Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_052296991.1 PYRFU_RS04105 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::Q9YEJ7 (270 letters) >NCBI__GCF_000223395.1:WP_052296991.1 Length = 340 Score = 281 bits (718), Expect = 2e-80 Identities = 152/266 (57%), Positives = 187/266 (70%), Gaps = 7/266 (2%) Query: 6 GVKLALKSEE--RRETVVEVEGVRIGGGSKAVIAGPCSVESWEQVREAALAVKEAGAHML 63 G KL L S E ++V + V +G VIAGPC +ES EQV EA AV AGAH++ Sbjct: 60 GSKLQLSSREWLGGDSVARIGNVEVGRDF-IVIAGPCGIESREQVEEAVSAVWSAGAHVV 118 Query: 64 RGGAFKPRTSPYSFQGLGLEGLKLLRRAGDEAGLPVVTEVLDPRHVETVSRYADMLQIGA 123 RGGA+KPRTSPYSFQG+GLE K L A GLP +TEV+DPR V D + +GA Sbjct: 119 RGGAWKPRTSPYSFQGIGLEAAKWLAEAAHSKGLPAITEVMDPRDARQVFNIVDGVWVGA 178 Query: 124 RNMQNFPLLREVGR----SGKPVLLKRGFGNTVEELLAAAEYILLEGNWQVVLVERGIRT 179 R+MQ PLLRE+GR +GK VL+KRGFGNT+EE L A+EY++LEG V L+ERG R Sbjct: 179 RSMQVTPLLRELGRLCRETGKAVLIKRGFGNTLEEWLLASEYVMLEGCSNVALIERGSRC 238 Query: 180 FEPSTRFTLDVAAVAVLKEATHLPVIVDPSHPAGRRSLVPALAKAGLAAGADGLIVEVHP 239 + +RF+LDVA + V + THLP+IVDPSHPAG+R LV LA A AAGA GL++EVHP Sbjct: 239 WASVSRFSLDVAIIPVARGKTHLPIIVDPSHPAGKRELVEPLALAATAAGAQGLMIEVHP 298 Query: 240 NPEEALSDAKQQLTPGEFARLMGELR 265 PE+ALSD +QQLTPGEF RLM +L+ Sbjct: 299 WPEKALSDKQQQLTPGEFKRLMEKLK 324 Lambda K H 0.318 0.136 0.392 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: 235 Number of extensions: 7 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: 270 Length of database: 340 Length adjustment: 27 Effective length of query: 243 Effective length of database: 313 Effective search space: 76059 Effective search space used: 76059 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: 48 (23.1 bits)
Align candidate WP_052296991.1 PYRFU_RS04105 (3-deoxy-7-phosphoheptulonate synthase)
to HMM TIGR01361 (aroF: 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))
# 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/TIGR01361.hmm # target sequence database: /tmp/gapView.887.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01361 [M=260] Accession: TIGR01361 Description: DAHP_synth_Bsub: 3-deoxy-7-phosphoheptulonate 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-100 320.0 0.0 6.6e-100 319.8 0.0 1.0 1 lcl|NCBI__GCF_000223395.1:WP_052296991.1 PYRFU_RS04105 3-deoxy-7-phosphoh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000223395.1:WP_052296991.1 PYRFU_RS04105 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 319.8 0.0 6.6e-100 6.6e-100 2 258 .. 65 324 .. 64 326 .. 0.97 Alignments for each domain: == domain 1 score: 319.8 bits; conditional E-value: 6.6e-100 TIGR01361 2 laskkvkkeetvvdvedvkiGegeliviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPysf 70 l s+++ ++v ++ +v++G + +iviaGPC +es+eq+ e+ av +aGa+++rGga+kPrtsPysf lcl|NCBI__GCF_000223395.1:WP_052296991.1 65 LSSREWLGGDSVARIGNVEVGRD-FIVIAGPCGIESREQVEEAVSAVWSAGAHVVRGGAWKPRTSPYSF 132 56888888999***********9.********************************************* PP TIGR01361 71 qGlgeeglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgk....skkPv 135 qG+g e+ k+l++a+++ gl+ +tev+d+rd + v + vD + +Gar mq + lL+e+g+ + k v lcl|NCBI__GCF_000223395.1:WP_052296991.1 133 QGIGLEAAKWLAEAAHSKGLPAITEVMDPRDARQVFNIVDGVWVGARSMQVTPLLRELGRlcreTGKAV 201 ***********************************************************744336899* PP TIGR01361 136 lLkrglaatieewleaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpsha 204 l+krg+++t+eewl a+eY++ eg++nv l+erG r + ++ rf+ld++ +++++ +thlP+ivDpsh+ lcl|NCBI__GCF_000223395.1:WP_052296991.1 202 LIKRGFGNTLEEWLLASEYVMLEGCSNVALIERGSRCWASVSRFSLDVAIIPVARGKTHLPIIVDPSHP 270 ********************************************************************* PP TIGR01361 205 aGrrdlvlplakaavavGadgllievhpdPekalsDseqqltpeefkelvkelk 258 aG+r+lv+pla aa a+Ga+gl+ievhp PekalsD +qqltp efk+l+++lk lcl|NCBI__GCF_000223395.1:WP_052296991.1 271 AGKRELVEPLALAATAAGAQGLMIEVHPWPEKALSDKQQQLTPGEFKRLMEKLK 324 ***************************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (260 nodes) Target sequences: 1 (340 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: 7.33 // [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