Align 4-oxalomesaconate tautomerase; Gallate degradation protein D; EC 5.3.2.8 (characterized)
to candidate Ac3H11_2325 2-methylaconitate cis-trans isomerase
Query= SwissProt::Q88JY0 (361 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2325 Length = 396 Score = 213 bits (542), Expect = 7e-60 Identities = 149/389 (38%), Positives = 206/389 (52%), Gaps = 48/389 (12%) Query: 3 QTRIPCLLMRGGTSKGAYFLHDDLPAP----GPLRDRVLLAVMGSPD--ARQIDGIGGAD 56 Q ++P +RGGTSKG +FL +DLPAP GP RD +LL V+GSPD +QIDG+G A Sbjct: 7 QIKVPATYLRGGTSKGVFFLLEDLPAPAQQPGPARDALLLRVLGSPDPYGKQIDGMGNAS 66 Query: 57 SLTSKVAIIRASQRDDADVDYLFAQVVVDEARVDYGQNCGNILAGVGPFALERGLVAAS- 115 S TSK I+ S R DVDYLF QV +++ VD+ NCGN+ A VGP A+ GL+ A+ Sbjct: 67 SSTSKAVILSRSTRPGHDVDYLFGQVSINQPFVDWSGNCGNLSAAVGPCAIHMGLIDAAR 126 Query: 116 ---GASTPVRIFMENTGQIAVAQVPTADGQVEYAGDTRIDGVPGRAAALVVTFADVA--G 170 + PVRI+ N G+ VA VP GQV+ GD +DGV AA + + F D A G Sbjct: 127 IPQNGTIPVRIWQANIGKTIVAHVPITHGQVQETGDFELDGVTFAAAEVALEFMDPADDG 186 Query: 171 ASCGALLPTGNSRDCVE-----GVEVTCIDNGMPVVLLCAEDLGVTGYEPCETLEADSAL 225 G + PTGN D +E T I+ G+P + L A++LG TG E + D+ Sbjct: 187 DEGGGMFPTGNVVDTLEVPGVGSFAATLINAGIPTIFLNAQELGYTGTELQGAINGDAVA 246 Query: 226 KTRLEAIR----LQLGPRMNLGDVSQR-NVPKMCLLSAPRNGGTVNTRSFIPHR------ 274 R EAIR L++G +LG+ + R + PK+ + APR T ++ I + Sbjct: 247 LARFEAIRAHGALRMGLIQHLGEATTRQHTPKIAFV-APRASYTASSGKAIDAKDIDLLV 305 Query: 275 --------CHASIGVFGAVSVATACLIEGSVAQGLASTSGGDRQRLAVEHPSGEFTVEIS 326 HA +G AV++ TA I G++ + GG R + HPSG T+ + Sbjct: 306 RAISMGQLHHAMMGT-AAVAIGTAAAIPGTLVN--LAAGGGVRSSVRFGHPSG--TLRVG 360 Query: 327 LEHGVIKGCGLV------RTARLLFDGVV 349 E I G V R+AR+L +G V Sbjct: 361 AEAAQINGQWKVTKALMSRSARILMEGWV 389 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: 422 Number of extensions: 32 Number of successful extensions: 5 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: 396 Length adjustment: 30 Effective length of query: 331 Effective length of database: 366 Effective search space: 121146 Effective search space used: 121146 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: 50 (23.9 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