Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate Pf1N1B4_4153 Glucose 1-dehydrogenase (EC 1.1.1.47)
Query= reanno::pseudo1_N1B4:Pf1N1B4_412 (272 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4153 Length = 254 Score = 130 bits (328), Expect = 2e-35 Identities = 88/251 (35%), Positives = 127/251 (50%), Gaps = 16/251 (6%) Query: 21 NKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVVAIKADVS 80 +KV L+TGAA GIG+AI ++ A+++ DI E V+ +A +V + AD++ Sbjct: 14 DKVALVTGAASGIGQAIALLLHARGAKVIAEDINPE-VQALAR------PGLVPLVADIT 66 Query: 81 RQQDLHAMARLAIELHGRIDVLVNCAGVNVFRDPLQMTEEDWHRCFAIDLDGAWYGCKAV 140 + LA+E GR+D+LVN AG+ + + + MT EDW R A++ A+ + Sbjct: 67 QDGAAERAVALAVEQFGRLDILVNNAGIIINKLVIDMTREDWERIQAVNATAAFLHSREA 126 Query: 141 LPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVNAIAP 200 + M+ GSI+NIAS S P Y +K L LTR L +E GIRVNA+ Sbjct: 127 VKAMMPNKSGSIVNIASYASYFAFPTIAAYTASKGALAQLTRTLALEVIGHGIRVNAVGV 186 Query: 201 GYIETQL---NVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPFINA 257 G + T + VD F H E P R QP E+A F+ASD A F+ Sbjct: 187 GDVVTNILNHVVDDGPAFLAQHGEAA------PIGRAAQPEEIAEVVAFIASDRASFMVG 240 Query: 258 SCITIDGGRSV 268 S + DGG +V Sbjct: 241 SVVMADGGMTV 251 Lambda K H 0.321 0.138 0.424 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: 151 Number of extensions: 9 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: 272 Length of database: 254 Length adjustment: 25 Effective length of query: 247 Effective length of database: 229 Effective search space: 56563 Effective search space used: 56563 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 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