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_012991967.1 THAL_RS04735 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_000025605.1:WP_012991967.1 Length = 363 Score = 296 bits (758), Expect = 6e-85 Identities = 153/365 (41%), Positives = 237/365 (64%), Gaps = 10/365 (2%) Query: 5 DQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKHI 64 ++L+ LR +ID +DE+I++L++ RA+ AQ++ +K K + PERE + + I Sbjct: 2 EELERLREKIDQIDEQIVELLNRRAQLAQQIGEIK-----KRLGLEIHAPERERQIFEKI 56 Query: 65 MELN----KGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVI 120 +++N K + + +FREI+S+CL+LE+P++VAYLGP+ TF+ AA ++FG S Sbjct: 57 IQINTQRYKETFPTKALLHIFREIISACLSLEKPIKVAYLGPKATFTHQAASEYFGLSAQ 116 Query: 121 SKPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHL 180 P +I +VF+EV ++GVVPVEN+TEG VN+TLD FLE D+ I GE+ + I HL Sbjct: 117 YIPAPSIRDVFQEVETDRADYGVVPVENTTEGVVNYTLDMFLESDLRIVGEIVIPIRLHL 176 Query: 181 LVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIA 240 L T +I +++SH Q+LAQCR WL+ + P V+ + S A A + E S+AIA Sbjct: 177 L-STCTDISQIKKVFSHRQALAQCRMWLEKNMPWVDLIETESTARACEIALEEEASSAIA 235 Query: 241 GDMAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELL 300 ++AA Y L LAE I+D P N TRFL+IG + + TG DKTS+I +++++PGAL+ L Sbjct: 236 SEVAAYTYHLHVLAENIQDNPNNYTRFLVIGKRSMKKTGKDKTSLIFAVKDEPGALYRAL 295 Query: 301 MPFHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSY 360 F+ ++LT+IE+RPS+ W YVFF+D GH +D ++ +E + +K+LGSY Sbjct: 296 ESFYLYNVNLTKIESRPSKKKAWDYVFFVDLEGHTEDEHVREAIELLKSRTQMVKLLGSY 355 Query: 361 PKAVL 365 P+A++ Sbjct: 356 PRALI 360 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: 302 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: 363 Length adjustment: 29 Effective length of query: 336 Effective length of database: 334 Effective search space: 112224 Effective search space used: 112224 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_012991967.1 THAL_RS04735 (prephenate dehydratase)
to HMM PF01817 (CM_2)
# 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/PF01817.25.hmm # target sequence database: /tmp/gapView.2818.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: CM_2 [M=79] Accession: PF01817.25 Description: Chorismate mutase type II 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-26 78.0 8.0 3.5e-26 77.8 5.4 2.4 2 lcl|NCBI__GCF_000025605.1:WP_012991967.1 THAL_RS04735 prephenate dehydrat Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025605.1:WP_012991967.1 THAL_RS04735 prephenate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 77.8 5.4 3.5e-26 3.5e-26 1 79 [] 8 89 .. 8 89 .. 0.95 2 ? -0.7 0.0 0.11 0.11 12 28 .. 339 355 .. 336 358 .. 0.83 Alignments for each domain: == domain 1 score: 77.8 bits; conditional E-value: 3.5e-26 CM_2 1 RkeIdeiDrelleLlaeRmelakeiaeyKkenglpvldpeReeevlerlre...gaeelgldpeavekifr 68 R++Id+iD++++eLl++R++la++i+e+Kk+ gl++ peRe++++e++ + + ++ ++ +a+ +ifr lcl|NCBI__GCF_000025605.1:WP_012991967.1 8 REKIDQIDEQIVELLNRRAQLAQQIGEIKKRLGLEIHAPERERQIFEKIIQintQRYKETFPTKALLHIFR 78 99*************************************************977555669*********** PP CM_2 69 eiisesralQk 79 eiis++++l+k lcl|NCBI__GCF_000025605.1:WP_012991967.1 79 EIISACLSLEK 89 *******9985 PP == domain 2 score: -0.7 bits; conditional E-value: 0.11 CM_2 12 leLlaeRmelakeiaey 28 +eLl+ R++++k + y lcl|NCBI__GCF_000025605.1:WP_012991967.1 339 IELLKSRTQMVKLLGSY 355 89*******99977765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (79 nodes) Target sequences: 1 (363 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: 9.69 // [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