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_013134238.1 ARNIT_RS02150 chorismate mutase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_000092245.1:WP_013134238.1 Length = 355 Score = 215 bits (548), Expect = 1e-60 Identities = 141/365 (38%), Positives = 196/365 (53%), Gaps = 14/365 (3%) Query: 1 MSEADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWV 60 MSEA L+ LR ++D++D+ +L+LI++R EV +K S YRPERE + Sbjct: 1 MSEAGLLE-LRKKLDAIDDELLELINKRMDLVHEVGLLKAKSG-----GAIYRPEREKAI 54 Query: 61 LKHIMELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVI 120 + + LNKG L+ + F EI + E P +AYLGPEG+F+ AA FG Sbjct: 55 IDRLDTLNKGKLNRAAIEAFFLEIFAISRNFELPENIAYLGPEGSFTHQAAEARFGAMSS 114 Query: 121 SKPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHL 180 + +I VFREV FGV+P+ENS+ G V+ T++ +D+ I EV L I HH Sbjct: 115 YISIGSIKGVFREVNTKKARFGVIPIENSSNGIVSDTINCLSTYDLKIIAEVVLNI-HHT 173 Query: 181 LVGETTKTDRITRIYSHAQSLAQCRKWLDAH-YPNVERVAVSSNADAAKRVKSEWNSAAI 239 L K I +IYS + QCR++L+ VE + V S AAK +E NSAAI Sbjct: 174 LATTCDKVKDIKKIYSKDIAFEQCRRFLENFGLDEVEHIPVESTTKAAKLALNEPNSAAI 233 Query: 240 AGDMAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHEL 299 + A+LY L L E IED+ N TRF II E +G+DKTSI+V + N G L E Sbjct: 234 CSHVGAKLYNLPILFENIEDKDNNKTRFFIISDFENAQSGNDKTSILVKLPNLQGVLVEF 293 Query: 300 LMPFHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGS 359 L F I+LT+I+ S + +FFID GH D +K + +K ++K LGS Sbjct: 294 LTDFDKAKINLTKIK---SHIVEGDSIFFIDFNGHKDDENVKEIFKK---HKESIKFLGS 347 Query: 360 YPKAV 364 Y K + Sbjct: 348 YVKEI 352 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: 292 Number of extensions: 18 Number of successful extensions: 4 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: 355 Length adjustment: 29 Effective length of query: 336 Effective length of database: 326 Effective search space: 109536 Effective search space used: 109536 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_013134238.1 ARNIT_RS02150 (chorismate mutase)
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.31062.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-28 85.6 0.9 3e-28 84.2 0.6 2.0 2 lcl|NCBI__GCF_000092245.1:WP_013134238.1 ARNIT_RS02150 chorismate mutase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092245.1:WP_013134238.1 ARNIT_RS02150 chorismate mutase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 84.2 0.6 3e-28 3e-28 1 76 [] 6 79 .. 6 79 .. 0.98 2 ? -3.3 0.0 0.6 0.6 61 73 .. 324 336 .. 323 337 .. 0.82 Alignments for each domain: == domain 1 score: 84.2 bits; conditional E-value: 3e-28 TIGR01807 1 LkelRnkiDaiDdrildLlseRaklakavgelKkksaseaviYRPeREaavlrrlkelnkGpLdqeavari 71 L elR+k+DaiDd++l+L+++R+ l+++vg lK k s+++iYRPeRE a++ rl lnkG L+ a+++ lcl|NCBI__GCF_000092245.1:WP_013134238.1 6 LLELRKKLDAIDDELLELINKRMDLVHEVGLLKAK--SGGAIYRPEREKAIIDRLDTLNKGKLNRAAIEAF 74 789********************************..********************************** PP TIGR01807 72 frEim 76 f Ei+ lcl|NCBI__GCF_000092245.1:WP_013134238.1 75 FLEIF 79 ***97 PP == domain 2 score: -3.3 bits; conditional E-value: 0.6 TIGR01807 61 GpLdqeavarifr 73 G d+e+v+ if+ lcl|NCBI__GCF_000092245.1:WP_013134238.1 324 GHKDDENVKEIFK 336 6678999999997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (76 nodes) Target sequences: 1 (355 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: 9.75 // [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