Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate AO353_23170 AO353_23170 short-chain dehydrogenase
Query= reanno::Korea:Ga0059261_1894 (259 letters) >FitnessBrowser__pseudo3_N2E3:AO353_23170 Length = 254 Score = 139 bits (349), Expect = 8e-38 Identities = 91/246 (36%), Positives = 125/246 (50%), Gaps = 5/246 (2%) Query: 16 LKGKRVLVTGGGSGIGAGIVEGFARQGADVTFFDIAGAESQLLVERLSADGHKACFERVD 75 L+G+RVLVTGG G+G + R GA V DI Q L A+G VD Sbjct: 8 LEGRRVLVTGGARGLGYAFAQAIGRAGAHVVIADILAERVQQSAAELVAEGLTVHGVAVD 67 Query: 76 LTDVASLQAVIARLIKGAGGFDILVNNAA--NDDRHAIDEITEAYWDERLSVNLKHIFFC 133 L S+ +A + GG D LVNNA+ N +E++ WD+ + VN++ + Sbjct: 68 LAQPDSIDTCVAETTRLLGGLDGLVNNASITNSGGKTCEELSLDTWDQVMHVNVRGTWLM 127 Query: 134 AQAVVPAMRARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGIRAT 193 +A +PA+RA G GAIVNL S + G +L+ Y K AI +TRSLAR+LG D I Sbjct: 128 TKACLPALRASGHGAIVNLASDTPLWGAPNLLAYVASKGAIIAMTRSLARELGTDNITVN 187 Query: 194 CVIPGNVRTPRQLKWYSPEGEAEIVAAQ-CLDGRLAPEDVAAMVLFLASDDARLVTGHSY 252 + PG V + Y PE + Q + PEDV+ VLF SD AR +TG + Sbjct: 188 AIAPGLVLV--EATAYVPEARHRLYNEQRAIQRPQLPEDVSGAVLFALSDLARFITGQTL 245 Query: 253 FVDAGW 258 V+ G+ Sbjct: 246 PVNGGF 251 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: 183 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: 259 Length of database: 254 Length adjustment: 24 Effective length of query: 235 Effective length of database: 230 Effective search space: 54050 Effective search space used: 54050 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