Citrus Sinensis ID: 003220
Local Sequence Feature Prediction
| Prediction and (Method) | Result |
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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 | Alignment graph | Length |
Definition |
RBH(Q2H) |
RBH(H2Q) |
Q cover |
H cover |
Identity |
E-value |
| Query | 838 | 2.2.26 [Sep-21-2011] | |||||||
| Q9SL79 | 701 | CRS2-associated factor 1, | yes | no | 0.556 | 0.664 | 0.674 | 0.0 | |
| Q5VMQ5 | 701 | CRS2-associated factor 1, | yes | no | 0.764 | 0.914 | 0.466 | 1e-159 | |
| Q84N49 | 674 | CRS2-associated factor 1, | N/A | no | 0.453 | 0.563 | 0.616 | 1e-146 | |
| Q9LDA9 | 564 | CRS2-associated factor 2, | no | no | 0.381 | 0.567 | 0.621 | 1e-119 | |
| Q84N48 | 611 | CRS2-associated factor 2, | N/A | no | 0.385 | 0.528 | 0.548 | 1e-110 | |
| Q657G7 | 607 | CRS2-associated factor 2, | no | no | 0.420 | 0.579 | 0.503 | 1e-109 | |
| Q6Z4U2 | 428 | CRS2-associated factor 1, | no | no | 0.344 | 0.675 | 0.496 | 2e-79 | |
| Q8VYD9 | 405 | CRS2-associated factor 1, | no | no | 0.372 | 0.770 | 0.432 | 2e-76 | |
| Q0J7J7 | 366 | CRS2-associated factor 2, | no | no | 0.318 | 0.729 | 0.468 | 2e-75 | |
| Q9FFU1 | 358 | CRS2-associated factor 2, | no | no | 0.324 | 0.759 | 0.460 | 1e-73 |
| >sp|Q9SL79|CAF1P_ARATH CRS2-associated factor 1, chloroplastic OS=Arabidopsis thaliana GN=At2g20020 PE=1 SV=2 | Back alignment and function desciption |
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Score = 699 bits (1803), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 331/491 (67%), Positives = 393/491 (80%), Gaps = 25/491 (5%)
Query: 1 MALKLIIPFPIFSPP--PNHNPNLNPNPPNHRPATEIRFSRWNNANAEEFNQRRRAQQEI 58
M+LKL PFPIF+P PNHNP R +EIRFSRW NANAE F QRRR+Q+E+
Sbjct: 1 MSLKLNTPFPIFAPSLFPNHNP---------RAPSEIRFSRWGNANAERFEQRRRSQEEL 51
Query: 59 EDDIRRHRRFDSATKITQSYDSSTSTATNGVA-FKSAGTPSSPSRPSIPGRKSKYSKPAT 117
E +IRR RRFD+ATKI ++DS + A + F+S GTPS PS SIPGR+SKYSKP +
Sbjct: 52 EAEIRRDRRFDAATKIVHTHDSEAAAAEPKTSPFRSRGTPSLPSARSIPGRRSKYSKPDS 111
Query: 118 NSSVDHPAFRKISKREKTTNKSPEKPAA--SKSNISITEDGLSYVIDGAPFEFKYSYTEA 175
+ R K + P+ P +K + ++EDGL+YVI+GAPFEFKYSYTE
Sbjct: 112 GPN-----------RPKNKPRVPDSPPQLDAKPEVKLSEDGLTYVINGAPFEFKYSYTET 160
Query: 176 PKAKPLKLREAAFSPFGPTTMGRPWTGRAPLPPSKKKLKEFDSFQLPPPNKKGVKPVQKP 235
PK KPLKLRE A++PFGPTTMGRPWTGRAPLP S+K +EFDSF+LPP KKG+KPVQKP
Sbjct: 161 PKVKPLKLREPAYAPFGPTTMGRPWTGRAPLPQSQKTPREFDSFRLPPVGKKGLKPVQKP 220
Query: 236 GPYLPGTGPRYVSTREEILGEPLTADEVRELVESAKRSSRQLNMGRDGLTHNMLDNIHAH 295
GP+ PG GPRYV ++EEILGEPLT +EVRELV S +++RQLNMGRDGLTHNML+NIH
Sbjct: 221 GPFRPGVGPRYVYSKEEILGEPLTKEEVRELVTSCLKTTRQLNMGRDGLTHNMLNNIHDL 280
Query: 296 WKRRRACKIKCKGVCTVDMDNVCEQLEERTGGKIIYRRGGVLYLFRGRNYNYRSRPRFPL 355
WKRRR CKIKCKGVCTVDMDNVCEQLEE+ GGK+IYRRGGVL+LFRGRNYN+R+RPRFPL
Sbjct: 281 WKRRRVCKIKCKGVCTVDMDNVCEQLEEKIGGKVIYRRGGVLFLFRGRNYNHRTRPRFPL 340
Query: 356 MLWKPVTPVYPRLIQQVPDGLTLEEATEMRKKGRKLIPICKLGKNGVYCDLAKNVREAFE 415
MLWKPV PVYPRLIQQVP+GLT +EAT MR+KGR+L+PICKLGKNGVYCDL KNV+EAFE
Sbjct: 341 MLWKPVAPVYPRLIQQVPEGLTRQEATNMRRKGRELMPICKLGKNGVYCDLVKNVKEAFE 400
Query: 416 VCELVRINCQGMNGSDYRKIGAKLRDLVPCVLISFEREHILMWRGQEWKSSILKPGNDSE 475
VCELVRI+CQGM GSD+RKIGAKL+DLVPCVL+SFE E IL+WRG+EWKSS+ P +
Sbjct: 401 VCELVRIDCQGMKGSDFRKIGAKLKDLVPCVLVSFENEQILIWRGREWKSSLTTPDKKGD 460
Query: 476 DAKESKVDGSI 486
++ +VD ++
Sbjct: 461 ILEDIEVDTAL 471
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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 | Back alignment and function description |
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| >sp|Q84N49|CAF1P_MAIZE CRS2-associated factor 1, chloroplastic OS=Zea mays GN=CAF1 PE=1 SV=1 | Back alignment and function description |
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| >sp|Q9LDA9|CAF2P_ARATH CRS2-associated factor 2, chloroplastic OS=Arabidopsis thaliana GN=At1g23400 PE=2 SV=1 | Back alignment and function description |
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| >sp|Q84N48|CAF2P_MAIZE CRS2-associated factor 2, chloroplastic OS=Zea mays GN=CAF2 PE=1 SV=1 | Back alignment and function description |
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| >sp|Q657G7|CAF2P_ORYSJ CRS2-associated factor 2, chloroplastic OS=Oryza sativa subsp. japonica GN=Os01g0323300 PE=2 SV=1 | Back alignment and function description |
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| >sp|Q6Z4U2|CAF1M_ORYSJ CRS2-associated factor 1, mitochondrial OS=Oryza sativa subsp. japonica GN=Os08g0174900 PE=2 SV=1 | Back alignment and function description |
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| >sp|Q8VYD9|CAF1M_ARATH CRS2-associated factor 1, mitochondrial OS=Arabidopsis thaliana GN=At4g31010 PE=2 SV=1 | Back alignment and function description |
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| >sp|Q0J7J7|CAF2M_ORYSJ CRS2-associated factor 2, mitochondrial OS=Oryza sativa subsp. japonica GN=Os08g0188000 PE=2 SV=2 | Back alignment and function description |
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| >sp|Q9FFU1|CAF2M_ARATH CRS2-associated factor 2, mitochondrial OS=Arabidopsis thaliana GN=At5g54890 PE=2 SV=1 | Back alignment and function description |
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Close Homologs in the Non-Redundant Database Detected by BLAST
Original result of BLAST against Nonredundant Database
| GI | Alignment Graph | Length |
Definition |
Q cover |
H cover |
Identity |
E-value |
| Query | 838 | ||||||
| 224113759 | 699 | predicted protein [Populus trichocarpa] | 0.829 | 0.994 | 0.536 | 0.0 | |
| 225445140 | 752 | PREDICTED: CRS2-associated factor 1, chl | 0.890 | 0.992 | 0.529 | 0.0 | |
| 449443167 | 745 | PREDICTED: CRS2-associated factor 1, chl | 0.878 | 0.987 | 0.528 | 0.0 | |
| 297738777 | 723 | unnamed protein product [Vitis vinifera] | 0.855 | 0.991 | 0.524 | 0.0 | |
| 255589857 | 748 | conserved hypothetical protein [Ricinus | 0.575 | 0.644 | 0.738 | 0.0 | |
| 356527769 | 723 | PREDICTED: CRS2-associated factor 1, chl | 0.847 | 0.982 | 0.490 | 0.0 | |
| 297836246 | 700 | hypothetical protein ARALYDRAFT_480467 [ | 0.556 | 0.665 | 0.682 | 0.0 | |
| 18399222 | 701 | CRS2-associated factor 1 [Arabidopsis th | 0.556 | 0.664 | 0.674 | 0.0 | |
| 357520913 | 698 | CRS2-associated factor [Medicago truncat | 0.779 | 0.935 | 0.501 | 0.0 | |
| 356495236 | 705 | PREDICTED: CRS2-associated factor 1, chl | 0.547 | 0.651 | 0.602 | 1e-168 |
| >gi|224113759|ref|XP_002332503.1| predicted protein [Populus trichocarpa] gi|222832483|gb|EEE70960.1| predicted protein [Populus trichocarpa] | Back alignment and taxonomy information |
|---|
Score = 794 bits (2050), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 452/842 (53%), Positives = 542/842 (64%), Gaps = 147/842 (17%)
Query: 1 MALKLI-IPFPIFSPPPNHNPNLNPNPPNHRPATEIRFSRWNNANAEEFNQRRRAQQEIE 59
MALKL PFPIF+PP +PNP +HRP+TE+ FSRW NANA++FNQR R+QQEIE
Sbjct: 1 MALKLFPTPFPIFAPP-------SPNP-SHRPSTEVHFSRWFNANADKFNQRYRSQQEIE 52
Query: 60 DDIRRHRRFDSATKITQSYDSSTSTATNGVAFKSAGTPSSPSRPSIPGRKSKYSKPATNS 119
+DI R RRF SA I +YD + + FKS GTPSSPS PSIPG+KSKYSKP +
Sbjct: 53 EDISRRRRFTSANNIVTNYDPKNAAEVDISFFKSTGTPSSPSSPSIPGKKSKYSKPLKKT 112
Query: 120 SVDHPAFRKISKREKTTNKSPEKPAASKSNISITEDGLSYVIDGAPFEFKYSYTEAPKAK 179
HPAF R + + P K++I ++EDG+SYVIDGAPFEFKYSYTE PK K
Sbjct: 113 ---HPAFLPKITRVPLPRNNAKPPIDRKADIKLSEDGVSYVIDGAPFEFKYSYTETPKVK 169
Query: 180 PLKLREAAFSPFGPTTMGRPWTGRAPLPPSKKKLKEFDSFQLPPPNKKGVKPVQKPGPYL 239
PLKLREA ++PFGP TM RPWTGRAPLPPSKKKL+EFDSF LPPP+KKGVKPVQ PGP+L
Sbjct: 170 PLKLREAPYAPFGPITMPRPWTGRAPLPPSKKKLREFDSFVLPPPDKKGVKPVQAPGPFL 229
Query: 240 PGTGPRYVSTREEILGEPLTADEVRELVESAKRSSRQLNMGRDGLTHNMLDNIHAHWKRR 299
PG GPRY TREEILG+PLT +E++ELV+ ++ RQLNMGRDGLTHNMLDNIHAHWKRR
Sbjct: 230 PGAGPRYAKTREEILGDPLTQEEIQELVDGCLKAKRQLNMGRDGLTHNMLDNIHAHWKRR 289
Query: 300 RACKIKCKGVCTVDMDNVCEQLEERTGGKIIYRRGGVLYLFRGRNYNYRSRPRFPLMLWK 359
R CKIKCKGVCTVDMDNVC+QLEERTGGKIIYR+GGVLYLFRGRNYNYR RPRFPLMLWK
Sbjct: 290 RVCKIKCKGVCTVDMDNVCQQLEERTGGKIIYRKGGVLYLFRGRNYNYRFRPRFPLMLWK 349
Query: 360 PVTPVYPRLIQQVPDGLTLEEATEMRKKGRKLIPICKLGKNGVYCDLAKNVREAFEVCEL 419
PVTPVYPRLIQ+ P+GLTL+EA+ MR KGRKLIPICKLGKNGVY DL +NVREAFE CEL
Sbjct: 350 PVTPVYPRLIQRAPEGLTLQEASGMRNKGRKLIPICKLGKNGVYRDLVRNVREAFEECEL 409
Query: 420 VRINCQGMNGSDYRKIGAKLRDLVPCVLISFEREHILMWRGQEWKSSILKPGNDSEDAKE 479
VRINCQGMNGSD+RKIGAKLRDLVPCVLISFE EHILMWRG++WKSS KP ND ++AK
Sbjct: 410 VRINCQGMNGSDFRKIGAKLRDLVPCVLISFECEHILMWRGRDWKSSFTKPVNDGDEAKN 469
Query: 480 SKVDGSISVAPPTAGNGSAPSLTQMLLVEGGSLNTFNSSISPKGYEEVQSALRENLSSID 539
S +DG+ S P L+EG TF+ + S L S +D
Sbjct: 470 SSIDGATSATP---------------LLEGLQNETFSVKDA--------STLNLKTSRMD 506
Query: 540 GEEPFSVTKKLSFADDNEQLSADESLSLADDDEPFSDSENLSSADDDEPFLASDSTTNVM 599
E+ E+LS D DE F A +
Sbjct: 507 AED---------------------------------QGEDLSQKDIDETFAAKIFISTST 533
Query: 600 EINETISATGCSNDKSDAMKNIYENVNKLENSGVGNDTSEPVSDTNECQTVLDNKGSVLG 659
EI E S T ND S A+
Sbjct: 534 EIYE--SKTTPDNDDSSAVT---------------------------------------- 551
Query: 660 ESAALSVGSETTLGSAESTRDQSEHFYVGSLNHDYQQNPSEVPEDHNVLTRLHGPSLEIV 719
+S A+ + S + L + SE + LN Y Q E+
Sbjct: 552 KSEAMRIASGSELQNVSEGSHVSE---LAKLNESYTQGVLEL------------------ 590
Query: 720 LHLMRQAVENGSALVLDDATLDADSIYERSVAFAKSAPPGPVFQQRSRKIAIQKGEKKEA 779
++QAVE GSA+VL DA LDAD++Y+++VAFA+SAPPGPVF+++ R +QK E +E
Sbjct: 591 ---LKQAVEIGSAVVL-DANLDADAVYQKAVAFAQSAPPGPVFRRQPRNTVVQKSEMQEN 646
Query: 780 GHLKMKREVPNMVVSENR---GNVRQSNRKKTKNSDEIEHGLDVVLSPQGSLKIDELAKL 836
G L++K+ V S ++ G+ R+S++ + K + E +D V PQGSL++DELAKL
Sbjct: 647 GELEVKQ-----VTSFSKMGGGSERKSSKVRRKYFN--EQYVDSV--PQGSLRVDELAKL 697
Query: 837 LA 838
LA
Sbjct: 698 LA 699
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Source: Populus trichocarpa Species: Populus trichocarpa Genus: Populus Family: Salicaceae Order: Malpighiales Class: Phylum: Streptophyta Superkingdom: Eukaryota |
| >gi|225445140|ref|XP_002280611.1| PREDICTED: CRS2-associated factor 1, chloroplastic [Vitis vinifera] | Back alignment and taxonomy information |
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| >gi|449443167|ref|XP_004139352.1| PREDICTED: CRS2-associated factor 1, chloroplastic-like [Cucumis sativus] gi|449521361|ref|XP_004167698.1| PREDICTED: CRS2-associated factor 1, chloroplastic-like [Cucumis sativus] | Back alignment and taxonomy information |
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| >gi|297738777|emb|CBI28022.3| unnamed protein product [Vitis vinifera] | Back alignment and taxonomy information |
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| >gi|255589857|ref|XP_002535109.1| conserved hypothetical protein [Ricinus communis] gi|223524018|gb|EEF27274.1| conserved hypothetical protein [Ricinus communis] | Back alignment and taxonomy information |
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| >gi|356527769|ref|XP_003532480.1| PREDICTED: CRS2-associated factor 1, chloroplastic-like [Glycine max] | Back alignment and taxonomy information |
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| >gi|297836246|ref|XP_002886005.1| hypothetical protein ARALYDRAFT_480467 [Arabidopsis lyrata subsp. lyrata] gi|297331845|gb|EFH62264.1| hypothetical protein ARALYDRAFT_480467 [Arabidopsis lyrata subsp. lyrata] | Back alignment and taxonomy information |
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| >gi|18399222|ref|NP_565462.1| CRS2-associated factor 1 [Arabidopsis thaliana] gi|75266026|sp|Q9SL79.2|CAF1P_ARATH RecName: Full=CRS2-associated factor 1, chloroplastic; AltName: Full=Chloroplastic group IIA intron splicing facilitator CRS2-associated factor 1; Flags: Precursor gi|15028051|gb|AAK76556.1| unknown protein [Arabidopsis thaliana] gi|20197570|gb|AAD24394.2| expressed protein [Arabidopsis thaliana] gi|28393847|gb|AAO42331.1| unknown protein [Arabidopsis thaliana] gi|330251862|gb|AEC06956.1| CRS2-associated factor 1 [Arabidopsis thaliana] | Back alignment and taxonomy information |
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| >gi|357520913|ref|XP_003630745.1| CRS2-associated factor [Medicago truncatula] gi|355524767|gb|AET05221.1| CRS2-associated factor [Medicago truncatula] | Back alignment and taxonomy information |
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| >gi|356495236|ref|XP_003516485.1| PREDICTED: CRS2-associated factor 1, chloroplastic-like [Glycine max] | Back alignment and taxonomy information |
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Prediction of Gene Ontology (GO) Terms
Close Homologs with Gene Ontology terms Detected by BLAST
Original result of BLAST against Gene Ontology (AMIGO)
| ID |
Alignment graph |
Length |
Definition |
Q cover |
H cover |
Identity |
E-value |
| Query | 838 | ||||||
| TAIR|locus:2061604 | 701 | CAF1 [Arabidopsis thaliana (ta | 0.612 | 0.731 | 0.582 | 1.3e-178 | |
| TAIR|locus:2028100 | 564 | CAF2 [Arabidopsis thaliana (ta | 0.415 | 0.617 | 0.558 | 1.1e-105 | |
| TAIR|locus:2126694 | 405 | AT4G31010 [Arabidopsis thalian | 0.281 | 0.582 | 0.487 | 3.7e-74 | |
| TAIR|locus:2160195 | 358 | AT5G54890 [Arabidopsis thalian | 0.258 | 0.606 | 0.520 | 2e-73 | |
| TAIR|locus:2096662 | 1011 | CFM2 "CRM family member 2" [Ar | 0.102 | 0.085 | 0.337 | 7.3e-14 | |
| TAIR|locus:2094558 | 881 | CFM3A "CRM family member 3A" [ | 0.109 | 0.104 | 0.304 | 1.9e-09 | |
| TAIR|locus:2094997 | 848 | EMB1865 "embryo defective 1865 | 0.114 | 0.113 | 0.309 | 1.8e-08 | |
| SGD|S000001431 | 995 | YIL169C "Putative protein of u | 0.249 | 0.210 | 0.236 | 0.00061 |
| TAIR|locus:2061604 CAF1 [Arabidopsis thaliana (taxid:3702)] | Back alignment and assigned GO terms |
|---|
Score = 1570 (557.7 bits), Expect = 1.3e-178, Sum P(2) = 1.3e-178
Identities = 311/534 (58%), Positives = 386/534 (72%)
Query: 33 TEIRFSRWNNANAEEFNQRRRAQQEIEDDIRRHRRFDSATKITQSYDSSTSTATNGVA-F 91
+EIRFSRW NANAE F QRRR+Q+E+E +IRR RRFD+ATKI ++DS + A + F
Sbjct: 26 SEIRFSRWGNANAERFEQRRRSQEELEAEIRRDRRFDAATKIVHTHDSEAAAAEPKTSPF 85
Query: 92 KSAGTXXXXXXXXXXGRKSKYSKPATNSSVDHPAFRKISKREKTTNKSPEKPAASKSNIS 151
+S GT GR+SKYSKP +S + P + + + P+ A K +
Sbjct: 86 RSRGTPSLPSARSIPGRRSKYSKP--DSGPNRP-----KNKPRVPDSPPQLDA--KPEVK 136
Query: 152 ITEDGLSYVIDGAPFEFKYSYTEAPKAKPLKLREAAFSPFGPTTMGRPWTGRAPLPPSKK 211
++EDGL+YVI+GAPFEFKYSYTE PK KPLKLRE A++PFGPTTMGRPWTGRAPLP S+K
Sbjct: 137 LSEDGLTYVINGAPFEFKYSYTETPKVKPLKLREPAYAPFGPTTMGRPWTGRAPLPQSQK 196
Query: 212 KLKEFDSFQLXXXXXXXXXXXXXXXXYLPGTGPRYVSTREEILGEPLTADEVRELVESAK 271
+EFDSF+L + PG GPRYV ++EEILGEPLT +EVRELV S
Sbjct: 197 TPREFDSFRLPPVGKKGLKPVQKPGPFRPGVGPRYVYSKEEILGEPLTKEEVRELVTSCL 256
Query: 272 RSSRQLNMGRDGLTHNMLDNIHAHWKRRRACKIKCKGVCTVDMDNVCEQLEERTGGKIIY 331
+++RQLNMGRDGLTHNML+NIH WKRRR CKIKCKGVCTVDMDNVCEQLEE+ GGK+IY
Sbjct: 257 KTTRQLNMGRDGLTHNMLNNIHDLWKRRRVCKIKCKGVCTVDMDNVCEQLEEKIGGKVIY 316
Query: 332 RRGGVLYLFRGRNYNYRSRPRFPLMLWKPVTPVYPRLIQQVPDGLTLEEATEMRKKGRKL 391
RRGGVL+LFRGRNYN+R+RPRFPLMLWKPV PVYPRLIQQVP+GLT +EAT MR+KGR+L
Sbjct: 317 RRGGVLFLFRGRNYNHRTRPRFPLMLWKPVAPVYPRLIQQVPEGLTRQEATNMRRKGREL 376
Query: 392 IPICKLGKNGVYCDLAKNVREAFEVCELVRINCQGMNGSDYRKIGAKLRDLVPCVLISFE 451
+PICKLGKNGVYCDL KNV+EAFEVCELVRI+CQGM GSD+RKIGAKL+DLVPCVL+SFE
Sbjct: 377 MPICKLGKNGVYCDLVKNVKEAFEVCELVRIDCQGMKGSDFRKIGAKLKDLVPCVLVSFE 436
Query: 452 REHILMWRGQEWKSSILKPGNDSEDAKESKVDGSISVAPPTAGNGSAPSLTQMLLVEGGS 511
E IL+WRG+EWKSS+ P + ++ +VD ++ P +P+ +Q + +
Sbjct: 437 NEQILIWRGREWKSSLTTPDKKGDILEDIEVDTAL---PEDDEPSVSPNQSQTM-TQNPP 492
Query: 512 LNTFNSSISPKGYE----EVQSALREN-LSSIDGEEPFSVTKKL--SFADDNEQ 558
L++ P G++ V S+ E ++S+ VT+ SF D E+
Sbjct: 493 LDSMELQNDPDGHDLSPSTVDSSEMEGTINSLQSWSTKDVTEPTVDSFLRDLEE 546
|
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| TAIR|locus:2028100 CAF2 [Arabidopsis thaliana (taxid:3702)] | Back alignment and assigned GO terms |
|---|
| TAIR|locus:2126694 AT4G31010 [Arabidopsis thaliana (taxid:3702)] | Back alignment and assigned GO terms |
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| TAIR|locus:2160195 AT5G54890 [Arabidopsis thaliana (taxid:3702)] | Back alignment and assigned GO terms |
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| TAIR|locus:2096662 CFM2 "CRM family member 2" [Arabidopsis thaliana (taxid:3702)] | Back alignment and assigned GO terms |
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| TAIR|locus:2094558 CFM3A "CRM family member 3A" [Arabidopsis thaliana (taxid:3702)] | Back alignment and assigned GO terms |
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| TAIR|locus:2094997 EMB1865 "embryo defective 1865" [Arabidopsis thaliana (taxid:3702)] | Back alignment and assigned GO terms |
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| SGD|S000001431 YIL169C "Putative protein of unknown function" [Saccharomyces cerevisiae (taxid:4932)] | Back alignment and assigned GO terms |
|---|
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
Fail to connect to STRING server
Conserved Domains and Related Protein Families
Conserved Domains Detected by RPS-BLAST
Original result of RPS-BLAST against CDD database part I
| ID | Alignment Graph | Length |
Definition |
E-value |
| Query | 838 | |||
| pfam01985 | 84 | pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain | 1e-24 | |
| smart01103 | 84 | smart01103, CRS1_YhbY, Escherichia coli YhbY is as | 4e-22 | |
| smart01103 | 84 | smart01103, CRS1_YhbY, Escherichia coli YhbY is as | 1e-18 | |
| pfam01985 | 84 | pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain | 1e-15 | |
| COG1534 | 97 | COG1534, COG1534, Predicted RNA-binding protein co | 3e-05 |
| >gnl|CDD|190184 pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain | Back alignment and domain information |
|---|
Score = 97.9 bits (245), Expect = 1e-24
Identities = 22/84 (26%), Positives = 41/84 (48%)
Query: 258 LTADEVRELVESAKRSSRQLNMGRDGLTHNMLDNIHAHWKRRRACKIKCKGVCTVDMDNV 317
LT + R L A + +G++GLT +++ I ++ K+K G D +
Sbjct: 1 LTGKQRRYLRSLAHHLKPVVQIGKNGLTEGVVEEIDEALEKHELIKVKVLGNDREDRKEI 60
Query: 318 CEQLEERTGGKIIYRRGGVLYLFR 341
E+L E+TG +++ G + L+R
Sbjct: 61 AEELAEKTGAELVQVIGRTIVLYR 84
|
Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. Length = 84 |
| >gnl|CDD|198171 smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly | Back alignment and domain information |
|---|
| >gnl|CDD|198171 smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly | Back alignment and domain information |
|---|
| >gnl|CDD|190184 pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain | Back alignment and domain information |
|---|
| >gnl|CDD|224451 COG1534, COG1534, Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
|---|
Conserved Domains Detected by HHsearch
Original result of HHsearch against CDD database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 838 | |||
| PF01985 | 84 | CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR | 99.93 | |
| PRK10343 | 97 | RNA-binding protein YhbY; Provisional | 99.93 | |
| TIGR00253 | 95 | RNA_bind_YhbY putative RNA-binding protein, YhbY f | 99.93 | |
| COG1534 | 97 | Predicted RNA-binding protein containing KH domain | 99.91 | |
| TIGR00253 | 95 | RNA_bind_YhbY putative RNA-binding protein, YhbY f | 99.91 | |
| PRK10343 | 97 | RNA-binding protein YhbY; Provisional | 99.91 | |
| PF01985 | 84 | CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR | 99.9 | |
| COG1534 | 97 | Predicted RNA-binding protein containing KH domain | 99.89 | |
| KOG1990 | 564 | consensus Poly(A)-specific exoribonuclease PARN [R | 99.76 | |
| KOG1990 | 564 | consensus Poly(A)-specific exoribonuclease PARN [R | 99.25 |
| >PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain | Back alignment and domain information |
|---|
Probab=99.93 E-value=3.4e-26 Score=199.37 Aligned_cols=84 Identities=29% Similarity=0.522 Sum_probs=75.7
Q ss_pred CCHHHHHHHHHhhhcCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCEEEEEECCEE
Q 003220 258 LTADEVRELVESAKRSSRQLNMGRDGLTHNMLDNIHAHWKRRRACKIKCKGVCTVDMDNVCEQLEERTGGKIIYRRGGVL 337 (838)
Q Consensus 258 LTsKQRR~LRklAhkLKPvV~IGKnGLTenVVeEIheAWkkHELVKVK~lg~~~eDmkeIaEeLEekTGGeVVQrIG~vI 337 (838)
||++|+++||++||+|+|+|+|||+|||++|+++|+++|++||||||||.+++..++++++++|+++|||++||+||+++
T Consensus 1 Lt~ke~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~iG~~~ 80 (84)
T PF01985_consen 1 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVIGRTI 80 (84)
T ss_dssp --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEETTEE
T ss_pred CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEECCEE
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEc
Q 003220 338 YLFR 341 (838)
Q Consensus 338 VLYR 341 (838)
||||
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. |
| >PRK10343 RNA-binding protein YhbY; Provisional | Back alignment and domain information |
|---|
| >TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family | Back alignment and domain information |
|---|
| >COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
|---|
| >TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family | Back alignment and domain information |
|---|
| >PRK10343 RNA-binding protein YhbY; Provisional | Back alignment and domain information |
|---|
| >PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain | Back alignment and domain information |
|---|
| >COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
|---|
| >KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair] | Back alignment and domain information |
|---|
| >KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair] | Back alignment and domain information |
|---|
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
| >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 | Back alignment and structure |
|---|
Score = 68.5 bits (168), Expect = 3e-14
Identities = 17/84 (20%), Positives = 31/84 (36%)
Query: 258 LTADEVRELVESAKRSSRQLNMGRDGLTHNMLDNIHAHWKRRRACKIKCKGVCTVDMDNV 317
L+ + + L A + + +G +GLT +L I K+K G +
Sbjct: 3 LSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQLI 62
Query: 318 CEQLEERTGGKIIYRRGGVLYLFR 341
+ T + G +L L+R
Sbjct: 63 INAIVRETKAAQVQTIGHILVLYR 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 | Back alignment and structure |
|---|
| >1rq8_A Conserved hypothetical protein; structural genomics, SAV1595, YHBY, UPF0044, unknown function; NMR {Staphylococcus aureus} SCOP: d.68.4.1 Length = 104 | Back alignment and structure |
|---|
| >1rq8_A Conserved hypothetical protein; structural genomics, SAV1595, YHBY, UPF0044, unknown function; NMR {Staphylococcus aureus} SCOP: d.68.4.1 Length = 104 | Back alignment and structure |
|---|
| >1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 | Back alignment and structure |
|---|
| >1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 | Back alignment and structure |
|---|
Structure Templates Detected by HHsearch
Original result of HHsearch against PDB70 database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 838 | |||
| 1jo0_A | 98 | Hypothetical protein HI1333; structural genomics, | 99.95 | |
| 1rq8_A | 104 | Conserved hypothetical protein; structural genomic | 99.95 | |
| 1rq8_A | 104 | Conserved hypothetical protein; structural genomic | 99.93 | |
| 1jo0_A | 98 | Hypothetical protein HI1333; structural genomics, | 99.93 |
| >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 | Back alignment and structure |
|---|
Probab=99.95 E-value=9.6e-28 Score=214.90 Aligned_cols=88 Identities=19% Similarity=0.269 Sum_probs=86.5
Q ss_pred CCCHHHHHHHHHhhhcCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCEEEEEECCE
Q 003220 257 PLTADEVRELVESAKRSSRQLNMGRDGLTHNMLDNIHAHWKRRRACKIKCKGVCTVDMDNVCEQLEERTGGKIIYRRGGV 336 (838)
Q Consensus 257 ~LTsKQRR~LRklAhkLKPvV~IGKnGLTenVVeEIheAWkkHELVKVK~lg~~~eDmkeIaEeLEekTGGeVVQrIG~v 336 (838)
+||++|+++||++||+|+|+|+|||+|||++|+++|+++|++||||||||++++.+|+++++++|+++|||++||+||++
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 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEccCC
Q 003220 337 LYLFRGRN 344 (838)
Q Consensus 337 IVLYRGsN 344 (838)
+||||++.
T Consensus 82 ~vLyR~~~ 89 (98)
T 1jo0_A 82 LVLYRPSE 89 (98)
T ss_dssp EEEECCCS
T ss_pred EEEEccCC
Confidence 99999884
|
| >1rq8_A Conserved hypothetical protein; structural genomics, SAV1595, YHBY, UPF0044, unknown function; NMR {Staphylococcus aureus} SCOP: d.68.4.1 | Back alignment and structure |
|---|
| >1rq8_A Conserved hypothetical protein; structural genomics, SAV1595, YHBY, UPF0044, unknown function; NMR {Staphylococcus aureus} SCOP: d.68.4.1 | Back alignment and structure |
|---|
| >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 | Back alignment and structure |
|---|
Homologous Structure Domains
Structure Domains Detected by RPS-BLAST
Original result of RPS-BLAST against SCOP70(version1.75) database
| ID | Alignment Graph | Length |
Definition |
E-value |
| 838 | ||||
| d1rq8a_ | 96 | d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphy | 5e-21 | |
| d1rq8a_ | 96 | d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphy | 4e-16 | |
| d1jo0a_ | 97 | d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i | 2e-19 | |
| d1jo0a_ | 97 | d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i | 2e-15 |
| >d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]} Length = 96 | Back information, alignment and structure |
|---|
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 = 86.3 bits (214), Expect = 5e-21
Identities = 20/89 (22%), Positives = 35/89 (39%)
Query: 258 LTADEVRELVESAKRSSRQLNMGRDGLTHNMLDNIHAHWKRRRACKIKCKGVCTVDMDNV 317
LT + R L A +G+ G+ NM+ I + R K+ D +
Sbjct: 2 LTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKEL 61
Query: 318 CEQLEERTGGKIIYRRGGVLYLFRGRNYN 346
E L E T +++ G ++ ++R N
Sbjct: 62 AETLSEATRSELVQVIGSMIVIYRESKEN 90
|
| >d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]} Length = 96 | Back information, alignment and structure |
|---|
| >d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]} Length = 97 | Back information, alignment and structure |
|---|
| >d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]} Length = 97 | Back information, alignment and structure |
|---|
Homologous Domains Detected by HHsearch
Original result of HHsearch against SCOP70(version1.75) database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 838 | |||
| d1rq8a_ | 96 | Hypothetical protein SAV1595 {Staphylococcus aureu | 99.94 | |
| d1jo0a_ | 97 | YhbY homologue HI1333 {Haemophilus influenzae [Tax | 99.94 | |
| d1rq8a_ | 96 | Hypothetical protein SAV1595 {Staphylococcus aureu | 99.92 | |
| d1jo0a_ | 97 | YhbY homologue HI1333 {Haemophilus influenzae [Tax | 99.92 |
| >d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]} | Back information, alignment and structure |
|---|
class: Alpha and beta proteins (a+b) fold: IF3-like superfamily: YhbY-like family: YhbY-like domain: Hypothetical protein SAV1595 species: Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]
Probab=99.94 E-value=1.7e-27 Score=209.49 Aligned_cols=90 Identities=22% Similarity=0.335 Sum_probs=88.1
Q ss_pred CCCHHHHHHHHHhhhcCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCEEEEEECCE
Q 003220 257 PLTADEVRELVESAKRSSRQLNMGRDGLTHNMLDNIHAHWKRRRACKIKCKGVCTVDMDNVCEQLEERTGGKIIYRRGGV 336 (838)
Q Consensus 257 ~LTsKQRR~LRklAhkLKPvV~IGKnGLTenVVeEIheAWkkHELVKVK~lg~~~eDmkeIaEeLEekTGGeVVQrIG~v 336 (838)
|||++|+++||++||+|+|+|+|||+|||++|+++|+++|++||||||||.+.+..|+++++++|+++|||++||+||++
T Consensus 1 mLt~kqr~~LR~~ah~l~p~v~IGk~Glt~~vi~ei~~~l~~~ELIKvk~~~~~~~~~~~~~~~l~~~t~a~~V~~iG~~ 80 (96)
T d1rq8a_ 1 MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVIGSM 80 (96)
T ss_dssp CCCHHHHHHHHHHTTSSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEETTE
T ss_pred CcCHHHHHHHHHHhcCCCCEEEECCCCCCHHHHHHHHHHHHhCCeeEEEecCCCHHHHHHHHHHHHHHhCCEEEEEECCE
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEccCCCC
Q 003220 337 LYLFRGRNYN 346 (838)
Q Consensus 337 IVLYRGsNY~ 346 (838)
+||||+++++
T Consensus 81 ~vlyR~~~~~ 90 (96)
T d1rq8a_ 81 IVIYRESKEN 90 (96)
T ss_dssp EEEEECCCSC
T ss_pred EEEEeCCCCC
Confidence 9999998765
|
| >d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]} | Back information, alignment and structure |
|---|
| >d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]} | Back information, alignment and structure |
|---|
| >d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]} | Back information, alignment and structure |
|---|