Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS; Vegetative protein 105; VEG105 (uncharacterized)
to candidate GFF1617 PS417_08225 acetolactate synthase
Query= curated2:P37251 (574 letters) >FitnessBrowser__WCS417:GFF1617 Length = 571 Score = 275 bits (702), Expect = 5e-78 Identities = 179/556 (32%), Positives = 284/556 (51%), Gaps = 20/556 (3%) Query: 34 EMIFGYP--GGAVLPIYDKLYNSGLVHILP-RHEQGAIHAAEGYARVSGKP--GVVIATS 88 ++++GY GG + + D + G ++ HEQGA AA +R + GV + TS Sbjct: 15 KVLYGYELIGGMITHLVDSINQLGKTKLVSVHHEQGAAFAASAVSRATHHEVLGVALGTS 74 Query: 89 GPGATNLVTGLADAMIDSLPLVVFTGQVATSVIGSD------AFQEADILGITMPVTKHS 142 GPGATNL+TG+AD +DS P + TGQV T + + FQE D + + +TK++ Sbjct: 75 GPGATNLITGIADCWLDSHPCLFLTGQVNTYELKGERNIRQQGFQELDSVALVSSITKYA 134 Query: 143 YQVRQPEDLPRIIKEAFHIATTGRPGPVLIDIPKDVATIEGEFSYDHEMNLPGYQPTTEP 202 YQVR ++L +++A +A GRPGPVL+DIP D+ + + + LP Q P Sbjct: 135 YQVRHVDELLPCLQKAIDLAREGRPGPVLLDIPMDIQRTDIDDAAVSAFLLPCAQQIAAP 194 Query: 203 -NYLQIRKLVEAVSSAKKPVILAGAGVLHGKASEELKNYAEQQQIPVAHTLLGLGGFPAD 261 + + A++ A+ P+IL G G ++ N E IP +L G PA Sbjct: 195 LQAADLETISNALACARNPLILLGGGAVNTPNFAHWLNQLETSGIPYVASLKGAEKIPAS 254 Query: 262 HPLFLGMAGMHGTYTANMALHECDLLISIGARFDDRVTG-NLKHFARNAKIAHIDIDPAE 320 +LGM G +GT AN A+ CD L+ +G+R D R TG + FAR AK+ ID+ + Sbjct: 255 AN-YLGMLGAYGTRAANHAVQNCDFLLVLGSRLDVRQTGAKPEDFARKAKVFQIDLMEGQ 313 Query: 321 IGKIMKTQIPVVGDSKIVLQELIKQDGKQSDSSEWKKQLAEWKEEYPLWYVDNEEE-GFK 379 + +K V + + + +++ + W A+ + ++ +VD + Sbjct: 314 LNNRVKAHASYVMELNTFFADFPLCEVQEN--AAWNAWAADLRADFDQSFVDEYTDWSVS 371 Query: 380 PQKLIEYIHQFTKGEAI-VATDVGQHQMWSAQFYPFQKADKWVTSGGLGTMGFGLPAAIG 438 P + + TKG + DVG +QMW+A SGGLGTMGF +PAAIG Sbjct: 372 PFVICSTLGALTKGHGVDFVADVGNNQMWAAHTLRLSPGQSMHHSGGLGTMGFAIPAAIG 431 Query: 439 AQLAEKDATVVAVVGDGGFQMTLQELDVIRELNLPVKVVILNNACLGMVRQWQEIFYEER 498 A A + V+ + GDGG Q+ +QELD+I LPV +++LNN LGMVR +QE+++E R Sbjct: 432 ACNAG-NKPVIVITGDGGAQLNIQELDIIARDQLPVLIIVLNNHSLGMVRGFQEMYFEGR 490 Query: 499 YSESKF-ASQPDFVKLSEAYGIKGIRISSEAEAKEKLEEALTSREPVVIDVRVASEEKVF 557 S + + F + EAYGI +S+ E ++ + S P +I++ + + Sbjct: 491 NSSTYWNGYTSQFKAIGEAYGISSTVVSTHEEFAAQVGMFIESPRPALIELMMPDARECR 550 Query: 558 PMVAPGKGLHEMVGVK 573 P + G+ + + + K Sbjct: 551 PRLEFGRSIDQQLPEK 566 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: 757 Number of extensions: 39 Number of successful extensions: 8 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: 571 Length adjustment: 36 Effective length of query: 538 Effective length of database: 535 Effective search space: 287830 Effective search space used: 287830 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