Align Short-chain dehydrogenase (characterized, see rationale)
to candidate 8501727 DvMF_2444 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__Miya:8501727 Length = 306 Score = 94.7 bits (234), Expect = 2e-24 Identities = 88/284 (30%), Positives = 123/284 (43%), Gaps = 46/284 (16%) Query: 5 LQDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGL----------- 53 L +V +VTGGA GIG I L A G + A + D + A L G Sbjct: 25 LAGRVALVTGGAQGIGRGIVEHLLACG---MRVAAMDADAEALAELAGALSAELAAEPVA 81 Query: 54 --------------QPRAALFQL-----ELQDEARCGEAVAETVRRFGRLDGLVNNAGVN 94 P + F + + D+A VA TV RFG L LVNNAG+ Sbjct: 82 DNEASLPAHPDASAAPHSPTFPMLTLHGSVADQADADRCVAATVARFGGLHLLVNNAGIA 141 Query: 95 -------DSVGLDAGRNEFVASLERNLIHYYVMAHYCVPHLKATRGAILNVSSKTALTGQ 147 D +D R + + L+ NL M VPHL+A RGA++N++S A+ + Sbjct: 142 NPHSGPADVAAMDMDRWQHM--LDVNLTGPMRMVRAAVPHLRAARGAVVNIASTRAVQSE 199 Query: 148 GNTSGYCASKGAQLSLTREWAAALRDDGVRVNALIPAEVMTPLYEKWIATFENPQEKLDA 207 +T Y ASKG ++LT A +L + V VN + P + K A DA Sbjct: 200 PHTEAYAASKGGLVALTHALAVSLGPE-VPVNCISPGWIEVRHLRK--AAHRETPVHTDA 256 Query: 208 ITSKIPLGKRFTTSEEMADMAVFLLSGRSSHTTGQWVFVDGGYT 251 ++ P+G R T ++A + FL + TGQ VDGG T Sbjct: 257 DRAQHPVG-RVGTVRDVAALVAFLAGDDAGFVTGQNWLVDGGMT 299 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: 182 Number of extensions: 12 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: 306 Length adjustment: 26 Effective length of query: 232 Effective length of database: 280 Effective search space: 64960 Effective search space used: 64960 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