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_077243516.1 B1A74_RS01045 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_001995255.1:WP_077243516.1 Length = 361 Score = 388 bits (997), Expect = e-112 Identities = 196/363 (53%), Positives = 258/363 (71%), Gaps = 4/363 (1%) Query: 1 MSEADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWV 60 MSE + L +LR RID++D +L L+SERARCA+ VARVK + EE VFYRPEREA + Sbjct: 1 MSEGESLASLRARIDAIDGELLALLSERARCAESVARVKRDN---GEEPVFYRPEREAEI 57 Query: 61 LKHIMELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVI 120 L+ + E N GPL ++ + RLFREIMS CLALE PL VAYLGPEGTF+ AA KHFGH+V Sbjct: 58 LRRVREENPGPLADDVIVRLFREIMSECLALEHPLTVAYLGPEGTFTHLAARKHFGHAVT 117 Query: 121 SKPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHL 180 + P+A+ID VF V G FGVVP+ENS+EG V HT+D F++ + ICGEV IHHHL Sbjct: 118 TTPLASIDAVFGAVETGRAQFGVVPIENSSEGVVTHTVDCFMDSSLQICGEVVTPIHHHL 177 Query: 181 LVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIA 240 L ++ + ++ +HAQ+LAQCR+WLD P+ ER AV+SNA AA+ + ++AAIA Sbjct: 178 L-SQSAGLGEVRQVLAHAQALAQCREWLDTWLPHAERHAVASNARAAELAAGDGSAAAIA 236 Query: 241 GDMAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELL 300 +AA+ YG+ E +EDR N+TRFLIIG+ P+G D+TSI++S N+PG+L+ LL Sbjct: 237 SRVAAEHYGVPVQVEHVEDRADNTTRFLIIGTATTRPSGADRTSIMLSTANRPGSLYALL 296 Query: 301 MPFHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSY 360 P GI LTRIE+RPSR +WTYVFF+D +GH +DP I LE++ A +K+LGSY Sbjct: 297 KPIAEAGISLTRIESRPSRCAQWTYVFFLDLLGHQEDPEIAGCLEQLRETADTVKILGSY 356 Query: 361 PKA 363 P+A Sbjct: 357 PRA 359 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: 387 Number of extensions: 15 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: 361 Length adjustment: 29 Effective length of query: 336 Effective length of database: 332 Effective search space: 111552 Effective search space used: 111552 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_077243516.1 B1A74_RS01045 (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.2010149.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-32 97.9 1.0 3.2e-32 96.9 1.0 1.5 1 NCBI__GCF_001995255.1:WP_077243516.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001995255.1:WP_077243516.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 96.9 1.0 3.2e-32 3.2e-32 1 76 [] 7 82 .. 7 82 .. 0.99 Alignments for each domain: == domain 1 score: 96.9 bits; conditional E-value: 3.2e-32 TIGR01807 1 LkelRnkiDaiDdrildLlseRaklakavgelKkksaseaviYRPeREaavlrrlkelnkGpLdqeavarifrEi 75 L+ lR++iDaiD ++l LlseRa++a++v+++K+ + +e v+YRPeREa +lrr++e n+GpL ++ + r+frEi NCBI__GCF_001995255.1:WP_077243516.1 7 LASLRARIDAIDGELLALLSERARCAESVARVKRDNGEEPVFYRPEREAEILRRVREENPGPLADDVIVRLFREI 81 789************************************************************************ PP TIGR01807 76 m 76 m NCBI__GCF_001995255.1:WP_077243516.1 82 M 82 9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (76 nodes) Target sequences: 1 (361 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: 15.27 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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