Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_078715956.1 B5D49_RS01965 3-oxoacyl-[acyl-carrier-protein] reductase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >NCBI__GCF_900167125.1:WP_078715956.1 Length = 247 Score = 112 bits (281), Expect = 6e-30 Identities = 77/244 (31%), Positives = 120/244 (49%), Gaps = 7/244 (2%) Query: 23 VVLLTGAAQGIGEAIVAAFASQQARLVISDI-QAEKVETVAAHWRERGADVHALKADVSN 81 V L+TG ++GIG A A+ + ++ + + E ETV + G A++ D S+ Sbjct: 7 VALVTGGSRGIGRACAERLAADGFEVWLTYVSKPEAAETVVQTIADAGGTARAVQLDSSD 66 Query: 82 QQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGCKAVL 141 ++ + + + ++ + LVN AG+ + M EDW I+L GA+ + Sbjct: 67 REAVASFFKDEIKGKVHLAALVNNAGITRDGLLIRMKPEDWDSVLDINLTGAFSCLQEAA 126 Query: 142 PQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNAIAPG 201 M Q GSIINI+S G Y AK GL+GLT+A E A +GVRVNA+APG Sbjct: 127 KIMARQRGGSIINISSVVGQMGNAGQANYVAAKAGLIGLTKAAARELAGRGVRVNAVAPG 186 Query: 202 YIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFINASCIT 261 +IET + D P + + P R+G P ++A FLA + A +I + Sbjct: 187 FIETDMTKDL------PEKTVESMKTMIPLSRLGSPGDIAAAVSFLAGNGAGYITGQVLA 240 Query: 262 IDGG 265 ++GG Sbjct: 241 VNGG 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: 143 Number of extensions: 4 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: 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 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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