Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_106715655.1 CU100_RS06510 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_003010935.1:WP_106715655.1 Length = 364 Score = 426 bits (1094), Expect = e-124 Identities = 223/367 (60%), Positives = 266/367 (72%), Gaps = 16/367 (4%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+ NT G LFRVTT+GESHGLALGC+VDG PPGI +EA++Q LD+R+PG SRYTTQRR Sbjct: 1 MSHNTFGHLFRVTTWGESHGLALGCVVDGCPPGISFSEAEIQSYLDKRKPGQSRYTTQRR 60 Query: 61 EPDQVKILSGVF---EGVT---TGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQK 114 EPDQVK+LSG +G+T TGT I ++IENTDQRS+DY I +RPGHADYTY+ K Sbjct: 61 EPDQVKVLSGFMLQDDGMTMISTGTPISMMIENTDQRSKDYGDIARQYRPGHADYTYDVK 120 Query: 115 YGLRDYRGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIK--DWSQ 172 YG+RDYRGGGRSSARETA RVAAGAIA+K + G+ +RG L MG +D DW + Sbjct: 121 YGIRDYRGGGRSSARETAARVAAGAIARKVVP---GLLVRGALVGMGIHSIDRSRWDWDE 177 Query: 173 VEQNPFFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAH 232 V NPFF PD +D + ++K G SIGA V VVA VPAGLG PV+ +LD DIA Sbjct: 178 VGNNPFFTPDLQSVDVFASYLDGIRKAGSSIGAVVEVVAENVPAGLGAPVYGKLDQDIAS 237 Query: 233 ALMSINAVKGVEIGDGFDVVALRGSQNRDEIT--KDG---FQSNHAGGILGGISSGQQII 287 LMSINAVKGVEIGDGFD L G +N DE+ DG F SNHAGGILGGISSG ++ Sbjct: 238 NLMSINAVKGVEIGDGFDTARLTGEENADEMRMGNDGKPIFLSNHAGGILGGISSGAPVV 297 Query: 288 AHMALKPTSSITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQ 347 A A+KPTSSI P R+I+ G +VE++T+GRHDPCVGIRAVPI EAM+A + DH LR Sbjct: 298 ARFAVKPTSSILTPRRSIDADGNQVEVMTRGRHDPCVGIRAVPIGEAMVACAIADHYLRH 357 Query: 348 RAQNADV 354 R Q + Sbjct: 358 RGQTGRI 364 Lambda K H 0.319 0.138 0.404 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: 478 Number of extensions: 14 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: 361 Length of database: 364 Length adjustment: 29 Effective length of query: 332 Effective length of database: 335 Effective search space: 111220 Effective search space used: 111220 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_106715655.1 CU100_RS06510 (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.2182697.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-124 400.1 0.1 4.5e-124 399.9 0.1 1.0 1 NCBI__GCF_003010935.1:WP_106715655.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010935.1:WP_106715655.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 399.9 0.1 4.5e-124 4.5e-124 1 350 [. 10 360 .. 10 361 .. 0.96 Alignments for each domain: == domain 1 score: 399.9 bits; conditional E-value: 4.5e-124 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvf...eGkT... 67 +r+tt+GeSHg alg+++dG+P+g++ +e++iq++l++R+pgqsr+t++r+E D+v++lsG + G T NCBI__GCF_003010935.1:WP_106715655.1 10 FRVTTWGESHGLALGCVVDGCPPGISFSEAEIQSYLDKRKPGQSRYTTQRREPDQVKVLSGFMlqdDGMTmis 82 89***********************************************************864447988555 PP TIGR00033 68 tGaPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketa 140 tG+Pi+++i+N+d+rskdy di++++RPgHadyty +KYgi+d++gggrsSaReTaarvaaGa+a+k + NCBI__GCF_003010935.1:WP_106715655.1 83 TGTPISMMIENTDQRSKDYGDIARQYRPGHADYTYDVKYGIRDYRGGGRSSARETAARVAAGAIARKVVPG-- 153 7******************************************************************9987.. PP TIGR00033 141 gieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvg 213 + + + +v +g +++++ + +++ ++p++ pd + + ++d ++k+g s+G+vvevv++nvp+g NCBI__GCF_003010935.1:WP_106715655.1 154 -LLVRGALVGMGIHSIDRSRWD---WDEVGNNPFFTPDLQSVDVFASYLDGIRKAGSSIGAVVEVVAENVPAG 222 .569999999999999987777...478999****************************************** PP TIGR00033 214 lGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrktnnsGGieGGitnGed 285 lG p++ kld +as l+sinAvKgveiGdGF++a+ +G e De+ + d+k + +n+ GGi+GGi+ G + NCBI__GCF_003010935.1:WP_106715655.1 223 LGAPVYGKLDQDIASNLMSINAVKGVEIGDGFDTARLTGEENADEMRMGnDGKPIFLSNHAGGILGGISSGAP 295 ***********************************************9989999******************* PP TIGR00033 286 irvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladallekras 350 ++ r avKp+++i +p++++d ++++ +t+gRhDpcv +ravp+ Eamva +ad++l++r++ NCBI__GCF_003010935.1:WP_106715655.1 296 VVARFAVKPTSSILTPRRSIDADGNQVEVMTRGRHDPCVGIRAVPIGEAMVACAIADHYLRHRGQ 360 *************************************************************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (364 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 17.68 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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