Align Short-chain dehydrogenase (characterized, see rationale)
to candidate HSERO_RS22305 HSERO_RS22305 oxidoreductase
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__HerbieS:HSERO_RS22305 Length = 249 Score = 99.4 bits (246), Expect = 6e-26 Identities = 75/249 (30%), Positives = 113/249 (45%), Gaps = 4/249 (1%) Query: 1 MDLNLQDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQPRAALF 60 M+ L K+ +VTGG SGIG A + +LAA+GA VF + A + + A Sbjct: 1 MNKQLNGKIALVTGGTSGIGLATAQELAAQGA--QVFITGRRQAELDAAVASIGAAATGI 58 Query: 61 QLELQDEARCGEAVAETVRRFGRLDGLVNNAGVNDSVGLDAGRNEFVASLERNLIHYYVM 120 + + + A+ + GRLD L NAG D + L A E + + + Sbjct: 59 RADASVLSELDTVYAQIAKSAGRLDILFANAGGGDMMPLGAITEEHFDRIFGTNVRGVLF 118 Query: 121 AHYCVPHLKATRGAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVRVNA 180 L +++ SS T++ G N S Y ASK A + R WA L+D +RVN Sbjct: 119 TVQKALPLLVDGASVILTSSTTSVLGTANFSVYSASKAAVRNFARSWALDLKDRAIRVNV 178 Query: 181 LIPAEVMTPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGRSSHTT 240 + P + TP + + + Q D + S++PLG R +E+ FL S +S Sbjct: 179 VSPGPIRTPGLGELVPD-DARQGLFDYLASQVPLG-RLGEPQEIGKAVAFLASDAASFVN 236 Query: 241 GQWVFVDGG 249 G +FVDGG Sbjct: 237 GIELFVDGG 245 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: 154 Number of extensions: 11 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: 258 Length of database: 249 Length adjustment: 24 Effective length of query: 234 Effective length of database: 225 Effective search space: 52650 Effective search space used: 52650 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: 47 (22.7 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