Align 4-hydroxy-2-oxohexanoate aldolase (EC 4.1.3.43) (characterized)
to candidate WP_012407235.1 NPUN_RS02205 homocitrate synthase
Query= BRENDA::Q53WI0 (347 letters) >NCBI__GCF_000020025.1:WP_012407235.1 Length = 377 Score = 90.1 bits (222), Expect = 8e-23 Identities = 82/275 (29%), Positives = 123/275 (44%), Gaps = 36/275 (13%) Query: 12 VVVDTTLRDGSHAHRHQYTVEEARAIAQALDEAGVYAIEV---SHGDGLGGSSLQYGFSR 68 ++ DTTLRDG A +T++E AIA+ LD G+ +EV + GD Sbjct: 5 IINDTTLRDGEQAAGVAFTLQEKVAIAKFLDSIGIPELEVGIPAMGD------------- 51 Query: 69 TDEMELIRAVRETVRRAKVAALLLPGIGTRKELKEAVEAGIQMVRIATQCTEADISEQHF 128 +E I A+ + +AK LL ++K ++ G+ V IA + I+ + Sbjct: 52 -EETRAIAAISDLGLQAK---LLGWNRAVISDIKASIACGLNRVHIAIPVSGIQIAAKFH 107 Query: 129 GM--------------AKEMGLEAVGFLMMSHMRPPEFLAEQARLMEGYGADVVYIVDSA 174 G A + GL S FL + A + +GA D+ Sbjct: 108 GQWRVSLQKLKDCISFAVDQGLWVAVGGEDSSRADENFLLDVALYAQEWGASRFRFCDTV 167 Query: 175 GAMLPEDAYARVKALKEALSRAKVGFHAHNNLGLAIGNTLAALAAGADWVDATLRGYGAG 234 G + P Y +VK L AL + H HN+ GLA N LA + AGA V+ T+ G G Sbjct: 168 GVLDPFTTYTKVKRLVSALM-IPLEIHTHNDFGLATANALAGIKAGALSVNTTVNGLGER 226 Query: 235 AGNAPL-EVLAAVLDKAGLNPGLDVFKLLDAAEYV 268 AGNA L EV+ A+ G++ G+D LL+ ++ V Sbjct: 227 AGNAALEEVVMAIKRIYGVDLGIDTPGLLELSQLV 261 Lambda K H 0.319 0.135 0.386 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: 297 Number of extensions: 20 Number of successful extensions: 3 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: 347 Length of database: 377 Length adjustment: 29 Effective length of query: 318 Effective length of database: 348 Effective search space: 110664 Effective search space used: 110664 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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