Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate WP_078715956.1 B5D49_RS01965 3-oxoacyl-[acyl-carrier-protein] reductase
Query= reanno::Burk376:H281DRAFT_00644 (263 letters) >NCBI__GCF_900167125.1:WP_078715956.1 Length = 247 Score = 94.7 bits (234), Expect = 2e-24 Identities = 76/249 (30%), Positives = 113/249 (45%), Gaps = 18/249 (7%) Query: 17 VSAGAAGIGLAIAEAFIEAQAEVYICDVNQAAIDEATSRFPKLHAGIA-----DVSKQAQ 71 V+ G+ GIG A AE EV++ V++ E + G A D S + Sbjct: 10 VTGGSRGIGRACAERLAADGFEVWLTYVSKPEAAETVVQTIADAGGTARAVQLDSSDREA 69 Query: 72 VDQIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFYFLRKAVPV 131 V D + L LVNNAGI G + + P W+S + NL F L++A + Sbjct: 70 VASFFKDEIKGKVHLAALVNNAGITRD-GLLIRMKPEDWDSVLDINLTGAFSCLQEAAKI 128 Query: 132 LKETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVRVNAILPGV 191 + SII +SSV G++G + Y + K ++GL K+ A EL VRVNA+ PG Sbjct: 129 MARQRG-GSIINISSVVGQMGNAGQANYVAAKAGLIGLTKAAARELAGRGVRVNAVAPGF 187 Query: 192 VEGERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALFLASPAGSNVTG 251 +E + +P + E I L R+ + DIAA FLA +TG Sbjct: 188 IETDM----------TKDLPEKTV-ESMKTMIPLSRLGSPGDIAAAVSFLAGNGAGYITG 236 Query: 252 QAISVDGNV 260 Q ++V+G + Sbjct: 237 QVLAVNGGM 245 Lambda K H 0.318 0.134 0.375 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: 109 Number of extensions: 7 Number of successful extensions: 2 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: 263 Length of database: 247 Length adjustment: 24 Effective length of query: 239 Effective length of database: 223 Effective search space: 53297 Effective search space used: 53297 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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