Align Maleylacetoacetate isomerase; MAAI; EC 5.2.1.2 (uncharacterized)
to candidate AZOBR_RS27895 AZOBR_RS27895 glutathione S-transferase
Query= curated2:Q9X4F7 (213 letters) >FitnessBrowser__azobra:AZOBR_RS27895 Length = 204 Score = 82.0 bits (201), Expect = 7e-21 Identities = 63/197 (31%), Positives = 96/197 (48%), Gaps = 8/197 (4%) Query: 7 LYDYWRSSASYRVRIALNLCGEAYRSVPVDLLAKAHRAPEHLARNPQGLVPVLDIDGERL 66 LY + S ++R R+ ++L G + V VDL A AH+ PE LA NP G VPVLD DG + Sbjct: 3 LYHHPLSGHAHRARLFVSLLGLPHELVEVDLKAGAHKTPEFLALNPFGQVPVLDDDGVVV 62 Query: 67 TQSLAIIEYLAETRDGTGLLPAHPIDRQRVRALSYAVAMDIHPVCNLGVVARVMAGAGDG 126 + S AI+ YLA+ + LP D + A+ +++ V AR++ G G Sbjct: 63 SDSNAILVYLAKKAGRSDWLPE---DARNAAAVQRWLSVAAGEVAYGPAAARLVTVFGAG 119 Query: 127 EAARREWMQKFIGEGLAAFERMLDHPATGAFCHGDRPTMADLCLVPQVYNARRWDVDLAA 186 + IG +R+ H + + G +PT+AD+ + V A +VDL+ Sbjct: 120 FNP-----DEVIGRAHTLLKRLDSHLSGRDWLVGLQPTIADVAIYSYVARAPEGNVDLSG 174 Query: 187 CPLLVAIDRRCAGIDAF 203 P + A RR G+ F Sbjct: 175 YPAVNAFLRRVEGLPGF 191 Lambda K H 0.324 0.138 0.433 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: 100 Number of extensions: 4 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: 213 Length of database: 204 Length adjustment: 21 Effective length of query: 192 Effective length of database: 183 Effective search space: 35136 Effective search space used: 35136 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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