Citrus Sinensis ID: 041912

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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-------36
Protein Sequence
MLAKLPKTLKTLNLIPVKKQNLLLFTQIHSSSEYIDDDPPFSPKRQKPQNPRTQQNPPVPSSNTNKLPLKSDLPFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALAPKEVDRVRFEEERNRVLGDPLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNINILLLYRGRNYDPKDRPVIPLMLWRPYAPIYPKVVKNVADGLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWRGKEQAMDSDPLIDPTNP
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccccHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHccEEEEEEcccccccHHHHHHHHHHHHccEEEEEEccEEEEEEccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccEEEEcccccHHHHHHHHHHHHHHccEEEEEccccccccHHHHHHHHHcccccEEEEEcccEEEEEcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccHccccccccccccEEEccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccHHHHHHHHHHHcccccHHHccccccccHHHHHHHHHHHHHcccEEEEEEccccHHHHHHHHHHHHHHcccEEEEEcccEEEEEEcccccccccccccEEccccccccccHHcccccccccHHHHHHHHHHcccccHHHHHcccccEEcHHHHHHHHHccccEEEEEcccccHHHHHHHHHHHHHcccEEEEEEcccEEEEEEccccccccccccccccc
Coil and Loop (DISEMBL)
mlaklpktlktlnlipvkkqNLLLFTQIhssseyidddppfspkrqkpqnprtqqnppvpssntnklplksdlpfdfkysysennpavepigfrepkrfspfgpgrldrkwtgttalapkevdrvRFEEernrvlgdpltEEEIAELVERYRHsdcarqinlgkwgvtHNMLDDLHNHWKRAEAVRIkclgvptldmdnvcfhleeksggkiiyRNINILLlyrgrnydpkdrpviplmlwrpyapiypkvVKNVADGLTFEETKEmrnrglhspplmkltrngvYVNVVAKVREAFKTEEVVRldcshvgtndckkigvklrdlvpcvpilfkdEQIILWRgkeqamdsdplidptnp
Flexible Loop (DISEMBL)
mlaklpktlktlnlipvkkQNLLLFTQIHSSSEYIDDDPPFSPKRQKpqnprtqqnppvpssntnklplKSDLPFDFKYSYSENnpavepigfrepkrfspfgpgrldrkwtgttalapkevdrvrfeeernrvlgdplteEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLeeksggkiiyrNINILLlyrgrnydpkDRPVIPLMLWRPYAPIYPKVVKNVADGLTFEETKemrnrglhspplmkltrngVYVNVVAKVREAfkteevvrldcshvgtndckkigvklrdlvpcvPILFKDEQIILWrgkeqamdsdplidptnp
Low Complexity Region (SEG)
MLAKLPKTLKTLNLIPVKKQNLLLFTQIHSSSEYIDDDPPFSPKRQKPQNPRTQQNPPVPSSNTNKLPLKSDLPFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALAPKEVDRVRFEEERNRVLGDPLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKiiyrninilllyrGRNYDPKDRPVIPLMLWRPYAPIYPKVVKNVADGLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWRGKEQAMDSDPLIDPTNP
Disordered region (IsUnstruct)
********LKTLNLIPVKKQNLLLFTQIH********************************************************************************KWTGTTAL****************VLGDPLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNINILLLYRGRNYDPKDRPVIPLMLWRPYAPIYPKVVKNVADGLTFEE************PLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWRG****************
Disordered Region (DISOPRED)
************************************************************************LPF********************************************************************IAELVERY********INLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNINILLLYRGRNYDPKDRPVIPLMLWRP*************************NRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWRGKEQA************
Disordered Region (DISEMBL)
MLAKLPKTLKTLNLIPVKKQNLLLFTQIHSSSEYIDDDPP***********************TNKLPLKSDLPFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALAPKEVDRVRFEEERNRVLGDPLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNINILLLYRGRNYDPKDRPVIPLMLWRPYAPIYPKVVKNVADGLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWRGKEQA************
Disordered Region (DISPRO)
****LPKTLKTLNLIPVKKQNLLLFTQIHSSSEYIDDDPPF************************KLPLKSDLPFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALA******************DPLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNINILLLYRGRNYDPKDRPVIPLMLWRPYAPIYPKVVKNVADGLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWRGKEQAMDSDPLIDP***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLAKLPKTLKTLNLIPVKKQNLLLFTQIHSSSEYIDDDPPFSPKRQKPQNPRTQQNPPVPSSNTNKLPLKSDLPFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALAPKEVDRVRFEEERNRVLGDPLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNINILLLYRGRNYDPKDRPVIPLMLWRPYAPIYPKVVKNVADGLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWRGKEQAMDSDPLIDPTNP
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	359	2.2.26 [Sep-21-2011]
Q9FFU1	358	CRS2-associated factor 2,	yes	no	0.941	0.944	0.702	1e-142
Q0J7J7	366	CRS2-associated factor 2,	yes	no	0.796	0.781	0.772	1e-129
Q6Z4U2	428	CRS2-associated factor 1,	no	no	0.766	0.642	0.547	2e-88
Q8VYD9	405	CRS2-associated factor 1,	no	no	0.793	0.703	0.545	3e-87
Q84N49	674	CRS2-associated factor 1,	N/A	no	0.768	0.409	0.443	8e-74
Q9SL79	701	CRS2-associated factor 1,	no	no	0.746	0.382	0.453	1e-73
Q5VMQ5	701	CRS2-associated factor 1,	no	no	0.768	0.393	0.443	2e-73
Q84N48	611	CRS2-associated factor 2,	N/A	no	0.777	0.456	0.444	1e-72
Q657G7	607	CRS2-associated factor 2,	no	no	0.777	0.459	0.438	2e-71
Q9LDA9	564	CRS2-associated factor 2,	no	no	0.746	0.475	0.447	2e-69

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

 Score =  505 bits (1300), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 243/346 (70%), Positives = 284/346 (82%), Gaps = 8/346 (2%)

Query: 10  KTLNLIPVKKQNLLLFTQIHSSSEYIDD-DPPFSP-------KRQKPQNPRTQQNPPVPS 61
           ++L L    K   L    + +     DD DPPFSP        ++K +    +Q+     
Sbjct: 6   RSLTLAKEPKDLFLFLCNLRARCVSTDDYDPPFSPLSKPTKPPKEKKKQKTKKQDQSSEL 65

Query: 62  SNTNKLPLKSDLPFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALAPKE 121
            N  K+P+ SDLPFDF+YSYSE NP +EPIGFREPKRFSPFGPGRLDRKWTGTTALA  E
Sbjct: 66  VNDLKIPVISDLPFDFRYSYSETNPEIEPIGFREPKRFSPFGPGRLDRKWTGTTALASPE 125

Query: 122 VDRVRFEEERNRVLGDPLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKR 181
           +D+ ++ EER RVLG+ LTE+E+ EL+ERYRHSDC RQINLGK GVTHNM+DD+HNHWK+
Sbjct: 126 IDQSQWVEERARVLGETLTEDEVTELIERYRHSDCTRQINLGKGGVTHNMIDDIHNHWKK 185

Query: 182 AEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNINILLLYRGRNYDPKDRPVIPLMLW 241
           AEAVRIKCLGVPTLDMDN+CFHLEEKSGGKI+YRNINIL+LYRGRNYDPK RP+IPLMLW
Sbjct: 186 AEAVRIKCLGVPTLDMDNICFHLEEKSGGKIVYRNINILVLYRGRNYDPKSRPIIPLMLW 245

Query: 242 RPYAPIYPKVVKNVADGLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEE 301
           +P+ PIYP++VKNVADGL FEETKEMRNRGLHSP LMKLTRNGVYVNVV +VRE F+TEE
Sbjct: 246 KPHPPIYPRLVKNVADGLEFEETKEMRNRGLHSPALMKLTRNGVYVNVVGRVREEFETEE 305

Query: 302 VVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWRGKEQA 347
           +VRLDC+HVG +DCK+IGVKL+++VPCVPILFKDEQIILWRGK   
Sbjct: 306 IVRLDCTHVGMSDCKRIGVKLKEMVPCVPILFKDEQIILWRGKRTG 351

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 =  462 bits (1190), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 221/286 (77%), Positives = 248/286 (86%)

Query: 68  PLKSDLPFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALAPKEVDRVRF 127
           P  SDLPFDF+YSYSE +PA  PIGFREP RFSPFGPGRLDR W G  A A +       
Sbjct: 74  PASSDLPFDFRYSYSETDPAWRPIGFREPTRFSPFGPGRLDRPWDGVAAAAARGEGAGAA 133

Query: 128 EEERNRVLGDPLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRI 187
              R  VLG+PL EEE+A+LVERYRHSDC+RQINLGK GVTHNM+DD+HNHWKRAEAVRI
Sbjct: 134 ATSREEVLGEPLAEEEVAQLVERYRHSDCSRQINLGKGGVTHNMIDDIHNHWKRAEAVRI 193

Query: 188 KCLGVPTLDMDNVCFHLEEKSGGKIIYRNINILLLYRGRNYDPKDRPVIPLMLWRPYAPI 247
           KCLGVPTLDMDN+CFHLE+K+GGK+IYRNINIL+LYRGRNYDPK RP IPLMLW+P API
Sbjct: 194 KCLGVPTLDMDNICFHLEDKTGGKVIYRNINILILYRGRNYDPKQRPQIPLMLWKPLAPI 253

Query: 248 YPKVVKNVADGLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDC 307
           YP++V+NVADGLTFE+TKE+RN GL+S PLMKLTRNGVYVNVV +VREAFKT EVVRLDC
Sbjct: 254 YPRLVQNVADGLTFEKTKELRNTGLNSSPLMKLTRNGVYVNVVDRVREAFKTVEVVRLDC 313

Query: 308 SHVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWRGKEQAMDSDPL 353
           SHVG++DCKKIGVKLRDLVPCVP+LFKDEQIILWRGK +  +S  L
Sbjct: 314 SHVGSSDCKKIGVKLRDLVPCVPLLFKDEQIILWRGKVKQENSVSL 359

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  325 bits (834), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 160/292 (54%), Positives = 209/292 (71%), Gaps = 17/292 (5%)

Query: 70  KSDLPFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALAPKEVDRVRFEE 129
           +SDLPFDF++SY+E++P  +PIG REPK +SPFGPGRLDR WTG  A A     R    +
Sbjct: 73  RSDLPFDFRFSYTESSPGDKPIGLREPK-YSPFGPGRLDRPWTGLCAPAVDTTLRDAHAD 131

Query: 130 ERNR----------------VLGDPLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLD 173
           +                   VLG+PLT  E A LV + + S   +QINLG+ G+THNML+
Sbjct: 132 DPAPAAERELEEARRRERERVLGEPLTPAERAFLVSKCQKSRTKKQINLGRDGLTHNMLN 191

Query: 174 DLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNINILLLYRGRNYDPKDR 233
           D+HNHWK  EAVR+KCLGVPT+DM NVC  LE+K+GG II+R+   L+LYRGR+Y+PK R
Sbjct: 192 DIHNHWKNDEAVRVKCLGVPTVDMQNVCHQLEDKTGGLIIHRHGGQLILYRGRHYNPKKR 251

Query: 234 PVIPLMLWRPYAPIYPKVVKNVADGLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKV 293
           PVIPLMLW+P  P+YP+++K   +GLT EETKEMR +GL+ P L KL +NG Y ++V  V
Sbjct: 252 PVIPLMLWKPAEPVYPRLIKTTIEGLTVEETKEMRKKGLYVPVLTKLAKNGYYASLVPMV 311

Query: 294 REAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWRGKE 345
           R+AF T+E+VR+D   +  +D +KIGVKLRDLVPC+ + F  EQII+WRGK+
Sbjct: 312 RDAFLTDELVRIDSKGLPKSDYRKIGVKLRDLVPCIIVSFDKEQIIVWRGKD 363

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  322 bits (824), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 162/297 (54%), Positives = 211/297 (71%), Gaps = 12/297 (4%)

Query: 60  PSSNTNKLPLKSDLPFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALA- 118
           PSS      + SDLPFDF++SY+E+   V PIG REPK +SPFGP RLDR+WTG  A A 
Sbjct: 70  PSSLEGVKTVHSDLPFDFRFSYTESCSNVRPIGLREPK-YSPFGPDRLDREWTGVCAPAV 128

Query: 119 -PK--EVDRV---RFEEERNRV----LGDPLTEEEIAELVERYRHSDCARQINLGKWGVT 168
            PK   VD V   + EE+R +V     G  LTE E   LVE  + +   RQ+NLG+ G+T
Sbjct: 129 NPKVESVDGVEDPKLEEKRRKVREKIQGASLTEAERKFLVELCQRNKTKRQVNLGRDGLT 188

Query: 169 HNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNINILLLYRGRNY 228
           HNML+D++NHWK AEAVR+KCLGVPTLDM NV FHLE+K+ G+++ ++   L+LYRGRNY
Sbjct: 189 HNMLNDVYNHWKHAEAVRVKCLGVPTLDMKNVIFHLEDKTFGQVVSKHSGTLVLYRGRNY 248

Query: 229 DPKDRPVIPLMLWRPYAPIYPKVVKNVADGLTFEETKEMRNRGLHSPPLMKLTRNGVYVN 288
           DPK RP IPLMLW+P+ P+YP+++K   DGL+ +ETK MR +GL  P L KL +NG Y +
Sbjct: 249 DPKKRPKIPLMLWKPHEPVYPRLIKTTIDGLSIDETKAMRKKGLAVPALTKLAKNGYYGS 308

Query: 289 VVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWRGKE 345
           +V  VR+AF   E+VR+DC  +   D KKIG KLRDLVPC+ + F  EQ+++WRGK+
Sbjct: 309 LVPMVRDAFLVSELVRIDCLGLERKDYKKIGAKLRDLVPCILVTFDKEQVVIWRGKD 365

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  277 bits (709), Expect = 8e-74,   Method: Compositional matrix adjust.
 Identities = 138/311 (44%), Positives = 191/311 (61%), Gaps = 35/311 (11%)

Query: 74  PFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALAPKEVDRVRFEE---- 129
           PF+F+YSY+E  P   P+  RE   F PFGP    R WTG   L     +   F+     
Sbjct: 91  PFEFQYSYTEA-PRARPVALREAP-FMPFGPEATPRPWTGRKPLPKSRKELPEFDSFVLP 148

Query: 130 ---------------------------ERNRVLGDPLTEEEIAELVERYRHSDCARQINL 162
                                       R  +LG+PLT+EE++ELV+    S   RQ+N+
Sbjct: 149 APGKKGVKPVQSPGPFLAGMEPRYQSVSREDILGEPLTKEEVSELVKGSLKSK--RQLNM 206

Query: 163 GKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNINILLL 222
           G+ G+THNML+++H+HWKR    +IKC GV T+DMDN+C  LEEK GGK+I+R   ++ L
Sbjct: 207 GRDGLTHNMLENIHSHWKRKRVCKIKCKGVCTIDMDNICHQLEEKVGGKVIHRQGGVIFL 266

Query: 223 YRGRNYDPKDRPVIPLMLWRPYAPIYPKVVKNVADGLTFEETKEMRNRGLHSPPLMKLTR 282
           +RGRNY+ + RP  PLMLW+P AP+YP++V  V  GLT +E  EMR RG   PP+ KL +
Sbjct: 267 FRGRNYNYRTRPCFPLMLWKPVAPVYPRLVTKVPGGLTPDEATEMRTRGHQLPPICKLGK 326

Query: 283 NGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWR 342
           NGVY N+V +VREAF+  ++VR+DCS +  +DC+KIG KL+DLVPC+ + F+ E I++WR
Sbjct: 327 NGVYANLVNQVREAFEACDLVRVDCSGLNKSDCRKIGAKLKDLVPCILLSFEFEHILMWR 386

Query: 343 GKEQAMDSDPL 353
           G +      PL
Sbjct: 387 GSDWKSSLPPL 397

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

 Score =  276 bits (707), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 137/302 (45%), Positives = 194/302 (64%), Gaps = 34/302 (11%)

Query: 74  PFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTAL-----APKEVDRVR-- 126
           PF+FKYSY+E  P V+P+  REP  ++PFGP  + R WTG   L      P+E D  R  
Sbjct: 150 PFEFKYSYTET-PKVKPLKLREPA-YAPFGPTTMGRPWTGRAPLPQSQKTPREFDSFRLP 207

Query: 127 -----------------------FEEERNRVLGDPLTEEEIAELVERYRHSDCARQINLG 163
                                  +   +  +LG+PLT+EE+ ELV     +   RQ+N+G
Sbjct: 208 PVGKKGLKPVQKPGPFRPGVGPRYVYSKEEILGEPLTKEEVRELVTSCLKT--TRQLNMG 265

Query: 164 KWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNINILLLY 223
           + G+THNML+++H+ WKR    +IKC GV T+DMDNVC  LEEK GGK+IYR   +L L+
Sbjct: 266 RDGLTHNMLNNIHDLWKRRRVCKIKCKGVCTVDMDNVCEQLEEKIGGKVIYRRGGVLFLF 325

Query: 224 RGRNYDPKDRPVIPLMLWRPYAPIYPKVVKNVADGLTFEETKEMRNRGLHSPPLMKLTRN 283
           RGRNY+ + RP  PLMLW+P AP+YP++++ V +GLT +E   MR +G    P+ KL +N
Sbjct: 326 RGRNYNHRTRPRFPLMLWKPVAPVYPRLIQQVPEGLTRQEATNMRRKGRELMPICKLGKN 385

Query: 284 GVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWRG 343
           GVY ++V  V+EAF+  E+VR+DC  +  +D +KIG KL+DLVPCV + F++EQI++WRG
Sbjct: 386 GVYCDLVKNVKEAFEVCELVRIDCQGMKGSDFRKIGAKLKDLVPCVLVSFENEQILIWRG 445

Query: 344 KE 345
           +E
Sbjct: 446 RE 447

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

 Score =  276 bits (705), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 138/311 (44%), Positives = 193/311 (62%), Gaps = 35/311 (11%)

Query: 74  PFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALAPKEVDRVRFEE---- 129
           PF+F+YSY+E  P   P+  RE   F PFGP    R WTG   L     +   F+     
Sbjct: 91  PFEFQYSYTET-PRARPVALREAP-FLPFGPEVTPRPWTGRKPLPKSRKELPEFDSFMLP 148

Query: 130 ---------------------------ERNRVLGDPLTEEEIAELVERYRHSDCARQINL 162
                                       R  VLG+PLT+EE+ ELV+    +   RQ+N+
Sbjct: 149 PPGKKGVKPVQSPGPFLAGTEPRYQAASREEVLGEPLTKEEVDELVKATLKTK--RQLNI 206

Query: 163 GKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNINILLL 222
           G+ G+THNML+++H+HWKR    +IKC GV T+DMDNVC  LEEK GGK+I+    ++ L
Sbjct: 207 GRDGLTHNMLENIHSHWKRKRVCKIKCKGVCTVDMDNVCQQLEEKVGGKVIHHQGGVIFL 266

Query: 223 YRGRNYDPKDRPVIPLMLWRPYAPIYPKVVKNVADGLTFEETKEMRNRGLHSPPLMKLTR 282
           +RGRNY+ + RP+ PLMLW+P AP+YP++VK + DGLT +E ++MR RG   PP+ KL +
Sbjct: 267 FRGRNYNYRTRPIYPLMLWKPAAPVYPRLVKKIPDGLTPDEAEDMRKRGRQLPPICKLGK 326

Query: 283 NGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWR 342
           NGVY+N+V +VREAF+  ++VR+DCS +  +DC+KIG KL+DLVPC  + F+ E I++WR
Sbjct: 327 NGVYLNLVKQVREAFEACDLVRVDCSGLNKSDCRKIGAKLKDLVPCTLLSFEFEHILMWR 386

Query: 343 GKEQAMDSDPL 353
           G +      PL
Sbjct: 387 GNDWKSSLPPL 397

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 =  273 bits (699), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 145/326 (44%), Positives = 196/326 (60%), Gaps = 47/326 (14%)

Query: 60  PSSNTNKLPLKSDLPFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALAP 119
           PS  + +LP     PFDF++SYSE  P   P+  REP  F PF P  + R WTG   L  
Sbjct: 120 PSGLSFRLP---GAPFDFQFSYSEA-PRAPPLAIREPA-FLPFAPPTMPRPWTGKAPLLT 174

Query: 120 KE--------------------------------------VDRVRFEEERNR--VLGDPL 139
           KE                                      + RV   + R+R  VLG+PL
Sbjct: 175 KEEKARRRGVRLHTPLGQETPQTVSAHGIMMEVRERRKMDLARVSPGDGRSREEVLGEPL 234

Query: 140 TEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDN 199
           T  E+  LV+   H    RQ+N+G+ G+THNML+ +H HW+R E  +++C GVPT+DM N
Sbjct: 235 TPSEVRALVKP--HISHNRQLNIGRDGLTHNMLEMIHCHWRRQEICKVRCRGVPTVDMKN 292

Query: 200 VCFHLEEKSGGKIIYRNINILLLYRGRNYDPKDRPVIPLMLWRPYAPIYPKVVKNVADGL 259
           +C+HLEEKSGGK+I+R   ++ LYRGR+YDPK RP  PLMLW+P  P+YPK++K   DG 
Sbjct: 293 LCYHLEEKSGGKVIHRVGGVVFLYRGRHYDPKTRPRYPLMLWKPATPVYPKLIKEAPDGF 352

Query: 260 TFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIG 319
           T EE  EMR +G    P+ KL +NG+Y+ +V  VR+AF+  ++V++DC  +  +D KKIG
Sbjct: 353 TKEEADEMRRKGRDLLPICKLAKNGIYITLVKDVRDAFEGSDLVKIDCEGLNPSDYKKIG 412

Query: 320 VKLRDLVPCVPILFKDEQIILWRGKE 345
            KLRDLVPCV + F DEQI++ RGKE
Sbjct: 413 AKLRDLVPCVLLSFDDEQILMHRGKE 438

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

 Score =  270 bits (689), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 143/326 (43%), Positives = 199/326 (61%), Gaps = 47/326 (14%)

Query: 60  PSSNTNKLPLKSDLPFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALAP 119
           PS  + +LP     PFDF++SYSE  P   P+  REP  F PF P  + R WTG   L  
Sbjct: 116 PSGLSFRLP---GAPFDFRFSYSEC-PRAPPVAIREPA-FLPFAPPTMPRPWTGKAPLLT 170

Query: 120 KE--------------------------------------VDRVRFEEERNR--VLGDPL 139
           KE                                      + RV   + R+R  VLG+PL
Sbjct: 171 KEEKARRRGVRLHTPLGEEAPRTVSAHGIMMEVRGRRKLDLARVSPGDGRSREEVLGEPL 230

Query: 140 TEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDN 199
           T  E+ +LV+   H    RQ+N+G+ G+THNML+ +H HW+R E  +++C GVPT+DM N
Sbjct: 231 TAAEVRDLVKP--HISHNRQLNIGRDGLTHNMLEMIHCHWRRQEICKVRCRGVPTVDMKN 288

Query: 200 VCFHLEEKSGGKIIYRNINILLLYRGRNYDPKDRPVIPLMLWRPYAPIYPKVVKNVADGL 259
           +C+HLEEKSGGK+I+R   ++ LYRGRNY+P+ RP  PLMLW+P  P+YPK+++   +GL
Sbjct: 289 LCYHLEEKSGGKVIHRVGGVVFLYRGRNYNPRTRPRYPLMLWKPATPVYPKLIQEAPEGL 348

Query: 260 TFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIG 319
           T EE  EMR RG    P+ KL +NG+Y+ +V  VR+AF+  ++V++DC  +  +D KKIG
Sbjct: 349 TKEEADEMRRRGKDLLPICKLAKNGIYIYLVRDVRDAFEGSDLVKIDCEGLNPSDYKKIG 408

Query: 320 VKLRDLVPCVPILFKDEQIILWRGKE 345
            KLRDLVPCV + F +EQI+++RGKE
Sbjct: 409 AKLRDLVPCVLLSFDNEQILMFRGKE 434

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 =  263 bits (672), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 135/302 (44%), Positives = 191/302 (63%), Gaps = 34/302 (11%)

Query: 74  PFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALA--------------- 118
           PF+F++SYSE  P V+P+G REP  F PF P  + R WTG   L                
Sbjct: 110 PFEFQFSYSET-PKVKPVGIREPA-FMPFAPPTMPRPWTGKAPLKKSKKKIPLFDSFNPP 167

Query: 119 PKEVDRVRFEE---------------ERNRVLGDPLTEEEIAELVERYRHSDCARQINLG 163
           P     V++ E                R  VLG+PL   E   L++ + H +  RQ+NLG
Sbjct: 168 PAGKSGVKYVEMPGPLPFGRYPKEGMNREEVLGEPLKRWEKGMLIKPHMHDN--RQVNLG 225

Query: 164 KWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNINILLLY 223
           + G THNML+ +H+HWKR    +++C GVPT+DM+NVC  LEEK+GG+II+R   ++ L+
Sbjct: 226 RDGFTHNMLELIHSHWKRRRVCKVRCKGVPTVDMNNVCRVLEEKTGGEIIHRVGGVVYLF 285

Query: 224 RGRNYDPKDRPVIPLMLWRPYAPIYPKVVKNVADGLTFEETKEMRNRGLHSPPLMKLTRN 283
           RGRNY+ + RP  PLMLW+P AP+YPK+++ V +GLT EE  E R +G    P+ KL++N
Sbjct: 286 RGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEVPEGLTKEEAHEFRVKGKSLRPICKLSKN 345

Query: 284 GVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWRG 343
           GVYV++V  VR+AF+   +V++DC  +  +D KKIG KL++LVPCV + F DEQI++WRG
Sbjct: 346 GVYVSLVKDVRDAFELSSLVKVDCPGLEPSDYKKIGAKLKELVPCVLLSFDDEQILMWRG 405

Query: 344 KE 345
           +E
Sbjct: 406 RE 407

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)

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	359
224124340	354	predicted protein [Populus trichocarpa]	0.944	0.957	0.763	1e-147
15240416	358	CRS2-associated factor 2 [Arabidopsis th	0.941	0.944	0.702	1e-140
225461009	452	PREDICTED: CRS2-associated factor 2, mit	0.791	0.628	0.809	1e-138
449468496	358	PREDICTED: CRS2-associated factor 2, mit	0.871	0.874	0.755	1e-137
297737420	343	unnamed protein product [Vitis vinifera]	0.832	0.871	0.773	1e-136
297792957	362	hypothetical protein ARALYDRAFT_331830 [	0.935	0.928	0.719	1e-136
255563935	409	conserved hypothetical protein [Ricinus	0.927	0.814	0.749	1e-133
356496030	358	PREDICTED: CRS2-associated factor 2, mit	0.888	0.891	0.719	1e-128
226530577	362	LOC100281604 [Zea mays] gi|195615022|gb|	0.768	0.762	0.783	1e-128
356530475	388	PREDICTED: CRS2-associated factor 2, mit	0.888	0.822	0.716	1e-128

>gi|224124340|ref|XP_002319307.1| predicted protein [Populus trichocarpa] gi|222857683|gb|EEE95230.1| predicted protein [Populus trichocarpa]

 Score =  527 bits (1357), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 262/343 (76%), Positives = 294/343 (85%), Gaps = 4/343 (1%)

Query: 10  KTLNLIPVKKQNLLLFTQIHSSSEYIDDDPPFS-PKRQKPQNPRTQQNPPVPSSNTNKLP 68
           KTL   P  K   + +   H+ S+    DPPFS  K+ KP+N    +  P P+ N  KLP
Sbjct: 11  KTLTQNPKSKSLYVSYFLNHTLSQ-DQYDPPFSLTKKPKPKNTTEPKETPDPN-NHPKLP 68

Query: 69  LKSDLPFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALAPKEVDRVRFE 128
           +KSDL FDF+YSYSE+NPA+EPIG+REPKRFSPFGPGRLDRKWTGT A    E D  +  
Sbjct: 69  VKSDLAFDFRYSYSESNPAIEPIGYREPKRFSPFGPGRLDRKWTGTAAPTQLETDMDKLM 128

Query: 129 EERNRVLGDPLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIK 188
           EERNRVLGDPLTEEE+AELVERYRHSDC+RQINLGK GVTHNMLDD+HNHWKRAEAVRIK
Sbjct: 129 EERNRVLGDPLTEEEVAELVERYRHSDCSRQINLGKGGVTHNMLDDIHNHWKRAEAVRIK 188

Query: 189 CLGVPTLDMDNVCFHLEEKSGGKIIYRNINILLLYRGRNYDPKDRPVIPLMLWRPYAPIY 248
           CLGVPTLDMDNVCFHLE+KSGGK++YRNINILLLYRGRNYDP++RPVIPLMLW+PYAPIY
Sbjct: 189 CLGVPTLDMDNVCFHLEDKSGGKVVYRNINILLLYRGRNYDPENRPVIPLMLWKPYAPIY 248

Query: 249 PKVVKNVADGLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCS 308
           PK+VKNVADGLTFEETKEMRNRGL+S PLMKLTRNGVYVNVV +VR+AF+TEEVVRLDC 
Sbjct: 249 PKLVKNVADGLTFEETKEMRNRGLNSLPLMKLTRNGVYVNVVDRVRDAFETEEVVRLDCK 308

Query: 309 HVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWRGKE-QAMDS 350
           HVG +DCKKIGVKL+DLVPCVPILFKDEQIILWRGK  Q ++S
Sbjct: 309 HVGMSDCKKIGVKLKDLVPCVPILFKDEQIILWRGKRNQELES 351

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15240416|ref|NP_200300.1| CRS2-associated factor 2 [Arabidopsis thaliana] gi|75170294|sp|Q9FFU1.1|CAF2M_ARATH RecName: Full=CRS2-associated factor 2, mitochondrial; Flags: Precursor gi|9758269|dbj|BAB08768.1| unnamed protein product [Arabidopsis thaliana] gi|332009170|gb|AED96553.1| CRS2-associated factor 2 [Arabidopsis thaliana]

 Score =  505 bits (1300), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 243/346 (70%), Positives = 284/346 (82%), Gaps = 8/346 (2%)

Query: 10  KTLNLIPVKKQNLLLFTQIHSSSEYIDD-DPPFSP-------KRQKPQNPRTQQNPPVPS 61
           ++L L    K   L    + +     DD DPPFSP        ++K +    +Q+     
Sbjct: 6   RSLTLAKEPKDLFLFLCNLRARCVSTDDYDPPFSPLSKPTKPPKEKKKQKTKKQDQSSEL 65

Query: 62  SNTNKLPLKSDLPFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALAPKE 121
            N  K+P+ SDLPFDF+YSYSE NP +EPIGFREPKRFSPFGPGRLDRKWTGTTALA  E
Sbjct: 66  VNDLKIPVISDLPFDFRYSYSETNPEIEPIGFREPKRFSPFGPGRLDRKWTGTTALASPE 125

Query: 122 VDRVRFEEERNRVLGDPLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKR 181
           +D+ ++ EER RVLG+ LTE+E+ EL+ERYRHSDC RQINLGK GVTHNM+DD+HNHWK+
Sbjct: 126 IDQSQWVEERARVLGETLTEDEVTELIERYRHSDCTRQINLGKGGVTHNMIDDIHNHWKK 185

Query: 182 AEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNINILLLYRGRNYDPKDRPVIPLMLW 241
           AEAVRIKCLGVPTLDMDN+CFHLEEKSGGKI+YRNINIL+LYRGRNYDPK RP+IPLMLW
Sbjct: 186 AEAVRIKCLGVPTLDMDNICFHLEEKSGGKIVYRNINILVLYRGRNYDPKSRPIIPLMLW 245

Query: 242 RPYAPIYPKVVKNVADGLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEE 301
           +P+ PIYP++VKNVADGL FEETKEMRNRGLHSP LMKLTRNGVYVNVV +VRE F+TEE
Sbjct: 246 KPHPPIYPRLVKNVADGLEFEETKEMRNRGLHSPALMKLTRNGVYVNVVGRVREEFETEE 305

Query: 302 VVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWRGKEQA 347
           +VRLDC+HVG +DCK+IGVKL+++VPCVPILFKDEQIILWRGK   
Sbjct: 306 IVRLDCTHVGMSDCKRIGVKLKEMVPCVPILFKDEQIILWRGKRTG 351

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225461009|ref|XP_002278505.1| PREDICTED: CRS2-associated factor 2, mitochondrial-like [Vitis vinifera]

 Score =  496 bits (1277), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 230/284 (80%), Positives = 257/284 (90%)

Query: 61  SSNTNKLPLKSDLPFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALAPK 120
           S      P KSDLPFDF+YSYSE NP+V PIGFREP RFSPFGP RLDRKWTGT A A +
Sbjct: 70  SKKGQTFPFKSDLPFDFRYSYSEANPSVHPIGFREPPRFSPFGPARLDRKWTGTAAPAEE 129

Query: 121 EVDRVRFEEERNRVLGDPLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWK 180
            VD     E+R  VLG+PL+E+EIAELVERYRHSDC+RQINLGK GVTHNMLDD+HNHWK
Sbjct: 130 VVDPAVVSEQRKAVLGEPLSEDEIAELVERYRHSDCSRQINLGKGGVTHNMLDDIHNHWK 189

Query: 181 RAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNINILLLYRGRNYDPKDRPVIPLML 240
           RAEAVRIKCLGVPTLDM+NVCFHLE+K GGKIIYRNINI+LLYRGRNYDPK+RPV+PLML
Sbjct: 190 RAEAVRIKCLGVPTLDMENVCFHLEDKCGGKIIYRNINIILLYRGRNYDPKNRPVVPLML 249

Query: 241 WRPYAPIYPKVVKNVADGLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTE 300
           W+PYAPIYPK+VK VADGLTFEETKEMRNRGL+ PP+MKLT+NGVYVNVV +VREAF++E
Sbjct: 250 WKPYAPIYPKLVKPVADGLTFEETKEMRNRGLNLPPVMKLTKNGVYVNVVERVREAFRSE 309

Query: 301 EVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWRGK 344
           EVVRLDC+HVG++DCK+IGVKLRDLVPCVPILFKDEQIILW+GK
Sbjct: 310 EVVRLDCTHVGSSDCKRIGVKLRDLVPCVPILFKDEQIILWKGK 353

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449468496|ref|XP_004151957.1| PREDICTED: CRS2-associated factor 2, mitochondrial-like [Cucumis sativus] gi|449489970|ref|XP_004158472.1| PREDICTED: CRS2-associated factor 2, mitochondrial-like [Cucumis sativus]

 Score =  494 bits (1272), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 241/319 (75%), Positives = 278/319 (87%), Gaps = 6/319 (1%)

Query: 38  DPPFSPKRQKPQNPRTQQNPPVPSSNTNK---LPLKSDLPFDFKYSYSENNPAVEPIGFR 94
           DPPFSP  +  +  + ++     +SN+N+   LPLKS LPFDF YSYSE NP V PIG+R
Sbjct: 40  DPPFSPVSKLQKAKKKKEKAHGGNSNSNENPTLPLKSYLPFDFFYSYSETNPLVSPIGYR 99

Query: 95  EPKRFSPFGPGRLDRKWTGTTALAPKEVDRVRFEEERNRVLGDPLTEEEIAELVERYRHS 154
           E  +FSPFGPGRLDRKWTGT+A +  EV+     EER R+LGDPL +EE+AELVE+YRHS
Sbjct: 100 ESPKFSPFGPGRLDRKWTGTSAPSAVEVNINEVLEERKRILGDPLLDEEVAELVEQYRHS 159

Query: 155 DCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIY 214
           DC+RQINLGK GVTHNMLDD+HNHWKRAEAVRIKCLGVPTLDMDN+CFHLE+KSGGKIIY
Sbjct: 160 DCSRQINLGKGGVTHNMLDDIHNHWKRAEAVRIKCLGVPTLDMDNICFHLEDKSGGKIIY 219

Query: 215 RNINILLLYRGRNYDPKDRPVIPLMLWRPYAPIYPKVVKNVADGLTFEETKEMRNRGLHS 274
           R+INILLLYRGRNYDPK+RP IPLMLW+PYAPIYPK+VKNVAD L+F+ETKEMR+RGL+S
Sbjct: 220 RHINILLLYRGRNYDPKNRPAIPLMLWKPYAPIYPKLVKNVADDLSFDETKEMRSRGLNS 279

Query: 275 PPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFK 334
           PPLMKLTRNGVYVNVV +VREAFK EEVVRLDC+HVG++DCK+IGVKLRDLVPCVPILFK
Sbjct: 280 PPLMKLTRNGVYVNVVDRVREAFKFEEVVRLDCTHVGSSDCKQIGVKLRDLVPCVPILFK 339

Query: 335 DEQIILWRGK---EQAMDS 350
           +EQIILWRGK   E+ M+S
Sbjct: 340 NEQIILWRGKKDHEEDMNS 358

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297737420|emb|CBI26621.3| unnamed protein product [Vitis vinifera]

 Score =  491 bits (1265), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 236/305 (77%), Positives = 265/305 (86%), Gaps = 6/305 (1%)

Query: 46  QKPQNPRTQQNPPV-----PSSNTNK-LPLKSDLPFDFKYSYSENNPAVEPIGFREPKRF 99
           Q P  P    +PP      P  N  +  P KSDLPFDF+YSYSE NP+V PIGFREP RF
Sbjct: 30  QSPPLPDHIHDPPFSLTSNPKDNKGQTFPFKSDLPFDFRYSYSEANPSVHPIGFREPPRF 89

Query: 100 SPFGPGRLDRKWTGTTALAPKEVDRVRFEEERNRVLGDPLTEEEIAELVERYRHSDCARQ 159
           SPFGP RLDRKWTGT A A + VD     E+R  VLG+PL+E+EIAELVERYRHSDC+RQ
Sbjct: 90  SPFGPARLDRKWTGTAAPAEEVVDPAVVSEQRKAVLGEPLSEDEIAELVERYRHSDCSRQ 149

Query: 160 INLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNINI 219
           INLGK GVTHNMLDD+HNHWKRAEAVRIKCLGVPTLDM+NVCFHLE+K GGKIIYRNINI
Sbjct: 150 INLGKGGVTHNMLDDIHNHWKRAEAVRIKCLGVPTLDMENVCFHLEDKCGGKIIYRNINI 209

Query: 220 LLLYRGRNYDPKDRPVIPLMLWRPYAPIYPKVVKNVADGLTFEETKEMRNRGLHSPPLMK 279
           +LLYRGRNYDPK+RPV+PLMLW+PYAPIYPK+VK VADGLTFEETKEMRNRGL+ PP+MK
Sbjct: 210 ILLYRGRNYDPKNRPVVPLMLWKPYAPIYPKLVKPVADGLTFEETKEMRNRGLNLPPVMK 269

Query: 280 LTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQII 339
           LT+NGVYVNVV +VREAF++EEVVRLDC+HVG++DCK+IGVKLRDLVPCVPILFKDEQII
Sbjct: 270 LTKNGVYVNVVERVREAFRSEEVVRLDCTHVGSSDCKRIGVKLRDLVPCVPILFKDEQII 329

Query: 340 LWRGK 344
           LW+GK
Sbjct: 330 LWKGK 334

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297792957|ref|XP_002864363.1| hypothetical protein ARALYDRAFT_331830 [Arabidopsis lyrata subsp. lyrata] gi|297310198|gb|EFH40622.1| hypothetical protein ARALYDRAFT_331830 [Arabidopsis lyrata subsp. lyrata]

 Score =  491 bits (1263), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 244/339 (71%), Positives = 286/339 (84%), Gaps = 3/339 (0%)

Query: 12  LNLIPVKKQNLLLFTQIHSSSEYIDD-DPPFSPKRQKPQNPRTQQNPPVPSSNTN--KLP 68
           L L   +K   LL   + +     D+ DPPFSP  +  + P+ ++        ++  K+P
Sbjct: 9   LTLAKEQKDLFLLLCNLRARFVSTDNYDPPFSPLSKPTKPPKEKKKTKKKQDQSSELKIP 68

Query: 69  LKSDLPFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALAPKEVDRVRFE 128
           + SDLPFDF+YSYSE NP +EPIGFREPKRFSPFGPGRLDRKWTGT+AL   E+D+ ++ 
Sbjct: 69  MISDLPFDFRYSYSETNPEIEPIGFREPKRFSPFGPGRLDRKWTGTSALVSPEIDQSQWV 128

Query: 129 EERNRVLGDPLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIK 188
           EER RVLG+PLTEEE+ ELVERYRHSDC+RQINLGK GVTHNM+DD+HNHWK+AEAVRIK
Sbjct: 129 EERARVLGEPLTEEEVTELVERYRHSDCSRQINLGKGGVTHNMIDDIHNHWKKAEAVRIK 188

Query: 189 CLGVPTLDMDNVCFHLEEKSGGKIIYRNINILLLYRGRNYDPKDRPVIPLMLWRPYAPIY 248
           CLGVPTLDMDN+CFHLEEKSGGKI+YR+INIL+LYRGRNYDPK RP+IPLMLW+PY PIY
Sbjct: 189 CLGVPTLDMDNICFHLEEKSGGKIVYRHINILVLYRGRNYDPKSRPIIPLMLWKPYPPIY 248

Query: 249 PKVVKNVADGLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCS 308
           P++VKNVADGLTFEETKEMRNRG+HSP LMKLTRNGVYVNVV +VRE F+TEE+VRLDC+
Sbjct: 249 PRLVKNVADGLTFEETKEMRNRGIHSPALMKLTRNGVYVNVVGRVREEFETEEIVRLDCT 308

Query: 309 HVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWRGKEQA 347
           HVG +DCK+IGVKL+DLVPCVPILFKDEQIILWRGK   
Sbjct: 309 HVGMSDCKRIGVKLKDLVPCVPILFKDEQIILWRGKRNG 347

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255563935|ref|XP_002522967.1| conserved hypothetical protein [Ricinus communis] gi|223537779|gb|EEF39397.1| conserved hypothetical protein [Ricinus communis]

 Score =  479 bits (1233), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 254/339 (74%), Positives = 286/339 (84%), Gaps = 6/339 (1%)

Query: 10  KTLNLIPVKKQ-NLLLFTQIHSSSEYIDDDPPFSPKRQKPQNPRTQQNPPVPSSNTNK-- 66
           KTL   P     N   +   H+ SE + D PPF+    KP+  +   N P  + N NK  
Sbjct: 54  KTLTKTPASYPFNYFTYFLSHTLSEDLYD-PPFT-LASKPKAKKAPTNQPGSNENPNKDP 111

Query: 67  -LPLKSDLPFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALAPKEVDRV 125
            LPLKSDLPFDF+YSYSE++ A++PIG+REPKRFSPFGPGRLDRKWTG  A    EVD  
Sbjct: 112 KLPLKSDLPFDFRYSYSESDSAIQPIGYREPKRFSPFGPGRLDRKWTGVAAPVQSEVDME 171

Query: 126 RFEEERNRVLGDPLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAV 185
              EER RVLGDPLTEEE+ ELVERYRHSDC+RQINLGK GVTHNMLDD+HNHWK+AEAV
Sbjct: 172 IVMEERRRVLGDPLTEEEVEELVERYRHSDCSRQINLGKGGVTHNMLDDIHNHWKKAEAV 231

Query: 186 RIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNINILLLYRGRNYDPKDRPVIPLMLWRPYA 245
           RIKCLGVPTLDMDNVCFHLE+KSGGKIIYR+INILLLYRGRNYDPK+RPVIP+MLW+PYA
Sbjct: 232 RIKCLGVPTLDMDNVCFHLEDKSGGKIIYRHINILLLYRGRNYDPKNRPVIPIMLWKPYA 291

Query: 246 PIYPKVVKNVADGLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRL 305
           PI+PK+VKNVADGL+FEETKE+RNRGL+SP LMKLTRNGVYV VV +VREAF+TEEVVRL
Sbjct: 292 PIFPKLVKNVADGLSFEETKEIRNRGLNSPALMKLTRNGVYVYVVERVREAFQTEEVVRL 351

Query: 306 DCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWRGK 344
           DC+HVG++DCKKIGVKLRDLVPCVPILFKDEQIILWRGK
Sbjct: 352 DCTHVGSSDCKKIGVKLRDLVPCVPILFKDEQIILWRGK 390

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356496030|ref|XP_003516873.1| PREDICTED: CRS2-associated factor 2, mitochondrial-like [Glycine max]

 Score =  464 bits (1194), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 241/335 (71%), Positives = 277/335 (82%), Gaps = 16/335 (4%)

Query: 32  SEYIDD---DPPFSPKRQ---KPQNPRTQQNPPVPSSNTN-------KLPLKSDLPFDFK 78
           S +I D   DPPFSP  +   K +    ++     S N +       KLP KS+LPFDF+
Sbjct: 22  SHFIPDHQYDPPFSPSPKPYYKSKKNHAEKKKKNNSENGDPNKNGAPKLPFKSNLPFDFR 81

Query: 79  YSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALAPKEVDRVRFEEERNRVLGDP 138
           YSYSE++P+V PI FRE  +FSPFGPGR+DRKWTG +A    E DR R EEERNR+LG+P
Sbjct: 82  YSYSESDPSVGPISFRESPKFSPFGPGRIDRKWTGVSAPVQGEPDRERVEEERNRILGEP 141

Query: 139 LTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMD 198
           L+E E+AEL+ERYRHSDCARQINLGK GVTHNML D+HNHWK+AEAVRIKCLGVPTLDMD
Sbjct: 142 LSEVEVAELIERYRHSDCARQINLGKGGVTHNMLGDIHNHWKKAEAVRIKCLGVPTLDMD 201

Query: 199 NVCFHLEEKSGGKIIYRNINILLLYRGRNYDPKDRPVIPLMLWRPYAPIYPKVVKNVADG 258
           NVCFHLE+KSGGK+IYRNINILLLYRGRNYD K+ PVIPLMLW+PYAPIYP++VKNV +G
Sbjct: 202 NVCFHLEDKSGGKVIYRNINILLLYRGRNYDTKNCPVIPLMLWKPYAPIYPRLVKNVIEG 261

Query: 259 LTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKI 318
           LT+EETKEMR  GL+S PL+KLTRNGVYVNVV +VREAFKT+EVV+LDC HVGT+DCKKI
Sbjct: 262 LTYEETKEMRKSGLNSDPLLKLTRNGVYVNVVERVREAFKTQEVVKLDCIHVGTSDCKKI 321

Query: 319 GVKLRDLVPCVPILFKDEQIILWRG---KEQAMDS 350
           GVKLRDLVPCVPILFKDEQIILWRG   +EQ  DS
Sbjct: 322 GVKLRDLVPCVPILFKDEQIILWRGNFKEEQPSDS 356

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226530577|ref|NP_001147995.1| LOC100281604 [Zea mays] gi|195615022|gb|ACG29341.1| CRS2-associated factor 1 [Zea mays]

 Score =  463 bits (1192), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 217/277 (78%), Positives = 244/277 (88%), Gaps = 1/277 (0%)

Query: 68  PLKSDLPFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALAPKEVDRVRF 127
           P  SDLPFDF+YSYSE +P   PIGFREP RFSPFGPGRLDR W GT A    + D    
Sbjct: 71  PAHSDLPFDFRYSYSETDPTWRPIGFREPTRFSPFGPGRLDRPWDGTAAARVGD-DASGD 129

Query: 128 EEERNRVLGDPLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRI 187
           E  R  VLG+PL+EEE+A LVE+YRHSDC+RQINLGK GVTHNMLDD+HNHWKRAEAVRI
Sbjct: 130 ERSREEVLGEPLSEEEVAALVEKYRHSDCSRQINLGKGGVTHNMLDDIHNHWKRAEAVRI 189

Query: 188 KCLGVPTLDMDNVCFHLEEKSGGKIIYRNINILLLYRGRNYDPKDRPVIPLMLWRPYAPI 247
           KCLGVPTLDMDN+CFHLE+K+GGK++ R+INI++LYRGRNYDP+ RP +PLMLW+P API
Sbjct: 190 KCLGVPTLDMDNICFHLEDKTGGKVVSRSINIIILYRGRNYDPQKRPGVPLMLWKPLAPI 249

Query: 248 YPKVVKNVADGLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDC 307
           YPK+V+NVA+GLTFEETKE+RNRGL+SPPL KLTRNGVYVNVV KVREAFKT EVVRLDC
Sbjct: 250 YPKLVQNVAEGLTFEETKELRNRGLNSPPLTKLTRNGVYVNVVDKVREAFKTVEVVRLDC 309

Query: 308 SHVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWRGK 344
           +HVGT DCKKIGVKLRDLVPC+PILFKDEQIILWRGK
Sbjct: 310 THVGTTDCKKIGVKLRDLVPCIPILFKDEQIILWRGK 346

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356530475|ref|XP_003533806.1| PREDICTED: CRS2-associated factor 2, mitochondrial-like [Glycine max]

 Score =  463 bits (1191), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 240/335 (71%), Positives = 276/335 (82%), Gaps = 16/335 (4%)

Query: 32  SEYIDD---DPPFSPKRQ---KPQNPRTQQNPPVPSSNTN-------KLPLKSDLPFDFK 78
           S +I D   DPPFSP  +   K +    ++     S N +       KLP KS+LPFDF+
Sbjct: 22  SHFIPDHQYDPPFSPSPKPYYKSKKNHAEKKKKNNSENGDPNKNGAPKLPFKSNLPFDFR 81

Query: 79  YSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALAPKEVDRVRFEEERNRVLGDP 138
           YSYSE++P+V PI FRE  +FSPFGPGR+DRKWTG +A    E DR R EEERNR+LG+P
Sbjct: 82  YSYSESDPSVGPISFRESPKFSPFGPGRIDRKWTGVSAPVQGEPDRERVEEERNRILGEP 141

Query: 139 LTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMD 198
           L+E E+AEL+ERYRHSDCARQINLGK GVTHNML D+HNHWK+AE VRIKCLGVPTLDMD
Sbjct: 142 LSEVEVAELIERYRHSDCARQINLGKGGVTHNMLGDIHNHWKKAEVVRIKCLGVPTLDMD 201

Query: 199 NVCFHLEEKSGGKIIYRNINILLLYRGRNYDPKDRPVIPLMLWRPYAPIYPKVVKNVADG 258
           NVCFHLE+KSGGK+IYRNINILLLYRGRNYD K+ PVIPLMLW+PYAPIYP++VKNV +G
Sbjct: 202 NVCFHLEDKSGGKVIYRNINILLLYRGRNYDTKNCPVIPLMLWKPYAPIYPRLVKNVIEG 261

Query: 259 LTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKI 318
           LT+EETKEMR  GL+S PL+KLTRNGVYVNVV +VREAFKT+EVV+LDC HVGT+DCKKI
Sbjct: 262 LTYEETKEMRKSGLNSDPLLKLTRNGVYVNVVERVREAFKTQEVVKLDCIHVGTSDCKKI 321

Query: 319 GVKLRDLVPCVPILFKDEQIILWRG---KEQAMDS 350
           GVKLRDLVPCVPILFKDEQIILWRG   +EQ  DS
Sbjct: 322 GVKLRDLVPCVPILFKDEQIILWRGNFKEEQPSDS 356

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	359
TAIR|locus:2160195	358	AT5G54890 [Arabidopsis thalian	0.933	0.935	0.688	7.6e-128
TAIR|locus:2126694	405	AT4G31010 [Arabidopsis thalian	0.866	0.767	0.507	4.5e-82
TAIR|locus:2028100	564	CAF2 [Arabidopsis thaliana (ta	0.618	0.393	0.473	2.2e-69
TAIR|locus:2061604	701	CAF1 [Arabidopsis thaliana (ta	0.607	0.310	0.477	2.9e-68
TAIR|locus:2096662	1011	CFM2 "CRM family member 2" [Ar	0.298	0.105	0.263	1.2e-06

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

 Score = 1255 (446.8 bits), Expect = 7.6e-128, P = 7.6e-128
 Identities = 236/343 (68%), Positives = 272/343 (79%)

Query:    10 KTLNLIPVKKQNLLLFTQIHSSSEYIDD-DPPFSP--KRQKPQNPRTQQNPPVP--SS-- 62
             ++L L    K   L    + +     DD DPPFSP  K  KP   + +Q       SS  
Sbjct:     6 RSLTLAKEPKDLFLFLCNLRARCVSTDDYDPPFSPLSKPTKPPKEKKKQKTKKQDQSSEL 65

Query:    63 -NTNKLPLKSDLPFDFKYSYSENNPAVEPIGFREPKRFSPFGPGRLDRKWTGTTALAPKE 121
              N  K+P+ SDLPFDF+YSYSE NP +EPIGFREPKRFSPFGPGRLDRKWTGTTALA  E
Sbjct:    66 VNDLKIPVISDLPFDFRYSYSETNPEIEPIGFREPKRFSPFGPGRLDRKWTGTTALASPE 125

Query:   122 VDRVRFEEERNRVLGDPLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKR 181
             +D+ ++ EER RVLG+ LTE+E+ EL+ERYRHSDC RQINLGK GVTHNM+DD+HNHWK+
Sbjct:   126 IDQSQWVEERARVLGETLTEDEVTELIERYRHSDCTRQINLGKGGVTHNMIDDIHNHWKK 185

Query:   182 AEAVRIKCLGVPTLDMDNVCFHLEEKSGGKXXXXXXXXXXXXXGRNYDPKDRPVIPLMLW 241
             AEAVRIKCLGVPTLDMDN+CFHLEEKSGGK             GRNYDPK RP+IPLMLW
Sbjct:   186 AEAVRIKCLGVPTLDMDNICFHLEEKSGGKIVYRNINILVLYRGRNYDPKSRPIIPLMLW 245

Query:   242 RPYAPIYPKVVKNVADGLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEE 301
             +P+ PIYP++VKNVADGL FEETKEMRNRGLHSP LMKLTRNGVYVNVV +VRE F+TEE
Sbjct:   246 KPHPPIYPRLVKNVADGLEFEETKEMRNRGLHSPALMKLTRNGVYVNVVGRVREEFETEE 305

Query:   302 VVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWRGK 344
             +VRLDC+HVG +DCK+IGVKL+++VPCVPILFKDEQIILWRGK
Sbjct:   306 IVRLDCTHVGMSDCKRIGVKLKEMVPCVPILFKDEQIILWRGK 348

GO:0003723 "RNA binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 823 (294.8 bits), Expect = 4.5e-82, P = 4.5e-82
 Identities = 165/325 (50%), Positives = 214/325 (65%)

Query:    32 SEYIDDDPPFSPKRQKPQNPRTQQNPPVPSSNTNKLPLKSDLPFDFKYSYSENNPAVEPI 91
             S    ++P F+ K    + P+ Q  PP  SS      + SDLPFDF++SY+E+   V PI
Sbjct:    44 SSSASENPDFNQKNNNKKKPKPQYRPP--SSLEGVKTVHSDLPFDFRFSYTESCSNVRPI 101

Query:    92 GFREPKRFSPFGPGRLDRKWTGTTALA--PK--EVDRV---RFEEERNRVL----GDPLT 140
             G REPK +SPFGP RLDR+WTG  A A  PK   VD V   + EE+R +V     G  LT
Sbjct:   102 GLREPK-YSPFGPDRLDREWTGVCAPAVNPKVESVDGVEDPKLEEKRRKVREKIQGASLT 160

Query:   141 EEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNV 200
             E E   LVE  + +   RQ+NLG+ G+THNML+D++NHWK AEAVR+KCLGVPTLDM NV
Sbjct:   161 EAERKFLVELCQRNKTKRQVNLGRDGLTHNMLNDVYNHWKHAEAVRVKCLGVPTLDMKNV 220

Query:   201 CFHLEEKSGGKXXXXXXXXXXXXXGRNYDPKDRPVIPLMLWRPYAPIYPKVVKNVADGLT 260
              FHLE+K+ G+             GRNYDPK RP IPLMLW+P+ P+YP+++K   DGL+
Sbjct:   221 IFHLEDKTFGQVVSKHSGTLVLYRGRNYDPKKRPKIPLMLWKPHEPVYPRLIKTTIDGLS 280

Query:   261 FEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGV 320
              +ETK MR +GL  P L KL +NG Y ++V  VR+AF   E+VR+DC  +   D KKIG 
Sbjct:   281 IDETKAMRKKGLAVPALTKLAKNGYYGSLVPMVRDAFLVSELVRIDCLGLERKDYKKIGA 340

Query:   321 KLRDLVPCVPILFKDEQIILWRGKE 345
             KLRDLVPC+ + F  EQ+++WRGK+
Sbjct:   341 KLRDLVPCILVTFDKEQVVIWRGKD 365

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:2028100 CAF2 [Arabidopsis thaliana (taxid:3702)]

 Score = 565 (203.9 bits), Expect = 2.2e-69, Sum P(3) = 2.2e-69
 Identities = 107/226 (47%), Positives = 152/226 (67%)

Query:   131 RNRVLGDPLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCL 190
             R  VLG+PL   E   L++ + H +  RQ+NLG+ G THNML+ +H+HWKR    +++C 
Sbjct:   195 REEVLGEPLKRWEKGMLIKPHMHDN--RQVNLGRDGFTHNMLELIHSHWKRRRVCKVRCK 252

Query:   191 GVPTLDMDNVCFHLEEKSGGKXXXXXXXXXXXXXGRNYDPKDRPVIPLMLWRPYAPIYPK 250
             GVPT+DM+NVC  LEEK+GG+             GRNY+ + RP  PLMLW+P AP+YPK
Sbjct:   253 GVPTVDMNNVCRVLEEKTGGEIIHRVGGVVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPK 312

Query:   251 VVKNVADGLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHV 310
             +++ V +GLT EE  E R +G    P+ KL++NGVYV++V  VR+AF+   +V++DC  +
Sbjct:   313 LIQEVPEGLTKEEAHEFRVKGKSLRPICKLSKNGVYVSLVKDVRDAFELSSLVKVDCPGL 372

Query:   311 GTNDCKKIGVKLRDLVPCVPILFKDEQIILWRGKE--QAMDSDPLI 354
               +D KKIG KL++LVPCV + F DEQI++WRG+E       +PLI
Sbjct:   373 EPSDYKKIGAKLKELVPCVLLSFDDEQILMWRGREWKSRFVDNPLI 418

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

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

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

 Score = 570 (205.7 bits), Expect = 2.9e-68, Sum P(2) = 2.9e-68
 Identities = 105/220 (47%), Positives = 151/220 (68%)

Query:   126 RFEEERNRVLGDPLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAV 185
             R+   +  +LG+PLT+EE+ ELV     +   RQ+N+G+ G+THNML+++H+ WKR    
Sbjct:   230 RYVYSKEEILGEPLTKEEVRELVTSCLKT--TRQLNMGRDGLTHNMLNNIHDLWKRRRVC 287

Query:   186 RIKCLGVPTLDMDNVCFHLEEKSGGKXXXXXXXXXXXXXGRNYDPKDRPVIPLMLWRPYA 245
             +IKC GV T+DMDNVC  LEEK GGK             GRNY+ + RP  PLMLW+P A
Sbjct:   288 KIKCKGVCTVDMDNVCEQLEEKIGGKVIYRRGGVLFLFRGRNYNHRTRPRFPLMLWKPVA 347

Query:   246 PIYPKVVKNVADGLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRL 305
             P+YP++++ V +GLT +E   MR +G    P+ KL +NGVY ++V  V+EAF+  E+VR+
Sbjct:   348 PVYPRLIQQVPEGLTRQEATNMRRKGRELMPICKLGKNGVYCDLVKNVKEAFEVCELVRI 407

Query:   306 DCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQIILWRGKE 345
             DC  +  +D +KIG KL+DLVPCV + F++EQI++WRG+E
Sbjct:   408 DCQGMKGSDFRKIGAKLKDLVPCVLVSFENEQILIWRGRE 447

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

 Score = 103 (41.3 bits), Expect = 1.2e-06, Sum P(2) = 1.2e-06
 Identities = 29/110 (26%), Positives = 49/110 (44%)

Query:   120 KEVDRVRFEEERNRVLGD-PLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNH 178
             KE +  R +EE+   L +  L   E+  L  R       +++ +GK G+T  +++ +H  
Sbjct:   146 KETEMERKKEEKVPSLAELTLPPAELRRL--RTVGIRLTKKLKIGKAGITEGIVNGIHER 203

Query:   179 WKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKXXXXXXXXXXXXXGRNY 228
             W+  E V+I C  +  ++M      LE K+GG              G NY
Sbjct:   204 WRTTEVVKIFCEDISRMNMKRTHDVLETKTGGLVIWRSGSKILLYRGVNY 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

---

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)
Q0J7J7	CAF2M_ORYSJ	No assigned EC number	0.7727	0.7966	0.7814	yes	no
Q9FFU1	CAF2M_ARATH	No assigned EC number	0.7023	0.9415	0.9441	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: gw1.XIII.2995.1 hypothetical protein (276 aa) (Populus trichocarpa)

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	359
pfam01985	84	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	8e-20
smart01103	84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	2e-19
smart01103	84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	3e-17
pfam01985	84	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	8e-17

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

 Score = 82.5 bits (205), Expect = 8e-20
 Identities = 20/86 (23%), Positives = 42/86 (48%), Gaps = 2/86 (2%)

Query: 139 LTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMD 198
           LT ++   L     H      + +GK G+T  +++++    ++ E +++K LG    D  
Sbjct: 1   LTGKQRRYLRSLAHHLK--PVVQIGKNGLTEGVVEEIDEALEKHELIKVKVLGNDREDRK 58

Query: 199 NVCFHLEEKSGGKIIYRNINILLLYR 224
            +   L EK+G +++      ++LYR
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 = 81.4 bits (202), Expect = 2e-19
 Identities = 20/86 (23%), Positives = 42/86 (48%), Gaps = 2/86 (2%)

Query: 139 LTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMD 198
           LT ++   L     H      + +GK G+T  +L+++    ++ E +++K LG    D  
Sbjct: 1   LTGKQKRYLRSLAHHLKP--VVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRK 58

Query: 199 NVCFHLEEKSGGKIIYRNINILLLYR 224
            +   L E++G +++      ++LYR
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 = 75.6 bits (187), Expect = 3e-17
 Identities = 18/84 (21%), Positives = 44/84 (52%)

Query: 259 LTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKI 318
           LT ++ + +R+   H  P++++ +NG+   V+ ++ EA +  E++++        D K+I
Sbjct: 1   LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEI 60

Query: 319 GVKLRDLVPCVPILFKDEQIILWR 342
             +L +      +    + I+L+R
Sbjct: 61  AEELAEETGAELVQVIGKTIVLYR 84

GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. Length = 84

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

 Score = 74.1 bits (183), Expect = 8e-17
 Identities = 19/84 (22%), Positives = 43/84 (51%)

Query: 259 LTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKI 318
           LT ++ + +R+   H  P++++ +NG+   VV ++ EA +  E++++        D K+I
Sbjct: 1   LTGKQRRYLRSLAHHLKPVVQIGKNGLTEGVVEEIDEALEKHELIKVKVLGNDREDRKEI 60

Query: 319 GVKLRDLVPCVPILFKDEQIILWR 342
             +L +      +      I+L+R
Sbjct: 61  AEELAEKTGAELVQVIGRTIVLYR 84

Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. Length = 84

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	359
PRK10343	97	RNA-binding protein YhbY; Provisional	99.95
PF01985	84	CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR	99.95
TIGR00253	95	RNA_bind_YhbY putative RNA-binding protein, YhbY f	99.95
TIGR00253	95	RNA_bind_YhbY putative RNA-binding protein, YhbY f	99.94
PRK10343	97	RNA-binding protein YhbY; Provisional	99.93
PF01985	84	CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR	99.93
COG1534	97	Predicted RNA-binding protein containing KH domain	99.93
COG1534	97	Predicted RNA-binding protein containing KH domain	99.91
KOG1990	564	consensus Poly(A)-specific exoribonuclease PARN [R	99.87
KOG1990	564	consensus Poly(A)-specific exoribonuclease PARN [R	99.68

>PRK10343 RNA-binding protein YhbY; Provisional

Probab=99.95  E-value=1.1e-27  Score=198.92  Aligned_cols=89  Identities=16%  Similarity=0.166  Sum_probs=86.9

Q ss_pred             CCCCHHHHHHHHHhhccCCCCceEEeCCCCCCHHHHHHHHHHHHHcceEEEEecCCChhhHHHHHHHHHHHhCCeEEEEE
Q 041912          137 DPLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRN  216 (359)
Q Consensus       137 ~~LT~kErk~LR~lAh~~kLkp~v~IGK~GlTe~vl~~I~~awe~hELVKIK~~g~~~~d~k~~ae~Le~~TGg~vVqri  216 (359)
                      +.||++|+++||++||+  |+|+|+|||+|||++|+++|+++|++||||||++++++.++.++++++|++.|||++||+|
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 MNLSTKQKQHLKGLAHP--LKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVI   78 (97)
T ss_pred             CCCCHHHHHHHHHhcCC--CCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeee
Confidence            47999999999999998  9999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccEEEEEeCCC
Q 041912          217 INILLLYRGRN  227 (359)
Q Consensus       217 G~~iVLYRgkn  227 (359)
                      |+++||||.+.
T Consensus        79 G~~~vlYR~~~   89 (97)
T PRK10343         79 GKTLVLYRPTK   89 (97)
T ss_pred             CcEEEEEecCC
Confidence            99999999985

>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=1.1e-27  Score=193.10  Aligned_cols=84  Identities=26%  Similarity=0.423  Sum_probs=75.4

Q ss_pred             CCHHHHHHHHHhhccCCCCceEEeCCCCCCHHHHHHHHHHHHHcceEEEEecCCChhhHHHHHHHHHHHhCCeEEEEEcc
Q 041912          139 LTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNIN  218 (359)
Q Consensus       139 LT~kErk~LR~lAh~~kLkp~v~IGK~GlTe~vl~~I~~awe~hELVKIK~~g~~~~d~k~~ae~Le~~TGg~vVqriG~  218 (359)
                      ||++|+++||++||+  ++|+|+|||+|+|++|+++|+++|++||||||+|.+++.++++++|++|+++|||++||++|+
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 LTSKERKFLRKLAHH--LKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVIGR   78 (84)
T ss_dssp             --HHHHHHHHHHHTT--C--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEETT
T ss_pred             CCHHHHHHHHHHhcC--CCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEECC
Confidence            799999999999998  999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEe
Q 041912          219 ILLLYR  224 (359)
Q Consensus       219 ~iVLYR  224 (359)
                      ++||||
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.

>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family

Probab=99.95  E-value=2.5e-27  Score=196.01  Aligned_cols=88  Identities=18%  Similarity=0.245  Sum_probs=85.9

Q ss_pred             CCHHHHHHHHHhhccCCCCceEEeCCCCCCHHHHHHHHHHHHHcceEEEEecCCChhhHHHHHHHHHHHhCCeEEEEEcc
Q 041912          139 LTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNIN  218 (359)
Q Consensus       139 LT~kErk~LR~lAh~~kLkp~v~IGK~GlTe~vl~~I~~awe~hELVKIK~~g~~~~d~k~~ae~Le~~TGg~vVqriG~  218 (359)
                      ||++|+++||++||+  |+|+|+|||+|||++|+++|+++|++||||||++++++.++.+++|++|++.|||++||+||+
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 LTGKQKRHLRGKAHH--LKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVIGK   78 (95)
T ss_pred             CCHHHHHHHHHHhCC--CCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEEcc
Confidence            799999999999998  999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEeCCCC
Q 041912          219 ILLLYRGRNY  228 (359)
Q Consensus       219 ~iVLYRgkny  228 (359)
                      ++||||++..
T Consensus        79 ~~vlYR~~~~   88 (95)
T TIGR00253        79 TIVLYRPTKE   88 (95)
T ss_pred             EEEEEecCCc
Confidence            9999999754

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.

>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family

Probab=99.94  E-value=1.8e-26  Score=190.97  Aligned_cols=88  Identities=18%  Similarity=0.359  Sum_probs=86.2

Q ss_pred             CCHHHHHHHHhccCCCCCceecccCCccHHHHHHHHHHHhhCCeEEEEecCCCCccHHHHHHHHHhhCCCeEEEEeCCEE
Q 041912          259 LTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQI  338 (359)
Q Consensus       259 LT~kEr~~LR~la~~l~pi~~LGKnGv~~~lv~~I~~a~e~rELVKI~vl~n~~~d~keiA~~L~~~tg~~lVq~ig~~I  338 (359)
                      ||+|||++||++||+|+|+++|||+|++++++++|++||++||||||.+++++.+|.+++|++|++.|||++||+||+++
T Consensus         1 Lt~kqr~~Lr~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~iG~~~   80 (95)
T TIGR00253         1 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVIGKTI   80 (95)
T ss_pred             CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEEccEE
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCCCC
Q 041912          339 ILWRGKEQ  346 (359)
Q Consensus       339 VLYRgk~y  346 (359)
                      ||||+++-
T Consensus        81 vlYR~~~~   88 (95)
T TIGR00253        81 VLYRPTKE   88 (95)
T ss_pred             EEEecCCc
Confidence            99999853

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=99.93  E-value=3.7e-26  Score=189.75  Aligned_cols=88  Identities=14%  Similarity=0.258  Sum_probs=86.4

Q ss_pred             CCCHHHHHHHHhccCCCCCceecccCCccHHHHHHHHHHHhhCCeEEEEecCCCCccHHHHHHHHHhhCCCeEEEEeCCE
Q 041912          258 GLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQ  337 (359)
Q Consensus       258 ~LT~kEr~~LR~la~~l~pi~~LGKnGv~~~lv~~I~~a~e~rELVKI~vl~n~~~d~keiA~~L~~~tg~~lVq~ig~~  337 (359)
                      .||++||+|||++||+++|+++|||+|++++++++|++|+++||||||.+++++.+|.+++|++|++.|||++||+||++
T Consensus         2 ~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~IG~~   81 (97)
T PRK10343          2 NLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKT   81 (97)
T ss_pred             CCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeeeCcE
Confidence            49999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCC
Q 041912          338 IILWRGKE  345 (359)
Q Consensus       338 IVLYRgk~  345 (359)
                      +||||.+.
T Consensus        82 ~vlYR~~~   89 (97)
T PRK10343         82 LVLYRPTK   89 (97)
T ss_pred             EEEEecCC
Confidence            99999985

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

Probab=99.93  E-value=2.5e-26  Score=185.15  Aligned_cols=84  Identities=24%  Similarity=0.384  Sum_probs=75.7

Q ss_pred             CCHHHHHHHHhccCCCCCceecccCCccHHHHHHHHHHHhhCCeEEEEecCCCCccHHHHHHHHHhhCCCeEEEEeCCEE
Q 041912          259 LTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQI  338 (359)
Q Consensus       259 LT~kEr~~LR~la~~l~pi~~LGKnGv~~~lv~~I~~a~e~rELVKI~vl~n~~~d~keiA~~L~~~tg~~lVq~ig~~I  338 (359)
                      ||++|+++||++|++|+|+++|||+|++++++++|+++|++||||||.|++++..|.+++|++|++.|||++|+++|+++
T Consensus         1 Lt~ke~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~iG~~~   80 (84)
T PF01985_consen    1 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVIGRTI   80 (84)
T ss_dssp             --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEETTEE
T ss_pred             CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEECCEE
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEc
Q 041912          339 ILWR  342 (359)
Q Consensus       339 VLYR  342 (359)
                      ||||
T Consensus        81 vlyR   84 (84)
T PF01985_consen   81 VLYR   84 (84)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9998

The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.

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

Probab=99.93  E-value=2.1e-25  Score=184.89  Aligned_cols=89  Identities=21%  Similarity=0.330  Sum_probs=85.7

Q ss_pred             CCCHHHHHHHHHhhccCCCCceEEeCCCCCCHHHHHHHHHHHHHcceEEEEecCCChhhHHHHHHHHHHHhCCeEEEEEc
Q 041912          138 PLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNI  217 (359)
Q Consensus       138 ~LT~kErk~LR~lAh~~kLkp~v~IGK~GlTe~vl~~I~~awe~hELVKIK~~g~~~~d~k~~ae~Le~~TGg~vVqriG  217 (359)
                      .||++|+++||+.||+  ++|+|+|||+|||++|+++|+++|++||||||++.+++.+|.+++|+.|++.+||++||+||
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 MLTGKQKRFLRSKAHH--LKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVIG   78 (97)
T ss_pred             CCcHHHHHHHHHhhcc--CCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeeee
Confidence            5899999999999998  99999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEEeCCCC
Q 041912          218 NILLLYRGRNY  228 (359)
Q Consensus       218 ~~iVLYRgkny  228 (359)
                      +++||||.+..
T Consensus        79 ~~~vlyr~~~e   89 (97)
T COG1534          79 KTLVLYRESKE   89 (97)
T ss_pred             eEEEEEecCcc
Confidence            99999995443

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

Probab=99.91  E-value=2e-24  Score=179.11  Aligned_cols=87  Identities=18%  Similarity=0.359  Sum_probs=85.0

Q ss_pred             CCCHHHHHHHHhccCCCCCceecccCCccHHHHHHHHHHHhhCCeEEEEecCCCCccHHHHHHHHHhhCCCeEEEEeCCE
Q 041912          258 GLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQ  337 (359)
Q Consensus       258 ~LT~kEr~~LR~la~~l~pi~~LGKnGv~~~lv~~I~~a~e~rELVKI~vl~n~~~d~keiA~~L~~~tg~~lVq~ig~~  337 (359)
                      .||+||+++||++||+++|+|+|||||++++++++|++++++||||||.+++++.+|.+++|+.|++.+||++||++|++
T Consensus         1 ~Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqviG~~   80 (97)
T COG1534           1 MLTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVIGKT   80 (97)
T ss_pred             CCcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeeeeeE
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCC
Q 041912          338 IILWRGK  344 (359)
Q Consensus       338 IVLYRgk  344 (359)
                      +||||.+
T Consensus        81 ~vlyr~~   87 (97)
T COG1534          81 LVLYRES   87 (97)
T ss_pred             EEEEecC
Confidence            9999944

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

Probab=99.87  E-value=1.8e-22  Score=210.45  Aligned_cols=254  Identities=20%  Similarity=0.270  Sum_probs=212.5

Q ss_pred             CCCCCCCcCCCCCCCccCCCCCccccch----hh-hhccccCC--CCCCHHHHHHHHHhhccCCCCceEEeCCCCCCHHH
Q 041912           99 FSPFGPGRLDRKWTGTTALAPKEVDRVR----FE-EERNRVLG--DPLTEEEIAELVERYRHSDCARQINLGKWGVTHNM  171 (359)
Q Consensus        99 ~~~fGP~~~~r~W~g~~plpvd~~~~p~----~~-~~r~~~lg--~~LT~kErk~LR~lAh~~kLkp~v~IGK~GlTe~v  171 (359)
                      |...||++.+  |+|..+++++++..|+    |. +.|..-+|  ..|+..|...+|.++..  .+++|.+|.++.-+++
T Consensus       130 ~~~~~~~~~~--~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~--~p~~~~~~~~~~~~~~  205 (564)
T KOG1990|consen  130 LDSLGPELSD--WGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLLRRLGYK--LPPHFALGRSRKLQGL  205 (564)
T ss_pred             hhccCccccc--CCCCCCccchhhhchhhhhcccChhccCCCCChhhhhhHHHHHHHHhccc--ccccceehhccccccc
Confidence            6699999998  9999999999977555    43 23333345  58999999999999987  9999999999999999


Q ss_pred             HHHHHHHHHHcceEEEEec-CCChhhHHHHHHHH--HHHhCCeEEEEEccEEEEEeCCCCCC------C--CC-----Cc
Q 041912          172 LDDLHNHWKRAEAVRIKCL-GVPTLDMDNVCFHL--EEKSGGKIIYRNINILLLYRGRNYDP------K--DR-----PV  235 (359)
Q Consensus       172 l~~I~~awe~hELVKIK~~-g~~~~d~k~~ae~L--e~~TGg~vVqriG~~iVLYRgkny~p------~--~R-----p~  235 (359)
                      .-.++..|++|+.+|+.+. +.+....+.++.++  ...||+.+|.++|-..++||+++|..      .  ..     |.
T Consensus       206 ~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~hN~~~dv~y~~~~Fl~~lp~~l~~f~~~~~~fp~  285 (564)
T KOG1990|consen  206 AVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVLHNKLLDVMYRYKNFLSPLPSTLEEFTDSSSMFPN  285 (564)
T ss_pred             hhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEeeccceeeeeehhhcccccchhHHHhhhhhhhhhh
Confidence            9999999999999999998 77778888999999  89999999999999999999999973      1  11     11


Q ss_pred             -------------cc--c---c--------ccCCC---------------------------------------------
Q 041912          236 -------------IP--L---M--------LWRPY---------------------------------------------  244 (359)
Q Consensus       236 -------------~p--l---m--------lW~~~---------------------------------------------  244 (359)
                                   ..  +   +        .|...                                             
T Consensus       286 ~~~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  365 (564)
T KOG1990|consen  286 IEDTKRLAKLSEYQKLNLKATLLELARAKAKKEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILA  365 (564)
T ss_pred             hHHHHHhhccccccchhhhhhHHHHHHHhcccccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhh
Confidence                         00  0   0        02110                                             


Q ss_pred             CCCCc---ccccccCCCCCHHHHHHHHhccCCCCCceecccCCccHHHHHHHHHHHhhCCeEEEEecCCCC-ccHHHHHH
Q 041912          245 APIYP---KVVKNVADGLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGT-NDCKKIGV  320 (359)
Q Consensus       245 ~Pv~~---~l~~~~~e~LT~kEr~~LR~la~~l~pi~~LGKnGv~~~lv~~I~~a~e~rELVKI~vl~n~~-~d~keiA~  320 (359)
                      .+.++   -+....++.+|.||+.+++++|..++..+.+|+.|++++++.++|.||+++|++|+.|..... .+.+..|.
T Consensus       366 ~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~  445 (564)
T KOG1990|consen  366 KLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYAS  445 (564)
T ss_pred             cccccccccccccchhhcChHHHHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHH
Confidence            00000   022256899999999999999999999999999999999999999999999999999977665 99999999


Q ss_pred             HHHhhCCCeEEEEeC----CEEEEEcCCCCCCCCCCCCCCCC
Q 041912          321 KLRDLVPCVPILFKD----EQIILWRGKEQAMDSDPLIDPTN  358 (359)
Q Consensus       321 ~L~~~tg~~lVq~ig----~~IVLYRgk~y~~~~~~~~~~~~  358 (359)
                      .++.++|+++|+++.    +.|+.|||++|.++..  ++|.|
T Consensus       446 ~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~--l~P~~  485 (564)
T KOG1990|consen  446 ALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTS--LRPRN  485 (564)
T ss_pred             HHHHHhCCceeeeccCCchhhHHHhhhhhccCCcc--cCchh
Confidence            999999999999975    4589999999999887  67654

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

Probab=99.68  E-value=4.6e-17  Score=170.12  Aligned_cols=213  Identities=17%  Similarity=0.139  Sum_probs=186.9

Q ss_pred             CCCCCHHHHHHHHHhhccCCCCceEEeCCCCCCHHHHHHHHHHHHHcceEEEEecCCChhhHHHHHHHHHHHhCC-eEEE
Q 041912          136 GDPLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGG-KIIY  214 (359)
Q Consensus       136 g~~LT~kErk~LR~lAh~~kLkp~v~IGK~GlTe~vl~~I~~awe~hELVKIK~~g~~~~d~k~~ae~Le~~TGg-~vVq  214 (359)
                      ...+.+.+..+||..|..  +.-..  +++|+|+.++++|+.-|+.+|+++++|....+.+|.++.+.++..||| -+||
T Consensus        11 ~~~~~~~~~~~l~~~~~~--~~~~~--~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~n~~~~   86 (564)
T KOG1990|consen   11 ELTVDEADLRRLRLVATG--MTSAP--WKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMSTGGNFVVW   86 (564)
T ss_pred             HhhcCHHHHHHHhhhhcc--ceecc--cccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccCCCceeee
Confidence            457889999999999976  54444  999999999999999999999999999988899999999999999999 8999


Q ss_pred             EEccEEEEEeCCCCC-C-----CC---CCc-cc-----------------ccccCC--CCCCCcc---------------
Q 041912          215 RNINILLLYRGRNYD-P-----KD---RPV-IP-----------------LMLWRP--YAPIYPK---------------  250 (359)
Q Consensus       215 riG~~iVLYRgkny~-p-----~~---Rp~-~p-----------------lmlW~~--~~Pv~~~---------------  250 (359)
                      +.|.....|++..|. +     +.   .-. .+                 .+.|+.  ..|++.|               
T Consensus        87 ~~g~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~  166 (564)
T KOG1990|consen   87 SRGDSISSPEFLCQRSPVDFVARQQENQAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRT  166 (564)
T ss_pred             ecCccccCCccceeecchhhhhhhchhhhhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhcc
Confidence            999999999776665 2     22   111 01                 134874  4677777               


Q ss_pred             cccccCCCCCHHHHHHHHhccCCCCCceecccCCccHHHHHHHHHHHhhCCeEEEEe-cCCCCccHHHHHHHH--HhhCC
Q 041912          251 VVKNVADGLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDC-SHVGTNDCKKIGVKL--RDLVP  327 (359)
Q Consensus       251 l~~~~~e~LT~kEr~~LR~la~~l~pi~~LGKnGv~~~lv~~I~~a~e~rELVKI~v-l~n~~~d~keiA~~L--~~~tg  327 (359)
                      ++.+++..||.+|..++|.+|...+++|.+|.++..++++..|+..|++++.+|+.+ ++.+......+|..+  ...+|
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            577889999999999999999999999999999999999999999999999999888 888899999999999  99999


Q ss_pred             CeEEEEeCCEEEEEcCCCCCCCCCC
Q 041912          328 CVPILFKDEQIILWRGKEQAMDSDP  352 (359)
Q Consensus       328 ~~lVq~ig~~IVLYRgk~y~~~~~~  352 (359)
                      +.||..++..+|+||+++|..+.+.
T Consensus       247 ~~lv~hN~~~dv~y~~~~Fl~~lp~  271 (564)
T KOG1990|consen  247 KVLVLHNKLLDVMYRYKNFLSPLPS  271 (564)
T ss_pred             CeEEeeccceeeeeehhhcccccch
Confidence            9999999999999999999995443

---

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	359
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	2e-11
1rq8_A	104	Conserved hypothetical protein; structural genomic	2e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05

>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 = 59.2 bits (144), Expect = 2e-11
 Identities = 20/100 (20%), Positives = 40/100 (40%), Gaps = 7/100 (7%)

Query: 139 LTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMD 198
           L+ ++   L     H +    + LG  G+T  +L ++ N     E +++K  G       
Sbjct: 3   LSTKQKQFLKGLAHHLN--PVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQ 60

Query: 199 NVCFHLEEKSGGKIIYRNINILLLYRGRNYDPKDRPVIPL 238
            +   +  ++    +    +IL+LYR     P +   I L
Sbjct: 61  LIINAIVRETKAAQVQTIGHILVLYR-----PSEEAKIQL 95

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

 Score = 56.6 bits (137), Expect = 2e-10
 Identities = 16/84 (19%), Positives = 36/84 (42%), Gaps = 4/84 (4%)

Query: 160 INLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNINI 219
             +GK G+  NM+  + +  +  E +++  L     D   +   L E +  +++    ++
Sbjct: 21  FQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVIGSM 80

Query: 220 LLLYRGRNYDPKDRPVIPLMLWRP 243
           +++YR      K+   I L L   
Sbjct: 81  IVIYRES----KENKEIELPLEHH 100

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 46.0 bits (108), Expect = 2e-05
 Identities = 53/349 (15%), Positives = 101/349 (28%), Gaps = 107/349 (30%)

Query: 69  LKSDLPFDF-KYSYSENNPAVEPIGF--------REPKRFSPFGPGRLD-----RKW--- 111
           L+ +  F        +  P++    +         + + F+ +   RL      R+    
Sbjct: 87  LRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLE 146

Query: 112 --------------TGTTALAPKEVDRVRFEEER-NRV----LGDPLTEEEIAELVER-Y 151
                         +G T +A       + + +   ++    L +  + E + E++++  
Sbjct: 147 LRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLL 206

Query: 152 RHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRI-------KCLGVPTLDMDNVC--- 201
              D             H+    L  H  +AE  R+        CL    L + NV    
Sbjct: 207 YQIDPNWTSRS-----DHSSNIKLRIHSIQAELRRLLKSKPYENCL----LVLLNVQNAK 257

Query: 202 ----FHLEEKSGGKIIYRNINILLLYRGRNYDPKDRPVIPLMLWRPYAPIYPKVVKNVAD 257
               F+L  K           ILL  R        + V   +       I    + + + 
Sbjct: 258 AWNAFNLSCK-----------ILLTTR-------FKQVTDFLSAATTTHI---SLDHHSM 296

Query: 258 GLTFEETKEMRNRGLHSP----PLMKLTRNGVYVNVVAKVREAFKTEEVVRLD-CSHVGT 312
            LT +E K +  + L       P   LT N   ++++A        + +   D   HV  
Sbjct: 297 TLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIA----ESIRDGLATWDNWKHVNC 352

Query: 313 NDCKK-IGVKLRDLVP---------CVPILFKDEQI------ILWRGKE 345
           +     I   L  L P            +      I      ++W    
Sbjct: 353 DKLTTIIESSLNVLEPAEYRKMFDRLS-VFPPSAHIPTILLSLIWFDVI 400

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	359
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,	99.95
1rq8_A	104	Conserved hypothetical protein; structural genomic	99.94

>1jo0_A Hypothetical protein HI1333; structural genomics, YHBY_HAEI structure 2 function project, S2F, unknown function; 1.37A {Haemophilus influenzae} SCOP: d.68.4.1 PDB: 1ln4_A

Probab=99.96  E-value=1.9e-29  Score=208.35  Aligned_cols=89  Identities=19%  Similarity=0.242  Sum_probs=86.7

Q ss_pred             CCCHHHHHHHHHhhccCCCCceEEeCCCCCCHHHHHHHHHHHHHcceEEEEecCCChhhHHHHHHHHHHHhCCeEEEEEc
Q 041912          138 PLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNI  217 (359)
Q Consensus       138 ~LT~kErk~LR~lAh~~kLkp~v~IGK~GlTe~vl~~I~~awe~hELVKIK~~g~~~~d~k~~ae~Le~~TGg~vVqriG  217 (359)
                      .||++|+++||++||+  |+|+|+|||+|||++|+++|+++|++||||||+|++++.+|++++|++|+++|||++||+||
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 TLSTKQKQFLKGLAHH--LNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTIG   79 (98)
T ss_dssp             CCCHHHHHHHHHHHTT--BCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEEEET
T ss_pred             CCCHHHHHHHHHHhcC--CCCeEEECCCCCCHHHHHHHHHHHHHCCeEEEEEeCCCHHHHHHHHHHHHHHhCCEEEEEEC
Confidence            6999999999999998  99999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEEeCCCC
Q 041912          218 NILLLYRGRNY  228 (359)
Q Consensus       218 ~~iVLYRgkny  228 (359)
                      +++||||++..
T Consensus        80 ~~~vLyR~~~~   90 (98)
T 1jo0_A           80 HILVLYRPSEE   90 (98)
T ss_dssp             TEEEEECCCSS
T ss_pred             CEEEEEccCCC
Confidence            99999999843

>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=5e-29  Score=207.95  Aligned_cols=90  Identities=17%  Similarity=0.261  Sum_probs=87.3

Q ss_pred             CCCHHHHHHHHHhhccCCCCceEEeCCCCCCHHHHHHHHHHHHHcceEEEEecCCChhhHHHHHHHHHHHhCCeEEEEEc
Q 041912          138 PLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNI  217 (359)
Q Consensus       138 ~LT~kErk~LR~lAh~~kLkp~v~IGK~GlTe~vl~~I~~awe~hELVKIK~~g~~~~d~k~~ae~Le~~TGg~vVqriG  217 (359)
                      +||++|+++||++||+  |+|+|+|||+|||++|+++|+++|++||||||+|++++.+|++++|++|+++|||++||+||
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 MLTGKQKRYLRSLAHN--IDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVIG   78 (104)
T ss_dssp             CCCHHHHHHHHHHTTS--SCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEET
T ss_pred             CCCHHHHHHHHHHhcC--CCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCHHHHHHHHHHHHHHhCCEEEEEEC
Confidence            5999999999999998  99999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEEeCCCCC
Q 041912          218 NILLLYRGRNYD  229 (359)
Q Consensus       218 ~~iVLYRgkny~  229 (359)
                      +++||||++..+
T Consensus        79 ~~~VLYR~~~~~   90 (104)
T 1rq8_A           79 SMIVIYRESKEN   90 (104)
T ss_dssp             TEEEEEECCCSC
T ss_pred             CEEEEEeCCCCC
Confidence            999999998744

>1jo0_A Hypothetical protein HI1333; structural genomics, YHBY_HAEI structure 2 function project, S2F, unknown function; 1.37A {Haemophilus influenzae} SCOP: d.68.4.1 PDB: 1ln4_A

Probab=99.95  E-value=1.3e-27  Score=197.39  Aligned_cols=89  Identities=16%  Similarity=0.265  Sum_probs=86.9

Q ss_pred             CCCHHHHHHHHhccCCCCCceecccCCccHHHHHHHHHHHhhCCeEEEEecCCCCccHHHHHHHHHhhCCCeEEEEeCCE
Q 041912          258 GLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQ  337 (359)
Q Consensus       258 ~LT~kEr~~LR~la~~l~pi~~LGKnGv~~~lv~~I~~a~e~rELVKI~vl~n~~~d~keiA~~L~~~tg~~lVq~ig~~  337 (359)
                      .||++||+|||++||+|+|+|+|||+|++++++++|++||++||||||.|++++.+|.+++|++|++.|||++||+||++
T Consensus         2 ~Lt~kqr~~Lr~~ah~l~pvv~IGk~GlT~~vi~ei~~aL~~~ELIKVkvl~~~~~~~~e~a~~la~~t~a~~Vq~IG~~   81 (98)
T 1jo0_A            2 TLSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTIGHI   81 (98)
T ss_dssp             CCCHHHHHHHHHHHTTBCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEEEETTE
T ss_pred             CCCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHHCCeEEEEEeCCCHHHHHHHHHHHHHHhCCEEEEEECCE
Confidence            59999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCCC
Q 041912          338 IILWRGKEQ  346 (359)
Q Consensus       338 IVLYRgk~y  346 (359)
                      +||||+++-
T Consensus        82 ~vLyR~~~~   90 (98)
T 1jo0_A           82 LVLYRPSEE   90 (98)
T ss_dssp             EEEECCCSS
T ss_pred             EEEEccCCC
Confidence            999999843

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

Probab=99.94  E-value=2.1e-27  Score=198.17  Aligned_cols=88  Identities=14%  Similarity=0.326  Sum_probs=86.5

Q ss_pred             CCCHHHHHHHHhccCCCCCceecccCCccHHHHHHHHHHHhhCCeEEEEecCCCCccHHHHHHHHHhhCCCeEEEEeCCE
Q 041912          258 GLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQ  337 (359)
Q Consensus       258 ~LT~kEr~~LR~la~~l~pi~~LGKnGv~~~lv~~I~~a~e~rELVKI~vl~n~~~d~keiA~~L~~~tg~~lVq~ig~~  337 (359)
                      .||++||+|||++|++|+|+|+|||+|++++++++|++||++||||||.|+++|..|.+++|++|++.|||++||+||++
T Consensus         1 mLt~kqr~~LR~~ah~Lkpvv~IGK~GlTe~vi~ei~~aL~~hELIKVkvl~~~~~d~~e~a~~la~~t~a~vVq~IG~~   80 (104)
T 1rq8_A            1 MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVIGSM   80 (104)
T ss_dssp             CCCHHHHHHHHHHTTSSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEETTE
T ss_pred             CCCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCHHHHHHHHHHHHHHhCCEEEEEECCE
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCC
Q 041912          338 IILWRGKE  345 (359)
Q Consensus       338 IVLYRgk~  345 (359)
                      +||||+++
T Consensus        81 ~VLYR~~~   88 (104)
T 1rq8_A           81 IVIYRESK   88 (104)
T ss_dssp             EEEEECCC
T ss_pred             EEEEeCCC
Confidence            99999986

---

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	359
d1rq8a_	96	d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphy	3e-18
d1rq8a_	96	d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphy	3e-13
d1jo0a_	97	d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i	1e-16
d1jo0a_	97	d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i	1e-12

>d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]} Length = 96

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: Hypothetical protein SAV1595
species: Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]

 Score = 77.0 bits (190), Expect = 3e-18
 Identities = 16/93 (17%), Positives = 40/93 (43%), Gaps = 2/93 (2%)

Query: 139 LTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMD 198
           LT ++   L     + D      +GK G+  NM+  + +  +  E +++  L     D  
Sbjct: 2   LTGKQKRYLRSLAHNIDP--IFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKK 59

Query: 199 NVCFHLEEKSGGKIIYRNINILLLYRGRNYDPK 231
            +   L E +  +++    +++++YR    + +
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 = 62.8 bits (153), Expect = 3e-13
 Identities = 12/88 (13%), Positives = 43/88 (48%)

Query: 259 LTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKI 318
           LT ++ + +R+   +  P+ ++ + G+  N++ ++ +  +  E++++       +D K++
Sbjct: 2   LTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKEL 61

Query: 319 GVKLRDLVPCVPILFKDEQIILWRGKEQ 346
              L +      +      I+++R  ++
Sbjct: 62  AETLSEATRSELVQVIGSMIVIYRESKE 89

>d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]} Length = 97

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

 Score = 72.4 bits (178), Expect = 1e-16
 Identities = 20/100 (20%), Positives = 40/100 (40%), Gaps = 7/100 (7%)

Query: 139 LTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMD 198
           L+ ++   L     H +    + LG  G+T  +L ++ N     E +++K  G       
Sbjct: 3   LSTKQKQFLKGLAHHLNPV--VMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQ 60

Query: 199 NVCFHLEEKSGGKIIYRNINILLLYRGRNYDPKDRPVIPL 238
            +   +  ++    +    +IL+LYR     P +   I L
Sbjct: 61  LIINAIVRETKAAQVQTIGHILVLYR-----PSEEAKIQL 95

>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 = 61.2 bits (149), Expect = 1e-12
 Identities = 15/89 (16%), Positives = 39/89 (43%)

Query: 259 LTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKI 318
           L+ ++ + ++    H  P++ L  NG+   V+A++  A    E++++  +       + I
Sbjct: 3   LSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLI 62

Query: 319 GVKLRDLVPCVPILFKDEQIILWRGKEQA 347
              +        +      ++L+R  E+A
Sbjct: 63  INAIVRETKAAQVQTIGHILVLYRPSEEA 91

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	359
d1rq8a_	96	Hypothetical protein SAV1595 {Staphylococcus aureu	99.96
d1jo0a_	97	YhbY homologue HI1333 {Haemophilus influenzae [Tax	99.96
d1rq8a_	96	Hypothetical protein SAV1595 {Staphylococcus aureu	99.94
d1jo0a_	97	YhbY homologue HI1333 {Haemophilus influenzae [Tax	99.94

>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=8.1e-29  Score=201.49  Aligned_cols=91  Identities=16%  Similarity=0.256  Sum_probs=88.4

Q ss_pred             CCCHHHHHHHHHhhccCCCCceEEeCCCCCCHHHHHHHHHHHHHcceEEEEecCCChhhHHHHHHHHHHHhCCeEEEEEc
Q 041912          138 PLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRNI  217 (359)
Q Consensus       138 ~LT~kErk~LR~lAh~~kLkp~v~IGK~GlTe~vl~~I~~awe~hELVKIK~~g~~~~d~k~~ae~Le~~TGg~vVqriG  217 (359)
                      +||++|+++||++||+  |+|+|+|||+|+|++|+++|+++|++||||||+|.+.+..|++++|++|+++|||++||+||
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 MLTGKQKRYLRSLAHN--IDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVIG   78 (96)
T ss_dssp             CCCHHHHHHHHHHTTS--SCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEET
T ss_pred             CcCHHHHHHHHHHhcC--CCCEEEECCCCCCHHHHHHHHHHHHhCCeeEEEecCCCHHHHHHHHHHHHHHhCCEEEEEEC
Confidence            5899999999999998  99999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEEeCCCCCC
Q 041912          218 NILLLYRGRNYDP  230 (359)
Q Consensus       218 ~~iVLYRgkny~p  230 (359)
                      +++||||+++++|
T Consensus        79 ~~~vlyR~~~~~~   91 (96)
T d1rq8a_          79 SMIVIYRESKENK   91 (96)
T ss_dssp             TEEEEEECCCSCC
T ss_pred             CEEEEEeCCCCCC
Confidence            9999999998764

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

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

Probab=99.96  E-value=8.5e-29  Score=201.70  Aligned_cols=89  Identities=19%  Similarity=0.252  Sum_probs=86.7

Q ss_pred             CCCCHHHHHHHHHhhccCCCCceEEeCCCCCCHHHHHHHHHHHHHcceEEEEecCCChhhHHHHHHHHHHHhCCeEEEEE
Q 041912          137 DPLTEEEIAELVERYRHSDCARQINLGKWGVTHNMLDDLHNHWKRAEAVRIKCLGVPTLDMDNVCFHLEEKSGGKIIYRN  216 (359)
Q Consensus       137 ~~LT~kErk~LR~lAh~~kLkp~v~IGK~GlTe~vl~~I~~awe~hELVKIK~~g~~~~d~k~~ae~Le~~TGg~vVqri  216 (359)
                      .+||++|+++||++||+  |+|+|+||++|||++|+++|+++|++||||||+|.+.+..|++++|++|+++|||++||+|
T Consensus         1 ttLt~kqr~~LR~~ah~--lkp~v~IGk~Glt~~vi~ei~~al~~~ELIKvki~~~~~~~~~~~~~~l~~~t~~~vV~~i   78 (97)
T d1jo0a_           1 TTLSTKQKQFLKGLAHH--LNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTI   78 (97)
T ss_dssp             CCCCHHHHHHHHHHHTT--BCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEEEE
T ss_pred             CCCCHHHHHHHHHHhcC--CCCEEEECCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHHHhCCEEEEEE
Confidence            37999999999999998  9999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccEEEEEeCCC
Q 041912          217 INILLLYRGRN  227 (359)
Q Consensus       217 G~~iVLYRgkn  227 (359)
                      |+++||||+++
T Consensus        79 G~~~ilYR~~~   89 (97)
T d1jo0a_          79 GHILVLYRPSE   89 (97)
T ss_dssp             TTEEEEECCCS
T ss_pred             CCEEEEEcCCC
Confidence            99999999975

>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=99.94  E-value=2.9e-27  Score=192.26  Aligned_cols=91  Identities=13%  Similarity=0.315  Sum_probs=88.1

Q ss_pred             CCCHHHHHHHHhccCCCCCceecccCCccHHHHHHHHHHHhhCCeEEEEecCCCCccHHHHHHHHHhhCCCeEEEEeCCE
Q 041912          258 GLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQ  337 (359)
Q Consensus       258 ~LT~kEr~~LR~la~~l~pi~~LGKnGv~~~lv~~I~~a~e~rELVKI~vl~n~~~d~keiA~~L~~~tg~~lVq~ig~~  337 (359)
                      .||++||++||++||+|+|+++|||+|++++++++|++||++||||||.|++++..|.+++|++|++.|||++||++|++
T Consensus         1 mLt~kqr~~LR~~ah~l~p~v~IGk~Glt~~vi~ei~~~l~~~ELIKvk~~~~~~~~~~~~~~~l~~~t~a~~V~~iG~~   80 (96)
T d1rq8a_           1 MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVIGSM   80 (96)
T ss_dssp             CCCHHHHHHHHHHTTSSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEETTE
T ss_pred             CcCHHHHHHHHHHhcCCCCEEEECCCCCCHHHHHHHHHHHHhCCeeEEEecCCCHHHHHHHHHHHHHHhCCEEEEEECCE
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCCCCC
Q 041912          338 IILWRGKEQAM  348 (359)
Q Consensus       338 IVLYRgk~y~~  348 (359)
                      +||||+++..+
T Consensus        81 ~vlyR~~~~~~   91 (96)
T d1rq8a_          81 IVIYRESKENK   91 (96)
T ss_dssp             EEEEECCCSCC
T ss_pred             EEEEeCCCCCC
Confidence            99999987654

>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=99.94  E-value=2.8e-27  Score=192.64  Aligned_cols=88  Identities=16%  Similarity=0.261  Sum_probs=86.6

Q ss_pred             CCCHHHHHHHHhccCCCCCceecccCCccHHHHHHHHHHHhhCCeEEEEecCCCCccHHHHHHHHHhhCCCeEEEEeCCE
Q 041912          258 GLTFEETKEMRNRGLHSPPLMKLTRNGVYVNVVAKVREAFKTEEVVRLDCSHVGTNDCKKIGVKLRDLVPCVPILFKDEQ  337 (359)
Q Consensus       258 ~LT~kEr~~LR~la~~l~pi~~LGKnGv~~~lv~~I~~a~e~rELVKI~vl~n~~~d~keiA~~L~~~tg~~lVq~ig~~  337 (359)
                      +||++||+|||++|++|+|+|+|||+|++++++++|++||++||||||.|++++.+|.+++|++|++.|||++||++|++
T Consensus         2 tLt~kqr~~LR~~ah~lkp~v~IGk~Glt~~vi~ei~~al~~~ELIKvki~~~~~~~~~~~~~~l~~~t~~~vV~~iG~~   81 (97)
T d1jo0a_           2 TLSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTIGHI   81 (97)
T ss_dssp             CCCHHHHHHHHHHHTTBCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEEEETTE
T ss_pred             CCCHHHHHHHHHHhcCCCCEEEECCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHHHhCCEEEEEECCE
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCC
Q 041912          338 IILWRGKE  345 (359)
Q Consensus       338 IVLYRgk~  345 (359)
                      +||||+++
T Consensus        82 ~ilYR~~~   89 (97)
T d1jo0a_          82 LVLYRPSE   89 (97)
T ss_dssp             EEEECCCS
T ss_pred             EEEEcCCC
Confidence            99999975