Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_012470721.1 GLOV_RS13260 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_000020385.1:WP_012470721.1 Length = 339 Score = 338 bits (867), Expect = 1e-97 Identities = 173/336 (51%), Positives = 236/336 (70%), Gaps = 2/336 (0%) Query: 1 MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRY-VVADKFESLDCV 59 MI+V+K G+ ++D +VVK + K HI G R VIG IGD+R +V E++ V Sbjct: 1 MIIVMKAGAGKKDRDEVVKRIKELGYKPHIIHGTTRDVIGAIGDERAKLVLQSLENMHGV 60 Query: 60 ESVVRVLKPYKLVSREFHPEDTVIDLGD-VKIGNGYFTIIAGPCSVEGREMLMETAHFLS 118 ESVV +L+PYKL S E E + + +GD V IG ++AGPCSVE E ++E+A + Sbjct: 61 ESVVPILQPYKLASSEVKHEPSQVKVGDSVVIGGSRVVVMAGPCSVESEEQIIESARLVK 120 Query: 119 ELGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYA 178 E G +LRGGA+KPRTSPYSFQGL E+GL+ L +A D G+ VTE + + + VA+YA Sbjct: 121 EAGATMLRGGAFKPRTSPYSFQGLEEEGLKMLAKARDLTGLPFVTEVINPETVDLVADYA 180 Query: 179 DIIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERG 238 D++QIGARN+QNF LL K G KP+LLKRG TI+EFL+SAEYI + GN ++LCERG Sbjct: 181 DMLQIGARNSQNFALLKKVGQCGKPILLKRGMAMTIQEFLMSAEYIMSEGNQGVVLCERG 240 Query: 239 IRTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVE 298 IRTFE ATRNTLD+SA+P+++ ++HLP+++DPSH G V P+ AA+A GA G+IVE Sbjct: 241 IRTFETATRNTLDLSAIPVLKLKTHLPVVIDPSHGTGNYHYVAPMCYAAVAAGADGLIVE 300 Query: 299 VHPEPEKALSDGKQSLDFELFKELVQEMKKLADALG 334 VHP+PE+A SDG QSL + F ++Q+++ A+A G Sbjct: 301 VHPDPERASSDGPQSLKPKKFAAMMQKLRLFAEADG 336 Lambda K H 0.318 0.138 0.388 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: 330 Number of extensions: 6 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: 338 Length of database: 339 Length adjustment: 28 Effective length of query: 310 Effective length of database: 311 Effective search space: 96410 Effective search space used: 96410 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: 49 (23.5 bits)
Align candidate WP_012470721.1 GLOV_RS13260 (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.11633.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-124 399.7 0.0 3.3e-124 399.4 0.0 1.1 1 lcl|NCBI__GCF_000020385.1:WP_012470721.1 GLOV_RS13260 3-deoxy-7-phosphohe Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020385.1:WP_012470721.1 GLOV_RS13260 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 399.4 0.0 3.3e-124 3.3e-124 2 258 .. 72 329 .. 71 331 .. 0.98 Alignments for each domain: == domain 1 score: 399.4 bits; conditional E-value: 3.3e-124 TIGR01361 2 laskkvkkeetvvdved.vkiGegeliviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPys 69 las++vk+e + v+v d v iG+ +++v+aGPCsveseeqi+e+a+ vkeaGa++lrGgafkPrtsPys lcl|NCBI__GCF_000020385.1:WP_012470721.1 72 LASSEVKHEPSQVKVGDsVVIGGSRVVVMAGPCSVESEEQIIESARLVKEAGATMLRGGAFKPRTSPYS 140 68999999999988876599************************************************* PP TIGR01361 70 fqGlgeeglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlLk 138 fqGl+eeglk+l++a+d tgl++vtev++++ v++va+y+D+lqiGarn+qnf+lLk+vg+ kP+lLk lcl|NCBI__GCF_000020385.1:WP_012470721.1 141 FQGLEEEGLKMLAKARDLTGLPFVTEVINPETVDLVADYADMLQIGARNSQNFALLKKVGQCGKPILLK 209 ********************************************************************* PP TIGR01361 139 rglaatieewleaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpshaaGr 207 rg+a ti+e+l++aeYi+segn+ v+lcerGirtfe+atr+tldlsa+++lk +thlPv++Dpsh++G+ lcl|NCBI__GCF_000020385.1:WP_012470721.1 210 RGMAMTIQEFLMSAEYIMSEGNQGVVLCERGIRTFETATRNTLDLSAIPVLKLKTHLPVVIDPSHGTGN 278 ********************************************************************* PP TIGR01361 208 rdlvlplakaavavGadgllievhpdPekalsDseqqltpeefkelvkelk 258 ++v p++ aava+Gadgl++evhpdPe+a sD++q+l+p++f++++++l+ lcl|NCBI__GCF_000020385.1:WP_012470721.1 279 YHYVAPMCYAAVAAGADGLIVEVHPDPERASSDGPQSLKPKKFAAMMQKLR 329 ************************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (260 nodes) Target sequences: 1 (339 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.31 // [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