Align Bifunctional chorismate mutase/prephenate dehydratase; Chorismate mutase-prephenate dehydratase; P-protein; EC 5.4.99.5; EC 4.2.1.51 (characterized)
to candidate GFF1941 Psest_1984 chorismate mutase domain of proteobacterial P-protein, clade 2
Query= SwissProt::P27603 (365 letters) >FitnessBrowser__psRCH2:GFF1941 Length = 365 Score = 690 bits (1780), Expect = 0.0 Identities = 347/365 (95%), Positives = 357/365 (97%) Query: 1 MSEADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWV 60 MS+ADQLKALRVRIDSLDERILDLISERARCAQEVARVKTA+ + E AVFYRPEREAWV Sbjct: 1 MSDADQLKALRVRIDSLDERILDLISERARCAQEVARVKTAALAEGESAVFYRPEREAWV 60 Query: 61 LKHIMELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVI 120 LKHIMELN+GPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGH+VI Sbjct: 61 LKHIMELNRGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHAVI 120 Query: 121 SKPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHL 180 S PMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHL Sbjct: 121 STPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHL 180 Query: 181 LVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIA 240 LVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIA Sbjct: 181 LVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIA 240 Query: 241 GDMAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELL 300 GDMAAQLYGL+KLAEKIEDRP NSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELL Sbjct: 241 GDMAAQLYGLTKLAEKIEDRPDNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELL 300 Query: 301 MPFHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSY 360 +PFH+NGIDLTRIETRPSRSGKWTYVFFID +GHHQDPLIK+VLEKIG EAVALKVLGSY Sbjct: 301 VPFHANGIDLTRIETRPSRSGKWTYVFFIDFLGHHQDPLIKDVLEKIGQEAVALKVLGSY 360 Query: 361 PKAVL 365 PKAVL Sbjct: 361 PKAVL 365 Lambda K H 0.319 0.133 0.390 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: 546 Number of extensions: 9 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: 365 Length of database: 365 Length adjustment: 30 Effective length of query: 335 Effective length of database: 335 Effective search space: 112225 Effective search space used: 112225 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 (21.8 bits) S2: 49 (23.5 bits)
Align candidate GFF1941 Psest_1984 (chorismate mutase domain of proteobacterial P-protein, clade 2)
to HMM TIGR01807 (pheA: 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/TIGR01807.hmm # target sequence database: /tmp/gapView.3447.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01807 [M=76] Accession: TIGR01807 Description: CM_P2: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-38 115.1 1.0 7.1e-38 115.1 1.0 1.9 2 lcl|FitnessBrowser__psRCH2:GFF1941 Psest_1984 chorismate mutase dom Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF1941 Psest_1984 chorismate mutase domain of proteobacterial P-protein, clade 2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 115.1 1.0 7.1e-38 7.1e-38 1 76 [] 7 85 .. 7 85 .. 0.96 2 ? -2.5 0.0 0.34 0.34 67 76 .] 126 135 .. 123 135 .. 0.80 Alignments for each domain: == domain 1 score: 115.1 bits; conditional E-value: 7.1e-38 TIGR01807 1 LkelRnkiDaiDdrildLlseRaklakavgelKkks...aseaviYRPeREaavlrrlkelnkGpLdqeavarifrE 74 Lk+lR++iD++D+rildL+seRa++a++v+++K+++ + av+YRPeREa+vl++++eln+GpLd+e++ar+frE lcl|FitnessBrowser__psRCH2:GFF1941 7 LKALRVRIDSLDERILDLISERARCAQEVARVKTAAlaeGESAVFYRPEREAWVLKHIMELNRGPLDNEEMARLFRE 83 799*******************************987666789********************************** PP TIGR01807 75 im 76 im lcl|FitnessBrowser__psRCH2:GFF1941 84 IM 85 *9 PP == domain 2 score: -2.5 bits; conditional E-value: 0.34 TIGR01807 67 avarifrEim 76 a++ +frE++ lcl|FitnessBrowser__psRCH2:GFF1941 126 AIDEVFREVV 135 78999**995 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (76 nodes) Target sequences: 1 (365 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: 9.45 // [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