Align Short-chain dehydrogenase (characterized, see rationale)
to candidate 5210989 Shew_3415 short chain dehydrogenase (RefSeq)
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__PV4:5210989 Length = 268 Score = 95.1 bits (235), Expect = 1e-24 Identities = 79/243 (32%), Positives = 118/243 (48%), Gaps = 26/243 (10%) Query: 5 LQDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQPRAA------ 58 L DKVVI+TG + GIG A++ +A G V+ ARS+ RL LQ + Sbjct: 4 LADKVVIITGASEGIGRALAKAMAPLGCRLVLTARSQ------GRLHSLQQELSSIASVP 57 Query: 59 --LFQLELQDEARCGEAVAETVRRFGRLDGLVNNAGVNDSVGLDAGRNEFVASLER---- 112 + ++ D A C + V F RLD LVNNAG+ D E ++ LER Sbjct: 58 PLVIPADVTDAAACQGLIDACVAHFDRLDILVNNAGMTMWSRFD--ELEDLSILERVMQV 115 Query: 113 NLIHYYVMAHYCVPHLKATRGAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALR 172 N + ++ H+ +PHLKA+RG I+ V+S LTG SGY ASK A + L Sbjct: 116 NYLAPAMLTHFALPHLKASRGQIVVVASVAGLTGVPTRSGYSASKHAVMGFFDSLRIELV 175 Query: 173 DDGVRVNALIPAEVMTPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLL 232 + V V + P V++ ++++ + NP K +KI T+E+ A M + + Sbjct: 176 EHDVAVTHICPDFVVSEIHKRALDGQGNPLGKSPMQEAKI------ITAEQCAQMMLPAI 229 Query: 233 SGR 235 +GR Sbjct: 230 AGR 232 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: 157 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: 258 Length of database: 268 Length adjustment: 25 Effective length of query: 233 Effective length of database: 243 Effective search space: 56619 Effective search space used: 56619 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