Align lactoylglutathione lyase (EC 4.4.1.5) (characterized)
to candidate H281DRAFT_04643 H281DRAFT_04643 methylmalonyl-CoA epimerase
Query= BRENDA::P0A0T3 (138 letters) >FitnessBrowser__Burk376:H281DRAFT_04643 Length = 128 Score = 216 bits (550), Expect = 1e-61 Identities = 99/127 (77%), Positives = 114/127 (89%) Query: 1 MRLLHTMLRVGNLEKSLDFYQNVLGMKLLRRKDYPEGRFTLAFVGYGDETDSTVLELTHN 60 MRLLHTMLRVG+L++S+ FY +LGMKLLRR+DYP+G+FTLAFVGY DE D TV+ELTHN Sbjct: 1 MRLLHTMLRVGDLDRSIAFYTELLGMKLLRREDYPDGKFTLAFVGYTDERDGTVIELTHN 60 Query: 61 WDTERYDLGNAYGHIAVEVDDAYEACERVKRQGGNVVREAGPMKHGTTVIAFVEDPDGYK 120 WDT YDLGN +GH+AVEV+DAY AC+++K QGG VVREAGPMKHGTTVIAFV DPDGYK Sbjct: 61 WDTPAYDLGNGFGHLAVEVEDAYAACDKIKAQGGTVVREAGPMKHGTTVIAFVTDPDGYK 120 Query: 121 IEFIQKK 127 IEFIQKK Sbjct: 121 IEFIQKK 127 Lambda K H 0.318 0.137 0.405 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: 135 Number of extensions: 2 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: 138 Length of database: 128 Length adjustment: 15 Effective length of query: 123 Effective length of database: 113 Effective search space: 13899 Effective search space used: 13899 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 (21.7 bits) S2: 42 (20.8 bits)
Align candidate H281DRAFT_04643 H281DRAFT_04643 (methylmalonyl-CoA epimerase)
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.6554.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-68 214.1 0.1 3.4e-68 214.0 0.1 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_04643 H281DRAFT_04643 methylmalonyl-Co Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_04643 H281DRAFT_04643 methylmalonyl-CoA epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 214.0 0.1 3.4e-68 3.4e-68 17 143 .. 2 128 .] 1 128 [] 0.99 Alignments for each domain: == domain 1 score: 214.0 bits; conditional E-value: 3.4e-68 TIGR00068 17 lllhtmlrvgdldksldfytevlGmkllrkkdfpeekfslaflgyedessaavieLtynwgtekyd 82 +llhtmlrvgdld+s+ fyte+lGmkllr++d+p+ kf+laf+gy de + +vieLt+nw+t yd lcl|FitnessBrowser__Burk376:H281DRAFT_04643 2 RLLHTMLRVGDLDRSIAFYTELLGMKLLRREDYPDGKFTLAFVGYTDERDGTVIELTHNWDTPAYD 67 79**************************************************************** PP TIGR00068 83 lGngfGhiaiavddvykacervkakGgkvvrepgpvkggtkviafvkDPDGykiellekkk 143 lGngfGh+a++v+d+y+ac+++ka+Gg vvre+gp+k+gt+viafv DPDGykie+++kkk lcl|FitnessBrowser__Burk376:H281DRAFT_04643 68 LGNGFGHLAVEVEDAYAACDKIKAQGGTVVREAGPMKHGTTVIAFVTDPDGYKIEFIQKKK 128 **********************************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (150 nodes) Target sequences: 1 (128 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 3.69 // [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