Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_035253776.1 H567_RS0108260 3-oxoacyl-ACP reductase FabG
Query= metacyc::MONOMER-16230 (256 letters) >NCBI__GCF_000422285.1:WP_035253776.1 Length = 254 Score = 145 bits (365), Expect = 1e-39 Identities = 92/261 (35%), Positives = 146/261 (55%), Gaps = 14/261 (5%) Query: 1 MLLIDKTVIVTGASRGIGRAAARECARQGARVVIGHSG-SDEGRAGALSLAEEIAAFGGT 59 M L D+ +VTG +RG+GRA A A++GAR+++ + D+ R I GG Sbjct: 1 MRLKDRVAVVTGGARGLGRAFALRLAQEGARIMVMNIVLRDKDREDMQETVRLIEELGGE 60 Query: 60 AIAVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGIC------PFHSFLDMPRELYLKT 113 A + D + + A V AFG +D+L+NNA I PF +D+ + + Sbjct: 61 ARSFAGDVTSEADTKAMAEATVAAFGRIDILINNAAIYDGLVRKPFDE-IDLGE--WDRV 117 Query: 114 VGTNLNGAYFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSC 173 +G N+ GA+ V+A MK Q + G I+ + S +A G HY +K G+L+L ++ Sbjct: 118 MGVNVKGAFLAVRAVFPVMKAQ-QSGKIVNLCSETAFTGSHGFVHYVSSKGGILALTRAL 176 Query: 174 AIALGPYGIRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLA 233 AI LGPY I NAV PG T+ ++ L+D+ + + T++ PL RLG P+D+ G +FLA Sbjct: 177 AIELGPYNICINAVAPGFTDTEASR-SLADVTRYD--TTKTPLKRLGTPEDITGAALFLA 233 Query: 234 SDMARYVTGASLLVDGGLFVN 254 S + ++TG +L+VDGG +++ Sbjct: 234 SAESDFITGQTLVVDGGRYMH 254 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: 144 Number of extensions: 8 Number of successful extensions: 5 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: 254 Length adjustment: 24 Effective length of query: 232 Effective length of database: 230 Effective search space: 53360 Effective search space used: 53360 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