Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate GFF2263 HP15_2213 3-ketoacyl-(acyl-carrier-protein) reductase
Query= metacyc::MONOMER-16230 (256 letters) >FitnessBrowser__Marino:GFF2263 Length = 247 Score = 147 bits (372), Expect = 2e-40 Identities = 97/253 (38%), Positives = 142/253 (56%), Gaps = 7/253 (2%) Query: 1 MLLIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTA 60 M L KT +VTGA+RGIG+A AR A QGA VV G+ AGA S+ ++ + G Sbjct: 1 MSLEGKTALVTGATRGIGQAIARALAAQGAEVV----GTATSEAGAESITNDLQSAGYKG 56 Query: 61 IAVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNG 120 + + AD S E + E G+ +LVNNAGI + + + + + + TNL+ Sbjct: 57 YGMVMNVADPASIEAGLKELTEKSGAPLILVNNAGITRDNLLMRLKDDDWASVLETNLSS 116 Query: 121 AYFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPY 180 Y T +A R M + + G II +SS+ A +G A Q +Y KAG+ +S A + Sbjct: 117 VYRTSKAVLRGMAK-AKWGRIINISSVVAGMGNAGQGNYCAAKAGVEGFTRSLAKEMSNR 175 Query: 181 GIRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYV 240 GI N V PG I TD+ K+ D ++R M +P GRLGEP+++A + FLASD A YV Sbjct: 176 GITANCVAPGFIDTDMTKK--LDDKQRGAMLEIIPAGRLGEPEEVAAVVAFLASDAAGYV 233 Query: 241 TGASLLVDGGLFV 253 TG ++ V+GG+++ Sbjct: 234 TGETINVNGGMYM 246 Lambda K H 0.319 0.136 0.383 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: 143 Number of extensions: 9 Number of successful extensions: 4 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: 256 Length of database: 247 Length adjustment: 24 Effective length of query: 232 Effective length of database: 223 Effective search space: 51736 Effective search space used: 51736 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: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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