Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate AO353_21495 AO353_21495 short-chain dehydrogenase
Query= SwissProt::Q8P3K4 (300 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21495 Length = 255 Score = 118 bits (296), Expect = 1e-31 Identities = 83/251 (33%), Positives = 127/251 (50%), Gaps = 15/251 (5%) Query: 57 LQGKRCLITAAGAGIGRESALACARAGAHVIATDIDAAALQ----ALAAESDAITTQLLD 112 L GK ++ A GIG A A+ GAHVI + Q A+ A+ T Sbjct: 9 LDGKIAFVSGASRGIGEAIAKLLAQQGAHVIVSSRKLDGCQHVADAIIADGGKATAVACH 68 Query: 113 VTDAAAITALVAA----HGPFDVLFNCAGYVHQG-SILDCDEPAWRRSFSINVDAMYYTC 167 + + IT + A+ G D+L N A Q ++LD D A++++ +N+ ++ Sbjct: 69 IGEMEQITQVFASIREQFGRLDILVNNAATNPQFCNVLDTDLGAFQKTVDVNIRGYFFMS 128 Query: 168 KAVLPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQGVRCN 227 M E G GSIIN++S+ G+ + +Y VTKAAVI ++K A + G+RCN Sbjct: 129 VEAGKLMRENGGGSIINVASINGISPGI-FQGIYSVTKAAVINMTKVFAKECAQFGIRCN 187 Query: 228 AICPGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDESSFT 287 A+ PG T V+ A+ K+ + P+ R+ DP E+A V+YLASD SS+T Sbjct: 188 ALLPGLTDTKFASALVK-----NDAILKTALQQIPLKRVADPSEMAGAVLYLASDASSYT 242 Query: 288 TGQTHIIDGGW 298 TG + +DGG+ Sbjct: 243 TGVSLNVDGGF 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: 162 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: 255 Length adjustment: 25 Effective length of query: 275 Effective length of database: 230 Effective search space: 63250 Effective search space used: 63250 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