Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate WP_011383117.1 AMB_RS03465 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= BRENDA::Q9I299 (655 letters) >NCBI__GCF_000009985.1:WP_011383117.1 Length = 665 Score = 669 bits (1727), Expect = 0.0 Identities = 362/660 (54%), Positives = 451/660 (68%), Gaps = 19/660 (2%) Query: 10 RLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSYLRG 69 ++L+ANRGEIACRVMR+A+ LGI +VAV+S+ D +A HVA AD AV +G A A+SYL+G Sbjct: 4 KILIANRGEIACRVMRTAKRLGIRTVAVYSEADANAMHVAMADEAVLIGPAAAAESYLKG 63 Query: 70 DRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAKALM 129 D I+ AA +GAQAIHPGYGFLSENA FA AC +AG++F+GPP AI AMGSK+ +K LM Sbjct: 64 DVILEAAKRTGAQAIHPGYGFLSENAGFAEACAKAGVVFIGPPVGAIHAMGSKAESKRLM 123 Query: 130 EEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEALSS 189 E AGVPLVPGYHG+ Q LE REA IGYPVL+KA+AGGGGKGM+VV + LAEA++S Sbjct: 124 EAAGVPLVPGYHGKGQTLEELTREAAIIGYPVLVKASAGGGGKGMRVVSEASGLAEAVAS 183 Query: 190 AQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVEEAP 249 A+REAKAAFGD +L+E YL +PRHVEIQVF D HG+ +YL ERDCSIQRRHQKV+EEAP Sbjct: 184 AKREAKAAFGDDSLLLETYLGRPRHVEIQVFCDTHGNGVYLFERDCSIQRRHQKVIEEAP 243 Query: 250 APGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEHPVTEAI 309 AP L E RRAMGEAAV AAQA+ YVGAGTVEFL + G+FFF+EMNTRLQVEHPVTE I Sbjct: 244 APALADETRRAMGEAAVAAAQAVDYVGAGTVEFLYQD-GRFFFIEMNTRLQVEHPVTEMI 302 Query: 310 TGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYREAAA 369 TGLDLV WQ+ VA G LPL QEQ+ GHA E RLYAEDP DFLPA G+L+ + Sbjct: 303 TGLDLVEWQLLVASGGKLPLAQEQLSRKGHAFEARLYAEDPSRDFLPAIGKLVHLAPPSE 362 Query: 370 GPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTNLAFL 429 RVD+GVR+GD+V+PFYDPM+AKLI W E R+ A +RL LA+ V G+ TN++FL Sbjct: 363 NRHVRVDTGVRQGDQVTPFYDPMIAKLIVWDEDRDSALRRLRRALADYQVAGVTTNVSFL 422 Query: 430 RRILGHPAFAAAELDTGFIARHQDDLLPAPQALPE---HFWQAAAEAWLQSEPGH--RRD 484 I HPAFAA E+DTGFI R++ DL P +P F A W + + R Sbjct: 423 GAIAAHPAFAALEIDTGFIERYRADLQPPAAPVPAMGLAFASLALLLWREEDSARTAARS 482 Query: 485 DDPHSPWSRNDGWRSALARESDL-MLRCRDERRC------------VRLRHASPSQYRLD 531 DPHSPW + +GWR D + DERR + + S + L Sbjct: 483 GDPHSPWHQTNGWRLNDDNHHDFRFMDGADERRVTVHFVADGWSLDLPDQTLSARRATLS 542 Query: 532 GDDLVSRVDGVTRRSAALRRGRQLFLEWEGELLAIEAVDPIAEAEAAHAHQGGLSAPMNG 591 G L + + G R ++ +R G + + +G I+ DP A A G L+APM G Sbjct: 543 GTTLSAEIGGERRTASVVRSGFDITVLHDGHAWKIKLDDPSATAAEREGGDGRLAAPMPG 602 Query: 592 SIVRVLVEPGQTVEAGATLVVLEAMKMEHSIRAPHAGVVKALYCSEGELVEEGTPLVELD 651 ++V+VLV+PG V AG L+V+EAMKMEH+I+AP G V A++ G+ V EG L+ + Sbjct: 603 TVVQVLVQPGDAVTAGQPLIVVEAMKMEHAIKAPAEGKVAAIHFKVGDTVAEGVELLAFE 662 Lambda K H 0.319 0.135 0.397 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: 1082 Number of extensions: 44 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 655 Length of database: 665 Length adjustment: 38 Effective length of query: 617 Effective length of database: 627 Effective search space: 386859 Effective search space used: 386859 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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