Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_077275131.1 BW732_RS01515 glucose 1-dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_20240 (272 letters) >NCBI__GCF_001998885.1:WP_077275131.1 Length = 261 Score = 139 bits (351), Expect = 5e-38 Identities = 91/256 (35%), Positives = 141/256 (55%), Gaps = 14/256 (5%) Query: 19 LKDKVVLLTGAAQGIGEAIVAAFASQQARLVI---SDIQA--QKVEAVAAHWRERGADVH 73 L KV ++TG ++GIG AI ++ ++V+ SD Q VEAV A G D Sbjct: 5 LNGKVAVITGGSKGIGTAISERLGKEKMKVVVNYHSDEAGANQAVEAVKA----AGGDGI 60 Query: 74 ALQADVSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGA 133 A+QA+V ++ +Q + A+ +G +D+ +N AG+ + ++ EDW R ++L G Sbjct: 61 AVQANVGSEEGVQKLVDVALSEYGTLDLWINNAGMENQCETHKLPLEDWERVINVNLTGV 120 Query: 134 WYGCKAVLPQMIEQGV-GSIINIASVHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKG 192 + G KA L +E G+IINI+SVH P Y +K G+ LT + +EYA + Sbjct: 121 FLGTKAALSYFVENNKKGNIINISSVHEQIPWPTFAHYSASKGGVKLLTETVAMEYANRN 180 Query: 193 VRVNAIAPGYIETQLNVDYWNGFADPHAERQRALDLHPPRRVGQPIEVAMTAVFLASDEA 252 +RVN I PG I+T +N + FADP + Q + P +R+G P EVA A +LASDEA Sbjct: 181 IRVNNIGPGAIKTPINAE---KFADPE-QLQTTKETIPMQRIGNPEEVAAAAAWLASDEA 236 Query: 253 PFINASCITIDGGRSV 268 ++ + +DGG ++ Sbjct: 237 SYVTGITLFVDGGMTL 252 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: 154 Number of extensions: 6 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: 261 Length adjustment: 25 Effective length of query: 247 Effective length of database: 236 Effective search space: 58292 Effective search space used: 58292 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