Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_028996623.1 H537_RS0102440 3-oxoacyl-ACP reductase
Query= reanno::pseudo5_N2C3_1:AO356_20240 (272 letters) >NCBI__GCF_000430725.1:WP_028996623.1 Length = 245 Score = 157 bits (397), Expect = 2e-43 Identities = 92/250 (36%), Positives = 142/250 (56%), Gaps = 11/250 (4%) Query: 18 RLKDKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAQKVEAVAAHWRERGA-DVHALQ 76 R +DKV ++TGAA GIG A+ + AR++++D+ A K A R+ GA D A Sbjct: 2 RFQDKVAIVTGAASGIGLAVARRLGQEGARVLVADLDAGKAGAAVQQLRDDGAPDALAQA 61 Query: 77 ADVSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYG 136 DV++++ + A + ++ GR+DV+VN AG+ VF+ E T +DW R +DL GA++ Sbjct: 62 CDVAQEEQVAAAVQAVLQRWGRLDVVVNNAGLMVFKPLQEHTADDWMRVLCVDLMGAFFF 121 Query: 137 CKAVLPQMIEQGVGSIINIASVHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVN 196 + M + G+I+N++S+H+ P Y AK LL LTR+ IE KG+R N Sbjct: 122 TRQAFVHM--RPGGAIVNVSSIHAEETTPLVASYAAAKAALLSLTRSTAIEGKAKGIRAN 179 Query: 197 AIAPGYIETQLNVDYWNGFADPHAERQRALDLHPPRRVGQPIEVAMTAVFLASDEAPFIN 256 AI PG ++T + W A+P+ + ++ VGQP +VA FLASDEA F+ Sbjct: 180 AILPGAVDTPM---LW---ANPNL--KSGIETVSLADVGQPQDVAAAVAFLASDEAVFVQ 231 Query: 257 ASCITIDGGR 266 + + +DGGR Sbjct: 232 GAALRVDGGR 241 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: 140 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: 245 Length adjustment: 24 Effective length of query: 248 Effective length of database: 221 Effective search space: 54808 Effective search space used: 54808 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