Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate GFF846 HP15_825 short-chain dehydrogenase/reductase SDR
Query= SwissProt::Q8P3K4 (300 letters) >FitnessBrowser__Marino:GFF846 Length = 256 Score = 117 bits (293), Expect = 3e-31 Identities = 86/251 (34%), Positives = 129/251 (51%), Gaps = 15/251 (5%) Query: 57 LQGKRCLITAAGAGIGRESALACARAGAHVIATD--ID-----AAALQALAAESDAITTQ 109 L GK LIT A GIG A A GAHVI + ID A++++ ++A Sbjct: 9 LTGKVALITGASRGIGESIARTLAEYGAHVIVSSRKIDGCEAVASSIRDAGGSAEAYACH 68 Query: 110 LLDVTDAAAITALV-AAHGPFDVLFN-CAGYVHQGSILDCDEPAWRRSFSINVDAMYYTC 167 + D+ +I A + HG D+L N A + G + D D A+ ++ +N+ ++ C Sbjct: 69 IGDMDQIESIWAHIDQTHGKLDILVNNAAANPYFGPVEDTDLGAFNKTVDVNIRGYFFMC 128 Query: 168 KAVLPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQGVRCN 227 M + G GSI+N++SV + + + +Y VTKAAVI ++K+ A + Q +R N Sbjct: 129 ARGAQMMKKAGGGSIVNVASV-NGVNPGHYQGIYSVTKAAVISMTKSFAMELGQQKIRVN 187 Query: 228 AICPGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDESSFT 287 A+ PG T + AL +E A+ K PM R+ DP E+A V+YL SD SS+T Sbjct: 188 ALLPGLTDT----KFASALTTNE-AIKKQAMAHIPMKRVADPGEMAGTVLYLVSDASSYT 242 Query: 288 TGQTHIIDGGW 298 TG DGG+ Sbjct: 243 TGACINADGGY 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: 156 Number of extensions: 12 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: 256 Length adjustment: 25 Effective length of query: 275 Effective length of database: 231 Effective search space: 63525 Effective search space used: 63525 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