Align lactoylglutathione lyase (EC 4.4.1.5) (characterized)
to candidate WP_086509516.1 BZY95_RS08510 lactoylglutathione lyase
Query= BRENDA::Q9HU72 (176 letters) >NCBI__GCF_002151265.1:WP_086509516.1 Length = 177 Score = 192 bits (488), Expect = 3e-54 Identities = 100/177 (56%), Positives = 126/177 (71%), Gaps = 4/177 (2%) Query: 1 MSFNTEVQPGICMEPDAITQEYVFNHTMLRVKDPKRSLDFYSRVLGMRLLRRLDFEEGRF 60 MSF E PG+ P A +Q + NHTMLRVKDP+++L FY+RV GMR++RRLDFEE F Sbjct: 1 MSFKGEQHPGV-QTPTADSQGFRLNHTMLRVKDPEKALAFYTRVFGMRVMRRLDFEEMSF 59 Query: 61 SLYFLA-MTRGEEVPDAVDERQRYTFGRQSVLELTHNWGSES-DDSQYHNGNQDPRGFGH 118 SLYFLA + GE+VP+ ER +TF + +LELTHNWG+ES DD YH+GN P+GFGH Sbjct: 60 SLYFLARLDDGEQVPEDQGERTVWTFSQTGLLELTHNWGTESQDDFAYHDGNAQPQGFGH 119 Query: 119 ICFSVPDLVAACERFETLGVNFVKPLDRG-MKNVAFISDPDGYWVEIVQASLNGEMG 174 ICFSVPDL AA F+ V FVK D+G MK+V F+ D DGYW+E++QA +G Sbjct: 120 ICFSVPDLDAAEAWFDANDVTFVKRSDQGKMKDVIFVKDVDGYWIEVIQADRLSALG 176 Lambda K H 0.322 0.139 0.428 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: 139 Number of extensions: 8 Number of successful extensions: 4 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: 176 Length of database: 177 Length adjustment: 19 Effective length of query: 157 Effective length of database: 158 Effective search space: 24806 Effective search space used: 24806 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 WP_086509516.1 BZY95_RS08510 (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.19507.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.7e-46 141.6 0.0 8.3e-46 141.3 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086509516.1 BZY95_RS08510 lactoylglutathione Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086509516.1 BZY95_RS08510 lactoylglutathione lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 141.3 0.0 8.3e-46 8.3e-46 10 144 .. 15 172 .. 6 176 .. 0.94 Alignments for each domain: == domain 1 score: 141.3 bits; conditional E-value: 8.3e-46 TIGR00068 10 deatkkylllhtmlrvgdldksldfytevlGmkllrkkdfpeekfslaflgyedessa........... 67 +++++l htmlrv+d++k+l fyt+v+Gm+++r+ df+e+ fsl+fl+ d+ ++ lcl|NCBI__GCF_002151265.1:WP_086509516.1 15 TADSQGFRLNHTMLRVKDPEKALAFYTRVFGMRVMRRLDFEEMSFSLYFLARLDDGEQvpedqgertvw 83 556789*********************************************98888888********** PP TIGR00068 68 .....avieLtynwgtek.....ydlGn....gfGhiaiavddvykacervkakGgkvvrepgpvkggt 122 +eLt+nwgte+ y+ Gn gfGhi +v+d+ +a + a+ + +v+++ ++g++ lcl|NCBI__GCF_002151265.1:WP_086509516.1 84 tfsqtGLLELTHNWGTESqddfaYHDGNaqpqGFGHICFSVPDLDAAEAWFDANDVTFVKRS--DQGKM 150 ***9999**********99*******************************************..9**** PP TIGR00068 123 kviafvkDPDGykiellekkkt 144 k + fvkD DGy+ie+++ ++ lcl|NCBI__GCF_002151265.1:WP_086509516.1 151 KDVIFVKDVDGYWIEVIQADRL 172 *****************98765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (150 nodes) Target sequences: 1 (177 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: 6.48 // [ok]
This GapMind analysis is from Sep 24 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