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 WP_057506775.1 ABB28_RS00665 chorismate mutase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_001431535.1:WP_057506775.1 Length = 398 Score = 330 bits (847), Expect = 3e-95 Identities = 173/360 (48%), Positives = 242/360 (67%), Gaps = 7/360 (1%) Query: 7 LKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAV-FYRPEREAWVLKHIM 65 L +R +ID +D I LI+ERAR A +V + K K AV +YRPEREA VL+ ++ Sbjct: 43 LADVRGKIDQIDRDIQSLIAERARFAHQVGKAKG----KLAAAVDYYRPEREAQVLRMVV 98 Query: 66 ELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKPMA 125 + N+GPL +E + ++REIMS+CLA ++PL++ YLGPEGTFSQ A LKHFG S + PMA Sbjct: 99 DRNEGPLSDELLVHVYREIMSACLAQQEPLKIGYLGPEGTFSQQAVLKHFGRSALGLPMA 158 Query: 126 AIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVGET 185 +I+EVF+EV AG +FGVVPVENS +G + TLD FL ++ ICGE ELR+ +++ + Sbjct: 159 SIEEVFQEVEAGNADFGVVPVENSGQGTIQITLDMFLTSNLKICGEAELRVQQYIM-SRS 217 Query: 186 TKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMAA 245 + I RIY+H QS Q WL A+ P E++ VSSNA+ A+R ++ ++AAI G+ A Sbjct: 218 GHLEDIERIYAHPQSFMQTSAWLRANLPKAEKIPVSSNAEGARRARNADDAAAIGGENAG 277 Query: 246 QLYGLSKLAEK-IEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELLMPFH 304 +Y L K+ K I++ N+TRFL+IG P +G D+TS++V + +KPGAL ++L PF Sbjct: 278 HVYNLKKVVTKPIQNDADNTTRFLVIGRSLFPSSGHDRTSVLVLIHDKPGALFDVLSPFA 337 Query: 305 SNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYPKAV 364 +GI + RIE+RPS GKW Y FFID GH D ++ L ++ A +KVLGSYP AV Sbjct: 338 RHGISMNRIESRPSHHGKWEYGFFIDLSGHIDDAPMQAALAELEGHAAQIKVLGSYPVAV 397 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: 385 Number of extensions: 17 Number of successful extensions: 4 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: 398 Length adjustment: 30 Effective length of query: 335 Effective length of database: 368 Effective search space: 123280 Effective search space used: 123280 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: 50 (23.9 bits)
Align candidate WP_057506775.1 ABB28_RS00665 (chorismate mutase)
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.18942.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-27 81.3 1.1 2.2e-26 78.3 0.7 2.4 2 lcl|NCBI__GCF_001431535.1:WP_057506775.1 ABB28_RS00665 chorismate mutase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057506775.1 ABB28_RS00665 chorismate mutase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 78.3 0.7 2.2e-26 2.2e-26 1 76 [] 43 118 .. 43 118 .. 0.98 2 ? 0.4 0.0 0.042 0.042 50 75 .. 143 167 .. 140 168 .. 0.83 Alignments for each domain: == domain 1 score: 78.3 bits; conditional E-value: 2.2e-26 TIGR01807 1 LkelRnkiDaiDdrildLlseRaklakavgelKkksaseaviYRPeREaavlrrlkelnkGpLdqeava 69 L+++R kiD iD i L+ eRa++a++vg+ K+k a+ YRPeREa+vlr + ++n+GpL +e + lcl|NCBI__GCF_001431535.1:WP_057506775.1 43 LADVRGKIDQIDRDIQSLIAERARFAHQVGKAKGKLAAAVDYYRPEREAQVLRMVVDRNEGPLSDELLV 111 6789***************************************************************** PP TIGR01807 70 rifrEim 76 ++rEim lcl|NCBI__GCF_001431535.1:WP_057506775.1 112 HVYREIM 118 ******9 PP == domain 2 score: 0.4 bits; conditional E-value: 0.042 TIGR01807 50 avlrrlkelnkGpLdqeavarifrEi 75 avl+++ G L+ +++ +f+E+ lcl|NCBI__GCF_001431535.1:WP_057506775.1 143 AVLKHFGRSALG-LPMASIEEVFQEV 167 678888777777.8999********8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (76 nodes) Target sequences: 1 (398 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: 8.53 // [ok]
This GapMind analysis is from Apr 10 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