Align Aconitate-delta-isomerase 1; Itaconic acid/2-hydroxyparaconate biosynthesis cluster protein ADI1; EC 5.-.-.- (characterized)
to candidate 14894 b0769 hypothetical protein (NCBI)
Query= SwissProt::A0A0U2X0E4 (443 letters) >FitnessBrowser__Keio:14894 Length = 350 Score = 264 bits (674), Expect = 4e-75 Identities = 160/356 (44%), Positives = 213/356 (59%), Gaps = 12/356 (3%) Query: 5 IDTTIYRAGTSRGLYFLASDLPAEPSERDAALISIMGSGHPLQIDGMGGGNSLTSKVAIV 64 I + R GTSRG + LA LP + ++RD L++IMGSG+ L+IDG+GGGN LTSKVAI+ Sbjct: 4 IPCVMMRGGTSRGAFLLAEHLPEDQTQRDKILMAIMGSGNDLEIDGIGGGNPLTSKVAII 63 Query: 65 SASTQRSEFDVDYLFCQVGITERFVDTAPNCGNLMSGVAAFAIERGLVQPHPSDTTCLVR 124 S S+ DVDYLF QV + E+ VDT PNCGN++SGV AFAIE GL+ T VR Sbjct: 64 SRSSD-PRADVDYLFAQVIVHEQRVDTTPNCGNMLSGVGAFAIENGLIAATSPVTR--VR 120 Query: 125 IFNLNSRQASELVIPVYNGRVHYDDIDDMH-MQRPSARVGLRFLDTVGSCTGKLLPTGNA 183 I N+N+ E + NG V Y+ + + +A V L FL+ G+ TGK+ PT N Sbjct: 121 IRNVNTGTFIEADVQTPNGVVEYEGSARIDGVPGTAAPVALTFLNAAGTKTGKVFPTDNQ 180 Query: 184 SDWIDGLKVSIIDSAVPVVFIRQHDVGITGSEAPATLNANTALLDRLERVRLEAGRRMGL 243 D+ D + V+ ID A+PVV I +G TG E PA L+A+ ALL R+E +RL+AG+ MGL Sbjct: 181 IDYFDDVPVTCIDMAMPVVIIPAEYLGKTGYELPAELDADKALLARIESIRLQAGKAMGL 240 Query: 244 GDVSGSVVPKLSLIGPGTETTTFTARYFTPKACHNAHAVTGAICTAGAAYIDGSVVCEIL 303 GDVS V+PK LI P + RYF P +CH A A+TGAI + + ++G+V +I+ Sbjct: 241 GDVSNMVIPKPVLISPAQKGGAINVRYFMPHSCHRALAITGAIAISSSCALEGTVTRQIV 300 Query: 304 SSRASACSASQRRISIEHPSGVLEVGLVPPENAAQSLVDVAVVERSVALIAHARVY 359 S I+IEHPSG L+V L A +L A V R+ I VY Sbjct: 301 P------SVGYGNINIEHPSGALDVHLSNEGQDATTL--RASVIRTTRKIFSGEVY 348 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: 384 Number of extensions: 13 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: 350 Length adjustment: 31 Effective length of query: 412 Effective length of database: 319 Effective search space: 131428 Effective search space used: 131428 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