Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_047007388.1 AAW01_RS11455 SDR family oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_20240 (272 letters) >NCBI__GCF_001010925.1:WP_047007388.1 Length = 266 Score = 145 bits (367), Expect = 7e-40 Identities = 92/263 (34%), Positives = 142/263 (53%), Gaps = 12/263 (4%) Query: 18 RLKDKVVLLTGAAQ--GIGEAIVAAFASQQARLVISDIQAQ-KVEAVAAHWRERGADVHA 74 R K +++TG+ + G+G+ I+ AFA + A V+SD++ +V+ VA R+RGA V Sbjct: 3 RFTGKTIVVTGSGKEKGLGQGILQAFADEGANCVVSDVRLDDEVDGVADELRQRGAKVAT 62 Query: 75 LQADVSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPL--EMTEEDWRRCFAIDLDG 132 +Q DVS QA+ +A++ G +DV VN AG+ PL T ++W + A++L G Sbjct: 63 VQCDVSDAASCQALVAQALDHFGSVDVFVNNAGIGFKMKPLLDVDTADEWDQVLAVNLSG 122 Query: 133 AWYGCKAVLPQMIEQGVGS-IINIASVHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPK 191 A+Y +A M++ G G IINIAS + P Y +KHG++GLTRA +E Sbjct: 123 AFYCTQAAARAMVDAGKGGRIINIASQAAKTGFPHLPAYVSSKHGMVGLTRASAVELGAH 182 Query: 192 GVRVNAIAPGYIETQLNV---DYWN---GFADPHAERQRALDLHPPRRVGQPIEVAMTAV 245 G+ VNAI P ++ T L +Y++ GFA +P R G P + A + Sbjct: 183 GITVNAICPNHVTTGLGAQQNEYFSKLLGFAKVEDYLANMAAKNPMGRPGLPSDTAAACL 242 Query: 246 FLASDEAPFINASCITIDGGRSV 268 +LASDEA ++ + I GG + Sbjct: 243 WLASDEAVYVTGEALNISGGEEM 265 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: 172 Number of extensions: 13 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: 266 Length adjustment: 25 Effective length of query: 247 Effective length of database: 241 Effective search space: 59527 Effective search space used: 59527 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