Align Short-chain dehydrogenase (characterized, see rationale)
to candidate 3607850 Dshi_1258 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__Dino:3607850 Length = 247 Score = 107 bits (266), Expect = 3e-28 Identities = 84/247 (34%), Positives = 125/247 (50%), Gaps = 13/247 (5%) Query: 6 QDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQPRAALFQLELQ 65 Q + ++TGGA GIG A + LAAEGA ++ + + ARL G A + ++ Sbjct: 3 QTPLALITGGAQGIGYACAEALAAEGARIILADIQDSVQEAAARLGG-----AGYLCDMG 57 Query: 66 DEARCGEAVAETVRRFGRLDGLVNNAGVNDSVG-LDAGRNEFVASLERNLIHYYVMAHYC 124 D A G G + LVNNAG+ LD F L+ NL +V Sbjct: 58 DAAAVGALFDRIEAEHGAVTYLVNNAGIAAPGDFLDYDLATFDRVLDINLRGVFVATQRA 117 Query: 125 VPHLKA--TRGAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVRVNALI 182 + A +GA++N+SS A + YCASKG + LT+ A AL G+RVNA+ Sbjct: 118 GRSMVAHGIKGAVVNMSSINAQVAIPSIPAYCASKGGLMQLTKVAALALAPHGIRVNAVG 177 Query: 183 PAEVMTPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGRSSHTTGQ 242 P + T E NP E ++ + S+ PL KR T++E+A++ FL S ++S+ TG+ Sbjct: 178 PGSIDT---EMMAGVNANP-EAMNMVLSRTPL-KRVGTAQEIANVVAFLCSDKASYVTGE 232 Query: 243 WVFVDGG 249 ++VDGG Sbjct: 233 TIYVDGG 239 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: 168 Number of extensions: 9 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: 247 Length adjustment: 24 Effective length of query: 234 Effective length of database: 223 Effective search space: 52182 Effective search space used: 52182 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 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