Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate AZOBR_RS28175 AZOBR_RS28175 short-chain dehydrogenase
Query= reanno::Korea:Ga0059261_1894 (259 letters) >FitnessBrowser__azobra:AZOBR_RS28175 Length = 251 Score = 134 bits (338), Expect = 1e-36 Identities = 86/245 (35%), Positives = 129/245 (52%), Gaps = 4/245 (1%) Query: 16 LKGKRVLVTGGGSGIGAGIVEGFARQGADVTFFDIAGAESQLLVERLSADGHKACFERVD 75 + G LVTGG SGIG FA+ GA AE V+ + G +A F + D Sbjct: 4 MSGGVALVTGGTSGIGRATALAFAKAGATAIVTGRREAEGLETVDLVRQAGGRAVFVQAD 63 Query: 76 LTDVASLQAVIARLIKGAGGFDILVNNAANDDRHAIDEITEAYWDERLSVNLKHIFFCAQ 135 + D + A+ AR+ + G D NNA ++ + TEA +D ++VN+K ++ C + Sbjct: 64 VADAEEVAALFARIERDHGRLDYAFNNAGIHFGRSVADTTEADFDRMVAVNIKGVWLCLK 123 Query: 136 AVVPAMRARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGIRATCV 195 +P M +G GAIV+ GS+ +GL+ +Y KAA+EG+TRS+A ++ + G+R V Sbjct: 124 HELPIMLRQGKGAIVSTGSVLGQIGLAGNSVYSASKAAVEGMTRSVAIEVAKSGVRVNAV 183 Query: 196 IPGNVRTPRQLKWYSPEGEAEIVAAQCLD--GRLA-PEDVAAMVLFLASDDARLVTGHSY 252 P ++TP + E EA A L GR+ P +VA V++L SD A +TG S Sbjct: 184 CPAIIQTPMSAGSFGGE-EAVNAALGPLHPVGRVGQPREVADTVVWLCSDAASFITGQSI 242 Query: 253 FVDAG 257 VD G Sbjct: 243 NVDGG 247 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: 138 Number of extensions: 12 Number of successful extensions: 2 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: 251 Length adjustment: 24 Effective length of query: 235 Effective length of database: 227 Effective search space: 53345 Effective search space used: 53345 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