Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_010877210.1 MTH_RS07675 thiamine pyrophosphate-binding protein
Query= curated2:O08353 (599 letters) >NCBI__GCF_000008645.1:WP_010877210.1 Length = 524 Score = 332 bits (851), Expect = 2e-95 Identities = 203/549 (36%), Positives = 297/549 (54%), Gaps = 40/549 (7%) Query: 4 AEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARASGK 63 AE + LE +FG+PG +LP Y+AL S L H+L RHEQ A HAADGYARASG Sbjct: 5 AEVLAGILEEAGFTHIFGHPGEQILPLYEALRKSGLEHVLMRHEQGAVHAADGYARASGG 64 Query: 64 VGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPIVK 123 GVC+ T GPGA NLV GVA A +DS P++A+TG +P + G FQE+D +F + + Sbjct: 65 PGVCVATGGPGALNLVMGVAAASTDSVPLIAMTGDLP-RGGGPGRFQEVDLEAVFRALTR 123 Query: 124 HNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLIGYN 183 + + + + + G G +HI+LP+DV LE D PS+V Sbjct: 124 MSMTPGSGDEASMMLADSISSLRRGLTGVIHINLPRDV--LEEDACPPVGPSEV------ 175 Query: 184 PTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMGKGC 243 + +A++L+ SA+RP+ILAGGGV+ A E + +E IPV TT +G Sbjct: 176 ---FRELPDMSRALELLGSARRPLILAGGGVIWGNAVGEFREFIENARIPVVTTYSARGV 232 Query: 244 ISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHIDID 303 I E+HPL LGM G GT AN+ DVL+ +G R S+R + N ++IH++ D Sbjct: 233 IPEDHPLCLGMTGTRGTPAANHAAGNCDVLLVLGARLSERTL----AATGNPRVIHVNTD 288 Query: 304 PAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSLKKSS 363 P+ + +V +++ VGD L E+ + W + + + ++ + Sbjct: 289 PSVLRGDVVLEMD-VGDFLRELPEL------------------KGPEGWFKELAAYRRDN 329 Query: 364 IPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPRSFLS 423 P+ + P V AV L+ + I D G + W+ + + RS + Sbjct: 330 PPISELQ--PPGGGAFVTS-SAVRGILDAAPDATIVNDAGSHTTWVTLHRRVLRERSLIF 386 Query: 424 SGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICIFDNR 483 SGG G MG+G P+AIGAK+A P VI I GDGGF M QELGT+AE +P+ +CI +N+ Sbjct: 387 SGGFGPMGYGLPAAIGAKLADPSRDVIMIAGDGGFQMTIQELGTVAELELPITMCILNNQ 446 Query: 484 TLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEAINCDE 543 L ++ QWQ + YG SV PDFI+LA++YGI A RI +++ A++ A+ E Sbjct: 447 KLDVIRQWQEMNYG-TSYSVELKN-PDFIRLADAYGIGAERILRLEDVSGAVERALESGE 504 Query: 544 PYLLDFAID 552 P LL+F ++ Sbjct: 505 PRLLEFMVE 513 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: 813 Number of extensions: 37 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: 524 Length adjustment: 36 Effective length of query: 563 Effective length of database: 488 Effective search space: 274744 Effective search space used: 274744 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