Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_013260015.1 DEBA_RS16120 sulfoacetaldehyde acetyltransferase
Query= curated2:O08353 (599 letters) >NCBI__GCF_000143965.1:WP_013260015.1 Length = 574 Score = 256 bits (654), Expect = 2e-72 Identities = 170/569 (29%), Positives = 282/569 (49%), Gaps = 28/569 (4%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 M +EA+++ L AE V+ +FG G A + D + + + HEQAAAHAADG AR Sbjct: 4 MTPSEALVETLVAEGVQNVFGIVGSAFMDALDLFPAAGIRFIPVAHEQAAAHAADGLARV 63 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 SG+ CI +GPGA N V+ + A+ SP+VA+T + T IG FQE+D + +F Sbjct: 64 SGRPQACIAQNGPGAANFVSAMVAAYWAHSPVVAITPETGTMGIGTGGFQELDQMAMFEK 123 Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180 + ++ + ++ E+ R F +A+ GP +++P+D + +P + Sbjct: 124 QTVYQVRVNQPQRMAELARRCFYMAK-NLNGPTQLNIPRDFFYGLCHDEIYPTARVSR-- 180 Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240 +G + +++A +L+A AK P+ILAGGGV + A EEL L E L+ PV + + Sbjct: 181 -----GLGSVQSLREAARLLAEAKFPVILAGGGVSQADAVEELTALAEYLSAPVVNSYLH 235 Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCR---FSDRITGDIKSFATNAKI 297 H LA G +G G+K A ++++DV++++G R F DI + AKI Sbjct: 236 NDTFPAEHALAAGPIGYCGSKAAMRLIAKADVVLALGSRLGPFGTLPQYDIDYWPKTAKI 295 Query: 298 IHIDIDPAEIGKNVNVDVPIVGDAK---LILKEVIKQLDYIINKDSKENNDKENISQ-WI 353 I +D++ +G + VDV D K L +K+L + D+ D Q W Sbjct: 296 IQVDVNIEVLGLSKRVDVASCADVKEYTPALLAAVKELRPGLAADAARLADVAREKQIWA 355 Query: 354 ENVNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYF 413 + + S ++ P+ P++ + EL I +II TD+G N YF Sbjct: 356 DELAQWSAS-------NEKPMHPRRFLSELSQAIP-----AGSIIATDIGNNSSMCNAYF 403 Query: 414 KTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGF-MMNCQELGTIAEYN 472 + PR +S+ G GF + +A+GAK+ P+ V C GDG + + QE+ T + Sbjct: 404 RFNGPRQHISALSWGNCGFAYGAAMGAKIGAPERPVFCFQGDGAYGISGIQEVMTAVRED 463 Query: 473 IPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEIN 532 IPV+ + +N G + Q +Y R N PD+ LAE G K +E+P+++ Sbjct: 464 IPVIAVVANNFEWGAEKKNQIDYYESRFVGANLPANPDYAALAEVMGAKGYVVEAPDQVG 523 Query: 533 EALKEAINCDEPYLLDFAIDPSSALSMVP 561 + ++EA+ P +++ I+ + + P Sbjct: 524 DVVREAVASGRPCVINAKIEGGARVLAEP 552 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: 746 Number of extensions: 40 Number of successful extensions: 5 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: 574 Length adjustment: 37 Effective length of query: 562 Effective length of database: 537 Effective search space: 301794 Effective search space used: 301794 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 09 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