Align Aconitate-delta-isomerase 1; Itaconic acid/2-hydroxyparaconate biosynthesis cluster protein ADI1; EC 5.-.-.- (characterized)
to candidate Ac3H11_4370 FIG00786362: hypothetical protein
Query= SwissProt::A0A0U2X0E4 (443 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4370 Length = 396 Score = 301 bits (772), Expect = 2e-86 Identities = 168/340 (49%), Positives = 223/340 (65%), Gaps = 8/340 (2%) Query: 9 IYRAGTSRGLYFLASDLPAEPSERDAALISIMGSGHPLQIDGMGGGNSLTSKVAIVSAST 68 + R GTSRG +FLA LP P RD LI+ +GS H LQIDG+GGGNSLTSKVAIVS ST Sbjct: 43 LMRGGTSRGPFFLADWLPQAPEARDRTLIAALGSPHELQIDGLGGGNSLTSKVAIVSRST 102 Query: 69 QRSEFDVDYLFCQVGITERFVDTAPNCGNLMSGVAAFAIERGLVQPHPSDTTCLVRIFNL 128 Q + DVDYLF QV + E VDT PNCGN+++GV FAIE+GLV P TT VR++N+ Sbjct: 103 Q-PDCDVDYLFAQVSVQEARVDTRPNCGNMLAGVGPFAIEQGLVAPSGQGTT-RVRVYNV 160 Query: 129 NSRQASELVIPVYNGRVHYD-DIDDMHMQRPSARVGLRFLDTVGSCTGKLLPTGNASDWI 187 N+R ++ + G+VHYD D+ ++ +A V + FLD G+ TG++ PTG D I Sbjct: 161 NTRSRIDVQVCTAGGQVHYDGDVRIDGVKGTAAPVLMNFLDAWGAVTGQIFPTGQRIDHI 220 Query: 188 DGLKVSIIDSAVPVVFIRQHDVGITGSEAPATLNANTALLDRLERVRLEAGRRMGLGDVS 247 GL V+ ID+A +V +R D+G+ G E PA L+ NTALL RLE +RLEAG+RMG+GDV+ Sbjct: 221 QGLDVTCIDAAQVMVLVRAADLGLRGDETPAELDTNTALLARLEALRLEAGQRMGMGDVT 280 Query: 248 GSVVPKLSLIGPGTETTTFTARYFTPKACHNAHAVTGAICTAGAAYIDGSVVCEILSSRA 307 SV+PK ++ PGT +RYFTP CH +HAVTGAI A A+ + G+V + Sbjct: 281 HSVLPKPVIVSPGTSPGCVVSRYFTPHQCHRSHAVTGAIGVAAASVLPGTVA----TDER 336 Query: 308 SACSASQRRISIEHPSGVLEVGLVPPENAAQ-SLVDVAVV 346 S SA RR+ ++HP+G ++V + E Q LV A+V Sbjct: 337 SPPSAGLRRVEVQHPAGRIQVEVELSEVDGQFKLVQAALV 376 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: 471 Number of extensions: 20 Number of successful extensions: 4 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: 396 Length adjustment: 32 Effective length of query: 411 Effective length of database: 364 Effective search space: 149604 Effective search space used: 149604 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