Align Hydroxyacylglutathione hydrolase GloC; Accessory type II glyoxalase; Glyoxalase II 2; GlxII-2; EC 3.1.2.6 (characterized)
to candidate WP_109969325.1 DK846_RS12745 MBL fold metallo-hydrolase
Query= SwissProt::P75849 (215 letters) >NCBI__GCF_003173355.1:WP_109969325.1 Length = 223 Score = 66.2 bits (160), Expect = 4e-16 Identities = 61/201 (30%), Positives = 97/201 (48%), Gaps = 21/201 (10%) Query: 8 VTAFSQNCSLIWCEQTRLAALVDPGGDAE---KIKQEVDDSGLTLMQILLTHGHLDHVGA 64 V + NC +I ++ L P A+ I+ ++ L I+LTH H+DHVG Sbjct: 10 VDGVNGNCFIIVRDELTLIDTGMPKNSAKIVTYIQDTLNRKPSDLKTIILTHFHIDHVGD 69 Query: 65 AAELAQHYGVPVFGPEKEDEFW----LQGLP--AQSRMFGLE-----ECQPLTPDRWLNE 113 A ++ + G V E + ++ +Q +P +F L +P+ P+ L + Sbjct: 70 ADDIKKLSGAKVAIHEADADYVAGRKIQPVPKGVMGWIFKLLIPLFFGSRPVEPEIKLKD 129 Query: 114 GDTISIGNVTLQVLHCPGHTPGHVVFFDDRAKLLISGDVI-FKGGVGRSDFPRGDHNQLI 172 GDTI+ L +H PGHTPG + FD +K+L +GDV+ F G R D N++ Sbjct: 130 GDTIA----GLISIHTPGHTPGSICLFDPASKILFAGDVLRFNGNKIRIGPSSLDLNEIK 185 Query: 173 SSIKDKLLPLGDDVIFIPGHG 193 SI +K+ + D I + GHG Sbjct: 186 QSI-NKIAAIDFD-IMLSGHG 204 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: 175 Number of extensions: 13 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: 215 Length of database: 223 Length adjustment: 22 Effective length of query: 193 Effective length of database: 201 Effective search space: 38793 Effective search space used: 38793 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 24 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