Align 4-oxalomesaconate tautomerase; Gallate degradation protein D; EC 5.3.2.8 (characterized)
to candidate AZOBR_RS28105 AZOBR_RS28105 hypothetical protein
Query= SwissProt::Q88JY0 (361 letters) >FitnessBrowser__azobra:AZOBR_RS28105 Length = 374 Score = 304 bits (778), Expect = 3e-87 Identities = 170/356 (47%), Positives = 223/356 (62%), Gaps = 12/356 (3%) Query: 3 QTRIPCLLMRGGTSKGAYFLHDDLPAPGPLRDRVLLAVMGSPDARQIDGIGGADSLTSKV 62 Q IPC++MRGGTS+G +FL DLPA RD +LL+VMG+ + IDGIGG + LTSKV Sbjct: 8 QIGIPCVMMRGGTSRGPFFLASDLPASPAERDALLLSVMGAGNDLGIDGIGGGNPLTSKV 67 Query: 63 AIIRASQRDDADVDYLFAQVVVDEARVDYGQNCGNILAGVGPFALERGLVAASGASTPVR 122 AI+ + ADVDYLFAQV V E VD NCGN+LA V PFA+E GLV A+ T VR Sbjct: 68 AIVGPATLAGADVDYLFAQVRVQEGIVDTSPNCGNMLAAVAPFAIEAGLVPATDGVTVVR 127 Query: 123 IFMENTGQIAVAQVPTADGQVEYAGDTRIDGVPGRAAALVVTFADVAGASCGALLPTGNS 182 I NTG++ A+V T DG+V Y G+ IDGVPG AA + + F D AGA+ G LLPTG Sbjct: 128 IHNVNTGKLIEARVQTPDGRVTYEGEAVIDGVPGTAAPIHLAFLDAAGANTGRLLPTGAP 187 Query: 183 RDCV------EGVEVTCIDNGMPVVLLCAEDLGVTGYEPCETLEADSALKTRLEAIRLQL 236 D + +G+EV+CID +PV+L+ A DLG TG+EP ++ D RLEA+R++ Sbjct: 188 VDRIIGIDGTDGIEVSCIDAAIPVMLVRAADLGKTGHEPMDSYRLDRVFMARLEALRVEA 247 Query: 237 GPRMNLGDVSQRNVPKMCLLSAPRNGGTVNTRSFIPHRCHASIGVFGAVSVATACLIEGS 296 G RM + + +PK LL+ P GGT+ R F+PH CH ++ + GAV+ ATAC I G+ Sbjct: 248 GRRMGFPNAAGMVIPKPVLLAPPTRGGTLAVRYFMPHDCHRAMAITGAVATATACTIPGT 307 Query: 297 VAQGLASTSG--GDRQRLAVEHPSGEFTVEISLEHG-VIKGCGLVRTARLLFDGVV 349 VA LA GD + EHP+G TV + G ++RT+R LF+G V Sbjct: 308 VASALAGRMALPGD---VTFEHPAGRLTVRLDPGAGQSAPTASILRTSRRLFEGTV 360 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: 486 Number of extensions: 25 Number of successful extensions: 2 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: 374 Length adjustment: 30 Effective length of query: 331 Effective length of database: 344 Effective search space: 113864 Effective search space used: 113864 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