Citrus Sinensis ID: 024461

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------
Protein Sequence
MDPKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKDSAPCKEIPSLQLINQTLSYARELERIV
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHcccHHHHHHHHHHccHHHHcccccHHHHHHHHHHHHcHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHccccHHHHHHHHHHHcccccccccEEEEcccccccccccccHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHcccHccccccHHHHHHHHHHHHHHHHHccHHHHHHHHHHccHHHHccccccccHHHHHHHHHccHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHccccHHHHHHHHHHccccEEEcccEEEEcccccccccccccHHHHHHHHHHHHHHHHHHc
Coil and Loop (DISEMBL)
MDPKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGfrslpplfedtpNAIRELTLARDIYEHAVLLSVKVEDQDAFERDFfqlkpyytdagkrlppspneyMILGLNLLRLLVQNRIAEFHTELELLsstalenpciKHAVELEQSFMEGAYNRVLSakqnvpnetyGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKeehpewemkdgFVFFqkakdsapckeipslqlINQTLSYARELERIV
Flexible Loop (DISEMBL)
MDPKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKDSAPckeipslqlinqtlsyareleriv
Low Complexity Region (SEG)
MDPKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIlglnllrllVQNRIAEFHtelellsstaleNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKDSAPCKEIPSLQLINQTLSYARELERIV
Disordered region (IsUnstruct)
**************FKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKDSAPCKEIPSLQLINQTLSY********
Disordered Region (DISOPRED)
*********QQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQ**************QLINQTLSYARELERIV
Disordered Region (DISEMBL)
********SQQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKDSAPCKEIPSLQLINQTLSYARELERIV
Disordered Region (DISPRO)
**PKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKDSAPCKEIPSLQLINQTLSYARELERIV
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDPKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKDSAPCKEIPSLQLINQTLSYARELERIV
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	267	2.2.26 [Sep-21-2011]
Q9SGW3	267	26S proteasome non-ATPase	yes	no	1.0	1.0	0.831	1e-124
Q9FHY0	233	26S proteasome non-ATPase	no	no	0.872	1.0	0.621	5e-88
P02889	263	Probable 26S proteasome n	yes	no	0.970	0.984	0.4	7e-51
Q5RE15	289	26S proteasome non-ATPase	yes	no	0.970	0.896	0.404	6e-39
Q3SYT7	287	26S proteasome non-ATPase	yes	no	0.962	0.895	0.408	7e-39
Q9CX56	353	26S proteasome non-ATPase	yes	no	0.955	0.722	0.413	8e-39
P48556	350	26S proteasome non-ATPase	yes	no	0.970	0.74	0.404	2e-38
P50524	270	26S proteasome regulatory	yes	no	0.887	0.877	0.342	1e-32
Q23449	250	26S proteasome non-ATPase	yes	no	0.749	0.8	0.357	8e-28
P32496	274	26S proteasome regulatory	yes	no	0.966	0.941	0.282	3e-17

>sp|Q9SGW3|RP12A_ARATH 26S proteasome non-ATPase regulatory subunit RPN12A OS=Arabidopsis thaliana GN=RPN12A PE=1 SV=1

 Score =  443 bits (1140), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 222/267 (83%), Positives = 243/267 (91%)

Query: 1   MDPKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTL 60
           MDP+LTEVSQQF+RFKAA  RKDYNTC+ LLSQLKVLLT F SLPPLFE++PNA +ELT+
Sbjct: 1   MDPQLTEVSQQFERFKAAFARKDYNTCSDLLSQLKVLLTKFTSLPPLFENSPNAAKELTI 60

Query: 61  ARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQN 120
           ARDIYEHAV+LSVK EDQDAFERDFFQLKPYY DA  R+P SP E +ILGLNLLRLLVQN
Sbjct: 61  ARDIYEHAVVLSVKTEDQDAFERDFFQLKPYYVDARNRIPQSPQENLILGLNLLRLLVQN 120

Query: 121 RIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLA 180
           RIAEFHTELELLSS  LE+PCIKHAVELEQSFMEGAYNRVLSA+Q  P+ TY YFMDLLA
Sbjct: 121 RIAEFHTELELLSSATLEDPCIKHAVELEQSFMEGAYNRVLSARQTAPDATYVYFMDLLA 180

Query: 181 KTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKD 240
           KT+RDEIAGCSEKAYDY+SI DA QMLLF+SDQELL YV +EHPEWE+K+GFV FQKAK+
Sbjct: 181 KTIRDEIAGCSEKAYDYVSISDARQMLLFSSDQELLTYVTDEHPEWEVKEGFVVFQKAKE 240

Query: 241 SAPCKEIPSLQLINQTLSYARELERIV 267
           +APCKEIPSLQLINQTLSYARELERIV
Sbjct: 241 TAPCKEIPSLQLINQTLSYARELERIV 267

Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. May help to control the degradation of one or more factors that repress cytokinin signaling.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9FHY0|RP12B_ARATH 26S proteasome non-ATPase regulatory subunit RPN12B OS=Arabidopsis thaliana GN=RPN12B PE=2 SV=2

 Score =  324 bits (830), Expect = 5e-88,   Method: Compositional matrix adjust.
 Identities = 166/267 (62%), Positives = 194/267 (72%), Gaps = 34/267 (12%)

Query: 1   MDPKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTL 60
           MDP+L EVSQQF+RFKAA   KD++TC+ LLSQLK+                        
Sbjct: 1   MDPQLMEVSQQFERFKAAFIIKDFDTCSSLLSQLKLF----------------------- 37

Query: 61  ARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQN 120
             D Y  ++ L+  +    A          ++     R+PPSP E +I+GLNLLRLLVQN
Sbjct: 38  --DHYLISLSLNALLLLTCAL---------FFLCTRNRIPPSPQENLIMGLNLLRLLVQN 86

Query: 121 RIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLA 180
           RIAEFHTEL LLSS  LENPCIKHAVELEQSFMEGAYNRVLSA+Q  P+ETY YFMDLLA
Sbjct: 87  RIAEFHTELGLLSSATLENPCIKHAVELEQSFMEGAYNRVLSARQTAPDETYVYFMDLLA 146

Query: 181 KTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKD 240
           KT+RDEIAGCSEKAYD+LSI +  +MLLF+SDQ+LL YV EEHPEWE+KDG V FQK ++
Sbjct: 147 KTIRDEIAGCSEKAYDHLSISEGCKMLLFSSDQQLLTYVNEEHPEWEVKDGLVVFQKTRE 206

Query: 241 SAPCKEIPSLQLINQTLSYARELERIV 267
           +APCKEIPSLQLINQTLSY RELERI+
Sbjct: 207 TAPCKEIPSLQLINQTLSYTRELERIL 233

Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.

Arabidopsis thaliana (taxid: 3702)

>sp|P02889|PSMD8_DICDI Probable 26S proteasome non-ATPase regulatory subunit 8 OS=Dictyostelium discoideum GN=psmD8-1 PE=3 SV=2

 Score =  200 bits (509), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 106/265 (40%), Positives = 167/265 (63%), Gaps = 6/265 (2%)

Query: 5   LTEVSQQFDRFKAAMT-RKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIR-ELTLAR 62
            + + Q  + FK  +    D    T +L QLK+  T     P    +  + ++ +L LAR
Sbjct: 3   FSSIEQNLNNFKKLVAGNSDKAQITPVLVQLKLAATIHLEKPTSLSNVSDKVKKDLVLAR 62

Query: 63  DIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRI 122
           +I E   L S+K++D D+FER F QLK YY D    + PS  EY I+GLNL+RLL +++ 
Sbjct: 63  EILELISLYSIKIKDIDSFERTFNQLKTYYYDYKSIIAPSTLEYQIIGLNLMRLLAKHKT 122

Query: 123 AEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKT 182
           +EFH+E+EL+    L+N  IK  + +E+S  EG+YN+++ ++  VP+E Y  F+D+LA +
Sbjct: 123 SEFHSEIELIEFNNLDNSFIKFPLLVEKSITEGSYNKIIQSRSGVPSEYYQVFLDILADS 182

Query: 183 VRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKDSA 242
           ++++IA CSEK++  LS+KDA ++LLF  + +  +Y+KE +  W+++   + F    +  
Sbjct: 183 IKEDIANCSEKSFKTLSLKDAEKVLLFNDNNQFQQYIKERN--WKVQGDVIQF--GNNDN 238

Query: 243 PCKEIPSLQLINQTLSYARELERIV 267
              EIPSLQLI+QTL YA+ELERIV
Sbjct: 239 QTVEIPSLQLIHQTLHYAKELERIV 263

Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.

Dictyostelium discoideum (taxid: 44689)

>sp|Q5RE15|PSMD8_PONAB 26S proteasome non-ATPase regulatory subunit 8 (Fragment) OS=Pongo abelii GN=PSMD8 PE=2 SV=2

 Score =  160 bits (406), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 108/267 (40%), Positives = 155/267 (58%), Gaps = 8/267 (2%)

Query: 5   LTEVSQQFDRFKAAMTRKDYN--TCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLAR 62
           L   +  +++ K    RK  N   C + L +LK++L     LP     T    ++L LAR
Sbjct: 27  LQAATGMYEQLKGEWNRKSPNLSKCGEELGRLKLVLLELNFLPT--TGTKLTKQQLILAR 84

Query: 63  DIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRI 122
           DI E     S+  +D  +FER   QLK YY D  ++LP S   + +LGLNLL LL QNR+
Sbjct: 85  DILEIGAQWSILRKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLSQNRV 144

Query: 123 AEFHTELELLSSTALE-NPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAK 181
           AEFHTELE L +  ++ N  IKH V LEQ  MEG+YN+V  AK N+P E+Y +F+D+L  
Sbjct: 145 AEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYAFFIDILLD 204

Query: 182 TVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK-DGFVFFQKAKD 240
           T+RDEIAGC EKAY+ +   +A ++L F + +++ +Y K+    W +  + +  F   + 
Sbjct: 205 TIRDEIAGCIEKAYEKILFTEATRILFFNTPKKMTDYAKKRG--WVLGPNNYYSFASQQQ 262

Query: 241 SAPCKEIPSLQLINQTLSYARELERIV 267
                 IPS +L  Q + YAR+LE IV
Sbjct: 263 KPEDTTIPSTELAKQVIEYARQLEMIV 289

Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. Necessary for activation of the CDC28 kinase.

Pongo abelii (taxid: 9601)

>sp|Q3SYT7|PSMD8_BOVIN 26S proteasome non-ATPase regulatory subunit 8 OS=Bos taurus GN=PSMD8 PE=2 SV=3

 Score =  160 bits (406), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 110/269 (40%), Positives = 158/269 (58%), Gaps = 12/269 (4%)

Query: 5   LTEVSQQFDRFKAAMTRKDYN--TCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLAR 62
           L   +  +++ K    RK  N   C + L +LK++L     LP     T    ++L LAR
Sbjct: 25  LQAAAGMYEQLKGEWNRKSPNLSKCGEELGRLKLVLLELNFLPT--TGTKLTKQQLILAR 82

Query: 63  DIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRI 122
           DI E     S+  +D  +FER   QLK YY D  ++LP S   + +LGLNLL LL QNR+
Sbjct: 83  DIQEIGAQWSILRKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLSQNRV 142

Query: 123 AEFHTELELLSSTALE-NPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAK 181
           AEFHTELE L +  ++ N  IKH V LEQ  MEG+YN+V  AK N+P E+Y +F+D+L  
Sbjct: 143 AEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLD 202

Query: 182 TVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFF---QKA 238
           T+RDEIAGC EKAY+ +   +A ++L F + +++ +Y K+      + + + F    QK 
Sbjct: 203 TIRDEIAGCIEKAYEKILFTEATRILFFNTPKKMTDYAKKRGWVLGINNYYSFASQQQKP 262

Query: 239 KDSAPCKEIPSLQLINQTLSYARELERIV 267
           +D+     IPS +L  Q + YAR+LE IV
Sbjct: 263 EDTT----IPSTELAKQVIEYARQLEMIV 287

Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. Necessary for activation of the CDC28 kinase.

Bos taurus (taxid: 9913)

>sp|Q9CX56|PSMD8_MOUSE 26S proteasome non-ATPase regulatory subunit 8 OS=Mus musculus GN=Psmd8 PE=1 SV=2

 Score =  160 bits (405), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 112/271 (41%), Positives = 161/271 (59%), Gaps = 16/271 (5%)

Query: 5   LTEVSQQFDRFKAAMTRKDYN--TCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLAR 62
           L   +  +++ K    RK+ N   C + L +LK++L     LP     T    ++L LAR
Sbjct: 91  LQAAAGMYEQLKDEWNRKNPNLSKCGEELGRLKLVLLELNFLPTT--GTKLTKQQLILAR 148

Query: 63  DIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRI 122
           DI E     S+  +D  +FER   QLK YY D  ++LP S   + +LGLNLL LL QNR+
Sbjct: 149 DILEIGAQWSILCKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLSQNRV 208

Query: 123 AEFHTELELLSSTALE-NPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAK 181
           AEFHTELE L +  ++ N  IKH V LEQ  MEG+YN+V  AK N+P E+Y +F+D+L  
Sbjct: 209 AEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLD 268

Query: 182 TVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK-DGFVFF----Q 236
           T+RDEIAGC EKAY+ +   +A ++L F++ +++ +Y K+    W +  + +  F    Q
Sbjct: 269 TIRDEIAGCIEKAYEKILFAEATRILFFSTPKKMTDYAKKRG--WVLGPNNYYSFASQQQ 326

Query: 237 KAKDSAPCKEIPSLQLINQTLSYARELERIV 267
           K +DS     IPS +L  Q + YAR+LE IV
Sbjct: 327 KPEDST----IPSTELAKQVIEYARQLEMIV 353

Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. Necessary for activation of the CDC28 kinase.

Mus musculus (taxid: 10090)

>sp|P48556|PSMD8_HUMAN 26S proteasome non-ATPase regulatory subunit 8 OS=Homo sapiens GN=PSMD8 PE=1 SV=2

 Score =  159 bits (403), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 108/267 (40%), Positives = 155/267 (58%), Gaps = 8/267 (2%)

Query: 5   LTEVSQQFDRFKAAMTRKDYN--TCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLAR 62
           L   +  +++ K    RK  N   C + L +LK++L     LP     T    ++L LAR
Sbjct: 88  LQAATGMYEQLKGEWNRKSPNLSKCGEELGRLKLVLLELNFLPT--TGTKLTKQQLILAR 145

Query: 63  DIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRI 122
           DI E     S+  +D  +FER   QLK YY D  ++LP S   + +LGLNLL LL QNR+
Sbjct: 146 DILEIGAQWSILRKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLSQNRV 205

Query: 123 AEFHTELELLSSTALE-NPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAK 181
           AEFHTELE L +  ++ N  IKH V LEQ  MEG+YN+V  AK N+P E+Y +F+D+L  
Sbjct: 206 AEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLD 265

Query: 182 TVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK-DGFVFFQKAKD 240
           T+RDEIAGC EKAY+ +   +A ++L F + +++ +Y K+    W +  + +  F   + 
Sbjct: 266 TIRDEIAGCIEKAYEKILFTEATRILFFNTPKKMTDYAKKRG--WVLGPNNYYSFASQQQ 323

Query: 241 SAPCKEIPSLQLINQTLSYARELERIV 267
                 IPS +L  Q + YAR+LE IV
Sbjct: 324 KPEDTTIPSTELAKQVIEYARQLEMIV 350

Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. Necessary for activation of the CDC28 kinase.

Homo sapiens (taxid: 9606)

>sp|P50524|RPN12_SCHPO 26S proteasome regulatory subunit rpn12 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpn12 PE=1 SV=1

 Score =  140 bits (352), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 91/266 (34%), Positives = 146/266 (54%), Gaps = 29/266 (10%)

Query: 21  RKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLARDIYEHAVLLSVKVEDQDA 80
           RKD+N C + L +LKV L        LF  T +   + + AR+++E+ VL+S++  D ++
Sbjct: 15  RKDWNACKKELLKLKVELAK----QNLFVPTSDK-EKASFARNVFEYGVLVSIQTCDIES 69

Query: 81  FERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTAL--E 138
           F R   Q+ P+Y D+   L PS    ++ GLNLL LL +NRIAEFHT LE +   +L   
Sbjct: 70  FARYASQVIPFYHDS---LVPSSRMGLVTGLNLLYLLSENRIAEFHTALESVPDKSLFER 126

Query: 139 NPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYL 198
           +P ++  + LEQ+ MEGA+++V S  ++     + YFM ++   VR+EIA C+EK Y  +
Sbjct: 127 DPYVEWVISLEQNVMEGAFDKVASMIRSCNFPEFSYFMKIVMSMVRNEIATCAEKVYSEI 186

Query: 199 SIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKDS----------------- 241
            + +A  +L   + +E  E + EE   W+++DG ++F K  ++                 
Sbjct: 187 PLSNATSLLYLENTKE-TEKLAEERG-WDIRDGVIYFPKEANALETEDGMLIDEEDELEL 244

Query: 242 APCKEIPSLQLINQTLSYARELERIV 267
            P     ++  I Q LSY  ELE+IV
Sbjct: 245 PPTASKHTISSIRQLLSYTSELEQIV 270

Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q23449|PSMD8_CAEEL 26S proteasome non-ATPase regulatory subunit 8 OS=Caenorhabditis elegans GN=rpn-12 PE=1 SV=1

 Score =  124 bits (310), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 75/210 (35%), Positives = 128/210 (60%), Gaps = 10/210 (4%)

Query: 61  ARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQN 120
           ++D+YE +VLL++   D + F+    Q+  YYT A +    S N++++ GL+L+ LL  N
Sbjct: 48  SKDLYEISVLLAILKHDFETFDDYINQMHTYYTMAPEN---SENKHLMTGLHLMFLLAAN 104

Query: 121 RIAEFHTELELL-SSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLL 179
           R+++FH  LE +       N  I   V +EQS MEGAYN+V+  ++N+P+  Y  F+ ++
Sbjct: 105 RLSDFHMLLEQIPQKEQTSNAYISTPVRIEQSLMEGAYNKVVLTEKNIPSPFYTIFIRIM 164

Query: 180 AKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDG--FVFFQK 237
             T+R EIA   EK++  L+ KDA  MLLF +D+++ ++ +E   +W + DG  +VF  +
Sbjct: 165 LDTIRREIATSIEKSFKVLTAKDATVMLLFDNDEQMKKFGQER--KWHL-DGERYVFEIE 221

Query: 238 AKDSAPCKEIPSLQLINQTLSYARELERIV 267
                P   + ++++  QTL YA++LE+IV
Sbjct: 222 VAQEKPVN-LDTVRVATQTLFYAKQLEQIV 250

Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.

Caenorhabditis elegans (taxid: 6239)

>sp|P32496|RPN12_YEAST 26S proteasome regulatory subunit RPN12 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPN12 PE=1 SV=3

 Score = 89.4 bits (220), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 79/280 (28%), Positives = 138/280 (49%), Gaps = 22/280 (7%)

Query: 3   PKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKV-LLTGFRSLPPLFEDTPNAIRELTLA 61
           P L E+++       A    DY  C +LL  +K+ L+     +P L       + +L + 
Sbjct: 2   PSLAELTKSL---SIAFENGDYAACEKLLPPIKIELIKNNLLIPDLSIQNDIYLNDLMIT 58

Query: 62  RDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNR 121
           + I E   L S++  + D+FE  F QLKPYY     +L  S  +  ++ L LL LL QN 
Sbjct: 59  KRILEVGALASIQTFNFDSFENYFNQLKPYYFSNNHKLSESDKKSKLISLYLLNLLSQNN 118

Query: 122 IAEFHTELELLS---STALENPCIKHAVELEQSFMEGAYNRVL----SAKQNVPNETYGY 174
             +FH+EL+ L        ++  + + ++L++  MEG+Y +      S  QN+    +  
Sbjct: 119 TTKFHSELQYLDKHIKNLEDDSLLSYPIKLDRWLMEGSYQKAWDLLQSGSQNIS--EFDS 176

Query: 175 FMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVF 234
           F D+L   +RDEIA  +E +YD+L + +   +L F +++E  ++  E +  W + +  V+
Sbjct: 177 FTDILKSAIRDEIAKNTELSYDFLPLSNIKALLFFNNEKETEKFALERN--WPIVNSKVY 234

Query: 235 F-----QKA--KDSAPCKEIPSLQLINQTLSYARELERIV 267
           F     +KA  +D    +E     +I + + YA  +E IV
Sbjct: 235 FNNQSKEKADYEDEMMHEEDQKTNIIEKAMDYAISIENIV 274

Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. Necessary for activation of the CDC28 kinase.

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

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	267
359807666	267	uncharacterized protein LOC100785835 [Gl	1.0	1.0	0.876	1e-129
449517868	267	PREDICTED: 26S proteasome non-ATPase reg	1.0	1.0	0.868	1e-128
356524925	267	PREDICTED: 26S proteasome non-ATPase reg	1.0	1.0	0.868	1e-128
357437525	267	26S proteasome non-ATPase regulatory sub	1.0	1.0	0.868	1e-128
449462515	267	PREDICTED: 26S proteasome non-ATPase reg	1.0	1.0	0.865	1e-127
388511026	267	unknown [Medicago truncatula]	1.0	1.0	0.865	1e-127
224072240	267	predicted protein [Populus trichocarpa]	1.0	1.0	0.865	1e-126
225426245	267	PREDICTED: 26S proteasome non-ATPase reg	1.0	1.0	0.853	1e-126
255646695	267	unknown [Glycine max]	1.0	1.0	0.857	1e-125
224058123	267	predicted protein [Populus trichocarpa]	1.0	1.0	0.850	1e-123

>gi|359807666|ref|NP_001241171.1| uncharacterized protein LOC100785835 [Glycine max] gi|255634606|gb|ACU17665.1| unknown [Glycine max]

 Score =  465 bits (1197), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 234/267 (87%), Positives = 249/267 (93%)

Query: 1   MDPKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTL 60
           MDPKL EVSQ FDRFKA+  R D++TC+ LLSQLKVLLTGFRSLPPLF DTPNA+ ELT+
Sbjct: 1   MDPKLKEVSQLFDRFKASFIRNDFDTCSNLLSQLKVLLTGFRSLPPLFADTPNAVHELTI 60

Query: 61  ARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQN 120
           ARDIYEHAV+LSVK EDQDAFERDFFQLKPYYTDA  RLPPSP EY ILGLNLLRLLVQN
Sbjct: 61  ARDIYEHAVVLSVKNEDQDAFERDFFQLKPYYTDACNRLPPSPQEYPILGLNLLRLLVQN 120

Query: 121 RIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLA 180
           RIAEFHTELELLSS ALENPCIKHAVELEQSFMEGAYNRVLSA+Q VP++TY YFMDLLA
Sbjct: 121 RIAEFHTELELLSSAALENPCIKHAVELEQSFMEGAYNRVLSARQTVPHDTYVYFMDLLA 180

Query: 181 KTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKD 240
           KTVRDEIAGCSEKAYDYLSIKDA QMLLF+SDQELLEY+KEEHPEWE+K+G VFFQKAK+
Sbjct: 181 KTVRDEIAGCSEKAYDYLSIKDAKQMLLFSSDQELLEYIKEEHPEWEIKNGSVFFQKAKE 240

Query: 241 SAPCKEIPSLQLINQTLSYARELERIV 267
           SAPCKEIPSLQLINQTLSYARELERIV
Sbjct: 241 SAPCKEIPSLQLINQTLSYARELERIV 267

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449517868|ref|XP_004165966.1| PREDICTED: 26S proteasome non-ATPase regulatory subunit RPN12A-like [Cucumis sativus]

 Score =  463 bits (1191), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 232/267 (86%), Positives = 248/267 (92%)

Query: 1   MDPKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTL 60
           MDPKLTEVSQ F+RFKAA+ R DY++C  LLSQLKV LTGFRSLPPLFEDTPNA+ ELT+
Sbjct: 1   MDPKLTEVSQHFERFKAALVRHDYDSCDNLLSQLKVFLTGFRSLPPLFEDTPNAVEELTI 60

Query: 61  ARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQN 120
           AR+IYEHAVLLSVKVEDQ AFERDFFQLKPYYTDA  RLPPSP EY ILGLNLLRLLVQN
Sbjct: 61  ARNIYEHAVLLSVKVEDQGAFERDFFQLKPYYTDAHNRLPPSPQEYPILGLNLLRLLVQN 120

Query: 121 RIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLA 180
           RIAEFHTELELLS +ALENPCIKHAVELEQSFMEGAYNRVLSA+Q VP+ETYGYFMDLLA
Sbjct: 121 RIAEFHTELELLSPSALENPCIKHAVELEQSFMEGAYNRVLSARQTVPHETYGYFMDLLA 180

Query: 181 KTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKD 240
           KTVRDEIAGCSEKAYDYLSI DA QMLLF+SDQELL+YVKEEHPEWE+ +G V+FQKAK+
Sbjct: 181 KTVRDEIAGCSEKAYDYLSINDACQMLLFSSDQELLDYVKEEHPEWEVTNGNVYFQKAKE 240

Query: 241 SAPCKEIPSLQLINQTLSYARELERIV 267
           S PCKEIPSLQLINQTLSYARELERIV
Sbjct: 241 SGPCKEIPSLQLINQTLSYARELERIV 267

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356524925|ref|XP_003531078.1| PREDICTED: 26S proteasome non-ATPase regulatory subunit RPN12A-like [Glycine max]

 Score =  462 bits (1190), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 232/267 (86%), Positives = 248/267 (92%)

Query: 1   MDPKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTL 60
           MDPKL EVSQ FDRFKA+  R D++ C+ LLSQLKVLLTGFRSLPPLF DTPNA+ ELT+
Sbjct: 1   MDPKLKEVSQLFDRFKASFLRNDFDNCSNLLSQLKVLLTGFRSLPPLFADTPNAVHELTI 60

Query: 61  ARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQN 120
           ARDIYEHAV+LSVK+EDQDAFERDFFQLKPYYTDA  RLPPSP EY ILGLNLLRLLVQN
Sbjct: 61  ARDIYEHAVVLSVKIEDQDAFERDFFQLKPYYTDACNRLPPSPQEYPILGLNLLRLLVQN 120

Query: 121 RIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLA 180
           RIAEFHTELELLSS ALENPCIKHAVELEQSFMEGAYNRVLSA+Q VP++TY YFMDLLA
Sbjct: 121 RIAEFHTELELLSSAALENPCIKHAVELEQSFMEGAYNRVLSARQTVPHDTYVYFMDLLA 180

Query: 181 KTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKD 240
           KTVRDEIAGCSEKAYDYLSIKDA QMLLF+SDQELLEY+KEEHPEWE+K+  VFFQKAK+
Sbjct: 181 KTVRDEIAGCSEKAYDYLSIKDAKQMLLFSSDQELLEYIKEEHPEWEIKNDSVFFQKAKE 240

Query: 241 SAPCKEIPSLQLINQTLSYARELERIV 267
           SAPCKEIPSLQLINQTLSYARELERIV
Sbjct: 241 SAPCKEIPSLQLINQTLSYARELERIV 267

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357437525|ref|XP_003589038.1| 26S proteasome non-ATPase regulatory subunit [Medicago truncatula] gi|217074312|gb|ACJ85516.1| unknown [Medicago truncatula] gi|355478086|gb|AES59289.1| 26S proteasome non-ATPase regulatory subunit [Medicago truncatula]

 Score =  462 bits (1190), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 232/267 (86%), Positives = 248/267 (92%)

Query: 1   MDPKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTL 60
           MDPK TEVSQ FDRFKAA  R D+++ + LLSQLKVLLTGFRSLPPLF DTPNA++ELT+
Sbjct: 1   MDPKFTEVSQLFDRFKAAFLRNDFDSASNLLSQLKVLLTGFRSLPPLFADTPNAVQELTI 60

Query: 61  ARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQN 120
           ARDIYEHAV+LSVK+EDQDAFERDFFQLKPYYTDA  RLP SP EY ILGLNLLRLLVQN
Sbjct: 61  ARDIYEHAVVLSVKIEDQDAFERDFFQLKPYYTDARNRLPQSPQEYPILGLNLLRLLVQN 120

Query: 121 RIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLA 180
           RIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSA+Q VP+ETY YFMDLLA
Sbjct: 121 RIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSARQTVPHETYVYFMDLLA 180

Query: 181 KTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKD 240
           KT+RDEIAGCSEKAYDYLSI DA QMLLFT DQELLEY+KEEHPEWE+K+G V+FQKAKD
Sbjct: 181 KTIRDEIAGCSEKAYDYLSINDAKQMLLFTKDQELLEYIKEEHPEWEIKNGSVYFQKAKD 240

Query: 241 SAPCKEIPSLQLINQTLSYARELERIV 267
           SAPCKEIPSLQLINQTLSYARELERIV
Sbjct: 241 SAPCKEIPSLQLINQTLSYARELERIV 267

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462515|ref|XP_004148986.1| PREDICTED: 26S proteasome non-ATPase regulatory subunit RPN12A-like [Cucumis sativus]

 Score =  460 bits (1183), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 231/267 (86%), Positives = 247/267 (92%)

Query: 1   MDPKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTL 60
           MDPKLTEVSQ F+RFKAA+ R DY++C  LLSQLKV LTGFRSLPPLFEDTPNA+ ELT+
Sbjct: 1   MDPKLTEVSQHFERFKAALVRHDYDSCDNLLSQLKVFLTGFRSLPPLFEDTPNAVEELTI 60

Query: 61  ARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQN 120
           AR+IYEHAVLLSVKVEDQ AFERDFFQLKPYY DA  RLPPSP EY ILGLNLLRLLVQN
Sbjct: 61  ARNIYEHAVLLSVKVEDQGAFERDFFQLKPYYIDARNRLPPSPQEYPILGLNLLRLLVQN 120

Query: 121 RIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLA 180
           RIAEFHTELELLS +ALENPCIKHAVELEQSFMEGAYNRVLSA+Q VP+ETYGYFMDLLA
Sbjct: 121 RIAEFHTELELLSPSALENPCIKHAVELEQSFMEGAYNRVLSARQTVPHETYGYFMDLLA 180

Query: 181 KTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKD 240
           KTVRDEIAGCSEKAYDYLSI DA QMLLF+SDQELL+YVKEEHPEWE+ +G V+FQKAK+
Sbjct: 181 KTVRDEIAGCSEKAYDYLSINDACQMLLFSSDQELLDYVKEEHPEWEVTNGNVYFQKAKE 240

Query: 241 SAPCKEIPSLQLINQTLSYARELERIV 267
           S PCKEIPSLQLINQTLSYARELERIV
Sbjct: 241 SGPCKEIPSLQLINQTLSYARELERIV 267

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388511026|gb|AFK43579.1| unknown [Medicago truncatula]

 Score =  459 bits (1181), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 231/267 (86%), Positives = 247/267 (92%)

Query: 1   MDPKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTL 60
           MDPK TEVSQ FDRFKAA  R D+++ + LLSQLKVLLTGFRSLPPLF DTPNA++ELT+
Sbjct: 1   MDPKFTEVSQLFDRFKAAFLRNDFDSASNLLSQLKVLLTGFRSLPPLFADTPNAVQELTI 60

Query: 61  ARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQN 120
           ARDIYEHAV+LSVK+EDQDAFERDFFQLKPYYTDA  RLP SP EY ILGLNLLRLLVQN
Sbjct: 61  ARDIYEHAVVLSVKIEDQDAFERDFFQLKPYYTDARNRLPQSPQEYPILGLNLLRLLVQN 120

Query: 121 RIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLA 180
           RIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSA+Q VP+ETY YFMDLLA
Sbjct: 121 RIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSARQTVPHETYVYFMDLLA 180

Query: 181 KTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKD 240
           KT+RDEIA CSEKAYDYLSI DA QMLLFT DQELLEY+KEEHPEWE+K+G V+FQKAKD
Sbjct: 181 KTIRDEIARCSEKAYDYLSINDAKQMLLFTKDQELLEYIKEEHPEWEIKNGSVYFQKAKD 240

Query: 241 SAPCKEIPSLQLINQTLSYARELERIV 267
           SAPCKEIPSLQLINQTLSYARELERIV
Sbjct: 241 SAPCKEIPSLQLINQTLSYARELERIV 267

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224072240|ref|XP_002303668.1| predicted protein [Populus trichocarpa] gi|118488523|gb|ABK96074.1| unknown [Populus trichocarpa] gi|222841100|gb|EEE78647.1| predicted protein [Populus trichocarpa]

 Score =  456 bits (1172), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 231/267 (86%), Positives = 248/267 (92%)

Query: 1   MDPKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTL 60
           MDPKLTEVSQ F+RFKAA TR+D+NT T LLSQLKVLLTGFRSLPPLFE+TPNA++ELT+
Sbjct: 1   MDPKLTEVSQLFERFKAACTREDFNTSTNLLSQLKVLLTGFRSLPPLFENTPNAVQELTI 60

Query: 61  ARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQN 120
           ARD++EHAVLLSVK+ DQ+AFERDFFQLKPYYTDA   LP SP EYMILGLNLLRLLVQN
Sbjct: 61  ARDVFEHAVLLSVKIGDQEAFERDFFQLKPYYTDASSCLPQSPQEYMILGLNLLRLLVQN 120

Query: 121 RIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLA 180
           RIAEFHTELELLS TALENPCIKHAVELEQSFMEGAYNRVLSAKQNVP +TY YFMDLLA
Sbjct: 121 RIAEFHTELELLSPTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPYKTYDYFMDLLA 180

Query: 181 KTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKD 240
           KTVRDEIAGCSEKAYDYLSI DA QMLLF S+ ELLEY+KEEHPEWE+K+G V FQKAK+
Sbjct: 181 KTVRDEIAGCSEKAYDYLSISDARQMLLFPSENELLEYIKEEHPEWEIKNGSVVFQKAKE 240

Query: 241 SAPCKEIPSLQLINQTLSYARELERIV 267
           SAPCKEIPSLQLINQTLSYARELERIV
Sbjct: 241 SAPCKEIPSLQLINQTLSYARELERIV 267

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225426245|ref|XP_002264255.1| PREDICTED: 26S proteasome non-ATPase regulatory subunit RPN12A [Vitis vinifera] gi|297742385|emb|CBI34534.3| unnamed protein product [Vitis vinifera]

 Score =  456 bits (1172), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 228/267 (85%), Positives = 245/267 (91%)

Query: 1   MDPKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTL 60
           MDPKL EVSQ  +RFKAA  R D++TCT+LLSQLKVLLT FRSLPPLFED+PNA+ EL +
Sbjct: 1   MDPKLREVSQGLERFKAAFVRSDFDTCTKLLSQLKVLLTEFRSLPPLFEDSPNAVHELKI 60

Query: 61  ARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQN 120
           ARDIYEHAV+LSVK EDQDAFERDFFQLKPYYTD G RLPPSP EY ILGLNLLRLLVQN
Sbjct: 61  ARDIYEHAVVLSVKTEDQDAFERDFFQLKPYYTDTGGRLPPSPQEYPILGLNLLRLLVQN 120

Query: 121 RIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLA 180
           RIAEFHTELELLS+TALEN CIKHAVELEQSFMEGAYNRVLSA+Q VP+ETY YFMDLLA
Sbjct: 121 RIAEFHTELELLSATALENACIKHAVELEQSFMEGAYNRVLSARQTVPHETYVYFMDLLA 180

Query: 181 KTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKD 240
           KTVRDEIAGCSEKAYDYLSI DA  MLLF+SDQEL EY+KEEHPEWE+K+G VFFQ+AK+
Sbjct: 181 KTVRDEIAGCSEKAYDYLSINDARHMLLFSSDQELFEYIKEEHPEWEIKNGHVFFQRAKE 240

Query: 241 SAPCKEIPSLQLINQTLSYARELERIV 267
           SAPCKEIPSLQLINQTLSYARELERIV
Sbjct: 241 SAPCKEIPSLQLINQTLSYARELERIV 267

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255646695|gb|ACU23821.1| unknown [Glycine max]

 Score =  454 bits (1167), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 229/267 (85%), Positives = 245/267 (91%)

Query: 1   MDPKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTL 60
           MDPKL EVSQ FDRFKA+  R D++ C+ LLSQLKVLLTGFRSLPPLF DTPNA+ ELT+
Sbjct: 1   MDPKLKEVSQLFDRFKASFLRNDFDNCSNLLSQLKVLLTGFRSLPPLFADTPNAVHELTI 60

Query: 61  ARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQN 120
           ARDIYEHAV+LSVK+EDQDAFERDFFQLKPYYTDA  RLPPSP EY ILGLNLLRLLVQN
Sbjct: 61  ARDIYEHAVVLSVKIEDQDAFERDFFQLKPYYTDACNRLPPSPQEYPILGLNLLRLLVQN 120

Query: 121 RIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLA 180
           RIAEFHTELELLSS ALENPCIKHAVELEQSFMEGAYNRVLSA+Q VP++TY YFMDLLA
Sbjct: 121 RIAEFHTELELLSSAALENPCIKHAVELEQSFMEGAYNRVLSARQTVPHDTYVYFMDLLA 180

Query: 181 KTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKD 240
           KTVRDEIAGCSEKAYDYLSIKDA QMLLF+SDQELLEY+KEEHPEWE+K+  VFFQKAK+
Sbjct: 181 KTVRDEIAGCSEKAYDYLSIKDAKQMLLFSSDQELLEYIKEEHPEWEIKNDSVFFQKAKE 240

Query: 241 SAPCKEIPSLQLINQTLSYARELERIV 267
            APCKEIP LQLINQTLSYAR LERIV
Sbjct: 241 FAPCKEIPFLQLINQTLSYARGLERIV 267

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224058123|ref|XP_002299452.1| predicted protein [Populus trichocarpa] gi|118482756|gb|ABK93296.1| unknown [Populus trichocarpa] gi|222846710|gb|EEE84257.1| predicted protein [Populus trichocarpa]

 Score =  446 bits (1148), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 227/267 (85%), Positives = 243/267 (91%)

Query: 1   MDPKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTL 60
           MDPKLTEVSQ F+RFKAA TR D+NT T LLSQLKVLL GFRSLPPLFE+TP++++EL +
Sbjct: 1   MDPKLTEVSQLFERFKAACTRDDFNTSTNLLSQLKVLLIGFRSLPPLFENTPHSVQELII 60

Query: 61  ARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQN 120
           ARDIYEHAVLLSVK+ DQDAFERDFFQLKPYYTDAG RL PSP EYMILGLNLLRLLVQN
Sbjct: 61  ARDIYEHAVLLSVKIGDQDAFERDFFQLKPYYTDAGGRLAPSPQEYMILGLNLLRLLVQN 120

Query: 121 RIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLA 180
           RIAEFHTELELLS  ALENPCIKHAVELEQSFMEGAYNRVLSAKQNVP +T+ YFMDLLA
Sbjct: 121 RIAEFHTELELLSPAALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPYKTFDYFMDLLA 180

Query: 181 KTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKD 240
           KTVRDEIAGCSEKAYDYLSI DA QMLLF+SD ELLEY+KE H EWE+K+G V FQKA +
Sbjct: 181 KTVRDEIAGCSEKAYDYLSISDARQMLLFSSDDELLEYIKEGHLEWEIKNGSVVFQKANE 240

Query: 241 SAPCKEIPSLQLINQTLSYARELERIV 267
           SAPCKEIPSL LINQTLSYARELERIV
Sbjct: 241 SAPCKEIPSLHLINQTLSYARELERIV 267

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	267
TAIR|locus:2019504	267	RPN12a "regulatory particle no	1.0	1.0	0.760	1.5e-106
TAIR|locus:2165750	233	RPN12b "regulatory particle no	0.636	0.729	0.705	2.5e-73
DICTYBASE|DDB_G0273979	263	psmD8-2 "26S proteasome regula	0.966	0.980	0.363	2.6e-40
DICTYBASE|DDB_G0272564	263	psmD8-1 "26S proteasome regula	0.966	0.980	0.363	2.6e-40
ZFIN|ZDB-GENE-040625-136	267	psmd8 "proteasome (prosome, ma	0.970	0.970	0.370	1.4e-39
MGI|MGI:1888669	353	Psmd8 "proteasome (prosome, ma	0.970	0.733	0.355	2.1e-36
UNIPROTKB|Q5RE15	289	PSMD8 "26S proteasome non-ATPa	0.970	0.896	0.355	2.7e-36
RGD|1309842	285	Psmd8 "proteasome (prosome, ma	0.970	0.908	0.355	3.5e-36
UNIPROTKB|F1LMQ3	353	Psmd8 "Protein Psmd8" [Rattus	0.970	0.733	0.355	3.5e-36
UNIPROTKB|P48556	350	PSMD8 "26S proteasome non-ATPa	0.970	0.74	0.355	4.4e-36

TAIR|locus:2019504 RPN12a "regulatory particle non-ATPase 12A" [Arabidopsis thaliana (taxid:3702)]

 Score = 1054 (376.1 bits), Expect = 1.5e-106, P = 1.5e-106
 Identities = 203/267 (76%), Positives = 224/267 (83%)

Query:     1 MDPKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTL 60
             MDP+LTEVSQQF+RFKAA  RKDYNTC+ LLSQLKVLLT F SLPPLFE++PNA +ELT+
Sbjct:     1 MDPQLTEVSQQFERFKAAFARKDYNTCSDLLSQLKVLLTKFTSLPPLFENSPNAAKELTI 60

Query:    61 ARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXVQN 120
             ARDIYEHAV+LSVK EDQDAFERDFFQLKPYY DA  R+P SP E +I         VQN
Sbjct:    61 ARDIYEHAVVLSVKTEDQDAFERDFFQLKPYYVDARNRIPQSPQENLILGLNLLRLLVQN 120

Query:   121 RIAEFHXXXXXXXXXXXXNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLA 180
             RIAEFH            +PCIKHAVELEQSFMEGAYNRVLSA+Q  P+ TY YFMDLLA
Sbjct:   121 RIAEFHTELELLSSATLEDPCIKHAVELEQSFMEGAYNRVLSARQTAPDATYVYFMDLLA 180

Query:   181 KTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKD 240
             KT+RDEIAGCSEKAYDY+SI DA QMLLF+SDQELL YV +EHPEWE+K+GFV FQKAK+
Sbjct:   181 KTIRDEIAGCSEKAYDYVSISDARQMLLFSSDQELLTYVTDEHPEWEVKEGFVVFQKAKE 240

Query:   241 SAPCKEIPSLQLINQTLSYARELERIV 267
             +APCKEIPSLQLINQTLSYARELERIV
Sbjct:   241 TAPCKEIPSLQLINQTLSYARELERIV 267

GO:0005634 "nucleus" evidence=ISM;TAS

GO:0005838 "proteasome regulatory particle" evidence=IEA

GO:0006508 "proteolysis" evidence=IEA

GO:0008233 "peptidase activity" evidence=ISS

GO:0008541 "proteasome regulatory particle, lid subcomplex" evidence=ISS

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

GO:0030163 "protein catabolic process" evidence=TAS

GO:0000502 "proteasome complex" evidence=IDA

GO:0009647 "skotomorphogenesis" evidence=IMP

GO:0009733 "response to auxin stimulus" evidence=IMP

GO:0009735 "response to cytokinin stimulus" evidence=IEP;RCA;IMP

GO:0009908 "flower development" evidence=IMP

GO:0031540 "regulation of anthocyanin biosynthetic process" evidence=IMP

GO:0048366 "leaf development" evidence=IMP

GO:0048528 "post-embryonic root development" evidence=IMP

GO:0048825 "cotyledon development" evidence=IMP

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0009408 "response to heat" evidence=IMP

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

GO:0043248 "proteasome assembly" evidence=RCA;IMP

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

GO:0005829 "cytosol" evidence=IDA

GO:0006635 "fatty acid beta-oxidation" evidence=RCA

GO:0009407 "toxin catabolic process" evidence=RCA

GO:0042023 "DNA endoreduplication" evidence=RCA

GO:0048767 "root hair elongation" evidence=RCA

GO:0051510 "regulation of unidimensional cell growth" evidence=RCA

GO:0051604 "protein maturation" evidence=RCA

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

TAIR|locus:2165750 RPN12b "regulatory particle non-ATPase 12B" [Arabidopsis thaliana (taxid:3702)]

 Score = 629 (226.5 bits), Expect = 2.5e-73, Sum P(2) = 2.5e-73
 Identities = 120/170 (70%), Positives = 135/170 (79%)

Query:    98 RLPPSPNEYMIXXXXXXXXXVQNRIAEFHXXXXXXXXXXXXNPCIKHAVELEQSFMEGAY 157
             R+PPSP E +I         VQNRIAEFH            NPCIKHAVELEQSFMEGAY
Sbjct:    64 RIPPSPQENLIMGLNLLRLLVQNRIAEFHTELGLLSSATLENPCIKHAVELEQSFMEGAY 123

Query:   158 NRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLE 217
             NRVLSA+Q  P+ETY YFMDLLAKT+RDEIAGCSEKAYD+LSI +  +MLLF+SDQ+LL 
Sbjct:   124 NRVLSARQTAPDETYVYFMDLLAKTIRDEIAGCSEKAYDHLSISEGCKMLLFSSDQQLLT 183

Query:   218 YVKEEHPEWEMKDGFVFFQKAKDSAPCKEIPSLQLINQTLSYARELERIV 267
             YV EEHPEWE+KDG V FQK +++APCKEIPSLQLINQTLSY RELERI+
Sbjct:   184 YVNEEHPEWEVKDGLVVFQKTRETAPCKEIPSLQLINQTLSYTRELERIL 233

GO:0005838 "proteasome regulatory particle" evidence=IEA;ISS

GO:0006508 "proteolysis" evidence=IEA;ISS

GO:0008233 "peptidase activity" evidence=ISS

DICTYBASE|DDB_G0273979 psmD8-2 "26S proteasome regulatory subunit S14" [Dictyostelium discoideum (taxid:44689)]

 Score = 429 (156.1 bits), Expect = 2.6e-40, P = 2.6e-40
 Identities = 96/264 (36%), Positives = 151/264 (57%)

Query:     6 TEVSQQFDRFKAAMT-RKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIR-ELTLARD 63
             + + Q  + FK  +    D    T +L QLK+  T     P    +  + ++ +L LAR+
Sbjct:     4 SSIEQNLNNFKKLVAGNSDKAQITPVLVQLKLAATIHLEKPTSLSNVSDKVKKDLVLARE 63

Query:    64 IYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXVQNRIA 123
             I E   L S+K++D D+FER F QLK YY D    + PS  EY I          +++ +
Sbjct:    64 ILELISLYSIKIKDIDSFERTFNQLKTYYYDYKSIIAPSTLEYQIIGLNLMRLLAKHKTS 123

Query:   124 EFHXXXXXXXXXXXXNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTV 183
             EFH            N  IK  + +E+S  EG+YN+++ ++  VP+E Y  F+D+LA ++
Sbjct:   124 EFHSEIELIEFNNLDNSFIKFPLLVEKSITEGSYNKIIQSRSGVPSEYYQVFLDILADSI 183

Query:   184 RDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKDSAP 243
             +++IA CSEK++  LS+KDA ++LLF  + +  +Y+KE +  W+++   + F    D+  
Sbjct:   184 KEDIANCSEKSFKTLSLKDAEKVLLFNDNNQFQQYIKERN--WKVQGDVIQFGN-NDNQT 240

Query:   244 CKEIPSLQLINQTLSYARELERIV 267
               EIPSLQLI+QTL YA+ELERIV
Sbjct:   241 V-EIPSLQLIHQTLHYAKELERIV 263

GO:0006508 "proteolysis" evidence=IEA

GO:0005838 "proteasome regulatory particle" evidence=IEA

GO:0004175 "endopeptidase activity" evidence=ISS

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0000502 "proteasome complex" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

DICTYBASE|DDB_G0272564 psmD8-1 "26S proteasome regulatory subunit S14" [Dictyostelium discoideum (taxid:44689)]

 Score = 429 (156.1 bits), Expect = 2.6e-40, P = 2.6e-40
 Identities = 96/264 (36%), Positives = 151/264 (57%)

Query:     6 TEVSQQFDRFKAAMT-RKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIR-ELTLARD 63
             + + Q  + FK  +    D    T +L QLK+  T     P    +  + ++ +L LAR+
Sbjct:     4 SSIEQNLNNFKKLVAGNSDKAQITPVLVQLKLAATIHLEKPTSLSNVSDKVKKDLVLARE 63

Query:    64 IYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXVQNRIA 123
             I E   L S+K++D D+FER F QLK YY D    + PS  EY I          +++ +
Sbjct:    64 ILELISLYSIKIKDIDSFERTFNQLKTYYYDYKSIIAPSTLEYQIIGLNLMRLLAKHKTS 123

Query:   124 EFHXXXXXXXXXXXXNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTV 183
             EFH            N  IK  + +E+S  EG+YN+++ ++  VP+E Y  F+D+LA ++
Sbjct:   124 EFHSEIELIEFNNLDNSFIKFPLLVEKSITEGSYNKIIQSRSGVPSEYYQVFLDILADSI 183

Query:   184 RDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKDSAP 243
             +++IA CSEK++  LS+KDA ++LLF  + +  +Y+KE +  W+++   + F    D+  
Sbjct:   184 KEDIANCSEKSFKTLSLKDAEKVLLFNDNNQFQQYIKERN--WKVQGDVIQFGN-NDNQT 240

Query:   244 CKEIPSLQLINQTLSYARELERIV 267
               EIPSLQLI+QTL YA+ELERIV
Sbjct:   241 V-EIPSLQLIHQTLHYAKELERIV 263

GO:0006508 "proteolysis" evidence=IEA

GO:0005838 "proteasome regulatory particle" evidence=IEA

GO:0004175 "endopeptidase activity" evidence=ISS

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0000502 "proteasome complex" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

ZFIN|ZDB-GENE-040625-136 psmd8 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 8" [Danio rerio (taxid:7955)]

 Score = 422 (153.6 bits), Expect = 1.4e-39, P = 1.4e-39
 Identities = 99/267 (37%), Positives = 142/267 (53%)

Query:     5 LTEVSQQFDRFKAAMTRKD--YNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLAR 62
             L E +  ++  KA   +K+   N C +LLS+LK+ L     LP     T    ++L LAR
Sbjct:     5 LKETAGLYETLKAEWNKKNPNLNKCGELLSKLKISLLELNFLPTT--GTKLTKQQLILAR 62

Query:    63 DIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXVQNRI 122
             D+ E   L S+  +D  +FER   QLK YY D    LP S   + +          QNR+
Sbjct:    63 DVLEIGALWSILKKDIPSFERYMAQLKCYYFDYKDELPESAYRHQLLGLNLLFLLSQNRV 122

Query:   123 AEFHXXXXXXXXXXX-XNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAK 181
             +EFH             N  I+H V LEQ  MEG+YN+V  AK N+P E+Y +F+D L  
Sbjct:   123 SEFHTELERLSAKDIQTNVYIRHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDTLLD 182

Query:   182 TVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEW-EMKDGFVFFQKAKD 240
             T+RDEIAGC EKAY+ +   +A ++L F+S +++ +Y K+ +  W +  DG+  F     
Sbjct:   183 TIRDEIAGCIEKAYEQIQFNEATRVLFFSSPKKMTDYAKKRN--WTQSPDGYYSFSTQHQ 240

Query:   241 SAPCKEIPSLQLINQTLSYARELERIV 267
                   IPS +L  Q + YAR+LE IV
Sbjct:   241 KTEEVTIPSTELAKQVIEYARQLEMIV 267

GO:0005838 "proteasome regulatory particle" evidence=IEA

GO:0006508 "proteolysis" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

MGI|MGI:1888669 Psmd8 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 8" [Mus musculus (taxid:10090)]

 Score = 392 (143.0 bits), Expect = 2.1e-36, P = 2.1e-36
 Identities = 95/267 (35%), Positives = 141/267 (52%)

Query:     5 LTEVSQQFDRFKAAMTRKDYNT--CTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLAR 62
             L   +  +++ K    RK+ N   C + L +LK++L     LP     T    ++L LAR
Sbjct:    91 LQAAAGMYEQLKDEWNRKNPNLSKCGEELGRLKLVLLELNFLPTT--GTKLTKQQLILAR 148

Query:    63 DIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXVQNRI 122
             DI E     S+  +D  +FER   QLK YY D  ++LP S   + +          QNR+
Sbjct:   149 DILEIGAQWSILCKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLSQNRV 208

Query:   123 AEFHXXXXXX-XXXXXXNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAK 181
             AEFH             N  IKH V LEQ  MEG+YN+V  AK N+P E+Y +F+D+L  
Sbjct:   209 AEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLD 268

Query:   182 TVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEM-KDGFVFFQKAKD 240
             T+RDEIAGC EKAY+ +   +A ++L F++ +++ +Y K+    W +  + +  F   + 
Sbjct:   269 TIRDEIAGCIEKAYEKILFAEATRILFFSTPKKMTDYAKKRG--WVLGPNNYYSFASQQQ 326

Query:   241 SAPCKEIPSLQLINQTLSYARELERIV 267
                   IPS +L  Q + YAR+LE IV
Sbjct:   327 KPEDSTIPSTELAKQVIEYARQLEMIV 353

GO:0000502 "proteasome complex" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0005838 "proteasome regulatory particle" evidence=IEA

GO:0006508 "proteolysis" evidence=IEA

GO:0022624 "proteasome accessory complex" evidence=IDA

UNIPROTKB|Q5RE15 PSMD8 "26S proteasome non-ATPase regulatory subunit 8" [Pongo abelii (taxid:9601)]

 Score = 391 (142.7 bits), Expect = 2.7e-36, P = 2.7e-36
 Identities = 95/267 (35%), Positives = 139/267 (52%)

Query:     5 LTEVSQQFDRFKAAMTRKDYNT--CTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLAR 62
             L   +  +++ K    RK  N   C + L +LK++L     LP     T    ++L LAR
Sbjct:    27 LQAATGMYEQLKGEWNRKSPNLSKCGEELGRLKLVLLELNFLPTT--GTKLTKQQLILAR 84

Query:    63 DIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXVQNRI 122
             DI E     S+  +D  +FER   QLK YY D  ++LP S   + +          QNR+
Sbjct:    85 DILEIGAQWSILRKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLSQNRV 144

Query:   123 AEFHXXXXXX-XXXXXXNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAK 181
             AEFH             N  IKH V LEQ  MEG+YN+V  AK N+P E+Y +F+D+L  
Sbjct:   145 AEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYAFFIDILLD 204

Query:   182 TVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEM-KDGFVFFQKAKD 240
             T+RDEIAGC EKAY+ +   +A ++L F + +++ +Y K+    W +  + +  F   + 
Sbjct:   205 TIRDEIAGCIEKAYEKILFTEATRILFFNTPKKMTDYAKKRG--WVLGPNNYYSFASQQQ 262

Query:   241 SAPCKEIPSLQLINQTLSYARELERIV 267
                   IPS +L  Q + YAR+LE IV
Sbjct:   263 KPEDTTIPSTELAKQVIEYARQLEMIV 289

GO:0022624 "proteasome accessory complex" evidence=ISS

RGD|1309842 Psmd8 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 8" [Rattus norvegicus (taxid:10116)]

 Score = 390 (142.3 bits), Expect = 3.5e-36, P = 3.5e-36
 Identities = 95/267 (35%), Positives = 140/267 (52%)

Query:     5 LTEVSQQFDRFKAAMTRKDYNT--CTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLAR 62
             L   +  +++ K    RK  N   C + L +LK++L     LP     T    ++L LAR
Sbjct:    23 LQAAAGMYEQLKDEWNRKSPNLSKCGEELGRLKLVLLELNFLPTT--GTKLTKQQLILAR 80

Query:    63 DIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXVQNRI 122
             DI E     S+  +D  +FER   QLK YY D  ++LP S   + +          QNR+
Sbjct:    81 DILEIGAQWSILCKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLSQNRV 140

Query:   123 AEFHXXXXXX-XXXXXXNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAK 181
             AEFH             N  IKH V LEQ  MEG+YN+V  AK N+P E+Y +F+D+L  
Sbjct:   141 AEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLD 200

Query:   182 TVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEM-KDGFVFFQKAKD 240
             T+RDEIAGC EKAY+ +   +A ++L F++ +++ +Y K+    W +  + +  F   + 
Sbjct:   201 TIRDEIAGCIEKAYEKILFAEATRILFFSTPKKMTDYAKKRG--WLLGPNNYYSFASQQQ 258

Query:   241 SAPCKEIPSLQLINQTLSYARELERIV 267
                   IPS +L  Q + YAR+LE IV
Sbjct:   259 KPEDSTIPSTELARQVIEYARQLEMIV 285

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0022624 "proteasome accessory complex" evidence=ISO

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|F1LMQ3 Psmd8 "Protein Psmd8" [Rattus norvegicus (taxid:10116)]

 Score = 390 (142.3 bits), Expect = 3.5e-36, P = 3.5e-36
 Identities = 95/267 (35%), Positives = 140/267 (52%)

Query:     5 LTEVSQQFDRFKAAMTRKDYNT--CTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLAR 62
             L   +  +++ K    RK  N   C + L +LK++L     LP     T    ++L LAR
Sbjct:    91 LQAAAGMYEQLKDEWNRKSPNLSKCGEELGRLKLVLLELNFLPTT--GTKLTKQQLILAR 148

Query:    63 DIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXVQNRI 122
             DI E     S+  +D  +FER   QLK YY D  ++LP S   + +          QNR+
Sbjct:   149 DILEIGAQWSILCKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLSQNRV 208

Query:   123 AEFHXXXXXX-XXXXXXNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAK 181
             AEFH             N  IKH V LEQ  MEG+YN+V  AK N+P E+Y +F+D+L  
Sbjct:   209 AEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLD 268

Query:   182 TVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEM-KDGFVFFQKAKD 240
             T+RDEIAGC EKAY+ +   +A ++L F++ +++ +Y K+    W +  + +  F   + 
Sbjct:   269 TIRDEIAGCIEKAYEKILFAEATRILFFSTPKKMTDYAKKRG--WLLGPNNYYSFASQQQ 326

Query:   241 SAPCKEIPSLQLINQTLSYARELERIV 267
                   IPS +L  Q + YAR+LE IV
Sbjct:   327 KPEDSTIPSTELARQVIEYARQLEMIV 353

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005838 "proteasome regulatory particle" evidence=IEA

GO:0006508 "proteolysis" evidence=IEA

UNIPROTKB|P48556 PSMD8 "26S proteasome non-ATPase regulatory subunit 8" [Homo sapiens (taxid:9606)]

 Score = 389 (142.0 bits), Expect = 4.4e-36, P = 4.4e-36
 Identities = 95/267 (35%), Positives = 139/267 (52%)

Query:     5 LTEVSQQFDRFKAAMTRKDYNT--CTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLAR 62
             L   +  +++ K    RK  N   C + L +LK++L     LP     T    ++L LAR
Sbjct:    88 LQAATGMYEQLKGEWNRKSPNLSKCGEELGRLKLVLLELNFLPTT--GTKLTKQQLILAR 145

Query:    63 DIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXVQNRI 122
             DI E     S+  +D  +FER   QLK YY D  ++LP S   + +          QNR+
Sbjct:   146 DILEIGAQWSILRKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLSQNRV 205

Query:   123 AEFHXXXXXX-XXXXXXNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAK 181
             AEFH             N  IKH V LEQ  MEG+YN+V  AK N+P E+Y +F+D+L  
Sbjct:   206 AEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLD 265

Query:   182 TVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEM-KDGFVFFQKAKD 240
             T+RDEIAGC EKAY+ +   +A ++L F + +++ +Y K+    W +  + +  F   + 
Sbjct:   266 TIRDEIAGCIEKAYEKILFTEATRILFFNTPKKMTDYAKKRG--WVLGPNNYYSFASQQQ 323

Query:   241 SAPCKEIPSLQLINQTLSYARELERIV 267
                   IPS +L  Q + YAR+LE IV
Sbjct:   324 KPEDTTIPSTELAKQVIEYARQLEMIV 350

GO:0005838 "proteasome regulatory particle" evidence=IEA

GO:0022624 "proteasome accessory complex" evidence=ISS

GO:0000502 "proteasome complex" evidence=TAS

GO:0000075 "cell cycle checkpoint" evidence=TAS

GO:0000082 "G1/S transition of mitotic cell cycle" evidence=TAS

GO:0000084 "S phase of mitotic cell cycle" evidence=TAS

GO:0000209 "protein polyubiquitination" evidence=TAS

GO:0000216 "M/G1 transition of mitotic cell cycle" evidence=TAS

GO:0000278 "mitotic cell cycle" evidence=TAS

GO:0002474 "antigen processing and presentation of peptide antigen via MHC class I" evidence=TAS

GO:0002479 "antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006521 "regulation of cellular amino acid metabolic process" evidence=TAS

GO:0006915 "apoptotic process" evidence=TAS

GO:0006977 "DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0031145 "anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process" evidence=TAS

GO:0034641 "cellular nitrogen compound metabolic process" evidence=TAS

GO:0042590 "antigen processing and presentation of exogenous peptide antigen via MHC class I" evidence=TAS

GO:0042981 "regulation of apoptotic process" evidence=TAS

GO:0044281 "small molecule metabolic process" evidence=TAS

GO:0051436 "negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0051437 "positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0051439 "regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P02889	PSMD8_DICDI	No assigned EC number	0.4	0.9700	0.9847	yes	no
P50524	RPN12_SCHPO	No assigned EC number	0.3421	0.8876	0.8777	yes	no
Q3SYT7	PSMD8_BOVIN	No assigned EC number	0.4089	0.9625	0.8954	yes	no
Q9SGW3	RP12A_ARATH	No assigned EC number	0.8314	1.0	1.0	yes	no
Q5RE15	PSMD8_PONAB	No assigned EC number	0.4044	0.9700	0.8961	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_Genewise1_v1.C_LG_III1640	SubName- Full=Putative uncharacterized protein; (267 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	eugene3.00150698	hypothetical protein (386 aa)				•	•	•	•		0.600
	eugene3.00120862	hypothetical protein (386 aa)				•	•	•	•		0.590
	estExt_fgenesh4_pg.C_LG_II1158	hypothetical protein (310 aa)				•	•	•	•		0.578
	estExt_fgenesh4_pg.C_290270	hypothetical protein (386 aa)				•	•	•	•		0.574
	estExt_fgenesh4_pm.C_400098	SubName- Full=Putative uncharacterized protein; (312 aa)				•	•	•	•		0.574
	grail3.0018005001	hypothetical protein (387 aa)				•	•	•	•		0.556
	estExt_fgenesh4_pg.C_LG_VII0646	SubName- Full=Putative uncharacterized protein; (442 aa)				•	•	•	•		0.544
	estExt_fgenesh4_pg.C_LG_VIII0552	hypothetical protein (311 aa)				•	•	•	•		0.541
	eugene3.00050260	hypothetical protein (442 aa)				•	•	•	•		0.534
	estExt_fgenesh4_pm.C_LG_X0754	SubName- Full=Putative uncharacterized protein; (311 aa)				•	•	•	•		0.533

---

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	267
pfam03399	155	pfam03399, SAC3_GANP, SAC3/GANP/Nin1/mts3/eIF-3 p2	3e-36
pfam10075	144	pfam10075, PCI_Csn8, COP9 signalosome, subunit CSN	4e-27

>gnl|CDD|217534 pfam03399, SAC3_GANP, SAC3/GANP/Nin1/mts3/eIF-3 p25 family

 Score =  125 bits (317), Expect = 3e-36
 Identities = 48/149 (32%), Positives = 71/149 (47%), Gaps = 4/149 (2%)

Query: 59  TLARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLV 118
            L   + E    ++++  D + F +   QLK  Y D    L  SPNE   +   LL LL 
Sbjct: 10  PLKVAVLEIGARIALEKGDLEQFNQCLSQLKELYDD---LLGKSPNEAEFIAYYLLYLLS 66

Query: 119 QNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDL 178
            N I++FHTELELL      +P I+ A+ELEQ+ MEG Y+R     +  P   Y   ++ 
Sbjct: 67  NNPISDFHTELELLPDEIRNDPYIQFALELEQALMEGNYHRFFRLLKKAPYL-YACLLER 125

Query: 179 LAKTVRDEIAGCSEKAYDYLSIKDAGQML 207
               +R E      KAY  + +    ++L
Sbjct: 126 FLDRIRKEALKAISKAYRSIPLSYLAELL 154

This large family includes diverse proteins involved in large complexes. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3, and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits. Length = 155

>gnl|CDD|220553 pfam10075, PCI_Csn8, COP9 signalosome, subunit CSN8

 Score =  101 bits (255), Expect = 4e-27
 Identities = 43/121 (35%), Positives = 64/121 (52%), Gaps = 2/121 (1%)

Query: 103 PNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALE-NPCIKHAVELEQSFMEGAYNRVL 161
             +  + GL LL+LL QN IA+F   L+ +     E NP I+  + L Q   E  Y +  
Sbjct: 1   ELKTELYGLILLKLLTQNDIADFRLLLKRIPQAIKESNPEIQQLLTLGQLLWENDYAKFW 60

Query: 162 SA-KQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVK 220
              + N  +E Y  F+  L  T+RDEIA    KAY  +SI D  ++L  +SD+EL ++ K
Sbjct: 61  QTLRSNDWSEDYTPFIAGLEDTIRDEIAALVGKAYSSISIDDLAELLGLSSDEELEKFAK 120

Query: 221 E 221
           +
Sbjct: 121 K 121

This PCI_Csn8 domain is conserved from plants to humans. It is a signature protein motif found in components of CSN (COP9 signalosome). It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development. Length = 144

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	267
KOG3151	260	consensus 26S proteasome regulatory complex, subun	100.0
PF10075	143	PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro	99.95
PF03399	204	SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; I	99.95
KOG1861	540	consensus Leucine permease transcriptional regulat	99.95
KOG4414	197	consensus COP9 signalosome, subunit CSN8 [Posttran	99.48
KOG3252	217	consensus Uncharacterized conserved protein [Funct	97.59
KOG1860	927	consensus Nuclear protein export factor [Intracell	97.47
COG5079	646	SAC3 Nuclear protein export factor [Intracellular	97.26
PF01399	105	PCI: PCI domain; InterPro: IPR000717 A homology do	97.08
KOG2908	380	consensus 26S proteasome regulatory complex, subun	95.04
smart00088	88	PINT motif in proteasome subunits, Int-6, Nip-1 an	94.87
smart00753	88	PAM PCI/PINT associated module.	94.87
KOG2582	422	consensus COP9 signalosome, subunit CSN3 [Posttran	88.87

>KOG3151 consensus 26S proteasome regulatory complex, subunit RPN12/PSMD8 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.3e-81  Score=552.95  Aligned_cols=257  Identities=54%  Similarity=0.803  Sum_probs=242.8

Q ss_pred             HHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHhcCCCCCCCCCCChhhHHHHHHHHHHHHHHHHHHhhccChHHHHHHHhh
Q 024461            9 SQQFDRFKAAMTRK-DYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLARDIYEHAVLLSVKVEDQDAFERDFFQ   87 (267)
Q Consensus         9 ~~l~~~L~~~~~~~-~~~~~~~lL~~lKi~L~~~~~L~~~~~~~~~~~~~l~lar~vlEi~al~si~~~D~~~F~r~~~q   87 (267)
                      .+++++|+++|..+ |+.+|+++|.+||++|++.+++||+.+.++.++++|.+||+|||+||++||.+.|+++|+|||+|
T Consensus         2 s~l~~~l~a~w~k~~d~~aC~klL~~lKveL~K~n~l~~~~~~~~~~k~~l~~aR~ilEi~vl~SI~t~D~~sFerY~~Q   81 (260)
T KOG3151|consen    2 SELYKNLKAEWAKRPDLVACEKLLDQLKVELTKNNLLPPDLNISDIDKQQLIIARDILEIGVLLSILTKDFESFERYMNQ   81 (260)
T ss_pred             chHHHHHHHHHhcCCcHHHHHHHHhHHHHHHHHHhcCCCCcccchhhHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHH
Confidence            57899999999966 99999999999999999999999987777788999999999999999999999999999999999


Q ss_pred             hhhhhhhcCCCCCCCcchhhHHHHHHHHHHhcCCHHHHHHHHHhccHhhh-cCchhhhhHHHHHHHHhcchHHHHHhhhc
Q 024461           88 LKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTAL-ENPCIKHAVELEQSFMEGAYNRVLSAKQN  166 (267)
Q Consensus        88 Lk~~Y~~~~~~l~~S~~~~~llgL~LL~LLsqn~i~efh~~LE~l~~~~~-~~~~I~~~i~leq~LmeG~Y~kv~~~~~~  166 (267)
                      |+|||+|+...+|+|+++++++||||||||||||++||||+||+||...+ .||||+|||+||||+|||+|||||.++++
T Consensus        82 lk~YY~d~~~~l~~S~~~~~l~GLnLL~LLsqNRiaeFHteLe~lp~~~l~~~~~I~~~v~LEq~~MEGaYnKv~~a~~s  161 (260)
T KOG3151|consen   82 LKPYYFDYNEKLSESEKKHKLLGLNLLYLLSQNRIAEFHTELELLPKKILQHNPYISHPVSLEQSLMEGAYNKVLSAKQS  161 (260)
T ss_pred             hcchhcccccccCcchhhhHHHHHHHHHHHHhccHHHHHHHHHhccHHHhhccchhhhHHHHHHHHHhhHHHHHHHHHhc
Confidence            99999999999999999999999999999999999999999999999988 77999999999999999999999999999


Q ss_pred             CCCccHHHHHHHHHHHHHHHHHHhHHHccCCCCHHHHHHhhCCCCHHHHHHHHhhcCCCceeeCCeEEEecCCCCCCCCC
Q 024461          167 VPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKDSAPCKE  246 (267)
Q Consensus       167 ~P~~~~~~fm~~L~~tiR~eia~~iekAY~sl~l~~a~~lL~f~s~~e~~~f~~~~~rgW~v~~g~i~f~~~~~~~~~~~  246 (267)
                      +|+++|.+|||+|++|||+|||.|+||||+.||+++|++||+|++++++..|+  .+|+|.++.+.++++...+.+...+
T Consensus       162 ~p~~~y~~FmdIl~~tiRdEIA~c~EKsYd~l~~s~a~~~L~f~~~~e~~~~~--~~r~W~l~~~~~~~~~~~~~~p~~~  239 (260)
T KOG3151|consen  162 IPSEEYTYFMDILLDTIRDEIAGCIEKSYDKLSASDATQMLLFNNDKELKKFA--TERQWPLDEKGVFSFASKETAPYEE  239 (260)
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHhcCChHHHHHHH--HhcCCcccccccccchhhccCchhc
Confidence            99999999999999999999999999999999999999999999999999997  4689999866666665444455567


Q ss_pred             CChHHHHHHHHhHHHHhhhcC
Q 024461          247 IPSLQLINQTLSYARELERIV  267 (267)
Q Consensus       247 ips~~li~~~L~YA~eLE~IV  267 (267)
                      +|+.++++|+|+||+|||+||
T Consensus       240 ~ps~~la~qtlsYar~LE~Iv  260 (260)
T KOG3151|consen  240 IPSTELAEQTLSYARELEMIV  260 (260)
T ss_pred             cCcHHHHHHHHHHHHHHHhcC
Confidence            999999999999999999998

>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8

Probab=99.95  E-value=2.1e-28  Score=203.60  Aligned_cols=130  Identities=28%  Similarity=0.447  Sum_probs=104.5

Q ss_pred             chhhHHHHHHHHHHhcCCHHHHHHHHHhccHhhhc-CchhhhhHHHHHHHHhcchHHHHHh-hhcCCCccHHHHHHHHHH
Q 024461          104 NEYMILGLNLLRLLVQNRIAEFHTELELLSSTALE-NPCIKHAVELEQSFMEGAYNRVLSA-KQNVPNETYGYFMDLLAK  181 (267)
Q Consensus       104 ~~~~llgL~LL~LLsqn~i~efh~~LE~l~~~~~~-~~~I~~~i~leq~LmeG~Y~kv~~~-~~~~P~~~~~~fm~~L~~  181 (267)
                      ....+.|++|+.+|.+|++++||.+|++||.+++. ||+|+.+|.|+|+||+|+|+++|.. +.+.|++.|..||..|.+
T Consensus         2 ~~~~~~~~~Ll~~L~~~~~~df~~~~~rip~~~~~~~~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~   81 (143)
T PF10075_consen    2 LNPEIYALILLKYLMQNDLSDFRLLWKRIPEELKQSDPEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGFED   81 (143)
T ss_dssp             --HHHHHHHHHHHHHTTTSTHHHHHHHTS-HHHHTS-TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTHHH
T ss_pred             CchhHHHHHHHHHHHcCCchHHHHHHHcCCHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHHHH
Confidence            35789999999999999999999999999999995 7999999999999999999999995 445788999999999999


Q ss_pred             HHHHHHHHhHHHccCCCCHHHHHHhhCCCCHHHHHHHHhhcCCCceeeCCeEEEe
Q 024461          182 TVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQ  236 (267)
Q Consensus       182 tiR~eia~~iekAY~sl~l~~a~~lL~f~s~~e~~~f~~~~~rgW~v~~g~i~f~  236 (267)
                      +||++|+.||++||++|++++++++||++ ++++.+|++  ++||+++++.++|+
T Consensus        82 ~iR~~i~~~i~~aY~sIs~~~la~~Lg~~-~~el~~~~~--~~gW~~d~~~~~~~  133 (143)
T PF10075_consen   82 TIRERIAHLISKAYSSISLSDLAEMLGLS-EEELEKFIK--SRGWTVDGDGVLFP  133 (143)
T ss_dssp             HHHHHHHHHHHHH-SEE-HHHHHHHTTS--HHHHHHHHH--HHT-EE-----EE-
T ss_pred             HHHHHHHHHHHHHHhHcCHHHHHHHhCCC-HHHHHHHHH--HcCCEECCCccEEe
Confidence            99999999999999999999999999999 999999995  46999995555555

In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.

>PF03399 SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; InterPro: IPR005062 This large family includes diverse proteins involved in large complexes [, , ]

Probab=99.95  E-value=1.1e-27  Score=208.04  Aligned_cols=147  Identities=35%  Similarity=0.554  Sum_probs=128.1

Q ss_pred             HHHHHHHHHHHHhhccChHHHHHHHhhhhhhhhhcCCCCCCCcchhhHHHHHHHHHHhcCCHHHHHHHHHhccHhhhcCc
Q 024461           61 ARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENP  140 (267)
Q Consensus        61 ar~vlEi~al~si~~~D~~~F~r~~~qLk~~Y~~~~~~l~~S~~~~~llgL~LL~LLsqn~i~efh~~LE~l~~~~~~~~  140 (267)
                      +++|||.+|+++|..+|.++|++|++||+.+|.+. ...++++++.+++|+|||++|++|+.++||..++.+|.+..+||
T Consensus        55 ~i~v~E~~ar~~i~~~d~~qf~~c~~~L~~lY~~~-~~~~~~~~~~ef~~y~lL~~l~~~~~~~~~~~l~~l~~~~~~~~  133 (204)
T PF03399_consen   55 AIKVYERIARFAIESGDLEQFNQCLSQLKELYDDL-RDLPPSPNEAEFIAYYLLYLLCQNNIPDFHMELELLPSEILSSP  133 (204)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHT---TTHHHHHHHHHHHTT-T---THHHHHHTTS-HHHHTSH
T ss_pred             HHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHhh-ccCCCCCCHHHHHHHHHHHHHHcccchHHHHHHHHCchhhhcCH
Confidence            99999999999999999999999999999999996 33577899999999999999999999999999999999988999


Q ss_pred             hhhhhHHHHHHHHhcchHHHHHhh--hcCCCccHHHHHHHHHHHHHHHHHHhHHHccCC-CCHHHHHHhhCC
Q 024461          141 CIKHAVELEQSFMEGAYNRVLSAK--QNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDY-LSIKDAGQMLLF  209 (267)
Q Consensus       141 ~I~~~i~leq~LmeG~Y~kv~~~~--~~~P~~~~~~fm~~L~~tiR~eia~~iekAY~s-l~l~~a~~lL~f  209 (267)
                      .|+++++|++++++|||.++|+..  .++| ..++.+|+.++++||..++.++++||.+ +|++.++++|+|
T Consensus       134 ~i~~al~l~~a~~~gny~~ff~l~~~~~~~-~l~~~l~~~~~~~iR~~al~~i~~ay~~~i~l~~l~~~L~F  204 (204)
T PF03399_consen  134 YIQFALELCRALMEGNYVRFFRLYRSKSAP-YLFACLMERFFNRIRLRALQSISKAYRSSIPLSFLAELLGF  204 (204)
T ss_dssp             HHHHHHHHHHHH--TTHHHHHHHHT-TTS--HHHHHHHGGGHHHHHHHHHHHHHHHS-T-EEHHHHHHHTT-
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHhccCCC-hHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCC
Confidence            999999999999999999999987  5544 5899999999999999999999999998 999999999987

The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3 [], and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit [, , ]. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits [].; PDB: 3T5V_D.

>KOG1861 consensus Leucine permease transcriptional regulator [Transcription]

Probab=99.95  E-value=2.4e-27  Score=226.55  Aligned_cols=171  Identities=19%  Similarity=0.345  Sum_probs=156.6

Q ss_pred             HHHHHHHHHHHHHHhhccChHHHHHHHhhhhhhhhhcCCCCCCCcchhhHHHHHHHHHHhcCCHHHHHHHHHhccHhhhc
Q 024461           59 TLARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALE  138 (267)
Q Consensus        59 ~lar~vlEi~al~si~~~D~~~F~r~~~qLk~~Y~~~~~~l~~S~~~~~llgL~LL~LLsqn~i~efh~~LE~l~~~~~~  138 (267)
                      .++++|||+||++|+++||.++|++|++|||.+|.   .++|+.  ..+|+++.|||.+-..+..+..++|..|+.++++
T Consensus       345 eFTveVYEtHARIALEkGD~~EfNQCQtQLk~LY~---egipg~--~~EF~AYriLY~i~tkN~~di~sll~~lt~E~ke  419 (540)
T KOG1861|consen  345 EFTVEVYETHARIALEKGDLEEFNQCQTQLKALYS---EGIPGA--YLEFTAYRILYYIFTKNYPDILSLLRDLTEEDKE  419 (540)
T ss_pred             ceeeeeehhhhHHHHhcCCHHHHHHHHHHHHHHHc---cCCCCc--hhhHHHHHHHHHHHhcCchHHHHHHHhccHhhcc
Confidence            35789999999999999999999999999999995   347765  7999999999977666666999999999999999


Q ss_pred             CchhhhhHHHHHHHHhcchHHHHHhhhcCCCccHHHHHHHHHHHHHHHHHHhHHHccC-CCCHHHHHHhhCCCCHHHHHH
Q 024461          139 NPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYD-YLSIKDAGQMLLFTSDQELLE  217 (267)
Q Consensus       139 ~~~I~~~i~leq~LmeG~Y~kv~~~~~~~P~~~~~~fm~~L~~tiR~eia~~iekAY~-sl~l~~a~~lL~f~s~~e~~~  217 (267)
                      |++|.|+++|+.++..|||+|+|+.+.++|. +-+++||.|+++.|..+...|.|||+ +||++.+++.|.|++-++|..
T Consensus       420 d~~V~hAL~vR~A~~~GNY~kFFrLY~~AP~-M~~yLmdlF~erER~~Al~ii~KsyrP~i~~~fi~~~laf~~~e~c~~  498 (540)
T KOG1861|consen  420 DEAVAHALEVRSAVTLGNYHKFFRLYLTAPN-MSGYLMDLFLERERKKALTIICKSYRPTITVDFIASELAFDSMEDCVN  498 (540)
T ss_pred             CHHHHHHHHHHHHHHhccHHHHHHHHhhccc-chhHHHHHHHHHHHHHHHHHHHHHcCCCccHHHHhhhhhhchHHHHHH
Confidence            9999999999999999999999999999997 78999999999999999999999999 999999999999999999999


Q ss_pred             HHhhcCCCceee-CCeEEEec
Q 024461          218 YVKEEHPEWEMK-DGFVFFQK  237 (267)
Q Consensus       218 f~~~~~rgW~v~-~g~i~f~~  237 (267)
                      |.  ++.+|+-+ .|..+...
T Consensus       499 ~l--~~~~~~~~~~g~~~~~~  517 (540)
T KOG1861|consen  499 FL--NEQNLTYDSLGPQILDK  517 (540)
T ss_pred             HH--hccCccccccCCccccc
Confidence            97  46889987 56555544

>KOG4414 consensus COP9 signalosome, subunit CSN8 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=99.48  E-value=3.3e-13  Score=113.04  Aligned_cols=133  Identities=11%  Similarity=0.126  Sum_probs=117.4

Q ss_pred             CCCCCc--chhhHHHHHHHHHHhcCCHHHHHHHHHhccHhhh-cCchhhhhHHHHHHHHhcchHHHHHhhhcCC-CccHH
Q 024461           98 RLPPSP--NEYMILGLNLLRLLVQNRIAEFHTELELLSSTAL-ENPCIKHAVELEQSFMEGAYNRVLSAKQNVP-NETYG  173 (267)
Q Consensus        98 ~l~~S~--~~~~llgL~LL~LLsqn~i~efh~~LE~l~~~~~-~~~~I~~~i~leq~LmeG~Y~kv~~~~~~~P-~~~~~  173 (267)
                      |+...+  -+...++.|++    -|+-.+...+|+|||+.++ .+|++.-+|.++|.+|..+|..||.+.+.-. |++..
T Consensus        33 GIa~~~dw~Ya~~L~~Yf~----~dD~dnARfLWKRIP~AIKe~k~El~aaWgiGQkiWq~Df~GiYeaI~~~dWSeeak  108 (197)
T KOG4414|consen   33 GIATHDDWPYAIHLAGYFL----HDDCDNARFLWKRIPPAIKEAKPELGAAWGIGQKIWQHDFAGIYEAINAHDWSEEAK  108 (197)
T ss_pred             CccCCCcchHHHHHHHHHH----hccchhHHHHHHhCCHHHhhcCchhhhhhhhhHHHHhcccchHHHHHhhhcchHHHH
Confidence            555444  67778888888    8999999999999999999 8999999999999999999999999876555 88999


Q ss_pred             HHHHHHHHHHHHHHHHhHHHccCCCCHHHHHHhhCCCCHHHHHHHHhhcCCCceee-CCeEE-Eec
Q 024461          174 YFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK-DGFVF-FQK  237 (267)
Q Consensus       174 ~fm~~L~~tiR~eia~~iekAY~sl~l~~a~~lL~f~s~~e~~~f~~~~~rgW~v~-~g~i~-f~~  237 (267)
                      .+|..|-|..|.+....+-.||+||..++.+..||+. +++...++.  +.||+++ ..++. .++
T Consensus       109 ~imaAf~D~~~kR~FaLl~qAYssI~~~D~A~FlGl~-~ddAtk~il--EnGWqaDaasqMasl~k  171 (197)
T KOG4414|consen  109 DIMAAFRDATRKRAFALLLQAYSSIIADDFAAFLGLP-EDDATKGIL--ENGWQADAASQMASLKK  171 (197)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-HHHHHHHHH--HcccchhhHHHHhhccc
Confidence            9999999999999999999999999999999999999 888888884  5799998 55555 444

>KOG3252 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.59  E-value=0.00054  Score=59.91  Aligned_cols=130  Identities=13%  Similarity=0.145  Sum_probs=106.0

Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhccHhhhcCchhhhhHHHHHHHHhcchHHHHHhhhcCCCccHHHHHHHHHHHHHH
Q 024461          106 YMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRD  185 (267)
Q Consensus       106 ~~llgL~LL~LLsqn~i~efh~~LE~l~~~~~~~~~I~~~i~leq~LmeG~Y~kv~~~~~~~P~~~~~~fm~~L~~tiR~  185 (267)
                      ..+++-=||.-|..=--+||-...=.||...+.+..++..+.|...|-.|+|..+|.....-| .++..+ -=|-|.||.
T Consensus        62 t~itaqILlKaL~~lP~tDF~l~kcli~~~~~~ee~~r~ii~L~~~LEt~~Fq~FW~~~~~N~-~mle~i-tGFedsvr~  139 (217)
T KOG3252|consen   62 TTITAQILLKALTNLPHTDFTLAKCLIDERVQMEEPFRSIIDLGDYLETCRFQQFWQEADENR-DMLEGI-TGFEDSVRK  139 (217)
T ss_pred             hHHHHHHHHHHHhcCCCcchhHHHHhcCHHHhcccchhHHHhHHHHHhhchHHHHhhhhccch-HHhcCC-CcHHHHHHH
Confidence            446666667777777788999999999998889999999999999999999999998543212 122221 226899999


Q ss_pred             HHHHhHHHccCCCCHHHHHHhhCCCCHHHHHHHHhhcCCCceee-CCeEEEecCC
Q 024461          186 EIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK-DGFVFFQKAK  239 (267)
Q Consensus       186 eia~~iekAY~sl~l~~a~~lL~f~s~~e~~~f~~~~~rgW~v~-~g~i~f~~~~  239 (267)
                      =+...+.-+|.+|+-.-.+++||-.+..++..+++  ..||..+ .|.|+.+..+
T Consensus       140 yachvv~iTyQkI~k~lLaellG~~sDs~le~~~~--~~GW~a~e~G~ifv~~qE  192 (217)
T KOG3252|consen  140 YACHVVGITYQKIDKWLLAELLGGLSDSQLEVWMT--KYGWIADESGQIFVASQE  192 (217)
T ss_pred             HHHHheechHhhchHHHHHHhhCcccHHHHHHHHH--HccceecCCceEEEeccc
Confidence            99999999999999999999999999999999984  5799999 7766666643

>KOG1860 consensus Nuclear protein export factor [Intracellular trafficking, secretion, and vesicular transport; Cell cycle control, cell division, chromosome partitioning]

Probab=97.47  E-value=0.0018  Score=67.88  Aligned_cols=168  Identities=18%  Similarity=0.251  Sum_probs=127.2

Q ss_pred             HHHHHHHHHHHHHhhc----cCh-HHH---------HHHHhhhhhhhhhcCCCCCCCcchhhHHHHHHHHHHhcCCHHHH
Q 024461           60 LARDIYEHAVLLSVKV----EDQ-DAF---------ERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEF  125 (267)
Q Consensus        60 lar~vlEi~al~si~~----~D~-~~F---------~r~~~qLk~~Y~~~~~~l~~S~~~~~llgL~LL~LLsqn~i~ef  125 (267)
                      .|..++|-.|++=|..    .|. +.|         .-|..-|..+|.|.+.+=-+.++..++-|||+|.  +-|+- +.
T Consensus       215 ~Av~llE~i~RfhI~~~h~Lce~~~~Fda~~nlEQL~K~l~sL~elYdD~r~~g~~cpnE~EFR~Y~vLl--~Lgd~-~~  291 (927)
T KOG1860|consen  215 EAVELLERIARFHILFRHRLCEEPEQFDAQQNLEQLQKCLQSLGELYDDLRKGGIPCPNEPEFRGYYVLL--SLGDP-QV  291 (927)
T ss_pred             HHHHHHHHHHHHHHHHHHHhccCcccCChhHHHHHHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHH--hcCCc-hH
Confidence            3556666665544422    233 344         3444556778999866666789999999999984  44443 44


Q ss_pred             HHHHHhccHhhhcCchhhhhHHHHHHHHhcchHHHHH-----------------hhhcCC-C-ccHHHHHHHHHHHHHHH
Q 024461          126 HTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLS-----------------AKQNVP-N-ETYGYFMDLLAKTVRDE  186 (267)
Q Consensus       126 h~~LE~l~~~~~~~~~I~~~i~leq~LmeG~Y~kv~~-----------------~~~~~P-~-~~~~~fm~~L~~tiR~e  186 (267)
                      -.....+|+++..++.+++++.+.++.-.|||-.+|+                 .....| . ..-..++..+..-||.-
T Consensus       292 ~~~iq~~~~evr~~~~Vk~al~~~~a~~~nn~~~~~r~~~~~t~a~~~l~~~~~~l~q~p~~~~L~~~v~~~~f~~ir~~  371 (927)
T KOG1860|consen  292 VRDIQAWPDEVRQDSEVKLALCLRRAFQSNNFRRFFRLSSLRTEALQNLYTRFFKLMQSPALPYLMGCVLELFFPDIRWA  371 (927)
T ss_pred             HHHHHhcCcccccchhHHHHHHHHHHhccCCeeeeeeccchhHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHH
Confidence            5677888999999999999999999999999999863                 122334 1 13466788889999999


Q ss_pred             HHHhHHHccC----CCCHHHHHHhhCCCCHHHHHHHHhhcCCCceeeCCe
Q 024461          187 IAGCSEKAYD----YLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGF  232 (267)
Q Consensus       187 ia~~iekAY~----sl~l~~a~~lL~f~s~~e~~~f~~~~~rgW~v~~g~  232 (267)
                      +...++.+|.    .+|+.....+|.|+++++...+.  +.+|-+++.|.
T Consensus       372 al~~~~~~~~~~~~~vp~~~l~~~l~f~~~e~~~~~~--~~y~Leis~~~  419 (927)
T KOG1860|consen  372 ALRAMSHAYNSKHVPVPLGKLDRILLFDGEEELKVVC--NYYGLEISVDD  419 (927)
T ss_pred             HHHHHHHHHhccCCCcchhHHHHHHhcCChhhhHhhh--hheeeEeeccc
Confidence            9999999995    79999999999999999999998  47898887343

>COG5079 SAC3 Nuclear protein export factor [Intracellular trafficking and secretion / Cell division and chromosome partitioning]

Probab=97.26  E-value=0.0077  Score=59.87  Aligned_cols=161  Identities=20%  Similarity=0.245  Sum_probs=117.5

Q ss_pred             HHHHHHHHHHHHhh----ccChHHHHHHHh--hhh-------hhhhhcCCCCCCCcchhhHHHHHHHHHHhcCCHHHHHH
Q 024461           61 ARDIYEHAVLLSVK----VEDQDAFERDFF--QLK-------PYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHT  127 (267)
Q Consensus        61 ar~vlEi~al~si~----~~D~~~F~r~~~--qLk-------~~Y~~~~~~l~~S~~~~~llgL~LL~LLsqn~i~efh~  127 (267)
                      |+++.|-.|++-|-    ..|...|.+=+.  ||+       .+|.+.+.+-...+|..++-++-+|-=|  +| ...-.
T Consensus       181 AV~c~EriaRfhIl~lh~L~~~p~Fs~qqeleQL~ksL~sL~elYdd~r~~~~~cpneaEFraYaiL~sl--gD-p~yv~  257 (646)
T COG5079         181 AVECHERIARFHILFLHLLHDHPHFSKQQELEQLKKSLASLIELYDDGRAGKKECPNEAEFRAYAILASL--GD-PRYVA  257 (646)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCccccHHhHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHh--CC-chhhh
Confidence            56677777765543    245566655443  544       6899988777889999999999877333  32 23445


Q ss_pred             HHHhccHhhhcCchhhhhHHHHHHHHhcchH---------------HHHHhhhcCCCccHHHHHHHHHH----HHHHHHH
Q 024461          128 ELELLSSTALENPCIKHAVELEQSFMEGAYN---------------RVLSAKQNVPNETYGYFMDLLAK----TVRDEIA  188 (267)
Q Consensus       128 ~LE~l~~~~~~~~~I~~~i~leq~LmeG~Y~---------------kv~~~~~~~P~~~~~~fm~~L~~----tiR~eia  188 (267)
                      -...+|..+..++-++-++.+.|-...|+|.               ++|+..+   ++...+||..|++    .||.-++
T Consensus       258 ~iq~wp~~if~d~~vq~alkl~~laq~nn~r~~~~rnteac~nlytrFfkl~q---Spsv~~lmg~lle~h~~sir~~aL  334 (646)
T COG5079         258 GIQGWPGGIFCDLPVQIALKLMQLAQSNNFRLLGRRNTEACFNLYTRFFKLIQ---SPSVQYLMGCLLEKHNISIRGGAL  334 (646)
T ss_pred             ccccCCccccccchHHHHHHHHHHhhccCeeeccccchhhhhHHHHHHHHHHh---CccHHHHHHHHHHHhhHHHHHHHH
Confidence            5678888888999999999999988888754               4444433   3457888887766    5787777


Q ss_pred             HhHHHcc----CCCCHHHHHHhhCCCCHHHHHHHHhhcCCCceee
Q 024461          189 GCSEKAY----DYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK  229 (267)
Q Consensus       189 ~~iekAY----~sl~l~~a~~lL~f~s~~e~~~f~~~~~rgW~v~  229 (267)
                      ..++++|    ..+|.-+...+|.|++.++..+|++  -.|-++.
T Consensus       335 kAm~k~~~sahk~ipf~~l~~il~f~~~~e~~efck--yy~lei~  377 (646)
T COG5079         335 KAMEKEIESAHKNIPFVDLSGILDFEEKGEGEEFCK--YYGLEIR  377 (646)
T ss_pred             HHHHHHHHHhhcCCCeehhhhhccccccchhHHHhh--hcceeee
Confidence            6655555    6899999999999999999999984  4677775

>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins

Probab=97.08  E-value=0.012  Score=44.94  Aligned_cols=49  Identities=16%  Similarity=0.282  Sum_probs=42.5

Q ss_pred             cHHHHHHHHHHHHHHHHHHhHHHccCCCCHHHHHHhhCCCCHHHHHHHHh
Q 024461          171 TYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVK  220 (267)
Q Consensus       171 ~~~~fm~~L~~tiR~eia~~iekAY~sl~l~~a~~lL~f~s~~e~~~f~~  220 (267)
                      .....++.+...+|......+.+.|++++++.++++++++ .++++.++.
T Consensus        34 ~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~-~~~vE~~l~   82 (105)
T PF01399_consen   34 FLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLS-EEEVESILI   82 (105)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCC-HHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccc-hHHHHHHHH
Confidence            3445778899999999999999999999999999999999 799988884

This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.

>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]

Probab=95.04  E-value=2.6  Score=40.49  Aligned_cols=197  Identities=20%  Similarity=0.224  Sum_probs=119.1

Q ss_pred             CCCCHHHHHHHHHHHHHHHhcCCCCCCCCCCChhhHHHHHHHHHHHHHHHHHHhhccChHHHHHHHhhhhhhhhhc-CCC
Q 024461           20 TRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDA-GKR   98 (267)
Q Consensus        20 ~~~~~~~~~~lL~~lKi~L~~~~~L~~~~~~~~~~~~~l~lar~vlEi~al~si~~~D~~~F~r~~~qLk~~Y~~~-~~~   98 (267)
                      +.+|+..|+++|..+|-.|-+.+..||.            +.-..|=.++.+-=..+|+++|-|+-   -.|-... .+.
T Consensus       127 ~i~DLk~~kk~ldd~~~~ld~~~~v~~~------------Vh~~fY~lssqYyk~~~d~a~yYr~~---L~YL~~~d~~~  191 (380)
T KOG2908|consen  127 EINDLKEIKKLLDDLKSMLDSLDGVTSN------------VHSSFYSLSSQYYKKIGDFASYYRHA---LLYLGCSDIDD  191 (380)
T ss_pred             hcccHHHHHHHHHHHHHHHhcccCCChh------------hhhhHHHHHHHHHHHHHhHHHHHHHH---HHHhccccccc
Confidence            4689999999999999988877666552            22234444555555556666654433   2232211 456


Q ss_pred             CCCCcchhhHHHHHHHHHHhcCCHHHHHHHHHhccHhhhcCchhhhhHHHHHHHHhcchHHHHHhhh---cCCCccHHHH
Q 024461           99 LPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQ---NVPNETYGYF  175 (267)
Q Consensus        99 l~~S~~~~~llgL~LL~LLsqn~i~efh~~LE~l~~~~~~~~~I~~~i~leq~LmeG~Y~kv~~~~~---~~P~~~~~~f  175 (267)
                      +|.|+....-.-|-+--||..| +=+|-.+|-.=--+-..+-...+-.++=.++-.|+..++.+..+   ..|  ..+--
T Consensus       192 l~~se~~~lA~~L~~aALLGe~-iyNfGELL~HPilesL~gT~~eWL~dll~Afn~Gdl~~f~~l~~~~~~~p--~L~~~  268 (380)
T KOG2908|consen  192 LSESEKQDLAFDLSLAALLGEN-IYNFGELLAHPILESLKGTNREWLKDLLIAFNSGDLKRFESLKGVWGKQP--DLASN  268 (380)
T ss_pred             cCHHHHHHHHHHHHHHHHhccc-cccHHHHHhhHHHHHhcCCcHHHHHHHHHHhccCCHHHHHHHHHHhccCc--hHHHH
Confidence            7888743333333334445543 44565444322112235666777888889999999999988654   334  34444


Q ss_pred             HHHHHHHHHHHHHHhHHHccC------CCCHHHHHHhhCCCCHHHHHHHH-----hhcCCCceee-CCeEEEec
Q 024461          176 MDLLAKTVRDEIAGCSEKAYD------YLSIKDAGQMLLFTSDQELLEYV-----KEEHPEWEMK-DGFVFFQK  237 (267)
Q Consensus       176 m~~L~~tiR~eia~~iekAY~------sl~l~~a~~lL~f~s~~e~~~f~-----~~~~rgW~v~-~g~i~f~~  237 (267)
                      -+.|.+.||  +.+.||-.|.      ++|++++++...++ .++++-.+     .+-=+||-=+ +|.+++.-
T Consensus       269 e~~L~qKI~--LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip-~~eVE~LVMKAlslgLikG~Idqv~~~v~~sw  339 (380)
T KOG2908|consen  269 EDFLLQKIR--LLALIEITFSRPANERTLSFKEIAEATKIP-NKEVELLVMKALSLGLIKGSIDQVEGVVYMSW  339 (380)
T ss_pred             HHHHHHHHH--HHHHHHHHhcCcchhccccHHHHHHHhCCC-HHHHHHHHHHHHhccceeeeecccccEEEEec
Confidence            455666665  4577887774      69999999999998 45544333     1112355433 67777765

>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15

Probab=94.87  E-value=0.14  Score=38.39  Aligned_cols=62  Identities=18%  Similarity=0.267  Sum_probs=49.8

Q ss_pred             HHHHHHHHHHHHHHhHHHccCCCCHHHHHHhhCCCCHHHHHHHHhh----cCCCceee--CCeEEEecC
Q 024461          176 MDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKE----EHPEWEMK--DGFVFFQKA  238 (267)
Q Consensus       176 m~~L~~tiR~eia~~iekAY~sl~l~~a~~lL~f~s~~e~~~f~~~----~~rgW~v~--~g~i~f~~~  238 (267)
                      .+.+...+|........+.|++|+++++++.++++ .++++.++..    ..-..+++  +|.++|...
T Consensus         3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~   70 (88)
T smart00088        3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEV   70 (88)
T ss_pred             HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCC
Confidence            46688999999999999999999999999999998 5578887742    23467887  677777653

Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.

>smart00753 PAM PCI/PINT associated module

Probab=94.87  E-value=0.14  Score=38.39  Aligned_cols=62  Identities=18%  Similarity=0.267  Sum_probs=49.8

Q ss_pred             HHHHHHHHHHHHHHhHHHccCCCCHHHHHHhhCCCCHHHHHHHHhh----cCCCceee--CCeEEEecC
Q 024461          176 MDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKE----EHPEWEMK--DGFVFFQKA  238 (267)
Q Consensus       176 m~~L~~tiR~eia~~iekAY~sl~l~~a~~lL~f~s~~e~~~f~~~----~~rgW~v~--~g~i~f~~~  238 (267)
                      .+.+...+|........+.|++|+++++++.++++ .++++.++..    ..-..+++  +|.++|...
T Consensus         3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~   70 (88)
T smart00753        3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEV   70 (88)
T ss_pred             HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCC
Confidence            46688999999999999999999999999999998 5578887742    23467887  677777653

>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=88.87  E-value=2.5  Score=41.05  Aligned_cols=75  Identities=17%  Similarity=0.284  Sum_probs=51.4

Q ss_pred             HHHHHHHHHHHhHHHccCCCCHHHHHHhhCCCCHHHHHHHHhh---cCCCceeeCCeEEEecCCCCCCCCCCChHHHHHH
Q 024461          179 LAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKE---EHPEWEMKDGFVFFQKAKDSAPCKEIPSLQLINQ  255 (267)
Q Consensus       179 L~~tiR~eia~~iekAY~sl~l~~a~~lL~f~s~~e~~~f~~~---~~rgW~v~~g~i~f~~~~~~~~~~~ips~~li~~  255 (267)
                      .+...-.+-.....|.|.||++++++++..+.+.+|+.+++-+   ..+-..+-||.|+|...+     .+.+|.++++|
T Consensus       299 av~sl~k~nI~rltktF~sLsL~dIA~~vQLa~~qevek~Ilqmie~~~i~a~iNG~v~f~~n~-----e~~~SpeM~~n  373 (422)
T KOG2582|consen  299 AVSSLYKKNIQRLTKTFLSLSLSDIASRVQLASAQEVEKYILQMIEDGEIFASINGMVFFTDNP-----EKYNSPEMHEN  373 (422)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcchHHHHHHHHHHhccCceEEEecceEEEecCc-----ccCCCHHHHhh
Confidence            3334444445566789999999999999999999999999853   234455458888887644     23455566664


Q ss_pred             HHh
Q 024461          256 TLS  258 (267)
Q Consensus       256 ~L~  258 (267)
                      -+.
T Consensus       374 k~~  376 (422)
T KOG2582|consen  374 KID  376 (422)
T ss_pred             HHH
Confidence            333

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	267
4b0z_A	229	Crystal Structure Of S. Pombe Rpn12 Length = 229		3e-24
4b4t_T	274	Near-Atomic Resolution Structural Model Of The Yeas		5e-16

>pdb|4B0Z|A Chain A, Crystal Structure Of S. Pombe Rpn12 Length = 229

Iteration: 1
 Score =  108 bits (270), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 69/219 (31%), Positives = 117/219 (53%), Gaps = 12/219 (5%)
Query: 21  RKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLARDIYEHAVLLSVKVEDQDA 80
           RKD+N C + L +LKV L        LF  T +   + + AR+++E+ VL+S++  D ++
Sbjct: 20  RKDWNACKKELLKLKVELAK----QNLFVPTSDK-EKASFARNVFEYGVLVSIQTCDIES 74
Query: 81  FERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXVQNRIAEFHXXXXXX--XXXXXX 138
           F R   Q+ P+Y D+   L PS    ++          +NRIAEFH              
Sbjct: 75  FARYASQVIPFYHDS---LVPSSRMGLVTGLNLLYLLSENRIAEFHTALESVPDKSLFER 131
Query: 139 NPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYL 198
           +P ++  + LEQ+ MEGA+++V S  ++     + YFM ++   VR+EIA C+EK Y  +
Sbjct: 132 DPYVEWVISLEQNVMEGAFDKVASMIRSCNFPEFSYFMKIVMSMVRNEIATCAEKVYSEI 191
Query: 199 SIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQK 237
            + +A  +L   + +E  E + EE   W+++DG ++F K
Sbjct: 192 PLSNATSLLYLENTKE-TEKLAEERG-WDIRDGVIYFPK 228

>pdb|4B4T|T Chain T, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 274

Iteration: 1
 Score = 81.3 bits (199), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 71/280 (25%), Positives = 126/280 (45%), Gaps = 22/280 (7%)
Query: 3   PKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKV-LLTGFRSLPPLFEDTPNAIRELTLA 61
           P L E+++       A    DY  C +LL  +K+ L+     +P L       + +L + 
Sbjct: 2   PSLAELTKSL---SIAFENGDYAACEKLLPPIKIELIKNNLLIPDLSIQNDIYLNDLMIT 58
Query: 62  RDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXVQNR 121
           + I E   L S++  + D+FE  F QLKPYY     +L  S  +  +          QN 
Sbjct: 59  KRILEVGALASIQTFNFDSFENYFNQLKPYYFSNNHKLSESDKKSKLISLYLLNLLSQNN 118
Query: 122 IAEFHXXXX---XXXXXXXXNPCIKHAVELEQSFMEGAYNRVL----SAKQNVPNETYGY 174
             +FH               +  + + ++L++  MEG+Y +      S  QN+    +  
Sbjct: 119 TTKFHSELQYLDKHIKNLEDDSLLSYPIKLDRWLMEGSYQKAWDLLQSGSQNIS--EFDS 176
Query: 175 FMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVF 234
           F D+L   +RDEIA  +E +YD+L + +   +L F +++E  ++  E +  W + +  V+
Sbjct: 177 FTDILKSAIRDEIAKNTELSYDFLPLSNIKALLFFNNEKETEKFALERN--WPIVNSKVY 234
Query: 235 F-----QKA--KDSAPCKEIPSLQLINQTLSYARELERIV 267
           F     +KA  +D    +E     +I + + YA  +E IV
Sbjct: 235 FNNQSKEKADYEDEMMHEEDQKTNIIEKAMDYAISIENIV 274

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	267
3t5v_A	316	Nuclear mRNA export protein SAC3; PCI, mRNA nuclea	2e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04

>3t5v_A Nuclear mRNA export protein SAC3; PCI, mRNA nuclear export, mRNA, nuclear, transcription; 2.90A {Saccharomyces cerevisiae} Length = 316

 Score = 47.5 bits (112), Expect = 2e-06
 Identities = 33/216 (15%), Positives = 59/216 (27%), Gaps = 23/216 (10%)

Query: 55  IRELTLARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLL 114
           +R   L   I   + +     ++ +   +    L   Y D        PNE       LL
Sbjct: 65  VRIHLLILHIMVKSNVEFSLQQELEQLHKSLITLSEIYDDVRSSGGTCPNEAEFRAYALL 124

Query: 115 RLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETY-- 172
             +   +  E    ++ L     ++  ++ A+   +     AY      K       Y  
Sbjct: 125 SKIRDPQYDE---NIQRLPKHIFQDKLVQMALCFRRVISNSAYTERGFVKTENCLNFYAR 181

Query: 173 --------------GYFMDLLAKTVRDEIAGCSEKAY----DYLSIKDAGQMLLFTSDQE 214
                         G+F+ +    +R                 +       MLLF + QE
Sbjct: 182 FFQLMQSPSLPLLMGFFLQMHLTDIRFYALRALSHTLNKKHKPIPFIYLENMLLFNNRQE 241

Query: 215 LLEYVKEEHPEWEMKDGFVFFQKAKDSAPCKEIPSL 250
           ++E+      E    D          S    E   L
Sbjct: 242 IIEFCNYYSIEIINGDAADLKTLQHYSHKLSETQPL 277

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 46.4 bits (109), Expect = 5e-06
 Identities = 41/298 (13%), Positives = 94/298 (31%), Gaps = 65/298 (21%)

Query: 26  TCTQLLSQL-KVLLTGFRSLPPLFEDT-PNAI-------RELTLARDIYEH------AVL 70
           T  ++ S L K L    + LP     T P  +       R+     D ++H        +
Sbjct: 299 TPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTI 358

Query: 71  LSVKVEDQDAFERDFFQLKPYYTD-----AGKRLPP----------SPNEYMILGLNLL- 114
           +   +   +  E      +  +           +P             ++ M++ +N L 
Sbjct: 359 IESSLNVLEPAE-----YRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVV-VNKLH 412

Query: 115 -RLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQN--VPNET 171
              LV+ +  E    +  +         +++   L +S ++  YN   +   +  +P   
Sbjct: 413 KYSLVEKQPKESTISIPSIYLELKVK--LENEYALHRSIVD-HYNIPKTFDSDDLIPPYL 469

Query: 172 YGYFMDLLA----KTVRDEIAGCSEKAY-DY--LS--IKDAGQMLLFTSD-----QEL-- 215
             YF   +          E        + D+  L   I+        +       Q+L  
Sbjct: 470 DQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKF 529

Query: 216 -LEYVKEEHPEWEM--KDGFVFFQKAKDS---APCKEIPSLQLINQTLSYARELERIV 267
              Y+ +  P++E        F  K +++   +   ++  + L+ +  +   E  + V
Sbjct: 530 YKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQV 587

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 46.0 bits (108), Expect = 7e-06
 Identities = 43/268 (16%), Positives = 88/268 (32%), Gaps = 55/268 (20%)

Query: 5   LTEVSQQFDRFKAAMTRKDYN--------TCTQ-------LLSQLKVLLTGFRSLPPLFE 49
           L++  +   +F   + R +Y            Q        + Q   L    +       
Sbjct: 72  LSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNV 131

Query: 50  DTP-------NAIRELTLARDIYEHAVL------LSVKVEDQDAFERDF-FQLKPYYTDA 95
                      A+ EL  A+++    VL      +++ V      +    F++  ++ + 
Sbjct: 132 SRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKI--FWLNL 189

Query: 96  GKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEG 155
                 SP   + +   LL  +  N    + +  +  S+  L    I+   EL +     
Sbjct: 190 KNCN--SPETVLEMLQKLLYQIDPN----WTSRSDHSSNIKLRIHSIQA--ELRRLLKSK 241

Query: 156 AYNRVLSAKQNVPN-ETYGYFMDLLAKTV---RDE--IAGCSEKAYDYLSIKDAGQMLLF 209
            Y   L    NV N + +  F +L  K +   R +      S     ++S+      +  
Sbjct: 242 PYENCLLVLLNVQNAKAWNAF-NLSCKILLTTRFKQVTDFLSAATTTHISLDH--HSMTL 298

Query: 210 TSDQ--ELL-EYVK---EEHPEWEMKDG 231
           T D+   LL +Y+    ++ P  E+   
Sbjct: 299 TPDEVKSLLLKYLDCRPQDLPR-EVLTT 325

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 41.8 bits (97), Expect = 2e-04
 Identities = 39/280 (13%), Positives = 73/280 (26%), Gaps = 71/280 (25%)

Query: 25  NTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLARDIYEHA--VLLSVK-VEDQDAF 81
               Q+            ++          +R L  ++  YE+   VLL+V+  +  +AF
Sbjct: 204 KLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKP-YENCLLVLLNVQNAKAWNAF 262

Query: 82  E---------RD---FFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTEL 129
                     R       L    T     +    +   +    +  LL++          
Sbjct: 263 NLSCKILLTTRFKQVTDFLSAATT---THISLDHHSMTLTPDEVKSLLLKY----LDCRP 315

Query: 130 ELLSSTALE-NPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIA 188
           + L    L  NP          S +         + ++    T+  +  +    +   I 
Sbjct: 316 QDLPREVLTTNP-------RRLS-IIAE------SIRDGLA-TWDNWKHVNCDKLTTIIE 360

Query: 189 GCSE--------KAYDYLSIKDAGQMLLFTSD----QELLE----YVKEEHPEWEMKDGF 232
                       K +D LS+        F         LL      V +      +    
Sbjct: 361 SSLNVLEPAEYRKMFDRLSV--------FPPSAHIPTILLSLIWFDVIKSDVMVVVNK-- 410

Query: 233 VFFQK---AKDSAPCK-EIPSLQL-INQTLSYARELERIV 267
              +     K        IPS+ L +   L     L R +
Sbjct: 411 -LHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSI 449

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	267
4b4t_T	274	26S proteasome regulatory subunit RPN12; hydrolase	100.0
4b0z_A	229	RPN12, 26S proteasome regulatory subunit RPN12; pr	100.0
1rz4_A	226	Eukaryotic translation initiation factor 3 subuni;	99.96
3t5v_A	316	Nuclear mRNA export protein SAC3; PCI, mRNA nuclea	99.87
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	97.69
4b4t_O	393	26S proteasome regulatory subunit RPN9; hydrolase,	97.35
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	97.25
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	97.15
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	96.73
1ufm_A	84	COP9 complex subunit 4; helix-turn-helix, structur	93.25
3t5x_A	203	PCI domain-containing protein 2; PCI, mRNA nuclear	80.98
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	80.86

>4b4t_T 26S proteasome regulatory subunit RPN12; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=9.8e-76  Score=535.66  Aligned_cols=260  Identities=27%  Similarity=0.478  Sum_probs=162.2

Q ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcCCCCCCC-CCCChhhHHHHHHHHHHHHHHHHHHhhccChHHHHHH
Q 024461            6 TEVSQQFDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPL-FEDTPNAIRELTLARDIYEHAVLLSVKVEDQDAFERD   84 (267)
Q Consensus         6 ~~~~~l~~~L~~~~~~~~~~~~~~lL~~lKi~L~~~~~L~~~-~~~~~~~~~~l~lar~vlEi~al~si~~~D~~~F~r~   84 (267)
                      .++.+++++|+++|+++|+++|.++|.++|+.|+++++|+|+ ..+++...+||.+||+|||+||++||+.+|+++|+||
T Consensus         2 ~~l~~l~~~l~~~~~~~d~~~~~~lL~~lK~~L~~~~~l~p~~~~~~~~~~~el~~ar~v~E~~a~~si~~~D~~~F~~~   81 (274)
T 4b4t_T            2 PSLAELTKSLSIAFENGDYAACEKLLPPIKIELIKNNLLIPDLSIQNDIYLNDLMITKRILEVGALASIQTFNFDSFENY   81 (274)
T ss_dssp             -----------------------------------------------------------CHHHHHHCCSSCSSHHHHHHH
T ss_pred             ccHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHHhccCcCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            457889999999999999999999999999999999999885 3345566789999999999999999999999999999


Q ss_pred             HhhhhhhhhhcCCCCCCCcchhhHHHHHHHHHHhcCCHHHHHHHHHhccHh---hhcCchhhhhHHHHHHHHhcchHHHH
Q 024461           85 FFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSST---ALENPCIKHAVELEQSFMEGAYNRVL  161 (267)
Q Consensus        85 ~~qLk~~Y~~~~~~l~~S~~~~~llgL~LL~LLsqn~i~efh~~LE~l~~~---~~~~~~I~~~i~leq~LmeG~Y~kv~  161 (267)
                      ++|||+||+|+.+++|+|+++++|+||||||||+|||++|||++||.||..   +++||+|+||++||+++|+|||+|+|
T Consensus        82 ~~QLk~~Y~d~~~~l~~s~~~~e~~~~~LLylL~~n~~~efh~~Le~L~~~~~~~~~d~~Ik~al~le~al~eGnY~kff  161 (274)
T 4b4t_T           82 FNQLKPYYFSNNHKLSESDKKSKLISLYLLNLLSQNNTTKFHSELQYLDKHIKNLEDDSLLSYPIKLDRWLMEGSYQKAW  161 (274)
T ss_dssp             HHHHHHHTTTTSSCSSCSHHHHHHHHHHHHHHHHHHCSTHHHHHHHSSSCSSSTTTCCHHHHHHHHHHHHHHHTCSHHHH
T ss_pred             HHHHHHHHHhhhccCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHhcchhhHhHhcChHHHHHHHHHHHHHcCCHHHHH
Confidence            999999999999999999999999999999999999999999999999963   45899999999999999999999999


Q ss_pred             HhhhcC--CCccHHHHHHHHHHHHHHHHHHhHHHccCCCCHHHHHHhhCCCCHHHHHHHHhhcCCCceeeCCeEEEecCC
Q 024461          162 SAKQNV--PNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAK  239 (267)
Q Consensus       162 ~~~~~~--P~~~~~~fm~~L~~tiR~eia~~iekAY~sl~l~~a~~lL~f~s~~e~~~f~~~~~rgW~v~~g~i~f~~~~  239 (267)
                      +..++.  |+++|++||++|++|||.+||+||+|||++||+++++++|+|+|++|+.+|++  +|||+++||.++|+..+
T Consensus       162 ~l~~~~~~p~~~~~~f~d~l~~~iR~~a~~~i~kaY~~i~l~~~~~~L~F~s~~e~~~F~~--~~gW~~~~~~v~F~~~~  239 (274)
T 4b4t_T          162 DLLQSGSQNISEFDSFTDILKSAIRDEIAKNTELSYDFLPLSNIKALLFFNNEKETEKFAL--ERNWPIVNSKVYFNNQS  239 (274)
T ss_dssp             HHHHTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHCSSCCHHHHHHHHTCCSHHHHHHHHH--HTTCCCCSSCCCC----
T ss_pred             HHHhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHhCCCCHHHHHHHHH--HcCCEEeCCEeEECCcc
Confidence            976654  56789999999999999999999999999999999999999999999999984  68999999999998754


Q ss_pred             CCC-------CCCCCChHHHHHHHHhHHHHhhhcC
Q 024461          240 DSA-------PCKEIPSLQLINQTLSYARELERIV  267 (267)
Q Consensus       240 ~~~-------~~~~ips~~li~~~L~YA~eLE~IV  267 (267)
                      +..       ...++||.++|+|+|+||+|||+||
T Consensus       240 ~~~~~~~~~~~~~~ips~~li~~~l~YA~elE~IV  274 (274)
T 4b4t_T          240 KEKADYEDEMMHEEDQKTNIIEKAMDYAISIENIV  274 (274)
T ss_dssp             -----------------------------------
T ss_pred             ccccccccccccccCcHHHHHHHHHHHHHHhhhcC
Confidence            221       2356899999999999999999998

>4b0z_A RPN12, 26S proteasome regulatory subunit RPN12; protein binding, proteasome ubitquitin; HET: SGM GOL; 1.58A {Schizosaccharomyces pombe}

Probab=100.00  E-value=2.7e-61  Score=429.58  Aligned_cols=216  Identities=34%  Similarity=0.624  Sum_probs=203.8

Q ss_pred             HHHHHHHhCCCCHHHHHHHHHHHHHHHhcCCCCCCCCCCChhhHHHHHHHHHHHHHHHHHHhhccChHHHHHHHhhhhhh
Q 024461           12 FDRFKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLARDIYEHAVLLSVKVEDQDAFERDFFQLKPY   91 (267)
Q Consensus        12 ~~~L~~~~~~~~~~~~~~lL~~lKi~L~~~~~L~~~~~~~~~~~~~l~lar~vlEi~al~si~~~D~~~F~r~~~qLk~~   91 (267)
                      +++|+.+|+++|+++|.++|+++|+.|++.+.++|+.     ..+++.+||+|||+||++||+.+|+++|+||++|||+|
T Consensus        11 l~~L~~~~~~~d~~~~~~lL~~lk~~L~~~~~~~p~~-----~~~~~~~ar~vyE~~a~~al~~~D~~~F~~~~~qLk~~   85 (229)
T 4b0z_A           11 LNHLADLYDRKDWNACKKELLKLKVELAKQNLFVPTS-----DKEKASFARNVFEYGVLVSIQTCDIESFARYASQVIPF   85 (229)
T ss_dssp             SHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCSSCCS-----CHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHHHHHhcCCCCCCC-----ChHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            5678888999999999999999999999999999842     24788999999999999999999999999999999999


Q ss_pred             hhhcCCCCCCCcchhhHHHHHHHHHHhcCCHHHHHHHHHhccHhh--hcCchhhhhHHHHHHHHhcchHHHHHhhhcCCC
Q 024461           92 YTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTA--LENPCIKHAVELEQSFMEGAYNRVLSAKQNVPN  169 (267)
Q Consensus        92 Y~~~~~~l~~S~~~~~llgL~LL~LLsqn~i~efh~~LE~l~~~~--~~~~~I~~~i~leq~LmeG~Y~kv~~~~~~~P~  169 (267)
                      |.++   +++|+++.+++||||||+|++|+++|||++|+.+|++.  ++||+|+||++|||++|+|||++||++.+++|+
T Consensus        86 Y~~~---~~~s~~~~e~~~~~LL~lL~~~~~~ef~~~le~l~~~~~~~~~~~I~~al~l~~al~~GnY~kff~l~~~~p~  162 (229)
T 4b0z_A           86 YHDS---LVPSSRMGLVTGLNLLYLLSENRIAEFHTALESVPDKSLFERDPYVEWVISLEQNVMEGAFDKVASMIRSCNF  162 (229)
T ss_dssp             HSSC---CCCCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHCSCTTHHHHCHHHHHHHHHHHHHHTTCHHHHHHHHHTCCC
T ss_pred             HHcc---CCCCccHHHHHHHHHHHHHHcCCchHHHHHHHhcChHHHhhcCHHHHHHHHHHHHHHcCCHHHHHHHHhcCcc
Confidence            9875   78899999999999999999999999999999999764  599999999999999999999999999999999


Q ss_pred             ccHHHHHHHHHHHHHHHHHHhHHHccCCCCHHHHHHhhCCCCHHHHHHHHhhcCCCceeeCCeEEEec
Q 024461          170 ETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQK  237 (267)
Q Consensus       170 ~~~~~fm~~L~~tiR~eia~~iekAY~sl~l~~a~~lL~f~s~~e~~~f~~~~~rgW~v~~g~i~f~~  237 (267)
                      +.|++||+.|++|+|.+|++||+|||++||+++++++|+|+|++++.+|++  ++||+++||.|||++
T Consensus       163 ~~~~~~~~~l~~~vR~~~l~~i~kaY~~i~l~~~~~~L~f~s~~e~~~f~~--~~gw~i~dg~i~F~~  228 (229)
T 4b0z_A          163 PEFSYFMKIVMSMVRNEIATCAEKVYSEIPLSNATSLLYLENTKETEKLAE--ERGWDIRDGVIYFPK  228 (229)
T ss_dssp             GGGHHHHHHHHHHHHHHHHHHHHHHCSEEEHHHHHHHTTCSSHHHHHHHHH--HHTCEEETTEEECC-
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHH--HcCCEEeCCEEecCC
Confidence            999999999999999999999999999999999999999999999999985  589999999999986

>1rz4_A Eukaryotic translation initiation factor 3 subuni; heat analogous motif, winged-helix, biosynthetic protein; 2.10A {Homo sapiens} SCOP: a.4.5.53 a.118.1.18

Probab=99.96  E-value=1.5e-29  Score=224.93  Aligned_cols=158  Identities=15%  Similarity=0.132  Sum_probs=130.2

Q ss_pred             ChHHHHHHHhh--hhhhhhhcCC----C---CCCCcchhhHHHHHHHHHHhcCCHHHHHHHHHhccHhhhcCchhhhhHH
Q 024461           77 DQDAFERDFFQ--LKPYYTDAGK----R---LPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVE  147 (267)
Q Consensus        77 D~~~F~r~~~q--Lk~~Y~~~~~----~---l~~S~~~~~llgL~LL~LLsqn~i~efh~~LE~l~~~~~~~~~I~~~i~  147 (267)
                      .++.|++|++|  .+++|+...+    .   +.|+....+++|++||.+|+++..+|||+.++.||+++.+||+|+++|.
T Consensus        25 ~l~~le~Yv~qq~~~~~YD~~anlalLklYq~~p~~~~~~ii~~iLlk~L~~~p~~DF~~~l~LIp~~~~~~~~I~~i~~  104 (226)
T 1rz4_A           25 NLATLERYVETQAKENAYDLEANLAVLKLYQFNPAFFQTTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILY  104 (226)
T ss_dssp             GHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTTTSTHHHHHHHTSCHHHHTSTTHHHHHH
T ss_pred             HHHHHHHHHHHHHhcccccHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHcCCHHHHHHHHHhCChhhhcCHHHHHHHH
Confidence            45667777777  5666642211    1   3567778999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcchHHHHHhhhcCCCccHHHHHHHHHHHHHHHHHHhHHHccCCCCHHHHHHhhCCCCHHHHHHHHhhcCCCce
Q 024461          148 LEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWE  227 (267)
Q Consensus       148 leq~LmeG~Y~kv~~~~~~~P~~~~~~fm~~L~~tiR~eia~~iekAY~sl~l~~a~~lL~f~s~~e~~~f~~~~~rgW~  227 (267)
                      |+++||+|+|++||...+.-|  .+..++.-|.++||.+|+.|+++||++||+++++++||+.|++++.+|++  ++||+
T Consensus       105 L~~~L~~~~y~~fW~~l~~~~--~l~~~i~gf~dsIR~~I~~~i~~aY~sI~~~~la~lLg~~s~~el~~fi~--~~GW~  180 (226)
T 1rz4_A          105 LGDLLETCHFQAFWQALDENM--DLLEGITGFEDSVRKFICHVVGITYQHIDRWLLAEMLGDLSDSQLKVWMS--KYGWS  180 (226)
T ss_dssp             HHHHHHTTCHHHHHHHSCTTC--HHHHTSTTHHHHHHHHHHHHHHHHCSEECHHHHHHHTTSCCHHHHHHHHH--HHTCE
T ss_pred             HHHHHHcCCHHHHHHHHhcCh--hHHHHHhHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHcCCCHHHHHHHHH--HCCCE
Confidence            999999999999999876522  23333344999999999999999999999999999998778999999996  46999


Q ss_pred             ee-CCeEEEecC
Q 024461          228 MK-DGFVFFQKA  238 (267)
Q Consensus       228 v~-~g~i~f~~~  238 (267)
                      ++ +|.|+|++.
T Consensus       181 vd~~g~I~~~n~  192 (226)
T 1rz4_A          181 ADESGQIFICSQ  192 (226)
T ss_dssp             ECC--CEECCCH
T ss_pred             ECCCccEEeCCC
Confidence            97 778877654

>3t5v_A Nuclear mRNA export protein SAC3; PCI, mRNA nuclear export, mRNA, nuclear, transcription; 2.90A {Saccharomyces cerevisiae}

Probab=99.87  E-value=1.2e-21  Score=181.75  Aligned_cols=190  Identities=16%  Similarity=0.223  Sum_probs=155.5

Q ss_pred             CCHHHHHHHHHHHHHHHhcCCCCCCCCCCChhhHHHHHHHHHHHHHHHHHHh------hccCh--------HHHHHHHhh
Q 024461           22 KDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLARDIYEHAVLLSV------KVEDQ--------DAFERDFFQ   87 (267)
Q Consensus        22 ~~~~~~~~lL~~lKi~L~~~~~L~~~~~~~~~~~~~l~lar~vlEi~al~si------~~~D~--------~~F~r~~~q   87 (267)
                      .++.=+..-+.-++-.|+--+.-      +       ..|.+|||.+|++.|      ..+|.        +.+..|..+
T Consensus        31 ~~y~fi~Dr~RsIRqDltvQ~i~------~-------~~~v~v~E~~aRf~i~~~~~L~~~~~~f~~~~~~eQl~~~L~s   97 (316)
T 3t5v_A           31 ESEGFLWDRMRSIRQDFTYQNYS------G-------PEAVDCNERIVRIHLLILHIMVKSNVEFSLQQELEQLHKSLIT   97 (316)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTTCC------S-------HHHHHHHHHHHHHHHHHHHHHHHSCCCCCHHHHHHHHHHHHHH
T ss_pred             hhhHHHHhhhhhhccCceeeccC------C-------chHHHHHHHHHHHHHHHHHHHhhCCCccchHHHHHHHHHHHHH
Confidence            56777777777777777764431      1       237899999999986      34443        245555668


Q ss_pred             hhhhhhhcCCCCCCCcchhhHHHHHHHHHHhcCCHHHHHHHHHhccHhhhcCchhhhhHHHHHHHH--------------
Q 024461           88 LKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFM--------------  153 (267)
Q Consensus        88 Lk~~Y~~~~~~l~~S~~~~~llgL~LL~LLsqn~i~efh~~LE~l~~~~~~~~~I~~~i~leq~Lm--------------  153 (267)
                      |+.+|.+.+..-..+++..++.||+||+.|.+.   +++..+..+|+++++||.|++++.|++++.              
T Consensus        98 L~~lY~d~~~~~~~~~ne~EF~aY~lL~~l~~~---~~~~~l~~Lp~~i~~~p~Vq~AL~l~~a~~~~~~~e~~~~~~~~  174 (316)
T 3t5v_A           98 LSEIYDDVRSSGGTCPNEAEFRAYALLSKIRDP---QYDENIQRLPKHIFQDKLVQMALCFRRVISNSAYTERGFVKTEN  174 (316)
T ss_dssp             HHHHHHHHHHTTCCCTTHHHHHHHHHHHSTTCT---HHHHHHTTSCHHHHTSHHHHHHHHHHHHHCCTTCCCTTCCCCSS
T ss_pred             HHHHHHHHhhcCCCCCCHHHHHHHHHHHHhccc---hHHHHHHhCCHHHhcCHHHHHHHHHHHHHHhccccccccccccc
Confidence            888899853322357899999999999988764   788899999999999999999999999985              


Q ss_pred             -hcchHHHHHhhhcCCCccH--HHHHHHHHHHHHHHHHHhHHHcc----CCCCHHHHHHhhCCCCHHHHHHHHhhcCCCc
Q 024461          154 -EGAYNRVLSAKQNVPNETY--GYFMDLLAKTVRDEIAGCSEKAY----DYLSIKDAGQMLLFTSDQELLEYVKEEHPEW  226 (267)
Q Consensus       154 -eG~Y~kv~~~~~~~P~~~~--~~fm~~L~~tiR~eia~~iekAY----~sl~l~~a~~lL~f~s~~e~~~f~~~~~rgW  226 (267)
                       .|||+++|+...+ |+..|  +.+|+.+++++|..++.||.+||    .++|+++++++|+|+|++|+.+|+.  ..||
T Consensus       175 ~~gNY~rFFrL~~~-~~~pyL~aclle~~~~~vR~~AL~~i~kay~~k~~~~pl~~L~~~L~Fds~ee~~~F~~--~~gl  251 (316)
T 3t5v_A          175 CLNFYARFFQLMQS-PSLPLLMGFFLQMHLTDIRFYALRALSHTLNKKHKPIPFIYLENMLLFNNRQEIIEFCN--YYSI  251 (316)
T ss_dssp             CCCCHHHHHHHHTC-TTSCHHHHHHHGGGHHHHHHHHHHHHHHHSCTTCCCEEHHHHHHHTTCSSHHHHHHHHH--HTTC
T ss_pred             ccchHHHHHHHHhc-cCCChHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcCHHHHHHHhCCCCHHHHHHHHH--HCCC
Confidence             3999999999887 32234  89999999999999999999999    4899999999999999999999994  6899


Q ss_pred             eeeC
Q 024461          227 EMKD  230 (267)
Q Consensus       227 ~v~~  230 (267)
                      ++.+
T Consensus       252 ~~~~  255 (316)
T 3t5v_A          252 EIIN  255 (316)
T ss_dssp             CEET
T ss_pred             eEeC
Confidence            9985

>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha solenoid, regulatory PART LID, hydrolase, protein binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A

Probab=97.69  E-value=0.014  Score=55.20  Aligned_cols=198  Identities=8%  Similarity=0.078  Sum_probs=130.1

Q ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCCCCCCChhhHHHHHHHHHHHHHHHHHHh-hccChHH-HHHHHhhhhhhhhhcCCC
Q 024461           21 RKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLARDIYEHAVLLSV-KVEDQDA-FERDFFQLKPYYTDAGKR   98 (267)
Q Consensus        21 ~~~~~~~~~lL~~lKi~L~~~~~L~~~~~~~~~~~~~l~lar~vlEi~al~si-~~~D~~~-F~r~~~qLk~~Y~~~~~~   98 (267)
                      -+|+.+++..+.+.+-....   .++    +|      .+-=.+-|.+.++.+ ..+|+.. |..++.-.+. |..    
T Consensus       152 ~~n~~k~k~~l~~a~~~~~a---i~~----~p------~i~a~i~~~~Gi~~l~~~rdyk~A~~~F~eaf~~-f~~----  213 (394)
T 3txn_A          152 LSNLPKARAALTSARTTANA---IYC----PP------KVQGALDLQSGILHAADERDFKTAFSYFYEAFEG-FDS----  213 (394)
T ss_dssp             TTCHHHHHHHHHHHHHHHHH---SCC----CH------HHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHH-HTT----
T ss_pred             hccHHHHHHHHHHHHhhhcc---CCC----CH------HHHHHHHHHhhHHHHHhccCHHHHHHHHHHHHhc-ccc----
Confidence            46777777777776554322   211    12      234567789999999 8999754 3333333222 321    


Q ss_pred             CCCCcchhhHHHHHHHHHHhcCCHHHHHHHHHhccHhhhcCchhhhhHHHHHHHHhcchHHHHHhhh----cCCCc-cHH
Q 024461           99 LPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQ----NVPNE-TYG  173 (267)
Q Consensus        99 l~~S~~~~~llgL~LL~LLsqn~i~efh~~LE~l~~~~~~~~~I~~~i~leq~LmeG~Y~kv~~~~~----~~P~~-~~~  173 (267)
                       .+++.+..++-+-+|.-|..++..|+...+..=......+|.|.....|-++.-.|+|..+.....    .+..+ ...
T Consensus       214 -~~~~~~~~~lkYlvL~aLl~~~r~el~~~l~~~~~~~~~~pei~~l~~L~~a~~~~dl~~f~~iL~~~~~~l~~D~~l~  292 (394)
T 3txn_A          214 -VDSVKALTSLKYMLLCKIMLGQSDDVNQLVSGKLAITYSGRDIDAMKSVAEASHKRSLADFQAALKEYKKELAEDVIVQ  292 (394)
T ss_dssp             -TCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHSHHHHTTCSHHHHHHHHHHHHHHTTCHHHHHHHHHHSTTTTTTSHHHH
T ss_pred             -cccHHHHHHHHHHHHHHHHcCCHHHHHHHhccccccccCCccHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcChHHH
Confidence             234555666666556666677778887543211001127899999999999999999988776432    22222 224


Q ss_pred             HHHHHHHHHHHHHHHHhHHHccCCCCHHHHHHhhCCCCHHHHHHHHhh----cCCCceee--CCeEEEecC
Q 024461          174 YFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKE----EHPEWEMK--DGFVFFQKA  238 (267)
Q Consensus       174 ~fm~~L~~tiR~eia~~iekAY~sl~l~~a~~lL~f~s~~e~~~f~~~----~~rgW~v~--~g~i~f~~~  238 (267)
                      ...+.|...||.....-+-+.|++|+++++++.++++ +++++..+..    ..-.=++|  +|.++|..+
T Consensus       293 ~h~~~L~~~Ir~~~L~~i~~pYsrIsl~~iA~~l~ls-~~evE~~L~~lI~dg~I~a~IDq~~giv~~~~~  362 (394)
T 3txn_A          293 AHLGTLYDTMLEQNLCRIIEPYSRVQVAHVAESIQLP-MPQVEKKLSQMILDKKFSGILDQGEGVLIVFEE  362 (394)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCSEEEHHHHHHHHTCC-HHHHHHHHHHHHHTTSSCEEEETTTTEEEECCC
T ss_pred             HHHHHHHHHHHHHHHHHHhHhhceeeHHHHHHHHCcC-HHHHHHHHHHHHHCCCeeEEEcCCCCEEEECCC
Confidence            4467899999999999999999999999999999995 8888777732    22222677  677777654

>4b4t_O 26S proteasome regulatory subunit RPN9; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.35  E-value=0.0089  Score=56.14  Aligned_cols=198  Identities=14%  Similarity=0.149  Sum_probs=132.3

Q ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCCCCCCChhhHHHHHHHHHHHHHHHHHHhhccChHHHHHHHhhhhhhhhhcCCCCC
Q 024461           21 RKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLP  100 (267)
Q Consensus        21 ~~~~~~~~~lL~~lKi~L~~~~~L~~~~~~~~~~~~~l~lar~vlEi~al~si~~~D~~~F~r~~~qLk~~Y~~~~~~l~  100 (267)
                      .+|...|...|.++|..+-..+...|            .+.-.+|+..+.+.-..+|.++|-++.-+--..|... ..+ 
T Consensus       140 ~~d~~~a~~~l~~~~~~l~~~~~~~~------------~v~~~~y~~~~~~~~~~~~~a~~y~~~l~~l~~~~~~-~~~-  205 (393)
T 4b4t_O          140 KNDLVKARDLLDDLEKTLDKKDSIPL------------RITNSFYSTNSQYFKFKNDFNSFYYTSLLYLSTLEPS-TSI-  205 (393)
T ss_dssp             HSCHHHHHHHHHHHHHHHHHSCCSSS------------HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTS-SSC-
T ss_pred             cCCHHHHHHHHHHHHHhhhccCCccH------------HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcccc-ccC-
Confidence            46889999999999987766543322            4567889999999999999988877655444444322 112 


Q ss_pred             CCcchhhHHHHHHHH-HHhcCCHHHHHHHHHhccHhhh-cCchhhhhHHHHHHHHhcchHHHHHhhh----cCCCccHHH
Q 024461          101 PSPNEYMILGLNLLR-LLVQNRIAEFHTELELLSSTAL-ENPCIKHAVELEQSFMEGAYNRVLSAKQ----NVPNETYGY  174 (267)
Q Consensus       101 ~S~~~~~llgL~LL~-LLsqn~i~efh~~LE~l~~~~~-~~~~I~~~i~leq~LmeG~Y~kv~~~~~----~~P~~~~~~  174 (267)
                       +...-.-+++.++. -|...++-.|-.+|..-..... ++|.+....+|=+..-.|+|..+-....    +.|  ....
T Consensus       206 -~~~~~~~~a~~l~~~all~~~i~~f~eLL~~p~i~~L~~~~~~~~l~~Ll~~f~~g~~~~f~~~~~~~~~~~~--~l~~  282 (393)
T 4b4t_O          206 -TLAERQQLAYDLSISALLGDKIYNFGELLHHPIMETIVNDSNYDWLFQLLNALTVGDFDKFDSLIKVQISKIP--ILAQ  282 (393)
T ss_dssp             -SHHHHHHHHHHHHHHHHHCCSSCSTHHHHHSCCTTSSCSSSSTTHHHHHHHHHHHTCHHHHHHHCCHHHHHSH--HHHH
T ss_pred             -CHHHHHHHHHHHHHHHHcCCCCCChHHHhCChHHHHhhcCCchHHHHHHHHHHhcCCHHHHHHHHHHhhhhCc--chhh
Confidence             23333344555444 4667778888887765443434 6788888899999999999999866321    222  3444


Q ss_pred             HHHHHHHHHHHHHHHhHH--HccCCCCHHHHHHhhCCCCHHHHHHHHhh-----cCCCceee--CCeEEEec
Q 024461          175 FMDLLAKTVRDEIAGCSE--KAYDYLSIKDAGQMLLFTSDQELLEYVKE-----EHPEWEMK--DGFVFFQK  237 (267)
Q Consensus       175 fm~~L~~tiR~eia~~ie--kAY~sl~l~~a~~lL~f~s~~e~~~f~~~-----~~rgW~v~--~g~i~f~~  237 (267)
                      ....+...+|.-....+.  +.|++||++++++.|+++ +++++.++..     .=+| ++|  +|.|+|..
T Consensus       283 ~~~~l~~kirll~l~~l~~~~~~~~i~f~~ia~~l~i~-~~evE~lli~aI~~glI~G-kIDQv~~~v~v~~  352 (393)
T 4b4t_O          283 HESFLRQKICLMTLIETVFVKNIRMLSFEDISKATHLP-KDNVEHLVMRAISLGLLKG-SIDQVNELVTISW  352 (393)
T ss_dssp             HHHHHHHHHHHHHHHHHHCSSSCCCEEHHHHHHHHTCC-HHHHHHHHHHHHHHSCSSS-CEETTTTEECC--
T ss_pred             hHHHHHHHHHHHHHHHHhccCCCCcCcHHHHHHHhCcC-HHHHHHHHHHHHHcCCEEE-EEcCCCCEEEEEe
Confidence            455566677765554333  457899999999999997 8999998842     1235 345  66666543

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.25  E-value=0.023  Score=54.06  Aligned_cols=202  Identities=13%  Similarity=0.092  Sum_probs=127.4

Q ss_pred             hCCCCHHHHHHHHHHHHHHHhcCCCCCCCCCCChhhHHHHHHHHHHHHHHHHHHhhccChHHHHHHHhhhhhhhhhcCCC
Q 024461           19 MTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKR   98 (267)
Q Consensus        19 ~~~~~~~~~~~lL~~lKi~L~~~~~L~~~~~~~~~~~~~l~lar~vlEi~al~si~~~D~~~F~r~~~qLk~~Y~~~~~~   98 (267)
                      ...+|+.++..++.+++......+   +    +    .  .+--.+++.++.+....+|+.+--+|+-++-.-|...   
T Consensus       188 l~~~d~~~a~~~~~ki~~~~~~~~---~----~----~--~lk~~~~~~~~~~~~~e~~y~~a~~~y~e~~~~~~~~---  251 (445)
T 4b4t_P          188 ILKGDYSQATVLSRKILKKTFKNP---K----Y----E--SLKLEYYNLLVKISLHKREYLEVAQYLQEIYQTDAIK---  251 (445)
T ss_dssp             HHHTCHHHHHHHHHHHHHHHHHSS---C----C----H--HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH---
T ss_pred             HHCCCHHHHHHHHHHHHHhhcccC---C----c----H--HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhccccc---
Confidence            345677777777777665444321   1    1    1  2345789999999999999877766666554444432   


Q ss_pred             CCCCcchhhHHHHHHHHHHhcCCHHHHHHHHHhccHhhhcCchhhhhHHHHHHHHhcch---HHHHHhhhcC--CC----
Q 024461           99 LPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAY---NRVLSAKQNV--PN----  169 (267)
Q Consensus        99 l~~S~~~~~llgL~LL~LLsqn~i~efh~~LE~l~~~~~~~~~I~~~i~leq~LmeG~Y---~kv~~~~~~~--P~----  169 (267)
                       ..+......+..-+++++-.+...++...+.++-.+. ..+.|..--.|.+....++.   ..+.......  |.    
T Consensus       252 -~d~~~~~~~L~~~v~~~iLa~~~~~~~~ll~~~~~~~-~~~~l~~~~~L~k~f~~~~L~~~~~~~~~~~~~L~~~~~~~  329 (445)
T 4b4t_P          252 -SDEAKWKPVLSHIVYFLVLSPYGNLQNDLIHKIQNDN-NLKKLESQESLVKLFTTNELMRWPIVQKTYEPVLNEDDLAF  329 (445)
T ss_dssp             -SCHHHHHHHHHHHHHHHHHSSCSSTTHHHHHSHHHHS-SCHHHHHHHHHHHHHHHCCSSSHHHHHHHTCSSTTTCCSSC
T ss_pred             -CCHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHhhcc-cccccHHHHHHHHHHHhchHhhhHHHHHHHHHHhcccchhh
Confidence             1122334455566666555555556666666654322 33555555667777777754   4444433211  11    


Q ss_pred             --ccHHHHHHHHHHHHHHHHHHhHHHccCCCCHHHHHHhhCCCCHHHHHHHHhh----cCCCceee--CCeEEEecCC
Q 024461          170 --ETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKE----EHPEWEMK--DGFVFFQKAK  239 (267)
Q Consensus       170 --~~~~~fm~~L~~tiR~eia~~iekAY~sl~l~~a~~lL~f~s~~e~~~f~~~----~~rgW~v~--~g~i~f~~~~  239 (267)
                        +....-...|..++++.-...+.+.|++|+++.++++|+++ +++++.++..    ..-.=++|  +|.|+|..++
T Consensus       330 ~~~~~~~~~~~L~~~v~ehnl~~i~k~Ys~I~l~~la~lL~l~-~~evE~~ls~mI~~g~i~akIDq~~giV~F~~~~  406 (445)
T 4b4t_P          330 GGEANKHHWEDLQKRVIEHNLRVISEYYSRITLLRLNELLDLT-ESQTETYISDLVNQGIIYAKVNRPAKIVNFEKPK  406 (445)
T ss_dssp             CCSCSSHHHHHHHHHHHHHHHHHHHHHEEEEEHHHHHHHHTSC-HHHHHHHHHHHHHHTSSCCEEETTTTEEEC----
T ss_pred             hcchhhHHHHHHHHHHHHHHHHHHHHHhceeeHHHHHHHhCcC-HHHHHHHHHHHHHCCCEEEEEcCCCCEEEECCCC
Confidence              11144567799999999999999999999999999999997 8999999842    11222566  7777887643

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.15  E-value=0.031  Score=52.77  Aligned_cols=201  Identities=10%  Similarity=0.045  Sum_probs=124.1

Q ss_pred             HhCCCCHHHHHHHHHHHHHHHhcCCCCCCCCCCChhhHHHHHHHHHHHHHHHHHHhhccChHHHHHHHhhhhhhhhhcCC
Q 024461           18 AMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGK   97 (267)
Q Consensus        18 ~~~~~~~~~~~~lL~~lKi~L~~~~~L~~~~~~~~~~~~~l~lar~vlEi~al~si~~~D~~~F~r~~~qLk~~Y~~~~~   97 (267)
                      ....+|+..+...+.+++....+.+        .+.    +.  -.+-..++++.+..+|+..=-+++-..-.-|.    
T Consensus       178 ~l~~~d~~~~~~~~~ka~~~~~~~~--------d~~----~~--~~lk~~~gl~~l~~r~f~~Aa~~f~e~~~t~~----  239 (429)
T 4b4t_R          178 GFFYNDQLYVKEKLEAVNSMIEKGG--------DWE----RR--NRYKTYYGIHCLAVRNFKEAAKLLVDSLATFT----  239 (429)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHHTTCC--------CTH----HH--HHHHHHHHHGGGGTSCHHHHHHHHHHHHHHSC----
T ss_pred             HHHhccHHHHHHHHHHHHHhhhcCC--------CHH----HH--HHHHHHHHHHHHHhChHHHHHHHHHHHhccCC----
Confidence            3446788888888888876544311        111    11  13456678888888887665554433322221    


Q ss_pred             CCCCCcchhhHHHHHHHHHHhcCCHHHHHHHHHhccH--hh-hcCchhhhhHHHHHHHHhcchHHHHHhh----hcCC--
Q 024461           98 RLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSS--TA-LENPCIKHAVELEQSFMEGAYNRVLSAK----QNVP--  168 (267)
Q Consensus        98 ~l~~S~~~~~llgL~LL~LLsqn~i~efh~~LE~l~~--~~-~~~~~I~~~i~leq~LmeG~Y~kv~~~~----~~~P--  168 (267)
                       ..+......+.-+..|.-+...+-.++..-+-.-|.  .. ..+|.+.....+=.++..++|..+|...    .+..  
T Consensus       240 -~~e~~~~~~~~~y~~l~al~~~~r~~l~~~v~~~~~~~~~l~~~p~~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~  318 (429)
T 4b4t_R          240 -SIELTSYESIATYASVTGLFTLERTDLKSKVIDSPELLSLISTTAALQSISSLTISLYASDYASYFPYLLETYANVLIP  318 (429)
T ss_dssp             -CSCHHHHHHHHHHHHHHHHHTTCHHHHHHSSSSSHHHHHGGGSHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHSTTTTT
T ss_pred             -ccchhhHHHHHHHHHHHHHhcCCHHHHHHHHhcCHHHHhhccCChhHHHHHHHHHHHHhccHHHHHHHHHHHHHhhhcc
Confidence             122233444444444444444444444432211111  11 2567888888888999999999998742    1211  


Q ss_pred             CccHHHHHHHHHHHHHHHHHHhHHHccCCCCHHHHHHhhCCCCHHHHHHHH----hhcCCCceee--CCeEEEecC
Q 024461          169 NETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYV----KEEHPEWEMK--DGFVFFQKA  238 (267)
Q Consensus       169 ~~~~~~fm~~L~~tiR~eia~~iekAY~sl~l~~a~~lL~f~s~~e~~~f~----~~~~rgW~v~--~g~i~f~~~  238 (267)
                      .+....-.+.|...||..+...+-+.|++|+++.+++.|+++ ++++++++    .+..-.=++|  +|.|++..+
T Consensus       319 d~~l~~h~~~l~~~ir~~~l~q~~~~Ys~I~l~~mA~~l~~s-~~~~E~~L~~lI~~g~l~akID~~~giv~~~~~  393 (429)
T 4b4t_R          319 CKYLNRHADFFVREMRRKVYAQLLESYKTLSLKSMASAFGVS-VAFLDNDLGKFIPNKQLNCVIDRVNGIVETNRP  393 (429)
T ss_dssp             CTTSTTTHHHHHHHHHHHHHHHHHHTCSEEEHHHHHHHHTSC-HHHHHHHHHHHHHHTSSCEEEETTTTEEEECC-
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHHHHHHcCCeEEEEcCCCCEEEECCC
Confidence            223344467789999999999999999999999999999997 66666555    3333345677  677777654

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.73  E-value=0.26  Score=43.93  Aligned_cols=203  Identities=10%  Similarity=0.110  Sum_probs=124.9

Q ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCCCCCCChhhHHHHHHHHHHHHHHHHHHhhccChHHHHHHHhhhhhhhhhcCCCCC
Q 024461           21 RKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLARDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLP  100 (267)
Q Consensus        21 ~~~~~~~~~lL~~lKi~L~~~~~L~~~~~~~~~~~~~l~lar~vlEi~al~si~~~D~~~F~r~~~qLk~~Y~~~~~~l~  100 (267)
                      .+|+.++...+.+....-..   .+.    ++      .+--.+++.+..+....+|...-.+|+.+.-..|... ....
T Consensus       188 ~~~~~~A~~~~~~al~~~~~---~~~----~~------~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~~~~~~~-~~~~  253 (434)
T 4b4t_Q          188 LRNLAKSKASLTAARTAANS---IYC----PT------QTVAELDLMSGILHCEDKDYKTAFSYFFESFESYHNL-TTHN  253 (434)
T ss_dssp             TTCHHHHHHHHHHHHHHHHH---SCC----CH------HHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHHHHHHT-TTSS
T ss_pred             hCcHHHHHHHHHHHHHHhhc---CCC----ch------HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhhhh-hhhh
Confidence            46777777777665443222   111    11      2234678888888889999888777777665555543 1111


Q ss_pred             CCcchhhHHHHHHHHHHhcCCHHHHHHHHHhccHhh-hcCchhhhhHHHHHHHHhcchHHHHHhhhc----C-CCccHHH
Q 024461          101 PSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTA-LENPCIKHAVELEQSFMEGAYNRVLSAKQN----V-PNETYGY  174 (267)
Q Consensus       101 ~S~~~~~llgL~LL~LLsqn~i~efh~~LE~l~~~~-~~~~~I~~~i~leq~LmeG~Y~kv~~~~~~----~-P~~~~~~  174 (267)
                      ........+.+.++.....+...+....+....... ..++.+..-..+......+++.........    . ..+....
T Consensus       254 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~  333 (434)
T 4b4t_Q          254 SYEKACQVLKYMLLSKIMLNLIDDVKNILNAKYTKETYQSRGIDAMKAVAEAYNNRSLLDFNTALKQYEKELMGDELTRS  333 (434)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHCSSSSTTCCCHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHTCSHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHhccchhHHHhHHHHHHHHHHhcchhhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHcccHHHHH
Confidence            222334455555555555555555555544432222 256777777778888888877666543221    1 1223455


Q ss_pred             HHHHHHHHHHHHHHHhHHHccCCCCHHHHHHhhCCCCHHHHHHHHhh----cCCCceee--CCeEEEecC
Q 024461          175 FMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKE----EHPEWEMK--DGFVFFQKA  238 (267)
Q Consensus       175 fm~~L~~tiR~eia~~iekAY~sl~l~~a~~lL~f~s~~e~~~f~~~----~~rgW~v~--~g~i~f~~~  238 (267)
                      .++.+..++|.....-+.+.|++|+++.++++|+++ +++++.++..    ..-.=+++  +|.+++...
T Consensus       334 ~~~~l~~~~~~~~l~~~~~~y~~i~l~~la~~l~~~-~~~~E~~l~~lI~~~~i~a~id~~~g~v~~~~~  402 (434)
T 4b4t_Q          334 HFNALYDTLLESNLCKIIEPFECVEISHISKIIGLD-TQQVEGKLSQMILDKIFYGVLDQGNGWLYVYET  402 (434)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSCSCEEHHHHHHHHTCC-HHHHHHHHHHHHHHTSSCCEEETTTTEEECC--
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHhCcC-HHHHHHHHHHHHhCCCcceecccccCeEeeCCC
Confidence            677889999999999999999999999999999997 7888776632    11122445  667766543

>1ufm_A COP9 complex subunit 4; helix-turn-helix, structural genomics, riken structural genomics/proteomics initiative, RSGI, signaling protein; NMR {Mus musculus} SCOP: a.4.5.47

Probab=93.25  E-value=0.25  Score=36.65  Aligned_cols=59  Identities=17%  Similarity=0.287  Sum_probs=43.5

Q ss_pred             HHHHHHHHHHHhHHHccCCCCHHHHHHhhCCCCHHHHHHHHhh----cCCCceee--CCeEEEecC
Q 024461          179 LAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKE----EHPEWEMK--DGFVFFQKA  238 (267)
Q Consensus       179 L~~tiR~eia~~iekAY~sl~l~~a~~lL~f~s~~e~~~f~~~----~~rgW~v~--~g~i~f~~~  238 (267)
                      |.+++.++-...+.+-|++|+++.++++|+++ ++++.+++..    ..-.=++|  +|.|+|..+
T Consensus        12 L~~~v~E~nl~~is~~Y~~Isl~~La~ll~ls-~~~vE~~ls~mI~~~~l~akIDq~~g~V~f~~~   76 (84)
T 1ufm_A           12 LDRAVIEHNLLSASKLYNNITFEELGALLEIP-AAKAEKIASQMITEGRMNGFIDQIDGIVHFETR   76 (84)
T ss_dssp             CCHHHHHHHHHHHHHSCSEEEHHHHHHHTTSC-HHHHHHHHHHHHHTTSSCEEEETTTTEEEECCS
T ss_pred             HHHHHHHHHHHHHHHhcCeeeHHHHHHHHCcC-HHHHHHHHHHHHhCCcEEEEEeCCCCEEEeCCc
Confidence            45566666667788899999999999999998 8888888742    22223555  677887653

>3t5x_A PCI domain-containing protein 2; PCI, mRNA nuclear export, transcription; 2.12A {Homo sapiens}

Probab=80.98  E-value=4.6  Score=34.19  Aligned_cols=71  Identities=15%  Similarity=0.095  Sum_probs=53.6

Q ss_pred             HHHHHHHHhcchHHHHHhhhcCCCccHHHHHHH----HHHHHHHHHHHhHHH------ccCCCCHHHHHHhhCCC-----
Q 024461          146 VELEQSFMEGAYNRVLSAKQNVPNETYGYFMDL----LAKTVRDEIAGCSEK------AYDYLSIKDAGQMLLFT-----  210 (267)
Q Consensus       146 i~leq~LmeG~Y~kv~~~~~~~P~~~~~~fm~~----L~~tiR~eia~~iek------AY~sl~l~~a~~lL~f~-----  210 (267)
                      ..|=+++-.||..++-....+-.    ..|++.    +++++|.-+....-|      .|+.||+++++.-|.++     
T Consensus        84 ~~L~~Avr~Gdl~~f~~~l~~~~----~~f~~~~~~lll~rlr~~v~r~l~rkv~~~~~~~rI~l~~i~~~l~~~~~~~~  159 (203)
T 3t5x_A           84 AEVTRAVSEGNLLLLHEALAKHE----AFFIRCGIFLILEKLKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQVEDV  159 (203)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHTH----HHHHHHTCHHHHHTHHHHHHHHHHHHHHHHHCCSEEEHHHHHHHHHHTTCTTC
T ss_pred             HHHHHHHHhCCHHHHHHHHHHhH----HHHHHCChHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCCC
Confidence            36779999999998877655411    345543    788888877766655      79999999999999774     


Q ss_pred             CHHHHHHHHh
Q 024461          211 SDQELLEYVK  220 (267)
Q Consensus       211 s~~e~~~f~~  220 (267)
                      +++|++..+.
T Consensus       160 ~~~evE~ila  169 (203)
T 3t5x_A          160 DIDEVQCILA  169 (203)
T ss_dssp             CHHHHHHHHH
T ss_pred             CHHHHHHHHH
Confidence            6888887763

>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha solenoid, regulatory PART LID, hydrolase, protein binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A

Probab=80.86  E-value=8  Score=36.24  Aligned_cols=141  Identities=12%  Similarity=0.100  Sum_probs=100.1

Q ss_pred             HHHHHHHHHHHHhhccChHHHHHHHhhh-hhhhhhcCCCCCCCcchhhHHH-HHHHHHHhcCCHHHHHHHHHhccHhhhc
Q 024461           61 ARDIYEHAVLLSVKVEDQDAFERDFFQL-KPYYTDAGKRLPPSPNEYMILG-LNLLRLLVQNRIAEFHTELELLSSTALE  138 (267)
Q Consensus        61 ar~vlEi~al~si~~~D~~~F~r~~~qL-k~~Y~~~~~~l~~S~~~~~llg-L~LL~LLsqn~i~efh~~LE~l~~~~~~  138 (267)
                      +.+++-++++.++..+|..++....++= ...|. .          .++-. ..|+.....+++.+|-..|+...+....
T Consensus       219 ~~~~lkYlvL~aLl~~~r~el~~~l~~~~~~~~~-~----------pei~~l~~L~~a~~~~dl~~f~~iL~~~~~~l~~  287 (394)
T 3txn_A          219 ALTSLKYMLLCKIMLGQSDDVNQLVSGKLAITYS-G----------RDIDAMKSVAEASHKRSLADFQAALKEYKKELAE  287 (394)
T ss_dssp             HHHHHHHHHHHHHHTTCGGGHHHHHHSHHHHTTC-S----------HHHHHHHHHHHHHHTTCHHHHHHHHHHSTTTTTT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHhccccccccC-C----------ccHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhc
Confidence            4678888999999999998888766543 22242 1          12323 3456678899999999999998777779


Q ss_pred             Cchhh-hhHHHHHHHHhcchHHHHHhhhcCCCccHHHHHHHHHHHHHHHHHHhHHHccCCCCHHHHHHhhCCCCH
Q 024461          139 NPCIK-HAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSD  212 (267)
Q Consensus       139 ~~~I~-~~i~leq~LmeG~Y~kv~~~~~~~P~~~~~~fm~~L~~tiR~eia~~iekAY~sl~l~~a~~lL~f~s~  212 (267)
                      ||+++ |.-.|.+.+.+.++-+++..+..+.-+.-+-....=.+-+-..++.+|...-=.=.++....++.+..+
T Consensus       288 D~~l~~h~~~L~~~Ir~~~L~~i~~pYsrIsl~~iA~~l~ls~~evE~~L~~lI~dg~I~a~IDq~~giv~~~~~  362 (394)
T 3txn_A          288 DVIVQAHLGTLYDTMLEQNLCRIIEPYSRVQVAHVAESIQLPMPQVEKKLSQMILDKKFSGILDQGEGVLIVFEE  362 (394)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHHTTCSEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSCEEEETTTTEEEECCC
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHhHhhceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCeeEEEcCCCCEEEECCC
Confidence            99975 467899999999999999887766532222222222667777888888765545556777777777543

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	267
d1rz4a1	85	Eukaryotic translation initiation factor 3 subunit	98.13
d1ufma_	84	COP9 signalosome complex subunit 4, GSN4 {Mouse (M	95.89

>d1rz4a1 a.4.5.53 (A:132-216) Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain
domain: Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.13  E-value=4.8e-06  Score=61.21  Aligned_cols=59  Identities=19%  Similarity=0.201  Sum_probs=50.8

Q ss_pred             HHHHHHHHHHHhHHHccCCCCHHHHHHhhCCCCHHHHHHHHhhcCCCceeeCCeEEEecCC
Q 024461          179 LAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAK  239 (267)
Q Consensus       179 L~~tiR~eia~~iekAY~sl~l~~a~~lL~f~s~~e~~~f~~~~~rgW~v~~g~i~f~~~~  239 (267)
                      |-+.||.-|+..+.-+|.+|+.+.++++|+..++.++.+|++  .-||++++|..+|+..+
T Consensus         3 FedsIR~~i~~vv~iTyq~I~~~~L~e~LG~~~d~~L~~~i~--~~gW~~~~~g~v~v~nq   61 (85)
T d1rz4a1           3 FEDSVRKFICHVVGITYQHIDRWLLAEMLGDLSDSQLKVWMS--KYGWSADESGQIFICSQ   61 (85)
T ss_dssp             HHHHHHHHHHHHHHHHCSEECHHHHHHHTTSCCHHHHHHHHH--HHTCEECC--CEECCCH
T ss_pred             HHHHHHHHHHhheeeeeeEEcHHHHHHHhCCCCHHHHHHHHH--HcCCEEcCCCEEEecCh
Confidence            578999999999999999999999999999999999999995  36999996665576653

>d1ufma_ a.4.5.47 (A:) COP9 signalosome complex subunit 4, GSN4 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PCI domain (PINT motif)
domain: COP9 signalosome complex subunit 4, GSN4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.89  E-value=0.01  Score=42.56  Aligned_cols=60  Identities=17%  Similarity=0.289  Sum_probs=47.0

Q ss_pred             HHHHHHHHHHHhHHHccCCCCHHHHHHhhCCCCHHHHHHHHhh----cCCCceee--CCeEEEecCC
Q 024461          179 LAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKE----EHPEWEMK--DGFVFFQKAK  239 (267)
Q Consensus       179 L~~tiR~eia~~iekAY~sl~l~~a~~lL~f~s~~e~~~f~~~----~~rgW~v~--~g~i~f~~~~  239 (267)
                      |.+.|++.-...+.+.|++|++++++++|+++ +++++.++..    ..-.=++|  +|.|+|..++
T Consensus        12 L~~~i~Ehni~~is~~Y~~Isl~~la~~l~l~-~~evE~~l~~mI~~~~i~akIDq~~g~V~F~~~e   77 (84)
T d1ufma_          12 LDRAVIEHNLLSASKLYNNITFEELGALLEIP-AAKAEKIASQMITEGRMNGFIDQIDGIVHFETRE   77 (84)
T ss_dssp             CCHHHHHHHHHHHHHSCSEEEHHHHHHHTTSC-HHHHHHHHHHHHHTTSSCEEEETTTTEEEECCSS
T ss_pred             HHHHHHHHHHHHHHHhhceeeHHHHHHHHCCC-HHHHHHHHHHHHhcCeEEEEEeCCCCEEEECCCC
Confidence            45677777778889999999999999999997 8888888742    23344566  7888888764