Align 4-oxalomesaconate tautomerase; Gallate degradation protein D; EC 5.3.2.8 (characterized)
to candidate PP_2337 PP_2337 aconitate isomerase
Query= SwissProt::Q88JY0 (361 letters) >FitnessBrowser__Putida:PP_2337 Length = 396 Score = 203 bits (516), Expect = 7e-57 Identities = 144/395 (36%), Positives = 209/395 (52%), Gaps = 45/395 (11%) Query: 3 QTRIPCLLMRGGTSKGAYFLHDDLPA----PGPLRDRVLLAVMGSPD--ARQIDGIGGAD 56 Q +IP +RGGTSKG +F DLP PGP RD +LL V+GSPD +QIDG+GGA Sbjct: 6 QIKIPATYIRGGTSKGVFFRLQDLPEQAQIPGPARDALLLRVIGSPDPYGKQIDGMGGAT 65 Query: 57 SLTSKVAIIRASQRDDADVDYLFAQVVVDEARVDYGQNCGNILAGVGPFALERGL----- 111 S TSK I+ S + + DVDYLF QV +D+A VD+ NCGN+ A VG FA+ GL Sbjct: 66 SSTSKTVILSQSIKPEHDVDYLFGQVSIDKAFVDWSGNCGNLSAAVGSFAISSGLVDPAR 125 Query: 112 VAASGASTPVRIFMENTGQIAVAQVPTADGQVEYAGDTRIDGVPGRAAALVVTFADVAG- 170 V +G +T VRI+ N G+ +A VP +G+V+ GD +DGV AA + + F D A Sbjct: 126 VPRNGIAT-VRIWQANIGKTIIAHVPITEGEVQETGDFELDGVTFPAAEVQLEFLDPAAD 184 Query: 171 --ASCGALLPTGNSRDCVE--GV---EVTCIDNGMPVVLLCAEDLGVTGYEPCETLEADS 223 GA+ PTGN D +E GV + T I+ G+P + + A D+G TG E + + D Sbjct: 185 EDGGGGAMFPTGNLVDDLEVPGVGTFKATLINAGIPTIFVNAADIGYTGTELQDAINGDP 244 Query: 224 ALKTRLEAIRLQLGPRMNLGD-----VSQRNVPKMCLLSAPRN----------GGTVN-- 266 R E IR RM L D +++ PK+ ++ P G ++ Sbjct: 245 QALLRFETIRAYGAVRMGLIDNVDQAAGRQHTPKVAFVAPPSTYTASSGKAVPAGEIDLL 304 Query: 267 TRSFIPHRCHASIGVFGAVSVATACLIEGSVAQGLASTSGGDRQRLAVEHPSGEFTV--- 323 R+ + H ++ AV++ TA I G++ + GG+R + HPSG V Sbjct: 305 VRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVN--LAAGGGERSAVRFGHPSGTLRVGAE 362 Query: 324 --EISLEHGVIKGCGLVRTARLLFDGVVCIGRDTW 356 +++ E V K + R+AR+L +G V + D++ Sbjct: 363 ARQVNGEWTVTKAI-MSRSARVLMEGWVRVPGDSF 396 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: 32 Number of successful extensions: 6 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