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_086508931.1 BZY95_RS05310 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_002151265.1:WP_086508931.1 Length = 363 Score = 516 bits (1328), Expect = e-151 Identities = 260/361 (72%), Positives = 299/361 (82%), Gaps = 3/361 (0%) Query: 5 DQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKHI 64 + L LR RID +D IL LIS RA CA++VA VKT S + AVFYRPEREA VL+ I Sbjct: 6 NNLDTLRQRIDEIDNDILRLISARAECAKQVAEVKTKS---DKGAVFYRPEREAQVLRRI 62 Query: 65 MELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKPM 124 MELN+GPL++EEMARLFREIMS+CLALEQP +VAYLGPEGTF+Q AALKHFG S +S PM Sbjct: 63 MELNQGPLNSEEMARLFREIMSACLALEQPTKVAYLGPEGTFTQQAALKHFGQSAVSMPM 122 Query: 125 AAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVGE 184 AAIDEVFREV AGAVN+GVVPVENSTEG V+HTLDSF++ I ICGEV LRIHHHLLV + Sbjct: 123 AAIDEVFREVEAGAVNYGVVPVENSTEGVVSHTLDSFMDSSIRICGEVVLRIHHHLLVAD 182 Query: 185 TTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMA 244 TT D+++R+YSH QSLAQCRKWLDAHYP ERV VSSNA+AAK +K EW+SAAIAGDMA Sbjct: 183 TTLRDKVSRVYSHPQSLAQCRKWLDAHYPRAERVPVSSNAEAAKMIKGEWHSAAIAGDMA 242 Query: 245 AQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELLMPFH 304 A+LYGL K+AEKIEDRP NSTRFLIIGSQ VP +G+DKTSI+V+MRN+PGALHELL PFH Sbjct: 243 AKLYGLEKVAEKIEDRPDNSTRFLIIGSQHVPMSGEDKTSIVVAMRNQPGALHELLEPFH 302 Query: 305 SNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYPKAV 364 + IDLTR+ETRPSR+G W YVFFID GH +P + VLE++ A LKVLGSYP V Sbjct: 303 RHSIDLTRLETRPSRTGVWNYVFFIDFKGHVDEPRVAAVLEEVRLRASELKVLGSYPVGV 362 Query: 365 L 365 L Sbjct: 363 L 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: 442 Number of extensions: 10 Number of successful extensions: 2 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_086508931.1 BZY95_RS05310 (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.31688.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-36 110.6 2.1 2.7e-36 110.0 1.1 1.9 2 lcl|NCBI__GCF_002151265.1:WP_086508931.1 BZY95_RS05310 prephenate dehydra Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086508931.1 BZY95_RS05310 prephenate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 110.0 1.1 2.7e-36 2.7e-36 1 76 [] 8 83 .. 8 83 .. 0.98 2 ? -2.7 0.0 0.4 0.4 64 75 .. 121 132 .. 117 132 .. 0.81 Alignments for each domain: == domain 1 score: 110.0 bits; conditional E-value: 2.7e-36 TIGR01807 1 LkelRnkiDaiDdrildLlseRaklakavgelKkksaseaviYRPeREaavlrrlkelnkGpLdqeavari 71 L lR++iD iD+ il+L+s Ra++ak+v+e+K+ks ++av+YRPeREa+vlrr++eln+GpL++e++ar+ lcl|NCBI__GCF_002151265.1:WP_086508931.1 8 LDTLRQRIDEIDNDILRLISARAECAKQVAEVKTKSDKGAVFYRPEREAQVLRRIMELNQGPLNSEEMARL 78 6789******************************************************************* PP TIGR01807 72 frEim 76 frEim lcl|NCBI__GCF_002151265.1:WP_086508931.1 79 FREIM 83 ****9 PP == domain 2 score: -2.7 bits; conditional E-value: 0.4 TIGR01807 64 dqeavarifrEi 75 + a++ +frE+ lcl|NCBI__GCF_002151265.1:WP_086508931.1 121 PMAAIDEVFREV 132 567899999998 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: 9.68 // [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