Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_010997705.1 AVA_RS17890 acetolactate synthase large subunit
Query= curated2:O08353 (599 letters) >NCBI__GCF_000204075.1:WP_010997705.1 Length = 547 Score = 345 bits (884), Expect = 4e-99 Identities = 209/561 (37%), Positives = 302/561 (53%), Gaps = 41/561 (7%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 MN AE +++ LE E V+ +FG PG L +AL HS + + TRHEQ AA AD Y R Sbjct: 1 MNTAELLVQCLENEGVQYVFGLPGEENLHVLEALKHSSIQFITTRHEQGAAFMADVYGRL 60 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 +GK GVC+ T GPGATNL+TGVA A+ D +P+VA+TGQV T + ++ Q +D + +F P Sbjct: 61 TGKAGVCLSTLGPGATNLMTGVADANLDGAPLVAITGQVGTDRMHIESHQYLDLVAMFAP 120 Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180 + K N QI + PE+ R AF+ +Q+ +PG VHIDLP+++ + P+ K Sbjct: 121 VTKWNKQIVRPSITPEVVRKAFKRSQSEKPGAVHIDLPENIAAM-------PVEGKPLQK 173 Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240 T I+ A I+ A P+IL G G + + A++ + + +NIPV T MG Sbjct: 174 DNIEKTYASFASIRAAAAAISQAVNPLILVGNGAIRAKASDAVTQFATQMNIPVANTFMG 233 Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAK--II 298 KG I HPLAL VG+ +D++I+IG D I K + K I+ Sbjct: 234 KGVIPYTHPLALWSVGLQQRDFITCGFDNTDLVIAIG---YDLIEFSPKKWNPEGKIPIV 290 Query: 299 HIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLD-------YIINKDSKENNDKENISQ 351 HI D AEI + +V ++GD L E++K D Y I S N +E+ Q Sbjct: 291 HIGADSAEIDSSYIPNVSVIGDISDSLVEILKVADRQGKPNPYAI---SLRGNIREDYEQ 347 Query: 352 WIENVNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAH 411 + + D PIKPQK++ +L V + + I+ +DVG ++MW+A Sbjct: 348 YAND--------------DGYPIKPQKLIYDLRQV-----MGPDDIVISDVGAHKMWIAR 388 Query: 412 YFKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEY 471 ++ +P + + S G MG P A+ AK+ P+ KV+ TGDGGFMMNCQEL T Sbjct: 389 HYHCHSPNTCIISNGFAAMGIAIPGALAAKLVYPNRKVVAATGDGGFMMNCQELETALRV 448 Query: 472 NIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEI 531 P V IF++ G++ Q +GK Q S G PDF+KLAES G+K R+ES ++ Sbjct: 449 GTPFVTLIFNDGGYGLIEWKQENQFGKGQSSFVHFGNPDFVKLAESMGLKGYRVESALDL 508 Query: 532 NEALKEAINCDEPYLLDFAID 552 LKEA+ D P ++D +D Sbjct: 509 IPVLKEALAQDVPAVIDCPVD 529 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: 815 Number of extensions: 30 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: 547 Length adjustment: 36 Effective length of query: 563 Effective length of database: 511 Effective search space: 287693 Effective search space used: 287693 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