Align lactoylglutathione lyase (EC 4.4.1.5) (characterized)
to candidate 3607221 Dshi_0637 Glyoxalase/bleomycin resistance protein/dioxygenase (RefSeq)
Query= BRENDA::Q9CJC0 (389 letters) >FitnessBrowser__Dino:3607221 Length = 307 Score = 118 bits (296), Expect = 2e-31 Identities = 93/294 (31%), Positives = 128/294 (43%), Gaps = 22/294 (7%) Query: 16 TLGGVHHVTAITSSAQKIYDFFTNILGLRLAKLTVNQDDYETYHLFFTEEDGH-GADMTF 74 T+ G+HHVTAI+ Q DFFT LG RL K TVN D +TYHL++ E G +TF Sbjct: 5 TIPGLHHVTAISGPPQDNLDFFTGTLGQRLVKKTVNFDAPDTYHLYYGNETAEPGTILTF 64 Query: 75 FDFKDIPKGNHGVNNIERASFRVPTDASLDYWTRRFDNAHVKHGEISSKFGQKTLEFEDF 134 F F D G G ++ VP D W R + +FGQ+ + D Sbjct: 65 FPFVDAGPGRAGPGMASAYAYAVPA-GRFDGWMARLAEDAIDFNGPVERFGQRVITLRDP 123 Query: 135 DGQLYQLISDQNNSGDDSKGRSWQLSNVPQEHGITGLGPVFVKVENAENLRTILETVFGF 194 DG +LI +++ P + G V + + E +L VFG+ Sbjct: 124 DGAPVELIETD------------RVAQAP----LDGFHSVTLWEADPEPTAKLLTEVFGY 167 Query: 195 RYAGQEDD---LHLFEVANGGNGAALILQEAGEKEAYAYQGYGTIHHLALGTANPETLNY 251 G E L VA G A++ + + G GTIHH+A + +T Sbjct: 168 TDGGTETGEGIERLRLVAPGDARGAVVDLIRTDTPSIGRSGAGTIHHVAFRAQDHDTHMG 227 Query: 252 WIERIKAFRLPHSGLVDRFYFSSEYVRVAPGVLFEIATYTPGIGALDMAKSGLG 305 W E++ + ++DR YF + Y R GVLFEIAT PG A D LG Sbjct: 228 WREKLLGLGHGLTPVIDRQYFDAIYFREPGGVLFEIATDPPGF-ATDEPMEALG 280 Lambda K H 0.316 0.135 0.399 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: 347 Number of extensions: 21 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 389 Length of database: 307 Length adjustment: 29 Effective length of query: 360 Effective length of database: 278 Effective search space: 100080 Effective search space used: 100080 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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