Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate Synpcc7942_0684 Synpcc7942_0684 3-oxoacyl-[acyl-carrier-protein] reductase
Query= metacyc::MONOMER-16230 (256 letters) >FitnessBrowser__SynE:Synpcc7942_0684 Length = 249 Score = 164 bits (414), Expect = 2e-45 Identities = 106/251 (42%), Positives = 146/251 (58%), Gaps = 12/251 (4%) Query: 3 LIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALS-LAEEIAAFGGTAI 61 L D+ +VTGASRGIGRA A E A GA+V + ++ S AGA + IAA GG A Sbjct: 6 LTDRIALVTGASRGIGRAIALELAAAGAKVAVNYASS----AGAADEVVAAIAAAGGEAF 61 Query: 62 AVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGA 121 AV AD + E L AA +E +G +DVLVNNAGI L M R+ + + NL G Sbjct: 62 AVKADVSQESEVEALFAAVIERWGRLDVLVNNAGITRDTLLLRMKRDDWQSVLDLNLGGV 121 Query: 122 YFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYG 181 + +AAA+ M +Q R G II ++S+ +G Q +Y+ KAG++ L ++ A L G Sbjct: 122 FLCSRAAAKIMLKQ-RSGRIINIASVVGEMGNPGQANYSAAKAGVIGLTKTVAKELASRG 180 Query: 182 IRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASD-MARYV 240 I NAV PG IATD+ E + E++ +PLGR GE ++AG + FLA+D A Y+ Sbjct: 181 ITVNAVAPGFIATDMTSELAA-----EKLLEVIPLGRYGEAAEVAGVVRFLAADPAAAYI 235 Query: 241 TGASLLVDGGL 251 TG + +DGGL Sbjct: 236 TGQVINIDGGL 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: 163 Number of extensions: 9 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: 249 Length adjustment: 24 Effective length of query: 232 Effective length of database: 225 Effective search space: 52200 Effective search space used: 52200 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