Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate WP_009780934.1 MED217_RS12720 SDR family oxidoreductase
Query= reanno::Korea:Ga0059261_1894 (259 letters) >NCBI__GCF_000152985.1:WP_009780934.1 Length = 246 Score = 127 bits (320), Expect = 2e-34 Identities = 79/238 (33%), Positives = 127/238 (53%), Gaps = 5/238 (2%) Query: 22 LVTGGGSGIGAGIVEGFARQGADVTFFDIAGAESQLLVERLSADGHKACFERVDLTDVAS 81 +VTGG SG+G I F G V I G + + G DL ++ + Sbjct: 7 VVTGGNSGLGYAIARKFCDAGYKVY---IIGRNEEKTRQAADNLGELVVPIVFDLNNLEA 63 Query: 82 LQAVIARLIKGAGGFDILVNNAANDDRHAIDEITEAYWDERLSVNLKHIFFCAQAVVPAM 141 + +I L++ G D+LVNNA + + E+T+A +D L N+K +F ++ VV +M Sbjct: 64 IPKLIDELLQATGKIDVLVNNAGINMKKDFAEVTDAEFDRILHTNVKSVFAISREVVKSM 123 Query: 142 RARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGIRATCVIPGNVR 201 + GG+IVN+ S++ G+ ++ Y K AIEG+TR++A DL + IR CV PG ++ Sbjct: 124 KGNYGGSIVNISSMAAQYGIPQVIAYTASKTAIEGMTRAMAVDLAQYNIRVNCVAPGFIK 183 Query: 202 TPRQLK-WYSPEGEAEIVAAQCLDGRL-APEDVAAMVLFLASDDARLVTGHSYFVDAG 257 TP K S + + V ++ G++ APED+A V +LA +++ +TG VD G Sbjct: 184 TPMTAKALNSDKQRKDRVFSRTPMGKMGAPEDIADAVFYLAGKESKFITGTVLCVDGG 241 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: 136 Number of extensions: 6 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: 246 Length adjustment: 24 Effective length of query: 235 Effective length of database: 222 Effective search space: 52170 Effective search space used: 52170 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: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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