Citrus Sinensis ID: 021078

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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-------
Protein Sequence
MTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHcccEEEEEccccHHHHHHHHHHHHHHHccEEEEEEEccEEEEEEcccccccccccccccccccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHcccccHHcccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccccHHHHHHHHHHcccccccccccccccccccHHHHHHcHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHcHccccccccccccccHHHHHHHHHHHccccEEEEEEccccHHHHHHHHHHHHHHcccEEEEEEcccEEEEEEcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHccccHcccccHcccccHcHcccccccccccccccccccccccccccccccccccccccccHHHHccccccccccHcHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MTAEEKILYKLRKARKKEERIVEGLkkiepkessemthdpeiltpeeHFYFLKMGrkcknyvpvgrrgiYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIImyrgknyaqppteimspritlsrkkaldkskyrDGLRAVKKYIPKLEQELELLRAQAETrsenrsdaaedvqnteldkpdfgsipsmmecsendptteslmasdsedlsdifetdseteteekaelrplyldqfdkfpvqndeehEDFEEHLRQISIDsrnakslgkdedsshfdEVDKMFLRAASLLKKQKR
Flexible Loop (DISEMBL)
MTAEEKILYklrkarkkeeriveglkkiepkessemthdpeiltPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIImyrgknyaqppteimspritlsrkkaldkskyrdglravKKYIPKLEQELELLRAQAetrsenrsdaaedvqnteldkpdfgsipSMMECSENDPTTESLMASDSEDLSDIFETDseteteekaelrplyldQFDKFPVQNDEEHEDFEEHLRQisidsrnakslgkdedsshfdevDKMFLRAASLLKKQKR
Low Complexity Region (SEG)
MTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKleqelellraqaeTRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR
Disordered region (IsUnstruct)
********************************************PEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYA***************************LRAVKKYIP*****************************************************************************************************************************************************
Disordered Region (DISOPRED)
****EKI*YKLRK*********************************EHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSR*KA******************KLEQELELL****************************************************************************YL*******************************************DEVDKMFLRAASLL*****
Disordered Region (DISEMBL)
MTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQ***************QNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDI************AELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRN************FDEVDKMFLRAASLLKKQKR
Disordered Region (DISPRO)
*TAEEKILYKLRKARKKEERIVEGLKKIEP*********PEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSE*R************************************************************ELRPLYLDQFDKFPV****EHEDFEEHLRQISID************SSHFDEVDKMFLRAASLLKK***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGxxxxxxxxxxxxxxxxxxxxxxxxxxxxRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR
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	317	2.2.26 [Sep-21-2011]
Q67XL4	444	Uncharacterized CRM domai	yes	no	0.962	0.686	0.670	1e-109
Q9FYT6	715	Chloroplastic group IIA i	N/A	no	0.454	0.201	0.393	1e-17
Q6YYA3	725	Chloroplastic group IIA i	no	no	0.454	0.198	0.373	1e-15
Q9LF10	720	Chloroplastic group IIA i	no	no	0.457	0.201	0.328	4e-14
Q5VMQ5	701	CRS2-associated factor 1,	no	no	0.283	0.128	0.307	7e-07
Q84N49	674	CRS2-associated factor 1,	N/A	no	0.331	0.155	0.318	3e-06
Q6Z4U2	428	CRS2-associated factor 1,	no	no	0.283	0.210	0.268	2e-05
Q0J7J7	366	CRS2-associated factor 2,	no	no	0.230	0.199	0.283	0.0003
Q657G7	607	CRS2-associated factor 2,	no	no	0.208	0.108	0.289	0.0005
Q84N48	611	CRS2-associated factor 2,	N/A	no	0.280	0.145	0.271	0.0005

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

 Score =  395 bits (1014), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 216/322 (67%), Positives = 253/322 (78%), Gaps = 17/322 (5%)

Query: 1   MTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKN 60
           MT+EEKIL KLRKARKKEER++E +KK+EP ES+E THDPEILTPEEHFY+LKMG KCKN
Sbjct: 135 MTSEEKILNKLRKARKKEERLMETMKKLEPSESAETTHDPEILTPEEHFYYLKMGLKCKN 194

Query: 61  YVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE 120
           YVPVGRRGIYQGVILNMHLHWKKHQTL+V++KTF+ +EVKEIA ELARLTGGIVL++HE 
Sbjct: 195 YVPVGRRGIYQGVILNMHLHWKKHQTLQVVIKTFTPDEVKEIAVELARLTGGIVLDVHEG 254

Query: 121 NTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQ 180
           NTIIMYRGKNY QPPTEIMSPRITL RKKALDKSK RD LRAV+KYIP+LEQEL+LL+AQ
Sbjct: 255 NTIIMYRGKNYVQPPTEIMSPRITLPRKKALDKSKCRDALRAVRKYIPRLEQELQLLQAQ 314

Query: 181 AETRSENRSDAAEDVQ--NTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFET 238
           AET+ +  +   +D Q  + EL K    S   + +  E D     L A+DS DLSDIFET
Sbjct: 315 AETKRDYTNVKVDDNQERSEELKKIIERSEECLEDEQEEDEAGLEL-ATDS-DLSDIFET 372

Query: 239 DSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDED---S 295
           DSE E + K E RPL+L++F+KFP  N+ E EDF         D   AKS G++ D   S
Sbjct: 373 DSELE-DAKTE-RPLFLEEFEKFPAINNREDEDFG--------DLGKAKSEGEENDDDKS 422

Query: 296 SHFDEVDKMFLRAASLLKKQKR 317
            +FDEVDKMFLRAA LLKK++R
Sbjct: 423 PNFDEVDKMFLRAAFLLKKKRR 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 = 1e-17,   Method: Compositional matrix adjust.
 Identities = 59/150 (39%), Positives = 84/150 (56%), Gaps = 6/150 (4%)

Query: 9   YKLRKARKKEERIVEGLKKIEPKES-SEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRR 67
           +KL    KK ER  + L K+    S SE + D E LT EE   F ++GRK    V +GRR
Sbjct: 529 WKLSVLNKKIERSNQALAKLHSSWSPSEQSADREHLTEEEKIMFRRIGRKMDGLVLLGRR 588

Query: 68  GIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT---II 124
           GI+ GVI  +H HWK  + +KVI K     ++   A+ L   TGGI++ + +  T   II
Sbjct: 589 GIFDGVIEEIHQHWKHKEVVKVITKQNQTRQIMYAASLLEVETGGILIAVEKLTTSHAII 648

Query: 125 MYRGKNYAQPPTEIMSPRITLSRKKALDKS 154
           +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 = 84.0 bits (206), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 56/150 (37%), Positives = 84/150 (56%), Gaps = 6/150 (4%)

Query: 9   YKLRKARKKEERIVEGLKKIEPKES-SEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRR 67
           ++L    KK ER  + L K+    S S+   D E+LT EE   F K+G K   +V +GRR
Sbjct: 531 WRLSMLTKKIERSNQVLAKLHSSWSPSKKDGDRELLTEEERRIFRKIGLKMDEHVLLGRR 590

Query: 68  GIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT---II 124
           G+++GVI  +H HWK  + +KVI K   A ++   +  L   TGG ++ I    T   II
Sbjct: 591 GVFEGVIEEIHQHWKHKEVVKVITKQNQASQITYTSMMLEVETGGTLIAIERFTTSHAII 650

Query: 125 MYRGKNYAQPPTEIMSPRITLSRKKALDKS 154
           +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 = 4e-14,   Method: Compositional matrix adjust.
 Identities = 49/149 (32%), Positives = 83/149 (55%), Gaps = 4/149 (2%)

Query: 34  SEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKT 93
           SE   D EILT EE     ++G K  + + +GRRG++ GV+  +H HWK  +  KVI   
Sbjct: 563 SEGDDDIEILTNEERECLRRIGLKMNSSLVLGRRGVFFGVMEGLHQHWKHREVAKVITMQ 622

Query: 94  FSAEEVKEIAAELARLTGGIVLEIH---EENTIIMYRGKNYAQPPTEIMSPRITLSRKKA 150
                V   A  L   + G+++ I    E + I++YRGKNY +P +++M+  + L+++KA
Sbjct: 623 KLFSRVVYTAKALETESNGVLISIEKLKEGHAILIYRGKNYKRPSSKLMAQNL-LTKRKA 681

Query: 151 LDKSKYRDGLRAVKKYIPKLEQELELLRA 179
           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 = 55.1 bits (131), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 28/91 (30%), Positives = 47/91 (51%), Gaps = 1/91 (1%)

Query: 41  EILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVK 100
           E LT EE    +K   K K  + +GR G+   ++ N+H HWK+ +  K+  K     ++ 
Sbjct: 183 EPLTKEEVDELVKATLKTKRQLNIGRDGLTHNMLENIHSHWKRKRVCKIKCKGVCTVDMD 242

Query: 101 EIAAELARLTGGIVLEIHEENTIIMYRGKNY 131
            +  +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 = 3e-06,   Method: Compositional matrix adjust.
 Identities = 35/110 (31%), Positives = 55/110 (50%), Gaps = 5/110 (4%)

Query: 25  LKKIEPKESSEMTHD--PEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWK 82
           L  +EP+  S    D   E LT EE    +K   K K  + +GR G+   ++ N+H HWK
Sbjct: 165 LAGMEPRYQSVSREDILGEPLTKEEVSELVKGSLKSKRQLNMGRDGLTHNMLENIHSHWK 224

Query: 83  KHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTII-MYRGKNY 131
           + +  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 = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/93 (26%), Positives = 50/93 (53%), Gaps = 3/93 (3%)

Query: 41  EILTPEEHFYFLKMGRK--CKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEE 98
           E LTP E  + +   +K   K  + +GR G+   ++ ++H HWK  + ++V        +
Sbjct: 155 EPLTPAERAFLVSKCQKSRTKKQINLGRDGLTHNMLNDIHNHWKNDEAVRVKCLGVPTVD 214

Query: 99  VKEIAAELARLTGGIVLEIHEENTIIMYRGKNY 131
           ++ +  +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 = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 58  CKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEI 117
           C   + +G+ G+   +I ++H HWK+ + +++        ++  I   L   TGG V+  
Sbjct: 162 CSRQINLGKGGVTHNMIDDIHNHWKRAEAVRIKCLGVPTLDMDNICFHLEDKTGGKVI-Y 220

Query: 118 HEENTIIMYRGKNY 131
              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|Q657G7|CAF2P_ORYSJ CRS2-associated factor 2, chloroplastic OS=Oryza sativa subsp. japonica GN=Os01g0323300 PE=2 SV=1

 Score = 45.8 bits (107), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 3/69 (4%)

Query: 64  VGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENTI 123
           +GR G+   ++  +H HW++ +  KV  +     ++K +   L   +GG V  IH    +
Sbjct: 251 IGRDGLTHNMLEMIHCHWRRQEICKVRCRGVPTVDMKNLCYHLEEKSGGKV--IHRVGGV 308

Query: 124 I-MYRGKNY 131
           + +YRG+NY
Sbjct: 309 VFLYRGRNY 317

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

 Score = 45.4 bits (106), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 25/92 (27%), Positives = 45/92 (48%), Gaps = 3/92 (3%)

Query: 41  EILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVK 100
           E LTP E    +K        + +GR G+   ++  +H HW++ +  KV  +     ++K
Sbjct: 232 EPLTPSEVRALVKPHISHNRQLNIGRDGLTHNMLEMIHCHWRRQEICKVRCRGVPTVDMK 291

Query: 101 EIAAELARLTGGIVLEIHEENTII-MYRGKNY 131
            +   L   +GG V  IH    ++ +YRG++Y
Sbjct: 292 NLCYHLEEKSGGKV--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	317
297739537	331	unnamed protein product [Vitis vinifera]	0.996	0.954	0.719	1e-132
225448146	401	PREDICTED: uncharacterized CRM domain-co	0.996	0.788	0.719	1e-131
255572670	458	conserved hypothetical protein [Ricinus	0.993	0.687	0.710	1e-129
224132018	413	predicted protein [Populus trichocarpa]	0.971	0.745	0.692	1e-124
356498434	383	PREDICTED: uncharacterized CRM domain-co	0.981	0.812	0.678	1e-121
356501797	382	PREDICTED: uncharacterized CRM domain-co	0.962	0.798	0.698	1e-120
357439975	443	CRM domain-containing protein, putative	0.981	0.702	0.670	1e-119
449458069	500	PREDICTED: uncharacterized CRM domain-co	0.996	0.632	0.633	1e-115
357439925	472	CRM domain-containing protein, putative	0.981	0.658	0.617	1e-114
297831446	1055	predicted protein [Arabidopsis lyrata su	0.952	0.286	0.664	1e-109

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

 Score =  476 bits (1224), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 239/332 (71%), Positives = 276/332 (83%), Gaps = 16/332 (4%)

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

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

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

Query: 181 AETRSENRSDAAEDVQNTELDKPDFGSIPSMM---------------ECSENDPTTESLM 225
           A+ ++EN+++A ED QN  +D  +   I ++                E SE +  T+S  
Sbjct: 181 AKMQAENKTEAVEDFQNANIDSINSQGISNLQPENSDKLRELLAGNNESSEEESLTDSGT 240

Query: 226 ASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRN 285
            S SE LSDIFE+DS+T+T+EKAE + LYL++F+KFPV++D E EDFEEHLRQIS DSR 
Sbjct: 241 ESCSEALSDIFESDSDTDTKEKAE-QLLYLNEFEKFPVESDGEPEDFEEHLRQISADSRK 299

Query: 286 AKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 317
           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|225448146|ref|XP_002263852.1| PREDICTED: uncharacterized CRM domain-containing protein At3g25440, chloroplastic-like [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: 1   MTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKN 60
           MTAEEKILYKLRKAR+KEER+ E L KIEPKESSE THDPEILTPEEHF+FLKMG KCKN
Sbjct: 71  MTAEEKILYKLRKARRKEERLAEALTKIEPKESSETTHDPEILTPEEHFFFLKMGLKCKN 130

Query: 61  YVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE 120
           YVP+GRRGIYQGVILNMHLHWKKHQTL+V+VKTFS EEVKEIA ELARLTGGIVL+IHEE
Sbjct: 131 YVPIGRRGIYQGVILNMHLHWKKHQTLQVVVKTFSPEEVKEIAVELARLTGGIVLDIHEE 190

Query: 121 NTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQ 180
           NTIIMYRGKNY+QPPTEIMSPRITLSRKKALDKSKYRDGLRAV+KYIP+LE +LELL+AQ
Sbjct: 191 NTIIMYRGKNYSQPPTEIMSPRITLSRKKALDKSKYRDGLRAVRKYIPRLEGDLELLQAQ 250

Query: 181 AETRSENRSDAAEDVQNTELDKPDFGSIPSMM---------------ECSENDPTTESLM 225
           A+ ++EN+++A ED QN  +D  +   I ++                E SE +  T+S  
Sbjct: 251 AKMQAENKTEAVEDFQNANIDSINSQGISNLQPENSDKLRELLAGNNESSEEESLTDSGT 310

Query: 226 ASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRN 285
            S SE LSDIFE+DS+T+T+EKAE + LYL++F+KFPV++D E EDFEEHLRQIS DSR 
Sbjct: 311 ESCSEALSDIFESDSDTDTKEKAE-QLLYLNEFEKFPVESDGEPEDFEEHLRQISADSRK 369

Query: 286 AKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 317
           AKSL KD D    DEVD+MFLRAASLLKK++R
Sbjct: 370 AKSLEKDADLPQLDEVDQMFLRAASLLKKKRR 401

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  468 bits (1204), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 236/332 (71%), Positives = 274/332 (82%), Gaps = 17/332 (5%)

Query: 1   MTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKN 60
           MTAEEK+LYKL+KA+KKEER V+ LKKIEP +SSE THDPEILTPEEHF+FLKMG KCKN
Sbjct: 129 MTAEEKLLYKLKKAQKKEERYVQALKKIEPVDSSETTHDPEILTPEEHFFFLKMGLKCKN 188

Query: 61  YVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE 120
           YVPVGRRGIYQGVILNMHLHWKKHQT++V+VKTFS EEVKEIAAELARLTGGIVL+IHEE
Sbjct: 189 YVPVGRRGIYQGVILNMHLHWKKHQTVQVVVKTFSPEEVKEIAAELARLTGGIVLDIHEE 248

Query: 121 NTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQ 180
           NTIIMYRGKNY+QPPTEIMSPRITLSRKKALDKSKYRDGLRAV+ YIP+LEQ+LELL+ Q
Sbjct: 249 NTIIMYRGKNYSQPPTEIMSPRITLSRKKALDKSKYRDGLRAVRNYIPRLEQDLELLKVQ 308

Query: 181 AETRSENRSDAAEDVQNTELDKPDFGSIPSMM---------------ECSENDPTTESLM 225
           +  ++E  S +AE+   T+ D  + G +PS                 ECSE +   +  M
Sbjct: 309 SMGKAECGSASAEETLYTD-DGAESGGVPSTPLENSEKLKKITDGQEECSEEESPMDLGM 367

Query: 226 ASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRN 285
            SDSEDLSDIFETDS+TETE+K + RPLYL++F KFP+Q +EE EDFEEHLRQ+S+DSR 
Sbjct: 368 LSDSEDLSDIFETDSDTETEDKVK-RPLYLEEFKKFPIQGNEEPEDFEEHLRQLSVDSRK 426

Query: 286 AKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 317
            +S  KD D   FDEVD++FLRAASLLKK+KR
Sbjct: 427 VESSEKDSDIPSFDEVDRLFLRAASLLKKKKR 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 =  452 bits (1162), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 232/335 (69%), Positives = 276/335 (82%), Gaps = 27/335 (8%)

Query: 1   MTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKN 60
           MTAEEKILYKLRKA++KEER V+ LKKIEPKESSE THDPEILTPEEHF+FLKMG KCKN
Sbjct: 88  MTAEEKILYKLRKAQRKEERFVQALKKIEPKESSEATHDPEILTPEEHFFFLKMGLKCKN 147

Query: 61  YVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE 120
           YVPVGRRGIYQGVILNMHLHWKKHQTLKV+VKTF+ EEVKEIAAELAR TGGIVL+IHEE
Sbjct: 148 YVPVGRRGIYQGVILNMHLHWKKHQTLKVVVKTFTPEEVKEIAAELARFTGGIVLDIHEE 207

Query: 121 NTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQ 180
           NTIIMYRGKNY+QPPTEIMSPR+TLSRKKALDKSK RDGLRA+++YIP+L+Q+LELL A+
Sbjct: 208 NTIIMYRGKNYSQPPTEIMSPRVTLSRKKALDKSKCRDGLRALRRYIPRLQQDLELLHAR 267

Query: 181 AETRS-----ENRSDAAEDVQNTE-----LDKPDFGSIPSMMECSENDPTTESLMASDSE 230
           A  ++     E+RS +++ ++N+E     +D+ D        E SE+ P T+  +ASDSE
Sbjct: 268 AGGKTDIDGAESRSISSKQLENSEKLKEIIDRQD--------EGSEDGPDTDLGIASDSE 319

Query: 231 DLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLG 290
           DLSDIFETDS+ +TEE ++ RPLYL++F+KF V+ D E EDFEEHLRQIS+ S+   + G
Sbjct: 320 DLSDIFETDSDADTEETSK-RPLYLEEFEKFSVEADGEPEDFEEHLRQISLGSKKGVTSG 378

Query: 291 K--------DEDSSHFDEVDKMFLRAASLLKKQKR 317
           K        D DS  FDEVD+MFLRAASLLK++KR
Sbjct: 379 KDVDIPTGVDVDSPSFDEVDRMFLRAASLLKRKKR 413

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  441 bits (1134), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 224/330 (67%), Positives = 266/330 (80%), Gaps = 19/330 (5%)

Query: 1   MTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKN 60
           MTAEEK LYKL KARKKEER+ E LKKIEP ESSE THDPEILTPEEHF+FLKMG K KN
Sbjct: 56  MTAEEKNLYKLLKARKKEERLCEALKKIEPAESSETTHDPEILTPEEHFFFLKMGLKSKN 115

Query: 61  YVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE 120
           YVPVGRRGIYQGVILNMHLHWKKHQTLKV+VKTFSAEEVKEIAAELARL+GGIVL+IHE+
Sbjct: 116 YVPVGRRGIYQGVILNMHLHWKKHQTLKVVVKTFSAEEVKEIAAELARLSGGIVLDIHED 175

Query: 121 NTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQ 180
           NTIIMYRGKNY+QPPTEIMSPR++LSRKKALDKSKYRD LRAV++YIP+LEQELE+LRAQ
Sbjct: 176 NTIIMYRGKNYSQPPTEIMSPRVSLSRKKALDKSKYRDALRAVRRYIPRLEQELEILRAQ 235

Query: 181 AETRSENRSDAAEDVQNTELDKPDFGSIPS-----------MMEC----SENDPTTESLM 225
            ++ +E+ +DAAE +QN+  +  + GSI +           MM      +E++    S +
Sbjct: 236 FKSSAESNTDAAEAIQNSGRESIESGSISNFQLQNSYKDREMMNVNIGSTEDETDMNSEL 295

Query: 226 ASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRN 285
            SDS+ LSDIFETDS+TE   K E +PLYLD+FD FP Q+D E  DFEEH+RQ+S+ S+N
Sbjct: 296 DSDSDKLSDIFETDSDTENFVKEE-KPLYLDEFDNFPEQSDGEMNDFEEHMRQMSLKSKN 354

Query: 286 AKSLGKDEDSSHFDEVDKMFLRAASLLKKQ 315
              + KD++    DEVDK+FL+A S LKK+
Sbjct: 355 ---MEKDDNLPKLDEVDKIFLQATSFLKKK 381

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  437 bits (1124), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 220/315 (69%), Positives = 260/315 (82%), Gaps = 10/315 (3%)

Query: 1   MTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKN 60
           MTAEEKILYKL KARKKEER+ E LKKIEP ESSE THDPEILTPEEHF+FLKMG K KN
Sbjct: 76  MTAEEKILYKLLKARKKEERLCEALKKIEPAESSETTHDPEILTPEEHFFFLKMGLKSKN 135

Query: 61  YVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE 120
           YVPVGRRGIYQGVILNMHLHWKKHQTLKV+VKTFSAEEVKEIA ELARL+GGIVL+IHE+
Sbjct: 136 YVPVGRRGIYQGVILNMHLHWKKHQTLKVVVKTFSAEEVKEIATELARLSGGIVLDIHED 195

Query: 121 NTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQ 180
           NTIIMYRGKNY+QPPTEIMSPR++LSRKKALDKSKYRD LRAV+++IP+LEQELE+LRAQ
Sbjct: 196 NTIIMYRGKNYSQPPTEIMSPRVSLSRKKALDKSKYRDALRAVRRHIPRLEQELEILRAQ 255

Query: 181 AETRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDS 240
            ++ +E+ +DAAE +QN      D       + C+E++    S + SDS+ LSDIFETDS
Sbjct: 256 FKSSAESNTDAAEAIQNNRERMND------NIGCTEDETDMNSELDSDSDKLSDIFETDS 309

Query: 241 ETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDE 300
           +TE   K E +PLYLD+FD FP Q+D E  DFEEHLRQ+S+ S+N   + K+++    DE
Sbjct: 310 DTENFIKEE-KPLYLDEFDNFPEQSDGEMNDFEEHLRQMSLKSKN---MEKEDNLPKLDE 365

Query: 301 VDKMFLRAASLLKKQ 315
           VDK+FL+A S LKK+
Sbjct: 366 VDKIFLQATSFLKKK 380

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  432 bits (1112), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 224/334 (67%), Positives = 267/334 (79%), Gaps = 23/334 (6%)

Query: 1   MTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKN 60
           MT EE+ILYKL KARKKEER+ E LKKIEP ESSE  HDPEILTPEEHF+FLKMG K KN
Sbjct: 116 MTTEERILYKLLKARKKEERLREALKKIEPTESSETIHDPEILTPEEHFFFLKMGLKSKN 175

Query: 61  YVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE 120
           YVPVGRRGIYQGVILNMHLHWKKHQTL+V+VKTFSAEEVKEIA ELARLTGGIVL IHEE
Sbjct: 176 YVPVGRRGIYQGVILNMHLHWKKHQTLQVVVKTFSAEEVKEIATELARLTGGIVLGIHEE 235

Query: 121 NTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQ 180
           +TIIMYRGKNY+QPPTEIMSPR+TL RKKALDKSKYRDGLRAV++YIPKLEQELE+LRAQ
Sbjct: 236 DTIIMYRGKNYSQPPTEIMSPRVTLPRKKALDKSKYRDGLRAVRRYIPKLEQELEILRAQ 295

Query: 181 AETRSENRSDAAEDVQ-------------NTELDKPDFGSIPSMME----CSENDPTTES 223
            ++ +E+ ++AAE +Q             N +L+K D   + +M      CSE++   +S
Sbjct: 296 FQSTAESNTEAAEGIQISDKVSVEPSSVSNLQLEKLD--KVGAMFNDNNSCSEDEAHMDS 353

Query: 224 LMASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDS 283
            + S S+ LSDIFETDS+TE   K E +PLYLD+F+ FP Q+D + +DFEEHL+QIS +S
Sbjct: 354 DLDSYSDKLSDIFETDSDTEDLVKEE-KPLYLDEFNNFPEQSDGDTDDFEEHLQQISYNS 412

Query: 284 RNAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 317
           +N   + KD D   FDEVD++FLRAAS LKK+++
Sbjct: 413 KN---MEKDADLPKFDEVDQIFLRAASFLKKKRK 443

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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 =  421 bits (1083), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 211/333 (63%), Positives = 265/333 (79%), Gaps = 17/333 (5%)

Query: 1   MTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKN 60
           MT+EEKIL+K+ KARKKE+R+VE L+KIEP +SS+ THDPEILTPEEHFYFLKMG K KN
Sbjct: 169 MTSEEKILFKMNKARKKEKRLVEALEKIEPADSSDTTHDPEILTPEEHFYFLKMGIKGKN 228

Query: 61  YVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE 120
           YVPVGRRGIYQGVILNMHLHWKKHQT+KV+VKTFS EEVKEIAAELARLTGG+VL+IHEE
Sbjct: 229 YVPVGRRGIYQGVILNMHLHWKKHQTVKVVVKTFSPEEVKEIAAELARLTGGLVLDIHEE 288

Query: 121 NTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQ 180
           +TIIMYRGKNY+QPPTEIMSPR++LSRKKALDKSKYRDGLRAV+K+IPKLEQEL  L++Q
Sbjct: 289 DTIIMYRGKNYSQPPTEIMSPRVSLSRKKALDKSKYRDGLRAVRKHIPKLEQELRFLQSQ 348

Query: 181 AETRSENRSDAAEDVQNTELDKPDFGSIPSM----------------MECSENDPTTESL 224
           A+   ++  ++ E +Q T  D     +I S+                 + S++    ++ 
Sbjct: 349 AKLNCKSNGESVEHMQETVDDTNKSKAISSLNLENLDDSSNAMRSVSKDWSDDSSPIDTG 408

Query: 225 MASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSR 284
           M+SDSEDLSD+FETD ++E +EK E +PL+L +F+ F  + ++E ED  + LRQIS+DS+
Sbjct: 409 MSSDSEDLSDMFETDIDSEADEKME-KPLFLKEFENFAAETEDEIEDLSDQLRQISMDSK 467

Query: 285 NAKSLGKDEDSSHFDEVDKMFLRAASLLKKQKR 317
            AK L  D +S  FDEVD++FLR+ASLLKK++R
Sbjct: 468 QAKILENDVNSPEFDEVDRLFLRSASLLKKKRR 500

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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 =  417 bits (1072), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 224/363 (61%), Positives = 267/363 (73%), Gaps = 52/363 (14%)

Query: 1   MTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKN 60
           MT EE+ILYKL KARKKEER+ E LKKIEP ESSE  HDPEILTPEEHF+FLKMG K KN
Sbjct: 116 MTTEERILYKLLKARKKEERLREALKKIEPTESSETIHDPEILTPEEHFFFLKMGLKSKN 175

Query: 61  YVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE 120
           YVPVGRRGIYQGVILNMHLHWKKHQTL+V+VKTFSAEEVKEIA ELARLTGGIVL IHEE
Sbjct: 176 YVPVGRRGIYQGVILNMHLHWKKHQTLQVVVKTFSAEEVKEIATELARLTGGIVLGIHEE 235

Query: 121 NTIIMYRGKNYAQPPTEIMSPRITLSRKK-----------------------------AL 151
           +TIIMYRGKNY+QPPTEIMSPR+TL RKK                             AL
Sbjct: 236 DTIIMYRGKNYSQPPTEIMSPRVTLPRKKVLHVPKDCLHHTIKDCFTFLFAYFPSLISAL 295

Query: 152 DKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENRSDAAEDVQ-------------NT 198
           DKSKYRDGLRAV++YIPKLEQELE+LRAQ ++ +E+ ++AAE +Q             N 
Sbjct: 296 DKSKYRDGLRAVRRYIPKLEQELEILRAQFQSTAESNTEAAEGIQISDKVSVEPSSVSNL 355

Query: 199 ELDKPDFGSIPSMME----CSENDPTTESLMASDSEDLSDIFETDSETETEEKAELRPLY 254
           +L+K D   + +M      CSE++   +S + S S+ LSDIFETDS+TE   K E +PLY
Sbjct: 356 QLEKLD--KVGAMFNDNNSCSEDEAHMDSDLDSYSDKLSDIFETDSDTEDLVKEE-KPLY 412

Query: 255 LDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKK 314
           LD+F+ FP Q+D + +DFEEHL+QIS +S+N   + KD D   FDEVD++FLRAAS LKK
Sbjct: 413 LDEFNNFPEQSDGDTDDFEEHLQQISYNSKN---MEKDADLPKFDEVDQIFLRAASFLKK 469

Query: 315 QKR 317
           +++
Sbjct: 470 KRK 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 =  400 bits (1027), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 214/322 (66%), Positives = 255/322 (79%), Gaps = 20/322 (6%)

Query: 1    MTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKN 60
            MTAEEKIL KL KARKKEER++E +KK+EP ES+E THDPEILTPEEHFY+LKMG KCKN
Sbjct: 749  MTAEEKILNKLTKARKKEERLMETMKKLEPSESAETTHDPEILTPEEHFYYLKMGLKCKN 808

Query: 61   YVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE 120
            YVPVGRRGIYQGVILNMHLHWKKHQTL+V++KTF+ +EV EIA ELARLTGGIVL++HE 
Sbjct: 809  YVPVGRRGIYQGVILNMHLHWKKHQTLQVVIKTFTPDEVNEIAVELARLTGGIVLDVHEG 868

Query: 121  NTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQ 180
            NTIIMYRGKNY QPPTEIMSPRITL RKKALDKSK RD LRAV+KYIP+LEQEL+LL+AQ
Sbjct: 869  NTIIMYRGKNYVQPPTEIMSPRITLPRKKALDKSKCRDALRAVRKYIPRLEQELQLLQAQ 928

Query: 181  AETRSENRSDAAEDVQ--NTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFET 238
            AET+ E  +   +D+Q  + EL K    S   + +  E +    S +A+DS DLSDIFET
Sbjct: 929  AETKREYLNVKVDDIQERSDELKKIIERSEECLED-EEEEEDAGSELATDS-DLSDIFET 986

Query: 239  DSETETEEKAELRPLYLDQFDKFP-VQNDEEHEDFEEHLRQISIDSRNAKSLGKDED--S 295
            DSE E E+   +RPL+L++F+KFP + N+ E EDF +           AKS G++ D  S
Sbjct: 987  DSELEDEKT--VRPLFLEEFEKFPAINNNREDEDFGK-----------AKSEGEENDDKS 1033

Query: 296  SHFDEVDKMFLRAASLLKKQKR 317
             +FDEVDKMFLRAASLLKK++R
Sbjct: 1034 PNFDEVDKMFLRAASLLKKKRR 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	317
TAIR|locus:2094438	444	LOH1 "LAG One Homologue 1" [Ar	0.952	0.680	0.630	1.1e-96
TAIR|locus:2056558	372	AT2G28480 [Arabidopsis thalian	0.772	0.658	0.378	5.9e-41
TAIR|locus:2091458	491	AT3G27550 [Arabidopsis thalian	0.526	0.340	0.461	8.4e-41
TAIR|locus:2123276	343	AT4G13070 [Arabidopsis thalian	0.514	0.475	0.511	8.7e-40
TAIR|locus:2094558	881	CFM3A "CRM family member 3A" [	0.750	0.270	0.300	1.8e-23
TAIR|locus:2094997	848	EMB1865 "embryo defective 1865	0.709	0.265	0.329	1.5e-21
TAIR|locus:2096662	1011	CFM2 "CRM family member 2" [Ar	0.955	0.299	0.252	8.6e-21
TAIR|locus:2181372	720	CRS1 "ortholog of maize chloro	0.482	0.212	0.339	2e-13

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

 Score = 961 (343.3 bits), Expect = 1.1e-96, P = 1.1e-96
 Identities = 205/325 (63%), Positives = 242/325 (74%)

Query:     1 MTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKN 60
             MT+EEKIL KLRKARKKEER++E +KK+EP ES+E THDPEILTPEEHFY+LKMG KCKN
Sbjct:   135 MTSEEKILNKLRKARKKEERLMETMKKLEPSESAETTHDPEILTPEEHFYYLKMGLKCKN 194

Query:    61 YVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE 120
             YVPVGRRGIYQGVILNMHLHWKKHQTL+V++KTF+ +EVKEIA ELARLTGGIVL++HE 
Sbjct:   195 YVPVGRRGIYQGVILNMHLHWKKHQTLQVVIKTFTPDEVKEIAVELARLTGGIVLDVHEG 254

Query:   121 NTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKXXXXXXXXXXX 180
             NTIIMYRGKNY QPPTEIMSPRITL RKKALDKSK RD LRAV+KYIP+           
Sbjct:   255 NTIIMYRGKNYVQPPTEIMSPRITLPRKKALDKSKCRDALRAVRKYIPRLEQELQLLQAQ 314

Query:   181 XXTRSENRSDAAEDVQ--NTELDKPDFGSIPSMMECSENDPTTESL---MASDSEDLSDI 235
               T+ +  +   +D Q  + EL K     I    EC E++   +     +A+DS DLSDI
Sbjct:   315 AETKRDYTNVKVDDNQERSEELKK----IIERSEECLEDEQEEDEAGLELATDS-DLSDI 369

Query:   236 FETDSETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDED- 294
             FETDSE E + K E RPL+L++F+KFP  N+ E EDF         D   AKS G++ D 
Sbjct:   370 FETDSELE-DAKTE-RPLFLEEFEKFPAINNREDEDFG--------DLGKAKSEGEENDD 419

Query:   295 --SSHFDEVDKMFLRAASLLKKQKR 317
               S +FDEVDKMFLRAA LLKK++R
Sbjct:   420 DKSPNFDEVDKMFLRAAFLLKKKRR 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:2056558 AT2G28480 [Arabidopsis thaliana (taxid:3702)]

 Score = 435 (158.2 bits), Expect = 5.9e-41, P = 5.9e-41
 Identities = 95/251 (37%), Positives = 143/251 (56%)

Query:     1 MTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKN 60
             + AEE+I YKL KA+ KE  ++E LK+ E  +       P  +T EE FY  KMG+K  N
Sbjct:   122 VNAEERIKYKLEKAKIKEALLIERLKRYEVAKVQGPEVRPHEITGEERFYLKKMGQKRSN 181

Query:    61 YVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE 120
             YVP+GRRG++ GVILNMHLHWKKH+T+KVI       +V++ A ELA+L+GG+ + I  +
Sbjct:   182 YVPIGRRGVFGGVILNMHLHWKKHETVKVICNNSKPGQVQQYAEELAKLSGGVPVNIIGD 241

Query:   121 NTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKXXXXXXXXXXX 180
             +TII YRGK Y QP  ++MSP  TLS+K+A +KSKY   L +V+ +I             
Sbjct:   242 DTIIFYRGKGYVQP--QVMSPIDTLSKKRAYEKSKYEQSLESVRHFIAIAEKELELYYRH 299

Query:   181 XXTRSE-NRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETD 239
                  + N  +    + ++  +          + CS+ D ++E     + E+L ++ +  
Sbjct:   300 VALYDDPNNRNPLSILDDSPSESRQHHENEFFLSCSDTDSSSED--EDEDEELCEL-DNG 356

Query:   240 SETETEEKAEL 250
             S + +  K EL
Sbjct:   357 SSSSSSAKEEL 367

GO:0003723 "RNA binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

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

 Score = 401 (146.2 bits), Expect = 8.4e-41, Sum P(2) = 8.4e-41
 Identities = 78/169 (46%), Positives = 115/169 (68%)

Query:     1 MTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKN 60
             MT EE+++Y L++A+KK   +++ LKK +  E     HDPE+ T E+   F K+G K KN
Sbjct:    50 MTDEERLIYNLKRAKKKVALLLQKLKKYDLPELPSPVHDPELFTSEQVQAFKKIGFKNKN 109

Query:    61 YVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE 120
             YVPVG RG++ GV+ NMH+HWK H+T++V    F  E++KE+A+ +ARL+GG+V+ IH  
Sbjct:   110 YVPVGVRGVFGGVVQNMHMHWKFHETVQVCCDNFPKEKIKEMASMIARLSGGVVINIHNV 169

Query:   121 NTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPK 169
              TIIM+RG+NY QP   I  P  TL+++KAL K+++   L + K  I K
Sbjct:   170 KTIIMFRGRNYRQPKNLI--PVNTLTKRKALFKARFEQALESQKLNIKK 216

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

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

 Score = 424 (154.3 bits), Expect = 8.7e-40, P = 8.7e-40
 Identities = 86/168 (51%), Positives = 118/168 (70%)

Query:     4 EEKILYKLRKARKKEERIVEGLKKIE-PKESSEMTHDPEILTPEEHFYFLKMGRKCKNYV 62
             E +I YKL KA++KEE ++E L+K + PK  +E  +DPE LT EE  Y  + G K KN+V
Sbjct:   143 EVRIRYKLEKAKRKEEWLIEKLRKYDVPKSPAE-PYDPESLTEEEQHYLKRTGEKRKNFV 201

Query:    63 PVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAE-EVKEIAAELARLTGGIVLEIHEEN 121
              VGRRG++ GV+LN+HLHWKKH+T+KVI K  +   +V E A ELARL+ GIV+++   N
Sbjct:   202 LVGRRGVFGGVVLNLHLHWKKHETVKVICKPCNKPGQVHEYAEELARLSKGIVIDVKPNN 261

Query:   122 TIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPK 169
             TI++YRGKNY +P  E+MSP  TLS+ KAL+K +Y   L    ++I K
Sbjct:   262 TIVLYRGKNYVRP--EVMSPVDTLSKDKALEKYRYEQSLEHTSEFIEK 307

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 = 281 (104.0 bits), Expect = 1.8e-23, P = 1.8e-23
 Identities = 74/246 (30%), Positives = 126/246 (51%)

Query:     6 KILYKLRKARKKEERIVEGLKKIEP-KESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPV 64
             K+  KL  A +K  +   GL K+E   + +E   DPE +T EE F F K+G K K ++ +
Sbjct:   600 KLERKLAFAERKLLKAERGLAKVEVCLKPAEQREDPESITDEERFMFRKLGLKMKAFLLL 659

Query:    65 GRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN--- 121
             GRRG++ G + NMHLHWK  + +K+IVK  + + VK++A  L   +GGI++ I +     
Sbjct:   660 GRRGVFDGTVENMHLHWKYRELVKIIVKAKTFDGVKKVALALEAESGGILVSIDKVTKGY 719

Query:   122 TIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKXXXXXXXXXXXX 181
              II+YRG++Y +P   ++ P+  L+++KAL +S        + K+I              
Sbjct:   720 AIIVYRGQDYKRPT--MLRPKNLLTKRKALARSIELQRREGLLKHI-STMQAKAKQLRAE 776

Query:   182 XTRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETD-S 240
               + E  +D  ++    +LD     S     E  ++D   E+    +  +  +I   + S
Sbjct:   777 IEQMEKVTDKGDEELYNKLDMAYASSDEETDEEDDDDAFPETYAEGEDGEEGEILAGELS 836

Query:   241 ETETEE 246
             ETE ++
Sbjct:   837 ETEDKD 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 = 1.5e-21, P = 1.5e-21
 Identities = 78/237 (32%), Positives = 125/237 (52%)

Query:     5 EKILYKLRKARKKEERIVEGLKKIEPKE-SSEMTHDPEILTPEEHFYFLKMGRKCKNYVP 63
             ++I +KL  A+ K +R  + L KIE     +   +D E+++ EE   F K+G K K Y+P
Sbjct:   614 KRIQHKLNLAQSKFQRAEKLLSKIEASMIPNGPDYDQEVISEEERAMFRKVGLKMKAYLP 673

Query:    64 VGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN-- 121
             +G RG++ GVI NMHLHWK  + +K+I K  +   V+E A  L   +GG+++ I +    
Sbjct:   674 IGIRGVFDGVIENMHLHWKHRELVKLISKQKNQAFVEETARLLEYESGGVLVAIEKVPKG 733

Query:   122 -TIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKXXXXXXXXXXX 180
               +I YRGKNY +P +  + PR  L++ KAL +S       A+ ++I +           
Sbjct:   734 FALIYYRGKNYRRPIS--LRPRNLLTKAKALKRSIAMQRHEALSQHISELERTIEQMQSQ 791

Query:   181 XXTRSENRSDAAEDVQNTELDKPDFGSIPSMMECSEND--PTT-ESLMASDSE-DLS 233
                 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 = 257 (95.5 bits), Expect = 8.6e-21, P = 8.6e-21
 Identities = 80/317 (25%), Positives = 147/317 (46%)

Query:     5 EKILYKLRKARKKEERIVEGLKKIEPKESSEMTH-DPEILTPEEHFYFLKMGRKCKNYVP 63
             EK   KL  A +K+    + L  +E +ES +++  D E +T +E +   K+G K K ++ 
Sbjct:   540 EKTSMKLSMALEKKANAEKVLADLENRESPQLSDIDKEGITNDEKYMLRKIGLKMKPFLL 599

Query:    64 VGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN-- 121
             +GRRG++ G I NMHLHWK  + +K+I   +S E   ++A  L   +GGI++ +   +  
Sbjct:   600 LGRRGVFDGTIENMHLHWKYRELVKIICNEYSIEAAHKVAEILEAESGGILVAVEMVSKG 659

Query:   122 -TIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKXXXXXXXXXXX 180
               II+YRGKNY +P  + + P+  LS+++AL +S      +++K ++ K           
Sbjct:   660 YAIIVYRGKNYERP--QCLRPQTLLSKREALKRSVEAQRRKSLKLHVLKLSNNIEELNRQ 717

Query:   181 XXTRSENRSDAAEDVQNTELDKPDFGSIPSMMECSENDPTTESLMASDSEDLSDIFETDS 240
                 S   ++   D +++ +   +     +  + +E +   E +    S DLS     + 
Sbjct:   718 LVEDSAT-NETWSDGESSNMMVEE----ETENQHTEPEKAREKIELGYSSDLSVPSSGEE 772

Query:   241 ETETEEKAELRPLYLDQFDKFPVQNDEEHEDFEEHLRQISIDSRNAKSLGKDEDSSHFDE 300
               E + + E+ PL     +    Q DE      +     S+DS    S+  +  S++   
Sbjct:   773 NWEDDSEGEVDPLTTSSQE---YQEDESESASSQRHEGNSLDSTANLSVFAETGSANASS 829

Query:   301 VDKMFLRAASLLKKQKR 317
                  L   S L   ++
Sbjct:   830 FHDRSLPHNSFLNANRK 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 = 200 (75.5 bits), Expect = 2.0e-13, P = 2.0e-13
 Identities = 55/162 (33%), Positives = 89/162 (54%)

Query:     9 YKLRKARKKEERIVEGLKKIEPK-ESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRR 67
             +KL   + K E+    L K+    + SE   D EILT EE     ++G K  + + +GRR
Sbjct:   537 HKLSILKSKIEKSNMELFKLNSLWKPSEGDDDIEILTNEERECLRRIGLKMNSSLVLGRR 596

Query:    68 GIYQGVILNMHLHWKKHQTLKVIV--KTFSAEEVKEIAAELARLTGGIVLEIH---EENT 122
             G++ GV+  +H HWK  +  KVI   K FS   V   A  L   + G+++ I    E + 
Sbjct:   597 GVFFGVMEGLHQHWKHREVAKVITMQKLFS--RVVYTAKALETESNGVLISIEKLKEGHA 654

Query:   123 IIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVK 164
             I++YRGKNY +P +++M+  + L+++KAL +S     L ++K
Sbjct:   655 ILIYRGKNYKRPSSKLMAQNL-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        0.312   0.130   0.360    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      317       304   0.00098  115 3  11 23  0.47    34
                                                     33  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:  591 (63 KB)
  Total size of DFA:  200 KB (2113 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:  31.47u 0.13s 31.60t   Elapsed:  00:00:01
  Total cpu time:  31.47u 0.13s 31.60t   Elapsed:  00:00:01
  Start:  Sat May 11 00:33:52 2013   End:  Sat May 11 00:33:53 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	0.6708	0.9621	0.6869	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	317
smart01103	84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	1e-21
pfam01985	84	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	5e-20

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

 Score = 86.4 bits (215), Expect = 1e-21
 Identities = 28/85 (32%), Positives = 46/85 (54%), Gaps = 1/85 (1%)

Query: 43  LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEI 102
           LT ++  Y   +    K  V +G+ G+ +GV+  +    +KH+ +KV V     E+ KEI
Sbjct: 1   LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEI 60

Query: 103 AAELARLTGGIVLEIHEENTIIMYR 127
           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 = 82.5 bits (205), Expect = 5e-20
 Identities = 28/85 (32%), Positives = 46/85 (54%), Gaps = 1/85 (1%)

Query: 43  LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEI 102
           LT ++  Y   +    K  V +G+ G+ +GV+  +    +KH+ +KV V     E+ KEI
Sbjct: 1   LTGKQRRYLRSLAHHLKPVVQIGKNGLTEGVVEEIDEALEKHELIKVKVLGNDREDRKEI 60

Query: 103 AAELARLTGGIVLEIHEENTIIMYR 127
           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	317
PRK10343	97	RNA-binding protein YhbY; Provisional	99.96
TIGR00253	95	RNA_bind_YhbY putative RNA-binding protein, YhbY f	99.96
PF01985	84	CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR	99.95
COG1534	97	Predicted RNA-binding protein containing KH domain	99.95
KOG1990	564	consensus Poly(A)-specific exoribonuclease PARN [R	99.94
KOG1990	564	consensus Poly(A)-specific exoribonuclease PARN [R	97.91

>PRK10343 RNA-binding protein YhbY; Provisional

Probab=99.96  E-value=2.9e-29  Score=204.98  Aligned_cols=89  Identities=21%  Similarity=0.340  Sum_probs=86.5

Q ss_pred             CCCCHHHHHHHHhccccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEeeC
Q 021078           41 EILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE  120 (317)
Q Consensus        41 E~LT~kERk~LRklAhkLKPvV~IGK~GVTdgVIeeI~~aLk~HELVKVKv~~~~~ed~keiAeeLe~~SGgeLVqV~IG  120 (317)
                      |+||++||++||++||+|+|+|+||++|||++|+.+|+.+|++||||||++.+++++++++++++|++.|||++||+ ||
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            46999999999999999999999999999999999999999999999999999999999999999999999999996 99


Q ss_pred             cEEEEEeCCC
Q 021078          121 NTIIMYRGKN  130 (317)
Q Consensus       121 ~tIILYRgkN  130 (317)
                      +++||||++.
T Consensus        80 ~~~vlYR~~~   89 (97)
T PRK10343         80 KTLVLYRPTK   89 (97)
T ss_pred             cEEEEEecCC
Confidence            9999999974

>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family

Probab=99.96  E-value=5e-29  Score=202.63  Aligned_cols=87  Identities=28%  Similarity=0.369  Sum_probs=85.0

Q ss_pred             CCHHHHHHHHhccccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEeeCcE
Q 021078           43 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT  122 (317)
Q Consensus        43 LT~kERk~LRklAhkLKPvV~IGK~GVTdgVIeeI~~aLk~HELVKVKv~~~~~ed~keiAeeLe~~SGgeLVqV~IG~t  122 (317)
                      ||++||++||++||+|+|+|+|||+|||++|+++|+.+|++||||||++.++++++++++|++|++.|||++||+ ||++
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            799999999999999999999999999999999999999999999999999999999999999999999999996 9999


Q ss_pred             EEEEeCCC
Q 021078          123 IIMYRGKN  130 (317)
Q Consensus       123 IILYRgkN  130 (317)
                      +||||++.
T Consensus        80 ~vlYR~~~   87 (95)
T TIGR00253        80 IVLYRPTK   87 (95)
T ss_pred             EEEEecCC
Confidence            99999964

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=99.95  E-value=2.7e-28  Score=192.27  Aligned_cols=84  Identities=36%  Similarity=0.522  Sum_probs=75.1

Q ss_pred             CCHHHHHHHHhccccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEeeCcE
Q 021078           43 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT  122 (317)
Q Consensus        43 LT~kERk~LRklAhkLKPvV~IGK~GVTdgVIeeI~~aLk~HELVKVKv~~~~~ed~keiAeeLe~~SGgeLVqV~IG~t  122 (317)
                      ||++||++||++||+|+|+|+|||+|||++|+++|+.+|++||||||+|.+++..+++++|+.|++.|||++|++ +|++
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            799999999999999999999999999999999999999999999999999999999999999999999999995 9999


Q ss_pred             EEEEe
Q 021078          123 IIMYR  127 (317)
Q Consensus       123 IILYR  127 (317)
                      +||||
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=99.95  E-value=4.2e-27  Score=192.58  Aligned_cols=91  Identities=26%  Similarity=0.421  Sum_probs=86.4

Q ss_pred             CCCHHHHHHHHhccccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEeeCc
Q 021078           42 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  121 (317)
Q Consensus        42 ~LT~kERk~LRklAhkLKPvV~IGK~GVTdgVIeeI~~aLk~HELVKVKv~~~~~ed~keiAeeLe~~SGgeLVqV~IG~  121 (317)
                      +||++|+++||+.||+++|+|+||++|||++||.+|+.+|++||||||++.+++.++++++|+.|++.+||.+||+ ||+
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            5899999999999999999999999999999999999999999999999999999999999999999999999996 999


Q ss_pred             EEEEEeCCCCCCC
Q 021078          122 TIIMYRGKNYAQP  134 (317)
Q Consensus       122 tIILYRgkNY~~P  134 (317)
                      ++||||. +..++
T Consensus        80 ~~vlyr~-~~e~~   91 (97)
T COG1534          80 TLVLYRE-SKEKR   91 (97)
T ss_pred             EEEEEec-Ccccc
Confidence            9999994 44443

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

Probab=99.94  E-value=1.5e-27  Score=241.77  Aligned_cols=184  Identities=42%  Similarity=0.616  Sum_probs=173.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhcccCCC-CCCCCCCCCCCCCHHHHHHHHhccccCCCeeeeCCCCCcHHHHHHHHHHHH
Q 021078            4 EEKILYKLRKARKKEERIVEGLKKIEPK-ESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWK   82 (317)
Q Consensus         4 e~ri~~kl~~a~~K~e~~~e~L~K~e~~-~pse~~~D~E~LT~kERk~LRklAhkLKPvV~IGK~GVTdgVIeeI~~aLk   82 (317)
                      .+++.+++..|++|++++...|++++.+ .|++..++++.+|.+++.+++++|.++++++.+|++|+++||+.++|.||+
T Consensus       343 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk  422 (564)
T KOG1990|consen  343 TEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWK  422 (564)
T ss_pred             HHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCCcccccceeecchhhhh
Confidence            4789999999999999999999999987 688999999999999999999999999999999999999999999999999


Q ss_pred             hCCeeeEEecCCCH-HHHHHHHHHHHHHhCCeEEEE---eeCcEEEEEeCCCCCCCCCCcCCcccccchHHHHhHHHHHh
Q 021078           83 KHQTLKVIVKTFSA-EEVKEIAAELARLTGGIVLEI---HEENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRD  158 (317)
Q Consensus        83 ~HELVKVKv~~~~~-ed~keiAeeLe~~SGgeLVqV---~IG~tIILYRgkNY~~P~~~i~~P~~lLtKrkAL~rS~~~q  158 (317)
                      +||++||+|+.... ..++..|..++..+|+++|++   ..|+.|+.|||+||.+|.+  |+|.++|+||+|+.+|+++|
T Consensus       423 ~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~--l~P~~~l~~~k~~~~~~~~~  500 (564)
T KOG1990|consen  423 SRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTS--LRPRNLLSRRKALERSLEEQ  500 (564)
T ss_pred             hcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCcc--cCchhhhcccCCccccHHHH
Confidence            99999999988665 999999999999999999997   3566699999999999977  99999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhhccCCcc
Q 021078          159 GLRAVKKYIPKLEQELELLRAQAETRSENRS  189 (317)
Q Consensus       159 r~~sl~~~i~~le~~i~~l~~~~~~~~~~~~  189 (317)
                      +.+|+++||+.++++++++++++..+..++.
T Consensus       501 ~~~a~~~~i~~~~~~~e~~~~~~~~~~~~~~  531 (564)
T KOG1990|consen  501 RKEALKSHISDLEQEIEQLQASVEAMPAINK  531 (564)
T ss_pred             HHHHHhhhcchhhhhHHHhhcchhccccccc
Confidence            9999999999999999999999988766665

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

Probab=97.91  E-value=1.1e-05  Score=83.23  Aligned_cols=117  Identities=26%  Similarity=0.372  Sum_probs=100.7

Q ss_pred             HHHHHHHhhcccCCCCCCCCCCCCCCCCHHHHHHHHhccccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCC-C
Q 021078           17 KEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTF-S   95 (317)
Q Consensus        17 K~e~~~e~L~K~e~~~pse~~~D~E~LT~kERk~LRklAhkLKPvV~IGK~GVTdgVIeeI~~aLk~HELVKVKv~~~-~   95 (317)
                      ....+.+.+..+..|...-|...+..||..+..++|.+|-...|++.+|.++.-.++...|..+|..|+..|+.+... .
T Consensus       149 ~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~  228 (564)
T KOG1990|consen  149 DADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVL  228 (564)
T ss_pred             hhhhchhhhhcccChhccCCCCChhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcch
Confidence            345566777777777777777788899999999999999999999999999999999999999999999999888653 4


Q ss_pred             HHHHHHHHHHH--HHHhCCeEEEEeeCcEEEEEeCCCCCCC
Q 021078           96 AEEVKEIAAEL--ARLTGGIVLEIHEENTIIMYRGKNYAQP  134 (317)
Q Consensus        96 ~ed~keiAeeL--e~~SGgeLVqV~IG~tIILYRgkNY~~P  134 (317)
                      ......++..+  -..+|+.||. +-|..+|+||++++-.|
T Consensus       229 ~~~~~~~a~~l~~~~~tg~~lv~-hN~~~dv~y~~~~Fl~~  268 (564)
T KOG1990|consen  229 ETRKERMADELQELLLTGKVLVL-HNKLLDVMYRYKNFLSP  268 (564)
T ss_pred             hhhccchHHHHHHHHhcCCeEEe-eccceeeeeehhhcccc
Confidence            44556777777  8899999998 79999999999999775

---

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	317
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	2e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-06
1rq8_A	104	Conserved hypothetical protein; structural genomic	9e-10

>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 = 55.7 bits (135), Expect = 2e-10
 Identities = 20/106 (18%), Positives = 41/106 (38%), Gaps = 10/106 (9%)

Query: 43  LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEI 102
           L+ ++  +   +       V +G  G+ +GV+  +      H+ +KV V     E  + I
Sbjct: 3   LSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLI 62

Query: 103 AAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRK 148
              + R T    ++    + +++YR              +I L RK
Sbjct: 63  INAIVRETKAAQVQTI-GHILVLYRPSE---------EAKIQLPRK 98

>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 = 6e-10
 Identities = 58/307 (18%), Positives = 94/307 (30%), Gaps = 79/307 (25%)

Query: 77  MHLHWKK--HQTLKVIVKTF-------------SAEEVKEIAAELARLTGG----IVLEI 117
               +K          V  F             S EE+  I      ++G       L  
Sbjct: 14  HQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLS 73

Query: 118 HEENTIIMYRG----KNYAQPPTEIMSPRITLSRKKALDKSKY---RDGL----RAVKKY 166
            +E  +  +       NY      +MSP  T  R+ ++    Y   RD L    +   KY
Sbjct: 74  KQEEMVQKFVEEVLRINYKF----LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKY 129

Query: 167 -IPKLEQELELLRAQAETRSENR------------SDAAEDVQNTEL-DKPDFGSI--PS 210
            + +L+  L+L +A  E R                  A +   + ++  K DF  I   +
Sbjct: 130 NVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFK-IFWLN 188

Query: 211 MMECSENDPTTESL------MASDSEDLSDIFETDSETETEEKAELRPLYLDQFDKFP-- 262
           +  C+  +   E L      +  +    SD            +AELR L   +   +   
Sbjct: 189 LKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK--PYENC 246

Query: 263 ------VQNDEEHEDFEEH---L---RQISI-DSRNAK-----SLGKDEDSSHFDEVDKM 304
                 VQN +    F      L   R   + D  +A      SL     +   DEV  +
Sbjct: 247 LLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL 306

Query: 305 FLRAASL 311
            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 = 46.4 bits (109), Expect = 8e-06
 Identities = 53/362 (14%), Positives = 97/362 (26%), Gaps = 120/362 (33%)

Query: 39  DPEILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEE 98
           + +       F        CK  + +  R  ++ V   +      H +L     T + +E
Sbjct: 255 NAKAW---NAFNL-----SCK--ILLTTR--FKQVTDFLSAATTTHISLDHHSMTLTPDE 302

Query: 99  VKEIAA--------ELAR--------LTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPR 142
           VK +          +L R            I   I +          N+     + ++  
Sbjct: 303 VKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLA----TWDNWKHVNCDKLTTI 358

Query: 143 ITLSRKKALDKSKYRDGLRA-------VKKYIPKLEQELELLRAQAETRSE--------N 187
           I  S    L+ ++YR                IP     L L+                  
Sbjct: 359 IESSLN-VLEPAEYRKMFDRLSVFPPSAH--IP--TILLSLIWFDVIKSDVMVVVNKLHK 413

Query: 188 RSDAAEDVQNTELDKPDFGSIPSM---MECS-ENDPTTESLM--------ASDSEDLSDI 235
            S   +  + + +      SIPS+   ++   EN+      +          DS+DL   
Sbjct: 414 YSLVEKQPKESTI------SIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPP 467

Query: 236 FETD----------SETE-TEEKAELRPLYLD---------------------------- 256
           +                E  E     R ++LD                            
Sbjct: 468 YLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQL 527

Query: 257 -QFDKFPVQNDEEHE----DFEEHLRQISIDSRNAKSLG------KDEDSSHFDEVDKMF 305
             +  +   ND ++E       + L +I  +   +K           ED + F+E  K  
Sbjct: 528 KFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQV 587

Query: 306 LR 307
            R
Sbjct: 588 QR 589

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

 Score = 54.2 bits (131), Expect = 9e-10
 Identities = 20/109 (18%), Positives = 45/109 (41%), Gaps = 9/109 (8%)

Query: 42  ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKE 101
           +LT ++  Y   +         +G+ GI + +I  +    +  + +KV V   + ++ KE
Sbjct: 1   MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKE 60

Query: 102 IAAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPRITLSRKKA 150
           +A  L+  T   +++    + I++YR     +         I L  +  
Sbjct: 61  LAETLSEATRSELVQ-VIGSMIVIYR-----ESKEN---KEIELPLEHH 100

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	317
1rq8_A	104	Conserved hypothetical protein; structural genomic	99.97
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	99.97

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

Probab=99.97  E-value=1.8e-30  Score=212.92  Aligned_cols=88  Identities=20%  Similarity=0.365  Sum_probs=86.3

Q ss_pred             CCCHHHHHHHHhccccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEeeCc
Q 021078           42 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  121 (317)
Q Consensus        42 ~LT~kERk~LRklAhkLKPvV~IGK~GVTdgVIeeI~~aLk~HELVKVKv~~~~~ed~keiAeeLe~~SGgeLVqV~IG~  121 (317)
                      |||++||++||++||+|+|+|+|||+|||++|+++|+.+|++||||||+|.++++++++++|++|++.|||++||+ ||+
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            6999999999999999999999999999999999999999999999999999999999999999999999999995 999


Q ss_pred             EEEEEeCCC
Q 021078          122 TIIMYRGKN  130 (317)
Q Consensus       122 tIILYRgkN  130 (317)
                      ++||||++.
T Consensus        80 ~~VLYR~~~   88 (104)
T 1rq8_A           80 MIVIYRESK   88 (104)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEeCCC
Confidence            999999976

>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=99.97  E-value=3.1e-30  Score=209.13  Aligned_cols=89  Identities=18%  Similarity=0.304  Sum_probs=86.3

Q ss_pred             CCCHHHHHHHHhccccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEeeCc
Q 021078           42 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  121 (317)
Q Consensus        42 ~LT~kERk~LRklAhkLKPvV~IGK~GVTdgVIeeI~~aLk~HELVKVKv~~~~~ed~keiAeeLe~~SGgeLVqV~IG~  121 (317)
                      .||++||++||++||+|+|+|+||++|||++|+.+|+.||++||||||+|.++++++++++|++|++.|||++||+ ||+
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            6999999999999999999999999999999999999999999999999999999999999999999999999995 999


Q ss_pred             EEEEEeCCCC
Q 021078          122 TIIMYRGKNY  131 (317)
Q Consensus       122 tIILYRgkNY  131 (317)
                      ++||||++..
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	317
d1rq8a_	96	d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphy	8e-19
d1jo0a_	97	d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i	2e-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 = 8e-19
 Identities = 18/90 (20%), Positives = 41/90 (45%), Gaps = 1/90 (1%)

Query: 42  ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKE 101
           +LT ++  Y   +         +G+ GI + +I  +    +  + +KV V   + ++ KE
Sbjct: 1   MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKE 60

Query: 102 IAAELARLTGGIVLEIHEENTIIMYRGKNY 131
           +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 = 76.7 bits (189), Expect = 2e-18
 Identities = 19/100 (19%), Positives = 40/100 (40%), Gaps = 5/100 (5%)

Query: 43  LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEI 102
           L+ ++  +   +       V +G  G+ +GV+  +      H+ +KV V     E  + I
Sbjct: 3   LSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLI 62

Query: 103 AAELARLTGGIVLEIHEENTIIMYRGKNYAQPPTEIMSPR 142
              + 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	317
d1jo0a_	97	YhbY homologue HI1333 {Haemophilus influenzae [Tax	99.97
d1rq8a_	96	Hypothetical protein SAV1595 {Staphylococcus aureu	99.96

>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=99.97  E-value=2.7e-30  Score=206.23  Aligned_cols=88  Identities=18%  Similarity=0.317  Sum_probs=85.7

Q ss_pred             CCCHHHHHHHHhccccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEeeCc
Q 021078           42 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  121 (317)
Q Consensus        42 ~LT~kERk~LRklAhkLKPvV~IGK~GVTdgVIeeI~~aLk~HELVKVKv~~~~~ed~keiAeeLe~~SGgeLVqV~IG~  121 (317)
                      +||++||++||++||+|+|+|+||++|||++|+.+|+.+|++||||||+|.+++++++++++++|++.|||.|||+ ||+
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            6999999999999999999999999999999999999999999999999999999999999999999999999995 999


Q ss_pred             EEEEEeCCC
Q 021078          122 TIIMYRGKN  130 (317)
Q Consensus       122 tIILYRgkN  130 (317)
                      ++||||++.
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=99.96  E-value=4.2e-30  Score=204.79  Aligned_cols=90  Identities=20%  Similarity=0.346  Sum_probs=87.1

Q ss_pred             CCCHHHHHHHHhccccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCeEEEEeeCc
Q 021078           42 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN  121 (317)
Q Consensus        42 ~LT~kERk~LRklAhkLKPvV~IGK~GVTdgVIeeI~~aLk~HELVKVKv~~~~~ed~keiAeeLe~~SGgeLVqV~IG~  121 (317)
                      |||++||++||++||+|+|+|+||++|||++|+.+|+.+|+.||||||+|.+++..+++++|++|++.|||++||+ ||+
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            6999999999999999999999999999999999999999999999999999999999999999999999999995 999


Q ss_pred             EEEEEeCCCCC
Q 021078          122 TIIMYRGKNYA  132 (317)
Q Consensus       122 tIILYRgkNY~  132 (317)
                      ++||||++++.
T Consensus        80 ~~vlyR~~~~~   90 (96)
T d1rq8a_          80 MIVIYRESKEN   90 (96)
T ss_dssp             EEEEEECCCSC
T ss_pred             EEEEEeCCCCC
Confidence            99999997653