Align Probable hydroxyacylglutathione hydrolase C13B11.03c; Glyoxalase II; Glx II; EC 3.1.2.6 (characterized)
to candidate Pf6N2E2_1531 FIG146518: Zn-dependent hydrolases, including glyoxylases
Query= SwissProt::O94250 (256 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1531 Length = 292 Score = 77.4 bits (189), Expect = 3e-19 Identities = 69/229 (30%), Positives = 101/229 (44%), Gaps = 37/229 (16%) Query: 19 AYLLLCEETRQAAIVDPA---------EVNVVMPILKKKLKNKEIDLQAILTTHHHADHS 69 +YL+L + TRQ A++D L ++ E +Q IL TH HADH Sbjct: 19 SYLVLDKTTRQCALIDSVLDFDPKSGRTTTTSADKLMARVLELEAKVQWILETHVHADHL 78 Query: 70 ----------GGNLNLKKEFPHV-----TIY--GGS---DQNGVSHVLQDKETLRIGNVQ 109 GG + + + V T++ GG D + H+ + E+ IG +Q Sbjct: 79 TAAPYLKEKLGGTIGIGSQIATVQEVFGTLFNTGGEMPRDGSQFDHLFVNDESFTIGTLQ 138 Query: 110 IEALHTPCHTRDSICFYAHSSNEHAVFTGDTLFNAGCGR----FFEGTAAEMHIALNAVL 165 ALHTP HT + + E A F GDTLF G F G A + ++N VL Sbjct: 139 CHALHTPGHTPACMTYVISDGQETAAFVGDTLFMPDYGTARCDFPGGNAHTLFRSINKVL 198 Query: 166 SSLPNNTVIYPGHEYTKS--NVKFASKHLQSEALN-HLEGLCNHNQFIA 211 SLP NT++Y H+Y V+F+S + A N H+ + F+A Sbjct: 199 -SLPANTLLYTCHDYQPGGREVQFSSTVAEQRADNVHVRNGISEEAFVA 246 Lambda K H 0.319 0.134 0.404 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: 213 Number of extensions: 13 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: 256 Length of database: 292 Length adjustment: 25 Effective length of query: 231 Effective length of database: 267 Effective search space: 61677 Effective search space used: 61677 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 (21.8 bits) S2: 47 (22.7 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