Align lactoylglutathione lyase (EC 4.4.1.5) (characterized)
to candidate 6937695 Sama_1837 lactoylglutathione lyase (RefSeq)
Query= BRENDA::P0AC81 (135 letters) >FitnessBrowser__SB2B:6937695 Length = 136 Score = 183 bits (464), Expect = 9e-52 Identities = 91/134 (67%), Positives = 108/134 (80%), Gaps = 1/134 (0%) Query: 2 RLLHTMLRVGDLQRSIDFYTKVLGMKLLRTSENPEYKYSLAFVGYGPETE-EAVIELTYN 60 ++LHTM+RV +L++SI FYT+VLGM LLRTSENPEY+YSLAFVGYG E + AVIELT+N Sbjct: 3 QILHTMVRVANLEKSIAFYTEVLGMTLLRTSENPEYRYSLAFVGYGEEAKGAAVIELTWN 62 Query: 61 WGVDKYELGTAYGHIALSVDNAAEACEKIRQNGGNVTREAGPVKGGTTVIAFVEDPDGYK 120 W DKYELGT +GHIA+ + +ACE I + GG VTR GPV GGTT IAFVEDPDGYK Sbjct: 63 WDTDKYELGTGFGHIAIGKADIYKACEDIAKAGGKVTRAPGPVAGGTTEIAFVEDPDGYK 122 Query: 121 IELIEEKDAGRGLG 134 IELI+ K A +GLG Sbjct: 123 IELIQMKSAMQGLG 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: 116 Number of extensions: 2 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 6937695 Sama_1837 (lactoylglutathione lyase (RefSeq))
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.3119077.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-65 203.6 0.0 5.8e-65 203.4 0.0 1.0 1 FitnessBrowser__SB2B:6937695 Domain annotation for each sequence (and alignments): >> FitnessBrowser__SB2B:6937695 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 203.4 0.0 5.8e-65 5.8e-65 17 148 .. 3 135 .. 1 136 [] 0.96 Alignments for each domain: == domain 1 score: 203.4 bits; conditional E-value: 5.8e-65 TIGR00068 17 lllhtmlrvgdldksldfytevlGmkllrkkdfpeekfslaflgyedess.aavieLtynwgtekydlGngfGhiaiavdd 96 ++lhtm+rv +l+ks+ fytevlGm+llr++++pe+++slaf+gy++e++ aavieLt+nw+t+ky+lG+gfGhiai+ d FitnessBrowser__SB2B:6937695 3 QILHTMVRVANLEKSIAFYTEVLGMTLLRTSENPEYRYSLAFVGYGEEAKgAAVIELTWNWDTDKYELGTGFGHIAIGKAD 83 699*******************************************99872689*************************** PP TIGR00068 97 vykacervkakGgkvvrepgpvkggtkviafvkDPDGykiellekkktkeal 148 +ykace + ++Ggkv+r pgpv ggt++iafv+DPDGykiel++ k++ ++l FitnessBrowser__SB2B:6937695 84 IYKACEDIAKAGGKVTRAPGPVAGGTTEIAFVEDPDGYKIELIQMKSAMQGL 135 **********************************************988765 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 9.48 // [ok]
This GapMind analysis is from Apr 09 2024. 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