Align SDR family oxidoreductase (characterized, see rationale)
to candidate Pf1N1B4_4954 Enoyl-[acyl-carrier-protein] reductase [NADPH] (EC 1.3.1.10)
Query= uniprot:A0A4P7ABK7 (254 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4954 Length = 248 Score = 127 bits (318), Expect = 3e-34 Identities = 82/253 (32%), Positives = 135/253 (53%), Gaps = 14/253 (5%) Query: 7 RLAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIAGVETHLLDV--- 63 RL GK LIT GIG + + F EGARVI T ++ + +I G E +L Sbjct: 3 RLQGKRTLITGGTSGIGLETAKQFLAEGARVIVTGVNPESMANAQAILGSEVLVLRADSA 62 Query: 64 ---TDDDAIKALVAKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAV 120 + +A+ + G +DV F AG I + +++ +D SF++N K + ++A+ Sbjct: 63 SVAAQKELAQAVQSHYGQLDVAFLNAGVSVWMPIEDWNEEMFDRSFDINVKGPYFLLQAL 122 Query: 121 LPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAIC 180 LP + + A ++N ++ S+ G A Y A+KAA + ++K+++++ + +G+R NA+ Sbjct: 123 LP-VFSNPASVVLN--TSVSAHLGAARSSIYAATKAAFLNMSKTLSSELLPRGVRVNAVS 179 Query: 181 PGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESNF 240 PG I++P + +A ++V A P GR G EEVA LYLASDES + Sbjct: 180 PGPIDTP-----LYDKAGIPDAYREQVNKDIAATIPFGRFGTPEEVAKAVLYLASDESRW 234 Query: 241 TTGSIHMIDGGWS 253 T G+ ++DGG S Sbjct: 235 TVGTEIIVDGGRS 247 Lambda K H 0.316 0.129 0.359 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: 121 Number of extensions: 8 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: 254 Length of database: 248 Length adjustment: 24 Effective length of query: 230 Effective length of database: 224 Effective search space: 51520 Effective search space used: 51520 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