Align 4-oxalomesaconate tautomerase; Gallate degradation protein D; EC 5.3.2.8 (characterized)
to candidate Pf1N1B4_4463 FIG00958979: hypothetical protein
Query= SwissProt::Q88JY0 (361 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4463 Length = 360 Score = 323 bits (828), Expect = 4e-93 Identities = 176/348 (50%), Positives = 225/348 (64%), Gaps = 3/348 (0%) Query: 5 RIPCLLMRGGTSKGAYFLHDDLPAPGPLRDRVLLAVMGSPDARQIDGIGGADSLTSKVAI 64 RIPC+LMRGGTSKG FL DLP RD +LLAVMGS +IDGIGG TSKVAI Sbjct: 3 RIPCVLMRGGTSKGPVFLAWDLPVSIEERDELLLAVMGSGHELEIDGIGGGSPQTSKVAI 62 Query: 65 IRASQRDDADVDYLFAQVVVDEARVDYGQNCGNILAGVGPFALERGLVAASGASTPVRIF 124 + S DADVDYLF QV+V + RVD NCGN+L VGPFA+E+GLV A G T VRI Sbjct: 63 VSPSLHPDADVDYLFVQVMVSQRRVDTAPNCGNMLCAVGPFAIEQGLVKAVGELTRVRIR 122 Query: 125 MENTGQIAVAQVPTADGQVEYAGDTRIDGVPGRAAALVVTFADVAGASCGALLPTGNSRD 184 NTG + V T +G+V Y GDT IDGVPG AA + +TF D AG+ G L PTG+++D Sbjct: 123 NLNTGTFVTSDVQTPNGKVSYEGDTAIDGVPGSAAPVQLTFLDAAGSKTGKLFPTGSTQD 182 Query: 185 CVEGVEVTCIDNGMPVVLLCAEDLGVTGYEPCETLEADSALKTRLEAIRLQLGPRMNLGD 244 + + VTCID MP++++ A LG G E L+AD RLEA+RL+ G M LGD Sbjct: 183 WFDDIPVTCIDMAMPMLIIEARHLGKRGDETPAELDADKDFMRRLEALRLRAGMAMGLGD 242 Query: 245 VSQRNVPKMCLLSAPRNGGTVNTRSFIPHRCHASIGVFGAVSVATACLIEGS-VAQGLAS 303 VS + +PK L++ + GGT+ R F+PH CH ++ + G++ +ATAC+ EGS VAQ L + Sbjct: 243 VSDKVIPKPVLVAPAKAGGTLQVRYFMPHNCHRALAITGSIGLATACVSEGSVVAQMLGN 302 Query: 304 TSGGDRQRLAVEHPSGEFTVEISL--EHGVIKGCGLVRTARLLFDGVV 349 T G Q++ +EHPSG V +S ++G +VRTAR LF G V Sbjct: 303 TGGPRLQQVRIEHPSGGIDVVLSYTGKNGDTIRASVVRTARRLFSGFV 350 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: 443 Number of extensions: 16 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: 360 Length adjustment: 29 Effective length of query: 332 Effective length of database: 331 Effective search space: 109892 Effective search space used: 109892 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