Align 4-oxalomesaconate tautomerase; Gallate degradation protein D; EC 5.3.2.8 (characterized)
to candidate GFF2273 Psest_2318 probable AcnD-accessory protein PrpF
Query= SwissProt::Q88JY0 (361 letters) >FitnessBrowser__psRCH2:GFF2273 Length = 395 Score = 208 bits (530), Expect = 2e-58 Identities = 143/396 (36%), Positives = 209/396 (52%), Gaps = 44/396 (11%) Query: 1 MGQTRIPCLLMRGGTSKGAYFLHDDLP----APGPLRDRVLLAVMGSPD--ARQIDGIGG 54 + Q RIP MRGGTSKG +F DLP PG RD++ + V+GSPD + IDG+GG Sbjct: 4 VSQVRIPATYMRGGTSKGVFFRLQDLPESCQVPGAARDKLFMRVIGSPDPYSAHIDGMGG 63 Query: 55 ADSLTSKVAIIRASQRDDADVDYLFAQVVVDEARVDYGQNCGNILAGVGPFALERGLVAA 114 A S TSK I+ S R D DV+YL+ QV +D+ VD+ NCGN+ G G FAL GLV A Sbjct: 64 ATSSTSKCVILSKSTRPDHDVEYLYGQVSIDKPFVDWSGNCGNLSTGAGAFALHAGLVDA 123 Query: 115 ----SGASTPVRIFMENTGQIAVAQVPTADGQVEYAGDTRIDGVPGRAAALVVTFADVA- 169 + VRI+ N G+ +A VP DGQ + GD +DGV AA +V+ F D + Sbjct: 124 ERIPQNGTCVVRIWQANIGKTIIAHVPVTDGQAQETGDFELDGVTFPAAEIVLEFLDPSD 183 Query: 170 -GASCGALLPTGNSRDCVE-----GVEVTCIDNGMPVVLLCAEDLGVTGYEPCETLEADS 223 G G++ PTGN D +E ++ T I G+P V + AED+G G E E + + Sbjct: 184 DGEEGGSMFPTGNLVDELEVPGVGTLKATMISAGIPTVFVNAEDIGYQGTELREDINGNP 243 Query: 224 ALKTRLEAIRLQLGPRMNL-----GDVSQRNVPKMCLLSAPR-----NGGTVN------- 266 RLEAIR+ RM L +++++ PK+ +S P+ +G T++ Sbjct: 244 EALARLEAIRVAGALRMGLIKTAEEALTRQHTPKVAFVSRPKSYRASSGKTIDAAEVDLL 303 Query: 267 TRSFIPHRCHASIGVFGAVSVATACLIEGSVAQGLASTSGGDRQRLAVEHPSGEFTVEIS 326 R+ + H ++ AV++ TA + G++ + GG+RQ + HPSG T+ + Sbjct: 304 VRALSMGKLHHAMMGTCAVAIGTAAAVPGTLVN--LAAGGGERQAVRFGHPSG--TLRVG 359 Query: 327 LEHGVIKGCGLV------RTARLLFDGVVCIGRDTW 356 E + G V R+AR+L +G V + D + Sbjct: 360 AEAKQVDGQWTVTKAIMSRSARVLMEGWVRVPGDAF 395 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: 24 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: 395 Length adjustment: 30 Effective length of query: 331 Effective length of database: 365 Effective search space: 120815 Effective search space used: 120815 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