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_011802172.1 PNAP_RS13950 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_000015505.1:WP_011802172.1 Length = 360 Score = 313 bits (803), Expect = 4e-90 Identities = 165/359 (45%), Positives = 229/359 (63%), Gaps = 10/359 (2%) Query: 7 LKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKHIME 66 L LRV+ID+LD+ +L L++ RA A++V VK K E F+RP+R A V++ I + Sbjct: 5 LDDLRVQIDALDKELLTLLNRRALVAEQVGEVK-----KREGTPFFRPDRVAQVIEKIQQ 59 Query: 67 LNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKPMAA 126 N GPL NE +A ++REIMS+CLALE P+RVAYLGP GTFS+ AAL+ FG+S+ + Sbjct: 60 ANMGPLKNEHVAAVWREIMSACLALESPVRVAYLGPAGTFSEQAALQFFGNSIEHVSCVS 119 Query: 127 IDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVGETT 186 IDEVFR AG+ +GVVPVENSTEG V+ +LD L + I GE+ L + HHLL T Sbjct: 120 IDEVFRATAAGSAGYGVVPVENSTEGVVSRSLDLLLNSPLHIVGEISLMVRHHLL-RLTD 178 Query: 187 KTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMAAQ 246 + I +Y+H Q+LAQC WL H P+VER A SSNA+ A+ + A IA D AA Sbjct: 179 SLENIEIVYAHPQALAQCHGWLTTHLPHVERRAASSNAEGARLASTNPAWAGIASDRAAT 238 Query: 247 LYGLSKLAEKIEDRPVNSTRFLIIGSQEV----PPTGDDKTSIIVSMRNKPGALHELLMP 302 + L +A I+D N TRF ++ + P +G D TS++VS+ N+PGA+H++L+P Sbjct: 239 QFALHTVAHAIQDDAFNRTRFAVVCLPQTLPAPPASGKDCTSLVVSVPNRPGAVHDILVP 298 Query: 303 FHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYP 361 ++G+ +TR E+RP+RSG+W Y F+ID GH +K L + KVLG+YP Sbjct: 299 LKTHGVSMTRFESRPARSGQWEYYFYIDLQGHPSQDHVKAALADLQQLCAFYKVLGTYP 357 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: 331 Number of extensions: 8 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: 360 Length adjustment: 29 Effective length of query: 336 Effective length of database: 331 Effective search space: 111216 Effective search space used: 111216 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_011802172.1 PNAP_RS13950 (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.28145.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.3e-31 92.8 0.3 1.2e-30 91.9 0.3 1.5 1 lcl|NCBI__GCF_000015505.1:WP_011802172.1 PNAP_RS13950 prephenate dehydrat Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015505.1:WP_011802172.1 PNAP_RS13950 prephenate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 91.9 0.3 1.2e-30 1.2e-30 1 76 [] 5 78 .. 5 78 .. 0.98 Alignments for each domain: == domain 1 score: 91.9 bits; conditional E-value: 1.2e-30 TIGR01807 1 LkelRnkiDaiDdrildLlseRaklakavgelKkksaseaviYRPeREaavlrrlkelnkGpLdqeavari 71 L +lR++iDa+D+++l+Ll+ Ra +a++vge+Kk+ ++++++RP+R a+v+ +++++n GpL++e va++ lcl|NCBI__GCF_000015505.1:WP_011802172.1 5 LDDLRVQIDALDKELLTLLNRRALVAEQVGEVKKR--EGTPFFRPDRVAQVIEKIQQANMGPLKNEHVAAV 73 678********************************..********************************** PP TIGR01807 72 frEim 76 +rEim lcl|NCBI__GCF_000015505.1:WP_011802172.1 74 WREIM 78 ****9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (76 nodes) Target sequences: 1 (360 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: 8.44 // [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