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_038150466.1 B076_RS0106700 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_000483485.1:WP_038150466.1 Length = 368 Score = 332 bits (852), Expect = 7e-96 Identities = 177/365 (48%), Positives = 242/365 (66%), Gaps = 3/365 (0%) Query: 1 MSEADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWV 60 M+E QL +R RIDS+DE+I +LI +RA CAQ+VA +KT E +FYRPEREA V Sbjct: 5 MTEQQQLTEIRNRIDSIDEQIQELIGQRAACAQKVADIKTQGGKV--ETIFYRPEREAQV 62 Query: 61 LKHIMELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVI 120 L+ + + N L + EMARLFREIMS+CLALEQP+ VAYLGPEG++S A+ +K FG S Sbjct: 63 LRAVKQRNTSLLPDNEMARLFREIMSACLALEQPISVAYLGPEGSYSHASVIKQFGSSAH 122 Query: 121 SKPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHL 180 +++I+EVF V G N+G+VPVENS+EG V +T + + I GEV+L +HH L Sbjct: 123 PIAVSSIEEVFATVEKGDANYGIVPVENSSEGVVKNTEKEMIHTGLTISGEVDLAVHHCL 182 Query: 181 LVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIA 240 L + + + I ++ +H+Q+L QC WL + P E AV SNA AAK + + + AAIA Sbjct: 183 L-SKGDEVELIRKVVAHSQALGQCEHWLKNNMPWAELEAVDSNALAAKMAQEDGSLAAIA 241 Query: 241 GDMAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELL 300 + AAQLYGL L IED+ N+T+F +IG + P+G+DKT++IVS+ NK GAL ELL Sbjct: 242 SEQAAQLYGLRILESNIEDQRDNTTKFWVIGRETTQPSGEDKTAMIVSIPNKSGALLELL 301 Query: 301 MPFHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSY 360 F I +TRI +RPS KW Y+FFID +GH D ++ LE++ +A K+LGSY Sbjct: 302 SCFSKRDISMTRIISRPSTDKKWDYLFFIDVLGHQVDENVRQALEEVKDKASFFKILGSY 361 Query: 361 PKAVL 365 P + L Sbjct: 362 PVSPL 366 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: 352 Number of extensions: 13 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: 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_038150466.1 B076_RS0106700 (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.5917.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-31 93.6 0.6 7.6e-31 92.5 0.6 1.6 1 lcl|NCBI__GCF_000483485.1:WP_038150466.1 B076_RS0106700 prephenate dehydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000483485.1:WP_038150466.1 B076_RS0106700 prephenate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 92.5 0.6 7.6e-31 7.6e-31 1 76 [] 11 87 .. 11 87 .. 0.97 Alignments for each domain: == domain 1 score: 92.5 bits; conditional E-value: 7.6e-31 TIGR01807 1 LkelRnkiDaiDdrildLlseRaklakavgelKkks.aseaviYRPeREaavlrrlkelnkGpLdqeavar 70 L+e+Rn+iD+iD++i +L+ +Ra +a++v+++K+++ e+++YRPeREa+vlr +k++n+ +L+++++ar lcl|NCBI__GCF_000483485.1:WP_038150466.1 11 LTEIRNRIDSIDEQIQELIGQRAACAQKVADIKTQGgKVETIFYRPEREAQVLRAVKQRNTSLLPDNEMAR 81 789*******************************996789******************************* PP TIGR01807 71 ifrEim 76 +frEim lcl|NCBI__GCF_000483485.1:WP_038150466.1 82 LFREIM 87 *****9 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 9.25 // [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