Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate 8501727 DvMF_2444 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= reanno::Korea:Ga0059261_1894 (259 letters) >FitnessBrowser__Miya:8501727 Length = 306 Score = 94.7 bits (234), Expect = 2e-24 Identities = 92/286 (32%), Positives = 119/286 (41%), Gaps = 36/286 (12%) Query: 5 AAASAAAVYPSLKGKRVLVTGGGSGIGAGIVEGFARQGADVTFFD--------IAGAESQ 56 AA +A +P L G+ LVTGG GIG GIVE G V D +AGA S Sbjct: 15 AARPLSAAHP-LAGRVALVTGGAQGIGRGIVEHLLACGMRVAAMDADAEALAELAGALSA 73 Query: 57 LLVERLSADG--------------HKACFERVDL----TDVASLQAVIARLIKGAGGFDI 98 L AD H F + L D A +A + GG + Sbjct: 74 ELAAEPVADNEASLPAHPDASAAPHSPTFPMLTLHGSVADQADADRCVAATVARFGGLHL 133 Query: 99 LVNNAANDDRHA----IDEITEAYWDERLSVNLKHIFFCAQAVVPAMRARGGGAIVNLGS 154 LVNNA + H+ + + W L VNL +A VP +RA GA+VN+ S Sbjct: 134 LVNNAGIANPHSGPADVAAMDMDRWQHMLDVNLTGPMRMVRAAVPHLRA-ARGAVVNIAS 192 Query: 155 ISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGIRATCVIPG--NVRTPRQLKWYSPE 212 Y K + LT +LA LG + + C+ PG VR R+ Sbjct: 193 TRAVQSEPHTEAYAASKGGLVALTHALAVSLGPE-VPVNCISPGWIEVRHLRKAAHRETP 251 Query: 213 GEAEIVAAQCLDGRLAP-EDVAAMVLFLASDDARLVTGHSYFVDAG 257 + AQ GR+ DVAA+V FLA DDA VTG ++ VD G Sbjct: 252 VHTDADRAQHPVGRVGTVRDVAALVAFLAGDDAGFVTGQNWLVDGG 297 Lambda K H 0.321 0.137 0.409 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: 158 Number of extensions: 14 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: 259 Length of database: 306 Length adjustment: 26 Effective length of query: 233 Effective length of database: 280 Effective search space: 65240 Effective search space used: 65240 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 (21.9 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