Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_051326919.1 G491_RS0100345 thiamine pyrophosphate-binding protein
Query= curated2:O08353 (599 letters) >NCBI__GCF_000429905.1:WP_051326919.1 Length = 568 Score = 260 bits (664), Expect = 1e-73 Identities = 174/572 (30%), Positives = 285/572 (49%), Gaps = 34/572 (5%) Query: 3 GAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARASG 62 GA+ +AL VE++F GG + P Y L +D+ + TRHEQAA A+ Y R + Sbjct: 10 GAQLAAEALVDLGVEVIFTLSGGHITPIYQFLEDTDIKLMDTRHEQAAVFMAEAYGRMTR 69 Query: 63 KVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPIV 122 K G+ + T+GPG TN +T +A A ++P+V ++G V + + Q++ + P+V Sbjct: 70 KPGIAMVTAGPGFTNALTPIANARLSNTPLVLISGVVGIESVDKLDLQDMRQAPVIEPMV 129 Query: 123 KHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLIGY 182 K ++ E A IA TGRPGPV+++LP D+ ++ P +KVK + Sbjct: 130 KKALVCHHPERVYEYIDMAMRIASTGRPGPVYLELPVDM------LNCKPEAAKVKRLAT 183 Query: 183 NPTTIGHPRQIKKA---IKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLM 239 P + KA +++I A P+I+AG G S A +EL K VE+ NIP+ T+ Sbjct: 184 QVEC--RPADLSKAPAILEMIEQANTPMIIAGSGAWYSDAGDELQKFVEMTNIPIFTSTQ 241 Query: 240 GKGCISENHPLALGMVGMHGTKPANYCLS--ESDVLISIGCRFS-DRITGDIKSFATNAK 296 G+G +S++HPL G +P ++ +D+LI +G RFS I GDI F K Sbjct: 242 GRGIVSDDHPLC--FEGSLAIRPGAAMMASFSTDLLIMLGSRFSLYYIFGDI--FPPTCK 297 Query: 297 IIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENV 356 I+ +DI+P E+G N VD+P+ D K ++ E+I+ ++ + +E + W++ + Sbjct: 298 IVQVDIEPQELGHNKAVDLPVTSDIKPLIAEMIR----LVEEKGNGAAMQEKYAGWVKTL 353 Query: 357 NSL----KKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHY 412 + + + + PI P ++ +E +D+ ++ I+ D G +WM Sbjct: 354 EQANIDGRVEANAQWESPESPIHPMRLARE----VDNFMNLESDIVCADGGDTSVWMGMT 409 Query: 413 FKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYN 472 + ++L SG G +G G P A AK PDS+V ITGDG N E T Sbjct: 410 RTVRKGGTYLDSGLYGCLGVGIPYANAAKFHNPDSRVCLITGDGSTGFNFMEFETSIRKG 469 Query: 473 IPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEIN 532 +P+V+ I ++ GM+ Q L G + G D+ K+ E G +E P +I Sbjct: 470 LPIVVVISNDLGWGMIRHSQELRLGHAIEDGTWIGRVDYHKMIEPLGGVGFLVEKPEDIR 529 Query: 533 EALKEAINCDEPYLLDFAIDPSSALSMVPPGA 564 AL+EA + ++ DP++ + PG+ Sbjct: 530 PALEEAFKTGKTCCINVMTDPTT----ISPGS 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: 802 Number of extensions: 37 Number of successful extensions: 4 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: 568 Length adjustment: 36 Effective length of query: 563 Effective length of database: 532 Effective search space: 299516 Effective search space used: 299516 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 Apr 10 2024. The underlying query database was built on Apr 09 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