Align L-fucose dehydrogenase (EC 1.1.1.122) (characterized)
to candidate WP_011650309.1 RL_RS02715 aldo/keto reductase
Query= reanno::BFirm:BPHYT_RS34225 (346 letters) >NCBI__GCF_000009265.1:WP_011650309.1 Length = 339 Score = 275 bits (703), Expect = 1e-78 Identities = 150/303 (49%), Positives = 188/303 (62%) Query: 13 RRIGRGPLQVTGLGLGTAPLGGLYRDLSDEEAHATIAAAWDAGVRYFDTAPHYGNTKAEH 72 RRIG+ L+VT + G A LGGLYR E A T+ AAWD+G+RYFD AP YG AE Sbjct: 4 RRIGKTKLEVTEISFGAAALGGLYRACPREVAMDTLQAAWDSGIRYFDVAPWYGLGLAER 63 Query: 73 RLGDALRRYPRADYVLSTKVGRRFVPRTTPFDDKEGWQNPLPFEAIYDYTHDGILRSFED 132 R+GD LR P YVLSTKVGR P T + +PL F+A YDY++DGI+RS E Sbjct: 64 RVGDFLRDQPDGSYVLSTKVGRLLRPVPTGTVPDYSYVDPLSFDADYDYSYDGIMRSVEF 123 Query: 133 SQQRLGIVDIDILLVHDIGRVTHGDNHPHYWRQLTEGGGFRALDALRSSGAIKAVGLGVN 192 S RLG+ IDIL VHD+G THG ++ G +AL+ L+SSGAI A GLGVN Sbjct: 124 SYARLGLNRIDILYVHDLGVYTHGAAKNAVHQKQFLDSGVKALEELKSSGAISAFGLGVN 183 Query: 193 EGAAILDAMAEFDIDCALLAGRYTLLEQTTLDDLLPACEKRGVSILLGGAFNSGILARGV 252 E LD D+DC LLAGRYTLL+++ + +LLP C ++G S+++GG FNSGILA G Sbjct: 184 EVPVCLDVTRHSDLDCILLAGRYTLLDRSAVAELLPLCREKGTSLVVGGVFNSGILATGP 243 Query: 253 QGDLKFNYGEAPPEVIERVARLEAVCRTHGVPLAAAALQFPYAHPTVATVLTGARSADEL 312 F+Y A +V+ +V +EA+ HGVPLAA ALQFP VA+VL G L Sbjct: 244 VPGSHFDYMPADDDVLAKVGAMEAIANRHGVPLAAPALQFPLREAIVASVLIGTAKPSSL 303 Query: 313 REN 315 N Sbjct: 304 TRN 306 Lambda K H 0.320 0.139 0.421 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: 311 Number of extensions: 9 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: 346 Length of database: 339 Length adjustment: 29 Effective length of query: 317 Effective length of database: 310 Effective search space: 98270 Effective search space used: 98270 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: 49 (23.5 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