Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_245926541.1 DK846_RS12300 thiamine pyrophosphate-binding protein
Query= curated2:O08353 (599 letters) >NCBI__GCF_003173355.1:WP_245926541.1 Length = 635 Score = 262 bits (670), Expect = 3e-74 Identities = 176/558 (31%), Positives = 288/558 (51%), Gaps = 42/558 (7%) Query: 4 AEAMIKALEAEKVEILFGYPGGALLPFYDALH-HSDLIHLLTRHEQAAAHAADGYARASG 62 ++ +I+ L + + FG PG + L +A+ + D L RHE+ AA AA Y + +G Sbjct: 98 SDVLIRQLTSFGIHEFFGIPGTSSLGIIEAIRKNKDARFTLFRHEENAALAASAYHKFTG 157 Query: 63 KVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPIV 122 K+ VC+ +GPGATNL TG+ A D +P+++L GQV + G FQEID F PI Sbjct: 158 KIAVCVTIAGPGATNLATGLYDAKEDKTPVLSLNGQVSMQYAGPGGFQEIDQDAFFRPIT 217 Query: 123 KHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLIGY 182 +N I +I A + A R G I +P DVQ+ +LD + + + + Sbjct: 218 VYNNTIYDRKMTQKILILALQHAIV-RSGVAQISVPNDVQKQQLDGKVYSLQGSIPSLKI 276 Query: 183 NPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMGKG 242 P + + +A ++ A+ P+ILAG G + L + ++ P+ +T KG Sbjct: 277 VPDS----DTLSRAAAMLDMAENPVILAGWGAF--SYADILSSFSKAIDAPILSTFRAKG 330 Query: 243 CISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHIDI 302 + + HP +G++G G+ A + ++D+LI++G FS + +I+ ID Sbjct: 331 ILPDGHPQYVGILGSVGSPQARELVEQADLLITLGVGFSKK-----TMVPEQVQILQIDR 385 Query: 303 DPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENND---KENISQWIENVNSL 359 +P +GK + +P+ GD + EV+ +L I+ + + N+ KE + W L Sbjct: 386 EPLMLGKG-DKTLPVYGD----VGEVLSRLIPIVRQRGRPNSPRRVKEIVESWDA---QL 437 Query: 360 KKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPR 419 +K + P + PI+P I+K L VI D + +I+ D+G+N W FK + R Sbjct: 438 EKEADP----NAKPIRPPYIMKVLSEVIPD-----DALISIDIGENAWWFGRNFKMKKQR 488 Query: 420 SFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICI 479 F SG L TMGFG P AI AK+A P+S+V CITGDGGF M + T +YN+P+V+ + Sbjct: 489 -FAMSGYLATMGFGLPGAIAAKLAYPESQVFCITGDGGFAMAMADFVTAVKYNLPMVVVV 547 Query: 480 FDNRTLGMVYQWQNLFYGKRQCSVNFG---GAPDFIKLAESYGIKARRIESPNEINEALK 536 +N LGM+ Q K + NF PDF A++ G + + + P+++ A++ Sbjct: 548 LNNHQLGMIRVEQ-----KVENYENFATDLKNPDFAMYAKACGGEGKHVFEPDDLGRAVR 602 Query: 537 EAINCDEPYLLDFAIDPS 554 A+ ++P ++D DP+ Sbjct: 603 WAMQLNKPVIIDVNTDPN 620 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: 888 Number of extensions: 50 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: 599 Length of database: 635 Length adjustment: 37 Effective length of query: 562 Effective length of database: 598 Effective search space: 336076 Effective search space used: 336076 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 09 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