Align lactoylglutathione lyase (EC 4.4.1.5) (characterized)
to candidate PP_3766 PP_3766 Lactoylglutathione lyase
Query= BRENDA::Q88GF8 (175 letters) >FitnessBrowser__Putida:PP_3766 Length = 175 Score = 365 bits (937), Expect = e-106 Identities = 175/175 (100%), Positives = 175/175 (100%) Query: 1 MSLHDLQTLPGVTAQPDAATAQFVFNHTMLRVKDIEKSLDFYTRVLGFRLVDKRDFPEAA 60 MSLHDLQTLPGVTAQPDAATAQFVFNHTMLRVKDIEKSLDFYTRVLGFRLVDKRDFPEAA Sbjct: 1 MSLHDLQTLPGVTAQPDAATAQFVFNHTMLRVKDIEKSLDFYTRVLGFRLVDKRDFPEAA 60 Query: 61 FSLYFLALVDPAQIPADDTARHQWMKSIPGVLELTHNHGTENDADFAYHNGNTDPRGFGH 120 FSLYFLALVDPAQIPADDTARHQWMKSIPGVLELTHNHGTENDADFAYHNGNTDPRGFGH Sbjct: 61 FSLYFLALVDPAQIPADDTARHQWMKSIPGVLELTHNHGTENDADFAYHNGNTDPRGFGH 120 Query: 121 ICISVPDVRAACARFEELEVPFQKRLQDGRMNHLAFVKDPDGYWVEVIQPTELEG 175 ICISVPDVRAACARFEELEVPFQKRLQDGRMNHLAFVKDPDGYWVEVIQPTELEG Sbjct: 121 ICISVPDVRAACARFEELEVPFQKRLQDGRMNHLAFVKDPDGYWVEVIQPTELEG 175 Lambda K H 0.323 0.139 0.431 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: 261 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: 175 Length of database: 175 Length adjustment: 19 Effective length of query: 156 Effective length of database: 156 Effective search space: 24336 Effective search space used: 24336 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 44 (21.6 bits)
Align candidate PP_3766 PP_3766 (Lactoylglutathione lyase)
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.31651.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-50 156.3 0.0 2.3e-50 156.1 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_3766 PP_3766 Lactoylglutathione lyase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_3766 PP_3766 Lactoylglutathione lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 156.1 0.0 2.3e-50 2.3e-50 7 143 .. 14 172 .. 7 175 .] 0.96 Alignments for each domain: == domain 1 score: 156.1 bits; conditional E-value: 2.3e-50 TIGR00068 7 avedeatkkylllhtmlrvgdldksldfytevlGmkllrkkdfpeekfslaflgyedessa.............. 67 a+ d at ++++ htmlrv+d++ksldfyt+vlG +l+ k+dfpe fsl+fl+ d ++ lcl|FitnessBrowser__Putida:PP_3766 14 AQPDAATAQFVFNHTMLRVKDIEKSLDFYTRVLGFRLVDKRDFPEAAFSLYFLALVDPAQIpaddtarhqwmksi 88 577899****************************************************99999************ PP TIGR00068 68 .avieLtynwgtek.....ydlGn....gfGhiaiavddvykacervkakGgkvvrepgpvkggtkviafvkDPD 132 v+eLt+n+gte+ y++Gn gfGhi i+v+dv +ac r++++ + + ++ ++g+++++afvkDPD lcl|FitnessBrowser__Putida:PP_3766 89 pGVLELTHNHGTENdadfaYHNGNtdprGFGHICISVPDVRAACARFEELEVPFQKRL--QDGRMNHLAFVKDPD 161 *************99******************************************9..*************** PP TIGR00068 133 Gykiellekkk 143 Gy++e+++ + lcl|FitnessBrowser__Putida:PP_3766 162 GYWVEVIQPTE 172 *******9865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (150 nodes) Target sequences: 1 (175 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: 5.79 // [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