Align 4-oxalomesaconate tautomerase; Gallate degradation protein D; EC 5.3.2.8 (characterized)
to candidate H281DRAFT_02982 H281DRAFT_02982 2-methylaconitate cis-trans isomerase
Query= SwissProt::Q88JY0 (361 letters) >FitnessBrowser__Burk376:H281DRAFT_02982 Length = 393 Score = 207 bits (527), Expect = 4e-58 Identities = 143/389 (36%), Positives = 208/389 (53%), Gaps = 47/389 (12%) Query: 3 QTRIPCLLMRGGTSKGAYFLHDDLP----APGPLRDRVLLAVMGSPD--ARQIDGIGGAD 56 Q RIP MRGGTSKG +F DLP PG RD +LL V+GSPD +QIDG+GGA Sbjct: 6 QIRIPATYMRGGTSKGVFFRLQDLPDAAQTPGAARDALLLRVIGSPDPYGKQIDGMGGAT 65 Query: 57 SLTSKVAIIRASQRDDADVDYLFAQVVVDEARVDYGQNCGNILAGVGPFALERGLVAAS- 115 S TSK II S + D DVDYLF QV +D+ VD+ NCGN+ A VGPFA+ GLV A+ Sbjct: 66 SSTSKTVIIAKSSKPDHDVDYLFGQVSIDKPFVDWSGNCGNLSAAVGPFAISAGLVEANR 125 Query: 116 ----GASTPVRIFMENTGQIAVAQVPTADGQVEYAGDTRIDGVPGRAAALVVTFADVAGA 171 G +T VRI+ N G+ +A VP +DG V+ GD +DGV AA + + F D A Sbjct: 126 IPRDGVAT-VRIWQANIGKTIIAHVPMSDGAVQETGDFELDGVTFPAAEVQLEFMDPAAE 184 Query: 172 SCGA---LLPTGNSRDCVE-----GVEVTCIDNGMPVVLLCAEDLGVTGYEPCETLEADS 223 GA + PTGN D ++ ++ T I+ G+P + + AE +G G E + + +D Sbjct: 185 EAGAGGSMFPTGNLVDDLDVPGVGTLKATMINAGIPTIFVNAEAIGYKGTELQDAINSDE 244 Query: 224 ALKTRLEAIR----LQLGPRMNLGDVSQR-NVPKMCLLSAPRN------------GGTVN 266 E IR L++G +L +++ R + PK+ ++ P + + Sbjct: 245 KALAMFETIRAHGALRMGLIKHLDEIATRQHTPKIAFVAKPADYVSSSGKRIGSGDADLL 304 Query: 267 TRSFIPHRCHASIGVFGAVSVATACLIEGSVAQGLASTSGGDRQRLAVEHPSGEFTVEIS 326 R+ + H ++ AV++ TA I G++ + GG+R+ + HPSG T+ + Sbjct: 305 VRAMSMGKLHHAMMGTAAVAIGTAAAIPGTLVN--LAAGGGEREAVRFGHPSG--TLRVG 360 Query: 327 LEHGVIKGCGLV------RTARLLFDGVV 349 E V+ G +V R+AR+L +G V Sbjct: 361 AEAAVVGGEWVVRKAVMSRSARVLMEGWV 389 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: 387 Number of extensions: 26 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: 393 Length adjustment: 30 Effective length of query: 331 Effective length of database: 363 Effective search space: 120153 Effective search space used: 120153 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