Align 4-hydroxy-2-oxovalerate aldolase; HOA; EC 4.1.3.39; 4-hydroxy-2-keto-pentanoic acid aldolase; 4-hydroxy-2-oxopentanoate aldolase (uncharacterized)
to candidate SMc02546 SMc02546 alpha-isopropylmalate/homocitrate synthase family transferase
Query= curated2:A5D523 (339 letters) >FitnessBrowser__Smeli:SMc02546 Length = 538 Score = 87.0 bits (214), Expect = 1e-21 Identities = 85/324 (26%), Positives = 139/324 (42%), Gaps = 41/324 (12%) Query: 7 IRIMDTTLRDGMHAMAHQFTPEQMAQVAAALDEAGVDVIEVTHGDGLAGSSFQYGFAAAT 66 I + DTTLRDG F+ E +A+ LD+ G+D +E + G + ++ T Sbjct: 6 IYLFDTTLRDGQQTPGIDFSVEDKIAIASLLDQFGMDYVEGGY-PGANPTDTEFFKCRRT 64 Query: 67 DEEYLEAVAPVLKKAKLAALILPGIGTCRDMRM-AVQAGVKVFRIATHVTEADISEEHMG 125 D+ A + K+A ++A PG+ + A+ K + V +EE++ Sbjct: 65 DKASFVAFG-MTKRAGVSASNDPGLSALLSAKSDAICLVAKSWDYHVEVALGCTNEENLD 123 Query: 126 LAKEMGAEVVGFLMMSHTVGKEKIAEQAKLMESYGADVVY-----------------MVD 168 + VV G+E + + + Y A+ Y + D Sbjct: 124 NIRASVEAVVAS-------GREAMVDCEHFFDGYKANSAYALACAKTAFEAGARWVVLCD 176 Query: 169 SAGAMIPPEVTEKIGYL--KEVLNIPVGFHAHNNLGLAVGNTLAAVAAGATAVDGTLRGL 226 + G PPE+ E + + + V +G HAHN+ G AV N+LAAV AG + GTL G+ Sbjct: 177 TNGGTQPPEIREIVSAVIAEGVPGANLGIHAHNDTGQAVANSLAAVEAGVRQIQGTLNGI 236 Query: 227 GAGAGNTSTEVLVAALK-----KAGYQVGVD---LYKIMDAATVLEPMMRR---PQV-ID 274 G GN + L+A L + ++ G+D L ++ A + ++ R PQ Sbjct: 237 GERCGNANLVTLIATLALKETYSSRFETGIDAERLQELTKLAHAFDELLNRSPDPQAPYV 296 Query: 275 NASIILGYAGVYSSFLLHTYRAAE 298 AS AG+++S LL R E Sbjct: 297 GASAFATKAGIHASALLKDPRTYE 320 Lambda K H 0.319 0.134 0.373 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: 334 Number of extensions: 15 Number of successful extensions: 2 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: 339 Length of database: 538 Length adjustment: 32 Effective length of query: 307 Effective length of database: 506 Effective search space: 155342 Effective search space used: 155342 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 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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