Align Hydroxyacylglutathione hydrolase GloC; Accessory type II glyoxalase; Glyoxalase II 2; GlxII-2; EC 3.1.2.6 (characterized)
to candidate AZOBR_RS19250 AZOBR_RS19250 hypothetical protein
Query= SwissProt::P75849 (215 letters) >FitnessBrowser__azobra:AZOBR_RS19250 Length = 210 Score = 278 bits (711), Expect = 5e-80 Identities = 119/206 (57%), Positives = 155/206 (75%) Query: 5 IIPVTAFSQNCSLIWCEQTRLAALVDPGGDAEKIKQEVDDSGLTLMQILLTHGHLDHVGA 64 I+PVT F QNC+++WC +T A VDPGGD ++ + G+TL +IL+THGH+DH GA Sbjct: 5 IVPVTPFQQNCTVLWCPETMKGAAVDPGGDLPRVLRAAQSKGVTLEKILVTHGHIDHAGA 64 Query: 65 AAELAQHYGVPVFGPEKEDEFWLQGLPAQSRMFGLEECQPLTPDRWLNEGDTISIGNVTL 124 A+LA +P+ GP +ED+FW+ G+P QS+MFG + TPDRWL EGDT+++GN+TL Sbjct: 65 VADLADELKLPIEGPHREDQFWIDGMPMQSQMFGFPPVRSFTPDRWLEEGDTVTVGNLTL 124 Query: 125 QVLHCPGHTPGHVVFFDDRAKLLISGDVIFKGGVGRSDFPRGDHNQLISSIKDKLLPLGD 184 V HCPGHTPGHVVF +K+ I GDV+F+G +GR+DFP+G+H LI SI+ KL PLGD Sbjct: 125 DVHHCPGHTPGHVVFVHKPSKIAIVGDVLFQGSIGRTDFPKGNHGDLIESIRSKLFPLGD 184 Query: 185 DVIFIPGHGPLSTLGYERLHNPFLQD 210 DV FIPGHGP ST+G ERL+NPFL D Sbjct: 185 DVTFIPGHGPTSTIGEERLYNPFLND 210 Lambda K H 0.321 0.142 0.453 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: 265 Number of extensions: 13 Number of successful extensions: 1 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: 215 Length of database: 210 Length adjustment: 21 Effective length of query: 194 Effective length of database: 189 Effective search space: 36666 Effective search space used: 36666 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: 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