Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS; Vegetative protein 105; VEG105 (uncharacterized)
to candidate GFF1219 PGA1_c12350 acetolactate synthase, catabolic
Query= curated2:P37251 (574 letters) >FitnessBrowser__Phaeo:GFF1219 Length = 554 Score = 173 bits (439), Expect = 1e-47 Identities = 158/555 (28%), Positives = 240/555 (43%), Gaps = 30/555 (5%) Query: 6 QVDSASAECTQTMSGALMLIESLKKEKVEMIFGYPGGAVLPIYDKLYNSGLVHILPRHEQ 65 + +SA+A T + A +L + L FG PGG VL + D L +G+ L +HE Sbjct: 3 ETNSAAAAATDPLRAADVLAQRLYAAGCRHAFGMPGGEVLTLVDALTKAGISFHLAKHEN 62 Query: 66 GAIHAAEGYARVSGKPGVVIATSGPGATNLVTGLADAMIDSLPLVVFTGQVATSVIGSDA 125 A EG G P +++AT GPGA N V +A+A D +P++V TG V + + Sbjct: 63 SAGFMGEGVYHSDGAPVILVATLGPGALNGVNVVANAHQDRVPMLVLTGCVDAAEAATYT 122 Query: 126 FQEADILGITMPVTKHSYQVRQPEDLPRIIKEAFHIATTGRPGPVLIDIPKDVATIEGEF 185 Q D + P+TK +Y++ E I +A IAT R GPV ID+P VA Sbjct: 123 HQVLDHQAVFAPITKATYRL-NAEAAGVIADKALRIATQPRNGPVHIDVPISVADAP--- 178 Query: 186 SYDHEMNLPGYQPTTEPNYLQIRKLVEAVSSAKKPVILAGAGVLHGKASEELKNYAEQQQ 245 + H L + T+P + + ++ A +PV + G + A L+ + E Q Sbjct: 179 AGPHRPYLAPAR-ATQPQPADLAQARAWLAEADRPVAVVGLDAVAEDAGASLRAFLEHYQ 237 Query: 246 IPVAHTLLGLGGFPADHPLFLGMAGMHGTYTANM--ALHECDLLISIGARFDDRVTGNLK 303 IP + G P DHPL LG AG+ ++ L E DL++++G +D ++ Sbjct: 238 IPFVTSYKAKGILPEDHPLCLGGAGLSPLADRHLLPLLREADLILALG--YDPI---EMR 292 Query: 304 HFARNA----KIAHIDIDPAEIGKIMKT-QIPVVGDSKIVLQELIKQDGKQSDSSEWKKQ 358 RNA + IDI + M T + VV L+ L D+ + Sbjct: 293 PGWRNAWDCSRQRVIDICAEDNTHYMHTASLTVVAGLAPSLRALTVGAQLADDAPQGN-- 350 Query: 359 LAEWKEEYPLWYVDNEEEGFK------PQKLIEYIHQFTKGEAIVATDVGQHQMWSAQFY 412 A W + P D F P +I + + D G H++ +Q + Sbjct: 351 -AHWPDGQPEAARDALAAAFAADADWGPAAIIAECQATLPADTLATADSGAHRILLSQMW 409 Query: 413 PFQKADKWVTSGGLGTMGFGLPAAIGAQLAEKDATVVAVVGDGGFQMTLQELDVIRELNL 472 + + S GL TMG +P AIG +LAE TVV+ GD GF M EL EL + Sbjct: 410 HCYEPRALIQSSGLCTMGCAVPMAIGRKLAEPQRTVVSFSGDAGFLMVAGELSTAAELGV 469 Query: 473 PVKVVILNNACLGMVRQWQEIFYEERYSESKF-ASQPDFVKLSEAYGIKGIRISSEAEAK 531 V+ +A L ++ Q + R + DF + A+G G+R+ A + Sbjct: 470 APIFVVFVDASLALIDLKQR---QRRLDNAGVDFGLHDFAAMGRAFGGNGVRVRDRASLR 526 Query: 532 EKLEEALTSREPVVI 546 L EA + VI Sbjct: 527 AALSEAQQAERFTVI 541 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: 683 Number of extensions: 33 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 574 Length of database: 554 Length adjustment: 36 Effective length of query: 538 Effective length of database: 518 Effective search space: 278684 Effective search space used: 278684 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