Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate SMc02034 SMc02034 oxidoreductase
Query= SwissProt::Q8P3K4 (300 letters) >FitnessBrowser__Smeli:SMc02034 Length = 257 Score = 145 bits (365), Expect = 1e-39 Identities = 93/256 (36%), Positives = 139/256 (54%), Gaps = 21/256 (8%) Query: 57 LQGKRCLITAAGAGIGRESALACARAGAHVIATDIDA----AALQALAAESDAITTQLLD 112 L G+ ++T AG GIG A A AGA V+ TDI A A ALAA+ + T L+D Sbjct: 8 LSGRVAVVTGAGQGIGLACAEALCEAGAAVVLTDISAERCEAGRAALAAKGYVVETDLID 67 Query: 113 VTDAAAITA----LVAAHGPFDVLFNCAGYVHQG----SILDCDEPAWRRSFSINVDAMY 164 + D+A++ A L + D+L AG H G + D D W R IN+ + Sbjct: 68 IGDSASVNAVADRLAVSGRAADILVANAGIAHAGVPAEELSDAD---WERMIGINLSGAF 124 Query: 165 YTCKAVLPGMLERGRGSIINMSSVASSIKGVPNRFV-YGVTKAAVIGLSKAIAADYVAQG 223 +C+A ML +GRGSI+ + S++ +I P + V Y KA V L++++AA++ A+G Sbjct: 125 RSCRAFGRHMLAKGRGSIVTIGSMSGTIVNRPQQQVHYNAAKAGVHHLTRSLAAEWAARG 184 Query: 224 VRCNAICPGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDE 283 VR N++ P I TP L +++ +++ + D PM RLG P EIA +V++LASD Sbjct: 185 VRVNSVAPTYIDTPLL-----TFAKEDKPMYEQWLDMTPMHRLGQPDEIASVVLFLASDA 239 Query: 284 SSFTTGQTHIIDGGWS 299 SS TG D G++ Sbjct: 240 SSLMTGSIVAADAGYT 255 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: 171 Number of extensions: 9 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: 257 Length adjustment: 25 Effective length of query: 275 Effective length of database: 232 Effective search space: 63800 Effective search space used: 63800 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