Align Muconolactone Delta-isomerase; MIase; EC 5.3.3.4 (characterized)
to candidate HSERO_RS06530 HSERO_RS06530 muconolactone delta-isomerase
Query= SwissProt::P80573 (92 letters) >FitnessBrowser__HerbieS:HSERO_RS06530 Length = 95 Score = 114 bits (284), Expect = 3e-31 Identities = 52/91 (57%), Positives = 70/91 (76%) Query: 1 MLYLVRMDVNLPHDMPAAQADDIKAREKAYAQQLQHEGKWQQLYRVVGEYANYSIFDVGS 60 ML++V+M VN+P + A AD +K EK +Q+LQ EGKW+ L+RVVG+YAN SIF+V Sbjct: 1 MLFMVQMQVNIPATLDKAVADQLKKDEKEMSQKLQREGKWRDLWRVVGQYANVSIFNVSG 60 Query: 61 HDELHTLLSGLPLFPYMKIHVTPLAKHPSSI 91 +DELH +LS LPL+P+M I VTPL +HPS+I Sbjct: 61 NDELHNILSALPLYPFMTISVTPLTQHPSAI 91 Lambda K H 0.321 0.136 0.413 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: 46 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: 92 Length of database: 95 Length adjustment: 10 Effective length of query: 82 Effective length of database: 85 Effective search space: 6970 Effective search space used: 6970 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: 39 (21.0 bits) S2: 39 (19.6 bits)
Align candidate HSERO_RS06530 HSERO_RS06530 (muconolactone delta-isomerase)
to HMM TIGR03221 (catC: muconolactone delta-isomerase (EC 5.3.3.4))
# 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/TIGR03221.hmm # target sequence database: /tmp/gapView.11251.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03221 [M=90] Accession: TIGR03221 Description: muco_delta: muconolactone delta-isomerase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-46 141.8 0.1 3.3e-46 141.6 0.1 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS06530 HSERO_RS06530 muconolactone delt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS06530 HSERO_RS06530 muconolactone delta-isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 141.6 0.1 3.3e-46 3.3e-46 1 90 [] 2 91 .. 2 91 .. 0.99 Alignments for each domain: == domain 1 score: 141.6 bits; conditional E-value: 3.3e-46 TIGR03221 1 lflvrmdvnlPedlpaekaaelkaeekalaqelqreGkwrhlwrvvGeyanvsifdvesndelhellsgl 70 lf+v+m+vn+P l+++ a++lk +ek+++q+lqreGkwr+lwrvvG+yanvsif+v+ ndelh++ls+l lcl|FitnessBrowser__HerbieS:HSERO_RS06530 2 LFMVQMQVNIPATLDKAVADQLKKDEKEMSQKLQREGKWRDLWRVVGQYANVSIFNVSGNDELHNILSAL 71 8********************************************************************* PP TIGR03221 71 PlfpymdievtalarhPsai 90 Pl+p+m i+vt+l++hPsai lcl|FitnessBrowser__HerbieS:HSERO_RS06530 72 PLYPFMTISVTPLTQHPSAI 91 ******************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (90 nodes) Target sequences: 1 (95 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 2.75 // [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