Psyllid ID: psy9642

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-------380-------390-------400-------410-------420-------430-------

MATALEQFVNNVRQLSAQGSFRELTEIIQKSMDVLTKYGQHLDNVLETLETFQHSLGILAILSAKLTLLSSSNTGSEYQEELFSQIQEFLNMCNPDQIRHAGDLYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPALAVSHIMLEGYKKYLLIYLIVYGKAPNLPKNVSQAICRYIKPLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRDENTGLTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRFNNPLTFAQIESNIRACMHLDGKFQAMEEEILVNPLYVKKAASPSDEETGSSKPGGRVMEVENSIY

ccHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHccccHHHHHcccccHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHcccHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHcccccHHHHHHHHHHcccHHHHHHHHHHcHHHHHccccccHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHcccccHHHHHHHHHHHHHccEEEEEEEccccEEEEcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHccccccccccccccccccccccccc

cccHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHcHHHHHHHHHHccHHHccHHHHHEEEEEEccccccccccccHHHHHHHHHHHHHHccHHHHHHcHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHccccHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHcHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHcccccHHHHHHHHHHHHHcccEEEEEEccccEEEEcccccHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHcccccccccEEcHHHHcc

MATALEQFVNNVRQLSAQGSFRELTEIIQKSMDVLTKYGQHLDNVLETLETFQHSLGILAILSAKLTLlsssntgseYQEELFSQIQEFLNMCNPDQIRHAGDLYAELSHQYTKTVmdlktpqrgiPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNfkpalefldvdittianegpqfdtkYFLQYFYYGGMIYLALKNYERALYFFEVIITTPALAVSHIMLEGYKKYLLIYLIVYgkapnlpknVSQAICRYIkplsqpylDLVSVYTNNNSTELQHLLLKYADVfsrdentgLTKQIVASLYKNNIKRLTKTFLTLSLADVasrvqlgtpvQAEIYILKMISQNEIYATinkkdgmvvfndnpqrfnnpltFAQIESNIRACMHLDGKFQAMEEEILVNplyvkkaaspsdeetgsskpggrvmeVENSIY

MATALEqfvnnvrqlsaqgsfRELTEIIQKSMDVLTKYGQHLDNVLETLETFQHSLGILAILSAKLTLLSSSNTGSEYQEELFSQIQEFLNMCNPDQIRHAGDLYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIanegpqfdtKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPALAVSHIMLEGYKKYLLIYLIVYGKAPNLPKNVSQAICRYIKPLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRDENTGLTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRFNNPLTFAQIESNIRACMHLDGKFQAMEEEILVNPlyvkkaaspsdeetgsskpggrvmevensiy

MATALEQFVNNVRQLSAQGSFRELTEIIQKSMDVLTKYGQHLDNVLETLETFQHSLGILAILSAKLTLLSSSNTGSEYQEELFSQIQEFLNMCNPDQIRHAGDLYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPALAVSHIMLEGykkylliyliVYGKAPNLPKNVSQAICRYIKPLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRDENTGLTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRFNNPLTFAQIESNIRACMHLDGKFQAMEEEILVNPLYVKKAASPSDEETGSSKPGGRVMEVENSIY

***********VRQLSAQGSFRELTEIIQKSMDVLTKYGQHLDNVLETLETFQHSLGILAILSAKLTLLSSS***SEYQEELFSQIQEFLNMCNPDQIRHAGDLYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPALAVSHIMLEGYKKYLLIYLIVYGKAPNLPKNVSQAICRYIKPLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRDENTGLTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRFNNPLTFAQIESNIRACMHLDGKFQAMEEEILVNPLYV****************************

**TALEQFVNNVR*****************************DNVLETLETFQHSLGILAILSAKLTLLSSSNTGSEYQEELFSQIQEFLNMCNPDQIRHAGDLYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPALAVSHIMLEGYKKYLLIYLIVYGKAPNLPKNVSQAICRYIKPLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRDENTGLTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNP*****PL**AQIESNIRACMHLDGKFQAMEEEI******************************ENSIY

****LEQFVNNVRQLSAQGSFRELTEIIQKSMDVLTKYGQHLDNVLETLETFQHSLGILAILSAKLTLLSSSNTGSEYQEELFSQIQEFLNMCNPDQIRHAGDLYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPALAVSHIMLEGYKKYLLIYLIVYGKAPNLPKNVSQAICRYIKPLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRDENTGLTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRFNNPLTFAQIESNIRACMHLDGKFQAMEEEILVNPLYVKKAASPSDEE******************

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		437	2.2.26 [Sep-21-2011]
Q6P2U9		423	COP9 signalosome complex	yes	N/A	0.954	0.985	0.537	1e-131
A6H7B5		423	COP9 signalosome complex	yes	N/A	0.958	0.990	0.534	1e-131
O88543		423	COP9 signalosome complex	yes	N/A	0.958	0.990	0.536	1e-131
Q5RFS2		423	COP9 signalosome complex	yes	N/A	0.958	0.990	0.536	1e-130
Q4R898		423	COP9 signalosome complex	N/A	N/A	0.958	0.990	0.536	1e-130
Q9UNS2		423	COP9 signalosome complex	yes	N/A	0.958	0.990	0.536	1e-130
Q68FW9		423	COP9 signalosome complex	yes	N/A	0.958	0.990	0.536	1e-130
Q5ZJF1		423	COP9 signalosome complex	yes	N/A	0.958	0.990	0.534	1e-130
Q28IV6		423	COP9 signalosome complex	yes	N/A	0.958	0.990	0.534	1e-128
Q7ZTN8		423	COP9 signalosome complex	N/A	N/A	0.958	0.990	0.529	1e-127

>sp\|Q6P2U9\|CSN3_DANRE COP9 signalosome complex subunit 3 OS=Danio rerio GN=cops3 PE=2 SV=1	Back alignment and function desciption

 Score =  469 bits (1207), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 227/422 (53%), Positives = 307/422 (72%), Gaps = 5/422 (1%)

Query: 1   MATALEQFVNNVRQLSAQGSFRELTEIIQKSMDVLTKYGQHLDNVLETLETFQHSLGILA 60
           MA+ALEQFVNNVRQLSAQG   +L E+I KS ++L K   HLD VL  L+  +HSLG+LA
Sbjct: 1   MASALEQFVNNVRQLSAQGQMTQLCELINKSGELLAKNLSHLDTVLGALDIQEHSLGVLA 60

Query: 61  ILSAKLTLLSSSNTGSEYQEELFSQIQEFLNMCNPDQIRHAGDLYAELSHQYTKTVMDLK 120
           +L  K ++ +  +      E LFSQ+Q F++ CN + IR+A D +A L HQ T  +++ K
Sbjct: 61  VLFVKFSMPNIPDF-----ETLFSQVQLFISTCNGEHIRYATDTFAGLCHQLTNALVERK 115

Query: 121 TPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQ 180
            P RGI +++ AI K+Q + +QLTS+H+DLCQLCLLA+ FKPA+ FL++D+  I  E   
Sbjct: 116 QPLRGISILKQAIDKMQMNTNQLTSVHADLCQLCLLAKCFKPAVPFLELDMMDICKENGA 175

Query: 181 FDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPALAVSHIMLEGYKKYLLIYLIVY 240
           +D K+FL Y+YYGGMIY  LKN+ERALYFFE  ITTPA+AVSHIMLE YKKY+L+ LI++
Sbjct: 176 YDAKHFLCYYYYGGMIYTGLKNFERALYFFEQAITTPAMAVSHIMLEAYKKYILVSLILH 235

Query: 241 GKAPNLPKNVSQAICRYIKPLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRDENTGLT 300
           GK   LPK  SQ + R+IKPLS  Y +L  +Y  NN  EL+ L+ K+++ F+RD NTGL 
Sbjct: 236 GKVQQLPKYTSQIVGRFIKPLSNAYHELAQIYATNNPAELRALVNKHSETFTRDNNTGLV 295

Query: 301 KQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKD 360
           KQ ++SLYK NI+RLTKTFLTLSL D+ASRVQL  P +AE Y+L MI   EIYA+IN+KD
Sbjct: 296 KQCLSSLYKKNIQRLTKTFLTLSLQDMASRVQLSGPQEAEKYVLHMIEDGEIYASINQKD 355

Query: 361 GMVVFNDNPQRFNNPLTFAQIESNIRACMHLDGKFQAMEEEILVNPLYVKKAASPSDEET 420
           GMV F+DNP+++NNP    +I+  +  C+ LD K ++M++EI VNP +V+K+    +++ 
Sbjct: 356 GMVCFHDNPEKYNNPAMLHKIDQEMLKCIELDEKLKSMDQEITVNPQFVQKSMGTQEDDV 415

Query: 421 GS 422
           GS
Sbjct: 416 GS 417

Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of E3 ligase complexes, leading to modify the Ubl ligase activity.
Danio rerio (taxid: 7955)

>sp\|A6H7B5\|CSN3_BOVIN COP9 signalosome complex subunit 3 OS=Bos taurus GN=COPS3 PE=2 SV=1	Back alignment and function description

>sp\|O88543\|CSN3_MOUSE COP9 signalosome complex subunit 3 OS=Mus musculus GN=Cops3 PE=1 SV=3	Back alignment and function description

>sp\|Q5RFS2\|CSN3_PONAB COP9 signalosome complex subunit 3 OS=Pongo abelii GN=COPS3 PE=2 SV=1	Back alignment and function description

>sp\|Q4R898\|CSN3_MACFA COP9 signalosome complex subunit 3 OS=Macaca fascicularis GN=COPS3 PE=2 SV=1	Back alignment and function description

>sp\|Q9UNS2\|CSN3_HUMAN COP9 signalosome complex subunit 3 OS=Homo sapiens GN=COPS3 PE=1 SV=3	Back alignment and function description

>sp\|Q68FW9\|CSN3_RAT COP9 signalosome complex subunit 3 OS=Rattus norvegicus GN=Cops3 PE=2 SV=1	Back alignment and function description

>sp\|Q5ZJF1\|CSN3_CHICK COP9 signalosome complex subunit 3 OS=Gallus gallus GN=COPS3 PE=2 SV=1	Back alignment and function description

>sp\|Q28IV6\|CSN3_XENTR COP9 signalosome complex subunit 3 OS=Xenopus tropicalis GN=cops3 PE=2 SV=1	Back alignment and function description

>sp\|Q7ZTN8\|CSN3_XENLA COP9 signalosome complex subunit 3 OS=Xenopus laevis GN=cops3 PE=2 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		437
307203254		445	COP9 signalosome complex subunit 3 [Harp	0.972	0.955	0.598	1e-140
332018929		445	COP9 signalosome complex subunit 3 [Acro	0.972	0.955	0.602	1e-139
242017347		427	COP9 signalosome complex subunit, putati	0.963	0.985	0.599	1e-138
427789621		430	Putative 26s proteasome regulatory subun	0.965	0.981	0.552	1e-134
346468841		430	hypothetical protein [Amblyomma maculatu	0.956	0.972	0.547	1e-132
156537217		441	PREDICTED: COP9 signalosome complex subu	0.965	0.956	0.555	1e-132
442753283		430	Putative cop9 signalosome subunit csn3 [	0.970	0.986	0.537	1e-131
348502345		423	PREDICTED: COP9 signalosome complex subu	0.954	0.985	0.542	1e-130
432955711		423	PREDICTED: COP9 signalosome complex subu	0.954	0.985	0.545	1e-130
55976433		423	RecName: Full=COP9 signalosome complex s	0.954	0.985	0.537	1e-129

>gi\|307203254\|gb\|EFN82409.1\| COP9 signalosome complex subunit 3 [Harpegnathos saltator]	Back alignment and taxonomy information

 Score =  505 bits (1300), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 255/426 (59%), Positives = 329/426 (77%), Gaps = 1/426 (0%)

Query: 1   MATALEQFVNNVRQLSAQGSFRELTEIIQKSMDVLTKYGQHLDNVLETLETFQHSLGILA 60
           MA+ALEQFVNNVR LS QG+FREL E+I KS +VLTK+GQHLDNVLETL+  QHSLGILA
Sbjct: 1   MASALEQFVNNVRTLSKQGNFRELCEVISKSAEVLTKHGQHLDNVLETLDLQQHSLGILA 60

Query: 61  ILSAKLTLLS-SSNTGSEYQEELFSQIQEFLNMCNPDQIRHAGDLYAELSHQYTKTVMDL 119
           +L AK +L + +    S+  + LF+Q+QEF+  CN +Q+R A D YAEL H  T+++++ 
Sbjct: 61  VLCAKFSLPNPNGGNNSDANKSLFNQVQEFIIGCNGEQVRLAPDTYAELCHLLTQSLVES 120

Query: 120 KTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGP 179
           K P RGI L++ AI+KIQ  DSQLTS+H+DLCQLCLL++  KPALEFLD+D+T I+ EG 
Sbjct: 121 KAPLRGIELLRRAIRKIQLFDSQLTSIHADLCQLCLLSKCMKPALEFLDIDVTGISQEGG 180

Query: 180 QFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPALAVSHIMLEGYKKYLLIYLIV 239
           QFD+KYFL Y+YYGGMIY ALKNY+RALYFFEV +TTPA+AVS+IMLE YKKY+L+ LI+
Sbjct: 181 QFDSKYFLLYYYYGGMIYTALKNYDRALYFFEVCVTTPAMAVSYIMLEAYKKYILVSLIL 240

Query: 240 YGKAPNLPKNVSQAICRYIKPLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRDENTGL 299
           +GK  NLP+  SQ I RYIKPLSQ Y +L + Y+ N+  E+Q ++ KY  +F RD N GL
Sbjct: 241 HGKVLNLPRYTSQVINRYIKPLSQQYQELATAYSINSCEEVQSIITKYQQLFIRDHNLGL 300

Query: 300 TKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKK 359
            KQ++A LYK NI+RLTKTFLTLSL+DVASRVQL  P  AE YIL MI   EI+ATIN+K
Sbjct: 301 VKQVLAYLYKKNIQRLTKTFLTLSLSDVASRVQLSGPADAENYILNMIEDGEIFATINQK 360

Query: 360 DGMVVFNDNPQRFNNPLTFAQIESNIRACMHLDGKFQAMEEEILVNPLYVKKAASPSDEE 419
           DGMVVF+D+P+++N+P   A  E  + AC  LD + Q MEEE+++ P YV+KA   +D++
Sbjct: 361 DGMVVFHDDPEKYNSPQMLANFEKEMAACTELDKRVQEMEEEVILTPQYVRKACGQNDQD 420

Query: 420 TGSSKP 425
             ++ P
Sbjct: 421 DQAAGP 426

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi\|332018929\|gb\|EGI59475.1\| COP9 signalosome complex subunit 3 [Acromyrmex echinatior]	Back alignment and taxonomy information

>gi\|242017347\|ref\|XP_002429151.1\| COP9 signalosome complex subunit, putative [Pediculus humanus corporis] gi\|212514024\|gb\|EEB16413.1\| COP9 signalosome complex subunit, putative [Pediculus humanus corporis]	Back alignment and taxonomy information

>gi\|427789621\|gb\|JAA60262.1\| Putative 26s proteasome regulatory subunit [Rhipicephalus pulchellus]	Back alignment and taxonomy information

>gi\|346468841\|gb\|AEO34265.1\| hypothetical protein [Amblyomma maculatum]	Back alignment and taxonomy information

>gi\|156537217\|ref\|XP_001605022.1\| PREDICTED: COP9 signalosome complex subunit 3-like [Nasonia vitripennis]	Back alignment and taxonomy information

>gi\|442753283\|gb\|JAA68801.1\| Putative cop9 signalosome subunit csn3 [Ixodes ricinus]	Back alignment and taxonomy information

>gi\|348502345\|ref\|XP_003438728.1\| PREDICTED: COP9 signalosome complex subunit 3-like [Oreochromis niloticus]	Back alignment and taxonomy information

>gi\|432955711\|ref\|XP_004085613.1\| PREDICTED: COP9 signalosome complex subunit 3-like [Oryzias latipes]	Back alignment and taxonomy information

>gi\|55976433\|sp\|Q6P2U9.1\|CSN3_DANRE RecName: Full=COP9 signalosome complex subunit 3; Short=Signalosome subunit 3 gi\|39795809\|gb\|AAH64288.1\| COP9 constitutive photomorphogenic homolog subunit 3 [Danio rerio]	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		437
ZFIN\|ZDB-GENE-030131-7660		423	cops3 "COP9 constitutive photo	0.954	0.985	0.521	7.3e-114
UNIPROTKB\|A6H7B5		423	COPS3 "COP9 signalosome comple	0.958	0.990	0.517	1.9e-113
UNIPROTKB\|E2RD70		423	COPS3 "Uncharacterized protein	0.958	0.990	0.52	1.9e-113
UNIPROTKB\|Q9UNS2		423	COPS3 "COP9 signalosome comple	0.958	0.990	0.52	2.5e-113
MGI\|MGI:1349409		423	Cops3 "COP9 (constitutive phot	0.958	0.990	0.52	2.5e-113
RGD\|1303002		423	Cops3 "COP9 signalosome subuni	0.958	0.990	0.52	3.2e-113
UNIPROTKB\|Q5ZJF1		423	COPS3 "COP9 signalosome comple	0.958	0.990	0.517	6.6e-113
UNIPROTKB\|F1SB16		423	COPS3 "Uncharacterized protein	0.958	0.990	0.515	7.6e-112
FB\|FBgn0027055		445	CSN3 "COP9 complex homolog sub	0.963	0.946	0.486	3.8e-101
DICTYBASE\|DDB_G0291848		418	csn3 "proteasome component reg	0.842	0.880	0.356	7.3e-59

ZFIN\|ZDB-GENE-030131-7660 cops3 "COP9 constitutive photomorphogenic homolog subunit 3" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

 Score = 1123 (400.4 bits), Expect = 7.3e-114, P = 7.3e-114
 Identities = 220/422 (52%), Positives = 298/422 (70%)

Query:     1 MATALEQFVNNVRQLSAQGSFRELTEIIQKSMDVLTKYGQHLDNVLETLETFQHSLGILA 60
             MA+ALEQFVNNVRQLSAQG   +L E+I KS ++L K   HLD VL  L+  +HSLG+LA
Sbjct:     1 MASALEQFVNNVRQLSAQGQMTQLCELINKSGELLAKNLSHLDTVLGALDIQEHSLGVLA 60

Query:    61 ILSAKLTLLSSSNTGSEYQEELFSQIQEFLNMCNPDQIRHAGDLYAELSHQYTKTVMDLK 120
             +L  K ++ +  +      E LFSQ+Q F++ CN + IR+A D +A L HQ T  +++ K
Sbjct:    61 VLFVKFSMPNIPDF-----ETLFSQVQLFISTCNGEHIRYATDTFAGLCHQLTNALVERK 115

Query:   121 TPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQ 180
              P RGI +++ AI K+Q + +QLTS+H+DLCQLCLLA+ FKPA+ FL++D+  I  E   
Sbjct:   116 QPLRGISILKQAIDKMQMNTNQLTSVHADLCQLCLLAKCFKPAVPFLELDMMDICKENGA 175

Query:   181 FDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPALAVSHIMLEGXXXXXXXXXXVY 240
             +D K+FL Y+YYGGMIY  LKN+ERALYFFE  ITTPA+AVSHIMLE           ++
Sbjct:   176 YDAKHFLCYYYYGGMIYTGLKNFERALYFFEQAITTPAMAVSHIMLEAYKKYILVSLILH 235

Query:   241 GKAPNLPKNVSQAICRYIKPLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRDENTGLT 300
             GK   LPK  SQ + R+IKPLS  Y +L  +Y  NN  EL+ L+ K+++ F+RD NTGL 
Sbjct:   236 GKVQQLPKYTSQIVGRFIKPLSNAYHELAQIYATNNPAELRALVNKHSETFTRDNNTGLV 295

Query:   301 KQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKD 360
             KQ ++SLYK NI+RLTKTFLTLSL D+ASRVQL  P +AE Y+L MI   EIYA+IN+KD
Sbjct:   296 KQCLSSLYKKNIQRLTKTFLTLSLQDMASRVQLSGPQEAEKYVLHMIEDGEIYASINQKD 355

Query:   361 GMVVFNDNPQRFNNPLTFAQIESNIRACMHLDGKFQAMEEEILVNPLYVKKAASPSDEET 420
             GMV F+DNP+++NNP    +I+  +  C+ LD K ++M++EI VNP +V+K+    +++ 
Sbjct:   356 GMVCFHDNPEKYNNPAMLHKIDQEMLKCIELDEKLKSMDQEITVNPQFVQKSMGTQEDDV 415

Query:   421 GS 422
             GS
Sbjct:   416 GS 417

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0008180 "signalosome" evidence=IEA

UNIPROTKB\|A6H7B5 COPS3 "COP9 signalosome complex subunit 3" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|E2RD70 COPS3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|Q9UNS2 COPS3 "COP9 signalosome complex subunit 3" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

MGI\|MGI:1349409 Cops3 "COP9 (constitutive photomorphogenic) homolog, subunit 3 (Arabidopsis thaliana)" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

RGD\|1303002 Cops3 "COP9 signalosome subunit 3" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5ZJF1 COPS3 "COP9 signalosome complex subunit 3" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|F1SB16 COPS3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

FB\|FBgn0027055 CSN3 "COP9 complex homolog subunit 3" [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0291848 csn3 "proteasome component region PCI (PINT) domain-containing protein" [Dictyostelium discoideum (taxid:44689)]	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)
Q4R898	CSN3_MACFA	No assigned EC number	0.5364	0.9588	0.9905	N/A	N/A
Q68FW9	CSN3_RAT	No assigned EC number	0.5364	0.9588	0.9905	yes	N/A
Q28IV6	CSN3_XENTR	No assigned EC number	0.5341	0.9588	0.9905	yes	N/A
Q8W575	CSN3_ARATH	No assigned EC number	0.3773	0.8237	0.8391	yes	N/A
Q9UNS2	CSN3_HUMAN	No assigned EC number	0.5364	0.9588	0.9905	yes	N/A
O88543	CSN3_MOUSE	No assigned EC number	0.5364	0.9588	0.9905	yes	N/A
Q8SYG2	CSN3_DROME	No assigned EC number	0.4954	0.9633	0.9460	yes	N/A
Q54E53	CSN3_DICDI	No assigned EC number	0.3773	0.8421	0.8803	yes	N/A
Q5RFS2	CSN3_PONAB	No assigned EC number	0.5364	0.9588	0.9905	yes	N/A
A6H7B5	CSN3_BOVIN	No assigned EC number	0.5341	0.9588	0.9905	yes	N/A
Q7ZTN8	CSN3_XENLA	No assigned EC number	0.5294	0.9588	0.9905	N/A	N/A
Q5ZJF1	CSN3_CHICK	No assigned EC number	0.5341	0.9588	0.9905	yes	N/A
Q6P2U9	CSN3_DANRE	No assigned EC number	0.5379	0.9542	0.9858	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		437
pfam01399		100	pfam01399, PCI, PCI domain	2e-13
smart00753		88	smart00753, PAM, PCI/PINT associated module	8e-10
smart00088		88	smart00088, PINT, motif in proteasome subunits, In	8e-10

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

 Score = 65.7 bits (161), Expect = 2e-13
 Identities = 25/101 (24%), Positives = 53/101 (52%), Gaps = 1/101 (0%)

Query: 265 YLDLVSVYTNNNSTELQHLLLKYADVFSRDENTGLTKQIVASLYKNNIKRLTKTFLTLSL 324
           Y DL+  + + + ++ + +L    D    D    L + +   + + N++RL K + ++SL
Sbjct: 1   YRDLLRAFYSGDLSDFEEILADNEDELLDDGLAELLEDLRRKIRELNLRRLAKPYSSISL 60

Query: 325 ADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVF 365
           +D+A  + L +  + E  + K+I    I   I++ +G+VVF
Sbjct: 61  SDLAKLLGL-SVDEVEKILSKLIRDGRIRGKIDQVNGIVVF 100

This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15). Length = 100

>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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		437
KOG2582\|consensus		422		100.0
KOG2581\|consensus		493		100.0
KOG1498\|consensus		439		99.91
KOG1463\|consensus		411		99.8
COG5071		439	RPN5 26S proteasome regulatory complex component [	99.78
PF01399		105	PCI: PCI domain; InterPro: IPR000717 A homology do	99.7
COG5159		421	RPN6 26S proteasome regulatory complex component [	99.65
KOG1464\|consensus		440		99.62
KOG1497\|consensus		399		99.58
COG5600		413	Transcription-associated recombination protein [DN	99.44
KOG2688\|consensus		394		99.4
smart00753		88	PAM PCI/PINT associated module.	99.26
smart00088		88	PINT motif in proteasome subunits, Int-6, Nip-1 an	99.26
KOG2908\|consensus		380		99.07
KOG1076\|consensus		843		98.27
KOG0687\|consensus		393		98.23
COG5187		412	RPN7 26S proteasome regulatory complex component,	98.15
PF10255		404	Paf67: RNA polymerase I-associated factor PAF67; I	98.1
KOG0686\|consensus		466		98.01
KOG2072\|consensus		988		97.91
KOG2753\|consensus		378		97.48
PF08375		68	Rpn3_C: Proteasome regulatory subunit C-terminal;	97.41
PF10075		143	PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro	96.51
KOG2758\|consensus		432		96.31
PF14938		282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	95.8
PF13432		65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	94.98
PF13371		73	TPR_9: Tetratricopeptide repeat	94.58
PF13414		69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	94.56
PF12895		84	Apc3: Anaphase-promoting complex, cyclosome, subun	94.34
PF09976		145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	94.25
TIGR02552		135	LcrH_SycD type III secretion low calcium response	94.07
PF07719		34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	93.89
TIGR02795		119	tol_pal_ybgF tol-pal system protein YbgF. Members	93.43
PF13424		78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	93.13
PF00515		34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	92.76
PF08784		102	RPA_C: Replication protein A C terminal; InterPro:	92.72
PF09012		69	FeoC: FeoC like transcriptional regulator; InterPr	92.44
cd00189		100	TPR Tetratricopeptide repeat domain; typically con	92.05
PF09295		395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	91.76
PRK15359		144	type III secretion system chaperone protein SscB;	91.73
PLN03088		356	SGT1, suppressor of G2 allele of SKP1; Provisional	91.21
PRK12370		553	invasion protein regulator; Provisional	90.91
PF13174		33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	90.78
PF13181		34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	90.19
PRK10803		263	tol-pal system protein YbgF; Provisional	87.6
PF13412		48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	87.2
PLN03218		1060	maturation of RBCL 1; Provisional	86.92
TIGR02521		234	type_IV_pilW type IV pilus biogenesis/stability pr	86.61
PRK15359		144	type III secretion system chaperone protein SscB;	85.58
PF12569		517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	85.56
PRK10370		198	formate-dependent nitrite reductase complex subuni	85.49
TIGR03302		235	OM_YfiO outer membrane assembly lipoprotein YfiO.	85.4
PF09986		214	DUF2225: Uncharacterized protein conserved in bact	85.17
PF14559		68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	84.87
PRK11788		389	tetratricopeptide repeat protein; Provisional	84.33
KOG4414\|consensus		197		83.96
smart00028		34	TPR Tetratricopeptide repeats. Repeats present in	83.52
TIGR02552		135	LcrH_SycD type III secretion low calcium response	83.41
PF14853		53	Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repe	82.98
PLN03218		1060	maturation of RBCL 1; Provisional	82.34
cd00189		100	TPR Tetratricopeptide repeat domain; typically con	82.24
PF10602		177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	82.01
smart00550		68	Zalpha Z-DNA-binding domain in adenosine deaminase	81.62
PF12802		62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	80.64
PF01047		59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	80.51
PF03399		204	SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; I	80.47

>KOG2582\|consensus	Back alignment and domain information

Probab=100.00  E-value=2.5e-80  Score=600.70  Aligned_cols=416  Identities=47%  Similarity=0.772  Sum_probs=403.1

Q ss_pred             CchhHHHHHHHHhhhccCCCHHHHHHHHHhhHHHHHhccccchhhhhccCcchhhHHHHHHHHHHhccccCCCCCCccHH
Q psy9642           1 MATALEQFVNNVRQLSAQGSFRELTEIIQKSMDVLTKYGQHLDNVLETLETFQHSLGILAILSAKLTLLSSSNTGSEYQE   80 (437)
Q Consensus         1 ~~~~l~~~v~~v~~~s~~~~~~~L~~~l~~~~~~l~~~~~~~~~~L~~ldp~~hsl~~L~vL~~~~~~~~~~~~~~~~~~   80 (437)
                      |++.++..+++++++|++++.++|.+.|.++.+.+.+++.+++++|..|||++||+|++|+|.+++..+.+    .++++
T Consensus         1 ~gs~l~a~i~~~~~~~~~~~~~eL~~~i~~~~ell~k~~~~~~~~L~~ld~~~hSlgml~~l~~~f~~~~~----~~~~~   76 (422)
T KOG2582|consen    1 LGSMLEAAINELCSLSHSSNVGELAELIVKSKELLAKNSSDLDAVLLHLDPQVHSLGMLAVLKVKFHTPSA----NPDPE   76 (422)
T ss_pred             CcHHHHHHHHHHHhhhcCCcHHHHHHHHHhhHHHHHhCcchHHHHHHhcCccccchhhhhhhhccccCccc----CCCHH
Confidence            56789999999999999999999999999999999999999999999999999999999999999988764    47889


Q ss_pred             HHHHHHHHHHHhcChhhhhhhHHHHHHHHHHHHHHHhhhCCCCcchHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCc
Q psy9642          81 ELFSQIQEFLNMCNPDQIRHAGDLYAELSHQYTKTVMDLKTPQRGIPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNF  160 (437)
Q Consensus        81 ~~~~~~~~fl~~fd~~Qir~a~~~~~~l~~~~~~~~~~~~~~~~~i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y  160 (437)
                      .+++++.+|+.+||.+|+|+|+..|..+|+.+++++...++|.+|+.++..|+.+++|++.++|++|.+++++||.+++|
T Consensus        77 ~li~~~~~FV~~~n~eqlr~as~~f~~lc~~l~~~~~~~~~p~~gi~ii~~av~k~~~~~~qlT~~H~~l~~~~L~ak~y  156 (422)
T KOG2582|consen   77 TLIELLNDFVDENNGEQLRLASEIFFPLCHDLTEAVVKKNKPLRGIRIIMQAVDKMQPSNGQLTSIHADLLQLCLEAKDY  156 (422)
T ss_pred             HHHHHHHHHHHhcChHHHhhHHHHHHHHHHHHHHHHHhcCCccccchHHHHHHHHhccCccchhhhHHHHHHHHHHhhcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHHHHHhhHHHHHHHHHHHhcccccccCHHHHHHHHHHHHHHHHHh
Q psy9642         161 KPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIYLALKNYERALYFFEVIITTPALAVSHIMLEGYKKYLLIYLIVY  240 (437)
Q Consensus       161 ~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~~~~k~y~~A~~~~~~ai~~P~~~~s~i~vea~Kk~iLv~Lil~  240 (437)
                      ..++|++|.+|.++|..++..+++.++.|+||||||++++|||++|..||+.|+++|+.+++.++.||||||+||+||+.
T Consensus       157 ~~~~p~ld~divei~~~n~h~~~k~fL~Y~yYgg~iciglk~fe~Al~~~e~~v~~Pa~~vs~~hlEaYkkylLvsLI~~  236 (422)
T KOG2582|consen  157 ASVLPYLDDDIVEICKANPHLDPKYFLLYLYYGGMICIGLKRFERALYLLEICVTTPAMAVSHIHLEAYKKYLLVSLILT  236 (422)
T ss_pred             cccCCccchhHHHHhccCCCCCHHHHHHHHHhcceeeeccccHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHhhhc
Confidence            99999999999999998889999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCccccHHHhHhhccCCHHHHHHHHHHhcCCHHHHHHHHHhccccccccchhhHHHHHHHHHHHHHHHHHHHhhc
Q psy9642         241 GKAPNLPKNVSQAICRYIKPLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRDENTGLTKQIVASLYKNNIKRLTKTFL  320 (437)
Q Consensus       241 G~~~~lp~~~s~~~~r~~k~~~~pY~~L~~af~~~d~~~~~~~~~~~~~~f~~D~n~~Lv~~l~~~v~r~~I~~l~k~Ys  320 (437)
                      ||+..+|+.+|+.+.|.+|+...||++|+++|.++...+++.++.+|.+.|.+|||+|++++++..+++|+|++++|+|+
T Consensus       237 GK~~ql~k~ts~~~~r~~K~ms~pY~ef~~~Y~~~~~~eLr~lVk~~~~rF~kDnnt~l~k~av~sl~k~nI~rltktF~  316 (422)
T KOG2582|consen  237 GKVFQLPKNTSQNAGRFFKPMSNPYHEFLNVYLKDSSTELRTLVKKHSERFTKDNNTGLAKQAVSSLYKKNIQRLTKTFL  316 (422)
T ss_pred             CceeeccccchhhhHHhcccCCchHHHHHHHHhcCCcHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy9642         321 TLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQRFNNPLTFAQIESNIRACMHLDGKFQAMEE  400 (437)
Q Consensus       321 ~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~~~~~~e~~~~l~~~i~~~~~L~~~~~~~d~  400 (437)
                      +|+|+|||++++|.+.+|||++|.+||++|+|.|.||   |||.|.+++++|.++|+...   .|..|.+|.+++++||+
T Consensus       317 sLsL~dIA~~vQLa~~qevek~Ilqmie~~~i~a~iN---G~v~f~~n~e~~~SpeM~~n---k~~~~~~L~e~l~~~e~  390 (422)
T KOG2582|consen  317 SLSLSDIASRVQLASAQEVEKYILQMIEDGEIFASIN---GMVFFTDNPEKYNSPEMHEN---KIDLCIQLIEALKAMEE  390 (422)
T ss_pred             HhhHHHHHHHHHhcchHHHHHHHHHHhccCceEEEec---ceEEEecCcccCCCHHHHhh---HHHHHHHHHHHHHhcch
Confidence            9999999999999999999999999999999999997   99999999999999988765   89999999999999999


Q ss_pred             HhhCCHHHHHHhcCCCCcccCCCCCCC
Q psy9642         401 EILVNPLYVKKAASPSDEETGSSKPGG  427 (437)
Q Consensus       401 ~l~~~~~yi~k~~~~~~~~~~~~~~~~  427 (437)
                      .+.++|-|++|+++.|.++ +|++|..
T Consensus       391 si~l~s~~~~K~m~~~~d~-~~~~p~t  416 (422)
T KOG2582|consen  391 SIRLNSVYVSKSMGSQEDD-GGSMPPT  416 (422)
T ss_pred             heeeCceeeehhhhhhhcc-ccCCCCc
Confidence            9999999999999999988 8887754

>KOG2581\|consensus	Back alignment and domain information

>KOG1498\|consensus	Back alignment and domain information

>KOG1463\|consensus	Back alignment and domain information

>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]	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

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

>KOG1464\|consensus	Back alignment and domain information

>KOG1497\|consensus	Back alignment and domain information

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

>KOG2688\|consensus	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

>KOG2908\|consensus	Back alignment and domain information

>KOG1076\|consensus	Back alignment and domain information

>KOG0687\|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

>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

>KOG0686\|consensus	Back alignment and domain information

>KOG2072\|consensus	Back alignment and domain information

>KOG2753\|consensus	Back alignment and domain information

>PF08375 Rpn3_C: Proteasome regulatory subunit C-terminal; InterPro: IPR013586 Intracellular proteins, including short-lived proteins such as cyclin, Mos, Myc, p53, NF-kappaB, and IkappaB, are degraded by the ubiquitin-proteasome system	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

>KOG2758\|consensus	Back alignment and domain information

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A	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

>PF13371 TPR_9: Tetratricopeptide repeat	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

>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

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

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

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]	Back alignment and domain information

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF	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

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]	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

>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

>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

>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

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

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

>PRK12370 invasion protein regulator; 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

>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A	Back alignment and domain information

>PRK10803 tol-pal system protein YbgF; Provisional	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

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

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

>PRK15359 type III secretion system chaperone protein SscB; Provisional	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

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

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

>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function	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

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

>KOG4414\|consensus	Back alignment and domain information

>smart00028 TPR Tetratricopeptide repeats	Back alignment and domain information

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

>PF14853 Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repeat; PDB: 1IYG_A 1PC2_A 1NZN_A 3UUX_C 1Y8M_A 2PQR_A 2PQN_A 3O48_A	Back alignment and domain information

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

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

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

>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B	Back alignment and domain information

>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance	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

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		437
3txn_A		394	26S proteasome regulatory complex subunit P42B; PC	4e-18
3t5x_A		203	PCI domain-containing protein 2; PCI, mRNA nuclear	1e-13
1ufm_A		84	COP9 complex subunit 4; helix-turn-helix, structur	9e-10
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-08
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
3t5v_B		455	Nuclear mRNA export protein THP1; PCI, mRNA nuclea	2e-06

>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 = 84.9 bits (209), Expect = 4e-18
 Identities = 51/365 (13%), Positives = 128/365 (35%), Gaps = 26/365 (7%)

Query: 20  SFRELTEIIQKSMDVLTKYGQHLDNVLETLETFQHSLGILA------ILSAKLTLLSSSN 73
             R   + I +  ++  + G+    + + ++  +  L  ++      ++ + + +    +
Sbjct: 14  RIRIKEQGILQQGELYKQEGK-AKELADLIKVTRPFLSSISKAKAAKLVRSLVDMFLDMD 72

Query: 74  TGSEYQEELFSQIQEFLNMCNPDQIRHAGDLYAELSHQYTKTVMDLKTPQRGIPLIQTAI 133
            G+  + +L     E+        +R +      L  +      D       + L    +
Sbjct: 73  AGTGIEVQLCKDCIEWAKQEKRTFLRQS------LEARLIALYFDTALYTEALALGAQLL 126

Query: 134 KKIQTSD--SQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFY 191
           ++++  D  + L  +     +      N   A   L     T AN               
Sbjct: 127 RELKKLDDKNLLVEVQLLESKTYHALSNLPKARAALT-SARTTANAIYCPPKVQGALDLQ 185

Query: 192 YGGMIYLALKNYERALYFFEVIITTPALAVSHIMLEGYKKYLLIYLIVYGKAPNLPKNVS 251
            G +     ++++ A  +F           S   L    KY+L+  I+ G++ ++ + VS
Sbjct: 186 SGILHAADERDFKTAFSYFYEAFEGFDSVDSVKALT-SLKYMLLCKIMLGQSDDVNQLVS 244

Query: 252 QAIC-RYIKPLSQPYLDLVSVYTNNNSTELQHLLLKYADVFSRDENTGLTKQIVASLYKN 310
             +   Y          +       +  + Q  L +Y    + D    + +  + +LY  
Sbjct: 245 GKLAITYSGRDIDAMKSVAEASHKRSLADFQAALKEYKKELAEDV---IVQAHLGTLYDT 301

Query: 311 ----NIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFN 366
               N+ R+ + +  + +A VA  +QL  P Q E  + +MI   +    +++ +G+++  
Sbjct: 302 MLEQNLCRIIEPYSRVQVAHVAESIQLPMP-QVEKKLSQMILDKKFSGILDQGEGVLIVF 360

Query: 367 DNPQR 371
           +    
Sbjct: 361 EETPV 365

PyMOL of 3txn

>3t5x_A PCI domain-containing protein 2; PCI, mRNA nuclear export, transcription; 2.12A {Homo sapiens} Length = 203	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 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

>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

>3t5v_B Nuclear mRNA export protein THP1; PCI, mRNA nuclear export, mRNA, nuclear, transcription; 2.90A {Saccharomyces cerevisiae} Length = 455	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		437
4b4t_S		523	RPN3, 26S proteasome regulatory subunit RPN3; hydr	100.0
4b4t_P		445	26S proteasome regulatory subunit RPN5; hydrolase,	99.95
3t5x_A		203	PCI domain-containing protein 2; PCI, mRNA nuclear	99.94
3txn_A		394	26S proteasome regulatory complex subunit P42B; PC	99.92
3t5v_B		455	Nuclear mRNA export protein THP1; PCI, mRNA nuclea	99.9
4b4t_Q		434	26S proteasome regulatory subunit RPN6; hydrolase,	99.81
4b4t_R		429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	99.81
1ufm_A		84	COP9 complex subunit 4; helix-turn-helix, structur	99.49
4b4t_O		393	26S proteasome regulatory subunit RPN9; hydrolase,	99.46
4b0z_A		229	RPN12, 26S proteasome regulatory subunit RPN12; pr	98.92
3chm_A		169	COP9 signalosome complex subunit 7; heat/ARM repea	98.17
2xev_A		129	YBGF; tetratricopeptide, alpha-helical, metal bind	95.7
3ro2_A		338	PINS homolog, G-protein-signaling modulator 2; TPR	95.45
3k9i_A		117	BH0479 protein; putative protein binding protein,	95.43
1qqe_A		292	Vesicular transport protein SEC17; helix-turn-heli	95.36
2vgx_A		148	Chaperone SYCD; alternative dimer assembly, tetrat	95.1
2xcb_A		142	PCRH, regulatory protein PCRH; protein transport,	94.98
2dba_A		148	Smooth muscle cell associated protein-1, isoform 2	94.97
3sf4_A		406	G-protein-signaling modulator 2; tetratricopeptide	94.9
3sz7_A		164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	94.89
3rkv_A		162	Putative peptidylprolyl isomerase; structural geno	94.89
2qfc_A		293	PLCR protein; TPR, HTH, transcription regulation;	94.88
3gyz_A		151	Chaperone protein IPGC; asymmetric homodimer, tetr	94.87
1elr_A		131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	94.85
3ro3_A		164	PINS homolog, G-protein-signaling modulator 2; asy	94.76
3ro3_A		164	PINS homolog, G-protein-signaling modulator 2; asy	94.75
4gcn_A		127	Protein STI-1; structural genomics, PSI-biology, m	94.52
3gw4_A		203	Uncharacterized protein; structural genomics, PSI-	94.52
3qky_A		261	Outer membrane assembly lipoprotein YFIO; membrane	94.49
1elw_A		118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	94.35
2fbn_A		198	70 kDa peptidylprolyl isomerase, putative; sulfur	94.32
4gco_A		126	Protein STI-1; structural genomics, PSI-biology, m	94.22
2vyi_A		131	SGTA protein; chaperone, TPR repeat, phosphoprotei	94.21
3upv_A		126	Heat shock protein STI1; TPR-fold, adaptor protein	94.17
1hxi_A		121	PEX5, peroxisome targeting signal 1 receptor PEX5;	94.1
3q15_A		378	PSP28, response regulator aspartate phosphatase H;	93.96
4a1s_A		411	PINS, partner of inscuteable; cell cycle, LGN, mit	93.95
3ma5_A		100	Tetratricopeptide repeat domain protein; NESG, str	93.72
2l6j_A		111	TPR repeat-containing protein associated with HSP;	93.69
3ieg_A		359	DNAJ homolog subfamily C member 3; TPR motif, chap	93.69
2e2e_A		177	Formate-dependent nitrite reductase complex NRFG;	93.67
2lni_A		133	Stress-induced-phosphoprotein 1; structural genomi	93.6
2ifu_A		307	Gamma-SNAP; membrane fusion, snare complex disasse	93.57
3nf1_A		311	KLC 1, kinesin light chain 1; TPR, structural geno	93.54
3q49_B		137	STIP1 homology and U box-containing protein 1; E3	93.46
2kat_A		115	Uncharacterized protein; NESG, structure, structur	93.39
4ga2_A		150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	93.38
3edt_B		283	KLC 2, kinesin light chain 2; superhelical, struct	93.36
3edt_B		283	KLC 2, kinesin light chain 2; superhelical, struct	93.21
2kc7_A		99	BFR218_protein; tetratricopeptide repeat, all-alph	93.09
3u3w_A		293	Transcriptional activator PLCR protein; ternary co	93.06
3q15_A		378	PSP28, response regulator aspartate phosphatase H;	93.05
4b4t_Q		434	26S proteasome regulatory subunit RPN6; hydrolase,	93.02
4b4t_T		274	26S proteasome regulatory subunit RPN12; hydrolase	92.78
1na0_A		125	Designed protein CTPR3; de novo protein; HET: IPT;	92.78
3ulq_A		383	Response regulator aspartate phosphatase F; tetrat	92.75
3nf1_A		311	KLC 1, kinesin light chain 1; TPR, structural geno	92.73
1na3_A		91	Designed protein CTPR2; de novo protein; HET: IPT;	92.45
1a17_A		166	Serine/threonine protein phosphatase 5; hydrolase,	92.41
1kt0_A		457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	92.25
1ihg_A		370	Cyclophilin 40; ppiase immunophilin tetratricopept	92.19
2pzi_A		681	Probable serine/threonine-protein kinase PKNG; ATP	92.01
1p5q_A		336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	92.01
2kck_A		112	TPR repeat; tetratricopeptide repeat, structural g	91.98
3u4t_A		272	TPR repeat-containing protein; structural genomics	91.95
1rz4_A		226	Eukaryotic translation initiation factor 3 subuni;	91.68
4gcn_A		127	Protein STI-1; structural genomics, PSI-biology, m	91.62
2ho1_A		252	Type 4 fimbrial biogenesis protein PILF; type IV p	91.55
2vq2_A		225	PILW, putative fimbrial biogenesis and twitching m	91.5
3uq3_A		258	Heat shock protein STI1; HSP90, peptide binding, c	91.47
3u3w_A		293	Transcriptional activator PLCR protein; ternary co	91.43
4i17_A		228	Hypothetical protein; TPR repeats protein, structu	91.28
3ulq_A		383	Response regulator aspartate phosphatase F; tetrat	91.23
1hxi_A		121	PEX5, peroxisome targeting signal 1 receptor PEX5;	91.12
3gw4_A		203	Uncharacterized protein; structural genomics, PSI-	91.07
3upv_A		126	Heat shock protein STI1; TPR-fold, adaptor protein	90.89
3vtx_A		184	MAMA; tetratricopeptide repeats (TPR) containing p	90.76
3hym_B		330	Cell division cycle protein 16 homolog; APC, anaph	90.71
4gco_A		126	Protein STI-1; structural genomics, PSI-biology, m	90.68
3gyz_A		151	Chaperone protein IPGC; asymmetric homodimer, tetr	90.58
2xcb_A		142	PCRH, regulatory protein PCRH; protein transport,	90.56
2lni_A		133	Stress-induced-phosphoprotein 1; structural genomi	90.54
1elr_A		131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	90.47
2ho1_A		252	Type 4 fimbrial biogenesis protein PILF; type IV p	90.45
2vgx_A		148	Chaperone SYCD; alternative dimer assembly, tetrat	90.34
3hym_B		330	Cell division cycle protein 16 homolog; APC, anaph	90.29
3sz7_A		164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	90.22
2xev_A		129	YBGF; tetratricopeptide, alpha-helical, metal bind	90.21
3as5_A		186	MAMA; tetratricopeptide repeats (TPR) containing p	90.17
2qfc_A		293	PLCR protein; TPR, HTH, transcription regulation;	90.04
1elw_A		118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	90.0
2fo7_A		136	Synthetic consensus TPR protein; tetratricopeptide	89.95
3q49_B		137	STIP1 homology and U box-containing protein 1; E3	89.94
3urz_A		208	Uncharacterized protein; tetratricopeptide repeats	89.85
3uq3_A		258	Heat shock protein STI1; HSP90, peptide binding, c	89.66
3qky_A		261	Outer membrane assembly lipoprotein YFIO; membrane	89.59
1hh8_A		213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	89.42
3as5_A		186	MAMA; tetratricopeptide repeats (TPR) containing p	89.22
2fo7_A		136	Synthetic consensus TPR protein; tetratricopeptide	89.15
3urz_A		208	Uncharacterized protein; tetratricopeptide repeats	89.01
2y4t_A		450	DNAJ homolog subfamily C member 3; chaperone, endo	88.91
1hh8_A		213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	88.88
4i17_A		228	Hypothetical protein; TPR repeats protein, structu	88.83
1xnf_A		275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	88.6
2q7f_A		243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	88.45
1pc2_A		152	Mitochondria fission protein; unknown function; NM	88.45
3ffl_A		167	Anaphase-promoting complex subunit 7; tetratricope	88.41
2hr2_A		159	Hypothetical protein; alpha-alpha superhelix fold,	88.29
1qgp_A		77	Protein (double stranded RNA adenosine deaminase);	88.08
2yhc_A		225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	88.0
1qqe_A		292	Vesicular transport protein SEC17; helix-turn-heli	87.99
2if4_A		338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	87.81
1wao_1		477	Serine/threonine protein phosphatase 5; hydrolase,	87.72
3u4t_A		272	TPR repeat-containing protein; structural genomics	87.71
2vyi_A		131	SGTA protein; chaperone, TPR repeat, phosphoprotei	87.6
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	87.56
1fch_A		368	Peroxisomal targeting signal 1 receptor; protein-p	87.4
2kck_A		112	TPR repeat; tetratricopeptide repeat, structural g	86.99
1xnf_A		275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	86.98
1wi9_A		72	Protein C20ORF116 homolog; helix-turn-helix motif,	86.82
2q7f_A		243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	86.76
2pl2_A		217	Hypothetical conserved protein TTC0263; TPR, prote	86.74
3cv0_A		327	Peroxisome targeting signal 1 receptor PEX5; TPR m	86.68
3vtx_A		184	MAMA; tetratricopeptide repeats (TPR) containing p	86.37
2pl2_A		217	Hypothetical conserved protein TTC0263; TPR, prote	86.3
2dba_A		148	Smooth muscle cell associated protein-1, isoform 2	86.12
2vq2_A		225	PILW, putative fimbrial biogenesis and twitching m	86.08
4abn_A		474	Tetratricopeptide repeat protein 5; P53 cofactor,	85.63
1a17_A		166	Serine/threonine protein phosphatase 5; hydrolase,	85.61
4eqf_A		365	PEX5-related protein; accessory protein, tetratric	85.52
1na0_A		125	Designed protein CTPR3; de novo protein; HET: IPT;	85.44
2xpi_A		597	Anaphase-promoting complex subunit CUT9; cell cycl	85.18
2ond_A		308	Cleavage stimulation factor 77 kDa subunit; HAT do	85.14
1qbj_A		81	Protein (double-stranded RNA specific adenosine D	85.13
3ieg_A		359	DNAJ homolog subfamily C member 3; TPR motif, chap	84.76
2h6f_A		382	Protein farnesyltransferase/geranylgeranyltransfer	84.72
2v5f_A		104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	83.95
3mkr_A		291	Coatomer subunit epsilon; tetratricopeptide repeat	83.73
2h6f_A		382	Protein farnesyltransferase/geranylgeranyltransfer	83.57
1fch_A		368	Peroxisomal targeting signal 1 receptor; protein-p	82.3
3rkv_A		162	Putative peptidylprolyl isomerase; structural geno	81.7
4eqf_A		365	PEX5-related protein; accessory protein, tetratric	81.36
2e2e_A		177	Formate-dependent nitrite reductase complex NRFG;	81.29
2y4t_A		450	DNAJ homolog subfamily C member 3; chaperone, endo	81.12
4ga2_A		150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	81.06
2heo_A		67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	80.88
3sf4_A		406	G-protein-signaling modulator 2; tetratricopeptide	80.42
4gyw_A		723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	80.18

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

Probab=100.00  E-value=3e-49  Score=410.60  Aligned_cols=350  Identities=16%  Similarity=0.176  Sum_probs=212.8

Q ss_pred             cchhhHHHHHHHHHHhccccCCCCCCccHHHHHHHHH--HHHHhcChhhhhhhH---HHHHHHHHHHHHHHhhh-CC---
Q psy9642          51 TFQHSLGILAILSAKLTLLSSSNTGSEYQEELFSQIQ--EFLNMCNPDQIRHAG---DLYAELSHQYTKTVMDL-KT---  121 (437)
Q Consensus        51 p~~hsl~~L~vL~~~~~~~~~~~~~~~~~~~~~~~~~--~fl~~fd~~Qir~a~---~~~~~l~~~~~~~~~~~-~~---  121 (437)
                      |+...+.+|.++..+++...     ..+...+...++  +.+..+|++.+....   .+|++++++....+... +.   
T Consensus       132 pE~~~y~~lL~~i~L~d~k~-----~~~~~~~~~~~~~~~~l~~~nrrtlD~l~ak~~fY~s~~~e~~~~~~~~~~~~~~  206 (523)
T 4b4t_S          132 AEINCFMHLLVQLFLWDSKE-----LEQLVEFNRKVVIPNLLCYYNLRSLNLINAKLWFYIYLSHETLARSSEEINSDNQ  206 (523)
T ss_dssp             ----------------------------------------------------------------------------CHHH
T ss_pred             hHHHHHHHHHHHHHHhcccc-----HHHHHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHHHHHHhcccccccccccc
Confidence            55666666666666665443     445566777666  678889999887555   34555666543322210 00   


Q ss_pred             --CCcc--hHHHHHHHHHhCCCCcchhhHHHHHHHHHHHhCCchHHHhhhhHhhhhhhcCCCCCChHhhHHHHHHHHHHH
Q psy9642         122 --PQRG--IPLIQTAIKKIQTSDSQLTSLHSDLCQLCLLAQNFKPALEFLDVDITTIANEGPQFDTKYFLQYFYYGGMIY  197 (437)
Q Consensus       122 --~~~~--i~~l~~ai~rl~~~~~~lT~~h~~l~~l~L~~~~y~~Al~il~~~I~~~~~~~~~~~~~~~l~Y~Yy~G~I~  197 (437)
                        .+|+  +..+++|++|.|+  .+-+++|..++|.+|..+.|.+|..++++..+.    ....+.++.++|+||.|+|+
T Consensus       207 ~~~ir~~Ll~~~rta~lr~D~--~~qa~l~nllLRnYL~~~~y~qA~~lvsk~~fP----~~~~sn~q~~rY~YY~GRI~  280 (523)
T 4b4t_S          207 NIILRSTMMKFLKIASLKHDN--ETKAMLINLILRDFLNNGEVDSASDFISKLEYP----HTDVSSSLEARYFFYLSKIN  280 (523)
T ss_dssp             HHHHHTHHHHHHHHCCSCSSS--CHHHHHHHHHHHHHHHSSCSTTHHHHHHHHCSC----TTTSCHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHhcccCc--chhHHHHHHHHHHHHccCcHHHHHHHHhcCcCC----cccCCHHHHHHHHHHHHHHH
Confidence              0232  3467888878775  567889999999999999999999999998652    12357788999999999999


Q ss_pred             HHHhhHHHHHHHHHHHhc-ccccc-cCHHHHHHHHHHHHHHHHHhCCCCCCCccccHHHhHhhccCCHHHHHHHHHHhcC
Q psy9642         198 LALKNYERALYFFEVIIT-TPALA-VSHIMLEGYKKYLLIYLIVYGKAPNLPKNVSQAICRYIKPLSQPYLDLVSVYTNN  275 (437)
Q Consensus       198 ~~~k~y~~A~~~~~~ai~-~P~~~-~s~i~vea~Kk~iLv~Lil~G~~~~lp~~~s~~~~r~~k~~~~pY~~L~~af~~~  275 (437)
                      +.+++|.+|.++|..|++ +|... ...+...++|++|+|.|+ .|++|+.+.+..+.    +++.+.||.+|++||+.|
T Consensus       281 a~q~~Y~eA~~~L~~A~rkap~~~~a~gfr~~a~K~lI~V~LL-lG~iP~r~lf~q~~----l~~~L~pY~~Lv~Avr~G  355 (523)
T 4b4t_S          281 AIQLDYSTANEYIIAAIRKAPHNSKSLGFLQQSNKLHCCIQLL-MGDIPELSFFHQSN----MQKSLLPYYHLTKAVKLG  355 (523)
T ss_dssp             HHTTCHHHHHHHHHHHTSSCSCSSSCSHHHHHHHHHHHHHHHH-HTCCCCHHHHTTTS----CHHHHHHHHHHHHHHHHT
T ss_pred             HHhccHHHHHHHHHHHHHhCCcchhhhhHHHHHHHHHHhHHhh-cCCCCChHHhhchh----HHHHHHHHHHHHHHHHcC
Confidence            999999999999999999 88765 457889999999999996 59999877664432    334578999999999999


Q ss_pred             CHHHHHHHHHhccccccccchhhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEE
Q psy9642         276 NSTELQHLLLKYADVFSRDENTGLTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYAT  355 (437)
Q Consensus       276 d~~~~~~~~~~~~~~f~~D~n~~Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~  355 (437)
                      |+..|.+++++|+..|.+|||++||++|+.+++|++|++++++|++||++|||.+++++++++||++|++||.+|.|.|+
T Consensus       356 dL~~F~~~L~~h~~~F~~Dgty~LI~rLr~~vir~~irkis~~YsrIsL~dIa~kL~L~s~eeaE~iVAkmI~dG~I~A~  435 (523)
T 4b4t_S          356 DLKKFTSTITKYKQLLLKDDTYQLCVRLRSNVIKTGIRIISLTYKKISLRDICLKLNLDSEQTVEYMVSRAIRDGVIEAK  435 (523)
T ss_dssp             CHHHHHHHHHHTHHHHHHTTCTHHHHHHHHHHHHHHHHHSCCCSSEECHHHHHHHHHHHHSSCHHHHHHHHHHHTSSCCE
T ss_pred             CHHHHHHHHHHhcceeccCChhHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHhCCCCHHHHHHHHHHHHHcCCceEE
Confidence            99999999999999999999999999999999999999999999999999999999998788999999999999999999


Q ss_pred             EecCCCEEEEccCCCCCCchHHHHHHHHHHHHHHHHHH-HHHHHHHHhhCCH-HHHHHhcCCC
Q psy9642         356 INKKDGMVVFNDNPQRFNNPLTFAQIESNIRACMHLDG-KFQAMEEEILVNP-LYVKKAASPS  416 (437)
Q Consensus       356 Id~~~g~v~F~~~~~~~~~~e~~~~l~~~i~~~~~L~~-~~~~~d~~l~~~~-~yi~k~~~~~  416 (437)
                      |||++|+|+|.+.++.|++.||+..|+++|++|++|++ .+++|+..-...+ ++.++..+.+
T Consensus       436 Idh~~g~v~ske~~d~yst~ep~~af~~RI~~cl~L~ne~vkaMryp~~~~~~~~~~~~~~~~  498 (523)
T 4b4t_S          436 INHEDGFIETTELLNIYDSEDPQQVFDERIKFANQLHDEYLVSMRYPEDKKTQQNEKSENGEN  498 (523)
T ss_dssp             ECTTTCCEECCSSSCC-----------------------------------------------
T ss_pred             EecCCCEEEeCccccccccHHHHHHHHHHHHHHHHHHHHHHHHccCCcccchhhHHHHHHHhh
Confidence            99999999999999999999999999999999999987 8999997655444 4444433333

PyMOL of 4b4t

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

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

>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

>3t5v_B Nuclear mRNA export protein THP1; PCI, mRNA nuclear export, mRNA, nuclear, transcription; 2.90A {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

>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

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

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

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

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

>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

>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

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

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

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

>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

>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

>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

>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

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

>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

>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

>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

>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

>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

>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

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

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

>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

>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

>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

>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

>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

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

>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

>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

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

>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

>4b4t_Q 26S proteasome regulatory subunit RPN6; 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

>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

>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

>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

>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

>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

>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

>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

>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

>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

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

>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

>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

>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

>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

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

>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

>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

>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

>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

>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

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

>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

>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

>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

>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

>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

>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

>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

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

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

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

>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

>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

>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

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

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

>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

>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

>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

>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

>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

>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

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

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

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1	Back alignment and structure

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}	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

>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

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

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

>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

>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

>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

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

>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

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

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

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

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

>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

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

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

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

>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

>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

>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

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

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

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

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

>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

>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

>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

>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

>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

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		437
d1ufma_		84	a.4.5.47 (A:) COP9 signalosome complex subunit 4,	3e-09

>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 = 51.3 bits (123), Expect = 3e-09
 Identities = 12/73 (16%), Positives = 34/73 (46%), Gaps = 5/73 (6%)

Query: 300 TKQIVASLYKN----NIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYAT 355
           +    + L +     N+   +K +  ++  ++ + +++    +AE    +MI++  +   
Sbjct: 5   SSGGSSILDRAVIEHNLLSASKLYNNITFEELGALLEI-PAAKAEKIASQMITEGRMNGF 63

Query: 356 INKKDGMVVFNDN 368
           I++ DG+V F   
Sbjct: 64  IDQIDGIVHFETR 76

PyMOL of d1ufma_

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		437
d1ufma_		84	COP9 signalosome complex subunit 4, GSN4 {Mouse (M	99.53
d1qqea_		290	Vesicular transport protein sec17 {Baker's yeast (	96.18
d1hxia_		112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	95.38
d1p5qa1		170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	95.28
d1tjca_		95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	94.62
d1elwa_		117	Hop {Human (Homo sapiens) [TaxId: 9606]}	93.73
d2fbna1		153	Putative 70 kda peptidylprolyl isomerase PFL2275c	93.7
d1kt1a1		168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	92.74
d2c2la1		201	STIP1 homology and U box-containing protein 1, STU	92.44
d1a17a_		159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	92.19
d1hxia_		112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	92.02
d2cfxa1		63	Transcriptional regulator LrpC {Bacillus subtilis	91.77
d1hz4a_		366	Transcription factor MalT domain III {Escherichia	91.71
d2pqrb1		124	Mitochondria fission protein Fis1 {Baker's yeast (	91.58
d1wi9a_		72	Hypothetical protein C20orf116 homolog {Mouse (Mus	89.9
d2cg4a1		63	Regulatory protein AsnC {Escherichia coli [TaxId:	89.76
d1a17a_		159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	89.64
d1elra_		128	Hop {Human (Homo sapiens) [TaxId: 9606]}	89.64
d1ihga1		169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	89.28
d1nzna_		122	Mitochondria fission protein Fis1 {Human (Homo sap	88.9
d1fcha_		323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	88.79
d1i1ga1		60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	88.66
d2c2la1		201	STIP1 homology and U box-containing protein 1, STU	88.56
d2cyya1		60	Putative transcriptional regulator PH1519 {Archaeo	88.38
d1z05a1		71	Transcriptional regulator VC2007 N-terminal domain	88.03
d1xnfa_		259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	87.97
d2hr2a1		156	Hypothetical protein CT2138 {Chlorobium tepidum [T	87.84
d1xnfa_		259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	87.72
d1hh8a_		192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	87.65
d1elwa_		117	Hop {Human (Homo sapiens) [TaxId: 9606]}	87.6
d1dpua_		69	C-terminal domain of RPA32 {Human (Homo sapiens) [	87.58
d2h6fa1		315	Protein farnesyltransferase alpha-subunit {Human (	87.57
d1lj9a_		144	Transcriptional regulator SlyA {Enterococcus faeca	87.19
d1elra_		128	Hop {Human (Homo sapiens) [TaxId: 9606]}	85.5
d1z6ra1		70	Mlc protein N-terminal domain {Escherichia coli [T	85.28
d1w3ba_		388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	85.16
d1hz4a_		366	Transcription factor MalT domain III {Escherichia	85.03
d1rz4a1		85	Eukaryotic translation initiation factor 3 subunit	84.24
d1sfxa_		109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	83.72
d1hh8a_		192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	82.8
d1fcha_		323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	82.67
d1w3ba_		388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	81.25
d1ub9a_		100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	80.5

>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=99.53  E-value=2.9e-15  Score=117.81  Aligned_cols=75  Identities=16%  Similarity=0.335  Sum_probs=67.8

Q ss_pred             chhhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHhCCCChHHHHHHHHHhHHcCceEEEEecCCCEEEEccCCC
Q psy9642         295 ENTGLTKQIVASLYKNNIKRLTKTFLTLSLADVASRVQLGTPVQAEIYILKMISQNEIYATINKKDGMVVFNDNPQ  370 (437)
Q Consensus       295 ~n~~Lv~~l~~~v~r~~I~~l~k~Ys~IsL~dIa~~l~L~~~~eaE~~l~~mI~~G~I~A~Id~~~g~v~F~~~~~  370 (437)
                      |+.+...-|.+++++|||++++++|++|++++||++++++ ++++|.+|++||.+|.|+|+||+.+|+|.|.+...
T Consensus         4 ~~~~~~t~L~~~i~Ehni~~is~~Y~~Isl~~la~~l~l~-~~evE~~l~~mI~~~~i~akIDq~~g~V~F~~~e~   78 (84)
T d1ufma_           4 GSSGGSSILDRAVIEHNLLSASKLYNNITFEELGALLEIP-AAKAEKIASQMITEGRMNGFIDQIDGIVHFETREA   78 (84)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHHSCSEEEHHHHHHHTTSC-HHHHHHHHHHHHHTTSSCEEEETTTTEEEECCSSC
T ss_pred             cccchhHHHHHHHHHHHHHHHHHhhceeeHHHHHHHHCCC-HHHHHHHHHHHHhcCeEEEEEeCCCCEEEECCCCc
Confidence            4445555578899999999999999999999999999997 89999999999999999999999999999987643

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

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

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

>d1elwa_ a.118.8.1 (A:) Hop {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

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

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {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

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}	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

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	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

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

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

>d1elra_ 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

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {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

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	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

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

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	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

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}	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

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

>d1lj9a_ a.4.5.28 (A:) Transcriptional regulator SlyA {Enterococcus faecalis [TaxId: 1351]}	Back information, alignment and structure

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}	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

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {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

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

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}	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

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

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