Align 4-oxalomesaconate tautomerase; Gallate degradation protein D; EC 5.3.2.8 (characterized)
to candidate BPHYT_RS30140 BPHYT_RS30140 3-methylitaconate isomerase
Query= SwissProt::Q88JY0 (361 letters) >FitnessBrowser__BFirm:BPHYT_RS30140 Length = 395 Score = 199 bits (507), Expect = 8e-56 Identities = 140/391 (35%), Positives = 204/391 (52%), Gaps = 41/391 (10%) Query: 3 QTRIPCLLMRGGTSKGAYFLHDDLP----APGPLRDRVLLAVMGSPD--ARQIDGIGGAD 56 Q +IP MRGGTSKG +F DLP PG RD +L+ V+GSPD +QIDG+GGA Sbjct: 6 QIKIPATYMRGGTSKGVFFRLQDLPEAAQVPGAARDALLMRVIGSPDPYGKQIDGMGGAT 65 Query: 57 SLTSKVAIIRASQRDDADVDYLFAQVVVDEARVDYGQNCGNILAGVGPFALERGLVAAS- 115 S TSK II S R D DVDYLF QV +D+A +D+ NCGN+ A VGPFA+ GLV S Sbjct: 66 SSTSKTVIIAKSSRPDHDVDYLFGQVSIDKAFIDWTGNCGNLSAAVGPFAISAGLVDPSR 125 Query: 116 ---GASTPVRIFMENTGQIAVAQVPTADGQVEYAGDTRIDGVPGRAAALVVTFADVAG-- 170 VRI+ N G+ + VP DG V+ GD +DGV AA + + F D A Sbjct: 126 IPRDGVAVVRIWQANIGKTIIGHVPMTDGAVQETGDFELDGVTFPAAEVQLEFMDPAAEE 185 Query: 171 -ASCGALLPTGNSRDCVE-----GVEVTCIDNGMPVVLLCAEDLGVTGYEPCETLEADSA 224 + G++ PTGN D +E ++ T I+ G+P + + AE +G G E + + +D Sbjct: 186 EGAGGSMFPTGNLVDDLEVPGVGTLKATMINAGIPTIFVDAESIGYKGTELQDAINSDDK 245 Query: 225 LKTRLEAIR----LQLGPRMNLGDVSQR-NVPKMCLLSAPR----------NGGTVN--T 267 E IR L++G NL +++ R + PK+ ++ P G V+ Sbjct: 246 ALAMFETIRAHGALRMGLIKNLDEIATRQHTPKVAFVAKPAAYVASSGKQIGAGDVDLLV 305 Query: 268 RSFIPHRCHASIGVFGAVSVATACLIEGSVAQGLASTSGGDRQRLAVEHPSGEFTV--EI 325 R+ + H ++ AV++ TA I G++ + GG ++ + HPSG V E Sbjct: 306 RAMSMGKLHHAMMGTAAVAIGTAAAIAGTLVN--LAAGGGAKESVRFGHPSGTLRVGAEA 363 Query: 326 SLEHG--VIKGCGLVRTARLLFDGVVCIGRD 354 S G + + R+AR+L +G V + ++ Sbjct: 364 SESGGEWTVTKAIMSRSARVLMEGWVRVPQE 394 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: 391 Number of extensions: 25 Number of successful extensions: 4 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