Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate 208820 DVU3293 thiamine pyrophosphate-requiring enzyme
Query= curated2:O08353 (599 letters) >MicrobesOnline__882:208820 Length = 547 Score = 269 bits (688), Expect = 2e-76 Identities = 167/559 (29%), Positives = 273/559 (48%), Gaps = 34/559 (6%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 MN A ++ LEAE V+ +FG PG L F +AL S + +LTRHEQAA A Y R Sbjct: 1 MNAATLFVRCLEAEGVDHIFGIPGEENLAFLEALRTSSIRLVLTRHEQAAGFMAATYGRL 60 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 +G+ GVC+ T GPGATNLVT VA A P++ +TGQ P K FQ +D + + P Sbjct: 61 TGRPGVCLSTLGPGATNLVTAVAYARLGGMPLIVITGQKPIKHSKQGRFQILDVVRMMEP 120 Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180 I K Q+ IP + R AF +A +PGPVHI+LP+D+ E+ H PS V+ Sbjct: 121 ITKSTRQVASGSAIPSLVREAFRLAAKEKPGPVHIELPEDIAAEEVATTPH-TPSLVRPA 179 Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240 +P +G +A + I AKRP++L G L + ++ + +T MG Sbjct: 180 QADPELVG------EAARRIRKAKRPLLLMAAGANRHDVCGHLRRFIDTTGMFFFSTQMG 233 Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHI 300 KG + + HP +LG + + + +D ++++G ++ +IH+ Sbjct: 234 KGAVDQRHPRSLGTAALSDHDYLHCAIERADCIVNVGHDVVEK-PPFFMHRDDGRTVIHV 292 Query: 301 DIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENND-----KENISQWIEN 355 ++ PA++ + +VGD + E ++ + I+ + ++D KE+I + Sbjct: 293 NVFPAQVDDVYFPQLEVVGD----IGESLQLMADIVGRCPGADDDYLRRIKEHIDAHVYA 348 Query: 356 VNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKT 415 + P PQ IV E+ + + N ++ D G ++W A ++ Sbjct: 349 TGLT----------NSFPPTPQSIVSEVREAMPE-----NGVLALDNGMYKLWFARNYRA 393 Query: 416 QTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPV 475 P + L L TMG G PSA+ + +P + V + GDGGFMMN QEL T + + Sbjct: 394 YAPNTLLLDNALATMGAGLPSALAVALLRPGTPVAALCGDGGFMMNSQELETAVRLGVDL 453 Query: 476 VICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEAL 535 + + + GM+ +W+ ++FG PDF++ AESYG R+ +P+ + + L Sbjct: 454 TVMVLRDDGYGMI-KWKQAGMELPVHGLDFGN-PDFVRYAESYGATGHRVSAPDGLRQTL 511 Query: 536 KEAINCDEPYLLDFAIDPS 554 + + +L++ +D S Sbjct: 512 RRCLATPGVHLIEVPVDYS 530 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: 704 Number of extensions: 28 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: 547 Length adjustment: 36 Effective length of query: 563 Effective length of database: 511 Effective search space: 287693 Effective search space used: 287693 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 09 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