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 HSERO_RS18430 HSERO_RS18430 chorismate mutase
Query= SwissProt::P27603 (365 letters) >FitnessBrowser__HerbieS:HSERO_RS18430 Length = 357 Score = 336 bits (861), Expect = 7e-97 Identities = 168/357 (47%), Positives = 239/357 (66%), Gaps = 6/357 (1%) Query: 5 DQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKHI 64 D+L LR +ID++D +ILDL+++RAR AQEV VK + A +RPEREA VL+ Sbjct: 4 DKLLPLRQKIDAIDAQILDLLNQRARVAQEVGHVKAET-----NAPVFRPEREAQVLRRA 58 Query: 65 MELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKPM 124 + N GPL ++ +FRE+MS+C ALE+ + VAYLGPEGTFS+ A + FGH++ Sbjct: 59 ADRNPGPLLGADIQTIFREVMSACRALEKRVVVAYLGPEGTFSEQAVYQQFGHAIEGLSC 118 Query: 125 AAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVGE 184 +IDEVFR+ AG +FGVVP+ENS+EG +N TLD L+ + I GEV + +HH L+ Sbjct: 119 VSIDEVFRDAEAGTADFGVVPIENSSEGVINRTLDLLLQTTLTISGEVSIPVHHSLMTA- 177 Query: 185 TTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMA 244 + K + ITRI +H+Q+LAQC WL+ +YP++ER AV+SNA+AA+ + + AAIAG++A Sbjct: 178 SGKMEGITRICAHSQALAQCNAWLNQNYPSIERQAVASNAEAARMAGEDQSVAAIAGEIA 237 Query: 245 AQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELLMPFH 304 Q Y L + I+D P N TRF +IG P+G D+TSI++S+ NK GA++ LL P Sbjct: 238 GQKYNLQTVNAHIQDDPHNRTRFAVIGRLRTAPSGRDQTSIVLSVPNKAGAVYNLLAPLA 297 Query: 305 SNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYP 361 +G+ +TR E+RP+R G W Y F++D GH QD + LE++ A K+LGSYP Sbjct: 298 RHGVSMTRFESRPARMGAWEYYFYVDLEGHEQDEKVAQALEELRQNAAFFKLLGSYP 354 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: 336 Number of extensions: 6 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: 357 Length adjustment: 29 Effective length of query: 336 Effective length of database: 328 Effective search space: 110208 Effective search space used: 110208 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 HSERO_RS18430 HSERO_RS18430 (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.14647.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-32 96.6 0.2 1.1e-31 95.2 0.2 1.8 1 lcl|FitnessBrowser__HerbieS:HSERO_RS18430 HSERO_RS18430 chorismate mutase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS18430 HSERO_RS18430 chorismate mutase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 95.2 0.2 1.1e-31 1.1e-31 1 76 [] 6 79 .. 6 79 .. 0.98 Alignments for each domain: == domain 1 score: 95.2 bits; conditional E-value: 1.1e-31 TIGR01807 1 LkelRnkiDaiDdrildLlseRaklakavgelKkksaseaviYRPeREaavlrrlkelnkGpLdqeavar 70 L +lR+kiDaiD++ildLl++Ra++a++vg++K + +a+++RPeREa+vlrr ++n+GpL +++ lcl|FitnessBrowser__HerbieS:HSERO_RS18430 6 LLPLRQKIDAIDAQILDLLNQRARVAQEVGHVKAE--TNAPVFRPEREAQVLRRAADRNPGPLLGADIQT 73 789********************************..999****************************** PP TIGR01807 71 ifrEim 76 ifrE+m lcl|FitnessBrowser__HerbieS:HSERO_RS18430 74 IFREVM 79 *****9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (76 nodes) Target sequences: 1 (357 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: 7.95 // [ok]
This GapMind analysis is from Apr 09 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