Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_013645606.1 METBO_RS10055 pyruvate dehydrogenase
Query= curated2:O08353 (599 letters) >NCBI__GCF_000191585.1:WP_013645606.1 Length = 585 Score = 275 bits (704), Expect = 3e-78 Identities = 183/539 (33%), Positives = 279/539 (51%), Gaps = 35/539 (6%) Query: 19 LFGYPGGALLPFYDALHHSDLIHLL-TRHEQAAAHAADGYARASGKVGVCIGTSGPGATN 77 +FG PG ++L DA+ ++ + + RHEQ AA A Y + +G V C+ +GPGATN Sbjct: 74 VFGIPGTSILGVVDAIKNNPKLEFIQVRHEQTAAFMASAYGKLTGNVAACLTVAGPGATN 133 Query: 78 LVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPIVKHNFQIQKTCQIPEI 137 L TG+ A D SP+VALTG V +LIG +FQEID F P+ N + Q + Sbjct: 134 LATGLYDAKLDHSPVVALTGMVKRQLIGPGSFQEIDQYSFFEPLTVFNKILMSRDQTTTL 193 Query: 138 FRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLIGYNPTTIGHPRQ--IKK 195 A + + R G HI +P DVQ+L D +P K G PT P + I++ Sbjct: 194 ATLAIKHSLIER-GVSHIGIPNDVQKL--DHQTKLVPFK----GNFPTRATKPTEYLIER 246 Query: 196 AIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMGKGCISENHPLALGMV 255 A K+I ++RP+I+AG G + G E LLK E + P+ TT KG + E L +G Sbjct: 247 AAKIIDKSERPVIIAGFGSIEQG--EALLKFAEKIKAPITTTFRAKGVVDEYEDLYVGSH 304 Query: 256 GMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHIDIDPAEIGKNVNVDV 315 G G+ + + ++D+LI IG FSD K K + IDIDP I + V+V Sbjct: 305 GGIGSTASTKLVDDADLLIVIGSSFSDMTQIPEK------KTVQIDIDPLMISRRFPVEV 358 Query: 316 PIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSLKKSSIPVMDYDDIPIK 375 ++G+ IL + + + KD E K +WIE + +S D P++ Sbjct: 359 GLIGNCSEILPMLHDLVKEVERKDYMEEMAKLK-KEWIELLKQEFES-------DKTPLR 410 Query: 376 PQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPRSFLSSGGLGTMGFGFP 435 I+ L +ID K+ IIT DVG++ W F + + + SG L +MGFGFP Sbjct: 411 APYILGVLNEMID-----KDAIITLDVGEHCWWFGRNFWMKKTQKMIMSGNLASMGFGFP 465 Query: 436 SAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICIFDNRTLGMVYQWQNL- 494 +A+ +++ PD +V+CITGDGGF M + T +Y +P+ + IF+N+ LGM+ Q Q + Sbjct: 466 AALTSQLMYPDKQVVCITGDGGFSMVMADFLTAVKYELPIKVFIFNNKQLGMIMQEQKME 525 Query: 495 FYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEAINCDEPYLLDFAIDP 553 Y Q + D+ + GIK +E P ++ A+++A+ ++P ++D DP Sbjct: 526 GYENWQTELQDLNYADYARCCGGVGIK---VEKPEDLPAAVEKALKSEKPVIVDINTDP 581 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: 832 Number of extensions: 43 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 599 Length of database: 585 Length adjustment: 37 Effective length of query: 562 Effective length of database: 548 Effective search space: 307976 Effective search space used: 307976 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