Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_011881501.1 acetolactate synthase
Query= curated2:O08353 (599 letters) >NCBI__GCF_000016205.1:WP_011881501.1 Length = 546 Score = 267 bits (683), Expect = 7e-76 Identities = 175/556 (31%), Positives = 271/556 (48%), Gaps = 29/556 (5%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 M ++ +KALEAE VE +FG PG L ++L S + +LTRHEQAA A Y R Sbjct: 1 MKASDLFVKALEAEGVEYVFGIPGEENLDLLESLRRSKIKLVLTRHEQAAGFMAATYGRL 60 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 +G+ GVC+ T GPGATN VT A A PM+ +TGQ P K FQ +D +G+ P Sbjct: 61 TGRTGVCLATLGPGATNFVTAAAYAQLGGMPMLMITGQKPIKSSKQGHFQIVDVVGMMQP 120 Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180 + K QI IP R AF A+ RPG H++LP+D+ E D PIP Sbjct: 121 LTKFTRQIVSIGNIPSAVREAFRRAEEERPGAAHLELPEDIAHEE--GDGKPIPR----- 173 Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240 ++ I + + A+ I +A+ P+++ G G + LL+ V+ IP TT MG Sbjct: 174 SFSRRPIAEQKAVAHAVDAIQAARHPLLMIGAGGNRKTTCKMLLEFVDETGIPFFTTQMG 233 Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAK-IIH 299 KG I E HPL LG + + + +D +I++G D I T+ K +IH Sbjct: 234 KGVIDETHPLWLGNATLSDGDFVHRAIEHADCIINVG---HDVIEKPPFFMRTDDKTVIH 290 Query: 300 IDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSL 359 ++ A++ + +VGD + + Q+ I + ++ + + + Sbjct: 291 VNFLGAQVDPVYFPQIEVVGD----IANAVWQMKEAIAPQPHWDFERFTMIKAHFEAHLQ 346 Query: 360 KKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPR 419 K P P+ P +IV +L + + I+ D G ++W A Y++ P Sbjct: 347 KGQHDP-----RFPMYPVRIVNDLYNALP-----VDGIVCLDNGMYKIWFARYWRAHEPN 396 Query: 420 SFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICI 479 S L L +MG G PSAI ++ P KVI + GDGGFMMN QEL T + +V+ I Sbjct: 397 SLLLDNALASMGAGLPSAIATRIVHPQRKVIAVCGDGGFMMNSQELETAVRLKLDLVVMI 456 Query: 480 FDNRTLGMV-YQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEA 538 + GM+ ++ +N+ + ++ PDF+ A+SYG R+E+ +++ L+E Sbjct: 457 LRDDAFGMIRWKQENMNFPDFAMTLK---NPDFVAYAQSYGAHGHRVEAADDLEPLLREC 513 Query: 539 INCDEPYLLDFAIDPS 554 +++D ID S Sbjct: 514 FATPGVHVIDVPIDYS 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: 765 Number of extensions: 34 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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 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