Citrus Sinensis ID: 026921

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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-
Protein Sequence
MLFFLHIAAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDDPSQGTIRSSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGASSSMAEYEDGSQSENYDEDEFYPEDDFNDDDEFYDSDSSDVVPLGSLPVDHIAERLQRK
Secondary Structure (PSIPRED)
ccEEEEEcccccEEEEHHHHHHHHHccccEEEEcccccccHHHHHHHHHHHccccEEEEEEcccEEEEEEccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHccccccccccccEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHcccEEEEcHHHHHHHccccEEEEEcccccHHHHHHHHHHHHHcccEEEEEEcccEEEEEEccccccccccccccccccccccccccccccccccccccHHHcccHHHHHHHHHHHHcccEEEHHHccccHHHHHHHHHHHHHHHHHHHccccEEEEEcccccccccccccccccccccccccccccccccccHHHHHcccccccccccccHHHHHHHHccc
Coil and Loop (DISEMBL)
MLFFLHIAAKNGVYLTLVRDVRnafegsslvkvnckgmhasdyKKLGAKLKELvpcvllsfddeQILMWRGkdwksmypeppsfsnpvdldiagdadgsgtpsddpsqgtirsspKMISLWKRAIESTKALVLDeinlgpddLLKKVEEFEGISQAAEHSYPALvlsredgasssmaeyedgsqsenydedefypeddfndddefydsdssdvvplgslpvdHIAERLQRK
Flexible Loop (DISEMBL)
MLFFLHIAAKNGVYLTLVRDVRNAFEGsslvkvnckgMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGKDWKSMYPEPPSFSNPVDLDIAGDADGsgtpsddpsqgtirsspKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISqaaehsypaLVLSREDGASSSMAEyedgsqsenydeDEFYPEDDFNDDDEFYDSDssdvvplgslpvdhiaerlqrk
Low Complexity Region (SEG)
MLFFLHIAAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDDPSQGTIRSSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGASSSMAEYEDGSQSenydedefypeddfndddefydsdssdVVPLGSLPVDHIAERLQRK
Disordered region (IsUnstruct)
*LFFLHIAAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGKDWKSM****************************************ISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGI******************************************************************************
Disordered Region (DISOPRED)
MLFFLH*AAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGKD**********************************************LWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSY*******************************************FYD***SDVVPLGSLPVDHIAERL***
Disordered Region (DISEMBL)
MLFFLHIAAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGKDWKSMYPEPPSFSNPVDLDIAGDA***************RSSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSRE********************EDEFYPEDDFNDDDEFYDSDSSDVVPLGSLPVDHIAERLQRK
Disordered Region (DISPRO)
MLFFLHIAAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGKDWKSMYPEPPSF**************************IRSSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSR****************************DDFNDDDEFYDSDSSDVVPLGSLPVDHIAERLQ**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLFFLHIAAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDDPSQGTIRSSPKMISLWKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGASSSMAEYEDGSQSENYDEDEFYPEDDFNDDDEFYDSDSSDVVPLGSLPVDHIAERLQRK
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	231	2.2.26 [Sep-21-2011]
Q9LDA9	564	CRS2-associated factor 2,	yes	no	0.935	0.382	0.550	1e-57
Q84N48	611	CRS2-associated factor 2,	N/A	no	0.948	0.358	0.495	3e-50
Q657G7	607	CRS2-associated factor 2,	yes	no	0.948	0.360	0.457	2e-46
Q9SL79	701	CRS2-associated factor 1,	no	no	0.316	0.104	0.589	3e-22
Q5VMQ5	701	CRS2-associated factor 1,	no	no	0.307	0.101	0.647	4e-22
Q84N49	674	CRS2-associated factor 1,	N/A	no	0.307	0.105	0.633	2e-21
Q8VYD9	405	CRS2-associated factor 1,	no	no	0.290	0.165	0.582	5e-18
Q6Z4U2	428	CRS2-associated factor 1,	no	no	0.285	0.154	0.560	1e-16
Q0J7J7	366	CRS2-associated factor 2,	no	no	0.277	0.174	0.515	8e-14
Q9FFU1	358	CRS2-associated factor 2,	no	no	0.277	0.178	0.5	1e-13

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

 Score =  223 bits (567), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 125/227 (55%), Positives = 166/227 (73%), Gaps = 11/227 (4%)

Query: 9   AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
           +KNGVY++LV+DVR+AFE SSLVKV+C G+  SDYKK+GAKLKELVPCVLLSFDDEQILM
Sbjct: 343 SKNGVYVSLVKDVRDAFELSSLVKVDCPGLEPSDYKKIGAKLKELVPCVLLSFDDEQILM 402

Query: 69  WRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDDPS---QGTIRSSPKMISLWKRAI 125
           WRG++WKS + + P   +  + +   + D S  PS++ +     T  SSPKMISLW+RA+
Sbjct: 403 WRGREWKSRFVDNPLIPSLSETNTTNELDPSDKPSEEQTVANPSTTISSPKMISLWQRAL 462

Query: 126 ESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGASSSMAEYEDGSQS 185
           ES+KA++L+E++LGPDDLLKKVEE EG S AAEH+Y A+VLS  DGA+    + +D S+ 
Sbjct: 463 ESSKAVILEELDLGPDDLLKKVEELEGTSLAAEHTYTAMVLSNTDGAAEDYVDEKDRSE- 521

Query: 186 ENYDEDEFYPEDDFNDDDEFYDSDSSDVV-PLGSLPVDHIAERLQRK 231
                 E+Y + D + DDE  D +S D V P+GSLPVD I  +L+ +
Sbjct: 522 ------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 =  198 bits (503), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 117/236 (49%), Positives = 154/236 (65%), Gaps = 17/236 (7%)

Query: 9   AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
           AKNG+Y+TLV+DVR+AFEGS LVK++C+G++ SDYKK+GAKL++LVPCVLLSFDDEQILM
Sbjct: 374 AKNGIYITLVKDVRDAFEGSDLVKIDCEGLNPSDYKKIGAKLRDLVPCVLLSFDDEQILM 433

Query: 69  WRGKDWKSMYPEPPSFSNPV---DLDIAGDADGSGTPSDDPSQGTIRS--SPKMISLWKR 123
            RGK+WKS Y +P +    V   +L +    + S   SD  +Q  IR    PKM  LWK 
Sbjct: 434 HRGKEWKSRYSKPLTLIPKVPKNNLAMTSVMNSSDEVSDANTQVAIREVLRPKMFKLWKS 493

Query: 124 AIESTKALVLDEI---NLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGASSSM-AEY 179
           A++S+ AL+LD+    NL PD LL  VEEF   SQA EHS+PAL+++  D ++ S+ AEY
Sbjct: 494 AVDSSLALLLDDAEANNLTPDSLLTLVEEFSVTSQAVEHSFPALLVTNGDASTDSLSAEY 553

Query: 180 ---EDGSQSENYDEDEFYPEDDFNDDDEFYDSDS----SDVVPLGSLPVDHIAERL 228
              E  +     +E +     D  DD+ F D D        VPLGSLP+D + ERL
Sbjct: 554 MNDEPETSVAGNEEGQLEQSPDLRDDEHF-DVDMFERLESSVPLGSLPIDSMIERL 608

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 =  185 bits (470), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 109/238 (45%), Positives = 155/238 (65%), Gaps = 19/238 (7%)

Query: 9   AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
           AKNG+Y+ LVRDVR+AFEGS LVK++C+G++ SDYKK+GAKL++LVPCVLLSFD+EQILM
Sbjct: 370 AKNGIYIYLVRDVRDAFEGSDLVKIDCEGLNPSDYKKIGAKLRDLVPCVLLSFDNEQILM 429

Query: 69  WRGKDWKSMYPEPPSFSNPV---DLDIAGDADGSGTPSDDPSQGTIRS--SPKMISLWKR 123
           +RGK+WKS YP+P +    +   ++ ++ D   S   +DD  +  +R    PKM  LW  
Sbjct: 430 FRGKEWKSRYPKPLTLIPKIRKNNVPMSSDESSSDEATDDDDRLAVREVLRPKMFELWTN 489

Query: 124 AIESTKALVLDEIN---LGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGASSSM-AEY 179
           AIES+ AL+LD+     L PD LL +VE+F   SQ  EHS+PA++++ ++     + AEY
Sbjct: 490 AIESSVALMLDDAEVDALTPDSLLTRVEDFSVTSQVVEHSFPAVLVANDESNPDVLNAEY 549

Query: 180 -----EDGS---QSENYDEDEFYPEDDFNDDDEFYDSDSSDVVPLGSLPVDHIAERLQ 229
                E G+   Q   + E     EDD  +DD     +SS  VPLG+LP+D + ++L 
Sbjct: 550 TEDEPETGTLEPQQHEFTESSDVAEDDHFEDDMLKRLESS--VPLGALPIDAVVKQLN 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|Q9SL79|CAF1P_ARATH CRS2-associated factor 1, chloroplastic OS=Arabidopsis thaliana GN=At2g20020 PE=1 SV=2

 Score =  105 bits (261), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 43/73 (58%), Positives = 60/73 (82%)

Query: 9   AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
            KNGVY  LV++V+ AFE   LV+++C+GM  SD++K+GAKLK+LVPCVL+SF++EQIL+
Sbjct: 383 GKNGVYCDLVKNVKEAFEVCELVRIDCQGMKGSDFRKIGAKLKDLVPCVLVSFENEQILI 442

Query: 69  WRGKDWKSMYPEP 81
           WRG++WKS    P
Sbjct: 443 WRGREWKSSLTTP 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|Q5VMQ5|CAF1P_ORYSJ CRS2-associated factor 1, chloroplastic OS=Oryza sativa subsp. japonica GN=Os01g0495900 PE=2 SV=1

 Score =  105 bits (261), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 46/71 (64%), Positives = 55/71 (77%)

Query: 9   AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
            KNGVYL LV+ VR AFE   LV+V+C G++ SD +K+GAKLK+LVPC LLSF+ E ILM
Sbjct: 325 GKNGVYLNLVKQVREAFEACDLVRVDCSGLNKSDCRKIGAKLKDLVPCTLLSFEFEHILM 384

Query: 69  WRGKDWKSMYP 79
           WRG DWKS  P
Sbjct: 385 WRGNDWKSSLP 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.

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  102 bits (254), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 45/71 (63%), Positives = 54/71 (76%)

Query: 9   AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
            KNGVY  LV  VR AFE   LV+V+C G++ SD +K+GAKLK+LVPC+LLSF+ E ILM
Sbjct: 325 GKNGVYANLVNQVREAFEACDLVRVDCSGLNKSDCRKIGAKLKDLVPCILLSFEFEHILM 384

Query: 69  WRGKDWKSMYP 79
           WRG DWKS  P
Sbjct: 385 WRGSDWKSSLP 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|Q8VYD9|CAF1M_ARATH CRS2-associated factor 1, mitochondrial OS=Arabidopsis thaliana GN=At4g31010 PE=2 SV=1

 Score = 91.3 bits (225), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 39/67 (58%), Positives = 55/67 (82%)

Query: 9   AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
           AKNG Y +LV  VR+AF  S LV+++C G+   DYKK+GAKL++LVPC+L++FD EQ+++
Sbjct: 301 AKNGYYGSLVPMVRDAFLVSELVRIDCLGLERKDYKKIGAKLRDLVPCILVTFDKEQVVI 360

Query: 69  WRGKDWK 75
           WRGKD+K
Sbjct: 361 WRGKDYK 367

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 86.7 bits (213), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 37/66 (56%), Positives = 53/66 (80%)

Query: 9   AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
           AKNG Y +LV  VR+AF    LV+++ KG+  SDY+K+G KL++LVPC+++SFD EQI++
Sbjct: 299 AKNGYYASLVPMVRDAFLTDELVRIDSKGLPKSDYRKIGVKLRDLVPCIIVSFDKEQIIV 358

Query: 69  WRGKDW 74
           WRGKD+
Sbjct: 359 WRGKDY 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 = 77.4 bits (189), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 33/64 (51%), Positives = 48/64 (75%)

Query: 9   AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
            +NGVY+ +V  VR AF+   +V+++C  + +SD KK+G KL++LVPCV L F DEQI++
Sbjct: 287 TRNGVYVNVVDRVREAFKTVEVVRLDCSHVGSSDCKKIGVKLRDLVPCVPLLFKDEQIIL 346

Query: 69  WRGK 72
           WRGK
Sbjct: 347 WRGK 350

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score = 77.0 bits (188), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 32/64 (50%), Positives = 46/64 (71%)

Query: 9   AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
            +NGVY+ +V  VR  FE   +V+++C  +  SD K++G KLKE+VPCV + F DEQI++
Sbjct: 285 TRNGVYVNVVGRVREEFETEEIVRLDCTHVGMSDCKRIGVKLKEMVPCVPILFKDEQIIL 344

Query: 69  WRGK 72
           WRGK
Sbjct: 345 WRGK 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	231
224110940	506	predicted protein [Populus trichocarpa]	0.956	0.436	0.651	1e-70
297739073	422	unnamed protein product [Vitis vinifera]	0.935	0.511	0.630	2e-70
255568848	561	conserved hypothetical protein [Ricinus	0.965	0.397	0.647	4e-70
359473240	560	PREDICTED: LOW QUALITY PROTEIN: CRS2-ass	0.926	0.382	0.631	5e-70
225425575	561	PREDICTED: CRS2-associated factor 2, chl	0.935	0.385	0.634	4e-69
356524038	593	PREDICTED: CRS2-associated factor 2, chl	0.852	0.332	0.572	3e-58
449434945	602	PREDICTED: LOW QUALITY PROTEIN: CRS2-ass	0.913	0.350	0.552	5e-58
449478585	603	PREDICTED: LOW QUALITY PROTEIN: CRS2-ass	0.913	0.349	0.552	6e-58
147771140	306	hypothetical protein VITISV_034260 [Viti	0.878	0.663	0.577	4e-57
307135966	603	RNA splicing factor [Cucumis melo subsp.	0.926	0.354	0.555	5e-57

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

 Score =  272 bits (695), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 148/227 (65%), Positives = 178/227 (78%), Gaps = 6/227 (2%)

Query: 9   AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
           AKNGVY+TLVRDVR AFEGS LVKV+CKGM  SDYKKLGAKLK+LVPCVLLSFDDEQILM
Sbjct: 282 AKNGVYITLVRDVRAAFEGSPLVKVDCKGMEPSDYKKLGAKLKDLVPCVLLSFDDEQILM 341

Query: 69  WRGKDWKSMYPEP-PSFSNPVDLDIAGDADGSGTPSDDPSQG---TIRSSPKMISLWKRA 124
           WRG+DWKSMYPE  PS S P +LDIA  +D SG   DD        + SSPKM+ LWK A
Sbjct: 342 WRGQDWKSMYPEARPSISFPAELDIASGSDDSGKSDDDCDNSDAKILSSSPKMMLLWKHA 401

Query: 125 IESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGASSSMAEYEDGSQ 184
           +ES KA++LDEI+LGPD LL KVEEFEGISQA EHSYPALV+S EDG+S+S++ +ED S 
Sbjct: 402 LESNKAILLDEIDLGPDALLTKVEEFEGISQATEHSYPALVMSSEDGSSNSISTFEDDSH 461

Query: 185 SENYDEDEFYPEDDFNDDDEFYDSDSSDVVPLGSLPVDHIAERLQRK 231
           SEN+ ED+ Y +D++ D + F + ++S   P GSL +D IAE+L +K
Sbjct: 462 SENFSEDDMYSDDEYYDSESFEELETS--APPGSLSIDLIAEKLDKK 506

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297739073|emb|CBI28562.3| unnamed protein product [Vitis vinifera]

 Score =  271 bits (693), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 145/230 (63%), Positives = 170/230 (73%), Gaps = 14/230 (6%)

Query: 9   AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
            KNGVY++LV+DVR+AFEGS LVK++CKGMHASDYKK+GAKLKE VPCVLLSFDDEQIL 
Sbjct: 167 VKNGVYISLVKDVRDAFEGSPLVKIDCKGMHASDYKKIGAKLKESVPCVLLSFDDEQILT 226

Query: 69  WRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDDPSQ---GTIRSSPKMISLWKRAI 125
           WRG  WKSMY   PSF  PV  D+A   +GSG P  +  +     + +SPKM+SLWK AI
Sbjct: 227 WRGHGWKSMYQGAPSFLIPVVADVASGLEGSGVPKSNHHRLDTKAVSASPKMMSLWKSAI 286

Query: 126 ESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGASSSMAEYEDGSQS 185
           ES+KAL+LDEI LGPD LLK VEEFEGISQA EHSYPALV+S EDG   + AE+E G  S
Sbjct: 287 ESSKALLLDEIGLGPDALLKVVEEFEGISQATEHSYPALVMSSEDGTGGTKAEHE-GYNS 345

Query: 186 ENYDEDEFYPEDDFNDDDEFYDSDSS-----DVVPLGSLPVDHIAERLQR 230
           E+Y EDE Y     NDDD+ Y  + S       VPLGSLPVD +A++L R
Sbjct: 346 EDYSEDEMY-----NDDDDEYLVNESLEEMESPVPLGSLPVDLLAKQLDR 390

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 =  270 bits (690), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 149/230 (64%), Positives = 182/230 (79%), Gaps = 7/230 (3%)

Query: 9   AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
           AKNGVY+TLVRDVRNAFEGS LVK++CKGM+ SDYKKLGAKLKELVPCVLLSFDDE ILM
Sbjct: 332 AKNGVYITLVRDVRNAFEGSPLVKIDCKGMNPSDYKKLGAKLKELVPCVLLSFDDEHILM 391

Query: 69  WRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDDPSQ---GTIRSSPKMISLWKRAI 125
           WRG++WK MYPE PS S P   D    +D SG   DDPS      +RSSPKM+SLW+ AI
Sbjct: 392 WRGQNWKPMYPEVPSVSTPDAADFTSGSDDSGKFEDDPSNRDANVVRSSPKMMSLWECAI 451

Query: 126 ESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGASSSMAEYEDGSQS 185
           ES+KA++LD+I+LGPDDLL+KVEEFE ISQA EHSYPA++LS EDGA++++A + D S S
Sbjct: 452 ESSKAILLDQIDLGPDDLLRKVEEFECISQATEHSYPAVILSSEDGANNTVAAFGDDSLS 511

Query: 186 ENYDEDEFYPEDDFNDDDEFYDSDSSD----VVPLGSLPVDHIAERLQRK 231
            ++ E++    DD  +DDE+YDSDS +     VPLGSLPVD +AERL ++
Sbjct: 512 GSFTEEDDTYTDDEYEDDEYYDSDSFEEVDTAVPLGSLPVDRLAERLHQE 561

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  270 bits (689), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 144/228 (63%), Positives = 169/228 (74%), Gaps = 14/228 (6%)

Query: 9   AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
            KNGVY++LV+DVR+AFEGS LVK++CKGMHASDYKK+GAKLKE VPCVLLSFDDEQIL 
Sbjct: 336 VKNGVYISLVKDVRDAFEGSPLVKIDCKGMHASDYKKIGAKLKESVPCVLLSFDDEQILT 395

Query: 69  WRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDDPSQ---GTIRSSPKMISLWKRAI 125
           WRG  WKSMY   PSF  PV  D+A   +GSG P  +  +     + +SPKM+SLWK AI
Sbjct: 396 WRGHGWKSMYQGAPSFLIPVVADVASGLEGSGVPKSNHHRLDTKAVSASPKMMSLWKSAI 455

Query: 126 ESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGASSSMAEYEDGSQS 185
           ES+KAL+LDEI LGPD LLK VEEFEGISQA EHSYPALV+S EDG   + AE+E G  S
Sbjct: 456 ESSKALLLDEIGLGPDALLKVVEEFEGISQATEHSYPALVMSSEDGTGGTKAEHE-GYNS 514

Query: 186 ENYDEDEFYPEDDFNDDDEFYDSDSS-----DVVPLGSLPVDHIAERL 228
           E+Y EDE Y     NDDD+ Y  + S       VPLGSLPVD +A++L
Sbjct: 515 EDYSEDEMY-----NDDDDEYLVNESLEEMESPVPLGSLPVDLLAKQL 557

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  266 bits (681), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 144/227 (63%), Positives = 171/227 (75%), Gaps = 11/227 (4%)

Query: 9   AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
            KNGVY++LV+DVR+AFEGS LVK++CKGMHASDYKK+GAKLKELVPCVLLSFDDEQIL 
Sbjct: 336 VKNGVYISLVKDVRDAFEGSPLVKIDCKGMHASDYKKIGAKLKELVPCVLLSFDDEQILT 395

Query: 69  WRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDDPSQ---GTIRSSPKMISLWKRAI 125
           WRG  WKSMY   PSF  PV  D+A   +GSG P  +  +     + +SPKM+SLWK AI
Sbjct: 396 WRGHGWKSMYQGAPSFLIPVVADVASGLEGSGIPKSNHHRLDTKAVSASPKMMSLWKSAI 455

Query: 126 ESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGASSSMAEYEDGSQS 185
           ES+KAL+LDE  LGPD LLK VEEFEGISQA EHSYPALV+S EDG   + AEYE G  S
Sbjct: 456 ESSKALLLDETGLGPDALLKVVEEFEGISQATEHSYPALVMSSEDGTGGTKAEYE-GYNS 514

Query: 186 ENYDEDEFYPEDDFNDDDEFYDSDS----SDVVPLGSLPVDHIAERL 228
           E+Y EDE Y   + +DDDE+  ++S       VPLGSLPVD +A++L
Sbjct: 515 EDYSEDEMY---NDDDDDEYLVNESLEEMESPVPLGSLPVDLLAKQL 558

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  230 bits (587), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 118/206 (57%), Positives = 152/206 (73%), Gaps = 9/206 (4%)

Query: 9   AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
           AKNGVY +LV+DVR+AFEGS LVK+NCKG+  SDYKK+GAKLK+LVPCVLLSFDDEQILM
Sbjct: 337 AKNGVYTSLVKDVRDAFEGSILVKINCKGLDPSDYKKIGAKLKDLVPCVLLSFDDEQILM 396

Query: 69  WRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDDPSQ---GTIRSSPKMISLWKRAI 125
           WRGKDWKS YP+P     P   +I G+ + SG   D+  +     + +SPKM+SLWKRAI
Sbjct: 397 WRGKDWKSRYPQPLPVFTPSKANIVGNLENSGETDDNQYKHDGNMVNTSPKMLSLWKRAI 456

Query: 126 ESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVL-SREDGASSSMAEYEDGSQ 184
           +S+KAL+LDE NLGPD LL+KVEEF+ +SQA EHS+PA  L S+E+ A  S A +E+   
Sbjct: 457 QSSKALLLDEFNLGPDALLEKVEEFDTVSQALEHSHPAFSLSSKENDAEGSSANFEN--- 513

Query: 185 SENYDEDEFYPEDDFNDDDEFYDSDS 210
             +Y  D  + E+D+   ++ Y SD+
Sbjct: 514 --SYSSDGLHTEEDYAKFEDSYSSDA 537

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  229 bits (585), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 126/228 (55%), Positives = 161/228 (70%), Gaps = 17/228 (7%)

Query: 9   AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
           AKNGVY++LV DVR+AFEGS LVK++C GMH SDYKKLGAKLKELVPCVLLSFD+EQILM
Sbjct: 381 AKNGVYISLVNDVRHAFEGSILVKIDCTGMHESDYKKLGAKLKELVPCVLLSFDNEQILM 440

Query: 69  WRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDD--------PSQGTIRSSPKMISL 120
           WRGKDWKS+  +  S   P     A   D  G+P +          +  TI++SPKM  L
Sbjct: 441 WRGKDWKSIISDDRSAPLPSR---ASSNDSLGSPGESLENSDLLHGNHHTIKTSPKMKLL 497

Query: 121 WKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGASSSMAEYE 180
           W+ AI+S KAL+LDEI L PDDLL+KVEEFE ISQA EHSYPA + S ED +S      +
Sbjct: 498 WEHAIDSNKALLLDEIGLAPDDLLEKVEEFERISQATEHSYPAFITSSEDVSSP-----D 552

Query: 181 DGSQSENYDEDEFYPEDDFNDDDEFYDSDSSDVVPLGSLPVDHIAERL 228
           D  +S+++ E  +  +DD   +++ +D ++  +VPLGSLPVD IA++L
Sbjct: 553 DSPKSQDHTEANYNSDDDVGREEDLFD-NADPLVPLGSLPVDIIAKKL 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 =  229 bits (584), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 126/228 (55%), Positives = 161/228 (70%), Gaps = 17/228 (7%)

Query: 9   AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
           AKNGVY++LV DVR+AFEGS LVK++C GMH SDYKKLGAKLKELVPCVLLSFD+EQILM
Sbjct: 382 AKNGVYISLVNDVRHAFEGSILVKIDCTGMHESDYKKLGAKLKELVPCVLLSFDNEQILM 441

Query: 69  WRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDD--------PSQGTIRSSPKMISL 120
           WRGKDWKS+  +  S   P     A   D  G+P +          +  TI++SPKM  L
Sbjct: 442 WRGKDWKSIISDDCSAPLP---SRASSNDSLGSPGESLENSDLLHDNHHTIKTSPKMKLL 498

Query: 121 WKRAIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGASSSMAEYE 180
           W+ AI+S KAL+LDEI L PDDLL+KVEEFE ISQA EHSYPA + S ED +S      +
Sbjct: 499 WEHAIDSNKALLLDEIGLAPDDLLEKVEEFERISQATEHSYPAFITSSEDVSSP-----D 553

Query: 181 DGSQSENYDEDEFYPEDDFNDDDEFYDSDSSDVVPLGSLPVDHIAERL 228
           D  +S+++ E  +  +DD   +++ +D ++  +VPLGSLPVD IA++L
Sbjct: 554 DSPKSQDHTEANYNSDDDVGREEDLFD-NADPLVPLGSLPVDIIAKKL 600

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147771140|emb|CAN74182.1| hypothetical protein VITISV_034260 [Vitis vinifera]

 Score =  227 bits (578), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 131/227 (57%), Positives = 158/227 (69%), Gaps = 24/227 (10%)

Query: 9   AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
            KNGVY++LV+DVR+AFEGS LVK++CKGMHASDYKK+GAKLK              IL 
Sbjct: 94  VKNGVYISLVKDVRDAFEGSPLVKIDCKGMHASDYKKIGAKLK--------------ILT 139

Query: 69  WRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDDPSQ---GTIRSSPKMISLWKRAI 125
           WRG  WKSMY   PSF  PV  D+A   +GSG P     +     + +SPKM+SLWK AI
Sbjct: 140 WRGHGWKSMYQGAPSFLIPVVADVASGLEGSGIPKSXHHRLDTKAVSASPKMMSLWKSAI 199

Query: 126 ESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGASSSMAEYEDGSQS 185
           ES+KAL+LDEI LGPD LLK VEEFEGISQA EHSYPALV+S EDG   + AE E G  S
Sbjct: 200 ESSKALLLDEIGLGPDALLKVVEEFEGISQATEHSYPALVMSSEDGTGGTKAEXE-GYNS 258

Query: 186 ENYDEDEFYPEDDFNDDDEFYDSDSSD----VVPLGSLPVDHIAERL 228
           E+Y EDE Y  +D +DDDE+  ++S +     VPLGSLPVD +A++L
Sbjct: 259 EDYSEDEMY--NDDDDDDEYLVNESLEEMESPVPLGSLPVDLLAKQL 303

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  226 bits (576), Expect = 5e-57,   Method: Compositional matrix adjust.
 Identities = 125/225 (55%), Positives = 162/225 (72%), Gaps = 11/225 (4%)

Query: 9   AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
           AKNGVY++LV DVR+AFEGS LVK++C GMH SDYKKLGAKLKELVPCVLLSFD+EQILM
Sbjct: 382 AKNGVYISLVDDVRHAFEGSILVKIDCTGMHESDYKKLGAKLKELVPCVLLSFDNEQILM 441

Query: 69  WRGKDWKSMYPE---PPSFSNPVDLDIAGDADGSGTPSD--DPSQGTIRSSPKMISLWKR 123
           WRGKDWKS+  +    P  S     D  G +  S   SD  + +  TI++SPKM  LW+R
Sbjct: 442 WRGKDWKSVISDDRSAPLPSRASSNDSLGSSGESVENSDLLNGNHHTIKTSPKMKLLWER 501

Query: 124 AIESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGASSSMAEYEDGS 183
           AI+S KAL+LDEI L PD+LL++VEEFE ISQA EHSYPA + S E+ +S +     D  
Sbjct: 502 AIDSNKALMLDEIGLAPDELLERVEEFERISQATEHSYPAFITSSEEVSSPA-----DSP 556

Query: 184 QSENYDEDEFYPEDDFNDDDEFYDSDSSDVVPLGSLPVDHIAERL 228
           +S+++ E  +  +DD   +++ +D +   +VPLGSLPVD IA++L
Sbjct: 557 ESQDHSEANYNSDDDVGREEDLFD-NVDPLVPLGSLPVDIIAKKL 600

Source: Cucumis melo subsp. melo

Species: Cucumis melo

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	231
TAIR|locus:2028100	564	CAF2 [Arabidopsis thaliana (ta	0.939	0.384	0.513	4.3e-54
TAIR|locus:2061604	701	CAF1 [Arabidopsis thaliana (ta	0.480	0.158	0.451	1.6e-23
TAIR|locus:2126694	405	AT4G31010 [Arabidopsis thalian	0.432	0.246	0.457	3.2e-18
TAIR|locus:2160195	358	AT5G54890 [Arabidopsis thalian	0.272	0.175	0.507	2.7e-13

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

 Score = 559 (201.8 bits), Expect = 4.3e-54, P = 4.3e-54
 Identities = 116/226 (51%), Positives = 153/226 (67%)

Query:     9 AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
             +KNGVY++LV+DVR+AFE SSLVKV+C G+  SDYKK+GAKLKELVPCVLLSFDDEQILM
Sbjct:   343 SKNGVYVSLVKDVRDAFELSSLVKVDCPGLEPSDYKKIGAKLKELVPCVLLSFDDEQILM 402

Query:    69 WRGKDWKSMYPEPPSFSNPVDLDIAGDADGSGTPSDDPS---QGTIRSSPKMISLWKRAI 125
             WRG++WKS + + P   +  + +   + D S  PS++ +     T  SSPKMISLW+RA+
Sbjct:   403 WRGREWKSRFVDNPLIPSLSETNTTNELDPSDKPSEEQTVANPSTTISSPKMISLWQRAL 462

Query:   126 ESTKALVLDEINLGPDDLLKKVEEFEGISQAAEHSYPALVLSREDGASSSMAEYEDGSQS 185
             ES+KA++L+E++LGPDDLLKKVEE EG S AAEH+Y A+VLS  DGA+    + +D S+ 
Sbjct:   463 ESSKAVILEELDLGPDDLLKKVEELEGTSLAAEHTYTAMVLSNTDGAAEDYVDEKDRSEE 522

Query:   186 XXXXXXXXXXXXXXXXXXXXXXXXXXXVVPLGSLPVDHIAERLQRK 231
                                        V P+GSLPVD I  +L+ +
Sbjct:   523 YYSDIDDDFDDECSDDESLDP------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 = 266 (98.7 bits), Expect = 1.6e-23, Sum P(2) = 1.6e-23
 Identities = 51/113 (45%), Positives = 78/113 (69%)

Query:    10 KNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMW 69
             KNGVY  LV++V+ AFE   LV+++C+GM  SD++K+GAKLK+LVPCVL+SF++EQIL+W
Sbjct:   384 KNGVYCDLVKNVKEAFEVCELVRIDCQGMKGSDFRKIGAKLKDLVPCVLVSFENEQILIW 443

Query:    70 RGKDWKSMYPEPPSFSNPV-DLDIAGDADGSGTPSDDPSQG-TIRSSPKMISL 120
             RG++WKS    P    + + D+++         PS  P+Q  T+  +P + S+
Sbjct:   444 RGREWKSSLTTPDKKGDILEDIEVDTALPEDDEPSVSPNQSQTMTQNPPLDSM 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 = 225 (84.3 bits), Expect = 3.2e-18, P = 3.2e-18
 Identities = 49/107 (45%), Positives = 69/107 (64%)

Query:     9 AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
             AKNG Y +LV  VR+AF  S LV+++C G+   DYKK+GAKL++LVPC+L++FD EQ+++
Sbjct:   301 AKNGYYGSLVPMVRDAFLVSELVRIDCLGLERKDYKKIGAKLRDLVPCILVTFDKEQVVI 360

Query:    69 WRGKDWKSMYP--EPPSF---SNPVDLDIAGDADGSGTPSDDPSQGT 110
             WRGKD+K      E  SF    + +D D+  D   S    D P + T
Sbjct:   361 WRGKDYKPPKEDDEYSSFIHRESSIDSDV--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 = 179 (68.1 bits), Expect = 2.7e-13, P = 2.7e-13
 Identities = 32/63 (50%), Positives = 46/63 (73%)

Query:    10 KNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMW 69
             +NGVY+ +V  VR  FE   +V+++C  +  SD K++G KLKE+VPCV + F DEQI++W
Sbjct:   286 RNGVYVNVVGRVREEFETEEIVRLDCTHVGMSDCKRIGVKLKEMVPCVPILFKDEQIILW 345

Query:    70 RGK 72
             RGK
Sbjct:   346 RGK 348


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.314   0.133   0.386    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      231       204   0.00094  111 3  11 23  0.40    33
                                                     31  0.46    35


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  4
  No. of states in DFA:  604 (64 KB)
  Total size of DFA:  169 KB (2099 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  19.07u 0.11s 19.18t   Elapsed:  00:00:00
  Total cpu time:  19.07u 0.11s 19.18t   Elapsed:  00:00:00
  Start:  Thu May  9 13:45:44 2013   End:  Thu May  9 13:45:44 2013

GO:0003723 "RNA binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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	231
pfam01985	84	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	4e-11
smart01103	84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	1e-09

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

 Score = 57.1 bits (139), Expect = 4e-11
 Identities = 17/61 (27%), Positives = 29/61 (47%)

Query: 10 KNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMW 69
          KNG+   +V ++  A E   L+KV   G    D K++  +L E     L+      I+++
Sbjct: 24 KNGLTEGVVEEIDEALEKHELIKVKVLGNDREDRKEIAEELAEKTGAELVQVIGRTIVLY 83

Query: 70 R 70
          R
Sbjct: 84 R 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 = 53.2 bits (129), Expect = 1e-09
 Identities = 16/61 (26%), Positives = 30/61 (49%)

Query: 10 KNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMW 69
          KNG+   ++ ++  A E   L+KV   G    D K++  +L E     L+    + I+++
Sbjct: 24 KNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEIAEELAEETGAELVQVIGKTIVLY 83

Query: 70 R 70
          R
Sbjct: 84 R 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	231
PF01985	84	CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR	99.13
TIGR00253	95	RNA_bind_YhbY putative RNA-binding protein, YhbY f	97.3
COG1534	97	Predicted RNA-binding protein containing KH domain	97.02
PRK10343	97	RNA-binding protein YhbY; Provisional	96.24
KOG1990	564	consensus Poly(A)-specific exoribonuclease PARN [R	95.86

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

Probab=99.13  E-value=3.7e-11  Score=89.36  Aligned_cols=69  Identities=25%  Similarity=0.341  Sum_probs=61.4

Q ss_pred             chhhhhhccCceEeehhHHHHHhhccCceEEEcCCCCCchhHHHhhhhhhcccCeeEEeecCceEEEEe
Q 026921            2 LFFLHIAAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWR   70 (231)
Q Consensus         2 l~~l~kL~kNGvY~~lV~~VrdAF~~~elVrIDC~gl~~sDyKKIGaKLrdLVpCvllsF~~eqIlmWR   70 (231)
                      |=|+..++|||++-++++.+++||+.+|||||.|.+-.+.|.+.+...|.+..+|.++...+.++++||
T Consensus        16 l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~iG~~~vlyR   84 (84)
T PF01985_consen   16 LKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVIGRTIVLYR   84 (84)
T ss_dssp             C--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEETTEEEEEE
T ss_pred             CCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEECCEEEEEC
Confidence            347788999999999999999999999999999999999999999999999999999999999999998

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=97.30  E-value=0.00045  Score=53.87  Aligned_cols=70  Identities=17%  Similarity=0.256  Sum_probs=65.1

Q ss_pred             hhhhhhccCceEeehhHHHHHhhccCceEEEcCCCCCchhHHHhhhhhhcccCeeEEeecCceEEEEecC
Q 026921            3 FFLHIAAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGK   72 (231)
Q Consensus         3 ~~l~kL~kNGvY~~lV~~VrdAF~~~elVrIDC~gl~~sDyKKIGaKLrdLVpCvllsF~~eqIlmWRGk   72 (231)
                      =|+...||||+--+++..+.+|++.+|||||---.-.++|.+.+...|-.-..|.++..-+..+++||..
T Consensus        17 ~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~iG~~~vlYR~~   86 (95)
T TIGR00253        17 KPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVIGKTIVLYRPT   86 (95)
T ss_pred             CCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEEccEEEEEecC
Confidence            4677889999999999999999999999999877777889999999999999999999999999999985

A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.

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

Probab=97.02  E-value=0.00098  Score=52.97  Aligned_cols=75  Identities=19%  Similarity=0.259  Sum_probs=67.8

Q ss_pred             hhhhhhccCceEeehhHHHHHhhccCceEEEcCCCCCchhHHHhhhhhhcccCeeEEeecCceEEEEecCCCCCCC
Q 026921            3 FFLHIAAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGKDWKSMY   78 (231)
Q Consensus         3 ~~l~kL~kNGvY~~lV~~VrdAF~~~elVrIDC~gl~~sDyKKIGaKLrdLVpCvllsF~~eqIlmWRGk~~k~~~   78 (231)
                      -|+...+|||+=-++++.+.+|.+.+||||+.--.=...|-+.|-.+|-+-+.|-++..-+..+++|| .+|....
T Consensus        18 ~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqviG~~~vlyr-~~~e~~~   92 (97)
T COG1534          18 KPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVIGKTLVLYR-ESKEKRK   92 (97)
T ss_pred             CceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeeeeeEEEEEe-cCccccc
Confidence            46778899999999999999999999999998777777899999999999999999999999999999 6665533

>PRK10343 RNA-binding protein YhbY; Provisional

Probab=96.24  E-value=0.006  Score=48.01  Aligned_cols=70  Identities=11%  Similarity=0.153  Sum_probs=65.2

Q ss_pred             hhhhhhccCceEeehhHHHHHhhccCceEEEcCCCCCchhHHHhhhhhhcccCeeEEeecCceEEEEecC
Q 026921            3 FFLHIAAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGK   72 (231)
Q Consensus         3 ~~l~kL~kNGvY~~lV~~VrdAF~~~elVrIDC~gl~~sDyKKIGaKLrdLVpCvllsF~~eqIlmWRGk   72 (231)
                      =|+...||||+=-+++..+.+|++.+|||||--..-.+.|-+.+...|-+-..|-++.-=+..+++||=.
T Consensus        19 ~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~IG~~~vlYR~~   88 (97)
T PRK10343         19 KPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGKTLVLYRPT   88 (97)
T ss_pred             CCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeeeCcEEEEEecC
Confidence            4677889999999999999999999999999988888889999999999999999999999999999965

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

Probab=95.86  E-value=0.0036  Score=60.96  Aligned_cols=76  Identities=25%  Similarity=0.465  Sum_probs=68.1

Q ss_pred             hhccCceEeehhHHHHHhhccCceEEEcCCCCCc-hhHHHhhhhhhcccCeeEEeec-C---ceEEEEecCCCCCCCCCC
Q 026921            7 IAAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHA-SDYKKLGAKLKELVPCVLLSFD-D---EQILMWRGKDWKSMYPEP   81 (231)
Q Consensus         7 kL~kNGvY~~lV~~VrdAF~~~elVrIDC~gl~~-sDyKKIGaKLrdLVpCvllsF~-~---eqIlmWRGk~~k~~~~~~   81 (231)
                      -+++.|+|..++.+++-+|+..|+|++.|...+. +.-+..+..+..+...++++.+ +   .+|+.+||++|..+..-.
T Consensus       403 ~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~l~  482 (564)
T KOG1990|consen  403 LSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTSLR  482 (564)
T ss_pred             ccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCcccC
Confidence            3678999999999999999999999999999999 9999999999999999999993 3   349999999999887533


Q ss_pred             C
Q 026921           82 P   82 (231)
Q Consensus        82 ~   82 (231)
                      |
T Consensus       483 P  483 (564)
T KOG1990|consen  483 P  483 (564)
T ss_pred             c
Confidence            3

---

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

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	231
1jo0_A	98	Hypothetical protein HI1333; structural genomics,	98.4
1rq8_A	104	Conserved hypothetical protein; structural genomic	98.15

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

Probab=98.40  E-value=1.6e-07  Score=71.97  Aligned_cols=71  Identities=14%  Similarity=0.200  Sum_probs=67.8

Q ss_pred             chhhhhhccCceEeehhHHHHHhhccCceEEEcCCCCCchhHHHhhhhhhcccCeeEEeecCceEEEEecC
Q 026921            2 LFFLHIAAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGK   72 (231)
Q Consensus         2 l~~l~kL~kNGvY~~lV~~VrdAF~~~elVrIDC~gl~~sDyKKIGaKLrdLVpCvllsF~~eqIlmWRGk   72 (231)
                      |=|+...||||+--+++..+++|++.+|||||-|.+-.+.|.+.+...|.+...|.++..-+..+++||+.
T Consensus        18 l~pvv~IGk~GlT~~vi~ei~~aL~~~ELIKVkvl~~~~~~~~e~a~~la~~t~a~~Vq~IG~~~vLyR~~   88 (98)
T 1jo0_A           18 LNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTIGHILVLYRPS   88 (98)
T ss_dssp             BCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEEEETTEEEEECCC
T ss_pred             CCCeEEECCCCCCHHHHHHHHHHHHHCCeEEEEEeCCCHHHHHHHHHHHHHHhCCEEEEEECCEEEEEccC
Confidence            34778899999999999999999999999999999999999999999999999999999999999999987

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

Probab=98.15  E-value=2.8e-06  Score=66.02  Aligned_cols=71  Identities=20%  Similarity=0.310  Sum_probs=67.5

Q ss_pred             hhhhhhccCceEeehhHHHHHhhccCceEEEcCCCCCchhHHHhhhhhhcccCeeEEeecCceEEEEecCC
Q 026921            3 FFLHIAAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGKD   73 (231)
Q Consensus         3 ~~l~kL~kNGvY~~lV~~VrdAF~~~elVrIDC~gl~~sDyKKIGaKLrdLVpCvllsF~~eqIlmWRGk~   73 (231)
                      =|+...||||+--++++.+.+|++.+|||||-|.+-.+.|-+.+...|.+-..|.++..-+..+++||+..
T Consensus        18 kpvv~IGK~GlTe~vi~ei~~aL~~hELIKVkvl~~~~~d~~e~a~~la~~t~a~vVq~IG~~~VLYR~~~   88 (104)
T 1rq8_A           18 DPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVIGSMIVIYRESK   88 (104)
T ss_dssp             CCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEETTEEEEEECCC
T ss_pred             CCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCHHHHHHHHHHHHHHhCCEEEEEECCEEEEEeCCC
Confidence            36778899999999999999999999999999999899999999999999999999999999999999875

---

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	231
d1jo0a_	97	d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i	3e-08

>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 = 47.8 bits (114), Expect = 3e-08
 Identities = 9/65 (13%), Positives = 24/65 (36%)

Query: 9  AKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILM 68
            NG+   ++ ++ NA     L+KV   G      + +   +        +      +++
Sbjct: 25 GGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTIGHILVL 84

Query: 69 WRGKD 73
          +R  +
Sbjct: 85 YRPSE 89

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	231
d1jo0a_	97	YhbY homologue HI1333 {Haemophilus influenzae [Tax	99.25
d1rq8a_	96	Hypothetical protein SAV1595 {Staphylococcus aureu	99.18

>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=99.25  E-value=2e-12  Score=96.23  Aligned_cols=72  Identities=14%  Similarity=0.210  Sum_probs=68.7

Q ss_pred             chhhhhhccCceEeehhHHHHHhhccCceEEEcCCCCCchhHHHhhhhhhcccCeeEEeecCceEEEEecCC
Q 026921            2 LFFLHIAAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGKD   73 (231)
Q Consensus         2 l~~l~kL~kNGvY~~lV~~VrdAF~~~elVrIDC~gl~~sDyKKIGaKLrdLVpCvllsF~~eqIlmWRGk~   73 (231)
                      |-|+.+++|||++.++|+.+.+||+.+|||||.|.+..++|.+.+..+|.+..+|.+|.+-+.++++||+..
T Consensus        18 lkp~v~IGk~Glt~~vi~ei~~al~~~ELIKvki~~~~~~~~~~~~~~l~~~t~~~vV~~iG~~~ilYR~~~   89 (97)
T d1jo0a_          18 LNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLIINAIVRETKAAQVQTIGHILVLYRPSE   89 (97)
T ss_dssp             BCCSEEECTTCSCHHHHHHHHHHHHHHSEEEEEETTCCHHHHHHHHHHHHHHHCCEEEEEETTEEEEECCCS
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHHhCCeEEEEEcCCCHHHHHHHHHHHHHHhCCEEEEEECCEEEEEcCCC
Confidence            457889999999999999999999999999999999999999999999999999999999999999999743

>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=99.18  E-value=9.7e-12  Score=92.26  Aligned_cols=73  Identities=19%  Similarity=0.295  Sum_probs=68.8

Q ss_pred             chhhhhhccCceEeehhHHHHHhhccCceEEEcCCCCCchhHHHhhhhhhcccCeeEEeecCceEEEEecCCC
Q 026921            2 LFFLHIAAKNGVYLTLVRDVRNAFEGSSLVKVNCKGMHASDYKKLGAKLKELVPCVLLSFDDEQILMWRGKDW   74 (231)
Q Consensus         2 l~~l~kL~kNGvY~~lV~~VrdAF~~~elVrIDC~gl~~sDyKKIGaKLrdLVpCvllsF~~eqIlmWRGk~~   74 (231)
                      |-|+..++|||++-++++.+++||+.+|||||.|.+-.++|.+.+..+|.+..+|.+|.+-+.++++||+...
T Consensus        17 l~p~v~IGk~Glt~~vi~ei~~~l~~~ELIKvk~~~~~~~~~~~~~~~l~~~t~a~~V~~iG~~~vlyR~~~~   89 (96)
T d1rq8a_          17 IDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVIGSMIVIYRESKE   89 (96)
T ss_dssp             SCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEETTEEEEEECCCS
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHHhCCeeEEEecCCCHHHHHHHHHHHHHHhCCEEEEEECCEEEEEeCCCC
Confidence            3467889999999999999999999999999999999999999999999999999999999999999997643