Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_011034264.1 MM_RS12135 acetolactate synthase large subunit
Query= curated2:O08353 (599 letters) >NCBI__GCF_000007065.1:WP_011034264.1 Length = 544 Score = 272 bits (696), Expect = 2e-77 Identities = 175/557 (31%), Positives = 289/557 (51%), Gaps = 33/557 (5%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 M ++ + L+ E VE +FG PG L ++L +SD+ ++TRHEQAAA A Y R Sbjct: 1 MKASDLFVAQLKEEGVEYVFGLPGEENLDLLESLRNSDIKLIITRHEQAAAFMAAAYGRL 60 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGN--DAFQEIDALGLF 118 +GK GVC T GPGATNLVTGVA A +P+++++GQ LI N FQ +D + + Sbjct: 61 TGKAGVCFSTLGPGATNLVTGVAQAQLTGAPLISISGQ--KALIDNWQARFQLVDVVRMM 118 Query: 119 MPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVK 178 P+ K I IP + R+AF+ A+ RPG VHI+LP+DV + D + V+ Sbjct: 119 EPLCKKAVTISDPGMIPTVLRNAFKHAEAERPGAVHIELPEDVAGEDTD-------AVVQ 171 Query: 179 LIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTL 238 P+ I+ A +I AK P+I+ G EEL I V T Sbjct: 172 KRSETSIPSPDPKAIETAAGMIREAKNPLIIVSSGANRKAVTEELEDFANRTGIYVVHTQ 231 Query: 239 MGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKII 298 MGKG + ++ P +L G+H N + +D++I++G + + + + KI+ Sbjct: 232 MGKGVVPDDCPYSLFATGIHARDYVNCGIDGADLIITVGYDIVE-YPPYLWNGKLDKKIV 290 Query: 299 HIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWI-ENVN 357 +ID + + N V ++GD ++++ ++ + +E EN +I E +N Sbjct: 291 NIDFVESVPDRYFNPAVEVIGDISSSVRQLAAKV-----PEKREFPVFENTRTFIEEKIN 345 Query: 358 SLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQT 417 S K S P PI PQ++VK + V + + II+ D G ++W + ++ Sbjct: 346 SPVKKSYP-------PI-PQEVVKSVREV-----LGREDIISLDNGIYKLWFSRLYRAYA 392 Query: 418 PRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVI 477 P + L L TMG GF + + AK+ P+ +++ + GDGGF+MNCQEL T Y IP+V+ Sbjct: 393 PNTVLLDNALATMGAGFSAGLVAKLLHPERRILAVCGDGGFIMNCQELETAVRYGIPLVV 452 Query: 478 CIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKE 537 I ++ G + +W+ ++++G PDF LAES+G +++ +++ E L++ Sbjct: 453 LILNDNAFGFI-KWKQKKMRFEDFALDYGN-PDFALLAESFGATGIKVKENDDLKEVLEK 510 Query: 538 AINCDEPYLLDFAIDPS 554 A + ++ +++ ID S Sbjct: 511 AFSLNKLVVIECPIDYS 527 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: 743 Number of extensions: 38 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: 544 Length adjustment: 36 Effective length of query: 563 Effective length of database: 508 Effective search space: 286004 Effective search space used: 286004 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