Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate WP_066329803.1 BLR17_RS09120 SDR family oxidoreductase
Query= uniprot:B2T9V3 (247 letters) >NCBI__GCF_900100165.1:WP_066329803.1 Length = 254 Score = 164 bits (415), Expect = 2e-45 Identities = 99/251 (39%), Positives = 140/251 (55%), Gaps = 15/251 (5%) Query: 5 LAGKTALITAAGQGIGLATAELFAREGARVIATDIRIDGLA---------GKPVEARKLD 55 L K A+IT G GIG A + LFA++GA V ++ + G V A + Sbjct: 4 LKDKKAIITGGGSGIGKAISVLFAKQGAEVHIIELTAESAQSTVDEITAEGGKVFAHACN 63 Query: 56 VRDDAAIKALAAEIGAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRMIRAFLP 115 V + A +IG + +L N AG H G + E D+D D+NVK +Y + A +P Sbjct: 64 VAKHDEVVATFEKIGNIHILVNNAGIAHVGKVDTTPEADFDRIMDVNVKGVYNCLFASIP 123 Query: 116 AMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCNAICPG 175 GGGSI+NM+S AS V G+ +RFAYS +K AV+ +T SVA D+I +RCN+I P Sbjct: 124 QFRKSGGGSIVNMASIASWV-GISDRFAYSTAKGAVMSMTLSVARDYINENIRCNSISPA 182 Query: 176 TVASPSLEQRIVAQAQAQGATL-DAVQAAFVARQPMGRIGKPEEIAALALYLGSDESSFT 234 V +P ++ I A + D + + QP+GR+GKPEEIA LAL+L S+E+ F Sbjct: 183 RVHTPFVDGFIAKNYPGNEAEIFDKLSKS----QPIGRMGKPEEIATLALFLASEEAGFI 238 Query: 235 TGHAHVIDGGW 245 TG + IDGG+ Sbjct: 239 TGSDYPIDGGF 249 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: 181 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: 254 Length adjustment: 24 Effective length of query: 223 Effective length of database: 230 Effective search space: 51290 Effective search space used: 51290 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 24 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