Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_059150016.1 V474_RS02810 acetolactate synthase large subunit
Query= curated2:O08353 (599 letters) >NCBI__GCF_001046635.1:WP_059150016.1 Length = 557 Score = 268 bits (686), Expect = 3e-76 Identities = 171/556 (30%), Positives = 273/556 (49%), Gaps = 30/556 (5%) Query: 4 AEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHL-LTRHEQAAAHAADGYARASG 62 ++ I+ LE E VE +FG PG L F D+L S I L LTRHEQ A A Y R +G Sbjct: 10 SDLFIECLEQEGVEYIFGVPGEENLDFLDSLSRSKQIKLILTRHEQGAGFMAATYGRHTG 69 Query: 63 KVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPIV 122 K GVC+ T GPGATN VT A A PM+ +TGQ P K FQ +D + + PI Sbjct: 70 KAGVCLSTLGPGATNFVTAAAYATLGGMPMLMITGQKPIKKSKQGRFQILDVVSMMQPIT 129 Query: 123 KHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLIGY 182 K+ Q+ + IP R AF IA+ +PG HI+LP+D+ + D P+P + I Sbjct: 130 KYAHQMASSDNIPSRVREAFRIAEEEKPGATHIELPEDIADEH--TDSRPVP---RSIVR 184 Query: 183 NPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMGKG 242 PT + I +A+ + AKRP+++ G G ++ L + VE IP TT +GKG Sbjct: 185 RPT--ADVKSIVQAVDALQKAKRPVLVIGAGANRKMTSKMLGEFVEKTGIPFLTTQLGKG 242 Query: 243 CISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDR----ITGDIKSFATNAKII 298 I E HP LG + + + ++D +++IG ++ +T D + +I Sbjct: 243 VIDERHPKFLGCAALSAGDFVHRAIEDADCIVNIGHDVIEKPPFFMTND--GTRDDRTVI 300 Query: 299 HIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNS 358 H+ AE+ + ++GD + ++ K++ ++K + + + Sbjct: 301 HVSTKTAEVDPVYFPHIEVIGDIANAMWQI---------KEAITPSEKWSFDAMLRYRQA 351 Query: 359 LKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTP 418 + + + + PI P V+++ + D + II D G ++W A + + P Sbjct: 352 EVEHTAKLAADERFPIFPPHAVQQVRDALPD-----DAIICLDNGIYKIWFARGYSARGP 406 Query: 419 RSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVIC 478 + L L TMG G PSA+ + + P KV+ + GDGGFMMN QE+ T + + + Sbjct: 407 NTVLLDNALATMGAGLPSAMASAMVYPGRKVLAVCGDGGFMMNSQEVETAVRLGLDLTVL 466 Query: 479 IFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEA 538 I ++ GM+ +W+ G +++G PDF+K AE+YG R+ES + E L Sbjct: 467 ILNDNAYGMI-RWKQANMGFADFGLSYGN-PDFVKYAEAYGANGYRVESSGHLQELLVHC 524 Query: 539 INCDEPYLLDFAIDPS 554 + +++D +D S Sbjct: 525 RDTPGVHIIDCPVDYS 540 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: 761 Number of extensions: 39 Number of successful extensions: 5 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: 557 Length adjustment: 36 Effective length of query: 563 Effective length of database: 521 Effective search space: 293323 Effective search space used: 293323 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