Psyllid ID: psy4083

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370----

MAGAMMFERSASQISITGNSYKTGYEEENHDEEVKAKEQNILQLGEKYKQEGKAIELAELIKKTRPFLSQISKAKAAKLVRSLVDFFLDLETRTGMEVALCKECIEWAKEERRTFLRQSLEARLIALYFDTGEYTEALKLSSSLLKELKKLDDKNLLVEVLLLESKTYHALSNLSTSRASLTSARTTANSIYCPPKMQAALDLQSGILHAADEQDFKTAFSYFYEAFEGFSTVDHNHAMMSLKYMLLSKIMLNTPEDVNQILSELEDDTIVKAHIGTLYDNMLEQNLCRIIEPYSRVEVGFIAKSIKLDELAVEKKLSQMILDKKFHGILDQGEKVLIVFEGAEIDKTYEKALETITSMGKVIDTLYQKAKKLT

ccccccccccHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccccHHHHHHHHHHcccHHHcccccHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHcccHHHHHHHHHHHHHccccEEEEEccccEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcc

cHHHHHHHHHccHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHcccEcccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHccccEEEHHHHHHHHcccHHHHHHHHHHHHHHccEEEEEEccccEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcc

magammfersasqisitgnsyktgyeeenhdeEVKAKEQNILQLGEKYKQEGKAIELAELIKKTRPFLSQISKAKAAKLVRSLVDFFLDLETRTGMEVALCKECIEWAKEERRTFLRQSLEARLIALYFDTGEYTEALKLSSSLLKELKKLDDKNLLVEVLLLESKTYHALSNLSTSRASLtsarttansiycppkmQAALDLQSGILHAADEQDFKTAFSYFYEAFegfstvdhNHAMMSLKYMLLSKIMLNTPEDVNQILSELEDDTIVKAHIGTLYDNMLEQNLcriiepysrveVGFIAKSIKLDELAVEKKLSQMILDKKFHGILDQGEKVLIVFEGAEIDKTYEKALETITSMGKVIDTLYQKAKKLT

magammfersasqisitgnsYKTGYEEENHDEEVKAKEQNILQLGEKYKQEGKAIELAELIKKTRPFLSQISKAKAAKLVRSLVDFFLDLETRTGMEVALCKECIEWAKEERRTFLRQSLEARLIALYFDTGEYTEALKLSSSLLKELKKLDDKNLLVEVLLLEsktyhalsnlstsraslTSARTTANSIYCPPKMQAALDLQSGILHAADEQDFKTAFSYFYEAFEGFSTVDHNHAMMSLKYMLLSKIMLNTPEDVNQILSELEDDTIVKAHIGTLYDNMLEQNLCRIIEPYSRVEVGFIAKSIKLDELAVEKKLSQMILDKKFHGILDQGEKVLIVFEGAEIDKTYEKALETITSMGKVIDTLYQKAKKLT

MAGAMMFERSASQISITGNSYKTGYEEENHDEEVKAKEQNILQLGEKYKQEGKAIELAELIKKTRPFLSQISKAKAAKLVRSLVDFFLDLETRTGMEVALCKECIEWAKEERRTFLRQSLEARLIALYFDTGEYTEAlklsssllkelkklddknllvevllleskTYHalsnlstsrasltsarttansIYCPPKMQAALDLQSGILHAADEQDFKTAFSYFYEAFEGFSTVDHNHAMMSLKYMLLSKIMLNTPEDVNQILSELEDDTIVKAHIGTLYDNMLEQNLCRIIEPYSRVEVGFIAKSIKLDELAVEKKLSQMILDKKFHGILDQGEKVLIVFEGAEIDKTYEKALETITSMGKVIDTLYQKAKKLT

***************************************************GKAIELAELIKKTRPFLSQISKAKAAKLVRSLVDFFLDLETRTGMEVALCKECIEWAKEERRTFLRQSLEARLIALYFDTGEYTEALKLSSSLLKELKKLDDKNLLVEVLLLESKTYHALSNL***********TTANSIYCPPKMQAALDLQSGILHAADEQDFKTAFSYFYEAFEGFSTVDHNHAMMSLKYMLLSKIMLNTPEDVNQILSELEDDTIVKAHIGTLYDNMLEQNLCRIIEPYSRVEVGFIAKSIKLDELAVEKKLSQMILDKKFHGILDQGEKVLIVFEGAEIDKTYEKALETITSMGKVIDTLY*******

**********************************KAKEQNILQLGEKYKQEGKAIELAELIKKTRPFLSQISKAKAAKLVRSLVDFFLDLETRTGMEVALCKECIEWAKEERRTFLRQSLEARLIALYFDTGEYTEALKL************DKNLLVEVLLLESKTYHALSNLSTSRASLTSARTTANSIYCPPKMQAALDLQSGILHAADEQDFKTAFSYFYEAFEGFSTVDHNHAMMSLKYMLLSKIMLNTPEDVNQILSELEDDTIVKAHIGTLYDNMLEQNLCRIIEPYSRVEVGFIAKSIKLDELAVEKKLSQMILDKKFHGILDQGEKVLIVFEGAEI*KTYEKALETITSMGKVIDTLYQKAKK**

********RSASQISITGNSYKTGYEEENHDEEVKAKEQNILQLGEKYKQEGKAIELAELIKKTRPFLSQISKAKAAKLVRSLVDFFLDLETRTGMEVALCKECIEWAKEERRTFLRQSLEARLIALYFDTGEYTEALKLSSSLLKELKKLDDKNLLVEVLLLESKTYHALSNLSTSRASLTSARTTANSIYCPPKMQAALDLQSGILHAADEQDFKTAFSYFYEAFEGFSTVDHNHAMMSLKYMLLSKIMLNTPEDVNQILSELEDDTIVKAHIGTLYDNMLEQNLCRIIEPYSRVEVGFIAKSIKLDELAVEKKLSQMILDKKFHGILDQGEKVLIVFEGAEIDKTYEKALETITSMGKVIDTLYQKAKKLT

*************ISITG*********ENHDEEVKAKEQNILQLGEKYKQEGKAIELAELIKKTRPFLSQISKAKAAKLVRSLVDFFLDLETRTGMEVALCKECIEWAKEERRTFLRQSLEARLIALYFDTGEYTEALKLSSSLLKELKKLDDKNLLVEVLLLESKTYHALSNLSTSRASLTSARTTANSIYCPPKMQAALDLQSGILHAADEQDFKTAFSYFYEAFEGFSTVDHNHAMMSLKYMLLSKIMLNTPEDVNQILSELEDDTIVKAHIGTLYDNMLEQNLCRIIEPYSRVEVGFIAKSIKLDELAVEKKLSQMILDKKFHGILDQGEKVLIVFEGAEIDKTYEKALETITSMGKVIDTLYQKAKK**

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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MAGAMMFERSASQISITGNSYKTGYExxxxxxxxxxxxxxxxxxxxxYKQEGKAIELAELIKKTRPFLSQISKAKAAKLVRSLVDFFLDLETRTGMEVALCKECIEWAKEERRTFLRQSLEARLIALYFDTGEYTEALKLSSSLLKELKKLDDKNLLVEVLLLESKTYHALSNLSTSRASLTSARTTANSIYCPPKMQAALDLQSGILHAADEQDFKTAFSYFYEAFEGFSTVDHNHAMMSLKYMLLSKIMLNTPEDVNQILSELEDDTIVKAHIGTLYDNMLEQNLCRIIEPYSRVEVGFIAKSIKLDELAVEKKLSQMILDKKFHGILDQGEKVLIVFEGAEIDKTYEKALETITSMGKVIDTLYQKAKKLT

no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		374	2.2.26 [Sep-21-2011]
Q7KLV9		422	26S proteasome non-ATPase	yes	N/A	1.0	0.886	0.651	1e-150
F1LMZ8		422	26S proteasome non-ATPase	yes	N/A	0.930	0.824	0.609	1e-133
O00231		422	26S proteasome non-ATPase	yes	N/A	0.930	0.824	0.609	1e-133
Q2KI42		422	26S proteasome non-ATPase	yes	N/A	0.930	0.824	0.609	1e-133
Q8BG32		422	26S proteasome non-ATPase	yes	N/A	0.930	0.824	0.609	1e-133
F6XBL2		422	26S proteasome non-ATPase	yes	N/A	0.994	0.881	0.582	1e-132
F1QGH9		422	26S proteasome non-ATPase	yes	N/A	0.997	0.883	0.575	1e-132
F6P3G4		421	26S proteasome non-ATPase	no	N/A	0.994	0.883	0.569	1e-131
Q20938		438	Probable 26S proteasome r	yes	N/A	0.919	0.785	0.519	1e-105
Q9P7S2		421	Probable 26S proteasome r	yes	N/A	0.895	0.795	0.485	3e-99

>sp\|Q7KLV9\|PSD11_DROME 26S proteasome non-ATPase regulatory subunit 11 OS=Drosophila melanogaster GN=Rpn6 PE=1 SV=1	Back alignment and function desciption

 Score =  533 bits (1372), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 275/422 (65%), Positives = 313/422 (74%), Gaps = 48/422 (11%)

Query: 1   MAGAMMFERSASQISITGNSYKTGY---------EEENHDEEVKAKEQNILQLGEKYKQE 51
           MAGA +FER+ +  S+      +             EN +E ++ KEQ ILQ GE YKQE
Sbjct: 1   MAGATLFERAQALSSVNREEQDSSLLNKLVRDQEGAENDEERIRIKEQGILQQGELYKQE 60

Query: 52  GKAIELAELIKKTRPFLSQISKAKAAKLVRSLVDFFLDLETRTGMEVALCKECIEWAKEE 111
           GKA ELA+LIK TRPFLS ISKAKAAKLVRSLVD FLD++  TG+EV LCK+CIEWAK+E
Sbjct: 61  GKAKELADLIKVTRPFLSSISKAKAAKLVRSLVDMFLDMDAGTGIEVQLCKDCIEWAKQE 120

Query: 112 RRTFLRQSLEARLIALYFDTGEYTEALKLSSSLLKELKKLDDKNLLVEVLLLESKTYHAL 171
           +RTFLRQSLEARLIALYFDT  YTEAL L + LL+ELKKLDDKNLLVEV LLESKTYHAL
Sbjct: 121 KRTFLRQSLEARLIALYFDTALYTEALALGAQLLRELKKLDDKNLLVEVQLLESKTYHAL 180

Query: 172 SNLSTSRASLTSARTTANSIYCPPKMQAALDLQSGILHAADEQDFKTAFSYFYEAFEGFS 231
           SNL  +RA+LTSARTTAN+IYCPPK+Q ALDLQSGILHAADE+DFKTAFSYFYEAFEGF 
Sbjct: 181 SNLPKARAALTSARTTANAIYCPPKVQGALDLQSGILHAADERDFKTAFSYFYEAFEGFD 240

Query: 232 TVDHNHAMMSLKYMLLSKIMLNTPEDVNQILS---------------------------- 263
           +VD   A+ SLKYMLL KIML   +DVNQ++S                            
Sbjct: 241 SVDSVKALTSLKYMLLCKIMLGQSDDVNQLVSGKLAITYSGRDIDAMKSVAEASHKRSLA 300

Query: 264 -----------ELEDDTIVKAHIGTLYDNMLEQNLCRIIEPYSRVEVGFIAKSIKLDELA 312
                      EL +D IV+AH+GTLYD MLEQNLCRIIEPYSRV+V  +A+SI+L    
Sbjct: 301 DFQAALKEYKKELAEDVIVQAHLGTLYDTMLEQNLCRIIEPYSRVQVAHVAESIQLPMPQ 360

Query: 313 VEKKLSQMILDKKFHGILDQGEKVLIVFEGAEIDKTYEKALETITSMGKVIDTLYQKAKK 372
           VEKKLSQMILDKKF GILDQGE VLIVFE   +DKTYE+ LETI SMGKV+DTLYQKAKK
Sbjct: 361 VEKKLSQMILDKKFSGILDQGEGVLIVFEETPVDKTYERVLETIQSMGKVVDTLYQKAKK 420

Query: 373 LT 374
           L+
Sbjct: 421 LS 422

Component of the lid subcomplex of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. In the complex, RPN6 is required for proteasome assembly (By similarity). May act as linker between 19S regulatory subunit and the 20S proteasome core.
Drosophila melanogaster (taxid: 7227)

>sp\|F1LMZ8\|PSD11_RAT 26S proteasome non-ATPase regulatory subunit 11 OS=Rattus norvegicus GN=Psmd11 PE=2 SV=2	Back alignment and function description

>sp\|O00231\|PSD11_HUMAN 26S proteasome non-ATPase regulatory subunit 11 OS=Homo sapiens GN=PSMD11 PE=1 SV=3	Back alignment and function description

>sp\|Q2KI42\|PSD11_BOVIN 26S proteasome non-ATPase regulatory subunit 11 OS=Bos taurus GN=PSMD11 PE=2 SV=3	Back alignment and function description

>sp\|Q8BG32\|PSD11_MOUSE 26S proteasome non-ATPase regulatory subunit 11 OS=Mus musculus GN=Psmd11 PE=1 SV=3	Back alignment and function description

>sp\|F6XBL2\|PSD11_XENTR 26S proteasome non-ATPase regulatory subunit 11 OS=Xenopus tropicalis GN=psmd11 PE=3 SV=2	Back alignment and function description

>sp\|F1QGH9\|PS11B_DANRE 26S proteasome non-ATPase regulatory subunit 11B OS=Danio rerio GN=psmd11b PE=2 SV=1	Back alignment and function description

>sp\|F6P3G4\|PS11A_DANRE 26S proteasome non-ATPase regulatory subunit 11A OS=Danio rerio GN=psmd11a PE=2 SV=1	Back alignment and function description

>sp\|Q20938\|PS11A_CAEEL Probable 26S proteasome regulatory subunit rpn-6.1 OS=Caenorhabditis elegans GN=rpn-6.1 PE=2 SV=2	Back alignment and function description

>sp\|Q9P7S2\|RPN6_SCHPO Probable 26S proteasome regulatory subunit rpn6 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpn6 PE=3 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		374
270013942		630	hypothetical protein TcasGA2_TC012621 [T	0.991	0.588	0.697	1e-161
189241162		417	PREDICTED: similar to Proteasome p44.5 s	0.991	0.889	0.697	1e-160
171919759		421	Rpn6-PB-like protein [Stratiomys singula	1.0	0.888	0.676	1e-153
340723582		423	PREDICTED: 26S proteasome non-ATPase reg	0.994	0.879	0.670	1e-152
350426717		423	PREDICTED: 26S proteasome non-ATPase reg	0.994	0.879	0.670	1e-152
48097764		423	PREDICTED: 26S proteasome non-ATPase reg	0.994	0.879	0.668	1e-151
383857417		423	PREDICTED: 26S proteasome non-ATPase reg	0.994	0.879	0.668	1e-151
332018792		423	26S proteasome non-ATPase regulatory sub	0.994	0.879	0.665	1e-151
307208985		423	26S proteasome non-ATPase regulatory sub	0.994	0.879	0.663	1e-151
157132413		416	26S proteasome subunit S9 [Aedes aegypti	0.991	0.891	0.673	1e-151

>gi\|270013942\|gb\|EFA10390.1\| hypothetical protein TcasGA2_TC012621 [Tribolium castaneum]	Back alignment and taxonomy information

 Score =  572 bits (1475), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 293/420 (69%), Positives = 330/420 (78%), Gaps = 49/420 (11%)

Query: 1   MAGAMMFERSASQISITGNSY------KTGYEEENHDEE-VKAKEQNILQLGEKYKQEGK 53
           MAGAM+FER+ S   +  +++      K   E+ ++DEE +K+KEQ+IL LGE+YK+EGK
Sbjct: 214 MAGAMLFERAQS---VPNSNHEKLLKLKRASEDPDNDEENIKSKEQDILNLGEQYKKEGK 270

Query: 54  AIELAELIKKTRPFLSQISKAKAAKLVRSLVDFFLDLETRTGMEVALCKECIEWAKEERR 113
           A ELAELIK TRPFLS ISKAKAAKLVRSLVDFFLDLE   G+EV LCKECIEWAKEERR
Sbjct: 271 AKELAELIKATRPFLSMISKAKAAKLVRSLVDFFLDLEAGIGIEVQLCKECIEWAKEERR 330

Query: 114 TFLRQSLEARLIALYFDTGEYTEALKLSSSLLKELKKLDDKNLLVEVLLLESKTYHALSN 173
           TFLRQSLEARLIALYFDTG +TEAL+L S+LLKELKKLDDKNLLVEV LLESKTYHALSN
Sbjct: 331 TFLRQSLEARLIALYFDTGMFTEALQLGSTLLKELKKLDDKNLLVEVQLLESKTYHALSN 390

Query: 174 LSTSRASLTSARTTANSIYCPPKMQAALDLQSGILHAADEQDFKTAFSYFYEAFEGFSTV 233
           L  +RA+LTSARTTAN+IYCPPKMQAALDLQSGILHAADE+DFKTA+SYFYEAFEGF +V
Sbjct: 391 LPKARAALTSARTTANAIYCPPKMQAALDLQSGILHAADEKDFKTAYSYFYEAFEGFDSV 450

Query: 234 DHNHAMMSLKYMLLSKIMLNTPEDVNQILS------------------------------ 263
           +   A+ +LKYMLLSKIMLN PEDV QI+S                              
Sbjct: 451 ESPKALTALKYMLLSKIMLNNPEDVQQIVSGKLAIKYAGKDIDAMKAVAQASHKRSLADF 510

Query: 264 ---------ELEDDTIVKAHIGTLYDNMLEQNLCRIIEPYSRVEVGFIAKSIKLDELAVE 314
                    ELEDD IV+AH+GTLYDNMLEQNLCRIIEPYSRV+V ++AK+IKL    VE
Sbjct: 511 QQAVKQFKHELEDDVIVRAHLGTLYDNMLEQNLCRIIEPYSRVQVDYVAKTIKLPMPQVE 570

Query: 315 KKLSQMILDKKFHGILDQGEKVLIVFEGAEIDKTYEKALETITSMGKVIDTLYQKAKKLT 374
           KKLSQMILD KFHGILDQGE VLIVFE   +DKTYE ALETI SM KV+DTLYQKAKKL+
Sbjct: 571 KKLSQMILDAKFHGILDQGEGVLIVFEETPVDKTYEMALETIQSMSKVVDTLYQKAKKLS 630

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi\|189241162\|ref\|XP_974687.2\| PREDICTED: similar to Proteasome p44.5 subunit CG10149-PB [Tribolium castaneum]	Back alignment and taxonomy information

>gi\|171919759\|gb\|ACB59075.1\| Rpn6-PB-like protein [Stratiomys singularior]	Back alignment and taxonomy information

>gi\|340723582\|ref\|XP_003400168.1\| PREDICTED: 26S proteasome non-ATPase regulatory subunit 11-like [Bombus terrestris]	Back alignment and taxonomy information

>gi\|350426717\|ref\|XP_003494522.1\| PREDICTED: 26S proteasome non-ATPase regulatory subunit 11-like [Bombus impatiens]	Back alignment and taxonomy information

>gi\|48097764\|ref\|XP_391945.1\| PREDICTED: 26S proteasome non-ATPase regulatory subunit 11-like isoform 1 [Apis mellifera] gi\|380022637\|ref\|XP_003695146.1\| PREDICTED: 26S proteasome non-ATPase regulatory subunit 11-like [Apis florea]	Back alignment and taxonomy information

>gi\|383857417\|ref\|XP_003704201.1\| PREDICTED: 26S proteasome non-ATPase regulatory subunit 11-like [Megachile rotundata]	Back alignment and taxonomy information

>gi\|332018792\|gb\|EGI59353.1\| 26S proteasome non-ATPase regulatory subunit 11 [Acromyrmex echinatior]	Back alignment and taxonomy information

>gi\|307208985\|gb\|EFN86185.1\| 26S proteasome non-ATPase regulatory subunit 11 [Harpegnathos saltator]	Back alignment and taxonomy information

>gi\|157132413\|ref\|XP_001656032.1\| 26S proteasome subunit S9 [Aedes aegypti] gi\|157132415\|ref\|XP_001656033.1\| 26S proteasome subunit S9 [Aedes aegypti] gi\|108871190\|gb\|EAT35415.1\| AAEL012419-PA [Aedes aegypti] gi\|403183277\|gb\|EJY57979.1\| AAEL012419-PB [Aedes aegypti]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		374
FB\|FBgn0028689		422	Rpn6 "Regulatory particle non-	0.703	0.623	0.562	5.5e-113
UNIPROTKB\|Q2KI42		422	PSMD11 "26S proteasome non-ATP	0.679	0.601	0.511	3.2e-100
UNIPROTKB\|E2RJ26		422	PSMD11 "Uncharacterized protei	0.679	0.601	0.511	3.2e-100
UNIPROTKB\|O00231		422	PSMD11 "26S proteasome non-ATP	0.679	0.601	0.511	3.2e-100
MGI\|MGI:1916327		422	Psmd11 "proteasome (prosome, m	0.679	0.601	0.511	3.2e-100
RGD\|1306450		422	Psmd11 "proteasome (prosome, m	0.679	0.601	0.511	3.2e-100
UNIPROTKB\|F1RKW8		392	PSMD11 "Uncharacterized protei	0.633	0.604	0.527	5.3e-100
UNIPROTKB\|F6XBL2		422	psmd11 "26S proteasome non-ATP	0.697	0.618	0.492	3.7e-99
ZFIN\|ZDB-GENE-030131-2711		421	psmd11a "proteasome (prosome,	0.679	0.603	0.5	2.6e-98
ZFIN\|ZDB-GENE-030131-984		422	psmd11b "proteasome (prosome,	0.679	0.601	0.492	5.3e-98

FB\|FBgn0028689 Rpn6 "Regulatory particle non-ATPase 6" [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

 Score = 714 (256.4 bits), Expect = 5.5e-113, Sum P(2) = 5.5e-113
 Identities = 153/272 (56%), Positives = 176/272 (64%)

Query:     1 MAGAMMFERSASQISITGNSYKTGY-------EE--ENHDEEVKAKEQNILQLGEKYKQE 51
             MAGA +FER+ +  S+      +         +E  EN +E ++ KEQ ILQ GE YKQE
Sbjct:     1 MAGATLFERAQALSSVNREEQDSSLLNKLVRDQEGAENDEERIRIKEQGILQQGELYKQE 60

Query:    52 GKAIELAELIKKTRPFLSQISKAKAAKLVRSLVDFFLDLETRTGMEVALCKECIEWAKEE 111
             GKA ELA+LIK TRPFLS ISKAKAAKLVRSLVD FLD++  TG+EV LCK+CIEWAK+E
Sbjct:    61 GKAKELADLIKVTRPFLSSISKAKAAKLVRSLVDMFLDMDAGTGIEVQLCKDCIEWAKQE 120

Query:   112 RRTFLRQSLEARLIALYFDTGEYTEAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTYHXX 171
             +RTFLRQSLEARLIALYFDT  YTEA                             TYH  
Sbjct:   121 KRTFLRQSLEARLIALYFDTALYTEALALGAQLLRELKKLDDKNLLVEVQLLESKTYHAL 180

Query:   172 XXXXXXXXXXXXXXXXXXXIYCPPKMQAALDLQSGILHAADEQDFKTAFSYFYEAFEGFS 231
                                IYCPPK+Q ALDLQSGILHAADE+DFKTAFSYFYEAFEGF 
Sbjct:   181 SNLPKARAALTSARTTANAIYCPPKVQGALDLQSGILHAADERDFKTAFSYFYEAFEGFD 240

Query:   232 TVDHNHAMMSLKYMLLSKIMLNTPEDVNQILS 263
             +VD   A+ SLKYMLL KIML   +DVNQ++S
Sbjct:   241 SVDSVKALTSLKYMLLCKIMLGQSDDVNQLVS 272

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

GO:0004175 "endopeptidase activity" evidence=IDA

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

GO:0006508 "proteolysis" evidence=ISS;IDA

GO:0005875 "microtubule associated complex" evidence=IDA

UNIPROTKB\|Q2KI42 PSMD11 "26S proteasome non-ATPase regulatory subunit 11" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|E2RJ26 PSMD11 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|O00231 PSMD11 "26S proteasome non-ATPase regulatory subunit 11" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

MGI\|MGI:1916327 Psmd11 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 11" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

RGD\|1306450 Psmd11 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 11" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|F1RKW8 PSMD11 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|F6XBL2 psmd11 "26S proteasome non-ATPase regulatory subunit 11" [Xenopus (Silurana) tropicalis (taxid:8364)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-030131-2711 psmd11a "proteasome (prosome, macropain) 216S subunit, non-ATPase, 11a" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-030131-984 psmd11b "proteasome (prosome, macropain) 216S subunit, non-ATPase, 11b" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

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)
O00231	PSD11_HUMAN	No assigned EC number	0.6098	0.9304	0.8246	yes	N/A
Q20938	PS11A_CAEEL	No assigned EC number	0.5194	0.9197	0.7853	yes	N/A
Q54UB5	PSD11_DICDI	No assigned EC number	0.4497	0.9010	0.8159	yes	N/A
Q8BG32	PSD11_MOUSE	No assigned EC number	0.6098	0.9304	0.8246	yes	N/A
Q7KLV9	PSD11_DROME	No assigned EC number	0.6516	1.0	0.8862	yes	N/A
F1QGH9	PS11B_DANRE	No assigned EC number	0.5751	0.9973	0.8838	yes	N/A
Q9P7S2	RPN6_SCHPO	No assigned EC number	0.4854	0.8957	0.7957	yes	N/A
F6P3G4	PS11A_DANRE	No assigned EC number	0.5690	0.9946	0.8836	no	N/A
Q9LP45	PSD11_ARATH	No assigned EC number	0.4668	0.9411	0.8400	yes	N/A
F1LMZ8	PSD11_RAT	No assigned EC number	0.6098	0.9304	0.8246	yes	N/A
Q12377	RPN6_YEAST	No assigned EC number	0.4289	0.9144	0.7880	yes	N/A
Q2KI42	PSD11_BOVIN	No assigned EC number	0.6098	0.9304	0.8246	yes	N/A
F6XBL2	PSD11_XENTR	No assigned EC number	0.5825	0.9946	0.8815	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Alignment Graph	Length	Definition	E-value
Query		374
COG5159		421	COG5159, RPN6, 26S proteasome regulatory complex c	1e-116
smart00753		88	smart00753, PAM, PCI/PINT associated module	2e-15
smart00088		88	smart00088, PINT, motif in proteasome subunits, In	2e-15
pfam01399		100	pfam01399, PCI, PCI domain	1e-13

>gnl\|CDD\|227488 COG5159, RPN6, 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

 Score =  343 bits (882), Expect = e-116
 Identities = 165/378 (43%), Positives = 225/378 (59%), Gaps = 42/378 (11%)

Query: 37  KEQNILQLGEKYKQEGKAIELAELIKKTRPFLSQISKAKAAKLVRSLVDFFLDLETRTGM 96
           +E  +L+L + Y  +G    L + I  +R  +   +K K  K++R+L++ F         
Sbjct: 44  QEATVLELFKLYVSKGDYCSLGDTITSSREAMEDFTKPKITKIIRTLIEKFPYSSDSLED 103

Query: 97  EVALCKECIEWAKEERRTFLRQSLEARLIALYFDTGEYTEALKLSSSLLKELKKLDDKNL 156
           ++ +    IEWA  E+R FLR  LE +LI L + TG+Y++AL L + LL ELKK DDK  
Sbjct: 104 QIKVLTALIEWADREKRKFLRLELECKLIYLLYKTGKYSDALALINPLLHELKKYDDKIN 163

Query: 157 LVEVLLLESKTYHALSNLSTSRASLTSARTTANSIYCPPKMQAALDLQSGILHAADEQDF 216
           L+ V LLESK YH + N+S S+ASLT+ART ANS YCPP++QA LDL SGILH  D++D+
Sbjct: 164 LITVHLLESKVYHEIRNVSKSKASLTAARTLANSAYCPPQLQAQLDLLSGILH-CDDRDY 222

Query: 217 KTAFSYFYEAFEGFSTVD-HNHAMMSLKYMLLSKIMLNTPEDVNQILS------------ 263
           KTA SYF EA EGF+ +     A +SLKYMLLSKIMLN  E+V  +L             
Sbjct: 223 KTASSYFIEALEGFTLLKMDVKACVSLKYMLLSKIMLNRREEVKAVLRNKNTLKHYDDRM 282

Query: 264 ----------------------------ELEDDTIVKAHIGTLYDNMLEQNLCRIIEPYS 295
                                       EL  D+ +++H+  LYD +LE+NL +IIEP+S
Sbjct: 283 IRAMLAVAEAFGNRSLKDFSDALAQYSDELHQDSFIRSHLQYLYDVLLEKNLVKIIEPFS 342

Query: 296 RVEVGFIAKSIKLDELAVEKKLSQMILDKKFHGILDQGEKVLIVFEGAEIDKTYEKALET 355
            VE+  IA  I LD   VE KLSQMILDK F+G LDQG+  LIV+     D TY++ALE 
Sbjct: 343 VVEISHIADVIGLDTNQVEGKLSQMILDKIFYGTLDQGDGCLIVYGEPAQDNTYDEALEQ 402

Query: 356 ITSMGKVIDTLYQKAKKL 373
           + ++  V+D+LY+KA  L
Sbjct: 403 VEALDCVVDSLYEKASAL 420

Length = 421

>gnl\|CDD\|214803 smart00753, PAM, PCI/PINT associated module	Back alignment and domain information

>gnl\|CDD\|214509 smart00088, PINT, motif in proteasome subunits, Int-6, Nip-1 and TRIP-15	Back alignment and domain information

>gnl\|CDD\|216479 pfam01399, PCI, PCI domain	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		374
KOG1463\|consensus		411		100.0
COG5159		421	RPN6 26S proteasome regulatory complex component [	100.0
KOG1464\|consensus		440		100.0
KOG0687\|consensus		393		100.0
KOG1498\|consensus		439		100.0
COG5187		412	RPN7 26S proteasome regulatory complex component,	100.0
COG5071		439	RPN5 26S proteasome regulatory complex component [	100.0
KOG0686\|consensus		466		99.97
KOG1497\|consensus		399		99.85
KOG2758\|consensus		432		99.79
PF10602		177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	99.72
smart00753		88	PAM PCI/PINT associated module.	99.54
smart00088		88	PINT motif in proteasome subunits, Int-6, Nip-1 an	99.54
PF01399		105	PCI: PCI domain; InterPro: IPR000717 A homology do	99.5
KOG2908\|consensus		380		99.36
KOG2581\|consensus		493		99.19
KOG2582\|consensus		422		98.7
KOG1076\|consensus		843		98.45
KOG2753\|consensus		378		98.15
PF14938		282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.91
KOG2072\|consensus		988		97.67
PRK11788		389	tetratricopeptide repeat protein; Provisional	97.23
PF14938		282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.22
COG5600		413	Transcription-associated recombination protein [DN	97.19
PF09976		145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.15
KOG2688\|consensus		394		96.96
PF09976		145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	96.77
KOG1840\|consensus		508		96.7
TIGR02521		234	type_IV_pilW type IV pilus biogenesis/stability pr	96.54
TIGR02795		119	tol_pal_ybgF tol-pal system protein YbgF. Members	96.47
KOG1840\|consensus		508		96.41
PRK11788		389	tetratricopeptide repeat protein; Provisional	96.36
TIGR00990		615	3a0801s09 mitochondrial precursor proteins import	96.35
TIGR00990		615	3a0801s09 mitochondrial precursor proteins import	96.24
TIGR03302		235	OM_YfiO outer membrane assembly lipoprotein YfiO.	96.16
PF04190		260	DUF410: Protein of unknown function (DUF410) ; Int	95.79
PF13424		78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	95.79
cd00189		100	TPR Tetratricopeptide repeat domain; typically con	95.77
PF10255		404	Paf67: RNA polymerase I-associated factor PAF67; I	95.75
TIGR02521		234	type_IV_pilW type IV pilus biogenesis/stability pr	95.56
PF09756		188	DDRGK: DDRGK domain; InterPro: IPR019153 This is a	95.55
TIGR03302		235	OM_YfiO outer membrane assembly lipoprotein YfiO.	95.32
TIGR00540		409	hemY_coli hemY protein. This is an uncharacterized	95.29
TIGR02917		899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	95.07
PF10075		143	PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro	95.03
CHL00033		168	ycf3 photosystem I assembly protein Ycf3	94.98
PRK02603		172	photosystem I assembly protein Ycf3; Provisional	94.95
TIGR02917		899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	94.9
PF09012		69	FeoC: FeoC like transcriptional regulator; InterPr	94.71
COG3063		250	PilF Tfp pilus assembly protein PilF [Cell motilit	94.71
PRK10747		398	putative protoheme IX biogenesis protein; Provisio	94.6
KOG2003\|consensus		840		94.54
KOG2003\|consensus		840		94.36
PRK10866		243	outer membrane biogenesis protein BamD; Provisiona	94.36
PF13432		65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	94.33
COG2956		389	Predicted N-acetylglucosaminyl transferase [Carboh	94.0
PF12895		84	Apc3: Anaphase-promoting complex, cyclosome, subun	93.93
TIGR02552		135	LcrH_SycD type III secretion low calcium response	93.86
PRK10049		765	pgaA outer membrane protein PgaA; Provisional	93.85
PRK10370		198	formate-dependent nitrite reductase complex subuni	93.36
PF13414		69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	93.18
KOG1125\|consensus		579		93.17
PRK11447		1157	cellulose synthase subunit BcsC; Provisional	93.07
PF13424		78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	93.06
KOG3081\|consensus		299		92.56
PF08784		102	RPA_C: Replication protein A C terminal; InterPro:	92.34
PF13525		203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	92.28
PLN03088		356	SGT1, suppressor of G2 allele of SKP1; Provisional	92.1
PF08220		57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	92.02
PRK15359		144	type III secretion system chaperone protein SscB;	92.0
PRK11447		1157	cellulose synthase subunit BcsC; Provisional	92.0
cd05804		355	StaR_like StaR_like; a well-conserved protein foun	91.92
KOG3054\|consensus		299		91.87
cd00189		100	TPR Tetratricopeptide repeat domain; typically con	91.4
KOG3060\|consensus		289		91.11
PRK04841		903	transcriptional regulator MalT; Provisional	91.08
TIGR02795		119	tol_pal_ybgF tol-pal system protein YbgF. Members	90.87
PRK15431		78	ferrous iron transport protein FeoC; Provisional	90.81
PRK10803		263	tol-pal system protein YbgF; Provisional	90.73
PF04733		290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	90.58
KOG2002\|consensus		1018		90.35
COG3355		126	Predicted transcriptional regulator [Transcription	90.21
KOG1861\|consensus		540		90.15
TIGR02552		135	LcrH_SycD type III secretion low calcium response	90.07
PF12569		517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	89.88
PF04733		290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	89.59
KOG1155\|consensus		559		89.42
PF13371		73	TPR_9: Tetratricopeptide repeat	89.15
PRK14574		822	hmsH outer membrane protein; Provisional	88.94
PRK04841		903	transcriptional regulator MalT; Provisional	88.87
KOG0548\|consensus		539		88.84
PRK15174		656	Vi polysaccharide export protein VexE; Provisional	88.63
PRK15174		656	Vi polysaccharide export protein VexE; Provisional	88.59
PF13429		280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	88.46
PF13525		203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	88.36
PF12895		84	Apc3: Anaphase-promoting complex, cyclosome, subun	88.34
PF13429		280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	88.09
PF14559		68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	87.83
KOG0495\|consensus		913		87.18
COG3071		400	HemY Uncharacterized enzyme of heme biosynthesis [	87.09
KOG2300\|consensus		629		87.06
PF13414		69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	86.97
PF09295		395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	86.88
COG2956		389	Predicted N-acetylglucosaminyl transferase [Carboh	86.87
KOG0495\|consensus		913		86.75
TIGR00540		409	hemY_coli hemY protein. This is an uncharacterized	86.74
PF13176		36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	86.68
PLN03218		1060	maturation of RBCL 1; Provisional	86.21
smart00550		68	Zalpha Z-DNA-binding domain in adenosine deaminase	86.09
PLN03218		1060	maturation of RBCL 1; Provisional	85.99
PF13174		33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	85.69
KOG0543\|consensus		397		85.1
PRK10049		765	pgaA outer membrane protein PgaA; Provisional	85.03
smart00345		60	HTH_GNTR helix_turn_helix gluconate operon transcr	84.77
KOG2002\|consensus		1018		84.55
PRK15179		694	Vi polysaccharide biosynthesis protein TviE; Provi	84.11
PRK09782		987	bacteriophage N4 receptor, outer membrane subunit;	83.21
KOG4626\|consensus		966		83.2
PLN03088		356	SGT1, suppressor of G2 allele of SKP1; Provisional	82.81
PRK11189		296	lipoprotein NlpI; Provisional	82.8
PF03399		204	SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; I	82.69
TIGR03504		44	FimV_Cterm FimV C-terminal domain. This protein is	82.59
smart00420		53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	82.47
PF13412		48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	82.41
KOG3617\|consensus		1416		82.34
cd05804		355	StaR_like StaR_like; a well-conserved protein foun	82.11
PF08279		55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	81.82
KOG4234\|consensus		271		81.73
PF10602		177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	81.43
PF04703		62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	81.02
PF10345		608	Cohesin_load: Cohesin loading factor; InterPro: IP	80.66
KOG1126\|consensus		638		80.54
PF12688		120	TPR_5: Tetratrico peptide repeat	80.05

>KOG1463\|consensus	Back alignment and domain information

Probab=100.00  E-value=1.5e-76  Score=556.77  Aligned_cols=361  Identities=64%  Similarity=0.965  Sum_probs=341.2

Q ss_pred             Ccchhh-hHhhhhhcccCccc---------ccCCcCCCCchHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhhhh
Q psy4083           1 MAGAMM-FERSASQISITGNS---------YKTGYEEENHDEEVKAKEQNILQLGEKYKQEGKAIELAELIKKTRPFLSQ   70 (374)
Q Consensus         1 ~~~~~~-~~~~~~~~~~~~~~---------~~~~~~~~~~~~~~k~~e~~~~~l~~~~~~~~~~~~l~~~l~~l~~~~~~   70 (374)
                      |++... +++++...+.++.+         +++...++++|...+.+|+.|.++++++.+.|+++++.++++++|||+.+
T Consensus         1 m~~~~~~~e~~~~~~~~~~~~~~~~il~~vl~~~~~~~s~e~~i~~kE~~Ilel~~ll~~~~~~~~lr~li~~~Rpf~~~   80 (411)
T KOG1463|consen    1 MSSAASLLERAQNLVSVNQVEEAINILKSVLNKAQGASSDEARIKEKEQSILELGDLLAKEGDAEELRDLITSLRPFLSS   80 (411)
T ss_pred             CCchHHHHHHHHHhcccchhhhhHHHHHHHhhhhccccCCHHHHHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHH
Confidence            344444 77887766666522         44322377899999999999999999999999999999999999999999


Q ss_pred             hhhHHHHHHHHHHHHHhhccccchhhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHHH
Q psy4083          71 ISKAKAAKLVRSLVDFFLDLETRTGMEVALCKECIEWAKEERRTFLRQSLEARLIALYFDTGEYTEALKLSSSLLKELKK  150 (374)
Q Consensus        71 ~~k~~~~k~i~~ild~~~~~~~~~~~~~~l~~e~i~~~~~~~r~~lr~~l~~kLa~~~~~~g~~~~Al~~~~~ll~el~~  150 (374)
                      ++|++++|+||.++|.+..++++.+.++.+|.++|+||+.++|+|||+.|++||+.+|++.++|.+|+.+++.+++|+++
T Consensus        81 v~KakaaKlvR~Lvd~~~~~~~~~~~~i~l~~~cIeWA~~ekRtFLRq~Learli~Ly~d~~~YteAlaL~~~L~rElKK  160 (411)
T KOG1463|consen   81 VSKAKAAKLVRSLVDMFLKIDDGTGDQIELCTECIEWAKREKRTFLRQSLEARLIRLYNDTKRYTEALALINDLLRELKK  160 (411)
T ss_pred             hhhHHHHHHHHHHHHHHccCCCCcchHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccchhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhccccCCChhhhHHHHHHHHHHhhcccccHHHHHHHHHHhccCc
Q psy4083         151 LDDKNLLVEVLLLESKTYHALSNLSTSRASLTSARTTANSIYCPPKMQAALDLQSGILHAADEQDFKTAFSYFYEAFEGF  230 (374)
Q Consensus       151 ~dd~~~~lev~l~ei~l~~~~~n~~~a~~~~~~a~~~~~~~~~~~~~~~~i~~~~G~~~~~~~rdy~~A~~~F~eaf~~f  230 (374)
                      .||+..++|++++|++.|+.++|.+|++++++.||+.+|++||||.+|+.++.++|++|. .++||++|++||||||++|
T Consensus       161 lDDK~lLvev~llESK~y~~l~Nl~KakasLTsART~AnaiYcpPqlQa~lDLqSGIlha-~ekDykTafSYFyEAfEgf  239 (411)
T KOG1463|consen  161 LDDKILLVEVHLLESKAYHALRNLPKAKASLTSARTTANAIYCPPQLQATLDLQSGILHA-AEKDYKTAFSYFYEAFEGF  239 (411)
T ss_pred             cccccceeeehhhhhHHHHHHhcchhHHHHHHHHHHhhcccccCHHHHHHHHHhccceee-cccccchHHHHHHHHHccc
Confidence            999999999999999999999999999999999999999999999999999999999999 8999999999999999999


Q ss_pred             Ccccc-hhHHHHHHHHHHHHHhcCCchhHHHHHH---------------------------------------HHhcChH
Q psy4083         231 STVDH-NHAMMSLKYMLLSKIMLNTPEDVNQILS---------------------------------------ELEDDTI  270 (374)
Q Consensus       231 ~~~~~-~~~~~~LkY~vL~~iL~~~~~~v~~ll~---------------------------------------~l~~D~~  270 (374)
                      ++.++ ..+...||||+||+||.|.+++|..+++                                       +|..||+
T Consensus       240 ~s~~~~v~A~~sLKYMlLcKIMln~~ddv~~lls~K~~l~y~g~~i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~i  319 (411)
T KOG1463|consen  240 DSLDDDVKALTSLKYMLLCKIMLNLPDDVAALLSAKLALKYAGRDIDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPI  319 (411)
T ss_pred             cccCCcHHHHHHHHHHHHHHHHhcCHHHHHHHHhhHHHHhccCcchHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChH
Confidence            99998 6999999999999999999998877766                                       7999999


Q ss_pred             HHhhHHHHHHHHHHHHHHHhhccccceeHHHHHhHhCCChHHHHHHHHHHhhcCccceeecCCCCeEEEecCCcchHHHH
Q psy4083         271 VKAHIGTLYDNMLEQNLCRIIEPYSRVEVGFIAKSIKLDELAVEKKLSQMILDKKFHGILDQGEKVLIVFEGAEIDKTYE  350 (374)
Q Consensus       271 l~~h~~~L~~~ire~~l~~~~~pYs~I~l~~lA~~l~ls~~~vE~~L~~lI~dgkl~akID~~~giv~~~~~~~~~~~y~  350 (374)
                      ++.|+..|++++.|+|+++++||||+|.++|+|+.+|++++.||++|++||+|++++|.+||++||++++++++.+++|+
T Consensus       320 vr~Hl~~Lyd~lLEknl~riIEPyS~Vei~hIA~~IGl~~~~VEkKLsqMILDKkf~G~LDQg~g~Liv~~e~~~d~~y~  399 (411)
T KOG1463|consen  320 VRSHLQSLYDNLLEKNLCRIIEPYSRVEISHIAEVIGLDVPQVEKKLSQMILDKKFYGTLDQGEGCLIVFEEPPADNTYD  399 (411)
T ss_pred             HHHHHHHHHHHHHHHhHHHHcCchhhhhHHHHHHHHCCCcHHHHHHHHHHHHHHHhhcccccCCCeEEEeCCCCcchHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q psy4083         351 KALETITSMGKV  362 (374)
Q Consensus       351 ~~~~~i~~l~~~  362 (374)
                      +++++|++++.+
T Consensus       400 ~aLetI~~m~kV  411 (411)
T KOG1463|consen  400 AALETIQNMGKV  411 (411)
T ss_pred             HHHHHHHhccCC
Confidence            999999998753

>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG1464\|consensus	Back alignment and domain information

>KOG0687\|consensus	Back alignment and domain information

>KOG1498\|consensus	Back alignment and domain information

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

>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG0686\|consensus	Back alignment and domain information

>KOG1497\|consensus	Back alignment and domain information

>KOG2758\|consensus	Back alignment and domain information

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome	Back alignment and domain information

>smart00753 PAM PCI/PINT associated module	Back alignment and domain information

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

>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	Back alignment and domain information

>KOG2908\|consensus	Back alignment and domain information

>KOG2581\|consensus	Back alignment and domain information

>KOG2582\|consensus	Back alignment and domain information

>KOG1076\|consensus	Back alignment and domain information

>KOG2753\|consensus	Back alignment and domain information

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A	Back alignment and domain information

>KOG2072\|consensus	Back alignment and domain information

>PRK11788 tetratricopeptide repeat protein; Provisional	Back alignment and domain information

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A	Back alignment and domain information

>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]	Back alignment and domain information

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function	Back alignment and domain information

>KOG2688\|consensus	Back alignment and domain information

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function	Back alignment and domain information

>KOG1840\|consensus	Back alignment and domain information

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW	Back alignment and domain information

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF	Back alignment and domain information

>KOG1840\|consensus	Back alignment and domain information

>PRK11788 tetratricopeptide repeat protein; Provisional	Back alignment and domain information

>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70)	Back alignment and domain information

>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70)	Back alignment and domain information

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO	Back alignment and domain information

>PF04190 DUF410: Protein of unknown function (DUF410) ; InterPro: IPR007317 This is a family of conserved eukaryotic proteins with undetermined function	Back alignment and domain information

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H	Back alignment and domain information

>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C

Back alignment and domain information

>PF10255 Paf67: RNA polymerase I-associated factor PAF67; InterPro: IPR019382 RNA polymerase I is a multi-subunit enzyme and its transcription competence is dependent on the presence of PAF67 []	Back alignment and domain information

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW	Back alignment and domain information

>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues	Back alignment and domain information

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO	Back alignment and domain information

>TIGR00540 hemY_coli hemY protein	Back alignment and domain information

>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein	Back alignment and domain information

>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	Back alignment and domain information

>CHL00033 ycf3 photosystem I assembly protein Ycf3	Back alignment and domain information

>PRK02603 photosystem I assembly protein Ycf3; Provisional	Back alignment and domain information

>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein	Back alignment and domain information

>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif	Back alignment and domain information

>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]	Back alignment and domain information

>PRK10747 putative protoheme IX biogenesis protein; Provisional	Back alignment and domain information

>KOG2003\|consensus	Back alignment and domain information

>KOG2003\|consensus	Back alignment and domain information

>PRK10866 outer membrane biogenesis protein BamD; Provisional	Back alignment and domain information

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B	Back alignment and domain information

>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]	Back alignment and domain information

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A	Back alignment and domain information

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD	Back alignment and domain information

>PRK10049 pgaA outer membrane protein PgaA; Provisional	Back alignment and domain information

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional	Back alignment and domain information

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A	Back alignment and domain information

>KOG1125\|consensus	Back alignment and domain information

>PRK11447 cellulose synthase subunit BcsC; Provisional	Back alignment and domain information

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H	Back alignment and domain information

>KOG3081\|consensus	Back alignment and domain information

>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A)	Back alignment and domain information

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A	Back alignment and domain information

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional	Back alignment and domain information

>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism	Back alignment and domain information

>PRK15359 type III secretion system chaperone protein SscB; Provisional	Back alignment and domain information

>PRK11447 cellulose synthase subunit BcsC; Provisional	Back alignment and domain information

>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals	Back alignment and domain information

>KOG3054\|consensus	Back alignment and domain information

Back alignment and domain information

>KOG3060\|consensus	Back alignment and domain information

>PRK04841 transcriptional regulator MalT; Provisional	Back alignment and domain information

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF	Back alignment and domain information

>PRK15431 ferrous iron transport protein FeoC; Provisional	Back alignment and domain information

>PRK10803 tol-pal system protein YbgF; Provisional	Back alignment and domain information

>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment	Back alignment and domain information

>KOG2002\|consensus	Back alignment and domain information

>COG3355 Predicted transcriptional regulator [Transcription]	Back alignment and domain information

>KOG1861\|consensus	Back alignment and domain information

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD	Back alignment and domain information

>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala	Back alignment and domain information

>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment	Back alignment and domain information

>KOG1155\|consensus	Back alignment and domain information

>PF13371 TPR_9: Tetratricopeptide repeat	Back alignment and domain information

>PRK14574 hmsH outer membrane protein; Provisional	Back alignment and domain information

>PRK04841 transcriptional regulator MalT; Provisional	Back alignment and domain information

>KOG0548\|consensus	Back alignment and domain information

>PRK15174 Vi polysaccharide export protein VexE; Provisional	Back alignment and domain information

>PRK15174 Vi polysaccharide export protein VexE; Provisional	Back alignment and domain information

>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B	Back alignment and domain information

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A	Back alignment and domain information

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A	Back alignment and domain information

>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B	Back alignment and domain information

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A	Back alignment and domain information

>KOG0495\|consensus	Back alignment and domain information

>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]	Back alignment and domain information

>KOG2300\|consensus	Back alignment and domain information

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A	Back alignment and domain information

>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi	Back alignment and domain information

>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]	Back alignment and domain information

>KOG0495\|consensus	Back alignment and domain information

>TIGR00540 hemY_coli hemY protein	Back alignment and domain information

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A	Back alignment and domain information

>PLN03218 maturation of RBCL 1; Provisional	Back alignment and domain information

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases	Back alignment and domain information

>PLN03218 maturation of RBCL 1; Provisional	Back alignment and domain information

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A	Back alignment and domain information

>KOG0543\|consensus	Back alignment and domain information

>PRK10049 pgaA outer membrane protein PgaA; Provisional	Back alignment and domain information

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor	Back alignment and domain information

>KOG2002\|consensus	Back alignment and domain information

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional	Back alignment and domain information

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional	Back alignment and domain information

>KOG4626\|consensus	Back alignment and domain information

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional	Back alignment and domain information

>PRK11189 lipoprotein NlpI; Provisional	Back alignment and domain information

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

>TIGR03504 FimV_Cterm FimV C-terminal domain	Back alignment and domain information

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor	Back alignment and domain information

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A	Back alignment and domain information

>KOG3617\|consensus	Back alignment and domain information

>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals	Back alignment and domain information

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets	Back alignment and domain information

>KOG4234\|consensus	Back alignment and domain information

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome	Back alignment and domain information

>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A	Back alignment and domain information

>PF10345 Cohesin_load: Cohesin loading factor; InterPro: IPR019440 Cohesin loading factor is a conserved protein that has been characterised in fungi	Back alignment and domain information

>KOG1126\|consensus	Back alignment and domain information

>PF12688 TPR_5: Tetratrico peptide repeat	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		374
3txm_A		394	Crystal Structure Of Rpn6 From Drosophila Melanogas		1e-122
4b4t_Q		434	Near-Atomic Resolution Structural Model Of The Yeas		1e-56

>pdb|3TXM|A Chain A, Crystal Structure Of Rpn6 From Drosophila Melanogaster, Gd(3+) Complex Length = 394

Back alignment and structure

Iteration: 1

Score = 434 bits (1116), Expect = e-122, Method: Compositional matrix adjust. Identities = 228/386 (59%), Positives = 256/386 (66%), Gaps = 39/386 (10%) Query: 28 ENHDEEVKAKEQNILQLGEKYKQEGKAIELAELIKKTRPFLSQISKAKAAKLVRSLVDFF 87 EN +E ++ KEQ ILQ GE YKQEGKA ELA+LIK TRPFLS ISKAKAAKLVRSLVD F Sbjct: 9 ENDEERIRIKEQGILQQGELYKQEGKAKELADLIKVTRPFLSSISKAKAAKLVRSLVDMF 68 Query: 88 LDLETRTGMEVALCKECIEWAKEERRTFLRQSLEARLIALYFDTGEYTEAXXXXXXXXXX 147 LD++ TG+EV LCK+CIEWAK+E+RTFLRQSLEARLIALYFDT YTEA Sbjct: 69 LDMDAGTGIEVQLCKDCIEWAKQEKRTFLRQSLEARLIALYFDTALYTEALALGAQLLRE 128 Query: 148 XXXXXXXXXXXXXXXXXXXTYHXXXXXXXXXXXXXXXXXXXXXIYCPPKMQAALDLQSGI 207 TYH IYCPPK+Q ALDLQSGI Sbjct: 129 LKKLDDKNLLVEVQLLESKTYHALSNLPKARAALTSARTTANAIYCPPKVQGALDLQSGI 188 Query: 208 LHAADEQDFKTAFSYFYEAFEGFSTVDHNHAMMSLKYMLLSKIMLNTPEDVNQILS---- 263 LHAADE+DFKTAFSYFYEAFEGF +VD A+ SLKYMLL KIML +DVNQ++S Sbjct: 189 LHAADERDFKTAFSYFYEAFEGFDSVDSVKALTSLKYMLLCKIMLGQSDDVNQLVSGKLA 248 Query: 264 -----------------------------------ELEDDTIVKAHIGTLYDNMLEQNLC 288 EL +D IV+AH+GTLYD MLEQNLC Sbjct: 249 ITYSGRDIDAMKSVAEASHKRSLADFQAALKEYKKELAEDVIVQAHLGTLYDTMLEQNLC 308 Query: 289 RIIEPYSRVEVGFIAKSIKLDELAVEKKLSQMILDKKFHGILDQGEKVLIVFEGAEIDKT 348 RIIEPYSRV+V +A+SI+L VEKKLSQMILDKKF GILDQGE VLIVFE +DKT Sbjct: 309 RIIEPYSRVQVAHVAESIQLPMPQVEKKLSQMILDKKFSGILDQGEGVLIVFEETPVDKT 368 Query: 349 YEKALETITSMGKVIDTLYQKAKKLT 374 YE+ LETI SMGKV+DTLYQKAKKL+ Sbjct: 369 YERVLETIQSMGKVVDTLYQKAKKLS 394

PyMOL of 3txm

>pdb|4B4T|Q Chain Q, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 434

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		374
3txn_A		394	26S proteasome regulatory complex subunit P42B; PC	2e-93
1ufm_A		84	COP9 complex subunit 4; helix-turn-helix, structur	9e-12
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-05

>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 Length = 394	Back alignment and structure

 Score =  284 bits (727), Expect = 2e-93
 Identities = 267/388 (68%), Positives = 300/388 (77%), Gaps = 39/388 (10%)

Query: 26  EEENHDEEVKAKEQNILQLGEKYKQEGKAIELAELIKKTRPFLSQISKAKAAKLVRSLVD 85
             EN +E ++ KEQ ILQ GE YKQEGKA ELA+LIK TRPFLS ISKAKAAKLVRSLVD
Sbjct: 7   GAENDEERIRIKEQGILQQGELYKQEGKAKELADLIKVTRPFLSSISKAKAAKLVRSLVD 66

Query: 86  FFLDLETRTGMEVALCKECIEWAKEERRTFLRQSLEARLIALYFDTGEYTEALKLSSSLL 145
            FLD++  TG+EV LCK+CIEWAK+E+RTFLRQSLEARLIALYFDT  YTEAL L + LL
Sbjct: 67  MFLDMDAGTGIEVQLCKDCIEWAKQEKRTFLRQSLEARLIALYFDTALYTEALALGAQLL 126

Query: 146 KELKKLDDKNLLVEVLLLESKTYHALSNLSTSRASLTSARTTANSIYCPPKMQAALDLQS 205
           +ELKKLDDKNLLVEV LLESKTYHALSNL  +RA+LTSARTTAN+IYCPPK+Q ALDLQS
Sbjct: 127 RELKKLDDKNLLVEVQLLESKTYHALSNLPKARAALTSARTTANAIYCPPKVQGALDLQS 186

Query: 206 GILHAADEQDFKTAFSYFYEAFEGFSTVDHNHAMMSLKYMLLSKIMLNTPEDVNQILS-- 263
           GILHAADE+DFKTAFSYFYEAFEGF +VD   A+ SLKYMLL KIML   +DVNQ++S  
Sbjct: 187 GILHAADERDFKTAFSYFYEAFEGFDSVDSVKALTSLKYMLLCKIMLGQSDDVNQLVSGK 246

Query: 264 -------------------------------------ELEDDTIVKAHIGTLYDNMLEQN 286
                                                EL +D IV+AH+GTLYD MLEQN
Sbjct: 247 LAITYSGRDIDAMKSVAEASHKRSLADFQAALKEYKKELAEDVIVQAHLGTLYDTMLEQN 306

Query: 287 LCRIIEPYSRVEVGFIAKSIKLDELAVEKKLSQMILDKKFHGILDQGEKVLIVFEGAEID 346
           LCRIIEPYSRV+V  +A+SI+L    VEKKLSQMILDKKF GILDQGE VLIVFE   +D
Sbjct: 307 LCRIIEPYSRVQVAHVAESIQLPMPQVEKKLSQMILDKKFSGILDQGEGVLIVFEETPVD 366

Query: 347 KTYEKALETITSMGKVIDTLYQKAKKLT 374
           KTYE+ LETI SMGKV+DTLYQKAKKL+
Sbjct: 367 KTYERVLETIQSMGKVVDTLYQKAKKLS 394

PyMOL of 3txn

>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 Length = 84	Back alignment and structure

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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		374
3txn_A		394	26S proteasome regulatory complex subunit P42B; PC	100.0
4b4t_P		445	26S proteasome regulatory subunit RPN5; hydrolase,	100.0
4b4t_Q		434	26S proteasome regulatory subunit RPN6; hydrolase,	100.0
4b4t_R		429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	100.0
4b4t_O		393	26S proteasome regulatory subunit RPN9; hydrolase,	99.81
1ufm_A		84	COP9 complex subunit 4; helix-turn-helix, structur	99.71
3t5x_A		203	PCI domain-containing protein 2; PCI, mRNA nuclear	99.64
4b4t_S		523	RPN3, 26S proteasome regulatory subunit RPN3; hydr	99.53
3t5v_B		455	Nuclear mRNA export protein THP1; PCI, mRNA nuclea	99.35
3ro2_A		338	PINS homolog, G-protein-signaling modulator 2; TPR	98.58
3ro2_A		338	PINS homolog, G-protein-signaling modulator 2; TPR	98.55
3sf4_A		406	G-protein-signaling modulator 2; tetratricopeptide	98.5
3u3w_A		293	Transcriptional activator PLCR protein; ternary co	98.48
3sf4_A		406	G-protein-signaling modulator 2; tetratricopeptide	98.47
4a1s_A		411	PINS, partner of inscuteable; cell cycle, LGN, mit	98.46
4a1s_A		411	PINS, partner of inscuteable; cell cycle, LGN, mit	98.44
3q15_A		378	PSP28, response regulator aspartate phosphatase H;	98.35
3ulq_A		383	Response regulator aspartate phosphatase F; tetrat	98.34
2qfc_A		293	PLCR protein; TPR, HTH, transcription regulation;	98.3
3nf1_A		311	KLC 1, kinesin light chain 1; TPR, structural geno	98.29
3ulq_A		383	Response regulator aspartate phosphatase F; tetrat	98.29
2ifu_A		307	Gamma-SNAP; membrane fusion, snare complex disasse	98.26
3gw4_A		203	Uncharacterized protein; structural genomics, PSI-	98.24
1qqe_A		292	Vesicular transport protein SEC17; helix-turn-heli	98.24
3edt_B		283	KLC 2, kinesin light chain 2; superhelical, struct	98.22
3ro3_A		164	PINS homolog, G-protein-signaling modulator 2; asy	98.21
3ro3_A		164	PINS homolog, G-protein-signaling modulator 2; asy	98.16
3q15_A		378	PSP28, response regulator aspartate phosphatase H;	98.13
3nf1_A		311	KLC 1, kinesin light chain 1; TPR, structural geno	98.09
3gw4_A		203	Uncharacterized protein; structural genomics, PSI-	98.02
1hz4_A		373	MALT regulatory protein; two-helix bundles, helix	97.87
4b4t_Q		434	26S proteasome regulatory subunit RPN6; hydrolase,	97.84
3uq3_A		258	Heat shock protein STI1; HSP90, peptide binding, c	97.76
1qqe_A		292	Vesicular transport protein SEC17; helix-turn-heli	97.74
4gcn_A		127	Protein STI-1; structural genomics, PSI-biology, m	97.72
3qky_A		261	Outer membrane assembly lipoprotein YFIO; membrane	97.69
3chm_A		169	COP9 signalosome complex subunit 7; heat/ARM repea	97.67
3vtx_A		184	MAMA; tetratricopeptide repeats (TPR) containing p	97.65
3uq3_A		258	Heat shock protein STI1; HSP90, peptide binding, c	97.64
2qfc_A		293	PLCR protein; TPR, HTH, transcription regulation;	97.63
4b0z_A		229	RPN12, 26S proteasome regulatory subunit RPN12; pr	97.62
1hz4_A		373	MALT regulatory protein; two-helix bundles, helix	97.61
3fp2_A		537	TPR repeat-containing protein YHR117W; TOM71, mito	97.56
3edt_B		283	KLC 2, kinesin light chain 2; superhelical, struct	97.55
2ifu_A		307	Gamma-SNAP; membrane fusion, snare complex disasse	97.53
2vq2_A		225	PILW, putative fimbrial biogenesis and twitching m	97.51
3hym_B		330	Cell division cycle protein 16 homolog; APC, anaph	97.46
3ieg_A		359	DNAJ homolog subfamily C member 3; TPR motif, chap	97.45
2ho1_A		252	Type 4 fimbrial biogenesis protein PILF; type IV p	97.39
3hym_B		330	Cell division cycle protein 16 homolog; APC, anaph	97.39
3as5_A		186	MAMA; tetratricopeptide repeats (TPR) containing p	97.34
4i17_A		228	Hypothetical protein; TPR repeats protein, structu	97.33
3ieg_A		359	DNAJ homolog subfamily C member 3; TPR motif, chap	97.29
2q7f_A		243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	97.27
1fch_A		368	Peroxisomal targeting signal 1 receptor; protein-p	97.25
2xpi_A		597	Anaphase-promoting complex subunit CUT9; cell cycl	97.24
3u3w_A		293	Transcriptional activator PLCR protein; ternary co	97.22
4eqf_A		365	PEX5-related protein; accessory protein, tetratric	97.21
2ho1_A		252	Type 4 fimbrial biogenesis protein PILF; type IV p	97.21
2xev_A		129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.16
2pl2_A		217	Hypothetical conserved protein TTC0263; TPR, prote	97.11
1elr_A		131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.11
2y4t_A		450	DNAJ homolog subfamily C member 3; chaperone, endo	97.1
2gw1_A		514	Mitochondrial precursor proteins import receptor;	97.09
4eqf_A		365	PEX5-related protein; accessory protein, tetratric	97.08
2xpi_A		597	Anaphase-promoting complex subunit CUT9; cell cycl	97.08
3u4t_A		272	TPR repeat-containing protein; structural genomics	97.02
2vq2_A		225	PILW, putative fimbrial biogenesis and twitching m	96.98
2pl2_A		217	Hypothetical conserved protein TTC0263; TPR, prote	96.93
1fch_A		368	Peroxisomal targeting signal 1 receptor; protein-p	96.92
2y4t_A		450	DNAJ homolog subfamily C member 3; chaperone, endo	96.91
2yhc_A		225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	96.91
2yhc_A		225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	96.9
4gco_A		126	Protein STI-1; structural genomics, PSI-biology, m	96.89
2q7f_A		243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	96.88
3vtx_A		184	MAMA; tetratricopeptide repeats (TPR) containing p	96.87
3cv0_A		327	Peroxisome targeting signal 1 receptor PEX5; TPR m	96.86
3rkv_A		162	Putative peptidylprolyl isomerase; structural geno	96.84
3cv0_A		327	Peroxisome targeting signal 1 receptor PEX5; TPR m	96.83
3qky_A		261	Outer membrane assembly lipoprotein YFIO; membrane	96.77
4gyw_A		723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	96.66
1a17_A		166	Serine/threonine protein phosphatase 5; hydrolase,	96.66
3fp2_A		537	TPR repeat-containing protein YHR117W; TOM71, mito	96.66
4gcn_A		127	Protein STI-1; structural genomics, PSI-biology, m	96.63
3upv_A		126	Heat shock protein STI1; TPR-fold, adaptor protein	96.52
1w3b_A		388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	96.51
4i17_A		228	Hypothetical protein; TPR repeats protein, structu	96.49
2fo7_A		136	Synthetic consensus TPR protein; tetratricopeptide	96.46
2kck_A		112	TPR repeat; tetratricopeptide repeat, structural g	96.46
4ga2_A		150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	96.38
3urz_A		208	Uncharacterized protein; tetratricopeptide repeats	96.38
3sz7_A		164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	96.38
1wi9_A		72	Protein C20ORF116 homolog; helix-turn-helix motif,	96.37
3q49_B		137	STIP1 homology and U box-containing protein 1; E3	96.35
1hh8_A		213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	96.26
2lni_A		133	Stress-induced-phosphoprotein 1; structural genomi	96.24
1w3b_A		388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	96.24
1xnf_A		275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	96.23
2dba_A		148	Smooth muscle cell associated protein-1, isoform 2	96.18
1elr_A		131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	96.17
1elw_A		118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	96.16
2gw1_A		514	Mitochondrial precursor proteins import receptor;	96.13
3as5_A		186	MAMA; tetratricopeptide repeats (TPR) containing p	96.12
3u4t_A		272	TPR repeat-containing protein; structural genomics	96.03
2vyi_A		131	SGTA protein; chaperone, TPR repeat, phosphoprotei	95.96
3rkv_A		162	Putative peptidylprolyl isomerase; structural geno	95.93
4ga2_A		150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	95.77
3n71_A		490	Histone lysine methyltransferase SMYD1; heart deve	95.77
3mkr_A		291	Coatomer subunit epsilon; tetratricopeptide repeat	95.77
2fbn_A		198	70 kDa peptidylprolyl isomerase, putative; sulfur	95.75
4abn_A		474	Tetratricopeptide repeat protein 5; P53 cofactor,	95.72
3mv2_B		310	Coatomer subunit epsilon; vesicular membrane coat	95.72
3n71_A		490	Histone lysine methyltransferase SMYD1; heart deve	95.69
1p5q_A		336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	95.68
1a17_A		166	Serine/threonine protein phosphatase 5; hydrolase,	95.67
2fbn_A		198	70 kDa peptidylprolyl isomerase, putative; sulfur	95.65
3mkr_A		291	Coatomer subunit epsilon; tetratricopeptide repeat	95.58
1ihg_A		370	Cyclophilin 40; ppiase immunophilin tetratricopept	95.57
2xcb_A		142	PCRH, regulatory protein PCRH; protein transport,	95.57
2vgx_A		148	Chaperone SYCD; alternative dimer assembly, tetrat	95.52
1na0_A		125	Designed protein CTPR3; de novo protein; HET: IPT;	95.48
3gyz_A		151	Chaperone protein IPGC; asymmetric homodimer, tetr	95.48
4gco_A		126	Protein STI-1; structural genomics, PSI-biology, m	95.46
2xev_A		129	YBGF; tetratricopeptide, alpha-helical, metal bind	95.39
2fo7_A		136	Synthetic consensus TPR protein; tetratricopeptide	95.39
3lpz_A		336	GET4 (YOR164C homolog); protein targeting, tail-an	95.38
3upv_A		126	Heat shock protein STI1; TPR-fold, adaptor protein	95.38
2l6j_A		111	TPR repeat-containing protein associated with HSP;	95.37
1hxi_A		121	PEX5, peroxisome targeting signal 1 receptor PEX5;	95.35
4abn_A		474	Tetratricopeptide repeat protein 5; P53 cofactor,	95.23
2wpv_A		312	GET4, UPF0363 protein YOR164C; golgi-ER traffickin	95.11
1kt0_A		457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	95.05
3gyz_A		151	Chaperone protein IPGC; asymmetric homodimer, tetr	94.92
2xcb_A		142	PCRH, regulatory protein PCRH; protein transport,	94.88
1hh8_A		213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	94.84
2v5f_A		104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	94.81
2lni_A		133	Stress-induced-phosphoprotein 1; structural genomi	94.81
4g1t_A		472	Interferon-induced protein with tetratricopeptide	94.68
1p5q_A		336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	94.66
3sz7_A		164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	94.64
4g1t_A		472	Interferon-induced protein with tetratricopeptide	94.61
1xnf_A		275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	94.61
1kt0_A		457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	94.61
2e2e_A		177	Formate-dependent nitrite reductase complex NRFG;	94.53
1ihg_A		370	Cyclophilin 40; ppiase immunophilin tetratricopept	94.51
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	94.39
3k9i_A		117	BH0479 protein; putative protein binding protein,	94.29
3urz_A		208	Uncharacterized protein; tetratricopeptide repeats	94.25
3qww_A		433	SET and MYND domain-containing protein 2; methyltr	94.24
3q49_B		137	STIP1 homology and U box-containing protein 1; E3	94.1
2vyi_A		131	SGTA protein; chaperone, TPR repeat, phosphoprotei	93.81
2vgx_A		148	Chaperone SYCD; alternative dimer assembly, tetrat	93.78
2ond_A		308	Cleavage stimulation factor 77 kDa subunit; HAT do	93.75
1elw_A		118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	93.66
1ouv_A		273	Conserved hypothetical secreted protein; TPR repea	93.25
1na0_A		125	Designed protein CTPR3; de novo protein; HET: IPT;	93.18
4f3v_A		282	ESX-1 secretion system protein ECCA1; tetratricope	93.17
3qwp_A		429	SET and MYND domain-containing protein 3; SMYD3,SE	93.04
2dba_A		148	Smooth muscle cell associated protein-1, isoform 2	92.99
2k02_A		87	Ferrous iron transport protein C; FEOC, iron-sulfu	92.87
3qww_A		433	SET and MYND domain-containing protein 2; methyltr	92.82
4gyw_A		723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	92.78
1xn7_A		78	Hypothetical protein YHGG; alpha+beta, GFT structu	92.77
1ouv_A		273	Conserved hypothetical secreted protein; TPR repea	92.73
2if4_A		338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	92.61
2hr2_A		159	Hypothetical protein; alpha-alpha superhelix fold,	92.47
2h6f_A		382	Protein farnesyltransferase/geranylgeranyltransfer	92.4
1qgp_A		77	Protein (double stranded RNA adenosine deaminase);	92.35
1b89_A		449	Protein (clathrin heavy chain); triskelion, coated	92.14
2pzi_A		681	Probable serine/threonine-protein kinase PKNG; ATP	91.98
3qwp_A		429	SET and MYND domain-containing protein 3; SMYD3,SE	91.98
3ma5_A		100	Tetratricopeptide repeat domain protein; NESG, str	91.93
2if4_A		338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	91.92
2hr2_A		159	Hypothetical protein; alpha-alpha superhelix fold,	91.92
2vsy_A		568	XCC0866; transferase, glycosyl transferase, GT-B,	91.78
2ond_A		308	Cleavage stimulation factor 77 kDa subunit; HAT do	91.69
1na3_A		91	Designed protein CTPR2; de novo protein; HET: IPT;	91.56
2vsy_A		568	XCC0866; transferase, glycosyl transferase, GT-B,	91.52
2jt1_A		77	PEFI protein; solution structure, winged helix-tur	91.26
2kck_A		112	TPR repeat; tetratricopeptide repeat, structural g	90.99
3k9i_A		117	BH0479 protein; putative protein binding protein,	90.91
2r5s_A		176	Uncharacterized protein VP0806; APC090868.1, vibri	90.71
4b0z_A		229	RPN12, 26S proteasome regulatory subunit RPN12; pr	90.64
1xi4_A		1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	90.49
2pzi_A		681	Probable serine/threonine-protein kinase PKNG; ATP	90.45
2e2e_A		177	Formate-dependent nitrite reductase complex NRFG;	90.18
1wao_1		477	Serine/threonine protein phosphatase 5; hydrolase,	89.93
1qbj_A		81	Protein (double-stranded RNA specific adenosine D	89.7
1xi4_A		1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	89.64
2kc7_A		99	BFR218_protein; tetratricopeptide repeat, all-alph	89.61
2ooe_A		530	Cleavage stimulation factor 77 kDa subunit; HAT do	89.59
3qou_A		287	Protein YBBN; thioredoxin-like fold, tetratricopep	89.26
3r0a_A		123	Putative transcriptional regulator; structural gen	89.09
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	88.79
3qou_A		287	Protein YBBN; thioredoxin-like fold, tetratricopep	88.7
2kat_A		115	Uncharacterized protein; NESG, structure, structur	88.59
3mv2_B		310	Coatomer subunit epsilon; vesicular membrane coat	87.75
1z7u_A		112	Hypothetical protein EF0647; winged-helix-turn-hel	87.59
1sfx_A		109	Conserved hypothetical protein AF2008; structural	87.26
1rz4_A		226	Eukaryotic translation initiation factor 3 subuni;	87.02
2heo_A		67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	86.96
4b4t_P		445	26S proteasome regulatory subunit RPN5; hydrolase,	86.02
4b4t_T		274	26S proteasome regulatory subunit RPN12; hydrolase	85.9
2hzt_A		107	Putative HTH-type transcriptional regulator YTCD;	85.59
1ub9_A		100	Hypothetical protein PH1061; helix-turn-helix moti	85.49
1b89_A		449	Protein (clathrin heavy chain); triskelion, coated	85.15
2r5s_A		176	Uncharacterized protein VP0806; APC090868.1, vibri	85.06
1wao_1		477	Serine/threonine protein phosphatase 5; hydrolase,	84.95
4ham_A		134	LMO2241 protein; structural genomics, PSI-biology,	84.71
2htj_A		81	P fimbrial regulatory protein KS71A; winged helix-	83.61
1hxi_A		121	PEX5, peroxisome targeting signal 1 receptor PEX5;	83.15
3tqn_A		113	Transcriptional regulator, GNTR family; regulatory	80.36
3i4p_A		162	Transcriptional regulator, ASNC family; PSI, struc	80.3
2fsw_A		107	PG_0823 protein; alpha-beta structure, helix-turn-	80.23

>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	Back alignment and structure

Probab=100.00  E-value=1.4e-75  Score=581.33  Aligned_cols=349  Identities=77%  Similarity=1.114  Sum_probs=302.2

Q ss_pred             CCCCchHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHhhccccchhhhHHHHHHHH
Q psy4083          26 EEENHDEEVKAKEQNILQLGEKYKQEGKAIELAELIKKTRPFLSQISKAKAAKLVRSLVDFFLDLETRTGMEVALCKECI  105 (374)
Q Consensus        26 ~~~~~~~~~k~~e~~~~~l~~~~~~~~~~~~l~~~l~~l~~~~~~~~k~~~~k~i~~ild~~~~~~~~~~~~~~l~~e~i  105 (374)
                      ++++++...+.+|++|++|+++|++.|+++++.++++.++++++.++|++++|+|++++|.++.+|++.+.++++|+++|
T Consensus         7 ~~~~~~~~~~~~e~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~kak~~k~v~~l~~~~~~~~~~~~~~~~~~~~~~   86 (394)
T 3txn_A            7 GAENDEERIRIKEQGILQQGELYKQEGKAKELADLIKVTRPFLSSISKAKAAKLVRSLVDMFLDMDAGTGIEVQLCKDCI   86 (394)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTTTGGGGSCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHH
T ss_pred             cCcCcHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHH
Confidence            45667888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Q psy4083         106 EWAKEERRTFLRQSLEARLIALYFDTGEYTEALKLSSSLLKELKKLDDKNLLVEVLLLESKTYHALSNLSTSRASLTSAR  185 (374)
Q Consensus       106 ~~~~~~~r~~lr~~l~~kLa~~~~~~g~~~~Al~~~~~ll~el~~~dd~~~~lev~l~ei~l~~~~~n~~~a~~~~~~a~  185 (374)
                      +||++++|+|||++++.|||++|++.|+|++|++++.++++++++.||+.+++|++++|+++|+..+|+++++++|++|+
T Consensus        87 ~~a~~~~r~flr~~l~~kL~~l~~~~~~y~~a~~~i~~l~~~~~~~dd~~~llev~lle~~~~~~~~n~~k~k~~l~~a~  166 (394)
T 3txn_A           87 EWAKQEKRTFLRQSLEARLIALYFDTALYTEALALGAQLLRELKKLDDKNLLVEVQLLESKTYHALSNLPKARAALTSAR  166 (394)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSSCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccccCCChhhhHHHHHHHHHHhhcccccHHHHHHHHHHhccCcCcccchhHHHHHHHHHHHHHhcCCchhHHHHHH--
Q psy4083         186 TTANSIYCPPKMQAALDLQSGILHAADEQDFKTAFSYFYEAFEGFSTVDHNHAMMSLKYMLLSKIMLNTPEDVNQILS--  263 (374)
Q Consensus       186 ~~~~~~~~~~~~~~~i~~~~G~~~~~~~rdy~~A~~~F~eaf~~f~~~~~~~~~~~LkY~vL~~iL~~~~~~v~~ll~--  263 (374)
                      ++++++++||+++|.|++|+|++|++.+|||++|+++|+|||++|+++|++++.++++|++||+||++++.++.+++.  
T Consensus       167 ~~~~ai~~~p~i~a~i~~~~Gi~~l~~~rdyk~A~~~F~eaf~~f~~~~~~~~~~~lkYlvL~aLl~~~r~el~~~l~~~  246 (394)
T 3txn_A          167 TTANAIYCPPKVQGALDLQSGILHAADERDFKTAFSYFYEAFEGFDSVDSVKALTSLKYMLLCKIMLGQSDDVNQLVSGK  246 (394)
T ss_dssp             HHHHHSCCCHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHSH
T ss_pred             hhhccCCCCHHHHHHHHHHhhHHHHHhccCHHHHHHHHHHHHhcccccccHHHHHHHHHHHHHHHHcCCHHHHHHHhccc
Confidence            999888899999999999999999945999999999999999999999999999999999999999988655433221  


Q ss_pred             -------------------------------------HHhcChHHHhhHHHHHHHHHHHHHHHhhccccceeHHHHHhHh
Q psy4083         264 -------------------------------------ELEDDTIVKAHIGTLYDNMLEQNLCRIIEPYSRVEVGFIAKSI  306 (374)
Q Consensus       264 -------------------------------------~l~~D~~l~~h~~~L~~~ire~~l~~~~~pYs~I~l~~lA~~l  306 (374)
                                                           .+..|+|+++|+..|+++||++|++++++||++|++++||+.|
T Consensus       247 ~~~~~~~pei~~l~~L~~a~~~~dl~~f~~iL~~~~~~l~~D~~l~~h~~~L~~~Ir~~~L~~i~~pYsrIsl~~iA~~l  326 (394)
T 3txn_A          247 LAITYSGRDIDAMKSVAEASHKRSLADFQAALKEYKKELAEDVIVQAHLGTLYDTMLEQNLCRIIEPYSRVQVAHVAESI  326 (394)
T ss_dssp             HHHTTCSHHHHHHHHHHHHHHTTCHHHHHHHHHHSTTTTTTSHHHHHHHHHHHHHHHHHHHHHHHTTCSEEEHHHHHHHH
T ss_pred             cccccCCccHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHHHHHHHHhHhhceeeHHHHHHHH
Confidence                                                 4788999999999999999999999999999999999999999


Q ss_pred             CCChHHHHHHHHHHhhcCccceeecCCCCeEEEecCCcchHHHHHHHHHHHHHHHHHHHHHHHhcccC
Q psy4083         307 KLDELAVEKKLSQMILDKKFHGILDQGEKVLIVFEGAEIDKTYEKALETITSMGKVIDTLYQKAKKLT  374 (374)
Q Consensus       307 ~ls~~~vE~~L~~lI~dgkl~akID~~~giv~~~~~~~~~~~y~~~~~~i~~l~~~vd~l~~~~~~~~  374 (374)
                      |+|++++|++|++||.+|+|+|+|||++|+|+++++++++.+|+++++++++|+++||.||+||++++
T Consensus       327 ~ls~~evE~~L~~lI~dg~I~a~IDq~~giv~~~~~~~r~~~y~~ale~l~~ls~vVd~L~~~~~~~~  394 (394)
T 3txn_A          327 QLPMPQVEKKLSQMILDKKFSGILDQGEGVLIVFEETPVDKTYERVLETIQSMGKVVDTLYQKAKKLS  394 (394)
T ss_dssp             TCCHHHHHHHHHHHHHTTSSCEEEETTTTEEEECCC--------------------------------
T ss_pred             CcCHHHHHHHHHHHHHCCCeeEEEcCCCCEEEECCCcchhhHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence            99999999999999999999999999999999999999999999999999999999999999999874

PyMOL of 3txn

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

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

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

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

>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	Back alignment and structure

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

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

>3t5v_B Nuclear mRNA export protein THP1; PCI, mRNA nuclear export, mRNA, nuclear, transcription; 2.90A {Saccharomyces cerevisiae}	Back alignment and structure

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}	Back alignment and structure

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}	Back alignment and structure

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}	Back alignment and structure

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A	Back alignment and structure

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}	Back alignment and structure

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}	Back alignment and structure

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}	Back alignment and structure

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}	Back alignment and structure

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}	Back alignment and structure

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}	Back alignment and structure

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}	Back alignment and structure

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}	Back alignment and structure

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}	Back alignment and structure

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}	Back alignment and structure

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1	Back alignment and structure

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A	Back alignment and structure

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}	Back alignment and structure

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}	Back alignment and structure

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}	Back alignment and structure

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}	Back alignment and structure

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}	Back alignment and structure

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2	Back alignment and structure

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

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}	Back alignment and structure

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1	Back alignment and structure

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}	Back alignment and structure

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}	Back alignment and structure

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

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A	Back alignment and structure

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}	Back alignment and structure

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}	Back alignment and structure

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

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2	Back alignment and structure

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A	Back alignment and structure

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A	Back alignment and structure

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}	Back alignment and structure

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}	Back alignment and structure

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}	Back alignment and structure

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}	Back alignment and structure

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A	Back alignment and structure

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}	Back alignment and structure

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A	Back alignment and structure

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}	Back alignment and structure

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}	Back alignment and structure

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1	Back alignment and structure

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A	Back alignment and structure

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}	Back alignment and structure

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A	Back alignment and structure

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}	Back alignment and structure

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A	Back alignment and structure

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}	Back alignment and structure

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}	Back alignment and structure

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A	Back alignment and structure

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A	Back alignment and structure

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}	Back alignment and structure

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}	Back alignment and structure

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}	Back alignment and structure

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}	Back alignment and structure

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}	Back alignment and structure

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}	Back alignment and structure

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A	Back alignment and structure

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A	Back alignment and structure

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A	Back alignment and structure

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A	Back alignment and structure

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}	Back alignment and structure

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1	Back alignment and structure

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A	Back alignment and structure

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A	Back alignment and structure

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}	Back alignment and structure

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A	Back alignment and structure

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}	Back alignment and structure

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*	Back alignment and structure

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A	Back alignment and structure

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A	Back alignment and structure

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}	Back alignment and structure

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}	Back alignment and structure

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1	Back alignment and structure

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}	Back alignment and structure

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A	Back alignment and structure

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}	Back alignment and structure

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*	Back alignment and structure

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}	Back alignment and structure

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}	Back alignment and structure

>1wi9_A Protein C20ORF116 homolog; helix-turn-helix motif, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: a.4.5.47	Back alignment and structure

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*	Back alignment and structure

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*	Back alignment and structure

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}	Back alignment and structure

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1	Back alignment and structure

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1	Back alignment and structure

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A	Back alignment and structure

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1	Back alignment and structure

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}	Back alignment and structure

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A	Back alignment and structure

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}	Back alignment and structure

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1	Back alignment and structure

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}	Back alignment and structure

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*	Back alignment and structure

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}	Back alignment and structure

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}	Back alignment and structure

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1	Back alignment and structure

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}	Back alignment and structure

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B	Back alignment and structure

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}	Back alignment and structure

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A	Back alignment and structure

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A	Back alignment and structure

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1	Back alignment and structure

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}	Back alignment and structure

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A	Back alignment and structure

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A	Back alignment and structure

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*	Back alignment and structure

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A	Back alignment and structure

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A	Back alignment and structure

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}	Back alignment and structure

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}	Back alignment and structure

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A	Back alignment and structure

>3lpz_A GET4 (YOR164C homolog); protein targeting, tail-anchored protein biogenesis, GET PAT GET5 binding, protein transport; 1.98A {Chaetomium thermophilum}	Back alignment and structure

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}	Back alignment and structure

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}	Back alignment and structure

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1	Back alignment and structure

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}	Back alignment and structure

>2wpv_A GET4, UPF0363 protein YOR164C; golgi-ER trafficking, tail-anchored protein, protein binding GET4; 1.99A {Saccharomyces cerevisiae} PDB: 3lku_A	Back alignment and structure

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A	Back alignment and structure

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A	Back alignment and structure

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A	Back alignment and structure

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*	Back alignment and structure

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A	Back alignment and structure

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}	Back alignment and structure

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}	Back alignment and structure

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A	Back alignment and structure

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}	Back alignment and structure

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}	Back alignment and structure

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1	Back alignment and structure

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A	Back alignment and structure

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}	Back alignment and structure

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A	Back alignment and structure

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2	Back alignment and structure

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}	Back alignment and structure

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}	Back alignment and structure

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*	Back alignment and structure

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*	Back alignment and structure

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1	Back alignment and structure

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*	Back alignment and structure

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7	Back alignment and structure

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1	Back alignment and structure

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1	Back alignment and structure

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A	Back alignment and structure

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}	Back alignment and structure

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*	Back alignment and structure

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}	Back alignment and structure

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*	Back alignment and structure

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*	Back alignment and structure

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62	Back alignment and structure

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1	Back alignment and structure

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}	Back alignment and structure

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8	Back alignment and structure

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Back alignment and structure

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19	Back alignment and structure

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3	Back alignment and structure

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}	Back alignment and structure

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*	Back alignment and structure

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A	Back alignment and structure

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}	Back alignment and structure

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8	Back alignment and structure

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*	Back alignment and structure

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7	Back alignment and structure

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A	Back alignment and structure

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*	Back alignment and structure

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}	Back alignment and structure

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}	Back alignment and structure

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}	Back alignment and structure

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}	Back alignment and structure

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

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A	Back alignment and structure

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}	Back alignment and structure

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}	Back alignment and structure

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3	Back alignment and structure

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A	Back alignment and structure

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A	Back alignment and structure

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}	Back alignment and structure

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7	Back alignment and structure

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*	Back alignment and structure

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}	Back alignment and structure

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2	Back alignment and structure

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*	Back alignment and structure

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}	Back alignment and structure

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B	Back alignment and structure

>1z7u_A Hypothetical protein EF0647; winged-helix-turn-helix, MARR, structural genomics, PSI, Pro structure initiative; 2.20A {Enterococcus faecalis} SCOP: a.4.5.69	Back alignment and structure

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50	Back alignment and structure

>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	Back alignment and structure

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A	Back alignment and structure

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

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

>2hzt_A Putative HTH-type transcriptional regulator YTCD; DNA-binding protein, HTH-type transcription regulators, structural genomics, PSI-2; HET: CSU MSE; 2.00A {Bacillus subtilis} SCOP: a.4.5.69	Back alignment and structure

>1ub9_A Hypothetical protein PH1061; helix-turn-helix motif, winged helix motif, structural genom transcription; 2.05A {Pyrococcus horikoshii} SCOP: a.4.5.28	Back alignment and structure

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3	Back alignment and structure

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}	Back alignment and structure

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3	Back alignment and structure

>4ham_A LMO2241 protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, winged helix-turn-helix, four helix bundle; 1.91A {Listeria monocytogenes}	Back alignment and structure

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73	Back alignment and structure

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1	Back alignment and structure

>3tqn_A Transcriptional regulator, GNTR family; regulatory functions; 2.80A {Coxiella burnetii}	Back alignment and structure

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}	Back alignment and structure

>2fsw_A PG_0823 protein; alpha-beta structure, helix-turn-helix, winged-helix-turn-HE structural genomics, PSI, protein structure initiative; HET: MSE; 2.16A {Porphyromonas gingivalis} SCOP: a.4.5.69	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		374
d1ufma_		84	a.4.5.47 (A:) COP9 signalosome complex subunit 4,	7e-14

>d1ufma_ a.4.5.47 (A:) COP9 signalosome complex subunit 4, GSN4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 84	Back information, alignment and structure


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]

 Score = 64.4 bits (157), Expect = 7e-14
 Identities = 17/67 (25%), Positives = 33/67 (49%), Gaps = 1/67 (1%)

Query: 278 LYDNMLEQNLCRIIEPYSRVEVGFIAKSIKLDELAVEKKLSQMILDKKFHGILDQGEKVL 337
           L   ++E NL    + Y+ +    +   +++     EK  SQMI + + +G +DQ + + 
Sbjct: 12  LDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGI- 70

Query: 338 IVFEGAE 344
           + FE  E
Sbjct: 71  VHFETRE 77

PyMOL of d1ufma_

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		374
d1ufma_		84	COP9 signalosome complex subunit 4, GSN4 {Mouse (M	99.65
d1qqea_		290	Vesicular transport protein sec17 {Baker's yeast (	98.39
d1qqea_		290	Vesicular transport protein sec17 {Baker's yeast (	97.74
d1elra_		128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.49
d1hz4a_		366	Transcription factor MalT domain III {Escherichia	97.45
d1hz4a_		366	Transcription factor MalT domain III {Escherichia	97.24
d1fcha_		323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.19
d1fcha_		323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	96.96
d1kt1a1		168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	96.91
d1w3ba_		388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	96.76
d1p5qa1		170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	96.73
d2c2la1		201	STIP1 homology and U box-containing protein 1, STU	96.39
d1w3ba_		388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	96.25
d1kt1a1		168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	96.21
d1elwa_		117	Hop {Human (Homo sapiens) [TaxId: 9606]}	96.21
d1wi9a_		72	Hypothetical protein C20orf116 homolog {Mouse (Mus	96.18
d1ihga1		169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	96.09
d1a17a_		159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	96.06
d1p5qa1		170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	96.06
d2fbna1		153	Putative 70 kda peptidylprolyl isomerase PFL2275c	95.82
d1hxia_		112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	95.62
d1a17a_		159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	95.54
d1tjca_		95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	95.51
d2fbna1		153	Putative 70 kda peptidylprolyl isomerase PFL2275c	95.46
d2hr2a1		156	Hypothetical protein CT2138 {Chlorobium tepidum [T	95.32
d1xnfa_		259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	95.3
d1hh8a_		192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	94.98
d1hh8a_		192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	94.69
d1xnfa_		259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	94.63
d2h6fa1		315	Protein farnesyltransferase alpha-subunit {Human (	93.94
d2c2la1		201	STIP1 homology and U box-containing protein 1, STU	92.92
d1elwa_		117	Hop {Human (Homo sapiens) [TaxId: 9606]}	92.54
d1ihga1		169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	92.5
d1elra_		128	Hop {Human (Homo sapiens) [TaxId: 9606]}	92.45
d1tjca_		95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	92.03
d1hxia_		112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	91.39
d1nzna_		122	Mitochondria fission protein Fis1 {Human (Homo sap	90.46
d2hr2a1		156	Hypothetical protein CT2138 {Chlorobium tepidum [T	90.17
d1ub9a_		100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	89.27
d2cfxa1		63	Transcriptional regulator LrpC {Bacillus subtilis	89.11
d3bwga1		78	Transcriptional regulator YydK {Bacillus subtilis	87.84
d2ff4a2		179	Probable regulatory protein EmbR, middle domain {M	87.36
d1dpua_		69	C-terminal domain of RPA32 {Human (Homo sapiens) [	87.35
d2cg4a1		63	Regulatory protein AsnC {Escherichia coli [TaxId:	87.27
d2cyya1		60	Putative transcriptional regulator PH1519 {Archaeo	86.22
d1i1ga1		60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	85.57
d1sfxa_		109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	85.34
d1nzna_		122	Mitochondria fission protein Fis1 {Human (Homo sap	84.94
d1z05a1		71	Transcriptional regulator VC2007 N-terminal domain	83.9
d2hs5a1		69	Putative transcriptional regulator RHA1_ro03477 {R	81.88
d1z6ra1		70	Mlc protein N-terminal domain {Escherichia coli [T	81.37

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

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=99.65  E-value=5.1e-17  Score=124.82  Aligned_cols=67  Identities=21%  Similarity=0.301  Sum_probs=64.1

Q ss_pred             HHHHHHHHHHHHhhccccceeHHHHHhHhCCChHHHHHHHHHHhhcCccceeecCCCCeEEEecCCc
Q psy4083         278 LYDNMLEQNLCRIIEPYSRVEVGFIAKSIKLDELAVEKKLSQMILDKKFHGILDQGEKVLIVFEGAE  344 (374)
Q Consensus       278 L~~~ire~~l~~~~~pYs~I~l~~lA~~l~ls~~~vE~~L~~lI~dgkl~akID~~~giv~~~~~~~  344 (374)
                      |++++++||++.+.+||++|+|++||+.|+++++++|.+|++||.+|+|+|+|||++|+|+|.++..
T Consensus        12 L~~~i~Ehni~~is~~Y~~Isl~~la~~l~l~~~evE~~l~~mI~~~~i~akIDq~~g~V~F~~~e~   78 (84)
T d1ufma_          12 LDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVHFETREA   78 (84)
T ss_dssp             CCHHHHHHHHHHHHHSCSEEEHHHHHHHTTSCHHHHHHHHHHHHHTTSSCEEEETTTTEEEECCSSC
T ss_pred             HHHHHHHHHHHHHHHhhceeeHHHHHHHHCCCHHHHHHHHHHHHhcCeEEEEEeCCCCEEEECCCCc
Confidence            6789999999999999999999999999999999999999999999999999999999999977654

PyMOL of d1ufma_

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}	Back information, alignment and structure

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}	Back information, alignment and structure

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wi9a_ a.4.5.47 (A:) Hypothetical protein C20orf116 homolog {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	Back information, alignment and structure

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}	Back information, alignment and structure

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}	Back information, alignment and structure

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}	Back information, alignment and structure

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}	Back information, alignment and structure

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	Back information, alignment and structure

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}	Back information, alignment and structure

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}	Back information, alignment and structure

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}	Back information, alignment and structure

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}	Back information, alignment and structure

>d3bwga1 a.4.5.6 (A:5-82) Transcriptional regulator YydK {Bacillus subtilis [TaxId: 1423]}	Back information, alignment and structure

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}	Back information, alignment and structure

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}	Back information, alignment and structure

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}	Back information, alignment and structure

>d2hs5a1 a.4.5.6 (A:25-93) Putative transcriptional regulator RHA1_ro03477 {Rhodococcus sp. RHA1 [TaxId: 101510]}	Back information, alignment and structure

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure