Citrus Sinensis ID: 028424

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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-------21
Protein Sequence
MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKDSAPCKEIPSLQLINQTLSYARELERIV
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHcccHHHHHHHHHHccHHHHcccccHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHccccHHHHHHHHHHHcccccccccEEEEcccccccccccccHHHHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHcccHccccccHHHHHHHHHHHHHHHHHccHHHHHHHHHHccHHHHccccccccHHHHHHHHHccHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHccccHHHHHHHHHHccccEEEcccEEEEcccccccccccccHHHHHHHHHHHHHHHHHHc
Coil and Loop (DISEMBL)
MVSGDIYEHAVLLSVKVEDQDAFERDFfqlkpyytdagkrlppspneyMILGLNLLRLLVQNRIAEFHTELELLsstalenpciKHAVELEQSFMEGAYNRVLSakqnvpnetyGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKeehpewemkdgFVFFqkakdsapckeipslqlINQTLSYARELERIV
Flexible Loop (DISEMBL)
mvsgdiyeHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKDSAPckeipslqlinqtlsyareleriv
Low Complexity Region (SEG)
MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIlglnllrllVQNRIAEFHtelellsstaleNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKDSAPCKEIPSLQLINQTLSYARELERIV
Disordered region (IsUnstruct)
*****IYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKDSAPCKEIPSLQLINQTLSY********
Disordered Region (DISOPRED)
MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQ**************QLINQTLSYARELERIV
Disordered Region (DISEMBL)
MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKDSAPCKEIPSLQLINQTLSYARELERIV
Disordered Region (DISPRO)
MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKDSAPCKEIPSLQLINQTLSYARELERIV
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKDSAPCKEIPSLQLINQTLSYARELERIV
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	209	2.2.26 [Sep-21-2011]
Q9SGW3	267	26S proteasome non-ATPase	yes	no	0.995	0.779	0.831	6e-94
Q9FHY0	233	26S proteasome non-ATPase	no	no	0.846	0.759	0.774	2e-79
P02889	263	Probable 26S proteasome n	yes	no	0.980	0.779	0.435	2e-46
Q9CX56	353	26S proteasome non-ATPase	yes	no	0.971	0.575	0.441	2e-34
Q5RE15	289	26S proteasome non-ATPase	no	no	0.990	0.716	0.431	3e-34
Q3SYT7	287	26S proteasome non-ATPase	yes	no	0.980	0.714	0.436	3e-34
P48556	350	26S proteasome non-ATPase	yes	no	0.990	0.591	0.431	5e-34
P50524	270	26S proteasome regulatory	yes	no	0.956	0.740	0.339	2e-28
Q23449	250	26S proteasome non-ATPase	yes	no	0.966	0.808	0.358	3e-28
P32496	274	26S proteasome regulatory	yes	no	0.980	0.748	0.295	2e-14

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

 Score =  343 bits (879), Expect = 6e-94,   Method: Compositional matrix adjust.
 Identities = 173/208 (83%), Positives = 189/208 (90%)

Query: 2   VSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQ 61
           ++ DIYEHAV+LSVK EDQDAFERDFFQLKPYY DA  R+P SP E +ILGLNLLRLLVQ
Sbjct: 60  IARDIYEHAVVLSVKTEDQDAFERDFFQLKPYYVDARNRIPQSPQENLILGLNLLRLLVQ 119

Query: 62  NRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLL 121
           NRIAEFHTELELLSS  LE+PCIKHAVELEQSFMEGAYNRVLSA+Q  P+ TY YFMDLL
Sbjct: 120 NRIAEFHTELELLSSATLEDPCIKHAVELEQSFMEGAYNRVLSARQTAPDATYVYFMDLL 179

Query: 122 AKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAK 181
           AKT+RDEIAGCSEKAYDY+SI DA QMLLF+SDQELL YV +EHPEWE+K+GFV FQKAK
Sbjct: 180 AKTIRDEIAGCSEKAYDYVSISDARQMLLFSSDQELLTYVTDEHPEWEVKEGFVVFQKAK 239

Query: 182 DSAPCKEIPSLQLINQTLSYARELERIV 209
           ++APCKEIPSLQLINQTLSYARELERIV
Sbjct: 240 ETAPCKEIPSLQLINQTLSYARELERIV 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 =  295 bits (754), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 137/177 (77%), Positives = 155/177 (87%)

Query: 33  YYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQ 92
           ++     R+PPSP E +I+GLNLLRLLVQNRIAEFHTEL LLSS  LENPCIKHAVELEQ
Sbjct: 57  FFLCTRNRIPPSPQENLIMGLNLLRLLVQNRIAEFHTELGLLSSATLENPCIKHAVELEQ 116

Query: 93  SFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFT 152
           SFMEGAYNRVLSA+Q  P+ETY YFMDLLAKT+RDEIAGCSEKAYD+LSI +  +MLLF+
Sbjct: 117 SFMEGAYNRVLSARQTAPDETYVYFMDLLAKTIRDEIAGCSEKAYDHLSISEGCKMLLFS 176

Query: 153 SDQELLEYVKEEHPEWEMKDGFVFFQKAKDSAPCKEIPSLQLINQTLSYARELERIV 209
           SDQ+LL YV EEHPEWE+KDG V FQK +++APCKEIPSLQLINQTLSY RELERI+
Sbjct: 177 SDQQLLTYVNEEHPEWEVKDGLVVFQKTRETAPCKEIPSLQLINQTLSYTRELERIL 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 =  185 bits (470), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 91/209 (43%), Positives = 144/209 (68%), Gaps = 4/209 (1%)

Query: 1   MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLV 60
           +++ +I E   L S+K++D D+FER F QLK YY D    + PS  EY I+GLNL+RLL 
Sbjct: 59  VLAREILELISLYSIKIKDIDSFERTFNQLKTYYYDYKSIIAPSTLEYQIIGLNLMRLLA 118

Query: 61  QNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDL 120
           +++ +EFH+E+EL+    L+N  IK  + +E+S  EG+YN+++ ++  VP+E Y  F+D+
Sbjct: 119 KHKTSEFHSEIELIEFNNLDNSFIKFPLLVEKSITEGSYNKIIQSRSGVPSEYYQVFLDI 178

Query: 121 LAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKA 180
           LA +++++IA CSEK++  LS+KDA ++LLF  + +  +Y+KE +  W+++   + F   
Sbjct: 179 LADSIKEDIANCSEKSFKTLSLKDAEKVLLFNDNNQFQQYIKERN--WKVQGDVIQF--G 234

Query: 181 KDSAPCKEIPSLQLINQTLSYARELERIV 209
            +     EIPSLQLI+QTL YA+ELERIV
Sbjct: 235 NNDNQTVEIPSLQLIHQTLHYAKELERIV 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|Q9CX56|PSMD8_MOUSE 26S proteasome non-ATPase regulatory subunit 8 OS=Mus musculus GN=Psmd8 PE=1 SV=2

 Score =  145 bits (366), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 95/215 (44%), Positives = 136/215 (63%), Gaps = 12/215 (5%)

Query: 1   MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLV 60
           +++ DI E     S+  +D  +FER   QLK YY D  ++LP S   + +LGLNLL LL 
Sbjct: 145 ILARDILEIGAQWSILCKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLS 204

Query: 61  QNRIAEFHTELELLSSTALE-NPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMD 119
           QNR+AEFHTELE L +  ++ N  IKH V LEQ  MEG+YN+V  AK N+P E+Y +F+D
Sbjct: 205 QNRVAEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFID 264

Query: 120 LLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK-DGFVFF- 177
           +L  T+RDEIAGC EKAY+ +   +A ++L F++ +++ +Y K+    W +  + +  F 
Sbjct: 265 ILLDTIRDEIAGCIEKAYEKILFAEATRILFFSTPKKMTDYAKKRG--WVLGPNNYYSFA 322

Query: 178 ---QKAKDSAPCKEIPSLQLINQTLSYARELERIV 209
              QK +DS     IPS +L  Q + YAR+LE IV
Sbjct: 323 SQQQKPEDST----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|Q5RE15|PSMD8_PONAB 26S proteasome non-ATPase regulatory subunit 8 (Fragment) OS=Pongo abelii GN=PSMD8 PE=2 SV=2

 Score =  145 bits (365), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 91/211 (43%), Positives = 131/211 (62%), Gaps = 4/211 (1%)

Query: 1   MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLV 60
           +++ DI E     S+  +D  +FER   QLK YY D  ++LP S   + +LGLNLL LL 
Sbjct: 81  ILARDILEIGAQWSILRKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLS 140

Query: 61  QNRIAEFHTELELLSSTALE-NPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMD 119
           QNR+AEFHTELE L +  ++ N  IKH V LEQ  MEG+YN+V  AK N+P E+Y +F+D
Sbjct: 141 QNRVAEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYAFFID 200

Query: 120 LLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK-DGFVFFQ 178
           +L  T+RDEIAGC EKAY+ +   +A ++L F + +++ +Y K+    W +  + +  F 
Sbjct: 201 ILLDTIRDEIAGCIEKAYEKILFTEATRILFFNTPKKMTDYAKKRG--WVLGPNNYYSFA 258

Query: 179 KAKDSAPCKEIPSLQLINQTLSYARELERIV 209
             +       IPS +L  Q + YAR+LE IV
Sbjct: 259 SQQQKPEDTTIPSTELAKQVIEYARQLEMIV 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 =  144 bits (364), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 93/213 (43%), Positives = 134/213 (62%), Gaps = 8/213 (3%)

Query: 1   MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLV 60
           +++ DI E     S+  +D  +FER   QLK YY D  ++LP S   + +LGLNLL LL 
Sbjct: 79  ILARDIQEIGAQWSILRKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLS 138

Query: 61  QNRIAEFHTELELLSSTALE-NPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMD 119
           QNR+AEFHTELE L +  ++ N  IKH V LEQ  MEG+YN+V  AK N+P E+Y +F+D
Sbjct: 139 QNRVAEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFID 198

Query: 120 LLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFF-- 177
           +L  T+RDEIAGC EKAY+ +   +A ++L F + +++ +Y K+      + + + F   
Sbjct: 199 ILLDTIRDEIAGCIEKAYEKILFTEATRILFFNTPKKMTDYAKKRGWVLGINNYYSFASQ 258

Query: 178 -QKAKDSAPCKEIPSLQLINQTLSYARELERIV 209
            QK +D+     IPS +L  Q + YAR+LE IV
Sbjct: 259 QQKPEDTT----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|P48556|PSMD8_HUMAN 26S proteasome non-ATPase regulatory subunit 8 OS=Homo sapiens GN=PSMD8 PE=1 SV=2

 Score =  144 bits (362), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 91/211 (43%), Positives = 131/211 (62%), Gaps = 4/211 (1%)

Query: 1   MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLV 60
           +++ DI E     S+  +D  +FER   QLK YY D  ++LP S   + +LGLNLL LL 
Sbjct: 142 ILARDILEIGAQWSILRKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLS 201

Query: 61  QNRIAEFHTELELLSSTALE-NPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMD 119
           QNR+AEFHTELE L +  ++ N  IKH V LEQ  MEG+YN+V  AK N+P E+Y +F+D
Sbjct: 202 QNRVAEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFID 261

Query: 120 LLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK-DGFVFFQ 178
           +L  T+RDEIAGC EKAY+ +   +A ++L F + +++ +Y K+    W +  + +  F 
Sbjct: 262 ILLDTIRDEIAGCIEKAYEKILFTEATRILFFNTPKKMTDYAKKRG--WVLGPNNYYSFA 319

Query: 179 KAKDSAPCKEIPSLQLINQTLSYARELERIV 209
             +       IPS +L  Q + YAR+LE IV
Sbjct: 320 SQQQKPEDTTIPSTELAKQVIEYARQLEMIV 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 =  125 bits (314), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 76/224 (33%), Positives = 125/224 (55%), Gaps = 24/224 (10%)

Query: 5   DIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRI 64
           +++E+ VL+S++  D ++F R   Q+ P+Y D+   L PS    ++ GLNLL LL +NRI
Sbjct: 52  NVFEYGVLVSIQTCDIESFARYASQVIPFYHDS---LVPSSRMGLVTGLNLLYLLSENRI 108

Query: 65  AEFHTELELLSSTAL--ENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLA 122
           AEFHT LE +   +L   +P ++  + LEQ+ MEGA+++V S  ++     + YFM ++ 
Sbjct: 109 AEFHTALESVPDKSLFERDPYVEWVISLEQNVMEGAFDKVASMIRSCNFPEFSYFMKIVM 168

Query: 123 KTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAKD 182
             VR+EIA C+EK Y  + + +A  +L   + +E  E + EE   W+++DG ++F K  +
Sbjct: 169 SMVRNEIATCAEKVYSEIPLSNATSLLYLENTKE-TEKLAEERG-WDIRDGVIYFPKEAN 226

Query: 183 S-----------------APCKEIPSLQLINQTLSYARELERIV 209
           +                  P     ++  I Q LSY  ELE+IV
Sbjct: 227 ALETEDGMLIDEEDELELPPTASKHTISSIRQLLSYTSELEQIV 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 (312), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 76/212 (35%), Positives = 128/212 (60%), Gaps = 10/212 (4%)

Query: 1   MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLV 60
           + S D+YE +VLL++   D + F+    Q+  YYT A +    S N++++ GL+L+ LL 
Sbjct: 46  LASKDLYEISVLLAILKHDFETFDDYINQMHTYYTMAPEN---SENKHLMTGLHLMFLLA 102

Query: 61  QNRIAEFHTELELL-SSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMD 119
            NR+++FH  LE +       N  I   V +EQS MEGAYN+V+  ++N+P+  Y  F+ 
Sbjct: 103 ANRLSDFHMLLEQIPQKEQTSNAYISTPVRIEQSLMEGAYNKVVLTEKNIPSPFYTIFIR 162

Query: 120 LLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDG--FVFF 177
           ++  T+R EIA   EK++  L+ KDA  MLLF +D+++ ++ +E   +W + DG  +VF 
Sbjct: 163 IMLDTIRREIATSIEKSFKVLTAKDATVMLLFDNDEQMKKFGQER--KWHL-DGERYVFE 219

Query: 178 QKAKDSAPCKEIPSLQLINQTLSYARELERIV 209
            +     P   + ++++  QTL YA++LE+IV
Sbjct: 220 IEVAQEKPVN-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 = 79.3 bits (194), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 66/223 (29%), Positives = 115/223 (51%), Gaps = 18/223 (8%)

Query: 1   MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLV 60
           M++  I E   L S++  + D+FE  F QLKPYY     +L  S  +  ++ L LL LL 
Sbjct: 56  MITKRILEVGALASIQTFNFDSFENYFNQLKPYYFSNNHKLSESDKKSKLISLYLLNLLS 115

Query: 61  QNRIAEFHTELELLS---STALENPCIKHAVELEQSFMEGAYNRVL----SAKQNVPNET 113
           QN   +FH+EL+ L        ++  + + ++L++  MEG+Y +      S  QN+    
Sbjct: 116 QNNTTKFHSELQYLDKHIKNLEDDSLLSYPIKLDRWLMEGSYQKAWDLLQSGSQNIS--E 173

Query: 114 YGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDG 173
           +  F D+L   +RDEIA  +E +YD+L + +   +L F +++E  ++  E +  W + + 
Sbjct: 174 FDSFTDILKSAIRDEIAKNTELSYDFLPLSNIKALLFFNNEKETEKFALERN--WPIVNS 231

Query: 174 FVFF-----QKA--KDSAPCKEIPSLQLINQTLSYARELERIV 209
            V+F     +KA  +D    +E     +I + + YA  +E IV
Sbjct: 232 KVYFNNQSKEKADYEDEMMHEEDQKTNIIEKAMDYAISIENIV 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	209
357437525	267	26S proteasome non-ATPase regulatory sub	0.995	0.779	0.889	4e-99
359807666	267	uncharacterized protein LOC100785835 [Gl	0.995	0.779	0.894	6e-99
356524925	267	PREDICTED: 26S proteasome non-ATPase reg	0.995	0.779	0.889	8e-99
388511026	267	unknown [Medicago truncatula]	0.995	0.779	0.884	2e-98
225426245	267	PREDICTED: 26S proteasome non-ATPase reg	0.995	0.779	0.875	1e-97
449517868	267	PREDICTED: 26S proteasome non-ATPase reg	0.995	0.779	0.879	5e-97
449462515	267	PREDICTED: 26S proteasome non-ATPase reg	0.995	0.779	0.875	3e-96
255646695	267	unknown [Glycine max]	0.995	0.779	0.875	4e-96
224072240	267	predicted protein [Populus trichocarpa]	0.995	0.779	0.865	4e-95
224058123	267	predicted protein [Populus trichocarpa]	1.0	0.782	0.861	2e-94

>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 =  366 bits (939), Expect = 4e-99,   Method: Compositional matrix adjust.
 Identities = 185/208 (88%), Positives = 196/208 (94%)

Query: 2   VSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQ 61
           ++ DIYEHAV+LSVK+EDQDAFERDFFQLKPYYTDA  RLP SP EY ILGLNLLRLLVQ
Sbjct: 60  IARDIYEHAVVLSVKIEDQDAFERDFFQLKPYYTDARNRLPQSPQEYPILGLNLLRLLVQ 119

Query: 62  NRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLL 121
           NRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSA+Q VP+ETY YFMDLL
Sbjct: 120 NRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSARQTVPHETYVYFMDLL 179

Query: 122 AKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAK 181
           AKT+RDEIAGCSEKAYDYLSI DA QMLLFT DQELLEY+KEEHPEWE+K+G V+FQKAK
Sbjct: 180 AKTIRDEIAGCSEKAYDYLSINDAKQMLLFTKDQELLEYIKEEHPEWEIKNGSVYFQKAK 239

Query: 182 DSAPCKEIPSLQLINQTLSYARELERIV 209
           DSAPCKEIPSLQLINQTLSYARELERIV
Sbjct: 240 DSAPCKEIPSLQLINQTLSYARELERIV 267

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  365 bits (937), Expect = 6e-99,   Method: Compositional matrix adjust.
 Identities = 186/208 (89%), Positives = 197/208 (94%)

Query: 2   VSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQ 61
           ++ DIYEHAV+LSVK EDQDAFERDFFQLKPYYTDA  RLPPSP EY ILGLNLLRLLVQ
Sbjct: 60  IARDIYEHAVVLSVKNEDQDAFERDFFQLKPYYTDACNRLPPSPQEYPILGLNLLRLLVQ 119

Query: 62  NRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLL 121
           NRIAEFHTELELLSS ALENPCIKHAVELEQSFMEGAYNRVLSA+Q VP++TY YFMDLL
Sbjct: 120 NRIAEFHTELELLSSAALENPCIKHAVELEQSFMEGAYNRVLSARQTVPHDTYVYFMDLL 179

Query: 122 AKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAK 181
           AKTVRDEIAGCSEKAYDYLSIKDA QMLLF+SDQELLEY+KEEHPEWE+K+G VFFQKAK
Sbjct: 180 AKTVRDEIAGCSEKAYDYLSIKDAKQMLLFSSDQELLEYIKEEHPEWEIKNGSVFFQKAK 239

Query: 182 DSAPCKEIPSLQLINQTLSYARELERIV 209
           +SAPCKEIPSLQLINQTLSYARELERIV
Sbjct: 240 ESAPCKEIPSLQLINQTLSYARELERIV 267

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  365 bits (936), Expect = 8e-99,   Method: Compositional matrix adjust.
 Identities = 185/208 (88%), Positives = 197/208 (94%)

Query: 2   VSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQ 61
           ++ DIYEHAV+LSVK+EDQDAFERDFFQLKPYYTDA  RLPPSP EY ILGLNLLRLLVQ
Sbjct: 60  IARDIYEHAVVLSVKIEDQDAFERDFFQLKPYYTDACNRLPPSPQEYPILGLNLLRLLVQ 119

Query: 62  NRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLL 121
           NRIAEFHTELELLSS ALENPCIKHAVELEQSFMEGAYNRVLSA+Q VP++TY YFMDLL
Sbjct: 120 NRIAEFHTELELLSSAALENPCIKHAVELEQSFMEGAYNRVLSARQTVPHDTYVYFMDLL 179

Query: 122 AKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAK 181
           AKTVRDEIAGCSEKAYDYLSIKDA QMLLF+SDQELLEY+KEEHPEWE+K+  VFFQKAK
Sbjct: 180 AKTVRDEIAGCSEKAYDYLSIKDAKQMLLFSSDQELLEYIKEEHPEWEIKNDSVFFQKAK 239

Query: 182 DSAPCKEIPSLQLINQTLSYARELERIV 209
           +SAPCKEIPSLQLINQTLSYARELERIV
Sbjct: 240 ESAPCKEIPSLQLINQTLSYARELERIV 267

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  363 bits (932), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 184/208 (88%), Positives = 195/208 (93%)

Query: 2   VSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQ 61
           ++ DIYEHAV+LSVK+EDQDAFERDFFQLKPYYTDA  RLP SP EY ILGLNLLRLLVQ
Sbjct: 60  IARDIYEHAVVLSVKIEDQDAFERDFFQLKPYYTDARNRLPQSPQEYPILGLNLLRLLVQ 119

Query: 62  NRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLL 121
           NRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSA+Q VP+ETY YFMDLL
Sbjct: 120 NRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSARQTVPHETYVYFMDLL 179

Query: 122 AKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAK 181
           AKT+RDEIA CSEKAYDYLSI DA QMLLFT DQELLEY+KEEHPEWE+K+G V+FQKAK
Sbjct: 180 AKTIRDEIARCSEKAYDYLSINDAKQMLLFTKDQELLEYIKEEHPEWEIKNGSVYFQKAK 239

Query: 182 DSAPCKEIPSLQLINQTLSYARELERIV 209
           DSAPCKEIPSLQLINQTLSYARELERIV
Sbjct: 240 DSAPCKEIPSLQLINQTLSYARELERIV 267

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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 =  361 bits (926), Expect = 1e-97,   Method: Compositional matrix adjust.
 Identities = 182/208 (87%), Positives = 194/208 (93%)

Query: 2   VSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQ 61
           ++ DIYEHAV+LSVK EDQDAFERDFFQLKPYYTD G RLPPSP EY ILGLNLLRLLVQ
Sbjct: 60  IARDIYEHAVVLSVKTEDQDAFERDFFQLKPYYTDTGGRLPPSPQEYPILGLNLLRLLVQ 119

Query: 62  NRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLL 121
           NRIAEFHTELELLS+TALEN CIKHAVELEQSFMEGAYNRVLSA+Q VP+ETY YFMDLL
Sbjct: 120 NRIAEFHTELELLSATALENACIKHAVELEQSFMEGAYNRVLSARQTVPHETYVYFMDLL 179

Query: 122 AKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAK 181
           AKTVRDEIAGCSEKAYDYLSI DA  MLLF+SDQEL EY+KEEHPEWE+K+G VFFQ+AK
Sbjct: 180 AKTVRDEIAGCSEKAYDYLSINDARHMLLFSSDQELFEYIKEEHPEWEIKNGHVFFQRAK 239

Query: 182 DSAPCKEIPSLQLINQTLSYARELERIV 209
           +SAPCKEIPSLQLINQTLSYARELERIV
Sbjct: 240 ESAPCKEIPSLQLINQTLSYARELERIV 267

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  359 bits (921), Expect = 5e-97,   Method: Compositional matrix adjust.
 Identities = 183/208 (87%), Positives = 195/208 (93%)

Query: 2   VSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQ 61
           ++ +IYEHAVLLSVKVEDQ AFERDFFQLKPYYTDA  RLPPSP EY ILGLNLLRLLVQ
Sbjct: 60  IARNIYEHAVLLSVKVEDQGAFERDFFQLKPYYTDAHNRLPPSPQEYPILGLNLLRLLVQ 119

Query: 62  NRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLL 121
           NRIAEFHTELELLS +ALENPCIKHAVELEQSFMEGAYNRVLSA+Q VP+ETYGYFMDLL
Sbjct: 120 NRIAEFHTELELLSPSALENPCIKHAVELEQSFMEGAYNRVLSARQTVPHETYGYFMDLL 179

Query: 122 AKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAK 181
           AKTVRDEIAGCSEKAYDYLSI DA QMLLF+SDQELL+YVKEEHPEWE+ +G V+FQKAK
Sbjct: 180 AKTVRDEIAGCSEKAYDYLSINDACQMLLFSSDQELLDYVKEEHPEWEVTNGNVYFQKAK 239

Query: 182 DSAPCKEIPSLQLINQTLSYARELERIV 209
           +S PCKEIPSLQLINQTLSYARELERIV
Sbjct: 240 ESGPCKEIPSLQLINQTLSYARELERIV 267

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  356 bits (914), Expect = 3e-96,   Method: Compositional matrix adjust.
 Identities = 182/208 (87%), Positives = 194/208 (93%)

Query: 2   VSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQ 61
           ++ +IYEHAVLLSVKVEDQ AFERDFFQLKPYY DA  RLPPSP EY ILGLNLLRLLVQ
Sbjct: 60  IARNIYEHAVLLSVKVEDQGAFERDFFQLKPYYIDARNRLPPSPQEYPILGLNLLRLLVQ 119

Query: 62  NRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLL 121
           NRIAEFHTELELLS +ALENPCIKHAVELEQSFMEGAYNRVLSA+Q VP+ETYGYFMDLL
Sbjct: 120 NRIAEFHTELELLSPSALENPCIKHAVELEQSFMEGAYNRVLSARQTVPHETYGYFMDLL 179

Query: 122 AKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAK 181
           AKTVRDEIAGCSEKAYDYLSI DA QMLLF+SDQELL+YVKEEHPEWE+ +G V+FQKAK
Sbjct: 180 AKTVRDEIAGCSEKAYDYLSINDACQMLLFSSDQELLDYVKEEHPEWEVTNGNVYFQKAK 239

Query: 182 DSAPCKEIPSLQLINQTLSYARELERIV 209
           +S PCKEIPSLQLINQTLSYARELERIV
Sbjct: 240 ESGPCKEIPSLQLINQTLSYARELERIV 267

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  356 bits (913), Expect = 4e-96,   Method: Compositional matrix adjust.
 Identities = 182/208 (87%), Positives = 194/208 (93%)

Query: 2   VSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQ 61
           ++ DIYEHAV+LSVK+EDQDAFERDFFQLKPYYTDA  RLPPSP EY ILGLNLLRLLVQ
Sbjct: 60  IARDIYEHAVVLSVKIEDQDAFERDFFQLKPYYTDACNRLPPSPQEYPILGLNLLRLLVQ 119

Query: 62  NRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLL 121
           NRIAEFHTELELLSS ALENPCIKHAVELEQSFMEGAYNRVLSA+Q VP++TY YFMDLL
Sbjct: 120 NRIAEFHTELELLSSAALENPCIKHAVELEQSFMEGAYNRVLSARQTVPHDTYVYFMDLL 179

Query: 122 AKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAK 181
           AKTVRDEIAGCSEKAYDYLSIKDA QMLLF+SDQELLEY+KEEHPEWE+K+  VFFQKAK
Sbjct: 180 AKTVRDEIAGCSEKAYDYLSIKDAKQMLLFSSDQELLEYIKEEHPEWEIKNDSVFFQKAK 239

Query: 182 DSAPCKEIPSLQLINQTLSYARELERIV 209
           + APCKEIP LQLINQTLSYAR LERIV
Sbjct: 240 EFAPCKEIPFLQLINQTLSYARGLERIV 267

Source: Glycine max

Species: Glycine max

Genus: Glycine

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 =  352 bits (904), Expect = 4e-95,   Method: Compositional matrix adjust.
 Identities = 180/208 (86%), Positives = 192/208 (92%)

Query: 2   VSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQ 61
           ++ D++EHAVLLSVK+ DQ+AFERDFFQLKPYYTDA   LP SP EYMILGLNLLRLLVQ
Sbjct: 60  IARDVFEHAVLLSVKIGDQEAFERDFFQLKPYYTDASSCLPQSPQEYMILGLNLLRLLVQ 119

Query: 62  NRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLL 121
           NRIAEFHTELELLS TALENPCIKHAVELEQSFMEGAYNRVLSAKQNVP +TY YFMDLL
Sbjct: 120 NRIAEFHTELELLSPTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPYKTYDYFMDLL 179

Query: 122 AKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAK 181
           AKTVRDEIAGCSEKAYDYLSI DA QMLLF S+ ELLEY+KEEHPEWE+K+G V FQKAK
Sbjct: 180 AKTVRDEIAGCSEKAYDYLSISDARQMLLFPSENELLEYIKEEHPEWEIKNGSVVFQKAK 239

Query: 182 DSAPCKEIPSLQLINQTLSYARELERIV 209
           +SAPCKEIPSLQLINQTLSYARELERIV
Sbjct: 240 ESAPCKEIPSLQLINQTLSYARELERIV 267

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  350 bits (899), Expect = 2e-94,   Method: Compositional matrix adjust.
 Identities = 180/209 (86%), Positives = 191/209 (91%)

Query: 1   MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLV 60
           +++ DIYEHAVLLSVK+ DQDAFERDFFQLKPYYTDAG RL PSP EYMILGLNLLRLLV
Sbjct: 59  IIARDIYEHAVLLSVKIGDQDAFERDFFQLKPYYTDAGGRLAPSPQEYMILGLNLLRLLV 118

Query: 61  QNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDL 120
           QNRIAEFHTELELLS  ALENPCIKHAVELEQSFMEGAYNRVLSAKQNVP +T+ YFMDL
Sbjct: 119 QNRIAEFHTELELLSPAALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPYKTFDYFMDL 178

Query: 121 LAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKA 180
           LAKTVRDEIAGCSEKAYDYLSI DA QMLLF+SD ELLEY+KE H EWE+K+G V FQKA
Sbjct: 179 LAKTVRDEIAGCSEKAYDYLSISDARQMLLFSSDDELLEYIKEGHLEWEIKNGSVVFQKA 238

Query: 181 KDSAPCKEIPSLQLINQTLSYARELERIV 209
            +SAPCKEIPSL LINQTLSYARELERIV
Sbjct: 239 NESAPCKEIPSLHLINQTLSYARELERIV 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	209
TAIR|locus:2019504	267	RPN12a "regulatory particle no	0.995	0.779	0.740	9.7e-80
TAIR|locus:2165750	233	RPN12b "regulatory particle no	0.813	0.729	0.705	1.6e-61
DICTYBASE|DDB_G0273979	263	psmD8-2 "26S proteasome regula	0.980	0.779	0.387	1.5e-35
DICTYBASE|DDB_G0272564	263	psmD8-1 "26S proteasome regula	0.980	0.779	0.387	1.5e-35
ZFIN|ZDB-GENE-040625-136	267	psmd8 "proteasome (prosome, ma	0.990	0.775	0.374	4.1e-33
MGI|MGI:1888669	353	Psmd8 "proteasome (prosome, ma	0.990	0.586	0.369	9.8e-32
RGD|1309842	285	Psmd8 "proteasome (prosome, ma	0.990	0.726	0.369	1.3e-31
UNIPROTKB|F1LMQ3	353	Psmd8 "Protein Psmd8" [Rattus	0.990	0.586	0.369	1.3e-31
UNIPROTKB|Q5RE15	289	PSMD8 "26S proteasome non-ATPa	0.990	0.716	0.369	1.6e-31
UNIPROTKB|P48556	350	PSMD8 "26S proteasome non-ATPa	0.990	0.591	0.369	2.6e-31

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

 Score = 801 (287.0 bits), Expect = 9.7e-80, P = 9.7e-80
 Identities = 154/208 (74%), Positives = 170/208 (81%)

Query:     2 VSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXVQ 61
             ++ DIYEHAV+LSVK EDQDAFERDFFQLKPYY DA  R+P SP E +I         VQ
Sbjct:    60 IARDIYEHAVVLSVKTEDQDAFERDFFQLKPYYVDARNRIPQSPQENLILGLNLLRLLVQ 119

Query:    62 NRIAEFHXXXXXXXXXXXXNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLL 121
             NRIAEFH            +PCIKHAVELEQSFMEGAYNRVLSA+Q  P+ TY YFMDLL
Sbjct:   120 NRIAEFHTELELLSSATLEDPCIKHAVELEQSFMEGAYNRVLSARQTAPDATYVYFMDLL 179

Query:   122 AKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKAK 181
             AKT+RDEIAGCSEKAYDY+SI DA QMLLF+SDQELL YV +EHPEWE+K+GFV FQKAK
Sbjct:   180 AKTIRDEIAGCSEKAYDYVSISDARQMLLFSSDQELLTYVTDEHPEWEVKEGFVVFQKAK 239

Query:   182 DSAPCKEIPSLQLINQTLSYARELERIV 209
             ++APCKEIPSLQLINQTLSYARELERIV
Sbjct:   240 ETAPCKEIPSLQLINQTLSYARELERIV 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 = 1.6e-61, P = 1.6e-61
 Identities = 120/170 (70%), Positives = 135/170 (79%)

Query:    40 RLPPSPNEYMIXXXXXXXXXVQNRIAEFHXXXXXXXXXXXXNPCIKHAVELEQSFMEGAY 99
             R+PPSP E +I         VQNRIAEFH            NPCIKHAVELEQSFMEGAY
Sbjct:    64 RIPPSPQENLIMGLNLLRLLVQNRIAEFHTELGLLSSATLENPCIKHAVELEQSFMEGAY 123

Query:   100 NRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLE 159
             NRVLSA+Q  P+ETY YFMDLLAKT+RDEIAGCSEKAYD+LSI +  +MLLF+SDQ+LL 
Sbjct:   124 NRVLSARQTAPDETYVYFMDLLAKTIRDEIAGCSEKAYDHLSISEGCKMLLFSSDQQLLT 183

Query:   160 YVKEEHPEWEMKDGFVFFQKAKDSAPCKEIPSLQLINQTLSYARELERIV 209
             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 = 384 (140.2 bits), Expect = 1.5e-35, P = 1.5e-35
 Identities = 81/209 (38%), Positives = 128/209 (61%)

Query:     1 MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXV 60
             +++ +I E   L S+K++D D+FER F QLK YY D    + PS  EY I          
Sbjct:    59 VLAREILELISLYSIKIKDIDSFERTFNQLKTYYYDYKSIIAPSTLEYQIIGLNLMRLLA 118

Query:    61 QNRIAEFHXXXXXXXXXXXXNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDL 120
             +++ +EFH            N  IK  + +E+S  EG+YN+++ ++  VP+E Y  F+D+
Sbjct:   119 KHKTSEFHSEIELIEFNNLDNSFIKFPLLVEKSITEGSYNKIIQSRSGVPSEYYQVFLDI 178

Query:   121 LAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKA 180
             LA +++++IA CSEK++  LS+KDA ++LLF  + +  +Y+KE +  W+++   + F   
Sbjct:   179 LADSIKEDIANCSEKSFKTLSLKDAEKVLLFNDNNQFQQYIKERN--WKVQGDVIQFGN- 235

Query:   181 KDSAPCKEIPSLQLINQTLSYARELERIV 209
              D+    EIPSLQLI+QTL YA+ELERIV
Sbjct:   236 NDNQTV-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 = 384 (140.2 bits), Expect = 1.5e-35, P = 1.5e-35
 Identities = 81/209 (38%), Positives = 128/209 (61%)

Query:     1 MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXV 60
             +++ +I E   L S+K++D D+FER F QLK YY D    + PS  EY I          
Sbjct:    59 VLAREILELISLYSIKIKDIDSFERTFNQLKTYYYDYKSIIAPSTLEYQIIGLNLMRLLA 118

Query:    61 QNRIAEFHXXXXXXXXXXXXNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDL 120
             +++ +EFH            N  IK  + +E+S  EG+YN+++ ++  VP+E Y  F+D+
Sbjct:   119 KHKTSEFHSEIELIEFNNLDNSFIKFPLLVEKSITEGSYNKIIQSRSGVPSEYYQVFLDI 178

Query:   121 LAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKA 180
             LA +++++IA CSEK++  LS+KDA ++LLF  + +  +Y+KE +  W+++   + F   
Sbjct:   179 LADSIKEDIANCSEKSFKTLSLKDAEKVLLFNDNNQFQQYIKERN--WKVQGDVIQFGN- 235

Query:   181 KDSAPCKEIPSLQLINQTLSYARELERIV 209
              D+    EIPSLQLI+QTL YA+ELERIV
Sbjct:   236 NDNQTV-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 = 361 (132.1 bits), Expect = 4.1e-33, P = 4.1e-33
 Identities = 79/211 (37%), Positives = 115/211 (54%)

Query:     1 MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXV 60
             +++ D+ E   L S+  +D  +FER   QLK YY D    LP S   + +          
Sbjct:    59 ILARDVLEIGALWSILKKDIPSFERYMAQLKCYYFDYKDELPESAYRHQLLGLNLLFLLS 118

Query:    61 QNRIAEFHXXXXXXXXXXX-XNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMD 119
             QNR++EFH             N  I+H V LEQ  MEG+YN+V  AK N+P E+Y +F+D
Sbjct:   119 QNRVSEFHTELERLSAKDIQTNVYIRHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFID 178

Query:   120 LLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEW-EMKDGFVFFQ 178
              L  T+RDEIAGC EKAY+ +   +A ++L F+S +++ +Y K+ +  W +  DG+  F 
Sbjct:   179 TLLDTIRDEIAGCIEKAYEQIQFNEATRVLFFSSPKKMTDYAKKRN--WTQSPDGYYSFS 236

Query:   179 KAKDSAPCKEIPSLQLINQTLSYARELERIV 209
                       IPS +L  Q + YAR+LE IV
Sbjct:   237 TQHQKTEEVTIPSTELAKQVIEYARQLEMIV 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 = 348 (127.6 bits), Expect = 9.8e-32, P = 9.8e-32
 Identities = 78/211 (36%), Positives = 116/211 (54%)

Query:     1 MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXV 60
             +++ DI E     S+  +D  +FER   QLK YY D  ++LP S   + +          
Sbjct:   145 ILARDILEIGAQWSILCKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLS 204

Query:    61 QNRIAEFHXXXXXX-XXXXXXNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMD 119
             QNR+AEFH             N  IKH V LEQ  MEG+YN+V  AK N+P E+Y +F+D
Sbjct:   205 QNRVAEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFID 264

Query:   120 LLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEM-KDGFVFFQ 178
             +L  T+RDEIAGC EKAY+ +   +A ++L F++ +++ +Y K+    W +  + +  F 
Sbjct:   265 ILLDTIRDEIAGCIEKAYEKILFAEATRILFFSTPKKMTDYAKKRG--WVLGPNNYYSFA 322

Query:   179 KAKDSAPCKEIPSLQLINQTLSYARELERIV 209
               +       IPS +L  Q + YAR+LE IV
Sbjct:   323 SQQQKPEDSTIPSTELAKQVIEYARQLEMIV 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

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

 Score = 347 (127.2 bits), Expect = 1.3e-31, P = 1.3e-31
 Identities = 78/211 (36%), Positives = 116/211 (54%)

Query:     1 MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXV 60
             +++ DI E     S+  +D  +FER   QLK YY D  ++LP S   + +          
Sbjct:    77 ILARDILEIGAQWSILCKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLS 136

Query:    61 QNRIAEFHXXXXXX-XXXXXXNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMD 119
             QNR+AEFH             N  IKH V LEQ  MEG+YN+V  AK N+P E+Y +F+D
Sbjct:   137 QNRVAEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFID 196

Query:   120 LLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEM-KDGFVFFQ 178
             +L  T+RDEIAGC EKAY+ +   +A ++L F++ +++ +Y K+    W +  + +  F 
Sbjct:   197 ILLDTIRDEIAGCIEKAYEKILFAEATRILFFSTPKKMTDYAKKRG--WLLGPNNYYSFA 254

Query:   179 KAKDSAPCKEIPSLQLINQTLSYARELERIV 209
               +       IPS +L  Q + YAR+LE IV
Sbjct:   255 SQQQKPEDSTIPSTELARQVIEYARQLEMIV 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 = 347 (127.2 bits), Expect = 1.3e-31, P = 1.3e-31
 Identities = 78/211 (36%), Positives = 116/211 (54%)

Query:     1 MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXV 60
             +++ DI E     S+  +D  +FER   QLK YY D  ++LP S   + +          
Sbjct:   145 ILARDILEIGAQWSILCKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLS 204

Query:    61 QNRIAEFHXXXXXX-XXXXXXNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMD 119
             QNR+AEFH             N  IKH V LEQ  MEG+YN+V  AK N+P E+Y +F+D
Sbjct:   205 QNRVAEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFID 264

Query:   120 LLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEM-KDGFVFFQ 178
             +L  T+RDEIAGC EKAY+ +   +A ++L F++ +++ +Y K+    W +  + +  F 
Sbjct:   265 ILLDTIRDEIAGCIEKAYEKILFAEATRILFFSTPKKMTDYAKKRG--WLLGPNNYYSFA 322

Query:   179 KAKDSAPCKEIPSLQLINQTLSYARELERIV 209
               +       IPS +L  Q + YAR+LE IV
Sbjct:   323 SQQQKPEDSTIPSTELARQVIEYARQLEMIV 353

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005838 "proteasome regulatory particle" evidence=IEA

GO:0006508 "proteolysis" evidence=IEA

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

 Score = 346 (126.9 bits), Expect = 1.6e-31, P = 1.6e-31
 Identities = 78/211 (36%), Positives = 115/211 (54%)

Query:     1 MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXV 60
             +++ DI E     S+  +D  +FER   QLK YY D  ++LP S   + +          
Sbjct:    81 ILARDILEIGAQWSILRKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLS 140

Query:    61 QNRIAEFHXXXXXX-XXXXXXNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMD 119
             QNR+AEFH             N  IKH V LEQ  MEG+YN+V  AK N+P E+Y +F+D
Sbjct:   141 QNRVAEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYAFFID 200

Query:   120 LLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEM-KDGFVFFQ 178
             +L  T+RDEIAGC EKAY+ +   +A ++L F + +++ +Y K+    W +  + +  F 
Sbjct:   201 ILLDTIRDEIAGCIEKAYEKILFTEATRILFFNTPKKMTDYAKKRG--WVLGPNNYYSFA 258

Query:   179 KAKDSAPCKEIPSLQLINQTLSYARELERIV 209
               +       IPS +L  Q + YAR+LE IV
Sbjct:   259 SQQQKPEDTTIPSTELAKQVIEYARQLEMIV 289

GO:0022624 "proteasome accessory complex" evidence=ISS

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

 Score = 344 (126.2 bits), Expect = 2.6e-31, P = 2.6e-31
 Identities = 78/211 (36%), Positives = 115/211 (54%)

Query:     1 MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXV 60
             +++ DI E     S+  +D  +FER   QLK YY D  ++LP S   + +          
Sbjct:   142 ILARDILEIGAQWSILRKDIPSFERYMAQLKCYYFDYKEQLPESAYMHQLLGLNLLFLLS 201

Query:    61 QNRIAEFHXXXXXX-XXXXXXNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMD 119
             QNR+AEFH             N  IKH V LEQ  MEG+YN+V  AK N+P E+Y +F+D
Sbjct:   202 QNRVAEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFID 261

Query:   120 LLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEM-KDGFVFFQ 178
             +L  T+RDEIAGC EKAY+ +   +A ++L F + +++ +Y K+    W +  + +  F 
Sbjct:   262 ILLDTIRDEIAGCIEKAYEKILFTEATRILFFNTPKKMTDYAKKRG--WVLGPNNYYSFA 319

Query:   179 KAKDSAPCKEIPSLQLINQTLSYARELERIV 209
               +       IPS +L  Q + YAR+LE IV
Sbjct:   320 SQQQKPEDTTIPSTELAKQVIEYARQLEMIV 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)
Q23449	PSMD8_CAEEL	No assigned EC number	0.3584	0.9665	0.808	yes	no
Q9SGW3	RP12A_ARATH	No assigned EC number	0.8317	0.9952	0.7790	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:
	GSVIVG00006696001	SubName- Full=Chromosome chr2 scaffold_176, whole genome shotgun sequence; (267 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00036762001	SubName- Full=Chromosome chr4 scaffold_83, whole genome shotgun sequence; (440 aa)				•	•	•	•		0.975
	GSVIVG00010470001	SubName- Full=Chromosome chr17 scaffold_263, whole genome shotgun sequence; (386 aa)				•	•	•	•		0.974
	GSVIVG00014791001	SubName- Full=Putative uncharacterized protein (Chromosome chr18 scaffold_1, whole genome shotg [...] (309 aa)				•	•	•	•		0.971
	GSVIVG00015634001	SubName- Full=Chromosome chr2 scaffold_11, whole genome shotgun sequence; (365 aa)				•	•	•	•		0.948
	GSVIVG00023752001	SubName- Full=Putative uncharacterized protein (Chromosome chr7 scaffold_31, whole genome shotg [...] (205 aa)				•	•	•	•		0.936
	GSVIVG00015420001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (191 aa)				•	•	•	•		0.916
	GSVIVG00030725001	RecName- Full=Proteasome subunit beta type; EC=3.4.25.1;; The proteasome is a multicatalytic pr [...] (250 aa)				•	•	•	•		0.915
	GSVIVG00019352001	SubName- Full=Chromosome chr7 scaffold_20, whole genome shotgun sequence; (320 aa)				•	•	•	•		0.912
	GSVIVG00024499001	RecName- Full=Proteasome subunit beta type; EC=3.4.25.1;; The proteasome is a multicatalytic pr [...] (245 aa)				•	•	•	•		0.907
	GSVIVG00026350001	RecName- Full=Proteasome subunit beta type; EC=3.4.25.1;; The proteasome is a multicatalytic pr [...] (223 aa)				•	•	•	•		0.906

---

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	209
pfam03399	155	pfam03399, SAC3_GANP, SAC3/GANP/Nin1/mts3/eIF-3 p2	1e-35
pfam10075	144	pfam10075, PCI_Csn8, COP9 signalosome, subunit CSN	7e-28

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

 Score =  122 bits (309), Expect = 1e-35
 Identities = 47/145 (32%), Positives = 70/145 (48%), Gaps = 4/145 (2%)

Query: 5   DIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRI 64
            + E    ++++  D + F +   QLK  Y D    L  SPNE   +   LL LL  N I
Sbjct: 14  AVLEIGARIALEKGDLEQFNQCLSQLKELYDD---LLGKSPNEAEFIAYYLLYLLSNNPI 70

Query: 65  AEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKT 124
           ++FHTELELL      +P I+ A+ELEQ+ MEG Y+R     +  P   Y   ++     
Sbjct: 71  SDFHTELELLPDEIRNDPYIQFALELEQALMEGNYHRFFRLLKKAPYL-YACLLERFLDR 129

Query: 125 VRDEIAGCSEKAYDYLSIKDAGQML 149
           +R E      KAY  + +    ++L
Sbjct: 130 IRKEALKAISKAYRSIPLSYLAELL 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 =  102 bits (256), Expect = 7e-28
 Identities = 43/121 (35%), Positives = 64/121 (52%), Gaps = 2/121 (1%)

Query: 45  PNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALE-NPCIKHAVELEQSFMEGAYNRVL 103
             +  + GL LL+LL QN IA+F   L+ +     E NP I+  + L Q   E  Y +  
Sbjct: 1   ELKTELYGLILLKLLTQNDIADFRLLLKRIPQAIKESNPEIQQLLTLGQLLWENDYAKFW 60

Query: 104 SA-KQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVK 162
              + N  +E Y  F+  L  T+RDEIA    KAY  +SI D  ++L  +SD+EL ++ K
Sbjct: 61  QTLRSNDWSEDYTPFIAGLEDTIRDEIAALVGKAYSSISIDDLAELLGLSSDEELEKFAK 120

Query: 163 E 163
           +
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	209
KOG3151	260	consensus 26S proteasome regulatory complex, subun	100.0
KOG1861	540	consensus Leucine permease transcriptional regulat	100.0
PF10075	143	PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro	99.96
PF03399	204	SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; I	99.96
KOG4414	197	consensus COP9 signalosome, subunit CSN8 [Posttran	99.71
KOG1860	927	consensus Nuclear protein export factor [Intracell	98.1
COG5079	646	SAC3 Nuclear protein export factor [Intracellular	97.68
KOG3252	217	consensus Uncharacterized conserved protein [Funct	97.53
PF01399	105	PCI: PCI domain; InterPro: IPR000717 A homology do	97.42
smart00088	88	PINT motif in proteasome subunits, Int-6, Nip-1 an	96.01
smart00753	88	PAM PCI/PINT associated module.	96.01
KOG0687	393	consensus 26S proteasome regulatory complex, subun	91.3
KOG2582	422	consensus COP9 signalosome, subunit CSN3 [Posttran	90.37
COG5187	412	RPN7 26S proteasome regulatory complex component,	89.24
KOG2581	493	consensus 26S proteasome regulatory complex, subun	88.43

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

Probab=100.00  E-value=4.3e-69  Score=455.54  Aligned_cols=207  Identities=57%  Similarity=0.873  Sum_probs=196.0

Q ss_pred             ChHHHHHHHHHHHHhhhcChHHHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHHHHHHHhccHhhh-
Q 028424            1 MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTAL-   79 (209)
Q Consensus         1 ~~ar~vlEi~a~~sl~~~D~~~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~efh~~Le~l~~~~~-   79 (209)
                      ++||+|||+||++||.++|+++|+|||+||+|||+|+...+|+|+++++++||||||||||||+++||++||+||...+ 
T Consensus        53 ~~aR~ilEi~vl~SI~t~D~~sFerY~~Qlk~YY~d~~~~l~~S~~~~~l~GLnLL~LLsqNRiaeFHteLe~lp~~~l~  132 (260)
T KOG3151|consen   53 IIARDILEIGVLLSILTKDFESFERYMNQLKPYYFDYNEKLSESEKKHKLLGLNLLYLLSQNRIAEFHTELELLPKKILQ  132 (260)
T ss_pred             HHHHHHHHHHHHHHHHhccHHHHHHHHHHhcchhcccccccCcchhhhHHHHHHHHHHHHhccHHHHHHHHHhccHHHhh
Confidence            3799999999999999999999999999999999999999999999999999999999999999999999999999988 


Q ss_pred             cCchhhhHHHHHHHHHhcChHHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHH
Q 028424           80 ENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLE  159 (209)
Q Consensus        80 ~~~~I~~~~~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~  159 (209)
                      .||||+||++|||++|||+|+|||.+++++|++.|++|||+|++|||+|||.|+||||..||+++|+.||+|++++++..
T Consensus       133 ~~~~I~~~v~LEq~~MEGaYnKv~~a~~s~p~~~y~~FmdIl~~tiRdEIA~c~EKsYd~l~~s~a~~~L~f~~~~e~~~  212 (260)
T KOG3151|consen  133 HNPYISHPVSLEQSLMEGAYNKVLSAKQSIPSEEYTYFMDILLDTIRDEIAGCIEKSYDKLSASDATQMLLFNNDKELKK  212 (260)
T ss_pred             ccchhhhHHHHHHHHHhhHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHhcCChHHHHH
Confidence            77999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhCCCceeeCCeEEEecCCCCCCCCCCChHHHHHHHHhHHHHhhhcC
Q 028424          160 YVKEEHPEWEMKDGFVFFQKAKDSAPCKEIPSLQLINQTLSYARELERIV  209 (209)
Q Consensus       160 f~~~~~~gW~~~~~~i~f~~~~~~~~~~~~~~~~li~~~l~Ya~elE~IV  209 (209)
                      |+  .+|+|.++.+.++++...+.+...++|+.+++.++|+||+|||+||
T Consensus       213 ~~--~~r~W~l~~~~~~~~~~~~~~p~~~~ps~~la~qtlsYar~LE~Iv  260 (260)
T KOG3151|consen  213 FA--TERQWPLDEKGVFSFASKETAPYEEIPSTELAEQTLSYARELEMIV  260 (260)
T ss_pred             HH--HhcCCcccccccccchhhccCchhccCcHHHHHHHHHHHHHHHhcC
Confidence            96  4789999966666665545555568999999999999999999998

>KOG1861 consensus Leucine permease transcriptional regulator [Transcription]

Probab=100.00  E-value=4.5e-33  Score=254.61  Aligned_cols=170  Identities=19%  Similarity=0.349  Sum_probs=156.5

Q ss_pred             hHHHHHHHHHHHHhhhcChHHHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHHHHHHHhccHhhhcC
Q 028424            2 VSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALEN   81 (209)
Q Consensus         2 ~ar~vlEi~a~~sl~~~D~~~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~efh~~Le~l~~~~~~~   81 (209)
                      ++.+|||+||+||+++||++|||||++|||.+|..+   +|+.  ..+|+||+|||++.+.|..+..++|..|+.|+|+|
T Consensus       346 FTveVYEtHARIALEkGD~~EfNQCQtQLk~LY~eg---ipg~--~~EF~AYriLY~i~tkN~~di~sll~~lt~E~ked  420 (540)
T KOG1861|consen  346 FTVEVYETHARIALEKGDLEEFNQCQTQLKALYSEG---IPGA--YLEFTAYRILYYIFTKNYPDILSLLRDLTEEDKED  420 (540)
T ss_pred             eeeeeehhhhHHHHhcCCHHHHHHHHHHHHHHHccC---CCCc--hhhHHHHHHHHHHHhcCchHHHHHHHhccHhhccC
Confidence            356899999999999999999999999999999654   6654  79999999999888777789999999999999999


Q ss_pred             chhhhHHHHHHHHHhcChHHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHHhccC-CccHHHHHHhhCCCCHHHHHHH
Q 028424           82 PCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYD-YLSIKDAGQMLLFTSDQELLEY  160 (209)
Q Consensus        82 ~~I~~~~~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~~tiR~~ia~~iekAY~-sl~l~~a~~lL~f~~~~e~~~f  160 (209)
                      ++|.|+++|+.++..|||++||+++.++|. |.+|+||.|++++|..++..|+|||+ +||++++++.|.|++.++|..|
T Consensus       421 ~~V~hAL~vR~A~~~GNY~kFFrLY~~AP~-M~~yLmdlF~erER~~Al~ii~KsyrP~i~~~fi~~~laf~~~e~c~~~  499 (540)
T KOG1861|consen  421 EAVAHALEVRSAVTLGNYHKFFRLYLTAPN-MSGYLMDLFLERERKKALTIICKSYRPTITVDFIASELAFDSMEDCVNF  499 (540)
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHhhccc-chhHHHHHHHHHHHHHHHHHHHHHcCCCccHHHHhhhhhhchHHHHHHH
Confidence            999999999999999999999999999998 79999999999999999999999999 9999999999999999999999


Q ss_pred             HhhhCCCceee-CCeEEEec
Q 028424          161 VKEEHPEWEMK-DGFVFFQK  179 (209)
Q Consensus       161 ~~~~~~gW~~~-~~~i~f~~  179 (209)
                      ..  +.+|+-+ .|..+..+
T Consensus       500 l~--~~~~~~~~~g~~~~~~  517 (540)
T KOG1861|consen  500 LN--EQNLTYDSLGPQILDK  517 (540)
T ss_pred             Hh--ccCccccccCCccccc
Confidence            74  6789887 55555444

>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=99.96  E-value=3.6e-30  Score=205.10  Aligned_cols=130  Identities=28%  Similarity=0.444  Sum_probs=104.7

Q ss_pred             hhHHHHHHHHHHHhhCCHHHHHHHHHhccHhhhc-CchhhhHHHHHHHHHhcChHHHHHHhh-cCCCcchHHHHHHHHHH
Q 028424           47 EYMILGLNLLRLLVQNRIAEFHTELELLSSTALE-NPCIKHAVELEQSFMEGAYNRVLSAKQ-NVPNETYGYFMDLLAKT  124 (209)
Q Consensus        47 ~~~il~l~LL~LL~~n~i~efh~~Le~l~~~~~~-~~~I~~~~~leq~L~eGnY~kv~~~~~-~~P~~~~~~fm~~L~~t  124 (209)
                      ...+.|++|+.+|.+|++++||.+|++||+++++ ||+|+.+|.|+|+||+|+|+++|...+ +.|++.+.+||..|.++
T Consensus         3 ~~~~~~~~Ll~~L~~~~~~df~~~~~rip~~~~~~~~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~   82 (143)
T PF10075_consen    3 NPEIYALILLKYLMQNDLSDFRLLWKRIPEELKQSDPEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGFEDT   82 (143)
T ss_dssp             -HHHHHHHHHHHHHTTTSTHHHHHHHTS-HHHHTS-TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTHHHH
T ss_pred             chhHHHHHHHHHHHcCCchHHHHHHHcCCHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHHHHH
Confidence            4689999999999999999999999999999995 799999999999999999999999654 56788999999999999


Q ss_pred             HHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhhhCCCceeeCCeEEEec
Q 028424          125 VRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQK  179 (209)
Q Consensus       125 iR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~~~~gW~~~~~~i~f~~  179 (209)
                      +|++|+.||++||++|++++++++||++ ++|+.+|++  ++||+++++.++|+.
T Consensus        83 iR~~i~~~i~~aY~sIs~~~la~~Lg~~-~~el~~~~~--~~gW~~d~~~~~~~~  134 (143)
T PF10075_consen   83 IRERIAHLISKAYSSISLSDLAEMLGLS-EEELEKFIK--SRGWTVDGDGVLFPP  134 (143)
T ss_dssp             HHHHHHHHHHHH-SEE-HHHHHHHTTS--HHHHHHHHH--HHT-EE-----EE--
T ss_pred             HHHHHHHHHHHHHhHcCHHHHHHHhCCC-HHHHHHHHH--HcCCEECCCccEEec
Confidence            9999999999999999999999999999 999999985  469999966655553

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=99.96  E-value=2.7e-29  Score=208.68  Aligned_cols=147  Identities=34%  Similarity=0.546  Sum_probs=127.9

Q ss_pred             HHHHHHHHHHHHhhhcChHHHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHHHHHHHhccHhhhcCc
Q 028424            3 SGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENP   82 (209)
Q Consensus         3 ar~vlEi~a~~sl~~~D~~~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~efh~~Le~l~~~~~~~~   82 (209)
                      +++|||.+|+++|..+|.++|++|++||+.+|.+. ...++++++.+|+|++||++|++|+.++||..+..+|++.++||
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            78999999999999999999999999999999986 33577899999999999999999999999999999999999999


Q ss_pred             hhhhHHHHHHHHHhcChHHHHHHh--hcCCCcchHHHHHHHHHHHHHHHHHHHHhccCC-ccHHHHHHhhCC
Q 028424           83 CIKHAVELEQSFMEGAYNRVLSAK--QNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDY-LSIKDAGQMLLF  151 (209)
Q Consensus        83 ~I~~~~~leq~L~eGnY~kv~~~~--~~~P~~~~~~fm~~L~~tiR~~ia~~iekAY~s-l~l~~a~~lL~f  151 (209)
                      .|+++++|.+++++|||.++|+..  .++| ..++.+|+.+++++|..++.++++||.+ +|++.++++|+|
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            999999999999999999999988  5654 5799999999999999999999999998 999999999997

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.

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

Probab=99.71  E-value=7.4e-17  Score=129.39  Aligned_cols=134  Identities=11%  Similarity=0.124  Sum_probs=119.0

Q ss_pred             CCCCCc--chhHHHHHHHHHHHhhCCHHHHHHHHHhccHhhh-cCchhhhHHHHHHHHHhcChHHHHHHhhcCC-CcchH
Q 028424           40 RLPPSP--NEYMILGLNLLRLLVQNRIAEFHTELELLSSTAL-ENPCIKHAVELEQSFMEGAYNRVLSAKQNVP-NETYG  115 (209)
Q Consensus        40 ~l~~s~--~~~~il~l~LL~LL~~n~i~efh~~Le~l~~~~~-~~~~I~~~~~leq~L~eGnY~kv~~~~~~~P-~~~~~  115 (209)
                      |+...+  -+...++.|+|    -|+..+...+|+|||+.+| .+|++.-+|.++|.+|..+|..||.+.+... |++..
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            565555  56777777777    8999999999999999999 9999999999999999999999999987655 88999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhhhCCCceee-CCeEE-EecC
Q 028424          116 YFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK-DGFVF-FQKA  180 (209)
Q Consensus       116 ~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~~~~gW~~~-~~~i~-f~~~  180 (209)
                      .+|..|-|..|.+....+..||+||..++++..||+. +++....+-  +.||++| .+++. .+++
T Consensus       109 ~imaAf~D~~~kR~FaLl~qAYssI~~~D~A~FlGl~-~ddAtk~il--EnGWqaDaasqMasl~kk  172 (197)
T KOG4414|consen  109 DIMAAFRDATRKRAFALLLQAYSSIIADDFAAFLGLP-EDDATKGIL--ENGWQADAASQMASLKKK  172 (197)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-HHHHHHHHH--HcccchhhHHHHhhccch
Confidence            9999999999999999999999999999999999999 888888874  6799999 55665 5543

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

Probab=98.10  E-value=0.00011  Score=73.28  Aligned_cols=172  Identities=18%  Similarity=0.287  Sum_probs=131.8

Q ss_pred             hHHHHHHHHHHHHhhh----cCh-HHH---------HHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHH
Q 028424            2 VSGDIYEHAVLLSVKV----EDQ-DAF---------ERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEF   67 (209)
Q Consensus         2 ~ar~vlEi~a~~sl~~----~D~-~~F---------~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~ef   67 (209)
                      .|..++|-.|+.=|..    .|. +.|         ..|..-|..+|.|+..+-.+.++..+|-|||+|  |+-|+ .+.
T Consensus       215 ~Av~llE~i~RfhI~~~h~Lce~~~~Fda~~nlEQL~K~l~sL~elYdD~r~~g~~cpnE~EFR~Y~vL--l~Lgd-~~~  291 (927)
T KOG1860|consen  215 EAVELLERIARFHILFRHRLCEEPEQFDAQQNLEQLQKCLQSLGELYDDLRKGGIPCPNEPEFRGYYVL--LSLGD-PQV  291 (927)
T ss_pred             HHHHHHHHHHHHHHHHHHHhccCcccCChhHHHHHHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHH--HhcCC-chH
Confidence            4677888777765543    233 344         445566778898886555668999999999977  55565 355


Q ss_pred             HHHHHhccHhhhcCchhhhHHHHHHHHHhcChHHHHH-----------------HhhcCC-C-cchHHHHHHHHHHHHHH
Q 028424           68 HTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLS-----------------AKQNVP-N-ETYGYFMDLLAKTVRDE  128 (209)
Q Consensus        68 h~~Le~l~~~~~~~~~I~~~~~leq~L~eGnY~kv~~-----------------~~~~~P-~-~~~~~fm~~L~~tiR~~  128 (209)
                      -.....+|+++..++.+++++.+.++...|||..+++                 .....| . ..-..++..+..-+|.-
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            6677889999999999999999999999999998863                 122334 1 13466788889999999


Q ss_pred             HHHHHHhccC----CccHHHHHHhhCCCCHHHHHHHHhhhCCCceee-CCeEEEe
Q 028424          129 IAGCSEKAYD----YLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK-DGFVFFQ  178 (209)
Q Consensus       129 ia~~iekAY~----sl~l~~a~~lL~f~~~~e~~~f~~~~~~gW~~~-~~~i~f~  178 (209)
                      +...++.+|.    .+|+.+...+|+|+++++...+..  .+|-+++ +..+..+
T Consensus       372 al~~~~~~~~~~~~~vp~~~l~~~l~f~~~e~~~~~~~--~y~Leis~~~~~~~~  424 (927)
T KOG1860|consen  372 ALRAMSHAYNSKHVPVPLGKLDRILLFDGEEELKVVCN--YYGLEISVDDKIVLS  424 (927)
T ss_pred             HHHHHHHHHhccCCCcchhHHHHHHhcCChhhhHhhhh--heeeEeecccccccc
Confidence            9999999996    599999999999999999999974  6888887 3334433

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

Probab=97.68  E-value=0.0017  Score=61.70  Aligned_cols=161  Identities=19%  Similarity=0.233  Sum_probs=119.5

Q ss_pred             HHHHHHHHHHHHhhh----cChHHHHHHHH--hh-------HHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHHHH
Q 028424            3 SGDIYEHAVLLSVKV----EDQDAFERDFF--QL-------KPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHT   69 (209)
Q Consensus         3 ar~vlEi~a~~sl~~----~D~~~F~~~~~--qL-------k~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~efh~   69 (209)
                      |.++.|..|++-|..    .|...|++=|.  ||       -.+|.++..+-...+|..+|-+|-+|-  +-+| ...-.
T Consensus       181 AV~c~EriaRfhIl~lh~L~~~p~Fs~qqeleQL~ksL~sL~elYdd~r~~~~~cpneaEFraYaiL~--slgD-p~yv~  257 (646)
T COG5079         181 AVECHERIARFHILFLHLLHDHPHFSKQQELEQLKKSLASLIELYDDGRAGKKECPNEAEFRAYAILA--SLGD-PRYVA  257 (646)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCccccHHhHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHH--HhCC-chhhh
Confidence            667788888766543    45577765543  55       468999877778889999999998873  3332 23444


Q ss_pred             HHHhccHhhhcCchhhhHHHHHHHHHhcCh---------------HHHHHHhhcCCCcchHHHHHHHHH----HHHHHHH
Q 028424           70 ELELLSSTALENPCIKHAVELEQSFMEGAY---------------NRVLSAKQNVPNETYGYFMDLLAK----TVRDEIA  130 (209)
Q Consensus        70 ~Le~l~~~~~~~~~I~~~~~leq~L~eGnY---------------~kv~~~~~~~P~~~~~~fm~~L~~----tiR~~ia  130 (209)
                      -...+|..+..++-++-++.+.|-...|||               .++|+..+. |  ...|||..|++    .+|.-++
T Consensus       258 ~iq~wp~~if~d~~vq~alkl~~laq~nn~r~~~~rnteac~nlytrFfkl~qS-p--sv~~lmg~lle~h~~sir~~aL  334 (646)
T COG5079         258 GIQGWPGGIFCDLPVQIALKLMQLAQSNNFRLLGRRNTEACFNLYTRFFKLIQS-P--SVQYLMGCLLEKHNISIRGGAL  334 (646)
T ss_pred             ccccCCccccccchHHHHHHHHHHhhccCeeeccccchhhhhHHHHHHHHHHhC-c--cHHHHHHHHHHHhhHHHHHHHH
Confidence            566788888899999999999999888875               455665544 4  46777776655    5788888


Q ss_pred             HHHHhcc----CCccHHHHHHhhCCCCHHHHHHHHhhhCCCceee
Q 028424          131 GCSEKAY----DYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK  171 (209)
Q Consensus       131 ~~iekAY----~sl~l~~a~~lL~f~~~~e~~~f~~~~~~gW~~~  171 (209)
                      ..++++|    ..+|.-+...+|.|++.+|..+|++  --|-++.
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            7555555    5799999999999999999999975  4577764

>KOG3252 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.53  E-value=0.00095  Score=55.93  Aligned_cols=129  Identities=13%  Similarity=0.146  Sum_probs=104.6

Q ss_pred             hHHHHHHHHHHHhhCCHHHHHHHHHhccHhhhcCchhhhHHHHHHHHHhcChHHHHHHhhcCCCcchHHHHHHHHHHHHH
Q 028424           48 YMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRD  127 (209)
Q Consensus        48 ~~il~l~LL~LL~~n~i~efh~~Le~l~~~~~~~~~I~~~~~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~~tiR~  127 (209)
                      ..+++==||.-|..=--+||-...=.||+....+..++.++.|...|-.|+|..+|.....-|. +... |.=|-|.||.
T Consensus        62 t~itaqILlKaL~~lP~tDF~l~kcli~~~~~~ee~~r~ii~L~~~LEt~~Fq~FW~~~~~N~~-mle~-itGFedsvr~  139 (217)
T KOG3252|consen   62 TTITAQILLKALTNLPHTDFTLAKCLIDERVQMEEPFRSIIDLGDYLETCRFQQFWQEADENRD-MLEG-ITGFEDSVRK  139 (217)
T ss_pred             hHHHHHHHHHHHhcCCCcchhHHHHhcCHHHhcccchhHHHhHHHHHhhchHHHHhhhhccchH-HhcC-CCcHHHHHHH
Confidence            3455556666676667788999999999988888999999999999999999999986542221 2222 2336889999


Q ss_pred             HHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhhhCCCceee-CCeEEEecC
Q 028424          128 EIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMK-DGFVFFQKA  180 (209)
Q Consensus       128 ~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~~~~gW~~~-~~~i~f~~~  180 (209)
                      =+--.+.-.|.+|+-.-++++||-.+..++..+++  +-||..+ .|.|+++..
T Consensus       140 yachvv~iTyQkI~k~lLaellG~~sDs~le~~~~--~~GW~a~e~G~ifv~~q  191 (217)
T KOG3252|consen  140 YACHVVGITYQKIDKWLLAELLGGLSDSQLEVWMT--KYGWIADESGQIFVASQ  191 (217)
T ss_pred             HHHHheechHhhchHHHHHHhhCcccHHHHHHHHH--HccceecCCceEEEecc
Confidence            99999999999999999999999999999999985  6799999 777777654

>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=97.42  E-value=0.0027  Score=46.36  Aligned_cols=73  Identities=16%  Similarity=0.258  Sum_probs=55.3

Q ss_pred             HHHHHHHhcChHHHHHHhhcC-----CCcchHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHh
Q 028424           89 ELEQSFMEGAYNRVLSAKQNV-----PNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVK  162 (209)
Q Consensus        89 ~leq~L~eGnY~kv~~~~~~~-----P~~~~~~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~  162 (209)
                      ++-+++-.|+|..+.+.....     ..+.....++.+...+|......+.+.|++|+++.++++++++ .++++.++.
T Consensus         5 ~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~-~~~vE~~l~   82 (105)
T PF01399_consen    5 ELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLS-EEEVESILI   82 (105)
T ss_dssp             HHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCC-HHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccc-hHHHHHHHH
Confidence            455566666666665544433     1334556889999999999999999999999999999999999 788888875

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.

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

Probab=96.01  E-value=0.036  Score=39.78  Aligned_cols=62  Identities=18%  Similarity=0.277  Sum_probs=49.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhh----hCCCceee--CCeEEEec
Q 028424          117 FMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKE----EHPEWEMK--DGFVFFQK  179 (209)
Q Consensus       117 fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~----~~~gW~~~--~~~i~f~~  179 (209)
                      ..+.+...+|........+.|++|++++++..++++ .+++..++..    ..-..++|  +|.+.|..
T Consensus         2 ~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~   69 (88)
T smart00088        2 LVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVSKAIRDGEISAKIDQVNGIVEFEE   69 (88)
T ss_pred             hHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHHHHHHCCCeEEEEcCcCCEEEECC
Confidence            356789999999999999999999999999999998 5577777652    23367787  56666665

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

>smart00753 PAM PCI/PINT associated module

Probab=96.01  E-value=0.036  Score=39.78  Aligned_cols=62  Identities=18%  Similarity=0.277  Sum_probs=49.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhh----hCCCceee--CCeEEEec
Q 028424          117 FMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKE----EHPEWEMK--DGFVFFQK  179 (209)
Q Consensus       117 fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~----~~~gW~~~--~~~i~f~~  179 (209)
                      ..+.+...+|........+.|++|++++++..++++ .+++..++..    ..-..++|  +|.+.|..
T Consensus         2 ~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~   69 (88)
T smart00753        2 LVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVSKAIRDGEISAKIDQVNGIVEFEE   69 (88)
T ss_pred             hHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHHHHHHCCCeEEEEcCcCCEEEECC
Confidence            356789999999999999999999999999999998 5577777652    23367787  56666665

>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]

Probab=91.30  E-value=12  Score=34.51  Aligned_cols=170  Identities=13%  Similarity=0.096  Sum_probs=118.0

Q ss_pred             HHHHHHhhhcChHHHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHHHHH-HHhcc------------
Q 028424            9 HAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTE-LELLS------------   75 (209)
Q Consensus         9 i~a~~sl~~~D~~~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~efh~~-Le~l~------------   75 (209)
                      .-+++.+--.|..=-++.+...|..|..+    ...++++.+-.++=+|..+-.|..++-.+ ++.+|            
T Consensus       146 ~~iRlglfy~D~~lV~~~iekak~liE~G----gDWeRrNRlKvY~Gly~msvR~Fk~Aa~Lfld~vsTFtS~El~~Y~~  221 (393)
T KOG0687|consen  146 YKIRLGLFYLDHDLVTESIEKAKSLIEEG----GDWERRNRLKVYQGLYCMSVRNFKEAADLFLDSVSTFTSYELMSYET  221 (393)
T ss_pred             HHHHHHHhhccHHHHHHHHHHHHHHHHhC----CChhhhhhHHHHHHHHHHHHHhHHHHHHHHHHHcccccceecccHHH
Confidence            34556666788888899999999999887    34578888999999999998888877655 34444            


Q ss_pred             ---------------Hhh--h--cCchhhh-------HHHHHHHHHhcChHHHHHHhh-----c-CCCcchHHHHHHHHH
Q 028424           76 ---------------STA--L--ENPCIKH-------AVELEQSFMEGAYNRVLSAKQ-----N-VPNETYGYFMDLLAK  123 (209)
Q Consensus        76 ---------------~~~--~--~~~~I~~-------~~~leq~L~eGnY~kv~~~~~-----~-~P~~~~~~fm~~L~~  123 (209)
                                     +++  |  ..|+|.-       ..++=-.|-+-+|..+|....     + -+.-..+++-+-++-
T Consensus       222 ~v~Ytv~~g~i~leR~dlktKVi~~~Evl~vl~~l~~~~q~l~SLY~C~Y~~Ff~~L~~~~~~~lk~D~~l~~h~~yyvR  301 (393)
T KOG0687|consen  222 FVRYTVITGLIALERVDLKTKVIKCPEVLEVLHKLPSVSQLLNSLYECDYSDFFNDLAAVEAKQLKDDRYLGPHYRYYVR  301 (393)
T ss_pred             HHHHHHHHhhheeccchHHhhhcCcHHHHHHhhcCchHHHHHHHHHhccHHHHHHHHHHHHHHhhccchhcchHHHHHHH
Confidence                           111  1  3454433       334445677899999988542     1 123344555666677


Q ss_pred             HHHHHHHHHHHhccCCccHHHHHHhhCCC---CHHHHHHHHhhhCCCcee-e-CCeEEEecCCCC
Q 028424          124 TVRDEIAGCSEKAYDYLSIKDAGQMLLFT---SDQELLEYVKEEHPEWEM-K-DGFVFFQKAKDS  183 (209)
Q Consensus       124 tiR~~ia~~iekAY~sl~l~~a~~lL~f~---~~~e~~~f~~~~~~gW~~-~-~~~i~f~~~~~~  183 (209)
                      -.|.++-.-.--+|++++++..|+-.|.+   -+.|+..|+. ..|-|.. | =+.|+.-++|+.
T Consensus       302 EMR~rvY~QlLESYrsl~l~~MA~aFgVSVefiDreL~rFI~-~grL~ckIDrVnGVVEtNrpD~  365 (393)
T KOG0687|consen  302 EMRRRVYAQLLESYRSLTLESMAKAFGVSVEFIDRELGRFIA-AGRLHCKIDRVNGVVETNRPDE  365 (393)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHHhHHHHhhc-cCceeeeeecccceeecCCccc
Confidence            78888888877899999999999999987   2358999995 4566765 4 234555554433

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

Probab=90.37  E-value=1.8  Score=40.19  Aligned_cols=77  Identities=17%  Similarity=0.270  Sum_probs=53.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhh---hCCCceeeCCeEEEecCCCCCCCCCCChHH
Q 028424          117 FMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKE---EHPEWEMKDGFVFFQKAKDSAPCKEIPSLQ  193 (209)
Q Consensus       117 fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~---~~~gW~~~~~~i~f~~~~~~~~~~~~~~~~  193 (209)
                      |....+...-.+-.....|.|.||+|++++++..+.+.+|+.+++-+   ..+-..+-||.|+|-..+.     +.+|.+
T Consensus       295 l~k~av~sl~k~nI~rltktF~sLsL~dIA~~vQLa~~qevek~Ilqmie~~~i~a~iNG~v~f~~n~e-----~~~Spe  369 (422)
T KOG2582|consen  295 LAKQAVSSLYKKNIQRLTKTFLSLSLSDIASRVQLASAQEVEKYILQMIEDGEIFASINGMVFFTDNPE-----KYNSPE  369 (422)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcchHHHHHHHHHHhccCceEEEecceEEEecCcc-----cCCCHH
Confidence            44455555566666778899999999999999999999999888753   2334444488887776432     244555


Q ss_pred             HHHHH
Q 028424          194 LINQT  198 (209)
Q Consensus       194 li~~~  198 (209)
                      ++.|-
T Consensus       370 M~~nk  374 (422)
T KOG2582|consen  370 MHENK  374 (422)
T ss_pred             HHhhH
Confidence            55543

>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]

Probab=89.24  E-value=17  Score=33.17  Aligned_cols=173  Identities=14%  Similarity=0.122  Sum_probs=118.8

Q ss_pred             HHHHHHHHHHhhhcChHHHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHHHHHHHhc-c--------
Q 028424            5 DIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELL-S--------   75 (209)
Q Consensus         5 ~vlEi~a~~sl~~~D~~~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~efh~~Le~l-~--------   75 (209)
                      +|+=.-+++.+--+|.---++-...+++.|.-+    ...++++.+..++=+++++-.+..++-.+|-.+ |        
T Consensus       153 Dv~l~kiRlg~~y~d~~vV~e~lE~~~~~iEkG----gDWeRrNRyK~Y~Gi~~m~~RnFkeAa~Ll~d~l~tF~S~El~  228 (412)
T COG5187         153 DVFLCKIRLGLIYGDRKVVEESLEVADDIIEKG----GDWERRNRYKVYKGIFKMMRRNFKEAAILLSDILPTFESSELI  228 (412)
T ss_pred             hhHHHHHHHHHhhccHHHHHHHHHHHHHHHHhC----CCHHhhhhHHHHHHHHHHHHHhhHHHHHHHHHHhccccccccc
Confidence            344445666677788888888888888888765    234677777778878888877777776665322 2        


Q ss_pred             -----------------------------Hh---hh-cCchhhhHHHHHHHHHhcChHHHHHHhh------cCCCcchHH
Q 028424           76 -----------------------------ST---AL-ENPCIKHAVELEQSFMEGAYNRVLSAKQ------NVPNETYGY  116 (209)
Q Consensus        76 -----------------------------~~---~~-~~~~I~~~~~leq~L~eGnY~kv~~~~~------~~P~~~~~~  116 (209)
                                                   ++   +. ++.-++...++--.|-+-+|...|....      =.|.....-
T Consensus       229 sY~~~vrYa~~~Gl~~leR~diktki~dspevl~vi~~~e~l~sl~~l~~SLy~cdY~~~F~~ll~~~~n~L~~d~fl~r  308 (412)
T COG5187         229 SYSRAVRYAIFCGLLRLERRDIKTKILDSPEVLDVIGSSEKLGSLVQLATSLYECDYGGDFMNLLYLFCNSLQDDVFLGR  308 (412)
T ss_pred             cHHHHHHHHHHhhhheeehhhhhhhhcCCHHHHHhccchhhhhhHHHHHHHHHHhccchhhHHHHHHHHhhccchHHHHH
Confidence                                         11   11 3445566677777888888887765221      123445566


Q ss_pred             HHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCC---CHHHHHHHHhhhCCCceee--CCeEEEecCCC
Q 028424          117 FMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFT---SDQELLEYVKEEHPEWEMK--DGFVFFQKAKD  182 (209)
Q Consensus       117 fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~---~~~e~~~f~~~~~~gW~~~--~~~i~f~~~~~  182 (209)
                      +.|.++--.|.++-.-+-.+|+.++++..|.-.|.+   -+-++-+|+- ..+-|.+-  =+.|++.++|+
T Consensus       309 h~d~fvREMRrrvYaQlLESYr~lsl~sMA~tFgVSV~yvdrDLg~FIp-~~~LncvIDRvnGvVetnrpd  378 (412)
T COG5187         309 HVDLFVREMRRRVYAQLLESYRLLSLESMAQTFGVSVEYVDRDLGEFIP-EGRLNCVIDRVNGVVETNRPD  378 (412)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhCccHHHHhhhHHhhCC-CCceeeeeecccceEeccCcc
Confidence            778888889999988888899999999999999987   1237888985 45677764  23455555543

>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]

Probab=88.43  E-value=3.6  Score=38.82  Aligned_cols=75  Identities=16%  Similarity=0.222  Sum_probs=51.3

Q ss_pred             hhhhHHHHHHHHHhcChHHHHHHhhcCCCcchHHHHH----HHHHHHHHHH----HHHHHhccCCccHHHHHHhhCCCCH
Q 028424           83 CIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMD----LLAKTVRDEI----AGCSEKAYDYLSIKDAGQMLLFTSD  154 (209)
Q Consensus        83 ~I~~~~~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~----~L~~tiR~~i----a~~iekAY~sl~l~~a~~lL~f~~~  154 (209)
                      .+.+=..|-++.-.||-.|+=.-..+.-    .-|+.    .|.-|.|..+    ...|.-+|+.||+.|+|+-|+++|+
T Consensus       317 sL~~Yf~Lt~AVr~gdlkkF~~~leq~k----~~f~~D~ty~LivRLR~NVIkTgIR~ISlsYSRISl~DIA~kL~l~Se  392 (493)
T KOG2581|consen  317 SLRPYFKLTQAVRLGDLKKFNETLEQFK----DKFQADGTYTLIVRLRHNVIKTGIRKISLSYSRISLQDIAKKLGLNSE  392 (493)
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHH----HHHhhCCcchHHHHHHHHHHHHhhhheeeeeeeccHHHHHHHhcCCCc
Confidence            6777778888888888888744332210    11111    2344555544    4688999999999999999999987


Q ss_pred             HHHHHHH
Q 028424          155 QELLEYV  161 (209)
Q Consensus       155 ~e~~~f~  161 (209)
                      +++.-.+
T Consensus       393 ed~EyiV  399 (493)
T KOG2581|consen  393 EDAEYIV  399 (493)
T ss_pred             hhHHHHH
Confidence            7655444

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	209
4b0z_A	229	Crystal Structure Of S. Pombe Rpn12 Length = 229		5e-20
4b4t_T	274	Near-Atomic Resolution Structural Model Of The Yeas		4e-13

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

Iteration: 1
 Score = 94.0 bits (232), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 54/177 (30%), Positives = 96/177 (54%), Gaps = 7/177 (3%)
Query: 5   DIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXVQNRI 64
           +++E+ VL+S++  D ++F R   Q+ P+Y D+   L PS    ++          +NRI
Sbjct: 57  NVFEYGVLVSIQTCDIESFARYASQVIPFYHDS---LVPSSRMGLVTGLNLLYLLSENRI 113
Query: 65  AEFHXXXXXX--XXXXXXNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLA 122
           AEFH              +P ++  + LEQ+ MEGA+++V S  ++     + YFM ++ 
Sbjct: 114 AEFHTALESVPDKSLFERDPYVEWVISLEQNVMEGAFDKVASMIRSCNFPEFSYFMKIVM 173
Query: 123 KTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQK 179
             VR+EIA C+EK Y  + + +A  +L   + +E  E + EE   W+++DG ++F K
Sbjct: 174 SMVRNEIATCAEKVYSEIPLSNATSLLYLENTKE-TEKLAEERG-WDIRDGVIYFPK 228

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

Iteration: 1
 Score = 70.9 bits (172), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 58/223 (26%), Positives = 103/223 (46%), Gaps = 18/223 (8%)
Query: 1   MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXV 60
           M++  I E   L S++  + D+FE  F QLKPYY     +L  S  +  +          
Sbjct: 56  MITKRILEVGALASIQTFNFDSFENYFNQLKPYYFSNNHKLSESDKKSKLISLYLLNLLS 115
Query: 61  QNRIAEFHXXXX---XXXXXXXXNPCIKHAVELEQSFMEGAYNRVL----SAKQNVPNET 113
           QN   +FH               +  + + ++L++  MEG+Y +      S  QN+    
Sbjct: 116 QNNTTKFHSELQYLDKHIKNLEDDSLLSYPIKLDRWLMEGSYQKAWDLLQSGSQNIS--E 173
Query: 114 YGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDG 173
           +  F D+L   +RDEIA  +E +YD+L + +   +L F +++E  ++  E +  W + + 
Sbjct: 174 FDSFTDILKSAIRDEIAKNTELSYDFLPLSNIKALLFFNNEKETEKFALERN--WPIVNS 231
Query: 174 FVFF-----QKA--KDSAPCKEIPSLQLINQTLSYARELERIV 209
            V+F     +KA  +D    +E     +I + + YA  +E IV
Sbjct: 232 KVYFNNQSKEKADYEDEMMHEEDQKTNIIEKAMDYAISIENIV 274

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	209
3t5v_A	316	Nuclear mRNA export protein SAC3; PCI, mRNA nuclea	7e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-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 = 7e-07
 Identities = 30/194 (15%), Positives = 52/194 (26%), Gaps = 23/194 (11%)

Query: 19  DQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTA 78
           + +   +    L   Y D        PNE       LL  +   +  E    ++ L    
Sbjct: 87  ELEQLHKSLITLSEIYDDVRSSGGTCPNEAEFRAYALLSKIRDPQYDE---NIQRLPKHI 143

Query: 79  LENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETY----------------GYFMDLLA 122
            ++  ++ A+   +     AY      K       Y                G+F+ +  
Sbjct: 144 FQDKLVQMALCFRRVISNSAYTERGFVKTENCLNFYARFFQLMQSPSLPLLMGFFLQMHL 203

Query: 123 KTVRDEIAGCSEKAY----DYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQ 178
             +R                 +       MLLF + QE++E+      E    D      
Sbjct: 204 TDIRFYALRALSHTLNKKHKPIPFIYLENMLLFNNRQEIIEFCNYYSIEIINGDAADLKT 263

Query: 179 KAKDSAPCKEIPSL 192
               S    E   L
Sbjct: 264 LQHYSHKLSETQPL 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 = 40.2 bits (93), Expect = 3e-04
 Identities = 34/245 (13%), Positives = 82/245 (33%), Gaps = 42/245 (17%)

Query: 1   MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPP----------SPNEYMI 50
            V+ D     +  S+ V +   + + F +L  +   A   +P             ++ M+
Sbjct: 349 HVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSA--HIPTILLSLIWFDVIKSDVMV 406

Query: 51  LGLNLL--RLLVQNRIAEFHTELELLSSTALENPCIKHAVELEQSFMEGAYNRVLSAKQN 108
           + +N L    LV+ +  E    +  +         +++   L +S ++  YN   +   +
Sbjct: 407 V-VNKLHKYSLVEKQPKESTISIPSIYLELKVK--LENEYALHRSIVD-HYNIPKTFDSD 462

Query: 109 --VPNETYGYFMDLLA----KTVRDEIAGCSEKAY---DYLS--IKDAGQMLLFTSD--- 154
             +P     YF   +          E        +    +L   I+        +     
Sbjct: 463 DLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILN 522

Query: 155 --QEL---LEYVKEEHPEWEM--KDGFVFFQKAKDS---APCKEIPSLQLINQTLSYARE 204
             Q+L     Y+ +  P++E        F  K +++   +   ++  + L+ +  +   E
Sbjct: 523 TLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEE 582

Query: 205 LERIV 209
             + V
Sbjct: 583 AHKQV 587

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	209
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	99.91
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	97.69
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	97.47
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	97.16
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	97.07
4b4t_O	393	26S proteasome regulatory subunit RPN9; hydrolase,	96.55
1ufm_A	84	COP9 complex subunit 4; helix-turn-helix, structur	95.51
3t5x_A	203	PCI domain-containing protein 2; PCI, mRNA nuclear	92.77
4b4t_S	523	RPN3, 26S proteasome regulatory subunit RPN3; hydr	88.45
3chm_A	169	COP9 signalosome complex subunit 7; heat/ARM repea	84.17
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	81.78

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

Probab=100.00  E-value=3.7e-66  Score=451.98  Aligned_cols=206  Identities=29%  Similarity=0.522  Sum_probs=162.4

Q ss_pred             hHHHHHHHHHHHHhhhcChHHHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHHHHHHHhccHh---h
Q 028424            2 VSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSST---A   78 (209)
Q Consensus         2 ~ar~vlEi~a~~sl~~~D~~~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~efh~~Le~l~~~---~   78 (209)
                      +||+|||+||++||+++|+++|+||++|||+||+++.+++|+|+++.+|+||||||||++|+++|||++||.||..   +
T Consensus        57 ~ar~v~E~~a~~si~~~D~~~F~~~~~QLk~~Y~d~~~~l~~s~~~~e~~~~~LLylL~~n~~~efh~~Le~L~~~~~~~  136 (274)
T 4b4t_T           57 ITKRILEVGALASIQTFNFDSFENYFNQLKPYYFSNNHKLSESDKKSKLISLYLLNLLSQNNTTKFHSELQYLDKHIKNL  136 (274)
T ss_dssp             ----CHHHHHHCCSSCSSHHHHHHHHHHHHHHTTTTSSCSSCSHHHHHHHHHHHHHHHHHHCSTHHHHHHHSSSCSSSTT
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhhccCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHhcchhhHhH
Confidence            7999999999999999999999999999999999998999999999999999999999999999999999999964   5


Q ss_pred             hcCchhhhHHHHHHHHHhcChHHHHHHhhcC--CCcchHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHH
Q 028424           79 LENPCIKHAVELEQSFMEGAYNRVLSAKQNV--PNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQE  156 (209)
Q Consensus        79 ~~~~~I~~~~~leq~L~eGnY~kv~~~~~~~--P~~~~~~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e  156 (209)
                      ++||+|+||++||+++|+|||+|||++.++.  |+++|++||++|++|+|.+||+||+|||++||+++++++|+|+|++|
T Consensus       137 ~~d~~Ik~al~le~al~eGnY~kff~l~~~~~~p~~~~~~f~d~l~~~iR~~a~~~i~kaY~~i~l~~~~~~L~F~s~~e  216 (274)
T 4b4t_T          137 EDDSLLSYPIKLDRWLMEGSYQKAWDLLQSGSQNISEFDSFTDILKSAIRDEIAKNTELSYDFLPLSNIKALLFFNNEKE  216 (274)
T ss_dssp             TCCHHHHHHHHHHHHHHHTCSHHHHHHHHTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHCSSCCHHHHHHHHTCCSHHH
T ss_pred             hcChHHHHHHHHHHHHHcCCHHHHHHHHhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHhCCCCHHH
Confidence            5899999999999999999999999987765  46678999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhCCCceeeCCeEEEecCCCCC-------CCCCCChHHHHHHHHhHHHHhhhcC
Q 028424          157 LLEYVKEEHPEWEMKDGFVFFQKAKDSA-------PCKEIPSLQLINQTLSYARELERIV  209 (209)
Q Consensus       157 ~~~f~~~~~~gW~~~~~~i~f~~~~~~~-------~~~~~~~~~li~~~l~Ya~elE~IV  209 (209)
                      +.+|++  ++||++++|.++|+..+.+.       ...++|+.++|+|+|+||+|||+||
T Consensus       217 ~~~F~~--~~gW~~~~~~v~F~~~~~~~~~~~~~~~~~~ips~~li~~~l~YA~elE~IV  274 (274)
T 4b4t_T          217 TEKFAL--ERNWPIVNSKVYFNNQSKEKADYEDEMMHEEDQKTNIIEKAMDYAISIENIV  274 (274)
T ss_dssp             HHHHHH--HTTCCCCSSCCCC---------------------------------------
T ss_pred             HHHHHH--HcCCEEeCCEeEECCccccccccccccccccCcHHHHHHHHHHHHHHhhhcC
Confidence            999985  68999999999998653221       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=2e-54  Score=368.68  Aligned_cols=173  Identities=35%  Similarity=0.667  Sum_probs=166.0

Q ss_pred             hHHHHHHHHHHHHhhhcChHHHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHHHHHHHhccHhh--h
Q 028424            2 VSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTA--L   79 (209)
Q Consensus         2 ~ar~vlEi~a~~sl~~~D~~~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~efh~~Le~l~~~~--~   79 (209)
                      +||+|||+||++||+.+|+++|+||++|||+||.++   +++|+++.+|+||||||+|++|+++|||++|+.+|++.  +
T Consensus        54 ~ar~vyE~~a~~al~~~D~~~F~~~~~qLk~~Y~~~---~~~s~~~~e~~~~~LL~lL~~~~~~ef~~~le~l~~~~~~~  130 (229)
T 4b0z_A           54 FARNVFEYGVLVSIQTCDIESFARYASQVIPFYHDS---LVPSSRMGLVTGLNLLYLLSENRIAEFHTALESVPDKSLFE  130 (229)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHSSC---CCCCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHCSCTTHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHcc---CCCCccHHHHHHHHHHHHHHcCCchHHHHHHHhcChHHHhh
Confidence            699999999999999999999999999999999875   78899999999999999999999999999999999763  6


Q ss_pred             cCchhhhHHHHHHHHHhcChHHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHH
Q 028424           80 ENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLE  159 (209)
Q Consensus        80 ~~~~I~~~~~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~  159 (209)
                      +||+|+||++|+|++|+|||++||++.+++|++.+++||+.|++|+|.+|++||+|||++||+++++++|||+|++|+.+
T Consensus       131 ~~~~I~~al~l~~al~~GnY~kff~l~~~~p~~~~~~~~~~l~~~vR~~~l~~i~kaY~~i~l~~~~~~L~f~s~~e~~~  210 (229)
T 4b0z_A          131 RDPYVEWVISLEQNVMEGAFDKVASMIRSCNFPEFSYFMKIVMSMVRNEIATCAEKVYSEIPLSNATSLLYLENTKETEK  210 (229)
T ss_dssp             HCHHHHHHHHHHHHHHTTCHHHHHHHHHTCCCGGGHHHHHHHHHHHHHHHHHHHHHHCSEEEHHHHHHHTTCSSHHHHHH
T ss_pred             cCHHHHHHHHHHHHHHcCCHHHHHHHHhcCccchHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhCCCceeeCCeEEEec
Q 028424          160 YVKEEHPEWEMKDGFVFFQK  179 (209)
Q Consensus       160 f~~~~~~gW~~~~~~i~f~~  179 (209)
                      |++  ++||+++||.|+|++
T Consensus       211 f~~--~~gw~i~dg~i~F~~  228 (229)
T 4b0z_A          211 LAE--ERGWDIRDGVIYFPK  228 (229)
T ss_dssp             HHH--HHTCEEETTEEECC-
T ss_pred             HHH--HcCCEEeCCEEecCC
Confidence            985  579999999999986

>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=1.4e-29  Score=215.48  Aligned_cols=159  Identities=16%  Similarity=0.137  Sum_probs=130.2

Q ss_pred             cChHHHHHHHHh--hHHHHhcCCC-------CCCCCcchhHHHHHHHHHHHhhCCHHHHHHHHHhccHhhhcCchhhhHH
Q 028424           18 EDQDAFERDFFQ--LKPYYTDAGK-------RLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCIKHAV   88 (209)
Q Consensus        18 ~D~~~F~~~~~q--Lk~~Y~~~~~-------~l~~s~~~~~il~l~LL~LL~~n~i~efh~~Le~l~~~~~~~~~I~~~~   88 (209)
                      ..++.|++|++|  ++++|....+       .+.|+....+++|++||.+|+++..+|||+.++.||+..++||+|+++|
T Consensus        24 ~~l~~le~Yv~qq~~~~~YD~~anlalLklYq~~p~~~~~~ii~~iLlk~L~~~p~~DF~~~l~LIp~~~~~~~~I~~i~  103 (226)
T 1rz4_A           24 ENLATLERYVETQAKENAYDLEANLAVLKLYQFNPAFFQTTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQIL  103 (226)
T ss_dssp             GGHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTTTSTHHHHHHHTSCHHHHTSTTHHHHH
T ss_pred             HHHHHHHHHHHHHHhcccccHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHcCCHHHHHHHHHhCChhhhcCHHHHHHH
Confidence            456778888887  4444421100       0245667789999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcChHHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhhhCCCc
Q 028424           89 ELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEW  168 (209)
Q Consensus        89 ~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~~~~gW  168 (209)
                      .|+++||+|+|++||++.+.-  +.+...|.-|.+++|.+|+.|+++||++||+++++++||+.+++++.+|++  ++||
T Consensus       104 ~L~~~L~~~~y~~fW~~l~~~--~~l~~~i~gf~dsIR~~I~~~i~~aY~sI~~~~la~lLg~~s~~el~~fi~--~~GW  179 (226)
T 1rz4_A          104 YLGDLLETCHFQAFWQALDEN--MDLLEGITGFEDSVRKFICHVVGITYQHIDRWLLAEMLGDLSDSQLKVWMS--KYGW  179 (226)
T ss_dssp             HHHHHHHTTCHHHHHHHSCTT--CHHHHTSTTHHHHHHHHHHHHHHHHCSEECHHHHHHHTTSCCHHHHHHHHH--HHTC
T ss_pred             HHHHHHHcCCHHHHHHHHhcC--hhHHHHHhHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHcCCCHHHHHHHHH--HCCC
Confidence            999999999999999997653  234445555999999999999999999999999999998778999999986  4699


Q ss_pred             eee-CCeEEEecC
Q 028424          169 EMK-DGFVFFQKA  180 (209)
Q Consensus       169 ~~~-~~~i~f~~~  180 (209)
                      +++ +|.|+|+..
T Consensus       180 ~vd~~g~I~~~n~  192 (226)
T 1rz4_A          180 SADESGQIFICSQ  192 (226)
T ss_dssp             EECC--CEECCCH
T ss_pred             EECCCccEEeCCC
Confidence            997 678877653

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

Probab=99.91  E-value=6.1e-24  Score=188.61  Aligned_cols=168  Identities=17%  Similarity=0.266  Sum_probs=139.4

Q ss_pred             hHHHHHHHHHHHHh------hhcChH-----HHHHHH---HhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHH
Q 028424            2 VSGDIYEHAVLLSV------KVEDQD-----AFERDF---FQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEF   67 (209)
Q Consensus         2 ~ar~vlEi~a~~sl------~~~D~~-----~F~~~~---~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~ef   67 (209)
                      .+.+|||.+|++.|      ..+|.+     +++||+   .+|+.+|.+....-..+++..+|.||+||+.|.+   .++
T Consensus        56 ~~v~v~E~~aRf~i~~~~~L~~~~~~f~~~~~~eQl~~~L~sL~~lY~d~~~~~~~~~ne~EF~aY~lL~~l~~---~~~  132 (316)
T 3t5v_A           56 EAVDCNERIVRIHLLILHIMVKSNVEFSLQQELEQLHKSLITLSEIYDDVRSSGGTCPNEAEFRAYALLSKIRD---PQY  132 (316)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCCCTTHHHHHHHHHHHSTTC---THH
T ss_pred             hHHHHHHHHHHHHHHHHHHHhhCCCccchHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHhcc---chH
Confidence            36789999999986      445542     444555   4778889874221135789999999999998875   478


Q ss_pred             HHHHHhccHhhhcCchhhhHHHHHHHHH---------------hcChHHHHHHhhc--CCCcchHHHHHHHHHHHHHHHH
Q 028424           68 HTELELLSSTALENPCIKHAVELEQSFM---------------EGAYNRVLSAKQN--VPNETYGYFMDLLAKTVRDEIA  130 (209)
Q Consensus        68 h~~Le~l~~~~~~~~~I~~~~~leq~L~---------------eGnY~kv~~~~~~--~P~~~~~~fm~~L~~tiR~~ia  130 (209)
                      ...+..||+++++||.|+++++|++++.               .|||+++|++..+  +|- +-+++|+.+++++|..++
T Consensus       133 ~~~l~~Lp~~i~~~p~Vq~AL~l~~a~~~~~~~e~~~~~~~~~~gNY~rFFrL~~~~~~py-L~aclle~~~~~vR~~AL  211 (316)
T 3t5v_A          133 DENIQRLPKHIFQDKLVQMALCFRRVISNSAYTERGFVKTENCLNFYARFFQLMQSPSLPL-LMGFFLQMHLTDIRFYAL  211 (316)
T ss_dssp             HHHHTTSCHHHHTSHHHHHHHHHHHHHCCTTCCCTTCCCCSSCCCCHHHHHHHHTCTTSCH-HHHHHHGGGHHHHHHHHH
T ss_pred             HHHHHhCCHHHhcCHHHHHHHHHHHHHHhcccccccccccccccchHHHHHHHHhccCCCh-HHHHHHHHHHHHHHHHHH
Confidence            8899999999999999999999999985               4999999999987  332 348999999999999999


Q ss_pred             HHHHhccC----CccHHHHHHhhCCCCHHHHHHHHhhhCCCceeeC-CeE
Q 028424          131 GCSEKAYD----YLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKD-GFV  175 (209)
Q Consensus       131 ~~iekAY~----sl~l~~a~~lL~f~~~~e~~~f~~~~~~gW~~~~-~~i  175 (209)
                      .+|.+||.    ++|+++++++|+|++++|+.+|++  ..||++.+ +.+
T Consensus       212 ~~i~kay~~k~~~~pl~~L~~~L~Fds~ee~~~F~~--~~gl~~~~~~~~  259 (316)
T 3t5v_A          212 RALSHTLNKKHKPIPFIYLENMLLFNNRQEIIEFCN--YYSIEIINGDAA  259 (316)
T ss_dssp             HHHHHHSCTTCCCEEHHHHHHHTTCSSHHHHHHHHH--HTTCCEETTTEE
T ss_pred             HHHHHHhccCCCCcCHHHHHHHhCCCCHHHHHHHHH--HCCCeEeCCCCc
Confidence            99999994    899999999999999999999995  68999985 434

>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=0.0039  Score=56.46  Aligned_cols=168  Identities=8%  Similarity=0.071  Sum_probs=114.7

Q ss_pred             HHHHHHHHHHh-hhcChHH-HHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHHHHHHHhccHhh-hcC
Q 028424            5 DIYEHAVLLSV-KVEDQDA-FERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTA-LEN   81 (209)
Q Consensus         5 ~vlEi~a~~sl-~~~D~~~-F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~efh~~Le~l~~~~-~~~   81 (209)
                      .+-|.+.++.+ ..+|+.. +..++.-.+. |..     .+++.+..++-|-+|.-|..++..|+...+.. +... ..+
T Consensus       181 ~i~~~~Gi~~l~~~rdyk~A~~~F~eaf~~-f~~-----~~~~~~~~~lkYlvL~aLl~~~r~el~~~l~~-~~~~~~~~  253 (394)
T 3txn_A          181 ALDLQSGILHAADERDFKTAFSYFYEAFEG-FDS-----VDSVKALTSLKYMLLCKIMLGQSDDVNQLVSG-KLAITYSG  253 (394)
T ss_dssp             HHHHHHHHHHHHTTSCHHHHHHHHHHHHHH-HTT-----TCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHS-HHHHTTCS
T ss_pred             HHHHHhhHHHHHhccCHHHHHHHHHHHHhc-ccc-----cccHHHHHHHHHHHHHHHHcCCHHHHHHHhcc-ccccccCC
Confidence            45678888888 8888754 3333333322 321     23455566666666666677887888754321 1111 178


Q ss_pred             chhhhHHHHHHHHHhcChHHHHHHhhc----CC-CcchHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHH
Q 028424           82 PCIKHAVELEQSFMEGAYNRVLSAKQN----VP-NETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQE  156 (209)
Q Consensus        82 ~~I~~~~~leq~L~eGnY~kv~~~~~~----~P-~~~~~~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e  156 (209)
                      |.|.....|-++...|++..+......    .. .+......+.|..++|......+-+.|++|+++++++.++++ +++
T Consensus       254 pei~~l~~L~~a~~~~dl~~f~~iL~~~~~~l~~D~~l~~h~~~L~~~Ir~~~L~~i~~pYsrIsl~~iA~~l~ls-~~e  332 (394)
T 3txn_A          254 RDIDAMKSVAEASHKRSLADFQAALKEYKKELAEDVIVQAHLGTLYDTMLEQNLCRIIEPYSRVQVAHVAESIQLP-MPQ  332 (394)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHSTTTTTTSHHHHHHHHHHHHHHHHHHHHHHHTTCSEEEHHHHHHHHTCC-HHH
T ss_pred             ccHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHHHHHHHHhHhhceeeHHHHHHHHCcC-HHH
Confidence            999999999999999999888775432    22 222344567899999999999999999999999999999995 887


Q ss_pred             HHHHHh----hhCCCceee--CCeEEEecC
Q 028424          157 LLEYVK----EEHPEWEMK--DGFVFFQKA  180 (209)
Q Consensus       157 ~~~f~~----~~~~gW~~~--~~~i~f~~~  180 (209)
                      +...+.    ...-.=++|  +|.+++..+
T Consensus       333 vE~~L~~lI~dg~I~a~IDq~~giv~~~~~  362 (394)
T 3txn_A          333 VEKKLSQMILDKKFSGILDQGEGVLIVFEE  362 (394)
T ss_dssp             HHHHHHHHHHTTSSCEEEETTTTEEEECCC
T ss_pred             HHHHHHHHHHCCCeeEEEcCCCCEEEECCC
Confidence            776664    222233677  676777654

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

Probab=97.47  E-value=0.0043  Score=56.03  Aligned_cols=165  Identities=13%  Similarity=0.100  Sum_probs=114.1

Q ss_pred             HHHHhhhcChHHHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHHHHHHHh-----------------
Q 028424           11 VLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELEL-----------------   73 (209)
Q Consensus        11 a~~sl~~~D~~~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~efh~~Le~-----------------   73 (209)
                      +++++..+|...-..+..+.+......    +....+..+-.+.-+++++.++.-++...+-.                 
T Consensus       175 irl~l~~~d~~~~~~~~~ka~~~~~~~----~d~~~~~~lk~~~gl~~l~~r~f~~Aa~~f~e~~~t~~~~e~~~~~~~~  250 (429)
T 4b4t_R          175 ARLGFFYNDQLYVKEKLEAVNSMIEKG----GDWERRNRYKTYYGIHCLAVRNFKEAAKLLVDSLATFTSIELTSYESIA  250 (429)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHTTC----CCTHHHHHHHHHHHHGGGGTSCHHHHHHHHHHHHHHSCCSCHHHHHHHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHHhhhcC----CCHHHHHHHHHHHHHHHHHhChHHHHHHHHHHHhccCCccchhhHHHHH
Confidence            567888999999999999988887654    33455667777777777777776654332211                 


Q ss_pred             ----------ccH-h----h----------hcCchhhhHHHHHHHHHhcChHHHHHHhh----cCC--CcchHHHHHHHH
Q 028424           74 ----------LSS-T----A----------LENPCIKHAVELEQSFMEGAYNRVLSAKQ----NVP--NETYGYFMDLLA  122 (209)
Q Consensus        74 ----------l~~-~----~----------~~~~~I~~~~~leq~L~eGnY~kv~~~~~----~~P--~~~~~~fm~~L~  122 (209)
                                .+. +    +          ..+|.+....++-.++..++|..+|....    +..  .+..+.-.+.|.
T Consensus       251 ~y~~l~al~~~~r~~l~~~v~~~~~~~~~l~~~p~~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~d~~l~~h~~~l~  330 (429)
T 4b4t_R          251 TYASVTGLFTLERTDLKSKVIDSPELLSLISTTAALQSISSLTISLYASDYASYFPYLLETYANVLIPCKYLNRHADFFV  330 (429)
T ss_dssp             HHHHHHHHHTTCHHHHHHSSSSSHHHHHGGGSHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHSTTTTTCTTSTTTHHHHH
T ss_pred             HHHHHHHHhcCCHHHHHHHHhcCHHHHhhccCChhHHHHHHHHHHHHhccHHHHHHHHHHHHHhhhccCHHHHHHHHHHH
Confidence                      010 0    1          13456666677788889999999987431    111  234455577899


Q ss_pred             HHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHH----HHhhhCCCceee--CCeEEEecC
Q 028424          123 KTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLE----YVKEEHPEWEMK--DGFVFFQKA  180 (209)
Q Consensus       123 ~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~----f~~~~~~gW~~~--~~~i~f~~~  180 (209)
                      ..+|..+...+.+.|++|+++.+|+.||++ ++++.+    ++.+..-.=++|  +|.|++..+
T Consensus       331 ~~ir~~~l~q~~~~Ys~I~l~~mA~~l~~s-~~~~E~~L~~lI~~g~l~akID~~~giv~~~~~  393 (429)
T 4b4t_R          331 REMRRKVYAQLLESYKTLSLKSMASAFGVS-VAFLDNDLGKFIPNKQLNCVIDRVNGIVETNRP  393 (429)
T ss_dssp             HHHHHHHHHHHHHTCSEEEHHHHHHHHTSC-HHHHHHHHHHHHHHTSSCEEEETTTTEEEECC-
T ss_pred             HHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHHHHHHcCCeEEEEcCCCCEEEECCC
Confidence            999999999999999999999999999998 665554    554434455677  666666553

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

Probab=97.16  E-value=0.0091  Score=54.31  Aligned_cols=170  Identities=11%  Similarity=0.076  Sum_probs=112.4

Q ss_pred             HHHHHHHHHHhhhcChHHHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHHHHHHHhccHhhhcCchh
Q 028424            5 DIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTALENPCI   84 (209)
Q Consensus         5 ~vlEi~a~~sl~~~D~~~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~efh~~Le~l~~~~~~~~~I   84 (209)
                      ..++.++++....+|+.+--+|+-++-.-|...    ..+......+.+-+++++-.+...+...++.++-.+ ...+.|
T Consensus       219 ~~~~~~~~~~~~e~~y~~a~~~y~e~~~~~~~~----~d~~~~~~~L~~~v~~~iLa~~~~~~~~ll~~~~~~-~~~~~l  293 (445)
T 4b4t_P          219 EYYNLLVKISLHKREYLEVAQYLQEIYQTDAIK----SDEAKWKPVLSHIVYFLVLSPYGNLQNDLIHKIQND-NNLKKL  293 (445)
T ss_dssp             HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH----SCHHHHHHHHHHHHHHHHHSSCSSTTHHHHHSHHHH-SSCHHH
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHhccccc----CCHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHhhc-cccccc
Confidence            578999999999999987777766665555432    112233445555566655555555666666665432 334566


Q ss_pred             hhHHHHHHHHHhcCh---HHHHHHhhcC--CCc------chHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCC
Q 028424           85 KHAVELEQSFMEGAY---NRVLSAKQNV--PNE------TYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTS  153 (209)
Q Consensus        85 ~~~~~leq~L~eGnY---~kv~~~~~~~--P~~------~~~~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~  153 (209)
                      ...-.|.++...++.   ..+...+...  |.+      ....-...|..+++......+.+-|++|+++.++.+|+++ 
T Consensus       294 ~~~~~L~k~f~~~~L~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~L~~~v~ehnl~~i~k~Ys~I~l~~la~lL~l~-  372 (445)
T 4b4t_P          294 ESQESLVKLFTTNELMRWPIVQKTYEPVLNEDDLAFGGEANKHHWEDLQKRVIEHNLRVISEYYSRITLLRLNELLDLT-  372 (445)
T ss_dssp             HHHHHHHHHHHHCCSSSHHHHHHHTCSSTTTCCSSCCCSCSSHHHHHHHHHHHHHHHHHHHHHEEEEEHHHHHHHHTSC-
T ss_pred             HHHHHHHHHHHhchHhhhHHHHHHHHHHhcccchhhhcchhhHHHHHHHHHHHHHHHHHHHHHhceeeHHHHHHHhCcC-
Confidence            666677888887764   5554443311  111      1145578899999999999999999999999999999998 


Q ss_pred             HHHHHHHHhh----hCCCceee--CCeEEEecC
Q 028424          154 DQELLEYVKE----EHPEWEMK--DGFVFFQKA  180 (209)
Q Consensus       154 ~~e~~~f~~~----~~~gW~~~--~~~i~f~~~  180 (209)
                      ++++..++..    ..-.=.+|  +|.|+|..+
T Consensus       373 ~~evE~~ls~mI~~g~i~akIDq~~giV~F~~~  405 (445)
T 4b4t_P          373 ESQTETYISDLVNQGIIYAKVNRPAKIVNFEKP  405 (445)
T ss_dssp             HHHHHHHHHHHHHHTSSCCEEETTTTEEEC---
T ss_pred             HHHHHHHHHHHHHCCCEEEEEcCCCCEEEECCC
Confidence            8899888752    12223667  676777654

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

Probab=97.07  E-value=0.048  Score=46.63  Aligned_cols=173  Identities=11%  Similarity=0.118  Sum_probs=111.2

Q ss_pred             HHHHHHHHHHhhhcChHHHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHHHHhhCCHHHHHHHHHhccHhh-hcCch
Q 028424            5 DIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLRLLVQNRIAEFHTELELLSSTA-LENPC   83 (209)
Q Consensus         5 ~vlEi~a~~sl~~~D~~~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~LL~~n~i~efh~~Le~l~~~~-~~~~~   83 (209)
                      .+++.+..+....+|..+-.+|+.+.-..|.... ...........+.+.++.....+...+....+....... ..++.
T Consensus       217 ~~~~~~g~~~~~~~~y~~A~~~~~~a~~~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  295 (434)
T 4b4t_Q          217 ELDLMSGILHCEDKDYKTAFSYFFESFESYHNLT-THNSYEKACQVLKYMLLSKIMLNLIDDVKNILNAKYTKETYQSRG  295 (434)
T ss_dssp             HHHHHHHHHTTSSSCHHHHHHHHHHHHHHHHHTT-TSSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHCSSSSTTCCCHH
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHhhhhh-hhhhHHHHHHHHHHHHHHHHhccchhHHHhHHHHHHHHHHhcchh
Confidence            4566777777778888877777766655554421 111222334455555555555566555555554433222 26677


Q ss_pred             hhhHHHHHHHHHhcChHHHHHHhhcC-----CCcchHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHH
Q 028424           84 IKHAVELEQSFMEGAYNRVLSAKQNV-----PNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELL  158 (209)
Q Consensus        84 I~~~~~leq~L~eGnY~kv~~~~~~~-----P~~~~~~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~  158 (209)
                      +.....+......+++..+-......     ..+.....++.+..++|.....-+.+.|++|+++.++..|+++ ++++.
T Consensus       296 ~~~~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~y~~i~l~~la~~l~~~-~~~~E  374 (434)
T 4b4t_Q          296 IDAMKAVAEAYNNRSLLDFNTALKQYEKELMGDELTRSHFNALYDTLLESNLCKIIEPFECVEISHISKIIGLD-TQQVE  374 (434)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHTHHHHTCSHHHHHHHHHHHHHHHHHHHHHHHSSCSCEEHHHHHHHHTCC-HHHHH
T ss_pred             hhHHHHHHHHHHhhhHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHhCcC-HHHHH
Confidence            77777888888888877765543211     1233456678889999999999999999999999999999997 77777


Q ss_pred             HHHhh----hCCCceee--CCeEEEec
Q 028424          159 EYVKE----EHPEWEMK--DGFVFFQK  179 (209)
Q Consensus       159 ~f~~~----~~~gW~~~--~~~i~f~~  179 (209)
                      .++..    ..-.=.+|  +|.+++..
T Consensus       375 ~~l~~lI~~~~i~a~id~~~g~v~~~~  401 (434)
T 4b4t_Q          375 GKLSQMILDKIFYGVLDQGNGWLYVYE  401 (434)
T ss_dssp             HHHHHHHHHTSSCCEEETTTTEEECC-
T ss_pred             HHHHHHHhCCCcceecccccCeEeeCC
Confidence            66542    12222455  56666654

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

Probab=96.55  E-value=0.049  Score=48.76  Aligned_cols=155  Identities=12%  Similarity=0.097  Sum_probs=103.4

Q ss_pred             HHHHHHHHHHHhhhcChHHHHHHHHhhHHHHhcCCCCCCCCcchhHHHHHHHHH-HHhhCCHHHHHHHHHhccHhh-hcC
Q 028424            4 GDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMILGLNLLR-LLVQNRIAEFHTELELLSSTA-LEN   81 (209)
Q Consensus         4 r~vlEi~a~~sl~~~D~~~F~~~~~qLk~~Y~~~~~~l~~s~~~~~il~l~LL~-LL~~n~i~efh~~Le~l~~~~-~~~   81 (209)
                      -.+|+..+.+.-..+|.++|-++.-+--..|... ..+  ++..-.-+++.++- .|...++-.|-.+|..-.... .++
T Consensus       169 ~~~y~~~~~~~~~~~~~a~~y~~~l~~l~~~~~~-~~~--~~~~~~~~a~~l~~~all~~~i~~f~eLL~~p~i~~L~~~  245 (393)
T 4b4t_O          169 NSFYSTNSQYFKFKNDFNSFYYTSLLYLSTLEPS-TSI--TLAERQQLAYDLSISALLGDKIYNFGELLHHPIMETIVND  245 (393)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTS-SSC--SHHHHHHHHHHHHHHHHHCCSSCSTHHHHHSCCTTSSCSS
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcccc-ccC--CHHHHHHHHHHHHHHHHcCCCCCChHHHhCChHHHHhhcC
Confidence            3567888888888888888777665544444422 112  22333344444443 566677778877776543333 367


Q ss_pred             chhhhHHHHHHHHHhcChHHHHHHhh-cCC-CcchHHHHHHHHHHHHHHHHHHHH--hccCCccHHHHHHhhCCCCHHHH
Q 028424           82 PCIKHAVELEQSFMEGAYNRVLSAKQ-NVP-NETYGYFMDLLAKTVRDEIAGCSE--KAYDYLSIKDAGQMLLFTSDQEL  157 (209)
Q Consensus        82 ~~I~~~~~leq~L~eGnY~kv~~~~~-~~P-~~~~~~fm~~L~~tiR~~ia~~ie--kAY~sl~l~~a~~lL~f~~~~e~  157 (209)
                      |......+|=+....|++..+-.... +.+ .+..+...+.+...+|.-....+.  +.|++||.+.+++.|+++ ++|+
T Consensus       246 ~~~~~l~~Ll~~f~~g~~~~f~~~~~~~~~~~~~l~~~~~~l~~kirll~l~~l~~~~~~~~i~f~~ia~~l~i~-~~ev  324 (393)
T 4b4t_O          246 SNYDWLFQLLNALTVGDFDKFDSLIKVQISKIPILAQHESFLRQKICLMTLIETVFVKNIRMLSFEDISKATHLP-KDNV  324 (393)
T ss_dssp             SSTTHHHHHHHHHHHTCHHHHHHHCCHHHHHSHHHHHHHHHHHHHHHHHHHHHHHCSSSCCCEEHHHHHHHHTCC-HHHH
T ss_pred             CchHHHHHHHHHHhcCCHHHHHHHHHHhhhhCcchhhhHHHHHHHHHHHHHHHHhccCCCCcCcHHHHHHHhCcC-HHHH
Confidence            88999999999999999999976432 111 123445555667777766665443  457799999999999997 8899


Q ss_pred             HHHHh
Q 028424          158 LEYVK  162 (209)
Q Consensus       158 ~~f~~  162 (209)
                      ..++-
T Consensus       325 E~lli  329 (393)
T 4b4t_O          325 EHLVM  329 (393)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            88875

>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=95.51  E-value=0.047  Score=38.89  Aligned_cols=59  Identities=17%  Similarity=0.287  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhh----hCCCceee--CCeEEEecC
Q 028424          121 LAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKE----EHPEWEMK--DGFVFFQKA  180 (209)
Q Consensus       121 L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~----~~~gW~~~--~~~i~f~~~  180 (209)
                      |.+++.+.....+.+-|++|+++.++++|+++ ++++.+++..    ..-.=++|  +|.|.|..+
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            45667777777888999999999999999998 8888777642    22233556  667777553

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

Probab=92.77  E-value=0.38  Score=39.21  Aligned_cols=71  Identities=17%  Similarity=0.121  Sum_probs=54.7

Q ss_pred             HHHHHHHHhcChHHHHHHhhcCCCcchHHHHH----HHHHHHHHHHHHHHHh------ccCCccHHHHHHhhCCC-----
Q 028424           88 VELEQSFMEGAYNRVLSAKQNVPNETYGYFMD----LLAKTVRDEIAGCSEK------AYDYLSIKDAGQMLLFT-----  152 (209)
Q Consensus        88 ~~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~----~L~~tiR~~ia~~iek------AY~sl~l~~a~~lL~f~-----  152 (209)
                      ..|=+++-.||..++-+..++..    ..|++    .+++++|.-+...+-|      .|+.||+++++.-|.+.     
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            47889999999999988766522    34554    3788999887766655      69999999999999774     


Q ss_pred             CHHHHHHHHh
Q 028424          153 SDQELLEYVK  162 (209)
Q Consensus       153 ~~~e~~~f~~  162 (209)
                      +++|++..+.
T Consensus       160 ~~~evE~ila  169 (203)
T 3t5x_A          160 DIDEVQCILA  169 (203)
T ss_dssp             CHHHHHHHHH
T ss_pred             CHHHHHHHHH
Confidence            6888877764

>4b4t_S RPN3, 26S proteasome regulatory subunit RPN3; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=88.45  E-value=0.36  Score=45.18  Aligned_cols=75  Identities=19%  Similarity=0.171  Sum_probs=53.7

Q ss_pred             HHHHHHHHHhcChHHHHHHhhcCC-----CcchHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHH
Q 028424           87 AVELEQSFMEGAYNRVLSAKQNVP-----NETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYV  161 (209)
Q Consensus        87 ~~~leq~L~eGnY~kv~~~~~~~P-----~~~~~~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~  161 (209)
                      =..|-++...||-.++-....+.-     ...| -++..+...+...-...+.++|++||+.+++..|++++++++...+
T Consensus       345 Y~~Lv~Avr~GdL~~F~~~L~~h~~~F~~Dgty-~LI~rLr~~vir~~irkis~~YsrIsL~dIa~kL~L~s~eeaE~iV  423 (523)
T 4b4t_S          345 YYHLTKAVKLGDLKKFTSTITKYKQLLLKDDTY-QLCVRLRSNVIKTGIRIISLTYKKISLRDICLKLNLDSEQTVEYMV  423 (523)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHTHHHHHHTTCT-HHHHHHHHHHHHHHHHHSCCCSSEECHHHHHHHHHHHHSSCHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHhcceeccCChh-HHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHhCCCCHHHHHHHH
Confidence            346778888899888766443211     1112 2456666677777788999999999999999999998777666655


Q ss_pred             h
Q 028424          162 K  162 (209)
Q Consensus       162 ~  162 (209)
                      .
T Consensus       424 A  424 (523)
T 4b4t_S          424 S  424 (523)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3chm_A COP9 signalosome complex subunit 7; heat/ARM repeats, winged helix motif, developmental protein, phosphoprotein; 1.50A {Arabidopsis thaliana}

Probab=84.17  E-value=8.7  Score=30.36  Aligned_cols=99  Identities=13%  Similarity=0.122  Sum_probs=72.6

Q ss_pred             HHhhCCHHHHHHHHHhccH-hhhcCchhhhHHHHHHHHHhcChHHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHHhc
Q 028424           58 LLVQNRIAEFHTELELLSS-TALENPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKA  136 (209)
Q Consensus        58 LL~~n~i~efh~~Le~l~~-~~~~~~~I~~~~~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~~tiR~~ia~~iekA  136 (209)
                      -|...++=.|..+| .+|. ...++..-+...+|=+....|+|...-....+.|.  ..   +.+...+|.=.+..+...
T Consensus        33 Al~~p~vf~F~eLL-~~p~v~~L~~~~~~~~~~LL~iF~~G~~~~y~~~~~~~p~--L~---~~~~~KlrlLtL~sLa~~  106 (169)
T 3chm_A           33 ATSHPSLFAFSEIL-ALPNVAQLEGTTDSVYLDLLRLFAHGTWGDYKCNATRLPH--LS---PDQILKLKQLTVLTLAES  106 (169)
T ss_dssp             HHHCTTCCCCHHHH-TCHHHHTTTTSTTHHHHHHHHHHHHCCHHHHHHHGGGSCC--CC---HHHHHHHHHHHHHHHHHH
T ss_pred             HhcCCCeeehHHHh-CChHHHHhcCCChhHHHHHHHHHhcCCHHHHHHhHHhCcc--hH---HHHHHHHHHHHHHHHHHh
Confidence            44455566676666 4443 22233334777889999999999987766666673  22   677788888777766666


Q ss_pred             cCCccHHHHHHhhCCCCHHHHHHHHh
Q 028424          137 YDYLSIKDAGQMLLFTSDQELLEYVK  162 (209)
Q Consensus       137 Y~sl~l~~a~~lL~f~~~~e~~~f~~  162 (209)
                      -+.||.+++++-|+++|.+|+..|+-
T Consensus       107 ~~~lsy~~I~~~l~i~~~~evE~lvI  132 (169)
T 3chm_A          107 NKVLPYDTLMVELDVSNVRELEDFLI  132 (169)
T ss_dssp             CSEEEHHHHHHHHTCCSHHHHHHHHH
T ss_pred             CCCcCHHHHHHHhCCCCHHHHHHHHH
Confidence            78999999999999999999999986

>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=81.78  E-value=8.1  Score=34.55  Aligned_cols=140  Identities=11%  Similarity=0.087  Sum_probs=100.7

Q ss_pred             HHHHHHHHHHHhhhcChHHHHHHHHhh-HHHHhcCCCCCCCCcchhHHHH-HHHHHHHhhCCHHHHHHHHHhccHhhhcC
Q 028424            4 GDIYEHAVLLSVKVEDQDAFERDFFQL-KPYYTDAGKRLPPSPNEYMILG-LNLLRLLVQNRIAEFHTELELLSSTALEN   81 (209)
Q Consensus         4 r~vlEi~a~~sl~~~D~~~F~~~~~qL-k~~Y~~~~~~l~~s~~~~~il~-l~LL~LL~~n~i~efh~~Le~l~~~~~~~   81 (209)
                      .+++=++++.++..+|..++....++= ...| ..          +++-. ..|+.....+++.+|...|+...+....|
T Consensus       220 ~~~lkYlvL~aLl~~~r~el~~~l~~~~~~~~-~~----------pei~~l~~L~~a~~~~dl~~f~~iL~~~~~~l~~D  288 (394)
T 3txn_A          220 LTSLKYMLLCKIMLGQSDDVNQLVSGKLAITY-SG----------RDIDAMKSVAEASHKRSLADFQAALKEYKKELAED  288 (394)
T ss_dssp             HHHHHHHHHHHHHTTCGGGHHHHHHSHHHHTT-CS----------HHHHHHHHHHHHHHTTCHHHHHHHHHHSTTTTTTS
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHhcccccccc-CC----------ccHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcC
Confidence            567888999999999988888766543 1223 21          12222 34666778999999999999988877899


Q ss_pred             chhh-hHHHHHHHHHhcChHHHHHHhhcCCCcchHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCH
Q 028424           82 PCIK-HAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSD  154 (209)
Q Consensus        82 ~~I~-~~~~leq~L~eGnY~kv~~~~~~~P~~~~~~fm~~L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~  154 (209)
                      |+++ |.-.|.+.+.+.++-+++..++.+.-+..+-....=.+-+-..++.+|...=-.=.++....++.+..+
T Consensus       289 ~~l~~h~~~L~~~Ir~~~L~~i~~pYsrIsl~~iA~~l~ls~~evE~~L~~lI~dg~I~a~IDq~~giv~~~~~  362 (394)
T 3txn_A          289 VIVQAHLGTLYDTMLEQNLCRIIEPYSRVQVAHVAESIQLPMPQVEKKLSQMILDKKFSGILDQGEGVLIVFEE  362 (394)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTCSEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSCEEEETTTTEEEECCC
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhHhhceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCeeEEEcCCCCEEEECCC
Confidence            9976 467899999999999999888776422222222222667777888888766656667778888877644

---

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	209
d1rz4a1	85	Eukaryotic translation initiation factor 3 subunit	98.35
d1ufma_	84	COP9 signalosome complex subunit 4, GSN4 {Mouse (M	96.68

>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=98.35  E-value=1.4e-06  Score=61.47  Aligned_cols=58  Identities=19%  Similarity=0.196  Sum_probs=50.2

Q ss_pred             HHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhhhCCCceeeCCeEEEecC
Q 028424          121 LAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQKA  180 (209)
Q Consensus       121 L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~~~~gW~~~~~~i~f~~~  180 (209)
                      |-|.||.-|+-.+.-+|.+|+.+-++++||..+++++.+|++  .-||++++|..+|+.+
T Consensus         3 FedsIR~~i~~vv~iTyq~I~~~~L~e~LG~~~d~~L~~~i~--~~gW~~~~~g~v~v~n   60 (85)
T d1rz4a1           3 FEDSVRKFICHVVGITYQHIDRWLLAEMLGDLSDSQLKVWMS--KYGWSADESGQIFICS   60 (85)
T ss_dssp             HHHHHHHHHHHHHHHHCSEECHHHHHHHTTSCCHHHHHHHHH--HHTCEECC--CEECCC
T ss_pred             HHHHHHHHHHhheeeeeeEEcHHHHHHHhCCCCHHHHHHHHH--HcCCEEcCCCEEEecC
Confidence            578999999999999999999999999999999999999996  3699998666556654

>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=96.68  E-value=0.0024  Score=43.95  Aligned_cols=60  Identities=17%  Similarity=0.289  Sum_probs=46.7

Q ss_pred             HHHHHHHHHHHHHHhccCCccHHHHHHhhCCCCHHHHHHHHhh----hCCCceee--CCeEEEecCC
Q 028424          121 LAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKE----EHPEWEMK--DGFVFFQKAK  181 (209)
Q Consensus       121 L~~tiR~~ia~~iekAY~sl~l~~a~~lL~f~~~~e~~~f~~~----~~~gW~~~--~~~i~f~~~~  181 (209)
                      |.+++++.-...+.+.|++|++++++++|+++ ++++..++..    ..-.=++|  +|.|+|..++
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            45677788888899999999999999999997 8888777652    23355566  7778887754