS---AEEIARKALKIAADIC  159 (171)
T ss_pred             HhccCcCceEEEEEEeCCCcEEEECCCCCEeccCCCeEEEeCCHHHHHHHHHHhhccCCCC---HHHHHHHHHHHHHhhC
Confidence                                                                357885 99   5599999999999999


Q ss_pred             CCCCCcEEEEE
Q 040809          115 SLTSEKLELAE  125 (161)
Q Consensus       115 ~~~~~~iei~i  125 (161)
                      ..++++|.|-.
T Consensus       160 ~~tg~~i~~~~  170 (171)
T cd01913         160 IYTNHNITVEE  170 (171)
T ss_pred             cccCCCEEEEe
Confidence            99999998753

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

>PRK05456 ATP-dependent protease subunit HslV; Provisional

Probab=99.69  E-value=1.1e-16  Score=120.40  Aligned_cols=105  Identities=20%  Similarity=0.247  Sum_probs=91.1

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEe-cCceEEEEeccHHHHHHHHHHHHHHHHHHHHH------------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKI-DDHVACAVAGIMSDANILINTARVQARRYAYA------------   82 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I-~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~------------   82 (161)
                      ++-|.|. | |||+|+|.+.+.++.++..+||++| ++|++|+.||..+|++.|.+.++.+++.|+..            
T Consensus         4 ivgi~~~dgVvlaaD~r~s~g~~v~~~~~~KI~~i~~d~i~~~~aG~~aD~q~l~~~l~~~~~~y~~~~~~~~a~l~~~l   83 (172)
T PRK05456          4 ILAVRRNGKVAIAGDGQVTLGNTVMKGNARKVRRLYNGKVLAGFAGSTADAFTLFERFEAKLEEHQGNLLRAAVELAKDW   83 (172)
T ss_pred             EEEEEECCEEEEEECCceEeCcEEEcCCCceEEEeCCCCEEEEEeccHHHHHHHHHHHHHHHHHccCccHHHHHHHHHHH
Confidence            5677887 4 9999999999999999999999999 99999999999999999999999987777621            


Q ss_pred             ----hCCCc-------------------------------------------cCCC-CCCCHHHHHHHHHHHHHHhhccC
Q 040809           83 ----YQEPI-------------------------------------------QDYK-DDMTRQEAVQLALKVLRKTMDST  114 (161)
Q Consensus        83 ----~~~~i-------------------------------------------~~y~-~~mt~eeai~la~~al~~~~~~~  114 (161)
                          |..++                                           ++|+ |+|   ||++++++|+..+.+||
T Consensus        84 ~~~~~~~~l~~~~lv~d~~~ly~id~~G~~~~~~~~~~a~GSGs~~a~g~ld~~y~~~~m---eA~~la~kai~~A~~Rd  160 (172)
T PRK05456         84 RTDRYLRRLEAMLIVADKEHSLIISGNGDVIEPEDGIIAIGSGGNYALAAARALLENTDL---SAEEIAEKALKIAADIC  160 (172)
T ss_pred             HhccCCCccEEEEEEEcCCcEEEECCCCcEeccCCCeEEEecCHHHHHHHHHHhhhcCCC---CHHHHHHHHHHHHHHhC
Confidence                11111                                           3578 999   99999999999999999


Q ss_pred             CCCCCcEEEEE
Q 040809          115 SLTSEKLELAE  125 (161)
Q Consensus       115 ~~~~~~iei~i  125 (161)
                      ..+++++.|-.
T Consensus       161 ~~sg~~i~v~~  171 (172)
T PRK05456        161 IYTNHNITIEE  171 (172)
T ss_pred             eeCCCcEEEEE
Confidence            99999998754

>TIGR03692 ATP_dep_HslV ATP-dependent protease HslVU, peptidase subunit

Probab=99.65  E-value=6.1e-16  Score=116.01  Aligned_cols=105  Identities=19%  Similarity=0.249  Sum_probs=91.2

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEe-cCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc-------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKI-DDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI-------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I-~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i-------   87 (161)
                      ++-|.|. | |||+|+|.+.+.++.++..+||++| ++|++|+.||..+|++.|.+++|.+++.|+...++.+       
T Consensus         3 ivgi~~~dgVvlaaD~r~s~g~~v~~~~~~Ki~~i~~d~i~~~~aG~~aD~q~l~~~~~~~~~~y~~~~~~~~a~l~~~~   82 (171)
T TIGR03692         3 ILAVRRNGKVVIAGDGQVTLGNTVMKGNARKVRRLYNGKVLAGFAGSTADAFTLFERFEAKLEEYQGNLTRAAVELAKDW   82 (171)
T ss_pred             EEEEEECCEEEEEECCceEeceEEEcCCCCeEEEeCCCCEEEEecchHHHHHHHHHHHHHHHHHccCchHHHHHHHHHHH
Confidence            5667787 4 9999999999999999999999999 5999999999999999999999999999986432222       


Q ss_pred             ----------------------------------------------------cCC-CCCCCHHHHHHHHHHHHHHhhccC
Q 040809           88 ----------------------------------------------------QDY-KDDMTRQEAVQLALKVLRKTMDST  114 (161)
Q Consensus        88 ----------------------------------------------------~~y-~~~mt~eeai~la~~al~~~~~~~  114 (161)
                                                                          ..| +++|+   |+++|++|++.+++||
T Consensus        83 ~~~~~~~~l~a~~iv~~~~~ly~i~~~G~~ie~~~~~~a~GSGS~~a~g~ld~~y~~~~~s---a~~la~~Av~~A~~rd  159 (171)
T TIGR03692        83 RTDRYLRRLEAMLIVADKETSLLISGTGDVIEPEDGIAAIGSGGNYALAAARALLRNTDLS---AEEIAREALKIAADIC  159 (171)
T ss_pred             hhcccccccEEEEEEEcCCCEEEEcCCCcEeccCCCeEEEeCCHHHHHHHHHHhhhcCCCC---HHHHHHHHHHHHHhhC
Confidence                                                                246 46777   9999999999999999


Q ss_pred             CCCCCcEEEEE
Q 040809          115 SLTSEKLELAE  125 (161)
Q Consensus       115 ~~~~~~iei~i  125 (161)
                      ..++++|.|-.
T Consensus       160 ~~sg~~i~v~~  170 (171)
T TIGR03692       160 IYTNHNITIEE  170 (171)
T ss_pred             ccCCCCEEEEe
Confidence            99999998753

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

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

Probab=99.65  E-value=1.8e-15  Score=117.35  Aligned_cols=121  Identities=16%  Similarity=0.215  Sum_probs=108.0

Q ss_pred             cccCCCCc-eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCC
Q 040809           10 TVFSPEGR-LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEP   86 (161)
Q Consensus        10 ~~fsp~Gr-l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~   86 (161)
                      ..|...|. |.-|-|- | ||++|+|.+.+-.+++++.+||+.|.++|+||.+|-.+|...+.+.+..+...|+++.++.
T Consensus        31 p~~tkTGTtIvgv~~k~gvIlgADtRaT~G~IvaDKnC~KIH~ia~~IyccGAGtAADte~vt~m~ss~l~Lh~l~t~R~  110 (271)
T KOG0173|consen   31 PKATKTGTTIVGVIFKDGVILGADTRATEGPIVADKNCEKIHFIAPNIYCCGAGTAADTEMVTRMISSNLELHRLNTGRK  110 (271)
T ss_pred             CcccccCcEEEEEEeCCeEEEeecccccCCCeeecchhHHHhhcccceEEccCCchhhHHHHHHHHHHHHHHHHhccCCC
Confidence            34555666 6666666 5 9999999999999999999999999999999999999999999999999999999888877


Q ss_pred             c-----------------------------------------------------------------cCCCCCCCHHHHHH
Q 040809           87 I-----------------------------------------------------------------QDYKDDMTRQEAVQ  101 (161)
Q Consensus        87 i-----------------------------------------------------------------~~y~~~mt~eeai~  101 (161)
                      +                                                                 .+|+|+|+.|||++
T Consensus       111 ~rVv~A~~mlkQ~LFrYqG~IgA~LiiGGvD~TGpHLy~i~phGStd~~Pf~alGSGslaAmsvlEsr~k~dlt~eea~~  190 (271)
T KOG0173|consen  111 PRVVTALRMLKQHLFRYQGHIGAALILGGVDPTGPHLYSIHPHGSTDKLPFTALGSGSLAAMSVLESRWKPDLTKEEAIK  190 (271)
T ss_pred             CceeeHHHHHHHHHHHhcCcccceeEEccccCCCCceEEEcCCCCcCccceeeeccchHHHHHHHHHhcCcccCHHHHHH
Confidence            6                                                                 36999999999999


Q ss_pred             HHHHHHHHhhccCCCCCCcEEEEEEEeCC
Q 040809          102 LALKVLRKTMDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus       102 la~~al~~~~~~~~~~~~~iei~ii~~~~  130 (161)
                      |+.+|+...+-.|-.+|.||.++||++.+
T Consensus       191 Lv~eAi~AGi~nDLgSGsnvdlcVI~~~~  219 (271)
T KOG0173|consen  191 LVCEAIAAGIFNDLGSGSNVDLCVITKKG  219 (271)
T ss_pred             HHHHHHHhhhccccCCCCceeEEEEeCCC
Confidence            99999999998888999999999999643

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

Probab=99.64  E-value=1.1e-15  Score=114.20  Aligned_cols=105  Identities=18%  Similarity=0.201  Sum_probs=99.9

Q ss_pred             EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc------------------
Q 040809           26 CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI------------------   87 (161)
Q Consensus        26 Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i------------------   87 (161)
                      +||+|+....++...+.+.+|+++|++|+.|+.+|-.||+-.+.+++...++.|+.++|.++                  
T Consensus        14 ilAsDt~~~~si~~~k~~~dK~~~ls~~~lm~~~Ge~GDt~qF~eyi~~Ni~LYkirnGyeLSp~~aahFtR~~La~~LR   93 (200)
T KOG0177|consen   14 ILASDTSAARSILVLKDDHDKIHRLSDHILMATVGEAGDTVQFTEYIQKNIQLYKIRNGYELSPSAAAHFTRRELAESLR   93 (200)
T ss_pred             EEeecchhhcceEEecccccceEEeccceeeeeecCCCceehHHHHHHhhhhHHhhhcCCcCCHHHHHHHHHHHHHHHHh
Confidence            78999999989888888999999999999999999999999999999999999999999988                  


Q ss_pred             ---------------------------------------------------cCCCCCCCHHHHHHHHHHHHHHhhccCCC
Q 040809           88 ---------------------------------------------------QDYKDDMTRQEAVQLALKVLRKTMDSTSL  116 (161)
Q Consensus        88 ---------------------------------------------------~~y~~~mt~eeai~la~~al~~~~~~~~~  116 (161)
                                                                         ++|+|+||.+||+.+..+|+.+.-.|..+
T Consensus        94 sr~~yqV~~LvaGYd~~~gp~L~~iDyla~~~~vpy~~hGy~~~f~~sIlDr~Y~pdmt~eea~~lmkKCv~El~kRlvi  173 (200)
T KOG0177|consen   94 SRTPYQVNILVAGYDPEEGPELYYIDYLATLVSVPYAAHGYGSYFCLSILDRYYKPDMTIEEALDLMKKCVLELKKRLVI  173 (200)
T ss_pred             cCCCceEEEEEeccCCCCCCceeeehhhhhcccCCcccccchhhhhHHHHHhhhCCCCCHHHHHHHHHHHHHHHHHhccc
Confidence                                                               36899999999999999999999999999


Q ss_pred             CCCcEEEEEEEeCC
Q 040809          117 TSEKLELAEVFLLP  130 (161)
Q Consensus       117 ~~~~iei~ii~~~~  130 (161)
                      ...++.|.||+|++
T Consensus       174 n~~~f~v~IVdkdG  187 (200)
T KOG0177|consen  174 NLPGFIVKIVDKDG  187 (200)
T ss_pred             CCCCcEEEEEcCCC
Confidence            99999999999985

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

Probab=99.39  E-value=4.6e-14  Score=71.03  Aligned_cols=20  Identities=65%  Similarity=1.250  Sum_probs=19.5

Q ss_pred             CCCCCcccCCCCceeeEecc
Q 040809            5 YDRQTTVFSPEGRLYQVDYM   24 (161)
Q Consensus         5 y~~~~~~fsp~Grl~qveya   24 (161)
                      ||+++|+|||+|||+|||||
T Consensus         1 YD~~~t~FSp~Grl~QVEYA   20 (23)
T PF10584_consen    1 YDRSITTFSPDGRLFQVEYA   20 (23)
T ss_dssp             TSSSTTSBBTTSSBHHHHHH
T ss_pred             CCCCceeECCCCeEEeeEee
Confidence            89999999999999999998

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 ....

>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=99.17  E-value=4.3e-10  Score=81.61  Aligned_cols=68  Identities=28%  Similarity=0.430  Sum_probs=60.5

Q ss_pred             eEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc
Q 040809           20 QVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI   87 (161)
Q Consensus        20 qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i   87 (161)
                      -+.+. | |||+|++.+.++........||+.++++++++++|+.+|++.+.++++.+++.|++.++.++
T Consensus         5 ~i~~~~gvila~d~~~~~~~~~~~~~~~ki~~~~~~~~~~~sG~~~d~~~~~~~~~~~~~~~~~~~~~~~   74 (164)
T cd01901           5 AIKGKGGVVLAADKRLSSGLPVAGSPVIKIGKNEDGIAWGLAGLAADAQTLVRRLREALQLYRLRYGEPI   74 (164)
T ss_pred             EEEeCCEEEEEEecccCccCeecCCCcceEEEecCCeEEEEecChHHHHHHHHHHHHHHHHHHHHHCCCC
Confidence            34444 5 99999999999887555889999999999999999999999999999999999999888765

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

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

Probab=98.76  E-value=7.9e-08  Score=74.48  Aligned_cols=113  Identities=17%  Similarity=0.243  Sum_probs=90.7

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHH-HhCCCc-------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAY-AYQEPI-------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~-~~~~~i-------   87 (161)
                      +..+.|. | |+|+|+..+-+.+--=+.++|||+|++++.+++||=.+|.+.+.+.+.....+... -=|..+       
T Consensus        44 Vla~ky~~GVviaaD~lgSYGslaR~~nVeRi~kVgdntllG~sGdisD~Q~i~r~L~~l~iedn~~~Dg~~l~Pk~ih~  123 (256)
T KOG0185|consen   44 VLALKYKDGVVIAADTLGSYGSLARYKNVERIFKVGDNTLLGASGDISDFQYIQRVLEQLVIEDNRLDDGQSLGPKAIHS  123 (256)
T ss_pred             EEEEEecCceEEEecccccchhhhhhcCceeeEEecCceEEecCccHHHHHHHHHHHHHHHhcccccccccccChHHHHH
Confidence            7788887 7 99999988765333224899999999999999999999999999999888776431 111222       


Q ss_pred             --------------------------------------------------------------cCCC---CCCCHHHHHHH
Q 040809           88 --------------------------------------------------------------QDYK---DDMTRQEAVQL  102 (161)
Q Consensus        88 --------------------------------------------------------------~~y~---~~mt~eeai~l  102 (161)
                                                                                    +.|.   ++++.+||..+
T Consensus       124 yltrvlY~rRsKmnPlwntlvVgGv~~~g~~~lg~V~~~G~~Y~~~~vATGfg~hLa~P~lR~~~~~k~~~~s~eeA~~l  203 (256)
T KOG0185|consen  124 YLTRVLYARRSKMNPLWNTLVVGGVDNTGEPFLGYVDLLGVAYESPVVATGFGAHLALPLLRDEWEKKGEDLSREEAEAL  203 (256)
T ss_pred             HHHHHHHHhhhccCchhhheeEeeecCCCCeeEEEEeeccccccCchhhhhhHHHhhhHHHHHhhhccchhhHHHHHHHH
Confidence                                                                          1222   67899999999


Q ss_pred             HHHHHHHhhccCCCCCCcEEEEEEEeCC
Q 040809          103 ALKVLRKTMDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus       103 a~~al~~~~~~~~~~~~~iei~ii~~~~  130 (161)
                      +.+|++-..-||.-+...++|++|+.++
T Consensus       204 i~~cMrVL~YRD~ra~n~fqva~v~~eG  231 (256)
T KOG0185|consen  204 IEKCMRVLYYRDARASNEFQVATVDEEG  231 (256)
T ss_pred             HHHHHHHHhccccccccceEEEEEcccc
Confidence            9999999999999999999999999864

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

Probab=94.98  E-value=0.017  Score=42.96  Aligned_cols=55  Identities=22%  Similarity=0.298  Sum_probs=45.2

Q ss_pred             EEEEEcccCCCCcccCCCCCceEEecC-ceEEEEeccHHHHHHHHHHHHHHHHHHH
Q 040809           26 CLVGENNVTSKLLQTSTSAEKMYKIDD-HVACAVAGIMSDANILINTARVQARRYA   80 (161)
Q Consensus        26 Vlaadkr~~~~l~~~~~~~~KI~~I~~-~i~~~~sG~~~D~~~l~~~~r~~~~~y~   80 (161)
                      |+++|-..+-+-.+...+..|+-+|.. .+..+++|-.+|+..|..++..+++.|.
T Consensus        17 ~iagDGQVtlG~tvmK~narKvRkl~~gkvlaGFAGstADaftLfe~fe~kle~~~   72 (178)
T COG5405          17 VIAGDGQVTLGNTVMKGNARKVRRLYNGKVLAGFAGSTADAFTLFERFEAKLEQYQ   72 (178)
T ss_pred             EEecCceEeecceeeeccHHHHHHHcCCcEEEEecccchhHHHHHHHHHHHHHHcc
Confidence            788888877766666656666666654 8999999999999999999999998884

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

Probab=80.11  E-value=3.4  Score=32.06  Aligned_cols=40  Identities=23%  Similarity=0.102  Sum_probs=32.5

Q ss_pred             CCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCC
Q 040809           91 KDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus        91 ~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~  130 (161)
                      .-+++++|+.+.|+-++...+.....-|-.+.+-++.+|.
T Consensus       163 ~~~~pLeea~kcaLvS~DSTlkSNiSVGlPldLl~~e~ds  202 (255)
T COG3484         163 TYDTPLEEAAKCALVSFDSTLKSNISVGLPLDLLVYEADS  202 (255)
T ss_pred             hccCCHHHHhhheEEecchhhhccccccCCceeEEEeccc
Confidence            4588999999999999999887655556678888888764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	161
1z7q_C	258	Crystal Structure Of The 20s Proteasome From Yeast		1e-17
1z7q_C	258	Crystal Structure Of The 20s Proteasome From Yeast		3e-07
1ryp_C	244	Crystal Structure Of The 20s Proteasome From Yeast		1e-17
1ryp_C	244	Crystal Structure Of The 20s Proteasome From Yeast		4e-07
1g0u_B	245	A Gated Channel Into The Proteasome Core Particle L		1e-17
1g0u_B	245	A Gated Channel Into The Proteasome Core Particle L		4e-07
3unb_B	261	Mouse Constitutive 20s Proteasome In Complex With P		4e-15
3unb_B	261	Mouse Constitutive 20s Proteasome In Complex With P		5e-05
1iru_C	261	Crystal Structure Of The Mammalian 20s Proteasome A		5e-15
1iru_C	261	Crystal Structure Of The Mammalian 20s Proteasome A		1e-04
3oeu_B	235	Structure Of Yeast 20s Open-Gate Proteasome With Co		1e-13
3oeu_B	235	Structure Of Yeast 20s Open-Gate Proteasome With Co		4e-07
3h4p_A	264	Proteasome 20s Core Particle From Methanocaldococcu		1e-12
1j2p_A	246	Alpha-Ring From The Proteasome From Archaeoglobus F		6e-12
1vsy_C	232	Proteasome Activator Complex Length = 232		6e-12
1vsy_C	232	Proteasome Activator Complex Length = 232		4e-07
3unb_D	241	Mouse Constitutive 20s Proteasome In Complex With P		3e-11
1iru_E	241	Crystal Structure Of The Mammalian 20s Proteasome A		3e-11
1j2q_A	237	20s Proteasome In Complex With Calpain-inhibitor I		7e-11
2z5c_C	262	Crystal Structure Of A Novel Chaperone Complex For		1e-09
4g4s_E	261	Structure Of Proteasome-Pba1-Pba2 Complex Length =		1e-09
1fnt_E	260	Crystal Structure Of The 20s Proteasome From Yeast		1e-09
1vsy_E	250	Proteasome Activator Complex Length = 250		2e-09
1g0u_D	241	A Gated Channel Into The Proteasome Core Particle L		2e-09
3jrm_A	227	Crystal Structure Of Archaeal 20s Proteasome In Com		6e-09
2ku1_A	237	Dynamic Regulation Of Archaeal Proteasome Gate Open		6e-09
1pma_A	233	Proteasome From Thermoplasma Acidophilum Length = 2		7e-09
1ryp_E	242	Crystal Structure Of The 20s Proteasome From Yeast		1e-08
1yar_A	233	Structure Of Archeabacterial 20s Proteasome Mutant		4e-08
1yau_A	233	Structure Of Archeabacterial 20s Proteasome- Pa26 C		2e-07
2ku2_A	237	Dynamic Regulation Of Archaeal Proteasome Gate Open		3e-07
1ryp_D	241	Crystal Structure Of The 20s Proteasome From Yeast		3e-07
1g0u_C	243	A Gated Channel Into The Proteasome Core Particle L		3e-07
1fnt_D	254	Crystal Structure Of The 20s Proteasome From Yeast		3e-07
1iru_A	246	Crystal Structure Of The Mammalian 20s Proteasome A		8e-07
1iru_D	248	Crystal Structure Of The Mammalian 20s Proteasome A		1e-06
3une_C	248	Mouse Constitutive 20s Proteasome Length = 248		1e-06
3unb_G	246	Mouse Constitutive 20s Proteasome In Complex With P		1e-06
3unb_C	248	Mouse Constitutive 20s Proteasome In Complex With P		2e-06
3unb_E	263	Mouse Constitutive 20s Proteasome In Complex With P		5e-06
1iru_F	263	Crystal Structure Of The Mammalian 20s Proteasome A		5e-06
3unb_F	255	Mouse Constitutive 20s Proteasome In Complex With P		6e-06
1iru_G	254	Crystal Structure Of The Mammalian 20s Proteasome A		7e-06
1g0u_E	234	A Gated Channel Into The Proteasome Core Particle L		2e-05
3sdi_E	233	Structure Of Yeast 20s Open-Gate Proteasome With Co		2e-05
1ryp_F	233	Crystal Structure Of The 20s Proteasome From Yeast		2e-05
1fnt_F	234	Crystal Structure Of The 20s Proteasome From Yeast		3e-05
4g4s_F	235	Structure Of Proteasome-Pba1-Pba2 Complex Length =		3e-05
3oeu_F	242	Structure Of Yeast 20s Open-Gate Proteasome With Co		6e-05
1g0u_F	248	A Gated Channel Into The Proteasome Core Particle L		6e-05
1ryp_G	244	Crystal Structure Of The 20s Proteasome From Yeast		6e-05
1z7q_G	288	Crystal Structure Of The 20s Proteasome From Yeast		7e-05
1fnt_G	287	Crystal Structure Of The 20s Proteasome From Yeast		7e-05
1g0u_G	252	A Gated Channel Into The Proteasome Core Particle L		1e-04
1ryp_A	243	Crystal Structure Of The 20s Proteasome From Yeast		1e-04

>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 = 85.5 bits (210), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 45/88 (51%), Positives = 56/88 (63%), Gaps = 18/88 (20%)
Query: 2  SRRYDRQTTVFSPEGRLYQVDYM-------GCLVG-----------ENNVTSKLLQTSTS 43
          SRRYD +TT+FSPEGRLYQV+Y        G  +G           E  VTS LL+  TS
Sbjct: 3  SRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTS 62
Query: 44 AEKMYKIDDHVACAVAGIMSDANILINT 71
           EK+YK++D +A AVAG+ +DA ILINT
Sbjct: 63 TEKLYKLNDKIAVAVAGLTADAEILINT 90

>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 = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 27/68 (39%), Positives = 43/68 (63%), Gaps = 1/68 (1%)
Query: 89  DYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPS-GKVKYRICSPESLTML 147
           DYKDDM   +A++LALK L KT DS++LT ++LE A +    + G+V  +I  P+ +  +
Sbjct: 179 DYKDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDI 238
Query: 148 LENFGVAQ 155
           L   G+ +
Sbjct: 239 LVKTGITK 246

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

Iteration: 1
 Score = 85.5 bits (210), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 45/88 (51%), Positives = 56/88 (63%), Gaps = 18/88 (20%)
Query: 2  SRRYDRQTTVFSPEGRLYQVDYM-------GCLVG-----------ENNVTSKLLQTSTS 43
          SRRYD +TT+FSPEGRLYQV+Y        G  +G           E  VTS LL+  TS
Sbjct: 2  SRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTS 61
Query: 44 AEKMYKIDDHVACAVAGIMSDANILINT 71
           EK+YK++D +A AVAG+ +DA ILINT
Sbjct: 62 TEKLYKLNDKIAVAVAGLTADAEILINT 89

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 27/66 (40%), Positives = 42/66 (63%), Gaps = 1/66 (1%)
Query: 89  DYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPS-GKVKYRICSPESLTML 147
           DYKDDM   +A++LALK L KT DS++LT ++LE A +    + G+V  +I  P+ +  +
Sbjct: 178 DYKDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDI 237
Query: 148 LENFGV 153
           L   G+
Sbjct: 238 LVKTGI 243

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

Iteration: 1
 Score = 85.5 bits (210), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 45/88 (51%), Positives = 56/88 (63%), Gaps = 18/88 (20%)
Query: 2  SRRYDRQTTVFSPEGRLYQVDYM-------GCLVG-----------ENNVTSKLLQTSTS 43
          SRRYD +TT+FSPEGRLYQV+Y        G  +G           E  VTS LL+  TS
Sbjct: 3  SRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTS 62
Query: 44 AEKMYKIDDHVACAVAGIMSDANILINT 71
           EK+YK++D +A AVAG+ +DA ILINT
Sbjct: 63 TEKLYKLNDKIAVAVAGLTADAEILINT 90

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 27/66 (40%), Positives = 42/66 (63%), Gaps = 1/66 (1%)
Query: 89  DYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPS-GKVKYRICSPESLTML 147
           DYKDDM   +A++LALK L KT DS++LT ++LE A +    + G+V  +I  P+ +  +
Sbjct: 179 DYKDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDI 238
Query: 148 LENFGV 153
           L   G+
Sbjct: 239 LVKTGI 244

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

Iteration: 1
 Score = 77.0 bits (188), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 44/105 (41%), Positives = 56/105 (53%), Gaps = 18/105 (17%)
Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MGC-------LVGENNVTSKLLQTST 42
           MSRRYD +TT+FSPEGRLYQV+Y           +G        L  E     KLL    
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF 60
Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTXXXXXXXXXXXXXEPI 87
            +EK+YK+++ +AC+VAGI SDAN+L N              EPI
Sbjct: 61  FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPI 105

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 26/62 (41%), Positives = 40/62 (64%), Gaps = 2/62 (3%)
Query: 88  QDYKD-DMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTM 146
           QDYK+ +MT + A+ LA+KVL KTMD + L++EK+E+A      SGK   R+   + +  
Sbjct: 177 QDYKEGEMTLKSALALAVKVLNKTMDVSKLSAEKVEIA-TLTRESGKTVIRVLKQKEVEQ 235
Query: 147 LL 148
           L+
Sbjct: 236 LI 237

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

Iteration: 1
 Score = 77.0 bits (188), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 44/105 (41%), Positives = 56/105 (53%), Gaps = 18/105 (17%)
Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MGC-------LVGENNVTSKLLQTST 42
           MSRRYD +TT+FSPEGRLYQV+Y           +G        L  E     KLL    
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF 60
Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTXXXXXXXXXXXXXEPI 87
            +EK+YK+++ +AC+VAGI SDAN+L N              EPI
Sbjct: 61  FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPI 105

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/62 (40%), Positives = 40/62 (64%), Gaps = 2/62 (3%)
Query: 88  QDYKD-DMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTM 146
           QDYK+ +MT + A+ LA+KVL KTMD + L++EK+E+A      +GK   R+   + +  
Sbjct: 177 QDYKEGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIA-TLTRENGKTVIRVLKQKEVEQ 235
Query: 147 LL 148
           L+
Sbjct: 236 LI 237

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

Iteration: 1
 Score = 72.4 bits (176), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 39/80 (48%), Positives = 49/80 (61%), Gaps = 18/80 (22%)
Query: 10 TVFSPEGRLYQVDYM-------GCLVG-----------ENNVTSKLLQTSTSAEKMYKID 51
          T+FSPEGRLYQV+Y        G  +G           E  VTS LL+  TS EK+YK++
Sbjct: 1  TIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTSTEKLYKLN 60
Query: 52 DHVACAVAGIMSDANILINT 71
          D +A AVAG+ +DA ILINT
Sbjct: 61 DKIAVAVAGLTADAEILINT 80

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 27/66 (40%), Positives = 42/66 (63%), Gaps = 1/66 (1%)
Query: 89  DYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPS-GKVKYRICSPESLTML 147
           DYKDDM   +A++LALK L KT DS++LT ++LE A +    + G+V  +I  P+ +  +
Sbjct: 169 DYKDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDI 228
Query: 148 LENFGV 153
           L   G+
Sbjct: 229 LVKTGI 234

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 37/84 (44%), Positives = 52/84 (61%), Gaps = 19/84 (22%)
Query: 5  YDRQTTVFSPEGRLYQVDY-------------MGC-----LVGENNVTSKLLQTSTSAEK 46
          YDR  TVFSPEGRLYQV+Y             + C     L  +  +TSKL++   S EK
Sbjct: 12 YDRAITVFSPEGRLYQVEYAREAVRRGTTAIGIACKDGVVLAVDRRITSKLVKIR-SIEK 70
Query: 47 MYKIDDHVACAVAGIMSDANILIN 70
          +++IDDHVA A +G+++DA +LI+
Sbjct: 71 IFQIDDHVAAATSGLVADARVLID 94

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 35/84 (41%), Positives = 51/84 (60%), Gaps = 19/84 (22%)
Query: 5  YDRQTTVFSPEGRLYQVDY-------------MGC-----LVGENNVTSKLLQTSTSAEK 46
          YDR  TVFSP+GRL+QV+Y             + C     L+ +  V SKLL+  T  EK
Sbjct: 8  YDRAITVFSPDGRLFQVEYAREAVKRGATAIGIKCKEGVILIADKRVGSKLLEKDT-IEK 66
Query: 47 MYKIDDHVACAVAGIMSDANILIN 70
          +YKID+H+  A +G+++DA +LI+
Sbjct: 67 IYKIDEHICAATSGLVADARVLID 90

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 37/77 (48%), Positives = 46/77 (59%), Gaps = 18/77 (23%)
Query: 13 SPEGRLYQVDYM-------GCLVG-----------ENNVTSKLLQTSTSAEKMYKIDDHV 54
          SPEGRLYQV+Y        G  +G           E  VTS LL+  TS EK+YK++D +
Sbjct: 1  SPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTSTEKLYKLNDKI 60
Query: 55 ACAVAGIMSDANILINT 71
          A AVAG+ +DA ILINT
Sbjct: 61 AVAVAGLTADAEILINT 77

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 27/66 (40%), Positives = 42/66 (63%), Gaps = 1/66 (1%)
Query: 89  DYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPS-GKVKYRICSPESLTML 147
           DYKDDM   +A++LALK L KT DS++LT ++LE A +    + G+V  +I  P+ +  +
Sbjct: 166 DYKDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDI 225
Query: 148 LENFGV 153
           L   G+
Sbjct: 226 LVKTGI 231

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 34/85 (40%), Positives = 49/85 (57%), Gaps = 19/85 (22%)
Query: 4  RYDRQTTVFSPEGRLYQVDY------MG------------CLVGENNVTSKLLQTSTSAE 45
           YDR    FSPEGRL+QV+Y      +G            CL  E  +TS L++ S S E
Sbjct: 7  EYDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEPS-SIE 65
Query: 46 KMYKIDDHVACAVAGIMSDANILIN 70
          K+ +ID H+ CA++G+++DA  LI+
Sbjct: 66 KIVEIDAHIGCAMSGLIADAKTLID 90

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 34/85 (40%), Positives = 49/85 (57%), Gaps = 19/85 (22%)
Query: 4  RYDRQTTVFSPEGRLYQVDY------MG------------CLVGENNVTSKLLQTSTSAE 45
           YDR    FSPEGRL+QV+Y      +G            CL  E  +TS L++ S S E
Sbjct: 7  EYDRGVNTFSPEGRLFQVEYDIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEPS-SIE 65
Query: 46 KMYKIDDHVACAVAGIMSDANILIN 70
          K+ +ID H+ CA++G+++DA  LI+
Sbjct: 66 KIVEIDAHIGCAMSGLIADAKTLID 90

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

Iteration: 1
 Score = 63.2 bits (152), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 36/99 (36%), Positives = 52/99 (52%), Gaps = 19/99 (19%)
Query: 7  RQTTVFSPEGRLYQVDY-------------MGC-----LVGENNVTSKLLQTSTSAEKMY 48
          R  TVFSP+GRL+QV+Y             + C     L+ +  V SKLL+  T  EK+Y
Sbjct: 1  RAITVFSPDGRLFQVEYAREAVKRGATAIGIKCKEGVILIADKRVGSKLLEADT-IEKIY 59
Query: 49 KIDDHVACAVAGIMSDANILINTXXXXXXXXXXXXXEPI 87
          KID+H+  A +G+++DA +LI+              EPI
Sbjct: 60 KIDEHICAATSGLVADARVLIDRARIEAQINRLTYDEPI 98

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 33/83 (39%), Positives = 47/83 (56%), Gaps = 19/83 (22%)
Query: 5  YDRQTTVFSPEGRLYQVDYM-----------------GCLVG-ENNVTSKLLQTSTSAEK 46
          YDR  + FSPEGRL+QV+Y                  G ++G E   TS LL+ S S EK
Sbjct: 10 YDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE-SDSIEK 68
Query: 47 MYKIDDHVACAVAGIMSDANILI 69
          + +ID H+ CA++G+ +DA  +I
Sbjct: 69 IVEIDRHIGCAMSGLTADARSMI 91

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 33/83 (39%), Positives = 47/83 (56%), Gaps = 19/83 (22%)
Query: 5  YDRQTTVFSPEGRLYQVDYM-----------------GCLVG-ENNVTSKLLQTSTSAEK 46
          YDR  + FSPEGRL+QV+Y                  G ++G E   TS LL+ S S EK
Sbjct: 9  YDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE-SDSIEK 67
Query: 47 MYKIDDHVACAVAGIMSDANILI 69
          + +ID H+ CA++G+ +DA  +I
Sbjct: 68 IVEIDRHIGCAMSGLTADARSMI 90

>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 = 58.9 bits (141), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 33/83 (39%), Positives = 47/83 (56%), Gaps = 19/83 (22%)
Query: 5  YDRQTTVFSPEGRLYQVDYM-----------------GCLVG-ENNVTSKLLQTSTSAEK 46
          YDR  + FSPEGRL+QV+Y                  G ++G E   TS LL+ S S EK
Sbjct: 8  YDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE-SDSIEK 66
Query: 47 MYKIDDHVACAVAGIMSDANILI 69
          + +ID H+ CA++G+ +DA  +I
Sbjct: 67 IVEIDRHIGCAMSGLTADARSMI 89

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/83 (39%), Positives = 47/83 (56%), Gaps = 19/83 (22%)
Query: 5  YDRQTTVFSPEGRLYQVDYM-----------------GCLVG-ENNVTSKLLQTSTSAEK 46
          YDR  + FSPEGRL+QV+Y                  G ++G E   TS LL+ S S EK
Sbjct: 8  YDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE-SDSIEK 66
Query: 47 MYKIDDHVACAVAGIMSDANILI 69
          + +ID H+ CA++G+ +DA  +I
Sbjct: 67 IVEIDRHIGCAMSGLTADARSMI 89

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/83 (39%), Positives = 47/83 (56%), Gaps = 19/83 (22%)
Query: 5  YDRQTTVFSPEGRLYQVDYM-----------------GCLVG-ENNVTSKLLQTSTSAEK 46
          YDR  + FSPEGRL+QV+Y                  G ++G E   TS LL+ S S EK
Sbjct: 8  YDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE-SDSIEK 66
Query: 47 MYKIDDHVACAVAGIMSDANILI 69
          + +ID H+ CA++G+ +DA  +I
Sbjct: 67 IVEIDRHIGCAMSGLTADARSMI 89

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 31/84 (36%), Positives = 50/84 (59%), Gaps = 19/84 (22%)
Query: 5  YDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAEK 46
          YDR  TVFSP+GRL+QV+Y           +G        L+ +  V S+L++ + S EK
Sbjct: 2  YDRAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQN-SIEK 60
Query: 47 MYKIDDHVACAVAGIMSDANILIN 70
          +  IDD+VA   +G+++DA +L++
Sbjct: 61 IQLIDDYVAAVTSGLVADARVLVD 84

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 31/84 (36%), Positives = 50/84 (59%), Gaps = 19/84 (22%)
Query: 5  YDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAEK 46
          YDR  TVFSP+GRL+QV+Y           +G        L+ +  V S+L++ + S EK
Sbjct: 12 YDRAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQN-SIEK 70
Query: 47 MYKIDDHVACAVAGIMSDANILIN 70
          +  IDD+VA   +G+++DA +L++
Sbjct: 71 IQLIDDYVAAVTSGLVADARVLVD 94

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 31/84 (36%), Positives = 50/84 (59%), Gaps = 19/84 (22%)
Query: 5  YDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAEK 46
          YDR  TVFSP+GRL+QV+Y           +G        L+ +  V S+L++ + S EK
Sbjct: 8  YDRAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQN-SIEK 66
Query: 47 MYKIDDHVACAVAGIMSDANILIN 70
          +  IDD+VA   +G+++DA +L++
Sbjct: 67 IQLIDDYVAAVTSGLVADARVLVD 90

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 32/82 (39%), Positives = 46/82 (56%), Gaps = 19/82 (23%)
Query: 6  DRQTTVFSPEGRLYQVDYM-----------------GCLVG-ENNVTSKLLQTSTSAEKM 47
          DR  + FSPEGRL+QV+Y                  G ++G E   TS LL+ S S EK+
Sbjct: 1  DRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE-SDSIEKI 59
Query: 48 YKIDDHVACAVAGIMSDANILI 69
           +ID H+ CA++G+ +DA  +I
Sbjct: 60 VEIDRHIGCAMSGLTADARSMI 81

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 30/84 (35%), Positives = 49/84 (58%), Gaps = 19/84 (22%)
Query: 5  YDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAEK 46
          Y R  TVFSP+GRL+QV+Y           +G        L+ +  V S+L++ + S EK
Sbjct: 8  YSRAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQN-SIEK 66
Query: 47 MYKIDDHVACAVAGIMSDANILIN 70
          +  IDD+VA   +G+++DA +L++
Sbjct: 67 IQLIDDYVAAVTSGLVADARVLVD 90

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/82 (35%), Positives = 48/82 (58%), Gaps = 19/82 (23%)
Query: 7  RQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAEKMY 48
          R  TVFSP+GRL+QV+Y           +G        L+ +  V S+L++ + S EK+ 
Sbjct: 10 RAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQN-SIEKIQ 68
Query: 49 KIDDHVACAVAGIMSDANILIN 70
           IDD+VA   +G+++DA +L++
Sbjct: 69 LIDDYVAAVTSGLVADARVLVD 90

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/82 (35%), Positives = 48/82 (58%), Gaps = 19/82 (23%)
Query: 7  RQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAEKMY 48
          R  TVFSP+GRL+QV+Y           +G        L+ +  V S+L++ + S EK+ 
Sbjct: 14 RAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQN-SIEKIQ 72
Query: 49 KIDDHVACAVAGIMSDANILIN 70
           IDD+VA   +G+++DA +L++
Sbjct: 73 LIDDYVAAVTSGLVADARVLVD 94

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 42/83 (50%), Gaps = 18/83 (21%)
Query: 5  YDRQTTVFSPEGRLYQVDYM-------GCLVG-----------ENNVTSKLLQTSTSAEK 46
          YDR  ++FSP+G ++QV+Y         C VG           E   T KL  T  +  K
Sbjct: 2  YDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSK 61
Query: 47 MYKIDDHVACAVAGIMSDANILI 69
          + KID HV  + +G+ +D+ ILI
Sbjct: 62 VSKIDSHVVLSFSGLNADSRILI 84

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 42/83 (50%), Gaps = 18/83 (21%)
Query: 5  YDRQTTVFSPEGRLYQVDYM-------GCLVG-----------ENNVTSKLLQTSTSAEK 46
          YDR  ++FSP+G ++QV+Y         C VG           E   T KL  T  +  K
Sbjct: 4  YDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSK 63
Query: 47 MYKIDDHVACAVAGIMSDANILI 69
          + KID HV  + +G+ +D+ ILI
Sbjct: 64 VSKIDSHVVLSFSGLNADSRILI 86

>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 = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 42/83 (50%), Gaps = 18/83 (21%)
Query: 5  YDRQTTVFSPEGRLYQVDYM-------GCLVG-----------ENNVTSKLLQTSTSAEK 46
          YDR  ++FSP+G ++QV+Y         C VG           E   T KL  T  +  K
Sbjct: 4  YDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSK 63
Query: 47 MYKIDDHVACAVAGIMSDANILI 69
          + KID HV  + +G+ +D+ ILI
Sbjct: 64 VSKIDSHVVLSFSGLNADSRILI 86

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 27/83 (32%), Positives = 42/83 (50%), Gaps = 20/83 (24%)
Query: 2  SRRYDRQTTVFSPEGRLYQVDYM-------------------GCLVGENNVTSKLLQTST 42
          S  +DR  T+FSPEGRLYQV+Y                      +V +  V  KLL +ST
Sbjct: 6  SAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSST 65
Query: 43 SAEKMYKIDDHVACAVAGIMSDA 65
              ++KI +++ C + G+ +D+
Sbjct: 66 VTH-LFKITENIGCVMTGMTADS 87

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 41/83 (49%), Gaps = 17/83 (20%)
Query: 5  YDRQTTVFSPEGRLYQVDYMG-----------------CLVGENNVTSKLLQTSTSAEKM 47
          YDR  TVFSP+G L+QV+Y                    ++G    +   LQ   +  K+
Sbjct: 3  YDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVRKI 62
Query: 48 YKIDDHVACAVAGIMSDANILIN 70
            +DD+V  A AG+ +DA I+IN
Sbjct: 63 CALDDNVCMAFAGLTADARIVIN 85

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 41/83 (49%), Gaps = 17/83 (20%)
Query: 5  YDRQTTVFSPEGRLYQVDYMG-----------------CLVGENNVTSKLLQTSTSAEKM 47
          YDR  TVFSP+G L+QV+Y                    ++G    +   LQ   +  K+
Sbjct: 3  YDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGKDIVVLGVEKKSVAKLQDERTVRKI 62
Query: 48 YKIDDHVACAVAGIMSDANILIN 70
            +DD+V  A AG+ +DA I+IN
Sbjct: 63 CALDDNVCMAFAGLTADARIVIN 85

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/83 (32%), Positives = 41/83 (49%), Gaps = 20/83 (24%)
Query: 2  SRRYDRQTTVFSPEGRLYQVDYM-------------------GCLVGENNVTSKLLQTST 42
          S  +DR  T+FSPEGRLYQV+Y                      +V +  V  KLL +ST
Sbjct: 6  SAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSST 65
Query: 43 SAEKMYKIDDHVACAVAGIMSDA 65
              ++KI + + C + G+ +D+
Sbjct: 66 VTH-LFKITESIGCVMTGMTADS 87

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 41/83 (49%), Gaps = 17/83 (20%)
Query: 5  YDRQTTVFSPEGRLYQVDYMG-----------------CLVGENNVTSKLLQTSTSAEKM 47
          YDR  TVFSP+G L+QV+Y                    ++G    +   LQ   +  K+
Sbjct: 3  YDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGKDIVVLGVAKKSVAKLQDERTVRKI 62
Query: 48 YKIDDHVACAVAGIMSDANILIN 70
            +DD+V  A AG+ +DA I+IN
Sbjct: 63 CALDDNVCMAFAGLTADARIVIN 85

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 44/82 (53%), Gaps = 15/82 (18%)
Query: 4  RYDRQTTVFSPEGRLYQVDYM-------GCLVGENNVTSKLL--------QTSTSAEKMY 48
          +YD   TV+SP+GR++Q++Y           VG  + T  +L        + +   +K+ 
Sbjct: 5  QYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQKKIL 64
Query: 49 KIDDHVACAVAGIMSDANILIN 70
           +D+H+  ++AG+ +DA +L N
Sbjct: 65 HVDNHIGISIAGLTADARLLCN 86

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 44/82 (53%), Gaps = 15/82 (18%)
Query: 4  RYDRQTTVFSPEGRLYQVDYM-------GCLVGENNVTSKLL--------QTSTSAEKMY 48
          +YD   TV+SP+GR++Q++Y           VG  + T  +L        + +   +K+ 
Sbjct: 5  QYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQKKIL 64
Query: 49 KIDDHVACAVAGIMSDANILIN 70
           +D+H+  ++AG+ +DA +L N
Sbjct: 65 HVDNHIGISIAGLTADARLLCN 86

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 19/84 (22%)
Query: 5  YDRQTTVFSPEGRLYQVDYM-----------------GCLVG-ENNVTSKLLQTSTSAEK 46
          YD   + FSP+GR++QV+Y                  G + G E  V SKL +  ++ ++
Sbjct: 8  YDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEGSN-KR 66
Query: 47 MYKIDDHVACAVAGIMSDANILIN 70
          ++ +D HV  AVAG+++DA  L +
Sbjct: 67 LFNVDRHVGMAVAGLLADARSLAD 90

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 19/84 (22%)
Query: 5  YDRQTTVFSPEGRLYQVDYM-----------------GCLVG-ENNVTSKLLQTSTSAEK 46
          YD   + FSP+GR++QV+Y                  G + G E  V SKL +  ++ ++
Sbjct: 7  YDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEGSN-KR 65
Query: 47 MYKIDDHVACAVAGIMSDANILIN 70
          ++ +D HV  AVAG+++DA  L +
Sbjct: 66 LFNVDRHVGMAVAGLLADARSLAD 89

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 15/81 (18%)
Query: 5  YDRQTTVFSPEGRLYQVDYMGCLVGENNVTSKLL---------------QTSTSAEKMYK 49
          YD  T  FSP GRL+QV+Y    + + +VT  L                + S+  +K+ K
Sbjct: 6  YDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQKKIIK 65
Query: 50 IDDHVACAVAGIMSDANILIN 70
           D+H+  ++AG+  DA +L N
Sbjct: 66 CDEHMGLSLAGLAPDARVLSN 86

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 15/81 (18%)
Query: 5  YDRQTTVFSPEGRLYQVDYMGCLVGENNVTSKLL---------------QTSTSAEKMYK 49
          YD  T  FSP GRL+QV+Y    + + +VT  L                + S+  +K+ K
Sbjct: 5  YDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQKKIIK 64
Query: 50 IDDHVACAVAGIMSDANILIN 70
           D+H+  ++AG+  DA +L N
Sbjct: 65 CDEHMGLSLAGLAPDARVLSN 85

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 15/81 (18%)
Query: 5  YDRQTTVFSPEGRLYQVDYMGCLVGENNVTSKLL---------------QTSTSAEKMYK 49
          YD  T  FSP GRL+QV+Y    + + +VT  L                + S+  +K+ K
Sbjct: 5  YDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQKKIIK 64
Query: 50 IDDHVACAVAGIMSDANILIN 70
           D+H+  ++AG+  DA +L N
Sbjct: 65 CDEHMGLSLAGLAPDARVLSN 85

>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 = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 15/81 (18%)
Query: 5  YDRQTTVFSPEGRLYQVDYMGCLVGENNVTSKLL---------------QTSTSAEKMYK 49
          YD  T  FSP GRL+QV+Y    + + +VT  L                + S+  +K+ K
Sbjct: 6  YDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQKKIIK 65
Query: 50 IDDHVACAVAGIMSDANILIN 70
           D+H+  ++AG+  DA +L N
Sbjct: 66 CDEHMGLSLAGLAPDARVLSN 86

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 15/81 (18%)
Query: 5  YDRQTTVFSPEGRLYQVDYMGCLVGENNVTSKLL---------------QTSTSAEKMYK 49
          YD  T  FSP GRL+QV+Y    + + +VT  L                + S+  +K+ K
Sbjct: 7  YDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQKKIIK 66
Query: 50 IDDHVACAVAGIMSDANILIN 70
           D+H+  ++AG+  DA +L N
Sbjct: 67 CDEHMGLSLAGLAPDARVLSN 87

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 41/84 (48%), Gaps = 19/84 (22%)
Query: 5  YDRQTTVFSPEGRLYQVDY-------------MGCLVG-----ENNVTSKLLQTSTSAEK 46
          YD   +VFSP+GR +QV+Y             + C  G     E  +TSKLL    +  K
Sbjct: 2  YDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNV-K 60
Query: 47 MYKIDDHVACAVAGIMSDANILIN 70
          +  +D H+ C  +G++ D   L+N
Sbjct: 61 IQVVDRHIGCVYSGLIPDGRHLVN 84

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 41/84 (48%), Gaps = 19/84 (22%)
Query: 5  YDRQTTVFSPEGRLYQVDY-------------MGCLVG-----ENNVTSKLLQTSTSAEK 46
          YD   +VFSP+GR +QV+Y             + C  G     E  +TSKLL    +  K
Sbjct: 8  YDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNV-K 66
Query: 47 MYKIDDHVACAVAGIMSDANILIN 70
          +  +D H+ C  +G++ D   L+N
Sbjct: 67 IQVVDRHIGCVYSGLIPDGRHLVN 90

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 41/84 (48%), Gaps = 19/84 (22%)
Query: 5  YDRQTTVFSPEGRLYQVDY-------------MGCLVG-----ENNVTSKLLQTSTSAEK 46
          YD   +VFSP+GR +QV+Y             + C  G     E  +TSKLL    +  K
Sbjct: 4  YDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNV-K 62
Query: 47 MYKIDDHVACAVAGIMSDANILIN 70
          +  +D H+ C  +G++ D   L+N
Sbjct: 63 IQVVDRHIGCVYSGLIPDGRHLVN 86

>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 = 43.1 bits (100), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 41/84 (48%), Gaps = 19/84 (22%)
Query: 5  YDRQTTVFSPEGRLYQVDY-------------MGCLVG-----ENNVTSKLLQTSTSAEK 46
          YD   +VFSP+GR +QV+Y             + C  G     E  +TSKLL    +  K
Sbjct: 8  YDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNV-K 66
Query: 47 MYKIDDHVACAVAGIMSDANILIN 70
          +  +D H+ C  +G++ D   L+N
Sbjct: 67 IQVVDRHIGCVYSGLIPDGRHLVN 90

>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 = 43.1 bits (100), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 41/84 (48%), Gaps = 19/84 (22%)
Query: 5  YDRQTTVFSPEGRLYQVDY-------------MGCLVG-----ENNVTSKLLQTSTSAEK 46
          YD   +VFSP+GR +QV+Y             + C  G     E  +TSKLL    +  K
Sbjct: 7  YDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNV-K 65
Query: 47 MYKIDDHVACAVAGIMSDANILIN 70
          +  +D H+ C  +G++ D   L+N
Sbjct: 66 IQVVDRHIGCVYSGLIPDGRHLVN 89

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 17/31 (54%), Positives = 21/31 (67%)
Query: 5  YDRQTTVFSPEGRLYQVDYMGCLVGENNVTS 35
          YDR  T+FSPEGRLYQV+Y      + N+ S
Sbjct: 12 YDRHITIFSPEGRLYQVEYAFKATNQTNINS 42

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 17/31 (54%), Positives = 21/31 (67%)
Query: 5  YDRQTTVFSPEGRLYQVDYMGCLVGENNVTS 35
          YDR  T+FSPEGRLYQV+Y      + N+ S
Sbjct: 3  YDRHITIFSPEGRLYQVEYAFKATNQTNINS 33

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	161
1iru_C	261	20S proteasome; cell cycle, immune response, prote	4e-33
1iru_C	261	20S proteasome; cell cycle, immune response, prote	1e-08
1iru_E	241	20S proteasome; cell cycle, immune response, prote	6e-33
1iru_E	241	20S proteasome; cell cycle, immune response, prote	1e-07
1ryp_B	250	20S proteasome; multicatalytic proteinase, protein	1e-32
1ryp_B	250	20S proteasome; multicatalytic proteinase, protein	2e-06
1iru_A	246	20S proteasome; cell cycle, immune response, prote	2e-32
1iru_A	246	20S proteasome; cell cycle, immune response, prote	2e-05
1iru_B	233	20S proteasome; cell cycle, immune response, prote	3e-32
1iru_B	233	20S proteasome; cell cycle, immune response, prote	1e-08
1ryp_C	244	20S proteasome; multicatalytic proteinase, protein	4e-32
1ryp_C	244	20S proteasome; multicatalytic proteinase, protein	8e-12
3nzj_F	288	Proteasome component C1; ubiquitin, protein degrad	9e-32
3nzj_F	288	Proteasome component C1; ubiquitin, protein degrad	1e-06
1ryp_D	241	20S proteasome; multicatalytic proteinase, protein	3e-31
1ryp_D	241	20S proteasome; multicatalytic proteinase, protein	4e-05
1ryp_A	243	20S proteasome; multicatalytic proteinase, protein	4e-31
1ryp_A	243	20S proteasome; multicatalytic proteinase, protein	8e-07
1iru_F	263	20S proteasome; cell cycle, immune response, prote	5e-31
1iru_F	263	20S proteasome; cell cycle, immune response, prote	2e-05
1iru_D	248	20S proteasome; cell cycle, immune response, prote	1e-30
1iru_G	254	20S proteasome; cell cycle, immune response, prote	1e-30
1iru_G	254	20S proteasome; cell cycle, immune response, prote	6e-08
1ryp_G	244	20S proteasome; multicatalytic proteinase, protein	1e-30
1ryp_G	244	20S proteasome; multicatalytic proteinase, protein	6e-07
1yar_A	233	Proteasome alpha subunit; proteasome 20S, PA26 pro	3e-29
1yar_A	233	Proteasome alpha subunit; proteasome 20S, PA26 pro	2e-07
3h4p_A	264	Proteasome subunit alpha; core particle, cytoplasm	4e-28
3h4p_A	264	Proteasome subunit alpha; core particle, cytoplasm	3e-07
1j2p_A	246	Alpha-ring, proteasome alpha subunit; hydrolase; 2	1e-27
1j2p_A	246	Alpha-ring, proteasome alpha subunit; hydrolase; 2	1e-07
1ryp_F	233	20S proteasome; multicatalytic proteinase, protein	1e-27
1ryp_F	233	20S proteasome; multicatalytic proteinase, protein	5e-07
1ryp_E	242	20S proteasome; multicatalytic proteinase, protein	2e-27
1ryp_E	242	20S proteasome; multicatalytic proteinase, protein	1e-07
3unf_H	234	Proteasome subunit beta type-10; antigen presentat	3e-13
3unf_H	234	Proteasome subunit beta type-10; antigen presentat	4e-07
3mi0_A	248	Proteasome subunit alpha; enzyme inhibitors, lacto	1e-11
3mi0_A	248	Proteasome subunit alpha; enzyme inhibitors, lacto	5e-09
1ryp_I	222	20S proteasome; multicatalytic proteinase, protein	1e-09
1ryp_I	222	20S proteasome; multicatalytic proteinase, protein	7e-05
3nzj_H	261	Proteasome component PUP1; ubiquitin, protein degr	1e-09
3nzj_H	261	Proteasome component PUP1; ubiquitin, protein degr	2e-04
1iru_I	234	20S proteasome; cell cycle, immune response, prote	2e-09
1iru_I	234	20S proteasome; cell cycle, immune response, prote	1e-04
1q5q_A	259	Proteasome alpha-type subunit 1; proteasome assemb	3e-09
1q5q_A	259	Proteasome alpha-type subunit 1; proteasome assemb	4e-08
1q5q_H	235	Proteasome beta-type subunit 1; proteasome assembl	2e-08
1yar_H	217	Proteasome beta subunit; proteasome 20S, PA26 prot	1e-07
1q5r_H	294	Proteasome beta-type subunit 1; proteasome assembl	4e-06
3nzj_K	287	Proteasome component PRE2; ubiquitin, protein degr	9e-06
1j2q_H	202	Proteasome beta subunit; ubiquitin, CP, hydrolase;	1e-05
1ryp_L	212	20S proteasome; multicatalytic proteinase, protein	1e-05
1ryp_L	212	20S proteasome; multicatalytic proteinase, protein	2e-05
2jay_A	291	Proteasome; hydrolase; 1.99A {Mycobacterium tuberc	3e-05
1ryp_H	205	20S proteasome; multicatalytic proteinase, protein	3e-05
1iru_L	204	20S proteasome; cell cycle, immune response, prote	3e-05
1iru_H	205	20S proteasome; cell cycle, immune response, prote	7e-05
3unf_N	199	Proteasome subunit beta type-9; antigen presentati	1e-04
1g0u_M	266	Proteasome component PRE4; ubiquitin, degradation,	1e-04
1ryp_M	222	20S proteasome; multicatalytic proteinase, protein	1e-04
1ryp_N	233	20S proteasome; multicatalytic proteinase, protein	2e-04
1iru_M	213	20S proteasome; cell cycle, immune response, prote	2e-04
1iru_J	205	20S proteasome; cell cycle, immune response, prote	3e-04
1ryp_K	198	20S proteasome; multicatalytic proteinase, protein	8e-04

>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 =  116 bits (293), Expect = 4e-33
 Identities = 49/105 (46%), Positives = 62/105 (59%), Gaps = 18/105 (17%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDYMG------------------CLVGENNVTSKLLQTST 42
           MSRRYD +TT+FSPEGRLYQV+Y                     L  E     KLL    
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF 60

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
            +EK+YK+++ +AC+VAGI SDAN+L N  R+ A+RY   YQEPI
Sbjct: 61  FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPI 105

>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 = 51.2 bits (123), Expect = 1e-08
 Identities = 26/73 (35%), Positives = 44/73 (60%), Gaps = 2/73 (2%)

Query: 88  QDYKD-DMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTM 146
           QDYK+ +MT + A+ LA+KVL KTMD + L++EK+E+A      +GK   R+   + +  
Sbjct: 177 QDYKEGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIA-TLTRENGKTVIRVLKQKEVEQ 235

Query: 147 LLENFGVAQPASE 159
           L++     +  +E
Sbjct: 236 LIKKHEEEEAKAE 248

>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 =  115 bits (291), Expect = 6e-33
 Identities = 40/106 (37%), Positives = 62/106 (58%), Gaps = 20/106 (18%)

Query: 1   MSR-RYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTS 41
           ++R  YDR    FSPEGRL+QV+Y           +G       CL  E  +TS L++ S
Sbjct: 3   LTRSEYDRGVNTFSPEGRLFQVEYDIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEPS 62

Query: 42  TSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
            S EK+ +ID H+ CA++G+++DA  LI+ ARV+ + + + Y E +
Sbjct: 63  -SIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETM 107

>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 = 48.7 bits (117), Expect = 1e-07
 Identities = 15/63 (23%), Positives = 33/63 (52%), Gaps = 5/63 (7%)

Query: 88  QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTML 147
           + Y   MT +EA++ +L +L++ M+   L +  +ELA V         + + + E L  +
Sbjct: 183 ELYHKSMTLKEAIKSSLIILKQVME-EKLNATNIELATV----QPGQNFHMFTKEELEEV 237

Query: 148 LEN 150
           +++
Sbjct: 238 IKD 240

>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 =  115 bits (290), Expect = 1e-32
 Identities = 26/106 (24%), Positives = 42/106 (39%), Gaps = 20/106 (18%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTST 42
           M+ RY    T FSP G+L Q+DY           +G        +  E   +S L  + T
Sbjct: 1   MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET 60

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQAR-RYAYAYQEPI 87
              K+  +   +    +G+  D  +L++ +R  A   Y   Y E  
Sbjct: 61  L-SKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYP 105

>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 = 45.3 bits (108), Expect = 2e-06
 Identities = 11/74 (14%), Positives = 33/74 (44%), Gaps = 12/74 (16%)

Query: 88  QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEV-----------FLLPSGKVKY 136
           + + D++  ++A+ +AL  L+++++      + +ELA +            +      ++
Sbjct: 177 KRWNDELELEDAIHIALLTLKESVE-GEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRF 235

Query: 137 RICSPESLTMLLEN 150
           R  + + +   LE 
Sbjct: 236 RKLTSQEINDRLEA 249

>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 =  114 bits (288), Expect = 2e-32
 Identities = 34/110 (30%), Positives = 54/110 (49%), Gaps = 24/110 (21%)

Query: 1   MSR----RYDRQTTVFSPEGRLYQVDY------------MG-------CLVGENNVTSKL 37
           MSR     +DR  T+FSPEGRLYQV+Y            +         +V +  V  KL
Sbjct: 1   MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL 60

Query: 38  LQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           L +S +   ++KI +++ C + G+ +D+   +  AR +A  + Y Y   I
Sbjct: 61  LDSS-TVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEI 109

>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 = 41.8 bits (99), Expect = 2e-05
 Identities = 12/65 (18%), Positives = 24/65 (36%), Gaps = 6/65 (9%)

Query: 88  QDYKD--DMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLT 145
           +  K   D T ++ V+ A+  L   +        ++E+  V        K+RI +   + 
Sbjct: 181 KKVKKKFDWTFEQTVETAITCLSTVLS-IDFKPSEIEVGVV---TVENPKFRILTEAEID 236

Query: 146 MLLEN 150
             L  
Sbjct: 237 AHLVA 241

>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 =  113 bits (286), Expect = 3e-32
 Identities = 31/104 (29%), Positives = 44/104 (42%), Gaps = 19/104 (18%)

Query: 2   SRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTS 43
            R Y    T FSP G+L Q++Y           +G        L  E    S L     S
Sbjct: 2   ERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDER-S 60

Query: 44  AEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
             K+  I  H+    +G+  D  +L++ AR  A++Y   YQEPI
Sbjct: 61  VHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPI 104

>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 = 51.4 bits (124), Expect = 1e-08
 Identities = 10/65 (15%), Positives = 29/65 (44%), Gaps = 6/65 (9%)

Query: 88  QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTML 147
           + Y +D+  ++A+  A+  L+++ +   +T + +E+         +  +R  +P  +   
Sbjct: 175 KRYNEDLELEDAIHTAILTLKESFE-GQMTEDNIEVGIC-----NEAGFRRLTPTEVKDY 228

Query: 148 LENFG 152
           L    
Sbjct: 229 LAAIA 233

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

 Score =  113 bits (286), Expect = 4e-32
 Identities = 52/104 (50%), Positives = 65/104 (62%), Gaps = 18/104 (17%)

Query: 2   SRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTS 43
           SRRYD +TT+FSPEGRLYQV+Y           +G        L  E  VTS LL+  TS
Sbjct: 2   SRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTS 61

Query: 44  AEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
            EK+YK++D +A AVAG+ +DA ILINTAR+ A+ Y   Y E I
Sbjct: 62  TEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDI 105

>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 = 60.0 bits (146), Expect = 8e-12
 Identities = 27/67 (40%), Positives = 41/67 (61%), Gaps = 1/67 (1%)

Query: 88  QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEV-FLLPSGKVKYRICSPESLTM 146
            DYKDDM   +A++LALK L KT DS++LT ++LE A +      G+V  +I  P+ +  
Sbjct: 177 MDYKDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKD 236

Query: 147 LLENFGV 153
           +L   G+
Sbjct: 237 ILVKTGI 243

>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 =  113 bits (286), Expect = 9e-32
 Identities = 31/105 (29%), Positives = 49/105 (46%), Gaps = 19/105 (18%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTST 42
           +   YD   +VFSP+GR +QV+Y           +G           E  +TSKLL    
Sbjct: 4   IGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQK 63

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           +  K+  +D H+ C  +G++ D   L+N  R +A  +   Y+ PI
Sbjct: 64  N-VKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPI 107

>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 = 45.8 bits (109), Expect = 1e-06
 Identities = 9/66 (13%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 84  QEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPES 143
           ++ +  + + ++ +EAV+ A K++    +       +LE++   L  +    ++    + 
Sbjct: 177 EKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNG-LHKFVKGDL 235

Query: 144 LTMLLE 149
           L   ++
Sbjct: 236 LQEAID 241

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

 Score =  111 bits (279), Expect = 3e-31
 Identities = 33/101 (32%), Positives = 53/101 (52%), Gaps = 18/101 (17%)

Query: 5   YDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAEK 46
           YDR  ++FSP+G ++QV+Y           +G        L  E   T KL  T  +  K
Sbjct: 2   YDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSK 61

Query: 47  MYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           + KID HV  + +G+ +D+ ILI  ARV+A+ +    ++P+
Sbjct: 62  VSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPV 102

>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 = 41.1 bits (97), Expect = 4e-05
 Identities = 9/68 (13%), Positives = 24/68 (35%), Gaps = 7/68 (10%)

Query: 84  QEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPES 143
           ++     +   T +E V+L ++ L + +      ++ +E+  V             S E 
Sbjct: 174 EKNYDRKEPPATVEECVKLTVRSLLEVVQ---TGAKNIEITVV----KPDSDIVALSSEE 226

Query: 144 LTMLLENF 151
           +   +   
Sbjct: 227 INQYVTQI 234

>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 =  111 bits (279), Expect = 4e-31
 Identities = 28/103 (27%), Positives = 44/103 (42%), Gaps = 20/103 (19%)

Query: 4   RYDRQTTVFSPEGRLYQVDY------------MG-------CLVGENNVTSKLLQTSTSA 44
            YDR  T+FSPEGRLYQV+Y            +         ++ +  V  KLL  + + 
Sbjct: 2   GYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPT-TV 60

Query: 45  EKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
             ++ I   +   V G + DA      A+ +A  + Y Y   +
Sbjct: 61  SYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDM 103

>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 = 46.1 bits (110), Expect = 8e-07
 Identities = 11/68 (16%), Positives = 29/68 (42%), Gaps = 6/68 (8%)

Query: 83  YQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPE 142
           +++   D+ ++ + ++ V+ A+  +   +  T  +   LE+         K K+   S E
Sbjct: 177 FKKSKIDHINEESWEKVVEFAITHMIDALG-TEFSKNDLEVGVA-----TKDKFFTLSAE 230

Query: 143 SLTMLLEN 150
           ++   L  
Sbjct: 231 NIEERLVA 238

>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 =  111 bits (280), Expect = 5e-31
 Identities = 28/106 (26%), Positives = 50/106 (47%), Gaps = 22/106 (20%)

Query: 1   MSR-RYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTS 41
           M R +YD   TV+SP+GR++Q++Y           +G        LV      S+L    
Sbjct: 1   MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQ 60

Query: 42  TSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
               K+  +D+H+  ++AG+ +DA +L N  R +     + +  P+
Sbjct: 61  K---KILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPL 103

>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 = 42.3 bits (100), Expect = 2e-05
 Identities = 13/67 (19%), Positives = 30/67 (44%), Gaps = 7/67 (10%)

Query: 88  QDYKDDM--TRQEAVQLALKVLRKTMDST-SLTSEKLELAEVFLLPSGKVKYRICSPESL 144
           +   + M     E V+  L+ LR+T+ +   LT++ + +  V       +++ I   + +
Sbjct: 174 RHMSEFMECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIV----GKDLEFTIYDDDDV 229

Query: 145 TMLLENF 151
           +  LE  
Sbjct: 230 SPFLEGL 236

>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 =  110 bits (277), Expect = 1e-30
 Identities = 35/101 (34%), Positives = 52/101 (51%), Gaps = 19/101 (18%)

Query: 5   YDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAEK 46
           YDR  TVFSP+G L+QV+Y           +G        L  E    +KL    T   K
Sbjct: 3   YDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTV-RK 61

Query: 47  MYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           +  +DD+V  A AG+ +DA I+IN ARV+ + +    ++P+
Sbjct: 62  ICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPV 102

>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 =  110 bits (277), Expect = 1e-30
 Identities = 31/105 (29%), Positives = 51/105 (48%), Gaps = 19/105 (18%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTST 42
           +   YD   + FSP+GR++QV+Y           +G           E  V SKL +   
Sbjct: 3   IGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEG- 61

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           S ++++ +D HV  AVAG+++DA  L + AR +A  +   +   I
Sbjct: 62  SNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNI 106

>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 = 49.3 bits (118), Expect = 6e-08
 Identities = 14/72 (19%), Positives = 30/72 (41%), Gaps = 3/72 (4%)

Query: 88  QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTML 147
           +    +MT ++ V+   K++    D     + +LEL+ V  L +G+ +     P+ +   
Sbjct: 178 KLQMKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEI---VPKDIREE 234

Query: 148 LENFGVAQPASE 159
            E +       E
Sbjct: 235 AEKYAKESLKEE 246

>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 =  110 bits (276), Expect = 1e-30
 Identities = 31/102 (30%), Positives = 48/102 (47%), Gaps = 19/102 (18%)

Query: 4   RYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAE 45
            YD   +VFSP+GR +QV+Y           +G           E  +TSKLL    +  
Sbjct: 3   GYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKN-V 61

Query: 46  KMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           K+  +D H+ C  +G++ D   L+N  R +A  +   Y+ PI
Sbjct: 62  KIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPI 103

>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 = 46.5 bits (111), Expect = 6e-07
 Identities = 9/66 (13%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 84  QEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPES 143
           ++ +  + + ++ +EAV+ A K++    +       +LE++   L  +    ++    + 
Sbjct: 173 EKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNG-LHKFVKGDL 231

Query: 144 LTMLLE 149
           L   ++
Sbjct: 232 LQEAID 237

>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 =  106 bits (266), Expect = 3e-29
 Identities = 35/108 (32%), Positives = 59/108 (54%), Gaps = 22/108 (20%)

Query: 1   MSR---RYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQ 39
           M +    Y R  TVFSP+GRL+QV+Y           +G        L+ +  V S+L++
Sbjct: 1   MQQGQMAYSRAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIE 60

Query: 40  TSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
            + S EK+  IDD+VA   +G+++DA +L++ AR+ A++    Y   +
Sbjct: 61  QN-SIEKIQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLV 107

>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 = 47.6 bits (114), Expect = 2e-07
 Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 5/61 (8%)

Query: 88  QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTML 147
           ++YK+++  +EAV L +K L+ +++      +  E+A +    +   KYRI   E +   
Sbjct: 178 REYKENLPEKEAVTLGIKALKSSLE-EGEELKAPEIASI----TVGNKYRIYDQEEVKKF 232

Query: 148 L 148
           L
Sbjct: 233 L 233

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

 Score =  103 bits (260), Expect = 4e-28
 Identities = 44/104 (42%), Positives = 62/104 (59%), Gaps = 19/104 (18%)

Query: 2   SRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTS 43
              YDR  TVFSPEGRLYQV+Y           +G        L  +  +TSKL++   S
Sbjct: 9   PSAYDRAITVFSPEGRLYQVEYAREAVRRGTTAIGIACKDGVVLAVDRRITSKLVKIR-S 67

Query: 44  AEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
            EK+++IDDHVA A +G+++DA +LI+ AR++A+ Y   Y E I
Sbjct: 68  IEKIFQIDDHVAAATSGLVADARVLIDRARLEAQIYRLTYGEEI 111

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

 Score = 47.3 bits (113), Expect = 3e-07
 Identities = 13/74 (17%), Positives = 32/74 (43%), Gaps = 5/74 (6%)

Query: 88  QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTML 147
           ++Y+DD+T  E ++LA+  L K  +   +  E +++    ++     +++    E +  L
Sbjct: 182 KEYRDDITLDEGLELAITALTKANE--DIKPENVDVC---IITVKDAQFKKIPVEEIKKL 236

Query: 148 LENFGVAQPASEVS 161
           +E            
Sbjct: 237 IEKVKKKLNEENKK 250

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

 Score =  102 bits (256), Expect = 1e-27
 Identities = 40/106 (37%), Positives = 62/106 (58%), Gaps = 20/106 (18%)

Query: 1   MSRR-YDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTS 41
           + +  YDR  TVFSP+GRL+QV+Y           +G        L+ +  V SKLL+  
Sbjct: 3   LPQMGYDRAITVFSPDGRLFQVEYAREAVKRGATAIGIKCKEGVILIADKRVGSKLLEKD 62

Query: 42  TSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
            + EK+YKID+H+  A +G+++DA +LI+ AR++A+     Y  PI
Sbjct: 63  -TIEKIYKIDEHICAATSGLVADARVLIDRARIEAQINRLTYDIPI 107

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

 Score = 48.5 bits (116), Expect = 1e-07
 Identities = 15/64 (23%), Positives = 32/64 (50%), Gaps = 4/64 (6%)

Query: 88  QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTML 147
           ++Y+DD++  +A+ L L  +  +++ + L  E +E+  V         ++  SPE L   
Sbjct: 177 KEYRDDLSFDDAMVLGLVAMGLSIE-SELVPENIEVGYV---KVDDRTFKEVSPEELKPY 232

Query: 148 LENF 151
           +E  
Sbjct: 233 VERA 236

>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 =  101 bits (255), Expect = 1e-27
 Identities = 29/102 (28%), Positives = 45/102 (44%), Gaps = 21/102 (20%)

Query: 4   RYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAE 45
            YD  T  FSP GRL+QV+Y           +G        LV       +L   S+  +
Sbjct: 4   NYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADEL---SSYQK 60

Query: 46  KMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           K+ K D+H+  ++AG+  DA +L N  R Q    +  +   +
Sbjct: 61  KIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKL 102

>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 = 46.5 bits (111), Expect = 5e-07
 Identities = 11/58 (18%), Positives = 25/58 (43%), Gaps = 4/58 (6%)

Query: 91  KDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLL 148
           K D    E ++  ++ + +++   SLT + L +A V         + I   E++   +
Sbjct: 180 KIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIV----GKDTPFTIYDGEAVAKYI 233

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

 Score =  101 bits (254), Expect = 2e-27
 Identities = 37/100 (37%), Positives = 52/100 (52%), Gaps = 19/100 (19%)

Query: 6  DRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAEKM 47
          DR  + FSPEGRL+QV+Y           +G        L  E   TS LL++  S EK+
Sbjct: 1  DRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESD-SIEKI 59

Query: 48 YKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           +ID H+ CA++G+ +DA  +I  AR  A  +   Y E I
Sbjct: 60 VEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDI 99

>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 = 48.4 bits (116), Expect = 1e-07
 Identities = 13/63 (20%), Positives = 30/63 (47%), Gaps = 5/63 (7%)

Query: 88  QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTML 147
            ++   +T +EA  L LK+L++ M+   L     +L+ +    + +  ++I   E    L
Sbjct: 177 NEWHSSLTLKEAELLVLKILKQVME-EKLDENNAQLSCI----TKQDGFKIYDNEKTAEL 231

Query: 148 LEN 150
           ++ 
Sbjct: 232 IKE 234

>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 = 64.2 bits (157), Expect = 3e-13
 Identities = 11/55 (20%), Positives = 22/55 (40%)

Query: 33 VTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           T+  +    S EK++ I   + C  AG+ +D  +    A  +   +A +     
Sbjct: 20 ATNDSVVADKSCEKIHFIAPKIYCCGAGVAADTEMTTRMAASKMELHALSTGREP 74

>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 = 46.9 bits (112), Expect = 4e-07
 Identities = 8/48 (16%), Positives = 21/48 (43%), Gaps = 2/48 (4%)

Query: 79  YAYAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEV 126
            A A  E    ++ +MT + A +L ++ +   + S   +   ++   +
Sbjct: 133 AAVALLE--DRFQPNMTLEAAQELLVEAITAGILSDLGSGGNVDACVI 178

>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 = 59.9 bits (145), Expect = 1e-11
 Identities = 18/85 (21%), Positives = 29/85 (34%), Gaps = 11/85 (12%)

Query: 13 SPEGRLYQ-VDYM-------GCLVG---ENNVTSKLLQTSTSAEKMYKIDDHVACAVAGI 61
          SPE  + +  +           +V       V       S S +K+ ++ D V  A AG 
Sbjct: 8  SPEQAMRERSELARKGIARAKSVVALAYAGGVLFVAENPSRSLQKISELYDRVGFAAAGK 67

Query: 62 MSDANILINTARVQARRYAYAYQEP 86
           ++ + L       A    YAY   
Sbjct: 68 FNEFDNLRRGGIQFADTRGYAYDRR 92

>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 = 52.2 bits (125), Expect = 5e-09
 Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 7/80 (8%)

Query: 88  QDYKDDMTRQEAVQLALKVLRKTMDSTS------LTSEKLELAEVFLLPSGKVKYRICSP 141
           + Y ++ +  +A+++A+  LR     TS      L    LE+A V      +  +R  + 
Sbjct: 169 ESYAENASLTDALRIAVAALRAGSADTSGGDQPTLGVASLEVA-VLDANRPRRAFRRITG 227

Query: 142 ESLTMLLENFGVAQPASEVS 161
            +L  LL +    Q   E S
Sbjct: 228 SALQALLVDQESPQSDGESS 247

>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 = 53.8 bits (130), Expect = 1e-09
 Identities = 8/55 (14%), Positives = 18/55 (32%)

Query: 33 VTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           T   +    +  K+++I   + CA AG  +D   +          ++       
Sbjct: 20 STQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREP 74

>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 = 40.3 bits (95), Expect = 7e-05
 Identities = 10/46 (21%), Positives = 24/46 (52%), Gaps = 2/46 (4%)

Query: 79  YAYAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELA 124
            A A  E    +K D+T++EA++LA   ++  + +   +   +++ 
Sbjct: 133 AAMAVLE--SHWKQDLTKEEAIKLASDAIQAGIWNDLGSGSNVDVC 176

>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 = 54.3 bits (131), Expect = 1e-09
 Identities = 8/55 (14%), Positives = 18/55 (32%)

Query: 33  VTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
            T   +    +  K+++I   + CA AG  +D   +          ++       
Sbjct: 49  STQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREP 103

>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 = 39.6 bits (93), Expect = 2e-04
 Identities = 10/46 (21%), Positives = 24/46 (52%), Gaps = 2/46 (4%)

Query: 79  YAYAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELA 124
            A A  E    +K D+T++EA++LA   ++  + +   +   +++ 
Sbjct: 162 AAMAVLE--SHWKQDLTKEEAIKLASDAIQAGIWNDLGSGSNVDVC 205

>1iru_I 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_H* 3une_H Length = 234

 Score = 53.5 bits (129), Expect = 2e-09
 Identities = 7/55 (12%), Positives = 20/55 (36%)

Query: 33 VTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           T  ++    +  K++ I  ++ C  AG  +D ++           ++ +     
Sbjct: 20 ATEGMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGRLP 74

>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 = 40.0 bits (94), Expect = 1e-04
 Identities = 9/48 (18%), Positives = 20/48 (41%), Gaps = 2/48 (4%)

Query: 79  YAYAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEV 126
            A A  E    ++ DM  +EA  L  + +   + +   +   ++L  +
Sbjct: 133 AAMAVFE--DKFRPDMEEEEAKNLVSEAIAAGIFNDLGSGSNIDLCVI 178

>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 = 53.5 bits (128), Expect = 3e-09
 Identities = 13/59 (22%), Positives = 22/59 (37%)

Query: 27 LVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQE 85
          L   + V       ST+  K+ ++ D +  A  G  ++   L     V A    Y+Y  
Sbjct: 33 LTFRDGVLFVAENPSTALHKVSELYDRLGFAAVGKYNEFENLRRAGIVHADMRGYSYDR 91

>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 = 50.0 bits (119), Expect = 4e-08
 Identities = 16/76 (21%), Positives = 30/76 (39%), Gaps = 5/76 (6%)

Query: 88  QDYKDDMTRQEAVQLALKVLRKTMDSTS----LTSEKLELAEVFLLPSGKVKYRICSPES 143
           + Y+ D+  + AV +A+  LR+          +    LE+A V      +  +R  +  +
Sbjct: 169 ESYRADLDLEAAVGIAVNALRQGGAGEGEKRNVDVASLEVA-VLDQSRPRRAFRRIAGTA 227

Query: 144 LTMLLENFGVAQPASE 159
           L  L+     A   S 
Sbjct: 228 LEQLVPAEPAAASESA 243

>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 = 50.6 bits (121), Expect = 2e-08
 Identities = 17/61 (27%), Positives = 25/61 (40%)

Query: 27 LVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEP 86
          L G+   T   L  S   EK+Y  D++ A  +AG    A  L+    V+   Y      P
Sbjct: 14 LAGDRRATQGNLIASRDVEKVYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEGVP 73

Query: 87 I 87
          +
Sbjct: 74 L 74

>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 = 48.4 bits (116), Expect = 1e-07
 Identities = 9/47 (19%), Positives = 24/47 (51%)

Query: 41 STSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
            + +K+++ID +    +AG++ DA +L+   + +   Y    +  +
Sbjct: 36 HKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKAELELYRLQRRVNM 82

>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 = 44.2 bits (104), Expect = 4e-06
 Identities = 16/61 (26%), Positives = 24/61 (39%)

Query: 27  LVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEP 86
           L G+   T   L  S   E +Y  D++ A  +AG    A  L+    V+   Y      P
Sbjct: 79  LAGDRRATQGNLIASRDVEAVYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEGVP 138

Query: 87  I 87
           +
Sbjct: 139 L 139

>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 = 43.2 bits (102), Expect = 9e-06
 Identities = 10/47 (21%), Positives = 20/47 (42%)

Query: 41  STSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           S + +K+ +I+  +   +AG  +D          Q R +    +E I
Sbjct: 103 SQTVKKVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREKERI 149

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 14/47 (29%), Positives = 24/47 (51%)

Query: 41 STSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
          S +A+K+Y+I D +A   AG + DA  L    +++A  Y    +   
Sbjct: 28 SKAAKKIYQIADRMAMTTAGSVGDAQFLARIIKIEANLYEIRRERKP 74

>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 = 42.2 bits (100), Expect = 1e-05
 Identities = 9/47 (19%), Positives = 20/47 (42%)

Query: 41 STSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
          S + +++ +I+  +   +AG  +D          Q R +    +E I
Sbjct: 28 SQTVKRVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREKERI 74

>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 = 41.8 bits (98), Expect = 3e-05
 Identities = 13/68 (19%), Positives = 22/68 (32%), Gaps = 7/68 (10%)

Query: 41  STSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQDYKDDMTRQEAV 100
                K+Y  DD+ A  +AG  + A        V+   Y      P       +T    +
Sbjct: 85  GRDVRKVYITDDYTATGIAGTAAVAVEFARLYAVELEHYEKLEGVP-------LTFAGKI 137

Query: 101 QLALKVLR 108
                ++R
Sbjct: 138 NRLAIMVR 145

>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 = 41.4 bits (98), Expect = 3e-05
 Identities = 8/47 (17%), Positives = 19/47 (40%)

Query: 41 STSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
          +   +K+ ++ D + C  +G  +D   + +  +     Y   Y  P 
Sbjct: 37 NRVTDKLTRVHDKIWCCRSGSAADTQAIADIVQYHLELYTSQYGTPS 83

>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 = 41.0 bits (97), Expect = 3e-05
 Identities = 11/47 (23%), Positives = 22/47 (46%)

Query: 41 STSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
          S + +K+ +I+ ++   +AG  +D +        Q R Y    +E I
Sbjct: 28 SQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQCRIYELRNKERI 74

>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 = 40.3 bits (95), Expect = 7e-05
 Identities = 9/47 (19%), Positives = 19/47 (40%)

Query: 41 STSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
          +   +K+  I D + C  +G  +D   + +    Q   ++    EP 
Sbjct: 28 NRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPP 74

>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 = 39.9 bits (94), Expect = 1e-04
 Identities = 10/47 (21%), Positives = 22/47 (46%)

Query: 41 STSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
          +   +K+  +   + CA++G  +DA  + + A  Q   +    +EP 
Sbjct: 28 NRVFDKLSPLHQRIFCALSGSAADAQAIADMAAYQLELHGLELEEPP 74

>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 = 40.1 bits (94), Expect = 1e-04
 Identities = 10/67 (14%), Positives = 25/67 (37%), Gaps = 2/67 (2%)

Query: 41  STSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQDYKDDMTRQEAV 100
               E++  + D+    ++G +SD   +    +        AY  P+ D ++ +      
Sbjct: 69  FNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTE--NAYDNPLADAEEALEPSYIF 126

Query: 101 QLALKVL 107
           +    V+
Sbjct: 127 EYLATVM 133

>1ryp_M 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_M* 1jd2_L* 1g65_L 1vsy_M 1z7q_M 2f16_L* 2fak_L* 2fny_L* 2gpl_L* 3d29_L* 3dy3_L* 3dy4_L* 3e47_L* 3gpj_L* 3gpt_L* 3gpw_L* 3hye_L* 3l5q_Q 3mg0_L* 3mg4_L* ... Length = 222

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 7/45 (15%), Positives = 20/45 (44%)

Query: 41 STSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQE 85
          S    K++   D++  +  G  +D + L+   +   + Y + + +
Sbjct: 37 SRYEPKVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHND 81

>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 = 39.6 bits (93), Expect = 2e-04
 Identities = 10/71 (14%), Positives = 21/71 (29%), Gaps = 6/71 (8%)

Query: 41  STSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQDYKDDMTRQEAV 100
               E++  + D+    ++G +SD   +    +      AY       +   D       
Sbjct: 36  FNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAY------DNPLADAEEALEP 89

Query: 101 QLALKVLRKTM 111
               + L   M
Sbjct: 90  SYIFEYLATVM 100

>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 = 39.1 bits (92), Expect = 2e-04
 Identities = 8/47 (17%), Positives = 18/47 (38%)

Query: 41 STSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
          +  + K YK+ D      +G   D   L      + + Y ++  + +
Sbjct: 37 TRDSPKCYKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAM 83

>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 = 38.7 bits (91), Expect = 3e-04
 Identities = 8/47 (17%), Positives = 20/47 (42%)

Query: 41 STSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
          +T  +K++ + D +   +AG+ +D   +    + +   Y       I
Sbjct: 36 TTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFRLNLYELKEGRQI 82

>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 = 37.2 bits (87), Expect = 8e-04
 Identities = 7/47 (14%), Positives = 15/47 (31%)

Query: 41 STSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
            S +K  ++  H   + AG   D        +   + Y+      +
Sbjct: 29 KDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYIQANIQLYSIREDYEL 75

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	161
1iru_C	261	20S proteasome; cell cycle, immune response, prote	100.0
1iru_G	254	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_C	244	20S proteasome; multicatalytic proteinase, protein	100.0
1j2p_A	246	Alpha-ring, proteasome alpha subunit; hydrolase; 2	100.0
3h4p_A	264	Proteasome subunit alpha; core particle, cytoplasm	100.0
1iru_B	233	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_B	250	20S proteasome; multicatalytic proteinase, protein	100.0
1ryp_D	241	20S proteasome; multicatalytic proteinase, protein	100.0
1ryp_A	243	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_A	246	20S proteasome; cell cycle, immune response, prote	100.0
1iru_D	248	20S proteasome; cell cycle, immune response, prote	100.0
1iru_E	241	20S proteasome; cell cycle, immune response, prote	100.0
1yar_A	233	Proteasome alpha subunit; proteasome 20S, PA26 pro	100.0
1ryp_E	242	20S proteasome; multicatalytic proteinase, protein	100.0
3nzj_F	288	Proteasome component C1; ubiquitin, protein degrad	100.0
1iru_F	263	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_G	244	20S proteasome; multicatalytic proteinase, protein	100.0
1ryp_F	233	20S proteasome; multicatalytic proteinase, protein	100.0
3h4p_a	219	Proteasome subunit beta; core particle, cytoplasm,	99.95
1q5q_A	259	Proteasome alpha-type subunit 1; proteasome assemb	99.94
1iru_L	204	20S proteasome; cell cycle, immune response, prote	99.94
1j2q_H	202	Proteasome beta subunit; ubiquitin, CP, hydrolase;	99.93
1yar_H	217	Proteasome beta subunit; proteasome 20S, PA26 prot	99.92
1ryp_L	212	20S proteasome; multicatalytic proteinase, protein	99.92
3unf_N	199	Proteasome subunit beta type-9; antigen presentati	99.92
1iru_H	205	20S proteasome; cell cycle, immune response, prote	99.92
3nzj_K	287	Proteasome component PRE2; ubiquitin, protein degr	99.92
3mi0_A	248	Proteasome subunit alpha; enzyme inhibitors, lacto	99.91
3unf_H	234	Proteasome subunit beta type-10; antigen presentat	99.9
1iru_J	205	20S proteasome; cell cycle, immune response, prote	99.89
1ryp_K	198	20S proteasome; multicatalytic proteinase, protein	99.89
1iru_M	213	20S proteasome; cell cycle, immune response, prote	99.89
1ryp_J	204	20S proteasome; multicatalytic proteinase, protein	99.88
1q5q_H	235	Proteasome beta-type subunit 1; proteasome assembl	99.88
2jay_A	291	Proteasome; hydrolase; 1.99A {Mycobacterium tuberc	99.88
1ryp_I	222	20S proteasome; multicatalytic proteinase, protein	99.88
1ryp_M	222	20S proteasome; multicatalytic proteinase, protein	99.88
1q5r_H	294	Proteasome beta-type subunit 1; proteasome assembl	99.88
3nzj_H	261	Proteasome component PUP1; ubiquitin, protein degr	99.88
1ryp_N	233	20S proteasome; multicatalytic proteinase, protein	99.88
1iru_I	234	20S proteasome; cell cycle, immune response, prote	99.87
1iru_N	219	20S proteasome; cell cycle, immune response, prote	99.87
1ryp_H	205	20S proteasome; multicatalytic proteinase, protein	99.87
1g0u_M	266	Proteasome component PRE4; ubiquitin, degradation,	99.87
1iru_K	201	20S proteasome; cell cycle, immune response, prote	99.87
1g3k_A	174	ATP-dependent protease HSLV; hydrolase; 1.90A {Hae	99.68
2z3b_A	180	ATP-dependent protease HSLV; N-terminal nucleophIl	99.65
1m4y_A	171	ATP-dependent protease HSLV; N-terminal catalytic	99.61

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

Probab=100.00  E-value=1.1e-39  Score=258.75  Aligned_cols=157  Identities=47%  Similarity=0.740  Sum_probs=143.0

Q ss_pred             CCCCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccH
Q 040809            1 MSRRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIM   62 (161)
Q Consensus         1 m~~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~   62 (161)
                      |.++||+++|+|||||||||||||                 | |||+|+|.++++++.++..+|||+|++||+|++||+.
T Consensus         1 m~~~yd~~~t~fsp~Grl~QvEYA~~av~~Gtt~vgi~~~dgVVlaaD~r~~~g~~~~~~~~~KI~~i~~~i~~~~aG~~   80 (261)
T 1iru_C            1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVFFSEKIYKLNEDMACSVAGIT   80 (261)
T ss_dssp             -CTTTCCCTTCCCTTSCCHHHHHHHHHHTTSCCEEEEBCSSEEEEEECCCCCCTTBCCCSSCSSEEECSSSEEEEEEECH
T ss_pred             CCCccCCCCccCCCCCeehHHHhHHHHHhcCCcEEEEEeCCEEEEEEecccCCcccccCCCCccEEEecCCEEEEEeEcH
Confidence            889999999999999999999999                 6 9999999999999988669999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCc-------------------------------------------------------
Q 040809           63 SDANILINTARVQARRYAYAYQEPI-------------------------------------------------------   87 (161)
Q Consensus        63 ~D~~~l~~~~r~~~~~y~~~~~~~i-------------------------------------------------------   87 (161)
                      +|++.|++++|.+++.|++++++++                                                       
T Consensus        81 aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rP~~v~~lvaG~D~~~gp~Ly~idp~G~~~~~~  160 (261)
T 1iru_C           81 SDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWK  160 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBSSCCCCCEEEEEEEEETTTEEEEEEEETTTEEEECS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccccCcCcceEEEEEEEEeCCCCcEEEEECCCceEEeee
Confidence            9999999999999999999999887                                                       


Q ss_pred             ----------------cCCCC-CCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 040809           88 ----------------QDYKD-DMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLEN  150 (161)
Q Consensus        88 ----------------~~y~~-~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~  150 (161)
                                      +.|++ +||++||++++++||..+++++..++++++|++|++++. ...|++|+++||++++..
T Consensus       161 ~~aiGsgs~~a~~~Le~~~~~~~ms~eeA~~la~~al~~~~~~d~~sg~~i~v~vi~~~~~-~~~~~~l~~~ei~~~l~~  239 (261)
T 1iru_C          161 ATCIGNNSAAAVSMLKQDYKEGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENG-KTVIRVLKQKEVEQLIKK  239 (261)
T ss_dssp             EEEESTTTTHHHHHHHHHCCTTCCCHHHHHHHHHHHHHHSSSCTTCCSTTCEEEEEECCSS-SCEEEECCHHHHHHHHHH
T ss_pred             eEEeCcccHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHhccCCCCCcEEEEEEEcCCC-eeeEEECCHHHHHHHHHH
Confidence                            35789 999999999999999999999899999999999999752 224999999999999999


Q ss_pred             hcccCCCC
Q 040809          151 FGVAQPAS  158 (161)
Q Consensus       151 ~~~~~~~~  158 (161)
                      +.+..+++
T Consensus       240 ~~~~~~~~  247 (261)
T 1iru_C          240 HEEEEAKA  247 (261)
T ss_dssp             HHTTTTTT
T ss_pred             HHhchhhh
Confidence            95444433

>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=2.8e-38  Score=249.66  Aligned_cols=151  Identities=28%  Similarity=0.403  Sum_probs=138.7

Q ss_pred             CCCCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccH
Q 040809            1 MSRRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIM   62 (161)
Q Consensus         1 m~~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~   62 (161)
                      |.++||+++|+|||+|||||||||                 | |||+|+|.++++++++ +.+|||+|++||+|++||+.
T Consensus         3 ~~~~yd~~~t~fsp~Grl~QvEyA~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~-~~~KI~~i~~~i~~~~aG~~   81 (254)
T 1iru_G            3 IGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEG-SNKRLFNVDRHVGMAVAGLL   81 (254)
T ss_dssp             CCSSTTSCTTCCCTTSCCHHHHHHHHHHHTSCCEEEEECSSBEEEEEEEECSCTTBCTT-TTCCEEEEETTEEEEEEECH
T ss_pred             cccccCCCCccCCcCCccHHHHhHHHHHhcCCCEEEEEECCEEEEEEecccCCCCcCcC-cCCcEEEECCCEEEEEecCh
Confidence            568999999999999999999999                 5 9999999999999974 88999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCc-------------------------------------------------------
Q 040809           63 SDANILINTARVQARRYAYAYQEPI-------------------------------------------------------   87 (161)
Q Consensus        63 ~D~~~l~~~~r~~~~~y~~~~~~~i-------------------------------------------------------   87 (161)
                      +|++.|++++|.+++.|+++|+++|                                                       
T Consensus        82 aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rP~~v~~lvaG~D~~~gp~Ly~idp~G~~~~~~  161 (254)
T 1iru_G           82 ADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYW  161 (254)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSBSSBCCCSEEEEEEEEETTTEEEEEEECTTCCEEEBS
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhccccccccceEEEEEEEEeCCCCcEEEEEcCCCCEEeee
Confidence            9999999999999999999999988                                                       


Q ss_pred             ----------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHh
Q 040809           88 ----------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENF  151 (161)
Q Consensus        88 ----------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~  151 (161)
                                      +.|+++||++||++++++||..+++++..++++++|++|+++.+|  .|++++++||+++++.+
T Consensus       162 ~~aiGsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~~~~~~~~iev~vi~~~~~g--~~~~l~~~~i~~~~~~~  239 (254)
T 1iru_G          162 GCAIGKARQAAKTEIEKLQMKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNG--RHEIVPKDIREEAEKYA  239 (254)
T ss_dssp             EEEESTTHHHHHHHHTTSCGGGCCHHHHHHHHHHHHHHHSCSSSSCCEEEEEEECBTTTTT--CCEECCHHHHHHHHHHH
T ss_pred             eEEecCccHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHhhccCCCCcEEEEEEEcCCCC--CeEECCHHHHHHHHHHH
Confidence                            357899999999999999999999887678999999999987443  59999999999999877


Q ss_pred             ccc
Q 040809          152 GVA  154 (161)
Q Consensus       152 ~~~  154 (161)
                      .+.
T Consensus       240 ~~~  242 (254)
T 1iru_G          240 KES  242 (254)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            443

>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=8.6e-38  Score=245.28  Aligned_cols=151  Identities=52%  Similarity=0.806  Sum_probs=138.3

Q ss_pred             CCCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHH
Q 040809            2 SRRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMS   63 (161)
Q Consensus         2 ~~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~   63 (161)
                      +++||+++|+|||||||||||||                 | |||+|+|.++++++.+++.+|||+|++||+|++||+.+
T Consensus         2 ~~~yd~~~t~fsp~Grl~QvEyA~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~a   81 (244)
T 1ryp_C            2 SRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTSTEKLYKLNDKIAVAVAGLTA   81 (244)
T ss_dssp             CGGGCCCTTCBCTTSCBHHHHHHHHHHTTSCCEEEEEETTEEEEEEECSSCCSSBCSTTCCSSEEESSSSEEEEEEECHH
T ss_pred             CCccCCCCceECcCCeeHHHHhHHHHHhcCCcEEEEEeCCEEEEEEeeccCCcCccCCCCCCcEEEECCCEEEEEEEcHH
Confidence            35899999999999999999999                 5 89999999999998556899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCc--------------------------------------------------------
Q 040809           64 DANILINTARVQARRYAYAYQEPI--------------------------------------------------------   87 (161)
Q Consensus        64 D~~~l~~~~r~~~~~y~~~~~~~i--------------------------------------------------------   87 (161)
                      |++.|++++|.+++.|++++++++                                                        
T Consensus        82 D~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rp~~v~~lvaG~D~~~gp~Ly~idp~G~~~~~~~  161 (244)
T 1ryp_C           82 DAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKA  161 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSCCCCCEEEEEEEEETTTEEEEEEECTTCCEEEBSE
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhccCCccceEEEEEEEEEcCCCCCEEEEECCCccEEeeeE
Confidence            999999999999999999999887                                                        


Q ss_pred             ---------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEE--eCCCCceeEEECCHHHHHHHHHH
Q 040809           88 ---------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVF--LLPSGKVKYRICSPESLTMLLEN  150 (161)
Q Consensus        88 ---------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~--~~~~g~~~~~~l~~~ei~~~l~~  150 (161)
                                     +.|+++||++||++++++||..+++++.+++++++|++|+  +++. ...|++|+++||++++++
T Consensus       162 ~aiGsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~rd~~sg~~i~v~vi~~~~~~~-~~~~~~l~~~ei~~~~~~  240 (244)
T 1ryp_C          162 ISVGANTSAAQTLLQMDYKDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDG-EVYQKIFKPQEIKDILVK  240 (244)
T ss_dssp             EEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCSSSSCCGGGEEEEEEECCSSSS-SCEEEECCHHHHHHHHHH
T ss_pred             EEECCCcHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHhccccCCCCcEEEEEEEeecCCC-ceeEEECCHHHHHHHHHH
Confidence                           3589999999999999999999999877789999999999  8752 113999999999999998


Q ss_pred             hcc
Q 040809          151 FGV  153 (161)
Q Consensus       151 ~~~  153 (161)
                      +..
T Consensus       241 ~~~  243 (244)
T 1ryp_C          241 TGI  243 (244)
T ss_dssp             HTC
T ss_pred             hhc
Confidence            753

>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=3.3e-38  Score=248.09  Aligned_cols=152  Identities=37%  Similarity=0.627  Sum_probs=138.5

Q ss_pred             CCCCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccH
Q 040809            1 MSRRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIM   62 (161)
Q Consensus         1 m~~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~   62 (161)
                      |+++||+++|+|||||||+|||||                 | |||+|+|.++++.+. ++.+|||+|++||+|++||+.
T Consensus         4 ~~~~yd~~~t~fsp~Grl~QvEya~~av~~Gtt~vgi~~~dgVvlaaD~r~~~~l~~~-~~~~KI~~i~~~i~~~~aG~~   82 (246)
T 1j2p_A            4 PQMGYDRAITVFSPDGRLFQVEYAREAVKRGATAIGIKCKEGVILIADKRVGSKLLEK-DTIEKIYKIDEHICAATSGLV   82 (246)
T ss_dssp             CCTTSSSCTTCCCTTSCCHHHHHHHHHHHTSCCEEEEEETTEEEEEEECCCSCTTBCG-GGCCSEEECSSSEEEEEEECH
T ss_pred             cccCcCCCCceECCCCeehHHHhHHHHHHcCCcEEEEEECCEEEEEEeccCCcccccc-CccCcEEEECCCEEEEEeEcc
Confidence            457999999999999999999999                 5 899999999998774 489999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCc-------------------------------------------------------
Q 040809           63 SDANILINTARVQARRYAYAYQEPI-------------------------------------------------------   87 (161)
Q Consensus        63 ~D~~~l~~~~r~~~~~y~~~~~~~i-------------------------------------------------------   87 (161)
                      +|++.|++++|.+++.|++++++++                                                       
T Consensus        83 aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~y~~~~~~rp~~v~~lvaG~D~gp~Ly~idp~G~~~~~~~~  162 (246)
T 1j2p_A           83 ADARVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQYGGVRPFGVSLLIAGVNEVPKLYETDPSGALLEYKAT  162 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCEEEEEEEESSSEEEEEECTTCCEEEBSEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCcccccEEEEEEEECCCCEEEEECCCceEEeeeEE
Confidence            9999999999999999999999877                                                       


Q ss_pred             --------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEE-eCCCCceeEEECCHHHHHHHHHHhc
Q 040809           88 --------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVF-LLPSGKVKYRICSPESLTMLLENFG  152 (161)
Q Consensus        88 --------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~-~~~~g~~~~~~l~~~ei~~~l~~~~  152 (161)
                                    +.|+++||++||++++++||..++++ ..++++++|++|+ +++    .|++++++||++++.++.
T Consensus       163 aiGsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~-~~sg~~i~v~vi~~~~~----~~~~l~~~ei~~~~~~~~  237 (246)
T 1j2p_A          163 AIGMGRMAVTEFFEKEYRDDLSFDDAMVLGLVAMGLSIES-ELVPENIEVGYVKVDDR----TFKEVSPEELKPYVERAN  237 (246)
T ss_dssp             EESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHHTS-CCCGGGEEEEEEETTTC----CCEECCHHHHHHHHHHHH
T ss_pred             EECCCcHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhc-cCCCCcEEEEEEEcCCC----ceEECCHHHHHHHHHHHH
Confidence                          35889999999999999999999998 8899999999999 643    599999999999999986


Q ss_pred             ccCCCC
Q 040809          153 VAQPAS  158 (161)
Q Consensus       153 ~~~~~~  158 (161)
                      +++.+.
T Consensus       238 ~~~~~~  243 (246)
T 1j2p_A          238 ERIREL  243 (246)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            655443

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

Probab=100.00  E-value=1.3e-38  Score=253.06  Aligned_cols=150  Identities=38%  Similarity=0.676  Sum_probs=132.3

Q ss_pred             CCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHH
Q 040809            3 RRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSD   64 (161)
Q Consensus         3 ~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D   64 (161)
                      .+||+++|+|||+|||||||||                 | |||+|+|.++++... ++.+|||+|++||+|++||+.+|
T Consensus        10 ~~yd~~~t~fSp~Grl~QvEYA~~av~~Gtt~vgi~~~dgVVlaaD~r~~~~li~~-~~~~KI~~i~d~i~~~~aG~~aD   88 (264)
T 3h4p_A           10 SAYDRAITVFSPEGRLYQVEYAREAVRRGTTAIGIACKDGVVLAVDRRITSKLVKI-RSIEKIFQIDDHVAAATSGLVAD   88 (264)
T ss_dssp             ------CCCCCSSSSCHHHHHHHHHHHHSCCEEEECCSSEEEEEEECCCCSTTBCT-TTCCCEEEEETTEEEEEEECSHH
T ss_pred             cccCCCcceECCCCeeHHHHhHHHHHhcCCcEEEEEECCEEEEEEecCccCCcccc-CccccEEEecCcEEEEeccchHH
Confidence            7899999999999999999999                 5 999999999987654 58999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCc---------------------------------------------------------
Q 040809           65 ANILINTARVQARRYAYAYQEPI---------------------------------------------------------   87 (161)
Q Consensus        65 ~~~l~~~~r~~~~~y~~~~~~~i---------------------------------------------------------   87 (161)
                      ++.|++++|.+++.|++.|++++                                                         
T Consensus        89 ~~~l~~~~r~~~~~y~~~~~~~i~v~~la~~l~~~~~~yt~~~~~rP~~v~~lvaG~D~~gp~Ly~iDp~G~~~~~~~~a  168 (264)
T 3h4p_A           89 ARVLIDRARLEAQIYRLTYGEEISIEMLAKKICDIKQAYTQHGGVRPFGVSLLIAGIDKNEARLFETDPSGALIEYKATA  168 (264)
T ss_dssp             HHHHHTTHHHHHHHHHHTTCSCCCHHHHHHHHHHHHHHTTSBSSCCCCSEEEEEEEEETTEEEEEEECTTCCCEEESEEE
T ss_pred             HHHHHHHHHHHHHhhHHhcCCCCCHHHHHHHHHHHHHHHhhccCCCCeeEEEEEEEEeCCcCEEEEECCCceEEecCeEE
Confidence            99999999999999999999988                                                         


Q ss_pred             -------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhccc
Q 040809           88 -------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFGVA  154 (161)
Q Consensus        88 -------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~~~  154 (161)
                                   +.|+++||++||++++++||..++++  .++++++|++|++++.   .|++|+++||+++++++.+.
T Consensus       169 iGsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~a~~~--~sg~~iev~vi~~~~~---~~~~l~~~ei~~~~~~~~~~  243 (264)
T 3h4p_A          169 IGSGRPVVMELLEKEYRDDITLDEGLELAITALTKANED--IKPENVDVCIITVKDA---QFKKIPVEEIKKLIEKVKKK  243 (264)
T ss_dssp             ESTTHHHHTTTHHHHCCTTCCSHHHHHHHHHHHHHHSSS--CCTTSEEEEEEETTTT---EEEECCTTTTGGGTTTTTTS
T ss_pred             ECCCHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHhc--cCCCeEEEEEEEeCCC---cEEECCHHHHHHHHHHHHHh
Confidence                         35899999999999999999999986  7999999999998754   69999999999999988666


Q ss_pred             CCCC
Q 040809          155 QPAS  158 (161)
Q Consensus       155 ~~~~  158 (161)
                      .+++
T Consensus       244 ~~~~  247 (264)
T 3h4p_A          244 LNEE  247 (264)
T ss_dssp             SSCC
T ss_pred             hhcc
Confidence            5544

>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=2.2e-37  Score=241.49  Aligned_cols=144  Identities=28%  Similarity=0.514  Sum_probs=133.2

Q ss_pred             CCCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHH
Q 040809            2 SRRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMS   63 (161)
Q Consensus         2 ~~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~   63 (161)
                      +++||+++|+|||||||||||||                 | |||+|+|.++++... ++.+||++|++||+|++||+.+
T Consensus         2 ~~~yd~~~t~fsp~Grl~QvEya~~av~~Gtt~vgi~~~dgVvlaaD~r~~~~l~~~-~~~~Ki~~i~~~i~~~~aG~~a   80 (233)
T 1iru_B            2 ERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDE-RSVHKVEPITKHIGLVYSGMGP   80 (233)
T ss_dssp             CCCCCSBSCCCCTTSCCHHHHHHHHHHHTSCCEEEEECSSCEEEEEECCCCCSSBCS-TTCCSSEESSSSEEEEEEECHH
T ss_pred             CCCccCCceeECCCCeEehhHhHHHHHHcCCcEEEEEeCCEEEEEEEecCCcccccc-ccCCeEEEECCCEEEEEEEccH
Confidence            47899999999999999999999                 5 899999999776654 4889999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCc--------------------------------------------------------
Q 040809           64 DANILINTARVQARRYAYAYQEPI--------------------------------------------------------   87 (161)
Q Consensus        64 D~~~l~~~~r~~~~~y~~~~~~~i--------------------------------------------------------   87 (161)
                      |++.|++++|.+++.|++++++++                                                        
T Consensus        81 D~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~y~~~~~~rP~~v~~lvaG~D~~gp~Ly~id~~G~~~~~~~~  160 (233)
T 1iru_B           81 DYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKAT  160 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCSEEEEEEEECSSSEEEEEECTTSCEEEBSEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCcCCCCCcEEEEEEEEEeCCCCeEEEECCCCCEEEeeEE
Confidence            999999999999999999999887                                                        


Q ss_pred             --------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhc
Q 040809           88 --------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFG  152 (161)
Q Consensus        88 --------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~  152 (161)
                                    +.|+++||++||++++++||..+++++ .++++++|++|+++     .|++++++||++++++++
T Consensus       161 aiG~gs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~d-~sg~~i~v~vi~~~-----g~~~l~~~ei~~~~~~~~  233 (233)
T 1iru_B          161 AMGKNYVNGKTFLEKRYNEDLELEDAIHTAILTLKESFEGQ-MTEDNIEVGICNEA-----GFRRLTPTEVKDYLAAIA  233 (233)
T ss_dssp             EESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHTTCCSC-CCSSSEEEEEEETT-----EEEECCHHHHHHHHTTCC
T ss_pred             EECCCCHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhcc-CCCCCEEEEEEECC-----CEEECCHHHHHHHHHhcC
Confidence                          358999999999999999999999987 88999999999987     499999999999998753

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

Probab=100.00  E-value=2.7e-37  Score=243.37  Aligned_cols=149  Identities=24%  Similarity=0.432  Sum_probs=133.8

Q ss_pred             CCCCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccH
Q 040809            1 MSRRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIM   62 (161)
Q Consensus         1 m~~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~   62 (161)
                      |.++||+++|+|||||||||||||                 | |||+|+|.+.++... ++.+||++|++||+|++||+.
T Consensus         1 ~~~~yd~~~t~fsp~Grl~QvEyA~~av~~Gtt~vgi~~~dgVvlaaD~r~~~~l~~~-~~~~Ki~~i~~~i~~~~aG~~   79 (250)
T 1ryp_B            1 MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMS-ETLSKVSLLTPDIGAVYSGMG   79 (250)
T ss_dssp             CCCCCCSBSSCBCTTSCBHHHHHHHHHHHTSCCEEEEEETTEEEEEEECCCSCSSBCG-GGCCSSEEEETTEEEEEEECH
T ss_pred             CCCcccCCceeECCCCccHHHHhHHHHHHcCCcEEEEEECCEEEEEEeccCCCccccC-cccCceEEECCCEEEEeeeCH
Confidence            889999999999999999999998                 5 899999998766554 489999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHH-HHHHhCCCc------------------------------------------------------
Q 040809           63 SDANILINTARVQARR-YAYAYQEPI------------------------------------------------------   87 (161)
Q Consensus        63 ~D~~~l~~~~r~~~~~-y~~~~~~~i------------------------------------------------------   87 (161)
                      +|++.+++++|.+++. |++.|++++                                                      
T Consensus        80 aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~~a~~~~~~~~~~~~rp~~v~~lvaG~D~~~gp~Ly~idp~G~~~~~  159 (250)
T 1ryp_B           80 PDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPW  159 (250)
T ss_dssp             HHHHHHHHHHHHHHHHTTHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCCEEEEEEEEETTTEEEEEEECTTSCEEEB
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHhcCCcccceEEEEEEEEcCCCCcEEEEECCCCCEEee
Confidence            9999999999999999 999998876                                                      


Q ss_pred             -----------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCC-----------CceeEEEC
Q 040809           88 -----------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPS-----------GKVKYRIC  139 (161)
Q Consensus        88 -----------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~-----------g~~~~~~l  139 (161)
                                       +.|+++||++||++++++||..++++ .+++++++|++|++++.           +...|++|
T Consensus       160 ~~~aiGsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~-~~sg~~i~v~vi~~~~~~~~~~~~~~~~~~~~~~~l  238 (250)
T 1ryp_B          160 KATAIGKGSVAAKTFLEKRWNDELELEDAIHIALLTLKESVEG-EFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKL  238 (250)
T ss_dssp             SEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCCS-CCSTTTEEEEEECSCCGGGTSEESCSSCCCCSEEEC
T ss_pred             ceeEecCccHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhcc-ccCCCCEEEEEEEccccccccccccccCCCCCeEEC
Confidence                             35899999999999999999999987 67899999999998620           11259999


Q ss_pred             CHHHHHHHHHHh
Q 040809          140 SPESLTMLLENF  151 (161)
Q Consensus       140 ~~~ei~~~l~~~  151 (161)
                      +++||+++++++
T Consensus       239 ~~~ei~~~l~~~  250 (250)
T 1ryp_B          239 TSQEINDRLEAL  250 (250)
T ss_dssp             CHHHHHHHHTTC
T ss_pred             CHHHHHHHHHhC
Confidence            999999999753

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

Probab=100.00  E-value=3.9e-37  Score=241.26  Aligned_cols=145  Identities=29%  Similarity=0.477  Sum_probs=136.3

Q ss_pred             CCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHH
Q 040809            4 RYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDA   65 (161)
Q Consensus         4 ~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~   65 (161)
                      +||+++|+|||||||||||||                 | |||+|+|.++++++.+++.+|||+|++||+|++||+.+|+
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            699999999999999999999                 5 9999999999999988789999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCc----------------------------------------------------------
Q 040809           66 NILINTARVQARRYAYAYQEPI----------------------------------------------------------   87 (161)
Q Consensus        66 ~~l~~~~r~~~~~y~~~~~~~i----------------------------------------------------------   87 (161)
                      +.|++++|.+++.|+++++++|                                                          
T Consensus        81 ~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rP~~v~~lvaG~D~~~~gp~Ly~idp~G~~~~~~~~  160 (241)
T 1ryp_D           81 RILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQ  160 (241)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSSTTBCCCSEEEEEEECCTTCCSCEEEEECTTSCEEEBSEE
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHccCCCCCCcceeeEEEEEcCCCCCeeEEEECCCCCEEEeeeE
Confidence            9999999999999999999987                                                          


Q ss_pred             --------------cCC---CCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 040809           88 --------------QDY---KDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLEN  150 (161)
Q Consensus        88 --------------~~y---~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~  150 (161)
                                    +.|   +++||++||++++++||..+++   .++++++|++|++++    .|++++++||++++.+
T Consensus       161 aiG~gs~~a~~~Le~~~~~~~~~ms~eea~~l~~~al~~~~~---~sg~~i~v~vi~~~~----~~~~l~~~ei~~~~~~  233 (241)
T 1ryp_D          161 TIGRNSKTVREFLEKNYDRKEPPATVEECVKLTVRSLLEVVQ---TGAKNIEITVVKPDS----DIVALSSEEINQYVTQ  233 (241)
T ss_dssp             EESTTHHHHHHHHHTTCCTTSCCCSHHHHHHHHHHHHHHHHC---SCSTTEEEEEEETTT----EEEECCHHHHHHHHHH
T ss_pred             EECCCcHHHHHHHHHhhhcccCCCCHHHHHHHHHHHHHHHhc---CCCCcEEEEEEECCC----cEEECCHHHHHHHHHH
Confidence                          468   8999999999999999999996   789999999999975    5999999999999999


Q ss_pred             hcccC
Q 040809          151 FGVAQ  155 (161)
Q Consensus       151 ~~~~~  155 (161)
                      +.+++
T Consensus       234 ~~~~~  238 (241)
T 1ryp_D          234 IEQEK  238 (241)
T ss_dssp             HTHHH
T ss_pred             Hhhhh
Confidence            86544

>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=1.8e-37  Score=243.43  Aligned_cols=145  Identities=26%  Similarity=0.457  Sum_probs=133.8

Q ss_pred             CCCCCCCcccCCCCceeeEecc------------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHH
Q 040809            3 RRYDRQTTVFSPEGRLYQVDYM------------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMS   63 (161)
Q Consensus         3 ~~y~~~~~~fsp~Grl~qveya------------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~   63 (161)
                      .+||+++|+|||||||||||||                  | |||+|+|.+.++... ++.+|||+|++||+|++||+.+
T Consensus         1 ~~yd~~~t~fsp~Grl~QvEYA~~av~~~Gtt~vgi~~~dgVvlaad~r~~~~l~~~-~~~~Ki~~i~~~i~~~~aG~~a   79 (243)
T 1ryp_A            1 AGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDP-TTVSYIFCISRTIGMVVNGPIP   79 (243)
T ss_dssp             CGGGGTSSSCCTTSCCHHHHHHHHHTTTTCCCEEEEECSSEEEEEEECCCCCTTBCG-GGCCSEEECSSSCEEEEESCHH
T ss_pred             CCCCCCCceECCCCeeHHHHHHHHHHhcCCCcEEEEEeCCEEEEEEEecCCccccCC-CcCCceEEECCCEEEEEEecHH
Confidence            4899999999999999999998                  5 999999999777664 4899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCc--------------------------------------------------------
Q 040809           64 DANILINTARVQARRYAYAYQEPI--------------------------------------------------------   87 (161)
Q Consensus        64 D~~~l~~~~r~~~~~y~~~~~~~i--------------------------------------------------------   87 (161)
                      |++.+++++|.+++.|+++++++|                                                        
T Consensus        80 D~~~l~~~~r~~~~~~~~~~~~~~~v~~la~~l~~~l~~y~~~~~~rP~~v~~lvaG~D~~~gp~Ly~~dp~G~~~~~~~  159 (243)
T 1ryp_A           80 DARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKA  159 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTSCCCSCEEEEEEEETTTEEEEEEECTTSCEEEBSE
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhccCCccccceEEEEEEEcCCCCcEEEEEcCCCCEEEEEE
Confidence            999999999999999999999988                                                        


Q ss_pred             ---------------cCCCC-------CCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHH
Q 040809           88 ---------------QDYKD-------DMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLT  145 (161)
Q Consensus        88 ---------------~~y~~-------~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~  145 (161)
                                     +.|++       +||++||++++++||..+++++ +++++++|++|+++     .|++++++||+
T Consensus       160 ~a~G~gs~~a~~~Le~~~~~~~~~~~~~ms~eea~~l~~~al~~~~~rd-~s~~~iev~vi~~~-----g~~~l~~~ei~  233 (243)
T 1ryp_A          160 TATGPKQQEITTNLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTE-FSKNDLEVGVATKD-----KFFTLSAENIE  233 (243)
T ss_dssp             EEESTTHHHHHHHHHHHHHHHCSSSCCCSSHHHHHHHHHHHHHHHHTCC-CCTTSEEEEEEETT-----EEEECCHHHHH
T ss_pred             EEECCCcHHHHHHHHHHhhhcccccccCCCHHHHHHHHHHHHHHHhccc-CCCCcEEEEEEECC-----CeEECCHHHHH
Confidence                           24677       9999999999999999999997 89999999999987     49999999999


Q ss_pred             HHHHHhccc
Q 040809          146 MLLENFGVA  154 (161)
Q Consensus       146 ~~l~~~~~~  154 (161)
                      ++++.++++
T Consensus       234 ~~~~~~~~~  242 (243)
T 1ryp_A          234 ERLVAIAEQ  242 (243)
T ss_dssp             HHHHHHTTT
T ss_pred             HHHHHhhcc
Confidence            999998543

>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=4.3e-37  Score=241.64  Aligned_cols=147  Identities=29%  Similarity=0.550  Sum_probs=135.0

Q ss_pred             CCCCCCCcccCCCCceeeEecc------------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHH
Q 040809            3 RRYDRQTTVFSPEGRLYQVDYM------------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMS   63 (161)
Q Consensus         3 ~~y~~~~~~fsp~Grl~qveya------------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~   63 (161)
                      .+||+++|+|||+|||+|||||                  | |||+|+|.+.++... ++.+||++|++||+|++||+.+
T Consensus         7 ~~yd~~~t~fsp~Grl~QvEya~~av~~~Gtt~vgi~~~dgVvlaaD~r~~~~l~~~-~~~~Ki~~i~~~i~~~~aG~~a   85 (246)
T 1iru_A            7 AGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDS-STVTHLFKITENIGCVMTGMTA   85 (246)
T ss_dssp             CTTTTTSSCCCTTSCCHHHHHHHHHHHTTCCEEEEEECSSEEEEEEECCCCCSSBCG-GGCCSEEESSSSCEEEEEECHH
T ss_pred             CCcCCCCccCCCCCeehHHHHHHHHHhcCCCCEEEEEeCCEEEEEEeecCCCcccCC-CccCceEEECCCEEEEEeccHH
Confidence            4899999999999999999998                  5 999999999766654 4889999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCc--------------------------------------------------------
Q 040809           64 DANILINTARVQARRYAYAYQEPI--------------------------------------------------------   87 (161)
Q Consensus        64 D~~~l~~~~r~~~~~y~~~~~~~i--------------------------------------------------------   87 (161)
                      |++.|++++|.+++.|++++++++                                                        
T Consensus        86 D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~y~~~~~~rp~~v~~lvaG~D~~~gp~Ly~idp~G~~~~~~~  165 (246)
T 1iru_A           86 DSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKA  165 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSBCCCSEEEEEEEEETTTEEEEEEECTTSCEEEBSE
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcCCCCCCcceEEEEEEEeCCCCeEEEEEcCCeeEEEeeE
Confidence            999999999999999999999987                                                        


Q ss_pred             ---------------cCCCC--CCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 040809           88 ---------------QDYKD--DMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLEN  150 (161)
Q Consensus        88 ---------------~~y~~--~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~  150 (161)
                                     +.|++  +||++||++++++||..+++++ .++++++|++|++++.   .|++++++||+++++.
T Consensus       166 ~aiG~gs~~a~~~Le~~~~~~~~ms~eea~~la~~al~~~~~rd-~sg~~i~v~vi~~~g~---~~~~l~~~ei~~~~~~  241 (246)
T 1iru_A          166 TAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCLSTVLSID-FKPSEIEVGVVTVENP---KFRILTEAEIDAHLVA  241 (246)
T ss_dssp             EEEETTHHHHHHHHHHHTTSCCCCCHHHHHHHHHHHHHHHTTCC-CCTTSEEEEEEETTEE---EEEECCHHHHHHHHHH
T ss_pred             EEECCCcHHHHHHHHHhhcccCCCCHHHHHHHHHHHHHHHhccc-CCCCcEEEEEEECCCC---eEEECCHHHHHHHHHH
Confidence                           35788  9999999999999999999997 9999999999998742   4999999999999999


Q ss_pred             hccc
Q 040809          151 FGVA  154 (161)
Q Consensus       151 ~~~~  154 (161)
                      ++++
T Consensus       242 ~~~~  245 (246)
T 1iru_A          242 LAER  245 (246)
T ss_dssp             HHTC
T ss_pred             hhcc
Confidence            8543

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

Probab=100.00  E-value=2e-37  Score=243.92  Aligned_cols=149  Identities=32%  Similarity=0.530  Sum_probs=135.8

Q ss_pred             CCCCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccH
Q 040809            1 MSRRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIM   62 (161)
Q Consensus         1 m~~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~   62 (161)
                      |+  ||+++|+|||||||||||||                 | |||+|+|.++++... ++.+|||+|++||+|++||+.
T Consensus         1 ~~--yd~~~t~fsp~Grl~QvEYA~~av~~Gtt~vgi~~~dgVvlaaD~r~~~~l~~~-~~~~KI~~i~~~i~~~~aG~~   77 (248)
T 1iru_D            1 MS--YDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDE-RTVRKICALDDNVCMAFAGLT   77 (248)
T ss_dssp             -C--CCCCCSCCCTTSCCHHHHHHHHHHHTSCCEEEECCSSEEEEEECCCCCCSSSCG-GGGCSEEESSSSCEEEEEECH
T ss_pred             CC--ccCCCceECCCCcchHHHHHHHHHHcCCCEEEEEeCCEEEEEEeecccccCccC-CCCCcEEEEcCCEEEEEeecH
Confidence            66  99999999999999999999                 5 999999999997654 488999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCc-------------------------------------------------------
Q 040809           63 SDANILINTARVQARRYAYAYQEPI-------------------------------------------------------   87 (161)
Q Consensus        63 ~D~~~l~~~~r~~~~~y~~~~~~~i-------------------------------------------------------   87 (161)
                      +|++.|++++|.+++.|+++++++|                                                       
T Consensus        78 aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rp~~v~~lvaG~D~~~gp~Ly~idp~G~~~~~~  157 (248)
T 1iru_D           78 ADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWK  157 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCEEEEEEEECSSSCEEEEEECTTSCEEEBS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhccCCcccccEEEEEEEEeCCCCcEEEEEcCCCcEEEee
Confidence            9999999999999999999999987                                                       


Q ss_pred             ----------------cCCCCCC--CHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHH
Q 040809           88 ----------------QDYKDDM--TRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLE  149 (161)
Q Consensus        88 ----------------~~y~~~m--t~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~  149 (161)
                                      +.|+++|  |++||++++++||..+++   .++++++|++|++++    .|++++++||++++.
T Consensus       158 ~~aiG~gs~~a~~~Le~~~~~~m~~s~eea~~la~~al~~~~~---~sg~~i~v~vi~~~g----~~~~l~~~ei~~~~~  230 (248)
T 1iru_D          158 ANAIGRGAKSVREFLEKNYTDEAIETDDLTIKLVIKALLEVVQ---SGGKNIELAVMRRDQ----SLKILNPEEIEKYVA  230 (248)
T ss_dssp             EEEESTTHHHHHHHHTTTCCSSTTCSHHHHHHHHHHHHHTTSC---TTSTTCCEEEEESSS----CEECCCHHHHHHHTT
T ss_pred             EEEECCCcHHHHHHHHHhhcccccCCHHHHHHHHHHHHHHHHc---CCCCcEEEEEEECCC----cEEECCHHHHHHHHH
Confidence                            3689999  999999999999999996   578999999999975    599999999999999


Q ss_pred             HhcccCCCCC
Q 040809          150 NFGVAQPASE  159 (161)
Q Consensus       150 ~~~~~~~~~~  159 (161)
                      .+.+++++++
T Consensus       231 ~~~~~~~~~~  240 (248)
T 1iru_D          231 EIEKEKEENE  240 (248)
T ss_dssp             TTTTTTTTTT
T ss_pred             HHHhcchhhh
Confidence            9977665543

>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=4.5e-37  Score=240.88  Aligned_cols=145  Identities=37%  Similarity=0.706  Sum_probs=131.4

Q ss_pred             CCC-CCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEecc
Q 040809            1 MSR-RYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGI   61 (161)
Q Consensus         1 m~~-~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~   61 (161)
                      |++ +||+++|+|||||||+|||||                 | |||+|+|.++++.+ +++.+||++|++||+|++||+
T Consensus         3 m~~~~yd~~~t~fsp~Grl~QvEya~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~-~~~~~Ki~~i~~~i~~~~aG~   81 (241)
T 1iru_E            3 LTRSEYDRGVNTFSPEGRLFQVEYDIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLME-PSSIEKIVEIDAHIGCAMSGL   81 (241)
T ss_dssp             -----CCCCTTCBCTTSCBHHHHHHHHHHTTSCCEEEEEETTEEEEEEECCCCCTTBC-TTSCCSEEEEETTEEEEEEEC
T ss_pred             CccCCCCCCCceECCCCccHHHHHHHHHHHcCCcEEEEEcCCEEEEEEecccCCcCcC-ccccceEEEEcCCEEEEEeeC
Confidence            554 899999999999999999999                 5 89999999999988 568999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCc------------------------------------------------------
Q 040809           62 MSDANILINTARVQARRYAYAYQEPI------------------------------------------------------   87 (161)
Q Consensus        62 ~~D~~~l~~~~r~~~~~y~~~~~~~i------------------------------------------------------   87 (161)
                      .+|++.+++++|.+++.|++++++++                                                      
T Consensus        82 ~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a~~l~~~~~~y~~~~~~~~l~~rp~~v~~lvaG~D~~gp~Ly~idp~G~  161 (241)
T 1iru_E           82 IADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMSRPFGVALLFGGVDEKGPQLFHMDPSGT  161 (241)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCBCSTTCCSSCBSSCCCEEEEEEEEETTEEEEEEECTTSC
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhccccccccccccceEEEEEEEEeCCCCEEEEECCCCc
Confidence            99999999999999999998887755                                                      


Q ss_pred             ---------------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHH
Q 040809           88 ---------------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTM  146 (161)
Q Consensus        88 ---------------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~  146 (161)
                                           +.|+++||++||++++++||..++++ .+++++++|++|++++    .|++|+++||++
T Consensus       162 ~~~~~~~aiGsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~-~~sg~~i~v~vi~~~~----~~~~l~~~ei~~  236 (241)
T 1iru_E          162 FVQCDARAIGSASEGAQSSLQELYHKSMTLKEAIKSSLIILKQVMEE-KLNATNIELATVQPGQ----NFHMFTKEELEE  236 (241)
T ss_dssp             EEEBSEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCSS-CCCTTSEEEEEECSSS----CCEECCHHHHHH
T ss_pred             EEecceEEECCCcHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhc-cCCCCCEEEEEEECCC----CeEECCHHHHHH
Confidence                                 24789999999999999999999998 8899999999999885    499999999999


Q ss_pred             HHHHh
Q 040809          147 LLENF  151 (161)
Q Consensus       147 ~l~~~  151 (161)
                      +++++
T Consensus       237 ~~~~~  241 (241)
T 1iru_E          237 VIKDI  241 (241)
T ss_dssp             HHTTC
T ss_pred             HHHhC
Confidence            99753

>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=2.1e-37  Score=241.53  Aligned_cols=142  Identities=35%  Similarity=0.644  Sum_probs=123.2

Q ss_pred             CCC-CCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEecc
Q 040809            1 MSR-RYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGI   61 (161)
Q Consensus         1 m~~-~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~   61 (161)
                      |++ +||+++|+|||||||+|||||                 | |||+|+|.++++.. .++.+||++|++||+|++||+
T Consensus         3 m~~~~yd~~~t~fsp~Grl~QvEya~~av~~Gtt~vgi~~~dgVvlaaD~r~~~~~~~-~~~~~Ki~~i~~~i~~~~aG~   81 (233)
T 1yar_A            3 QGQMAYSRAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIE-QNSIEKIQLIDDYVAAVTSGL   81 (233)
T ss_dssp             ----------CCCCTTSCCHHHHHHHHHHTTSCCEEEEEETTEEEEEECCCCCCTTBC-STTCCSEEEEETTEEEEEEEB
T ss_pred             cccccCCCCCceECcCCeeHHHHhHHHHHhcCCcEEEEEECCEEEEEEeccCCccccc-ccccCeEEEecCCEEEEEeeC
Confidence            554 899999999999999999999                 5 89999999998765 458899999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCc------------------------------------------------------
Q 040809           62 MSDANILINTARVQARRYAYAYQEPI------------------------------------------------------   87 (161)
Q Consensus        62 ~~D~~~l~~~~r~~~~~y~~~~~~~i------------------------------------------------------   87 (161)
                      .+|++.+++++|.+++.|++++++++                                                      
T Consensus        82 ~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a~~l~~~~~~~~~~~~~rp~~v~~lvaG~D~~gp~Ly~id~~G~~~~~~  161 (233)
T 1yar_A           82 VADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGVSLIFAGIDQIGPRLFDCDPAGTINEYK  161 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBTTBCCCCEEEEEEEECSSCEEEEEECTTCCEEEBS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCcCCcCcceEEEEEEEEeCCCCEEEEECCCCCEEeee
Confidence            99999999999999999999999887                                                      


Q ss_pred             ----------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHH
Q 040809           88 ----------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLL  148 (161)
Q Consensus        88 ----------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l  148 (161)
                                      +.|+++||++||++++++||..+++++. ++++++|++|++++    .|++++++||+++|
T Consensus       162 ~~aiG~gs~~a~~~Le~~~~~~~s~eea~~la~~al~~~~~~d~-s~~~i~v~vi~~~~----~~~~~~~~ei~~~l  233 (233)
T 1yar_A          162 ATAIGSGKDAVVSFLEREYKENLPEKEAVTLGIKALKSSLEEGE-ELKAPEIASITVGN----KYRIYDQEEVKKFL  233 (233)
T ss_dssp             EEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHTSCSSC-CCCCCEEEEEETTS----CCEECCHHHHHTTC
T ss_pred             EEEEcCCcHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhccC-CCCcEEEEEEECCC----CEEECCHHHHHhhC
Confidence                            3589999999999999999999999865 89999999999885    49999999998764

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

Probab=100.00  E-value=1.7e-36  Score=237.58  Aligned_cols=146  Identities=36%  Similarity=0.573  Sum_probs=134.4

Q ss_pred             CCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHH
Q 040809            6 DRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANI   67 (161)
Q Consensus         6 ~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~   67 (161)
                      |+++|+|||||||||||||                 | |||+|+|.++++++ +++.+|||+|++||+|++||+.+|++.
T Consensus         1 d~~~t~fsp~Grl~QvEyA~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~-~~~~~Ki~~i~~~i~~~~aG~~aD~~~   79 (242)
T 1ryp_E            1 DRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE-SDSIEKIVEIDRHIGCAMSGLTADARS   79 (242)
T ss_dssp             CCCTTCBCTTSCBHHHHHHHHHHTTSCCEEEEECSSCEEEEEECCCSSTTBC-GGGCCCEEEEETTEEEEEEESGGGHHH
T ss_pred             CCCCceECCCCcChHHHhHHHHHHcCCCEEEEEECCEEEEEEeecCCCcCcc-CccCCceEEEcCCEEEEEeecHHHHHH
Confidence            7899999999999999999                 5 99999999999988 558999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhCCCc------------------------------------------------------------
Q 040809           68 LINTARVQARRYAYAYQEPI------------------------------------------------------------   87 (161)
Q Consensus        68 l~~~~r~~~~~y~~~~~~~i------------------------------------------------------------   87 (161)
                      +++++|.+++.|++++++++                                                            
T Consensus        80 l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~~~~l~~RP~~v~~lvaG~D~~~gp~Ly~idp~G~~~~~  159 (242)
T 1ryp_E           80 MIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRY  159 (242)
T ss_dssp             HHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCCBSSCTTSCCCBSSCCSEEEEEEEEETTTEEEEEEECTTSCEEEB
T ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccccCcccccccCcceEEEEEEEEeCCCCCEEEEECCCCCEecc
Confidence            99999999999999877655                                                            


Q ss_pred             -----------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 040809           88 -----------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLEN  150 (161)
Q Consensus        88 -----------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~  150 (161)
                                       +.|+++||++||++++++||..++++ ..++.+++|++|++++    .|++++++||++++++
T Consensus       160 ~~~aiGsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~-~~sg~~i~v~vi~~~~----~~~~~~~~ei~~~~~~  234 (242)
T 1ryp_E          160 NAKAIGSGSEGAQAELLNEWHSSLTLKEAELLVLKILKQVMEE-KLDENNAQLSCITKQD----GFKIYDNEKTAELIKE  234 (242)
T ss_dssp             SEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCSS-CCCTTSEEEEEEETTT----EEEECCHHHHHHHHHH
T ss_pred             CEEEECCCCHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHhhc-cCCCCcEEEEEEECCC----CeEECCHHHHHHHHHH
Confidence                             35789999999999999999999998 8899999999999875    5999999999999999


Q ss_pred             hcccCCC
Q 040809          151 FGVAQPA  157 (161)
Q Consensus       151 ~~~~~~~  157 (161)
                      +.+++++
T Consensus       235 ~~~~~~~  241 (242)
T 1ryp_E          235 LKEKEAA  241 (242)
T ss_dssp             HHHHHTT
T ss_pred             Hhhhhcc
Confidence            9665543

>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=4.3e-36  Score=241.08  Aligned_cols=142  Identities=29%  Similarity=0.473  Sum_probs=129.5

Q ss_pred             CCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHH
Q 040809            3 RRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSD   64 (161)
Q Consensus         3 ~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D   64 (161)
                      .+||+++|+|||+|||||||||                 | |||+|+|.++++++++ ..+|||+|++||+|++||+.+|
T Consensus         6 ~~yd~~~t~fSP~Grl~QvEYA~kAv~~GtT~Vgik~kdGVVlAaD~r~t~gl~~~~-~~~KI~~I~d~i~~~~aG~~aD   84 (288)
T 3nzj_F            6 TGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQ-KNVKIQVVDRHIGCVYSGLIPD   84 (288)
T ss_dssp             CCTTSSTTCCCTTSCCHHHHHHHHHHHTSCCEEEEEETTEEEEEEEEEECCTTBCTT-CSCCCEEETTTEEEEEEECHHH
T ss_pred             CCccCCcccCCCCCchHHHHHHHHHHhcCCcEEEEEECCEEEEEEcCCcccCCcccc-ccceEEEEcCCEEEEecCcHHH
Confidence            7899999999999999999999                 6 9999999999999987 7899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCc---------------------------------------------------------
Q 040809           65 ANILINTARVQARRYAYAYQEPI---------------------------------------------------------   87 (161)
Q Consensus        65 ~~~l~~~~r~~~~~y~~~~~~~i---------------------------------------------------------   87 (161)
                      ++.|++++|.+++.|+++|+++|                                                         
T Consensus        85 ~~~l~~~lr~e~~~y~~~~~~~i~v~~lA~~l~~~l~~yt~~~~~rP~gv~~lvaG~D~~Gp~Ly~iDp~G~~~~~~~~a  164 (288)
T 3nzj_F           85 GRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAA  164 (288)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSCTTBCCCCEEEEEEEEETTEEEEEEECTTSCEEEBSEEE
T ss_pred             HHHHHHHHHHHHHHHHHHcCCcCCHHHHHHHHHHHHHHHHHhccCCCceEEEEEEEEeCCCCEEEEECCCCCEEEcCEEE
Confidence            99999999999999999999988                                                         


Q ss_pred             -------------cC---CCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEe-CCCCceeEEECCHHHHHHH
Q 040809           88 -------------QD---YKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFL-LPSGKVKYRICSPESLTML  147 (161)
Q Consensus        88 -------------~~---y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~-~~~g~~~~~~l~~~ei~~~  147 (161)
                                   +.   |+++||++||++++++||..+++++..+++++||+||++ +.+|  .++.++.+++++.
T Consensus       165 iGsgs~~a~~~Lek~~~~~~~~ms~eEAv~la~~al~~a~~~~~~~~~~iev~vIt~~~~~~--~~~~vp~~~~~~~  239 (288)
T 3nzj_F          165 TGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNG--LHKFVKGDLLQEA  239 (288)
T ss_dssp             ESTTHHHHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHGGGGTTSEEEEEEEEEETTTSTT--CCEECCHHHHHHH
T ss_pred             EcCcHHHHHHHHHHhccccCCCCCHHHHHHHHHHHHHHHHhcccCCCCeEEEEEEEecCCCc--eEEECCHHHHHHH
Confidence                         35   899999999999999999999999888999999999998 5444  5666666665543

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

Probab=100.00  E-value=1.8e-36  Score=240.52  Aligned_cols=145  Identities=26%  Similarity=0.499  Sum_probs=133.0

Q ss_pred             CC-CCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEecc
Q 040809            1 MS-RRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGI   61 (161)
Q Consensus         1 m~-~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~   61 (161)
                      |. ++||+++|+|||+|||||||||                 | |||+|+|.++++.   ++.+|||+|++||+|++||+
T Consensus         1 m~~~~yd~~~t~fsP~Grl~QvEYA~~av~~Gtt~vgi~~~dgVVlaaD~r~~~gl~---~~~~KI~~i~~~i~~~~aG~   77 (263)
T 1iru_F            1 MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELA---AHQKKILHVDNHIGISIAGL   77 (263)
T ss_dssp             ---CTTTSCTTCCCTTSCCHHHHHHHHHHHHSCCEEEEECSSEEEEEEECCCSSTTB---CCCCCEEEEETTEEEEEEEC
T ss_pred             CCcCCCCCCCccCCCCCeehHHHHHHHHHHcCCcEEEEEeCCEEEEEEecccccccc---cchhcEEEEcCCEEEEEeCC
Confidence            55 5899999999999999999999                 5 9999999999974   36799999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCc------------------------------------------------------
Q 040809           62 MSDANILINTARVQARRYAYAYQEPI------------------------------------------------------   87 (161)
Q Consensus        62 ~~D~~~l~~~~r~~~~~y~~~~~~~i------------------------------------------------------   87 (161)
                      .+|++.|++++|.+++.|+++|+++|                                                      
T Consensus        78 ~aD~~~l~~~~~~~~~~~~~~~~~~i~v~~la~~l~~~l~~~t~~~~~RP~~v~~lvaG~D~~gp~Ly~idp~G~~~~~~  157 (263)
T 1iru_F           78 TADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAGYDDMGPHIFQTCPSANYFDCR  157 (263)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEETTEEEEEEECSSSCEEEES
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHhhcccccccceEEEEEEEEcCCCCEEEEECCCCCEEEee
Confidence            99999999999999999999999988                                                      


Q ss_pred             ----------------cCCCC--CCCHHHHHHHHHHHHHHhhccC-CCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHH
Q 040809           88 ----------------QDYKD--DMTRQEAVQLALKVLRKTMDST-SLTSEKLELAEVFLLPSGKVKYRICSPESLTMLL  148 (161)
Q Consensus        88 ----------------~~y~~--~mt~eeai~la~~al~~~~~~~-~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l  148 (161)
                                      +.|++  +||++||++++++||..+++++ .+++++++|++|++++    .|++++++||++++
T Consensus       158 ~~aiGsgs~~a~~~Le~~~~~~~~ms~eea~~la~~al~~~~~rd~~~sg~~iev~vi~~~~----~~~~l~~~ei~~~~  233 (263)
T 1iru_F          158 AMSIGARSQSARTYLERHMSEFMECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDL----EFTIYDDDDVSPFL  233 (263)
T ss_dssp             EEEESTTHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCTTCCCCTTTEEEEEEETTE----EEEEECSGGGHHHH
T ss_pred             EEEcCcccHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHhccccCCCCcEEEEEEECCC----CeEECCHHHHHHHH
Confidence                            24666  9999999999999999999998 4899999999999875    59999999999999


Q ss_pred             HHhc
Q 040809          149 ENFG  152 (161)
Q Consensus       149 ~~~~  152 (161)
                      .++.
T Consensus       234 ~~~~  237 (263)
T 1iru_F          234 EGLE  237 (263)
T ss_dssp             TTCC
T ss_pred             HHHh
Confidence            9885

>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=3.2e-35  Score=230.93  Aligned_cols=147  Identities=28%  Similarity=0.439  Sum_probs=133.1

Q ss_pred             CCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHH
Q 040809            3 RRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSD   64 (161)
Q Consensus         3 ~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D   64 (161)
                      ++||+++|+|||+|||||||||                 | |||+|+|.++++++++ ..+||++|++||+|++||+.+|
T Consensus         2 ~~yd~~~t~fsp~Grl~QvEya~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~-~~~KI~~i~~~i~~~~aG~~aD   80 (244)
T 1ryp_G            2 TGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQ-KNVKIQVVDRHIGCVYSGLIPD   80 (244)
T ss_dssp             CCTTSSTTCCCTTSCCHHHHHHHHHHHTSCCEEEEEETTEEEEEEEEECCCTTBCTT-TSCCCEEETTTEEEEEEECHHH
T ss_pred             CCccCCcccCCcCCchHHHHhHHHHHHCCCCEEEEEECCEEEEEEecccCCCCcccc-ccCceEEecCCEEEEEcccHHH
Confidence            5899999999999999999999                 6 9999999999999987 4699999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCc---------------------------------------------------------
Q 040809           65 ANILINTARVQARRYAYAYQEPI---------------------------------------------------------   87 (161)
Q Consensus        65 ~~~l~~~~r~~~~~y~~~~~~~i---------------------------------------------------------   87 (161)
                      ++.|++++|.+++.|++++++++                                                         
T Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rp~~v~~lvaG~D~~gp~Ly~idp~G~~~~~~~~a  160 (244)
T 1ryp_G           81 GRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAA  160 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSCTTBCCCCEEEEEEEEETTEEEEEEECTTSCEEEBSEEE
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCccCceEEEEEEEEeCCcCEEEEECCCCCEEEeeEEE
Confidence            99999999999999999999977                                                         


Q ss_pred             -------------cC---CCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEe-CCCCceeEEECCHHHHHHHHHH
Q 040809           88 -------------QD---YKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFL-LPSGKVKYRICSPESLTMLLEN  150 (161)
Q Consensus        88 -------------~~---y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~-~~~g~~~~~~l~~~ei~~~l~~  150 (161)
                                   +.   |+++||++||++++++||..+++++..++.+++|++|++ +.+   .++++.++++.+...+
T Consensus       161 iG~gs~~a~~~Le~~~~~~~~~ms~eea~~la~~al~~~~~~d~~s~~~iev~vi~~~~~~---g~~~~~~~~~~~~~~~  237 (244)
T 1ryp_G          161 TGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETN---GLHKFVKGDLLQEAID  237 (244)
T ss_dssp             ESTTHHHHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHGGGGTTSCEEEEEEEEETTTTT---TSEEECCTHHHHHHHH
T ss_pred             ECCChHHHHHHHHHhHhhcCCCCCHHHHHHHHHHHHHHHHhccCCCCCeEEEEEEEecCCC---CeeeeChHHHHHHHHH
Confidence                         23   899999999999999999999999888999999999997 222   3678888888777766


Q ss_pred             hcc
Q 040809          151 FGV  153 (161)
Q Consensus       151 ~~~  153 (161)
                      .++
T Consensus       238 ~~~  240 (244)
T 1ryp_G          238 FAQ  240 (244)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            644

>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=6.7e-36  Score=233.15  Aligned_cols=138  Identities=27%  Similarity=0.451  Sum_probs=126.8

Q ss_pred             CCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHH
Q 040809            3 RRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSD   64 (161)
Q Consensus         3 ~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D   64 (161)
                      ++||+++|+|||||||+|||||                 | |||+|+|.++++.  . +.+||++|++||+|++||+.+|
T Consensus         3 ~~yd~~~t~fsp~Grl~QvEyA~~av~~Gtt~vgi~~~dgVvlaaD~r~~~~l~--~-~~~Ki~~i~~~i~~~~aG~~aD   79 (233)
T 1ryp_F            3 NNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELS--S-YQKKIIKCDEHMGLSLAGLAPD   79 (233)
T ss_dssp             HHHSSCTTCCCTTSCCHHHHHHHHHHHTSCCEEEEECSSEEEEEEECCCSSTTB--C-CCCCEEEEETTEEEEEEECHHH
T ss_pred             CcccCCCccCCCCCeehHHHHHHHHHHcCCCEEEEEcCCEEEEEEEeccccccc--c-ccCcEEEEcCCEEEEEEechHH
Confidence            4799999999999999999999                 5 9999999999875  2 6799999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCc---------------------------------------------------------
Q 040809           65 ANILINTARVQARRYAYAYQEPI---------------------------------------------------------   87 (161)
Q Consensus        65 ~~~l~~~~r~~~~~y~~~~~~~i---------------------------------------------------------   87 (161)
                      ++.+++++|.+++.|+++++++|                                                         
T Consensus        80 ~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rp~~v~~lvaG~D~~gp~Ly~idp~G~~~~~~~~a  159 (233)
T 1ryp_F           80 ARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTA  159 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEETTEEEEEEECTTSCEEEESEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcccCCcCcceEEEEEEEeCCcCEEEEECCCCCeeeeeEEE
Confidence            99999999999999999999988                                                         


Q ss_pred             -------------cCCCC--CC--CHHHHHHHHHHHHHHhhccC-CCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHH
Q 040809           88 -------------QDYKD--DM--TRQEAVQLALKVLRKTMDST-SLTSEKLELAEVFLLPSGKVKYRICSPESLTMLL  148 (161)
Q Consensus        88 -------------~~y~~--~m--t~eeai~la~~al~~~~~~~-~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l  148 (161)
                                   +.|++  +|  |++||++++++||..++ ++ .+++++++|++|++++    .|++++++||+++|
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 IGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVEAISQSL-RDESLTVDNLSIAIVGKDT----PFTIYDGEAVAKYI  233 (233)
T ss_dssp             ESTTHHHHHHHHHHHHHHHTTCCSCHHHHHHHHHHHHTTSC-CSSCCCTTTEEEEEEETTE----EEEEEEGGGGGGGC
T ss_pred             ECCCcHHHHHHHHHHhccccccCCCHHHHHHHHHHHHHHHh-hcccCCCCcEEEEEEECCC----CEEECCHHHHHhhC
Confidence                         24677  99  99999999999999999 66 5799999999999875    59999999998764

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

Probab=99.95  E-value=1.1e-26  Score=179.47  Aligned_cols=137  Identities=23%  Similarity=0.351  Sum_probs=120.8

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +.-|.+. | |||+|+|.+++.++.+++.+|||+|++||+|++||+.+|++.|++++|.+++.|++.|++++        
T Consensus         4 ~vgi~~~dgVvlaaD~r~~~g~~i~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~   83 (219)
T 3h4p_a            4 TVGLICDDAVILATDKRASLGNLVADKEAKKLYKIDDYIAMTIAGSVGDAQAIVRLLIAEAKLYKMRTGRNIPPLACATL   83 (219)
T ss_dssp             EEEEEETTEEEEECCCCEEETTEEEETTCCCEEEEETTEEEECCSCHHHHHHHHHHHHHHHHHHHHHTSSCCCHHHHHHH
T ss_pred             EEEEEECCEEEEEEcCCcccCCEeeccccceeEEecCCEEEEeeEcHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            5566666 6 99999999998776667899999999999999999999999999999999999999999988        


Q ss_pred             ------------------------------------------------------------cCCCCCCCHHHHHHHHHHHH
Q 040809           88 ------------------------------------------------------------QDYKDDMTRQEAVQLALKVL  107 (161)
Q Consensus        88 ------------------------------------------------------------~~y~~~mt~eeai~la~~al  107 (161)
                                                                                  +.|+++||++||++++++||
T Consensus        84 l~~~~~~~~~~P~~v~~lvaG~D~~~gp~Ly~idp~G~~~~~~~~~aiG~gs~~a~~~Le~~~~~~ms~eea~~la~~al  163 (219)
T 3h4p_a           84 LSNILHSSRMFPFLTQIIIGGYDLLEGAKLFSLDPLGGMNEEKTFTATGSGSPIAYGVLEAGYDRDMSVEEGIKLALNAL  163 (219)
T ss_dssp             HHHHHHHTTTTTCCCCCEEEEEETTTEEEEEEECSSCCEEECSSEEEESTTHHHHHHHHHTSCCTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCceEEEEEEEEeCCCCcEEEEECCCCceEecCCEEEEcCCHHHHHHHHHHhcCCCCCHHHHHHHHHHHH
Confidence                                                                        36899999999999999999


Q ss_pred             HHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhcccCCCCC
Q 040809          108 RKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFGVAQPASE  159 (161)
Q Consensus       108 ~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~~~~~~~~  159 (161)
                      ..++++|..++++++|++|+++     .|++|+++||+++|++++.+++++.
T Consensus       164 ~~~~~rd~~sg~~i~v~vi~~~-----g~~~l~~~ei~~~l~~~~~~~~~~~  210 (219)
T 3h4p_a          164 KSAMERDTFSGNGISLAVITKD-----GVKIFEDEEIEKILDSMKAKPKKKT  210 (219)
T ss_dssp             HHHHTSCSSCCSCCCEEEEETT-----EEEECCHHHHHHHHHHCC-------
T ss_pred             HHHHhhcCCCCCcEEEEEEeCC-----CeEEcCHHHHHHHHHHhhccccccc
Confidence            9999999999999999999987     4999999999999999987776654

>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=99.94  E-value=6.9e-27  Score=185.00  Aligned_cols=139  Identities=23%  Similarity=0.279  Sum_probs=112.5

Q ss_pred             cccCCCCcee-eEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHH
Q 040809           10 TVFSPEGRLY-QVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILIN   70 (161)
Q Consensus        10 ~~fsp~Grl~-qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~   70 (161)
                      ..|||+|++. |||||                 | |||+|+|        +++.+|||+|++||+|++||+.+|++.|++
T Consensus         5 ~~~sPe~~~~~qvEYA~~av~~Gtt~vgi~~~dgVVlaaD~r--------s~~~~KI~~I~d~i~~~~aG~~aD~~~l~~   76 (259)
T 1q5q_A            5 YYASAEQIMRDRSELARKGIARGRSVVVLTFRDGVLFVAENP--------STALHKVSELYDRLGFAAVGKYNEFENLRR   76 (259)
T ss_dssp             ----CHHHHHHHHHHHHHHHHTSCCEEEEECSSEEEEEECCS--------CSSSCSEEEEETTEEEEEEECHHHHHHHHH
T ss_pred             cccCHHHHHHHHHHHHHHHHhcCCcEEEEEeCCEEEEEEecC--------CCCcCcEEEeCCCEEEEEccCHHHHHHHHH
Confidence            3589999995 99999                 6 9999998        247899999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhCC-Cc--------------------------------------------------------------
Q 040809           71 TARVQARRYAYAYQE-PI--------------------------------------------------------------   87 (161)
Q Consensus        71 ~~r~~~~~y~~~~~~-~i--------------------------------------------------------------   87 (161)
                      ++|.+++.|++.|+. +|                                                              
T Consensus        77 ~~~~~~~~~~~~~~~~~i~v~~la~~l~~~l~q~yt~~~rP~~v~~lvaG~D~~~~~~gp~Ly~idp~G~~~~~~~~~ai  156 (259)
T 1q5q_A           77 AGIVHADMRGYSYDRRDVTGRSLANAYAQTLGTIFTEQPKPYEVEICVAEVGRVGSPKAPQLYRITYDGSIVDEQHFVVM  156 (259)
T ss_dssp             HHHHHHHHHHHHSCGGGCCHHHHHHHHHHHHHHHHHHSSSCCCEEEEEEECCCSSCCCCCEEEEEETTSCEEEESSEEEE
T ss_pred             HHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHhccCCCCceEEEEEEEEcccCCCCCCEEEEECCCCceeeCCCEEEE
Confidence            999999999988874 55                                                              


Q ss_pred             ------------cCCCCCCCHHHHHHHHHHHHHHhh-----ccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 040809           88 ------------QDYKDDMTRQEAVQLALKVLRKTM-----DSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLEN  150 (161)
Q Consensus        88 ------------~~y~~~mt~eeai~la~~al~~~~-----~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~  150 (161)
                                  +.|+++||++||++++++||..++     +++. ++.+++|++|++++.+ +.|++|+++||++++.+
T Consensus       157 G~gs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~~~~~rd~-sg~~iev~vi~~~~~~-~~~~~l~~~ei~~~~~~  234 (259)
T 1q5q_A          157 GGTTEPIATAMRESYRADLDLEAAVGIAVNALRQGGAGEGEKRNV-DVASLEVAVLDQSRPR-RAFRRIAGTALEQLVPA  234 (259)
T ss_dssp             SSSHHHHHHHHHHHCCTTCCHHHHHHHHHHHHTTCC--------C-CSSCSEEEEEETTSSS-CCEEECCHHHHHTTSCC
T ss_pred             CCChHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHhhcccccccC-CCCcEEEEEEECCCCc-CCeEECCHHHHHHHHHH
Confidence                        246899999999999999999999     7766 9999999999998422 25999999999999988


Q ss_pred             hcccCCCC
Q 040809          151 FGVAQPAS  158 (161)
Q Consensus       151 ~~~~~~~~  158 (161)
                      +.+...++
T Consensus       235 ~~~~~~~~  242 (259)
T 1q5q_A          235 EPAAASES  242 (259)
T ss_dssp             C-------
T ss_pred             hhhccccc
Confidence            85554433

>1iru_L 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_K* 3une_K 3unf_K* 3unh_K

Probab=99.94  E-value=4.1e-26  Score=174.24  Aligned_cols=133  Identities=18%  Similarity=0.250  Sum_probs=118.3

Q ss_pred             eeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc---------
Q 040809           19 YQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI---------   87 (161)
Q Consensus        19 ~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i---------   87 (161)
                      .-+.+. | |||+|+|.+++.++.+++.+|||+|++||+|++||+.+|++.|++++|.+++.|++++++++         
T Consensus         4 vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l   83 (204)
T 1iru_L            4 LAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQCRIYELRNKERISVAAASKLL   83 (204)
T ss_dssp             EEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEECCBCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHH
T ss_pred             EEEEeCCEEEEEEcCCcccCCEEEcCcccceEEcCCCEEEEccCcHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHH
Confidence            445555 5 89999999986555556899999999999999999999999999999999999999999887         


Q ss_pred             ---------------------------------------------------------cCCCCCCCHHHHHHHHHHHHHHh
Q 040809           88 ---------------------------------------------------------QDYKDDMTRQEAVQLALKVLRKT  110 (161)
Q Consensus        88 ---------------------------------------------------------~~y~~~mt~eeai~la~~al~~~  110 (161)
                                                                               +.|+++||++||++++++||..+
T Consensus        84 ~~~~~~~r~~~~~v~~lvaG~D~~gp~Ly~idp~G~~~~~~~~aiG~gs~~a~~~Le~~~~~~~s~eea~~l~~~al~~~  163 (204)
T 1iru_L           84 ANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNRISGATFSVGSGSVYAYGVMDRGYSYDLEVEQAYDLARRAIYQA  163 (204)
T ss_dssp             HHHHHTTTTSCCCBEEEEEEECSSSEEEEEEESSSCEEECSEEEESTTHHHHHHHHHTTCCTTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCCeeEEEEEEEEeCCCCEEEEECCCCcEEEeCCEEEEcCHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHH
Confidence                                                                     36899999999999999999999


Q ss_pred             hccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhcccCC
Q 040809          111 MDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFGVAQP  156 (161)
Q Consensus       111 ~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~~~~~  156 (161)
                      ++++..++++++|++|+++     .|+.++++||+++++++.+++|
T Consensus       164 ~~rd~~s~~~i~v~vi~~~-----g~~~l~~~ei~~~~~~~~~~~~  204 (204)
T 1iru_L          164 TYRDAYSGGAVNLYHVRED-----GWIRVSSDNVADLHEKYSGSTP  204 (204)
T ss_dssp             HHHBTTCCSEEEEEEECSS-----CEEEEEEEEHHHHHHHHTC---
T ss_pred             HHhCccCCCceEEEEEeCC-----ceEEeCHHHHHHHHHHhccCCC
Confidence            9998889999999999986     4999999999999999977654

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

Probab=99.93  E-value=2.8e-25  Score=169.37  Aligned_cols=130  Identities=22%  Similarity=0.372  Sum_probs=117.2

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +.-|-+. | |||+|+|.+++.++.+++.+|||+|++||+|++||+.+|++.|++++|.+++.|+++++++|        
T Consensus         3 ~vgi~~~dgVvlaad~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~   82 (202)
T 1j2q_H            3 TVGLVCKDGVVMATEKRATMGNFIASKAAKKIYQIADRMAMTTAGSVGDAQFLARIIKIEANLYEIRRERKPTVRAIATL   82 (202)
T ss_dssp             EEEEEETTEEEEEEECCEEETTEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHH
T ss_pred             EEEEEeCCEEEEEECCCcCcCCEEeeccccCEEEcCCCEEEEecccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
Confidence            3445555 5 99999999986555556899999999999999999999999999999999999999999987        


Q ss_pred             -----------------------------------------------------------cCCCCCCCHHHHHHHHHHHHH
Q 040809           88 -----------------------------------------------------------QDYKDDMTRQEAVQLALKVLR  108 (161)
Q Consensus        88 -----------------------------------------------------------~~y~~~mt~eeai~la~~al~  108 (161)
                                                                                 +.|+++||++||++++++||.
T Consensus        83 l~~~~~~~r~rp~~~~~lvaG~D~~gp~Ly~id~~G~~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s~eea~~la~~al~  162 (202)
T 1j2q_H           83 TSNLLNSYRYFPYLVQLLIGGIDSEGKSIYSIDPIGGAIEEKDIVATGSGSLTAYGVLEDRFTPEIGVDEAVELAVRAIY  162 (202)
T ss_dssp             HHHHHHHTTTSCCCEEEEEEEEETTEEEEEEECTTCCEEEESSEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHhhCCCCceEEEEEEEEeCCCCEEEEECCCCCeeecCCEEEEcCCHHHHHHHHHhhcCCCcCHHHHHHHHHHHHH
Confidence                                                                       358999999999999999999


Q ss_pred             HhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhc
Q 040809          109 KTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFG  152 (161)
Q Consensus       109 ~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~  152 (161)
                      .+++++..++++++|++|+++     .|++++++||++++++++
T Consensus       163 ~~~~~d~~s~~~i~v~vi~~~-----g~~~l~~~ei~~~~~~~~  201 (202)
T 1j2q_H          163 SAMKRDSASGDGIDVVKITED-----EFYQYSPEEVEQILAKFR  201 (202)
T ss_dssp             HHHTTCTTSCSCEEEEEECSS-----CEEECHHHHHHHHGGGTT
T ss_pred             HHHhcCCCCCCcEEEEEEeCC-----CeEEeCHHHHHHHHHHhh
Confidence            999998889999999999987     399999999999998875

>1yar_H Proteasome beta subunit; proteasome 20S, PA26 proteasome activator 11S, hydrolase-HYD activator complex; 1.90A {Thermoplasma acidophilum} SCOP: d.153.1.4 PDB: 1ya7_H 1yau_H 3ipm_H 1pma_B 3jrm_H 3c92_H 3c91_H 3jse_H 3jtl_H

Probab=99.92  E-value=1.7e-24  Score=166.99  Aligned_cols=133  Identities=17%  Similarity=0.317  Sum_probs=120.0

Q ss_pred             CceeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc------
Q 040809           16 GRLYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI------   87 (161)
Q Consensus        16 Grl~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i------   87 (161)
                      +.+.-|.+. | |||+|+|.+++.++.+++.+||++|++||+|++||+.+|++.+++++|.+++.|++++++++      
T Consensus         9 tt~vgi~~~dgVvlaaD~r~~~g~l~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la   88 (217)
T 1yar_H            9 TTTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKAELELYRLQRRVNMPIEAVA   88 (217)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             ccEEEEEeCCEEEEEEcCCCCCCCEEecCccCCeEEeCCCEEEEeCcCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            347777777 6 99999999986555556899999999999999999999999999999999999999999887      


Q ss_pred             -----------------------------------------------------------cCCCCCCCHHHHHHHHHHHHH
Q 040809           88 -----------------------------------------------------------QDYKDDMTRQEAVQLALKVLR  108 (161)
Q Consensus        88 -----------------------------------------------------------~~y~~~mt~eeai~la~~al~  108 (161)
                                                                                 +.|+++||++||++++++||.
T Consensus        89 ~~l~~~~~~~r~rp~~v~~lvaG~D~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~s~eea~~la~~al~  168 (217)
T 1yar_H           89 TLLSNMLNQVKYMPYMVQLLVGGIDTAPHVFSIDAAGGSVEDIYASTGSGSPFVYGVLESQYSEKMTVDEGVDLVIRAIS  168 (217)
T ss_dssp             HHHHHHHHHTTTSCCCEEEEEEEESSSEEEEEECTTCCEEEESEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCCCceEEEEEEEECCCCEEEEECCCCCeEecCEEEEcCCHHHHHHHHHhhcccCCCHHHHHHHHHHHHH
Confidence                                                                       358999999999999999999


Q ss_pred             HhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhc
Q 040809          109 KTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFG  152 (161)
Q Consensus       109 ~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~  152 (161)
                      .+.++|..++++++|++|+++.    .|++++++||+++++++.
T Consensus       169 ~~~~rd~~s~~~i~v~vi~~~~----g~~~~~~~ei~~~~~~~~  208 (217)
T 1yar_H          169 AAKQRDSASGGMIDVAVITRKD----GYVQLPTDQIESRIRKLG  208 (217)
T ss_dssp             HHHHHCTTCCSCCEEEEEETTT----EEEECCHHHHHHHHHHHT
T ss_pred             HHHhccCCCCCcEEEEEEECCC----CEEEcCHHHHHHHHHHHH
Confidence            9999988899999999999843    599999999999998775

>1ryp_L 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_L 1vsy_L 1z7q_L 3l5q_P 1g65_K* 1g0u_K* 1jd2_K* 2f16_K* 2fak_K* 2fny_K* 2gpl_K* 2zcy_K* 3bdm_K* 3d29_K* 3dy3_K* 3dy4_K* 3e47_K* 3gpj_K* 3gpt_K* 3gpw_K* ...

Probab=99.92  E-value=3.6e-25  Score=169.98  Aligned_cols=136  Identities=14%  Similarity=0.146  Sum_probs=120.6

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +.-|.+. | |||+|+|.+++.++.+++.+|||+|++||+|++||+.+|++.|++++|.+++.|++++++++        
T Consensus         3 ~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~   82 (212)
T 1ryp_L            3 TLAFRFQGGIIVAVDSRATAGNWVASQTVKRVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREKERISVAAASKI   82 (212)
T ss_dssp             EEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEECCBCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHH
T ss_pred             EEEEEeCCEEEEEEcCCcccCCeEecCcccceeeeCCcEEEEccccHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            3445565 5 99999999986555555899999999999999999999999999999999999999999887        


Q ss_pred             -----------------------------------------------------------cCCCCCCCHHHHHHHHHHHHH
Q 040809           88 -----------------------------------------------------------QDYKDDMTRQEAVQLALKVLR  108 (161)
Q Consensus        88 -----------------------------------------------------------~~y~~~mt~eeai~la~~al~  108 (161)
                                                                                 +.|+++||++||++++++||.
T Consensus        83 l~~~~~~~~~~p~~v~~lvaG~D~~~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~s~eea~~la~~al~  162 (212)
T 1ryp_L           83 LSNLVYQYKGAGLSMGTMICGYTRKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSIL  162 (212)
T ss_dssp             HHHHHHHTTTSCCCBEEEEEEEETTTEEEEEEEETTCCEEECSEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHhhCCCCceEEEEEEEEeCCCCCEEEEEcCCceeEecCCEEEcCCHHHHHHHHHhhCCCCCCHHHHHHHHHHHHH
Confidence                                                                       358999999999999999999


Q ss_pred             HhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhcccCCCC
Q 040809          109 KTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFGVAQPAS  158 (161)
Q Consensus       109 ~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~~~~~~~  158 (161)
                      .+++++..++++++|++|+++     .|++++++||++++.++.+++.++
T Consensus       163 ~~~~rd~~s~~~i~v~vi~~~-----g~~~~~~~ei~~~~~~~~~~~~~~  207 (212)
T 1ryp_L          163 AAAHRDAYSGGSVNLYHVTED-----GWIYHGNHDVGELFWKVKEEEGSF  207 (212)
T ss_dssp             HHHHHBTTCCSEEEEEEEETT-----EEEEEEEEEHHHHHHHHHHHHCCC
T ss_pred             HHHHhccccCCceEEEEEcCC-----ceEEECHHHHHHHHHHHHHhhhhh
Confidence            999998899999999999976     499999999999999886655443

>3unf_N Proteasome subunit beta type-9; antigen presentation, drug development, protein degradation, hydrolase-hydrolase inhibitor complex; HET: 04C; 2.90A {Mus musculus} PDB: 3unh_N

Probab=99.92  E-value=1.9e-25  Score=169.80  Aligned_cols=128  Identities=17%  Similarity=0.285  Sum_probs=115.4

Q ss_pred             eeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc---------
Q 040809           19 YQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI---------   87 (161)
Q Consensus        19 ~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i---------   87 (161)
                      .-|.+. | |||+|+|.+++.++.+++.+|||+|++||+|++||+.+|++.+++++|.+++.|++++++++         
T Consensus         4 vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a~~l   83 (199)
T 3unf_N            4 MAVEFDGGVVVGSDSRVSAGTAVVNRVFDKLSPLHQRIFCALSGSAADAQAIADMAAYQLELHGLELEEPPLVLAAANVV   83 (199)
T ss_dssp             EEEECSSCEEEEECCCEEETTEEEESSCCCEEEEETTEEEEECSCHHHHHHHHHHHHHHHHHHHHHTTSCCCHHHHHHHH
T ss_pred             EEEEeCCeEEEEECCcccCCceeEccccCceEEcCCCEEEEecccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Confidence            445565 5 99999999998666667899999999999999999999999999999999999999999988         


Q ss_pred             --------------------------------------------------------cCCCCCCCHHHHHHHHHHHHHHhh
Q 040809           88 --------------------------------------------------------QDYKDDMTRQEAVQLALKVLRKTM  111 (161)
Q Consensus        88 --------------------------------------------------------~~y~~~mt~eeai~la~~al~~~~  111 (161)
                                                                              +.|+++||++||++++++||..++
T Consensus        84 ~~~l~~~~~p~~v~~lvaG~D~~~~p~ly~p~G~~~~~~~~~~~Gsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~  163 (199)
T 3unf_N           84 KNISYKYREDLLAHLIVAGWDQREGGQVYGTMGGMLIRQPFTIGGSGSSYIYGYVDAAYKPGMTPEECRRFTTNAITLAM  163 (199)
T ss_dssp             HHHHHHTTTTCCCCEEEEEEETTTEEEEEECGGGCCEECSEEEEEGGGGGGHHHHHHHCCSSCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCCCceEEEEEEEEeCCCCcEEEEECCCceecCCEEEEccCHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHH
Confidence                                                                    358999999999999999999999


Q ss_pred             ccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHH
Q 040809          112 DSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLE  149 (161)
Q Consensus       112 ~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~  149 (161)
                      ++|..++++++|++|++++.   .|+.|+++||+++++
T Consensus       164 ~~d~~sg~~i~v~vi~~~g~---~~~~l~~~ei~~~~~  198 (199)
T 3unf_N          164 NRDGSSGGVIYLVTITAAGV---DHRVILGDELPKFYD  198 (199)
T ss_dssp             HHCTTCCSCEEEEEECSSCE---EEEEECGGGSCCCCC
T ss_pred             HhccccCCCeEEEEEcCCCE---EEEEcCcccCccccc
Confidence            99989999999999999853   699999999987653

>1iru_H 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_N* 3une_N

Probab=99.92  E-value=4.7e-25  Score=168.49  Aligned_cols=130  Identities=17%  Similarity=0.289  Sum_probs=116.2

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +.-|.+. | |||+|+|.+++.++.+++.+|||+|++||+|++||+.+|++.+++++|.+++.|++++++++        
T Consensus         3 ~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~   82 (205)
T 1iru_H            3 IMAVQFDGGVVLGADSRTTTGSYIANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASL   82 (205)
T ss_dssp             EEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHH
T ss_pred             EEEEEeCCEEEEEEcCCcccCcEEecCCcCceEEcCCCEEEEcCccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHH
Confidence            3445555 6 99999999999555566889999999999999999999999999999999999999999887        


Q ss_pred             ----------------------------------------------------------cCCCCCCCHHHHHHHHHHHHHH
Q 040809           88 ----------------------------------------------------------QDYKDDMTRQEAVQLALKVLRK  109 (161)
Q Consensus        88 ----------------------------------------------------------~~y~~~mt~eeai~la~~al~~  109 (161)
                                                                                +.|+++||++||++++++||..
T Consensus        83 l~~~~~~~~~p~~~~~lvaG~D~~~gp~ly~~d~~G~~~~~~~~a~Gsgs~~a~~~Le~~~~~~~s~eea~~l~~~al~~  162 (205)
T 1iru_H           83 FKEMCYRYREDLMAGIIIAGWDPQEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREGMTKEECLQFTANALAL  162 (205)
T ss_dssp             HHHHHHHTTTTCCEEEEEEEEETTTEEEEEEECTTSCCEECSEEEESGGGGGGHHHHHHHCCTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCcCccEEEEEEEEeCCCCCEEEEECCCCcEEecCEEEECCCHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Confidence                                                                      3589999999999999999999


Q ss_pred             hhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 040809          110 TMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLEN  150 (161)
Q Consensus       110 ~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~  150 (161)
                      +++++..++++++|++|++++.   .|++|+++||++++++
T Consensus       163 ~~~~d~~s~~~i~v~vi~~~g~---~~~~l~~~ei~~~~~~  200 (205)
T 1iru_H          163 AMERDGSSGGVIRLAAIAESGV---ERQVLLGDQIPKFAVA  200 (205)
T ss_dssp             HHHHBTTCCSCEEEEEEETTEE---EEEEECGGGSCCCCCC
T ss_pred             HHHhccccCCcEEEEEEeCCCe---EEEEeChHHhhHHHhh
Confidence            9999889999999999998752   5899999999888764

>3nzj_K Proteasome component PRE2; ubiquitin, protein degradation, N-terminal nucleophilic HYDR 19S regulatory particle; HET: TY5 TRO MES; 2.40A {Saccharomyces cerevisiae} PDB: 3nzw_K* 3nzx_K* 4b4t_5

Probab=99.92  E-value=1.3e-24  Score=174.22  Aligned_cols=133  Identities=15%  Similarity=0.159  Sum_probs=120.8

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +.-|.|. | |||+|+|.+.+.++.+++.+||++|++||+|++||+.+|++.+++++|.+++.|++++++++        
T Consensus        78 ~vgik~~dGVVlAaD~r~t~G~li~~~~~~KI~~I~d~i~~~~aG~~AD~~~l~~~lr~~~~~y~~~~~~~isv~~la~~  157 (287)
T 3nzj_K           78 TLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREKERISVAAASKI  157 (287)
T ss_dssp             EEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEECEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHH
T ss_pred             EEEEEECCEEEEEEccccccCceeecCCcceEEEEcCcEEEEecCCHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHH
Confidence            4444444 6 99999999987766677899999999999999999999999999999999999999999987        


Q ss_pred             -----------------------------------------------------------cCCCCCCCHHHHHHHHHHHHH
Q 040809           88 -----------------------------------------------------------QDYKDDMTRQEAVQLALKVLR  108 (161)
Q Consensus        88 -----------------------------------------------------------~~y~~~mt~eeai~la~~al~  108 (161)
                                                                                 +.|+++||++||++++++||.
T Consensus       158 ls~~l~~~r~~p~~v~~lvaG~D~~~gp~Ly~iDp~G~~~~~~~~AiGsgs~~a~~~Le~~y~~dms~eEAi~la~~aL~  237 (287)
T 3nzj_K          158 LSNLVYQYKGAGLSMGTMICGYTRKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSIL  237 (287)
T ss_dssp             HHHHHHHTTTSCCCEEEEEEEEETTTEEEEEEEETTCCEEECSEEEESTTHHHHHHHHHTSCCTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHhhcCCCceEEEEEEEEcCCCCCEEEEECCCceEEEcCeEEEecchHHHHHHHHHhhcCCCCHHHHHHHHHHHHH
Confidence                                                                       468999999999999999999


Q ss_pred             HhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhcccC
Q 040809          109 KTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFGVAQ  155 (161)
Q Consensus       109 ~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~~~~  155 (161)
                      .+.++|..++++++|++|+++     .|++++++||++++.++++++
T Consensus       238 ~a~~rD~~sg~~i~V~vItkd-----g~~~l~~~ev~~~l~~~~e~~  279 (287)
T 3nzj_K          238 AAAHRDAYSGGSVNLYHVTED-----GWIYHGNHDVGELFWKVKEEE  279 (287)
T ss_dssp             HHHHHBTTCCSEEEEEEEETT-----EEEEEEEEEHHHHHHHHHHHH
T ss_pred             HHHhhCcCCCCceEEEEEeCC-----CEEEeCHHHHHHHHHHHHHhh
Confidence            999999999999999999988     499999999999999887654

>3mi0_A Proteasome subunit alpha; enzyme inhibitors, lactones, proteasome endopeptidase comple mycobacterium tuberculosis, hydrolase; HET: SA6; 2.20A {Mycobacterium tuberculosis} SCOP: d.153.1.4 PDB: 3h6f_A 3krd_A* 3h6i_A* 3mka_A 2fhh_A* 2fhg_A 3hfa_D 3hf9_A 3mfe_D

Probab=99.91  E-value=4.4e-24  Score=168.01  Aligned_cols=125  Identities=26%  Similarity=0.342  Sum_probs=99.7

Q ss_pred             e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhC-CCc---------------
Q 040809           25 G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQ-EPI---------------   87 (161)
Q Consensus        25 G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~-~~i---------------   87 (161)
                      | |||+|+|        +++.+|||+|++||+|++||+.+|++.|.+.++..++.|+++|+ ++|               
T Consensus        38 gVVlaadkr--------~~~~~KI~~I~d~i~~~~aG~~aD~~~l~~~~~~~~~l~~~~~~~~~i~v~~la~~l~~~l~q  109 (248)
T 3mi0_A           38 GVLFVAENP--------SRSLQKISELYDRVGFAAAGKFNEFDNLRRGGIQFADTRGYAYDRRDVTGRQLANVYAQTLGT  109 (248)
T ss_dssp             EEEEEEECC--------CSSSCSEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHHHHHHH
T ss_pred             EEEEEEeCC--------CCCCCCeEEECCCEEEEEccCHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHH
Confidence            5 9999999        23789999999999999999999999999999999999999999 666               


Q ss_pred             -----------------------------------------------------------cCCCCCCCHHHHHHHHHHHHH
Q 040809           88 -----------------------------------------------------------QDYKDDMTRQEAVQLALKVLR  108 (161)
Q Consensus        88 -----------------------------------------------------------~~y~~~mt~eeai~la~~al~  108 (161)
                                                                                 ++|+++||++||++++++||+
T Consensus       110 ~yt~~~rP~gv~~liaG~D~~~~~~gp~Ly~~Dp~G~~~~e~~~~a~Gsgs~~a~~~Le~~y~~~mt~eeai~la~~aL~  189 (248)
T 3mi0_A          110 IFTEQAKPYEVELCVAEVAHYGETKRPELYRITYDGSIADEPHFVVMGGTTEPIANALKESYAENASLTDALRIAVAALR  189 (248)
T ss_dssp             HHHHSSSCCCEEEEEEECCCTTCCCCCEEEEECTTSCEEEESSEEEESSCHHHHHHHHHHHCCTTCCHHHHHHHHHHHHH
T ss_pred             HhccCCCCceEEEEEEEEcCCCCCCCCEEEEECCCeEEeecccEEEECccHHHHHHHHHhhcCCCCCHHHHHHHHHHHHH
Confidence                                                                       247899999999999999999


Q ss_pred             Hhh-------ccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhcccCCCCC
Q 040809          109 KTM-------DSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFGVAQPASE  159 (161)
Q Consensus       109 ~~~-------~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~~~~~~~~  159 (161)
                      .++       ++ .++++++||+||++++. .+.|++|+++||+++|+++...+-+.|
T Consensus       190 ~~~~~~~~~~~~-~~~~~~iev~vv~~~g~-~~~f~~l~~~ei~~~l~~~~~~~~~~~  245 (248)
T 3mi0_A          190 AGSADTSGGDQP-TLGVASLEVAVLDANRP-RRAFRRITGSALQALLVDQESPQSDGE  245 (248)
T ss_dssp             HC-------------CCTTEEEEEEETTSS-SCCEEECCHHHHHHTC-----------
T ss_pred             HHHhhcccCccc-ccCCCcEEEEEEECCCC-cccEEECCHHHHHHHHHHcCCCccccc
Confidence            999       44 68899999999999852 237999999999999998865544433

>3unf_H Proteasome subunit beta type-10; antigen presentation, drug development, protein degradation, hydrolase-hydrolase inhibitor complex; HET: 04C; 2.90A {Mus musculus} PDB: 3unh_H

Probab=99.90  E-value=9.4e-24  Score=164.81  Aligned_cols=122  Identities=16%  Similarity=0.172  Sum_probs=111.1

Q ss_pred             eeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc---------
Q 040809           19 YQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI---------   87 (161)
Q Consensus        19 ~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i---------   87 (161)
                      .-+-|. | |||+|+|.++++++.+++.+|||+|++||+|++||+.+|++.+++++|.+++.|++++++++         
T Consensus         4 vgi~~kdgVVlaaD~r~t~g~~v~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l   83 (234)
T 3unf_H            4 AGLVFRDGVILGADTRATNDSVVADKSCEKIHFIAPKIYCCGAGVAADTEMTTRMAASKMELHALSTGREPRVATVTRIL   83 (234)
T ss_dssp             EEEECSSEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHCSCCCHHHHHHHH
T ss_pred             EEEEeCCEEEEEECCCcccCCEeccCccccEEEecCCEEEEecccHHHHHHHHHHHHHHHHhhHHhcCCCCCHHHHHHHH
Confidence            345555 6 99999999999988877899999999999999999999999999999999999999999988         


Q ss_pred             --------------------------------------------------------cCCCCCCCHHHHHHHHHHHHHHhh
Q 040809           88 --------------------------------------------------------QDYKDDMTRQEAVQLALKVLRKTM  111 (161)
Q Consensus        88 --------------------------------------------------------~~y~~~mt~eeai~la~~al~~~~  111 (161)
                                                                              +.|+++||++||++++++||..++
T Consensus        84 ~~~l~~~~~p~~v~llvaG~D~~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~ms~eeA~~la~~al~~~~  163 (234)
T 3unf_H           84 RQTLFRYQGHVGASLVVGGVDLNGPQLYEVHPHGSYSRLPFTALGSGQGAAVALLEDRFQPNMTLEAAQELLVEAITAGI  163 (234)
T ss_dssp             HHHHHHTTTCSCEEEEEEEEETTEEEEEEECTTSCEEECSEEEEETTHHHHHHHHHHHCCSSCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCCCccEEEEEEEEeCCCCEEEEECCCCCEEeccEEEEcCCchhhHHHHHhccCCCCCHHHHHHHHHHHHHHHH
Confidence                                                                    358999999999999999999999


Q ss_pred             ccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHH
Q 040809          112 DSTSLTSEKLELAEVFLLPSGKVKYRICSPESLT  145 (161)
Q Consensus       112 ~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~  145 (161)
                      .+|..++++++|++|++++     ++.+++.+++
T Consensus       164 ~~D~~sg~~iev~vi~~dg-----~~~l~~~~i~  192 (234)
T 3unf_H          164 LSDLGSGGNVDACVITAGG-----AKLQRALSTP  192 (234)
T ss_dssp             HHBTTCCSCEEEEEEESSC-----EEEEEEEECC
T ss_pred             hhcCCCCCcEEEEEEECCC-----EEEeCceecc
Confidence            9988899999999999983     8888877764

>1iru_J 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_I* 3une_I 3unf_I* 3unh_I

Probab=99.89  E-value=2.4e-22  Score=153.37  Aligned_cols=119  Identities=10%  Similarity=0.170  Sum_probs=108.9

Q ss_pred             cCCCCc-eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc-
Q 040809           12 FSPEGR-LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI-   87 (161)
Q Consensus        12 fsp~Gr-l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i-   87 (161)
                      +...|. +.-|.+. | |||+|+|.++++++.+++.+|||+|++||+|++||+.+|++.|++++|.+++.|++.+++++ 
T Consensus         4 ~~~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~   83 (205)
T 1iru_J            4 MSYNGGAVMAMKGKNCVAIAADRRFGIQAQLVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFRLNLYELKEGRQIK   83 (205)
T ss_dssp             TTSSCCEEEEEECSSEEEEEEECCEEETTEEEESCCCCEEECSTTEEEECCSCHHHHHHHHHHHHHHHHHHHHHSSSCCC
T ss_pred             ccCCCCeEEEEEeCCEEEEEECCccccCCeEeecCCccEEEeCCCEEEEccccHHHHHHHHHHHHHHHHHHHhhcCCCCC
Confidence            334443 7888888 5 99999999999999887899999999999999999999999999999999999999999887 


Q ss_pred             --------------------------------------------------------------------cCCCCCCCHHHH
Q 040809           88 --------------------------------------------------------------------QDYKDDMTRQEA   99 (161)
Q Consensus        88 --------------------------------------------------------------------~~y~~~mt~eea   99 (161)
                                                                                          +.|+++||++||
T Consensus        84 v~~la~~l~~~~y~~r~~P~~v~~lvaG~D~~~~~p~Ly~idp~G~~~~~~~~~aiG~gs~~a~~~Le~~~~~~~s~eea  163 (205)
T 1iru_J           84 PYTLMSMVANLLYEKRFGPYYTEPVIAGLDPKTFKPFICSLDLIGCPMVTDDFVVSGTCAEQMYGMCESLWEPNMDPDHL  163 (205)
T ss_dssp             HHHHHHHHHHHHHTTTTSCCSCCCEEEEECTTSCCEEEEEECTTCCEEECSSEEEEETTHHHHHHHHHHHCCSSCCHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCCceEEEEEEEEeCCCCCeEEEEECCCCCccccCCeeEeeeCHHHHHHHHhcccCCCCCHHHH
Confidence                                                                                357899999999


Q ss_pred             HHHHHHHHHHhhccCCCCCCcEEEEEEEeCC
Q 040809          100 VQLALKVLRKTMDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus       100 i~la~~al~~~~~~~~~~~~~iei~ii~~~~  130 (161)
                      ++++++||..+++++..++++++|++|++++
T Consensus       164 ~~l~~~al~~~~~~d~~s~~~i~v~vi~~~g  194 (205)
T 1iru_J          164 FETISQAMLNAVDRDAVSGMGVIVHIIEKDK  194 (205)
T ss_dssp             HHHHHHHHHHHGGGBTTSCSCEEEEEEESSB
T ss_pred             HHHHHHHHHHHHHhCcccCCceEEEEEcCCC
Confidence            9999999999999988899999999999875

>1ryp_K 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_K 1g0u_J* 1jd2_J* 1g65_J 1vsy_K 1z7q_K 2f16_J* 2fak_J* 2fny_J* 2gpl_J* 2zcy_J* 3bdm_J* 3d29_J* 3dy3_J* 3dy4_J* 3e47_J* 3gpj_J* 3gpt_J* 3gpw_J* 3hye_J* ...

Probab=99.89  E-value=1.9e-22  Score=153.16  Aligned_cols=118  Identities=15%  Similarity=0.162  Sum_probs=106.9

Q ss_pred             eeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc---------
Q 040809           19 YQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI---------   87 (161)
Q Consensus        19 ~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i---------   87 (161)
                      .-|.+. | |||+|+|.++++++.+++.+|||+|++||+|++||+.+|++.|++++|.+++.|++++++++         
T Consensus         5 vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l   84 (198)
T 1ryp_K            5 LGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYIQANIQLYSIREDYELSPQAVSSFV   84 (198)
T ss_dssp             EEEECSSCEEEEEECCEEETTEEEESCCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHH
T ss_pred             EEEEECCEEEEEECCCcccCCEEEecCCCceEEeCCCEEEEeccCHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHH
Confidence            445555 5 89999999999988777899999999999999999999999999999999999999999877         


Q ss_pred             -------------------------------------------------------------cCCCCCCCHHHHHHHHHHH
Q 040809           88 -------------------------------------------------------------QDYKDDMTRQEAVQLALKV  106 (161)
Q Consensus        88 -------------------------------------------------------------~~y~~~mt~eeai~la~~a  106 (161)
                                                                                   +.|+++||++||++++++|
T Consensus        85 ~~~l~~~~~~r~p~~v~~lvaG~D~~~~~p~Ly~idp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s~eea~~l~~~a  164 (198)
T 1ryp_K           85 RQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQIDYLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLC  164 (198)
T ss_dssp             HHHHHHHTTSSSCCCEEEEEEEEETTTTEEEEEEECTTCCEEECSEEECTTHHHHHHHHHHHHCCTTCCHHHHHHHHHHH
T ss_pred             HHHHHHhcccCCCceEEEEEEEEeCCCCCcEEEEECCCCCEEECCEEEEcccHHHHHHHHHhhcCCCCCHHHHHHHHHHH
Confidence                                                                         3589999999999999999


Q ss_pred             HHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCH
Q 040809          107 LRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSP  141 (161)
Q Consensus       107 l~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~  141 (161)
                      |..+.+++..++++++|++|+++     +++++++
T Consensus       165 l~~~~~~d~~s~~~i~v~vi~~~-----g~~~~~~  194 (198)
T 1ryp_K          165 VQELEKRMPMDFKGVIVKIVDKD-----GIRQVDD  194 (198)
T ss_dssp             HHHHHHHCSBCCCCEEEEEEETT-----EEEEECC
T ss_pred             HHHHHHhCccCCCceEEEEEcCC-----CEEEecc
Confidence            99999998899999999999987     4777764

>1iru_M 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_L* 3une_L 3unf_L* 3unh_L

Probab=99.89  E-value=4.7e-22  Score=152.61  Aligned_cols=115  Identities=13%  Similarity=0.202  Sum_probs=106.5

Q ss_pred             CceeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc------
Q 040809           16 GRLYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI------   87 (161)
Q Consensus        16 Grl~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i------   87 (161)
                      +.+.-|.+. | |||+|+|.++++++.+++.+|||+|++||+|++||+.+|++.|++++|.+++.|++++++++      
T Consensus        10 tt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la   89 (213)
T 1iru_M           10 GTILAIAGEDFAIVASDTRLSEGFSIHTRDSPKCYKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMTTGAIA   89 (213)
T ss_dssp             CEEEEEEETTEEEEEEECCEEETTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             CcEEEEEeCCEEEEEECCCcccCCEEecCCCCcEEEcCCCEEEEccccHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHH
Confidence            348888888 6 99999999999998877899999999999999999999999999999999999999999877      


Q ss_pred             -------------------------------------------------------------cC---------CCCCCCHH
Q 040809           88 -------------------------------------------------------------QD---------YKDDMTRQ   97 (161)
Q Consensus        88 -------------------------------------------------------------~~---------y~~~mt~e   97 (161)
                                                                                   +.         |+++||++
T Consensus        90 ~~l~~~~y~~r~~P~~v~~lvaG~D~~g~p~Ly~id~~G~~~~~~~~aiGsg~~~a~~~Le~~~~~~~~~~~~~~~~s~e  169 (213)
T 1iru_M           90 AMLSTILYSRRFFPYYVYNIIGGLDEEGKGAVYSFDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVEHVPLSLD  169 (213)
T ss_dssp             HHHHHHHHHTTTSCCCEEEEEEEECTTSCEEEEEECTTSCEEEESEEEEETTHHHHHHHHHHHTTCCSCSSCCCCCCCHH
T ss_pred             HHHHHHHHhhCCCCceEEEEEEEEcCCCCEEEEEECCCCCEEECCEEEEeeCHHHHHHHHhhccccccccccCCCCCCHH
Confidence                                                                         23         88999999


Q ss_pred             HHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCC
Q 040809           98 EAVQLALKVLRKTMDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus        98 eai~la~~al~~~~~~~~~~~~~iei~ii~~~~  130 (161)
                      ||++++++||..+.+++..++++++|++|++++
T Consensus       170 ea~~l~~~al~~~~~~d~~s~~~i~v~vi~~~g  202 (213)
T 1iru_M          170 RAMRLVKDVFISAAERDVYTGDALRICIVTKEG  202 (213)
T ss_dssp             HHHHHHHHHHHHHHHHBTTSCSEEEEEEEETTE
T ss_pred             HHHHHHHHHHHHHHHhCCccCCcEEEEEEcCCC
Confidence            999999999999999988999999999999874

>1ryp_J 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_I* 1g65_I 1vsy_J 2f16_I* 2fak_I* 2fny_I* 2gpl_I* 3d29_I* 3dy3_I* 3dy4_I* 3e47_I* 3gpj_I* 3gpt_I* 3gpw_I* 3hye_I* 3l5q_N 3mg0_I* 3mg4_I* 3oeu_I* 3oev_I* ...

Probab=99.88  E-value=5.8e-22  Score=151.18  Aligned_cols=119  Identities=16%  Similarity=0.178  Sum_probs=109.2

Q ss_pred             ccCCCCc-eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc
Q 040809           11 VFSPEGR-LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI   87 (161)
Q Consensus        11 ~fsp~Gr-l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i   87 (161)
                      +|+..|. +.-|.+. | |||+|+|.++++++.+++.+|||+|+ ||+|++||+.+|++.|++++|.+++.|++++++++
T Consensus         3 ~~~~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~-~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~   81 (204)
T 1ryp_J            3 PSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYG-HVFLGITGLATDVTTLNEMFRYKTNLYKLKEERAI   81 (204)
T ss_dssp             GGGSSCCEEEEEECSSEEEEEEECCEEETTEEEESCCCCEEEET-TEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCC
T ss_pred             CcCCCCCeEEEEEeCCEEEEEEcCCcccCCEEeeCCcceEEEeC-CEEEEeeEcHHHHHHHHHHHHHHHHHHhhccCCCC
Confidence            4555554 8888888 5 99999999999999888899999999 99999999999999999999999999999999887


Q ss_pred             ---------------------------------------------------------------------cCCCCCCCHHH
Q 040809           88 ---------------------------------------------------------------------QDYKDDMTRQE   98 (161)
Q Consensus        88 ---------------------------------------------------------------------~~y~~~mt~ee   98 (161)
                                                                                           +.|+++||++|
T Consensus        82 ~v~~la~~l~~~~y~~~~~P~~v~~lvaG~D~~~~gp~Ly~idp~G~~~~~~~~~aiG~gs~~a~~~Le~~~~~~~s~ee  161 (204)
T 1ryp_J           82 EPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPFIAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPED  161 (204)
T ss_dssp             CHHHHHHHHHHHHHTTTTSCCCEEEEEEEECTTTCCEEEEEECTTCCEECCSSEEEEETTHHHHHHHHHHHCCSSCCHHH
T ss_pred             CHHHHHHHHHHHHHHhcCCCceEEEEEEEEeCCCCceEEEEECCCCCccccCceeEeccCHHHHHHHHhhhcCCCcCHHH
Confidence                                                                                 35789999999


Q ss_pred             HHHHHHHHHHHhhccCCCCCCcEEEEEEEeCC
Q 040809           99 AVQLALKVLRKTMDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus        99 ai~la~~al~~~~~~~~~~~~~iei~ii~~~~  130 (161)
                      |++++++||..+++++..++++++|++|++++
T Consensus       162 a~~l~~~al~~~~~~d~~s~~~i~v~vi~~~g  193 (204)
T 1ryp_J          162 LFETISQALLNAADRDALSGWGAVVYIIKKDE  193 (204)
T ss_dssp             HHHHHHHHHHHHHTTBTTSCSCEEEEEEESSC
T ss_pred             HHHHHHHHHHHHHHhCcccCCcEEEEEEcCCC
Confidence            99999999999999988999999999999875

>1q5q_H Proteasome beta-type subunit 1; proteasome assembly, Pro-peptide, inter-subunit contacts, RH erythropolis, hydrolase; 2.60A {Rhodococcus erythropolis} SCOP: d.153.1.4

Probab=99.88  E-value=3.7e-22  Score=155.66  Aligned_cols=135  Identities=22%  Similarity=0.252  Sum_probs=115.6

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +.-|-+. | |||+|+|.+++.++.+++.+|||+|++||+|++||+.+|++.|++++|.+++.|+++|++++        
T Consensus         3 ~vgi~~~dgVVlaaD~r~~~g~l~~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~   82 (235)
T 1q5q_H            3 IVALTYKGGVLLAGDRRATQGNLIASRDVEKVYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEGVPLTFDGKANR   82 (235)
T ss_dssp             EEEEECSSCEEEEECCCEEETTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHH
T ss_pred             EEEEEECCEEEEEECCCCCcCCEEecCCcCcEEEeCCcEEEEcCCcHHHHHHHHHHHHHHHHHhHHHhCCCCCHHHHHHH
Confidence            3455566 5 99999999986555556899999999999999999999999999999999999999988877        


Q ss_pred             ---------------------------------------------------------------------cCCCCCCCHHH
Q 040809           88 ---------------------------------------------------------------------QDYKDDMTRQE   98 (161)
Q Consensus        88 ---------------------------------------------------------------------~~y~~~mt~ee   98 (161)
                                                                                           +.|+++||++|
T Consensus        83 l~~~~~~~~~~~~rp~~v~~lvaG~D~~~g~~~~~p~Ly~idp~G~~~~~~~~~~aiGsgs~~a~~~Le~~~~~~ms~ee  162 (235)
T 1q5q_H           83 LASMVRGNLGAAMQGLAVVPLLVGYDLDADDESRAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALKKIYSPDSDEET  162 (235)
T ss_dssp             HHHHHHTTHHHHTTTCCEEEEEEEECTTCSSTTSCEEEEEECTTSCEEECCSSEEEESTTHHHHHHHHHHHCCTTCCHHH
T ss_pred             HHHHHHHHHHhhhcccceEEEEEEEECCCCccCCCCEEEEECCCCceEEeCCCeEEECCCHHHHHHHHHhhcCCCCCHHH
Confidence                                                                                 23689999999


Q ss_pred             HHHHHHHHHHHhhccCCCCCC--cE-----EEEEEEeCCCCceeEEECCHHHHHHHHHHhcccCCC
Q 040809           99 AVQLALKVLRKTMDSTSLTSE--KL-----ELAEVFLLPSGKVKYRICSPESLTMLLENFGVAQPA  157 (161)
Q Consensus        99 ai~la~~al~~~~~~~~~~~~--~i-----ei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~~~~~~  157 (161)
                      |++++++||..++++|..++.  ++     +|++|+++     .|++++++|+++++.++.+++.+
T Consensus       163 A~~la~~al~~a~~~d~~sg~~~~i~~~~~ev~vi~~~-----g~~~l~~~ei~~~~~~~~~~~~~  223 (235)
T 1q5q_H          163 ALRAAIESLYDAADDDSATGGPDLTRGIYPTAVTITQA-----GAVHVSEETTSELARRIVAERTE  223 (235)
T ss_dssp             HHHHHHHHHHHHHHHCTTTCCCBTTTTBCCEEEEEETT-----EEEECCHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhhCcccCCcccccccccEEEEEeCC-----CeEEeCHHHHHHHHHHHHHHHhh
Confidence            999999999999998777664  23     99999976     49999999999999998665443

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

Probab=99.88  E-value=3.4e-22  Score=160.51  Aligned_cols=124  Identities=17%  Similarity=0.165  Sum_probs=96.3

Q ss_pred             e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc----------------
Q 040809           25 G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI----------------   87 (161)
Q Consensus        25 G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i----------------   87 (161)
                      | |||+|+|.+++.++.+++.+|||+|++||+|++||+.+|++.|++++|.+++.|++.+++++                
T Consensus        68 GVVlAaD~r~t~g~li~~~~~~KI~~i~d~i~~~~aG~~aD~~~l~~~lr~~~~~y~~~~~~~i~v~~la~~la~~l~~~  147 (291)
T 2jay_A           68 GVVMAGDRRSTQGNMISGRDVRKVYITDDYTATGIAGTAAVAVEFARLYAVELEHYEKLEGVPLTFAGKINRLAIMVRGN  147 (291)
T ss_dssp             EEEEEECCC--------CCCCCCEEEEETTEEEEEESCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHTC
T ss_pred             EEEEEECCCccCCCeeecCCcccEEEeCCcEEEEEcccHHHHHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHHh
Confidence            5 99999999998777777899999999999999999999999999999999999999988877                


Q ss_pred             -------------------------------------------------------------cCCCCCCCHHHHHHHHHHH
Q 040809           88 -------------------------------------------------------------QDYKDDMTRQEAVQLALKV  106 (161)
Q Consensus        88 -------------------------------------------------------------~~y~~~mt~eeai~la~~a  106 (161)
                                                                                   +.|+++||++||++++++|
T Consensus       148 ~~~~~rpf~v~~lvaG~D~~g~~~~~~p~Ly~iDp~G~~~e~~~~~~aiGsgs~~a~~~Le~~~~~~ms~eEAi~la~~a  227 (291)
T 2jay_A          148 LAAAMQGLLALPLLAGYDIHASDPQSAGRIVSFDAAGGWNIEEEGYQAVGSGSLFAKSSMKKLYSQVTDGDSGLRVAVEA  227 (291)
T ss_dssp             HHHHHHTCCCEEEEEEECTTCSCSTTCEEEEEECTTSCEEECSSSEEEESTTHHHHHHHHHHHGGGCCSHHHHHHHHHHH
T ss_pred             hhhhccccceeEEEEEEeCCCCcCCCCCEEEEECCCCcEEecCCCEEEEecCHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Confidence                                                                         2367999999999999999


Q ss_pred             HHHhhccCCCCCCcE--------EEEEEEeCCCCceeEEECCHHHHHHHHHHhccc
Q 040809          107 LRKTMDSTSLTSEKL--------ELAEVFLLPSGKVKYRICSPESLTMLLENFGVA  154 (161)
Q Consensus       107 l~~~~~~~~~~~~~i--------ei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~~~  154 (161)
                      |..++++|..++ ++        +|++|+++     .|++++++||++++..+.++
T Consensus       228 L~~a~~~D~~sg-~~e~vr~~~~~v~vi~~d-----g~~~l~~~ei~~~~~~~~~~  277 (291)
T 2jay_A          228 LYDAADDDSATG-GPDLVRGIFPTAVIIDAD-----GAVDVPESRIAELARAIIES  277 (291)
T ss_dssp             HHHC-----------------CCEEEEEETT-----EEEECCHHHHHHHHHHC---
T ss_pred             HHHHHhhCCCCC-CcccccccCCEEEEEECC-----CeEEcCHHHHHHHHHHHHHh
Confidence            999999876655 44        69999987     49999999999999988554

>1ryp_I 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1g0u_H* 1jd2_H* 1g65_H 1vsy_I 1z7q_I 2f16_H* 2fak_H* 2fny_H* 2gpl_H* 3d29_H* 3dy3_H* 3dy4_H* 3e47_H* 3gpj_H* 3gpt_H* 3gpw_H* 3hye_H* 3l5q_M 3mg0_H* 3mg4_H* ...

Probab=99.88  E-value=2.4e-22  Score=155.52  Aligned_cols=113  Identities=15%  Similarity=0.247  Sum_probs=103.8

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +.-|.+. | |||+|+|.++++++.+++.+||++|++||+|++||+.+|++.|++++|.+++.|++++++++        
T Consensus         3 ~vgi~~~dgVvlaaD~r~t~g~~~~~~~~~KI~~i~d~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a~~   82 (222)
T 1ryp_I            3 IVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQM   82 (222)
T ss_dssp             EEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHH
T ss_pred             EEEEEECCEEEEEEcCCcccCCeeecCCcccEEEecCCEEEEecccHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            3445565 5 99999999999988887899999999999999999999999999999999999999999987        


Q ss_pred             ---------------------------------------------------------cCCCCCCCHHHHHHHHHHHHHHh
Q 040809           88 ---------------------------------------------------------QDYKDDMTRQEAVQLALKVLRKT  110 (161)
Q Consensus        88 ---------------------------------------------------------~~y~~~mt~eeai~la~~al~~~  110 (161)
                                                                               +.|+++||++||++++++||..+
T Consensus        83 l~~~l~~~~~p~~v~~lvaG~D~~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~ms~eeA~~la~~al~~~  162 (222)
T 1ryp_I           83 LKQHLFKYQGHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKLASDAIQAG  162 (222)
T ss_dssp             HHHHHHHTTTCSCEEEEEEEEETTEEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHHCCSSCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHhhcCCCCCeeEEEEEEeCCCCEEEEECCCCCEEecCEEEECCCHHHHHHHHHhhCCCCcCHHHHHHHHHHHHHHH
Confidence                                                                     35899999999999999999999


Q ss_pred             hccCCCCCCcEEEEEEEeCC
Q 040809          111 MDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus       111 ~~~~~~~~~~iei~ii~~~~  130 (161)
                      +++|..++++++|++|++++
T Consensus       163 ~~~d~~sg~~i~v~vi~~~g  182 (222)
T 1ryp_I          163 IWNDLGSGSNVDVCVMEIGK  182 (222)
T ss_dssp             HHHCTTCCSCEEEEEEETTS
T ss_pred             HhccccCCCcEEEEEEECCC
Confidence            99988899999999999874

>1ryp_M 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_M* 1jd2_L* 1g65_L 1vsy_M 1z7q_M 2f16_L* 2fak_L* 2fny_L* 2gpl_L* 3d29_L* 3dy3_L* 3dy4_L* 3e47_L* 3gpj_L* 3gpt_L* 3gpw_L* 3hye_L* 3l5q_Q 3mg0_L* 3mg4_L* ...

Probab=99.88  E-value=5.8e-22  Score=153.26  Aligned_cols=115  Identities=13%  Similarity=0.216  Sum_probs=106.6

Q ss_pred             CceeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhC-CCc-----
Q 040809           16 GRLYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQ-EPI-----   87 (161)
Q Consensus        16 Grl~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~-~~i-----   87 (161)
                      +.+.-|.+. | |||+|+|.++++++.+++.+|||+|++||+|++||+.+|++.|++++|.+++.|+++++ +++     
T Consensus        10 tt~vgi~~~dgVvlaaD~r~~~g~~i~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~v~~l   89 (222)
T 1ryp_M           10 GTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKLSINSA   89 (222)
T ss_dssp             CEEEEEECSSCEEEEEECCEEETTEEEESCCCCCEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHTTTCCCCHHHH
T ss_pred             ccEEEEEeCCEEEEEEecccccCCEecCCCcCcEEEeCCCEEEEccccHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHH
Confidence            348888888 5 99999999999988777899999999999999999999999999999999999999999 877     


Q ss_pred             --------------------------------------------------------------cC----------------
Q 040809           88 --------------------------------------------------------------QD----------------   89 (161)
Q Consensus        88 --------------------------------------------------------------~~----------------   89 (161)
                                                                                    +.                
T Consensus        90 a~~l~~~ly~~r~~P~~v~~ivaG~D~~g~p~Ly~~dp~G~~~~~~~~a~Gsg~~~a~~~Le~~~~~~~~~~~~~~~~~~  169 (222)
T 1ryp_M           90 ARNIQHLLYGKRFFPYYVHTIIAGLDEDGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYEPGTNGKVK  169 (222)
T ss_dssp             HHHHHHHHHTTTTSCCCEEEEEEEECTTSCEEEEEECTTSCEEEESEEEEETTHHHHHHHHHHHTSCTTCBCTTSTTCSB
T ss_pred             HHHHHHHHHhcCCCCceEEEEEEEEcCCCCeEEEEECCCcCEEecCEEEEcCcHHHHHHHHhcccccccccccccccccc
Confidence                                                                          12                


Q ss_pred             -CCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCC
Q 040809           90 -YKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus        90 -y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~  130 (161)
                       |+++||+|||++++++||..+.+++..++++++|++|++++
T Consensus       170 ~~~~~~s~eeA~~la~~al~~a~~rd~~sg~~i~v~vi~~~g  211 (222)
T 1ryp_M          170 KPLKYLSVEEVIKLVRDSFTSATERHIQVGDGLEILIVTKDG  211 (222)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTE
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHHhcccCCCcEEEEEEcCCC
Confidence             88999999999999999999999998999999999999874

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

Probab=99.88  E-value=1.2e-21  Score=157.57  Aligned_cols=135  Identities=21%  Similarity=0.243  Sum_probs=114.9

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +.-|-|. | |||+|+|.+++.++.+++.+|||+|++||+|++||+.+|++.|++++|.+++.|+++|++++        
T Consensus        68 iVgIk~kdGVVlAaD~r~t~G~li~~~~~~KI~~I~~~i~~~~aG~~aD~~~l~~~~r~~~~~y~~~~g~~isv~~la~~  147 (294)
T 1q5r_H           68 IVALTYKGGVLLAGDRRATQGNLIASRDVEAVYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEGVPLTFDGKANR  147 (294)
T ss_dssp             EEEEECSSCEEEEECCCEEETTEEEESCCCCEEEEETTEEEEEEEBHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHH
T ss_pred             EEEEEECCEEEEEEcCccccCceeecCCcceEEEECCcEEEEEeecHHHHHHHHHHHHHHHHHhhHhhCCCCCHHHHHHH
Confidence            5555555 5 99999999986555556899999999999999999999999999999999999999988877        


Q ss_pred             ---------------------------------------------------------------------cCCCCCCCHHH
Q 040809           88 ---------------------------------------------------------------------QDYKDDMTRQE   98 (161)
Q Consensus        88 ---------------------------------------------------------------------~~y~~~mt~ee   98 (161)
                                                                                           +.|+++||++|
T Consensus       148 la~~l~~~~~~~~rp~~v~lLvaG~D~~~g~~~~~p~Ly~iDp~G~~~e~~~~~~AiGsgs~~a~~~Le~~y~~~ms~eE  227 (294)
T 1q5r_H          148 LASMVRGNLGAAMQGLAVVPLLVGYDLDADDESRAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALKKIYSPDSDEET  227 (294)
T ss_dssp             HHHHHHHHHHHHTTTTCEEEEEEEECTTCSCTTSCEEEEEECSSSCEEECCSSEEEESTTHHHHHHHHHHHCCSSCCHHH
T ss_pred             HHHHHHHHHhhhcCCcceEEEEEEEeCCCCcCCCCCEEEEECCCCeEEecCCCeEEEecCcHHHHHHHHHhccCCCCHHH
Confidence                                                                                 24679999999


Q ss_pred             HHHHHHHHHHHhhccCCCCCC--cE-----EEEEEEeCCCCceeEEECCHHHHHHHHHHhcccCCC
Q 040809           99 AVQLALKVLRKTMDSTSLTSE--KL-----ELAEVFLLPSGKVKYRICSPESLTMLLENFGVAQPA  157 (161)
Q Consensus        99 ai~la~~al~~~~~~~~~~~~--~i-----ei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~~~~~~  157 (161)
                      |++++++||..++++|..++.  ++     +|++|+++     .|++++++||++++.++.++..+
T Consensus       228 Ai~la~~aL~~a~~rD~~sG~~~~ir~i~~ev~vI~~~-----g~~~l~~~ei~~~l~~i~~~~~~  288 (294)
T 1q5r_H          228 ALRAAIESLYDAADDDSATGGPDLTRGIYPTAVTITQA-----GAVHVSEETTSELARRIVAERTE  288 (294)
T ss_dssp             HHHHHHHHHHHHHHHCTTTCCCBTTTTBCCEEEEEETT-----EEEECCHHHHHHHHHHHCC----
T ss_pred             HHHHHHHHHHHHHhhccccCCchhhcccCCEEEEEECC-----CEEEcCHHHHHHHHHHHHHHhhh
Confidence            999999999999998777653  36     99999976     49999999999999999666543

>3nzj_H Proteasome component PUP1; ubiquitin, protein degradation, N-terminal nucleophilic HYDR 19S regulatory particle; HET: TY5 TRO MES; 2.40A {Saccharomyces cerevisiae} PDB: 3nzw_H* 3nzx_H* 4b4t_2

Probab=99.88  E-value=9e-22  Score=155.86  Aligned_cols=114  Identities=15%  Similarity=0.244  Sum_probs=105.2

Q ss_pred             ceeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc-------
Q 040809           17 RLYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI-------   87 (161)
Q Consensus        17 rl~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i-------   87 (161)
                      .+.-|.|. | |||+|+|.+++.++.+++.+|||+|++||+|++||+.+|++.+++++|.+++.|++++++++       
T Consensus        31 Tivgi~~kdGVVlAaD~r~t~g~li~~~~~~KI~~I~d~i~~~~aG~~aD~~~l~~~lr~~~~~~~~~~~~~~~v~~~a~  110 (261)
T 3nzj_H           31 TIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQ  110 (261)
T ss_dssp             CEEEEEETTEEEEEEECCEEETTEEEETTCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHH
T ss_pred             eEEEEEECCEEEEEEcCCcccCCeeccCCcceEEEEcCCEEEEeccCHHHHHHHHHHHHHHHHHhHHhhCCCCCHHHHHH
Confidence            46666666 6 99999999998777777899999999999999999999999999999999999999999887       


Q ss_pred             ----------------------------------------------------------cCCCCCCCHHHHHHHHHHHHHH
Q 040809           88 ----------------------------------------------------------QDYKDDMTRQEAVQLALKVLRK  109 (161)
Q Consensus        88 ----------------------------------------------------------~~y~~~mt~eeai~la~~al~~  109 (161)
                                                                                +.|+++||+|||++++++||..
T Consensus       111 ~l~~~l~~~~~~~gv~llvaG~D~~Gp~Ly~iDp~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~ms~eEA~~la~~al~~  190 (261)
T 3nzj_H          111 MLKQHLFKYQGHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKLASDAIQA  190 (261)
T ss_dssp             HHHHHHHHTTTCSCEEEEEEEEETTEEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHHCCSSCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCcccEEEEEEEEeCCCCEEEEECCCccEEecCeEEeccchHHHHHHHHHHhccCCCHHHHHHHHHHHHHH
Confidence                                                                      3689999999999999999999


Q ss_pred             hhccCCCCCCcEEEEEEEeCC
Q 040809          110 TMDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus       110 ~~~~~~~~~~~iei~ii~~~~  130 (161)
                      ++.+|..++++++|++|++++
T Consensus       191 a~~rD~~sg~~iev~vI~kdg  211 (261)
T 3nzj_H          191 GIWNDLGSGSNVDVCVMEIGK  211 (261)
T ss_dssp             HHHHCTTCCSCEEEEEEETTS
T ss_pred             HHhhCCCCCCcEEEEEEECCC
Confidence            999988899999999999985

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

Probab=99.88  E-value=1.6e-22  Score=157.45  Aligned_cols=128  Identities=15%  Similarity=0.153  Sum_probs=114.5

Q ss_pred             CceeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHH-----HhCCCc-
Q 040809           16 GRLYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAY-----AYQEPI-   87 (161)
Q Consensus        16 Grl~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~-----~~~~~i-   87 (161)
                      +.+.-|.+. | |||+|+|.+.+.++.+++.+|||+|++||+|++||+.+|++.|++++|.+++.|++     .+++++ 
T Consensus         9 tt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   88 (233)
T 1ryp_N            9 TSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLADAEEALE   88 (233)
T ss_dssp             CCEEEEEETTEEEEEEECCEEETTEEEESCCCCEEEETTTEEEEEEEEHHHHHHHHHHHHHHHHHHHTTCTTTTTTTSCC
T ss_pred             ceEEEEEECCEEEEEEcCccccCCeeecCCcCceEEeCCCEEEEccccHHHHHHHHHHHHHHHHHHhhccchhhcCCCCC
Confidence            346677777 5 99999999987666666899999999999999999999999999999999999999     899887 


Q ss_pred             --------------------------------------------------------------------cCCCC-----CC
Q 040809           88 --------------------------------------------------------------------QDYKD-----DM   94 (161)
Q Consensus        88 --------------------------------------------------------------------~~y~~-----~m   94 (161)
                                                                                          +.|++     +|
T Consensus        89 v~~la~~l~~~ly~~r~~~~P~~v~~lvaG~D~~~gp~Ly~id~~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~~~~~m  168 (233)
T 1ryp_N           89 PSYIFEYLATVMYQRRSKMNPLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFGAHMANPLLRKVVDRESDIPKT  168 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCCCEEEEEEEECTTSCEEEEEEETTCCEECCSEEECTHHHHHHHHHHTTTCSSGGGGGGC
T ss_pred             HHHHHHHHHHHHHHhcCCCCCceEEEEEEEEcCCCCEEEEEECCCcCeEEcCEEEECcCHHHHHHHHHHhhccccccCCC
Confidence                                                                                36788     99


Q ss_pred             CHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHH
Q 040809           95 TRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTML  147 (161)
Q Consensus        95 t~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~  147 (161)
                      |++||++++++||..+++++..++.+++|++|+++.    .++.++++||+++
T Consensus       169 s~eea~~la~~al~~~~~rd~~sg~~i~v~vi~~~~----g~~~~~~~~i~~~  217 (233)
T 1ryp_N          169 TVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKNT----GLTFKKNLQVENM  217 (233)
T ss_dssp             CHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTT----EEEEEEEEECCSC
T ss_pred             CHHHHHHHHHHHHHHHHHhcccCCCcEEEEEEECCC----CeEEcChHhcccc
Confidence            999999999999999999998999999999999874    4899998888765

>1iru_I 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_H* 3une_H

Probab=99.87  E-value=7.5e-22  Score=153.90  Aligned_cols=119  Identities=16%  Similarity=0.231  Sum_probs=106.8

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +.-|.+. | |||+|+|.++++++.+++.+|||+|++||+|++||+.+|++.+++++|.+++.|++.+++++        
T Consensus         3 ivgi~~~dgVVlaaD~r~t~g~~~~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~   82 (234)
T 1iru_I            3 IAGVVYKDGIVLGADTRATEGMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGRLPRVVTANRM   82 (234)
T ss_dssp             EEEEEETTEEEEEECCCEESSSBEEESSCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHCSCCCHHHHHHH
T ss_pred             EEEEEeCCEEEEEEcCCcccCceeccCcccceEEecCCEEEEecCcHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHH
Confidence            3445565 6 99999999999988877889999999999999999999999999999999999999999987        


Q ss_pred             ---------------------------------------------------------cCCCCCCCHHHHHHHHHHHHHHh
Q 040809           88 ---------------------------------------------------------QDYKDDMTRQEAVQLALKVLRKT  110 (161)
Q Consensus        88 ---------------------------------------------------------~~y~~~mt~eeai~la~~al~~~  110 (161)
                                                                               +.|+++||++||++++++||..+
T Consensus        83 l~~~l~~~~~~~~v~llvaG~D~~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~ms~eeA~~la~~al~~a  162 (234)
T 1iru_I           83 LKQMLFRYRGYIGAALVLGGVDVTGPHLYSIYPHGSTDKLPYVTMGSGSLAAMAVFEDKFRPDMEEEEAKNLVSEAIAAG  162 (234)
T ss_dssp             HHHHHHHTTTCSCEEEEEEEECSSCEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHSCCTTCCHHHHHTHHHHHHHHH
T ss_pred             HHHHHHhcCCCCceeEEEEEEcCCCCEEEEECCCCCEEecCEEEECCchHHHHHHHHHhccCCCCHHHHHHHHHHHHHHH
Confidence                                                                     36899999999999999999999


Q ss_pred             hccCCCCCCcEEEEEEEeCCCCceeEEECCH
Q 040809          111 MDSTSLTSEKLELAEVFLLPSGKVKYRICSP  141 (161)
Q Consensus       111 ~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~  141 (161)
                      ++++..++++++|++|+++     .++.+.+
T Consensus       163 ~~~d~~sg~~i~v~vi~k~-----g~~~~~~  188 (234)
T 1iru_I          163 IFNDLGSGSNIDLCVISKN-----KLDFLRP  188 (234)
T ss_dssp             HHHCTTCCSCEEEEEEETT-----EEECCSE
T ss_pred             HHhcccCCCCEEEEEEECC-----cEEEEcc
Confidence            9998888999999999987     3555543

>1iru_N 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_M* 3une_M 3unf_M* 3unh_M

Probab=99.87  E-value=2e-22  Score=155.40  Aligned_cols=127  Identities=12%  Similarity=0.097  Sum_probs=112.5

Q ss_pred             CceeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHH-HhCCCc-----
Q 040809           16 GRLYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAY-AYQEPI-----   87 (161)
Q Consensus        16 Grl~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~-~~~~~i-----   87 (161)
                      +.+.-|.+. | |||+|+|.+++.++.+++.+|||+|++||+|++||+.+|++.|++++|.+++.|++ .+++++     
T Consensus         9 tt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~v~~l   88 (219)
T 1iru_N            9 TSVLGVKFEGGVVIAADMLGSYGSLARFRNISRIMRVNNSTMLGASGDYADFQYLKQVLGQMVIDEELLGDGHSYSPRAI   88 (219)
T ss_dssp             CCCEEEEETTEEEEEEECCEEETTEEEECSCCCEEEETTTEEEEEEEEHHHHHHHHHHHHHHHHHHHHHCSSCCCCHHHH
T ss_pred             ceEEEEEeCCEEEEEECCccccCcEEecCCCCceEEeCCCEEEEeccCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHH
Confidence            346667777 5 99999999986666556899999999999999999999999999999999999998 888887     


Q ss_pred             ---------------------------------------------------------------cCCCC--CCCHHHHHHH
Q 040809           88 ---------------------------------------------------------------QDYKD--DMTRQEAVQL  102 (161)
Q Consensus        88 ---------------------------------------------------------------~~y~~--~mt~eeai~l  102 (161)
                                                                                     +.|++  +||++||+++
T Consensus        89 a~~l~~~ly~~r~~~~P~~v~~lvaG~D~~gp~Ly~id~~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~~mt~eea~~l  168 (219)
T 1iru_N           89 HSWLTRAMYSRRSKMNPLWNTMVIGGYADGESFLGYVDMLGVAYEAPSLATGYGAYLAQPLLREVLEKQPVLSQTEARDL  168 (219)
T ss_dssp             HHHHHHHHHHHHHTTCCCCEEEEEEEEETTEEEEEEECSSCCEEECSEEECTTHHHHTHHHHHHHHTSCSCCCHHHHHHH
T ss_pred             HHHHHHHHHHhcccCCCceEEEEEEEEECCCCEEEEECCCCCeEECCeEEECccHHHHHHHHHhhcCCCCCCCHHHHHHH
Confidence                                                                           24678  9999999999


Q ss_pred             HHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHH
Q 040809          103 ALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTML  147 (161)
Q Consensus       103 a~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~  147 (161)
                      +++||..+++++..++++++|++|+++     .++.++++||+..
T Consensus       169 ~~~al~~~~~~d~~sg~~i~v~vi~~~-----g~~~~~~~~i~~~  208 (219)
T 1iru_N          169 VERCMRVLYYRDARSYNRFQTATVTEK-----GVEIEGPLSTETN  208 (219)
T ss_dssp             HHHHHHHHHHHBTTCCSCEEEEEEETT-----EEEEEEEECCCCC
T ss_pred             HHHHHHHHHHhcCcCCCcEEEEEEcCC-----CEEEcCCeeccch
Confidence            999999999998899999999999987     4899998887653

>1ryp_H 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 3nzj_N* 3nzw_N* 3nzx_N* 1vsy_H 3l5q_B 1g65_N* 1fnt_H 1g0u_N* 1jd2_N* 1z7q_H 2f16_N* 2fak_N* 2fny_N* 2gpl_N* 2zcy_N* 3bdm_N* 3d29_N* 3dy3_N* 3dy4_N* 3e47_N* ...

Probab=99.87  E-value=2.3e-21  Score=148.03  Aligned_cols=114  Identities=13%  Similarity=0.323  Sum_probs=104.3

Q ss_pred             CceeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc------
Q 040809           16 GRLYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI------   87 (161)
Q Consensus        16 Grl~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i------   87 (161)
                      +.+.-|.+. | |||+|+|.+++.++.+++.+||++|++||+|++||+.+|++.+++++|.+++.|++++++ +      
T Consensus        10 tt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~-~~v~~la   88 (205)
T 1ryp_H           10 ASIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKIWCCRSGSAADTQAIADIVQYHLELYTSQYGT-PSTETAA   88 (205)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEEBHHHHHHHHHHHHHHHHHHHHHHSS-CCHHHHH
T ss_pred             ceEEEEEeCCEEEEEEcCCcccCcEEEcCCcCceEEcCCCEEEEccCCHHHHHHHHHHHHHHHHHHHHHhCC-CCHHHHH
Confidence            447778887 5 999999999986666668899999999999999999999999999999999999999998 7      


Q ss_pred             ------------------------------------------------------------cCCCCCCCHHHHHHHHHHHH
Q 040809           88 ------------------------------------------------------------QDYKDDMTRQEAVQLALKVL  107 (161)
Q Consensus        88 ------------------------------------------------------------~~y~~~mt~eeai~la~~al  107 (161)
                                                                                  +.|+++||++||++++++||
T Consensus        89 ~~l~~~~~~~~~~~~~~~lvaG~D~~~gp~Ly~id~~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~s~eea~~l~~~al  168 (205)
T 1ryp_H           89 SVFKELCYENKDNLTAGIIVAGYDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSL  168 (205)
T ss_dssp             HHHHHHHHHTTTTCCEEEEEEEEETTTEEEEEEECTTSCCEEESEEEESGGGGGGHHHHHHHCCTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhcCceEEEEEEEEecCCCcEEEEECCCccEEecCEEEEEecHHHHHHHHHhccCCCCCHHHHHHHHHHHH
Confidence                                                                        35899999999999999999


Q ss_pred             HHhhccCCCCCCcEEEEEEEeCC
Q 040809          108 RKTMDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus       108 ~~~~~~~~~~~~~iei~ii~~~~  130 (161)
                      ..+++++..++++++|++|++++
T Consensus       169 ~~a~~~d~~sg~~i~v~vi~~~g  191 (205)
T 1ryp_H          169 SQAIKWDGSSGGVIRMVVLTAAG  191 (205)
T ss_dssp             HHHHHHBTTCCSCEEEEEEETTE
T ss_pred             HHHHHhCCccCCeEEEEEEcCCC
Confidence            99999988899999999999875

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

Probab=99.87  E-value=3.7e-22  Score=158.38  Aligned_cols=126  Identities=15%  Similarity=0.158  Sum_probs=112.3

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHH-----HhCCCc---
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAY-----AYQEPI---   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~-----~~~~~i---   87 (161)
                      +.-|.+. | |||+|+|.+.+.++.+++.+|||+|++||+|++||+.+|++.|++++|.+++.|++     .+++++   
T Consensus        44 ~vgi~~~dgVVlAaD~r~t~g~~i~~~~~~KI~~i~d~i~~~~aG~~aD~~~l~~~lr~~~~~~~~~~~~~~~~~~~~v~  123 (266)
T 1g0u_M           44 VISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLADAEEALEPS  123 (266)
T ss_dssp             EEEEEETTEEEEEEECCEEETTEEEECCCCCEEECTTSEEEEEEEEHHHHHHHHHHHHHHHHHHHTTCTTTTTTTSCCHH
T ss_pred             EEEEEECCEEEEEEcCCcccCceeecCCcCcEEEcCCCEEEEeccCHHHHHHHHHHHHHHHHHhhhccchhhcCCCCCHH
Confidence            5555555 5 99999999987666666899999999999999999999999999999999999998     888887   


Q ss_pred             ------------------------------------------------------------------cCCCC-----CCCH
Q 040809           88 ------------------------------------------------------------------QDYKD-----DMTR   96 (161)
Q Consensus        88 ------------------------------------------------------------------~~y~~-----~mt~   96 (161)
                                                                                        +.|++     +||+
T Consensus       124 ~la~~l~~~ly~~r~~~~P~~v~~lvaG~D~~~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~~~~~ms~  203 (266)
T 1g0u_M          124 YIFEYLATVMYQRRSKMNPLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFGAHMANPLLRKVVDRESDIPKTTV  203 (266)
T ss_dssp             HHHHHHHHHHHHHHHTTCCCCEEEEEEEECTTSCEEEEEEETTCCEECCSEEECTHHHHTHHHHHTTTCSSGGGGGGCCH
T ss_pred             HHHHHHHHHHHHhccCCCCceEEEEEEEEcCCCCEEEEEECCCCCEEeCCEEEEccCHHHHHHHHHHhhcccccCCCCCH
Confidence                                                                              36788     9999


Q ss_pred             HHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHH
Q 040809           97 QEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTML  147 (161)
Q Consensus        97 eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~  147 (161)
                      +||++++++||..+++++..++.+++|++|+++.    .|+.++++||+++
T Consensus       204 eeA~~la~~al~~a~~rd~~sg~~i~v~vI~k~~----g~~~~~~~ei~~~  250 (266)
T 1g0u_M          204 QVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKNT----GLTFKKNLQVENM  250 (266)
T ss_dssp             HHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTT----EEEEEEEEECCCC
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCcEEEEEEECCC----CeEEcCHHHhhhh
Confidence            9999999999999999999999999999999874    4899998888765

>1iru_K 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_J* 3une_J 3unf_J* 3unh_J

Probab=99.87  E-value=2.1e-21  Score=147.74  Aligned_cols=117  Identities=14%  Similarity=0.153  Sum_probs=103.6

Q ss_pred             eeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc---------
Q 040809           19 YQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI---------   87 (161)
Q Consensus        19 ~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i---------   87 (161)
                      .-|.+. | |||+|+|.+++.++.+++.+|||+|++||+|++||+.+|++.+++++|.+++.|++++++++         
T Consensus         5 vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a~~~   84 (201)
T 1iru_K            5 IGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYIQKNVQLYKMRNGYELSPTAAANFT   84 (201)
T ss_dssp             EEEECSSEEEEEEECCEEETTEEEESSCCCEEECSSSEEEEEEESTTHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHH
T ss_pred             EEEEeCCEEEEEEcCccccCcEEEccCcceEEEecCCEEEEeCcCHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            345555 5 89999999986555556899999999999999999999999999999999999999999876         


Q ss_pred             ------------------------------------------------------------cCCCCCCCHHHHHHHHHHHH
Q 040809           88 ------------------------------------------------------------QDYKDDMTRQEAVQLALKVL  107 (161)
Q Consensus        88 ------------------------------------------------------------~~y~~~mt~eeai~la~~al  107 (161)
                                                                                  +.|+++||++||++++++||
T Consensus        85 ~~~l~~~~~~~~p~~~~~lvaG~D~~~gp~Ly~id~~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~s~eea~~l~~~al  164 (201)
T 1iru_K           85 RRNLADCLRSRTPYHVNLLLAGYDEHEGPALYYMDYLAALAKAPFAAHGYGAFLTLSILDRYYTPTISRERAVELLRKCL  164 (201)
T ss_dssp             HHHHHHHHTSSSCCCEEEEEEEEETTTEEEEEEECTTCCEEECSEEEESHHHHHHHHHHHHHCCTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCCccEEEEEEEEeCCCCeEEEEECCCcCeEECCEEEECCcHHHHHHHHHhcccCCCCHHHHHHHHHHHH
Confidence                                                                        35899999999999999999


Q ss_pred             HHhhccCCCCCCcEEEEEEEeCCCCceeEEECC
Q 040809          108 RKTMDSTSLTSEKLELAEVFLLPSGKVKYRICS  140 (161)
Q Consensus       108 ~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~  140 (161)
                      ..+.+++..++.+++|++|++++     ++.+.
T Consensus       165 ~~a~~rd~~sg~~i~v~vi~~~g-----~~~~~  192 (201)
T 1iru_K          165 EELQKRFILNLPTFSVRIIDKNG-----IHDLD  192 (201)
T ss_dssp             HHHHHTBCBCCCCEEEEEEETTE-----EECCC
T ss_pred             HHHHhhccccCCceEEEEEcCCC-----eEEee
Confidence            99999998999999999999873     66654

>1g3k_A ATP-dependent protease HSLV; hydrolase; 1.90A {Haemophilus influenzae} SCOP: d.153.1.4 PDB: 1g3i_G 1jjw_A 1kyi_G* 1ofh_G* 1ofi_G* 1e94_A* 1g4a_B* 1g4b_M 1hqy_A* 1ht1_C* 1ht2_A* 1ned_A

Probab=99.68  E-value=3.5e-17  Score=121.92  Aligned_cols=107  Identities=16%  Similarity=0.153  Sum_probs=88.7

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEe-cCceEEEEeccHHHHHHHHHHHHHHHHHHHHHh-----------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKI-DDHVACAVAGIMSDANILINTARVQARRYAYAY-----------   83 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I-~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~-----------   83 (161)
                      +.-|-+. | |||+|+|.+++.++.+++.+|||+| ++|++|++||+.+|++.|.+++|.+++.|++..           
T Consensus         3 ~vgi~~~dgVvlaaD~r~t~g~~i~~~~~~Ki~~i~~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~   82 (174)
T 1g3k_A            3 IVSVRRNGQVVVGGDGQVSLGNTVMKGNARKVRRLYNGKVLAGFAGGTADAFTLFELFERKLEMHQGHLLKSAVELAKDW   82 (174)
T ss_dssp             EEEEEETTEEEEEECCCEEETTEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             EEEEEECCEEEEEECCCCccCCeeEeCCCCcEEEECCCCEEEEeCccHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            3445555 5 9999999998866666789999999 999999999999999999999999998885311           


Q ss_pred             -----CCCc--------------------------------------------cCCC-CCCCHHHHHHHHHHHHHHhhcc
Q 040809           84 -----QEPI--------------------------------------------QDYK-DDMTRQEAVQLALKVLRKTMDS  113 (161)
Q Consensus        84 -----~~~i--------------------------------------------~~y~-~~mt~eeai~la~~al~~~~~~  113 (161)
                           ..++                                            +.|+ ++||.+   +++.+||..+.++
T Consensus        83 ~~~~~~r~~~~~l~g~d~p~Ly~~d~~G~~~~~~~~~~~a~Gsgs~~a~~~le~~~~~~~mt~~---~l~~~al~~a~~r  159 (174)
T 1g3k_A           83 RTDRALRKLEAMLIVADEKESLIITGIGDVVQPEEDQILAIGSGGNYALSAARALVENTELSAH---EIVEKSLRIAGDI  159 (174)
T ss_dssp             HHSTTGGGCCCEEEEECSSCEEEEETTTEEECCCTTCEEEESTTHHHHHHHHHHHHHHCCCCHH---HHHHHHHHHHHHH
T ss_pred             HhccCcCcceEEEEEECCCEEEEEcCCCcEEecCCCcEEEEcccHHHHHHHHHHhcccCCCCHH---HHHHHHHHHHHHh
Confidence                 1111                                            2467 999965   6899999999999


Q ss_pred             CCCCCCcEEEEEEE
Q 040809          114 TSLTSEKLELAEVF  127 (161)
Q Consensus       114 ~~~~~~~iei~ii~  127 (161)
                      |..++++++|++|+
T Consensus       160 d~~sg~~i~v~~i~  173 (174)
T 1g3k_A          160 CVFTNTNFTIEELP  173 (174)
T ss_dssp             CTTCCSCCEEEEEC
T ss_pred             ccccCCceEEEEec
Confidence            99999999999985

>2z3b_A ATP-dependent protease HSLV; N-terminal nucleophIle hydrolase; 2.50A {Bacillus subtilis} SCOP: d.153.1.4 PDB: 2z3a_A 1yyf_D* 3ty6_A

Probab=99.65  E-value=2.6e-16  Score=117.97  Aligned_cols=108  Identities=20%  Similarity=0.267  Sum_probs=90.6

Q ss_pred             CceeeEecc-e-EEEEEcccCCCCc-ccCCCCCceEEe-cCceEEEEeccHHHHHHHHHHHHHHHHHHH---H-------
Q 040809           16 GRLYQVDYM-G-CLVGENNVTSKLL-QTSTSAEKMYKI-DDHVACAVAGIMSDANILINTARVQARRYA---Y-------   81 (161)
Q Consensus        16 Grl~qveya-G-Vlaadkr~~~~l~-~~~~~~~KI~~I-~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~---~-------   81 (161)
                      +.+.-|.+. | |||+|+|.+.+.+ +.+++.+|||+| ++|++|++||+.+|++.|.+++|.+++.|+   .       
T Consensus         6 tTivgi~~~dgVvlaaD~r~t~g~~~i~~~~~~KI~~i~~~~i~~~~aG~~aD~~~l~~~~~~~~~~y~g~~~~~~~~l~   85 (180)
T 2z3b_A            6 TTIFAVQHKGRSAMSGDGQVTFGQAVVMKHTARKVRKLFNGKVLAGFAGSVADAFTLFEKFEAKLEEYNGNLKRAAVELA   85 (180)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTTEEEESCCCCEEEETTTTEEEEECSCHHHHHHHHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             eEEEEEEECCEEEEEECCCccCCCceEecCCCCcEEEECCCCEEEEeCchHHHHHHHHHHHHHHHHHhcCChHHHHHHHH
Confidence            457888888 5 9999999998654 556689999999 999999999999999999999999999986   1       


Q ss_pred             ----Hh--CCCc-------------------------------------------cCCCC---CCCHHHHHHHHHHHHHH
Q 040809           82 ----AY--QEPI-------------------------------------------QDYKD---DMTRQEAVQLALKVLRK  109 (161)
Q Consensus        82 ----~~--~~~i-------------------------------------------~~y~~---~mt~eeai~la~~al~~  109 (161)
                          .+  .+|.                                           +.|++   +||.||   ++.+||..
T Consensus        86 ~~~~~~~~~rp~~~~~lvad~p~ly~~d~~G~~~~~~~~~~a~Gsgs~~a~~~le~~~~~~~~~mt~ee---l~~~al~~  162 (180)
T 2z3b_A           86 KEWRSDKVLRKLEAMLIVMNQDTLLLVSGTGEVIEPDDGILAIGSGGNYALAAGRALKKHAGESMSASE---IARAALET  162 (180)
T ss_dssp             HHHHHCTTGGGCCCCEEEECSSCEEEECTTCCEECCSSSEEEESTTHHHHHHHHHHHHHHHGGGCCHHH---HHHHHHHH
T ss_pred             HHHHhhhCcCcceEEEEEEcCCeEEEECCCCcEEEeCCCEEEECCCHHHHHHHHHHhhhccCCCCCHHH---HHHHHHHH
Confidence                11  1111                                           24677   999999   46799999


Q ss_pred             hhccCCCCCCcEEEEEE
Q 040809          110 TMDSTSLTSEKLELAEV  126 (161)
Q Consensus       110 ~~~~~~~~~~~iei~ii  126 (161)
                      +.++|..++++++|.+|
T Consensus       163 a~~rd~~sg~~i~v~~i  179 (180)
T 2z3b_A          163 AGEICVYTNDQIILEEL  179 (180)
T ss_dssp             HHHHCTTCCSCCEEEEE
T ss_pred             HHHhcCccCCeEEEEEE
Confidence            99999999999999988

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

Probab=99.61  E-value=3.5e-16  Score=116.09  Aligned_cols=105  Identities=18%  Similarity=0.216  Sum_probs=86.4

Q ss_pred             eeEecc-e-EEEEEcccCCCCcccCCCCCceEEe-cCceEEEEeccHHHHHHHHHHHHHHHHHHHH--------------
Q 040809           19 YQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKI-DDHVACAVAGIMSDANILINTARVQARRYAY--------------   81 (161)
Q Consensus        19 ~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I-~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~--------------   81 (161)
                      .-|.+. | |||+|+|.+.+.++.+++.+|||+| ++|++|++||+.+|++.+++++|.+++.|++              
T Consensus         4 vgi~~~dgVvlaaD~r~~~g~~i~~~~~~Ki~~i~~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~   83 (171)
T 1m4y_A            4 LVVRRNGQTVMGGDGQVTFGSTVLKGNARKVRKLGEGKVLAGFAGSVADAMTLFDRFEAKLREWGGNLTKAAVELAKDWR   83 (171)
T ss_dssp             EEEEETTEEEEEECCCEEETTEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             EEEEECCEEEEEECCCcccCCEEEeCCcceEEEeCCCCEEEEeCccHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            445555 5 9999999998766666689999999 9999999999999999999999999998751              


Q ss_pred             Hh--CCCc-------------------------------------------cCCC-CCCCHHHHHHHHHHHHHHhhccCC
Q 040809           82 AY--QEPI-------------------------------------------QDYK-DDMTRQEAVQLALKVLRKTMDSTS  115 (161)
Q Consensus        82 ~~--~~~i-------------------------------------------~~y~-~~mt~eeai~la~~al~~~~~~~~  115 (161)
                      .+  ..|.                                           +.|+ ++||.   ++++++||..+.+||.
T Consensus        84 ~~~~~~~~~~~~lv~D~p~Ly~~d~~G~~~~~~~~~~a~Gsgs~~a~~~le~~~~~~~ms~---~~l~~~al~~a~~rd~  160 (171)
T 1m4y_A           84 TDRVLRRLEALLLVADKENIFIISGNGEVIQPDDDAAAIGSGGPYALAAAKALLRNTDLSA---REIVEKAMTIAGEICI  160 (171)
T ss_dssp             HCTTGGGCCCEEEEECSSCEEEECTTSCEECCSSSEEEESTTHHHHHHHHHHHHHHCCCCH---HHHHHHHHHHHHHHCT
T ss_pred             HhCCCCceEEEEEEEcCCEEEEECCCCCEEecCCCEEEECCcHHHHHHHHHHhcccCCCCH---HHHHHHHHHHHHHhCc
Confidence            11  1111                                           3467 89997   5689999999999999


Q ss_pred             CCCCcEEEEEE
Q 040809          116 LTSEKLELAEV  126 (161)
Q Consensus       116 ~~~~~iei~ii  126 (161)
                      .++++++|.++
T Consensus       161 ~sg~~i~v~~~  171 (171)
T 1m4y_A          161 YTNQNIVIEEV  171 (171)
T ss_dssp             TCCSCCEEEEC
T ss_pred             ccCCeEEEEEC
Confidence            99999999864

---

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	161
d1rypc_	244	d.153.1.4 (C:) Proteasome alpha subunit (non-catal	1e-21
d1rypc_	244	d.153.1.4 (C:) Proteasome alpha subunit (non-catal	4e-10
d1iruc_	250	d.153.1.4 (C:) Proteasome alpha subunit (non-catal	4e-21
d1iruc_	250	d.153.1.4 (C:) Proteasome alpha subunit (non-catal	2e-08
d1rypf_	233	d.153.1.4 (F:) Proteasome alpha subunit (non-catal	6e-20
d1rypf_	233	d.153.1.4 (F:) Proteasome alpha subunit (non-catal	5e-04
d1irug_	245	d.153.1.4 (G:) Proteasome alpha subunit (non-catal	3e-19
d1irug_	245	d.153.1.4 (G:) Proteasome alpha subunit (non-catal	3e-09
d1irua_	244	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	3e-18
d1irua_	244	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	2e-04
d1rypg_	244	d.153.1.4 (G:) Proteasome alpha subunit (non-catal	6e-18
d1rypg_	244	d.153.1.4 (G:) Proteasome alpha subunit (non-catal	2e-07
d1rypd_	241	d.153.1.4 (D:) Proteasome alpha subunit (non-catal	8e-18
d1irue_	234	d.153.1.4 (E:) Proteasome alpha subunit (non-catal	1e-17
d1irue_	234	d.153.1.4 (E:) Proteasome alpha subunit (non-catal	9e-06
d1irub_	233	d.153.1.4 (B:) Proteasome alpha subunit (non-catal	5e-17
d1rypb_	250	d.153.1.4 (B:) Proteasome alpha subunit (non-catal	5e-17
d1rypb_	250	d.153.1.4 (B:) Proteasome alpha subunit (non-catal	9e-05
d1j2pa_	243	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	9e-17
d1j2pa_	243	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	1e-05
d1irud_	243	d.153.1.4 (D:) Proteasome alpha subunit (non-catal	1e-16
d1rype_	242	d.153.1.4 (E:) Proteasome alpha subunit (non-catal	2e-16
d1rype_	242	d.153.1.4 (E:) Proteasome alpha subunit (non-catal	9e-06
d1iruf_	238	d.153.1.4 (F:) Proteasome alpha subunit (non-catal	2e-16
d1iruf_	238	d.153.1.4 (F:) Proteasome alpha subunit (non-catal	5e-04
d1rypa_	243	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	1e-15
d1rypa_	243	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	7e-04
d1yara1	221	d.153.1.4 (A:13-233) Proteasome alpha subunit (non	5e-14
d1yara1	221	d.153.1.4 (A:13-233) Proteasome alpha subunit (non	2e-04
d1ryp2_	233	d.153.1.4 (2:) Proteasome beta subunit (catalytic)	3e-10
d1q5qa_	227	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	3e-09
d1q5qa_	227	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	4e-05
d1ryp1_	222	d.153.1.4 (1:) Proteasome beta subunit (catalytic)	2e-08
d1rypi_	222	d.153.1.4 (I:) Proteasome beta subunit (catalytic)	4e-08
d1rypi_	222	d.153.1.4 (I:) Proteasome beta subunit (catalytic)	0.001
d1irul_	201	d.153.1.4 (L:) Proteasome beta subunit (catalytic)	2e-07
d1irul_	201	d.153.1.4 (L:) Proteasome beta subunit (catalytic)	4e-05
d1iruk_	199	d.153.1.4 (K:) Proteasome beta subunit (catalytic)	2e-07
d1iruk_	199	d.153.1.4 (K:) Proteasome beta subunit (catalytic)	3e-04
d1rypk_	198	d.153.1.4 (K:) Proteasome beta subunit (catalytic)	4e-07
d1irui_	220	d.153.1.4 (I:) Proteasome beta subunit (catalytic)	5e-07
d1iruh_	202	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	1e-06
d1iruh_	202	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	6e-04
d1iru2_	217	d.153.1.4 (2:) Proteasome beta subunit (catalytic)	2e-06
d1iru2_	217	d.153.1.4 (2:) Proteasome beta subunit (catalytic)	8e-04
d1yarh1	203	d.153.1.4 (H:1-203) Proteasome beta subunit (catal	3e-06
d1yarh1	203	d.153.1.4 (H:1-203) Proteasome beta subunit (catal	2e-05
d1iru1_	213	d.153.1.4 (1:) Proteasome beta subunit (catalytic)	4e-06
d1ryph_	205	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	7e-06
d1q5qh_	224	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	1e-05
d1j2qh_	202	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	1e-05
d1j2qh_	202	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	1e-05
d1rypl_	212	d.153.1.4 (L:) Proteasome beta subunit (catalytic)	3e-05
d1rypl_	212	d.153.1.4 (L:) Proteasome beta subunit (catalytic)	0.001

>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 = 85.1 bits (210), Expect = 1e-21
 Identities = 51/103 (49%), Positives = 64/103 (62%), Gaps = 18/103 (17%)

Query: 2   SRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTS 43
           SRRYD +TT+FSPEGRLYQV+Y           +G        L  E  VTS LL+  TS
Sbjct: 2   SRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTS 61

Query: 44  AEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEP 86
            EK+YK++D +A AVAG+ +DA ILINTAR+ A+ Y   Y E 
Sbjct: 62  TEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNED 104

>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 = 54.3 bits (130), Expect = 4e-10
 Identities = 32/105 (30%), Positives = 48/105 (45%), Gaps = 1/105 (0%)

Query: 50  IDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQDYKDDMTRQEAVQLALKVLRK 109
            DD     +       N     A       + A      DYKDDM   +A++LALK L K
Sbjct: 139 YDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKDDMKVDDAIELALKTLSK 198

Query: 110 TMDSTSLTSEKLELAEVFL-LPSGKVKYRICSPESLTMLLENFGV 153
           T DS++LT ++LE A +      G+V  +I  P+ +  +L   G+
Sbjct: 199 TTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVKTGI 243

>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 = 84.0 bits (207), Expect = 4e-21
 Identities = 49/105 (46%), Positives = 63/105 (60%), Gaps = 18/105 (17%)

Query: 2   SRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTS 43
           SRRYD +TT+FSPEGRLYQV+Y           +G        L  E     KLL     
Sbjct: 1   SRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVFF 60

Query: 44  AEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQ 88
           +EK+YK+++ +AC+VAGI SDAN+L N  R+ A+RY   YQEPI 
Sbjct: 61  SEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIP 105

>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 = 49.7 bits (118), Expect = 2e-08
 Identities = 30/101 (29%), Positives = 47/101 (46%), Gaps = 2/101 (1%)

Query: 50  IDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQDY-KDDMTRQEAVQLALKVLR 108
            D H    +       N     A       A A     QDY + +MT + A+ LA+KVL 
Sbjct: 138 WDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYKEGEMTLKSALALAIKVLN 197

Query: 109 KTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLE 149
           KTMD + L++EK+E+A      +GK   R+   + +  L++
Sbjct: 198 KTMDVSKLSAEKVEIA-TLTRENGKTVIRVLKQKEVEQLIK 237

>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 = 80.9 bits (199), Expect = 6e-20
 Identities = 29/102 (28%), Positives = 45/102 (44%), Gaps = 21/102 (20%)

Query: 4   RYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAE 45
            YD  T  FSP GRL+QV+Y           +G        LV       +L   S+  +
Sbjct: 4   NYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADEL---SSYQK 60

Query: 46  KMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           K+ K D+H+  ++AG+  DA +L N  R Q    +  +   +
Sbjct: 61  KIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKL 102

>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 = 37.0 bits (85), Expect = 5e-04
 Identities = 13/92 (14%), Positives = 29/92 (31%), Gaps = 8/92 (8%)

Query: 61  IMSDANILINTARVQARRYAYAYQEPIQDYKD----DMTRQEAVQLALKVLRKTMDSTSL 116
                N+          R   A     +        D    E ++  ++ + +++   SL
Sbjct: 146 FQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVEAISQSLRDESL 205

Query: 117 TSEKLELAEVFLLPSGKVKYRICSPESLTMLL 148
           T + L +A V         + I   E++   +
Sbjct: 206 TVDNLSIAIV----GKDTPFTIYDGEAVAKYI 233

>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 = 78.9 bits (194), Expect = 3e-19
 Identities = 31/105 (29%), Positives = 50/105 (47%), Gaps = 19/105 (18%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTST 42
           +   YD   + FSP+GR++QV+Y           +G           E  V SKL     
Sbjct: 3   IGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLY-EEG 61

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           S ++++ +D HV  AVAG+++DA  L + AR +A  +   +   I
Sbjct: 62  SNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNI 106

>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 = 52.0 bits (124), Expect = 3e-09
 Identities = 12/77 (15%), Positives = 25/77 (32%)

Query: 50  IDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQDYKDDMTRQEAVQLALKVLRK 109
              +    +  I               +    A  E  +    +MT ++ V+   K++  
Sbjct: 140 YSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQMKEMTCRDIVKEVAKIIYI 199

Query: 110 TMDSTSLTSEKLELAEV 126
             D     + +LEL+ V
Sbjct: 200 VHDEVKDKAFELELSWV 216

>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 = 76.6 bits (188), Expect = 3e-18
 Identities = 32/104 (30%), Positives = 51/104 (49%), Gaps = 20/104 (19%)

Query: 2   SRRYDRQTTVFSPEGRLYQVDY------------MGC-------LVGENNVTSKLLQTST 42
           S  +DR  T+FSPEGRLYQV+Y            +         +V +  V  KLL +ST
Sbjct: 5   SAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSST 64

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEP 86
               ++KI +++ C + G+ +D+   +  AR +A  + Y Y   
Sbjct: 65  V-THLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYE 107

>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 = 38.1 bits (88), Expect = 2e-04
 Identities = 12/70 (17%), Positives = 27/70 (38%), Gaps = 4/70 (5%)

Query: 81  YAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICS 140
            ++ E     K D T ++ V+ A+  L   +        ++E+    ++     K+RI +
Sbjct: 175 TSFLEKKVKKKFDWTFEQTVETAITCLSTVLS-IDFKPSEIEVG---VVTVENPKFRILT 230

Query: 141 PESLTMLLEN 150
              +   L  
Sbjct: 231 EAEIDAHLVA 240

>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 = 75.4 bits (185), Expect = 6e-18
 Identities = 31/101 (30%), Positives = 48/101 (47%), Gaps = 19/101 (18%)

Query: 5   YDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAEK 46
           YD   +VFSP+GR +QV+Y           +G           E  +TSKLL    +  K
Sbjct: 4   YDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKN-VK 62

Query: 47  MYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           +  +D H+ C  +G++ D   L+N  R +A  +   Y+ PI
Sbjct: 63  IQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPI 103

>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 = 46.2 bits (109), Expect = 2e-07
 Identities = 12/52 (23%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 76  ARRYAYAYQEPIQD-YKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEV 126
            R+ A A  E + D + + ++ +EAV+ A K++    +       +LE++  
Sbjct: 164 GRQSAKAELEKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWC 215

>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 = 75.1 bits (184), Expect = 8e-18
 Identities = 33/101 (32%), Positives = 53/101 (52%), Gaps = 18/101 (17%)

Query: 5   YDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAEK 46
           YDR  ++FSP+G ++QV+Y           +G        L  E   T KL  T  +  K
Sbjct: 2   YDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSK 61

Query: 47  MYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           + KID HV  + +G+ +D+ ILI  ARV+A+ +    ++P+
Sbjct: 62  VSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPV 102

>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 = 74.3 bits (182), Expect = 1e-17
 Identities = 38/101 (37%), Positives = 59/101 (58%), Gaps = 19/101 (18%)

Query: 5   YDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAEK 46
           YDR    FSPEGRL+QV+Y           +G       CL  E  +TS L++ S+  EK
Sbjct: 1   YDRGVNTFSPEGRLFQVEYDIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEPSSI-EK 59

Query: 47  MYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           + +ID H+ CA++G+++DA  LI+ ARV+ + + + Y E +
Sbjct: 60  IVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETM 100

>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 = 41.9 bits (98), Expect = 9e-06
 Identities = 16/74 (21%), Positives = 34/74 (45%), Gaps = 5/74 (6%)

Query: 77  RRYAYAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKY 136
                A     + Y   MT +EA++ +L +L++ M+   L +  +ELA V         +
Sbjct: 165 SASEGAQSSLQELYHKSMTLKEAIKSSLIILKQVMEE-KLNATNIELATV----QPGQNF 219

Query: 137 RICSPESLTMLLEN 150
            + + E L  ++++
Sbjct: 220 HMFTKEELEEVIKD 233

>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 = 73.2 bits (179), Expect = 5e-17
 Identities = 30/103 (29%), Positives = 43/103 (41%), Gaps = 19/103 (18%)

Query: 2   SRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTS 43
            R Y    T FSP G+L Q++Y           +G        L  E    S L     S
Sbjct: 2   ERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILY-DERS 60

Query: 44  AEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEP 86
             K+  I  H+    +G+  D  +L++ AR  A++Y   YQEP
Sbjct: 61  VHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEP 103

>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 = 73.2 bits (179), Expect = 5e-17
 Identities = 26/106 (24%), Positives = 42/106 (39%), Gaps = 20/106 (18%)

Query: 1   MSRRYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTST 42
           M+ RY    T FSP G+L Q+DY           +G        +  E   +S L   S 
Sbjct: 1   MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAM-SE 59

Query: 43  SAEKMYKIDDHVACAVAGIMSDANILINTARVQAR-RYAYAYQEPI 87
           +  K+  +   +    +G+  D  +L++ +R  A   Y   Y E  
Sbjct: 60  TLSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYP 105

>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 = 38.9 bits (90), Expect = 9e-05
 Identities = 16/111 (14%), Positives = 45/111 (40%), Gaps = 12/111 (10%)

Query: 50  IDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQDYKDDMTRQEAVQLALKVLRK 109
            D+    ++  +    +     A    +    A     + + D++  ++A+ +AL  L++
Sbjct: 139 HDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWNDELELEDAIHIALLTLKE 198

Query: 110 TMDSTSLTSEKLELAEV----------FLLPSGKV-KYRICSPESLTMLLE 149
           +++      + +ELA +            +P+ K  ++R  + + +   LE
Sbjct: 199 SVE-GEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTSQEINDRLE 248

>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 = 72.4 bits (177), Expect = 9e-17
 Identities = 39/100 (39%), Positives = 58/100 (58%), Gaps = 19/100 (19%)

Query: 5   YDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAEK 46
           YDR  TVFSP+GRL+QV+Y           +G        L+ +  V SKLL    + EK
Sbjct: 5   YDRAITVFSPDGRLFQVEYAREAVKRGATAIGIKCKEGVILIADKRVGSKLL-EKDTIEK 63

Query: 47  MYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEP 86
           +YKID+H+  A +G+++DA +LI+ AR++A+     Y  P
Sbjct: 64  IYKIDEHICAATSGLVADARVLIDRARIEAQINRLTYDIP 103

>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 = 41.6 bits (97), Expect = 1e-05
 Identities = 17/74 (22%), Positives = 35/74 (47%), Gaps = 6/74 (8%)

Query: 76  ARRYAYAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVK 135
            R     + E  ++Y+DD++  +A+ L L  +  +++ + L  E +E+  V         
Sbjct: 164 GRMAVTEFFE--KEYRDDLSFDDAMVLGLVAMGLSIE-SELVPENIEVGYV---KVDDRT 217

Query: 136 YRICSPESLTMLLE 149
           ++  SPE L   +E
Sbjct: 218 FKEVSPEELKPYVE 231

>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 = 72.4 bits (177), Expect = 1e-16
 Identities = 34/102 (33%), Positives = 52/102 (50%), Gaps = 19/102 (18%)

Query: 5   YDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAEK 46
           YDR  TVFSP+G L+QV+Y           +G        L  E    +KL     +  K
Sbjct: 2   YDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQ-DERTVRK 60

Query: 47  MYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQ 88
           +  +DD+V  A AG+ +DA I+IN ARV+ + +    ++P+ 
Sbjct: 61  ICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVT 102

>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 = 71.7 bits (175), Expect = 2e-16
 Identities = 36/100 (36%), Positives = 52/100 (52%), Gaps = 19/100 (19%)

Query: 6  DRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAEKM 47
          DR  + FSPEGRL+QV+Y           +G        L  E   TS LL++ +  EK+
Sbjct: 1  DRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESDS-IEKI 59

Query: 48 YKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           +ID H+ CA++G+ +DA  +I  AR  A  +   Y E I
Sbjct: 60 VEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDI 99

>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 = 42.0 bits (98), Expect = 9e-06
 Identities = 17/102 (16%), Positives = 37/102 (36%), Gaps = 5/102 (4%)

Query: 50  IDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQDYKDDMTRQEAVQLALKVLRK 109
            D      +             A+        A  E + ++   +T +EA  L LK+L++
Sbjct: 139 HDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNEWHSSLTLKEAELLVLKILKQ 198

Query: 110 TMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENF 151
            M+   L     +L+ +    + +  ++I   E    L++  
Sbjct: 199 VMEE-KLDENNAQLSCI----TKQDGFKIYDNEKTAELIKEL 235

>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 = 71.6 bits (175), Expect = 2e-16
 Identities = 26/101 (25%), Positives = 49/101 (48%), Gaps = 21/101 (20%)

Query: 4  RYDRQTTVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAE 45
          +YD   TV+SP+GR++Q++Y           +G        LV      S+L   +   +
Sbjct: 2  QYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSEL---AAHQK 58

Query: 46 KMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEP 86
          K+  +D+H+  ++AG+ +DA +L N  R +     + +  P
Sbjct: 59 KILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRP 99

>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 = 36.5 bits (84), Expect = 5e-04
 Identities = 15/73 (20%), Positives = 31/73 (42%), Gaps = 5/73 (6%)

Query: 79  YAYAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDS-TSLTSEKLELAEVFLLPSGKVKYR 137
            A  Y E       +    E V+  L+ LR+T+ +   LT++ + +  V       +++ 
Sbjct: 164 SARTYLERHMSEFMECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIV----GKDLEFT 219

Query: 138 ICSPESLTMLLEN 150
           I   + ++  LE 
Sbjct: 220 IYDDDDVSPFLEG 232

>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 = 69.4 bits (169), Expect = 1e-15
 Identities = 27/101 (26%), Positives = 39/101 (38%), Gaps = 18/101 (17%)

Query: 5   YDRQTTVFSPEGRLYQVDYM------------------GCLVGENNVTSKLLQTSTSAEK 46
           YDR  T+FSPEGRLYQV+Y                     +V         L   T+   
Sbjct: 3   YDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPTTVSY 62

Query: 47  MYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI 87
           ++ I   +   V G + DA      A+ +A  + Y Y   +
Sbjct: 63  IFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDM 103

>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 = 36.2 bits (83), Expect = 7e-04
 Identities = 11/67 (16%), Positives = 29/67 (43%), Gaps = 6/67 (8%)

Query: 83  YQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPE 142
           +++   D+ ++ + ++ V+ A+  +   +  T  +   LE+         K K+   S E
Sbjct: 177 FKKSKIDHINEESWEKVVEFAITHMIDALG-TEFSKNDLEVGVA-----TKDKFFTLSAE 230

Query: 143 SLTMLLE 149
           ++   L 
Sbjct: 231 NIEERLV 237

>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 = 64.7 bits (157), Expect = 5e-14
 Identities = 32/97 (32%), Positives = 53/97 (54%), Gaps = 19/97 (19%)

Query: 10 TVFSPEGRLYQVDY-----------MG-------CLVGENNVTSKLLQTSTSAEKMYKID 51
          TVFSP+GRL+QV+Y           +G        L+ +  V S+L+    S EK+  ID
Sbjct: 1  TVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLI-EQNSIEKIQLID 59

Query: 52 DHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQ 88
          D+VA   +G+++DA +L++ AR+ A++    Y   + 
Sbjct: 60 DYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVN 96

>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 = 37.8 bits (87), Expect = 2e-04
 Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 7/70 (10%)

Query: 79  YAYAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRI 138
              ++ E  ++YK+++  +EAV L +K L+ +++      +  E+A +    +   KYRI
Sbjct: 159 AVVSFLE--REYKENLPEKEAVTLGIKALKSSLEE-GEELKAPEIASI----TVGNKYRI 211

Query: 139 CSPESLTMLL 148
              E +   L
Sbjct: 212 YDQEEVKKFL 221

>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 = 54.4 bits (130), Expect = 3e-10
 Identities = 14/100 (14%), Positives = 36/100 (36%), Gaps = 2/100 (2%)

Query: 27  LVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEP 86
           +  +N  +   L      E++  + D+    ++G +SD   +    +        AY  P
Sbjct: 22  IAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTE--NAYDNP 79

Query: 87  IQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEV 126
           + D ++ +      +    V+ +     +     + +A V
Sbjct: 80  LADAEEALEPSYIFEYLATVMYQRRSKMNPLWNAIIVAGV 119

>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 = 51.6 bits (123), Expect = 3e-09
 Identities = 14/71 (19%), Positives = 26/71 (36%), Gaps = 6/71 (8%)

Query: 41  STSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQDYKDDMTRQEAV 100
           ST+  K+ ++ D +  A  G  ++   L     V A    Y+Y       + D+T +   
Sbjct: 39  STALHKVSELYDRLGFAAVGKYNEFENLRRAGIVHADMRGYSYD------RRDVTGRSLA 92

Query: 101 QLALKVLRKTM 111
               + L    
Sbjct: 93  NAYAQTLGTIF 103

>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 = 40.0 bits (93), Expect = 4e-05
 Identities = 23/154 (14%), Positives = 47/154 (30%), Gaps = 20/154 (12%)

Query: 15  EGRLYQVDYMGCLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSD---------- 64
              +    Y    V   ++ +   QT  +          V   VA +             
Sbjct: 73  HADMRGYSYDRRDVTGRSLANAYAQTLGTIFTEQPKPYEVEICVAEVGRVGSPKAPQLYR 132

Query: 65  ----ANILINTARVQARRYAYAYQEPIQD-YKDDMTRQEAVQLALKVLRKTMDSTS---- 115
                +I+     V            +++ Y+ D+  + AV +A+  LR+          
Sbjct: 133 ITYDGSIVDEQHFVVMGGTTEPIATAMRESYRADLDLEAAVGIAVNALRQGGAGEGEKRN 192

Query: 116 LTSEKLELAEVFLLPSGKVKYRICSPESLTMLLE 149
           +    LE+A V      +  +R  +  +L  L+ 
Sbjct: 193 VDVASLEVA-VLDQSRPRRAFRRIAGTALEQLVP 225

>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 = 49.4 bits (117), Expect = 2e-08
 Identities = 9/62 (14%), Positives = 24/62 (38%)

Query: 26 CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQE 85
           L G+    +     S    K++   D++  +  G  +D + L+   +   + Y + + +
Sbjct: 22 VLAGDTRNITDYSINSRYEPKVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHND 81

Query: 86 PI 87
            
Sbjct: 82 KK 83

>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 = 48.2 bits (114), Expect = 4e-08
 Identities = 8/62 (12%), Positives = 20/62 (32%)

Query: 26 CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQE 85
           +  +   T   +    +  K+++I   + CA AG  +D   +          ++     
Sbjct: 13 VIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSR 72

Query: 86 PI 87
            
Sbjct: 73 EP 74

>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 = 35.5 bits (81), Expect = 0.001
 Identities = 15/116 (12%), Positives = 35/116 (30%), Gaps = 10/116 (8%)

Query: 19  YQVDYMGCLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINT------- 71
             ++               LQ        Y+        VAG+    + L +        
Sbjct: 61  SNIELHSLYTSREPRVVSALQMLKQHLFKYQGHIGAYLIVAGVDPTGSHLFSIHAHGSTD 120

Query: 72  ---ARVQARRYAYAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELA 124
                        A       +K D+T++EA++LA   ++  + +   +   +++ 
Sbjct: 121 VGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKLASDAIQAGIWNDLGSGSNVDVC 176

>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 = 46.3 bits (109), Expect = 2e-07
 Identities = 12/64 (18%), Positives = 27/64 (42%)

Query: 27 LVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEP 86
          +  ++  T+     S + +K+ +I+ ++   +AG  +D +        Q R Y    +E 
Sbjct: 14 VAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQCRIYELRNKER 73

Query: 87 IQDY 90
          I   
Sbjct: 74 ISVA 77

>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 = 39.7 bits (92), Expect = 4e-05
 Identities = 16/101 (15%), Positives = 36/101 (35%), Gaps = 5/101 (4%)

Query: 51  DDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQDYKDDMTRQEAVQLALKVLRKT 110
            D     +  + S+ N +            YAY    + Y  D+  ++A  LA + + + 
Sbjct: 104 WDKRGPGLYYVDSEGNRISGATFSVGSGSVYAYGVMDRGYSYDLEVEQAYDLARRAIYQA 163

Query: 111 MDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENF 151
               + +   + L  V      +  +   S +++  L E +
Sbjct: 164 TYRDAYSGGAVNLYHV-----REDGWIRVSSDNVADLHEKY 199

>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 = 46.4 bits (109), Expect = 2e-07
 Identities = 8/62 (12%), Positives = 20/62 (32%)

Query: 26 CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQE 85
           +  +    S ++Q     +KM+K+ + +     G   D        +   + Y      
Sbjct: 14 LVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYIQKNVQLYKMRNGY 73

Query: 86 PI 87
           +
Sbjct: 74 EL 75

>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 = 37.5 bits (86), Expect = 3e-04
 Identities = 12/77 (15%), Positives = 24/77 (31%)

Query: 50  IDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQDYKDDMTRQEAVQLALKVLRK 109
            D+H   A+  +   A +                    + Y   ++R+ AV+L  K L +
Sbjct: 107 YDEHEGPALYYMDYLAALAKAPFAAHGYGAFLTLSILDRYYTPTISRERAVELLRKCLEE 166

Query: 110 TMDSTSLTSEKLELAEV 126
                 L      +  +
Sbjct: 167 LQKRFILNLPTFSVRII 183

>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 = 45.5 bits (107), Expect = 4e-07
 Identities = 10/63 (15%), Positives = 19/63 (30%)

Query: 26 CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQE 85
           L     VT  +     S +K  ++  H   + AG   D        +   + Y+     
Sbjct: 14 ILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYIQANIQLYSIREDY 73

Query: 86 PIQ 88
           + 
Sbjct: 74 ELS 76

>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 = 45.2 bits (106), Expect = 5e-07
 Identities = 8/61 (13%), Positives = 22/61 (36%)

Query: 27 LVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEP 86
          L  +   T  ++    +  K++ I  ++ C  AG  +D ++           ++ +    
Sbjct: 14 LGADTRATEGMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGRL 73

Query: 87 I 87
           
Sbjct: 74 P 74

>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 = 44.3 bits (104), Expect = 1e-06
 Identities = 11/61 (18%), Positives = 24/61 (39%)

Query: 27 LVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEP 86
          L  ++  T+     +   +K+  I D + C  +G  +D   + +    Q   ++    EP
Sbjct: 14 LGADSRTTTGSYIANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEP 73

Query: 87 I 87
           
Sbjct: 74 P 74

>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 = 36.6 bits (84), Expect = 6e-04
 Identities = 12/64 (18%), Positives = 26/64 (40%), Gaps = 3/64 (4%)

Query: 81  YAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICS 140
           Y Y      Y++ MT++E +Q     L   M+    +   + LA +       V+ ++  
Sbjct: 134 YIYGYVDATYREGMTKEECLQFTANALALAMERDGSSGGVIRLAAI---AESGVERQVLL 190

Query: 141 PESL 144
            + +
Sbjct: 191 GDQI 194

>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 = 43.6 bits (102), Expect = 2e-06
 Identities = 4/61 (6%), Positives = 16/61 (26%)

Query: 26 CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQE 85
           +  +   +   L    +  ++ ++++      +G  +D   L                 
Sbjct: 21 VIAADMLGSYGSLARFRNISRIMRVNNSTMLGASGDYADFQYLKQVLGQMVIDEELLGDG 80

Query: 86 P 86
           
Sbjct: 81 H 81

>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 = 36.3 bits (83), Expect = 8e-04
 Identities = 7/51 (13%), Positives = 19/51 (37%)

Query: 76  ARRYAYAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEV 126
               A      + + +  +++ EA  L  + +R      + +  + + A V
Sbjct: 142 GAYLAQPLLREVLEKQPVLSQTEARDLVERCMRVLYYRDARSYNRFQTATV 192

>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 = 43.2 bits (101), Expect = 3e-06
 Identities = 12/62 (19%), Positives = 29/62 (46%)

Query: 26 CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQE 85
           +  E  VT +      + +K+++ID +    +AG++ DA +L+   + +   Y    + 
Sbjct: 13 IMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKAELELYRLQRRV 72

Query: 86 PI 87
           +
Sbjct: 73 NM 74

>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 = 40.5 bits (94), Expect = 2e-05
 Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 6/75 (8%)

Query: 79  YAYAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRI 138
           + Y   E    Y + MT  E V L ++ +       S +   +++A +    + K  Y  
Sbjct: 133 FVYGVLE--SQYSEKMTVDEGVDLVIRAISAAKQRDSASGGMIDVAVI----TRKDGYVQ 186

Query: 139 CSPESLTMLLENFGV 153
              + +   +   G+
Sbjct: 187 LPTDQIESRIRKLGL 201

>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 = 43.0 bits (100), Expect = 4e-06
 Identities = 8/76 (10%), Positives = 23/76 (30%)

Query: 26  CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQE 85
            +  +  ++      +  + K YK+ D      +G   D   L      + + Y ++  +
Sbjct: 22  IVASDTRLSEGFSIHTRDSPKCYKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNK 81

Query: 86  PIQDYKDDMTRQEAVQ 101
            +            + 
Sbjct: 82  AMTTGAIAAMLSTILY 97

>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 = 42.0 bits (98), Expect = 7e-06
 Identities = 10/62 (16%), Positives = 24/62 (38%)

Query: 27 LVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEP 86
          L  ++  T+     +   +K+ ++ D + C  +G  +D   + +  +     Y   Y  P
Sbjct: 23 LGADSRTTTGAYIANRVTDKLTRVHDKIWCCRSGSAADTQAIADIVQYHLELYTSQYGTP 82

Query: 87 IQ 88
            
Sbjct: 83 ST 84

>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 = 41.8 bits (97), Expect = 1e-05
 Identities = 17/62 (27%), Positives = 25/62 (40%)

Query: 27 LVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEP 86
          L G+   T   L  S   EK+Y  D++ A  +AG    A  L+    V+   Y      P
Sbjct: 14 LAGDRRATQGNLIASRDVEKVYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEGVP 73

Query: 87 IQ 88
          + 
Sbjct: 74 LT 75

>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 = 41.3 bits (96), Expect = 1e-05
 Identities = 16/100 (16%), Positives = 36/100 (36%), Gaps = 5/100 (5%)

Query: 50  IDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPIQDYKDDMTRQEAVQLALKVLRK 109
           ID       +       I              AY      +  ++   EAV+LA++ +  
Sbjct: 104 IDSEGKSIYSIDPIGGAIEEKDIVATGSGSLTAYGVLEDRFTPEIGVDEAVELAVRAIYS 163

Query: 110 TMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLE 149
            M   S + + +++ ++      + ++   SPE +  +L 
Sbjct: 164 AMKRDSASGDGIDVVKI-----TEDEFYQYSPEEVEQILA 198

>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 = 41.3 bits (96), Expect = 1e-05
 Identities = 16/63 (25%), Positives = 27/63 (42%)

Query: 26 CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQE 85
           +  E   T      S +A+K+Y+I D +A   AG + DA  L    +++A  Y    + 
Sbjct: 13 VMATEKRATMGNFIASKAAKKIYQIADRMAMTTAGSVGDAQFLARIIKIEANLYEIRRER 72

Query: 86 PIQ 88
             
Sbjct: 73 KPT 75

>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 = 40.1 bits (93), Expect = 3e-05
 Identities = 10/61 (16%), Positives = 25/61 (40%)

Query: 27 LVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEP 86
          +  ++  T+     S + +++ +I+  +   +AG  +D          Q R +    +E 
Sbjct: 14 VAVDSRATAGNWVASQTVKRVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREKER 73

Query: 87 I 87
          I
Sbjct: 74 I 74

>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 = 35.5 bits (81), Expect = 0.001
 Identities = 12/66 (18%), Positives = 25/66 (37%)

Query: 61  IMSDANILINTARVQARRYAYAYQEPIQDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEK 120
           + SD   L            +AY     +YK D++ ++A+ L  + +       + +   
Sbjct: 115 VDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAAHRDAYSGGS 174

Query: 121 LELAEV 126
           + L  V
Sbjct: 175 VNLYHV 180

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	161
d1iruc_	250	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rypb_	250	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1j2pa_	243	Proteasome alpha subunit (non-catalytic) {Archaeon	100.0
d1rypc_	244	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1irua_	244	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rypd_	241	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1irub_	233	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1irue_	234	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1irug_	245	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1iruf_	238	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rypf_	233	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1irud_	243	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rypa_	243	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1rype_	242	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1rypg_	244	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1yara1	221	Proteasome alpha subunit (non-catalytic) {Archaeon	100.0
d1yarh1	203	Proteasome beta subunit (catalytic) {Archaeon Ther	99.94
d1j2qh_	202	Proteasome beta subunit (catalytic) {Archaeon Arch	99.93
d1rypl_	212	Proteasome beta subunit (catalytic) {Baker's yeast	99.93
d1irul_	201	Proteasome beta subunit (catalytic) {Cow (Bos taur	99.93
d1ryph_	205	Proteasome beta subunit (catalytic) {Baker's yeast	99.93
d1q5qa_	227	Proteasome alpha subunit (non-catalytic) {Rhodococ	99.93
d1q5qh_	224	Proteasome beta subunit (catalytic) {Rhodococcus e	99.92
d1iruh_	202	Proteasome beta subunit (catalytic) {Cow (Bos taur	99.91
d1rypk_	198	Proteasome beta subunit (catalytic) {Baker's yeast	99.9
d1iruj_	204	Proteasome beta subunit (catalytic) {Cow (Bos taur	99.88
d1rypi_	222	Proteasome beta subunit (catalytic) {Baker's yeast	99.88
d1irui_	220	Proteasome beta subunit (catalytic) {Cow (Bos taur	99.88
d1ryp2_	233	Proteasome beta subunit (catalytic) {Baker's yeast	99.87
d1iruk_	199	Proteasome beta subunit (catalytic) {Cow (Bos taur	99.86
d1iru1_	213	Proteasome beta subunit (catalytic) {Cow (Bos taur	99.86
d1ryp1_	222	Proteasome beta subunit (catalytic) {Baker's yeast	99.85
d1rypj_	204	Proteasome beta subunit (catalytic) {Baker's yeast	99.84
d1iru2_	217	Proteasome beta subunit (catalytic) {Cow (Bos taur	99.82
d2z3ba1	180	HslV (ClpQ) protease {Bacillus subtilis [TaxId: 14	99.45
d1m4ya_	171	HslV (ClpQ) protease {Thermotoga maritima [TaxId:	99.28
d1g3ka_	173	HslV (ClpQ) protease {Haemophilus influenzae [TaxI	99.22

>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=1e-40  Score=261.08  Aligned_cols=156  Identities=47%  Similarity=0.736  Sum_probs=143.9

Q ss_pred             CCCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHH
Q 040809            2 SRRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMS   63 (161)
Q Consensus         2 ~~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~   63 (161)
                      +++||+++|+|||||||+|||||                 | |||+|+|.++++++.++..+|||+|++||+|++||+.+
T Consensus         1 ~~~yd~~~t~fsp~Grl~QvEyA~kav~~G~tvvgik~~dgVvlaad~~~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~   80 (250)
T d1iruc_           1 SRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVFFSEKIYKLNEDMACSVAGITS   80 (250)
T ss_dssp             CTTTCCCTTCCCTTSCCHHHHHHHHHHTTSCCEEEEBCSSEEEEEECCCCCCTTBCCCSSCSSEEECSSSEEEEEEECHH
T ss_pred             CCccCCCCeeECCCCcchHHHHHHHHHhcCCcEEEEEeCCEEEEEEeCccccCCcccCcccceEEECCCcEEEEeecccc
Confidence            58999999999999999999999                 6 99999999999998887889999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCc--------------------------------------------------------
Q 040809           64 DANILINTARVQARRYAYAYQEPI--------------------------------------------------------   87 (161)
Q Consensus        64 D~~~l~~~~r~~~~~y~~~~~~~i--------------------------------------------------------   87 (161)
                      |++.+++++|.++..|++.|++++                                                        
T Consensus        81 D~~~l~~~~r~~~~~~~~~~~~~i~~~~la~~l~~~~~~~~~~~~~rP~~~~~li~G~D~~~gp~Ly~~Dp~G~~~~~~~  160 (250)
T d1iruc_          81 DANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKA  160 (250)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBSSCCCCCEEEEEEEEETTTEEEEEEEETTTEEEECSE
T ss_pred             hHHHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHHHhhhccCCcceEEEEEEEEcCCCCCEEEEEcccccEeeeeE
Confidence            999999999999999999999988                                                        


Q ss_pred             ---------------cCCCC-CCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHh
Q 040809           88 ---------------QDYKD-DMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENF  151 (161)
Q Consensus        88 ---------------~~y~~-~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~  151 (161)
                                     ++|++ +||++||++++++||+.+++++..+++++||++|+++++ .+.|+.|+++||+++++++
T Consensus       161 ~a~G~gs~~a~~~Le~~y~~~~ms~eeai~la~~al~~~~~~d~~~~~~iei~ii~~~~~-~~~~~~l~~~Ei~~~l~~~  239 (250)
T d1iruc_         161 TCIGNNSAAAVSMLKQDYKEGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENG-KTVIRVLKQKEVEQLIKKH  239 (250)
T ss_dssp             EEESTTTTHHHHHHHHHCCTTCCCHHHHHHHHHHHHHHSSSCTTCCSTTCEEEEEECCSS-SCEEEECCHHHHHHHHHHH
T ss_pred             EEeCcChHHHHHHHHhhcccCCCCHHHHHHHHHHHHHHHhcccCCCCCeEEEEEEEcCCC-ceeEEECCHHHHHHHHHHH
Confidence                           35775 899999999999999999998999999999999999863 4469999999999999998


Q ss_pred             cccCCCC
Q 040809          152 GVAQPAS  158 (161)
Q Consensus       152 ~~~~~~~  158 (161)
                      .++..++
T Consensus       240 ~e~~~~a  246 (250)
T d1iruc_         240 EEEEAKA  246 (250)
T ss_dssp             HTTTTTT
T ss_pred             HHHhhhH
Confidence            7665544

>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=5.4e-39  Score=251.16  Aligned_cols=149  Identities=24%  Similarity=0.435  Sum_probs=135.1

Q ss_pred             CCCCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccH
Q 040809            1 MSRRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIM   62 (161)
Q Consensus         1 m~~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~   62 (161)
                      |+++||+++|+|||||||+|||||                 | |||+|+|.++++.+.+ ..+|||+|++|++|++||+.
T Consensus         1 m~~~yd~~~t~fsp~G~l~QvEyA~kav~~G~tvvgi~~~dgVvlaad~r~~~~~~~~~-~~~ki~~I~~~i~~~~sG~~   79 (250)
T d1rypb_           1 MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSE-TLSKVSLLTPDIGAVYSGMG   79 (250)
T ss_dssp             CCCCCCSBSSCBCTTSCBHHHHHHHHHHHTSCCEEEEEETTEEEEEEECCCSCSSBCGG-GCCSSEEEETTEEEEEEECH
T ss_pred             CCccccCCCceECCCCeehHHHHHHHHHHcCCCEEEEEeCCEEEEEEecccCCcccccc-ccceeEeccCCEEEEeeecc
Confidence            999999999999999999999999                 5 8999999998888765 78999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHH-HHHHhCCCc------------------------------------------------------
Q 040809           63 SDANILINTARVQARR-YAYAYQEPI------------------------------------------------------   87 (161)
Q Consensus        63 ~D~~~l~~~~r~~~~~-y~~~~~~~i------------------------------------------------------   87 (161)
                      +|++.++++++.+++. |++.+++++                                                      
T Consensus        80 ~D~~~l~~~~~~~~~~~y~~~~~~~~~~~~la~~~~~~~~~~~~~~~~rp~~v~~li~G~D~~~gp~Ly~id~~G~~~~~  159 (250)
T d1rypb_          80 PDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPW  159 (250)
T ss_dssp             HHHHHHHHHHHHHHHHTTHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCCEEEEEEEEETTTEEEEEEECTTSCEEEB
T ss_pred             cHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhcCCcCeeEEEEEEEecCCCCCEEEEEcCcEEEEEe
Confidence            9999999999999975 899999887                                                      


Q ss_pred             -----------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCC-----------ceeEEEC
Q 040809           88 -----------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSG-----------KVKYRIC  139 (161)
Q Consensus        88 -----------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g-----------~~~~~~l  139 (161)
                                       ++|+++|+++||++++++||+++++++ +++++++|+||++++..           .+.|++|
T Consensus       160 ~~~a~G~gs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~d-~s~~~iev~vi~~~~~~~~~~~~v~~~~~~~fr~l  238 (250)
T d1rypb_         160 KATAIGKGSVAAKTFLEKRWNDELELEDAIHIALLTLKESVEGE-FNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKL  238 (250)
T ss_dssp             SEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCCSC-CSTTTEEEEEECSCCGGGTSEESCSSCCCCSEEEC
T ss_pred             eEEecCcchHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHhhcc-CCCCCEEEEEEeCCCcccccccccccccCCceEEC
Confidence                             368999999999999999999999885 78999999999886420           1369999


Q ss_pred             CHHHHHHHHHHh
Q 040809          140 SPESLTMLLENF  151 (161)
Q Consensus       140 ~~~ei~~~l~~~  151 (161)
                      +++||+++|+.+
T Consensus       239 s~eei~~~l~~l  250 (250)
T d1rypb_         239 TSQEINDRLEAL  250 (250)
T ss_dssp             CHHHHHHHHTTC
T ss_pred             CHHHHHHHHHhC
Confidence            999999999864

>d1j2pa_ d.153.1.4 (A:) Proteasome alpha subunit (non-catalytic) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=100.00  E-value=5.5e-39  Score=250.32  Aligned_cols=150  Identities=37%  Similarity=0.658  Sum_probs=138.3

Q ss_pred             CCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHH
Q 040809            3 RRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSD   64 (161)
Q Consensus         3 ~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D   64 (161)
                      -|||+++|+|||||||+|||||                 | |||+|+|.++++.+.. ..+|||+|++||+|++||+.+|
T Consensus         3 ~gyd~~~t~fsp~Grl~QvEya~kav~~G~t~Igik~~dgVvlaad~r~~~~~~~~~-~~~KI~~I~~~i~~~~sG~~~D   81 (243)
T d1j2pa_           3 MGYDRAITVFSPDGRLFQVEYAREAVKRGATAIGIKCKEGVILIADKRVGSKLLEKD-TIEKIYKIDEHICAATSGLVAD   81 (243)
T ss_dssp             TTSSSCTTCCCTTSCCHHHHHHHHHHHTSCCEEEEEETTEEEEEEECCCSCTTBCGG-GCCSEEECSSSEEEEEEECHHH
T ss_pred             CCcCCCCccCCCCCcchHHHHHHHHHHcCCCEEEEEECCEEEEEEecCccccCcccc-ccccEeecCCcEEEEeeecccH
Confidence            4899999999999999999998                 6 9999999999988765 7899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCc---------------------------------------------------------
Q 040809           65 ANILINTARVQARRYAYAYQEPI---------------------------------------------------------   87 (161)
Q Consensus        65 ~~~l~~~~r~~~~~y~~~~~~~i---------------------------------------------------------   87 (161)
                      ++.+++++|.+++.|++.+++++                                                         
T Consensus        82 ~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~rP~~~~~il~G~D~~p~Ly~~Dp~G~~~~~~~~a~  161 (243)
T d1j2pa_          82 ARVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQYGGVRPFGVSLLIAGVNEVPKLYETDPSGALLEYKATAI  161 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCEEEEEEEESSSEEEEEECTTCCEEEBSEEEE
T ss_pred             HHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHHHHhhhccCCccceeEEEEEecCCceEEEEeccCceeeeeEEEe
Confidence            99999999999999999999988                                                         


Q ss_pred             ------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhcccC
Q 040809           88 ------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFGVAQ  155 (161)
Q Consensus        88 ------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~~~~  155 (161)
                                  +.|+++||++||+++|++||+.+++++ .+++++||++|+++++   .|++|+++||++++++++++.
T Consensus       162 G~g~~~a~~~Le~~y~~~ms~eeai~la~~~l~~~~~~d-~~~~~iei~iv~~~~~---~~~~l~~~ei~~~~~~~~e~~  237 (243)
T d1j2pa_         162 GMGRMAVTEFFEKEYRDDLSFDDAMVLGLVAMGLSIESE-LVPENIEVGYVKVDDR---TFKEVSPEELKPYVERANERI  237 (243)
T ss_dssp             STTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHHTSC-CCGGGEEEEEEETTTC---CCEECCHHHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHhhcccCCCHHHHHHHHHHHHHHHHhcc-cCCCceEEEEEEeCCC---cEEECCHHHHHHHHHHHHHHH
Confidence                        368999999999999999999999874 6778999999998865   599999999999999987765


Q ss_pred             CC
Q 040809          156 PA  157 (161)
Q Consensus       156 ~~  157 (161)
                      ++
T Consensus       238 ~~  239 (243)
T d1j2pa_         238 RE  239 (243)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=2.7e-38  Score=246.34  Aligned_cols=151  Identities=52%  Similarity=0.812  Sum_probs=140.1

Q ss_pred             CCCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHH
Q 040809            2 SRRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMS   63 (161)
Q Consensus         2 ~~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~   63 (161)
                      +++||+++|+|||||||+|||||                 | |||+|+|.++++++.++..+|||+|+++|+|++||+.+
T Consensus         2 ~~~yd~~~t~fsp~G~~~Qveya~~ai~~G~T~vgi~~~dgVvlaad~r~s~~~~~~~~~~~KI~~i~~~i~~~~sG~~~   81 (244)
T d1rypc_           2 SRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTSTEKLYKLNDKIAVAVAGLTA   81 (244)
T ss_dssp             CGGGCCCTTCBCTTSCBHHHHHHHHHHTTSCCEEEEEETTEEEEEEECSSCCSSBCSTTCCSSEEESSSSEEEEEEECHH
T ss_pred             CCccCCCceeECCCCcChHHHHHHHHHhcCCCEEEEEeCCEEEEEEeCCccCCCcccCCccceEEEcCCCeEEEEecccC
Confidence            57899999999999999999999                 6 89999999999999888899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCc--------------------------------------------------------
Q 040809           64 DANILINTARVQARRYAYAYQEPI--------------------------------------------------------   87 (161)
Q Consensus        64 D~~~l~~~~r~~~~~y~~~~~~~i--------------------------------------------------------   87 (161)
                      |++.+++.+|.+++.|++.+++++                                                        
T Consensus        82 D~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~rP~~~~~ll~G~d~~~gp~Ly~id~~Gs~~~~~~  161 (244)
T d1rypc_          82 DAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKA  161 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSCCCCCEEEEEEEEETTTEEEEEEECTTCCEEEBSE
T ss_pred             cHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhhhhccccCccceeEEEEEEecCCCceEEEecCCCcEeeeee
Confidence            999999999999999999999998                                                        


Q ss_pred             ---------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCC-CceeEEECCHHHHHHHHHHh
Q 040809           88 ---------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPS-GKVKYRICSPESLTMLLENF  151 (161)
Q Consensus        88 ---------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~-g~~~~~~l~~~ei~~~l~~~  151 (161)
                                     +.|+++||++||+.++++||+.+++++..+++++||++|++++. +...++.++++||+++|.+.
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                           36899999999999999999999999999999999999998753 22358899999999999875


Q ss_pred             c
Q 040809          152 G  152 (161)
Q Consensus       152 ~  152 (161)
                      .
T Consensus       242 ~  242 (244)
T d1rypc_         242 G  242 (244)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=4.1e-38  Score=245.53  Aligned_cols=148  Identities=30%  Similarity=0.541  Sum_probs=135.8

Q ss_pred             CCCCCCCCcccCCCCceeeEecc------------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccH
Q 040809            2 SRRYDRQTTVFSPEGRLYQVDYM------------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIM   62 (161)
Q Consensus         2 ~~~y~~~~~~fsp~Grl~qveya------------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~   62 (161)
                      ..|||+++|+|||||||+|||||                  | |||+|+|.++++.+.+ ..+|||+|++||+|++||+.
T Consensus         5 ~~gyd~~~t~Fsp~Grl~QvEYA~kav~~gg~t~igIk~~dgVVlaad~r~~~~~~~~~-~~~KI~~I~~~i~~~~sG~~   83 (244)
T d1irua_           5 SAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSS-TVTHLFKITENIGCVMTGMT   83 (244)
T ss_dssp             CCTTTTTSSCCCTTSCCHHHHHHHHHHHTTCCEEEEEECSSEEEEEEECCCCCSSBCGG-GCCSEEESSSSCEEEEEECH
T ss_pred             CCCcCCCCceECCCCeEhHHHHHHHHHHhCCccEEEEEcCCEEEEEEecccccccccCC-ccceEEEecCCcEEEEecch
Confidence            36899999999999999999999                  5 8999999998888876 78999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCc-------------------------------------------------------
Q 040809           63 SDANILINTARVQARRYAYAYQEPI-------------------------------------------------------   87 (161)
Q Consensus        63 ~D~~~l~~~~r~~~~~y~~~~~~~i-------------------------------------------------------   87 (161)
                      +|++.+++++|.+++.|++.|++++                                                       
T Consensus        84 ~D~~~l~~~~r~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rP~~v~~ll~G~D~~~g~~Ly~~Dp~G~~~~~~  163 (244)
T d1irua_          84 ADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFK  163 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSBCCCSEEEEEEEEETTTEEEEEEECTTSCEEEBS
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCCCchHHHHHHHHHHHHHhcccccCccceeeEEEEEcCCCCcEEEEEcCCccEEecc
Confidence            9999999999999999999999998                                                       


Q ss_pred             ----------------cCC--CCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHH
Q 040809           88 ----------------QDY--KDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLE  149 (161)
Q Consensus        88 ----------------~~y--~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~  149 (161)
                                      ++|  +++|+++||++++++||+.+++++ .+++++||+||+++++   .|++|+++||+++|.
T Consensus       164 ~~a~G~gs~~~~~~Le~~~~~~~d~t~eeai~l~~~~l~~~~~~d-~~~~~iev~ii~~~~~---~~~~l~~~ei~~~l~  239 (244)
T d1irua_         164 ATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCLSTVLSID-FKPSEIEVGVVTVENP---KFRILTEAEIDAHLV  239 (244)
T ss_dssp             EEEEETTHHHHHHHHHHHTTSCCCCCHHHHHHHHHHHHHHHTTCC-CCTTSEEEEEEETTEE---EEEECCHHHHHHHHH
T ss_pred             eEeccCchhHHHHHHHhccccccCCCHHHHHHHHHHHHHHHHhcC-CCCCcEEEEEEEeCCC---cEEECCHHHHHHHHH
Confidence                            246  458999999999999999999975 6778999999998864   699999999999999


Q ss_pred             Hhccc
Q 040809          150 NFGVA  154 (161)
Q Consensus       150 ~~~~~  154 (161)
                      +++++
T Consensus       240 ~~~~r  244 (244)
T d1irua_         240 ALAER  244 (244)
T ss_dssp             HHHTC
T ss_pred             HHhcC
Confidence            98763

>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=1e-37  Score=242.77  Aligned_cols=148  Identities=28%  Similarity=0.472  Sum_probs=136.6

Q ss_pred             CCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHH
Q 040809            4 RYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDA   65 (161)
Q Consensus         4 ~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~   65 (161)
                      |||+++|+|||||||+|||||                 | |||+|+|.++++++.+.+.+|||+|++|++|++||+.+|+
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            799999999999999999998                 5 9999999999999888788999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCc----------------------------------------------------------
Q 040809           66 NILINTARVQARRYAYAYQEPI----------------------------------------------------------   87 (161)
Q Consensus        66 ~~l~~~~r~~~~~y~~~~~~~i----------------------------------------------------------   87 (161)
                      +.+++++|.+++.|++.++++|                                                          
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            9999999999999999999998                                                          


Q ss_pred             --------------cCCC---CCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 040809           88 --------------QDYK---DDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLEN  150 (161)
Q Consensus        88 --------------~~y~---~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~  150 (161)
                                    +.|+   ++||++|++++|++||+++.++   +++++||+|+++++    .|++|+++||+++|.+
T Consensus       161 a~G~gs~~~~~~Le~~~~~~~~~~t~~e~i~lal~al~~~~~~---~~~~iei~ii~~d~----~~~~l~~~ei~~~l~~  233 (241)
T d1rypd_         161 TIGRNSKTVREFLEKNYDRKEPPATVEECVKLTVRSLLEVVQT---GAKNIEITVVKPDS----DIVALSSEEINQYVTQ  233 (241)
T ss_dssp             EESTTHHHHHHHHHTTCCTTSCCCSHHHHHHHHHHHHHHHHCS---CSTTEEEEEEETTT----EEEECCHHHHHHHHHH
T ss_pred             EECcCHHHHHHHHHHhhhcccCCCCHHHHHHHHHHHHHHHhcC---CCCcEEEEEEECCC----CEEECCHHHHHHHHHH
Confidence                          3574   4699999999999999998854   57899999999986    6999999999999999


Q ss_pred             hcccCCCC
Q 040809          151 FGVAQPAS  158 (161)
Q Consensus       151 ~~~~~~~~  158 (161)
                      ++++++++
T Consensus       234 i~~~~~~~  241 (241)
T d1rypd_         234 IEQEKQEQ  241 (241)
T ss_dssp             HTHHHHCC
T ss_pred             HHHHHhcC
Confidence            98876653

>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=1.2e-37  Score=240.60  Aligned_cols=144  Identities=28%  Similarity=0.514  Sum_probs=133.3

Q ss_pred             CCCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHH
Q 040809            2 SRRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMS   63 (161)
Q Consensus         2 ~~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~   63 (161)
                      .+|||+++|+|||||||+|||||                 | |||+|+|.+.+++.. +..+|||+|++|++|+.||+.+
T Consensus         2 ~~gyd~~~t~fsp~Gr~~Qveya~kav~~G~tvigik~~dgVvlaaD~r~~~~~~~~-~~~~ki~~i~~~i~~~~sG~~~   80 (233)
T d1irub_           2 ERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDE-RSVHKVEPITKHIGLVYSGMGP   80 (233)
T ss_dssp             CCCCCSBSCCCCTTSCCHHHHHHHHHHHTSCCEEEEECSSCEEEEEECCCCCSSBCS-TTCCSSEESSSSEEEEEEECHH
T ss_pred             CCCcCCCCCeECCCCcChHHHHHHHHHHcCCCEEEEEeCCEEEEEEeCCcccCCccc-cccceEEEecCceEEEEeccch
Confidence            48999999999999999999999                 5 899999999988764 4889999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCc--------------------------------------------------------
Q 040809           64 DANILINTARVQARRYAYAYQEPI--------------------------------------------------------   87 (161)
Q Consensus        64 D~~~l~~~~r~~~~~y~~~~~~~i--------------------------------------------------------   87 (161)
                      |++.+++++|.+++.|++.+++++                                                        
T Consensus        81 D~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~p~~~~~li~g~d~~~~~ly~id~~G~~~~~~~~  160 (233)
T d1irub_          81 DYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKAT  160 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCSEEEEEEEECSSSEEEEEECTTSCEEEBSEE
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhccccccceEEEeeeecccCCceEEEEcCCcceEeccce
Confidence            999999999999999999999988                                                        


Q ss_pred             --------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhc
Q 040809           88 --------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFG  152 (161)
Q Consensus        88 --------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~  152 (161)
                                    +.|+++||++||++++++||+.+++++ .++.+++|++|+++     ++++|+++||+++|+.++
T Consensus       161 a~G~gs~~~~~~Le~~~~~~ms~eea~~l~~~~L~~~~~~d-~~~~~vev~ii~~~-----g~~~l~~~eI~~~l~~i~  233 (233)
T d1irub_         161 AMGKNYVNGKTFLEKRYNEDLELEDAIHTAILTLKESFEGQ-MTEDNIEVGICNEA-----GFRRLTPTEVKDYLAAIA  233 (233)
T ss_dssp             EESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHTTCCSC-CCSSSEEEEEEETT-----EEEECCHHHHHHHHTTCC
T ss_pred             ecCCcHHHHHHHHHhhcccCccHHHHHHHHHHHHHHHHhcc-CCCCcEEEEEEeCC-----CeEECCHHHHHHHHHHhC
Confidence                          368999999999999999999999875 57789999999977     599999999999998763

>d1irue_ d.153.1.4 (E:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=2.4e-37  Score=239.66  Aligned_cols=141  Identities=38%  Similarity=0.704  Sum_probs=131.2

Q ss_pred             CCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHH
Q 040809            5 YDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDAN   66 (161)
Q Consensus         5 y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~   66 (161)
                      ||+++|+|||||||+|||||                 | |||+|+|.+.++...+ ..+|||+|++||+|++||+.+|++
T Consensus         1 yd~~~t~fsp~G~l~QvEYa~kav~~G~t~vgik~~dgVvlaad~~~~~~~~~~~-~~~KI~~I~~~i~~~~sG~~~D~~   79 (234)
T d1irue_           1 YDRGVNTFSPEGRLFQVEYDIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEPS-SIEKIVEIDAHIGCAMSGLIADAK   79 (234)
T ss_dssp             CCCCTTCBCTTSCBHHHHHHHHHHTTSCCEEEEEETTEEEEEEECCCCCTTBCTT-SCCSEEEEETTEEEEEEECHHHHH
T ss_pred             CCCCCceECCCCcchHHHHHHHHHHcCCCEEEEEeCCEEEEEEecCccCCCcccC-cccCEEEccCcEEEEEeeccchHH
Confidence            89999999999999999998                 6 8999999999987765 789999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCc-----------------------------------------------------------
Q 040809           67 ILINTARVQARRYAYAYQEPI-----------------------------------------------------------   87 (161)
Q Consensus        67 ~l~~~~r~~~~~y~~~~~~~i-----------------------------------------------------------   87 (161)
                      .+++.+|.++..|++.+++++                                                           
T Consensus        80 ~l~~~~~~~~~~~~~~~~~~i~~~~la~~i~~~~~~~t~~~~~~~~~~rP~~~~~il~G~D~~gp~Ly~idp~G~~~~~~  159 (234)
T d1irue_          80 TLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMSRPFGVALLFGGVDEKGPQLFHMDPSGTFVQCD  159 (234)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCBCSTTCCSSCBSSCCCEEEEEEEEETTEEEEEEECTTSCEEEBS
T ss_pred             HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHhhcccccccccccceEEEEEEEEcCCCCEEEEEecCcccceee
Confidence            999999999999999999887                                                           


Q ss_pred             ----------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHh
Q 040809           88 ----------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENF  151 (161)
Q Consensus        88 ----------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~  151 (161)
                                      +.|+++|+++||+++|++||+.+.++ ..++.++||++|+++.    .|++|+++||+++++++
T Consensus       160 ~~a~G~gs~~~~~~Le~~~~~~~~~eeai~~a~~al~~~~~~-~~~~~~iei~ii~~~~----~~k~l~~~ei~~~l~~i  234 (234)
T d1irue_         160 ARAIGSASEGAQSSLQELYHKSMTLKEAIKSSLIILKQVMEE-KLNATNIELATVQPGQ----NFHMFTKEELEEVIKDI  234 (234)
T ss_dssp             EEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCSS-CCCTTSEEEEEECSSS----CCEECCHHHHHHHHTTC
T ss_pred             eEEeCCchHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHhc-cCCCCCEEEEEEECCC----CEEECCHHHHHHHHHhC
Confidence                            36899999999999999999999876 5888999999999875    59999999999999864

>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=9.4e-38  Score=243.74  Aligned_cols=150  Identities=29%  Similarity=0.440  Sum_probs=136.3

Q ss_pred             CCCCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccH
Q 040809            1 MSRRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIM   62 (161)
Q Consensus         1 m~~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~   62 (161)
                      |..+||+++|+|||||||+|||||                 | |||+|+|.+.+++..+ ..+|||+|++||+|++||+.
T Consensus         3 ~~~~yd~~~t~Fsp~Grl~QvEYa~~av~~G~t~VGik~~dgVvlaad~~~~~~~~~~~-~~~Ki~~I~~~i~~~~sG~~   81 (245)
T d1irug_           3 IGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEG-SNKRLFNVDRHVGMAVAGLL   81 (245)
T ss_dssp             CCSSTTSCTTCCCTTSCCHHHHHHHHHHHTSCCEEEEECSSBEEEEEEEECSCTTBCTT-TTCCEEEEETTEEEEEEECH
T ss_pred             CccccCCCCceECCCCeehHHHHHHHHHHcCCcEEEEEeCCEEEEEEeccccccccccC-ccceEEEcCCCEEEEeccCc
Confidence            568999999999999999999999                 5 9999999999888765 78999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCc-------------------------------------------------------
Q 040809           63 SDANILINTARVQARRYAYAYQEPI-------------------------------------------------------   87 (161)
Q Consensus        63 ~D~~~l~~~~r~~~~~y~~~~~~~i-------------------------------------------------------   87 (161)
                      +|++.+++++|.+++.|+++|++++                                                       
T Consensus        82 ~D~~~l~~~~~~~~~~~~~~~g~~i~~~~la~~la~~~~~~t~~~~~rP~~vs~li~G~D~~~gp~Ly~iDp~G~~~~~~  161 (245)
T d1irug_          82 ADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYW  161 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSBSSBCCCSEEEEEEEEETTTEEEEEEECTTCCEEEBS
T ss_pred             hhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhccccccccceEEEEEEEcCCCCceEEEEcCCceEEeee
Confidence            9999999999999999999999998                                                       


Q ss_pred             ----------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHh
Q 040809           88 ----------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENF  151 (161)
Q Consensus        88 ----------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~  151 (161)
                                      +.|+++||.+||++++++||+.+++++..++.+|||++|++++++   ++++.++|+.+.+.++
T Consensus       162 ~~a~G~gs~~a~~~Le~~~~~dmt~eea~~l~~~~l~~~~~~~~~~~~~iei~~v~~~~~~---~~~~~~~e~~~~~~~~  238 (245)
T d1irug_         162 GCAIGKARQAAKTEIEKLQMKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNG---RHEIVPKDIREEAEKY  238 (245)
T ss_dssp             EEEESTTHHHHHHHHTTSCGGGCCHHHHHHHHHHHHHHHSCSSSSCCEEEEEEECBTTTTT---CCEECCHHHHHHHHHH
T ss_pred             EEEECCccHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEEEEecCCC---eEEEChHHHHHHHHHH
Confidence                            468999999999999999999999888888999999999987654   5677788888887777


Q ss_pred             ccc
Q 040809          152 GVA  154 (161)
Q Consensus       152 ~~~  154 (161)
                      +++
T Consensus       239 ~~~  241 (245)
T d1irug_         239 AKE  241 (245)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            554

>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=1e-37  Score=242.44  Aligned_cols=146  Identities=25%  Similarity=0.468  Sum_probs=132.8

Q ss_pred             CCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHH
Q 040809            3 RRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSD   64 (161)
Q Consensus         3 ~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D   64 (161)
                      ++||+++|+|||||||+|||||                 | |||+|+|.++++.+   +.+|||+|+++|+|++||+.+|
T Consensus         1 ~~yd~~~tiFsp~Grl~QvEYA~kav~~G~t~vgik~~dgVvlaad~~~~~~~~~---~~~KI~~I~~~i~~~~sG~~~D   77 (238)
T d1iruf_           1 NQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAA---HQKKILHVDNHIGISIAGLTAD   77 (238)
T ss_dssp             CTTTSCTTCCCTTSCCHHHHHHHHHHHHSCCEEEEECSSEEEEEEECCCSSTTBC---CCCCEEEEETTEEEEEEECHHH
T ss_pred             CCCCCCCeeECCCCcchHHHHHHHHHhcCCCEEEEEeCCEEEEEEecccccCCCC---ccceEEEeCCceEEEEeccchH
Confidence            5899999999999999999999                 5 89999999999875   4589999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCc---------------------------------------------------------
Q 040809           65 ANILINTARVQARRYAYAYQEPI---------------------------------------------------------   87 (161)
Q Consensus        65 ~~~l~~~~r~~~~~y~~~~~~~i---------------------------------------------------------   87 (161)
                      ++.+++++|.++..|+++|++++                                                         
T Consensus        78 ~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~l~~~~~~y~~~~~~rP~~v~~il~G~D~~gp~Ly~~D~~G~~~~~~~~a  157 (238)
T d1iruf_          78 ARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAGYDDMGPHIFQTCPSANYFDCRAMS  157 (238)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEETTEEEEEEECSSSCEEEESEEE
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHHHhhccCCCcccceEEEEEEcCCCceEEEEcCCCCEEeeeeEE
Confidence            99999999999999999999998                                                         


Q ss_pred             -------------cCCCCC--CCHHHHHHHHHHHHHHhhccC-CCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHh
Q 040809           88 -------------QDYKDD--MTRQEAVQLALKVLRKTMDST-SLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENF  151 (161)
Q Consensus        88 -------------~~y~~~--mt~eeai~la~~al~~~~~~~-~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~  151 (161)
                                   ++|+++  ++++||+++|++||++++.++ .+++.+|||++|++++    .|++++++||+++|+++
T Consensus       158 ~G~g~~~~~~~Lek~~~~~~~~~~~eav~lai~al~~~~~~~~~~~~~~iev~ii~k~~----~~~~l~~~ei~~~l~~i  233 (238)
T d1iruf_         158 IGARSQSARTYLERHMSEFMECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDL----EFTIYDDDDVSPFLEGL  233 (238)
T ss_dssp             ESTTHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCTTCCCCTTTEEEEEEETTE----EEEEECSGGGHHHHTTC
T ss_pred             ECCCchhhHHHHHhhcccccCCCHHHHHHHHHHHHHHHHhhcccCCCCcEEEEEEeCCC----CEEECCHHHHHHHHHHH
Confidence                         246775  489999999999999998654 5789999999999875    69999999999999999


Q ss_pred             cccC
Q 040809          152 GVAQ  155 (161)
Q Consensus       152 ~~~~  155 (161)
                      ++.+
T Consensus       234 ~ek~  237 (238)
T d1iruf_         234 EERP  237 (238)
T ss_dssp             CCCC
T ss_pred             HhCc
Confidence            7754

>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=7.7e-38  Score=242.46  Aligned_cols=140  Identities=27%  Similarity=0.418  Sum_probs=129.9

Q ss_pred             CCCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHH
Q 040809            2 SRRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMS   63 (161)
Q Consensus         2 ~~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~   63 (161)
                      +++||+++|+|||||||+|||||                 | |||+|+|.++++..   +.+|||+|++|++|++||+.+
T Consensus         2 ~~~yd~~~t~FspdGrl~QvEyA~kav~~g~t~igi~~~dgvvlaad~~~~~~l~~---~~~KI~~I~~~i~~~~sG~~~   78 (233)
T d1rypf_           2 RNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSS---YQKKIIKCDEHMGLSLAGLAP   78 (233)
T ss_dssp             HHHHSSCTTCCCTTSCCHHHHHHHHHHHTSCCEEEEECSSEEEEEEECCCSSTTBC---CCCCEEEEETTEEEEEEECHH
T ss_pred             CccccCCCceECCCCcChHHHHHHHHHHcCCCEEEEEECCeEEEEEeccccccCCc---chheEEEcCCCEEEEEeeccc
Confidence            36899999999999999999999                 6 99999999988743   678999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCc--------------------------------------------------------
Q 040809           64 DANILINTARVQARRYAYAYQEPI--------------------------------------------------------   87 (161)
Q Consensus        64 D~~~l~~~~r~~~~~y~~~~~~~i--------------------------------------------------------   87 (161)
                      |++.+++++|.+++.|++.|+++|                                                        
T Consensus        79 D~~~l~~~~r~~~~~~~~~~~~~i~~~~la~~l~~~~~~~t~~~~~RP~gv~~il~G~d~~g~~Ly~idp~G~~~~~~~~  158 (233)
T d1rypf_          79 DARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGT  158 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEETTEEEEEEECTTSCEEEESEE
T ss_pred             cHHHHHHHHHHHHHhhhhhcCCCCcHHHHHHHHHHHHHHHhcccccCCccceEEEEEEcCCCCEEEEEccccceecccEE
Confidence            999999999999999999999998                                                        


Q ss_pred             ------------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHH
Q 040809           88 ------------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLL  148 (161)
Q Consensus        88 ------------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l  148 (161)
                                        +.|+++|+++|+++++++||..+++++.++++++||+||++++    +|++|+++||+++|
T Consensus       159 aiG~gs~~a~~~Le~~~~~~~~~dms~eeai~l~~~~l~~~~~~d~~~~~~iev~ii~k~~----~~~~l~~~ei~~~i  233 (233)
T d1rypf_         159 AIGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDT----PFTIYDGEAVAKYI  233 (233)
T ss_dssp             EESTTHHHHHHHHHHHHHHHTTCCSCHHHHHHHHHHHHTTSCCSSCCCTTTEEEEEEETTE----EEEEEEGGGGGGGC
T ss_pred             EecCchHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHHhccCCCCCeEEEEEEECCC----CeEECCHHHHHhhC
Confidence                              1367899999999999999999999999999999999999986    69999999998764

>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=8.4e-37  Score=237.82  Aligned_cols=149  Identities=31%  Similarity=0.512  Sum_probs=135.1

Q ss_pred             CCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHH
Q 040809            4 RYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDA   65 (161)
Q Consensus         4 ~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~   65 (161)
                      .||+++|+|||||||+|||||                 | |||+|+|.+.++...+ ..+|||+|+++|+|++||+.+|+
T Consensus         1 ~yd~~~t~Fsp~Grl~QvEya~kav~~G~Tvvgik~~dgVvla~d~r~~~~~~~~~-~~~KI~~i~~~i~~~~sG~~~D~   79 (243)
T d1irud_           1 SYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDER-TVRKICALDDNVCMAFAGLTADA   79 (243)
T ss_dssp             CCCCCCSCCCTTSCCHHHHHHHHHHHTSCCEEEECCSSEEEEEECCCCCCSSSCGG-GGCSEEESSSSCEEEEEECHHHH
T ss_pred             CCCCCCeeECCCCcchHHHHHHHHHhcCCCEEEEEeCCEEEEEEeccccCcccCCC-ccccEEECCCCEEEEEEEchhhH
Confidence            599999999999999999999                 6 9999999887777654 88999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCc----------------------------------------------------------
Q 040809           66 NILINTARVQARRYAYAYQEPI----------------------------------------------------------   87 (161)
Q Consensus        66 ~~l~~~~r~~~~~y~~~~~~~i----------------------------------------------------------   87 (161)
                      +.+++.+|.+++.|++.|+++|                                                          
T Consensus        80 ~~l~~~~~~~~~~~~~~~~~~i~v~~la~~ls~~~~~~t~~~~~rp~~v~~li~G~D~~~~p~Ly~idp~G~~~~~~~~a  159 (243)
T d1irud_          80 RIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANA  159 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCEEEEEEEECSSSCEEEEEECTTSCEEEBSEEE
T ss_pred             HHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHhcccCCccceEEEEEEEcCCCCCEEEEecCcEEEEeccEEE
Confidence            9999999999999999999988                                                          


Q ss_pred             -------------cCCCCCC--CHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhc
Q 040809           88 -------------QDYKDDM--TRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFG  152 (161)
Q Consensus        88 -------------~~y~~~m--t~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~  152 (161)
                                   +.|+++|  +.++++++|+++|.....   .++++++|++|+++.    .|++++++||++++.+++
T Consensus       160 ~G~gs~~a~~~Lek~~~~~~~~~~~~~i~~ai~~l~~~~~---~~~~~vei~ii~k~~----~~~~l~~~eI~~~l~~i~  232 (243)
T d1irud_         160 IGRGAKSVREFLEKNYTDEAIETDDLTIKLVIKALLEVVQ---SGGKNIELAVMRRDQ----SLKILNPEEIEKYVAEIE  232 (243)
T ss_dssp             ESTTHHHHHHHHTTTCCSSTTCSHHHHHHHHHHHHHTTSC---TTSTTCCEEEEESSS----CEECCCHHHHHHHTTTTT
T ss_pred             ECCChHHHHHHHHHhcccCCCccHHHHHHHHHHHHHHHhc---CCCCcEEEEEEECCC----CEEECCHHHHHHHHHHHH
Confidence                         4688988  678899999999998764   467899999999875    599999999999999999


Q ss_pred             ccCCCCCC
Q 040809          153 VAQPASEV  160 (161)
Q Consensus       153 ~~~~~~~~  160 (161)
                      ++..++|.
T Consensus       233 ~~~~~~~~  240 (243)
T d1irud_         233 KEKEENEK  240 (243)
T ss_dssp             TTTTTTTS
T ss_pred             hhhhhhhh
Confidence            88888764

>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=6.7e-37  Score=238.32  Aligned_cols=144  Identities=26%  Similarity=0.463  Sum_probs=132.0

Q ss_pred             CCCCCCcccCCCCceeeEecc------------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHH
Q 040809            4 RYDRQTTVFSPEGRLYQVDYM------------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSD   64 (161)
Q Consensus         4 ~y~~~~~~fsp~Grl~qveya------------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D   64 (161)
                      |||+++|+|||+|||+|||||                  | |||+|+|.++++.... ..+||++|++||+|++||+.+|
T Consensus         2 gyd~~~t~fsp~Grl~QvEYA~~av~~~g~T~igik~~dgVvlaad~r~~~~l~~~~-~~~KI~~i~~~i~~~~sG~~~D   80 (243)
T d1rypa_           2 GYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPT-TVSYIFCISRTIGMVVNGPIPD   80 (243)
T ss_dssp             GGGGTSSSCCTTSCCHHHHHHHHHTTTTCCCEEEEECSSEEEEEEECCCCCTTBCGG-GCCSEEECSSSCEEEEESCHHH
T ss_pred             CCCCCCCeECCCCeehHHHHHHHHHHccCceEEEEEcCCEEEEEEeccccccccccC-cccceEecCCCEEEEEecCcHH
Confidence            899999999999999999998                  5 9999999998887665 7899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCc---------------------------------------------------------
Q 040809           65 ANILINTARVQARRYAYAYQEPI---------------------------------------------------------   87 (161)
Q Consensus        65 ~~~l~~~~r~~~~~y~~~~~~~i---------------------------------------------------------   87 (161)
                      ++.+++++|.+++.|++.+++++                                                         
T Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~ls~~~~~~~~~~~~rP~~v~~ll~G~D~~~g~~Ly~~Dp~G~~~~~~~~  160 (243)
T d1rypa_          81 ARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKAT  160 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTSCCCSCEEEEEEEETTTEEEEEEECTTSCEEEBSEE
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcccccCccceEEEEEEccCCCCeEEEEcCCEEEEecceE
Confidence            99999999999999999999988                                                         


Q ss_pred             --------------cCCC-------CCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHH
Q 040809           88 --------------QDYK-------DDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTM  146 (161)
Q Consensus        88 --------------~~y~-------~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~  146 (161)
                                    ++|+       +++|++|++++|++||+.+.+++ .+++++||++++++     +|++|+++||++
T Consensus       161 a~G~gs~~~~~~Le~~~~~~~~~~~~~~s~eeav~la~~~l~~~~~~d-~~~~~iei~iitk~-----g~~~l~~eeI~~  234 (243)
T d1rypa_         161 ATGPKQQEITTNLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTE-FSKNDLEVGVATKD-----KFFTLSAENIEE  234 (243)
T ss_dssp             EESTTHHHHHHHHHHHHHHHCSSSCCCSSHHHHHHHHHHHHHHHHTCC-CCTTSEEEEEEETT-----EEEECCHHHHHH
T ss_pred             EeCccHHHHHHHHHHHhhcccccccccccHHHHHHHHHHHHHHHhhcc-CCCCcEEEEEEeCC-----ceEEeCHHHHHH
Confidence                          2344       46799999999999999999985 68899999999987     599999999999


Q ss_pred             HHHHhccc
Q 040809          147 LLENFGVA  154 (161)
Q Consensus       147 ~l~~~~~~  154 (161)
                      +|..+.+.
T Consensus       235 ~l~~i~e~  242 (243)
T d1rypa_         235 RLVAIAEQ  242 (243)
T ss_dssp             HHHHHTTT
T ss_pred             HHHHHhcc
Confidence            99998764

>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=4.4e-36  Score=233.42  Aligned_cols=147  Identities=35%  Similarity=0.569  Sum_probs=134.8

Q ss_pred             CCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHH
Q 040809            6 DRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANI   67 (161)
Q Consensus         6 ~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~   67 (161)
                      |+++|+|||||||+|||||                 | |||+|+|.+.++...+ +.+|||+|+++|+|++||+.+|++.
T Consensus         1 d~~~t~fsp~G~l~Qveya~~a~~~G~t~Vgi~~~dgVvla~d~r~~~~~~~~~-~~~Ki~~i~~~i~~~~sG~~~D~~~   79 (242)
T d1rype_           1 DRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESD-SIEKIVEIDRHIGCAMSGLTADARS   79 (242)
T ss_dssp             CCCTTCBCTTSCBHHHHHHHHHHTTSCCEEEEECSSCEEEEEECCCSSTTBCGG-GCCCEEEEETTEEEEEEESGGGHHH
T ss_pred             CCCcceECCCCcchHHHHHHHHHHcCCCEEEEEeCCEEEEEEeCCccCcCcccC-ccceEEEcCCCEEEEEeecchhHHH
Confidence            7899999999999999999                 5 9999999999876654 7899999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhCCCc------------------------------------------------------------
Q 040809           68 LINTARVQARRYAYAYQEPI------------------------------------------------------------   87 (161)
Q Consensus        68 l~~~~r~~~~~y~~~~~~~i------------------------------------------------------------   87 (161)
                      +++++|.+++.|++.+++++                                                            
T Consensus        80 l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~rP~~~~~ii~G~D~~~~p~L~~idp~G~~~~~  159 (242)
T d1rype_          80 MIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRY  159 (242)
T ss_dssp             HHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCCBSSCTTSCCCBSSCCSEEEEEEEEETTTEEEEEEECTTSCEEEB
T ss_pred             HHHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHhccccccchhccccceEEEEEEEeccccceEEEEEcCCCceecc
Confidence            99999999999999999887                                                            


Q ss_pred             -----------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 040809           88 -----------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLEN  150 (161)
Q Consensus        88 -----------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~  150 (161)
                                       ++|+++||++||+.++++||+.++++ ..++++++|++|+++.    +|++++++||++++.+
T Consensus       160 ~~~a~G~gs~~~~~~Le~~~~~~ms~~ea~~la~~~l~~~~~~-~~~~~~~~v~~i~~~~----g~~~l~~~~i~~~~~~  234 (242)
T d1rype_         160 NAKAIGSGSEGAQAELLNEWHSSLTLKEAELLVLKILKQVMEE-KLDENNAQLSCITKQD----GFKIYDNEKTAELIKE  234 (242)
T ss_dssp             SEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCSS-CCCTTSEEEEEEETTT----EEEECCHHHHHHHHHH
T ss_pred             ceeecccchHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHhc-cCCCCceEEEEEECCC----CeEECCHHHHHHHHHH
Confidence                             36899999999999999999999986 4677789999999875    5999999999999999


Q ss_pred             hcccCCCC
Q 040809          151 FGVAQPAS  158 (161)
Q Consensus       151 ~~~~~~~~  158 (161)
                      +.++.++|
T Consensus       235 i~e~~~~e  242 (242)
T d1rype_         235 LKEKEAAE  242 (242)
T ss_dssp             HHHHHTTC
T ss_pred             HHHhhhcC
Confidence            98877654

>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=5.5e-36  Score=233.45  Aligned_cols=149  Identities=27%  Similarity=0.434  Sum_probs=133.4

Q ss_pred             CCCCCCCcccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHH
Q 040809            3 RRYDRQTTVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSD   64 (161)
Q Consensus         3 ~~y~~~~~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D   64 (161)
                      .|||+++|+|||||||+|||||                 | |||+|+|.++++.+++ ..+||++|++||+|+.||+.+|
T Consensus         2 ~gyd~~~t~fsp~Grl~QvEya~kav~~G~t~igik~~dgVvlaad~~~~~~~~~~~-~~~KI~~I~~~i~~~~sG~~~D   80 (244)
T d1rypg_           2 TGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQ-KNVKIQVVDRHIGCVYSGLIPD   80 (244)
T ss_dssp             CCTTSSTTCCCTTSCCHHHHHHHHHHHTSCCEEEEEETTEEEEEEEEECCCTTBCTT-TSCCCEEETTTEEEEEEECHHH
T ss_pred             CCcCCCCceECCCCeehHHHHHHHHHHcCCCEEEEEeCCEEEEEEecccCCCCcccc-ccceEEEccCceEEEEccchhh
Confidence            5899999999999999999999                 6 8999999999998876 5789999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCc---------------------------------------------------------
Q 040809           65 ANILINTARVQARRYAYAYQEPI---------------------------------------------------------   87 (161)
Q Consensus        65 ~~~l~~~~r~~~~~y~~~~~~~i---------------------------------------------------------   87 (161)
                      ++.+++++|.+++.|++.|++++                                                         
T Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~t~~~~~RP~~~~~iiaG~D~~gp~Ly~idp~Gs~~~~~~~a  160 (244)
T d1rypg_          81 GRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAA  160 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSCTTBCCCCEEEEEEEEETTEEEEEEECTTSCEEEBSEEE
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhcccccCCceEEEEEEEEeCCCCEEEEEcCCccEEecCeEe
Confidence            99999999999999999999998                                                         


Q ss_pred             ----------------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHh
Q 040809           88 ----------------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENF  151 (161)
Q Consensus        88 ----------------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~  151 (161)
                                      ..|+++||++||++++++||+.+++++..++.++||++|+.++.+ ..++.++.++++++++..
T Consensus       161 ~G~gs~~~~~~Lek~~~~~~~~mt~eeai~la~~~L~~~~~~~~~~~~~iev~ii~~~~~~-~~~~~~~~e~~~~~~~~~  239 (244)
T d1rypg_         161 TGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETN-GLHKFVKGDLLQEAIDFA  239 (244)
T ss_dssp             ESTTHHHHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHGGGGTTSCEEEEEEEEETTTTT-TSEEECCTHHHHHHHHHH
T ss_pred             cCCccHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHhcccCCCCeEEEEEEEEEcCC-CeEEECCHHHHHHHHHHH
Confidence                            148999999999999999999999888888899999999864321 157777777788888776


Q ss_pred             cc
Q 040809          152 GV  153 (161)
Q Consensus       152 ~~  153 (161)
                      .+
T Consensus       240 ~~  241 (244)
T d1rypg_         240 QK  241 (244)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

>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=4.6e-35  Score=224.86  Aligned_cols=133  Identities=36%  Similarity=0.653  Sum_probs=122.8

Q ss_pred             cccCCCCceeeEecc-----------------e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHH
Q 040809           10 TVFSPEGRLYQVDYM-----------------G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINT   71 (161)
Q Consensus        10 ~~fsp~Grl~qveya-----------------G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~   71 (161)
                      |+|||||||+|||||                 | |||+|+|.++++...+ ..+|||+|++|++|++||+.+|++.+.+.
T Consensus         1 t~fsp~G~l~QvEYa~~av~~G~t~vgi~~~dgVvlaad~r~~~~~~~~~-~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~   79 (221)
T d1yara1           1 TVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQN-SIEKIQLIDDYVAAVTSGLVADARVLVDF   79 (221)
T ss_dssp             CCCCTTSCCHHHHHHHHHHTTSCCEEEEEETTEEEEEECCCCCCTTBCST-TCCSEEEEETTEEEEEEEBHHHHHHHHHH
T ss_pred             CeECCCCcchHHHHHHHHHhcCCcEEEEEeCCEEEEEEecccCCcccccC-ccceEEEecCCceEEeeeccchHHHHHHH
Confidence            799999999999999                 6 8999999987777654 78999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhCCCc----------------------------------------------------------------
Q 040809           72 ARVQARRYAYAYQEPI----------------------------------------------------------------   87 (161)
Q Consensus        72 ~r~~~~~y~~~~~~~i----------------------------------------------------------------   87 (161)
                      +|.+++.|++.|++++                                                                
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~l~~~~a~~~~~~~~~~~~rP~~~~~li~G~d~~gp~Ly~id~~G~~~~~~~~a~G~g~~~  159 (221)
T d1yara1          80 ARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGVSLIFAGIDQIGPRLFDCDPAGTINEYKATAIGSGKDA  159 (221)
T ss_dssp             HHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBTTBCCCCEEEEEEEECSSCEEEEEECTTCCEEEBSEEEESTTHHH
T ss_pred             HHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhhhccCCCcceEEEEEEEecCCCeEEEEcCCccEEEeeEEEECCchHH
Confidence            9999999999999998                                                                


Q ss_pred             ------cCCCCCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHH
Q 040809           88 ------QDYKDDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLL  148 (161)
Q Consensus        88 ------~~y~~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l  148 (161)
                            ++|+|+||++||+++|++||+.++++ ..++++++|++|++++    .|++|+++||+++|
T Consensus       160 ~~~~Le~~~~~~ms~~ea~~la~~~l~~~~~~-~~~~~~~ei~~i~~~~----~~r~l~~~ei~~~l  221 (221)
T d1yara1         160 VVSFLEREYKENLPEKEAVTLGIKALKSSLEE-GEELKAPEIASITVGN----KYRIYDQEEVKKFL  221 (221)
T ss_dssp             HHHHHHHHCCTTCCHHHHHHHHHHHHHHTSCS-SCCCCCCEEEEEETTS----CCEECCHHHHHTTC
T ss_pred             HHHHHHHHhhccccHHHHHHHHHHHHHHHHhc-cCCCCCcEEEEEEcCC----CEEECCHHHHHHhC
Confidence                  36899999999999999999999986 5788899999999875    59999999999864

>d1yarh1 d.153.1.4 (H:1-203) Proteasome beta subunit (catalytic) {Archaeon Thermoplasma acidophilum [TaxId: 2303]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

Probab=99.94  E-value=4e-26  Score=172.24  Aligned_cols=131  Identities=17%  Similarity=0.325  Sum_probs=119.6

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +.-+-|. | |||+|+|.+.+.++.+++.+|||+|+++++|++||..+|++.+++++|.+++.|++.+++++        
T Consensus         3 ~igi~~kdgVvia~D~r~s~~~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~   82 (203)
T d1yarh1           3 TVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKAELELYRLQRRVNMPIEAVATL   82 (203)
T ss_dssp             EEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHH
T ss_pred             EEEEEECCEEEEEECCCcccCCEeecCCcccEEEecCCeeeecCCCcchHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHH
Confidence            3445666 6 99999999887777777899999999999999999999999999999999999999999988        


Q ss_pred             ---------------------------------------------------------cCCCCCCCHHHHHHHHHHHHHHh
Q 040809           88 ---------------------------------------------------------QDYKDDMTRQEAVQLALKVLRKT  110 (161)
Q Consensus        88 ---------------------------------------------------------~~y~~~mt~eeai~la~~al~~~  110 (161)
                                                                               ++|+++||++||++++++||+.+
T Consensus        83 l~~~~~~~~~~p~~~~~lvaG~d~~p~l~~~d~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~eea~~l~~~~l~~~  162 (203)
T d1yarh1          83 LSNMLNQVKYMPYMVQLLVGGIDTAPHVFSIDAAGGSVEDIYASTGSGSPFVYGVLESQYSEKMTVDEGVDLVIRAISAA  162 (203)
T ss_dssp             HHHHHHHTTTSCCCEEEEEEEESSSEEEEEECTTCCEEEESEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhccCCccceeEEEEEcCCCeeEecCCccceecccccccCCCcHHHHHHHHHhccCCCCHHHHHHHHHHHHHHH
Confidence                                                                     36899999999999999999999


Q ss_pred             hccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhc
Q 040809          111 MDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFG  152 (161)
Q Consensus       111 ~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~  152 (161)
                      .+++..++++++|++|++++    +|++++++||+++++++.
T Consensus       163 ~~~d~~~~~~v~v~ii~~~~----g~~~l~~~ei~~~~~~~~  200 (203)
T d1yarh1         163 KQRDSASGGMIDVAVITRKD----GYVQLPTDQIESRIRKLG  200 (203)
T ss_dssp             HHHCTTCCSCCEEEEEETTT----EEEECCHHHHHHHHHHHT
T ss_pred             HHhcCCCCCeEEEEEEECCC----CEEECCHHHHHHHHHHhC
Confidence            99999999999999999864    599999999999999874

>d1j2qh_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.93  E-value=1.1e-25  Score=169.26  Aligned_cols=131  Identities=22%  Similarity=0.365  Sum_probs=119.9

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +.-+.|. | |||+|+|.+.+.++.+++.+|||+|+++|+|++||..+|++.+++.+|.+++.|++.++.++        
T Consensus         3 ~vgi~~~dgVvlaaD~r~s~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~   82 (202)
T d1j2qh_           3 TVGLVCKDGVVMATEKRATMGNFIASKAAKKIYQIADRMAMTTAGSVGDAQFLARIIKIEANLYEIRRERKPTVRAIATL   82 (202)
T ss_dssp             EEEEEETTEEEEEEECCEEETTEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHH
T ss_pred             EEEEEECCEEEEEECCCcccCCeeccCccceEEEecCcEEEEecCcchhHHHHHHHHHHHhhhhhhccCCCccHHHHHHH
Confidence            3456666 6 99999999888777777889999999999999999999999999999999999999999987        


Q ss_pred             -----------------------------------------------------------cCCCCCCCHHHHHHHHHHHHH
Q 040809           88 -----------------------------------------------------------QDYKDDMTRQEAVQLALKVLR  108 (161)
Q Consensus        88 -----------------------------------------------------------~~y~~~mt~eeai~la~~al~  108 (161)
                                                                                 ++|+|+|+++||+.++++||.
T Consensus        83 ~~~~~~~~~~~p~~~~~lvaG~d~~~~~l~~~d~~G~~~~~~~~~a~G~g~~~~~~~Le~~~~~~ms~~ea~~l~~~al~  162 (202)
T d1j2qh_          83 TSNLLNSYRYFPYLVQLLIGGIDSEGKSIYSIDPIGGAIEEKDIVATGSGSLTAYGVLEDRFTPEIGVDEAVELAVRAIY  162 (202)
T ss_dssp             HHHHHHHTTTSCCCEEEEEEEEETTEEEEEEECTTCCEEEESSEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHhhhcccceeeEEEEEEEcCCCceEEEEeCCCCeEeecceEEccCChHHHHHHHHhhcCCCCCHHHHHHHHHHHHH
Confidence                                                                       368999999999999999999


Q ss_pred             HhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhcc
Q 040809          109 KTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFGV  153 (161)
Q Consensus       109 ~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~~  153 (161)
                      .+++++..++++++|++|+++     ++++++++||++++.++.+
T Consensus       163 ~~~~~d~~~g~~v~v~~i~~~-----g~~~~~~~ei~~~l~~~~k  202 (202)
T d1j2qh_         163 SAMKRDSASGDGIDVVKITED-----EFYQYSPEEVEQILAKFRK  202 (202)
T ss_dssp             HHHTTCTTSCSCEEEEEECSS-----CEEECHHHHHHHHGGGTTC
T ss_pred             HHHHhcCCCCCeEEEEEEECC-----CEEEeCHHHHHHHHHHhhC
Confidence            999999999999999999987     3899999999999998864

>d1rypl_ d.153.1.4 (L:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.93  E-value=4.3e-26  Score=173.32  Aligned_cols=136  Identities=14%  Similarity=0.146  Sum_probs=123.4

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +..+-|. | |||+|+|.+.+.++.+++.+|||+|++||+|++||..+|++.+++++|.+++.|++.+++++        
T Consensus         3 ~iai~~kdgVvlaaD~r~t~g~~i~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~   82 (212)
T d1rypl_           3 TLAFRFQGGIIVAVDSRATAGNWVASQTVKRVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREKERISVAAASKI   82 (212)
T ss_dssp             EEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEECCBCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHH
T ss_pred             EEEEEECCEEEEEEcCccccCceeecCCcceEEEECCcEEEEeccchHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHH
Confidence            4556676 6 99999999988888777899999999999999999999999999999999999999999888        


Q ss_pred             -----------------------------------------------------------cCCCCCCCHHHHHHHHHHHHH
Q 040809           88 -----------------------------------------------------------QDYKDDMTRQEAVQLALKVLR  108 (161)
Q Consensus        88 -----------------------------------------------------------~~y~~~mt~eeai~la~~al~  108 (161)
                                                                                 +.|+++||++||++++++||+
T Consensus        83 ls~~~~~~~~~p~~~~~~l~G~~~~~g~~Ly~id~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~mt~~ea~~l~~~al~  162 (212)
T d1rypl_          83 LSNLVYQYKGAGLSMGTMICGYTRKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSIL  162 (212)
T ss_dssp             HHHHHHHTTTSCCCBEEEEEEEETTTEEEEEEEETTCCEEECSEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhccCCcceEeeeeEeecCCCCEEEEECCCceEEecceEEEccCcccchhHHHHhccCCCCHHHHHHHHHHHHH
Confidence                                                                       368999999999999999999


Q ss_pred             HhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhcccCCCC
Q 040809          109 KTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFGVAQPAS  158 (161)
Q Consensus       109 ~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~~~~~~~  158 (161)
                      .+..+|..++++++|++|+++     ++++++++||.+++.++.++.-++
T Consensus       163 ~~~~rd~~sg~~v~v~vi~~~-----g~~~~~~~ev~~~~~~~~~~~~~~  207 (212)
T d1rypl_         163 AAAHRDAYSGGSVNLYHVTED-----GWIYHGNHDVGELFWKVKEEEGSF  207 (212)
T ss_dssp             HHHHHBTTCCSEEEEEEEETT-----EEEEEEEEEHHHHHHHHHHHHCCC
T ss_pred             HHHHhcCCCCCceEEEEEcCC-----ceEEeCHHHHHHHHHHHHHhhccc
Confidence            999999999999999999987     499999999999998886655443

>d1irul_ d.153.1.4 (L:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=99.93  E-value=1.3e-25  Score=169.33  Aligned_cols=130  Identities=18%  Similarity=0.237  Sum_probs=120.3

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +.-|.|. | |||+|+|.+.+.++.+++.+|||+|+++|+|++||..+|++.+.+.++.+++.|++.+++++        
T Consensus         3 ~igi~~~dgVvlaaD~~~t~g~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~   82 (201)
T d1irul_           3 TLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQCRIYELRNKERISVAAASKL   82 (201)
T ss_dssp             EEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEECCBCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHH
T ss_pred             EEEEEECCEEEEEEcCccccCCEeecCCcccEEEeCCcEEEEEcCccchHHHHHHHHHHHHHHHHHhcCCCCchhHHHHH
Confidence            4567777 6 99999999998888888889999999999999999999999999999999999999999888        


Q ss_pred             ----------------------------------------------------------cCCCCCCCHHHHHHHHHHHHHH
Q 040809           88 ----------------------------------------------------------QDYKDDMTRQEAVQLALKVLRK  109 (161)
Q Consensus        88 ----------------------------------------------------------~~y~~~mt~eeai~la~~al~~  109 (161)
                                                                                +.|+++||.+||++++++||+.
T Consensus        83 l~~~~~~~~~~p~~~~~lvaG~d~~~~~l~~~d~~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~ms~eea~~l~~~~l~~  162 (201)
T d1irul_          83 LANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNRISGATFSVGSGSVYAYGVMDRGYSYDLEVEQAYDLARRAIYQ  162 (201)
T ss_dssp             HHHHHHTTTTSCCCBEEEEEEECSSSEEEEEEESSSCEEECSEEEESTTHHHHHHHHHTTCCTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHhhhccCCCceEEEEEEEEecCCceEEEEccCceEEEeeeEEecCchHHHHHHHHhhccCCCCHHHHHHHHHHHHHH
Confidence                                                                      4689999999999999999999


Q ss_pred             hhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhc
Q 040809          110 TMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFG  152 (161)
Q Consensus       110 ~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~  152 (161)
                      +.++|..++++++|++|++++     +++++++||.++.++++
T Consensus       163 ~~~~d~~sg~~~~v~~i~~~G-----~~~i~~~ev~~~~~~~~  200 (201)
T d1irul_         163 ATYRDAYSGGAVNLYHVREDG-----WIRVSSDNVADLHEKYS  200 (201)
T ss_dssp             HHHHBTTCCSEEEEEEECSSC-----EEEEEEEEHHHHHHHHT
T ss_pred             HHHhCCCCCCceEEEEEeCCc-----eEEECHHHHHHHHHhhc
Confidence            999999999999999999873     88899999999998864

>d1ryph_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.93  E-value=1.3e-25  Score=170.06  Aligned_cols=128  Identities=14%  Similarity=0.328  Sum_probs=117.2

Q ss_pred             CceeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc------
Q 040809           16 GRLYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI------   87 (161)
Q Consensus        16 Grl~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i------   87 (161)
                      +.+.-+-|. | |||+|+|.+.+.++.++..+||++|++|++|++||..+|++.+++++|.+++.|++++++++      
T Consensus        10 tTivgi~~~dgVvlaaD~r~s~g~~i~~~~~~ki~~i~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   89 (205)
T d1ryph_          10 ASIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKIWCCRSGSAADTQAIADIVQYHLELYTSQYGTPSTETAAS   89 (205)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEEBHHHHHHHHHHHHHHHHHHHHHHSSCCHHHHHH
T ss_pred             ceEEEEEECCEEEEEECCccccCceeeccccceEEEccCceEEeeccchhHHHHHHHHHHHHHHHHHHHcCCccHHHHHH
Confidence            347788888 6 99999999998888888899999999999999999999999999999999999999999877      


Q ss_pred             -----------------------------------------------------------cCCCCCCCHHHHHHHHHHHHH
Q 040809           88 -----------------------------------------------------------QDYKDDMTRQEAVQLALKVLR  108 (161)
Q Consensus        88 -----------------------------------------------------------~~y~~~mt~eeai~la~~al~  108 (161)
                                                                                 +.|+++||++||++++++||+
T Consensus        90 ~~~~~~~~~~~p~~~~~lvaG~d~~~~p~Ly~~d~~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~ms~~ea~~l~~~al~  169 (205)
T d1ryph_          90 VFKELCYENKDNLTAGIIVAGYDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSLS  169 (205)
T ss_dssp             HHHHHHHHTTTTCCEEEEEEEEETTTEEEEEEECTTSCCEEESEEEESGGGGGGHHHHHHHCCTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCccCceEEEEEEeecCCCCcEEEEECCCCcEEecCeEEeecCcHHHHHHHHhhhhcccCHHHHHHHHHHHHH
Confidence                                                                       368999999999999999999


Q ss_pred             HhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHH
Q 040809          109 KTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTM  146 (161)
Q Consensus       109 ~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~  146 (161)
                      .++++|..++++++|++|++++-   .++.+.++|+++
T Consensus       170 ~a~~rD~~sg~~v~v~iitk~G~---~~~~~~~~e~~~  204 (205)
T d1ryph_         170 QAIKWDGSSGGVIRMVVLTAAGV---ERLIFYPDEYEQ  204 (205)
T ss_dssp             HHHHHBTTCCSCEEEEEEETTEE---EEEEECHHHHTC
T ss_pred             HHHHhcCcCCCCEEEEEEcCCce---EEEecCcccccc
Confidence            99999999999999999999852   567789999875

>d1q5qa_ d.153.1.4 (A:) Proteasome alpha subunit (non-catalytic) {Rhodococcus erythropolis [TaxId: 1833]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Rhodococcus erythropolis [TaxId: 1833]

Probab=99.93  E-value=7.5e-26  Score=174.04  Aligned_cols=116  Identities=23%  Similarity=0.343  Sum_probs=100.6

Q ss_pred             e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCC-Cc---------------
Q 040809           25 G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQE-PI---------------   87 (161)
Q Consensus        25 G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~-~i---------------   87 (161)
                      | |||+|+|.+        +.+|||+|++||+||+||+.+|++.|++++|.+|+.|++.|+. ++               
T Consensus        30 GVvlaad~r~~--------s~~KI~~i~~~i~~~~sG~~aD~~~l~~~~r~~~~~~~~~~~~~~~~~~~la~~~~~~~~~  101 (227)
T d1q5qa_          30 GVLFVAENPST--------ALHKVSELYDRLGFAAVGKYNEFENLRRAGIVHADMRGYSYDRRDVTGRSLANAYAQTLGT  101 (227)
T ss_dssp             EEEEEECCSCS--------SSCSEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHHHHHHH
T ss_pred             EEEEEEccCCC--------CcceEEEecCceEEEecCchHHHHHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHH
Confidence            6 999999853        4689999999999999999999999999999999999999985 33               


Q ss_pred             -----------------------------------------------------------cCCCCCCCHHHHHHHHHHHHH
Q 040809           88 -----------------------------------------------------------QDYKDDMTRQEAVQLALKVLR  108 (161)
Q Consensus        88 -----------------------------------------------------------~~y~~~mt~eeai~la~~al~  108 (161)
                                                                                 ++|+++||++||+++|++||+
T Consensus       102 ~~~~~~rP~gvs~lvaG~D~~g~~~~p~Ly~vDpsG~~~~~~~~~~~g~~s~~~~~~Le~~y~~~ms~eea~~la~~aL~  181 (227)
T d1q5qa_         102 IFTEQPKPYEVEICVAEVGRVGSPKAPQLYRITYDGSIVDEQHFVVMGGTTEPIATAMRESYRADLDLEAAVGIAVNALR  181 (227)
T ss_dssp             HHHHSSSCCCEEEEEEECCCSSCCCCCEEEEEETTSCEEEESSEEEESSSHHHHHHHHHHHCCTTCCHHHHHHHHHHHHT
T ss_pred             HHHhcCCCceEEEEEEEEecCCCCCCCEEEEEccccceeeecccccCCCchHHHHHHHHHhccCCCCHHHHHHHHHHHHH
Confidence                                                                       368999999999999999999


Q ss_pred             HhhccC----CCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHH
Q 040809          109 KTMDST----SLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLE  149 (161)
Q Consensus       109 ~~~~~~----~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~  149 (161)
                      .+++++    .++++++||+|+++++. .+.|++|+++||+++|.
T Consensus       182 ~a~~~d~~~~~~~~~~ievavi~k~~~-~~~fr~l~~~ei~~~l~  225 (227)
T d1q5qa_         182 QGGAGEGEKRNVDVASLEVAVLDQSRP-RRAFRRIAGTALEQLVP  225 (227)
T ss_dssp             TCC--------CCSSCSEEEEEETTSS-SCCEEECCHHHHHTTSC
T ss_pred             HHhhcccccCCcCcceEEEEEEECCCC-ccceEEcCHHHHHHHhc
Confidence            999764    25788999999998753 34799999999999874

>d1q5qh_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Rhodococcus erythropolis [TaxId: 1833]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Rhodococcus erythropolis [TaxId: 1833]

Probab=99.92  E-value=1.6e-24  Score=165.16  Aligned_cols=135  Identities=22%  Similarity=0.249  Sum_probs=121.9

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +.-|.|. | |||+|+|.+++.++..+..+||++|++|++|+++|..+|++.+.+.++.+++.|++.++.++        
T Consensus         3 ivgi~~kdgVvlaaD~r~s~g~~i~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (224)
T d1q5qh_           3 IVALTYKGGVLLAGDRRATQGNLIASRDVEKVYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEGVPLTFDGKANR   82 (224)
T ss_dssp             EEEEECSSCEEEEECCCEEETTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHH
T ss_pred             EEEEEECCEEEEEECCCcccCCEeecCCcceEEEeCCcEEEEecccchHHHHHHHHHHHHhHHHHHhhCCCccHHHHHHH
Confidence            5567777 5 99999999998787777899999999999999999999999999999999999999999987        


Q ss_pred             ---------------------------------------------------------------------cCCCCCCCHHH
Q 040809           88 ---------------------------------------------------------------------QDYKDDMTRQE   98 (161)
Q Consensus        88 ---------------------------------------------------------------------~~y~~~mt~ee   98 (161)
                                                                                           ++|+++||++|
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~g~~~~g~d~~~~~~l~~~d~~G~~~~~~~~~~a~GsG~~~a~~~Le~~~~~~mt~~e  162 (224)
T d1q5qh_          83 LASMVRGNLGAAMQGLAVVPLLVGYDLDADDESRAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALKKIYSPDSDEET  162 (224)
T ss_dssp             HHHHHHTTHHHHTTTCCEEEEEEEECTTCSSTTSCEEEEEECTTSCEEECCSSEEEESTTHHHHHHHHHHHCCTTCCHHH
T ss_pred             HHHHHHHhhcccccCccceeeEEEeecccccccCCceEEEEEccCcEEEeccceeeecCccHHHHHHHHHhhcccCCHHH
Confidence                                                                                 35899999999


Q ss_pred             HHHHHHHHHHHhhccCCCCCC-------cEEEEEEEeCCCCceeEEECCHHHHHHHHHHhcccCCC
Q 040809           99 AVQLALKVLRKTMDSTSLTSE-------KLELAEVFLLPSGKVKYRICSPESLTMLLENFGVAQPA  157 (161)
Q Consensus        99 ai~la~~al~~~~~~~~~~~~-------~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~~~~~~  157 (161)
                      |++++++||..++++|..+|+       ++++++++++     .|++++++||+++++++.+++.+
T Consensus       163 a~~l~~~al~~a~~rD~~SGg~~~~~~~~~~~~~i~~~-----g~~~l~~~ei~~~~~~~~~~~~~  223 (224)
T d1q5qh_         163 ALRAAIESLYDAADDDSATGGPDLTRGIYPTAVTITQA-----GAVHVSEETTSELARRIVAERTE  223 (224)
T ss_dssp             HHHHHHHHHHHHHHHCTTTCCCBTTTTBCCEEEEEETT-----EEEECCHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhhccccCCcccccccceEEEEEeCC-----cEEEcCHHHHHHHHHHHHHHHhc
Confidence            999999999999999888876       4789999987     49999999999999999776544

>d1iruh_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=99.91  E-value=1.4e-24  Score=163.76  Aligned_cols=127  Identities=17%  Similarity=0.305  Sum_probs=114.9

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +..|-|. | |||+|+|.+.+.++.+++.+||++|++|++|+++|+.+|++.+.+.+|.+++.|+++++.++        
T Consensus         3 ivai~~~dgVvlaaD~r~t~g~~i~~~~~~KI~~i~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~   82 (202)
T d1iruh_           3 IMAVQFDGGVVLGADSRTTTGSYIANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASL   82 (202)
T ss_dssp             EEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHH
T ss_pred             EEEEEECCEEEEEECCccccCCeeecCCcceEEEcCCcEEEEeccchHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHH
Confidence            4456666 5 99999999999898888899999999999999999999999999999999999999999887        


Q ss_pred             ----------------------------------------------------------cCCCCCCCHHHHHHHHHHHHHH
Q 040809           88 ----------------------------------------------------------QDYKDDMTRQEAVQLALKVLRK  109 (161)
Q Consensus        88 ----------------------------------------------------------~~y~~~mt~eeai~la~~al~~  109 (161)
                                                                                +.|+++||++||++++++||..
T Consensus        83 l~~~l~~~~~p~~~~~lvaG~d~~~~~~l~~~d~~g~~~~~~~~a~G~g~~~a~~~L~~~~~~~~~~~ea~~l~~~al~~  162 (202)
T d1iruh_          83 FKEMCYRYREDLMAGIIIAGWDPQEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREGMTKEECLQFTANALAL  162 (202)
T ss_dssp             HHHHHHHTTTTCCEEEEEEEEETTTEEEEEEECTTSCCEECSEEEESGGGGGGHHHHHHHCCTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhccceeEEEEEEEeecCCCcEEEEECCCCceeecceeEEeCCHHHHHHHHHHhhccCCcHHHHHHHHHHHHHH
Confidence                                                                      3589999999999999999999


Q ss_pred             hhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHH
Q 040809          110 TMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTML  147 (161)
Q Consensus       110 ~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~  147 (161)
                      ++++|..++++++|++|++++.   .++.++.+||+.+
T Consensus       163 a~~rD~~sg~~i~v~vi~~~G~---~~~~~~~d~~~~~  197 (202)
T d1iruh_         163 AMERDGSSGGVIRLAAIAESGV---ERQVLLGDQIPKF  197 (202)
T ss_dssp             HHHHBTTCCSCEEEEEEETTEE---EEEEECGGGSCCC
T ss_pred             HHhhCCCCCCCEEEEEEeCCCe---EEEEcCHHHhhhh
Confidence            9999999999999999999752   6788999887654

>d1rypk_ d.153.1.4 (K:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.90  E-value=8.3e-24  Score=158.92  Aligned_cols=122  Identities=15%  Similarity=0.151  Sum_probs=111.6

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +.-|.|. | |||+|+|.+.+.++.+++.+|||+|++|++|++||..+|++.+.+.+|.+++.|++++++++        
T Consensus         4 iigi~~~dgVvlaaD~r~s~g~~~~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (198)
T d1rypk_           4 ILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYIQANIQLYSIREDYELSPQAVSSF   83 (198)
T ss_dssp             EEEEECSSCEEEEEECCEEETTEEEESCCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHH
T ss_pred             EEEEEECCEEEEEEcCCcccCCEeecCccceEEEecCCEEEEecCCcccHHHHHHHHHHHHHHHHHHhCCCcchHHHHHH
Confidence            3455666 6 99999999999998887899999999999999999999999999999999999999999988        


Q ss_pred             --------------------------------------------------------------cCCCCCCCHHHHHHHHHH
Q 040809           88 --------------------------------------------------------------QDYKDDMTRQEAVQLALK  105 (161)
Q Consensus        88 --------------------------------------------------------------~~y~~~mt~eeai~la~~  105 (161)
                                                                                    ++|+++||++||++++.+
T Consensus        84 i~~~~~~~~~~~~P~~~~~liaG~D~~~~~p~L~~id~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~eea~~l~~~  163 (198)
T d1rypk_          84 VRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQIDYLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKL  163 (198)
T ss_dssp             HHHHHHHHTTSSSCCCEEEEEEEEETTTTEEEEEEECTTCCEEECSEEECTTHHHHHHHHHHHHCCTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHhcccccceEEEEEEEecCCCceEEEEecccccEEecceEEEeccchhhHHHHHhcccccCCHHHHHHHHHH
Confidence                                                                          368999999999999999


Q ss_pred             HHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHH
Q 040809          106 VLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESL  144 (161)
Q Consensus       106 al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei  144 (161)
                      ||+.+.+++..++++++|++|+++     +++++++.|+
T Consensus       164 ~l~~~~~~d~~s~~~~~v~vi~~d-----G~~~~~~~~~  197 (198)
T d1rypk_         164 CVQELEKRMPMDFKGVIVKIVDKD-----GIRQVDDFQA  197 (198)
T ss_dssp             HHHHHHHHCSBCCCCEEEEEEETT-----EEEEECCCSC
T ss_pred             HHHHHHHhcCcCCCcEEEEEEcCC-----CeEEcchhcc
Confidence            999999999999999999999987     4889888765

>d1iruj_ d.153.1.4 (J:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=99.88  E-value=1.9e-22  Score=151.99  Aligned_cols=115  Identities=10%  Similarity=0.172  Sum_probs=108.5

Q ss_pred             CceeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc------
Q 040809           16 GRLYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI------   87 (161)
Q Consensus        16 Grl~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i------   87 (161)
                      |.+..+.|. | |||+|+|.+.+.++.++..+|||+|++|++|+++|..+|++.+++.+|.+++.|++.++.++      
T Consensus         8 ~Tvigi~~~dgVvlaaD~r~s~g~~~~~~~~~Ki~~I~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~a   87 (204)
T d1iruj_           8 GAVMAMKGKNCVAIAADRRFGIQAQLVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFRLNLYELKEGRQIKPYTLM   87 (204)
T ss_dssp             CEEEEEECSSEEEEEEECCEEETTEEEESCCCCEEECSTTEEEECCSCHHHHHHHHHHHHHHHHHHHHHSSSCCCHHHHH
T ss_pred             ceEEEEEECCEEEEEECCCcccCCeeEcCcccEEEEeCCCeEEEeccCchHHHHHHHHHHHhhhhhhhhcccccchHHHH
Confidence            458888888 6 99999999999888888999999999999999999999999999999999999999999988      


Q ss_pred             ---------------------------------------------------------------cCCCCCCCHHHHHHHHH
Q 040809           88 ---------------------------------------------------------------QDYKDDMTRQEAVQLAL  104 (161)
Q Consensus        88 ---------------------------------------------------------------~~y~~~mt~eeai~la~  104 (161)
                                                                                     +.|+++||.+||+++++
T Consensus        88 ~~l~~~~~~~~~~p~~~~~lvaG~D~~~~~~~~~~~d~~g~~~~~~~~~~~G~g~~~~~~~l~~~~~~~ms~~ea~~l~~  167 (204)
T d1iruj_          88 SMVANLLYEKRFGPYYTEPVIAGLDPKTFKPFICSLDLIGCPMVTDDFVVSGTCAEQMYGMCESLWEPNMDPDHLFETIS  167 (204)
T ss_dssp             HHHHHHHHTTTTSCCSCCCEEEEECTTSCCEEEEEECTTCCEEECSSEEEEETTHHHHHHHHHHHCCSSCCHHHHHHHHH
T ss_pred             HHHHHHHHHhhhccceeEEEEEEEcCCCCceEEEEecCCCceeeecceEEechhHHHHHHHHHhccccCCCHHHHHHHHH
Confidence                                                                           35899999999999999


Q ss_pred             HHHHHhhccCCCCCCcEEEEEEEeCC
Q 040809          105 KVLRKTMDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus       105 ~al~~~~~~~~~~~~~iei~ii~~~~  130 (161)
                      +||+.+.++|..++++++|++|++++
T Consensus       168 ~al~~a~~rd~~sg~~~~v~ii~k~g  193 (204)
T d1iruj_         168 QAMLNAVDRDAVSGMGVIVHIIEKDK  193 (204)
T ss_dssp             HHHHHHGGGBTTSCSCEEEEEEESSB
T ss_pred             HHHHHHHhhcccCCCcEEEEEEeCCC
Confidence            99999999999999999999999985

>d1rypi_ d.153.1.4 (I:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.88  E-value=3.2e-23  Score=158.52  Aligned_cols=113  Identities=15%  Similarity=0.247  Sum_probs=104.6

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +.-+.|. | |||+|+|.+.+.++.+++.+|||+|++||+||++|..+|++.+.+++|.+++.|++.++.++        
T Consensus         3 iVgik~~dGVviaaD~r~s~g~~~~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~l~~~~~~~~~~~~~~~~v~~~a~~   82 (222)
T d1rypi_           3 IVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQM   82 (222)
T ss_dssp             EEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHH
T ss_pred             EEEEEECCEEEEEECCCcccCceeecCCcccEEEEcCCEEEEecccchHHHHHHHHHHHHHHHhhhhhCCCCcHHHHHHH
Confidence            4556677 6 99999999988888777889999999999999999999999999999999999999999888        


Q ss_pred             ---------------------------------------------------------cCCCCCCCHHHHHHHHHHHHHHh
Q 040809           88 ---------------------------------------------------------QDYKDDMTRQEAVQLALKVLRKT  110 (161)
Q Consensus        88 ---------------------------------------------------------~~y~~~mt~eeai~la~~al~~~  110 (161)
                                                                               +.|+|+||++||++++++||+.+
T Consensus        83 l~~~~~~~~~p~~~~~l~aG~d~~g~~Ly~id~~G~~~~~~~~a~Gsg~~~a~~~Le~~~k~~ms~eea~~l~~~al~~a  162 (222)
T d1rypi_          83 LKQHLFKYQGHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKLASDAIQAG  162 (222)
T ss_dssp             HHHHHHHTTTCSCEEEEEEEEETTEEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHHCCSSCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhhhccceeEEEEEEcCCCcEEEEEecCcceEEeeEEEECCCcHHHHHHHHhhccCCCCHHHHHHHHHHHHHHH
Confidence                                                                     36899999999999999999999


Q ss_pred             hccCCCCCCcEEEEEEEeCC
Q 040809          111 MDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus       111 ~~~~~~~~~~iei~ii~~~~  130 (161)
                      .++|..++++++|++|+++.
T Consensus       163 ~~~D~~sg~~i~i~vi~~~~  182 (222)
T d1rypi_         163 IWNDLGSGSNVDVCVMEIGK  182 (222)
T ss_dssp             HHHCTTCCSCEEEEEEETTS
T ss_pred             hcccCCCCCcEEEEEEEcCC
Confidence            99999999999999999875

>d1irui_ d.153.1.4 (I:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=99.88  E-value=1.5e-22  Score=154.39  Aligned_cols=122  Identities=15%  Similarity=0.216  Sum_probs=111.1

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +.-+.|. | |||+|+|.+.+.++.+++.+|||+|++|++|++||..+|++.+++.++.+++.|++.+|.++        
T Consensus         3 ivgi~~~dgVvlaaD~r~s~g~~i~~~~~~KI~~i~~~i~~~~aG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~   82 (220)
T d1irui_           3 IAGVVYKDGIVLGADTRATEGMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGRLPRVVTANRM   82 (220)
T ss_dssp             EEEEEETTEEEEEECCCEESSSBEEESSCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHCSCCCHHHHHHH
T ss_pred             EEEEEECCEEEEEEcCCcccCCEeecCCcccEEEecCcEEEEEccccHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHH
Confidence            4556676 6 99999999999999888889999999999999999999999999999999999999999988        


Q ss_pred             ---------------------------------------------------------cCCCCCCCHHHHHHHHHHHHHHh
Q 040809           88 ---------------------------------------------------------QDYKDDMTRQEAVQLALKVLRKT  110 (161)
Q Consensus        88 ---------------------------------------------------------~~y~~~mt~eeai~la~~al~~~  110 (161)
                                                                               +.|+++||++||++++++||+.+
T Consensus        83 l~~~~y~~~~p~~~~~ivaG~D~~g~~L~~id~~G~~~~~~~~a~Gsgs~~a~~~L~~~~~~~~s~~ea~~l~~~al~~~  162 (220)
T d1irui_          83 LKQMLFRYRGYIGAALVLGGVDVTGPHLYSIYPHGSTDKLPYVTMGSGSLAAMAVFEDKFRPDMEEEEAKNLVSEAIAAG  162 (220)
T ss_dssp             HHHHHHHTTTCSCEEEEEEEECSSCEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHSCCTTCCHHHHHTHHHHHHHHH
T ss_pred             HHhhhhhcccccceeEEEEEEeCCCcEEEEEeCCCcEEEeeEEEEccccHHHHHHHHHhcccCCCHHHHHHHHHHHHHHh
Confidence                                                                     36899999999999999999999


Q ss_pred             hccCCCCCCcEEEEEEEeCCCCceeEEECCHHHH
Q 040809          111 MDSTSLTSEKLELAEVFLLPSGKVKYRICSPESL  144 (161)
Q Consensus       111 ~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei  144 (161)
                      .++|..++++++|++|++++     .+.+.+.++
T Consensus       163 ~~~D~~sg~~i~i~vitkdg-----~~~~~~~~~  191 (220)
T d1irui_         163 IFNDLGSGSNIDLCVISKNK-----LDFLRPYTV  191 (220)
T ss_dssp             HHHCTTCCSCEEEEEEETTE-----EECCSEEEC
T ss_pred             hccCCCCCCcEEEEEEECCC-----eEEeCcccc
Confidence            99999999999999999883     667766554

>d1ryp2_ d.153.1.4 (2:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.87  E-value=1.6e-22  Score=155.27  Aligned_cols=134  Identities=14%  Similarity=0.130  Sum_probs=114.4

Q ss_pred             CceeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCC-----c-
Q 040809           16 GRLYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEP-----I-   87 (161)
Q Consensus        16 Grl~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~-----i-   87 (161)
                      +.+.-+-|. | |||+|+|.+.+.++.+++.+|||+|++|++|++||+.+|++.+.+.++.+++.|++.++.+     + 
T Consensus         9 tTivgi~~~dgVvlaaD~r~s~g~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~l~~~~~~~~~~~~~~~~~~~~~   88 (233)
T d1ryp2_           9 TSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLADAEEALE   88 (233)
T ss_dssp             CCEEEEEETTEEEEEEECCEEETTEEEESCCCCEEEETTTEEEEEEEEHHHHHHHHHHHHHHHHHHHTTCTTTTTTTSCC
T ss_pred             ceEEEEEECCEEEEEECCCcccCCeeecCCcceEEEeCCCEEEEeccCchHHHHHHHHHHHHHHHHHHhhCCCCCCcccC
Confidence            457777787 6 9999999886655656688999999999999999999999999999999999999877532     2 


Q ss_pred             --------------------------------------------------------------------cCCC-----CCC
Q 040809           88 --------------------------------------------------------------------QDYK-----DDM   94 (161)
Q Consensus        88 --------------------------------------------------------------------~~y~-----~~m   94 (161)
                                                                                          +.|+     |+|
T Consensus        89 ~~~~a~~l~~~~y~~~~~~~P~~~~~liaG~d~~g~~~ly~~d~~G~~~~~~~~a~G~g~~~a~~~Le~~~~~~~~~~~m  168 (233)
T d1ryp2_          89 PSYIFEYLATVMYQRRSKMNPLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFGAHMANPLLRKVVDRESDIPKT  168 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCCCEEEEEEEECTTSCEEEEEEETTCCEECCSEEECTHHHHHHHHHHTTTCCSGGGGGGC
T ss_pred             HHHHHHHHHHHHHhhccccCCceeEEEEEEEcCCCCeEEEEEcCCCcEEeeeeEEecCccHHHHHHHHHHHhhccccccc
Confidence                                                                                2465     799


Q ss_pred             CHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhcc
Q 040809           95 TRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPESLTMLLENFGV  153 (161)
Q Consensus        95 t~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~ei~~~l~~~~~  153 (161)
                      |++||++++++||+.++.||..++++++|++|++++    .++++.+++|+.+...+++
T Consensus       169 s~eeA~~l~~~al~~~~~rD~~sg~~i~i~~itkd~----g~~~~~~~~ie~~~~~~a~  223 (233)
T d1ryp2_         169 TVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKNT----GLTFKKNLQVENMKWDFAK  223 (233)
T ss_dssp             CHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTT----EEEEEEEEECCSCCCGGGG
T ss_pred             CHHHHHHHHHHHHHHHHHhcccCCCCEEEEEEECCC----CEEECChhcchhhhhhHhh
Confidence            999999999999999999999999999999999985    5899999888765444443

>d1iruk_ d.153.1.4 (K:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=99.86  E-value=2.5e-21  Score=143.41  Aligned_cols=120  Identities=14%  Similarity=0.150  Sum_probs=107.6

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +..|-+- | |||+|+|.+.+..+.+++.+|||+|+++++|+++|..+|++.+.+.+|.+++.|++.++.++        
T Consensus         4 ivgi~~kdgVviaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~~G~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (199)
T d1iruk_           4 LIGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYIQKNVQLYKMRNGYELSPTAAANF   83 (199)
T ss_dssp             EEEEECSSEEEEEEECCEEETTEEEESSCCCEEECSSSEEEEEEESTTHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHH
T ss_pred             EEEEEECCEEEEEECCCccCCCeeecCCcceEEEecCcEEEEecccchHHHHHHHHHHHHhhhhhhhcCCcCcHHHHHHH
Confidence            3444554 5 99999999998888777889999999999999999999999999999999999999999988        


Q ss_pred             -------------------------------------------------------------cCCCCCCCHHHHHHHHHHH
Q 040809           88 -------------------------------------------------------------QDYKDDMTRQEAVQLALKV  106 (161)
Q Consensus        88 -------------------------------------------------------------~~y~~~mt~eeai~la~~a  106 (161)
                                                                                   +.|+++|+++||++++++|
T Consensus        84 l~~~~~~~~~~~~~~~~~~~~aG~d~~~~~~l~~~~~~g~~~~~~~~a~G~gs~~a~~~l~~~~~~~~~~~ea~~l~~~a  163 (199)
T d1iruk_          84 TRRNLADCLRSRTPYHVNLLLAGYDEHEGPALYYMDYLAALAKAPFAAHGYGAFLTLSILDRYYTPTISRERAVELLRKC  163 (199)
T ss_dssp             HHHHHHHHHTSSSCCCEEEEEEEEETTTEEEEEEECTTCCEEECSEEEESHHHHHHHHHHHHHCCTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHhhccCCcceeeeecceeccCCceEEeecccceEEeeeeeeecccchhhhHHHHHhccCCCCHHHHHHHHHHH
Confidence                                                                         3589999999999999999


Q ss_pred             HHHhhccCCCCCCcEEEEEEEeCCCCceeEEECCHH
Q 040809          107 LRKTMDSTSLTSEKLELAEVFLLPSGKVKYRICSPE  142 (161)
Q Consensus       107 l~~~~~~~~~~~~~iei~ii~~~~~g~~~~~~l~~~  142 (161)
                      |..+.++|..++++++|++|++++     ++++++.
T Consensus       164 l~~~~~~d~~sg~~~~v~vv~~~g-----~~~~~~~  194 (199)
T d1iruk_         164 LEELQKRFILNLPTFSVRIIDKNG-----IHDLDNI  194 (199)
T ss_dssp             HHHHHHTBCBCCCCEEEEEEETTE-----EECCCCB
T ss_pred             HHHHHHhcCCcCCceEEEEEcCCC-----eEEcCCc
Confidence            999999999999999999999873     6776553

>d1iru1_ d.153.1.4 (1:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=99.86  E-value=5.2e-21  Score=143.84  Aligned_cols=115  Identities=13%  Similarity=0.191  Sum_probs=106.2

Q ss_pred             CceeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc------
Q 040809           16 GRLYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI------   87 (161)
Q Consensus        16 Grl~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i------   87 (161)
                      |.+..|-|. | |||+|+|.+.+.++.+++.+||++|++|++++++|..+|++.+.+++|.+++.|++.++.++      
T Consensus        10 ~Tivai~~~dgVviaaD~r~t~g~~~~~~~~~KI~~i~~~i~~~~aG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   89 (213)
T d1iru1_          10 GTILAIAGEDFAIVASDTRLSEGFSIHTRDSPKCYKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMTTGAIA   89 (213)
T ss_dssp             CEEEEEEETTEEEEEEECCEEETTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             cEEEEEEECCEEEEEECCccccCceeeccccCEEEEcCCCEEEEecCccchHHHHHHHHHHHHHHHHHhhCCchhHHHHH
Confidence            448999998 5 99999999998888777889999999999999999999999999999999999999999988      


Q ss_pred             ----------------------------------------------------------------------cCCCCCCCHH
Q 040809           88 ----------------------------------------------------------------------QDYKDDMTRQ   97 (161)
Q Consensus        88 ----------------------------------------------------------------------~~y~~~mt~e   97 (161)
                                                                                            ..|.++||++
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~g~d~~~~~~l~~~d~~g~~~~~~~~a~G~g~~~a~~~l~~~~~~~~~~~~~~~~~s~~  169 (213)
T d1iru1_          90 AMLSTILYSRRFFPYYVYNIIGGLDEEGKGAVYSFDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVEHVPLSLD  169 (213)
T ss_dssp             HHHHHHHHTTTTSCCCEEEEEEEECTTSCEEEEEECTTSCEEEESEEEEETTHHHHHHHHHHHTTCCSCSSCCCCCCCHH
T ss_pred             HHHHHHHHHHHhhhcccccceEEEecCCCcEEEecCCcceeeecCeeeecCccHHHHHHHHHhhcccchhcccccCCCHH
Confidence                                                                                  1245899999


Q ss_pred             HHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCC
Q 040809           98 EAVQLALKVLRKTMDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus        98 eai~la~~al~~~~~~~~~~~~~iei~ii~~~~  130 (161)
                      ||++++++||..+.+++..++.+++|++|++++
T Consensus       170 ea~~~~~~~l~~~~~~d~~sg~~~~v~~i~k~G  202 (213)
T d1iru1_         170 RAMRLVKDVFISAAERDVYTGDALRICIVTKEG  202 (213)
T ss_dssp             HHHHHHHHHHHHHHHHBTTSCSEEEEEEEETTE
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCceEEEEEeCCC
Confidence            999999999999999999999999999999985

>d1ryp1_ d.153.1.4 (1:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.85  E-value=2.7e-21  Score=147.06  Aligned_cols=116  Identities=13%  Similarity=0.221  Sum_probs=105.1

Q ss_pred             CC-ceeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc----
Q 040809           15 EG-RLYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI----   87 (161)
Q Consensus        15 ~G-rl~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i----   87 (161)
                      .| .+..+.+. | |||+|+|.+.++++.+++.+|||+|++|++|++||+.+|++.+++++|.+++.|++.++...    
T Consensus         8 nG~Tivgi~~~dgVviaaD~r~s~~~~i~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~   87 (222)
T d1ryp1_           8 NGGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKLSIN   87 (222)
T ss_dssp             CCCEEEEEECSSCEEEEEECCEEETTEEEESCCCCCEECSTTCEEEEEESHHHHHHHHHHHHHHHHHHHHHTTTCCCCHH
T ss_pred             CCcEEEEEEECCEEEEEECCCcccCCEeccCCcceEEEecCCEEEEeccChHHHHHHHHHHHHHhhhhhhhcCCCCCcHH
Confidence            44 59999998 5 99999999999988887899999999999999999999999999999999999999987543    


Q ss_pred             ----------------------------------------------------------------cCCC------------
Q 040809           88 ----------------------------------------------------------------QDYK------------   91 (161)
Q Consensus        88 ----------------------------------------------------------------~~y~------------   91 (161)
                                                                                      +.|+            
T Consensus        88 ~~~~~~~~~~~~~~~~p~~~~~li~G~d~~~~~~Ly~~D~~G~~~~~~~~a~G~g~~~a~~~Le~~~~~~~~~~~~~~~~  167 (222)
T d1ryp1_          88 SAARNIQHLLYGKRFFPYYVHTIIAGLDEDGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYEPGTNGK  167 (222)
T ss_dssp             HHHHHHHHHHHTTTTSCCCEEEEEEEECTTSCEEEEEECTTSCEEEESEEEEETTHHHHHHHHHHHTSCTTCBCTTSTTC
T ss_pred             HHHHHHHHHHHhhhhhhheeeeeEEEEeCCCCeEEEEECCCcEEEEeceEEEcccHHHHHHHHHHhhccccccCcccchh
Confidence                                                                            1233            


Q ss_pred             -----CCCCHHHHHHHHHHHHHHhhccCCCCCCcEEEEEEEeCC
Q 040809           92 -----DDMTRQEAVQLALKVLRKTMDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus        92 -----~~mt~eeai~la~~al~~~~~~~~~~~~~iei~ii~~~~  130 (161)
                           ++||++||++++++||..+.++|..++++++|++|++++
T Consensus       168 ~~~~~~~lt~~ea~~l~~~al~~a~~rd~~sg~~v~v~iitkdG  211 (222)
T d1ryp1_         168 VKKPLKYLSVEEVIKLVRDSFTSATERHIQVGDGLEILIVTKDG  211 (222)
T ss_dssp             SBCCCCCCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTE
T ss_pred             hhcccccccHHHHHHHHHHHHHHHHHhcccCCCcEEEEEEeCCC
Confidence                 689999999999999999999999999999999999984

>d1rypj_ d.153.1.4 (J:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.84  E-value=1.9e-20  Score=140.54  Aligned_cols=114  Identities=16%  Similarity=0.193  Sum_probs=106.6

Q ss_pred             CceeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc------
Q 040809           16 GRLYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI------   87 (161)
Q Consensus        16 Grl~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i------   87 (161)
                      |.+..|.+. | |||+|+|.+.+.++.++..+|||+| +|++|+++|..+|++.+.+.+|.+++.|++.++.++      
T Consensus         9 ~Tivgi~~~d~VvlaaD~r~~~~~~~~~~~~~Ki~~i-~~i~~~~~G~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la   87 (204)
T d1rypj_           9 GIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHY-GHVFLGITGLATDVTTLNEMFRYKTNLYKLKEERAIEPETFT   87 (204)
T ss_dssp             CEEEEEECSSEEEEEEECCEEETTEEEESCCCCEEEE-TTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             eEEEEEEECCEEEEEEcCCcccCCEeecCcccEEEEc-CCEEEEecCcchHHHHHHHHHHHHHHHHHHhcCCCCcchHHH
Confidence            558888888 6 9999999999988888889999999 599999999999999999999999999999999987      


Q ss_pred             ---------------------------------------------------------------cCCCCCCCHHHHHHHHH
Q 040809           88 ---------------------------------------------------------------QDYKDDMTRQEAVQLAL  104 (161)
Q Consensus        88 ---------------------------------------------------------------~~y~~~mt~eeai~la~  104 (161)
                                                                                     +.|+++||.+||+++++
T Consensus        88 ~~l~~~l~~~~~~p~~v~~li~G~d~~~g~~~L~~~D~~G~~~~~~~~~~~G~g~~~a~~~l~~~~~~~ms~~ea~~l~~  167 (204)
T d1rypj_          88 QLVSSSLYERRFGPYFVGPVVAGINSKSGKPFIAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETIS  167 (204)
T ss_dssp             HHHHHHHHTTTTSCCCEEEEEEEECTTTCCEEEEEECTTCCEECCSSEEEEETTHHHHHHHHHHHCCSSCCHHHHHHHHH
T ss_pred             HHHHHHHHhhcccceeeeEEEEEEecCCCcceEEEeCCCCccccccCcEEeecchHHHHHHHHhccccCCCHHHHHHHHH
Confidence                                                                           35899999999999999


Q ss_pred             HHHHHhhccCCCCCCcEEEEEEEeCC
Q 040809          105 KVLRKTMDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus       105 ~al~~~~~~~~~~~~~iei~ii~~~~  130 (161)
                      +||..+.+++..++++++|++|++++
T Consensus       168 ~al~~a~~~d~~sg~~~~v~ii~kdg  193 (204)
T d1rypj_         168 QALLNAADRDALSGWGAVVYIIKKDE  193 (204)
T ss_dssp             HHHHHHHTTBTTSCSCEEEEEEESSC
T ss_pred             HHHHHHHHhcCccCCeEEEEEEECCc
Confidence            99999999999999999999999985

>d1iru2_ d.153.1.4 (2:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=99.82  E-value=3.2e-20  Score=140.86  Aligned_cols=115  Identities=10%  Similarity=0.097  Sum_probs=102.4

Q ss_pred             CceeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHh-CCCc-----
Q 040809           16 GRLYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAY-QEPI-----   87 (161)
Q Consensus        16 Grl~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~-~~~i-----   87 (161)
                      +.+..|.|. | |||+|+|.+.+.++.+++.+||++|++|++|+.+|..+|++.+++.++.++..|++.+ +.++     
T Consensus         9 tTivgi~~~dgVviaaD~r~t~g~~~~~~~~~KI~~i~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~v~~~   88 (217)
T d1iru2_           9 TSVLGVKFEGGVVIAADMLGSYGSLARFRNISRIMRVNNSTMLGASGDYADFQYLKQVLGQMVIDEELLGDGHSYSPRAI   88 (217)
T ss_dssp             CCCEEEEETTEEEEEEECCEEETTEEEECSCCCEEEETTTEEEEEEEEHHHHHHHHHHHHHHHHHHHHHCSSCCCCHHHH
T ss_pred             cEEEEEEECCEEEEEEcCCcccCCeeecCCcceEEEeCCCeEEEeccccHHHHHHHHHHHHHHHHhhhhcCCCCCCHHHH
Confidence            457888888 5 9999999988877777789999999999999999999999999999999999988765 4555     


Q ss_pred             ---------------------------------------------------------------c--CCCCCCCHHHHHHH
Q 040809           88 ---------------------------------------------------------------Q--DYKDDMTRQEAVQL  102 (161)
Q Consensus        88 ---------------------------------------------------------------~--~y~~~mt~eeai~l  102 (161)
                                                                                     +  .|+++||.+||+++
T Consensus        89 a~~l~~~~y~~~~~~~p~~~~~li~G~d~~~~~l~~~D~~G~~~~~~~~a~G~g~~~a~~~Le~~~~~~~~lt~~ea~~l  168 (217)
T d1iru2_          89 HSWLTRAMYSRRSKMNPLWNTMVIGGYADGESFLGYVDMLGVAYEAPSLATGYGAYLAQPLLREVLEKQPVLSQTEARDL  168 (217)
T ss_dssp             HHHHHHHHHHHHHTTCCCCEEEEEEEEETTEEEEEEECSSCCEEECSEEECTTHHHHTHHHHHHHHTSCSCCCHHHHHHH
T ss_pred             HHHHHHHHHHhccccCcccceEEEEEEcCCCcEEEEEecCceeEeeeEEeccCcHHHHHHHHHHHhcccCCCCHHHHHHH
Confidence                                                                           1  34689999999999


Q ss_pred             HHHHHHHhhccCCCCCCcEEEEEEEeCC
Q 040809          103 ALKVLRKTMDSTSLTSEKLELAEVFLLP  130 (161)
Q Consensus       103 a~~al~~~~~~~~~~~~~iei~ii~~~~  130 (161)
                      +++||+.+.++|..++++++|++|++++
T Consensus       169 ~~~al~~a~~rd~~sg~~i~i~vi~~~G  196 (217)
T d1iru2_         169 VERCMRVLYYRDARSYNRFQTATVTEKG  196 (217)
T ss_dssp             HHHHHHHHHHHBTTCCSCEEEEEEETTE
T ss_pred             HHHHHHHHHHhcCcCCCcEEEEEEeCCC
Confidence            9999999999999999999999999874

>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=99.45  E-value=1.1e-14  Score=106.67  Aligned_cols=113  Identities=19%  Similarity=0.195  Sum_probs=91.1

Q ss_pred             CCCc-eeeEecc-e-EEEEEcccCCCCcccC-CCCCceEEecCc-eEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc-
Q 040809           14 PEGR-LYQVDYM-G-CLVGENNVTSKLLQTS-TSAEKMYKIDDH-VACAVAGIMSDANILINTARVQARRYAYAYQEPI-   87 (161)
Q Consensus        14 p~Gr-l~qveya-G-Vlaadkr~~~~l~~~~-~~~~KI~~I~~~-i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i-   87 (161)
                      +.|. +..|.|. | |||+|+|.+.+.++.. ...+|+++++++ ++++.+|...|.+.+.+..+.+...++.....+. 
T Consensus         3 ~~GTTivai~~~dGVvlAaDtR~S~G~~i~~~~~~~ki~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (180)
T d2z3ba1           3 FHATTIFAVQHKGRSAMSGDGQVTFGQAVVMKHTARKVRKLFNGKVLAGFAGSVADAFTLFEKFEAKLEEYNGNLKRAAV   82 (180)
T ss_dssp             BCCCCEEEEEETTEEEEEECCCEEETTTEEEESCCCCEEEETTTTEEEEECSCHHHHHHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             CCCeEEEEEEECCEEEEEECCcccCCceeEecccceEEEEecccceecccchHHHHHHHHHHHHHHHHHhhccccchhHH
Confidence            3444 8899999 5 9999999998654444 357899999885 7788899999999999888877766542222111 


Q ss_pred             ----------------------------------------------------------cCCCCCCCHHHHHHHHHHHHHH
Q 040809           88 ----------------------------------------------------------QDYKDDMTRQEAVQLALKVLRK  109 (161)
Q Consensus        88 ----------------------------------------------------------~~y~~~mt~eeai~la~~al~~  109 (161)
                                                                                ..|+++||.+||++|+++||+.
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~GSGs~~A~g~l~~~~~~~~s~~eA~~l~~~Al~~  162 (180)
T d2z3ba1          83 ELAKEWRSDKVLRKLEAMLIVMNQDTLLLVSGTGEVIEPDDGILAIGSGGNYALAAGRALKKHAGESMSASEIARAALET  162 (180)
T ss_dssp             HHHHHHHHCTTGGGCCCCEEEECSSCEEEECTTCCEECCSSSEEEESTTHHHHHHHHHHHHHHHGGGCCHHHHHHHHHHH
T ss_pred             HHHHHHhHHHHHHHhhcceeeeeccccccccCCceeecccccEEEEcCchHHHHHHHHHHhhcCCCccCHHHHHHHHHHH
Confidence                                                                      3578999999999999999999


Q ss_pred             hhccCCCCCCcEEEEEE
Q 040809          110 TMDSTSLTSEKLELAEV  126 (161)
Q Consensus       110 ~~~~~~~~~~~iei~ii  126 (161)
                      |.++|.+++++++|-+|
T Consensus       163 A~e~dvyT~~~~~~~~i  179 (180)
T d2z3ba1         163 AGEICVYTNDQIILEEL  179 (180)
T ss_dssp             HHHHCTTCCSCCEEEEE
T ss_pred             HHhhcEEcCCcEEEEEe
Confidence            99999999999999876

>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=99.28  E-value=1.5e-12  Score=93.89  Aligned_cols=106  Identities=14%  Similarity=0.038  Sum_probs=83.7

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEEEEeccHHHHHHHHHHHHHHHHHHHHHhCCCc--------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVACAVAGIMSDANILINTARVQARRYAYAYQEPI--------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i--------   87 (161)
                      +.-|.|. | |||+|+|.+.+.++.++..+||++|+++++++.+|..+|...+..........+........        
T Consensus         3 ivav~~~~gVviAaDtR~S~G~~i~~r~~~Ki~~i~~~~~~~~~g~~ad~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (171)
T d1m4ya_           3 ILVVRRNGQTVMGGDGQVTFGSTVLKGNARKVRKLGEGKVLAGFAGSVADAMTLFDRFEAKLREWGGNLTKAAVELAKDW   82 (171)
T ss_dssp             EEEEEETTEEEEEECCCEEETTEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             EEEEEECCEEEEEECCCcccCCEEEeCCcceEEEecCCcEEEEEeechhhHHHHHHHHHHHHHHhhccchhhHHHHHHHH
Confidence            6678888 4 99999999999999999999999999999999999999999888776666554432211111        


Q ss_pred             ----------------------------------------------------cCC-CCCCCHHHHHHHHHHHHHHhhccC
Q 040809           88 ----------------------------------------------------QDY-KDDMTRQEAVQLALKVLRKTMDST  114 (161)
Q Consensus        88 ----------------------------------------------------~~y-~~~mt~eeai~la~~al~~~~~~~  114 (161)
                                                                          ..| +++|+   |.+++++||..|.++|
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~l~~~~~~~~~~---a~el~~~Ai~~A~e~d  159 (171)
T d1m4ya_          83 RTDRVLRRLEALLLVADKENIFIISGNGEVIQPDDDAAAIGSGGPYALAAAKALLRNTDLS---AREIVEKAMTIAGEIC  159 (171)
T ss_dssp             HHCTTGGGCCCEEEEECSSCEEEECTTSCEECCSSSEEEESTTHHHHHHHHHHHHHHCCCC---HHHHHHHHHHHHHHHC
T ss_pred             HHhhhhcccccccceecCCcceEEecCCceeeecCCEEEEcchHHHHHHHHHhhccCCCCC---HHHHHHHHHHHHHhhc
Confidence                                                                122 35675   5668999999999999


Q ss_pred             CCCCCcEEEEEE
Q 040809          115 SLTSEKLELAEV  126 (161)
Q Consensus       115 ~~~~~~iei~ii  126 (161)
                      .+++++++|-.|
T Consensus       160 vyTg~~~~i~~~  171 (171)
T d1m4ya_         160 IYTNQNIVIEEV  171 (171)
T ss_dssp             TTCCSCCEEEEC
T ss_pred             eEcCCcEEEEEC
Confidence            999999998653

>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=99.22  E-value=1.5e-12  Score=94.21  Aligned_cols=109  Identities=17%  Similarity=0.097  Sum_probs=76.1

Q ss_pred             eeeEecc-e-EEEEEcccCCCCcccCCCCCceEEecCceEE-EEeccHHHHHHHHHHHHHHHHHHHHHhCCCc-------
Q 040809           18 LYQVDYM-G-CLVGENNVTSKLLQTSTSAEKMYKIDDHVAC-AVAGIMSDANILINTARVQARRYAYAYQEPI-------   87 (161)
Q Consensus        18 l~qveya-G-Vlaadkr~~~~l~~~~~~~~KI~~I~~~i~~-~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i-------   87 (161)
                      +..|.|. | |||+|+|.+.+.++.++..+||++|++++++ +.+|...+...+.+..+.....++.......       
T Consensus         3 ivai~~~dGVVlAaDtRaS~G~~i~~r~~~Ki~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (173)
T d1g3ka_           3 IVSVRRNGQVVVGGDGQVSLGNTVMKGNARKVRRLYNGKVLAGFAGGTADAFTLFELFERKLEMHQGHLLKSAVELAKDW   82 (173)
T ss_dssp             EEEEEETTEEEEEECCCEEETTEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             EEEEEECCEEEEEECCCcccCCEeEcCCcceEEEecCCcEEEEeeehhHhHHHHHHHHHHHHHhhcCcchhHHHHHHHHH
Confidence            5678888 5 9999999999999999999999999888555 5555555555544433322222211000000       


Q ss_pred             ---------------------------------------------------cCCCCCCCHHHHHHHHHHHHHHhhccCCC
Q 040809           88 ---------------------------------------------------QDYKDDMTRQEAVQLALKVLRKTMDSTSL  116 (161)
Q Consensus        88 ---------------------------------------------------~~y~~~mt~eeai~la~~al~~~~~~~~~  116 (161)
                                                                         .+|+.+++.+||.+++++||..|.++|.+
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~GSGs~~A~~~l~~~~~~~~~~A~ela~~Ai~~Aae~dvy  162 (173)
T d1g3ka_          83 RTDRALRKLEAMLIVADEKESLIITGIGDVVQPEEDQILAIGSGGNYALSAARALVENTELSAHEIVEKSLRIAGDICVF  162 (173)
T ss_dssp             HHSTTGGGCCCEEEEECSSCEEEEETTTEEECCCTTCEEEESTTHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCTT
T ss_pred             HHhhhhcccccccccccCCCcceecccCceEEecCCCEEEecchHHHHHHHHHHhhhcCCCCHHHHHHHHHHHHHhhcEE
Confidence                                                               01234455567889999999999999999


Q ss_pred             CCCcEEEEEE
Q 040809          117 TSEKLELAEV  126 (161)
Q Consensus       117 ~~~~iei~ii  126 (161)
                      ++++++|-.|
T Consensus       163 Tgd~~~i~~~  172 (173)
T d1g3ka_         163 TNTNFTIEEL  172 (173)
T ss_dssp             CCSCCEEEEE
T ss_pred             cCCcEEEEEC
Confidence            9999998765