Citrus Sinensis ID: 004280

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760----

MSTYAKPEAALNQAEALINVGQKQDALQVLHDLITSKRHRAWQKILEKIMFKYVELCVDMRRGKFAKDGLIQYRIVCQQVNVTSLEEVIKHFMHLSTEKAEQARSQAQALEEALDVDDLEADKRPEDLMLSYVSGEKGKDRSDRELVTPWFKFLWETYRTVLEILRNNSKLEALYAMTAHRAFQFCKQYKRTTEFRRLCEIIRNHLLNLNKYRDQRDRPDLSSPESLQLYLDTRFEQLKVATDLQLWQEAFYSVEDIHGLMCMVKKTPKPSLLVVYYAKLTEIFWISSSHLYHAYAWFKLFTLQKTYNKNLSLKDLQLIASSVVLAALLVVPYDRSRSASHLELENEKDRNLRMANLIGFELDPKFDSREALSRSSLLSELVSKGVMSCATQEVKDLYNLLEHEFLPLDLASKVQPLLAKISKYGGKLASASSVPEVQLSRYIPALEKLVTLRVLQQVSEVYQMMRIESLSQMIPFFDFAVVEKISVEAVKHNFIAMKIDHMRGVVVFCNLGLESDGLRDHLTIFAQSLNKVRALIYPPANKASKLGEMLAGLGEIVDKEHKRLLARKSIIEKRKEEHERQLIEMEREEESRRLKQQKITEEAEQKRLAAEFEHRKNQRILREIEERELEEAQALLEEAEKRNKKKGGKKPILEGEKVLHEREQQLEVELSRQRHDGDLREKYRLSRMLDNKNTFQERVLNRRRVEVDRRKVEREERISLIIKARKQEREAKRKKIFYVRTEEEKIKRLREEEEARKREGIHIN

ccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHccccccccccHHHHcHHHHHHHHHHccccccccHHHHHHHHHHHHccccHHHHHcHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHEEEHHHHHcccccccHHHHHHHHHHHHHHccccEEEEccccEEEEcccccccHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccc

ccccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHcccccHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHcccHHHccHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHcccccHHHHHHHHHHHHHcccEEEEEEccccEEEEccccccHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccc

MSTYAKPEAALNQAEALINVGQKQDALQVLHDLITSKRHRAWQKILEKIMFKYVELCVDMrrgkfakdglIQYRIVCQQVNVTSLEEVIKHFMHLSTEKAEQARSQAQALEEALdvddleadkrpedLMLSYvsgekgkdrsdrelvtPWFKFLWETYRTVLEILRNNSKLEALYAMTAHRAFQFCKQYKRTTEFRRLCEIIRNHLLNlnkyrdqrdrpdlsspesLQLYLDTRFEQLKVATDLQLWQEAFYSVEDIHGLMcmvkktpkpsLLVVYYAKLTEIFWIssshlyhaYAWFKLFTLQKTynknlslkDLQLIASSVVLAALLVVpydrsrsashleleNEKDRNLRMANLIGfeldpkfdsrealSRSSLLSELVSKGVMSCATQEVKDLYNLleheflpldlaSKVQPLLAKISKYggklasassvpevqlsryipaLEKLVTLRVLQQVSEVYQMMRIESLSQMIPFFDFAVVEKISVEAVKHNFIAMKIDHMRGVVVFCNLglesdglrDHLTIFAQSLNKVRaliyppankasKLGEMLAGLGEIVDKEHKRLLARKSIIEKRKEEHERQLIEMEREEESRRLKQQKITEEAEQKRLAAEFEHRKNQRILREIEERELEEAQALLEEAEKRNkkkggkkpilegeKVLHEREQQLEVELSRqrhdgdlreKYRLSRMLDNKNTFQERVLNRRRVEVDRRKVEREERISLIIKARKQEREAKRKKIFYVRTEEEKIKRLREEEEARKREGIHIN

mstyakpeAALNQAEALINVGQKQDALQVLHDLITSKRHRAWQKILEKIMFKYVELCVDMRRGKFAKDGLIQYRIVCQQVNVTSLEEVIKHFMHLSTEKAEQARSQAQALEEAldvddleadkrpeDLMLsyvsgekgkdrsdrelvTPWFKFLWETYRTVLEILRNNSKLEALYAMTAHRAFQFCKQYKRTTEFRRLCEIIRNHllnlnkyrdqrdrpdlsspESLQLYLDTRFEQLKVATDLQLWQEAFYSVEDIHGLMCMVKKTPKPSLLVVYYAKLTEIFWISSSHLYHAYAWFKLFTLQKTYNKNLSLKDLQLIASSVVLAALLVVPydrsrsashlelenekdrnLRMANLIGFELDPKFDSREALSRSSLLSELVSKGVMSCATQEVKDLYNLLEHEFLPLDLASKVQPLLAKISKYGgklasassvpevQLSRYIPALEKLVTLRVLQQVSEVYQMMRIESLSQMIPFFDFAVVEKISVEAVKHNFIAMKIDHMRGVVVFCNLGLESDGLRDHLTIFAQSLNKVRALIYPPANKASKLGEMLAGLGEIVDKEHKRLLARKSIIEKRKEEHERQLIEMEREEESRRLKQQKITEEAEQKRlaaefehrknqrILREIEERELEEAQALLEEaekrnkkkggkkpilegekvlhEREQQLevelsrqrhdgdlrekyrlsrmldnkntfqervlnrrrvevdrrkvereerisLIIKarkqereakrkkifyvrteeekikrlreeeearkregihin

MSTYAKPEAALNQAEALINVGQKQDALQVLHDLITSKRHRAWQKILEKIMFKYVELCVDMRRGKFAKDGLIQYRIVCQQVNVTSLEEVIKHFMHLSTEKAEQARSQAQaleealdvddleadKRPEDLMLSYVSGEKGKDRSDRELVTPWFKFLWETYRTVLEILRNNSKLEALYAMTAHRAFQFCKQYKRTTEFRRLCEIIRNHLLNLNKYRDQRDRPDLSSPESLQLYLDTRFEQLKVATDLQLWQEAFYSVEDIHGLMCMVKKTPKPSLLVVYYAKLTEIFWISSSHLYHAYAWFKLFTLQKTYNKNLSLKDLQLIassvvlaallvvPYDRSRSASHLELENEKDRNLRMANLIGFELDPKFDsrealsrssllselvsKGVMSCATQEVKDLYNLLEHEFLPLDLASKVQPLLAKISKYGGKLASASSVPEVQLSRYIPALEKLVTLRVLQQVSEVYQMMRIESLSQMIPFFDFAVVEKISVEAVKHNFIAMKIDHMRGVVVFCNLGLESDGLRDHLTIFAQSLNKVRALIYPPANKASKLGEMLAGLGEIVDKEHKRLLARKSIIEKRKeeherqliemereeesrrLKQQKITEEAEQKRLAAEFEHRKNqrilreieereleeaqalleeaekrnkkkggkkpilegekVLHEREQQLEVELSRQRHDGDLREKYRLSRMLDNKNTFQervlnrrrvevdrrkvereerISLIIkarkqereakrkkIFYVrteeekikrlreeeearkreGIHIN

***************ALINVGQKQDALQVLHDLITSKRHRAWQKILEKIMFKYVELCVDMRRGKFAKDGLIQYRIVCQQVNVTSLEEVIKHFMHL*************************************************ELVTPWFKFLWETYRTVLEILRNNSKLEALYAMTAHRAFQFCKQYKRTTEFRRLCEIIRNHLLNLNKY**************LQLYLDTRFEQLKVATDLQLWQEAFYSVEDIHGLMCMVKKTPKPSLLVVYYAKLTEIFWISSSHLYHAYAWFKLFTLQKTYNKNLSLKDLQLIASSVVLAALLVVPYD*******************MANLIGFEL***************LSELVSKGVMSCATQEVKDLYNLLEHEFLPLDLASKVQPLLAKISKYGGKLASASSVPEVQLSRYIPALEKLVTLRVLQQVSEVYQMMRIESLSQMIPFFDFAVVEKISVEAVKHNFIAMKIDHMRGVVVFCNLGLESDGLRDHLTIFAQSLNKVRALIYPPANKASKLGEMLAGLGEIVDKE***L************************************************************************************************************************************************************I**************IFY**************************

***YAKPEAALNQAEALINVGQKQDALQVLHDLITSKRHRAWQKILEKIMFKYVELCVDMRRGKFAKDGLIQYRIVCQQVNVTSLEEVIKHFMHLSTEKA******************LEADKRPEDLMLSYVSGE****RSDRELVTPWFKFLWETYRTVLEILRNNSKLEALYAMTAHRAFQFCKQYKRTTEFRRLCEIIRNHLLNLNK*********LSSPESLQLYLDTRFEQLKVATDLQLWQEAFYSVEDIHGLMCMVKKTPKPSLLVVYYAKLTEIFWISSSHLYHAYAWFKLFTL***************IASSVVLAALLVV**********************MANLIGFEL*************SLLSELVSKGVMSCATQEVKDLYNLLEHEFLPLDLASKVQPLLAKISKYGG*******VPEVQLSRYIPALEKLVTLRVLQQVSEVYQMMRIESLSQMIPFFDFAVVEKISVEAVKHNFIAMKIDHMRGVVVFCNLGLESDGLRDHLTIFAQSLN******************************************************************************************************************************************************************************************************************************************

MSTYAKPEAALNQAEALINVGQKQDALQVLHDLITSKRHRAWQKILEKIMFKYVELCVDMRRGKFAKDGLIQYRIVCQQVNVTSLEEVIKHFMHLS*************LEEALDVDDLEADKRPEDLMLSYVS*********RELVTPWFKFLWETYRTVLEILRNNSKLEALYAMTAHRAFQFCKQYKRTTEFRRLCEIIRNHLLNLNKYRD********SPESLQLYLDTRFEQLKVATDLQLWQEAFYSVEDIHGLMCMVKKTPKPSLLVVYYAKLTEIFWISSSHLYHAYAWFKLFTLQKTYNKNLSLKDLQLIASSVVLAALLVVPYDRSRSASHLELENEKDRNLRMANLIGFELDPKFDSREALSRSSLLSELVSKGVMSCATQEVKDLYNLLEHEFLPLDLASKVQPLLAKISKY**********PEVQLSRYIPALEKLVTLRVLQQVSEVYQMMRIESLSQMIPFFDFAVVEKISVEAVKHNFIAMKIDHMRGVVVFCNLGLESDGLRDHLTIFAQSLNKVRALIYPPANKASKLGEMLAGLGEIVDKEHKRLLARKSIIEKRKEEHERQLIEM***************EEAEQKRLAAEFEHRKNQRILREIEERELEEAQALLEEA**********KPILEGEKVLHEREQQLEVELSRQRHDGDLREKYRLSRMLDNKNTFQERVLNRRRVEVDRRKVEREERISLIIKARKQEREAKRKKIFYVRTEEEKIKRLRE*************

**TYAKPEAALNQAEALINVGQKQDALQVLHDLITSKRHRAWQKILEKIMFKYVELCVDMRRGKFAKDGLIQYRIVCQQVNVTSLEEVIKHFMHLSTEKAEQARSQAQALEEALDVDDLEADKRPEDLMLSYVSG*KGKDRSDRELVTPWFKFLWETYRTVLEILRNNSKLEALYAMTAHRAFQFCKQYKRTTEFRRLCEIIRNHLLNLNKYRDQRDRPDLSSPESLQLYLDTRFEQLKVATDLQLWQEAFYSVEDIHGLMCMVKKTPKPSLLVVYYAKLTEIFWISSSHLYHAYAWFKLFTLQKTYNKNLSLKDLQLIASSVVLAALLVVPYDRSRSASHLELENEKDRNLRMANLIGFELDPKFDSREALSRSSLLSELVSKGVMSCATQEVKDLYNLLEHEFLPLDLASKVQPLLAKISKYG*******SVPEVQLSRYIPALEKLVTLRVLQQVSEVYQMMRIESLSQMIPFFDFAVVEKISVEAVKHNFIAMKIDHMRGVVVFCNLGLESDGLRDHLTIFAQSLNKVRALIYPPANKASKLGEMLAGLGEIVDKEHKRLLARKSIIEKRKEEHERQLIEMEREEESRRLKQQKITEEAEQKRLAAEFEHRKNQRILREIEERELEEAQALLEEAEKRNKKKGGKKPILEGEKVLHEREQQLEVELSRQRHDGDLREKYRLSRMLDNKNTFQERVLNRRRVEVDRRKVEREERISLIIKARKQEREAKRKKIFYVRTEEEKIKRLREEEEARKRE*****

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MSTYAKPEAALNQAEALINVGQKQDALQVLHDLITSKRHRAWQKILEKIMFKYVELCVDMRRGKFAKDGLIQYRIVCQQVNVTSLEEVIKHFxxxxxxxxxxxxxxxxxxxxxxxxxxxxADKRPEDLMLSYVSGEKGKDRSDRELVTPWFKFLWETYRTVLEILRNNSKLEALYAMTAHRAFQFCKQYKRTTEFRRLCEIIRNHLLNLNKYRDQRDRPDLSSPESLQLYLDTRFEQLKVATDLQLWQEAFYSVEDIHGLMCMVKKTPKPSLLVVYYAKLTEIFWISSSHLYHAYAWFKLFTLQKTYNKNLSLKDLQLIASSVVLAALLVVPYDRSRSASHLELENEKDRNLRMANLIGFELDPKFDSREALSRSSLLSELVSKGVMSCATQEVKDLYNLLEHEFLPLDLASKVQPLLAKISKYGGKLASASSVPEVQLSRYIPALEKLVTLRVLQQVSEVYQMMRIESLSQMIPFFDFAVVEKISVEAVKHNFIAMKIDHMRGVVVFCNLGLESDGLRDHLTIFAQSLNKVRALIYPPANKASKLGEMLAGLGEIVDKExxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxKRLAAEFEHxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxKPILEGEKVLHEREQQLEVELSRQRHDGDLREKYRLSRMLDNKNTFQERVLNRRRVEVDRRKVEREERISLIIKARKQEREAKRKKIFYxxxxxxxxxxxxxxxxxxxxxGIHIN

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		764	2.2.26 [Sep-21-2011]
Q40554		958	Eukaryotic translation in	N/A	no	0.980	0.781	0.717	0.0
Q9LD55		987	Eukaryotic translation in	yes	no	0.979	0.757	0.711	0.0
Q9XHR2		962	Eukaryotic translation in	N/A	no	0.972	0.772	0.654	0.0
A2VD00		1424	Eukaryotic translation in	N/A	no	0.789	0.423	0.388	1e-124
A4II09		1391	Eukaryotic translation in	yes	no	0.789	0.433	0.382	1e-123
Q6PCR7		1267	Eukaryotic translation in	yes	no	0.787	0.475	0.387	1e-122
Q1JU68		1354	Eukaryotic translation in	yes	no	0.782	0.441	0.397	1e-122
P23116		1344	Eukaryotic translation in	yes	no	0.787	0.447	0.391	1e-121
Q14152		1382	Eukaryotic translation in	yes	no	0.787	0.435	0.392	1e-121
Q0CUP6		1040	Eukaryotic translation in	N/A	no	0.802	0.589	0.387	1e-120

>sp\|Q40554\|EIF3A_TOBAC Eukaryotic translation initiation factor 3 subunit A OS=Nicotiana tabacum GN=TIF3A1 PE=2 SV=1	Back alignment and function desciption

 Score = 1129 bits (2921), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 578/806 (71%), Positives = 667/806 (82%), Gaps = 57/806 (7%)

Query: 1   MSTYAKPEAALNQAEALINVGQKQDALQVLHDLITSKRHRAWQKILEKIMFKYVELCVDM 60
           M+T+AKPE AL +AE LI VGQKQ+ALQ LHDLITS+R+RAWQK LE+IMFKYVELCVDM
Sbjct: 1   MATFAKPENALKRAEELITVGQKQEALQALHDLITSRRYRAWQKTLERIMFKYVELCVDM 60

Query: 61  RRGKFAKDGLIQYRIVCQQVNVTSLEEVIKHFMHLSTEKAEQARSQAQALEEALDVDDLE 120
           RRG+FAKDGLIQYRIVCQQVN+ SLEEVIKHFMHL+TE+AE AR+QAQALEEALDV+DLE
Sbjct: 61  RRGRFAKDGLIQYRIVCQQVNINSLEEVIKHFMHLATERAELARNQAQALEEALDVEDLE 120

Query: 121 ADKRPEDLMLSYVSGEKGKDRSDRELVTPWFKFLWETYRTVLEILRNNSKLEALYAMTAH 180
           ADKRPEDLMLSYVSGEKGKDRSDRELVTPWFKFLWETYRTVLEILRNNS+LEALYAMTAH
Sbjct: 121 ADKRPEDLMLSYVSGEKGKDRSDRELVTPWFKFLWETYRTVLEILRNNSRLEALYAMTAH 180

Query: 181 RAFQFCKQYKRTTEFRRLCEIIRNHLLNLNKYRDQRDRPDLSSPESLQLYLDTRFEQLKV 240
           RAFQFCKQYKRTTEFRRLCEIIRNHL NLNKYRDQRDRPDLS+PESLQLYLDTRFEQLKV
Sbjct: 181 RAFQFCKQYKRTTEFRRLCEIIRNHLANLNKYRDQRDRPDLSAPESLQLYLDTRFEQLKV 240

Query: 241 ATDLQLWQEAFYSVEDIHGLMCMVKKTPKPSLLVVYYAKLTEIFWISSSHLYHAYAWFKL 300
           AT+L LWQEAF S+EDI+GLMCMVKKTPK SL+VVYY KLTEIFW+SS+HLYHAYAW KL
Sbjct: 241 ATELGLWQEAFRSIEDIYGLMCMVKKTPKASLMVVYYGKLTEIFWMSSNHLYHAYAWLKL 300

Query: 301 FTLQKTYNKNLSLKDLQLIASSVVLAALLVVPYDRSRSASHLELENEKDRNLRMANLIGF 360
           F+LQK++NKNLS KDLQLIASSVVLAAL V PYD+S  ASHLELENEK+R+LR+ANLIGF
Sbjct: 301 FSLQKSFNKNLSQKDLQLIASSVVLAALSVPPYDQSYGASHLELENEKERSLRVANLIGF 360

Query: 361 ELDPKFDSREALSRSSLLSELVSKGVMSCATQEVKDLYNLLEHEFLPLDLASKVQPLLAK 420
           E++PK ++R ALSRSSLLSELVSKGVMSC TQEVKDLY+LLE+EFLPLDLA KVQP+L+K
Sbjct: 361 EVEPKAENRVALSRSSLLSELVSKGVMSCVTQEVKDLYHLLENEFLPLDLALKVQPVLSK 420

Query: 421 ISKYGGKLASASSVPEVQLSRYIPALEKLVTLRVLQQVSEVYQMMRIESLSQMIPFFDFA 480
           ISK GGKL+S SSVPEVQLS+Y+PALEKL TLR+LQQVS+VYQ ++I+++S+MIPFFDF 
Sbjct: 421 ISKLGGKLSSVSSVPEVQLSQYVPALEKLATLRLLQQVSQVYQTIQIDNISKMIPFFDFT 480

Query: 481 VVEKISVEAVKHNFIAMKIDHMRGVVVFCNLGLESDGLRDHLTIFAQSLNKVRALIYPPA 540
           V+EKISV+AV+ NF+A+K+DHM+G+    N  L            A+SL+K R +IYPPA
Sbjct: 481 VIEKISVDAVRRNFLAIKVDHMKGLSSLVNRVLRRKDSGIICLFLAESLSKARTMIYPPA 540

Query: 541 NKASKLGEMLAGLGEIVDKEHKRLLARKSIIEKRKEEHERQLIEMEREEESRRLKQQKIT 600
            KA+KLGE L+ L EIV+KEHKRLLARKSIIEKRKEE ER L+EMER EE++R   QK+T
Sbjct: 541 KKAAKLGEALSNLAEIVEKEHKRLLARKSIIEKRKEEQERLLLEMERVEETKRRDVQKMT 600

Query: 601 EEAEQKRLAAEFEHRKNQRILREIEERELEEAQALLEEAEKRNKKKG-----GKK----- 650
           EEAEQKR+AAE+E R+NQRIL+EIE+RELEEAQALL EAEKR+K+K      G+K     
Sbjct: 601 EEAEQKRIAAEYEQRRNQRILKEIEDRELEEAQALLHEAEKRSKRKKKPVLEGEKMTKKV 660

Query: 651 ---------------------------------------PILEG--------EKVLHERE 663
                                                  P++E         E  LHERE
Sbjct: 661 IMELALNEQLRERQEMEKKLLKFAKSMDHLERAKREEAAPLIESAFKQRLAEEAALHERE 720

Query: 664 QQLEVELSRQRHDGDLREKYRLSRMLDNKNTFQERVLNRRRVEVDRRKVEREERISLIIK 723
           QQ E+ELSRQRH GDL EK RL+RML+NK   QE+V++ R  E  R K ER+ERIS II+
Sbjct: 721 QQQEIELSRQRHAGDLEEKRRLARMLENKRILQEKVVSSREAEFTRMKRERQERISQIIQ 780

Query: 724 ARKQEREAKRKKIFYVRTEEEKIKRL 749
           +RKQEREA+RK IF++R+EEE+ KRL
Sbjct: 781 SRKQEREARRKMIFFLRSEEERQKRL 806

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome.
Nicotiana tabacum (taxid: 4097)

>sp\|Q9LD55\|EIF3A_ARATH Eukaryotic translation initiation factor 3 subunit A OS=Arabidopsis thaliana GN=TIF3A1 PE=1 SV=1	Back alignment and function description

>sp\|Q9XHR2\|EIF3A_MAIZE Eukaryotic translation initiation factor 3 subunit A OS=Zea mays GN=TIF3A1 PE=2 SV=1	Back alignment and function description

>sp\|A2VD00\|EIF3A_XENLA Eukaryotic translation initiation factor 3 subunit A OS=Xenopus laevis GN=eif3a PE=2 SV=1	Back alignment and function description

>sp\|A4II09\|EIF3A_XENTR Eukaryotic translation initiation factor 3 subunit A OS=Xenopus tropicalis GN=eif3a PE=2 SV=1	Back alignment and function description

>sp\|Q6PCR7\|EIF3A_DANRE Eukaryotic translation initiation factor 3 subunit A OS=Danio rerio GN=eif3a PE=2 SV=1	Back alignment and function description

>sp\|Q1JU68\|EIF3A_RAT Eukaryotic translation initiation factor 3 subunit A OS=Rattus norvegicus GN=Eif3a PE=2 SV=2	Back alignment and function description

>sp\|P23116\|EIF3A_MOUSE Eukaryotic translation initiation factor 3 subunit A OS=Mus musculus GN=Eif3a PE=1 SV=5	Back alignment and function description

>sp\|Q14152\|EIF3A_HUMAN Eukaryotic translation initiation factor 3 subunit A OS=Homo sapiens GN=EIF3A PE=1 SV=1	Back alignment and function description

>sp\|Q0CUP6\|EIF3A_ASPTN Eukaryotic translation initiation factor 3 subunit A OS=Aspergillus terreus (strain NIH 2624 / FGSC A1156) GN=tif32 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		764
296089739		884	unnamed protein product [Vitis vinifera]	0.976	0.843	0.778	0.0
225450669		977	PREDICTED: eukaryotic translation initia	0.976	0.763	0.778	0.0
255542824		994	Eukaryotic translation initiation factor	0.980	0.753	0.774	0.0
224125084		994	predicted protein [Populus trichocarpa]	0.980	0.753	0.779	0.0
356572345		957	PREDICTED: eukaryotic translation initia	0.993	0.793	0.722	0.0
356505122		958	PREDICTED: eukaryotic translation initia	0.993	0.792	0.719	0.0
224123680		972	predicted protein [Populus trichocarpa]	0.980	0.770	0.776	0.0
449522901		970	PREDICTED: LOW QUALITY PROTEIN: eukaryot	0.979	0.771	0.724	0.0
449435518		816	PREDICTED: eukaryotic translation initia	0.988	0.925	0.733	0.0
297813615		982	hypothetical protein ARALYDRAFT_489971 [	0.980	0.762	0.713	0.0

>gi\|296089739\|emb\|CBI39558.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score = 1233 bits (3190), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 626/804 (77%), Positives = 691/804 (85%), Gaps = 58/804 (7%)

Query: 1   MSTYAKPEAALNQAEALINVGQKQDALQVLHDLITSKRHRAWQKILEKIMFKYVELCVDM 60
           M+T+AKPE AL +AE LINVGQKQDALQ LHDLITSKR+RAWQK LE+IMFKYVELCVDM
Sbjct: 1   MATFAKPENALKRAEELINVGQKQDALQALHDLITSKRYRAWQKTLERIMFKYVELCVDM 60

Query: 61  RRGKFAKDGLIQYRIVCQQVNVTSLEEVIKHFMHLSTEKAEQARSQAQALEEALDVDDLE 120
           RRG+FAKDGLIQYRIVCQQVNVTSLEEVIKHFMHLSTEKAEQAR+QAQALEEALDVDDLE
Sbjct: 61  RRGRFAKDGLIQYRIVCQQVNVTSLEEVIKHFMHLSTEKAEQARNQAQALEEALDVDDLE 120

Query: 121 ADKRPEDLMLSYVSGEKGKDRSDRELVTPWFKFLWETYRTVLEILRNNSKLEALYAMTAH 180
           ADKRPEDLMLSYVSGEKGKDRSDRELVTPWFKFLWETYRTVLEILRNNSKLEALYAMTAH
Sbjct: 121 ADKRPEDLMLSYVSGEKGKDRSDRELVTPWFKFLWETYRTVLEILRNNSKLEALYAMTAH 180

Query: 181 RAFQFCKQYKRTTEFRRLCEIIRNHLLNLNKYRDQRDRPDLSSPESLQLYLDTRFEQLKV 240
           RAFQFCKQYKRTTEFRRLCEIIRNHL NLNKYRDQRDRPDLS+PESLQLYLDTRFEQLK+
Sbjct: 181 RAFQFCKQYKRTTEFRRLCEIIRNHLSNLNKYRDQRDRPDLSAPESLQLYLDTRFEQLKI 240

Query: 241 ATDLQLWQEAFYSVEDIHGLMCMVKKTPKPSLLVVYYAKLTEIFWISSSHLYHAYAWFKL 300
           AT+L+LWQEAF SVEDIHGLMCMVKKTPK SL+VVYYAKLTEIFW+SSSHLYHAYAWFKL
Sbjct: 241 ATELELWQEAFRSVEDIHGLMCMVKKTPKASLMVVYYAKLTEIFWVSSSHLYHAYAWFKL 300

Query: 301 FTLQKTYNKNLSLKDLQLIASSVVLAALLVVPYDRSRSASHLELENEKDRNLRMANLIGF 360
           F+LQK++NKNLS KDLQLIASSVVLAAL V PYD +R ASHLELENEK+RNLRMANLIGF
Sbjct: 301 FSLQKSFNKNLSQKDLQLIASSVVLAALSVTPYDLTRGASHLELENEKERNLRMANLIGF 360

Query: 361 ELDPKFDSREALSRSSLLSELVSKGVMSCATQEVKDLYNLLEHEFLPLDLASKVQPLLAK 420
            L+PK D RE LSRS+LLSELVSKGVM+C TQEVKDLY+LLEHEFLPLDLAS+VQPLLAK
Sbjct: 361 NLEPKLDGREVLSRSALLSELVSKGVMTCVTQEVKDLYHLLEHEFLPLDLASRVQPLLAK 420

Query: 421 ISKYGGKLASASSVPEVQLSRYIPALEKLVTLRVLQQVSEVYQMMRIESLSQMIPFFDFA 480
           ISK GGKL+SASSV EVQLS+Y+PALEKL TLR+LQQVS+VYQ M+IESLS++I FFDF+
Sbjct: 421 ISKLGGKLSSASSVSEVQLSQYVPALEKLATLRLLQQVSQVYQTMKIESLSKVIQFFDFS 480

Query: 481 VVEKISVEAVKHNFIAMKIDHMRGVVVFCNLGLESDGLRDHLTIFAQSLNKVRALIYPPA 540
           VVEKISV+AVKH FIAMK+DHM+GV++F NLGLESD +RDHLT+FA+ LNK RALI+PPA
Sbjct: 481 VVEKISVDAVKHGFIAMKVDHMKGVILFGNLGLESDRMRDHLTVFAEFLNKARALIHPPA 540

Query: 541 NKASKLGEMLAGLGEIVDKEHKRLLARKSIIEKRKEEHERQLIEMEREEESRRLKQQKIT 600
            KASKLG+ML+GL E VDKEHKRLLARKSIIEKRKEE ERQL+EMEREEES+RLK QKIT
Sbjct: 541 KKASKLGDMLSGLAETVDKEHKRLLARKSIIEKRKEEQERQLLEMEREEESKRLKLQKIT 600

Query: 601 EEAEQKRLAAEFEHRKNQRILREIEERELEEAQALLEEAEK------------------- 641
           EEAEQKRLA+E+E RK QRILREIEERELEEAQALL+EAEK                   
Sbjct: 601 EEAEQKRLASEYEQRKTQRILREIEERELEEAQALLQEAEKRSKKKGKKPIAEGEKVTKQ 660

Query: 642 -----------RNKKKGGKK--------------------PILEG--------EKVLHER 662
                      R +++  KK                    P++E         EK  HE 
Sbjct: 661 SLMELALSEQLRERQEMEKKLQKLAKTMDYLERAKREEAAPLIEAAFQQRLVEEKAFHEH 720

Query: 663 EQQLEVELSRQRHDGDLREKYRLSRMLDNKNTFQERVLNRRRVEVDRRKVEREERISLII 722
           EQQ E+E+SRQRHDGDLREK RL RMLD K  FQERV+NRR+ E  R + EREERIS II
Sbjct: 721 EQQQEIEVSRQRHDGDLREKNRLVRMLDKKMIFQERVMNRRQAEYSRLRAEREERISQII 780

Query: 723 KARKQEREAKRKKIFYVRTEEEKI 746
           ++RKQEREAKRK +FY+R+EEE++
Sbjct: 781 QSRKQEREAKRKMLFYLRSEEERM 804

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|225450669\|ref\|XP_002283093.1\| PREDICTED: eukaryotic translation initiation factor 3 subunit A [Vitis vinifera]	Back alignment and taxonomy information

>gi\|255542824\|ref\|XP_002512475.1\| Eukaryotic translation initiation factor 3 subunit, putative [Ricinus communis] gi\|223548436\|gb\|EEF49927.1\| Eukaryotic translation initiation factor 3 subunit, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|224125084\|ref\|XP_002319496.1\| predicted protein [Populus trichocarpa] gi\|222857872\|gb\|EEE95419.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356572345\|ref\|XP_003554329.1\| PREDICTED: eukaryotic translation initiation factor 3 subunit A-like [Glycine max] gi\|47076999\|dbj\|BAD18434.1\| unnamed protein product [Homo sapiens]	Back alignment and taxonomy information

>gi\|356505122\|ref\|XP_003521341.1\| PREDICTED: eukaryotic translation initiation factor 3 subunit A-like [Glycine max]	Back alignment and taxonomy information

>gi\|224123680\|ref\|XP_002330181.1\| predicted protein [Populus trichocarpa] gi\|222871637\|gb\|EEF08768.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|449522901\|ref\|XP_004168464.1\| PREDICTED: LOW QUALITY PROTEIN: eukaryotic translation initiation factor 3 subunit A-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449435518\|ref\|XP_004135542.1\| PREDICTED: eukaryotic translation initiation factor 3 subunit A-like, partial [Cucumis sativus]	Back alignment and taxonomy information

>gi\|297813615\|ref\|XP_002874691.1\| hypothetical protein ARALYDRAFT_489971 [Arabidopsis lyrata subsp. lyrata] gi\|297320528\|gb\|EFH50950.1\| hypothetical protein ARALYDRAFT_489971 [Arabidopsis lyrata subsp. lyrata]	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		764
TAIR\|locus:2123076		987	EIF3A "AT4G11420" [Arabidopsis	0.806	0.624	0.727	2.2e-253
UNIPROTKB\|E1BSS3		1365	EIF3A "Uncharacterized protein	0.774	0.433	0.365	9.4e-105
UNIPROTKB\|F1S4P6		1378	EIF3A "Uncharacterized protein	0.774	0.429	0.364	2.8e-103
RGD\|1307269		1354	Eif3a "eukaryotic translation	0.774	0.437	0.364	3.6e-103
UNIPROTKB\|F1LRG1		1344	Eif3a "Eukaryotic translation	0.774	0.440	0.364	3.6e-103
UNIPROTKB\|E2RSR5		1350	EIF3A "Uncharacterized protein	0.774	0.438	0.362	3.6e-103
UNIPROTKB\|E1B7R4		1378	EIF3A "Uncharacterized protein	0.774	0.429	0.362	3.7e-103
UNIPROTKB\|Q14152		1382	EIF3A "Eukaryotic translation	0.774	0.428	0.362	6.6e-103
MGI\|MGI:95301		1344	Eif3a "eukaryotic translation	0.774	0.440	0.359	7.4e-103
ZFIN\|ZDB-GENE-030131-5726		1267	eif3s10 "eukaryotic translatio	0.774	0.467	0.356	1.2e-102

TAIR\|locus:2123076 EIF3A "AT4G11420" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 2330 (825.3 bits), Expect = 2.2e-253, Sum P(2) = 2.2e-253
 Identities = 448/616 (72%), Positives = 517/616 (83%)

Query:     1 MSTYAKPEAALNQAEALINVGQKQDALQVLHDLITSKRHRAWQKILEKIMFKYVELCVDM 60
             M+ +AKPE AL +A+ LINVGQKQDALQ LHDLITSKR+RAWQK LEKIMFKY++LCVD+
Sbjct:     1 MANFAKPENALKRADELINVGQKQDALQALHDLITSKRYRAWQKPLEKIMFKYLDLCVDL 60

Query:    61 RRGKFAKDGLIQYRIVCQQVNVTSLEEVIKHFMHLSTEKAEQARSQAQXXXXXXXXXXXX 120
             +RG+FAKDGLIQYRIVCQQVNV+SLEEVIKHF+HL+T+KAEQARSQA             
Sbjct:    61 KRGRFAKDGLIQYRIVCQQVNVSSLEEVIKHFLHLATDKAEQARSQADALEEALDVDDLE 120

Query:   121 XXKRPEDLMLSYVSGEKGKDRSDRELVTPWFKFLWETYRTVLEILRNNSKLEALYAMTAH 180
               ++PEDL LS VSGEKGKDRSDRELVTPWFKFLWETYRTVLEILRNNSKLEALYAMTAH
Sbjct:   121 ADRKPEDLQLSIVSGEKGKDRSDRELVTPWFKFLWETYRTVLEILRNNSKLEALYAMTAH 180

Query:   181 RAFQFCKQYKRTTEFRRLCEIIRNHLLNLNKYRDQRDRPDLSSPESLQLYLDTRFEQLKV 240
             +AFQFCKQYKRTTEFRRLCEIIRNHL NLNKYRDQRDRPDLS+PESLQLYLDTRF+QLKV
Sbjct:   181 KAFQFCKQYKRTTEFRRLCEIIRNHLANLNKYRDQRDRPDLSAPESLQLYLDTRFDQLKV 240

Query:   241 ATDLQLWQEAFYSVEDIHGLMCMVKKTPKPSLLVVYYAKLTEIFWISSSHLYHAYAWFKL 300
             AT+L LWQEAF SVEDI+GLMCMVKKTPK SLL+VYY+KLTEIFWISSSHLYHAYAWFKL
Sbjct:   241 ATELGLWQEAFRSVEDIYGLMCMVKKTPKSSLLMVYYSKLTEIFWISSSHLYHAYAWFKL 300

Query:   301 FTLQKTYNKNLSLKDLQLIXXXXXXXXXXXXPYDRSRSASHLELENEKDRNLRMANLIGF 360
             F+LQK +NKNLS KDLQLI            P+DR++SASH+ELENEK+RNLRMANLIGF
Sbjct:   301 FSLQKNFNKNLSQKDLQLIASSVVLAALSIPPFDRAQSASHMELENEKERNLRMANLIGF 360

Query:   361 ELDPKFDXXXXXXXXXXXXXXXXKGVMSCATQEVKDLYNLLEHEFLPLDLASKVQPLLAK 420
              L+PKF+                KGV+SCA+QEVKDL+++LEHEF PLDL SK+QPLL K
Sbjct:   361 NLEPKFEGKDMLSRSALLSELVSKGVLSCASQEVKDLFHVLEHEFHPLDLGSKIQPLLEK 420

Query:   421 ISKYGGKLASASSVPEVQLSRYIPALEKLVTLRVLQQVSEVYQMMRIESLSQMIPFFDFA 480
             ISK GGKL+SA S+PEVQLS+Y+P+LEKL TLR+LQQVS++YQ +RIESLSQ++PFF F+
Sbjct:   421 ISKSGGKLSSAPSLPEVQLSQYVPSLEKLATLRLLQQVSKIYQTIRIESLSQLVPFFQFS 480

Query:   481 VVEKISVEAVKHNFIAMKIDHMRGVVVFCNLGLESDGLRDHLTIFAQSLNKVRALIYPPA 540
              VEKISV+AVK+NF+AMK+DHM+GVV+F NLG+ESDGLRDHL +FA+SL+KVRA++YP  
Sbjct:   481 EVEKISVDAVKNNFVAMKVDHMKGVVIFGNLGIESDGLRDHLAVFAESLSKVRAMLYPVP 540

Query:   541 NKASKLGEMLAGLGEIVDKEHKRLLARKSIIEKRKXXXXXXXXXXXXXXXXXXLKQQKIT 600
             +KASKL  ++  L + V+KEHKRLLARKSIIEKRK                  LK QK+T
Sbjct:   541 SKASKLAGVIPNLADTVEKEHKRLLARKSIIEKRKEDQERQQLEMEREEEQKRLKLQKLT 600

Query:   601 EEAEQKRLAAEFEHRK 616
             EEAEQKRLAAE   R+
Sbjct:   601 EEAEQKRLAAELAERR 616

GO:0003743 "translation initiation factor activity" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=ISS

GO:0006413 "translational initiation" evidence=TAS

GO:0005886 "plasma membrane" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

UNIPROTKB\|E1BSS3 EIF3A "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|F1S4P6 EIF3A "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

RGD\|1307269 Eif3a "eukaryotic translation initiation factor 3, subunit A" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|F1LRG1 Eif3a "Eukaryotic translation initiation factor 3 subunit A" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|E2RSR5 EIF3A "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|E1B7R4 EIF3A "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|Q14152 EIF3A "Eukaryotic translation initiation factor 3 subunit A" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

MGI\|MGI:95301 Eif3a "eukaryotic translation initiation factor 3, subunit A" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-030131-5726 eif3s10 "eukaryotic translation initiation factor 3, subunit 10 (theta)" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9LD55	EIF3A_ARATH	No assigned EC number	0.7116	0.9790	0.7578	yes	no
Q40554	EIF3A_TOBAC	No assigned EC number	0.7171	0.9803	0.7818	N/A	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00022664001	SubName- Full=Chromosome chr14 scaffold_27, whole genome shotgun sequence; (977 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00025658001	SubName- Full=Chromosome chr8 scaffold_34, whole genome shotgun sequence; (437 aa)	•	•	•	•	0.949
	GSVIVG00015309001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (363 aa)	•	•	•	•	0.939
	GSVIVG00023929001	SubName- Full=Chromosome chr6 scaffold_3, whole genome shotgun sequence; (269 aa)	•	•	•	•	0.931
	GSVIVG00031929001	SubName- Full=Putative uncharacterized protein (Chromosome undetermined scaffold_60, whole geno [...] (464 aa)	•	•	•	•	0.913
	GSVIVG00024042001	SubName- Full=Chromosome chr6 scaffold_3, whole genome shotgun sequence; (344 aa)	•	•	•	•	0.912
	GSVIVG00029350001	SubName- Full=Chromosome chr13 scaffold_48, whole genome shotgun sequence; (344 aa)	•	•	•	•	0.912
	GSVIVG00033547001	SubName- Full=Chromosome chr5 scaffold_67, whole genome shotgun sequence; (333 aa)	•	•	•	•	0.855
	GSVIVG00025451001	SubName- Full=Chromosome chr8 scaffold_34, whole genome shotgun sequence; (605 aa)	•	•	•	•	0.851
	GSVIVG00030682001	SubName- Full=Putative uncharacterized protein (Chromosome chr1 scaffold_5, whole genome shotgu [...] (326 aa)	•	•	•	•	0.828
	GSVIVG00022319001	SubName- Full=Chromosome chr14 scaffold_26, whole genome shotgun sequence; (116 aa)			•		0.800

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		764
PTZ00121		2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-07
smart00753		88	smart00753, PAM, PCI/PINT associated module	6e-07
smart00088		88	smart00088, PINT, motif in proteasome subunits, In	6e-07
PTZ00121		2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-06
PTZ00121		2084	PTZ00121, PTZ00121, MAEBL; Provisional	9e-06
COG1196		1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-05
TIGR02169		1164	TIGR02169, SMC_prok_A, chromosome segregation prot	3e-05
COG1196		1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-05
PTZ00121		2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-05
COG1196		1163	COG1196, Smc, Chromosome segregation ATPases [Cell	5e-05
pfam01399		100	pfam01399, PCI, PCI domain	5e-05
TIGR02169		1164	TIGR02169, SMC_prok_A, chromosome segregation prot	1e-04
PRK02224		880	PRK02224, PRK02224, chromosome segregation protein	2e-04
PTZ00121		2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-04
pfam00716		326	pfam00716, Peptidase_S21, Assemblin (Peptidase fam	4e-04
PTZ00121		2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-04
PTZ00121		2084	PTZ00121, PTZ00121, MAEBL; Provisional	6e-04
COG1196		1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.001
COG1196		1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.001
pfam05279		240	pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylas	0.001
TIGR02168		1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.001
COG1196		1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
COG1196		1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
COG0419		908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.002
PRK03918		880	PRK03918, PRK03918, chromosome segregation protein	0.002
PRK12704		520	PRK12704, PRK12704, phosphodiesterase; Provisional	0.002
pfam02463		1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.002
PTZ00121		2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.003
PTZ00121		2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.004

>gnl\|CDD\|173412 PTZ00121, PTZ00121, MAEBL; Provisional	Back alignment and domain information

 Score = 55.1 bits (132), Expect = 1e-07
 Identities = 44/212 (20%), Positives = 97/212 (45%), Gaps = 22/212 (10%)

Query: 559  KEHKRLLARKSIIEKRKEEHERQLIEMEREEESRRLKQQKITEE---AEQKRLAAEFEHR 615
            +E K+    K   E +K +  ++  E ++ +E ++ ++ K  EE   AE+ + A E ++ 
Sbjct: 1519 EEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNM 1578

Query: 616  KNQR--ILREIEERELEEAQALLEEAEKRNKKKGGK--KPILEGEKVLHEREQQLEVELS 671
              ++    ++ EE  +EE   L EE +K   ++  K  +  ++ E++    E++ +VE  
Sbjct: 1579 ALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQL 1638

Query: 672  RQRHDGDLREKYRLSRMLDNKNTFQERVLNRRRVEVDRRKVEREERISLIIKARKQEREA 731
            +++   + ++   L +  +            ++ E D++K E         +A+K E + 
Sbjct: 1639 KKKEAEEKKKAEELKKAEEENKIKAAEE--AKKAEEDKKKAE---------EAKKAEEDE 1687

Query: 732  KRKKIFYVRTEEEKIK----RLREEEEARKRE 759
            K+      +  EE  K    + +E EE +K E
Sbjct: 1688 KKAAEALKKEAEEAKKAEELKKKEAEEKKKAE 1719

Length = 2084

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

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

>gnl\|CDD\|173412 PTZ00121, PTZ00121, MAEBL; Provisional	Back alignment and domain information

>gnl\|CDD\|173412 PTZ00121, PTZ00121, MAEBL; Provisional	Back alignment and domain information

>gnl\|CDD\|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	Back alignment and domain information

>gnl\|CDD\|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type	Back alignment and domain information

>gnl\|CDD\|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	Back alignment and domain information

>gnl\|CDD\|173412 PTZ00121, PTZ00121, MAEBL; Provisional	Back alignment and domain information

>gnl\|CDD\|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	Back alignment and domain information

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

>gnl\|CDD\|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type	Back alignment and domain information

>gnl\|CDD\|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional	Back alignment and domain information

>gnl\|CDD\|173412 PTZ00121, PTZ00121, MAEBL; Provisional	Back alignment and domain information

>gnl\|CDD\|216078 pfam00716, Peptidase_S21, Assemblin (Peptidase family S21)	Back alignment and domain information

>gnl\|CDD\|173412 PTZ00121, PTZ00121, MAEBL; Provisional	Back alignment and domain information

>gnl\|CDD\|173412 PTZ00121, PTZ00121, MAEBL; Provisional	Back alignment and domain information

>gnl\|CDD\|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	Back alignment and domain information

>gnl\|CDD\|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	Back alignment and domain information

>gnl\|CDD\|191249 pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylase N-terminal region	Back alignment and domain information

>gnl\|CDD\|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type	Back alignment and domain information

>gnl\|CDD\|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	Back alignment and domain information

>gnl\|CDD\|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	Back alignment and domain information

>gnl\|CDD\|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional	Back alignment and domain information

>gnl\|CDD\|237177 PRK12704, PRK12704, phosphodiesterase; Provisional	Back alignment and domain information

>gnl\|CDD\|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	Back alignment and domain information

>gnl\|CDD\|173412 PTZ00121, PTZ00121, MAEBL; Provisional	Back alignment and domain information

>gnl\|CDD\|173412 PTZ00121, PTZ00121, MAEBL; Provisional	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		764
KOG2072		988	consensus Translation initiation factor 3, subunit	100.0
PF01399		105	PCI: PCI domain; InterPro: IPR000717 A homology do	98.98
smart00753		88	PAM PCI/PINT associated module.	98.9
smart00088		88	PINT motif in proteasome subunits, Int-6, Nip-1 an	98.9
KOG1498		439	consensus 26S proteasome regulatory complex, subun	97.88
PTZ00121		2084	MAEBL; Provisional	97.69
KOG2072		988	consensus Translation initiation factor 3, subunit	97.46
PTZ00121		2084	MAEBL; Provisional	97.32
COG5071		439	RPN5 26S proteasome regulatory complex component [	97.24
KOG1497		399	consensus COP9 signalosome, subunit CSN4 [Posttran	95.65
KOG1029		1118	consensus Endocytic adaptor protein intersectin [S	95.54
KOG2581		493	consensus 26S proteasome regulatory complex, subun	94.69
KOG1464		440	consensus COP9 signalosome, subunit CSN2 [Posttran	92.75
KOG2753		378	consensus Uncharacterized conserved protein, conta	91.39
KOG1029		1118	consensus Endocytic adaptor protein intersectin [S	91.12
KOG0163		1259	consensus Myosin class VI heavy chain [Cytoskeleto	90.92
KOG1144		1064	consensus Translation initiation factor 5B (eIF-5B	90.81
PTZ00266		1021	NIMA-related protein kinase; Provisional	90.57
KOG2582		422	consensus COP9 signalosome, subunit CSN3 [Posttran	90.22
KOG2908		380	consensus 26S proteasome regulatory complex, subun	89.85
KOG2758		432	consensus Translation initiation factor 3, subunit	89.02
PF10075		143	PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro	88.67
PTZ00266		1021	NIMA-related protein kinase; Provisional	88.34
KOG4364		811	consensus Chromatin assembly factor-I [Chromatin s	87.45
KOG0163		1259	consensus Myosin class VI heavy chain [Cytoskeleto	86.11
KOG1076		843	consensus Translation initiation factor 3, subunit	82.94

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

Probab=100.00  E-value=5e-217  Score=1804.35  Aligned_cols=740  Identities=50%  Similarity=0.782  Sum_probs=700.3

Q ss_pred             CCC-CCChhhHHHhHHHHHhcCChHHHHHHHHHHHhcccccchhchHHHHHHHHHHHHhhcccccchhhhhHHHHHhhhc
Q 004280            1 MST-YAKPEAALNQAEALINVGQKQDALQVLHDLITSKRHRAWQKILEKIMFKYVELCVDMRRGKFAKDGLIQYRIVCQQ   79 (764)
Q Consensus         1 M~~-~~kPEnALKRA~ELi~vGq~~~AL~~L~d~i~skr~r~w~~~lE~Im~~~ieLCVel~kg~~aKdgL~QYk~~~Q~   79 (764)
                      ||+ |+|||||||||+|||+||++++|||+|||+|++||+|+|+++||||||+|++|||+|+||++||||||||||+||+
T Consensus         1 Ma~y~~kPENALKRAdElI~VGkkq~ALqsLhd~i~~kr~r~~q~~~EpIMfKyleLCVdLkKg~lAKdGL~QYk~~~Qq   80 (988)
T KOG2072|consen    1 MAPYFQKPENALKRADELIEVGKKQDALQSLHDTITAKRHRWWQTVLEPIMFKYLELCVDLKKGHLAKDGLFQYKNLCQQ   80 (988)
T ss_pred             CCCCCCCcHHHHHHHHHHHHcCCccHHHHHHHHHHHHHHHhhhccchHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHH
Confidence            675 8999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCccccccCCChhHHHHHhhcCccccCcccccccchHHHHHHHHHH
Q 004280           80 VNVTSLEEVIKHFMHLSTEKAEQARSQAQALEEALDVDDLEADKRPEDLMLSYVSGEKGKDRSDRELVTPWFKFLWETYR  159 (764)
Q Consensus        80 ~nv~SLe~Vir~fl~lae~K~~~a~~ka~~~~~~~~~dDLE~~~tPE~lLLsavs~e~~~drtdr~~vtPwlkFLWEsYR  159 (764)
                      +||.|||+||+|||++|++|+++||.+|++++.++++||||++.||||||||+|||++++|||||++|||||||||||||
T Consensus        81 vnv~SlE~VvrhflklAe~kte~Aq~qad~l~~ve~vdDLe~~~tPEslllSvVsGe~sqdR~DR~lltPWlkFLWeSYR  160 (988)
T KOG2072|consen   81 VNVKSLENVVRHFLKLAEEKTEAAQEQADELQKVEEVDDLEAGVTPESLLLSVVSGEDSQDRSDRELLTPWLKFLWESYR  160 (988)
T ss_pred             hchHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccccCCChHHHHHHHhcccccccccchHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhccchhhHHHHHHHHHHHHHHHHhhCchhHHHHHHHHHHHHHHHHhhccccCCCCCCCChhHHHHHHHHHHHhHH
Q 004280          160 TVLEILRNNSKLEALYAMTAHRAFQFCKQYKRTTEFRRLCEIIRNHLLNLNKYRDQRDRPDLSSPESLQLYLDTRFEQLK  239 (764)
Q Consensus       160 ~vLdiLRnNskLE~lY~~ta~~Af~FClkY~RktEFrRLce~LR~Hl~~~~K~~~~~~~~~ls~peT~q~~LetRf~QL~  239 (764)
                      +||||||||++||.+||+||++||+||+||+||||||||||+||+||++++|++++++.||||||||+|+||||||.||+
T Consensus       161 ~vLdlLRNNa~lE~lY~~ia~~aFqFCLkYqRktEFRrLCe~LR~HL~~i~k~~nq~~~v~Ln~~Etlql~LDtRf~QLd  240 (988)
T KOG2072|consen  161 TVLDLLRNNARLEALYHDIARKAFQFCLKYQRKTEFRRLCELLRMHLDNINKHQNQSTRVDLNDPETLQLYLDTRFQQLD  240 (988)
T ss_pred             HHHHHHhhhHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhhccCcCCCCCCHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhcHHHHHHHHhHHHHHhhhhcCCCchhHHHHHHHHHHHHHHHcCchHHHHHHHHHHHhhhhhhCCCCCHHHHHHH
Q 004280          240 VATDLQLWQEAFYSVEDIHGLMCMVKKTPKPSLLVVYYAKLTEIFWISSSHLYHAYAWFKLFTLQKTYNKNLSLKDLQLI  319 (764)
Q Consensus       240 ~Av~LeLWqEAFrsvEDI~~Lm~~skk~pkp~~ma~YYekLa~IFw~s~n~LfHA~A~~k~f~l~k~~~~~~t~ee~~~~  319 (764)
                      |||+||||||||||||||||||++||+||||++|+|||+||++|||+|||+||||+||++||.|+++++||+|++|++.|
T Consensus       241 vAi~lELWQEAyrSiEDIhgLm~lSKrtPkp~~laNYY~KL~~VF~~sgn~LfHAaAw~k~f~l~k~~~K~~Tqde~q~~  320 (988)
T KOG2072|consen  241 VAIELELWQEAYRSIEDIHGLMKLSKRTPKPSTLANYYEKLAKVFWKSGNPLFHAAAWLKLFKLYKNMNKNLTQDELQRM  320 (988)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHhcccccHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccCcCC-CCCcchhhhhhhh-HhHHHHHHHhhCCCCCCCccccccccHHHHHHHHHHcCCcccccHHHHHH
Q 004280          320 ASSVVLAALLVVPYD-RSRSASHLELENE-KDRNLRMANLIGFELDPKFDSREALSRSSLLSELVSKGVMSCATQEVKDL  397 (764)
Q Consensus       320 AS~vlLAaLsIP~~~-~~~~~~~~~~d~~-~~k~~Rla~LLgl~~~pk~~~~~iPtR~~Ll~~l~~~~vl~~a~~~v~~L  397 (764)
                      ||+|||||||||+++ ++.++..++.|+. ++|+.|||+||||+.+        |||.+||+++++.||+++|+++|++|
T Consensus       321 as~VlLaaLSIP~~~~~~~~~r~~e~e~~~~ek~~rla~LL~L~~~--------PTR~~ll~e~v~~gV~~~v~qe~kdL  392 (988)
T KOG2072|consen  321 ASRVLLAALSIPIPDARSDSARLIEIEDIGKEKNLRLANLLGLPAP--------PTRKGLLKEAVREGVLSKVDQEVKDL  392 (988)
T ss_pred             HHHHHHHHhcCCCCCcccccccccccccchhhHHHHHHHHhCCCCC--------ccHHHHHHHHHHhccHhhhhHHHHHH
Confidence            999999999999764 4444555565554 9999999999999977        99999999999999999999999999


Q ss_pred             HHHHhhcCChhhhHHhhHHHHHHHhhhcCCcccCCCCChhhhhhhHHHHHHHHHHHHHHHHHHHhheeehhhhhhccCCC
Q 004280          398 YNLLEHEFLPLDLASKVQPLLAKISKYGGKLASASSVPEVQLSRYIPALEKLVTLRVLQQVSEVYQMMRIESLSQMIPFF  477 (764)
Q Consensus       398 y~lLE~~f~Pl~l~~k~~p~l~~l~~~~~~~~~~~~~~~~~~~~Y~~~L~~vi~~Rll~qlSqvY~ti~i~~L~~l~~f~  477 (764)
                      |+|||++||||+||++|+|||++|++            .|+.+|||+||++||++|+|+|+||+|+||++++|++|+||+
T Consensus       393 Y~iLEveF~PL~l~k~lq~ll~~ls~------------~~~~~QYI~sLq~v~~~RllqQvSqiY~sIs~~~l~~La~F~  460 (988)
T KOG2072|consen  393 YNILEVEFHPLKLCKKLQPLLDKLSE------------SPDKSQYIPSLQDVIILRLLQQVSQIYESISFERLYKLAPFF  460 (988)
T ss_pred             HHHHHhcCCHHHHHHHHHHHHHHHHc------------CCCccccchhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhc
Confidence            99999999999999999999999997            477899999999999999999999999999999999999999


Q ss_pred             ChHHHHHHHHHHHhcCceeEEEeccCCeEEEecCC----------------CCchhHhhHHHHHHHHHHHHHhhcCCchh
Q 004280          478 DFAVVEKISVEAVKHNFIAMKIDHMRGVVVFCNLG----------------LESDGLRDHLTIFAQSLNKVRALIYPPAN  541 (764)
Q Consensus       478 ~~~~iEk~lv~a~~~~~l~vrIDH~~~~I~F~~~~----------------~~s~~ir~qL~~la~~L~~~~~~i~p~~~  541 (764)
                      ++++||++||+|+++|+|+|+|||.+|||+||+|.                ++|+.||+||+.|+.+|..++.++||...
T Consensus       461 ~~~~lEk~~v~a~k~~~v~iriDH~~~~v~FgsDl~~s~~~~~~eg~~lqs~~sE~ir~~L~~m~~~L~~~~e~~dp~~~  540 (988)
T KOG2072|consen  461 SAFELEKLLVEAAKHNDVSIRIDHESNSVSFGSDLFLSKEEDEPEGPELQSMPSEGIRSQLTAMAESLSKVVEELDPVII  540 (988)
T ss_pred             CHHHHHHHHHHHHhccceeEEeccccceeeeccccccccccccCCCchhhcCchHhHHHHHHHHHHHHHHHHHhhChHHH
Confidence            99999999999999999999999999999999864                47889999999999999999999999732


Q ss_pred             h---hhhHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 004280          542 K---ASKLGEMLAGLGEIVDKEHKRLLARKSIIEKRKEEHERQLIEMEREEESRRLKQQKITEEAEQKRLAAEFEHRKNQ  618 (764)
Q Consensus       542 ~---~~~~~~~~~~~~~~~~~eh~~~l~R~~~ie~rKE~~e~~~~~~e~ee~~~r~~~~~~~~~ae~~Rl~eE~~~Re~e  618 (764)
                      .   ......++.++..+.+.||+++++|+++||+|||.+|+++.+++++++.++...+++.++||++|+.+|..+|+.+
T Consensus       541 r~~~~~~~~~~v~~~~~~v~~E~krilaRk~liE~rKe~~E~~~~~re~Eea~~q~~e~~~~r~aE~kRl~ee~~Ere~~  620 (988)
T KOG2072|consen  541 RNSRAKKKEGAVTNYLKNVDKEHKRILARKSLIEKRKEDLEKQNVEREAEEAQEQAKEQRQAREAEEKRLIEEKKEREAK  620 (988)
T ss_pred             HHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            2   5567788999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHH-----------------------------------------HHHHHhhhcCCCCChhhhhH
Q 004280          619 RILREIEERELEEAQALLE-----------------------------------------EAEKRNKKKGGKKPILEGEK  657 (764)
Q Consensus       619 r~~~E~e~~~~~e~~k~~~-----------------------------------------e~~kk~~~~~kk~d~~era~  657 (764)
                      |+++|+++|+.+++++.+.                                         ||+.||+.++||+||+|||+
T Consensus       621 R~l~E~e~i~~k~~ke~~~~~~~te~~aK~~k~~d~ed~e~lD~d~i~~~q~eel~Ke~kElq~rL~~q~KkiDh~ERA~  700 (988)
T KOG2072|consen  621 RILREKEAIRKKELKERLEQLKQTEVGAKGGKEKDLEDLEKLDADQIKARQIEELEKERKELQSRLQYQEKKIDHLERAK  700 (988)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCChHHhhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHH
Confidence            9999999999888766542                                         34448899999999999997


Q ss_pred             --------------------HHHHHHHHHHHHHHHHhhHhhHHHHhhhhhccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 004280          658 --------------------VLHEREQQLEVELSRQRHDGDLREKYRLSRMLDNKNTFQERVLNRRRVEVDRRKVEREER  717 (764)
Q Consensus       658 --------------------~~~e~~~~~~~~~ak~~h~~~~~~k~RL~r~~~d~~~f~~~~~~~r~~e~~~~~~e~~~r  717 (764)
                                          ++|+.+++++++.++++|+.+|++|+||++|++|+..|+..|...|+++|++...+++++
T Consensus       701 R~EeiPL~e~~~~~~~~~d~e~~e~~Ek~Ri~~~~ae~e~~vk~k~~l~rm~~d~~~f~e~vk~~rqs~~~e~~~~~ea~  780 (988)
T KOG2072|consen  701 RLEEIPLIEKAYDERQEEDRELYEAREKQRIEAAIAERESAVKDKKRLSRMYDDRDKFKEHVKGERQSEYEEKLKQFEAR  780 (988)
T ss_pred             HHHhhhhHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence                                999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHH---HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhhh
Q 004280          718 ISLII---KARKQEREAKRKKIFYVRTEEEKIKRLREEEEARKREG  760 (764)
Q Consensus       718 l~~~~---~~r~~er~~~Rr~~~~~~~eEer~~r~~eeee~~~~ee  760 (764)
                      |+.++   ++|+.+|..+||.+++++.||++..|+.|++.+.+.++
T Consensus       781 leaer~rl~erk~~R~eerk~~~~re~EEEr~Rr~EEe~~ae~~ee  826 (988)
T KOG2072|consen  781 LEAERNRLAERKRARIEERKQAYYREIEEERARREEEEANAERQEE  826 (988)
T ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99544   56666677778888999988888555555554444444

>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

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

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

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

>PTZ00121 MAEBL; Provisional	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

>PTZ00121 MAEBL; Provisional	Back alignment and domain information

>COG5071 RPN5 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

>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

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

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

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

>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>KOG0163 consensus Myosin class VI heavy chain [Cytoskeleton]	Back alignment and domain information

>KOG1144 consensus Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PTZ00266 NIMA-related protein kinase; Provisional	Back alignment and domain information

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

>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]	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

>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

>PTZ00266 NIMA-related protein kinase; Provisional	Back alignment and domain information

>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]	Back alignment and domain information

>KOG0163 consensus Myosin class VI heavy chain [Cytoskeleton]	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

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		764
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-17
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-12
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
2dfs_A		1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-08
2dfs_A		1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	6e-08
2dfs_A		1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	3e-05
1i84_S		1184	Smooth muscle myosin heavy chain; muscle protein,	4e-08
1i84_S		1184	Smooth muscle myosin heavy chain; muscle protein,	6e-07
1i84_S		1184	Smooth muscle myosin heavy chain; muscle protein,	3e-04
2zuo_A		861	MVP, major vault protein; repeat domains, protein-	1e-07
2zuo_A		861	MVP, major vault protein; repeat domains, protein-	3e-05
2zuo_A		861	MVP, major vault protein; repeat domains, protein-	1e-04
3lvg_D		190	LCB, clathrin light chain B; SELF assembly, coated	7e-06
3lvg_D		190	LCB, clathrin light chain B; SELF assembly, coated	1e-04
1g8x_A		1010	Myosin II heavy chain fused to alpha-actinin 3; mo	8e-05
2qag_B		427	Septin-6, protein NEDD5; cell cycle, cell division	4e-04
1f5n_A		592	Interferon-induced guanylate-binding protein 1; GB	6e-04

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

 Score = 84.1 bits (207), Expect = 9e-17
 Identities = 101/688 (14%), Positives = 179/688 (26%), Gaps = 224/688 (32%)

Query: 91  HFMHLSTEKAEQARSQAQALEEALD--VDDLEADKRPEDLMLSYVSGEKGKD---RSDRE 145
           H  H+  E  E        L    D  VD+ +  K  +D+  S +S E+        D  
Sbjct: 3   HHHHMDFETGEHQYQYKDILSVFEDAFVDNFDC-KDVQDMPKSILSKEEIDHIIMSKDAV 61

Query: 146 LVTPWFKFLWETYRTVLEILRNNSKLEALYAMTAHRAFQFCKQYKRTTEFRRLCEIIRNH 205
                      T R +   L   SK E +         +    YK       +    R  
Sbjct: 62  S---------GTLR-LFWTLL--SKQEEMVQKFVEEVLR--INYKFLMS--PIKTEQRQP 105

Query: 206 LLNLNKYRDQRDRPDLSSPESLQLYLDTRFEQLKVATDLQLWQEAFYSVED-----IHGL 260
            +    Y +QRDR   +  +    Y  +R +       L+L ++A   +       I G 
Sbjct: 106 SMMTRMYIEQRDRL-YNDNQVFAKYNVSRLQPY-----LKL-RQALLELRPAKNVLIDG- 157

Query: 261 M------CMVKKTPKPSLLVVYYAKLTEIFWISSSH-------------LYHAYAWFKLF 301
           +       +         +        +IFW++  +             L +        
Sbjct: 158 VLGSGKTWVALDVCLSYKVQCKMD--FKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTS 215

Query: 302 TLQKTYNKNLSLKDLQ-----LIASSVVLAALLVVPYDRSRSASHLELENEKDRNL---R 353
               + N  L +  +Q     L+ S      LLV+     ++A      N   + L   R
Sbjct: 216 RSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVL--LNVQNAKAWNAFNLSCKILLTTR 273

Query: 354 MANLIGFELDPKFDSREALSRSSLLSELVSKGVMSCATQEVKDLY-NLLEHEF--LPLDL 410
              +         D   A + + +  +  S  +      EVK L    L+     LP + 
Sbjct: 274 FKQVT--------DFLSAATTTHISLDHHSMTL---TPDEVKSLLLKYLDCRPQDLPRE- 321

Query: 411 ASKVQPLLAKISKYGGKLASASSVPEVQLSRYIPALEKLVTLRVLQQVSEVYQMMRIESL 470
                P    I                     I        +R      + ++ +  + L
Sbjct: 322 VLTTNPRRLSI---------------------IAES-----IRDGLATWDNWKHVNCDKL 355

Query: 471 SQMIPFFDFAVVEKISVEAVKHNFIAMKIDHMRGVVVFCNLGLESDGLRDH---LTIFAQ 527
           + +I         + S+                         LE    R     L++F  
Sbjct: 356 TTII---------ESSLNV-----------------------LEPAEYRKMFDRLSVFPP 383

Query: 528 SLNKVRALIYPPANKASKL-GEML-AGLGEIVDKEHKRLLARKSIIEKRKEEHERQLIEM 585
           S +     I  P    S +  +++ + +  +V+K HK  L  K   E         L   
Sbjct: 384 SAH-----I--PTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELK 436

Query: 586 EREEESRRLKQQKITEEAEQKRLAAEFEHRKNQRILREIEERELEEAQALLEEAEKRNKK 645
            + E    L                   HR                   +++        
Sbjct: 437 VKLENEYAL-------------------HRS------------------IVDHYNIPKTF 459

Query: 646 KGGKKPILEGEKV--------LHEREQQLEVELSRQ------------RHDG-------- 677
                     ++         L   E    + L R             RHD         
Sbjct: 460 DSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGS 519

Query: 678 ------DLREKYRLSRMLDNKNTFQERV 699
                  L+  Y+   + DN   ++  V
Sbjct: 520 ILNTLQQLK-FYK-PYICDNDPKYERLV 545

PyMOL of 1vt4

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

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

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080	Back alignment and structure

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080	Back alignment and structure

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080	Back alignment and structure

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184	Back alignment and structure

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184	Back alignment and structure

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184	Back alignment and structure

>2zuo_A MVP, major vault protein; repeat domains, protein-protein complex, cytoplasm, ribonucleoprotein, structural protein; 3.50A {Rattus norvegicus} PDB: 2zv4_N 2zv5_a 2qzv_A Length = 861	Back alignment and structure

>2zuo_A MVP, major vault protein; repeat domains, protein-protein complex, cytoplasm, ribonucleoprotein, structural protein; 3.50A {Rattus norvegicus} PDB: 2zv4_N 2zv5_a 2qzv_A Length = 861	Back alignment and structure

>2zuo_A MVP, major vault protein; repeat domains, protein-protein complex, cytoplasm, ribonucleoprotein, structural protein; 3.50A {Rattus norvegicus} PDB: 2zv4_N 2zv5_a 2qzv_A Length = 861	Back alignment and structure

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190	Back alignment and structure

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190	Back alignment and structure

>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM, protein engineering, structural protein; HET: ADP; 2.80A {Dictyostelium discoideum} SCOP: k.1.1.1 Length = 1010	Back alignment and structure

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens} Length = 427	Back alignment and structure

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		764
4b4t_P		445	26S proteasome regulatory subunit RPN5; hydrolase,	99.15
4b4t_Q		434	26S proteasome regulatory subunit RPN6; hydrolase,	99.03
3txn_A		394	26S proteasome regulatory complex subunit P42B; PC	98.96
4b4t_R		429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	98.48
4b4t_O		393	26S proteasome regulatory subunit RPN9; hydrolase,	98.4
1ufm_A		84	COP9 complex subunit 4; helix-turn-helix, structur	97.75
4b4t_S		523	RPN3, 26S proteasome regulatory subunit RPN3; hydr	97.52
3t5x_A		203	PCI domain-containing protein 2; PCI, mRNA nuclear	95.87
3t5v_B		455	Nuclear mRNA export protein THP1; PCI, mRNA nuclea	90.67
4b0z_A		229	RPN12, 26S proteasome regulatory subunit RPN12; pr	88.31
1rz4_A		226	Eukaryotic translation initiation factor 3 subuni;	87.71
3chm_A		169	COP9 signalosome complex subunit 7; heat/ARM repea	83.79

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

Probab=99.15  E-value=8.2e-09  Score=115.16  Aligned_cols=407  Identities=16%  Similarity=0.142  Sum_probs=218.4

Q ss_pred             hhHHHhHHHHHhcCChHHHHHHHHHHHhcccccchhchHHHHHHHHHHHHhhcccccchhhhhHHHHHhhhccCcCcHHH
Q 004280            8 EAALNQAEALINVGQKQDALQVLHDLITSKRHRAWQKILEKIMFKYVELCVDMRRGKFAKDGLIQYRIVCQQVNVTSLEE   87 (764)
Q Consensus         8 EnALKRA~ELi~vGq~~~AL~~L~d~i~skr~r~w~~~lE~Im~~~ieLCVel~kg~~aKdgL~QYk~~~Q~~nv~SLe~   87 (764)
                      ++.+..|+.|.. |++++|++.|..+-..-|.-.=..+.-.+....+.||++.+.-.   .-..++..++...|.  +-.
T Consensus        18 ~~~~~~~~~l~~-~~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~---~l~e~i~~Lskkr~q--lk~   91 (445)
T 4b4t_P           18 KEEFPKIDSLAQ-NDCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWD---DLNEQLTLLSKKHGQ--LKL   91 (445)
T ss_dssp             ----------CH-HHHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHH---HHHHHHHHHHTTTTT--SHH
T ss_pred             HHHHHHHHHHHc-CCHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHH---HHHHHHHHHHHHhhh--hHH
Confidence            567888888855 89999999998877654322111333445556678999887632   223344444543321  233


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhccCccccccCCChhHHHHHhhcCccccCcccccccchHHHHHHHHHHHHHHHhcc
Q 004280           88 VIKHFMHLSTEKAEQARSQAQALEEALDVDDLEADKRPEDLMLSYVSGEKGKDRSDRELVTPWFKFLWETYRTVLEILRN  167 (764)
Q Consensus        88 Vir~fl~lae~K~~~a~~ka~~~~~~~~~dDLE~~~tPE~lLLsavs~e~~~drtdr~~vtPwlkFLWEsYR~vLdiLRn  167 (764)
                      .+.+.+..+..-+...                   .+++                            -+++-.++++|+.
T Consensus        92 ai~~~V~~~~~~l~~~-------------------~~~d----------------------------~~~~~~~i~~l~~  124 (445)
T 4b4t_P           92 SIQYMIQKVMEYLKSS-------------------KSLD----------------------------LNTRISVIETIRV  124 (445)
T ss_dssp             HHHHHHHHHHHHHHHH-------------------CTTH----------------------------HHHHHHHHHCCSS
T ss_pred             HHHHHHHHHHHHHhcC-------------------Cchh----------------------------HHHHHHHHHHHHH
Confidence            3334443332222110                   0000                            0122233344431


Q ss_pred             c--hh--hHHHHHHHHHHHHHHHHhhCchhHHHHHHHHHHHHHHHHhhccccCCCCCCCChhHHHHHHHHHHHhHHHHHh
Q 004280          168 N--SK--LEALYAMTAHRAFQFCKQYKRTTEFRRLCEIIRNHLLNLNKYRDQRDRPDLSSPESLQLYLDTRFEQLKVATD  243 (764)
Q Consensus       168 N--sk--LE~lY~~ta~~Af~FClkY~RktEFrRLce~LR~Hl~~~~K~~~~~~~~~ls~peT~q~~LetRf~QL~~Av~  243 (764)
                      -  .|  ||...   |+=...+|.=|....++...+++|..=....  +  +    ..+..+    =++.-+.|+.....
T Consensus       125 vte~kiflE~er---arl~~~La~i~e~~g~~~eA~~iL~~l~~Et--~--~----~~~~~~----kve~~l~q~rl~l~  189 (445)
T 4b4t_P          125 VTENKIFVEVER---ARVTKDLVEIKKEEGKIDEAADILCELQVET--Y--G----SMEMSE----KIQFILEQMELSIL  189 (445)
T ss_dssp             SSSCCCCCCHHH---HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH--C--S----SSCHHH----HHHHHHHHHHHHHH
T ss_pred             HhccchHHHHHH---HHHHHHHHHHHHHccCHHHHHHHHHHHHHHH--H--h----cccHHH----HHHHHHHHHHHHHH
Confidence            1  11  22222   2223445666777788888888776522111  1  1    012223    45666679999999


Q ss_pred             hhcHHHHHHHHhHHHHHhhhhcCCCchhHHHHHHHHHHHHHHHcCchHHHHHHHHHHHhhhhhhCCCCCHHHHHHHHHHH
Q 004280          244 LQLWQEAFYSVEDIHGLMCMVKKTPKPSLLVVYYAKLTEIFWISSSHLYHAYAWFKLFTLQKTYNKNLSLKDLQLIASSV  323 (764)
Q Consensus       244 LeLWqEAFrsvEDI~~Lm~~skk~pkp~~ma~YYekLa~IFw~s~n~LfHA~A~~k~f~l~k~~~~~~t~ee~~~~AS~v  323 (764)
                      .+-|..|--.+.=|..-.  ...+|.|.+++.||.-++.++..-++|+=-+-.|+-.|....   -.-.+......-..+
T Consensus       190 ~~d~~~a~~~~~ki~~~~--~~~~~~~~lk~~~~~~~~~~~~~e~~y~~a~~~y~e~~~~~~---~~~d~~~~~~~L~~~  264 (445)
T 4b4t_P          190 KGDYSQATVLSRKILKKT--FKNPKYESLKLEYYNLLVKISLHKREYLEVAQYLQEIYQTDA---IKSDEAKWKPVLSHI  264 (445)
T ss_dssp             HTCHHHHHHHHHHHHHHH--HHSSCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH---HHSCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhh--cccCCcHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhccc---ccCCHHHHHHHHHHH
Confidence            999999987766654321  234566899999999999999999999865555444443322   112333444445555


Q ss_pred             HHHhhccCcCCCCCcchhhhhhhhHhHHHHHHHhhCCCCCCCccccccccHHHHHHHHHHcCCcccccHHHHHHHHHHhh
Q 004280          324 VLAALLVVPYDRSRSASHLELENEKDRNLRMANLIGFELDPKFDSREALSRSSLLSELVSKGVMSCATQEVKDLYNLLEH  403 (764)
Q Consensus       324 lLAaLsIP~~~~~~~~~~~~~d~~~~k~~Rla~LLgl~~~pk~~~~~iPtR~~Ll~~l~~~~vl~~a~~~v~~Ly~lLE~  403 (764)
                      |+.++--|.++..              ..-++.+..-.     .++.+|.-..|++......+..+  |.+...|.   .
T Consensus       265 v~~~iLa~~~~~~--------------~~ll~~~~~~~-----~~~~l~~~~~L~k~f~~~~L~~~--~~~~~~~~---~  320 (445)
T 4b4t_P          265 VYFLVLSPYGNLQ--------------NDLIHKIQNDN-----NLKKLESQESLVKLFTTNELMRW--PIVQKTYE---P  320 (445)
T ss_dssp             HHHHHHSSCSSTT--------------HHHHHSHHHHS-----SCHHHHHHHHHHHHHHHCCSSSH--HHHHHHTC---S
T ss_pred             HHHHHhCCCCchH--------------HHHHHHHhhcc-----cccccHHHHHHHHHHHhchHhhh--HHHHHHHH---H
Confidence            5555555553321              01111111111     12356777788877777666543  22222221   1


Q ss_pred             cCChhhhHHhhHHHHHHHhhhcCCcccCCCCChhhhhhhHHHHHHHHHHHHHHHHHHHhheeehhhhhhccCCCChHHHH
Q 004280          404 EFLPLDLASKVQPLLAKISKYGGKLASASSVPEVQLSRYIPALEKLVTLRVLQQVSEVYQMMRIESLSQMIPFFDFAVVE  483 (764)
Q Consensus       404 ~f~Pl~l~~k~~p~l~~l~~~~~~~~~~~~~~~~~~~~Y~~~L~~vi~~Rll~qlSqvY~ti~i~~L~~l~~f~~~~~iE  483 (764)
                      .+.|.                      .....+.....++..|.+.++...|..+|+.|++|++++|.+++. .+..++|
T Consensus       321 ~L~~~----------------------~~~~~~~~~~~~~~~L~~~v~ehnl~~i~k~Ys~I~l~~la~lL~-l~~~evE  377 (445)
T 4b4t_P          321 VLNED----------------------DLAFGGEANKHHWEDLQKRVIEHNLRVISEYYSRITLLRLNELLD-LTESQTE  377 (445)
T ss_dssp             STTTC----------------------CSSCCCSCSSHHHHHHHHHHHHHHHHHHHHHEEEEEHHHHHHHHT-SCHHHHH
T ss_pred             Hhccc----------------------chhhhcchhhHHHHHHHHHHHHHHHHHHHHHhceeeHHHHHHHhC-cCHHHHH
Confidence            11110                      000112233567889999999999999999999999999999987 5899999


Q ss_pred             HHHHHHHhcCceeEEEeccCCeEEEecCCCCchhHhhHHHHHHHHHHHHHhhcCC
Q 004280          484 KISVEAVKHNFIAMKIDHMRGVVVFCNLGLESDGLRDHLTIFAQSLNKVRALIYP  538 (764)
Q Consensus       484 k~lv~a~~~~~l~vrIDH~~~~I~F~~~~~~s~~ir~qL~~la~~L~~~~~~i~p  538 (764)
                      .+|.+++..|.|..+||..+|+|+|+...-++    ..|+.|+..+...++.|+.
T Consensus       378 ~~ls~mI~~g~i~akIDq~~giV~F~~~~~~~----~~l~~W~~~i~~l~~~v~k  428 (445)
T 4b4t_P          378 TYISDLVNQGIIYAKVNRPAKIVNFEKPKNSS----QLLNEWSHNVDELLEHIET  428 (445)
T ss_dssp             HHHHHHHHHTSSCCEEETTTTEEEC------------------------------
T ss_pred             HHHHHHHHCCCEEEEEcCCCCEEEECCCCChH----HHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999754333    4566666666666665543

PyMOL of 4b4t

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

>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha solenoid, regulatory PART LID, hydrolase, protein binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A	Back alignment and structure

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

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

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

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

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

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

>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

>3chm_A COP9 signalosome complex subunit 7; heat/ARM repeats, winged helix motif, developmental protein, phosphoprotein; 1.50A {Arabidopsis thaliana}	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		764
d1vzva_		221	b.57.1.1 (A:) VZV protease {Varicella-Zoster virus	0.001
d1ufma_		84	a.4.5.47 (A:) COP9 signalosome complex subunit 4,	0.003
d1at3a_		231	b.57.1.1 (A:) HSV-2 protease {Herpes simplex virus	0.004

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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		764
d1ufma_		84	COP9 signalosome complex subunit 4, GSN4 {Mouse (M	98.2

>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=98.20  E-value=8.5e-07  Score=75.68  Aligned_cols=66  Identities=24%  Similarity=0.349  Sum_probs=61.2

Q ss_pred             HHHHHHHHHHHHHHHHhheeehhhhhhccCCCChHHHHHHHHHHHhcCceeEEEeccCCeEEEecCC
Q 004280          446 LEKLVTLRVLQQVSEVYQMMRIESLSQMIPFFDFAVVEKISVEAVKHNFIAMKIDHMRGVVVFCNLG  512 (764)
Q Consensus       446 L~~vi~~Rll~qlSqvY~ti~i~~L~~l~~f~~~~~iEk~lv~a~~~~~l~vrIDH~~~~I~F~~~~  512 (764)
                      |++.++...+..+|++|.+|+|++|.+++.+ +..++|.+|++.+.++.|..+||+.+|+|+|.+..
T Consensus        12 L~~~i~Ehni~~is~~Y~~Isl~~la~~l~l-~~~evE~~l~~mI~~~~i~akIDq~~g~V~F~~~e   77 (84)
T d1ufma_          12 LDRAVIEHNLLSASKLYNNITFEELGALLEI-PAAKAEKIASQMITEGRMNGFIDQIDGIVHFETRE   77 (84)
T ss_dssp             CCHHHHHHHHHHHHHSCSEEEHHHHHHHTTS-CHHHHHHHHHHHHHTTSSCEEEETTTTEEEECCSS
T ss_pred             HHHHHHHHHHHHHHHhhceeeHHHHHHHHCC-CHHHHHHHHHHHHhcCeEEEEEeCCCCEEEECCCC
Confidence            5677888999999999999999999999875 89999999999999999999999999999998753

PyMOL of d1ufma_