Align (4E)-oxalomesaconate Delta-isomerase; OMA isomerase; 1,3-allylic isomerase LigU; EC 5.3.3.- (characterized)
to candidate PP_2055 PP_2055 putative isomerase
Query= SwissProt::Q0KJL4 (357 letters) >FitnessBrowser__Putida:PP_2055 Length = 359 Score = 308 bits (789), Expect = 1e-88 Identities = 166/352 (47%), Positives = 223/352 (63%), Gaps = 5/352 (1%) Query: 8 MDSAPCMWMRGGTSKGGYFLRADLPADTAARDAFLLAVMGSPDPRQIDGMGGADPLTSKV 67 M PC+ MRGGTSKG +F DLPA+ RD L+ +MGS +IDG+GG P TSKV Sbjct: 1 MQRIPCVLMRGGTSKGPFFHAWDLPANVVERDELLINLMGSGHELEIDGIGGGSPQTSKV 60 Query: 68 AVVSKSERPGIDVDYLFLQVFVDQAIVTDAQNCGNILAGVGPFAIERGLVAASGDETRVA 127 A++S S DVDYLF+QV V Q V A NCGN+L VGPFAIE+GLV +T V Sbjct: 61 AIISPSLHADADVDYLFVQVMVAQRRVDTAPNCGNMLCAVGPFAIEQGLVKGQEGKTLVR 120 Query: 128 IFMENTGQVAVATVRTPGGSVTYAGDAAIDGVPGTHAPIPTEFRDTAGSSCGALLPSGNA 187 I NTG + V TPGG V Y G AIDGVPGT AP+ F D GS G L P+G A Sbjct: 121 IRNLNTGTFVNSLVETPGGIVRYEGRTAIDGVPGTAAPVHLTFLDAVGSKTGKLFPTGKA 180 Query: 188 VDVVNGLPVTLIDNGMPCVVMKAADVGITGYEDRDSLDANAELKAKIEAIRLAVGELMNL 247 DV++G+PVT ID MP +V++A+ +G++G E LDAN+ L ++EA+RL G+ M L Sbjct: 181 QDVIDGVPVTCIDMAMPMMVVEASQLGVSGSETPAQLDANSALLERLEALRLKAGKAMGL 240 Query: 248 GDVTEKSVPKMMLVAPPRDGGAVCVRSFIPHRAHATIGVLGAVSVATACLIPGSPAAEVA 307 GDV+ +PK +LV+ PR G + VR F+PH H + + GAV +ATAC+ PG+ A+ Sbjct: 241 GDVSGMVIPKPVLVSKPRYDGTLQVRYFMPHNCHRALAITGAVGLATACVSPGTVIAD-- 298 Query: 308 VVPEGARK--TLSIEHPTGEMSCVLEVDDA-GNVVSAALLRTARKLMDGVVF 356 ++ EGA++ + +EHP+G + L A G + A+++RTAR+L G V+ Sbjct: 299 LLGEGAQQLAQVRLEHPSGGIDVALTRSGAEGQTIQASVVRTARRLFSGFVY 350 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: 385 Number of extensions: 18 Number of successful extensions: 2 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: 359 Length adjustment: 29 Effective length of query: 328 Effective length of database: 330 Effective search space: 108240 Effective search space used: 108240 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: 49 (23.5 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