Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_028487187.1 B076_RS0110000 acetolactate synthase large subunit
Query= curated2:O08353 (599 letters) >NCBI__GCF_000483485.1:WP_028487187.1 Length = 543 Score = 338 bits (868), Expect = 3e-97 Identities = 207/561 (36%), Positives = 313/561 (55%), Gaps = 31/561 (5%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 M AE ++ LE E+VE +FG PG L DAL S + +LTRHEQ AA AD Y R Sbjct: 1 MKAAELFVRCLENEEVEYIFGIPGEENLDLMDALLDSHIQFILTRHEQGAAFMADVYGRL 60 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 +G+ GVC+ T GPGATNLVTGVA A+ D +P+VA+ GQ T + ++ Q +D + LF P Sbjct: 61 TGQAGVCLSTLGPGATNLVTGVADANMDRAPVVAIAGQAATSRLHKESHQVLDLVNLFEP 120 Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180 I K++ QI IPE+ R AF++AQ+ +PG ID P+++ E ++K P+ + L Sbjct: 121 ISKYSTQILTPDIIPEVVRKAFKVAQSEKPGCSFIDFPENIASFE--VNKPPLKKQSAL- 177 Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240 P H ++K+A ++I+ A PII+AG GV+ S A+ L + LNIPV TT M Sbjct: 178 --PPEPNSH--KVKQAAEVISQAHYPIIIAGNGVVRSNASHALEEFASKLNIPVATTFMA 233 Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHI 300 KG +S H L+LG VG+ + + +DV+I +G + + + KIIHI Sbjct: 234 KGVLSCGHELSLGTVGLQANDYISCGIDRADVVICVGYDIVE-YQPHLWNHNPGCKIIHI 292 Query: 301 DIDPAEIGKNVNVDVPIVGDAKLILKEV--IKQLDYIINKDSKENNDKENISQWIENVNS 358 D PAE+ + V+ ++GD L ++ I Q +K N K++I E + + Sbjct: 293 DSQPAEVDEFYIVEAGLIGDIGSALAKISAISQR----HKTPFYQNLKQHID---ERMQA 345 Query: 359 LKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTP 418 K D P+KPQKI+ +L + I+ +DVG ++MW+A F+T P Sbjct: 346 YK-------DDSGFPLKPQKILHDLRRA-----LQPEDIVISDVGAHKMWIARMFQTLAP 393 Query: 419 RSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVIC 478 + + S G +MG P AI AK+AKP + +TGD GF+MN QE+ T IP+++ Sbjct: 394 NTCIISNGFASMGIALPGAIAAKLAKPKQVAVAVTGDAGFLMNMQEIETAVRLQIPIIVL 453 Query: 479 IFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEA 538 I+++ G++ +W+ + R+ V F PDF+KLA+++G K RIE +++ LK+A Sbjct: 454 IWNDAHYGLI-KWKQENHFGRESHVAFTN-PDFVKLADAFGAKGYRIEKASDLLPTLKKA 511 Query: 539 INCDEPYLLDFAIDPSSALSM 559 I D L+D +D S L + Sbjct: 512 ITDDCVVLIDCPVDYSENLKL 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: 724 Number of extensions: 26 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 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