Citrus Sinensis ID: 008379

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-------57

MMKDVEDKSSAEYQRLTWDALRKSINGLVNKVNATNIKNIIPELFAENLIRGRGLFCRSCMKSQMASPGFTDVFAALVAVVNTKFTAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQVAHEIIALELLTILLENPTDDSVEVAVGFVKECGSILQDLSPKGLHGIFERFRGILHEGEIDKRVQFLIEGLFAIRKAKFQGYPAVRPELDLVDIEDQLTHEISLQDEIDPEITLDIFKPDPNFLDNEKRYEDMKKDLLGETSEDEEGSDAGSGDEDDSEEEEEEEDEEQMKIKDETETNLVNLRRTIYLTIMSSVDFEEAGHKLLKIKLEPGQEMELCIMLLECCSQERTYLRYYGLLGQRFCMINKVHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGTHALPWHVLAYIRLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERLTDPTMQDSFESIFPRDNPKNTRFAINFFTSIGLGGITENLREYLKNMPRLIMQQQKQVSESEPDSEADNESESSDSSDSDTSSSQSESEDSSSSDESNRDKRHSKRRRRH

ccccccccccHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHcccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHccccccccHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHcHHHHHHHHcccccHHHHHHHccccccccHHHHHHHHHHHccHHHHHHHHHHHHcccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccc

cHHHccccccHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHcccccHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHccccccccccHHcccccccccEEEEEccccccccHccccEEcccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHccccEEEcccHHHHHHHHHHHHHHHHccccHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHEEEEEcccccccHHHHHHHHHHHHHHHHccHHHHHHHHccccHHHHHccccccccccccEEEEHHHHHHcccHcHHHHHHHHHccccccHHHcHHHHccccccccccccccccccccccccccccccccccccccccccccHHHHccc

mmkdvedkSSAEYQRLTWDALRKSINGLVNKVNATNIKNIIPELFAENLIRGRGLFCRScmksqmaspgfTDVFAALVAVVNTKFTAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQVAHEIIALELLTILlenptddsvEVAVGFVKECGsilqdlspkglhGIFERFRGILHEGEIDKRVQFLIEGLFAIRKAKfqgypavrpeldlvdIEDQLTHEislqdeidpeitldifkpdpnfldnekRYEDMKKDLlgetsedeegsdagsgdeddseeeeeEEDEEQMKIKDETETNLVNLRRTIYLTIMSSVDFEEAGHKLLKIKLEPGQEMELCIMLLECCSQERTYLRYYGLLGQRFCMINKVHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGTHALPWHVLAYIRLteedttssSRIFIKILFQELSEHLGIRLlnerltdptmqdsfesifprdnpkntrFAINFFTSIGLGGITENLREYLKNMPRLIMQQQkqvsesepdseadnesessdssdsdtsssqsesedssssdesnrdkrhskrrrrh

MMKDVEDKSSAEYQRLTWDALRKSINGLVNKVNATNIKNIIPELFAENLIRGRGLFCRSCMKSQMASPGFTDVFAALVAVVNTKFTAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQVAHEIIALELLTILLENPTDDSVEVAVGFVKECGSilqdlspkglHGIFERFRGILHEGEIDKRVQFLIEGLFAIRKAKFQGYPAVRPELDLVDIEDQLTHEislqdeidpeitldifkpdpnfldnEKRYEDMKKDLlgetsedeegsdagsgdeddseeeeeeedeeqmkikdetetnlvnLRRTIYLTIMSSVDFEEAGHKLLKIKLEPGQEMELCIMLLECCSQERTYLRYYGLLGQRFCMINKVHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGTHALPWHVLAYIRLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERLTDPTMQDSFEsifprdnpknTRFAINFFtsiglggiTENLREYLKNMPRLIMQQQkqvsesepdseadnesessdssdsdtsssqsesedssssdesnrdkrhskrrrrh

MMKDVEDKSSAEYQRLTWDALRKSINGLVNKVNATNIKNIIPELFAENLIRGRGLFCRSCMKSQMASPGFTDVFAALVAVVNTKFTAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQVAHeiialelltilleNPTDDSVEVAVGFVKECGSILQDLSPKGLHGIFERFRGILHEGEIDKRVQFLIEGLFAIRKAKFQGYPAVRPELDLVDIEDQLTHEISLQDEIDPEITLDIFKPDPNFLDNEKRYEDMKKDLLgetsedeegsdagsgdeddseeeeeeedeeQMKIKDETETNLVNLRRTIYLTIMSSVDFEEAGHKLLKIKLEPGQEMELCIMLLECCSQERTYLRYYGLLGQRFCMINKVHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGTHALPWHVLAYIRLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERLTDPTMQDSFESIFPRDNPKNTRFAINFFTSIGLGGITENLREYLKNMPRLIMQQQKQVsesepdseadnesessdssdsdtsssqsesedssssdesNrdkrhskrrrrh

************YQRLTWDALRKSINGLVNKVNATNIKNIIPELFAENLIRGRGLFCRSCMKSQMASPGFTDVFAALVAVVNTKFTAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQVAHEIIALELLTILLENPTDDSVEVAVGFVKECGSILQDLSPKGLHGIFERFRGILHEGEIDKRVQFLIEGLFAIRKAKFQGYPAVRPELDLVDIEDQLTHEISLQDEIDPEITLDIFK************************************************************NLVNLRRTIYLTIMSSVDFEEAGHKLLKIKLEPGQEMELCIMLLECCSQERTYLRYYGLLGQRFCMINKVHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGTHALPWHVLAYIRLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERLTD*********IF*****KNTRFAINFFTSIGLGGITENLREYLKNMPRL************************************************************

*******************ALRKSINGLVNKVNATNIKNIIPELFAENLIRGRGLFCRSCMKSQMASPGFTDVFAALVAVVNTKFTAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQVAHEIIALELLTILLENPTDDSVEVAVGFVKECGSILQDLSPKGLHGIFE****************FLIEGLFAIRKAKFQGYPAVRPELDLVDIEDQLTH*I*******PEITLDIFKPDPNFLDNEKRYEDMKKDLLGET********************************DETETNLVNLRRTIYLTIMSSVDFEEAGHKLLKIKLEPGQEMELCIMLLECCSQERTYLRYYGLLGQRFCMINKVHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGTHALPWHVLAYIRLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERLTDPTMQDSFESIFPRDNPKNTRFAINFFTSIGLGGITENLREYL******************************************************************

***********EYQRLTWDALRKSINGLVNKVNATNIKNIIPELFAENLIRGRGLFCRSCMKSQMASPGFTDVFAALVAVVNTKFTAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQVAHEIIALELLTILLENPTDDSVEVAVGFVKECGSILQDLSPKGLHGIFERFRGILHEGEIDKRVQFLIEGLFAIRKAKFQGYPAVRPELDLVDIEDQLTHEISLQDEIDPEITLDIFKPDPNFLDNEKRYEDMKKDLLG********************************IKDETETNLVNLRRTIYLTIMSSVDFEEAGHKLLKIKLEPGQEMELCIMLLECCSQERTYLRYYGLLGQRFCMINKVHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGTHALPWHVLAYIRLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERLTDPTMQDSFESIFPRDNPKNTRFAINFFTSIGLGGITENLREYLKNMPRLIM**********************************************************

******DKSSAEYQRLTWDALRKSINGLVNKVNATNIKNIIPELFAENLIRGRGLFCRSCMKSQMASPGFTDVFAALVAVVNTKFTAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQVAHEIIALELLTILLENPTDDSVEVAVGFVKECGSILQDLSPKGLHGIFERFRGILHEGEIDKRVQFLIEGLFAIRKAKFQGYPAVRPELDLVDIEDQLTHEISLQDEIDPEITLDIFKPDPNFLDNEKRYEDMKKDLLG****************************EQMKIKDETETNLVNLRRTIYLTIMSSVDFEEAGHKLLKIKLEPGQEMELCIMLLECCSQERTYLRYYGLLGQRFCMINKVHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGTHALPWHVLAYIRLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERLTDPTMQDSFESIFPRDNPKNTRFAINFFTSIGLGGITENLREYLKNMPRLIMQQQ*******************************************************

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MMKDVEDKSSAEYQRLTWDALRKSINGLVNKVNATNIKNIIPELFAENLIRGRGLFCRSCMKSQMASPGFTDVFAALVAVVNTKFTAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQVAHEIIALELLTILLENPTDDSVEVAVGFVKECGSILQDLSPKGLHGIFERFRGILHEGEIDKRVQFLIEGLFAIRKAKFQGYPAVRPELDLVDIEDQLTHEISLQDEIDPEITLDIFKPDPNFLDNEKRYEDMKKDLLGETSEDEEGSDAGSGDEDDxxxxxxxxxxxxxxxxxxxxxNLVNLRRTIYLTIMSSVDFEEAGHKLLKIKLEPGQEMELCIMLLECCSQERTYLRYYGLLGQRFCMINKVHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGTHALPWHVLAYIRLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERLTDPTMQDSFESIFPRDNPKNTRFAINFFTSIGLGGITENLREYLKNMPRLIMQQQKQVSESEPDSEADNESESSDSSDSDTSSSQSESEDSSSSDESNRDKRHSKRRRRH

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		568	2.2.26 [Sep-21-2011]
Q08C72		985	Pre-mRNA-splicing factor	yes	no	0.908	0.523	0.567	1e-171
P0CM97		831	Pre-mRNA-splicing factor	N/A	no	0.883	0.604	0.554	1e-170
P0CM96		831	Pre-mRNA-splicing factor	yes	no	0.883	0.604	0.554	1e-170
Q5ZKA3		926	Pre-mRNA-splicing factor	yes	no	0.908	0.557	0.576	1e-170
Q8C5N3		908	Pre-mRNA-splicing factor	yes	no	0.915	0.572	0.567	1e-170
Q9HCG8		908	Pre-mRNA-splicing factor	yes	no	0.915	0.572	0.570	1e-169
Q52KN9		803	Pre-mRNA-splicing factor	N/A	no	0.906	0.641	0.560	1e-169
Q5RA93		908	Pre-mRNA-splicing factor	yes	no	0.915	0.572	0.568	1e-168
Q4WKB9		881	Pre-mRNA-splicing factor	yes	no	0.883	0.569	0.564	1e-168
Q9VJ87		1330	Pre-mRNA-splicing factor	yes	no	0.896	0.382	0.558	1e-167

>sp\|Q08C72\|CWC22_DANRE Pre-mRNA-splicing factor CWC22 homolog OS=Danio rerio GN=cwc22 PE=2 SV=1	Back alignment and function desciption

 Score =  600 bits (1548), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 295/520 (56%), Positives = 399/520 (76%), Gaps = 4/520 (0%)

Query: 1   MMKDVEDKSSAEYQRLTWDALRKSINGLVNKVNATNIKNIIPELFAENLIRGRGLFCRSC 60
           M   + DKSS EYQR++W+AL+KSINGL+NKVN +NI NII EL  EN++RGRGL  RS 
Sbjct: 236 MQAQITDKSSLEYQRMSWEALKKSINGLINKVNVSNIANIIQELLQENIVRGRGLLARSI 295

Query: 61  MKSQMASPGFTDVFAALVAVVNTKFTAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIA 120
           +++Q ASP FT V++A+VA++N+KF  +GEL+LKR++L  ++ Y+RNDK Q L A KF+ 
Sbjct: 296 LQAQAASPIFTHVYSAVVAIINSKFPQIGELILKRLILNFRKGYRRNDKQQCLTASKFVG 355

Query: 121 HLVNQQVAHEIIALELLTILLENPTDDSVEVAVGFVKECGSILQDLSPKGLHGIFERFRG 180
           HL+NQ VAHE++ LE+LT+LLE PTDDSVEVA+ F+KECG  L ++SP+G++ IFER R 
Sbjct: 356 HLINQNVAHEVLCLEMLTLLLERPTDDSVEVAISFLKECGLKLTEVSPRGINAIFERLRN 415

Query: 181 ILHEGEIDKRVQFLIEGLFAIRKAKFQGYPAVRPELDLVDIEDQLTHEISLQDEIDPEIT 240
           ILHE EIDKRVQ++IE +FAIRK  F+ +P +   LDLV+ EDQ TH + L+DE + E  
Sbjct: 416 ILHESEIDKRVQYMIEVMFAIRKDGFKDHPIIPEGLDLVEEEDQFTHMLPLEDEYNTEDI 475

Query: 241 LDIFKPDPNFLDNEKRYEDMKKDLLGE----TSEDEEGSDAGSGDEDDSEEEEEEEDEEQ 296
           L++FK DPNFL+NE++Y+ +K+++L E    + +D  GS     D+++ EE    E++E+
Sbjct: 476 LNVFKLDPNFLENEEKYKTIKREILDEGSSDSGDDAGGSGDDEDDDEEDEEAAAGEEQEK 535

Query: 297 MKIKDETETNLVNLRRTIYLTIMSSVDFEEAGHKLLKIKLEPGQEMELCIMLLECCSQER 356
           + I D+TE NLV  RRTIYL I SS+DFEE  HKL+K+     Q  ELC M+L+CC+Q+R
Sbjct: 536 VTIFDQTEVNLVAFRRTIYLAIQSSLDFEECAHKLIKMDFPESQTKELCNMILDCCAQQR 595

Query: 357 TYLRYYGLLGQRFCMINKVHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGTHALP 416
           TY +++GLL  RFC++ K + E+FE  F +QY  IHRLETNKLRNVA+ FAHLL T ++P
Sbjct: 596 TYEKFFGLLAGRFCLLKKEYMESFEAIFQEQYETIHRLETNKLRNVARIFAHLLYTDSVP 655

Query: 417 WHVLAYIRLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERLTDPTMQDSFESIFPRDNP 476
           W VL  +R++E+ TTSSSRIF+KILFQEL  ++G+  LNERL D T+Q  FE +FPRDNP
Sbjct: 656 WSVLECVRMSEDTTTSSSRIFVKILFQELCAYMGLPKLNERLKDTTLQPFFEGLFPRDNP 715

Query: 477 KNTRFAINFFTSIGLGGITENLREYLKNMPRLIMQQQKQV 516
           +NTRFAINFFTSIGLGG+T+ LRE+LKN P++IM Q ++V
Sbjct: 716 RNTRFAINFFTSIGLGGLTDELREHLKNAPKMIMTQNQEV 755

May be involved in pre-mRNA splicing.
Danio rerio (taxid: 7955)

>sp\|P0CM97\|CWC22_CRYNB Pre-mRNA-splicing factor CWC22 OS=Cryptococcus neoformans var. neoformans serotype D (strain B-3501A) GN=CWC22 PE=3 SV=1	Back alignment and function description

>sp\|P0CM96\|CWC22_CRYNJ Pre-mRNA-splicing factor CWC22 OS=Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565) GN=CWC22 PE=3 SV=1	Back alignment and function description

>sp\|Q5ZKA3\|CWC22_CHICK Pre-mRNA-splicing factor CWC22 homolog OS=Gallus gallus GN=CWC22 PE=2 SV=2	Back alignment and function description

>sp\|Q8C5N3\|CWC22_MOUSE Pre-mRNA-splicing factor CWC22 homolog OS=Mus musculus GN=Cwc22 PE=1 SV=1	Back alignment and function description

>sp\|Q9HCG8\|CWC22_HUMAN Pre-mRNA-splicing factor CWC22 homolog OS=Homo sapiens GN=CWC22 PE=1 SV=3	Back alignment and function description

>sp\|Q52KN9\|CWC22_XENLA Pre-mRNA-splicing factor CWC22 homolog OS=Xenopus laevis GN=cwc22 PE=2 SV=1	Back alignment and function description

>sp\|Q5RA93\|CWC22_PONAB Pre-mRNA-splicing factor CWC22 homolog OS=Pongo abelii GN=CWC22 PE=2 SV=1	Back alignment and function description

>sp\|Q4WKB9\|CWC22_ASPFU Pre-mRNA-splicing factor cwc22 OS=Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) GN=cwc22 PE=3 SV=1	Back alignment and function description

>sp\|Q9VJ87\|CWC22_DROME Pre-mRNA-splicing factor CWC22 homolog OS=Drosophila melanogaster GN=ncm PE=1 SV=3	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		568
225454072		785	PREDICTED: pre-mRNA-splicing factor CWC2	0.987	0.714	0.864	0.0
449448752		797	PREDICTED: pre-mRNA-splicing factor CWC2	0.908	0.647	0.907	0.0
449503636		780	PREDICTED: LOW QUALITY PROTEIN: pre-mRNA	0.908	0.661	0.903	0.0
356524175		871	PREDICTED: pre-mRNA-splicing factor CWC2	0.908	0.592	0.905	0.0
356546225		860	PREDICTED: pre-mRNA-splicing factor CWC2	0.908	0.6	0.905	0.0
224139202		933	predicted protein [Populus trichocarpa]	0.908	0.553	0.898	0.0
15220892		900	pre-mRNA-splicing factor CWC22 [Arabidop	0.906	0.572	0.876	0.0
297839843		897	hypothetical protein ARALYDRAFT_895889 [	0.906	0.574	0.866	0.0
242053847		792	hypothetical protein SORBIDRAFT_03g02981	0.903	0.647	0.867	0.0
115488040		787	Os12g0256300 [Oryza sativa Japonica Grou	0.904	0.653	0.850	0.0

>gi\|225454072\|ref\|XP_002265479.1\| PREDICTED: pre-mRNA-splicing factor CWC22 homolog [Vitis vinifera]	Back alignment and taxonomy information

 Score =  951 bits (2458), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 496/574 (86%), Positives = 527/574 (91%), Gaps = 13/574 (2%)

Query: 1   MMKDVEDKSSAEYQRLTWDALRKSINGLVNKVNATNIKNIIPELFAENLIRGRGLFCRSC 60
           MMK+V+DKSS EYQRLTWDALRKSINGLVNKVNATNIKNIIPELF ENLIRGRGLFCRSC
Sbjct: 217 MMKEVQDKSSIEYQRLTWDALRKSINGLVNKVNATNIKNIIPELFGENLIRGRGLFCRSC 276

Query: 61  MKSQMASPGFTDVFAALVAVVNTKFTAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIA 120
           MKSQMASPGFTDVFAALVAVVNTKF  VGELL++RIVLQ KRAYKRNDK QLLAAVKFIA
Sbjct: 277 MKSQMASPGFTDVFAALVAVVNTKFPEVGELLMRRIVLQFKRAYKRNDKHQLLAAVKFIA 336

Query: 121 HLVNQQVAHEIIALELLTILLENPTDDSVEVAVGFVKECGSILQDLSPKGLHGIFERFRG 180
           HLVNQQVAHEIIALELL ++LENPTDDSVEVAVGFVKECGSILQDLSPKGLHGIFERFRG
Sbjct: 337 HLVNQQVAHEIIALELLALMLENPTDDSVEVAVGFVKECGSILQDLSPKGLHGIFERFRG 396

Query: 181 ILHEGEIDKRVQFLIEGLFAIRKAKFQGYPAVRPELDLVDIEDQLTHEISLQDEIDPEIT 240
           ILHEGEIDKRVQFLIEGLFAIRKAKFQG+PAVRPELDLV+ EDQLTHEISL+++IDPEIT
Sbjct: 397 ILHEGEIDKRVQFLIEGLFAIRKAKFQGHPAVRPELDLVEQEDQLTHEISLEEKIDPEIT 456

Query: 241 LDIFKPDPNFLDNEKRYEDMKKDLLGETSEDEEGSDAGS-------GDEDDSEEEEEEED 293
           LDIFKPDP FL++EKRYE++KK +LGE SEDE GSDAGS        D++D +E+++EED
Sbjct: 457 LDIFKPDPQFLESEKRYEELKKTILGEESEDEAGSDAGSDDEDEDEDDDEDDDEDDDEED 516

Query: 294 EEQMKIKDETETNLVNLRRTIYLTIMSSVDFEEAGHKLLKIKLEPGQEMELCIMLLECCS 353
           E+QMKIKDETETNLVNLRRTIYLTIMSS+DFEEAGHKLLKIKLEPGQEMELCIMLLECCS
Sbjct: 517 EQQMKIKDETETNLVNLRRTIYLTIMSSIDFEEAGHKLLKIKLEPGQEMELCIMLLECCS 576

Query: 354 QERTYLRYYGLLGQRFCMINKVHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGTH 413
           QERTYLRYYGLLGQRFCMINKVHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGT 
Sbjct: 577 QERTYLRYYGLLGQRFCMINKVHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGTD 636

Query: 414 ALPWHVLAYIRLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERLTDPTMQDSFESIFPR 473
           ALPWHVLAYIRLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERLTDP+MQDSFESIFP+
Sbjct: 637 ALPWHVLAYIRLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERLTDPSMQDSFESIFPK 696

Query: 474 DNPKNTRFAINFFTSIGLGGITENLREYLKNMPRLIMQQQKQVSESEPDSEADNESESSD 533
           DNPKNTRF+INFFTSIGLGGITENLREYLKNMPRLIMQQQK      P SE+D+ESES  
Sbjct: 697 DNPKNTRFSINFFTSIGLGGITENLREYLKNMPRLIMQQQK------PVSESDDESESGS 750

Query: 534 SSDSDTSSSQSESEDSSSSDESNRDKRHSKRRRR 567
            S    SS      + SS  ES RD+RH KRRRR
Sbjct: 751 GSSGSDSSGSESESEQSSPSESERDERHKKRRRR 784

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|449448752\|ref\|XP_004142129.1\| PREDICTED: pre-mRNA-splicing factor CWC22 homolog [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449503636\|ref\|XP_004162101.1\| PREDICTED: LOW QUALITY PROTEIN: pre-mRNA-splicing factor CWC22 homolog, partial [Cucumis sativus]	Back alignment and taxonomy information

>gi\|356524175\|ref\|XP_003530707.1\| PREDICTED: pre-mRNA-splicing factor CWC22 homolog [Glycine max]	Back alignment and taxonomy information

>gi\|356546225\|ref\|XP_003541530.1\| PREDICTED: pre-mRNA-splicing factor CWC22 homolog [Glycine max]	Back alignment and taxonomy information

>gi\|224139202\|ref\|XP_002323005.1\| predicted protein [Populus trichocarpa] gi\|222867635\|gb\|EEF04766.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi|15220892|ref|NP_178208.1| pre-mRNA-splicing factor CWC22 [Arabidopsis thaliana] gi|6503305|gb|AAF14681.1|AC011713_29 Contains similarity to gb|U19615 LET 858 gene from Caenorhabditis elegans. ESTs gb|AI995150, gb|H76674 and gb|R84035 come from this gene [Arabidopsis thaliana] gi|22654971|gb|AAM98078.1| At1g80930/F23A5_23 [Arabidopsis thaliana] gi|28416525|gb|AAO42793.1| At1g80930/F23A5_23 [Arabidopsis thaliana] gi|332198347|gb|AEE36468.1| pre-mRNA-splicing factor CWC22 [Arabidopsis thaliana]

Back alignment and taxonomy information

>gi\|297839843\|ref\|XP_002887803.1\| hypothetical protein ARALYDRAFT_895889 [Arabidopsis lyrata subsp. lyrata] gi\|297333644\|gb\|EFH64062.1\| hypothetical protein ARALYDRAFT_895889 [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|242053847\|ref\|XP_002456069.1\| hypothetical protein SORBIDRAFT_03g029810 [Sorghum bicolor] gi\|241928044\|gb\|EES01189.1\| hypothetical protein SORBIDRAFT_03g029810 [Sorghum bicolor]	Back alignment and taxonomy information

>gi|115488040|ref|NP_001066507.1| Os12g0256300 [Oryza sativa Japonica Group] gi|77554176|gb|ABA96972.1| Pre-mRNA splicing factor cwc22, putative, expressed [Oryza sativa Japonica Group] gi|113649014|dbj|BAF29526.1| Os12g0256300 [Oryza sativa Japonica Group] gi|156622336|emb|CAO82941.1| putative pre-mRNA-splicing factor cwc-22 [Oryza sativa Japonica Group] gi|215707245|dbj|BAG93705.1| unnamed protein product [Oryza sativa Japonica Group]

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		568
TAIR\|locus:2025797		900	AT1G80930 "AT1G80930" [Arabido	0.904	0.571	0.818	2.5e-223
UNIPROTKB\|F1RYP5		904	CWC22 "Uncharacterized protein	0.908	0.570	0.538	6e-151
ZFIN\|ZDB-GENE-060929-452		985	cwc22 "CWC22 spliceosome-assoc	0.908	0.523	0.534	6e-151
UNIPROTKB\|F1MWG3		899	CWC22 "Uncharacterized protein	0.908	0.573	0.538	7.6e-151
RGD\|1565385		905	Cwc22 "CWC22 spliceosome-assoc	0.903	0.566	0.537	2e-150
MGI\|MGI:2136773		908	Cwc22 "CWC22 spliceosome-assoc	0.906	0.567	0.536	3.3e-150
UNIPROTKB\|J9P9J1		908	CWC22 "Uncharacterized protein	0.908	0.568	0.536	4.2e-150
UNIPROTKB\|B7WP74		745	CWC22 "Pre-mRNA-splicing facto	0.908	0.692	0.536	5.4e-150
UNIPROTKB\|Q9HCG8		908	CWC22 "Pre-mRNA-splicing facto	0.908	0.568	0.536	5.4e-150
DICTYBASE\|DDB_G0267796		925	DDB_G0267796 "initiation facto	0.380	0.233	0.623	7.4e-150

TAIR\|locus:2025797 AT1G80930 "AT1G80930" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 2156 (764.0 bits), Expect = 2.5e-223, P = 2.5e-223
 Identities = 423/517 (81%), Positives = 452/517 (87%)

Query:     1 MMKDVEDKSSAEYQRLTWDALRKSINGLVNKVNATNIKNIIPELFAENLIRGRGLFCRSC 60
             MMK+VEDKSS EYQRLTWDALRKSINGLVNKVNA+NIKNIIPELFAENLIRGRGLFCRSC
Sbjct:   342 MMKEVEDKSSVEYQRLTWDALRKSINGLVNKVNASNIKNIIPELFAENLIRGRGLFCRSC 401

Query:    61 MKSQMASPGFTDVFAALVAVVNTKFTAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIA 120
             MKSQMASPGFTDVFAALVAV+N KF  V ELLLKR+VLQLKRAYKRNDKPQLLAAVKFIA
Sbjct:   402 MKSQMASPGFTDVFAALVAVINAKFPEVAELLLKRVVLQLKRAYKRNDKPQLLAAVKFIA 461

Query:   121 HLVNQQVAHXXXXXXXXXXXXXNPTDDSVEVAVGFVKECGSILQDLSPKGLHGIFERFRG 180
             HLVNQQVA              +PTDDSVEVAVGFV ECG++LQD+SP+GL+GIFERFRG
Sbjct:   462 HLVNQQVAEEIIALELVTILLGDPTDDSVEVAVGFVTECGAMLQDVSPRGLNGIFERFRG 521

Query:   181 ILHEGEIDKRVQFLIEGLFAIRKAKFQGYPAVRPELDLVDIEDQLTHEISLQDEIDPEIT 240
             ILHEGEIDKRVQ+LIE LFA RKAKFQG+PAVRPELDLV  E++ +H++SL  EIDPE  
Sbjct:   522 ILHEGEIDKRVQYLIESLFATRKAKFQGHPAVRPELDLV--EEKYSHDLSLDHEIDPETA 579

Query:   241 LDIFKPDPNFLDNEKRYEDMKKDLLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-QMKI 299
             LDIFKPDP+F++NEK+YE +KK+LL                               QM+I
Sbjct:   580 LDIFKPDPDFVENEKKYEALKKELLGDEESEDEDGSDASSEDNDEEEDESDEEDEEQMRI 639

Query:   300 KDETETNLVNLRRTIYLTIMSSVDFEEAGHKLLKIKLEPGQEMELCIMLLECCSQERTYL 359
             +DETETNLVNLRRTIYLTIMSSVDFEEAGHKLLKIKLEPGQEMELCIMLLECCSQERTYL
Sbjct:   640 RDETETNLVNLRRTIYLTIMSSVDFEEAGHKLLKIKLEPGQEMELCIMLLECCSQERTYL 699

Query:   360 RYYGLLGQRFCMINKVHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGTHALPWHV 419
             RYYGLLGQRFCMINK+HQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGT ALPWHV
Sbjct:   700 RYYGLLGQRFCMINKIHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGTDALPWHV 759

Query:   420 LAYIRLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERLTDPTMQDSFESIFPRDNPKNT 479
             LAYIRLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERL DPTMQ+S ESIFP+DNPKNT
Sbjct:   760 LAYIRLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERLQDPTMQESLESIFPKDNPKNT 819

Query:   480 RFAINFFTSIGLGGITENLREYLKNMPRLIMQQQKQV 516
             RFAINFFTSIGLGGITENLREYLKNMP LIMQ+QKQV
Sbjct:   820 RFAINFFTSIGLGGITENLREYLKNMPSLIMQRQKQV 856

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0006412 "translation" evidence=ISS

GO:0016070 "RNA metabolic process" evidence=IEA

GO:0005829 "cytosol" evidence=IDA

UNIPROTKB\|F1RYP5 CWC22 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-060929-452 cwc22 "CWC22 spliceosome-associated protein homolog (S. cerevisiae)" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|F1MWG3 CWC22 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

RGD\|1565385 Cwc22 "CWC22 spliceosome-associated protein homolog (S. cerevisiae)" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

MGI\|MGI:2136773 Cwc22 "CWC22 spliceosome-associated protein homolog (S. cerevisiae)" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|J9P9J1 CWC22 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|B7WP74 CWC22 "Pre-mRNA-splicing factor CWC22 homolog" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|Q9HCG8 CWC22 "Pre-mRNA-splicing factor CWC22 homolog" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0267796 DDB_G0267796 "initiation factor eIF-4 gamma, MA3 domain-containing protein" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P0CM96	CWC22_CRYNJ	No assigned EC number	0.5546	0.8838	0.6040	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	eugene3.00161151	hypothetical protein (933 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	estExt_Genewise1_v1.C_LG_IV2251	hypothetical protein (909 aa)	•	•	0.437
	eugene3.00012679	hypothetical protein (230 aa)		•	0.409

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		568
pfam02854		198	pfam02854, MIF4G, MIF4G domain	2e-29
smart00543		200	smart00543, MIF4G, Middle domain of eukaryotic ini	1e-27
pfam02847		113	pfam02847, MA3, MA3 domain	2e-25
smart00544		113	smart00544, MA3, Domain in DAP-5, eIF4G, MA-3 and	2e-25
TIGR00927		1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	4e-05
PTZ00248		319	PTZ00248, PTZ00248, eukaryotic translation initiat	3e-04
pfam04931		784	pfam04931, DNA_pol_phi, DNA polymerase phi	0.001
COG5271		4600	COG5271, MDN1, AAA ATPase containing von Willebran	0.002
pfam05110		1154	pfam05110, AF-4, AF-4 proto-oncoprotein	0.003

>gnl\|CDD\|217253 pfam02854, MIF4G, MIF4G domain	Back alignment and domain information

 Score =  114 bits (288), Expect = 2e-29
 Identities = 57/198 (28%), Positives = 97/198 (48%), Gaps = 14/198 (7%)

Query: 22  RKSINGLVNKVNATNIKNIIPELFAEN--LIRGRGLFCRSCMKSQMASPGFTDVFAALVA 79
            K + GL+NK++ +N + II EL   N               +  +  P F   +A L A
Sbjct: 1   LKKVKGLLNKLSPSNFEKIIDELLKLNMSDKNLLKYILELIFEKAVEEPNFIPAYARLCA 60

Query: 80  VVNTKFTAVGELLLKRIVLQLKRAY---KRNDKPQLLAAVKFIAHLVNQQVAHEIIALEL 136
            +N+K    GELLL R+  + ++     +R ++ + L  V+F+  L N +V  E I LE 
Sbjct: 61  GLNSKNPDFGELLLNRLQEEFEKGVEEEERGNRKRRLGLVRFLGELFNFKVLTEKIILEC 120

Query: 137 LTILLENPT------DDSVEVAVGFVKECG-SILQDLSPKGLHGIFERFRGILH--EGEI 187
           L  LLE+ T      + S+E+ +  +  CG  + ++   K +  I ER +  L   + E+
Sbjct: 121 LKELLESLTEEDPRDEFSLEILLLLLTTCGKLLDREKLKKLMDEILERIQKYLLSADPEL 180

Query: 188 DKRVQFLIEGLFAIRKAK 205
             R++F++E L  +RK K
Sbjct: 181 SSRLRFMLEDLIELRKNK 198

MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Length = 198

>gnl\|CDD\|214713 smart00543, MIF4G, Middle domain of eukaryotic initiation factor 4G (eIF4G)	Back alignment and domain information

>gnl\|CDD\|111714 pfam02847, MA3, MA3 domain	Back alignment and domain information

>gnl\|CDD\|214714 smart00544, MA3, Domain in DAP-5, eIF4G, MA-3 and other proteins	Back alignment and domain information

>gnl\|CDD\|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	Back alignment and domain information

>gnl\|CDD\|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional	Back alignment and domain information

>gnl\|CDD\|218333 pfam04931, DNA_pol_phi, DNA polymerase phi	Back alignment and domain information

>gnl\|CDD\|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]	Back alignment and domain information

>gnl\|CDD\|218440 pfam05110, AF-4, AF-4 proto-oncoprotein	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		568
KOG2140		739	consensus Uncharacterized conserved protein [Gener	100.0
KOG2141		822	consensus Protein involved in high osmolarity sign	100.0
smart00543		200	MIF4G Middle domain of eukaryotic initiation facto	99.94
PF02854		209	MIF4G: MIF4G domain; InterPro: IPR003890 This entr	99.94
smart00544		113	MA3 Domain in DAP-5, eIF4G, MA-3 and other protein	99.77
PF02847		113	MA3: MA3 domain; InterPro: IPR003891 This entry re	99.68
KOG0401		970	consensus Translation initiation factor 4F, riboso	99.38
KOG2051		1128	consensus Nonsense-mediated mRNA decay 2 protein [	99.36
KOG1104		759	consensus Nuclear cap-binding complex, subunit NCB	99.22
KOG2051		1128	consensus Nonsense-mediated mRNA decay 2 protein [	98.24
PF02854		209	MIF4G: MIF4G domain; InterPro: IPR003890 This entr	96.62
smart00543		200	MIF4G Middle domain of eukaryotic initiation facto	95.36
PHA03308		1463	transcriptional regulator ICP4; Provisional	94.55
PF09088		191	MIF4G_like: MIF4G like; InterPro: IPR015172 This e	94.48
PF10500		225	SR-25: Nuclear RNA-splicing-associated protein; In	94.48
KOG3942		348	consensus MIF4G domain-containing protein [Transla	94.33
PF07817		256	GLE1: GLE1-like protein; InterPro: IPR012476 The m	93.53
KOG2140		739	consensus Uncharacterized conserved protein [Gener	92.88
KOG2297		412	consensus Predicted translation factor, contains W	92.29
KOG2130		407	consensus Phosphatidylserine-specific receptor Ptd	91.85
KOG2412		591	consensus Nuclear-export-signal (NES)-containing p	91.62
PHA03308		1463	transcriptional regulator ICP4; Provisional	89.99
KOG2130		407	consensus Phosphatidylserine-specific receptor Ptd	87.35

>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]	Back alignment and domain information

Probab=100.00  E-value=2.7e-170  Score=1322.53  Aligned_cols=539  Identities=65%  Similarity=1.055  Sum_probs=505.0

Q ss_pred             CCccccCCCCHHHHHHHHHHHHHHHHHHhhcCChhhHHHHHHHHHHhhhhhhhhHHHHHHhhhccCCCChHHHHHHHHHH
Q 008379            1 MMKDVEDKSSAEYQRLTWDALRKSINGLVNKVNATNIKNIIPELFAENLIRGRGLFCRSCMKSQMASPGFTDVFAALVAV   80 (568)
Q Consensus         1 ~~~~~~~~~s~e~qr~~w~~Lkk~I~gllNKLs~~Ni~~i~~eL~~~Ni~rgrgll~~si~~~q~~~~~f~~vyAaLva~   80 (568)
                      ||++|+|++|.+|||++|++|||+|+|+|||||.+||..|++|||++|++|||||+|++||++|+++|.|++|||||+|+
T Consensus       144 mq~qi~Dk~s~~yQRmnWEalkksInglInkvn~sNi~~ii~eLfqeNiirgRgl~crsv~~aq~asp~ft~vyaALvAv  223 (739)
T KOG2140|consen  144 MQAQITDKNSIEYQRMNWEALKKSINGLINKVNASNIQEIIRELFQENIIRGRGLLCRSVMQAQAASPGFTPVYAALVAV  223 (739)
T ss_pred             HHHHhcccchHHHHHHHHHHHHHHhHHHHhhhhHHHHHHHHHHHHHHHHHhccchhHHHHHHHHhcCCCCcHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhcCCchHHHHHHHHHHHHHHHHHHhCChhhhhhhHHHHHHHHhhhhccHHHHHHHHHHHhhCCCCCcHHHHHHHHHHHh
Q 008379           81 VNTKFTAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQVAHEIIALELLTILLENPTDDSVEVAVGFVKECG  160 (568)
Q Consensus        81 ln~~~pe~G~lll~rlv~~F~~~~~~~dk~~~~n~i~fIa~Lyn~~Vv~~~lildii~~LLe~~te~sVE~ll~lLr~~G  160 (568)
                      ||++||+||++|++|++.+|+++|+|||+..|.|.++|||||+||+|+|++++++|+.+||+.||+++||+++.+|+.||
T Consensus       224 iNskfP~IgElLlkrLilqf~r~f~RnDk~~c~~~~kfiahLinq~VahEIv~Leil~lLLe~PTddSvevaI~flkecG  303 (739)
T KOG2140|consen  224 INSKFPQIGELLLKRLILQFKRSFRRNDKVSCLNASKFIAHLINQQVAHEIVALEILTLLLERPTDDSVEVAIAFLKECG  303 (739)
T ss_pred             HccCCchHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhccCChhHHHHHHHHHHHHhhcCCCChhHHHHHHHHHHHHHhccCCCCCCCCCccccccccceeeeeeccCcCCcccc
Q 008379          161 SILQDLSPKGLHGIFERFRGILHEGEIDKRVQFLIEGLFAIRKAKFQGYPAVRPELDLVDIEDQLTHEISLQDEIDPEIT  240 (568)
Q Consensus       161 ~~Lr~~~p~~lk~I~~~l~~il~e~~is~R~~fmIE~l~~lr~nk~k~~~~i~~~ldlve~~~~~th~i~l~~~~~~e~~  240 (568)
                      .+|..++|.+++.||++||.|||+|++++|+|||||+||++|+++|+++|++.++||+|+++||+||.+++++.++|++.
T Consensus       304 akL~~VSpr~~n~IfErlR~ILhe~Eld~rvqy~iEtlf~iRkdkfk~~p~v~~~LDlvee~dq~tH~l~l~de~dpe~~  383 (739)
T KOG2140|consen  304 AKLAEVSPRALNGIFERLRYILHEGELDRRVQYMIETLFQIRKDKFKSHPAVLEELDLVEEEDQITHSLSLEDEDDPEKE  383 (739)
T ss_pred             HHHHHhChHHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHhhccCCccccccCccchhhheeeeeecccccChhhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcccCCcccccchHHHHhhhhcccCCCCC-CcCCCCCCCCCCCCchhhhhhhhHHHhhhhhhhhcchhhhhhhhhhhhh
Q 008379          241 LDIFKPDPNFLDNEKRYEDMKKDLLGETSE-DEEGSDAGSGDEDDSEEEEEEEDEEQMKIKDETETNLVNLRRTIYLTIM  319 (568)
Q Consensus       241 l~~f~~D~~~~~~e~~~~~~k~~ilG~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~d~t~~n~t~~RR~Ifl~IM  319 (568)
                      |++|++||+|.+||++|+++|++|+|.... ++++++.++++++++++++++++++.++|.|+|.+|++++||+||||||
T Consensus       384 L~vFk~dp~f~ene~kydaikkeiLgn~dsen~d~~~~s~E~~~eee~e~~ee~~e~~qI~D~T~~Nlv~frr~IYLti~  463 (739)
T KOG2140|consen  384 LGVFKKDPNFEENEEKYDAIKKEILGNEDSENEDDEDGSSEDDDEEEDESVEEDEEKLQIIDMTETNLVNFRRTIYLTIQ  463 (739)
T ss_pred             hcccccCccHHHHHHHHHHHHHHHhcCCcccccccccccccccccccccccccccccceeeccccchhHHhhhhheeeee
Confidence            999999999999999999999999997543 2333333333333333444456677899999999999999999999999


Q ss_pred             cCCCHHHHHHHHHcccCCCCcchHHHHHHHHhhcccCcchhhHHHHHHHHhhccHhhHHHHHHHHHHHhhhhhcCchhhH
Q 008379          320 SSVDFEEAGHKLLKIKLEPGQEMELCIMLLECCSQERTYLRYYGLLGQRFCMINKVHQENFEKCFVQQYSMIHRLETNKL  399 (568)
Q Consensus       320 SS~d~~eA~hKLlkL~lk~~qe~EI~~vli~Cc~qEktYn~yY~llaerlC~~~~~~~~~f~~~f~~~y~~i~~le~~kl  399 (568)
                      ||+||+||+||||||.|+++|+.|+|+|||+||+||+||.+|||+|++|||.+|+.||.+|+.||.++|.+||++|++||
T Consensus       464 SSldfeEaaHKLLKmkip~~q~~elc~mii~cc~QerTy~kFYglL~eRfc~l~r~~q~~fe~~f~q~YstIhr~EtnkL  543 (739)
T KOG2140|consen  464 SSLDFEEAAHKLLKMKIPESQEKELCNMIIDCCAQERTYEKFYGLLGERFCMLHREWQEAFEKCFKQQYSTIHRYETNKL  543 (739)
T ss_pred             ccCcHHHHHHHHHhccCCchhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhcCCcCcccccccccCCcccCchHHHHHHHHHHHHHHHHchHHHHhhcCCcchhhhhhccCCCCCCCCc
Q 008379          400 RNVAKFFAHLLGTHALPWHVLAYIRLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERLTDPTMQDSFESIFPRDNPKNT  479 (568)
Q Consensus       400 rNlakf~ahLl~~~~l~l~vLk~i~l~e~dttss~riFik~LfqeL~~~lg~~~l~~rl~d~~~~~~~~glfp~d~~~~~  479 (568)
                      ||+||||||||++|+|||.||++|+|||++|||++||||||||||||++|||++|++||+||++||+|+||||+|||+|+
T Consensus       544 RnlakffahLlstd~lpw~vl~~ikLTEEdTtsssRIfiKilFqELve~lGl~~L~~RL~dptl~~~l~glFP~dnp~n~  623 (739)
T KOG2140|consen  544 RNLAKFFAHLLSTDALPWDVLACIKLTEEDTTSSSRIFIKILFQELVEALGLDKLNERLNDPTLQPKLEGLFPRDNPRNT  623 (739)
T ss_pred             HHHHHHHHHHhcccccchHHHHHhhcccccCCccceehHHHHHHHHHHHhChHHHHHHhcCcchhhhhhccCcCCCcccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eehhhHHHhcCchhhhHHHHHHHHhCChhHHHhhhhccCCCCCCcccCCCCCCCCCCCCC
Q 008379          480 RFAINFFTSIGLGGITENLREYLKNMPRLIMQQQKQVSESEPDSEADNESESSDSSDSDT  539 (568)
Q Consensus       480 rfsinfft~IgLg~lt~~~R~~l~~~~~~~~~~~~~~~~~~s~~~~~~~s~~~~~~~~~~  539 (568)
                      ||||||||+||||+||++||++|++.|+.+++++.++..++|+++|+|+++|++.|+|++
T Consensus       624 RfsINfFTsIGLGgLTeelRe~L~~~pk~~~a~~eq~~~ses~~ss~sss~ses~s~s~~  683 (739)
T KOG2140|consen  624 RFSINFFTSIGLGGLTEELREYLKNMPKVEDAEKEQVAESESGSSSSSSSDSESESDSGD  683 (739)
T ss_pred             eeeeehhhhhccccchHHHHHHHHhcchhhhhhHHHHhhcccccccccccccccCCCCCC
Confidence            999999999999999999999999999998866665554444444444444443343333

>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]	Back alignment and domain information

>smart00543 MIF4G Middle domain of eukaryotic initiation factor 4G (eIF4G)	Back alignment and domain information

>PF02854 MIF4G: MIF4G domain; InterPro: IPR003890 This entry represents an MIF4G-like domain	Back alignment and domain information

>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins	Back alignment and domain information

>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]	Back alignment and domain information

>KOG0401 consensus Translation initiation factor 4F, ribosome/mRNA-bridging subunit (eIF-4G) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]	Back alignment and domain information

>KOG1104 consensus Nuclear cap-binding complex, subunit NCBP1/CBP80 [RNA processing and modification]	Back alignment and domain information

>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]	Back alignment and domain information

>PF02854 MIF4G: MIF4G domain; InterPro: IPR003890 This entry represents an MIF4G-like domain	Back alignment and domain information

>smart00543 MIF4G Middle domain of eukaryotic initiation factor 4G (eIF4G)	Back alignment and domain information

>PHA03308 transcriptional regulator ICP4; Provisional	Back alignment and domain information

>PF09088 MIF4G_like: MIF4G like; InterPro: IPR015172 This entry represents an MIF4G-like domain	Back alignment and domain information

>PF10500 SR-25: Nuclear RNA-splicing-associated protein; InterPro: IPR019532 SR-25, otherwise known as ADP-ribosylation factor-like factor 6-interacting protein 4, is expressed in virtually all tissue types	Back alignment and domain information

>KOG3942 consensus MIF4G domain-containing protein [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PF07817 GLE1: GLE1-like protein; InterPro: IPR012476 The members of this family are sequences that are similar to the human protein GLE1 (O75458 from SWISSPROT)	Back alignment and domain information

>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]	Back alignment and domain information

>KOG2297 consensus Predicted translation factor, contains W2 domain [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG2130 consensus Phosphatidylserine-specific receptor PtdSerR, contains JmjC domain [Chromatin structure and dynamics; Signal transduction mechanisms]	Back alignment and domain information

>KOG2412 consensus Nuclear-export-signal (NES)-containing protein/polyadenylated-RNA export factor [RNA processing and modification]	Back alignment and domain information

>PHA03308 transcriptional regulator ICP4; Provisional	Back alignment and domain information

>KOG2130 consensus Phosphatidylserine-specific receptor PtdSerR, contains JmjC domain [Chromatin structure and dynamics; Signal transduction mechanisms]	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		568
1h2v_C		771	80 kDa nuclear CAP binding protein; CAP-binding-co	1e-37
1hu3_A		260	EIF4GII; heat repeat, translation; 2.37A {Homo sap	6e-19
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-12
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04
3rk6_A		234	Polyadenylate-binding protein-interacting protein;	2e-11
2vso_E		284	Eukaryotic initiation factor 4F subunit P150; acet	5e-08
2i2o_A		224	EIF4G-like protein; protein structure initiative,	1e-04

>1h2v_C 80 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: a.118.1.14 a.118.1.14 a.118.1.14 PDB: 1n52_A* 1n54_A 3fex_A 3fey_A 1h6k_A 1h2t_C* 1h2u_A* Length = 771	Back alignment and structure

 Score =  147 bits (371), Expect = 1e-37
 Identities = 66/556 (11%), Positives = 167/556 (30%), Gaps = 56/556 (10%)

Query: 14  QRLTWDALRKSINGLVNKVNATNIKNI------IPELFAENLIRGRGLFCRSCMKSQMAS 67
           +    +     +  L+ KV   +  ++      +  +   +L   +    R         
Sbjct: 1   KTSDANETEDHLESLICKVGEKSACSLESNLEGLAGVLEADLPNYKSKILRLLCTVARLL 60

Query: 68  PGFTDVFAALVAVVNTKFTAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQV 127
           P    ++  LV ++N +    G   ++ ++ QLK + K N+  + +  V+F++ LVN  V
Sbjct: 61  PEKLTIYTTLVGLLNARNYNFGGEFVEAMIRQLKESLKANNYNEAVYLVRFLSDLVNCHV 120

Query: 128 AHEIIALELLTILLE---------NPTDDSVEVAVGFVKECGSILQDLSPKGLHGIFERF 178
                 + +    +             D  V   +  +   G  L +     +  IF   
Sbjct: 121 IAAPSMVAMFENFVSVTQEEDVPQVRRDWYVYAFLSSLPWVGKELYEKKDAEMDRIFANT 180

Query: 179 RGILHEGEIDKRVQFLIEGLFAIRKAKFQGYPAVRPELDLVDIEDQLTHEISLQDEIDPE 238
                   + +R +  +  L        Q + A +P      ++        L+ +   E
Sbjct: 181 ESY-----LKRRQKTHVPML--------QVWTADKPHPQEEYLDCLWAQIQKLKKDRWQE 227

Query: 239 ITLDIFKPDPNFLDNEKRYEDMKKDLLGETSEDEEGSDAGSGDEDDSEEEEEEEDEEQMK 298
             +      P +L  +    +  +  L   +      D+            +  D+ +  
Sbjct: 228 RHI----LRP-YLAFDSILCEALQHNLPPFTPPPHTEDSVYPMPRVIFRMFDYTDDPEGP 282

Query: 299 IKDETETNLVNLRRTIYLTIMSSVDFE--EAGHKLLKIKLEPGQEMELCI-------MLL 349
           +   + +    +       I+ S   E      +L+    +    +   I       +  
Sbjct: 283 VMPGSHSVERFVIEENLHCIIKSHWKERKTCAAQLVSYPGKNKIPLNYHIVEVIFAELFQ 342

Query: 350 ECCSQERTYLRYYGLLGQRFCMIN-KVHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAH 408
                       Y  L    C +      +   +     Y  +  + T  +     +F+H
Sbjct: 343 LPAPPHIDV--MYTTLLIELCKLQPGSLPQVLAQATEMLYMRLDTMNTTCVDRFINWFSH 400

Query: 409 LLGTHALPWHVLAYIRLTEEDTTSSSRIFIKILFQELSEHLGIRL-LNERLTDPTMQDSF 467
            L      W    +     +D  S    F++ + ++      +RL  ++R+ D  +  +F
Sbjct: 401 HLSNFQFRWSWEDWSDCLSQDPESPKPKFVREVLEKC-----MRLSYHQRILD-IVPPTF 454

Query: 468 ESIFPRDNPKNTRFAINFFTSIGLGGITENLREYLKNMPRLIMQQQKQVSESEPDSEADN 527
            ++ P +     ++      S+    +   L    K+         +  S  +     + 
Sbjct: 455 SALCPSNPTCIYKYGDESSNSLPGHSVALCLAVAFKSKA----TNDEIFSILKDVPNPNQ 510

Query: 528 ESESSDSSDSDTSSSQ 543
           + +  +    +    +
Sbjct: 511 DDDDDEGFSFNPLKIE 526

PyMOL of 1h2v

>1hu3_A EIF4GII; heat repeat, translation; 2.37A {Homo sapiens} SCOP: a.118.1.14 Length = 260	Back alignment and structure

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

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

>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

>3rk6_A Polyadenylate-binding protein-interacting protein; heat fold, PABP, EIF4A, EIF3, translation regulator; 2.00A {Homo sapiens} Length = 234	Back alignment and structure

>2vso_E Eukaryotic initiation factor 4F subunit P150; acetylation, ATP-binding, phosphoprotein, protein biosynthesis, translation regulation; HET: AMP; 2.6A {Saccharomyces cerevisiae} PDB: 2vsx_E* Length = 284	Back alignment and structure

>2i2o_A EIF4G-like protein; protein structure initiative, PSI, cente eukaryotic structural genomics, CESG, structural genomics, function; HET: MSE; 1.92A {Danio rerio} Length = 224	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		568
1h2v_C		771	80 kDa nuclear CAP binding protein; CAP-binding-co	100.0
1hu3_A		260	EIF4GII; heat repeat, translation; 2.37A {Homo sap	100.0
2vso_E		284	Eukaryotic initiation factor 4F subunit P150; acet	100.0
3rk6_A		234	Polyadenylate-binding protein-interacting protein;	99.96
2i2o_A		224	EIF4G-like protein; protein structure initiative,	99.85
1uw4_B		248	UPF2, regulator of nonsense transcripts 2; nonsens	99.36
1ug3_A		339	EIF4GI, eukaryotic protein synthesis initiation fa	96.58
4gmj_A		229	CCR4-NOT transcription complex subunit 1; mRNA dec	95.19
3l6a_A		364	Eukaryotic translation initiation factor 4 gamma;	95.09
4b89_A		249	General negative regulator of transcription subun;	93.85
1hu3_A		260	EIF4GII; heat repeat, translation; 2.37A {Homo sap	92.45
2vso_E		284	Eukaryotic initiation factor 4F subunit P150; acet	89.86
3pev_B		297	Nucleoporin GLE1; RECA, heat, DEAD-BOX, ATPase, he	87.3
2rg8_A		165	Programmed cell death protein 4; MA3 domain, heat	86.24
2i2o_A		224	EIF4G-like protein; protein structure initiative,	83.59
3rk6_A		234	Polyadenylate-binding protein-interacting protein;	82.75
2nsz_A		129	Programmed cell death protein 4; PDCD4, tumor supp	82.21
1h2v_C		771	80 kDa nuclear CAP binding protein; CAP-binding-co	80.21

>1h2v_C 80 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: a.118.1.14 a.118.1.14 a.118.1.14 PDB: 1n52_A* 1n54_A 3fex_A 3fey_A 1h6k_A 1h2t_C* 1h2u_A*	Back alignment and structure

Probab=100.00  E-value=1.2e-46  Score=429.41  Aligned_cols=415  Identities=15%  Similarity=0.221  Sum_probs=336.2

Q ss_pred             HHHHHHHHHhhcCCh---hhHHHHHHHHHH---hhhhhhhhHHHHHHhhhccCCCChHHHHHHHHHHHhcCCchHHHHHH
Q 008379           20 ALRKSINGLVNKVNA---TNIKNIIPELFA---ENLIRGRGLFCRSCMKSQMASPGFTDVFAALVAVVNTKFTAVGELLL   93 (568)
Q Consensus        20 ~Lkk~I~gllNKLs~---~Ni~~i~~eL~~---~Ni~rgrgll~~si~~~q~~~~~f~~vyAaLva~ln~~~pe~G~lll   93 (568)
                      .++.+|+++|-|+++   +|++.-+..|+.   .|+.+|||.|++++++++...|.++++||+||++||++.|+||++++
T Consensus         7 ~~~~~l~~lI~rlge~~~~s~~~~l~~L~~~l~~~l~~~r~~i~~~l~~~~~~~P~Kt~vyAaLVgllN~k~pe~G~~lv   86 (771)
T 1h2v_C            7 ETEDHLESLICKVGEKSACSLESNLEGLAGVLEADLPNYKSKILRLLCTVARLLPEKLTIYTTLVGLLNARNYNFGGEFV   86 (771)
T ss_dssp             ---CHHHHHHHTTTSSCSSCHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             cHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCCCcchHHHHHHHHHHcCChhHHHHHH
Confidence            468899999999999   666655555543   58999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhCChhhhhhhHHHHHHHHhhhhccHHHHHHHHHHHhhCCCCCcH---------HHHHHHHHHHhHhhc
Q 008379           94 KRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQVAHEIIALELLTILLENPTDDSV---------EVAVGFVKECGSILQ  164 (568)
Q Consensus        94 ~rlv~~F~~~~~~~dk~~~~n~i~fIa~Lyn~~Vv~~~lildii~~LLe~~te~sV---------E~ll~lLr~~G~~Lr  164 (568)
                      ++++.+|+++++++++..|..+++|||+|+|++|+++..+++++..|++.++++++         .+++..|.+||+.|.
T Consensus        87 ~~l~~~f~~~l~~~~~~~~k~~lrFLa~L~n~~Vv~~~~il~lL~~Ll~~~~e~~~~q~r~D~~v~~vL~~Lp~~G~~L~  166 (771)
T 1h2v_C           87 EAMIRQLKESLKANNYNEAVYLVRFLSDLVNCHVIAAPSMVAMFENFVSVTQEEDVPQVRRDWYVYAFLSSLPWVGKELY  166 (771)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTSBCHHHHHHHHHHHHHGGGCSSCCHHHHHHHHHHHHTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccChHHHHHHHHHHHHhccCCeecHHHHHHHHHHHHHhhhhcCCcccchhHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999998886554         569999999999999


Q ss_pred             cCChhHHHHHHHHHHHHh-hcCC----------------CChhHHHHHHHHHHHHHhccCCCCCCCCCccccc--cccce
Q 008379          165 DLSPKGLHGIFERFRGIL-HEGE----------------IDKRVQFLIEGLFAIRKAKFQGYPAVRPELDLVD--IEDQL  225 (568)
Q Consensus       165 ~~~p~~lk~I~~~l~~il-~e~~----------------is~R~~fmIE~l~~lr~nk~k~~~~i~~~ldlve--~~~~~  225 (568)
                      +..|.++++|+++++..+ +.+.                .+.|+++|++.|..+|+|+|+. |.++..++..+  ..++.
T Consensus       167 e~~~~~l~~lle~~~~yl~~r~~~~~~ll~~~~~~~~~~~~~~l~~L~~ql~~lr~~~w~~-~~iprp~~~f~~~l~d~~  245 (771)
T 1h2v_C          167 EKKDAEMDRIFANTESYLKRRQKTHVPMLQVWTADKPHPQEEYLDCLWAQIQKLKKDRWQE-RHILRPYLAFDSILCEAL  245 (771)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTCCCTTHHHHCSBCCCSSCCCCBHHHHHHHHHHHHHHTTTCC-SCCCCGGGGGTTTCCGGG
T ss_pred             hcCHHHHHHHHHHHHHHHHhcCccchhhhhccccCCCCchhhHHHHHHHHHHHHHHCCCCC-cCCCchhhhccccccccc
Confidence            999999999999999866 4332                2579999999999999999985 56655554443  45677


Q ss_pred             eeeee-ccCcCCccccCCcccCCcccccchHHHHhhhhcccCCCCCCcCCCCCCCCCCCCchhhhhhhhHHHhhhhhhhh
Q 008379          226 THEIS-LQDEIDPEITLDIFKPDPNFLDNEKRYEDMKKDLLGETSEDEEGSDAGSGDEDDSEEEEEEEDEEQMKIKDETE  304 (568)
Q Consensus       226 th~i~-l~~~~~~e~~l~~f~~D~~~~~~e~~~~~~k~~ilG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~d~t~  304 (568)
                      +|.+. +......+        ++.|.     |-.+...+.|..+.++ +                      ..+.+.+.
T Consensus       246 ~H~lp~~~~p~~~~--------~~~yp-----~p~~~f~if~~~d~~e-~----------------------~~~p~~~~  289 (771)
T 1h2v_C          246 QHNLPPFTPPPHTE--------DSVYP-----MPRVIFRMFDYTDDPE-G----------------------PVMPGSHS  289 (771)
T ss_dssp             CBCCCCCCCCCCCT--------TCCCC-----CCCBCCCCCCGGGCTT-S----------------------SCCCCTTS
T ss_pred             cCCCCCCCCCCCcc--------cccCC-----ccceeeeccCCccccc-c----------------------ccCCCcch
Confidence            88765 33221111        22222     2223444555432110 0                      01223344


Q ss_pred             cchhhhhhhhhhhhhcCC--CHHHHHHHHHcccCCCCcchHHHHHHHHhhccc-------CcchhhHHHHHHHHhhcc-H
Q 008379          305 TNLVNLRRTIYLTIMSSV--DFEEAGHKLLKIKLEPGQEMELCIMLLECCSQE-------RTYLRYYGLLGQRFCMIN-K  374 (568)
Q Consensus       305 ~n~t~~RR~Ifl~IMSS~--d~~eA~hKLlkL~lk~~qe~EI~~vli~Cc~qE-------ktYn~yY~llaerlC~~~-~  374 (568)
                      .+ ..+.|++|+.||++.  +..||+|+|+++.  .+++.++++|+|+||.+|       ++|..||+.|+.+||+.+ +
T Consensus       290 id-r~l~re~ildIi~~~~~nrkecA~~Ll~l~--~~~~~~~e~~iVE~i~~el~~LP~p~~~~iyY~sll~eLCkl~P~  366 (771)
T 1h2v_C          290 VE-RFVIEENLHCIIKSHWKERKTCAAQLVSYP--GKNKIPLNYHIVEVIFAELFQLPAPPHIDVMYTTLLIELCKLQPG  366 (771)
T ss_dssp             HH-HHHHHHHHHHHHHHHTTCHHHHHHHHHTCC--CSSCCCHHHHHHHHHHHHHTCSSCCSSCHHHHHHHHHHHHHHSTT
T ss_pred             HH-HHHHHHHHHHHHHHccCCHHHHHHHHhcCC--CCCcccHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHhChH
Confidence            44 678999999999999  7799999999985  557788999999999999       999999999999999999 6


Q ss_pred             hhHHHHHHHHHHHhhhhhcCchhhHHHHHHHHHHHHhcC--CcCcccccccccCCcccCchHHHHHHHHHHHHHHHHchH
Q 008379          375 VHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGTH--ALPWHVLAYIRLTEEDTTSSSRIFIKILFQELSEHLGIR  452 (568)
Q Consensus       375 ~~~~~f~~~f~~~y~~i~~le~~klrNlakf~ahLl~~~--~l~l~vLk~i~l~e~dttss~riFik~LfqeL~~~lg~~  452 (568)
                      .|...|..||...|+++|+++++.+++++.+|+|+|+++  ..+|+.|..+  ++.++++++|+|+|.+|++++.---. 
T Consensus       367 ~~~~v~~~ai~~lY~~i~~md~e~~~Rf~dwFShhLSNF~f~W~W~eW~~~--~e~~~~~p~r~Fik~ll~k~~RLSy~-  443 (771)
T 1h2v_C          367 SLPQVLAQATEMLYMRLDTMNTTCVDRFINWFSHHLSNFQFRWSWEDWSDC--LSQDPESPKPKFVREVLEKCMRLSYH-  443 (771)
T ss_dssp             THHHHHHHHHHHHHHTGGGBCHHHHHHHHHHHHHHHTTTTTCCCGGGGGGG--TTSCTTSHHHHHHHHHHHHHHHTSCH-
T ss_pred             hHHHHHHHHHHHHHHhhcccCHHHHHHHHHHHHHHHhcCCcCccHHHhHHh--hcCCccCcHHHHHHHHHHHHHhhhhH-
Confidence            899999999999999999999999999999999999999  6788888665  56778889999999999999863333 


Q ss_pred             HHHhhcCCcchhhhhhccCCCCCCCCcee
Q 008379          453 LLNERLTDPTMQDSFESIFPRDNPKNTRF  481 (568)
Q Consensus       453 ~l~~rl~d~~~~~~~~glfp~d~~~~~rf  481 (568)
                         +|+.+ .+.+.|.+++|.++.-+-+|
T Consensus       444 ---~rIk~-~lP~~~~~llp~~p~p~f~y  468 (771)
T 1h2v_C          444 ---QRILD-IVPPTFSALCPSNPTCIYKY  468 (771)
T ss_dssp             ---HHHHT-TSCGGGGGGSCCCCCCCCTT
T ss_pred             ---HHHHH-hCcHHHHhhCCCCCCCCcee
Confidence               34444 66667889999754333333

PyMOL of 1h2v

>1hu3_A EIF4GII; heat repeat, translation; 2.37A {Homo sapiens} SCOP: a.118.1.14	Back alignment and structure

>2vso_E Eukaryotic initiation factor 4F subunit P150; acetylation, ATP-binding, phosphoprotein, protein biosynthesis, translation regulation; HET: AMP; 2.6A {Saccharomyces cerevisiae} PDB: 2vsx_E*	Back alignment and structure

>3rk6_A Polyadenylate-binding protein-interacting protein; heat fold, PABP, EIF4A, EIF3, translation regulator; 2.00A {Homo sapiens}	Back alignment and structure

>2i2o_A EIF4G-like protein; protein structure initiative, PSI, cente eukaryotic structural genomics, CESG, structural genomics, function; HET: MSE; 1.92A {Danio rerio}	Back alignment and structure

>1uw4_B UPF2, regulator of nonsense transcripts 2; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: a.118.1.14	Back alignment and structure

>1ug3_A EIF4GI, eukaryotic protein synthesis initiation factor 4G; heat repeat, translation; 2.24A {Homo sapiens} SCOP: a.118.1.14 a.118.1.14	Back alignment and structure

>4gmj_A CCR4-NOT transcription complex subunit 1; mRNA decay, deadenylase, RNA bindin; HET: GOL; 2.70A {Homo sapiens} PDB: 4gml_A	Back alignment and structure

>3l6a_A Eukaryotic translation initiation factor 4 gamma; C-terminal region, MA2 domain, W2 domain, EIF4G2, EIF family translation; HET: MES PG4; 2.00A {Homo sapiens}	Back alignment and structure

>4b89_A General negative regulator of transcription subun; 1.50A {Saccharomyces cerevisiae S288C} PDB: 4b8a_A 4b8c_B	Back alignment and structure

>1hu3_A EIF4GII; heat repeat, translation; 2.37A {Homo sapiens} SCOP: a.118.1.14	Back alignment and structure

>2vso_E Eukaryotic initiation factor 4F subunit P150; acetylation, ATP-binding, phosphoprotein, protein biosynthesis, translation regulation; HET: AMP; 2.6A {Saccharomyces cerevisiae} PDB: 2vsx_E*	Back alignment and structure

>3pev_B Nucleoporin GLE1; RECA, heat, DEAD-BOX, ATPase, helicase, mRNA export, nuclear hydrolase; HET: IHP; 2.50A {Saccharomyces cerevisiae} PDB: 3peu_B* 3pex_B* 3pez_B* 3rrm_B* 3rrn_B*	Back alignment and structure

>2rg8_A Programmed cell death protein 4; MA3 domain, heat repeats, anti-oncogene, apoptosis, cell cycle, cytoplasm, nucleus, phosphorylation, polymorphism; 1.80A {Homo sapiens} PDB: 2kzt_A	Back alignment and structure

>2i2o_A EIF4G-like protein; protein structure initiative, PSI, cente eukaryotic structural genomics, CESG, structural genomics, function; HET: MSE; 1.92A {Danio rerio}	Back alignment and structure

>3rk6_A Polyadenylate-binding protein-interacting protein; heat fold, PABP, EIF4A, EIF3, translation regulator; 2.00A {Homo sapiens}	Back alignment and structure

>2nsz_A Programmed cell death protein 4; PDCD4, tumor suppressor, translation, antitumor protein; 1.15A {Mus musculus} SCOP: a.118.1.14 PDB: 2kzt_B 2hm8_A 2ggf_A	Back alignment and structure

>1h2v_C 80 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: a.118.1.14 a.118.1.14 a.118.1.14 PDB: 1n52_A* 1n54_A 3fex_A 3fey_A 1h6k_A 1h2t_C* 1h2u_A*	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	E-value
Query		568
d1h2vc1		262	a.118.1.14 (C:29-290) CBP80, 80KDa nuclear cap-bin	2e-41
d1hu3a_		243	a.118.1.14 (A:) Eukaryotic initiation factor eIF4G	1e-25
d1uw4b_		248	a.118.1.14 (B:) Regulator of nonsense transcripts	5e-24

>d1h2vc1 a.118.1.14 (C:29-290) CBP80, 80KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 262	Back information, alignment and structure


class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: MIF4G domain-like
domain: CBP80, 80KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  148 bits (374), Expect = 2e-41
 Identities = 44/259 (16%), Positives = 86/259 (33%), Gaps = 31/259 (11%)

Query: 19  DALRKSINGLVNKVNATNIKNI--IPELFAENLIRGRGLFCRSCMKSQMASPGFTDVFAA 76
           D L   I  +  K   +   N+  +  +   +L   +    R         P    ++  
Sbjct: 1   DHLESLICKVGEKSACSLESNLEGLAGVLEADLPNYKSKILRLLCTVARLLPEKLTIYTT 60

Query: 77  LVAVVNTKFTAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQVAHEIIALEL 136
           LV ++N +    G   ++ ++ QLK + K N+  + +  V+F++ LVN  V      + +
Sbjct: 61  LVGLLNARNYNFGGEFVEAMIRQLKESLKANNYNEAVYLVRFLSDLVNCHVIAAPSMVAM 120

Query: 137 LTILLENPTDDS---------VEVAVGFVKECGSILQDLSPKGLHGIFERFRGIL----- 182
               +    ++          V   +  +   G  L +     +  IF      L     
Sbjct: 121 FENFVSVTQEEDVPQVRRDWYVYAFLSSLPWVGKELYEKKDAEMDRIFANTESYLKRRQK 180

Query: 183 ------------HEGEIDKRVQFLIEGLFAIRKAKFQGYPAVRPELDLVDIEDQ-LTHEI 229
                            ++ +  L   +  ++K ++Q    +RP L    I  + L H  
Sbjct: 181 THVPMLQVWTADKPHPQEEYLDCLWAQIQKLKKDRWQERHILRPYLAFDSILCEALQHN- 239

Query: 230 SLQDEIDPEITLDIFKPDP 248
            L     P  T D   P P
Sbjct: 240 -LPPFTPPPHTEDSVYPMP 257

PyMOL of d1h2vc1

>d1hu3a_ a.118.1.14 (A:) Eukaryotic initiation factor eIF4G {Human (Homo sapiens) [TaxId: 9606]} Length = 243	Back information, alignment and structure

>d1uw4b_ a.118.1.14 (B:) Regulator of nonsense transcripts 2, UPF2 {Human (Homo sapiens) [TaxId: 9606]} Length = 248	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		568
d1hu3a_		243	Eukaryotic initiation factor eIF4G {Human (Homo sa	99.97
d1uw4b_		248	Regulator of nonsense transcripts 2, UPF2 {Human (	99.92
d1h2vc1		262	CBP80, 80KDa nuclear cap-binding protein {Human (H	99.91
d1h2vc2		190	CBP80, 80KDa nuclear cap-binding protein {Human (H	96.79
d1ug3a1		193	Eukaryotic initiation factor eIF4G {Human (Homo sa	94.98
d1hu3a_		243	Eukaryotic initiation factor eIF4G {Human (Homo sa	94.96
d1h2vc1		262	CBP80, 80KDa nuclear cap-binding protein {Human (H	92.38
d1uw4b_		248	Regulator of nonsense transcripts 2, UPF2 {Human (	89.46

>d1hu3a_ a.118.1.14 (A:) Eukaryotic initiation factor eIF4G {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: MIF4G domain-like
domain: Eukaryotic initiation factor eIF4G
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=1.2e-30  Score=257.54  Aligned_cols=193  Identities=16%  Similarity=0.298  Sum_probs=169.2

Q ss_pred             HHHHHHHHHHHHHHhhcCChhhHHHHHHHHHHhhhhhhh--hHHHHHHhhhccCCCChHHHHHHHHHHHhcCCc------
Q 008379           15 RLTWDALRKSINGLVNKVNATNIKNIIPELFAENLIRGR--GLFCRSCMKSQMASPGFTDVFAALVAVVNTKFT------   86 (568)
Q Consensus        15 r~~w~~Lkk~I~gllNKLs~~Ni~~i~~eL~~~Ni~rgr--gll~~si~~~q~~~~~f~~vyAaLva~ln~~~p------   86 (568)
                      ...++.|+|+|+|+|||||++|+..|+.++....+....  ..++..|+..++.+|+|+++||.||+.|+...|      
T Consensus         5 ~~~~~~l~r~v~~lLNKLt~~n~~~i~~ei~~l~~~~~~~l~~~v~~I~~kai~e~~f~~~YA~Lc~~l~~~~~~~~~~~   84 (243)
T d1hu3a_           5 NIKTQELFRKVRSILNKLTPQMFNQLMKQVSGLTVDTEERLKGVIDLVFEKAIDEPSFSVAYANMCRCLVTLKVPMADKP   84 (243)
T ss_dssp             HHHHHHHHHHHHHHHTCSSCCCHHHHHHHHTTCCCCSHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHTTCCCC-----
T ss_pred             HHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHcCccccHHHHHHHHHHHHhcCcccccc
Confidence            456779999999999999999999999999765433322  346778888888899999999999999987654      


Q ss_pred             ----hHHHHHHHHHHHHHHHHHHh--------------------------------CChhhhhhhHHHHHHHHhhhhccH
Q 008379           87 ----AVGELLLKRIVLQLKRAYKR--------------------------------NDKPQLLAAVKFIAHLVNQQVAHE  130 (568)
Q Consensus        87 ----e~G~lll~rlv~~F~~~~~~--------------------------------~dk~~~~n~i~fIa~Lyn~~Vv~~  130 (568)
                          .|+..|+++|+..|.+....                                +.+++..|+++||||||+++|+++
T Consensus        85 ~~~~~F~~~Ll~~~q~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~k~~~~g~i~figeLy~~~~v~~  164 (243)
T d1hu3a_          85 GNTVNFRKLLLNRCQKEFEKDKADDDVFEKKQKELEAASAPEERTRLHDELEEAKDKARRRSIGNIKFIGELFKLKMLTE  164 (243)
T ss_dssp             ----CHHHHHHHHHHHHHHHHTC------------------------------CCSSHHHHHHHHHHHHHHHHTTTCSCH
T ss_pred             ccchHHHHHHHHHHHHHHHHhhhhhhhhHhhhcccccccchHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHccccchH
Confidence                58899999999999876431                                114578899999999999999999


Q ss_pred             HHHHHHHHHHhhCCCCCcHHHHHHHHHHHhHhhccCCh-hHHHHHHHHHHHHhhcCCCChhHHHHHHHHHHHHHhccC
Q 008379          131 IIALELLTILLENPTDDSVEVAVGFVKECGSILQDLSP-KGLHGIFERFRGILHEGEIDKRVQFLIEGLFAIRKAKFQ  207 (568)
Q Consensus       131 ~lildii~~LLe~~te~sVE~ll~lLr~~G~~Lr~~~p-~~lk~I~~~l~~il~e~~is~R~~fmIE~l~~lr~nk~k  207 (568)
                      .++++|+..|+.+|+|++||++|.+|++||+.|+..+| ..++.+|++++.+...+++++|++|||++|+++|+++|+
T Consensus       165 ~~i~~~l~~Ll~~~~e~~ie~l~~lL~~~G~~L~~~~~~~~~~~~~~~l~~~~~~~~~s~Rirfml~~l~elR~~~W~  242 (243)
T d1hu3a_         165 AIMHDCVVKLLKNHDEESLECLCRLLTTIGKDLDFEKAKPRMDQYFNQMEKIVKERKTSSRIRFMLQDVIDLRLCNWV  242 (243)
T ss_dssp             HHHHHHHHHHHHSCSHHHHHHHHHHHHHHHHHHCCTTTHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHcCCC
Confidence            99999999999999999999999999999999998876 457889999999999999999999999999999999997

PyMOL of d1hu3a_

>d1uw4b_ a.118.1.14 (B:) Regulator of nonsense transcripts 2, UPF2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1h2vc1 a.118.1.14 (C:29-290) CBP80, 80KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1h2vc2 a.118.1.14 (C:291-480) CBP80, 80KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1ug3a1 a.118.1.14 (A:1235-1427) Eukaryotic initiation factor eIF4G {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1hu3a_ a.118.1.14 (A:) Eukaryotic initiation factor eIF4G {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1h2vc1 a.118.1.14 (C:29-290) CBP80, 80KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1uw4b_ a.118.1.14 (B:) Regulator of nonsense transcripts 2, UPF2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure