Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_019895419.1 A377_RS0106440 acetolactate synthase large subunit
Query= curated2:O08353 (599 letters) >NCBI__GCF_000384235.1:WP_019895419.1 Length = 563 Score = 280 bits (717), Expect = 9e-80 Identities = 175/551 (31%), Positives = 275/551 (49%), Gaps = 25/551 (4%) Query: 4 AEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARASGK 63 ++ ++ALEAE VE +FG PG L ++L S + +LTRHEQAA A Y R +G Sbjct: 13 SDLFVQALEAEGVEYIFGIPGEENLDLLNSLKDSSIKLVLTRHEQAAGFMAATYGRLTGM 72 Query: 64 VGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPIVK 123 GVC+ T GPGATNLVT A A PMV +TGQ P K FQ ID + + PI K Sbjct: 73 AGVCLSTLGPGATNLVTAAAYAQLGGMPMVMITGQKPIKTSKQGQFQIIDVVDMMHPITK 132 Query: 124 HNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLIGYN 183 + QI IP R AF A T RPG H++LP+D+ D S+V G + Sbjct: 133 YTCQIHSGYNIPSRVREAFRSAMTERPGATHMELPEDIAAEITD-------SQVIEQGLH 185 Query: 184 PTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMGKGC 243 + + ++ A+++I AKRP+IL G G A + L + ++ IP TT MGKG Sbjct: 186 RRPLAEEKAVRTAVQMIEKAKRPLILIGAGANRKTAGKMLRQFIDKTGIPFFTTQMGKGV 245 Query: 244 ISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHIDID 303 + E H L LG + + L ++D++I++G ++ ++ AK+IHI+ Sbjct: 246 VDERHHLYLGCAALSDHDFVHCALRDTDLIINVGHDVIEKPPFFMQH--GGAKVIHINFT 303 Query: 304 PAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSLKKSS 363 AEI +VGD + ++ ++++ ++ D +++ + K Sbjct: 304 NAEIDPVYFPQAEVVGDIGNAIYQIKERIERQMHWD---------FDCFMQAKRYIDKDI 354 Query: 364 IPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPRSFLS 423 + D D P+ PQ++V ++ + D +I D G ++W A + + L Sbjct: 355 VKHADDDRFPMLPQRVVADIRGYMPDTG-----MIALDNGVYKIWFARNYLAYHHNTVLL 409 Query: 424 SGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICIFDNR 483 L +MG G PSAI AK+ PD KV+ I GDGGFMMN QE+ T + +V+ + ++ Sbjct: 410 DNALASMGAGLPSAIAAKLVHPDRKVMAICGDGGFMMNSQEMETAVRLKLDLVVIVLNDN 469 Query: 484 TLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEAINCDE 543 GM+ +W+ G ++ G A +F++ A+SYG RI + E+ + Sbjct: 470 AFGMI-KWKQANMGFDDFGLDVGNA-NFVEYAQSYGAHGHRISTAEELQSRIDACYEAGG 527 Query: 544 PYLLDFAIDPS 554 +L++ +D S Sbjct: 528 VHLIEVPVDYS 538 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: 784 Number of extensions: 40 Number of successful extensions: 4 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: 563 Length adjustment: 36 Effective length of query: 563 Effective length of database: 527 Effective search space: 296701 Effective search space used: 296701 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