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_072905145.1 BUB13_RS02375 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_900142125.1:WP_072905145.1 Length = 368 Score = 295 bits (755), Expect = 1e-84 Identities = 154/359 (42%), Positives = 229/359 (63%), Gaps = 6/359 (1%) Query: 5 DQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKHI 64 ++L LR +ID +D +ILDL+++RA V + K +S + FY P RE + + + Sbjct: 4 EELNKLREQIDGIDNQILDLLNKRAEIVIGVGKAKESS-----DGTFYVPSREKAIYERL 58 Query: 65 MELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKPM 124 N GP N+ + ++FREI+S+ L +E P++VA+LGP+ TF+ AA++ FG S P+ Sbjct: 59 TAQNAGPFPNDAVVKVFREIISASLNMELPMQVAFLGPQSTFTHMAAMQQFGLSAQLVPL 118 Query: 125 AAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVGE 184 +I VF EV G ++GVVPVENSTEG VNHTLD F D+ + E+ L I H+LL + Sbjct: 119 KSIPAVFEEVERGRAHYGVVPVENSTEGVVNHTLDMFSGSDLQVIAEIMLEISHNLL-SK 177 Query: 185 TTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMA 244 T ++I+++ SH Q+LAQCR W + + P+V V V+S A AA+ + ++AAIA + A Sbjct: 178 TGNIEQISKVVSHPQALAQCRHWFEQNLPDVPLVDVASTAAAAQMAAEDESAAAIASEAA 237 Query: 245 AQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELLMPFH 304 YGL + KIED P N TRFLIIG++ +G+DKTSI+ S++++PG L+ +L PF Sbjct: 238 VVQYGLKVVKAKIEDNPNNFTRFLIIGTKTPEKSGNDKTSIMFSIKDEPGILYRMLEPFS 297 Query: 305 SNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYPKA 363 I+L++IE+RP + W Y+FF+D +GH D I +E++ LKVLGSYP A Sbjct: 298 KRQINLSKIESRPMKHKAWEYIFFLDLIGHIDDQPISEAVEELRDYCHFLKVLGSYPIA 356 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: 318 Number of extensions: 14 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: 368 Length adjustment: 30 Effective length of query: 335 Effective length of database: 338 Effective search space: 113230 Effective search space used: 113230 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_072905145.1 BUB13_RS02375 (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.17595.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.1e-27 79.5 0.0 1.8e-26 78.5 0.0 1.5 1 lcl|NCBI__GCF_900142125.1:WP_072905145.1 BUB13_RS02375 prephenate dehydra Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900142125.1:WP_072905145.1 BUB13_RS02375 prephenate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 78.5 0.0 1.8e-26 1.8e-26 1 76 [] 6 79 .. 6 79 .. 0.98 Alignments for each domain: == domain 1 score: 78.5 bits; conditional E-value: 1.8e-26 TIGR01807 1 LkelRnkiDaiDdrildLlseRaklakavgelKkksaseaviYRPeREaavlrrlkelnkGpLdqeavari 71 L++lR++iD iD++ildLl++Ra+++ vg+ K++ s++++Y P RE a+ rl +n Gp +++av ++ lcl|NCBI__GCF_900142125.1:WP_072905145.1 6 LNKLREQIDGIDNQILDLLNKRAEIVIGVGKAKES--SDGTFYVPSREKAIYERLTAQNAGPFPNDAVVKV 74 789******************************99..99******************************** PP TIGR01807 72 frEim 76 frEi+ lcl|NCBI__GCF_900142125.1:WP_072905145.1 75 FREII 79 ***97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (76 nodes) Target sequences: 1 (368 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: 8.12 // [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