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_019556286.1 F612_RS0103095 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_000381085.1:WP_019556286.1 Length = 363 Score = 321 bits (823), Expect = 2e-92 Identities = 175/364 (48%), Positives = 242/364 (66%), Gaps = 3/364 (0%) Query: 2 SEADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVL 61 +E QL +R +ID++D +I DLI +RA CAQ+VA +KT +AVFYRPEREA VL Sbjct: 3 TEQMQLTEIRNQIDTIDAQIQDLIGQRAACAQKVADIKTQG--DNVDAVFYRPEREAQVL 60 Query: 62 KHIMELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVIS 121 + + N L +EEMA+LFREIMS+CLALEQP VAYLGPEG++S A+ +K FG SV S Sbjct: 61 RAVKARNTSLLPDEEMAKLFREIMSACLALEQPTTVAYLGPEGSYSHASVIKQFGSSVHS 120 Query: 122 KPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLL 181 ++ I+EVF V G ++G+VPVENS+EG V T ++ + D+ + GEV L IHH LL Sbjct: 121 IAVSTIEEVFEAVEKGDASYGMVPVENSSEGVVKSTQNALVTTDLKVSGEVALEIHHCLL 180 Query: 182 VGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAG 241 T + I +I +H Q+L QC +W+ + P E AV+SNA AAK K++ AAIA Sbjct: 181 SKSKT-VENIHKIVAHQQALGQCEQWIKNNLPWAEIEAVASNALAAKMAKTDSAVAAIAS 239 Query: 242 DMAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELLM 301 + AAQLY L+ L IED+ NST+F ++G +G+DKT++IVSM+N+ GAL ++L Sbjct: 240 EQAAQLYQLNILESHIEDQSDNSTKFWVVGRDATQSSGEDKTAMIVSMKNQSGALLDILS 299 Query: 302 PFHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYP 361 F S GI++TRI +RPS W Y FFID MGH +D +K L ++ ++ K+LGS+P Sbjct: 300 CFSSRGINMTRIISRPSLDTTWDYQFFIDVMGHQEDENLKQALAEVKSKSAFFKLLGSFP 359 Query: 362 KAVL 365 + L Sbjct: 360 VSPL 363 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: 317 Number of extensions: 9 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: 365 Length of database: 363 Length adjustment: 29 Effective length of query: 336 Effective length of database: 334 Effective search space: 112224 Effective search space used: 112224 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 WP_019556286.1 F612_RS0103095 (prephenate dehydratase)
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.17627.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-31 93.4 1.1 8.6e-31 92.4 0.4 2.0 2 lcl|NCBI__GCF_000381085.1:WP_019556286.1 F612_RS0103095 prephenate dehydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000381085.1:WP_019556286.1 F612_RS0103095 prephenate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 92.4 0.4 8.6e-31 8.6e-31 1 76 [] 8 84 .. 8 84 .. 0.98 2 ? -3.1 0.0 0.55 0.55 25 37 .. 338 350 .. 334 351 .. 0.77 Alignments for each domain: == domain 1 score: 92.4 bits; conditional E-value: 8.6e-31 TIGR01807 1 LkelRnkiDaiDdrildLlseRaklakavgelKkks.aseaviYRPeREaavlrrlkelnkGpLdqeavar 70 L+e+Rn+iD+iD++i dL+ +Ra +a++v+++K+++ +av+YRPeREa+vlr +k +n+ +L++e++a+ lcl|NCBI__GCF_000381085.1:WP_019556286.1 8 LTEIRNQIDTIDAQIQDLIGQRAACAQKVADIKTQGdNVDAVFYRPEREAQVLRAVKARNTSLLPDEEMAK 78 789********************************97789******************************* PP TIGR01807 71 ifrEim 76 +frEim lcl|NCBI__GCF_000381085.1:WP_019556286.1 79 LFREIM 84 *****9 PP == domain 2 score: -3.1 bits; conditional E-value: 0.55 TIGR01807 25 lakavgelKkksa 37 l +a++e+K ksa lcl|NCBI__GCF_000381085.1:WP_019556286.1 338 LKQALAEVKSKSA 350 5688999999865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (76 nodes) Target sequences: 1 (363 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: 9.16 // [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