Align Short-chain dehydrogenase (characterized, see rationale)
to candidate WP_011840077.1 RSPH17029_RS20910 SDR family oxidoreductase
Query= uniprot:A0A2E7P8M8 (258 letters) >NCBI__GCF_000015985.1:WP_011840077.1 Length = 248 Score = 86.3 bits (212), Expect = 6e-22 Identities = 75/251 (29%), Positives = 118/251 (47%), Gaps = 14/251 (5%) Query: 3 LNLQDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQPRAALFQL 62 ++L +V +VTGGA GIG A++ +L A GA ++ R D + A + FQ+ Sbjct: 4 IDLAGRVAVVTGGAQGIGRAVAERLIASGARVCLWDR---DAERAAATAAELGGNSFFQV 60 Query: 63 ELQDEARCGEAVAE-TVRRFGRLDGLVNNAGVNDSVG--LDAGRNEFVASLERNLIHYYV 119 Q + +A + T GR+D L+ NAG+ S D E+ ++ NL + Sbjct: 61 VDQVDFTAVKAATDATEATGGRIDILIANAGIAGSNAPVADYPVEEWHRIIDINLNGVFH 120 Query: 120 MAHYCVPHLKATR-GAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVRV 178 VP +KA G I+ V+S G N + Y ASK ++LT+ + + V Sbjct: 121 CCKAVVPGMKARGYGRIVTVASIAGKEGNPNAAAYSASKAGVIALTKSLGKEVAGQDIAV 180 Query: 179 NALIPAEVMTPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGRSSH 238 N + PA T +++ + Q +D + S+IP G RF +E A M +L S +S Sbjct: 181 NCVTPAAARTQIFD------QMAQSHIDYMLSRIPRG-RFLDLDEAAAMIAWLASAENSF 233 Query: 239 TTGQWVFVDGG 249 TTG + GG Sbjct: 234 TTGAVFDLSGG 244 Lambda K H 0.318 0.134 0.394 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: 136 Number of extensions: 8 Number of successful extensions: 2 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: 258 Length of database: 248 Length adjustment: 24 Effective length of query: 234 Effective length of database: 224 Effective search space: 52416 Effective search space used: 52416 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 (21.7 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Apr 10 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