Align 4-oxalomesaconate tautomerase; Gallate degradation protein D; EC 5.3.2.8 (characterized)
to candidate N515DRAFT_0030 N515DRAFT_0030 2-methylaconitate cis-trans isomerase
Query= SwissProt::Q88JY0 (361 letters) >FitnessBrowser__Dyella79:N515DRAFT_0030 Length = 399 Score = 203 bits (516), Expect = 7e-57 Identities = 143/390 (36%), Positives = 206/390 (52%), Gaps = 49/390 (12%) Query: 3 QTRIPCLLMRGGTSKGAYFLHDDLPA----PGPLRDRVLLAVMGSPD--ARQIDGIGGAD 56 Q RIP +RGGTSKG +F DLPA PG RD +L V+GSPD +QIDG+GGA Sbjct: 11 QLRIPATYLRGGTSKGVFFRLQDLPAAAQVPGAARDALLQRVIGSPDPYGKQIDGMGGAT 70 Query: 57 SLTSKVAIIRASQRDDADVDYLFAQVVVDEARVDYGQNCGNILAGVGPFALERGLVAASG 116 S TSK I+ S R D DVDYLF QV +D+A VD+ NCGN+ A VGPFA+ GLV Sbjct: 71 SSTSKTVIVSRSSRADHDVDYLFGQVAIDKAFVDWSGNCGNLSAAVGPFAIANGLV--DP 128 Query: 117 ASTP------VRIFMENTGQIAVAQVPTADGQVEYAGDTRIDGVPGRAAALVVTFADVAG 170 A P VRI+ N G+ +A+VP DG V+ GD +DGV AA + + F D A Sbjct: 129 ARVPRDGIAIVRIWQANIGKTIIARVPITDGAVQETGDFELDGVTFPAAEVQLEFVDPAA 188 Query: 171 ---ASCGALLPTGNSRDCVE-----GVEVTCIDNGMPVVLLCAEDLGVTGYEPCETLEAD 222 + GA+ PTG+ D +E ++ T I+ G+P + + A +G TG E + + +D Sbjct: 189 EEDGAGGAMFPTGHVVDDLEVPGVGTLKATMINAGIPTIFVEAAAIGYTGTELQDAINSD 248 Query: 223 SALKTRLEAIR----LQLGPRMNLGDVSQR-NVPKMCLLSAPRN----------GGTVN- 266 + E IR L++G L +++ R + PK+ ++ P + G V+ Sbjct: 249 AKALAMFETIRAHGALRMGLIATLEEIATRQHTPKVAFVAGPADYLASSGKRVAAGDVDL 308 Query: 267 -TRSFIPHRCHASIGVFGAVSVATACLIEGSVAQGLASTSGGDRQRLAVEHPSGEFTVEI 325 R+ + H ++ AV++ TA I G++ + GG+R + HPSG T+ + Sbjct: 309 LVRAMSMGKLHHAMMGTAAVAIGTAAAIPGTLVN--VAAGGGERHAVRFGHPSG--TLRV 364 Query: 326 SLEHGVIKGCGLV------RTARLLFDGVV 349 E + G V R+AR+L +G V Sbjct: 365 GAEAAQVDGAWTVTKAVMSRSARVLMEGWV 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: 426 Number of extensions: 36 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: 399 Length adjustment: 30 Effective length of query: 331 Effective length of database: 369 Effective search space: 122139 Effective search space used: 122139 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