Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_029329105.1 ON01_RS12165 acetolactate synthase large subunit
Query= curated2:O08353 (599 letters) >NCBI__GCF_000224785.1:WP_029329105.1 Length = 546 Score = 319 bits (818), Expect = 2e-91 Identities = 195/572 (34%), Positives = 303/572 (52%), Gaps = 32/572 (5%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 MN AE ++K LE E VE +FG PG + DA + SD+ ++TRHE +AA A Y R Sbjct: 4 MNVAELLVKCLEQEGVEYVFGVPGEENVDLMDAFYDSDIEFIVTRHETSAAFMAATYGRL 63 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 +G GVC+ T GPGATNL+TGVA A+ D +P+VA+TGQ + Q D + ++ P Sbjct: 64 TGTPGVCLATLGPGATNLMTGVANANMDHAPLVAITGQAGLDRQHKISHQYYDLINMYEP 123 Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180 + K N QI+ PE+ R AF++A + G HIDLP+D+ ++++ P++ Sbjct: 124 VTKWNAQIKSAKITPEVVRKAFQVAGQEKWGATHIDLPEDIAGMDIEKATPLNPNE---- 179 Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240 P T I++A+ +I A+ P+ILAG G+ A EE V + IPV + MG Sbjct: 180 --RPHTKASESIIEQAVNMIEKAEHPLILAGNGISRQQATEEFRAFVRKVKIPVVHSFMG 237 Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHI 300 KG IS + L+L G+ G +ESD++I++G ++ + +N +IIH+ Sbjct: 238 KGAISWENDLSLLTAGIGGNDYITCGFNESDLIITVGFDIAEYPPKNWN--RSNTQIIHL 295 Query: 301 DIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENIS-QWIENVNSL 359 D + AE N V + I+GD L+++ EN + N W+ NV Sbjct: 296 DTEEAETDANYPVGLNILGDIPANLQQL------------GENIESPNADFAWVSNVRKQ 343 Query: 360 KKSSIPVMDYD-DIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTP 418 + + + D P+KPQKI+ +L V +N++ I +DVG ++MWMA + T P Sbjct: 344 ALNELEAFEEDTHFPVKPQKIISDLRKV-----LNEDAIAISDVGAHKMWMARMYHTHQP 398 Query: 419 RSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVIC 478 + L S GL +MG PSAI AK+ PD V+ + GDG F M EL T +P+++ Sbjct: 399 NTCLISNGLASMGVAVPSAIAAKMVHPDRNVVAVCGDGSFQMTGAELETARRLELPIIVL 458 Query: 479 IFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEA 538 ++ + G++ +W L R + FG PD+ +LA SYG + I +E+ AL++A Sbjct: 459 MWRDDGYGLI-EWHQLKKFDRSSYIKFGN-PDYQQLAASYGFEVMTITKADELKPALEKA 516 Query: 539 INCDEPYLLDFAIDPSSALSMVPPGAKLTNII 570 ++P +D +D S + + KL +II Sbjct: 517 AASNQPTFIDCPVDYSENMKLT---EKLGDII 545 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: 760 Number of extensions: 33 Number of successful extensions: 6 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: 546 Length adjustment: 36 Effective length of query: 563 Effective length of database: 510 Effective search space: 287130 Effective search space used: 287130 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 Jul 26 2024. The underlying query database was built on Jul 25 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