Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_085218863.1 B9N75_RS11115 thiamine pyrophosphate-binding protein
Query= curated2:Q7U5G1 (617 letters) >NCBI__GCF_900177405.1:WP_085218863.1 Length = 552 Score = 219 bits (559), Expect = 2e-61 Identities = 177/533 (33%), Positives = 249/533 (46%), Gaps = 57/533 (10%) Query: 19 QTISGAAALMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHAA 78 Q +G L+D L G D IF PG + L DALH + + ++ R E + A Sbjct: 3 QLRTGGRILIDNLLAQGCDRIFCVPGESYLAALDALHDTPA---IDLVVCRQEGGVAYMA 59 Query: 79 DAYARATGKVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQETDI 138 +A + TG+ GV F T GPGATN G+ A+ DS PMV++ G V R + FQE D Sbjct: 60 EADGKMTGRPGVAFVTRGPGATNASVGVHVARQDSTPMVLLIGDVARGDRDREGFQEVDF 119 Query: 139 FGITLPIVKHSWVVR--DPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFNYVPVE 196 + P+ K WV R D + VA+A+ A +GRPGPV++ +P+D+ +++ V Sbjct: 120 LTMFAPLAK--WVARIEDARRIPEYVARAWRTATAGRPGPVVLVLPEDMLRDEVEAVDRP 177 Query: 197 PGSVIPGGFHQPEPPLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQLP 256 I Q PL AV + + L++ A PL VGGG + A R AER LP Sbjct: 178 ANPCIA----QAADPL--AVGSLMTLLQDACAPLAIVGGGGWCSGAGHYFRDFAERIGLP 231 Query: 257 VTTTLMGKGAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVTGKLDTFA- 315 V T + A + + G LG V DLL+ VGAR + T A Sbjct: 232 VATAFRRQDAIGADSPVYAGNLGYGPNPKLVERVKNADLLLVVGARLGEATTDGYTLIAP 291 Query: 316 --PRARVVHFEIDPAEIGKNRKADVAVLGDLGLSLARMVE-------ISLQRTAEPRTAA 366 P +VH DP E+G + D+ + D+ A +V IS AE Sbjct: 292 DHPGQTLVHVHPDPNELGSVYRTDLPICADM-REFAELVADWEEQEVISFDAGAEAH-RE 349 Query: 367 WLERINTWKDRYPLTIPPAEGAIYPQE---VLLAVRDLAP-DAIVTTDVGQ-----HQMW 417 WLE W ++P A G P + V+ A+RD P D I+ G H+ W Sbjct: 350 WLE----W------SMPRATGG--PLDLGLVVEAMRDALPADTIICNGAGNFSGWWHRFW 397 Query: 418 --AAQHLRNGPRGWISSAGLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGT 475 AA + P G+MG+G PAA+ A + PDR VV +AGD LMN QEL T Sbjct: 398 PYAALPSQLAPTN-------GSMGYGPPAAVAAALRFPDRTVVAVAGDGDFLMNGQELAT 450 Query: 476 LAAYGLPVKVVIVNNHWQGMVRQWQESFYDERYSASDMLNGMPDFIALARSFG 528 + + V++++N G +R QE Y ER + ++N PDF A++FG Sbjct: 451 AMRHDTDMLVLVIDNASYGTIRMHQEREYPERVVGTGLVN--PDFAQFAKAFG 501 Lambda K H 0.320 0.136 0.414 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: 927 Number of extensions: 47 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: 617 Length of database: 552 Length adjustment: 36 Effective length of query: 581 Effective length of database: 516 Effective search space: 299796 Effective search space used: 299796 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 (21.8 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