Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_027723082.1 H589_RS0116710 3-oxoacyl-ACP reductase FabG
Query= uniprot:A0A4P7ABK7 (254 letters) >NCBI__GCF_000425265.1:WP_027723082.1 Length = 240 Score = 97.8 bits (242), Expect = 2e-25 Identities = 72/250 (28%), Positives = 121/250 (48%), Gaps = 24/250 (9%) Query: 11 KTVLITAAAQGIGRASTELFAREGARVI----ATDISKTHLEELASIAGVETHLL--DVT 64 K LIT A++GIG A A +G + + D E G + LL DVT Sbjct: 3 KIALITGASKGIGAAIAVQLAEDGYDIWLNYRSDDAGAHKTAEQIKQHGQQCTLLKFDVT 62 Query: 65 DDDAIKALVAKVGTVDVLF---NCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAVL 121 D+ A++ ++ + V + N AG+ ++ D W+ ++ F+ + V+ Sbjct: 63 DEKAVEENLSSLLEKKVPYIVVNNAGFTRDSIMMMMDSSDWNKVLQVHLTGFFNVTKPVV 122 Query: 122 PGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAICP 181 ML K+ G I+NIAS + GVA + Y A+KA ++G TKS+A + + I NA+ P Sbjct: 123 SRMLRKRTGRIINIASTSGET-GVAGQTNYCAAKAGLIGATKSLAMEVAKRNILVNAVTP 181 Query: 182 GTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESNFT 241 G I++ L++ + K T P+ R+G +EVA + +L SD++++ Sbjct: 182 GFIDTDMLSELPVDEIKNT--------------IPLKRLGTPKEVAGVVSFLCSDKASYI 227 Query: 242 TGSIHMIDGG 251 TG ++GG Sbjct: 228 TGQTIAVNGG 237 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: 117 Number of extensions: 7 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: 254 Length of database: 240 Length adjustment: 24 Effective length of query: 230 Effective length of database: 216 Effective search space: 49680 Effective search space used: 49680 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 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