Align lactoylglutathione lyase (EC 4.4.1.5) (characterized)
to candidate 15772 b1651 glyoxalase I, Ni-dependent (NCBI)
Query= BRENDA::P0AC81 (135 letters) >FitnessBrowser__Keio:15772 Length = 135 Score = 275 bits (703), Expect = 2e-79 Identities = 135/135 (100%), Positives = 135/135 (100%) Query: 1 MRLLHTMLRVGDLQRSIDFYTKVLGMKLLRTSENPEYKYSLAFVGYGPETEEAVIELTYN 60 MRLLHTMLRVGDLQRSIDFYTKVLGMKLLRTSENPEYKYSLAFVGYGPETEEAVIELTYN Sbjct: 1 MRLLHTMLRVGDLQRSIDFYTKVLGMKLLRTSENPEYKYSLAFVGYGPETEEAVIELTYN 60 Query: 61 WGVDKYELGTAYGHIALSVDNAAEACEKIRQNGGNVTREAGPVKGGTTVIAFVEDPDGYK 120 WGVDKYELGTAYGHIALSVDNAAEACEKIRQNGGNVTREAGPVKGGTTVIAFVEDPDGYK Sbjct: 61 WGVDKYELGTAYGHIALSVDNAAEACEKIRQNGGNVTREAGPVKGGTTVIAFVEDPDGYK 120 Query: 121 IELIEEKDAGRGLGN 135 IELIEEKDAGRGLGN Sbjct: 121 IELIEEKDAGRGLGN 135 Lambda K H 0.315 0.137 0.397 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: 177 Number of extensions: 1 Number of successful extensions: 1 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: 135 Length of database: 135 Length adjustment: 15 Effective length of query: 120 Effective length of database: 120 Effective search space: 14400 Effective search space used: 14400 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: 42 (22.0 bits) S2: 42 (20.8 bits)
Align candidate 15772 b1651 (glyoxalase I, Ni-dependent (NCBI))
to HMM TIGR00068 (gloA: lactoylglutathione lyase (EC 4.4.1.5))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR00068.hmm # target sequence database: /tmp/gapView.15715.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00068 [M=150] Accession: TIGR00068 Description: glyox_I: lactoylglutathione lyase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-73 230.0 0.0 4.2e-73 229.9 0.0 1.0 1 lcl|FitnessBrowser__Keio:15772 b1651 glyoxalase I, Ni-dependent Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:15772 b1651 glyoxalase I, Ni-dependent (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 229.9 0.0 4.2e-73 4.2e-73 17 149 .. 2 134 .. 1 135 [] 0.98 Alignments for each domain: == domain 1 score: 229.9 bits; conditional E-value: 4.2e-73 TIGR00068 17 lllhtmlrvgdldksldfytevlGmkllrkkdfpeekfslaflgyedessaavieLtynwgtekydlGngfGhiaiavd 95 +llhtmlrvgdl++s+dfyt+vlGmkllr++++pe+k+slaf+gy++e+++avieLtynwg++ky+lG+++Ghia++vd lcl|FitnessBrowser__Keio:15772 2 RLLHTMLRVGDLQRSIDFYTKVLGMKLLRTSENPEYKYSLAFVGYGPETEEAVIELTYNWGVDKYELGTAYGHIALSVD 80 79***************************************************************************** PP TIGR00068 96 dvykacervkakGgkvvrepgpvkggtkviafvkDPDGykiellekkktkealg 149 ++++ace+++++Gg+v+re+gpvkggt+viafv+DPDGykiel+e+k++ ++lg lcl|FitnessBrowser__Keio:15772 81 NAAEACEKIRQNGGNVTREAGPVKGGTTVIAFVEDPDGYKIELIEEKDAGRGLG 134 ***********************************************9998876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (150 nodes) Target sequences: 1 (135 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 4.12 // [ok]
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