Align L-arabinose 1-dehydrogenase (NAD(P)(+)); D-galactose 1-dehydrogenase; EC 1.1.1.376; EC 1.1.1.120; EC 1.1.1.48 (characterized)
to candidate Echvi_1123 Echvi_1123 Predicted dehydrogenases and related proteins
Query= SwissProt::Q53TZ2 (309 letters) >FitnessBrowser__Cola:Echvi_1123 Length = 343 Score = 85.5 bits (210), Expect = 2e-21 Identities = 59/183 (32%), Positives = 92/183 (50%), Gaps = 9/183 (4%) Query: 1 MSDQVSLGVVGIGKIARDQHLPAIDAEPGFKLTACASRHAEVT-----GVRNYRDLRALL 55 M+ + G+VG G++A+ H P I EP LTA RH + + V YR L ALL Sbjct: 1 MTQPLKTGLVGFGRVAQTMHAPLIHQEPLLDLTAVVERHHQKSKEKYPAVTVYRSLEALL 60 Query: 56 AAERELDAVSLCAPPQVRYAQARAALEAGKHVMLEKPPGATLGEVAVLEALARERGLTLF 115 A E ++D + +C P + ++QA+ ALEAGKHV+++KP + E L +LA+ +G L Sbjct: 61 A-EADVDLIVICTPNEYHFSQAKMALEAGKHVVVDKPITVSSSEAEALLSLAKSKGKLLS 119 Query: 116 ATWHSRCASAVEPAREWLATRAI-RAVQVRWKEDVRRWHPGQQWIWE--PGGLGVFDPGI 172 A + R + + L + R V D R P + W + PG ++D G Sbjct: 120 AFQNRRWDGDFQTITKLLHEGTLGRIVHFESHFDRFRPEPTENWREQQVPGSGILYDLGA 179 Query: 173 NAL 175 + + Sbjct: 180 HLI 182 Lambda K H 0.321 0.136 0.421 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: 220 Number of extensions: 11 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: 309 Length of database: 343 Length adjustment: 28 Effective length of query: 281 Effective length of database: 315 Effective search space: 88515 Effective search space used: 88515 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: 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