Align Short-chain dehydrogenase (characterized, see rationale)
to candidate 3607199 Dshi_0620 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__Dino:3607199 Length = 250 Score = 112 bits (279), Expect = 1e-29 Identities = 82/247 (33%), Positives = 121/247 (48%), Gaps = 10/247 (4%) Query: 5 LQDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQPRAALFQLEL 64 + K +VTG A GIG A + L G + R P L GL + ++ Sbjct: 1 MTSKTAVVTGAARGIGLATTKLLLERGWKVAMIDRD--GPALAEALQGLDGVHGI-DCDV 57 Query: 65 QDEARCGEAVAETVRRFGRLDGLVNNAGVNDSVGLD-AGRNEFVASLERNLIHYYVMAHY 123 D +AET+R FG++D LVNNAGV D ++ + +E NL ++ Sbjct: 58 SDPEAVEGMIAETLREFGQIDALVNNAGVADFGPIEETSFARWKTVMETNLDGPFLCVQA 117 Query: 124 CVPHLKATRGAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVRVNALIP 183 P LKAT+GA++N++S + L Y SK A + LT + A L + G+R N + P Sbjct: 118 ATPALKATKGAVVNIASISGLRASTLRVAYGTSKAAVIQLTLQQAVELGEHGIRANCVCP 177 Query: 184 AEVMTPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGRSSHTTGQW 243 V T L A + QE +DA IPL R+ + +E+A+ +FL S R+S TGQ Sbjct: 178 GPVRTKL-----AMAVHSQEIIDAYHDAIPL-NRYGSEQEIAEAILFLCSERASFITGQV 231 Query: 244 VFVDGGY 250 + DGG+ Sbjct: 232 LAADGGF 238 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: 127 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: 250 Length adjustment: 24 Effective length of query: 234 Effective length of database: 226 Effective search space: 52884 Effective search space used: 52884 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