Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate H281DRAFT_01343 H281DRAFT_01343 3-methylcrotonoyl-CoA carboxylase, alpha subunit
Query= SwissProt::Q5LUF3 (681 letters) >FitnessBrowser__Burk376:H281DRAFT_01343 Length = 677 Score = 506 bits (1304), Expect = e-147 Identities = 295/680 (43%), Positives = 393/680 (57%), Gaps = 22/680 (3%) Query: 1 MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60 MFNKILIANRGEIACRV T +++GI++VA+YSDAD A HV DEAVHIG A +SY Sbjct: 1 MFNKILIANRGEIACRVAATCKRLGIASVAVYSDADADAKHVSACDEAVHIGGATAAESY 60 Query: 61 IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120 + + +++ A RATGAQAVHPGYGFLSEN FA A EA G++F+GPP AI AMG K +K Sbjct: 61 LRVARIIEAARATGAQAVHPGYGFLSENEDFAHACEAAGIVFIGPPVEAIAAMGSKAAAK 120 Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180 + A V VPGY G ++ + + ++ IGYPV++KASAGGGGKGMR+ ++ Sbjct: 121 ALMHAAAVPLVPGYHGDDQNPELLHREADAIGYPVLLKASAGGGGKGMRVVERSEDFLAA 180 Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240 S K EAA+SFG+DR+ IEK++T+PRH+E+QV D HG +YL +R+CS+QRR+QKV+E Sbjct: 181 LASCKREAASSFGNDRVLIEKYLTRPRHVEVQVFADRHGGAVYLFDRDCSVQRRHQKVLE 240 Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300 EAP+P L +R MGE AVA A+AV Y AGTVEFI+ +FYF+EMNTRLQVEHPVT Sbjct: 241 EAPAPGLSAQIKREMGEAAVAAARAVNYVGAGTVEFIMTATGDFYFMEMNTRLQVEHPVT 300 Query: 301 ELITGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTRYRP 360 E+ITG DLVE +RVAAG+PL +TQ +K+ G AIE R+YAE P RGFLPS G L R Sbjct: 301 EMITGQDLVEWQLRVAAGQPLPLTQDQLKIDGHAIEARIYAEHPARGFLPSTGTLKHLRM 360 Query: 361 PAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRAAAI 420 P G S +A VR D+GV EG I+ +YDPMIAKL TR A+ Sbjct: 361 PEGVEF------AIHAGAGESRKAPVRIDSGVREGDTITPFYDPMIAKLIVHGATREEAL 414 Query: 421 EAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAEEYPEGFEGVNLPETDLR 480 M AL + EV G N+ FL +++ F +GD+ T I + F V P + Sbjct: 415 ARMSRALHACEVVGPHTNVEFLQRIVESEPFATGDLDTGLIERHHEALFAPVKKPFKEAL 474 Query: 481 RVAAAAAAMHRVAEIRRTRVSGRMDNHERRVG----TEWVVTLQGAD--FPVTIAADHDG 534 +A AA + + G W+ + P T+A DG Sbjct: 475 ALACAALLTREGGTAHGASPWDALSHWRLNSGFTQTLGWLAIESSGETGSPFTVAFARDG 534 Query: 535 STVSFDDGSSMRVTSDWTPGDQLANLMVDGAPLVLKVGKISGGFRIRTRGADLKVHVRTP 594 +T + + +R W+ G L +G R+ G V Sbjct: 535 ATQTLEH-DGVREAFSWSSGAGLHEYRA-------TIGDARATGRVFIDGDTFHVFCLGH 586 Query: 595 RQA-ELARLMPEKLPPDTSK-MLLCPMPGLIVKVDVEVGQEVQEGQALCTIEAMKMENIL 652 A E L+ + + L PMPG ++ V VE G V++G L +EAMKME+ + Sbjct: 587 ALAFEWQNLLAHAADAEHGEGRLTAPMPGKVIAVLVEPGAVVEKGTPLIVMEAMKMEHTI 646 Query: 653 RAEKKGVVAKINASAGNSLA 672 A G V+++ + G+ +A Sbjct: 647 GAPAAGTVSEVLYAVGDQVA 666 Lambda K H 0.317 0.134 0.387 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1147 Number of extensions: 51 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 681 Length of database: 677 Length adjustment: 39 Effective length of query: 642 Effective length of database: 638 Effective search space: 409596 Effective search space used: 409596 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory