Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_047214213.1 PATSB16_RS11230 glucose 1-dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_20240 (272 letters) >NCBI__GCF_001931675.1:WP_047214213.1 Length = 255 Score = 141 bits (356), Expect = 1e-38 Identities = 92/250 (36%), Positives = 134/250 (53%), Gaps = 6/250 (2%) Query: 18 RLKDKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQ-AQKVEAVAAHWRERGADVHALQ 76 R+ D V L+TG+AQGIG AI A + A++V+ D Q A E A R G+D + Sbjct: 2 RMNDTVALVTGSAQGIGRAIAVRLAQEGAKIVVEDRQDADAAEQTLAQVRAAGSDGCVIA 61 Query: 77 ADVSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYG 136 +V D + + AV GRIDVLVN AGV LE++E D+ ++L GA++ Sbjct: 62 GNVGSVHDARGVVDAAVAKLGRIDVLVNNAGVERNAPFLEVSEADYDLVLDVNLKGAFFM 121 Query: 137 CKAVLPQMIEQGVGS-IINIASVHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRV 195 +AV+ + + G I+NI+SVH P Y +K G+ + R L IE AP G+ V Sbjct: 122 TQAVVRHLRDSHRGGRIVNISSVHEELPFPHFTSYCASKGGMKMMVRNLAIELAPLGITV 181 Query: 196 NAIAPGYIETQLNVDYWNGFADPHAERQRALDLHPPRRVGQPIEVAMTAVFLASDEAPFI 255 N +APG + T +N N AE L P +R+G+ +VA +FLASDEA ++ Sbjct: 182 NNVAPGAVGTAIN----NKLLHDPAELSALLANIPLKRLGKVEDVANAVLFLASDEASYV 237 Query: 256 NASCITIDGG 265 + + +DGG Sbjct: 238 TGTTVYVDGG 247 Lambda K H 0.321 0.137 0.419 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: 156 Number of extensions: 5 Number of successful extensions: 4 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: 272 Length of database: 255 Length adjustment: 25 Effective length of query: 247 Effective length of database: 230 Effective search space: 56810 Effective search space used: 56810 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 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