Align Muconolactone isomerase (EC 5.3.3.4) (characterized)
to candidate Pf1N1B4_5804 Muconolactone isomerase (EC 5.3.3.4)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3823 (96 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5804 Length = 96 Score = 186 bits (472), Expect = 6e-53 Identities = 89/96 (92%), Positives = 93/96 (96%) Query: 1 MLFHVKMTVNLPVDMNPEVAAKLKADEKALAQRLQEQGKWRHLWRIAGHYANYSVFDVDS 60 MLFHVKMTVNLPVDMNPE AA+LKADEKALAQRLQEQGKWRHLWRIAG YANYSVFDVDS Sbjct: 1 MLFHVKMTVNLPVDMNPERAAQLKADEKALAQRLQEQGKWRHLWRIAGLYANYSVFDVDS 60 Query: 61 VQELHDLLMQLPLFPYMAIEIDAMCRHPSSIRDDDR 96 VQELHDLLMQLPL+PYMAIE+ AMCRHPSSIR+DDR Sbjct: 61 VQELHDLLMQLPLYPYMAIEVTAMCRHPSSIREDDR 96 Lambda K H 0.324 0.136 0.422 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: 87 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: 96 Length of database: 96 Length adjustment: 10 Effective length of query: 86 Effective length of database: 86 Effective search space: 7396 Effective search space used: 7396 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 39 (21.1 bits) S2: 39 (19.6 bits)
Align candidate Pf1N1B4_5804 (Muconolactone isomerase (EC 5.3.3.4))
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.32026.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-50 154.7 0.1 3e-50 154.6 0.1 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5804 Muconolactone isomerase (EC 5.3. Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5804 Muconolactone isomerase (EC 5.3.3.4) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 154.6 0.1 3e-50 3e-50 1 90 [] 2 91 .. 2 91 .. 0.99 Alignments for each domain: == domain 1 score: 154.6 bits; conditional E-value: 3e-50 TIGR03221 1 lflvrmdvnlPedlpaekaaelkaeekalaqelqreGkwrhlwrvvGeyanvsifdvesndelhel 66 lf+v+m+vnlP+d+++e+aa+lka+ekalaq+lq++Gkwrhlwr++G yan+s+fdv+s +elh+l lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5804 2 LFHVKMTVNLPVDMNPERAAQLKADEKALAQRLQEQGKWRHLWRIAGLYANYSVFDVDSVQELHDL 67 8***************************************************************** PP TIGR03221 67 lsglPlfpymdievtalarhPsai 90 l++lPl+pym ievta++rhPs+i lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5804 68 LMQLPLYPYMAIEVTAMCRHPSSI 91 **********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (90 nodes) Target sequences: 1 (96 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: 4.06 // [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