Citrus Sinensis ID: 018444

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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------
Protein Sequence
MLVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDDPSQGTIRSSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGASSSMAEYEDGSQSENYDEDEFYPEDDFNDDDEFYDSDSSDVVPLGSLPVDHIAERLQRK
Secondary Structure (PSIPRED)
cccccHHHccccccccccccHHHHHHHHHHHHHcccEEEEEEcccccccHHHHHHHHHHHHccEEEEEEccEEEEEEccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccEEEEccccHHHHHHHHHHHHHccccEEEEEccccccccHHHHHHHHHcccccEEEcccccEEEEEEccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccHHHHHHcccEEcccccHHHHHHHHHHHHHHHccEEEEEEcccccccHHHHHHHHHHHcccEEEEEcccEEEEEEcccccccccccccEEEcccccccccHHHccccccccHHHHHHHHHHcccccHHHHHHHcccEEEHHHHHHHHHccccEEEEEcccccHHHHHHHHHHHHHcccEEEEEEcccEEEEEEcccccccccccccccccccccccccccccccccccccccHHcccHHHHHHHHHHHHccHEEEHHHccccHHHHHHHHHHHHHHHHHHHccccEEEEEcccccccccccccccccccccccccccccccccHHHHHHHcccccccccccccHHHHHHHHccc
Coil and Loop (DISEMBL)
mlvkpllkdnrqvnlgrdgLTHNMLELIHSHWKRRRVIKikckgvptvdmdnVCRRLeektggkiifrVGGLVYLfrgrnynyrtrpqyplmlwkpaapvypkliqeapegltkHEADELRRKgksllpicklakngVYLTLVRDVRnafegsslvkvnckgmhasdyKKLGAKLKELvpcvllsfddeQILMWRGkdwksmypeppsfsnpvdldiagdadgsgtpsddpsqgtirsspKMISLWKRAIESTKALVLDeinlgpddLLKKVEEFEGISQAAEHSYPALvlsredgasssmaeyedgsqsenydedefypeddfndddefydsdssdvvplgslpvdHIAERLQRK
Flexible Loop (DISEMBL)
mlvkpllkdnrqvnlgrdgltHNMLELIHSHWKRRRVIKikckgvptvdmdnvcrrleektggkiifrvgglvYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADELRrkgksllpicklakNGVYLTLVRDVRNAFegsslvkvnckgMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGKDWKSMYPEPPSFSNPVDLDIAGDADGsgtpsddpsqgtirsspKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISqaaehsypaLVLSREDGASSSMAEyedgsqsenydeDEFYPEDDFNDDDEFYDSDssdvvplgslpvdhiaerlqrk
Low Complexity Region (SEG)
MLVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDDPSQGTIRSSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGASSSMAEYEDGSQSenydedefypeddfndddefydsdssdVVPLGSLPVDHIAERLQRK
Disordered region (IsUnstruct)
*************NLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQE*****************KSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGKDWKSM****************************************ISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGI******************************************************************************
Disordered Region (DISOPRED)
*L*******N**VNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYLFRGRNYNYRTRPQ****LWK**APV***********************GKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGKD*************************************************************************************************************************************************LPVDH*AERL***
Disordered Region (DISEMBL)
MLVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGKDWKSMYPEPPSFSNPVDLDIAGDA***************RSSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSRE********************EDEFYPEDDFNDDDEFYDSDSSDVVPLGSLPVDHIAERLQRK
Disordered Region (DISPRO)
MLVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGKDWKSM*********************************IRSSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSR**************************PEDDFNDDDEFYDSDSSDVVPLGSLPVDHIAERLQ**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDDPSQGTIRSSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGASSSMAEYEDGSQSENYDEDEFYPEDDFNDDDEFYDSDSSDVVPLGSLPVDHIAERLQRK
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	356	2.2.26 [Sep-21-2011]
Q9LDA9	564	CRS2-associated factor 2,	yes	no	0.980	0.618	0.663	1e-131
Q84N48	611	CRS2-associated factor 2,	N/A	no	0.988	0.576	0.569	1e-115
Q657G7	607	CRS2-associated factor 2,	yes	no	0.985	0.578	0.562	1e-114
Q5VMQ5	701	CRS2-associated factor 1,	no	no	0.991	0.503	0.482	2e-85
Q9SL79	701	CRS2-associated factor 1,	no	no	0.575	0.292	0.673	4e-85
Q84N49	674	CRS2-associated factor 1,	N/A	no	0.564	0.298	0.679	9e-83
Q6Z4U2	428	CRS2-associated factor 1,	no	no	0.539	0.448	0.578	1e-63
Q0J7J7	366	CRS2-associated factor 2,	no	no	0.528	0.513	0.542	2e-59
Q8VYD9	405	CRS2-associated factor 1,	no	no	0.542	0.476	0.533	6e-59
Q9FFU1	358	CRS2-associated factor 2,	no	no	0.528	0.525	0.505	5e-56

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

 Score =  468 bits (1204), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 239/360 (66%), Positives = 287/360 (79%), Gaps = 11/360 (3%)

Query: 1   MLVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEK 60
           ML+KP + DNRQVNLGRDG THNMLELIHSHWKRRRV K++CKGVPTVDM+NVCR LEEK
Sbjct: 210 MLIKPHMHDNRQVNLGRDGFTHNMLELIHSHWKRRRVCKVRCKGVPTVDMNNVCRVLEEK 269

Query: 61  TGGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADEL 120
           TGG+II RVGG+VYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQE PEGLTK EA E 
Sbjct: 270 TGGEIIHRVGGVVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEVPEGLTKEEAHEF 329

Query: 121 RRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVP 180
           R KGKSL PICKL+KNGVY++LV+DVR+AFE SSLVKV+C G+  SDYKK+GAKLKELVP
Sbjct: 330 RVKGKSLRPICKLSKNGVYVSLVKDVRDAFELSSLVKVDCPGLEPSDYKKIGAKLKELVP 389

Query: 181 CVLLSFDDEQILMWRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDDPS---QGTIR 237
           CVLLSFDDEQILMWRG++WKS + + P   +  + +   + D S  PS++ +     T  
Sbjct: 390 CVLLSFDDEQILMWRGREWKSRFVDNPLIPSLSETNTTNELDPSDKPSEEQTVANPSTTI 449

Query: 238 SSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGA 297
           SSPKMISLW+RA+ES+KA++L+E++LGPDDLLKKVEE EG S AAEH+Y A+VLS  DGA
Sbjct: 450 SSPKMISLWQRALESSKAVILEELDLGPDDLLKKVEELEGTSLAAEHTYTAMVLSNTDGA 509

Query: 298 SSSMAEYEDGSQSENYDEDEFYPEDDFNDDDEFYDSDSSDVV-PLGSLPVDHIAERLQRK 356
           +    + +D S+       E+Y + D + DDE  D +S D V P+GSLPVD I  +L+ +
Sbjct: 510 AEDYVDEKDRSE-------EYYSDIDDDFDDECSDDESLDPVGPVGSLPVDKIVRKLRER 562

Essential protein required for the splicing of group IIB introns in chloroplasts. Forms splicing particles with CRS2. Interacts with RNA and confers intron specificity of the splicing particles.
Arabidopsis thaliana (taxid: 3702)

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

 Score =  414 bits (1065), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 210/369 (56%), Positives = 271/369 (73%), Gaps = 17/369 (4%)

Query: 2   LVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKT 61
           LVKP +  NRQ+N+GRDGLTHNMLE+IH HW+R+ + K++C+GVPTVDM N+C  LEEK+
Sbjct: 242 LVKPHISHNRQLNIGRDGLTHNMLEMIHCHWRRQEICKVRCRGVPTVDMKNLCYHLEEKS 301

Query: 62  GGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADELR 121
           GGK+I RVGG+V+L+RGR+Y+ +TRP+YPLMLWKPA PVYPKLI+EAP+G TK EADE+R
Sbjct: 302 GGKVIHRVGGVVFLYRGRHYDPKTRPRYPLMLWKPATPVYPKLIKEAPDGFTKEEADEMR 361

Query: 122 RKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPC 181
           RKG+ LLPICKLAKNG+Y+TLV+DVR+AFEGS LVK++C+G++ SDYKK+GAKL++LVPC
Sbjct: 362 RKGRDLLPICKLAKNGIYITLVKDVRDAFEGSDLVKIDCEGLNPSDYKKIGAKLRDLVPC 421

Query: 182 VLLSFDDEQILMWRGKDWKSMYPEPPSFSNPV---DLDIAGDADGSGTPSDDPSQGTIRS 238
           VLLSFDDEQILM RGK+WKS Y +P +    V   +L +    + S   SD  +Q  IR 
Sbjct: 422 VLLSFDDEQILMHRGKEWKSRYSKPLTLIPKVPKNNLAMTSVMNSSDEVSDANTQVAIRE 481

Query: 239 --SPKMISLWKRAIESTKALVLDEI---NLGPDDLLKKVEEFEGISQAAEHSYPALVLSR 293
              PKM  LWK A++S+ AL+LD+    NL PD LL  VEEF   SQA EHS+PAL+++ 
Sbjct: 482 VLRPKMFKLWKSAVDSSLALLLDDAEANNLTPDSLLTLVEEFSVTSQAVEHSFPALLVTN 541

Query: 294 EDGASSSM-AEY---EDGSQSENYDEDEFYPEDDFNDDDEFYDSDS----SDVVPLGSLP 345
            D ++ S+ AEY   E  +     +E +     D  DD+ F D D        VPLGSLP
Sbjct: 542 GDASTDSLSAEYMNDEPETSVAGNEEGQLEQSPDLRDDEHF-DVDMFERLESSVPLGSLP 600

Query: 346 VDHIAERLQ 354
           +D + ERL 
Sbjct: 601 IDSMIERLN 609

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 =  410 bits (1054), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 208/370 (56%), Positives = 273/370 (73%), Gaps = 19/370 (5%)

Query: 2   LVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKT 61
           LVKP +  NRQ+N+GRDGLTHNMLE+IH HW+R+ + K++C+GVPTVDM N+C  LEEK+
Sbjct: 238 LVKPHISHNRQLNIGRDGLTHNMLEMIHCHWRRQEICKVRCRGVPTVDMKNLCYHLEEKS 297

Query: 62  GGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADELR 121
           GGK+I RVGG+V+L+RGRNYN RTRP+YPLMLWKPA PVYPKLIQEAPEGLTK EADE+R
Sbjct: 298 GGKVIHRVGGVVFLYRGRNYNPRTRPRYPLMLWKPATPVYPKLIQEAPEGLTKEEADEMR 357

Query: 122 RKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPC 181
           R+GK LLPICKLAKNG+Y+ LVRDVR+AFEGS LVK++C+G++ SDYKK+GAKL++LVPC
Sbjct: 358 RRGKDLLPICKLAKNGIYIYLVRDVRDAFEGSDLVKIDCEGLNPSDYKKIGAKLRDLVPC 417

Query: 182 VLLSFDDEQILMWRGKDWKSMYPEPPSFSNPV---DLDIAGDADGSGTPSDDPSQGTIRS 238
           VLLSFD+EQILM+RGK+WKS YP+P +    +   ++ ++ D   S   +DD  +  +R 
Sbjct: 418 VLLSFDNEQILMFRGKEWKSRYPKPLTLIPKIRKNNVPMSSDESSSDEATDDDDRLAVRE 477

Query: 239 --SPKMISLWKRAIESTKALVLDEIN---LGPDDLLKKVEEFEGISQAAEHSYPALVLSR 293
              PKM  LW  AIES+ AL+LD+     L PD LL +VE+F   SQ  EHS+PA++++ 
Sbjct: 478 VLRPKMFELWTNAIESSVALMLDDAEVDALTPDSLLTRVEDFSVTSQVVEHSFPAVLVAN 537

Query: 294 EDGASSSM-AEY-----EDGS---QSENYDEDEFYPEDDFNDDDEFYDSDSSDVVPLGSL 344
           ++     + AEY     E G+   Q   + E     EDD  +DD     +SS  VPLG+L
Sbjct: 538 DESNPDVLNAEYTEDEPETGTLEPQQHEFTESSDVAEDDHFEDDMLKRLESS--VPLGAL 595

Query: 345 PVDHIAERLQ 354
           P+D + ++L 
Sbjct: 596 PIDAVVKQLN 605

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

 Score =  316 bits (809), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 177/367 (48%), Positives = 229/367 (62%), Gaps = 14/367 (3%)

Query: 2   LVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKT 61
           LVK  LK  RQ+N+GRDGLTHNMLE IHSHWKR+RV KIKCKGV TVDMDNVC++LEEK 
Sbjct: 193 LVKATLKTKRQLNIGRDGLTHNMLENIHSHWKRKRVCKIKCKGVCTVDMDNVCQQLEEKV 252

Query: 62  GGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADELR 121
           GGK+I   GG+++LFRGRNYNYRTRP YPLMLWKPAAPVYP+L+++ P+GLT  EA+++R
Sbjct: 253 GGKVIHHQGGVIFLFRGRNYNYRTRPIYPLMLWKPAAPVYPRLVKKIPDGLTPDEAEDMR 312

Query: 122 RKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPC 181
           ++G+ L PICKL KNGVYL LV+ VR AFE   LV+V+C G++ SD +K+GAKLK+LVPC
Sbjct: 313 KRGRQLPPICKLGKNGVYLNLVKQVREAFEACDLVRVDCSGLNKSDCRKIGAKLKDLVPC 372

Query: 182 VLLSFDDEQILMWRGKDWKSMYP--EPPSFSNPVDLDIAGDADGSG---TPSDDPSQGTI 236
            LLSF+ E ILMWRG DWKS  P  E   F    D  +     GSG   TP +  +  T 
Sbjct: 373 TLLSFEFEHILMWRGNDWKSSLPPLEENDFKVASDQILNSKEAGSGSALTPIELVNNATS 432

Query: 237 RSSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDG 296
                +I   ++  +S K+   + + LG       V   EGI      +   +  S  + 
Sbjct: 433 LKKCNLIEGAEKLEDSMKSSFENGMILGSACGNPGVCNSEGIDGTESSADAPIEFSPSNS 492

Query: 297 A-----SSSMAEYEDGS---QSENYDEDEFYPEDDFNDDDEFYDSDSSDVVPLGSLPVDH 348
           A     S +   Y   S   +SEN +  E YP D   + ++  D   +    +GS    H
Sbjct: 493 ARDLDPSQTSTLYCQSSLLDKSENGELIEMYP-DRCGNSEQSPDVPEALTCLMGSSDEIH 551

Query: 349 IAERLQR 355
             E ++R
Sbjct: 552 ELETMRR 558

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

 Score =  315 bits (807), Expect = 4e-85,   Method: Compositional matrix adjust.
 Identities = 138/205 (67%), Positives = 172/205 (83%)

Query: 2   LVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKT 61
           LV   LK  RQ+N+GRDGLTHNML  IH  WKRRRV KIKCKGV TVDMDNVC +LEEK 
Sbjct: 251 LVTSCLKTTRQLNMGRDGLTHNMLNNIHDLWKRRRVCKIKCKGVCTVDMDNVCEQLEEKI 310

Query: 62  GGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADELR 121
           GGK+I+R GG+++LFRGRNYN+RTRP++PLMLWKP APVYP+LIQ+ PEGLT+ EA  +R
Sbjct: 311 GGKVIYRRGGVLFLFRGRNYNHRTRPRFPLMLWKPVAPVYPRLIQQVPEGLTRQEATNMR 370

Query: 122 RKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPC 181
           RKG+ L+PICKL KNGVY  LV++V+ AFE   LV+++C+GM  SD++K+GAKLK+LVPC
Sbjct: 371 RKGRELMPICKLGKNGVYCDLVKNVKEAFEVCELVRIDCQGMKGSDFRKIGAKLKDLVPC 430

Query: 182 VLLSFDDEQILMWRGKDWKSMYPEP 206
           VL+SF++EQIL+WRG++WKS    P
Sbjct: 431 VLVSFENEQILIWRGREWKSSLTTP 455

Required for the splicing of group IIB introns in chloroplasts. Forms splicing particles with CRS2. Interacts with RNA and confers intron specificity of the splicing particles.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  307 bits (786), Expect = 9e-83,   Method: Compositional matrix adjust.
 Identities = 138/203 (67%), Positives = 163/203 (80%)

Query: 2   LVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKT 61
           LVK  LK  RQ+N+GRDGLTHNMLE IHSHWKR+RV KIKCKGV T+DMDN+C +LEEK 
Sbjct: 193 LVKGSLKSKRQLNMGRDGLTHNMLENIHSHWKRKRVCKIKCKGVCTIDMDNICHQLEEKV 252

Query: 62  GGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADELR 121
           GGK+I R GG+++LFRGRNYNYRTRP +PLMLWKP APVYP+L+ + P GLT  EA E+R
Sbjct: 253 GGKVIHRQGGVIFLFRGRNYNYRTRPCFPLMLWKPVAPVYPRLVTKVPGGLTPDEATEMR 312

Query: 122 RKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPC 181
            +G  L PICKL KNGVY  LV  VR AFE   LV+V+C G++ SD +K+GAKLK+LVPC
Sbjct: 313 TRGHQLPPICKLGKNGVYANLVNQVREAFEACDLVRVDCSGLNKSDCRKIGAKLKDLVPC 372

Query: 182 VLLSFDDEQILMWRGKDWKSMYP 204
           +LLSF+ E ILMWRG DWKS  P
Sbjct: 373 ILLSFEFEHILMWRGSDWKSSLP 395

Required for the splicing of group IIB introns in chloroplasts. Forms splicing particles with CRS2. Interacts with RNA and confers intron specificity of the splicing particles.

Zea mays (taxid: 4577)

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

 Score =  243 bits (620), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 111/192 (57%), Positives = 146/192 (76%)

Query: 8   KDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIF 67
           +  +Q+NLGRDGLTHNML  IH+HWK    +++KC GVPTVDM NVC +LE+KTGG II 
Sbjct: 173 RTKKQINLGRDGLTHNMLNDIHNHWKNDEAVRVKCLGVPTVDMQNVCHQLEDKTGGLIIH 232

Query: 68  RVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADELRRKGKSL 127
           R GG + L+RGR+YN + RP  PLMLWKPA PVYP+LI+   EGLT  E  E+R+KG  +
Sbjct: 233 RHGGQLILYRGRHYNPKKRPVIPLMLWKPAEPVYPRLIKTTIEGLTVEETKEMRKKGLYV 292

Query: 128 LPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFD 187
             + KLAKNG Y +LV  VR+AF    LV+++ KG+  SDY+K+G KL++LVPC+++SFD
Sbjct: 293 PVLTKLAKNGYYASLVPMVRDAFLTDELVRIDSKGLPKSDYRKIGVKLRDLVPCIIVSFD 352

Query: 188 DEQILMWRGKDW 199
            EQI++WRGKD+
Sbjct: 353 KEQIIVWRGKDY 364

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  230 bits (586), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 102/188 (54%), Positives = 143/188 (76%)

Query: 10  NRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRV 69
           +RQ+NLG+ G+THNM++ IH+HWKR   ++IKC GVPT+DMDN+C  LE+KTGGK+I+R 
Sbjct: 163 SRQINLGKGGVTHNMIDDIHNHWKRAEAVRIKCLGVPTLDMDNICFHLEDKTGGKVIYRN 222

Query: 70  GGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADELRRKGKSLLP 129
             ++ L+RGRNY+ + RPQ PLMLWKP AP+YP+L+Q   +GLT  +  ELR  G +  P
Sbjct: 223 INILILYRGRNYDPKQRPQIPLMLWKPLAPIYPRLVQNVADGLTFEKTKELRNTGLNSSP 282

Query: 130 ICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDE 189
           + KL +NGVY+ +V  VR AF+   +V+++C  + +SD KK+G KL++LVPCV L F DE
Sbjct: 283 LMKLTRNGVYVNVVDRVREAFKTVEVVRLDCSHVGSSDCKKIGVKLRDLVPCVPLLFKDE 342

Query: 190 QILMWRGK 197
           QI++WRGK
Sbjct: 343 QIILWRGK 350

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 =  228 bits (581), Expect = 6e-59,   Method: Compositional matrix adjust.
 Identities = 103/193 (53%), Positives = 145/193 (75%)

Query: 8   KDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIF 67
           K  RQVNLGRDGLTHNML  +++HWK    +++KC GVPT+DM NV   LE+KT G+++ 
Sbjct: 175 KTKRQVNLGRDGLTHNMLNDVYNHWKHAEAVRVKCLGVPTLDMKNVIFHLEDKTFGQVVS 234

Query: 68  RVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADELRRKGKSL 127
           +  G + L+RGRNY+ + RP+ PLMLWKP  PVYP+LI+   +GL+  E   +R+KG ++
Sbjct: 235 KHSGTLVLYRGRNYDPKKRPKIPLMLWKPHEPVYPRLIKTTIDGLSIDETKAMRKKGLAV 294

Query: 128 LPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFD 187
             + KLAKNG Y +LV  VR+AF  S LV+++C G+   DYKK+GAKL++LVPC+L++FD
Sbjct: 295 PALTKLAKNGYYGSLVPMVRDAFLVSELVRIDCLGLERKDYKKIGAKLRDLVPCILVTFD 354

Query: 188 DEQILMWRGKDWK 200
            EQ+++WRGKD+K
Sbjct: 355 KEQVVIWRGKDYK 367

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  218 bits (555), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 95/188 (50%), Positives = 137/188 (72%)

Query: 10  NRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRV 69
            RQ+NLG+ G+THNM++ IH+HWK+   ++IKC GVPT+DMDN+C  LEEK+GGKI++R 
Sbjct: 161 TRQINLGKGGVTHNMIDDIHNHWKKAEAVRIKCLGVPTLDMDNICFHLEEKSGGKIVYRN 220

Query: 70  GGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADELRRKGKSLLP 129
             ++ L+RGRNY+ ++RP  PLMLWKP  P+YP+L++   +GL   E  E+R +G     
Sbjct: 221 INILVLYRGRNYDPKSRPIIPLMLWKPHPPIYPRLVKNVADGLEFEETKEMRNRGLHSPA 280

Query: 130 ICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDE 189
           + KL +NGVY+ +V  VR  FE   +V+++C  +  SD K++G KLKE+VPCV + F DE
Sbjct: 281 LMKLTRNGVYVNVVGRVREEFETEEIVRLDCTHVGMSDCKRIGVKLKEMVPCVPILFKDE 340

Query: 190 QILMWRGK 197
           QI++WRGK
Sbjct: 341 QIILWRGK 348

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

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	356
224110940	506	predicted protein [Populus trichocarpa]	0.994	0.699	0.722	1e-146
225425575	561	PREDICTED: CRS2-associated factor 2, chl	0.980	0.622	0.719	1e-144
359473240	560	PREDICTED: LOW QUALITY PROTEIN: CRS2-ass	0.974	0.619	0.714	1e-144
255568848	561	conserved hypothetical protein [Ricinus	0.997	0.632	0.704	1e-140
356524038	593	PREDICTED: CRS2-associated factor 2, chl	0.926	0.556	0.687	1e-132
307135966	603	RNA splicing factor [Cucumis melo subsp.	0.974	0.575	0.667	1e-131
449434945	602	PREDICTED: LOW QUALITY PROTEIN: CRS2-ass	0.966	0.571	0.662	1e-131
449478585	603	PREDICTED: LOW QUALITY PROTEIN: CRS2-ass	0.966	0.570	0.662	1e-131
297850808	565	hypothetical protein ARALYDRAFT_335585 [	0.971	0.612	0.687	1e-130
22329751	564	CRS2-associated factor 2 [Arabidopsis th	0.980	0.618	0.663	1e-129

>gi|224110940|ref|XP_002315689.1| predicted protein [Populus trichocarpa] gi|222864729|gb|EEF01860.1| predicted protein [Populus trichocarpa]

 Score =  524 bits (1350), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 260/360 (72%), Positives = 301/360 (83%), Gaps = 6/360 (1%)

Query: 1   MLVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEK 60
           +L+KP L DNRQVNLG DGLTHNMLEL+HSHWKRRRV K++CKGVPTVDMDNVCR LEEK
Sbjct: 149 LLIKPHLSDNRQVNLGEDGLTHNMLELVHSHWKRRRVCKVRCKGVPTVDMDNVCRHLEEK 208

Query: 61  TGGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADEL 120
           TGGKII RVGG+VYLFRGRNYNYRTRPQYP+MLWKPA PVYPKLIQEAPEGLTK +ADE 
Sbjct: 209 TGGKIIHRVGGVVYLFRGRNYNYRTRPQYPVMLWKPATPVYPKLIQEAPEGLTKAQADEF 268

Query: 121 RRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVP 180
           R+KGK+LLPICKLAKNGVY+TLVRDVR AFEGS LVKV+CKGM  SDYKKLGAKLK+LVP
Sbjct: 269 RKKGKNLLPICKLAKNGVYITLVRDVRAAFEGSPLVKVDCKGMEPSDYKKLGAKLKDLVP 328

Query: 181 CVLLSFDDEQILMWRGKDWKSMYPEP-PSFSNPVDLDIA---GDADGSGTPSDDPSQGTI 236
           CVLLSFDDEQILMWRG+DWKSMYPE  PS S P +LDIA    D+  S    D+     +
Sbjct: 329 CVLLSFDDEQILMWRGQDWKSMYPEARPSISFPAELDIASGSDDSGKSDDDCDNSDAKIL 388

Query: 237 RSSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDG 296
            SSPKM+ LWK A+ES KA++LDEI+LGPD LL KVEEFEGISQA EHSYPALV+S EDG
Sbjct: 389 SSSPKMMLLWKHALESNKAILLDEIDLGPDALLTKVEEFEGISQATEHSYPALVMSSEDG 448

Query: 297 ASSSMAEYEDGSQSENYDEDEFYPEDDFNDDDEFYDSDSSDVVPLGSLPVDHIAERLQRK 356
           +S+S++ +ED S SEN+ ED+ Y +D++ D + F + ++S   P GSL +D IAE+L +K
Sbjct: 449 SSNSISTFEDDSHSENFSEDDMYSDDEYYDSESFEELETS--APPGSLSIDLIAEKLDKK 506

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225425575|ref|XP_002267079.1| PREDICTED: CRS2-associated factor 2, chloroplastic [Vitis vinifera] gi|297739063|emb|CBI28552.3| unnamed protein product [Vitis vinifera]

 Score =  516 bits (1329), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 259/360 (71%), Positives = 295/360 (81%), Gaps = 11/360 (3%)

Query: 1   MLVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEK 60
           MLVKP L  NRQVNLGRDGLTHNMLELIHSHWKR+RV K++CKGVPT+DMDNVC  LEEK
Sbjct: 203 MLVKPYLSHNRQVNLGRDGLTHNMLELIHSHWKRQRVCKVRCKGVPTIDMDNVCHHLEEK 262

Query: 61  TGGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADEL 120
           TGGKII RVGG+VYLFRGRNYNYRTRPQYP+MLWKPAAPVYPKLIQEAPEGLTK EADEL
Sbjct: 263 TGGKIIHRVGGVVYLFRGRNYNYRTRPQYPVMLWKPAAPVYPKLIQEAPEGLTKFEADEL 322

Query: 121 RRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVP 180
           R KGK+L+PIC+L KNGVY++LV+DVR+AFEGS LVK++CKGMHASDYKK+GAKLKELVP
Sbjct: 323 RMKGKNLIPICRLVKNGVYISLVKDVRDAFEGSPLVKIDCKGMHASDYKKIGAKLKELVP 382

Query: 181 CVLLSFDDEQILMWRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDDPSQ---GTIR 237
           CVLLSFDDEQIL WRG  WKSMY   PSF  PV  D+A   +GSG P  +  +     + 
Sbjct: 383 CVLLSFDDEQILTWRGHGWKSMYQGAPSFLIPVVADVASGLEGSGIPKSNHHRLDTKAVS 442

Query: 238 SSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGA 297
           +SPKM+SLWK AIES+KAL+LDE  LGPD LLK VEEFEGISQA EHSYPALV+S EDG 
Sbjct: 443 ASPKMMSLWKSAIESSKALLLDETGLGPDALLKVVEEFEGISQATEHSYPALVMSSEDGT 502

Query: 298 SSSMAEYEDGSQSENYDEDEFYPEDDFNDDDEFYDSDS----SDVVPLGSLPVDHIAERL 353
             + AEYE G  SE+Y EDE Y   + +DDDE+  ++S       VPLGSLPVD +A++L
Sbjct: 503 GGTKAEYE-GYNSEDYSEDEMY---NDDDDDEYLVNESLEEMESPVPLGSLPVDLLAKQL 558

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359473240|ref|XP_003631275.1| PREDICTED: LOW QUALITY PROTEIN: CRS2-associated factor 2, chloroplastic-like [Vitis vinifera]

 Score =  516 bits (1329), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 258/361 (71%), Positives = 291/361 (80%), Gaps = 14/361 (3%)

Query: 1   MLVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEK 60
           MLVKP L  NRQVNLGRDGLTHNMLELIHSHWKR+RV K+ CKGVPT+DMDNVC  LEEK
Sbjct: 203 MLVKPYLSHNRQVNLGRDGLTHNMLELIHSHWKRQRVCKVWCKGVPTIDMDNVCHHLEEK 262

Query: 61  TGGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADEL 120
           TGGKII RVGG+VYLFRGRNYNYRTRPQYP+MLWKPAAPVYPKLIQEAPEGLTK EADEL
Sbjct: 263 TGGKIIHRVGGVVYLFRGRNYNYRTRPQYPVMLWKPAAPVYPKLIQEAPEGLTKFEADEL 322

Query: 121 RRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVP 180
           R KG +L+PIC+L KNGVY++LV+DVR+AFEGS LVK++CKGMHASDYKK+GAKLKE VP
Sbjct: 323 RMKGXNLIPICRLVKNGVYISLVKDVRDAFEGSPLVKIDCKGMHASDYKKIGAKLKESVP 382

Query: 181 CVLLSFDDEQILMWRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDDPSQ---GTIR 237
           CVLLSFDDEQIL WRG  WKSMY   PSF  PV  D+A   +GSG P  +  +     + 
Sbjct: 383 CVLLSFDDEQILTWRGHGWKSMYQGAPSFLIPVVADVASGLEGSGVPKSNHHRLDTKAVS 442

Query: 238 SSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGA 297
           +SPKM+SLWK AIES+KAL+LDEI LGPD LLK VEEFEGISQA EHSYPALV+S EDG 
Sbjct: 443 ASPKMMSLWKSAIESSKALLLDEIGLGPDALLKVVEEFEGISQATEHSYPALVMSSEDGT 502

Query: 298 SSSMAEYEDGSQSENYDEDEFYPEDDFNDDDEFYDSDSS-----DVVPLGSLPVDHIAER 352
             + AE+E G  SE+Y EDE Y     NDDD+ Y  + S       VPLGSLPVD +A++
Sbjct: 503 GGTKAEHE-GYNSEDYSEDEMY-----NDDDDEYLVNESLEEMESPVPLGSLPVDLLAKQ 556

Query: 353 L 353
           L
Sbjct: 557 L 557

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255568848|ref|XP_002525395.1| conserved hypothetical protein [Ricinus communis] gi|223535358|gb|EEF37033.1| conserved hypothetical protein [Ricinus communis]

 Score =  504 bits (1299), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 255/362 (70%), Positives = 304/362 (83%), Gaps = 7/362 (1%)

Query: 2   LVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKT 61
           LVKPLL DNRQVNLGRDGLTHNMLELIHSHW+R  V K++CKG+PTVDM+N+CR LEE+T
Sbjct: 200 LVKPLLSDNRQVNLGRDGLTHNMLELIHSHWRRSPVCKVRCKGIPTVDMNNICRHLEERT 259

Query: 62  GGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADELR 121
           GGKII+R+GG+VYLF GRNY+YR+R +YP+MLWKPAAPVYPKLIQ+APEGLTK EADE R
Sbjct: 260 GGKIIYRIGGVVYLFCGRNYDYRSRVRYPVMLWKPAAPVYPKLIQDAPEGLTKAEADEFR 319

Query: 122 RKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPC 181
            KGK+LLPICKLAKNGVY+TLVRDVRNAFEGS LVK++CKGM+ SDYKKLGAKLKELVPC
Sbjct: 320 EKGKNLLPICKLAKNGVYITLVRDVRNAFEGSPLVKIDCKGMNPSDYKKLGAKLKELVPC 379

Query: 182 VLLSFDDEQILMWRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDDPSQ---GTIRS 238
           VLLSFDDE ILMWRG++WK MYPE PS S P   D    +D SG   DDPS      +RS
Sbjct: 380 VLLSFDDEHILMWRGQNWKPMYPEVPSVSTPDAADFTSGSDDSGKFEDDPSNRDANVVRS 439

Query: 239 SPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGAS 298
           SPKM+SLW+ AIES+KA++LD+I+LGPDDLL+KVEEFE ISQA EHSYPA++LS EDGA+
Sbjct: 440 SPKMMSLWECAIESSKAILLDQIDLGPDDLLRKVEEFECISQATEHSYPAVILSSEDGAN 499

Query: 299 SSMAEYEDGSQSENYDEDEFYPEDDFNDDDEFYDSDSSD----VVPLGSLPVDHIAERLQ 354
           +++A + D S S ++ E++    DD  +DDE+YDSDS +     VPLGSLPVD +AERL 
Sbjct: 500 NTVAAFGDDSLSGSFTEEDDTYTDDEYEDDEYYDSDSFEEVDTAVPLGSLPVDRLAERLH 559

Query: 355 RK 356
           ++
Sbjct: 560 QE 561

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356524038|ref|XP_003530640.1| PREDICTED: CRS2-associated factor 2, chloroplastic-like [Glycine max]

 Score =  477 bits (1227), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 233/339 (68%), Positives = 274/339 (80%), Gaps = 9/339 (2%)

Query: 1   MLVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEK 60
           MLVKP++  NRQVNLGRDGLTHNMLELIHSHWKRRRV KI+C GVPTVDMDNVC  +EEK
Sbjct: 204 MLVKPMMSYNRQVNLGRDGLTHNMLELIHSHWKRRRVCKIRCLGVPTVDMDNVCHHIEEK 263

Query: 61  TGGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADEL 120
           TGGKII RVGG+VYLFRGRNYNY TRPQYP+MLWKPAAPVYPKLIQ+AP GLTK EADEL
Sbjct: 264 TGGKIIHRVGGVVYLFRGRNYNYSTRPQYPVMLWKPAAPVYPKLIQDAPGGLTKDEADEL 323

Query: 121 RRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVP 180
           R KGKSLLPICKLAKNGVY +LV+DVR+AFEGS LVK+NCKG+  SDYKK+GAKLK+LVP
Sbjct: 324 RMKGKSLLPICKLAKNGVYTSLVKDVRDAFEGSILVKINCKGLDPSDYKKIGAKLKDLVP 383

Query: 181 CVLLSFDDEQILMWRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDDPSQ---GTIR 237
           CVLLSFDDEQILMWRGKDWKS YP+P     P   +I G+ + SG   D+  +     + 
Sbjct: 384 CVLLSFDDEQILMWRGKDWKSRYPQPLPVFTPSKANIVGNLENSGETDDNQYKHDGNMVN 443

Query: 238 SSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVL-SREDG 296
           +SPKM+SLWKRAI+S+KAL+LDE NLGPD LL+KVEEF+ +SQA EHS+PA  L S+E+ 
Sbjct: 444 TSPKMLSLWKRAIQSSKALLLDEFNLGPDALLEKVEEFDTVSQALEHSHPAFSLSSKEND 503

Query: 297 ASSSMAEYEDGSQSENYDEDEFYPEDDFNDDDEFYDSDS 335
           A  S A +E+     +Y  D  + E+D+   ++ Y SD+
Sbjct: 504 AEGSSANFEN-----SYSSDGLHTEEDYAKFEDSYSSDA 537

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|307135966|gb|ADN33825.1| RNA splicing factor [Cucumis melo subsp. melo]

 Score =  475 bits (1223), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 239/358 (66%), Positives = 286/358 (79%), Gaps = 11/358 (3%)

Query: 1   MLVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEK 60
           MLVKP L  NRQVNLGRDGLTHNMLELIHSHWKR+RV K++CKGVPTVDMDN+C  +EEK
Sbjct: 249 MLVKPHLSHNRQVNLGRDGLTHNMLELIHSHWKRQRVCKVRCKGVPTVDMDNICHHIEEK 308

Query: 61  TGGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADEL 120
           TGGKII RVGG++YLFRGRNYNYRTRPQYP+MLWKPAAPVYPKLIQEAPEGLTK EA+EL
Sbjct: 309 TGGKIIHRVGGVLYLFRGRNYNYRTRPQYPVMLWKPAAPVYPKLIQEAPEGLTKEEANEL 368

Query: 121 RRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVP 180
           R KGK+LLPICKLAKNGVY++LV DVR+AFEGS LVK++C GMH SDYKKLGAKLKELVP
Sbjct: 369 RMKGKNLLPICKLAKNGVYISLVDDVRHAFEGSILVKIDCTGMHESDYKKLGAKLKELVP 428

Query: 181 CVLLSFDDEQILMWRGKDWKSMYPE---PPSFSNPVDLDIAGDADGSGTPSD--DPSQGT 235
           CVLLSFD+EQILMWRGKDWKS+  +    P  S     D  G +  S   SD  + +  T
Sbjct: 429 CVLLSFDNEQILMWRGKDWKSVISDDRSAPLPSRASSNDSLGSSGESVENSDLLNGNHHT 488

Query: 236 IRSSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSRED 295
           I++SPKM  LW+RAI+S KAL+LDEI L PD+LL++VEEFE ISQA EHSYPA + S E+
Sbjct: 489 IKTSPKMKLLWERAIDSNKALMLDEIGLAPDELLERVEEFERISQATEHSYPAFITSSEE 548

Query: 296 GASSSMAEYEDGSQSENYDEDEFYPEDDFNDDDEFYDSDSSDVVPLGSLPVDHIAERL 353
            +S +     D  +S+++ E  +  +DD   +++ +D +   +VPLGSLPVD IA++L
Sbjct: 549 VSSPA-----DSPESQDHSEANYNSDDDVGREEDLFD-NVDPLVPLGSLPVDIIAKKL 600

Source: Cucumis melo subsp. melo

Species: Cucumis melo

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449434945|ref|XP_004135256.1| PREDICTED: LOW QUALITY PROTEIN: CRS2-associated factor 2, chloroplastic-like [Cucumis sativus]

 Score =  475 bits (1222), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 239/361 (66%), Positives = 284/361 (78%), Gaps = 17/361 (4%)

Query: 1   MLVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEK 60
           MLVKP L  NRQVNLGRDGLTHNMLELIHSHWKR+RV K++CKGVPTVDMDN+C  +EEK
Sbjct: 248 MLVKPHLSHNRQVNLGRDGLTHNMLELIHSHWKRQRVCKVRCKGVPTVDMDNICHHIEEK 307

Query: 61  TGGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADEL 120
           TGGKII RVGG++YLFRGRNYNYRTRPQYP+MLWKPAAPVYPKLIQEAPEGLTK EA+ L
Sbjct: 308 TGGKIIHRVGGVLYLFRGRNYNYRTRPQYPVMLWKPAAPVYPKLIQEAPEGLTKKEANVL 367

Query: 121 RRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVP 180
           R KGK+LLPICKLAKNGVY++LV DVR+AFEGS LVK++C GMH SDYKKLGAKLKELVP
Sbjct: 368 RMKGKNLLPICKLAKNGVYISLVNDVRHAFEGSILVKIDCTGMHESDYKKLGAKLKELVP 427

Query: 181 CVLLSFDDEQILMWRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDD--------PS 232
           CVLLSFD+EQILMWRGKDWKS+  +  S   P     A   D  G+P +          +
Sbjct: 428 CVLLSFDNEQILMWRGKDWKSIISDDRSAPLP---SRASSNDSLGSPGESLENSDLLHGN 484

Query: 233 QGTIRSSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLS 292
             TI++SPKM  LW+ AI+S KAL+LDEI L PDDLL+KVEEFE ISQA EHSYPA + S
Sbjct: 485 HHTIKTSPKMKLLWEHAIDSNKALLLDEIGLAPDDLLEKVEEFERISQATEHSYPAFITS 544

Query: 293 REDGASSSMAEYEDGSQSENYDEDEFYPEDDFNDDDEFYDSDSSDVVPLGSLPVDHIAER 352
            ED +S      +D  +S+++ E  +  +DD   +++ +D ++  +VPLGSLPVD IA++
Sbjct: 545 SEDVSSP-----DDSPKSQDHTEANYNSDDDVGREEDLFD-NADPLVPLGSLPVDIIAKK 598

Query: 353 L 353
           L
Sbjct: 599 L 599

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449478585|ref|XP_004155360.1| PREDICTED: LOW QUALITY PROTEIN: CRS2-associated factor 2, chloroplastic-like [Cucumis sativus]

 Score =  475 bits (1222), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 239/361 (66%), Positives = 284/361 (78%), Gaps = 17/361 (4%)

Query: 1   MLVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEK 60
           MLVKP L  NRQVNLGRDGLTHNMLELIHSHWKR+RV K++CKGVPTVDMDN+C  +EEK
Sbjct: 249 MLVKPHLSHNRQVNLGRDGLTHNMLELIHSHWKRQRVCKVRCKGVPTVDMDNICHHIEEK 308

Query: 61  TGGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADEL 120
           TGGKII RVGG++YLFRGRNYNYRTRPQYP+MLWKPAAPVYPKLIQEAPEGLTK EA+ L
Sbjct: 309 TGGKIIHRVGGVLYLFRGRNYNYRTRPQYPVMLWKPAAPVYPKLIQEAPEGLTKKEANVL 368

Query: 121 RRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVP 180
           R KGK+LLPICKLAKNGVY++LV DVR+AFEGS LVK++C GMH SDYKKLGAKLKELVP
Sbjct: 369 RMKGKNLLPICKLAKNGVYISLVNDVRHAFEGSILVKIDCTGMHESDYKKLGAKLKELVP 428

Query: 181 CVLLSFDDEQILMWRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDD--------PS 232
           CVLLSFD+EQILMWRGKDWKS+  +  S   P     A   D  G+P +          +
Sbjct: 429 CVLLSFDNEQILMWRGKDWKSIISDDCSAPLP---SRASSNDSLGSPGESLENSDLLHDN 485

Query: 233 QGTIRSSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLS 292
             TI++SPKM  LW+ AI+S KAL+LDEI L PDDLL+KVEEFE ISQA EHSYPA + S
Sbjct: 486 HHTIKTSPKMKLLWEHAIDSNKALLLDEIGLAPDDLLEKVEEFERISQATEHSYPAFITS 545

Query: 293 REDGASSSMAEYEDGSQSENYDEDEFYPEDDFNDDDEFYDSDSSDVVPLGSLPVDHIAER 352
            ED +S      +D  +S+++ E  +  +DD   +++ +D ++  +VPLGSLPVD IA++
Sbjct: 546 SEDVSSP-----DDSPKSQDHTEANYNSDDDVGREEDLFD-NADPLVPLGSLPVDIIAKK 599

Query: 353 L 353
           L
Sbjct: 600 L 600

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297850808|ref|XP_002893285.1| hypothetical protein ARALYDRAFT_335585 [Arabidopsis lyrata subsp. lyrata] gi|297339127|gb|EFH69544.1| hypothetical protein ARALYDRAFT_335585 [Arabidopsis lyrata subsp. lyrata]

 Score =  469 bits (1208), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 249/362 (68%), Positives = 289/362 (79%), Gaps = 16/362 (4%)

Query: 1   MLVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEK 60
           ML+KP + DNRQVNLGRDG THNMLELIHSHWKRRRV K++CKGVPTVDMDNVCR LEEK
Sbjct: 212 MLIKPHMHDNRQVNLGRDGFTHNMLELIHSHWKRRRVCKVRCKGVPTVDMDNVCRVLEEK 271

Query: 61  TGGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADEL 120
           TGG+II RVGG+VYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQE PEGLTK EA E 
Sbjct: 272 TGGEIIHRVGGVVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEVPEGLTKEEALEF 331

Query: 121 RRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVP 180
           R KGKSL PICKL+KNGVY++LV+DVR+AFE S LVKV+C G+  SDYKK+GAKLKELVP
Sbjct: 332 RVKGKSLRPICKLSKNGVYVSLVKDVRDAFELSPLVKVDCPGLEPSDYKKIGAKLKELVP 391

Query: 181 CVLLSFDDEQILMWRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSD-----DPSQGT 235
           CVLLSFDDEQILMWRG+DWKS + + P   +  + +IA + D S  PSD     DPS  T
Sbjct: 392 CVLLSFDDEQILMWRGRDWKSRFVDNPLIPSLSETNIANELDPSDKPSDEQTVSDPSS-T 450

Query: 236 IRSSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSRED 295
           I SSPKMISLWKRA+ES+KA++L+E++LGPDDLLKKVEE EG S AAEHSY A+VLS  D
Sbjct: 451 I-SSPKMISLWKRALESSKAVILEELDLGPDDLLKKVEELEGTSLAAEHSYTAMVLSNTD 509

Query: 296 GASSSMAEYEDGSQSENYDEDEFYPEDDFNDDDEFYDSDSSDVV-PLGSLPVDHIAERLQ 354
           GA+    +Y D     + D  E Y + D + DDE  D +S D V P+G+LPVD I  +L+
Sbjct: 510 GAAE---DYVD-----DKDRSEEYSDIDDDFDDECSDDESLDPVGPVGTLPVDKIVRKLR 561

Query: 355 RK 356
            +
Sbjct: 562 ER 563

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22329751|ref|NP_173754.2| CRS2-associated factor 2 [Arabidopsis thaliana] gi|75173812|sp|Q9LDA9.1|CAF2P_ARATH RecName: Full=CRS2-associated factor 2, chloroplastic; AltName: Full=Chloroplastic group IIA intron splicing facilitator CRS2-associated factor 2; Flags: Precursor gi|8778588|gb|AAF79596.1|AC007945_16 F28C11.4 [Arabidopsis thaliana] gi|9295699|gb|AAF87005.1|AC005292_14 F26F24.27 [Arabidopsis thaliana] gi|17065312|gb|AAL32810.1| Unknown protein [Arabidopsis thaliana] gi|21387129|gb|AAM47968.1| unknown protein [Arabidopsis thaliana] gi|332192262|gb|AEE30383.1| CRS2-associated factor 2 [Arabidopsis thaliana]

 Score =  468 bits (1204), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 239/360 (66%), Positives = 287/360 (79%), Gaps = 11/360 (3%)

Query: 1   MLVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEK 60
           ML+KP + DNRQVNLGRDG THNMLELIHSHWKRRRV K++CKGVPTVDM+NVCR LEEK
Sbjct: 210 MLIKPHMHDNRQVNLGRDGFTHNMLELIHSHWKRRRVCKVRCKGVPTVDMNNVCRVLEEK 269

Query: 61  TGGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADEL 120
           TGG+II RVGG+VYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQE PEGLTK EA E 
Sbjct: 270 TGGEIIHRVGGVVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEVPEGLTKEEAHEF 329

Query: 121 RRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVP 180
           R KGKSL PICKL+KNGVY++LV+DVR+AFE SSLVKV+C G+  SDYKK+GAKLKELVP
Sbjct: 330 RVKGKSLRPICKLSKNGVYVSLVKDVRDAFELSSLVKVDCPGLEPSDYKKIGAKLKELVP 389

Query: 181 CVLLSFDDEQILMWRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDDPS---QGTIR 237
           CVLLSFDDEQILMWRG++WKS + + P   +  + +   + D S  PS++ +     T  
Sbjct: 390 CVLLSFDDEQILMWRGREWKSRFVDNPLIPSLSETNTTNELDPSDKPSEEQTVANPSTTI 449

Query: 238 SSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGA 297
           SSPKMISLW+RA+ES+KA++L+E++LGPDDLLKKVEE EG S AAEH+Y A+VLS  DGA
Sbjct: 450 SSPKMISLWQRALESSKAVILEELDLGPDDLLKKVEELEGTSLAAEHTYTAMVLSNTDGA 509

Query: 298 SSSMAEYEDGSQSENYDEDEFYPEDDFNDDDEFYDSDSSDVV-PLGSLPVDHIAERLQRK 356
           +    + +D S+       E+Y + D + DDE  D +S D V P+GSLPVD I  +L+ +
Sbjct: 510 AEDYVDEKDRSE-------EYYSDIDDDFDDECSDDESLDPVGPVGSLPVDKIVRKLRER 562

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	356
TAIR|locus:2028100	564	CAF2 [Arabidopsis thaliana (ta	0.983	0.620	0.640	1.1e-119
TAIR|locus:2061604	701	CAF1 [Arabidopsis thaliana (ta	0.685	0.348	0.593	1.2e-90
TAIR|locus:2126694	405	AT4G31010 [Arabidopsis thalian	0.634	0.558	0.484	1.6e-56
TAIR|locus:2160195	358	AT5G54890 [Arabidopsis thalian	0.525	0.522	0.508	2.4e-53
TAIR|locus:2096662	1011	CFM2 "CRM family member 2" [Ar	0.205	0.072	0.356	2.4e-11
TAIR|locus:2094997	848	EMB1865 "embryo defective 1865	0.196	0.082	0.3	2.5e-09
TAIR|locus:2094558	881	CFM3A "CRM family member 3A" [	0.176	0.071	0.333	9e-08

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

 Score = 1178 (419.7 bits), Expect = 1.1e-119, P = 1.1e-119
 Identities = 230/359 (64%), Positives = 274/359 (76%)

Query:     1 MLVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEK 60
             ML+KP + DNRQVNLGRDG THNMLELIHSHWKRRRV K++CKGVPTVDM+NVCR LEEK
Sbjct:   210 MLIKPHMHDNRQVNLGRDGFTHNMLELIHSHWKRRRVCKVRCKGVPTVDMNNVCRVLEEK 269

Query:    61 TGGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADEL 120
             TGG+II RVGG+VYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQE PEGLTK EA E 
Sbjct:   270 TGGEIIHRVGGVVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEVPEGLTKEEAHEF 329

Query:   121 RRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVP 180
             R KGKSL PICKL+KNGVY++LV+DVR+AFE SSLVKV+C G+  SDYKK+GAKLKELVP
Sbjct:   330 RVKGKSLRPICKLSKNGVYVSLVKDVRDAFELSSLVKVDCPGLEPSDYKKIGAKLKELVP 389

Query:   181 CVLLSFDDEQILMWRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDDPS---QGTIR 237
             CVLLSFDDEQILMWRG++WKS + + P   +  + +   + D S  PS++ +     T  
Sbjct:   390 CVLLSFDDEQILMWRGREWKSRFVDNPLIPSLSETNTTNELDPSDKPSEEQTVANPSTTI 449

Query:   238 SSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGA 297
             SSPKMISLW+RA+ES+KA++L+E++LGPDDLLKKVEE EG S AAEH+Y A+VLS  DGA
Sbjct:   450 SSPKMISLWQRALESSKAVILEELDLGPDDLLKKVEELEGTSLAAEHTYTAMVLSNTDGA 509

Query:   298 SSSMAEYEDGSQSXXXXXXXXXXXXXXXXXXXXXXXXXXXVVPLGSLPVDHIAERLQRK 356
             +    + +D S+                            V P+GSLPVD I  +L+ +
Sbjct:   510 AEDYVDEKDRSEEYYSDIDDDFDDECSDDESLDP------VGPVGSLPVDKIVRKLRER 562

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 = 797 (285.6 bits), Expect = 1.2e-90, Sum P(4) = 1.2e-90
 Identities = 146/246 (59%), Positives = 190/246 (77%)

Query:     2 LVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKT 61
             LV   LK  RQ+N+GRDGLTHNML  IH  WKRRRV KIKCKGV TVDMDNVC +LEEK 
Sbjct:   251 LVTSCLKTTRQLNMGRDGLTHNMLNNIHDLWKRRRVCKIKCKGVCTVDMDNVCEQLEEKI 310

Query:    62 GGKIIFRVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADELR 121
             GGK+I+R GG+++LFRGRNYN+RTRP++PLMLWKP APVYP+LIQ+ PEGLT+ EA  +R
Sbjct:   311 GGKVIYRRGGVLFLFRGRNYNHRTRPRFPLMLWKPVAPVYPRLIQQVPEGLTRQEATNMR 370

Query:   122 RKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPC 181
             RKG+ L+PICKL KNGVY  LV++V+ AFE   LV+++C+GM  SD++K+GAKLK+LVPC
Sbjct:   371 RKGRELMPICKLGKNGVYCDLVKNVKEAFEVCELVRIDCQGMKGSDFRKIGAKLKDLVPC 430

Query:   182 VLLSFDDEQILMWRGKDWKSMYPEPPSFSNPV-DLDIAGDADGSGTPSDDPSQG-TIRSS 239
             VL+SF++EQIL+WRG++WKS    P    + + D+++         PS  P+Q  T+  +
Sbjct:   431 VLVSFENEQILIWRGREWKSSLTTPDKKGDILEDIEVDTALPEDDEPSVSPNQSQTMTQN 490

Query:   240 PKMISL 245
             P + S+
Sbjct:   491 PPLDSM 496

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:2126694 AT4G31010 [Arabidopsis thaliana (taxid:3702)]

 Score = 582 (209.9 bits), Expect = 1.6e-56, P = 1.6e-56
 Identities = 113/233 (48%), Positives = 159/233 (68%)

Query:     8 KDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIF 67
             K  RQVNLGRDGLTHNML  +++HWK    +++KC GVPT+DM NV   LE+KT G+++ 
Sbjct:   175 KTKRQVNLGRDGLTHNMLNDVYNHWKHAEAVRVKCLGVPTLDMKNVIFHLEDKTFGQVVS 234

Query:    68 RVGGLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADELRRKGKSL 127
             +  G + L+RGRNY+ + RP+ PLMLWKP  PVYP+LI+   +GL+  E   +R+KG ++
Sbjct:   235 KHSGTLVLYRGRNYDPKKRPKIPLMLWKPHEPVYPRLIKTTIDGLSIDETKAMRKKGLAV 294

Query:   128 LPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFD 187
               + KLAKNG Y +LV  VR+AF  S LV+++C G+   DYKK+GAKL++LVPC+L++FD
Sbjct:   295 PALTKLAKNGYYGSLVPMVRDAFLVSELVRIDCLGLERKDYKKIGAKLRDLVPCILVTFD 354

Query:   188 DEQILMWRGKDWKSMYP--EPPSF---SNPVDLDIAGDADGSGTPSDDPSQGT 235
              EQ+++WRGKD+K      E  SF    + +D D+  D   S    D P + T
Sbjct:   355 KEQVVIWRGKDYKPPKEDDEYSSFIHRESSIDSDV--DLSCSRGAQDSPDETT 405

GO:0003723 "RNA binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

GO:0010048 "vernalization response" evidence=RCA

GO:0048573 "photoperiodism, flowering" evidence=RCA

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

 Score = 552 (199.4 bits), Expect = 2.4e-53, P = 2.4e-53
 Identities = 95/187 (50%), Positives = 137/187 (73%)

Query:    11 RQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVG 70
             RQ+NLG+ G+THNM++ IH+HWK+   ++IKC GVPT+DMDN+C  LEEK+GGKI++R  
Sbjct:   162 RQINLGKGGVTHNMIDDIHNHWKKAEAVRIKCLGVPTLDMDNICFHLEEKSGGKIVYRNI 221

Query:    71 GLVYLFRGRNYNYRTRPQYPLMLWKPAAPVYPKLIQEAPEGLTKHEADELRRKGKSLLPI 130
              ++ L+RGRNY+ ++RP  PLMLWKP  P+YP+L++   +GL   E  E+R +G     +
Sbjct:   222 NILVLYRGRNYDPKSRPIIPLMLWKPHPPIYPRLVKNVADGLEFEETKEMRNRGLHSPAL 281

Query:   131 CKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQ 190
              KL +NGVY+ +V  VR  FE   +V+++C  +  SD K++G KLKE+VPCV + F DEQ
Sbjct:   282 MKLTRNGVYVNVVGRVREEFETEEIVRLDCTHVGMSDCKRIGVKLKEMVPCVPILFKDEQ 341

Query:   191 ILMWRGK 197
             I++WRGK
Sbjct:   342 IILWRGK 348

GO:0003723 "RNA binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 147 (56.8 bits), Expect = 2.4e-11, Sum P(2) = 2.4e-11
 Identities = 26/73 (35%), Positives = 44/73 (60%)

Query:    11 RQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVG 70
             +++ +G+ G+T  ++  IH  W+   V+KI C+ +  ++M      LE KTGG +I+R G
Sbjct:   183 KKLKIGKAGITEGIVNGIHERWRTTEVVKIFCEDISRMNMKRTHDVLETKTGGLVIWRSG 242

Query:    71 GLVYLFRGRNYNY 83
               + L+RG NY Y
Sbjct:   243 SKILLYRGVNYQY 255

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;RCA

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

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

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

 Score = 123 (48.4 bits), Expect = 2.5e-09, Sum P(2) = 2.5e-09
 Identities = 21/70 (30%), Positives = 43/70 (61%)

Query:    12 QVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGG 71
             ++N+ + GLT  ++E I+  W++  ++++K   V   DM      +E +TGG +I+R G 
Sbjct:   261 RINIPKAGLTQAVMEKIYDTWRKEELVRLKFHEVLARDMKTAHEIVERRTGGMVIWRAGS 320

Query:    72 LVYLFRGRNY 81
             ++ ++RG +Y
Sbjct:   321 VMVVYRGLDY 330

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009793 "embryo development ending in seed dormancy" evidence=NAS

GO:0009737 "response to abscisic acid stimulus" evidence=IDA

GO:0006655 "phosphatidylglycerol biosynthetic process" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0016117 "carotenoid biosynthetic process" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

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

 Score = 113 (44.8 bits), Expect = 9.0e-08, Sum P(2) = 9.0e-08
 Identities = 21/63 (33%), Positives = 38/63 (60%)

Query:    19 GLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYLFRG 78
             G+T   ++ I   WK   ++++K +G   ++M  +   LE+KTGG +I+R G  + L+RG
Sbjct:   246 GVTQVAVDAIKEKWKSAEIVRLKIEGASALNMRKMHEILEKKTGGLVIWRSGTSISLYRG 305

Query:    79 RNY 81
              +Y
Sbjct:   306 VSY 308

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;IDA

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

GO:0048316 "seed development" evidence=IGI

---

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)
Q9LDA9	CAF2P_ARATH	No assigned EC number	0.6638	0.9803	0.6187	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.X.5327.1 hypothetical protein (506 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	356
pfam01985	84	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	5e-21
smart01103	84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	2e-18
pfam01985	84	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	3e-17
smart01103	84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	3e-15
COG1534	97	COG1534, COG1534, Predicted RNA-binding protein co	7e-04

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

 Score = 85.6 bits (213), Expect = 5e-21
 Identities = 21/77 (27%), Positives = 37/77 (48%)

Query: 1  MLVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEK 60
           L          V +G++GLT  ++E I    ++  +IK+K  G    D   +   L EK
Sbjct: 8  YLRSLAHHLKPVVQIGKNGLTEGVVEEIDEALEKHELIKVKVLGNDREDRKEIAEELAEK 67

Query: 61 TGGKIIFRVGGLVYLFR 77
          TG +++  +G  + L+R
Sbjct: 68 TGAELVQVIGRTIVLYR 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 = 78.7 bits (195), Expect = 2e-18
 Identities = 21/77 (27%), Positives = 37/77 (48%)

Query: 1  MLVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEK 60
           L          V +G++GLT  +LE I    ++  +IK+K  G    D   +   L E+
Sbjct: 8  YLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEIAEELAEE 67

Query: 61 TGGKIIFRVGGLVYLFR 77
          TG +++  +G  + L+R
Sbjct: 68 TGAELVQVIGKTIVLYR 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 = 75.2 bits (186), Expect = 3e-17
 Identities = 23/84 (27%), Positives = 39/84 (46%)

Query: 112 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKL 171
           LT  +   LR     L P+ ++ KNG+   +V ++  A E   L+KV   G    D K++
Sbjct: 1   LTGKQRRYLRSLAHHLKPVVQIGKNGLTEGVVEEIDEALEKHELIKVKVLGNDREDRKEI 60

Query: 172 GAKLKELVPCVLLSFDDEQILMWR 195
             +L E     L+      I+++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

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

 Score = 69.8 bits (172), Expect = 3e-15
 Identities = 22/84 (26%), Positives = 40/84 (47%)

Query: 112 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKL 171
           LT  +   LR     L P+ ++ KNG+   ++ ++  A E   L+KV   G    D K++
Sbjct: 1   LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEI 60

Query: 172 GAKLKELVPCVLLSFDDEQILMWR 195
             +L E     L+    + I+++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|224451 COG1534, COG1534, Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]

 Score = 38.0 bits (89), Expect = 7e-04
 Identities = 18/65 (27%), Positives = 35/65 (53%)

Query: 13 VNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGL 72
          V +G++GLT  +++ I    + R +IK+K       D   +   L E+TG +++  +G  
Sbjct: 21 VQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVIGKT 80

Query: 73 VYLFR 77
          + L+R
Sbjct: 81 LVLYR 85

Length = 97

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	356
PF01985	84	CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR	99.9
PF01985	84	CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR	99.89
TIGR00253	95	RNA_bind_YhbY putative RNA-binding protein, YhbY f	99.87
TIGR00253	95	RNA_bind_YhbY putative RNA-binding protein, YhbY f	99.87
PRK10343	97	RNA-binding protein YhbY; Provisional	99.87
PRK10343	97	RNA-binding protein YhbY; Provisional	99.87
COG1534	97	Predicted RNA-binding protein containing KH domain	99.84
COG1534	97	Predicted RNA-binding protein containing KH domain	99.82
KOG1990	564	consensus Poly(A)-specific exoribonuclease PARN [R	99.8
KOG1990	564	consensus Poly(A)-specific exoribonuclease PARN [R	99.28

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

Probab=99.90  E-value=7.9e-24  Score=169.95  Aligned_cols=84  Identities=27%  Similarity=0.439  Sum_probs=75.7

Q ss_pred             CCHHHHHHHHHccCCCcceeecccccccHHHHHHHHHHhhcCceEEEEeeCCCCCcHHHHHHHHHhhcCcEEEEEeCCEE
Q 018444          112 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQI  191 (356)
Q Consensus       112 LT~kErtyLRrla~~l~Pif~LGKngv~~gLv~aI~ea~Ek~ELVKI~vkg~~~~D~keiA~eLk~lTg~vLVs~~g~~I  191 (356)
                      ||++|+.+||++|+.++|+++|||+|++++++.+|+.+|++||||||.|+++|..+.+++|++|++.|||++|+++|+++
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             EEEe
Q 018444          192 LMWR  195 (356)
Q Consensus       192 VLYR  195 (356)
                      ||||
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.

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

Probab=99.89  E-value=3.3e-23  Score=166.38  Aligned_cols=76  Identities=28%  Similarity=0.476  Sum_probs=68.2

Q ss_pred             cccCcccCCCeeeeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcEEEEEe
Q 018444            2 LVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYLFR   77 (356)
Q Consensus         2 l~K~~lkmkpvV~IGK~GVTd~VVeeIh~awk~rELVKVK~l~~~~~dmk~iae~Le~kTGg~VVqrIG~~iVLYR   77 (356)
                      |-+.|++++|+|+|||+|||++|+++|+++|++||||||||.+++..+++++++.|+++|||++||++|+++||||
T Consensus         9 Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~iG~~~vlyR   84 (84)
T PF01985_consen    9 LRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVIGRTIVLYR   84 (84)
T ss_dssp             HHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEETTEEEEEE
T ss_pred             HHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEECCEEEEEC
Confidence            4578999999999999999999999999999999999999999999999999999999999999999999999998

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=99.87  E-value=3.8e-22  Score=165.03  Aligned_cols=77  Identities=22%  Similarity=0.315  Sum_probs=74.9

Q ss_pred             cCcccCCCeeeeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcEEEEEeccC
Q 018444            4 KPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYLFRGRN   80 (356)
Q Consensus         4 K~~lkmkpvV~IGK~GVTd~VVeeIh~awk~rELVKVK~l~~~~~dmk~iae~Le~kTGg~VVqrIG~~iVLYRg~n   80 (356)
                      ..|++++|+|+|||+|||++|+++|+++|++|||||||+++++..+.+++++.|+++|||++||.||+++||||++.
T Consensus        11 ~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~iG~~~vlYR~~~   87 (95)
T TIGR00253        11 GKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVIGKTIVLYRPTK   87 (95)
T ss_pred             HHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEEccEEEEEecCC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999974

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=99.87  E-value=4.3e-22  Score=164.70  Aligned_cols=86  Identities=22%  Similarity=0.348  Sum_probs=85.0

Q ss_pred             CCHHHHHHHHHccCCCcceeecccccccHHHHHHHHHHhhcCceEEEEeeCCCCCcHHHHHHHHHhhcCcEEEEEeCCEE
Q 018444          112 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQI  191 (356)
Q Consensus       112 LT~kErtyLRrla~~l~Pif~LGKngv~~gLv~aI~ea~Ek~ELVKI~vkg~~~~D~keiA~eLk~lTg~vLVs~~g~~I  191 (356)
                      ||++|+.+||++|+.+.|+++|||+|++++++..|.++|++||||||.++++|..|.+++|++|++.|||++||++|+.+
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             EEEecC
Q 018444          192 LMWRGK  197 (356)
Q Consensus       192 VLYRGk  197 (356)
                      ||||+.
T Consensus        81 vlYR~~   86 (95)
T TIGR00253        81 VLYRPT   86 (95)
T ss_pred             EEEecC
Confidence            999986

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=99.87  E-value=6.7e-22  Score=164.23  Aligned_cols=86  Identities=15%  Similarity=0.256  Sum_probs=85.2

Q ss_pred             CCHHHHHHHHHccCCCcceeecccccccHHHHHHHHHHhhcCceEEEEeeCCCCCcHHHHHHHHHhhcCcEEEEEeCCEE
Q 018444          112 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQI  191 (356)
Q Consensus       112 LT~kErtyLRrla~~l~Pif~LGKngv~~gLv~aI~ea~Ek~ELVKI~vkg~~~~D~keiA~eLk~lTg~vLVs~~g~~I  191 (356)
                      ||++|+.|||++|+++.|+++|||+|++++++..|.+++++||||||.++++|..+.+++|++|++.|||++||++|+++
T Consensus         3 Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~IG~~~   82 (97)
T PRK10343          3 LSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKTL   82 (97)
T ss_pred             CCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeeeCcEE
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecC
Q 018444          192 LMWRGK  197 (356)
Q Consensus       192 VLYRGk  197 (356)
                      ||||..
T Consensus        83 vlYR~~   88 (97)
T PRK10343         83 VLYRPT   88 (97)
T ss_pred             EEEecC
Confidence            999986

>PRK10343 RNA-binding protein YhbY; Provisional

Probab=99.87  E-value=8.6e-22  Score=163.59  Aligned_cols=77  Identities=21%  Similarity=0.241  Sum_probs=75.0

Q ss_pred             cCcccCCCeeeeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcEEEEEeccC
Q 018444            4 KPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYLFRGRN   80 (356)
Q Consensus         4 K~~lkmkpvV~IGK~GVTd~VVeeIh~awk~rELVKVK~l~~~~~dmk~iae~Le~kTGg~VVqrIG~~iVLYRg~n   80 (356)
                      ..|++++|+|+|||+|||++|+++|.++|++|||||||+++++.++.++++++|+++||+++||+||+++||||++.
T Consensus        13 ~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~IG~~~vlYR~~~   89 (97)
T PRK10343         13 GLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKTLVLYRPTK   89 (97)
T ss_pred             HhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeeeCcEEEEEecCC
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999999985

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

Probab=99.84  E-value=8.3e-21  Score=157.77  Aligned_cols=79  Identities=24%  Similarity=0.403  Sum_probs=75.7

Q ss_pred             cccCcccCCCeeeeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcEEEEEeccC
Q 018444            2 LVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYLFRGRN   80 (356)
Q Consensus         2 l~K~~lkmkpvV~IGK~GVTd~VVeeIh~awk~rELVKVK~l~~~~~dmk~iae~Le~kTGg~VVqrIG~~iVLYRg~n   80 (356)
                      |.+.|++++|+|+|||+|||++|+++|.++|++||||||++.+++.++.+++|+.|++++|+.+||+||+++||||.+.
T Consensus        10 Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqviG~~~vlyr~~~   88 (97)
T COG1534          10 LRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVIGKTLVLYRESK   88 (97)
T ss_pred             HHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeeeeeEEEEEecCc
Confidence            5678999999999999999999999999999999999999999999999999999999999999999999999999443

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

Probab=99.82  E-value=4.2e-20  Score=153.58  Aligned_cols=84  Identities=26%  Similarity=0.416  Sum_probs=83.6

Q ss_pred             CCHHHHHHHHHccCCCcceeecccccccHHHHHHHHHHhhcCceEEEEeeCCCCCcHHHHHHHHHhhcCcEEEEEeCCEE
Q 018444          112 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQI  191 (356)
Q Consensus       112 LT~kErtyLRrla~~l~Pif~LGKngv~~gLv~aI~ea~Ek~ELVKI~vkg~~~~D~keiA~eLk~lTg~vLVs~~g~~I  191 (356)
                      ||.+|+.+||++|+++.|+|++||||++.++++.|..+++.+|||||.+++++..|-+++|++|++.|||.+||++|+.+
T Consensus         2 Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqviG~~~   81 (97)
T COG1534           2 LTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVIGKTL   81 (97)
T ss_pred             CcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeeeeeEE
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEe
Q 018444          192 LMWR  195 (356)
Q Consensus       192 VLYR  195 (356)
                      ||||
T Consensus        82 vlyr   85 (97)
T COG1534          82 VLYR   85 (97)
T ss_pred             EEEe
Confidence            9999

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

Probab=99.80  E-value=4e-20  Score=191.67  Aligned_cols=192  Identities=21%  Similarity=0.182  Sum_probs=172.3

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCC-eEEEEECcEEEEEeccCCCCCC---------
Q 018444           16 GRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGG-KIIFRVGGLVYLFRGRNYNYRT---------   85 (356)
Q Consensus        16 GK~GVTd~VVeeIh~awk~rELVKVK~l~~~~~dmk~iae~Le~kTGg-~VVqrIG~~iVLYRg~nY~~~~---------   85 (356)
                      +++|+|+++++.|++.|+.+|+++++|....+.+|.+.++.++..||| .+||+.|-+...|++..|..+.         
T Consensus        34 ~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~n~~~~~~g~~~s~~~~~~~~~~~~~~~~~~~~  113 (564)
T KOG1990|consen   34 WKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMSTGGNFVVWSRGDSISSPEFLCQRSPVDFVARQQEN  113 (564)
T ss_pred             cccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccCCCceeeeecCccccCCccceeecchhhhhhhchh
Confidence            999999999999999999999999999999999999999999999999 9999999999999777776541         


Q ss_pred             --------------------CCCCCccccCCCCCCCc-----------cccccCCC----CCCHHHHHHHHHccCCCcce
Q 018444           86 --------------------RPQYPLMLWKPAAPVYP-----------KLIQEAPE----GLTKHEADELRRKGKSLLPI  130 (356)
Q Consensus        86 --------------------rPr~~~m~w~p~~Pv~p-----------~l~~~~Pe----~LT~kErtyLRrla~~l~Pi  130 (356)
                                          .|++-+|+..++.|++.           .+++.+|.    .||..+.+++|++|...+||
T Consensus       114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~  193 (564)
T KOG1990|consen  114 QAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLPPH  193 (564)
T ss_pred             hhhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCChhhhhhHHHHHHHHhccccccc
Confidence                                15555666566666544           44555554    49999999999999999999


Q ss_pred             eecccccccHHHHHHHHHHhhcCceEEEEee-CCCCCcHHHHHHHH--HhhcCcEEEEEeCCEEEEEecCCCCCCCCCCC
Q 018444          131 CKLAKNGVYLTLVRDVRNAFEGSSLVKVNCK-GMHASDYKKLGAKL--KELVPCVLLSFDDEQILMWRGKDWKSMYPEPP  207 (356)
Q Consensus       131 f~LGKngv~~gLv~aI~ea~Ek~ELVKI~vk-g~~~~D~keiA~eL--k~lTg~vLVs~~g~~IVLYRGkd~~~~~v~~~  207 (356)
                      |.+|+++..++++.+++.+|++++.+|+.|+ |.+.+..+.+|.++  ..+||++||.+|+..+|+|||++|++ .++.+
T Consensus       194 ~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~hN~~~dv~y~~~~Fl~-~lp~~  272 (564)
T KOG1990|consen  194 FALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVLHNKLLDVMYRYKNFLS-PLPST  272 (564)
T ss_pred             ceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEeeccceeeeeehhhccc-ccchh
Confidence            9999999999999999999999999999999 99999999999999  99999999999999999999999999 66555


Q ss_pred             C
Q 018444          208 S  208 (356)
Q Consensus       208 ~  208 (356)
                      .
T Consensus       273 l  273 (564)
T KOG1990|consen  273 L  273 (564)
T ss_pred             H
Confidence            3

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

Probab=99.28  E-value=1.7e-12  Score=135.35  Aligned_cols=209  Identities=21%  Similarity=0.271  Sum_probs=168.7

Q ss_pred             ccCcccCCCeeeeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCC-hhhHHHHHHHH--HHHhCCeEEEEECcEEEEEecc
Q 018444            3 VKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVP-TVDMDNVCRRL--EEKTGGKIIFRVGGLVYLFRGR   79 (356)
Q Consensus         3 ~K~~lkmkpvV~IGK~GVTd~VVeeIh~awk~rELVKVK~l~~~-~~dmk~iae~L--e~kTGg~VVqrIG~~iVLYRg~   79 (356)
                      -+++-+..+.+.+|..+.-+++.-.+...|..|+..|+.+...- ......++..+  -..||+.+|-+-|-..+.||++
T Consensus       184 r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~hN~~~dv~y~~~  263 (564)
T KOG1990|consen  184 RRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVLHNKLLDVMYRYK  263 (564)
T ss_pred             HHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEeeccceeeeeehh
Confidence            35677788999999999999999999999999999998887653 44556778888  8899999999999999999998


Q ss_pred             CCCCCC-------CC---CCCcc-----------------------------ccC-CCCC--------------------
Q 018444           80 NYNYRT-------RP---QYPLM-----------------------------LWK-PAAP--------------------   99 (356)
Q Consensus        80 nY~~~~-------rP---r~~~m-----------------------------~w~-p~~P--------------------   99 (356)
                      +|-.+-       +.   .||.+                             .|- |+.+                    
T Consensus       264 ~Fl~~lp~~l~~f~~~~~~fp~~~~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~  343 (564)
T KOG1990|consen  264 NFLSPLPSTLEEFTDSSSMFPNIEDTKRLAKLSEYQKLNLKATLLELARAKAKKEKEIERRSISSRLKLEFEKASSEKLT  343 (564)
T ss_pred             hcccccchhHHHhhhhhhhhhhhHHHHHhhccccccchhhhhhHHHHHHHhcccccCcccccccchhhhhhhccchhhHH
Confidence            887631       11   12211                             011 1111                    


Q ss_pred             ---------------------------CCccccccCCCCCCHHHHHHHHHccCCCcceeecccccccHHHHHHHHHHhhc
Q 018444          100 ---------------------------VYPKLIQEAPEGLTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEG  152 (356)
Q Consensus       100 ---------------------------v~p~l~~~~Pe~LT~kErtyLRrla~~l~Pif~LGKngv~~gLv~aI~ea~Ek  152 (356)
                                                 -.|..-+..|+..|.+++.++++.|..+....-+|+.|+++|++.+++.+|..
T Consensus       344 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~  423 (564)
T KOG1990|consen  344 EAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKS  423 (564)
T ss_pred             HHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCCcccccceeecchhhhhh
Confidence                                       01111124567899999999999999999999999999999999999999999


Q ss_pred             CceEEEEee-CCCCCcHHHHHHHHHhhcCcEEEEEeCC-E---EEEEecCCCCCCCCCCCCCCC
Q 018444          153 SSLVKVNCK-GMHASDYKKLGAKLKELVPCVLLSFDDE-Q---ILMWRGKDWKSMYPEPPSFSN  211 (356)
Q Consensus       153 ~ELVKI~vk-g~~~~D~keiA~eLk~lTg~vLVs~~g~-~---IVLYRGkd~~~~~v~~~~~~~  211 (356)
                      +|++|+.|+ .+.+...+..|..+...+|+++|+++.. .   |+.|||++|..+....|....
T Consensus       424 ~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~l~P~~~l  487 (564)
T KOG1990|consen  424 RELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTSLRPRNLL  487 (564)
T ss_pred             cccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCcccCchhhh
Confidence            999999999 6666999999999999999999998543 2   899999999997776665533

---

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	356
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	5e-12
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	6e-05
1rq8_A	104	Conserved hypothetical protein; structural genomic	3e-11
1rq8_A	104	Conserved hypothetical protein; structural genomic	9e-04

>1jo0_A Hypothetical protein HI1333; structural genomics, YHBY_HAEI structure 2 function project, S2F, unknown function; 1.37A {Haemophilus influenzae} SCOP: d.68.4.1 PDB: 1ln4_A Length = 98

 Score = 60.7 bits (148), Expect = 5e-12
 Identities = 16/65 (24%), Positives = 29/65 (44%)

Query: 13 VNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGL 72
          V LG +GLT  +L  I +      +IK+K  G        +   +  +T    +  +G +
Sbjct: 22 VMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTIGHI 81

Query: 73 VYLFR 77
          + L+R
Sbjct: 82 LVLYR 86

>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 = 40.7 bits (96), Expect = 6e-05
 Identities = 13/72 (18%), Positives = 26/72 (36%)

Query: 112 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKL 171
           L+  +   L+     L P+  L  NG+   ++ ++ NA     L+KV   G      + +
Sbjct: 3   LSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLI 62

Query: 172 GAKLKELVPCVL 183
              +        
Sbjct: 63  INAIVRETKAAQ 74

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

 Score = 58.9 bits (143), Expect = 3e-11
 Identities = 14/65 (21%), Positives = 31/65 (47%)

Query: 13 VNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGL 72
            +G+ G+  NM++ I    + R +IK+        D   +   L E T  +++  +G +
Sbjct: 21 FQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVIGSM 80

Query: 73 VYLFR 77
          + ++R
Sbjct: 81 IVIYR 85

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

 Score = 37.3 bits (87), Expect = 9e-04
 Identities = 18/72 (25%), Positives = 33/72 (45%)

Query: 112 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKL 171
           LT  +   LR    ++ PI ++ K G+   +++ + +  E   L+KV+    +  D K+L
Sbjct: 2   LTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKEL 61

Query: 172 GAKLKELVPCVL 183
              L E     L
Sbjct: 62  AETLSEATRSEL 73

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	356
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	99.91
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	99.9
1rq8_A	104	Conserved hypothetical protein; structural genomic	99.9
1rq8_A	104	Conserved hypothetical protein; structural genomic	99.9

>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=99.91  E-value=2.5e-24  Score=177.40  Aligned_cols=79  Identities=23%  Similarity=0.313  Sum_probs=76.0

Q ss_pred             cccCcccCCCeeeeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcEEEEEeccC
Q 018444            2 LVKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYLFRGRN   80 (356)
Q Consensus         2 l~K~~lkmkpvV~IGK~GVTd~VVeeIh~awk~rELVKVK~l~~~~~dmk~iae~Le~kTGg~VVqrIG~~iVLYRg~n   80 (356)
                      |-..|++++|+|+|||+|||++|+++|++||++||||||+|++++..+++++|++|+++|||++||+||+++||||++.
T Consensus        11 Lr~~ah~l~pvv~IGk~GlT~~vi~ei~~aL~~~ELIKVkvl~~~~~~~~e~a~~la~~t~a~~Vq~IG~~~vLyR~~~   89 (98)
T 1jo0_A           11 LKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTIGHILVLYRPSE   89 (98)
T ss_dssp             HHHHHTTBCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEEEETTEEEEECCCS
T ss_pred             HHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHHCCeEEEEEeCCCHHHHHHHHHHHHHHhCCEEEEEECCEEEEEccCC
Confidence            3457899999999999999999999999999999999999999999999999999999999999999999999999984

>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=99.90  E-value=2.9e-24  Score=177.01  Aligned_cols=87  Identities=16%  Similarity=0.255  Sum_probs=85.8

Q ss_pred             CCCHHHHHHHHHccCCCcceeecccccccHHHHHHHHHHhhcCceEEEEeeCCCCCcHHHHHHHHHhhcCcEEEEEeCCE
Q 018444          111 GLTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQ  190 (356)
Q Consensus       111 ~LT~kErtyLRrla~~l~Pif~LGKngv~~gLv~aI~ea~Ek~ELVKI~vkg~~~~D~keiA~eLk~lTg~vLVs~~g~~  190 (356)
                      .||++|+.|||++|+++.|+|+|||+|++++++..|+++|++||||||.|+++|..|.+++|++|++.|||++||++|+.
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            49999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEecC
Q 018444          191 ILMWRGK  197 (356)
Q Consensus       191 IVLYRGk  197 (356)
                      +||||+.
T Consensus        82 ~vLyR~~   88 (98)
T 1jo0_A           82 LVLYRPS   88 (98)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999987

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

Probab=99.90  E-value=5.4e-24  Score=177.34  Aligned_cols=78  Identities=18%  Similarity=0.348  Sum_probs=75.7

Q ss_pred             ccCcccCCCeeeeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcEEEEEeccC
Q 018444            3 VKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYLFRGRN   80 (356)
Q Consensus         3 ~K~~lkmkpvV~IGK~GVTd~VVeeIh~awk~rELVKVK~l~~~~~dmk~iae~Le~kTGg~VVqrIG~~iVLYRg~n   80 (356)
                      -..|++++|+|+|||+|||++|+++|+++|++||||||||++++..+++++|+.|+++|||++||+||+++||||++.
T Consensus        11 R~~ah~Lkpvv~IGK~GlTe~vi~ei~~aL~~hELIKVkvl~~~~~d~~e~a~~la~~t~a~vVq~IG~~~VLYR~~~   88 (104)
T 1rq8_A           11 RSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVIGSMIVIYRESK   88 (104)
T ss_dssp             HHHTTSSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEETTEEEEEECCC
T ss_pred             HHHhcCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCHHHHHHHHHHHHHHhCCEEEEEECCEEEEEeCCC
Confidence            357899999999999999999999999999999999999999999999999999999999999999999999999986

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

Probab=99.90  E-value=1.2e-23  Score=175.38  Aligned_cols=87  Identities=23%  Similarity=0.387  Sum_probs=85.8

Q ss_pred             CCHHHHHHHHHccCCCcceeecccccccHHHHHHHHHHhhcCceEEEEeeCCCCCcHHHHHHHHHhhcCcEEEEEeCCEE
Q 018444          112 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQI  191 (356)
Q Consensus       112 LT~kErtyLRrla~~l~Pif~LGKngv~~gLv~aI~ea~Ek~ELVKI~vkg~~~~D~keiA~eLk~lTg~vLVs~~g~~I  191 (356)
                      ||++|+.|||++|+.+.|+|+|||+|++++++.+|.++|+++|||||.|+++|..|.+++|++|++.|||++||++|+.+
T Consensus         2 Lt~kqr~~LR~~ah~Lkpvv~IGK~GlTe~vi~ei~~aL~~hELIKVkvl~~~~~d~~e~a~~la~~t~a~vVq~IG~~~   81 (104)
T 1rq8_A            2 LTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVIGSMI   81 (104)
T ss_dssp             CCHHHHHHHHHHTTSSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEETTEE
T ss_pred             CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCHHHHHHHHHHHHHHhCCEEEEEECCEE
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCC
Q 018444          192 LMWRGKD  198 (356)
Q Consensus       192 VLYRGkd  198 (356)
                      ||||++.
T Consensus        82 VLYR~~~   88 (104)
T 1rq8_A           82 VIYRESK   88 (104)
T ss_dssp             EEEECCC
T ss_pred             EEEeCCC
Confidence            9999875

---

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	356
d1rq8a_	96	d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphy	5e-18
d1rq8a_	96	d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphy	4e-13
d1jo0a_	97	d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i	3e-17
d1jo0a_	97	d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i	2e-13

>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 = 76.3 bits (188), Expect = 5e-18
 Identities = 15/70 (21%), Positives = 32/70 (45%)

Query: 13 VNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGL 72
            +G+ G+  NM++ I    + R +IK+        D   +   L E T  +++  +G +
Sbjct: 21 FQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVIGSM 80

Query: 73 VYLFRGRNYN 82
          + ++R    N
Sbjct: 81 IVIYRESKEN 90

>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 = 62.4 bits (152), Expect = 4e-13
 Identities = 22/101 (21%), Positives = 41/101 (40%), Gaps = 6/101 (5%)

Query: 112 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKL 171
           LT  +   LR    ++ PI ++ K G+   +++ + +  E   L+KV+    +  D K+L
Sbjct: 2   LTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKEL 61

Query: 172 GAKLKELVPCVLLSFDDEQILMWRGKDWKSMYPEPPSFSNP 212
              L E     L+      I+++R         E      P
Sbjct: 62  AETLSEATRSELVQVIGSMIVIYRES------KENKEIELP 96

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

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

 Score = 74.3 bits (183), Expect = 3e-17
 Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 3/78 (3%)

Query: 13 VNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGL 72
          V LG +GLT  +L  I +      +IK+K  G        +   +  +T    +  +G +
Sbjct: 22 VMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTIGHI 81

Query: 73 VYLFRGRNYNYRTRPQYP 90
          + L+R    +   + Q P
Sbjct: 82 LVLYRP---SEEAKIQLP 96

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

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

 Score = 63.2 bits (154), Expect = 2e-13
 Identities = 14/87 (16%), Positives = 33/87 (37%)

Query: 112 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKL 171
           L+  +   L+     L P+  L  NG+   ++ ++ NA     L+KV   G      + +
Sbjct: 3   LSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLI 62

Query: 172 GAKLKELVPCVLLSFDDEQILMWRGKD 198
              +        +      ++++R  +
Sbjct: 63  INAIVRETKAAQVQTIGHILVLYRPSE 89

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	356
d1jo0a_	97	YhbY homologue HI1333 {Haemophilus influenzae [Tax	99.9
d1rq8a_	96	Hypothetical protein SAV1595 {Staphylococcus aureu	99.9
d1rq8a_	96	Hypothetical protein SAV1595 {Staphylococcus aureu	99.89
d1jo0a_	97	YhbY homologue HI1333 {Haemophilus influenzae [Tax	99.89

>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=99.90  E-value=4.4e-24  Score=173.02  Aligned_cols=87  Identities=16%  Similarity=0.255  Sum_probs=85.5

Q ss_pred             CCCHHHHHHHHHccCCCcceeecccccccHHHHHHHHHHhhcCceEEEEeeCCCCCcHHHHHHHHHhhcCcEEEEEeCCE
Q 018444          111 GLTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQ  190 (356)
Q Consensus       111 ~LT~kErtyLRrla~~l~Pif~LGKngv~~gLv~aI~ea~Ek~ELVKI~vkg~~~~D~keiA~eLk~lTg~vLVs~~g~~  190 (356)
                      .||++|+.+||++|+++.|+|+|||+|++++++..|+++|++||||||.|++++..|.+++|++|++.|||++|+++|++
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            59999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEecC
Q 018444          191 ILMWRGK  197 (356)
Q Consensus       191 IVLYRGk  197 (356)
                      +||||+.
T Consensus        82 ~ilYR~~   88 (97)
T d1jo0a_          82 LVLYRPS   88 (97)
T ss_dssp             EEEECCC
T ss_pred             EEEEcCC
Confidence            9999984

>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=99.90  E-value=7.1e-24  Score=171.50  Aligned_cols=89  Identities=22%  Similarity=0.365  Sum_probs=86.4

Q ss_pred             CCHHHHHHHHHccCCCcceeecccccccHHHHHHHHHHhhcCceEEEEeeCCCCCcHHHHHHHHHhhcCcEEEEEeCCEE
Q 018444          112 LTKHEADELRRKGKSLLPICKLAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQI  191 (356)
Q Consensus       112 LT~kErtyLRrla~~l~Pif~LGKngv~~gLv~aI~ea~Ek~ELVKI~vkg~~~~D~keiA~eLk~lTg~vLVs~~g~~I  191 (356)
                      ||++|+.+||++|+++.|+++|||+|++++++..|+++|+++|||||.|++++..|.+++|++|+++|||++||++|+++
T Consensus         2 Lt~kqr~~LR~~ah~l~p~v~IGk~Glt~~vi~ei~~~l~~~ELIKvk~~~~~~~~~~~~~~~l~~~t~a~~V~~iG~~~   81 (96)
T d1rq8a_           2 LTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVIGSMI   81 (96)
T ss_dssp             CCHHHHHHHHHHTTSSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEETTEE
T ss_pred             cCHHHHHHHHHHhcCCCCEEEECCCCCCHHHHHHHHHHHHhCCeeEEEecCCCHHHHHHHHHHHHHHhCCEEEEEECCEE
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCCC
Q 018444          192 LMWRGKDWK  200 (356)
Q Consensus       192 VLYRGkd~~  200 (356)
                      ||||++...
T Consensus        82 vlyR~~~~~   90 (96)
T d1rq8a_          82 VIYRESKEN   90 (96)
T ss_dssp             EEEECCCSC
T ss_pred             EEEeCCCCC
Confidence            999987443

>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=99.89  E-value=1.2e-23  Score=170.11  Aligned_cols=80  Identities=19%  Similarity=0.344  Sum_probs=77.0

Q ss_pred             ccCcccCCCeeeeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcEEEEEeccCCC
Q 018444            3 VKPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYLFRGRNYN   82 (356)
Q Consensus         3 ~K~~lkmkpvV~IGK~GVTd~VVeeIh~awk~rELVKVK~l~~~~~dmk~iae~Le~kTGg~VVqrIG~~iVLYRg~nY~   82 (356)
                      -+.|++++|+|+|||+|||++|+++|+++|++||||||+|.+++..+++++++.|+++|||.+||+||+++||||+++++
T Consensus        11 R~~ah~l~p~v~IGk~Glt~~vi~ei~~~l~~~ELIKvk~~~~~~~~~~~~~~~l~~~t~a~~V~~iG~~~vlyR~~~~~   90 (96)
T d1rq8a_          11 RSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVIGSMIVIYRESKEN   90 (96)
T ss_dssp             HHHTTSSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEETTEEEEEECCCSC
T ss_pred             HHHhcCCCCEEEECCCCCCHHHHHHHHHHHHhCCeeEEEecCCCHHHHHHHHHHHHHHhCCEEEEEECCEEEEEeCCCCC
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999999998765

>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=99.89  E-value=2.1e-23  Score=169.02  Aligned_cols=77  Identities=22%  Similarity=0.311  Sum_probs=74.8

Q ss_pred             cCcccCCCeeeeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcEEEEEeccC
Q 018444            4 KPLLKDNRQVNLGRDGLTHNMLELIHSHWKRRRVIKIKCKGVPTVDMDNVCRRLEEKTGGKIIFRVGGLVYLFRGRN   80 (356)
Q Consensus         4 K~~lkmkpvV~IGK~GVTd~VVeeIh~awk~rELVKVK~l~~~~~dmk~iae~Le~kTGg~VVqrIG~~iVLYRg~n   80 (356)
                      +.|++|+|+|+|||+|||++|+++|+++|++||||||||.+++..++++++++|+++|||.+||+||+++||||++.
T Consensus        13 ~~ah~lkp~v~IGk~Glt~~vi~ei~~al~~~ELIKvki~~~~~~~~~~~~~~l~~~t~~~vV~~iG~~~ilYR~~~   89 (97)
T d1jo0a_          13 GLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTIGHILVLYRPSE   89 (97)
T ss_dssp             HHHTTBCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEEEETTEEEEECCCS
T ss_pred             HHhcCCCCEEEECCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHHHhCCEEEEEECCEEEEEcCCC
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999999865