Align (4E)-oxalomesaconate Delta-isomerase; OMA isomerase; 1,3-allylic isomerase LigU; EC 5.3.3.- (characterized)
to candidate WP_007153590.1 MDG893_RS09680 2-methylaconitate cis-trans isomerase PrpF
Query= SwissProt::Q0KJL4 (357 letters) >NCBI__GCF_000170835.1:WP_007153590.1 Length = 390 Score = 188 bits (478), Expect = 2e-52 Identities = 143/381 (37%), Positives = 195/381 (51%), Gaps = 38/381 (9%) Query: 12 PCMWMRGGTSKGGYFLRADLPADTAA----RDAFLLAVMGSPDP--RQIDGMGGADPLTS 65 P +MRGGTSKG +F DLP RD+ L+ V+GSPDP +QIDG+G TS Sbjct: 10 PATYMRGGTSKGVFFRLEDLPEGAQTPGPIRDSLLMRVIGSPDPYQKQIDGLGNGTSSTS 69 Query: 66 KVAVVSKSERPGIDVDYLFLQVFVDQAIVTDAQNCGNILAGVGPFAIERGLVAASGDE-- 123 K +VS+SERP DVDYLF QV +D+A V + NCGN+ VG FAI GLVAA E Sbjct: 70 KTVIVSRSERPDHDVDYLFGQVGIDRAFVDWSGNCGNLTTAVGAFAISAGLVAADTLEQN 129 Query: 124 --TRVAIFMENTGQVAVATVRTPGGSVTYAGDAAIDGVPGTHAPIPTEFRDTAGSSCGAL 181 V I+ N G+ +A V G V GD +DGV A I EF D AG GA+ Sbjct: 130 SVAAVRIWQANIGKTIIARVPMTDGQVQETGDFELDGVAFPAAKIALEFLDPAGDE-GAI 188 Query: 182 LPSGNAVDV--VNGL---PVTLIDNGMPCVVMKAADVGITGYEDRDSLDANAELKAKIEA 236 P+GN VD V GL VT+I G+P + ++A VG TG E +D+++ + + A E+ Sbjct: 189 FPTGNPVDELDVPGLGKFRVTMITAGIPTIFVEADAVGYTGTELQDAINNDPQALAMFES 248 Query: 237 IR----LAVGELMNLGDVTEKS-VPKMMLVAPPRDGGA------------VCVRSFIPHR 279 IR L +G + L + + PK+ VA P D A + VR + Sbjct: 249 IRGHGALQMGLVETLAEAENRQHTPKIAFVAGPSDYVAASGKRITIDDVDLLVRGLSMGK 308 Query: 280 AHATIGVLGAVSVATACLIPGSPAAEVAVVPEGARKTLSIEHPTGEMSCVLEVDDAGN-- 337 H + AV++ A IPG+ A G + ++ HP+G + E ++ Sbjct: 309 LHHAMPGTVAVAIGAAHAIPGTIVNTAA--GGGNQTSVRFGHPSGTLRVGAEARESNGEW 366 Query: 338 -VVSAALLRTARKLMDGVVFV 357 V A + R+AR LM+G V V Sbjct: 367 VVEKAIMSRSARVLMEGWVRV 387 Lambda K H 0.318 0.135 0.396 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: 393 Number of extensions: 21 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: 357 Length of database: 390 Length adjustment: 30 Effective length of query: 327 Effective length of database: 360 Effective search space: 117720 Effective search space used: 117720 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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