Align 4-oxalomesaconate tautomerase; Gallate degradation protein D; EC 5.3.2.8 (characterized)
to candidate 14894 b0769 hypothetical protein (NCBI)
Query= SwissProt::Q88JY0 (361 letters) >FitnessBrowser__Keio:14894 Length = 350 Score = 321 bits (822), Expect = 2e-92 Identities = 169/347 (48%), Positives = 224/347 (64%), Gaps = 4/347 (1%) Query: 5 RIPCLLMRGGTSKGAYFLHDDLPAPGPLRDRVLLAVMGSPDARQIDGIGGADSLTSKVAI 64 +IPC++MRGGTS+GA+ L + LP RD++L+A+MGS + +IDGIGG + LTSKVAI Sbjct: 3 KIPCVMMRGGTSRGAFLLAEHLPEDQTQRDKILMAIMGSGNDLEIDGIGGGNPLTSKVAI 62 Query: 65 IRASQRDDADVDYLFAQVVVDEARVDYGQNCGNILAGVGPFALERGLVAASGASTPVRIF 124 I S ADVDYLFAQV+V E RVD NCGN+L+GVG FA+E GL+AA+ T VRI Sbjct: 63 ISRSSDPRADVDYLFAQVIVHEQRVDTTPNCGNMLSGVGAFAIENGLIAATSPVTRVRIR 122 Query: 125 MENTGQIAVAQVPTADGQVEYAGDTRIDGVPGRAAALVVTFADVAGASCGALLPTGNSRD 184 NTG A V T +G VEY G RIDGVPG AA + +TF + AG G + PT N D Sbjct: 123 NVNTGTFIEADVQTPNGVVEYEGSARIDGVPGTAAPVALTFLNAAGTKTGKVFPTDNQID 182 Query: 185 CVEGVEVTCIDNGMPVVLLCAEDLGVTGYEPCETLEADSALKTRLEAIRLQLGPRMNLGD 244 + V VTCID MPVV++ AE LG TGYE L+AD AL R+E+IRLQ G M LGD Sbjct: 183 YFDDVPVTCIDMAMPVVIIPAEYLGKTGYELPAELDADKALLARIESIRLQAGKAMGLGD 242 Query: 245 VSQRNVPKMCLLSAPRNGGTVNTRSFIPHRCHASIGVFGAVSVATACLIEGSVAQGLAST 304 VS +PK L+S + GG +N R F+PH CH ++ + GA++++++C +EG+V + + + Sbjct: 243 VSNMVIPKPVLISPAQKGGAINVRYFMPHSCHRALAITGAIAISSSCALEGTVTRQIVPS 302 Query: 305 SGGDRQRLAVEHPSGEFTVEISLE--HGVIKGCGLVRTARLLFDGVV 349 G + +EHPSG V +S E ++RT R +F G V Sbjct: 303 VG--YGNINIEHPSGALDVHLSNEGQDATTLRASVIRTTRKIFSGEV 347 Lambda K H 0.320 0.138 0.412 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: 418 Number of extensions: 18 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: 361 Length of database: 350 Length adjustment: 29 Effective length of query: 332 Effective length of database: 321 Effective search space: 106572 Effective search space used: 106572 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: 49 (23.5 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