Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_011611556.1 TERY_RS09095 acetolactate synthase large subunit
Query= curated2:O08353 (599 letters) >NCBI__GCF_000014265.1:WP_011611556.1 Length = 545 Score = 340 bits (873), Expect = 7e-98 Identities = 208/562 (37%), Positives = 303/562 (53%), Gaps = 45/562 (8%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 MN AE +IK LE E V+ +FG PG L +AL +S + + TRHEQ AA AD Y R Sbjct: 1 MNTAELLIKCLENEGVKYIFGLPGEENLNILEALKNSSIQFITTRHEQGAAFMADVYGRL 60 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 +GK GVC+ T GPGATNL+TGVA A+ D +P+VA+TGQV T + ++ Q +D + +F P Sbjct: 61 TGKAGVCLSTLGPGATNLMTGVADANLDGAPLVAITGQVGTDRMHIESHQYLDLVAMFSP 120 Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180 + K N QI + PEI R AF++AQ +PG +HIDLP+++ + ++ P+ + Sbjct: 121 VTKWNAQILRPSNTPEIVRKAFKVAQQEKPGAIHIDLPENI--AAMSVEGKPLKQDKREK 178 Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240 Y+ + + +A I+ AK P+IL G G L A+E + + LNIPV T MG Sbjct: 179 SYSAY-----QSMTEAAVAISKAKNPMILVGNGALRGNASEIVTEFATRLNIPVANTFMG 233 Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKI--I 298 KG I HPL+L G+ ++D++I++G D I K + KI I Sbjct: 234 KGVIPYTHPLSLWTTGLQQRDFITCAFEQTDLVIAVG---YDLIEYSPKKWNPQGKIPVI 290 Query: 299 HIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNS 358 H+ AEI + IVGD L E++++ E I+Q V+ Sbjct: 291 HVGAKYAEIDSSYIPIAEIVGDISDSLNEILRR--------------SERINQLSPTVSE 336 Query: 359 LKKSSIPVMDY--------DDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMA 410 ++KS M Y D PIKPQK++ +L V + I+ +DVG ++MW+A Sbjct: 337 IRKS----MRYEYEGHGKDDGFPIKPQKLIYDLRQV-----MGPEDIVISDVGAHKMWIA 387 Query: 411 HYFKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAE 470 ++ + P + L S G MG P AI AK+ P+ KV+ TGDGGFMMNCQEL T Sbjct: 388 RHYHCERPNTCLISNGFAAMGIAIPGAIAAKLVYPERKVVAATGDGGFMMNCQELETALR 447 Query: 471 YNIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNE 530 V IF++ G++ +W+ + + FG PDF+K AES+G+K R+ES + Sbjct: 448 VGTNFVTLIFNDGGYGLI-EWKQENHFGESSFIKFGN-PDFVKFAESFGLKGYRVESAAD 505 Query: 531 INEALKEAINCDEPYLLDFAID 552 + LKEA+ D P ++D ID Sbjct: 506 LIPTLKEALAQDVPAVIDCPID 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: 794 Number of extensions: 36 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: 545 Length adjustment: 36 Effective length of query: 563 Effective length of database: 509 Effective search space: 286567 Effective search space used: 286567 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