Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_015930013.1 MNOD_RS16255 3-oxoacyl-ACP reductase FabG
Query= metacyc::MONOMER-16230 (256 letters) >NCBI__GCF_000022085.1:WP_015930013.1 Length = 262 Score = 149 bits (377), Expect = 4e-41 Identities = 97/248 (39%), Positives = 133/248 (53%), Gaps = 6/248 (2%) Query: 3 LIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIA 62 L K +VTG++RGIG A AR AR+GA VVI +D A A A + GG A+A Sbjct: 5 LAGKVALVTGSARGIGLAIARAFAREGASVVI----ADVNEASAEEAASGLLREGGRAMA 60 Query: 63 VGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAY 122 V D AD S ++ A + G +D+LVNNAG+ FL+ + + +G NL GA+ Sbjct: 61 VAVDVADPTSIAGMMEAILRRHGRLDILVNNAGVGGNTPFLETSLADWNRIIGINLTGAF 120 Query: 123 FTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGI 182 QA AR M G GG I+ ++S+S GG + Y KAGL L + A+ L + I Sbjct: 121 LVAQACAREMVRVG-GGKIVNIASLSGQRGGNGRAAYGAAKAGLELLTKVMAVELAEHNI 179 Query: 183 RCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVTG 242 N + PG I T++ K D R +P+ R G P+++A VFL SD +RYV G Sbjct: 180 NVNNIAPGAIETEMAK-FAHDEATRAAYNYLIPMTRYGTPEEIADAAVFLCSDESRYVHG 238 Query: 243 ASLLVDGG 250 +L VDGG Sbjct: 239 HTLNVDGG 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: 172 Number of extensions: 8 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: 262 Length adjustment: 24 Effective length of query: 232 Effective length of database: 238 Effective search space: 55216 Effective search space used: 55216 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: 47 (22.7 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