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 BPHYT_RS14910 BPHYT_RS14910 chorismate mutase
Query= SwissProt::P27603 (365 letters) >FitnessBrowser__BFirm:BPHYT_RS14910 Length = 360 Score = 327 bits (839), Expect = 2e-94 Identities = 172/358 (48%), Positives = 242/358 (67%), Gaps = 6/358 (1%) Query: 6 QLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKHIM 65 +LK LR RID+LD +++ L+++RA A EV VK K A +RPERE V+ + Sbjct: 8 RLKPLRERIDALDAQLIALLNQRAAVALEVGEVK-----KHFNAPVFRPEREQQVIARLQ 62 Query: 66 ELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKPMA 125 ++++GPL +E ++ ++REIM++ ALE+ ++ AYLGP GT+S+ A ++FG S+ P Sbjct: 63 DMSEGPLASEHISAIWREIMAASRALEKTIKAAYLGPVGTYSEQAMHEYFGQSIEGLPCP 122 Query: 126 AIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVGET 185 +IDEVFR V AGA FGVVPVENSTEGAV+ TLD L+ + I GE+ L IHH+LL Sbjct: 123 SIDEVFRSVEAGAAEFGVVPVENSTEGAVSRTLDLLLQTQLTIGGELALPIHHNLLTLNG 182 Query: 186 TKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMAA 245 T +TR+ +HAQ+LAQC++WL + P++ER AVSSNA+AA+ + AAIAGD AA Sbjct: 183 GLTG-VTRVCAHAQALAQCQRWLSTNAPHLERQAVSSNAEAARMAAEDPTVAAIAGDRAA 241 Query: 246 QLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELLMPFHS 305 YGL I+D P N TRF++IG Q P+G D+TS+IVS+ N+PGA+ +LL P Sbjct: 242 THYGLQVAYALIQDDPHNRTRFVMIGKQPAGPSGYDQTSLIVSVVNEPGAMVKLLEPLAR 301 Query: 306 NGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYPKA 363 + + +TR E+RP+R G W Y F+ID GH DP + L ++G +A LK+LGSYP+A Sbjct: 302 HSVSMTRFESRPARVGTWEYYFYIDVEGHRDDPAVAAALTELGEKAAFLKILGSYPRA 359 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: 330 Number of extensions: 9 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: 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 BPHYT_RS14910 BPHYT_RS14910 (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.382.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-30 91.8 0.2 2.5e-30 90.9 0.2 1.5 1 lcl|FitnessBrowser__BFirm:BPHYT_RS14910 BPHYT_RS14910 chorismate mutase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS14910 BPHYT_RS14910 chorismate mutase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 90.9 0.2 2.5e-30 2.5e-30 1 76 [] 9 82 .. 9 82 .. 0.98 Alignments for each domain: == domain 1 score: 90.9 bits; conditional E-value: 2.5e-30 TIGR01807 1 LkelRnkiDaiDdrildLlseRaklakavgelKkksaseaviYRPeREaavlrrlkelnkGpLdqeavarif 72 Lk+lR++iDa+D+++ Ll++Ra +a +vge+Kk+ +a+++RPeRE++v+ rl+++ +GpL +e + +i+ lcl|FitnessBrowser__BFirm:BPHYT_RS14910 9 LKPLRERIDALDAQLIALLNQRAAVALEVGEVKKH--FNAPVFRPEREQQVIARLQDMSEGPLASEHISAIW 78 89*********************************..89999****************************** PP TIGR01807 73 rEim 76 rEim lcl|FitnessBrowser__BFirm:BPHYT_RS14910 79 REIM 82 ***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: 11.63 // [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