Citrus Sinensis ID: 011932

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Local Sequence Feature Prediction

Residue Number Marker
--------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----
Protein Sequence
MGGRVLVSSASMALRKSPQFKILLSKFHIFKPFSYNKYPFQRISSMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVVEKQESSENSSSADGAGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKVLLIFLIHTLYKYAECIIFFFLLLTALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR
Secondary Structure (PSIPRED)
cccccccccHHHHHHccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccEEEEEEccccccccHHccccccccccccccccHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHcccEEEEEEcccHHHHHHHHHHHHHHHccEEEEEEEccEEEEEEccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccHEHHHHHHHHHccHcccEEEccccccccccccccccccccccEEEEEEcccccccEEEccccccEEEEcccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHcHccccccccccccccHHHHHHHHHHHHcccEEEEEEccccHHHHHHHHHHHHHHcccEEEEEccccEEEEEEcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHccccccccccccccHHHccccccccccccccccccccHHcccccccccccccccccccccHHHHccccccccccccHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MGGRVLVSSAsmalrkspqfkillskfhifkpfsynkypfqrISSMVDVLCKafgpcyglkrfsiegrlwihsapLRHYIEKVVEKqessensssadgaGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLkkiepkessemthdpeiltpeeHFYFLKMGrkcknyvpvgrrgiYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIImyrgknyaqppteimspritlsRKKVLLIFLIHTLYKYAECIIFFFLLLTALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETrsenrsdaaedvqnteldkpdfgsipsmmecsendptteslmasdsedlsdifetdseteteekaelrplyldqfdkfpvqndeehEDFEEHLRQISIDsrnakslgkdedsshfdEVDKMFLRAASLLKKQKR
Flexible Loop (DISEMBL)
mggrvlvssasmalrksPQFKILLSKFHIFKPFSYNKYPFQRISSMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVVekqessensssadgagvakvkrkklkgkravvrwlkhfrykkkkeyermtaeeKILYklrkarkkeeriveglkkiepkessemthdpeiltPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKVLLIFLIHTLYKYAECIIFFFLLLTALDKSKYRDGLRAVKKYIPKLEQELELLRAQAetrsenrsdaaedvqnteldkpdfgsipSMMECSENDPTTESLMASDSEDLSDIFETDseteteekaelrplyldQFDKFPVQNDEEHEDFEEHLRQisidsrnakslgkdedsshfdevDKMFLRAASLLKKQKR
Low Complexity Region (SEG)
MGGRVLVSSASMALRKSPQFKILLSKFHIFKPFSYNKYPFQRISSMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVVEKQESSENSSSADgagvakvkrkklkgkravvrWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKVLLIFLIHTLYKYAECIIFFFLLLTALDKSKYRDGLRAVKKYIPKleqelellraqaeTRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR
Disordered region (IsUnstruct)
******************QFKILLSKFHIFKPFSYNKYPFQRISSMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVV*************************KGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKL*********************************PEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKVLLIFLIHTLYKYAECIIFFFLLLTALDKSKYRDGLRAVKKYIPKLE**************************************************************************************************************************************************
Disordered Region (DISOPRED)
********SASMALRKSPQFKILLSKFHIF*****************DVLCKAFGPCYGLKRFSIEGRLWIH***********************************************************************RKA**K****************************EEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRI*******************AECIIFFFLLLTALDKSKYRDGLRAVKKYIPKLEQELE***************************************************************************************************************************DEVDKMFLRAASLL*****
Disordered Region (DISEMBL)
*********ASMALRKSPQFKILLSKFHIFKPFSYNKYPFQRISSMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKV****************************KRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKVLLIFLIHTLYKYAECIIFFFLLLTALDKSKYRDGLRAVKKYIPKLEQELELLRAQ***************QNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDI************AELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRN************FDEVDKMFLRAASLLKKQKR
Disordered Region (DISPRO)
*************LRKSPQFKILLSKFHIFKPFSYNKYPFQRISSMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLR************************AKVK**K*KGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPK*****THDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKVLLIFLIHTLYKYAECIIFFFLLLTALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETR****************************************************************ELRPLYLDQFDKFPV*****HEDFEEHLRQISID************SSHFDEVDKMFLRAASLLKK***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGGRVLVSSASMALRKSPQFKILLSKFHIFKPFSYNKYPFQRISSMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVVEKQESSENSSSADGAGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKVLLIFLIHTLYKYAECIIFFFLLLTALDKSKYRDGxxxxxxxxxxxxxxxxxxxxxxxxxxxxRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	474	2.2.26 [Sep-21-2011]
Q67XL4	444	Uncharacterized CRM domai	yes	no	0.888	0.948	0.569	1e-123
Q9FYT6	715	Chloroplastic group IIA i	N/A	no	0.265	0.176	0.415	9e-17
Q6YYA3	725	Chloroplastic group IIA i	no	no	0.293	0.191	0.374	4e-15
Q9LF10	720	Chloroplastic group IIA i	no	no	0.246	0.162	0.341	3e-12
Q5VMQ5	701	CRS2-associated factor 1,	no	no	0.189	0.128	0.307	9e-07
Q84N49	674	CRS2-associated factor 1,	N/A	no	0.221	0.155	0.318	4e-06
Q6Z4U2	428	CRS2-associated factor 1,	no	no	0.189	0.210	0.268	2e-05
Q84N48	611	CRS2-associated factor 2,	N/A	no	0.318	0.247	0.236	0.0003
Q0J7J7	366	CRS2-associated factor 2,	no	no	0.154	0.199	0.283	0.0004

>sp|Q67XL4|Y3544_ARATH Uncharacterized CRM domain-containing protein At3g25440, chloroplastic OS=Arabidopsis thaliana GN=At3g25440 PE=2 SV=1

 Score =  442 bits (1138), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 277/486 (56%), Positives = 328/486 (67%), Gaps = 65/486 (13%)

Query: 4   RVLVSSASMALR-KSPQFKILLSKFHIFKPFSYNKYPFQRISSMVDVLCKAFGPCYGLKR 62
           RV  S+ASM LR KS Q   L S   +F  F+       R  S  +++CK       L +
Sbjct: 9   RVSTSAASMLLRRKSRQLGFLASSSPLFSSFN----SMNRTISSCNIVCKV------LHK 58

Query: 63  FSIEGRLW---------IHSAPLRHYIEKVVEKQESSENSSSADGAGVAKVKRKKLKGKR 113
            S+   +W          HS P R   +  + K   SENSSS DG    K+KRKKLKGKR
Sbjct: 59  ESLTRPMWNVSFLRSSSFHSTPARETGDDDISK---SENSSSQDGDSCTKLKRKKLKGKR 115

Query: 114 AVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPE 173
           AVVRWLK FR+KKKKE+ERMT+EEKIL KLRKARKKEER++E +KK+EP ES+E THDPE
Sbjct: 116 AVVRWLKFFRWKKKKEFERMTSEEKILNKLRKARKKEERLMETMKKLEPSESAETTHDPE 175

Query: 174 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKE 233
           ILTPEEHFY+LKMG KCKNYVPVGRRGIYQGVILNMHLHWKKHQTL+V++KTF+ +EVKE
Sbjct: 176 ILTPEEHFYYLKMGLKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLQVVIKTFTPDEVKE 235

Query: 234 IAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKVLLIFLIHTLYK 293
           IA ELARLTGGIVL++HE NTIIMYRGKNY QPPTEIMSPRITL RKK            
Sbjct: 236 IAVELARLTGGIVLDVHEGNTIIMYRGKNYVQPPTEIMSPRITLPRKK------------ 283

Query: 294 YAECIIFFFLLLTALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQ 353
                        ALDKSK RD LRAV+KYIP+LEQEL+LL+AQAET+ +  +   +D Q
Sbjct: 284 -------------ALDKSKCRDALRAVRKYIPRLEQELQLLQAQAETKRDYTNVKVDDNQ 330

Query: 354 --NTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLY 411
             + EL K    S   + +  E D     L A+DS DLSDIFETDSE E + K E RPL+
Sbjct: 331 ERSEELKKIIERSEECLEDEQEEDEAGLEL-ATDS-DLSDIFETDSELE-DAKTE-RPLF 386

Query: 412 LDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDED---SSHFDEVDKMFLRAASL 468
           L++F+KFP  N+ E EDF         D   AKS G++ D   S +FDEVDKMFLRAA L
Sbjct: 387 LEEFEKFPAINNREDEDFG--------DLGKAKSEGEENDDDKSPNFDEVDKMFLRAAFL 438

Query: 469 LKKQKR 474
           LKK++R
Sbjct: 439 LKKKRR 444

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FYT6|CRS1_MAIZE Chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic OS=Zea mays GN=CRS1 PE=1 SV=1

 Score = 88.6 bits (218), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 54/130 (41%), Positives = 74/130 (56%), Gaps = 4/130 (3%)

Query: 141 YKLRKARKKEERIVEGLKKIEPKES-SEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRR 199
           +KL    KK ER  + L K+    S SE + D E LT EE   F ++GRK    V +GRR
Sbjct: 529 WKLSVLNKKIERSNQALAKLHSSWSPSEQSADREHLTEEEKIMFRRIGRKMDGLVLLGRR 588

Query: 200 GIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT---II 256
           GI+ GVI  +H HWK  + +KVI K     ++   A+ L   TGGI++ + +  T   II
Sbjct: 589 GIFDGVIEEIHQHWKHKEVVKVITKQNQTRQIMYAASLLEVETGGILIAVEKLTTSHAII 648

Query: 257 MYRGKNYAQP 266
           +YRGKNY +P
Sbjct: 649 LYRGKNYRRP 658

Required for the splicing of group IIA introns in chloroplasts, and especially for atpF, by regulating the intron folding. Forms splicing particles with RNA. Also involved in chloroplast protein translation.

Zea mays (taxid: 4577)

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

 Score = 83.2 bits (204), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 55/147 (37%), Positives = 81/147 (55%), Gaps = 8/147 (5%)

Query: 141 YKLRKARKKEERIVEGLKKIEPKES-SEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRR 199
           ++L    KK ER  + L K+    S S+   D E+LT EE   F K+G K   +V +GRR
Sbjct: 531 WRLSMLTKKIERSNQVLAKLHSSWSPSKKDGDRELLTEEERRIFRKIGLKMDEHVLLGRR 590

Query: 200 GIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT---II 256
           G+++GVI  +H HWK  + +KVI K   A ++   +  L   TGG ++ I    T   II
Sbjct: 591 GVFEGVIEEIHQHWKHKEVVKVITKQNQASQITYTSMMLEVETGGTLIAIERFTTSHAII 650

Query: 257 MYRGKNYAQP----PTEIMSPRITLSR 279
           +YRGKNY +P    P+ +++ R  L R
Sbjct: 651 LYRGKNYRRPTKSAPSNLLTKREALQR 677

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|Q9LF10|CRS1_ARATH Chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic OS=Arabidopsis thaliana GN=At5g16180 PE=2 SV=2

 Score = 73.6 bits (179), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 41/120 (34%), Positives = 65/120 (54%), Gaps = 3/120 (2%)

Query: 166 SEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKT 225
           SE   D EILT EE     ++G K  + + +GRRG++ GV+  +H HWK  +  KVI   
Sbjct: 563 SEGDDDIEILTNEERECLRRIGLKMNSSLVLGRRGVFFGVMEGLHQHWKHREVAKVITMQ 622

Query: 226 FSAEEVKEIAAELARLTGGIVLEIH---EENTIIMYRGKNYAQPPTEIMSPRITLSRKKV 282
                V   A  L   + G+++ I    E + I++YRGKNY +P +++M+  +   RK +
Sbjct: 623 KLFSRVVYTAKALETESNGVLISIEKLKEGHAILIYRGKNYKRPSSKLMAQNLLTKRKAL 682

Required for the splicing of group IIA introns in chloroplasts, by regulating the intron folding. Forms splicing particles with RNA. May also be involved in chloroplast protein translation.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 55.5 bits (132), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 28/91 (30%), Positives = 47/91 (51%), Gaps = 1/91 (1%)

Query: 173 EILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVK 232
           E LT EE    +K   K K  + +GR G+   ++ N+H HWK+ +  K+  K     ++ 
Sbjct: 183 EPLTKEEVDELVKATLKTKRQLNIGRDGLTHNMLENIHSHWKRKRVCKIKCKGVCTVDMD 242

Query: 233 EIAAELARLTGGIVLEIHEENTIIMYRGKNY 263
            +  +L    GG V+  H+   I ++RG+NY
Sbjct: 243 NVCQQLEEKVGGKVIH-HQGGVIFLFRGRNY 272

Required for the splicing of group IIB introns in chloroplasts. Forms splicing particles with CRS2. Interacts with RNA and confers intron specificity of the splicing particles.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q84N49|CAF1P_MAIZE CRS2-associated factor 1, chloroplastic OS=Zea mays GN=CAF1 PE=1 SV=1

 Score = 53.1 bits (126), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 35/110 (31%), Positives = 55/110 (50%), Gaps = 5/110 (4%)

Query: 157 LKKIEPKESSEMTHD--PEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWK 214
           L  +EP+  S    D   E LT EE    +K   K K  + +GR G+   ++ N+H HWK
Sbjct: 165 LAGMEPRYQSVSREDILGEPLTKEEVSELVKGSLKSKRQLNMGRDGLTHNMLENIHSHWK 224

Query: 215 KHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTII-MYRGKNY 263
           + +  K+  K     ++  I  +L    GG V  IH +  +I ++RG+NY
Sbjct: 225 RKRVCKIKCKGVCTIDMDNICHQLEEKVGGKV--IHRQGGVIFLFRGRNY 272

Required for the splicing of group IIB introns in chloroplasts. Forms splicing particles with CRS2. Interacts with RNA and confers intron specificity of the splicing particles.

Zea mays (taxid: 4577)

>sp|Q6Z4U2|CAF1M_ORYSJ CRS2-associated factor 1, mitochondrial OS=Oryza sativa subsp. japonica GN=Os08g0174900 PE=2 SV=1

 Score = 51.2 bits (121), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/93 (26%), Positives = 50/93 (53%), Gaps = 3/93 (3%)

Query: 173 EILTPEEHFYFLKMGRK--CKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEE 230
           E LTP E  + +   +K   K  + +GR G+   ++ ++H HWK  + ++V        +
Sbjct: 155 EPLTPAERAFLVSKCQKSRTKKQINLGRDGLTHNMLNDIHNHWKNDEAVRVKCLGVPTVD 214

Query: 231 VKEIAAELARLTGGIVLEIHEENTIIMYRGKNY 263
           ++ +  +L   TGG+++  H    +I+YRG++Y
Sbjct: 215 MQNVCHQLEDKTGGLIIHRH-GGQLILYRGRHY 246

May be involved for the splicing of group IIB introns in mitochondrions.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q84N48|CAF2P_MAIZE CRS2-associated factor 2, chloroplastic OS=Zea mays GN=CAF2 PE=1 SV=1

 Score = 47.0 bits (110), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 40/169 (23%), Positives = 76/169 (44%), Gaps = 18/169 (10%)

Query: 99  AGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLK 158
            G A +  K+ K +R  VR          +E  +  +   I+ ++R+ RK +      L 
Sbjct: 167 TGKAPLLTKEEKARRRGVR----LHTPLGQETPQTVSAHGIMMEVRERRKMD------LA 216

Query: 159 KIEPKES---SEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKK 215
           ++ P +     E+  +P  LTP E    +K        + +GR G+   ++  +H HW++
Sbjct: 217 RVSPGDGRSREEVLGEP--LTPSEVRALVKPHISHNRQLNIGRDGLTHNMLEMIHCHWRR 274

Query: 216 HQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTII-MYRGKNY 263
            +  KV  +     ++K +   L   +GG V  IH    ++ +YRG++Y
Sbjct: 275 QEICKVRCRGVPTVDMKNLCYHLEEKSGGKV--IHRVGGVVFLYRGRHY 321

Required for the splicing of group IIB introns in chloroplasts. Forms splicing particles with CRS2. Interacts with RNA and confers intron specificity of the splicing particles.

Zea mays (taxid: 4577)

>sp|Q0J7J7|CAF2M_ORYSJ CRS2-associated factor 2, mitochondrial OS=Oryza sativa subsp. japonica GN=Os08g0188000 PE=2 SV=2

 Score = 46.6 bits (109), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 190 CKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEI 249
           C   + +G+ G+   +I ++H HWK+ + +++        ++  I   L   TGG V+  
Sbjct: 162 CSRQINLGKGGVTHNMIDDIHNHWKRAEAVRIKCLGVPTLDMDNICFHLEDKTGGKVI-Y 220

Query: 250 HEENTIIMYRGKNY 263
              N +I+YRG+NY
Sbjct: 221 RNINILILYRGRNY 234

May be involved for the splicing of group IIB introns in mitochondrions.

Oryza sativa subsp. japonica (taxid: 39947)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	474
255572670	458	conserved hypothetical protein [Ricinus	0.883	0.914	0.619	1e-146
224132018	413	predicted protein [Populus trichocarpa]	0.824	0.946	0.621	1e-144
225448146	401	PREDICTED: uncharacterized CRM domain-co	0.805	0.952	0.653	1e-140
356501797	382	PREDICTED: uncharacterized CRM domain-co	0.782	0.971	0.644	1e-135
356498434	383	PREDICTED: uncharacterized CRM domain-co	0.765	0.947	0.643	1e-132
357439925	472	CRM domain-containing protein, putative	0.913	0.917	0.582	1e-130
297739537	331	unnamed protein product [Vitis vinifera]	0.666	0.954	0.669	1e-127
449458069	500	PREDICTED: uncharacterized CRM domain-co	0.816	0.774	0.561	1e-126
357439975	443	CRM domain-containing protein, putative	0.867	0.927	0.572	1e-125
9279724	1115	unnamed protein product [Arabidopsis tha	0.873	0.371	0.561	1e-122

>gi|255572670|ref|XP_002527268.1| conserved hypothetical protein [Ricinus communis] gi|223533361|gb|EEF35112.1| conserved hypothetical protein [Ricinus communis]

 Score =  524 bits (1349), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 290/468 (61%), Positives = 342/468 (73%), Gaps = 49/468 (10%)

Query: 28  HIFKPFSYNKYPFQRISSMVDVLCK------AFGPCYGLKRFSIEGRLWIHSAPLRHYIE 81
           ++F PF  +   + R +S+  ++CK      AF P Y L+   I G  WIH  P    I+
Sbjct: 19  YLFTPFFSDSLTY-RTTSLFHIICKVFSQAPAFRPVYVLEGPHIGGHRWIHFGPTLTDID 77

Query: 82  KVVEKQESSENSSSADGAGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILY 141
           K  E    S  S+  +G+G AKVKRKKLKGKRAVVRWLK FR+KKKKEYERMTAEEK+LY
Sbjct: 78  KDGEPPPLSGQSTMVEGSGCAKVKRKKLKGKRAVVRWLKFFRWKKKKEYERMTAEEKLLY 137

Query: 142 KLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGI 201
           KL+KA+KKEER V+ LKKIEP +SSE THDPEILTPEEHF+FLKMG KCKNYVPVGRRGI
Sbjct: 138 KLKKAQKKEERYVQALKKIEPVDSSETTHDPEILTPEEHFFFLKMGLKCKNYVPVGRRGI 197

Query: 202 YQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGK 261
           YQGVILNMHLHWKKHQT++V+VKTFS EEVKEIAAELARLTGGIVL+IHEENTIIMYRGK
Sbjct: 198 YQGVILNMHLHWKKHQTVQVVVKTFSPEEVKEIAAELARLTGGIVLDIHEENTIIMYRGK 257

Query: 262 NYAQPPTEIMSPRITLSRKKVLLIFLIHTLYKYAECIIFFFLLLTALDKSKYRDGLRAVK 321
           NY+QPPTEIMSPRITLSRKK                         ALDKSKYRDGLRAV+
Sbjct: 258 NYSQPPTEIMSPRITLSRKK-------------------------ALDKSKYRDGLRAVR 292

Query: 322 KYIPKLEQELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSMM------------ 369
            YIP+LEQ+LELL+ Q+  ++E  S +AE+   T+ D  + G +PS              
Sbjct: 293 NYIPRLEQDLELLKVQSMGKAECGSASAEETLYTD-DGAESGGVPSTPLENSEKLKKITD 351

Query: 370 ---ECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEH 426
              ECSE +   +  M SDSEDLSDIFETDS+TETE+K + RPLYL++F KFP+Q +EE 
Sbjct: 352 GQEECSEEESPMDLGMLSDSEDLSDIFETDSDTETEDKVK-RPLYLEEFKKFPIQGNEEP 410

Query: 427 EDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 474
           EDFEEHLRQ+S+DSR  +S  KD D   FDEVD++FLRAASLLKK+KR
Sbjct: 411 EDFEEHLRQLSVDSRKVESSEKDSDIPSFDEVDRLFLRAASLLKKKKR 458

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224132018|ref|XP_002321235.1| predicted protein [Populus trichocarpa] gi|222862008|gb|EEE99550.1| predicted protein [Populus trichocarpa]

 Score =  519 bits (1337), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 278/447 (62%), Positives = 333/447 (74%), Gaps = 56/447 (12%)

Query: 50  LCKAFG--PCYGLKR--FSIEGRLWIHSAPLRHYIEKVVEKQESSENSSSADGAGVAKVK 105
           +CK  G  P Y +K     + G LWIHS P  + ++KVVE  E+ E +++       KVK
Sbjct: 1   MCKVLGQRPVYNVKGHLVPLVGHLWIHSCPSLNNVDKVVEPTENFEKTAAVFSGSDVKVK 60

Query: 106 RKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKES 165
           R KLKGKRAVVRWLK FR+KKKKEYERMTAEEKILYKLRKA++KEER V+ LKKIEPKES
Sbjct: 61  RPKLKGKRAVVRWLKFFRWKKKKEYERMTAEEKILYKLRKAQRKEERFVQALKKIEPKES 120

Query: 166 SEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKT 225
           SE THDPEILTPEEHF+FLKMG KCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKV+VKT
Sbjct: 121 SEATHDPEILTPEEHFFFLKMGLKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVVVKT 180

Query: 226 FSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKVLLI 285
           F+ EEVKEIAAELAR TGGIVL+IHEENTIIMYRGKNY+QPPTEIMSPR+TLSRKK    
Sbjct: 181 FTPEEVKEIAAELARFTGGIVLDIHEENTIIMYRGKNYSQPPTEIMSPRVTLSRKK---- 236

Query: 286 FLIHTLYKYAECIIFFFLLLTALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRS--- 342
                                ALDKSK RDGLRA+++YIP+L+Q+LELL A+A  ++   
Sbjct: 237 ---------------------ALDKSKCRDGLRALRRYIPRLQQDLELLHARAGGKTDID 275

Query: 343 --ENRSDAAEDVQNTE-----LDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFET 395
             E+RS +++ ++N+E     +D+ D G        SE+ P T+  +ASDSEDLSDIFET
Sbjct: 276 GAESRSISSKQLENSEKLKEIIDRQDEG--------SEDGPDTDLGIASDSEDLSDIFET 327

Query: 396 DSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGK------- 448
           DS+ +TEE ++ RPLYL++F+KF V+ D E EDFEEHLRQIS+ S+   + GK       
Sbjct: 328 DSDADTEETSK-RPLYLEEFEKFSVEADGEPEDFEEHLRQISLGSKKGVTSGKDVDIPTG 386

Query: 449 -DEDSSHFDEVDKMFLRAASLLKKQKR 474
            D DS  FDEVD+MFLRAASLLK++KR
Sbjct: 387 VDVDSPSFDEVDRMFLRAASLLKRKKR 413

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225448146|ref|XP_002263852.1| PREDICTED: uncharacterized CRM domain-containing protein At3g25440, chloroplastic-like [Vitis vinifera]

 Score =  504 bits (1299), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 277/424 (65%), Positives = 323/424 (76%), Gaps = 42/424 (9%)

Query: 67  GRLWIHSAPLRHYIE-KVVEKQESSENSSSADGAGVAKVKRKKLKGKRAVVRWLKHFRYK 125
            R  +H+  L H +E  V E ++   +S++A G    KVKRKKLKGKRAVVRWLK FR+K
Sbjct: 4   ARFLVHNLLLGHSMEYGVAEPEKLPVDSTTAAGTVETKVKRKKLKGKRAVVRWLKFFRWK 63

Query: 126 KKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLK 185
           KKKEYERMTAEEKILYKLRKAR+KEER+ E L KIEPKESSE THDPEILTPEEHF+FLK
Sbjct: 64  KKKEYERMTAEEKILYKLRKARRKEERLAEALTKIEPKESSETTHDPEILTPEEHFFFLK 123

Query: 186 MGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGI 245
           MG KCKNYVP+GRRGIYQGVILNMHLHWKKHQTL+V+VKTFS EEVKEIA ELARLTGGI
Sbjct: 124 MGLKCKNYVPIGRRGIYQGVILNMHLHWKKHQTLQVVVKTFSPEEVKEIAVELARLTGGI 183

Query: 246 VLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKVLLIFLIHTLYKYAECIIFFFLLL 305
           VL+IHEENTIIMYRGKNY+QPPTEIMSPRITLSRKK                        
Sbjct: 184 VLDIHEENTIIMYRGKNYSQPPTEIMSPRITLSRKK------------------------ 219

Query: 306 TALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSI 365
            ALDKSKYRDGLRAV+KYIP+LE +LELL+AQA+ ++EN+++A ED QN  +D  +   I
Sbjct: 220 -ALDKSKYRDGLRAVRKYIPRLEGDLELLQAQAKMQAENKTEAVEDFQNANIDSINSQGI 278

Query: 366 PSMM---------------ECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPL 410
            ++                E SE +  T+S   S SE LSDIFE+DS+T+T+EKAE + L
Sbjct: 279 SNLQPENSDKLRELLAGNNESSEEESLTDSGTESCSEALSDIFESDSDTDTKEKAE-QLL 337

Query: 411 YLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLK 470
           YL++F+KFPV++D E EDFEEHLRQIS DSR AKSL KD D    DEVD+MFLRAASLLK
Sbjct: 338 YLNEFEKFPVESDGEPEDFEEHLRQISADSRKAKSLEKDADLPQLDEVDQMFLRAASLLK 397

Query: 471 KQKR 474
           K++R
Sbjct: 398 KKRR 401

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356501797|ref|XP_003519710.1| PREDICTED: uncharacterized CRM domain-containing protein At3g25440, chloroplastic-like [Glycine max]

 Score =  488 bits (1256), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 263/408 (64%), Positives = 311/408 (76%), Gaps = 37/408 (9%)

Query: 67  GRLWIHSAPLRHYIEKVVEKQESSENSSSA--DGAGVAKVKRKKLKGKRAVVRWLKHFRY 124
           G    HS P   + +KVVE+Q+ S+ +SSA  DG G AKVKR KLKGKRAVVRWLK FR+
Sbjct: 8   GNASFHSCPFLKFNDKVVEQQQDSQKASSANVDGDGNAKVKRNKLKGKRAVVRWLKFFRF 67

Query: 125 KKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFL 184
           KKKKEYERMTAEEKILYKL KARKKEER+ E LKKIEP ESSE THDPEILTPEEHF+FL
Sbjct: 68  KKKKEYERMTAEEKILYKLLKARKKEERLCEALKKIEPAESSETTHDPEILTPEEHFFFL 127

Query: 185 KMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGG 244
           KMG K KNYVPVGRRGIYQGVILNMHLHWKKHQTLKV+VKTFSAEEVKEIA ELARL+GG
Sbjct: 128 KMGLKSKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVVVKTFSAEEVKEIATELARLSGG 187

Query: 245 IVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKVLLIFLIHTLYKYAECIIFFFLL 304
           IVL+IHE+NTIIMYRGKNY+QPPTEIMSPR++LSRKK                       
Sbjct: 188 IVLDIHEDNTIIMYRGKNYSQPPTEIMSPRVSLSRKK----------------------- 224

Query: 305 LTALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQNTELDKPDFGS 364
             ALDKSKYRD LRAV+++IP+LEQELE+LRAQ ++ +E+ +DAAE +QN          
Sbjct: 225 --ALDKSKYRDALRAVRRHIPRLEQELEILRAQFKSSAESNTDAAEAIQNNR------ER 276

Query: 365 IPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDE 424
           +   + C+E++    S + SDS+ LSDIFETDS+TE   K E +PLYLD+FD FP Q+D 
Sbjct: 277 MNDNIGCTEDETDMNSELDSDSDKLSDIFETDSDTENFIKEE-KPLYLDEFDNFPEQSDG 335

Query: 425 EHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQ 472
           E  DFEEHLRQ+S+ S+N   + K+++    DEVDK+FL+A S LKK+
Sbjct: 336 EMNDFEEHLRQMSLKSKN---MEKEDNLPKLDEVDKIFLQATSFLKKK 380

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356498434|ref|XP_003518057.1| PREDICTED: uncharacterized CRM domain-containing protein At3g25440, chloroplastic-like, partial [Glycine max]

 Score =  478 bits (1231), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 264/410 (64%), Positives = 312/410 (76%), Gaps = 47/410 (11%)

Query: 81  EKVVEKQ-ESSENSSSA--DGAGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEE 137
           +KVVE+Q + S+ +SSA  DG G AKVKR KLKGKRAVVRWLK FR+KKKKEYERMTAEE
Sbjct: 1   DKVVEQQHQDSQKASSANVDGDGNAKVKRNKLKGKRAVVRWLKFFRFKKKKEYERMTAEE 60

Query: 138 KILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVG 197
           K LYKL KARKKEER+ E LKKIEP ESSE THDPEILTPEEHF+FLKMG K KNYVPVG
Sbjct: 61  KNLYKLLKARKKEERLCEALKKIEPAESSETTHDPEILTPEEHFFFLKMGLKSKNYVPVG 120

Query: 198 RRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIM 257
           RRGIYQGVILNMHLHWKKHQTLKV+VKTFSAEEVKEIAAELARL+GGIVL+IHE+NTIIM
Sbjct: 121 RRGIYQGVILNMHLHWKKHQTLKVVVKTFSAEEVKEIAAELARLSGGIVLDIHEDNTIIM 180

Query: 258 YRGKNYAQPPTEIMSPRITLSRKKVLLIFLIHTLYKYAECIIFFFLLLTALDKSKYRDGL 317
           YRGKNY+QPPTEIMSPR++LSRKK                         ALDKSKYRD L
Sbjct: 181 YRGKNYSQPPTEIMSPRVSLSRKK-------------------------ALDKSKYRDAL 215

Query: 318 RAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPS---------- 367
           RAV++YIP+LEQELE+LRAQ ++ +E+ +DAAE +QN+  +  + GSI +          
Sbjct: 216 RAVRRYIPRLEQELEILRAQFKSSAESNTDAAEAIQNSGRESIESGSISNFQLQNSYKDR 275

Query: 368 -MMEC----SENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQN 422
            MM      +E++    S + SDS+ LSDIFETDS+TE   K E +PLYLD+FD FP Q+
Sbjct: 276 EMMNVNIGSTEDETDMNSELDSDSDKLSDIFETDSDTENFVKEE-KPLYLDEFDNFPEQS 334

Query: 423 DEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQ 472
           D E  DFEEH+RQ+S+ S+N   + KD++    DEVDK+FL+A S LKK+
Sbjct: 335 DGEMNDFEEHMRQMSLKSKN---MEKDDNLPKLDEVDKIFLQATSFLKKK 381

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357439925|ref|XP_003590240.1| CRM domain-containing protein, putative [Medicago truncatula] gi|355479288|gb|AES60491.1| CRM domain-containing protein, putative [Medicago truncatula]

 Score =  472 bits (1215), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 281/482 (58%), Positives = 345/482 (71%), Gaps = 49/482 (10%)

Query: 23  LLSKFHIFKPFSYNKYPFQRISSMVDVLCKAFGP---CYGLKRFSIE-GRLWIHSAP-LR 77
           LL+KF      S   +  +  +S+  V+CK +      + L   S   G L  HS P L+
Sbjct: 10  LLNKFQFLS--SSTTFLLRHKTSLNYVICKVYAQEHHQFKLPSTSTRVGCLSFHSTPFLK 67

Query: 78  HYIEKVVEKQESSENSSSADGAGVAKV-KRKKLKGKRAVVRWLKHFRYKKKKEYERMTAE 136
              +KVVE+ + S+        G  KV  RKKLKGKRAVVRWLK FR+KKKKE++RMT E
Sbjct: 68  CNHDKVVEQPQDSD--------GDVKVPARKKLKGKRAVVRWLKFFRFKKKKEFQRMTTE 119

Query: 137 EKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPV 196
           E+ILYKL KARKKEER+ E LKKIEP ESSE  HDPEILTPEEHF+FLKMG K KNYVPV
Sbjct: 120 ERILYKLLKARKKEERLREALKKIEPTESSETIHDPEILTPEEHFFFLKMGLKSKNYVPV 179

Query: 197 GRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTII 256
           GRRGIYQGVILNMHLHWKKHQTL+V+VKTFSAEEVKEIA ELARLTGGIVL IHEE+TII
Sbjct: 180 GRRGIYQGVILNMHLHWKKHQTLQVVVKTFSAEEVKEIATELARLTGGIVLGIHEEDTII 239

Query: 257 MYRGKNYAQPPTEIMSPRITLSRKKVLLI---FLIHTLYKYAECIIFFFL----LLTALD 309
           MYRGKNY+QPPTEIMSPR+TL RKKVL +    L HT+    +C  F F     L++ALD
Sbjct: 240 MYRGKNYSQPPTEIMSPRVTLPRKKVLHVPKDCLHHTI---KDCFTFLFAYFPSLISALD 296

Query: 310 KSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQ-------------NTE 356
           KSKYRDGLRAV++YIPKLEQELE+LRAQ ++ +E+ ++AAE +Q             N +
Sbjct: 297 KSKYRDGLRAVRRYIPKLEQELEILRAQFQSTAESNTEAAEGIQISDKVSVEPSSVSNLQ 356

Query: 357 LDKPDFGSIPSMME----CSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYL 412
           L+K D   + +M      CSE++   +S + S S+ LSDIFETDS+TE   K E +PLYL
Sbjct: 357 LEKLD--KVGAMFNDNNSCSEDEAHMDSDLDSYSDKLSDIFETDSDTEDLVKEE-KPLYL 413

Query: 413 DQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQ 472
           D+F+ FP Q+D + +DFEEHL+QIS +S+N   + KD D   FDEVD++FLRAAS LKK+
Sbjct: 414 DEFNNFPEQSDGDTDDFEEHLQQISYNSKN---MEKDADLPKFDEVDQIFLRAASFLKKK 470

Query: 473 KR 474
           ++
Sbjct: 471 RK 472

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297739537|emb|CBI29719.3| unnamed protein product [Vitis vinifera]

 Score =  461 bits (1185), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 239/357 (66%), Positives = 276/357 (77%), Gaps = 41/357 (11%)

Query: 133 MTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKN 192
           MTAEEKILYKLRKAR+KEER+ E L KIEPKESSE THDPEILTPEEHF+FLKMG KCKN
Sbjct: 1   MTAEEKILYKLRKARRKEERLAEALTKIEPKESSETTHDPEILTPEEHFFFLKMGLKCKN 60

Query: 193 YVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE 252
           YVP+GRRGIYQGVILNMHLHWKKHQTL+V+VKTFS EEVKEIA ELARLTGGIVL+IHEE
Sbjct: 61  YVPIGRRGIYQGVILNMHLHWKKHQTLQVVVKTFSPEEVKEIAVELARLTGGIVLDIHEE 120

Query: 253 NTIIMYRGKNYAQPPTEIMSPRITLSRKKVLLIFLIHTLYKYAECIIFFFLLLTALDKSK 312
           NTIIMYRGKNY+QPPTEIMSPRITLSRKK                         ALDKSK
Sbjct: 121 NTIIMYRGKNYSQPPTEIMSPRITLSRKK-------------------------ALDKSK 155

Query: 313 YRDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSMM--- 369
           YRDGLRAV+KYIP+LE +LELL+AQA+ ++EN+++A ED QN  +D  +   I ++    
Sbjct: 156 YRDGLRAVRKYIPRLEGDLELLQAQAKMQAENKTEAVEDFQNANIDSINSQGISNLQPEN 215

Query: 370 ------------ECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDK 417
                       E SE +  T+S   S SE LSDIFE+DS+T+T+EKAE + LYL++F+K
Sbjct: 216 SDKLRELLAGNNESSEEESLTDSGTESCSEALSDIFESDSDTDTKEKAE-QLLYLNEFEK 274

Query: 418 FPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 474
           FPV++D E EDFEEHLRQIS DSR AKSL KD D    DEVD+MFLRAASLLKK++R
Sbjct: 275 FPVESDGEPEDFEEHLRQISADSRKAKSLEKDADLPQLDEVDQMFLRAASLLKKKRR 331

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449458069|ref|XP_004146770.1| PREDICTED: uncharacterized CRM domain-containing protein At3g25440, chloroplastic-like [Cucumis sativus] gi|449516505|ref|XP_004165287.1| PREDICTED: uncharacterized CRM domain-containing protein At3g25440, chloroplastic-like [Cucumis sativus]

 Score =  458 bits (1179), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 251/447 (56%), Positives = 316/447 (70%), Gaps = 60/447 (13%)

Query: 53  AFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVVEKQESSENSSS---ADGAGVAKVKRKKL 109
           +F   YGL   S+ G  WIHS        K VE  E SE  S+    DG+G+ + ++K+ 
Sbjct: 89  SFNGVYGLT--SVVGYRWIHST-------KSVEPLEKSEGKSAIGFTDGSGIEEEEKKEK 139

Query: 110 KGK------RAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPK 163
           K +      RAVVRWLK FR+KKKKEYERMT+EEKIL+K+ KARKKE+R+VE L+KIEP 
Sbjct: 140 KTRKKLKGKRAVVRWLKLFRWKKKKEYERMTSEEKILFKMNKARKKEKRLVEALEKIEPA 199

Query: 164 ESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIV 223
           +SS+ THDPEILTPEEHFYFLKMG K KNYVPVGRRGIYQGVILNMHLHWKKHQT+KV+V
Sbjct: 200 DSSDTTHDPEILTPEEHFYFLKMGIKGKNYVPVGRRGIYQGVILNMHLHWKKHQTVKVVV 259

Query: 224 KTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKVL 283
           KTFS EEVKEIAAELARLTGG+VL+IHEE+TIIMYRGKNY+QPPTEIMSPR++LSRKK  
Sbjct: 260 KTFSPEEVKEIAAELARLTGGLVLDIHEEDTIIMYRGKNYSQPPTEIMSPRVSLSRKK-- 317

Query: 284 LIFLIHTLYKYAECIIFFFLLLTALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSE 343
                                  ALDKSKYRDGLRAV+K+IPKLEQEL  L++QA+   +
Sbjct: 318 -----------------------ALDKSKYRDGLRAVRKHIPKLEQELRFLQSQAKLNCK 354

Query: 344 NRSDAAEDVQNTELDKPDFGSIPSMM----------------ECSENDPTTESLMASDSE 387
           +  ++ E +Q T  D     +I S+                 + S++    ++ M+SDSE
Sbjct: 355 SNGESVEHMQETVDDTNKSKAISSLNLENLDDSSNAMRSVSKDWSDDSSPIDTGMSSDSE 414

Query: 388 DLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLG 447
           DLSD+FETD ++E +EK E +PL+L +F+ F  + ++E ED  + LRQIS+DS+ AK L 
Sbjct: 415 DLSDMFETDIDSEADEKME-KPLFLKEFENFAAETEDEIEDLSDQLRQISMDSKQAKILE 473

Query: 448 KDEDSSHFDEVDKMFLRAASLLKKQKR 474
            D +S  FDEVD++FLR+ASLLKK++R
Sbjct: 474 NDVNSPEFDEVDRLFLRSASLLKKKRR 500

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357439975|ref|XP_003590265.1| CRM domain-containing protein, putative [Medicago truncatula] gi|355479313|gb|AES60516.1| CRM domain-containing protein, putative [Medicago truncatula]

 Score =  455 bits (1170), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 272/475 (57%), Positives = 331/475 (69%), Gaps = 64/475 (13%)

Query: 23  LLSKFHIFKPFSYNKYPFQRISSMVDVLCKAFGP---CYGLKRFSIE-GRLWIHSAP-LR 77
           LL+KF      S   +  +  +S+  V+CK +      + L   S   G L  HS P L+
Sbjct: 10  LLNKFQFLS--SSTTFLLRHKTSLNYVICKVYAQEHHQFKLPSTSTRVGCLSFHSTPFLK 67

Query: 78  HYIEKVVEKQESSENSSSADGAGVAKV-KRKKLKGKRAVVRWLKHFRYKKKKEYERMTAE 136
              +KVVE+ + S+        G  KV  RKKLKGKRAVVRWLK FR+KKKKE++RMT E
Sbjct: 68  CNHDKVVEQPQDSD--------GDVKVPARKKLKGKRAVVRWLKFFRFKKKKEFQRMTTE 119

Query: 137 EKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPV 196
           E+ILYKL KARKKEER+ E LKKIEP ESSE  HDPEILTPEEHF+FLKMG K KNYVPV
Sbjct: 120 ERILYKLLKARKKEERLREALKKIEPTESSETIHDPEILTPEEHFFFLKMGLKSKNYVPV 179

Query: 197 GRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTII 256
           GRRGIYQGVILNMHLHWKKHQTL+V+VKTFSAEEVKEIA ELARLTGGIVL IHEE+TII
Sbjct: 180 GRRGIYQGVILNMHLHWKKHQTLQVVVKTFSAEEVKEIATELARLTGGIVLGIHEEDTII 239

Query: 257 MYRGKNYAQPPTEIMSPRITLSRKKVLLIFLIHTLYKYAECIIFFFLLLTALDKSKYRDG 316
           MYRGKNY+QPPTEIMSPR+TL RKK                         ALDKSKYRDG
Sbjct: 240 MYRGKNYSQPPTEIMSPRVTLPRKK-------------------------ALDKSKYRDG 274

Query: 317 LRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQ-------------NTELDKPDFG 363
           LRAV++YIPKLEQELE+LRAQ ++ +E+ ++AAE +Q             N +L+K D  
Sbjct: 275 LRAVRRYIPKLEQELEILRAQFQSTAESNTEAAEGIQISDKVSVEPSSVSNLQLEKLD-- 332

Query: 364 SIPSMME----CSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFP 419
            + +M      CSE++   +S + S S+ LSDIFETDS+TE   K E +PLYLD+F+ FP
Sbjct: 333 KVGAMFNDNNSCSEDEAHMDSDLDSYSDKLSDIFETDSDTEDLVKEE-KPLYLDEFNNFP 391

Query: 420 VQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 474
            Q+D + +DFEEHL+QIS +S+N   + KD D   FDEVD++FLRAAS LKK+++
Sbjct: 392 EQSDGDTDDFEEHLQQISYNSKN---MEKDADLPKFDEVDQIFLRAASFLKKKRK 443

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|9279724|dbj|BAB01314.1| unnamed protein product [Arabidopsis thaliana]

 Score =  444 bits (1143), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 277/493 (56%), Positives = 329/493 (66%), Gaps = 79/493 (16%)

Query: 4    RVLVSSASMALR-KSPQFKILLSKFHIFKPFSYNKYPFQRISSMVDVLCKAFGPCYGLKR 62
            RV  S+ASM LR KS Q   L S   +F  F+       R  S  +++CK       L +
Sbjct: 680  RVSTSAASMLLRRKSRQLGFLASSSPLFSSFN----SMNRTISSCNIVCKV------LHK 729

Query: 63   FSIEGRLW---------IHSAPLRHYIEKVVEKQESSENSSSADGAGVAKVKRKKLKGKR 113
             S+   +W          HS P R   +  + K   SENSSS DG    K+KRKKLKGKR
Sbjct: 730  ESLTRPMWNVSFLRSSSFHSTPARETGDDDISK---SENSSSQDGDSCTKLKRKKLKGKR 786

Query: 114  AVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPE 173
            AVVRWLK FR+KKKKE+ERMT+EEKIL KLRKARKKEER++E +KK+EP ES+E THDPE
Sbjct: 787  AVVRWLKFFRWKKKKEFERMTSEEKILNKLRKARKKEERLMETMKKLEPSESAETTHDPE 846

Query: 174  ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKE 233
            ILTPEEHFY+LKMG KCKNYVPVGRRGIYQGVILNMHLHWKKHQTL+V++KTF+ +EVKE
Sbjct: 847  ILTPEEHFYYLKMGLKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLQVVIKTFTPDEVKE 906

Query: 234  IAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKVLLIFLIHTLYK 293
            IA ELARLTGGIVL++HE NTIIMYRGKNY QPPTEIMSPRITL RKK            
Sbjct: 907  IAVELARLTGGIVLDVHEGNTIIMYRGKNYVQPPTEIMSPRITLPRKK------------ 954

Query: 294  YAECIIFFFLLLTALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQ 353
                         ALDKSK RD LRAV+KYIP+LEQEL+LL+AQAET+ +  +   +D Q
Sbjct: 955  -------------ALDKSKCRDALRAVRKYIPRLEQELQLLQAQAETKRDYTNVKVDDNQ 1001

Query: 354  --NTELDKPDFGSIPSMMECSENDPTTESL-------MASDSEDLSDIFETDSETETEEK 404
              + EL K        ++E SE     E         +A+DS DLSDIFETDSE E + K
Sbjct: 1002 ERSEELKK--------IIERSEECLEDEQEEDEAGLELATDS-DLSDIFETDSELE-DAK 1051

Query: 405  AELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDED---SSHFDEVDKM 461
             E RPL+L++F+KFP  N+ E EDF         D   AKS G++ D   S +FDEVDKM
Sbjct: 1052 TE-RPLFLEEFEKFPAINNREDEDFG--------DLGKAKSEGEENDDDKSPNFDEVDKM 1102

Query: 462  FLRAASLLKKQKR 474
            FLRAA LLKK++R
Sbjct: 1103 FLRAAFLLKKKRR 1115

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	474
TAIR|locus:2094438	444	LOH1 "LAG One Homologue 1" [Ar	0.563	0.601	0.596	3.1e-108
TAIR|locus:2056558	372	AT2G28480 [Arabidopsis thalian	0.320	0.408	0.506	4.6e-40
TAIR|locus:2091458	491	AT3G27550 [Arabidopsis thalian	0.343	0.331	0.460	9.4e-40
TAIR|locus:2123276	343	AT4G13070 [Arabidopsis thalian	0.341	0.472	0.508	9.9e-39
TAIR|locus:2094558	881	CFM3A "CRM family member 3A" [	0.327	0.175	0.371	1.1e-19
TAIR|locus:2096662	1011	CFM2 "CRM family member 2" [Ar	0.339	0.159	0.335	1.9e-17
TAIR|locus:2094997	848	EMB1865 "embryo defective 1865	0.305	0.170	0.377	1.1e-16
TAIR|locus:2181372	720	CRS1 "ortholog of maize chloro	0.322	0.212	0.317	1.1e-11

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

 Score = 804 (288.1 bits), Expect = 3.1e-108, Sum P(2) = 3.1e-108
 Identities = 173/290 (59%), Positives = 200/290 (68%)

Query:     4 RVLVSSASMALR-KSPQFKILLSKFHIFKPFSYNKYPFQRISSMVDVLCKAFGPCYGLKR 62
             RV  S+ASM LR KS Q   L S   +F   S+N     R  S  +++CK       L +
Sbjct:     9 RVSTSAASMLLRRKSRQLGFLASSSPLFS--SFNS--MNRTISSCNIVCKV------LHK 58

Query:    63 FSIEGRLW---------IHSAPLRHYIEKVVEKQESSENSSSADXXXXXXXXXXXXXXXX 113
              S+   +W          HS P R   +  + K   SENSSS D                
Sbjct:    59 ESLTRPMWNVSFLRSSSFHSTPARETGDDDISK---SENSSSQDGDSCTKLKRKKLKGKR 115

Query:   114 XXXXWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPE 173
                 WLK FR+KKKKE+ERMT+EEKIL KLRKARKKEER++E +KK+EP ES+E THDPE
Sbjct:   116 AVVRWLKFFRWKKKKEFERMTSEEKILNKLRKARKKEERLMETMKKLEPSESAETTHDPE 175

Query:   174 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKE 233
             ILTPEEHFY+LKMG KCKNYVPVGRRGIYQGVILNMHLHWKKHQTL+V++KTF+ +EVKE
Sbjct:   176 ILTPEEHFYYLKMGLKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLQVVIKTFTPDEVKE 235

Query:   234 IAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKVL 283
             IA ELARLTGGIVL++HE NTIIMYRGKNY QPPTEIMSPRITL RKK L
Sbjct:   236 IAVELARLTGGIVLDVHEGNTIIMYRGKNYVQPPTEIMSPRITLPRKKAL 285

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

GO:0042761 "very long-chain fatty acid biosynthetic process" evidence=IGI

GO:0050291 "sphingosine N-acyltransferase activity" evidence=IGI

TAIR|locus:2056558 AT2G28480 [Arabidopsis thaliana (taxid:3702)]

 Score = 390 (142.3 bits), Expect = 4.6e-40, Sum P(2) = 4.6e-40
 Identities = 79/156 (50%), Positives = 108/156 (69%)

Query:   126 KKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLK 185
             KKK++  + AEE+I YKL KA+ KE  ++E LK+ E  +       P  +T EE FY  K
Sbjct:   117 KKKKF--VNAEERIKYKLEKAKIKEALLIERLKRYEVAKVQGPEVRPHEITGEERFYLKK 174

Query:   186 MGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGI 245
             MG+K  NYVP+GRRG++ GVILNMHLHWKKH+T+KVI       +V++ A ELA+L+GG+
Sbjct:   175 MGQKRSNYVPIGRRGVFGGVILNMHLHWKKHETVKVICNNSKPGQVQQYAEELAKLSGGV 234

Query:   246 VLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKK 281
              + I  ++TII YRGK Y QP  ++MSP  TLS+K+
Sbjct:   235 PVNIIGDDTIIFYRGKGYVQP--QVMSPIDTLSKKR 268

GO:0003723 "RNA binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2091458 AT3G27550 [Arabidopsis thaliana (taxid:3702)]

 Score = 391 (142.7 bits), Expect = 9.4e-40, Sum P(2) = 9.4e-40
 Identities = 76/165 (46%), Positives = 112/165 (67%)

Query:   119 LKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPE 178
             L+  R  KK + + MT EE+++Y L++A+KK   +++ LKK +  E     HDPE+ T E
Sbjct:    36 LREIRRAKKLKKKLMTDEERLIYNLKRAKKKVALLLQKLKKYDLPELPSPVHDPELFTSE 95

Query:   179 EHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAEL 238
             +   F K+G K KNYVPVG RG++ GV+ NMH+HWK H+T++V    F  E++KE+A+ +
Sbjct:    96 QVQAFKKIGFKNKNYVPVGVRGVFGGVVQNMHMHWKFHETVQVCCDNFPKEKIKEMASMI 155

Query:   239 ARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKVL 283
             ARL+GG+V+ IH   TIIM+RG+NY QP   I  P  TL+++K L
Sbjct:   156 ARLSGGVVINIHNVKTIIMFRGRNYRQPKNLI--PVNTLTKRKAL 198

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2123276 AT4G13070 [Arabidopsis thaliana (taxid:3702)]

 Score = 414 (150.8 bits), Expect = 9.9e-39, P = 9.9e-39
 Identities = 85/167 (50%), Positives = 116/167 (69%)

Query:   119 LKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIE-PKESSEMTHDPEILTP 177
             L+ +R K KK+      E +I YKL KA++KEE ++E L+K + PK  +E  +DPE LT 
Sbjct:   126 LRFYRLKAKKKMNSPNPEVRIRYKLEKAKRKEEWLIEKLRKYDVPKSPAE-PYDPESLTE 184

Query:   178 EEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAE-EVKEIAA 236
             EE  Y  + G K KN+V VGRRG++ GV+LN+HLHWKKH+T+KVI K  +   +V E A 
Sbjct:   185 EEQHYLKRTGEKRKNFVLVGRRGVFGGVVLNLHLHWKKHETVKVICKPCNKPGQVHEYAE 244

Query:   237 ELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKVL 283
             ELARL+ GIV+++   NTI++YRGKNY +P  E+MSP  TLS+ K L
Sbjct:   245 ELARLSKGIVIDVKPNNTIVLYRGKNYVRP--EVMSPVDTLSKDKAL 289

GO:0003723 "RNA binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2094558 CFM3A "CRM family member 3A" [Arabidopsis thaliana (taxid:3702)]

 Score = 265 (98.3 bits), Expect = 1.1e-19, Sum P(2) = 1.1e-19
 Identities = 61/164 (37%), Positives = 98/164 (59%)

Query:   127 KKEYERMTAEE---KILYKLRKARKKEERIVEGLKKIEP-KESSEMTHDPEILTPEEHFY 182
             K+E E +  E    K+  KL  A +K  +   GL K+E   + +E   DPE +T EE F 
Sbjct:   586 KQEVEILRHENLVRKLERKLAFAERKLLKAERGLAKVEVCLKPAEQREDPESITDEERFM 645

Query:   183 FLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLT 242
             F K+G K K ++ +GRRG++ G + NMHLHWK  + +K+IVK  + + VK++A  L   +
Sbjct:   646 FRKLGLKMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKAKTFDGVKKVALALEAES 705

Query:   243 GGIVLEIHEEN---TIIMYRGKNYAQPPTEIMSPRITLSRKKVL 283
             GGI++ I +      II+YRG++Y +P   ++ P+  L+++K L
Sbjct:   706 GGILVSIDKVTKGYAIIVYRGQDYKRPT--MLRPKNLLTKRKAL 747

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;IDA

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

GO:0048316 "seed development" evidence=IGI

TAIR|locus:2096662 CFM2 "CRM family member 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 245 (91.3 bits), Expect = 1.9e-17, Sum P(2) = 1.9e-17
 Identities = 57/170 (33%), Positives = 97/170 (57%)

Query:   121 HFRYKKKKEYERMTAE---EKILYKLRKARKKEERIVEGLKKIEPKESSEMTH-DPEILT 176
             H +  + K  +R + E   EK   KL  A +K+    + L  +E +ES +++  D E +T
Sbjct:   521 HIQTHQMKSRQRNSPEAILEKTSMKLSMALEKKANAEKVLADLENRESPQLSDIDKEGIT 580

Query:   177 PEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAA 236
              +E +   K+G K K ++ +GRRG++ G I NMHLHWK  + +K+I   +S E   ++A 
Sbjct:   581 NDEKYMLRKIGLKMKPFLLLGRRGVFDGTIENMHLHWKYRELVKIICNEYSIEAAHKVAE 640

Query:   237 ELARLTGGIVLEIHEEN---TIIMYRGKNYAQPPTEIMSPRITLSRKKVL 283
              L   +GGI++ +   +    II+YRGKNY +P  + + P+  LS+++ L
Sbjct:   641 ILEAESGGILVAVEMVSKGYAIIVYRGKNYERP--QCLRPQTLLSKREAL 688

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;RCA

GO:0000372 "Group I intron splicing" evidence=IMP

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

TAIR|locus:2094997 EMB1865 "embryo defective 1865" [Arabidopsis thaliana (taxid:3702)]

 Score = 241 (89.9 bits), Expect = 1.1e-16, Sum P(2) = 1.1e-16
 Identities = 57/151 (37%), Positives = 89/151 (58%)

Query:   137 EKILYKLRKARKKEERIVEGLKKIEPKE-SSEMTHDPEILTPEEHFYFLKMGRKCKNYVP 195
             ++I +KL  A+ K +R  + L KIE     +   +D E+++ EE   F K+G K K Y+P
Sbjct:   614 KRIQHKLNLAQSKFQRAEKLLSKIEASMIPNGPDYDQEVISEEERAMFRKVGLKMKAYLP 673

Query:   196 VGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN-- 253
             +G RG++ GVI NMHLHWK  + +K+I K  +   V+E A  L   +GG+++ I +    
Sbjct:   674 IGIRGVFDGVIENMHLHWKHRELVKLISKQKNQAFVEETARLLEYESGGVLVAIEKVPKG 733

Query:   254 -TIIMYRGKNYAQPPTEIMSPRITLSRKKVL 283
               +I YRGKNY +P +  + PR  L++ K L
Sbjct:   734 FALIYYRGKNYRRPIS--LRPRNLLTKAKAL 762

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;IDA

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

GO:0009737 "response to abscisic acid stimulus" evidence=IDA

GO:0006655 "phosphatidylglycerol biosynthetic process" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0016117 "carotenoid biosynthetic process" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

TAIR|locus:2181372 CRS1 "ortholog of maize chloroplast splicing factor CRS1" [Arabidopsis thaliana (taxid:3702)]

 Score = 191 (72.3 bits), Expect = 1.1e-11, P = 1.1e-11
 Identities = 52/164 (31%), Positives = 85/164 (51%)

Query:   125 KKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFL 184
             K + E E  + E K+     K  K    + +     +P E  +   D EILT EE     
Sbjct:   525 KARLEKELKSQEHKLSILKSKIEKSNMELFKLNSLWKPSEGDD---DIEILTNEERECLR 581

Query:   185 KMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIV--KTFSAEEVKEIAAELARLT 242
             ++G K  + + +GRRG++ GV+  +H HWK  +  KVI   K FS   V   A  L   +
Sbjct:   582 RIGLKMNSSLVLGRRGVFFGVMEGLHQHWKHREVAKVITMQKLFS--RVVYTAKALETES 639

Query:   243 GGIVLEIH---EENTIIMYRGKNYAQPPTEIMSPRITLSRKKVL 283
              G+++ I    E + I++YRGKNY +P +++M+  + L+++K L
Sbjct:   640 NGVLISIEKLKEGHAILIYRGKNYKRPSSKLMAQNL-LTKRKAL 682


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.318   0.134   0.381    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      474       441   0.00089  118 3  11 22  0.40    34
                                                     34  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  8
  No. of states in DFA:  606 (64 KB)
  Total size of DFA:  263 KB (2140 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  43.93u 0.12s 44.05t   Elapsed:  00:00:02
  Total cpu time:  43.93u 0.12s 44.05t   Elapsed:  00:00:02
  Start:  Mon May 20 22:52:00 2013   End:  Mon May 20 22:52:02 2013

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

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

---

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)
Q67XL4	Y3544_ARATH	No assigned EC number	0.5699	0.8881	0.9481	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: gw1.XIV.4068.1 hypothetical protein (388 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	474
smart01103	84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	4e-21
pfam01985	84	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	1e-19

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

 Score = 87.1 bits (217), Expect = 4e-21
 Identities = 28/85 (32%), Positives = 46/85 (54%), Gaps = 1/85 (1%)

Query: 175 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEI 234
           LT ++  Y   +    K  V +G+ G+ +GV+  +    +KH+ +KV V     E+ KEI
Sbjct: 1   LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEI 60

Query: 235 AAELARLTGGIVLEIHEENTIIMYR 259
           A ELA  TG  +++     TI++YR
Sbjct: 61  AEELAEETGAELVQ-VIGKTIVLYR 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

 Score = 82.9 bits (206), Expect = 1e-19
 Identities = 28/85 (32%), Positives = 46/85 (54%), Gaps = 1/85 (1%)

Query: 175 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEI 234
           LT ++  Y   +    K  V +G+ G+ +GV+  +    +KH+ +KV V     E+ KEI
Sbjct: 1   LTGKQRRYLRSLAHHLKPVVQIGKNGLTEGVVEEIDEALEKHELIKVKVLGNDREDRKEI 60

Query: 235 AAELARLTGGIVLEIHEENTIIMYR 259
           A ELA  TG  +++     TI++YR
Sbjct: 61  AEELAEKTGAELVQ-VIGRTIVLYR 84

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	474
PRK10343	97	RNA-binding protein YhbY; Provisional	99.95
TIGR00253	95	RNA_bind_YhbY putative RNA-binding protein, YhbY f	99.95
PF01985	84	CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR	99.94
KOG1990	564	consensus Poly(A)-specific exoribonuclease PARN [R	99.94
COG1534	97	Predicted RNA-binding protein containing KH domain	99.93
KOG1990	564	consensus Poly(A)-specific exoribonuclease PARN [R	97.7

>PRK10343 RNA-binding protein YhbY; Provisional

Probab=99.95  E-value=2.1e-27  Score=202.03  Aligned_cols=89  Identities=21%  Similarity=0.340  Sum_probs=86.4

Q ss_pred             CCCCHHHHHHHHhcccCCCceeeeCCCCCcHHHHHHHHHHHHhcCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEEeC
Q 011932          173 EILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE  252 (474)
Q Consensus       173 E~LT~EERk~LRKlAhkLKPVV~IGKrGVTDgVIeeIh~ALK~HELVKVKVkq~s~ed~keIAeeLAe~SGGeLVQViIG  252 (474)
                      ++||++||++||++||+|+|+|+||++||||+|+++|+++|++||||||++.+++.+++++++++|++.|||++||+ ||
T Consensus         1 m~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~-IG   79 (97)
T PRK10343          1 MNLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQV-IG   79 (97)
T ss_pred             CCCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEee-eC
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999998 69


Q ss_pred             CEEEEEeCCC
Q 011932          253 NTIIMYRGKN  262 (474)
Q Consensus       253 ~tIILYRGKN  262 (474)
                      +++||||++.
T Consensus        80 ~~~vlYR~~~   89 (97)
T PRK10343         80 KTLVLYRPTK   89 (97)
T ss_pred             cEEEEEecCC
Confidence            9999999875

>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family

Probab=99.95  E-value=3.4e-27  Score=199.68  Aligned_cols=87  Identities=28%  Similarity=0.369  Sum_probs=84.9

Q ss_pred             CCHHHHHHHHhcccCCCceeeeCCCCCcHHHHHHHHHHHHhcCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEEeCCE
Q 011932          175 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT  254 (474)
Q Consensus       175 LT~EERk~LRKlAhkLKPVV~IGKrGVTDgVIeeIh~ALK~HELVKVKVkq~s~ed~keIAeeLAe~SGGeLVQViIG~t  254 (474)
                      ||++||++||++||+|+|+|+||++|||++||++|+++|++||||||++.+++.++++++|++|++.|||++||+ +|++
T Consensus         1 Lt~kqr~~Lr~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~-iG~~   79 (95)
T TIGR00253         1 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQV-IGKT   79 (95)
T ss_pred             CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEE-EccE
Confidence            799999999999999999999999999999999999999999999999999999999999999999999999998 5999


Q ss_pred             EEEEeCCC
Q 011932          255 IIMYRGKN  262 (474)
Q Consensus       255 IILYRGKN  262 (474)
                      +||||++.
T Consensus        80 ~vlYR~~~   87 (95)
T TIGR00253        80 IVLYRPTK   87 (95)
T ss_pred             EEEEecCC
Confidence            99999874

A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.

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

Probab=99.94  E-value=1.1e-26  Score=190.15  Aligned_cols=84  Identities=36%  Similarity=0.522  Sum_probs=75.0

Q ss_pred             CCHHHHHHHHhcccCCCceeeeCCCCCcHHHHHHHHHHHHhcCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEEeCCE
Q 011932          175 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT  254 (474)
Q Consensus       175 LT~EERk~LRKlAhkLKPVV~IGKrGVTDgVIeeIh~ALK~HELVKVKVkq~s~ed~keIAeeLAe~SGGeLVQViIG~t  254 (474)
                      ||++|+++||++||+|+|+|+||++|||++|+++|+++|++||||||+|.+++.++++++|++|++.|||++||+ +|++
T Consensus         1 Lt~ke~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~-iG~~   79 (84)
T PF01985_consen    1 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQV-IGRT   79 (84)
T ss_dssp             --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEE-ETTE
T ss_pred             CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEE-ECCE
Confidence            799999999999999999999999999999999999999999999999999999999999999999999999997 6999


Q ss_pred             EEEEe
Q 011932          255 IIMYR  259 (474)
Q Consensus       255 IILYR  259 (474)
                      +||||
T Consensus        80 ~vlyR   84 (84)
T PF01985_consen   80 IVLYR   84 (84)
T ss_dssp             EEEEE
T ss_pred             EEEEC
Confidence            99998

The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. 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 [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.

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

Probab=99.94  E-value=4.7e-27  Score=246.66  Aligned_cols=214  Identities=41%  Similarity=0.580  Sum_probs=194.1

Q ss_pred             hhhhhhhhhhhhhhhhhhhhhh-----hHhhhccChH---HHHHHHHHHHHHHHHHHHHhhcccCCC-CCCCCCCCCCCC
Q 011932          105 KRKKLKGKRAVVRWLKHFRYKK-----KKEYERMTAE---EKILYKLRKARKKEERIVEGLKKIEPK-ESSEMTHDPEIL  175 (474)
Q Consensus       105 ~r~k~k~k~a~~~~lk~~r~k~-----kke~~~m~~e---~ri~~KL~~AkkK~er~~e~LaKiE~~-~paEp~~DpE~L  175 (474)
                      ++.-..-.++.++|.+.+.+..     +.+.+++..+   +.+.+++..+++|++++...|++++.+ .|++..+|++.+
T Consensus       304 ~~t~~e~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~  383 (564)
T KOG1990|consen  304 KATLLELARAKAKKEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESI  383 (564)
T ss_pred             hhhHHHHHHHhcccccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhc
Confidence            3344455667778887777765     7777788776   788899999999999999999999987 899999999999


Q ss_pred             CHHHHHHHHhcccCCCceeeeCCCCCcHHHHHHHHHHHHhcCeeeEEecCCCH-HHHHHHHHHHHHHhCCeEEEEE---e
Q 011932          176 TPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSA-EEVKEIAAELARLTGGIVLEIH---E  251 (474)
Q Consensus       176 T~EERk~LRKlAhkLKPVV~IGKrGVTDgVIeeIh~ALK~HELVKVKVkq~s~-ed~keIAeeLAe~SGGeLVQVi---I  251 (474)
                      |.+++.+++++|.+|++++.+|++|+++|||.++|.||++||++||+|+.... .+++..|..++..+|+.+|++.   .
T Consensus       384 t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~  463 (564)
T KOG1990|consen  384 TEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPK  463 (564)
T ss_pred             ChHHHHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCc
Confidence            99999999999999999999999999999999999999999999999998665 9999999999999999999976   4


Q ss_pred             CCEEEEEeCCCCCCCCCCCCCCCcchhhhhhHHHHHhhhhchhhHHHHHHHHHHHHHHHHHHHhhHHHHHhhHHHHHHHH
Q 011932          252 ENTIIMYRGKNYAQPPTEIMSPRITLSRKKVLLIFLIHTLYKYAECIIFFFLLLTALDKSKYRDGLRAVKKYIPKLEQEL  331 (474)
Q Consensus       252 G~tIILYRGKNY~rP~~eim~P~~~Ltkrk~~~~~~~~~~~~~~~~~~~~~~~~~AL~rS~~~qr~~alk~~I~~le~~i  331 (474)
                      |..|+.|||+||.+|.+  |+|.++|+||+                         |+.+++++|+.+|+++||+.+++++
T Consensus       464 ~~ai~~yr~k~y~~p~~--l~P~~~l~~~k-------------------------~~~~~~~~~~~~a~~~~i~~~~~~~  516 (564)
T KOG1990|consen  464 GYAIIAYRGKNYDRPTS--LRPRNLLSRRK-------------------------ALERSLEEQRKEALKSHISDLEQEI  516 (564)
T ss_pred             hhhHHHhhhhhccCCcc--cCchhhhcccC-------------------------CccccHHHHHHHHHhhhcchhhhhH
Confidence            66699999999999976  99999999999                         9999999999999999999999999


Q ss_pred             HHHHHHhccccccc
Q 011932          332 ELLRAQAETRSENR  345 (474)
Q Consensus       332 e~l~~~~~~~~~~~  345 (474)
                      +++++++.......
T Consensus       517 e~~~~~~~~~~~~~  530 (564)
T KOG1990|consen  517 EQLQASVEAMPAIN  530 (564)
T ss_pred             HHhhcchhcccccc
Confidence            99999988755543

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

Probab=99.93  E-value=1.5e-25  Score=191.26  Aligned_cols=91  Identities=26%  Similarity=0.429  Sum_probs=86.5

Q ss_pred             CCCHHHHHHHHhcccCCCceeeeCCCCCcHHHHHHHHHHHHhcCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEEeCC
Q 011932          174 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  253 (474)
Q Consensus       174 ~LT~EERk~LRKlAhkLKPVV~IGKrGVTDgVIeeIh~ALK~HELVKVKVkq~s~ed~keIAeeLAe~SGGeLVQViIG~  253 (474)
                      +||++|+++||+.||+++|+|+||++|||++||.+|+++|++||||||++.+++.++++++|+.|++.+||.+||+ +|+
T Consensus         1 ~Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqv-iG~   79 (97)
T COG1534           1 MLTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQV-IGK   79 (97)
T ss_pred             CCcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeee-eee
Confidence            6999999999999999999999999999999999999999999999999999999999999999999999999998 599


Q ss_pred             EEEEEeCCCCCCC
Q 011932          254 TIIMYRGKNYAQP  266 (474)
Q Consensus       254 tIILYRGKNY~rP  266 (474)
                      ++|||| .+...+
T Consensus        80 ~~vlyr-~~~e~~   91 (97)
T COG1534          80 TLVLYR-ESKEKR   91 (97)
T ss_pred             EEEEEe-cCcccc
Confidence            999999 444444

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

Probab=97.70  E-value=2.6e-05  Score=83.69  Aligned_cols=152  Identities=21%  Similarity=0.290  Sum_probs=128.5

Q ss_pred             hhhhhhhhhhhhhhHhhhccChHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCCCCCCCCCCCHHHHHHHHhcccCCCce
Q 011932          114 AVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNY  193 (474)
Q Consensus       114 a~~~~lk~~r~k~kke~~~m~~e~ri~~KL~~AkkK~er~~e~LaKiE~~~paEp~~DpE~LT~EERk~LRKlAhkLKPV  193 (474)
                      +..-|+-.++..++.-...|.++..-.|-..........+.+.+..+..|...-+...+..||..+.-++|.+|-...|+
T Consensus       114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~  193 (564)
T KOG1990|consen  114 QAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLPPH  193 (564)
T ss_pred             hhhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCChhhhhhHHHHHHHHhccccccc
Confidence            44557777777888888888888666665555666677888888888888778888889999999999999999999999


Q ss_pred             eeeCCCCCcHHHHHHHHHHHHhcCeeeEEecCCC-HHHHHHHHHHH--HHHhCCeEEEEEeCCEEEEEeCCCCCCC
Q 011932          194 VPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFS-AEEVKEIAAEL--ARLTGGIVLEIHEENTIIMYRGKNYAQP  266 (474)
Q Consensus       194 V~IGKrGVTDgVIeeIh~ALK~HELVKVKVkq~s-~ed~keIAeeL--Ae~SGGeLVQViIG~tIILYRGKNY~rP  266 (474)
                      +.+|.++.-+++...|..+|..|+..|+-+...- ......+|..+  -..+|+.||.. -|..+++||++||-.|
T Consensus       194 ~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~h-N~~~dv~y~~~~Fl~~  268 (564)
T KOG1990|consen  194 FALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVLH-NKLLDVMYRYKNFLSP  268 (564)
T ss_pred             ceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEee-ccceeeeeehhhcccc
Confidence            9999999999999999999999999998886643 44556788888  88999999964 6889999999999885

---

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	Length	Definition	E-value
Query	474
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	2e-10
1rq8_A	104	Conserved hypothetical protein; structural genomic	1e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-07

>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

 Score = 56.1 bits (136), Expect = 2e-10
 Identities = 20/106 (18%), Positives = 41/106 (38%), Gaps = 10/106 (9%)

Query: 175 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEI 234
           L+ ++  +   +       V +G  G+ +GV+  +      H+ +KV V     E  + I
Sbjct: 3   LSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLI 62

Query: 235 AAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRK 280
              + R T    ++    + +++YR              +I L RK
Sbjct: 63  INAIVRETKAAQVQTI-GHILVLYRPSE---------EAKIQLPRK 98

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

 Score = 54.6 bits (132), Expect = 1e-09
 Identities = 20/108 (18%), Positives = 45/108 (41%), Gaps = 9/108 (8%)

Query: 174 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKE 233
           +LT ++  Y   +         +G+ GI + +I  +    +  + +KV V   + ++ KE
Sbjct: 1   MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKE 60

Query: 234 IAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKK 281
           +A  L+  T   +++    + I++YR     +         I L  + 
Sbjct: 61  LAETLSEATRSELVQ-VIGSMIVIYR-----ESKEN---KEIELPLEH 99

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

 Score = 56.0 bits (134), Expect = 2e-08
 Identities = 82/576 (14%), Positives = 157/576 (27%), Gaps = 185/576 (32%)

Query: 20  FKILLSK-FHIFKPF-----SYNKYPFQRISSMVDVLCKAFGPCYGLKRFSIE-GRLWIH 72
           F  LLSK   + + F       N Y F  + S +    +   P    + +  +  RL+  
Sbjct: 68  FWTLLSKQEEMVQKFVEEVLRIN-YKF--LMSPIKTEQR--QPSMMTRMYIEQRDRLYND 122

Query: 73  SAPLRHY----IEKVVEKQESSENSSSAD--------GAG----VAKVKR-KKLKGKRAV 115
           +     Y    ++  ++ +++      A         G+G       V    K++ K   
Sbjct: 123 NQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDF 182

Query: 116 -VRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKE----ERIVEGLKKIEPKESSEMTH 170
            + WL   +     E   +   +K+LY++             I   +  I+ +    +  
Sbjct: 183 KIFWLN-LKNCNSPE-TVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKS 240

Query: 171 --------------DPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKH 216
                         + +       F        CK  + +  R  ++ V   +      H
Sbjct: 241 KPYENCLLVLLNVQNAKAW---NAFNL-----SCK--ILLTTR--FKQVTDFLSAATTTH 288

Query: 217 QTLKVIVKTFSAEEVKEIAA--------ELAR--------LTGGIVLEIHEENTIIMYRG 260
            +L     T + +EVK +          +L R            I   I +         
Sbjct: 289 ISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLA----TW 344

Query: 261 KNYAQPPTEIMSPRITLSRKKVLLIFLIHTLYK--YAECIIFFFLLLTALDKSKYRDGLR 318
            N+     + ++  I  S     L  L    Y+  +    +F                  
Sbjct: 345 DNWKHVNCDKLTTIIESS-----LNVLEPAEYRKMFDRLSVF-------------PPS-- 384

Query: 319 AVKKYIPKLEQELELLRAQAETRSE--------NRSDAAEDVQNTELDKPDFGSIPSM-- 368
                IP     L L+                   S   +  + + +      SIPS+  
Sbjct: 385 -AH--IP--TILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTI------SIPSIYL 433

Query: 369 -MECS-ENDPTTESLM--------ASDSEDLSDIFETD----------SETE-TEEKAEL 407
            ++   EN+      +          DS+DL   +                E  E     
Sbjct: 434 ELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLF 493

Query: 408 RPLYLD-----------------------------QFDKFPVQNDEEHE----DFEEHLR 434
           R ++LD                              +  +   ND ++E       + L 
Sbjct: 494 RMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLP 553

Query: 435 QISIDSRNAKSLG------KDEDSSHFDEVDKMFLR 464
           +I  +   +K           ED + F+E  K   R
Sbjct: 554 KIEENLICSKYTDLLRIALMAEDEAIFEEAHKQVQR 589

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

 Score = 51.0 bits (121), Expect = 7e-07
 Identities = 56/324 (17%), Positives = 93/324 (28%), Gaps = 88/324 (27%)

Query: 209 MHLHWKK--HQTLKVIVKTF-------------SAEEVKEIAAELARLTGG----IVLEI 249
               +K          V  F             S EE+  I      ++G       L  
Sbjct: 14  HQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLS 73

Query: 250 HEENTIIMYRG----KNYAQPPTEIMSPRITLSRKKVLLIFLIHTLYKYAECIIFFFLLL 305
            +E  +  +       NY      +MSP              I T  +    +   +  +
Sbjct: 74  KQEEMVQKFVEEVLRINYKF----LMSP--------------IKTEQRQPSMMTRMY--I 113

Query: 306 TALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENR------------SDAAEDVQ 353
              D+  Y D     K  + +L+  L+L +A  E R                  A +   
Sbjct: 114 EQRDRL-YNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCL 172

Query: 354 NTEL-DKPDFGSI--PSMMECSENDPTTESL------MASDSEDLSDIFETDSETETEEK 404
           + ++  K DF  I   ++  C+  +   E L      +  +    SD            +
Sbjct: 173 SYKVQCKMDFK-IFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQ 231

Query: 405 AELRPLYLDQFDKFP--------VQNDEEHEDFEEH---L---RQISI-DSRNAK----- 444
           AELR L   +   +         VQN +    F      L   R   + D  +A      
Sbjct: 232 AELRRLLKSK--PYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHI 289

Query: 445 SLGKDEDSSHFDEVDKMFLRAASL 468
           SL     +   DEV  + L+    
Sbjct: 290 SLDHHSMTLTPDEVKSLLLKYLDC 313

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	474
1rq8_A	104	Conserved hypothetical protein; structural genomic	99.96
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	99.95

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

Probab=99.96  E-value=9.5e-29  Score=210.93  Aligned_cols=91  Identities=20%  Similarity=0.354  Sum_probs=87.5

Q ss_pred             CCCHHHHHHHHhcccCCCceeeeCCCCCcHHHHHHHHHHHHhcCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEEeCC
Q 011932          174 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  253 (474)
Q Consensus       174 ~LT~EERk~LRKlAhkLKPVV~IGKrGVTDgVIeeIh~ALK~HELVKVKVkq~s~ed~keIAeeLAe~SGGeLVQViIG~  253 (474)
                      |||++||++||++||+|+|+|+||++|||++|+++|+++|++||||||+|.+++.++++++|++||+.|||++||+ ||+
T Consensus         1 mLt~kqr~~LR~~ah~Lkpvv~IGK~GlTe~vi~ei~~aL~~hELIKVkvl~~~~~d~~e~a~~la~~t~a~vVq~-IG~   79 (104)
T 1rq8_A            1 MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQV-IGS   79 (104)
T ss_dssp             CCCHHHHHHHHHHTTSSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEE-ETT
T ss_pred             CCCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCHHHHHHHHHHHHHHhCCEEEEE-ECC
Confidence            7999999999999999999999999999999999999999999999999999999999999999999999999997 599


Q ss_pred             EEEEEeCCCCCCC
Q 011932          254 TIIMYRGKNYAQP  266 (474)
Q Consensus       254 tIILYRGKNY~rP  266 (474)
                      ++||||++. ..|
T Consensus        80 ~~VLYR~~~-~~~   91 (104)
T 1rq8_A           80 MIVIYRESK-ENK   91 (104)
T ss_dssp             EEEEEECCC-SCC
T ss_pred             EEEEEeCCC-CCC
Confidence            999999886 444

>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

Probab=99.95  E-value=2.9e-28  Score=205.47  Aligned_cols=88  Identities=18%  Similarity=0.317  Sum_probs=85.7

Q ss_pred             CCCHHHHHHHHhcccCCCceeeeCCCCCcHHHHHHHHHHHHhcCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEEeCC
Q 011932          174 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  253 (474)
Q Consensus       174 ~LT~EERk~LRKlAhkLKPVV~IGKrGVTDgVIeeIh~ALK~HELVKVKVkq~s~ed~keIAeeLAe~SGGeLVQViIG~  253 (474)
                      .||++||++||++||+|+|+|+||++|||++|+++|++||++||||||+|.+++.++++++|++|++.|||++||+ ||+
T Consensus         2 ~Lt~kqr~~Lr~~ah~l~pvv~IGk~GlT~~vi~ei~~aL~~~ELIKVkvl~~~~~~~~e~a~~la~~t~a~~Vq~-IG~   80 (98)
T 1jo0_A            2 TLSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQT-IGH   80 (98)
T ss_dssp             CCCHHHHHHHHHHHTTBCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEEE-ETT
T ss_pred             CCCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHHCCeEEEEEeCCCHHHHHHHHHHHHHHhCCEEEEE-ECC
Confidence            6999999999999999999999999999999999999999999999999999999999999999999999999997 699


Q ss_pred             EEEEEeCCC
Q 011932          254 TIIMYRGKN  262 (474)
Q Consensus       254 tIILYRGKN  262 (474)
                      ++||||++.
T Consensus        81 ~~vLyR~~~   89 (98)
T 1jo0_A           81 ILVLYRPSE   89 (98)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEEccCC
Confidence            999999874

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	474
d1rq8a_	96	d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphy	1e-18
d1jo0a_	97	d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i	3e-18

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

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 = 78.6 bits (194), Expect = 1e-18
 Identities = 18/90 (20%), Positives = 41/90 (45%), Gaps = 1/90 (1%)

Query: 174 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKE 233
           +LT ++  Y   +         +G+ GI + +I  +    +  + +KV V   + ++ KE
Sbjct: 1   MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKE 60

Query: 234 IAAELARLTGGIVLEIHEENTIIMYRGKNY 263
           +A  L+  T   +++    + I++YR    
Sbjct: 61  LAETLSEATRSELVQ-VIGSMIVIYRESKE 89

>d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]} Length = 97

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]

 Score = 77.4 bits (191), Expect = 3e-18
 Identities = 19/100 (19%), Positives = 40/100 (40%), Gaps = 5/100 (5%)

Query: 175 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEI 234
           L+ ++  +   +       V +G  G+ +GV+  +      H+ +KV V     E  + I
Sbjct: 3   LSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLI 62

Query: 235 AAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPR 274
              + R T    ++    + +++YR         +I  PR
Sbjct: 63  INAIVRETKAAQVQ-TIGHILVLYRPS----EEAKIQLPR 97

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	474
d1jo0a_	97	YhbY homologue HI1333 {Haemophilus influenzae [Tax	99.96
d1rq8a_	96	Hypothetical protein SAV1595 {Staphylococcus aureu	99.95

>d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]}

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=99.96  E-value=1e-28  Score=204.62  Aligned_cols=88  Identities=18%  Similarity=0.317  Sum_probs=85.6

Q ss_pred             CCCHHHHHHHHhcccCCCceeeeCCCCCcHHHHHHHHHHHHhcCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEEeCC
Q 011932          174 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  253 (474)
Q Consensus       174 ~LT~EERk~LRKlAhkLKPVV~IGKrGVTDgVIeeIh~ALK~HELVKVKVkq~s~ed~keIAeeLAe~SGGeLVQViIG~  253 (474)
                      +||++||++||++||+|+|+|+||++|||++|+.+|++||++||||||+|.+++.++++++|++|++.|||.+||+ +|+
T Consensus         2 tLt~kqr~~LR~~ah~lkp~v~IGk~Glt~~vi~ei~~al~~~ELIKvki~~~~~~~~~~~~~~l~~~t~~~vV~~-iG~   80 (97)
T d1jo0a_           2 TLSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQT-IGH   80 (97)
T ss_dssp             CCCHHHHHHHHHHHTTBCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEEE-ETT
T ss_pred             CCCHHHHHHHHHHhcCCCCEEEECCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHHHhCCEEEEE-ECC
Confidence            6999999999999999999999999999999999999999999999999999999999999999999999999987 699


Q ss_pred             EEEEEeCCC
Q 011932          254 TIIMYRGKN  262 (474)
Q Consensus       254 tIILYRGKN  262 (474)
                      ++||||+++
T Consensus        81 ~~ilYR~~~   89 (97)
T d1jo0a_          81 ILVLYRPSE   89 (97)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEEcCCC
Confidence            999999865

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

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]

Probab=99.95  E-value=1.5e-28  Score=203.32  Aligned_cols=89  Identities=20%  Similarity=0.351  Sum_probs=86.7

Q ss_pred             CCCHHHHHHHHhcccCCCceeeeCCCCCcHHHHHHHHHHHHhcCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEEeCC
Q 011932          174 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  253 (474)
Q Consensus       174 ~LT~EERk~LRKlAhkLKPVV~IGKrGVTDgVIeeIh~ALK~HELVKVKVkq~s~ed~keIAeeLAe~SGGeLVQViIG~  253 (474)
                      |||++||++||++||+|+|+|+||++|||++|+.+|+.+|+.||||||+|.+++.++++++|++||+.|||++||+ +|+
T Consensus         1 mLt~kqr~~LR~~ah~l~p~v~IGk~Glt~~vi~ei~~~l~~~ELIKvk~~~~~~~~~~~~~~~l~~~t~a~~V~~-iG~   79 (96)
T d1rq8a_           1 MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQV-IGS   79 (96)
T ss_dssp             CCCHHHHHHHHHHTTSSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEE-ETT
T ss_pred             CcCHHHHHHHHHHhcCCCCEEEECCCCCCHHHHHHHHHHHHhCCeeEEEecCCCHHHHHHHHHHHHHHhCCEEEEE-ECC
Confidence            7999999999999999999999999999999999999999999999999999999999999999999999999997 699


Q ss_pred             EEEEEeCCCC
Q 011932          254 TIIMYRGKNY  263 (474)
Q Consensus       254 tIILYRGKNY  263 (474)
                      ++||||++++
T Consensus        80 ~~vlyR~~~~   89 (96)
T d1rq8a_          80 MIVIYRESKE   89 (96)
T ss_dssp             EEEEEECCCS
T ss_pred             EEEEEeCCCC
Confidence            9999998765