Citrus Sinensis ID: 011352

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------49

MTQDVEMKDKENPSNSLSSPFTPSTLHHLKEIASLMETGAHAREVRRIMRAVRLTMALRRKLKAPVLSAFLNFALAPGSEAHSRLLSYLPKEDEHEMEVDTASSGAPAPAKHPLPELEIYCYLLVLIFLIDKKRYNEAKACSSASIARLKNMNRRTVDVLAARLYFYYSLCYELTGDLAEIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLRSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAALGFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFSSTFSSDRTNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVRALRFPPNSHKEKESAEKRRERQQQEQELAKHIAEEDDDEF

ccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHcccccHHHHHHHcccccccccccccccccccccccccccccHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHcccHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHcccHHHHHHHHHcccHHHHHHHHHHccHHHHcccHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHcccccccHHHHHHHHHHHHHcccEEEEEEccccEEEEcccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccc

ccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHccHHHHHHHHHHHcccccHHHHHHHHHccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHcccccHHHHccHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHcccccEHHHHHHHHHHHHHHHHEEEEEccccHHHHHHHHccccHccHHHHHHHHHHHHHcccEEEEEEccccEEEEccccEEEccccHHHHHHHHHHHHHHHHHHHHHHHcccccHcccHHHHHHHHHHHHHHHHHHHHHHccccccc

mtqdvemkdkenpsnslsspftpstLHHLKEIASLMETGAHAREVRRIMRAVRLTMALRRKLKAPVLSAFLNFALAPGSEAHSRLlsylpkedehemevdtassgapapakhplpelEIYCYLLVLIFLIDKKRYNEAKACSSASIARLKNMNRRTVDVLAARLYFYYSLCYELTGDLAEIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLrskaprfeahsnQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAALGFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFSstfssdrtnNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLrldsanpvadAESIVSKAIRDgaidatvdhangwmvsketgdiystnepqlafNSRIAFCLNMHNEAvralrfppnshkekeSAEKRRERQQQEQELAKHIAEEDDDEF

mtqdvemkdkenpsnslsspftpSTLHHLKEIASLMetgahareVRRIMRAVRLTMALRRKLKAPVLSAFLNFALAPGSEAHSRLLSYLPKEDEHEMEVDTASSGAPAPAKHPLPELEIYCYLLVLIFLIDKKRYNEAKACSSasiarlknmnrrTVDVLAARLYFYYSLCYELTGDLAEIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLRSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAALGFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFsstfssdrtnnliVRLRhnvirtglrnisisysrISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVralrfppnshkekesaEKRRERQQQEQELakhiaeedddef

MTQDVEMKDKENPSNSLSSPFTPSTLHHLKEIASLMETGAHAREVRRIMRAVRLTMALRRKLKAPVLSAFLNFALAPGSEAHSRLLSYLPKEDEHEMEVDTASSGAPAPAKHPLPELEIYCYLLVLIFLIDKKRYNEAKACSSASIARLKNMNRRTVDVLAARLYFYYSLCYELTGDLAEIRGNLLALHRIATLRHDELGQETllnlllrnylhynlyDQAEKLRSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAALGFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFSSTFSSDRTNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVRALRFPPNSHkekesaekrrerqqqeqeLAKHIAEEDDDEF

******************************EIASLMETGAHAREVRRIMRAVRLTMALRRKLKAPVLSAFLNFALAP***************************************LEIYCYLLVLIFLIDKKRYNEAKACSSASIARLKNMNRRTVDVLAARLYFYYSLCYELTGDLAEIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLR****RFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAALGFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFSSTFSSDRTNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVRAL**************************************

*TQDVE********************HHLKEIASLMETGAHAREVRRIMRAVRLTMALRRKLKAPVLSAFLNFALAPGSEAHSRLLSYLP**********************PLPELEIYCYLLVLIFLIDKKRYNEAKACSSASIARLKNMNRRTVDVLAARLYFYYSLCYELTGDLAEIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLRSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAALGFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFSSTFSSDRTNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVRA********************************EE*****

*******************PFTPSTLHHLKEIASLMETGAHAREVRRIMRAVRLTMALRRKLKAPVLSAFLNFALAPGSEAHSRLLSYLPKE****************PAKHPLPELEIYCYLLVLIFLIDKKRYNEAKACSSASIARLKNMNRRTVDVLAARLYFYYSLCYELTGDLAEIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLRSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAALGFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFSSTFSSDRTNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVRALRFPP**********************************

********************FTPSTLHHLKEIASLMETGAHAREVRRIMRAVRLTMALRRKLKAPVLSAFLNFALAPGSEAHSRLLSYLPK*******************KHPLPELEIYCYLLVLIFLIDKKRYNEAKACSSASIARLKNMNRRTVDVLAARLYFYYSLCYELTGDLAEIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLRSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAALGFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFSSTFSSDRTNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVRALRFPPNS*******************L*KHIAE******

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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		488	2.2.26 [Sep-21-2011]
P93768		488	Probable 26S proteasome n	N/A	no	0.997	0.997	0.910	0.0
Q06364		489	Probable 26S proteasome n	N/A	no	0.997	0.995	0.877	0.0
Q9LNU4		488	Probable 26S proteasome n	yes	no	0.997	0.997	0.826	0.0
Q9LQR8		487	Probable 26S proteasome n	no	no	0.997	1.0	0.811	0.0
P25161		494	Probable 26S proteasome n	yes	no	0.938	0.927	0.477	1e-109
O43242		534	26S proteasome non-ATPase	yes	no	0.944	0.863	0.482	1e-108
Q2KJ46		534	26S proteasome non-ATPase	yes	no	0.944	0.863	0.482	1e-108
P14685		530	26S proteasome non-ATPase	yes	no	0.944	0.869	0.482	1e-107
O61470		496	Probable 26S proteasome n	yes	no	0.979	0.963	0.470	1e-104
Q9U5Z8		500	Probable 26S proteasome n	N/A	no	0.979	0.956	0.472	1e-104

>sp\|P93768\|PSMD3_TOBAC Probable 26S proteasome non-ATPase regulatory subunit 3 OS=Nicotiana tabacum GN=21D7 PE=2 SV=1	Back alignment and function desciption

 Score =  862 bits (2227), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 445/489 (91%), Positives = 463/489 (94%), Gaps = 2/489 (0%)

Query: 1   MTQDVEMKDKENP-SNSLSSPFTPSTLHHLKEIASLMETGAHAREVRRIMRAVRLTMALR 59
           MTQDVEMK++  P SNSLSS   PS  HHLKEIASL+ETGA+AREVRRI RAVRLTMALR
Sbjct: 1   MTQDVEMKEQAAPPSNSLSST-APSIFHHLKEIASLIETGAYAREVRRISRAVRLTMALR 59

Query: 60  RKLKAPVLSAFLNFALAPGSEAHSRLLSYLPKEDEHEMEVDTASSGAPAPAKHPLPELEI 119
           +KLKA  LSAFLN+ L PGSE HSRL S+LPKEDE +MEVDTA+SGA AP K+PLPELEI
Sbjct: 60  KKLKASSLSAFLNYVLVPGSEVHSRLSSFLPKEDEQDMEVDTATSGAQAPIKNPLPELEI 119

Query: 120 YCYLLVLIFLIDKKRYNEAKACSSASIARLKNMNRRTVDVLAARLYFYYSLCYELTGDLA 179
           YCYLLVLIFLID+K+YNEAKACSSASIARLK +NRRTVDVLA+RLYFYYSLCYELTGDLA
Sbjct: 120 YCYLLVLIFLIDQKKYNEAKACSSASIARLKTVNRRTVDVLASRLYFYYSLCYELTGDLA 179

Query: 180 EIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLRSKAPRFEAHSNQQF 239
           EIRG LLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLRSKAPRFEAHSNQQF
Sbjct: 180 EIRGYLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLRSKAPRFEAHSNQQF 239

Query: 240 CRYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAALGFRVQCNKWAIIVRLLLGEIPERT 299
            RYLFYLGKIRTIQLEYTDAKESLLQAARKAP AALGFRVQCNKWAIIVRLLLGEIPERT
Sbjct: 240 SRYLFYLGKIRTIQLEYTDAKESLLQAARKAPQAALGFRVQCNKWAIIVRLLLGEIPERT 299

Query: 300 VFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFSSTFSSDRTNNLIVRLRHNVIRTG 359
           VFMQKGMEKALRPYFELTNAVRIGDLELF+ VAEKFSSTFSSD TNNLIVRLRHNVIRTG
Sbjct: 300 VFMQKGMEKALRPYFELTNAVRIGDLELFRKVAEKFSSTFSSDGTNNLIVRLRHNVIRTG 359

Query: 360 LRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHANGWMVSKET 419
           LRNISISYSRISL DVAKKLRLDS NPVADAESIVSKAIRDGAIDAT+DHANGWMVSKET
Sbjct: 360 LRNISISYSRISLVDVAKKLRLDSPNPVADAESIVSKAIRDGAIDATLDHANGWMVSKET 419

Query: 420 GDIYSTNEPQLAFNSRIAFCLNMHNEAVRALRFPPNSHKEKESAEKRRERQQQEQELAKH 479
           GDIYSTNEPQ+AFNSRIAFCLNMHNEAVRALRFPPNSHKEKESAEKRRERQQQEQELAKH
Sbjct: 420 GDIYSTNEPQIAFNSRIAFCLNMHNEAVRALRFPPNSHKEKESAEKRRERQQQEQELAKH 479

Query: 480 IAEEDDDEF 488
           IAEEDDD+F
Sbjct: 480 IAEEDDDDF 488

Acts as a regulatory subunit of the 26 proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.
Nicotiana tabacum (taxid: 4097)

>sp\|Q06364\|PSMD3_DAUCA Probable 26S proteasome non-ATPase regulatory subunit 3 OS=Daucus carota GN=21D7 PE=1 SV=2	Back alignment and function description

>sp\|Q9LNU4\|PSD31_ARATH Probable 26S proteasome non-ATPase regulatory subunit 3a OS=Arabidopsis thaliana GN=EMB2719 PE=1 SV=3	Back alignment and function description

>sp\|Q9LQR8\|PSD32_ARATH Probable 26S proteasome non-ATPase regulatory subunit 3b OS=Arabidopsis thaliana GN=At1g75990 PE=2 SV=2	Back alignment and function description

>sp\|P25161\|PSMD3_DROME Probable 26S proteasome non-ATPase regulatory subunit 3 OS=Drosophila melanogaster GN=Rpn3 PE=2 SV=1	Back alignment and function description

>sp\|O43242\|PSMD3_HUMAN 26S proteasome non-ATPase regulatory subunit 3 OS=Homo sapiens GN=PSMD3 PE=1 SV=2	Back alignment and function description

>sp\|Q2KJ46\|PSMD3_BOVIN 26S proteasome non-ATPase regulatory subunit 3 OS=Bos taurus GN=PSMD3 PE=2 SV=1	Back alignment and function description

>sp\|P14685\|PSMD3_MOUSE 26S proteasome non-ATPase regulatory subunit 3 OS=Mus musculus GN=Psmd3 PE=1 SV=3	Back alignment and function description

>sp\|O61470\|PSMD3_ANOGA Probable 26S proteasome non-ATPase regulatory subunit 3 OS=Anopheles gambiae GN=Dox-A2 PE=3 SV=2	Back alignment and function description

>sp\|Q9U5Z8\|PSMD3_ANOST Probable 26S proteasome non-ATPase regulatory subunit 3 OS=Anopheles stephensi GN=DOXA2 PE=3 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		488
225428067		487	PREDICTED: probable 26S proteasome non-A	0.997	1.0	0.899	0.0
3914467		488	RecName: Full=Probable 26S proteasome no	0.997	0.997	0.910	0.0
255560521		491	26S proteasome regulatory subunit S3, pu	1.0	0.993	0.890	0.0
12230970		489	RecName: Full=Probable 26S proteasome no	0.997	0.995	0.877	0.0
356517716		487	PREDICTED: probable 26S proteasome non-A	0.997	1.0	0.862	0.0
356509165		487	PREDICTED: probable 26S proteasome non-A	0.997	1.0	0.862	0.0
357467057		490	26S proteasome non-ATPase regulatory sub	0.997	0.993	0.859	0.0
224080636		488	predicted protein [Populus trichocarpa]	1.0	1.0	0.887	0.0
356553349		490	PREDICTED: probable 26S proteasome non-A	0.997	0.993	0.835	0.0
224103165		486	predicted protein [Populus trichocarpa]	0.995	1.0	0.903	0.0

>gi\|225428067\|ref\|XP_002279715.1\| PREDICTED: probable 26S proteasome non-ATPase regulatory subunit 3 [Vitis vinifera]	Back alignment and taxonomy information

 Score =  866 bits (2237), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 439/488 (89%), Positives = 466/488 (95%), Gaps = 1/488 (0%)

Query: 1   MTQDVEMKDKENPSNSLSSPFTPSTLHHLKEIASLMETGAHAREVRRIMRAVRLTMALRR 60
           MTQDVEMK+   PSNS++S  TPSTL HLKEIASL+E+ A+AREVRRI+RA+RLTM LRR
Sbjct: 1   MTQDVEMKELPAPSNSVTST-TPSTLQHLKEIASLIESSAYAREVRRIVRAIRLTMILRR 59

Query: 61  KLKAPVLSAFLNFALAPGSEAHSRLLSYLPKEDEHEMEVDTASSGAPAPAKHPLPELEIY 120
           KLKA VLS FLN+AL PGSE H+RL SYLPKEDEH+MEVDTA+S    PAKHPLPELEIY
Sbjct: 60  KLKATVLSGFLNYALNPGSEVHTRLSSYLPKEDEHDMEVDTATSATQTPAKHPLPELEIY 119

Query: 121 CYLLVLIFLIDKKRYNEAKACSSASIARLKNMNRRTVDVLAARLYFYYSLCYELTGDLAE 180
           CYLLVLIFLID+K+Y EAKACS+ASI RLKN+NRRT+DVLA+RLY YYSL YELTGDLAE
Sbjct: 120 CYLLVLIFLIDQKKYKEAKACSAASITRLKNLNRRTIDVLASRLYSYYSLSYELTGDLAE 179

Query: 181 IRGNLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLRSKAPRFEAHSNQQFC 240
           IRGNLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLRSKAPRFEAHSNQQFC
Sbjct: 180 IRGNLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLRSKAPRFEAHSNQQFC 239

Query: 241 RYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAALGFRVQCNKWAIIVRLLLGEIPERTV 300
           RYLFYLGKIRTIQLEYTDAKESLLQAARKAPV+ALGFRVQCNKWA+IVRLLLGEIPERTV
Sbjct: 240 RYLFYLGKIRTIQLEYTDAKESLLQAARKAPVSALGFRVQCNKWAVIVRLLLGEIPERTV 299

Query: 301 FMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFSSTFSSDRTNNLIVRLRHNVIRTGL 360
           FMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFS+TFSSDRT+NLIVRLRHNVIRTGL
Sbjct: 300 FMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFSTTFSSDRTHNLIVRLRHNVIRTGL 359

Query: 361 RNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHANGWMVSKETG 420
           RNISISYSRISLADVA+KLRLDSANP+ADAESIV+KAIRDGAIDAT+DHANGWMVSKETG
Sbjct: 360 RNISISYSRISLADVAQKLRLDSANPIADAESIVAKAIRDGAIDATLDHANGWMVSKETG 419

Query: 421 DIYSTNEPQLAFNSRIAFCLNMHNEAVRALRFPPNSHKEKESAEKRRERQQQEQELAKHI 480
           DIYSTNEPQ AFNSRIAFCLNMHN+AVRALRFPPNSHKEKESAEKRRERQQQEQELAKHI
Sbjct: 420 DIYSTNEPQFAFNSRIAFCLNMHNDAVRALRFPPNSHKEKESAEKRRERQQQEQELAKHI 479

Query: 481 AEEDDDEF 488
           AEEDDDEF
Sbjct: 480 AEEDDDEF 487

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|3914467\|sp\|P93768.1\|PSMD3_TOBAC RecName: Full=Probable 26S proteasome non-ATPase regulatory subunit 3; Short=26S proteasome subunit S3; AltName: Full=26S proteasome regulatory subunit RPN3; AltName: Full=Nuclear antigen 21D7 gi\|1864003\|dbj\|BAA19252.1\| 21D7 [Nicotiana tabacum]	Back alignment and taxonomy information

>gi\|255560521\|ref\|XP_002521275.1\| 26S proteasome regulatory subunit S3, putative [Ricinus communis] gi\|223539543\|gb\|EEF41131.1\| 26S proteasome regulatory subunit S3, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|12230970\|sp\|Q06364.2\|PSMD3_DAUCA RecName: Full=Probable 26S proteasome non-ATPase regulatory subunit 3; Short=26S proteasome subunit S3; AltName: Full=26S proteasome regulatory subunit RPN3; AltName: Full=Nuclear antigen 21D7	Back alignment and taxonomy information

>gi\|356517716\|ref\|XP_003527532.1\| PREDICTED: probable 26S proteasome non-ATPase regulatory subunit 3-like [Glycine max]	Back alignment and taxonomy information

>gi\|356509165\|ref\|XP_003523322.1\| PREDICTED: probable 26S proteasome non-ATPase regulatory subunit 3-like [Glycine max]	Back alignment and taxonomy information

>gi\|357467057\|ref\|XP_003603813.1\| 26S proteasome non-ATPase regulatory subunit [Medicago truncatula] gi\|355492861\|gb\|AES74064.1\| 26S proteasome non-ATPase regulatory subunit [Medicago truncatula]	Back alignment and taxonomy information

>gi\|224080636\|ref\|XP_002306189.1\| predicted protein [Populus trichocarpa] gi\|222849153\|gb\|EEE86700.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356553349\|ref\|XP_003545019.1\| PREDICTED: probable 26S proteasome non-ATPase regulatory subunit 3-like [Glycine max]	Back alignment and taxonomy information

>gi\|224103165\|ref\|XP_002312950.1\| predicted protein [Populus trichocarpa] gi\|222849358\|gb\|EEE86905.1\| predicted protein [Populus trichocarpa]	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		488
TAIR\|locus:2198561		488	EMB2719 "EMBRYO DEFECTIVE 2719	0.997	0.997	0.766	1e-194
TAIR\|locus:2204385		487	AT1G75990 [Arabidopsis thalian	0.997	1.0	0.754	4.6e-192
ZFIN\|ZDB-GENE-040426-1444		503	psmd3 "proteasome (prosome, ma	0.983	0.954	0.422	7e-93
UNIPROTKB\|Q2KJ46		534	PSMD3 "26S proteasome non-ATPa	0.944	0.863	0.427	2.7e-91
UNIPROTKB\|E2QUY7		534	PSMD3 "Uncharacterized protein	0.944	0.863	0.427	2.7e-91
UNIPROTKB\|O43242		534	PSMD3 "26S proteasome non-ATPa	0.944	0.863	0.427	2.7e-91
MGI\|MGI:98858		530	Psmd3 "proteasome (prosome, ma	0.944	0.869	0.427	3.5e-91
RGD\|1311470		530	Psmd3 "proteasome (prosome, ma	0.944	0.869	0.427	3.5e-91
UNIPROTKB\|F1RXA7		536	LOC100512253 "Uncharacterized	0.944	0.860	0.429	1.2e-90
FB\|FBgn0261396		494	Rpn3 "Regulatory particle non-	0.938	0.927	0.426	2.3e-87

TAIR\|locus:2198561 EMB2719 "EMBRYO DEFECTIVE 2719" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1886 (669.0 bits), Expect = 1.0e-194, P = 1.0e-194
 Identities = 375/489 (76%), Positives = 415/489 (84%)

Query:     1 MTQDVEMKDKENPSNSLSSPFTPSTLHHLKEIASLMETGAHAREVRRIMRAVRLTMALRR 60
             MTQDVEMKD   PS S+ S  T ST+ +LKEIA+L++TG++ +EVRRI RAVRLT+ LR+
Sbjct:     1 MTQDVEMKDNNTPSQSIISSST-STMQNLKEIAALIDTGSYTKEVRRIARAVRLTIGLRQ 59

Query:    61 KLKAPVLSAFLNFALAPGSEAHSRLLSYLPKEDEHEMEVDTASSGAPA-PAKHPLPELEI 119
             KL   VLS+FL+FAL PGSEAHSRL S++PK DEH+MEVDTASS   A P+KH   ELEI
Sbjct:    60 KLTGSVLSSFLDFALVPGSEAHSRLSSFVPKGDEHDMEVDTASSATQAAPSKHLPAELEI 119

Query:   120 YCYLLVLIFLIDKKRYNEAKACSSASIARLKNMNRRTVDVLAARLYFYYSLCYELTGDLA 179
             YCY +VL+FLID+K+YNEAKACSSASIARLKN+NRRT+DV+A+RLYFYYSL YE TGDLA
Sbjct:   120 YCYFIVLLFLIDQKKYNEAKACSSASIARLKNVNRRTIDVIASRLYFYYSLSYEQTGDLA 179

Query:   180 EIRGNLLALHRIATLRHDELGQETXXXXXXXXXXXXXXXDQAEKLRSKAPRFEAHSNQQF 239
             EIRG LLALH  ATLRHDELGQET               DQAEKLRSKAPRFEAHSNQQF
Sbjct:   180 EIRGTLLALHHSATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLRSKAPRFEAHSNQQF 239

Query:   240 CRYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAALGFRVQCNKWAIIVRLLLGEIPERT 299
             CRYLFYLGKIRTIQLEYTDAKESLLQAARKAP+AALGFR+QCNKWAI+VRLLLGEIPER+
Sbjct:   240 CRYLFYLGKIRTIQLEYTDAKESLLQAARKAPIAALGFRIQCNKWAILVRLLLGEIPERS 299

Query:   300 VFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFSSTFSSDRTNNLIVRLRHNVIRTG 359
             +F QKGMEKALRPYFELTNAVRIGDLELF++V EKF  TF+ DRT+NLIVRLRHNVIRTG
Sbjct:   300 IFTQKGMEKALRPYFELTNAVRIGDLELFRTVQEKFLDTFAQDRTHNLIVRLRHNVIRTG 359

Query:   360 LRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHANGWMVSKET 419
             LRNISISYSRISL DVAKKLRL+S NPVADAESIV+KAIRDGAIDAT+DH NG MVSKET
Sbjct:   360 LRNISISYSRISLPDVAKKLRLNSENPVADAESIVAKAIRDGAIDATIDHKNGCMVSKET 419

Query:   420 GDIYSTNEPQLAFNSRIAFCLNMHNEAVRALRFPPNSHXXXXXXXXXXXXXXXXXXLAKH 479
             GDIYSTNEPQ AFNSRIAFCLNMHNEAVRALRFPPN+H                  LAKH
Sbjct:   420 GDIYSTNEPQTAFNSRIAFCLNMHNEAVRALRFPPNTHKEKESDEKRRERKQQEEELAKH 479

Query:   480 IAEEDDDEF 488
             +AEEDDD+F
Sbjct:   480 MAEEDDDDF 488

GO:0000502 "proteasome complex" evidence=IEA;IDA

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0030234 "enzyme regulator activity" evidence=IEA

GO:0042176 "regulation of protein catabolic process" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

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

GO:0009407 "toxin catabolic process" evidence=RCA

GO:0042023 "DNA endoreduplication" evidence=RCA

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

GO:0043248 "proteasome assembly" evidence=RCA

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

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

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

TAIR\|locus:2204385 AT1G75990 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-040426-1444 psmd3 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 3" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|Q2KJ46 PSMD3 "26S proteasome non-ATPase regulatory subunit 3" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|E2QUY7 PSMD3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|O43242 PSMD3 "26S proteasome non-ATPase regulatory subunit 3" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

MGI\|MGI:98858 Psmd3 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 3" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

RGD\|1311470 Psmd3 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 3" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|F1RXA7 LOC100512253 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

FB\|FBgn0261396 Rpn3 "Regulatory particle non-ATPase 3" [Drosophila melanogaster (taxid:7227)]	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)
Q9LNU4	PSD31_ARATH	No assigned EC number	0.8261	0.9979	0.9979	yes	no
O61470	PSMD3_ANOGA	No assigned EC number	0.4702	0.9795	0.9637	yes	no
O43242	PSMD3_HUMAN	No assigned EC number	0.4828	0.9446	0.8632	yes	no
P14685	PSMD3_MOUSE	No assigned EC number	0.4828	0.9446	0.8698	yes	no
P93768	PSMD3_TOBAC	No assigned EC number	0.9100	0.9979	0.9979	N/A	no
O42897	RPN3_SCHPO	No assigned EC number	0.4403	0.9077	0.8913	yes	no
Q9LQR8	PSD32_ARATH	No assigned EC number	0.8114	0.9979	1.0	no	no
Q1ZXD3	PSMD3_DICDI	No assigned EC number	0.4252	0.9446	0.9146	yes	no
P25161	PSMD3_DROME	No assigned EC number	0.4776	0.9385	0.9271	yes	no
Q06364	PSMD3_DAUCA	No assigned EC number	0.8775	0.9979	0.9959	N/A	no
Q04908	PSMD3_CAEEL	No assigned EC number	0.3795	0.9795	0.9484	yes	no
Q2KJ46	PSMD3_BOVIN	No assigned EC number	0.4828	0.9446	0.8632	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

Fail to connect to STRING server

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		488
pfam08375		68	pfam08375, Rpn3_C, Proteasome regulatory subunit C	8e-27
pfam01399		100	pfam01399, PCI, PCI domain	6e-21
smart00753		88	smart00753, PAM, PCI/PINT associated module	3e-19
smart00088		88	smart00088, PINT, motif in proteasome subunits, In	3e-19

>gnl\|CDD\|149439 pfam08375, Rpn3_C, Proteasome regulatory subunit C-terminal	Back alignment and domain information

 Score =  102 bits (256), Expect = 8e-27
 Identities = 39/68 (57%), Positives = 52/68 (76%), Gaps = 1/68 (1%)

Query: 421 DIYSTNEPQLAFNSRIAFCLNMHNEAVRALRFPPNSHK-EKESAEKRRERQQQEQELAKH 479
           D+YST EPQ AF+ RI FCL +HN+AV+A+R+PP+  K E+E AE+ RER Q E ELAK 
Sbjct: 1   DVYSTKEPQQAFDERIQFCLQLHNDAVKAMRYPPDKEKKEEEKAEEARERDQLELELAKE 60

Query: 480 IAEEDDDE 487
           ++E D D+
Sbjct: 61  LSEGDLDD 68

This eukaryotic domain is found at the C-terminus of 26S proteasome regulatory subunits such as the non-ATPase Rpn3 subunit which is essential for proteasomal function. It occurs together with the PCI/PINT domain (pfam01399). Length = 68

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

>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		488
KOG2581		493	consensus 26S proteasome regulatory complex, subun	100.0
KOG2688		394	consensus Transcription-associated recombination p	100.0
COG5600		413	Transcription-associated recombination protein [DN	99.97
KOG2582		422	consensus COP9 signalosome, subunit CSN3 [Posttran	99.95
PF08375		68	Rpn3_C: Proteasome regulatory subunit C-terminal;	99.92
KOG1463		411	consensus 26S proteasome regulatory complex, subun	99.92
COG5159		421	RPN6 26S proteasome regulatory complex component [	99.82
KOG1497		399	consensus COP9 signalosome, subunit CSN4 [Posttran	99.78
KOG1464		440	consensus COP9 signalosome, subunit CSN2 [Posttran	99.75
PF01399		105	PCI: PCI domain; InterPro: IPR000717 A homology do	99.7
KOG1498		439	consensus 26S proteasome regulatory complex, subun	99.49
KOG2908		380	consensus 26S proteasome regulatory complex, subun	99.29
smart00088		88	PINT motif in proteasome subunits, Int-6, Nip-1 an	99.1
smart00753		88	PAM PCI/PINT associated module.	99.1
COG5071		439	RPN5 26S proteasome regulatory complex component [	99.03
KOG0687		393	consensus 26S proteasome regulatory complex, subun	98.23
KOG1076		843	consensus Translation initiation factor 3, subunit	97.99
COG5187		412	RPN7 26S proteasome regulatory complex component,	97.83
PF14938		282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.6
KOG0686		466	consensus COP9 signalosome, subunit CSN1 [Posttran	97.55
PF10255		404	Paf67: RNA polymerase I-associated factor PAF67; I	97.32
KOG2753		378	consensus Uncharacterized conserved protein, conta	96.87
KOG2758		432	consensus Translation initiation factor 3, subunit	96.68
KOG2072		988	consensus Translation initiation factor 3, subunit	96.42
PLN03081		697	pentatricopeptide (PPR) repeat-containing protein;	96.29
PF09976		145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	96.21
TIGR03302		235	OM_YfiO outer membrane assembly lipoprotein YfiO.	95.93
PF13371		73	TPR_9: Tetratricopeptide repeat	95.61
PF07719		34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	95.37
PRK11788		389	tetratricopeptide repeat protein; Provisional	95.35
TIGR00990		615	3a0801s09 mitochondrial precursor proteins import	95.19
PF14938		282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	95.17
PF13432		65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	95.04
PRK11788		389	tetratricopeptide repeat protein; Provisional	95.0
TIGR02521		234	type_IV_pilW type IV pilus biogenesis/stability pr	94.99
PF10075		143	PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro	94.93
cd00189		100	TPR Tetratricopeptide repeat domain; typically con	94.4
PF13424		78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	94.19
TIGR02552		135	LcrH_SycD type III secretion low calcium response	94.07
TIGR02521		234	type_IV_pilW type IV pilus biogenesis/stability pr	94.05
PF13525		203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	93.75
TIGR00990		615	3a0801s09 mitochondrial precursor proteins import	93.22
PF00515		34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	93.09
PLN03081		697	pentatricopeptide (PPR) repeat-containing protein;	93.04
TIGR02917		899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	92.7
KOG4162		799	consensus Predicted calmodulin-binding protein [Si	92.69
KOG2300		629	consensus Uncharacterized conserved protein [Funct	92.58
PF10602		177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	92.51
TIGR02917		899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	92.44
TIGR02795		119	tol_pal_ybgF tol-pal system protein YbgF. Members	91.95
PF12569		517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	91.66
PF13414		69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	91.56
PF13174		33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	91.42
PF12895		84	Apc3: Anaphase-promoting complex, cyclosome, subun	90.77
PF03399		204	SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; I	90.67
PF09012		69	FeoC: FeoC like transcriptional regulator; InterPr	90.58
PF04733		290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	90.33
PRK15359		144	type III secretion system chaperone protein SscB;	90.1
PRK11447		1157	cellulose synthase subunit BcsC; Provisional	89.98
PF13181		34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	89.78
KOG1840		508	consensus Kinesin light chain [Cytoskeleton]	89.69
PRK04841		903	transcriptional regulator MalT; Provisional	89.57
PRK10370		198	formate-dependent nitrite reductase complex subuni	89.47
PRK11189		296	lipoprotein NlpI; Provisional	89.4
PRK12370		553	invasion protein regulator; Provisional	89.33
PRK10049		765	pgaA outer membrane protein PgaA; Provisional	89.28
cd05804		355	StaR_like StaR_like; a well-conserved protein foun	89.0
cd00189		100	TPR Tetratricopeptide repeat domain; typically con	88.99
PLN03077		857	Protein ECB2; Provisional	88.61
PLN03218		1060	maturation of RBCL 1; Provisional	88.39
PF13414		69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	87.97
CHL00033		168	ycf3 photosystem I assembly protein Ycf3	87.79
PRK15174		656	Vi polysaccharide export protein VexE; Provisional	87.61
PF09295		395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	87.22
PRK04841		903	transcriptional regulator MalT; Provisional	87.22
KOG2002		1018	consensus TPR-containing nuclear phosphoprotein th	86.99
cd05804		355	StaR_like StaR_like; a well-conserved protein foun	86.9
KOG1840		508	consensus Kinesin light chain [Cytoskeleton]	86.8
PRK14574		822	hmsH outer membrane protein; Provisional	86.74
PF13429		280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	86.23
TIGR03302		235	OM_YfiO outer membrane assembly lipoprotein YfiO.	85.83
PRK02603		172	photosystem I assembly protein Ycf3; Provisional	85.73
PLN03088		356	SGT1, suppressor of G2 allele of SKP1; Provisional	85.66
PRK10866		243	outer membrane biogenesis protein BamD; Provisiona	85.09
PLN03218		1060	maturation of RBCL 1; Provisional	84.83
PRK12370		553	invasion protein regulator; Provisional	84.64
PRK15174		656	Vi polysaccharide export protein VexE; Provisional	84.21
PLN03077		857	Protein ECB2; Provisional	84.2
PF08784		102	RPA_C: Replication protein A C terminal; InterPro:	84.12
KOG1173		611	consensus Anaphase-promoting complex (APC), Cdc16	83.9
PRK11189		296	lipoprotein NlpI; Provisional	83.46
PF12569		517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	82.53
PRK10049		765	pgaA outer membrane protein PgaA; Provisional	82.31
PF13176		36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	82.23
PF10345		608	Cohesin_load: Cohesin loading factor; InterPro: IP	81.66
PF12895		84	Apc3: Anaphase-promoting complex, cyclosome, subun	81.5
smart00028		34	TPR Tetratricopeptide repeats. Repeats present in	81.44
PF14559		68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	81.35
PRK02603		172	photosystem I assembly protein Ycf3; Provisional	81.12
KOG2002		1018	consensus TPR-containing nuclear phosphoprotein th	80.9
PRK15331		165	chaperone protein SicA; Provisional	80.58
PF13428		44	TPR_14: Tetratricopeptide repeat	80.39
PF13424		78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	80.31
PRK11906		458	transcriptional regulator; Provisional	80.28

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

Probab=100.00  E-value=4.1e-116  Score=879.69  Aligned_cols=485  Identities=57%  Similarity=0.846  Sum_probs=458.7

Q ss_pred             CCccccCCCCCC--CCCCCCCCCCcchHHHHHHHHHHHHhhhcccchhHHHHHHhhhHHHhcccChHHHHHHHHHHcCCC
Q 011352            1 MTQDVEMKDKEN--PSNSLSSPFTPSTLHHLKEIASLMETGAHAREVRRIMRAVRLTMALRRKLKAPVLSAFLNFALAPG   78 (488)
Q Consensus         1 m~~~~~~~~~~~--~~~~~~~~~~~~~~~~i~~~~~li~k~v~~~~~r~~~r~lr~~~~~r~~l~~~~l~~~~~~~~~~~   78 (488)
                      |++||||++.+.  +..+.+...+..++++|++++.+|+|+|.++|||||||+||.++++|++|+..+|..+++.++|++
T Consensus         4 ~~~~~e~d~~~~~~~~~~~~k~~~~~~vq~ike~~~~i~kg~~tke~r~I~R~lr~l~~~r~kln~~vL~~~v~~~~~~~   83 (493)
T KOG2581|consen    4 GAQDVEMDDNGVADTATQSKKSADTSTVQNIKEQLAQIDKGVYTKEPRFILRALRLLPSTRRKLNGAVLYKLVSSLLSSG   83 (493)
T ss_pred             cceeeeecccccccccchhcccccHHHHHHHHHHHHHHhccccccchHHHHHHHHhhhhhHhhhhHHHHHHHHHHHcCCc
Confidence            567899998742  223333334888999999999999999999999999999999999999999999999999999999


Q ss_pred             chhHHHHHhcCCCCCCcccccccCCCCCCC-CC-CCCCCHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHHHhhhhhh
Q 011352           79 SEAHSRLLSYLPKEDEHEMEVDTASSGAPA-PA-KHPLPELEIYCYLLVLIFLIDKKRYNEAKACSSASIARLKNMNRRT  156 (488)
Q Consensus        79 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~-~~-~~~~p~~e~~~~ll~~~~l~d~~~~~~A~~~~~~lv~~l~~~~~r~  156 (488)
                      +++++.++++++......++.+...+.+++ +. .+..||+|+|+++|++++++|+++|++|.+++.+++..+..+|+|+
T Consensus        84 se~~~~~l~fv~~~~~~~~p~~~~s~~t~~a~~~k~~~~Ei~aY~~lLv~Lfl~d~K~~kea~~~~~~~l~~i~~~nrRt  163 (493)
T KOG2581|consen   84 SEAMDRLLRFVPAFDKNIKPLDTDSPNTQSALKRKPLPAEIEAYLYLLVLLFLIDQKEYKEADKISDALLASISIQNRRT  163 (493)
T ss_pred             hHHHHHHHhhcccccccCCcccccccccccccccCCchHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcchhh
Confidence            999999999998877655544443222222 23 5566799999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHhhhcCCcccHHHHHHHHHHHHHccCCHHHHHHHHhcCCCCccCCh
Q 011352          157 VDVLAARLYFYYSLCYELTGDLAEIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLRSKAPRFEAHSN  236 (488)
Q Consensus       157 ld~l~ak~~~y~s~~~e~~~~l~~~r~~L~~~~rta~~~~~~~~~~~l~n~llr~Yl~~~~~~~a~~li~~~~~pe~~~~  236 (488)
                      +|.+.||+|||+++++|..+++..+|+.|++.+|||+++|+..||++++|||||+|++.+.|++|+++++++.+|++.++
T Consensus       164 lD~i~ak~~fy~~l~~E~~~~l~~~rs~l~~~lrtAtLrhd~e~qavLiN~LLr~yL~n~lydqa~~lvsK~~~pe~~sn  243 (493)
T KOG2581|consen  164 LDLIAAKLYFYLYLSYELEGRLADIRSFLHALLRTATLRHDEEGQAVLINLLLRNYLHNKLYDQADKLVSKSVYPEAASN  243 (493)
T ss_pred             HHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHhhhcCcchhHHHHHHHHHHHHhhhHHHHHHHHHhhcccCcccccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCCc-cchhhHHHHHHHHHHHHHhcCCCCCcchhcchhhhhhhhhHHH
Q 011352          237 QQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPV-AALGFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFE  315 (488)
Q Consensus       237 ~~~v~Y~YY~Gri~~~~~dy~~A~~~L~~A~~~~P~-~~~~~~~~alK~lIlv~LL~G~iP~~~ll~~~~l~~~l~~Y~~  315 (488)
                      ++++||+||.|+|.++++||+.|.+||.+|++++|+ .+.||++++.|++|+++||+|+||+++.|+++++++.|.||+.
T Consensus       244 ne~ARY~yY~GrIkaiqldYssA~~~~~qa~rkapq~~alGf~q~v~k~~ivv~ll~geiPers~F~Qp~~~ksL~~Yf~  323 (493)
T KOG2581|consen  244 NEWARYLYYLGRIKAIQLDYSSALEYFLQALRKAPQHAALGFRQQVNKLMIVVELLLGEIPERSVFRQPGMRKSLRPYFK  323 (493)
T ss_pred             HHHHHHHHHHhhHHHhhcchhHHHHHHHHHHHhCcchhhhhHHHHHHHHHHHHHHHcCCCcchhhhcCccHHHHHHHHHH
Confidence            999999999999999999999999999999999997 6799999999999999999999999999999999999999999


Q ss_pred             HHHHHhcCCHHHHHHHHHHcchhhhcCcchHHHHHHHHHHHHHhHHHHHHhhccccHHHHHHHhcCCCCCChHHHHHHHH
Q 011352          316 LTNAVRIGDLELFKSVAEKFSSTFSSDRTNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVS  395 (488)
Q Consensus       316 L~~Av~~Gdl~~f~~~l~~~~~~f~~D~~~~Lv~rLr~~vir~~ir~i~~~YsrIsL~dIa~~L~l~~~~d~eeaE~ila  395 (488)
                      |++|||.||+++|++++++|...|..||+|.|+.|||+||||++||+|+.+|||||+.|||.+|+++++   ++||+||+
T Consensus       324 Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~LivRLR~NVIkTgIR~ISlsYSRISl~DIA~kL~l~Se---ed~EyiVa  400 (493)
T KOG2581|consen  324 LTQAVRLGDLKKFNETLEQFKDKFQADGTYTLIVRLRHNVIKTGIRKISLSYSRISLQDIAKKLGLNSE---EDAEYIVA  400 (493)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhheeeeeeeccHHHHHHHhcCCCc---hhHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999999997   88999999


Q ss_pred             HHHHcCCcceEeeCCCcEEEEcccCcccCCccccHHHHHHHHHHHHhhHHHHHhcCCCCCCCcchhhHHHHHHhhHHHHH
Q 011352          396 KAIRDGAIDATVDHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVRALRFPPNSHKEKESAEKRRERQQQEQE  475 (488)
Q Consensus       396 ~mI~dG~I~A~Id~~~G~v~~~~~~dv~s~~ep~~~l~~rI~~~l~l~~~~v~amr~p~~~~~~~~~~~~~~~~~~~~~e  475 (488)
                      ++|+||.|+|+|||++|||.+++..++|++.+|+.+|+.||+||++|||++|+||||||+.++++|++|++||||||+.|
T Consensus       401 kAIRDGvIea~Id~~~g~m~skE~~diy~t~epQ~~f~~rI~fCl~LhN~~vkamRyPp~~~~~~Es~E~~rereqq~~e  480 (493)
T KOG2581|consen  401 KAIRDGVIEAKIDHEDGFMQSKETFDIYSTREPQTAFDERIRFCLQLHNEAVKAMRYPPKKKKDLESAEKRREREQQELE  480 (493)
T ss_pred             HHHHhccceeeeccccCceehhhhhhhhccCCchhhHhHHHHHHHHHHHHHHHHhcCCCcchhhHHHHHHhhhhhhhHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhcccCCCCC
Q 011352          476 LAKHIAEEDDDEF  488 (488)
Q Consensus       476 ~~~~~~~~~~~~~  488 (488)
                      +||||+|+|||||
T Consensus       481 ~akemae~Ddd~F  493 (493)
T KOG2581|consen  481 LAKEMAEEDDDDF  493 (493)
T ss_pred             HHHHhhhcccCCC
Confidence            9999999999999

>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

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

>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

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

>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]	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

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

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

>COG5071 RPN5 26S proteasome regulatory complex component [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

>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

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

>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]	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

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

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

>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional	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

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

>PF13371 TPR_9: Tetratricopeptide repeat	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

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

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

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

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

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

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW	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

>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

>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

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

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

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A	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

>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

>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional	Back alignment and domain information

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

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]	Back alignment and domain information

>KOG2300 consensus Uncharacterized conserved protein [Function unknown]	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

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

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF	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

>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

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

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

>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

>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

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

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

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

>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

>KOG1840 consensus Kinesin light chain [Cytoskeleton]	Back alignment and domain information

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

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

>PRK11189 lipoprotein NlpI; Provisional	Back alignment and domain information

>PRK12370 invasion protein regulator; Provisional	Back alignment and domain information

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

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

Back alignment and domain information

>PLN03077 Protein ECB2; Provisional	Back alignment and domain information

>PLN03218 maturation of RBCL 1; 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

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

>PRK15174 Vi polysaccharide export protein VexE; Provisional	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

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

>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]	Back alignment and domain information

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

>KOG1840 consensus Kinesin light chain [Cytoskeleton]	Back alignment and domain information

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

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

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

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

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

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

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

>PRK12370 invasion protein regulator; Provisional	Back alignment and domain information

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

>PLN03077 Protein ECB2; Provisional	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

>KOG1173 consensus Anaphase-promoting complex (APC), Cdc16 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PRK11189 lipoprotein NlpI; Provisional	Back alignment and domain information

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

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

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

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

>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

>smart00028 TPR Tetratricopeptide repeats	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

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

>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]	Back alignment and domain information

>PRK15331 chaperone protein SicA; Provisional	Back alignment and domain information

>PF13428 TPR_14: Tetratricopeptide repeat	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

>PRK11906 transcriptional regulator; 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		488
4b4t_S		523	Near-Atomic Resolution Structural Model Of The Yeas		1e-56

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

Back alignment and structure

Iteration: 1

Score = 217 bits (552), Expect = 1e-56, Method: Compositional matrix adjust. Identities = 128/356 (35%), Positives = 197/356 (55%), Gaps = 20/356 (5%) Query: 116 ELEIYCYLLVLIFLIDKKRYNEAKACSSASIA--RLKNMNRRTVDVLAARLYFYYSLCYE 173 E+ + +LLV +FL D K + + + L N R+++++ A+L+FY L +E Sbjct: 133 EINCFMHLLVQLFLWDSKELEQLVEFNRKVVIPNLLCYYNLRSLNLINAKLWFYIYLSHE 192 Query: 174 LTGDLAE----------IRGNLLALHRIATLRHDELGQETXXXXXXXXXXXXXXXDQAEK 223 +E +R ++ +IA+L+HD + D A Sbjct: 193 TLARSSEEINSDNQNIILRSTMMKFLKIASLKHDNETKAMLINLILRDFLNNGEVDSASD 252 Query: 224 LRSKA--PRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAP--VAALGFRV 279 SK P + S+ + RY FYL KI IQL+Y+ A E ++ A RKAP +LGF Sbjct: 253 FISKLEYPHTDVSSSLE-ARYFFYLSKINAIQLDYSTANEYIIAAIRKAPHNSKSLGFLQ 311 Query: 280 QCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFSSTF 339 Q NK ++LL+G+IPE + F Q M+K+L PY+ LT AV++GDL+ F S K+ Sbjct: 312 QSNKLHCCIQLLMGDIPELSFFHQSNMQKSLLPYYHLTKAVKLGDLKKFTSTITKYKQLL 371 Query: 340 SSDRTNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIR 399 D T L VRLR NVI+TG+R IS++Y +ISL D+ KL LDS V E +VS+AIR Sbjct: 372 LKDDTYQLCVRLRSNVIKTGIRIISLTYKKISLRDICLKLNLDSEQTV---EYMVSRAIR 428 Query: 400 DGAIDATVDHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVRALRFPPN 455 DG I+A ++H +G++ + E +IY + +PQ F+ RI F +H+E + ++R+P + Sbjct: 429 DGVIEAKINHEDGFIETTELLNIYDSEDPQQVFDERIKFANQLHDEYLVSMRYPED 484

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		488
3t5v_B		455	Nuclear mRNA export protein THP1; PCI, mRNA nuclea	7e-54
3t5x_A		203	PCI domain-containing protein 2; PCI, mRNA nuclear	5e-50
3txn_A		394	26S proteasome regulatory complex subunit P42B; PC	9e-17
1ufm_A		84	COP9 complex subunit 4; helix-turn-helix, structur	2e-06
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-04

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

 Score =  186 bits (474), Expect = 7e-54
 Identities = 39/278 (14%), Positives = 88/278 (31%), Gaps = 39/278 (14%)

Query: 204 LLNLLLRNYLHYNLYDQAEKL------RSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYT 257
           L+N L   Y           +      +S    F  +   Q   Y + LG+   +  +  
Sbjct: 178 LVNKLNNIYFRIESPQLCSNIFKNFQPKSMLAHFNEYQLDQQIEYRYLLGRYYLLNSQVH 237

Query: 258 DAKESLLQAARKAPVAALGFRVQ------CNKWAIIVRLLLGEIPERTVFMQKGMEKALR 311
           +A     +A +      L  +           + I   L+LG++ +         ++ + 
Sbjct: 238 NAFVQFNEAFQSLLNLPLTNQAITRNGTRILNYMIPTGLILGKMVKWGPLRPFLSQETID 297

Query: 312 PYFELTNAVRIGDLELFKSVAEKFSSTFSSDRTNNLIV-RLRHNVIRTGLRNISISY--- 367
            +  L   VR G+++       +      + +   +++ +L     R  ++ +  S+   
Sbjct: 298 NWSVLYKHVRYGNIQGVSLWLRQNERHLCARQLLIVLLEKLPMVTYRNLIKTVIKSWTTE 357

Query: 368 ---SRISLADVAKKLRLDSANPVA-----------------DAESIVSKAIRDGAIDATV 407
              +++  + + + L+L                        + E+++   I  G + A  
Sbjct: 358 WGQNKLPYSLIERVLQLSIGPTFEDPGAQEITIYNGIHSPKNVENVLVTLINLGLLRANC 417

Query: 408 DHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNE 445
                  V K+T  I    E     N RI      H+ 
Sbjct: 418 FPQLQLCVVKKTTMI---QEIVPPVNERITKMFPAHSH 452

PyMOL of 3t5v

>3t5x_A PCI domain-containing protein 2; PCI, mRNA nuclear export, transcription; 2.12A {Homo sapiens} Length = 203	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 Length = 394	Back alignment and structure

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

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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		488
4b4t_S		523	RPN3, 26S proteasome regulatory subunit RPN3; hydr	100.0
3t5v_B		455	Nuclear mRNA export protein THP1; PCI, mRNA nuclea	100.0
3t5x_A		203	PCI domain-containing protein 2; PCI, mRNA nuclear	100.0
4b4t_P		445	26S proteasome regulatory subunit RPN5; hydrolase,	99.94
3txn_A		394	26S proteasome regulatory complex subunit P42B; PC	99.94
4b4t_Q		434	26S proteasome regulatory subunit RPN6; hydrolase,	99.87
4b4t_R		429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	99.7
4b4t_O		393	26S proteasome regulatory subunit RPN9; hydrolase,	99.68
4b0z_A		229	RPN12, 26S proteasome regulatory subunit RPN12; pr	99.49
1ufm_A		84	COP9 complex subunit 4; helix-turn-helix, structur	99.19
1qqe_A		292	Vesicular transport protein SEC17; helix-turn-heli	98.28
3ro3_A		164	PINS homolog, G-protein-signaling modulator 2; asy	98.16
3chm_A		169	COP9 signalosome complex subunit 7; heat/ARM repea	98.14
3ulq_A		383	Response regulator aspartate phosphatase F; tetrat	98.11
3ro2_A		338	PINS homolog, G-protein-signaling modulator 2; TPR	98.02
3gw4_A		203	Uncharacterized protein; structural genomics, PSI-	98.01
3sf4_A		406	G-protein-signaling modulator 2; tetratricopeptide	97.96
3sf4_A		406	G-protein-signaling modulator 2; tetratricopeptide	97.95
3ro2_A		338	PINS homolog, G-protein-signaling modulator 2; TPR	97.94
4a1s_A		411	PINS, partner of inscuteable; cell cycle, LGN, mit	97.91
4a1s_A		411	PINS, partner of inscuteable; cell cycle, LGN, mit	97.88
3q15_A		378	PSP28, response regulator aspartate phosphatase H;	97.88
2ifu_A		307	Gamma-SNAP; membrane fusion, snare complex disasse	97.81
3ulq_A		383	Response regulator aspartate phosphatase F; tetrat	97.69
3gw4_A		203	Uncharacterized protein; structural genomics, PSI-	97.57
3q15_A		378	PSP28, response regulator aspartate phosphatase H;	97.55
3ro3_A		164	PINS homolog, G-protein-signaling modulator 2; asy	97.45
3nf1_A		311	KLC 1, kinesin light chain 1; TPR, structural geno	97.39
3u3w_A		293	Transcriptional activator PLCR protein; ternary co	97.37
1qqe_A		292	Vesicular transport protein SEC17; helix-turn-heli	97.35
2qfc_A		293	PLCR protein; TPR, HTH, transcription regulation;	97.34
3nf1_A		311	KLC 1, kinesin light chain 1; TPR, structural geno	97.32
4b4t_Q		434	26S proteasome regulatory subunit RPN6; hydrolase,	97.32
2ifu_A		307	Gamma-SNAP; membrane fusion, snare complex disasse	97.32
1hz4_A		373	MALT regulatory protein; two-helix bundles, helix	97.27
2ho1_A		252	Type 4 fimbrial biogenesis protein PILF; type IV p	97.25
3uq3_A		258	Heat shock protein STI1; HSP90, peptide binding, c	97.22
3edt_B		283	KLC 2, kinesin light chain 2; superhelical, struct	97.21
3edt_B		283	KLC 2, kinesin light chain 2; superhelical, struct	97.19
1hh8_A		213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	97.17
1hz4_A		373	MALT regulatory protein; two-helix bundles, helix	97.15
3u3w_A		293	Transcriptional activator PLCR protein; ternary co	97.08
2qfc_A		293	PLCR protein; TPR, HTH, transcription regulation;	97.07
3uq3_A		258	Heat shock protein STI1; HSP90, peptide binding, c	96.93
2vq2_A		225	PILW, putative fimbrial biogenesis and twitching m	96.93
4i17_A		228	Hypothetical protein; TPR repeats protein, structu	96.88
3qky_A		261	Outer membrane assembly lipoprotein YFIO; membrane	96.87
4eqf_A		365	PEX5-related protein; accessory protein, tetratric	96.83
3as5_A		186	MAMA; tetratricopeptide repeats (TPR) containing p	96.77
2ho1_A		252	Type 4 fimbrial biogenesis protein PILF; type IV p	96.74
2yhc_A		225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	96.62
3qky_A		261	Outer membrane assembly lipoprotein YFIO; membrane	96.56
2q7f_A		243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	96.54
3hym_B		330	Cell division cycle protein 16 homolog; APC, anaph	96.52
2vq2_A		225	PILW, putative fimbrial biogenesis and twitching m	96.48
3as5_A		186	MAMA; tetratricopeptide repeats (TPR) containing p	96.48
2fo7_A		136	Synthetic consensus TPR protein; tetratricopeptide	96.45
3vtx_A		184	MAMA; tetratricopeptide repeats (TPR) containing p	96.37
2vyi_A		131	SGTA protein; chaperone, TPR repeat, phosphoprotei	96.25
2q7f_A		243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	96.25
1fch_A		368	Peroxisomal targeting signal 1 receptor; protein-p	96.18
3hym_B		330	Cell division cycle protein 16 homolog; APC, anaph	96.16
4eqf_A		365	PEX5-related protein; accessory protein, tetratric	96.06
1elr_A		131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	95.96
3sz7_A		164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	95.91
3ieg_A		359	DNAJ homolog subfamily C member 3; TPR motif, chap	95.88
3urz_A		208	Uncharacterized protein; tetratricopeptide repeats	95.87
2y4t_A		450	DNAJ homolog subfamily C member 3; chaperone, endo	95.86
1fch_A		368	Peroxisomal targeting signal 1 receptor; protein-p	95.7
3rkv_A		162	Putative peptidylprolyl isomerase; structural geno	95.63
1na0_A		125	Designed protein CTPR3; de novo protein; HET: IPT;	95.62
3vtx_A		184	MAMA; tetratricopeptide repeats (TPR) containing p	95.61
3fp2_A		537	TPR repeat-containing protein YHR117W; TOM71, mito	95.6
3u4t_A		272	TPR repeat-containing protein; structural genomics	95.59
2gw1_A		514	Mitochondrial precursor proteins import receptor;	95.54
3mkr_A		291	Coatomer subunit epsilon; tetratricopeptide repeat	95.45
3ieg_A		359	DNAJ homolog subfamily C member 3; TPR motif, chap	95.41
2xpi_A		597	Anaphase-promoting complex subunit CUT9; cell cycl	95.35
2vgx_A		148	Chaperone SYCD; alternative dimer assembly, tetrat	95.32
1xnf_A		275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	95.26
3gyz_A		151	Chaperone protein IPGC; asymmetric homodimer, tetr	95.21
2pl2_A		217	Hypothetical conserved protein TTC0263; TPR, prote	95.18
1xnf_A		275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	95.15
3cv0_A		327	Peroxisome targeting signal 1 receptor PEX5; TPR m	95.14
2fbn_A		198	70 kDa peptidylprolyl isomerase, putative; sulfur	95.12
2xev_A		129	YBGF; tetratricopeptide, alpha-helical, metal bind	95.11
3fp2_A		537	TPR repeat-containing protein YHR117W; TOM71, mito	95.07
2xcb_A		142	PCRH, regulatory protein PCRH; protein transport,	95.04
4b4t_T		274	26S proteasome regulatory subunit RPN12; hydrolase	95.03
4i17_A		228	Hypothetical protein; TPR repeats protein, structu	94.98
3q49_B		137	STIP1 homology and U box-containing protein 1; E3	94.96
3cv0_A		327	Peroxisome targeting signal 1 receptor PEX5; TPR m	94.93
2y4t_A		450	DNAJ homolog subfamily C member 3; chaperone, endo	94.93
2lni_A		133	Stress-induced-phosphoprotein 1; structural genomi	94.81
1a17_A		166	Serine/threonine protein phosphatase 5; hydrolase,	94.76
4gco_A		126	Protein STI-1; structural genomics, PSI-biology, m	94.66
2gw1_A		514	Mitochondrial precursor proteins import receptor;	94.64
1elw_A		118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	94.64
1a17_A		166	Serine/threonine protein phosphatase 5; hydrolase,	94.58
2dba_A		148	Smooth muscle cell associated protein-1, isoform 2	94.58
2xpi_A		597	Anaphase-promoting complex subunit CUT9; cell cycl	94.55
2fo7_A		136	Synthetic consensus TPR protein; tetratricopeptide	94.53
3upv_A		126	Heat shock protein STI1; TPR-fold, adaptor protein	94.52
1w3b_A		388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	94.47
3u4t_A		272	TPR repeat-containing protein; structural genomics	94.39
4gyw_A		723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	94.38
1kt0_A		457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	94.36
2pl2_A		217	Hypothetical conserved protein TTC0263; TPR, prote	94.08
4abn_A		474	Tetratricopeptide repeat protein 5; P53 cofactor,	93.99
1p5q_A		336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	93.98
2e2e_A		177	Formate-dependent nitrite reductase complex NRFG;	93.91
1w3b_A		388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	93.91
4abn_A		474	Tetratricopeptide repeat protein 5; P53 cofactor,	93.87
4ga2_A		150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	93.63
2vsy_A		568	XCC0866; transferase, glycosyl transferase, GT-B,	93.59
4gcn_A		127	Protein STI-1; structural genomics, PSI-biology, m	93.56
2h6f_A		382	Protein farnesyltransferase/geranylgeranyltransfer	93.38
2kck_A		112	TPR repeat; tetratricopeptide repeat, structural g	93.09
1p5q_A		336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	93.04
1ihg_A		370	Cyclophilin 40; ppiase immunophilin tetratricopept	93.0
2l6j_A		111	TPR repeat-containing protein associated with HSP;	92.6
3k9i_A		117	BH0479 protein; putative protein binding protein,	92.58
2vsy_A		568	XCC0866; transferase, glycosyl transferase, GT-B,	92.51
1na3_A		91	Designed protein CTPR2; de novo protein; HET: IPT;	92.43
3mv2_B		310	Coatomer subunit epsilon; vesicular membrane coat	92.37
2yhc_A		225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	92.34
4ga2_A		150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	92.26
3ma5_A		100	Tetratricopeptide repeat domain protein; NESG, str	92.19
2kc7_A		99	BFR218_protein; tetratricopeptide repeat, all-alph	91.87
2pzi_A		681	Probable serine/threonine-protein kinase PKNG; ATP	91.72
3n71_A		490	Histone lysine methyltransferase SMYD1; heart deve	91.52
1hxi_A		121	PEX5, peroxisome targeting signal 1 receptor PEX5;	91.22
2ond_A		308	Cleavage stimulation factor 77 kDa subunit; HAT do	91.04
1hh8_A		213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	90.89
1ouv_A		273	Conserved hypothetical secreted protein; TPR repea	90.84
2kat_A		115	Uncharacterized protein; NESG, structure, structur	90.52
1elw_A		118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	90.5
2xev_A		129	YBGF; tetratricopeptide, alpha-helical, metal bind	89.97
3sz7_A		164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	89.95
1elr_A		131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	89.46
3q49_B		137	STIP1 homology and U box-containing protein 1; E3	89.4
2kck_A		112	TPR repeat; tetratricopeptide repeat, structural g	89.29
2hr2_A		159	Hypothetical protein; alpha-alpha superhelix fold,	89.24
3urz_A		208	Uncharacterized protein; tetratricopeptide repeats	89.22
3mv2_B		310	Coatomer subunit epsilon; vesicular membrane coat	89.12
3mkr_A		291	Coatomer subunit epsilon; tetratricopeptide repeat	88.92
2h6f_A		382	Protein farnesyltransferase/geranylgeranyltransfer	88.55
4gco_A		126	Protein STI-1; structural genomics, PSI-biology, m	88.48
3upv_A		126	Heat shock protein STI1; TPR-fold, adaptor protein	88.37
4gcn_A		127	Protein STI-1; structural genomics, PSI-biology, m	88.28
1ouv_A		273	Conserved hypothetical secreted protein; TPR repea	88.22
3n71_A		490	Histone lysine methyltransferase SMYD1; heart deve	88.21
2vyi_A		131	SGTA protein; chaperone, TPR repeat, phosphoprotei	88.21
1na0_A		125	Designed protein CTPR3; de novo protein; HET: IPT;	88.17
3qww_A		433	SET and MYND domain-containing protein 2; methyltr	88.16
2dba_A		148	Smooth muscle cell associated protein-1, isoform 2	88.01
2lni_A		133	Stress-induced-phosphoprotein 1; structural genomi	87.87
1hxi_A		121	PEX5, peroxisome targeting signal 1 receptor PEX5;	87.78
2xcb_A		142	PCRH, regulatory protein PCRH; protein transport,	87.75
2vgx_A		148	Chaperone SYCD; alternative dimer assembly, tetrat	87.43
2ond_A		308	Cleavage stimulation factor 77 kDa subunit; HAT do	87.41
4g1t_A		472	Interferon-induced protein with tetratricopeptide	87.14
2pzi_A		681	Probable serine/threonine-protein kinase PKNG; ATP	86.52
3gyz_A		151	Chaperone protein IPGC; asymmetric homodimer, tetr	86.36
2if4_A		338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	85.89
4g1t_A		472	Interferon-induced protein with tetratricopeptide	85.77
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	85.75
4gyw_A		723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	85.18
2v5f_A		104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	84.21
2fbn_A		198	70 kDa peptidylprolyl isomerase, putative; sulfur	83.96
2l6j_A		111	TPR repeat-containing protein associated with HSP;	83.88
3ma5_A		100	Tetratricopeptide repeat domain protein; NESG, str	83.72
1wao_1		477	Serine/threonine protein phosphatase 5; hydrolase,	83.5
1wao_1		477	Serine/threonine protein phosphatase 5; hydrolase,	83.01
3qwp_A		429	SET and MYND domain-containing protein 3; SMYD3,SE	82.81
2ooe_A		530	Cleavage stimulation factor 77 kDa subunit; HAT do	82.28
2r5s_A		176	Uncharacterized protein VP0806; APC090868.1, vibri	82.22
1ihg_A		370	Cyclophilin 40; ppiase immunophilin tetratricopept	81.64
3rkv_A		162	Putative peptidylprolyl isomerase; structural geno	80.89
1rz4_A		226	Eukaryotic translation initiation factor 3 subuni;	80.66
1wi9_A		72	Protein C20ORF116 homolog; helix-turn-helix motif,	80.61
3rjv_A		212	Putative SEL1 repeat protein; alpha-alpha superhel	80.27
2heo_A		67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	80.24

>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=2.5e-106  Score=857.08  Aligned_cols=458  Identities=32%  Similarity=0.545  Sum_probs=234.5

Q ss_pred             CcchHHHHHHHHHHHHhhhcccchhHHHHHHhhhHHHhcc--cChHHHHHHHHHHcCCCchhHHHHHhcCCCCCCccc--
Q 011352           22 TPSTLHHLKEIASLMETGAHAREVRRIMRAVRLTMALRRK--LKAPVLSAFLNFALAPGSEAHSRLLSYLPKEDEHEM--   97 (488)
Q Consensus        22 ~~~~~~~i~~~~~li~k~v~~~~~r~~~r~lr~~~~~r~~--l~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~--   97 (488)
                      ++.++++|++++++|||||.++|+|||+||||.++++||+  |++++|..+|+.+||++++.+..|+++|+.++..++  
T Consensus        27 ~~~~~~~i~~~~~~i~k~v~~~~~r~~~r~lr~~~~~rk~~~l~~~~l~~~i~~~~~~~~~~~~~ll~~l~~~~~~~~~~  106 (523)
T 4b4t_S           27 EEDQVQELLKVLNEISKTTLTLDPRYIWRSLKDLSSLRNQELLNAETLCFTVNVLYPDSSSFKKNLLKFITSNHKSSVPG  106 (523)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhhhhhcccccCCHHHHHHHHHHHCCCCcHHHHHHHHHhcccccccccc
Confidence            7888999999999999999999999999999999999999  999999999999999999999999999986543222  


Q ss_pred             --ccccCCCC------CCCCCCCCCCHHHHHHHHHHHHHHHcccCHHHHHHHHHHHH--HHHHhhhhhhHHHHHHHHHHH
Q 011352           98 --EVDTASSG------APAPAKHPLPELEIYCYLLVLIFLIDKKRYNEAKACSSASI--ARLKNMNRRTVDVLAARLYFY  167 (488)
Q Consensus        98 --~~~~~~~~------~~~~~~~~~p~~e~~~~ll~~~~l~d~~~~~~A~~~~~~lv--~~l~~~~~r~ld~l~ak~~~y  167 (488)
                        +.+...+.      ...+..+++||+|+|+++|++++++|+++|++|.+|+..++  +.++.+||||+|.|.||+|||
T Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~~~~pE~~~y~~lL~~i~L~d~k~~~~~~~~~~~~~~~~~l~~~nrrtlD~l~ak~~fY  186 (523)
T 4b4t_S          107 SAELRNSYPASFYSVNTEKKTIEVTAEINCFMHLLVQLFLWDSKELEQLVEFNRKVVIPNLLCYYNLRSLNLINAKLWFY  186 (523)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             chhccccCcccccccCCCCCCCCCChHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHH
Confidence              22111111      11245667999999999999999999999999999999999  679999999999999999999


Q ss_pred             HHHHHHhhccHH----------HHHHHHHHHHHHhhhcCCcccHHHHHHHHHHHHHccCCHHHHHHHHhcCCCCcc-CCh
Q 011352          168 YSLCYELTGDLA----------EIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLRSKAPRFEA-HSN  236 (488)
Q Consensus       168 ~s~~~e~~~~l~----------~~r~~L~~~~rta~~~~~~~~~~~l~n~llr~Yl~~~~~~~a~~li~~~~~pe~-~~~  236 (488)
                      |+++||+.+++.          ++|+.|++++|||++|||..||++++|+++|+|++.|.|+||.+++++++||++ .++
T Consensus       187 ~s~~~e~~~~~~~~~~~~~~~~~ir~~Ll~~~rta~lr~D~~~qa~l~nllLRnYL~~~~y~qA~~lvsk~~fP~~~~sn  266 (523)
T 4b4t_S          187 IYLSHETLARSSEEINSDNQNIILRSTMMKFLKIASLKHDNETKAMLINLILRDFLNNGEVDSASDFISKLEYPHTDVSS  266 (523)
T ss_dssp             ----------------CHHHHHHHHTHHHHHHHHCCSCSSSCHHHHHHHHHHHHHHHSSCSTTHHHHHHHHCSCTTTSCH
T ss_pred             HHHHHHHhcccccccccccchhhHHHHHHHHHHHHhcccCcchhHHHHHHHHHHHHccCcHHHHHHHHhcCcCCcccCCH
Confidence            999999988664          489999999999999999999999999999999999999999999999999986 899


Q ss_pred             hHHHHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCCc--cchhhHHHHHHHHHHHHHhcCCCCCcchhcchhhhhhhhhHH
Q 011352          237 QQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPV--AALGFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYF  314 (488)
Q Consensus       237 ~~~v~Y~YY~Gri~~~~~dy~~A~~~L~~A~~~~P~--~~~~~~~~alK~lIlv~LL~G~iP~~~ll~~~~l~~~l~~Y~  314 (488)
                      +|+++|+||.|||++++++|.+|+++|.+|+++||+  .+.+|++.++||+|+|+||+|++|++++|.++.+++.|.||.
T Consensus       267 ~q~~rY~YY~GRI~a~q~~Y~eA~~~L~~A~rkap~~~~a~gfr~~a~K~lI~V~LLlG~iP~r~lf~q~~l~~~L~pY~  346 (523)
T 4b4t_S          267 SLEARYFFYLSKINAIQLDYSTANEYIIAAIRKAPHNSKSLGFLQQSNKLHCCIQLLMGDIPELSFFHQSNMQKSLLPYY  346 (523)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTSSCSCSSSCSHHHHHHHHHHHHHHHHHTCCCCHHHHTTTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCcchhhhhHHHHHHHHHHhHHhhcCCCCChHHhhchhHHHHHHHHH
Confidence            999999999999999999999999999999999998  357999999999999999999999999999999998999999


Q ss_pred             HHHHHHhcCCHHHHHHHHHHcchhhhcCcchHHHHHHHHHHHHHhHHHHHHhhccccHHHHHHHhcCCCCCChHHHHHHH
Q 011352          315 ELTNAVRIGDLELFKSVAEKFSSTFSSDRTNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIV  394 (488)
Q Consensus       315 ~L~~Av~~Gdl~~f~~~l~~~~~~f~~D~~~~Lv~rLr~~vir~~ir~i~~~YsrIsL~dIa~~L~l~~~~d~eeaE~il  394 (488)
                      +|++||+.||+..|++++++|+..|.+||||+||+||+++|+|++||+++++|++||++|||.+|+++++   ++|||+|
T Consensus       347 ~Lv~Avr~GdL~~F~~~L~~h~~~F~~Dgty~LI~rLr~~vir~~irkis~~YsrIsL~dIa~kL~L~s~---eeaE~iV  423 (523)
T 4b4t_S          347 HLTKAVKLGDLKKFTSTITKYKQLLLKDDTYQLCVRLRSNVIKTGIRIISLTYKKISLRDICLKLNLDSE---QTVEYMV  423 (523)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHTHHHHHHTTCTHHHHHHHHHHHHHHHHHSCCCSSEECHHHHHHHHHHHHS---SCHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHhcceeccCChhHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHhCCCCH---HHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999999876   8999999


Q ss_pred             HHHHHcCCcceEeeCCCcEEEEcccCcccCCccccHHHHHHHHHHHHhhHHHHHhcCCCCCCCc-chhhHHHHHHhhH-H
Q 011352          395 SKAIRDGAIDATVDHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVRALRFPPNSHK-EKESAEKRRERQQ-Q  472 (488)
Q Consensus       395 a~mI~dG~I~A~Id~~~G~v~~~~~~dv~s~~ep~~~l~~rI~~~l~l~~~~v~amr~p~~~~~-~~~~~~~~~~~~~-~  472 (488)
                      ++||.||+|+|+|||++|||.|++..|+|++.+|+.+|++||+||++||||+||+||||++.++ +.+++++++++++ .
T Consensus       424 AkmI~dG~I~A~Idh~~g~v~ske~~d~yst~ep~~af~~RI~~cl~L~ne~vkaMryp~~~~~~~~~~~~~~~~~~~~~  503 (523)
T 4b4t_S          424 SRAIRDGVIEAKINHEDGFIETTELLNIYDSEDPQQVFDERIKFANQLHDEYLVSMRYPEDKKTQQNEKSENGENDDDTL  503 (523)
T ss_dssp             HHHHHHTSSCCEECTTTCCEECCSSSCC----------------------------------------------------
T ss_pred             HHHHHcCCceEEEecCCCEEEeCccccccccHHHHHHHHHHHHHHHHHHHHHHHHccCCcccchhhHHHHHHHhhhhhhh
Confidence            9999999999999999999999999999999999999999999999999999999999999998 7777776665532 4


Q ss_pred             HHHHHHhhcc
Q 011352          473 EQELAKHIAE  482 (488)
Q Consensus       473 ~~e~~~~~~~  482 (488)
                      +.+++.+++|
T Consensus       504 ~~~~~d~~~d  513 (523)
T 4b4t_S          504 DGDLMDDMSD  513 (523)
T ss_dssp             ----------
T ss_pred             hhcccccccc
Confidence            5555555543

PyMOL of 4b4t

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

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

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

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

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

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

>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

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

>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

>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

>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

>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

>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

>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

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

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

>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

>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

>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

>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

>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

>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

>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

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

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

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

>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

>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

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

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

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

>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

>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

>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

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

>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

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

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

>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

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

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

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

>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

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

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

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

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

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

>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

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

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

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

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

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

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

>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

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

>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

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

>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

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

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

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

>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

>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

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

>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

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

>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

>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

>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

>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

>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

>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

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

>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

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

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

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

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

>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

>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

>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

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

>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

>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

>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

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

>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

>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

>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

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

>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

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

>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

>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

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

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

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

>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

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

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

>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

>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

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

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

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

>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

>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

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

>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

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

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

Back alignment and structure

>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

>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

>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

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

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

>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

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

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

>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

>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

>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

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

>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

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

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

>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

>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

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

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

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

>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

>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

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

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

>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

>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

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

>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

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}	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

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		488
d1ufma_		84	a.4.5.47 (A:) COP9 signalosome complex subunit 4,	2e-14

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


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

 Score = 66.3 bits (162), Expect = 2e-14
 Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 6/73 (8%)

Query: 351 LRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHA 410
           L   VI   L + S  Y+ I+  ++   L +    P A AE I S+ I +G ++  +D  
Sbjct: 12  LDRAVIEHNLLSASKLYNNITFEELGALLEI----PAAKAEKIASQMITEGRMNGFIDQI 67

Query: 411 NG--WMVSKETGD 421
           +G     ++E   
Sbjct: 68  DGIVHFETREASG 80

PyMOL of d1ufma_

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		488
d1ufma_		84	COP9 signalosome complex subunit 4, GSN4 {Mouse (M	99.29
d1qqea_		290	Vesicular transport protein sec17 {Baker's yeast (	98.2
d1hz4a_		366	Transcription factor MalT domain III {Escherichia	96.89
d1qqea_		290	Vesicular transport protein sec17 {Baker's yeast (	96.06
d1w3ba_		388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	95.97
d1hz4a_		366	Transcription factor MalT domain III {Escherichia	95.22
d1p5qa1		170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	95.18
d2hr2a1		156	Hypothetical protein CT2138 {Chlorobium tepidum [T	94.9
d1xnfa_		259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	94.86
d1elwa_		117	Hop {Human (Homo sapiens) [TaxId: 9606]}	94.75
d1xnfa_		259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	94.74
d1hh8a_		192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	94.73
d1a17a_		159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	94.39
d1fcha_		323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	94.33
d2c2la1		201	STIP1 homology and U box-containing protein 1, STU	94.02
d1ihga1		169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	93.95
d2fbna1		153	Putative 70 kda peptidylprolyl isomerase PFL2275c	93.13
d1tjca_		95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	93.01
d1kt1a1		168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	92.91
d1hxia_		112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	91.37
d1w3ba_		388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	91.32
d1fcha_		323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	89.88
d1hxia_		112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	89.46
d1nzna_		122	Mitochondria fission protein Fis1 {Human (Homo sap	88.75
d1tjca_		95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	88.38
d2cfxa1		63	Transcriptional regulator LrpC {Bacillus subtilis	88.32
d2c2la1		201	STIP1 homology and U box-containing protein 1, STU	86.93
d2pqrb1		124	Mitochondria fission protein Fis1 {Baker's yeast (	86.89
d1a17a_		159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	86.47
d1hh8a_		192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	86.35
d1elra_		128	Hop {Human (Homo sapiens) [TaxId: 9606]}	85.21
d2onda1		308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	84.96
d1elwa_		117	Hop {Human (Homo sapiens) [TaxId: 9606]}	83.92
d2h6fa1		315	Protein farnesyltransferase alpha-subunit {Human (	81.63
d1wi9a_		72	Hypothetical protein C20orf116 homolog {Mouse (Mus	80.9
d1i1ga1		60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	80.59
d2cyya1		60	Putative transcriptional regulator PH1519 {Archaeo	80.18

>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=99.29  E-value=1.8e-12  Score=104.07  Aligned_cols=74  Identities=23%  Similarity=0.339  Sum_probs=65.7

Q ss_pred             chHHHHHHHHHHHHHhHHHHHHhhccccHHHHHHHhcCCCCCChHHHHHHHHHHHHcCCcceEeeCCCcEEEEcccCc
Q 011352          344 TNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHANGWMVSKETGD  421 (488)
Q Consensus       344 ~~~Lv~rLr~~vir~~ir~i~~~YsrIsL~dIa~~L~l~~~~d~eeaE~ila~mI~dG~I~A~Id~~~G~v~~~~~~d  421 (488)
                      +++...-|+.++++++|++++++|++|+|+++|+.++++.    +++|.+|++||.+|.|+|+|||.+|+|.|.....
T Consensus         5 ~~~~~t~L~~~i~Ehni~~is~~Y~~Isl~~la~~l~l~~----~evE~~l~~mI~~~~i~akIDq~~g~V~F~~~e~   78 (84)
T d1ufma_           5 SSGGSSILDRAVIEHNLLSASKLYNNITFEELGALLEIPA----AKAEKIASQMITEGRMNGFIDQIDGIVHFETREA   78 (84)
T ss_dssp             CCCSSCCCCHHHHHHHHHHHHHSCSEEEHHHHHHHTTSCH----HHHHHHHHHHHHTTSSCEEEETTTTEEEECCSSC
T ss_pred             ccchhHHHHHHHHHHHHHHHHHhhceeeHHHHHHHHCCCH----HHHHHHHHHHHhcCeEEEEEeCCCCEEEECCCCc
Confidence            3333334678899999999999999999999999999986    9999999999999999999999999999987643

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

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

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

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

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

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

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

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

>d1elwa_ a.118.8.1 (A:) Hop {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

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {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

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {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

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	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

>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

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

>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

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {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

>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

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

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

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

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {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

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

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

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