Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_036376286.1 MVAN_RS13285 chorismate synthase
Query= SwissProt::P9WPY1 (401 letters) >NCBI__GCF_000015305.1:WP_036376286.1 Length = 404 Score = 666 bits (1719), Expect = 0.0 Identities = 344/404 (85%), Positives = 370/404 (91%), Gaps = 3/404 (0%) Query: 1 MLRWITAGESHGRALVAVVEGMVAGVHVTSADIADQLARRRLGYGRGARMTFERDAVTVL 60 MLRW TAGESHGRALVA+VEGMVAGVHVT+ DI+ QLARRRLGYGRGARM FE+D VT+L Sbjct: 1 MLRWTTAGESHGRALVAMVEGMVAGVHVTTQDISAQLARRRLGYGRGARMKFEQDQVTML 60 Query: 61 SGIRHGSTLGGPIAIEIGNTEWPKWETVMAADPVDPAELAD-VARNAPLTRPRPGHADYA 119 +G+RHG TLGGPIAIEIGNTEWPKWETVMA DPVDPA LAD ARNAPLTRPRPGHADYA Sbjct: 61 TGLRHGVTLGGPIAIEIGNTEWPKWETVMAPDPVDPAVLADSAARNAPLTRPRPGHADYA 120 Query: 120 GMLKYGFDDARPVLERASARETAARVAAGTVARAFLRQALGVEVLSHVISIGASAPYEGP 179 GMLKYGFDDARPVLERASARETAARVAAGTVARAFL+QALGVE++SHVISIGAS PY+GP Sbjct: 121 GMLKYGFDDARPVLERASARETAARVAAGTVARAFLQQALGVEIVSHVISIGASKPYDGP 180 Query: 180 PPRAEDLPAIDASPVRAYDKAAEADMIAQIEAAKKDGDTLGGVVEAVALGLPVGLGSFTS 239 PP+A DL AIDASPVRA+D A+EA MI +IEAAK+DGDTLGGVVE VA GLPVGLGSFTS Sbjct: 181 PPQAADLTAIDASPVRAFDAASEALMIDEIEAAKRDGDTLGGVVEVVAHGLPVGLGSFTS 240 Query: 240 GDHRLDSQLAAAVMGIQAIKGVEIGDGFQTARRRGSRAHDEMYPGPDGVVRSTNRAGGLE 299 GD+RLDSQLA AVMGIQAIKGVEIGDGF+TARRRGS AHDE+YPG DGV+RSTNRAGGLE Sbjct: 241 GDNRLDSQLAGAVMGIQAIKGVEIGDGFETARRRGSVAHDEIYPGADGVMRSTNRAGGLE 300 Query: 300 GGMTNGQPLRVRAAMKPISTVPRALATVDLATGDEAVAIHQRSDVCAVPAAGVVVETMVA 359 GGMTNG P+RVRAAMKPISTVPRALATVD+ATG+EAVAIHQRSDVCAVPAA VVVETMVA Sbjct: 301 GGMTNGLPVRVRAAMKPISTVPRALATVDMATGEEAVAIHQRSDVCAVPAAAVVVETMVA 360 Query: 360 LVLARAALEKFGGDSLAETQRNIAAYQRSVADRE--APAARVSG 401 LVLARA LEKFGGDSLAET+ NI +Y R+VA RE AR SG Sbjct: 361 LVLARAVLEKFGGDSLAETRANIDSYLRAVATREPSTDGARASG 404 Lambda K H 0.317 0.133 0.380 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: 589 Number of extensions: 16 Number of successful extensions: 2 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: 401 Length of database: 404 Length adjustment: 31 Effective length of query: 370 Effective length of database: 373 Effective search space: 138010 Effective search space used: 138010 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_036376286.1 MVAN_RS13285 (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.9830.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-129 418.1 1.0 1.5e-129 417.8 1.0 1.0 1 lcl|NCBI__GCF_000015305.1:WP_036376286.1 MVAN_RS13285 chorismate synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015305.1:WP_036376286.1 MVAN_RS13285 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 417.8 1.0 1.5e-129 1.5e-129 1 350 [. 2 373 .. 2 374 .. 0.96 Alignments for each domain: == domain 1 score: 417.8 bits; conditional E-value: 1.5e-129 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 lr+tt+GeSHg+al+a+++G+ ag+++t++di+ +l+rRr g++r++rm+ E+D+v++l+G+++G T G lcl|NCBI__GCF_000015305.1:WP_036376286.1 2 LRWTTAGESHGRALVAMVEGMVAGVHVTTQDISAQLARRRLGYGRGARMKFEQDQVTMLTGLRHGVTLG 70 69******************************************************************* PP TIGR00033 70 aPiallikNkd.......vrskdyed...........ikelpRPgHadytylkKYgikd.regggrsSa 119 Pia+ i N++ +++++++ ++pRPgHady+++ KYg++d r ++r+Sa lcl|NCBI__GCF_000015305.1:WP_036376286.1 71 GPIAIEIGNTEwpkwetvMAPDPVDPavladsaarnaPLTRPRPGHADYAGMLKYGFDDaRPVLERASA 139 ******************899999889999999999899********************99******** PP TIGR00033 120 ReTaarvaaGavakklLketagieivayvvklgevelee.esakeiskerldkspvrcpdaeaekemee 187 ReTaarvaaG+va+++L++ g+eiv++v+++g + + + ++d+spvr+ da e+ m + lcl|NCBI__GCF_000015305.1:WP_036376286.1 140 RETAARVAAGTVARAFLQQALGVEIVSHVISIGASKPYDgPPPQAADLTAIDASPVRAFDAASEALMID 208 *********************************96655405555777899******************* PP TIGR00033 188 eidkakkdgdsvGgvvevvvsnvpvglG..eplfdkldaelasallsinAvKgveiGdGFeaasvrGse 254 ei+ ak+dgd++Ggvvevv++++pvglG +++ld++la a+++i+A+KgveiGdGFe+a++rGs lcl|NCBI__GCF_000015305.1:WP_036376286.1 209 EIEAAKRDGDTLGGVVEVVAHGLPVGLGsfTSGDNRLDSQLAGAVMGIQAIKGVEIGDGFETARRRGSV 277 ****************************88899************************************ PP TIGR00033 255 anDelvleddkirrktnnsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpc 323 a+De++ d++ r tn+ GG+eGG+tnG ++rvr+a+Kpi+t+ ++l+tvd++t e+a a ++R+D+c lcl|NCBI__GCF_000015305.1:WP_036376286.1 278 AHDEIYPGADGVMRSTNRAGGLEGGMTNGLPVRVRAAMKPISTVPRALATVDMATGEEAVAIHQRSDVC 346 ********************************************************************* PP TIGR00033 324 vvpravpvvEamvalvladallekras 350 +vp+a++vvE+mvalvla a+lek++ lcl|NCBI__GCF_000015305.1:WP_036376286.1 347 AVPAAAVVVETMVALVLARAVLEKFGG 373 ***********************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (404 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.11 // [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