Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate GFF3176 HP15_3118 acetolactate synthase, large subunit, biosynthetic type
Query= curated2:O08353 (599 letters) >FitnessBrowser__Marino:GFF3176 Length = 556 Score = 281 bits (718), Expect = 7e-80 Identities = 181/557 (32%), Positives = 281/557 (50%), Gaps = 31/557 (5%) Query: 2 NGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARAS 61 NGAE I+ALE E VE +F PG L F +AL S + +L RHEQAA A Y R + Sbjct: 10 NGAELFIRALENEGVEYIFAVPGEENLAFLEALRTSSIQLVLNRHEQAAGFMAATYGRLT 69 Query: 62 GKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPI 121 G+VGVC+ T GPGATN VT A A PM+ ++GQ P K FQ +D + L P+ Sbjct: 70 GRVGVCLSTLGPGATNFVTAAAYAQLGGMPMMMISGQKPIKSSKQGLFQILDVVDLMRPL 129 Query: 122 VKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPI-PSKVKLI 180 K+ QI IP R AF +A RPG VH++LP+D+ + + D H PS + Sbjct: 130 TKYTRQISNANTIPAKVREAFRLASEERPGAVHLELPEDIADEAPESDTHIFKPSDAR-- 187 Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240 P+ P+ ++ A +++ A+ P+I+ G G ++ LL LV + IP TT MG Sbjct: 188 --RPS--ASPKSLEMACEMLREARHPLIMIGAGANRKRVSQALLHLVNVTGIPFFTTQMG 243 Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFAT--NAKII 298 KG + E HP LG + + + +D++I++G + F T K+I Sbjct: 244 KGVVDERHPRYLGNAALSAGDFVHCAIDRADLVINVG----HDVVEKPPFFMTPGGKKVI 299 Query: 299 HIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYII-NKDSKENNDKENISQWIENVN 357 H++ A++ +VGD + ++Y+ N N+D + + E V+ Sbjct: 300 HVNFSAADVDPVYFPQHEVVGD-------IANSVEYMAENCGQCANHDFTRLMEVKEAVD 352 Query: 358 SLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQT 417 + + + D P+ PQ+IV ++ V+ D + IIT D G ++W A ++ Sbjct: 353 AHLQER---AEDDRFPVIPQRIVHDVRQVMPD-----DGIITLDNGMYKLWFARNYRAYD 404 Query: 418 PRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVI 477 + L L +MG G PS + A + PD KV+ I GDGGFMMN QEL T N+ +V+ Sbjct: 405 NNTVLLDNALASMGAGLPSGMMASMLYPDLKVMAICGDGGFMMNSQELETAVRLNLNLVV 464 Query: 478 CIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKE 537 I ++ GM+ +W+ G +++ PDF+ A+SYG K R+ ++ L+ Sbjct: 465 LIINDSAYGMI-KWKQGQEGYSDFGLDYRN-PDFVTYAQSYGAKGHRLTRTEDLRPTLEG 522 Query: 538 AINCDEPYLLDFAIDPS 554 A+ +++D +D S Sbjct: 523 ALAEGGVHVVDVPVDYS 539 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: 750 Number of extensions: 38 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: 556 Length adjustment: 36 Effective length of query: 563 Effective length of database: 520 Effective search space: 292760 Effective search space used: 292760 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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