Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate WP_043920347.1 jaqu_RS17725 SDR family oxidoreductase
Query= SwissProt::Q8P3K4 (300 letters) >NCBI__GCF_000877395.1:WP_043920347.1 Length = 251 Score = 145 bits (365), Expect = 1e-39 Identities = 91/257 (35%), Positives = 139/257 (54%), Gaps = 12/257 (4%) Query: 47 VSIPTTPNTRLQGKRCLITAAGAGIGRESALACARAGAHVIATDIDAAALQALAAE---- 102 + +P TP+ RL+G+R + G+G A+A A AGA V+ A A++A AA Sbjct: 1 MDLPRTPSFRLEGRRAFVPGGSRGLGLGCAVALAEAGAEVVIAARSADAVEAAAAAMREA 60 Query: 103 SDAITTQLLDVTDAAAITALVAAHGPFDVLFNCAGYVHQGSILDCDEPAWRRSFSINVDA 162 A T LDVTD AA+ A + PFD+L N AG G L+ + + ++N+ A Sbjct: 61 GHAATGVALDVTDLAAVDAFLDGEAPFDILCNAAGVARHGPALETEPDDFDAVAALNLRA 120 Query: 163 MYYTCKAVLPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQ 222 Y+ + V GM +RG GSII +SS + GV +R VY TK V G++KA+A ++ + Sbjct: 121 AYFLAQRVARGM-DRG-GSIIQISSQMGHVGGV-DRAVYCATKHGVEGMTKAMAIEWGPR 177 Query: 223 GVRCNAICPGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASD 282 +R N ICP I+TP E+ W ++ + R+G+ +I VV+LAS+ Sbjct: 178 DIRVNTICPTFIRTP---LTAATFADPERRAW--IDEKIKLPRVGEVEDIMGAVVFLASE 232 Query: 283 ESSFTTGQTHIIDGGWS 299 S+ TG + ++DGGW+ Sbjct: 233 ASAMVTGTSLLVDGGWT 249 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: 166 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: 251 Length adjustment: 25 Effective length of query: 275 Effective length of database: 226 Effective search space: 62150 Effective search space used: 62150 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 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