Align chorismate mutase (EC 5.4.99.5) (characterized)
to candidate CA265_RS11635 CA265_RS11635 3-deoxy-7-phosphoheptulonate synthase
Query= reanno::Pedo557:CA265_RS11635 (379 letters) >FitnessBrowser__Pedo557:CA265_RS11635 Length = 379 Score = 751 bits (1938), Expect = 0.0 Identities = 379/379 (100%), Positives = 379/379 (100%) Query: 1 MKLNLNIQSLNTWLNVNNEPLIISGPCSAETEEQLLTTAHLLAATGKVSVLRAGIWKPRT 60 MKLNLNIQSLNTWLNVNNEPLIISGPCSAETEEQLLTTAHLLAATGKVSVLRAGIWKPRT Sbjct: 1 MKLNLNIQSLNTWLNVNNEPLIISGPCSAETEEQLLTTAHLLAATGKVSVLRAGIWKPRT 60 Query: 61 RPGEFEGIGSIGLEWLKRAKAETGLPTAVEVANAKHVEEALAAGVDILWIGARSTVNPFT 120 RPGEFEGIGSIGLEWLKRAKAETGLPTAVEVANAKHVEEALAAGVDILWIGARSTVNPFT Sbjct: 61 RPGEFEGIGSIGLEWLKRAKAETGLPTAVEVANAKHVEEALAAGVDILWIGARSTVNPFT 120 Query: 121 VQEIADALKGHDVPVLIKNPVNPDLQLWIGAIERINGAGITKIGAIHRGFSSFEKSSFRN 180 VQEIADALKGHDVPVLIKNPVNPDLQLWIGAIERINGAGITKIGAIHRGFSSFEKSSFRN Sbjct: 121 VQEIADALKGHDVPVLIKNPVNPDLQLWIGAIERINGAGITKIGAIHRGFSSFEKSSFRN 180 Query: 181 EPMWELAIQLKTLCPELPIINDPSHICGNRELIPYISQKALDLDMQGLMIESHVDPSVAW 240 EPMWELAIQLKTLCPELPIINDPSHICGNRELIPYISQKALDLDMQGLMIESHVDPSVAW Sbjct: 181 EPMWELAIQLKTLCPELPIINDPSHICGNRELIPYISQKALDLDMQGLMIESHVDPSVAW 240 Query: 241 TDAKQQVTPAALAELVDRLTVREPEAPNEAFADKLADLRKSIDKIDDVLLQKLGERMAIV 300 TDAKQQVTPAALAELVDRLTVREPEAPNEAFADKLADLRKSIDKIDDVLLQKLGERMAIV Sbjct: 241 TDAKQQVTPAALAELVDRLTVREPEAPNEAFADKLADLRKSIDKIDDVLLQKLGERMAIV 300 Query: 301 EKIGEFKRDNQVTILQVNRWDAIIKKGHAFAKALKLDLNFTEKFLELVHGESIRKQTEIM 360 EKIGEFKRDNQVTILQVNRWDAIIKKGHAFAKALKLDLNFTEKFLELVHGESIRKQTEIM Sbjct: 301 EKIGEFKRDNQVTILQVNRWDAIIKKGHAFAKALKLDLNFTEKFLELVHGESIRKQTEIM 360 Query: 361 NAGKAEQGIAAEQHTEVKA 379 NAGKAEQGIAAEQHTEVKA Sbjct: 361 NAGKAEQGIAAEQHTEVKA 379 Lambda K H 0.317 0.134 0.389 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: 620 Number of extensions: 16 Number of successful extensions: 3 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: 379 Length of database: 379 Length adjustment: 30 Effective length of query: 349 Effective length of database: 349 Effective search space: 121801 Effective search space used: 121801 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: 41 (21.6 bits) S2: 50 (23.9 bits)
Align candidate CA265_RS11635 CA265_RS11635 (3-deoxy-7-phosphoheptulonate synthase)
to HMM PF01817 (CM_2)
# 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/PF01817.25.hmm # target sequence database: /tmp/gapView.443.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CM_2 [M=79] Accession: PF01817.25 Description: Chorismate mutase type II 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-21 63.3 0.7 2.8e-21 62.0 0.7 1.7 1 lcl|FitnessBrowser__Pedo557:CA265_RS11635 CA265_RS11635 3-deoxy-7-phosphoh Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS11635 CA265_RS11635 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 62.0 0.7 2.8e-21 2.8e-21 1 78 [. 279 356 .. 279 357 .. 0.98 Alignments for each domain: == domain 1 score: 62.0 bits; conditional E-value: 2.8e-21 CM_2 1 RkeIdeiDrelleLlaeRmelakeiaeyKkenglpvldpeReeevlerlregaeelgldpeavekifr 68 Rk+Id+iD+ ll+ l eRm+++++i+e+K++n++++l+ +R+++++++ + a++l+ld +++ek+++ lcl|FitnessBrowser__Pedo557:CA265_RS11635 279 RKSIDKIDDVLLQKLGERMAIVEKIGEFKRDNQVTILQVNRWDAIIKKGHAFAKALKLDLNFTEKFLE 346 99****************************************************************** PP CM_2 69 eiisesralQ 78 ++ es++ Q lcl|FitnessBrowser__Pedo557:CA265_RS11635 347 LVHGESIRKQ 356 ********99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (79 nodes) Target sequences: 1 (379 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: 10.98 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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