Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_086509739.1 BZY95_RS09495 5-guanidino-2-oxopentanoate decarboxylase
Query= curated2:Q7U5G1 (617 letters) >NCBI__GCF_002151265.1:WP_086509739.1 Length = 537 Score = 230 bits (587), Expect = 1e-64 Identities = 168/538 (31%), Positives = 260/538 (48%), Gaps = 38/538 (7%) Query: 33 RHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHAADAYARATGKVGVCF 92 R+GVDT+FG PG + +Y L E V+H+ RHEQ AD YARATG+ GVC Sbjct: 14 RYGVDTVFGIPGVHTVALYRGLE----ESGVRHVTPRHEQGAGFMADGYARATGRPGVCL 69 Query: 93 GTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQETDIFG---ITLPIVKHS 149 +GPG TN+ T + A DSVPM+VI+ R +G + ++ + + + S Sbjct: 70 IITGPGMTNIATAMGQALADSVPMLVISSVNRRDTLGRGQGRLHELPSQQQLMAGVSRFS 129 Query: 150 WVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFNYVPVEPGSVIPGGFHQPE 209 + DP+ L ++A+AF + RPGPV I+IP D+ + P P +P Sbjct: 130 HTLLDPSALPEVLARAFAVFQGQRPGPVHIEIPIDLFDAPVTSTELPP----PARLFRPA 185 Query: 210 PPLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQLPVTTTLMGKGAFDE 269 P A +A A D + A+RPL+ +GGG + A A + R L ER P TT+ KG Sbjct: 186 PD-PAGLALAADWLRAAKRPLVLLGGGCVEAPA--AARALVERLDAPTVTTINAKGVLGR 242 Query: 270 NDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVTGKL--DTFAPRARVVHFEIDP 327 L +G E D+++AVG + + D F R R++ ++D Sbjct: 243 AHPLDLG--ANAALPAVRELAREADVVLAVGTELGETDYDVVFDDGFELRGRLIRIDLDA 300 Query: 328 AEIGKNRKADVAVLGDLGLSLARMVE---ISLQRTAEPRTAAWLERINTWKDRYPLTIPP 384 ++ +N++ + ++ D G +LA + E L R RTA L +N D P Sbjct: 301 QQLVRNQQVALGLVADAGRTLALLAEHFSAPLSRGGAQRTADTLAALNLKGD-------P 353 Query: 385 AEGAIYPQEVLLAVRDLAPDAIVTTDVGQHQMWAAQHLRNGP---RGWISSAGLGTMGFG 441 A P L + PDAI+ D ++A HL + P R + +S G GT+G+G Sbjct: 354 AFAPFVPFYATLG--ETLPDAILVGD-STAPVYAGNHLVSQPEPRRYFNASTGYGTLGYG 410 Query: 442 MPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKVVIVNNHWQGMVRQWQE 501 +PAA+GAQ+ +P VV + GD ++ + EL T LPV VV+ +N +R++ + Sbjct: 411 LPAALGAQLGLPGLPVVALVGDGGVMFTLSELATAVEARLPVVVVLWHNQGYEEIRRYMD 470 Query: 502 SFYDERYSASDMLNGMPDFIALARSFGVDGVKITDRELLHRDLAAALQSPTPTMIDVH 559 + R PDF +A FG V+++D L + LA+ P +++V+ Sbjct: 471 AHGVTRCGVDIQ---APDFQVVAAGFGCQAVRVSDPAGLTQALASR-PLDAPLLVEVN 524 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: 926 Number of extensions: 59 Number of successful extensions: 7 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: 537 Length adjustment: 36 Effective length of query: 581 Effective length of database: 501 Effective search space: 291081 Effective search space used: 291081 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 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