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_090444924.1 BLS63_RS12620 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_900100495.1:WP_090444924.1 Length = 364 Score = 640 bits (1651), Expect = 0.0 Identities = 322/365 (88%), Positives = 344/365 (94%), Gaps = 1/365 (0%) Query: 1 MSEADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWV 60 MSE +L+ALR+RIDSLDE+IL+LIS+RARCA+EVARVK + P+ E+ VFYRPEREA V Sbjct: 1 MSE-QELQALRLRIDSLDEKILELISDRARCAEEVARVKMKALPEGEKPVFYRPEREAQV 59 Query: 61 LKHIMELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVI 120 LK IME N GPL NEEMARLFREIMSSCLALE PL+VAYLGPEGTFSQAAA+KHFGH+VI Sbjct: 60 LKRIMERNAGPLGNEEMARLFREIMSSCLALENPLKVAYLGPEGTFSQAAAMKHFGHAVI 119 Query: 121 SKPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHL 180 S PMAAIDEVFREV AGAVNFGVVPVENSTEGA+NHTLDSFLEHD+VICGEVELRIHHHL Sbjct: 120 SVPMAAIDEVFREVAAGAVNFGVVPVENSTEGAINHTLDSFLEHDMVICGEVELRIHHHL 179 Query: 181 LVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIA 240 LVGE TKTD+ITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIA Sbjct: 180 LVGENTKTDKITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIA 239 Query: 241 GDMAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELL 300 GDMAA LYGL+KLAEKIEDRP NSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELL Sbjct: 240 GDMAASLYGLTKLAEKIEDRPDNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELL 299 Query: 301 MPFHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSY 360 +PFH+NGIDLTRIETRPSRSGKWTYVFFID +GHH+DPLIK+VLEKI EAVALKVLGSY Sbjct: 300 VPFHNNGIDLTRIETRPSRSGKWTYVFFIDFVGHHRDPLIKDVLEKINQEAVALKVLGSY 359 Query: 361 PKAVL 365 PKAVL Sbjct: 360 PKAVL 364 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: 518 Number of extensions: 13 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: 364 Length adjustment: 29 Effective length of query: 336 Effective length of database: 335 Effective search space: 112560 Effective search space used: 112560 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_090444924.1 BLS63_RS12620 (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.10026.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-34 102.7 2.9 5.1e-34 102.7 1.2 1.9 2 lcl|NCBI__GCF_900100495.1:WP_090444924.1 BLS63_RS12620 prephenate dehydra Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900100495.1:WP_090444924.1 BLS63_RS12620 prephenate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 102.7 1.2 5.1e-34 5.1e-34 1 76 [] 6 84 .. 6 84 .. 0.96 2 ? -2.7 0.0 0.41 0.41 66 75 .. 124 133 .. 121 134 .. 0.80 Alignments for each domain: == domain 1 score: 102.7 bits; conditional E-value: 5.1e-34 TIGR01807 1 LkelRnkiDaiDdrildLlseRaklakavgelKkks...aseaviYRPeREaavlrrlkelnkGpLdqeav 68 L++lR +iD++D++il+L+s+Ra++a++v+++K k+ ++ v+YRPeREa+vl+r++e+n GpL +e++ lcl|NCBI__GCF_900100495.1:WP_090444924.1 6 LQALRLRIDSLDEKILELISDRARCAEEVARVKMKAlpeGEKPVFYRPEREAQVLKRIMERNAGPLGNEEM 76 789*******************************9876667889*************************** PP TIGR01807 69 arifrEim 76 ar+frEim lcl|NCBI__GCF_900100495.1:WP_090444924.1 77 ARLFREIM 84 *******9 PP == domain 2 score: -2.7 bits; conditional E-value: 0.41 TIGR01807 66 eavarifrEi 75 a++ +frE+ lcl|NCBI__GCF_900100495.1:WP_090444924.1 124 AAIDEVFREV 133 5899999998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (76 nodes) Target sequences: 1 (364 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: 11.22 // [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