Citrus Sinensis ID: 013147

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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-------45
Protein Sequence
MGGRVLVSSASMALRKSPQFKILLSKFHIFKPFSYNKYPFQRISSMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVVEKQESSENSSSADGAGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR
Secondary Structure (PSIPRED)
cccccccccHHHHHHccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccEEEccEEcccccEEEcccccccccccccccHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHcccEEEEEEcccHHHHHHHHHHHHHHHccEEEEEEEccEEEEEEcccccccccccccccccccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccccHHHHHHHHHHcccccccccccccccccccHHHHHHccHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccHEHHHHHHHHHccHHHcHEEcccccccccccccccccccccccEEEEEEccccccEEEccccccEEEEcccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHcHHcccccccccccccHHHHHHHHHHHccccEEEEEEccccHHHHHHHHHHHHHHcccEEEEEccccEEEEEEcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHccccHHccccHcccccHcHcccccccccccccccccccccccccccccccccccccccccHHHHccccccccccHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MGGRVLVSSAsmalrkspqfkillskfhifkpfsynkypfqrISSMVDVLCKafgpcyglkrfsiegrlwihsapLRHYIEKVVEKqessensssadgaGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLkkiepkessemthdpeiltpeeHFYFLKMGrkcknyvpvgrrgiYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIImyrgknyaqppteimspritlsrkkaldkskyrDGLRAVKKYIPKLEQELELLRAQAETrsenrsdaaedvqnteldkpdfgsipsmmecsendptteslmasdsedlsdifetdseteteekaelrplyldqfdkfpvqndeehEDFEEHLRQISIDsrnakslgkdedsshfdEVDKMFLRAASLLKKQKR
Flexible Loop (DISEMBL)
mggrvlvssasmalrksPQFKILLSKFHIFKPFSYNKYPFQRISSMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVVekqessensssadgagvakvkrkklkgkravvrwlkhfrykkkkeyermtaeeKILYklrkarkkeeriveglkkiepkessemthdpeiltPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIImyrgknyaqppteimspritlsrkkaldkskyrdglravKKYIPKLEQELELLRAQAetrsenrsdaaedvqnteldkpdfgsipSMMECSENDPTTESLMASDSEDLSDIFETDseteteekaelrplyldQFDKFPVQNDEEHEDFEEHLRQisidsrnakslgkdedsshfdevDKMFLRAASLLKKQKR
Low Complexity Region (SEG)
MGGRVLVSSASMALRKSPQFKILLSKFHIFKPFSYNKYPFQRISSMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVVEKQESSENSSSADgagvakvkrkklkgkravvrWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKleqelellraqaeTRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR
Disordered region (IsUnstruct)
******************QFKILLSKFHIFKPFSYNKYPFQRISSMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVV*************************KGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKL*********************************PEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYA***************************LRAVKKYIP*****************************************************************************************************************************************************
Disordered Region (DISOPRED)
********SASMALRKSPQFKILLSKFHIFK****************DVLCKAFGPCYGLKRFSIEGRLWIH*********************************************************************KLRKARKKEER*************************EEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLS**********************KLEQELEL**************************************************************************************************************************DEVDKMFLRAASLL*****
Disordered Region (DISEMBL)
*********ASMALRKSPQFKILLSKFHIFKPFSYNKYPFQRISSMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKV****************************KRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQ***************QNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDI************AELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRN************FDEVDKMFLRAASLLKKQKR
Disordered Region (DISPRO)
************ALRKSPQFKILLSKFHIFKPFSYNKYPFQRISSMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLR************************AKVKR*KLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPK*****THDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSE**************************************************************ELRPLYLDQFDKFPV****EHEDFEEHLRQISID************SSHFDEVDKMFLRAASLLKK***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGGRVLVSSASMALRKSPQFKILLSKFHIFKPFSYNKYPFQRISSMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVVEKQESSENSSSADGAGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGxxxxxxxxxxxxxxxxxxxxxxxxxxxxRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR
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	449	2.2.26 [Sep-21-2011]
Q67XL4	444	Uncharacterized CRM domai	yes	no	0.937	0.948	0.600	1e-127
Q9FYT6	715	Chloroplastic group IIA i	N/A	no	0.320	0.201	0.393	3e-17
Q6YYA3	725	Chloroplastic group IIA i	no	no	0.320	0.198	0.373	2e-15
Q9LF10	720	Chloroplastic group IIA i	no	no	0.322	0.201	0.328	8e-14
Q5VMQ5	701	CRS2-associated factor 1,	no	no	0.200	0.128	0.307	8e-07
Q84N49	674	CRS2-associated factor 1,	N/A	no	0.233	0.155	0.318	5e-06
Q6Z4U2	428	CRS2-associated factor 1,	no	no	0.200	0.210	0.268	2e-05
Q84N48	611	CRS2-associated factor 2,	N/A	no	0.336	0.247	0.236	0.0003
Q0J7J7	366	CRS2-associated factor 2,	no	no	0.162	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 =  457 bits (1175), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 277/461 (60%), Positives = 328/461 (71%), Gaps = 40/461 (8%)

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 IAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLR 293
           IA ELARLTGGIVL++HE NTIIMYRGKNY QPPTEIMSPRITL RKKALDKSK RD LR
Sbjct: 236 IAVELARLTGGIVLDVHEGNTIIMYRGKNYVQPPTEIMSPRITLPRKKALDKSKCRDALR 295

Query: 294 AVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQ--NTELDKPDFGSIPSMMECSENDP 351
           AV+KYIP+LEQEL+LL+AQAET+ +  +   +D Q  + EL K    S   + +  E D 
Sbjct: 296 AVRKYIPRLEQELQLLQAQAETKRDYTNVKVDDNQERSEELKKIIERSEECLEDEQEEDE 355

Query: 352 TTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQI 411
               L A+DS DLSDIFETDSE E + K E RPL+L++F+KFP  N+ E EDF       
Sbjct: 356 AGLEL-ATDS-DLSDIFETDSELE-DAKTE-RPLFLEEFEKFPAINNREDEDFG------ 405

Query: 412 SIDSRNAKSLGKDED---SSHFDEVDKMFLRAASLLKKQKR 449
             D   AKS G++ D   S +FDEVDKMFLRAA LLKK++R
Sbjct: 406 --DLGKAKSEGEENDDDKSPNFDEVDKMFLRAAFLLKKKRR 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 = 90.1 bits (222), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 59/150 (39%), Positives = 84/150 (56%), Gaps = 6/150 (4%)

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 MYRGKNYAQPPTEIMSPRITLSRKKALDKS 286
           +YRGKNY +P     S    L++++AL +S
Sbjct: 649 LYRGKNYRRPAKSSFSN--LLTKREALRRS 676

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 = 84.3 bits (207), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 56/150 (37%), Positives = 84/150 (56%), Gaps = 6/150 (4%)

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 MYRGKNYAQPPTEIMSPRITLSRKKALDKS 286
           +YRGKNY +P     +P   L++++AL +S
Sbjct: 651 LYRGKNYRRPTKS--APSNLLTKREALQRS 678

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 = 79.0 bits (193), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 49/149 (32%), Positives = 83/149 (55%), Gaps = 4/149 (2%)

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

Query: 226 FSAEEVKEIAAELARLTGGIVLEIH---EENTIIMYRGKNYAQPPTEIMSPRITLSRKKA 282
                V   A  L   + G+++ I    E + I++YRGKNY +P +++M+  + L+++KA
Sbjct: 623 KLFSRVVYTAKALETESNGVLISIEKLKEGHAILIYRGKNYKRPSSKLMAQNL-LTKRKA 681

Query: 283 LDKSKYRDGLRAVKKYIPKLEQELELLRA 311
           L +S     L ++K +  + E+ +E L+ 
Sbjct: 682 LQRSVVMQRLGSLKFFAYQRERAIEDLKV 710

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 = 8e-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 = 52.8 bits (125), Expect = 5e-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	449
255572670	458	conserved hypothetical protein [Ricinus	0.933	0.914	0.654	1e-150
224132018	413	predicted protein [Populus trichocarpa]	0.870	0.946	0.658	1e-149
225448146	401	PREDICTED: uncharacterized CRM domain-co	0.850	0.952	0.694	1e-145
356501797	382	PREDICTED: uncharacterized CRM domain-co	0.826	0.971	0.686	1e-140
356498434	383	PREDICTED: uncharacterized CRM domain-co	0.808	0.947	0.685	1e-137
297739537	331	unnamed protein product [Vitis vinifera]	0.703	0.954	0.719	1e-131
449458069	500	PREDICTED: uncharacterized CRM domain-co	0.861	0.774	0.594	1e-130
357439975	443	CRM domain-containing protein, putative	0.915	0.927	0.604	1e-130
9279724	1115	unnamed protein product [Arabidopsis tha	0.922	0.371	0.591	1e-126
79417439	444	uncharacterized CRM domain-containing pr	0.937	0.948	0.600	1e-126

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

 Score =  539 bits (1388), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 290/443 (65%), Positives = 342/443 (77%), Gaps = 24/443 (5%)

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 NYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRS 321
           NY+QPPTEIMSPRITLSRKKALDKSKYRDGLRAV+ YIP+LEQ+LELL+ Q+  ++E  S
Sbjct: 258 NYSQPPTEIMSPRITLSRKKALDKSKYRDGLRAVRNYIPRLEQDLELLKVQSMGKAECGS 317

Query: 322 DAAEDVQNTELDKPDFGSIPSMM---------------ECSENDPTTESLMASDSEDLSD 366
            +AE+   T+ D  + G +PS                 ECSE +   +  M SDSEDLSD
Sbjct: 318 ASAEETLYTD-DGAESGGVPSTPLENSEKLKKITDGQEECSEEESPMDLGMLSDSEDLSD 376

Query: 367 IFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDED 426
           IFETDS+TETE+K + RPLYL++F KFP+Q +EE EDFEEHLRQ+S+DSR  +S  KD D
Sbjct: 377 IFETDSDTETEDKVK-RPLYLEEFKKFPIQGNEEPEDFEEHLRQLSVDSRKVESSEKDSD 435

Query: 427 SSHFDEVDKMFLRAASLLKKQKR 449
              FDEVD++FLRAASLLKK+KR
Sbjct: 436 IPSFDEVDRLFLRAASLLKKKKR 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 =  534 bits (1375), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 278/422 (65%), Positives = 333/422 (78%), Gaps = 31/422 (7%)

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 FSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDK 285
           F+ EEVKEIAAELAR TGGIVL+IHEENTIIMYRGKNY+QPPTEIMSPR+TLSRKKALDK
Sbjct: 181 FTPEEVKEIAAELARFTGGIVLDIHEENTIIMYRGKNYSQPPTEIMSPRVTLSRKKALDK 240

Query: 286 SKYRDGLRAVKKYIPKLEQELELLRAQAETRS-----ENRSDAAEDVQNTE-----LDKP 335
           SK RDGLRA+++YIP+L+Q+LELL A+A  ++     E+RS +++ ++N+E     +D+ 
Sbjct: 241 SKCRDGLRALRRYIPRLQQDLELLHARAGGKTDIDGAESRSISSKQLENSEKLKEIIDRQ 300

Query: 336 DFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPV 395
           D G        SE+ P T+  +ASDSEDLSDIFETDS+ +TEE ++ RPLYL++F+KF V
Sbjct: 301 DEG--------SEDGPDTDLGIASDSEDLSDIFETDSDADTEETSK-RPLYLEEFEKFSV 351

Query: 396 QNDEEHEDFEEHLRQISIDSRNAKSLGK--------DEDSSHFDEVDKMFLRAASLLKKQ 447
           + D E EDFEEHLRQIS+ S+   + GK        D DS  FDEVD+MFLRAASLLK++
Sbjct: 352 EADGEPEDFEEHLRQISLGSKKGVTSGKDVDIPTGVDVDSPSFDEVDRMFLRAASLLKRK 411

Query: 448 KR 449
           KR
Sbjct: 412 KR 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 =  520 bits (1339), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 277/399 (69%), Positives = 323/399 (80%), Gaps = 17/399 (4%)

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 VLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQE 305
           VL+IHEENTIIMYRGKNY+QPPTEIMSPRITLSRKKALDKSKYRDGLRAV+KYIP+LE +
Sbjct: 184 VLDIHEENTIIMYRGKNYSQPPTEIMSPRITLSRKKALDKSKYRDGLRAVRKYIPRLEGD 243

Query: 306 LELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSMM---------------ECSEND 350
           LELL+AQA+ ++EN+++A ED QN  +D  +   I ++                E SE +
Sbjct: 244 LELLQAQAKMQAENKTEAVEDFQNANIDSINSQGISNLQPENSDKLRELLAGNNESSEEE 303

Query: 351 PTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQ 410
             T+S   S SE LSDIFE+DS+T+T+EKAE + LYL++F+KFPV++D E EDFEEHLRQ
Sbjct: 304 SLTDSGTESCSEALSDIFESDSDTDTKEKAE-QLLYLNEFEKFPVESDGEPEDFEEHLRQ 362

Query: 411 ISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 449
           IS DSR AKSL KD D    DEVD+MFLRAASLLKK++R
Sbjct: 363 ISADSRKAKSLEKDADLPQLDEVDQMFLRAASLLKKKRR 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 =  503 bits (1294), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 263/383 (68%), Positives = 311/383 (81%), Gaps = 12/383 (3%)

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 IVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQ 304
           IVL+IHE+NTIIMYRGKNY+QPPTEIMSPR++LSRKKALDKSKYRD LRAV+++IP+LEQ
Sbjct: 188 IVLDIHEDNTIIMYRGKNYSQPPTEIMSPRVSLSRKKALDKSKYRDALRAVRRHIPRLEQ 247

Query: 305 ELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDL 364
           ELE+LRAQ ++ +E+ +DAAE +QN          +   + C+E++    S + SDS+ L
Sbjct: 248 ELEILRAQFKSSAESNTDAAEAIQNNR------ERMNDNIGCTEDETDMNSELDSDSDKL 301

Query: 365 SDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKD 424
           SDIFETDS+TE   K E +PLYLD+FD FP Q+D E  DFEEHLRQ+S+ S+N   + K+
Sbjct: 302 SDIFETDSDTENFIKEE-KPLYLDEFDNFPEQSDGEMNDFEEHLRQMSLKSKN---MEKE 357

Query: 425 EDSSHFDEVDKMFLRAASLLKKQ 447
           ++    DEVDK+FL+A S LKK+
Sbjct: 358 DNLPKLDEVDKIFLQATSFLKKK 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 =  493 bits (1269), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 264/385 (68%), Positives = 312/385 (81%), Gaps = 22/385 (5%)

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 YRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRS 317
           YRGKNY+QPPTEIMSPR++LSRKKALDKSKYRD LRAV++YIP+LEQELE+LRAQ ++ +
Sbjct: 181 YRGKNYSQPPTEIMSPRVSLSRKKALDKSKYRDALRAVRRYIPRLEQELEILRAQFKSSA 240

Query: 318 ENRSDAAEDVQNTELDKPDFGSIPS-----------MMEC----SENDPTTESLMASDSE 362
           E+ +DAAE +QN+  +  + GSI +           MM      +E++    S + SDS+
Sbjct: 241 ESNTDAAEAIQNSGRESIESGSISNFQLQNSYKDREMMNVNIGSTEDETDMNSELDSDSD 300

Query: 363 DLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLG 422
            LSDIFETDS+TE   K E +PLYLD+FD FP Q+D E  DFEEH+RQ+S+ S+N   + 
Sbjct: 301 KLSDIFETDSDTENFVKEE-KPLYLDEFDNFPEQSDGEMNDFEEHMRQMSLKSKN---ME 356

Query: 423 KDEDSSHFDEVDKMFLRAASLLKKQ 447
           KD++    DEVDK+FL+A S LKK+
Sbjct: 357 KDDNLPKLDEVDKIFLQATSFLKKK 381

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  476 bits (1224), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 239/332 (71%), Positives = 276/332 (83%), Gaps = 16/332 (4%)

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 NTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQ 312
           NTIIMYRGKNY+QPPTEIMSPRITLSRKKALDKSKYRDGLRAV+KYIP+LE +LELL+AQ
Sbjct: 121 NTIIMYRGKNYSQPPTEIMSPRITLSRKKALDKSKYRDGLRAVRKYIPRLEGDLELLQAQ 180

Query: 313 AETRSENRSDAAEDVQNTELDKPDFGSIPSMM---------------ECSENDPTTESLM 357
           A+ ++EN+++A ED QN  +D  +   I ++                E SE +  T+S  
Sbjct: 181 AKMQAENKTEAVEDFQNANIDSINSQGISNLQPENSDKLRELLAGNNESSEEESLTDSGT 240

Query: 358 ASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRN 417
            S SE LSDIFE+DS+T+T+EKAE + LYL++F+KFPV++D E EDFEEHLRQIS DSR 
Sbjct: 241 ESCSEALSDIFESDSDTDTKEKAE-QLLYLNEFEKFPVESDGEPEDFEEHLRQISADSRK 299

Query: 418 AKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 449
           AKSL KD D    DEVD+MFLRAASLLKK++R
Sbjct: 300 AKSLEKDADLPQLDEVDQMFLRAASLLKKKRR 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 =  472 bits (1214), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 251/422 (59%), Positives = 316/422 (74%), Gaps = 35/422 (8%)

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 KTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKAL 283
           KTFS EEVKEIAAELARLTGG+VL+IHEE+TIIMYRGKNY+QPPTEIMSPR++LSRKKAL
Sbjct: 260 KTFSPEEVKEIAAELARLTGGLVLDIHEEDTIIMYRGKNYSQPPTEIMSPRVSLSRKKAL 319

Query: 284 DKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSM 343
           DKSKYRDGLRAV+K+IPKLEQEL  L++QA+   ++  ++ E +Q T  D     +I S+
Sbjct: 320 DKSKYRDGLRAVRKHIPKLEQELRFLQSQAKLNCKSNGESVEHMQETVDDTNKSKAISSL 379

Query: 344 M----------------ECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYL 387
                            + S++    ++ M+SDSEDLSD+FETD ++E +EK E +PL+L
Sbjct: 380 NLENLDDSSNAMRSVSKDWSDDSSPIDTGMSSDSEDLSDMFETDIDSEADEKME-KPLFL 438

Query: 388 DQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQ 447
            +F+ F  + ++E ED  + LRQIS+DS+ AK L  D +S  FDEVD++FLR+ASLLKK+
Sbjct: 439 KEFENFAAETEDEIEDLSDQLRQISMDSKQAKILENDVNSPEFDEVDRLFLRSASLLKKK 498

Query: 448 KR 449
           +R
Sbjct: 499 RR 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 =  470 bits (1210), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 272/450 (60%), Positives = 331/450 (73%), Gaps = 39/450 (8%)

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 MYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETR 316
           MYRGKNY+QPPTEIMSPR+TL RKKALDKSKYRDGLRAV++YIPKLEQELE+LRAQ ++ 
Sbjct: 240 MYRGKNYSQPPTEIMSPRVTLPRKKALDKSKYRDGLRAVRRYIPKLEQELEILRAQFQST 299

Query: 317 SENRSDAAEDVQ-------------NTELDKPDFGSIPSMME----CSENDPTTESLMAS 359
           +E+ ++AAE +Q             N +L+K D   + +M      CSE++   +S + S
Sbjct: 300 AESNTEAAEGIQISDKVSVEPSSVSNLQLEKLD--KVGAMFNDNNSCSEDEAHMDSDLDS 357

Query: 360 DSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAK 419
            S+ LSDIFETDS+TE   K E +PLYLD+F+ FP Q+D + +DFEEHL+QIS +S+N  
Sbjct: 358 YSDKLSDIFETDSDTEDLVKEE-KPLYLDEFNNFPEQSDGDTDDFEEHLQQISYNSKN-- 414

Query: 420 SLGKDEDSSHFDEVDKMFLRAASLLKKQKR 449
            + KD D   FDEVD++FLRAAS LKK+++
Sbjct: 415 -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 =  458 bits (1179), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 277/468 (59%), Positives = 329/468 (70%), Gaps = 54/468 (11%)

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  IAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLR 293
            IA ELARLTGGIVL++HE NTIIMYRGKNY QPPTEIMSPRITL RKKALDKSK RD LR
Sbjct: 907  IAVELARLTGGIVLDVHEGNTIIMYRGKNYVQPPTEIMSPRITLPRKKALDKSKCRDALR 966

Query: 294  AVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQ--NTELDKPDFGSIPSMMECSENDP 351
            AV+KYIP+LEQEL+LL+AQAET+ +  +   +D Q  + EL K        ++E SE   
Sbjct: 967  AVRKYIPRLEQELQLLQAQAETKRDYTNVKVDDNQERSEELKK--------IIERSEECL 1018

Query: 352  TTESL-------MASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDF 404
              E         +A+DS DLSDIFETDSE E + K E RPL+L++F+KFP  N+ E EDF
Sbjct: 1019 EDEQEEDEAGLELATDS-DLSDIFETDSELE-DAKTE-RPLFLEEFEKFPAINNREDEDF 1075

Query: 405  EEHLRQISIDSRNAKSLGKDED---SSHFDEVDKMFLRAASLLKKQKR 449
                     D   AKS G++ D   S +FDEVDKMFLRAA LLKK++R
Sbjct: 1076 G--------DLGKAKSEGEENDDDKSPNFDEVDKMFLRAAFLLKKKRR 1115

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|79417439|ref|NP_189171.2| uncharacterized CRM domain-containing protein [Arabidopsis thaliana] gi|75116513|sp|Q67XL4.1|Y3544_ARATH RecName: Full=Uncharacterized CRM domain-containing protein At3g25440, chloroplastic; Flags: Precursor gi|51971805|dbj|BAD44567.1| unknown protein [Arabidopsis thaliana] gi|332643490|gb|AEE77011.1| uncharacterized CRM domain-containing protein [Arabidopsis thaliana]

 Score =  457 bits (1175), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 277/461 (60%), Positives = 328/461 (71%), Gaps = 40/461 (8%)

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 IAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLR 293
           IA ELARLTGGIVL++HE NTIIMYRGKNY QPPTEIMSPRITL RKKALDKSK RD LR
Sbjct: 236 IAVELARLTGGIVLDVHEGNTIIMYRGKNYVQPPTEIMSPRITLPRKKALDKSKCRDALR 295

Query: 294 AVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQ--NTELDKPDFGSIPSMMECSENDP 351
           AV+KYIP+LEQEL+LL+AQAET+ +  +   +D Q  + EL K    S   + +  E D 
Sbjct: 296 AVRKYIPRLEQELQLLQAQAETKRDYTNVKVDDNQERSEELKKIIERSEECLEDEQEEDE 355

Query: 352 TTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQI 411
               L A+DS DLSDIFETDSE E + K E RPL+L++F+KFP  N+ E EDF       
Sbjct: 356 AGLEL-ATDS-DLSDIFETDSELE-DAKTE-RPLFLEEFEKFPAINNREDEDFG------ 405

Query: 412 SIDSRNAKSLGKDED---SSHFDEVDKMFLRAASLLKKQKR 449
             D   AKS G++ D   S +FDEVDKMFLRAA LLKK++R
Sbjct: 406 --DLGKAKSEGEENDDDKSPNFDEVDKMFLRAAFLLKKKRR 444

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	449
TAIR|locus:2094438	444	LOH1 "LAG One Homologue 1" [Ar	0.930	0.941	0.543	6.1e-110
TAIR|locus:2091458	491	AT3G27550 [Arabidopsis thalian	0.403	0.368	0.448	2.8e-42
TAIR|locus:2123276	343	AT4G13070 [Arabidopsis thalian	0.400	0.524	0.491	4e-42
TAIR|locus:2056558	372	AT2G28480 [Arabidopsis thalian	0.556	0.672	0.379	8.4e-42
TAIR|locus:2094558	881	CFM3A "CRM family member 3A" [	0.554	0.282	0.3	2.7e-22
TAIR|locus:2094997	848	EMB1865 "embryo defective 1865	0.501	0.265	0.329	8.7e-20
TAIR|locus:2096662	1011	CFM2 "CRM family member 2" [Ar	0.710	0.315	0.25	1.2e-19
TAIR|locus:2181372	720	CRS1 "ortholog of maize chloro	0.369	0.230	0.316	3.3e-13

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

 Score = 1086 (387.4 bits), Expect = 6.1e-110, P = 6.1e-110
 Identities = 252/464 (54%), Positives = 302/464 (65%)

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 IAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLR 293
             IA ELARLTGGIVL++HE NTIIMYRGKNY QPPTEIMSPRITL RKKALDKSK RD LR
Sbjct:   236 IAVELARLTGGIVLDVHEGNTIIMYRGKNYVQPPTEIMSPRITLPRKKALDKSKCRDALR 295

Query:   294 AVKKYIPKXXXXXXXXXXXXXTRSENRSDAAEDVQ--NTELDKPDFGSIPSMMECSENDP 351
             AV+KYIP+             T+ +  +   +D Q  + EL K     I    EC E++ 
Sbjct:   296 AVRKYIPRLEQELQLLQAQAETKRDYTNVKVDDNQERSEELKK----IIERSEECLEDEQ 351

Query:   352 TTESL---MASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHL 408
               +     +A+DS DLSDIFETDSE E + K E RPL+L++F+KFP  N+ E EDF    
Sbjct:   352 EEDEAGLELATDS-DLSDIFETDSELE-DAKTE-RPLFLEEFEKFPAINNREDEDFG--- 405

Query:   409 RQISIDSRNAKSLGKDED---SSHFDEVDKMFLRAASLLKKQKR 449
                  D   AKS G++ D   S +FDEVDKMFLRAA LLKK++R
Sbjct:   406 -----DLGKAKSEGEENDDDKSPNFDEVDKMFLRAAFLLKKKRR 444

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:2091458 AT3G27550 [Arabidopsis thaliana (taxid:3702)]

 Score = 415 (151.1 bits), Expect = 2.8e-42, Sum P(2) = 2.8e-42
 Identities = 82/183 (44%), Positives = 122/183 (66%)

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 ARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKY 298
             ARL+GG+V+ IH   TIIM+RG+NY QP   I  P  TL+++KAL K+++   L + K  
Sbjct:   156 ARLSGGVVINIHNVKTIIMFRGRNYRQPKNLI--PVNTLTKRKALFKARFEQALESQKLN 213

Query:   299 IPK 301
             I K
Sbjct:   214 IKK 216

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

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

 Score = 446 (162.1 bits), Expect = 4.0e-42, P = 4.0e-42
 Identities = 91/185 (49%), Positives = 126/185 (68%)

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 ELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVK 296
             ELARL+ GIV+++   NTI++YRGKNY +P  E+MSP  TLS+ KAL+K +Y   L    
Sbjct:   245 ELARLSKGIVIDVKPNNTIVLYRGKNYVRP--EVMSPVDTLSKDKALEKYRYEQSLEHTS 302

Query:   297 KYIPK 301
             ++I K
Sbjct:   303 EFIEK 307

GO:0003723 "RNA binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

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

 Score = 443 (161.0 bits), Expect = 8.4e-42, P = 8.4e-42
 Identities = 98/258 (37%), Positives = 148/258 (57%)

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 VLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKXXXX 305
              + I  ++TII YRGK Y QP  ++MSP  TLS+K+A +KSKY   L +V+ +I      
Sbjct:   235 PVNIIGDDTIIFYRGKGYVQP--QVMSPIDTLSKKRAYEKSKYEQSLESVRHFIAIAEKE 292

Query:   306 XXXXXXXXXTRSE-NRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDL 364
                         + N  +    + ++  +          + CS+ D ++E     + E+L
Sbjct:   293 LELYYRHVALYDDPNNRNPLSILDDSPSESRQHHENEFFLSCSDTDSSSED--EDEDEEL 350

Query:   365 SDIFETDSETETEEKAEL 382
              ++ +  S + +  K EL
Sbjct:   351 CEL-DNGSSSSSSAKEEL 367

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 = 284 (105.0 bits), Expect = 2.7e-22, P = 2.7e-22
 Identities = 78/260 (30%), Positives = 132/260 (50%)

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---TIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYI 299
             GGI++ I +      II+YRG++Y +P   ++ P+  L+++KAL +S        + K+I
Sbjct:   706 GGILVSIDKVTKGYAIIVYRGQDYKRPT--MLRPKNLLTKRKALARSIELQRREGLLKHI 763

Query:   300 PKXXXXXXXXXXXXXTRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMAS 359
                             + E  +D  ++    +LD     S     E  ++D   E+    
Sbjct:   764 -STMQAKAKQLRAEIEQMEKVTDKGDEELYNKLDMAYASSDEETDEEDDDDAFPETYAEG 822

Query:   360 DSEDLSDIFETD-SETETEE 378
             +  +  +I   + SETE ++
Sbjct:   823 EDGEEGEILAGELSETEDKD 842

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

 Score = 263 (97.6 bits), Expect = 8.7e-20, P = 8.7e-20
 Identities = 78/237 (32%), Positives = 125/237 (52%)

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 -TIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKXXXXXXXXXXX 312
               +I YRGKNY +P +  + PR  L++ KAL +S       A+ ++I +           
Sbjct:   734 FALIYYRGKNYRRPIS--LRPRNLLTKAKALKRSIAMQRHEALSQHISELERTIEQMQSQ 791

Query:   313 XXTRSENRSDAAEDVQNTELDKPDFGSIPSMMECSEND--PTT-ESLMASDSE-DLS 365
                 S+N S +  + +N E D  D       +E +E+D   T  ES ++S  E D+S
Sbjct:   792 LT--SKNPSYSESEWENDEDDDDDEEEEKDDVEDNESDWDETDGESAISSIEEADMS 846

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

 Score = 263 (97.6 bits), Expect = 1.2e-19, P = 1.2e-19
 Identities = 84/336 (25%), Positives = 155/336 (46%)

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---TIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLR 293
              L   +GGI++ +   +    II+YRGKNY +P  + + P+  LS+++AL +S      +
Sbjct:   641 ILEAESGGILVAVEMVSKGYAIIVYRGKNYERP--QCLRPQTLLSKREALKRSVEAQRRK 698

Query:   294 AVKKYIPKXXXXXXXXXXXXXTRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTT 353
             ++K ++ K               S   ++   D +++ +   +     +  + +E +   
Sbjct:   699 SLKLHVLKLSNNIEELNRQLVEDSAT-NETWSDGESSNMMVEE----ETENQHTEPEKAR 753

Query:   354 ESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISI 413
             E +    S DLS     +   E + + E+ PL     +    Q DE      +     S+
Sbjct:   754 EKIELGYSSDLSVPSSGEENWEDDSEGEVDPLTTSSQE---YQEDESESASSQRHEGNSL 810

Query:   414 DSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 449
             DS    S+  +  S++        L   S L   ++
Sbjct:   811 DSTANLSVFAETGSANASSFHDRSLPHNSFLNANRK 846

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

 Score = 204 (76.9 bits), Expect = 3.3e-13, P = 3.3e-13
 Identities = 56/177 (31%), Positives = 92/177 (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---EENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVK 296
              G+++ I    E + I++YRGKNY +P +++M+  + L+++KAL +S     L ++K
Sbjct:   640 NGVLISIEKLKEGHAILIYRGKNYKRPSSKLMAQNL-LTKRKALQRSVVMQRLGSLK 695


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        0.315   0.132   0.373    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      449       416   0.00081  118 3  11 22  0.43    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:  602 (64 KB)
  Total size of DFA:  253 KB (2136 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:  43.56u 0.10s 43.66t   Elapsed:  00:00:02
  Total cpu time:  43.56u 0.10s 43.66t   Elapsed:  00:00:02
  Start:  Mon May 20 22:45:30 2013   End:  Mon May 20 22:45:32 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	0.6008	0.9376	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

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	Length	Definition	E-value
Query	449
smart01103	84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	3e-21
pfam01985	84	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	9e-20

>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 = 3e-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 = 9e-20
 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	449
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=1.3e-27  Score=202.58  Aligned_cols=89  Identities=21%  Similarity=0.340  Sum_probs=86.2

Q ss_pred             CCCCHHHHHHHHhhhccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeC
Q 013147          173 EILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE  252 (449)
Q Consensus       173 E~LT~EQRk~LRKlGhkLKPVV~IGKrGVTdgVIeeIh~Awk~HELVKVKVkqns~ed~keiAeeLee~SGGeLVQViIG  252 (449)
                      ++||++||+|||++||+|+|+|+||++|||++|+++|+.+|++||||||++.+++++++++++++|++.|||++||+ ||
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            46999999999999999999999999999999999999999999999999999999999999999999999999997 69


Q ss_pred             cEEEEEeCCC
Q 013147          253 NTIIMYRGKN  262 (449)
Q Consensus       253 ~tIILYRGKN  262 (449)
                      +++||||++.
T Consensus        80 ~~~vlYR~~~   89 (97)
T PRK10343         80 KTLVLYRPTK   89 (97)
T ss_pred             cEEEEEecCC
Confidence            9999999864

>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family

Probab=99.95  E-value=2.1e-27  Score=200.26  Aligned_cols=87  Identities=28%  Similarity=0.369  Sum_probs=84.7

Q ss_pred             CCHHHHHHHHhhhccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCcE
Q 013147          175 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT  254 (449)
Q Consensus       175 LT~EQRk~LRKlGhkLKPVV~IGKrGVTdgVIeeIh~Awk~HELVKVKVkqns~ed~keiAeeLee~SGGeLVQViIG~t  254 (449)
                      ||++||++||++||+|+|+|+||++|||++||++|+++|++||||||++.++++++++++|++|++.|||++||+ ||++
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            799999999999999999999999999999999999999999999999999999999999999999999999997 6999


Q ss_pred             EEEEeCCC
Q 013147          255 IIMYRGKN  262 (449)
Q Consensus       255 IILYRGKN  262 (449)
                      +||||++.
T Consensus        80 ~vlYR~~~   87 (95)
T TIGR00253        80 IVLYRPTK   87 (95)
T ss_pred             EEEEecCC
Confidence            99999863

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=8.9e-27  Score=190.15  Aligned_cols=84  Identities=36%  Similarity=0.522  Sum_probs=74.9

Q ss_pred             CCHHHHHHHHhhhccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCcE
Q 013147          175 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT  254 (449)
Q Consensus       175 LT~EQRk~LRKlGhkLKPVV~IGKrGVTdgVIeeIh~Awk~HELVKVKVkqns~ed~keiAeeLee~SGGeLVQViIG~t  254 (449)
                      ||++|+++||++||+|+|+|+||++|||++|+++|+.+|++||||||+|.+++.++++++|+.|++.|||++||+ +|++
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            799999999999999999999999999999999999999999999999999999999999999999999999986 6999


Q ss_pred             EEEEe
Q 013147          255 IIMYR  259 (449)
Q Consensus       255 IILYR  259 (449)
                      +||||
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=3.6e-27  Score=246.94  Aligned_cols=209  Identities=41%  Similarity=0.592  Sum_probs=188.4

Q ss_pred             hhhhhhhhhhhhhhhhhh-----hHHhhccChH---HHHHHHHHHHHHHHHHHHHhhcccCCC-CCCCCCCCCCCCCHHH
Q 013147          109 LKGKRAVVRWLKHFRYKK-----KKEYERMTAE---EKILYKLRKARKKEERIVEGLKKIEPK-ESSEMTHDPEILTPEE  179 (449)
Q Consensus       109 ~~~k~a~~~~l~~~r~~~-----kk~~~~~~~e---~ri~~KL~~A~kK~e~~~e~L~K~E~~-~paEp~~DpE~LT~EQ  179 (449)
                      ..-.+++++|.+.+.+..     +.+.+.+..+   +.+.+++..+++|++++...|++++.+ .|++..+|++.+|.++
T Consensus       308 ~e~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee  387 (564)
T KOG1990|consen  308 LELARAKAKKEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEE  387 (564)
T ss_pred             HHHHHHhcccccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHH
Confidence            344556667776666654     6666667655   788899999999999999999999986 8999999999999999


Q ss_pred             HHHHHhhhccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCH-HHHHHHHHHHHHHhCCEEEEEe---eCcEE
Q 013147          180 HFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSA-EEVKEIAAELARLTGGIVLEIH---EENTI  255 (449)
Q Consensus       180 Rk~LRKlGhkLKPVV~IGKrGVTdgVIeeIh~Awk~HELVKVKVkqns~-ed~keiAeeLee~SGGeLVQVi---IG~tI  255 (449)
                      +.+++++|.+|++++.+|++|+++||+.++|.||++||++||+|+.... .+++..|..++..+|+++|++.   .|..|
T Consensus       388 ~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai  467 (564)
T KOG1990|consen  388 RLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAI  467 (564)
T ss_pred             HHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhH
Confidence            9999999999999999999999999999999999999999999999765 9999999999999999999975   46669


Q ss_pred             EEEeCCCCCCCCCccCCCCcccchHHHHHHHHHHhhhHHHHhhHHHHHHHHHHHHHHHhhhccc
Q 013147          256 IMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSEN  319 (449)
Q Consensus       256 ILYRGKNY~rP~~~il~P~nlLtKrkAL~rS~e~Qr~eslk~~i~~le~~ie~l~~~~~~~~~~  319 (449)
                      +.|||+||.+|.+  |+|.++|+||+|+.+++++|+.+|+++||+.+++++++++.++...-.+
T Consensus       468 ~~yr~k~y~~p~~--l~P~~~l~~~k~~~~~~~~~~~~a~~~~i~~~~~~~e~~~~~~~~~~~~  529 (564)
T KOG1990|consen  468 IAYRGKNYDRPTS--LRPRNLLSRRKALERSLEEQRKEALKSHISDLEQEIEQLQASVEAMPAI  529 (564)
T ss_pred             HHhhhhhccCCcc--cCchhhhcccCCccccHHHHHHHHHhhhcchhhhhHHHhhcchhccccc
Confidence            9999999999976  9999999999999999999999999999999999999999987764443

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

Probab=99.93  E-value=6.8e-26  Score=192.53  Aligned_cols=91  Identities=26%  Similarity=0.429  Sum_probs=86.8

Q ss_pred             CCCHHHHHHHHhhhccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCc
Q 013147          174 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  253 (449)
Q Consensus       174 ~LT~EQRk~LRKlGhkLKPVV~IGKrGVTdgVIeeIh~Awk~HELVKVKVkqns~ed~keiAeeLee~SGGeLVQViIG~  253 (449)
                      +||++|+++||+.||+++|+|+||++|||++||.+|+.+|++||||||++.+++.++.+++|+.|++.+||.+||+ +|+
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 013147          254 TIIMYRGKNYAQP  266 (449)
Q Consensus       254 tIILYRGKNY~rP  266 (449)
                      ++|||| .+..++
T Consensus        80 ~~vlyr-~~~e~~   91 (97)
T COG1534          80 TLVLYR-ESKEKR   91 (97)
T ss_pred             EEEEEe-cCcccc
Confidence            999999 455554

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

Probab=97.70  E-value=1.8e-05  Score=84.57  Aligned_cols=152  Identities=22%  Similarity=0.308  Sum_probs=125.5

Q ss_pred             hhhhhhhhhhhhhhHHhhccChHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCCCCCCCCCCCHHHHHHHHhhhccCCCe
Q 013147          114 AVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNY  193 (449)
Q Consensus       114 a~~~~l~~~r~~~kk~~~~~~~e~ri~~KL~~A~kK~e~~~e~L~K~E~~~paEp~~DpE~LT~EQRk~LRKlGhkLKPV  193 (449)
                      +...|+..++..++.-...|.++..--|-..........+.+.+..+..|...-+...+..||..+..++|.+|-...|+
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            44557777777778888888888555554445556666788888888888777788888899999999999999999999


Q ss_pred             eeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCC-HHHHHHHHHHH--HHHhCCEEEEEeeCcEEEEEeCCCCCCC
Q 013147          194 VPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFS-AEEVKEIAAEL--ARLTGGIVLEIHEENTIIMYRGKNYAQP  266 (449)
Q Consensus       194 V~IGKrGVTdgVIeeIh~Awk~HELVKVKVkqns-~ed~keiAeeL--ee~SGGeLVQViIG~tIILYRGKNY~rP  266 (449)
                      +.+|.++.-.++...|..+|..|+..|+-+...- ......++..+  -..+|+.||. +-|..+++||++|+-.|
T Consensus       194 ~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~-hN~~~dv~y~~~~Fl~~  268 (564)
T KOG1990|consen  194 FALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVL-HNKLLDVMYRYKNFLSP  268 (564)
T ss_pred             ceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEe-eccceeeeeehhhcccc
Confidence            9999999999999999999999999998876643 44556777788  7889999996 46889999999999774

---

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	449
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	3e-10
1rq8_A	104	Conserved hypothetical protein; structural genomic	1e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-09
1j0a_A	325	1-aminocyclopropane-1-carboxylate deaminase; PLP d	8e-04

>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 = 3e-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 = 20/109 (18%), Positives = 45/109 (41%), Gaps = 9/109 (8%)

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

Query: 234 IAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKA 282
           +A  L+  T   +++    + I++YR     +         I L  +  
Sbjct: 61  LAETLSEATRSELVQ-VIGSMIVIYR-----ESKEN---KEIELPLEHH 100

>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 = 59.5 bits (143), Expect = 1e-09
 Identities = 58/307 (18%), Positives = 94/307 (30%), Gaps = 79/307 (25%)

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

Query: 250 HEENTIIMYRG----KNYAQPPTEIMSPRITLSRKKALDKSKY---RDGL----RAVKKY 298
            +E  +  +       NY      +MSP  T  R+ ++    Y   RD L    +   KY
Sbjct: 74  KQEEMVQKFVEEVLRINYKF----LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKY 129

Query: 299 -IPKLEQELELLRAQAETRSENR------------SDAAEDVQNTEL-DKPDFGSI--PS 342
            + +L+  L+L +A  E R                  A +   + ++  K DF  I   +
Sbjct: 130 NVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFK-IFWLN 188

Query: 343 MMECSENDPTTESL------MASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFP-- 394
           +  C+  +   E L      +  +    SD            +AELR L   +   +   
Sbjct: 189 LKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK--PYENC 246

Query: 395 ------VQNDEEHEDFEEH---L---RQISI-DSRNAK-----SLGKDEDSSHFDEVDKM 436
                 VQN +    F      L   R   + D  +A      SL     +   DEV  +
Sbjct: 247 LLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL 306

Query: 437 FLRAASL 443
            L+    
Sbjct: 307 LLKYLDC 313

>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 = 58.3 bits (140), Expect = 3e-09
 Identities = 81/556 (14%), Positives = 156/556 (28%), Gaps = 170/556 (30%)

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 KNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRA-------VKKYIPKLEQELELLRAQA 313
            N+     + ++  I  S    L+ ++YR                IP     L L+    
Sbjct: 345 DNWKHVNCDKLTTIIESSLN-VLEPAEYRKMFDRLSVFPPSAH--IP--TILLSLIWFDV 399

Query: 314 ETRSE--------NRSDAAEDVQNTELDKPDFGSIPSM---MECS-ENDPTTESLM---- 357
                          S   +  + + +      SIPS+   ++   EN+      +    
Sbjct: 400 IKSDVMVVVNKLHKYSLVEKQPKESTI------SIPSIYLELKVKLENEYALHRSIVDHY 453

Query: 358 ----ASDSEDLSDIFETD----------SETE-TEEKAELRPLYLD-------------- 388
                 DS+DL   +                E  E     R ++LD              
Sbjct: 454 NIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTA 513

Query: 389 ---------------QFDKFPVQNDEEHE----DFEEHLRQISIDSRNAKSLG------K 423
                           +  +   ND ++E       + L +I  +   +K          
Sbjct: 514 WNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALM 573

Query: 424 DEDSSHFDEVDKMFLR 439
            ED + F+E  K   R
Sbjct: 574 AEDEAIFEEAHKQVQR 589

>1j0a_A 1-aminocyclopropane-1-carboxylate deaminase; PLP dependent, lyase; HET: PLP; 2.50A {Pyrococcus horikoshii} SCOP: c.79.1.1 PDB: 1j0b_A* Length = 325

 Score = 40.4 bits (94), Expect = 8e-04
 Identities = 20/143 (13%), Positives = 49/143 (34%), Gaps = 8/143 (5%)

Query: 129 EYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGR 188
            +E M   E+I  +L++  +K   I  G        +S +     +    E     ++ +
Sbjct: 130 SFELMKYAEEIAEELKREGRKPYVIPPG-------GASPIGTLGYVRAVGEIATQSEV-K 181

Query: 189 KCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLE 248
                V  G  G   G+ L + +  +  + + + V  F      ++   +      + ++
Sbjct: 182 FDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEAAELLGVK 241

Query: 249 IHEENTIIMYRGKNYAQPPTEIM 271
           +     +  Y    Y +   E+ 
Sbjct: 242 VEVRPELYDYSFGEYGKITGEVA 264

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	449
1rq8_A	104	Conserved hypothetical protein; structural genomic	99.96
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	99.96

>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=4.1e-29  Score=212.42  Aligned_cols=91  Identities=20%  Similarity=0.354  Sum_probs=87.5

Q ss_pred             CCCHHHHHHHHhhhccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCc
Q 013147          174 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  253 (449)
Q Consensus       174 ~LT~EQRk~LRKlGhkLKPVV~IGKrGVTdgVIeeIh~Awk~HELVKVKVkqns~ed~keiAeeLee~SGGeLVQViIG~  253 (449)
                      |||++||+|||++||+|+|+|+||++|||++|+++|++||++||||||+|.+++.++++++|++|++.|||++||+ ||+
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 699


Q ss_pred             EEEEEeCCCCCCC
Q 013147          254 TIIMYRGKNYAQP  266 (449)
Q Consensus       254 tIILYRGKNY~rP  266 (449)
                      ++||||++. ..|
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            999999976 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=99.96  E-value=1.5e-28  Score=206.53  Aligned_cols=88  Identities=18%  Similarity=0.317  Sum_probs=85.6

Q ss_pred             CCCHHHHHHHHhhhccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCc
Q 013147          174 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  253 (449)
Q Consensus       174 ~LT~EQRk~LRKlGhkLKPVV~IGKrGVTdgVIeeIh~Awk~HELVKVKVkqns~ed~keiAeeLee~SGGeLVQViIG~  253 (449)
                      .||++||+|||++||+|+|+|+||++|||++|+++|++||++||||||+|.++++++++++|++|++.|||++||+ ||+
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 013147          254 TIIMYRGKN  262 (449)
Q Consensus       254 tIILYRGKN  262 (449)
                      ++||||++.
T Consensus        81 ~~vLyR~~~   89 (98)
T 1jo0_A           81 ILVLYRPSE   89 (98)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEEccCC
Confidence            999999873

---

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	449
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	4e-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 = 77.0 bits (190), Expect = 4e-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	449
d1rq8a_	96	Hypothetical protein SAV1595 {Staphylococcus aureu	99.96
d1jo0a_	97	YhbY homologue HI1333 {Haemophilus influenzae [Tax	99.96

>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=99.96  E-value=6.9e-29  Score=204.71  Aligned_cols=91  Identities=20%  Similarity=0.344  Sum_probs=87.2

Q ss_pred             CCCHHHHHHHHhhhccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCc
Q 013147          174 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  253 (449)
Q Consensus       174 ~LT~EQRk~LRKlGhkLKPVV~IGKrGVTdgVIeeIh~Awk~HELVKVKVkqns~ed~keiAeeLee~SGGeLVQViIG~  253 (449)
                      |||++||++||++||+|+|+|+||++|||++|+.+|+.||+.||||||+|..++.++++++|++||+.|||++||+ +|+
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             EEEEEeCCCCCCC
Q 013147          254 TIIMYRGKNYAQP  266 (449)
Q Consensus       254 tIILYRGKNY~rP  266 (449)
                      ++||||++++ .|
T Consensus        80 ~~vlyR~~~~-~~   91 (96)
T d1rq8a_          80 MIVIYRESKE-NK   91 (96)
T ss_dssp             EEEEEECCCS-CC
T ss_pred             EEEEEeCCCC-CC
Confidence            9999998654 44

>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=7.9e-29  Score=204.71  Aligned_cols=88  Identities=18%  Similarity=0.317  Sum_probs=85.5

Q ss_pred             CCCHHHHHHHHhhhccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCc
Q 013147          174 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  253 (449)
Q Consensus       174 ~LT~EQRk~LRKlGhkLKPVV~IGKrGVTdgVIeeIh~Awk~HELVKVKVkqns~ed~keiAeeLee~SGGeLVQViIG~  253 (449)
                      +||++||++||++||+|+|+|+||++|||++||.+|+.||++||||||+|.+++.+++++++++|++.|||.|||+ +|+
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 013147          254 TIIMYRGKN  262 (449)
Q Consensus       254 tIILYRGKN  262 (449)
                      ++||||++.
T Consensus        81 ~~ilYR~~~   89 (97)
T d1jo0a_          81 ILVLYRPSE   89 (97)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEEcCCC
Confidence            999999854