Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate CA265_RS15450 CA265_RS15450 3-oxoacyl-[acyl-carrier-protein] reductase
Query= metacyc::MONOMER-16231 (254 letters) >FitnessBrowser__Pedo557:CA265_RS15450 Length = 247 Score = 152 bits (384), Expect = 6e-42 Identities = 96/249 (38%), Positives = 132/249 (53%), Gaps = 3/249 (1%) Query: 1 MKLLEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIA 60 MKLLEGKT LVTGAS GIGR A A+ GA+VA Y S ++ E+++ G + Sbjct: 1 MKLLEGKTALVTGASKGIGRKIAEKFAEQGANVAFTYLSSVEKGEALEQELQSFGTKVKG 60 Query: 61 VKGDVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAY 120 + D + A+ + V FG +D++V+NAGI + M + + +NL + Sbjct: 61 YRSDASKFAEAEQLINDIVAEFGTIDIVVNNAGITKDGLLMRMSEENWDDVININLK-SI 119 Query: 121 FMVQAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGI 180 F V AA +++ + G + + SI G Q +Y +KAG+ +S A LG I Sbjct: 120 FNVTKAASKVMMKARKGVFINMGSIVGTTGNGGQANYAASKAGIIGFTKSIAKELGSRNI 179 Query: 181 RCNSVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTG 240 R N V PG I TE+ D+ D + E E PL R G ED+A VFLASDM+AYVTG Sbjct: 180 RANVVAPGFIRTEMT--DILDPKVVEGWEKDIPLKRAGETEDIANVCVFLASDMSAYVTG 237 Query: 241 AALLVDGGM 249 L V GGM Sbjct: 238 QTLSVCGGM 246 Lambda K H 0.318 0.133 0.379 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: 112 Number of extensions: 6 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: 254 Length of database: 247 Length adjustment: 24 Effective length of query: 230 Effective length of database: 223 Effective search space: 51290 Effective search space used: 51290 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 17 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