Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate AO353_28090 AO353_28090 dehydrogenase
Query= BRENDA::P31867 (318 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28090 Length = 316 Score = 191 bits (486), Expect = 2e-53 Identities = 111/269 (41%), Positives = 157/269 (58%), Gaps = 16/269 (5%) Query: 12 MPAVGFGCWKVDVDTCSEQIYRAIKTGYRLFDGAEDYANEKLVGAGVKKAIDEGIVKRED 71 MPAVGFG D+ ++ I A++TG+R FD AE Y NE VG +K+ ++ G V+RED Sbjct: 24 MPAVGFGTLFRDLSVTTQAIKHALETGFRHFDCAERYRNEDKVGVAIKEFLETGKVRRED 83 Query: 72 LFLTSKLWNNYHHPDNVEKALNRTLSDLQVDYVDLFLIHFPVTFKFVPLEEKYPPGFYCG 131 LF+T+KLWN H P+ V A + LQVDY+D +LIH P F F P E++ P Sbjct: 84 LFITTKLWNTNHRPERVLPAFEASCRRLQVDYIDCYLIHTP--FAFQPGEDQEPRD---E 138 Query: 132 KGDNFDYEDVPILETWKALEKLVKAGKIRSIGVSNFPGALLLDLLRGATIKPSVLQVEHH 191 +G V ++ETW+ALE+LV G+ +SIG+S+ L +++ A IKP+V+QVE H Sbjct: 139 QGRIIYDSGVTLIETWRALERLVDEGRCKSIGLSDITLQALQEIVAVARIKPAVVQVESH 198 Query: 192 PYLQQPRLIEFAQSRGIAVTAYSSFGPQSFVELNQGRALNTSPLFENETIKAIAAKHGKS 251 PYL + L+EF + GI V A F L G N + E+ I +A + ++ Sbjct: 199 PYLPEWELLEFCRQHGIIVLA--------FAPLGHGMQPN---VLEDAVITGVARRLQQT 247 Query: 252 PAQVLLRWSSQRGIAIIPKSNTVPRLLEN 280 PAQV L WS QRG+A + S T+ + EN Sbjct: 248 PAQVALAWSVQRGVAFLTTSATLSHIQEN 276 Lambda K H 0.320 0.139 0.423 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: 272 Number of extensions: 15 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: 318 Length of database: 316 Length adjustment: 27 Effective length of query: 291 Effective length of database: 289 Effective search space: 84099 Effective search space used: 84099 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 (21.8 bits) S2: 48 (23.1 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