Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS; Vegetative protein 105; VEG105 (uncharacterized)
to candidate WP_011383235.1 AMB_RS04050 thiamine pyrophosphate-binding protein
Query= curated2:P37251 (574 letters) >NCBI__GCF_000009985.1:WP_011383235.1 Length = 613 Score = 259 bits (662), Expect = 2e-73 Identities = 171/558 (30%), Positives = 278/558 (49%), Gaps = 39/558 (6%) Query: 24 LIESLKKEKVEMIFGYPGGAVLPIYDKLYNSGLV-HILPRHEQGAIHAAEGYARVSGKPG 82 +I L +E ++ IF G A + D + ++ HEQG AAE YA++ G PG Sbjct: 7 VINRLAEEGIDKIFVVYGAANGDLIDAFTRTNKTEYVATMHEQGGGFAAEAYAKIKGIPG 66 Query: 83 VVIATSGPGATNLVTGLADAMIDSLPLVVFTGQVATSVIGSD------AFQEADILGITM 136 IATSGPG NL+T + + DS+P V TGQ+ + + D FQE DI+G+ Sbjct: 67 ATIATSGPGGQNLLTSMGNCFYDSIPCVFMTGQINSQFLRPDPSIRQVGFQETDIVGMAK 126 Query: 137 PVTKHSYQVRQPEDLPRIIKEAFHIATTGRPGPVLIDIPKDVATIEGE----FSYD---- 188 PVTK++ + ++ +++A IA GRPGPVL+DIP ++ + + F +D Sbjct: 127 PVTKYAKMITSAAEIRYEVEKALFIAKEGRPGPVLLDIPLNIQKQDIDPDKLFGFDTVAA 186 Query: 189 -HEMNLPGYQPTTEPNYLQIRKLVEAVSSAKKPVILAGAGVLHGKASEELKNYAEQQQIP 247 NL + + K +K+P I+ G GV A ++L E +P Sbjct: 187 QRSWNLDAVDAAIDTYLADLAK-------SKRPTIMVGGGVRLANAVDDLVELGEVLGVP 239 Query: 248 VAHTLLGLGGFPADHPLFLGMAGMHGTYTANMALHECDLLISIGARFDDRVTG-NLKHFA 306 + T L +D P + G G +G N + DLL+++G+R R+TG N+ FA Sbjct: 240 MFPTWNALDVVTSDLPQYGGRIGTYGGAGRNFGIQNSDLLLAVGSRISGRITGGNIHSFA 299 Query: 307 RNAKIAHIDIDPAEIGKIMKTQIP----VVGDSKIVLQELI------KQDGKQSDSSEWK 356 R AK +D+D + K ++ Q+P V+ D+ I L+ L+ + +G D W Sbjct: 300 REAKKYVVDVDETLLQKHLQ-QVPLDVNVLCDAGIFLRRLVARAKALRANGGLGDHKAWL 358 Query: 357 KQLAEWKEEY-PLWYVDNEEEG-FKPQKLIEYIHQFTKGEAIVATDVGQHQMWSAQFYPF 414 ++ +W++ Y P+ E++G P + + + KG IV D G + + ++ + Sbjct: 359 SKVLDWRDRYDPVLPEFFEQKGTVHPYAFVRKLSEMMKGGDIVVGDCGGNIVVTSHAFET 418 Query: 415 QKADKWVTSGGLGTMGFGLPAAIGAQLAEKDATVVAVVGDGGFQMTLQELDVIRELNLPV 474 ++ + +T+ G MGF A+GA A + VV ++GDGG M +QEL + V Sbjct: 419 KRGQRLLTNNGNSPMGFSFAGAMGAWFAAPNNQVVCIIGDGGMNMNIQELQTFVNYGVKV 478 Query: 475 KVVILNNACLGMVRQWQEIFYEERYSE--SKFASQPDFVKLSEAYGIKGIRISSEAEAKE 532 K ILNN G+ + +QE + R K + PDFVK+++AYG+K + I ++ E + Sbjct: 479 KTFILNNHIYGITKAYQETNFNGRAEACGPKGYAPPDFVKIAQAYGVKTVTIETQQEMEA 538 Query: 533 KLEEALTSREPVVIDVRV 550 K+ E L + VV DV + Sbjct: 539 KIAEVLAADCAVVCDVNM 556 Lambda K H 0.317 0.135 0.391 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: 807 Number of extensions: 40 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: 574 Length of database: 613 Length adjustment: 37 Effective length of query: 537 Effective length of database: 576 Effective search space: 309312 Effective search space used: 309312 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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