Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate WP_085770280.1 B1812_RS02990 3-oxoacyl-[acyl-carrier-protein] reductase
Query= uniprot:B2T9V3 (247 letters) >NCBI__GCF_002117405.1:WP_085770280.1 Length = 246 Score = 138 bits (348), Expect = 9e-38 Identities = 91/250 (36%), Positives = 130/250 (52%), Gaps = 22/250 (8%) Query: 5 LAGKTALITAAGQGIGLATAELFAREGARVIATDIR---IDGLAGKPVEARKL------- 54 L GKTAL+T A G+GLA A + GA V + R ++ LAG+ E + Sbjct: 4 LTGKTALVTGASSGLGLAIARTLHQAGATVGLSGTRREALETLAGELKERAHILPCNLSD 63 Query: 55 DVRDDAAIKALAAEIGAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRMIRAFL 114 D I A +G VD+L N AG + +EDWD +N+ A +R+ RA L Sbjct: 64 RAETDKLIPAAEGAMGGVDILVNNAGITRDMLFMRMKDEDWDAVLAVNLTAAFRLSRAVL 123 Query: 115 PAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCNAICP 174 M+ K G IIN++S A +V G P + YSA+KA + G+TKS+A + +RGV N + P Sbjct: 124 RGMMRKRHGRIINITSVAGAV-GNPGQANYSAAKAGLTGMTKSLANEVASRGVTVNCVAP 182 Query: 175 GTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSDESSFT 234 G + SP + ++ +AQ + + PM R G +EI A LYL SDE++F Sbjct: 183 GVIESPMTQ--VLNEAQRE---------RLLKLIPMERFGSADEIGAAVLYLASDEAAFI 231 Query: 235 TGHAHVIDGG 244 TG I+GG Sbjct: 232 TGQTLHINGG 241 Lambda K H 0.320 0.133 0.381 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: 147 Number of extensions: 7 Number of successful extensions: 4 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: 247 Length of database: 246 Length adjustment: 24 Effective length of query: 223 Effective length of database: 222 Effective search space: 49506 Effective search space used: 49506 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 Apr 09 2024. 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