MLTKLSGSVMILGSHILDPGDDYGEVDDRLTLSYKIETKAPDDESHHEEP
GREEPTASSEARTGSTIPENKGEPETLAPTGKKRKIQEGQNSEGTSVTRE
EKKVKTITIRPLNMADFREAKNQVAASYAAEGSAMNKLKQWNELYGEGGS
RKKE*
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| The polypeptide, DCAR_005009, derives from mRNA, DCAR_005009. |
Analysis Date: 2021-12-09
Analysis Name: DCAR peptide blastp to SwissProt and TrEMBL without DCAR
Total hits: 20
Match: A0A2R6PHW5 ((Spastin like {ECO:0000313|EMBL:PSR91464.1}))
HSP 1 Score: 109.768 bits (273), Expect = 6.444e-26
Identity = 53/80 (66.25%), Postives = 65/80 (81.25%), Query Frame = 0
Query: 75 ETLAPTGKKRKIQEGQNSEGTSVTREEKKVKTITIRPLNMADFREAKNQVAASYAAEGSAMNKLKQWNELYGEGGSRKKE 154
E L KK++ +EG+NS+ T E+K+ + ITIRPLNM DFREA+NQVAAS+AAEGS MN+LKQWN+LYGEGGSRKKE
Sbjct: 746 ERLKDLEKKQRAEEGENSKDNQDTVEDKEERVITIRPLNMQDFREARNQVAASFAAEGSIMNELKQWNDLYGEGGSRKKE 825
HSP 2 Score: 60.8474 bits (146), Expect = 6.443e-9
Identity = 29/48 (60.42%), Postives = 36/48 (75.00%), Query Frame = 0
Query: 1 MLTKLSGSVMILGSHILDPGDDYGEVDDRLT--LSYKIETKAPDDESH 46
ML KLSG V+ILGS I+D G DY EVD+RL+ Y IE +AP+DE+H
Sbjct: 290 MLKKLSGPVLILGSRIVDMGTDYKEVDERLSALFPYNIEIRAPEDENH 337
Match: A0A5J4ZU26 (AAA domain-containing protein {ECO:0000259|SMART:SM00382})
HSP 1 Score: 109.768 bits (273), Expect = 6.470e-26
Identity = 56/80 (70.00%), Postives = 65/80 (81.25%), Query Frame = 0
Query: 75 ETLAPTGKKRKIQEGQNSEGTSVTREEKKVKTITIRPLNMADFREAKNQVAASYAAEGSAMNKLKQWNELYGEGGSRKKE 154
E L +KR+ +EGQNSE TS T E++ + ITIRPLNM DFR AKNQVAAS+AAEGS M++LKQWNELYGEGGSRKKE
Sbjct: 642 ERLKDLERKRRAEEGQNSEDTSATAGEEE-RVITIRPLNMEDFRVAKNQVAASFAAEGSIMSELKQWNELYGEGGSRKKE 720
HSP 2 Score: 68.9366 bits (167), Expect = 1.147e-11
Identity = 33/48 (68.75%), Postives = 37/48 (77.08%), Query Frame = 0
Query: 1 MLTKLSGSVMILGSHILDPGDDYGEVDDRLT--LSYKIETKAPDDESH 46
ML KLSGSV+ILGS ILDPG+DY EVD+RLT Y IE K P DE+H
Sbjct: 266 MLKKLSGSVLILGSRILDPGNDYREVDERLTSLFPYNIEIKPPKDETH 313
Match: A0A2P2Q985 (AAA_lid_3 domain-containing protein {ECO:0000259|Pfam:PF17862})
HSP 1 Score: 99.7525 bits (247), Expect = 2.500e-25
Identity = 48/73 (65.75%), Postives = 61/73 (83.56%), Query Frame = 0
Query: 82 KKRKIQEGQNSEGTSVTREEKKVKTITIRPLNMADFREAKNQVAASYAAEGSAMNKLKQWNELYGEGGSRKKE 154
+K+K +EG +SE S ++EE + IT+RPLNM D R+AKNQVAAS+AAEGS M++LKQWNELYGEGGSRKK+
Sbjct: 36 RKQKAKEGTSSEDASDSKEESTEEKITLRPLNMEDMRQAKNQVAASFAAEGSIMSELKQWNELYGEGGSRKKQ 108
Match: A0A834LJJ0 ((Uncharacterized protein {ECO:0000313|EMBL:KAF7139488.1}))
HSP 1 Score: 107.071 bits (266), Expect = 4.825e-25
Identity = 53/80 (66.25%), Postives = 63/80 (78.75%), Query Frame = 0
Query: 75 ETLAPTGKKRKIQEGQNSEGTSVTREEKKVKTITIRPLNMADFREAKNQVAASYAAEGSAMNKLKQWNELYGEGGSRKKE 154
E L KK+K QEG+N + T EK+ + ITIRPLNM DFREA+NQVAAS+AAEGS MN+LKQWN+LYG+GGSRKKE
Sbjct: 749 ERLKDLEKKQKAQEGKNLKDAPDTEVEKEERVITIRPLNMQDFREARNQVAASFAAEGSIMNELKQWNDLYGDGGSRKKE 828
HSP 2 Score: 64.3142 bits (155), Expect = 4.041e-10
Identity = 30/48 (62.50%), Postives = 37/48 (77.08%), Query Frame = 0
Query: 1 MLTKLSGSVMILGSHILDPGDDYGEVDDRLT--LSYKIETKAPDDESH 46
ML +LSG V+ILGS I+D G +YGEVD+RLT Y IE KAP+DE+H
Sbjct: 293 MLKRLSGPVLILGSRIVDSGSNYGEVDERLTALFPYNIEIKAPEDETH 340
Match: M1BRP3 ((ATP binding protein {ECO:0000313|EnsemblPlants:PGSC0003DMT400051398}))
HSP 1 Score: 99.3673 bits (246), Expect = 1.162e-24
Identity = 48/74 (64.86%), Postives = 62/74 (83.78%), Query Frame = 0
Query: 82 KKRKIQEGQNSEGTSVTREEK-KVKTITIRPLNMADFREAKNQVAASYAAEGSAMNKLKQWNELYGEGGSRKKE 154
KKR +EGQ++EG S +EE + + IT+RPLNM D R+AKNQVAAS+A+EGS M++LKQWN+LYGEGGSRKK+
Sbjct: 69 KKRSAEEGQSAEGNSDEKEEAAEERVITLRPLNMEDMRQAKNQVAASFASEGSVMSELKQWNDLYGEGGSRKKQ 142
Match: A0A7C9DQ97 (AAA_lid_3 domain-containing protein {ECO:0000259|Pfam:PF17862})
HSP 1 Score: 100.138 bits (248), Expect = 1.388e-24
Identity = 46/82 (56.10%), Postives = 64/82 (78.05%), Query Frame = 0
Query: 73 EPETLAPTGKKRKIQEGQNSEGTSVTREEKKVKTITIRPLNMADFREAKNQVAASYAAEGSAMNKLKQWNELYGEGGSRKKE 154
+ E L G ++K ++GQ+S+G S + K+ + +++RPLNM DFR+AKNQ AAS+A+EG+ MN+LKQWN LYGEGGSRKKE
Sbjct: 94 QQERLKDMGNQQKSEQGQSSDGESNNEDVKEERVMSLRPLNMEDFRQAKNQAAASFASEGAVMNELKQWNNLYGEGGSRKKE 175
Match: A0A6A4LVU3 (AAA domain-containing protein {ECO:0000259|SMART:SM00382} (Fragment))
HSP 1 Score: 105.531 bits (262), Expect = 1.622e-24
Identity = 52/80 (65.00%), Postives = 62/80 (77.50%), Query Frame = 0
Query: 75 ETLAPTGKKRKIQEGQNSEGTSVTREEKKVKTITIRPLNMADFREAKNQVAASYAAEGSAMNKLKQWNELYGEGGSRKKE 154
E L KK+ QEG+N + T EK+ + ITIRPLNM DFREA+NQVAAS+AAEGS MN+LKQWN+LYG+GGSRKKE
Sbjct: 709 ERLKDLEKKQTAQEGKNLKDAPDTEAEKEERVITIRPLNMQDFREARNQVAASFAAEGSVMNELKQWNDLYGDGGSRKKE 788
HSP 2 Score: 64.3142 bits (155), Expect = 3.682e-10
Identity = 30/48 (62.50%), Postives = 37/48 (77.08%), Query Frame = 0
Query: 1 MLTKLSGSVMILGSHILDPGDDYGEVDDRLT--LSYKIETKAPDDESH 46
ML +LSG V+ILGS I+D G +YGEVD+RLT Y IE KAP+DE+H
Sbjct: 253 MLKRLSGPVLILGSRIVDSGSNYGEVDERLTALFPYNIEIKAPEDETH 300
Match: A0A7J7C7D6 ((Putative ATP binding protein {ECO:0000313|EMBL:KAF5730041.1}))
HSP 1 Score: 105.145 bits (261), Expect = 2.325e-24
Identity = 47/73 (64.38%), Postives = 64/73 (87.67%), Query Frame = 0
Query: 82 KKRKIQEGQNSEGTSVTREEKKVKTITIRPLNMADFREAKNQVAASYAAEGSAMNKLKQWNELYGEGGSRKKE 154
K++++ EGQ+SE S T+E K+ + IT+RPLNM DF++AKNQ+AAS+AAEGS M++LKQWN+LYGEGGSRKK+
Sbjct: 539 KQQQVAEGQHSEDVSDTKEGKEERVITLRPLNMEDFKQAKNQIAASFAAEGSIMSELKQWNDLYGEGGSRKKQ 611
HSP 2 Score: 53.5286 bits (127), Expect = 2.388e-6
Identity = 26/48 (54.17%), Postives = 35/48 (72.92%), Query Frame = 0
Query: 1 MLTKLSGSVMILGSHILDPGDDYGEVDDRLT--LSYKIETKAPDDESH 46
ML KLS SV+ILGS I+D +D ++D+RLT YKI+ K P+DE+H
Sbjct: 80 MLKKLSRSVLILGSQIVDQDNDSNQLDERLTAVFPYKIDIKPPEDETH 127
Match: A0A0V0I5N4 ((Putative ovule protein {ECO:0000313|EMBL:JAP27932.1}))
HSP 1 Score: 98.9821 bits (245), Expect = 2.982e-24
Identity = 48/74 (64.86%), Postives = 62/74 (83.78%), Query Frame = 0
Query: 82 KKRKIQEGQNSEGTSVTREEK-KVKTITIRPLNMADFREAKNQVAASYAAEGSAMNKLKQWNELYGEGGSRKKE 154
KKR +EGQ++EG S +EE + + IT+RPLNM D R+AKNQVAAS+A+EGS M++LKQWN+LYGEGGSRKK+
Sbjct: 96 KKRNAEEGQSAEGNSDEKEEAAEERVITLRPLNMEDMRQAKNQVAASFASEGSVMSELKQWNDLYGEGGSRKKQ 169
Match: A0A2G9HRE0 ((Adenosinetriphosphatase {ECO:0000313|EMBL:PIN20087.1}) (3.6.1.3 {ECO:0000313|EMBL:PIN20087.1}))
HSP 1 Score: 98.2117 bits (243), Expect = 3.195e-24
Identity = 47/73 (64.38%), Postives = 59/73 (80.82%), Query Frame = 0
Query: 82 KKRKIQEGQNSEGTSVTREEKKVKTITIRPLNMADFREAKNQVAASYAAEGSAMNKLKQWNELYGEGGSRKKE 154
KK+ EG++S+ S +EE K K I++RPLNM D R+AKNQVAAS+A+EGS M +LKQWNELYGEGGSRKK+
Sbjct: 69 KKQTDDEGKSSKDASSCQEETKEKVISLRPLNMEDLRQAKNQVAASFASEGSIMAELKQWNELYGEGGSRKKQ 141
| Match Name | Stats | Description |
|---|---|---|
| A0A2R6PHW5 | E-Value: 6.444e-26, PID: 66.25 | (Spastin like {ECO:0000313|EMBL:PSR91464.1})[more] |
| A0A5J4ZU26 | E-Value: 6.470e-26, PID: 70.00 | AAA domain-containing protein {ECO:0000259|SMART:S... [more] |
| A0A2P2Q985 | E-Value: 2.500e-25, PID: 65.75 | AAA_lid_3 domain-containing protein {ECO:0000259|P... [more] |
| A0A834LJJ0 | E-Value: 4.825e-25, PID: 66.25 | (Uncharacterized protein {ECO:0000313|EMBL:KAF7139... [more] |
| M1BRP3 | E-Value: 1.162e-24, PID: 64.86 | (ATP binding protein {ECO:0000313|EnsemblPlants:PG... [more] |
| A0A7C9DQ97 | E-Value: 1.388e-24, PID: 56.10 | AAA_lid_3 domain-containing protein {ECO:0000259|P... [more] |
| A0A6A4LVU3 | E-Value: 1.622e-24, PID: 65.00 | AAA domain-containing protein {ECO:0000259|SMART:S... [more] |
| A0A7J7C7D6 | E-Value: 2.325e-24, PID: 64.38 | (Putative ATP binding protein {ECO:0000313|EMBL:KA... [more] |
| A0A0V0I5N4 | E-Value: 2.982e-24, PID: 64.86 | (Putative ovule protein {ECO:0000313|EMBL:JAP27932... [more] |
| A0A2G9HRE0 | E-Value: 3.195e-24, PID: 64.38 | (Adenosinetriphosphatase {ECO:0000313|EMBL:PIN2008... [more] |
Pages
back to top| Name | Description |
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An orange, doubled-haploid, Nantes-type carrot (DH1) was used for genome sequencing. We used BAC end sequences and a newly developed linkage map with 2,075 markers to correct 135 scaffolds with one or more chimeric regions. The resulting v2.0 assembly spans 421.5 Mb and contains 4,907 scaffolds (N50 of 12.7 Mb), accounting for ∼90% of the estimated genome size of 473 Mb. The scaftig N50 of 31.2 kb is similar to those of other high-quality genome assemblies such as potato and pepper. About 86% (362 Mb) of the assembled genome is included in only 60 superscaffolds anchored to the nine pseudomolecules. The longest superscaffold spans 30.2 Mb, 85% of chromosome 4. There are a few different naming schemes for this assembly. First there is the Phytozome genome ID 388: The authors' sequences and gene predictions were also submitted to Phytozome, and can be accessed at this address: https://phytozome-next.jgi.doe.gov/info/Dcarota_v2_0 LNRQ01: These sequences were then assigned GenBank accession numbers starting at LNRQ01000001.1 which corresponds to DCARv2_Chr1, up to LNRQ01004826.1 which corresponds to an unincorporated contig, DCARv2_C10750146. These reside in bioproject PRJNA268187, which is a subproject of umbrella project PRJNA285926. Assembly GCA_001625215.1: The genome assembly was later defined an accession number GCA_001625215.1 for assembly ASM162521v1 which consists of only the 9 chromosome sequences and the plastid assembly, which have accession numbers from CM004278.1 to CM004286.1 for the chromosomes and CM004358.1 for the plastid. The mitochondrial genome was not included because it is classified as an incomplete sequence. RefSeq: The assembly was then later added to RefSeq, and there another new set of identifiers was defined from NC_030381.1 to NC_030389.1 for the chromosomes, and from NW_016089425.1 to NW_016094239.1 for unincorporated scaffolds and contigs. These reside in bioproject PRJNA326436. Note that NCBI substituted different assembled organellar genomes from different genotypes for the RefSeq records. The NCBI Sequence report lists the correspondences between the various naming methods Link to the LNRQ01000000.1 master record at NCBI Raw Reads: Link to SRA accessions used for the genome assembly This genome is available in the CarrotOmics Blast Search | |
This analysis is a blastp search of all of the DCAR V1.0 Gene Prediction polypeptide sequences against combined ExPASy SwissProt and TrEMBL databases from Nov. 17, 2021. Prior to performing the blast search, the database was filtered to remove organisms not in the Viridiplantae, and also filtered to remove these same DCAR gene predictions. | |
For gene model prediction, mobile element–related repeats were masked using RepeatMasker. De novo prediction using AUGUSTUS v2.5.5, GENSCAN v.1.1.0, and GlimmerHMM-3.0.1 was trained using model species A. thaliana and S. lycoperisum training sets. The protein sequences of S. lycoperisum, Solanum tuberosum, A. thaliana, Brassica rapa, and Oryza sativa were mapped to the carrot genome using TBLASTN (BLAST All 2.2.23) and analyzed with GeneWise version 2.2.0. Carrot ESTs were aligned to the genome using BLAT and analyzed with PASA to detect spliced gene models. RNA-seq reads from 20 DH1 libraries were aligned with TopHat 2.0.9. Transcripts were predicted by Cufflinks. All gene models produced by de novo prediction, protein homology searches, and prediction and transcript-based evidence were integrated using GLEAN v1.1. Putative gene functions were assigned using the best BLASTP match to SwissProt and TrEMBL databases. Gene motifs and domains were determined with InterProScan version 4.7 against the ProDom, PRINTS, Pfam, SMART, PANTHER, and PROSITE protein databases. GO IDs for each gene were obtained from the corresponding InterPro entries. All genes were aligned against KEGG (release 58) proteins. Data from this analysis can be viewed in JBrowse here. |