Align lactoylglutathione lyase (EC 4.4.1.5) (characterized)
to candidate 201201 SO2044 lactoylglutathione lyase (NCBI ptt file)
Query= BRENDA::P0AC81 (135 letters) >FitnessBrowser__MR1:201201 Length = 136 Score = 193 bits (490), Expect = 9e-55 Identities = 96/134 (71%), Positives = 109/134 (81%), Gaps = 1/134 (0%) Query: 2 RLLHTMLRVGDLQRSIDFYTKVLGMKLLRTSENPEYKYSLAFVGYGPE-TEEAVIELTYN 60 +LLHTM+RVG+L+RSI FYT+VLGMKLLRTSENPEYKYSLAFVGYG E T +AVIELTYN Sbjct: 3 QLLHTMIRVGNLERSIAFYTQVLGMKLLRTSENPEYKYSLAFVGYGEESTGQAVIELTYN 62 Query: 61 WGVDKYELGTAYGHIALSVDNAAEACEKIRQNGGNVTREAGPVKGGTTVIAFVEDPDGYK 120 WG +KY+LGT +GHIA+ D+ CE I GG VTR GPV GGTT IAFVEDPDGYK Sbjct: 63 WGTEKYDLGTGFGHIAIGDDDIYARCEAIAAAGGKVTRAPGPVAGGTTEIAFVEDPDGYK 122 Query: 121 IELIEEKDAGRGLG 134 IE I+ K A +GLG Sbjct: 123 IEFIQMKSATQGLG 136 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: 125 Number of extensions: 3 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: 135 Length of database: 136 Length adjustment: 15 Effective length of query: 120 Effective length of database: 121 Effective search space: 14520 Effective search space used: 14520 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 201201 SO2044 (lactoylglutathione lyase (NCBI ptt file))
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.15349.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-67 211.8 0.0 1.6e-67 211.7 0.0 1.0 1 lcl|FitnessBrowser__MR1:201201 SO2044 lactoylglutathione lyase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:201201 SO2044 lactoylglutathione lyase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 211.7 0.0 1.6e-67 1.6e-67 17 148 .. 3 135 .. 1 136 [] 0.96 Alignments for each domain: == domain 1 score: 211.7 bits; conditional E-value: 1.6e-67 TIGR00068 17 lllhtmlrvgdldksldfytevlGmkllrkkdfpeekfslaflgyedess.aavieLtynwgtekydlGngfGhiaiav 94 +llhtm+rvg+l++s+ fyt+vlGmkllr++++pe+k+slaf+gy++es+ +avieLtynwgtekydlG+gfGhiai+ lcl|FitnessBrowser__MR1:201201 3 QLLHTMIRVGNLERSIAFYTQVLGMKLLRTSENPEYKYSLAFVGYGEESTgQAVIELTYNWGTEKYDLGTGFGHIAIGD 81 79*******************************************99976369************************** PP TIGR00068 95 ddvykacervkakGgkvvrepgpvkggtkviafvkDPDGykiellekkktkeal 148 dd+y+ ce++ a+Ggkv+r pgpv ggt++iafv+DPDGykie+++ k+++++l lcl|FitnessBrowser__MR1:201201 82 DDIYARCEAIAAAGGKVTRAPGPVAGGTTEIAFVEDPDGYKIEFIQMKSATQGL 135 ************************************************998876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (150 nodes) Target sequences: 1 (136 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: 5.18 // [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