Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_093428106.1 BM272_RS07235 acetolactate synthase large subunit
Query= curated2:O08353 (599 letters) >NCBI__GCF_900112605.1:WP_093428106.1 Length = 543 Score = 311 bits (797), Expect = 4e-89 Identities = 189/564 (33%), Positives = 299/564 (53%), Gaps = 37/564 (6%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 M AE ++ LE E VE +FG PG L DAL SD+ + RHEQ AA AD Y R Sbjct: 1 MKTAELFVRCLENEGVEYIFGLPGEENLDVMDALVDSDIQFITVRHEQGAAFMADVYGRL 60 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 +G+ GVC+ T GPGATNL+TGVA A+ D +P+VA+ GQ T + ++ Q +D LF P Sbjct: 61 TGRAGVCLATLGPGATNLITGVADANMDHAPLVAIAGQASTNRLHKESHQVLDLQNLFRP 120 Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180 + K++ ++ E+ R AF++AQ+ + G I+ P+++ E+ I+ P+ + + Sbjct: 121 VTKYSSRLLTPAITTEVVRKAFKLAQSEKTGACFIEFPENI--AEMPIEDEPLTVRQPVA 178 Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240 P +++ A I++A PIILAG GV+ SGA E L + E +NIPV T M Sbjct: 179 PEPPGD-----RVEAAAAAISAANNPIILAGNGVIRSGACEALAEFAEAMNIPVANTFMA 233 Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIG---CRFSDRITGDIKSFATNAKI 297 KG I HP+ALG G+ + ++D+++ IG + + +S ++ Sbjct: 234 KGAIPFKHPMALGSAGLQAKDYVSCGFDQADLVLCIGYDLVEYHPYLWNPTRS----NRL 289 Query: 298 IHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVN 357 +HID PAE+ +VDV +VGD L+ + + + ++ IE++N Sbjct: 290 VHIDNTPAEVDAFYSVDVGVVGDITHSLQRIAEAATPRAGQFARPLR-----RALIEDMN 344 Query: 358 SLKKSSIPVMDYDDIPIKPQKIVKELMAV--IDDLNINKNTIITTDVGQNQMWMAHYFKT 415 + S P+KPQKI+ +L +DD+ I DVG ++MWMA F+ Sbjct: 345 EHAEDS-------RFPVKPQKIIWDLRTAMQLDDIAI-------CDVGAHKMWMARMFRA 390 Query: 416 QTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPV 475 + P + L S G MG P A+GA++A+P V+ +TGD GF+MN QEL T I + Sbjct: 391 ERPNTCLISNGFAAMGIALPGAVGARLARPGVNVVAVTGDAGFLMNAQELETAVRQGISM 450 Query: 476 VICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEAL 535 V+ ++++ G++ +W+ L R +V+F PD + A+S+G RIE ++ L Sbjct: 451 VVLVWNDAGYGLI-EWKQLNAYGRTSAVDFNN-PDLVTFAQSFGAHGYRIERTEDLLPTL 508 Query: 536 KEAINCDEPYLLDFAIDPSSALSM 559 +EA+ ++D +D S L + Sbjct: 509 REALADGGVSVIDCPVDYSENLKL 532 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: 710 Number of extensions: 28 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: 543 Length adjustment: 36 Effective length of query: 563 Effective length of database: 507 Effective search space: 285441 Effective search space used: 285441 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 25 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