Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate BPHYT_RS16940 BPHYT_RS16940 short-chain dehydrogenase
Query= SwissProt::Q8P3K4 (300 letters) >FitnessBrowser__BFirm:BPHYT_RS16940 Length = 258 Score = 153 bits (386), Expect = 5e-42 Identities = 100/253 (39%), Positives = 136/253 (53%), Gaps = 11/253 (4%) Query: 56 RLQGKRCLITAAGAGIGRESALACARAGAHVIATDIDAAALQALAAESDAITTQLL---- 111 RL GK L+T AG GIG A A AR GA V+ ++D + A A T + Sbjct: 3 RLAGKVALVTGAGRGIGSAIAHAFAREGAAVVLAELDIETARQTAEHIKAQTGARVLAVH 62 Query: 112 -DVTDAAAITALVA----AHGPFDVLFNCAGYVHQGSILDCDEPAWRRSFSINVDAMYYT 166 DVT +A++ V+ A G DVL N AG L + WRR F++++D ++ Sbjct: 63 TDVTQSASVQHAVSEAERAFGALDVLVNNAGINVFCDPLTMTDDDWRRCFAVDLDGVWNG 122 Query: 167 CKAVLPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQGVRC 226 C+A LPGM+ERG GSI+N++S S K +P F Y V K VIGL++A+ +Y + VR Sbjct: 123 CRAALPGMVERGAGSIVNIAS-THSFKIIPGCFPYPVAKHGVIGLTRALGIEYAPRNVRV 181 Query: 227 NAICPGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDESSF 286 NAI PG I+T L D A ++ D QPM R+G P E+A V+LASDE+ F Sbjct: 182 NAIAPGYIET-QLTHDWWNEQADPAAAQQATLDLQPMKRIGRPEEVAMTAVFLASDEAPF 240 Query: 287 TTGQTHIIDGGWS 299 +DGG S Sbjct: 241 INATCITVDGGRS 253 Lambda K H 0.320 0.133 0.395 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: 147 Number of extensions: 8 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: 300 Length of database: 258 Length adjustment: 25 Effective length of query: 275 Effective length of database: 233 Effective search space: 64075 Effective search space used: 64075 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 Sep 17 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