Align Hydroxyacylglutathione hydrolase GloC; Accessory type II glyoxalase; Glyoxalase II 2; GlxII-2; EC 3.1.2.6 (characterized)
to candidate 350674 BT1146 putative metallo-beta-lactamase (NCBI ptt file)
Query= SwissProt::P75849 (215 letters) >FitnessBrowser__Btheta:350674 Length = 203 Score = 145 bits (367), Expect = 4e-40 Identities = 73/204 (35%), Positives = 122/204 (59%), Gaps = 7/204 (3%) Query: 11 FSQNCSLIWCEQTRLAALVDPGGDAEKIKQEVDD----SGLTLMQILLTHGHLDHVGAAA 66 F NC ++W + T+ A ++DPG E+ KQ + + LT+ +L TH HLDH+ Sbjct: 2 FPVNCYVLW-DDTKEAVVIDPGCFYEEEKQALKKFILTNELTVKHLLNTHLHLDHIFGNP 60 Query: 67 ELAQHYGVPVFGPEKEDEFWLQGLPAQSRMFGLE-ECQPLTPDRWLNEGDTISIGNVTLQ 125 + + +G+ K DEFW+ P QSRMFG + + +P+ ++L++GD I+ G+ L+ Sbjct: 61 FMLKEFGLSAEA-NKADEFWIDEAPKQSRMFGFQLQEEPVPLGKYLHDGDIITFGHTKLE 119 Query: 126 VLHCPGHTPGHVVFFDDRAKLLISGDVIFKGGVGRSDFPRGDHNQLISSIKDKLLPLGDD 185 +H PGH+PG +V++ + SGDV+F+G +GR+D G+ ++LI I +L L ++ Sbjct: 120 AIHVPGHSPGSLVYYCKEENCMFSGDVLFQGSIGRADLSGGNFDELIDHICSRLFVLPNE 179 Query: 186 VIFIPGHGPLSTLGYERLHNPFLQ 209 + PGHG +T+G E+ NPF + Sbjct: 180 TVVYPGHGAPTTIGMEKAENPFFR 203 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: 191 Number of extensions: 15 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: 215 Length of database: 203 Length adjustment: 21 Effective length of query: 194 Effective length of database: 182 Effective search space: 35308 Effective search space used: 35308 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