Align Chorismate synthase ARO2; 5-enolpyruvylshikimate-3-phosphate phospholyase; Aromatic amino acid requiring protein 2; EC 1.5.1.38; EC 4.2.3.5 (characterized)
to candidate WP_035236562.1 Q366_RS04200 chorismate synthase
Query= SwissProt::P28777 (376 letters) >NCBI__GCF_000745975.1:WP_035236562.1 Length = 368 Score = 427 bits (1098), Expect = e-124 Identities = 226/367 (61%), Positives = 265/367 (72%), Gaps = 11/367 (2%) Query: 2 STFGKLFRVTTYGESHCKSVGCIVDGVPPGMSLTEADIQPQLTRRRPGQSKLSTPRDEKD 61 S+FGKLFRV+T+GESHC VG +VDG PGM+LTE DIQ QL RRRPGQS +ST R E D Sbjct: 3 SSFGKLFRVSTFGESHCPGVGVVVDGCLPGMALTEPDIQCQLDRRRPGQSAVSTDRQESD 62 Query: 62 RVEIQSGTEFGKTLGTPIAMMIKNEDQRPHDYSDMDKFPRPSHADFTYSEKYGIKASSGG 121 RV IQSGTE G TLGTPI++ + N+DQRP DY M PRPSHADFTY KYGI+ASSGG Sbjct: 63 RVAIQSGTEHGLTLGTPISLFVPNKDQRPGDYKSMADIPRPSHADFTYQSKYGIRASSGG 122 Query: 122 GRASARETIGRVASGAIAEKFLAQNSNVEIVAFVTQIGEIKMNRDSFDPEFQHLLNTITR 181 GR+SARETIGRV +GAIAEK L ++IVA+V+Q+G+IK PE L +TR Sbjct: 123 GRSSARETIGRVCAGAIAEKMLKTALGIDIVAWVSQVGQIKA------PETDGL--NLTR 174 Query: 182 EKVDSMGPIRCPDASVAGLMVKEIEKYRGNKDSIGGVVTCVVRNLPTGLGEPCFDKLEAM 241 VD+ IRCPD A M + + + KDSIGGVV+CV ++P G GEP FDKLEA+ Sbjct: 175 AMVDA-SMIRCPDKDAAKAMEAVVLRAKEEKDSIGGVVSCVCTHVPAGFGEPVFDKLEAL 233 Query: 242 LAHAMLSIPASKGFEIGSGFQGVSVPGSKHNDPFYFEKETNRLRTKTNNSGGVQGGISNG 301 LAHAMLSIPA+KGFEIGSGF G + GS HNDPF + RL T TN SGG+QGGISNG Sbjct: 234 LAHAMLSIPATKGFEIGSGFAGAQMRGSVHNDPFVL--KDGRLGTTTNFSGGIQGGISNG 291 Query: 302 ENIYFSVPFKSVATISQEQKTATYDGEEGILAAKGRHDPAVTPRAIPIVEAMTALVLADA 361 E I F V FK ATI Q+T + G + LAAKGRHDP V RA+PIVE+M ALVLAD Sbjct: 292 EPIVFRVAFKPPATIGHAQETVDFQGRQATLAAKGRHDPCVVSRAVPIVESMAALVLADV 351 Query: 362 LLIQKAR 368 +L Q+AR Sbjct: 352 MLQQQAR 358 Lambda K H 0.316 0.133 0.383 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: 453 Number of extensions: 12 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: 376 Length of database: 368 Length adjustment: 30 Effective length of query: 346 Effective length of database: 338 Effective search space: 116948 Effective search space used: 116948 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_035236562.1 Q366_RS04200 (chorismate synthase)
to HMM TIGR00033 (aroC: chorismate synthase (EC 4.2.3.5))
# 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/TIGR00033.hmm # target sequence database: /tmp/gapView.9215.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00033 [M=351] Accession: TIGR00033 Description: aroC: chorismate synthase 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-145 469.5 0.1 3.4e-145 469.4 0.1 1.0 1 lcl|NCBI__GCF_000745975.1:WP_035236562.1 Q366_RS04200 chorismate synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745975.1:WP_035236562.1 Q366_RS04200 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 469.4 0.1 3.4e-145 3.4e-145 1 349 [. 9 357 .. 9 359 .. 0.99 Alignments for each domain: == domain 1 score: 469.4 bits; conditional E-value: 3.4e-145 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +r+ tfGeSH++ +g+++dG+ +g+ lte diq +l+rRrpgqs +++ r+E+D+v i+sG+++G T G lcl|NCBI__GCF_000745975.1:WP_035236562.1 9 FRVSTFGESHCPGVGVVVDGCLPGMALTEPDIQCQLDRRRPGQSAVSTDRQESDRVAIQSGTEHGLTLG 77 89******************************************************************* PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 +Pi+l + Nkd+r+ dy++++++pRP+Had+ty+ KYgi++++gggrsSaReT++rv aGa+a+k+Lk lcl|NCBI__GCF_000745975.1:WP_035236562.1 78 TPISLFVPNKDQRPGDYKSMADIPRPSHADFTYQSKYGIRASSGGGRSSARETIGRVCAGAIAEKMLKT 146 ********************************************************************* PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 gi iva+v+++g+++++e+ + ++ +d+s +rcpd++a+k+me+++ +ak+++ds+Ggvv++v lcl|NCBI__GCF_000745975.1:WP_035236562.1 147 ALGIDIVAWVSQVGQIKAPETDGLNLTRAMVDASMIRCPDKDAAKAMEAVVLRAKEEKDSIGGVVSCVC 215 ********************999999******************************************* PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGi 276 + vp+g+Gep+fdkl+a la+a+lsi+A Kg+eiG+GF+ a++rGs +nD++vl+d+++ + tn sGGi lcl|NCBI__GCF_000745975.1:WP_035236562.1 216 THVPAGFGEPVFDKLEALLAHAMLSIPATKGFEIGSGFAGAQMRGSVHNDPFVLKDGRLGTTTNFSGGI 284 ********************************************************************* PP TIGR00033 277 eGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladall 345 +GGi+nGe+i++r+a+Kp +ti+++++tvd ++++++ a+kgRhDpcvv ravp+vE+m alvlad +l lcl|NCBI__GCF_000745975.1:WP_035236562.1 285 QGGISNGEPIVFRVAFKPPATIGHAQETVDFQGRQATLAAKGRHDPCVVSRAVPIVESMAALVLADVML 353 ********************************************************************* PP TIGR00033 346 ekra 349 +++a lcl|NCBI__GCF_000745975.1:WP_035236562.1 354 QQQA 357 *986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (368 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 7.11 // [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