Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_011869278.1 MMARC5_RS07785 thiamine pyrophosphate-binding protein
Query= curated2:O08353 (599 letters) >NCBI__GCF_000016125.1:WP_011869278.1 Length = 501 Score = 247 bits (631), Expect = 7e-70 Identities = 181/556 (32%), Positives = 288/556 (51%), Gaps = 78/556 (14%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLL-TRHEQAAAHAADGYAR 59 M + +I E + V+ +F YPG +LP Y ALH + I+ + +HEQA+AHAADGY R Sbjct: 1 MKYLDFIIDFFENKGVKSVFAYPGEQILPIYGALHENSKINCIDVKHEQASAHAADGYFR 60 Query: 60 ASGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFM 119 + +VGVC+ T+GPGATNL TG+ATA DSS ++AL+G+ T +G + FQEI F+ Sbjct: 61 ITNEVGVCLATAGPGATNLTTGIATAFKDSSSVLALSGRCSTNYLGKNYFQEIPM--DFL 118 Query: 120 PIVKHNF-QIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVK 178 K F + + + + ++E+ + PV I++P D+ +LE+ I S++ Sbjct: 119 NFEKGYFVENSDSKYLINSYDDSYELKK-----PVSINIPADIYDLEV------IDSEID 167 Query: 179 LIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVEL---LNIPVC 235 LI N ++ IK +AK P++L G G+ + E+L++ E+ L IP+ Sbjct: 168 LINKNTESL---ETTISTIKKHENAKNPVLLLGQGIYGNLKYSEILEINEILKKLQIPIL 224 Query: 236 TTLMGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNA 295 TT +G I EN GMVG G+ +N + +SD + SIG S + + Sbjct: 225 TTYPARGVIDENFENVYGMVGRRGSLQSNELILKSDAVFSIGASLSYNTLPE----SVRD 280 Query: 296 KIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIEN 355 KI++ ++ P + G N D IK + N++ + K + Sbjct: 281 KILY-NVIPLKFGINSTND--------------IKTIVNTFNENVFSGHVK-------PS 318 Query: 356 VNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKT 415 + L ++ DY K +I++ N+ K+TIITTD G + ++++ K Sbjct: 319 GHDLSRNEFKFGDYS---TKIHEILE---------NLPKDTIITTDAGNHTVFVSLLKKC 366 Query: 416 QTPRSFLSSGGLGTMGFGFPSAIGAKVAKPD----SKVICITGDGGFMMNCQELGTIAEY 471 PR+ +SS +GTMGFG P++IG K D +V+ I+GDGGF M QELGT+AE Sbjct: 367 VAPRNIISSHSMGTMGFGLPASIGVKFGCNDYNINREVVSISGDGGFQMTIQELGTVAEN 426 Query: 472 NIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEI 531 N+ ++I + N L M +GK +N PDF K+A++YGI+ I++ +EI Sbjct: 427 NLKILIVVMKNNHLNM--------FGK----IN---TPDFNKIADAYGIENVYIQNSDEI 471 Query: 532 NEALKEAINCDEPYLL 547 E + + PY++ Sbjct: 472 GENISYFLKKSIPYVM 487 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: 733 Number of extensions: 39 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 599 Length of database: 501 Length adjustment: 36 Effective length of query: 563 Effective length of database: 465 Effective search space: 261795 Effective search space used: 261795 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