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_068167039.1 HTA01S_RS02955 chorismate mutase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_001592305.1:WP_068167039.1 Length = 365 Score = 304 bits (778), Expect = 3e-87 Identities = 160/364 (43%), Positives = 233/364 (64%), Gaps = 10/364 (2%) Query: 2 SEADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVL 61 ++++ L ALRV+IDSLD+++L L+++RAR A++V +K +AE + F+RP+R A V+ Sbjct: 5 TQSEALGALRVQIDSLDQQLLSLLNQRARVAEQVGEIK-----RAEGSPFFRPDRVAQVI 59 Query: 62 KHIMELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVIS 121 + I N+GPL N+ +A ++REIMS+CLALE P RVA LGP+GTF + AA++ FG + Sbjct: 60 EKIQAANQGPLLNQHVASIWREIMSACLALEAPQRVAVLGPQGTFCEQAAIEFFGGAANL 119 Query: 122 KPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLL 181 A DEVF AG +GVV +ENSTEG V +LD FL + + GEV L + H+LL Sbjct: 120 IYCANFDEVFHATAAGTAQYGVVGMENSTEGVVARSLDLFLRSPVHVVGEVSLLVRHNLL 179 Query: 182 VGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAG 241 + + I + +H Q+LAQC+ WL H PN ER AV SNA+ A+ + A +A Sbjct: 180 -RQVNDLNGIEVVMAHPQALAQCQNWLSQHLPNAERRAVDSNAEGARLAATNPAWAGLAS 238 Query: 242 DMAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEV----PPTGDDKTSIIVSMRNKPGALH 297 + AA +GL +A I+D N TRF +I + P TG D TS++VS+ N+PGA+H Sbjct: 239 ERAAAQFGLHIVAHAIQDEAYNRTRFAVICLPQTLAMPPATGKDCTSLVVSVPNRPGAVH 298 Query: 298 ELLMPFHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVL 357 +LL+P +NG+ +TR E+RP++SG+W Y F+ID GH P + LE++ KVL Sbjct: 299 DLLVPLKNNGVSMTRFESRPAKSGQWEYYFYIDIAGHPSQPHVAAALEELKGLCAFYKVL 358 Query: 358 GSYP 361 G+YP Sbjct: 359 GAYP 362 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: 341 Number of extensions: 10 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: 365 Length adjustment: 30 Effective length of query: 335 Effective length of database: 335 Effective search space: 112225 Effective search space used: 112225 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_068167039.1 HTA01S_RS02955 (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.19108.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.3e-30 89.1 0.1 1.6e-29 88.3 0.1 1.4 1 lcl|NCBI__GCF_001592305.1:WP_068167039.1 HTA01S_RS02955 chorismate mutase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001592305.1:WP_068167039.1 HTA01S_RS02955 chorismate mutase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 88.3 0.1 1.6e-29 1.6e-29 1 76 [] 10 83 .. 10 83 .. 0.98 Alignments for each domain: == domain 1 score: 88.3 bits; conditional E-value: 1.6e-29 TIGR01807 1 LkelRnkiDaiDdrildLlseRaklakavgelKkksaseaviYRPeREaavlrrlkelnkGpLdqeavari 71 L +lR++iD++D+++l Ll++Ra++a++vge+K++ ++++++RP+R a+v+ +++ +n+GpL ++ va i lcl|NCBI__GCF_001592305.1:WP_068167039.1 10 LGALRVQIDSLDQQLLSLLNQRARVAEQVGEIKRA--EGSPFFRPDRVAQVIEKIQAANQGPLLNQHVASI 78 5689*****************************99..9********************************* PP TIGR01807 72 frEim 76 +rEim lcl|NCBI__GCF_001592305.1:WP_068167039.1 79 WREIM 83 ****9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (76 nodes) Target sequences: 1 (365 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: 10.18 // [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