Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_011974156.1 MAEO_RS07420 thiamine pyrophosphate-binding protein
Query= curated2:O08353 (599 letters) >NCBI__GCF_000017185.1:WP_011974156.1 Length = 507 Score = 231 bits (588), Expect = 7e-65 Identities = 172/563 (30%), Positives = 284/563 (50%), Gaps = 87/563 (15%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 MN + ++ L + ++ +F YPG +LP Y+ L+ S + +++ R EQ A+H ADGY+R Sbjct: 1 MNFTDEILDFLIKKNIKTVFSYPGEQILPLYNGLNESPIKNIMVRSEQGASHMADGYSRI 60 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 + VGVC+ T+GPGATNL+TG+ATA+ DSS ++A+TG+ + I + FQEI+ L Sbjct: 61 TNHVGVCLATAGPGATNLMTGIATAYKDSSSVIAITGRCKKEYINKNYFQEINMDFL--- 117 Query: 121 IVKHNFQIQKTCQIPEI--FRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVK 178 N Q P+I F AF + + P+H+++P V L+ + D + Sbjct: 118 ----NLQNGYFVDAPDIKYFEKAFNESINTKK-PIHLNIPYGVL-LDSNDDNNR------ 165 Query: 179 LIGYNPTTIGHPRQIKKAIKLIAS------AKRPIILAGGGVLLSGANEELLKLVELL-- 230 N + KK I + +P++L G G+ + + ++LK+ ++L Sbjct: 166 --NNNENNYKDEKNNKKDNTSILNNIDYNTTGKPLLLIGQGIYGNLSYNDILKINDILKN 223 Query: 231 -NIPVCTTLMGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIK 289 +IP+ TT +G I EN+P+ LG+VG GT+ AN + D + +G S Sbjct: 224 SHIPIATTYPARGVIDENNPICLGLVGGRGTEKANQYILNCDTVYCLGASLS-------- 275 Query: 290 SFATNAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENI 349 + T +I I P K++ +++ + D +L+ I L+Y K NN Sbjct: 276 -YNTLPPLIRDKIIPKI--KDIPININNLEDIELL----INTLNY------KYNN----- 317 Query: 350 SQWIENV-NSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMW 408 +I N+ N++ ++ DY +K +I+ N+ +TIITTD G + ++ Sbjct: 318 -VYINNIGNNINPNNKLCGDYS---LKINEILN---------NLPDDTIITTDAGNHTVF 364 Query: 409 MAHYFKTQTPRSFLSSGGLGTMGFGFPSAIGAKVA----KPDSKVICITGDGGFMMNCQE 464 ++ P++ +SS +GTMGFG P++IG K D +V+ I GDGGF MN QE Sbjct: 365 VSLLKTCGAPKNIISSHSMGTMGFGLPASIGVKFGCLDNNIDREVVSINGDGGFQMNIQE 424 Query: 465 LGTIAEYNIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARR 524 L T++E N+ ++I I N L + +N PDF K+A+ Y I Sbjct: 425 LATVSENNLKILIIIMKNNRLNIFGDIKN---------------PDFNKIADGYNIDNIY 469 Query: 525 IESPNEINEALKEAINCDEPYLL 547 I +EI +K +N ++PYL+ Sbjct: 470 ISDIDEIENNIKYYLNNNKPYLM 492 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: 742 Number of extensions: 34 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 599 Length of database: 507 Length adjustment: 36 Effective length of query: 563 Effective length of database: 471 Effective search space: 265173 Effective search space used: 265173 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