Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate GFF3010 PS417_15405 glutathione S-transferase
Query= reanno::MR1:200836 (216 letters) >FitnessBrowser__WCS417:GFF3010 Length = 205 Score = 62.4 bits (150), Expect = 6e-15 Identities = 56/184 (30%), Positives = 89/184 (48%), Gaps = 17/184 (9%) Query: 7 WRSSAAYRVRIALNLKGVSAEQLSVHLVRDGGEQHKADYIALNPQELVPTLVVDDEQDGD 66 + S A V + L KG++ + +++ L D +QH AD+ L+ + VPTLV +GD Sbjct: 9 YTSPYALSVFVTLREKGLAFDTITLDL--DAAQQHAADFARLSLTQRVPTLV-----EGD 61 Query: 67 -ALTQSLAIIEYLDELYPKTPLLPASALERAHVRAMALTIACEIHPLNNLR--VLQYLTQ 123 AL++S AI EYL++ YP TP+ PA RA R + + ++ P+ R ++ + Q Sbjct: 62 FALSESSAITEYLEQAYPGTPVYPADPKLRARARQVQAWLRSDLLPIRQERSTMVVFYGQ 121 Query: 124 KLTVNEEAKSAWYHHWVATGFTALETQLVRHSGRYCFGDKVTIADLCLVPQVYNAQRFNV 183 K+ A A + L+ + Y FGD +IAD+ L + N N Sbjct: 122 KMPPLSPVAEA-----AAAKLISAAQDLLVGNPAYLFGD-WSIADVDLAVML-NRLILNG 174 Query: 184 DLTP 187 D P Sbjct: 175 DSVP 178 Lambda K H 0.321 0.134 0.408 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: 114 Number of extensions: 5 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 216 Length of database: 205 Length adjustment: 21 Effective length of query: 195 Effective length of database: 184 Effective search space: 35880 Effective search space used: 35880 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