Citrus Sinensis ID: 041729

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----

MPTAPWMRSPIVLQPDEIIKPSKPKTKKSFKKTDKGLTAKESGVRGKQAMKKIIENIEKLQKDQILDETQKKVMEKFEFKGCFEENVSHEEDLRGGFGGKVPWLREDRFVFRRMKKERMVTKAETMLDGELLERLKDEARKMRKWVKVKKAGVTESVVFEIRLAWRRNELAMVKFDVPLCRNMDRAREILELKTGGLVIWTKKDAHVVYRGDGSKSSVKMCPRSADDQEAPLSKSTHLHLEKKVNVSWIKSNTATLDQNRSLKDGEENSLPTSIFMDKNLRIDKSLYEREGDRLLDGLGPRFVDWWMWKPLPVDGDLLPEVVPGFKPPFRLSPPDARSKLTDDELTYLRKLAHPLPTHFVLGRNRGLQGLATAILKLWEKSLVAKITVKWGIPNTDNEQMANELKASLAKWKPNFKFSDDGVLLMQHLTGGVLLLRNKFLIILYRGKDFLPCGVENLIVERERELQICQNHEEGARLKAIETFHLPDEPLEKTSKAGTLSEFQNIQSDFGDLKMGNREFELQLEAEIEDLERELRKQERKLLLEQDPDLEMITEEERQCLHKIGMKINSNLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLFAQVIYTAKSLVAESGGILISVDKLKEGHAIIIYRGKNYRRPLKLMTQNLLSKRQALRRSLEMQRLGSLKFFRIPETAGHLQFENQTYLPKKAKLLAHLPLYCLLSQISSVRIYFPSSSDSSLQVFRHEGNNCDEMMGYA

ccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccHHHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHccEEEccccccHHHHHHHHHHHHHcccEEEEEEcccccHHHHHHHHHHHHHHccEEEEEEccEEEEEEcccccccccccccccccccccccccHHHHHHHHccccccccccHHHHHccccccccccccccccccccccccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccEEccccccHHHHHHHHHHHHHHHHHHHEEcccccccccHHHHHHHHHHHHHccccccccccccccccEEEccEEEEEEcccEEEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHcccEEEEEccccHHHHHHHHHHHHHHHccEEEEEEEcccccEEEEEcccccccccccccHHHccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccHHHHHHHHcccccccccccccccccccccccccccccccccccHHHHcccc

cccccccccccccccccccccccccccccccccHHHccccccccccHHHHHHHHHHHHHHHHccccccccHHHHHHHHHcccHHHHEEEHHccccccccccccHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHccEEEEEEcccccHcHHHHHHHHHHHcccEEEEEcccEEEEEEccccccccccccccccccHHHHHHHHHHcccccccHHccccccccHHHHHccccccccccccccccccccccccHHHHHHHHHHHHcccccccccccccccccccccccccccccccccEcccccccccccHHHHHHHHHHHccccccEEccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcccEEEEccccEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHccccccccccccccccccHHHHHHHHHccccEEEEEEccccHHHHHHHHHHHHHHcccEEEEEEEcccccEEEEEEcccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccEEcccccccccccccccccccccEEEccccccHHHHcccc

mptapwmrspivlqpdeiikpskpktkksfkktdkgltakesgvrGKQAMKKIIENIEKLQKDQILDETQKKVMEKFEfkgcfeenvsheedlrggfggkvpwlREDRFVFRRMKKERMVTKAETMLDGELLERLKDEARKMRKWVKVKKAGVTESVVFEIRLAWRRNELAMVKFDVPLCRNMDRAREILELKtgglviwtkkdahvvyrgdgskssvkmcprsaddqeaplsksthlhlekKVNVSWIKSNtatldqnrslkdgeenslptsifmdknlridksLYEREGdrlldglgprfvdwwmwkplpvdgdllpevvpgfkppfrlsppdarskltdDELTYLRKlahplpthfvlgrnrgLQGLATAILKLWEKSLVAKITVkwgipntdneQMANELKASLAKwkpnfkfsddgVLLMQHLTGGVLLLRNKFLIILYrgkdflpcgveNLIVERERELQICQNHEEGARLKAIEtfhlpdeplektskagtlSEFQNIQsdfgdlkmgnrEFELQLEAEIEDLERELRKQERKLLleqdpdlemITEEERQCLHKIGMKinsnlllgrrgvFDGVIEGLHQHWKYREVARVITKQKLFAQVIYTAKSLVAESGGILISVDKLKEGHAIIIYRgknyrrplKLMTQNLLSKRQALRRSLEMQRlgslkffripetaghlqfenqtyLPKKAKLLAHLPLYCllsqissvriyfpsssdsslQVFRhegnncdemmgya

mptapwmrspivlqpdeiikpskpktkksfkktdkgltakesgvrgkqAMKKIIENIEKLQKDQILDETQKKVMEKFEFKGCFeenvsheedlrggfggkvpwlredrfvfrrmkkermvtkaetmldgelleRLKDEARKMrkwvkvkkagvtesvVFEIRLawrrnelamvkfdvplcRNMDRAREILElktgglviwtkkdahvvyrgdgskssvkmcpRSADDqeaplsksthlhlekkvnvswiksntatldqnrslkdgeenslptsifmdknlriDKSLYEREGDRLLDGLGPRFVDWWMWKPLPVDGDLLPEVVPGFkppfrlsppdarSKLTDDELTYLRKLAHPLPTHFVLGRNRGLQGLATAILKLWEKSLVAKITVKwgipntdnEQMANELKASLAKWKPNFKFSDDGVLLMQHLTGGVLLLRNKFLIILYRGKDFLPCGVENLIVERERELQICQNHEEGARLKAIETFHLPDEPLEKtskagtlsEFQNIQSDFGDLKMGNREFELQLEAEIEDLERELRKQERKllleqdpdlemITEEERQCLHKIGMKINSNLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLFAQVIYTAKSLVAESGgilisvdklkeGHAIIiyrgknyrrplKLMTQNLLSKRQALRRSLEMQRLGSLKFFRIPETAGHLQFENQTYLPKKAKLLAHLPLYCLLSQISSVRIYFPSSSDSSLQVFRHEGNNCDEMMGYA

MPTAPWMRSPIVLQPDEIIkpskpktkksfkktdkGLTAKESGVRGKQAMKKIIENIEKLQKDQILDETQKKVMEKFEFKGCFEENVSHEEDLRGGFGGKVPWLREDRFVFRRMKKERMVTKAETMLDGELLERLKDEARKMRKWVKVKKAGVTESVVFEIRLAWRRNELAMVKFDVPLCRNMDRAREILELKTGGLVIWTKKDAHVVYRGDGSKSSVKMCPRSADDQEAPLSKSTHLHLEKKVNVSWIKSNTATLDQNRSLKDGEENSLPTSIFMDKNLRIDKSLYEREGDRLLDGLGPRFVDWWMWKPLPVDGDLLPEVVPGFKPPFRLSPPDARSKLTDDELTYLRKLAHPLPTHFVLGRNRGLQGLATAILKLWEKSLVAKITVKWGIPNTDNEQMANELKASLAKWKPNFKFSDDGVLLMQHLTGGVLLLRNKFLIILYRGKDFLPCGVENLIVERERELQICQNHEEGARLKAIETFHLPDEPLEKTSKAGTLSEFQNIQSDFGDLKMGNREFELQLEAEIEDlerelrkqerkllleqDPDLEMITEEERQCLHKIGMKINSNLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLFAQVIYTAKSLVAESGGILISVDKLKEGHAIIIYRGKNYRRPLKLMTQNLLSKRQALRRSLEMQRLGSLKFFRIPETAGHLQFENQTYlpkkakllahlplYCLLSQISSVRIYFPSSSDSSLQVFRHEGNNCDEMMGYA

***********************************************************************KVMEKFEFKGCFEENVSHEEDLRGGFGGKVPWLREDRFVFRRMKKERMVTKAETMLDGELLERLKDEARKMRKWVKVKKAGVTESVVFEIRLAWRRNELAMVKFDVPLCRNMDRAREILELKTGGLVIWTKKDAHVVYR*********************************VNVSWI************************IFMDKNLRIDKSLYEREGDRLLDGLGPRFVDWWMWKPLPVDGDLLPEVVPGFK****************DELTYLRKLAHPLPTHFVLGRNRGLQGLATAILKLWEKSLVAKITVKWGIPNTDNEQMANELKASLAKWKPNFKFSDDGVLLMQHLTGGVLLLRNKFLIILYRGKDFLPCGVENLIVERERELQICQNHEEGARLKAIETFH***********************************************************************ERQCLHKIGMKINSNLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLFAQVIYTAKSLVAESGGILISVDKLKEGHAIIIYRGKNYRRPLKLMTQNLLSKRQALRRSLEMQRLGSLKFFRIPETAGHLQFENQTYLPKKAKLLAHLPLYCLLSQISSVRIYFP************************

**TAPW************************************************************************************************************************LDGELLERLKDEARKMRKWVKVKKAGVTESVVFEIRLAWRRNELAMVKFDVPLCRNMDRAREILELKTGGLVIWTKKDAHVVYRGDGSKS***********************************************************************EREGDRLLDGLGPRFVDWWMWKPLPVDGDLLPEVVPGFKPPFRLSPPDARSKLTDDELTYLRKLAHPLPTHFVLGRNRGLQGLATAILKLWEKSLVAKITVKWGIPNTDNEQMANELKASLAKWKPNFKFSDDGVLLMQHLTGGVLLLRNKFLIILYRGKDFLPCGVENLIV******************************************FQN*************************************************EEERQCLHKIGMKINSNLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLFAQVIYTAKSLVAESGGILISVDKLKEGHAIIIYRGKNYRRPLKLMTQNLLSKRQALRRSLEMQ***SL**FRIPETAGHL***************************************************C*EMMGY*

MPTAPWMRSPIVLQPDEIIKPS**************LTAKESGVRGKQAMKKIIENIEKLQKDQILDETQKKVMEKFEFKGCFEENVSHEEDLRGGFGGKVPWLREDRFVFRRMKKERMVTKAETMLDGELLERLKDEARKMRKWVKVKKAGVTESVVFEIRLAWRRNELAMVKFDVPLCRNMDRAREILELKTGGLVIWTKKDAHVVYR************************STHLHLEKKVNVSWIKSNTATLDQNRSLKDGEENSLPTSIFMDKNLRIDKSLYEREGDRLLDGLGPRFVDWWMWKPLPVDGDLLPEVVPGFKPPFRLSPPDARSKLTDDELTYLRKLAHPLPTHFVLGRNRGLQGLATAILKLWEKSLVAKITVKWGIPNTDNEQMANELKASLAKWKPNFKFSDDGVLLMQHLTGGVLLLRNKFLIILYRGKDFLPCGVENLIVERERELQICQNHEEGARLKAIETFHLPDEPLEKTSKAGTLSEFQNIQSDFGDLKMGNREFELQLEAEIEDLERELRKQERKLLLEQDPDLEMITEEERQCLHKIGMKINSNLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLFAQVIYTAKSLVAESGGILISVDKLKEGHAIIIYRGKNYRRPLKLMTQNLLSKRQALRRSLEMQRLGSLKFFRIPETAGHLQFENQTYLPKKAKLLAHLPLYCLLSQISSVRIYFPSSSDSSLQVFRHEGNNCDEMMGYA

*PTAPWMRSPIVLQPDEIIKPS***********************GKQAMKKIIENIEKLQKDQILDETQKKVMEKFEFKGCFEENVSHEEDLRGGFGGKVPWLRED**VFR********TKAETMLDGELLERLKDEARKMRKWVKVKKAGVTESVVFEIRLAWRRNELAMVKFDVPLCRNMDRAREILELKTGGLVIWTKKDAHVVYRGDGSKSSVKMCP***********************************************************IDKSLYEREGDRLLDGLGPRFVDWWMWKPLPVDGDLLPEVVPGFKPPFRLSPPDARSKLTDDELTYLRKLAHPLPTHFVLGRNRGLQGLATAILKLWEKSLVAKITVKWGIPNTDNEQMANELKASLAKWKPNFKFSDDGVLLMQHLTGGVLLLRNKFLIILYRGKDFLPCGVENLIVERERELQICQNHEEGARLKAIETFH************GTLSEFQNIQSDFGDLKMGNREFELQLEAEIEDLERELRKQERKLL**QD**LEMITEEERQCLHKIGMKINSNLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLFAQVIYTAKSLVAESGGILISVDKLKEGHAIIIYRGKNYRRPLKLMTQNLLSKRQALRRSLEMQRLGSLKFFRIPETAGHLQFENQTYLPKKAKLLAHLP*Y**LS****************L*********CD*****A

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MPTAPWMRSPIVLQPDEIIKPSKPKTKKSFKKTDKGLTAKESGVRGKQAMKKIIENIEKLQKDQILDETQKKVMEKFEFKGCFEENVSHEEDLRGGFGGKVPWLREDRFVFRRMKKERMVTKAETMLDGELLERLKDEARKMRKWVKVKKAGVTESVVFEIRLAWRRNELAMVKFDVPLCRNMDRAREILELKTGGLVIWTKKDAHVVYRGDGSKSSVKMCPRSADDQEAPLSKSTHLHLEKKVNVSWIKSNTATLDQNRSLKDGEENSLPTSIFMDKNLRIDKSLYEREGDRLLDGLGPRFVDWWMWKPLPVDGDLLPEVVPGFKPPFRLSPPDARSKLTDDELTYLRKLAHPLPTHFVLGRNRGLQGLATAILKLWEKSLVAKITVKWGIPNTDNEQMANELKASLAKWKPNFKFSDDGVLLMQHLTGGVLLLRNKFLIILYRGKDFLPCGVENLIVERERELQICQNHEEGARLKAIETFHLPDEPLEKTSKAGTLSEFQNIQSDFGDLKMGxxxxxxxxxxxxxxxxxxxxxxxxxLLLEQDPDLEMITEEERQCLHKIGMKINSNLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLFAQVIYTAKSLVAESGGILISVDKLKEGHAIIIYRGKNYRRPLKLMTQNLLSKRQALRRSLEMQRLGSLKFFRIPETAGHLQFENQTYLPKKAKLLAHLPLYCLLSQISSVRIYFPSSSDSSLQVFRHEGNNCDEMMGYA

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		744	2.2.26 [Sep-21-2011]
Q6YYA3		725	Chloroplastic group IIA i	yes	no	0.731	0.750	0.465	1e-139
Q9FYT6		715	Chloroplastic group IIA i	N/A	no	0.806	0.839	0.439	1e-137
Q9LF10		720	Chloroplastic group IIA i	yes	no	0.497	0.513	0.569	1e-129
Q67XL4		444	Uncharacterized CRM domai	no	no	0.224	0.376	0.324	2e-13
Q5VMQ5		701	CRS2-associated factor 1,	no	no	0.120	0.128	0.297	7e-05
Q84N49		674	CRS2-associated factor 1,	N/A	no	0.120	0.133	0.297	0.0002

>sp\|Q6YYA3\|CRS1_ORYSJ Chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic OS=Oryza sativa subsp. japonica GN=Os08g0360100 PE=2 SV=1	Back alignment and function desciption

 Score =  496 bits (1277), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 283/608 (46%), Positives = 363/608 (59%), Gaps = 64/608 (10%)

Query: 96  GFGGKVPWL----REDRFVFRRMKKERMVTKAETMLDGELLERLKDEARKMRKWVKVKKA 151
           G    VPW      E + V RR KK R+ T+AET L+   LERL+  AR   +W + KKA
Sbjct: 120 GIRRAVPWAAARDEETKVVLRREKKTRVPTRAETELEAGELERLRRAARGKERWARAKKA 179

Query: 152 GVTESVVFEIRLAWRR-NELAMVKFDVPLCRNMDRAREILELKTGGLVIWTKKDAHVVYR 210
           G+T+ VV E+R  W +  ELA V+   PL R MDRAREILE+KTGGLV+WT+   H VYR
Sbjct: 180 GITDEVVEEVRGQWAKGQELAGVRIVEPLRRCMDRAREILEIKTGGLVVWTRGGIHFVYR 239

Query: 211 GDGSKSSVKMCPRSADDQEAPLSKSTHLHLEKKVNVSWIKSNTATLDQNRSLKDGEENSL 270
           G    S ++   R  D             +     +S + SN  T       KD    + 
Sbjct: 240 GS---SYLENAKRHRD------------FVNYNEELSPVTSNNPTSQGKYWSKDETLTND 284

Query: 271 PTSIFMDKNLRIDKSLYEREGDRLLDGLGPRFVDWWMWKPLPVDGDLLPEVVPGFKPPFR 330
                   +  I  +LYERE +RLLD LGPRF+DWW   PLPVD DLLPEVVP FK PFR
Sbjct: 285 NDEADDKDDKPIKGTLYEREVNRLLDSLGPRFIDWWWNTPLPVDADLLPEVVPDFKTPFR 344

Query: 331 LSPPDARSKLTDDELTYLRKLAHPLPTHFVLGRNRGLQGLATAILKLWEKSLVAKITVKW 390
             PP  R  L D+ELTYLRK A PLPTHFVLGRN  LQGLA AILKLWEKSL+AK+ VK 
Sbjct: 345 QCPPGVRPALADEELTYLRKHARPLPTHFVLGRNTKLQGLAAAILKLWEKSLIAKVAVKV 404

Query: 391 GIPNTDNEQMANELKASLAKWKPNFKFSDDGVLLMQHLTGGVLLLRNKFLIILYRGKDFL 450
           GI NT++EQMA  LK                      LTGG ++LRNK  II+YRGKDFL
Sbjct: 405 GIQNTNHEQMARNLK---------------------RLTGGTVILRNKDYIIIYRGKDFL 443

Query: 451 PCGVENLIVERERELQICQNHEEGARLKAIETFHLPDEPLEKTSKAGTLSEFQNIQSDFG 510
           P GV   ++ERE ++   Q  EE ARLK  ++  +      + S  GT  E+Q+      
Sbjct: 444 PGGVAESVIERESQVHDQQAKEEEARLKMADSLQMIVGLSSERSYVGTFREYQDFHDSHA 503

Query: 511 DLKMGNREFELQLEAEIEDLERELRKQERKLLL----------------------EQDPD 548
                N  F +QLEA+   LE+EL+ QE +L +                      ++D D
Sbjct: 504 RRTTEN-NFRIQLEAKKHRLEKELKDQEWRLSMLTKKIERSNQVLAKLHSSWSPSKKDGD 562

Query: 549 LEMITEEERQCLHKIGMKINSNLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLFAQV 608
            E++TEEER+   KIG+K++ ++LLGRRGVF+GVIE +HQHWK++EV +VITKQ   +Q+
Sbjct: 563 RELLTEEERRIFRKIGLKMDEHVLLGRRGVFEGVIEEIHQHWKHKEVVKVITKQNQASQI 622

Query: 609 IYTAKSLVAESGGILISVDKLKEGHAIIIYRGKNYRRPLKLMTQNLLSKRQALRRSLEMQ 668
            YT+  L  E+GG LI++++    HAII+YRGKNYRRP K    NLL+KR+AL+RS+E+Q
Sbjct: 623 TYTSMMLEVETGGTLIAIERFTTSHAIILYRGKNYRRPTKSAPSNLLTKREALQRSIEVQ 682

Query: 669 RLGSLKFF 676
           R GS+K+F
Sbjct: 683 RRGSMKYF 690

Required for the splicing of group IIA introns in chloroplasts, by regulating the intron folding. Forms splicing particles with RNA. Also involved in chloroplast protein translation.
Oryza sativa subsp. japonica (taxid: 39947)

>sp\|Q9FYT6\|CRS1_MAIZE Chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic OS=Zea mays GN=CRS1 PE=1 SV=1	Back alignment and function description

>sp\|Q9LF10\|CRS1_ARATH Chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic OS=Arabidopsis thaliana GN=At5g16180 PE=2 SV=2	Back alignment and function description

>sp\|Q67XL4\|Y3544_ARATH Uncharacterized CRM domain-containing protein At3g25440, chloroplastic OS=Arabidopsis thaliana GN=At3g25440 PE=2 SV=1	Back alignment and function description

>sp\|Q5VMQ5\|CAF1P_ORYSJ CRS2-associated factor 1, chloroplastic OS=Oryza sativa subsp. japonica GN=Os01g0495900 PE=2 SV=1	Back alignment and function description

>sp\|Q84N49\|CAF1P_MAIZE CRS2-associated factor 1, chloroplastic OS=Zea mays GN=CAF1 PE=1 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		744
225452088		1184	PREDICTED: chloroplastic group IIA intro	0.875	0.549	0.611	0.0
255551422		742	conserved hypothetical protein [Ricinus	0.831	0.834	0.602	0.0
224127512		687	predicted protein [Populus trichocarpa]	0.802	0.868	0.555	0.0
356567264		712	PREDICTED: chloroplastic group IIA intro	0.817	0.853	0.544	0.0
449441730		760	PREDICTED: chloroplastic group IIA intro	0.857	0.839	0.523	0.0
449490080		760	PREDICTED: LOW QUALITY PROTEIN: chloropl	0.846	0.828	0.522	0.0
297807647		727	ATCRS1/CRS1 [Arabidopsis lyrata subsp. l	0.795	0.814	0.496	0.0
296087258		529	unnamed protein product [Vitis vinifera]	0.502	0.706	0.676	1e-156
242078893		728	hypothetical protein SORBIDRAFT_07g01512	0.825	0.843	0.450	1e-142
326492786		730	predicted protein [Hordeum vulgare subsp	0.866	0.883	0.440	1e-142

>gi\|225452088\|ref\|XP_002280704.1\| PREDICTED: chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic-like [Vitis vinifera]	Back alignment and taxonomy information

 Score =  826 bits (2134), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 434/710 (61%), Positives = 520/710 (73%), Gaps = 59/710 (8%)

Query: 1   MPTAPWMRSPIVLQPDEIIKPSKPKTKK-----SFKKTDKGLTAKESGVRGKQAMKKIIE 55
           MPTAPWM+ P++LQP+E++  SK + KK       +K D+ LT K SG RG +AMKKI++
Sbjct: 75  MPTAPWMKGPLLLQPNEVLDLSKARPKKVAGSAGAEKPDRSLTEKVSGGRGAKAMKKIMQ 134

Query: 56  NIEKLQKDQILDETQKKVMEKFEFKGCFEENVSHEEDLRGGFGGKVPWLREDRFVFRRMK 115
           +I KLQ+    DETQ+   E+FEF G   E +  +E+ R   GGK+PWL+ ++ VFRR K
Sbjct: 135 SIVKLQETHTSDETQENT-EEFEF-GVSLEGIGGDENSR--IGGKMPWLKTEKVVFRRTK 190

Query: 116 KERMVTKAETMLDGELLERLKDEARKMRKWVKVKKAGVTESVVFEIRLAWRRNELAMVKF 175
           KE++VT AE  LD  LLERL+ EA KMRKWVKVKKAGVTESVV +I + W+ +ELAMVKF
Sbjct: 191 KEKVVTAAELTLDPMLLERLRGEAVKMRKWVKVKKAGVTESVVDQIHMVWKSDELAMVKF 250

Query: 176 DVPLCRNMDRAREILELKTGGLVIWTKKDAHVVYRGDGSKSSVK----MCPRSADDQEAP 231
           D+PLCRNMDRAREILE+KT GLVIW+KKD  VVYRG   +S+ K    M P      +A 
Sbjct: 251 DMPLCRNMDRAREILEIKTRGLVIWSKKDTLVVYRGSNYQSTSKHFQKMRPGLVAGADAS 310

Query: 232 LSKSTHLHLEKKVNVSWIKSNTATLDQNRSLKDGEENSLPTSIFMDKNLR---IDKSLYE 288
            SK    + E  + +S IK + +T  +    KDGEE+S PT IFM++ +    ++ SLYE
Sbjct: 311 NSKLNQSNFEDDLTISEIKFHESTTGEKMGRKDGEEDSSPTGIFMEEMVDSQPVNGSLYE 370

Query: 289 REGDRLLDGLGPRFVDWWMWKPLPVDGDLLPEVVPGFKPPFRLSPPDARSKLTDDELTYL 348
           RE DRLLDGLGPRF+DWW  KPLPVD DLLPEV+PGF+PPFRLSPP  RSKLTDDELTYL
Sbjct: 371 READRLLDGLGPRFIDWWRPKPLPVDADLLPEVLPGFRPPFRLSPPQTRSKLTDDELTYL 430

Query: 349 RKLAHPLPTHFVLGRNRGLQGLATAILKLWEKSLVAKITVKWGIPNTDNEQMANELKASL 408
           RKLA+ LPTHFVLGRNR LQGLA AILKLWEKSL+ KI +KWGIPNT NEQMANELK   
Sbjct: 431 RKLAYALPTHFVLGRNRKLQGLAAAILKLWEKSLIVKIAIKWGIPNTKNEQMANELKC-- 488

Query: 409 AKWKPNFKFSDDGVLLMQHLTGGVLLLRNKFLIILYRGKDFLPCGVENLIVERERELQIC 468
                              LTGGVLLLRNKF IILYRGKDFLPC V NLIVERE E + C
Sbjct: 489 -------------------LTGGVLLLRNKFFIILYRGKDFLPCRVANLIVEREMEFKGC 529

Query: 469 QNHEEGARLKAIETFHLPDEPLEKTSKAGTLSEFQNIQSDFGDLKMGNREFELQLEAEIE 528
           Q  EE ARLKAIET  + D+PL  TS  GTLSEFQNI+++F  LK GN E E++LEAE E
Sbjct: 530 QIREEDARLKAIETSFVTDKPLANTSTTGTLSEFQNIETEFRGLKDGNTEIEVELEAEKE 589

Query: 529 DLERELRKQERKLLL----------------------EQDPDLEMITEEERQCLHKIGMK 566
            LE+EL+KQER L +                      + D D EMITEEER+C  KIG K
Sbjct: 590 RLEKELKKQERNLFILKRKIERSAKVLAKLNSAWRPADHDADKEMITEEERECFRKIGQK 649

Query: 567 INSNLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLFAQVIYTAKSLVAESGGILISV 626
           ++S+LLLGRRGVFDGVIEGLHQHWK+RE+ +VIT Q+ F+QV+YTAK L +ESGG+L+S+
Sbjct: 650 MDSSLLLGRRGVFDGVIEGLHQHWKHREIVKVITMQRSFSQVLYTAKLLESESGGVLVSI 709

Query: 627 DKLKEGHAIIIYRGKNYRRPLKLMTQNLLSKRQALRRSLEMQRLGSLKFF 676
           DKLKEGHAIIIYRGKNYRRP+KL+ +NLL+KR+AL RSLEMQR+GSLKFF
Sbjct: 710 DKLKEGHAIIIYRGKNYRRPIKLVPKNLLTKREALNRSLEMQRIGSLKFF 759

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|255551422\|ref\|XP_002516757.1\| conserved hypothetical protein [Ricinus communis] gi\|223544130\|gb\|EEF45655.1\| conserved hypothetical protein [Ricinus communis]	Back alignment and taxonomy information

>gi\|224127512\|ref\|XP_002329296.1\| predicted protein [Populus trichocarpa] gi\|222870750\|gb\|EEF07881.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356567264\|ref\|XP_003551841.1\| PREDICTED: chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic-like [Glycine max]	Back alignment and taxonomy information

>gi\|449441730\|ref\|XP_004138635.1\| PREDICTED: chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449490080\|ref\|XP_004158502.1\| PREDICTED: LOW QUALITY PROTEIN: chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|297807647\|ref\|XP_002871707.1\| ATCRS1/CRS1 [Arabidopsis lyrata subsp. lyrata] gi\|297317544\|gb\|EFH47966.1\| ATCRS1/CRS1 [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|296087258\|emb\|CBI33632.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|242078893\|ref\|XP_002444215.1\| hypothetical protein SORBIDRAFT_07g015120 [Sorghum bicolor] gi\|241940565\|gb\|EES13710.1\| hypothetical protein SORBIDRAFT_07g015120 [Sorghum bicolor]	Back alignment and taxonomy information

>gi\|326492786\|dbj\|BAJ90249.1\| predicted protein [Hordeum vulgare subsp. vulgare]	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		744
TAIR\|locus:2181372		720	CRS1 "ortholog of maize chloro	0.513	0.530	0.504	1e-154
TAIR\|locus:2094997		848	EMB1865 "embryo defective 1865	0.369	0.324	0.412	4.4e-95
TAIR\|locus:2094558		881	CFM3A "CRM family member 3A" [	0.466	0.393	0.342	6e-90
TAIR\|locus:2096662		1011	CFM2 "CRM family member 2" [Ar	0.744	0.547	0.378	1.2e-87
TAIR\|locus:2091458		491	AT3G27550 [Arabidopsis thalian	0.180	0.272	0.371	1.4e-14
TAIR\|locus:2123276		343	AT4G13070 [Arabidopsis thalian	0.151	0.329	0.435	6.7e-14
TAIR\|locus:2056558		372	AT2G28480 [Arabidopsis thalian	0.163	0.327	0.392	7.9e-13
TAIR\|locus:2094438		444	LOH1 "LAG One Homologue 1" [Ar	0.181	0.304	0.347	8.7e-12

TAIR\|locus:2181372 CRS1 "ortholog of maize chloroplast splicing factor CRS1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 951 (339.8 bits), Expect = 1.0e-154, Sum P(2) = 1.0e-154
 Identities = 206/408 (50%), Positives = 281/408 (68%)

Query:   282 IDKSLYEREGDRLLDGLGPRFVDWWMWKPLPVDGDLLPEVVPGFKPPFRLSPPDARSKLT 341
             I  SLYERE DRLLDGLGPR++DWWM +P PVD DLLPEVV G+  P R  PP+ R+KLT
Sbjct:   303 ISSSLYEREADRLLDGLGPRYMDWWMRRPFPVDADLLPEVVNGYMTPSRRCPPNTRAKLT 362

Query:   342 DDELTYLRKLAHPLPTHFVLGRNRGLQGLATAILKLWEKSLVAKITVKWGIPNTDNEQMA 401
             D+ELTYLR +A PLP HFVLGRN GLQGLA+AI+KLWEK ++AKI +KWG  NT+NE+MA
Sbjct:   363 DEELTYLRNIAQPLPFHFVLGRNYGLQGLASAIVKLWEKCIIAKIAIKWGALNTNNEEMA 422

Query:   402 NELKASLAKWKPNFKFSDDGVLLMQHLTGGVLLLRNK-FL----IILYRGKDFLPCGVEN 456
             +EL+           +   GVL++++    ++L R K FL      L   ++ L    ++
Sbjct:   423 DELR-----------YLTGGVLILRNKYL-IVLYRGKDFLSDEVADLVEDRERLLSRYQH 470

Query:   457 LI-VERERELQICQNHEEGARLKAIETFHLPDEPLEKTSKAGTLSEFQNIQSDFG----D 511
                 +RE ++++ +    G +LK         E  E   K G +   +N++++      +
Sbjct:   471 FEETKRESDIELLEVVTNGKQLKETNKSGTLLEFQELQRKFGEMDP-RNLETEAEKARLE 529

Query:   512 LKMGNREFELQ-LEAEIEDXXXXXXXXXXXXX-XXXDPDLEMITEEERQCLHKIGMKINS 569
              ++ ++E +L  L+++IE                  D D+E++T EER+CL +IG+K+NS
Sbjct:   530 KELKSQEHKLSILKSKIEKSNMELFKLNSLWKPSEGDDDIEILTNEERECLRRIGLKMNS 589

Query:   570 NLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLFAQVIYTAKSLVAESGGILISVDKL 629
             +L+LGRRGVF GV+EGLHQHWK+REVA+VIT QKLF++V+YTAK+L  ES G+LIS++KL
Sbjct:   590 SLVLGRRGVFFGVMEGLHQHWKHREVAKVITMQKLFSRVVYTAKALETESNGVLISIEKL 649

Query:   630 KEGHAIIIYRGKNYRRPL-KLMTQNLLSKRQALRRSLEMQRLGSLKFF 676
             KEGHAI+IYRGKNY+RP  KLM QNLL+KR+AL+RS+ MQRLGSLKFF
Sbjct:   650 KEGHAILIYRGKNYKRPSSKLMAQNLLTKRKALQRSVVMQRLGSLKFF 697

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

GO:0000373 "Group II intron splicing" evidence=IDA

TAIR\|locus:2094997 EMB1865 "embryo defective 1865" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2094558 CFM3A "CRM family member 3A" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2096662 CFM2 "CRM family member 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2091458 AT3G27550 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2123276 AT4G13070 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2056558 AT2G28480 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2094438 LOH1 "LAG One Homologue 1" [Arabidopsis thaliana (taxid:3702)]	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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		744
smart01103		84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	2e-15
pfam01985		84	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	1e-14
smart01103		84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	7e-13
smart01103		84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	9e-13
pfam01985		84	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	1e-11
pfam01985		84	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	2e-11

>gnl\|CDD\|198171 smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly	Back alignment and domain information

 Score = 71.3 bits (176), Expect = 2e-15
 Identities = 19/88 (21%), Positives = 42/88 (47%), Gaps = 4/88 (4%)

Query: 552 ITEEERQCLHKIGMKINSNLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLFAQVIYT 611
           +T ++++ L  +   +   + +G+ G+ +GV+E + +  +  E+ +V             
Sbjct: 1   LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEI 60

Query: 612 AKSLVAESGGILISVDKLKEGHAIIIYR 639
           A+ L  E+G  L+ V     G  I++YR
Sbjct: 61  AEELAEETGAELVQV----IGKTIVLYR 84

GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. Length = 84

>gnl\|CDD\|190184 pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	Back alignment and domain information

>gnl\|CDD\|198171 smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly	Back alignment and domain information

>gnl\|CDD\|198171 smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly	Back alignment and domain information

>gnl\|CDD\|190184 pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	Back alignment and domain information

>gnl\|CDD\|190184 pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		744
KOG1990		564	consensus Poly(A)-specific exoribonuclease PARN [R	100.0
PRK10343		97	RNA-binding protein YhbY; Provisional	99.94
TIGR00253		95	RNA_bind_YhbY putative RNA-binding protein, YhbY f	99.93
PRK10343		97	RNA-binding protein YhbY; Provisional	99.92
PF01985		84	CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR	99.92
TIGR00253		95	RNA_bind_YhbY putative RNA-binding protein, YhbY f	99.91
PF01985		84	CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR	99.91
COG1534		97	Predicted RNA-binding protein containing KH domain	99.91
COG1534		97	Predicted RNA-binding protein containing KH domain	99.88
KOG1990		564	consensus Poly(A)-specific exoribonuclease PARN [R	97.32

>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]	Back alignment and domain information

Probab=100.00  E-value=1.6e-77  Score=669.50  Aligned_cols=494  Identities=42%  Similarity=0.566  Sum_probs=446.6

Q ss_pred             hhccccCcccccCCCHHHHHHHHHHhhcccceEEecCCCCCHHHHHHHHHHHHhCceEEEEecCCchhhHHHHHHHHHHH
Q 041729          114 MKKERMVTKAETMLDGELLERLKDEARKMRKWVKVKKAGVTESVVFEIRLAWRRNELAMVKFDVPLCRNMDRAREILELK  193 (744)
Q Consensus       114 ~~~~~~~s~AEl~L~~~ElrrLR~lA~~LkpvV~VGK~GVT~~VV~~Iheawk~~ELIKVKv~~~~~~dmk~v~e~LEek  193 (744)
                      .+.++ +++||+++++.++.+||..|..+...+  +++|+|+.+++.|++.|+.+|+++++|....+.+|++.+++++..
T Consensus         2 ~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~--~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~   78 (564)
T KOG1990|consen    2 SNFES-LSLAELTVDEADLRRLRLVATGMTSAP--WKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMS   78 (564)
T ss_pred             Ccccc-hhHHHhhcCHHHHHHHhhhhccceecc--cccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhcc
Confidence            45667 999999999999999999999998888  999999999999999999999999999999999999999999999


Q ss_pred             hCC-eEEEEeCCEEEEEecCCCCCCcccCCCCCCCCCCcccccccccccccccccccccccccccccccccCCCCCCCCc
Q 041729          194 TGG-LVIWTKKDAHVVYRGDGSKSSVKMCPRSADDQEAPLSKSTHLHLEKKVNVSWIKSNTATLDQNRSLKDGEENSLPT  272 (744)
Q Consensus       194 TGg-~VVqriG~viVLYRg~~Y~~p~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  272 (744)
                      ||| .+||+.|.+...|++..|..|+.-.++.                                        .+      
T Consensus        79 ~~~n~~~~~~g~~~s~~~~~~~~~~~~~~~~~----------------------------------------~~------  112 (564)
T KOG1990|consen   79 TGGNFVVWSRGDSISSPEFLCQRSPVDFVARQ----------------------------------------QE------  112 (564)
T ss_pred             CCCceeeeecCccccCCccceeecchhhhhhh----------------------------------------ch------
Confidence            999 9999999999999998887664321100                                        00      


Q ss_pred             ccccccccccchhhhhhhhhhhhccCCCCccCCCCCCCCCCCCCCCCcccCCCCCCcccCCCCCCCCCChHHHHHHHHhc
Q 041729          273 SIFMDKNLRIDKSLYEREGDRLLDGLGPRFVDWWMWKPLPVDGDLLPEVVPGFKPPFRLSPPDARSKLTDDELTYLRKLA  352 (744)
Q Consensus       273 s~~~~~~~~~~~~~~e~E~d~LLD~LGPRf~dW~g~~PlPVDaDLLP~vvpgyk~PfRllP~gvrp~Lt~~E~T~lRrla  352 (744)
                           .+......+++.|.+.+||++||||.|||+.+|+|||+||+|++||+|.+|||.||+|++++||..|+|.+|++|
T Consensus       113 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~  187 (564)
T KOG1990|consen  113 -----NQAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLLRRLG  187 (564)
T ss_pred             -----hhhhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCChhhhhhHHHHHHHHhc
Confidence                 011223467889999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCcEeecccccchhHHHHHHHHhhhcceeeeeeccCCCCCchHHHHHHH--HhhhcccCCCCcccccchhhcccccC
Q 041729          353 HPLPTHFVLGRNRGLQGLATAILKLWEKSLVAKITVKWGIPNTDNEQMANEL--KASLAKWKPNFKFSDDGVLLMQHLTG  430 (744)
Q Consensus       353 r~LPpHfaLGRNr~lqGLA~ai~KLWEks~iaKIavKrGvqnT~ne~MaeeL--K~~~~~~~~~~~f~~~~~~~~~~LTG  430 (744)
                      +.+||||++|+++.+||++.+|+++|++|+++||+|+||++++.++.||.++  +                     .+||
T Consensus       188 ~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~---------------------~~tg  246 (564)
T KOG1990|consen  188 YKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQEL---------------------LLTG  246 (564)
T ss_pred             ccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHH---------------------HhcC
Confidence            9999999999999999999999999999999999999999999999999999  7                     8999


Q ss_pred             eeEEeeeCcEEEEEecCCCCCcchhhhHHHHHHHHHHhhhhhhhhhhhhhhcccCCCCcccccCcccchHHHHHHHhhhc
Q 041729          431 GVLLLRNKFLIILYRGKDFLPCGVENLIVERERELQICQNHEEGARLKAIETFHLPDEPLEKTSKAGTLSEFQNIQSDFG  510 (744)
Q Consensus       431 gvLLsRnke~Iv~yRGkDFlp~~V~~al~eRe~~~~~~q~~EE~aR~~a~~~~~~~~~~~~~~~~agtl~E~~~~~~~~~  510 (744)
                      ++|++||++++|+|||++|++ .|.++|.++.......|+.++.+|+.++...       .....++|+.|+..+.++|+
T Consensus       247 ~~lv~hN~~~dv~y~~~~Fl~-~lp~~l~~f~~~~~~fp~~~~~~~~~~~~~~-------~~~~~~~t~~e~~~~~~~~~  318 (564)
T KOG1990|consen  247 KVLVLHNKLLDVMYRYKNFLS-PLPSTLEEFTDSSSMFPNIEDTKRLAKLSEY-------QKLNLKATLLELARAKAKKE  318 (564)
T ss_pred             CeEEeeccceeeeeehhhccc-ccchhHHHhhhhhhhhhhhHHHHHhhccccc-------cchhhhhhHHHHHHHhcccc
Confidence            999999999999999999999 9999999999998899999999999873221       23467899999999999999


Q ss_pred             ccccCch-HHHHHHHHHHHHHHHHHHHHHHhhcC----------------------CCCCccCCCCHHHHHHHHhhcccC
Q 041729          511 DLKMGNR-EFELQLEAEIEDLERELRKQERKLLL----------------------EQDPDLEMITEEERQCLHKIGMKI  567 (744)
Q Consensus       511 ~~~~~~~-~~~~~~ea~~~k~e~~l~~~E~kl~~----------------------~~~~d~e~LT~eQR~~LRklghkL  567 (744)
                      ....... ...+..+.++...++..+.+.+++..                      +...|++.+|.+++.+++++|.+|
T Consensus       319 ~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~  398 (564)
T KOG1990|consen  319 KEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKM  398 (564)
T ss_pred             cCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhh
Confidence            8875432 22344555666666555555555432                      566999999999999999999999


Q ss_pred             cceeeeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCCH-HHHHHHHHHHHHHhCCEEEeecccCcCcEEEEecCCCCCCC
Q 041729          568 NSNLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLF-AQVIYTAKSLVAESGGILISVDKLKEGHAIIIYRGKNYRRP  646 (744)
Q Consensus       568 KPvV~IGKrGVtdgVIeeIh~aLk~hELVKVkv~~~~~-~d~keiA~~Le~~SGg~LVqV~k~~IG~tiILYRgknY~rP  646 (744)
                      ++++.+|++|+|+|+|.+||.||++||++||+|+.... .++++.|..++.++|+++|+++++..|++|+.||++||++|
T Consensus       399 ~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p  478 (564)
T KOG1990|consen  399 KRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRP  478 (564)
T ss_pred             ccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCC
Confidence            99999999999999999999999999999999999776 99999999999999999999999999999999999999999


Q ss_pred             ccccccccccHHHHHHHHHHHHHhhhhhhccc--ccchhhhhhhcc
Q 041729          647 LKLMTQNLLSKRQALRRSLEMQRLGSLKFFRI--PETAGHLQFENQ  690 (744)
Q Consensus       647 ~~l~pknlLtKrkAl~rs~~~Qr~~sl~~~i~--~~~i~~l~~~~~  690 (744)
                      ..++|.++|+||+|+.+|+++|+.+|+++||.  +.++++++....
T Consensus       479 ~~l~P~~~l~~~k~~~~~~~~~~~~a~~~~i~~~~~~~e~~~~~~~  524 (564)
T KOG1990|consen  479 TSLRPRNLLSRRKALERSLEEQRKEALKSHISDLEQEIEQLQASVE  524 (564)
T ss_pred             cccCchhhhcccCCccccHHHHHHHHHhhhcchhhhhHHHhhcchh
Confidence            99999999999999999999999999999998  899999887654

>PRK10343 RNA-binding protein YhbY; Provisional	Back alignment and domain information

>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family	Back alignment and domain information

>PRK10343 RNA-binding protein YhbY; Provisional	Back alignment and domain information

>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain	Back alignment and domain information

>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family	Back alignment and domain information

>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain	Back alignment and domain information

>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]	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		744
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-16
1rq8_A		104	Conserved hypothetical protein; structural genomic	9e-10
1rq8_A		104	Conserved hypothetical protein; structural genomic	1e-06
1jo0_A		98	Hypothetical protein HI1333; structural genomics,	2e-07
1jo0_A		98	Hypothetical protein HI1333; structural genomics,	2e-05

>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 = 81.1 bits (199), Expect = 8e-16
 Identities = 114/722 (15%), Positives = 214/722 (29%), Gaps = 223/722 (30%)

Query: 51  KKIIE-NIEKLQKD----QILDETQKKVMEKFEFKGCFEENVSHEEDLRGGFGGKVPWLR 105
           K I+    +    +     + D   K ++ K E                  F     W  
Sbjct: 19  KDILSVFEDAFVDNFDCKDVQDMP-KSILSKEEIDHIIMSK-DAVSGTLRLF-----WTL 71

Query: 106 EDRFVFRRMKKERMVTKA-ETMLDGE---LLERLKDEARKMRKWVKVKKAGVTESVVFEI 161
                    K+E MV K  E +L      L+  +K E R+         + +T   + + 
Sbjct: 72  LS-------KQEEMVQKFVEEVLRINYKFLMSPIKTEQRQ--------PSMMTRMYIEQR 116

Query: 162 RLAWRRNELAMVKFDVPLCRNMDRAREILELKTGGLVIWTKKDAHVVYRGD-GS-KSSVK 219
              +  N++   K++V       R +  L+L+   L +  +   +V+  G  GS K+ V 
Sbjct: 117 DRLYNDNQV-FAKYNVS------RLQPYLKLRQALLEL--RPAKNVLIDGVLGSGKTWVA 167

Query: 220 MCPRSADDQEAPLSKSTHLHLEKKVNVSWIKSNTATLDQNRSLKDGEENSLPTSIFMDKN 279
           +        +  LS      ++    + W+                  NS  T + M + 
Sbjct: 168 L--------DVCLSYKVQCKMDF--KIFWLNL-------------KNCNSPETVLEMLQK 204

Query: 280 L--RIDKSLYEREGDRL------LDGLGPRFVDWWMWKPLPVDGDLL-------PEVVPG 324
           L  +ID +   R  D        +  +          KP      LL        +    
Sbjct: 205 LLYQIDPNWTSR-SDHSSNIKLRIHSIQAELRRLLKSKPYE--NCLLVLLNVQNAKAWNA 261

Query: 325 FKPPFRLSPPDARSKLTDDELTYLRKLAHPLPTHFVLGRNRGLQGLATAILKLWEKSLVA 384
           F         +   K+                   +  R + +    T  L     + ++
Sbjct: 262 F---------NLSCKI------------------LLTTRFKQV----TDFLSAATTTHIS 290

Query: 385 KITVKWGIPNTDNEQMANELKASLAKWKPNFKFSDDGVLLMQHLTGGVLLLRNKFLIILY 444
                  +  T +E     L   L K+  + +  D   L  + LT     L         
Sbjct: 291 LDHHSMTL--TPDEVK--SL---LLKYL-DCRPQD---LPREVLTTNPRRL--------- 330

Query: 445 RGKDFLPCGVENLIVERERE-LQICQN--HEEGARL-KAIETF--HLPDEPLEKTSKAGT 498
                      ++I E  R+ L    N  H    +L   IE+    L  EP E       
Sbjct: 331 -----------SIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVL--EPAEYRKMFDR 377

Query: 499 LSEFQ---NIQSDFGDLKMGNREFELQLEAEIEDLERELRKQERKLLLEQDP-------- 547
           LS F    +I +    L +      +  +    D+   + K  +  L+E+ P        
Sbjct: 378 LSVFPPSAHIPTIL--LSL------IWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIP 429

Query: 548 DLEM---ITEEERQCLHKIGMKINS-NLLLGRRG------VFDGVIEGLHQHWKY----- 592
            + +   +  E    LH+    ++  N+              D      + H  +     
Sbjct: 430 SIYLELKVKLENEYALHR--SIVDHYNIPKTFDSDDLIPPYLDQYF---YSHIGHHLKNI 484

Query: 593 REVARVITKQKLF-------AQVIYTAKSLVAESGGILISVDKLKEGHAIIIYRG---KN 642
               R+   + +F        ++ + + +  A SG IL ++ +LK       Y+     N
Sbjct: 485 EHPERMTLFRMVFLDFRFLEQKIRHDSTAWNA-SGSILNTLQQLK------FYKPYICDN 537

Query: 643 ---YRRPLKLMTQNLLSKRQALRRSLEMQRLGSLKFFRIPETAGHLQFENQTYLPKKAKL 699
              Y R +  +   L    + L  S         K+  +   A  L  E++    +  K 
Sbjct: 538 DPKYERLVNAILDFLPKIEENLICS---------KYTDLLRIA--LMAEDEAIFEEAHKQ 586

Query: 700 LA 701
           + 
Sbjct: 587 VQ 588

PyMOL of 1vt4

>1rq8_A Conserved hypothetical protein; structural genomics, SAV1595, YHBY, UPF0044, unknown function; NMR {Staphylococcus aureus} SCOP: d.68.4.1 Length = 104	Back alignment and structure

>1rq8_A Conserved hypothetical protein; structural genomics, SAV1595, YHBY, UPF0044, unknown function; NMR {Staphylococcus aureus} SCOP: d.68.4.1 Length = 104	Back alignment and structure

>1jo0_A Hypothetical protein HI1333; structural genomics, YHBY_HAEI structure 2 function project, S2F, unknown function; 1.37A {Haemophilus influenzae} SCOP: d.68.4.1 PDB: 1ln4_A Length = 98	Back alignment and structure

>1jo0_A Hypothetical protein HI1333; structural genomics, YHBY_HAEI structure 2 function project, S2F, unknown function; 1.37A {Haemophilus influenzae} SCOP: d.68.4.1 PDB: 1ln4_A Length = 98	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		744
1rq8_A		104	Conserved hypothetical protein; structural genomic	99.95
1jo0_A		98	Hypothetical protein HI1333; structural genomics,	99.94
1jo0_A		98	Hypothetical protein HI1333; structural genomics,	99.94
1rq8_A		104	Conserved hypothetical protein; structural genomic	99.94

>1rq8_A Conserved hypothetical protein; structural genomics, SAV1595, YHBY, UPF0044, unknown function; NMR {Staphylococcus aureus} SCOP: d.68.4.1	Back alignment and structure

Probab=99.95  E-value=2e-27  Score=214.98  Aligned_cols=96  Identities=22%  Similarity=0.373  Sum_probs=91.6

Q ss_pred             CCCHHHHHHHHhhcccCcceeeeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCCHHHHHHHHHHHHHHhCCEEEeecccC
Q 041729          551 MITEEERQCLHKIGMKINSNLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLFAQVIYTAKSLVAESGGILISVDKLK  630 (744)
Q Consensus       551 ~LT~eQR~~LRklghkLKPvV~IGKrGVtdgVIeeIh~aLk~hELVKVkv~~~~~~d~keiA~~Le~~SGg~LVqV~k~~  630 (744)
                      |||++||+|||++||+|+|+|+||++||||+||++|+++|++||||||+|.+++.++++++|++||+.|||++||+    
T Consensus         1 mLt~kqr~~LR~~ah~Lkpvv~IGK~GlTe~vi~ei~~aL~~hELIKVkvl~~~~~d~~e~a~~la~~t~a~vVq~----   76 (104)
T 1rq8_A            1 MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQV----   76 (104)
T ss_dssp             CCCHHHHHHHHHHTTSSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEE----
T ss_pred             CCCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCHHHHHHHHHHHHHHhCCEEEEE----
Confidence            7999999999999999999999999999999999999999999999999999999999999999999999999998    


Q ss_pred             cCcEEEEecCCCCCCCccccc
Q 041729          631 EGHAIIIYRGKNYRRPLKLMT  651 (744)
Q Consensus       631 IG~tiILYRgknY~rP~~l~p  651 (744)
                      ||+++||||+++ ..|.+.+|
T Consensus        77 IG~~~VLYR~~~-~~~~i~~~   96 (104)
T 1rq8_A           77 IGSMIVIYRESK-ENKEIELP   96 (104)
T ss_dssp             ETTEEEEEECCC-SCCSCCCC
T ss_pred             ECCEEEEEeCCC-CCCceecc
Confidence            899999999987 56666655

PyMOL of 1rq8

>1jo0_A Hypothetical protein HI1333; structural genomics, YHBY_HAEI structure 2 function project, S2F, unknown function; 1.37A {Haemophilus influenzae} SCOP: d.68.4.1 PDB: 1ln4_A	Back alignment and structure

>1jo0_A Hypothetical protein HI1333; structural genomics, YHBY_HAEI structure 2 function project, S2F, unknown function; 1.37A {Haemophilus influenzae} SCOP: d.68.4.1 PDB: 1ln4_A	Back alignment and structure

>1rq8_A Conserved hypothetical protein; structural genomics, SAV1595, YHBY, UPF0044, unknown function; NMR {Staphylococcus aureus} SCOP: d.68.4.1	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		744
d1rq8a_		96	d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphy	6e-19
d1rq8a_		96	d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphy	3e-16
d1rq8a_		96	d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphy	1e-11
d1jo0a_		97	d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i	3e-15
d1jo0a_		97	d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i	5e-14
d1jo0a_		97	d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i	8e-12

>d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]} Length = 96	Back information, alignment and structure


class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: Hypothetical protein SAV1595
species: Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]

 Score = 80.1 bits (198), Expect = 6e-19
 Identities = 22/99 (22%), Positives = 47/99 (47%), Gaps = 4/99 (4%)

Query: 551 MITEEERQCLHKIGMKINSNLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLFAQVIY 610
           M+T ++++ L  +   I+    +G+ G+ + +I+ +    + RE+ +V   Q  F     
Sbjct: 1   MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKE 60

Query: 611 TAKSLVAESGGILISVDKLKEGHAIIIYRGKNYRRPLKL 649
            A++L   +   L+ V     G  I+IYR     + ++L
Sbjct: 61  LAETLSEATRSELVQV----IGSMIVIYRESKENKEIEL 95

PyMOL of d1rq8a_

>d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]} Length = 96	Back information, alignment and structure

>d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]} Length = 96	Back information, alignment and structure

>d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]} Length = 97	Back information, alignment and structure

>d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]} Length = 97	Back information, alignment and structure

>d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]} Length = 97	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		744
d1jo0a_		97	YhbY homologue HI1333 {Haemophilus influenzae [Tax	99.94
d1rq8a_		96	Hypothetical protein SAV1595 {Staphylococcus aureu	99.94
d1jo0a_		97	YhbY homologue HI1333 {Haemophilus influenzae [Tax	99.93
d1rq8a_		96	Hypothetical protein SAV1595 {Staphylococcus aureu	99.93

>d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]}	Back information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: YhbY homologue HI1333
species: Haemophilus influenzae [TaxId: 727]

Probab=99.94  E-value=4.4e-27  Score=207.65  Aligned_cols=96  Identities=17%  Similarity=0.333  Sum_probs=91.9

Q ss_pred             CCCHHHHHHHHhhcccCcceeeeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCCHHHHHHHHHHHHHHhCCEEEeecccC
Q 041729          551 MITEEERQCLHKIGMKINSNLLLGRRGVFDGVIEGLHQHWKYREVARVITKQKLFAQVIYTAKSLVAESGGILISVDKLK  630 (744)
Q Consensus       551 ~LT~eQR~~LRklghkLKPvV~IGKrGVtdgVIeeIh~aLk~hELVKVkv~~~~~~d~keiA~~Le~~SGg~LVqV~k~~  630 (744)
                      +||++||++||++||+|+|+|.||++|||++||.+|++||++||||||+|.+++.+++++++++||+.|||.+||+    
T Consensus         2 tLt~kqr~~LR~~ah~lkp~v~IGk~Glt~~vi~ei~~al~~~ELIKvki~~~~~~~~~~~~~~l~~~t~~~vV~~----   77 (97)
T d1jo0a_           2 TLSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQT----   77 (97)
T ss_dssp             CCCHHHHHHHHHHHTTBCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEEE----
T ss_pred             CCCHHHHHHHHHHhcCCCCEEEECCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHHHhCCEEEEE----
Confidence            6999999999999999999999999999999999999999999999999999999999999999999999999998    


Q ss_pred             cCcEEEEecCCCCCCCcccccc
Q 041729          631 EGHAIIIYRGKNYRRPLKLMTQ  652 (744)
Q Consensus       631 IG~tiILYRgknY~rP~~l~pk  652 (744)
                      ||+++||||+++  .|.+.+|+
T Consensus        78 iG~~~ilYR~~~--~~~i~lPk   97 (97)
T d1jo0a_          78 IGHILVLYRPSE--EAKIQLPR   97 (97)
T ss_dssp             ETTEEEEECCCS--SCCBCCCC
T ss_pred             ECCEEEEEcCCC--CCCCCCCC
Confidence            899999999975  57777775

PyMOL of d1jo0a_

>d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]}	Back information, alignment and structure

>d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]}	Back information, alignment and structure

>d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]}	Back information, alignment and structure