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 N515DRAFT_1431 N515DRAFT_1431 chorismate mutase
Query= SwissProt::P27603 (365 letters) >FitnessBrowser__Dyella79:N515DRAFT_1431 Length = 362 Score = 375 bits (963), Expect = e-108 Identities = 188/358 (52%), Positives = 259/358 (72%), Gaps = 4/358 (1%) Query: 7 LKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKHIME 66 L+ +R RIDS+D +I +LISERA AQEVARVK A + +YRPEREA VL+ +++ Sbjct: 8 LEQVRERIDSIDRQIQELISERAGWAQEVARVKGAGLSAID---YYRPEREAHVLRMVVD 64 Query: 67 LNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKPMAA 126 N+GPL + EM RLFREIMSSCLA E PL+V +LGPEGTFS+ A KHFGH+ P+ + Sbjct: 65 RNRGPLSDTEMVRLFREIMSSCLAQEDPLKVGFLGPEGTFSEQAVRKHFGHAAYGLPLGS 124 Query: 127 IDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVGETT 186 I+EVF+EV AG +FGVVPVENS +G + TLD FL + ICGE+ELR+H L + Sbjct: 125 IEEVFQEVAAGHADFGVVPVENSGQGMIQITLDMFLTSEATICGEIELRVHQ-CLHSQGG 183 Query: 187 KTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMAAQ 246 + + I R+Y+HAQSL QC+ WL + P+VE +AVSSNA+AA+ + ++AAIAG+ A + Sbjct: 184 RMEDIKRVYAHAQSLQQCKTWLRINLPDVECIAVSSNAEAARMARHADDAAAIAGETAGR 243 Query: 247 LYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELLMPFHSN 306 +YGL LA IEDR N+TRFL+IG PP+G+D+TS+++++ +KPGAL+++L PF + Sbjct: 244 VYGLKTLATGIEDRADNTTRFLVIGRSLFPPSGNDRTSLLITVNDKPGALYDVLSPFAKH 303 Query: 307 GIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYPKAV 364 + L RIE+RP+ +GKW Y FFID GH QD I+ ++++G A ++VLGSYP A+ Sbjct: 304 DVSLNRIESRPAHTGKWQYAFFIDVSGHVQDAPIQAAMQEMGGAAAQVRVLGSYPVAL 361 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: 365 Number of extensions: 11 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: 362 Length adjustment: 29 Effective length of query: 336 Effective length of database: 333 Effective search space: 111888 Effective search space used: 111888 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 N515DRAFT_1431 N515DRAFT_1431 (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.19082.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8e-30 89.3 0.7 8.3e-29 86.0 1.0 2.2 2 lcl|FitnessBrowser__Dyella79:N515DRAFT_1431 N515DRAFT_1431 chorismate mutase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_1431 N515DRAFT_1431 chorismate mutase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 86.0 1.0 8.3e-29 8.3e-29 1 76 [] 8 83 .. 8 83 .. 0.98 2 ? 0.3 0.0 0.046 0.046 48 75 .. 106 132 .. 98 133 .. 0.84 Alignments for each domain: == domain 1 score: 86.0 bits; conditional E-value: 8.3e-29 TIGR01807 1 LkelRnkiDaiDdrildLlseRaklakavgelKkksaseaviYRPeREaavlrrlkelnkGpLdqeav 68 L+++R++iD+iD +i +L+seRa a++v+++K+++ s YRPeREa vlr + ++n+GpL + ++ lcl|FitnessBrowser__Dyella79:N515DRAFT_1431 8 LEQVRERIDSIDRQIQELISERAGWAQEVARVKGAGLSAIDYYRPEREAHVLRMVVDRNRGPLSDTEM 75 7899**************************************************************** PP TIGR01807 69 arifrEim 76 r+frEim lcl|FitnessBrowser__Dyella79:N515DRAFT_1431 76 VRLFREIM 83 *******9 PP == domain 2 score: 0.3 bits; conditional E-value: 0.046 TIGR01807 48 EaavlrrlkelnkGpLdqeavarifrEi 75 E+av +++ ++ G L+ +++ +f+E+ lcl|FitnessBrowser__Dyella79:N515DRAFT_1431 106 EQAVRKHFGHAAYG-LPLGSIEEVFQEV 132 67788888888877.78999*******8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (76 nodes) Target sequences: 1 (362 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: 8.21 // [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