Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_012470844.1 GLOV_RS13875 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_000020385.1:WP_012470844.1 Length = 338 Score = 355 bits (910), Expect = e-102 Identities = 170/334 (50%), Positives = 239/334 (71%), Gaps = 1/334 (0%) Query: 1 MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVE 60 M++V+ +++ DI KV+++ G ERT IG++G+ YV L V+ Sbjct: 1 MLIVMNHTASQADIDKVIEVVSGMGFTAAPIPGGERTAIGVLGNKGYVDDSTIRDLPGVQ 60 Query: 61 SVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYF-TIIAGPCSVEGREMLMETAHFLSE 119 + V KPYKLVSR+FHP++T++D+ VKIG G ++ GPC+VE E +++TA F+ + Sbjct: 61 QAIHVSKPYKLVSRDFHPDNTIVDVAGVKIGEGERPVVVGGPCAVESEEQILKTARFVKQ 120 Query: 120 LGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYAD 179 G +LRGGA+KPRT P++FQGL E+GL+ L +A G+ +VTE + D++ VAEYAD Sbjct: 121 CGADLLRGGAFKPRTGPHTFQGLREEGLKLLAKARTATGLPIVTEVMSPDNVALVAEYAD 180 Query: 180 IIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGI 239 ++Q+GARN QNF LL + G KP+LLKRG TIEEFL +AEYI GN ++ILCERGI Sbjct: 181 LLQVGARNMQNFDLLRELGRIRKPILLKRGMSATIEEFLAAAEYILAEGNDQVILCERGI 240 Query: 240 RTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEV 299 RTFE ATRNTLD++ VP++++ +HLP++VDPSH+ G+R LV P+S+AA+ GAHG++VEV Sbjct: 241 RTFETATRNTLDLAMVPLVKELTHLPVMVDPSHATGKRSLVTPMSKAALVAGAHGVLVEV 300 Query: 300 HPEPEKALSDGKQSLDFELFKELVQEMKKLADAL 333 HPEPEKALSDG QSL F F+ L+ ++KKL + L Sbjct: 301 HPEPEKALSDGPQSLTFPGFEALMADLKKLRNCL 334 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: 321 Number of extensions: 12 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: 338 Length of database: 338 Length adjustment: 28 Effective length of query: 310 Effective length of database: 310 Effective search space: 96100 Effective search space used: 96100 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_012470844.1 GLOV_RS13875 (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.31912.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-126 406.2 0.0 3.4e-126 405.9 0.0 1.0 1 lcl|NCBI__GCF_000020385.1:WP_012470844.1 GLOV_RS13875 3-deoxy-7-phosphohe Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020385.1:WP_012470844.1 GLOV_RS13875 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 405.9 0.0 3.4e-126 3.4e-126 2 259 .. 71 329 .. 70 330 .. 0.99 Alignments for each domain: == domain 1 score: 405.9 bits; conditional E-value: 3.4e-126 TIGR01361 2 laskkvkkeetvvdvedvkiGege.liviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPys 69 l+s+++++++t+vdv +vkiGege ++v+ GPC+veseeqi++ta++vk+ Ga+llrGgafkPrt P++ lcl|NCBI__GCF_000020385.1:WP_012470844.1 71 LVSRDFHPDNTIVDVAGVKIGEGErPVVVGGPCAVESEEQILKTARFVKQCGADLLRGGAFKPRTGPHT 139 789********************989999**************************************** PP TIGR01361 70 fqGlgeeglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlLk 138 fqGl eeglkll++a+ +tgl++vtev+ +++v +vaey+D+lq+Garnmqnf+lL+e+g+ +kP+lLk lcl|NCBI__GCF_000020385.1:WP_012470844.1 140 FQGLREEGLKLLAKARTATGLPIVTEVMSPDNVALVAEYADLLQVGARNMQNFDLLRELGRIRKPILLK 208 ********************************************************************* PP TIGR01361 139 rglaatieewleaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpshaaGr 207 rg++atiee+l+aaeYil+egn +vilcerGirtfe+atr+tldl+ v+l+k+lthlPv+vDpsha+G+ lcl|NCBI__GCF_000020385.1:WP_012470844.1 209 RGMSATIEEFLAAAEYILAEGNDQVILCERGIRTFETATRNTLDLAMVPLVKELTHLPVMVDPSHATGK 277 ********************************************************************* PP TIGR01361 208 rdlvlplakaavavGadgllievhpdPekalsDseqqltpeefkelvkelka 259 r+lv+p++kaa+ +Ga+g+l+evhp+PekalsD++q+lt+ f++l+ +lk+ lcl|NCBI__GCF_000020385.1:WP_012470844.1 278 RSLVTPMSKAALVAGAHGVLVEVHPEPEKALSDGPQSLTFPGFEALMADLKK 329 ***********************************************99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (260 nodes) Target sequences: 1 (338 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: 8.48 // [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