Align 4-oxalomesaconate tautomerase; Gallate degradation protein D; EC 5.3.2.8 (characterized)
to candidate WP_011382697.1 AMB_RS01270 4-oxalomesaconate tautomerase
Query= SwissProt::Q88JY0 (361 letters) >NCBI__GCF_000009985.1:WP_011382697.1 Length = 363 Score = 384 bits (987), Expect = e-111 Identities = 198/359 (55%), Positives = 245/359 (68%), Gaps = 3/359 (0%) Query: 3 QTRIPCLLMRGGTSKGAYFLHDDLPAPGPLRDRVLLAVMGSPDARQIDGIGGADSLTSKV 62 QT IPCL MRGGTS+G +FL DLPA LRD+VLLAVMGSP ARQIDG+GG LTSKV Sbjct: 2 QTPIPCLFMRGGTSRGPFFLESDLPADMALRDKVLLAVMGSPHARQIDGLGGGHPLTSKV 61 Query: 63 AIIRASQRDDADVDYLFAQVVVDEARVDYGQNCGNILAGVGPFALERGLVAASGASTPVR 122 I+R S D+D+LFAQ+ D VD NCGN+LA V PFALERG+V G +T +R Sbjct: 62 GIVRPSTTPGVDLDFLFAQLQPDRETVDTTPNCGNMLAAVVPFALERGIVRPQGDTTTLR 121 Query: 123 IFMENTGQIAVAQVPTADGQVEYAGDTRIDGVPGRAAALVVTFADVAGASCGALLPTGNS 182 + NT V T G++EY G+ RIDGVPG A+ + + F D AG+ C LLPTG + Sbjct: 122 VLTLNTDMQCDITVRTPGGRMEYQGEARIDGVPGTASPIAINFLDTAGSVCTGLLPTGRT 181 Query: 183 RDCVEGVEVTCIDNGMPVVLLCAEDLGVTGYEPCETLEADSALKTRLEAIRLQLGPRMNL 242 RD ++G+EVTCIDNGMP+VL A DLG TG E ETL AD+ LK R+E +RL+ G M L Sbjct: 182 RDVIDGLEVTCIDNGMPMVLFRAADLGRTGAESVETLNADTELKARIETLRLKAGHLMGL 241 Query: 243 GDVSQRNVPKMCLLSAPRNGGTVNTRSFIPHRCHASIGVFGAVSVATACLIEGSVAQGLA 302 GDV +N PKMCL++ P GG + TR FIPH CH +IGV AV+VATAC++EGSV +GLA Sbjct: 242 GDVGPKNYPKMCLVAPPSAGGALGTRCFIPHVCHDAIGVLAAVTVATACVLEGSVTEGLA 301 Query: 303 STSGGDRQRLAVEHPSGEFTVEISLEHG---VIKGCGLVRTARLLFDGVVCIGRDTWGG 358 + GG + +AVEHP+GEF+VE+ L+ + L+RTARLL G V I W G Sbjct: 302 NVPGGAVKTIAVEHPTGEFSVELELDLADPQKVVRAALLRTARLLMKGEVMIPAAIWEG 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: 454 Number of extensions: 18 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: 363 Length adjustment: 29 Effective length of query: 332 Effective length of database: 334 Effective search space: 110888 Effective search space used: 110888 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