Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate CCNA_01747 CCNA_01747 3-oxoacyl-(acyl-carrier protein) reductase
Query= SwissProt::Q8P3K4 (300 letters) >FitnessBrowser__Caulo:CCNA_01747 Length = 246 Score = 128 bits (322), Expect = 1e-34 Identities = 82/247 (33%), Positives = 127/247 (51%), Gaps = 14/247 (5%) Query: 57 LQGKRCLITAAGAGIGRESALACARAGAHVIATDIDAAALQALAAE-SDAITTQLLDVTD 115 L GK L+T A GIG A A GAHV+ + +AL L AE + +T + +++D Sbjct: 4 LTGKTALVTGATGGIGGAIARALHAQGAHVVLSGTRESALAELKAELGERASTVVANLSD 63 Query: 116 AAAITALVA-----AHGPFDVLFNCAGYVHQGSILDCDEPAWRRSFSINVDAMYYTCKAV 170 A + LVA A P D++ AG G I+ + W +N++ + +A Sbjct: 64 AEQVDGLVAKAEEAAGAPLDIVIANAGVTRDGLIVRMKDEDWDTVIKVNLEGYFRLSRAA 123 Query: 171 LPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQGVRCNAIC 230 GM++R G II ++S+ + G P + Y +KA +IG SKA+A + ++GV N + Sbjct: 124 AKGMMKRRAGRIIGITSIVG-VTGNPGQTNYAASKAGMIGFSKALAQELASRGVTVNCVA 182 Query: 231 PGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDESSFTTGQ 290 PG I +P AL ++A P G+LG+ +IA VYLASD++ + TGQ Sbjct: 183 PGFIASP----MTDALNEQQKA---GILSTIPAGKLGEGADIAAACVYLASDQAGYVTGQ 235 Query: 291 THIIDGG 297 T ++GG Sbjct: 236 TLHVNGG 242 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: 8 Number of successful extensions: 3 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: 246 Length adjustment: 25 Effective length of query: 275 Effective length of database: 221 Effective search space: 60775 Effective search space used: 60775 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