Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate 7025403 Shewana3_2558 3-oxoacyl-[acyl-carrier-protein] reductase (RefSeq)
Query= metacyc::MONOMER-16230 (256 letters) >FitnessBrowser__ANA3:7025403 Length = 248 Score = 135 bits (339), Expect = 1e-36 Identities = 88/251 (35%), Positives = 132/251 (52%), Gaps = 10/251 (3%) Query: 3 LIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIA 62 L K +VTGASRGIGRA A GA +V+G + S++G A G Sbjct: 7 LAGKVALVTGASRGIGRAIAETLVEAGA-IVVGTATSEKGAAAIQEY------LGDKGFG 59 Query: 63 VGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAY 122 + + D S L + E G VD+LVNNAGI + + M + + + TNL + Sbjct: 60 LVLNVTDSQSVTDLFDSIKEKAGDVDILVNNAGITRDNLLMRMKDDEWNDIIDTNLTSLF 119 Query: 123 FTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGI 182 + R M ++ R G II + S+ +G A Q +Y+ KAGL+ +S A + I Sbjct: 120 RLSKPVMRTMMKK-RFGRIINIGSVVGTMGNAGQVNYSAAKAGLIGFTKSLAREVASRQI 178 Query: 183 RCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVTG 242 NA+ PG I TD+ E D +K + S+VP+ RLG+ ++A ++FLASD A Y+TG Sbjct: 179 TVNAIAPGFIQTDMTDELTEDQQKA--IMSQVPMERLGQAQEIANAVLFLASDSAAYITG 236 Query: 243 ASLLVDGGLFV 253 +L V+GG+++ Sbjct: 237 ETLHVNGGMYM 247 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: 167 Number of extensions: 11 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