Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate PP_1946 PP_1946 Oxidoreductase, short chain dehydrogenase/reductase family
Query= SwissProt::Q8P3K4 (300 letters) >FitnessBrowser__Putida:PP_1946 Length = 262 Score = 139 bits (349), Expect = 9e-38 Identities = 91/259 (35%), Positives = 137/259 (52%), Gaps = 25/259 (9%) Query: 52 TPNTRLQGKRCLITAAGAGIGRESALACARAGAHV----IATDIDAAALQALAAESDAIT 107 T N GK L+T AG+GIGR +ALA A++GA V I+TD ++ + AE T Sbjct: 2 TVNYDFSGKVVLVTGAGSGIGRATALAFAQSGASVAVADISTDHGLKTVELVKAEGGEAT 61 Query: 108 TQLLDVTDAAAITAL----VAAHGPFDVLFNCAGY-VHQGSILDCDEPAWRRSFSINVDA 162 +DV ++ ++ VA +G D+ N AG + + + D WRR +N+ + Sbjct: 62 FFHVDVGSEPSVQSMLAGVVAHYGGLDIAHNNAGIEANIVPLAELDSDNWRRVIDVNLSS 121 Query: 163 MYYTCKAVLPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQ 222 ++Y K +P ML+RG G+I+N +S AS + G Y TK V+GL+KA A DY Q Sbjct: 122 VFYCLKGEIPLMLKRGGGAIVNTAS-ASGLIGGYRLSGYTATKHGVVGLTKAAAIDYANQ 180 Query: 223 GVRCNAICPGTIKTPSLGQRVQALGGDEQAVWKSFTDR----QPMGRLGDPREIAQLVVY 278 +R NA+CPG + +P L Q + DR P+GRL EIA+ V++ Sbjct: 181 NIRINAVCPGPVDSPFLADMPQPM-----------RDRLLFGTPIGRLATAEEIARSVLW 229 Query: 279 LASDESSFTTGQTHIIDGG 297 L SD++ + G + +DGG Sbjct: 230 LCSDDAKYVVGHSMSVDGG 248 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: 144 Number of extensions: 11 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: 262 Length adjustment: 26 Effective length of query: 274 Effective length of database: 236 Effective search space: 64664 Effective search space used: 64664 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