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_084057312.1 B9A12_RS07670 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_900176285.1:WP_084057312.1 Length = 374 Score = 276 bits (706), Expect = 6e-79 Identities = 142/364 (39%), Positives = 221/364 (60%), Gaps = 8/364 (2%) Query: 1 MSEADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAV-FYRPEREAW 59 M + L+ LR ID+LD+ ILD ++ R R +++ R+K AE+ + + P RE Sbjct: 1 MMKGQSLEELRRGIDALDQEILDRLNRRMRLVEQIGRIK------AEKGLDTFDPGREEA 54 Query: 60 VLKHIMELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSV 119 V + ++E + GPL E + ++REI+++ L+QPL+VA+LGPE T+S AAL FGHS Sbjct: 55 VCRRLVEASPGPLPAESVRAIYREILAASRKLQQPLKVAFLGPEWTYSHLAALSVFGHSA 114 Query: 120 ISKPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHH 179 P +A+ +VF + G VVP+ENS EG + T+D E + + GE L + H Sbjct: 115 HYLPQSALVDVFDHLSKGLARVAVVPIENSLEGGIGQTMDLLYERPVRVVGECYLEVAH- 173 Query: 180 LLVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAI 239 L + + ++Y+H +L QCR+W+ H + E +S A AA++ SE + AA+ Sbjct: 174 CLCSRASDPGSVRKLYAHPHALGQCRRWISEHLRHAEIYECASTAQAARQAASEASGAAL 233 Query: 240 AGDMAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHEL 299 AA+ YGLS LAE++ED N+TRF+++G +E PTGDDKTSI+ ++ +KPGAL+ + Sbjct: 234 CNVKAAENYGLSVLAERVEDHAGNTTRFIVLGFEENSPTGDDKTSILFAVADKPGALYRV 293 Query: 300 LMPFHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGS 359 L +G+++TRIE+RP+R W Y+FF D G+ +D ++ LE+ K+LGS Sbjct: 294 LEVLTQHGLNMTRIESRPNRLHPWQYLFFADIGGYERDERVRAALEEAASRTTFFKILGS 353 Query: 360 YPKA 363 YP+A Sbjct: 354 YPRA 357 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: 334 Number of extensions: 14 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: 374 Length adjustment: 30 Effective length of query: 335 Effective length of database: 344 Effective search space: 115240 Effective search space used: 115240 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_084057312.1 B9A12_RS07670 (prephenate dehydratase)
to HMM PF01817 (CM_2)
# 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/PF01817.25.hmm # target sequence database: /tmp/gapView.24261.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CM_2 [M=79] Accession: PF01817.25 Description: Chorismate mutase type II 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-27 81.5 0.4 5.1e-27 80.4 0.4 1.6 1 lcl|NCBI__GCF_900176285.1:WP_084057312.1 B9A12_RS07670 prephenate dehydra Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900176285.1:WP_084057312.1 B9A12_RS07670 prephenate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 80.4 0.4 5.1e-27 5.1e-27 1 79 [] 11 88 .. 11 88 .. 0.97 Alignments for each domain: == domain 1 score: 80.4 bits; conditional E-value: 5.1e-27 CM_2 1 RkeIdeiDrelleLlaeRmelakeiaeyKkenglpvldpeReeevlerlre...gaeelgldpeavekifr 68 R+ Id++D+e+l+ l++Rm+l+++i+++K+e+gl+ +dp Ree+v +rl e g+ l++e v++i+r lcl|NCBI__GCF_900176285.1:WP_084057312.1 11 RRGIDALDQEILDRLNRRMRLVEQIGRIKAEKGLDTFDPGREEAVCRRLVEaspGP----LPAESVRAIYR 77 899************************************************87777....*********** PP CM_2 69 eiisesralQk 79 ei+++sr+lQ+ lcl|NCBI__GCF_900176285.1:WP_084057312.1 78 EILAASRKLQQ 88 **********6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (79 nodes) Target sequences: 1 (374 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: 10.71 // [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