Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_010443464.1 G7G_RS0121085 acetolactate synthase large subunit
Query= curated2:Q7U5G1 (617 letters) >NCBI__GCF_000192475.1:WP_010443464.1 Length = 557 Score = 233 bits (594), Expect = 2e-65 Identities = 170/549 (30%), Positives = 267/549 (48%), Gaps = 34/549 (6%) Query: 27 LMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHAADAYARATG 86 L+ AL GV+ IF PG L + ++L ++ ++ +L RHEQ A Y R TG Sbjct: 18 LVAALEAEGVEYIFAVPGEENLDVLESLRTSK----IELVLTRHEQGAAFMAATYGRLTG 73 Query: 87 KVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQETDIFGITLPIV 146 K GVC T GPGATN T A A + +P+++ITGQ P FQ DI G+ PI Sbjct: 74 KAGVCMATLGPGATNFATPAAYAHLGGMPLIMITGQKPIKKSKQGQFQIVDIVGLFDPIC 133 Query: 147 KHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFNYVPVEPGSVIPGGFH 206 K S + + S++ +AF +A RPG VL+++P+D+ E+ + +EP H Sbjct: 134 KMSKQIVHGNTIPSLIREAFRVAQEERPGAVLLELPEDIAAEETSEHVLEP--------H 185 Query: 207 QPEPPL--DAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQLPVTTTLMGK 264 Q + DA + A ++I A+ PLL +G GA A +L Q+P T MGK Sbjct: 186 QRHYAVAGDAVLTEAAEMIRAARMPLLLLGAGANRKHARSALSKFVNDTQIPFFNTQMGK 245 Query: 265 GAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVTGKLDTFAPRARVVHFE 324 G DE L +G + Y + A+ DL+I VG ++ ++ +V+H Sbjct: 246 GVVDERSELFLGTAALSDGDYLHCAIERADLIINVGHDVVEKPPFFMEEGG--TKVIHVN 303 Query: 325 IDPAEIGKNRKADVAVLGDLGLSLARMVEISLQRTAEPRTAAWLERINTWKDRYPLTIPP 384 A++ + V V+GDL S++++ E LQ E ++ +R+ D + Sbjct: 304 YKAAQVDQVYFPQVEVVGDLAQSISKLGEF-LQGPLE-FDRSYFQRVKNETD-----LHT 356 Query: 385 AEGA------IYPQEVLLAVRDLAPDA-IVTTDVGQHQMWAAQHLR-NGPRGWISSAGLG 436 +EGA + PQ + R + D I+ D G +++W A++ + P + L Sbjct: 357 SEGADDPRFPVIPQRFVSDTRKVMGDCDIIALDNGIYKIWYARNYQAYQPNTVLLDNALA 416 Query: 437 TMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKVVIVNNHWQGMV 496 TMG G+P+AM A P+R+V+ I GD +MN QE+ T GL + V ++N+ GM+ Sbjct: 417 TMGAGLPSAMMAAKLYPERRVMAICGDGGFMMNSQEIETAVRLGLNLVVTVLNDSSYGMI 476 Query: 497 RQWQESFYDERYSASDMLNGMPDFIALARSFGVDGVKITDRELLHRDLAAALQSPTPTMI 556 R W++S + N PDF+ A S+G G ++ E L A ++ +I Sbjct: 477 R-WKQSHAGFDDWGLEFKN--PDFVQYANSYGATGHRVERTEDLVPTFEKAFEAGGVHLI 533 Query: 557 DVHVRRGEN 565 D+ V EN Sbjct: 534 DLPVDYSEN 542 Lambda K H 0.320 0.136 0.414 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: 726 Number of extensions: 34 Number of successful extensions: 6 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: 617 Length of database: 557 Length adjustment: 37 Effective length of query: 580 Effective length of database: 520 Effective search space: 301600 Effective search space used: 301600 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: 53 (25.0 bits)
This GapMind analysis is from Jul 26 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