Align Hydroxyacylglutathione hydrolase; EC 3.1.2.6; Glyoxalase II; Glx II (uncharacterized)
to candidate CA265_RS25095 CA265_RS25095 MBL fold metallo-hydrolase
Query= curated2:A6VVZ9 (257 letters) >FitnessBrowser__Pedo557:CA265_RS25095 Length = 470 Score = 67.0 bits (162), Expect = 7e-16 Identities = 46/136 (33%), Positives = 63/136 (46%), Gaps = 14/136 (10%) Query: 46 TLTGILITHHHKDHTGGVAELKQHSNCPV-YGPEHLTELVTHPVDDGDRILVFSKVFTVI 104 T+ I TH H D G +L + S + YGP TE +H DG++ + T + Sbjct: 46 TIKYIFETHFHADFVSGHVDLAEKSGAEIIYGPTAKTEFKSHMAKDGEQFKIGKLTITAL 105 Query: 105 ATPGHTLDHLCYFSEQET---PILLSGDTLFKGGCGR--IMEGTHEQM--LAAMI----- 152 TPGHTL+ Y E + SGDTLF G GR + + H M LA M+ Sbjct: 106 HTPGHTLESTTYLLTDENGKDHCIFSGDTLFIGDVGRPDLAQKGHLTMEDLAGMLYDSLN 165 Query: 153 -KISGLPNDTLIYGTH 167 KI L +D ++Y H Sbjct: 166 EKIKPLADDVIVYPAH 181 Lambda K H 0.319 0.136 0.411 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: 255 Number of extensions: 11 Number of successful extensions: 3 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: 257 Length of database: 470 Length adjustment: 29 Effective length of query: 228 Effective length of database: 441 Effective search space: 100548 Effective search space used: 100548 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 (21.7 bits) S2: 49 (23.5 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