Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_013843779.1 DESRU_RS19290 sulfoacetaldehyde acetyltransferase
Query= curated2:O08353 (599 letters) >NCBI__GCF_000215085.1:WP_013843779.1 Length = 579 Score = 294 bits (752), Expect = 8e-84 Identities = 181/568 (31%), Positives = 299/568 (52%), Gaps = 19/568 (3%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 M +EA+++ L EKVE + G G A + D + + + RHEQ+AAH D Y R Sbjct: 6 MTPSEAIVETLLQEKVEHVTGIVGSAFMDMLDLFPTAGIHFIPVRHEQSAAHMEDAYTRV 65 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 +GK GVC+G +GPG TN+VT VA A+ +P+V ++ T IG D FQE D + +F Sbjct: 66 TGKCGVCVGQNGPGITNMVTSVAAANMAHTPLVVISPSAGTPTIGWDGFQECDQVSVFRA 125 Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180 I K ++ + + R+AF IA R G V D+P+D EL+ ++ P + ++ Sbjct: 126 ITKATVRVPHPKRAADCLRTAFRIAYAER-GAVLYDIPRDYFYGELE-ERILAPHQYRV- 182 Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240 + G + +A++L+A A+RP+I++G GV+ S A + + K+ E L PV T + Sbjct: 183 --DARGCGSRESLNRAVELLAQAQRPVIVSGRGVVDSQAKDIVAKIAEHLTAPVAVTYLH 240 Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCR---FSDRITGDIKSFATNAKI 297 +H L +G +G G+K A Y L E+DV+++IG R F DI F +AKI Sbjct: 241 NDGFYADHELMVGPIGYMGSKAAMYSLQEADVILAIGTRLSVFGTLPQYDIHYFPEDAKI 300 Query: 298 IHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVN 357 I IDI+P I + V+V IVGDAK E++K L+ K + ++E ++Q Sbjct: 301 IQIDINPKHIARTHPVEVGIVGDAKEASLEILKGLE---AKIPQPQINEERLNQISARQQ 357 Query: 358 SLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQT 417 ++ ++ + D PI P++ + E+ + +N I+ TD+G Y + + Sbjct: 358 DWEEETVNLAMVDGNPINPRRALLEIQRALP-----QNAIVATDIGNVASTANTYLRFRD 412 Query: 418 PRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVI 477 +++ G GF +P+A+GA++ +P++ V I GDG + M+ E+ T E N+PVV Sbjct: 413 KGMHIAALTFGNTGFAYPAALGAQLGRPEAPVAAIIGDGAWGMSLHEVSTAVEQNLPVVA 472 Query: 478 CIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKE 537 C+F N + Q FY R + F+ +A++ G + R++SP+++ EAL + Sbjct: 473 CVFRNGAWCAEKKNQVDFYNNRFVGADIPNPESFVPVAQAMGAQGIRVDSPSQVGEALDQ 532 Query: 538 AINCDEPYLLDFAIDPSSALSMVPPGAK 565 A+ +P +L+ D + PP K Sbjct: 533 ALKSRKPTVLEIVCD---GTQLAPPFRK 557 Lambda K H 0.319 0.137 0.405 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: 745 Number of extensions: 39 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: 599 Length of database: 579 Length adjustment: 37 Effective length of query: 562 Effective length of database: 542 Effective search space: 304604 Effective search space used: 304604 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 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
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