Align Aconitate-delta-isomerase 1; Itaconic acid/2-hydroxyparaconate biosynthesis cluster protein ADI1; EC 5.-.-.- (characterized)
to candidate PP_2055 PP_2055 putative isomerase
Query= SwissProt::A0A0U2X0E4 (443 letters) >FitnessBrowser__Putida:PP_2055 Length = 359 Score = 277 bits (708), Expect = 4e-79 Identities = 163/359 (45%), Positives = 220/359 (61%), Gaps = 10/359 (2%) Query: 5 IDTTIYRAGTSRGLYFLASDLPAEPSERDAALISIMGSGHPLQIDGMGGGNSLTSKVAIV 64 I + R GTS+G +F A DLPA ERD LI++MGSGH L+IDG+GGG+ TSKVAI+ Sbjct: 4 IPCVLMRGGTSKGPFFHAWDLPANVVERDELLINLMGSGHELEIDGIGGGSPQTSKVAII 63 Query: 65 SASTQRSEFDVDYLFCQVGITERFVDTAPNCGNLMSGVAAFAIERGLVQPHPSDTTCLVR 124 S S ++ DVDYLF QV + +R VDTAPNCGN++ V FAIE+GLV+ T LVR Sbjct: 64 SPSLH-ADADVDYLFVQVMVAQRRVDTAPNCGNMLCAVGPFAIEQGLVKGQEGKT--LVR 120 Query: 125 IFNLNSRQASELVIPVYNGRVHYDDIDDMH-MQRPSARVGLRFLDTVGSCTGKLLPTGNA 183 I NLN+ ++ G V Y+ + + +A V L FLD VGS TGKL PTG A Sbjct: 121 IRNLNTGTFVNSLVETPGGIVRYEGRTAIDGVPGTAAPVHLTFLDAVGSKTGKLFPTGKA 180 Query: 184 SDWIDGLKVSIIDSAVPVVFIRQHDVGITGSEAPATLNANTALLDRLERVRLEAGRRMGL 243 D IDG+ V+ ID A+P++ + +G++GSE PA L+AN+ALL+RLE +RL+AG+ MGL Sbjct: 181 QDVIDGVPVTCIDMAMPMMVVEASQLGVSGSETPAQLDANSALLERLEALRLKAGKAMGL 240 Query: 244 GDVSGSVVPKLSLIGPGTETTTFTARYFTPKACHNAHAVTGAICTAGAAYIDGSVVCEIL 303 GDVSG V+PK L+ T RYF P CH A A+TGA+ A A G+V+ ++L Sbjct: 241 GDVSGMVIPKPVLVSKPRYDGTLQVRYFMPHNCHRALAITGAVGLATACVSPGTVIADLL 300 Query: 304 SSRASACSASQRRISIEHPSGVLEVGLVPPENAAQSLVDVAVVERSVALIAHARVYYTT 362 A + ++ +EHPSG ++V L + A+ A V R+ + VY T Sbjct: 301 GEGAQQLA----QVRLEHPSGGIDVALT--RSGAEGQTIQASVVRTARRLFSGFVYAPT 353 Lambda K H 0.318 0.133 0.389 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: 382 Number of extensions: 16 Number of successful extensions: 3 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: 443 Length of database: 359 Length adjustment: 31 Effective length of query: 412 Effective length of database: 328 Effective search space: 135136 Effective search space used: 135136 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 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