Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_013402459.1 CALHY_RS02575 SDR family oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_20240 (272 letters) >NCBI__GCF_000166355.1:WP_013402459.1 Length = 255 Score = 145 bits (366), Expect = 8e-40 Identities = 87/252 (34%), Positives = 133/252 (52%), Gaps = 3/252 (1%) Query: 20 KDKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAQKV---EAVAAHWRERGADVHALQ 76 KDKVVL+TGA GIG +A A++ ++ + K E R+ G + +Q Sbjct: 4 KDKVVLITGATSGIGRTTAVLYAKYGAKVAVNGRELNKDKNGETTIDEIRKIGGECIFIQ 63 Query: 77 ADVSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYG 136 DVSK D Q + VE +G+ID+LVN AG+ + M+EED+ + A+++ GA+ Sbjct: 64 GDVSKNDDAQRIVMETVEKYGKIDILVNNAGIVLPGRVDNMSEEDFDKTMAVNVKGAFLV 123 Query: 137 CKAVLPQMIEQGVGSIINIASVHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVN 196 K + QM +QG G I+N+ASV + Y +K ++ LT+A+ +Y +RVN Sbjct: 124 SKYAVLQMKKQGKGVIVNVASVAALKGHTDRSAYSASKGAIVSLTKAMAADYVKDNIRVN 183 Query: 197 AIAPGYIETQLNVDYWNGFADPHAERQRALDLHPPRRVGQPIEVAMTAVFLASDEAPFIN 256 + PG T + DP A R + P R+G+P E+A +F + DEA F+N Sbjct: 184 CVCPGTTLTPAVEEKIVNAPDPEAMRAAFIARQPMGRLGRPEEIAFAILFASCDEAEFMN 243 Query: 257 ASCITIDGGRSV 268 S I IDGG ++ Sbjct: 244 GSIIVIDGGMTI 255 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: 157 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: 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