Align Maleylacetoacetate isomerase; MAAI; EC 5.2.1.2 (uncharacterized)
to candidate PP_1320 PP_1320 stringent starvation protein A
Query= curated2:P57109 (212 letters) >FitnessBrowser__Putida:PP_1320 Length = 207 Score = 59.7 bits (143), Expect = 4e-14 Identities = 51/168 (30%), Positives = 73/168 (43%), Gaps = 12/168 (7%) Query: 12 SYRVRIALALKGLDYQSLPVNLIRDGGEHRQPAYLALNPQGRVPALQVDEGELLIQSPAI 71 S+RVR+ LA KG+ Q + V+ H +NP G VP L VD L +S + Sbjct: 18 SHRVRLVLAEKGVSVQLIDVD-----PAHLPRKLAEVNPYGSVPTL-VDRDLALYESTVV 71 Query: 72 IEYLEERYPQPALLSSDPLRRARERGVAALVGCDIHPLHNASVLNLLRQWGHDEEQVRQW 131 +EYLEERYP P L+ P+ R R + + D L + +VL+ E R Sbjct: 72 MEYLEERYPHPPLMPVYPVARGNSRLLMHRIQRDWCALAD-TVLD-----PRSSEAARTE 125 Query: 132 IGHWVGQGLAAVEQLIGDQGWCFGDRPGLADVYLVPQLYAAERFGVAL 179 + + L V L + D L D L+P L+ G+ L Sbjct: 126 ARKALRESLTGVSPLFSEFACFMSDEQSLVDCCLLPILWRLPVLGIEL 173 Lambda K H 0.321 0.138 0.434 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: 111 Number of extensions: 9 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: 212 Length of database: 207 Length adjustment: 21 Effective length of query: 191 Effective length of database: 186 Effective search space: 35526 Effective search space used: 35526 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 45 (21.9 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