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 Dsui_1940 Dsui_1940 chorismate mutase, clade 2
Query= SwissProt::P27603 (365 letters) >lcl|FitnessBrowser__PS:Dsui_1940 Dsui_1940 chorismate mutase, clade 2 Length = 374 Score = 386 bits (991), Expect = e-112 Identities = 192/360 (53%), Positives = 254/360 (70%), Gaps = 6/360 (1%) Query: 7 LKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKHIME 66 L +R+ ID++D ++LDL++ RARCAQ+V +K + YRPEREA VL+ I + Sbjct: 18 LSVVRMDIDAIDAQLLDLLNRRARCAQQVGEIKARH---GDAGFIYRPEREAQVLRRIQD 74 Query: 67 LNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKPMAA 126 +N+GPL +E + FRE+MS+CL+LEQPL +A+LGP GTFS++A+ KHFGH+ P A+ Sbjct: 75 MNQGPLSSESVTWFFREVMSACLSLEQPLGIAFLGPLGTFSESASTKHFGHAARLLPQAS 134 Query: 127 IDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVGETT 186 ID+VFREV AG N+GV PVENSTEGAV TLD L + ICGEV LRIH HLL + Sbjct: 135 IDDVFREVEAGHANYGVAPVENSTEGAVGRTLDLLLGTSLKICGEVVLRIHQHLLT-KAP 193 Query: 187 KTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMAAQ 246 DR+T++YSHAQSLAQC +WL+ H PNV R++V SNA AA+ E +AAIAG+ AA Sbjct: 194 SLDRVTKVYSHAQSLAQCHEWLNRHLPNVPRISVGSNAQAAQMAAQEEGAAAIAGEAAAD 253 Query: 247 LYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPT--GDDKTSIIVSMRNKPGALHELLMPFH 304 Y L +LAE IED P N+TRF+++G + P+ G DKTS+I+S+ N GALH LL+PF Sbjct: 254 RYDLPRLAESIEDEPNNTTRFVVLGRHDAGPSTAGKDKTSLIMSIPNNTGALHTLLVPFA 313 Query: 305 SNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYPKAV 364 G+ LTR+E+RP+R W YVFF+D GH +P +K L+++ A LKVLGSYP AV Sbjct: 314 DAGVSLTRLESRPARHTLWEYVFFVDVDGHRDEPRVKAALDELARRAAYLKVLGSYPVAV 373 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: 375 Number of extensions: 16 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: 374 Length adjustment: 30 Effective length of query: 335 Effective length of database: 344 Effective search space: 115240 Effective search space used: 115240 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 Dsui_1940 Dsui_1940 (chorismate mutase, clade 2)
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.7639.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-34 104.4 0.1 2.1e-33 100.8 0.1 2.3 2 lcl|FitnessBrowser__PS:Dsui_1940 Dsui_1940 chorismate mutase, cla Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_1940 Dsui_1940 chorismate mutase, clade 2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 100.8 0.1 2.1e-33 2.1e-33 2 76 .] 19 93 .. 18 93 .. 0.97 2 ? 0.9 0.0 0.03 0.03 62 75 .. 129 142 .. 120 143 .. 0.89 Alignments for each domain: == domain 1 score: 100.8 bits; conditional E-value: 2.1e-33 TIGR01807 2 kelRnkiDaiDdrildLlseRaklakavgelKkksaseaviYRPeREaavlrrlkelnkGpLdqeavarifrEim 76 +R iDaiD+++ldLl+ Ra++a++vge+K + + ++iYRPeREa+vlrr++++n+GpL +e+v frE+m lcl|FitnessBrowser__PS:Dsui_1940 19 SVVRMDIDAIDAQLLDLLNRRARCAQQVGEIKARHGDAGFIYRPEREAQVLRRIQDMNQGPLSSESVTWFFREVM 93 56899*********************************************************************9 PP == domain 2 score: 0.9 bits; conditional E-value: 0.03 TIGR01807 62 pLdqeavarifrEi 75 +L+q +++ +frE+ lcl|FitnessBrowser__PS:Dsui_1940 129 LLPQASIDDVFREV 142 799**********8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (76 nodes) Target sequences: 1 (374 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: 9.64 // [ok]
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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