Align Hydroxyacylglutathione hydrolase GloC; EC 3.1.2.6; Accessory type II glyoxalase; Glyoxalase II 2; GlxII-2 (uncharacterized)
to candidate AO353_15160 AO353_15160 MBL fold metallo-hydrolase
Query= curated2:Q57544 (212 letters) >FitnessBrowser__pseudo3_N2E3:AO353_15160 Length = 214 Score = 151 bits (382), Expect = 8e-42 Identities = 82/208 (39%), Positives = 120/208 (57%), Gaps = 5/208 (2%) Query: 4 EIIPVTAFQQNCSLIWDD-EKNAAIIDPGGEAERLIQRIEELDLNLKVLLLTHGHLDHVG 62 E PV Q NC++I D K A ++DPGG E ++ R+E L L + ++ TH HLDH Sbjct: 11 ETFPVGPLQCNCTIIGDPITKKAIVVDPGGNHELILARLEALGLKVVSIIHTHAHLDHFL 70 Query: 63 AAMQLKQHFGVEIWGSNEKDKFLFESLPEQAQRFGLPNIDAFLPDRWFNQEGEILKLDGF 122 A+ QLK+ G + +++D+FL+++L Q Q F +P PDRW + E+ G Sbjct: 71 ASGQLKEKTGATLH-LHKEDQFLWDNLEMQCQMFRVPYTPVPSPDRWLADDEELACGCGV 129 Query: 123 NFEILHLPGHTPGHIGFIEHEKKVAFTGDVLFQGGIGRTDFPRGDYETLISSIRTKLLPL 182 LH PGHTPG + F E K+ GD LF+ G+GRTD GD T++ SI+ +L L Sbjct: 130 ---ALHTPGHTPGSMSFWFSEAKLLIAGDTLFRRGVGRTDLWGGDQATIVRSIKQRLYTL 186 Query: 183 NDDIIIIAGHGSYTTIGQEKRSNPFLNS 210 +++ +I GHG T +G E R NPF+ + Sbjct: 187 DEEATVITGHGPDTRLGDEMRENPFVRA 214 Lambda K H 0.321 0.142 0.430 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: 152 Number of extensions: 7 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: 212 Length of database: 214 Length adjustment: 22 Effective length of query: 190 Effective length of database: 192 Effective search space: 36480 Effective search space used: 36480 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