Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate Echvi_4610 Echvi_4610 3-oxoacyl-(acyl-carrier-protein) reductase
Query= metacyc::MONOMER-16230 (256 letters) >FitnessBrowser__Cola:Echvi_4610 Length = 248 Score = 164 bits (414), Expect = 2e-45 Identities = 96/251 (38%), Positives = 152/251 (60%), Gaps = 8/251 (3%) Query: 2 LLIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGS-DEGRAGALSLAEEIAAFGGTA 60 LL KT ++TGAS+GIGRA A + A++GA V S ++G+A L +E+A FG A Sbjct: 3 LLTGKTALITGASKGIGRAIALKYAQEGANVAFTFLSSVEKGQA----LEKELAEFGVKA 58 Query: 61 IAVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNG 120 +DA+D + E+LV V+ FG++DVL+NNAG+ + + M E + + NL Sbjct: 59 KGFRSDASDFKAAEELVNEVVKEFGALDVLINNAGVTRDNLLMRMNEEAWDDVMNINLKS 118 Query: 121 AYFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPY 180 + TV+AA R + +Q + G+II ++S+ + G A Q +Y +KAG++ +S A+ LG Sbjct: 119 CFNTVKAATRTLMKQ-KAGSIINITSVVGIKGNAGQANYAASKAGIIGFTKSVALELGSR 177 Query: 181 GIRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYV 240 GIR NAV PG I T++ ++ D + + +P+ R G+P+++A VFL SDM+ YV Sbjct: 178 GIRSNAVAPGFIETEMT--EVLDEKTVQGWRDAIPMKRGGQPEEVANACVFLGSDMSSYV 235 Query: 241 TGASLLVDGGL 251 +G + VDG + Sbjct: 236 SGQVIQVDGAM 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: 138 Number of extensions: 10 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: 256 Length of database: 248 Length adjustment: 24 Effective length of query: 232 Effective length of database: 224 Effective search space: 51968 Effective search space used: 51968 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 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