Citrus Sinensis ID: 015090

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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---
Protein Sequence
MRLRLHCSSMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVVEKQESSENSSSADGAGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccEEEEcccccccccHHccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHcccEEEEEEcccHHHHHHHHHHHHHHHccEEEEEEEccEEEEEEcccccccccccccccccccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHccccHHHcccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHcccccccccccccccccccccccHHHHHHHHHHcccccccccccccccccccHHHHHHcHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccEEEEEccccEEEEEEEccccccEcccccccEEEEccccccccccccccccccccccccccccccHHHHHHHHcHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHcHccccccccccccccHHHHHHHHHHHccccEEEEEEccccHHHHHHHHHHHHHHcccEEEEEccccEEEEEEcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHccccHHccccHcccccHcHcccccccccccccccccccccccccccccccccccccccccHHHHccccccccccHcHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MRLRLHCSSMVDVLCKafgpcyglkrfsiegrlwihsapLRHYIEKVVEKqessensssadgaGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLkkiepkessemthdpeiltpeeHFYFLKMGrkcknyvpvgrrgiYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIImyrgknyaqppteimspritlsrkkaldkskyrDGLRAVKKYIPKLEQELELLRAQAETrsenrsdaaedvqnteldkpdfgsipsmmecsendptteslmasdsedlsdifetdseteteekaelrplyldqfdkfpvqndeehEDFEEHLRQISIDsrnakslgkdedsshfdEVDKMFLRAASLLKKQKR
Flexible Loop (DISEMBL)
MRLRLHCSSMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVVekqessensssadgagvakvkrkklkgkravvrwlkhfrykkkkeyermtaeeKILYklrkarkkeeriveglkkiepkessemthdpeiltPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIImyrgknyaqppteimspritlsrkkaldkskyrdglravKKYIPKLEQELELLRAQAetrsenrsdaaedvqnteldkpdfgsipSMMECSENDPTTESLMASDSEDLSDIFETDseteteekaelrplyldQFDKFPVQNDEEHEDFEEHLRQisidsrnakslgkdedsshfdevDKMFLRAASLLKKQKR
Low Complexity Region (SEG)
MRLRLHCSSMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVVEKQESSENSSSADgagvakvkrkklkgkravvrWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKleqelellraqaeTRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR
Disordered region (IsUnstruct)
****LHCSSMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVV*************************KGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKL*********************************PEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYA***************************LRAVKKYIP*****************************************************************************************************************************************************
Disordered Region (DISOPRED)
*************LCKAFGPCYGLKRFSIEGRLWIH*********************************************************************KLRKARKKEERI***********************PEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRIT*****************************LE***************************************************************************************************************************DEVDKMFLRAASLL*****
Disordered Region (DISEMBL)
MRLRLHCSSMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKV****************************KRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQ***************QNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDI************AELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRN************FDEVDKMFLRAASLLKKQKR
Disordered Region (DISPRO)
*RLRLHCSSMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPL*************************AKVK****KGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPK*****THDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSE**************************************************************ELRPLYLDQFDKFPV****EHEDFEEHLRQISID************SSHFDEVDKMFLRAASLLKK***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRLRLHCSSMVDVLCKAFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVVEKQESSENSSSADGAGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGxxxxxxxxxxxxxxxxxxxxxxxxxxxxRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR
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	413	2.2.26 [Sep-21-2011]
Q67XL4	444	Uncharacterized CRM domai	yes	no	0.929	0.864	0.622	1e-123
Q9FYT6	715	Chloroplastic group IIA i	N/A	no	0.348	0.201	0.393	3e-17
Q6YYA3	725	Chloroplastic group IIA i	no	no	0.348	0.198	0.373	2e-15
Q9LF10	720	Chloroplastic group IIA i	no	no	0.351	0.201	0.328	9e-14
Q5VMQ5	701	CRS2-associated factor 1,	no	no	0.217	0.128	0.307	1e-06
Q84N49	674	CRS2-associated factor 1,	N/A	no	0.254	0.155	0.318	8e-06
Q6Z4U2	428	CRS2-associated factor 1,	no	no	0.217	0.210	0.268	3e-05
Q0J7J7	366	CRS2-associated factor 2,	no	no	0.176	0.199	0.283	0.0005
Q84N48	611	CRS2-associated factor 2,	N/A	no	0.365	0.247	0.236	0.0007

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

 Score =  442 bits (1136), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 261/419 (62%), Positives = 309/419 (73%), Gaps = 35/419 (8%)

Query: 9   SMVDVLCKAFGPCYGLKRFSIEGRLW---------IHSAPLRHYIEKVVEKQESSENSSS 59
           S  +++CK       L + S+   +W          HS P R   +  + K   SENSSS
Sbjct: 47  SSCNIVCKV------LHKESLTRPMWNVSFLRSSSFHSTPARETGDDDISK---SENSSS 97

Query: 60  ADGAGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVE 119
            DG    K+KRKKLKGKRAVVRWLK FR+KKKKE+ERMT+EEKIL KLRKARKKEER++E
Sbjct: 98  QDGDSCTKLKRKKLKGKRAVVRWLKFFRWKKKKEFERMTSEEKILNKLRKARKKEERLME 157

Query: 120 GLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKK 179
            +KK+EP ES+E THDPEILTPEEHFY+LKMG KCKNYVPVGRRGIYQGVILNMHLHWKK
Sbjct: 158 TMKKLEPSESAETTHDPEILTPEEHFYYLKMGLKCKNYVPVGRRGIYQGVILNMHLHWKK 217

Query: 180 HQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRI 239
           HQTL+V++KTF+ +EVKEIA ELARLTGGIVL++HE NTIIMYRGKNY QPPTEIMSPRI
Sbjct: 218 HQTLQVVIKTFTPDEVKEIAVELARLTGGIVLDVHEGNTIIMYRGKNYVQPPTEIMSPRI 277

Query: 240 TLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQ--NTELD 297
           TL RKKALDKSK RD LRAV+KYIP+LEQEL+LL+AQAET+ +  +   +D Q  + EL 
Sbjct: 278 TLPRKKALDKSKCRDALRAVRKYIPRLEQELQLLQAQAETKRDYTNVKVDDNQERSEELK 337

Query: 298 KPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKF 357
           K    S   + +  E D     L A+DS DLSDIFETDSE E + K E RPL+L++F+KF
Sbjct: 338 KIIERSEECLEDEQEEDEAGLEL-ATDS-DLSDIFETDSELE-DAKTE-RPLFLEEFEKF 393

Query: 358 PVQNDEEHEDFEEHLRQISIDSRNAKSLGKDED---SSHFDEVDKMFLRAASLLKKQKR 413
           P  N+ E EDF         D   AKS G++ D   S +FDEVDKMFLRAA LLKK++R
Sbjct: 394 PAINNREDEDFG--------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: 105 YKLRKARKKEERIVEGLKKIEPKES-SEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRR 163
           +KL    KK ER  + L K+    S SE + D E LT EE   F ++GRK    V +GRR
Sbjct: 529 WKLSVLNKKIERSNQALAKLHSSWSPSEQSADREHLTEEEKIMFRRIGRKMDGLVLLGRR 588

Query: 164 GIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT---II 220
           GI+ GVI  +H HWK  + +KVI K     ++   A+ L   TGGI++ + +  T   II
Sbjct: 589 GIFDGVIEEIHQHWKHKEVVKVITKQNQTRQIMYAASLLEVETGGILIAVEKLTTSHAII 648

Query: 221 MYRGKNYAQPPTEIMSPRITLSRKKALDKS 250
           +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: 105 YKLRKARKKEERIVEGLKKIEPKES-SEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRR 163
           ++L    KK ER  + L K+    S S+   D E+LT EE   F K+G K   +V +GRR
Sbjct: 531 WRLSMLTKKIERSNQVLAKLHSSWSPSKKDGDRELLTEEERRIFRKIGLKMDEHVLLGRR 590

Query: 164 GIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT---II 220
           G+++GVI  +H HWK  + +KVI K   A ++   +  L   TGG ++ I    T   II
Sbjct: 591 GVFEGVIEEIHQHWKHKEVVKVITKQNQASQITYTSMMLEVETGGTLIAIERFTTSHAII 650

Query: 221 MYRGKNYAQPPTEIMSPRITLSRKKALDKS 250
           +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 = 78.6 bits (192), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 49/149 (32%), Positives = 83/149 (55%), Gaps = 4/149 (2%)

Query: 130 SEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKT 189
           SE   D EILT EE     ++G K  + + +GRRG++ GV+  +H HWK  +  KVI   
Sbjct: 563 SEGDDDIEILTNEERECLRRIGLKMNSSLVLGRRGVFFGVMEGLHQHWKHREVAKVITMQ 622

Query: 190 FSAEEVKEIAAELARLTGGIVLEIH---EENTIIMYRGKNYAQPPTEIMSPRITLSRKKA 246
                V   A  L   + G+++ I    E + I++YRGKNY +P +++M+  + L+++KA
Sbjct: 623 KLFSRVVYTAKALETESNGVLISIEKLKEGHAILIYRGKNYKRPSSKLMAQNL-LTKRKA 681

Query: 247 LDKSKYRDGLRAVKKYIPKLEQELELLRA 275
           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 = 54.7 bits (130), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/91 (30%), Positives = 47/91 (51%), Gaps = 1/91 (1%)

Query: 137 EILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVK 196
           E LT EE    +K   K K  + +GR G+   ++ N+H HWK+ +  K+  K     ++ 
Sbjct: 183 EPLTKEEVDELVKATLKTKRQLNIGRDGLTHNMLENIHSHWKRKRVCKIKCKGVCTVDMD 242

Query: 197 EIAAELARLTGGIVLEIHEENTIIMYRGKNY 227
            +  +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 = 52.0 bits (123), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 35/110 (31%), Positives = 55/110 (50%), Gaps = 5/110 (4%)

Query: 121 LKKIEPKESSEMTHD--PEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWK 178
           L  +EP+  S    D   E LT EE    +K   K K  + +GR G+   ++ N+H HWK
Sbjct: 165 LAGMEPRYQSVSREDILGEPLTKEEVSELVKGSLKSKRQLNMGRDGLTHNMLENIHSHWK 224

Query: 179 KHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTII-MYRGKNY 227
           + +  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 = 50.4 bits (119), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/93 (26%), Positives = 50/93 (53%), Gaps = 3/93 (3%)

Query: 137 EILTPEEHFYFLKMGRK--CKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEE 194
           E LTP E  + +   +K   K  + +GR G+   ++ ++H HWK  + ++V        +
Sbjct: 155 EPLTPAERAFLVSKCQKSRTKKQINLGRDGLTHNMLNDIHNHWKNDEAVRVKCLGVPTVD 214

Query: 195 VKEIAAELARLTGGIVLEIHEENTIIMYRGKNY 227
           ++ +  +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|Q0J7J7|CAF2M_ORYSJ CRS2-associated factor 2, mitochondrial OS=Oryza sativa subsp. japonica GN=Os08g0188000 PE=2 SV=2

 Score = 46.2 bits (108), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 154 CKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEI 213
           C   + +G+ G+   +I ++H HWK+ + +++        ++  I   L   TGG V+  
Sbjct: 162 CSRQINLGKGGVTHNMIDDIHNHWKRAEAVRIKCLGVPTLDMDNICFHLEDKTGGKVI-Y 220

Query: 214 HEENTIIMYRGKNY 227
              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)

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

 Score = 45.4 bits (106), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 40/169 (23%), Positives = 76/169 (44%), Gaps = 18/169 (10%)

Query: 63  AGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLK 122
            G A +  K+ K +R  VR          +E  +  +   I+ ++R+ RK +      L 
Sbjct: 167 TGKAPLLTKEEKARRRGVR----LHTPLGQETPQTVSAHGIMMEVRERRKMD------LA 216

Query: 123 KIEPKES---SEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKK 179
           ++ P +     E+  +P  LTP E    +K        + +GR G+   ++  +H HW++
Sbjct: 217 RVSPGDGRSREEVLGEP--LTPSEVRALVKPHISHNRQLNIGRDGLTHNMLEMIHCHWRR 274

Query: 180 HQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTII-MYRGKNY 227
            +  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)

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	413
224132018	413	predicted protein [Populus trichocarpa]	0.946	0.946	0.658	1e-149
255572670	458	conserved hypothetical protein [Ricinus	0.990	0.893	0.664	1e-149
225448146	401	PREDICTED: uncharacterized CRM domain-co	0.924	0.952	0.694	1e-145
356501797	382	PREDICTED: uncharacterized CRM domain-co	0.898	0.971	0.689	1e-140
356498434	383	PREDICTED: uncharacterized CRM domain-co	0.878	0.947	0.685	1e-137
297739537	331	unnamed protein product [Vitis vinifera]	0.765	0.954	0.719	1e-131
449458069	500	PREDICTED: uncharacterized CRM domain-co	0.937	0.774	0.594	1e-130
357439975	443	CRM domain-containing protein, putative	0.953	0.889	0.621	1e-130
357439925	472	CRM domain-containing protein, putative	0.953	0.834	0.582	1e-125
297831446	1055	predicted protein [Arabidopsis lyrata su	0.929	0.363	0.618	1e-123

>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: 14  LCKAFG--PCYGLKR--FSIEGRLWIHSAPLRHYIEKVVEKQESSENSSSADGAGVAKVK 69
           +CK  G  P Y +K     + G LWIHS P  + ++KVVE  E+ E +++       KVK
Sbjct: 1   MCKVLGQRPVYNVKGHLVPLVGHLWIHSCPSLNNVDKVVEPTENFEKTAAVFSGSDVKVK 60

Query: 70  RKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKES 129
           R KLKGKRAVVRWLK FR+KKKKEYERMTAEEKILYKLRKA++KEER V+ LKKIEPKES
Sbjct: 61  RPKLKGKRAVVRWLKFFRWKKKKEYERMTAEEKILYKLRKAQRKEERFVQALKKIEPKES 120

Query: 130 SEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKT 189
           SE THDPEILTPEEHF+FLKMG KCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKV+VKT
Sbjct: 121 SEATHDPEILTPEEHFFFLKMGLKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVVVKT 180

Query: 190 FSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDK 249
           F+ EEVKEIAAELAR TGGIVL+IHEENTIIMYRGKNY+QPPTEIMSPR+TLSRKKALDK
Sbjct: 181 FTPEEVKEIAAELARFTGGIVLDIHEENTIIMYRGKNYSQPPTEIMSPRVTLSRKKALDK 240

Query: 250 SKYRDGLRAVKKYIPKLEQELELLRAQAETRS-----ENRSDAAEDVQNTE-----LDKP 299
           SK RDGLRA+++YIP+L+Q+LELL A+A  ++     E+RS +++ ++N+E     +D+ 
Sbjct: 241 SKCRDGLRALRRYIPRLQQDLELLHARAGGKTDIDGAESRSISSKQLENSEKLKEIIDRQ 300

Query: 300 DFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPV 359
           D        E SE+ P T+  +ASDSEDLSDIFETDS+ +TEE ++ RPLYL++F+KF V
Sbjct: 301 D--------EGSEDGPDTDLGIASDSEDLSDIFETDSDADTEETSK-RPLYLEEFEKFSV 351

Query: 360 QNDEEHEDFEEHLRQISIDSRNAKSLGK--------DEDSSHFDEVDKMFLRAASLLKKQ 411
           + D E EDFEEHLRQIS+ S+   + GK        D DS  FDEVD+MFLRAASLLK++
Sbjct: 352 EADGEPEDFEEHLRQISLGSKKGVTSGKDVDIPTGVDVDSPSFDEVDRMFLRAASLLKRK 411

Query: 412 KR 413
           KR
Sbjct: 412 KR 413

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  533 bits (1374), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 287/432 (66%), Positives = 335/432 (77%), Gaps = 23/432 (5%)

Query: 3   LRLHCSSMVDVLCK------AFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVVEKQESSEN 56
           L    +S+  ++CK      AF P Y L+   I G  WIH  P    I+K  E    S  
Sbjct: 29  LTYRTTSLFHIICKVFSQAPAFRPVYVLEGPHIGGHRWIHFGPTLTDIDKDGEPPPLSGQ 88

Query: 57  SSSADGAGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEER 116
           S+  +G+G AKVKRKKLKGKRAVVRWLK FR+KKKKEYERMTAEEK+LYKL+KA+KKEER
Sbjct: 89  STMVEGSGCAKVKRKKLKGKRAVVRWLKFFRWKKKKEYERMTAEEKLLYKLKKAQKKEER 148

Query: 117 IVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLH 176
            V+ LKKIEP +SSE THDPEILTPEEHF+FLKMG KCKNYVPVGRRGIYQGVILNMHLH
Sbjct: 149 YVQALKKIEPVDSSETTHDPEILTPEEHFFFLKMGLKCKNYVPVGRRGIYQGVILNMHLH 208

Query: 177 WKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMS 236
           WKKHQT++V+VKTFS EEVKEIAAELARLTGGIVL+IHEENTIIMYRGKNY+QPPTEIMS
Sbjct: 209 WKKHQTVQVVVKTFSPEEVKEIAAELARLTGGIVLDIHEENTIIMYRGKNYSQPPTEIMS 268

Query: 237 PRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQNTEL 296
           PRITLSRKKALDKSKYRDGLRAV+ YIP+LEQ+LELL+ Q+  ++E  S +AE+   T+ 
Sbjct: 269 PRITLSRKKALDKSKYRDGLRAVRNYIPRLEQDLELLKVQSMGKAECGSASAEETLYTD- 327

Query: 297 DKPDFGSIPSMM---------------ECSENDPTTESLMASDSEDLSDIFETDSETETE 341
           D  + G +PS                 ECSE +   +  M SDSEDLSDIFETDS+TETE
Sbjct: 328 DGAESGGVPSTPLENSEKLKKITDGQEECSEEESPMDLGMLSDSEDLSDIFETDSDTETE 387

Query: 342 EKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMF 401
           +K + RPLYL++F KFP+Q +EE EDFEEHLRQ+S+DSR  +S  KD D   FDEVD++F
Sbjct: 388 DKVK-RPLYLEEFKKFPIQGNEEPEDFEEHLRQLSVDSRKVESSEKDSDIPSFDEVDRLF 446

Query: 402 LRAASLLKKQKR 413
           LRAASLLKK+KR
Sbjct: 447 LRAASLLKKKKR 458

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

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: 31  GRLWIHSAPLRHYIE-KVVEKQESSENSSSADGAGVAKVKRKKLKGKRAVVRWLKHFRYK 89
            R  +H+  L H +E  V E ++   +S++A G    KVKRKKLKGKRAVVRWLK FR+K
Sbjct: 4   ARFLVHNLLLGHSMEYGVAEPEKLPVDSTTAAGTVETKVKRKKLKGKRAVVRWLKFFRWK 63

Query: 90  KKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLK 149
           KKKEYERMTAEEKILYKLRKAR+KEER+ E L KIEPKESSE THDPEILTPEEHF+FLK
Sbjct: 64  KKKEYERMTAEEKILYKLRKARRKEERLAEALTKIEPKESSETTHDPEILTPEEHFFFLK 123

Query: 150 MGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGI 209
           MG KCKNYVP+GRRGIYQGVILNMHLHWKKHQTL+V+VKTFS EEVKEIA ELARLTGGI
Sbjct: 124 MGLKCKNYVPIGRRGIYQGVILNMHLHWKKHQTLQVVVKTFSPEEVKEIAVELARLTGGI 183

Query: 210 VLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQE 269
           VL+IHEENTIIMYRGKNY+QPPTEIMSPRITLSRKKALDKSKYRDGLRAV+KYIP+LE +
Sbjct: 184 VLDIHEENTIIMYRGKNYSQPPTEIMSPRITLSRKKALDKSKYRDGLRAVRKYIPRLEGD 243

Query: 270 LELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSMM---------------ECSEND 314
           LELL+AQA+ ++EN+++A ED QN  +D  +   I ++                E SE +
Sbjct: 244 LELLQAQAKMQAENKTEAVEDFQNANIDSINSQGISNLQPENSDKLRELLAGNNESSEEE 303

Query: 315 PTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQ 374
             T+S   S SE LSDIFE+DS+T+T+EKAE + LYL++F+KFPV++D E EDFEEHLRQ
Sbjct: 304 SLTDSGTESCSEALSDIFESDSDTDTKEKAE-QLLYLNEFEKFPVESDGEPEDFEEHLRQ 362

Query: 375 ISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 413
           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 = 264/383 (68%), Positives = 311/383 (81%), Gaps = 12/383 (3%)

Query: 31  GRLWIHSAPLRHYIEKVVEKQESSENSSSA--DGAGVAKVKRKKLKGKRAVVRWLKHFRY 88
           G    HS P   + +KVVE+Q+ S+ +SSA  DG G AKVKR KLKGKRAVVRWLK FR+
Sbjct: 8   GNASFHSCPFLKFNDKVVEQQQDSQKASSANVDGDGNAKVKRNKLKGKRAVVRWLKFFRF 67

Query: 89  KKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFL 148
           KKKKEYERMTAEEKILYKL KARKKEER+ E LKKIEP ESSE THDPEILTPEEHF+FL
Sbjct: 68  KKKKEYERMTAEEKILYKLLKARKKEERLCEALKKIEPAESSETTHDPEILTPEEHFFFL 127

Query: 149 KMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGG 208
           KMG K KNYVPVGRRGIYQGVILNMHLHWKKHQTLKV+VKTFSAEEVKEIA ELARL+GG
Sbjct: 128 KMGLKSKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVVVKTFSAEEVKEIATELARLSGG 187

Query: 209 IVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQ 268
           IVL+IHE+NTIIMYRGKNY+QPPTEIMSPR++LSRKKALDKSKYRD LRAV+++IP+LEQ
Sbjct: 188 IVLDIHEDNTIIMYRGKNYSQPPTEIMSPRVSLSRKKALDKSKYRDALRAVRRHIPRLEQ 247

Query: 269 ELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDL 328
           ELE+LRAQ ++ +E+ +DAAE +QN      D       + C+E++    S + SDS+ L
Sbjct: 248 ELEILRAQFKSSAESNTDAAEAIQNNRERMND------NIGCTEDETDMNSELDSDSDKL 301

Query: 329 SDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKD 388
           SDIFETDS+TE   K E +PLYLD+FD FP Q+D E  DFEEHLRQ+S+ S+N   + K+
Sbjct: 302 SDIFETDSDTENFIKEE-KPLYLDEFDNFPEQSDGEMNDFEEHLRQMSLKSKN---MEKE 357

Query: 389 EDSSHFDEVDKMFLRAASLLKKQ 411
           ++    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 (1270), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 264/385 (68%), Positives = 312/385 (81%), Gaps = 22/385 (5%)

Query: 45  EKVVEKQ-ESSENSSSA--DGAGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEE 101
           +KVVE+Q + S+ +SSA  DG G AKVKR KLKGKRAVVRWLK FR+KKKKEYERMTAEE
Sbjct: 1   DKVVEQQHQDSQKASSANVDGDGNAKVKRNKLKGKRAVVRWLKFFRFKKKKEYERMTAEE 60

Query: 102 KILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVG 161
           K LYKL KARKKEER+ E LKKIEP ESSE THDPEILTPEEHF+FLKMG K KNYVPVG
Sbjct: 61  KNLYKLLKARKKEERLCEALKKIEPAESSETTHDPEILTPEEHFFFLKMGLKSKNYVPVG 120

Query: 162 RRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIM 221
           RRGIYQGVILNMHLHWKKHQTLKV+VKTFSAEEVKEIAAELARL+GGIVL+IHE+NTIIM
Sbjct: 121 RRGIYQGVILNMHLHWKKHQTLKVVVKTFSAEEVKEIAAELARLSGGIVLDIHEDNTIIM 180

Query: 222 YRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRS 281
           YRGKNY+QPPTEIMSPR++LSRKKALDKSKYRD LRAV++YIP+LEQELE+LRAQ ++ +
Sbjct: 181 YRGKNYSQPPTEIMSPRVSLSRKKALDKSKYRDALRAVRRYIPRLEQELEILRAQFKSSA 240

Query: 282 ENRSDAAEDVQNTELDKPDFGSIPS-----------MMEC----SENDPTTESLMASDSE 326
           E+ +DAAE +QN+  +  + GSI +           MM      +E++    S + SDS+
Sbjct: 241 ESNTDAAEAIQNSGRESIESGSISNFQLQNSYKDREMMNVNIGSTEDETDMNSELDSDSD 300

Query: 327 DLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLG 386
            LSDIFETDS+TE   K E +PLYLD+FD FP Q+D E  DFEEH+RQ+S+ S+N   + 
Sbjct: 301 KLSDIFETDSDTENFVKEE-KPLYLDEFDNFPEQSDGEMNDFEEHMRQMSLKSKN---ME 356

Query: 387 KDEDSSHFDEVDKMFLRAASLLKKQ 411
           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 (1223), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 239/332 (71%), Positives = 276/332 (83%), Gaps = 16/332 (4%)

Query: 97  MTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKN 156
           MTAEEKILYKLRKAR+KEER+ E L KIEPKESSE THDPEILTPEEHF+FLKMG KCKN
Sbjct: 1   MTAEEKILYKLRKARRKEERLAEALTKIEPKESSETTHDPEILTPEEHFFFLKMGLKCKN 60

Query: 157 YVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE 216
           YVP+GRRGIYQGVILNMHLHWKKHQTL+V+VKTFS EEVKEIA ELARLTGGIVL+IHEE
Sbjct: 61  YVPIGRRGIYQGVILNMHLHWKKHQTLQVVVKTFSPEEVKEIAVELARLTGGIVLDIHEE 120

Query: 217 NTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQ 276
           NTIIMYRGKNY+QPPTEIMSPRITLSRKKALDKSKYRDGLRAV+KYIP+LE +LELL+AQ
Sbjct: 121 NTIIMYRGKNYSQPPTEIMSPRITLSRKKALDKSKYRDGLRAVRKYIPRLEGDLELLQAQ 180

Query: 277 AETRSENRSDAAEDVQNTELDKPDFGSIPSMM---------------ECSENDPTTESLM 321
           A+ ++EN+++A ED QN  +D  +   I ++                E SE +  T+S  
Sbjct: 181 AKMQAENKTEAVEDFQNANIDSINSQGISNLQPENSDKLRELLAGNNESSEEESLTDSGT 240

Query: 322 ASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRN 381
            S SE LSDIFE+DS+T+T+EKAE + LYL++F+KFPV++D E EDFEEHLRQIS DSR 
Sbjct: 241 ESCSEALSDIFESDSDTDTKEKAE-QLLYLNEFEKFPVESDGEPEDFEEHLRQISADSRK 299

Query: 382 AKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 413
           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 (1215), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 251/422 (59%), Positives = 316/422 (74%), Gaps = 35/422 (8%)

Query: 17  AFGPCYGLKRFSIEGRLWIHSAPLRHYIEKVVEKQESSENSSS---ADGAGVAKVKRKKL 73
           +F   YGL   S+ G  WIHS        K VE  E SE  S+    DG+G+ + ++K+ 
Sbjct: 89  SFNGVYGLT--SVVGYRWIHST-------KSVEPLEKSEGKSAIGFTDGSGIEEEEKKEK 139

Query: 74  KGK------RAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPK 127
           K +      RAVVRWLK FR+KKKKEYERMT+EEKIL+K+ KARKKE+R+VE L+KIEP 
Sbjct: 140 KTRKKLKGKRAVVRWLKLFRWKKKKEYERMTSEEKILFKMNKARKKEKRLVEALEKIEPA 199

Query: 128 ESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIV 187
           +SS+ THDPEILTPEEHFYFLKMG K KNYVPVGRRGIYQGVILNMHLHWKKHQT+KV+V
Sbjct: 200 DSSDTTHDPEILTPEEHFYFLKMGIKGKNYVPVGRRGIYQGVILNMHLHWKKHQTVKVVV 259

Query: 188 KTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKAL 247
           KTFS EEVKEIAAELARLTGG+VL+IHEE+TIIMYRGKNY+QPPTEIMSPR++LSRKKAL
Sbjct: 260 KTFSPEEVKEIAAELARLTGGLVLDIHEEDTIIMYRGKNYSQPPTEIMSPRVSLSRKKAL 319

Query: 248 DKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSM 307
           DKSKYRDGLRAV+K+IPKLEQEL  L++QA+   ++  ++ E +Q T  D     +I S+
Sbjct: 320 DKSKYRDGLRAVRKHIPKLEQELRFLQSQAKLNCKSNGESVEHMQETVDDTNKSKAISSL 379

Query: 308 M----------------ECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYL 351
                            + S++    ++ M+SDSEDLSD+FETD ++E +EK E +PL+L
Sbjct: 380 NLENLDDSSNAMRSVSKDWSDDSSPIDTGMSSDSEDLSDMFETDIDSEADEKME-KPLFL 438

Query: 352 DQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQ 411
            +F+ F  + ++E ED  + LRQIS+DS+ AK L  D +S  FDEVD++FLR+ASLLKK+
Sbjct: 439 KEFENFAAETEDEIEDLSDQLRQISMDSKQAKILENDVNSPEFDEVDRLFLRSASLLKKK 498

Query: 412 KR 413
           +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 =  469 bits (1208), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 268/431 (62%), Positives = 324/431 (75%), Gaps = 37/431 (8%)

Query: 6   HCSSMVDVLCKAFGP---CYGLKRFSIE-GRLWIHSAP-LRHYIEKVVEKQESSENSSSA 60
           H +S+  V+CK +      + L   S   G L  HS P L+   +KVVE+ + S+     
Sbjct: 27  HKTSLNYVICKVYAQEHHQFKLPSTSTRVGCLSFHSTPFLKCNHDKVVEQPQDSD----- 81

Query: 61  DGAGVAKV-KRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVE 119
              G  KV  RKKLKGKRAVVRWLK FR+KKKKE++RMT EE+ILYKL KARKKEER+ E
Sbjct: 82  ---GDVKVPARKKLKGKRAVVRWLKFFRFKKKKEFQRMTTEERILYKLLKARKKEERLRE 138

Query: 120 GLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKK 179
            LKKIEP ESSE  HDPEILTPEEHF+FLKMG K KNYVPVGRRGIYQGVILNMHLHWKK
Sbjct: 139 ALKKIEPTESSETIHDPEILTPEEHFFFLKMGLKSKNYVPVGRRGIYQGVILNMHLHWKK 198

Query: 180 HQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRI 239
           HQTL+V+VKTFSAEEVKEIA ELARLTGGIVL IHEE+TIIMYRGKNY+QPPTEIMSPR+
Sbjct: 199 HQTLQVVVKTFSAEEVKEIATELARLTGGIVLGIHEEDTIIMYRGKNYSQPPTEIMSPRV 258

Query: 240 TLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQ------- 292
           TL RKKALDKSKYRDGLRAV++YIPKLEQELE+LRAQ ++ +E+ ++AAE +Q       
Sbjct: 259 TLPRKKALDKSKYRDGLRAVRRYIPKLEQELEILRAQFQSTAESNTEAAEGIQISDKVSV 318

Query: 293 ------NTELDKPDFGSIPSMME----CSENDPTTESLMASDSEDLSDIFETDSETETEE 342
                 N +L+K D   + +M      CSE++   +S + S S+ LSDIFETDS+TE   
Sbjct: 319 EPSSVSNLQLEKLD--KVGAMFNDNNSCSEDEAHMDSDLDSYSDKLSDIFETDSDTEDLV 376

Query: 343 KAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFL 402
           K E +PLYLD+F+ FP Q+D + +DFEEHL+QIS +S+N   + KD D   FDEVD++FL
Sbjct: 377 KEE-KPLYLDEFNNFPEQSDGDTDDFEEHLQQISYNSKN---MEKDADLPKFDEVDQIFL 432

Query: 403 RAASLLKKQKR 413
           RAAS LKK+++
Sbjct: 433 RAASFLKKKRK 443

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  453 bits (1165), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 268/460 (58%), Positives = 324/460 (70%), Gaps = 66/460 (14%)

Query: 6   HCSSMVDVLCKAFGP---CYGLKRFSIE-GRLWIHSAP-LRHYIEKVVEKQESSENSSSA 60
           H +S+  V+CK +      + L   S   G L  HS P L+   +KVVE+ + S+     
Sbjct: 27  HKTSLNYVICKVYAQEHHQFKLPSTSTRVGCLSFHSTPFLKCNHDKVVEQPQDSD----- 81

Query: 61  DGAGVAKV-KRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVE 119
              G  KV  RKKLKGKRAVVRWLK FR+KKKKE++RMT EE+ILYKL KARKKEER+ E
Sbjct: 82  ---GDVKVPARKKLKGKRAVVRWLKFFRFKKKKEFQRMTTEERILYKLLKARKKEERLRE 138

Query: 120 GLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKK 179
            LKKIEP ESSE  HDPEILTPEEHF+FLKMG K KNYVPVGRRGIYQGVILNMHLHWKK
Sbjct: 139 ALKKIEPTESSETIHDPEILTPEEHFFFLKMGLKSKNYVPVGRRGIYQGVILNMHLHWKK 198

Query: 180 HQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRI 239
           HQTL+V+VKTFSAEEVKEIA ELARLTGGIVL IHEE+TIIMYRGKNY+QPPTEIMSPR+
Sbjct: 199 HQTLQVVVKTFSAEEVKEIATELARLTGGIVLGIHEEDTIIMYRGKNYSQPPTEIMSPRV 258

Query: 240 TLSRKK-----------------------------ALDKSKYRDGLRAVKKYIPKLEQEL 270
           TL RKK                             ALDKSKYRDGLRAV++YIPKLEQEL
Sbjct: 259 TLPRKKVLHVPKDCLHHTIKDCFTFLFAYFPSLISALDKSKYRDGLRAVRRYIPKLEQEL 318

Query: 271 ELLRAQAETRSENRSDAAEDVQ-------------NTELDKPDFGSIPSMME----CSEN 313
           E+LRAQ ++ +E+ ++AAE +Q             N +L+K D   + +M      CSE+
Sbjct: 319 EILRAQFQSTAESNTEAAEGIQISDKVSVEPSSVSNLQLEKLD--KVGAMFNDNNSCSED 376

Query: 314 DPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLR 373
           +   +S + S S+ LSDIFETDS+TE   K E +PLYLD+F+ FP Q+D + +DFEEHL+
Sbjct: 377 EAHMDSDLDSYSDKLSDIFETDSDTEDLVKEE-KPLYLDEFNNFPEQSDGDTDDFEEHLQ 435

Query: 374 QISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 413
           QIS +S+N   + KD D   FDEVD++FLRAAS LKK+++
Sbjct: 436 QISYNSKN---MEKDADLPKFDEVDQIFLRAASFLKKKRK 472

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297831446|ref|XP_002883605.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297329445|gb|EFH59864.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  448 bits (1153), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 258/417 (61%), Positives = 311/417 (74%), Gaps = 33/417 (7%)

Query: 8    SSMVDVLCKAF------GPCYGLKRFSIEGRLWIHSAPLRHYIEKVVEKQESSENSSSAD 61
            SS  +++CK        GP + +   S     W HS    + + +  +    SENSSS D
Sbjct: 661  SSSGNIVCKVLLKESLNGPMWNV---SFLRSSWFHS----NSVPETGDCLSKSENSSSQD 713

Query: 62   GAGVAKVKRKKLKGKRAVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGL 121
            G    K+KRKKLKGKRAVVRWLK FR+KKKKE+ERMTAEEKIL KL KARKKEER++E +
Sbjct: 714  GGSSTKLKRKKLKGKRAVVRWLKFFRWKKKKEFERMTAEEKILNKLTKARKKEERLMETM 773

Query: 122  KKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQ 181
            KK+EP ES+E THDPEILTPEEHFY+LKMG KCKNYVPVGRRGIYQGVILNMHLHWKKHQ
Sbjct: 774  KKLEPSESAETTHDPEILTPEEHFYYLKMGLKCKNYVPVGRRGIYQGVILNMHLHWKKHQ 833

Query: 182  TLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITL 241
            TL+V++KTF+ +EV EIA ELARLTGGIVL++HE NTIIMYRGKNY QPPTEIMSPRITL
Sbjct: 834  TLQVVIKTFTPDEVNEIAVELARLTGGIVLDVHEGNTIIMYRGKNYVQPPTEIMSPRITL 893

Query: 242  SRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQ--NTELDKP 299
             RKKALDKSK RD LRAV+KYIP+LEQEL+LL+AQAET+ E  +   +D+Q  + EL K 
Sbjct: 894  PRKKALDKSKCRDALRAVRKYIPRLEQELQLLQAQAETKREYLNVKVDDIQERSDELKKI 953

Query: 300  DFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFP- 358
               S   + +  E +    S +A+DS DLSDIFETDSE E E+   +RPL+L++F+KFP 
Sbjct: 954  IERSEECLED-EEEEEDAGSELATDS-DLSDIFETDSELEDEKT--VRPLFLEEFEKFPA 1009

Query: 359  VQNDEEHEDFEEHLRQISIDSRNAKSLGKDED--SSHFDEVDKMFLRAASLLKKQKR 413
            + N+ E EDF +           AKS G++ D  S +FDEVDKMFLRAASLLKK++R
Sbjct: 1010 INNNREDEDFGK-----------AKSEGEENDDKSPNFDEVDKMFLRAASLLKKKRR 1055

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

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	413
TAIR|locus:2094438	444	LOH1 "LAG One Homologue 1" [Ar	0.871	0.810	0.593	1.2e-106
TAIR|locus:2091458	491	AT3G27550 [Arabidopsis thalian	0.438	0.368	0.448	2.8e-42
TAIR|locus:2123276	343	AT4G13070 [Arabidopsis thalian	0.435	0.524	0.491	4e-42
TAIR|locus:2056558	372	AT2G28480 [Arabidopsis thalian	0.605	0.672	0.379	8.4e-42
TAIR|locus:2094558	881	CFM3A "CRM family member 3A" [	0.602	0.282	0.3	8.8e-24
TAIR|locus:2094997	848	EMB1865 "embryo defective 1865	0.544	0.265	0.329	3.4e-20
TAIR|locus:2096662	1011	CFM2 "CRM family member 2" [Ar	0.772	0.315	0.25	4.5e-20
TAIR|locus:2181372	720	CRS1 "ortholog of maize chloro	0.401	0.230	0.316	2.4e-13

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

 Score = 1055 (376.4 bits), Expect = 1.2e-106, P = 1.2e-106
 Identities = 229/386 (59%), Positives = 270/386 (69%)

Query:    36 HSAPLRHYIEKVVEKQESSENSSSADXXXXXXXXXXXXXXXXXXXXWLKHFRYKKKKEYE 95
             HS P R   +  + K   SENSSS D                    WLK FR+KKKKE+E
Sbjct:    77 HSTPARETGDDDISK---SENSSSQDGDSCTKLKRKKLKGKRAVVRWLKFFRWKKKKEFE 133

Query:    96 RMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCK 155
             RMT+EEKIL KLRKARKKEER++E +KK+EP ES+E THDPEILTPEEHFY+LKMG KCK
Sbjct:   134 RMTSEEKILNKLRKARKKEERLMETMKKLEPSESAETTHDPEILTPEEHFYYLKMGLKCK 193

Query:   156 NYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHE 215
             NYVPVGRRGIYQGVILNMHLHWKKHQTL+V++KTF+ +EVKEIA ELARLTGGIVL++HE
Sbjct:   194 NYVPVGRRGIYQGVILNMHLHWKKHQTLQVVIKTFTPDEVKEIAVELARLTGGIVLDVHE 253

Query:   216 ENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKXXXXXXXXXX 275
              NTIIMYRGKNY QPPTEIMSPRITL RKKALDKSK RD LRAV+KYIP+          
Sbjct:   254 GNTIIMYRGKNYVQPPTEIMSPRITLPRKKALDKSKCRDALRAVRKYIPRLEQELQLLQA 313

Query:   276 XXXTRSENRSDAAEDVQ--NTELDKPDFGSIPSMMECSENDPTTESL---MASDSEDLSD 330
                T+ +  +   +D Q  + EL K     I    EC E++   +     +A+DS DLSD
Sbjct:   314 QAETKRDYTNVKVDDNQERSEELKK----IIERSEECLEDEQEEDEAGLELATDS-DLSD 368

Query:   331 IFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDED 390
             IFETDSE E + K E RPL+L++F+KFP  N+ E EDF         D   AKS G++ D
Sbjct:   369 IFETDSELE-DAKTE-RPLFLEEFEKFPAINNREDEDFG--------DLGKAKSEGEEND 418

Query:   391 ---SSHFDEVDKMFLRAASLLKKQKR 413
                S +FDEVDKMFLRAA LLKK++R
Sbjct:   419 DDKSPNFDEVDKMFLRAAFLLKKKRR 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:    83 LKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPE 142
             L+  R  KK + + MT EE+++Y L++A+KK   +++ LKK +  E     HDPE+ T E
Sbjct:    36 LREIRRAKKLKKKLMTDEERLIYNLKRAKKKVALLLQKLKKYDLPELPSPVHDPELFTSE 95

Query:   143 EHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAEL 202
             +   F K+G K KNYVPVG RG++ GV+ NMH+HWK H+T++V    F  E++KE+A+ +
Sbjct:    96 QVQAFKKIGFKNKNYVPVGVRGVFGGVVQNMHMHWKFHETVQVCCDNFPKEKIKEMASMI 155

Query:   203 ARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKY 262
             ARL+GG+V+ IH   TIIM+RG+NY QP   I  P  TL+++KAL K+++   L + K  
Sbjct:   156 ARLSGGVVINIHNVKTIIMFRGRNYRQPKNLI--PVNTLTKRKALFKARFEQALESQKLN 213

Query:   263 IPK 265
             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:    83 LKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIE-PKESSEMTHDPEILTP 141
             L+ +R K KK+      E +I YKL KA++KEE ++E L+K + PK  +E  +DPE LT 
Sbjct:   126 LRFYRLKAKKKMNSPNPEVRIRYKLEKAKRKEEWLIEKLRKYDVPKSPAE-PYDPESLTE 184

Query:   142 EEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAE-EVKEIAA 200
             EE  Y  + G K KN+V VGRRG++ GV+LN+HLHWKKH+T+KVI K  +   +V E A 
Sbjct:   185 EEQHYLKRTGEKRKNFVLVGRRGVFGGVVLNLHLHWKKHETVKVICKPCNKPGQVHEYAE 244

Query:   201 ELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVK 260
             ELARL+ GIV+++   NTI++YRGKNY +P  E+MSP  TLS+ KAL+K +Y   L    
Sbjct:   245 ELARLSKGIVIDVKPNNTIVLYRGKNYVRP--EVMSPVDTLSKDKALEKYRYEQSLEHTS 302

Query:   261 KYIPK 265
             ++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:    90 KKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLK 149
             KKK++  + AEE+I YKL KA+ KE  ++E LK+ E  +       P  +T EE FY  K
Sbjct:   117 KKKKF--VNAEERIKYKLEKAKIKEALLIERLKRYEVAKVQGPEVRPHEITGEERFYLKK 174

Query:   150 MGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGI 209
             MG+K  NYVP+GRRG++ GVILNMHLHWKKH+T+KVI       +V++ A ELA+L+GG+
Sbjct:   175 MGQKRSNYVPIGRRGVFGGVILNMHLHWKKHETVKVICNNSKPGQVQQYAEELAKLSGGV 234

Query:   210 VLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKXXXX 269
              + I  ++TII YRGK Y QP  ++MSP  TLS+K+A +KSKY   L +V+ +I      
Sbjct:   235 PVNIIGDDTIIFYRGKGYVQP--QVMSPIDTLSKKRAYEKSKYEQSLESVRHFIAIAEKE 292

Query:   270 XXXXXXXXXTRSE-NRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDL 328
                         + N  +    + ++  +          + CS+ D ++E     + E+L
Sbjct:   293 LELYYRHVALYDDPNNRNPLSILDDSPSESRQHHENEFFLSCSDTDSSSED--EDEDEEL 350

Query:   329 SDIFETDSETETEEKAEL 346
              ++ +  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 = 8.8e-24, P = 8.8e-24
 Identities = 78/260 (30%), Positives = 132/260 (50%)

Query:    91 KKEYERMTAEE---KILYKLRKARKKEERIVEGLKKIEP-KESSEMTHDPEILTPEEHFY 146
             K+E E +  E    K+  KL  A +K  +   GL K+E   + +E   DPE +T EE F 
Sbjct:   586 KQEVEILRHENLVRKLERKLAFAERKLLKAERGLAKVEVCLKPAEQREDPESITDEERFM 645

Query:   147 FLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLT 206
             F K+G K K ++ +GRRG++ G + NMHLHWK  + +K+IVK  + + VK++A  L   +
Sbjct:   646 FRKLGLKMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKAKTFDGVKKVALALEAES 705

Query:   207 GGIVLEIHEEN---TIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYI 263
             GGI++ I +      II+YRG++Y +P   ++ P+  L+++KAL +S        + K+I
Sbjct:   706 GGILVSIDKVTKGYAIIVYRGQDYKRPT--MLRPKNLLTKRKALARSIELQRREGLLKHI 763

Query:   264 PKXXXXXXXXXXXXXTRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMAS 323
                             + E  +D  ++    +LD     S     E  ++D   E+    
Sbjct:   764 -STMQAKAKQLRAEIEQMEKVTDKGDEELYNKLDMAYASSDEETDEEDDDDAFPETYAEG 822

Query:   324 DSEDLSDIFETD-SETETEE 342
             +  +  +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 = 3.4e-20, P = 3.4e-20
 Identities = 78/237 (32%), Positives = 125/237 (52%)

Query:   101 EKILYKLRKARKKEERIVEGLKKIEPKE-SSEMTHDPEILTPEEHFYFLKMGRKCKNYVP 159
             ++I +KL  A+ K +R  + L KIE     +   +D E+++ EE   F K+G K K Y+P
Sbjct:   614 KRIQHKLNLAQSKFQRAEKLLSKIEASMIPNGPDYDQEVISEEERAMFRKVGLKMKAYLP 673

Query:   160 VGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN-- 217
             +G RG++ GVI NMHLHWK  + +K+I K  +   V+E A  L   +GG+++ I +    
Sbjct:   674 IGIRGVFDGVIENMHLHWKHRELVKLISKQKNQAFVEETARLLEYESGGVLVAIEKVPKG 733

Query:   218 -TIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKXXXXXXXXXXX 276
               +I YRGKNY +P +  + PR  L++ KAL +S       A+ ++I +           
Sbjct:   734 FALIYYRGKNYRRPIS--LRPRNLLTKAKALKRSIAMQRHEALSQHISELERTIEQMQSQ 791

Query:   277 XXTRSENRSDAAEDVQNTELDKPDFGSIPSMMECSEND--PTT-ESLMASDSE-DLS 329
                 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 = 4.5e-20, P = 4.5e-20
 Identities = 84/336 (25%), Positives = 155/336 (46%)

Query:    85 HFRYKKKKEYERMTAE---EKILYKLRKARKKEERIVEGLKKIEPKESSEMTH-DPEILT 140
             H +  + K  +R + E   EK   KL  A +K+    + L  +E +ES +++  D E +T
Sbjct:   521 HIQTHQMKSRQRNSPEAILEKTSMKLSMALEKKANAEKVLADLENRESPQLSDIDKEGIT 580

Query:   141 PEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAA 200
              +E +   K+G K K ++ +GRRG++ G I NMHLHWK  + +K+I   +S E   ++A 
Sbjct:   581 NDEKYMLRKIGLKMKPFLLLGRRGVFDGTIENMHLHWKYRELVKIICNEYSIEAAHKVAE 640

Query:   201 ELARLTGGIVLEIHEEN---TIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLR 257
              L   +GGI++ +   +    II+YRGKNY +P  + + P+  LS+++AL +S      +
Sbjct:   641 ILEAESGGILVAVEMVSKGYAIIVYRGKNYERP--QCLRPQTLLSKREALKRSVEAQRRK 698

Query:   258 AVKKYIPKXXXXXXXXXXXXXTRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTT 317
             ++K ++ K               S   ++   D +++ +   +     +  + +E +   
Sbjct:   699 SLKLHVLKLSNNIEELNRQLVEDSAT-NETWSDGESSNMMVEE----ETENQHTEPEKAR 753

Query:   318 ESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISI 377
             E +    S DLS     +   E + + E+ PL     +    Q DE      +     S+
Sbjct:   754 EKIELGYSSDLSVPSSGEENWEDDSEGEVDPLTTSSQE---YQEDESESASSQRHEGNSL 810

Query:   378 DSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 413
             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 = 2.4e-13, P = 2.4e-13
 Identities = 56/177 (31%), Positives = 92/177 (51%)

Query:    89 KKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFL 148
             K + E E  + E K+     K  K    + +     +P E  +   D EILT EE     
Sbjct:   525 KARLEKELKSQEHKLSILKSKIEKSNMELFKLNSLWKPSEGDD---DIEILTNEERECLR 581

Query:   149 KMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIV--KTFSAEEVKEIAAELARLT 206
             ++G K  + + +GRRG++ GV+  +H HWK  +  KVI   K FS   V   A  L   +
Sbjct:   582 RIGLKMNSSLVLGRRGVFFGVMEGLHQHWKHREVAKVITMQKLFS--RVVYTAKALETES 639

Query:   207 GGIVLEIH---EENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVK 260
              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   0.131   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      413       380   0.00090  117 3  11 23  0.44    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:  243 KB (2132 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:  42.40u 0.10s 42.50t   Elapsed:  00:00:02
  Total cpu time:  42.40u 0.10s 42.50t   Elapsed:  00:00:02
  Start:  Fri May 10 03:21:39 2013   End:  Fri May 10 03:21:41 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	0.6229	0.9297	0.8648	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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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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	413
smart01103	84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	6e-21
pfam01985	84	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	2e-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 = 86.0 bits (214), Expect = 6e-21
 Identities = 28/85 (32%), Positives = 46/85 (54%), Gaps = 1/85 (1%)

Query: 139 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEI 198
           LT ++  Y   +    K  V +G+ G+ +GV+  +    +KH+ +KV V     E+ KEI
Sbjct: 1   LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEI 60

Query: 199 AAELARLTGGIVLEIHEENTIIMYR 223
           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 = 82.1 bits (204), Expect = 2e-19
 Identities = 28/85 (32%), Positives = 46/85 (54%), Gaps = 1/85 (1%)

Query: 139 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEI 198
           LT ++  Y   +    K  V +G+ G+ +GV+  +    +KH+ +KV V     E+ KEI
Sbjct: 1   LTGKQRRYLRSLAHHLKPVVQIGKNGLTEGVVEEIDEALEKHELIKVKVLGNDREDRKEI 60

Query: 199 AAELARLTGGIVLEIHEENTIIMYR 223
           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	413
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	97.77

>PRK10343 RNA-binding protein YhbY; Provisional

Probab=99.95  E-value=2e-27  Score=199.73  Aligned_cols=89  Identities=21%  Similarity=0.340  Sum_probs=86.2

Q ss_pred             CCCCHHHHHHHHhhcccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeC
Q 015090          137 EILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE  216 (413)
Q Consensus       137 E~LT~eERk~LRKlAhkLKPVV~IGKrGVTdgVIeeIh~AwK~HELVKVKvk~~s~ed~keiAeeLee~TGGeLVQviiG  216 (413)
                      ++||++||+|||++||+|+|+|+||++|||++|+++|+.+|++||||||++.+++.+++++++++|++.|||++||+ ||
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 015090          217 NTIIMYRGKN  226 (413)
Q Consensus       217 ~tIILYRGKN  226 (413)
                      +++||||++.
T Consensus        80 ~~~vlYR~~~   89 (97)
T PRK10343         80 KTLVLYRPTK   89 (97)
T ss_pred             cEEEEEecCC
Confidence            9999999964

>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family

Probab=99.95  E-value=3.1e-27  Score=197.64  Aligned_cols=87  Identities=28%  Similarity=0.369  Sum_probs=84.7

Q ss_pred             CCHHHHHHHHhhcccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCcE
Q 015090          139 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT  218 (413)
Q Consensus       139 LT~eERk~LRKlAhkLKPVV~IGKrGVTdgVIeeIh~AwK~HELVKVKvk~~s~ed~keiAeeLee~TGGeLVQviiG~t  218 (413)
                      ||++||++||++||+|+|+|+||++|||++||++|+++|++||||||++.+++.++++++|++|++.|||++||+ +|++
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 015090          219 IIMYRGKN  226 (413)
Q Consensus       219 IILYRGKN  226 (413)
                      +||||++.
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=8.7e-27  Score=188.84  Aligned_cols=84  Identities=36%  Similarity=0.522  Sum_probs=74.9

Q ss_pred             CCHHHHHHHHhhcccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCcE
Q 015090          139 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT  218 (413)
Q Consensus       139 LT~eERk~LRKlAhkLKPVV~IGKrGVTdgVIeeIh~AwK~HELVKVKvk~~s~ed~keiAeeLee~TGGeLVQviiG~t  218 (413)
                      ||++|+++||++||+|+|+|+||++|||++|+++|+.+|++||||||+|.+++.++++++|+.|++.|||++|++ +|++
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 015090          219 IIMYR  223 (413)
Q Consensus       219 IILYR  223 (413)
                      +||||
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=1.7e-27  Score=247.83  Aligned_cols=208  Identities=41%  Similarity=0.596  Sum_probs=188.2

Q ss_pred             hhhhhhhhhhhhhhhhhhh-----hHHhhhcChH---HHHHHHHHHHHHHHHHHHHhhcccCCC-CCCCCCCCCCCCCHH
Q 015090           72 KLKGKRAVVRWLKHFRYKK-----KKEYERMTAE---EKILYKLRKARKKEERIVEGLKKIEPK-ESSEMTHDPEILTPE  142 (413)
Q Consensus        72 k~~~k~a~~~~~~~~r~~~-----kke~~~~~~e---~ri~~KL~~A~~K~e~~~e~L~K~E~~-~paE~~~DpE~LT~e  142 (413)
                      -..-..++++|.+.+.+..     +.+.+.+..+   +.+.+++..+++|++++...|++++.+ .|++..+|++.+|.+
T Consensus       307 ~~e~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~e  386 (564)
T KOG1990|consen  307 LLELARAKAKKEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEE  386 (564)
T ss_pred             HHHHHHHhcccccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChH
Confidence            3344566677777666654     6677777655   788999999999999999999999986 899999999999999


Q ss_pred             HHHHHHhhcccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCH-HHHHHHHHHHHHHhCCEEEEEe---eCcE
Q 015090          143 EHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSA-EEVKEIAAELARLTGGIVLEIH---EENT  218 (413)
Q Consensus       143 ERk~LRKlAhkLKPVV~IGKrGVTdgVIeeIh~AwK~HELVKVKvk~~s~-ed~keiAeeLee~TGGeLVQvi---iG~t  218 (413)
                      ++.+++++|.+|++++.+|++|+++|+|.++|.||++||++||+|+.... .+++..|..++..+|+++|++.   .|..
T Consensus       387 e~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~a  466 (564)
T KOG1990|consen  387 ERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYA  466 (564)
T ss_pred             HHHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhh
Confidence            99999999999999999999999999999999999999999999998665 9999999999999999999975   4666


Q ss_pred             EEEEeCCCCCCCCCccCCCCcccchHHHHHHHHHHhhhHHHHhhHHHHHHHHHHHHHHHhhhc
Q 015090          219 IIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRS  281 (413)
Q Consensus       219 IILYRGKNY~rP~~~~~~P~~lLtKrkAL~rS~~~Qr~eslk~~i~~le~~ie~l~~~~~~~~  281 (413)
                      |++|||+||.+|.+  |+|.++|+||+|+.+++++|+.+|+++||..+++++++++.++....
T Consensus       467 i~~yr~k~y~~p~~--l~P~~~l~~~k~~~~~~~~~~~~a~~~~i~~~~~~~e~~~~~~~~~~  527 (564)
T KOG1990|consen  467 IIAYRGKNYDRPTS--LRPRNLLSRRKALERSLEEQRKEALKSHISDLEQEIEQLQASVEAMP  527 (564)
T ss_pred             HHHhhhhhccCCcc--cCchhhhcccCCccccHHHHHHHHHhhhcchhhhhHHHhhcchhccc
Confidence            99999999999975  99999999999999999999999999999999999999999876543

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

Probab=99.93  E-value=1.5e-25  Score=188.95  Aligned_cols=91  Identities=26%  Similarity=0.421  Sum_probs=86.5

Q ss_pred             CCCHHHHHHHHhhcccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCc
Q 015090          138 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  217 (413)
Q Consensus       138 ~LT~eERk~LRKlAhkLKPVV~IGKrGVTdgVIeeIh~AwK~HELVKVKvk~~s~ed~keiAeeLee~TGGeLVQviiG~  217 (413)
                      +||++|+++||+.||+++|+|+||++|||++||.+|+.+|++||||||++.+++.++.+++|+.|++.+||.+||+ +|+
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            6999999999999999999999999999999999999999999999999999999999999999999999999997 699


Q ss_pred             EEEEEeCCCCCCC
Q 015090          218 TIIMYRGKNYAQP  230 (413)
Q Consensus       218 tIILYRGKNY~rP  230 (413)
                      ++||||. +..++
T Consensus        80 ~~vlyr~-~~e~~   91 (97)
T COG1534          80 TLVLYRE-SKEKR   91 (97)
T ss_pred             EEEEEec-Ccccc
Confidence            9999994 44444

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

Probab=97.77  E-value=1.3e-05  Score=84.96  Aligned_cols=152  Identities=22%  Similarity=0.306  Sum_probs=125.4

Q ss_pred             hhhhhhhhhhhhhhHHhhhcChHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCCCCCCCCCCCHHHHHHHHhhcccCCCe
Q 015090           78 AVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNY  157 (413)
Q Consensus        78 a~~~~~~~~r~~~kke~~~~~~e~ri~~KL~~A~~K~e~~~e~L~K~E~~~paE~~~DpE~LT~eERk~LRKlAhkLKPV  157 (413)
                      +...|+..++..++.-...|.++..--|-..........+.+.+..+..|...-+...+..||..+.-++|.+|-...|+
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            45557777777778888888888544444444555666778888888888777778888899999999999999999999


Q ss_pred             eeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCC-CHHHHHHHHHHH--HHHhCCEEEEEeeCcEEEEEeCCCCCCC
Q 015090          158 VPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTF-SAEEVKEIAAEL--ARLTGGIVLEIHEENTIIMYRGKNYAQP  230 (413)
Q Consensus       158 V~IGKrGVTdgVIeeIh~AwK~HELVKVKvk~~-s~ed~keiAeeL--ee~TGGeLVQviiG~tIILYRGKNY~rP  230 (413)
                      +.+|.++.-.++.-.|..+|..|+..|+-+... .......+|..+  -..+|+.||. +-|..+|+||++|+-.|
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            999999999999999999999999999877654 344556778888  8899999996 46889999999999775

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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	413
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	4e-10
1rq8_A	104	Conserved hypothetical protein; structural genomic	2e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07
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 = 55.4 bits (134), Expect = 4e-10
 Identities = 20/106 (18%), Positives = 41/106 (38%), Gaps = 10/106 (9%)

Query: 139 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEI 198
           L+ ++  +   +       V +G  G+ +GV+  +      H+ +KV V     E  + I
Sbjct: 3   LSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLI 62

Query: 199 AAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRK 244
              + 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 = 53.9 bits (130), Expect = 2e-09
 Identities = 20/109 (18%), Positives = 45/109 (41%), Gaps = 9/109 (8%)

Query: 138 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKE 197
           +LT ++  Y   +         +G+ GI + +I  +    +  + +KV V   + ++ KE
Sbjct: 1   MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKE 60

Query: 198 IAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKA 246
           +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 = 59.1 bits (142), Expect = 2e-09
 Identities = 58/307 (18%), Positives = 94/307 (30%), Gaps = 79/307 (25%)

Query: 173 MHLHWKK--HQTLKVIVKTF-------------SAEEVKEIAAELARLTGG----IVLEI 213
               +K          V  F             S EE+  I      ++G       L  
Sbjct: 14  HQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLS 73

Query: 214 HEENTIIMYRG----KNYAQPPTEIMSPRITLSRKKALDKSKY---RDGL----RAVKKY 262
            +E  +  +       NY      +MSP  T  R+ ++    Y   RD L    +   KY
Sbjct: 74  KQEEMVQKFVEEVLRINYKF----LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKY 129

Query: 263 -IPKLEQELELLRAQAETRSENR------------SDAAEDVQNTEL-DKPDFGSI--PS 306
            + +L+  L+L +A  E R                  A +   + ++  K DF  I   +
Sbjct: 130 NVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFK-IFWLN 188

Query: 307 MMECSENDPTTESL------MASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFP-- 358
           +  C+  +   E L      +  +    SD            +AELR L   +   +   
Sbjct: 189 LKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK--PYENC 246

Query: 359 ------VQNDEEHEDFEEH---L---RQISI-DSRNAK-----SLGKDEDSSHFDEVDKM 400
                 VQN +    F      L   R   + D  +A      SL     +   DEV  +
Sbjct: 247 LLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL 306

Query: 401 FLRAASL 407
            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 = 52.2 bits (124), Expect = 2e-07
 Identities = 70/501 (13%), Positives = 137/501 (27%), Gaps = 158/501 (31%)

Query: 32  RLWIHSAPLRHY----IEKVVEKQESSENSSSAD--------GAG----VAKVKR-KKLK 74
           RL+  +     Y    ++  ++ +++      A         G+G       V    K++
Sbjct: 118 RLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQ 177

Query: 75  GKRAV-VRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKE----ERIVEGLKKIEPKES 129
            K    + WL   +     E   +   +K+LY++             I   +  I+ +  
Sbjct: 178 CKMDFKIFWLN-LKNCNSPE-TVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELR 235

Query: 130 SEMTH--------------DPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHL 175
             +                + +       F        CK  + +  R  ++ V   +  
Sbjct: 236 RLLKSKPYENCLLVLLNVQNAKAW---NAFNL-----SCK--ILLTTR--FKQVTDFLSA 283

Query: 176 HWKKHQTLKVIVKTFSAEEVKEIAA--------ELAR--------LTGGIVLEIHEENTI 219
               H +L     T + +EVK +          +L R            I   I +    
Sbjct: 284 ATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLA- 342

Query: 220 IMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRA-------VKKYIPKLEQELEL 272
                 N+     + ++  I  S    L+ ++YR                IP     L L
Sbjct: 343 ---TWDNWKHVNCDKLTTIIESSLN-VLEPAEYRKMFDRLSVFPPSAH--IP--TILLSL 394

Query: 273 LRAQAETRSE--------NRSDAAEDVQNTELDKPDFGSIPSM---MECS-ENDPTTESL 320
           +                   S   +  + + +      SIPS+   ++   EN+      
Sbjct: 395 IWFDVIKSDVMVVVNKLHKYSLVEKQPKESTI------SIPSIYLELKVKLENEYALHRS 448

Query: 321 M--------ASDSEDLSDIFETD----------SETE-TEEKAELRPLYLD--------- 352
           +          DS+DL   +                E  E     R ++LD         
Sbjct: 449 IVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIR 508

Query: 353 --------------------QFDKFPVQNDEEHE----DFEEHLRQISIDSRNAKSLG-- 386
                                +  +   ND ++E       + L +I  +   +K     
Sbjct: 509 HDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLL 568

Query: 387 ----KDEDSSHFDEVDKMFLR 403
                 ED + F+E  K   R
Sbjct: 569 RIALMAEDEAIFEEAHKQVQR 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: 93  EYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGR 152
            +E M   E+I  +L++  +K   I  G        +S +     +    E     ++ +
Sbjct: 130 SFELMKYAEEIAEELKREGRKPYVIPPG-------GASPIGTLGYVRAVGEIATQSEV-K 181

Query: 153 KCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLE 212
                V  G  G   G+ L + +  +  + + + V  F      ++   +      + ++
Sbjct: 182 FDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEAAELLGVK 241

Query: 213 IHEENTIIMYRGKNYAQPPTEIM 235
           +     +  Y    Y +   E+ 
Sbjct: 242 VEVRPELYDYSFGEYGKITGEVA 264

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	413
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=6.7e-29  Score=209.48  Aligned_cols=91  Identities=20%  Similarity=0.354  Sum_probs=87.3

Q ss_pred             CCCHHHHHHHHhhcccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCc
Q 015090          138 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  217 (413)
Q Consensus       138 ~LT~eERk~LRKlAhkLKPVV~IGKrGVTdgVIeeIh~AwK~HELVKVKvk~~s~ed~keiAeeLee~TGGeLVQviiG~  217 (413)
                      |||++||+|||++||+|+|+|+||++|||++|+++|++||++||||||+|.+++.++++++|++|++.|||++||+ ||+
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            7999999999999999999999999999999999999999999999999999999999999999999999999996 699


Q ss_pred             EEEEEeCCCCCCC
Q 015090          218 TIIMYRGKNYAQP  230 (413)
Q Consensus       218 tIILYRGKNY~rP  230 (413)
                      ++||||++. ..|
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=99.96  E-value=1.5e-28  Score=204.90  Aligned_cols=89  Identities=18%  Similarity=0.304  Sum_probs=86.0

Q ss_pred             CCCHHHHHHHHhhcccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCc
Q 015090          138 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  217 (413)
Q Consensus       138 ~LT~eERk~LRKlAhkLKPVV~IGKrGVTdgVIeeIh~AwK~HELVKVKvk~~s~ed~keiAeeLee~TGGeLVQviiG~  217 (413)
                      .||++||+|||++||+|+|+|+||++|||++|+++|++||++||||||+|.+++.++++++|++|++.|||++||+ ||+
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            6999999999999999999999999999999999999999999999999999999999999999999999999996 699


Q ss_pred             EEEEEeCCCC
Q 015090          218 TIIMYRGKNY  227 (413)
Q Consensus       218 tIILYRGKNY  227 (413)
                      ++||||++..
T Consensus        81 ~~vLyR~~~~   90 (98)
T 1jo0_A           81 ILVLYRPSEE   90 (98)
T ss_dssp             EEEEECCCSS
T ss_pred             EEEEEccCCC
Confidence            9999998743

---

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	413
d1rq8a_	96	d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphy	2e-18
d1jo0a_	97	d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i	6e-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 = 77.8 bits (192), Expect = 2e-18
 Identities = 18/90 (20%), Positives = 41/90 (45%), Gaps = 1/90 (1%)

Query: 138 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKE 197
           +LT ++  Y   +         +G+ GI + +I  +    +  + +KV V   + ++ KE
Sbjct: 1   MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKE 60

Query: 198 IAAELARLTGGIVLEIHEENTIIMYRGKNY 227
           +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 = 76.3 bits (188), Expect = 6e-18
 Identities = 19/100 (19%), Positives = 40/100 (40%), Gaps = 5/100 (5%)

Query: 139 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEI 198
           L+ ++  +   +       V +G  G+ +GV+  +      H+ +KV V     E  + I
Sbjct: 3   LSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLI 62

Query: 199 AAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPR 238
              + 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	413
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=7.7e-29  Score=202.95  Aligned_cols=89  Identities=20%  Similarity=0.351  Sum_probs=86.4

Q ss_pred             CCCHHHHHHHHhhcccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCc
Q 015090          138 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  217 (413)
Q Consensus       138 ~LT~eERk~LRKlAhkLKPVV~IGKrGVTdgVIeeIh~AwK~HELVKVKvk~~s~ed~keiAeeLee~TGGeLVQviiG~  217 (413)
                      |||++||++||++||+|+|+|+||++|||++|+.+|+.||+.||||||+|.+++.++++++|++|++.|||++||+ +|+
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 699


Q ss_pred             EEEEEeCCCC
Q 015090          218 TIIMYRGKNY  227 (413)
Q Consensus       218 tIILYRGKNY  227 (413)
                      ++||||++++
T Consensus        80 ~~vlyR~~~~   89 (96)
T d1rq8a_          80 MIVIYRESKE   89 (96)
T ss_dssp             EEEEEECCCS
T ss_pred             EEEEEeCCCC
Confidence            9999998655

>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=9.8e-29  Score=202.63  Aligned_cols=88  Identities=18%  Similarity=0.317  Sum_probs=85.4

Q ss_pred             CCCHHHHHHHHhhcccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCc
Q 015090          138 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  217 (413)
Q Consensus       138 ~LT~eERk~LRKlAhkLKPVV~IGKrGVTdgVIeeIh~AwK~HELVKVKvk~~s~ed~keiAeeLee~TGGeLVQviiG~  217 (413)
                      +||++||++||++||+|+|+|+||++|||++||.+|+.||++||||||+|.+++.++++++|++|++.|||+|||+ +|+
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 015090          218 TIIMYRGKN  226 (413)
Q Consensus       218 tIILYRGKN  226 (413)
                      ++||||+++
T Consensus        81 ~~ilYR~~~   89 (97)
T d1jo0a_          81 ILVLYRPSE   89 (97)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEEcCCC
Confidence            999999854