Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_013091146.1 BC1002_RS16535 beta-ketoacyl-ACP reductase
Query= uniprot:Q8EGC1 (252 letters) >NCBI__GCF_000092885.1:WP_013091146.1 Length = 246 Score = 132 bits (333), Expect = 5e-36 Identities = 83/259 (32%), Positives = 141/259 (54%), Gaps = 23/259 (8%) Query: 3 LKDKVVVITGGAGGLGLAMAHNFAQAG-AKLALIDVDQDKLERACADLGSSTEVQGYAL- 60 + ++V +TGG GG+G A+ + +A + + R D + G+ Sbjct: 1 MANRVAYVTGGMGGIGTAICQRLHKENYTVIAGCGPNSTRKARWLED----QKALGFNFI 56 Query: 61 ----DITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQS 116 ++ D E F + ++ G+++VLVNNAGI RDGM K M+++ +Q+ Sbjct: 57 ASEGNVADWESTAKAFEKVRKEVGEVDVLVNNAGITRDGMFRK---------MTYEDWQA 107 Query: 117 VINVNLTGTFLCGREAAAAMIESGQAGVIVNISSL-AKAGNVGQSNYAASKAGVAAMSVG 175 VI+ NLT F ++ M++ G G I+NISS+ + G GQ+NY+ +KAG+ ++ Sbjct: 108 VIDTNLTSLFNVTKQVIEGMVDRG-FGRIINISSVNGQKGQFGQTNYSTAKAGIHGFTMA 166 Query: 176 WAKELARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIE 235 A+E+A N+ V+PG I T+M A++PE LE++ +PV RLG +EIAS V +I Sbjct: 167 LAQEVATKNVTVNTVSPGYIGTDMVKAIRPEVLEKIVATIPVRRLGTPDEIASIVAWIAS 226 Query: 236 ND--YVNGRVFEVDGGIRL 252 ++ + G F ++GG+ + Sbjct: 227 DEAGFATGADFSLNGGLHM 245 Lambda K H 0.317 0.134 0.369 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: 164 Number of extensions: 12 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: 252 Length of database: 246 Length adjustment: 24 Effective length of query: 228 Effective length of database: 222 Effective search space: 50616 Effective search space used: 50616 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 (21.7 bits) S2: 46 (22.3 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