Citrus Sinensis ID: 012934

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---

METGAHAREVRRIMRAVRLTMALRRKLKAPVLSAFLNFALAPGSEAHSRLLSYLPKEDEHEMEVDTASSGAPAPAKHPLPELEIYCYLLVLIFLIDKKRYNEAKACSSASIARLKNMNRRTVDVLAARLYFYYSLCYELTGDLAEIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLRSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAALGFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFSSTFSSDRTNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVRALRFPPNSHKEKESAEKRRERQQQEQELAKHIAEEDDDEF

ccccccccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHcccccHHHHHHHHcccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHcccHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHcccHHHHHHHHHcccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHcccccccHHHHHHHHHHHHHcccEEEEEEccccEEEEcccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccc

ccccHccccHHHHHHHHHHHHHHHHHccHHHHHHHHHHHcccccHHHHHHHHHccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHcccccHHHHccHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHEEEEEccccHHHHHHHHccccHccHHHHHHHHHHHHHcccEEEEEEccccEEEEccccEEEccccHHHHHHHHHHHHHHHHHHHHHHHcccccHcccHHHHHHHHHHHHHHHHHHHHHHccccccc

METGAHAREVRRIMRAVRLTMALRRKLKAPVLSAFLNFALAPGSEAHSRLlsylpkedehemevdtassgapapakhplpelEIYCYLLVLIFLIDKKRYNEAKACSSASIARLKNMNRRTVDVLAARLYFYYSLCYELTGDLAEIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLrskaprfeahsnQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAALGFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFSstfssdrtnNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLrldsanpvadAESIVSKAIRDgaidatvdhangwmvsketgdiystnepqlafNSRIAFCLNMHNEAvralrfppnshkekeSAEKRRERQQQEQELAKHIAEEDDDEF

metgaharevrrIMRAVRLTMALRRKLKAPVLSAFLNFALAPGSEAHSRLLSYLPKEDEHEMEVDTASSGAPAPAKHPLPELEIYCYLLVLIFLIDKKRYNEAKACSSasiarlknmnrrTVDVLAARLYFYYSLCYELTGDLAEIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLRSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAALGFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFsstfssdrtnnliVRLRhnvirtglrnisisysrISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVralrfppnshkekesaEKRRERQQQEQELakhiaeedddef

METGAHAREVRRIMRAVRLTMALRRKLKAPVLSAFLNFALAPGSEAHSRLLSYLPKEDEHEMEVDTASSGAPAPAKHPLPELEIYCYLLVLIFLIDKKRYNEAKACSSASIARLKNMNRRTVDVLAARLYFYYSLCYELTGDLAEIRGNLLALHRIATLRHDELGQETllnlllrnylhynlyDQAEKLRSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAALGFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFSSTFSSDRTNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVRALRFPPNSHkekesaekrrerqqqeqeLAKHIAEEDDDEF

**********RRIMRAVRLTMALRRKLKAPVLSAFLNFALAP***************************************LEIYCYLLVLIFLIDKKRYNEAKACSSASIARLKNMNRRTVDVLAARLYFYYSLCYELTGDLAEIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLR****RFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAALGFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFSSTFSSDRTNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVRAL**************************************

*ETGAHAREVRRIMRAVRLTMALRRKLKAPVLSAFLNFALAPGSEAHSRLL***************************LPELEIYCYLLVLIFLIDKKRYNEAKACSSASIARLKNMNRRTVDVLAARLYFYYSLCYELTGDLAEIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLRSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAALGFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFSSTFSSDRTNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVR*********************************EED****

********EVRRIMRAVRLTMALRRKLKAPVLSAFLNFALAPGSEAHSRLLSYLPKE****************PAKHPLPELEIYCYLLVLIFLIDKKRYNEAKACSSASIARLKNMNRRTVDVLAARLYFYYSLCYELTGDLAEIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLRSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAALGFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFSSTFSSDRTNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVRALRFPP**********************************

M*TGAHAREVRRIMRAVRLTMALRRKLKAPVLSAFLNFALAPGSEAHSRLLSYLPK*******************KHPLPELEIYCYLLVLIFLIDKKRYNEAKACSSASIARLKNMNRRTVDVLAARLYFYYSLCYELTGDLAEIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLRSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAALGFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFSSTFSSDRTNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVRALRFPPNS*******E***********L*KHIAE******

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

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		453	2.2.26 [Sep-21-2011]
P93768		488	Probable 26S proteasome n	N/A	no	1.0	0.928	0.924	0.0
Q06364		489	Probable 26S proteasome n	N/A	no	1.0	0.926	0.894	0.0
Q9LNU4		488	Probable 26S proteasome n	yes	no	1.0	0.928	0.843	0.0
Q9LQR8		487	Probable 26S proteasome n	no	no	1.0	0.930	0.825	0.0
P25161		494	Probable 26S proteasome n	yes	no	0.984	0.902	0.487	1e-108
O43242		534	26S proteasome non-ATPase	yes	no	0.993	0.842	0.485	1e-106
P14685		530	26S proteasome non-ATPase	yes	no	0.993	0.849	0.485	1e-106
Q2KJ46		534	26S proteasome non-ATPase	yes	no	0.993	0.842	0.485	1e-106
O61470		496	Probable 26S proteasome n	yes	no	0.973	0.889	0.496	1e-104
Q9U5Z8		500	Probable 26S proteasome n	N/A	no	0.973	0.882	0.498	1e-103

>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 =  819 bits (2116), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 419/453 (92%), Positives = 435/453 (96%)

Query: 1   METGAHAREVRRIMRAVRLTMALRRKLKAPVLSAFLNFALAPGSEAHSRLLSYLPKEDEH 60
           +ETGA+AREVRRI RAVRLTMALR+KLKA  LSAFLN+ L PGSE HSRL S+LPKEDE 
Sbjct: 36  IETGAYAREVRRISRAVRLTMALRKKLKASSLSAFLNYVLVPGSEVHSRLSSFLPKEDEQ 95

Query: 61  EMEVDTASSGAPAPAKHPLPELEIYCYLLVLIFLIDKKRYNEAKACSSASIARLKNMNRR 120
           +MEVDTA+SGA AP K+PLPELEIYCYLLVLIFLID+K+YNEAKACSSASIARLK +NRR
Sbjct: 96  DMEVDTATSGAQAPIKNPLPELEIYCYLLVLIFLIDQKKYNEAKACSSASIARLKTVNRR 155

Query: 121 TVDVLAARLYFYYSLCYELTGDLAEIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHY 180
           TVDVLA+RLYFYYSLCYELTGDLAEIRG LLALHRIATLRHDELGQETLLNLLLRNYLHY
Sbjct: 156 TVDVLASRLYFYYSLCYELTGDLAEIRGYLLALHRIATLRHDELGQETLLNLLLRNYLHY 215

Query: 181 NLYDQAEKLRSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAAL 240
           NLYDQAEKLRSKAPRFEAHSNQQF RYLFYLGKIRTIQLEYTDAKESLLQAARKAP AAL
Sbjct: 216 NLYDQAEKLRSKAPRFEAHSNQQFSRYLFYLGKIRTIQLEYTDAKESLLQAARKAPQAAL 275

Query: 241 GFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKF 300
           GFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELF+ VAEKF
Sbjct: 276 GFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFRKVAEKF 335

Query: 301 SSTFSSDRTNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVS 360
           SSTFSSD TNNLIVRLRHNVIRTGLRNISISYSRISL DVAKKLRLDS NPVADAESIVS
Sbjct: 336 SSTFSSDGTNNLIVRLRHNVIRTGLRNISISYSRISLVDVAKKLRLDSPNPVADAESIVS 395

Query: 361 KAIRDGAIDATVDHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVRALRFPPN 420
           KAIRDGAIDAT+DHANGWMVSKETGDIYSTNEPQ+AFNSRIAFCLNMHNEAVRALRFPPN
Sbjct: 396 KAIRDGAIDATLDHANGWMVSKETGDIYSTNEPQIAFNSRIAFCLNMHNEAVRALRFPPN 455

Query: 421 SHKEKESAEKRRERQQQEQELAKHIAEEDDDEF 453
           SHKEKESAEKRRERQQQEQELAKHIAEEDDD+F
Sbjct: 456 SHKEKESAEKRRERQQQEQELAKHIAEEDDDDF 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\|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\|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\|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		453
255560521		491	26S proteasome regulatory subunit S3, pu	1.0	0.922	0.920	0.0
225428067		487	PREDICTED: probable 26S proteasome non-A	1.0	0.930	0.911	0.0
3914467		488	RecName: Full=Probable 26S proteasome no	1.0	0.928	0.924	0.0
12230970		489	RecName: Full=Probable 26S proteasome no	1.0	0.926	0.894	0.0
224080636		488	predicted protein [Populus trichocarpa]	1.0	0.928	0.909	0.0
449454524		485	PREDICTED: probable 26S proteasome non-A	0.993	0.927	0.898	0.0
356509165		487	PREDICTED: probable 26S proteasome non-A	1.0	0.930	0.874	0.0
449454221		481	PREDICTED: probable 26S proteasome non-A	0.993	0.935	0.887	0.0
224103165		486	predicted protein [Populus trichocarpa]	1.0	0.932	0.916	0.0
356517716		487	PREDICTED: probable 26S proteasome non-A	1.0	0.930	0.869	0.0

>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

 Score =  820 bits (2119), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 417/453 (92%), Positives = 441/453 (97%)

Query: 1   METGAHAREVRRIMRAVRLTMALRRKLKAPVLSAFLNFALAPGSEAHSRLLSYLPKEDEH 60
           +ETGA+AREVRRI+RAVRLTMALRRKLKA +LSAFLN  L PGS+ ++RL S+LPKED+H
Sbjct: 39  IETGAYAREVRRIVRAVRLTMALRRKLKAQLLSAFLNSILTPGSDPYTRLSSFLPKEDDH 98

Query: 61  EMEVDTASSGAPAPAKHPLPELEIYCYLLVLIFLIDKKRYNEAKACSSASIARLKNMNRR 120
           EMEVDTA+S   APAKHPLPELE+YCYLLVLI+LID+K+YNEAKACS+A IARLKN+NRR
Sbjct: 99  EMEVDTATSVTQAPAKHPLPELEMYCYLLVLIYLIDQKKYNEAKACSTACIARLKNLNRR 158

Query: 121 TVDVLAARLYFYYSLCYELTGDLAEIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHY 180
           TVDVLA+RLYFYYSL YELTGDLAEIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHY
Sbjct: 159 TVDVLASRLYFYYSLSYELTGDLAEIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHY 218

Query: 181 NLYDQAEKLRSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAAL 240
           NLYDQAEKLRSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARK+PVAAL
Sbjct: 219 NLYDQAEKLRSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKSPVAAL 278

Query: 241 GFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKF 300
           GFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKF
Sbjct: 279 GFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKF 338

Query: 301 SSTFSSDRTNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVS 360
           S+ FS+DRT+NLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIV+
Sbjct: 339 STIFSADRTHNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVA 398

Query: 361 KAIRDGAIDATVDHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVRALRFPPN 420
           KAIRDGAIDAT+DHANGWMVSKETGDIYSTNEPQ+AFNSRIAFCLNMHNEAVRALRFPPN
Sbjct: 399 KAIRDGAIDATLDHANGWMVSKETGDIYSTNEPQIAFNSRIAFCLNMHNEAVRALRFPPN 458

Query: 421 SHKEKESAEKRRERQQQEQELAKHIAEEDDDEF 453
           SHKEKESAEKRRERQQQEQELAKHIAEEDDDEF
Sbjct: 459 SHKEKESAEKRRERQQQEQELAKHIAEEDDDEF 491

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

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

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

>gi\|449454524\|ref\|XP_004145004.1\| PREDICTED: probable 26S proteasome non-ATPase regulatory subunit 3-like [Cucumis sativus] gi\|449498909\|ref\|XP_004160668.1\| PREDICTED: probable 26S proteasome non-ATPase regulatory subunit 3-like [Cucumis sativus]	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\|449454221\|ref\|XP_004144854.1\| PREDICTED: probable 26S proteasome non-ATPase regulatory subunit 3-like [Cucumis sativus]	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

>gi\|356517716\|ref\|XP_003527532.1\| PREDICTED: probable 26S proteasome non-ATPase regulatory subunit 3-like [Glycine max]	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		453
TAIR\|locus:2198561		488	EMB2719 "EMBRYO DEFECTIVE 2719	1.0	0.928	0.777	2e-184
TAIR\|locus:2204385		487	AT1G75990 [Arabidopsis thalian	1.0	0.930	0.763	5.4e-182
UNIPROTKB\|Q2KJ46		534	PSMD3 "26S proteasome non-ATPa	0.993	0.842	0.428	1.1e-89
UNIPROTKB\|E2QUY7		534	PSMD3 "Uncharacterized protein	0.993	0.842	0.428	1.1e-89
UNIPROTKB\|O43242		534	PSMD3 "26S proteasome non-ATPa	0.993	0.842	0.428	1.1e-89
MGI\|MGI:98858		530	Psmd3 "proteasome (prosome, ma	0.993	0.849	0.428	1.1e-89
RGD\|1311470		530	Psmd3 "proteasome (prosome, ma	0.993	0.849	0.428	1.1e-89
ZFIN\|ZDB-GENE-040426-1444		503	psmd3 "proteasome (prosome, ma	0.993	0.894	0.430	1.7e-89
UNIPROTKB\|F1RXA7		536	LOC100512253 "Uncharacterized	0.993	0.839	0.431	4.6e-89
FB\|FBgn0261396		494	Rpn3 "Regulatory particle non-	0.984	0.902	0.435	6e-87

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

 Score = 1789 (634.8 bits), Expect = 2.0e-184, P = 2.0e-184
 Identities = 353/454 (77%), Positives = 389/454 (85%)

Query:     1 METGAHAREVRRIMRAVRLTMALRRKLKAPVLSAFLNFALAPGSEAHSRLLSYLPKEDEH 60
             ++TG++ +EVRRI RAVRLT+ LR+KL   VLS+FL+FAL PGSEAHSRL S++PK DEH
Sbjct:    35 IDTGSYTKEVRRIARAVRLTIGLRQKLTGSVLSSFLDFALVPGSEAHSRLSSFVPKGDEH 94

Query:    61 EMEVDTASSGAPA-PAKHPLPELEIYCYLLVLIFLIDKKRYNEAKACSSASIARLKNMNR 119
             +MEVDTASS   A P+KH   ELEIYCY +VL+FLID+K+YNEAKACSSASIARLKN+NR
Sbjct:    95 DMEVDTASSATQAAPSKHLPAELEIYCYFIVLLFLIDQKKYNEAKACSSASIARLKNVNR 154

Query:   120 RTVDVLAARLYFYYSLCYELTGDLAEIRGNLLALHRIATLRHDELGQETXXXXXXXXXXX 179
             RT+DV+A+RLYFYYSL YE TGDLAEIRG LLALH  ATLRHDELGQET           
Sbjct:   155 RTIDVIASRLYFYYSLSYEQTGDLAEIRGTLLALHHSATLRHDELGQETLLNLLLRNYLH 214

Query:   180 XXXXDQAEKLRSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPVAA 239
                 DQAEKLRSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAP+AA
Sbjct:   215 YNLYDQAEKLRSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPIAA 274

Query:   240 LGFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEK 299
             LGFR+QCNKWAI+VRLLLGEIPER++F QKGMEKALRPYFELTNAVRIGDLELF++V EK
Sbjct:   275 LGFRIQCNKWAILVRLLLGEIPERSIFTQKGMEKALRPYFELTNAVRIGDLELFRTVQEK 334

Query:   300 FSSTFSSDRTNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIV 359
             F  TF+ DRT+NLIVRLRHNVIRTGLRNISISYSRISL DVAKKLRL+S NPVADAESIV
Sbjct:   335 FLDTFAQDRTHNLIVRLRHNVIRTGLRNISISYSRISLPDVAKKLRLNSENPVADAESIV 394

Query:   360 SKAIRDGAIDATVDHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVRALRFPP 419
             +KAIRDGAIDAT+DH NG MVSKETGDIYSTNEPQ AFNSRIAFCLNMHNEAVRALRFPP
Sbjct:   395 AKAIRDGAIDATIDHKNGCMVSKETGDIYSTNEPQTAFNSRIAFCLNMHNEAVRALRFPP 454

Query:   420 NSHXXXXXXXXXXXXXXXXXXLAKHIAEEDDDEF 453
             N+H                  LAKH+AEEDDD+F
Sbjct:   455 NTHKEKESDEKRRERKQQEEELAKHMAEEDDDDF 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

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

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\|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	0.8436	1.0	0.9282	yes	no
O61470	PSMD3_ANOGA	No assigned EC number	0.4966	0.9735	0.8891	yes	no
O43242	PSMD3_HUMAN	No assigned EC number	0.4857	0.9933	0.8426	yes	no
P14685	PSMD3_MOUSE	No assigned EC number	0.4857	0.9933	0.8490	yes	no
P93768	PSMD3_TOBAC	No assigned EC number	0.9249	1.0	0.9282	N/A	no
O42897	RPN3_SCHPO	No assigned EC number	0.4422	0.9558	0.8712	yes	no
Q9LQR8	PSD32_ARATH	No assigned EC number	0.8256	1.0	0.9301	no	no
Q1ZXD3	PSMD3_DICDI	No assigned EC number	0.4267	0.9933	0.8928	yes	no
P25161	PSMD3_DROME	No assigned EC number	0.4879	0.9845	0.9028	yes	no
Q06364	PSMD3_DAUCA	No assigned EC number	0.8940	1.0	0.9263	N/A	no
Q04908	PSMD3_CAEEL	No assigned EC number	0.4052	0.9668	0.8690	yes	no
Q2KJ46	PSMD3_BOVIN	No assigned EC number	0.4857	0.9933	0.8426	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		453
pfam08375		68	pfam08375, Rpn3_C, Proteasome regulatory subunit C	5e-27
pfam01399		100	pfam01399, PCI, PCI domain	6e-21
smart00753		88	smart00753, PAM, PCI/PINT associated module	2e-19
smart00088		88	smart00088, PINT, motif in proteasome subunits, In	2e-19

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

 Score =  102 bits (257), Expect = 5e-27
 Identities = 39/68 (57%), Positives = 52/68 (76%), Gaps = 1/68 (1%)

Query: 386 DIYSTNEPQLAFNSRIAFCLNMHNEAVRALRFPPNSHK-EKESAEKRRERQQQEQELAKH 444
           D+YST EPQ AF+ RI FCL +HN+AV+A+R+PP+  K E+E AE+ RER Q E ELAK 
Sbjct: 1   DVYSTKEPQQAFDERIQFCLQLHNDAVKAMRYPPDKEKKEEEKAEEARERDQLELELAKE 60

Query: 445 IAEEDDDE 452
           ++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		453
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	100.0
KOG2582		422	consensus COP9 signalosome, subunit CSN3 [Posttran	99.94
KOG1463		411	consensus 26S proteasome regulatory complex, subun	99.92
PF08375		68	Rpn3_C: Proteasome regulatory subunit C-terminal;	99.92
COG5159		421	RPN6 26S proteasome regulatory complex component [	99.81
KOG1497		399	consensus COP9 signalosome, subunit CSN4 [Posttran	99.77
KOG1464		440	consensus COP9 signalosome, subunit CSN2 [Posttran	99.73
PF01399		105	PCI: PCI domain; InterPro: IPR000717 A homology do	99.71
KOG1498		439	consensus 26S proteasome regulatory complex, subun	99.67
KOG2908		380	consensus 26S proteasome regulatory complex, subun	99.35
COG5071		439	RPN5 26S proteasome regulatory complex component [	99.34
smart00088		88	PINT motif in proteasome subunits, Int-6, Nip-1 an	99.13
smart00753		88	PAM PCI/PINT associated module.	99.13
KOG0687		393	consensus 26S proteasome regulatory complex, subun	98.16
KOG1076		843	consensus Translation initiation factor 3, subunit	98.09
COG5187		412	RPN7 26S proteasome regulatory complex component,	97.93
KOG0686		466	consensus COP9 signalosome, subunit CSN1 [Posttran	97.7
PF14938		282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.65
PF10255		404	Paf67: RNA polymerase I-associated factor PAF67; I	97.45
KOG2753		378	consensus Uncharacterized conserved protein, conta	97.28
KOG2758		432	consensus Translation initiation factor 3, subunit	96.89
KOG2072		988	consensus Translation initiation factor 3, subunit	96.65
PLN03081		697	pentatricopeptide (PPR) repeat-containing protein;	96.15
PF09976		145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	96.07
TIGR00990		615	3a0801s09 mitochondrial precursor proteins import	95.89
PF10075		143	PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro	95.77
TIGR03302		235	OM_YfiO outer membrane assembly lipoprotein YfiO.	95.56
PF07719		34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	95.34
TIGR02521		234	type_IV_pilW type IV pilus biogenesis/stability pr	95.21
PRK11788		389	tetratricopeptide repeat protein; Provisional	95.19
PRK11788		389	tetratricopeptide repeat protein; Provisional	95.05
PF13371		73	TPR_9: Tetratricopeptide repeat	95.0
TIGR02552		135	LcrH_SycD type III secretion low calcium response	94.69
PF13432		65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	94.37
cd00189		100	TPR Tetratricopeptide repeat domain; typically con	94.37
PF14938		282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	94.24
PLN03077		857	Protein ECB2; Provisional	94.02
KOG2300		629	consensus Uncharacterized conserved protein [Funct	93.99
PF13424		78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	93.81
TIGR02521		234	type_IV_pilW type IV pilus biogenesis/stability pr	93.68
PF00515		34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	93.22
PF04733		290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	93.08
PLN03081		697	pentatricopeptide (PPR) repeat-containing protein;	92.99
TIGR02917		899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	92.84
TIGR00990		615	3a0801s09 mitochondrial precursor proteins import	92.71
TIGR02795		119	tol_pal_ybgF tol-pal system protein YbgF. Members	92.34
PF10602		177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	92.21
PF13525		203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	92.21
PF13414		69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	91.85
PF09012		69	FeoC: FeoC like transcriptional regulator; InterPr	91.66
TIGR02917		899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	91.65
PF03399		204	SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; I	91.27
PF12895		84	Apc3: Anaphase-promoting complex, cyclosome, subun	91.26
KOG4162		799	consensus Predicted calmodulin-binding protein [Si	91.23
PF13174		33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	91.07
KOG1840		508	consensus Kinesin light chain [Cytoskeleton]	90.33
PRK10049		765	pgaA outer membrane protein PgaA; Provisional	90.04
PRK15359		144	type III secretion system chaperone protein SscB;	90.03
PF12569		517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	89.92
PLN03077		857	Protein ECB2; Provisional	89.81
PF13181		34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	89.79
PRK11189		296	lipoprotein NlpI; Provisional	89.15
KOG1840		508	consensus Kinesin light chain [Cytoskeleton]	89.02
PRK10370		198	formate-dependent nitrite reductase complex subuni	88.98
PRK12370		553	invasion protein regulator; Provisional	88.91
PF13414		69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	88.75
PRK15174		656	Vi polysaccharide export protein VexE; Provisional	88.75
PRK04841		903	transcriptional regulator MalT; Provisional	88.44
cd00189		100	TPR Tetratricopeptide repeat domain; typically con	87.92
cd05804		355	StaR_like StaR_like; a well-conserved protein foun	87.66
PRK11447		1157	cellulose synthase subunit BcsC; Provisional	87.48
PLN03088		356	SGT1, suppressor of G2 allele of SKP1; Provisional	87.35
cd05804		355	StaR_like StaR_like; a well-conserved protein foun	86.88
PF08784		102	RPA_C: Replication protein A C terminal; InterPro:	86.64
PLN03218		1060	maturation of RBCL 1; Provisional	86.34
PRK04841		903	transcriptional regulator MalT; Provisional	86.2
CHL00033		168	ycf3 photosystem I assembly protein Ycf3	86.14
PLN03218		1060	maturation of RBCL 1; Provisional	85.72
PF13429		280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	84.62
TIGR03302		235	OM_YfiO outer membrane assembly lipoprotein YfiO.	84.28
PRK14574		822	hmsH outer membrane protein; Provisional	84.28
PRK02603		172	photosystem I assembly protein Ycf3; Provisional	83.83
KOG2002		1018	consensus TPR-containing nuclear phosphoprotein th	83.81
KOG2300		629	consensus Uncharacterized conserved protein [Funct	83.49
PF13424		78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	83.1
PF09295		395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	82.83
smart00028		34	TPR Tetratricopeptide repeats. Repeats present in	82.74
PRK15174		656	Vi polysaccharide export protein VexE; Provisional	82.73
PF13176		36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	82.07
PF04190		260	DUF410: Protein of unknown function (DUF410) ; Int	82.07
KOG1173		611	consensus Anaphase-promoting complex (APC), Cdc16	81.89
PRK10049		765	pgaA outer membrane protein PgaA; Provisional	81.85
PRK11189		296	lipoprotein NlpI; Provisional	81.69
PRK10866		243	outer membrane biogenesis protein BamD; Provisiona	81.5
PRK15331		165	chaperone protein SicA; Provisional	80.3
PRK15363		157	pathogenicity island 2 chaperone protein SscA; Pro	80.29

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

Probab=100.00  E-value=1.6e-111  Score=836.50  Aligned_cols=450  Identities=59%  Similarity=0.888  Sum_probs=433.7

Q ss_pred             CcccccccchhHHHHHHHhhHHHhccCChHHHHHHHHHHcCCCchhHHHHHhcCCCCCCcccccccCCCCCCC-CC-CCC
Q 012934            1 METGAHAREVRRIMRAVRLTMALRRKLKAPVLSAFLNFALAPGSEAHSRLLSYLPKEDEHEMEVDTASSGAPA-PA-KHP   78 (453)
Q Consensus         1 ~~~~~~~~~~r~~~r~~r~~~~~r~~l~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~-~~-~~~   78 (453)
                      |+|+|.++|+|||||+||.++++|++|+..+|..+++.++|+++++++.++.+++.+++..++.+.....+++ +. ++.
T Consensus        41 i~kg~~tke~r~I~R~lr~l~~~r~kln~~vL~~~v~~~~~~~se~~~~~l~fv~~~~~~~~p~~~~s~~t~~a~~~k~~  120 (493)
T KOG2581|consen   41 IDKGVYTKEPRFILRALRLLPSTRRKLNGAVLYKLVSSLLSSGSEAMDRLLRFVPAFDKNIKPLDTDSPNTQSALKRKPL  120 (493)
T ss_pred             HhccccccchHHHHHHHHhhhhhHhhhhHHHHHHHHHHHcCCchHHHHHHHhhcccccccCCcccccccccccccccCCc
Confidence            6899999999999999999999999999999999999999999999999999999877766655544222222 23 556


Q ss_pred             CCHHHHHHHHHHHHHHhcccCHHHHHHHHHHHHHHHHhhchhhhHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHhh
Q 012934           79 LPELEIYCYLLVLIFLIDKKRYNEAKACSSASIARLKNMNRRTVDVLAARLYFYYSLCYELTGDLAEIRGNLLALHRIAT  158 (453)
Q Consensus        79 ~p~~e~~~~ll~~~~l~d~~~~~~A~~~~~~lv~~l~~~~~r~~d~l~ak~~~~~~~~~e~~~~l~~~r~~l~~~~rta~  158 (453)
                      .||+|+|+++|++++++|+++|++|.+++.+++..+..+|+|++|.+.||+|||+++++|..+++..+|+.|++.+|||+
T Consensus       121 ~~Ei~aY~~lLv~Lfl~d~K~~kea~~~~~~~l~~i~~~nrRtlD~i~ak~~fy~~l~~E~~~~l~~~rs~l~~~lrtAt  200 (493)
T KOG2581|consen  121 PAEIEAYLYLLVLLFLIDQKEYKEADKISDALLASISIQNRRTLDLIAAKLYFYLYLSYELEGRLADIRSFLHALLRTAT  200 (493)
T ss_pred             hHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcchhhHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHhh
Confidence            67999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccCccchHHHHHHHHHHHHhcCChHHHHHHHhcCCcCccCChhhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCc-
Q 012934          159 LRHDELGQETLLNLLLRNYLHYNLYDQAEKLRSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAPV-  237 (453)
Q Consensus       159 ~~~~~~~~~~l~n~llr~Yl~~~~~~~a~~li~~~~~p~~~~~~~~v~Y~YY~G~i~~~~~dy~~A~~~L~~A~~~~p~-  237 (453)
                      ++|+..||++++|+|||+|++.+.|++|+++++++.+|+..++++++||+||.|+|.++|+||++|.++|.+|++++|+ 
T Consensus       201 Lrhd~e~qavLiN~LLr~yL~n~lydqa~~lvsK~~~pe~~snne~ARY~yY~GrIkaiqldYssA~~~~~qa~rkapq~  280 (493)
T KOG2581|consen  201 LRHDEEGQAVLINLLLRNYLHNKLYDQADKLVSKSVYPEAASNNEWARYLYYLGRIKAIQLDYSSALEYFLQALRKAPQH  280 (493)
T ss_pred             hcCcchhHHHHHHHHHHHHhhhHHHHHHHHHhhcccCccccccHHHHHHHHHHhhHHHhhcchhHHHHHHHHHHHhCcch
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999999997 


Q ss_pred             CchHhHHHHHHHHHhHHHhcCCCCChhhhhhhhhhhhhhhHHHHHHHHhcCCHHHHHHHHHhcchhhccCccHHHHHHHH
Q 012934          238 AALGFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFSSTFSSDRTNNLIVRLR  317 (453)
Q Consensus       238 ~~~~~~~~alK~lIlv~LL~G~iP~~~ll~~~~l~~~l~~Y~~L~~Av~~Gdl~~f~~~l~~~~~~f~~Dg~~~Lv~rLr  317 (453)
                      .+.||++++.|++|+++||+|+||++++|.|+.++++|.||+.|++|||.||+++|++++++|...|.+||+|.|+.|||
T Consensus       281 ~alGf~q~v~k~~ivv~ll~geiPers~F~Qp~~~ksL~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~LivRLR  360 (493)
T KOG2581|consen  281 AALGFRQQVNKLMIVVELLLGEIPERSVFRQPGMRKSLRPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYTLIVRLR  360 (493)
T ss_pred             hhhhHHHHHHHHHHHHHHHcCCCcchhhhcCccHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcchHHHHHH
Confidence            67999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhcccccHHHHHHHhCCCCCCChHHHHHHHHHhHHcCCceeEeeCCCcEEEecccccccCCccccHHH
Q 012934          318 HNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHANGWMVSKETGDIYSTNEPQLAF  397 (453)
Q Consensus       318 ~~vir~~irki~~~YsrIsL~dIa~~L~l~~~~d~~eaE~iva~mI~dG~I~A~Id~~~G~v~~~~~~~v~s~~ep~~~l  397 (453)
                      +|||+++||+|+.+|||||+.|||.+|+++|+   ++||+||+++|+||.|+|+|||++|||.+++..++|++.+|+.+|
T Consensus       361 ~NVIkTgIR~ISlsYSRISl~DIA~kL~l~Se---ed~EyiVakAIRDGvIea~Id~~~g~m~skE~~diy~t~epQ~~f  437 (493)
T KOG2581|consen  361 HNVIKTGIRKISLSYSRISLQDIAKKLGLNSE---EDAEYIVAKAIRDGVIEAKIDHEDGFMQSKETFDIYSTREPQTAF  437 (493)
T ss_pred             HHHHHHhhhheeeeeeeccHHHHHHHhcCCCc---hhHHHHHHHHHHhccceeeeccccCceehhhhhhhhccCCchhhH
Confidence            99999999999999999999999999999997   889999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCchhhhhHHHHHHhhHHHHHHHHhhcccCCCCC
Q 012934          398 NSRIAFCLNMHNEAVRALRFPPNSHKEKESAEKRRERQQQEQELAKHIAEEDDDEF  453 (453)
Q Consensus       398 ~~rI~~~l~l~~~~v~amr~p~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~  453 (453)
                      +.||+||++|||++|+||||||+.++++|++|++||||||++|+||||+|+|||||
T Consensus       438 ~~rI~fCl~LhN~~vkamRyPp~~~~~~Es~E~~rereqq~~e~akemae~Ddd~F  493 (493)
T KOG2581|consen  438 DERIRFCLQLHNEAVKAMRYPPKKKKDLESAEKRREREQQELELAKEMAEEDDDDF  493 (493)
T ss_pred             hHHHHHHHHHHHHHHHHhcCCCcchhhHHHHHHhhhhhhhHHHHHHHhhhcccCCC
Confidence            99999999999999999999999999999999999999999999999999999999

>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

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

>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

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

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

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

>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

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

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

>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

>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

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO	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

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

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

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

>PF13371 TPR_9: Tetratricopeptide repeat	Back alignment and domain information

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

>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

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

>PLN03077 Protein ECB2; Provisional	Back alignment and domain information

>KOG2300 consensus Uncharacterized conserved protein [Function unknown]	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

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW	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

>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

>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

>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

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF	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

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

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

>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

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

>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

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

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

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

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

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

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

>PLN03077 Protein ECB2; 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

>PRK11189 lipoprotein NlpI; Provisional	Back alignment and domain information

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

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

>PRK12370 invasion protein regulator; 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

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

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

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

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

>PLN03088 SGT1, suppressor of G2 allele of SKP1; 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

>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

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

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

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

>PLN03218 maturation of RBCL 1; 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

>PRK14574 hmsH outer membrane protein; Provisional	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

>KOG2300 consensus Uncharacterized conserved protein [Function unknown]	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

>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

>smart00028 TPR Tetratricopeptide repeats	Back alignment and domain information

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

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

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

>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

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

>PRK11189 lipoprotein NlpI; Provisional	Back alignment and domain information

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

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

>PRK15363 pathogenicity island 2 chaperone protein SscA; 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		453
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 = 216 bits (551), Expect = 1e-56, Method: Compositional matrix adjust. Identities = 128/356 (35%), Positives = 197/356 (55%), Gaps = 20/356 (5%) Query: 81 ELEIYCYLLVLIFLIDKKRYNEAKACSSASIA--RLKNMNRRTVDVLAARLYFYYSLCYE 138 E+ + +LLV +FL D K + + + L N R+++++ A+L+FY L +E Sbjct: 133 EINCFMHLLVQLFLWDSKELEQLVEFNRKVVIPNLLCYYNLRSLNLINAKLWFYIYLSHE 192 Query: 139 LTGDLAE----------IRGNLLALHRIATLRHDELGQETXXXXXXXXXXXXXXXDQAEK 188 +E +R ++ +IA+L+HD + D A Sbjct: 193 TLARSSEEINSDNQNIILRSTMMKFLKIASLKHDNETKAMLINLILRDFLNNGEVDSASD 252 Query: 189 LRSKA--PRFEAHSNQQFCRYLFYLGKIRTIQLEYTDAKESLLQAARKAP--VAALGFRV 244 SK P + S+ + RY FYL KI IQL+Y+ A E ++ A RKAP +LGF Sbjct: 253 FISKLEYPHTDVSSSLE-ARYFFYLSKINAIQLDYSTANEYIIAAIRKAPHNSKSLGFLQ 311 Query: 245 QCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELFKSVAEKFSSTF 304 Q NK ++LL+G+IPE + F Q M+K+L PY+ LT AV++GDL+ F S K+ Sbjct: 312 QSNKLHCCIQLLMGDIPELSFFHQSNMQKSLLPYYHLTKAVKLGDLKKFTSTITKYKQLL 371 Query: 305 SSDRTNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIR 364 D T L VRLR NVI+TG+R IS++Y +ISL D+ KL LDS V E +VS+AIR Sbjct: 372 LKDDTYQLCVRLRSNVIKTGIRIISLTYKKISLRDICLKLNLDSEQTV---EYMVSRAIR 428 Query: 365 DGAIDATVDHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVRALRFPPN 420 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		453
3t5v_B		455	Nuclear mRNA export protein THP1; PCI, mRNA nuclea	5e-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

>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 (472), Expect = 5e-54
 Identities = 39/278 (14%), Positives = 88/278 (31%), Gaps = 39/278 (14%)

Query: 169 LLNLLLRNYLHYNLYDQAEKL------RSKAPRFEAHSNQQFCRYLFYLGKIRTIQLEYT 222
           L+N L   Y           +      +S    F  +   Q   Y + LG+   +  +  
Sbjct: 178 LVNKLNNIYFRIESPQLCSNIFKNFQPKSMLAHFNEYQLDQQIEYRYLLGRYYLLNSQVH 237

Query: 223 DAKESLLQAARKAPVAALGFRVQCN------KWAIIVRLLLGEIPERTVFMQKGMEKALR 276
           +A     +A +      L  +           + I   L+LG++ +         ++ + 
Sbjct: 238 NAFVQFNEAFQSLLNLPLTNQAITRNGTRILNYMIPTGLILGKMVKWGPLRPFLSQETID 297

Query: 277 PYFELTNAVRIGDLELFKSVAEKFSSTFSSDRTNNLIV-RLRHNVIRTGLRNISISY--- 332
            +  L   VR G+++       +      + +   +++ +L     R  ++ +  S+   
Sbjct: 298 NWSVLYKHVRYGNIQGVSLWLRQNERHLCARQLLIVLLEKLPMVTYRNLIKTVIKSWTTE 357

Query: 333 ---SRISLADVAKKLRLDSANPVA-----------------DAESIVSKAIRDGAIDATV 372
              +++  + + + L+L                        + E+++   I  G + A  
Sbjct: 358 WGQNKLPYSLIERVLQLSIGPTFEDPGAQEITIYNGIHSPKNVENVLVTLINLGLLRANC 417

Query: 373 DHANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNE 410
                  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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		453
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,	99.95
3txn_A		394	26S proteasome regulatory complex subunit P42B; PC	99.94
4b4t_Q		434	26S proteasome regulatory subunit RPN6; hydrolase,	99.88
4b4t_R		429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	99.73
4b4t_O		393	26S proteasome regulatory subunit RPN9; hydrolase,	99.68
4b0z_A		229	RPN12, 26S proteasome regulatory subunit RPN12; pr	99.5
1ufm_A		84	COP9 complex subunit 4; helix-turn-helix, structur	99.24
1qqe_A		292	Vesicular transport protein SEC17; helix-turn-heli	98.29
3chm_A		169	COP9 signalosome complex subunit 7; heat/ARM repea	98.18
3ro3_A		164	PINS homolog, G-protein-signaling modulator 2; asy	98.14
3ulq_A		383	Response regulator aspartate phosphatase F; tetrat	98.04
3gw4_A		203	Uncharacterized protein; structural genomics, PSI-	97.99
3ro2_A		338	PINS homolog, G-protein-signaling modulator 2; TPR	97.98
3ro2_A		338	PINS homolog, G-protein-signaling modulator 2; TPR	97.95
3sf4_A		406	G-protein-signaling modulator 2; tetratricopeptide	97.92
3sf4_A		406	G-protein-signaling modulator 2; tetratricopeptide	97.92
4a1s_A		411	PINS, partner of inscuteable; cell cycle, LGN, mit	97.88
4a1s_A		411	PINS, partner of inscuteable; cell cycle, LGN, mit	97.87
3q15_A		378	PSP28, response regulator aspartate phosphatase H;	97.8
2ifu_A		307	Gamma-SNAP; membrane fusion, snare complex disasse	97.8
3ulq_A		383	Response regulator aspartate phosphatase F; tetrat	97.65
3gw4_A		203	Uncharacterized protein; structural genomics, PSI-	97.62
3q15_A		378	PSP28, response regulator aspartate phosphatase H;	97.49
3ro3_A		164	PINS homolog, G-protein-signaling modulator 2; asy	97.46
2ho1_A		252	Type 4 fimbrial biogenesis protein PILF; type IV p	97.37
3u3w_A		293	Transcriptional activator PLCR protein; ternary co	97.37
3nf1_A		311	KLC 1, kinesin light chain 1; TPR, structural geno	97.31
3nf1_A		311	KLC 1, kinesin light chain 1; TPR, structural geno	97.31
4b4t_Q		434	26S proteasome regulatory subunit RPN6; hydrolase,	97.31
2qfc_A		293	PLCR protein; TPR, HTH, transcription regulation;	97.27
2ifu_A		307	Gamma-SNAP; membrane fusion, snare complex disasse	97.26
1hz4_A		373	MALT regulatory protein; two-helix bundles, helix	97.26
1qqe_A		292	Vesicular transport protein SEC17; helix-turn-heli	97.25
3edt_B		283	KLC 2, kinesin light chain 2; superhelical, struct	97.25
3uq3_A		258	Heat shock protein STI1; HSP90, peptide binding, c	97.23
3u3w_A		293	Transcriptional activator PLCR protein; ternary co	97.2
1hh8_A		213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	97.17
3edt_B		283	KLC 2, kinesin light chain 2; superhelical, struct	97.16
2qfc_A		293	PLCR protein; TPR, HTH, transcription regulation;	97.13
1hz4_A		373	MALT regulatory protein; two-helix bundles, helix	97.07
2vq2_A		225	PILW, putative fimbrial biogenesis and twitching m	96.9
2q7f_A		243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	96.9
3uq3_A		258	Heat shock protein STI1; HSP90, peptide binding, c	96.86
4eqf_A		365	PEX5-related protein; accessory protein, tetratric	96.82
4i17_A		228	Hypothetical protein; TPR repeats protein, structu	96.79
2ho1_A		252	Type 4 fimbrial biogenesis protein PILF; type IV p	96.76
3qky_A		261	Outer membrane assembly lipoprotein YFIO; membrane	96.75
3as5_A		186	MAMA; tetratricopeptide repeats (TPR) containing p	96.7
3hym_B		330	Cell division cycle protein 16 homolog; APC, anaph	96.58
2vq2_A		225	PILW, putative fimbrial biogenesis and twitching m	96.51
2fo7_A		136	Synthetic consensus TPR protein; tetratricopeptide	96.5
3as5_A		186	MAMA; tetratricopeptide repeats (TPR) containing p	96.49
3qky_A		261	Outer membrane assembly lipoprotein YFIO; membrane	96.4
2yhc_A		225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	96.33
2q7f_A		243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	96.28
1fch_A		368	Peroxisomal targeting signal 1 receptor; protein-p	96.26
3vtx_A		184	MAMA; tetratricopeptide repeats (TPR) containing p	96.26
3mkr_A		291	Coatomer subunit epsilon; tetratricopeptide repeat	96.22
4eqf_A		365	PEX5-related protein; accessory protein, tetratric	96.06
2vyi_A		131	SGTA protein; chaperone, TPR repeat, phosphoprotei	96.04
3ieg_A		359	DNAJ homolog subfamily C member 3; TPR motif, chap	96.04
1elr_A		131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	96.03
3hym_B		330	Cell division cycle protein 16 homolog; APC, anaph	95.98
2y4t_A		450	DNAJ homolog subfamily C member 3; chaperone, endo	95.97
3ieg_A		359	DNAJ homolog subfamily C member 3; TPR motif, chap	95.97
3sz7_A		164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	95.93
2vgx_A		148	Chaperone SYCD; alternative dimer assembly, tetrat	95.9
3urz_A		208	Uncharacterized protein; tetratricopeptide repeats	95.87
4gco_A		126	Protein STI-1; structural genomics, PSI-biology, m	95.79
1fch_A		368	Peroxisomal targeting signal 1 receptor; protein-p	95.79
3rkv_A		162	Putative peptidylprolyl isomerase; structural geno	95.79
3fp2_A		537	TPR repeat-containing protein YHR117W; TOM71, mito	95.77
2gw1_A		514	Mitochondrial precursor proteins import receptor;	95.72
3u4t_A		272	TPR repeat-containing protein; structural genomics	95.69
1na0_A		125	Designed protein CTPR3; de novo protein; HET: IPT;	95.61
2xcb_A		142	PCRH, regulatory protein PCRH; protein transport,	95.59
2lni_A		133	Stress-induced-phosphoprotein 1; structural genomi	95.59
4i17_A		228	Hypothetical protein; TPR repeats protein, structu	95.5
3vtx_A		184	MAMA; tetratricopeptide repeats (TPR) containing p	95.48
2xpi_A		597	Anaphase-promoting complex subunit CUT9; cell cycl	95.46
2pl2_A		217	Hypothetical conserved protein TTC0263; TPR, prote	95.46
3gyz_A		151	Chaperone protein IPGC; asymmetric homodimer, tetr	95.43
1xnf_A		275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	95.42
2e2e_A		177	Formate-dependent nitrite reductase complex NRFG;	95.38
3u4t_A		272	TPR repeat-containing protein; structural genomics	95.35
1xnf_A		275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	95.19
2fbn_A		198	70 kDa peptidylprolyl isomerase, putative; sulfur	95.1
2y4t_A		450	DNAJ homolog subfamily C member 3; chaperone, endo	95.04
1w3b_A		388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	95.04
3fp2_A		537	TPR repeat-containing protein YHR117W; TOM71, mito	95.02
2xpi_A		597	Anaphase-promoting complex subunit CUT9; cell cycl	95.0
4b4t_T		274	26S proteasome regulatory subunit RPN12; hydrolase	94.99
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	94.88
1a17_A		166	Serine/threonine protein phosphatase 5; hydrolase,	94.88
2xev_A		129	YBGF; tetratricopeptide, alpha-helical, metal bind	94.88
2gw1_A		514	Mitochondrial precursor proteins import receptor;	94.85
3cv0_A		327	Peroxisome targeting signal 1 receptor PEX5; TPR m	94.85
1w3b_A		388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	94.64
3upv_A		126	Heat shock protein STI1; TPR-fold, adaptor protein	94.62
2fo7_A		136	Synthetic consensus TPR protein; tetratricopeptide	94.6
1elw_A		118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	94.59
1kt0_A		457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	94.56
2dba_A		148	Smooth muscle cell associated protein-1, isoform 2	94.55
1a17_A		166	Serine/threonine protein phosphatase 5; hydrolase,	94.46
4gyw_A		723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	94.26
1ihg_A		370	Cyclophilin 40; ppiase immunophilin tetratricopept	94.08
1hxi_A		121	PEX5, peroxisome targeting signal 1 receptor PEX5;	94.0
2pl2_A		217	Hypothetical conserved protein TTC0263; TPR, prote	93.99
4abn_A		474	Tetratricopeptide repeat protein 5; P53 cofactor,	93.97
4gcn_A		127	Protein STI-1; structural genomics, PSI-biology, m	93.93
1p5q_A		336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	93.91
4abn_A		474	Tetratricopeptide repeat protein 5; P53 cofactor,	93.83
2vsy_A		568	XCC0866; transferase, glycosyl transferase, GT-B,	93.81
2kck_A		112	TPR repeat; tetratricopeptide repeat, structural g	93.1
1p5q_A		336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	92.66
3mv2_B		310	Coatomer subunit epsilon; vesicular membrane coat	92.56
4ga2_A		150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	92.52
3k9i_A		117	BH0479 protein; putative protein binding protein,	92.5
2vsy_A		568	XCC0866; transferase, glycosyl transferase, GT-B,	92.47
2yhc_A		225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	92.43
3ma5_A		100	Tetratricopeptide repeat domain protein; NESG, str	92.38
3n71_A		490	Histone lysine methyltransferase SMYD1; heart deve	92.05
2l6j_A		111	TPR repeat-containing protein associated with HSP;	92.04
2h6f_A		382	Protein farnesyltransferase/geranylgeranyltransfer	91.78
2kc7_A		99	BFR218_protein; tetratricopeptide repeat, all-alph	91.64
4ga2_A		150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	91.64
1na3_A		91	Designed protein CTPR2; de novo protein; HET: IPT;	91.64
1ouv_A		273	Conserved hypothetical secreted protein; TPR repea	91.27
2pzi_A		681	Probable serine/threonine-protein kinase PKNG; ATP	91.18
1hh8_A		213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	90.74
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	90.68
2kat_A		115	Uncharacterized protein; NESG, structure, structur	90.4
2hr2_A		159	Hypothetical protein; alpha-alpha superhelix fold,	90.28
2pzi_A		681	Probable serine/threonine-protein kinase PKNG; ATP	90.13
2ond_A		308	Cleavage stimulation factor 77 kDa subunit; HAT do	90.02
3mv2_B		310	Coatomer subunit epsilon; vesicular membrane coat	89.81
2xev_A		129	YBGF; tetratricopeptide, alpha-helical, metal bind	89.66
1elw_A		118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	89.64
4gyw_A		723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	89.55
3mkr_A		291	Coatomer subunit epsilon; tetratricopeptide repeat	89.46
3sz7_A		164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	89.31
3urz_A		208	Uncharacterized protein; tetratricopeptide repeats	89.01
4gcn_A		127	Protein STI-1; structural genomics, PSI-biology, m	88.79
1elr_A		131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	88.6
4gco_A		126	Protein STI-1; structural genomics, PSI-biology, m	88.52
3q49_B		137	STIP1 homology and U box-containing protein 1; E3	88.51
3n71_A		490	Histone lysine methyltransferase SMYD1; heart deve	88.51
3qww_A		433	SET and MYND domain-containing protein 2; methyltr	88.49
1ouv_A		273	Conserved hypothetical secreted protein; TPR repea	88.19
1wao_1		477	Serine/threonine protein phosphatase 5; hydrolase,	88.08
2vyi_A		131	SGTA protein; chaperone, TPR repeat, phosphoprotei	87.98
2h6f_A		382	Protein farnesyltransferase/geranylgeranyltransfer	87.51
2xcb_A		142	PCRH, regulatory protein PCRH; protein transport,	87.48
3upv_A		126	Heat shock protein STI1; TPR-fold, adaptor protein	87.42
2kck_A		112	TPR repeat; tetratricopeptide repeat, structural g	87.42
4g1t_A		472	Interferon-induced protein with tetratricopeptide	87.36
2if4_A		338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	87.29
2vgx_A		148	Chaperone SYCD; alternative dimer assembly, tetrat	87.05
1hxi_A		121	PEX5, peroxisome targeting signal 1 receptor PEX5;	86.8
4g1t_A		472	Interferon-induced protein with tetratricopeptide	86.7
2dba_A		148	Smooth muscle cell associated protein-1, isoform 2	86.5
1na0_A		125	Designed protein CTPR3; de novo protein; HET: IPT;	86.45
2lni_A		133	Stress-induced-phosphoprotein 1; structural genomi	86.29
2ond_A		308	Cleavage stimulation factor 77 kDa subunit; HAT do	85.76
3gyz_A		151	Chaperone protein IPGC; asymmetric homodimer, tetr	85.66
2r5s_A		176	Uncharacterized protein VP0806; APC090868.1, vibri	84.36
3qwp_A		429	SET and MYND domain-containing protein 3; SMYD3,SE	84.35
2fbn_A		198	70 kDa peptidylprolyl isomerase, putative; sulfur	84.3
2l6j_A		111	TPR repeat-containing protein associated with HSP;	83.59
1rz4_A		226	Eukaryotic translation initiation factor 3 subuni;	83.3
2v5f_A		104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	83.07
3rkv_A		162	Putative peptidylprolyl isomerase; structural geno	82.44
1wi9_A		72	Protein C20ORF116 homolog; helix-turn-helix motif,	81.58
2heo_A		67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	81.52
3rjv_A		212	Putative SEL1 repeat protein; alpha-alpha superhel	81.19

>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=9.2e-103  Score=819.66  Aligned_cols=444  Identities=33%  Similarity=0.554  Sum_probs=234.4

Q ss_pred             CcccccccchhHHHHHHHhhHHHhcc--CChHHHHHHHHHHcCCCchhHHHHHhcCCCCCCcccc----cccCCC-----
Q 012934            1 METGAHAREVRRIMRAVRLTMALRRK--LKAPVLSAFLNFALAPGSEAHSRLLSYLPKEDEHEME----VDTASS-----   69 (453)
Q Consensus         1 ~~~~~~~~~~r~~~r~~r~~~~~r~~--l~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~----~~~~~~-----   69 (453)
                      |||||.++|+|||+||||.++++||+  |++++|..+|+.+||++++.+..|+++|++++..+++    .+...+     
T Consensus        41 i~k~v~~~~~r~~~r~lr~~~~~rk~~~l~~~~l~~~i~~~~~~~~~~~~~ll~~l~~~~~~~~~~~~~~~~~~~~~~~~  120 (523)
T 4b4t_S           41 ISKTTLTLDPRYIWRSLKDLSSLRNQELLNAETLCFTVNVLYPDSSSFKKNLLKFITSNHKSSVPGSAELRNSYPASFYS  120 (523)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHhcchHHHHHHHHHhhhhhcccccCCHHHHHHHHHHHCCCCcHHHHHHHHHhccccccccccchhccccCcccccc
Confidence            79999999999999999999999999  9999999999999999999999999999865443221    111111     


Q ss_pred             -CCCCCCCCCCCHHHHHHHHHHHHHHhcccCHHHHHHHHHHHH--HHHHhhchhhhHHHHHHHHHHHHHHHHhhcCHH--
Q 012934           70 -GAPAPAKHPLPELEIYCYLLVLIFLIDKKRYNEAKACSSASI--ARLKNMNRRTVDVLAARLYFYYSLCYELTGDLA--  144 (453)
Q Consensus        70 -~~~~~~~~~~p~~e~~~~ll~~~~l~d~~~~~~A~~~~~~lv--~~l~~~~~r~~d~l~ak~~~~~~~~~e~~~~l~--  144 (453)
                       ...++..+++||+|+|+++|++++++|+++|++|.+|+..++  +.++.+||||+|.+.||+||||+++||+.+++.  
T Consensus       121 ~~~~~~~~~~~pE~~~y~~lL~~i~L~d~k~~~~~~~~~~~~~~~~~l~~~nrrtlD~l~ak~~fY~s~~~e~~~~~~~~  200 (523)
T 4b4t_S          121 VNTEKKTIEVTAEINCFMHLLVQLFLWDSKELEQLVEFNRKVVIPNLLCYYNLRSLNLINAKLWFYIYLSHETLARSSEE  200 (523)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cCCCCCCCCCChHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHHHHHHhcccccc
Confidence             112245678999999999999999999999999999999999  679999999999999999999999999988664  


Q ss_pred             --------HHHHHHHHHHHHhhhccCccchHHHHHHHHHHHHhcCChHHHHHHHhcCCcCcc-CChhhHHHHHHHHHHHH
Q 012934          145 --------EIRGNLLALHRIATLRHDELGQETLLNLLLRNYLHYNLYDQAEKLRSKAPRFEA-HSNQQFCRYLFYLGKIR  215 (453)
Q Consensus       145 --------~~r~~l~~~~rta~~~~~~~~~~~l~n~llr~Yl~~~~~~~a~~li~~~~~p~~-~~~~~~v~Y~YY~G~i~  215 (453)
                              ++|+.|++++|||++|||..||++++|+++|+|++.|.|++|.+++++++||+. .+++|+++|+||.|+|+
T Consensus       201 ~~~~~~~~~ir~~Ll~~~rta~lr~D~~~qa~l~nllLRnYL~~~~y~qA~~lvsk~~fP~~~~sn~q~~rY~YY~GRI~  280 (523)
T 4b4t_S          201 INSDNQNIILRSTMMKFLKIASLKHDNETKAMLINLILRDFLNNGEVDSASDFISKLEYPHTDVSSSLEARYFFYLSKIN  280 (523)
T ss_dssp             --CHHHHHHHHTHHHHHHHHCCSCSSSCHHHHHHHHHHHHHHHSSCSTTHHHHHHHHCSCTTTSCHHHHHHHHHHHHHHH
T ss_pred             cccccchhhHHHHHHHHHHHHhcccCcchhHHHHHHHHHHHHccCcHHHHHHHHhcCcCCcccCCHHHHHHHHHHHHHHH
Confidence                    489999999999999999999999999999999999999999999999999986 89999999999999999


Q ss_pred             HHHhhHHHHHHHHHHHHHcCCc--CchHhHHHHHHHHHhHHHhcCCCCChhhhhhhhhhhhhhhHHHHHHHHhcCCHHHH
Q 012934          216 TIQLEYTDAKESLLQAARKAPV--AALGFRVQCNKWAIIVRLLLGEIPERTVFMQKGMEKALRPYFELTNAVRIGDLELF  293 (453)
Q Consensus       216 ~~~~dy~~A~~~L~~A~~~~p~--~~~~~~~~alK~lIlv~LL~G~iP~~~ll~~~~l~~~l~~Y~~L~~Av~~Gdl~~f  293 (453)
                      +++++|.+|+++|.+|+++||+  .+.+|++.++|++|+|+||+|++|++++|.++.+++.|.||.+|++||+.||+..|
T Consensus       281 a~q~~Y~eA~~~L~~A~rkap~~~~a~gfr~~a~K~lI~V~LLlG~iP~r~lf~q~~l~~~L~pY~~Lv~Avr~GdL~~F  360 (523)
T 4b4t_S          281 AIQLDYSTANEYIIAAIRKAPHNSKSLGFLQQSNKLHCCIQLLMGDIPELSFFHQSNMQKSLLPYYHLTKAVKLGDLKKF  360 (523)
T ss_dssp             HHTTCHHHHHHHHHHHTSSCSCSSSCSHHHHHHHHHHHHHHHHHTCCCCHHHHTTTSCHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHhccHHHHHHHHHHHHHhCCcchhhhhHHHHHHHHHHhHHhhcCCCCChHHhhchhHHHHHHHHHHHHHHHHcCCHHHH
Confidence            9999999999999999999997  35799999999999999999999999999999998899999999999999999999


Q ss_pred             HHHHHhcchhhccCccHHHHHHHHHHHHHHHHHHHHhhcccccHHHHHHHhCCCCCCChHHHHHHHHHhHHcCCceeEee
Q 012934          294 KSVAEKFSSTFSSDRTNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVD  373 (453)
Q Consensus       294 ~~~l~~~~~~f~~Dg~~~Lv~rLr~~vir~~irki~~~YsrIsL~dIa~~L~l~~~~d~~eaE~iva~mI~dG~I~A~Id  373 (453)
                      ++++++|+..|.+||||+||+||+++|+|++||+|+++|++||++|||.+|+++++   ++|||+|++||.||+|+|+||
T Consensus       361 ~~~L~~h~~~F~~Dgty~LI~rLr~~vir~~irkis~~YsrIsL~dIa~kL~L~s~---eeaE~iVAkmI~dG~I~A~Id  437 (523)
T 4b4t_S          361 TSTITKYKQLLLKDDTYQLCVRLRSNVIKTGIRIISLTYKKISLRDICLKLNLDSE---QTVEYMVSRAIRDGVIEAKIN  437 (523)
T ss_dssp             HHHHHHTHHHHHHTTCTHHHHHHHHHHHHHHHHHSCCCSSEECHHHHHHHHHHHHS---SCHHHHHHHHHHHTSSCCEEC
T ss_pred             HHHHHHhcceeccCChhHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHhCCCCH---HHHHHHHHHHHHcCCceEEEe
Confidence            99999999999999999999999999999999999999999999999999999876   899999999999999999999


Q ss_pred             CCCcEEEecccccccCCccccHHHHHHHHHHHHHHHHHHHhcCCCCCCch-hhhhHHHHHHhhH-HHHHHHHhhcc
Q 012934          374 HANGWMVSKETGDIYSTNEPQLAFNSRIAFCLNMHNEAVRALRFPPNSHK-EKESAEKRRERQQ-QEQELAKHIAE  447 (453)
Q Consensus       374 ~~~G~v~~~~~~~v~s~~ep~~~l~~rI~~~l~l~~~~v~amr~p~~~~~-~~~~~~~~~~~~~-~~~e~~~~~~~  447 (453)
                      |++|+|.|++..++|++.+|+.+|++||+||++||||+|||||||++.++ +.+++++++++++ .+.+++.+++|
T Consensus       438 h~~g~v~ske~~d~yst~ep~~af~~RI~~cl~L~ne~vkaMryp~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~d  513 (523)
T 4b4t_S          438 HEDGFIETTELLNIYDSEDPQQVFDERIKFANQLHDEYLVSMRYPEDKKTQQNEKSENGENDDDTLDGDLMDDMSD  513 (523)
T ss_dssp             TTTCCEECCSSSCC--------------------------------------------------------------
T ss_pred             cCCCEEEeCccccccccHHHHHHHHHHHHHHHHHHHHHHHHccCCcccchhhHHHHHHHhhhhhhhhhcccccccc
Confidence            99999999999999999999999999999999999999999999999997 7777776655532 45555555543

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

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

>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

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

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

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

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

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

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

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

>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

>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

>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

>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

>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

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

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

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

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

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

>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

>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

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

>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

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

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

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

>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

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

>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

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

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

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

>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

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

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

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

>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

>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

>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

>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

>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

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

>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

>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

>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

>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

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

>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

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

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

>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

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

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

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

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

>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

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

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

>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

>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

>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

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

>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

>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

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

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

>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

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

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

>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

>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

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; 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

>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

>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

>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

>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

>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

>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

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

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

>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

>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

>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

>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

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

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

>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

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

>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

>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

>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

>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

>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

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

>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

>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

>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

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

>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

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

>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

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

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

>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

>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

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

>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

>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

>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

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

>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

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

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

>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

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

>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

>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

>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

>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

>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

>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

>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

>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

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

>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

>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

>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

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		453
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: 316 LRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHA 375
           L   VI   L + S  Y+ I+  ++   L +    P A AE I S+ I +G ++  +D  
Sbjct: 12  LDRAVIEHNLLSASKLYNNITFEELGALLEI----PAAKAEKIASQMITEGRMNGFIDQI 67

Query: 376 NG--WMVSKETGD 386
           +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		453
d1ufma_		84	COP9 signalosome complex subunit 4, GSN4 {Mouse (M	99.33
d1qqea_		290	Vesicular transport protein sec17 {Baker's yeast (	98.23
d1hz4a_		366	Transcription factor MalT domain III {Escherichia	96.76
d1w3ba_		388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	95.98
d1qqea_		290	Vesicular transport protein sec17 {Baker's yeast (	95.71
d1p5qa1		170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	95.39
d1elwa_		117	Hop {Human (Homo sapiens) [TaxId: 9606]}	95.32
d1xnfa_		259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	95.16
d1hh8a_		192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	95.12
d1hz4a_		366	Transcription factor MalT domain III {Escherichia	94.94
d2hr2a1		156	Hypothetical protein CT2138 {Chlorobium tepidum [T	94.92
d1a17a_		159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	94.81
d2c2la1		201	STIP1 homology and U box-containing protein 1, STU	94.53
d1ihga1		169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	94.42
d1xnfa_		259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	94.32
d1fcha_		323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	94.26
d2fbna1		153	Putative 70 kda peptidylprolyl isomerase PFL2275c	93.97
d1hxia_		112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	93.85
d1kt1a1		168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	93.66
d1w3ba_		388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	93.14
d1tjca_		95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	92.59
d1fcha_		323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	90.48
d2cfxa1		63	Transcriptional regulator LrpC {Bacillus subtilis	89.73
d2cg4a1		63	Regulatory protein AsnC {Escherichia coli [TaxId:	89.53
d1hxia_		112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	89.36
d1nzna_		122	Mitochondria fission protein Fis1 {Human (Homo sap	88.35
d1elra_		128	Hop {Human (Homo sapiens) [TaxId: 9606]}	87.87
d1tjca_		95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	87.15
d2pqrb1		124	Mitochondria fission protein Fis1 {Baker's yeast (	86.93
d2cyya1		60	Putative transcriptional regulator PH1519 {Archaeo	86.67
d1hh8a_		192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	86.57
d1a17a_		159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	86.53
d2c2la1		201	STIP1 homology and U box-containing protein 1, STU	86.34
d1elwa_		117	Hop {Human (Homo sapiens) [TaxId: 9606]}	84.59
d2onda1		308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	83.46
d1i1ga1		60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	83.38
d1wi9a_		72	Hypothetical protein C20orf116 homolog {Mouse (Mus	82.32

>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=99.33  E-value=3.1e-13  Score=107.25  Aligned_cols=75  Identities=23%  Similarity=0.330  Sum_probs=66.6

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHhhcccccHHHHHHHhCCCCCCChHHHHHHHHHhHHcCCceeEeeCCCcEEEeccccc
Q 012934          308 RTNNLIVRLRHNVIRTGLRNISISYSRISLADVAKKLRLDSANPVADAESIVSKAIRDGAIDATVDHANGWMVSKETGD  386 (453)
Q Consensus       308 g~~~Lv~rLr~~vir~~irki~~~YsrIsL~dIa~~L~l~~~~d~~eaE~iva~mI~dG~I~A~Id~~~G~v~~~~~~~  386 (453)
                      |+++...-|+.++++++|++++++|++|+|+++|+.++++.    +++|.+|++||.+|.|+|+||+.+|+|.|.....
T Consensus         4 ~~~~~~t~L~~~i~Ehni~~is~~Y~~Isl~~la~~l~l~~----~evE~~l~~mI~~~~i~akIDq~~g~V~F~~~e~   78 (84)
T d1ufma_           4 GSSGGSSILDRAVIEHNLLSASKLYNNITFEELGALLEIPA----AKAEKIASQMITEGRMNGFIDQIDGIVHFETREA   78 (84)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHHSCSEEEHHHHHHHTTSCH----HHHHHHHHHHHHTTSSCEEEETTTTEEEECCSSC
T ss_pred             cccchhHHHHHHHHHHHHHHHHHhhceeeHHHHHHHHCCCH----HHHHHHHHHHHhcCeEEEEEeCCCCEEEECCCCc
Confidence            33333344778899999999999999999999999999986    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

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

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

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

>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

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

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

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

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

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

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

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

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

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

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

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

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

>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

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

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

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

>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

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

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

>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

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