Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_024852225.1 N745_RS0111220 acetolactate synthase large subunit
Query= curated2:O08353 (599 letters) >NCBI__GCF_000526715.1:WP_024852225.1 Length = 547 Score = 310 bits (795), Expect = 8e-89 Identities = 197/557 (35%), Positives = 301/557 (54%), Gaps = 31/557 (5%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 M ++ ++ LE E VE +FG PG + DAL S + + RHEQ AA AD Y R Sbjct: 1 MKASQLFVQCLENEGVEYIFGIPGEENMDVMDALVDSKIQFITCRHEQGAAFMADVYGRL 60 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 +GK GVC+ T GPGATNLVTGVA A+ D+SP+VA+ GQ T + ++ Q +D + +F P Sbjct: 61 TGKAGVCLSTLGPGATNLVTGVADANMDNSPVVAIAGQAATTRMHKESHQVLDLVSMFRP 120 Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180 I K+ QI + IPE+ R AF++AQ +PG ID P+++ E+E I + P+P + Sbjct: 121 ISKYAIQILEPETIPEVMRKAFKLAQAEKPGASFIDFPENISEME--IVESPLP-----V 173 Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240 + T+ + I A ++I AK+P+IL G G + + A+ L NIPV T M Sbjct: 174 INSKLTLADSQLILDAAEIIKQAKKPLILVGNGAVRAKASGSLFAFSNHYNIPVINTFMA 233 Query: 241 KGCISE-NHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNA--KI 297 KG + +PL++G G+ N +E+D++I IG D + + N KI Sbjct: 234 KGVVPHYKNPLSMGTAGLQKGDYNNGGFAEADLVICIG---FDMVEYHPHLWNPNREHKI 290 Query: 298 IHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVN 357 IHID AE+ + V ++G+ L + +KQ K S + ++++ +E V+ Sbjct: 291 IHIDTKAAEVDYSYIPHVELIGNIGFNL-DALKQALPEKPKTSIQFPLRQSLFDEMERVS 349 Query: 358 SLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQT 417 + D P+KPQKI+ +L + K I +DVG ++MWMA F+ + Sbjct: 350 QSQ----------DWPMKPQKIIWDLRTA-----MKKKDIAISDVGAHKMWMARMFRCEL 394 Query: 418 PRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVI 477 P + + S G +MG P A+GAK+A PD ++ +TGD GFMMN QE+ T P VI Sbjct: 395 PNTCIISNGFASMGIAVPGAVGAKLAFPDRAIVAVTGDAGFMMNSQEIETALRCETPFVI 454 Query: 478 CIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKE 537 I+++ G++ Q YG R ++F PDF+K AES+G RI + +E+ ALK Sbjct: 455 LIWNDNQYGLINWKQKRRYG-RPAYIDFKN-PDFVKYAESFGATGIRINAADELLPALKT 512 Query: 538 AINCDEPYLLDFAIDPS 554 A+ + ++D +D S Sbjct: 513 ALTANTVTVIDCPVDYS 529 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: 756 Number of extensions: 28 Number of successful extensions: 7 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 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