Citrus Sinensis ID: 017893

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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----
Protein Sequence
MIFNRFSRQKPSLRSQPFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPNPTLNPNKNFKKKSKPQYRPPSSLDAPKKKYTDLPFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRSWFRISFLASL
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccHHHHHHHHHHccccccccHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHccEEEEEEcccccccHHHHHHHHHHHcccEEEEEEccEEEEEEccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccccccccHHHHHHHHHHccEEEEEcccccccHHHHHHHHHHccccEEEcccc
Secondary Structure Prediction (SSPRO)
cHHHHHHcccccccccccEccccccccccccHHHcccccHHHcccccccccccccccccccccccccHccccccccccccccccccccccccccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccHcccccHHHHHcccccHHHHHHHHHHHHccccccEEEcccccHHHHHHHHHHHHHHHccEEEEEEccccHHHHHHHHHHHHHHcccEEEEEcccEEEEEEcccccccccccccEEEcccccccccHHHccccccccHHHHHHHHHHcccccHHHHHcccccEEEHHHHHHHHHccccEEEEEcccccHHHHHHHHHHHHHcccEEEEEcc
Coil and Loop (DISEMBL)
mifnrfsrqkpslrsqpftlLTCCLsataanttnnssklydhysfkpppslspkpenpnptlnpnknfkkkskpqyrppssldapkkkytdlpfdfrysytetnqnvrpiglrepkyspfgpgrlerewtgvcapaadpkvksaeegaedpnleeKRILVREriqgepltnAERKALVEKCHRNRTKRQinlgrdglthNMLNDIHNHWKHAEAVRIKclgvptvdmknvcfqledktfgkiifrhGGTLVLyrgrnynpkkrpviplmlwrphepvypkLIKTTIEGLSIEETKEMRKRGLAVPVLTKlakngyygslvpMVRDAFLVSELVRIdcqglersdykkigcklrsWFRISFLASL
Flexible Loop (DISEMBL)
mifnrfsrqkpslrsqpfTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPNPTlnpnknfkkkskpqyrppssldapkkkytdLPFDFRYSYTetnqnvrpiglrepkYSPFGPGRLEREWTGVCAPaadpkvksaeegaedpnleekrilvreriqgepltnaerkalvekchrnrtkrqinlgrdglTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDktfgkiifrhggtlvlyrgrnynpkkrpviplmlwrphepvypkLIKTTIEGlsieetkemrkrglavpvLTKLAKNGYYGSLVPMVRDAFLVSELVRIdcqglersdykkigcklrswfrisflasl
Low Complexity Region (SEG)
MIFNRFSRQKPSLRSQPFtlltcclsataanttnnssKLYDHYSFkpppslspkpenpnpTLnpnknfkkkskpQYRPPSSLDAPKKKYTDLPFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRSWFRISFLASL
Disordered region (IsUnstruct)
*****************FTLLTCCLSATAA***********************************************************TDLPFDFRYSYTETNQNVRPIGL************LEREWTGVC********************************************VEKCHR*RTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRSWFRISFL***
Disordered Region (DISOPRED)
*******************************************************************************************LPFDF********************YSPFGPGRLEREWTGVC******************************************ALV**********QINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNY******************************************GLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRSWFRISFLASL
Disordered Region (DISEMBL)
*************RSQPFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPNPTLNPNKNF***************APKKKYTDLPFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRSWFRISFLASL
Disordered Region (DISPRO)
MIFNRFSR********PFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLS**************************PSSLDAPKKKYTDLPFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVC******************************IQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRSWFRISFLASL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MIFNRFSRQKPSLRSQPFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPNPTLNPNKNFKKKSKPQYRPPSSLDAPKKKYTDLPFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRSWFRISFLASL
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	364	2.2.26 [Sep-21-2011]
Q8VYD9	405	CRS2-associated factor 1,	yes	no	0.945	0.849	0.720	1e-136
Q6Z4U2	428	CRS2-associated factor 1,	yes	no	0.859	0.731	0.665	1e-112
Q9FFU1	358	CRS2-associated factor 2,	no	no	0.692	0.703	0.562	1e-83
Q0J7J7	366	CRS2-associated factor 2,	no	no	0.708	0.704	0.546	4e-77
Q9SL79	701	CRS2-associated factor 1,	no	no	0.708	0.368	0.491	8e-70
Q657G7	607	CRS2-associated factor 2,	no	no	0.730	0.438	0.484	1e-66
Q84N48	611	CRS2-associated factor 2,	N/A	no	0.730	0.435	0.471	2e-66
Q5VMQ5	701	CRS2-associated factor 1,	no	no	0.725	0.376	0.458	2e-66
Q9LDA9	564	CRS2-associated factor 2,	no	no	0.706	0.455	0.489	8e-66
Q84N49	674	CRS2-associated factor 1,	N/A	no	0.708	0.382	0.475	1e-64

>sp|Q8VYD9|CAF1M_ARATH CRS2-associated factor 1, mitochondrial OS=Arabidopsis thaliana GN=At4g31010 PE=2 SV=1

 Score =  483 bits (1244), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 255/354 (72%), Positives = 286/354 (80%), Gaps = 10/354 (2%)

Query: 1   MIFNRFSRQKPSLRSQPFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPNP 60
           M   R SR  PS     FTLLT  L     + T +SS+L D Y+F+ PP LS      NP
Sbjct: 1   MFLIRLSRHNPS----SFTLLTRRLH----DQTISSSRLRDLYNFQSPPPLSSSASE-NP 51

Query: 61  TLNPNKNFKKKSKPQYRPPSSLDAPKKKYTDLPFDFRYSYTETNQNVRPIGLREPKYSPF 120
             N   N KKK KPQYRPPSSL+  K  ++DLPFDFR+SYTE+  NVRPIGLREPKYSPF
Sbjct: 52  DFNQKNNNKKKPKPQYRPPSSLEGVKTVHSDLPFDFRFSYTESCSNVRPIGLREPKYSPF 111

Query: 121 GPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEK 180
           GP RL+REWTGVCAPA +PKV+S + G EDP LEEKR  VRE+IQG  LT AERK LVE 
Sbjct: 112 GPDRLDREWTGVCAPAVNPKVESVD-GVEDPKLEEKRRKVREKIQGASLTEAERKFLVEL 170

Query: 181 CHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFG 240
           C RN+TKRQ+NLGRDGLTHNMLND++NHWKHAEAVR+KCLGVPT+DMKNV F LEDKTFG
Sbjct: 171 CQRNKTKRQVNLGRDGLTHNMLNDVYNHWKHAEAVRVKCLGVPTLDMKNVIFHLEDKTFG 230

Query: 241 KIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKR 300
           +++ +H GTLVLYRGRNY+PKKRP IPLMLW+PHEPVYP+LIKTTI+GLSI+ETK MRK+
Sbjct: 231 QVVSKHSGTLVLYRGRNYDPKKRPKIPLMLWKPHEPVYPRLIKTTIDGLSIDETKAMRKK 290

Query: 301 GLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRS 354
           GLAVP LTKLAKNGYYGSLVPMVRDAFLVSELVRIDC GLER DYKKIG KLR 
Sbjct: 291 GLAVPALTKLAKNGYYGSLVPMVRDAFLVSELVRIDCLGLERKDYKKIGAKLRD 344

May be involved for the splicing of group IIB introns in mitochondrions.
Arabidopsis thaliana (taxid: 3702)

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

 Score =  404 bits (1039), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 215/323 (66%), Positives = 249/323 (77%), Gaps = 10/323 (3%)

Query: 37  SKLYDHYSFKPPPSLSPKPENPNPTLNPNKNFKKKSKPQYRPPSSLDAPKK--KYTDLPF 94
           S L D Y F PP SL+P     + + +     ++  KP YRPPSSLD   +    +DLPF
Sbjct: 23  SGLLDRYGFVPPASLTPH----SASDDGGAKKRRPKKPPYRPPSSLDRGGRPAARSDLPF 78

Query: 95  DFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLE 154
           DFR+SYTE++   +PIGLREPKYSPFGPGRL+R WTG+CAPA D  ++ A      P  E
Sbjct: 79  DFRFSYTESSPGDKPIGLREPKYSPFGPGRLDRPWTGLCAPAVDTTLRDAHADDPAPAAE 138

Query: 155 EKRILVRER----IQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWK 210
            +    R R    + GEPLT AER  LV KC ++RTK+QINLGRDGLTHNMLNDIHNHWK
Sbjct: 139 RELEEARRRERERVLGEPLTPAERAFLVSKCQKSRTKKQINLGRDGLTHNMLNDIHNHWK 198

Query: 211 HAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLML 270
           + EAVR+KCLGVPTVDM+NVC QLEDKT G II RHGG L+LYRGR+YNPKKRPVIPLML
Sbjct: 199 NDEAVRVKCLGVPTVDMQNVCHQLEDKTGGLIIHRHGGQLILYRGRHYNPKKRPVIPLML 258

Query: 271 WRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVS 330
           W+P EPVYP+LIKTTIEGL++EETKEMRK+GL VPVLTKLAKNGYY SLVPMVRDAFL  
Sbjct: 259 WKPAEPVYPRLIKTTIEGLTVEETKEMRKKGLYVPVLTKLAKNGYYASLVPMVRDAFLTD 318

Query: 331 ELVRIDCQGLERSDYKKIGCKLR 353
           ELVRID +GL +SDY+KIG KLR
Sbjct: 319 ELVRIDSKGLPKSDYRKIGVKLR 341

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

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9FFU1|CAF2M_ARATH CRS2-associated factor 2, mitochondrial OS=Arabidopsis thaliana GN=At5g54890 PE=2 SV=1

 Score =  310 bits (793), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 149/265 (56%), Positives = 191/265 (72%), Gaps = 13/265 (4%)

Query: 90  TDLPFDFRYSYTETNQNVRPIGLREPK-YSPFGPGRLEREWTGVCAPAADPKVKSAEEGA 148
           +DLPFDFRYSY+ETN  + PIG REPK +SPFGPGRL+R+WTG  A A+ P++  ++   
Sbjct: 75  SDLPFDFRYSYSETNPEIEPIGFREPKRFSPFGPGRLDRKWTGTTALAS-PEIDQSQWVE 133

Query: 149 EDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNH 208
           E           R R+ GE LT  E   L+E+   +   RQINLG+ G+THNM++DIHNH
Sbjct: 134 E-----------RARVLGETLTEDEVTELIERYRHSDCTRQINLGKGGVTHNMIDDIHNH 182

Query: 209 WKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPL 268
           WK AEAVRIKCLGVPT+DM N+CF LE+K+ GKI++R+   LVLYRGRNY+PK RP+IPL
Sbjct: 183 WKKAEAVRIKCLGVPTLDMDNICFHLEEKSGGKIVYRNINILVLYRGRNYDPKSRPIIPL 242

Query: 269 MLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFL 328
           MLW+PH P+YP+L+K   +GL  EETKEMR RGL  P L KL +NG Y ++V  VR+ F 
Sbjct: 243 MLWKPHPPIYPRLVKNVADGLEFEETKEMRNRGLHSPALMKLTRNGVYVNVVGRVREEFE 302

Query: 329 VSELVRIDCQGLERSDYKKIGCKLR 353
             E+VR+DC  +  SD K+IG KL+
Sbjct: 303 TEEIVRLDCTHVGMSDCKRIGVKLK 327

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  288 bits (737), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 148/271 (54%), Positives = 188/271 (69%), Gaps = 13/271 (4%)

Query: 85  PKKKYTDLPFDFRYSYTETNQNVRPIGLREP-KYSPFGPGRLEREWTGVCAPAADPKVKS 143
           P+   +DLPFDFRYSY+ET+   RPIG REP ++SPFGPGRL+R W GV A AA  +   
Sbjct: 72  PEPASSDLPFDFRYSYSETDPAWRPIGFREPTRFSPFGPGRLDRPWDGVAAAAARGEGAG 131

Query: 144 AEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLN 203
           A   +            RE + GEPL   E   LVE+   +   RQINLG+ G+THNM++
Sbjct: 132 AAATS------------REEVLGEPLAEEEVAQLVERYRHSDCSRQINLGKGGVTHNMID 179

Query: 204 DIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKR 263
           DIHNHWK AEAVRIKCLGVPT+DM N+CF LEDKT GK+I+R+   L+LYRGRNY+PK+R
Sbjct: 180 DIHNHWKRAEAVRIKCLGVPTLDMDNICFHLEDKTGGKVIYRNINILILYRGRNYDPKQR 239

Query: 264 PVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMV 323
           P IPLMLW+P  P+YP+L++   +GL+ E+TKE+R  GL    L KL +NG Y ++V  V
Sbjct: 240 PQIPLMLWKPLAPIYPRLVQNVADGLTFEKTKELRNTGLNSSPLMKLTRNGVYVNVVDRV 299

Query: 324 RDAFLVSELVRIDCQGLERSDYKKIGCKLRS 354
           R+AF   E+VR+DC  +  SD KKIG KLR 
Sbjct: 300 REAFKTVEVVRLDCSHVGSSDCKKIGVKLRD 330

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

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9SL79|CAF1P_ARATH CRS2-associated factor 1, chloroplastic OS=Arabidopsis thaliana GN=At2g20020 PE=1 SV=2

 Score =  264 bits (675), Expect = 8e-70,   Method: Compositional matrix adjust.
 Identities = 137/279 (49%), Positives = 179/279 (64%), Gaps = 21/279 (7%)

Query: 93  PFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCA-----------------P 135
           PF+F+YSYTET + V+P+ LREP Y+PFGP  + R WTG                    P
Sbjct: 150 PFEFKYSYTETPK-VKPLKLREPAYAPFGPTTMGRPWTGRAPLPQSQKTPREFDSFRLPP 208

Query: 136 AADPKVKSAEE-GAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGR 194
                +K  ++ G   P +  + +  +E I GEPLT  E + LV  C +  T RQ+N+GR
Sbjct: 209 VGKKGLKPVQKPGPFRPGVGPRYVYSKEEILGEPLTKEEVRELVTSCLK--TTRQLNMGR 266

Query: 195 DGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYR 254
           DGLTHNMLN+IH+ WK     +IKC GV TVDM NVC QLE+K  GK+I+R GG L L+R
Sbjct: 267 DGLTHNMLNNIHDLWKRRRVCKIKCKGVCTVDMDNVCEQLEEKIGGKVIYRRGGVLFLFR 326

Query: 255 GRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNG 314
           GRNYN + RP  PLMLW+P  PVYP+LI+   EGL+ +E   MR++G  +  + KL KNG
Sbjct: 327 GRNYNHRTRPRFPLMLWKPVAPVYPRLIQQVPEGLTRQEATNMRRKGRELMPICKLGKNG 386

Query: 315 YYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLR 353
            Y  LV  V++AF V ELVRIDCQG++ SD++KIG KL+
Sbjct: 387 VYCDLVKNVKEAFEVCELVRIDCQGMKGSDFRKIGAKLK 425

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.

Arabidopsis thaliana (taxid: 3702)

>sp|Q657G7|CAF2P_ORYSJ CRS2-associated factor 2, chloroplastic OS=Oryza sativa subsp. japonica GN=Os01g0323300 PE=2 SV=1

 Score =  253 bits (647), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 145/299 (48%), Positives = 182/299 (60%), Gaps = 33/299 (11%)

Query: 93  PFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCAPAADPKVKSAEEGA---- 148
           PFDFR+SY+E  +   P+ +REP + PF P  + R WTG  AP    + K+   G     
Sbjct: 127 PFDFRFSYSECPR-APPVAIREPAFLPFAPPTMPRPWTGK-APLLTKEEKARRRGVRLHT 184

Query: 149 ----EDP----------------NLEEKRIL-----VRERIQGEPLTNAERKALVEKCHR 183
               E P                 L+  R+       RE + GEPLT AE + LV K H 
Sbjct: 185 PLGEEAPRTVSAHGIMMEVRGRRKLDLARVSPGDGRSREEVLGEPLTAAEVRDLV-KPHI 243

Query: 184 NRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKII 243
           +   RQ+N+GRDGLTHNML  IH HW+  E  +++C GVPTVDMKN+C+ LE+K+ GK+I
Sbjct: 244 SHN-RQLNIGRDGLTHNMLEMIHCHWRRQEICKVRCRGVPTVDMKNLCYHLEEKSGGKVI 302

Query: 244 FRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLA 303
            R GG + LYRGRNYNP+ RP  PLMLW+P  PVYPKLI+   EGL+ EE  EMR+RG  
Sbjct: 303 HRVGGVVFLYRGRNYNPRTRPRYPLMLWKPATPVYPKLIQEAPEGLTKEEADEMRRRGKD 362

Query: 304 VPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRSWFRISFLA 362
           +  + KLAKNG Y  LV  VRDAF  S+LV+IDC+GL  SDYKKIG KLR       L+
Sbjct: 363 LLPICKLAKNGIYIYLVRDVRDAFEGSDLVKIDCEGLNPSDYKKIGAKLRDLVPCVLLS 421

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 =  253 bits (646), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 141/299 (47%), Positives = 184/299 (61%), Gaps = 33/299 (11%)

Query: 93  PFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCAPAADPKVKSAEEGA---- 148
           PFDF++SY+E  +   P+ +REP + PF P  + R WTG  AP    + K+   G     
Sbjct: 131 PFDFQFSYSEAPR-APPLAIREPAFLPFAPPTMPRPWTGK-APLLTKEEKARRRGVRLHT 188

Query: 149 ----EDPN----------LEEKRIL-----------VRERIQGEPLTNAERKALVEKCHR 183
               E P           + E+R +            RE + GEPLT +E +ALV K H 
Sbjct: 189 PLGQETPQTVSAHGIMMEVRERRKMDLARVSPGDGRSREEVLGEPLTPSEVRALV-KPHI 247

Query: 184 NRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKII 243
           +   RQ+N+GRDGLTHNML  IH HW+  E  +++C GVPTVDMKN+C+ LE+K+ GK+I
Sbjct: 248 SHN-RQLNIGRDGLTHNMLEMIHCHWRRQEICKVRCRGVPTVDMKNLCYHLEEKSGGKVI 306

Query: 244 FRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLA 303
            R GG + LYRGR+Y+PK RP  PLMLW+P  PVYPKLIK   +G + EE  EMR++G  
Sbjct: 307 HRVGGVVFLYRGRHYDPKTRPRYPLMLWKPATPVYPKLIKEAPDGFTKEEADEMRRKGRD 366

Query: 304 VPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRSWFRISFLA 362
           +  + KLAKNG Y +LV  VRDAF  S+LV+IDC+GL  SDYKKIG KLR       L+
Sbjct: 367 LLPICKLAKNGIYITLVKDVRDAFEGSDLVKIDCEGLNPSDYKKIGAKLRDLVPCVLLS 425

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

 Score =  253 bits (646), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 134/292 (45%), Positives = 176/292 (60%), Gaps = 28/292 (9%)

Query: 93  PFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTG-----------------VCAP 135
           PF+F+YSYTET +  RP+ LRE  + PFGP    R WTG                 +  P
Sbjct: 91  PFEFQYSYTETPR-ARPVALREAPFLPFGPEVTPRPWTGRKPLPKSRKELPEFDSFMLPP 149

Query: 136 AADPKVKSAEE-----GAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQI 190
                VK  +         +P  +      RE + GEPLT  E   LV+     +TKRQ+
Sbjct: 150 PGKKGVKPVQSPGPFLAGTEPRYQAAS---REEVLGEPLTKEEVDELVKATL--KTKRQL 204

Query: 191 NLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTL 250
           N+GRDGLTHNML +IH+HWK     +IKC GV TVDM NVC QLE+K  GK+I   GG +
Sbjct: 205 NIGRDGLTHNMLENIHSHWKRKRVCKIKCKGVCTVDMDNVCQQLEEKVGGKVIHHQGGVI 264

Query: 251 VLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKL 310
            L+RGRNYN + RP+ PLMLW+P  PVYP+L+K   +GL+ +E ++MRKRG  +P + KL
Sbjct: 265 FLFRGRNYNYRTRPIYPLMLWKPAAPVYPRLVKKIPDGLTPDEAEDMRKRGRQLPPICKL 324

Query: 311 AKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRSWFRISFLA 362
            KNG Y +LV  VR+AF   +LVR+DC GL +SD +KIG KL+     + L+
Sbjct: 325 GKNGVYLNLVKQVREAFEACDLVRVDCSGLNKSDCRKIGAKLKDLVPCTLLS 376

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|Q9LDA9|CAF2P_ARATH CRS2-associated factor 2, chloroplastic OS=Arabidopsis thaliana GN=At1g23400 PE=2 SV=1

 Score =  251 bits (640), Expect = 8e-66,   Method: Compositional matrix adjust.
 Identities = 137/280 (48%), Positives = 174/280 (62%), Gaps = 23/280 (8%)

Query: 93  PFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCA-----------------P 135
           PF+F++SY+ET + V+P+G+REP + PF P  + R WTG                    P
Sbjct: 110 PFEFQFSYSETPK-VKPVGIREPAFMPFAPPTMPRPWTGKAPLKKSKKKIPLFDSFNPPP 168

Query: 136 AADPKVKSAEEGAEDP-NLEEKRILVRERIQGEPLTNAERKALVE-KCHRNRTKRQINLG 193
           A    VK  E     P     K  + RE + GEPL   E+  L++   H NR   Q+NLG
Sbjct: 169 AGKSGVKYVEMPGPLPFGRYPKEGMNREEVLGEPLKRWEKGMLIKPHMHDNR---QVNLG 225

Query: 194 RDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLY 253
           RDG THNML  IH+HWK     +++C GVPTVDM NVC  LE+KT G+II R GG + L+
Sbjct: 226 RDGFTHNMLELIHSHWKRRRVCKVRCKGVPTVDMNNVCRVLEEKTGGEIIHRVGGVVYLF 285

Query: 254 RGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKN 313
           RGRNYN + RP  PLMLW+P  PVYPKLI+   EGL+ EE  E R +G ++  + KL+KN
Sbjct: 286 RGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEVPEGLTKEEAHEFRVKGKSLRPICKLSKN 345

Query: 314 GYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLR 353
           G Y SLV  VRDAF +S LV++DC GLE SDYKKIG KL+
Sbjct: 346 GVYVSLVKDVRDAFELSSLVKVDCPGLEPSDYKKIGAKLK 385

Essential protein 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.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  247 bits (630), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 133/280 (47%), Positives = 172/280 (61%), Gaps = 22/280 (7%)

Query: 93  PFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTG----------------VCAPA 136
           PF+F+YSYTE  +  RP+ LRE  + PFGP    R WTG                   PA
Sbjct: 91  PFEFQYSYTEAPR-ARPVALREAPFMPFGPEATPRPWTGRKPLPKSRKELPEFDSFVLPA 149

Query: 137 ADPK-VKSAEE-GAEDPNLEEK-RILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLG 193
              K VK  +  G     +E + + + RE I GEPLT  E   LV+   +  +KRQ+N+G
Sbjct: 150 PGKKGVKPVQSPGPFLAGMEPRYQSVSREDILGEPLTKEEVSELVKGSLK--SKRQLNMG 207

Query: 194 RDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLY 253
           RDGLTHNML +IH+HWK     +IKC GV T+DM N+C QLE+K  GK+I R GG + L+
Sbjct: 208 RDGLTHNMLENIHSHWKRKRVCKIKCKGVCTIDMDNICHQLEEKVGGKVIHRQGGVIFLF 267

Query: 254 RGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKN 313
           RGRNYN + RP  PLMLW+P  PVYP+L+     GL+ +E  EMR RG  +P + KL KN
Sbjct: 268 RGRNYNYRTRPCFPLMLWKPVAPVYPRLVTKVPGGLTPDEATEMRTRGHQLPPICKLGKN 327

Query: 314 GYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLR 353
           G Y +LV  VR+AF   +LVR+DC GL +SD +KIG KL+
Sbjct: 328 GVYANLVNQVREAFEACDLVRVDCSGLNKSDCRKIGAKLK 367

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	364
317106625	415	JHL05D22.2 [Jatropha curcas]	0.939	0.824	0.764	1e-154
255541412	411	conserved hypothetical protein [Ricinus	0.928	0.822	0.750	1e-145
225453847	418	PREDICTED: CRS2-associated factor 1, mit	0.953	0.830	0.753	1e-143
224130086	405	predicted protein [Populus trichocarpa]	0.914	0.822	0.736	1e-138
356560247	396	PREDICTED: CRS2-associated factor 1, mit	0.934	0.858	0.694	1e-137
297802930	408	DNA binding protein [Arabidopsis lyrata	0.947	0.845	0.717	1e-135
22329043	405	CRS2-associated factor 1 [Arabidopsis th	0.945	0.849	0.720	1e-134
449432211	392	PREDICTED: CRS2-associated factor 1, mit	0.752	0.698	0.833	1e-131
2980765	392	hypothetical protein [Arabidopsis thalia	0.942	0.875	0.696	1e-130
357144801	437	PREDICTED: CRS2-associated factor 1, mit	0.854	0.711	0.680	1e-123

>gi|317106625|dbj|BAJ53131.1| JHL05D22.2 [Jatropha curcas]

 Score =  550 bits (1416), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 272/356 (76%), Positives = 305/356 (85%), Gaps = 14/356 (3%)

Query: 2   IFNRFSRQKPSLRSQPFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPK-PENPNP 60
           +  R SRQKP     P + L   L A   ++ + SSKL+DHY+F+PPPSLSP+ P+NPNP
Sbjct: 3   LLARLSRQKPP----PPSSLCLTLLARHLSSASTSSKLHDHYAFRPPPSLSPQEPDNPNP 58

Query: 61  TLNPNKNFKKKSKPQYRPPSSLDAPKKK--YTDLPFDFRYSYTETNQNVRPIGLREPKYS 118
           T       +KK KP YRPPS+LD   KK  ++DLPFDFRYSYTE++Q+VRPIGLREPKYS
Sbjct: 59  TT------RKKQKPLYRPPSTLDRTGKKPTHSDLPFDFRYSYTESSQSVRPIGLREPKYS 112

Query: 119 PFGPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALV 178
           PFGP RL+R WTGVCAPA DPKVKS + G +DPNLEEKR L+RE+IQG+PLTNAERK LV
Sbjct: 113 PFGPDRLDRSWTGVCAPAVDPKVKSLD-GTDDPNLEEKRKLMREKIQGDPLTNAERKILV 171

Query: 179 EKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKT 238
            +C RN+TKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVC QLEDKT
Sbjct: 172 AQCQRNKTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCSQLEDKT 231

Query: 239 FGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMR 298
           FGKII RH G+LVLYRGRNYNPKKRPVIPLM+WRPHEP+YP+LIKTTI+GLSI+ETKEMR
Sbjct: 232 FGKIIHRHCGSLVLYRGRNYNPKKRPVIPLMMWRPHEPIYPRLIKTTIDGLSIDETKEMR 291

Query: 299 KRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRS 354
           KRGLAVP LTKLAKNGYY SLVPMVRDAFL +ELVRIDCQGLE+SDYKKIGCKLR 
Sbjct: 292 KRGLAVPALTKLAKNGYYASLVPMVRDAFLTNELVRIDCQGLEKSDYKKIGCKLRD 347

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255541412|ref|XP_002511770.1| conserved hypothetical protein [Ricinus communis] gi|223548950|gb|EEF50439.1| conserved hypothetical protein [Ricinus communis]

 Score =  520 bits (1338), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 268/357 (75%), Positives = 300/357 (84%), Gaps = 19/357 (5%)

Query: 1   MIFNRFSRQKPSLRSQPF-TLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPN 59
           ++ NR SR+KP     P+ TLL+  LS+ +A     SSKL+D YSF PPPSLSP+     
Sbjct: 2   LLLNRLSREKP-----PYPTLLSRYLSSASA-----SSKLHDQYSFMPPPSLSPQNHQ-- 49

Query: 60  PTLNPNKNFKKKSKPQYRPPSSLDAPKKK--YTDLPFDFRYSYTETNQNVRPIGLREPKY 117
              NPN   KKK KP YRPPSSLD   KK  ++DLPFDFRYSYTE++Q+VRPIGLREPKY
Sbjct: 50  ---NPNSTPKKKRKPLYRPPSSLDRTGKKPTHSDLPFDFRYSYTESSQSVRPIGLREPKY 106

Query: 118 SPFGPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKAL 177
           SPFGP RL+R WTGVCAP  +PK+K  + G+E+PNLEEKR   RE+IQG+PLTNAERK L
Sbjct: 107 SPFGPDRLDRAWTGVCAPVVEPKLKFVD-GSENPNLEEKRRWWREQIQGQPLTNAERKIL 165

Query: 178 VEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDK 237
           VE C R++TK+QINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVC QLEDK
Sbjct: 166 VESCQRHKTKKQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCTQLEDK 225

Query: 238 TFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEM 297
           TFGKII RH G LVLYRGRNY+PKKRPVIPLM+WRPHEP+YPKLIKTTIEGLSIEETKEM
Sbjct: 226 TFGKIIHRHCGLLVLYRGRNYHPKKRPVIPLMMWRPHEPIYPKLIKTTIEGLSIEETKEM 285

Query: 298 RKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRS 354
           RK+GLA+P LTKLAKNGYY SLVPMVRDAFLV+ELVRIDCQGL +SDYKKIGCKLR 
Sbjct: 286 RKKGLALPALTKLAKNGYYASLVPMVRDAFLVNELVRIDCQGLPKSDYKKIGCKLRD 342

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225453847|ref|XP_002272563.1| PREDICTED: CRS2-associated factor 1, mitochondrial [Vitis vinifera] gi|296089125|emb|CBI38828.3| unnamed protein product [Vitis vinifera]

 Score =  515 bits (1326), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 269/357 (75%), Positives = 293/357 (82%), Gaps = 10/357 (2%)

Query: 1   MIFNRFSRQKPSLRSQPFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPNP 60
            I  RFSRQ     S   TL T  LS++A  +   SS+L DHYSFK P  +SP  +NPNP
Sbjct: 2   FIVTRFSRQIRQSHSAAVTLSTRRLSSSAPPSP--SSRLLDHYSFKSP--VSPF-QNPNP 56

Query: 61  TLNPNKNFKKKSKPQYRPPSSLDAPKKK--YTDLPFDFRYSYTETNQNVRPIGLREPKYS 118
             NP  + KKK KP YRPPSSLD   KK   +DLPFDFRYSYTE++  VRPIGLREPKYS
Sbjct: 57  --NPEPSTKKKQKPPYRPPSSLDRTGKKPLRSDLPFDFRYSYTESSPAVRPIGLREPKYS 114

Query: 119 PFGPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALV 178
           PFGPG L+REWTGVCAPA DPKV+S + G EDP LEEKR  +RE+  GEPLT AERK LV
Sbjct: 115 PFGPGLLDREWTGVCAPAVDPKVRSVD-GKEDPKLEEKRRRMREKTLGEPLTAAERKILV 173

Query: 179 EKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKT 238
           EKC R+RTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKC+GVPTVDMKNVC QLEDKT
Sbjct: 174 EKCQRHRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCMGVPTVDMKNVCTQLEDKT 233

Query: 239 FGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMR 298
            GK+I R GG LVLYRGRNY+PKKRPVIPLMLWRPHEP+YP+LIKT I+GLSIEETKEMR
Sbjct: 234 SGKVIHRQGGLLVLYRGRNYHPKKRPVIPLMLWRPHEPIYPRLIKTVIDGLSIEETKEMR 293

Query: 299 KRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRSW 355
           KRGLAVP LTKLAKNGYYGSLVPMVRDAFL  EL+RIDCQGLER DYKKIGCKLR +
Sbjct: 294 KRGLAVPALTKLAKNGYYGSLVPMVRDAFLTDELIRIDCQGLERRDYKKIGCKLRDF 350

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224130086|ref|XP_002320749.1| predicted protein [Populus trichocarpa] gi|222861522|gb|EEE99064.1| predicted protein [Populus trichocarpa]

 Score =  497 bits (1279), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 254/345 (73%), Positives = 287/345 (83%), Gaps = 12/345 (3%)

Query: 13  LRSQPFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPNPTLNPNKNFKKKS 72
           L  Q    LT  LS++ A     SSKL+D Y FKPPPSLSP+     P  + N N KKK 
Sbjct: 7   LSGQKHFFLTRHLSSSTA-----SSKLHDIYCFKPPPSLSPE----KPQTSNNNNNKKKQ 57

Query: 73  KPQYRPPSSLDAPKKKY-TDLPFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTG 131
           KP+YRPPSSL+  KK   +DLPFDFR+SYTE+  +VRPIGLREPKYSPFGPGRL+R WTG
Sbjct: 58  KPEYRPPSSLETNKKPLRSDLPFDFRFSYTESCPDVRPIGLREPKYSPFGPGRLDRTWTG 117

Query: 132 VCAPAADPKVKSAEEGA--EDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQ 189
           VCAPA D KVKS ++G   E  +LEEKR ++RE+IQG+PLT AE K LV+KC RN+TK+Q
Sbjct: 118 VCAPAVDLKVKSVDDGVGEEGLDLEEKRTVMREKIQGKPLTKAEGKILVDKCQRNKTKKQ 177

Query: 190 INLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGT 249
           INLG DGLTHNMLNDIHNHWKH EAVR+KC+GVPTVDMKNVC QLEDKTFGKII RH G 
Sbjct: 178 INLGIDGLTHNMLNDIHNHWKHDEAVRVKCMGVPTVDMKNVCTQLEDKTFGKIIHRHCGL 237

Query: 250 LVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTK 309
           LVLYRGRNY+P+ RPVIPLMLW+PHEPVYP+LIKTTI+GLSIEETKEMRKRGLAVP LTK
Sbjct: 238 LVLYRGRNYHPRNRPVIPLMLWKPHEPVYPRLIKTTIDGLSIEETKEMRKRGLAVPALTK 297

Query: 310 LAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRS 354
           L++NGY+GSLVPMVRDAFLVSELVRIDCQGL+RSD KKIGCKLR 
Sbjct: 298 LSRNGYFGSLVPMVRDAFLVSELVRIDCQGLDRSDSKKIGCKLRD 342

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356560247|ref|XP_003548405.1| PREDICTED: CRS2-associated factor 1, mitochondrial-like [Glycine max]

 Score =  494 bits (1272), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 248/357 (69%), Positives = 288/357 (80%), Gaps = 17/357 (4%)

Query: 1   MIFNRFSRQKPSLRSQPFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPNP 60
            +  R +RQ PS      TLLT  LS+ A       SKL+ +Y+FKPP SL+P+P+  N 
Sbjct: 2   FLLTRLTRQNPSRA----TLLTRHLSSAA-------SKLHSNYTFKPPSSLAPQPQCSN- 49

Query: 61  TLNPNKNFKKKSKPQYRPPSSLDAPKKK---YTDLPFDFRYSYTETNQNVRPIGLREPKY 117
              P+K  +KK KP+YRPPSSLD   +K     DLPFDFR+SYTE++  VRPIGLREPKY
Sbjct: 50  -FPPSKPNQKKPKPRYRPPSSLDQAGRKPVRSNDLPFDFRFSYTESSAKVRPIGLREPKY 108

Query: 118 SPFGPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKAL 177
           SPFGPGR++R+WTGVCAPA DP V+S E G EDP LEE+R   RE IQG+PL++ ERKAL
Sbjct: 109 SPFGPGRVDRKWTGVCAPAVDPTVESLE-GPEDPKLEEQRKKKREMIQGKPLSSEERKAL 167

Query: 178 VEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDK 237
           V +  R++T R +NLGRDGLTHNMLN IHNHWK AEAVRIKC+GVPT+DM N+C QLEDK
Sbjct: 168 VSQFERSKTNRHVNLGRDGLTHNMLNVIHNHWKFAEAVRIKCMGVPTMDMNNICTQLEDK 227

Query: 238 TFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEM 297
           TFGK+IFRHGGTL+LYRGRNYNPKKRPVIP+MLW+PHEPVYP+LIKTTI+GLSI+ETKEM
Sbjct: 228 TFGKVIFRHGGTLILYRGRNYNPKKRPVIPVMLWKPHEPVYPRLIKTTIDGLSIKETKEM 287

Query: 298 RKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRS 354
           RKRGL+VP LTKLAKNGYY  LVPMVRDAFL  ELVRIDC+GLER DYKKIGCKLR 
Sbjct: 288 RKRGLSVPALTKLAKNGYYAFLVPMVRDAFLSCELVRIDCEGLERKDYKKIGCKLRD 344

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297802930|ref|XP_002869349.1| DNA binding protein [Arabidopsis lyrata subsp. lyrata] gi|297315185|gb|EFH45608.1| DNA binding protein [Arabidopsis lyrata subsp. lyrata]

 Score =  489 bits (1258), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 254/354 (71%), Positives = 286/354 (80%), Gaps = 9/354 (2%)

Query: 1   MIFNRFSRQKPSLRSQPFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPNP 60
           M   R SR  PS     FTLLT  L     + T +SS+L D Y+F+ PP       + NP
Sbjct: 1   MFLIRLSRHNPS----SFTLLTRRLH----DQTISSSRLRDLYNFQSPPPPLSSSASENP 52

Query: 61  TLNPNKNFKKKSKPQYRPPSSLDAPKKKYTDLPFDFRYSYTETNQNVRPIGLREPKYSPF 120
             N   N KKK KPQYRPPSSL+  K  ++DLPFDFR+SYTE++ NVRPIGLREPKYSPF
Sbjct: 53  DFNQKNNNKKKPKPQYRPPSSLEGVKTVHSDLPFDFRFSYTESSSNVRPIGLREPKYSPF 112

Query: 121 GPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEK 180
           GP RL+REWTGVCAPA DPKV+S + G EDP LEEKR  VRE+IQG  LT AERK LVE 
Sbjct: 113 GPDRLDREWTGVCAPAVDPKVESVD-GVEDPKLEEKRRKVREKIQGASLTEAERKFLVEL 171

Query: 181 CHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFG 240
           C RN+TKRQ+NLGRDGLTHNMLNDI+NHWKHAEAVR+KCLGVPT+DMKNV F LEDKTFG
Sbjct: 172 CQRNKTKRQVNLGRDGLTHNMLNDIYNHWKHAEAVRVKCLGVPTLDMKNVIFHLEDKTFG 231

Query: 241 KIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKR 300
           +++ +H GTLVLYRGRNY+PKKRP IPLMLW+PHEPVYP+LIKTTI+GLSI+ETK MRK+
Sbjct: 232 QVVSKHCGTLVLYRGRNYDPKKRPKIPLMLWKPHEPVYPRLIKTTIDGLSIDETKAMRKK 291

Query: 301 GLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRS 354
           GLAVP LTKLAKNGYYGSLVPMVRDAFLVSELVRIDC GL+R DYKKIG KLR 
Sbjct: 292 GLAVPALTKLAKNGYYGSLVPMVRDAFLVSELVRIDCLGLDRKDYKKIGAKLRD 345

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22329043|ref|NP_194830.2| CRS2-associated factor 1 [Arabidopsis thaliana] gi|75161464|sp|Q8VYD9.1|CAF1M_ARATH RecName: Full=CRS2-associated factor 1, mitochondrial; Flags: Precursor gi|18176015|gb|AAL59968.1| unknown protein [Arabidopsis thaliana] gi|20465409|gb|AAM20129.1| unknown protein [Arabidopsis thaliana] gi|332660446|gb|AEE85846.1| CRS2-associated factor 1 [Arabidopsis thaliana]

 Score =  483 bits (1244), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 255/354 (72%), Positives = 286/354 (80%), Gaps = 10/354 (2%)

Query: 1   MIFNRFSRQKPSLRSQPFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPNP 60
           M   R SR  PS     FTLLT  L     + T +SS+L D Y+F+ PP LS      NP
Sbjct: 1   MFLIRLSRHNPS----SFTLLTRRLH----DQTISSSRLRDLYNFQSPPPLSSSASE-NP 51

Query: 61  TLNPNKNFKKKSKPQYRPPSSLDAPKKKYTDLPFDFRYSYTETNQNVRPIGLREPKYSPF 120
             N   N KKK KPQYRPPSSL+  K  ++DLPFDFR+SYTE+  NVRPIGLREPKYSPF
Sbjct: 52  DFNQKNNNKKKPKPQYRPPSSLEGVKTVHSDLPFDFRFSYTESCSNVRPIGLREPKYSPF 111

Query: 121 GPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEK 180
           GP RL+REWTGVCAPA +PKV+S + G EDP LEEKR  VRE+IQG  LT AERK LVE 
Sbjct: 112 GPDRLDREWTGVCAPAVNPKVESVD-GVEDPKLEEKRRKVREKIQGASLTEAERKFLVEL 170

Query: 181 CHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFG 240
           C RN+TKRQ+NLGRDGLTHNMLND++NHWKHAEAVR+KCLGVPT+DMKNV F LEDKTFG
Sbjct: 171 CQRNKTKRQVNLGRDGLTHNMLNDVYNHWKHAEAVRVKCLGVPTLDMKNVIFHLEDKTFG 230

Query: 241 KIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKR 300
           +++ +H GTLVLYRGRNY+PKKRP IPLMLW+PHEPVYP+LIKTTI+GLSI+ETK MRK+
Sbjct: 231 QVVSKHSGTLVLYRGRNYDPKKRPKIPLMLWKPHEPVYPRLIKTTIDGLSIDETKAMRKK 290

Query: 301 GLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRS 354
           GLAVP LTKLAKNGYYGSLVPMVRDAFLVSELVRIDC GLER DYKKIG KLR 
Sbjct: 291 GLAVPALTKLAKNGYYGSLVPMVRDAFLVSELVRIDCLGLERKDYKKIGAKLRD 344

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449432211|ref|XP_004133893.1| PREDICTED: CRS2-associated factor 1, mitochondrial-like [Cucumis sativus] gi|449480099|ref|XP_004155799.1| PREDICTED: LOW QUALITY PROTEIN: CRS2-associated factor 1, mitochondrial-like [Cucumis sativus]

 Score =  474 bits (1221), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 231/277 (83%), Positives = 249/277 (89%), Gaps = 3/277 (1%)

Query: 80  SSLDAPKKK--YTDLPFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCAPAA 137
           SSLD   KK   ++LPFDF+YSYTET+ +VRPIGLREPKYSPFGPGRL+REWTGVCAPAA
Sbjct: 63  SSLDLGGKKPRRSNLPFDFQYSYTETSPSVRPIGLREPKYSPFGPGRLDREWTGVCAPAA 122

Query: 138 DPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGRDGL 197
           +PK  S E G EDP LE KR ++RE IQGEPL  AERKALVEKC +N+TKRQINLGRDGL
Sbjct: 123 NPKATSVE-GMEDPRLEGKRRVMREAIQGEPLPGAERKALVEKCQKNKTKRQINLGRDGL 181

Query: 198 THNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRN 257
           THNMLNDIHNHW+H EAVRIKCLGVPTVDMKNVC QLEDKTFGKII RHGG LVLYRGRN
Sbjct: 182 THNMLNDIHNHWRHGEAVRIKCLGVPTVDMKNVCTQLEDKTFGKIIHRHGGFLVLYRGRN 241

Query: 258 YNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYG 317
           YNPKKRP IPLMLWRPHEP+YP+LIKTTI+GLSI+ETKEMRK+GLAVP LTKLAKNGYYG
Sbjct: 242 YNPKKRPFIPLMLWRPHEPIYPRLIKTTIDGLSIDETKEMRKKGLAVPALTKLAKNGYYG 301

Query: 318 SLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRS 354
           SLVPMVRDAFL  ELVRIDC+GLERSDYKKIGCKLR 
Sbjct: 302 SLVPMVRDAFLSCELVRIDCKGLERSDYKKIGCKLRD 338

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|2980765|emb|CAA18192.1| hypothetical protein [Arabidopsis thaliana] gi|7270003|emb|CAB79819.1| hypothetical protein [Arabidopsis thaliana]

 Score =  472 bits (1215), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 255/366 (69%), Positives = 286/366 (78%), Gaps = 23/366 (6%)

Query: 1   MIFNRFSRQKPSLRSQPFTLLTCCLSATAANTTNNSSKLYDHYSFKPPPSLSPKPENPNP 60
           M   R SR  PS     FTLLT  L     + T +SS+L D Y+F+ PP LS      NP
Sbjct: 1   MFLIRLSRHNPS----SFTLLTRRLH----DQTISSSRLRDLYNFQSPPPLSSSASE-NP 51

Query: 61  TLNPNKNFKKKSKPQYRPPSSLDAPKKKYTDLPFDFRYSYTETNQNVRPIGLREPKYSPF 120
             N   N KKK KPQYRPPSSL+  K  ++DLPFDFR+SYTE+  NVRPIGLREPKYSPF
Sbjct: 52  DFNQKNNNKKKPKPQYRPPSSLEGVKTVHSDLPFDFRFSYTESCSNVRPIGLREPKYSPF 111

Query: 121 GPGRLEREWTGVCAPAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEK 180
           GP RL+REWTGVCAPA +PKV+S + G EDP LEEKR  VRE+IQG  LT AERK LVE 
Sbjct: 112 GPDRLDREWTGVCAPAVNPKVESVD-GVEDPKLEEKRRKVREKIQGASLTEAERKFLVEL 170

Query: 181 CHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFG 240
           C RN+TKRQ+NLGRDGLTHNMLND++NHWKHAEAVR+KCLGVPT+DMKNV F LEDKTFG
Sbjct: 171 CQRNKTKRQVNLGRDGLTHNMLNDVYNHWKHAEAVRVKCLGVPTLDMKNVIFHLEDKTFG 230

Query: 241 KIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKR 300
           +++ +H GTLVLYRGRNY+PKKRP IPLMLW+PHEPVYP+LIKTTI+GLSI+ETK MRK+
Sbjct: 231 QVVSKHSGTLVLYRGRNYDPKKRPKIPLMLWKPHEPVYPRLIKTTIDGLSIDETKAMRKK 290

Query: 301 GLAVPVLTKL-------------AKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKK 347
           GLAVP LTKL             AKNGYYGSLVPMVRDAFLVSELVRIDC GLER DYKK
Sbjct: 291 GLAVPALTKLGPYLFHAFLFLNSAKNGYYGSLVPMVRDAFLVSELVRIDCLGLERKDYKK 350

Query: 348 IGCKLR 353
           IG KLR
Sbjct: 351 IGAKLR 356

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357144801|ref|XP_003573418.1| PREDICTED: CRS2-associated factor 1, mitochondrial-like [Brachypodium distachyon]

 Score =  446 bits (1148), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 224/329 (68%), Positives = 260/329 (79%), Gaps = 18/329 (5%)

Query: 37  SKLYDHYSFKPPPSLSPKPENPNPTLNPNKNFKKK---SKPQYRPPSSLDAPKK--KYTD 91
           S+L DHY F PP SL+P     NP   P+   +KK    KP YRPPSSLD   +   ++D
Sbjct: 22  SRLLDHYGFAPPASLTP-----NPREAPHAAAEKKRRTKKPPYRPPSSLDRGGRPASHSD 76

Query: 92  LPFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCAPAADPKVKSAEEGAEDP 151
           LPFDFR+SYTE+  + +PIGLREPKYSPFGPGRL+R WTG+CAPA D  ++     AEDP
Sbjct: 77  LPFDFRFSYTESTPDAKPIGLREPKYSPFGPGRLDRPWTGLCAPAVDTTIRDVH--AEDP 134

Query: 152 ------NLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDI 205
                 +L+E R   RER+ GEPLT AER  +V+KC RNRTKRQ+NLGRDGLTHNMLNDI
Sbjct: 135 APAAEKDLQEARRRERERVLGEPLTPAERTFVVDKCQRNRTKRQVNLGRDGLTHNMLNDI 194

Query: 206 HNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPV 265
           HNHWKH EAVR+KCLGVPTVDM+NVC +LEDKT G II RHGG L+LYRGR+Y+PKKRPV
Sbjct: 195 HNHWKHGEAVRVKCLGVPTVDMQNVCHELEDKTGGLIIHRHGGQLILYRGRHYHPKKRPV 254

Query: 266 IPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRD 325
           IPLMLW+P EP+YP+LIKTTIEGL++ ETK MRK+GL VPVLTKLAKNGYY SLVPMVRD
Sbjct: 255 IPLMLWKPAEPIYPRLIKTTIEGLTVVETKAMRKKGLHVPVLTKLAKNGYYASLVPMVRD 314

Query: 326 AFLVSELVRIDCQGLERSDYKKIGCKLRS 354
           AFL  ELVRIDC+GL +SDY+KIG KLR 
Sbjct: 315 AFLTDELVRIDCKGLPKSDYRKIGVKLRD 343

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

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	364
TAIR|locus:2126694	405	AT4G31010 [Arabidopsis thalian	0.763	0.686	0.799	3.5e-123
TAIR|locus:2160195	358	AT5G54890 [Arabidopsis thalian	0.692	0.703	0.566	1.4e-78
TAIR|locus:2061604	701	CAF1 [Arabidopsis thaliana (ta	0.708	0.368	0.491	5.2e-65
TAIR|locus:2028100	564	CAF2 [Arabidopsis thaliana (ta	0.708	0.457	0.498	8.8e-63
TAIR|locus:2096662	1011	CFM2 "CRM family member 2" [Ar	0.203	0.073	0.378	4.2e-09
TAIR|locus:2094997	848	EMB1865 "embryo defective 1865	0.373	0.160	0.306	5.7e-06
TAIR|locus:2094558	881	CFM3A "CRM family member 3A" [	0.241	0.099	0.355	2.3e-05
TAIR|locus:2091458	491	AT3G27550 [Arabidopsis thalian	0.321	0.238	0.245	3.6e-05

TAIR|locus:2126694 AT4G31010 [Arabidopsis thaliana (taxid:3702)]

 Score = 1211 (431.4 bits), Expect = 3.5e-123, P = 3.5e-123
 Identities = 223/279 (79%), Positives = 249/279 (89%)

Query:    75 QYRPPSSLDAPKKKYTDLPFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCA 134
             QYRPPSSL+  K  ++DLPFDFR+SYTE+  NVRPIGLREPKYSPFGP RL+REWTGVCA
Sbjct:    66 QYRPPSSLEGVKTVHSDLPFDFRFSYTESCSNVRPIGLREPKYSPFGPDRLDREWTGVCA 125

Query:   135 PAADPKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGR 194
             PA +PKV+S + G EDP LEEKR  VRE+IQG  LT AERK LVE C RN+TKRQ+NLGR
Sbjct:   126 PAVNPKVESVD-GVEDPKLEEKRRKVREKIQGASLTEAERKFLVELCQRNKTKRQVNLGR 184

Query:   195 DGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYR 254
             DGLTHNMLND++NHWKHAEAVR+KCLGVPT+DMKNV F LEDKTFG+++ +H GTLVLYR
Sbjct:   185 DGLTHNMLNDVYNHWKHAEAVRVKCLGVPTLDMKNVIFHLEDKTFGQVVSKHSGTLVLYR 244

Query:   255 GRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNG 314
             GRNY+PKKRP IPLMLW+PHEPVYP+LIKTTI+GLSI+ETK MRK+GLAVP LTKLAKNG
Sbjct:   245 GRNYDPKKRPKIPLMLWKPHEPVYPRLIKTTIDGLSIDETKAMRKKGLAVPALTKLAKNG 304

Query:   315 YYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLR 353
             YYGSLVPMVRDAFLVSELVRIDC GLER DYKKIG KLR
Sbjct:   305 YYGSLVPMVRDAFLVSELVRIDCLGLERKDYKKIGAKLR 343

GO:0003723 "RNA binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA

GO:0010048 "vernalization response" evidence=RCA

GO:0048573 "photoperiodism, flowering" evidence=RCA

TAIR|locus:2160195 AT5G54890 [Arabidopsis thaliana (taxid:3702)]

 Score = 790 (283.2 bits), Expect = 1.4e-78, P = 1.4e-78
 Identities = 150/265 (56%), Positives = 192/265 (72%)

Query:    90 TDLPFDFRYSYTETNQNVRPIGLREPK-YSPFGPGRLEREWTGVCAPAADPKVKSAEEGA 148
             +DLPFDFRYSY+ETN  + PIG REPK +SPFGPGRL+R+WTG  A  A P++  ++   
Sbjct:    75 SDLPFDFRYSYSETNPEIEPIGFREPKRFSPFGPGRLDRKWTGTTA-LASPEIDQSQW-- 131

Query:   149 EDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNH 208
                 +EE     R R+ GE LT  E   L+E+   +   RQINLG+ G+THNM++DIHNH
Sbjct:   132 ----VEE-----RARVLGETLTEDEVTELIERYRHSDCTRQINLGKGGVTHNMIDDIHNH 182

Query:   209 WKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPL 268
             WK AEAVRIKCLGVPT+DM N+CF LE+K+ GKI++R+   LVLYRGRNY+PK RP+IPL
Sbjct:   183 WKKAEAVRIKCLGVPTLDMDNICFHLEEKSGGKIVYRNINILVLYRGRNYDPKSRPIIPL 242

Query:   269 MLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFL 328
             MLW+PH P+YP+L+K   +GL  EETKEMR RGL  P L KL +NG Y ++V  VR+ F 
Sbjct:   243 MLWKPHPPIYPRLVKNVADGLEFEETKEMRNRGLHSPALMKLTRNGVYVNVVGRVREEFE 302

Query:   329 VSELVRIDCQGLERSDYKKIGCKLR 353
               E+VR+DC  +  SD K+IG KL+
Sbjct:   303 TEEIVRLDCTHVGMSDCKRIGVKLK 327

GO:0003723 "RNA binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2061604 CAF1 [Arabidopsis thaliana (taxid:3702)]

 Score = 662 (238.1 bits), Expect = 5.2e-65, P = 5.2e-65
 Identities = 137/279 (49%), Positives = 179/279 (64%)

Query:    93 PFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCA-----------------P 135
             PF+F+YSYTET + V+P+ LREP Y+PFGP  + R WTG                    P
Sbjct:   150 PFEFKYSYTETPK-VKPLKLREPAYAPFGPTTMGRPWTGRAPLPQSQKTPREFDSFRLPP 208

Query:   136 AADPKVKSAEE-GAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGR 194
                  +K  ++ G   P +  + +  +E I GEPLT  E + LV  C +  T RQ+N+GR
Sbjct:   209 VGKKGLKPVQKPGPFRPGVGPRYVYSKEEILGEPLTKEEVRELVTSCLK--TTRQLNMGR 266

Query:   195 DGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYR 254
             DGLTHNMLN+IH+ WK     +IKC GV TVDM NVC QLE+K  GK+I+R GG L L+R
Sbjct:   267 DGLTHNMLNNIHDLWKRRRVCKIKCKGVCTVDMDNVCEQLEEKIGGKVIYRRGGVLFLFR 326

Query:   255 GRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNG 314
             GRNYN + RP  PLMLW+P  PVYP+LI+   EGL+ +E   MR++G  +  + KL KNG
Sbjct:   327 GRNYNHRTRPRFPLMLWKPVAPVYPRLIQQVPEGLTRQEATNMRRKGRELMPICKLGKNG 386

Query:   315 YYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLR 353
              Y  LV  V++AF V ELVRIDCQG++ SD++KIG KL+
Sbjct:   387 VYCDLVKNVKEAFEVCELVRIDCQGMKGSDFRKIGAKLK 425

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

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

GO:0006364 "rRNA processing" evidence=RCA

GO:0006399 "tRNA metabolic process" evidence=RCA

GO:0009658 "chloroplast organization" evidence=RCA

TAIR|locus:2028100 CAF2 [Arabidopsis thaliana (taxid:3702)]

 Score = 641 (230.7 bits), Expect = 8.8e-63, P = 8.8e-63
 Identities = 139/279 (49%), Positives = 177/279 (63%)

Query:    93 PFDFRYSYTETNQNVRPIGLREPKYSPFGPGRLEREWTGVCA--------PAAD-----P 139
             PF+F++SY+ET + V+P+G+REP + PF P  + R WTG           P  D     P
Sbjct:   110 PFEFQFSYSETPK-VKPVGIREPAFMPFAPPTMPRPWTGKAPLKKSKKKIPLFDSFNPPP 168

Query:   140 KVKSAEEGAEDPN-LE----EKRILVRERIQGEPLTNAERKALVEKCHRNRTKRQINLGR 194
               KS  +  E P  L      K  + RE + GEPL   E+  L+ K H +   RQ+NLGR
Sbjct:   169 AGKSGVKYVEMPGPLPFGRYPKEGMNREEVLGEPLKRWEKGMLI-KPHMH-DNRQVNLGR 226

Query:   195 DGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLVLYR 254
             DG THNML  IH+HWK     +++C GVPTVDM NVC  LE+KT G+II R GG + L+R
Sbjct:   227 DGFTHNMLELIHSHWKRRRVCKVRCKGVPTVDMNNVCRVLEEKTGGEIIHRVGGVVYLFR 286

Query:   255 GRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNG 314
             GRNYN + RP  PLMLW+P  PVYPKLI+   EGL+ EE  E R +G ++  + KL+KNG
Sbjct:   287 GRNYNYRTRPQYPLMLWKPAAPVYPKLIQEVPEGLTKEEAHEFRVKGKSLRPICKLSKNG 346

Query:   315 YYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLR 353
              Y SLV  VRDAF +S LV++DC GLE SDYKKIG KL+
Sbjct:   347 VYVSLVKDVRDAFELSSLVKVDCPGLEPSDYKKIGAKLK 385

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

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

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

 Score = 152 (58.6 bits), Expect = 4.2e-09, Sum P(2) = 4.2e-09
 Identities = 28/74 (37%), Positives = 45/74 (60%)

Query:   185 RTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIF 244
             R  +++ +G+ G+T  ++N IH  W+  E V+I C  +  ++MK     LE KT G +I+
Sbjct:   180 RLTKKLKIGKAGITEGIVNGIHERWRTTEVVKIFCEDISRMNMKRTHDVLETKTGGLVIW 239

Query:   245 RHGGTLVLYRGRNY 258
             R G  ++LYRG NY
Sbjct:   240 RSGSKILLYRGVNY 253

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;RCA

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

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

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

 Score = 140 (54.3 bits), Expect = 5.7e-06, Sum P(2) = 5.7e-06
 Identities = 45/147 (30%), Positives = 73/147 (49%)

Query:   139 PKVKSAEEGAEDPNLEEKRILVRERIQGEPLTNAERKALVEKCHRNRTKR-------QIN 191
             P  K+ EE A +  + E  + V ++ +    + AE    VE     R +R       +IN
Sbjct:   206 PWEKNEEEQAAERVVGEGGVAVMQKRRARAPSLAE--LTVEDSELRRLRRDGMYLRVRIN 263

Query:   192 LGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGGTLV 251
             + + GLT  ++  I++ W+  E VR+K   V   DMK     +E +T G +I+R G  +V
Sbjct:   264 IPKAGLTQAVMEKIYDTWRKEELVRLKFHEVLARDMKTAHEIVERRTGGMVIWRAGSVMV 323

Query:   252 LYRGRNYNPKKRPVIPLMLWRPHEPVY 278
             +YRG +Y  K  PVI   +  P E ++
Sbjct:   324 VYRGLDY--KGPPVISNQMAGPKETLF 348

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

 Score = 124 (48.7 bits), Expect = 2.3e-05, Sum P(2) = 2.3e-05
 Identities = 32/90 (35%), Positives = 49/90 (54%)

Query:   169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMK 228
             L  +E + L     R  +K +I  G  G+T   ++ I   WK AE VR+K  G   ++M+
Sbjct:   221 LPESELRRLRNLTFRTASKMRIRGG--GVTQVAVDAIKEKWKSAEIVRLKIEGASALNMR 278

Query:   229 NVCFQLEDKTFGKIIFRHGGTLVLYRGRNY 258
              +   LE KT G +I+R G ++ LYRG +Y
Sbjct:   279 KMHEILEKKTGGLVIWRSGTSISLYRGVSY 308

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

 Score = 127 (49.8 bits), Expect = 3.6e-05, P = 3.6e-05
 Identities = 30/122 (24%), Positives = 64/122 (52%)

Query:   185 RTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIF 244
             + K  + +G  G+   ++ ++H HWK  E V++ C   P   +K +   +   + G +I 
Sbjct:   106 KNKNYVPVGVRGVFGGVVQNMHMHWKFHETVQVCCDNFPKEKIKEMASMIARLSGGVVIN 165

Query:   245 RHG-GTLVLYRGRNYNPKKRPVIPLMLWRPHEPVYPKLIKTTIEG--LSIEETKE-MRKR 300
              H   T++++RGRNY   K  +IP+      + ++    +  +E   L+I++T++ +R+ 
Sbjct:   166 IHNVKTIIMFRGRNYRQPKN-LIPVNTLTKRKALFKARFEQALESQKLNIKKTEQQLRRM 224

Query:   301 GL 302
             G+
Sbjct:   225 GV 226


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        0.321   0.139   0.426    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      364       318   0.00083  116 3  11 22  0.38    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:  613 (65 KB)
  Total size of DFA:  238 KB (2130 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:  25.60u 0.11s 25.71t   Elapsed:  00:00:01
  Total cpu time:  25.60u 0.11s 25.71t   Elapsed:  00:00:01
  Start:  Fri May 10 04:03:36 2013   End:  Fri May 10 04:03:37 2013

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

---

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)
Q6Z4U2	CAF1M_ORYSJ	No assigned EC number	0.6656	0.8598	0.7313	yes	no
Q8VYD9	CAF1M_ARATH	No assigned EC number	0.7203	0.9450	0.8493	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00026315001 SubName- Full=Chromosome chr15 scaffold_37, whole genome shotgun sequence; (418 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	364
pfam01985	84	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	3e-26
smart01103	84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	5e-24
smart01103	84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	9e-09
pfam01985	84	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	2e-07
COG1534	97	COG1534, COG1534, Predicted RNA-binding protein co	1e-04

>gnl|CDD|190184 pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain

 Score = 99.9 bits (250), Expect = 3e-26
 Identities = 26/86 (30%), Positives = 46/86 (53%), Gaps = 2/86 (2%)

Query: 169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMK 228
           LT  +R+ L    H    K  + +G++GLT  ++ +I    +  E +++K LG    D K
Sbjct: 1   LTGKQRRYLRSLAHH--LKPVVQIGKNGLTEGVVEEIDEALEKHELIKVKVLGNDREDRK 58

Query: 229 NVCFQLEDKTFGKIIFRHGGTLVLYR 254
            +  +L +KT  +++   G T+VLYR
Sbjct: 59  EIAEELAEKTGAELVQVIGRTIVLYR 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

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

 Score = 94.1 bits (235), Expect = 5e-24
 Identities = 25/86 (29%), Positives = 46/86 (53%), Gaps = 2/86 (2%)

Query: 169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMK 228
           LT  +++ L    H    K  + +G++GLT  +L +I    +  E +++K LG    D K
Sbjct: 1   LTGKQKRYLRSLAHH--LKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRK 58

Query: 229 NVCFQLEDKTFGKIIFRHGGTLVLYR 254
            +  +L ++T  +++   G T+VLYR
Sbjct: 59  EIAEELAEETGAELVQVIGKTIVLYR 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|198171 smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly

 Score = 51.7 bits (125), Expect = 9e-09
 Identities = 14/64 (21%), Positives = 33/64 (51%)

Query: 289 LSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKI 348
           L+ ++ + +R     +  + ++ KNG    ++  + +A    EL+++   G +R D K+I
Sbjct: 1   LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEI 60

Query: 349 GCKL 352
             +L
Sbjct: 61  AEEL 64

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 = 47.5 bits (114), Expect = 2e-07
 Identities = 15/64 (23%), Positives = 33/64 (51%)

Query: 289 LSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKI 348
           L+ ++ + +R     +  + ++ KNG    +V  + +A    EL+++   G +R D K+I
Sbjct: 1   LTGKQRRYLRSLAHHLKPVVQIGKNGLTEGVVEEIDEALEKHELIKVKVLGNDREDRKEI 60

Query: 349 GCKL 352
             +L
Sbjct: 61  AEEL 64

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

>gnl|CDD|224451 COG1534, COG1534, Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]

 Score = 40.7 bits (96), Expect = 1e-04
 Identities = 27/98 (27%), Positives = 47/98 (47%), Gaps = 3/98 (3%)

Query: 169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMK 228
           LT  +++ L  K H  +   QI  G++GLT  ++ +I    +  E +++K L     D K
Sbjct: 2   LTGKQKRFLRSKAHHLKPIVQI--GKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKK 59

Query: 229 NVCFQLEDKTFGKIIFRHGGTLVLYR-GRNYNPKKRPV 265
            +   L ++T  +++   G TLVLYR  +       P 
Sbjct: 60  EIAEALAEETGAELVQVIGKTLVLYRESKEKRKISLPR 97

Length = 97

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	364
PF01985	84	CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR	99.95
PRK10343	97	RNA-binding protein YhbY; Provisional	99.95
TIGR00253	95	RNA_bind_YhbY putative RNA-binding protein, YhbY f	99.94
COG1534	97	Predicted RNA-binding protein containing KH domain	99.93
KOG1990	564	consensus Poly(A)-specific exoribonuclease PARN [R	99.53
PF01985	84	CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR	99.12
KOG1990	564	consensus Poly(A)-specific exoribonuclease PARN [R	98.31
TIGR00253	95	RNA_bind_YhbY putative RNA-binding protein, YhbY f	97.85
PRK10343	97	RNA-binding protein YhbY; Provisional	97.46
COG1534	97	Predicted RNA-binding protein containing KH domain	96.5

>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=2.1e-27  Score=191.02  Aligned_cols=84  Identities=36%  Similarity=0.543  Sum_probs=75.2

Q ss_pred             CCHHHHHHHHHHhhhCCCCceEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhcCCEEEEEECC
Q 017893          169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGG  248 (364)
Q Consensus       169 LT~kERk~LRk~Ah~~kLkPvV~IGK~GLTd~VVeeI~~aLk~hELVKVK~l~~~~~dmkeiae~LeekTGg~VVq~IG~  248 (364)
                      ||++|+++||+.||  +++|+|+|||+|||++|+++|+++|++||||||+|.+++..++++++++|+++|||++||++|+
T Consensus         1 Lt~ke~~~Lr~~a~--~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~iG~   78 (84)
T PF01985_consen    1 LTSKERKFLRKLAH--HLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVIGR   78 (84)
T ss_dssp             --HHHHHHHHHHHT--TC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEETT
T ss_pred             CCHHHHHHHHHHhc--CCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEECC
Confidence            79999999999999  6999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEc
Q 017893          249 TLVLYR  254 (364)
Q Consensus       249 tiVLYR  254 (364)
                      ++||||
T Consensus        79 ~~vlyR   84 (84)
T PF01985_consen   79 TIVLYR   84 (84)
T ss_dssp             EEEEEE
T ss_pred             EEEEEC
Confidence            999998

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.

>PRK10343 RNA-binding protein YhbY; Provisional

Probab=99.95  E-value=3.1e-27  Score=196.48  Aligned_cols=89  Identities=25%  Similarity=0.298  Sum_probs=86.3

Q ss_pred             CCCCHHHHHHHHHHhhhCCCCceEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhcCCEEEEEE
Q 017893          167 EPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRH  246 (364)
Q Consensus       167 e~LT~kERk~LRk~Ah~~kLkPvV~IGK~GLTd~VVeeI~~aLk~hELVKVK~l~~~~~dmkeiae~LeekTGg~VVq~I  246 (364)
                      ++||++||++||++||  +++|+|+|||+|||++|+++|+++|++||||||++++++.++.++++++|+++|||++||+|
T Consensus         1 m~Lt~kqr~~LR~~ah--~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~I   78 (97)
T PRK10343          1 MNLSTKQKQHLKGLAH--PLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVI   78 (97)
T ss_pred             CCCCHHHHHHHHHhcC--CCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeee
Confidence            3699999999999999  69999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCEEEEEcCCC
Q 017893          247 GGTLVLYRGRN  257 (364)
Q Consensus       247 G~tiVLYRgkn  257 (364)
                      |+++||||++.
T Consensus        79 G~~~vlYR~~~   89 (97)
T PRK10343         79 GKTLVLYRPTK   89 (97)
T ss_pred             CcEEEEEecCC
Confidence            99999999964

>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family

Probab=99.94  E-value=5.5e-27  Score=194.16  Aligned_cols=87  Identities=26%  Similarity=0.379  Sum_probs=85.0

Q ss_pred             CCHHHHHHHHHHhhhCCCCceEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhcCCEEEEEECC
Q 017893          169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHGG  248 (364)
Q Consensus       169 LT~kERk~LRk~Ah~~kLkPvV~IGK~GLTd~VVeeI~~aLk~hELVKVK~l~~~~~dmkeiae~LeekTGg~VVq~IG~  248 (364)
                      ||++||++||+.||  +|+|+|+|||+|||++|+++|+++|++||||||++++++.++.++++++|+++|||++||+||+
T Consensus         1 Lt~kqr~~Lr~~ah--~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~iG~   78 (95)
T TIGR00253         1 LTGKQKRHLRGKAH--HLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVIGK   78 (95)
T ss_pred             CCHHHHHHHHHHhC--CCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEEcc
Confidence            79999999999999  6999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEcCCC
Q 017893          249 TLVLYRGRN  257 (364)
Q Consensus       249 tiVLYRgkn  257 (364)
                      ++||||++.
T Consensus        79 ~~vlYR~~~   87 (95)
T TIGR00253        79 TIVLYRPTK   87 (95)
T ss_pred             EEEEEecCC
Confidence            999999964

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.

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

Probab=99.93  E-value=2.9e-25  Score=184.80  Aligned_cols=87  Identities=29%  Similarity=0.463  Sum_probs=84.6

Q ss_pred             CCCHHHHHHHHHHhhhCCCCceEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhcCCEEEEEEC
Q 017893          168 PLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHG  247 (364)
Q Consensus       168 ~LT~kERk~LRk~Ah~~kLkPvV~IGK~GLTd~VVeeI~~aLk~hELVKVK~l~~~~~dmkeiae~LeekTGg~VVq~IG  247 (364)
                      +||++|+++||+.||  +++|+|+|||+|||++|++||+++|++||||||++.+++.+|.+++++.|++++||.+||+||
T Consensus         1 ~Lt~kq~~~Lrs~Ah--~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqviG   78 (97)
T COG1534           1 MLTGKQKRFLRSKAH--HLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVIG   78 (97)
T ss_pred             CCcHHHHHHHHHhhc--cCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeeee
Confidence            589999999999999  599999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEEcCC
Q 017893          248 GTLVLYRGR  256 (364)
Q Consensus       248 ~tiVLYRgk  256 (364)
                      +++||||.+
T Consensus        79 ~~~vlyr~~   87 (97)
T COG1534          79 KTLVLYRES   87 (97)
T ss_pred             eEEEEEecC
Confidence            999999953

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

Probab=99.53  E-value=1.3e-14  Score=151.02  Aligned_cols=193  Identities=17%  Similarity=0.137  Sum_probs=164.5

Q ss_pred             CCCCCHHHHHHHHHHhhhCCCCceEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhcCC-EEEE
Q 017893          166 GEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFG-KIIF  244 (364)
Q Consensus       166 ~e~LT~kERk~LRk~Ah~~kLkPvV~IGK~GLTd~VVeeI~~aLk~hELVKVK~l~~~~~dmkeiae~LeekTGg-~VVq  244 (364)
                      ...+.+.+..+||..|.  ++...+  +++|+|+++++.|++.|+.+|+++++|....+..|....+.++..+++ -+||
T Consensus        11 ~~~~~~~~~~~l~~~~~--~~~~~~--~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~n~~~~   86 (564)
T KOG1990|consen   11 ELTVDEADLRRLRLVAT--GMTSAP--WKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMSTGGNFVVW   86 (564)
T ss_pred             HhhcCHHHHHHHhhhhc--cceecc--cccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccCCCceeee
Confidence            35688899999999997  455555  999999999999999999999999999999999999999999999999 9999


Q ss_pred             EECCEEEEEcCCCCCCC----CCC---cc--------------------cccccC--CCCCCchhhhhhh----------
Q 017893          245 RHGGTLVLYRGRNYNPK----KRP---VI--------------------PLMLWR--PHEPVYPKLIKTT----------  285 (364)
Q Consensus       245 ~IG~tiVLYRgknY~~~----~RP---~i--------------------plmlwk--p~~Pv~pklik~~----------  285 (364)
                      ..|.....|++..|.-+    .|.   ..                    ..+.|-  ...|++-+++.+.          
T Consensus        87 ~~g~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~  166 (564)
T KOG1990|consen   87 SRGDSISSPEFLCQRSPVDFVARQQENQAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRT  166 (564)
T ss_pred             ecCccccCCccceeecchhhhhhhchhhhhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhcc
Confidence            99999988866555311    111   00                    123344  5666766666443          


Q ss_pred             -----cCCCCHHHHHHHHhCCCCCCceEEeccCCCCCchhHHHHHHhhhcceEEEecc-CCCcchhHHHHHhh--hcccc
Q 017893          286 -----IEGLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQ-GLERSDYKKIGCKL--RSWFR  357 (364)
Q Consensus       286 -----~eGLs~eE~telRr~g~~lp~~~kLgRNg~~~~Lv~~V~~~we~s~ivKI~ck-G~~~sd~~kig~kL--k~L~~  357 (364)
                           ++.|+..|.+.+|+.|..+|+||.+|+++.+++++.++++.|+++++++|.|+ |+..+..+.||++|  +.+++
T Consensus       167 l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg  246 (564)
T KOG1990|consen  167 LPVGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTG  246 (564)
T ss_pred             CCCCChhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcC
Confidence                 35599999999999999999999999999999999999999999999999997 99999999999999  99999


Q ss_pred             eeecc
Q 017893          358 ISFLA  362 (364)
Q Consensus       358 ~vll~  362 (364)
                      ++|+.
T Consensus       247 ~~lv~  251 (564)
T KOG1990|consen  247 KVLVL  251 (564)
T ss_pred             CeEEe
Confidence            98864

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

Probab=99.12  E-value=5.2e-11  Score=96.06  Aligned_cols=74  Identities=26%  Similarity=0.322  Sum_probs=64.2

Q ss_pred             CCHHHHHHHHhCCCCCCceEEeccCCCCCchhHHHHHHhhhcceEEEeccCCCcchhHHHHHhhhcccceeecc
Q 017893          289 LSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRSWFRISFLA  362 (364)
Q Consensus       289 Ls~eE~telRr~g~~lp~~~kLgRNg~~~~Lv~~V~~~we~s~ivKI~ckG~~~sd~~kig~kLk~L~~~vll~  362 (364)
                      ||.+|..++|+.|..+.|++.+|+||...+++++|.++|+..|||||.|.+..+.|.+.|+++|.+.++|.+..
T Consensus         1 Lt~ke~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~   74 (84)
T PF01985_consen    1 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQ   74 (84)
T ss_dssp             --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEE
T ss_pred             CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEE
Confidence            68999999999999999999999999999999999999999999999999999999999999999999998863

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=98.31  E-value=6.2e-07  Score=94.26  Aligned_cols=194  Identities=19%  Similarity=0.194  Sum_probs=155.8

Q ss_pred             CCCCCHHHHHHHHHHhhhCCCCceEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCC-ChHhHHHHHHHH--HHhcCCEE
Q 017893          166 GEPLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGV-PTVDMKNVCFQL--EDKTFGKI  242 (364)
Q Consensus       166 ~e~LT~kERk~LRk~Ah~~kLkPvV~IGK~GLTd~VVeeI~~aLk~hELVKVK~l~~-~~~dmkeiae~L--eekTGg~V  242 (364)
                      ...|+..|.-.+|.++-  ...+.+.+|.++.-+++.-.+...|+.|+.+|+.+... .....+.++..+  -..+|+.+
T Consensus       172 ~~~l~~~~~~~~r~~~~--~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~l  249 (564)
T KOG1990|consen  172 PPLLTSIESTLLRRLGY--KLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVL  249 (564)
T ss_pred             hhhhhhHHHHHHHHhcc--cccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeE
Confidence            35799999999999998  79999999999999999999999999999999887754 444566777777  88899999


Q ss_pred             EEEECCEEEEEcCCCCCCCCCCc-----------ccc-----------------------------cccCC-CCC-----
Q 017893          243 IFRHGGTLVLYRGRNYNPKKRPV-----------IPL-----------------------------MLWRP-HEP-----  276 (364)
Q Consensus       243 Vq~IG~tiVLYRgknY~~~~RP~-----------ipl-----------------------------mlwkp-~~P-----  276 (364)
                      |.+.+...|+||++++-. .-|.           ||.                             ..|.+ .++     
T Consensus       250 v~hN~~~dv~y~~~~Fl~-~lp~~l~~f~~~~~~fp~~~~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~  328 (564)
T KOG1990|consen  250 VLHNKLLDVMYRYKNFLS-PLPSTLEEFTDSSSMFPNIEDTKRLAKLSEYQKLNLKATLLELARAKAKKEKEIERRSISS  328 (564)
T ss_pred             Eeeccceeeeeehhhccc-ccchhHHHhhhhhhhhhhhHHHHHhhccccccchhhhhhHHHHHHHhcccccCcccccccc
Confidence            999999999999887643 2110           110                             00110 000     


Q ss_pred             -C----------------chhh-------------------------hhhhcCCCCHHHHHHHHhCCCCCCceEEeccCC
Q 017893          277 -V----------------YPKL-------------------------IKTTIEGLSIEETKEMRKRGLAVPVLTKLAKNG  314 (364)
Q Consensus       277 -v----------------~pkl-------------------------ik~~~eGLs~eE~telRr~g~~lp~~~kLgRNg  314 (364)
                       +                +-++                         -..+++..|++|-.++++.|...-...-+||.|
T Consensus       329 ~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg  408 (564)
T KOG1990|consen  329 RLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRG  408 (564)
T ss_pred             hhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCCcc
Confidence             0                0000                         013567799999999999999999999999999


Q ss_pred             CCCchhHHHHHHhhhcceEEEeccCCCc-chhHHHHHhhhcccceeecc
Q 017893          315 YYGSLVPMVRDAFLVSELVRIDCQGLER-SDYKKIGCKLRSWFRISFLA  362 (364)
Q Consensus       315 ~~~~Lv~~V~~~we~s~ivKI~ckG~~~-sd~~kig~kLk~L~~~vll~  362 (364)
                      ++.|++.++..+|...+.+++.|+.-.. +.-+..|..|-.+-+++++.
T Consensus       409 ~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~  457 (564)
T KOG1990|consen  409 VFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVS  457 (564)
T ss_pred             cccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceee
Confidence            9999999999999999999999995555 99999999999999888764

>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family

Probab=97.85  E-value=4.1e-05  Score=64.06  Aligned_cols=73  Identities=16%  Similarity=0.219  Sum_probs=68.3

Q ss_pred             CCHHHHHHHHhCCCCCCceEEeccCCCCCchhHHHHHHhhhcceEEEeccCCCcchhHHHHHhhhcccceeec
Q 017893          289 LSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRSWFRISFL  361 (364)
Q Consensus       289 Ls~eE~telRr~g~~lp~~~kLgRNg~~~~Lv~~V~~~we~s~ivKI~ckG~~~sd~~kig~kLk~L~~~vll  361 (364)
                      ||.++..++|..|..+.|++-.|+||.-.+++..|.++|+..||+||-+..-...|-+.++++|-+-++|.+.
T Consensus         1 Lt~kqr~~Lr~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~V   73 (95)
T TIGR00253         1 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNV   73 (95)
T ss_pred             CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEE
Confidence            6889999999999999999999999999999999999999999999999866678889999999999988775

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.

>PRK10343 RNA-binding protein YhbY; Provisional

Probab=97.46  E-value=0.00036  Score=58.81  Aligned_cols=73  Identities=14%  Similarity=0.152  Sum_probs=68.4

Q ss_pred             CCHHHHHHHHhCCCCCCceEEeccCCCCCchhHHHHHHhhhcceEEEeccCCCcchhHHHHHhhhcccceeec
Q 017893          289 LSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRSWFRISFL  361 (364)
Q Consensus       289 Ls~eE~telRr~g~~lp~~~kLgRNg~~~~Lv~~V~~~we~s~ivKI~ckG~~~sd~~kig~kLk~L~~~vll  361 (364)
                      ||.++..++|..|..+.|++-.|+||.-.+++..|.++.+..||+||-+..-...|-+.++++|-+-++|-+.
T Consensus         3 Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~V   75 (97)
T PRK10343          3 LSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNV   75 (97)
T ss_pred             CCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEE
Confidence            7889999999999999999999999999999999999999999999999877888889999999998888764

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

Probab=96.50  E-value=0.007  Score=51.30  Aligned_cols=73  Identities=18%  Similarity=0.272  Sum_probs=68.0

Q ss_pred             CCHHHHHHHHhCCCCCCceEEeccCCCCCchhHHHHHHhhhcceEEEeccCCCcchhHHHHHhhhcccceeec
Q 017893          289 LSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRSWFRISFL  361 (364)
Q Consensus       289 Ls~eE~telRr~g~~lp~~~kLgRNg~~~~Lv~~V~~~we~s~ivKI~ckG~~~sd~~kig~kLk~L~~~vll  361 (364)
                      ||.++..++|.++..+-|++-.|+||.-.++.+.|.++-+..+++||-+-+-...|=+.+|++|-+-++|.|.
T Consensus         2 Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lV   74 (97)
T COG1534           2 LTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELV   74 (97)
T ss_pred             CcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEe
Confidence            6889999999999999999999999999999999999999999999998777777999999999999988775

---

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	364
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	3e-19
1rq8_A	104	Conserved hypothetical protein; structural genomic	4e-18

>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 = 81.2 bits (201), Expect = 3e-19
 Identities = 23/99 (23%), Positives = 44/99 (44%), Gaps = 5/99 (5%)

Query: 169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMK 228
           L+  +++ L  K   +     + LG +GLT  +L +I N   H E +++K  G      +
Sbjct: 3   LSTKQKQFL--KGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQ 60

Query: 229 NVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIP 267
            +   +  +T    +   G  LVLYR    + + +  +P
Sbjct: 61  LIINAIVRETKAAQVQTIGHILVLYRP---SEEAKIQLP 96

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

 Score = 78.1 bits (193), Expect = 4e-18
 Identities = 23/107 (21%), Positives = 46/107 (42%), Gaps = 6/107 (5%)

Query: 169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMK 228
           LT  +++ L  +   +       +G+ G+  NM+  I +  ++ E +++  L     D K
Sbjct: 2   LTGKQKRYL--RSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKK 59

Query: 229 NVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIPLMLWRPHE 275
            +   L + T  +++   G  +V+YR      K+   I L L   H 
Sbjct: 60  ELAETLSEATRSELVQVIGSMIVIYRES----KENKEIELPLEHHHH 102

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	364
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	99.96
1rq8_A	104	Conserved hypothetical protein; structural genomic	99.96
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	98.4
1rq8_A	104	Conserved hypothetical protein; structural genomic	98.24

>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=4.6e-29  Score=206.11  Aligned_cols=87  Identities=25%  Similarity=0.374  Sum_probs=85.5

Q ss_pred             CCCHHHHHHHHHHhhhCCCCceEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhcCCEEEEEEC
Q 017893          168 PLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHG  247 (364)
Q Consensus       168 ~LT~kERk~LRk~Ah~~kLkPvV~IGK~GLTd~VVeeI~~aLk~hELVKVK~l~~~~~dmkeiae~LeekTGg~VVq~IG  247 (364)
                      .||++|+++||+.||  +|+|+|+|||+|||++|+++|+++|++||||||+|++++.+|+++++++|+++|||++||+||
T Consensus         2 ~Lt~kqr~~Lr~~ah--~l~pvv~IGk~GlT~~vi~ei~~aL~~~ELIKVkvl~~~~~~~~e~a~~la~~t~a~~Vq~IG   79 (98)
T 1jo0_A            2 TLSTKQKQFLKGLAH--HLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTIG   79 (98)
T ss_dssp             CCCHHHHHHHHHHHT--TBCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEEEET
T ss_pred             CCCHHHHHHHHHHhc--CCCCeEEECCCCCCHHHHHHHHHHHHHCCeEEEEEeCCCHHHHHHHHHHHHHHhCCEEEEEEC
Confidence            699999999999999  699999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEEcCC
Q 017893          248 GTLVLYRGR  256 (364)
Q Consensus       248 ~tiVLYRgk  256 (364)
                      +++||||++
T Consensus        80 ~~~vLyR~~   88 (98)
T 1jo0_A           80 HILVLYRPS   88 (98)
T ss_dssp             TEEEEECCC
T ss_pred             CEEEEEccC
Confidence            999999986

>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=6e-29  Score=207.68  Aligned_cols=88  Identities=22%  Similarity=0.395  Sum_probs=86.2

Q ss_pred             CCCHHHHHHHHHHhhhCCCCceEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhcCCEEEEEEC
Q 017893          168 PLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHG  247 (364)
Q Consensus       168 ~LT~kERk~LRk~Ah~~kLkPvV~IGK~GLTd~VVeeI~~aLk~hELVKVK~l~~~~~dmkeiae~LeekTGg~VVq~IG  247 (364)
                      +||++||++||+.||  +|+|+|+|||+|||++|+++|+++|++||||||+|++++.+|+++++++|+++|||++||+||
T Consensus         1 mLt~kqr~~LR~~ah--~Lkpvv~IGK~GlTe~vi~ei~~aL~~hELIKVkvl~~~~~d~~e~a~~la~~t~a~vVq~IG   78 (104)
T 1rq8_A            1 MLTGKQKRYLRSLAH--NIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVIG   78 (104)
T ss_dssp             CCCHHHHHHHHHHTT--SSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEET
T ss_pred             CCCHHHHHHHHHHhc--CCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCHHHHHHHHHHHHHHhCCEEEEEEC
Confidence            699999999999999  699999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEEcCCC
Q 017893          248 GTLVLYRGRN  257 (364)
Q Consensus       248 ~tiVLYRgkn  257 (364)
                      +++||||++.
T Consensus        79 ~~~VLYR~~~   88 (104)
T 1rq8_A           79 SMIVIYRESK   88 (104)
T ss_dssp             TEEEEEECCC
T ss_pred             CEEEEEeCCC
Confidence            9999999976

>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=98.40  E-value=2.5e-07  Score=76.29  Aligned_cols=73  Identities=15%  Similarity=0.206  Sum_probs=70.3

Q ss_pred             CCHHHHHHHHhCCCCCCceEEeccCCCCCchhHHHHHHhhhcceEEEeccCCCcchhHHHHHhhhcccceeec
Q 017893          289 LSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRSWFRISFL  361 (364)
Q Consensus       289 Ls~eE~telRr~g~~lp~~~kLgRNg~~~~Lv~~V~~~we~s~ivKI~ckG~~~sd~~kig~kLk~L~~~vll  361 (364)
                      ||.+|..++|..|..+.|++-+|+||.-.++++.|.++|+..||+||-|.+....|-+.|+++|-+.++|.+.
T Consensus         3 Lt~kqr~~Lr~~ah~l~pvv~IGk~GlT~~vi~ei~~aL~~~ELIKVkvl~~~~~~~~e~a~~la~~t~a~~V   75 (98)
T 1jo0_A            3 LSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQV   75 (98)
T ss_dssp             CCHHHHHHHHHHHTTBCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEE
T ss_pred             CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHHCCeEEEEEeCCCHHHHHHHHHHHHHHhCCEEE
Confidence            7899999999999999999999999999999999999999999999999998899999999999999998764

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

Probab=98.24  E-value=1.3e-06  Score=72.98  Aligned_cols=73  Identities=15%  Similarity=0.244  Sum_probs=69.8

Q ss_pred             CCHHHHHHHHhCCCCCCceEEeccCCCCCchhHHHHHHhhhcceEEEeccCCCcchhHHHHHhhhcccceeec
Q 017893          289 LSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRSWFRISFL  361 (364)
Q Consensus       289 Ls~eE~telRr~g~~lp~~~kLgRNg~~~~Lv~~V~~~we~s~ivKI~ckG~~~sd~~kig~kLk~L~~~vll  361 (364)
                      ||.++..++|..|..+.|++-+|+||.-.++++.|.++|+..||+||-|.+....|-+.++++|-+.++|.+.
T Consensus         2 Lt~kqr~~LR~~ah~Lkpvv~IGK~GlTe~vi~ei~~aL~~hELIKVkvl~~~~~d~~e~a~~la~~t~a~vV   74 (104)
T 1rq8_A            2 LTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELV   74 (104)
T ss_dssp             CCHHHHHHHHHHTTSSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEE
T ss_pred             CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCHHHHHHHHHHHHHHhCCEEE
Confidence            7899999999999999999999999999999999999999999999999988889999999999999998774

---

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	364
d1rq8a_	96	d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphy	8e-24
d1rq8a_	96	d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphy	4e-07
d1jo0a_	97	d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i	6e-22
d1jo0a_	97	d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i	1e-06

>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 = 92.1 bits (229), Expect = 8e-24
 Identities = 20/93 (21%), Positives = 41/93 (44%), Gaps = 2/93 (2%)

Query: 169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMK 228
           LT  +++ L    H         +G+ G+  NM+  I +  ++ E +++  L     D K
Sbjct: 2   LTGKQKRYLRSLAHN--IDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKK 59

Query: 229 NVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPK 261
            +   L + T  +++   G  +V+YR    N +
Sbjct: 60  ELAETLSEATRSELVQVIGSMIVIYRESKENKE 92

>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 = 45.4 bits (108), Expect = 4e-07
 Identities = 10/64 (15%), Positives = 28/64 (43%)

Query: 289 LSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKI 348
           L+ ++ + +R     +  + ++ K G   +++  + D     EL+++        D K++
Sbjct: 2   LTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKEL 61

Query: 349 GCKL 352
              L
Sbjct: 62  AETL 65

>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 = 86.7 bits (215), Expect = 6e-22
 Identities = 23/99 (23%), Positives = 44/99 (44%), Gaps = 5/99 (5%)

Query: 169 LTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMK 228
           L+  +++ L  K   +     + LG +GLT  +L +I N   H E +++K  G      +
Sbjct: 3   LSTKQKQFL--KGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQ 60

Query: 229 NVCFQLEDKTFGKIIFRHGGTLVLYRGRNYNPKKRPVIP 267
            +   +  +T    +   G  LVLYR    + + +  +P
Sbjct: 61  LIINAIVRETKAAQVQTIGHILVLYRP---SEEAKIQLP 96

>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 = 43.9 bits (104), Expect = 1e-06
 Identities = 11/64 (17%), Positives = 28/64 (43%)

Query: 289 LSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKI 348
           LS ++ + ++     +  +  L  NG    ++  + +A    EL+++   G +R   + I
Sbjct: 3   LSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLI 62

Query: 349 GCKL 352
              +
Sbjct: 63  INAI 66

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	364
d1rq8a_	96	Hypothetical protein SAV1595 {Staphylococcus aureu	99.96
d1jo0a_	97	YhbY homologue HI1333 {Haemophilus influenzae [Tax	99.95
d1jo0a_	97	YhbY homologue HI1333 {Haemophilus influenzae [Tax	99.02
d1rq8a_	96	Hypothetical protein SAV1595 {Staphylococcus aureu	98.9

>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=9.2e-29  Score=200.85  Aligned_cols=90  Identities=22%  Similarity=0.390  Sum_probs=87.2

Q ss_pred             CCCHHHHHHHHHHhhhCCCCceEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhcCCEEEEEEC
Q 017893          168 PLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHG  247 (364)
Q Consensus       168 ~LT~kERk~LRk~Ah~~kLkPvV~IGK~GLTd~VVeeI~~aLk~hELVKVK~l~~~~~dmkeiae~LeekTGg~VVq~IG  247 (364)
                      +||++|+++||+.||  +|+|+|+|||+|||++|+++|+++|++||||||+|.+.+..|+++++++||++|||.+||+||
T Consensus         1 mLt~kqr~~LR~~ah--~l~p~v~IGk~Glt~~vi~ei~~~l~~~ELIKvk~~~~~~~~~~~~~~~l~~~t~a~~V~~iG   78 (96)
T d1rq8a_           1 MLTGKQKRYLRSLAH--NIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVIG   78 (96)
T ss_dssp             CCCHHHHHHHHHHTT--SSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEET
T ss_pred             CcCHHHHHHHHHHhc--CCCCEEEECCCCCCHHHHHHHHHHHHhCCeeEEEecCCCHHHHHHHHHHHHHHhCCEEEEEEC
Confidence            699999999999999  699999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEEcCCCCC
Q 017893          248 GTLVLYRGRNYN  259 (364)
Q Consensus       248 ~tiVLYRgknY~  259 (364)
                      +++||||+++++
T Consensus        79 ~~~vlyR~~~~~   90 (96)
T d1rq8a_          79 SMIVIYRESKEN   90 (96)
T ss_dssp             TEEEEEECCCSC
T ss_pred             CEEEEEeCCCCC
Confidence            999999997653

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

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: YhbY homologue HI1333
species: Haemophilus influenzae [TaxId: 727]

Probab=99.95  E-value=3.8e-28  Score=197.53  Aligned_cols=88  Identities=25%  Similarity=0.373  Sum_probs=85.6

Q ss_pred             CCCHHHHHHHHHHhhhCCCCceEEeCCCCCCHHHHHHHHHHHHhCCeeEEEeCCCChHhHHHHHHHHHHhcCCEEEEEEC
Q 017893          168 PLTNAERKALVEKCHRNRTKRQINLGRDGLTHNMLNDIHNHWKHAEAVRIKCLGVPTVDMKNVCFQLEDKTFGKIIFRHG  247 (364)
Q Consensus       168 ~LT~kERk~LRk~Ah~~kLkPvV~IGK~GLTd~VVeeI~~aLk~hELVKVK~l~~~~~dmkeiae~LeekTGg~VVq~IG  247 (364)
                      .||++|+++||++||  +|+|+|+|||+|||++|+++|+++|++||||||+|.+.+.+|+++++++||++|||.+||+||
T Consensus         2 tLt~kqr~~LR~~ah--~lkp~v~IGk~Glt~~vi~ei~~al~~~ELIKvki~~~~~~~~~~~~~~l~~~t~~~vV~~iG   79 (97)
T d1jo0a_           2 TLSTKQKQFLKGLAH--HLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTIG   79 (97)
T ss_dssp             CCCHHHHHHHHHHHT--TBCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEEEET
T ss_pred             CCCHHHHHHHHHHhc--CCCCEEEECCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHHHhCCEEEEEEC
Confidence            699999999999999  599999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEEcCCC
Q 017893          248 GTLVLYRGRN  257 (364)
Q Consensus       248 ~tiVLYRgkn  257 (364)
                      +++||||++.
T Consensus        80 ~~~ilYR~~~   89 (97)
T d1jo0a_          80 HILVLYRPSE   89 (97)
T ss_dssp             TEEEEECCCS
T ss_pred             CEEEEEcCCC
Confidence            9999999853

>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=99.02  E-value=9.1e-11  Score=94.23  Aligned_cols=75  Identities=15%  Similarity=0.195  Sum_probs=72.0

Q ss_pred             CCCHHHHHHHHhCCCCCCceEEeccCCCCCchhHHHHHHhhhcceEEEeccCCCcchhHHHHHhhhcccceeecc
Q 017893          288 GLSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRSWFRISFLA  362 (364)
Q Consensus       288 GLs~eE~telRr~g~~lp~~~kLgRNg~~~~Lv~~V~~~we~s~ivKI~ckG~~~sd~~kig~kLk~L~~~vll~  362 (364)
                      -||.+|..+||..|..+.|++.+|+||...++++.|.++|+..|||||.|.+....|.+.|+++|.+.|+|+++-
T Consensus         2 tLt~kqr~~LR~~ah~lkp~v~IGk~Glt~~vi~ei~~al~~~ELIKvki~~~~~~~~~~~~~~l~~~t~~~vV~   76 (97)
T d1jo0a_           2 TLSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQ   76 (97)
T ss_dssp             CCCHHHHHHHHHHHTTBCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEE
T ss_pred             CCCHHHHHHHHHHhcCCCCEEEECCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHHHhCCEEEE
Confidence            389999999999999999999999999999999999999999999999999889999999999999999998863

>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=98.90  E-value=7.2e-10  Score=88.74  Aligned_cols=74  Identities=15%  Similarity=0.240  Sum_probs=71.2

Q ss_pred             CCHHHHHHHHhCCCCCCceEEeccCCCCCchhHHHHHHhhhcceEEEeccCCCcchhHHHHHhhhcccceeecc
Q 017893          289 LSIEETKEMRKRGLAVPVLTKLAKNGYYGSLVPMVRDAFLVSELVRIDCQGLERSDYKKIGCKLRSWFRISFLA  362 (364)
Q Consensus       289 Ls~eE~telRr~g~~lp~~~kLgRNg~~~~Lv~~V~~~we~s~ivKI~ckG~~~sd~~kig~kLk~L~~~vll~  362 (364)
                      ||.+|..+||..|..+.|++.+|+||...++++.|.++|+..||+||.|.+....|-+.++++|.+.++|.++.
T Consensus         2 Lt~kqr~~LR~~ah~l~p~v~IGk~Glt~~vi~ei~~~l~~~ELIKvk~~~~~~~~~~~~~~~l~~~t~a~~V~   75 (96)
T d1rq8a_           2 LTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQ   75 (96)
T ss_dssp             CCHHHHHHHHHHTTSSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEE
T ss_pred             cCHHHHHHHHHHhcCCCCEEEECCCCCCHHHHHHHHHHHHhCCeeEEEecCCCHHHHHHHHHHHHHHhCCEEEE
Confidence            78999999999999999999999999999999999999999999999999888999999999999999998864