Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_037577100.1 BS73_RS27900 thiamine pyrophosphate-requiring protein
Query= curated2:O08353 (599 letters) >NCBI__GCF_000744815.1:WP_037577100.1 Length = 600 Score = 238 bits (608), Expect = 4e-67 Identities = 178/573 (31%), Positives = 278/573 (48%), Gaps = 34/573 (5%) Query: 4 AEAMIKALEAEKVEILFGYPGGALLPFYDALHHS--DLIHLLTRHEQAAAHAADGYARAS 61 ++ +++ L V+ +FGYPG + A + + RHE+ AA A GYA+ S Sbjct: 6 SDFILRRLREWDVDYVFGYPGDGINGLLSAWERAGDQPRFIQARHEEMAAFEAVGYAKFS 65 Query: 62 GKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPI 121 G+VGVC TSGPGA +L+ G+ A D P+VAL GQ IG QE+D L+ + Sbjct: 66 GRVGVCAATSGPGAIHLLNGLYDAKLDHVPVVALVGQTAQTAIGGSYQQEVDLPNLYKDV 125 Query: 122 VKHNFQIQKTC-QIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180 Q+ T Q+P + A IAQ R + +P DVQ+LE H + Sbjct: 126 ASEYCQLVTTPEQLPNVLDRAMRIAQ-ARKTVTAVIVPADVQDLEYSAPTHAFKMVPSSL 184 Query: 181 GYNPTT-IGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLM 239 G++ + + H + +A +++ S + ILAG G GA+ EL++ E+L V L+ Sbjct: 185 GFSGSAYVPHEDDLARAAEVLNSGSKVAILAGQGA--RGASAELIETAEVLGAGVAKALL 242 Query: 240 GKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIH 299 GK + ++ P G G+ GT+P + + D L+ IG F + + F A+ + Sbjct: 243 GKDVLPDDLPFVTGASGLLGTRPTYELMKDCDTLLVIGSSFP--YSQFLPEFG-QARAVQ 299 Query: 300 IDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSL 359 IDIDP IG +V +VGDA+ L+ ++ L ++ +E ++ N S+W E + Sbjct: 300 IDIDPGRIGMRYPFEVNLVGDARETLRRLLPLLSRKEDRGWREKIEQNN-SRWWEVMK-- 356 Query: 360 KKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPR 419 +++S+ + PI P+ V V+D L + IIT D G W A + + + Sbjct: 357 RRASV-----EADPINPEYAVH----VLDGL-LPGRAIITADSGSAANWYARHLRIREGI 406 Query: 420 SFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMN-CQELGTIAEY-----NI 473 + SG L TMG G P AIGAK + PD I + GDG MN EL T+ +Y + Sbjct: 407 NGSLSGTLATMGPGVPYAIGAKFSCPDRPAIALVGDGAMQMNGLAELITVGKYWQEWRDP 466 Query: 474 PVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPD--FIKLAESYGIKARRIESPNEI 531 +V+C+ +N+ L V W+ + PD + A G+ R+E P E+ Sbjct: 467 RLVVCVLNNQDLNQV-TWEMRSMSGSPQFLPSQQLPDVRYADFARGLGLHGIRVEKPEEV 525 Query: 532 NEALKEAINCDEPYLLDFAIDPSSALSMVPPGA 564 A + A+ D P +LD DP A+ +PP A Sbjct: 526 EPAWRAALESDRPCVLDVLTDP--AVPPIPPHA 556 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: 799 Number of extensions: 46 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: 600 Length adjustment: 37 Effective length of query: 562 Effective length of database: 563 Effective search space: 316406 Effective search space used: 316406 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 Jul 26 2024. The underlying query database was built on Jul 25 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