Align chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_084704279.1 BS73_RS23080 chorismate mutase
Query= BRENDA::P9WIC1 (105 letters) >NCBI__GCF_000744815.1:WP_084704279.1 Length = 107 Score = 66.2 bits (160), Expect = 1e-16 Identities = 35/71 (49%), Positives = 49/71 (69%), Gaps = 1/71 (1%) Query: 33 REEIDRLDAEILALVKRRAEVSKAIGKARMASGGTRLVHSREMKVIERY-SELGPDGKDL 91 RE ID LD E+L +VK R VS + +AR+A+GG RL +RE +++ R+ +ELG G +L Sbjct: 36 RERIDALDGELLRIVKERMAVSARVQRARIATGGPRLSLAREQQILARFHAELGRAGTEL 95 Query: 92 AILLLRLGRGR 102 +LLL L RGR Sbjct: 96 GMLLLELSRGR 106 Lambda K H 0.317 0.136 0.375 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: 40 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: 105 Length of database: 107 Length adjustment: 11 Effective length of query: 94 Effective length of database: 96 Effective search space: 9024 Effective search space used: 9024 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: 40 (21.2 bits) S2: 40 (20.0 bits)
Align candidate WP_084704279.1 BS73_RS23080 (chorismate mutase)
to HMM TIGR01808 (chorismate mutase (EC 5.4.99.5))
# 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.aa/TIGR01808.hmm # target sequence database: /tmp/gapView.1441759.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01808 [M=74] Accession: TIGR01808 Description: CM_M_hiGC-arch: chorismate mutase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-20 59.4 0.9 1.7e-20 59.2 0.9 1.1 1 NCBI__GCF_000744815.1:WP_084704279.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000744815.1:WP_084704279.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 59.2 0.9 1.7e-20 1.7e-20 2 74 .] 32 105 .. 31 105 .. 0.97 Alignments for each domain: == domain 1 score: 59.2 bits; conditional E-value: 1.7e-20 TIGR01808 2 ikklReEidrlDaeilslvKrRleisqaiGKirkesggtrlvrkREvevierf.aelGeegkelaellLrlgr 73 i + Re id lD e+l +vK R+ +s + ++r + gg+rl RE++++ rf aelG g el llL+l+r NCBI__GCF_000744815.1:WP_084704279.1 32 IAQARERIDALDGELLRIVKERMAVSARVQRARIATGGPRLSLAREQQILARFhAELGRAGTELGMLLLELSR 104 5678********************************************************************9 PP TIGR01808 74 g 74 g NCBI__GCF_000744815.1:WP_084704279.1 105 G 105 7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (74 nodes) Target sequences: 1 (107 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: 4.38 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
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