Citrus Sinensis ID: 014453

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----

MQSIENLVTQIQGLSSNASDITALKDYLKAAEDLLRSESTRLLSFLDQLDPSKHSLGYLYFLEPCMYCSITKERANTLVPIIARFITSCSAEQIRYVPEKFINVCKRYKDQVLLLEAPIRGVGPMLTAIRKIQSSTEHLTTLHPEFLQLCLLAKCYKAGLSVLEDDIYEINLPRDFFLYCYYGGMIFIGQKRFRKALELLHNVVTAPMSSINAIAVEAYKKYILVSLIHHGQFSSTLPKYTSSAAQRNLKNFSQPYMELVNTYNTGKIVELETYVQTNREKFESDNNLGLVKQVVSSMYKRNIQRLTQTYLTLSLQDIANTVQLNSSKEAEMHVLQMIQDGEIFATINQKDGMVRFLEDPEQYKTCEMIEHIDSSIQRIMSLSKKLTAMDELISCDPLYLGKAGRERQRFDFDDFDSVPQKFNI

cccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHcccccHHHcHHHHHHHHHHHHccHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHcccHHHHHHHHHHcccccHHHHHHHHHHcHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHccccHHHHHHHHHHHHHcccEEEEEEccccEEEEEccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHccccccccccccccccc

ccHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHcHHHHHHHHHHccHHHcHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHccHHHHHHcHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHcccccHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHcccccHHHHHHHHHHHHHcccEEEEEEccccEEEEccccHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHcccccccccccccccc

MQSIENLVTQIQglssnasdITALKDYLKAAEDLLRSESTRLLSFldqldpskhslgylyflepcmycsitkerANTLVPIIARFITSCSAEQIRYVPEKFINVCKRYKDQVLLleapirgvgpMLTAIRKIQSSTEHLTTLHPEFLQLCLLAKCYKAGLSVleddiyeinlprdffLYCYYGGMIFIGQKRFRKALELLHNVVTAPMSSINAIAVEAYKKYILVSLIhhgqfsstlpkytssAAQRNLKNFSQPYMELVNTYNTGKIVELETYVQTNRekfesdnnlgLVKQVVSSMYKRNIQRLTQTYLTLSLQDIANTVQLNSSKEAEMHVLQMIQDGEIFAtinqkdgmvrfledpeqyktcEMIEHIDSSIQRIMSLSKKLTAMdeliscdplylgkagrerqrfdfddfdsvpqkfni

MQSIENLVTQiqglssnasdITALKDYLKAAEDLLRSESTRLLSFLDQLDPSKHSLGYLYFLEPCMYCSITKERANTLVPIIARFITSCSAEQIRYVPEKFINVCKRYKDQVLLLEAPIRGVGPMLTAIRKIQSSTEHLTTLHPEFLQLCLLAKCYKAGLSVLEDDIYEINLPRDFFLYCYYGGMIFIGQKRFRKALELLHNVVTAPMSSINAIAVEAYKKYILVSLIHHGQFSSTLPKYTSSAAQRNLKNFSQPYMELVNTYNTGKIVELETYVQTNrekfesdnnlglVKQVVSSMYKRNIQRLTQTYLTLSLQDIANTVQLNSSKEAEMHVLQMIQDGEIFATINQKDGMVRFLEDPEQYKTCEMIEHIDSSIQRIMSLSKKLTAMDELISCDPLYLGKAGRERQrfdfddfdsvpqkfni

********************ITALKDYLKAAEDLLRSESTRLLSFLDQLDPSKHSLGYLYFLEPCMYCSITKERANTLVPIIARFITSCSAEQIRYVPEKFINVCKRYKDQVLLLEAPIRGVGPMLTAIRKIQSSTEHLTTLHPEFLQLCLLAKCYKAGLSVLEDDIYEINLPRDFFLYCYYGGMIFIGQKRFRKALELLHNVVTAPMSSINAIAVEAYKKYILVSLIHHGQFSSTLPKYT*****RNLKNFSQPYMELVNTYNTGKIVELETYVQTNREKFESDNNLGLVKQVVSSMYKRNIQRLTQTYLTLSLQDIANTVQLNSSKEAEMHVLQMIQDGEIFATINQKDGMVRFLEDPEQYKTCEMIEHIDSSIQRIMSLSKKLTAMDELISCDPLYLGKAG********************

**SIENLVTQIQGLS******TALKDYLKAAE*******TRLLSFLDQLDPSKHSLGYLYFLEPCMYCSI*KERANTLVPIIARFITSCSAEQIRYVPEKFINVCKRYKDQVLLLEAPIRGVGPMLTAIRKIQSSTEHLTTLHPEFLQLCLLAKCYKAGLSVLEDDIYEINLPRDFFLYCYYGGMIFIGQKRFRKALELLHNVVTAPMSSINAIAVEAYKKYILVSLIHHGQFSSTLPKYTSSAAQRNLKNFSQPYMELVNTYNTGKIVELETYVQTNREKFESDNNLGLVKQVVSSMYKRNIQRLTQTYLTLSLQDIANTVQLNSSKEAEMHVLQMIQDGEIFATINQKDGMVRFLEDPEQYKTCEMIEHIDSSIQRIMSLSKKLTAMDE*********************************

*QSIENLVTQIQGLSSNASDITALKDYLKAAEDLLRSESTRLLSFLDQLDPSKHSLGYLYFLEPCMYCSITKERANTLVPIIARFITSCSAEQIRYVPEKFINVCKRYKDQVLLLEAPIRGVGPMLTAIRKIQSSTEHLTTLHPEFLQLCLLAKCYKAGLSVLEDDIYEINLPRDFFLYCYYGGMIFIGQKRFRKALELLHNVVTAPMSSINAIAVEAYKKYILVSLIHHGQFSSTLPKYTSSAAQRNLKNFSQPYMELVNTYNTGKIVELETYVQTNREKFESDNNLGLVKQVVSSMYKRNIQRLTQTYLTLSLQDIANTVQLNSSKEAEMHVLQMIQDGEIFATINQKDGMVRFLEDPEQYKTCEMIEHIDSSIQRIMSLSKKLTAMDELISCDPLYLGKAGRERQ****************

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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		424	2.2.26 [Sep-21-2011]
Q8W575		429	COP9 signalosome complex	yes	no	1.0	0.988	0.663	1e-164
Q5RFS2		423	COP9 signalosome complex	yes	no	0.976	0.978	0.402	7e-82
Q4R898		423	COP9 signalosome complex	N/A	no	0.976	0.978	0.402	7e-82
Q9UNS2		423	COP9 signalosome complex	yes	no	0.976	0.978	0.402	7e-82
Q68FW9		423	COP9 signalosome complex	yes	no	0.976	0.978	0.402	8e-82
O88543		423	COP9 signalosome complex	yes	no	0.976	0.978	0.402	9e-82
Q28IV6		423	COP9 signalosome complex	yes	no	0.976	0.978	0.407	1e-81
Q7ZTN8		423	COP9 signalosome complex	N/A	no	0.976	0.978	0.405	2e-81
A6H7B5		423	COP9 signalosome complex	yes	no	0.976	0.978	0.400	2e-81
Q5ZJF1		423	COP9 signalosome complex	yes	no	0.976	0.978	0.402	3e-81

>sp\|Q8W575\|CSN3_ARATH COP9 signalosome complex subunit 3 OS=Arabidopsis thaliana GN=CSN3 PE=1 SV=2	Back alignment and function desciption

 Score =  577 bits (1487), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 282/425 (66%), Positives = 336/425 (79%), Gaps = 1/425 (0%)

Query: 1   MQSIENLVTQIQGLSSNASDITALKDYLKAAEDLLRSESTRLLSFLDQLDPSKHSLGYLY 60
           + S+E ++T IQGLS +  D++AL D L+ A+D LR+E     S LDQLD SKHSLGYLY
Sbjct: 5   VNSVEAVITSIQGLSGSPEDLSALHDLLRGAQDSLRAEPGVNFSTLDQLDASKHSLGYLY 64

Query: 61  FLEPCMYCSITKERANTLVPIIARFITSCSAEQIRYVPEKFINVCKRYKDQVLLLEAPIR 120
           FLE      ++KE+A   +PIIARFI SC A QIR    KF+++CK  KD V+ L  P+R
Sbjct: 65  FLEVLTCGPVSKEKAAYEIPIIARFINSCDAGQIRLASYKFVSLCKILKDHVIALGDPLR 124

Query: 121 GVGPMLTAIRKIQSSTEHLTTLHPEFLQLCLLAKCYKAGLSVLEDDIYEINLPRDFFLYC 180
           GVGP+L A++K+Q S++ LT LHP+ LQLCL AK YK+G S+L DDI EI+ PRDFFLY 
Sbjct: 125 GVGPLLNAVQKLQVSSKRLTALHPDVLQLCLQAKSYKSGFSILSDDIVEIDQPRDFFLYS 184

Query: 181 YYGGMIFIGQKRFRKALELLHNVVTAPMSSINAIAVEAYKKYILVSLIHHGQFSSTLPKY 240
           YYGGMI IG KRF+KALELL+NVVTAPM  +NAIA+EAYKKYILVSLIH+GQF++TLPK 
Sbjct: 185 YYGGMICIGLKRFQKALELLYNVVTAPMHQVNAIALEAYKKYILVSLIHNGQFTNTLPKC 244

Query: 241 TSSAAQRNLKNFSQPYMELVNTYNTGKIVELETYVQTNREKFESDNNLGLVKQVVSSMYK 300
            S+AAQR+ KN++ PY+EL N YN GKI ELE  V     +FE D NLGLVKQ VSS+YK
Sbjct: 245 ASTAAQRSFKNYTGPYIELGNCYNDGKIGELEALVVARNAEFEEDKNLGLVKQAVSSLYK 304

Query: 301 RNIQRLTQTYLTLSLQDIANTVQLNSSKEAEMHVLQMIQDGEIFATINQKDGMVRFLEDP 360
           RNI RLTQ YLTLSLQDIAN VQL ++KEAEMHVLQMIQDG+I A INQKDGMVRFLEDP
Sbjct: 305 RNILRLTQKYLTLSLQDIANMVQLGNAKEAEMHVLQMIQDGQIHALINQKDGMVRFLEDP 364

Query: 361 EQYKTCEMIEHIDSSIQRIMSLSKKLTAMDELISCDPLYLGKAGRERQRFDF-DDFDSVP 419
           EQYK+ EMIE +DS IQR + LSK L AMDE +SCDPLYLGK GRERQR+DF DDFD+VP
Sbjct: 365 EQYKSSEMIEIMDSVIQRTIGLSKNLLAMDESLSCDPLYLGKVGRERQRYDFGDDFDTVP 424

Query: 420 QKFNI 424
           QKF++
Sbjct: 425 QKFSM 429

Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes such as photomorphogenesis and auxin and jasmonate responses. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF. It is involved in repression of photomorphogenesis in darkness by regulating the activity of COP1-containing Ubl ligase complexes. The complex is also required for degradation of IAA6 by regulating the activity of the Ubl ligase SCF-TIR complex.
Arabidopsis thaliana (taxid: 3702)

>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\|O88543\|CSN3_MOUSE COP9 signalosome complex subunit 3 OS=Mus musculus GN=Cops3 PE=1 SV=3	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

>sp\|A6H7B5\|CSN3_BOVIN COP9 signalosome complex subunit 3 OS=Bos taurus 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

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		424
255536979		427	26S proteasome regulatory subunit S3, pu	0.995	0.988	0.834	0.0
225452159		424	PREDICTED: COP9 signalosome complex subu	1.0	1.0	0.792	0.0
224060219		423	predicted protein [Populus trichocarpa]	0.997	1.0	0.785	0.0
224141257		424	predicted protein [Populus trichocarpa]	1.0	1.0	0.773	0.0
356511828		423	PREDICTED: COP9 signalosome complex subu	0.997	1.0	0.773	0.0
356511830		423	PREDICTED: COP9 signalosome complex subu	0.997	1.0	0.771	0.0
356571399		423	PREDICTED: COP9 signalosome complex subu	0.997	1.0	0.768	0.0
356571401		425	PREDICTED: COP9 signalosome complex subu	0.992	0.990	0.770	0.0
449441398		423	PREDICTED: COP9 signalosome complex subu	0.997	1.0	0.745	0.0
449495275		423	PREDICTED: LOW QUALITY PROTEIN: COP9 sig	0.997	1.0	0.742	0.0

>gi\|255536979\|ref\|XP_002509556.1\| 26S proteasome regulatory subunit S3, putative [Ricinus communis] gi\|223549455\|gb\|EEF50943.1\| 26S proteasome regulatory subunit S3, putative [Ricinus communis]	Back alignment and taxonomy information

 Score =  741 bits (1912), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 353/423 (83%), Positives = 390/423 (92%), Gaps = 1/423 (0%)

Query: 3   SIENLVTQIQGLSSNASDITALKDYLKAAEDLLRSES-TRLLSFLDQLDPSKHSLGYLYF 61
           SIE+LVTQIQGLSS+A+DI+AL +YLK A+D L S+S TRLL FLDQLDPS HSLGYLYF
Sbjct: 5   SIESLVTQIQGLSSSATDISALHNYLKQADDSLHSDSPTRLLPFLDQLDPSVHSLGYLYF 64

Query: 62  LEPCMYCSITKERANTLVPIIARFITSCSAEQIRYVPEKFINVCKRYKDQVLLLEAPIRG 121
           LE C    I+KE+A TLV I+ARF+TSC+A+QIR  P+KFI+VCKR+KDQV+LLE P+RG
Sbjct: 65  LEACTSGPISKEQARTLVLILARFVTSCAADQIRLAPDKFISVCKRFKDQVMLLEEPMRG 124

Query: 122 VGPMLTAIRKIQSSTEHLTTLHPEFLQLCLLAKCYKAGLSVLEDDIYEINLPRDFFLYCY 181
           V P+L A+RK+QSS+ HLTTLHPEFLQLCLL+KCYK GLS+LEDDI+E++ PRD FLY Y
Sbjct: 125 VAPLLAAVRKLQSSSVHLTTLHPEFLQLCLLSKCYKTGLSILEDDIFEVDQPRDLFLYSY 184

Query: 182 YGGMIFIGQKRFRKALELLHNVVTAPMSSINAIAVEAYKKYILVSLIHHGQFSSTLPKYT 241
           YGGM+ IGQKRFRKALELLHNVVTAPMSSINAIAVEAYKKYIL SLIH GQFS++LPKY 
Sbjct: 185 YGGMVCIGQKRFRKALELLHNVVTAPMSSINAIAVEAYKKYILASLIHQGQFSTSLPKYA 244

Query: 242 SSAAQRNLKNFSQPYMELVNTYNTGKIVELETYVQTNREKFESDNNLGLVKQVVSSMYKR 301
           SSAAQRNLKNF QPY+EL N+Y+TGKI ELETYVQTNREKFESDNNLGLVKQVVSSMYKR
Sbjct: 245 SSAAQRNLKNFCQPYIELANSYSTGKIAELETYVQTNREKFESDNNLGLVKQVVSSMYKR 304

Query: 302 NIQRLTQTYLTLSLQDIANTVQLNSSKEAEMHVLQMIQDGEIFATINQKDGMVRFLEDPE 361
           NIQRLTQTYLTLSLQDIANTVQLNS KEAEMHVLQMIQDGEI+ATINQKDGMVRFLEDPE
Sbjct: 305 NIQRLTQTYLTLSLQDIANTVQLNSPKEAEMHVLQMIQDGEIYATINQKDGMVRFLEDPE 364

Query: 362 QYKTCEMIEHIDSSIQRIMSLSKKLTAMDELISCDPLYLGKAGRERQRFDFDDFDSVPQK 421
           QYKTCEMIEHIDSSIQRIM+LSKKLTAMDEL+SCDPLYL KAGRERQRFDFDDFD+VPQK
Sbjct: 365 QYKTCEMIEHIDSSIQRIMNLSKKLTAMDELMSCDPLYLAKAGRERQRFDFDDFDTVPQK 424

Query: 422 FNI 424
           FNI
Sbjct: 425 FNI 427

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|225452159\|ref\|XP_002263731.1\| PREDICTED: COP9 signalosome complex subunit 3 [Vitis vinifera] gi\|296090247\|emb\|CBI40066.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224060219\|ref\|XP_002300091.1\| predicted protein [Populus trichocarpa] gi\|222847349\|gb\|EEE84896.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|224141257\|ref\|XP_002323991.1\| predicted protein [Populus trichocarpa] gi\|222866993\|gb\|EEF04124.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356511828\|ref\|XP_003524624.1\| PREDICTED: COP9 signalosome complex subunit 3-like isoform 1 [Glycine max]	Back alignment and taxonomy information

>gi\|356511830\|ref\|XP_003524625.1\| PREDICTED: COP9 signalosome complex subunit 3-like isoform 2 [Glycine max]	Back alignment and taxonomy information

>gi\|356571399\|ref\|XP_003553864.1\| PREDICTED: COP9 signalosome complex subunit 3-like isoform 1 [Glycine max]	Back alignment and taxonomy information

>gi\|356571401\|ref\|XP_003553865.1\| PREDICTED: COP9 signalosome complex subunit 3-like isoform 2 [Glycine max]	Back alignment and taxonomy information

>gi\|449441398\|ref\|XP_004138469.1\| PREDICTED: COP9 signalosome complex subunit 3-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449495275\|ref\|XP_004159785.1\| PREDICTED: LOW QUALITY PROTEIN: COP9 signalosome complex subunit 3-like [Cucumis sativus]	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		424
TAIR\|locus:2145638		429	COP13 "AT5G14250" [Arabidopsis	1.0	0.988	0.649	1.9e-140
UNIPROTKB\|Q9UNS2		423	COPS3 "COP9 signalosome comple	0.938	0.940	0.415	5.5e-77
MGI\|MGI:1349409		423	Cops3 "COP9 (constitutive phot	0.938	0.940	0.415	7.1e-77
RGD\|1303002		423	Cops3 "COP9 signalosome subuni	0.938	0.940	0.415	7.1e-77
UNIPROTKB\|A6H7B5		423	COPS3 "COP9 signalosome comple	0.938	0.940	0.412	1.1e-76
UNIPROTKB\|Q5ZJF1		423	COPS3 "COP9 signalosome comple	0.938	0.940	0.415	1.5e-76
UNIPROTKB\|E2RD70		423	COPS3 "Uncharacterized protein	0.938	0.940	0.412	2.4e-76
UNIPROTKB\|F1SB16		423	COPS3 "Uncharacterized protein	0.938	0.940	0.410	3.1e-76
ZFIN\|ZDB-GENE-030131-7660		423	cops3 "COP9 constitutive photo	0.938	0.940	0.415	3.9e-76
DICTYBASE\|DDB_G0291848		418	csn3 "proteasome component reg	0.882	0.894	0.403	1.3e-66

TAIR\|locus:2145638 COP13 "AT5G14250" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1374 (488.7 bits), Expect = 1.9e-140, P = 1.9e-140
 Identities = 276/425 (64%), Positives = 329/425 (77%)

Query:     1 MQSIENLVTQIQGLSSNASDITALKDYLKAAEDLLRSESTRLLSFLDQLDPSKHSLGYLY 60
             + S+E ++T IQGLS +  D++AL D L+ A+D LR+E     S LDQLD SKHSLGYLY
Sbjct:     5 VNSVEAVITSIQGLSGSPEDLSALHDLLRGAQDSLRAEPGVNFSTLDQLDASKHSLGYLY 64

Query:    61 FLEPCMYCSITKERANTLVPIIARFITSCSAEQIRYVPEKFINVCKRYKDQVLLLEAPIR 120
             FLE      ++KE+A   +PIIARFI SC A QIR    KF+++CK  KD V+ L  P+R
Sbjct:    65 FLEVLTCGPVSKEKAAYEIPIIARFINSCDAGQIRLASYKFVSLCKILKDHVIALGDPLR 124

Query:   121 GVGPMLTAIRKIQSSTEHLTTLHPEFLQLCLLAKCYKAGLSVLEDDIYEINLPRDFFLYC 180
             GVGP+L A++K+Q S++ LT LHP+ LQLCL AK YK+G S+L DDI EI+ PRDFFLY 
Sbjct:   125 GVGPLLNAVQKLQVSSKRLTALHPDVLQLCLQAKSYKSGFSILSDDIVEIDQPRDFFLYS 184

Query:   181 YYGGMIFIGQKRFRKALELLHNVVTAPMSSINAIAVEAYKKYILVSLIHHGQFSSTLPKY 240
             YYGGMI IG KRF+KALELL+NVVTAPM  +NAIA+EAYKKYILVSLIH+GQF++TLPK 
Sbjct:   185 YYGGMICIGLKRFQKALELLYNVVTAPMHQVNAIALEAYKKYILVSLIHNGQFTNTLPKC 244

Query:   241 TSSAAQRNLKNFSQPYMELVNTYNTGKIVELETYVQTNREKFESDNNLGLVKQVVSSMYK 300
              S+AAQR+ KN++ PY+EL N YN GKI ELE  V     +FE D NLGLVKQ VSS+YK
Sbjct:   245 ASTAAQRSFKNYTGPYIELGNCYNDGKIGELEALVVARNAEFEEDKNLGLVKQAVSSLYK 304

Query:   301 RNIQRLTQTYLTLSLQDIANTVQLNSSKEAEMHVLQMIQDGEIFATINQKDGMVRFLEDP 360
             RNI RLTQ YLTLSLQDIAN VQL ++KEAEMHVLQMIQDG+I A INQKDGMVRFLEDP
Sbjct:   305 RNILRLTQKYLTLSLQDIANMVQLGNAKEAEMHVLQMIQDGQIHALINQKDGMVRFLEDP 364

Query:   361 EQYKTCEMIEHIDSSIQRIMSLSKKLTAMDELISCDPLYLGKAGRERQRXXXXXXX-SVP 419
             EQYK+ EMIE +DS IQR + LSK L AMDE +SCDPLYLGK GRERQR        +VP
Sbjct:   365 EQYKSSEMIEIMDSVIQRTIGLSKNLLAMDESLSCDPLYLGKVGRERQRYDFGDDFDTVP 424

Query:   420 QKFNI 424
             QKF++
Sbjct:   425 QKFSM 429

GO:0008180 "signalosome" evidence=TAS;IPI

GO:0009640 "photomorphogenesis" evidence=RCA;TAS

GO:0005515 "protein binding" evidence=IPI

GO:0010388 "cullin deneddylation" evidence=RCA;IMP

GO:0010971 "positive regulation of G2/M transition of mitotic cell cycle" evidence=IMP

GO:0005829 "cytosol" evidence=IDA

GO:0000278 "mitotic cell cycle" evidence=RCA

GO:0006312 "mitotic recombination" evidence=RCA

GO:0006396 "RNA processing" evidence=RCA

GO:0009560 "embryo sac egg cell differentiation" evidence=RCA

GO:0009793 "embryo development ending in seed dormancy" evidence=RCA

GO:0009845 "seed germination" evidence=RCA

GO:0009909 "regulation of flower development" evidence=RCA

GO:0009933 "meristem structural organization" evidence=RCA

GO:0010162 "seed dormancy process" evidence=RCA

GO:0010182 "sugar mediated signaling pathway" evidence=RCA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

GO:0016567 "protein ubiquitination" evidence=RCA

GO:0016571 "histone methylation" evidence=RCA

GO:0016579 "protein deubiquitination" evidence=RCA

GO:0019915 "lipid storage" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

GO:0050826 "response to freezing" evidence=RCA

GO:0051604 "protein maturation" evidence=RCA

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\|A6H7B5 COPS3 "COP9 signalosome complex subunit 3" [Bos taurus (taxid:9913)]	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\|E2RD70 COPS3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

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

ZFIN\|ZDB-GENE-030131-7660 cops3 "COP9 constitutive photomorphogenic homolog subunit 3" [Danio rerio (taxid:7955)]	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)
Q68FW9	CSN3_RAT	No assigned EC number	0.4028	0.9764	0.9787	yes	no
Q28IV6	CSN3_XENTR	No assigned EC number	0.4074	0.9764	0.9787	yes	no
Q8W575	CSN3_ARATH	No assigned EC number	0.6635	1.0	0.9883	yes	no
Q9UNS2	CSN3_HUMAN	No assigned EC number	0.4028	0.9764	0.9787	yes	no
Q8SYG2	CSN3_DROME	No assigned EC number	0.3593	0.9386	0.8943	yes	no
Q54E53	CSN3_DICDI	No assigned EC number	0.4005	0.8820	0.8947	yes	no
P68358	CSN3_BRAOL	No assigned EC number	0.9189	0.0872	0.6727	N/A	no
O88543	CSN3_MOUSE	No assigned EC number	0.4028	0.9764	0.9787	yes	no
Q5RFS2	CSN3_PONAB	No assigned EC number	0.4028	0.9764	0.9787	yes	no
A6H7B5	CSN3_BOVIN	No assigned EC number	0.4004	0.9764	0.9787	yes	no
Q5ZJF1	CSN3_CHICK	No assigned EC number	0.4028	0.9764	0.9787	yes	no
Q6P2U9	CSN3_DANRE	No assigned EC number	0.4152	0.9386	0.9408	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	fgenesh4_pg.C_LG_I002287	hypothetical protein (423 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	grail3.0012044601	SubName- Full=Putative uncharacterized protein; (398 aa)	•	•	•	0.662

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		424
pfam01399		100	pfam01399, PCI, PCI domain	2e-17
smart00753		88	smart00753, PAM, PCI/PINT associated module	1e-14
smart00088		88	smart00088, PINT, motif in proteasome subunits, In	1e-14

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

 Score = 76.9 bits (190), Expect = 2e-17
 Identities = 28/101 (27%), Positives = 56/101 (55%), Gaps = 1/101 (0%)

Query: 256 YMELVNTYNTGKIVELETYVQTNREKFESDNNLGLVKQVVSSMYKRNIQRLTQTYLTLSL 315
           Y +L+  + +G + + E  +  N ++   D    L++ +   + + N++RL + Y ++SL
Sbjct: 1   YRDLLRAFYSGDLSDFEEILADNEDELLDDGLAELLEDLRRKIRELNLRRLAKPYSSISL 60

Query: 316 QDIANTVQLNSSKEAEMHVLQMIQDGEIFATINQKDGMVRF 356
            D+A  + L S  E E  + ++I+DG I   I+Q +G+V F
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		424
KOG2582		422	consensus COP9 signalosome, subunit CSN3 [Posttran	100.0
KOG2581		493	consensus 26S proteasome regulatory complex, subun	100.0
KOG1498		439	consensus 26S proteasome regulatory complex, subun	99.89
KOG1464		440	consensus COP9 signalosome, subunit CSN2 [Posttran	99.73
KOG1463		411	consensus 26S proteasome regulatory complex, subun	99.73
PF01399		105	PCI: PCI domain; InterPro: IPR000717 A homology do	99.71
KOG1497		399	consensus COP9 signalosome, subunit CSN4 [Posttran	99.7
COG5071		439	RPN5 26S proteasome regulatory complex component [	99.69
KOG2688		394	consensus Transcription-associated recombination p	99.66
COG5600		413	Transcription-associated recombination protein [DN	99.52
COG5159		421	RPN6 26S proteasome regulatory complex component [	99.49
smart00088		88	PINT motif in proteasome subunits, Int-6, Nip-1 an	99.26
smart00753		88	PAM PCI/PINT associated module.	99.26
KOG2908		380	consensus 26S proteasome regulatory complex, subun	99.24
PF10255		404	Paf67: RNA polymerase I-associated factor PAF67; I	98.34
KOG1076		843	consensus Translation initiation factor 3, subunit	98.29
COG5187		412	RPN7 26S proteasome regulatory complex component,	98.28
KOG0687		393	consensus 26S proteasome regulatory complex, subun	98.25
KOG0686		466	consensus COP9 signalosome, subunit CSN1 [Posttran	98.06
KOG2072		988	consensus Translation initiation factor 3, subunit	97.82
PF08375		68	Rpn3_C: Proteasome regulatory subunit C-terminal;	97.7
KOG2758		432	consensus Translation initiation factor 3, subunit	97.04
KOG2753		378	consensus Uncharacterized conserved protein, conta	96.93
PF10075		143	PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro	96.38
PF13432		65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	95.78
PRK15359		144	type III secretion system chaperone protein SscB;	95.64
TIGR02552		135	LcrH_SycD type III secretion low calcium response	95.61
PF09976		145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	95.54
PF13371		73	TPR_9: Tetratricopeptide repeat	95.29
PF14938		282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	95.12
PF07719		34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	95.07
TIGR02795		119	tol_pal_ybgF tol-pal system protein YbgF. Members	95.04
PRK12370		553	invasion protein regulator; Provisional	94.91
PF12895		84	Apc3: Anaphase-promoting complex, cyclosome, subun	94.78
PF13414		69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	94.55
PLN03088		356	SGT1, suppressor of G2 allele of SKP1; Provisional	93.73
PF00515		34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	93.49
cd00189		100	TPR Tetratricopeptide repeat domain; typically con	93.19
PF09012		69	FeoC: FeoC like transcriptional regulator; InterPr	92.94
PRK10370		198	formate-dependent nitrite reductase complex subuni	92.23
PRK10803		263	tol-pal system protein YbgF; Provisional	91.77
TIGR03302		235	OM_YfiO outer membrane assembly lipoprotein YfiO.	91.63
PF13174		33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	91.38
PF13181		34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	90.99
PF09295		395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	90.84
PF08784		102	RPA_C: Replication protein A C terminal; InterPro:	90.76
PF13424		78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	90.35
KOG3677		525	consensus RNA polymerase I-associated factor - PAF	90.23
TIGR00990		615	3a0801s09 mitochondrial precursor proteins import	89.26
PRK15359		144	type III secretion system chaperone protein SscB;	88.92
PRK10747		398	putative protoheme IX biogenesis protein; Provisio	88.43
PF14559		68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	88.18
PF14853		53	Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repe	87.9
KOG1126		638	consensus DNA-binding cell division cycle control	87.76
PF13412		48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	87.73
TIGR02552		135	LcrH_SycD type III secretion low calcium response	87.39
TIGR00990		615	3a0801s09 mitochondrial precursor proteins import	86.94
PRK10803		263	tol-pal system protein YbgF; Provisional	86.79
TIGR02917		899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	86.62
PF10602		177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	86.03
cd00189		100	TPR Tetratricopeptide repeat domain; typically con	85.88
smart00028		34	TPR Tetratricopeptide repeats. Repeats present in	85.11
CHL00033		168	ycf3 photosystem I assembly protein Ycf3	85.1
TIGR02917		899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	84.64
PRK11788		389	tetratricopeptide repeat protein; Provisional	84.38
TIGR03302		235	OM_YfiO outer membrane assembly lipoprotein YfiO.	84.15
TIGR02521		234	type_IV_pilW type IV pilus biogenesis/stability pr	84.02
PF12569		517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	83.71
smart00550		68	Zalpha Z-DNA-binding domain in adenosine deaminase	82.91
PF13429		280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	82.85
TIGR02795		119	tol_pal_ybgF tol-pal system protein YbgF. Members	82.82
PRK09782		987	bacteriophage N4 receptor, outer membrane subunit;	82.81
PF13176		36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	82.41
PRK11189		296	lipoprotein NlpI; Provisional	82.36
PF09756		188	DDRGK: DDRGK domain; InterPro: IPR019153 This is a	82.14
PF12688		120	TPR_5: Tetratrico peptide repeat	81.72
PRK15174		656	Vi polysaccharide export protein VexE; Provisional	81.6
PRK15363		157	pathogenicity island 2 chaperone protein SscA; Pro	81.1
PF13414		69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	80.94
PF03399		204	SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; I	80.71
PRK02603		172	photosystem I assembly protein Ycf3; Provisional	80.69
PRK02603		172	photosystem I assembly protein Ycf3; Provisional	80.63

>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]	Back alignment and domain information

Probab=100.00  E-value=1.3e-70  Score=528.96  Aligned_cols=411  Identities=42%  Similarity=0.646  Sum_probs=396.2

Q ss_pred             HHHHHHHHhhcCCCcccHHHHHHHHHHhHHHHhhhcccccccccccCcchhhHHHHHHHhhccccccchhhhccHHHHHH
Q 014453            4 IENLVTQIQGLSSNASDITALKDYLKAAEDLLRSESTRLLSFLDQLDPSKHSLGYLYFLEPCMYCSITKERANTLVPIIA   83 (424)
Q Consensus         4 l~~~~~~i~~~~~~~~~~~~l~~~l~~~~~~l~~~~~~~~~~L~~ldp~~~sl~~l~ll~~~~~~~~~~~~~~~l~~~~~   83 (424)
                      ++..++.++++++++ ++.+|.+.+.++.+.|++++++++.+|..+||..||+|++|++..+.....+..+++++++++.
T Consensus         5 l~a~i~~~~~~~~~~-~~~eL~~~i~~~~ell~k~~~~~~~~L~~ld~~~hSlgml~~l~~~f~~~~~~~~~~~li~~~~   83 (422)
T KOG2582|consen    5 LEAAINELCSLSHSS-NVGELAELIVKSKELLAKNSSDLDAVLLHLDPQVHSLGMLAVLKVKFHTPSANPDPETLIELLN   83 (422)
T ss_pred             HHHHHHHHHhhhcCC-cHHHHHHHHHhhHHHHHhCcchHHHHHHhcCccccchhhhhhhhccccCcccCCCHHHHHHHHH
Confidence            788999999999999 9999999999999999999999999999999999999999999999987764457789999999


Q ss_pred             HHHhhCCchhhhcchHHHHHHHHHHHHHHHHhhccccchHHHHHHHHhhCCCCCCcchHHHHHHHHHHHccChHHHHhcc
Q 014453           84 RFITSCSAEQIRYVPEKFINVCKRYKDQVLLLEAPIRGVGPMLTAIRKIQSSTEHLTTLHPEFLQLCLLAKCYKAGLSVL  163 (424)
Q Consensus        84 ~fl~~fd~~Q~r~~~~~~~~l~~~~~~~~~~~~~~~~~i~~L~~A~~rl~~~~~~lT~~h~~l~rlcL~~~~y~~Al~il  163 (424)
                      +|+.++|.+|+|++++.|..+|+.+...+.+.++|.+|++++.+|+.++.+++.++|++|..++++||.+++|..+++++
T Consensus        84 ~FV~~~n~eqlr~as~~f~~lc~~l~~~~~~~~~p~~gi~ii~~av~k~~~~~~qlT~~H~~l~~~~L~ak~y~~~~p~l  163 (422)
T KOG2582|consen   84 DFVDENNGEQLRLASEIFFPLCHDLTEAVVKKNKPLRGIRIIMQAVDKMQPSNGQLTSIHADLLQLCLEAKDYASVLPYL  163 (422)
T ss_pred             HHHHhcChHHHhhHHHHHHHHHHHHHHHHHhcCCccccchHHHHHHHHhccCccchhhhHHHHHHHHHHhhcccccCCcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccccc------cCchhhHHHHHHHHHHHHhhhcHHHHHHHHHHHhcccCccccHHHHHHHHHHHHHHHHhcCCCCCCC
Q 014453          164 EDDIYEI------NLPRDFFLYCYYGGMIFIGQKRFRKALELLHNVVTAPMSSINAIAVEAYKKYILVSLIHHGQFSSTL  237 (424)
Q Consensus       164 ~~~i~~~------~~~~~~l~Y~YY~G~I~~~~~~y~~A~~~~~~a~~~P~~~~s~i~~ea~Kk~iLv~LL~~G~~~~p~  237 (424)
                      +.+|.++      .+|+.++.|+||||||+++.++|++|..+|+.|+++|+.+++.|+.|||||++||+||..|++. .+
T Consensus       164 d~divei~~~n~h~~~k~fL~Y~yYgg~iciglk~fe~Al~~~e~~v~~Pa~~vs~~hlEaYkkylLvsLI~~GK~~-ql  242 (422)
T KOG2582|consen  164 DDDIVEICKANPHLDPKYFLLYLYYGGMICIGLKRFERALYLLEICVTTPAMAVSHIHLEAYKKYLLVSLILTGKVF-QL  242 (422)
T ss_pred             chhHHHHhccCCCCCHHHHHHHHHhcceeeeccccHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHhhhcCcee-ec
Confidence            9999988      3478999999999999999999999999999999999999999999999999999999999999 89


Q ss_pred             CcccCHHHhhhhhhccHHHHHHHHHHhcCCHHHHHHHHHHcccccccccchhHHHHHHHHHHHHHHHHHHhhhhcccHHH
Q 014453          238 PKYTSSAAQRNLKNFSQPYMELVNTYNTGKIVELETYVQTNREKFESDNNLGLVKQVVSSMYKRNIQRLTQTYLTLSLQD  317 (424)
Q Consensus       238 p~~~s~~~~~~~k~~~~~Y~~L~~a~~~gdl~~~~~~l~~~~~~f~~Dgn~~Lv~~l~~~v~r~~I~~l~~~Ys~Isl~~  317 (424)
                      |+++|+.+.|.+|....||++|+++|-++...+++.++.+|.+.|.+|||.|+++++...+++++|.+++|+|++++|+|
T Consensus       243 ~k~ts~~~~r~~K~ms~pY~ef~~~Y~~~~~~eLr~lVk~~~~rF~kDnnt~l~k~av~sl~k~nI~rltktF~sLsL~d  322 (422)
T KOG2582|consen  243 PKNTSQNAGRFFKPMSNPYHEFLNVYLKDSSTELRTLVKKHSERFTKDNNTGLAKQAVSSLYKKNIQRLTKTFLSLSLSD  322 (422)
T ss_pred             cccchhhhHHhcccCCchHHHHHHHHhcCCcHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCHHHHHHHHHHhHHcCceEEEEecCCCEEEEecCCCccChHHHHHHHHHHHHHHHHHHHHHHHHhHHhhcCH
Q 014453          318 IANTVQLNSSKEAEMHVLQMIQDGEIFATINQKDGMVRFLEDPEQYKTCEMIEHIDSSIQRIMSLSKKLTAMDELISCDP  397 (424)
Q Consensus       318 Ia~~l~l~~~~eaE~~v~~mI~~G~I~A~Id~~~g~v~F~~~~~~~~~~~~~~~~~~~i~~~~~L~~~~~~~d~~l~~~~  397 (424)
                      ||++.+|.+.+|||..|.+||.+|+|.|.||   |+|.|.++++.|.++|+.   +..|..|.+|.++++.||+.|.++|
T Consensus       323 IA~~vQLa~~qevek~Ilqmie~~~i~a~iN---G~v~f~~n~e~~~SpeM~---~nk~~~~~~L~e~l~~~e~si~l~s  396 (422)
T KOG2582|consen  323 IASRVQLASAQEVEKYILQMIEDGEIFASIN---GMVFFTDNPEKYNSPEMH---ENKIDLCIQLIEALKAMEESIRLNS  396 (422)
T ss_pred             HHHHHHhcchHHHHHHHHHHhccCceEEEec---ceEEEecCcccCCCHHHH---hhHHHHHHHHHHHHHhcchheeeCc
Confidence            9999999999999999999999999999998   999999999999999874   4489999999999999999999999


Q ss_pred             HHHHHhhhhhccCCCCCCCCCCccc
Q 014453          398 LYLGKAGRERQRFDFDDFDSVPQKF  422 (424)
Q Consensus       398 ~yi~~~~~~~~~~~~~~~~~~~~~~  422 (424)
                      -|++|.++.+.+.-.++++.+|++|
T Consensus       397 ~~~~K~m~~~~d~~~~~p~t~s~~f  421 (422)
T KOG2582|consen  397 VYVSKSMGSQEDDGGSMPPTESKFF  421 (422)
T ss_pred             eeeehhhhhhhccccCCCCccCCCC
Confidence            9999999999988999999999987

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

>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]	Back alignment and domain information

>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [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

>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]	Back alignment and domain information

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

>KOG2688 consensus Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning]	Back alignment and domain information

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

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

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

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

>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [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

>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]	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

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

>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]	Back alignment and domain information

>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]	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

>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]	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

>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

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

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD	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

>PF13371 TPR_9: Tetratricopeptide repeat	Back alignment and domain information

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

>PRK12370 invasion protein regulator; Provisional	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

>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

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional	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

>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

>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

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

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

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO	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

>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

>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

>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

>KOG3677 consensus RNA polymerase I-associated factor - PAF67 [Translation, ribosomal structure and biogenesis; Transcription]	Back alignment and domain information

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

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

>PRK10747 putative protoheme IX biogenesis protein; Provisional	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

>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

>KOG1126 consensus DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning]	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

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

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

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

>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein	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

Back alignment and domain information

>smart00028 TPR Tetratricopeptide repeats	Back alignment and domain information

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

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

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

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

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW	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

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

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

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

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

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

>PRK11189 lipoprotein NlpI; Provisional	Back alignment and domain information

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

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

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

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional	Back alignment and domain information

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

>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

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

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

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		424
4b4t_S		523	Near-Atomic Resolution Structural Model Of The Yeas		1e-05

>pdb|4B4T|S Chain S, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 523

Back alignment and structure

Iteration: 1

Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust. Identities = 34/125 (27%), Positives = 60/125 (48%), Gaps = 8/125 (6%) Query: 246 QRNLKNFSQPYMELVNTYNTGKIVELETYVQTNREKFESDNNLGLVKQVVSSMYKRNIQR 305 Q N++ PY L G + + + + ++ D+ L ++ S++ K I+ Sbjct: 335 QSNMQKSLLPYYHLTKAVKLGDLKKFTSTITKYKQLLLKDDTYQLCVRLRSNVIKTGIRI 394 Query: 306 LTQTYLTLSLQDIANTVQLNSSKEAEMHVLQMIQDGEIFATINQKDGMVRFL-------- 357 ++ TY +SL+DI + L+S + E V + I+DG I A IN +DG + Sbjct: 395 ISLTYKKISLRDICLKLNLDSEQTVEYMVSRAIRDGVIEAKINHEDGFIETTELLNIYDS 454 Query: 358 EDPEQ 362 EDP+Q Sbjct: 455 EDPQQ 459

PyMOL of 4b4t

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		424
3txn_A		394	26S proteasome regulatory complex subunit P42B; PC	6e-14
1ufm_A		84	COP9 complex subunit 4; helix-turn-helix, structur	2e-11
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-11
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-08
3t5x_A		203	PCI domain-containing protein 2; PCI, mRNA nuclear	9e-10
3t5v_B		455	Nuclear mRNA export protein THP1; PCI, mRNA nuclea	2e-04

>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 = 72.2 bits (176), Expect = 6e-14
 Identities = 49/332 (14%), Positives = 113/332 (34%), Gaps = 15/332 (4%)

Query: 67  YCSITKERANTLVPIIARFITSCSAEQIRYVPEKF-INVCKRYKDQVLLLEAPIRGVGPM 125
                       V +    I     E+  ++ +     +   Y D  L  EA +     +
Sbjct: 67  MFLDMDAGTGIEVQLCKDCIEWAKQEKRTFLRQSLEARLIALYFDTALYTEA-LALGAQL 125

Query: 126 LTAIRKIQSSTEHLTTLHPEFLQLCLLAKCYKAGLSVLEDDIYEINL-----PRDFFLYC 180
           L  ++K+      L  +     +            + L       N           L  
Sbjct: 126 LRELKKLDDKN-LLVEVQLLESKTYHALSNLPKARAALTSARTTANAIYCPPKVQGALDL 184

Query: 181 YYGGMIFIGQKRFRKALELLHNVVTAPMSSINAIAVEAYKKYILVSLIHHGQFSSTLPKY 240
             G +    ++ F+ A    +       S  +  A+ + K Y+L+  I  GQ        
Sbjct: 185 QSGILHAADERDFKTAFSYFYEAFEGFDSVDSVKALTSLK-YMLLCKIMLGQSDDVNQLV 243

Query: 241 TSSAAQRNLKNFSQPYMELVNTYNTGKIVELETYVQTNREKFESDNNLGL-VKQVVSSMY 299
           +   A             +    +   + + +  ++  +++   D  +   +  +  +M 
Sbjct: 244 SGKLAITYSGRDIDAMKSVAEASHKRSLADFQAALKEYKKELAEDVIVQAHLGTLYDTML 303

Query: 300 KRNIQRLTQTYLTLSLQDIANTVQLNSSKEAEMHVLQMIQDGEIFATINQKDGMVRFLED 359
           ++N+ R+ + Y  + +  +A ++QL    + E  + QMI D +    ++Q +G++   E+
Sbjct: 304 EQNLCRIIEPYSRVQVAHVAESIQLPMP-QVEKKLSQMILDKKFSGILDQGEGVLIVFEE 362

Query: 360 PEQYKTC----EMIEHIDSSIQRIMSLSKKLT 387
               KT     E I+ +   +  +   +KKL+
Sbjct: 363 TPVDKTYERVLETIQSMGKVVDTLYQKAKKLS 394

PyMOL of 3txn

>1ufm_A COP9 complex subunit 4; helix-turn-helix, structural genomics, riken structural genomics/proteomics initiative, RSGI, signaling protein; NMR {Mus musculus} SCOP: a.4.5.47 Length = 84	Back alignment and structure

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

>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

>3t5x_A PCI domain-containing protein 2; PCI, mRNA nuclear export, transcription; 2.12A {Homo sapiens} Length = 203	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		424
4b4t_S		523	RPN3, 26S proteasome regulatory subunit RPN3; hydr	100.0
3t5x_A		203	PCI domain-containing protein 2; PCI, mRNA nuclear	99.96
3t5v_B		455	Nuclear mRNA export protein THP1; PCI, mRNA nuclea	99.95
4b4t_P		445	26S proteasome regulatory subunit RPN5; hydrolase,	99.94
3txn_A		394	26S proteasome regulatory complex subunit P42B; PC	99.91
4b4t_R		429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	99.78
4b4t_Q		434	26S proteasome regulatory subunit RPN6; hydrolase,	99.78
4b4t_O		393	26S proteasome regulatory subunit RPN9; hydrolase,	99.48
1ufm_A		84	COP9 complex subunit 4; helix-turn-helix, structur	99.43
4b0z_A		229	RPN12, 26S proteasome regulatory subunit RPN12; pr	99.09
3chm_A		169	COP9 signalosome complex subunit 7; heat/ARM repea	98.21
2xev_A		129	YBGF; tetratricopeptide, alpha-helical, metal bind	96.72
3gyz_A		151	Chaperone protein IPGC; asymmetric homodimer, tetr	96.28
4gco_A		126	Protein STI-1; structural genomics, PSI-biology, m	96.14
2xcb_A		142	PCRH, regulatory protein PCRH; protein transport,	96.13
2vgx_A		148	Chaperone SYCD; alternative dimer assembly, tetrat	96.13
3sz7_A		164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	96.04
3qky_A		261	Outer membrane assembly lipoprotein YFIO; membrane	95.87
2vyi_A		131	SGTA protein; chaperone, TPR repeat, phosphoprotei	95.84
2dba_A		148	Smooth muscle cell associated protein-1, isoform 2	95.69
3k9i_A		117	BH0479 protein; putative protein binding protein,	95.68
3upv_A		126	Heat shock protein STI1; TPR-fold, adaptor protein	95.62
4ga2_A		150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	95.62
1hxi_A		121	PEX5, peroxisome targeting signal 1 receptor PEX5;	95.53
2lni_A		133	Stress-induced-phosphoprotein 1; structural genomi	95.35
1qqe_A		292	Vesicular transport protein SEC17; helix-turn-heli	95.34
3q49_B		137	STIP1 homology and U box-containing protein 1; E3	95.28
2kat_A		115	Uncharacterized protein; NESG, structure, structur	95.21
3ro2_A		338	PINS homolog, G-protein-signaling modulator 2; TPR	95.12
3rkv_A		162	Putative peptidylprolyl isomerase; structural geno	95.11
1elw_A		118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	95.02
2fbn_A		198	70 kDa peptidylprolyl isomerase, putative; sulfur	94.88
3ro3_A		164	PINS homolog, G-protein-signaling modulator 2; asy	94.85
2ho1_A		252	Type 4 fimbrial biogenesis protein PILF; type IV p	94.78
4gcn_A		127	Protein STI-1; structural genomics, PSI-biology, m	94.76
1elr_A		131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	94.74
3u4t_A		272	TPR repeat-containing protein; structural genomics	94.58
3qky_A		261	Outer membrane assembly lipoprotein YFIO; membrane	94.51
2pzi_A		681	Probable serine/threonine-protein kinase PKNG; ATP	94.44
3sf4_A		406	G-protein-signaling modulator 2; tetratricopeptide	94.39
2e2e_A		177	Formate-dependent nitrite reductase complex NRFG;	94.26
2l6j_A		111	TPR repeat-containing protein associated with HSP;	94.26
3vtx_A		184	MAMA; tetratricopeptide repeats (TPR) containing p	94.25
1na0_A		125	Designed protein CTPR3; de novo protein; HET: IPT;	94.09
1a17_A		166	Serine/threonine protein phosphatase 5; hydrolase,	94.08
2kck_A		112	TPR repeat; tetratricopeptide repeat, structural g	93.96
3ma5_A		100	Tetratricopeptide repeat domain protein; NESG, str	93.96
4a1s_A		411	PINS, partner of inscuteable; cell cycle, LGN, mit	93.9
3vtx_A		184	MAMA; tetratricopeptide repeats (TPR) containing p	93.88
4i17_A		228	Hypothetical protein; TPR repeats protein, structu	93.86
3hym_B		330	Cell division cycle protein 16 homolog; APC, anaph	93.6
2q7f_A		243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	93.52
1hh8_A		213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	93.46
3ieg_A		359	DNAJ homolog subfamily C member 3; TPR motif, chap	93.43
2xev_A		129	YBGF; tetratricopeptide, alpha-helical, metal bind	93.37
3q15_A		378	PSP28, response regulator aspartate phosphatase H;	93.33
3uq3_A		258	Heat shock protein STI1; HSP90, peptide binding, c	93.33
2h6f_A		382	Protein farnesyltransferase/geranylgeranyltransfer	93.26
2h6f_A		382	Protein farnesyltransferase/geranylgeranyltransfer	93.18
3u4t_A		272	TPR repeat-containing protein; structural genomics	93.17
3q15_A		378	PSP28, response regulator aspartate phosphatase H;	93.14
3uq3_A		258	Heat shock protein STI1; HSP90, peptide binding, c	93.12
2vq2_A		225	PILW, putative fimbrial biogenesis and twitching m	93.08
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	93.07
3urz_A		208	Uncharacterized protein; tetratricopeptide repeats	93.03
2pl2_A		217	Hypothetical conserved protein TTC0263; TPR, prote	93.01
1p5q_A		336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	92.93
2pl2_A		217	Hypothetical conserved protein TTC0263; TPR, prote	92.93
2kc7_A		99	BFR218_protein; tetratricopeptide repeat, all-alph	92.92
2ifu_A		307	Gamma-SNAP; membrane fusion, snare complex disasse	92.91
1na3_A		91	Designed protein CTPR2; de novo protein; HET: IPT;	92.9
3urz_A		208	Uncharacterized protein; tetratricopeptide repeats	92.85
3gyz_A		151	Chaperone protein IPGC; asymmetric homodimer, tetr	92.82
3ulq_A		383	Response regulator aspartate phosphatase F; tetrat	92.8
2vq2_A		225	PILW, putative fimbrial biogenesis and twitching m	92.68
1ihg_A		370	Cyclophilin 40; ppiase immunophilin tetratricopept	92.66
2yhc_A		225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	92.65
3mkr_A		291	Coatomer subunit epsilon; tetratricopeptide repeat	92.63
4abn_A		474	Tetratricopeptide repeat protein 5; P53 cofactor,	92.63
2hr2_A		159	Hypothetical protein; alpha-alpha superhelix fold,	92.56
1kt0_A		457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	92.5
3upv_A		126	Heat shock protein STI1; TPR-fold, adaptor protein	92.5
2fo7_A		136	Synthetic consensus TPR protein; tetratricopeptide	92.47
3as5_A		186	MAMA; tetratricopeptide repeats (TPR) containing p	92.41
2xcb_A		142	PCRH, regulatory protein PCRH; protein transport,	92.41
4i17_A		228	Hypothetical protein; TPR repeats protein, structu	92.34
4gco_A		126	Protein STI-1; structural genomics, PSI-biology, m	92.29
3sz7_A		164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	92.26
3nf1_A		311	KLC 1, kinesin light chain 1; TPR, structural geno	92.23
2vgx_A		148	Chaperone SYCD; alternative dimer assembly, tetrat	92.2
4gyw_A		723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	92.12
2ho1_A		252	Type 4 fimbrial biogenesis protein PILF; type IV p	92.09
1fch_A		368	Peroxisomal targeting signal 1 receptor; protein-p	92.07
1w3b_A		388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	92.06
3ro3_A		164	PINS homolog, G-protein-signaling modulator 2; asy	92.06
3nf1_A		311	KLC 1, kinesin light chain 1; TPR, structural geno	91.99
3as5_A		186	MAMA; tetratricopeptide repeats (TPR) containing p	91.99
1hxi_A		121	PEX5, peroxisome targeting signal 1 receptor PEX5;	91.9
2dba_A		148	Smooth muscle cell associated protein-1, isoform 2	91.9
1xnf_A		275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	91.87
4eqf_A		365	PEX5-related protein; accessory protein, tetratric	91.87
2lni_A		133	Stress-induced-phosphoprotein 1; structural genomi	91.8
1rz4_A		226	Eukaryotic translation initiation factor 3 subuni;	91.74
3gw4_A		203	Uncharacterized protein; structural genomics, PSI-	91.74
4ga2_A		150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	91.67
3q49_B		137	STIP1 homology and U box-containing protein 1; E3	91.65
1elw_A		118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	91.61
2qfc_A		293	PLCR protein; TPR, HTH, transcription regulation;	91.59
1pc2_A		152	Mitochondria fission protein; unknown function; NM	91.54
4eqf_A		365	PEX5-related protein; accessory protein, tetratric	91.39
2fo7_A		136	Synthetic consensus TPR protein; tetratricopeptide	91.3
3gw4_A		203	Uncharacterized protein; structural genomics, PSI-	91.25
2qfc_A		293	PLCR protein; TPR, HTH, transcription regulation;	91.14
3qou_A		287	Protein YBBN; thioredoxin-like fold, tetratricopep	91.14
3fp2_A		537	TPR repeat-containing protein YHR117W; TOM71, mito	91.07
3sf4_A		406	G-protein-signaling modulator 2; tetratricopeptide	91.02
2ond_A		308	Cleavage stimulation factor 77 kDa subunit; HAT do	91.01
1elr_A		131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	90.98
2q7f_A		243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	90.97
4gyw_A		723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	90.94
1xnf_A		275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	90.88
3ulq_A		383	Response regulator aspartate phosphatase F; tetrat	90.82
3cv0_A		327	Peroxisome targeting signal 1 receptor PEX5; TPR m	90.7
3hym_B		330	Cell division cycle protein 16 homolog; APC, anaph	90.7
3ro2_A		338	PINS homolog, G-protein-signaling modulator 2; TPR	90.65
4a1s_A		411	PINS, partner of inscuteable; cell cycle, LGN, mit	90.52
1wao_1		477	Serine/threonine protein phosphatase 5; hydrolase,	90.47
1hh8_A		213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	90.43
2yhc_A		225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	90.36
4b4t_Q		434	26S proteasome regulatory subunit RPN6; hydrolase,	90.36
3ieg_A		359	DNAJ homolog subfamily C member 3; TPR motif, chap	90.28
2gw1_A		514	Mitochondrial precursor proteins import receptor;	90.27
4gcn_A		127	Protein STI-1; structural genomics, PSI-biology, m	90.21
1w3b_A		388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	90.19
2kck_A		112	TPR repeat; tetratricopeptide repeat, structural g	90.06
2y4t_A		450	DNAJ homolog subfamily C member 3; chaperone, endo	89.89
4abn_A		474	Tetratricopeptide repeat protein 5; P53 cofactor,	89.7
2vsy_A		568	XCC0866; transferase, glycosyl transferase, GT-B,	89.66
3edt_B		283	KLC 2, kinesin light chain 2; superhelical, struct	89.58
4b4t_T		274	26S proteasome regulatory subunit RPN12; hydrolase	89.51
1wi9_A		72	Protein C20ORF116 homolog; helix-turn-helix motif,	89.48
1fch_A		368	Peroxisomal targeting signal 1 receptor; protein-p	89.19
2vyi_A		131	SGTA protein; chaperone, TPR repeat, phosphoprotei	89.13
3edt_B		283	KLC 2, kinesin light chain 2; superhelical, struct	88.7
2y4t_A		450	DNAJ homolog subfamily C member 3; chaperone, endo	88.42
2xpi_A		597	Anaphase-promoting complex subunit CUT9; cell cycl	88.41
3u3w_A		293	Transcriptional activator PLCR protein; ternary co	88.26
2xpi_A		597	Anaphase-promoting complex subunit CUT9; cell cycl	88.15
2e2e_A		177	Formate-dependent nitrite reductase complex NRFG;	88.07
1a17_A		166	Serine/threonine protein phosphatase 5; hydrolase,	87.69
2vsy_A		568	XCC0866; transferase, glycosyl transferase, GT-B,	87.45
2gw1_A		514	Mitochondrial precursor proteins import receptor;	87.18
1na0_A		125	Designed protein CTPR3; de novo protein; HET: IPT;	87.06
3k9i_A		117	BH0479 protein; putative protein binding protein,	86.07
1qgp_A		77	Protein (double stranded RNA adenosine deaminase);	86.05
1qbj_A		81	Protein (double-stranded RNA specific adenosine D	85.64
3u3w_A		293	Transcriptional activator PLCR protein; ternary co	85.56
3fp2_A		537	TPR repeat-containing protein YHR117W; TOM71, mito	85.47
1qqe_A		292	Vesicular transport protein SEC17; helix-turn-heli	85.33
2if4_A		338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	85.06
2heo_A		67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	84.84
3cv0_A		327	Peroxisome targeting signal 1 receptor PEX5; TPR m	84.46
3ly7_A		372	Transcriptional activator CADC; alpha/beta domain,	84.13
4f3v_A		282	ESX-1 secretion system protein ECCA1; tetratricope	84.04
3mkr_A		291	Coatomer subunit epsilon; tetratricopeptide repeat	84.0
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	83.39
2ond_A		308	Cleavage stimulation factor 77 kDa subunit; HAT do	82.98
1hz4_A		373	MALT regulatory protein; two-helix bundles, helix	82.2
3rkv_A		162	Putative peptidylprolyl isomerase; structural geno	82.08
2ifu_A		307	Gamma-SNAP; membrane fusion, snare complex disasse	81.35
2r5s_A		176	Uncharacterized protein VP0806; APC090868.1, vibri	81.19
1nzn_A		126	CGI-135 protein, fission protein FIS1P; TPR, unkno	80.08

>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=1.9e-58  Score=476.24  Aligned_cols=346  Identities=19%  Similarity=0.155  Sum_probs=215.9

Q ss_pred             ccccccccCcchhhHHHHHHHhhccccccchhhhccHH--HHHHHHHhhCCchhhhcchHHHHHHHHHHHHHHHHhhcc-
Q 014453           42 LLSFLDQLDPSKHSLGYLYFLEPCMYCSITKERANTLV--PIIARFITSCSAEQIRYVPEKFINVCKRYKDQVLLLEAP-  118 (424)
Q Consensus        42 ~~~~L~~ldp~~~sl~~l~ll~~~~~~~~~~~~~~~l~--~~~~~fl~~fd~~Q~r~~~~~~~~l~~~~~~~~~~~~~~-  118 (424)
                      ..+++|++|.++|.|.++|+++.+....+. ...+.++  +++        ..++|+++|.+.+++|||+++++|..++ 
T Consensus       127 ~~~~~pE~~~y~~lL~~i~L~d~k~~~~~~-~~~~~~~~~~~l--------~~~nrrtlD~l~ak~~fY~s~~~e~~~~~  197 (523)
T 4b4t_S          127 TIEVTAEINCFMHLLVQLFLWDSKELEQLV-EFNRKVVIPNLL--------CYYNLRSLNLINAKLWFYIYLSHETLARS  197 (523)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCCCChHHHHHHHHHHHHHHhccccHHHHH-HHHHHHHHHHHH--------HHHhHHhHHHHHHHHHHHHHHHHHHhccc
Confidence            356899999999999999999999876552 2333333  233        4459999999999999999999886542 


Q ss_pred             ------------ccch--HHHHHHHHhhCCCCCCcchHHHHHHHHHHHccChHHHHhcccccccccc--CchhhHHHHHH
Q 014453          119 ------------IRGV--GPMLTAIRKIQSSTEHLTTLHPEFLQLCLLAKCYKAGLSVLEDDIYEIN--LPRDFFLYCYY  182 (424)
Q Consensus       119 ------------~~~i--~~L~~A~~rl~~~~~~lT~~h~~l~rlcL~~~~y~~Al~il~~~i~~~~--~~~~~l~Y~YY  182 (424)
                                  +|+.  ..+|+|++|.  +..+.+++|.+++|+||..+.|++|.++++|..|+..  ..+++++|+||
T Consensus       198 ~~~~~~~~~~~~ir~~Ll~~~rta~lr~--D~~~qa~l~nllLRnYL~~~~y~qA~~lvsk~~fP~~~~sn~q~~rY~YY  275 (523)
T 4b4t_S          198 SEEINSDNQNIILRSTMMKFLKIASLKH--DNETKAMLINLILRDFLNNGEVDSASDFISKLEYPHTDVSSSLEARYFFY  275 (523)
T ss_dssp             -----CHHHHHHHHTHHHHHHHHCCSCS--SSCHHHHHHHHHHHHHHHSSCSTTHHHHHHHHCSCTTTSCHHHHHHHHHH
T ss_pred             ccccccccchhhHHHHHHHHHHHHhccc--CcchhHHHHHHHHHHHHccCcHHHHHHHHhcCcCCcccCCHHHHHHHHHH
Confidence                        2332  3478888664  4567899999999999999999999999999988643  24688999999


Q ss_pred             HHHHHHhhhcHHHHHHHHHHHhc-ccCcc-ccHHHHHHHHHHHHHHHHhcCCCCCCCCcccCHHHhhhhhhccHHHHHHH
Q 014453          183 GGMIFIGQKRFRKALELLHNVVT-APMSS-INAIAVEAYKKYILVSLIHHGQFSSTLPKYTSSAAQRNLKNFSQPYMELV  260 (424)
Q Consensus       183 ~G~I~~~~~~y~~A~~~~~~a~~-~P~~~-~s~i~~ea~Kk~iLv~LL~~G~~~~p~p~~~s~~~~~~~k~~~~~Y~~L~  260 (424)
                      .|+|++.+++|.+|.++|..|++ ||... ..++.+.++|++|+|.||+ |++| +    ++.+.++.+++.+.||.+|+
T Consensus       276 ~GRI~a~q~~Y~eA~~~L~~A~rkap~~~~a~gfr~~a~K~lI~V~LLl-G~iP-~----r~lf~q~~l~~~L~pY~~Lv  349 (523)
T 4b4t_S          276 LSKINAIQLDYSTANEYIIAAIRKAPHNSKSLGFLQQSNKLHCCIQLLM-GDIP-E----LSFFHQSNMQKSLLPYYHLT  349 (523)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHTSSCSCSSSCSHHHHHHHHHHHHHHHHH-TCCC-C----HHHHTTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHhccHHHHHHHHHHHHHhCCcchhhhhHHHHHHHHHHhHHhhc-CCCC-C----hHHhhchhHHHHHHHHHHHH
Confidence            99999999999999999999998 88764 5688999999999999997 9999 3    56777777778899999999


Q ss_pred             HHHhcCCHHHHHHHHHHcccccccccchhHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHhCCCCHHHHHHHHHHhHHc
Q 014453          261 NTYNTGKIVELETYVQTNREKFESDNNLGLVKQVVSSMYKRNIQRLTQTYLTLSLQDIANTVQLNSSKEAEMHVLQMIQD  340 (424)
Q Consensus       261 ~a~~~gdl~~~~~~l~~~~~~f~~Dgn~~Lv~~l~~~v~r~~I~~l~~~Ys~Isl~~Ia~~l~l~~~~eaE~~v~~mI~~  340 (424)
                      +||+.||+..|.+++++|++.|.+|||++||++|+.+|+|++|++++++|++||++|||.+++++|+++||++|++||.+
T Consensus       350 ~Avr~GdL~~F~~~L~~h~~~F~~Dgty~LI~rLr~~vir~~irkis~~YsrIsL~dIa~kL~L~s~eeaE~iVAkmI~d  429 (523)
T 4b4t_S          350 KAVKLGDLKKFTSTITKYKQLLLKDDTYQLCVRLRSNVIKTGIRIISLTYKKISLRDICLKLNLDSEQTVEYMVSRAIRD  429 (523)
T ss_dssp             HHHHHTCHHHHHHHHHHTHHHHHHTTCTHHHHHHHHHHHHHHHHHSCCCSSEECHHHHHHHHHHHHSSCHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHhcceeccCChhHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHhCCCCHHHHHHHHHHHHHc
Confidence            99999999999999999999999999999999999999999999999999999999999999998789999999999999


Q ss_pred             CceEEEEecCCCEEEEecCCCccChHHHHHHHHHHHHHHHHHHH-HHHHHhHHhh-cCHHHHHHhh
Q 014453          341 GEIFATINQKDGMVRFLEDPEQYKTCEMIEHIDSSIQRIMSLSK-KLTAMDELIS-CDPLYLGKAG  404 (424)
Q Consensus       341 G~I~A~Id~~~g~v~F~~~~~~~~~~~~~~~~~~~i~~~~~L~~-~~~~~d~~l~-~~~~yi~~~~  404 (424)
                      |.|+|+|||++|+|.|++.+|.|+|.||+.+|++||++|++|++ .+++|...-. .++++.++..
T Consensus       430 G~I~A~Idh~~g~v~ske~~d~yst~ep~~af~~RI~~cl~L~ne~vkaMryp~~~~~~~~~~~~~  495 (523)
T 4b4t_S          430 GVIEAKINHEDGFIETTELLNIYDSEDPQQVFDERIKFANQLHDEYLVSMRYPEDKKTQQNEKSEN  495 (523)
T ss_dssp             TSSCCEECTTTCCEECCSSSCC--------------------------------------------
T ss_pred             CCceEEEecCCCEEEeCccccccccHHHHHHHHHHHHHHHHHHHHHHHHccCCcccchhhHHHHHH
Confidence            99999999999999999999999999999999999999999975 7999996433 3444444443

PyMOL of 4b4t

>3t5x_A PCI domain-containing protein 2; PCI, mRNA nuclear export, transcription; 2.12A {Homo sapiens}	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_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}	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

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

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

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

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

>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

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

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

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

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

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

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

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

>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

>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

>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

>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

>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

>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

>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

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

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

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

>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

>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

>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

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

>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

>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

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

>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

>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

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

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

>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

>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

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

>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

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

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

>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

>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

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

>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

>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

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

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

>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

>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

>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

>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

>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

>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

>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

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_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

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

>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

>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

>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

>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

>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

>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

>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

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

>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

>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

>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

>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

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

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

>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

>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

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

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

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

>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

>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

>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

>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

>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

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

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

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

>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

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

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

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

>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

>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

>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

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

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

>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

>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

>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

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

>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

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

>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

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

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

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

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

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

>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

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

>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

>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

>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

>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

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

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

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

>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

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

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {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

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

>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

>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

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

>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

>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

>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

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A	Back alignment and structure

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

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

>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

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

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

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

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_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		424
d1ufma_		84	a.4.5.47 (A:) COP9 signalosome complex subunit 4,	3e-10

>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 = 54.0 bits (130), Expect = 3e-10
 Identities = 14/57 (24%), Positives = 33/57 (57%), Gaps = 1/57 (1%)

Query: 300 KRNIQRLTQTYLTLSLQDIANTVQLNSSKEAEMHVLQMIQDGEIFATINQKDGMVRF 356
           + N+   ++ Y  ++ +++   +++ ++ +AE    QMI +G +   I+Q DG+V F
Sbjct: 18  EHNLLSASKLYNNITFEELGALLEIPAA-KAEKIASQMITEGRMNGFIDQIDGIVHF 73

PyMOL of d1ufma_

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		424
d1ufma_		84	COP9 signalosome complex subunit 4, GSN4 {Mouse (M	99.49
d1qqea_		290	Vesicular transport protein sec17 {Baker's yeast (	96.26
d1p5qa1		170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	95.82
d1elwa_		117	Hop {Human (Homo sapiens) [TaxId: 9606]}	95.78
d2c2la1		201	STIP1 homology and U box-containing protein 1, STU	95.5
d1a17a_		159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	95.01
d1hxia_		112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	94.73
d1nzna_		122	Mitochondria fission protein Fis1 {Human (Homo sap	94.25
d2fbna1		153	Putative 70 kda peptidylprolyl isomerase PFL2275c	93.88
d1tjca_		95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	93.77
d1a17a_		159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	93.43
d1kt1a1		168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	93.28
d1hxia_		112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	93.12
d2c2la1		201	STIP1 homology and U box-containing protein 1, STU	92.76
d1xnfa_		259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	92.75
d1fcha_		323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	92.52
d2cfxa1		63	Transcriptional regulator LrpC {Bacillus subtilis	92.23
d1hz4a_		366	Transcription factor MalT domain III {Escherichia	92.02
d1wi9a_		72	Hypothetical protein C20orf116 homolog {Mouse (Mus	91.99
d1elwa_		117	Hop {Human (Homo sapiens) [TaxId: 9606]}	91.96
d2pqrb1		124	Mitochondria fission protein Fis1 {Baker's yeast (	91.79
d2h6fa1		315	Protein farnesyltransferase alpha-subunit {Human (	91.76
d1elra_		128	Hop {Human (Homo sapiens) [TaxId: 9606]}	91.3
d1w3ba_		388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	91.28
d1w3ba_		388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	90.89
d1xnfa_		259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	90.51
d2cg4a1		63	Regulatory protein AsnC {Escherichia coli [TaxId:	90.41
d1ihga1		169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	89.98
d1hh8a_		192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	89.94
d1fcha_		323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	89.91
d1hh8a_		192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	89.02
d2cyya1		60	Putative transcriptional regulator PH1519 {Archaeo	88.78
d1i1ga1		60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	88.57
d2hr2a1		156	Hypothetical protein CT2138 {Chlorobium tepidum [T	88.22
d1z05a1		71	Transcriptional regulator VC2007 N-terminal domain	87.59
d1lj9a_		144	Transcriptional regulator SlyA {Enterococcus faeca	86.73
d1hz4a_		366	Transcription factor MalT domain III {Escherichia	86.03
d1elra_		128	Hop {Human (Homo sapiens) [TaxId: 9606]}	85.46
d1z6ra1		70	Mlc protein N-terminal domain {Escherichia coli [T	83.66
d1rz4a1		85	Eukaryotic translation initiation factor 3 subunit	81.88
d1ub9a_		100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	81.67
d1dpua_		69	C-terminal domain of RPA32 {Human (Homo sapiens) [	81.07

>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=99.49  E-value=6.8e-15  Score=114.72  Aligned_cols=75  Identities=20%  Similarity=0.348  Sum_probs=67.3

Q ss_pred             cchhHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHhCCCCHHHHHHHHHHhHHcCceEEEEecCCCEEEEecCCC
Q 014453          286 NNLGLVKQVVSSMYKRNIQRLTQTYLTLSLQDIANTVQLNSSKEAEMHVLQMIQDGEIFATINQKDGMVRFLEDPE  361 (424)
Q Consensus       286 gn~~Lv~~l~~~v~r~~I~~l~~~Ys~Isl~~Ia~~l~l~~~~eaE~~v~~mI~~G~I~A~Id~~~g~v~F~~~~~  361 (424)
                      |+.+...-|++++++|||+.++++|++|+++++|+.++++ ++++|.+|++||.+|.|+|+||+.+|+|.|.....
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            4444444568999999999999999999999999999997 89999999999999999999999999999986543

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

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {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

>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

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

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

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

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

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

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

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

>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

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

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

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

>d1elra_ a.118.8.1 (A:) Hop {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

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

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

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}	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

>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

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

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

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

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}	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

>d1lj9a_ a.4.5.28 (A:) Transcriptional regulator SlyA {Enterococcus faecalis [TaxId: 1351]}	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

>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

>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

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}	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