Citrus Sinensis ID: 013187

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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
MGGRVLVSSASMALRKSPQFKILLSKFHIFKPFSYNKYPFQRISMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVVEKQESSENSSSADGAGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR
Secondary Structure (PSIPRED)
ccccccccccHHHHcccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccHHccccccccccccccccHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHcccEEEEEEEcccHHHHHHHHHHHHHHHccEEEEEEEccEEEEEEcccccccccccccccccccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHccccHHHHccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccccHHHHHHHHHHcccccccccccccccccccHHHHHHccHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccHEHHHHHHHHHccccccEEEcccccccccccccccEEEEEcccEEEEEEcccccEEcccccccEEEEccccccccccccccccccccccccccccccHHHHHHHHcHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHcHHcccccccccccccHHHHHHHHHHHccccEEEEEEccccHHHHHHHHHHHHHHcccEEEEEccccEEEEEEcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHccccHHccccHcccccHcHcccccccccccccccccccccccccccccccccccccccccHHHHccccccccccHcHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MGGRVLVSSAsmalrkspqfkillskfhifkpfsynkypfqriSMVDVLCKafgpcyglkrfsiegrlwihsapLRHYIEKVVEKqessensssadgaGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLkkiepkessemthdpeiltpeeHFYFLKMGrkcknyvpvgrrgiYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIImyrgknyaqppteimspritlsrkkaldkskyrDGLRAVKKYIPKLEQELELLRAQAETrsenrsdaaedvqnteldkpdfgsipsmmecsendptteslmasdsedlsdifetdseteteekaelrplyldqfdkfpvqndeehEDFEEHLRQISIDsrnakslgkdedsshfdEVDKMFLRAASLLKKQKR
Flexible Loop (DISEMBL)
mggrvlvssasmalrksPQFKILLSKFHIFKPFSYNKYPFQRISMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVVekqessensssadgagvakvkrkklkgkravvrwlkhfrykkkkeyermtaeeKILYklrkarkkeeriveglkkiepkessemthdpeiltPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIImyrgknyaqppteimspritlsrkkaldkskyrdglravKKYIPKLEQELELLRAQAetrsenrsdaaedvqnteldkpdfgsipSMMECSENDPTTESLMASDSEDLSDIFETDseteteekaelrplyldQFDKFPVQNDEEHEDFEEHLRQisidsrnakslgkdedsshfdevDKMFLRAASLLKKQKR
Low Complexity Region (SEG)
MGGRVLVSSASMALRKSPQFKILLSKFHIFKPFSYNKYPFQRISMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVVEKQESSENSSSADgagvakvkrkklkgkravvrWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKleqelellraqaeTRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR
Disordered region (IsUnstruct)
******************QFKILLSKFHIFKPFSYNKYPFQRISMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVV*************************KGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKL*********************************PEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYA***************************LRAVKKYIP*****************************************************************************************************************************************************
Disordered Region (DISOPRED)
*********A****RKSPQFKILLSKFHIF*************SMVDVLCKAFGPCYGLKRFSIEGRLWI*********************************************************************YKLRKARKKEERI************************EEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSR*********************KLEQELEL**************************************************************************************************************************DEVDKMFLRAASLL*****
Disordered Region (DISEMBL)
*********ASMALRKSPQFKILLSKFHIFKPFSYNKYPFQRISMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKV****************************KRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQ***************QNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDI************AELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRN************FDEVDKMFLRAASLLKKQKR
Disordered Region (DISPRO)
*************LRKSPQFKILLSKFHIFKPFSYNKYPFQRISMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPL*************************AKVK****KGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPK*****THDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSE**************************************************************ELRPLYLDQFDKFPV****EHEDFEEHLRQISID************SSHFDEVDKMFLRAASLLKK***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGGRVLVSSASMALRKSPQFKILLSKFHIFKPFSYNKYPFQRISMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVVEKQESSENSSSADGAGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGxxxxxxxxxxxxxxxxxxxxxxxxxxxxRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR
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	448	2.2.26 [Sep-21-2011]
Q67XL4	444	Uncharacterized CRM domai	yes	no	0.937	0.945	0.605	1e-127
Q9FYT6	715	Chloroplastic group IIA i	N/A	no	0.321	0.201	0.393	3e-17
Q6YYA3	725	Chloroplastic group IIA i	no	no	0.321	0.198	0.373	2e-15
Q9LF10	720	Chloroplastic group IIA i	no	no	0.323	0.201	0.328	8e-14
Q5VMQ5	701	CRS2-associated factor 1,	no	no	0.200	0.128	0.307	9e-07
Q84N49	674	CRS2-associated factor 1,	N/A	no	0.234	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	0.337	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 = 279/461 (60%), Positives = 330/461 (71%), Gaps = 41/461 (8%)

Query: 4   RVLVSSASMALR-KSPQFKILLSKFHIFKPF-SYNKYPFQRISMVDVLCKAFGPCYGLKR 61
           RV  S+ASM LR KS Q   L S   +F  F S N+     IS  +++CK       L +
Sbjct: 9   RVSTSAASMLLRRKSRQLGFLASSSPLFSSFNSMNRT----ISSCNIVCKV------LHK 58

Query: 62  FSIEGRLW---------IHSAPLRHYIEKVVEKQESSENSSSADGAGVAKVKRKKLKGKR 112
            S+   +W          HS P R   +  + K   SENSSS DG    K+KRKKLKGKR
Sbjct: 59  ESLTRPMWNVSFLRSSSFHSTPARETGDDDISK---SENSSSQDGDSCTKLKRKKLKGKR 115

Query: 113 AVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPE 172
           AVVRWLK FR+KKKKE+ERMT+EEKIL KLRKARKKEER++E +KK+EP ES+E THDPE
Sbjct: 116 AVVRWLKFFRWKKKKEFERMTSEEKILNKLRKARKKEERLMETMKKLEPSESAETTHDPE 175

Query: 173 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKE 232
           ILTPEEHFY+LKMG KCKNYVPVGRRGIYQGVILNMHLHWKKHQTL+V++KTF+ +EVKE
Sbjct: 176 ILTPEEHFYYLKMGLKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLQVVIKTFTPDEVKE 235

Query: 233 IAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLR 292
           IA ELARLTGGIVL++HE NTIIMYRGKNY QPPTEIMSPRITL RKKALDKSK RD LR
Sbjct: 236 IAVELARLTGGIVLDVHEGNTIIMYRGKNYVQPPTEIMSPRITLPRKKALDKSKCRDALR 295

Query: 293 AVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQ--NTELDKPDFGSIPSMMECSENDP 350
           AV+KYIP+LEQEL+LL+AQAET+ +  +   +D Q  + EL K    S   + +  E D 
Sbjct: 296 AVRKYIPRLEQELQLLQAQAETKRDYTNVKVDDNQERSEELKKIIERSEECLEDEQEEDE 355

Query: 351 TTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQI 410
               L A+DS DLSDIFETDSE E + K E RPL+L++F+KFP  N+ E EDF       
Sbjct: 356 AGLEL-ATDS-DLSDIFETDSELE-DAKTE-RPLFLEEFEKFPAINNREDEDFG------ 405

Query: 411 SIDSRNAKSLGKDED---SSHFDEVDKMFLRAASLLKKQKR 448
             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 = 90.5 bits (223), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 59/150 (39%), Positives = 84/150 (56%), Gaps = 6/150 (4%)

Query: 140 YKLRKARKKEERIVEGLKKIEPKES-SEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRR 198
           +KL    KK ER  + L K+    S SE + D E LT EE   F ++GRK    V +GRR
Sbjct: 529 WKLSVLNKKIERSNQALAKLHSSWSPSEQSADREHLTEEEKIMFRRIGRKMDGLVLLGRR 588

Query: 199 GIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT---II 255
           GI+ GVI  +H HWK  + +KVI K     ++   A+ L   TGGI++ + +  T   II
Sbjct: 589 GIFDGVIEEIHQHWKHKEVVKVITKQNQTRQIMYAASLLEVETGGILIAVEKLTTSHAII 648

Query: 256 MYRGKNYAQPPTEIMSPRITLSRKKALDKS 285
           +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: 140 YKLRKARKKEERIVEGLKKIEPKES-SEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRR 198
           ++L    KK ER  + L K+    S S+   D E+LT EE   F K+G K   +V +GRR
Sbjct: 531 WRLSMLTKKIERSNQVLAKLHSSWSPSKKDGDRELLTEEERRIFRKIGLKMDEHVLLGRR 590

Query: 199 GIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT---II 255
           G+++GVI  +H HWK  + +KVI K   A ++   +  L   TGG ++ I    T   II
Sbjct: 591 GVFEGVIEEIHQHWKHKEVVKVITKQNQASQITYTSMMLEVETGGTLIAIERFTTSHAII 650

Query: 256 MYRGKNYAQPPTEIMSPRITLSRKKALDKS 285
           +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: 165 SEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKT 224
           SE   D EILT EE     ++G K  + + +GRRG++ GV+  +H HWK  +  KVI   
Sbjct: 563 SEGDDDIEILTNEERECLRRIGLKMNSSLVLGRRGVFFGVMEGLHQHWKHREVAKVITMQ 622

Query: 225 FSAEEVKEIAAELARLTGGIVLEIH---EENTIIMYRGKNYAQPPTEIMSPRITLSRKKA 281
                V   A  L   + G+++ I    E + I++YRGKNY +P +++M+  + L+++KA
Sbjct: 623 KLFSRVVYTAKALETESNGVLISIEKLKEGHAILIYRGKNYKRPSSKLMAQNL-LTKRKA 681

Query: 282 LDKSKYRDGLRAVKKYIPKLEQELELLRA 310
           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 = 9e-07,   Method: Compositional matrix adjust.
 Identities = 28/91 (30%), Positives = 47/91 (51%), Gaps = 1/91 (1%)

Query: 172 EILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVK 231
           E LT EE    +K   K K  + +GR G+   ++ N+H HWK+ +  K+  K     ++ 
Sbjct: 183 EPLTKEEVDELVKATLKTKRQLNIGRDGLTHNMLENIHSHWKRKRVCKIKCKGVCTVDMD 242

Query: 232 EIAAELARLTGGIVLEIHEENTIIMYRGKNY 262
            +  +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: 156 LKKIEPKESSEMTHD--PEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWK 213
           L  +EP+  S    D   E LT EE    +K   K K  + +GR G+   ++ N+H HWK
Sbjct: 165 LAGMEPRYQSVSREDILGEPLTKEEVSELVKGSLKSKRQLNMGRDGLTHNMLENIHSHWK 224

Query: 214 KHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTII-MYRGKNY 262
           + +  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: 172 EILTPEEHFYFLKMGRK--CKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEE 229
           E LTP E  + +   +K   K  + +GR G+   ++ ++H HWK  + ++V        +
Sbjct: 155 EPLTPAERAFLVSKCQKSRTKKQINLGRDGLTHNMLNDIHNHWKNDEAVRVKCLGVPTVD 214

Query: 230 VKEIAAELARLTGGIVLEIHEENTIIMYRGKNY 262
           ++ +  +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: 98  AGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLK 157
            G A +  K+ K +R  VR          +E  +  +   I+ ++R+ RK +      L 
Sbjct: 167 TGKAPLLTKEEKARRRGVR----LHTPLGQETPQTVSAHGIMMEVRERRKMD------LA 216

Query: 158 KIEPKES---SEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKK 214
           ++ P +     E+  +P  LTP E    +K        + +GR G+   ++  +H HW++
Sbjct: 217 RVSPGDGRSREEVLGEP--LTPSEVRALVKPHISHNRQLNIGRDGLTHNMLEMIHCHWRR 274

Query: 215 HQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTII-MYRGKNY 262
            +  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: 189 CKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEI 248
           C   + +G+ G+   +I ++H HWK+ + +++        ++  I   L   TGG V+  
Sbjct: 162 CSRQINLGKGGVTHNMIDDIHNHWKRAEAVRIKCLGVPTLDMDNICFHLEDKTGGKVI-Y 220

Query: 249 HEENTIIMYRGKNY 262
              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	448
255572670	458	conserved hypothetical protein [Ricinus	0.935	0.914	0.653	1e-151
224132018	413	predicted protein [Populus trichocarpa]	0.872	0.946	0.658	1e-149
225448146	401	PREDICTED: uncharacterized CRM domain-co	0.852	0.952	0.694	1e-145
356501797	382	PREDICTED: uncharacterized CRM domain-co	0.828	0.971	0.686	1e-139
356498434	383	PREDICTED: uncharacterized CRM domain-co	0.810	0.947	0.685	1e-137
297739537	331	unnamed protein product [Vitis vinifera]	0.705	0.954	0.719	1e-131
449458069	500	PREDICTED: uncharacterized CRM domain-co	0.863	0.774	0.594	1e-130
357439975	443	CRM domain-containing protein, putative	0.910	0.920	0.597	1e-129
9279724	1115	unnamed protein product [Arabidopsis tha	0.921	0.370	0.596	1e-126
79417439	444	uncharacterized CRM domain-containing pr	0.937	0.945	0.605	1e-126

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

 Score =  540 bits (1391), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 289/442 (65%), Positives = 341/442 (77%), Gaps = 23/442 (5%)

Query: 28  HIFKPFSYNKYPFQRISMVDVLCK------AFGPCYGLKRFSIEGRLWIHSAPLRHYIEK 81
           ++F PF  +   ++  S+  ++CK      AF P Y L+   I G  WIH  P    I+K
Sbjct: 19  YLFTPFFSDSLTYRTTSLFHIICKVFSQAPAFRPVYVLEGPHIGGHRWIHFGPTLTDIDK 78

Query: 82  VVEKQESSENSSSADGAGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYK 141
             E    S  S+  +G+G AKVKRKKLKGKRAVVRWLK FR+KKKKEYERMTAEEK+LYK
Sbjct: 79  DGEPPPLSGQSTMVEGSGCAKVKRKKLKGKRAVVRWLKFFRWKKKKEYERMTAEEKLLYK 138

Query: 142 LRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIY 201
           L+KA+KKEER V+ LKKIEP +SSE THDPEILTPEEHF+FLKMG KCKNYVPVGRRGIY
Sbjct: 139 LKKAQKKEERYVQALKKIEPVDSSETTHDPEILTPEEHFFFLKMGLKCKNYVPVGRRGIY 198

Query: 202 QGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKN 261
           QGVILNMHLHWKKHQT++V+VKTFS EEVKEIAAELARLTGGIVL+IHEENTIIMYRGKN
Sbjct: 199 QGVILNMHLHWKKHQTVQVVVKTFSPEEVKEIAAELARLTGGIVLDIHEENTIIMYRGKN 258

Query: 262 YAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRSD 321
           Y+QPPTEIMSPRITLSRKKALDKSKYRDGLRAV+ YIP+LEQ+LELL+ Q+  ++E  S 
Sbjct: 259 YSQPPTEIMSPRITLSRKKALDKSKYRDGLRAVRNYIPRLEQDLELLKVQSMGKAECGSA 318

Query: 322 AAEDVQNTELDKPDFGSIPSMM---------------ECSENDPTTESLMASDSEDLSDI 366
           +AE+   T+ D  + G +PS                 ECSE +   +  M SDSEDLSDI
Sbjct: 319 SAEETLYTD-DGAESGGVPSTPLENSEKLKKITDGQEECSEEESPMDLGMLSDSEDLSDI 377

Query: 367 FETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDS 426
           FETDS+TETE+K + RPLYL++F KFP+Q +EE EDFEEHLRQ+S+DSR  +S  KD D 
Sbjct: 378 FETDSDTETEDKVK-RPLYLEEFKKFPIQGNEEPEDFEEHLRQLSVDSRKVESSEKDSDI 436

Query: 427 SHFDEVDKMFLRAASLLKKQKR 448
             FDEVD++FLRAASLLKK+KR
Sbjct: 437 PSFDEVDRLFLRAASLLKKKKR 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 =  533 bits (1374), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 278/422 (65%), Positives = 333/422 (78%), Gaps = 31/422 (7%)

Query: 49  LCKAFG--PCYGLKR--FSIEGRLWIHSAPLRHYIEKVVEKQESSENSSSADGAGVAKVK 104
           +CK  G  P Y +K     + G LWIHS P  + ++KVVE  E+ E +++       KVK
Sbjct: 1   MCKVLGQRPVYNVKGHLVPLVGHLWIHSCPSLNNVDKVVEPTENFEKTAAVFSGSDVKVK 60

Query: 105 RKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKES 164
           R KLKGKRAVVRWLK FR+KKKKEYERMTAEEKILYKLRKA++KEER V+ LKKIEPKES
Sbjct: 61  RPKLKGKRAVVRWLKFFRWKKKKEYERMTAEEKILYKLRKAQRKEERFVQALKKIEPKES 120

Query: 165 SEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKT 224
           SE THDPEILTPEEHF+FLKMG KCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKV+VKT
Sbjct: 121 SEATHDPEILTPEEHFFFLKMGLKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVVVKT 180

Query: 225 FSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDK 284
           F+ EEVKEIAAELAR TGGIVL+IHEENTIIMYRGKNY+QPPTEIMSPR+TLSRKKALDK
Sbjct: 181 FTPEEVKEIAAELARFTGGIVLDIHEENTIIMYRGKNYSQPPTEIMSPRVTLSRKKALDK 240

Query: 285 SKYRDGLRAVKKYIPKLEQELELLRAQAETRS-----ENRSDAAEDVQNTE-----LDKP 334
           SK RDGLRA+++YIP+L+Q+LELL A+A  ++     E+RS +++ ++N+E     +D+ 
Sbjct: 241 SKCRDGLRALRRYIPRLQQDLELLHARAGGKTDIDGAESRSISSKQLENSEKLKEIIDRQ 300

Query: 335 DFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPV 394
           D G        SE+ P T+  +ASDSEDLSDIFETDS+ +TEE ++ RPLYL++F+KF V
Sbjct: 301 DEG--------SEDGPDTDLGIASDSEDLSDIFETDSDADTEETSK-RPLYLEEFEKFSV 351

Query: 395 QNDEEHEDFEEHLRQISIDSRNAKSLGK--------DEDSSHFDEVDKMFLRAASLLKKQ 446
           + D E EDFEEHLRQIS+ S+   + GK        D DS  FDEVD+MFLRAASLLK++
Sbjct: 352 EADGEPEDFEEHLRQISLGSKKGVTSGKDVDIPTGVDVDSPSFDEVDRMFLRAASLLKRK 411

Query: 447 KR 448
           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 (1338), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 277/399 (69%), Positives = 323/399 (80%), Gaps = 17/399 (4%)

Query: 66  GRLWIHSAPLRHYIE-KVVEKQESSENSSSADGAGVAKVKRKKLKGKRAVVRWLKHFRYK 124
            R  +H+  L H +E  V E ++   +S++A G    KVKRKKLKGKRAVVRWLK FR+K
Sbjct: 4   ARFLVHNLLLGHSMEYGVAEPEKLPVDSTTAAGTVETKVKRKKLKGKRAVVRWLKFFRWK 63

Query: 125 KKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLK 184
           KKKEYERMTAEEKILYKLRKAR+KEER+ E L KIEPKESSE THDPEILTPEEHF+FLK
Sbjct: 64  KKKEYERMTAEEKILYKLRKARRKEERLAEALTKIEPKESSETTHDPEILTPEEHFFFLK 123

Query: 185 MGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGI 244
           MG KCKNYVP+GRRGIYQGVILNMHLHWKKHQTL+V+VKTFS EEVKEIA ELARLTGGI
Sbjct: 124 MGLKCKNYVPIGRRGIYQGVILNMHLHWKKHQTLQVVVKTFSPEEVKEIAVELARLTGGI 183

Query: 245 VLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQE 304
           VL+IHEENTIIMYRGKNY+QPPTEIMSPRITLSRKKALDKSKYRDGLRAV+KYIP+LE +
Sbjct: 184 VLDIHEENTIIMYRGKNYSQPPTEIMSPRITLSRKKALDKSKYRDGLRAVRKYIPRLEGD 243

Query: 305 LELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSMM---------------ECSEND 349
           LELL+AQA+ ++EN+++A ED QN  +D  +   I ++                E SE +
Sbjct: 244 LELLQAQAKMQAENKTEAVEDFQNANIDSINSQGISNLQPENSDKLRELLAGNNESSEEE 303

Query: 350 PTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQ 409
             T+S   S SE LSDIFE+DS+T+T+EKAE + LYL++F+KFPV++D E EDFEEHLRQ
Sbjct: 304 SLTDSGTESCSEALSDIFESDSDTDTKEKAE-QLLYLNEFEKFPVESDGEPEDFEEHLRQ 362

Query: 410 ISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 448
           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 =  502 bits (1293), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 263/383 (68%), Positives = 311/383 (81%), Gaps = 12/383 (3%)

Query: 66  GRLWIHSAPLRHYIEKVVEKQESSENSSSA--DGAGVAKVKRKKLKGKRAVVRWLKHFRY 123
           G    HS P   + +KVVE+Q+ S+ +SSA  DG G AKVKR KLKGKRAVVRWLK FR+
Sbjct: 8   GNASFHSCPFLKFNDKVVEQQQDSQKASSANVDGDGNAKVKRNKLKGKRAVVRWLKFFRF 67

Query: 124 KKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFL 183
           KKKKEYERMTAEEKILYKL KARKKEER+ E LKKIEP ESSE THDPEILTPEEHF+FL
Sbjct: 68  KKKKEYERMTAEEKILYKLLKARKKEERLCEALKKIEPAESSETTHDPEILTPEEHFFFL 127

Query: 184 KMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGG 243
           KMG K KNYVPVGRRGIYQGVILNMHLHWKKHQTLKV+VKTFSAEEVKEIA ELARL+GG
Sbjct: 128 KMGLKSKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVVVKTFSAEEVKEIATELARLSGG 187

Query: 244 IVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQ 303
           IVL+IHE+NTIIMYRGKNY+QPPTEIMSPR++LSRKKALDKSKYRD LRAV+++IP+LEQ
Sbjct: 188 IVLDIHEDNTIIMYRGKNYSQPPTEIMSPRVSLSRKKALDKSKYRDALRAVRRHIPRLEQ 247

Query: 304 ELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDL 363
           ELE+LRAQ ++ +E+ +DAAE +QN          +   + C+E++    S + SDS+ L
Sbjct: 248 ELEILRAQFKSSAESNTDAAEAIQNNR------ERMNDNIGCTEDETDMNSELDSDSDKL 301

Query: 364 SDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKD 423
           SDIFETDS+TE   K E +PLYLD+FD FP Q+D E  DFEEHLRQ+S+ S+N   + K+
Sbjct: 302 SDIFETDSDTENFIKEE-KPLYLDEFDNFPEQSDGEMNDFEEHLRQMSLKSKN---MEKE 357

Query: 424 EDSSHFDEVDKMFLRAASLLKKQ 446
           ++    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: 80  EKVVEKQ-ESSENSSSA--DGAGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEE 136
           +KVVE+Q + S+ +SSA  DG G AKVKR KLKGKRAVVRWLK FR+KKKKEYERMTAEE
Sbjct: 1   DKVVEQQHQDSQKASSANVDGDGNAKVKRNKLKGKRAVVRWLKFFRFKKKKEYERMTAEE 60

Query: 137 KILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVG 196
           K LYKL KARKKEER+ E LKKIEP ESSE THDPEILTPEEHF+FLKMG K KNYVPVG
Sbjct: 61  KNLYKLLKARKKEERLCEALKKIEPAESSETTHDPEILTPEEHFFFLKMGLKSKNYVPVG 120

Query: 197 RRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIM 256
           RRGIYQGVILNMHLHWKKHQTLKV+VKTFSAEEVKEIAAELARL+GGIVL+IHE+NTIIM
Sbjct: 121 RRGIYQGVILNMHLHWKKHQTLKVVVKTFSAEEVKEIAAELARLSGGIVLDIHEDNTIIM 180

Query: 257 YRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRS 316
           YRGKNY+QPPTEIMSPR++LSRKKALDKSKYRD LRAV++YIP+LEQELE+LRAQ ++ +
Sbjct: 181 YRGKNYSQPPTEIMSPRVSLSRKKALDKSKYRDALRAVRRYIPRLEQELEILRAQFKSSA 240

Query: 317 ENRSDAAEDVQNTELDKPDFGSIPS-----------MMEC----SENDPTTESLMASDSE 361
           E+ +DAAE +QN+  +  + GSI +           MM      +E++    S + SDS+
Sbjct: 241 ESNTDAAEAIQNSGRESIESGSISNFQLQNSYKDREMMNVNIGSTEDETDMNSELDSDSD 300

Query: 362 DLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLG 421
            LSDIFETDS+TE   K E +PLYLD+FD FP Q+D E  DFEEH+RQ+S+ S+N   + 
Sbjct: 301 KLSDIFETDSDTENFVKEE-KPLYLDEFDNFPEQSDGEMNDFEEHMRQMSLKSKN---ME 356

Query: 422 KDEDSSHFDEVDKMFLRAASLLKKQ 446
           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 =  475 bits (1222), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 239/332 (71%), Positives = 276/332 (83%), Gaps = 16/332 (4%)

Query: 132 MTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKN 191
           MTAEEKILYKLRKAR+KEER+ E L KIEPKESSE THDPEILTPEEHF+FLKMG KCKN
Sbjct: 1   MTAEEKILYKLRKARRKEERLAEALTKIEPKESSETTHDPEILTPEEHFFFLKMGLKCKN 60

Query: 192 YVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE 251
           YVP+GRRGIYQGVILNMHLHWKKHQTL+V+VKTFS EEVKEIA ELARLTGGIVL+IHEE
Sbjct: 61  YVPIGRRGIYQGVILNMHLHWKKHQTLQVVVKTFSPEEVKEIAVELARLTGGIVLDIHEE 120

Query: 252 NTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQ 311
           NTIIMYRGKNY+QPPTEIMSPRITLSRKKALDKSKYRDGLRAV+KYIP+LE +LELL+AQ
Sbjct: 121 NTIIMYRGKNYSQPPTEIMSPRITLSRKKALDKSKYRDGLRAVRKYIPRLEGDLELLQAQ 180

Query: 312 AETRSENRSDAAEDVQNTELDKPDFGSIPSMM---------------ECSENDPTTESLM 356
           A+ ++EN+++A ED QN  +D  +   I ++                E SE +  T+S  
Sbjct: 181 AKMQAENKTEAVEDFQNANIDSINSQGISNLQPENSDKLRELLAGNNESSEEESLTDSGT 240

Query: 357 ASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRN 416
            S SE LSDIFE+DS+T+T+EKAE + LYL++F+KFPV++D E EDFEEHLRQIS DSR 
Sbjct: 241 ESCSEALSDIFESDSDTDTKEKAE-QLLYLNEFEKFPVESDGEPEDFEEHLRQISADSRK 299

Query: 417 AKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 448
           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: 52  AFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVVEKQESSENSSS---ADGAGVAKVKRKKL 108
           +F   YGL   S+ G  WIHS        K VE  E SE  S+    DG+G+ + ++K+ 
Sbjct: 89  SFNGVYGLT--SVVGYRWIHST-------KSVEPLEKSEGKSAIGFTDGSGIEEEEKKEK 139

Query: 109 KGK------RAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPK 162
           K +      RAVVRWLK FR+KKKKEYERMT+EEKIL+K+ KARKKE+R+VE L+KIEP 
Sbjct: 140 KTRKKLKGKRAVVRWLKLFRWKKKKEYERMTSEEKILFKMNKARKKEKRLVEALEKIEPA 199

Query: 163 ESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIV 222
           +SS+ THDPEILTPEEHFYFLKMG K KNYVPVGRRGIYQGVILNMHLHWKKHQT+KV+V
Sbjct: 200 DSSDTTHDPEILTPEEHFYFLKMGIKGKNYVPVGRRGIYQGVILNMHLHWKKHQTVKVVV 259

Query: 223 KTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKAL 282
           KTFS EEVKEIAAELARLTGG+VL+IHEE+TIIMYRGKNY+QPPTEIMSPR++LSRKKAL
Sbjct: 260 KTFSPEEVKEIAAELARLTGGLVLDIHEEDTIIMYRGKNYSQPPTEIMSPRVSLSRKKAL 319

Query: 283 DKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSM 342
           DKSKYRDGLRAV+K+IPKLEQEL  L++QA+   ++  ++ E +Q T  D     +I S+
Sbjct: 320 DKSKYRDGLRAVRKHIPKLEQELRFLQSQAKLNCKSNGESVEHMQETVDDTNKSKAISSL 379

Query: 343 M----------------ECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYL 386
                            + S++    ++ M+SDSEDLSD+FETD ++E +EK E +PL+L
Sbjct: 380 NLENLDDSSNAMRSVSKDWSDDSSPIDTGMSSDSEDLSDMFETDIDSEADEKME-KPLFL 438

Query: 387 DQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQ 446
            +F+ F  + ++E ED  + LRQIS+DS+ AK L  D +S  FDEVD++FLR+ASLLKK+
Sbjct: 439 KEFENFAAETEDEIEDLSDQLRQISMDSKQAKILENDVNSPEFDEVDRLFLRSASLLKKK 498

Query: 447 KR 448
           +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 =  468 bits (1204), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 272/455 (59%), Positives = 330/455 (72%), Gaps = 47/455 (10%)

Query: 27  FHIFKPFSYNKYPF----------QRISMVDVLCKAFGP---CYGLKRFSIE-GRLWIHS 72
           + IF     NK+ F           + S+  V+CK +      + L   S   G L  HS
Sbjct: 3   WRIFTSPLLNKFQFLSSSTTFLLRHKTSLNYVICKVYAQEHHQFKLPSTSTRVGCLSFHS 62

Query: 73  AP-LRHYIEKVVEKQESSENSSSADGAGVAKV-KRKKLKGKRAVVRWLKHFRYKKKKEYE 130
            P L+   +KVVE+ + S+        G  KV  RKKLKGKRAVVRWLK FR+KKKKE++
Sbjct: 63  TPFLKCNHDKVVEQPQDSD--------GDVKVPARKKLKGKRAVVRWLKFFRFKKKKEFQ 114

Query: 131 RMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCK 190
           RMT EE+ILYKL KARKKEER+ E LKKIEP ESSE  HDPEILTPEEHF+FLKMG K K
Sbjct: 115 RMTTEERILYKLLKARKKEERLREALKKIEPTESSETIHDPEILTPEEHFFFLKMGLKSK 174

Query: 191 NYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHE 250
           NYVPVGRRGIYQGVILNMHLHWKKHQTL+V+VKTFSAEEVKEIA ELARLTGGIVL IHE
Sbjct: 175 NYVPVGRRGIYQGVILNMHLHWKKHQTLQVVVKTFSAEEVKEIATELARLTGGIVLGIHE 234

Query: 251 ENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRA 310
           E+TIIMYRGKNY+QPPTEIMSPR+TL RKKALDKSKYRDGLRAV++YIPKLEQELE+LRA
Sbjct: 235 EDTIIMYRGKNYSQPPTEIMSPRVTLPRKKALDKSKYRDGLRAVRRYIPKLEQELEILRA 294

Query: 311 QAETRSENRSDAAEDVQ-------------NTELDKPDFGSIPSMME----CSENDPTTE 353
           Q ++ +E+ ++AAE +Q             N +L+K D   + +M      CSE++   +
Sbjct: 295 QFQSTAESNTEAAEGIQISDKVSVEPSSVSNLQLEKLD--KVGAMFNDNNSCSEDEAHMD 352

Query: 354 SLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISID 413
           S + S S+ LSDIFETDS+TE   K E +PLYLD+F+ FP Q+D + +DFEEHL+QIS +
Sbjct: 353 SDLDSYSDKLSDIFETDSDTEDLVKEE-KPLYLDEFNNFPEQSDGDTDDFEEHLQQISYN 411

Query: 414 SRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 448
           S+N   + KD D   FDEVD++FLRAAS LKK+++
Sbjct: 412 SKN---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 =  459 bits (1180), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 279/468 (59%), Positives = 331/468 (70%), Gaps = 55/468 (11%)

Query: 4    RVLVSSASMALR-KSPQFKILLSKFHIFKPF-SYNKYPFQRISMVDVLCKAFGPCYGLKR 61
            RV  S+ASM LR KS Q   L S   +F  F S N+     IS  +++CK       L +
Sbjct: 680  RVSTSAASMLLRRKSRQLGFLASSSPLFSSFNSMNR----TISSCNIVCKV------LHK 729

Query: 62   FSIEGRLW---------IHSAPLRHYIEKVVEKQESSENSSSADGAGVAKVKRKKLKGKR 112
             S+   +W          HS P R   +  + K   SENSSS DG    K+KRKKLKGKR
Sbjct: 730  ESLTRPMWNVSFLRSSSFHSTPARETGDDDISK---SENSSSQDGDSCTKLKRKKLKGKR 786

Query: 113  AVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPE 172
            AVVRWLK FR+KKKKE+ERMT+EEKIL KLRKARKKEER++E +KK+EP ES+E THDPE
Sbjct: 787  AVVRWLKFFRWKKKKEFERMTSEEKILNKLRKARKKEERLMETMKKLEPSESAETTHDPE 846

Query: 173  ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKE 232
            ILTPEEHFY+LKMG KCKNYVPVGRRGIYQGVILNMHLHWKKHQTL+V++KTF+ +EVKE
Sbjct: 847  ILTPEEHFYYLKMGLKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLQVVIKTFTPDEVKE 906

Query: 233  IAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLR 292
            IA ELARLTGGIVL++HE NTIIMYRGKNY QPPTEIMSPRITL RKKALDKSK RD LR
Sbjct: 907  IAVELARLTGGIVLDVHEGNTIIMYRGKNYVQPPTEIMSPRITLPRKKALDKSKCRDALR 966

Query: 293  AVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQ--NTELDKPDFGSIPSMMECSENDP 350
            AV+KYIP+LEQEL+LL+AQAET+ +  +   +D Q  + EL K        ++E SE   
Sbjct: 967  AVRKYIPRLEQELQLLQAQAETKRDYTNVKVDDNQERSEELKK--------IIERSEECL 1018

Query: 351  TTESL-------MASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDF 403
              E         +A+DS DLSDIFETDSE E + K E RPL+L++F+KFP  N+ E EDF
Sbjct: 1019 EDEQEEDEAGLELATDS-DLSDIFETDSELE-DAKTE-RPLFLEEFEKFPAINNREDEDF 1075

Query: 404  EEHLRQISIDSRNAKSLGKDED---SSHFDEVDKMFLRAASLLKKQKR 448
                     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 = 279/461 (60%), Positives = 330/461 (71%), Gaps = 41/461 (8%)

Query: 4   RVLVSSASMALR-KSPQFKILLSKFHIFKPF-SYNKYPFQRISMVDVLCKAFGPCYGLKR 61
           RV  S+ASM LR KS Q   L S   +F  F S N+     IS  +++CK       L +
Sbjct: 9   RVSTSAASMLLRRKSRQLGFLASSSPLFSSFNSMNRT----ISSCNIVCKV------LHK 58

Query: 62  FSIEGRLW---------IHSAPLRHYIEKVVEKQESSENSSSADGAGVAKVKRKKLKGKR 112
            S+   +W          HS P R   +  + K   SENSSS DG    K+KRKKLKGKR
Sbjct: 59  ESLTRPMWNVSFLRSSSFHSTPARETGDDDISK---SENSSSQDGDSCTKLKRKKLKGKR 115

Query: 113 AVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPE 172
           AVVRWLK FR+KKKKE+ERMT+EEKIL KLRKARKKEER++E +KK+EP ES+E THDPE
Sbjct: 116 AVVRWLKFFRWKKKKEFERMTSEEKILNKLRKARKKEERLMETMKKLEPSESAETTHDPE 175

Query: 173 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKE 232
           ILTPEEHFY+LKMG KCKNYVPVGRRGIYQGVILNMHLHWKKHQTL+V++KTF+ +EVKE
Sbjct: 176 ILTPEEHFYYLKMGLKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLQVVIKTFTPDEVKE 235

Query: 233 IAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLR 292
           IA ELARLTGGIVL++HE NTIIMYRGKNY QPPTEIMSPRITL RKKALDKSK RD LR
Sbjct: 236 IAVELARLTGGIVLDVHEGNTIIMYRGKNYVQPPTEIMSPRITLPRKKALDKSKCRDALR 295

Query: 293 AVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQ--NTELDKPDFGSIPSMMECSENDP 350
           AV+KYIP+LEQEL+LL+AQAET+ +  +   +D Q  + EL K    S   + +  E D 
Sbjct: 296 AVRKYIPRLEQELQLLQAQAETKRDYTNVKVDDNQERSEELKKIIERSEECLEDEQEEDE 355

Query: 351 TTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQI 410
               L A+DS DLSDIFETDSE E + K E RPL+L++F+KFP  N+ E EDF       
Sbjct: 356 AGLEL-ATDS-DLSDIFETDSELE-DAKTE-RPLFLEEFEKFPAINNREDEDFG------ 405

Query: 411 SIDSRNAKSLGKDED---SSHFDEVDKMFLRAASLLKKQKR 448
             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	448
TAIR|locus:2094438	444	LOH1 "LAG One Homologue 1" [Ar	0.930	0.939	0.545	3.8e-110
TAIR|locus:2091458	491	AT3G27550 [Arabidopsis thalian	0.404	0.368	0.448	2.8e-42
TAIR|locus:2123276	343	AT4G13070 [Arabidopsis thalian	0.401	0.524	0.491	4e-42
TAIR|locus:2056558	372	AT2G28480 [Arabidopsis thalian	0.558	0.672	0.379	8.4e-42
TAIR|locus:2094558	881	CFM3A "CRM family member 3A" [	0.555	0.282	0.3	2.6e-22
TAIR|locus:2094997	848	EMB1865 "embryo defective 1865	0.502	0.265	0.329	8.5e-20
TAIR|locus:2096662	1011	CFM2 "CRM family member 2" [Ar	0.712	0.315	0.25	1.1e-19
TAIR|locus:2181372	720	CRS1 "ortholog of maize chloro	0.370	0.230	0.316	3.3e-13

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

 Score = 1088 (388.1 bits), Expect = 3.8e-110, P = 3.8e-110
 Identities = 253/464 (54%), Positives = 303/464 (65%)

Query:     4 RVLVSSASMALR-KSPQFKILLSKFHIFKPF-SYNKYPFQRISMVDVLCKAFGPCYGLKR 61
             RV  S+ASM LR KS Q   L S   +F  F S N+     IS  +++CK       L +
Sbjct:     9 RVSTSAASMLLRRKSRQLGFLASSSPLFSSFNSMNR----TISSCNIVCKV------LHK 58

Query:    62 FSIEGRLW---------IHSAPLRHYIEKVVEKQESSENSSSADXXXXXXXXXXXXXXXX 112
              S+   +W          HS P R   +  + K   SENSSS D                
Sbjct:    59 ESLTRPMWNVSFLRSSSFHSTPARETGDDDISK---SENSSSQDGDSCTKLKRKKLKGKR 115

Query:   113 XXXXWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPE 172
                 WLK FR+KKKKE+ERMT+EEKIL KLRKARKKEER++E +KK+EP ES+E THDPE
Sbjct:   116 AVVRWLKFFRWKKKKEFERMTSEEKILNKLRKARKKEERLMETMKKLEPSESAETTHDPE 175

Query:   173 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKE 232
             ILTPEEHFY+LKMG KCKNYVPVGRRGIYQGVILNMHLHWKKHQTL+V++KTF+ +EVKE
Sbjct:   176 ILTPEEHFYYLKMGLKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLQVVIKTFTPDEVKE 235

Query:   233 IAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLR 292
             IA ELARLTGGIVL++HE NTIIMYRGKNY QPPTEIMSPRITL RKKALDKSK RD LR
Sbjct:   236 IAVELARLTGGIVLDVHEGNTIIMYRGKNYVQPPTEIMSPRITLPRKKALDKSKCRDALR 295

Query:   293 AVKKYIPKXXXXXXXXXXXXXTRSENRSDAAEDVQ--NTELDKPDFGSIPSMMECSENDP 350
             AV+KYIP+             T+ +  +   +D Q  + EL K     I    EC E++ 
Sbjct:   296 AVRKYIPRLEQELQLLQAQAETKRDYTNVKVDDNQERSEELKK----IIERSEECLEDEQ 351

Query:   351 TTESL---MASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHL 407
               +     +A+DS DLSDIFETDSE E + K E RPL+L++F+KFP  N+ E EDF    
Sbjct:   352 EEDEAGLELATDS-DLSDIFETDSELE-DAKTE-RPLFLEEFEKFPAINNREDEDFG--- 405

Query:   408 RQISIDSRNAKSLGKDED---SSHFDEVDKMFLRAASLLKKQKR 448
                  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:   118 LKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPE 177
             L+  R  KK + + MT EE+++Y L++A+KK   +++ LKK +  E     HDPE+ T E
Sbjct:    36 LREIRRAKKLKKKLMTDEERLIYNLKRAKKKVALLLQKLKKYDLPELPSPVHDPELFTSE 95

Query:   178 EHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAEL 237
             +   F K+G K KNYVPVG RG++ GV+ NMH+HWK H+T++V    F  E++KE+A+ +
Sbjct:    96 QVQAFKKIGFKNKNYVPVGVRGVFGGVVQNMHMHWKFHETVQVCCDNFPKEKIKEMASMI 155

Query:   238 ARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKY 297
             ARL+GG+V+ IH   TIIM+RG+NY QP   I  P  TL+++KAL K+++   L + K  
Sbjct:   156 ARLSGGVVINIHNVKTIIMFRGRNYRQPKNLI--PVNTLTKRKALFKARFEQALESQKLN 213

Query:   298 IPK 300
             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:   118 LKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIE-PKESSEMTHDPEILTP 176
             L+ +R K KK+      E +I YKL KA++KEE ++E L+K + PK  +E  +DPE LT 
Sbjct:   126 LRFYRLKAKKKMNSPNPEVRIRYKLEKAKRKEEWLIEKLRKYDVPKSPAE-PYDPESLTE 184

Query:   177 EEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAE-EVKEIAA 235
             EE  Y  + G K KN+V VGRRG++ GV+LN+HLHWKKH+T+KVI K  +   +V E A 
Sbjct:   185 EEQHYLKRTGEKRKNFVLVGRRGVFGGVVLNLHLHWKKHETVKVICKPCNKPGQVHEYAE 244

Query:   236 ELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVK 295
             ELARL+ GIV+++   NTI++YRGKNY +P  E+MSP  TLS+ KAL+K +Y   L    
Sbjct:   245 ELARLSKGIVIDVKPNNTIVLYRGKNYVRP--EVMSPVDTLSKDKALEKYRYEQSLEHTS 302

Query:   296 KYIPK 300
             ++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:   125 KKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLK 184
             KKK++  + AEE+I YKL KA+ KE  ++E LK+ E  +       P  +T EE FY  K
Sbjct:   117 KKKKF--VNAEERIKYKLEKAKIKEALLIERLKRYEVAKVQGPEVRPHEITGEERFYLKK 174

Query:   185 MGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGI 244
             MG+K  NYVP+GRRG++ GVILNMHLHWKKH+T+KVI       +V++ A ELA+L+GG+
Sbjct:   175 MGQKRSNYVPIGRRGVFGGVILNMHLHWKKHETVKVICNNSKPGQVQQYAEELAKLSGGV 234

Query:   245 VLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKXXXX 304
              + I  ++TII YRGK Y QP  ++MSP  TLS+K+A +KSKY   L +V+ +I      
Sbjct:   235 PVNIIGDDTIIFYRGKGYVQP--QVMSPIDTLSKKRAYEKSKYEQSLESVRHFIAIAEKE 292

Query:   305 XXXXXXXXXTRSE-NRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDL 363
                         + N  +    + ++  +          + CS+ D ++E     + E+L
Sbjct:   293 LELYYRHVALYDDPNNRNPLSILDDSPSESRQHHENEFFLSCSDTDSSSED--EDEDEEL 350

Query:   364 SDIFETDSETETEEKAEL 381
              ++ +  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 = 2.6e-22, P = 2.6e-22
 Identities = 78/260 (30%), Positives = 132/260 (50%)

Query:   126 KKEYERMTAEE---KILYKLRKARKKEERIVEGLKKIEP-KESSEMTHDPEILTPEEHFY 181
             K+E E +  E    K+  KL  A +K  +   GL K+E   + +E   DPE +T EE F 
Sbjct:   586 KQEVEILRHENLVRKLERKLAFAERKLLKAERGLAKVEVCLKPAEQREDPESITDEERFM 645

Query:   182 FLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLT 241
             F K+G K K ++ +GRRG++ G + NMHLHWK  + +K+IVK  + + VK++A  L   +
Sbjct:   646 FRKLGLKMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKAKTFDGVKKVALALEAES 705

Query:   242 GGIVLEIHEEN---TIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYI 298
             GGI++ I +      II+YRG++Y +P   ++ P+  L+++KAL +S        + K+I
Sbjct:   706 GGILVSIDKVTKGYAIIVYRGQDYKRPT--MLRPKNLLTKRKALARSIELQRREGLLKHI 763

Query:   299 PKXXXXXXXXXXXXXTRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMAS 358
                             + E  +D  ++    +LD     S     E  ++D   E+    
Sbjct:   764 -STMQAKAKQLRAEIEQMEKVTDKGDEELYNKLDMAYASSDEETDEEDDDDAFPETYAEG 822

Query:   359 DSEDLSDIFETD-SETETEE 377
             +  +  +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 = 8.5e-20, P = 8.5e-20
 Identities = 78/237 (32%), Positives = 125/237 (52%)

Query:   136 EKILYKLRKARKKEERIVEGLKKIEPKE-SSEMTHDPEILTPEEHFYFLKMGRKCKNYVP 194
             ++I +KL  A+ K +R  + L KIE     +   +D E+++ EE   F K+G K K Y+P
Sbjct:   614 KRIQHKLNLAQSKFQRAEKLLSKIEASMIPNGPDYDQEVISEEERAMFRKVGLKMKAYLP 673

Query:   195 VGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN-- 252
             +G RG++ GVI NMHLHWK  + +K+I K  +   V+E A  L   +GG+++ I +    
Sbjct:   674 IGIRGVFDGVIENMHLHWKHRELVKLISKQKNQAFVEETARLLEYESGGVLVAIEKVPKG 733

Query:   253 -TIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKXXXXXXXXXXX 311
               +I YRGKNY +P +  + PR  L++ KAL +S       A+ ++I +           
Sbjct:   734 FALIYYRGKNYRRPIS--LRPRNLLTKAKALKRSIAMQRHEALSQHISELERTIEQMQSQ 791

Query:   312 XXTRSENRSDAAEDVQNTELDKPDFGSIPSMMECSEND--PTT-ESLMASDSE-DLS 364
                 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 = 1.1e-19, P = 1.1e-19
 Identities = 84/336 (25%), Positives = 155/336 (46%)

Query:   120 HFRYKKKKEYERMTAE---EKILYKLRKARKKEERIVEGLKKIEPKESSEMTH-DPEILT 175
             H +  + K  +R + E   EK   KL  A +K+    + L  +E +ES +++  D E +T
Sbjct:   521 HIQTHQMKSRQRNSPEAILEKTSMKLSMALEKKANAEKVLADLENRESPQLSDIDKEGIT 580

Query:   176 PEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAA 235
              +E +   K+G K K ++ +GRRG++ G I NMHLHWK  + +K+I   +S E   ++A 
Sbjct:   581 NDEKYMLRKIGLKMKPFLLLGRRGVFDGTIENMHLHWKYRELVKIICNEYSIEAAHKVAE 640

Query:   236 ELARLTGGIVLEIHEEN---TIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLR 292
              L   +GGI++ +   +    II+YRGKNY +P  + + P+  LS+++AL +S      +
Sbjct:   641 ILEAESGGILVAVEMVSKGYAIIVYRGKNYERP--QCLRPQTLLSKREALKRSVEAQRRK 698

Query:   293 AVKKYIPKXXXXXXXXXXXXXTRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTT 352
             ++K ++ K               S   ++   D +++ +   +     +  + +E +   
Sbjct:   699 SLKLHVLKLSNNIEELNRQLVEDSAT-NETWSDGESSNMMVEE----ETENQHTEPEKAR 753

Query:   353 ESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISI 412
             E +    S DLS     +   E + + E+ PL     +    Q DE      +     S+
Sbjct:   754 EKIELGYSSDLSVPSSGEENWEDDSEGEVDPLTTSSQE---YQEDESESASSQRHEGNSL 810

Query:   413 DSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 448
             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:   124 KKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFL 183
             K + E E  + E K+     K  K    + +     +P E  +   D EILT EE     
Sbjct:   525 KARLEKELKSQEHKLSILKSKIEKSNMELFKLNSLWKPSEGDD---DIEILTNEERECLR 581

Query:   184 KMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIV--KTFSAEEVKEIAAELARLT 241
             ++G K  + + +GRRG++ GV+  +H HWK  +  KVI   K FS   V   A  L   +
Sbjct:   582 RIGLKMNSSLVLGRRGVFFGVMEGLHQHWKHREVAKVITMQKLFS--RVVYTAKALETES 639

Query:   242 GGIVLEIH---EENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVK 295
              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   0.374    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      448       415   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:  44.45u 0.12s 44.57t   Elapsed:  00:00:02
  Total cpu time:  44.45u 0.12s 44.57t   Elapsed:  00:00:02
  Start:  Mon May 20 23:38:05 2013   End:  Mon May 20 23:38:07 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	0.6052	0.9375	0.9459	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	448
smart01103	84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	3e-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 = 3e-21
 Identities = 28/85 (32%), Positives = 46/85 (54%), Gaps = 1/85 (1%)

Query: 174 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEI 233
           LT ++  Y   +    K  V +G+ G+ +GV+  +    +KH+ +KV V     E+ KEI
Sbjct: 1   LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEI 60

Query: 234 AAELARLTGGIVLEIHEENTIIMYR 258
           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: 174 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEI 233
           LT ++  Y   +    K  V +G+ G+ +GV+  +    +KH+ +KV V     E+ KEI
Sbjct: 1   LTGKQRRYLRSLAHHLKPVVQIGKNGLTEGVVEEIDEALEKHELIKVKVLGNDREDRKEI 60

Query: 234 AAELARLTGGIVLEIHEENTIIMYR 258
           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	448
KOG1990	564	consensus Poly(A)-specific exoribonuclease PARN [R	99.95
PRK10343	97	RNA-binding protein YhbY; Provisional	99.94
TIGR00253	95	RNA_bind_YhbY putative RNA-binding protein, YhbY f	99.94
PF01985	84	CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR	99.94
COG1534	97	Predicted RNA-binding protein containing KH domain	99.93
KOG1990	564	consensus Poly(A)-specific exoribonuclease PARN [R	97.8

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

Probab=99.95  E-value=6.4e-28  Score=252.72  Aligned_cols=210  Identities=41%  Similarity=0.590  Sum_probs=189.6

Q ss_pred             hhhhhhhhhhhhhhhhhh-----hHHhhccChH---HHHHHHHHHHHHHHHHHHHhhcccCCC-CCCCCCCCCCCCCHHH
Q 013187          108 LKGKRAVVRWLKHFRYKK-----KKEYERMTAE---EKILYKLRKARKKEERIVEGLKKIEPK-ESSEMTHDPEILTPEE  178 (448)
Q Consensus       108 ~k~k~a~~~~~~~~r~~~-----kke~~~~~~e---~ri~~KL~~A~kK~er~~e~L~K~E~~-~paEp~~DpE~LT~EE  178 (448)
                      ..-..+..+|.+.+.+..     +.+.+.+..+   +.+.+++..+++|++++...|++++.+ .|++..++++.+|.++
T Consensus       308 ~e~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee  387 (564)
T KOG1990|consen  308 LELARAKAKKEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEE  387 (564)
T ss_pred             HHHHHHhcccccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHH
Confidence            344556677776666554     6666666555   788999999999999999999999987 8899999999999999


Q ss_pred             HHHHHhhhccCCceeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCH-HHHHHHHHHHHHHhCCEEEEEe---eCcEE
Q 013187          179 HFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSA-EEVKEIAAELARLTGGIVLEIH---EENTI  254 (448)
Q Consensus       179 Rk~LRKlGhkLKPVV~IGKrGVTDgVIeeIh~AwK~HELVKVKvk~~s~-ed~keIAeeLee~SGGeLVQVi---IG~tI  254 (448)
                      +.+++++|.+|++++.+|++|+++||+.++|.||++||++||+|+.... .++++.|..++..+|+++|++.   .|..|
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             EEEeCCCCCCCCCccCCCCcccchHHHHHHHHHHhhhHHHHhhHHHHHHHHHHHHHHHhhhcccc
Q 013187          255 IMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENR  319 (448)
Q Consensus       255 ILYRGKNY~rP~~~i~~P~~lLtKrkAL~rS~e~Qr~eslk~~I~~le~~ie~l~~~~~~~~~~~  319 (448)
                      +.|||+||++|.+  |+|.++|+||+|+.+++++|+.+|+++||..+++++++++.++.......
T Consensus       468 ~~yr~k~y~~p~~--l~P~~~l~~~k~~~~~~~~~~~~a~~~~i~~~~~~~e~~~~~~~~~~~~~  530 (564)
T KOG1990|consen  468 IAYRGKNYDRPTS--LRPRNLLSRRKALERSLEEQRKEALKSHISDLEQEIEQLQASVEAMPAIN  530 (564)
T ss_pred             HHhhhhhccCCcc--cCchhhhcccCCccccHHHHHHHHHhhhcchhhhhHHHhhcchhcccccc
Confidence            9999999999975  99999999999999999999999999999999999999999987765444

>PRK10343 RNA-binding protein YhbY; Provisional

Probab=99.94  E-value=5.1e-27  Score=198.92  Aligned_cols=89  Identities=21%  Similarity=0.340  Sum_probs=86.3

Q ss_pred             CCCCHHHHHHHHhhhccCCceeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeC
Q 013187          172 EILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE  251 (448)
Q Consensus       172 E~LT~EERk~LRKlGhkLKPVV~IGKrGVTDgVIeeIh~AwK~HELVKVKvk~~s~ed~keIAeeLee~SGGeLVQViIG  251 (448)
                      ++||++||++||++||+|+|+|+||++||||+|+.+|+.+|++||||||++.+++.+++++++++|++.|||++||+ ||
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 013187          252 NTIIMYRGKN  261 (448)
Q Consensus       252 ~tIILYRGKN  261 (448)
                      +++||||++.
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=99.94  E-value=6e-27  Score=197.51  Aligned_cols=87  Identities=28%  Similarity=0.369  Sum_probs=84.8

Q ss_pred             CCHHHHHHHHhhhccCCceeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCcE
Q 013187          174 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT  253 (448)
Q Consensus       174 LT~EERk~LRKlGhkLKPVV~IGKrGVTDgVIeeIh~AwK~HELVKVKvk~~s~ed~keIAeeLee~SGGeLVQViIG~t  253 (448)
                      ||++||++||++||+|+|+|+||++|||++||++|+.+|++||||||++.+++.++++++|++|++.|||++||+ +|++
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 013187          254 IIMYRGKN  261 (448)
Q Consensus       254 IILYRGKN  261 (448)
                      +||||++.
T Consensus        80 ~vlYR~~~   87 (95)
T TIGR00253        80 IVLYRPTK   87 (95)
T ss_pred             EEEEecCC
Confidence            99999864

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=1.4e-26  Score=189.12  Aligned_cols=84  Identities=36%  Similarity=0.522  Sum_probs=74.9

Q ss_pred             CCHHHHHHHHhhhccCCceeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCcE
Q 013187          174 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT  253 (448)
Q Consensus       174 LT~EERk~LRKlGhkLKPVV~IGKrGVTDgVIeeIh~AwK~HELVKVKvk~~s~ed~keIAeeLee~SGGeLVQViIG~t  253 (448)
                      ||++|+++||++||+|+|+|+||++|||++|+++|+.+|++||||||+|.+++.++++++|+.|++.|||++|++ +|++
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 7999


Q ss_pred             EEEEe
Q 013187          254 IIMYR  258 (448)
Q Consensus       254 IILYR  258 (448)
                      +||||
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.

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

Probab=99.93  E-value=3.4e-25  Score=188.27  Aligned_cols=91  Identities=26%  Similarity=0.429  Sum_probs=86.4

Q ss_pred             CCCHHHHHHHHhhhccCCceeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCc
Q 013187          173 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  252 (448)
Q Consensus       173 ~LT~EERk~LRKlGhkLKPVV~IGKrGVTDgVIeeIh~AwK~HELVKVKvk~~s~ed~keIAeeLee~SGGeLVQViIG~  252 (448)
                      +||++|+++||+.||+++|+|+||++|||++||.+|+.+|++||||||++.+++.++.+++|+.|++.+||.+||+ +|+
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            5999999999999999999999999999999999999999999999999999999999999999999999999998 699


Q ss_pred             EEEEEeCCCCCCC
Q 013187          253 TIIMYRGKNYAQP  265 (448)
Q Consensus       253 tIILYRGKNY~rP  265 (448)
                      ++|||| .+...+
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=97.80  E-value=1.1e-05  Score=86.26  Aligned_cols=152  Identities=21%  Similarity=0.288  Sum_probs=125.6

Q ss_pred             hhhhhhhhhhhhhhHHhhccChHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCCCCCCCCCCCHHHHHHHHhhhccCCce
Q 013187          113 AVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNY  192 (448)
Q Consensus       113 a~~~~~~~~r~~~kke~~~~~~e~ri~~KL~~A~kK~er~~e~L~K~E~~~paEp~~DpE~LT~EERk~LRKlGhkLKPV  192 (448)
                      +...|+..++..++.-...|.++..--|-..........+.+.+..+..|...-+...+..||..+.-++|.+|-...|+
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            45557777777778888888888544444444555666778888888888777788889999999999999999999999


Q ss_pred             eeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCC-CHHHHHHHHHHH--HHHhCCEEEEEeeCcEEEEEeCCCCCCC
Q 013187          193 VPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTF-SAEEVKEIAAEL--ARLTGGIVLEIHEENTIIMYRGKNYAQP  265 (448)
Q Consensus       193 V~IGKrGVTDgVIeeIh~AwK~HELVKVKvk~~-s~ed~keIAeeL--ee~SGGeLVQViIG~tIILYRGKNY~rP  265 (448)
                      +.+|.++.-.++...|..+|..|+..|+-+... .......++..+  -..+|+.||.. -|..+|+||++||-.|
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            999999999999999999999999999877654 344456778888  88999999964 6889999999999774

---

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	448
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,	1e-08
1j0a_A	325	1-aminocyclopropane-1-carboxylate deaminase; PLP d	9e-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: 174 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEI 233
           L+ ++  +   +       V +G  G+ +GV+  +      H+ +KV V     E  + I
Sbjct: 3   LSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLI 62

Query: 234 AAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRK 279
              + 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: 173 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKE 232
           +LT ++  Y   +         +G+ GI + +I  +    +  + +KV V   + ++ KE
Sbjct: 1   MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKE 60

Query: 233 IAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKA 281
           +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: 208 MHLHWKK--HQTLKVIVKTF-------------SAEEVKEIAAELARLTGG----IVLEI 248
               +K          V  F             S EE+  I      ++G       L  
Sbjct: 14  HQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLS 73

Query: 249 HEENTIIMYRG----KNYAQPPTEIMSPRITLSRKKALDKSKY---RDGL----RAVKKY 297
            +E  +  +       NY      +MSP  T  R+ ++    Y   RD L    +   KY
Sbjct: 74  KQEEMVQKFVEEVLRINYKF----LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKY 129

Query: 298 -IPKLEQELELLRAQAETRSENR------------SDAAEDVQNTEL-DKPDFGSI--PS 341
            + +L+  L+L +A  E R                  A +   + ++  K DF  I   +
Sbjct: 130 NVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFK-IFWLN 188

Query: 342 MMECSENDPTTESL------MASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFP-- 393
           +  C+  +   E L      +  +    SD            +AELR L   +   +   
Sbjct: 189 LKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK--PYENC 246

Query: 394 ------VQNDEEHEDFEEH---L---RQISI-DSRNAK-----SLGKDEDSSHFDEVDKM 435
                 VQN +    F      L   R   + D  +A      SL     +   DEV  +
Sbjct: 247 LLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL 306

Query: 436 FLRAASL 442
            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 = 56.4 bits (135), Expect = 1e-08
 Identities = 81/557 (14%), Positives = 153/557 (27%), Gaps = 173/557 (31%)

Query: 20  FKILLSK-FHIFKPF-----SYNKYPF--QRISMVDVLCKAFGPCYGLKRFSIE-GRLWI 70
           F  LLSK   + + F       N Y F    I           P    + +  +  RL+ 
Sbjct: 68  FWTLLSKQEEMVQKFVEEVLRIN-YKFLMSPIKTEQR-----QPSMMTRMYIEQRDRLYN 121

Query: 71  HSAPLRHY----IEKVVEKQESSENSSSAD--------GAG----VAKVKR-KKLKGKRA 113
            +     Y    ++  ++ +++      A         G+G       V    K++ K  
Sbjct: 122 DNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMD 181

Query: 114 V-VRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKE----ERIVEGLKKIEPKESSEMT 168
             + WL   +     E   +   +K+LY++             I   +  I+ +    + 
Sbjct: 182 FKIFWLN-LKNCNSPE-TVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLK 239

Query: 169 H--------------DPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKK 214
                          + +       F        CK  + +  R  ++ V   +      
Sbjct: 240 SKPYENCLLVLLNVQNAKAW---NAFNL-----SCK--ILLTTR--FKQVTDFLSAATTT 287

Query: 215 HQTLKVIVKTFSAEEVKEIAA--------ELAR--------LTGGIVLEIHEENTIIMYR 258
           H +L     T + +EVK +          +L R            I   I +        
Sbjct: 288 HISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLA----T 343

Query: 259 GKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRA-------VKKYIPKLEQELELLRAQ 311
             N+     + ++  I  S    L+ ++YR                IP     L L+   
Sbjct: 344 WDNWKHVNCDKLTTIIESSLN-VLEPAEYRKMFDRLSVFPPSAH--IP--TILLSLIWFD 398

Query: 312 AETRSE--------NRSDAAEDVQNTELDKPDFGSIPSM---MECS-ENDPTTESLM--- 356
                           S   +  + + +      SIPS+   ++   EN+      +   
Sbjct: 399 VIKSDVMVVVNKLHKYSLVEKQPKESTI------SIPSIYLELKVKLENEYALHRSIVDH 452

Query: 357 -----ASDSEDLSDIFETD----------SETE-TEEKAELRPLYLD------------- 387
                  DS+DL   +                E  E     R ++LD             
Sbjct: 453 YNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDST 512

Query: 388 ----------------QFDKFPVQNDEEHE----DFEEHLRQISIDSRNAKSLG------ 421
                            +  +   ND ++E       + L +I  +   +K         
Sbjct: 513 AWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIAL 572

Query: 422 KDEDSSHFDEVDKMFLR 438
             ED + F+E  K   R
Sbjct: 573 MAEDEAIFEEAHKQVQR 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 = 9e-04
 Identities = 20/143 (13%), Positives = 49/143 (34%), Gaps = 8/143 (5%)

Query: 128 EYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGR 187
            +E M   E+I  +L++  +K   I  G        +S +     +    E     ++ +
Sbjct: 130 SFELMKYAEEIAEELKREGRKPYVIPPG-------GASPIGTLGYVRAVGEIATQSEV-K 181

Query: 188 KCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLE 247
                V  G  G   G+ L + +  +  + + + V  F      ++   +      + ++
Sbjct: 182 FDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEAAELLGVK 241

Query: 248 IHEENTIIMYRGKNYAQPPTEIM 270
           +     +  Y    Y +   E+ 
Sbjct: 242 VEVRPELYDYSFGEYGKITGEVA 264

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	448
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=1.6e-28  Score=208.88  Aligned_cols=91  Identities=20%  Similarity=0.354  Sum_probs=87.4

Q ss_pred             CCCHHHHHHHHhhhccCCceeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCc
Q 013187          173 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  252 (448)
Q Consensus       173 ~LT~EERk~LRKlGhkLKPVV~IGKrGVTDgVIeeIh~AwK~HELVKVKvk~~s~ed~keIAeeLee~SGGeLVQViIG~  252 (448)
                      |||++||++||++||+|+|+|+||++|||++|+++|++||++||||||+|.+++.++++++|++|++.|||++||+ ||+
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 013187          253 TIIMYRGKNYAQP  265 (448)
Q Consensus       253 tIILYRGKNY~rP  265 (448)
                      ++||||++. ..|
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 344

>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=3.4e-28  Score=204.41  Aligned_cols=88  Identities=18%  Similarity=0.317  Sum_probs=85.7

Q ss_pred             CCCHHHHHHHHhhhccCCceeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCc
Q 013187          173 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  252 (448)
Q Consensus       173 ~LT~EERk~LRKlGhkLKPVV~IGKrGVTDgVIeeIh~AwK~HELVKVKvk~~s~ed~keIAeeLee~SGGeLVQViIG~  252 (448)
                      .||++||++||++||+|+|+|+||++|||++|+++|++||++||||||+|.+++.++++++|++|++.|||++||+ ||+
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 013187          253 TIIMYRGKN  261 (448)
Q Consensus       253 tIILYRGKN  261 (448)
                      ++||||++.
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	448
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 = 78.2 bits (193), Expect = 1e-18
 Identities = 18/90 (20%), Positives = 41/90 (45%), Gaps = 1/90 (1%)

Query: 173 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKE 232
           +LT ++  Y   +         +G+ GI + +I  +    +  + +KV V   + ++ KE
Sbjct: 1   MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKE 60

Query: 233 IAAELARLTGGIVLEIHEENTIIMYRGKNY 262
           +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: 174 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEI 233
           L+ ++  +   +       V +G  G+ +GV+  +      H+ +KV V     E  + I
Sbjct: 3   LSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLI 62

Query: 234 AAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPR 273
              + 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	448
d1jo0a_	97	YhbY homologue HI1333 {Haemophilus influenzae [Tax	99.95
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=99.95  E-value=1.4e-28  Score=203.27  Aligned_cols=88  Identities=18%  Similarity=0.317  Sum_probs=85.6

Q ss_pred             CCCHHHHHHHHhhhccCCceeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCc
Q 013187          173 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  252 (448)
Q Consensus       173 ~LT~EERk~LRKlGhkLKPVV~IGKrGVTDgVIeeIh~AwK~HELVKVKvk~~s~ed~keIAeeLee~SGGeLVQViIG~  252 (448)
                      +||++||++||++||+|+|+|+||++|||++|+.+|+.||++||||||+|.+++.++++++|++|++.|||++||+ +|+
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            6999999999999999999999999999999999999999999999999999999999999999999999999986 699


Q ss_pred             EEEEEeCCC
Q 013187          253 TIIMYRGKN  261 (448)
Q Consensus       253 tIILYRGKN  261 (448)
                      ++||||++.
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=1.7e-28  Score=202.43  Aligned_cols=89  Identities=20%  Similarity=0.351  Sum_probs=86.5

Q ss_pred             CCCHHHHHHHHhhhccCCceeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCc
Q 013187          173 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  252 (448)
Q Consensus       173 ~LT~EERk~LRKlGhkLKPVV~IGKrGVTDgVIeeIh~AwK~HELVKVKvk~~s~ed~keIAeeLee~SGGeLVQViIG~  252 (448)
                      |||++||++||++||+|+|+|+||++|||++|+.+|+.||+.||||||+|.+++.++++++|++||+.|||++||+ +|+
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            7999999999999999999999999999999999999999999999999999999999999999999999999996 799


Q ss_pred             EEEEEeCCCC
Q 013187          253 TIIMYRGKNY  262 (448)
Q Consensus       253 tIILYRGKNY  262 (448)
                      ++||||++++
T Consensus        80 ~~vlyR~~~~   89 (96)
T d1rq8a_          80 MIVIYRESKE   89 (96)
T ss_dssp             EEEEEECCCS
T ss_pred             EEEEEeCCCC
Confidence            9999998765