Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_008538620.1 HMPREF9454_RS06290 3-oxoacyl-[acyl-carrier-protein] reductase
Query= reanno::pseudo5_N2C3_1:AO356_20240 (272 letters) >NCBI__GCF_000245775.1:WP_008538620.1 Length = 247 Score = 130 bits (328), Expect = 2e-35 Identities = 85/250 (34%), Positives = 127/250 (50%), Gaps = 11/250 (4%) Query: 19 LKDKVVLLTGAAQGIGEAIVAAFASQQARLVISDI-QAQKVEAVAAHWRERGADVHALQA 77 L KV L+TGA++GIG A+ A + A + I+ E V + G +QA Sbjct: 3 LDGKVALVTGASRGIGRAVAIELAKEGATVAINYAGNVAAAEEVKNIITDMGGKAMIVQA 62 Query: 78 DVSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPL--EMTEEDWRRCFAIDLDGAWY 135 DVS +Q M + + G+ID+LVN AG+ RD L M +DW +L G + Sbjct: 63 DVSDEQAASEMVEKVIAEFGQIDILVNNAGIT--RDGLFIRMKSQDWNAVINTNLTGIFN 120 Query: 136 GCKAVLPQMIEQGVGSIINIASVHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRV 195 K M+++ G IIN+ SV G Y AK G++G T++L E A +G+ V Sbjct: 121 CTKVAAKYMMKKRSGKIINMTSVSGIMGNIGQTNYSAAKAGVIGFTKSLAREMASRGITV 180 Query: 196 NAIAPGYIETQLNVDYWNGFADPHAERQRALDLHPPRRVGQPIEVAMTAVFLASDEAPFI 255 NA+APG+I T + A P + + + P ++GQP ++A VFLASD+A +I Sbjct: 181 NAVAPGFIATDMTA------AMPEKAQAQVVGSIPLGKMGQPEDIANAVVFLASDKASYI 234 Query: 256 NASCITIDGG 265 + +DGG Sbjct: 235 TGQVVNVDGG 244 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: 135 Number of extensions: 8 Number of successful extensions: 5 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: 247 Length adjustment: 24 Effective length of query: 248 Effective length of database: 223 Effective search space: 55304 Effective search space used: 55304 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